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

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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.

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Eric Coissac

2026-08-16 13:11:06 +02:00

parent 8615da59a8

commit eee71430a4

14 changed files with 1444 additions and 82 deletions

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iqtree.ufboot

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