phast - 1.4+dfsg-1 main

PHAST is a software package for comparative and evolutionary genomics.
It consists of about half a dozen major programs, plus more than a dozen
utilities for manipulating sequence alignments, phylogenetic trees, and
genomic annotations. For the most part, PHAST focuses on two kinds of
applications: the identification of novel functional elements, including
protein-coding exons and evolutionarily conserved sequences; and
statistical phylogenetic modeling, including estimation of model
parameters, detection of signatures of selection, and reconstruction of
ancestral sequences.
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PHAST does not support phylogeny reconstruction or sequence alignment,
and it is designed for use with DNA sequences only (see Comparison).