| bioperl-live | Top |
| LocalConfig |
| 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 | 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 |
| Graphics | Generate GD images of Bio::Seq objects |
| IdCollectionI | interface for objects with multiple identifiers |
| IdentifiableI | interface for objects with identifiers |
| JobI | |
| LocatableSeq | A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. |
| LocationI | Abstract interface of a Location on a Sequence |
| MapIO | A Map Factory object |
| OntologyIO | Parser factory for Ontology formats |
| Perl | Functional access to BioPerl for people who don't know objects |
| PrimarySeq | Bioperl lightweight Sequence Object |
| PrimarySeqI | [Developers] - Interface definition for a Bio::PrimarySeq |
| 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 |
| Species | Generic species object |
| Taxonomy | Conversion used bt the Taxonomy classes |
| TreeIO | Parser for Tree files |
| UpdateableSeqI(1) | Descendant of Bio::SeqI that allows updates |
| bioperl-live::Bio::Align | Top |
| AlignI | An interface for describing sequence alignments. |
| DNAStatistics | Calculate some statistics for a DNA alignment |
| PairwiseStatistics | Base statistic object for Pairwise Alignments |
| StatisticsI | Calculate some statistics for an alignment |
| Utilities(1) | A collection of utilities regarding converting and manipulating alignment objects |
| bioperl-live::Bio::AlignIO | Top |
| bl2seq | bl2seq sequence input/output stream |
| clustalw | clustalw sequence input/output stream |
| emboss | Parse EMBOSS alignment output (from applications water and needle) |
| fasta(1) | FastA MSA Sequence input/output stream |
| mase | mase sequence input/output stream |
| mega | Parse and Create MEGA format data files |
| meme | meme sequence input/output stream |
| msf | msf sequence input/output stream |
| nexus | NEXUS format sequence input/output stream |
| pfam | pfam sequence input/output stream |
| phylip | PHYLIP format sequence input/output stream |
| 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 |
| bioperl-live::Bio::Annotation | Top |
| AnnotationFactory | Instantiates a new Bio::AnnotationI (or derived class) through a factory |
| Collection(1) | Default Perl implementation of AnnotationCollectionI |
| Comment | A comment object, holding text |
| DBLink | DESCRIPTION of Object |
| OntologyTerm | An ontology term adapted to AnnotationI |
| Reference | Specialised DBLink object for Literature References |
| SimpleValue | A simple scalar |
| StructuredValue | A scalar with embedded structured information |
| TypeManager | Manages types for annotation collections |
| bioperl-live::Bio::Assembly | Top |
| Contig | Perl module to hold and manipulate sequence assembly contigs. |
| ContigAnalysis | Perform analysis on sequence assembly contigs. |
| IO(1) | Handler for Assembly::IO Formats |
| Scaffold | Perl module to hold and manipulate sequence assembly data. |
| ScaffoldI | Abstract Inteface of Sequence Assemblies |
| bioperl-live::Bio::Assembly::IO | Top |
| ace(1) | module to load phrap ACE files. |
| phrap | driver to load phrap.out files. |
| 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(2) | 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::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::ClusterIO | Top |
| dbsnp | dbSNP input stream |
| unigene | UniGene input stream |
| bioperl-live::Bio::Coordinate | Top |
| Chain(1) | Mapping locations through a chain of coordinate mappers |
| Collection(2) | 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 | 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 | An other name for Bio::Location::Simple |
| Match | An other name for Bio::Location::Simple |
| 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 |
| DBFetch | Database object for retrieving using the dbfetch script |
| EMBL(1) | Database object interface for EMBL entry retrieval |
| Failover | A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs |
| Fasta(1) | - Fast indexed access to a directory of fasta files |
| FileCache | In file cache for BioSeq objects |
| Flat | Interface for indexed flat files |
| GDB | Database object interface to GDB HTTP query |
| GFF(1) | - Storage and retrieval of sequence annotation data |
| GenBank(1) | Database object interface to GenBank |
| GenPept | Database object interface to GenPept |
| ID_Iterator | |
| InMemoryCache | Abstract interface for a sequence database |
