|
Bio::Align::AlignI
[source]
[v 1.006901]
|
An interface for describing sequence alignments. |
|
Bio::Align::DNAStatistics
[source]
[v 1.006901]
|
Calculate some statistics for a DNA alignment |
|
Bio::Align::Graphics
[source]
[v 1.006901]
|
Graphic Rendering of Bio::Align::AlignI Objects |
|
Bio::Align::PairwiseStatistics
[source]
[v 1.006901]
|
Base statistic object for Pairwise Alignments |
|
Bio::Align::ProteinStatistics
[source]
[v 1.006901]
|
Calculate Protein Alignment statistics (mostly distances) |
|
Bio::Align::StatisticsI
[source]
[v 1.006901]
|
Calculate some statistics for an alignment |
|
Bio::Align::Utilities
[source]
[v 1.006901]
|
A collection of utilities regarding converting |
|
Bio::AlignIO
[source]
[v 1.006901]
|
Handler for AlignIO Formats |
|
Bio::AlignIO::arp
[source]
[v 1.006901]
|
ARP MSA Sequence input/output stream |
|
Bio::AlignIO::bl2seq
[source]
[v 1.006901]
|
bl2seq sequence input/output stream |
|
Bio::AlignIO::clustalw
[source]
[v 1.006901]
|
clustalw sequence input/output stream |
|
Bio::AlignIO::emboss
[source]
[v 1.006901]
|
Parse EMBOSS alignment output (from applications water and needle) |
|
Bio::AlignIO::fasta
[source]
[v 1.006901]
|
fasta MSA Sequence input/output stream |
|
Bio::AlignIO::Handler::GenericAlignHandler
[source]
[v 1.006901]
|
Bio::HandlerI-based |
|
Bio::AlignIO::largemultifasta
[source]
[v 1.006901]
|
Largemultifasta MSA Sequence |
|
Bio::AlignIO::maf
[source]
[v 1.006901]
|
Multiple Alignment Format sequence input stream |
|
Bio::AlignIO::mase
[source]
[v 1.006901]
|
mase sequence input/output stream |
|
Bio::AlignIO::mega
[source]
[v 1.006901]
|
Parse and Create MEGA format data files |
|
Bio::AlignIO::meme
[source]
[v 1.006901]
|
meme sequence input/output stream |
|
Bio::AlignIO::metafasta
[source]
[v 1.006901]
|
Metafasta MSA Sequence input/output stream |
|
Bio::AlignIO::msf
[source]
[v 1.006901]
|
msf sequence input/output stream |
|
Bio::AlignIO::nexml
[source]
[v 1.006901]
|
NeXML format sequence alignment input/output stream driver |
|
Bio::AlignIO::nexus
[source]
[v 1.006901]
|
NEXUS format sequence input/output stream |
|
Bio::AlignIO::pfam
[source]
[v 1.006901]
|
pfam sequence input/output stream |
|
Bio::AlignIO::phylip
[source]
[v 1.006901]
|
PHYLIP format sequence input/output stream |
|
Bio::AlignIO::po
[source]
[v 1.006901]
|
po MSA Sequence input/output stream |
|
Bio::AlignIO::proda
[source]
[v 1.006901]
|
proda sequence input/output stream |
|
Bio::AlignIO::prodom
[source]
[v 1.006901]
|
prodom sequence input/output stream |
|
Bio::AlignIO::psi
[source]
[v 1.006901]
|
Read/Write PSI-BLAST profile alignment files |
|
Bio::AlignIO::selex
[source]
[v 1.006901]
|
selex sequence input/output stream |
|
Bio::AlignIO::stockholm
[source]
[v 1.006901]
|
stockholm sequence input/output stream |
|
Bio::AlignIO::xmfa
[source]
[v 1.006901]
|
XMFA MSA Sequence input/output stream |
|
Bio::AnalysisI
[source]
[v 1.006901]
|
An interface to any (local or remote) analysis tool |
|
Bio::AnalysisParserI
[source]
[v 1.006901]
|
Generic analysis output parser interface |
|
Bio::AnalysisResultI
[source]
[v 1.006901]
|
Interface for analysis result objects |
|
Bio::AnnotatableI
[source]
[v 1.006901]
|
the base interface an annotatable object must implement |
|
Bio::Annotation::AnnotationFactory
[source]
[v 1.006901]
|
Instantiates a new |
|
Bio::Annotation::Collection
[source]
[v 1.006901]
|
Default Perl implementation of |
|
Bio::Annotation::Comment
[source]
[v 1.006901]
|
A comment object, holding text |
|
Bio::Annotation::DBLink
[source]
[v 1.006901]
|
untyped links between databases |
|
Bio::Annotation::OntologyTerm
[source]
[v 1.006901]
|
An ontology term adapted to AnnotationI |
|
Bio::Annotation::Reference
[source]
[v 1.006901]
|
Specialised DBLink object for Literature References |
|
Bio::Annotation::Relation
[source]
[v 1.006901]
|
Relationship (pairwise) with other objects SeqI and NodeI; |
|
Bio::Annotation::SimpleValue
[source]
[v 1.006901]
|
A simple scalar |
|
Bio::Annotation::StructuredValue
[source]
[v 1.006901]
|
A scalar with embedded structured |
|
Bio::Annotation::TagTree
[source]
[v 1.006901]
|
AnnotationI with tree-like hierarchal key-value |
|
Bio::Annotation::Target
[source]
[v 1.006901]
|
Provides an object which represents a target (ie, a |
|
Bio::Annotation::Tree
[source]
[v 1.006901]
|
Provide a tree as an annotation to a Bio::AnnotatableI |
|
Bio::Annotation::TypeManager
[source]
[v 1.006901]
|
Manages types for annotation collections |
|
Bio::AnnotationCollectionI
[source]
[v 1.006901]
|
Interface for annotation collections |
|
Bio::AnnotationI
[source]
[v 1.006901]
|
Annotation interface |
|
Bio::Assembly::Contig
[source]
[v 1.006901]
|
Perl module to hold and manipulate |
|
Bio::Assembly::ContigAnalysis
[source]
[v 1.006901]
|
|
|
Bio::Assembly::IO
[source]
[v 1.006901]
|
Handler for Assembly::IO Formats |
|
Bio::Assembly::IO::ace
[source]
[v 1.006901]
|
module to load ACE files from various assembly programs |
|
Bio::Assembly::IO::bowtie
[source]
[v 1.006901]
|
An IO module for assemblies in Bowtie format *BETA* |
|
Bio::Assembly::IO::maq
[source]
[v 1.006901]
|
Driver to read assembly files in maq format *BETA* |
|
Bio::Assembly::IO::phrap
[source]
[v 1.006901]
|
driver to load phrap.out files. |
|
Bio::Assembly::IO::sam
[source]
[v 1.006901]
|
An IO module for assemblies in Sam format *BETA* |
|
Bio::Assembly::IO::tigr
[source]
[v 1.006901]
|
Driver to read and write assembly files in the TIGR |
|
Bio::Assembly::Scaffold
[source]
[v 1.006901]
|
Perl module to hold and manipulate sequence assembly |
|
Bio::Assembly::ScaffoldI
[source]
[v 1.006901]
|
Abstract Inteface of Sequence Assemblies |
|
Bio::Assembly::Singlet
[source]
[v 1.006901]
|
Perl module to hold and manipulate |
|
Bio::Assembly::Tools::ContigSpectrum
[source]
[v 1.006901]
|
create and manipulate contig spectra |
|
Bio::Biblio
[source]
[v 1.006901]
|
A Bibliographic Query Service module |
|
Bio::Biblio::Article
[source]
[v 1.006901]
|
Representation of a general article |
|
Bio::Biblio::BiblioBase
[source]
[v 1.006901]
|
An abstract base for other biblio classes |
|
Bio::Biblio::Book
[source]
[v 1.006901]
|
Representation of a book |
|
Bio::Biblio::BookArticle
[source]
[v 1.006901]
|
Representation of a book article |
|
Bio::Biblio::IO
[source]
[v 1.006901]
|
Handling the bibliographic references |
|
Bio::Biblio::IO::medline2ref
[source]
[v 1.006901]
|
A converter of a raw hash to MEDLINE citations |
|
Bio::Biblio::IO::medlinexml
[source]
[v 1.006901]
|
A converter of XML files with MEDLINE citations |
|
Bio::Biblio::IO::pubmed2ref
[source]
[v 1.006901]
|
A converter of a raw hash to PUBMED citations |
|
Bio::Biblio::IO::pubmedxml
[source]
[v 1.006901]
|
A converter of XML files with PUBMED citations |
|
Bio::Biblio::Journal
[source]
[v 1.006901]
|
Representation of a journal |
|
Bio::Biblio::JournalArticle
[source]
[v 1.006901]
|
Representation of a journal article |
|
Bio::Biblio::MedlineArticle
[source]
[v 1.006901]
|
Representation of a MEDLINE article |
|
Bio::Biblio::MedlineBook
[source]
[v 1.006901]
|
Representation of a MEDLINE book |
|
Bio::Biblio::MedlineBookArticle
[source]
[v 1.006901]
|
Representation of a MEDLINE book article |
|
Bio::Biblio::MedlineJournal
[source]
[v 1.006901]
|
Representation of a MEDLINE journal |
|
Bio::Biblio::MedlineJournalArticle
[source]
[v 1.006901]
|
Representation of a MEDLINE journal article |
|
Bio::Biblio::Organisation
[source]
[v 1.006901]
|
Representation of an organisation |
|
Bio::Biblio::Patent
[source]
[v 1.006901]
|
Representation of a patent |
|
Bio::Biblio::Person
[source]
[v 1.006901]
|
Representation of a person |
|
Bio::Biblio::Proceeding
[source]
[v 1.006901]
|
Representation of a conference proceeding |
|
Bio::Biblio::Provider
[source]
[v 1.006901]
|
Representation of a general provider |
|
Bio::Biblio::PubmedArticle
[source]
[v 1.006901]
|
Representation of a PUBMED article |
|
Bio::Biblio::PubmedBookArticle
[source]
[v 1.006901]
|
Representation of a PUBMED book article |
|
Bio::Biblio::PubmedJournalArticle
[source]
[v 1.006901]
|
Representation of a PUBMED journal article |
|
Bio::Biblio::Ref
[source]
[v 1.006901]
|
Representation of a bibliographic reference |
|
Bio::Biblio::Service
[source]
[v 1.006901]
|
Representation of a provider of type service |
|
Bio::Biblio::TechReport
[source]
[v 1.006901]
|
Representation of a technical report |
|
Bio::Biblio::Thesis
[source]
[v 1.006901]
|
Representation of thesis |
|
Bio::Biblio::WebResource
[source]
[v 1.006901]
|
Representation of a web resource |
|
Bio::Cluster::ClusterFactory
[source]
[v 1.006901]
|
Instantiates a new Bio::ClusterI (or derived class) through a factory |
|
Bio::Cluster::FamilyI
[source]
[v 1.006901]
|
Family Interface |
|
Bio::Cluster::SequenceFamily
[source]
[v 1.006901]
|
Sequence Family object |
|
Bio::Cluster::UniGene
[source]
[v 1.006901]
|
UniGene object |
|
Bio::Cluster::UniGeneI
[source]
[v 1.006901]
|
abstract interface of UniGene object |
|
Bio::ClusterI
[source]
[v 1.006901]
|
Cluster Interface |
|
Bio::ClusterIO
[source]
[v 1.006901]
|
Handler for Cluster Formats |
|
Bio::ClusterIO::dbsnp
[source]
[v 1.006901]
|
dbSNP input stream |
|
Bio::ClusterIO::unigene
[source]
[v 1.006901]
|
UniGene input stream |
|
Bio::CodonUsage::IO
[source]
[v 1.006901]
|
for reading and writing codon usage tables to file |
|
Bio::CodonUsage::Table
[source]
[v 1.006901]
|
for access to the Codon usage Database |
|
Bio::Coordinate::Chain
[source]
[v 1.006901]
|
Mapping locations through a chain of coordinate mappers |
|
Bio::Coordinate::Collection
[source]
[v 1.006901]
|
Noncontinuous match between two coordinate sets |
|
Bio::Coordinate::ExtrapolatingPair
[source]
[v 1.006901]
|
Continuous match between two coordinate sets |
|
Bio::Coordinate::GeneMapper
[source]
[v 1.006901]
|
transformations between gene related coordinate systems |
|
Bio::Coordinate::Graph
[source]
[v 1.006901]
|
Finds shortest path between nodes in a graph |
|
Bio::Coordinate::MapperI
[source]
[v 1.006901]
|
Interface describing coordinate mappers |
