Documentation
extracts BioPerl documentation and indexes it in a database for easy retrieval
check modules and scripts for authors not in AUTHORS file
check NAME in module POD has fully qualified object name
validate URLs located in module code and POD
convert cvs log messages to changelogs
check modules and scripts for dependencies not in core
Check modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.
inspect only hard-coded dependencies of sets of perl files
information about modules in BioPerl core
check the POD documentation syntax in modules and scripts
install script to create symbolic links
Bulk-load a Bio::DB::GFF database from GFF files.
Fast-load a Bio::DB::GFF database from GFF files.
Load a Bio::DB::GFF database from GENBANK files.
Genbank-gtgbrowse-friendly GFF3
Generate a histogram of Bio::DB::GFF features
Load a Bio::DB::GFF database from GFF files.
Get/set Bio::DB::GFF meta-data
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
Massage WormBase GFF files into a version suitable for the Generic Genome Browser
Load GFF into a SeqFeature database
an interactive command-line interface to Bio::DB::HIV and Bio::DB::Query::HIVQuery
Caching BioFetch-compatible web proxy for GenBank
index sequence files using Bio::DB::Flat
sequence retrieval using OBDA registry
finding flanking sequences for a variant in a sequence position
fetches sequences from bioperl indexed databases
indexes files for use by bp_fetch.pl
bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
a test for distinguishing between selection and population expansion.
turn FASTA -m 9 output into NCBI -m 9 tabular output
filters searchio results, outputting a tab delimited summary
turn HMMER output into tabular format
parse single/multiple HMMSEARCH results file(s) with different output options
turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
extract the corresponding sequence for a specified feature type
Convert an input mRNA/cDNA sequence into protein
generic BioPerl sequence format converter
Takes one or more sequence files and splits them into a number of load balanced files.
split a sequence (or stream) into a single file per sequence
splits a sequence into equal sized chunks with an optional overlapping range
translates a sequence
unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
amino acid composition of protein sequences
a chaos plot from DNA and RNA sequences
GC content of nucleotide sequences
oligo count and frequency
classify BLAST hits by taxonomic kingdom
query a local TaxonomyDB for species or taxonid
query Entrez taxonomy database and print out information
simple script which returns the NCBI Taxonomic id for a requested species
Building a taxonomic tree based on the full lineages of a set of species names
builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
convert nexus format trees (from PAUP* and MrBayes) to new hampshire
convert Bio::TreeIO parseable format trees to pagel format
script to split an input set of database(s) into smaller pieces
script to query Genbank and retrieve records
extract DNA sequences based on BLAST hits
mask sequence(s) based on its alignment results
implement a transformer of alignments from protein to mrna coordinates
randomly mutagenize a single protein or DNA sequence
a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
script to calculate pairwise Ka,Ks for a set of sequences
script for submitting jobs to a remote blast server (ncbi blast queue at this time)
Reverse translate a Profam-like protein motif
Turn SearchIO parseable reports(s) into a set of aligned blocks
Turn SearchIO parseable reports(s) into TRIBE matrix
lists the number of bases and number of sequences in specified sequence database files
convert sequence formats
Modules
An interface for describing sequence alignments.
Calculate some statistics for a DNA alignment
Graphic Rendering of Bio::Align::AlignI Objects
Base statistic object for Pairwise Alignments
Calculate Protein Alignment statistics (mostly distances)
Calculate some statistics for an alignment
A collection of utilities regarding converting and manipulating alignment objects
Handler for AlignIO Formats
Bio::HandlerI-based generic data handler class for alignment-based data
ARP MSA Sequence input/output stream
bl2seq sequence input/output stream
clustalw sequence input/output stream
Parse EMBOSS alignment output (from applications water and needle)
fasta MSA Sequence input/output stream
Largemultifasta MSA Sequence input/output stream
Multiple Alignment Format sequence input stream
mase sequence input/output stream
Parse and Create MEGA format data files
meme sequence input/output stream
Metafasta MSA Sequence input/output stream
msf sequence input/output stream
NeXML format sequence alignment input/output stream driver
NEXUS format sequence input/output stream
pfam sequence input/output stream
PHYLIP format sequence input/output stream
po MSA Sequence input/output stream
proda sequence input/output stream
prodom sequence input/output stream
Read/Write PSI-BLAST profile alignment files
selex sequence input/output stream
stockholm sequence input/output stream
XMFA MSA Sequence input/output stream
An interface to any (local or remote) analysis tool
Generic analysis output parser interface
Interface for analysis result objects
the base interface an annotatable object must implement
Instantiates a new Bio::AnnotationI (or derived class) through a factory
Default Perl implementation of AnnotationCollectionI
A comment object, holding text
untyped links between databases
An ontology term adapted to AnnotationI
Specialised DBLink object for Literature References
Relationship (pairwise) with other objects SeqI and NodeI;
A simple scalar
A scalar with embedded structured information
AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
Provide a tree as an annotation to a Bio::AnnotatableI object
Manages types for annotation collections
Interface for annotation collections
Annotation interface
Perl module to hold and manipulate sequence assembly contigs.
