Metadata
{
+
"abstracts_in_pod": { … - "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\ngeneric 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\ninput/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 \nFAST::Bio::AnnotationI (or derived class) through a factory",
- "FAST::Bio::Annotation::Collection": "Default Perl implementation of \nAnnotationCollectionI",
- "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\nrelationships ('structured tags') that can be represented as simple text.",
- "FAST::Bio::Annotation::Target": "Provides an object which represents a target (ie, a\nsimilarity 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\nwhich uses local flat files",
- "FAST::Bio::DB::Taxonomy::list": "An implementation of FAST::Bio::DB::Taxonomy\nthat 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\ngenerator 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::HandlerBaseI": "Interface class for handler methods which interact with any\nevent-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\nthat can be projected into a MSA or have coordinates relative to\nanother seq.",
- "FAST::Bio::Location::Atomic": "Implementation of a Atomic Location on a Sequence",
- "FAST::Bio::Location::CoordinatePolicyI": "Abstract interface for objects implementing\na certain policy of computing integer-valued coordinates of a Location",
- "FAST::Bio::Location::Fuzzy": "Implementation of a Location on a Sequence\nwhich has unclear start and/or end locations",
- "FAST::Bio::Location::FuzzyLocationI": "Abstract interface of a Location on a Sequence\nwhich has unclear start/end location",
- "FAST::Bio::Location::NarrowestCoordPolicy": "class implementing \nFAST::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\nwhich has multiple locations (start/end points)",
- "FAST::Bio::Location::SplitLocationI": "Abstract interface of a Location on a Sequence\nwhich has multiple locations (start/end points)",
- "FAST::Bio::Location::WidestCoordPolicy": "class implementing \nFAST::Bio::Location::CoordinatePolicy as the widest possible and reasonable range",
- "FAST::Bio::LocationI": "Abstract interface of a Location on a Sequence",
- "FAST::Bio::Ontology::DocumentRegistry": "Keep track of where to find ontologies.\nAllows lookups by name.",
- "FAST::Bio::Ontology::OBOEngine": "An Ontology Engine for OBO style flat file\nformat 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\nFAST::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\nFAST::Bio::Ontology::SimpleGOEngine",
- "FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02": "Graph adaptor (v02.x) for\nFAST::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 \nFAST::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::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\n 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::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\n results",
- "FAST::Bio::Search::Result::CrossMatchResult": "CrossMatch-specific subclass of FAST::Bio::Search::Result::GenericResult",
- "FAST::Bio::Search::Result::GenericResult": "Generic Implementation of\nFAST::Bio::Search::Result::ResultI interface applicable to most search\nresults.",
- "FAST::Bio::Search::Result::HmmpfamResult": "A parser and result object for hmmpfam\n results",
- "FAST::Bio::Search::Result::PullResultI": "FAST::Bio::Search::Result::ResultI interface for\n '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 \n(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\nSearchIO 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\na 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\nblast 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\nmegablast 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\nalignment output",
- "FAST::Bio::SearchIO::wise": "Parsing of wise output as alignments",
- "FAST::Bio::Seq": "Sequence object, with features",
- "FAST::Bio::Seq::GapSeqI": "GapSeq interface, for gapped sequences",
- "FAST::Bio::Seq::LargeLocatableSeq": "LocatableSeq object that stores sequence as\nfiles in the tempdir",
- "FAST::Bio::Seq::LargePrimarySeq": "PrimarySeq object that stores sequence as\nfiles in the tempdir (as found by File::Temp) or the default method in\nFAST::Bio::Root::Root",
- "FAST::Bio::Seq::LargeSeqI": "Interface class for sequences that cache their\nresidues in a temporary file",
- "FAST::Bio::Seq::Meta": "Generic superclass for sequence objects with\nresidue-based meta information",
- "FAST::Bio::Seq::Meta::Array": "array-based generic implementation of a\nsequence class with residue-based meta information",
- "FAST::Bio::Seq::MetaI": "Interface for sequence objects with residue-based\nmeta 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\n and trace values",
- "FAST::Bio::Seq::RichSeq": "Module implementing a sequence created from a rich\nsequence 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\n complex structure of a gene",
- "FAST::Bio::SeqFeature::Gene::Intron": "An intron feature",
- "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\n transcript of exons, promoter(s), UTR, and a poly-adenylation site.",
- "FAST::Bio::SeqFeature::Gene::UTR": "A feature representing an untranslated region\n 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\n of two sequences.",