|
Bio::Coordinate::Pair
[source]
[v 1.006901]
|
Continuous match between two coordinate sets |
|
Bio::Coordinate::Result
[source]
[v 1.006901]
|
Results from coordinate transformation |
|
Bio::Coordinate::Result::Gap
[source]
[v 1.006901]
|
Another name for Bio::Location::Simple |
|
Bio::Coordinate::Result::Match
[source]
[v 1.006901]
|
Another name for Bio::Location::Simple |
|
Bio::Coordinate::ResultI
[source]
[v 1.006901]
|
Interface to identify coordinate mapper results |
|
Bio::Coordinate::Utils
[source]
[v 1.006901]
|
Additional methods to create Bio::Coordinate objects |
|
Bio::Das::FeatureTypeI
[source]
[v 1.006901]
|
Simple interface to Sequence Ontology feature types |
|
Bio::Das::SegmentI
[source]
[v 1.006901]
|
DAS-style access to a feature database |
|
Bio::DasI
[source]
[v 1.006901]
|
DAS-style access to a feature database |
|
Bio::DB::Ace
[source]
[v 1.006901]
|
Database object interface to ACeDB servers |
|
Bio::DB::Biblio::biofetch
[source]
[v 1.006901]
|
A BioFetch-based access to a bibliographic |
|
Bio::DB::Biblio::eutils
[source]
[v 1.006901]
|
Access to PubMed's bibliographic query service |
|
Bio::DB::Biblio::soap
[source]
[v 1.006901]
|
A SOAP-based access to a bibliographic query service |
|
Bio::DB::BiblioI
[source]
[v 1.006901]
|
An interface to a Bibliographic Query Service |
|
Bio::DB::BioFetch
[source]
[v 1.006901]
|
Database object interface to BioFetch retrieval |
|
Bio::DB::CUTG
[source]
[v 1.006901]
|
for access to the Codon usage Database |
|
Bio::DB::DBFetch
[source]
[v 1.006901]
|
Database object for retrieving using the dbfetch script |
|
Bio::DB::EMBL
[source]
[v 1.006901]
|
Database object interface for EMBL entry retrieval |
|
Bio::DB::EntrezGene
[source]
[v 1.006901]
|
Database object interface to Entrez Gene |
|
Bio::DB::EUtilities
[source]
[v 1.006901]
|
webagent which interacts with and retrieves data from |
|
Bio::DB::Expression
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::DB::Expression::geo
[source]
[v 1.006901]
|
*** DESCRIPTION of Class |
|
Bio::DB::Failover
[source]
[v 1.006901]
|
A Bio::DB::RandomAccessI compliant class which |
|
Bio::DB::Fasta
[source]
[v 1.006901]
|
Fast indexed access to a directory of fasta files |
|
Bio::DB::FileCache
[source]
[v 1.006901]
|
In file cache for BioSeq objects |
|
Bio::DB::Flat
[source]
[v 1.006901]
|
Interface for indexed flat files |
|
Bio::DB::Flat::BDB
[source]
[v 1.006901]
|
Interface for BioHackathon standard BDB-indexed flat file |
|
Bio::DB::Flat::BDB::embl
[source]
[v 1.006901]
|
embl adaptor for Open-bio standard BDB-indexed flat file |
|
Bio::DB::Flat::BDB::fasta
[source]
[v 1.006901]
|
fasta adaptor for Open-bio standard BDB-indexed flat file |
|
Bio::DB::Flat::BDB::genbank
[source]
[v 1.006901]
|
genbank adaptor for Open-bio standard BDB-indexed flat file |
|
Bio::DB::Flat::BDB::swiss
[source]
[v 1.006901]
|
swissprot adaptor for Open-bio standard BDB-indexed flat file |
|
Bio::DB::Flat::BinarySearch
[source]
[v 1.006901]
|
BinarySearch search indexing system for sequence files |
|
Bio::DB::GenBank
[source]
[v 1.006901]
|
Database object interface to GenBank |
|
Bio::DB::GenericWebAgent
[source]
[v 1.006901]
|
helper base class for parameter-based remote server |
|
Bio::DB::GenPept
[source]
[v 1.006901]
|
Database object interface to GenPept |
|
Bio::DB::GFF
[source]
[v 1.006901]
|
Storage and retrieval of sequence annotation data |
|
Bio::DB::GFF::Adaptor::ace
[source]
[v 1.006901]
|
ace interface (for multiple inheritance) |
|
Bio::DB::GFF::Adaptor::berkeleydb
[source]
[v 1.006901]
|
Bio::DB::GFF database adaptor for in-memory databases |
|
Bio::DB::GFF::Adaptor::berkeleydb::iterator
[source]
[v 1.006901]
|
iterator for Bio::DB::GFF::Adaptor::berkeleydb |
|
Bio::DB::GFF::Adaptor::biofetch
[source]
[v 1.006901]
|
Cache BioFetch objects in a Bio::DB::GFF database |
|
Bio::DB::GFF::Adaptor::biofetch_oracle
[source]
[v 1.006901]
|
Cache BioFetch objects in a Bio::DB::GFF database |
|
Bio::DB::GFF::Adaptor::dbi
[source]
[v 1.006901]
|
Database adaptor for DBI (SQL) databases |
|
Bio::DB::GFF::Adaptor::dbi::caching_handle
[source]
[v 1.006901]
|
Cache for database handles |
|
Bio::DB::GFF::Adaptor::dbi::iterator
[source]
[v 1.006901]
|
iterator for Bio::DB::GFF::Adaptor::dbi |
|
Bio::DB::GFF::Adaptor::dbi::mysql
[source]
[v 1.006901]
|
Database adaptor for a specific mysql schema |
|
Bio::DB::GFF::Adaptor::dbi::mysqlace
[source]
[v 1.006901]
|
Unholy union between mysql GFF database and acedb database |
|
Bio::DB::GFF::Adaptor::dbi::mysqlcmap
[source]
[v 1.006901]
|
Database adaptor for an integraded |
|
Bio::DB::GFF::Adaptor::dbi::mysqlopt
[source]
[v 1.006901]
|
Deprecated database adaptor |
|
Bio::DB::GFF::Adaptor::dbi::oracle
[source]
[v 1.006901]
|
Database adaptor for a specific oracle schema |
|
Bio::DB::GFF::Adaptor::dbi::oracleace
[source]
[v 1.006901]
|
Unholy union between oracle GFF database and acedb database |
|
Bio::DB::GFF::Adaptor::dbi::pg
[source]
[v 1.006901]
|
Database adaptor for a specific postgres schema |
|
Bio::DB::GFF::Adaptor::dbi::pg_fts
[source]
[v 1.006901]
|
Database adaptor for a specific postgres schema with a TSearch2 implementation |
|
Bio::DB::GFF::Adaptor::memory
[source]
[v 1.006901]
|
Bio::DB::GFF database adaptor for in-memory databases |
|
Bio::DB::GFF::Adaptor::memory::feature_serializer
[source]
[v 1.006901]
|
utility methods for serializing and deserializing GFF features |
|
Bio::DB::GFF::Adaptor::memory::iterator
[source]
[v 1.006901]
|
iterator for Bio::DB::GFF::Adaptor::memory |
|
Bio::DB::GFF::Aggregator
[source]
[v 1.006901]
|
Aggregate GFF groups into composite features |
|
Bio::DB::GFF::Aggregator::alignment
[source]
[v 1.006901]
|
Alignment aggregator |
|
Bio::DB::GFF::Aggregator::clone
[source]
[v 1.006901]
|
Clone aggregator |
|
Bio::DB::GFF::Aggregator::coding
[source]
[v 1.006901]
|
The Coding Region Aggregator |
|
Bio::DB::GFF::Aggregator::gene
[source]
[v 1.006901]
|
Sequence Ontology Geene |
|
Bio::DB::GFF::Aggregator::match
[source]
[v 1.006901]
|
Match aggregator |
|
Bio::DB::GFF::Aggregator::none
[source]
[v 1.006901]
|
No aggregation |
|
Bio::DB::GFF::Aggregator::orf
[source]
[v 1.006901]
|
An aggregator for orf regions |
|
Bio::DB::GFF::Aggregator::processed_transcript
[source]
[v 1.006901]
|
Sequence Ontology Transcript |
|
Bio::DB::GFF::Aggregator::so_transcript
[source]
[v 1.006901]
|
Sequence Ontology Transcript |
|
Bio::DB::GFF::Aggregator::transcript
[source]
[v 1.006901]
|
Transcript aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_acembly
[source]
[v 1.006901]
|
UCSC acembly aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_ensgene
[source]
[v 1.006901]
|
UCSC ensGene aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_genscan
[source]
[v 1.006901]
|
UCSC genscan aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_refgene
[source]
[v 1.006901]
|
UCSC refGene aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_sanger22
[source]
[v 1.006901]
|
UCSC sanger22 aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo
[source]
[v 1.006901]
|
UCSC sanger22pseudo aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_softberry
[source]
[v 1.006901]
|
UCSC softberry aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_twinscan
[source]
[v 1.006901]
|
UCSC twinscan aggregator |
|
Bio::DB::GFF::Aggregator::ucsc_unigene
[source]
[v 1.006901]
|
UCSC UniGene aggregator |
|
Bio::DB::GFF::Featname
[source]
[v 1.006901]
|
The name of a feature |
|
Bio::DB::GFF::Feature
[source]
[v 1.006901]
|
A relative segment identified by a feature type |
|
Bio::DB::GFF::Homol
[source]
[v 1.006901]
|
A segment of DNA that is homologous to another |
|
Bio::DB::GFF::RelSegment
[source]
[v 1.006901]
|
Sequence segment with relative coordinate support |
|
Bio::DB::GFF::Segment
[source]
[v 1.006901]
|
Simple DNA segment object |
|
Bio::DB::GFF::Typename
[source]
[v 1.006901]
|
The name of a feature type |
|
Bio::DB::GFF::Util::Binning
[source]
[v 1.006901]
|
binning utility for Bio::DB::GFF index |
|
Bio::DB::GFF::Util::Rearrange
[source]
[v 1.006901]
|
rearrange utility |
|
Bio::DB::HIV
[source]
[v 1.006901]
|
Database object interface to the Los Alamos HIV Sequence Database |
|
Bio::DB::HIV::HIVAnnotProcessor [v 1.006901]
|
|
|
Bio::DB::HIV::HIVQueryHelper
[source]
[v 1.006901]
|
Routines and packages used by Bio::DB::HIV and |
|
Bio::DB::InMemoryCache
[source]
[v 1.006901]
|
Abstract interface for a sequence database |
|
Bio::DB::LocationI
[source]
[v 1.006901]
|
A RandomAccessI-like abstract interface for |
|
Bio::DB::MeSH
[source]
[v 1.006901]
|
Term retrieval from a Web MeSH database |
|
Bio::DB::NCBIHelper
[source]
[v 1.006901]
|
A collection of routines useful for queries to |
|
Bio::DB::Qual
[source]
[v 1.006901]
|
Fast indexed access to a directory of quality files |
|
Bio::DB::Query::GenBank
[source]
[v 1.006901]
|
Build a GenBank Entrez Query |
|
Bio::DB::Query::HIVQuery
[source]
[v 1.006901]
|
Query interface to the Los Alamos HIV Sequence Database |
|
Bio::DB::Query::WebQuery
[source]
[v 1.006901]
|
Helper class for web-based sequence queryies |
|
Bio::DB::QueryI
[source]
[v 1.006901]
|
Object Interface to queryable sequence databases |
|
Bio::DB::RandomAccessI
[source]
[v 1.006901]
|
Abstract interface for a sequence database |
|
Bio::DB::ReferenceI
[source]
[v 1.006901]
|
A RandomAccessI-like abstract interface for |
|
Bio::DB::RefSeq
[source]
[v 1.006901]
|
Database object interface for RefSeq retrieval |
|
Bio::DB::Registry
[source]
[v 1.006901]
|
Access to the Open Bio Database Access registry scheme |
|
Bio::DB::SeqFeature
[source]
[v 1.006901]
|
Normalized feature for use with Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::NormalizedFeature
[source]
[v 1.006901]
|
Normalized feature for use with Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::NormalizedFeatureI
[source]
[v 1.006901]
|
Interface for normalized features |
|
Bio::DB::SeqFeature::NormalizedTableFeatureI
[source]
[v 1.006901]
|
Interface for normalized features whose hierarchy is stored in a table |
|
