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 piBUSS, that employs the BEAGLE high performance library for phylogenetic computations within BEAST to rapidly generate large sequence alignments under complex evolutionary models. piBUSS 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. Analogous to BEAST model and analysis setup, more advanced simulation options are supported through an extensible markup language (XML) specification, which in addition to generating sequence output, also allows users to combine simulation and analysis in a single BEAST run. Conclusions: piBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, piBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. The software aims at implementing new models and data types that are continuously being developed as part of BEAST/BEAGLE.
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