Abstract Summary: We have developed an efficient program, the Perfect Phylogeny Haplotyper (PPH) that takes in unphased population genotype data, and determines if that data can be explained by haplotype pairs that could have evolved on a perfect phylogeny. Availability: Executable code for four common platforms is available at: http://wwwcsif.cs.ucdavis.edu/~gusfield Contact: gusfield@cs.ucdavis.edu * To whom correspondence should be addressed.