Eric Coissac
128db64564
Introduces --iqtree-min-freq (default 0.001) to treat low-frequency nucleotide states as missing data during IQ-TREE alignment generation when --free-loss is active. This triggers a recoding pass that folds rare states into the missing symbol, followed by non-informative site removal and alphabet recomputation to maintain output consistency. The change also adds Sankoff model configuration files and updates related tests and documentation.
168 lines
2.5 KiB
YAML
168 lines
2.5 KiB
YAML
ratio_ceiling: 0.5
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