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Bioinformatics Advance Access originally published online on March 3, 2005
Bioinformatics 2005 21(10):2463-2468; 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{at}oupjournals.org

Partition-distance via the assignment problem

Dmitry A. Konovalov *, Bruce Litow and Nigel Bajema

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

*To whom correspondence should be addressed.

Motivation: Accuracy testing of various pedigree reconstruction methods requires an efficient algorithm for the 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. The 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.

Contact: dmitry.konovalov{at}jcu.edu.au


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D. A. Konovalov, N. Bajema, and B. Litow
Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem
Bioinformatics, October 15, 2005; 21(20): 3912 - 3917.
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