πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

BMC Bioinformatics

Filip Bielejec¹  Philippe Lemey¹  Luiz Max Carvalho³  Guy Baele¹  Andrew Rambaut²  Marc A Suchard⁴ 

[1] Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium

[2] Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

[3] Program for Scientific Computing (PROCC), Fundação Oswaldo Cruz, Rio de Janeiro, Brazil

[4] Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA

关键词: Evolution;    BEAGLE;    BEAST;    Phylogenetics;    Monte Carlo;    Simulation;   

Others  :  818613
DOI  :  10.1186/1471-2105-15-133

 received in 2013-10-10, accepted in 2014-04-24,  发布年份 2014

【 摘 要 】

Background

Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies.

Results

We present a flexible Monte Carlo simulation tool, called πBUSS, that employs the BEAGLE high performance library for phylogenetic computations to rapidly generate large sequence alignments under complex evolutionary models. πBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. πBUSS may serve as an easy-to-use, standard sequence simulation tool, but the available models and data types are particularly useful to assess the performance of complex BEAST inferences. The connection with BEAST is further strengthened through the use of a common extensible markup language (XML), allowing to specify also more advanced evolutionary models. To support simulation under the latter, as well as to support simulation and analysis in a single run, we also add the πBUSS core simulation routine to the list of BEAST XML parsers.

Conclusions

πBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, πBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. Applications are not restricted to the BEAST framework, or even time-measured evolutionary histories, and πBUSS can be connected to various other programs using standard input and output format.

【 授权许可】

   
2014 Bielejec et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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