01755naa a2200229 a 450000100080000000500110000800800410001902200140006002400390007410000160011324500900012926000090021950002760022852007970050465300170130165300200131865300180133865300130135670000150136970000150138477301260139910609402020-03-23       2020    bl uuuu     u00u1 u    #d  a1367-48037 a10.1093/bioinformatics/btz7352DOI1 aFERRÉS, I.  asimurgbsimulate bacterial pangenomes in R. (Application note)h[electronic resource]  c2020  aArticle history: Received: 19 March 2019 / Revision received: 06 August 2019 / Accepted: 25 September 2019 / Published: 04 October 2019. Corresponding author:   Ferrés, I.; Microbial Genomics Laboratory, Institut Pasteur Montevideo, Uruguay; email:iferres@pasteur.edu.uy  aABSTRACT. Motivation: The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models. Results: We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses. © 2020 Oxford University Press. All rights reserved.  aBenchmarking  aGenome analysis  aMutation rate  aSoftware1 aFRESIA, P.1 aIRAOLA, G.  tBioinformatics, 15 February 2020, Volume 36, Issue 4, Pages 1273-1274. Doi: https://doi.org/10.1093/bioinformatics/btz735