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RPHAST

Siepel Lab

Major Programs

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

Utilities

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

Contact

Send feedback to: phast-help-l@cornell.edu

Description

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).

RPHAST

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.

Download

PHAST is freely available under a BSD-style license.


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Platforms and Dependencies

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.

Support

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.

Mailing List

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.

Documentation

HOWTO for phastCons.

Other documentation coming soon.

Funding

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).

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