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:



Problems addressed by this GENEPOP workflow

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


Detailed Workflow Usage & Specifications

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.

URL: http://www.loni.ucla.edu/twiki/bin/view/LONI/Pipeline_GenomicsInformatics_GENEPOP

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