| Alignment | Bio::EnsEMBL::Pipeline::Alignment.pm |
| AnaSubmission | |
| Analysis | |
| BatchSubmission | Bio::EnsEMBL::Pipeline::BatchSubmission |
| Flag | Bio::EnsEMBL::Pipeline::Flag |
| Job | Bio::EnsEMBL::Pipeline::Job |
| Monitor | |
| Rule | Bio::EnsEMBL::Pipeline::Rule |
| RuleManager | Bio::EnsEMBL::Pipeline::RuleManager |
| SeqFetcher | Bio::EnsEMBL::Pipeline::SeqFetcher |
| Status | small object storing job status tags |