The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.
 / 
FAST-1.06
River stage zero No dependents
3 ++

Changes for version 1.06

  • Fix in name of symbolic link to the popset data-file in t/data. Release corresponding to acceptance in Frontiers in Genetics

Documentation

alncut
filter sites in alignments based on variation and gap-content
fascodon
counts codon usage
fascomp
analysis of monomer frequencies
fasconvert
Convert sequences or alignments to or from fasta format.
fascut
select biosequence record data by character or field ranges
fasfilter
Select sequences by numerical values of name,value pairs
fasgrep
print sequence records matching a pattern
fashead
print first sequence records on input
faslen
annotate sequence lengths to descriptions
faspaste
concatenate sequence record data
fasrc
reverse complement nucleotide sequences and alignments
fassort
sort sequences based on identifiers
fassub
regex-based substitutions on sequence records
fastail
print last sequence records on input
fastax
select sequence records by NCBI taxonomic names or IDs
fastaxsort
sort sequence records based on NCBI taxonomy
fastr
character-based transformations on sequence records
fasuniq
Remove duplicate sequence records in a multifasta file or datastream.
faswc
tally sequences and sequence characters
fasxl
translate sequences by a genetic code.
gbfalncut
cut sites from alignments by regex-matching on features in an annotated GenBank file
gbfcut
search features from GenBank files and print corresponding sequences

Modules

FAST
FAST Analysis of Sequences Toolbox
FAST::Bio::Align::AlignI
An interface for describing sequence alignments.
FAST::Bio::AlignIO
Handler for AlignIO Formats
FAST::Bio::AlignIO::Handler::GenericAlignHandler
FAST::Bio::HandlerI-based generic data handler class for alignment-based data
FAST::Bio::AlignIO::arp
ARP MSA Sequence input/output stream
FAST::Bio::AlignIO::bl2seq
bl2seq sequence input/output stream
FAST::Bio::AlignIO::clustalw
clustalw sequence input/output stream
FAST::Bio::AlignIO::emboss
Parse EMBOSS alignment output (from applications water and needle)
FAST::Bio::AlignIO::fasta
fasta MSA Sequence input/output stream
FAST::Bio::AlignIO::largemultifasta
Largemultifasta MSA Sequence input/output stream
FAST::Bio::AlignIO::maf
Multiple Alignment Format sequence input stream
FAST::Bio::AlignIO::mase
mase sequence input/output stream
FAST::Bio::AlignIO::mega
Parse and Create MEGA format data files
FAST::Bio::AlignIO::meme
meme sequence input/output stream
FAST::Bio::AlignIO::metafasta
Metafasta MSA Sequence input/output stream
FAST::Bio::AlignIO::msf
msf sequence input/output stream
FAST::Bio::AlignIO::nexml
NeXML format sequence alignment input/output stream driver
FAST::Bio::AlignIO::nexus
NEXUS format sequence input/output stream
FAST::Bio::AlignIO::pfam
pfam sequence input/output stream
FAST::Bio::AlignIO::phylip
PHYLIP format sequence input/output stream
FAST::Bio::AlignIO::po
po MSA Sequence input/output stream
FAST::Bio::AlignIO::proda
proda sequence input/output stream
FAST::Bio::AlignIO::prodom
prodom sequence input/output stream
FAST::Bio::AlignIO::psi
Read/Write PSI-BLAST profile alignment files
FAST::Bio::AlignIO::selex
selex sequence input/output stream
FAST::Bio::AlignIO::stockholm
stockholm sequence input/output stream
FAST::Bio::AlignIO::xmfa
XMFA MSA Sequence input/output stream
FAST::Bio::AnalysisParserI
Generic analysis output parser interface
FAST::Bio::AnalysisResultI
Interface for analysis result objects
FAST::Bio::AnnotatableI
the base interface an annotatable object must implement
FAST::Bio::Annotation::AnnotationFactory
Instantiates a new FAST::Bio::AnnotationI (or derived class) through a factory
FAST::Bio::Annotation::Collection
Default Perl implementation of AnnotationCollectionI
FAST::Bio::Annotation::Comment
A comment object, holding text
FAST::Bio::Annotation::DBLink
untyped links between databases
FAST::Bio::Annotation::OntologyTerm
An ontology term adapted to AnnotationI
FAST::Bio::Annotation::Reference
Specialised DBLink object for Literature References
FAST::Bio::Annotation::SimpleValue
A simple scalar
FAST::Bio::Annotation::TagTree
AnnotationI with tree-like hierarchal key-value relationships ('structured tags') that can be represented as simple text.