| NCBIHelper | A collection of routines useful for queries to NCBI databases. |
| QueryI | Object Interface to queryable sequence databases |
| RandomAccessI | Abstract interface for a sequence database |
| RefSeq | Database object interface for RefSeq retrieval |
| Registry | Access to the Open Bio Database Access registry scheme |
| SeqI(2) | Abstract Interface for Sequence databases |
| SwissProt | Database object interface to SwissProt retrieval |
| 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 |
| XEMBL | Database object interface for XEMBL entry retrieval |
| XEMBLService | SOAP service definition for XEMBL |
| bioperl-live::Bio::DB::Biblio | Top |
| biofetch(1) | A BioFetch-based access to a bibliographic citation retrieval |
| soap | A SOAP-based access to a bibliographic query service |
| bioperl-live::Bio::DB::Flat | Top |
| BDB | Interface for BioHackathon standard BDB-indexed flat file |
| OBDAIndex | Binary search indexing system for sequence files |
| bioperl-live::Bio::DB::Flat::BDB | Top |
| embl(1) | embl adaptor for Open-bio standard BDB-indexed flat file |
| fasta(2) | fasta adaptor for Open-bio standard BDB-indexed flat file |
| 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 | - Simple DNA segment object |
| Typename | - The name of a feature type |
| bioperl-live::Bio::DB::GFF::Adaptor | Top |
| ace(2) | - ace interface (for multiple inheritance) |
| biofetch(2) | - Cache BioFetch objects in a Bio::DB::GFF database |
| dbi | - Database adaptor for DBI (SQL) databases |
| memory | - Database adaptor for a specific mysql schema |
| memory_iterator | iterator for Bio::DB::GFF::Adaptor::memory |
| bioperl-live::Bio::DB::GFF::Adaptor::dbi | Top |
| caching_handle | - Cache for database handles |
| faux_dbh | |
| iterator | iterator for Bio::DB::GFF::Adaptor::dbi |
| mysql | - Database adaptor for a specific mysql schema |
| mysqlace | - Unholy union between mysql GFF database and acedb database |
| mysqlopt | - Deprecated database adaptor |
| oracle | - Database adaptor for a specific oracle schema |
| oracleace | - Unholy union between oracle GFF database and acedb database |
| bioperl-live::Bio::DB::GFF::Aggregator | Top |
| alignment(1) | - Alignment aggregator |
| clone | - Clone aggregator |
| coding | - The Coding Region Aggregator |
| match | - Match aggregator |
| none | - No aggregation |
| processed_transcript(1) | - Sequence Ontology Transcript |
| transcript(1) | - 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::Util | Top |
| Binning | binning utility for Bio::DB::GFF index |
| Rearrange | rearrange utility |
| bioperl-live::Bio::DB::Query | Top |
| GenBank(2) | Build a GenBank Entrez Query |
| WebQuery | Helper class for web-based sequence queryies |
| bioperl-live::Bio::Das | Top |
| FeatureTypeI | Simple interface to Sequence Ontology feature types |
| SegmentI | DAS-style access to a feature database |
| bioperl-live::Bio::Event | Top |
| EventGeneratorI | This interface describes the basic event generator class. |
| EventHandlerI(1) | An Event Handler Interface |
| bioperl-live::Bio::Expression | Top |
| FeatureGroup | a set of DNA/RNA features. ISA Bio::Expression::FeatureI |
| FeatureI | an interface class for DNA/RNA features |
| ProbeI | an interface class for DNA/RNA probes |
| bioperl-live::Bio::Expression::FeatureGroup | Top |
| FeatureGroupMas50 |
| bioperl-live::Bio::Factory | Top |
| AnalysisI(2) | An interface to analysis tool factory |
| ApplicationFactoryI | Interface class for Application Factories |
| BlastHitFactory | Factory for Bio::Search::Hit::BlastHit objects |
| BlastResultFactory | Factory for Bio::Search::Result::BlastResult objects |
| DriverFactory | Base class for factory classes loading drivers |
| EMBOSS | EMBOSS appliaction factory class |
| FTLocationFactory | A FeatureTable Location Parser |
| HitFactoryI | Interface for an object that builds Bio::Search::Hit::HitI objects |
| LocationFactoryI | DESCRIPTION of Interface |
| 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 |
| ResultFactoryI | Interface for an object that builds Bio::Search::Result::ResultI objects |
| 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::Graphics | Top |
| Feature(2) | A simple feature object for use with Bio::Graphics::Panel |
| FeatureFile | - A set of Bio::Graphics features, stored in a file |
| Glyph | Base class for Bio::Graphics::Glyph objects |
