Software Taxonomy Biology


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








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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, a

  • Mesquite - Experimental, modular software for evolutionary biology, designed to help biologists software analyze comparative data about organisms.
  • GeneTree - Uses reconciled trees to compare gene trees and biology species trees, taxonomy explaining incongruence between the phylogenies by biology postulating horizontal transfer, gene taxonomy duplication and loss events. biology Reprints of papers describing the methods taxonomy are available biology from the GeneTree
  • Clann: Software for Supertree Methods - Clann implements a large number of supertree methods biology for reconstructing phylogenies from sets of input phylogenetic biology trees.
  • Phylodendron - Java application for drawing phylogenetic trees. Allows you software to save taxonomy in various formats, print, edit, modify, software and adorn the tree, taxonomy and should work on software any java runtime platform.
  • SuperTree - Implements various supertree building methods. Available in Linux/Unix software and PC taxonomy versions.
  • NONA - Freeware software for phylogenetic analyses using parsimony.
  • Component - For analysis of phylogenies. Includes a wide range of randomization biology methods, consensus methods, tree comparison measures, and calculates reconciled trees. biology Now aging, and available only for Windows machines, but still biology has some unique features. Much of the
  • TreeMap - Experimental program for comparing host and parasite trees.
  • MacClade - A powerful Macintosh package for phylogenetic analysis. Not intended as biology a stand-alone tool to infer phylogeny, but excels in studying biology character evolution. Also provides tools for entering and editing data biology and phylogenies and producing attractive tree diag
  • NONA - A Quick Guide to the Commands - A brief overview of using NONA for phylogenetic software analysis.
  • MrBayes - Open source software for estimation of phylogenies using software Bayesian inference.
  • TreeView - Simple program for displaying phylogenies.
  • Phylo-Win - Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.
  • 3I - Internet-accessible Interactive Identification - Program to create internet-accessible interactive taxonomic keys.
  • r8s - Open source software for estimating absolute rates of biology molecular evolution biology and divergence times on phylogenetic trees.
  • Tree Puzzle - Computer program to reconstruct phylogenetic trees from molecular biology sequence data software by maximum likelihood.
  • PAML - Phylogenetic analyses of DNA or protein sequences using maximum likelihood.


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