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bioperl-1.4
++

Changes for version 1.4

  • Since initial 1.2.0, 3000 separate changes have been made to make this release.
    • o installable scripts
    • o global module version from Bio::Root:Version
    • o Bio::Graphics
      • major improvements; SVG support
    • o Bio::Popgen
      • population genetics
      • support several population genetics types of questions.
      • Tests for statistical neutrality of mutations (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics. Tests of population structure (Wright's F-statistic: Fst) is in Bio::PopGen::PopStats. Calculating composite linkage disequilibrium (LD) is available in Bio::PopGen::Statistics as well.
      • Bio::PopGen::IO for reading in prettybase (SeattleSNPs) and csv (comma delimited formatted) data.
      • a directory for implementing population simulations has been added Bio::PopGen::Simulation and 2 simulations - a Coalescent and a simple single-locus multi-allele genetic drift simulation have been provided. This replaces the code in Bio::Tree::RandomTree which has been deprecated until proper methods for generating random phylogenetic trees are implemented.
    • o Bio::Restriction
      • new restrion analysis modules
    • o Bio::Tools::Analysis
      • web based DNA and Protein analysis framework and several implementations
    • o Bio::Seq::Meta
      • per residue annotable sequences
    • o Bio::Matrix
      • Bio::Matrix::PSM - Position Scoring Matrix
      • Bio::Matrix::IO has been added for generalized parsing of matrix data. Matrix::IO::scoring and Matrix::IO::phylip are initial implementations for parsing BLOSUM/PAM and Phylip Distance matricies respectively. A generic matrix implementation for general use was added in Bio::Matrix::Generic.
    • o Bio::Ontology
      • major changes
    • o Bio:Tree
    • o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
      • small inhibitory RNA
    • o Bio::SeqFeature::Tools
      • seqFeature mapping tools
      • Bio::SeqFeature::Tools::Unflattener.pm
        • deal with mapping GenBank feature collections into Chado/GFF3 processable feature sets (with SO term mappings)
    • o Bio::Tools::dpAlign
      • pure perl dynamic programming sequence alignment
      • needs Bioperl-ext
    • o new Bio::SearchIO formats
    • o new Bio::SeqIO formats
      • chado, tab, kegg, tigr, game
      • axt and psl: UCSC formats.
      • blasttable: NCBI -m 8 or -m 9 format from blastall
      • important fixes for old modules
    • o Bio::AlignIO: maf
    • o improved Bio::Tools::Genewise
    • o Bio::SeqIO now can recongnize sequence formats automatically from stream
    • o new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
    • o Bio::DB::Registry bugs fixed
      • BerkeleyDB-indexed flat files can be used by the OBDA system
      • Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all used by the OBDA system
    • o several new HOWTOs
      • SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat Databases
    • o hundreds of new and improved files
    • o o Bio::Tree::AlleleNode has been updated to be a container of an Bio::PopGen::Individual object for use in the Coalescent simulations.

Changes for version 1.4

Documentation

Bioperl
Biodesign
Bioperl
Bioscripts
BioPerlTutorial
a tutorial for bioperl
authors.pl
check modules and scripts for authors not in AUTHORS file
modules.pl
information about modules in BioPerl core
pod.pl
check the POD documentation syntax in modules and scripts

Modules

Bio::Align::AlignI
An interface for describing sequence alignments.
Bio::Align::DNAStatistics
Calculate some statistics for a DNA alignment
Bio::Align::PairwiseStatistics
Base statistic object for Pairwise Alignments
Bio::Align::StatisticsI
Calculate some statistics for an alignment
Bio::Align::Utilities
A collection of utilities regarding converting and manipulating alignment objects
Bio::AlignIO
Handler for AlignIO Formats
Bio::AlignIO::bl2seq
bl2seq sequence input/output stream
Bio::AlignIO::clustalw
clustalw sequence input/output stream
Bio::AlignIO::emboss
Parse EMBOSS alignment output (from applications water and needle)
Bio::AlignIO::fasta
FastA MSA Sequence input/output stream
Bio::AlignIO::maf
Multipla Alignment Format sequence input stream
Bio::AlignIO::mase
mase sequence input/output stream
Bio::AlignIO::mega
Parse and Create MEGA format data files
Bio::AlignIO::meme
meme sequence input/output stream
Bio::AlignIO::metafasta
Metafasta MSA Sequence input/output stream
Bio::AlignIO::msf
msf sequence input/output stream
Bio::AlignIO::nexus
NEXUS format sequence input/output stream
Bio::AlignIO::pfam
pfam sequence input/output stream
Bio::AlignIO::phylip
PHYLIP format sequence input/output stream
Bio::AlignIO::prodom
prodom sequence input/output stream
Bio::AlignIO::psi
Read/Write PSI-BLAST profile alignment files
Bio::AlignIO::selex
selex sequence input/output stream
Bio::AlignIO::stockholm
stockholm sequence input/output stream
Bio::AnalysisI
An interface to any (local or remote) analysis tool
Bio::AnalysisParserI
Generic analysis output parser interface
Bio::AnalysisResultI
Interface for analysis result objects
Bio::AnnotatableI
the base interface an annotatable object must implement
Bio::Annotation::AnnotationFactory
Instantiates a new Bio::AnnotationI (or derived class) through a factory
Bio::Annotation::Collection
Default Perl implementation of AnnotationCollectionI
Bio::Annotation::Comment
A comment object, holding text
Bio::Annotation::DBLink
DESCRIPTION of Object
Bio::Annotation::OntologyTerm
An ontology term adapted to AnnotationI
Bio::Annotation::Reference
Specialised DBLink object for Literature References
Bio::Annotation::SimpleValue
A simple scalar
Bio::Annotation::StructuredValue
A scalar with embedded structured information
Bio::Annotation::TypeManager
Manages types for annotation collections
Bio::AnnotationCollectionI
Interface for annotation collections
Bio::AnnotationI
Annotation interface
Bio::Assembly::Contig
Perl module to hold and manipulate sequence assembly contigs.
Bio::Assembly::ContigAnalysis
Perform analysis on sequence assembly contigs.
Bio::Assembly::IO
Handler for Assembly::IO Formats
Bio::Assembly::IO::ace
module to load phrap ACE files.
Bio::Assembly::IO::phrap
driver to load phrap.out files.
Bio::Assembly::Scaffold
Perl module to hold and manipulate sequence assembly data.
