| bioperl-live | Top |
| BioPerl(1) | Perl Modules for Biology |
| bioperl-live::_build | Top |
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| bioperl-live::_build::lib | Top |
| ModuleBuildBioperl |
| bioperl-live::ide | Top |
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| bioperl-live::ide::bioperl-mode | Top |
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| bioperl-live::ide::bioperl-mode::site-lisp | Top |
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| bioperl-live::ide::bioperl-mode::dist | Top |
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| bioperl-live::ide::bioperl-mode::etc | Top |
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| bioperl-live::ide::bioperl-mode::etc::images | Top |
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| bioperl-live::maintenance | Top |
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| bioperl-live::cover_db | Top |
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| bioperl-live::cover_db::runs | Top |
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| bioperl-live::cover_db::structure | Top |
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| bioperl-live::Bio | Top |
| AlignIO | Handler for AlignIO Formats |
| AnalysisI(1) | An interface to any (local or remote) analysis tool |
| AnalysisParserI | Generic analysis output parser interface |
| AnalysisResultI | Interface for analysis result objects |
| AnnotatableI | the base interface an annotatable object must implement |
| AnnotationCollectionI(1) | Interface for annotation collections |
| AnnotationI | Annotation interface |
| Biblio | A Bibliographic Query Service module |
| ClusterI | Cluster Interface |
| ClusterIO | Handler for Cluster Formats |
| DBLinkContainerI | Abstract interface for any object wanting to use database cross references |
| DasI | DAS-style access to a feature database |
| DescribableI | interface for objects with human readable names and descriptions |
| FeatureHolderI | the base interface an object with features must implement |
| FeatureIO | Handler for FeatureIO |
| HandlerBaseI | Interface class for handler methods which interact with any event-driven parsers (drivers). |
| IdCollectionI | interface for objects with multiple identifiers |
| IdentifiableI | interface for objects with identifiers |
| JobI | |
| LocatableSeq(1) | A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. |
| LocationI(1) | Abstract interface of a Location on a Sequence |
| MapIO | A Map Factory object |
| NexmlIO | stream handler for NeXML documents |
| OntologyIO | Parser factory for Ontology formats |
| ParameterBaseI | Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends. |
| Perl | Functional access to BioPerl for people who don't know objects |
| PhyloNetwork | Module to compute with Phylogenetic Networks |
| PrimarySeq | Bioperl lightweight Sequence Object |
| PrimarySeqI | Interface definition for a Bio::PrimarySeq |
| PullParserI | A base module for fast 'pull' parsing |
| Range(1) | Pure perl RangeI implementation |
| RangeI | Range interface |
| SearchDist | A perl wrapper around Sean Eddy's histogram object |
| SearchIO | Driver for parsing Sequence Database Searches (BLAST, FASTA, ...) |
| Seq | Sequence object, with features |
| SeqAnalysisParserI | Sequence analysis output parser interface |
| SeqFeatureI | Abstract interface of a Sequence Feature |
| SeqI(1) | [Developers] Abstract Interface of Sequence (with features) |
| SeqIO | Handler for SeqIO Formats |
| SeqUtils | Additional methods for PrimarySeq objects |
| SimpleAlign | Multiple alignments held as a set of sequences |
| SimpleAnalysisI | A simple interface to any (local or remote) analysis tool |
| Species | Generic species object |
| Taxon(1) | A node in a represented taxonomy |
| Taxonomy(1) | representing Taxonomy. |
| TreeIO | Parser for Tree files |
| UpdateableSeqI(1) | Descendant of Bio::SeqI that allows updates |
| WebAgent | A base class for Web (any protocol) access |
| bioperl-live::Bio::SearchIO | Top |
| EventHandlerI(1) | An abstract Event Handler for Search Result parsing |
| FastHitEventBuilder | Event Handler for SearchIO events. |
| IteratedSearchResultEventBuilder | Event Handler for SearchIO events. |
| SearchResultEventBuilder | Event Handler for SearchIO events. |
| SearchWriterI | Interface for outputting parsed Search results |
| axt | a parser for axt format reports |
| blast | Event generator for event based parsing of blast reports |
| blast_pull | A parser for BLAST output |
| blasttable | Driver module for SearchIO for parsing NCBI -m 8/9 format |
| blastxml | A SearchIO implementation of NCBI Blast XML parsing. |
| cross_match | CrossMatch-specific subclass of Bio::SearchIO |
| erpin | SearchIO-based ERPIN parser |
| exonerate | parser for Exonerate |
| fasta(1) | A SearchIO parser for FASTA results |
| gmap_f9 | Event generator for parsing gmap reports (Z format) |
| hmmer | A parser for HMMER output (hmmpfam, hmmsearch) |
| hmmer_pull | A parser for HMMER output |
| infernal | SearchIO-based Infernal parser |
| megablast | a driver module for Bio::SearchIO to parse megablast reports (format 0) |
| psl | A parser for PSL output (UCSC) |
| rnamotif | SearchIO-based RNAMotif parser |
| sim4 | parser for Sim4 alignments |
| waba | SearchIO parser for Jim Kent WABA program alignment output |
| wise | Parsing of wise output as alignments |
| bioperl-live::Bio::SearchIO::Writer | Top |
| BSMLResultWriter | BSML output writer |
| GbrowseGFF | Interface for outputting parsed search results in Gbrowse GFF format |
| HSPTableWriter | Tab-delimited data for Bio::Search::HSP::HSPI objects |
| HTMLResultWriter | write a Bio::Search::ResultI in HTML |
| HitTableWriter | Tab-delimited data for Bio::Search::Hit::HitI objects |
| ResultTableWriter | Outputs tab-delimited data for each Bio::Search::Result::ResultI object. |
| TextResultWriter | Object to implement writing a Bio::Search::ResultI in Text. |
| bioperl-live::Bio::SearchIO::XML | Top |
| BlastHandler | XML Handler for NCBI Blast XML parsing. |
| PsiBlastHandler | XML Handler for NCBI Blast PSIBLAST XML parsing. |
| bioperl-live::Bio::AlignIO | Top |
| arp | ARP MSA Sequence input/output stream |
| bl2seq | bl2seq sequence input/output stream |
| clustalw | clustalw sequence input/output stream |
| emboss | Parse EMBOSS alignment output (from applications water and needle) |
| fasta(2) | fasta MSA Sequence input/output stream |
| largemultifasta | Largemultifasta MSA Sequence input/output stream |
| maf | Multiple Alignment Format sequence input stream |
| mase | mase sequence input/output stream |
| mega | Parse and Create MEGA format data files |
| meme(1) | meme sequence input/output stream |
| metafasta(1) | Metafasta MSA Sequence input/output stream |
| msf | msf sequence input/output stream |
| nexml(1) | NeXML format sequence alignment input/output stream driver |
| nexus(1) | NEXUS format sequence input/output stream |
| pfam | pfam sequence input/output stream |
| phylip(1) | PHYLIP format sequence input/output stream |
| po | po MSA Sequence input/output stream |
| proda | proda sequence input/output stream This provides the basic capabilities to parse the output alignments from the ProDA multiple sequence alignment program (http://proda.stanford.edu) |
| prodom | prodom sequence input/output stream |
| psi | Read/Write PSI-BLAST profile alignment files |
| selex | selex sequence input/output stream |
| stockholm | stockholm sequence input/output stream |
