Changes for version 1.2.3
- o Bug #1475 - Fix and add speedup to spliced_seq for remote location handling. o Bug #1477 - Sel --> Sec abbreviation fixed o Fix bug #1487 where paring in-between locations when end < start caused the FTLocationFactory logic to fail. o Fix bug #1489 which was not dealing with keywords as an arrayref properly (this is fixed on the main trunk because keywords returns a string and the array is accessible via get_keywords). o Bio::Tree::Tree memory leak (bug #1480) fixed Added a new initialization option -nodelete which won't try and cleanup the containing nodes if this is true. o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed this was only present on the branch for the 1.2.1 and 1.2.2 series
- Also merged main trunk changes to the branch which make newick -> nhx round tripping more effective (storing branch length and bootstrap values in same locate for NodeNHX and Node implementations.) Fixes to TreeIO parsing for labeled internal also required small changes to TreeIO::nhx. Improved tests for this module as well.
- o Bio::SearchIO
- Fixed bugs in BLAST parsing which couldn't parse NCBI gapped blast properly (was losing hit significance values due to the extra unexpeted column).
- Parsing of blastcl3 (netblast from NCBI) now can handle case of integer overflow (# of letters in nt seq dbs is > MAX_INT) although doesn't try to correct it - will get the negative number for you. Added a test for this as well.
- Fixed HMMER parsing bug which prevented parsing when a hmmpfam report has no top-level family classification scores but does have scores and alignments for individual domains.
- Parsing FASTA reports where ungapped percent ID is < 10 and the regular expression to match the line was missing the possibility of an extra space. This is rare, which is why we probably did not catch it before.
- BLAST parsing picks up more of the statistics/parameter fields at the bottom of reports. Still not fully complete.
- SearchIO::Writer::HTMLResultWriter and TextResultWriter were fixed to include many improvements and added flexiblity in outputting the files. Bug #1495 was also fixed in the process.
- o Bio::DB::GFF
- Update for GFF3 compatibility.
- Added scripts for importing from UCSC and GenBank.
- Added a 1.2003 version number.
- o Bio::Graphics
- Updated tutorial.
- Added a 1.2003 version number.
- o SeqIO::swiss Bug #1504 fixed with swiss writing which was not properly writing keywords out. o Bio::SeqIO::genbank
- Fixed bug/enhancement #1513 where dates of the form D-MMM-YYYY were not parsed. Even though this is invalid format we can handle it - and also cleanup the date string so it is properly formatted.
- Bug/enhancement #1517 fixed so that SEGMENT line can be parsed and written with Genbank format. Similarly bug #1515 is fixed to parse in the ORIGIN text.
- o Bio::SeqIO::fasta, a new method called preferred_id_type allows you to specify the ID type, one of (accession accession.version display primary). See Bio::SeqIO::preferred_id_type method documentation for more information. o Unigene parsing updated to handle file format changes by NCBI
Documentation
Bioperl Design Documentation
Load a Bio::DB::GFF database from GENBANK files.
Bulk-load a Bio::DB::GFF database from GFF files.
Fast-load a Bio::DB::GFF database from GFF files.
Generate a histogram of Bio::DB::GFF features
Load a Bio::DB::GFF database from GFF files.
Bulk-load a Bio::DB::GFF database from GFF files.
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
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
generic CGI program to retrieve biological database entries in various formats and styles (using SRS)
Render a Bio::Graphics Feature File
fetches sequences from bioperl indexed databases
indexes files for use by bpfetch
perl script to find the longest ORF of a sequence
lists the number of bases and number of sequences in specified sequence database files
you will want to change this script
script for submitting jobs to a remote blast server (ncbi blast queue at this time)
builds a phylogenetic tree based on a sequence search (FastA,BLAST,HMMER)
Modules
An interface for describing sequence alignments.