Bio::Assembly::ScaffoldI
Abstract Inteface of Sequence Assemblies
Bio::Biblio
A Bibliographic Query Service module
Bio::Biblio::Article
Representation of a general article
Bio::Biblio::BiblioBase
An abstract base for other biblio classes
Bio::Biblio::Book
Representation of a book
Bio::Biblio::BookArticle
Representation of a book article
Bio::Biblio::IO
Handling the bibliographic references
Bio::Biblio::IO::medline2ref
A converter of a raw hash to MEDLINE citations
Bio::Biblio::IO::medlinexml
A converter of XML files with MEDLINE citations
Bio::Biblio::IO::pubmed2ref
A converter of a raw hash to PUBMED citations
Bio::Biblio::IO::pubmedxml
A converter of XML files with PUBMED citations
Bio::Biblio::Journal
Representation of a journal
Bio::Biblio::JournalArticle
Representation of a journal article
Bio::Biblio::MedlineArticle
Representation of a MEDLINE article
Bio::Biblio::MedlineBook
Representation of a MEDLINE book
Bio::Biblio::MedlineBookArticle
Representation of a MEDLINE book article
Bio::Biblio::MedlineJournal
Representation of a MEDLINE journal
Bio::Biblio::MedlineJournalArticle
Representation of a MEDLINE journal article
Bio::Biblio::Organisation
Representation of an organisation
Bio::Biblio::Patent
Representation of a patent
Bio::Biblio::Person
Representation of a person
Bio::Biblio::Proceeding
Representation of a conference proceeding
Bio::Biblio::Provider
Representation of a general provider
Bio::Biblio::PubmedArticle
Representation of a PUBMED article
Bio::Biblio::PubmedBookArticle
Representation of a PUBMED book article
Bio::Biblio::PubmedJournalArticle
Representation of a PUBMED journal article
Bio::Biblio::Ref
Representation of a bibliographic reference
Bio::Biblio::Service
Representation of a provider of type service
Bio::Biblio::TechReport
Representation of a technical report
Bio::Biblio::Thesis
Representation of thesis
Bio::Biblio::WebResource
Representation of a web resource
Bio::Cluster::ClusterFactory
Instantiates a new Bio::ClusterI (or derived class) through a factory
Bio::Cluster::FamilyI
Family Interface
Bio::Cluster::SequenceFamily
Sequence Family object
Bio::Cluster::UniGene
UniGene object
Bio::Cluster::UniGeneI
abstract interface of UniGene object
Bio::ClusterI
Cluster Interface
Bio::ClusterIO
Handler for Cluster Formats
Bio::ClusterIO::dbsnp
dbSNP input stream
Bio::ClusterIO::unigene
UniGene input stream
Bio::CodonUsage::IO
for reading and writing codon usage tables to file
Bio::CodonUsage::Table
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::Coordinate::Chain
Mapping locations through a chain of coordinate mappers
Bio::Coordinate::Collection
Noncontinuous match between two coordinate sets
Bio::Coordinate::ExtrapolatingPair
Continuous match between two coordinate sets
Bio::Coordinate::GeneMapper
transformations between gene related coordinate systems
Bio::Coordinate::Graph
Finds shortest path between nodes in a graph
Bio::Coordinate::MapperI
Interface describing coordinate mappers
Bio::Coordinate::Pair
Continuous match between two coordinate sets
Bio::Coordinate::Result
Results from coordinate transformation
Bio::Coordinate::Result::Gap
Another name for Bio::Location::Simple
Bio::Coordinate::Result::Match
Another name for Bio::Location::Simple
Bio::Coordinate::ResultI
Interface to identify coordinate mapper results
Bio::Coordinate::Utils
Additional methods to create Bio::Coordinate objects
Bio::DB::Ace
Database object interface to ACeDB servers
Bio::DB::Biblio::biofetch
A BioFetch-based access to a bibliographic citation retrieval
Bio::DB::Biblio::soap
A SOAP-based access to a bibliographic query service
Bio::DB::BiblioI
An interface to a Bibliographic Query Service
Bio::DB::BioFetch
Database object interface to BioFetch retrieval
Bio::DB::CUTG
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Bio::DB::DBFetch
Database object for retrieving using the dbfetch script
Bio::DB::EMBL
Database object interface for EMBL entry retrieval
Bio::DB::Failover
A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs
Bio::DB::Fasta
Fast indexed access to a directory of fasta files
Bio::DB::FileCache
In file cache for BioSeq objects
Bio::DB::Flat
Interface for indexed flat files
Bio::DB::Flat::BDB
Interface for BioHackathon standard BDB-indexed flat file
Bio::DB::Flat::BDB::embl
embl adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::fasta
fasta adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::genbank
genbank adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::swiss
swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BDB::swissprot
swissprot adaptor for Open-bio standard BDB-indexed flat file
Bio::DB::Flat::BinarySearch
BinarySearch search indexing system for sequence files
Bio::DB::GDB
Database object interface to GDB HTTP query
Bio::DB::GFF
Storage and retrieval of sequence annotation data
Bio::DB::GFF::Adaptor::ace
ace interface (for multiple inheritance)
Bio::DB::GFF::Adaptor::biofetch
Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::biofetch_oracle
Cache BioFetch objects in a Bio::DB::GFF database
Bio::DB::GFF::Adaptor::dbi
Database adaptor for DBI (SQL) databases
Bio::DB::GFF::Adaptor::dbi::caching_handle
Cache for database handles
Bio::DB::GFF::Adaptor::dbi::iterator
iterator for Bio::DB::GFF::Adaptor::dbi
Bio::DB::GFF::Adaptor::dbi::mysql
Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::dbi::mysqlace
Unholy union between mysql GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::mysqlopt
Deprecated database adaptor
Bio::DB::GFF::Adaptor::dbi::oracle
Database adaptor for a specific oracle schema
Bio::DB::GFF::Adaptor::dbi::oracleace
Unholy union between oracle GFF database and acedb database
Bio::DB::GFF::Adaptor::dbi::pg
Database adaptor for a specific postgres schema
Bio::DB::GFF::Adaptor::memory
Database adaptor for a specific mysql schema
Bio::DB::GFF::Adaptor::memory_iterator
iterator for Bio::DB::GFF::Adaptor::memory
Bio::DB::GFF::Aggregator
Aggregate GFF groups into composite features
Bio::DB::GFF::Aggregator::alignment
Alignment aggregator
Bio::DB::GFF::Aggregator::clone
Clone aggregator
Bio::DB::GFF::Aggregator::coding
The Coding Region Aggregator
Bio::DB::GFF::Aggregator::match
Match aggregator
Bio::DB::GFF::Aggregator::none
No aggregation
Bio::DB::GFF::Aggregator::processed_transcript
Sequence Ontology Transcript
Bio::DB::GFF::Aggregator::transcript
Transcript aggregator
Bio::DB::GFF::Aggregator::ucsc_acembly
UCSC acembly aggregator
Bio::DB::GFF::Aggregator::ucsc_ensgene
UCSC ensGene aggregator
Bio::DB::GFF::Aggregator::ucsc_genscan
UCSC genscan aggregator
Bio::DB::GFF::Aggregator::ucsc_refgene
UCSC refGene aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22
UCSC sanger22 aggregator
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo
UCSC sanger22pseudo aggregator
Bio::DB::GFF::Aggregator::ucsc_softberry
UCSC softberry aggregator
Bio::DB::GFF::Aggregator::ucsc_twinscan
UCSC twinscan aggregator
Bio::DB::GFF::Aggregator::ucsc_unigene
UCSC UniGene aggregator
Bio::DB::GFF::Featname
The name of a feature
Bio::DB::GFF::Feature
A relative segment identified by a feature type
Bio::DB::GFF::Homol
A segment of DNA that is homologous to another
Bio::DB::GFF::RelSegment
Sequence segment with relative coordinate support
Bio::DB::GFF::Segment
Simple DNA segment object
Bio::DB::GFF::Typename
The name of a feature type
Bio::DB::GFF::Util::Binning
binning utility for Bio::DB::GFF index
Bio::DB::GFF::Util::Rearrange
rearrange utility
Bio::DB::GenBank
Database object interface to GenBank
Bio::DB::GenPept
Database object interface to GenPept
Bio::DB::InMemoryCache
Abstract interface for a sequence database
Bio::DB::MeSH
Term retrieval from a Web MeSH database
Bio::DB::NCBIHelper
A collection of routines useful for queries to NCBI databases.