| xmfa | XMFA MSA Sequence input/output stream |
| bioperl-live::Bio::AlignIO::Handler | Top |
| GenericAlignHandler | Bio::HandlerI-based generic data handler class for alignment-based data |
| bioperl-live::Bio::Location | Top |
| Atomic | Implementation of a Atomic Location on a Sequence |
| AvWithinCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise |
| CoordinatePolicyI | Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location |
| Fuzzy | Implementation of a Location on a Sequence which has unclear start and/or end locations |
| FuzzyLocationI | Abstract interface of a Location on a Sequence which has unclear start/end location |
| NarrowestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range |
| Simple | Implementation of a Simple Location on a Sequence |
| Split | Implementation of a Location on a Sequence which has multiple locations (start/end points) |
| SplitLocationI | Abstract interface of a Location on a Sequence which has multiple locations (start/end points) |
| WidestCoordPolicy | class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range |
| bioperl-live::Bio::Coordinate | Top |
| Chain(1) | Mapping locations through a chain of coordinate mappers |
| Collection(1) | Noncontinuous match between two coordinate sets |
| ExtrapolatingPair | Continuous match between two coordinate sets |
| GeneMapper | transformations between gene related coordinate systems |
| Graph | Finds shortest path between nodes in a graph |
| MapperI | Interface describing coordinate mappers |
| Pair(1) | Continuous match between two coordinate sets |
| Result(1) | Results from coordinate transformation |
| ResultI(1) | Interface to identify coordinate mapper results |
| Utils | Additional methods to create Bio::Coordinate objects |
| bioperl-live::Bio::Coordinate::Result | Top |
| Gap | Another name for Bio::Location::Simple |
| Match(1) | Another name for Bio::Location::Simple |
| bioperl-live::Bio::MapIO | Top |
| fpc | A FPC Map reader |
| mapmaker | A Mapmaker Map reader |
| bioperl-live::Bio::Index | Top |
| Abstract | Abstract interface for indexing a flat file |
| AbstractSeq | base class for AbstractSeq |
| Blast | Indexes Blast reports and supports retrieval based on query accession(s) |
| BlastTable | Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s) |
| EMBL(1) | Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format). |
| Fasta(1) | Interface for indexing (multiple) fasta files |
| Fastq | Interface for indexing (multiple) fastq files |
| GenBank(1) | Interface for indexing one or more GenBank files (i.e. flat file GenBank format). |
| Hmmer | indexes HMMER reports and supports retreival based on query |
| Qual | Interface for indexing (multiple) fasta qual files |
| Stockholm | Indexes Stockholm format alignments (such as those from Pfam and Rfam. Retrieves raw stream data using the ID or a Bio::SimpleAlign (via Bio::AlignIO) |
| SwissPfam | Interface for indexing swisspfam files |
| Swissprot | Interface for indexing one or more Swissprot files. |
| bioperl-live::Bio::Seq | Top |
| BaseSeqProcessor | Base implementation for a SequenceProcessor |
| EncodedSeq | subtype of L |
| LargeLocatableSeq | LocatableSeq object that stores sequence as files in the tempdir |
| LargePrimarySeq | PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root |
| LargeSeq | SeqI compliant object that stores sequence as files in /tmp |
| LargeSeqI | Interface class for sequences that cache their residues in a temporary file |
| Meta | Generic superclass for sequence objects with residue-based meta information |
| MetaI | Interface for sequence objects with residue-based meta information |
| PrimaryQual | Bioperl lightweight Quality Object |
| PrimedSeq | A representation of a sequence and two primers flanking a target region |
| QualI | Interface definition for a Bio::Seq::Qual |
| Quality | Implementation of sequence with residue quality and trace values |
| RichSeq | Module implementing a sequence created from a rich sequence database entry |
| RichSeqI | interface for sequences from rich data sources, mostly databases |
| SeqBuilder | Configurable object builder for sequence stream parsers |
| SeqFactory | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
| SeqFastaSpeedFactory | Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
| SeqWithQuality | Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead! |
| SequenceTrace | Bioperl object packaging a sequence with its trace |
| TraceI | Interface definition for a Bio::Seq::Trace |
| bioperl-live::Bio::Seq::Meta | Top |
| Array | array-based generic implementation of a sequence class with residue-based meta information |
| bioperl-live::Bio::SeqIO | Top |
| FTHelper | Helper class for Embl/Genbank feature tables |
| MultiFile | Treating a set of files as a single input stream |
| abi | abi trace sequence input/output stream |
| ace(1) | ace sequence input/output stream |
| agave | AGAVE sequence output stream. |
| alf | alf trace sequence input/output stream |
| asciitree | asciitree sequence input/output stream |
| bsml | BSML sequence input/output stream |
| bsml_sax | BSML sequence input/output stream using SAX |
| chadoxml | chadoxml sequence output stream |
| chaos | chaos sequence input/output stream |
| chaosxml | chaosxml sequence input/output stream |
| ctf | ctf trace sequence input/output stream |
| embl(1) | EMBL sequence input/output stream |
| embldriver | EMBL sequence input/output stream |
| entrezgene | Entrez Gene ASN1 parser |
| excel | sequence input/output stream from a MSExcel-formatted table |
| exp | exp trace sequence input/output stream |
| fasta(3) | fasta sequence input/output stream |
| fastq | fastq sequence input/output stream |
| flybase_chadoxml | FlyBase variant of chadoxml with sequence output stream |
| game | - a class for parsing and writing game-XML |
| gbdriver | GenBank handler-based push parser |
| gcg | GCG sequence input/output stream |
| genbank(1) | GenBank sequence input/output stream |
| interpro(1) | InterProScan XML input/output stream |
| kegg | KEGG sequence input/output stream |
| largefasta | method i/o on very large fasta sequence files |
| lasergene | Lasergene sequence file input/output stream |
| locuslink | LocusLink input/output stream |
| metafasta(2) | metafasta sequence input/output stream |
| nexml(2) | NeXML sequence input/output stream |
| phd | .phd file input/output stream |
| pir | PIR sequence input/output stream |
| pln | pln trace sequence input/output stream |
| qual | .qual file input/output stream |
| raw | raw sequence file input/output stream |
| scf | .scf file input/output stream |
| seqxml | SeqXML sequence input/output stream |
| strider | DNA strider sequence input/output stream |
| swiss(1) | Swissprot sequence input/output stream |
| swissdriver | SwissProt/UniProt handler-based push parser |
| tab | nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n" |
| table | sequence input/output stream from a delimited table |
| tigr(1) | TIGR XML sequence input/output stream |
| tigrxml | Parse TIGR (new) XML |
| tinyseq | reading/writing sequences in NCBI TinySeq format |
| ztr | ztr trace sequence input/output stream |
| bioperl-live::Bio::SeqIO::tinyseq | Top |
| tinyseqHandler | XML event handlers to support NCBI TinySeq XML parsing |
| bioperl-live::Bio::SeqIO::game | Top |
| featHandler | - a class for handling feature elements |
| gameHandler | - PerlSAX handler for game-XML |
| gameSubs | - a base class for game-XML parsing |
