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http://paup.csit.fsu.edu/
Featured Site PAUP* Open in a new browser windowLink Details
- 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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http://evolution.genetics.washington.edu/phylip.html
Featured Site PHYLIP Open in a new browser windowLink Details
- 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, a
- http://evolution.genetics.washington.edu/phylip.html

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Regular Websites in this category

3I - Internet-accessible Interactive Identification Open in a new windowLink Details
- Program to create internet-accessible interactive taxonomic keys.
- http://ctap.inhs.uiuc.edu/dmitriev/

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r8s Open in a new windowLink Details
- Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
- http://ginger.ucdavis.edu/r8s/

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NONA Open in a new windowLink Details
- Freeware software for phylogenetic analyses using parsimony.
- http://www.cladistics.com/aboutNona.htm

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MrBayes Open in a new windowLink Details
- Open source software for estimation of phylogenies using Bayesian inference.
- http://mrbayes.csit.fsu.edu/

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Clann: Software for Supertree Methods Open in a new windowLink Details
- Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees.
- http://bioinf.may.ie/software/clann/

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Mesquite Open in a new windowLink Details
- 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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PAML Open in a new windowLink Details
- 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 Open in a new windowLink Details
- 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 Open in a new windowLink Details
- 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 Open in a new windowLink Details
- A brief overview of using NONA for phylogenetic analysis.
- http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html

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Tree Puzzle Open in a new windowLink Details
- Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
- http://www.tree-puzzle.de/

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GeneTree Open in a new windowLink Details
- 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
- http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html

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MacClade Open in a new windowLink Details
- 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 diag
- http://phylogeny.arizona.edu/macclade/macclade.html

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Phylodendron Open in a new windowLink Details
- 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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Component Open in a new windowLink Details
- For analysis of phylogenies. Includes a wide range of randomization 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
- http://taxonomy.zoology.gla.ac.uk/rod/cpw.html

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TreeView Open in a new windowLink Details
- Simple program for displaying phylogenies.
- http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

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TreeMap Open in a new windowLink Details
- Experimental program for comparing host and parasite trees.
- http://taxonomy.zoology.gla.ac.uk/rod/treemap.html

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