feat: add phylogenetic analysis CLI command and lazy distance traits

Introduce the `obikphylo` crate to support genome-vs-genome distance matrix computation and phylogenetic tree inference via Neighbor-Joining and UPGMA algorithms. Extend the `obikmer2` CLI with a new `phylo` command that exposes configurable metrics, presence thresholds, and CSV/Newick output options. Refactor `obikindex` to expose trait-based partial aggregation for efficient distance metric finalization without full matrix materialization. Update dependency graphs and remove obsolete storage modules.

src/Cargo.lock

@@ -1677,6 +1677,7 @@ dependencies = [
  "obikindex",
  "obikindexer",
  "obikmerge",
+ "obikphylo",
  "obikquery",
  "obikrebuild",
  "obikrope",
@@ -1712,6 +1713,7 @@ dependencies = [
 name = "obikphylo"
 version = "0.1.0"
 dependencies = [
+ "kodama",
  "memmap2",
  "ndarray",
  "obicompactvec",
@@ -1725,8 +1727,10 @@ dependencies = [
  "obiskbuilder",
  "obiskio",
  "obisys",
+ "petgraph",
  "rand 0.10.2",
  "rayon",
+ "speedytree",
  "tempfile",
  "tracing",
  "tracing-subscriber",

src/obikindex/src/layer/content_layer.rs

@@ -26,7 +26,8 @@ use std::path::{Path, PathBuf};
 
 use crate::layer::utils::LAYERNAME_SUFFIX;
 
-use obicompactvec::{PersistentBitMatrix, PersistentIntMatrix};
+use ndarray::{Array1, Array2};
+use obicompactvec::{BitPartials, ColumnWeights, CountPartials, PersistentBitMatrix, PersistentIntMatrix};
 use obikseq::CanonicalKmer;
 
 use crate::index::error::OKIResult;
@@ -349,3 +350,79 @@ impl KmerLayer {
         }
     }
 }
+
+// ── obicompactvec's statistics traits — read-only accessors, same spirit
+// as `col_weights`/`nonzero_iter` above, just formalised as trait impls so
+// generic aggregation code (`obikidxcache::IndexCache`'s callers) can rely
+// on `KmerLayer: ColumnWeights`/`CountPartials`/`BitPartials` rather than
+// duck-typing matching method names. `CountPartials`/`BitPartials` each
+// only make sense for the content this layer actually holds — calling the
+// wrong one panics, same convention as `col()`/`content()` above.
+
+impl ColumnWeights for KmerLayer {
+    fn col_weights(&self) -> Array1<u64> {
+        self.col_weights()
+    }
+}
+
+impl CountPartials for KmerLayer {
+    fn partial_bray(&self) -> Array2<u64> {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_bray(),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_bray() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_bray() called on an Empty layer"),
+        }
+    }
+    fn partial_euclidean(&self) -> Array2<f64> {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_euclidean(),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_euclidean() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_euclidean() called on an Empty layer"),
+        }
+    }
+    fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_threshold_jaccard(threshold),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_threshold_jaccard() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_threshold_jaccard() called on an Empty layer"),
+        }
+    }
+    fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_relfreq_bray(global),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_relfreq_bray() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_relfreq_bray() called on an Empty layer"),
+        }
+    }
+    fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_relfreq_euclidean(global),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_relfreq_euclidean() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_relfreq_euclidean() called on an Empty layer"),
+        }
+    }
+    fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
+        match self {
+            KmerLayer::Count { layer, .. } => layer.partial_hellinger(global),
+            KmerLayer::Presence { .. } => panic!("CountPartials::partial_hellinger() called on a Presence layer"),
+            KmerLayer::Empty { .. } => panic!("CountPartials::partial_hellinger() called on an Empty layer"),
+        }
+    }
+}
+
+impl BitPartials for KmerLayer {
+    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
+        match self {
+            KmerLayer::Presence { layer, .. } => layer.partial_jaccard(),
+            KmerLayer::Count { .. } => panic!("BitPartials::partial_jaccard() called on a Count layer"),
+            KmerLayer::Empty { .. } => panic!("BitPartials::partial_jaccard() called on an Empty layer"),
+        }
+    }
+    fn partial_hamming(&self) -> Array2<u64> {
+        match self {
+            KmerLayer::Presence { layer, .. } => layer.partial_hamming(),
+            KmerLayer::Count { .. } => panic!("BitPartials::partial_hamming() called on a Count layer"),
+            KmerLayer::Empty { .. } => panic!("BitPartials::partial_hamming() called on an Empty layer"),
+        }
+    }
+}

src/obikindex/src/layer/tests/typed_layer.rs

@@ -196,11 +196,11 @@ fn count_layer_reports_count_content_and_columnar_storage() {
     set_k(4);
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
-    TypedLayer::<PersistentIntMatrix>::build(dir.pat
-        h(), DEFAUL
-       T_BLOCK_BITS, &Index
-       Mode::Exact, |_| 1)
-       ,
+    TypedLayer::<PersistentIntMatrix>::build(
+        dir.path(),
+        DEFAULT_BLOCK_BITS,
+        &IndexMode::Exact,
+        |_| 1,
     ).unwrap();
     let layer = TypedLayer::<PersistentIntMatrix>::open(dir.path()).unwrap();
 

