feat(distance): add IQ-TREE output and optimize state index mapping

Introduce `--iqtree` and `--raw-snp-counts` flags to generate IQ-TREE model files, recoded FASTA alignments, and per-pair diagnostic counts. Centralize alphabet conversion by extracting a precomputed state index lookup table into the Sankoff module, eliminating redundant iterations across downstream adapters.

This commit is contained in:

Eric Coissac

2026-08-12 20:05:10 +02:00

parent adf5b52dc7

commit 28d841c7be

5 changed files with 285 additions and 8 deletions

.gitignore

View File

@@ -26,3 +26,4 @@ benchmark/specific_index_count
 benchmark/specific_index_presence
 TNT
 phyg
 *.tnt