Minnesota Supercomputing Institute
Wednesday, December 7, 2016
These programs include:
dnacompEstimates phylogenies from nucleic acid sequence data using the compatibility criterion.
dnadistComputes four different distances between species from nucleic acid sequences.
dnainvarFor nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants.
dnamlEstimates phylogenies from nucleotide sequences by maximum likelihood.
dnamlkSame as DNAML but assumes a molecular clock.
dnamoveInteractive construction of phylogenies from nucleic acid sequences.
dnaparsEstimates phylogenies by the parsimony method using nucleic acid sequences.
dnapennyFinds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search.
seqbootReads in a data set, and produces multiple data sets from it by bootstrap resampling.
consenseComputes consensus trees by the majority-rule consensus tree method.
protdistEstimates phylogenies from protein sequences using the parsimony method.
protparsComputes a distance measure for protein sequences.
restmlEstimation of phylogenies by maximum likelihood using restriction sites data.
fitchEstimates phylogenies from distance matrix data under the "additive tree model" .
kitschEstimates phylogenies from distance matrix data under the "ultrametric" model.
neighborAn implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method.
contmlEstimates phylogenies from gene frequency data by maximum likelihood under a model.
gendistComputes one of three different genetic distance formulas from gene frequency data.
contrastReads 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.
mixEstimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1).
moveInteractive construction of phylogenies from discrete character data with two states (0 and 1).
pennyFinds all most parsimonious phylogenies for discrete-character data with two states.
dollopEstimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1).
dolmoveInteractive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria.
dolpennyFinds 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.
cliqueFinds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.
factorTakes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1).
drawgramPlots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats.
drawtreeSimilar to DRAWGRAM but plots unrooted phylogenies.
retreeReads 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
Documentation (html files) can be found in the