Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event

Abstract. The haplotype inference (HI) problem is the problem of inferring 2n haplotype pairs from n observed genotype vectors. This is a key problem that arises in studying genetic variation in populations, for example in the ongoing HapMap project [5]. In order to have a hope of finding the haplotypes that actually generated the observed genotypes, we must use some (implicit or explicit) genetic model of the evolution of the underlying haplotypes. The Perfect Phylogeny Haplotyping (PPH) model was introduced in 2002 [9] to reflect the “neutral coalescent” or “perfect phylogeny” model of haplotype evolution. The PPH problem (which can be solved in polynomial time) is to determine whether there is an HI solution where the inferred haplotypes can be derived on a perfect phylogeny (tree).

• Type: Conference
• Year: 2005
• Where: WABI
• Authors: Yun S. Song, Yufeng Wu, Dan Gusfield
• Keywords: Algorithms, Haplotypes, Observed Genotypes, Perfect Phylogeny, WABI 2005