FAST::Bio::Annotation::Target
Provides an object which represents a target (ie, a similarity hit) from one object to something in another database
FAST::Bio::Annotation::TypeManager
Manages types for annotation collections
FAST::Bio::AnnotationCollectionI
Interface for annotation collections
FAST::Bio::AnnotationI
Annotation interface
FAST::Bio::Cluster::FamilyI
Family Interface
FAST::Bio::Cluster::SequenceFamily
Sequence Family object
FAST::Bio::ClusterI
Cluster Interface
FAST::Bio::DB::InMemoryCache
Abstract interface for a sequence database
FAST::Bio::DB::RandomAccessI
Abstract interface for a sequence database
FAST::Bio::DB::SeqI
Abstract Interface for Sequence databases
FAST::Bio::DB::Taxonomy
Access to a taxonomy database
FAST::Bio::DB::Taxonomy::entrez
Taxonomy Entrez driver
FAST::Bio::DB::Taxonomy::flatfile
An implementation of FAST::Bio::DB::Taxonomy which uses local flat files
FAST::Bio::DB::Taxonomy::list
An implementation of FAST::Bio::DB::Taxonomy that accepts lists of words to build a database
FAST::Bio::DescribableI
interface for objects with human readable names and descriptions
FAST::Bio::Event::EventGeneratorI
This interface describes the basic event generator class.
FAST::Bio::Event::EventHandlerI
An Event Handler Interface
FAST::Bio::Factory::FTLocationFactory
A FeatureTable Location Parser
FAST::Bio::Factory::LocationFactoryI
A factory interface for generating locations from a string
FAST::Bio::Factory::ObjectBuilderI
Interface for an object builder
FAST::Bio::Factory::ObjectFactory
Instantiates a new FAST::Bio::Root::RootI (or derived class) through a factory
FAST::Bio::Factory::ObjectFactoryI
A General object creator factory
FAST::Bio::Factory::SequenceFactoryI
This interface allows for generic building of sequences in factories which create sequences (like SeqIO)
FAST::Bio::Factory::SequenceStreamI
Interface describing the basics of a Sequence Stream.
FAST::Bio::FeatureHolderI
the base interface an object with features must implement
FAST::Bio::GapSeqI
GapSeq interface, for gapped sequences
FAST::Bio::HandlerBaseI
Interface class for handler methods which interact with any event-driven parsers (drivers).
FAST::Bio::IdentifiableI
interface for objects with identifiers
FAST::Bio::LocatableSeq
A FAST::Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq.
FAST::Bio::Location::Atomic
Implementation of a Atomic Location on a Sequence
FAST::Bio::Location::CoordinatePolicyI
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
FAST::Bio::Location::Fuzzy
Implementation of a Location on a Sequence which has unclear start and/or end locations
FAST::Bio::Location::FuzzyLocationI
Abstract interface of a Location on a Sequence which has unclear start/end location
FAST::Bio::Location::NarrowestCoordPolicy
class implementing FAST::Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
FAST::Bio::Location::Simple
Implementation of a Simple Location on a Sequence
FAST::Bio::Location::Split
Implementation of a Location on a Sequence which has multiple locations (start/end points)
FAST::Bio::Location::SplitLocationI
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
FAST::Bio::Location::WidestCoordPolicy
class implementing FAST::Bio::Location::CoordinatePolicy as the widest possible and reasonable range
FAST::Bio::LocationI
Abstract interface of a Location on a Sequence
FAST::Bio::MyPrimarySeqI
Interface definition for a FAST::Bio::PrimarySeq
FAST::Bio::MySeqI
Abstract Interface of Sequence (with features)
FAST::Bio::Ontology::DocumentRegistry
Keep track of where to find ontologies. Allows lookups by name.
