We address the combinatorial problem of inferring haplotypes in a population that forms a perfect phylogeny (PP) given a sample of genotypes. The problem is relevant because, in DNA sequencing, genotypes are easier to obtain than haplotyping by DNA sequencing. Since PP’s appear naturally and frequently on DNA sequences of restricted length, PP haplotyping is a favourable approach to facilitate ...

Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas fro...

BACKGROUND Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium. METHODS Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of...

Haplotype data is valuable in mapping disease-susceptibility genes in the study of Mendelian and complex diseases. We present algorithms for inferring a most likely haplotype configuration for general pedigrees, implemented in the newest version of the genetic linkage analysis system SUPERLINK. In SUPERLINK, genetic linkage analysis problems are represented internally using Bayesian networks. T...

Haplotyping via perfect phylogeny is a method for retrieving haplotypes from genotypes. Fast algorithms are known for computing perfect phylogenies from complete and error-free input instances—these instances can be organized as a genotype matrix whose rows are the genotypes and whose columns are the single nucleotide polymorphisms under consideration. Unfortunately, in the more realistic setti...