Add TNT configuration directives and tree export commands to script

Updates the generated TNT script with configuration parameters and appends tree management commands for saving and exporting results. Modifications are strictly limited to string literals written to the output stream.
Add diagnostic logging and minor internal refactoring
2026-08-17 11:39:51 +02:00 · 2026-08-17 11:29:31 +02:00 · 2026-08-17 11:24:23 +02:00 · 2026-08-17 11:19:44 +02:00 · 2026-08-17 11:16:42 +02:00 · 2026-08-17 11:06:03 +02:00
436 changed files with 104571 additions and 11980 deletions
@@ -1,4 +1,4 @@
-name: CI
+pname: CI

 on:
  pull_request:
@@ -25,8 +25,8 @@ jobs:
            ~/.cargo/registry
            ~/.cargo/git
            src/target
-          key: ${{ runner.os }}-cargo-${{ hashFiles('src/Cargo.lock') }}
-          restore-keys: ${{ runner.os }}-cargo-
+          key: ${{ runner.os }}-cargo-v2-${{ hashFiles('src/Cargo.lock') }}
+          restore-keys: ${{ runner.os }}-cargo-v2-

      - name: Build
        run: cargo build --release
@@ -104,19 +104,23 @@ jobs:

      - name: Build macOS binary
        run: |
-          docker run --rm \
-            -v "${{ github.workspace }}:/src" \
+          CID=$(docker create \
            -w /src/src \
            registry.metabarcoding.org/cibuilder/rustcrossosx:latest \
-            cargo build --release --target aarch64-apple-darwin --no-default-features
+            cargo build --release --target aarch64-apple-darwin --no-default-features)
+          docker cp . "$CID:/src"
+          docker start -a "$CID"
+          STATUS=$(docker wait "$CID")
+          mkdir -p /tmp/dist
+          docker cp "$CID:/src/src/target/aarch64-apple-darwin/release/obikmer" /tmp/dist/obikmer-macos-arm64
+          docker rm "$CID" > /dev/null
+          [ "$STATUS" -eq 0 ]

      - name: Prepare and upload artifact
        env:
          GITEA_TOKEN: ${{ secrets.GITEATOKEN }}
          RELEASE_ID: ${{ needs.create-release.outputs.release_id }}
        run: |
-          mkdir -p /tmp/dist
-          cp src/target/aarch64-apple-darwin/release/obikmer /tmp/dist/obikmer-macos-arm64
          curl -s -X POST \
            "${{ github.server_url }}/api/v1/repos/${{ github.repository }}/releases/$RELEASE_ID/assets" \
            -H "Authorization: token $GITEA_TOKEN" \
@@ -9,12 +9,17 @@ data-stress
 ./**/*.json
 *.bin
 *.log
+*.csv
 Betula_exilis--IGA-24-33
 benchmark/genomes
+benchmark/genomes_orig
 benchmark/simulated_data
 benchmark/specimen_index_presence
 benchmark/specimen_index_count
 benchmark/global_index_presence
+benchmark/global_index_presence_orig
+benchmark/global_index_presence_sav
+benchmark/all_specific
 benchmark/global_index_count
 benchmark/stats
 benchmark/reference_index
@@ -22,3 +27,16 @@ benchmark/reference_dist
 benchmark/obikmer_dist
 benchmark/specific_index_count
 benchmark/specific_index_presence
+TNT
+phyg
+biblio
+*.tnt
+*.tre
+*.phy
+*.treefile
+*.bionj
+*.iqtree
+*.mldist
+*.parstree
+*.ckp.gz
+*.model
@@ -12,8 +12,8 @@ Si une dépendance demandée pose problème (erreur de compilation, bug, API man
 Quand une nouvelle construction (type, itérateur, abstraction) rend du code historique injustifié, le signaler immédiatement et proposer de le supprimer — ne pas conserver les deux en parallèle par inertie. Le développeur demande explicitement de remettre en cause le code base : ne pas attendre qu'il insiste.

 Tu maintiens en **anglais**, dense et sans remplissage, les documents suivants :
- `docmd/index.md` — document de discussion de base, enrichi progressivement au fil de nos échanges ; il reflète l'état courant de la réflexion sur le projet
- les autres fichiers Markdown dans `docmd/` selon leur thème respectif
+- `DevDocMD/index.md` — document de discussion de base, enrichi progressivement au fil de nos échanges ; il reflète l'état courant de la réflexion sur le projet
+- les autres fichiers Markdown dans `DevDocMD/` selon leur thème respectif

 Les snippets de code y sont courts et illustrent uniquement des principes architecturaux. Nos échanges se font en **français**.

@@ -42,33 +42,35 @@ Les snippets de code y sont courts et illustrent uniquement des principes archit

 ## Infrastructure de documentation

-La documentation est gérée via **MkDocs + thème Material**, avec publication sur **GitHub Pages**.
+La documentation est gérée via **MkDocs + thème Material**, avec publication sur **GitHub Pages**. Deux arbres de documentation indépendants, deux configurations à la racine du dépôt (voir aussi `UserDocMD/` ci-dessous pour la doc utilisateur) :

 **Structure des répertoires**

 ```
-docmd/          ← sources Markdown + mkdocs.yml
-docmd/mkdocs.yml
-doc/            ← site HTML généré (servi par GitHub Pages)
+DevDocMD/       ← sources Markdown, doc développeur (discussion, historique, rationale)
+UserDocMD/      ← sources Markdown, doc utilisateur (état factuel courant, sans code Rust)
+mkdocs.yml      ← config doc développeur : docs_dir DevDocMD, site_dir DevDoc
+mkdocs-user.yml ← config doc utilisateur : docs_dir UserDocMD, site_dir doc
+DevDoc/         ← site HTML généré (doc développeur)
+doc/            ← site HTML généré (doc utilisateur — publié par GitHub Pages, répertoire par défaut)
 .venv/          ← environnement Python (ignoré par git)
 ```

-**Configuration `docmd/mkdocs.yml`**
- `docs_dir: .` (sources = `docmd/` lui-même)
- `site_dir: ../doc` (sortie = `doc/`)
-
 **Commandes Makefile**

 | Commande | Effet |
 |---|---|
-| `make doc` | Construit le HTML dans `doc/` |
-| `make doc-serve` | Serveur local avec rechargement automatique |
-| `make clean-doc` | Supprime `doc/` |
-| `make clean` | Supprime `doc/` et `.venv/` |
+| `make doc` | Construit la doc développeur dans `DevDoc/` |
+| `make doc-serve` | Serveur local (doc développeur), rechargement automatique |
+| `make clean-doc` | Supprime `DevDoc/` |
+| `make doc-user` | Construit la doc utilisateur dans `doc/` |
+| `make doc-user-serve` | Serveur local (doc utilisateur), rechargement automatique |
+| `make clean-doc-user` | Supprime `doc/` |
+| `make clean` | Supprime `DevDoc/`, `doc/` et `.venv/` |

-Le `.venv/` est dans `.gitignore`. Le répertoire `doc/` (sortie HTML) est versionné pour GitHub Pages.
+Le `.venv/` est dans `.gitignore`. `DevDoc/` et `doc/` (sorties HTML) sont versionnés — `doc/` spécifiquement parce que c'est le répertoire par défaut que GitHub Pages sert.

-Lors de l'ajout de nouveaux fichiers Markdown dans `docmd/`, mettre à jour la section `nav:` de `docmd/mkdocs.yml`.
+Lors de l'ajout de nouveaux fichiers Markdown dans `DevDocMD/`, mettre à jour la section `nav:` de `mkdocs.yml` ; dans `UserDocMD/`, mettre à jour `mkdocs-user.yml`.

 ---

@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -12,6 +12,8 @@
        <link rel="prev" href="../sequences/invariant/">
      
      
+        <link rel="next" href="../siblings/">
+      
      
        
      
@@ -180,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -189,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -210,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -361,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -383,10 +440,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -404,8 +461,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -786,14 +843,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -831,10 +972,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -852,8 +993,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1159,6 +1300,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -9,7 +9,7 @@
      
      
      
-        <link rel="prev" href="../../../implementation/rebuild_filter/">
+        <link rel="prev" href="../../../implementation/obitaxonomy/">
      