Perform analysis on sequence assembly contigs.
Handler for Assembly::IO Formats
module to load ACE files from various assembly programs
An IO module for assemblies in Bowtie format *BETA*
Driver to read assembly files in maq format *BETA*
driver to load phrap.out files.
An IO module for assemblies in Sam format *BETA*
Driver to read and write assembly files in the TIGR Assembler v2 default format.
Perl module to hold and manipulate sequence assembly data.
Abstract Inteface of Sequence Assemblies
Perl module to hold and manipulate singlets from sequence assembly contigs.
create and manipulate contig spectra
Instantiates a new Bio::ClusterI (or derived class) through a factory
Family Interface
Sequence Family object
UniGene object
abstract interface of UniGene object
Cluster Interface
Handler for Cluster Formats
dbSNP input stream
UniGene input stream
for reading and writing codon usage tables to file
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Database object interface to ACeDB servers
Database object interface to BioFetch retrieval
for access to the Codon usage Database at http://www.kazusa.or.jp/codon.
Database object for retrieving using the dbfetch script
Database object interface for EMBL entry retrieval
Database object interface to Entrez Gene
DESCRIPTION of Object
*** DESCRIPTION of Class
A Bio::DB::RandomAccessI compliant class which wraps a prioritized list of DBs
Fast indexed access to fasta files
In file cache for BioSeq objects
Interface for indexed flat files
Interface for BioHackathon standard BDB-indexed flat file
embl adaptor for Open-bio standard BDB-indexed flat file
fasta adaptor for Open-bio standard BDB-indexed flat file
genbank adaptor for Open-bio standard BDB-indexed flat file
swissprot adaptor for Open-bio standard BDB-indexed flat file
BinarySearch search indexing system for sequence files
Storage and retrieval of sequence annotation data
ace interface (for multiple inheritance)
Bio::DB::GFF database adaptor for in-memory databases
iterator for Bio::DB::GFF::Adaptor::berkeleydb
Cache BioFetch objects in a Bio::DB::GFF database
Cache BioFetch objects in a Bio::DB::GFF database
Database adaptor for DBI (SQL) databases
Cache for database handles
iterator for Bio::DB::GFF::Adaptor::dbi
Database adaptor for a specific mysql schema
Unholy union between mysql GFF database and acedb database
Database adaptor for an integraded CMap/GBrowse mysql schema
Deprecated database adaptor
Database adaptor for a specific oracle schema
Unholy union between oracle GFF database and acedb database
Database adaptor for a specific postgres schema
Database adaptor for a specific postgres schema with a TSearch2 implementation
Bio::DB::GFF database adaptor for in-memory databases
utility methods for serializing and deserializing GFF features
iterator for Bio::DB::GFF::Adaptor::memory
Aggregate GFF groups into composite features
Alignment aggregator
Clone aggregator
The Coding Region Aggregator
Sequence Ontology Geene
Match aggregator
No aggregation
An aggregator for orf regions
Sequence Ontology Transcript
Sequence Ontology Transcript
Transcript aggregator
UCSC acembly aggregator
UCSC ensGene aggregator
UCSC genscan aggregator
UCSC refGene aggregator
UCSC sanger22 aggregator
UCSC sanger22pseudo aggregator
UCSC softberry aggregator
UCSC twinscan aggregator
UCSC UniGene aggregator
The name of a feature
A relative segment identified by a feature type
A segment of DNA that is homologous to another
Sequence segment with relative coordinate support
Simple DNA segment object
The name of a feature type
binning utility for Bio::DB::GFF index
rearrange utility
Database object interface to GenBank
Database object interface to GenPept
helper base class for parameter-based remote server access and response retrieval.
Database object interface to the Los Alamos HIV Sequence Database
Adds HIV-specific annotations to Bio::SeqIO streams
Routines and packages used by Bio::DB::HIV and Bio::DB::Query::HIVQuery
Abstract interface for a sequence database
Base class for modules using indexed sequence files
A RandomAccessI-like abstract interface for retrieving location data from a sequence database and returning Bio::LocationI objects
Term retrieval from a Web MeSH database
A collection of routines useful for queries to NCBI databases.
