| rmsap-package | Statistical Analyses for Methylation Sensitive Amplification Polymorphism assays |
| methStatusEval | classify a locus as either MSL or NML. |
| msap | Diversity analysis of MSAP data |
| pcoa | Principal Coordinate Analyses |
| polymorphic | Checks polymorphic state |
| repMet | Report methylation levels |
| shannon | Shannon Index of phenotypic diversity |