_PG

Downloads
 

PGenome Contains all the described programs and one example with step by step instructions
Win





PGMerge Merges a phenotype file with sequences from a genotype file to create the basic input file (PGfile) for PGenome programs. PGMerge also sorts the file on up to 4 phenotypic fields per individual for association mapping.
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PGTheta Tests the association of specific nucleotides with a phenotype by a series of statistical tests. Association consistency is evaluated by a permutation test (Doerge & Churchill 1996, Churchill & Doerge 1994 ).
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PGCon tests the association between genotypes at a segregating site and phenotypes by contingency chi squere analysis with probabilities adjusted by the Bonferroni method. Additionally calculates the minimal effect that a nucleic acid substitution or a different genotype need exert in the phenotype with sample sizes used and maintain statistical significance.
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PGLD Calculates Ohta's Linkage Disequilibrium D Statistics for each segregating sites in a genotypic sequence (Ohta 1982a, Ohta 1982b). Dst' association with nucleotide distance is assessed through linear regression analysis and Mantel test is used for statistical significance (Mantel 1967).
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PGFis Lists allele frequencies at each segregating site and summarizes the relation between obseeved and expected heterozygotes (Wright's " F " and W&C "f") (Wright 1965, Weir and Cockerham 1984) at each segregating site.
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The final two programs are for testing isolation by distance in population genetics.

PGPW Calculates pairwise genetic distances, creating a genetic distance matrices that can be compared to a geographic distance matrix to test for isolation by distance in PGMan
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PGMan performs linear regression analysis and calculates Mantel probability (Mantel 1967) between the genetic distance matrix produce by PGPW and a geographic distance matrix to test isolation by distance.
Win


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Win (DOS executable (XP compatible) and test files)
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