Fast indexed access to quality files
Build a GenBank Entrez Query
Query interface to the Los Alamos HIV Sequence Database
Helper class for web-based sequence queryies
Object Interface to queryable sequence databases
Abstract interface for a sequence database
Database object interface for RefSeq retrieval
A RandomAccessI-like abstract interface for retrieving Reference data from a sequence database and returning Bio::Annotation::Reference objects
Access to the Open Bio Database Access registry scheme
Normalized feature for use with Bio::DB::SeqFeature::Store
Normalized feature for use with Bio::DB::SeqFeature::Store
Interface for normalized features
Interface for normalized features whose hierarchy is stored in a table
Location-based access to genome annotation data
Storage and retrieval of sequence annotation data
utility methods for creating and iterating over SeqFeature records
PostgreSQL implementation of Bio::DB::SeqFeature::Store
SQLite implementation of Bio::DB::SeqFeature::Store
Mysql implementation of Bio::DB::SeqFeature::Store
feature file loader for Bio::DB::SeqFeature::Store
GFF2 file loader for Bio::DB::SeqFeature::Store
GFF3 file loader for Bio::DB::SeqFeature::Store
Internal utility for Bio::DB::SeqFeature::Store
fetch and store objects from a BerkeleyDB
Storage and retrieval of sequence annotation data in Berkeleydb files
Storage and retrieval of sequence annotation data in Berkeleydb files
In-memory implementation of Bio::DB::SeqFeature::Store
Abstract Interface for Sequence databases
front end to querying databases for identifier versions
interface to NCBI Sequence Revision History page
Database object interface to SwissProt retrieval
Access to a Transcription Factor Binding Site database
An implementation of Bio::DB::TFBS which uses local flat files for transfac pro
Access to a taxonomy database
Taxonomy Entrez driver
Use the NCBI taxonomy from local indexed flat files
Use the Greengenes taxonomy
An implementation of Bio::DB::Taxonomy that accepts lists of words to build a database
Use the Silva taxonomy
SQLite-based implementation of Bio::DB::Taxonomy::flatfile
Artificial database that delegates to specific databases
An interface for writing to a database of sequences.
Object Interface to generalize Web Databases for retrieving sequences
Abstract interface for any object wanting to use database cross references
Simple interface to Sequence Ontology feature types
DAS-style access to a feature database
DAS-style access to a feature database
interface for objects with human readable names and descriptions
generate SVG output of Pictogram display for consensus motifs
This interface describes the basic event generator class.
An Event Handler Interface
An interface to analysis tool factory
Interface class for Application Factories
Base class for factory classes loading drivers
A FeatureTable Location Parser
A factory interface for generating locations from a string
A Factory for getting markers
Interface for an object builder
Instantiates a new Bio::Root::RootI (or derived class) through a factory
A General object creator factory
class capable of creating SeqAnalysisParserI compliant parsers
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
Interface for chained sequence processing algorithms
Interface describing the basics of a Sequence Stream.
Factory Interface for getting and writing trees from/to a data stream
the base interface an object with features must implement
Interface class for handler methods which interact with any event-driven parsers (drivers).
interface for objects with multiple identifiers
interface for objects with identifiers
Abstract interface for indexing a flat file
base class for AbstractSeq
Indexes Blast reports and supports retrieval based on query accession(s)
Indexes tabular Blast reports (-m 8 or -m 9 format) and supports retrieval based on query accession(s)
Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
Interface for indexing (multiple) fasta files
Interface for indexing (multiple) fastq files
Interface for indexing one or more GenBank files (i.e. flat file GenBank format).
indexes HMMER reports and supports retreival based on query
Interface for indexing (multiple) fasta qual files
Interface for indexing swisspfam files
Interface for indexing one or more Swissprot files.
AARange abstract class for LiveSeq
DoubleChain DataStructure for Perl
Double linked chain data structure
DNA object for LiveSeq
Range abstract class for LiveSeq
Range abstract class for LiveSeq
Loader for LiveSeq from EMBL entries with BioPerl
Parent Loader for LiveSeq
Range abstract class for LiveSeq
Mutation event descriptor class
Package mutating LiveSequences
Prim_Transcript class for LiveSeq
Range abstract class for LiveSeq
Repeat_Region class for LiveSeq
Repeat_Unit class for LiveSeq
Abstract sequence interface class for LiveSeq
Transcript class for LiveSeq
Translation class for LiveSeq
A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
Implementation of a Atomic Location on a Sequence
class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Implementation of a Location on a Sequence which has unclear start and/or end locations
Abstract interface of a Location on a Sequence which has unclear start/end location
class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Implementation of a Simple Location on a Sequence
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Abstract interface of a Location on a Sequence
An central map object representing a clone
A MapI implementation handling the contigs of a Physical Map (such as FPC)
A Bio::MapI compliant map implementation handling cytogenic bands
An object representing a marker.
