• 1 Introduction
    • 1.1 Purpose
    • 1.2 The two Genepop distributions
    • 1.3 Changes since version 4.0
  • 2 Installing Genepop and session examples
    • 2.1 Installation
      • 2.1.1 R package
      • 2.1.2 Stand-alone executable
    • 2.2 Example sessions
      • 2.2.1 Example 1: basic session
      • 2.2.2 Example 2: using the settings file
      • 2.2.3 Example 3: Batch processing
  • 3 The input file
  • 4 The settings file and command line arguments
  • 5 All menu options
    • 5.1 Option 1: Hardy-Weinberg (HW) exact tests
      • 5.1.1 Sub-options 1–3: Tests for each locus in each population
      • 5.1.2 Output
      • 5.1.3 Sub-options 4,5: Global tests across loci or across samples
      • 5.1.4 Analyzing a single genotypic matrix
      • 5.1.5 Code checks
    • 5.2 Option 2: Tests and tables for linkage disequilibrium
      • 5.2.1 Sub-option 1: Tests
      • 5.2.2 Output
      • 5.2.3 Sub-option 2: create tables
      • 5.2.4 Code checks
    • 5.3 Option 3: population differentiation
      • 5.3.1 Sub-options 1 or 2 (genic differentiation)
      • 5.3.2 Sub-options 3 or 4 (genotypic differentiation)
      • 5.3.3 Output
      • 5.3.4 Gene diversity as a test statistic
      • 5.3.5 Analyzing a single contingency table
      • 5.3.6 Code checks
    • 5.4 Option 4: private alleles
    • 5.5 Option 5: Basic information, \(F_\mathrm{IS}\), and gene diversities
      • 5.5.1 Sub-option 1: Allele and genotype frequencies
      • 5.5.2 Sub-option 2: Identity-based gene diversities and \(F_\mathrm{IS}\)
      • 5.5.3 Sub-option 3: Allele size-based gene diversities and \(\rho_{\mathrm{IS}}\)
    • 5.6 Option 6: Fst and other correlations, isolation by distance
      • 5.6.1 Sub-options 1–4: \(F\)-statistics and \(\rho\)-statistics
      • 5.6.2 Sub-option 5: isolation by distance between individuals
      • 5.6.3 Sub-option 6: isolation by distance between groups
      • 5.6.4 Former sub-option 5 of Genepop: analysis of isolation by distance from a genetic distance matrix
      • 5.6.5 User-provided geographic distance matrices
      • 5.6.6 Analysis of isolation by distance from multiple genetic distance matrices
      • 5.6.7 Analysis of mean differentiation
    • 5.7 Data selection for analyses of isolation by distance
      • 5.7.1 Selecting a subset of samples
    • 5.8 Option 7: File conversions
    • 5.9 Option 8: Null alleles and some input file utilities
      • 5.9.1 Sub-option 1: null alleles
      • 5.9.2 Sub-option 2: Diploidisation of haploid data
      • 5.9.3 Sub-option 3: Relabeling alleles names
      • 5.9.4 Sub-options 4 and 5: Conversion of population data to individual data
      • 5.9.5 Sub-option 6: Random sampling of haploid genotypes from diploid ones
  • 6 Evaluating the performance of inferences for Isolation by distance
  • 7 Methods
    • 7.1 Null alleles
    • 7.2 Exact tests
    • 7.3 Algorithms for exact tests
    • 7.4 Accuracy of P values estimated by the Markov chain algorithms
    • 7.5 Test statistics
    • 7.6 Estimating \(F\)-statistics and related quantities
      • 7.6.1 ANOVA estimators: single- and multilocus definitions
      • 7.6.2 Microsatellite allele sizes, \(R_\mathrm{ST}\), and \(\rho_\mathrm{ST}\)
      • 7.6.3 Robertson and Hill’s estimator of \(F_\mathrm{IS}\)
    • 7.7 Bootstraps
    • 7.8 Mantel test
      • 7.8.1 Misuse 1: tests of correlation at different distance
      • 7.8.2 Misuse 2: partial Mantel tests
  • 8 Code maintenance, credits, contact, etc.
    • 8.1 Code maintenance
    • 8.2 Credits for the current version
    • 8.3 Previous history
    • 8.4 Contact
      • 8.4.1 Bug fixes since release of Genepop version 3.4 in May 2003 until first release of Genepop 4.0:
  • 9 Copyright
  • Bibliography

Genepop version 4.7.1

9 Copyright

All contents of the R package are covered by its license, the GPL-compatible CeCill 2.1 license (see http://www.cecill.info/index.en.html).