MCMCSALUT is a program for the joint sampling of alignments and
mutation parameter values for given DNA sequences. It is freely
available under the terms of the
GNU General Public License (GPL). MCMCSALUT was
The following gzipped tar package contains the source code for Version 1.0 of MCMCSALUT:mcmcsalut.tgz
(It also contains a README file.)
MCMCSALUT is based on a sequence evolution model that allows insertions and deletions of fragments containing more than one site. There are many options for the substitution model. For a desription of the model, the algorithm behind MCMCSALUT and application examples see
D.Metzler (2003) Statistical alignment based on fragment insertion and deletion
Bioinformatics 19 pp. 490-499.
Supplementary figures for this paper are available from http://www.math.uni-frankfurt.de/~stoch/software/mcmcsalut/figures.html.
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