      
        <link rel="next" href="../../index_architecture/">
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -385,10 +440,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -406,8 +461,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -788,14 +843,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../../../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../../../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -833,10 +972,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -854,8 +993,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -931,6 +1070,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Danish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.da=function(){this.pipeline.reset(),this.pipeline.add(e.da.trimmer,e.da.stopWordFilter,e.da.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.da.stemmer))},e.da.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤﬀ-ﬆＡ-Ｚａ-ｚ",e.da.trimmer=e.trimmerSupport.generateTrimmer(e.da.wordCharacters),e.Pipeline.registerFunction(e.da.trimmer,"trimmer-da"),e.da.stemmer=function(){var r=e.stemmerSupport.Among,i=e.stemmerSupport.SnowballProgram,n=new function(){function e(){var e,r=f.cursor+3;if(d=f.limit,0<=r&&r<=f.limit){for(a=r;;){if(e=f.cursor,f.in_grouping(w,97,248)){f.cursor=e;break}if(f.cursor=e,e>=f.limit)return;f.cursor++}for(;!f.out_grouping(w,97,248);){if(f.cursor>=f.limit)return;f.cursor++}d=f.cursor,d<a&&(d=a)}}function n(){var e,r;if(f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(c,32),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del();break;case 2:f.in_grouping_b(p,97,229)&&f.slice_del()}}function t(){var e,r=f.limit-f.cursor;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.find_among_b(l,4)?(f.bra=f.cursor,f.limit_backward=e,f.cursor=f.limit-r,f.cursor>f.limit_backward&&(f.cursor--,f.bra=f.cursor,f.slice_del())):f.limit_backward=e)}function s(){var e,r,i,n=f.limit-f.cursor;if(f.ket=f.cursor,f.eq_s_b(2,"st")&&(f.bra=f.cursor,f.eq_s_b(2,"ig")&&f.slice_del()),f.cursor=f.limit-n,f.cursor>=d&&(r=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,e=f.find_among_b(m,5),f.limit_backward=r,e))switch(f.bra=f.cursor,e){case 1:f.slice_del(),i=f.limit-f.cursor,t(),f.cursor=f.limit-i;break;case 2:f.slice_from("løs")}}function o(){var e;f.cursor>=d&&(e=f.limit_backward,f.limit_backward=d,f.ket=f.cursor,f.out_grouping_b(w,97,248)?(f.bra=f.cursor,u=f.slice_to(u),f.limit_backward=e,f.eq_v_b(u)&&f.slice_del()):f.limit_backward=e)}var a,d,u,c=[new r("hed",-1,1),new r("ethed",0,1),new r("ered",-1,1),new r("e",-1,1),new r("erede",3,1),new r("ende",3,1),new r("erende",5,1),new r("ene",3,1),new r("erne",3,1),new r("ere",3,1),new r("en",-1,1),new r("heden",10,1),new r("eren",10,1),new r("er",-1,1),new r("heder",13,1),new r("erer",13,1),new r("s",-1,2),new r("heds",16,1),new r("es",16,1),new r("endes",18,1),new r("erendes",19,1),new r("enes",18,1),new r("ernes",18,1),new r("eres",18,1),new r("ens",16,1),new r("hedens",24,1),new r("erens",24,1),new r("ers",16,1),new r("ets",16,1),new r("erets",28,1),new r("et",-1,1),new r("eret",30,1)],l=[new r("gd",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("elig",1,1),new r("els",-1,1),new r("løst",-1,2)],w=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],p=[239,254,42,3,0,0,0,0,0,0,0,0,0,0,0,0,16],f=new i;this.setCurrent=function(e){f.setCurrent(e)},this.getCurrent=function(){return f.getCurrent()},this.stem=function(){var r=f.cursor;return e(),f.limit_backward=r,f.cursor=f.limit,n(),f.cursor=f.limit,t(),f.cursor=f.limit,s(),f.cursor=f.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return n.setCurrent(e),n.stem(),n.getCurrent()}):(n.setCurrent(e),n.stem(),n.getCurrent())}}(),e.Pipeline.registerFunction(e.da.stemmer,"stemmer-da"),e.da.stopWordFilter=e.generateStopWordFilter("ad af alle alt anden at blev blive bliver da de dem den denne der deres det dette dig din disse dog du efter eller en end er et for fra ham han hans har havde have hende hendes her hos hun hvad hvis hvor i ikke ind jeg jer jo kunne man mange med meget men mig min mine mit mod ned noget nogle nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hi=function(){this.pipeline.reset(),this.pipeline.add(e.hi.trimmer,e.hi.stopWordFilter,e.hi.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.hi.stemmer))},e.hi.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.hi.trimmer=e.trimmerSupport.generateTrimmer(e.hi.wordCharacters),e.Pipeline.registerFunction(e.hi.trimmer,"trimmer-hi"),e.hi.stopWordFilter=e.generateStopWordFilter("अत अपना अपनी अपने अभी अंदर आदि आप इत्यादि इन इनका इन्हीं इन्हें इन्हों इस इसका इसकी इसके इसमें इसी इसे उन उनका उनकी उनके उनको उन्हीं उन्हें उन्हों उस उसके उसी उसे एक एवं एस ऐसे और कई कर करता करते करना करने करें कहते कहा का काफ़ी कि कितना किन्हें किन्हों किया किर किस किसी किसे की कुछ कुल के को कोई कौन कौनसा गया घर जब जहाँ जा जितना जिन जिन्हें जिन्हों जिस जिसे जीधर जैसा जैसे जो तक तब तरह तिन तिन्हें तिन्हों तिस तिसे तो था थी थे दबारा दिया दुसरा दूसरे दो द्वारा न नके नहीं ना निहायत नीचे ने पर पहले पूरा पे फिर बनी बही बहुत बाद बाला बिलकुल भी भीतर मगर मानो मे में यदि यह यहाँ यही या यिह ये रखें रहा रहे ऱ्वासा लिए लिये लेकिन व वग़ैरह वर्ग वह वहाँ वहीं वाले वुह वे वो सकता सकते सबसे सभी साथ साबुत साभ सारा से सो संग ही हुआ हुई हुए है हैं हो होता होती होते होना होने".split(" ")),e.hi.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.hi.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var t=i.toString().toLowerCase().replace(/^\s+/,"");return r.cut(t).split("|")},e.Pipeline.registerFunction(e.hi.stemmer,"stemmer-hi"),e.Pipeline.registerFunction(e.hi.stopWordFilter,"stopWordFilter-hi")}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.hy=function(){this.pipeline.reset(),this.pipeline.add(e.hy.trimmer,e.hy.stopWordFilter)},e.hy.wordCharacters="[A-Za-z԰-֏ﬀ-ﭏ]",e.hy.trimmer=e.trimmerSupport.generateTrimmer(e.hy.wordCharacters),e.Pipeline.registerFunction(e.hy.trimmer,"trimmer-hy"),e.hy.stopWordFilter=e.generateStopWordFilter("դու և եք էիր էիք հետո նաև նրանք որը վրա է որ պիտի են այս մեջ ն իր ու ի այդ որոնք այն կամ էր մի ես համար այլ իսկ էին ենք հետ ին թ էինք մենք նրա նա դուք եմ էի ըստ որպես ում".split(" ")),e.Pipeline.registerFunction(e.hy.stopWordFilter,"stopWordFilter-hy"),e.hy.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}(),e.Pipeline.registerFunction(e.hy.stemmer,"stemmer-hy")}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.ja=function(){this.pipeline.reset(),this.pipeline.add(e.ja.trimmer,e.ja.stopWordFilter,e.ja.stemmer),r?this.tokenizer=e.ja.tokenizer:(e.tokenizer&&(e.tokenizer=e.ja.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.ja.tokenizer))};var t=new e.TinySegmenter;e.ja.tokenizer=function(i){var n,o,s,p,a,u,m,l,c,f;if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t.toLowerCase()):t.toLowerCase()});for(o=i.toString().toLowerCase().replace(/^\s+/,""),n=o.length-1;n>=0;n--)if(/\S/.test(o.charAt(n))){o=o.substring(0,n+1);break}for(a=[],s=o.length,c=0,l=0;c<=s;c++)if(u=o.charAt(c),m=c-l,u.match(/\s/)||c==s){if(m>0)for(p=t.segment(o.slice(l,c)).filter(function(e){return!!e}),f=l,n=0;n<p.length;n++)r?a.push(new e.Token(p[n],{position:[f,p[n].length],index:a.length})):a.push(p[n]),f+=p[n].length;l=c+1}return a},e.ja.stemmer=function(){return function(e){return e}}(),e.Pipeline.registerFunction(e.ja.stemmer,"stemmer-ja"),e.ja.wordCharacters="一二三四五六七八九十百千万億兆一-龠々〆ヵヶぁ-んァ-ヴーｱ-ﾝﾞa-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ja.trimmer=e.trimmerSupport.generateTrimmer(e.ja.wordCharacters),e.Pipeline.registerFunction(e.ja.trimmer,"trimmer-ja"),e.ja.stopWordFilter=e.generateStopWordFilter("これ それ あれ この その あの ここ そこ あそこ こちら どこ だれ なに なん 何 私 貴方 貴方方 我々 私達 あの人 あのかた 彼女 彼 です あります おります います は が の に を で え から まで より も どの と し それで しかし".split(" ")),e.Pipeline.registerFunction(e.ja.stopWordFilter,"stopWordFilter-ja"),e.jp=e.ja,e.Pipeline.registerFunction(e.jp.stemmer,"stemmer-jp"),e.Pipeline.registerFunction(e.jp.trimmer,"trimmer-jp"),e.Pipeline.registerFunction(e.jp.stopWordFilter,"stopWordFilter-jp")}});
@@ -0,0 +1 @@
+module.exports=require("./lunr.ja");
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.kn=function(){this.pipeline.reset(),this.pipeline.add(e.kn.trimmer,e.kn.stopWordFilter,e.kn.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.kn.stemmer))},e.kn.wordCharacters="ಀ-಄ಅ-ಔಕ-ಹಾ-ೌ಼-ಽೕ-ೖೝ-ೞೠ-ೡೢ-ೣ೤೥೦-೯ೱ-ೳ",e.kn.trimmer=e.trimmerSupport.generateTrimmer(e.kn.wordCharacters),e.Pipeline.registerFunction(e.kn.trimmer,"trimmer-kn"),e.kn.stopWordFilter=e.generateStopWordFilter("ಮತ್ತು ಈ ಒಂದು ರಲ್ಲಿ ಹಾಗೂ ಎಂದು ಅಥವಾ ಇದು ರ ಅವರು ಎಂಬ ಮೇಲೆ ಅವರ ತನ್ನ ಆದರೆ ತಮ್ಮ ನಂತರ ಮೂಲಕ ಹೆಚ್ಚು ನ ಆ ಕೆಲವು ಅನೇಕ ಎರಡು ಹಾಗು ಪ್ರಮುಖ ಇದನ್ನು ಇದರ ಸುಮಾರು ಅದರ ಅದು ಮೊದಲ ಬಗ್ಗೆ ನಲ್ಲಿ ರಂದು ಇತರ ಅತ್ಯಂತ ಹೆಚ್ಚಿನ ಸಹ ಸಾಮಾನ್ಯವಾಗಿ ನೇ ಹಲವಾರು ಹೊಸ ದಿ ಕಡಿಮೆ ಯಾವುದೇ ಹೊಂದಿದೆ ದೊಡ್ಡ ಅನ್ನು ಇವರು ಪ್ರಕಾರ ಇದೆ ಮಾತ್ರ ಕೂಡ ಇಲ್ಲಿ ಎಲ್ಲಾ ವಿವಿಧ ಅದನ್ನು ಹಲವು ರಿಂದ ಕೇವಲ ದ ದಕ್ಷಿಣ ಗೆ ಅವನ ಅತಿ ನೆಯ ಬಹಳ ಕೆಲಸ ಎಲ್ಲ ಪ್ರತಿ ಇತ್ಯಾದಿ ಇವು ಬೇರೆ ಹೀಗೆ ನಡುವೆ ಇದಕ್ಕೆ ಎಸ್ ಇವರ ಮೊದಲು ಶ್ರೀ ಮಾಡುವ ಇದರಲ್ಲಿ ರೀತಿಯ ಮಾಡಿದ ಕಾಲ ಅಲ್ಲಿ ಮಾಡಲು ಅದೇ ಈಗ ಅವು ಗಳು ಎ ಎಂಬುದು ಅವನು ಅಂದರೆ ಅವರಿಗೆ ಇರುವ ವಿಶೇಷ ಮುಂದೆ ಅವುಗಳ ಮುಂತಾದ ಮೂಲ ಬಿ ಮೀ ಒಂದೇ ಇನ್ನೂ ಹೆಚ್ಚಾಗಿ ಮಾಡಿ ಅವರನ್ನು ಇದೇ ಯ ರೀತಿಯಲ್ಲಿ ಜೊತೆ ಅದರಲ್ಲಿ ಮಾಡಿದರು ನಡೆದ ಆಗ ಮತ್ತೆ ಪೂರ್ವ ಆತ ಬಂದ ಯಾವ ಒಟ್ಟು ಇತರೆ ಹಿಂದೆ ಪ್ರಮಾಣದ ಗಳನ್ನು ಕುರಿತು ಯು ಆದ್ದರಿಂದ ಅಲ್ಲದೆ ನಗರದ ಮೇಲಿನ ಏಕೆಂದರೆ ರಷ್ಟು ಎಂಬುದನ್ನು ಬಾರಿ ಎಂದರೆ ಹಿಂದಿನ ಆದರೂ ಆದ ಸಂಬಂಧಿಸಿದ ಮತ್ತೊಂದು ಸಿ ಆತನ ".split(" ")),e.kn.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.kn.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var n=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(n).split("|")},e.Pipeline.registerFunction(e.kn.stemmer,"stemmer-kn"),e.Pipeline.registerFunction(e.kn.stopWordFilter,"stopWordFilter-kn")}});
