bali-phy - 4.0-1 main

BAli-Phy estimates multiple sequence alignments and evolutionary trees
from unaligned DNA, amino acid, or codon sequences. BAli-Phy uses MCMC
to estimate evolutionary trees, positive selection, and branch lengths
while averaging over alternative alignments. BAli-Phy can display
alignment ambiguity graphically in an alignment uncertainty (AU) plot.
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BAli-Phy can also estimate phylogenies from a fixed alignment (like MrBayes
and BEAST) using substitution models like GTR+gamma. BAli-Phy automatically
estimates relative rates for each gene.