src/obikindex/src/layer/typed_layer.rs

@@ -1,8 +1,10 @@
 // use crate::layer::utils::layer_dir;
 use obicompactvec::{
-    BinaryMatrix, ColBuilder, MatrixBuilder, PersistentBitMatrix, PersistentBitMatrixBuilder,
-    PersistentCompactIntMatrixBuilder, PersistentIntMatrix, PersistentSparseBitMatrix,
+    BinaryMatrix, BitPartials, ColBuilder, CountPartials, MatrixBuilder, PersistentBitMatrix,
+    PersistentBitMatrixBuilder, PersistentCompactIntMatrixBuilder, PersistentIntMatrix,
+    PersistentSparseBitMatrix,
 };
+use ndarray::{Array1, Array2};
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
 use std::collections::HashMap;
@@ -424,6 +426,29 @@ impl TypedLayer<PersistentIntMatrix> {
     ) -> Box<dyn Iterator<Item = (usize, usize, u32)> + 'a> {
         self.data.nonzero_iter(slots)
     }
+
+    /// `CountPartials`' required primitives, delegated straight to the
+    /// underlying matrix — see `obicompactvec::CountPartials` for what
+    /// each one means and how its provided finalisation methods
+    /// (`bray_dist_matrix`, `jaccard_dist_matrix`, ...) consume them.
+    pub fn partial_bray(&self) -> Array2<u64> {
+        CountPartials::partial_bray(&self.data)
+    }
+    pub fn partial_euclidean(&self) -> Array2<f64> {
+        CountPartials::partial_euclidean(&self.data)
+    }
+    pub fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
+        CountPartials::partial_threshold_jaccard(&self.data, threshold)
+    }
+    pub fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
+        CountPartials::partial_relfreq_bray(&self.data, global)
+    }
+    pub fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
+        CountPartials::partial_relfreq_euclidean(&self.data, global)
+    }
+    pub fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
+        CountPartials::partial_hellinger(&self.data, global)
+    }
 }
 
 // ── Mode 3 — presence/absence matrix ─────────────────────────────────────────
@@ -487,6 +512,15 @@ impl TypedLayer<PersistentBitMatrix> {
         self.data.nonzero_iter(slots)
     }
 
+    /// `BitPartials`' required primitives, delegated straight to the
+    /// underlying matrix.
+    pub fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
+        BitPartials::partial_jaccard(&self.data)
+    }
+    pub fn partial_hamming(&self) -> Array2<u64> {
+        BitPartials::partial_hamming(&self.data)
+    }
+
     pub fn append_genome_column(
         layer_dir: &Path,
         value_of: impl Fn(usize) -> bool,

src/obikmer2/Cargo.toml

@@ -23,6 +23,7 @@ obikrebuild   = { path = "../obikrebuild" }
 obikstats     = { path = "../obikstats" }
 obikquery     = { path = "../obikquery" }
 obikidxcache  = { path = "../obikidxcache" }
+obikphylo     = { path = "../obikphylo" }
 obikrope      = { path = "../obikrope" }
 obifastwrite  = { path = "../obifastwrite" }
 obiskbuilder  = { path = "../obiskbuilder" }

src/obikmer2/src/cmd/mod.rs

@@ -7,6 +7,7 @@ pub mod index;
 pub mod merge;
 pub mod pack;
 mod predicate;
+pub mod phylo;
 pub mod query;
 pub mod select;
 pub mod superkmer;

src/obikmer2/src/cmd/phylo/args.rs

@@ -0,0 +1,72 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikphylo::DistanceMetric;
+
+#[derive(clap::ValueEnum, Clone, Copy, Debug)]
+pub enum MetricArg {
+    Jaccard,
+    Mash,
+    Hamming,
+    BrayCurtis,
+    #[value(name = "relfreq-bray-curtis")]
+    RelfreqBrayCurtis,
+    Euclidean,
+    #[value(name = "relfreq-euclidean")]
+    RelfreqEuclidean,
+    Hellinger,
+    #[value(name = "hellinger-euclidean")]
+    HellingerEuclidean,
+}
+
+impl From<MetricArg> for DistanceMetric {
+    fn from(m: MetricArg) -> Self {
+        match m {
+            MetricArg::Jaccard            => DistanceMetric::Jaccard,
+            MetricArg::Mash               => DistanceMetric::Mash,
+            MetricArg::Hamming            => DistanceMetric::Hamming,
+            MetricArg::BrayCurtis         => DistanceMetric::BrayCurtis,
+            MetricArg::RelfreqBrayCurtis  => DistanceMetric::RelfreqBrayCurtis,
+            MetricArg::Euclidean          => DistanceMetric::Euclidean,
+            MetricArg::RelfreqEuclidean   => DistanceMetric::RelfreqEuclidean,
+            MetricArg::Hellinger          => DistanceMetric::Hellinger,
+            MetricArg::HellingerEuclidean => DistanceMetric::HellingerEuclidean,
+        }
+    }
+}
+
+/// Partial transfer of `obikmer`'s `phylo` command: the plain distance-metric
+/// path only (`--metric`/NJ/UPGMA) — everything sibling-annex-based
+/// (`--sibling-annex`, `--snp`, `--sankoff`, `--tnt`/`--phyg`/`--iqtree`, ...)
+/// stays in `obikmer` until `obikphylo::siblings` is reconnected (see the
+/// project memory on this).
+#[derive(Args)]
+pub struct PhyloArgs {
+    /// Index directory
+    pub index: PathBuf,
+
+    /// Distance metric to compute
+    #[arg(long, value_enum, default_value = "jaccard")]
+    pub metric: MetricArg,
+
+    /// Minimum count to consider a kmer present when computing Jaccard on count indexes
+    #[arg(long, default_value = "1")]
+    pub presence_threshold: u32,
+
+    /// Also output the shared-kmer count matrix (CSV)
+    #[arg(long)]
+    pub shared_kmers: bool,
+
+    /// Compute and write a Neighbor-Joining tree (Newick)
+    #[arg(long)]
+    pub nj: bool,
+
+    /// Compute and write a UPGMA tree (Newick)
+    #[arg(long)]
+    pub upgma: bool,
+
+    /// Output prefix: <prefix>_dist.csv, <prefix>_shared.csv, <prefix>_nj.nwk,
+    /// <prefix>_upgma.nwk. If omitted, the distance matrix is written to stdout.
+    #[arg(short, long)]
+    pub output: Option<PathBuf>,
+}