| gameWriter | - a class for writing game-XML |
| seqHandler | - a class for handling game-XML sequences |
| bioperl-live::Bio::SeqIO::Handler | Top |
| GenericRichSeqHandler | Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data |
| bioperl-live::Bio::ClusterIO | Top |
| dbsnp | dbSNP input stream |
| unigene | UniGene input stream |
| bioperl-live::Bio::Taxonomy | Top |
| FactoryI | interface to define how to access NCBI Taxonoy |
| Node(1) | A node in a represented taxonomy |
| Taxon(2) | Generic Taxonomic Entity object |
| Tree(1) | An Organism Level Implementation of TreeI interface. |
| bioperl-live::Bio::OntologyIO | Top |
| InterProParser | Parser for InterPro xml files. |
| dagflat | a base class parser for GO flat-file type formats |
| goflat | a parser for the Gene Ontology flat-file format |
| obo | a parser for OBO flat-file format from Gene Ontology Consortium |
| simplehierarchy | a base class parser for simple hierarchy-by-indentation type formats |
| soflat | a parser for the Sequence Ontology flat-file format |
| bioperl-live::Bio::OntologyIO::Handlers | Top |
| BaseSAXHandler | base class for SAX Handlers |
| InterProHandler | XML handler class for InterProParser |
| InterPro_BioSQL_Handler | parse an InterPro XML file and persist the resulting terms to a Biosql database |
| bioperl-live::Bio::PopGen | Top |
| Genotype | An implementation of GenotypeI which is just an allele container |
| GenotypeI | A marker and alleles for a specific individual |
| HtSNP | Select htSNP from a haplotype set |
| IO(1) | Input individual,marker,allele information |
| Individual | An implementation of an Individual who has Genotype or Sequence Results |
| IndividualI | An individual who has Genotype or Sequence Results |
| Marker(1) | A genetic marker which one uses to generate genotypes |
| MarkerI(1) | A Population Genetic conceptual marker |
| PopStats | A collection of methods for calculating statistics about a population or sets of populations |
| Population | A population of individuals |
| PopulationI | Interface for Populations |
| Statistics(1) | Population Genetics statistical tests |
| TagHaplotype | Haplotype tag object. |
| Utilities(1) | Utilities for working with PopGen data and objects |
| bioperl-live::Bio::PopGen::IO | Top |
| csv | Extract individual allele data from a CSV parser |
| hapmap | A parser for HapMap output data |
| phase | A parser for Phase format data |
| prettybase | Extract individual allele data from PrettyBase format |
| bioperl-live::Bio::PopGen::Simulation | Top |
| Coalescent | A Coalescent simulation factory |
| GeneticDrift | A simple genetic drift simulation |
| bioperl-live::Bio::Align | Top |
| AlignI | An interface for describing sequence alignments. |
| DNAStatistics | Calculate some statistics for a DNA alignment |
| Graphics | Graphic Rendering of Bio::Align::AlignI Objects |
| PairwiseStatistics | Base statistic object for Pairwise Alignments |
| ProteinStatistics | Calculate Protein Alignment statistics (mostly distances) |
| StatisticsI(1) | Calculate some statistics for an alignment |
| Utilities(2) | A collection of utilities regarding converting and manipulating alignment objects |
| bioperl-live::Bio::SeqEvolution | Top |
| DNAPoint | evolve a sequence by point mutations |
| EvolutionI | the interface for evolving sequences |
| Factory(1) | Factory object to instantiate sequence evolving classes |
| bioperl-live::Bio::Nexml | Top |
| Factory(2) | A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents |
| bioperl-live::Bio::Expression | Top |
| Contact | DESCRIPTION of Object |
| DataSet | DESCRIPTION of Object |
| FeatureGroup | a set of DNA/RNA features. ISA Bio::Expression::FeatureI |
| FeatureI | an interface class for DNA/RNA features |
| Platform | DESCRIPTION of Object |
| ProbeI | an interface class for DNA/RNA probes |
| Sample | DESCRIPTION of Object |
| bioperl-live::Bio::Expression::FeatureSet | Top |
| FeatureSetMas50 | utility class for Mas50 FeatureSet |
| bioperl-live::Bio::Expression::FeatureGroup | Top |
| FeatureGroupMas50 | utility class for Mas50 FeatureGroup |
| bioperl-live::Bio::SeqFeature | Top |
| Annotated | PLEASE PUT SOMETHING HERE |
| AnnotationAdaptor | integrates SeqFeatureIs annotation |
| Collection(2) | A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc. |
| CollectionI | An interface for a collection of SeqFeatureI objects. |
| Computation | Computation SeqFeature |
| FeaturePair | hold pair feature information e.g. blast hits |
| Generic(1) | Generic SeqFeature |
| Lite | Lightweight Bio::SeqFeatureI class |
| PositionProxy | handle features when truncation/revcom sequences span a feature |
| Primer | Primer Generic SeqFeature |
| Similarity | A sequence feature based on similarity |
| SimilarityPair | Sequence feature based on the similarity of two sequences. |
| TypedSeqFeatureI | a strongly typed SeqFeature |
| bioperl-live::Bio::SeqFeature::SiRNA | Top |
| Oligo | Perl object for small inhibitory RNAs. |
| Pair(2) | Perl object for small inhibitory RNA (SiRNA) oligo pairs |
| bioperl-live::Bio::SeqFeature::Gene | Top |
| Exon(1) | a feature representing an exon |
| ExonI | Interface for a feature representing an exon |
| GeneStructure | A feature representing an arbitrarily complex structure of a gene |
| GeneStructureI | A feature representing an arbitrarily complex structure of a gene |
| Intron(1) | An intron feature |
| NC_Feature | superclass for non-coding features |
| Poly_A_site | poly A feature |
| Promoter | Describes a promoter |
| Transcript(1) | A feature representing a transcript |
| TranscriptI | Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site. |
| UTR | A feature representing an untranslated region that is part of a transcriptional unit |
| bioperl-live::Bio::SeqFeature::Tools | Top |
| FeatureNamer | generates unique persistent names for features |
| IDHandler | maps $seq_feature-E |
| TypeMapper | maps $seq_feature-E |
| Unflattener | turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy |
| bioperl-live::Bio::Annotation | Top |
| AnnotationFactory | Instantiates a new Bio::AnnotationI (or derived class) through a factory |
| Collection(3) | Default Perl implementation of AnnotationCollectionI |
| Comment | A comment object, holding text |
| DBLink | untyped links between databases |
| OntologyTerm | An ontology term adapted to AnnotationI |
| Reference | Specialised DBLink object for Literature References |
| Relation | Relationship (pairwise) with other objects SeqI and NodeI; |
| SimpleValue | A simple scalar |
| StructuredValue | A scalar with embedded structured information |
| TagTree | AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text. |
| Target | Provides an object which represents a target (ie, a similarity hit) from one object to something in another database |
| Tree(2) | Provide a tree as an annotation to a Bio::AnnotatableI object |
| TypeManager | Manages types for annotation collections |
| bioperl-live::Bio::Tree | Top |
| AlleleNode | A Node with Alleles attached |
| AnnotatableNode | A Tree Node with support for annotation |
| Compatible | Testing compatibility of phylogenetic trees with nested taxa. |
| DistanceFactory | Construct a tree using distance based methods |
| Node(2) | A Simple Tree Node |
| NodeI | Interface describing a Tree Node |
| NodeNHX | A Simple Tree Node with support for NHX tags |
| RandomFactory(1) | TreeFactory for generating Random Trees |
| Statistics(2) | Calculate certain statistics for a Tree |
