Subcategories 4

Related categories 4

PAUP*
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
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.
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.
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.
Mesquite
Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.
MrBayes
Open source software for estimation of phylogenies using Bayesian inference.
NONA - A Quick Guide to the Commands
A brief overview of using NONA for phylogenetic analysis.
PAML
Phylogenetic analyses of DNA or protein sequences using maximum likelihood.
Phylo-Win
Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
Phylodendron
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.
r8s
Open source software for estimating absolute rates of molecular evolution and divergence times on phylogenetic trees.
Tree Puzzle
Computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.
TreeMap
Experimental program for comparing host and parasite trees.
TreeView
Simple program for displaying phylogenies.
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Last update:
August 5, 2016 at 18:54:10 UTC
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