Computational problems in perfect phylogeny haplotyping: Typing without calling the allele

Tamar Barzuza*, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vcctor of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics and is a variant of the PP haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is "full" genotypes, here, we assume less informative input and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by the tree they map onto and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes and present a linear algorithm for identifying those genotypes.

Original languageEnglish
Pages (from-to)101-109
Number of pages9
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Issue number1
StatePublished - 2008


  • Graph realization
  • Haplotypes
  • Perfect phylogeny
  • XOR-genotypes


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