| Eagle-package | Eagle for Genome-wide Association Mapping |
| AM | multiple-locus Association Mapping |
| Eagle | Eagle for Genome-wide Association Mapping |
| FPR4AM | Set the false positive rate for 'AM' |
| OpenGUI | Browser-based Graphical User Interface |
| PlotAM | Visualisation of multiple locus association mapping results |
| ReadMap | Read map file |
| ReadMarker | Read marker data. |
| ReadPheno | Read phenotype file |
| ReadZmat | Read Z matrix |
| SummaryAM | Summary of multiple locus association mapping results |