| 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 |
| 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 HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) |
| hmmer2 | A parser for HMMER output (hmmpfam, hmmsearch) |
| hmmer3 | DESCRIPTION of Object |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Bio::Index::Stockholm |
| SwissPfam | Interface for indexing swisspfam files |
| Swissprot | Interface for indexing one or more
Swissprot files. |
| BaseSeqProcessor | Base implementation for a SequenceProcessor |
| EncodedSeq | subtype of L to store DNA that encodes a protein |
| 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 |
| SimulatedRead | Read with sequencing errors taken from a reference sequence |
| TraceI | Interface definition for a Bio::Seq::Trace |
| 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 |
| gbxml | GenBank sequence input/output stream using SAX |
| 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 |
| mbsout | input stream for output by Teshima et al.'s mbs. |
| metafasta(2) | metafasta sequence input/output stream |
| msout | input stream for output by Hudson's ms |
| 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 |
| 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 |
| 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 |
| 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 |
| 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. |
| 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 |
| 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 |
| NewickParser | which implements a newick string parser as a finite state
machine which enables it to parse the full Newick specification.
Taken largely from the Ensembl Compara file with the same name
(Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the
parser to work with BioPerl's event handler-based parsing scheme.
This module is used by nhx.pm and newick.pm, and is NOT called
directly. Instead, both of those parsing modules extend this module in
order to gain access to the main parsing method. |
| 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 | Bio::TreeIO::newick |
| 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 |
| 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 |
| Build(2) | 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 |
| 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) | |
| FeatureIterator(1) | |
| 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 |
| 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 |
| 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. |
| hmmer3Hit | DESCRIPTION of Object |
| 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 |
| hmmer3HSP | DESCRIPTION of Object |
| 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 output |
| 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 |
| EUtilDataI | eutil data object interface |
| EUtilParameters | Manipulation of NCBI eutil-based
parameters for remote database requests. |
| History | 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 handling data output (XML) from
esummary. |