Mesquite is software for evolutionary biology, designed to
help biologists analyze comparative data about organisms. Its
emphasis is on phylogenetic analysis, but some of its modules
concern population genetics, while others
do non-phylogenetic multivariate analysis. Because it is
modular, the analyses available depend on the modules
installed. Written by Wayne and David Maddison.
PHYLIP (the PHYLogeny Inference Package) is a package of
programs for inferring phylogenies (evolutionary trees). It is
available free over the Internet, and written to work on as
many different kinds of computer systems as possible. The
source code is distributed (in C), and executables are also
distributed. In particular, already-compiled executables are
available for Windows (95/98/NT/2000/me/xp), MacOS 8 and 9,
MacOS X, and Linux systems. Complete documentation is available
on documentation files that come with the package.
COMPARE analyzes interspecific data in an evolutionary
context. It applies several Phylogenetic Comparative Methods
(e.g., independent contrasts, spatial autocorrelation,
phylogenetic GLS, phylogenetic mixed model), and can conduct
phylogenetic randomization tests (i.e., to generate random
phylogenies, branch lengths, or interspecific data on a
phylogeny).
CAIC (Comparative Analysis by Independent Contrasts) is a
freeware comparative analysis package for Macintosh. It and
finds and calculates phylogenetically independent contrasts in
one or more variables enabling you to test hypotheses of
correlated evolution.
MacClade is a computer program for phylogenetic analysis
written by David Maddison and Wayne Maddison. Its analytical
strength is in studies of character evolution. It also provides
many tools for entering and editing data and phylogenies, and
for producing tree diagrams and charts.
Phenotypic Diversity Analysis Programs by Theodore Garland,
Jr., Peter E. Midford, Jason A. Jones, Allan W. Dickerman, and
Ramon Diaz-Uriarte. PDAP is a set of Microsoft DOS
computer programs, but they will run fine in a DOS window under
Windows 95/98, Windows XP or Linux.