add name-tree command and fix --free-loss cost matrix

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.
2026-08-16 13:11:06 +02:00
parent 8615da59a8
commit eee71430a4
14 changed files with 1444 additions and 82 deletions
@@ -25,6 +25,7 @@ All functionality is exposed through a single binary, `obikmer`, organized as su
 | [`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 |
 | [`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) |