| Panel | Generate GD images of Bio::Seq objects |
| Util |
| bioperl-live::Bio::Graphics::Glyph | Top |
| Factory | Factory for Bio::Graphics::Glyph objects |
| alignment(2) | The "alignment" glyph |
| anchored_arrow | The "anchored_arrow" glyph |
| arrow | The "arrow" glyph |
| box | The "box" glyph |
| cds | The "cds" glyph |
| crossbox | The "crossbox" glyph |
| diamond | The "diamond" glyph |
| dna | The "dna" glyph |
| dot | The "dot" glyph |
| ellipse | The "ellipse" glyph |
| ex | The "crossbox" glyph |
| extending_arrow | - The "extending arrow" glyph |
| generic | The "generic" glyph |
| graded_segments | The "graded_segments" glyph |
| group | The "group" glyph |
| heterogeneous_segments | The "heterogeneous_segments" glyph |
| line | The "line" glyph |
| oval | The "oval" glyph |
| pinsertion | The "Drosophila P-element Insertion" glyph |
| primers | The "STS primers" glyph |
| processed_transcript(2) | The sequence ontology transcript glyph |
| redgreen_box | The "redgreen_box" glyph |
| redgreen_segment | The "redgreen_segments" glyph |
| rndrect | The "round rect" glyph |
| ruler_arrow | The "ruler_arrow" glyph |
| segmented_keyglyph | The "segmented_keyglyph" glyph |
| segments | The "segments" glyph |
| span | The "span" glyph |
| splice_site | The "splice_site" glyph |
| toomany | The "too many to show" glyph |
| track | The "track" glyph |
| transcript(2) | The "transcript" glyph |
| transcript2 | The "transcript2" glyph |
| translation | The "6-frame translation" glyph |
| triangle | The "triangle" glyph |
| xyplot | The xyplot glyph |
| bioperl-live::Bio::Index | Top |
| Abstract | Abstract interface for indexing a flat file |
| AbstractSeq | Base class for AbstractSeq s |
| Blast(1) | Indexes Blast reports and supports retrieval based on query accession(s) |
| EMBL(2) | Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format). |
| Fasta(2) | Interface for indexing (multiple) fasta files |
| Fastq | Interface for indexing (multiple) fastq files |
| GenBank(3) | Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format). |
| SwissPfam | Interface for indexing swisspfam files |
| Swissprot | Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). |
| bioperl-live::Bio::LiveSeq | Top |
| AARange | AARange abstract class for LiveSeq |
| Chain(2) | DoubleChain DataStructure for Perl |
| ChainI | Double linked chain data structure |
| DNA | DNA object for LiveSeq |
| Exon(1) | Range abstract class for LiveSeq |
| Gene(1) | Range abstract class for LiveSeq |
| Intron(1) | 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(1) | Transcript class for LiveSeq |
| Translation | Translation class for LiveSeq |
| bioperl-live::Bio::LiveSeq::IO | Top |
| BioPerl | Loader for LiveSeq from EMBL entries with BioPerl |
| Loader | Parent Loader for LiveSeq |
| SRS | Loader for LiveSeq from EMBL entries with SRS |
| 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(1) | 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::Map | Top |
| CytoMap | A Bio::MapI compliant map implementation handling cytogenic bands |
| CytoMarker | An object representing a marker. |
| CytoPosition | Marker class with cytogenetic band storing attributes |
| 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 |
| MappableI | An object that can be placed in a map |
| Marker | An central map object representing a generic marker that can have multiple location in several maps. |
| MarkerI | 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. |
| Position | A single position of a Marker in a Map |
| PositionI | Abstracts the notion of a position having a value in the context of a marker and a Map |
| SimpleMap | A MapI implementation handling the basics of a Map |
| bioperl-live::Bio::MapIO | Top |
| mapmaker | A Mapmaker Map reader |
| bioperl-live::Bio::Matrix | Top |
| PhylipDist | A Phylip Distance Matrix object |
| bioperl-live::Bio::Ontology | Top |
| GOterm | representation of GO terms |
| InterProTerm | Implementation of InterProI term interface |
| 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 |
| SimpleGOEngine | a Ontology Engine for GO implementing OntologyEngineI |
| SimpleOntologyEngine | Implementation of OntologyEngineI interface |
| Term | 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::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 |
| soflat | a parser for the Sequence Ontology flat-file format |
| bioperl-live::Bio::OntologyIO::Handlers | Top |