Bio::DB::SeqFeature::Segment
[source]
[v 1.006901]
|
Location-based access to genome annotation data |
|
Bio::DB::SeqFeature::Store
[source]
[v 1.006901]
|
Storage and retrieval of sequence annotation data |
|
Bio::DB::SeqFeature::Store::bdb
[source]
[v 1.006901]
|
fetch and store objects from a BerkeleyDB |
|
Bio::DB::SeqFeature::Store::berkeleydb
[source]
[v 1.006901]
|
Storage and retrieval of sequence annotation data in Berkeleydb files |
|
Bio::DB::SeqFeature::Store::berkeleydb3
[source]
[v 1.006901]
|
Storage and retrieval of sequence |
|
Bio::DB::SeqFeature::Store::DBI::Iterator
[source]
[v 1.006901]
|
utility methods for creating and iterating over SeqFeature records |
|
Bio::DB::SeqFeature::Store::DBI::mysql
[source]
[v 1.006901]
|
Mysql implementation of Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::DBI::Pg
[source]
[v 1.006901]
|
PostgreSQL implementation of Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::DBI::SQLite
[source]
[v 1.006901]
|
SQLite implementation of Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::FeatureFileLoader
[source]
[v 1.006901]
|
feature file loader for Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::GFF2Loader
[source]
[v 1.006901]
|
GFF2 file loader for Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::GFF3Loader
[source]
[v 1.006901]
|
GFF3 file loader for Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::Loader
[source]
[v 1.006901]
|
Loader |
|
Bio::DB::SeqFeature::Store::LoadHelper
[source]
[v 1.006901]
|
Internal utility for Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqFeature::Store::memory
[source]
[v 1.006901]
|
In-memory implementation of Bio::DB::SeqFeature::Store |
|
Bio::DB::SeqHound
[source]
[v 1.006901]
|
Database object interface to SeqHound |
|
Bio::DB::SeqI
[source]
[v 1.006901]
|
Abstract Interface for Sequence databases |
|
Bio::DB::SeqVersion
[source]
[v 1.006901]
|
front end to querying databases for identifier |
|
Bio::DB::SeqVersion::gi
[source]
[v 1.006901]
|
interface to NCBI Sequence Revision History page |
|
Bio::DB::SwissProt
[source]
[v 1.006901]
|
Database object interface to SwissProt retrieval |
|
Bio::DB::Taxonomy
[source]
[v 1.006901]
|
Access to a taxonomy database |
|
Bio::DB::Taxonomy::entrez
[source]
[v 1.006901]
|
Taxonomy Entrez driver |
|
Bio::DB::Taxonomy::flatfile
[source]
[v 1.006901]
|
An implementation of Bio::DB::Taxonomy |
|
Bio::DB::Taxonomy::list
[source]
[v 1.006901]
|
An implementation of Bio::DB::Taxonomy |
|
Bio::DB::TFBS
[source]
[v 1.006901]
|
Access to a Transcription Factor Binding Site database |
|
Bio::DB::TFBS::transfac_pro
[source]
[v 1.006901]
|
An implementation of Bio::DB::TFBS |
|
Bio::DB::Universal
[source]
[v 1.006901]
|
Artificial database that delegates to specific databases |
|
Bio::DB::UpdateableSeqI
[source]
[v 1.006901]
|
An interface for writing to a database of sequences. |
|
Bio::DB::WebDBSeqI
[source]
[v 1.006901]
|
Object Interface to generalize Web Databases |
|
Bio::DBLinkContainerI
[source]
[v 1.006901]
|
Abstract interface for any object wanting to use |
|
Bio::DescribableI
[source]
[v 1.006901]
|
interface for objects with human readable names and descriptions |
|
Bio::Draw::Pictogram
[source]
[v 1.006901]
|
generate SVG output of Pictogram display for consensus motifs |
|
Bio::Event::EventGeneratorI
[source]
[v 1.006901]
|
This interface describes the basic event |
|
Bio::Event::EventHandlerI
[source]
[v 1.006901]
|
An Event Handler Interface |
|
Bio::Factory::AnalysisI
[source]
[v 1.006901]
|
An interface to analysis tool factory |
|
Bio::Factory::ApplicationFactoryI
[source]
[v 1.006901]
|
Interface class for Application Factories |
|
Bio::Factory::DriverFactory
[source]
[v 1.006901]
|
Base class for factory classes loading drivers |
|
Bio::Factory::FTLocationFactory
[source]
[v 1.006901]
|
A FeatureTable Location Parser |
|
Bio::Factory::LocationFactoryI
[source]
[v 1.006901]
|
A factory interface for generating locations from a string |
|
Bio::Factory::MapFactoryI
[source]
[v 1.006901]
|
A Factory for getting markers |
|
Bio::Factory::ObjectBuilderI
[source]
[v 1.006901]
|
Interface for an object builder |
|
Bio::Factory::ObjectFactory
[source]
[v 1.006901]
|
Instantiates a new Bio::Root::RootI (or derived class) through a factory |
|
Bio::Factory::ObjectFactoryI
[source]
[v 1.006901]
|
A General object creator factory |
|
Bio::Factory::SeqAnalysisParserFactory
[source]
[v 1.006901]
|
class capable of creating |
|
Bio::Factory::SeqAnalysisParserFactoryI
[source]
[v 1.006901]
|
interface describing objects capable |
|
Bio::Factory::SequenceFactoryI
[source]
[v 1.006901]
|
This interface allows for generic building of sequences in factories which create sequences (like SeqIO) |
|
Bio::Factory::SequenceProcessorI
[source]
[v 1.006901]
|
Interface for chained sequence |
|
Bio::Factory::SequenceStreamI
[source]
[v 1.006901]
|
Interface describing the basics of a Sequence Stream. |
|
Bio::Factory::TreeFactoryI
[source]
[v 1.006901]
|
Factory Interface for getting and writing trees |
|
Bio::FeatureHolderI
[source]
[v 1.006901]
|
the base interface an object with features must implement |
|
Bio::FeatureIO
[source]
[v 1.006901]
|
Handler for FeatureIO |
|
Bio::FeatureIO::bed
[source]
[v 1.006901]
|
read/write features from UCSC BED format |
|
Bio::FeatureIO::gff
[source]
[v 1.006901]
|
read/write GFF feature files |
|
Bio::FeatureIO::gtf
[source]
[v 1.006901]
|
read write features in GTF format |
|
Bio::FeatureIO::interpro
[source]
[v 1.006901]
|
read features from InterPro XML |
|
Bio::FeatureIO::ptt
[source]
[v 1.006901]
|
read/write features in PTT format |
|
Bio::FeatureIO::vecscreen_simple
[source]
[v 1.006901]
|
read/write features from NCBI vecscreen -f 3 |
|
Bio::HandlerBaseI
[source]
[v 1.006901]
|
Interface class for handler methods which interact with any |
|
Bio::IdCollectionI
[source]
[v 1.006901]
|
interface for objects with multiple identifiers |
|
Bio::IdentifiableI
[source]
[v 1.006901]
|
interface for objects with identifiers |
|
Bio::Index::Abstract
[source]
[v 1.006901]
|
Abstract interface for indexing a flat file |
|
Bio::Index::AbstractSeq
[source]
[v 1.006901]
|
base class for AbstractSeq |
|
Bio::Index::Blast
[source]
[v 1.006901]
|
Indexes Blast reports and supports retrieval |
|
Bio::Index::BlastTable
[source]
[v 1.006901]
|
Indexes tabular Blast reports (-m 8 or -m 9 format) and |
|
Bio::Index::EMBL
[source]
[v 1.006901]
|
Interface for indexing (multiple) EMBL/Swissprot |
|
Bio::Index::Fasta
[source]
[v 1.006901]
|
Interface for indexing (multiple) fasta files |
|
Bio::Index::Fastq
[source]
[v 1.006901]
|
Interface for indexing (multiple) fastq files |
|
Bio::Index::GenBank
[source]
[v 1.006901]
|
Interface for indexing one or more GenBank |
|
Bio::Index::Hmmer
[source]
[v 1.006901]
|
indexes HMMER reports and supports retreival based on query |
|
Bio::Index::Qual
[source]
[v 1.006901]
|
Interface for indexing (multiple) fasta qual files |
|
Bio::Index::Stockholm
[source]
[v 1.006901]
|
Indexes Stockholm format alignments (such as those from |
|
Bio::Index::SwissPfam
[source]
[v 1.006901]
|
Interface for indexing swisspfam files |
|
Bio::Index::Swissprot
[source]
[v 1.006901]
|
Interface for indexing one or more |
|
Bio::LiveSeq::AARange
[source]
[v 1.006901]
|
AARange abstract class for LiveSeq |
|
Bio::LiveSeq::Chain
[source]
[v 1.006901]
|
DoubleChain DataStructure for Perl |
|
Bio::LiveSeq::ChainI
[source]
[v 1.006901]
|
Double linked chain data structure |
|
Bio::LiveSeq::DNA
[source]
[v 1.006901]
|
DNA object for LiveSeq |
|
Bio::LiveSeq::Exon
[source]
[v 1.006901]
|
Range abstract class for LiveSeq |
|
Bio::LiveSeq::Gene
[source]
[v 1.006901]
|
Range abstract class for LiveSeq |
|
Bio::LiveSeq::Intron
[source]
[v 1.006901]
|
Range abstract class for LiveSeq |
|
Bio::LiveSeq::IO::BioPerl
[source]
[v 1.006901]
|
Loader for LiveSeq from EMBL entries with BioPerl |
|
Bio::LiveSeq::IO::Loader
[source]
[v 1.006901]
|
Parent Loader for LiveSeq |
|
Bio::LiveSeq::Mutation
[source]
[v 1.006901]
|
Mutation event descriptor class |
|
Bio::LiveSeq::Mutator
[source]
[v 1.006901]
|
Package mutating LiveSequences |
|
Bio::LiveSeq::Prim_Transcript
[source]
[v 1.006901]
|
Prim_Transcript class for LiveSeq |
|
Bio::LiveSeq::Range
[source]
[v 1.006901]
|
Range abstract class for LiveSeq |
|
Bio::LiveSeq::Repeat_Region
[source]
[v 1.006901]
|
Repeat_Region class for LiveSeq |
|
Bio::LiveSeq::Repeat_Unit
[source]
[v 1.006901]
|
Repeat_Unit class for LiveSeq |
|
Bio::LiveSeq::SeqI
[source]
[v 1.006901]
|
Abstract sequence interface class for LiveSeq |
|
Bio::LiveSeq::Transcript
[source]
[v 1.006901]
|
Transcript class for LiveSeq |
|
Bio::LiveSeq::Translation
[source]
[v 1.006901]
|
Translation class for LiveSeq |
|
Bio::Location::Atomic
[source]
[v 1.006901]
|
Implementation of a Atomic Location on a Sequence |
|
Bio::Location::AvWithinCoordPolicy
[source]
[v 1.006901]
|
class implementing |
|
Bio::Location::CoordinatePolicyI
[source]
[v 1.006901]
|
Abstract interface for objects implementing |
|
Bio::Location::Fuzzy
[source]
[v 1.006901]
|
Implementation of a Location on a Sequence |
|
Bio::Location::FuzzyLocationI
[source]
[v 1.006901]
|
Abstract interface of a Location on a Sequence |
|
Bio::Location::NarrowestCoordPolicy
[source]
[v 1.006901]
|
class implementing |
|
Bio::Location::Simple
[source]
[v 1.006901]
|
Implementation of a Simple Location on a Sequence |
|
Bio::Location::Split
[source]
[v 1.006901]
|
Implementation of a Location on a Sequence |
|
Bio::Location::SplitLocationI
[source]
[v 1.006901]
|
Abstract interface of a Location on a Sequence |
|
Bio::Location::WidestCoordPolicy
[source]
[v 1.006901]
|
class implementing |
|
Bio::LocationI
[source]
[v 1.006901]
|
Abstract interface of a Location on a Sequence |
|
Bio::Map::Clone
[source]
[v 1.006901]
|
An central map object representing a clone |
|
Bio::Map::Contig
[source]
[v 1.006901]
|
A MapI implementation handling the contigs of a |
|
Bio::Map::CytoMap
[source]
[v 1.006901]
|
A Bio::MapI compliant map implementation handling cytogenic bands |
|
