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RPHAST
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
phastBias:Identification of GC-biased gene conversion using a phylo-HMM
Alignments: maf_parse, 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. It consists of over 60,000 lines of C code.
PHAST does not support phylogeny reconstruction or sequence alignment, and it is designed for use with DNA sequences only (see Comparison).
Many phast functions can now be accessed from within the R environment using the rphast package. It is available from the RPHAST webpage and also on CRAN.
PHAST is freely available under a BSD-style license.
PHAST is written in standard C and should compile cleanly on any standard UNIX platform (including Mac OS X). 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.
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).
