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Below is a list of software useful and appropriate for study
with MLST data.
Included is a description of the software and links to the
downloadable files
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Sequence Output by Nick Ross and
Brian Spratt |
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Sequence Output is a simple Macintosh program that allows
a set of sequences (in MEGA format) to be grouped into
those that are identical (i.e. allele assignment), and
allows all alleles to be compared to any selected 'master'
allele, to identify the variable sites.
More information
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Platform(s) - Windows DOS exe.
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FREE
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MEGA by Sudhir Kumar, Koichiro Tamura,
Ingrid Jakobsen and Masatoshi Nei |
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The scope of computational molecular evolutionary genetics
has expanded greatly with unparalleled growth of gene
sequence databases in recent years. Efficient handling
and analysis of these data for molecular evolutionary
analysis require the development of easy-to-use computer
programs. Therefore, the goal of the MEGA (Molecular
Evolutionary Genetics Analysis) software project has
been to make useful methods of comparative sequence
analysis easily accessible to the scientific community
for research and education.
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Platform(s) - Macintosh, Sun WorkStation and Windows.
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FREE
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PAUP by David Swofford |
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PAUP* version 4.0 is a major
upgrade and new release of the software package for inference
of evolutionary trees.
The influence of high-speed computer analysis of molecular,
morphological and/or behavioral data to infer phylogenetic
relationships has expanded well beyond its central role
in evolutionary biology, now encompassing applications
in areas as diverse as conservation biology, ecology,
and forensic studies.
The success of previous versions of PAUP: Phylogenetic
Analysis Using Parsimony has made it the most widely used
software package for the inference of evolutionary trees.
In addition, the PAUP manual has proven to be an essential
guide, serving as a comprehensive introduction to phylogenetic
analysis for beginning researchers, as well as an important
reference for experts in the field.
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Platform(s) - Windows, UNIX/VMS, or DOS-based formats.
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Purchase - Website
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$85-$150
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Phylip by Joe
Felsenstein |
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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.
It is the most widely-distributed phylogeny package, with
over 7,000 registered users, some of them satisfied. It
competes with PAUP* to be the program responsible for
the most published trees.
It has been distributed since October, 1980. .
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Platform(s) - pre-386 DOS, 386/486/Pentium DOS, Windows
3.1, Windows95/98/NT, 68k Macintosh, or PowerMac.
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Download - Website |
FREE
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by Keith
Jolley |
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The purpose of this program
is to bring together some of the analyses which can be
performed on MLST data into a single package. Written
for Windows.
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Platform(s) - Windows95/98/NT
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Download - Website |
FREE
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