bin/all_dists
bin/base_evolve
bin/chooseLines
bin/clean_genes
bin/consEntropy
bin/convert_coords
bin/display_rate_matrix
bin/dless
bin/dlessP
bin/draw_tree
bin/eval_predictions
bin/exoniphy
bin/hmm_train
bin/hmm_tweak
bin/hmm_view
bin/indelFit
bin/indelHistory
bin/maf_parse
bin/makeHKY
bin/modFreqs
bin/msa_diff
bin/msa_split
bin/msa_view
bin/pbsDecode
bin/pbsEncode
bin/pbsScoreMatrix
bin/pbsTrain
bin/phast
bin/phastBias
bin/phastCons
bin/phastMotif
bin/phastOdds
bin/phyloBoot
bin/phyloFit
bin/phyloP
bin/prequel
bin/refeature
bin/stringiphy
bin/treeGen
bin/tree_doctor
include/phast/bd_phylo_hmm.h
include/phast/bed.h
include/phast/bgc_hmm.h
include/phast/category_map.h
include/phast/complex.h
include/phast/complex_matrix.h
include/phast/complex_vector.h
include/phast/cons.h
include/phast/dgamma.h
include/phast/eigen.h
include/phast/em.h
include/phast/external_libs.h
include/phast/fit_column.h
include/phast/fit_em.h
include/phast/fit_feature.h
include/phast/gap_patterns.h
include/phast/genepred.h
include/phast/gff.h
include/phast/hashtable.h
include/phast/hmm.h
include/phast/indel_history.h
include/phast/indel_mod.h
include/phast/list_of_lists.h
include/phast/lists.h
include/phast/local_alignment.h
include/phast/maf.h
include/phast/maf_block.h
include/phast/markov_matrix.h
include/phast/matrix.h
include/phast/memory_handler.h
include/phast/misc.h
include/phast/motif.h
include/phast/ms.h
include/phast/msa.h
include/phast/multi_msa.h
include/phast/numerical_opt.h
include/phast/pbs_code.h
include/phast/phylo_fit.h
include/phast/phylo_hmm.h
include/phast/phylo_p.h
include/phast/phylo_p_print.h
include/phast/prob_matrix.h
include/phast/prob_vector.h
include/phast/pssm.h
include/phast/puzzler.h
include/phast/queues.h
include/phast/rph_util.h
include/phast/simplex_grid.h
include/phast/stacks.h
include/phast/stringsplus.h
include/phast/subst_distrib.h
include/phast/subst_mods.h
include/phast/sufficient_stats.h
include/phast/tfbs.h
include/phast/tree_likelihoods.h
include/phast/tree_model.h
include/phast/trees.h
include/phast/vector.h
include/phast/wig.h
lib/cmake/phast/phastConfig.cmake
lib/cmake/phast/phastConfigVersion.cmake
lib/cmake/phast/phastTargets-release.cmake
lib/cmake/phast/phastTargets.cmake
lib/libphast.a
