PPH
PPH 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, PPH 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.
This package was written by Ren-Hua Chung at U.C. Davis Computer Science under the
direction of Dan Gusfield.
For a discussion of the problem of inferring haplotypes and the general solution method
in this program, see:
"Haplotyping as Perfect Phylogeny: Conceptual Framework and Efficient Solutions"
in
recent papers
For a brief discussion of the details of the program see
Perfect Phylogeny Haplotyper: Haplotype Inferral Using a Tree Model" in
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 available for the following platforms:
Dan Gusfield's Homepage, gusfield@cs.ucdavis.edu
December
2002