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

TreeView

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).

TreeExplorer

View and manipulate MEGA format trees under Windows.


Tree building

CAFCA

Collection of APL Functions for Cladistic Analysis, written by Rino Zandee. Currently Macintosh only, but Windows version coming.

MrBayes

MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. Avaialble for Mac, PC, and Unix.

PAUP*

The standard program for phylogenetic analysis (Mac OS, Windows, Unix).

PHYLIP

The most comphrehensive, all imbracing collection of phylogenetic programs, including parsimony, maximum likelihood, and distance methods, plus utility programs. Runs on anything.

Spectronet

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).

Spectrum

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.

 


Models

HYPHY

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.

 

ModelTest

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

r8s

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)

Mesquite

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.

CAIC

Comparative method (Macintosh only)

COMPONENT

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

TreeMap

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

 


Sequence format converters

ForCon

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

SeqVerter

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

MACAW

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

SeAl

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.

SeqApp

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.

SeqPup

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

Mega2

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

BioEdit

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)

NEntrez

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

LoopDLoop

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

LoopDLoop

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

RNADraw

Compute and display secondary structures under Windows 95/NT.

RNAStructure

Compute and display secondary structures under Windows 95/NT.

RnaViz

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

SStructView

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


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