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Abstract Summary: 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 (SFSCODE) 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. Contact: rhernandez@uchicago. edu Supplementary information: An extensive user's manual, perfor-mance statistics, and comparisons of patterns of genetic variation generated by SFSCODE to theoretical expectations under various non-stationary demographic histories and models of natural selection are available on the project website: http: //sfscode. sourceforge. net.
Ryan D. Hernandez (Tue,) studied this question.