Important Phylogenetic Software
ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees.
ATV reads standard "New Hampshire" format tree files (as produced by all major phylogenetic
analysis software). ATV also implements an extended superset of New Hampshire format called
NHX format, which allows to extensively annotate a tree.
ATV can be used both as application and as Applet. It requires Java version 1.5 or higher. ATV is part of
FORESTER (a framework for
BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
It is entirely orientated towards rooted, time-measured phylogenies inferred using
strict or relaxed molecular clock models. It can be used as a method of reconstructing
phylogenies but is also a framework for testing evolutionary hypotheses without
conditioning on a single tree topology. BEAST uses MCMC to average over tree space,
so that each tree is weighted proportional to its posterior probability. We include
a simple to use user-interface program for setting up standard analyses and a suit
of programs for analysing the results.
Geneious provides sophisticated
genome & proteome research software, sequence alignment, protein or molecular visualization,
publication literature search and storage software and more, with revolutionary usability.
So you get more done. And faster results - faster to publication or faster to discovery.
Geneious Pro is an integrated bioinformatics software suite for manipulating, finding,
sharing, and exploring biological data such as DNA sequences or proteins, phylogenies,
3D structure information, publications, etc. It features sequence alignment and phylogenetic
analysis, contig assembly, primer design and restriction analysis, access to biological
databases, BLAST, protein structure viewing, NCBI, EMBL, PubMed auto-find, and more. It even
includes an API for creating your own plugins.
MacClade is a computer program for phylogenetic analysis written by
David Maddison and Wayne Maddison. Its analytical strength is in
studies of character evolution. It also provides many tools for
entering and editing data and phylogenies, and for producing tree
diagrams and charts.
Mesquite is software for evolutionary biology, designed to help biologists analyze
comparative data about organisms. Its emphasis is on phylogenetic analysis, but some
of its modules concern population genetics, while others do non-phylogenetic multivariate
analysis. The native file format is NEXUS file format, but Mesquite can also import
and export numerous
other file types.
MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of
phylogeny is based upon a quantity called the posterior probability distribution of trees,
which is the probability of a tree conditioned on the observations. The conditioning is
accomplished using Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation technique called
Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.
The program takes as input a character matrix in a
NEXUS file format.
Network - Free Phylogenetic Network Software
Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then
provide age estimates for any ancestor in the tree.
PAUP: Phylogenetic Analysis Using Parsimony. Tools for inferring and interpreting phylogenetic
NEXUS file format.
PHYLIP is a free package of programs for inferring phylogenies. It is distributed as
source code, documentation files, and a number of different types of executables.
Output is written onto special files with names like "outfile" and "treefile".
Trees written onto "treefile" are in the NEWICK
file format, an informal standard agreed to in 1986 by authors of a number of major phylogeny
r8s is a program for estimating absolute rates ("r8s") of molecular evolution
and divergence times on a phylogenetic tree. r8s generates combined matrix
representations of trees from tree file MRF Heuristic Supertree Software. r8s
uses NEXUS file format.
Tools for analyzing and visualizing evolutionary data. SplitsTree uses
NEXUS file format.
SplitsTree Reloaded - JSplits
jSplits - otherwise known as SplitsTree4.0, is an all-new implementation of the
SplitsTree software written in Java. Superficially, this new program is similar to previous versions
of this software. However, there are substantial differences. The new program has many new features.
TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs. TreeView
can read files of many file formats.
Joe Felsenstein's list of Phylogeny Programs
Joe Felsenstein of the Department of Genome Sciences at the University
of Washington, maintains a list of 324
phylogeny packages and 45 free servers, free and non-free, listed
by methods available, computer systems, data type to analyse, date.
Does not include data conversion utilities, clustering programmes,
tree alignment programmes that do not infer trees, programmes for
detecting evidence of recombination that are not using trees intensively
enough and sequence editors that do not submit jobs to phylogeny programs
More Software links
Online Software Tools
Build Supertree Server
Rod Page's Online software that implements one of three algorithms described in chapters by David Bryant,
Philip Daniel, Charles Semple, and Mike Steel in "Phylogenetic supertrees: Combining information to reveal the Tree of Life (Computational Biology)" edited by Olaf Bininda-Emonds.
PhyloFacts - Phylogenomic encyclopedias across the Tree of Life.
Phylodendron - Phylogenetic tree printer.
Supertree Construction Package - Computational Biology Laboratory
The Department of Computer Science
at Iowa State University hosts online software to build MRF, MRP, MC, or MMC supertrees.
There is also a page that links to
other phylogenetic databases.
Supertree Server - Computational Biology Laboratory
Information and tools to assist phylogenetic biologists and others interested in using supertrees in their
research or teaching. It provides background information on the theory and links to
examples with real data. It also provides a venue for archiving of software tools for
supertree construction as they become available, as well as links to other efforts in
Supertree Server - Rod Page
Online software to build mincut and modified mincut supertrees
TreeGen - Tree generation from distance data.
TreeTop - Phylogenetic Tree Prediction.
An online searchable relational database of phylogenetic information hosted by
the University at Buffalo. TreeBASE
stores phylogenetic trees and the data matrices used to generate them
from published research papers.
The Tree Of Life
The Tree Of Life is a collaborative Internet project containing
information about phylogeny and biodiversity. Each page contains
information about one group of organisms with links to their
closest related ancestors and predecessors.