Marker class with cytogenetic band storing attributes
An Entity Interface
An central map object representing a marker
An gene modelled as a mappable element.
A MapI implementation to represent the area around a gene
A typed position, suitable for modelling the various regions of a gene.
Represents being relative to named sub-regions of a gene.
A representation of a genetic linkage map.
Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap
Interface for describing Map objects in bioperl
An object representing a generic map element that can have multiple locations in several maps.
An object that can be placed in a map
An central map object representing a generic marker that can have multiple location in several maps.
Interface for basic marker functionality
An object representing a Microsatellite marker.
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.
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.
A class for handling a Physical Map (such as FPC)
A single position of a Marker, or the range over which that marker lies, in a Map
A Position Handler Implementation
A Position Handler Interface
Abstracts the notion of a position having a value in the context of a marker and a Map
A position with a sequence.
An object representing the predictions of something that can have multiple locations in several maps.
Represents what a Position's coordiantes are relative to.
Interface for describing what a Position's coordiantes are relative to.
A MapI implementation handling the basics of a Map
A transcription factor modelled as a mappable element
A Map Factory object
A FPC Map reader
A Mapmaker Map reader
A generic matrix implementation
A factory for Matrix parsing
A parser for the mlagan substitution matrix
A parser for PHYLIP distance matricies
A parser for PAM/BLOSUM matricies
An interface for describing a Matrix
A generic matrix with mlagan fields
PSM parser
PSM mast parser implementation
motif fasta format parser
PSM meme parser implementation
PSM psiblast parser
PSM transfac parser
A PSM site occurance
InstanceSite interface, holds an instance of a PSM
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) with log-odds scoring information.
handle combination of site matricies
handle combination of site matricies
PSM mast parser implementation
handles the header data from a PSM file
abstract interface to handler of site matricies
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
A Phylip Distance Matrix object
Object which can hold scoring matrix information
Codon Evolution Models
A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents
stream handler for NeXML documents
Keep track of where to find ontologies. Allows lookups by name.
representation of GO terms
Implementation of InterProI term interface
An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
representation of OBO terms
standard implementation of an Ontology
Interface a minimal Ontology implementation should satisfy
Interface for an ontology implementation
A repository of ontologies
a path for an ontology term graph
Interface for a path between ontology terms
a relationship for an ontology
Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory
Interface for a relationship between ontology terms
a relationship type for an ontology
Graph adaptor for Bio::Ontology::SimpleGOEngine
Implementation of OntologyEngineI interface
implementation of the interface for ontology terms
Instantiates a new Bio::Ontology::TermI (or derived class) through a factory
interface for ontology terms
Parser factory for Ontology formats
XML handler class for InterProParser
parse an InterPro XML file and persist the resulting terms to a Biosql database
Parser for InterPro xml files.
a base class parser for GO flat-file type formats
a parser for the Gene Ontology flat-file format
a base class parser for simple hierarchy-by-indentation type formats
a parser for the Sequence Ontology flat-file format
Simple interface class for any parameter-related data such as IDs, database name, program arguments, and other odds and ends.
Functional access to BioPerl for people who don't know objects
Representation of a correlating phenotype in a given species
A MeSH term
Context for a MeSH term
Representation of context/value(-range)/unit triplets
Representation of a Mini MIM entry
represents OMIM (Online Mendelian Inheritance in Man) database entries
Representation of a allelic variant of the OMIM database
parser for the OMIM database
A class for modeling phenotypes
An interface for classes modeling phenotypes
Module to compute with Phylogenetic Networks
Module to sequentially generate Phylogenetic Networks
Module to sequentially generate Phylogenetic Networks
Interface between PhyloNetwork and GraphViz
Module to generate random Phylogenetic Networks
Module to sequentially generate Phylogenetic Trees
Module to sequentially generate Phylogenetic Trees
Module to sequentially generate Phylogenetic Trees
Module to compute with vectors of arbitrary dimension
An implementation of GenotypeI which is just an allele container
A marker and alleles for a specific individual
Input individual,marker,allele information
A parser for HapMap output data
A parser for Phase format data
Extract individual allele data from PrettyBase format
An implementation of an Individual who has Genotype or Sequence Results
An individual who has Genotype or Sequence Results
A genetic marker which one uses to generate genotypes
A Population Genetic conceptual marker
A collection of methods for calculating statistics about a population or sets of populations
A population of individuals
Interface for Populations
A Coalescent simulation factory
A simple genetic drift simulation
Population Genetics statistical tests
Haplotype tag object.
