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Replace Sankoff cost matrix with cardinality-composition decomposition

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Replaced the legacy Sankoff parsimony pipeline with a new cardinality-composition decomposition that constructs row-normalized transition probability matrices symmetrized via geometric mean. This ensures reversibility, reduces free parameters from 240 to 120, and guarantees a zero diagonal. Tallies are now explicitly restricted to variable families to align with +ASC-corrected alignment populations. Additionally, fixed `--exclude-genome` handling to re-scan surviving sequences and drop newly monomorphic columns, preventing silent data corruption in downstream tree inference tools.
This commit is contained in:
Eric Coissac
2026-08-13 16:58:12 +02:00
parent c26623fa00
commit 0c86ea0385
9 changed files with 901 additions and 549 deletions
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iqtree.model
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