|Taxonomy, Systematics, and Bioinformatics
at the University of Glasgow
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| This is a list of some software we have found
useful. A much
more extensive list is provided by Joe Felsenstein.
View NEXUS and PHYLIP format tree files on Macs (68K and Power Mac) and Windows (16 and 32 bit). Unix version as well (TreeView X).
View and manipulate MEGA format trees under Windows.
Collection of APL Functions for Cladistic Analysis, written by Rino Zandee. Currently Macintosh only, but Windows version coming.
MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. Avaialble for Mac, PC, and Unix.
The standard program for phylogenetic analysis (Mac OS, Windows, Unix).
The most comphrehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood, and distance methods, plus utility programs. Runs on anything.
Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allowing the user to interactively analyze the resulting collection using tools such as Lento-plots and median networks (Windows only).
Finds bipartition spectra of molecular data (Macintosh and Windows95/NT).
Written by Daniel Huson, SplitsTree uses split decomposition to construct networks of relationship. The program supports the NEXUS file format, and runs on Apple Macintosh and Unix machines. There is also a Web version. The program can be downloaded from the SplitsTree ftp site.
HYPHY is a free multiplatform (Mac, Windows and UNIX) software package intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs.
The use of a model of DNA substitution is routine in the analysis of DNA sequences. Modeltest helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion.
Other lists of tree building programs
Mike Sanderson's program for estimating absolute rates ("r8s") of molecular evolution and divergence times on a phylogenetic tree .
Interactive character analysis using parsimony. Wonderful! (Macintosh only)
The inertia of the massive programs and the isolation and idiosyncracies of the small programs have prompted us to develop Mesquite, a new modular system that will allow many programmers to contribute building blocks to a common system. Mesquite began with an emphasis on phylogenetic analysis, but its flexibility allows for other uses in evolutionary biology. It is written in JavaŠ for ease of development and platform independence.
SeqPup which will run on Mac's, Windows PC's and Unix.
WWW version of Entrez). For Windows and Macintosh.