| Tree(3) | An Implementation of TreeI interface. |
| TreeFunctionsI | Decorated Interface implementing basic Tree exploration methods |
| TreeI | A Tree object suitable for lots of things, designed originally for Phylogenetic Trees. |
| bioperl-live::Bio::Tree::Draw | Top |
| Cladogram | Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. |
| bioperl-live::Bio::Ontology | Top |
| DocumentRegistry | Keep track of where to find ontologies. Allows lookups by name. |
| GOterm | representation of GO terms |
| InterProTerm | Implementation of InterProI term interface |
| OBOEngine | An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium |
| OBOterm | representation of OBO terms |
| Ontology | standard implementation of an Ontology |
| OntologyEngineI | Interface a minimal Ontology implementation should satisfy |
| OntologyI | Interface for an ontology implementation |
| OntologyStore | A repository of ontologies |
| Path | a path for an ontology term graph |
| PathI | Interface for a path between ontology terms |
| Relationship | a relationship for an ontology |
| RelationshipFactory | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory |
| RelationshipI | Interface for a relationship between ontology terms |
| RelationshipType | a relationship type for an ontology |
| SimpleOntologyEngine | Implementation of OntologyEngineI interface |
| Term(1) | implementation of the interface for ontology terms |
| TermFactory | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory |
| TermI | interface for ontology terms |
| bioperl-live::Bio::Ontology::SimpleGOEngine | Top |
| GraphAdaptor | Graph adaptor for Bio::Ontology::SimpleGOEngine |
| GraphAdaptor02 | Graph adaptor (v02.x) for Bio::Ontology::SimpleGOEngine |
| bioperl-live::Bio::FeatureIO | Top |
| bed | read/write features from UCSC BED format |
| gff | read/write GFF feature files |
| gtf | read write features in GTF format |
| interpro(2) | read features from InterPro XML |
| ptt | read/write features in PTT format |
| vecscreen_simple | read/write features from NCBI vecscreen -f 3 output |
| bioperl-live::Bio::Microarray | Top |
Nothing here |
| bioperl-live::Bio::Microarray::Tools | Top |
| MitoChipV2Parser | Class for parsing design file for Affy MitoChip V2.0 |
| ReseqChip | Class for analysing additional probe oligonucleotides of Resequencing Chips (for instance Affy Mitochip v2.0) |
| bioperl-live::Bio::PhyloNetwork | Top |
| Factory(3) | Module to sequentially generate Phylogenetic Networks |
| FactoryX | Module to sequentially generate Phylogenetic Networks |
| GraphViz | Interface between PhyloNetwork and GraphViz |
| RandomFactory(2) | Module to generate random Phylogenetic Networks |
| TreeFactory | Module to sequentially generate Phylogenetic Trees |
| TreeFactoryMulti | Module to sequentially generate Phylogenetic Trees |
| TreeFactoryX | Module to sequentially generate Phylogenetic Trees |
| muVector | Module to compute with vectors of arbitrary dimension |
| bioperl-live::Bio::Cluster | Top |
| ClusterFactory | Instantiates a new Bio::ClusterI (or derived class) through a factory |
| FamilyI | Family Interface |
| SequenceFamily | Sequence Family object |
| UniGene | UniGene object |
| UniGeneI | abstract interface of UniGene object |
| bioperl-live::Bio::Matrix | Top |
| Generic(2) | A generic matrix implementation |
| IO(2) | A factory for Matrix parsing |
| MatrixI | An interface for describing a Matrix |
| Mlagan | A generic matrix with mlagan fields |
| PhylipDist | A Phylip Distance Matrix object |
| Scoring | Object which can hold scoring matrix information |
| bioperl-live::Bio::Matrix::IO | Top |
| mlagan | A parser for the mlagan substitution matrix |
| phylip(2) | A parser for PHYLIP distance matricies |
| scoring | A parser for PAM/BLOSUM matricies |
| bioperl-live::Bio::Matrix::PSM | Top |
| IO(3) | PSM parser |
| InstanceSite | A PSM site occurance |
| InstanceSiteI | InstanceSite interface, holds an instance of a PSM |
| ProtMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information. |
| ProtPsm | handle combination of site matricies |
| Psm | handle combination of site matricies |
| PsmHeader | PSM mast parser implementation |
| PsmHeaderI | handles the header data from a PSM file |
| PsmI | abstract interface to handler of site matricies |
| SiteMatrix | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds |
| SiteMatrixI | SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds |
| bioperl-live::Bio::Matrix::PSM::IO | Top |
| mast | PSM mast parser implementation |
| masta | motif fasta format parser |
| meme(2) | PSM meme parser implementation |
| psiblast | PSM psiblast parser |
| transfac | PSM transfac parser |
| bioperl-live::Bio::Event | Top |
| EventGeneratorI | This interface describes the basic event generator class. |
| EventHandlerI(2) | An Event Handler Interface |
| bioperl-live::Bio::TreeIO | Top |
| TreeEventBuilder | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events |
| cluster | A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output |
| lintree | Parser for lintree output trees |
| newick | TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. |
| nexml(3) | A TreeIO driver module for parsing NeXML tree files |
| nexus(2) | A TreeIO driver module for parsing Nexus tree output from PAUP |
| nhx | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. |
| pag | Bio::TreeIO driver for Pagel format |
| phyloxml | TreeIO implementation for parsing PhyloXML format. |
| svggraph | A simple output format that converts a Tree object to an SVG output |
| tabtree | A simple output format which displays a tree as an ASCII drawing |
| bioperl-live::Bio::Map | Top |
| Clone | An central map object representing a clone |
| Contig(1) | A MapI implementation handling the contigs of a Physical Map (such as FPC) |
| CytoMap | A Bio::MapI compliant map implementation handling cytogenic bands |
| CytoMarker | An object representing a marker. |
| CytoPosition | Marker class with cytogenetic band storing attributes |
| EntityI | An Entity Interface |
| FPCMarker | An central map object representing a marker |
| Gene(1) | An gene modelled as a mappable element. |
| GeneMap | A MapI implementation to represent the area around a gene |
| GenePosition | A typed position, suitable for modelling the various regions of a gene. |
| GeneRelative | Represents being relative to named sub-regions of a gene. |
| LinkageMap | A representation of a genetic linkage map. |
| LinkagePosition | Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap |
| MapI | Interface for describing Map objects in bioperl |
| Mappable | An object representing a generic map element that can have multiple locations in several maps. |
| MappableI | An object that can be placed in a map |
| Marker(2) | An central map object representing a generic marker that can have multiple location in several maps. |
| MarkerI(2) | Interface for basic marker functionality |
| Microsatellite | An object representing a Microsatellite marker. |
| OrderedPosition | Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. |
| OrderedPositionWithDistance | Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. |
| Physical | A class for handling a Physical Map (such as FPC) |
| Position | A single position of a Marker, or the range over which that marker lies, in a Map |
| PositionHandler | A Position Handler Implementation |
| PositionHandlerI | A Position Handler Interface |