- "FAST::Bio::SeqFeature::Tools::FeatureNamer": "generates unique persistent names for features",
- "FAST::Bio::SeqFeature::Tools::IDHandler": "maps $seq_feature-E<gt>primary_tag",
- "FAST::Bio::SeqFeature::Tools::TypeMapper": "maps $seq_feature-E<gt>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\ndata 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\n 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\nstream. 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\nformat of the contents of a file, a string, or through a\nfilehandle.",
- "FAST::Bio::Tools::IUPAC": "Generates unique Seq objects from an ambiguous Seq object",
- "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::SeqStats": "Object holding statistics for one \nparticular 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\n originally for Phylogenetic Trees.",
- "FAST::Bio::UnivAln": "Bioperl alignment object",
- "FAST::Bio::WebAgent": "A base class for Web (any protocol) access",
- "FAST::FAST::Bio::Root::HTTPget": "module for fallback HTTP get operations when \nLWP:: is unavailable",
- "FAST::List::Gen": "provides functions for generating lists\r",
- "FAST::List::Gen::Benchmark": "performance tips for using L<FAST::List::Gen>\r",
- "FAST::List::Gen::Builtins": "perl builtin functions with partial + lazy application\r",
- "FAST::List::Gen::Cookbook": "how to get the most out of L<FAST::List::Gen>\r",
- "FAST::List::Gen::Haskell": "the haskell prelude in perl5\r",
- "FAST::List::Gen::Lazy": "perl6 / haskell like laziness in perl5\r",
- "FAST::List::Gen::Lazy::Ops": "perl ops with partial + lazy application\r",
- "FAST::List::Gen::Perl6": "perl6 meta operators in perl5",
- "FAST::List::Generator": "provides functions for generating lists\r",
- "alncut": "filter sites in alignments based on variation and gap-content",
- "alnpi": "calculate molecular population genetic statistics from DNA alignments",
- "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\nmultifasta 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",
- "verbose": "a boolean value, which if TRUE will cause\n C<rmtree> to print a message each time it\n examines a file, giving the name of the file, and\n indicating whether it's using C<rmdir> or\n C<unlink> to remove it, or that it's skipping it.\n (defaults to FALSE)"
},- "author": "DHARD",
- "buildfile_executable": 0,
- "dir_lib": "lib",
- "dir_t": "t",
+
"dirs_array": [ … - "bin",
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- "lib/FAST/Bio/Align",
- "lib/FAST/Bio/AlignIO/Handler",
- "lib/FAST/Bio/AlignIO",
- "lib/FAST/Bio/Annotation",
- "lib/FAST/Bio/Cluster",
- "lib/FAST/Bio/DB/Taxonomy",
- "lib/FAST/Bio/DB",
- "lib/FAST/Bio/Event",
- "lib/FAST/Bio/Factory",
- "lib/FAST/Bio/Location",
- "lib/FAST/Bio/Ontology/SimpleGOEngine",
- "lib/FAST/Bio/Ontology",
- "lib/FAST/Bio/OntologyIO/Handlers",
- "lib/FAST/Bio/OntologyIO",
- "lib/FAST/Bio/Root",
- "lib/FAST/Bio/Search/HSP",
- "lib/FAST/Bio/Search/Hit",
- "lib/FAST/Bio/Search/Result",
- "lib/FAST/Bio/Search",
- "lib/FAST/Bio/SearchIO/Writer",
- "lib/FAST/Bio/SearchIO/XML",
- "lib/FAST/Bio/SearchIO",
- "lib/FAST/Bio/Seq/Meta",
- "lib/FAST/Bio/Seq",
- "lib/FAST/Bio/SeqFeature/Gene",
- "lib/FAST/Bio/SeqFeature/Tools",
- "lib/FAST/Bio/SeqFeature",
- "lib/FAST/Bio/SeqIO/Handler",
- "lib/FAST/Bio/SeqIO/game",
- "lib/FAST/Bio/SeqIO/tinyseq",
- "lib/FAST/Bio/SeqIO",
- "lib/FAST/Bio/Tools/Run",
- "lib/FAST/Bio/Tools/SeqPattern",
- "lib/FAST/Bio/Tools",
- "lib/FAST/Bio/Tree",
- "lib/FAST/Bio",
- "lib/FAST/List/Gen/Lazy",
- "lib/FAST/List/Gen",
- "lib/FAST/List",
- "lib/FAST",
- "lib",
- "t/data",
- "t/lib/Test/Cmd",
- "t/lib/Test",
- "t/lib",
- "t"
],- "dist": "FAST",
- "dynamic_config": 1,
+
"error": { … - "consistent_version": "0.974,1.006924,1.01",
+
"prereq_matches_use": [ … - "Convert::Binary::C",
- "Data::Stag",
- "Data::Stag::XMLWriter",
- "Error",
- "Graph::Directed",
- "IO::String",
- "LWP::UserAgent",
- "List::MoreUtils",
- "Spreadsheet::ParseExcel",
- "XML::DOM",
- "XML::DOM::XPath",
- "XML::LibXML",
- "XML::LibXML::Reader",
- "XML::Parser::PerlSAX",
- "XML::SAX",
- "XML::SAX::Base",
- "XML::SAX::Writer",
- "XML::Writer",
- "parent",
- "version"
],- "use_strict": "FAST::Bio::Location::Split, FAST::Bio::Search::BlastUtils, FAST::Bio::SearchIO::SearchWriterI, FAST::Bio::SearchIO::XML::BlastHandler, FAST::Bio::SearchIO::XML::PsiBlastHandler, FAST::Bio::SearchIO::cross_match, FAST::Bio::SeqIO::game, FAST::List::Generator",
- "use_warnings": "FAST::Bio::Align::AlignI, FAST::Bio::AlignIO, FAST::Bio::AlignIO::arp, FAST::Bio::AlignIO::bl2seq, FAST::Bio::AlignIO::clustalw, FAST::Bio::AlignIO::emboss, FAST::Bio::AlignIO::fasta, FAST::Bio::AlignIO::largemultifasta, FAST::Bio::AlignIO::maf, FAST::Bio::AlignIO::mase, FAST::Bio::AlignIO::mega, FAST::Bio::AlignIO::meme, FAST::Bio::AlignIO::metafasta, FAST::Bio::AlignIO::msf, FAST::Bio::AlignIO::nexml, FAST::Bio::AlignIO::nexus, FAST::Bio::AlignIO::pfam, FAST::Bio::AlignIO::phylip, FAST::Bio::AlignIO::po, FAST::Bio::AlignIO::proda, FAST::Bio::AlignIO::prodom, FAST::Bio::AlignIO::psi, FAST::Bio::AlignIO::selex, FAST::Bio::AlignIO::stockholm, FAST::Bio::AlignIO::xmfa, FAST::Bio::AnalysisParserI, FAST::Bio::AnalysisResultI, FAST::Bio::AnnotatableI, FAST::Bio::Annotation::AnnotationFactory, FAST::Bio::Annotation::Collection, FAST::Bio::Annotation::Comment, FAST::Bio::Annotation::DBLink, FAST::Bio::Annotation::OntologyTerm, FAST::Bio::Annotation::Reference, FAST::Bio::Annotation::SimpleValue, FAST::Bio::Annotation::TagTree, FAST::Bio::Annotation::Target, FAST::Bio::Annotation::TypeManager, FAST::Bio::AnnotationCollectionI, FAST::Bio::AnnotationI, FAST::Bio::Cluster::FamilyI, FAST::Bio::Cluster::SequenceFamily, FAST::Bio::ClusterI, FAST::Bio::DB::InMemoryCache, FAST::Bio::DB::RandomAccessI, FAST::Bio::DB::SeqI, FAST::Bio::DB::Taxonomy, FAST::Bio::DB::Taxonomy::entrez, FAST::Bio::DB::Taxonomy::flatfile, FAST::Bio::DB::Taxonomy::list, FAST::Bio::DescribableI, FAST::Bio::Event::EventGeneratorI, FAST::Bio::Event::EventHandlerI, FAST::Bio::Factory::FTLocationFactory, FAST::Bio::Factory::LocationFactoryI, FAST::Bio::Factory::ObjectBuilderI, FAST::Bio::Factory::ObjectFactory, FAST::Bio::Factory::ObjectFactoryI, FAST::Bio::Factory::SequenceFactoryI, FAST::Bio::Factory::SequenceStreamI, FAST::Bio::FeatureHolderI, FAST::Bio::GapSeq, FAST::Bio::GapSeqI, FAST::Bio::IdentifiableI, FAST::Bio::LocatableSeq, FAST::Bio::Location::Atomic, FAST::Bio::Location::CoordinatePolicyI, FAST::Bio::Location::Fuzzy, FAST::Bio::Location::FuzzyLocationI, FAST::Bio::Location::NarrowestCoordPolicy, FAST::Bio::Location::Simple, FAST::Bio::Location::Split, FAST::Bio::Location::SplitLocationI, FAST::Bio::Location::WidestCoordPolicy, FAST::Bio::LocationI, FAST::Bio::MyPrimarySeqI, FAST::Bio::MySeqI, FAST::Bio::MySeqUtils, FAST::Bio::Ontology::DocumentRegistry, FAST::Bio::Ontology::OBOEngine, FAST::Bio::Ontology::Ontology, FAST::Bio::Ontology::OntologyEngineI, FAST::Bio::Ontology::OntologyI, FAST::Bio::Ontology::OntologyStore, FAST::Bio::Ontology::Relationship, FAST::Bio::Ontology::RelationshipFactory, FAST::Bio::Ontology::RelationshipI, FAST::Bio::Ontology::RelationshipType, FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor, FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02, FAST::Bio::Ontology::SimpleOntologyEngine, FAST::Bio::Ontology::Term, FAST::Bio::Ontology::TermFactory, FAST::Bio::Ontology::TermI, FAST::Bio::OntologyIO, FAST::Bio::OntologyIO::Handlers::BaseSAXHandler, FAST::Bio::OntologyIO::Handlers::InterProHandler, FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler, FAST::Bio::OntologyIO::InterProParser, FAST::Bio::OntologyIO::dagflat, FAST::Bio::OntologyIO::goflat, FAST::Bio::OntologyIO::obo, FAST::Bio::OntologyIO::simplehierarchy, FAST::Bio::OntologyIO::soflat, FAST::Bio::PrimarySeq, FAST::Bio::PrimarySeqI, FAST::Bio::PullParserI, FAST::Bio::Range, FAST::Bio::RangeI, FAST::Bio::Root::Exception, FAST::Bio::Root::IO, FAST::Bio::Root::Root, FAST::Bio::Root::RootI, FAST::Bio::Root::Version, FAST::Bio::Search::BlastUtils, FAST::Bio::Search::GenericStatistics, FAST::Bio::Search::HSP::BlastPullHSP, FAST::Bio::Search::HSP::GenericHSP, FAST::Bio::Search::HSP::HSPFactory, FAST::Bio::Search::HSP::HSPI, FAST::Bio::Search::HSP::HmmpfamHSP, FAST::Bio::Search::HSP::PullHSPI, FAST::Bio::Search::Hit::BlastPullHit, FAST::Bio::Search::Hit::GenericHit, FAST::Bio::Search::Hit::HitFactory, FAST::Bio::Search::Hit::HitI, FAST::Bio::Search::Hit::HmmpfamHit, FAST::Bio::Search::Hit::PullHitI, FAST::Bio::Search::Result::BlastPullResult, FAST::Bio::Search::Result::CrossMatchResult, FAST::Bio::Search::Result::GenericResult, FAST::Bio::Search::Result::HmmpfamResult, FAST::Bio::Search::Result::PullResultI, FAST::Bio::Search::Result::ResultFactory, FAST::Bio::Search::Result::ResultI, FAST::Bio::Search::SearchUtils, FAST::Bio::Search::StatisticsI, FAST::Bio::SearchIO::EventHandlerI, FAST::Bio::SearchIO::FastHitEventBuilder, FAST::Bio::SearchIO::IteratedSearchResultEventBuilder, FAST::Bio::SearchIO::SearchResultEventBuilder, FAST::Bio::SearchIO::SearchWriterI, FAST::Bio::SearchIO::Writer::BSMLResultWriter, FAST::Bio::SearchIO::Writer::GbrowseGFF, FAST::Bio::SearchIO::Writer::HSPTableWriter, FAST::Bio::SearchIO::Writer::HTMLResultWriter, FAST::Bio::SearchIO::Writer::HitTableWriter, FAST::Bio::SearchIO::Writer::ResultTableWriter, FAST::Bio::SearchIO::Writer::TextResultWriter, FAST::Bio::SearchIO::XML::BlastHandler, FAST::Bio::SearchIO::XML::PsiBlastHandler, FAST::Bio::SearchIO::axt, FAST::Bio::SearchIO::blast, FAST::Bio::SearchIO::blast_pull, FAST::Bio::SearchIO::blasttable, FAST::Bio::SearchIO::blastxml, FAST::Bio::SearchIO::cross_match, FAST::Bio::SearchIO::erpin, FAST::Bio::SearchIO::exonerate, FAST::Bio::SearchIO::fasta, FAST::Bio::SearchIO::hmmer, FAST::Bio::SearchIO::hmmer2, FAST::Bio::SearchIO::hmmer3, FAST::Bio::SearchIO::hmmer_pull, FAST::Bio::SearchIO::infernal, FAST::Bio::SearchIO::megablast, FAST::Bio::SearchIO::psl, FAST::Bio::SearchIO::rnamotif, FAST::Bio::SearchIO::sim4, FAST::Bio::SearchIO::waba, FAST::Bio::SearchIO::wise, FAST::Bio::Seq, FAST::Bio::Seq::LargeLocatableSeq, FAST::Bio::Seq::LargePrimarySeq, FAST::Bio::Seq::LargeSeqI, FAST::Bio::Seq::Meta, FAST::Bio::Seq::Meta::Array, FAST::Bio::Seq::MetaI, FAST::Bio::Seq::PrimaryQual, FAST::Bio::Seq::QualI, FAST::Bio::Seq::Quality, FAST::Bio::Seq::RichSeq, FAST::Bio::Seq::RichSeqI, FAST::Bio::Seq::SeqBuilder, FAST::Bio::Seq::SeqFactory, FAST::Bio::Seq::SeqFastaSpeedFactory, FAST::Bio::Seq::SequenceTrace, FAST::Bio::Seq::TraceI, FAST::Bio::SeqAnalysisParserI, FAST::Bio::SeqFeature::FeaturePair, FAST::Bio::SeqFeature::Gene::Exon, FAST::Bio