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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. jamescai@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.

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