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.
Win
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
).
Win
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.
Win
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).
Win

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.
Win
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
Win
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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