::SeqFeature::Gene::ExonI, FAST::Bio::SeqFeature::Gene::GeneStructure, FAST::Bio::SeqFeature::Gene::GeneStructureI, FAST::Bio::SeqFeature::Gene::Intron, FAST::Bio::SeqFeature::Gene::NC_Feature, FAST::Bio::SeqFeature::Gene::Poly_A_site, FAST::Bio::SeqFeature::Gene::Promoter, FAST::Bio::SeqFeature::Gene::Transcript, FAST::Bio::SeqFeature::Gene::TranscriptI, FAST::Bio::SeqFeature::Gene::UTR, FAST::Bio::SeqFeature::Generic, FAST::Bio::SeqFeature::Similarity, FAST::Bio::SeqFeature::SimilarityPair, FAST::Bio::SeqFeature::Tools::FeatureNamer, FAST::Bio::SeqFeature::Tools::IDHandler, FAST::Bio::SeqFeature::Tools::TypeMapper, FAST::Bio::SeqFeature::Tools::Unflattener, FAST::Bio::SeqFeatureI, FAST::Bio::SeqI, FAST::Bio::SeqIO::FTHelper, FAST::Bio::SeqIO::MultiFile, FAST::Bio::SeqIO::abi, FAST::Bio::SeqIO::ace, FAST::Bio::SeqIO::agave, FAST::Bio::SeqIO::alf, FAST::Bio::SeqIO::asciitree, FAST::Bio::SeqIO::bsml, FAST::Bio::SeqIO::bsml_sax, FAST::Bio::SeqIO::chadoxml, FAST::Bio::SeqIO::chaos, FAST::Bio::SeqIO::chaosxml, FAST::Bio::SeqIO::ctf, FAST::Bio::SeqIO::embl, FAST::Bio::SeqIO::embldriver, FAST::Bio::SeqIO::entrezgene, FAST::Bio::SeqIO::excel, FAST::Bio::SeqIO::exp, FAST::Bio::SeqIO::fastq, FAST::Bio::SeqIO::flybase_chadoxml, FAST::Bio::SeqIO::game, FAST::Bio::SeqIO::game::featHandler, FAST::Bio::SeqIO::game::gameHandler, FAST::Bio::SeqIO::game::gameSubs, FAST::Bio::SeqIO::game::gameWriter, FAST::Bio::SeqIO::game::seqHandler, FAST::Bio::SeqIO::gbxml, FAST::Bio::SeqIO::gcg, FAST::Bio::SeqIO::genbank, FAST::Bio::SeqIO::interpro, FAST::Bio::SeqIO::kegg, FAST::Bio::SeqIO::largefasta, FAST::Bio::SeqIO::lasergene, FAST::Bio::SeqIO::locuslink, FAST::Bio::SeqIO::mbsout, FAST::Bio::SeqIO::metafasta, FAST::Bio::SeqIO::msout, FAST::Bio::SeqIO::nexml, FAST::Bio::SeqIO::phd, FAST::Bio::SeqIO::pir, FAST::Bio::SeqIO::pln, FAST::Bio::SeqIO::qual, FAST::Bio::SeqIO::raw, FAST::Bio::SeqIO::scf, FAST::Bio::SeqIO::seqxml, FAST::Bio::SeqIO::swiss, FAST::Bio::SeqIO::swissdriver, FAST::Bio::SeqIO::tab, FAST::Bio::SeqIO::table, FAST::Bio::SeqIO::tigr, FAST::Bio::SeqIO::tigrxml, FAST::Bio::SeqIO::tinyseq, FAST::Bio::SeqIO::ztr, FAST::Bio::SeqUtils, FAST::Bio::SimpleAlign, FAST::Bio::Taxon, FAST::Bio::Tools::AnalysisResult, FAST::Bio::Tools::CodonTable, FAST::Bio::Tools::GFF, FAST::Bio::Tools::Genewise, FAST::Bio::Tools::Genomewise, FAST::Bio::Tools::IUPAC, FAST::Bio::Tools::MySeqStats, FAST::Bio::Tools::Run::GenericParameters, FAST::Bio::Tools::Run::ParametersI, FAST::Bio::Tools::SeqPattern, FAST::Bio::Tools::SeqStats, FAST::Bio::Tree::Node, FAST::Bio::Tree::NodeI, FAST::Bio::Tree::Tree, FAST::Bio::Tree::TreeFunctionsI, FAST::Bio::Tree::TreeI, FAST::Bio::UnivAln, FAST::Bio::WebAgent, FAST::List::Generator"
},- "extension": "tar.gz",
- "extractable": 1,
- "extracts_nicely": 1,
- "file__build": 0,
- "file_blib": 0,
- "file_build": 0,
- "file_changelog": "Changes",
- "file_makefile": 0,
- "file_makefile_pl": "Makefile.PL",
- "file_manifest": "MANIFEST",
- "file_meta_json": "META.json",
- "file_meta_yml": "META.yml",
- "file_pm_to_blib": 0,
- "file_readme": "README,README.md",
+
"files_array": [ … - "Changes",
- "INSTALL",
- "MANIFEST",
- "META.json",
- "META.yml",
- "Makefile.PL",
- "README",
- "README.md",
- "bin/alncut",
- "bin/alnpi",
- "bin/fascodon",
- "bin/fascomp",
- "bin/fasconvert",
- "bin/fascut",
- "bin/fasfilter",
- "bin/fasgrep",
- "bin/fashead",
- "bin/faslen",
- "bin/faspaste",
- "bin/fasrc",
- "bin/fassort",
- "bin/fassub",
- "bin/fastail",
- "bin/fastax",
- "bin/fastaxsort",
- "bin/fastr",
- "bin/fasuniq",
- "bin/faswc",
- "bin/fasxl",
- "bin/gbfalncut",
- "bin/gbfcut",
- "doc/FAST_Cookbook.html",
- "doc/FAST_Cookbook.org",
- "doc/FAST_Cookbook.pdf",
- "doc/FAST_Cookbook.tex",
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- "doc/org2pdf",
- "lib/FAST/Bio/Align/AlignI.pm",
- "lib/FAST/Bio/AlignIO/Handler/GenericAlignHandler.pm",
- "lib/FAST/Bio/AlignIO/arp.pm",
- "lib/FAST/Bio/AlignIO/bl2seq.pm",
- "lib/FAST/Bio/AlignIO/clustalw.pm",
- "lib/FAST/Bio/AlignIO/emboss.pm",
- "lib/FAST/Bio/AlignIO/fasta.pm",
- "lib/FAST/Bio/AlignIO/largemultifasta.pm",
- "lib/FAST/Bio/AlignIO/maf.pm",
- "lib/FAST/Bio/AlignIO/mase.pm",
- "lib/FAST/Bio/AlignIO/mega.pm",
- "lib/FAST/Bio/AlignIO/meme.pm",
- "lib/FAST/Bio/AlignIO/metafasta.pm",
- "lib/FAST/Bio/AlignIO/msf.pm",
- "lib/FAST/Bio/AlignIO/nexml.pm",
- "lib/FAST/Bio/AlignIO/nexus.pm",
- "lib/FAST/Bio/AlignIO/pfam.pm",
- "lib/FAST/Bio/AlignIO/phylip.pm",
- "lib/FAST/Bio/AlignIO/po.pm",
- "lib/FAST/Bio/AlignIO/proda.pm",
- "lib/FAST/Bio/AlignIO/prodom.pm",
- "lib/FAST/Bio/AlignIO/psi.pm",
- "lib/FAST/Bio/AlignIO/selex.pm",
- "lib/FAST/Bio/AlignIO/stockholm.pm",
- "lib/FAST/Bio/AlignIO/xmfa.pm",
- "lib/FAST/Bio/AlignIO.pm",
- "lib/FAST/Bio/AnalysisParserI.pm",
- "lib/FAST/Bio/AnalysisResultI.pm",
- "lib/FAST/Bio/AnnotatableI.pm",
- "lib/FAST/Bio/Annotation/AnnotationFactory.pm",
- "lib/FAST/Bio/Annotation/Collection.pm",
- "lib/FAST/Bio/Annotation/Comment.pm",
- "lib/FAST/Bio/Annotation/DBLink.pm",
- "lib/FAST/Bio/Annotation/OntologyTerm.pm",
- "lib/FAST/Bio/Annotation/Reference.pm",
- "lib/FAST/Bio/Annotation/SimpleValue.pm",
- "lib/FAST/Bio/Annotation/TagTree.pm",
- "lib/FAST/Bio/Annotation/Target.pm",
- "lib/FAST/Bio/Annotation/TypeManager.pm",
- "lib/FAST/Bio/AnnotationCollectionI.pm",
