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Bayesian Evolutionary
Analysis Sampling
Trees (BEAST) is a
program for Bayesian
Markov Chain Monte
Carlo (MCMC)
analysis of molecular
sequences. It is
oriented towards
rooted, time-measured
phylogenies inferred
using strict or relaxed
molecular clock
No
BEAST
models. It can be used
Free
programming
as a method of
reconstructing
phylogenies but is also
a framework for
testing evolutionary
hypotheses without
conditioning on a
single tree topology.
BEAST averages over
tree space, so that each
tree is weighted
proportional to its
posterior probability.
The Basic Local
Alignment Search Tool
(BLAST) finds regions
of local similarity
between genetic
sequences, comparing
BLAST
nucleotide or protein
(Basic Local sequences to sequence No
Free
Alignment databases and
programming
Search Tool) calculates the
statistical significance
of matches. BLAST
can be used to infer
functional and
evolutionary
relationships between
Additional Information
Lemey P, Rambaut A, Drummond AJ & Suchard MA
Computational Biology 5, e1000520.
Drummond AJ & Rambaut A (2007) "BEAST: Bayes
by sampling trees." BMC Evolutionary Biology 7, 214
Drummond AJ, Nicholls GK, Rodrigo AG & Solomon
161, 1307-1320.
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&P
Title
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sequences as well as
help identify members
of gene families. It is
used to compare a
novel sequence with
those contained in
nucleotide and protein
databases by aligning
the novel sequence
with previously
characterized genes.
Alternative
implementations
include AB-BLAST
(formerly known as
WU-BLAST), FSABLAST, and
ScalaBLAST.
ClustalW2, ClustallW,
and ClustalX are
general purpose,
multiple sequence
alignment tools.
Multiple alignments of
protein sequences can
identify conserved
sequence regions. This
is useful in designing
experiments to test and
ClustalW2 / modify the function of
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ClustalW / specific proteins, in
Free
programming
ClustalX
predicting the function
and structure of
proteins and in
identifying new
members of protein
families. Clustal is a
general purpose
multiple sequence
alignment program for
DNA or proteins.
ClustalW is the
command line version
Additional Information
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http://www.ebi.ac.uk/Tools/clustalw2/index.ht
Higgins D., Thompson J., Gibson T., Thompso
Gibson T.J.(1994)
CLUSTAL W: improving the sensitivity of pro
sequence alignment through sequence weighti
penalties and weight matrix choice.
Higgins, D.G., Thompson, J.D. and Gibson, T
CLUSTAL for multiple sequence alignments.
266:383-402. Nucleic Acids Research 22: 467
Larkin M.A., Blackshields G., Brown N.P., Ch
P.A., McWilliam H.*, Valentin F.*, Wallace I
R.*, Thompson J.D., Gibson T.J. and Higgins
and ClustalX version 2, Bioinformatics 2007 2
Using ClustalX for multiple sequence, Tuimal
http://www.clustal.org/)
Title
Mesquite
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Technical
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and ClustalX is the
graphical version of
Clustal. The current
version is ClustalW2.
It produces
biologically
meaningful multiple
sequence alignments of
divergent sequences by
calculating the best
match for the selected
sequences and lining
them up so that the
identities, similarities
and differences can be
seen. Evolutionary
relationships can be
seen via viewing
Cladograms or
Phylograms.
Mesquite is a modular
software system for
evolutionary analysis,
designed to help
biologists analyze
comparative data about
organisms. Although
its emphasis is on
phylogenetic analysis,
some of its modules
concern population
Basic
genetics, while others programming Free
do non-phylogenetic skills
multivariate analysis.
The analyses include:
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Reconstruction
of ancestral
states
(parsimony,
likelihood)
Tests of
process of
Additional Information
Example use: Tyler, Kevin M.; Wagner, Gerd K.; Wu
Katharina T., Functional Significance May Underlie t
Single Amino Acid Substitutions in Conserved Protei
Molecular Evolution (70:4), DOI: 10.1007/s00239-01
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character
evolution,
including
correlation
Analysis of
speciation and
extinction rates
Simulation of
character
evolution
(categorical,
DNA,
continuous)
Parametric
bootstrapping
(integration
with programs
such as PAUP*
and NONA)
Morphometrics
(PCA, CVA,
geometric
morphometrics)
Coalescence
(simulations,
other
calculations)
Tree
comparisons
and simulations
(tree similarity,
Markov
speciation
models)
Mesquite is not
primarily designed to
infer phylogenetic
trees, but rather for
diverse analyses using
already inferred trees.
Technical
Expertise Cost
Required
Additional Information
Title
MrBayes
PAUP*
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MrBayes is a program
for doing Bayesian
phylogenetic analysis
including phylogenetic
reconstruction.
Bayesian inference of
phylogeny is based on
the posterior
probability distribution
of trees, which is the
probability of a tree
conditioned on the
observations. The
conditioning is
accomplished using
Bayes's theorem. The
posterior probability
distribution of trees is
often impossible to
calculate analytically;
instead, MrBayes uses
a simulation technique
called Markov Chain
Monte Carlo (MCMC)
to approximate the
posterior probabilities
of trees.
PAUP* (Phylogenetic
Analysis Using
Parsimony *and other
methods) is a program
for phylogenetic
analysis using
parsimony, maximum
likelihood, and
distance methods. The
program has a
selection of analysis
options and model
choices, and
accommodates DNA,
RNA, protein and
general data types. It
Technical
Expertise Cost
Required
Additional Information
Huelsenbeck JP, Ronquist F., MRBAYES: Bayesian i
trees,Bioinformatics. 2001 Aug;17(8):754-5.
No
Fredrik Ronquist and Andrew R. Deans, Bayesian Phy
Free
programming
Influence on Insect Systematics, Annual Review of En
Vol. 55: 189-206 (Volume publication date January 2
online as a Review in Advance on October 5, 2009,DO
10.1146/annurev.ento.54.110807.090529
Maddison, David R., Swofford, David L. and Maddiso
NEXUS: an extensible file format for systematic infor
No
CostBiology 46: 590-621
programming basis
http://users.iab.uaf.edu/~derek_sikes/zool575/z575_la
Title
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has options for dealing
with phylogenetic trees
including importing,
combining, comparing,
constraining, rooting
and testing hypotheses.
PHYLIP (the
PHYLogeny Inference
Package) is a package
of programs for
inferring phylogenies
(evolutionary trees).
Methods that are
available in the
package include:
PHYLIP
parsimony, distance
(PHYLogeny
No
matrix, and likelihood
Free
Inference
programming
methods, including
Package)
bootstrapping and
consensus trees. Input
data types include
molecular sequences,
gene frequencies,
restriction sites and
fragments, distance
matrices, and discrete
characters.
Additional Information
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Joseph Felsenstein, Inferring Phylogenies, 200
Associates. ISBN 0-87893-177-5
http://www.facebook.com/pages/PHYLIP/115