Bio::DB::Query::GenBank
Build a GenBank Entrez Query
Bio::DB::Query::WebQuery
Helper class for web-based sequence queryies
Bio::DB::QueryI
Object Interface to queryable sequence databases
Bio::DB::RandomAccessI
Abstract interface for a sequence database
Bio::DB::RefSeq
Database object interface for RefSeq retrieval
Bio::DB::Registry
Access to the Open Bio Database Access registry scheme
Bio::DB::SeqI
Abstract Interface for Sequence databases
Bio::DB::SwissProt
Database object interface to SwissProt retrieval
Bio::DB::Taxonomy
Access to a taxonomy database
Bio::DB::Taxonomy::entrez
Taxonomy Entrez driver
Bio::DB::Taxonomy::flatfile
An implementation of Bio::DB::Taxonomy which uses local flat files
Bio::DB::Universal
Artificial database that delegates to specific databases
Bio::DB::UpdateableSeqI
An interface for writing to a database of sequences.
Bio::DB::WebDBSeqI
Object Interface to generalize Web Databases for retrieving sequences
Bio::DB::XEMBL
Database object interface for XEMBL entry retrieval
Bio::DB::XEMBLService
SOAP service definition for XEMBL
Bio::DBLinkContainerI
Abstract interface for any object wanting to use database cross references
Bio::Das::FeatureTypeI
Simple interface to Sequence Ontology feature types
Bio::Das::SegmentI
DAS-style access to a feature database
Bio::DasI
DAS-style access to a feature database
Bio::DescribableI
interface for objects with human readable names and descriptions
Bio::Event::EventGeneratorI
This interface describes the basic event generator class.
Bio::Event::EventHandlerI
An Event Handler Interface
Bio::Expression::FeatureGroup
a set of DNA/RNA features. ISA Bio::Expression::FeatureI
Bio::Expression::FeatureI
an interface class for DNA/RNA features
Bio::Factory::AnalysisI
An interface to analysis tool factory
Bio::Factory::ApplicationFactoryI
Interface class for Application Factories
Bio::Factory::DriverFactory
Base class for factory classes loading drivers
Bio::Factory::FTLocationFactory
A FeatureTable Location Parser
Bio::Factory::HitFactoryI
Interface for an object that builds Bio::Search::Hit::HitI objects
Bio::Factory::LocationFactoryI
DESCRIPTION of Interface
Bio::Factory::MapFactoryI
A Factory for getting markers
Bio::Factory::ObjectBuilderI
Interface for an object builder
Bio::Factory::ObjectFactory
Instantiates a new Bio::Root::RootI (or derived class) through a factory
Bio::Factory::ObjectFactoryI
A General object creator factory
Bio::Factory::ResultFactoryI
Interface for an object that builds Bio::Search::Result::ResultI objects
Bio::Factory::SeqAnalysisParserFactory
class capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SeqAnalysisParserFactoryI
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Bio::Factory::SequenceFactoryI
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Bio::Factory::SequenceProcessorI
Interface for chained sequence processing algorithms
Bio::Factory::SequenceStreamI
Interface describing the basics of a Sequence Stream.
Bio::Factory::TreeFactoryI
Factory Interface for getting and writing trees from/to a data stream
Bio::FeatureHolderI
the base interface an object with features must implement
Bio::Graphics
Generate GD images of Bio::Seq objects
Bio::Graphics::ConfiguratorI
A sectioned map of configuration options (a map of maps), with a default section. Intended to augment existing tag-gtvalue semantics (ie. of Bio::AnnotationCollectionI) for object-representation information (eg. foreground color), and for general interface preferences (eg. image width in gbrowse).
Bio::Graphics::Feature
A simple feature object for use with Bio::Graphics::Panel
Bio::Graphics::FeatureFile
A set of Bio::Graphics features, stored in a file
Bio::Graphics::FeatureFile::Iterator
Iterator across a Bio::Graphics::FeatureFile
Bio::Graphics::Glyph
Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::Factory
Factory for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph::alignment
The "alignment" glyph
Bio::Graphics::Glyph::anchored_arrow
The "anchored_arrow" glyph
Bio::Graphics::Glyph::arrow
The "arrow" glyph
Bio::Graphics::Glyph::box
The "box" glyph
Bio::Graphics::Glyph::cds
The "cds" glyph
Bio::Graphics::Glyph::crossbox
The "crossbox" glyph
Bio::Graphics::Glyph::diamond
The "diamond" glyph
Bio::Graphics::Glyph::dna
The "dna" glyph
Bio::Graphics::Glyph::dot
The "dot" glyph
Bio::Graphics::Glyph::ellipse
The "ellipse" glyph
Bio::Graphics::Glyph::ex
The "crossbox" glyph
Bio::Graphics::Glyph::extending_arrow
The "extending arrow" glyph
Bio::Graphics::Glyph::generic
The "generic" glyph
Bio::Graphics::Glyph::graded_segments
The "graded_segments" glyph
Bio::Graphics::Glyph::group
The "group" glyph
Bio::Graphics::Glyph::heterogeneous_segments
The "heterogeneous_segments" glyph
Bio::Graphics::Glyph::line
The "line" glyph
Bio::Graphics::Glyph::minmax
The minmax glyph
Bio::Graphics::Glyph::oval
The "oval" glyph
Bio::Graphics::Glyph::pinsertion
The "Drosophila P-element Insertion" glyph
Bio::Graphics::Glyph::primers
The "STS primers" glyph
Bio::Graphics::Glyph::processed_transcript
The sequence ontology transcript glyph
Bio::Graphics::Glyph::redgreen_box
The "redgreen_box" glyph
Bio::Graphics::Glyph::redgreen_segment
The "redgreen_segments" glyph
Bio::Graphics::Glyph::rndrect
The "round rect" glyph
Bio::Graphics::Glyph::ruler_arrow
The "ruler_arrow" glyph
Bio::Graphics::Glyph::segmented_keyglyph
The "segmented_keyglyph" glyph
Bio::Graphics::Glyph::segments
The "segments" glyph
Bio::Graphics::Glyph::span
The "span" glyph
Bio::Graphics::Glyph::splice_site
The "splice_site" glyph
Bio::Graphics::Glyph::toomany
The "too many to show" glyph
Bio::Graphics::Glyph::track
The "track" glyph
Bio::Graphics::Glyph::transcript
The "transcript" glyph
Bio::Graphics::Glyph::transcript2
The "transcript2" glyph
Bio::Graphics::Glyph::translation
The "6-frame translation" glyph
Bio::Graphics::Glyph::triangle
The "triangle" glyph
Bio::Graphics::Glyph::xyplot
The xyplot glyph
Bio::Graphics::Panel
Generate GD images of Bio::Seq objects
Bio::Graphics::Pictogram
Bio::Graphics::RendererI
A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
Bio::IdCollectionI
interface for objects with multiple identifiers
Bio::IdentifiableI
interface for objects with identifiers
Bio::Index::Abstract
Abstract interface for indexing a flat file
Bio::Index::AbstractSeq
Base class for AbstractSeq s
Bio::Index::Blast
Indexes Blast reports and supports retrieval based on query accession(s)
Bio::Index::EMBL
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Bio::Index::Fasta
Interface for indexing (multiple) fasta files
Bio::Index::Fastq
Interface for indexing (multiple) fastq files
Bio::Index::GenBank
Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format).
