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Supported Applications

PHAST

  • Description

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

  • Usage

    To list all executables provided by PHAST, run: $ biogrids-list phast Copy to clipboard

  • 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 Available operating systems: Linux 64, OS X INTEL

  • 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

  • Keywords

    Comparative Genomics

  • Default Versions

    Linux 64:  1.5 (40.4 MB)
    OS X INTEL:  1.5 (22.3 MB)

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