Bacmeta : simulator for genomic evolution in bacterial metapopulations

Show full item record



Sipola , A , Marttinen , P & Corander , J 2018 , ' Bacmeta : simulator for genomic evolution in bacterial metapopulations ' , Bioinformatics , vol. 34 , no. 13 , pp. 2308-2310 .

Title: Bacmeta : simulator for genomic evolution in bacterial metapopulations
Author: Sipola, Aleksi; Marttinen, Pekka; Corander, Jukka
Contributor organization: Department of Mathematics and Statistics
Jukka Corander / Principal Investigator
Biostatistics Helsinki
Date: 2018-07-01
Language: eng
Number of pages: 3
Belongs to series: Bioinformatics
ISSN: 1367-4803
Abstract: 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 under the BSD 3-clause license. Contact: or Supplementary information: Supplementary data are available at Bioinformatics online.
1183 Plant biology, microbiology, virology
112 Statistics and probability
Peer reviewed: Yes
Rights: unspecified
Usage restriction: openAccess
Self-archived version: acceptedVersion

Files in this item

Total number of downloads: Loading...

Files Size Format View
FixedSupplementary_1.pdf 158.1Kb PDF View/Open

This item appears in the following Collection(s)

Show full item record