Bio::Index::SwissPfam
Interface for indexing swisspfam files
Bio::Index::Swissprot
Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).
Bio::LiveSeq::AARange
AARange abstract class for LiveSeq
Bio::LiveSeq::Chain
DoubleChain DataStructure for Perl
Bio::LiveSeq::ChainI
Double linked chain data structure
Bio::LiveSeq::DNA
DNA object for LiveSeq
Bio::LiveSeq::Exon
Range abstract class for LiveSeq
Bio::LiveSeq::Gene
Range abstract class for LiveSeq
Bio::LiveSeq::IO::BioPerl
Loader for LiveSeq from EMBL entries with BioPerl
Bio::LiveSeq::IO::Loader
Parent Loader for LiveSeq
Bio::LiveSeq::IO::SRS
Loader for LiveSeq from EMBL entries with SRS
Bio::LiveSeq::Intron
Range abstract class for LiveSeq
Bio::LiveSeq::Mutation
Mutation event descriptor class
Bio::LiveSeq::Mutator
Package mutating LiveSequences
Bio::LiveSeq::Prim_Transcript
Prim_Transcript class for LiveSeq
Bio::LiveSeq::Range
Range abstract class for LiveSeq
Bio::LiveSeq::Repeat_Region
Repeat_Region class for LiveSeq
Bio::LiveSeq::Repeat_Unit
Repeat_Unit class for LiveSeq
Bio::LiveSeq::SeqI
Abstract sequence interface class for LiveSeq
Bio::LiveSeq::Transcript
Transcript class for LiveSeq
Bio::LiveSeq::Translation
Translation class for LiveSeq
Bio::LocatableSeq
A Sequence object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
Bio::Location::Atomic
Implementation of a Atomic Location on a Sequence
Bio::Location::AvWithinCoordPolicy
class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Bio::Location::CoordinatePolicyI
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Bio::Location::Fuzzy
Implementation of a Location on a Sequence which has unclear start and/or end locations
Bio::Location::FuzzyLocationI
Abstract interface of a Location on a Sequence which has unclear start/end location
Bio::Location::NarrowestCoordPolicy
class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Bio::Location::Simple
Implementation of a Simple Location on a Sequence
Bio::Location::Split
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::SplitLocationI
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
Bio::Location::WidestCoordPolicy
class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Bio::LocationI
Abstract interface of a Location on a Sequence
Bio::Map::CytoMap
A Bio::MapI compliant map implementation handling cytogenic bands
Bio::Map::CytoMarker
An object representing a marker.
Bio::Map::CytoPosition
Marker class with cytogenetic band storing attributes
Bio::Map::LinkageMap
A representation of a genetic linkage map.
Bio::Map::LinkagePosition
Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
Bio::Map::MapI
Interface for describing Map objects in bioperl
Bio::Map::MappableI
An object that can be placed in a map
Bio::Map::Marker
An central map object representing a generic marker that can have multiple location in several maps.
Bio::Map::MarkerI
Interface for basic marker functionality
Bio::Map::Microsatellite
An object representing a Microsatellite marker.
Bio::Map::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.
Bio::Map::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.
Bio::Map::Position
A single position of a Marker in a Map
Bio::Map::PositionI
Abstracts the notion of a position having a value in the context of a marker and a Map
Bio::Map::SimpleMap
A MapI implementation handling the basics of a Map
Bio::MapIO
A Map Factory object
Bio::MapIO::mapmaker
A Mapmaker Map reader
Bio::Matrix::Generic
A generic matrix implementation
Bio::Matrix::IO
A factory for Matrix parsing
Bio::Matrix::IO::phylip
A parser for PHYLIP distance matricies
Bio::Matrix::IO::scoring
A parser for PAM/BLOSUM matricies
Bio::Matrix::MatrixI
An interface for describing a Matrix
Bio::Matrix::PSM::IO
PSM parser
Bio::Matrix::PSM::IO::mast
PSM mast parser implementation
Bio::Matrix::PSM::IO::meme
PSM meme parser implementation
Bio::Matrix::PSM::IO::transfac
PSM transfac parser
Bio::Matrix::PSM::InstanceSite
A PSM site occurance
Bio::Matrix::PSM::InstanceSiteI
InstanceSite interface, holds an instance of a PSM
Bio::Matrix::PSM::Psm
handle combination of site matricies
Bio::Matrix::PSM::PsmHeader
PSM mast parser implementation
Bio::Matrix::PSM::PsmHeaderI
Bio::Matrix::PSM::PsmI
abstract interface to handler of site matricies
Bio::Matrix::PSM::SiteMatrix
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix)
Bio::Matrix::PSM::SiteMatrixI
SiteMatrix interface, holds a position scoring matrix (or position weight matrix)
Bio::Matrix::PhylipDist
A Phylip Distance Matrix object
Bio::Matrix::Scoring
Object which can hold scoring matrix information
Bio::Ontology::GOterm
representation of GO terms
Bio::Ontology::InterProTerm
Implementation of InterProI term interface
Bio::Ontology::Ontology
standard implementation of an Ontology
Bio::Ontology::OntologyEngineI
Interface a minimal Ontology implementation should satisfy
Bio::Ontology::OntologyI
Interface for an ontology implementation
Bio::Ontology::OntologyStore
A repository of ontologies
Bio::Ontology::Path
a path for an ontology term graph
Bio::Ontology::PathI
Interface for a path between ontology terms
Bio::Ontology::Relationship
a relationship for an ontology
Bio::Ontology::RelationshipFactory
Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Bio::Ontology::RelationshipI
Interface for a relationship between ontology terms
Bio::Ontology::RelationshipType
a relationship type for an ontology
Bio::Ontology::SimpleGOEngine
a Ontology Engine for GO implementing OntologyEngineI
Bio::Ontology::SimpleOntologyEngine
Implementation of OntologyEngineI interface
Bio::Ontology::Term
interface for ontology terms
Bio::Ontology::TermFactory
Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
Bio::Ontology::TermI
interface for ontology terms
Bio::OntologyIO
Parser factory for Ontology formats
Bio::OntologyIO::Handlers::BaseSAXHandler
Bio::OntologyIO::Handlers::InterProHandler
XML handler class for InterProParser
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
Bio::OntologyIO::InterProParser
Parser for InterPro xml files.
