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PHYLIP (the PHYLogeny Inference Package) is one of most popular package of programs for inferring phylogenies (evolutionary trees).
These programs include:
Estimates phylogenies from nucleic acid sequence data using the compatibility criterion.
Computes four different distances between species from nucleic acid sequences.
For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants.
Estimates phylogenies from nucleotide sequences by maximum likelihood.
Same as DNAML but assumes a molecular clock.
Interactive construction of phylogenies from nucleic acid sequences.
Estimates phylogenies by the parsimony method using nucleic acid sequences.
Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search.
Reads in a data set, and produces multiple data sets from it by bootstrap resampling.
Computes consensus trees by the majority-rule consensus tree method.
Estimates phylogenies from protein sequences using the parsimony method.
Computes a distance measure for protein sequences.
Estimation of phylogenies by maximum likelihood using restriction sites data.
Estimates phylogenies from distance matrix data under the "additive tree model" .
Estimates phylogenies from distance matrix data under the "ultrametric" model.
An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method.
Estimates phylogenies from gene frequency data by maximum likelihood under a model.
Computes one of three different genetic distance formulas from gene frequency data.
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.
Estimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1).
Interactive construction of phylogenies from discrete character data with two states (0 and 1).
Finds all most parsimonious phylogenies for discrete-character data with two states.
Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1).
Interactive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria.
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.
Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.
Takes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1).
Plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats.
Similar to DRAWGRAM but plots unrooted phylogenies.
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
Documentation (html files) can be found in the