ArticleBMC bioinformatics2014
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
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- Comparative performance of viral landscape phylogeography approaches.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation.PNAS nexus · 2025Article
- nosoi: A stochastic agent-based transmission chain simulation framework in r.Methods in ecology and evolution · 2020Article
- Global Spread of the B5 Subgenotype EV-A71 and the Phylogeographical Analysis of Chinese Migration Events.Frontiers in cellular and infection microbiology · 2020Article
- Divergence dating using mixed effects clock modelling: An application to HIV-1.Virus evolution · 2019Article
- Article
- Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling.Virus evolution · 2017Article
- Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.Molecular biology and evolution · 2017Article
- Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic.Scientific reports · 2016Article
- Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty.Systematic biology · 2016Article
- The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study.Virus evolution · 2016Article
- MERS-CoV recombination: implications about the reservoir and potential for adaptation.Virus evolution · 2016Article
- Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.PLoS computational biology · 2015Article
- Quantifying evolutionary constraints on B-cell affinity maturation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Article
- Host ecology determines the dispersal patterns of a plant virus.Virus evolution · 2015Article
- Trends in substitution models of molecular evolution.Frontiers in genetics · 2015Article
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6 authors.
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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.
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