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| | Clann: Software for Supertree Methods     |
| | 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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| | Component |
| | 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 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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| | 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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| | 3I - Internet-accessible Interactive Identification |
| | Program to create internet-accessible interactive taxonomic keys.
http://ctap.inhs.uiuc.edu/dmitriev/ |
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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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| | 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 |
| | Open source software for estimation of phylogenies using Bayesian inference.
http://mrbayes.csit.fsu.edu/ |
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| | NONA |
| | Freeware software for phylogenetic analyses using parsimony.
http://www.cladistics.com/aboutNona.htm |
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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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| | PAML |
| | Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
http://abacus.gene.ucl.ac.uk/software/paml.html |
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