src/obikmer2/src/cmd/phylo/mod.rs

@@ -0,0 +1,134 @@
+mod args;
+
+use std::io::{self, BufWriter, Write};
+use std::sync::Arc;
+
+use obikidxcache::index_cache::IndexCache;
+use obikindex::KmerIndex;
+use obikphylo::{Metrics, neighbor_joining_newick, upgma_newick};
+use obisys::{Reporter, Stage};
+use tracing::info;
+
+pub use args::PhyloArgs;
+
+pub fn run(args: PhyloArgs) {
+    let idx = Arc::new(KmerIndex::open(&args.index).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    }));
+
+    let labels: Vec<String> = idx
+        .meta()
+        .genomes()
+        .unwrap_or_else(|e| {
+            eprintln!("error reading index metadata: {e}");
+            std::process::exit(1);
+        })
+        .iter()
+        .map(|g| g.label.clone())
+        .collect();
+    let n = labels.len();
+
+    let mut rep = Reporter::new();
+
+    info!("computing {:?} distances for {} genome(s)", args.metric, n);
+
+    // Every partition/layer this needs is opened once, up front, and
+    // handed to `Metrics::distance` — see `obikquery`'s own use of
+    // `IndexCache` for the same reasoning (one open, many in-memory reads).
+    let cache = IndexCache::new(Arc::clone(&idx), None);
+
+    let need_shared = args.shared_kmers || args.nj || args.upgma;
+    let t = Stage::start("distance");
+    let result = cache
+        .distance(args.metric.into(), need_shared, args.presence_threshold)
+        .unwrap_or_else(|e| {
+            eprintln!("error computing distances: {e}");
+            std::process::exit(1);
+        });
+    rep.push(t.stop());
+
+    // ── Distance matrix → CSV ─────────────────────────────────────────────────
+    let write_dist_csv = |w: &mut dyn Write| {
+        write!(w, "genome").unwrap();
+        for g in &labels { write!(w, ",{g}").unwrap(); }
+        writeln!(w).unwrap();
+        for (i, g) in labels.iter().enumerate() {
+            write!(w, "{g}").unwrap();
+            for j in 0..n {
+                write!(w, ",{:.6}", result.matrix[[i, j]]).unwrap();
+            }
+            writeln!(w).unwrap();
+        }
+    };
+
+    match &args.output {
+        Some(prefix) => {
+            let path = format!("{}_dist.csv", prefix.display());
+            let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+                eprintln!("error creating {path}: {e}");
+                std::process::exit(1);
+            }));
+            write_dist_csv(&mut f);
+            info!("distance matrix → {path}");
+        }
+        None => {
+            let stdout = io::stdout();
+            let mut out = BufWriter::new(stdout.lock());
+            write_dist_csv(&mut out);
+        }
+    }
+
+    // ── Shared-kmer matrix → CSV ──────────────────────────────────────────────
+    if args.shared_kmers {
+        if let Some(shared) = &result.shared_kmers {
+            let path = args.output.as_ref()
+                .map(|p| format!("{}_shared.csv", p.display()))
+                .unwrap_or_else(|| "shared.csv".into());
+            let mut f = BufWriter::new(std::fs::File::create(&path).unwrap_or_else(|e| {
+                eprintln!("error creating {path}: {e}");
+                std::process::exit(1);
+            }));
+            write!(f, "genome").unwrap();
+            for g in &labels { write!(f, ",{g}").unwrap(); }
+            writeln!(f).unwrap();
+            for (i, g) in labels.iter().enumerate() {
+                write!(f, "{g}").unwrap();
+                for j in 0..n { write!(f, ",{}", shared[[i, j]]).unwrap(); }
+                writeln!(f).unwrap();
+            }
+            info!("shared-kmer matrix → {path}");
+        }
+    }
+
+    // ── NJ tree ────────────────────────────────────────────────────────────────
+    if args.nj {
+        let newick = neighbor_joining_newick(&result.matrix, &labels).unwrap_or_else(|e| {
+            eprintln!("error computing NJ tree: {e}");
+            std::process::exit(1);
+        });
+        let path = args.output.as_ref()
+            .map(|p| format!("{}_nj.nwk", p.display()))
+            .unwrap_or_else(|| "nj.nwk".into());
+        std::fs::write(&path, &newick).unwrap_or_else(|e| {
+            eprintln!("error writing {path}: {e}");
+            std::process::exit(1);
+        });
+        info!("NJ tree → {path}");
+    }
+
+    // ── UPGMA tree ───────────────────────────────────────────────────────────────
+    if args.upgma {
+        let newick = upgma_newick(&result.matrix, &labels);
+        let path = args.output.as_ref()
+            .map(|p| format!("{}_upgma.nwk", p.display()))
+            .unwrap_or_else(|| "upgma.nwk".into());
+        std::fs::write(&path, &newick).unwrap_or_else(|e| {
+            eprintln!("error writing {path}: {e}");
+            std::process::exit(1);
+        });
+        info!("UPGMA tree → {path}");
+    }
+
+    rep.print();
+}

