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UNLABELLED: Coalescent simulation has become an indispensable tool in population genetics, and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation by distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalized version of this algorithm as a freely available Python module. AVAILABILITY: Package available at http://pypi.python.org/pypi/ercs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original publication

DOI

10.1093/bioinformatics/btt067

Type

Journal article

Journal

Bioinformatics (Oxford, England)

Publication Date

04/2013

Volume

29

Pages

955 - 956

Addresses

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, West Mains Road, EH9 3JT, UK. jerome.kelleher@ed.ac.uk

Keywords

Pedigree, Genetics, Population, Evolution, Molecular, Genes, Algorithms, Models, Genetic, Computer Simulation, Software