Bio::Map::CytoMarker
[source]
[v 1.006901]
|
An object representing a marker. |
|
Bio::Map::CytoPosition
[source]
[v 1.006901]
|
Marker class with cytogenetic band storing attributes |
|
Bio::Map::EntityI
[source]
[v 1.006901]
|
An Entity Interface |
|
Bio::Map::FPCMarker
[source]
[v 1.006901]
|
An central map object representing a marker |
|
Bio::Map::Gene
[source]
[v 1.006901]
|
An gene modelled as a mappable element. |
|
Bio::Map::GeneMap
[source]
[v 1.006901]
|
A MapI implementation to represent the area around a gene |
|
Bio::Map::GenePosition
[source]
[v 1.006901]
|
A typed position, suitable for modelling the various |
|
Bio::Map::GeneRelative
[source]
[v 1.006901]
|
Represents being relative to named sub-regions of a |
|
Bio::Map::LinkageMap
[source]
[v 1.006901]
|
A representation of a genetic linkage map. |
|
Bio::Map::LinkagePosition
[source]
[v 1.006901]
|
Create a Position for a Marker that will be placed |
|
Bio::Map::MapI
[source]
[v 1.006901]
|
Interface for describing Map objects in bioperl |
|
Bio::Map::Mappable
[source]
[v 1.006901]
|
An object representing a generic map element |
|
Bio::Map::MappableI
[source]
[v 1.006901]
|
An object that can be placed in a map |
|
Bio::Map::Marker
[source]
[v 1.006901]
|
An central map object representing a generic marker |
|
Bio::Map::MarkerI
[source]
[v 1.006901]
|
Interface for basic marker functionality |
|
Bio::Map::Microsatellite
[source]
[v 1.006901]
|
An object representing a Microsatellite marker. |
|
Bio::Map::OrderedPosition
[source]
[v 1.006901]
|
Abstracts the notion of a member |
|
Bio::Map::OrderedPositionWithDistance
[source]
[v 1.006901]
|
Abstracts the notion of a member |
|
Bio::Map::Physical
[source]
[v 1.006901]
|
A class for handling a Physical Map (such as FPC) |
|
Bio::Map::Position
[source]
[v 1.006901]
|
A single position of a Marker, or the range over which |
|
Bio::Map::PositionHandler
[source]
[v 1.006901]
|
A Position Handler Implementation |
|
Bio::Map::PositionHandlerI
[source]
[v 1.006901]
|
A Position Handler Interface |
|
Bio::Map::PositionI
[source]
[v 1.006901]
|
Abstracts the notion of a position having a value in the context of a marker and a Map |
|
Bio::Map::PositionWithSequence
[source]
[v 1.006901]
|
A position with a sequence. |
|
Bio::Map::Prediction
[source]
[v 1.006901]
|
An object representing the predictions of something |
|
Bio::Map::Relative
[source]
[v 1.006901]
|
Represents what a Position's coordiantes are relative to. |
|
Bio::Map::RelativeI
[source]
[v 1.006901]
|
Interface for describing what a Position's coordiantes are |
|
Bio::Map::SimpleMap
[source]
[v 1.006901]
|
A MapI implementation handling the basics of a Map |
|
Bio::Map::TranscriptionFactor
[source]
[v 1.006901]
|
A transcription factor modelled as a mappable |
|
Bio::MapIO
[source]
[v 1.006901]
|
A Map Factory object |
|
Bio::MapIO::fpc
[source]
[v 1.006901]
|
A FPC Map reader |
|
Bio::MapIO::mapmaker
[source]
[v 1.006901]
|
A Mapmaker Map reader |
|
Bio::Matrix::Generic
[source]
[v 1.006901]
|
A generic matrix implementation |
|
Bio::Matrix::IO
[source]
[v 1.006901]
|
A factory for Matrix parsing |
|
Bio::Matrix::IO::mlagan
[source]
[v 1.006901]
|
A parser for the mlagan substitution matrix |
|
Bio::Matrix::IO::phylip
[source]
[v 1.006901]
|
A parser for PHYLIP distance matricies |
|
Bio::Matrix::IO::scoring
[source]
[v 1.006901]
|
A parser for PAM/BLOSUM matricies |
|
Bio::Matrix::MatrixI
[source]
[v 1.006901]
|
An interface for describing a Matrix |
|
Bio::Matrix::Mlagan
[source]
[v 1.006901]
|
A generic matrix with mlagan fields |
|
Bio::Matrix::PhylipDist
[source]
[v 1.006901]
|
A Phylip Distance Matrix object |
|
Bio::Matrix::PSM::InstanceSite
[source]
[v 1.006901]
|
A PSM site occurance |
|
Bio::Matrix::PSM::InstanceSiteI
[source]
[v 1.006901]
|
InstanceSite interface, holds an instance of a PSM |
|
Bio::Matrix::PSM::IO
[source]
[v 1.006901]
|
PSM parser |
|
Bio::Matrix::PSM::IO::mast
[source]
[v 1.006901]
|
PSM mast parser implementation |
|
Bio::Matrix::PSM::IO::masta
[source]
[v 1.006901]
|
motif fasta format parser |
|
Bio::Matrix::PSM::IO::meme
[source]
[v 1.006901]
|
PSM meme parser implementation |
|
Bio::Matrix::PSM::IO::psiblast
[source]
[v 1.006901]
|
PSM psiblast parser |
|
Bio::Matrix::PSM::IO::transfac
[source]
[v 1.006901]
|
PSM transfac parser |
|
Bio::Matrix::PSM::ProtMatrix
[source]
[v 1.006901]
|
SiteMatrixI implementation, holds a |
|
Bio::Matrix::PSM::ProtPsm
[source]
[v 1.006901]
|
handle combination of site matricies |
|
Bio::Matrix::PSM::Psm
[source]
[v 1.006901]
|
handle combination of site matricies |
|
Bio::Matrix::PSM::PsmHeader
[source]
[v 1.006901]
|
PSM mast parser implementation |
|
Bio::Matrix::PSM::PsmHeaderI
[source]
[v 1.006901]
|
handles the header data from a PSM file |
|
Bio::Matrix::PSM::PsmI
[source]
[v 1.006901]
|
abstract interface to handler of site matricies |
|
Bio::Matrix::PSM::SiteMatrix
[source]
[v 1.006901]
|
SiteMatrixI implementation, holds a |
|
Bio::Matrix::PSM::SiteMatrixI
[source]
[v 1.006901]
|
SiteMatrixI implementation, holds a |
|
Bio::Matrix::Scoring
[source]
[v 1.006901]
|
Object which can hold scoring matrix information |
|
Bio::MolEvol::CodonModel
[source]
[v 1.006901]
|
Codon Evolution Models |
|
Bio::Nexml::Factory
[source]
[v 1.006901]
|
A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents |
|
Bio::NexmlIO
[source]
[v 1.006901]
|
stream handler for NeXML documents |
|
Bio::Ontology::DocumentRegistry
[source]
[v 1.006901]
|
Keep track of where to find ontologies. |
|
Bio::Ontology::GOterm
[source]
[v 1.006901]
|
representation of GO terms |
|
Bio::Ontology::InterProTerm
[source]
[v 1.006901]
|
Implementation of InterProI term interface |
|
Bio::Ontology::OBOEngine
[source]
[v 1.006901]
|
An Ontology Engine for OBO style flat file |
|
Bio::Ontology::OBOterm
[source]
[v 1.006901]
|
representation of OBO terms |
|
Bio::Ontology::Ontology
[source]
[v 1.006901]
|
standard implementation of an Ontology |
|
Bio::Ontology::OntologyEngineI
[source]
[v 1.006901]
|
Interface a minimal Ontology implementation should satisfy |
|
Bio::Ontology::OntologyI
[source]
[v 1.006901]
|
Interface for an ontology implementation |
|
Bio::Ontology::OntologyStore
[source]
[v 1.006901]
|
A repository of ontologies |
|
Bio::Ontology::Path
[source]
[v 1.006901]
|
a path for an ontology term graph |
|
Bio::Ontology::PathI
[source]
[v 1.006901]
|
Interface for a path between ontology terms |
|
Bio::Ontology::Relationship
[source]
[v 1.006901]
|
a relationship for an ontology |
|
Bio::Ontology::RelationshipFactory
[source]
[v 1.006901]
|
Instantiates a new |
|
Bio::Ontology::RelationshipI
[source]
[v 1.006901]
|
Interface for a relationship between ontology terms |
|
Bio::Ontology::RelationshipType
[source]
[v 1.006901]
|
a relationship type for an ontology |
|
Bio::Ontology::SimpleGOEngine::GraphAdaptor
[source]
[v 1.006901]
|
Graph adaptor for |
|
Bio::Ontology::SimpleGOEngine::GraphAdaptor02
[source]
[v 1.006901]
|
Graph adaptor (v02.x) for |
|
Bio::Ontology::SimpleOntologyEngine
[source]
[v 1.006901]
|
Implementation of OntologyEngineI interface |
|
Bio::Ontology::Term
[source]
[v 1.006901]
|
implementation of the interface for ontology terms |
|
Bio::Ontology::TermFactory
[source]
[v 1.006901]
|
Instantiates a new |
|
Bio::Ontology::TermI
[source]
[v 1.006901]
|
interface for ontology terms |
|
Bio::OntologyIO
[source]
[v 1.006901]
|
Parser factory for Ontology formats |
|
Bio::OntologyIO::dagflat
[source]
[v 1.006901]
|
a base class parser for GO flat-file type formats |
|
Bio::OntologyIO::goflat
[source]
[v 1.006901]
|
a parser for the Gene Ontology flat-file format |
|
Bio::OntologyIO::Handlers::BaseSAXHandler [v 1.006901]
|
|
|
Bio::OntologyIO::Handlers::InterProHandler
[source]
[v 1.006901]
|
XML handler class for InterProParser |
|
Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
[source]
[v 1.006901]
|
parse an InterPro XML file and persist the resulting terms to a Biosql database |
|
Bio::OntologyIO::InterProParser
[source]
[v 1.006901]
|
Parser for InterPro xml files. |
|
Bio::OntologyIO::obo
[source]
[v 1.006901]
|
a parser for OBO flat-file format from Gene Ontology Consortium |
|
Bio::OntologyIO::simplehierarchy
[source]
[v 1.006901]
|
a base class parser for simple hierarchy-by-indentation |
|
Bio::OntologyIO::soflat
[source]
[v 1.006901]
|
a parser for the Sequence Ontology flat-file format |
|
Bio::ParameterBaseI
[source]
[v 1.006901]
|
Simple interface class for any parameter-related data such |
|
Bio::Perl
[source]
[v 1.006901]
|
Functional access to BioPerl for people who don't know objects |
|
Bio::Phenotype::Correlate
[source]
[v 1.006901]
|
Representation of a correlating phenotype in a given species |
|
Bio::Phenotype::Measure
[source]
[v 1.006901]
|
Representation of context/value(-range)/unit triplets |
|
Bio::Phenotype::MeSH::Term
[source]
[v 1.006901]
|
A MeSH term |
|
Bio::Phenotype::MeSH::Twig
[source]
[v 1.006901]
|
Context for a MeSH term |
|
Bio::Phenotype::OMIM::MiniMIMentry
[source]
[v 1.006901]
|
Representation of a Mini MIM entry |
|
Bio::Phenotype::OMIM::OMIMentry
[source]
[v 1.006901]
|
represents OMIM (Online Mendelian |
|
Bio::Phenotype::OMIM::OMIMentryAllelicVariant
[source]
[v 1.006901]
|
Representation of a allelic |
|
Bio::Phenotype::OMIM::OMIMparser
[source]
[v 1.006901]
|
parser for the OMIM database |
|
Bio::Phenotype::Phenotype
[source]
[v 1.006901]
|
A class for modeling phenotypes |
|
Bio::Phenotype::PhenotypeI
[source]
[v 1.006901]
|
An interface for classes modeling phenotypes |
|
Bio::PhyloNetwork
[source]
[v 1.006901]
|
Module to compute with Phylogenetic Networks |
|
Bio::PhyloNetwork::Factory
[source]
[v 1.006901]
|
Module to sequentially generate |
|
Bio::PhyloNetwork::FactoryX
[source]
[v 1.006901]
|
Module to sequentially generate |
|
Bio::PhyloNetwork::GraphViz
[source]
[v 1.006901]
|
Interface between PhyloNetwork and GraphViz |
|
Bio::PhyloNetwork::muVector
[source]
[v 1.006901]
|
Module to compute with vectors of arbitrary |
|
Bio::PhyloNetwork::RandomFactory
[source]
[v 1.006901]
|
Module to generate random |
