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PedPhase

PedPhase is a suite of computer programs for haplotype inference from genotypes on pedigree data. It consists of several different 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.


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  • PedPhase 3.0

    PedPhase 3.0 implements the DSS algorithm, which is described in details in An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. JBCB, 7(3): 521-545, 2009. It was released in Aug 2009 as a standalone program for windows and Linux platforms, with a brief description of the algorithm. The algorithm can effectively work for any pedigree structure and large number of SNPs, with no or very few recombinations and moderate missing. This algorithm should replace the Block-extension algorithm and the Constraint-finding algorithm implemented in version 1.0.


  • PedPhase 2.1

    PedPhase 2.0/2.1 implements the ILP algorithm, which is described in details in Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming. Journal of Computational Biology, 12:719-739, 2005. It is an exact algorithm. Version 2.1 has fix some bugs reported by users. Due to the ILP solver, Version 2.1 is only available on Windows.


  • PedPhase 1.0

    PedPhase 1.0 implements four algorithms, which are described in these two papers ( Efficient Inference of Haplotypes from Genotype on a Pedigree and Minimum Recombinant Haplotype Configuration on Tree Pedigrees.). Version 1.0 is available on Windows and Linux..


  • Citations


      Li, X. & Li, J. An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions. Journal of Bioinformatics and Computational Biology (JBCB), 7(3): 521-545, 2009.
      Jing Li and Tao Jiang. Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming. Journal of Computational Biology, 12:719-739, 2005.
      Jing Li and Tao Jiang. Efficient Inference of Haplotypes from Genotype on a Pedigree. Journal of Bioinformatics and Computational Biology(JBCB) 1(1):41-69. 2003
      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 Software

        Cyrillic Pedigree Draw Software
        Another Pedigree Draw Software by Dave Curtis
        PedCheck to check Mendelian errors
        SimWalk2, a statistical pedigree analysis package

    2. Updated 08/25/2009.