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){e.multiLanguage=function(){for(var t=Array.prototype.slice.call(arguments),i=t.join("-"),r="",n=[],s=[],p=0;p<t.length;++p)"en"==t[p]?(r+="\\w",n.unshift(e.stopWordFilter),n.push(e.stemmer),s.push(e.stemmer)):(r+=e[t[p]].wordCharacters,e[t[p]].stopWordFilter&&n.unshift(e[t[p]].stopWordFilter),e[t[p]].stemmer&&(n.push(e[t[p]].stemmer),s.push(e[t[p]].stemmer)));var o=e.trimmerSupport.generateTrimmer(r);return e.Pipeline.registerFunction(o,"lunr-multi-trimmer-"+i),n.unshift(o),function(){this.pipeline.reset(),this.pipeline.add.apply(this.pipeline,n),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add.apply(this.searchPipeline,s))}}}});
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Norwegian` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.no=function(){this.pipeline.reset(),this.pipeline.add(e.no.trimmer,e.no.stopWordFilter,e.no.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.no.stemmer))},e.no.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤﬀ-ﬆＡ-Ｚａ-ｚ",e.no.trimmer=e.trimmerSupport.generateTrimmer(e.no.wordCharacters),e.Pipeline.registerFunction(e.no.trimmer,"trimmer-no"),e.no.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,i=new function(){function e(){var e,r=w.cursor+3;if(a=w.limit,0<=r||r<=w.limit){for(s=r;;){if(e=w.cursor,w.in_grouping(d,97,248)){w.cursor=e;break}if(e>=w.limit)return;w.cursor=e+1}for(;!w.out_grouping(d,97,248);){if(w.cursor>=w.limit)return;w.cursor++}a=w.cursor,a<s&&(a=s)}}function i(){var e,r,n;if(w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(m,29),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:n=w.limit-w.cursor,w.in_grouping_b(c,98,122)?w.slice_del():(w.cursor=w.limit-n,w.eq_s_b(1,"k")&&w.out_grouping_b(d,97,248)&&w.slice_del());break;case 3:w.slice_from("er")}}function t(){var e,r=w.limit-w.cursor;w.cursor>=a&&(e=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,w.find_among_b(u,2)?(w.bra=w.cursor,w.limit_backward=e,w.cursor=w.limit-r,w.cursor>w.limit_backward&&(w.cursor--,w.bra=w.cursor,w.slice_del())):w.limit_backward=e)}function o(){var e,r;w.cursor>=a&&(r=w.limit_backward,w.limit_backward=a,w.ket=w.cursor,e=w.find_among_b(l,11),e?(w.bra=w.cursor,w.limit_backward=r,1==e&&w.slice_del()):w.limit_backward=r)}var s,a,m=[new r("a",-1,1),new r("e",-1,1),new r("ede",1,1),new r("ande",1,1),new r("ende",1,1),new r("ane",1,1),new r("ene",1,1),new r("hetene",6,1),new r("erte",1,3),new r("en",-1,1),new r("heten",9,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",12,1),new r("s",-1,2),new r("as",14,1),new r("es",14,1),new r("edes",16,1),new r("endes",16,1),new r("enes",16,1),new r("hetenes",19,1),new r("ens",14,1),new r("hetens",21,1),new r("ers",14,1),new r("ets",14,1),new r("et",-1,1),new r("het",25,1),new r("ert",-1,3),new r("ast",-1,1)],u=[new r("dt",-1,-1),new r("vt",-1,-1)],l=[new r("leg",-1,1),new r("eleg",0,1),new r("ig",-1,1),new r("eig",2,1),new r("lig",2,1),new r("elig",4,1),new r("els",-1,1),new r("lov",-1,1),new r("elov",7,1),new r("slov",7,1),new r("hetslov",9,1)],d=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,48,0,128],c=[119,125,149,1],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,i(),w.cursor=w.limit,t(),w.cursor=w.limit,o(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return i.setCurrent(e),i.stem(),i.getCurrent()}):(i.setCurrent(e),i.stem(),i.getCurrent())}}(),e.Pipeline.registerFunction(e.no.stemmer,"stemmer-no"),e.no.stopWordFilter=e.generateStopWordFilter("alle at av bare begge ble blei bli blir blitt både båe da de deg dei deim deira deires dem den denne der dere deres det dette di din disse ditt du dykk dykkar då eg ein eit eitt eller elles en enn er et ett etter for fordi fra før ha hadde han hans har hennar henne hennes her hjå ho hoe honom hoss hossen hun hva hvem hver hvilke hvilken hvis hvor hvordan hvorfor i ikke ikkje ikkje ingen ingi inkje inn inni ja jeg kan kom korleis korso kun kunne kva kvar kvarhelst kven kvi kvifor man mange me med medan meg meget mellom men mi min mine mitt mot mykje ned no noe noen noka noko nokon nokor nokre nå når og også om opp oss over på samme seg selv si si sia sidan siden sin sine sitt sjøl skal skulle slik so som som somme somt så sånn til um upp ut uten var vart varte ved vere verte vi vil ville vore vors vort vår være være vært å".split(" ")),e.Pipeline.registerFunction(e.no.stopWordFilter,"stopWordFilter-no")}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sa=function(){this.pipeline.reset(),this.pipeline.add(e.sa.trimmer,e.sa.stopWordFilter,e.sa.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sa.stemmer))},e.sa.wordCharacters="ऀ-ःऄ-एऐ-टठ-यर-िी-ॏॐ-य़ॠ-९॰-ॿ꣠-꣱ꣲ-ꣷ꣸-ꣻ꣼-ꣽꣾ-ꣿᆰ0-ᆰ9",e.sa.trimmer=e.trimmerSupport.generateTrimmer(e.sa.wordCharacters),e.Pipeline.registerFunction(e.sa.trimmer,"trimmer-sa"),e.sa.stopWordFilter=e.generateStopWordFilter('तथा अयम्‌ एकम्‌ इत्यस्मिन्‌ तथा तत्‌ वा अयम्‌ इत्यस्य ते आहूत उपरि तेषाम्‌  किन्तु तेषाम्‌ तदा इत्यनेन अधिकः इत्यस्य तत्‌ केचन बहवः द्वि तथा महत्वपूर्णः अयम्‌ अस्य  विषये अयं अस्ति तत्‌ प्रथमः विषये इत्युपरि इत्युपरि इतर अधिकतमः अधिकः अपि सामान्यतया ठ इतरेतर नूतनम्‌ द  न्यूनम्‌ कश्चित्‌ वा विशालः द  सः अस्ति तदनुसारम् तत्र अस्ति केवलम्‌ अपि अत्र सर्वे विविधाः तत्‌ बहवः यतः इदानीम्‌ द  दक्षिण इत्यस्मै तस्य उपरि नथ अतीव कार्यम्‌ सर्वे एकैकम्‌ इत्यादि। एते सन्ति  उत इत्थम्‌ मध्ये एतदर्थं . स कस्य प्रथमः श्री. करोति अस्मिन् प्रकारः निर्मिता कालः तत्र कर्तुं  समान अधुना ते सन्ति स एकः अस्ति सः अर्थात् तेषां कृते . स्थितम्  विशेषः अग्रिम तेषाम्‌ समान स्रोतः ख म समान इदानीमपि अधिकतया करोतु ते समान इत्यस्य वीथी सह यस्मिन्  कृतवान्‌ धृतः तदा पुनः पूर्वं सः आगतः किम्‌ कुल इतर पुरा  मात्रा स विषये उ अतएव अपि नगरस्य  उपरि यतः प्रतिशतं  कतरः कालः साधनानि भूत तथापि जात सम्बन्धि अन्यत्‌ ग अतः अस्माकं स्वकीयाः अस्माकं इदानीं अन्तः इत्यादयः भवन्तः इत्यादयः एते एताः तस्य अस्य इदम् एते तेषां तेषां तेषां तान् तेषां तेषां तेषां समानः सः एकः च तादृशाः बहवः अन्ये च वदन्ति यत् कियत् कस्मै  कस्मै  यस्मै  यस्मै  यस्मै  यस्मै न अतिनीचः किन्तु प्रथमं सम्पूर्णतया  ततः चिरकालानन्तरं पुस्तकं सम्पूर्णतया अन्तः  किन्तु अत्र वा इह इव श्रद्धाय अवशिष्यते  परन्तु अन्ये वर्गाः सन्ति ते सन्ति शक्नुवन्ति सर्वे मिलित्वा सर्वे एकत्र"'.split(" ")),e.sa.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var r=e.wordcut;r.init(),e.sa.tokenizer=function(t){if(!arguments.length||null==t||void 0==t)return[];if(Array.isArray(t))return t.map(function(r){return isLunr2?new e.Token(r.toLowerCase()):r.toLowerCase()});var i=t.toString().toLowerCase().replace(/^\s+/,"");return r.cut(i).split("|")},e.Pipeline.registerFunction(e.sa.stemmer,"stemmer-sa"),e.Pipeline.registerFunction(e.sa.stopWordFilter,"stopWordFilter-sa")}});
@@ -0,0 +1 @@
+!function(r,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(r.lunr)}(this,function(){return function(r){r.stemmerSupport={Among:function(r,t,i,s){if(this.toCharArray=function(r){for(var t=r.length,i=new Array(t),s=0;s<t;s++)i[s]=r.charCodeAt(s);return i},!r&&""!=r||!t&&0!=t||!i)throw"Bad Among initialisation: s:"+r+", substring_i: "+t+", result: "+i;this.s_size=r.length,this.s=this.toCharArray(r),this.substring_i=t,this.result=i,this.method=s},SnowballProgram:function(){var r;return{bra:0,ket:0,limit:0,cursor:0,limit_backward:0,setCurrent:function(t){r=t,this.cursor=0,this.limit=t.length,this.limit_backward=0,this.bra=this.cursor,this.ket=this.limit},getCurrent:function(){var t=r;return r=null,t},in_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},in_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e<=s&&e>=i&&(e-=i,t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},out_grouping:function(t,i,s){if(this.cursor<this.limit){var e=r.charCodeAt(this.cursor);if(e>s||e<i)return this.cursor++,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor++,!0}return!1},out_grouping_b:function(t,i,s){if(this.cursor>this.limit_backward){var e=r.charCodeAt(this.cursor-1);if(e>s||e<i)return this.cursor--,!0;if(e-=i,!(t[e>>3]&1<<(7&e)))return this.cursor--,!0}return!1},eq_s:function(t,i){if(this.limit-this.cursor<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor+s)!=i.charCodeAt(s))return!1;return this.cursor+=t,!0},eq_s_b:function(t,i){if(this.cursor-this.limit_backward<t)return!1;for(var s=0;s<t;s++)if(r.charCodeAt(this.cursor-t+s)!