src/obikmer2/src/main.rs

@@ -39,6 +39,9 @@ enum Commands {
     Utils(cmd::utils::UtilsArgs),
     /// Convert an index's evidence representation (exact/approximate/hybrid), in place
     Convert(cmd::convert::ConvertArgs),
+    /// Genome-vs-genome distance matrix (+ optional NJ/UPGMA tree) — partial transfer,
+    /// sibling-annex-based operations are not yet ported (see obikmer's own `phylo`)
+    Phylo(cmd::phylo::PhyloArgs),
 }
 
 fn main() {
@@ -64,5 +67,6 @@ fn main() {
         Commands::Annotate(args) => cmd::annotate::run(args),
         Commands::Utils(args) => cmd::utils::run(args),
         Commands::Convert(args) => cmd::convert::run(args),
+        Commands::Phylo(args) => cmd::phylo::run(args),
     }
 }

src/obikphylo/Cargo.toml

@@ -12,10 +12,13 @@ obicompactvec    = { path = "../obicompactvec" }
 obikidxcache     = { path = "../obikidxcache" }
 obiskbuilder     = { path = "../obiskbuilder" }
 obipipeline      = { path = "../obipipeline" }
+kodama           = "0.3.0"
 memmap2          = "0.9"
 ndarray          = "0.17"
+petgraph         = "0.6.4"
 rand             = "0.10"
 rayon            = "1"
+speedytree       = "0.1"
 tracing          = "0.1.44"
 
 [dev-dependencies]

src/obikphylo/src/distance.rs

@@ -1,10 +1,23 @@
-use ndarray::Array2;
-use obicompactvec::traits::{BitPartials, CountPartials};
-use obikidxcache::LayeredStore;
-use rayon::prelude::*;
+//! Genome-vs-genome distance matrices over a whole index — the aggregation
+//! (summing per-layer partials into one global partial) and the final
+//! distance calculation are both phylogenetic domain logic, so both live
+//! here, not in `obikidxcache` (which only ever hands out already-opened
+//! `KmerLayer`s via `IndexCache::iter()` — plain exposition, no
+//! computation of its own).
+//!
+//! [`AggregatedCount`]/[`AggregatedBit`] exist purely to "hang"
+//! `obicompactvec`'s `CountPartials`/`BitPartials` traits on a borrowed
+//! collection of `KmerLayer`s, so their already-written finalisation
+//! methods (`bray_dist_matrix`, `jaccard_dist_matrix`, ...) can be reused
+//! as-is instead of re-derived here — see `KmerLayer`'s own
+//! `ColumnWeights`/`CountPartials`/`BitPartials` impls (`obikindex`) for
+//! the per-layer primitives these sum.
 
+use ndarray::{Array1, Array2};
+use obicompactvec::{BitPartials, ColumnWeights, CountPartials};
+use obikidxcache::index_cache::IndexCache;
+use obikindex::layer::{KmerLayer, LayerContent};
 use obikindex::{OKIError, OKIResult};
-use obikindex::KmerIndex;
 
 // ── Public API ────────────────────────────────────────────────────────────────
 
@@ -51,43 +64,122 @@ impl DistanceMetric {
     }
 }
 
-// ── KmerIndex::distance ───────────────────────────────────────────────────────
+// ── Aggregators — sum every cached layer's own partials into one global
+// partial, then hand the result off to `CountPartials`/`BitPartials`'s own
+// provided finalisation methods.
 