|
Bio::PhyloNetwork::TreeFactory
[source]
[v 1.006901]
|
Module to sequentially generate |
|
Bio::PhyloNetwork::TreeFactoryMulti
[source]
[v 1.006901]
|
Module to sequentially generate |
|
Bio::PhyloNetwork::TreeFactoryX
[source]
[v 1.006901]
|
Module to sequentially generate |
|
Bio::PopGen::Genotype
[source]
[v 1.006901]
|
An implementation of GenotypeI which is just an allele container |
|
Bio::PopGen::GenotypeI
[source]
[v 1.006901]
|
A marker and alleles for a specific individual |
|
Bio::PopGen::HtSNP [v 1.006901]
|
|
|
Bio::PopGen::Individual
[source]
[v 1.006901]
|
An implementation of an Individual who has |
|
Bio::PopGen::IndividualI
[source]
[v 1.006901]
|
An individual who has Genotype or Sequence Results |
|
Bio::PopGen::IO
[source]
[v 1.006901]
|
Input individual,marker,allele information |
|
Bio::PopGen::IO::csv [v 1.006901]
|
|
|
Bio::PopGen::IO::hapmap
[source]
[v 1.006901]
|
A parser for HapMap output data |
|
Bio::PopGen::IO::phase
[source]
[v 1.006901]
|
A parser for Phase format data |
|
Bio::PopGen::IO::prettybase
[source]
[v 1.006901]
|
Extract individual allele data from PrettyBase format |
|
Bio::PopGen::Marker
[source]
[v 1.006901]
|
A genetic marker which one uses to generate genotypes |
|
Bio::PopGen::MarkerI
[source]
[v 1.006901]
|
A Population Genetic conceptual marker |
|
Bio::PopGen::PopStats
[source]
[v 1.006901]
|
A collection of methods for calculating |
|
Bio::PopGen::Population
[source]
[v 1.006901]
|
A population of individuals |
|
Bio::PopGen::PopulationI
[source]
[v 1.006901]
|
Interface for Populations |
|
Bio::PopGen::Simulation::Coalescent
[source]
[v 1.006901]
|
A Coalescent simulation factory |
|
Bio::PopGen::Simulation::GeneticDrift
[source]
[v 1.006901]
|
A simple genetic drift simulation |
|
Bio::PopGen::Statistics
[source]
[v 1.006901]
|
Population Genetics statistical tests |
|
Bio::PopGen::TagHaplotype
[source]
[v 1.006901]
|
Haplotype tag object. |
|
Bio::PopGen::Utilities
[source]
[v 1.006901]
|
Utilities for working with PopGen data and objects |
|
Bio::PrimarySeq
[source]
[v 1.006901]
|
Bioperl lightweight Sequence Object |
|
Bio::PrimarySeq::Fasta [v 1.006901]
|
|
|
Bio::PrimarySeqI
[source]
[v 1.006901]
|
Interface definition for a Bio::PrimarySeq |
|
Bio::PullParserI
[source]
[v 1.006901]
|
A base module for fast 'pull' parsing |
|
Bio::Range
[source]
[v 1.006901]
|
Pure perl RangeI implementation |
|
Bio::RangeI
[source]
[v 1.006901]
|
Range interface |
|
Bio::Restriction::Analysis
[source]
[v 1.006901]
|
cutting sequences with restriction |
|
Bio::Restriction::Enzyme
[source]
[v 1.006901]
|
A single restriction endonuclease |
|
Bio::Restriction::Enzyme::MultiCut
[source]
[v 1.006901]
|
A single restriction endonuclease |
|
Bio::Restriction::Enzyme::MultiSite
[source]
[v 1.006901]
|
A single restriction endonuclease |
|
Bio::Restriction::EnzymeCollection
[source]
[v 1.006901]
|
Set of restriction endonucleases |
|
Bio::Restriction::EnzymeI
[source]
[v 1.006901]
|
Interface class for restriction endonuclease |
|
Bio::Restriction::IO
[source]
[v 1.006901]
|
Handler for sequence variation IO Formats |
|
Bio::Restriction::IO::bairoch
[source]
[v 1.006901]
|
bairoch enzyme set |
|
Bio::Restriction::IO::base
[source]
[v 1.006901]
|
base enzyme set |
|
Bio::Restriction::IO::itype2
[source]
[v 1.006901]
|
itype2 enzyme set |
|
Bio::Restriction::IO::prototype
[source]
[v 1.006901]
|
prototype enzyme set |
|
Bio::Restriction::IO::withrefm
[source]
[v 1.006901]
|
withrefm enzyme set |
|
Bio::Root::Build
[source]
[v 1.006901]
|
A common Module::Build subclass base for BioPerl distributions |
|
Bio::Root::Exception
[source]
[v 1.006901]
|
Generic exception objects for Bioperl |
|
Bio::Root::HTTPget
[source]
[v 1.006901]
|
module for fallback HTTP get operations when |
|
Bio::Root::IO
[source]
[v 1.006901]
|
module providing several methods often needed when dealing with file IO |
|
Bio::Root::Root
[source]
[v 1.006901]
|
Hash-based implementation of Bio::Root::RootI |
|
Bio::Root::RootI
[source]
[v 1.006901]
|
Abstract interface to root object code |
|
Bio::Root::Storable
[source]
[v 1.006901]
|
object serialisation methods |
|
Bio::Root::Test
[source]
[v 1.006901]
|
A common base for all Bioperl test scripts. |
|
Bio::Root::Test::Warn
[source]
[v 1.006901]
|
Perl extension to test Bioperl methods for warnings |
|
Bio::Root::Utilities
[source]
[v 1.006901]
|
General-purpose utility module |
|
Bio::Root::Version
[source]
[v 1.006901]
|
provide global, distribution-level versioning |
|
Bio::Search::BlastStatistics
[source]
[v 1.006901]
|
An object for Blast statistics |
|
Bio::Search::BlastUtils
[source]
[v 1.006901]
|
Utility functions for Bio::Search:: BLAST objects |
|
Bio::Search::DatabaseI
[source]
[v 1.006901]
|
Interface for a database used in a sequence search |
|
Bio::Search::GenericDatabase
[source]
[v 1.006901]
|
Generic implementation of Bio::Search::DatabaseI |
|
Bio::Search::GenericStatistics
[source]
[v 1.006901]
|
An object for statistics |
|
Bio::Search::Hit::BlastHit
[source]
[v 1.006901]
|
Blast-specific subclass of Bio::Search::Hit::GenericHit |
|
Bio::Search::Hit::BlastPullHit
[source]
[v 1.006901]
|
A parser and hit object for BLASTN hits |
|
Bio::Search::Hit::Fasta
[source]
[v 1.006901]
|
Hit object specific for Fasta-generated hits |
|
Bio::Search::Hit::GenericHit
[source]
[v 1.006901]
|
A generic implementation of the Bio::Search::Hit::HitI interface |
|
Bio::Search::Hit::HitFactory
[source]
[v 1.006901]
|
A factory to create Bio::Search::Hit::HitI objects |
|
Bio::Search::Hit::HitI
[source]
[v 1.006901]
|
Interface for a hit in a similarity search result |
|
Bio::Search::Hit::hmmer3Hit
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::Search::Hit::HMMERHit
[source]
[v 1.006901]
|
A Hit module for HMMER hits |
|
Bio::Search::Hit::HmmpfamHit
[source]
[v 1.006901]
|
A parser and hit object for hmmpfam hits |
|
Bio::Search::Hit::ModelHit
[source]
[v 1.006901]
|
A model-based implementation of the Bio::Search::Hit::HitI interface |
|
Bio::Search::Hit::PsiBlastHit
[source]
[v 1.006901]
|
Bioperl BLAST Hit object |
|
Bio::Search::Hit::PullHitI
[source]
[v 1.006901]
|
Bio::Search::Hit::HitI interface for pull parsers. |
|
Bio::Search::HSP::BlastHSP
[source]
[v 1.006901]
|
Bioperl BLAST High-Scoring Pair object |
|
Bio::Search::HSP::BlastPullHSP
[source]
[v 1.006901]
|
A parser and HSP object for BlastN hsps |
|
Bio::Search::HSP::FastaHSP
[source]
[v 1.006901]
|
HSP object for FASTA specific data |
|
Bio::Search::HSP::GenericHSP
[source]
[v 1.006901]
|
A "Generic" implementation of a High Scoring Pair |
|
Bio::Search::HSP::hmmer3HSP
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::Search::HSP::HMMERHSP
[source]
[v 1.006901]
|
A HSP object for HMMER results |
|
Bio::Search::HSP::HmmpfamHSP
[source]
[v 1.006901]
|
A parser and HSP object for hmmpfam hsps |
|
Bio::Search::HSP::HSPFactory
[source]
[v 1.006901]
|
A factory to create Bio::Search::HSP::HSPI objects |
|
Bio::Search::HSP::ModelHSP
[source]
[v 1.006901]
|
A HSP object for model-based searches |
|
Bio::Search::HSP::PsiBlastHSP
[source]
[v 1.006901]
|
Bioperl BLAST High-Scoring Pair object |
|
Bio::Search::HSP::PSLHSP
[source]
[v 1.006901]
|
A HSP for PSL output |
|
Bio::Search::HSP::PullHSPI
[source]
[v 1.006901]
|
Bio::Search::HSP::HSPI interface for pull parsers. |
|
Bio::Search::HSP::WABAHSP
[source]
[v 1.006901]
|
HSP object suitable for describing WABA alignments |
|
Bio::Search::Iteration::GenericIteration
[source]
[v 1.006901]
|
A generic implementation of the Bio::Search::Iteration::IterationI interface. |
|
Bio::Search::Iteration::IterationI
[source]
[v 1.006901]
|
Abstract interface to an |
|
Bio::Search::Processor
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::Search::Result::BlastPullResult
[source]
[v 1.006901]
|
A parser and result object for BLASTN |
|
Bio::Search::Result::BlastResult
[source]
[v 1.006901]
|
Blast-specific subclass of Bio::Search::Result::GenericResult |
|
Bio::Search::Result::CrossMatchResult
[source]
[v 1.006901]
|
CrossMatch-specific subclass of Bio::Search::Result::GenericResult |
|
Bio::Search::Result::GenericResult
[source]
[v 1.006901]
|
Generic Implementation of |
|
Bio::Search::Result::hmmer3Result
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::Search::Result::HMMERResult
[source]
[v 1.006901]
|
A Result object for HMMER results |
|
Bio::Search::Result::HmmpfamResult
[source]
[v 1.006901]
|
A parser and result object for hmmpfam |
|
Bio::Search::Result::PullResultI
[source]
[v 1.006901]
|
Bio::Search::Result::ResultI interface for |
|
Bio::Search::Result::ResultFactory
[source]
[v 1.006901]
|
A factory to create Bio::Search::Result::ResultI objects |
|
Bio::Search::Result::ResultI
[source]
[v 1.006901]
|
Abstract interface to Search Result objects |
|
Bio::Search::Result::WABAResult
[source]
[v 1.006901]
|
Result object for WABA alignment output |
|
Bio::Search::SearchUtils
[source]
[v 1.006901]
|
Utility functions for Bio::Search:: objects |
|
Bio::Search::StatisticsI
[source]
[v 1.006901]
|
A Base object for statistics |
|
Bio::Search::Tiling::MapTileUtils
[source]
[v 1.006901]
|
utilities for manipulating closed intervals for an HSP tiling algorithm |
|
Bio::Search::Tiling::MapTiling
[source]
[v 1.006901]
|
An implementation of an HSP tiling |
|
Bio::Search::Tiling::TilingI
[source]
[v 1.006901]
|
Abstract interface for an HSP tiling module |
|
Bio::SearchDist
[source]
[v 1.006901]
|
A perl wrapper around Sean Eddy's histogram object |
|
Bio::SearchIO
[source]
[v 1.006901]
|
Driver for parsing Sequence Database Searches |
|
Bio::SearchIO::axt
[source]
[v 1.006901]
|
a parser for axt format reports |
|
Bio::SearchIO::blast
[source]
[v 1.006901]
|
Event generator for event based parsing of |
|
Bio::SearchIO::blasttable
[source]
[v 1.006901]
|
Driver module for SearchIO for parsing NCBI -m 8/9 format |
|
Bio::SearchIO::blastxml
[source]
[v 1.006901]
|
A SearchIO implementation of NCBI Blast XML parsing. |
|
Bio::SearchIO::blast_pull
[source]
[v 1.006901]
|
A parser for BLAST output |
|
