New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers
INFORMS Journal on Computing
Discovering kinship through small subsets
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
A Metric for Phylogenetic Trees Based on Matching
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Kinship inference is the task of identifying genealogically related individuals. Questions of kinship are important for determining mating structures, particularly in endangered populations. Although many solutions exist for reconstructing full-sibling relationships, few exist for half-siblings. We present SibJoin, a heuristic-based clustering approach based on Mendelian genetics, which is reasonably accurate and thousands of times faster than existing algorithms. We also identify issues with partition distance, the traditional method for assessing the quality of estimated sibship partitionings. We prefer an information theoretic alternative called variation of information, which takes into account the degree to which misplaced individuals harm sibship structures.