=i.charCodeAt(s))return!1;return this.cursor-=t,!0},find_among:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=l;m<_.s_size;m++){if(n+l==u){f=-1;break}if(f=r.charCodeAt(n+l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n+_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n+_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},find_among_b:function(t,i){for(var s=0,e=i,n=this.cursor,u=this.limit_backward,o=0,h=0,c=!1;;){for(var a=s+(e-s>>1),f=0,l=o<h?o:h,_=t[a],m=_.s_size-1-l;m>=0;m--){if(n-l==u){f=-1;break}if(f=r.charCodeAt(n-1-l)-_.s[m])break;l++}if(f<0?(e=a,h=l):(s=a,o=l),e-s<=1){if(s>0||e==s||c)break;c=!0}}for(;;){var _=t[s];if(o>=_.s_size){if(this.cursor=n-_.s_size,!_.method)return _.result;var b=_.method();if(this.cursor=n-_.s_size,b)return _.result}if((s=_.substring_i)<0)return 0}},replace_s:function(t,i,s){var e=s.length-(i-t),n=r.substring(0,t),u=r.substring(i);return r=n+s+u,this.limit+=e,this.cursor>=i?this.cursor+=e:this.cursor>t&&(this.cursor=t),e},slice_check:function(){if(this.bra<0||this.bra>this.ket||this.ket>this.limit||this.limit>r.length)throw"faulty slice operation"},slice_from:function(r){this.slice_check(),this.replace_s(this.bra,this.ket,r)},slice_del:function(){this.slice_from("")},insert:function(r,t,i){var s=this.replace_s(r,t,i);r<=this.bra&&(this.bra+=s),r<=this.ket&&(this.ket+=s)},slice_to:function(){return this.slice_check(),r.substring(this.bra,this.ket)},eq_v_b:function(r){return this.eq_s_b(r.length,r)}}}},r.trimmerSupport={generateTrimmer:function(r){var t=new RegExp("^[^"+r+"]+"),i=new RegExp("[^"+r+"]+$");return function(r){return"function"==typeof r.update?r.update(function(r){return r.replace(t,"").replace(i,"")}):r.replace(t,"").replace(i,"")}}}}});
@@ -0,0 +1,18 @@
+/*!
+ * Lunr languages, `Swedish` language
+ * https://github.com/MihaiValentin/lunr-languages
+ *
+ * Copyright 2014, Mihai Valentin
+ * http://www.mozilla.org/MPL/
+ */
+/*!
+ * based on
+ * Snowball JavaScript Library v0.3
+ * http://code.google.com/p/urim/
+ * http://snowball.tartarus.org/
+ *
+ * Copyright 2010, Oleg Mazko
+ * http://www.mozilla.org/MPL/
+ */
+
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.sv=function(){this.pipeline.reset(),this.pipeline.add(e.sv.trimmer,e.sv.stopWordFilter,e.sv.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.sv.stemmer))},e.sv.wordCharacters="A-Za-zªºÀ-ÖØ-öø-ʸˠ-ˤᴀ-ᴥᴬ-ᵜᵢ-ᵥᵫ-ᵷᵹ-ᶾḀ-ỿⁱⁿₐ-ₜKÅℲⅎⅠ-ↈⱠ-ⱿꜢ-ꞇꞋ-ꞭꞰ-ꞷꟷ-ꟿꬰ-ꭚꭜ-ꭤﬀ-ﬆＡ-Ｚａ-ｚ",e.sv.trimmer=e.trimmerSupport.generateTrimmer(e.sv.wordCharacters),e.Pipeline.registerFunction(e.sv.trimmer,"trimmer-sv"),e.sv.stemmer=function(){var r=e.stemmerSupport.Among,n=e.stemmerSupport.SnowballProgram,t=new function(){function e(){var e,r=w.cursor+3;if(o=w.limit,0<=r||r<=w.limit){for(a=r;;){if(e=w.cursor,w.in_grouping(l,97,246)){w.cursor=e;break}if(w.cursor=e,w.cursor>=w.limit)return;w.cursor++}for(;!w.out_grouping(l,97,246);){if(w.cursor>=w.limit)return;w.cursor++}o=w.cursor,o<a&&(o=a)}}function t(){var e,r=w.limit_backward;if(w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(u,37),w.limit_backward=r,e))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.in_grouping_b(d,98,121)&&w.slice_del()}}function i(){var e=w.limit_backward;w.cursor>=o&&(w.limit_backward=o,w.cursor=w.limit,w.find_among_b(c,7)&&(w.cursor=w.limit,w.ket=w.cursor,w.cursor>w.limit_backward&&(w.bra=--w.cursor,w.slice_del())),w.limit_backward=e)}function s(){var e,r;if(w.cursor>=o){if(r=w.limit_backward,w.limit_backward=o,w.cursor=w.limit,w.ket=w.cursor,e=w.find_among_b(m,5))switch(w.bra=w.cursor,e){case 1:w.slice_del();break;case 2:w.slice_from("lös");break;case 3:w.slice_from("full")}w.limit_backward=r}}var a,o,u=[new r("a",-1,1),new r("arna",0,1),new r("erna",0,1),new r("heterna",2,1),new r("orna",0,1),new r("ad",-1,1),new r("e",-1,1),new r("ade",6,1),new r("ande",6,1),new r("arne",6,1),new r("are",6,1),new r("aste",6,1),new r("en",-1,1),new r("anden",12,1),new r("aren",12,1),new r("heten",12,1),new r("ern",-1,1),new r("ar",-1,1),new r("er",-1,1),new r("heter",18,1),new r("or",-1,1),new r("s",-1,2),new r("as",21,1),new r("arnas",22,1),new r("ernas",22,1),new r("ornas",22,1),new r("es",21,1),new r("ades",26,1),new r("andes",26,1),new r("ens",21,1),new r("arens",29,1),new r("hetens",29,1),new r("erns",21,1),new r("at",-1,1),new r("andet",-1,1),new r("het",-1,1),new r("ast",-1,1)],c=[new r("dd",-1,-1),new r("gd",-1,-1),new r("nn",-1,-1),new r("dt",-1,-1),new r("gt",-1,-1),new r("kt",-1,-1),new r("tt",-1,-1)],m=[new r("ig",-1,1),new r("lig",0,1),new r("els",-1,1),new r("fullt",-1,3),new r("löst",-1,2)],l=[17,65,16,1,0,0,0,0,0,0,0,0,0,0,0,0,24,0,32],d=[119,127,149],w=new n;this.setCurrent=function(e){w.setCurrent(e)},this.getCurrent=function(){return w.getCurrent()},this.stem=function(){var r=w.cursor;return e(),w.limit_backward=r,w.cursor=w.limit,t(),w.cursor=w.limit,i(),w.cursor=w.limit,s(),!0}};return function(e){return"function"==typeof e.update?e.update(function(e){return t.setCurrent(e),t.stem(),t.getCurrent()}):(t.setCurrent(e),t.stem(),t.getCurrent())}}(),e.Pipeline.registerFunction(e.sv.stemmer,"stemmer-sv"),e.sv.stopWordFilter=e.generateStopWordFilter("alla allt att av blev bli blir blivit de dem den denna deras dess dessa det detta dig din dina ditt du där då efter ej eller en er era ert ett från för ha hade han hans har henne hennes hon honom hur här i icke ingen inom inte jag ju kan kunde man med mellan men mig min mina mitt mot mycket ni nu när någon något några och om oss på samma sedan sig sin sina sitta själv skulle som så sådan sådana sådant till under upp ut utan vad var vara varför varit varje vars vart vem vi vid vilka vilkas vilken vilket vår våra vårt än är åt över".split(" ")),e.Pipeline.registerFunction(e.sv.stopWordFilter,"stopWordFilter-sv")}});
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.ta=function(){this.pipeline.reset(),this.pipeline.add(e.ta.trimmer,e.ta.stopWordFilter,e.ta.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.ta.stemmer))},e.ta.wordCharacters="஀-உஊ-ஏஐ-ஙச-ட஠-னப-யர-ஹ஺-ிீ-௉ொ-௏ௐ-௙௚-௟௠-௩௪-௯௰-௹௺-௿a-zA-Zａ-ｚＡ-Ｚ0-9０-９",e.ta.trimmer=e.trimmerSupport.generateTrimmer(e.ta.wordCharacters),e.Pipeline.registerFunction(e.ta.trimmer,"trimmer-ta"),e.ta.stopWordFilter=e.generateStopWordFilter("அங்கு அங்கே அது அதை அந்த அவர் அவர்கள் அவள் அவன் அவை ஆக ஆகவே ஆகையால் ஆதலால் ஆதலினால் ஆனாலும் ஆனால் இங்கு இங்கே இது இதை இந்த இப்படி இவர் இவர்கள் இவள் இவன் இவை இவ்வளவு உனக்கு உனது உன் உன்னால் எங்கு எங்கே எது எதை எந்த எப்படி எவர் எவர்கள் எவள் எவன் எவை எவ்வளவு எனக்கு எனது எனவே என் என்ன என்னால் ஏது ஏன் தனது தன்னால் தானே தான் நாங்கள் நாம் நான் நீ நீங்கள்".split(" ")),e.ta.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.ta.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.ta.stemmer,"stemmer-ta"),e.Pipeline.registerFunction(e.ta.stopWordFilter,"stopWordFilter-ta")}});
@@ -0,0 +1 @@
+!function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():t()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.te=function(){this.pipeline.reset(),this.pipeline.add(e.te.trimmer,e.te.stopWordFilter,e.te.stemmer),this.searchPipeline&&(this.searchPipeline.reset(),this.searchPipeline.add(e.te.stemmer))},e.te.wordCharacters="ఀ-ఄఅ-ఔక-హా-ౌౕ-ౖౘ-ౚౠ-ౡౢ-ౣ౦-౯౸-౿఼ఽ్ౝ౷౤౥",e.te.trimmer=e.trimmerSupport.generateTrimmer(e.te.wordCharacters),e.Pipeline.registerFunction(e.te.trimmer,"trimmer-te"),e.te.stopWordFilter=e.generateStopWordFilter("అందరూ అందుబాటులో అడగండి అడగడం అడ్డంగా అనుగుణంగా అనుమతించు అనుమతిస్తుంది అయితే ఇప్పటికే ఉన్నారు ఎక్కడైనా ఎప్పుడు ఎవరైనా ఎవరో ఏ ఏదైనా ఏమైనప్పటికి ఒక ఒకరు కనిపిస్తాయి కాదు కూడా గా గురించి చుట్టూ చేయగలిగింది తగిన తర్వాత దాదాపు దూరంగా నిజంగా పై ప్రకారం ప్రక్కన మధ్య మరియు మరొక మళ్ళీ మాత్రమే మెచ్చుకో వద్ద వెంట వేరుగా వ్యతిరేకంగా సంబంధం".split(" ")),e.te.stemmer=function(){return function(e){return"function"==typeof e.update?e.update(function(e){return e}):e}}();var t=e.wordcut;t.init(),e.te.tokenizer=function(r){if(!arguments.length||null==r||void 0==r)return[];if(Array.isArray(r))return r.map(function(t){return isLunr2?new e.Token(t.toLowerCase()):t.toLowerCase()});var i=r.toString().toLowerCase().replace(/^\s+/,"");return t.cut(i).split("|")},e.Pipeline.registerFunction(e.te.stemmer,"stemmer-te"),e.Pipeline.registerFunction(e.te.stopWordFilter,"stopWordFilter-te")}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var r="2"==e.version[0];e.th=function(){this.pipeline.reset(),this.pipeline.add(e.th.trimmer),r?this.tokenizer=e.th.tokenizer:(e.tokenizer&&(e.tokenizer=e.th.tokenizer),this.tokenizerFn&&(this.tokenizerFn=e.th.tokenizer))},e.th.wordCharacters="[฀-๿]",e.th.trimmer=e.trimmerSupport.generateTrimmer(e.th.wordCharacters),e.Pipeline.registerFunction(e.th.trimmer,"trimmer-th");var t=e.wordcut;t.init(),e.th.tokenizer=function(i){if(!arguments.length||null==i||void 0==i)return[];if(Array.isArray(i))return i.map(function(t){return r?new e.Token(t):t});var n=i.toString().replace(/^\s+/,"");return t.cut(n).split("|")}}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");e.vi=function(){this.pipeline.reset(),this.pipeline.add(e.vi.stopWordFilter,e.vi.trimmer)},e.vi.wordCharacters="[A-Za-ẓ̀͐́͑̉̃̓ÂâÊêÔôĂ-ăĐ-đƠ-ơƯ-ư]",e.vi.trimmer=e.trimmerSupport.generateTrimmer(e.vi.wordCharacters),e.Pipeline.registerFunction(e.vi.trimmer,"trimmer-vi"),e.vi.stopWordFilter=e.generateStopWordFilter("là cái nhưng mà".split(" "))}});
