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Two general-purpose phylogenetic packages
are available to the users of the AMDeC Core Facility:
PHYLIP v. 3.5c (also available as EMBASSY-PHYLIP - The
EMBOSS version of PHYLIP) and PAUP 4.0. For phylogenetic
analysis by maximum likelihood the PAML package is installed.
For users of Windows based computers we recommend the
download and installation of the MEGA2 package (details
below).
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 uses a command line interface.
Web pages: http://evolution.genetics.washington.edu,
or 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.
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,
and similar to PHYLIP, intensive reference to the manual
is necessary for successful use of this package.
Web pages: http://paup.csit.fsu.edu/about.html
Though PHYLLIP and PAUP cover almost
all needs of modern phylogenetic analysis, in many cases
extensive study is required to learn the use of command
line features of these packages. The package MEGA2 (Molecular
Evolutionary Genetic Analysis) forn the Microsoft Windows
platform offers a convenient and easy-to-use graphical
user interface, which facilitates the use of most popular
methods of phylogenetic analysis. For MEGA2 users, PAUP
and PHYLIP remain as indispensable, highly sophisticated
tools for special cases. 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 manipulating and output
of trees in EMF or BMP formats.
MEGA2 is produced by Sudhir Kumar, Koichiro Tamura,
Ingrid Jakobsen and Masatoshi Nei.
The previous version, MEGA, was a DOS program, which
carried out parsimony as well as neighbor-joining methods,
with branch-and-bound search available for parsimony
and bootstrapping available for all methods.
Web pages: 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 is 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 .
Author: Pavel Morozov.
Last updated 4/16/2003.
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