Bio::OntologyIO::dagflat
a base class parser for GO flat-file type formats
Bio::OntologyIO::goflat
a parser for the Gene Ontology flat-file format
Bio::OntologyIO::simplehierarchy
a base class parser for simple hierarchy-by-indentation type formats
Bio::OntologyIO::soflat
a parser for the Sequence Ontology flat-file format
Bio::Perl
Functional access to BioPerl for people who don't know objects
Bio::Phenotype::Correlate
Representation of a correlating phenotype in a given species
Bio::Phenotype::MeSH::Term
A MeSH term
Bio::Phenotype::MeSH::Twig
Context for a MeSH term
Bio::Phenotype::Measure
Representation of context/value(-range)/unit triplets
Bio::Phenotype::OMIM::MiniMIMentry
Representation of a Mini MIM entry
Bio::Phenotype::OMIM::OMIMentry
represents OMIM (Online Mendelian Inheritance in Man) database entries
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
Representation of a allelic variant of the OMIM database
Bio::Phenotype::OMIM::OMIMparser
parser for the OMIM database
Bio::Phenotype::Phenotype
A class for modeling phenotypes
Bio::Phenotype::PhenotypeI
An interface for classes modeling phenotypes
Bio::PopGen::Genotype
An implementation of a genotype which is an allele container
Bio::PopGen::GenotypeI
A marker and alleles for a specific individual
Bio::PopGen::IO
Input individual,marker,allele information
Bio::PopGen::IO::csv
Bio::PopGen::IO::prettybase
Extract individual allele data from PrettyBase format
Bio::PopGen::Individual
An implementation of an Individual who has Genotype or Sequence Results
Bio::PopGen::IndividualI
An individual who has Genotype or Sequence Results
Bio::PopGen::Marker
A genetic marker which one uses to generate genotypes
Bio::PopGen::MarkerI
A Population Genetic conceptual marker
Bio::PopGen::PopStats
A collection of methods for calculating statistics about a population or sets of populations
Bio::PopGen::Population
A population of individuals
Bio::PopGen::PopulationI
Interface for Populations
Bio::PopGen::Simulation::Coalescent
A Coalescent simulation factory
Bio::PopGen::Simulation::GeneticDrift
A simple genetic drift simulation
Bio::PopGen::Statistics
Population Genetics statistical tests
Bio::PrimarySeq
Bioperl lightweight Sequence Object
Bio::PrimarySeqI
Bio::Range
Pure perl RangeI implementation
Bio::RangeI
Range interface
Bio::Restriction::Analysis
cutting sequences with restriction enzymes
Bio::Restriction::Enzyme
A single restriction endonuclease (cuts DNA at specific locations)
Bio::Restriction::Enzyme::MultiCut
A single restriction endonuclease
Bio::Restriction::Enzyme::MultiSite
A single restriction endonuclease
Bio::Restriction::EnzymeCollection
Set of restriction endonucleases
Bio::Restriction::EnzymeI
Interface class for restriction endonuclease
Bio::Restriction::IO
Handler for sequence variation IO Formats
Bio::Restriction::IO::bairoch
bairoch enzyme set
Bio::Restriction::IO::base
base enzyme set
Bio::Restriction::IO::itype2
itype2 enzyme set
Bio::Restriction::IO::withrefm
withrefm enzyme set
Bio::Root::Err
Exception class for Perl 5 objects
Bio::Root::Exception
Generic exception objects for Bioperl
Bio::Root::Global
Global variables and utility functions
Bio::Root::HTTPget
module for fallback HTTP get operations when LWP:: is unavailable
Bio::Root::IO
module providing several methods often needed when dealing with file IO
Bio::Root::IOManager
Input and output manager for Perl5 objects.
Bio::Root::Object
A core Perl 5 object.
Bio::Root::Root
Hash-based implementation of Bio::Root::RootI
Bio::Root::RootI
Abstract interface to root object code
Bio::Root::Storable
object serialisation methods
Bio::Root::Utilities
General-purpose utility module
Bio::Root::Vector
Interface for managing linked lists of Perl5 objects.
Bio::Root::Version
provide global, distribution-level versioning
Bio::Root::Xref
A generic cross-reference object.
Bio::Search::BlastUtils
Utility functions for Bio::Search:: BLAST objects
Bio::Search::DatabaseI
Interface for a database used in a sequence search
Bio::Search::GenericDatabase
Generic implementation of Bio::Search::DatabaseI
Bio::Search::HSP::BlastHSP
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::FastaHSP
HSP object for FASTA specific data
Bio::Search::HSP::GenericHSP
A "Generic" implementation of a High Scoring Pair
Bio::Search::HSP::HMMERHSP
A HSP object for HMMER results
Bio::Search::HSP::HSPFactory
A factory to create Bio::Search::HSP::HSPI objects
Bio::Search::HSP::HSPI
Interface for a High Scoring Pair in a similarity search result
Bio::Search::HSP::PSLHSP
A HSP for PSL output
Bio::Search::HSP::PsiBlastHSP
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::WABAHSP
HSP object suitable for describing WABA alignments
Bio::Search::Hit::BlastHit
Blast-specific subclass of Bio::Search::Hit::GenericHit
Bio::Search::Hit::Fasta
Hit object specific for Fasta-generated hits
Bio::Search::Hit::GenericHit
A generic implementation of the Bio::Search::Hit::HitI interface
Bio::Search::Hit::HMMERHit
A Hit module for HMMER hits
Bio::Search::Hit::HitFactory
A factory to create Bio::Search::Hit::HitI objects
Bio::Search::Hit::HitI
Interface for a hit in a similarity search result
Bio::Search::Hit::PsiBlastHit
Bioperl BLAST Hit object
Bio::Search::Iteration::GenericIteration
A generic implementation of the Bio::Search::Iteration::IterationI interface.