@@ -0,0 +1 @@
+!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r(require("@node-rs/jieba")):r()(e.lunr)}(this,function(e){return function(r,t){if(void 0===r)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===r.stemmerSupport)throw new Error("Lunr stemmer support is not present. Please include / require Lunr stemmer support before this script.");var i="2"==r.version[0];r.zh=function(){this.pipeline.reset(),this.pipeline.add(r.zh.trimmer,r.zh.stopWordFilter,r.zh.stemmer),i?this.tokenizer=r.zh.tokenizer:(r.tokenizer&&(r.tokenizer=r.zh.tokenizer),this.tokenizerFn&&(this.tokenizerFn=r.zh.tokenizer))},r.zh.tokenizer=function(n){if(!arguments.length||null==n||void 0==n)return[];if(Array.isArray(n))return n.map(function(e){return i?new r.Token(e.toLowerCase()):e.toLowerCase()});t&&e.load(t);var o=n.toString().trim().toLowerCase(),s=[];e.cut(o,!0).forEach(function(e){s=s.concat(e.split(" "))}),s=s.filter(function(e){return!!e});var u=0;return s.map(function(e,t){if(i){var n=o.indexOf(e,u),s={};return s.position=[n,e.length],s.index=t,u=n,new r.Token(e,s)}return e})},r.zh.wordCharacters="\\w一-龥",r.zh.trimmer=r.trimmerSupport.generateTrimmer(r.zh.wordCharacters),r.Pipeline.registerFunction(r.zh.trimmer,"trimmer-zh"),r.zh.stemmer=function(){return function(e){return e}}(),r.Pipeline.registerFunction(r.zh.stemmer,"stemmer-zh"),r.zh.stopWordFilter=r.generateStopWordFilter("的 一 不 在 人 有 是 为 為 以 于 於 上 他 而 后 後 之 来 來 及 了 因 下 可 到 由 这 這 与 與 也 此 但 并 並 个 個 其 已 无 無 小 我 们 們 起 最 再 今 去 好 只 又 或 很 亦 某 把 那 你 乃 它 吧 被 比 别 趁 当 當 从 從 得 打 凡 儿 兒 尔 爾 该 該 各 给 給 跟 和 何 还 還 即 几 幾 既 看 据 據 距 靠 啦 另 么 麽 每 嘛 拿 哪 您 凭 憑 且 却 卻 让 讓 仍 啥 如 若 使 谁 誰 虽 雖 随 隨 同 所 她 哇 嗡 往 些 向 沿 哟 喲 用 咱 则 則 怎 曾 至 致 着 著 诸 諸 自".split(" ")),r.Pipeline.registerFunction(r.zh.stopWordFilter,"stopWordFilter-zh")}});
@@ -0,0 +1,206 @@
+/**
+ * export the module via AMD, CommonJS or as a browser global
+ * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js
+ */
+;(function (root, factory) {
+    if (typeof define === 'function' && define.amd) {
+        // AMD. Register as an anonymous module.
+        define(factory)
+    } else if (typeof exports === 'object') {
+        /**
+         * Node. Does not work with strict CommonJS, but
+         * only CommonJS-like environments that support module.exports,
+         * like Node.
+         */
+        module.exports = factory()
+    } else {
+        // Browser globals (root is window)
+        factory()(root.lunr);
+    }
+}(this, function () {
+    /**
+     * Just return a value to define the module export.
+     * This example returns an object, but the module
+     * can return a function as the exported value.
+     */
+
+    return function(lunr) {
+        // TinySegmenter 0.1 -- Super compact Japanese tokenizer in Javascript
+        // (c) 2008 Taku Kudo <taku@chasen.org>
+        // TinySegmenter is freely distributable under the terms of a new BSD licence.
+        // For details, see http://chasen.org/~taku/software/TinySegmenter/LICENCE.txt
+
+        function TinySegmenter() {
+          var patterns = {
+            "[一二三四五六七八九十百千万億兆]":"M",
+            "[一-龠々〆ヵヶ]":"H",
+            "[ぁ-ん]":"I",
+            "[ァ-ヴーｱ-ﾝﾞｰ]":"K",
+            "[a-zA-Zａ-ｚＡ-Ｚ]":"A",
+            "[0-9０-９]":"N"
+          }
+          this.chartype_ = [];
+          for (var i in patterns) {
+            var regexp = new RegExp(i);
+            this.chartype_.push([regexp, patterns[i]]);
+          }
+
+          this.BIAS__ = -332
+          this.BC1__ = {"HH":6,"II":2461,"KH":406,"OH":-1378};
+          this.BC2__ = {"AA":-3267,"AI":2744,"AN":-878,"HH":-4070,"HM":-1711,"HN":4012,"HO":3761,"IA":1327,"IH":-1184,"II":-1332,"IK":1721,"IO":5492,"KI":3831,"KK":-8741,"MH":-3132,"MK":3334,"OO":-2920};
+          this.BC3__ = {"HH":996,"HI":626,"HK":-721,"HN":-1307,"HO":-836,"IH":-301,"KK":2762,"MK":1079,"MM":4034,"OA":-1652,"OH":266};
+          this.BP1__ = {"BB":295,"OB":304,"OO":-125,"UB":352};
+          this.BP2__ = {"BO":60,"OO":-1762};
+          this.BQ1__ = {"BHH":1150,"BHM":1521,"BII":-1158,"BIM":886,"BMH":1208,"BNH":449,"BOH":-91,"BOO":-2597,"OHI":451,"OIH":-296,"OKA":1851,"OKH":-1020,"OKK":904,"OOO":2965};
+          this.BQ2__ = {"BHH":118,"BHI":-1159,"BHM":466,"BIH":-919,"BKK":-1720,"BKO":864,"OHH":-1139,"OHM":-181,"OIH":153,"UHI":-1146};
+          this.BQ3__ = {"BHH":-792,"BHI":2664,"BII":-299,"BKI":419,"BMH":937,"BMM":8335,"BNN":998,"BOH":775,"OHH":2174,"OHM":439,"OII":280,"OKH":1798,"OKI":-793,"OKO":-2242,"OMH":-2402,"OOO":11699};
+          this.BQ4__ = {"BHH":-3895,"BIH":3761,"BII":-4654,"BIK":1348,"BKK":-1806,"BMI":-3385,"BOO":-12396,"OAH":926,"OHH":266,"OHK":-2036,"ONN":-973};
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+          return this;
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+        TinySegmenter.prototype.ctype_ = function(str) {
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+            if (str.match(this.chartype_[i][0])) {
+              return this.chartype_[i][1];
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+          return "O";
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+
+        TinySegmenter.prototype.ts_ = function(v) {
+          if (v) { return v; }
+          return 0;
+        }
+
+        TinySegmenter.prototype.segment = function(input) {
+          if (input == null || input == undefined || input == "") {
+            return [];
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+          var seg = ["B3","B2","B1"];
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+          seg.push("E2");
+          seg.push("E3");
+          ctype.push("O");
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+          var word = seg[3];
+          var p1 = "U";
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+          for (var i = 4; i < seg.length - 3; ++i) {
+            var score = this.BIAS__;
+            var w1 = seg[i-3];
+            var w2 = seg[i-2];
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+            var c4 = ctype[i];
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+            var c6 = ctype[i+2];
+            score += this.ts_(this.UP1__[p1]);
+            score += this.ts_(this.UP2__[p2]);
+            score += this.ts_(this.UP3__[p3]);
+            score += this.ts_(this.BP1__[p1 + p2]);
+            score += this.ts_(this.BP2__[p2 + p3]);
+            score += this.ts_(this.UW1__[w1]);
+            score += this.ts_(this.UW2__[w2]);
+            score += this.ts_(this.UW3__[w3]);
+            score += this.ts_(this.UW4__[w4]);
+            score += this.ts_(this.UW5__[w5]);
+            score += this.ts_(this.UW6__[w6]);
+            score += this.ts_(this.BW1__[w2 + w3]);
+            score += this.ts_(this.BW2__[w3 + w4]);
+            score += this.ts_(this.BW3__[w4 + w5]);
+            score += this.ts_(this.TW1__[w1 + w2 + w3]);
+            score += this.ts_(this.TW2__[w2 + w3 + w4]);
+            score += this.ts_(this.TW3__[w3 + w4 + w5]);
+            score += this.ts_(this.TW4__[w4 + w5 + w6]);
+            score += this.ts_(this.UC1__[c1]);
+            score += this.ts_(this.UC2__[c2]);
+            score += this.ts_(this.UC3__[c3]);
+            score += this.ts_(this.UC4__[c4]);
+            score += this.ts_(this.UC5__[c5]);
+            score += this.ts_(this.UC6__[c6]);
+            score += this.ts_(this.BC1__[c2 + c3]);
+            score += this.ts_(this.BC2__[c3 + c4]);
+            score += this.ts_(this.BC3__[c4 + c5]);
+            score += this.ts_(this.TC1__[c1 + c2 + c3]);
+            score += this.ts_(this.TC2__[c2 + c3 + c4]);
+            score += this.ts_(this.TC3__[c3 + c4 + c5]);
+            score += this.ts_(this.TC4__[c4 + c5 + c6]);
+        //  score += this.ts_(this.TC5__[c4 + c5 + c6]);    
+            score += this.ts_(this.UQ1__[p1 + c1]);
+            score += this.ts_(this.UQ2__[p2 + c2]);
+            score += this.ts_(this.UQ3__[p3 + c3]);
+            score += this.ts_(this.BQ1__[p2 + c2 + c3]);
+            score += this.ts_(this.BQ2__[p2 + c3 + c4]);
+            score += this.ts_(this.BQ3__[p3 + c2 + c3]);
+            score += this.ts_(this.BQ4__[p3 + c3 + c4]);
+            score += this.ts_(this.TQ1__[p2 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ2__[p2 + c2 + c3 + c4]);
+            score += this.ts_(this.TQ3__[p3 + c1 + c2 + c3]);
+            score += this.ts_(this.TQ4__[p3 + c2 + c3 + c4]);
+            var p = "O";
+            if (score > 0) {
+              result.push(word);
+              word = "";
+              p = "B";
+            }
+            p1 = p2;
+            p2 = p3;
+            p3 = p;
+            word += seg[i];
+          }
+          result.push(word);
+
+          return result;
+        }
+
+        lunr.TinySegmenter = TinySegmenter;
+    };
+
+}));
@@ -0,0 +1 @@
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@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -77,12 +77,24 @@
  

