A parsimonious tree-grow method for haplotype inference

MOTIVATION Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, such as disease genes mapping and drug design. Parsimony haplotyping is one of haplotyping problems belonging to NP-hard class. RESULTS In this paper, we aim to develop a novel algorithm for the haplotype inference problem with the parsimony criterion, based on a parsimonious tree-grow method (PTG). PTG is a heuristic algorithm that can find the minimum number of distinct haplotypes based on the criterion of keeping all genotypes resolved during tree-grow process. In addition, a block-partitioning method is also proposed to improve the computational efficiency. We show that the proposed approach is not only effective with a high accuracy, but also very efficient with the computational complexity in the order of O(m2n) time for n single nucleotide polymorphism sites in m individual genotypes. AVAILABILITY The software is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/ptg/ CONTACT [email protected] SUPPLEMENTARY INFORMATION Supporting materials is available from http://zhangroup.aporc.org/bioinfo/ptg/bti572supplementary.pdf