Bio::Search::Iteration::IterationI
Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
Bio::Search::Processor
DESCRIPTION of Object
Bio::Search::Result::BlastResult
Blast-specific subclass of Bio::Search::Result::GenericResult
Bio::Search::Result::GenericResult
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
Bio::Search::Result::HMMERResult
A Result object for HMMER results
Bio::Search::Result::ResultFactory
A factory to create Bio::Search::Result::ResultI objects
Bio::Search::Result::ResultI
Abstract interface to Search Result objects
Bio::Search::Result::WABAResult
Result object for WABA alignment output
Bio::Search::SearchUtils
Utility functions for Bio::Search:: objects
Bio::SearchDist
A perl wrapper around Sean Eddy's histogram object
Bio::SearchIO
Driver for parsing Sequence Database Searches (Blast,FASTA,...)
Bio::SearchIO::EventHandlerI
An abstract Event Handler for Search Result parsing
Bio::SearchIO::FastHitEventBuilder
Event Handler for SearchIO events.
Bio::SearchIO::IteratedSearchResultEventBuilder
Event Handler for SearchIO events.
Bio::SearchIO::SearchResultEventBuilder
Event Handler for SearchIO events.
Bio::SearchIO::SearchWriterI
Interface for outputting parsed Search results
Bio::SearchIO::Writer::BSMLResultWriter
DESCRIPTION of Object
Bio::SearchIO::Writer::GbrowseGFF
Interface for outputting parsed search results in Gbrowse GFF format
Bio::SearchIO::Writer::HSPTableWriter
Tab-delimited data for Bio::Search::HSP::HSPI objects
Bio::SearchIO::Writer::HTMLResultWriter
Object to implement writing a Bio::Search::ResultI in HTML.
Bio::SearchIO::Writer::HitTableWriter
Tab-delimited data for Bio::Search::Hit::HitI objects
Bio::SearchIO::Writer::ResultTableWriter
Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Bio::SearchIO::Writer::TextResultWriter
Object to implement writing a Bio::Search::ResultI in Text.
Bio::SearchIO::axt
a parser for axt format reports
Bio::SearchIO::blast
Event generator for event based parsing of blast reports
Bio::SearchIO::blasttable
Driver module for SearchIO for parsing NCBI -m 8/9 format
Bio::SearchIO::blastxml
A SearchIO implementation of NCBI Blast XML parsing.
Bio::SearchIO::exonerate
parser for Exonerate
Bio::SearchIO::fasta
A SearchIO parser for FASTA results
Bio::SearchIO::hmmer
A parser for HMMER output (hmmpfam, hmmsearch)
Bio::SearchIO::megablast
a driver module for Bio::SearchIO to parse megablast reports (format 0)
Bio::SearchIO::psl
A parser for PSL output (UCSC)
Bio::SearchIO::sim4
parser for Sim4 alignments
Bio::SearchIO::waba
SearchIO parser for Jim Kent WABA program alignment output
Bio::SearchIO::wise
Parsing of wise output as alignments
Bio::Seq
Sequence object, with features
Bio::Seq::BaseSeqProcessor
Base implementation for a SequenceProcessor
Bio::Seq::EncodedSeq
subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Seq::LargePrimarySeq
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
Bio::Seq::LargeSeq
SeqI compliant object that stores sequence as files in /tmp
Bio::Seq::Meta
Generic superclass for sequence objects with residue-based meta information
Bio::Seq::Meta::Array
array-based generic implementation of a sequence class with residue-based meta information
Bio::Seq::MetaI
Interface for sequence objects with residue-based meta information
Bio::Seq::PrimaryQual
Bioperl lightweight Quality Object
Bio::Seq::PrimedSeq
A representation of a sequence and two primers flanking a target region for amplification
Bio::Seq::QualI
Interface definition for a Bio::Seq::Qual
Bio::Seq::RichSeq
Module implementing a sequence created from a rich sequence database entry
Bio::Seq::RichSeqI
interface for sequences from rich data sources, mostly databases
Bio::Seq::SeqBuilder
Configurable object builder for sequence stream parsers
Bio::Seq::SeqFactory
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bio::Seq::SeqFastaSpeedFactory
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bio::Seq::SeqWithQuality
Bioperl object packaging a sequence with its quality
Bio::Seq::SequenceTrace
Bioperl object packaging a sequence with its trace
Bio::Seq::TraceI
Interface definition for a Bio::Seq::Trace
Bio::SeqAnalysisParserI
Sequence analysis output parser interface
Bio::SeqFeature::AnnotationAdaptor
integrates SeqFeatureIs annotation
Bio::SeqFeature::Collection
A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.
Bio::SeqFeature::CollectionI
An interface for a collection of SeqFeatureI objects.
Bio::SeqFeature::Computation
Computation SeqFeature
Bio::SeqFeature::FeaturePair
hold pair feature information e.g. blast hits
Bio::SeqFeature::Gene::Exon
a feature representing an exon
Bio::SeqFeature::Gene::ExonI
Interface for a feature representing an exon
Bio::SeqFeature::Gene::GeneStructure
A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::GeneStructureI
A feature representing an arbitrarily complex structure of a gene
Bio::SeqFeature::Gene::Intron
DESCRIPTION of Object
Bio::SeqFeature::Gene::NC_Feature
DESCRIPTION of Object
Bio::SeqFeature::Gene::Poly_A_site
DESCRIPTION of Object
Bio::SeqFeature::Gene::Promoter
Describes a promotor
Bio::SeqFeature::Gene::Transcript
A feature representing a transcript
Bio::SeqFeature::Gene::TranscriptI
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Bio::SeqFeature::Gene::UTR
A feature representing an untranslated region that is part of a transcriptional unit
Bio::SeqFeature::Generic
Generic SeqFeature
Bio::SeqFeature::PositionProxy
handle features when truncation/revcom sequences span a feature
Bio::SeqFeature::Primer
Primer Generic SeqFeature
Bio::SeqFeature::SiRNA::Oligo
Perl object for small inhibitory RNAs.
Bio::SeqFeature::SiRNA::Pair
Perl object for small inhibitory RNA (SiRNA) oligo pairs
Bio::SeqFeature::Similarity
A sequence feature based on similarity
Bio::SeqFeature::SimilarityPair
Sequence feature based on the similarity of two sequences.