| InterProHandler | XML handler class for InterProParser |
| 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::Root | Top |
| Err | Exception class for Perl 5 objects |
| Exception | Generic exception objects for Bioperl |
| Global | Global variables and utility functions |
| HTTPget | module for fallback HTTP get operations when LWP:: is unavailable |
| IO(3) | module providing several methods often needed when dealing with file IO |
| IOManager | Input and output manager for Perl5 objects. |
| Object | A core Perl 5 object. |
| Root | Hash-based implementation of Bio::Root::RootI |
| RootI | Abstract interface to root object code |
| Utilities(2) | General-purpose utility module |
| Vector | Interface for managing linked lists of Perl5 objects. |
| Xref | A generic cross-reference object.
B |
| bioperl-live::Bio::Search | Top |
| 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 |
| Processor | DESCRIPTION of Object |
| SearchUtils | Utility functions for Bio::Search:: objects |
| bioperl-live::Bio::Search::HSP | Top |
| BlastHSP | Bioperl BLAST High-Scoring Pair object |
| 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 | Interface for a High Scoring Pair in a similarity search result |
| WABAHSP | HSP object suitable for describing WABA alignments |
| bioperl-live::Bio::Search::Hit | Top |
| BlastHit | Bioperl BLAST Hit object |
| Fasta(3) | 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 |
| bioperl-live::Bio::Search::Result | Top |
| BlastResult | A top-level BLAST Report object |
| GenericResult | Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results. |
| HMMERResult | A Result object for HMMER results |
| 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::SearchIO | Top |
| EventHandlerI(2) | An abstract Event Handler for Search Result parsing |
| FastHitEventBuilder | Event Handler for SearchIO events. |
| SearchResultEventBuilder | Event Handler for SearchIO events. |
| SearchWriterI | Interface for outputting parsed Search results |
| blast | Event generator for event based parsing of blast reports |
| blastxml | A SearchIO implementation of NCBI Blast XML parsing. |
| chado(1) | chado sequence input/output stream |
| chadosxpr(1) | chadosxpr sequence input/output stream |
| exonerate | parser for Exonerate |
| fasta(3) | A SearchIO parser for FASTA results |
| hmmer | A parser for HMMER output (hmmpfam, hmmsearch) |
| psiblast | Parser for traditional BLAST and PSI-BLAST reports |
| waba | SearchIO parser for Jim Kent WABA program alignment output |
| bioperl-live::Bio::SearchIO::Writer | Top |
| HSPTableWriter | Tab-delimited data for Bio::Search::HSP::HSPI objects |
| HTMLResultWriter | Object to implement writing 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::Seq | Top |
| BaseSeqProcessor | Base implementation for a SequenceProcessor |
| EncodedSeq | subtype of L |
| 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 |
| PrimaryQual | Bioperl lightweight Quality Object |
| PrimedSeq | |
| QualI | Interface definition for a Bio::Seq::Qual |
| RichSeq | Module implementing a sequence created from a rich sequence database entry |
| RichSeqI | RichSeq interface, mainly for database orientated sequences |
| 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 |
| SequenceTrace | Bioperl object packaging a sequence with its trace |
| TraceI | Interface definition for a Bio::Seq::Trace |
| bioperl-live::Bio::SeqFeature | Top |
| AnnotationAdaptor | integrates SeqFeatureIs annotation |
| Collection(3) | 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 | Generic SeqFeature |
| 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. |
| bioperl-live::Bio::SeqFeature::Gene | Top |
| Exon(2) | 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(2) | DESCRIPTION of Object |
| NC_Feature | DESCRIPTION of Object |
| Poly_A_site | DESCRIPTION of Object |
| Promoter | Describes a promotor |
| Transcript(2) | 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 transcription unit |
| 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(3) | ace sequence input/output stream |
| alf | alf trace sequence input/output stream |
| bsml | BSML sequence input/output stream |
| chado(2) | chado sequence input/output stream |
| chadoitext | chadoitext sequence input/output stream |
| chadosxpr(2) | chadosxpr sequence input/output stream |
| chadoxml | chadoxml sequence input/output stream |
| ctf | ctf trace sequence input/output stream |
