Bioinformatics Links Directory : Phylogeny Reconstruction

This section contains links to tools and databases for phylogeny reconstruction, including taxonomy resources.

Eclair - (Found June 29, 2008 )

Eclair is a web service that implements the Eclat (EST CLAssification Tool) support vector machine (SVM) approach for the classification of species origin for, primarily, expressed sequence tags (ESTs)
http://eclair.btk.fi/

ITS2 - (Found June 29, 2008 )

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.
http://its2.bioapps.biozentrum.uni-wuerzburg.de/

Joes Site - Phylogeny Programs - (Found June 29, 2008 )

Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip.
http://evolution.genetics.washington.edu/phylip/software.html

MAVID - (Found June 29, 2008 )

MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.
http://baboon.math.berkeley.edu/mavid/

MEGA - (Found June 29, 2008 )

MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments.
http://www.megasoftware.net/

Mesquite - (Found June 29, 2008 )

Mesquite is an open source software project designed to deal with comparative data about organisms and evolutionary analyses. Mesquite contains modules for phylogenetic analysis, population genetics, and non-phylogenetic multivariate analysis.
http://mesquiteproject.org/mesquite/mesquite.html

MLST - (Found June 29, 2008 )

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.
http://www.mlst.net/

ModelTest Sever - (Found June 29, 2008 )

ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.
http://darwin.uvigo.es/software/modeltest_server.html

MultiPhyl - (Found June 29, 2008 )

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.
http://www.cs.nuim.ie/distributed/multiphyl.php

NJplot - (Found June 29, 2008 )

NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Available for several platforms including Windows, MacOS, Linux and Solaris.
http://pbil.univ-lyon1.fr/software/njplot.html