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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
1Department for Computer Science and Mathematics, Goethe-University, Frankfurt am Main, Germany. lin@linhi.de
Bioinformatics (Oxford, England)
|July 7, 2009
Summary
TreeTime software integrates paleontological data to improve phylogenetic tree estimation. It utilizes relaxed molecular clock models for accurate evolutionary rate calibration, enhancing evolutionary biology research.
Area of Science:
- Evolutionary Biology
- Computational Biology
- Phylogenetics
Background:
- Phylogenetic tree estimation from molecular data can be enhanced by incorporating paleontological knowledge.
- Calibrating phylogenetic tree branch lengths requires relaxed molecular clock models to account for varying mutation rates.
Purpose of the Study:
- To introduce TreeTime, a software tool for Bayesian phylogeny estimation.
- To enable the integration of prior information on tree topology and divergence times.
- To provide efficient and extensible relaxed molecular clock models.
Main Methods:
- Bayesian inference for phylogenetic tree estimation.
- Implementation of multiple relaxed molecular clock models.
- Utilizing prior information on topology and branching times.
Main Results:
- The TreeTime software effectively incorporates prior paleontological information into phylogenetic analyses.
- Several relaxed molecular clock models are available within the TreeTime software.
- TreeTime is developed in C++ for efficiency and extensibility.
Conclusions:
- TreeTime offers a robust platform for Bayesian phylogeny estimation, leveraging paleontological constraints.
- The software's flexibility with relaxed molecular clock models supports diverse evolutionary studies.
- TreeTime is freely available, promoting accessibility in computational evolutionary research.
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