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> Alignment Software
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1. Biology - Wikipedia, the free encyclopedia

For other uses, see Biology (disambiguation). Biology studies the variety of life (clockwise from top-left) E. coli, tree fern, ...
en.wikipedia.org

2. BBC - GCSE Bitesize - Science: Biology

www.bbc.co.uk

3. History of biology - Wikipedia, the free encyclopedia

The history of biology traces the study of the living world from ancient to modern times. Although the concept of biology as a single coherent field arose in the 19th ...
en.wikipedia.org

Component

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

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)

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)

Mesquite

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

MrBayes

Bayesian inference of phylogeny using Markov Chain Monte Carlo methods.
(http://morphbank.ebc.uu.se/mrbayes/)

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)

PAML

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

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.
(http://www.lms.si.edu/PAUP/)

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

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

Phylo-Win

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

RadCon

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.ht)

SuperTree

Implements various supertree building methods. Available in Linux/Unix and PC versions.
(http://www.tcd.ie/Botany/NS/SuperTree.html)

Tree Puzzle

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

TreeMap

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

TreeView

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

ZooKey

Software for creating taxonomic keys.
(http://www3.ufrgs.br/zookey/)

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