-impl KmerIndex {
-    pub fn distance(&self, metric: DistanceMetric, shared_kmers: bool, presence_threshold: u32) -> OKIResult<DistanceOutput> {
-        let n_genomes = self.meta.genomes().map_err(OKIError::Io)?.len();
+fn sum_array1(n: usize, items: impl Iterator<Item = Array1<u64>>) -> Array1<u64> {
+    items.fold(Array1::zeros(n), |acc, x| acc + x)
+}
+fn sum_array2_u64(n: usize, items: impl Iterator<Item = Array2<u64>>) -> Array2<u64> {
+    items.fold(Array2::zeros((n, n)), |acc, x| acc + x)
+}
+fn sum_array2_f64(n: usize, items: impl Iterator<Item = Array2<f64>>) -> Array2<f64> {
+    items.fold(Array2::zeros((n, n)), |acc, x| acc + x)
+}
+
+struct AggregatedCount<'a> {
+    n_genomes: usize,
+    layers: Vec<&'a KmerLayer>,
+}
+
+impl ColumnWeights for AggregatedCount<'_> {
+    fn col_weights(&self) -> Array1<u64> {
+        sum_array1(self.n_genomes, self.layers.iter().map(|l| l.col_weights()))
+    }
+}
+
+impl CountPartials for AggregatedCount<'_> {
+    fn partial_bray(&self) -> Array2<u64> {
+        sum_array2_u64(self.n_genomes, self.layers.iter().map(|l| l.partial_bray()))
+    }
+    fn partial_euclidean(&self) -> Array2<f64> {
+        sum_array2_f64(self.n_genomes, self.layers.iter().map(|l| l.partial_euclidean()))
+    }
+    fn partial_threshold_jaccard(&self, threshold: u32) -> (Array2<u64>, Array2<u64>) {
+        let n = self.n_genomes;
+        self.layers.iter().map(|l| l.partial_threshold_jaccard(threshold)).fold(
+            (Array2::zeros((n, n)), Array2::zeros((n, n))),
+            |(inter, union), (i, u)| (inter + i, union + u),
+        )
+    }
+    fn partial_relfreq_bray(&self, global: &Array1<u64>) -> Array2<f64> {
+        sum_array2_f64(self.n_genomes, self.layers.iter().map(|l| l.partial_relfreq_bray(global)))
+    }
+    fn partial_relfreq_euclidean(&self, global: &Array1<u64>) -> Array2<f64> {
+        sum_array2_f64(self.n_genomes, self.layers.iter().map(|l| l.partial_relfreq_euclidean(global)))
+    }
+    fn partial_hellinger(&self, global: &Array1<u64>) -> Array2<f64> {
+        sum_array2_f64(self.n_genomes, self.layers.iter().map(|l| l.partial_hellinger(global)))
+    }
+}
+
+struct AggregatedBit<'a> {
+    n_genomes: usize,
+    layers: Vec<&'a KmerLayer>,
+}
+
+impl ColumnWeights for AggregatedBit<'_> {
+    fn col_weights(&self) -> Array1<u64> {
+        sum_array1(self.n_genomes, self.layers.iter().map(|l| l.col_weights()))
+    }
+}
+
+impl BitPartials for AggregatedBit<'_> {
+    fn partial_jaccard(&self) -> (Array2<u64>, Array2<u64>) {
+        let n = self.n_genomes;
+        self.layers.iter().map(|l| l.partial_jaccard()).fold(
+            (Array2::zeros((n, n)), Array2::zeros((n, n))),
+            |(inter, union), (i, u)| (inter + i, union + u),
+        )
+    }
+    fn partial_hamming(&self) -> Array2<u64> {
+        sum_array2_u64(self.n_genomes, self.layers.iter().map(|l| l.partial_hamming()))
+    }
+}
+
+// ── Metrics — the domain-facing entry point ────────────────────────────────────
+
+/// Genome-vs-genome distance computation over a whole (already-cached)
+/// index. `IndexCache` is foreign to this crate, so this is an extension
+/// trait — same reasoning as every other `obikindex`/`obikidxcache`
+/// extension trait in this codebase.
+pub trait Metrics {
+    fn distance(&self, metric: DistanceMetric, shared_kmers: bool, presence_threshold: u32) -> OKIResult<DistanceOutput>;
+}
+
+impl Metrics for IndexCache {
+    fn distance(&self, metric: DistanceMetric, shared_kmers: bool, presence_threshold: u32) -> OKIResult<DistanceOutput> {
+        let n_genomes = self.meta().genomes().len();
         if n_genomes < 2 {
             return Err(OKIError::InvalidInput(
                 "distance requires at least 2 genomes in the index".into(),
             ));
         }
 
-        let use_counts = self.meta.config.with_counts;
+        let use_counts = self.meta().config().with_counts;
         if metric.requires_counts() && !use_counts {
             return Err(OKIError::InvalidInput(format!(
                 "{metric:?} requires a count index (with_counts = true)"
             )));
         }
 
-        let n_parts = self.n_partitions();
+        let kmer_size = self.meta().config().kmer_size;
 
         if use_counts {
-            let stores: Vec<_> = (0..n_parts)
-                .into_par_iter()
-                .map(|i| self.count_store(i).map_err(OKIError::Partition))
-                .collect::<OKIResult<_>>()?;
-            let global = LayeredStore::new(stores);
+            let layers: Vec<&KmerLayer> = self.iter().filter(|l| l.content() == LayerContent::Count).collect();
+            let agg = AggregatedCount { n_genomes, layers };
 
