Important Phylogenetic Software

ATV
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 automated phylogenomics).

BEAST
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
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
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
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
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*
PAUP: Phylogenetic Analysis Using Parsimony. Tools for inferring and interpreting phylogenetic trees. Uses NEXUS file format.

Phylip
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 packages.

r8s
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.

SplitsTree 3.2
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
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 this area.

Supertree Server - Rod Page
Online software to build mincut and modified mincut supertrees

TreeGen - Tree generation from distance data.

TreeTop - Phylogenetic Tree Prediction.

 

Online Databases

TreeBASE
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.