- Multi-thread computing
- Sample and SNPs filter
- Format conversion of genotype file
- Allele frequency and Genotype frequency
- Homozygosity and Heterozygosity
- Construct relationship matrix (XRM)
- Format conversion of XRM
- Calculate inbreeding and relationship coefficient
- Principal component analysis (PCA)
- LM, BLUP, PBLUP, GBLUP(rrBLUP), SSGBLUP
- Single trait model
- Repeat records of single trait model
- Multiple traits model
- Solve mixed model equation (MME)
- Fitting interaction for effects (E by E, G by G, G by E)
- Statistical tests of significance for effects
- Reliability and PEV
- Compute SNP effect
- Predicting GEBV/GPRS
- Genomic mating
- LD
- LD scores
- LD score regression
- Summary level BLUP (SBLUP)
- Multiple traits SBLUP (MT-SBLUP)