| Options | Attribute | Default | Detail |
| –single-trait | flag | – | to implement single trait model. |
| –multi-trait | flag | – | to implement multiple traits model. |
| –make-xrm | flag | – | to construct and output relationship matrix. |
| –trans-xrm | flag | – | to transform file format of relationship matrix. |
| –mme | flag | – | to solve the mixed model equation with provided （co)variance components. |
| –snp-effect | flag | – | to compute and output snp effect. |
| –maf | flag | – | to compute the minor allele frequency. |
| –mating | flag | – | to implement genomic mating. |
| –inbreeding | flag | – | to calculate the inbreeding coefficient. |
| –pheno | file | – | the path and name of phenotype file, header should be included, missing value should be represented by “NA”. |
| –pheno-pos | int | 2 | the position of the analyzed phenotype in columns of phenotype file. For multiple traits, please use comma as separator. |
| –pedigree | file | – | the path and name of pedigree file, header should be included, the order of columns should be “id”, “father”, “mother”. |
| –bfile | file | – | the prefix of genotype files in plink binary format. |
| –gebv | file | – | the estimated genomic breeding values, the first column should be id, header should be included. |
| –score | file | – | the estimated SNP effects, the first column should be SNP id, the rest columns are the SNP effects, header should be included. |
| –xrm | file | – | the prefix of binary relationship matrix (*.bin and *.id). For multiple relationship matrix, please use comma as separator. |
| –dcovar | int | – | the position of the discrete covariates (fixed effects, e.g. sex, year, …) in columns of phenotype file (e.g. “–dcovar 4,5”). For interaction, please use colon as separator (e.g. “–dcovar 4,5,4:5”). |
| –qcovar | int | – | the position of the quantitative covariates (e.g. height, weight, …) in columns of phenotype file. |
| –rand | int | – | the position of the random effects in columns of phenotype file. For interaction, please use colon as separator. |
| –rand-gxe | int:file | – | a mixture of digital value and prefix of XRM, specify genetic-environment interaction (e.g. “–rand-gxe 2:demo.GA”). |
| –add | flag | – | additive genetic effect. |
| –add-inv | flag | – | whether to compute the inverse of additive relationship matrix. |
| –dom | flag | – | dominant genetic effect. |
| –dom-inv | flag | – | whether to compute the inverse of dominant relationship matrix. |
| –vc-priors | double | – | the prior values of variance components for all random effects, please use comma as separator within a trait, and use space as separator among traits. |
| –covc-priors | double | – | the prior values of co-variance components among traits for all ‘xrm’, please use comma as separator among traits, and use space as separator among ‘xrm’. |
| –snp-weight | file | – | the path and name of a file containing weights for all SNPs when constructing GRM and calculating SNP effects, the fist column shoud be SNP id. |
| –vc-method | text | AI | the algorithms (AI, EM, EMAI, HE, HI) for variance components estimation. |
| –tol | double | 1.00E-06 | the tolerance for convergence of variance components estimation. |
| –ai-maxit | int | 20 | the maximum number of iteration for AIREML. |
| –em-maxit | int | 20 | the maximum number of iteration for EMREML. |
| –alpha | double | 0.05 | weight of pedigree based relationship matrix when constructing H matrix for SSGBLUP model. |
| –ridge-value | double | 0 | ridge regression value for solving uninvertible square matrix. |
| –triangle | flag | – | input/output a triangle matrix (in format of ‘i j value’). |
| –xrm-txt | file | – | the file path and name of relationship matrix in text format. |
| –xrm-id | file | – | the file path and name of id for all individuals. |
| –keep | file | – | the path and name of a file listing individuals to be used in analysis. |
| –remove | file | – | the path and name of a file listing individuals to be removed in analysis. |
| –extract | file | – | the path and name of a file listing markers to be used in analysis. |
| –exclude | file | – | the path and name of a file listing markers to be removed in analysis. |
| –pcg | flag | – | to solve the system of linear equations A*x = b for x using the Preconditioned Conjugate Gradients Method. |
| –pcg-num | int | 0 | the maximum number of iteration for Preconditioned Conjugate Gradients Method. |
| –step | int | 10000 | the number of markers that are loaded into RAM at a time when constructing GRM, smaller step helps to reduce the memory cost, but would cause lower computational efficiency. |
| –float-prec | flag | – | whether to use float precision, it can help to reduce the memory cost in analysis. |
| –threads | int | 0 | the number of threads used for analysis. |
| –out | text | hiblup | the prefix of output files. |