    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../installation/">
+<span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
  </span>
 </a>
 </li>
 <li class="md-nav__item md-nav__item--nested">
-<input class="md-nav__toggle md-toggle" id="__nav_2" type="checkbox"/>
-<label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+<input class="md-nav__toggle md-toggle" id="__nav_3" type="checkbox"/>
+<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
 <span class="md-ellipsis">
    
  
@@ -93,8 +105,8 @@
  </span>
 <span class="md-nav__icon md-icon"></span>
 </label>
-<nav aria-expanded="false" aria-labelledby="__nav_2_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_2">
+<nav aria-expanded="false" aria-labelledby="__nav_3_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_3">
 <span class="md-nav__icon md-icon"></span>
            
  
@@ -160,6 +172,18 @@
  

    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../theory/evolutionary_distances/">
+<span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
  </span>
 </a>
 </li>
@@ -167,8 +191,8 @@
 </nav>
 </li>
 <li class="md-nav__item md-nav__item--active md-nav__item--nested">
-<input checked="" class="md-nav__toggle md-toggle" id="__nav_3" type="checkbox"/>
-<label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+<input checked="" class="md-nav__toggle md-toggle" id="__nav_4" type="checkbox"/>
+<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
 <span class="md-ellipsis">
    
  
@@ -179,8 +203,8 @@
  </span>
 <span class="md-nav__icon md-icon"></span>
 </label>
-<nav aria-expanded="true" aria-labelledby="__nav_3_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_3">
+<nav aria-expanded="true" aria-labelledby="__nav_4_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_4">
 <span class="md-nav__icon md-icon"></span>
            
  
@@ -296,6 +320,15 @@
    </span>
 </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
+    </span>
+</a>
+</li>
 </ul>
 </nav>
 </li>
@@ -420,11 +453,47 @@
 </a>
 </li>
 <li class="md-nav__item">
-<a class="md-nav__link" href="../rebuild_filter/">
+<a class="md-nav__link" href="../merge_parallelism/">
 <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism &amp; memory
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../filtering/">
+<span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../select/">
+<span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../obitaxonomy/">
+<span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -435,8 +504,8 @@
 </nav>
 </li>
 <li class="md-nav__item md-nav__item--nested">
-<input class="md-nav__toggle md-toggle" id="__nav_4" type="checkbox"/>
-<label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+<input class="md-nav__toggle md-toggle" id="__nav_5" type="checkbox"/>
+<label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
 <span class="md-ellipsis">
    
  
@@ -447,8 +516,8 @@
  </span>
 <span class="md-nav__icon md-icon"></span>
 </label>
-<nav aria-expanded="false" aria-labelledby="__nav_4_label" class="md-nav" data-md-level="1">
-<label class="md-nav__title" for="__nav_4">
+<nav aria-expanded="false" aria-labelledby="__nav_5_label" class="md-nav" data-md-level="1">
+<label class="md-nav__title" for="__nav_5">
 <span class="md-nav__icon md-icon"></span>
            
  
@@ -478,6 +547,42 @@
  

    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/siblings/">
+<span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_worker_pools/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+</a>
+</li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="../../architecture/numa_partition_runner/">
+<span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
  </span>
 </a>
 </li>
@@ -552,6 +657,15 @@
    </span>
 </a>
 </li>
+<li class="md-nav__item">
+<a class="md-nav__link" href="#future-work-parallel-gzip-decompression-in-xopen">
+<span class="md-ellipsis">
+      
+        Future work — parallel gzip decompression in xopen
+      
+    </span>
+</a>
+</li>
 </ul>
 </nav>
 </div>
@@ -659,6 +773,16 @@ The stream path (<code>NucStream</code> / <code>NucPage</code>) is described in
    FoundAt      --&gt; InHeader  : other</code></pre>
 <p><code>restart</code> is updated each time a <code>+</code> is found. When any state fails its expected input, the scan jumps back to <code>restart</code> and continues from there — guaranteeing that a <code>@</code> in a quality line cannot be accepted as a record start, because the <code>\n+\n</code> structure immediately following it (going backward) will not be found.</p>
 <p>Returns the byte offset of the <code>@</code> that starts the last complete record.</p>
+<hr/>
+<h2 id="future-work-parallel-gzip-decompression-in-xopen">Future work — parallel gzip decompression in <code>xopen</code></h2>
+<p><code>obiread::xopen</code> (<code>xopen.rs</code>) decompresses gzip via <code>niffler</code> → <code>flate2</code>, which is single-threaded (standard DEFLATE has no parallel-decodable structure). For large local gzip inputs this single-threaded decompression can become the throughput bottleneck feeding the <code>query</code>/<code>index</code>/<code>superkmer</code> pipelines, since chunk/page production for a given file is serialized ahead of the worker pool.</p>
+<p>Candidate: special-case local, on-disk, gzip-magic-detected paths in <code>open_raw</code>/<code>xopen</code> to use <a href="https://github.com/alekseizarubin/rapidgzip-rs"><code>rapidgzip-rs</code></a> (<code>ReaderBuilder::new().parallelism(n).open(path)</code>, implements <code>Read + Seek</code>) instead of <code>niffler</code>, keeping <code>niffler</code> for every other case: <code>stdin</code> (<code>-</code>), HTTP(S) sources, and all non-gzip formats (bzip2, xz, zstd — less used in practice here).</p>
+<p>Constraints identified so far (not yet validated against real data):
+- Branch point must move earlier than the current <code>decompress()</code> call in <code>open_raw</code> — rapidgzip's fast path needs the file <strong>path</strong>, not an already-opened generic <code>Read</code>, so the gzip/local-file detection has to happen before the generic <code>File::open</code> + <code>niffler::send::get_reader</code> path is taken.
+- <code>stdin</code> and HTTP sources are not seekable — they stay on <code>niffler</code> regardless; the gain only applies to local on-disk <code>.gz</code> files.
+- <code>rapidgzip-sys</code> vendors a native C++ engine: requires CMake ≥ 3.17, a C++17 compiler, and <code>nasm</code> on x86 targets — a real build-toolchain addition, not just a pure-Rust crate.
+- Low maturity of the Rust binding at review time (2 GitHub stars, ~15 commits, April 2026 latest release) — the underlying C++ engine is validated (HPDC 2023 paper), but the binding itself has limited production track record.</p>
+<p>Decision: parked for now. Before adopting, validate on real data: throughput vs. <code>niffler</code> on representative large <code>.gz</code> inputs, and byte-for-byte correctness of decompressed output.</p>
 </article>
 </div>
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@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
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-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
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-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+
+    
+  </span>
+  
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+    </li>
+  
+
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+      <a href="../select/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+
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+  
+  
+
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+
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
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+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
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+          <label class="md-nav__title" for="__nav_5">
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+              
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
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+
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+  
+
+              
+            
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
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+    </li>
+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
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+    </li>
+  
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+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+  
+  <span class="md-ellipsis">
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+    Installation
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+
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+  </span>
+  
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+
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+    </li>
+  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
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            <span class="md-nav__icon md-icon"></span>
            
  
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+              
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
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+    Central-position SNP distance (discussion)
+  
+
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+      </a>
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+  
+
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
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+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -968,10 +1107,10 @@
      
        
        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
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+            
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@@ -9,10 +9,10 @@
      
      
      
-        <link rel="prev" href="../merge/">
+        <link rel="prev" href="../merge_parallelism/">
      
      
-        <link rel="next" href="../../architecture/sequences/invariant/">
+        <link rel="next" href="../select/">
      
      
        
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-        <title>Kmer filtering (rebuild/dump/unitig) - obikmer</title>
+        <title>Kmer filtering - obikmer</title>
      
    
    
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-              Kmer filtering (rebuild/dump/unitig)
+              Kmer filtering
            
          </span>
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@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
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+
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+  </span>
+  
+  
+
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+    </li>
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+
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+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
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+  
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+    
+  
+    Central-position SNP distance (discussion)
+  
+
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+  </span>
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+    </li>
+  
+
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+          <label class="md-nav__title" for="__nav_4">
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@@ -787,6 +842,34 @@
                
  
  
+  
+  
+    <li class="md-nav__item">
+      <a href="../merge_parallelism/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
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+    </li>
+  
+
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+            
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+                
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+  
    
  
  
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+    Kmer filtering
  

    
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    </span>
  </a>
  
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
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+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
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+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
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+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
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+      
+        Command-specific options
+      
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+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
      
        <li class="md-nav__item">
@@ -991,6 +1152,62 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -1013,10 +1230,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1034,8 +1251,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1101,6 +1318,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -1243,6 +1544,45 @@
    </span>
  </a>
  
+    <nav class="md-nav" aria-label="Quorum flags">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#negative-counts-offset-from-group-size" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Negative counts — offset from group size
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#validation" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Validation
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#conservative-rounding-of-fraction-thresholds" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Conservative rounding of fraction thresholds
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
      
        <li class="md-nav__item">
@@ -1254,6 +1594,45 @@
    </span>
  </a>
  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#command-specific-options" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        Command-specific options
+      
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="Command-specific options">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#dump-head-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        dump --head N
+      
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#phylo-presence-threshold-n" class="md-nav__link">
+    <span class="md-ellipsis">
+      
+        phylo --presence-threshold N
+      
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
      
