Taxonomy, Systematics, and Bioinformatics
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Software developed at Glasgow

Other software

Programming and other documents

This is a list of some software we have found useful. A much more extensive list is provided by Joe Felsenstein.

Tree viewing


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.

Tree building


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).

SplitsTree 2.0

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

Tree comparsion and interpretation


Mike Sanderson's program for estimating absolute rates ("r8s") of molecular evolution and divergence times on a phylogenetic tree .

MacClade 3.0

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.


Comparative method (Macintosh only)


Comphrehensive set of tree comparison, consensus, and randomisation methods (Windows only).


Software for comparing host and parasite phylogenies (Windows and Macintosh).


Sequence format converters


ForCon is a user-friendly software tool for the conversion of nucleic acid and amino acid sequence alignments. Requires Windows.


SeqVerter v. 1.4 is a free sequence file format conversion utility by GeneStudio, Inc. Requires Windows 95/NT (you may need to update your MFC librariers for this program).

Sequence alignment, analysis and searching


Multiple sequence alignments, for both Windows (3.1, NT on Intel and Alpha chips) and Macintosh.


Se-Al is a Macintosh application for creating multiple sequence alignments from nucleotide and amino acid sequences. At the moment it does not do any automatic alignments but is intended for the production of hand alignments and forpreparing input for alignment programs such as CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. It is particularly useful for manipulating protein coding DNA/RNA sequences.


Multiple sequence alignments, including Blast searches and links to other applications. For Macintosh only but see SeqPup which will run on Mac's, Windows PC's and Unix.


Multiple sequence alignments, including Blast searches and links to other applications. Written in Java.


Sequence and phylogentetic analysis program, now with a Windows interface. The DOS version of MEGA is still available


BioEdit is a graphical biological sequence alignment editor and analysis program for Windows 95. It is offered as is and free of charge to anyone who wants it. Features include manual and automated multiple sequence alignment, colored/shaded views, World Wide Web functions, BLAST accessories, and link to external analysis programs such as Clustal and TreeView. (for Windows 95/NT)


Interactive searching of GENBANK from your desktop via the Internet (see also NCBI's WWW version of Entrez). For Windows and Macintosh.

RNA secondary structure


A tool for drawing RNA secondary structures in molecular biology on Apple Macintosh computers.


A tool for drawing RNA secondary structures in molecular biology. Written in Java and runs on Macintosh, Windows and Unix machines.


Compute and display secondary structures under Windows 95/NT.


Compute and display secondary structures under Windows 95/NT.


A tool for drawing RNA secondary structures on PC's running Windows 95/NT or Linux (requires TCL).


A Java applet for displaying secondary structure in a Web browser.

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