Abstract
BackgroundSimulated 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.ResultsWe 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.ConclusionsπBUSS 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.
Highlights
Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods
We have developed a new simulation tool, called πBUSS, that we consider to be a rejuvenation of Seq-Gen [7], with several extensions to better integrate with the BEAST inference framework
Compared to Seq-Gen and other simulation software (Table 1), πBUSS covers a relatively wide range of models while, similar to Mesquite, offering a cross-platform, user-friendly graphical user interface (GUI). πBUSS is implemented in the Java programming language, and requires a Java runtime environment, and depends on the Broad-platform Evolutionary Analysis General Likelihood Evaluator (BEAGLE) library
Summary
We present a flexible Monte Carlo simulation tool, called π BUSS, that employs the BEAGLE high performance library for phylogenetic computations to rapidly generate large sequence alignments under complex evolutionary models. π BUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. We present a flexible Monte Carlo simulation tool, called π BUSS, that employs the BEAGLE high performance library for phylogenetic computations to rapidly generate large sequence alignments under complex evolutionary models. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. Π BUSS may serve as an easy-to-use, standard sequence simulation tool, but the available models and data types are 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 more advanced evolutionary models. Conclusions: π BUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Π BUSS 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 π BUSS can be connected to various other programs using standard input and output format
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