|
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.
Download the Program
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 2.0/2.1 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
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
Related Software
|
|
