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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti373
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 30, 2004
Revised February 15, 2005
Accepted March 2, 2005

Article

Partition distance via the assignment problem

Dmitry A. Konovalov 1*, Bruce Litow 1, and Nigel Bajema 1

1 School of Information Technology, James Cook University, Townsville, QLD 4811, Australia

* To whom correspondence should be addressed.
Dmitry A. Konovalov, E-mail: dmitry.konovalov{at}jcu.edu.au


  Abstract

Motivation: Accuracy testing of various pedigree reconstruction methods requires an efficient algorithm for calculation of distance between a known partition and its reconstruction. The currently used algorithm of Almudevar and Field takes a prohibitively long time for certain partitions and population sizes.

Results: We present an algorithm that very efficiently reduces the partition-distance calculation to the classic assignment problem of weighted bipartite graphs that has known polynomial-time solutions. Performance of the algorithm is tested against the Almudevar and Field partition-distance algorithm to verify the significant improvement in speed.

Availability: Computer code written in java is available upon request from the first author.


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[Abstract] [Full Text] [PDF]


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