Bio::SearchIO::cross_match
[source]
[v 1.006901]
|
CrossMatch-specific subclass of Bio::SearchIO |
|
Bio::SearchIO::erpin
[source]
[v 1.006901]
|
SearchIO-based ERPIN parser |
|
Bio::SearchIO::EventHandlerI
[source]
[v 1.006901]
|
An abstract Event Handler for Search Result parsing |
|
Bio::SearchIO::exonerate
[source]
[v 1.006901]
|
parser for Exonerate |
|
Bio::SearchIO::fasta
[source]
[v 1.006901]
|
A SearchIO parser for FASTA results |
|
Bio::SearchIO::FastHitEventBuilder
[source]
[v 1.006901]
|
Event Handler for SearchIO events. |
|
Bio::SearchIO::gmap_f9
[source]
[v 1.006901]
|
Event generator for parsing gmap reports (Z format) |
|
Bio::SearchIO::hmmer
[source]
[v 1.006901]
|
A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam) |
|
Bio::SearchIO::hmmer2
[source]
[v 1.006901]
|
A parser for HMMER output (hmmpfam, hmmsearch) |
|
Bio::SearchIO::hmmer3
[source]
[v 1.006901]
|
DESCRIPTION of Object |
|
Bio::SearchIO::hmmer_pull
[source]
[v 1.006901]
|
A parser for HMMER output |
|
Bio::SearchIO::infernal
[source]
[v 1.006901]
|
SearchIO-based Infernal parser |
|
Bio::SearchIO::IteratedSearchResultEventBuilder
[source]
[v 1.006901]
|
Event Handler for |
|
Bio::SearchIO::megablast
[source]
[v 1.006901]
|
a driver module for Bio::SearchIO to parse |
|
Bio::SearchIO::psl
[source]
[v 1.006901]
|
A parser for PSL output (UCSC) |
|
Bio::SearchIO::rnamotif
[source]
[v 1.006901]
|
SearchIO-based RNAMotif parser |
|
Bio::SearchIO::SearchResultEventBuilder
[source]
[v 1.006901]
|
Event Handler for SearchIO events. |
|
Bio::SearchIO::SearchWriterI
[source]
[v 1.006901]
|
Interface for outputting parsed Search results |
|
Bio::SearchIO::sim4
[source]
[v 1.006901]
|
parser for Sim4 alignments |
|
Bio::SearchIO::waba
[source]
[v 1.006901]
|
SearchIO parser for Jim Kent WABA program |
|
Bio::SearchIO::wise
[source]
[v 1.006901]
|
Parsing of wise output as alignments |
|
Bio::SearchIO::Writer::BSMLResultWriter
[source]
[v 1.006901]
|
BSML output writer |
|
Bio::SearchIO::Writer::GbrowseGFF
[source]
[v 1.006901]
|
Interface for outputting parsed search results in Gbrowse GFF format |
|
Bio::SearchIO::Writer::HitTableWriter
[source]
[v 1.006901]
|
Tab-delimited data for Bio::Search::Hit::HitI objects |
|
Bio::SearchIO::Writer::HSPTableWriter
[source]
[v 1.006901]
|
Tab-delimited data for Bio::Search::HSP::HSPI objects |
|
Bio::SearchIO::Writer::HTMLResultWriter
[source]
[v 1.006901]
|
write a Bio::Search::ResultI in HTML |
|
Bio::SearchIO::Writer::ResultTableWriter
[source]
[v 1.006901]
|
Outputs tab-delimited data for each Bio::Search::Result::ResultI object. |
|
Bio::SearchIO::Writer::TextResultWriter
[source]
[v 1.006901]
|
Object to implement writing |
|
Bio::SearchIO::XML::BlastHandler
[source]
[v 1.006901]
|
XML Handler for NCBI Blast XML parsing. |
|
Bio::SearchIO::XML::PsiBlastHandler
[source]
[v 1.006901]
|
XML Handler for NCBI Blast PSIBLAST XML parsing. |
|
Bio::Seq
[source]
[v 1.006901]
|
Sequence object, with features |
|
Bio::Seq::BaseSeqProcessor
[source]
[v 1.006901]
|
Base implementation for a SequenceProcessor |
|
Bio::Seq::EncodedSeq
[source]
[v 1.006901]
|
subtype of L<Bio::LocatableSeq|Bio::LocatableSeq> to store DNA that encodes a protein |
|
Bio::Seq::LargeLocatableSeq
[source]
[v 1.006901]
|
LocatableSeq object that stores sequence as |
|
Bio::Seq::LargePrimarySeq
[source]
[v 1.006901]
|
PrimarySeq object that stores sequence as |
|
Bio::Seq::LargeSeq
[source]
[v 1.006901]
|
SeqI compliant object that stores sequence as |
|
Bio::Seq::LargeSeqI
[source]
[v 1.006901]
|
Interface class for sequences that cache their |
|
Bio::Seq::Meta
[source]
[v 1.006901]
|
Generic superclass for sequence objects with |
|
Bio::Seq::Meta::Array
[source]
[v 1.006901]
|
array-based generic implementation of a |
|
Bio::Seq::MetaI
[source]
[v 1.006901]
|
Interface for sequence objects with residue-based |
|
Bio::Seq::PrimaryQual
[source]
[v 1.006901]
|
Bioperl lightweight Quality Object |
|
Bio::Seq::PrimaryQual::Qual [v 1.006901]
|
|
|
Bio::Seq::PrimedSeq
[source]
[v 1.006901]
|
A representation of a sequence and two primers |
|
Bio::Seq::QualI
[source]
[v 1.006901]
|
Interface definition for a Bio::Seq::Qual |
|
Bio::Seq::Quality
[source]
[v 1.006901]
|
Implementation of sequence with residue quality |
|
Bio::Seq::RichSeq
[source]
[v 1.006901]
|
Module implementing a sequence created from a rich |
|
Bio::Seq::RichSeqI
[source]
[v 1.006901]
|
interface for sequences from rich data sources, mostly databases |
|
Bio::Seq::SeqBuilder
[source]
[v 1.006901]
|
Configurable object builder for sequence stream parsers |
|
Bio::Seq::SeqFactory
[source]
[v 1.006901]
|
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
|
Bio::Seq::SeqFastaSpeedFactory
[source]
[v 1.006901]
|
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory |
|
Bio::Seq::SequenceTrace
[source]
[v 1.006901]
|
Bioperl object packaging a sequence with its trace |
|
Bio::Seq::SeqWithQuality
[source]
[v 1.006901]
|
Bioperl object packaging a sequence with its quality. |
|
Bio::Seq::TraceI
[source]
[v 1.006901]
|
Interface definition for a Bio::Seq::Trace |
|
Bio::SeqAnalysisParserI
[source]
[v 1.006901]
|
Sequence analysis output parser interface |
|
Bio::SeqEvolution::DNAPoint
[source]
[v 1.006901]
|
evolve a sequence by point mutations |
|
Bio::SeqEvolution::EvolutionI
[source]
[v 1.006901]
|
the interface for evolving sequences |
|
Bio::SeqEvolution::Factory
[source]
[v 1.006901]
|
Factory object to instantiate sequence evolving classes |
|
Bio::SeqFeature::Annotated
[source]
[v 1.006901]
|
PLEASE PUT SOMETHING HERE |
|
Bio::SeqFeature::AnnotationAdaptor
[source]
[v 1.006901]
|
integrates SeqFeatureIs annotation |
|
Bio::SeqFeature::Collection
[source]
[v 1.006901]
|
A container class for SeqFeatures |
|
Bio::SeqFeature::CollectionI
[source]
[v 1.006901]
|
An interface for a collection of SeqFeatureI objects. |
|
Bio::SeqFeature::Computation
[source]
[v 1.006901]
|
Computation SeqFeature |
|
Bio::SeqFeature::FeaturePair
[source]
[v 1.006901]
|
hold pair feature information e.g. blast hits |
|
Bio::SeqFeature::Gene::Exon
[source]
[v 1.006901]
|
a feature representing an exon |
|
Bio::SeqFeature::Gene::ExonI
[source]
[v 1.006901]
|
Interface for a feature representing an exon |
|
Bio::SeqFeature::Gene::GeneStructure
[source]
[v 1.006901]
|
A feature representing an arbitrarily complex structure of a gene |
|
Bio::SeqFeature::Gene::GeneStructureI
[source]
[v 1.006901]
|
A feature representing an arbitrarily |
|
Bio::SeqFeature::Gene::Intron
[source]
[v 1.006901]
|
An intron feature |
|
Bio::SeqFeature::Gene::NC_Feature
[source]
[v 1.006901]
|
superclass for non-coding features |
|
Bio::SeqFeature::Gene::Poly_A_site
[source]
[v 1.006901]
|
poly A feature |
|
Bio::SeqFeature::Gene::Promoter
[source]
[v 1.006901]
|
Describes a promoter |
|
Bio::SeqFeature::Gene::Transcript
[source]
[v 1.006901]
|
A feature representing a transcript |
|
Bio::SeqFeature::Gene::TranscriptI
[source]
[v 1.006901]
|
Interface for a feature representing a |
|
Bio::SeqFeature::Gene::UTR
[source]
[v 1.006901]
|
A feature representing an untranslated region |
|
Bio::SeqFeature::Generic
[source]
[v 1.006901]
|
Generic SeqFeature |
|
Bio::SeqFeature::Lite
[source]
[v 1.006901]
|
Lightweight Bio::SeqFeatureI class |
|
Bio::SeqFeature::PositionProxy
[source]
[v 1.006901]
|
handle features when truncation/revcom sequences span a feature |
|
Bio::SeqFeature::Primer
[source]
[v 1.006901]
|
Primer Generic SeqFeature |
|
Bio::SeqFeature::Similarity
[source]
[v 1.006901]
|
A sequence feature based on similarity |
|
Bio::SeqFeature::SimilarityPair
[source]
[v 1.006901]
|
Sequence feature based on the similarity |
|
Bio::SeqFeature::SiRNA::Oligo
[source]
[v 1.006901]
|
Perl object for small inhibitory RNAs. |
|
Bio::SeqFeature::SiRNA::Pair
[source]
[v 1.006901]
|
Perl object for small inhibitory RNA |
|
Bio::SeqFeature::Tools::FeatureNamer
[source]
[v 1.006901]
|
generates unique persistent names for features |
|
Bio::SeqFeature::Tools::IDHandler
[source]
[v 1.006901]
|
maps $seq_feature-E<gt>primary_tag |
|
Bio::SeqFeature::Tools::TypeMapper
[source]
[v 1.006901]
|
maps $seq_feature-E<gt>primary_tag |
|
Bio::SeqFeature::Tools::Unflattener
[source]
[v 1.006901]
|
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy |
|
Bio::SeqFeature::TypedSeqFeatureI
[source]
[v 1.006901]
|
a strongly typed SeqFeature |
|
Bio::SeqFeatureI
[source]
[v 1.006901]
|
Abstract interface of a Sequence Feature |
|
Bio::SeqI
[source]
[v 1.006901]
|
[Developers] Abstract Interface of Sequence (with features) |
|
Bio::SeqIO
[source]
[v 1.006901]
|
Handler for SeqIO Formats |
|
Bio::SeqIO::abi
[source]
[v 1.006901]
|
abi trace sequence input/output stream |
|
Bio::SeqIO::ace
[source]
[v 1.006901]
|
ace sequence input/output stream |
|
Bio::SeqIO::agave
[source]
[v 1.006901]
|
AGAVE sequence output stream. |
|
Bio::SeqIO::alf
[source]
[v 1.006901]
|
alf trace sequence input/output stream |
|
Bio::SeqIO::asciitree
[source]
[v 1.006901]
|
asciitree sequence input/output stream |
|
Bio::SeqIO::bsml
[source]
[v 1.006901]
|
BSML sequence input/output stream |
|
Bio::SeqIO::bsml_sax
[source]
[v 1.006901]
|
BSML sequence input/output stream using SAX |
|
Bio::SeqIO::chadoxml
[source]
[v 1.006901]
|
chadoxml sequence output stream |
|
Bio::SeqIO::chaos
[source]
[v 1.006901]
|
chaos sequence input/output stream |
|
Bio::SeqIO::chaosxml
[source]
[v 1.006901]
|
chaosxml sequence input/output stream |
|
Bio::SeqIO::ctf
[source]
[v 1.006901]
|
ctf trace sequence input/output stream |
|
Bio::SeqIO::embl
[source]
[v 1.006901]
|
EMBL sequence input/output stream |
|
Bio::SeqIO::embldriver
[source]
[v 1.006901]
|
EMBL sequence input/output stream |
|
Bio::SeqIO::entrezgene
[source]
[v 1.006901]
|
Entrez Gene ASN1 parser |
|
Bio::SeqIO::excel
[source]
[v 1.006901]
|
sequence input/output stream from a |
|
Bio::SeqIO::exp
[source]
[v 1.006901]
|
exp trace sequence input/output stream |
|
Bio::SeqIO::fasta
[source]
[v 1.006901]
|
fasta sequence input/output stream |
|
Bio::SeqIO::fastq
[source]
[v 1.006901]
|
