📦 phast

40 pages

A

  • all_dists(1)Given a tree in Newick (*.nh) format, report distances✨

B

  • base_evolve(1)Produce a synthetic alignment by simulating evolution according to✨

C

  • 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✨

D

  • 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✨

E

  • eval_predictions(1)Compares predicted genes with "real" (or annotated) genes.✨
  • exoniphy(1)Prediction of evolutionarily conserved protein-coding exons using Required argument <msa_fname> must be a multiple alignment file, in one of several possible formats (see --msa-format).✨

H

  • hmm_train(1)Estimate the transition probabilities of an HMM, based on multiple -g <gff_fname_list> [OPTIONS] > out.hmm✨
  • hmm_tweak(1)Alter transition probabilities in an HMM definition file.✨
  • hmm_view(1)produces a graphical description of the state-transition✨

I

  • 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✨

M

  • 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✨

P

  • 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 The phylogenetic model must be in the .mod format produced by the phyloFit program. The alignment file can be in any of several…✨
  • prequel(1)Compute marginal probability distributions for bases at ancestral✨

R

  • refeature(1)Read a file representing a set of features, optionally✨

S

  • stringiphy(1)Attempt to string together predicted exons into full transcripts✨

T

  • tree_doctor(1)Scale, prune, merge, and otherwise tweak phylogenetic trees.✨
  • treeGen(1)Enumerate rooted tree topologies, subject to constraints on✨