| 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).
 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 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
r8s
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.
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).
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).
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.
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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