Phylogenetics

From Bioinformatics.Org Wiki

Software

• ATV - a phylogenetic tree display tool
• Clann - Clann: Software for investigating phylogenomic information using supertrees. This implements several methods of Supertree analysis (which are used as optimality criteria) and allows exhaustive and heuristic searches of tree-space to find the best supert
• fastDNAml - Estimates maximum likelihood phylogenetic trees from nucleotide sequences
• Friend - Friend, an Integrated Front-end Application for Bioinformatics
• MOLPHY - A Computer Program Package for Molecular Phylogenetics including ProtML
• njplot - NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format
• PAML - Phylogenetic Analysis by Maximum Likelihood
• Paup - Software package for inference of evolutionary trees
• PHASE - PHASE performs molecular phylogenetic inference using maximum likelihood and Bayesian (MCMC) techniques. Specific RNA substitution models are implemented to account for the correlated mutations of paired bases in RNA helices.
• PHYLIP - PHYLIP is a free package of programs for inferring phylogenies.
• PhyloDraw - PhyloDraw is a drawing tool for creating phylogenetic trees. PhyloDraw supports various kinds of multialignment programs (Dialign2, Clustal-W, Phylip format, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cl
• PhyloGrapher - PhyloGrapher is a program designed to visualize and study evolutional relationship between families of homologous genes or proteins. PhyloGrapher is a drawing tool that generates custom graphs out of the given set of genes based on distance matrix file.
• phylowin - Phylo_win is a graphical colour interface for molecular phylogenetic inference.
• PyPhy - PyPhy is a set of python scripts and modules for automatic, large-scale reconstructions of phylogenetic relationships of complete microbial genomes.
• unrooted - Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.