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Plans

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

Instructions for Bug Reports

When reporting a bug in PHAST, please provide us with as much detail as possible. We cannot fix your bug if we cannot reproduce it. In particular, please send us:

• A clear description of the problem.
• The version of the software you are using, what platform (processor and operating system) you are using, and the version of CLAPACK (if any) you have linked to.
• Your exact command-line string, including all options.
• All input data files. If you encounter a problem with a large input file (say, >10MB), we very much appreciate your taking a few minutes to see if it can be reproduced with a smaller file. For example, see if you can reproduce the problem with a small "slice" of an input alignment obtained using the msa_view program with the --start, --end, and/or --seqs options. If you cannot reproduce the error with a small input file, please compress the large data file before emailing it, or (even better), post it for download by HTTP or FTP.

Please do not send us technical questions that are not directly related to PHAST — for example, basic questions about linux, cygwin, or CLAPACK.