# phylip

## Summary

+ **Module Name:** phylip
+ **Support Level:** Secondary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://evolution.genetics.washington.edu/phylip.html](http://evolution.genetics.washington.edu/phylip.html)

## Software Description

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.
## General Linux

To load this module for use in a Linux environment, you can run the command:

	module load phylip

Depending on where you are working, there may be more than one version of phylip available.
To see which modules are available for loading you can run:

	module avail phylip