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Bioinformatics. 2018 Jul 1;34(13):2308-2310. doi: 10.1093/bioinformatics/bty093.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

Author information

1
Department of Mathematics and Statistics, University of Helsinki, Finland.
2
Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Finland.
3
Department of Biostatistics, University of Oslo, Norway.

Abstract

Summary:

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and micro-epidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population and ultimately the whole metapopulation, is efficiently simulated using C++ objects and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g. large-scale simulations and likelihood-free inference.

Availability and implementation:

Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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