LPPH (Linear-Time Algorithm for Perfect Phylogeny Haplotyping) is a linear-time program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model.In more population genetic terms, LPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.
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A linear-time algorithm to the Perfect Phylogeny Haplotyping (PPH) Problem.
Z. Ding, V. Filkov and D. Gusfield
J Comput Biol. 2006 Mar;13(2):522-53.