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| D.make | Generate D Matrix |
| EM.MIM | EM Algorithm for QTL MIM |
| EM.MIM2 | EM Algorithm for QTL MIM with Seletive Genotyping |
| EQF.permu | EQF Permutation |
| EQF.plot | EQF plot |
| IM.search | QTL search by IM |
| IM.search2 | QTL search by IM with Seletive Genotyping |
| LOD.QTLdetect | QTL Detect by LOD |
| LRTthre | LRT Threshold |
| MIM.points | QTL Short Distance Correction by MIM |
| MIM.points2 | QTL Short Distance Correction by MIM with Seletive Genotyping |
| MIM.search | QTL search by MIM |
| MIM.search2 | QTL search by MIM with Seletive Genotyping |
| progeny | Progeny Simulation |
| Q.make | Generate Q Matrix |