FAST::Bio::Ontology::OBOEngine
An Ontology Engine for OBO style flat file format from the Gene Ontology Consortium
FAST::Bio::Ontology::Ontology
standard implementation of an Ontology
FAST::Bio::Ontology::OntologyEngineI
Interface a minimal Ontology implementation should satisfy
FAST::Bio::Ontology::OntologyI
Interface for an ontology implementation
FAST::Bio::Ontology::OntologyStore
A repository of ontologies
FAST::Bio::Ontology::Relationship
a relationship for an ontology
FAST::Bio::Ontology::RelationshipFactory
Instantiates a new FAST::Bio::Ontology::RelationshipI (or derived class) through a factory
FAST::Bio::Ontology::RelationshipI
Interface for a relationship between ontology terms
FAST::Bio::Ontology::RelationshipType
a relationship type for an ontology
FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor
Graph adaptor for FAST::Bio::Ontology::SimpleGOEngine
FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02
Graph adaptor (v02.x) for FAST::Bio::Ontology::SimpleGOEngine
FAST::Bio::Ontology::SimpleOntologyEngine
Implementation of OntologyEngineI interface
FAST::Bio::Ontology::Term
implementation of the interface for ontology terms
FAST::Bio::Ontology::TermFactory
Instantiates a new FAST::Bio::Ontology::TermI (or derived class) through a factory
FAST::Bio::Ontology::TermI
interface for ontology terms
FAST::Bio::OntologyIO
Parser factory for Ontology formats
FAST::Bio::OntologyIO::Handlers::BaseSAXHandler
FAST::Bio::OntologyIO::Handlers::InterProHandler
XML handler class for InterProParser
FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler
parse an InterPro XML file and persist the resulting terms to a Biosql database
FAST::Bio::OntologyIO::InterProParser
Parser for InterPro xml files.
FAST::Bio::OntologyIO::dagflat
a base class parser for GO flat-file type formats
FAST::Bio::OntologyIO::goflat
a parser for the Gene Ontology flat-file format
FAST::Bio::OntologyIO::obo
a parser for OBO flat-file format from Gene Ontology Consortium
FAST::Bio::OntologyIO::simplehierarchy
a base class parser for simple hierarchy-by-indentation type formats
FAST::Bio::OntologyIO::soflat
a parser for the Sequence Ontology flat-file format
FAST::Bio::PrimarySeq
Bioperl lightweight Sequence Object
FAST::Bio::PrimarySeqI
Interface definition for a FAST::Bio::PrimarySeq
FAST::Bio::PullParserI
A base module for fast 'pull' parsing
FAST::Bio::Range
Pure perl RangeI implementation
FAST::Bio::RangeI
Range interface
FAST::FAST::Bio::Root::HTTPget
module for fallback HTTP get operations when LWP:: is unavailable
FAST::Bio::Search::BlastUtils
Utility functions for FAST::Bio::Search:: BLAST objects
FAST::Bio::Search::GenericStatistics
An object for statistics
FAST::Bio::Search::HSP::BlastPullHSP
A parser and HSP object for BlastN hsps
FAST::Bio::Search::HSP::GenericHSP
A "Generic" implementation of a High Scoring Pair
FAST::Bio::Search::HSP::HSPFactory
A factory to create FAST::Bio::Search::HSP::HSPI objects
FAST::Bio::Search::HSP::HSPI
Interface for a High Scoring Pair in a similarity search result
FAST::Bio::Search::HSP::HmmpfamHSP
A parser and HSP object for hmmpfam hsps
FAST::Bio::Search::HSP::PullHSPI
FAST::Bio::Search::HSP::HSPI interface for pull parsers.
FAST::Bio::Search::Hit::BlastPullHit
A parser and hit object for BLASTN hits
FAST::Bio::Search::Hit::GenericHit
A generic implementation of the FAST::Bio::Search::Hit::HitI interface
FAST::Bio::Search::Hit::HitFactory
A factory to create FAST::Bio::Search::Hit::HitI objects
FAST::Bio::Search::Hit::HitI
Interface for a hit in a similarity search result
FAST::Bio::Search::Hit::HmmpfamHit
A parser and hit object for hmmpfam hits
FAST::Bio::Search::Hit::PullHitI
FAST::Bio::Search::Hit::HitI interface for pull parsers.