| PositionI | Abstracts the notion of a position having a value in the context of a marker and a Map |
| PositionWithSequence | A position with a sequence. |
| Prediction | An object representing the predictions of something that can have multiple locations in several maps. |
| Relative | Represents what a Position's coordiantes are relative to. |
| RelativeI | Interface for describing what a Position's coordiantes are relative to. |
| SimpleMap | A MapI implementation handling the basics of a Map |
| TranscriptionFactor | A transcription factor modelled as a mappable element |
| bioperl-live::Bio::Phenotype | Top |
| Correlate | Representation of a correlating phenotype in a given species |
| Measure | Representation of context/value(-range)/unit triplets |
| Phenotype | A class for modeling phenotypes |
| PhenotypeI | An interface for classes modeling phenotypes |
| bioperl-live::Bio::Phenotype::OMIM | Top |
| MiniMIMentry | Representation of a Mini MIM entry |
| OMIMentry | represents OMIM (Online Mendelian Inheritance in Man) database entries |
| OMIMentryAllelicVariant | Representation of a allelic variant of the OMIM database |
| OMIMparser | parser for the OMIM database |
| bioperl-live::Bio::Phenotype::MeSH | Top |
| Term(2) | A MeSH term |
| Twig | Context for a MeSH term |
| bioperl-live::Bio::Root | Top |
| Build | A common Module::Build subclass base for BioPerl distributions |
| Exception | Generic exception objects for Bioperl |
| HTTPget | module for fallback HTTP get operations when LWP:: is unavailable |
| IO(4) | module providing several methods often needed when dealing with file IO |
| Root | Hash-based implementation of Bio::Root::RootI |
| RootI | Abstract interface to root object code |
| Storable | object serialisation methods |
| Test | A common base for all Bioperl test scripts. |
| Utilities(3) | General-purpose utility module |
| Version | provide global, distribution-level versioning |
| bioperl-live::Bio::Root::Test | Top |
| Warn | Perl extension to test Bioperl methods for warnings |
| bioperl-live::Bio::Biblio | Top |
| Article | Representation of a general article |
| BiblioBase | An abstract base for other biblio classes |
| Book | Representation of a book |
| BookArticle | Representation of a book article |
| IO(5) | Handling the bibliographic references |
| Journal | Representation of a journal |
| JournalArticle | Representation of a journal article |
| MedlineArticle | Representation of a MEDLINE article |
| MedlineBook | Representation of a MEDLINE book |
| MedlineBookArticle | Representation of a MEDLINE book article |
| MedlineJournal | Representation of a MEDLINE journal |
| MedlineJournalArticle | Representation of a MEDLINE journal article |
| Organisation | Representation of an organisation |
| Patent | Representation of a patent |
| Person | Representation of a person |
| Proceeding | Representation of a conference proceeding |
| Provider | Representation of a general provider |
| PubmedArticle | Representation of a PUBMED article |
| PubmedBookArticle | Representation of a PUBMED book article |
| PubmedJournalArticle | Representation of a PUBMED journal article |
| Ref | Representation of a bibliographic reference |
| Service | Representation of a provider of type service |
| TechReport | Representation of a technical report |
| Thesis | Representation of thesis |
| WebResource | Representation of a web resource |
| bioperl-live::Bio::Biblio::IO | Top |
| medline2ref | A converter of a raw hash to MEDLINE citations |
| medlinexml | A converter of XML files with MEDLINE citations |
| pubmed2ref | A converter of a raw hash to PUBMED citations |
| pubmedxml | A converter of XML files with PUBMED citations |
| bioperl-live::Bio::Structure | Top |
| Atom | Bioperl structure Object, describes an Atom |
| Chain(2) | Bioperl structure Object, describes a chain |
| Entry | Bioperl structure Object, describes the whole entry |
| IO(6) | Handler for Structure Formats |
| Model | Bioperl structure Object, describes a Model |
| Residue | Bioperl structure Object, describes a Residue |
| StructureI | Abstract Interface for a Structure objects |
| bioperl-live::Bio::Structure::SecStr | Top |
Nothing here |
| bioperl-live::Bio::Structure::SecStr::DSSP | Top |
| Res(1) | Module for parsing/accessing dssp output |
| bioperl-live::Bio::Structure::SecStr::STRIDE | Top |
| Res(2) | Module for parsing/accessing stride output |
| bioperl-live::Bio::Structure::IO | Top |
| pdb | PDB input/output stream |
| bioperl-live::Bio::DB | Top |
| Ace | Database object interface to ACeDB servers |
| BiblioI | An interface to a Bibliographic Query Service |
| BioFetch | Database object interface to BioFetch retrieval |
| CUTG | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. |
| DBFetch | Database object for retrieving using the dbfetch script |
| EMBL(2) | Database object interface for EMBL entry retrieval |
| EUtilities(1) | webagent which interacts with and retrieves data from NCBI's eUtils |
| EntrezGene | Database object interface to Entrez Gene |
| Expression | DESCRIPTION of Object |
| Failover | A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs |
| Fasta(1) | - Fast indexed access to a directory of fasta files |
| Fasta(2) | |
| FileCache | In file cache for BioSeq objects |
| Flat | Interface for indexed flat files |
| GFF(1) | - Storage and retrieval of sequence annotation data |
| GenBank(2) | Database object interface to GenBank |
| GenPept | Database object interface to GenPept |
| GenericWebAgent | helper base class for parameter-based remote server access and response retrieval. |
| HIV | Database object interface to the Los Alamos HIV Sequence Database |
| ID_Iterator | |
| InMemoryCache | Abstract interface for a sequence database |
| LocationI(2) | A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects |
| MeSH | Term retrieval from a Web MeSH database |
| NCBIHelper | A collection of routines useful for queries to NCBI databases. |
| Qual(1) | - Fast indexed access to a directory of quality files |
| Qual(2) | |
| QueryI | Object Interface to queryable sequence databases |
| RandomAccessI | Abstract interface for a sequence database |
| RefSeq | Database object interface for RefSeq retrieval |
| ReferenceI | A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects |
| Registry | Access to the Open Bio Database Access registry scheme |
| SeqFeature | - Normalized feature for use with Bio::DB::SeqFeature::Store |
| SeqHound | Database object interface to SeqHound |
| SeqI(2) | Abstract Interface for Sequence databases |
| SeqVersion | front end to querying databases for identifier versions |
| Stream(1) | |
| Stream(2) | |
| SwissProt | Database object interface to SwissProt retrieval |
| TFBS | Access to a Transcription Factor Binding Site database |
| Taxonomy(2) | Access to a taxonomy database |
| Universal | Artificial database that delegates to specific databases |
| UpdateableSeqI(2) | An interface for writing to a database of sequences. |
| WebDBSeqI | Object Interface to generalize Web Databases for retrieving sequences |
| bioperl-live::Bio::DB::HIV | Top |
| AnnotationCollectionI(2) | |
| HIVAnnotProcessor | Adds HIV-specific annotations to Bio::SeqIO streams |
| HIVQueryHelper | Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery |
| HIVSchema | |
| Q | |
| QRY | |
| R |
| bioperl-live::Bio::DB::Taxonomy | Top |
| entrez | Taxonomy Entrez driver |
| flatfile | An implementation of Bio::DB::Taxonomy which uses local flat files |
