Introduction | Sample usage | gcat | Data Input | References

Introduction | Sample usage | lfa | af | Data Input | References

Introduction | Kinship and inbreeding coefficients | The generalized $\Fst$ | The individual-level pairwise $\Fst$ | Sample usage | Input genotype data | Load and clean sample data | Estimate and visualize kinship using genotypes and subpopulations | Estimate $\Fst$ and individual inbreeding from a kinship matrix | Estimate individual-level pairwise $\Fst$ matrix from a kinship matrix | Rescale kinship matrix in a subset of the data | Plot multiple kinship matrices together | Plot kinship matrices with multiple levels of labels | Coancestry estimation from allele frequencies | Admixture plot example | References

Introduction | The BN-PSD population structure | Random allele frequencies and genotypes | Simulation examples | Population structure: 1D geography | Draw random allele frequencies and genotypes | Customizing the allele frequency and genotype pipeline | Additional population structures | Circular 1D geography | Independent subpopulations | Intermediate subpopulations related by a tree | Admixture with intermediate tree structure | Draw random allele frequencies and genotypes for admixture with intermediate tree structure | References

Introduction | Quick Start Guide | Plotting | Writing Your Own Analysis Method | Reproducing or Adding to a Previous Run | Note on Subsampling