Utilities for working with PopGen data and objects
Bioperl lightweight sequence object
Interface definition for a Bio::PrimarySeq
A base module for fast 'pull' parsing
Pure perl RangeI implementation
Range interface
cutting sequences with restriction enzymes
A single restriction endonuclease (cuts DNA at specific locations)
A single restriction endonuclease
A single restriction endonuclease
Set of restriction endonucleases
Interface class for restriction endonuclease
Handler for sequence variation IO Formats
bairoch enzyme set
base enzyme set
itype2 enzyme set
prototype enzyme set
withrefm enzyme set
module for fallback HTTP get operations when LWP:: is unavailable
An implementation of TestInterface
An object for Blast statistics
Utility functions for Bio::Search:: BLAST objects
Interface for a database used in a sequence search
Generic implementation of Bio::Search::DatabaseI
An object for statistics
Bioperl BLAST High-Scoring Pair object
A parser and HSP object for BlastN hsps
HSP object for FASTA specific data
A "Generic" implementation of a High Scoring Pair
A HSP object for HMMER results
A factory to create Bio::Search::HSP::HSPI objects
Interface for a High Scoring Pair in a similarity search result
A parser and HSP object for hmmpfam hsps
A HSP object for model-based searches
A HSP for PSL output
Bioperl BLAST High-Scoring Pair object
Bio::Search::HSP::HSPI interface for pull parsers.
HSP object suitable for describing WABA alignments
Blast-specific subclass of Bio::Search::Hit::GenericHit
A parser and hit object for BLASTN hits
Hit object specific for Fasta-generated hits
A generic implementation of the Bio::Search::Hit::HitI interface
A Hit module for HMMER hits
A factory to create Bio::Search::Hit::HitI objects
Interface for a hit in a similarity search result
A parser and hit object for hmmpfam hits
A model-based implementation of the Bio::Search::Hit::HitI interface
Bioperl BLAST Hit object
Bio::Search::Hit::HitI interface for pull parsers.
DESCRIPTION of Object
A generic implementation of the Bio::Search::Iteration::IterationI interface.
Abstract interface to an iteration from an iterated search result, such as PSI-BLAST.
DESCRIPTION of Object
A parser and result object for BLASTN results
Blast-specific subclass of Bio::Search::Result::GenericResult
CrossMatch-specific subclass of Bio::Search::Result::GenericResult
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
A Result object for HMMER results
A parser and result object for hmmpfam results
A Result object for INFERNAL results
Bio::Search::Result::ResultI interface for 'pull' parsers
A factory to create Bio::Search::Result::ResultI objects
Abstract interface to Search Result objects
Result object for WABA alignment output
DESCRIPTION of Object
Utility functions for Bio::Search:: objects
A Base object for statistics
utilities for manipulating closed intervals for an HSP tiling algorithm
An implementation of an HSP tiling algorithm, with methods to obtain frequently-requested statistics
Abstract interface for an HSP tiling module
A perl wrapper around Sean Eddy's histogram object
Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
An abstract Event Handler for Search Result parsing
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Event Handler for SearchIO events.
Interface for outputting parsed Search results
Interface for outputting parsed search results in Gbrowse GFF format
Tab-delimited data for Bio::Search::HSP::HSPI objects
write a Bio::Search::ResultI in HTML
Tab-delimited data for Bio::Search::Hit::HitI objects
Outputs tab-delimited data for each Bio::Search::Result::ResultI object.