| list | An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database |
| bioperl-live::Bio::DB::Expression | Top |
| geo | *** DESCRIPTION of Class |
| bioperl-live::Bio::DB::SeqFeature | Top |
| NormalizedFeature | - Normalized feature for use with Bio::DB::SeqFeature::Store |
| NormalizedFeatureI | - Interface for normalized features |
| NormalizedTableFeatureI | - Interface for normalized features whose hierarchy is stored in a table |
| Segment(1) | - Location-based access to genome annotation data |
| Store | - Storage and retrieval of sequence annotation data |
| bioperl-live::Bio::DB::SeqFeature::Store | Top |
| FeatureFileLoader | - feature file loader for Bio::DB::SeqFeature::Store |
| GFF2Loader | - GFF2 file loader for Bio::DB::SeqFeature::Store |
| GFF3Loader | - GFF3 file loader for Bio::DB::SeqFeature::Store |
| Iterator(1) | |
| Iterator(2) | |
| LoadHelper | - Internal utility for Bio::DB::SeqFeature::Store |
| Loader(1) | - Loader |
| Subdir | |
| bdb | fetch and store objects from a BerkeleyDB |
| berkeleydb(1) | - Storage and retrieval of sequence annotation data in Berkeleydb files |
| berkeleydb3 | - Storage and retrieval of sequence annotation data in Berkeleydb files |
| memory(1) | - In-memory implementation of Bio::DB::SeqFeature::Store |
| bioperl-live::Bio::DB::SeqFeature::Store::DBI | Top |
| Iterator | utility methods for creating and iterating over SeqFeature records |
| Pg | - PostgreSQL implementation of Bio::DB::SeqFeature::Store |
| SQLite | - SQLite implementation of Bio::DB::SeqFeature::Store |
| mysql(1) | - Mysql implementation of Bio::DB::SeqFeature::Store |
| bioperl-live::Bio::DB::TFBS | Top |
| transfac_pro | An implementation of Bio::DB::TFBS which uses local flat files for transfac pro |
| bioperl-live::Bio::DB::GFF | Top |
| Aggregator | - Aggregate GFF groups into composite features |
| Featname | - The name of a feature |
| Feature(1) | - A relative segment identified by a feature type |
| Homol | - A segment of DNA that is homologous to another |
| RelSegment | - Sequence segment with relative coordinate support |
| Segment(2) | - Simple DNA segment object |
| Typename | - The name of a feature type |
| bioperl-live::Bio::DB::GFF::Util | Top |
| Binning | binning utility for Bio::DB::GFF index |
| Rearrange | rearrange utility |
| bioperl-live::Bio::DB::GFF::Aggregator | Top |
| alignment | - Alignment aggregator |
| clone | - Clone aggregator |
| coding | - The Coding Region Aggregator |
| gene | - Sequence Ontology Geene |
| match | - Match aggregator |
| none | - No aggregation |
| orf | - An aggregator for orf regions |
| processed_transcript | - Sequence Ontology Transcript |
| so_transcript | - Sequence Ontology Transcript |
| transcript | - Transcript aggregator |
| ucsc_acembly | - UCSC acembly aggregator |
| ucsc_ensgene | - UCSC ensGene aggregator |
| ucsc_genscan | - UCSC genscan aggregator |
| ucsc_refgene | - UCSC refGene aggregator |
| ucsc_sanger22 | - UCSC sanger22 aggregator |
| ucsc_sanger22pseudo | - UCSC sanger22pseudo aggregator |
| ucsc_softberry | - UCSC softberry aggregator |
| ucsc_twinscan | - UCSC twinscan aggregator |
| ucsc_unigene | - UCSC UniGene aggregator |
| bioperl-live::Bio::DB::GFF::Adaptor | Top |
| FeatureStore | |
| ace(2) | - ace interface (for multiple inheritance) |
| berkeleydb(2) | - Bio::DB::GFF database adaptor for in-memory databases |
| biofetch(1) | - Cache BioFetch objects in a Bio::DB::GFF database |
| biofetch_oracle | - Cache BioFetch objects in a Bio::DB::GFF database |
| dbi | - Database adaptor for DBI (SQL) databases |
| memory(2) | - Bio::DB::GFF database adaptor for in-memory databases |
| bioperl-live::Bio::DB::GFF::Adaptor::dbi | Top |
| caching_handle | - Cache for database handles |
| faux_dbh | |
| iterator(1) | iterator for Bio::DB::GFF::Adaptor::dbi |
| mysql(2) | - Database adaptor for a specific mysql schema |
| mysqlace | - Unholy union between mysql GFF database and acedb database |
| mysqlcmap | - Database adaptor for an integraded CMap/GBrowse mysql schema |
| mysqlopt | - Deprecated database adaptor |
| oracle | - Database adaptor for a specific oracle schema |
| oracleace | - Unholy union between oracle GFF database and acedb database |
| pg | - Database adaptor for a specific postgres schema |
| pg_fts | - Database adaptor for a specific postgres schema with a TSearch2 implementation |
| bioperl-live::Bio::DB::GFF::Adaptor::berkeleydb | Top |
| iterator(2) | iterator for Bio::DB::GFF::Adaptor::berkeleydb |
| bioperl-live::Bio::DB::GFF::Adaptor::memory | Top |
| feature_serializer | utility methods for serializing and deserializing GFF features |
| iterator(3) | iterator for Bio::DB::GFF::Adaptor::memory |
| bioperl-live::Bio::DB::Flat | Top |
| BDB | Interface for BioHackathon standard BDB-indexed flat file |
| BinarySearch | BinarySearch search indexing system for sequence files |
| bioperl-live::Bio::DB::Flat::BDB | Top |
| embl(2) | embl adaptor for Open-bio standard BDB-indexed flat file |
| fasta(4) | fasta adaptor for Open-bio standard BDB-indexed flat file |
| genbank(2) | genbank adaptor for Open-bio standard BDB-indexed flat file |
| swiss(2) | swissprot adaptor for Open-bio standard BDB-indexed flat file |
| bioperl-live::Bio::DB::Biblio | Top |
| biofetch(2) | A BioFetch-based access to a bibliographic citation retrieval |
| eutils | Access to PubMed's bibliographic query service |
| soap | A SOAP-based access to a bibliographic query service |
| bioperl-live::Bio::DB::SeqVersion | Top |
| gi | interface to NCBI Sequence Revision History page |
| bioperl-live::Bio::DB::Query | Top |
| GenBank(3) | Build a GenBank Entrez Query |
| HIVQuery | Query interface to the Los Alamos HIV Sequence Database |
| WebQuery | Helper class for web-based sequence queryies |
| bioperl-live::Bio::Draw | Top |
| Pictogram | generate SVG output of Pictogram display for consensus motifs |
| bioperl-live::Bio::Search | Top |
| BlastStatistics | An object for Blast statistics |
| BlastUtils | Utility functions for Bio::Search:: BLAST objects |
| DatabaseI | Interface for a database used in a sequence search |
| GenericDatabase | Generic implementation of Bio::Search::DatabaseI |
| GenericStatistics | An object for statistics |
| Processor | DESCRIPTION of Object |
| SearchUtils | Utility functions for Bio::Search:: objects |
| StatisticsI(2) | A Base object for statistics |
| bioperl-live::Bio::Search::Tiling | Top |
| HSPI(1) | |
| LocatableSeq(2) | |
| MapTileUtils | utilities for manipulating closed intervals for an HSP tiling algorithm |
| MapTiling | An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics |
| TilingI | Abstract interface for an HSP tiling module |
| bioperl-live::Bio::Search::Result | Top |
| BlastPullResult | A parser and result object for BLASTN results |
| BlastResult | Blast-specific subclass of Bio::Search::Result::GenericResult |
| CrossMatchResult(1) | CrossMatch-specific subclass of Bio::Search::Result::GenericResult |
| CrossMatchResult(2) | |
| GenericResult | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. |
| HMMERResult | A Result object for HMMER results |
| HmmpfamResult | A parser and result object for hmmpfam results |
| PullResultI | Bio::Search::Result::ResultI interface for 'pull' parsers |
| ResultFactory | A factory to create Bio::Search::Result::ResultI objects |
| ResultI(2) | Abstract interface to Search Result objects |
| WABAResult | Result object for WABA alignment output |
| bioperl-live::Bio::Search::Hit | Top |
