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| ABneutral | Run Model with no selection (ABneutral) |
| ABneutralSOMA | Model with no selection (outneutral) |
| ABnull | Run model that considers no accumulation of epimutations (ABnull) |
| ABselectMM | Run model with selection against spontaneous gain of methylation (ABselectMM) |
| ABselectMMSOMA | Model with selection against spontaneous gain of methylation (outselectMM) |
| ABselectUU | Run model with selection against spontaneous loss of methylation (ABselectUU) |
| ABselectUUSOMA | Model with selection against spontaneous loss of methylation (outselectUU) |
| BOOTmodel | Bootstrap analysis with the best model |
| convertDMATRIX | convertDMATRIX |
| dMatrix | Constructing D-Matrices |
| FtestRSS | Comparison of different models and selection of best model |
| makePHYLO | Generating tree pedigree data |
| rc.meth.lvl | Calculating rc.Meth.lvl |