NAME

       phast - phylogenetic analysis with space/time models

DESCRIPTION

       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.