- "lib/FAST/Bio/AnnotationI.pm",
- "lib/FAST/Bio/Cluster/FamilyI.pm",
- "lib/FAST/Bio/Cluster/SequenceFamily.pm",
- "lib/FAST/Bio/ClusterI.pm",
- "lib/FAST/Bio/DB/InMemoryCache.pm",
- "lib/FAST/Bio/DB/RandomAccessI.pm",
- "lib/FAST/Bio/DB/SeqI.pm",
- "lib/FAST/Bio/DB/Taxonomy/entrez.pm",
- "lib/FAST/Bio/DB/Taxonomy/flatfile.pm",
- "lib/FAST/Bio/DB/Taxonomy/list.pm",
- "lib/FAST/Bio/DB/Taxonomy.pm",
- "lib/FAST/Bio/DescribableI.pm",
- "lib/FAST/Bio/Event/EventGeneratorI.pm",
- "lib/FAST/Bio/Event/EventHandlerI.pm",
- "lib/FAST/Bio/Factory/FTLocationFactory.pm",
- "lib/FAST/Bio/Factory/LocationFactoryI.pm",
- "lib/FAST/Bio/Factory/ObjectBuilderI.pm",
- "lib/FAST/Bio/Factory/ObjectFactory.pm",
- "lib/FAST/Bio/Factory/ObjectFactoryI.pm",
- "lib/FAST/Bio/Factory/SequenceFactoryI.pm",
- "lib/FAST/Bio/Factory/SequenceStreamI.pm",
- "lib/FAST/Bio/FeatureHolderI.pm",
- "lib/FAST/Bio/GapSeq.pm",
- "lib/FAST/Bio/GapSeqI.pm",
- "lib/FAST/Bio/HandlerBaseI.pm",
- "lib/FAST/Bio/IdentifiableI.pm",
- "lib/FAST/Bio/LocatableSeq.pm",
- "lib/FAST/Bio/Location/Atomic.pm",
- "lib/FAST/Bio/Location/CoordinatePolicyI.pm",
- "lib/FAST/Bio/Location/Fuzzy.pm",
- "lib/FAST/Bio/Location/FuzzyLocationI.pm",
- "lib/FAST/Bio/Location/NarrowestCoordPolicy.pm",
- "lib/FAST/Bio/Location/Simple.pm",
- "lib/FAST/Bio/Location/Split.pm",
- "lib/FAST/Bio/Location/SplitLocationI.pm",
- "lib/FAST/Bio/Location/WidestCoordPolicy.pm",
- "lib/FAST/Bio/LocationI.pm",
- "lib/FAST/Bio/MyPrimarySeqI.pm",
- "lib/FAST/Bio/MySeqI.pm",
- "lib/FAST/Bio/MySeqUtils.pm",
- "lib/FAST/Bio/Ontology/DocumentRegistry.pm",
- "lib/FAST/Bio/Ontology/OBOEngine.pm",
- "lib/FAST/Bio/Ontology/Ontology.pm",
- "lib/FAST/Bio/Ontology/OntologyEngineI.pm",
- "lib/FAST/Bio/Ontology/OntologyI.pm",
- "lib/FAST/Bio/Ontology/OntologyStore.pm",
- "lib/FAST/Bio/Ontology/Relationship.pm",
- "lib/FAST/Bio/Ontology/RelationshipFactory.pm",
- "lib/FAST/Bio/Ontology/RelationshipI.pm",
- "lib/FAST/Bio/Ontology/RelationshipType.pm",
- "lib/FAST/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm",
- "lib/FAST/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm",
- "lib/FAST/Bio/Ontology/SimpleOntologyEngine.pm",
- "lib/FAST/Bio/Ontology/Term.pm",
- "lib/FAST/Bio/Ontology/TermFactory.pm",
- "lib/FAST/Bio/Ontology/TermI.pm",
- "lib/FAST/Bio/OntologyIO/Handlers/BaseSAXHandler.pm",
- "lib/FAST/Bio/OntologyIO/Handlers/InterProHandler.pm",
- "lib/FAST/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm",
- "lib/FAST/Bio/OntologyIO/InterProParser.pm",
- "lib/FAST/Bio/OntologyIO/dagflat.pm",
- "lib/FAST/Bio/OntologyIO/goflat.pm",
- "lib/FAST/Bio/OntologyIO/obo.pm",
- "lib/FAST/Bio/OntologyIO/simplehierarchy.pm",
- "lib/FAST/Bio/OntologyIO/soflat.pm",
- "lib/FAST/Bio/OntologyIO.pm",
- "lib/FAST/Bio/PrimarySeq.pm",
- "lib/FAST/Bio/PrimarySeqI.pm",
- "lib/FAST/Bio/PullParserI.pm",
- "lib/FAST/Bio/Range.pm",
- "lib/FAST/Bio/RangeI.pm",
- "lib/FAST/Bio/Root/Exception.pm",
- "lib/FAST/Bio/Root/HTTPget.pm",
- "lib/FAST/Bio/Root/IO.pm",
- "lib/FAST/Bio/Root/Root.pm",
- "lib/FAST/Bio/Root/RootI.pm",
- "lib/FAST/Bio/Root/Version.pm",
- "lib/FAST/Bio/Search/BlastUtils.pm",
- "lib/FAST/Bio/Search/GenericStatistics.pm",
- "lib/FAST/Bio/Search/HSP/BlastPullHSP.pm",
- "lib/FAST/Bio/Search/HSP/GenericHSP.pm",
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- "lib/FAST/Bio/Search/HSP/HSPI.pm",
- "lib/FAST/Bio/Search/HSP/HmmpfamHSP.pm",
- "lib/FAST/Bio/Search/HSP/PullHSPI.pm",
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- "lib/FAST/Bio/Search/Hit/GenericHit.pm",
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- "lib/FAST/Bio/Search/Result/CrossMatchResult.pm",
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},+
"lib/FAST/Bio/Event/EventGeneratorI.pm": { … - "FAST::Bio::Event::EventGeneratorI": "undef"
},+
"lib/FAST/Bio/Event/EventHandlerI.pm": { … - "FAST::Bio::Event::EventHandlerI": "undef"
},+
"lib/FAST/Bio/Factory/FTLocationFactory.pm": { … - "FAST::Bio::Factory::FTLocationFactory": "undef"
},+
"lib/FAST/Bio/Factory/LocationFactoryI.pm": { … - "FAST::Bio::Factory::LocationFactoryI": "undef"
},+
"lib/FAST/Bio/Factory/ObjectBuilderI.pm": { … - "FAST::Bio::Factory::ObjectBuilderI": "undef"
},+
"lib/FAST/Bio/Factory/ObjectFactory.pm": { … - "FAST::Bio::Factory::ObjectFactory": "undef"
},+
"lib/FAST/Bio/Factory/ObjectFactoryI.pm": { … - "FAST::Bio::Factory::ObjectFactoryI": "undef"
},+
"lib/FAST/Bio/Factory/SequenceFactoryI.pm": { … - "FAST::Bio::Factory::SequenceFactoryI": "undef"
},+
"lib/FAST/Bio/Factory/SequenceStreamI.pm": { … - "FAST::Bio::Factory::SequenceStreamI": "undef"
},+
"lib/FAST/Bio/FeatureHolderI.pm": { … - "FAST::Bio::FeatureHolderI": "undef"
},+
"lib/FAST/Bio/GapSeq.pm": { … - "FAST::Bio::GapSeq": "undef"
},+
"lib/FAST/Bio/GapSeqI.pm": { … - "FAST::Bio::GapSeqI": "undef"
},+
"lib/FAST/Bio/HandlerBaseI.pm": { … - "FAST::Bio::HandlerBaseI": "undef"
},+
"lib/FAST/Bio/IdentifiableI.pm": { … - "FAST::Bio::IdentifiableI": "undef"
},+
"lib/FAST/Bio/LocatableSeq.pm": { … - "FAST::Bio::LocatableSeq": "undef"
},+
"lib/FAST/Bio/Location/Atomic.pm": { … - "FAST::Bio::Location::Atomic": "undef"
},+
"lib/FAST/Bio/Location/CoordinatePolicyI.pm": { … - "FAST::Bio::Location::CoordinatePolicyI": "undef"
},+
"lib/FAST/Bio/Location/Fuzzy.pm": { … - "FAST::Bio::Location::Fuzzy": "undef"
},+
