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rename distance subcommand to phylo

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Rename the distance CLI subcommand to phylo across the codebase, documentation, and build configurations. Relocate source files from cmd/distance/ to a dedicated cmd/phylo/ module, update all internal routing references, and adjust benchmark scripts and Makefile targets to reflect the new command name.
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Eric Coissac
2026-08-15 10:07:03 +02:00
parent 79346c0c86
commit dd889854cb
19 changed files with 49 additions and 46 deletions
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UserDocMD/index.md
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@@ -24,7 +24,7 @@ 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 |
| [`distance`](usage/distance.md) | Compute pairwise distance matrices and phylogenetic exports |
| [`phylo`](usage/phylo.md) | Compute pairwise evolutionary-distance proxies, 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) |