Object to implement writing a Bio::Search::ResultI in Text.
a parser for axt format reports
Event generator for event based parsing of blast reports
A parser for BLAST output
Driver module for SearchIO for parsing NCBI -m 8/9 format
CrossMatch-specific subclass of Bio::SearchIO
SearchIO-based ERPIN parser
parser for Exonerate
A SearchIO parser for FASTA results
Event generator for parsing gmap reports (Z format)
A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
A parser for HMMER output (hmmpfam, hmmsearch)
A parser for HMMER output
SearchIO-based Infernal parser
a driver module for Bio::SearchIO to parse megablast reports (format 0)
A parser for PSL output (UCSC)
SearchIO-based RNAMotif parser
parser for Sim4 alignments
SearchIO parser for Jim Kent WABA program alignment output
Parsing of wise output as alignments
Sequence object, with features
Base implementation for a SequenceProcessor
subtype of Bio::LocatableSeq to store DNA that encodes a protein
LocatableSeq object that stores sequence as files in the tempdir
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root
SeqI compliant object that stores sequence as files in /tmp
Interface class for sequences that cache their residues in a temporary file
Generic superclass for sequence objects with residue-based meta information
array-based generic implementation of a sequence class with residue-based meta information
Interface for sequence objects with residue-based meta information
Bioperl lightweight Quality Object
A sequence and a pair of primers matching on it
Interface definition for a Bio::Seq::Qual
Implementation of sequence with residue quality and trace values
Module implementing a sequence created from a rich sequence database entry
interface for sequences from rich data sources, mostly databases
Configurable object builder for sequence stream parsers
Instantiation of generic Bio::PrimarySeqI (or derived) objects through a factory
Rapid creation of Bio::Seq objects through a factory
Bioperl object packaging a sequence with its quality. Deprecated class, use Bio::Seq::Quality instead!
Bioperl object packaging a sequence with its trace
Read with sequencing errors taken from a reference sequence
Interface definition for a Bio::Seq::Trace
Sequence analysis output parser interface
evolve a sequence by point mutations
the interface for evolving sequences
Factory object to instantiate sequence evolving classes
Amplicon feature
integrates SeqFeatureIs annotation
A container class for SeqFeatures suitable for performing operations such as finding features within a range, that match a certain feature type, etc.
An interface for a collection of SeqFeatureI objects.
Computation SeqFeature
hold pair feature information e.g. blast hits
a feature representing an exon
Interface for a feature representing an exon
A feature representing an arbitrarily complex structure of a gene
A feature representing an arbitrarily complex structure of a gene
An intron feature
superclass for non-coding features
poly A feature
Describes a promoter
A feature representing a transcript
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
A feature representing an untranslated region that is part of a transcriptional unit
Generic SeqFeature
Lightweight Bio::SeqFeatureI class
handle features when truncation/revcom sequences span a feature
Primer Generic SeqFeature
Perl object for small inhibitory RNAs.
Perl object for small inhibitory RNA (SiRNA) oligo pairs
A sequence feature based on similarity
Sequence feature based on the similarity of two sequences.
Feature representing a subsequence
generates unique persistent names for features
maps $seq_feature-gtprimary_tag
maps $seq_feature-gtprimary_tag
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
a strongly typed SeqFeature
Abstract interface of a Sequence Feature
[Developers] Abstract Interface of Sequence (with features)
Handler for SeqIO Formats
Helper class for EMBL/Genbank feature tables
Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
Treating a set of files as a single input stream
abi trace sequence input/output stream
ace sequence input/output stream
AGAVE sequence output stream.
alf trace sequence input/output stream
asciitree sequence input/output stream
BSML sequence input/output stream
BSML sequence input/output stream using SAX
chadoxml sequence output stream
chaos sequence input/output stream
chaosxml sequence input/output stream
ctf trace sequence input/output stream
EMBL sequence input/output stream
EMBL sequence input/output stream
Entrez Gene ASN1 parser
sequence input/output stream from a MSExcel-formatted table
exp trace sequence input/output stream
fasta sequence input/output stream
fastq sequence input/output stream
FlyBase variant of chadoxml with sequence output stream
a class for parsing and writing game-XML
a class for handling feature elements
PerlSAX handler for game-XML
a base class for game-XML parsing
a class for writing game-XML
a class for handling game-XML sequences
GenBank handler-based push parser
GenBank sequence input/output stream using SAX
GCG sequence input/output stream
GenBank sequence input/output stream
InterProScan XML input/output stream
KEGG sequence input/output stream
method i/o on very large fasta sequence files
Lasergene sequence file input/output stream
LocusLink input/output stream
input stream for output by Teshima et al.'s mbs.
metafasta sequence input/output stream
input stream for output by Hudson's ms
NeXML sequence input/output stream
phd file input/output stream
PIR sequence input/output stream
pln trace sequence input/output stream
.qual file input/output stream
raw sequence file input/output stream
.scf file input/output stream
SeqXML sequence input/output stream
DNA strider sequence input/output stream
Swissprot sequence input/output stream
SwissProt/UniProt handler-based push parser
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
sequence input/output stream from a delimited table
TIGR XML sequence input/output stream
Parse TIGR (new) XML
reading/writing sequences in NCBI TinySeq format
XML event handlers to support NCBI TinySeq XML parsing
ztr trace sequence input/output stream
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
A simple interface to any (local or remote) analysis tool
Generic species object.
