| Directory > Science > Biology > Taxonomy > Software PAUP*
PAUP is the most widely used package for phylogenetic inference, and now implements maximum
likelihood and distance methods as well as various forms of parsimony. Powerful and very easy to
use, particularly the Mac version.
http://paup.csit.fsu.edu/
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ZooKey
Software for creating taxonomic keys.
http://www3.ufrgs.br/zookey/
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Mesquite
Experimental, modular software for evolutionary biology, designed to help biologists analyze
comparative data about organisms.
http://mesquiteproject.org/mesquite/mesquite.html
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MrBayes
Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
http://morphbank.ebc.uu.se/mrbayes/
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PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
http://abacus.gene.ucl.ac.uk/software/paml.html
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Phylo-Win
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining,
parsimony, and maximum likelihood methods and bootstrap with any of them.
http://pbil.univ-lyon1.fr/software/phylowin.html
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SuperTree
Implements various supertree building methods. Available in Linux/Unix and PC versions.
http://www.tcd.ie/Botany/NS/SuperTree.html
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Nona - A Quick Guide to the Commands
A brief overview of using Nona for phylogenetic analysis.
http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html
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Tree Puzzle
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum
likelihood.
http://www.tree-puzzle.de/
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GeneTree
Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the
phylogenies by postulating horizontal transfer, gene duplication and loss events. Reprints of
papers describing the methods are available from the GeneTree web page. Available for Macintosh and
Windows.
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
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RadCon
A package implementing a wide range of consensus methods, including reduced consensus, and for
calculation of MRP supertrees. Currently only available for Macs.
http://taxonomy.zoology.gla.ac.uk/~jthorley/radcon/radcon.html
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MacClade
A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer
phylogeny, but excels in studying character evolution. Also provides tools for entering and editing
data and phylogenies and producing attractive tree diagrams and charts.
http://phylogeny.arizona.edu/macclade/macclade.html
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Phylodendron
Java application for drawing phylogenetic trees. Allows you to save in various formats, print,
edit, modify, and adorn the tree, and should work on any java runtime platform.
http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/
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PHYLIP
Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference
package. The most widely distributed phylogeny software. Includes distance, likelihood and
parsimony methods for a wide range of different types of data, and runs on most platforms.
http://evolution.genetics.washington.edu/phylip.html
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Component
For analysis of phlyogenies. Includes a wide range of randomisation methods, consensus methods,
tree comparison measures, and calculates reconciled trees. Now aging, and available only for
Windows machines, but still has some unique features. Much of the functionality is now replaced by
RadCon, GeneTree, TreeMap and the latest release of PAUP.
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html
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TreeView
Simple program for displaying phylogenies.
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
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TreeMap
Experimental program for comparing host and parasite trees.
http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
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