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Bioinformatics. 2008 Dec 1;24(23):2786-7. doi: 10.1093/bioinformatics/btn522. Epub 2008 Oct 7.

A flexible forward simulator for populations subject to selection and demography.

Author information

1
Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850, USA. rhernandez@uchicago.edu

Abstract

This article 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, sex-linked 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.

PMID:
18842601
PMCID:
PMC2639268
DOI:
10.1093/bioinformatics/btn522
[Indexed for MEDLINE]
Free PMC Article

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