| BPlite | Lightweight BLAST parser |
| BPliteWrapper | Bio::EnsEMBL::Analysis::Tools::BPliteWrapper |
| BasicFilter | Bio::EnsEMBL::Analysis::Tools::BasicFilter |
| BlastDB | |
| Blastz | Ensembl specific blastz output parser |
| CdnaUpdateTranscriptFilter | Bio::EnsEMBL::Analysis::Tools::CdnaUpdateTranscriptFilter |
| ClusterFilter | Bio::EnsEMBL::Analysis::Tools::ClusterFilter |
| ConfigUtils | |
| ExonerateTranscriptFilter | Bio::EnsEMBL::Analysis::Tools::ExonerateTranscriptFilter |
| FeatureFactory | Bio::EnsEMBL::Analysis::Tools::FeatureFactory |
| FeatureFilter | Bio::EnsEMBL::Analysis::Tools::FeatureFilter |
| FilterBPlite | Bio::EnsEMBL::Analysis::Tools::FilterBPlite |
| FragmentTranscriptFilter | Bio::EnsEMBL::Analysis::Tools::FragmentTranscriptFilter |
| GeneBuildUtils | base class for genebuild utility methods |
| IgTranscriptFilter | |
| KillList | |
| Logger | |
| MiniSeq | an artificially constructed cDNA on a genomic sequence |
| PairAlign | Dna pairwise alignment module |
| PolyAClipping | polA-clipping.pl |
| ProteinAnnotationFilter | Bio::EnsEMBL::Analysis::Tools::ProteinAnnotationFilter |
| Stashes | |
| Utilities | base class which exports utility methods which don't take Bio::XX objects |