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

Abstract

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. 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. 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).