| gwas.analysis | Performs GWAS analysis with five optional models and different optional thresholds. |
| gwas.cross | Read genomic data to perform GWAS analyses. |
| linkdis.plots | Linkage Disequilibrium heatmap plot |
| mq.g.diagnostics | Performs molecular markers quality diagnostics. |
| pca.analysis | Principal Component Analysis. |
| QA_geno | Name of the file containing genotypic (marker scores) information. |
| QA_map | Name of the file containing marker map information |
| QA_pheno | Name of the file containing phenotypic information |
| QA_sim | Name of the file containing phenotypic information |