This is a tutorial for the MORGAN (Monte Carlo Genetic Analysis) package, focusing on how to use the provided programs.
The current version of this document is written for MORGAN Version 3.1.1.
1. Get Started 2. Common Features and File Formats 3. Checking Pedigree Validity 4. Computing Kinship and One- or Two-Locus Inbreeding Coefficients 5. Simulating Marker and Trait Data in Pedigrees 6. Simulating Marker Data Conditional on Trait Data in Pedigrees 7. Estimating a priori ibd Probabilities by Monte Carlo 8. Using MCMC to Estimate Parameters of Interest in Pedigree Data 9. Estimating Conditional ibd Probabilities by MCMC 10. Estimating ibd Based Test Statistics by MCMC 11. Estimating Location lod Scores by MCMC 12. Population-based inference of IBD 13. Polygenic Modeling of Quantitative Traits by EM Algorithm 14. Estimating Genetic Maps from Marker Data References Concept Index Statement Index