| embl(2) | EMBL sequence input/output stream |
| exp | exp trace sequence input/output stream |
| fasta(4) | fasta sequence input/output stream |
| fastq | fastq sequence input/output stream |
| game | Parses GAME XML 0.1 and higher into and out of Bio::Seq objects. |
| gcg | GCG sequence input/output stream |
| genbank | GenBank sequence input/output stream |
| largefasta | method i/o on very large fasta sequence files |
| locuslink | DESCRIPTION of Object |
| 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 |
| swiss | Swissprot sequence input/output stream |
| ztr | ztr trace sequence input/output stream |
| bioperl-live::Bio::SeqIO::game | Top |
| featureHandler | GAME helper via PerlSAX helper. |
| idHandler | GAME helper via PerlSAX helper. |
| seqHandler | GAME helper via PerlSAX helper. |
| bioperl-live::Bio::Structure | Top |
| Atom | Bioperl structure Object, describes an Atom |
| Chain(3) | Bioperl structure Object, describes a chain |
| Entry | Bioperl structure Object, describes the whole entry |
| IO(4) | 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::IO | Top |
| pdb | PDB input/output stream |
| 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::Symbol | Top |
| Alphabet | DESCRIPTION of Object |
| 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 |
| bioperl-live::Bio::Taxonomy | Top |
| Taxon | Generic Taxonomic Entity object |
| Tree(1) | An Organism Level Implementation of TreeI interface. |
| bioperl-live::Bio::Tools | Top |
| 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(2) | 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(2) | 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 |
| bioperl-live::Bio::Tools::Alignment | Top |
| Consed | A module to work with objects from consed .ace files |
| Trim |
| bioperl-live::Bio::Tools::BPlite | Top |
| HSP(1) | Blast report High Scoring Pair (HSP) |
| Iteration | object for parsing single iteration of a PSIBLAST report |
| Sbjct(1) | A Blast Subject (database search Hit) |
| bioperl-live::Bio::Tools::Blast | Top |
| HSP(2) | Bioperl BLAST High-Scoring Segment Pair object |
| HTML | Bioperl Utility module for HTML formatting Blast reports |
| Sbjct(2) | Bioperl BLAST "Hit" object |
| bioperl-live::Bio::Tools::HMMER | Top |
| Domain | One particular domain hit from HMMER |
| Results(1) | Object representing HMMER output results |
| Set | Set of identical domains from HMMER matches |
| bioperl-live::Bio::Tools::Phylo | Top |
| Molphy | DESCRIPTION of Object |
| PAML | Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 |
| bioperl-live::Bio::Tools::Phylo::Molphy | Top |
| Result(2) | DESCRIPTION of Object |
| bioperl-live::Bio::Tools::Phylo::PAML | Top |
| Result(3) | A PAML result set object |
| bioperl-live::Bio::Tools::Phylo::Phylip | Top |
| ProtDist | DESCRIPTION of Object |
| bioperl-live::Bio::Tools::Prediction | Top |
| Exon(3) | A predicted exon feature |
| Gene(2) | a predicted gene structure feature |
| bioperl-live::Bio::Tools::Run | Top |
| 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) |
| WrapperBase | A Base object for wrappers around executables |
| bioperl-live::Bio::Tools::Sim4 | Top |
| Exon(4) | A single exon determined by an alignment |
| Results(2) | Results of one Sim4 run |
| bioperl-live::Bio::Tools::StateMachine | Top |
| AbstractStateMachine | Abstract state machine object |
| IOStateMachine | IO-based implementation of AbstractStateMachine |
| bioperl-live::Bio::Tree | Top |
| AlleleNode | DESCRIPTION of Object |
| Node | A Simple Tree Node |
| NodeI | Interface describing a Tree Node |
| NodeNHX | A Simple Tree Node with support for NHX tags |
| RandomFactory | TreeFactory for generating Random Trees |
| Statistics | Calculate certain statistics for a Tree |
| Tree(2) | 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::TreeIO | Top |
| TreeEventBuilder | Build Bio::Tree::Tree's and Bio::Tree::Node's from Events |
| newick | TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. |
| nhx | TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format. |
| tabtree | A simple output format which displays a tree as an ASCII drawing |
| 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(5) | 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::doc | Top |
Nothing here |
| bioperl-live::doc::faq | Top |
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| bioperl-live::doc::howto | Top |
