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Experimental program for comparing host and parasite trees.
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TreeMap Map is an experimental program for comparing host and parasite trees. It is available for both Windows and Apple Macs. TreeMap 2.0 by Michael Charleston and Roderic Page is available for Mac OS. Response to Ashley Dowling's critique of TreeMap...Simple program for displaying phylogenies.
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TreeView Tree drawing software for Apple Macintosh and Windows (and now Linux and Unix) TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs. It has the following features: runs on both the Apple Macintosh and Windows...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.
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COMPONENT Home Page T is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography View screen shot at actual size Features User-friendly interface:WYSIWYG tree printing, interactive...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
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.
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IUBio Archive Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology. Options allow you to save in various formats, print, edit, modify, and adorn the tree. This version of Phylodendron includes the ability to run as a Web service....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
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
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.
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GeneTree A program for comparing gene and species trees GeneTree is an experimental program for comparing gene and species trees. Currently it is available for Mac OS (System 7.5 or later running on a PowerMac and Windows 95/NT 4.0 or later....Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
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TREE-PUZZLE Maximum likelihood analysis for nucleotide, amino acid, and two-state data Copyright 2003-2004 by Heiko A. Schmidt, Korbinian Strimmer, and Arndt von Haeseler Copyright 1999-2003 by Heiko A. Schmidt, Korbinian Strimmer, Martin Vingron, and Arndt von Haeseler Copyright 1995-1999 by Korbinian...A brief overview of using Nona for phylogenetic analysis.
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The following is intended to provide a quick overview of the most commonly used commands for the phylogenetic analysis program Nona. A more complete guide is available in the document Piwe.doc that is distributed with the program and with Piwe....Implements various supertree building methods. Available in Linux/Unix and PC versions.
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SuperTree Home Page Tree is a program to compute MRP matrices from NEXUS/NEWICK phylogenetic trees. It does not perform parsimony analyses on these matrices, so you will need another program (PAUP*4, PHYLIP, or others) for that step. Other methods will be implemented in...Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
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Phylo_win Many distances can be used including Jukes Cantor, Kimura, Tajima Nei, HKY, Galtier Gouy (1995 LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected...Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
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Phylogenetic Analysis by Maximum Likelihood (PAML) How fast is my new computer? Get the benchmark speed2.tar.gz Downloading and Compiling PAML Running Programs in PAML To ask questions, go to Genetics Software Forum PAML Manual (pamlDOC.pdf) PAML FAQs (pamlFAQs.pdf) Old versions of paml PAML Resources on the...Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
http://morphbank.ebc.uu.se/mrbayes/
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
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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. Because it is modular, the...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/