Software Tools
Comprehensive catalog of software tools for animal breeding, quantitative genetics, and genomic analysis. From variance component estimation to breeding program simulation.
Variance Components
Software for estimating variance components in mixed models: BLUPF90, ASReml, DMU, GCTA
Evaluations
Run genetic evaluations and predict breeding values: MiXBLUP, BLUPF90, BOLT, Mix99
Inbreeding
Manage inbreeding and optimize mate selection: Matesel, AlphaMate, EVA, optiSel
Genomic Processing
Process SNP chip data and calculate genomic relationships: calc_grm, preGSf90, PLINK
GWAS
Genome-wide association studies and genomic prediction: JWAS, postGSf90, BGLR, GCTA
Imputation
Impute missing genotypes: Beagle, AlphaImpute, AlphaPeel, FImpute
Breed Composition
Estimate breed composition percentages: Structure, Admixture, Allele Frequency methods
Simulation
Simulate breeding programs: AlphaSimR, MoBPS, QMSim, ADAM
Selection Index
Design breeding schemes and calculate accuracy: SelAction, SelAction 2
Miscellaneous
Other useful tools: OpenMendel statistical genetics suite
About These Tools
Open Source & Commercial: This list includes both free/open-source tools and commercial software. Paid tools are clearly marked with a 💳 badge.
Active Development: Software development status is indicated with badges: ✓ Active, 🚧 In Development, ⚠️ Deprecated. Many tools are actively maintained by research groups.
University Resources: Check with your institution's IT department or library for potential site licenses for commercial software like ASReml or MiXBLUP.