        <li class="md-nav__item">
@@ -1285,11 +1664,12 @@


 <h1 id="kmer-filtering-and-ingroupoutgroup-predicates">Kmer filtering and ingroup/outgroup predicates</h1>
-<p>The <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> commands all share the same filtering
-system. Filters can select k-mers based on per-genome quorum counts, optionally
-restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived from genome
-metadata.</p>
-<p><code>rebuild</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
+<p>The <code>filter</code>, <code>dump</code>, and <code>unitig</code> commands share the same filtering system,
+implemented as a shared <code>FilterArgs</code> clap argument group embedded in each command
+via <code>#[command(flatten)]</code>. Filters select k-mers based on per-genome quorum
+counts, optionally restricted to <strong>ingroup</strong> and <strong>outgroup</strong> genome sets derived
+from genome metadata. All rules described here apply identically to all three commands.</p>
+<p><code>filter</code> additionally accepts <code>--min-total-count</code> / <code>--max-total-count</code> filters
 that operate on the sum of counts across all genomes.</p>
 <h2 id="predicate-syntax">Predicate syntax</h2>
 <p>Each <code>--ingroup</code> and <code>--outgroup</code> flag takes a predicate of the form:</p>
@@ -1327,16 +1707,44 @@ that operate on the sum of counts across all genomes.</p>
 </table>
 <p>Multiple values separated by <code>|</code> are always OR-ed within the predicate.</p>
 <h3 id="path-matching-and">Path matching (<code>~</code> and <code>!~</code>)</h3>
-<p>Metadata values can represent hierarchical taxonomic paths such as
+<p>Metadata values can represent hierarchical concept paths such as
 <code>/Eukaryota/Viridiplantae/Streptophyta/Betulaceae/Betula/nana</code>.</p>
+<p>Stored taxonomy values always start with <code>/</code> (the root of the path).
+Query patterns do <strong>not</strong> need to start with <code>/</code> — a leading <code>/</code> is an optional
+start anchor, not a requirement.</p>
+<table>
+<thead>
+<tr>
+<th>Pattern form</th>
+<th>Semantics</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>A/B</code></td>
+<td>contiguous sub-path A then B, anywhere in the value</td>
+</tr>
+<tr>
+<td><code>/A/B</code></td>
+<td>value starts with A then B</td>
+</tr>
+<tr>
+<td><code>A/B$</code></td>
+<td>value ends with A then B</td>
+</tr>
+<tr>
+<td><code>/A/B$</code></td>
+<td>value is exactly A then B</td>
+</tr>
+<tr>
+<td><code>A@x/B</code></td>
+<td>A with class <code>x</code> followed by B with any class</td>
+</tr>
+</tbody>
+</table>
 <ul>
-<li><strong>Absolute pattern</strong> (starts with <code>/</code>): the value must start with the pattern
-  at a segment boundary.
-  <code>taxon~/Betulaceae/Betula</code> matches <code>/Betulaceae/Betula/nana</code> and
-  <code>/Betulaceae/Betula</code> but not <code>/Betulaceae/Betuloides/…</code>.</li>
-<li><strong>Bare segment</strong> (no leading <code>/</code>): the value must contain the pattern as an
-  exact path component anywhere.
-  <code>taxon~Betula</code> matches any path that has <code>Betula</code> as one of its segments.</li>
+<li><code>taxon~/Betulaceae/Betula</code> matches any path that starts with <code>Betulaceae</code> then <code>Betula</code>.</li>
+<li><code>taxon~Betula</code> matches any path containing <code>Betula</code> as a segment, anywhere.</li>
 </ul>
 <h3 id="missing-metadata-key-na">Missing metadata key → NA</h3>
 <p>If a genome does not carry the queried metadata key, the predicate returns <strong>NA</strong>.
@@ -1422,12 +1830,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at least N ingroup genomes</td>
+<td>k-mer present in at least N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-count N</code></td>
 <td>ingroup</td>
-<td>k-mer present in at most N ingroup genomes</td>
+<td>k-mer present in at most N ingroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-frac F</code></td>
@@ -1442,12 +1850,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at least N outgroup genomes</td>
+<td>k-mer present in at least N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--max-outgroup-count N</code></td>
 <td>outgroup</td>
-<td>k-mer present in at most N outgroup genomes</td>
+<td>k-mer present in at most N outgroup genomes (N may be negative, see below)</td>
 </tr>
 <tr>
 <td><code>--min-outgroup-frac F</code></td>
@@ -1462,12 +1870,12 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 <tr>
 <td><code>--min-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≥ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≥ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--max-total-count N</code></td>
 <td>all genomes</td>
-<td>sum of per-genome counts ≤ N (<code>rebuild</code> only)</td>
+<td>sum of per-genome counts ≤ N (<code>filter</code> only)</td>
 </tr>
 <tr>
 <td><code>--presence-threshold N</code></td>
@@ -1476,15 +1884,184 @@ cannot be classified are <strong>ignored</strong> in all quorum counts.</p>
 </tr>
 </tbody>
 </table>
-<p>Defaults: mins = 0 (no lower bound), max counts = group size, max fracs = 1.0
-(no upper bound). A filter with all defaults is a no-op.</p>
+<h3 id="negative-counts-offset-from-group-size">Negative counts — offset from group size</h3>
+<p>The four integer count flags (<code>--min-count</code>, <code>--max-count</code>, <code>--min-outgroup-count</code>,
+<code>--max-outgroup-count</code>) accept <strong>negative</strong> values, interpreted as an offset counted
+down from the group size <code>n</code>, resolved at run time once <code>n</code> is known:</p>
+<table>
+<thead>
+<tr>
+<th>Value</th>
+<th>Effective threshold</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>N ≥ 0</code></td>
+<td>literal absolute count <code>N</code></td>
+</tr>
+<tr>
+<td><code>-x</code> (x &gt; 0)</td>
+<td><code>max(1, n − x)</code> — "all but x"</td>
+</tr>
+</tbody>
+</table>
+<p><code>-1</code> literally means <em>all but one</em>, <code>-2</code> <em>all but two</em>, and so on. This expresses
+a quorum relative to the group size that a plain fraction cannot state exactly
+(e.g. "present in every genome except at most one" is <code>n−1</code>, which is <code>0.9</code> for
+<code>n = 10</code> but <code>0.857…</code> for <code>n = 7</code>).</p>
+<p>The threshold is <strong>floored at 1</strong>, never 0: the negative form always keeps
+constraining the group. Without the floor, <code>--min-count -1</code> on a singleton
+ingroup (<code>n = 1</code>) would resolve to <code>0</code> ("at least 0") and silently drop the
+constraint; the floor makes it <code>1</code> ("present in that one genome") instead.</p>
+<p>To express a count of <code>0</code> (e.g. "absent from the ingroup"), use the literal <code>0</code>,
+not a negative — <code>0</code> and <code>-0</code> are indistinguishable, so the offset form starts at
+<code>-1</code>.</p>
+<blockquote>
+<p><strong>Edge case</strong> — on an <em>empty</em> group (<code>n = 0</code>, e.g. a predicate matching no
+genome), a negative count still resolves to <code>1</code>, an impossible constraint that
+rejects every k-mer. This is consistent with an empty group letting nothing
+through, but differs from the "no constraint" behaviour of the fraction flags.</p>
+</blockquote>
+<p><strong>Conditional defaults</strong> — the defaults for <code>--min-frac</code> and <code>--max-outgroup-count</code> depend on two conditions:
+whether the corresponding group was declared, <strong>and</strong> whether any quorum flag for that group was explicitly set.</p>
+<blockquote>
+<p><strong>Rule</strong>: declaring a group activates the smart default <strong>only if no quorum flag for that group is explicitly set</strong>.
+As soon as any quorum flag for a group is present on the command line, all defaults for that group revert to no-op values.</p>
+</blockquote>
+<table>
+<thead>
+<tr>
+<th><code>--ingroup</code></th>
+<th>Any ingroup quorum flag?</th>
+<th><code>--min-frac</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>0.0 (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>1.0</strong> — all ingroup genomes must carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>0.0 — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<table>
+<thead>
+<tr>
+<th><code>--outgroup</code></th>
+<th>Any outgroup quorum flag?</th>
+<th><code>--max-outgroup-count</code> default</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td>not set</td>
+<td>—</td>
+<td>outgroup size (no-op)</td>
+</tr>
+<tr>
+<td>set</td>
+<td>no</td>
+<td><strong>0</strong> — no outgroup genome may carry the k-mer</td>
+</tr>
+<tr>
+<td>set</td>
+<td>yes</td>
+<td>outgroup size — user controls quorum explicitly</td>
+</tr>
+</tbody>
+</table>
+<p>"Any ingroup quorum flag" means any of: <code>--min-count</code>, <code>--max-count</code>, <code>--min-frac</code>, <code>--max-frac</code>.<br />
+"Any outgroup quorum flag" means any of: <code>--min-outgroup-count</code>, <code>--max-outgroup-count</code>, <code>--min-outgroup-frac</code>, <code>--max-outgroup-frac</code>.</p>
+<p><strong>Why this rule?</strong> Setting any quorum flag signals explicit intent — the defaults are there to help when the user omits quorum entirely, not to interfere with deliberate constraints. Mixing implicit and explicit quorum on the same group would risk silent incoherence (e.g. <code>--max-count 0</code> with an implicit <code>--min-frac 1.0</code>).</p>
+<p>All other bounds default to 0 / group size / 0.0 / 1.0 regardless of whether groups are declared.</p>
+<h3 id="validation">Validation</h3>
+<p>After resolving defaults, the following are checked and cause an immediate error:</p>
+<table>
+<thead>
+<tr>
+<th>Condition</th>
+<th>Error</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-count &gt; --max-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-frac &gt; --max-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-count &gt; --max-outgroup-count</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td><code>--min-outgroup-frac &gt; --max-outgroup-frac</code></td>
+<td>incoherent bounds</td>
+</tr>
+<tr>
+<td>any fraction outside <code>[0.0, 1.0]</code></td>
+<td>invalid value</td>
+</tr>
+</tbody>
+</table>
+<p>The check applies to the <strong>effective</strong> values (after defaults are resolved), so an explicit <code>--max-frac 0.5</code> with an implicit <code>--min-frac 1.0</code> would have been caught — but the rule above prevents that situation from arising in the first place.</p>
 <p>Fractions are computed over the size of the classified group, not over total
 genome count. An empty group (no genome classified as ingroup/outgroup) never
 triggers a filter failure.</p>
+<h3 id="conservative-rounding-of-fraction-thresholds">Conservative rounding of fraction thresholds</h3>
+<p>When a fraction threshold <code>F</code> is applied to a group of size <code>N</code>, the effective
+integer threshold is determined by the direction of the bound:</p>
+<table>
+<thead>
+<tr>
+<th>Bound</th>
+<th>Effective count</th>
+<th>Rounding</th>
+<th>Rationale</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td><code>--min-frac F</code></td>
+<td>k-mer in ≥ ⌈F·N⌉ genomes</td>
+<td><strong>ceil</strong></td>
+<td>stricter — a kmer present in exactly ⌊F·N⌋ genomes does not meet the fraction</td>
+</tr>
+<tr>
+<td><code>--max-frac F</code></td>
+<td>k-mer in ≤ ⌊F·N⌋ genomes</td>
+<td><strong>floor</strong></td>
+<td>stricter — a kmer present in ⌈F·N⌉ genomes already exceeds the fraction</td>
+</tr>
+</tbody>
+</table>
+<p>The same rule applies symmetrically to <code>--min-outgroup-frac</code> (ceil) and
+<code>--max-outgroup-frac</code> (floor). The outgroup direction is not inverted: the
+conservative rounding depends only on whether the bound is a minimum or a
+maximum, not on which group it applies to.</p>
+<p><strong>Example</strong> — <code>--min-frac 0.5</code> with an ingroup of 3 genomes:
+<code>⌈0.5 × 3⌉ = ⌈1.5⌉ = 2</code> → at least 2 of 3 ingroup genomes must carry the k-mer.</p>
+<p><strong>Implementation note</strong> — the filter evaluates <code>n / denom &lt; min_frac</code> directly
+(integer <code>n</code>, float comparison) rather than pre-computing <code>⌈F·N⌉</code>. This is
+mathematically equivalent for integer counts: <code>n / N &lt; F</code> ↔ <code>n &lt; F·N</code> ↔
+<code>n ≤ ⌈F·N⌉ − 1</code> ↔ <code>n &lt; ⌈F·N⌉</code>. No explicit rounding is needed.</p>
 <h2 id="examples">Examples</h2>
 <p>Keep k-mers specific to <em>Betula nana</em> — present in at least 2 <em>B. nana</em> genomes
 and absent from every other genome in the index:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1492,7 +2069,7 @@ and absent from every other genome in the index:</p>
 </code></pre></div>
 <p>Keep k-mers found in at least 2 <em>Betula nana</em> genomes and absent from all
 other <em>Betula</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
@@ -1500,21 +2077,28 @@ other <em>Betula</em>:</p>
 </code></pre></div>
 <p>Use taxonomic paths — keep k-mers present in ≥ 50 % of the <em>Betula</em> clade
 and in fewer than 10 % of everything outside <em>Betulaceae</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;taxon~/Betulaceae/Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;taxon!~/Betulaceae&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--min-frac<span class="w"> </span><span class="m">0</span>.5<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-frac<span class="w"> </span><span class="m">0</span>.1
 </code></pre></div>
 <p>Multiple outgroup predicates (OR): exclude k-mers present in <em>Alnus</em> or <em>Carpinus</em>:</p>
-<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>rebuild<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Alnus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;genus=Carpinus&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
-<p>The same flags work identically for <code>dump</code> and <code>unitig</code>. To dump only k-mers
-specific to <em>Betula nana</em>:</p>
+<p>Noise-tolerant core — keep k-mers present in <em>all but one</em> ingroup genome
+(<code>-1</code> = <code>n−1</code>) and absent from <em>all but one</em> of the outgroup:</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>filter<span class="w"> </span>src<span class="w"> </span>--output<span class="w"> </span>dst<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;genus=Betula&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--min-count<span class="w"> </span>-1<span class="w"> </span><span class="se">\</span>
+<span class="w">  </span>--max-outgroup-count<span class="w"> </span>-1
+</code></pre></div>
+<p>To dump only k-mers specific to <em>Betula nana</em>:</p>
 <div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--ingroup<span class="w">  </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--outgroup<span class="w"> </span><span class="s2">&quot;*&quot;</span><span class="w"> </span><span class="se">\</span>
@@ -1528,6 +2112,21 @@ specific to <em>Betula nana</em>:</p>
 <span class="w">  </span>--min-count<span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="se">\</span>
 <span class="w">  </span>--max-outgroup-count<span class="w"> </span><span class="m">0</span>
 </code></pre></div>
+<h2 id="command-specific-options">Command-specific options</h2>
+<h3 id="dump-head-n"><code>dump --head N</code></h3>
+<p>Stops output after the first N k-mers that pass all active filters.
+Iteration terminates immediately — subsequent partitions and layers are not scanned.
+Useful for quick inspection of large indexes without loading the entire dataset.</p>
+<div class="highlight"><pre><span></span><code>obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">100</span>
+obikmer<span class="w"> </span>dump<span class="w"> </span>myindex<span class="w"> </span>--head<span class="w"> </span><span class="m">20</span><span class="w"> </span>--ingroup<span class="w"> </span><span class="s2">&quot;species=Betula_nana&quot;</span><span class="w"> </span>--min-count<span class="w"> </span><span class="m">1</span>
+</code></pre></div>
+<h3 id="phylo-presence-threshold-n"><code>phylo --presence-threshold N</code></h3>
+<p>When computing Jaccard distance on a <strong>count index</strong>, a k-mer is considered present in a genome if its count is ≥ N (default 1).
+This option is independent of the <code>--presence-threshold</code> used in filtering.</p>
+<div class="highlight"><pre><span></span><code><span class="c1"># Jaccard treating kmers with count ≥ 2 as present</span>
+obikmer<span class="w"> </span>phylo<span class="w"> </span>myindex<span class="w"> </span>--metric<span class="w"> </span>jaccard<span class="w"> </span>--presence-threshold<span class="w"> </span><span class="m">2</span>
+</code></pre></div>
+<p>This parameter has no effect on presence/absence indexes (where values are already 0/1) or on metrics other than Jaccard.</p>
 <h2 id="implementation">Implementation</h2>
 <ul>
 <li>
@@ -1539,14 +2138,14 @@ specific to <em>Betula nana</em>:</p>
 </li>
 <li>
 <p><strong><code>obikmer::cmd::predicate::FilterArgs</code></strong> — shared <code>clap</code> argument group
-  embedded via <code>#[command(flatten)]</code> in <code>RebuildArgs</code>, <code>DumpArgs</code>, and
+  embedded via <code>#[command(flatten)]</code> in <code>FilterArgs</code>, <code>DumpArgs</code>, and
  <code>UnitigArgs</code>. <code>FilterArgs::build_filters()</code> returns a ready-to-use filter
  list.</p>
 </li>
 <li>
 <p><strong><code>obikpartitionner::KmerPartition::iter_partition_kmers</code></strong> — accepts
  <code>filters: &amp;[Box&lt;dyn KmerFilter&gt;]</code> and applies them per-kmer before invoking
-  the callback. <code>rebuild</code>, <code>dump</code>, and <code>unitig</code> all go through this single
+  the callback. <code>filter</code>, <code>dump</code>, and <code>unitig</code> all go through this single
  entry point.</p>
 </li>
 </ul>
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -925,14 +980,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -968,10 +1107,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -989,8 +1128,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1056,6 +1195,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -12,7 +12,7 @@
        <link rel="prev" href="../persistent_bit_vec/">
      