             let matrix = match metric {
-                DistanceMetric::BrayCurtis        => CountPartials::bray_dist_matrix(&global),
-                DistanceMetric::RelfreqBrayCurtis => CountPartials::relfreq_bray_dist_matrix(&global),
-                DistanceMetric::Euclidean         => CountPartials::euclidean_dist_matrix(&global),
-                DistanceMetric::RelfreqEuclidean  => CountPartials::relfreq_euclidean_dist_matrix(&global),
-                DistanceMetric::Hellinger         => CountPartials::hellinger_dist_matrix(&global),
-                DistanceMetric::HellingerEuclidean => CountPartials::hellinger_euclidean_dist_matrix(&global),
-                DistanceMetric::Jaccard           => CountPartials::threshold_jaccard_dist_matrix(&global, presence_threshold),
-                DistanceMetric::Mash              => CountPartials::threshold_mash_dist_matrix(&global, self.kmer_size(), presence_threshold),
-                DistanceMetric::Hamming           => {
+                DistanceMetric::BrayCurtis         => agg.bray_dist_matrix(),
+                DistanceMetric::RelfreqBrayCurtis  => agg.relfreq_bray_dist_matrix(),
+                DistanceMetric::Euclidean          => agg.euclidean_dist_matrix(),
+                DistanceMetric::RelfreqEuclidean   => agg.relfreq_euclidean_dist_matrix(),
+                DistanceMetric::Hellinger          => agg.hellinger_dist_matrix(),
+                DistanceMetric::HellingerEuclidean => agg.hellinger_euclidean_dist_matrix(),
+                DistanceMetric::Jaccard            => agg.threshold_jaccard_dist_matrix(presence_threshold),
+                DistanceMetric::Mash               => agg.threshold_mash_dist_matrix(kmer_size, presence_threshold),
+                DistanceMetric::Hamming => {
                     return Err(OKIError::InvalidInput(
                         "Hamming is only available for presence/absence indexes".into(),
                     ));
@@ -95,7 +187,7 @@ impl KmerIndex {
             };
 
             let shared = if shared_kmers {
-                let (inter, _) = CountPartials::partial_threshold_jaccard(&global, presence_threshold);
+                let (inter, _) = agg.partial_threshold_jaccard(presence_threshold);
                 Some(inter)
             } else {
                 None
@@ -103,18 +195,13 @@ impl KmerIndex {
 
             Ok(DistanceOutput { matrix, shared_kmers: shared })
         } else {
-            let stores: Vec<_> = (0..n_parts)
-                .into_par_iter()
-                .map(|i| self.presence_store(i).map_err(OKIError::Partition))
-                .collect::<OKIResult<_>>()?;
-            let global = LayeredStore::new(stores);
+            let layers: Vec<&KmerLayer> = self.iter().filter(|l| l.content() == LayerContent::Presence).collect();
+            let agg = AggregatedBit { n_genomes, layers };
 
             let matrix = match metric {
-                DistanceMetric::Jaccard => BitPartials::jaccard_dist_matrix(&global),
-                DistanceMetric::Mash    => BitPartials::mash_dist_matrix(&global, self.kmer_size()),
-                DistanceMetric::Hamming => {
-                    BitPartials::hamming_dist_matrix(&global).mapv(|v| v as f64)
-                }
+                DistanceMetric::Jaccard => agg.jaccard_dist_matrix(),
+                DistanceMetric::Mash    => agg.mash_dist_matrix(kmer_size),
+                DistanceMetric::Hamming => agg.hamming_dist_matrix().mapv(|v| v as f64),
                 other => {
                     return Err(OKIError::InvalidInput(format!(
                         "{other:?} requires a count index; use --metric jaccard or --metric hamming"
@@ -123,7 +210,7 @@ impl KmerIndex {
             };
 
             let shared = if shared_kmers {
-                let (inter, _) = BitPartials::partial_jaccard(&global);
+                let (inter, _) = agg.partial_jaccard();
                 Some(inter)
             } else {
                 None

src/obikphylo/src/lib.rs

@@ -1,7 +1,7 @@
 //! Library-level phylogenetic functionality for `obikmer`, built as
-//! extension traits over `obikindex::KmerIndex` and `obikindex::layer`'s
-//! generic layer types — the `phylo` CLI command is a consumer of this
-//! crate, not the owner of this logic (see `DevDocMD/architecture/siblings.md`).
+//! extension traits over `obikindex`/`obikidxcache`'s foreign types — the
+//! `phylo` CLI command is a consumer of this crate, not the owner of this
+//! logic (see `DevDocMD/architecture/siblings.md`).
 //!
 //! Starts with [`siblings`] (family presence-mask annex, SNP distance,
 //! cardinality, pseudo-alignment); further phylo-domain functionality
@@ -15,7 +15,8 @@
 //! this crate until `siblings` comes back.
 
 mod distance;
-mod matrix_store;
+mod tree;
 // pub mod siblings; // temporarily disconnected — see module doc above.
 
-pub use distance::{DistanceMetric, DistanceOutput};
+pub use distance::{DistanceMetric, DistanceOutput, Metrics};
+pub use tree::{neighbor_joining_newick, upgma_newick};

