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David H. Ardell > FAST-1.02

FAST-1.02

This Release FAST-1.02  [Download] [Browse 10 Feb 2015
Latest Release FAST-1.06  [Download] [Browse 21 Apr 2015
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License The Perl 5 License (Artistic 1 & GPL 1)
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INSTALL
Makefile.PL
MANIFEST
META.json
README

Modules

FAST FAST Analysis of Sequences Toolbox     1.02
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::GapSeq      
FAST::Bio::GapSeqI      
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      
FAST::Bio::MySeqI      
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     1.00
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 base class for SAX Handlers      
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::Bio::Root::Exception      
FAST::Bio::Root::IO      
FAST::Bio::Root::Root      
FAST::Bio::Root::RootI      
FAST::Bio::Root::Version     1.006924
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->primary_tag      
FAST::Bio::SeqFeature::Tools::TypeMapper maps $seq_feature->primary_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      
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     1.01
FAST::Bio::WebAgent A base class for Web (any protocol) access      
FAST::FAST::Bio::Root::HTTPget module for fallback HTTP get operations when LWP:: is unavailable      
FAST::List::Gen provides functions for generating lists     0.974
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      
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      

Documentation

FAST::Bio::Seq::GapSeqI GapSeq interface, for gapped sequences  
FAST::List::Gen::Builtins perl builtin functions with partial + lazy application  
alncut filter sites in alignments based on variation and gap-content  
bin/alnpi  
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  

Other Files

README.md
doc/FAST_Cookbook.html