"lib/FAST/Bio/Location/FuzzyLocationI.pm": { … - "FAST::Bio::Location::FuzzyLocationI": "undef"
},+
"lib/FAST/Bio/Location/NarrowestCoordPolicy.pm": { … - "FAST::Bio::Location::NarrowestCoordPolicy": "undef"
},+
"lib/FAST/Bio/Location/Simple.pm": { … - "FAST::Bio::Location::Simple": "undef"
},+
"lib/FAST/Bio/Location/Split.pm": { … - "FAST::Bio::Location::Split": "undef"
},+
"lib/FAST/Bio/Location/SplitLocationI.pm": { … - "FAST::Bio::Location::SplitLocationI": "undef"
},+
"lib/FAST/Bio/Location/WidestCoordPolicy.pm": { … - "FAST::Bio::Location::WidestCoordPolicy": "undef"
},+
"lib/FAST/Bio/LocationI.pm": { … - "FAST::Bio::LocationI": "undef"
},+
"lib/FAST/Bio/MyPrimarySeqI.pm": { … - "FAST::Bio::MyPrimarySeqI": "undef"
},+
"lib/FAST/Bio/MySeqI.pm": { … - "FAST::Bio::MySeqI": "undef"
},+
"lib/FAST/Bio/Ontology/DocumentRegistry.pm": { … - "FAST::Bio::Ontology::DocumentRegistry": "undef"
},+
"lib/FAST/Bio/Ontology/OBOEngine.pm": { … - "FAST::Bio::Ontology::OBOEngine": "undef"
},+
"lib/FAST/Bio/Ontology/Ontology.pm": { … - "FAST::Bio::Ontology::Ontology": "undef"
},+
"lib/FAST/Bio/Ontology/OntologyEngineI.pm": { … - "FAST::Bio::Ontology::OntologyEngineI": "undef"
},+
"lib/FAST/Bio/Ontology/OntologyI.pm": { … - "FAST::Bio::Ontology::OntologyI": "undef"
},+
"lib/FAST/Bio/Ontology/OntologyStore.pm": { … - "FAST::Bio::Ontology::OntologyStore": "undef"
},+
"lib/FAST/Bio/Ontology/Relationship.pm": { … - "FAST::Bio::Ontology::Relationship": "undef"
},+
"lib/FAST/Bio/Ontology/RelationshipFactory.pm": { … - "FAST::Bio::Ontology::RelationshipFactory": "undef"
},+
"lib/FAST/Bio/Ontology/RelationshipI.pm": { … - "FAST::Bio::Ontology::RelationshipI": "undef"
},+
"lib/FAST/Bio/Ontology/RelationshipType.pm": { … - "FAST::Bio::Ontology::RelationshipType": "undef"
},+
"lib/FAST/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm": { … - "FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor": "undef"
},+
"lib/FAST/Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm": { … - "FAST::Bio::Ontology::SimpleGOEngine::GraphAdaptor02": "undef"
},+
"lib/FAST/Bio/Ontology/SimpleOntologyEngine.pm": { … - "FAST::Bio::Ontology::SimpleOntologyEngine": "undef"
},+
"lib/FAST/Bio/Ontology/Term.pm": { … - "FAST::Bio::Ontology::Term": "undef"
},+
"lib/FAST/Bio/Ontology/TermFactory.pm": { … - "FAST::Bio::Ontology::TermFactory": "undef"
},+
"lib/FAST/Bio/Ontology/TermI.pm": { … - "FAST::Bio::Ontology::TermI": "undef"
},+
"lib/FAST/Bio/OntologyIO.pm": { … - "FAST::Bio::OntologyIO": "undef"
},+
"lib/FAST/Bio/OntologyIO/Handlers/BaseSAXHandler.pm": { … - "FAST::Bio::OntologyIO::Handlers::BaseSAXHandler": "undef"
},+
"lib/FAST/Bio/OntologyIO/Handlers/InterProHandler.pm": { … - "FAST::Bio::OntologyIO::Handlers::InterProHandler": "undef"
},+
"lib/FAST/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm": { … - "FAST::Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler": "undef"
},+
"lib/FAST/Bio/OntologyIO/InterProParser.pm": { … - "FAST::Bio::OntologyIO::InterProParser": "undef"
},+
"lib/FAST/Bio/OntologyIO/dagflat.pm": { … - "FAST::Bio::OntologyIO::dagflat": "undef"
},+
"lib/FAST/Bio/OntologyIO/goflat.pm": { … - "FAST::Bio::OntologyIO::goflat": "undef"
},+
"lib/FAST/Bio/OntologyIO/obo.pm": { … - "FAST::Bio::OntologyIO::obo": "undef"
},+
"lib/FAST/Bio/OntologyIO/simplehierarchy.pm": { … - "FAST::Bio::OntologyIO::simplehierarchy": "undef"
},+
"lib/FAST/Bio/OntologyIO/soflat.pm": { … - "FAST::Bio::OntologyIO::soflat": "undef"
},+
"lib/FAST/Bio/PrimarySeq.pm": { … - "FAST::Bio::PrimarySeq": "undef"
},+
"lib/FAST/Bio/PrimarySeqI.pm": { … - "FAST::Bio::PrimarySeqI": "undef"
},+
"lib/FAST/Bio/PullParserI.pm": { … - "FAST::Bio::PullParserI": "undef"
},+
"lib/FAST/Bio/Range.pm": { … - "FAST::Bio::Range": "undef"
},+
"lib/FAST/Bio/RangeI.pm": { … - "FAST::Bio::RangeI": "undef"
},+
"lib/FAST/Bio/Root/Exception.pm": { … - "FAST::Bio::Root::Exception": "undef"
},+
"lib/FAST/Bio/Root/HTTPget.pm": { … - "FAST::FAST::Bio::Root::HTTPget": "undef"
},+
"lib/FAST/Bio/Root/IO.pm": { … - "FAST::Bio::Root::IO": "undef"
},+
"lib/FAST/Bio/Root/Root.pm": { … - "FAST::Bio::Root::Root": "undef"
},+
"lib/FAST/Bio/Root/RootI.pm": { … - "FAST::Bio::Root::RootI": "undef"
},+
"lib/FAST/Bio/Root/Version.pm": { … - "FAST::Bio::Root::Version": "1.006924"
},+
"lib/FAST/Bio/Search/BlastUtils.pm": { … - "FAST::Bio::Search::BlastUtils": "undef"
},+
"lib/FAST/Bio/Search/GenericStatistics.pm": { … - "FAST::Bio::Search::GenericStatistics": "undef"
},+
"lib/FAST/Bio/Search/HSP/BlastPullHSP.pm": { … - "FAST::Bio::Search::HSP::BlastPullHSP": "undef"
},+
"lib/FAST/Bio/Search/HSP/GenericHSP.pm": { … - "FAST::Bio::Search::HSP::GenericHSP": "undef"
},+
"lib/FAST/Bio/Search/HSP/HSPFactory.pm": { … - "FAST::Bio::Search::HSP::HSPFactory": "undef"
},+
"lib/FAST/Bio/Search/HSP/HSPI.pm": { … - "FAST::Bio::Search::HSP::HSPI": "undef"
},+
"lib/FAST/Bio/Search/HSP/HmmpfamHSP.pm": { … - "FAST::Bio::Search::HSP::HmmpfamHSP": "undef"
},+
"lib/FAST/Bio/Search/HSP/PullHSPI.pm": { … - "FAST::Bio::Search::HSP::PullHSPI": "undef"
},+
"lib/FAST/Bio/Search/Hit/BlastPullHit.pm": { … - "FAST::Bio::Search::Hit::BlastPullHit": "undef"
},+
"lib/FAST/Bio/Search/Hit/GenericHit.pm": { … - "FAST::Bio::Search::Hit::GenericHit": "undef"
},+
"lib/FAST/Bio/Search/Hit/HitFactory.pm": { … - "FAST::Bio::Search::Hit::HitFactory": "undef"
