Phast

• all_dists(1) Given a tree in Newick (*.nh) format, report distances
• base_evolve(1) Produce a synthetic alignment by simulating evolution according to
• chooseLines(1) Randomly choose k lines from a file of n lines, for 0 < k < n.
• clean_genes(1) Given a GFF describing a set of genes and a corresponding
• consEntropy(1) For use with phastCons. Given phylogenetic models for conserved and
• convert_coords(1) converts coordinates of features in a GFF file according to a multiple alignment
• display_rate_matrix(1) this tool is part of the PHAST suite
• dless(1) Attempts to identify elements under selection in all species or in
• dlessP(1) Computes various p-values and other stats of interest for dless
• draw_tree(1) Produces a simple postscript rendering of a tree
• eval_predictions(1) Compares predicted genes with "real" (or annotated) genes.
• exoniphy(1) Prediction of evolutionarily conserved protein-coding exons using
• hmm_train(1) Estimate the transition probabilities of an HMM, based on multiple
• hmm_tweak(1) Alter transition probabilities in an HMM definition file.
• hmm_view(1) produces a graphical description of the state-transition
• indelFit(1) Estimate the parameters of a simple indel model, given an indel history
• indelHistory(1) Obtain an "indel history" for an alignment and write it to a file
• maf_parse(1) Reads a MAF file and perform various operations on it.
• makeHKY(1) Generates an HKY tree model, given kappa (the transition/transversion
• modFreqs(1) Change background frequencies of reversible tree model in such
• msa_diff(1) Compare two multiple alignments and report differences.
• msa_split(1) Partitions a multiple sequence alignment either at designated
• msa_view(1) Provides various kinds of "views" of one or more multiple
• pbsDecode(1) Decode a binary encoding of a probabilistic biological sequence
• pbsEncode(1) Produce an approximate binary encoding of a probabilistic
• pbsScoreMatrix(1) Generate log-odds score matrices for use in alignment of
• pbsTrain(1) Estimate a discrete encoding scheme for probabilistic biological
• phast(1) phylogenetic analysis with space/time models
• phastBias(1) Identify regions of the alignment which are affected by gBGC,
• phastCons(1) Identify conserved elements or produce conservation scores, given
• phastMotif(1) Predicts motifs from a set of multiple alignments. Uses
• phastOdds(1) Compute log-odds scores based on two phylogenetic models or phylo-HMMs,
• phyloBoot(1) Generate simulated alignment data by parametric or nonparametric
• phyloFit(1) Fits one or more tree models to a multiple alignment of DNA
• phyloP(1) Compute conservation or acceleration p-values based on an alignment and
• prequel(1) Compute marginal probability distributions for bases at ancestral
• refeature(1) Read a file representing a set of features, optionally
• stringiphy(1) Attempt to string together predicted exons into full transcripts
• tree_doctor(1) Scale, prune, merge, and otherwise tweak phylogenetic trees.
• treeGen(1) Enumerate rooted tree topologies, subject to constraints on