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Bioinformatics Advance Access published online on July 3, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp417
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TreeTime: An extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.

Lin Himmelmann 1 and Dirk Metzler 2,*

1Goethe-University,Department for Computer Science and Mathematics, Frankfurt am Main, Germany, www.linhi.com
2University of Munich (LMU), Biology Department, Munich, Germany, www.zi.biol.lmu.de/evol/StatGen.html

*To whom correspondence should be addressed. Prof. Dirk Metzler, E-mail: metzler{at}bio.lmu.de


  Abstract

Motivation: For the estimation of phylogenetic trees from molecular data it is worthwhile to take prior paleontologic knowledge into account, if available. To calibrate the branch lengths of the tree with times assigned to geo-historical events or fossils, it is necessary to select a relaxed molecular clock model to specify how mutation rates can change along the phylogeny.

Results: We present the software TreeTime for Bayesian phylogeny estimation. It can take prior information about the topology of the tree and about branching times into account. Several relaxed molecular clock models are implemented in TreeTime. TreeTime is written in C++ and designed to be efficient and extensible.

Availability: TreeTime is freely available from http://www.zi.bio.lmu.de/evol/statgen/software/treetime under the terms of the GNU General Public Licence (GPL, version 3 or later)

Contact: lin{at}linhi.de, metzler{at}bio.lmu.de

Associate Editor: Prof. Martin Bishop

Received on March 11, 2009; revised on June 30, 2009; accepted on July 1, 2009

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