![]() ![]() However, PAML has very broad functionality for phylogenetic modeling, and several of its models and applications are not supported in PHAST. Like PAML, PHAST supports several different nucleotide substitution models and is optimized for fitting models to (potentially large) data sets conditional on a given tree topology, rather than for topology estimation (as are MrBayes, PhyML, RAxML, PHYLIP, and many other packages). In the realm of phylogenetic modeling, it is most similar to PAML. How does PHAST compare with PAML and other programs for phylogenetic modeling? Phylo-HMMs have been called "space/time models" because they describe DNA sequences by two Markov processes - one that operates in the dimension of time (along the branches of an evolutionary tree) and one that operates in space (along the sequences themselves) (see Yang, 1995). The name "PHAST" arose because several programs in the package (including phastCons, exoniphy, and dless) make use of phylogenetic hidden Markov models (phylo-HMMs). ![]()
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