Software Tools :: PHYLIP
Introduction
PHYLIP (PHYLogeny Inference Package) is a package of programs for
inferring phylogenies (evolutionary trees). It has been distributed since
1980, and has over 15,000 registered users, making it the most widely
distributed package of phylogeny programs. It is available free,
and can be obtained from
http://evolution.genetics.washington.edu/phylip.html
PHYLIP is written by Joseph Felsenstein, Department of Genetics,
University of Washington, Seattle WA.
Getting Help
Accessing the Programs
You can access PHYLIP in two ways:
- from the Unix prompt under your CGB Research account: type "use phylip" or
"use molbio" to initialize the system, then type the name of the program
- via the web interfaces provided below
| clique |
clique |
Finds the largest clique of mutually compatible
characters, and the phylogeny which they recommend, for discrete
character data with two states |
| consense |
consense |
Computes consensus trees by the majority-rule consensus
tree method |
| dnadist |
dnadist |
Computes four different distances between species from
nucleic acid sequences |
| dnapars |
dnapars |
Estimates phylogenies from nucleic acid sequences using
parsimony |
| dollop |
dollop |
Executes Dollo and Polymorphism Parsimony Program |
| drawgram |
drawgram |
Interactively plots a cladogram- or phenogram-like rooted tree diagram |
| drawtree |
drawtree |
Interactively plots an unrooted tree diagram |
| fitch |
fitch |
Estimates phylogenies from distance matrix data under
the "additive tree model" using the Fitch-Margoliash criterion and
some related least-squares criteria |
| kitsch |
kitsch |
Estimates phylogenies from distance matrix data under
the "ultrametric" model (same as the additive tree model except that
an evolutionary clock is assumed) |
| mix |
mix |
Estimates phylogenies by several parsimony methods for
discrete character data with two states |
| pars |
pars |
Executes Wagner parsimony method with multiple states |
| neighbor |
neighbor |
Estimates a phylogenetic tree using neighbor joining
(doesn't assume a clock) and UPGMA (assumes a clock) methods |
| protdist |
protdist |
Computes a distance measure for protein sequences using
maximum likelihood estimates based on one of three metrics |
| protpars |
protpars |
Estimates phylogenies from protein sequences using
parsimony |
| seqboot |
seqboot |
Produces multiple data sets from a single data set
by bootstrap resampling |
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