Microsatellite-based Ancestry and Parentage Analysis: GENEPOP Workflow

Created: 2011-04-05 22:10:32 Last updated: 2011-07-14 00:14:47

GENEPOP is genetics software package that does the following types of analyses:

This specific GENEPOP workflow computes the following:

Testing :
- Hardy-Weinberg exact tests (several options) ...................... 1
- Exact tests for genotypic disequilibrium (several options) ........ 2
- Exact tests for population differentiation (several options) ...... 3
Estimating:
- Nm estimates (private allele method) .............................. 4
- Allele frequencies, various Fis and gene diversities .............. 5
- Fst & other correlations, isolation by distance (several options).. 6
Ecumenicism and various utilities:
- Ecumenicism: file conversion (several options) .................... 7
- Null alleles and miscellaneous input file utilities ............... 8

Genepop implements a mixture of traditional methods and some more focused developments:

It computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci;
It computes estimates of F-statistics, null allele frequencies, allele size- based statistics for microsatellites, etc., and of number of immigrants by Barton & Slatkin’s 1986 private allele method;
It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including confidence intervals for “neighborhood size”.
Genepop converts data from the Genepop input format to formats of some softwares that were around in Genepop’s youth; there was little need to update this option as many more recent softwares for population genetic analyses read input files in the Genepop format.