FAST::Bio::Search::Result::BlastPullResult
A parser and result object for BLASTN results
FAST::Bio::Search::Result::CrossMatchResult
CrossMatch-specific subclass of FAST::Bio::Search::Result::GenericResult
FAST::Bio::Search::Result::GenericResult
Generic Implementation of FAST::Bio::Search::Result::ResultI interface applicable to most search results.
FAST::Bio::Search::Result::HmmpfamResult
A parser and result object for hmmpfam results
FAST::Bio::Search::Result::PullResultI
FAST::Bio::Search::Result::ResultI interface for 'pull' parsers
FAST::Bio::Search::Result::ResultFactory
A factory to create FAST::Bio::Search::Result::ResultI objects
FAST::Bio::Search::Result::ResultI
Abstract interface to Search Result objects
FAST::Bio::Search::SearchUtils
Utility functions for FAST::Bio::Search:: objects
FAST::Bio::Search::StatisticsI
A Base object for statistics
FAST::Bio::SearchIO
Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
FAST::Bio::SearchIO::EventHandlerI
An abstract Event Handler for Search Result parsing
FAST::Bio::SearchIO::FastHitEventBuilder
Event Handler for SearchIO events.
FAST::Bio::SearchIO::IteratedSearchResultEventBuilder
Event Handler for SearchIO events.
FAST::Bio::SearchIO::SearchResultEventBuilder
Event Handler for SearchIO events.
FAST::Bio::SearchIO::SearchWriterI
Interface for outputting parsed Search results
FAST::Bio::SearchIO::Writer::BSMLResultWriter
BSML output writer
FAST::Bio::SearchIO::Writer::GbrowseGFF
Interface for outputting parsed search results in Gbrowse GFF format
FAST::Bio::SearchIO::Writer::HSPTableWriter
Tab-delimited data for FAST::Bio::Search::HSP::HSPI objects
FAST::Bio::SearchIO::Writer::HTMLResultWriter
write a FAST::Bio::Search::ResultI in HTML
FAST::Bio::SearchIO::Writer::HitTableWriter
Tab-delimited data for FAST::Bio::Search::Hit::HitI objects
FAST::Bio::SearchIO::Writer::ResultTableWriter
Outputs tab-delimited data for each FAST::Bio::Search::Result::ResultI object.
FAST::Bio::SearchIO::Writer::TextResultWriter
Object to implement writing a FAST::Bio::Search::ResultI in Text.
FAST::Bio::SearchIO::XML::BlastHandler
XML Handler for NCBI Blast XML parsing.
FAST::Bio::SearchIO::XML::PsiBlastHandler
XML Handler for NCBI Blast PSIBLAST XML parsing.
FAST::Bio::SearchIO::axt
a parser for axt format reports
FAST::Bio::SearchIO::blast
Event generator for event based parsing of blast reports
FAST::Bio::SearchIO::blast_pull
A parser for BLAST output
FAST::Bio::SearchIO::blasttable
Driver module for SearchIO for parsing NCBI -m 8/9 format
FAST::Bio::SearchIO::blastxml
A SearchIO implementation of NCBI Blast XML parsing.
