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

Current and Planned Development

Several improvements and extensions to PHAST are underway or planned: