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

  1. Introduction to programming in Fortran 95/2003

Class notes

Assignments used in the class

Week 2. May 19-23

  1. Advanced programming in Fortran 95/2005
  2. Computer algorithms useful in animal breeding
  3. Efficient creation and solving of mixed model equations
  4. Introduction to BLUPF90 family of programs
    1. Design
    2. Models (multiple trait, maternal, random regression, competition,…)
    3. Advanced models (competition, threshold, censored,..)
    4. Associated programs (renumf90, inbupg,..)

BLUPF90 manual

Files used for Appendix I in BLUPF90 manual

Week 3. May 26 - 30

  1. Data simulation (including genomics)
  2. Data manipulation and scripts using Unix tools
  3. SNP effects, genomic relationships and genomic recursions
  4. GBLUP, GREML and G-GGIBBS
  5. Single-step GBLUP (prediction + GWAS)
  6. Computing with large number of genotypes

Class notes - week 3 Updated March, 2015.

Slides - week 3

Pictures

course_2014.jpg

course_materials_-_from_uga_2014.txt · Last modified: 2015/08/14 13:57 by andres
 
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