Two general-purpose phylogenetic
packages are available for the users of AMDeC Core
Facility: PHYLIP v. 3.5c (also available as EMBASSY-PHYLIP
- The EMBOSS version of PHYLIP) and PAUP 4.0. In
addition, for phylogenetic analysis by maximum likelihood
the PAML package is installed. Also, for users of
Windows based computers we recommend downloading
and installing the MEGA2 package.
PHYLIP is the most widely distributed
and popular phylogeny package, with over 7,000 registered
users. It is produced by Joe Felsenstein of the
Department of Genome Sciences at the University
of Washington.
PHYLIP includes programs to carry out parsimony,
distance matrix methods, maximum likelihood, and
other methods on a variety of types of data, including
DNA and RNA sequences, protein sequences, restriction
sites, 0/1 discrete characters data, gene frequencies,
continuous characters and distance matrices. This
package is available for most systems and has a
command line interface. See the web page: http://evolution.genetics.washington.edu,
or download by anonymous ftp: ftp://evolution.genetics.washington.edu/pub/phylip
The PAUP package is produced by
David Swofford of the Laboratory of Molecular Systematics,
National Museum of Natural History, Smithsonian
Institution, Washington, D.C. and is a commercial
software package. The Core Facility has a multi-user
license for this product. PAUP is the most sophisticated
parsimony program, with many options. It includes
parsimony, distance matrix, invariants, and maximum
likelihood methods and many indices and statistical
tests.
The package has a graphical user
interface but most operations still have to be done
on the command line. Similar to PHYLIP, intensive
use of the manual is necessary for successful use
of this package. See the web page at: http://paup.csit.fsu.edu/about.html.
MEGA2 - Though PHYLLIP and PAUP
covers almost all needs of modern phylogenetic analysis,
in many cases intensive study is required to learn
use of the command line features of these packages.
The package MEGA2 (Molecular Evolutionary Genetic
Analysis) for the Microsoft Windows platform offers
a convenient and easy-to-use graphical user interface.
MEGA2 carries out parsimony, distance matrix and
likelihood methods with branch-and-bound search
available for parsimony and bootstrapping available
for all methods and has a reasonably good set of
incorporated statistical tests and sequence evolution
models. The GUI allows sophisticated tree manipulation
and the output of trees in EMF or BMP formats.
MEGA2 is produced by Sudhir Kumar,
Koichiro Tamura, Ingrid Jakobsen and Masatoshi Nei.
See http://www.megasoftware.net
PAML (Phylogenetic Analysis by
Maximum Likelihood) is produced by Ziheng Yang of
the Department of Genetics and Biometry, University
College London. The strength of the package lies
in its rich implementation of evolutionary models,
though Yang comments that tree-making is not a strong
point of the current version. The programs can estimate
branch lengths in a tree and parameters in the evolutionary
model such as the transition/transversion rate ratio,
the gamma parameter for variable substitution rates
among sites, rate parameters for different genes,
and synonymous and nonsynonymous substitution rates.
They can also test evolutionary models, calculate
substitution rates at particular sites, reconstruct
ancestral nucleotide or amino acid sequences, simulate
DNA and protein sequence evolution, and of course
do phylogenetic tree reconstruction by maximum likelihood
and Bayesian Markov Chain Monte Carlo methods.
PAML distributed as ANSI C source
code and has a command line user interface. Thorough
reading of the manual is necessary before use of
the package. Web pages: http://abacus.gene.ucl.ac.uk/software/paml.html
For more extensive list of phylogenetic
software one should visit Joe
Felsenstein pages .
