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Siepel Lab
phastCons: Conservation scoring and identification of conserved elements
phastOdds: Log-odds scoring for
phylogenetic models or phylo-HMMs
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
exoniphy: Phylogenetic exon prediction
dless: Prediction of elements under lineage-specific selection
prequel: Probabilistic reconstruction of ancestral sequences
Alignments: msa_view, msa_split, msa_diff
Phylogenetic
models: tree_doctor, all_dists, draw_tree, consEntropy, indelFit, indelHistory
Sampling/bootstrapping: base_evolve, phyloBoot
Annotations: refeature, clean_genes, eval_predictions
...and others
Send feedback to: phast-help-l@cornell.edu
PHAST is a freely available 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 (see left panel). 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. The package does not support alignment or tree estimation, nor does it work with amino acid sequences. It consists of about 50,000 lines of C code.
PHAST is written in standard C and should compile cleanly on any standard UNIX platform (including Mac OS X). Several users have also reported success in compiling PHAST under Windows, typically using cygwin. PHAST is mostly self-contained, but it does depend on the LAPACK package for certain matrix operations (diagonalization and inversion). On Mac OS X (version 10.3 or later) LAPACK is built-in, but on other platforms, the C port of LAPACK, called CLAPACK, must be installed for PHAST to be fully functional. See the README for details.
PHAST is freely available under a BSD-style license.
Download current version: phast.v0_9_9_10b.tgz [updated 2/19/09]
Previous versions:
phast.v0_9_9_9b.tgz [updated 12/10/08]
phast.v0_9_9_8b.tgz [updated 11/22/08]
The most recent version can also be accessed through our subversion server at http://compgen.bscb.cornell.edu/svnrepo/phast/trunk.
For example, use the following command to download the source files:
svn checkout http://compgen.bscb.cornell.edu/svnrepo/phast/trunk phast
While we do our best to respond to questions, feature requests, bug reports, and other input from users, we must emphasize that PHAST is free, academic software with no guarantees of support. All requests for support should be sent by email to phast-help-l@cornell.edu and will be addressed in as timely a manner as possible. Before reporting a bug, please see these instructions.
Users interested in receiving occasional announcements about PHAST — advertising new features, new programs, major releases, etc. — may wish to join the PHAST mailing list. To join, send an email with a blank subject line and the single word "join" in the message body to phast-users-l-request@cornell.edu.
HOWTO for phastCons.
Other documentation coming soon.
PHAST development and maintenance is supported by NSF Grant DBI-0644111, NIH Grant R01-GM082901-01, and a David and Lucile Packard Fellowship for Science and Engineering. Past funding sources have included the National Human Genome Research Institute (NHGRI), an Achievement Rewards for College Scientists (ARCS) scholarship, and a Graduate Research and Education in Adaptive bio-Technology (GREAT) fellowship from the University of California Biotechnology Research and Education Program (UCBREP).