fastq sequence input/output stream |
|
Bio::SeqIO::flybase_chadoxml
[source]
[v 1.006901]
|
FlyBase variant of chadoxml with sequence output stream |
|
Bio::SeqIO::FTHelper
[source]
[v 1.006901]
|
Helper class for Embl/Genbank feature tables |
|
Bio::SeqIO::game
[source]
[v 1.006901]
|
a class for parsing and writing game-XML |
|
Bio::SeqIO::game::featHandler
[source]
[v 1.006901]
|
a class for handling feature elements |
|
Bio::SeqIO::game::gameHandler
[source]
[v 1.006901]
|
PerlSAX handler for game-XML |
|
Bio::SeqIO::game::gameSubs
[source]
[v 1.006901]
|
a base class for game-XML parsing |
|
Bio::SeqIO::game::gameWriter
[source]
[v 1.006901]
|
a class for writing game-XML |
|
Bio::SeqIO::game::seqHandler
[source]
[v 1.006901]
|
a class for handling game-XML sequences |
|
Bio::SeqIO::gbdriver
[source]
[v 1.006901]
|
GenBank handler-based push parser |
|
Bio::SeqIO::gbxml
[source]
[v 1.006901]
|
GenBank sequence input/output stream using SAX |
|
Bio::SeqIO::gcg
[source]
[v 1.006901]
|
GCG sequence input/output stream |
|
Bio::SeqIO::genbank
[source]
[v 1.006901]
|
GenBank sequence input/output stream |
|
Bio::SeqIO::Handler::GenericRichSeqHandler
[source]
[v 1.006901]
|
Bio::HandlerI-based |
|
Bio::SeqIO::interpro
[source]
[v 1.006901]
|
InterProScan XML input/output stream |
|
Bio::SeqIO::kegg
[source]
[v 1.006901]
|
KEGG sequence input/output stream |
|
Bio::SeqIO::largefasta
[source]
[v 1.006901]
|
method i/o on very large fasta sequence files |
|
Bio::SeqIO::lasergene
[source]
[v 1.006901]
|
Lasergene sequence file input/output stream |
|
Bio::SeqIO::locuslink
[source]
[v 1.006901]
|
LocusLink input/output stream |
|
Bio::SeqIO::mbsout
[source]
[v 1.006901]
|
input stream for output by Teshima et al.'s mbs. |
|
Bio::SeqIO::metafasta
[source]
[v 1.006901]
|
metafasta sequence input/output stream |
|
Bio::SeqIO::msout
[source]
[v 1.006901]
|
input stream for output by Hudson's ms |
|
Bio::SeqIO::MultiFile
[source]
[v 1.006901]
|
Treating a set of files as a single input stream |
|
Bio::SeqIO::nexml
[source]
[v 1.006901]
|
NeXML sequence input/output stream |
|
Bio::SeqIO::phd
[source]
[v 1.006901]
|
phd file input/output stream |
|
Bio::SeqIO::pir
[source]
[v 1.006901]
|
PIR sequence input/output stream |
|
Bio::SeqIO::pln
[source]
[v 1.006901]
|
pln trace sequence input/output stream |
|
Bio::SeqIO::qual
[source]
[v 1.006901]
|
.qual file input/output stream |
|
Bio::SeqIO::raw
[source]
[v 1.006901]
|
raw sequence file input/output stream |
|
Bio::SeqIO::scf
[source]
[v 1.006901]
|
.scf file input/output stream |
|
Bio::SeqIO::seqxml
[source]
[v 1.006901]
|
SeqXML sequence input/output stream |
|
Bio::SeqIO::strider
[source]
[v 1.006901]
|
DNA strider sequence input/output stream |
|
Bio::SeqIO::swiss
[source]
[v 1.006901]
|
Swissprot sequence input/output stream |
|
Bio::SeqIO::swissdriver
[source]
[v 1.006901]
|
SwissProt/UniProt handler-based push parser |
|
Bio::SeqIO::tab
[source]
[v 1.006901]
|
nearly raw sequence file input/output |
|
Bio::SeqIO::table
[source]
[v 1.006901]
|
sequence input/output stream from a delimited table |
|
Bio::SeqIO::tigr
[source]
[v 1.006901]
|
TIGR XML sequence input/output stream |
|
Bio::SeqIO::tigrxml
[source]
[v 1.006901]
|
Parse TIGR (new) XML |
|
Bio::SeqIO::tinyseq
[source]
[v 1.006901]
|
reading/writing sequences in NCBI TinySeq format |
|
Bio::SeqIO::tinyseq::tinyseqHandler
[source]
[v 1.006901]
|
XML event handlers to support NCBI TinySeq XML parsing |
|
Bio::SeqIO::ztr
[source]
[v 1.006901]
|
ztr trace sequence input/output stream |
|
Bio::SeqUtils
[source]
[v 1.006901]
|
Additional methods for PrimarySeq objects |
|
Bio::SimpleAlign
[source]
[v 1.006901]
|
Multiple alignments held as a set of sequences |
|
Bio::SimpleAnalysisI
[source]
[v 1.006901]
|
A simple interface to any (local or remote) analysis tool |
|
Bio::Species
[source]
[v 1.006901]
|
Generic species object. |
|
Bio::Structure::Atom
[source]
[v 1.006901]
|
Bioperl structure Object, describes an Atom |
|
Bio::Structure::Chain
[source]
[v 1.006901]
|
Bioperl structure Object, describes a chain |
|
Bio::Structure::Entry
[source]
[v 1.006901]
|
Bioperl structure Object, describes the whole entry |
|
Bio::Structure::IO
[source]
[v 1.006901]
|
Handler for Structure Formats |
|
Bio::Structure::IO::pdb
[source]
[v 1.006901]
|
PDB input/output stream |
|
Bio::Structure::Model
[source]
[v 1.006901]
|
Bioperl structure Object, describes a Model |
|
Bio::Structure::Residue
[source]
[v 1.006901]
|
Bioperl structure Object, describes a Residue |
|
Bio::Structure::SecStr::DSSP::Res
[source]
[v 1.006901]
|
Module for parsing/accessing dssp output |
|
Bio::Structure::SecStr::STRIDE::Res
[source]
[v 1.006901]
|
Module for parsing/accessing stride output |
|
Bio::Structure::StructureI
[source]
[v 1.006901]
|
Abstract Interface for a Structure objects |
|
Bio::Symbol::Alphabet
[source]
[v 1.006901]
|
BSANE/BioCORBA compliant symbol list alphabet |
|
Bio::Symbol::AlphabetI
[source]
[v 1.006901]
|
A Symbol Alphabet |
|
Bio::Symbol::DNAAlphabet
[source]
[v 1.006901]
|
A ready made DNA alphabet |
|
Bio::Symbol::ProteinAlphabet
[source]
[v 1.006901]
|
A ready made Protein alphabet |
|
Bio::Symbol::Symbol
[source]
[v 1.006901]
|
A biological symbol |
|
Bio::Symbol::SymbolI
[source]
[v 1.006901]
|
Interface for a Symbol |
|
Bio::Taxon
[source]
[v 1.006901]
|
A node in a represented taxonomy |
|
Bio::Taxonomy
[source]
[v 1.006901]
|
representing Taxonomy. |
|
Bio::Taxonomy::FactoryI
[source]
[v 1.006901]
|
interface to define how to access NCBI Taxonoy |
|
Bio::Taxonomy::Node
[source]
[v 1.006901]
|
A node in a represented taxonomy |
|
Bio::Taxonomy::Taxon
[source]
[v 1.006901]
|
Generic Taxonomic Entity object |
|
Bio::Taxonomy::Tree
[source]
[v 1.006901]
|
An Organism Level Implementation of TreeI interface. |
|
Bio::Tools::AlignFactory
[source]
[v 1.006901]
|
Base object for alignment factories |
|
Bio::Tools::Alignment::Consed
[source]
[v 1.006901]
|
A module to work with objects from consed .ace files |
|
Bio::Tools::Alignment::Trim
[source]
[v 1.006901]
|
A kludge to do specialized trimming of |
|
Bio::Tools::Analysis::DNA::ESEfinder
[source]
[v 1.006901]
|
a wrapper around ESEfinder |
|
Bio::Tools::Analysis::Protein::Domcut
[source]
[v 1.006901]
|
a wrapper around Domcut server |
|
Bio::Tools::Analysis::Protein::ELM
[source]
[v 1.006901]
|
a wrapper around the ELM server which predicts short functional motifs on amino acid sequences |
|
Bio::Tools::Analysis::Protein::GOR4
[source]
[v 1.006901]
|
a wrapper around GOR4 protein |
|
Bio::Tools::Analysis::Protein::HNN
[source]
[v 1.006901]
|
a wrapper around the HNN protein |
|
Bio::Tools::Analysis::Protein::Mitoprot
[source]
[v 1.006901]
|
a wrapper around Mitoprot |
|
Bio::Tools::Analysis::Protein::NetPhos
[source]
[v 1.006901]
|
a wrapper around NetPhos server |
|
Bio::Tools::Analysis::Protein::Scansite
[source]
[v 1.006901]
|
a wrapper around the Scansite server |
|
Bio::Tools::Analysis::Protein::Sopma
[source]
[v 1.006901]
|
a wrapper around the |
|
Bio::Tools::Analysis::SimpleAnalysisBase
[source]
[v 1.006901]
|
abstract superclass for |
|
Bio::Tools::AnalysisResult
[source]
[v 1.006901]
|
Base class for analysis result objects and parsers |
|
Bio::Tools::Blat
[source]
[v 1.006901]
|
parser for Blat program |
|
Bio::Tools::CodonTable
[source]
[v 1.006901]
|
Codon table object |
|
Bio::Tools::Coil
[source]
[v 1.006901]
|
parser for Coil output |
|
Bio::Tools::dpAlign
[source]
[v 1.006901]
|
Perl extension to do pairwise dynamic programming sequence alignment |
|
Bio::Tools::ECnumber
[source]
[v 1.006901]
|
representation of EC numbers (Enzyme Classification) |
|
Bio::Tools::EMBOSS::Palindrome
[source]
[v 1.006901]
|
parse EMBOSS palindrome output |
|
Bio::Tools::EPCR
[source]
[v 1.006901]
|
Parse ePCR output and make features |
|
Bio::Tools::Eponine
[source]
[v 1.006901]
|
Results of one Eponine run |
|
Bio::Tools::ERPIN
[source]
[v 1.006901]
|
a parser for ERPIN output |
|
Bio::Tools::Est2Genome
[source]
[v 1.006901]
|
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects |
|
Bio::Tools::ESTScan
[source]
[v 1.006901]
|
Results of one ESTScan run |
|
Bio::Tools::EUtilities
[source]
[v 1.006901]
|
NCBI eutil XML parsers |
|
Bio::Tools::EUtilities::EUtilDataI
[source]
[v 1.006901]
|
eutil data object interface |
|
Bio::Tools::EUtilities::EUtilParameters
[source]
[v 1.006901]
|
Manipulation of NCBI eutil-based |
|
Bio::Tools::EUtilities::History
[source]
[v 1.006901]
|
lightweight implementation of HistoryI |
|
Bio::Tools::EUtilities::HistoryI
[source]
[v 1.006901]
|
simple extension of EUtilDataI interface |
|
Bio::Tools::EUtilities::Info
[source]
[v 1.006901]
|
interface class for storing einfo data |
|
Bio::Tools::EUtilities::Info::FieldInfo
[source]
[v 1.006901]
|
class for storing einfo field data |
|
Bio::Tools::EUtilities::Info::LinkInfo
[source]
[v 1.006901]
|
class for storing einfo link data |
|
Bio::Tools::EUtilities::Link
[source]
[v 1.006901]
|
general API for accessing data retrieved from elink queries |
|
Bio::Tools::EUtilities::Link::LinkSet
[source]
[v 1.006901]
|
class for EUtils LinkSets |
|
Bio::Tools::EUtilities::Link::UrlLink
[source]
[v 1.006901]
|
class for EUtils UrlLinks |
|
Bio::Tools::EUtilities::Query
[source]
[v 1.006901]
|
parse and collect esearch, epost, espell, |
|
Bio::Tools::EUtilities::Query::GlobalQuery
[source]
[v 1.006901]
|
container class for egquery data |
|
Bio::Tools::EUtilities::Summary
[source]
[v 1.006901]
|
class for handling data output (XML) from |
|
Bio::Tools::EUtilities::Summary::DocSum
[source]
[v 1.006901]
|
data object for document summary data |
|
Bio::Tools::EUtilities::Summary::Item
[source]
[v 1.006901]
|
simple layered object for DocSum item data |
|
Bio::Tools::EUtilities::Summary::ItemContainerI
[source]
[v 1.006901]
|
abtract interface methods |
|
Bio::Tools::Fgenesh
[source]
[v 1.006901]
|
parse results of one Fgenesh run |
|
Bio::Tools::FootPrinter
[source]
[v 1.006901]
|
write sequence features in FootPrinter format |
|
Bio::Tools::Gel
[source]
[v 1.006901]
|