src/obikphylo/src/matrix_store.rs

@@ -1,47 +0,0 @@
-use obicompactvec::{PersistentBitMatrix, PersistentIntMatrix};
-use obikidxcache::LayeredStore;
-use obikindex::OKIResult;
-use obikindex::layer::open_data;
-
-use obikindex::KmerIndex;
-use obikindex::load_meta;
-
-impl KmerIndex {
-    /// Open all count matrices for partition `part`, one per layer.
-    /// Layers without a `counts/` directory are skipped.
-    pub fn count_store(&self, part: usize) -> OKIResult<LayeredStore<PersistentIntMatrix>> {
-        let index_dir = self.index_dir(part);
-        if !index_dir.exists() {
-            return Ok(LayeredStore::new(vec![]));
-        }
-        let n_layers = self.n_layers();
-        let matrices = (0..n_layers)
-            .filter_map(|l| {
-                self.layer_dir(part, l)
-                    .join("counts")
-                    .exists()
-                    .then(|| open_data(&index_dir, l))
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        Ok(LayeredStore::new(matrices))
-    }
-
-    /// Open all presence matrices for partition `part`, one per layer.
-    /// Layers without a `presence/` directory are skipped.
-    pub fn presence_store(&self, part: usize) -> OKIResult<LayeredStore<PersistentBitMatrix>> {
-        let index_dir = self.index_dir(part);
-        if !index_dir.exists() {
-            return Ok(LayeredStore::new(vec![]));
-        }
-        let n_layers = load_meta(&index_dir)?.n_layers;
-        let matrices = (0..n_layers)
-            .filter_map(|l| {
-                self.layer_dir(part, l)
-                    .join("presence")
-                    .exists()
-                    .then(|| open_data(&index_dir, l))
-            })
-            .collect::<OKIResult<Vec<_>>>()?;
-        Ok(LayeredStore::new(matrices))
-    }
-}

src/obikphylo/src/tree/mod.rs

@@ -0,0 +1,88 @@
+//! A minimal, write-only phylogenetic tree: just enough structure to unify
+//! whatever a reconstruction algorithm produces (NJ, UPGMA, ...) into one
+//! shared Newick serialisation, instead of each algorithm hand-rolling its
+//! own Newick writer. No reader — nothing in this crate ever needs to parse
+//! a Newick string back in, so there is no `from_newick`.
+
+mod newick;
+mod nj;
+mod upgma;
+
+pub use nj::neighbor_joining_newick;
+pub use upgma::upgma_newick;
+
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
+struct NodeId(usize);
+
+#[derive(Debug, Default)]
+struct Node {
+    name: Option<String>,
+    branch_length: Option<f64>,
+    bootstrap: Option<f64>,
+    children: Vec<NodeId>,
+}
+
+/// Arena-based tree: nodes are created detached ([`new_leaf`](Tree::new_leaf)/
+/// [`new_node`](Tree::new_node)) and wired together with
+/// [`attach`](Tree::attach) — the shape every bottom-up reconstruction
+/// algorithm (UPGMA's successive merges, NJ's already-built graph) needs:
+/// a node's parent is only known once *it* already exists.
+#[derive(Debug, Default)]
+struct Tree {
+    nodes: Vec<Node>,
+    root: Option<NodeId>,
+}
+
+impl Tree {
+    fn new() -> Self {
+        Self::default()
+    }
+
+    /// Create a new, detached leaf node.
+    fn new_leaf(&mut self, name: impl Into<String>) -> NodeId {
+        let id = self.new_node();
+        self.nodes[id.0].name = Some(name.into());
+        id
+    }
+
+    /// Create a new, detached internal node (no name).
+    fn new_node(&mut self) -> NodeId {
+        let id = NodeId(self.nodes.len());
+        self.nodes.push(Node::default());
+        id
+    }
+
+    /// Attach `child` under `parent`, recording the branch length between them.
+    fn attach(&mut self, parent: NodeId, child: NodeId, branch_length: f64) {
+        self.nodes[child.0].branch_length = Some(branch_length);
+        self.nodes[parent.0].children.push(child);
+    }
+
+    /// Record a bootstrap/support value for `node` — meaningful on an
+    /// internal node only; printed right after its closing parenthesis, per
+    /// Newick convention.
+    #[allow(dead_code)] // no current caller sets one (NJ/UPGMA don't produce support values); kept for the next algorithm that does.
+    fn set_bootstrap(&mut self, node: NodeId, value: f64) {
+        self.nodes[node.0].bootstrap = Some(value);
+    }
+
+    /// Mark `node` as the tree's root. Required exactly once before
+    /// [`to_newick`](Tree::to_newick).
+    fn set_root(&mut self, node: NodeId) {
+        self.root = Some(node);
+    }
+
+    /// Serialise to Newick (terminated with `;`). Panics if
+    /// [`set_root`](Tree::set_root) was never called — a tree with no
+    /// designated root is a builder bug, not a recoverable input.
+    fn to_newick(&self) -> String {
+        let root = self.root.expect("Tree::to_newick: root not set");
+        let mut out = newick::write_node(self, root);
+        out.push(';');
+        out
+    }
+
+    fn node(&self, id: NodeId) -> &Node {
+        &self.nodes[id.0]
+    }
+}

src/obikphylo/src/tree/newick.rs

@@ -0,0 +1,34 @@
+//! The one Newick writer every tree-reconstruction algorithm in this
+//! module shares.
+
+use super::{Node, NodeId, Tree};
+
+pub(super) fn write_node(tree: &Tree, id: NodeId) -> String {
+    let node: &Node = tree.node(id);
+    let mut s = String::new();
+
+    if node.children.is_empty() {
+        if let Some(name) = &node.name {
+            s.push_str(name);
+        }
+    } else {
+        s.push('(');
+        for (i, &child) in node.children.iter().enumerate() {
+            if i > 0 {
+                s.push(',');
+            }
+            s.push_str(&write_node(tree, child));
+        }
+        s.push(')');
+        if let Some(bootstrap) = node.bootstrap {
+            s.push_str(&format!("{bootstrap}"));
+        }
+    }
+
+    if let Some(branch_length) = node.branch_length {
+        s.push(':');
+        s.push_str(&format!("{branch_length:.6}"));
+    }
+
+    s
+}