| BlastHit | Blast-specific subclass of Bio::Search::Hit::GenericHit |
| BlastPullHit | A parser and hit object for BLASTN hits |
| Fasta(2) | Hit object specific for Fasta-generated hits |
| GenericHit | A generic implementation of the Bio::Search::Hit::HitI interface |
| HMMERHit | A Hit module for HMMER hits |
| HitFactory | A factory to create Bio::Search::Hit::HitI objects |
| HitI | Interface for a hit in a similarity search result |
| HmmpfamHit | A parser and hit object for hmmpfam hits |
| ModelHit | A model-based implementation of the Bio::Search::Hit::HitI interface |
| PsiBlastHit | Bioperl BLAST Hit object |
| PullHitI | Bio::Search::Hit::HitI interface for pull parsers. |
| bioperl-live::Bio::Search::Iteration | Top |
| GenericIteration | A generic implementation of the Bio::Search::Iteration::IterationI interface. |
| IterationI | Abstract interface to an iteration from an iterated search result, such as PSI-BLAST. |
| bioperl-live::Bio::Search::HSP | Top |
| BlastHSP | Bioperl BLAST High-Scoring Pair object |
| BlastPullHSP | A parser and HSP object for BlastN hsps |
| FastaHSP | HSP object for FASTA specific data |
| GenericHSP | A "Generic" implementation of a High Scoring Pair |
| HMMERHSP | A HSP object for HMMER results |
| HSPFactory | A factory to create Bio::Search::HSP::HSPI objects |
| HSPI(2) | Interface for a High Scoring Pair in a similarity search result |
| HmmpfamHSP | A parser and HSP object for hmmpfam hsps |
| ModelHSP | A HSP object for model-based searches |
| PSLHSP | A HSP for PSL output |
| PsiBlastHSP | Bioperl BLAST High-Scoring Pair object |
| PullHSPI | Bio::Search::HSP::HSPI interface for pull parsers. |
| WABAHSP | HSP object suitable for describing WABA alignments |
| bioperl-live::Bio::LiveSeq | Top |
| AARange | AARange abstract class for LiveSeq |
| Chain(3) | DoubleChain DataStructure for Perl |
| ChainI | Double linked chain data structure |
| DNA | DNA object for LiveSeq |
| Exon(2) | Range abstract class for LiveSeq |
| Gene(2) | Range abstract class for LiveSeq |
| Intron(2) | Range abstract class for LiveSeq |
| Mutation | Mutation event descriptor class |
| Mutator | Package mutating LiveSequences |
| Prim_Transcript | Prim_Transcript class for LiveSeq |
| Range(2) | Range abstract class for LiveSeq |
| Repeat_Region | Repeat_Region class for LiveSeq |
| Repeat_Unit | Repeat_Unit class for LiveSeq |
| SeqI(3) | Abstract sequence interface class for LiveSeq |
| Transcript(2) | Transcript class for LiveSeq |
| Translation | Translation class for LiveSeq |
| bioperl-live::Bio::LiveSeq::IO | Top |
| BioPerl(2) | Loader for LiveSeq from EMBL entries with BioPerl |
| Loader(2) | Parent Loader for LiveSeq |
| bioperl-live::Bio::CodonUsage | Top |
| IO(7) | for reading and writing codon usage tables to file |
| Table | for access to the Codon usage Database at http://www.kazusa.or.jp/codon. |
| bioperl-live::Bio::MolEvol | Top |
| CodonModel | Codon Evolution Models |
| bioperl-live::Bio::Factory | Top |
| AnalysisI(2) | An interface to analysis tool factory |
| ApplicationFactoryI | Interface class for Application Factories |
| DriverFactory | Base class for factory classes loading drivers |
| FTLocationFactory | A FeatureTable Location Parser |
| LocationFactoryI | A factory interface for generating locations from a string |
| MapFactoryI | A Factory for getting markers |
| ObjectBuilderI | Interface for an object builder |
| ObjectFactory | Instantiates a new Bio::Root::RootI (or derived class) through a factory |
| ObjectFactoryI | A General object creator factory |
| SeqAnalysisParserFactory | class capable of creating SeqAnalysisParserI compliant parsers |
| SeqAnalysisParserFactoryI | interface describing objects capable of creating SeqAnalysisParserI compliant parsers |
| SequenceFactoryI | This interface allows for generic building of sequences in factories which create sequences (like SeqIO) |
| SequenceProcessorI | Interface for chained sequence processing algorithms |
| SequenceStreamI | Interface describing the basics of a Sequence Stream. |
| TreeFactoryI | Factory Interface for getting and writing trees from/to a data stream |
| bioperl-live::Bio::Assembly | Top |
| Contig(2) | Perl module to hold and manipulate sequence assembly contigs. |
| ContigAnalysis | Perform analysis on sequence assembly contigs. |
| IO(8) | Handler for Assembly::IO Formats |
| Scaffold | Perl module to hold and manipulate sequence assembly data. |
| ScaffoldI | Abstract Inteface of Sequence Assemblies |
| Singlet | Perl module to hold and manipulate singlets from sequence assembly contigs. |
| bioperl-live::Bio::Assembly::IO | Top |
| ace(3) | module to load ACE files from various assembly programs |
| bowtie | An IO module for assemblies in Bowtie format *BETA* |
| maq | Driver to read assembly files in maq format *BETA* |
| phrap | driver to load phrap.out files. |
| sam | An IO module for assemblies in Sam format *BETA* |
| tigr(2) | Driver to read and write assembly files in the TIGR Assembler v2 default format. |
| bioperl-live::Bio::Assembly::Tools | Top |
| ContigSpectrum | create and manipulate contig spectra |
| bioperl-live::Bio::Variation | Top |
| AAChange | Sequence change class for polypeptides |
| AAReverseMutate | point mutation and codon information from single amino acid changes |
| Allele | Sequence object with allele-specific attributes |
| DNAMutation | DNA level mutation class |
| IO(9) | Handler for sequence variation IO Formats |
| RNAChange | Sequence change class for RNA level |
| SNP | submitted SNP |
| SeqDiff | Container class for mutation/variant descriptions |
| VariantI | Sequence Change SeqFeature abstract class |
| bioperl-live::Bio::Variation::IO | Top |
| flat | flat file sequence variation input/output stream |
| xml | XML sequence variation input/output stream |
| bioperl-live::Bio::Das | Top |
| FeatureTypeI | Simple interface to Sequence Ontology feature types |
| SegmentI | DAS-style access to a feature database |
| bioperl-live::Bio::Tools | Top |
| AlignFactory | Base object for alignment factories |
| AnalysisResult | Base class for analysis result objects and parsers |
| Blat | parser for Blat program |
| CodonTable | Codon table object |
| Coil | parser for Coil output |
| ECnumber | representation of EC numbers (Enzyme Classification) |
| EPCR | Parse ePCR output and make features |
| ERPIN | a parser for ERPIN output |
| ESTScan | Results of one ESTScan run |
| EUtilities(2) | NCBI eutil XML parsers |
| Eponine | Results of one Eponine run |
| Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects |
| Fgenesh | parse results of one Fgenesh run |
| FootPrinter | write sequence features in FootPrinter format |
| GFF(2) | A Bio::SeqAnalysisParserI compliant GFF format parser |
| Gel | Calculates relative electrophoretic migration distances |
| Geneid | Results of one geneid run |
| Genemark | Results of one Genemark run |
| Genewise | Results of one Genewise run |
| Genomewise | Results of one Genomewise run |
| Genscan | Results of one Genscan run |
| Glimmer | parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions |
| Grail | Results of one Grail run |
| GuessSeqFormat | Module for determining the sequence format of the contents of a file, a string, or through a filehandle. |
| Hmmpfam | Parser for Hmmpfam program |
| IUPAC | Generates unique Seq objects from an ambiguous Seq object |
| Infernal | A parser for Infernal output |
| Lucy | Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR |
