Eric Coissac
eee71430a4
Introduce the obikmer name-tree subcommand to map numeric leaf labels in phylogenetic tree exports back to taxon names using a reference FASTA file. Correct the --free-loss flag behavior by removing cardinality transition costs from pairwise cost calculations, ensuring sibling gains and losses are priced identically to whole-family events. Update documentation, configuration parameters, and add reference phylogenetic data files.
63 lines
1.7 KiB
YAML
63 lines
1.7 KiB
YAML
site_name: obikmer — User Guide
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docs_dir: UserDocMD
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site_dir: doc-user
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theme:
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name: material
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plugins:
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- mermaid2:
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- bibtex:
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bib_file: UserDocMD/references.bib
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csl_file: UserDocMD/ecology-letters.csl
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enable_inline_citations: false
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markdown_extensions:
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- admonition
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- footnotes
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- tables
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- pymdownx.superfences:
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custom_fences:
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- name: mermaid
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class: mermaid
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format: !!python/name:pymdownx.superfences.fence_code_format
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- pymdownx.arithmatex:
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generic: true
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extra_javascript:
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- https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
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nav:
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- Home: index.md
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- Installation: installation.md
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- Theory:
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- Kmers and super-kmers: theory/kmers_and_superkmers.md
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- DNA encoding: theory/encoding.md
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- Low-complexity kmer filter: theory/entropy_filter.md
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- Minimizer selection: theory/minimizer_selection.md
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- Partitioning and indexing architecture: theory/indexing_architecture.md
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- Usage:
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- superkmer: usage/superkmer.md
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- index: usage/index_command.md
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- merge: usage/merge.md
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- filter: usage/filter.md
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- select: usage/select.md
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- query: usage/query.md
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- dump: usage/dump.md
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- annotate: usage/annotate.md
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- phylo: usage/phylo.md
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- name-tree: usage/name-tree.md
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- unitig: usage/unitig.md
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- estimate: usage/estimate.md
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- reindex: usage/reindex.md
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- utils: usage/utils.md
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- pack: usage/pack.md
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- Predicates and taxonomy paths: usage/predicates.md
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- Formats:
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- Index construction and on-disk layout: formats/index_layout.md
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- Architecture notes: architecture.md
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watch:
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- UserDocMD
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- mkdocs-user.yml
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