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PedPhase

PedPhase is a computer program for inferring haplotypes from genotypes on pedigree data. It consists of five algorithms that 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. Please send your comments and suggestions to Jing Li.


  • Dowdload the Program

    The current version of PedPhase is 2.0. If you use PedPhase, please send your email to Jing Li, so that we can keep you informed of updates and we could have an idea of the level of interest in the program. Currently PedPhase Version 2.0 is only available on Windows.

    Old versions

    Version 1.0 on Windows and Linux..


  • Citation


      Jing Li and Tao Jiang. An Exact Solution for Finding Minimum Recombinant Haplotype Configurations on Pedigrees with Missing Data by Integer Linear Programming. RECOMB04 101--110. Full version submitted to Journal of Computational Biology
      Jing Li and Tao Jiang. Efficient Rule-Based Haplotyping Algorithm for Pedigree Data. In Proc. 7th Annual Conference on Research in Computational Molecular Biology (RECOMB03), 197-206.. Full version in Journal of Bioinformatics and Computational Biology(JBCB) 1(1):41-69. with title Efficient Inference of Haplotypes from Genotype on a Pedigree
      Koichiro Doi, Jing Li and Tao Jiang. Minimum Recombinant Haplotype Configuration on Tree Pedigrees. In Proc. WABI03 339-353.


  • Dataset

    We have applied the integer linear programming algorithm in PedPhase on the genotype data with pedigree information obtained from Gabriel et al. You may find the haplotype solutions here. Please refer to the readme file for more information about the data.

  • Related Links

      HapMap Project at National Human Genome Research Institute.
      Genotype data of the structure of haplotype blocks discovered by Whitehead Institute/MIT Center for Genome Research
      The SNP Consortium
      DIMACS Workshop on SNP


    1. Related Softwares

        Cyrillic Pedigree Draw Software
        Another Pedigree Draw Software by Dave Curtis
        PedCheck to check Mendelian errors
        SimWalk2, a statistical pedigree analysis package
      2. Updated 07/22/2004.