},+
"lib/FAST/Bio/Search/Hit/HitI.pm": { … - "FAST::Bio::Search::Hit::HitI": "undef"
},+
"lib/FAST/Bio/Search/Hit/HmmpfamHit.pm": { … - "FAST::Bio::Search::Hit::HmmpfamHit": "undef"
},+
"lib/FAST/Bio/Search/Hit/PullHitI.pm": { … - "FAST::Bio::Search::Hit::PullHitI": "undef"
},+
"lib/FAST/Bio/Search/Result/BlastPullResult.pm": { … - "FAST::Bio::Search::Result::BlastPullResult": "undef"
},+
"lib/FAST/Bio/Search/Result/CrossMatchResult.pm": { … - "FAST::Bio::Search::Result::CrossMatchResult": "undef"
},+
"lib/FAST/Bio/Search/Result/GenericResult.pm": { … - "FAST::Bio::Search::Result::GenericResult": "undef"
},+
"lib/FAST/Bio/Search/Result/HmmpfamResult.pm": { … - "FAST::Bio::Search::Result::HmmpfamResult": "undef"
},+
"lib/FAST/Bio/Search/Result/PullResultI.pm": { … - "FAST::Bio::Search::Result::PullResultI": "undef"
},+
"lib/FAST/Bio/Search/Result/ResultFactory.pm": { … - "FAST::Bio::Search::Result::ResultFactory": "undef"
},+
"lib/FAST/Bio/Search/Result/ResultI.pm": { … - "FAST::Bio::Search::Result::ResultI": "undef"
},+
"lib/FAST/Bio/Search/SearchUtils.pm": { … - "FAST::Bio::Search::SearchUtils": "undef"
},+
"lib/FAST/Bio/Search/StatisticsI.pm": { … - "FAST::Bio::Search::StatisticsI": "undef"
},+
"lib/FAST/Bio/SearchIO.pm": { … - "FAST::Bio::SearchIO": "undef"
},+
"lib/FAST/Bio/SearchIO/EventHandlerI.pm": { … - "FAST::Bio::SearchIO::EventHandlerI": "undef"
},+
"lib/FAST/Bio/SearchIO/FastHitEventBuilder.pm": { … - "FAST::Bio::SearchIO::FastHitEventBuilder": "undef"
},+
"lib/FAST/Bio/SearchIO/IteratedSearchResultEventBuilder.pm": { … - "FAST::Bio::SearchIO::IteratedSearchResultEventBuilder": "undef"
},+
"lib/FAST/Bio/SearchIO/SearchResultEventBuilder.pm": { … - "FAST::Bio::SearchIO::SearchResultEventBuilder": "undef"
},+
"lib/FAST/Bio/SearchIO/SearchWriterI.pm": { … - "FAST::Bio::SearchIO::SearchWriterI": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/BSMLResultWriter.pm": { … - "FAST::Bio::SearchIO::Writer::BSMLResultWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/GbrowseGFF.pm": { … - "FAST::Bio::SearchIO::Writer::GbrowseGFF": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/HSPTableWriter.pm": { … - "FAST::Bio::SearchIO::Writer::HSPTableWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/HTMLResultWriter.pm": { … - "FAST::Bio::SearchIO::Writer::HTMLResultWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/HitTableWriter.pm": { … - "FAST::Bio::SearchIO::Writer::HitTableWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/ResultTableWriter.pm": { … - "FAST::Bio::SearchIO::Writer::ResultTableWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/Writer/TextResultWriter.pm": { … - "FAST::Bio::SearchIO::Writer::TextResultWriter": "undef"
},+
"lib/FAST/Bio/SearchIO/XML/BlastHandler.pm": { … - "FAST::Bio::SearchIO::XML::BlastHandler": "undef"
},+
"lib/FAST/Bio/SearchIO/XML/PsiBlastHandler.pm": { … - "FAST::Bio::SearchIO::XML::PsiBlastHandler": "undef"
},+
"lib/FAST/Bio/SearchIO/axt.pm": { … - "FAST::Bio::SearchIO::axt": "undef"
},+
"lib/FAST/Bio/SearchIO/blast.pm": { … - "FAST::Bio::SearchIO::blast": "undef"
},+
"lib/FAST/Bio/SearchIO/blast_pull.pm": { … - "FAST::Bio::SearchIO::blast_pull": "undef"
},+
"lib/FAST/Bio/SearchIO/blasttable.pm": { … - "FAST::Bio::SearchIO::blasttable": "undef"
},+
"lib/FAST/Bio/SearchIO/blastxml.pm": { … - "FAST::Bio::SearchIO::blastxml": "undef"
},+
"lib/FAST/Bio/SearchIO/cross_match.pm": { … - "FAST::Bio::SearchIO::cross_match": "undef"
},+
"lib/FAST/Bio/SearchIO/erpin.pm": { … - "FAST::Bio::SearchIO::erpin": "undef"
},+
"lib/FAST/Bio/SearchIO/exonerate.pm": { … - "FAST::Bio::SearchIO::exonerate": "undef"
},+
"lib/FAST/Bio/SearchIO/fasta.pm": { … - "FAST::Bio::SearchIO::fasta": "undef"
},+
"lib/FAST/Bio/SearchIO/gmap_f9.pm": { … - "FAST::Bio::SearchIO::gmap_f9": "undef"
},+
"lib/FAST/Bio/SearchIO/hmmer.pm": { … - "FAST::Bio::SearchIO::hmmer": "undef"
},+
"lib/FAST/Bio/SearchIO/hmmer2.pm": { … - "FAST::Bio::SearchIO::hmmer2": "undef"
},+
"lib/FAST/Bio/SearchIO/hmmer3.pm": { … - "FAST::Bio::SearchIO::hmmer3": "undef"
},+
"lib/FAST/Bio/SearchIO/hmmer_pull.pm": { … - "FAST::Bio::SearchIO::hmmer_pull": "undef"
},+
"lib/FAST/Bio/SearchIO/infernal.pm": { … - "FAST::Bio::SearchIO::infernal": "undef"
},+
"lib/FAST/Bio/SearchIO/megablast.pm": { … - "FAST::Bio::SearchIO::megablast": "undef"
},+
"lib/FAST/Bio/SearchIO/psl.pm": { … - "FAST::Bio::SearchIO::psl": "undef"
},+
"lib/FAST/Bio/SearchIO/rnamotif.pm": { … - "FAST::Bio::SearchIO::rnamotif": "undef"
},+
"lib/FAST/Bio/SearchIO/sim4.pm": { … - "FAST::Bio::SearchIO::sim4": "undef"
},+
"lib/FAST/Bio/SearchIO/waba.pm": { … - "FAST::Bio::SearchIO::waba": "undef"
},+
"lib/FAST/Bio/SearchIO/wise.pm": { … - "FAST::Bio::SearchIO::wise": "undef"
},+
"lib/FAST/Bio/Seq.pm": { … - "FAST::Bio::Seq": "undef"
},+
"lib/FAST/Bio/Seq/LargeLocatableSeq.pm": { … - "FAST::Bio::Seq::LargeLocatableSeq": "undef"
},+
"lib/FAST/Bio/Seq/LargePrimarySeq.pm": { … - "FAST::Bio::Seq::LargePrimarySeq": "undef"
},+
"lib/FAST/Bio/Seq/LargeSeqI.pm": { … - "FAST::Bio::Seq::LargeSeqI": "undef"
},+
"lib/FAST/Bio/Seq/Meta.pm": { … - "FAST::Bio::Seq::Meta": "undef"
},+
"lib/FAST/Bio/Seq/Meta/Array.pm": { … - "FAST::Bio::Seq::Meta::Array": "undef"
},+
"lib/FAST/Bio/Seq/MetaI.pm": { … - "FAST::Bio::Seq::MetaI": "undef"
},+
"lib/FAST/Bio/Seq/PrimaryQual.pm": { … - "FAST::Bio::Seq::PrimaryQual": "undef"