FAST::Bio::SearchIO::cross_match
CrossMatch-specific subclass of FAST::Bio::SearchIO
FAST::Bio::SearchIO::erpin
SearchIO-based ERPIN parser
FAST::Bio::SearchIO::exonerate
parser for Exonerate
FAST::Bio::SearchIO::fasta
A SearchIO parser for FASTA results
FAST::Bio::SearchIO::gmap_f9
Event generator for parsing gmap reports (Z format)
FAST::Bio::SearchIO::hmmer
A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
FAST::Bio::SearchIO::hmmer2
A parser for HMMER output (hmmpfam, hmmsearch)
FAST::Bio::SearchIO::hmmer3
DESCRIPTION of Object
FAST::Bio::SearchIO::hmmer_pull
A parser for HMMER output
FAST::Bio::SearchIO::infernal
SearchIO-based Infernal parser
FAST::Bio::SearchIO::megablast
a driver module for FAST::Bio::SearchIO to parse megablast reports (format 0)
FAST::Bio::SearchIO::psl
A parser for PSL output (UCSC)
FAST::Bio::SearchIO::rnamotif
SearchIO-based RNAMotif parser
FAST::Bio::SearchIO::sim4
parser for Sim4 alignments
FAST::Bio::SearchIO::waba
SearchIO parser for Jim Kent WABA program alignment output
FAST::Bio::SearchIO::wise
Parsing of wise output as alignments
FAST::Bio::Seq
Sequence object, with features
FAST::Bio::Seq::LargeLocatableSeq
LocatableSeq object that stores sequence as files in the tempdir
FAST::Bio::Seq::LargePrimarySeq
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in FAST::Bio::Root::Root
FAST::Bio::Seq::LargeSeqI
Interface class for sequences that cache their residues in a temporary file
FAST::Bio::Seq::Meta
Generic superclass for sequence objects with residue-based meta information
FAST::Bio::Seq::Meta::Array
array-based generic implementation of a sequence class with residue-based meta information
FAST::Bio::Seq::MetaI
Interface for sequence objects with residue-based meta information
FAST::Bio::Seq::PrimaryQual
Bioperl lightweight Quality Object
FAST::Bio::Seq::QualI
Interface definition for a FAST::Bio::Seq::Qual
FAST::Bio::Seq::Quality
Implementation of sequence with residue quality and trace values
FAST::Bio::Seq::RichSeq
Module implementing a sequence created from a rich sequence database entry
FAST::Bio::Seq::RichSeqI
interface for sequences from rich data sources, mostly databases
FAST::Bio::Seq::SeqBuilder
Configurable object builder for sequence stream parsers
FAST::Bio::Seq::SeqFactory
Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory
FAST::Bio::Seq::SeqFastaSpeedFactory
Instantiates a new FAST::Bio::PrimarySeqI (or derived class) through a factory
FAST::Bio::Seq::SequenceTrace
Bioperl object packaging a sequence with its trace
FAST::Bio::Seq::TraceI
Interface definition for a FAST::Bio::Seq::Trace
FAST::Bio::SeqAnalysisParserI
Sequence analysis output parser interface
FAST::Bio::SeqFeature::FeaturePair
hold pair feature information e.g. blast hits
FAST::Bio::SeqFeature::Gene::Exon
a feature representing an exon
FAST::Bio::SeqFeature::Gene::ExonI
Interface for a feature representing an exon
FAST::Bio::SeqFeature::Gene::GeneStructure
A feature representing an arbitrarily complex structure of a gene
FAST::Bio::SeqFeature::Gene::GeneStructureI
A feature representing an arbitrarily complex structure of a gene
FAST::Bio::SeqFeature::Gene::Intron
An intron feature
FAST::Bio::SeqFeature::Gene::NC_Feature
superclass for non-coding features
FAST::Bio::SeqFeature::Gene::Poly_A_site
poly A feature
FAST::Bio::SeqFeature::Gene::Promoter
Describes a promoter
FAST::Bio::SeqFeature::Gene::Transcript
A feature representing a transcript
FAST::Bio::SeqFeature::Gene::TranscriptI
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
FAST::Bio::SeqFeature::Gene::UTR
A feature representing an untranslated region that is part of a transcriptional unit
FAST::Bio::SeqFeature::Generic
Generic SeqFeature
FAST::Bio::SeqFeature::Similarity
A sequence feature based on similarity
FAST::Bio::SeqFeature::SimilarityPair
Sequence feature based on the similarity of two sequences.
