PHAST

Phylogenetic Analysis with Space/Time models (PHAST) is a freely available software package consisting of a collection of command-line programs and supporting libraries for comparative and evolutionary genomics. Best known as the search engine behind the Conservation tracks in the University of California, Santa Cruz (UCSC) Genome Browser, PHAST also includes several tools for phylogenetic modeling, functional element identification, as well as utilities for manipulating alignments, trees and genomic annotations.

The PHAST project was initiated by Principal Investigator, Adam Siepel with extensions by Melissa Hubisz.

Many phast functions can be accessed from within the R environment using the rphast package. It is available from the RPHAST webpage and also on CRAN.

The phastWeb application was developed by Ritika Ramani.

phastCons: Conservation scoring and identification of conserved elements

phyloFit: Fitting of phylogenetic models to aligned DNA sequences

phyloP: Computation of p-values for conservation or acceleration, either lineage-specific or across all branches

phastOdds: Log-odds scoring for phylogenetic models or phylo-HMMs

exoniphy: Phylogenetic exon prediction

dless: Prediction of elements under lineage-specific selection

prequel: Probabilistic reconstruction of ancestral sequences

phastBias: Identification of GC-biased gene conversion using a phylo-HMM