TY - JOUR AU - Delaneau, Olivier AU - Coulonges, Cédric AU - Zagury, Jean-François PY - 2008 DA - 2008/12/16 TI - Shape-IT: new rapid and accurate algorithm for haplotype inference JO - BMC Bioinformatics SP - 540 VL - 9 IS - 1 AB - We have developed a new computational algorithm, Shape-IT, to infer haplotypes under the genetic model of coalescence with recombination developed by Stephens et al in Phase v2.1. It runs much faster than Phase v2.1 while exhibiting the same accuracy. The major algorithmic improvements rely on the use of binary trees to represent the sets of candidate haplotypes for each individual. These binary tree representations: (1) speed up the computations of posterior probabilities of the haplotypes by avoiding the redundant operations made in Phase v2.1, and (2) overcome the exponential aspect of the haplotypes inference problem by the smart exploration of the most plausible pathways (ie. haplotypes) in the binary trees. SN - 1471-2105 UR - https://doi.org/10.1186/1471-2105-9-540 DO - 10.1186/1471-2105-9-540 ID - Delaneau2008 ER -