Bio::SeqFeature::Tools::TypeMapper
maps $seq_feature-gtprimary_tag
Bio::SeqFeature::Tools::Unflattener
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
Bio::SeqFeatureI
Abstract interface of a Sequence Feature
Bio::SeqI
Bio::SeqIO
Handler for SeqIO Formats
Bio::SeqIO::FTHelper
Helper class for Embl/Genbank feature tables
Bio::SeqIO::MultiFile
Treating a set of files as a single input stream
Bio::SeqIO::abi
abi trace sequence input/output stream
Bio::SeqIO::ace
ace sequence input/output stream
Bio::SeqIO::alf
alf trace sequence input/output stream
Bio::SeqIO::asciitree
asciitree sequence input/output stream
Bio::SeqIO::bsml
BSML sequence input/output stream
Bio::SeqIO::chadoxml
chadoxml sequence input/output stream
Bio::SeqIO::ctf
ctf trace sequence input/output stream
Bio::SeqIO::embl
EMBL sequence input/output stream
Bio::SeqIO::exp
exp trace sequence input/output stream
Bio::SeqIO::fasta
fasta sequence input/output stream
Bio::SeqIO::fastq
fastq sequence input/output stream
Bio::SeqIO::game
a class for parsing and writing game-XML
Bio::SeqIO::game::featHandler
a class for handling feature elements
Bio::SeqIO::game::gameHandler
PerlSAX handler for game-XML
Bio::SeqIO::game::gameSubs
a base class for game-XML parsing
Bio::SeqIO::game::gameWriter
a class for writing game-XML
Bio::SeqIO::game::seqHandler
a class for handling game-XML sequences
Bio::SeqIO::gcg
GCG sequence input/output stream
Bio::SeqIO::genbank
GenBank sequence input/output stream
Bio::SeqIO::kegg
KEGG sequence input/output stream
Bio::SeqIO::largefasta
method i/o on very large fasta sequence files
Bio::SeqIO::locuslink
DESCRIPTION of Object
Bio::SeqIO::metafasta
metafasta sequence input/output stream
Bio::SeqIO::phd
.phd file input/output stream
Bio::SeqIO::pir
PIR sequence input/output stream
Bio::SeqIO::pln
pln trace sequence input/output stream
Bio::SeqIO::qual
.qual file input/output stream
Bio::SeqIO::raw
raw sequence file input/output stream
Bio::SeqIO::scf
.scf file input/output stream
Bio::SeqIO::swiss
Swissprot sequence input/output stream
Bio::SeqIO::tab
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
Bio::SeqIO::tigr
TIGR XML sequence input/output stream
Bio::SeqIO::ztr
ztr trace sequence input/output stream
Bio::SeqUtils
Additional methods for PrimarySeq objects
Bio::SimpleAlign
Multiple alignments held as a set of sequences
Bio::SimpleAnalysisI
A simple interface to any (local or remote) analysis tool
Bio::Species
Generic species object
Bio::Structure::Atom
Bioperl structure Object, describes an Atom
Bio::Structure::Chain
Bioperl structure Object, describes a chain
Bio::Structure::Entry
Bioperl structure Object, describes the whole entry
Bio::Structure::IO
Handler for Structure Formats
Bio::Structure::IO::pdb
PDB input/output stream
Bio::Structure::Model
Bioperl structure Object, describes a Model
Bio::Structure::Residue
Bioperl structure Object, describes a Residue
Bio::Structure::SecStr::DSSP::Res
Module for parsing/accessing dssp output
Bio::Structure::SecStr::STRIDE::Res
Module for parsing/accessing stride output
Bio::Structure::StructureI
Abstract Interface for a Structure objects
Bio::Symbol::Alphabet
DESCRIPTION of Object
Bio::Symbol::AlphabetI
A Symbol Alphabet
Bio::Symbol::DNAAlphabet
A ready made DNA alphabet
Bio::Symbol::ProteinAlphabet
A ready made Protein alphabet
Bio::Symbol::Symbol
A biological symbol
Bio::Symbol::SymbolI
Interface for a Symbol
Bio::Taxonomy
representing Taxonomy.
Bio::Taxonomy::FactoryI
interface to define how to access NCBI Taxonoy
Bio::Taxonomy::Node
A node in a represented taxonomy
Bio::Taxonomy::Taxon
Generic Taxonomic Entity object
Bio::Taxonomy::Tree
An Organism Level Implementation of TreeI interface.
Bio::Tools::AlignFactory
Base object for alignment factories
Bio::Tools::Alignment::Consed
A module to work with objects from consed .ace files
Bio::Tools::Alignment::Trim
A kludge to do specialized trimming of sequence based on quality.
Bio::Tools::Analysis::DNA::ESEfinder
a wrapper around ESEfinder server
Bio::Tools::Analysis::Protein::Domcut
a wrapper around Domcut server
Bio::Tools::Analysis::Protein::ELM
Bio::Tools::Analysis::Protein::GOR4
a wrapper around GOR4 protein secondary structure prediction server
Bio::Tools::Analysis::Protein::HNN
a wrapper around HNN protein secondary structure prediction server
Bio::Tools::Analysis::Protein::Mitoprot
a wrapper around Mitoprot server
Bio::Tools::Analysis::Protein::NetPhos
a wrapper around NetPhos server
Bio::Tools::Analysis::Protein::Scansite
a wrapper around the Scansite server
Bio::Tools::Analysis::Protein::Sopma
a wrapper around Sopma protein secondary structure prediction server
Bio::Tools::Analysis::SimpleAnalysisBase
abstact superclass for SimpleAnalysis implementations
Bio::Tools::AnalysisResult
Base class for analysis result objects and parsers
Bio::Tools::BPbl2seq
Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Bio::Tools::BPlite
Lightweight BLAST parser
Bio::Tools::BPlite::HSP
Blast report High Scoring Pair (HSP)
Bio::Tools::BPlite::Iteration
object for parsing single iteration of a PSIBLAST report
Bio::Tools::BPlite::Sbjct
A Blast Subject (database search Hit)
Bio::Tools::BPpsilite
Lightweight BLAST parser for (iterated) psiblast reports
Bio::Tools::Blast
Bioperl BLAST sequence analysis object
Bio::Tools::Blast::HSP
Bioperl BLAST High-Scoring Segment Pair object
Bio::Tools::Blast::HTML
Bioperl Utility module for HTML formatting Blast reports
Bio::Tools::Blast::Sbjct
Bioperl BLAST "Hit" object
Bio::Tools::Blat
Bio::Tools::CodonTable
Bioperl codon table object
Bio::Tools::Coil
Bio::Tools::ECnumber
representation of EC numbers
Bio::Tools::EMBOSS::Palindrome
parse EMBOSS palindrome output
Bio::Tools::EPCR
Parse ePCR output and make features
Bio::Tools::ESTScan
Results of one ESTScan run
Bio::Tools::Eponine
Results of one Eponine run
Bio::Tools::Est2Genome
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
Bio::Tools::FootPrinter
DESCRIPTION of Object
Bio::Tools::GFF
A Bio::SeqAnalysisParserI compliant GFF format parser
Bio::Tools::Gel
