Jambe
Probabilistic Divergence Measures for
Detecting Recombination
with Markov Chain Monte Carlo
Version 1.0 alpha
© Copyright 2001, Dirk Husmeier,
Biomathematics and Statistics Scotland (BioSS).
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JAMBE is a software package to detect recombination
in DNA sequence alignments, implementing the method
discussed in
Husmeier D., Wright F. (2001):
"Probabilistic Divergence Measures for Detecting Interspecies Recombination" ,
Bioinformatics 17, Suppl. 1, S123-S131
(also presented at ISMB 2001).
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The software package has been written in Java 1.1.
Some of the commands are deprecated and will not
run under Java 1.2.
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Jambe creates an output file called
results_histo.out,
which shows the posterior distribution on tree
topologies for all window positions.
This can be used for further analysis, like the computation
of the Kullback-Leibler divergence between various distributions,
as discussed in the paper cited above.
The current version of JAMBE does not do this for you, though,
but rather offers you a set of MATLAB functions for the
subsequent analysis.
Writing the respective Java classes should be straightforward,
especially since some
older (now obsolete) classes
already exist. However, I have not got round doing this yet ...
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The MCMC simulations are done with the C++ package
BAMBE, Version 1.01 or Version 2.02.
You are strongly advised to familiarise yourself
with this software package, compile and install it properly,
and especially understand the various
options of the BAMBE file
infile.
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One of the Java classes (
ExtractTopos.java)
invokes a UNIX command.
Consequently, the current version will not run on a PC with the
WINDOWS operating system, although a PC running LINUX might
be o.k.
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Last modified: February 2002