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Bioinformatics Advance Access originally published online on April 9, 2009
Bioinformatics 2009 25(12):1561-1563; doi:10.1093/bioinformatics/btp185
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients

Mark Abney

Department of Human Genetics, University of Chicago, 920 E 58th St., Chicago, IL 60637, USA


  Abstract

Summary: Computing the probability of identity by descent sharing among n genes given only the pedigree of those genes is a computationally challenging problem, if n or the pedigree size is large. Here, I present a novel graphical algorithm for efficiently computing all generalized kinship coefficients for n genes. The graphical description transforms the problem from doing many recursion on the pedigree to doing a single traversal of a structure referred to as the kinship graph.

Availability: The algorithm is implemented for n = 4 in the software package IdCoefs at http://home.uchicago.edu/abney/Software.html.

Contact: abney{at}bsd.uchicago.edu

Supplementary Information:Supplementary data are available at Bioinformatics online.

Associate Editor: Martin Bishop

Received on February 12, 2009; revised on March 30, 2009; accepted on March 31, 2009

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