BPPH (Perfect Phylogeny Haplotyper: The Berkeley method ) is a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent). In more population genetic terms, BPPH 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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“Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions”
D. Gusfield In Proceedings of RECOMB, Sixth Annual Conference on Research in Computational Molecular Biology, April 2002