Software Tools
Comprehensive catalog of software tools for animal breeding, quantitative genetics, and genomic analysis. From variance component estimation to breeding program simulation.
Nice short article by Ignacy Misztal on software in animal breeding:
View PDFVariance Components
Estimating variance components in mixed models.
Evaluations
Running genetic evaluations and predicting breeding values.
Inbreeding
Managing inbreeding and optimising mate selection.
Genomic Processing
Processing SNP data and building genomic relationships.
GWAS
Genome-wide association studies and genomic prediction.
Imputation
Imputing missing genotypes.
Breed Composition
Estimating breed composition percentages.
Simulation
Simulating breeding programs.
Selection Index
Designing breeding schemes and calculating accuracy.
Miscellaneous
Other useful tools.
About These Tools
This list includes both free open-source tools and commercial software. Paid tools are marked Commercial.
Most tools here are actively maintained by research groups. Anything in development or no longer maintained is labelled as such.
Check with your institution’s IT department or library for site licenses for commercial software like ASReml or MiXBLUP.