Programming and computer algorithms in animal breeding with focus on genomic selection and single-step GBLUP
The course was held from 9:00am to 5:00pm, from May 13 to May 30 in 2014 at UGA. Instructors were Ignacy Misztal, Shogo Tsuruta, Ignacio Aguilar, Zulma Vitezica, and Andres Legarra.
Computer programming in animal breeding
Week 1. May 13-16
Week 2. May 19-23
Advanced programming in Fortran 95/2005
Computer algorithms useful in animal breeding
Efficient creation and solving of mixed model equations
Introduction to BLUPF90 family of programs
Design
Models (multiple trait, maternal, random regression, competition,…)
Advanced models (competition, threshold, censored,..)
Associated programs (renumf90, inbupg,..)
BLUPF90 manual
Files used for Appendix I in BLUPF90 manual
Week 3. May 26 - 30
Data simulation (including genomics)
Data manipulation and scripts using Unix tools
SNP effects, genomic relationships and genomic recursions
GBLUP, GREML and G-GGIBBS
Single-step GBLUP (prediction + GWAS)
Computing with large number of genotypes
Class notes - week 3 Updated March, 2015.
Slides - week 3
Pictures