Add phylogenetic CLI options for family overlap and missing data

Introduces CLI flags for computing pairwise family overlap matrices and filtering genomes below a shared family threshold. Adds a free-loss mode that recodes locus non-detection states to missing data symbols in Sankoff-calibrated alignments, resolving ascertainment bias handling for IQ-TREE. Updates empirical transition parameters, removes the legacy model asset, and extends output writers for CSV diagnostics, FASTA pseudo-alignments, and Newick trees.

This commit is contained in:

Eric Coissac

2026-08-16 11:54:43 +02:00

parent e2b9374426

commit 8615da59a8

12 changed files with 833 additions and 465 deletions

.gitignore

View File

@@ -27,3 +27,12 @@ benchmark/specific_index_presence
 TNT
 phyg
 *.tnt
 *.tre
 *.phy
 *.treefile
 *.bionj
 *.iqtree
 *.mldist
 *.parstree
 *.ckp.gz
 *.model