Supported Applications


  • Description

    (Phylogenetic Analysis with Space/Time models) a software package for comparative and evolutionary genomics.

  • Usage Notes

    The PHAST package contains the following programs:

        all_dists            hmm_view        phastBias
        base_evolve          indelFit        phastCons
        chooseLines          indelHistory    phastMotif
        clean_genes          maf_parse       phastOdds
        consEntropy          makeHKY         phyloBoot
        convert_coords       modFreqs        phyloFit
        display_rate_matrix  msa_diff        phyloP
        dless                msa_split       prequel
        dlessP               msa_view        refeature
        draw_tree            pbsDecode       stringiphy
        eval_predictions     pbsEncode       test
        exoniphy             pbsScoreMatrix  tree_doctor
        hmm_train            pbsTrain        treeGen
        hmm_tweak            phast
    For help, type the program's name followed by -h in your command line window.
  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install phast Copy to clipboard
  • Primary Citation*

    A. Siepel and D. Haussler. 2004. Combining phylogenetic and hidden Markov models in biosequence analysis. Journal of computational biology : a journal of computational molecular cell biology. 11: 413-28.

    • *Full citation information available through