Search Software

  • Categories: Genetics | Service Level: Minimal | SW Module: phylip

    PHYLIP (the PHYLogeny Inference Package) is one of most popular package of programs for inferring phylogenies (evolutionary trees).

    These programs include:

    dnacomp
    Estimates phylogenies from nucleic acid sequence data using the compatibility criterion.

    dnadist
    Computes four different distances between species from nucleic acid sequences.

    dnainvar
    For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants.

    dnaml
    Estimates phylogenies from nucleotide sequences by maximum likelihood.

    dnamlk
    Same as DNAML but assumes a molecular clock.

    dnamove
    Interactive construction of phylogenies from nucleic acid sequences.

    dnapars
    Estimates phylogenies by the parsimony method using nucleic acid sequences.

    dnapenny
    Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search.

    seqboot
    Reads in a data set, and produces multiple data sets from it by bootstrap resampling.

    consense
    Computes consensus trees by the majority-rule consensus tree method.

    protdist
    Estimates phylogenies from protein sequences using the parsimony method.

    protpars
    Computes a distance measure for protein sequences.

    restml
    Estimation of phylogenies by maximum likelihood using restriction sites data.

    fitch
    Estimates phylogenies from distance matrix data under the "additive tree model" .

    kitsch
    Estimates phylogenies from distance matrix data under the "ultrametric" model.

    neighbor
    An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method.

    contml
    Estimates phylogenies from gene frequency data by maximum likelihood under a model.

    gendist
    Computes one of three different genetic distance formulas from gene frequency data.

    contrast
    Reads a tree from a tree file, and a data set with continuous characters data, and produces the independent contrasts for those characters, for use in any multivariate statistics package.

    mix
    Estimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1).

    move
    Interactive construction of phylogenies from discrete character data with two states (0 and 1).

    penny
    Finds all most parsimonious phylogenies for discrete-character data with two states.

    dollop
    Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1).

    dolmove
    Interactive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria.

    dolpenny
    Finds all most parsimonious phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of exact search.

    clique
    Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.

    factor
    Takes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1).

    drawgram
    Plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats.

    drawtree
    Similar to DRAWGRAM but plots unrooted phylogenies.

    retree
    Reads in a tree (with branch lengths if necessary) and allows you to reroot the tree, to flip branches, to change species names and branch lengths, and then write the result out.

    To run this software interactively in a Linux environment run the commands:

    module load phylip
    dnamove

    Home Page http://evolution.genetics.washington.edu/phylip.html

    Documentation (html files) can be found in the

    /soft/phylip/3.69/doc