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Bioinformatics Vol. 19 no. 4 2003
Pages 539-540
© 2003 Oxford University Press

Applications Note

PopHist: inferring population history from the spectrum of allele frequencies

Stephen Wooding

Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112-5330, USA

Received on February 14, 2002 ; revised on September 24, 2002 ; accepted on October 25, 2002

Summary: PopHist is a computer program that uses the frequency spectrum of alleles to: (a) estimate maximum likelihood parameters describing a population’s history; and (b) compare alternative hypotheses about population history using likelihood ratio tests. The program uses the matrix coalescent, a method for calculating theoretical frequency spectra that can be applied to sets of unlinked sites.

Availability: Source code and documentation are available at http://mombasa.anthro.utah.edu/wooding/PopHist

Contact: swooding{at}genetics.utah.edu


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