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J Hered. 2008 Jul-Aug;99(4):438-40. doi: 10.1093/jhered/esm127. Epub 2008 Feb 29.

PGEToolbox: A Matlab toolbox for population genetics and evolution.

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Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA.


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

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