A flexible forward simulator for populations subject to selection and demography

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

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Biological Evolution
  • Computer Simulation
  • Demography
  • Genetics, Population*
  • Genome, Human
  • Humans
  • Models, Genetic
  • Population / genetics*
  • Selection, Genetic
  • Software