Bioperl structure Object, describes an Atom
Bioperl structure Object, describes a chain
Bioperl structure Object, describes the whole entry
Handler for Structure Formats
PDB input/output stream
Bioperl structure Object, describes a Model
Bioperl structure Object, describes a Residue
Module for parsing/accessing dssp output
Module for parsing/accessing stride output
Abstract Interface for a Structure objects
BSANE/BioCORBA compliant symbol list alphabet
A Symbol Alphabet
A ready made DNA alphabet
A ready made Protein alphabet
A biological symbol
Interface for a Symbol
A node in a represented taxonomy
representing Taxonomy.
interface to define how to access NCBI Taxonoy
A node in a represented taxonomy
Generic Taxonomic Entity object
An Organism Level Implementation of TreeI interface.
Base object for alignment factories
A module to work with objects from consed .ace files
A kludge to do specialized trimming of sequence based on quality.
Find amplicons in a template using degenerate PCR primers
a wrapper around ESEfinder server
a wrapper around Domcut server
a wrapper around the ELM server which predicts short functional motifs on amino acid sequences
a wrapper around GOR4 protein secondary structure prediction server
a wrapper around the HNN protein secondary structure prediction server
a wrapper around NetPhos server
a wrapper around the Scansite server
a wrapper around the Sopma protein secondary structure prediction server
abstract superclass for SimpleAnalysis implementations
Base class for analysis result objects and parsers
parser for Blat program
Codon table object
parser for Coil output
representation of EC numbers (Enzyme Classification)
parse EMBOSS palindrome output
Parse ePCR output and make features
Results of one ESTScan run
Results of one Eponine run
Parse est2genome output, makes simple Bio::SeqFeature::Generic objects
parse results of one Fgenesh run
write sequence features in FootPrinter format
A Bio::SeqAnalysisParserI compliant GFF format parser
Calculates relative electrophoretic migration distances
Results of one geneid run
Results of one Genemark run
Results of one Genewise run
Results of one Genomewise run
Results of one Genscan run
parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
Results of one Grail run
Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
One particular domain hit from HMMER
Object representing HMMER output results
Set of identical domains from HMMER matches
Parser for Hmmpfam program
Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Results of one MZEF run
Parses output from Transfac's match(TM)
Object holding alternative alphabet coding for one protein sequence
Parses output from GERP
Parses output from gumby
parser for Molphy output
container for data parsed from a ProtML run
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
Parses output from the PAML program codeml.
A container for NSSite Model Result from PAML
A PAML result set object
parser for ProtDist output
A predicted exon feature
a predicted gene structure feature
base class for common assessor things
interface for assessing primer pairs
position of a single primer
two primers on left and right side
Create input for and work with the output from the program primer3
Parser for FingerPRINTScanII program
parse Profile output
parser for Promoterwise tab format output
Parser for ps_scan result
submit to and parse output from protparam ;
Results of one Pseudowise run
A Parser for qrna output
A set of routines useful for generating random data in different distributions
a parser for RepeatMasker output
An object for the parameters used to run programs
A Base object for the parameters used to run programs
Object for remote execution of the NCBI Blast via HTTP
parse seg output
represent a sequence pattern or motif
Object holding statistics for one particular sequence
Object holding n-mer statistics for a sequence
Perl object for designing small inhibitory RNAs.
Perl object implementing the Saigo group's rules for designing small inhibitory RNAs
Perl object implementing the tuschl group's rules for designing small inhibitory RNAs
Bioperl object for sigcleave analysis
parser for Signalp output
enhanced parser for Signalp output
A single exon determined by an alignment
Results of one Sim4 run
A single exon determined by an alignment
Results of a Spidey run
a parser for Tandem Repeats Finder output
Results of one TargetP run
parse TMHMM output (TransMembrane HMM)
Perl extension to do pairwise dynamic programming sequence alignment
Parse ipcress output and make features
Parse isPcr output and make features
calculate the isoelectric point of a protein
pairwise Smith Waterman object
A parser for tRNAscan-SE output
A Node with Alleles attached
A Tree Node with support for annotation
Testing compatibility of phylogenetic trees with nested taxa.
Construct a tree using distance based methods
Drawing phylogenetic trees in Encapsulated PostScript (EPS) format.
A Simple Tree Node
Interface describing a Tree Node
A Simple Tree Node with support for NHX tags
TreeFactory for generating Random Trees
Calculate certain statistics for a Tree
An implementation of the TreeI interface.