      
-        <link rel="next" href="../rebuild_filter/">
+        <link rel="next" href="../merge_parallelism/">
      
      
        
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -997,14 +1052,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1040,10 +1179,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1061,8 +1200,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1128,6 +1267,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
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          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1003,14 +1058,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
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+  
+
+              
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1046,10 +1185,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1067,8 +1206,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1134,6 +1273,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1103,14 +1158,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1146,10 +1285,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1167,8 +1306,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1234,6 +1373,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
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+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -953,14 +1008,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -996,10 +1135,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1084,6 +1223,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1065,14 +1120,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1108,10 +1247,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1129,8 +1268,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1196,6 +1335,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1048,14 +1103,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1091,10 +1230,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1112,8 +1251,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1179,6 +1318,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -914,14 +969,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -957,10 +1096,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -978,8 +1117,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1045,6 +1184,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -986,14 +1041,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1029,10 +1168,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1050,8 +1189,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1117,6 +1256,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -9,7 +9,7 @@
      
      
      
-        <link rel="prev" href="../../theory/indexing/">
+        <link rel="prev" href="../../theory/evolutionary_distances/">
      
      
        <link rel="next" href="../kmer/">
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -892,14 +947,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -935,10 +1074,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -956,8 +1095,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1023,6 +1162,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -182,6 +182,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
    
    
    
@@ -191,10 +218,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -212,8 +239,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -363,6 +390,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -387,10 +442,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -408,8 +463,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1014,14 +1069,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../rebuild_filter/" class="md-nav__link">
+      <a href="../merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -1057,10 +1196,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -1078,8 +1217,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1145,6 +1284,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
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+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -402,8 +457,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
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+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -178,6 +178,33 @@
  
  
  
+    <li class="md-nav__item">
+      <a href="../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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@@ -187,10 +214,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
        
          
-          <label class="md-nav__link" for="__nav_2" id="__nav_2_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -208,8 +235,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -359,6 +386,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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@@ -381,10 +436,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
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@@ -784,14 +839,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -827,10 +966,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -848,8 +987,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -915,6 +1054,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -9,7 +9,7 @@
      
      
      
-        <link rel="prev" href="..">
+        <link rel="prev" href="../installation/">
      
      
        <link rel="next" href="../theory/encoding/">
@@ -180,6 +180,33 @@
      
  
  
+  
+  
+    <li class="md-nav__item">
+      <a href="../installation/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Installation
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
    
  
  
@@ -193,10 +220,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
        
          
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+          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
            
  
  
@@ -214,8 +241,8 @@
            <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_2">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -462,6 +489,34 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../theory/evolutionary_distances/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Central-position SNP distance (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
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@@ -484,10 +539,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
        
          
-          <label class="md-nav__link" for="__nav_3" id="__nav_3_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
            
  
  
@@ -505,8 +560,8 @@
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_4">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -887,14 +942,98 @@
  
  
    <li class="md-nav__item">
-      <a href="../implementation/rebuild_filter/" class="md-nav__link">
+      <a href="../implementation/merge_parallelism/" class="md-nav__link">
        
  
  
  <span class="md-ellipsis">
    
  
-    Kmer filtering (rebuild/dump/unitig)
+    Merge parallelism & memory
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/filtering/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Kmer filtering
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/select/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Select command
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../implementation/obitaxonomy/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    obitaxonomy crate
  

    
@@ -930,10 +1069,10 @@
      
        
        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
        
          
-          <label class="md-nav__link" for="__nav_4" id="__nav_4_label" tabindex="0">
+          <label class="md-nav__link" for="__nav_5" id="__nav_5_label" tabindex="0">
            
  
  
@@ -951,8 +1090,8 @@
            <span class="md-nav__icon md-icon"></span>
          </label>
        
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
            <span class="md-nav__icon md-icon"></span>
            
  
@@ -1018,6 +1157,90 @@

              
            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/siblings/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    Sibling annex (discussion)
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_worker_pools/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware worker pools
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../architecture/numa_partition_runner/" class="md-nav__link">
+        
+  
+  
+  <span class="md-ellipsis">
+    
+  
+    NUMA-aware partition runner
+  
+
+    
+  </span>
+  
+  
+
+      </a>
+    </li>
+  
+
+              
+            
          </ul>
        </nav>
      
@@ -241,3 +241,21 @@
 	volume = 33,
 	year = 2017,
 	bdsk-url-1 = {http://dx.doi.org/10.1093/bioinformatics/btw832}}
+
+@misc{Mash-distances-doc,
+	author = {{Marbl Lab}},
+	howpublished = {Mash documentation},
+	title = {Mash Distance},
+	url = {https://mash.readthedocs.io/en/latest/distances.html},
+	urldate = {2026-07-09},
+	year = 2026}
+
+@article{Fan2015-mash-formula,
+	author = {Fan, Huan and Ives, Anthony R and Surget-Groba, Yann and Cannon, Charles H},
+	doi = {10.1186/s12864-015-1647-5},
+	journal = {BMC Genomics},
+	number = 1,
+	title = {An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data},
+	url = {https://doi.org/10.1186/s12864-015-1647-5},
+	volume = 16,
+	year = 2015}
@@ -0,0 +1,3 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
+</urlset>
--- a/Show More
+++ b/Show More
				`@@ -0,0 +1 @@`
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