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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

Utilities

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

Contact

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

Current and Planned Development

Several improvements and extensions to PHAST are underway or planned:

• A major expansion of the phyloP program is nearly complete. The program now can compute conservation/acceleration p-values by four different methods, including a likelihood ratio test, a score test, and a GERP-like method, as well as the original method described in the RECOMB 2006 paper. It can also now be used, like phastCons, to produce base-by-base conservation scores for large-scale data sets.
• A full-featured interface between PHAST and the R programming environment, called RPHAST, is under development. RPHAST will allow PHAST library functions to be called from R, enabling rapid development of new methods and convenient, on-the-fly visualization and postprocessing of results.
• PhD student Adam Diehl is developing an extension to dless, called dmotif, that models the gain and loss of transcription factor binding sites. The method is fully Bayesian and uses an efficient Gibbs sampling algorithm to infer posterior distributions for model parameters, binding site locations, and gain/loss events.
• Extensions to support likelihood ratio tests for lineage-specific changes in the pattern (as opposed to the rate) of substitution are planned, in collaboration with Katie Pollard.
• Improvements to the library and API documentation are planned.