Calculates relative electrophoretic migration distances
Bio::Tools::Geneid
Results of one geneid run
Bio::Tools::Genemark
Results of one Genemark run
Bio::Tools::Genewise
Results of one Genewise run
Bio::Tools::Genomewise
Results of one Genomewise run
Bio::Tools::Genscan
Results of one Genscan run
Bio::Tools::Glimmer
A parser for GLIMMER gene predictions
Bio::Tools::Grail
Results of one Grail run
Bio::Tools::GuessSeqFormat
Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
Bio::Tools::HMMER::Domain
One particular domain hit from HMMER
Bio::Tools::HMMER::Results
Object representing HMMER output results
Bio::Tools::HMMER::Set
Set of identical domains from HMMER matches
Bio::Tools::Hmmpfam
Bio::Tools::IUPAC
Generates unique Seq objects from an ambiguous Seq object
Bio::Tools::Lucy
Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Bio::Tools::MZEF
Results of one MZEF run
Bio::Tools::OddCodes
Object holding alternative alphabet coding for one protein sequence
Bio::Tools::Phylo::Molphy
DESCRIPTION of Object
Bio::Tools::Phylo::Molphy::Result
DESCRIPTION of Object
Bio::Tools::Phylo::PAML
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
Bio::Tools::Phylo::PAML::ModelResult
A container for NSSite Model Result from PAML
Bio::Tools::Phylo::PAML::Result
A PAML result set object
Bio::Tools::Phylo::Phylip::ProtDist
DESCRIPTION of Object
Bio::Tools::Prediction::Exon
A predicted exon feature
Bio::Tools::Prediction::Gene
a predicted gene structure feature
Bio::Tools::Primer::Assessor::Base
base class for common assessor things
Bio::Tools::Primer::AssessorI
interface for assessing primer pairs
Bio::Tools::Primer::Feature
position of a single primer
Bio::Tools::Primer::Pair
two primers on left and right side
Bio::Tools::Primer3
Create input for and work with the output from the program primer3
Bio::Tools::Prints
Parser for FingerPRINTScanII program
Bio::Tools::Profile
parse Profile output
Bio::Tools::Promoterwise
DESCRIPTION of Object
Bio::Tools::PrositeScan
Parser for ps_scan result
Bio::Tools::Pseudowise
Results of one Pseudowise run
Bio::Tools::QRNA
A Parser for qrna output
Bio::Tools::RandomDistFunctions
A set of routines useful for generating random data in different distributions
Bio::Tools::RepeatMasker
DESCRIPTION of Object
Bio::Tools::RestrictionEnzyme
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
Bio::Tools::Run::RemoteBlast
Object for remote execution of the NCBI Blast via HTTP
Bio::Tools::Run::StandAloneBlast
Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast.
Bio::Tools::Run::WrapperBase
A Base object for wrappers around executables
Bio::Tools::Seg
parse Seg output (filter low complexity protein sequence)
Bio::Tools::SeqAnal
Bioperl sequence analysis base class.
Bio::Tools::SeqPattern
Bioperl object for a sequence pattern or motif
Bio::Tools::SeqStats
Object holding statistics for one particular sequence
Bio::Tools::SeqWords
Object holding n-mer statistics for one sequence
Bio::Tools::SiRNA
Perl object for designing small inhibitory RNAs.
Bio::Tools::Sigcleave
Bioperl object for sigcleave analysis
Bio::Tools::Signalp
Bio::Tools::Sim4::Exon
A single exon determined by an alignment
Bio::Tools::Sim4::Results
Results of one Sim4 run
Bio::Tools::Tmhmm
parse TmHMM output (transmembrane HMM)
Bio::Tools::WWW
Bioperl manager for web resources related to biology.
Bio::Tools::dpAlign
Perl extension to do pairwise dynamic programming sequence alignment
Bio::Tools::pICalculator
Bio::Tools::pSW
pairwise Smith Waterman object
Bio::Tree::AlleleNode
A Node with Alleles attached
Bio::Tree::Node
A Simple Tree Node
Bio::Tree::NodeI
Interface describing a Tree Node
Bio::Tree::NodeNHX
A Simple Tree Node with support for NHX tags
Bio::Tree::RandomFactory
TreeFactory for generating Random Trees
Bio::Tree::Statistics
Calculate certain statistics for a Tree
Bio::Tree::Tree
An Implementation of TreeI interface.
Bio::Tree::TreeFunctionsI
Decorated Interface implementing basic Tree exploration methods
Bio::Tree::TreeI
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Bio::TreeIO
Parser for Tree files
Bio::TreeIO::TreeEventBuilder
Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
Bio::TreeIO::lintree
Parser for lintree output trees
Bio::TreeIO::newick
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
Bio::TreeIO::nexus
A TreeIO driver module for parsing Nexus tree output from PAUP
Bio::TreeIO::nhx
TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
Bio::TreeIO::svggraph
A simple output format that converts a Tree object to an SVG output
Bio::TreeIO::tabtree
A simple output format which displays a tree as an ASCII drawing
Bio::UpdateableSeqI
Descendant of Bio::SeqI that allows updates
Bio::Variation::AAChange
Sequence change class for polypeptides
Bio::Variation::AAReverseMutate
point mutation and codon information from single amino acid changes
Bio::Variation::Allele
Sequence object with allele-specific attributes
Bio::Variation::DNAMutation
DNA level mutation class
Bio::Variation::IO
Handler for sequence variation IO Formats
Bio::Variation::IO::flat
flat file sequence variation input/output stream
Bio::Variation::IO::xml
XML sequence variation input/output stream
Bio::Variation::RNAChange
Sequence change class for RNA level
Bio::Variation::SNP
submitted SNP
Bio::Variation::SeqDiff
Container class for mutation/variant descriptions
Bio::Variation::VariantI
Sequence Change SeqFeature abstract class
Bio::WebAgent
A base class for Web (any protocol) access
Bio::PrimarySeq
Bio::PrimarySeqI
Bio::Seq
Bio::SeqI
Error
TestInterface
TestObject

Provides

Bio::AnalysisI::JobI
in Bio/AnalysisI.pm
Bio::DB::Fasta::Stream
in Bio/DB/Fasta.pm
Bio::DB::GFF::Adaptor::dbi::faux_dbh
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
Bio::DB::GFF::ID_Iterator
in Bio/DB/GFF.pm
Bio::Expression::FeatureGroup::FeatureGroupMas50
in Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
Bio::Expression::FeatureSet::FeatureSetMas50
in Bio/Expression/FeatureSet/FeatureSetMas50.pm
Bio::Graphics::Util
in Bio/Graphics/Util.pm
Bio::PrimarySeq::Fasta
in Bio/DB/Fasta.pm

Examples

Other files