Changes for version 1.7.6 - 2019-08-28
- The program bp_classify_hits_kingdom has been removed and is now part of the examples documentation instead.
- GD is now listed as a suggestion instead of a requirement. The bp_chaos_plot program will now work with the GD module.
- New method Bio::Tree::Statistics::transfer_bootstrap_expectation to compute Transfer Bootstrap Expectation (TBE) for internal nodes based on the methods outlined in Lemoine et al, Nature, 2018.
- New method Bio::SeqIO::fasta::next_seq_fast to retrieve next sequence in the stream faster but not perfect.
Documentation
amino acid composition of protein sequences
index sequence files using Bio::DB::Flat
sequence retrieval using OBDA registry
a chaos plot from DNA and RNA sequences
script to split an input set of database(s) into smaller pieces
extract the corresponding sequence for a specified feature type
turn FASTA -m 9 output into NCBI -m 9 tabular output
fetches sequences from bioperl indexed databases
filters searchio results, outputting a tab delimited summary
extract DNA sequences based on BLAST hits
GC content of nucleotide sequences
Genbank-gtgbrowse-friendly GFF3
indexes files for use by bp_fetch.pl
query a local TaxonomyDB for species or taxonid
Convert an input mRNA/cDNA sequence into protein
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
convert nexus format trees (from PAUP* and MrBayes) to new hampshire
a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
oligo count and frequency
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
Reverse translate a Profam-like protein motif
Turn SearchIO parseable reports(s) into a set of aligned blocks
turn a SearchIO report into GFF
turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
Turn SearchIO parseable reports(s) into TRIBE matrix
lists the number of bases and number of sequences in specified sequence database files
generic BioPerl sequence format converter
cut FASTA sequences with a given range
Takes one or more sequence files and splits them into a number of load balanced files.
bioperl implementation of sequence fetch from local db (like EMBOSS seqret)
split a sequence (or stream) into a single file per sequence
splits a sequence into equal sized chunks with an optional overlapping range
convert sequence formats
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
translates a sequence
convert Bio::TreeIO parseable format trees to pagel format
unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy
Modules
An interface for describing sequence alignments.
Calculate some statistics for a DNA alignment
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
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
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
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 for retrieving using the dbfetch script
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
binning utility for Bio::DB::GFF index
rearrange utility
helper base class for parameter-based remote server access and response retrieval.
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
Fast indexed access to quality files
Helper class for web-based sequence queryies
Object Interface to queryable sequence databases
Abstract interface for a sequence database
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
Abstract Interface for Sequence databases
Access to a taxonomy database
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
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
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
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).
Interface for indexing (multiple) fasta qual files
Interface for indexing swisspfam files
Interface for indexing one or more Swissprot files.
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
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 occurrence
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
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
base class for SAX Handlers
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
parser for OBO 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.
Bioperl lightweight sequence object
Interface definition for a Bio::PrimarySeq
A base module for fast 'pull' parsing
Pure perl RangeI implementation
Range interface
BioPerl exceptions
module for fallback HTTP get operations when LWP:: is unavailable
BioPerl base IO handling class
implementation of Bio::Root::RootI interface
base interface for all BioPerl classes
Safely store/retrieve objects from disk
common base for all BioPerl test scripts
An implementation of TestInterface
general-purpose utilities
don't use, get version from each module
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 factory to create Bio::Search::HSP::HSPI objects
Interface for a High Scoring Pair in a similarity search result
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 factory to create Bio::Search::Hit::HitI objects
Interface for a hit in a similarity search result
A model-based implementation of the Bio::Search::Hit::HitI interface
Bioperl BLAST Hit object
Bio::Search::Hit::HitI interface for pull parsers.
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 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
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
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)
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 trace
Read with sequencing errors taken from a reference sequence
Interface definition for a Bio::Seq::Trace
Sequence analysis output parser interface
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
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
ace sequence input/output stream
asciitree sequence input/output stream
BSML sequence input/output stream
BSML sequence input/output stream using SAX
EMBL sequence input/output stream
EMBL sequence input/output stream
fasta sequence input/output stream
fastq sequence input/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
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
phd file input/output stream
PIR 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
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
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.
A node in a represented taxonomy
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
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
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.
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
parser for Molphy output
container for data parsed from a ProtML run
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
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
Module representing any (remote or local) analysis tool
A directory of analysis tools
An object for the parameters used to run programs
A Base object for the parameters used to run programs
A Base object for wrappers around executables
Extensions to WrapperBase for handling programs with commands *ALPHA*
parse seg output
represent a sequence pattern or motif
reverse translate protein patterns
Object holding statistics for one particular sequence
Object holding n-mer statistics for a sequence
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)
Parse ipcress output and make features
Parse isPcr output and make features
calculate the isoelectric point of a protein
A parser for tRNAscan-SE output
A Tree Node with support for annotation
Testing compatibility of phylogenetic trees with nested taxa.
Construct a tree using distance based methods
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
newick string parser
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
parsing and writing of Newick/PHYLIP/New Hampshire format
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 which displays a tree as an ASCII drawing
Descendant of Bio::SeqI that allows updates
A base class for Web (any protocol) access
Perl modules for biology
Provides
in lib/Bio/AnalysisI.pm
in lib/Bio/DB/IndexedBase.pm
in lib/Bio/Search/Tiling/MapTileUtils.pm
in lib/Bio/DB/Fasta.pm
in lib/Bio/Search/Tiling/MapTileUtils.pm
in lib/Bio/DB/Qual.pm
in lib/Bio/Tools/Run/Analysis.pm
in lib/Bio/Tools/Run/Analysis.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/simplealign.pl
- examples/classify_hits_kingdom
- examples/contributed/nmrpdb_parse.pl
- examples/contributed/prosite2perl.pl
- examples/contributed/rebase2list.pl
- examples/db/est_tissue_query.pl
- examples/db/get_seqs.pl
- examples/db/rfetch.pl
- examples/db/use_registry.pl
- examples/generate_random_seq.pl
- examples/longorf.pl
- examples/make_primers.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/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/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