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| bioperl-live::doc::howto::examples | Top |
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| bioperl-live::doc::howto::examples::graphics | Top |
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| bioperl-live::doc::howto::figs | Top |
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| bioperl-live::doc::howto::figs::graphics | Top |
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| bioperl-live::doc::howto::html | Top |
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| bioperl-live::doc::howto::pdf | Top |
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| bioperl-live::doc::howto::sgml | Top |
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| bioperl-live::examples | Top |
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| bioperl-live::examples::biographics | Top |
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| bioperl-live::examples::ontology | Top |
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| bioperl-live::examples::searchio | Top |
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| bioperl-live::models | Top |
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| bioperl-live::scripts | Top |
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| bioperl-live::scripts::Bio-DB-GFF | Top |
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| bioperl-live::scripts::DB | Top |
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| bioperl-live::scripts::align | Top |
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| bioperl-live::scripts::biblio | Top |
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| bioperl-live::scripts::biographics | Top |
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| bioperl-live::scripts::cluster | Top |
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| bioperl-live::scripts::contributed | Top |
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| bioperl-live::scripts::das | Top |
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| bioperl-live::scripts::exceptions | Top |
| Error | |
| Simple(2) | |
| TestInterface | A simple subclass of Interface |
| TestObject | An implementation of TestInterface |
| subs | Error/exception handling in an OO-ish way |
| bioperl-live::scripts::graphics | Top |
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| bioperl-live::scripts::index | Top |
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| bioperl-live::scripts::liveseq | Top |
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| bioperl-live::scripts::root_object | Top |
| Bar | |
| Foo | |
| Outer |
| bioperl-live::scripts::searchio | Top |
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| bioperl-live::scripts::seq | Top |
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| bioperl-live::scripts::seqstats | Top |
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| bioperl-live::scripts::structure | Top |
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| bioperl-live::scripts::taxa | Top |
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| bioperl-live::scripts::tk | Top |
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| bioperl-live::scripts::tools | Top |
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| bioperl-live::scripts::tree | Top |
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| bioperl-live::scripts::utilities | Top |
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| bioperl-live::t | Top |
| Test | provides a simple framework for writing test scripts |
| bioperl-live::t::data | Top |
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| bioperl-live::t::data::biodbgff | Top |
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| bioperl-live::t::data::biographics | Top |
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| bioperl-live::t::data::biographics::t1 | Top |
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| bioperl-live::t::data::biographics::t2 | Top |
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| bioperl-live::t::data::biographics::t3 | Top |
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| bioperl-live::t::data::consed_project | Top |
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| bioperl-live::t::data::consed_project::edit_dir | Top |
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| bioperl-live::t::data::consed_project::phd_dir | Top |
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| bioperl-live::t::data::dbfa | Top |