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Journal of Heredity Advance Access published online on February 29, 2008
Journal of Heredity, doi:10.1093/jhered/esm127
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© The American Genetic Association. 2008. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Computer Notes

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

James J. Cai

From the Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305

Address correspondence to James J. Cai at the address above, or e-mail: jamescai{at}stanford.edu.

Assessing genetic diversity within populations is vital for understanding the nature of evolutionary processes at the molecular level. PGEToolbox is a Matlab-based open-sourced software package for data analysis in population genetics. The main features of this software are as follows: 1) capability for handling both DNA sequence polymorphisms and single nucleotide polymorphisms (SNPs), which include genotype and haplotype data; 2) exhaustive population genetic analyses and neutrality tests based on the coalescent theory; 3) extendibility and scalability for complex and large genome-wide datasets; 4) simple yet effective graphic user interfaces and sophisticated visualization of data and results. For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox.

Corresponding Editor: Robert Wayne

Received August 1, 2008
Accepted December 7, 2008


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