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 ana - [Read more MEGA]
Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX. - [Read more PHYLIP]
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. - [Read more Mesquite]
NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Availiable for several platforms including Windows, MacOS, Linux and Solaris. - [Read more NJplot]
BLAST a protein sequence, then perform automated phylogenetic analysis on hits or on uploaded sequences; PHYLIP-based analyses. - [Read more PhyloBLAST]
The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and traini - [Read more CIPRes]
TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences. - [Read more TreeJuxtaposer]
"Phylogeny-Diversity of Life Through Time" is an on-line exhibit at the University of California Museum of Paleontology website. There is an introduction to phylogenetics and cladistics, and you can navigate through a very informative phylogenetic tree r - [Read more UCMP Phylogeny Wing]
Puzzleboot is a UNIX shell script facilitating bootstrap analysis using TREE-PUZZLE and PHYLIP. It enhances TREE-PUZZLE by allowing one to analyse multiple datasets, and can be used for both protein and DNA distance bootstrap analysis. - [Read more Puzzleboot]
Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download. - [Read more Ribosomal Database Project]
Weighbor is a tool for building phylogenetic trees from distance matrices. It employs a weighted version of the neighbour-joining method in which longer distances in the matrix are given less weight. - [Read more Weighbor]
