PedPhase: Haplotype Inference for Pedigree Data

Summary: We have developed a computer program consisting of four algorithms for inferring haplotypes from (unphased) genotypes on pedigree data. These algorithms are designed based on a combinatorial formulation of haplotype inference, namely the minimum-recombinant haplotype configuration (MRHC) problem, and are effective for different types of data. One of the algorithms, called block-extension, is an efficient heuristic algorithm for MRHC that performs very well when the input data requires few recombinants. The other three are exact algorithms for MRHC under various restrictions. Availability: Executable code for Windows and Linux is available at website http://www.cs.ucr.edu/ ̃jili/haplotyping.html. Contact: [email protected].