src/obikphylo/src/tree/nj.rs

@@ -0,0 +1,55 @@
+//! Neighbor-Joining, via `speedytree` — converts its own tree type
+//! (`petgraph::graph::UnGraph<String, f64>`) into this crate's [`super::Tree`]
+//! so its Newick output goes through the same writer as every other
+//! algorithm here.
+
+use ndarray::Array2;
+use obikindex::{OKIError, OKIResult};
+use petgraph::graph::NodeIndex;
+use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver};
+
+use super::{NodeId, Tree};
+
+/// Compute a Neighbor-Joining tree from a symmetric `n×n` distance `matrix`
+/// (genomes in `labels` order), returning it as a Newick string.
+pub fn neighbor_joining_newick(matrix: &Array2<f64>, labels: &[String]) -> OKIResult<String> {
+    let n = labels.len();
+    let rows: Vec<Vec<f64>> = (0..n).map(|i| (0..n).map(|j| matrix[[i, j]]).collect()).collect();
+    let dm = DistanceMatrix::build(rows, labels.to_vec())
+        .map_err(|e| OKIError::InvalidInput(format!("building NJ distance matrix: {e}")))?;
+    let graph = NeighborJoiningSolver::<Hybrid>::default(dm)
+        .solve()
+        .map_err(|e| OKIError::InvalidInput(format!("computing NJ tree: {e}")))?;
+
+    // speedytree's own Newick writer expects the same convention: the
+    // unrooted result's "display root" is whichever node still has all
+    // three of its original neighbours (every other node lost one to
+    // becoming somebody's child during the walk below).
+    let root = graph
+        .node_indices()
+        .find(|&node| graph.neighbors(node).count() == 3)
+        .ok_or_else(|| OKIError::InvalidInput("NJ tree has no trifurcating root".into()))?;
+
+    let mut tree = Tree::new();
+    let root_id = convert(&graph, root, root, &mut tree);
+    tree.set_root(root_id);
+    Ok(tree.to_newick())
+}
+
+/// Recursively convert `node` (and everything below it, i.e. every
+/// neighbour except `parent`) into this crate's `Tree`. Excluding just the
+/// immediate parent is enough to avoid revisiting — `graph` is a tree
+/// (no cycles), so that's the only edge that could lead back.
+fn convert(graph: &speedytree::Tree, node: NodeIndex, parent: NodeIndex, tree: &mut Tree) -> NodeId {
+    let label = &graph[node];
+    let id = if label.is_empty() { tree.new_node() } else { tree.new_leaf(label.clone()) };
+
+    for child in graph.neighbors(node).filter(|&c| c != parent) {
+        let edge = graph.find_edge(node, child).expect("adjacent nodes must share an edge");
+        let branch_length = *graph.edge_weight(edge).expect("edge must carry a weight");
+        let child_id = convert(graph, child, node, tree);
+        tree.attach(id, child_id, branch_length);
+    }
+
+    id
+}

src/obikphylo/src/tree/upgma.rs

@@ -0,0 +1,51 @@
+//! UPGMA (average-linkage hierarchical clustering), via `kodama` — converts
+//! its dendrogram (a flat list of merge steps) into this crate's
+//! [`super::Tree`], bottom-up, so its Newick output goes through the same
+//! writer as every other algorithm here.
+
+use kodama::{Method, linkage};
+use ndarray::Array2;
+
+use super::Tree;
+
+/// Compute a UPGMA tree from a symmetric `n×n` distance `matrix` (genomes in
+/// `labels` order), returning it as a Newick string.
+pub fn upgma_newick(matrix: &Array2<f64>, labels: &[String]) -> String {
+    let n = labels.len();
+    let mut condensed: Vec<f64> = Vec::with_capacity(n * (n - 1) / 2);
+    for i in 0..n {
+        for j in (i + 1)..n {
+            condensed.push(matrix[[i, j]]);
+        }
+    }
+    let dendro = linkage(&mut condensed, n, Method::Average);
+
+    let mut tree = Tree::new();
+    // `kodama` numbers clusters `0..n` for the original leaves and `n..`
+    // for each successive merge, in the order `dendro.steps()` yields them
+    // — so appending to `node_of` as we go keeps `node_of[cluster_id]`
+    // valid the moment a later step references it.
+    let mut node_of: Vec<super::NodeId> =
+        labels.iter().map(|label| tree.new_leaf(label.clone())).collect();
+    // height of each node: leaves = 0, internal = dissimilarity/2 (UPGMA is
+    // ultrametric: both children of a merge are equidistant from it).
+    let mut heights = vec![0.0f64; 2 * n - 1];
+
+    let mut root = None;
+    for (k, step) in dendro.steps().iter().enumerate() {
+        let new_node = n + k;
+        let h = step.dissimilarity / 2.0;
+        heights[new_node] = h;
+
+        let parent = tree.new_node();
+        for &cluster in &[step.cluster1, step.cluster2] {
+            let branch_length = (h - heights[cluster]).max(0.0);
+            tree.attach(parent, node_of[cluster], branch_length);
+        }
+        node_of.push(parent);
+        root = Some(parent);
+    }
+
+    tree.set_root(root.expect("at least one merge step for n >= 2 genomes"));
+    tree.to_newick()
+}