Calculate some statistics for a DNA alignment
Base statistic object for Pairwise Alignments
Calculate some statistics for an alignment
A collection of utilities regarding converting and manipulating alignment objects
Handler for AlignIO Formats
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
mase sequence input/output stream
Parse and Create MEGA format data files
meme 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
prodom sequence input/output stream
Read/Write PSI-BLAST profile alignment files
selex sequence input/output stream
stockholm 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
DESCRIPTION of Object
An ontology term adapted to AnnotationI
Specialised DBLink object for Literature References
A simple scalar
A scalar with embedded structured information
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 phrap ACE files.
driver to load phrap.out files.
Perl module to hold and manipulate sequence assembly data.
Abstract Inteface of Sequence Assemblies
A Bibliographic Query Service module
Representation of a general article
An abstract base for other biblio classes
Representation of a book
Representation of a book article
Handling the bibliographic references
A converter of a raw hash to MEDLINE citations
A converter of XML files with MEDLINE citations
A converter of a raw hash to PUBMED citations
A converter of XML files with PUBMED citations
Representation of a journal
Representation of a journal article
Representation of a MEDLINE article
Representation of a MEDLINE book
Representation of a MEDLINE book article
Representation of a MEDLINE journal
Representation of a MEDLINE journal article
Representation of an organisation
Representation of a patent
Representation of a person
Representation of a conference proceeding
Representation of a general provider
Representation of a PUBMED article
Representation of a PUBMED book article
Representation of a PUBMED journal article
Representation of a bibliographic reference
Representation of a provider of type service
Representation of a technical report
Representation of thesis
Representation of a web resource
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
Mapping locations through a chain of coordinate mappers
Noncontinuous match between two coordinate sets
Continuous match between two coordinate sets
transformations between gene related coordinate systems
Finds shortest path between nodes in a graph
Interface describing coordinate mappers
Continuous match between two coordinate sets
Results from coordinate transformation
An other name for Bio::Location::Simple
An other name for Bio::Location::Simple
Interface to identify coordinate mapper results
Additional methods to create Bio::Coordinate objects
Database object interface to ACeDB servers
A BioFetch-based access to a bibliographic citation retrieval
A SOAP-based access to a bibliographic query service
An interface to a Bibliographic Query Service
Database object interface to BioFetch retrieval
Database object for retrieving using the dbfetch script
Database object interface for EMBL entry retrieval
A Bio::DB::RandomAccessI compliant class which wraps a priority list of DBs
Fast indexed access to a directory of 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
Binary search indexing system for sequence files
Database object interface to GDB HTTP query
Storage and retrieval of sequence annotation data
ace interface (for multiple inheritance)
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
Deprecated database adaptor
Database adaptor for a specific oracle schema
Unholy union between oracle GFF database and acedb database
Database adaptor for a specific mysql schema
iterator for Bio::DB::GFF::Adaptor::memory
Aggregate GFF groups into composite features
Alignment aggregator
Clone aggregator
The Coding Region Aggregator
Match aggregator
No aggregation
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
Abstract interface for a sequence database
A collection of routines useful for queries to NCBI databases.
Build a GenBank Entrez Query
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
Access to the Open Bio Database Access registry scheme
Abstract Interface for Sequence databases
Database object interface to SwissProt retrieval
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
Database object interface for XEMBL entry retrieval
SOAP service definition for XEMBL
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
a set of DNA/RNA features. ISA Bio::Expression::FeatureI
an interface class for DNA/RNA features
an interface class for DNA/RNA probes
An interface to analysis tool factory
Interface class for Application Factories
Factory for Bio::Search::Hit::BlastHit objects
Factory for Bio::Search::Result::BlastResult objects
Base class for factory classes loading drivers
EMBOSS appliaction factory class
A FeatureTable Location Parser
Interface for an object that builds Bio::Search::Hit::HitI objects
DESCRIPTION of Interface
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
Interface for an object that builds Bio::Search::Result::ResultI objects
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
Generate GD images of Bio::Seq objects
A simple feature object for use with Bio::Graphics::Panel
A set of Bio::Graphics features, stored in a file
Base class for Bio::Graphics::Glyph objects
Factory for Bio::Graphics::Glyph objects
The "alignment" glyph
The "anchored_arrow" glyph
The "arrow" glyph
The "box" glyph
The "cds" glyph
The "crossbox" glyph
The "diamond" glyph
The "dna" glyph
The "dot" glyph
The "ellipse" glyph
The "crossbox" glyph
The "extending arrow" glyph
The "generic" glyph
The "graded_segments" glyph
The "group" glyph
The "heterogeneous_segments" glyph
The "line" glyph
The "oval" glyph
The "Drosophila P-element Insertion" glyph
The "STS primers" glyph
The sequence ontology transcript glyph
The "redgreen_box" glyph
The "redgreen_segments" glyph
The "round rect" glyph
The "ruler_arrow" glyph
The "segmented_keyglyph" glyph
The "segments" glyph
The "span" glyph
The "splice_site" glyph
The "too many to show" glyph
The "track" glyph
The "transcript" glyph
The "transcript2" glyph
The "6-frame translation" glyph
The "triangle" glyph
The xyplot glyph
Generate GD images of Bio::Seq objects
interface for objects with multiple identifiers
interface for objects with identifiers
Abstract interface for indexing a flat file
Base class for AbstractSeq s
Indexes Blast reports and supports retrieval based on query accession(s)
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Interface for indexing (multiple) fasta files
Interface for indexing (multiple) fastq files
Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format).
