Supported Applications

PHAST

  • 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

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