FAST::Bio::SeqFeature::Tools::FeatureNamer
generates unique persistent names for features
FAST::Bio::SeqFeature::Tools::IDHandler
maps $seq_feature-gtprimary_tag
FAST::Bio::SeqFeature::Tools::TypeMapper
maps $seq_feature-gtprimary_tag
FAST::Bio::SeqFeature::Tools::Unflattener
turns flat list of genbank-sourced features into a nested SeqFeatureI hierarchy
FAST::Bio::SeqFeatureI
Abstract interface of a Sequence Feature
FAST::Bio::SeqI
[Developers] Abstract Interface of Sequence (with features)
FAST::Bio::SeqIO
Handler for SeqIO Formats
FAST::Bio::SeqIO::FTHelper
Helper class for Embl/Genbank feature tables
FAST::Bio::SeqIO::Handler::GenericRichSeqHandler
FAST::Bio::HandlerI-based data handler for GenBank/EMBL/UniProt (and other) sequence data
FAST::Bio::SeqIO::MultiFile
Treating a set of files as a single input stream
FAST::Bio::SeqIO::abi
abi trace sequence input/output stream
FAST::Bio::SeqIO::ace
ace sequence input/output stream
FAST::Bio::SeqIO::agave
AGAVE sequence output stream.
FAST::Bio::SeqIO::alf
alf trace sequence input/output stream
FAST::Bio::SeqIO::asciitree
asciitree sequence input/output stream
FAST::Bio::SeqIO::bsml
BSML sequence input/output stream
FAST::Bio::SeqIO::bsml_sax
BSML sequence input/output stream using SAX
FAST::Bio::SeqIO::chadoxml
chadoxml sequence output stream
FAST::Bio::SeqIO::chaos
chaos sequence input/output stream
FAST::Bio::SeqIO::chaosxml
chaosxml sequence input/output stream
FAST::Bio::SeqIO::ctf
ctf trace sequence input/output stream
FAST::Bio::SeqIO::embl
EMBL sequence input/output stream
FAST::Bio::SeqIO::embldriver
EMBL sequence input/output stream
FAST::Bio::SeqIO::entrezgene
Entrez Gene ASN1 parser
FAST::Bio::SeqIO::excel
sequence input/output stream from a MSExcel-formatted table
FAST::Bio::SeqIO::exp
exp trace sequence input/output stream
FAST::Bio::SeqIO::fasta
fasta sequence input/output stream
FAST::Bio::SeqIO::fastq
fastq sequence input/output stream
FAST::Bio::SeqIO::flybase_chadoxml
FlyBase variant of chadoxml with sequence output stream
FAST::Bio::SeqIO::game
a class for parsing and writing game-XML
FAST::Bio::SeqIO::game::featHandler
a class for handling feature elements
FAST::Bio::SeqIO::game::gameHandler
PerlSAX handler for game-XML
FAST::Bio::SeqIO::game::gameSubs
a base class for game-XML parsing
FAST::Bio::SeqIO::game::gameWriter
a class for writing game-XML
FAST::Bio::SeqIO::game::seqHandler
a class for handling game-XML sequences
FAST::Bio::SeqIO::gbdriver
GenBank handler-based push parser
FAST::Bio::SeqIO::gbxml
GenBank sequence input/output stream using SAX
FAST::Bio::SeqIO::gcg
GCG sequence input/output stream
FAST::Bio::SeqIO::genbank
GenBank sequence input/output stream
FAST::Bio::SeqIO::interpro
InterProScan XML input/output stream
FAST::Bio::SeqIO::kegg
KEGG sequence input/output stream
FAST::Bio::SeqIO::largefasta
method i/o on very large fasta sequence files
FAST::Bio::SeqIO::lasergene
Lasergene sequence file input/output stream
FAST::Bio::SeqIO::locuslink
LocusLink input/output stream
FAST::Bio::SeqIO::mbsout
input stream for output by Teshima et al.'s mbs.