Interface for indexing swisspfam files
Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).
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
Loader for LiveSeq from EMBL entries with SRS
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 Sequence 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 Bio::MapI compliant map implementation handling cytogenic bands
An object representing a marker.
Marker class with cytogenetic band storing attributes
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 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 single position of a Marker in a Map
Abstracts the notion of a position having a value in the context of a marker and a Map
A MapI implementation handling the basics of a Map
A Map Factory object
A Mapmaker Map reader
A Phylip Distance Matrix object
representation of GO terms
Implementation of InterProI term interface
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
a Ontology Engine for GO implementing OntologyEngineI
Implementation of OntologyEngineI interface
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
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 parser for the Sequence Ontology flat-file format
Functional access to BioPerl for people who don't know objects
Representation of a correlating phenotype in a given species
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
Bioperl lightweight Sequence Object
Pure perl RangeI implementation
Range interface
Exception class for Perl 5 objects
Generic exception objects for Bioperl
Global variables and utility functions
module for fallback HTTP get operations when LWP:: is unavailable
module providing several methods often needed when dealing with file IO
Input and output manager for Perl5 objects.
A core Perl 5 object.
Hash-based implementation of Bio::Root::RootI
Abstract interface to root object code
General-purpose utility module
Interface for managing linked lists of Perl5 objects.
A generic cross-reference object.
Utility functions for Bio::Search:: BLAST objects
Interface for a database used in a sequence search
Generic implementation of Bio::Search::DatabaseI
Bioperl BLAST High-Scoring Pair object
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
HSP object suitable for describing WABA alignments
Bioperl BLAST Hit object
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
DESCRIPTION of Object
A top-level BLAST Report object
Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
A Result object for HMMER results
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 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.
Interface for outputting parsed Search results
Tab-delimited data for Bio::Search::HSP::HSPI objects
Object to implement writing 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.
Event generator for event based parsing of blast reports
A SearchIO implementation of NCBI Blast XML parsing.
chado sequence input/output stream
chadosxpr sequence input/output stream
parser for Exonerate
A SearchIO parser for FASTA results
A parser for HMMER output (hmmpfam, hmmsearch)
Parser for traditional BLAST and PSI-BLAST reports
SearchIO parser for Jim Kent WABA program alignment output
Sequence object, with features
Base implementation for a SequenceProcessor
subtype of Bio::LocatableSeq to store DNA that encodes a protein
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
Bioperl lightweight Quality Object
Interface definition for a Bio::Seq::Qual
Module implementing a sequence created from a rich sequence database entry
RichSeq interface, mainly for database orientated sequences
Configurable object builder for sequence stream parsers
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Instantiates a new Bio::PrimarySeqI (or derived class) through a factory
Bioperl object packaging a sequence with its quality
Bioperl object packaging a sequence with its trace
Interface definition for a Bio::Seq::Trace
Sequence analysis output parser interface
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
DESCRIPTION of Object
DESCRIPTION of Object
DESCRIPTION of Object
Describes a promotor
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 transcription unit
Generic SeqFeature
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.