Calculates relative electrophoretic migration distances |
|
Bio::Tools::Geneid
[source]
[v 1.006901]
|
Results of one geneid run |
|
Bio::Tools::Genemark
[source]
[v 1.006901]
|
Results of one Genemark run |
|
Bio::Tools::Genewise
[source]
[v 1.006901]
|
Results of one Genewise run |
|
Bio::Tools::Genomewise
[source]
[v 1.006901]
|
Results of one Genomewise run |
|
Bio::Tools::Genscan
[source]
[v 1.006901]
|
Results of one Genscan run |
|
Bio::Tools::GFF
[source]
[v 1.006901]
|
A Bio::SeqAnalysisParserI compliant GFF format parser |
|
Bio::Tools::Glimmer
[source]
[v 1.006901]
|
parser for Glimmer 2.X/3.X prokaryotic and |
|
Bio::Tools::Grail
[source]
[v 1.006901]
|
Results of one Grail run |
|
Bio::Tools::GuessSeqFormat
[source]
[v 1.006901]
|
Module for determining the sequence |
|
Bio::Tools::HMMER::Domain
[source]
[v 1.006901]
|
One particular domain hit from HMMER |
|
Bio::Tools::HMMER::Results
[source]
[v 1.006901]
|
Object representing HMMER output results |
|
Bio::Tools::HMMER::Set
[source]
[v 1.006901]
|
Set of identical domains from HMMER matches |
|
Bio::Tools::Hmmpfam
[source]
[v 1.006901]
|
Parser for Hmmpfam program |
|
Bio::Tools::Infernal
[source]
[v 1.006901]
|
A parser for Infernal output |
|
Bio::Tools::ipcress
[source]
[v 1.006901]
|
Parse ipcress output and make features |
|
Bio::Tools::isPcr
[source]
[v 1.006901]
|
Parse isPcr output and make features |
|
Bio::Tools::IUPAC
[source]
[v 1.006901]
|
Generates unique Seq objects from an ambiguous Seq object |
|
Bio::Tools::Lucy
[source]
[v 1.006901]
|
Object for analyzing the output from Lucy, |
|
Bio::Tools::Match
[source]
[v 1.006901]
|
Parses output from Transfac's match(TM) |
|
Bio::Tools::MZEF
[source]
[v 1.006901]
|
Results of one MZEF run |
|
Bio::Tools::OddCodes
[source]
[v 1.006901]
|
Object holding alternative alphabet coding for |
|
Bio::Tools::Phylo::Gerp
[source]
[v 1.006901]
|
Parses output from GERP |
|
Bio::Tools::Phylo::Gumby
[source]
[v 1.006901]
|
Parses output from gumby |
|
Bio::Tools::Phylo::Molphy
[source]
[v 1.006901]
|
parser for Molphy output |
|
Bio::Tools::Phylo::Molphy::Result
[source]
[v 1.006901]
|
container for data parsed from a ProtML run |
|
Bio::Tools::Phylo::PAML
[source]
[v 1.006901]
|
Parses output from the PAML programs codeml, |
|
Bio::Tools::Phylo::PAML::Codeml
[source]
[v 1.006901]
|
Parses output from the PAML program codeml. |
|
Bio::Tools::Phylo::PAML::ModelResult
[source]
[v 1.006901]
|
A container for NSSite Model Result from PAML |
|
Bio::Tools::Phylo::PAML::Result
[source]
[v 1.006901]
|
A PAML result set object |
|
Bio::Tools::Phylo::Phylip::ProtDist
[source]
[v 1.006901]
|
parser for ProtDist output |
|
Bio::Tools::pICalculator
[source]
[v 1.006901]
|
calculate the isoelectric point of a protein |
|
Bio::Tools::Prediction::Exon
[source]
[v 1.006901]
|
A predicted exon feature |
|
Bio::Tools::Prediction::Gene
[source]
[v 1.006901]
|
a predicted gene structure feature |
|
Bio::Tools::Primer3
[source]
[v 1.006901]
|
Create input for and work with the output from |
|
Bio::Tools::Primer::Assessor::Base
[source]
[v 1.006901]
|
base class for common assessor things |
|
Bio::Tools::Primer::AssessorI
[source]
[v 1.006901]
|
interface for assessing primer pairs |
|
Bio::Tools::Primer::Feature
[source]
[v 1.006901]
|
position of a single primer |
|
Bio::Tools::Primer::Pair
[source]
[v 1.006901]
|
two primers on left and right side |
|
Bio::Tools::Prints
[source]
[v 1.006901]
|
Parser for FingerPRINTScanII program |
|
Bio::Tools::Profile
[source]
[v 1.006901]
|
parse Profile output |
|
Bio::Tools::Promoterwise
[source]
[v 1.006901]
|
parser for Promoterwise tab format output |
|
Bio::Tools::PrositeScan
[source]
[v 1.006901]
|
Parser for ps_scan result |
|
Bio::Tools::Protparam
[source]
[v 1.006901]
|
submit to and parse output from protparam ; |
|
Bio::Tools::Pseudowise
[source]
[v 1.006901]
|
Results of one Pseudowise run |
|
Bio::Tools::pSW
[source]
[v 1.006901]
|
pairwise Smith Waterman object |
|
Bio::Tools::QRNA
[source]
[v 1.006901]
|
A Parser for qrna output |
|
Bio::Tools::RandomDistFunctions
[source]
[v 1.006901]
|
A set of routines useful for |
|
Bio::Tools::RepeatMasker
[source]
[v 1.006901]
|
a parser for RepeatMasker output |
|
Bio::Tools::RNAMotif
[source]
[v 1.006901]
|
A parser for RNAMotif output |
|
Bio::Tools::Run::GenericParameters
[source]
[v 1.006901]
|
An object for the parameters used to run programs |
|
Bio::Tools::Run::ParametersI
[source]
[v 1.006901]
|
A Base object for the parameters used to run programs |
|
Bio::Tools::Run::RemoteBlast
[source]
[v 1.006901]
|
Object for remote execution of the NCBI Blast |
|
Bio::Tools::Run::StandAloneBlast
[source]
[v 1.006901]
|
Object for the local execution |
|
Bio::Tools::Run::StandAloneNCBIBlast
[source]
[v 1.006901]
|
Object for the local execution |
|
Bio::Tools::Run::StandAloneWUBlast
[source]
[v 1.006901]
|
Object for the local execution |
|
Bio::Tools::Run::WrapperBase
[source]
[v 1.006901]
|
A Base object for wrappers around executables |
|
Bio::Tools::Seg
[source]
[v 1.006901]
|
parse C<seg> output |
|
Bio::Tools::SeqPattern
[source]
[v 1.006901]
|
represent a sequence pattern or motif |
|
Bio::Tools::SeqPattern::Backtranslate
[source]
[v 1.006901]
|
|
|
Bio::Tools::SeqStats
[source]
[v 1.006901]
|
Object holding statistics for one |
|
Bio::Tools::SeqWords
[source]
[v 1.006901]
|
Object holding n-mer statistics for a sequence |
|
Bio::Tools::Sigcleave
[source]
[v 1.006901]
|
Bioperl object for sigcleave analysis |
|
Bio::Tools::Signalp
[source]
[v 1.006901]
|
parser for Signalp output |
|
Bio::Tools::Signalp::ExtendedSignalp
[source]
[v 1.006901]
|
enhanced parser for Signalp output |
|
Bio::Tools::Sim4::Exon
[source]
[v 1.006901]
|
A single exon determined by an alignment |
|
Bio::Tools::Sim4::Results
[source]
[v 1.006901]
|
Results of one Sim4 run |
|
Bio::Tools::SiRNA [v 1.006901]
|
|
|
Bio::Tools::SiRNA::Ruleset::saigo
[source]
[v 1.006901]
|
Perl object implementing the Saigo |
|
Bio::Tools::SiRNA::Ruleset::tuschl
[source]
[v 1.006901]
|
Perl object implementing the |
|
Bio::Tools::Spidey::Exon
[source]
[v 1.006901]
|
A single exon determined by an alignment |
|
Bio::Tools::Spidey::Results
[source]
[v 1.006901]
|
Results of a Spidey run |
|
Bio::Tools::TandemRepeatsFinder
[source]
[v 1.006901]
|
a parser for Tandem Repeats Finder output |
|
Bio::Tools::TargetP
[source]
[v 1.006901]
|
Results of one TargetP run |
|
Bio::Tools::Tmhmm
[source]
[v 1.006901]
|
parse TMHMM output (TransMembrane HMM) |
|
Bio::Tools::tRNAscanSE
[source]
[v 1.006901]
|
A parser for tRNAscan-SE output |
|
Bio::Tree::AlleleNode
[source]
[v 1.006901]
|
A Node with Alleles attached |
|
Bio::Tree::AnnotatableNode
[source]
[v 1.006901]
|
A Tree Node with support for annotation |
|
Bio::Tree::Compatible
[source]
[v 1.006901]
|
Testing compatibility of phylogenetic trees |
|
Bio::Tree::DistanceFactory
[source]
[v 1.006901]
|
Construct a tree using distance based methods |
|
Bio::Tree::Draw::Cladogram
[source]
[v 1.006901]
|
Drawing phylogenetic trees in |
|
Bio::Tree::Node
[source]
[v 1.006901]
|
A Simple Tree Node |
|
Bio::Tree::NodeI
[source]
[v 1.006901]
|
Interface describing a Tree Node |
|
Bio::Tree::NodeNHX
[source]
[v 1.006901]
|
A Simple Tree Node with support for NHX tags |
|
Bio::Tree::RandomFactory
[source]
[v 1.006901]
|
TreeFactory for generating Random Trees |
|
Bio::Tree::Statistics
[source]
[v 1.006901]
|
Calculate certain statistics for a Tree |
|
Bio::Tree::Tree
[source]
[v 1.006901]
|
An Implementation of TreeI interface. |
|
Bio::Tree::TreeFunctionsI
[source]
[v 1.006901]
|
Decorated Interface implementing basic Tree exploration methods |
|
Bio::Tree::TreeI
[source]
[v 1.006901]
|
A Tree object suitable for lots of things, designed |
|
Bio::TreeIO
[source]
[v 1.006901]
|
Parser for Tree files |
|
Bio::TreeIO::cluster
[source]
[v 1.006901]
|
A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output |
|
Bio::TreeIO::lintree
[source]
[v 1.006901]
|
Parser for lintree output trees |
|
Bio::TreeIO::newick
[source]
[v 1.006901]
|
TreeIO implementation for parsing |
|
Bio::TreeIO::NewickParser [v 1.006901]
|
|
|
Bio::TreeIO::nexml
[source]
[v 1.006901]
|
A TreeIO driver module for parsing NeXML tree files |
|
Bio::TreeIO::nexus
[source]
[v 1.006901]
|
A TreeIO driver module for parsing Nexus tree output from PAUP |
|
Bio::TreeIO::nhx
[source]
[v 1.006901]
|
TreeIO implementation for parsing |
|
Bio::TreeIO::pag
[source]
[v 1.006901]
|
Bio::TreeIO driver for Pagel format |
|
Bio::TreeIO::phyloxml
[source]
[v 1.006901]
|
TreeIO implementation for parsing PhyloXML format. |
|
Bio::TreeIO::svggraph
[source]
[v 1.006901]
|
A simple output format that converts a Tree object to an SVG output |
|
Bio::TreeIO::tabtree
[source]
[v 1.006901]
|
A simple output format which displays a tree as an ASCII drawing |
|
Bio::TreeIO::TreeEventBuilder
[source]
[v 1.006901]
|
Build Bio::Tree::Tree's and |
|
Bio::UpdateableSeqI
[source]
[v 1.006901]
|
Descendant of Bio::SeqI that allows updates |
|
Bio::Variation::AAChange
[source]
[v 1.006901]
|
Sequence change class for polypeptides |
|
Bio::Variation::AAReverseMutate
[source]
[v 1.006901]
|
point mutation and codon |
|
Bio::Variation::Allele
[source]
[v 1.006901]
|
Sequence object with allele-specific attributes |
|
Bio::Variation::DNAMutation
[source]
[v 1.006901]
|
DNA level mutation class |
|
Bio::Variation::IO
[source]
[v 1.006901]
|
Handler for sequence variation IO Formats |
|
Bio::Variation::IO::flat
[source]
[v 1.006901]
|
flat file sequence variation input/output stream |
|
Bio::Variation::IO::xml
[source]
[v 1.006901]
|
XML sequence variation input/output stream |
|
Bio::Variation::RNAChange
[source]
[v 1.006901]
|
Sequence change class for RNA level |
|
Bio::Variation::SeqDiff
[source]
[v 1.006901]
|
Container class for mutation/variant descriptions |
|
Bio::Variation::SNP
[source]
[v 1.006901]
|
submitted SNP |
|
Bio::Variation::VariantI
[source]
[v 1.006901]
|
Sequence Change SeqFeature abstract class |
|
Bio::WebAgent
[source]
[v 1.006901]
|
A base class for Web (any protocol) access |
