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Bioinformatics Advance Access published online on January 12, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk049
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received November 7, 2005
Revised January 6, 2006
Accepted January 9, 2006

Applications note

Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting

Alun Thomas 1 * and Nicola J. Camp 1

1 Department of Medical Informatics, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA

* To whom correspondence should be addressed.
Alun Thomas, E-mail: alun{at}genepi.med.utah.edu


  Abstract

Summary: Graphical modeling is used to extend the gene counting method to compute maximum likelihood estimates of allele frequencies for samples of individuals related in extended pedigrees. Genotypes may be missing or partially observed, and error rates can be simultaneously estimated.

Availability: The Java classes and Javadocs pages for GeneCountAlleles can be obtained from bioinformatics.med.utah.edu/~alun, which also has more information on its use and file formats.

Associate Editor: Martin Bishop
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