PHAST logo

Navigation

Home / Download
FAQ
Comparison
Background & References
Plans

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: phasthelp@cshl.edu

Phast - Older Versions


Source Code
Version: 1.4phast.v1_4.tgz
Version: 1.3phast.v1_3.tgz
Version: 1.2.1phast.v1_2_1.tgz
Version: 1.1phast.v1_1.tgz
Version: 1.0phast.v1_0.tgz
Version: 0.9.9.10phast.v0_9_9_10b.tgz
Version: 0.9.9.9phast.v0_9_9_9b.tgz
Version: 0.9.9.8phast.v0_9_9_8b.tgz
Version: 0.9.9.7phast.v0_9_9_7b.tgz
Version: 0.9.9.6phast.v0_9_9_6b.tgz

Ubuntu/Debian
Version: 1.4phast.v1_4.x86_64.deb
Version: 1.3phast.v1_3.x86_64.deb
Version: 1.0phast.v1_0.i386.deb
Version: 1.0phast.v1_0.x86_64.deb

Fedora/Redhat/OpenSUSE
Version: 1.4phast.v1_4.x86_64.rpm
Version: 1.3phast.v1_3.x86_64.rpm
Version: 1.0phast.v1_0.i386.rpm
Version: 1.0phast.v1_0.x86_64.rpm

MacOSX
Version: 1.4phast.v1_4.pkg.zip
Version: 1.3phast.v1_3.pkg.zip
Version: 1.1phast.v1_1.mpkg.zip
Version: 1.0phast.v1_0.pkg.zip

Windows
Version: 1.3phast_v1_3.exe
Version: 1.2.1phast_v1_2_1.exe
Version: 1.2phast_v1_2.exe
Version: 1.1phast.v1_1.exe
Version: 1.0phast_v1_0.exe