Software & Tools
Software and computational tools developed by our lab and collaborators
JWAS.jl
An open-source software tool written in Julia for Bayesian multiple regression methods applied to genomic prediction and genome-wide association studies:
- Univariate (single-trait) analysis
- Multivariate (multi-trait) analysis
- No limitations on fixed effects (e.g., herd, year, age, sex)
- Random effects other than markers (e.g., litter, pen)
- Random effects using pedigree information
- Additive genetic effects, Maternal effects, Random permanent environmental effects
- Correlated residuals,Correlated random effects
- Unknown (or known) variance components
- Complete genomic data
- Incomplete genomic data (single-step)
- Neural Networks (NNMM) and Multi-class Bayesian Analysis
- Cross-validation and GWAS capabilities
XSim.jl
A fast and user-friendly tool to simulate sequence data and complicated pedigree structures:
- Efficient CPOS algorithm implementation
- Simulation using real genome sequence data
- Support for complex pedigree structures
- Modern breeding program simulation
- Multi-trait and multi-generation support
LPChoose.jl
Optimizing Sequencing Resources in Genotyped Livestock Populations by Linear Programming:
- Efficient allocation of sequencing resources in genotyped populations
- Minimum set cover approach for haplotype representation
- Budget-constrained selection for maximum haplotype coverage
- Integration with whole-genome sequence data
- Support for large-scale livestock breeding programs