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DPPH

DPPH is a program for inferring haplotypes from genotypes to determine if there are resulting haplotypes that fit a tree model (i.e. a perfect phylogeny, a coalescent).
In more population genetic terms, DPPH determines whether a set of SNP genotypes can be explained by haplotype pairs that could have evolved on a coalescent under the no-recombination, infinite sites model. Hence it determines for SNP genotype data what the three or four gametes test (depending on whether the tree is rooted or not) determines for haplotype data.

Program DPPH solves the same problem solved by program PPH (now called GPPH to distinguish it from the other programs for the PPH problem). However, program DPPH is faster than GPPH and it also outputs a representation of the set of all solutions.

This package was written by Ren-Hua Chung at U.C. Davis Computer Science under the
direction of Dan Gusfield.


To cite the general problem and first results, please use:
"Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions" D. Gusfield In Proceedings of RECOMB, Sixth Annual Conference on Research in Computational Molecular Biology, April 2002

To cite the specific method implemented in program DPPH, please use:
"Haplotyping as Perfect Phylogeny: A Direct Approach", "V. Bafna and D. Gusfield and G. Lancia and S. Yooseph",
Journal of Computational Biology, Vol. 10, No. 3 (2003), pp. 323-340
First released as: Techreport = "CSE-2002-21", "UC Davis, Department of Computer Science", "July 17, 2002"


Papers can be found at: recent papers

Copyright (C) 2002 R.H. Chung and D. Gusfield
We give no warranties, and no rights for commercial use.

Executable versions of this program are now available for the following platforms: