Skip Navigation


Bioinformatics Advance Access originally published online on July 3, 2009
Bioinformatics 2009 25(18):2440-2441; doi:10.1093/bioinformatics/btp417
This Article
Right arrow Full Text
Right arrow Full Text (Print PDF)
Right arrow All Versions of this Article:
25/18/2440    most recent
btp417v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Himmelmann, L.
Right arrow Articles by Metzler, D.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Himmelmann, L.
Right arrow Articles by Metzler, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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,*

1Department for Computer Science and Mathematics, Goethe-University, Frankfurt am Main and 2Department of Biology, University of Munich (LMU), Munich, Germany

*To whom correspondence should be addressed.


  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://evol.bio.lmu.de/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: Martin Bishop

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.