Homepage of MCMCSALUT (Markov Chain Monte Carlo Sequence Alignment Utility)

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 developed by Dirk Metzler.

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 models. 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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Dirk Metzler
Last modified: Tue Oct 29 16:02:55 CET 2002