Decorated Interface implementing basic Tree exploration methods
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
Parser for Tree files
Build Bio::Tree::Tree's and Bio::Tree::Node's from Events
A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output
Parser for lintree output trees
A TreeIO driver module for parsing NeXML tree files
A TreeIO driver module for parsing Nexus tree output from PAUP
TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
Bio::TreeIO driver for Pagel format
TreeIO implementation for parsing PhyloXML format.
A simple output format that converts a Tree object to an SVG output
A simple output format which displays a tree as an ASCII drawing
Descendant of Bio::SeqI that allows updates
Sequence change class for polypeptides
point mutation and codon information from single amino acid changes
Sequence object with allele-specific attributes
DNA level mutation class
Handler for sequence variation IO Formats
flat file sequence variation input/output stream
XML sequence variation input/output stream
Sequence change class for RNA level
submitted SNP
Container class for mutation/variant descriptions
Sequence Change SeqFeature abstract class
A base class for Web (any protocol) access
Perl Modules for Biology
get BioPerl method and package information from a Berkeley DB
Provides
in Bio/AnalysisI.pm
in Bio/DB/SeqFeature/Store/berkeleydb.pm
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
in Bio/DB/GFF.pm
in Bio/DB/GFF.pm
in Bio/DB/IndexedBase.pm
in Bio/DB/SeqFeature/Store.pm
in Bio/DB/SeqFeature/Store/berkeleydb.pm
in Bio/DB/SeqFeature/Store/memory.pm
in Bio/Search/Tiling/MapTileUtils.pm
in Bio/DB/Fasta.pm
in Bio/Root/Build.pm
in Bio/Root/Exception.pm
in Bio/Root/IO.pm
in Bio/Root/Root.pm
in Bio/Root/RootI.pm
in Bio/Root/Storable.pm
in Bio/Root/Test.pm
in Bio/Root/Utilities.pm
in Bio/Root/Version.pm
in Bio/Search/Tiling/MapTileUtils.pm
in Bio/DB/Qual.pm
in Bio/DB/GFF/Adaptor/berkeleydb.pm
Examples
- examples/Bio-DB-GFF/load_ucsc.pl
- examples/align/FastAlign.pl
- examples/align/align_on_codons.pl
- examples/align/aligntutorial.pl
- examples/align/clustalw.pl
- examples/align/simplealign.pl
- examples/bioperl.pl
- examples/cluster/dbsnp.pl
- examples/contributed/nmrpdb_parse.pl
- examples/contributed/prosite2perl.pl
- examples/contributed/rebase2list.pl
- examples/db/dbfetch
- examples/db/est_tissue_query.pl
- examples/db/gb2features.pl
- examples/db/getGenBank.pl
- examples/db/get_seqs.pl
- examples/db/rfetch.pl
- examples/db/use_registry.pl
- examples/generate_random_seq.pl
- examples/liveseq/change_gene.pl
- examples/longorf.pl
- examples/make_primers.pl
- examples/popgen/parse_calc_stats.pl
- examples/quality/svgtrace.pl
- examples/rev_and_trans.pl
- examples/revcom_dir.pl
- examples/root/README
- examples/root/exceptions1.pl
- examples/root/exceptions2.pl
- examples/root/exceptions3.pl
- examples/root/exceptions4.pl
- examples/searchio/blast_example.pl
- examples/searchio/custom_writer.pl
- examples/searchio/hitwriter.pl
- examples/searchio/hspwriter.pl
- examples/searchio/htmlwriter.pl
- examples/searchio/psiblast_features.pl
- examples/searchio/psiblast_iterations.pl
- examples/searchio/rawwriter.pl
- examples/searchio/resultwriter.pl
- examples/searchio/waba2gff.pl
- examples/searchio/waba2gff3.pl
- examples/sirna/TAG
- examples/sirna/rnai_finder.cgi
- examples/structure/structure-io.pl
- examples/subsequence.cgi
- examples/tk/gsequence.pl
- examples/tk/hitdisplay.pl
- examples/tools/extract_genes.pl
- examples/tools/gb_to_gff.pl
- examples/tools/gff2ps.pl
- examples/tools/parse_codeml.pl
- examples/tools/psw.pl
- examples/tools/reverse-translate.pl
- examples/tools/run_genscan.pl
- examples/tools/run_primer3.pl
- examples/tools/seq_pattern.pl
- examples/tools/standaloneblast.pl
- examples/tree/paup2phylip.pl