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| rplant-package | rplant |
| CheckJobStatus | Executing analytical applications |
| Clustal | ClustalW alignment |
| clustal | ClustalW alignment |
| ClustalW | ClustalW alignment |
| CompareNames | Resolving Names via TNRS |
| CopyDir | Directory management |
| CopyFile | File management |
| DeleteDir | Directory management |
| DeleteFile | File management |
| DeleteJob | Executing analytical applications |
| DNA.fasta | Data Sets |
| FastTree | FastTree Dispatcher |
| Fasttree | FastTree Dispatcher |
| fasttree | FastTree Dispatcher |
| FaST_LMM | FaST-LMM-2.07 |
| geno_test.tfam | Data Sets |
| geno_test.tped | Data Sets |
| GetAppInfo | Deployed applications |
| GetJobHistory | Executing analytical applications |
| GetPhylotasticToken | Resolving Names via TNRS |
| KillJob | Executing analytical applications |
| ListApps | Deployed applications |
| ListDir | Directory management |
| ListJobOutput | Executing analytical applications |
| Mafft | MAFFT Multiple Sequence Alignment |
| MakeDir | Directory management |
| MoveDir | Directory management |
| MoveFile | File management |
| Muscle | MUSCLE alignment |
| PermissionsDir | Directory management |
| PermissionsFile | File management |
| PHYLIP_Pars | PHYLIP 3.69 |
| PLINK | PLINK-1.07 |
| PLINKConversion | PLINKConversion |
| PROTEIN.fasta | Data Sets |
| RAXML | RAxML |
| RAxML | RAxML |
| Raxml | RAxML |
| raxml | RAxML |
| RenameDir | Directory management |
| RenameFile | File management |
| ResolveNames | Resolving Names via TNRS |
| RetrieveJob | Executing analytical applications |
| RetrieveTNRSNames | Resolving Names via TNRS |
| rPlant | rplant |
| rplant | rplant |
| ShareDir | Directory management |
| ShareFile | File management |
| SubmitJob | Executing analytical applications |
| SupportFile | File management |
| TNRS | Resolving Names via TNRS |
| UploadFile | File management |
| Validate | Authentication functions |
| Wait | Executing analytical applications |