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Update documentation for CLI command renames and new commands

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Renames the reindex command to convert across all usage guides and navigation menus. Adds documentation for the newly introduced name-tree command. Updates flag references, such as replacing --metric with --distance in pack and phylo modules, and adjusts MkDocs configuration to match the revised structure. All changes are strictly limited to documentation and configuration files.
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Eric Coissac
2026-08-28 23:06:05 +02:00
parent 95fa0c93b2
commit caf59b5658
38 changed files with 666 additions and 2433 deletions
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UserDocMD/index.md
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@@ -24,11 +24,10 @@ All functionality is exposed through a single binary, `obikmer`, organized as su
| [`query`](usage/query.md) | Query an index with sequences and annotate matches |
| [`dump`](usage/dump.md) | Dump indexed kmers as CSV |
| [`annotate`](usage/annotate.md) | Add, update, or dump genome metadata |
| [`phylo`](usage/phylo.md) | Compute pairwise evolutionary-distance proxies, trees, and phylogenetic exports |
| [`name-tree`](usage/name-tree.md) | Translate a TNT/PhyG numeric-label tree export back to real taxon names |
| [`phylo`](usage/phylo.md) | Compute pairwise genome distances, trees, and phylogenetic exports |
| [`unitig`](usage/unitig.md) | Dump the unitigs of an index as FASTA |
| [`estimate`](usage/estimate.md) | Estimate approximate-index parameters before indexing |
| [`reindex`](usage/reindex.md) | Convert an index's evidence representation (exact ↔ approximate) |
| [`convert`](usage/convert.md) | Convert an index's evidence representation (exact/approximate/hybrid), in place |
| [`utils`](usage/utils.md) | Miscellaneous index maintenance and inspection utilities |
| [`pack`](usage/pack.md) | Pack per-column matrix files into a single-file format |