Directory of Software Resources

Home > Science > Biology > Taxonomy > Software

Subcategories

• Alignment Software
• Comparative Methods
• Directories
• Taxonomic Databases

Resources in This Category

• Component

  http://taxonomy.zoology.gla.ac.uk/rod/cpw.html
  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.

• GeneTree

  http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.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.

• Mesquite

  http://mesquiteproject.org/mesquite/mesquite.html
  Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.

• MrBayes

  http://mrbayes.sourceforge.net/
  Open source software for estimation of phylogenies using Bayesian inference.

• NONA - A Quick Guide to the Commands

  http://www.gwu.edu/~clade/faculty/lipscomb/Nonadoc.html
  A brief overview of using NONA for phylogenetic analysis.

• PAML

  http://abacus.gene.ucl.ac.uk/software/paml.html
  Phylogenetic analyses of DNA or protein sequences using maximum likelihood.

• PAUP*

  http://paup.csit.fsu.edu/
  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.

• PHYLIP

  http://evolution.genetics.washington.edu/phylip.html
  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.

• Phylo-Win

  http://pbil.univ-lyon1.fr/software/phylowin.html
  Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.

• Phylodendron

  http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/
  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.

• Tree Puzzle

  http://www.tree-puzzle.de/
  Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

• TreeMap

  http://taxonomy.zoology.gla.ac.uk/rod/treemap.html
  Experimental program for comparing host and parasite trees.

• TreeView

  http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
  Simple program for displaying phylogenies.

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