Image from ScienceNOW, July 14, 2005
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PHAST (PHylogenetic Analysis with Space/Time models) includes several phylo-HMM-based programs and related tools for phylogenetic analysis and functional element identification. The phastCons, ExoniPhy, and DLESS programs (see research projects) are included in this package, as are the programs phyloFit (fitting of phylogenetic models to data; supports context-dependent models and parameter estimation by EM), phyloP (phylogenetic P-value computation), phastOdds (log-odds scoring with phylo-HMMs), and phyloBoot (parametric and nonparametric bootstrapping). PHAST is a work in progress but it is reasonably stable now and in fairly wide use in the comparative genomics community. (It has been downloaded more than 150 times.) The software is written in C and has been successfully installed and used on most common platforms. It is freely available for research purposes by request.
See new phastCons HOWTO.
This software package includes code to enumerate sorting reversals for signed permutations, and to compute reversal (inversion) medians (see related publications). RevMed is freely downloadable under the terms of the GNU General Public License, but GRAPPA is required for installation. Parts of RevMed have been incorporated into GRAPPA as of version 1.6.