Abstract interface of a Sequence Feature
Handler for SeqIO Formats
Helper class for Embl/Genbank feature tables
Treating a set of files as a single input stream
abi trace sequence input/output stream
ace sequence input/output stream
alf trace sequence input/output stream
BSML sequence input/output stream
chado sequence input/output stream
chadoitext sequence input/output stream
chadosxpr sequence input/output stream
chadoxml sequence input/output stream
ctf trace sequence input/output stream
EMBL sequence input/output stream
exp trace sequence input/output stream
fasta sequence input/output stream
fastq sequence input/output stream
Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.
GAME helper via PerlSAX helper.
GAME helper via PerlSAX helper.
GAME helper via PerlSAX helper.
GCG sequence input/output stream
GenBank sequence input/output stream
method i/o on very large fasta sequence files
DESCRIPTION of Object
.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
Swissprot sequence input/output stream
ztr trace sequence input/output stream
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
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
DESCRIPTION of Object
A Symbol Alphabet
A ready made DNA alphabet
A ready made Protein alphabet
A biological symbol
Interface for a Symbol
Conversion used bt the Taxonomy classes
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.
Base class for analysis result objects and parsers
Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Lightweight BLAST parser
Blast report High Scoring Pair (HSP)
object for parsing single iteration of a PSIBLAST report
A Blast Subject (database search Hit)
Lightweight BLAST parser for (iterated) psiblast reports
Bioperl BLAST sequence analysis object
Bioperl BLAST High-Scoring Segment Pair object
Bioperl Utility module for HTML formatting Blast reports
Bioperl BLAST "Hit" object
Bioperl codon table object
representation of EC numbers
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
DESCRIPTION of Object
A Bio::SeqAnalysisParserI compliant GFF format parser
Calculates relative electrophoretic migration distances
Results of one Genemark run
Results of one Genewise run
Results of one Genomewise run
Results of one Genscan run
Results of one Grail run
One particular domain hit from HMMER
Object representing HMMER output results
Set of identical domains from HMMER matches
Generates unique Seq objects from an ambiguous Seq object
Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Results of one MZEF run
Object holding alternative alphabet coding for one protein sequence
DESCRIPTION of Object
DESCRIPTION of Object
Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00
A PAML result set object
DESCRIPTION of Object
A predicted exon feature
a predicted gene structure feature
Create input for and work with the output from the program primer3
Parser for FingerPRINTScanII program
parse Profile output
DESCRIPTION of Object
Results of one Pseudowise run
DESCRIPTION of Object
Bioperl object for a restriction endonuclease (cuts DNA at specific locations)
Object for remote execution of the NCBI Blast via HTTP
Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq)
A Base object for wrappers around executables
parse Seg output (filter low complexity protein sequence)
Bioperl sequence analysis base class.
Bioperl object for a sequence pattern or motif
Object holding statistics for one particular sequence
Object holding n-mer statistics for one sequence
Bioperl object for sigcleave analysis
A single exon determined by an alignment
Results of one Sim4 run
Abstract state machine object
IO-based implementation of AbstractStateMachine
parse TmHMM output (transmembrane HMM)
Bioperl manager for web resources related to biology.
pairwise Smith Waterman object
DESCRIPTION of Object
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 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
TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format.
TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
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
Error/exception handling in an OO-ish way
A simple subclass of Interface
An implementation of TestInterface
Provides
in scripts/root_object/Bar.pm
in Bio/AnalysisI.pm
in Bio/DB/Fasta.pm
in Bio/DB/GFF/Adaptor/dbi/caching_handle.pm
in Bio/DB/GFF.pm
in Bio/Expression/FeatureGroup/FeatureGroupMas50.pm
in Bio/Graphics/Util.pm
in Bio/DB/Fasta.pm
in Bio/Seq/PrimedSeq.pm
in scripts/exceptions/Error.pm
in scripts/exceptions/Error.pm
in scripts/root_object/Foo.pm
in LocalConfig.pm
in scripts/root_object/Outer.pm