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Software (37)

Categories:

See Also:
Editor's Picks:

http://paup.csit.fsu.edu/
» PAUP* Open in a new browser windowEditor's Pick
   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/

http://evolution.genetics.washington.edu/phylip.html
» PHYLIP Open in a new browser windowEditor's Pick
   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


Sites:

http://ctap.inhs.uiuc.edu/dmitriev/
» 3I - Internet-accessible Interactive Identification Open in a new browser window
   Program to create internet-accessible interactive taxonomic keys.
   http://ctap.inhs.uiuc.edu/dmitriev/
http://bioinf.may.ie/software/clann/
» Clann: Software for Supertree Methods Open in a new browser window
   Clann implements a large number of supertree methods for reconstructing phylogenies from sets of input phylogenetic trees.
   http://bioinf.may.ie/software/clann/
http://taxonomy.zoology.gla.ac.uk/rod/cpw.html
» Component Open in a new browser window
   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
http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html
» GeneTree Open in a new browser window
   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
http://phylogeny.arizona.edu/macclade/macclade.html
» MacClade Open in a new browser window
   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
http://mesquiteproject.org/mesquite/mesquite.html
» Mesquite Open in a new browser window
   Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
   http://mesquiteproject.org/mesquite/mesquite.html
http://mrbayes.csit.fsu.edu/
» MrBayes Open in a new browser window
   Open source software for estimation of phylogenies using Bayesian inference.
   http://mrbayes.csit.fsu.edu/
http://www.cladistics.com/aboutNona.htm
» NONA Open in a new browser window
   Freeware software for phylogenetic analyses using parsimony.
   http://www.cladistics.com/aboutNona.htm
http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html
» NONA - A Quick Guide to the Commands Open in a new browser window
   A brief overview of using NONA for phylogenetic analysis.
   http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html
http://abacus.gene.ucl.ac.uk/software/paml.html
» PAML Open in a new browser window
   Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
   http://abacus.gene.ucl.ac.uk/software/paml.html
http://pbil.univ-lyon1.fr/software/phylowin.html
» Phylo-Win Open in a new browser window
   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
http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/
» Phylodendron Open in a new browser window
   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/
http://www.tree-puzzle.de/
» Tree Puzzle Open in a new browser window
   Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
   http://www.tree-puzzle.de/
http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
» TreeMap Open in a new browser window
   Experimental program for comparing host and parasite trees.
   http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
» TreeView Open in a new browser window
   Simple program for displaying phylogenies.
   http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
http://loco.biosci.arizona.edu/r8s/
» r8s Open in a new browser window
   Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
   http://loco.biosci.arizona.edu/r8s/

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Last Updated: 2007-01-02 17:59:41





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