| MZEF | Results of one MZEF run |
| Match(2) | Parses output from Transfac's match(TM) |
| 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 | parser for Promoterwise tab format output |
| PrositeScan | Parser for ps_scan result |
| Protparam | submit to and parse output from protparam ; |
| Pseudowise | Results of one Pseudowise run |
| QRNA | A Parser for qrna output |
| RNAMotif | A parser for RNAMotif output |
| RandomDistFunctions | A set of routines useful for generating random data in different distributions |
| RepeatMasker | a parser for RepeatMasker output |
| Seg | parse C |
| SeqPattern | represent a sequence pattern or motif |
| SeqStats | Object holding statistics for one particular sequence |
| SeqWords | Object holding n-mer statistics for a sequence |
| SiRNA | Perl object for designing small inhibitory RNAs. |
| Sigcleave | Bioperl object for sigcleave analysis |
| Signalp | parser for Signalp output |
| TandemRepeatsFinder | a parser for Tandem Repeats Finder output |
| TargetP | Results of one TargetP run |
| Tmhmm | parse TMHMM output (TransMembrane HMM) |
| dpAlign | Perl extension to do pairwise dynamic programming sequence alignment |
| ipcress | Parse ipcress output and make features |
| isPcr | Parse isPcr output and make features |
| pICalculator | calculate the isoelectric point of a protein |
| pSW | pairwise Smith Waterman object |
| tRNAscanSE | A parser for tRNAscan-SE output |
| bioperl-live::Bio::Tools::Run | Top |
| GenericParameters | An object for the parameters used to run programs |
| ParametersI | A Base object for the parameters used to run programs |
| RemoteBlast | Object for remote execution of the NCBI Blast via HTTP |
| StandAloneBlast | Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast. |
| StandAloneNCBIBlast | Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast. |
| StandAloneWUBlast | Object for the local execution of WU-Blast. |
| WrapperBase(1) | A Base object for wrappers around executables |
| bioperl-live::Bio::Tools::Run::WrapperBase | Top |
| WrapperBase(2) | Extensions to WrapperBase for handling programs with commands *ALPHA* |
| bioperl-live::Bio::Tools::Signalp | Top |
| ExtendedSignalp | enhanced parser for Signalp output |
| bioperl-live::Bio::Tools::SeqPattern | Top |
| Backtranslate | Bio::Tools::SeqPattern::Backtranslate |
| bioperl-live::Bio::Tools::EMBOSS | Top |
| Palindrome | parse EMBOSS palindrome output |
| bioperl-live::Bio::Tools::SiRNA | Top |
Nothing here |
| bioperl-live::Bio::Tools::SiRNA::Ruleset | Top |
| saigo | Perl object implementing the Saigo group's rules for designing small inhibitory RNAs |
| tuschl | Perl object implementing the tuschl group's rules for designing small inhibitory RNAs |
| bioperl-live::Bio::Tools::Phylo | Top |
| Gerp | Parses output from GERP |
| Gumby | Parses output from gumby |
| Molphy | parser for Molphy output |
| PAML | Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 |
| bioperl-live::Bio::Tools::Phylo::Molphy | Top |
| Result(2) | container for data parsed from a ProtML run |
| bioperl-live::Bio::Tools::Phylo::Phylip | Top |
| ProtDist | parser for ProtDist output |
| bioperl-live::Bio::Tools::Phylo::PAML | Top |
| ModelResult | A container for NSSite Model Result from PAML |
| Result(3) | A PAML result set object |
| bioperl-live::Bio::Tools::Primer | Top |
| AssessorI | interface for assessing primer pairs |
| Feature(2) | position of a single primer |
| Pair(3) | two primers on left and right side |
| bioperl-live::Bio::Tools::Primer::Assessor | Top |
| Base | base class for common assessor things |
| bioperl-live::Bio::Tools::Prediction | Top |
| Exon(3) | A predicted exon feature |
| Gene(3) | a predicted gene structure feature |
| bioperl-live::Bio::Tools::Sim4 | Top |
| Exon(4) | A single exon determined by an alignment |
| Results(1) | Results of one Sim4 run |
| bioperl-live::Bio::Tools::Spidey | Top |
| Exon(5) | A single exon determined by an alignment |
| Results(2) | Results of a Spidey run |
| bioperl-live::Bio::Tools::EUtilities | Top |
| EUtilDataI | eutil data object interface |
| EUtilParameters | Manipulation of NCBI eutil-based parameters for remote database requests. |
| History(1) | lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc). |
| History(2) | lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc). |
| HistoryI | simple extension of EUtilDataI interface class for classes which hold NCBI server history data |
| Info | interface class for storing einfo data |
| Link | general API for accessing data retrieved from elink queries |
| Query | parse and collect esearch, epost, espell, egquery information |
| Summary | class for handlign data output (XML) from esummary. |
| bioperl-live::Bio::Tools::EUtilities::Link | Top |
| LinkSet | class for EUtils LinkSets |
| UrlLink | class for EUtils UrlLinks |
| bioperl-live::Bio::Tools::EUtilities::Summary | Top |
| DocSum | data object for document summary data from esummary |
| Item | simple layered object for DocSum item data |
| ItemContainerI | abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered) |
| bioperl-live::Bio::Tools::EUtilities::Info | Top |
| FieldInfo | class for storing einfo field data |
| LinkInfo | class for storing einfo link data |
| bioperl-live::Bio::Tools::EUtilities::Query | Top |
| GlobalQuery | container class for egquery data |
| bioperl-live::Bio::Tools::Analysis | Top |
| SimpleAnalysisBase | abstract superclass for SimpleAnalysis implementations |
| bioperl-live::Bio::Tools::Analysis::Protein | Top |
| Domcut | a wrapper around Domcut server |
| ELM | a wrapper around the ELM server which predicts short functional motifs on amino acid sequences |
| GOR4 | a wrapper around GOR4 protein secondary structure prediction server |
| HNN | a wrapper around the HNN protein secondary structure prediction server |
| Mitoprot | a wrapper around Mitoprot server |
| NetPhos | a wrapper around NetPhos server |
| Scansite | a wrapper around the Scansite server |
| Sopma | a wrapper around the Sopma protein secondary structure prediction server |
| bioperl-live::Bio::Tools::Analysis::DNA | Top |
| ESEfinder | a wrapper around ESEfinder server |
| bioperl-live::Bio::Tools::HMMER | Top |
| Domain | One particular domain hit from HMMER |
| Results(3) | Object representing HMMER output results |
| Set | Set of identical domains from HMMER matches |
| bioperl-live::Bio::Tools::Alignment | Top |
| Consed | A module to work with objects from consed .ace files |
| Trim |
| bioperl-live::Bio::Restriction | Top |
| Analysis | cutting sequences with restriction enzymes |
| Enzyme | A single restriction endonuclease (cuts DNA at specific locations) |
| EnzymeCollection | Set of restriction endonucleases |
| EnzymeI | Interface class for restriction endonuclease |
| IO(10) | Handler for sequence variation IO Formats |
| bioperl-live::Bio::Restriction::Enzyme | Top |
| MultiCut | A single restriction endonuclease |
| MultiSite | A single restriction endonuclease |
| bioperl-live::Bio::Restriction::IO | Top |
| bairoch | bairoch enzyme set |
| base | base enzyme set |
| itype2 | itype2 enzyme set |
| prototype | prototype enzyme set |
| withrefm | withrefm enzyme set |
| bioperl-live::Bio::Symbol | Top |
| Alphabet | BSANE/BioCORBA compliant symbol list alphabet |
| AlphabetI | A Symbol Alphabet |
| DNAAlphabet | A ready made DNA alphabet |
| ProteinAlphabet | A ready made Protein alphabet |
| Symbol | A biological symbol |
| SymbolI | Interface for a Symbol |