PPH A program for inferring haplotypes from genotypes
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PPH Tags

analysis haplotype extended haplotypes haplotype analysis generate interacting genotypes create interacting genotypes progeny array genotypes phylogeny genetic population genotype analysis haplotypes analysis goat haplotypes 3 diploid genotypes

PPH Description

PPH was developed to be 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. In the program PPH, when asked for the format of the input data, select one of the numbers 1 through 7 as explained below. The input format determines the output format. Step by step to Use this program: 1. Type "pph.exe" to start the program. 2. Please input the filename: Input the filename of the file which contains genotype or haplotype information. 3. Please input the number of the file format: ( Please refer to the file "FORMAT.txt" ): This program can read seven different kinds of formats. Please refer to the file "FORMAT.txt" for more information of the formats. Input value should be from 1 to 7. 4. Please input the file name that holds the ancestral vector, i.e., the binary vector specifying the character states at the root of the tree. There are two special cases of particular importance. If the ancestral states are all-0, then just enter "d" for the default case; if you do not know the ancestral states, enter "m" for the majority vector). In that case, the program will determine if there is an unrooted tree that could evolve the given genotypes. 6. An output file will be generated. The name of the output file is "output". For information about the output formats, see the file FORMAT.txt 7. The program also checks for consistency of the output. That is, it checks that each output haplotype pair does actually correspond to the correct input genotype vector. The program reports the result of that verification step.

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