| AlignFactory | Base object for alignment factories |
| AnalysisResult | Base class for analysis result objects and parsers |
| BPbl2seq | Lightweight BLAST parser for pair-wise sequence
alignment using the BLAST algorithm. |
| BPlite | Lightweight BLAST parser |
| BPpsilite | Lightweight BLAST parser for (iterated) psiblast reports |
| Blast | Bioperl BLAST sequence analysis object |
| CodonTable | Bioperl codon table object |
| Coil | Bio::Tools::Coil |
| ECnumber | representation of EC numbers |
| EPCR | Parse ePCR output and make features |
| ESTScan | Results of one ESTScan run |
| Eponine | Results of one Eponine run |
| Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects |
| FootPrinter | DESCRIPTION of Object |
| GFF | A Bio::SeqAnalysisParserI compliant GFF format parser |
| Gel | Calculates relative electrophoretic migration distances |
| Genemark | Results of one Genemark run |
| Genewise | Results of one Genewise run |
| Genomewise | Results of one Genomewise run |
| Genscan | Results of one Genscan run |
| Grail | Results of one Grail run |
| Hmmpfam | Bio::Tools::Hmmpfam |
| IUPAC | Generates unique Seq objects from an ambiguous Seq object |
| Lucy | Object for analyzing the output from Lucy,
a vector and quality trimming program from TIGR |
| MZEF | Results of one MZEF run |
| OddCodes | Object holding alternative alphabet coding for
one protein sequence |
| Primer3 | Create input for and work with the output from the
program primer3 |
| Prints | Parser for FingerPRINTScanII program |
| Profile | parse Profile output |
| Promoterwise | DESCRIPTION of Object |
| Pseudowise | Results of one Pseudowise run |
| RepeatMasker | DESCRIPTION of Object |
| RestrictionEnzyme | Bioperl object for a restriction endonuclease
(cuts DNA at specific locations) |
| Seg | parse Seg output (filter low complexity protein sequence) |
| SeqAnal | Bioperl sequence analysis base class. |
| SeqPattern | Bioperl object for a sequence pattern or motif |
| SeqStats | Object holding statistics for one particular sequence |
| SeqWords | Object holding n-mer statistics for one sequence |
| Sigcleave | Bioperl object for sigcleave analysis |
| Signalp | Bio::Tools::SignalP |
| Tmhmm | parse TmHMM output (transmembrane HMM) |
| WWW | Bioperl manager for web resources related to biology. |
| pSW | pairwise Smith Waterman object |