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Bioinformatics Advance Access published online on October 7, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn522
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A Flexible Forward Simulator for Populations Subject to Selection and Demography

Ryan D. Hernandez

Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850 USA; Current Address: Department of Human Genetics, University of Chicago, 920 E. 58th St., CLSC 418, Chicago, Illinois 60637 USA

*To whom correspondence should be addressed. Dr. Ryan D. Hernandez, E-mail: rhernandez{at}uchicago.edu


  Abstract

Summary: This paper introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sexlinked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent).

Availability: The source code (written in the C programming language) is available at http://sfscode.sourceforge.net, and a web server (http://cbsuapps.tc.cornell.edu/sfscode.aspx) allows the user to perform simulations using the high performance computing cluster hosted by the Cornell University Computational Biology Service Unit.

Supplementary information: An extensive user's manual, performance statistics, and comparisons of patterns of genetic variation generated by SFS_CODE to theoretical expectations under various non-stationary demographic histories and models of natural selection are available on the project website: http://sfscode.sourceforge.net.

Contact: rhernandez{at}uchicago.edu

Associate Editor: Dr. Alex Bateman

Received on August 13, 2008; revised on September 19, 2008; accepted on October 4, 2008

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