This book takes the perfect phylogeny approach to the haplotype inference problem, and presents various perfect phylogeny based formulations and algorithms to solve the haplotype inference problem. One of the major results presented in this book is the linear-time opph algorithm for the perfect phylogeny haplotyping (PPH) problem. This algorithm is one of the first linear-time algorithms for the PPH problem. This book also presents algorithms for constructing near-perfect phylogenies from both haplotype and genotype data. Taking into account the fact that most biological data is incomplete, this book also presents some elegant heuristics for constructing perfect phylogenies from incomplete genotype data. The algorithms presented here will be useful in understanding and analyzing the increasingly large amounts of genotype data that are becoming available.