Dmitry A Konovalov1, Bruce Litow, Nigel Bajema. 1. School of Information Technology, James Cook University, Townsville, QLD 4811, Australia. dmitry.konovalov@jcu.edu.au
Abstract
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.
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.
Authors: Patrick Meyer; Fenja M Schophaus; Thomas Glassen; Jasmin Riedl; Julia M Rohrer; Gert G Wagner; Timo von Oertzen Journal: PLoS One Date: 2019-03-04 Impact factor: 3.240