| 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 |