FAST::Bio::SeqIO::metafasta
metafasta sequence input/output stream
FAST::Bio::SeqIO::msout
input stream for output by Hudson's ms
FAST::Bio::SeqIO::nexml
NeXML sequence input/output stream
FAST::Bio::SeqIO::phd
phd file input/output stream
FAST::Bio::SeqIO::pir
PIR sequence input/output stream
FAST::Bio::SeqIO::pln
pln trace sequence input/output stream
FAST::Bio::SeqIO::qual
.qual file input/output stream
FAST::Bio::SeqIO::raw
raw sequence file input/output stream
FAST::Bio::SeqIO::scf
.scf file input/output stream
FAST::Bio::SeqIO::seqxml
SeqXML sequence input/output stream
FAST::Bio::SeqIO::strider
DNA strider sequence input/output stream
FAST::Bio::SeqIO::swiss
Swissprot sequence input/output stream
FAST::Bio::SeqIO::swissdriver
SwissProt/UniProt handler-based push parser
FAST::Bio::SeqIO::tab
nearly raw sequence file input/output stream. Reads/writes id"\t"sequence"\n"
FAST::Bio::SeqIO::table
sequence input/output stream from a delimited table
FAST::Bio::SeqIO::tigr
TIGR XML sequence input/output stream
FAST::Bio::SeqIO::tigrxml
Parse TIGR (new) XML
FAST::Bio::SeqIO::tinyseq
reading/writing sequences in NCBI TinySeq format
FAST::Bio::SeqIO::tinyseq::tinyseqHandler
XML event handlers to support NCBI TinySeq XML parsing
FAST::Bio::SeqIO::ztr
ztr trace sequence input/output stream
FAST::Bio::SeqUtils
Additional methods for PrimarySeq objects
FAST::Bio::SimpleAlign
Multiple alignments held as a set of sequences
FAST::Bio::Species
Generic species object.
FAST::Bio::Taxon
A node in a represented taxonomy
FAST::Bio::Tools::AnalysisResult
Base class for analysis result objects and parsers
FAST::Bio::Tools::CodonTable
Codon table object
FAST::Bio::Tools::GFF
A FAST::Bio::SeqAnalysisParserI compliant GFF format parser
FAST::Bio::Tools::Genewise
Results of one Genewise run
FAST::Bio::Tools::Genomewise
Results of one Genomewise run
FAST::Bio::Tools::GuessSeqFormat
Module for determining the sequence format of the contents of a file, a string, or through a filehandle.
FAST::Bio::Tools::IUPAC
Generates unique Seq objects from an ambiguous Seq object
FAST::Bio::Tools::MySeqStats
Object holding statistics for one particular sequence
FAST::Bio::Tools::Run::GenericParameters
An object for the parameters used to run programs
FAST::Bio::Tools::Run::ParametersI
A Base object for the parameters used to run programs
FAST::Bio::Tools::SeqPattern
represent a sequence pattern or motif
FAST::Bio::Tools::SeqPattern::Backtranslate
FAST::Bio::Tools::SeqStats
Object holding statistics for one particular sequence
FAST::Bio::Tree::Node
A Simple Tree Node
FAST::Bio::Tree::NodeI
Interface describing a Tree Node
FAST::Bio::Tree::Tree
An Implementation of TreeI interface.
FAST::Bio::Tree::TreeFunctionsI
Decorated Interface implementing basic Tree exploration methods
FAST::Bio::Tree::TreeI
A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
FAST::Bio::UnivAln
Bioperl alignment object
FAST::Bio::WebAgent
A base class for Web (any protocol) access
FAST::List::Gen
provides functions for generating lists
FAST::List::Gen::Benchmark
performance tips for using FAST::List::Gen
FAST::List::Gen::Cookbook
how to get the most out of FAST::List::Gen
FAST::List::Gen::Haskell
the haskell prelude in perl5
FAST::List::Gen::Lazy
perl6 / haskell like laziness in perl5
FAST::List::Gen::Lazy::Builtins
perl builtin functions with partial + lazy application
FAST::List::Gen::Lazy::Ops
perl ops with partial + lazy application
FAST::List::Gen::Perl6
perl6 meta operators in perl5
FAST::List::Generator
provides functions for generating lists

Provides

FAST::Bio::GapSeq
in lib/FAST/Bio/GapSeq.pm
FAST::Bio::Root::Exception
in lib/FAST/Bio/Root/Exception.pm
FAST::Bio::Root::IO
in lib/FAST/Bio/Root/IO.pm
FAST::Bio::Root::Root
in lib/FAST/Bio/Root/Root.pm
FAST::Bio::Root::RootI
in lib/FAST/Bio/Root/RootI.pm
FAST::Bio::Root::Version
in lib/FAST/Bio/Root/Version.pm
FAST::Bio::SeqUtils
in lib/FAST/Bio/MySeqUtils.pm

Other files