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Bioinformatics Advance Access originally published online on January 18, 2005
Bioinformatics 2005 21(9):2106-2107; doi:10.1093/bioinformatics/bti274
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Mtreemix: a software package for learning and using mixture models of mutagenetic trees

Niko Beerenwinkel 1,*, Jörg Rahnenführer 1, Rolf Kaiser 2, Daniel Hoffmann 3, Joachim Selbig 4 and Thomas Lengauer 1

1Max Planck Institute for Informatics Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany
2Institute of Virology, University of Cologne Fürst-Pückler-Strasse 56, 50935 Köln, Germany
3Center of Advanced European Studies and Research Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
4Max Planck Institute of Molecular Plant Physiology Am Mühlenberg 1, 14476 Golm, Germany

*To whom correspondence should be addressed at Department of Mathematics, University of California, 898 Evans Hall, Berkeley, CA 94720, USA.

Summary: Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes. They have been applied to model the accumulation of chromosomal gains and losses in tumor development and the development of drug resistance-associated mutations in the HIV genome.

Mtreemix is a software package for estimating mutagenetic trees mixture models from observed cross-sectional data and for using these models for predictions. We provide programs for model fitting, model selection, simulation, likelihood computation and waiting time estimation.

Availability: Mtreemix, including source code, documentation, sample data files and precompiled Solaris and Linux binaries, is freely available for non-commercial users at http://mtreemix.bioinf.mpi-sb.mpg.de/

Contact: niko{at}math.berkeley.edu


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