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

Additional Resources