},+
"lib/FAST/Bio/Seq/QualI.pm": { … - "FAST::Bio::Seq::QualI": "undef"
},+
"lib/FAST/Bio/Seq/Quality.pm": { … - "FAST::Bio::Seq::Quality": "undef"
},+
"lib/FAST/Bio/Seq/RichSeq.pm": { … - "FAST::Bio::Seq::RichSeq": "undef"
},+
"lib/FAST/Bio/Seq/RichSeqI.pm": { … - "FAST::Bio::Seq::RichSeqI": "undef"
},+
"lib/FAST/Bio/Seq/SeqBuilder.pm": { … - "FAST::Bio::Seq::SeqBuilder": "undef"
},+
"lib/FAST/Bio/Seq/SeqFactory.pm": { … - "FAST::Bio::Seq::SeqFactory": "undef"
},+
"lib/FAST/Bio/Seq/SeqFastaSpeedFactory.pm": { … - "FAST::Bio::Seq::SeqFastaSpeedFactory": "undef"
},+
"lib/FAST/Bio/Seq/SequenceTrace.pm": { … - "FAST::Bio::Seq::SequenceTrace": "undef"
},+
"lib/FAST/Bio/Seq/TraceI.pm": { … - "FAST::Bio::Seq::TraceI": "undef"
},+
"lib/FAST/Bio/SeqAnalysisParserI.pm": { … - "FAST::Bio::SeqAnalysisParserI": "undef"
},+
"lib/FAST/Bio/SeqFeature/FeaturePair.pm": { … - "FAST::Bio::SeqFeature::FeaturePair": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/Exon.pm": { … - "FAST::Bio::SeqFeature::Gene::Exon": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/ExonI.pm": { … - "FAST::Bio::SeqFeature::Gene::ExonI": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/GeneStructure.pm": { … - "FAST::Bio::SeqFeature::Gene::GeneStructure": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/GeneStructureI.pm": { … - "FAST::Bio::SeqFeature::Gene::GeneStructureI": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/Intron.pm": { … - "FAST::Bio::SeqFeature::Gene::Intron": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/NC_Feature.pm": { … - "FAST::Bio::SeqFeature::Gene::NC_Feature": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/Poly_A_site.pm": { … - "FAST::Bio::SeqFeature::Gene::Poly_A_site": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/Promoter.pm": { … - "FAST::Bio::SeqFeature::Gene::Promoter": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/Transcript.pm": { … - "FAST::Bio::SeqFeature::Gene::Transcript": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/TranscriptI.pm": { … - "FAST::Bio::SeqFeature::Gene::TranscriptI": "undef"
},+
"lib/FAST/Bio/SeqFeature/Gene/UTR.pm": { … - "FAST::Bio::SeqFeature::Gene::UTR": "undef"
},+
"lib/FAST/Bio/SeqFeature/Generic.pm": { … - "FAST::Bio::SeqFeature::Generic": "undef"
},+
"lib/FAST/Bio/SeqFeature/Similarity.pm": { … - "FAST::Bio::SeqFeature::Similarity": "undef"
},+
"lib/FAST/Bio/SeqFeature/SimilarityPair.pm": { … - "FAST::Bio::SeqFeature::SimilarityPair": "undef"
},+
"lib/FAST/Bio/SeqFeature/Tools/FeatureNamer.pm": { … - "FAST::Bio::SeqFeature::Tools::FeatureNamer": "undef"
},+
"lib/FAST/Bio/SeqFeature/Tools/IDHandler.pm": { … - "FAST::Bio::SeqFeature::Tools::IDHandler": "undef"
},+
"lib/FAST/Bio/SeqFeature/Tools/TypeMapper.pm": { … - "FAST::Bio::SeqFeature::Tools::TypeMapper": "undef"
},+
"lib/FAST/Bio/SeqFeature/Tools/Unflattener.pm": { … - "FAST::Bio::SeqFeature::Tools::Unflattener": "undef"
},+
"lib/FAST/Bio/SeqFeatureI.pm": { … - "FAST::Bio::SeqFeatureI": "undef"
},+
"lib/FAST/Bio/SeqI.pm": { … - "FAST::Bio::SeqI": "undef"
},+
"lib/FAST/Bio/SeqIO.pm": { … - "FAST::Bio::SeqIO": "undef"
},+
"lib/FAST/Bio/SeqIO/FTHelper.pm": { … - "FAST::Bio::SeqIO::FTHelper": "undef"
},+
"lib/FAST/Bio/SeqIO/Handler/GenericRichSeqHandler.pm": { … - "FAST::Bio::SeqIO::Handler::GenericRichSeqHandler": "undef"
},+
"lib/FAST/Bio/SeqIO/MultiFile.pm": { … - "FAST::Bio::SeqIO::MultiFile": "undef"
},+
"lib/FAST/Bio/SeqIO/abi.pm": { … - "FAST::Bio::SeqIO::abi": "undef"
},+
"lib/FAST/Bio/SeqIO/ace.pm": { … - "FAST::Bio::SeqIO::ace": "undef"
},+
"lib/FAST/Bio/SeqIO/agave.pm": { … - "FAST::Bio::SeqIO::agave": "undef"
},+
"lib/FAST/Bio/SeqIO/alf.pm": { … - "FAST::Bio::SeqIO::alf": "undef"
},+
"lib/FAST/Bio/SeqIO/asciitree.pm": { … - "FAST::Bio::SeqIO::asciitree": "undef"
},+
"lib/FAST/Bio/SeqIO/bsml.pm": { … - "FAST::Bio::SeqIO::bsml": "undef"
},+
"lib/FAST/Bio/SeqIO/bsml_sax.pm": { … - "FAST::Bio::SeqIO::bsml_sax": "undef"
},+
"lib/FAST/Bio/SeqIO/chadoxml.pm": { … - "FAST::Bio::SeqIO::chadoxml": "undef"
},+
"lib/FAST/Bio/SeqIO/chaos.pm": { … - "FAST::Bio::SeqIO::chaos": "undef"
},+
"lib/FAST/Bio/SeqIO/chaosxml.pm": { … - "FAST::Bio::SeqIO::chaosxml": "undef"
},+
"lib/FAST/Bio/SeqIO/ctf.pm": { … - "FAST::Bio::SeqIO::ctf": "undef"
},+
"lib/FAST/Bio/SeqIO/embl.pm": { … - "FAST::Bio::SeqIO::embl": "undef"
},+
"lib/FAST/Bio/SeqIO/embldriver.pm": { … - "FAST::Bio::SeqIO::embldriver": "undef"
},+
"lib/FAST/Bio/SeqIO/entrezgene.pm": { … - "FAST::Bio::SeqIO::entrezgene": "undef"
},+
"lib/FAST/Bio/SeqIO/excel.pm": { … - "FAST::Bio::SeqIO::excel": "undef"
},+
"lib/FAST/Bio/SeqIO/exp.pm": { … - "FAST::Bio::SeqIO::exp": "undef"
},+
"lib/FAST/Bio/SeqIO/fasta.pm": { … - "FAST::Bio::SeqIO::fasta": "undef"
},+
"lib/FAST/Bio/SeqIO/fastq.pm": { … - "FAST::Bio::SeqIO::fastq": "undef"
},+
"lib/FAST/Bio/SeqIO/flybase_chadoxml.pm": { … - "FAST::Bio::SeqIO::flybase_chadoxml": "undef"
},+
"lib/FAST/Bio/SeqIO/game.pm": { … - "FAST::Bio::SeqIO::game": "undef"
},+
"lib/FAST/Bio/SeqIO/game/featHandler.pm": { … - "FAST::Bio::SeqIO::game::featHandler": "undef"
},+
"lib/FAST/Bio/SeqIO/game/gameHandler.pm": { … - "FAST::Bio::SeqIO::game::gameHandler": "undef"
},+
"lib/FAST/Bio/SeqIO/game/gameSubs.pm": { … - "FAST::Bio::SeqIO::game::gameSubs": "undef"
},+
"lib/FAST/Bio/SeqIO/game/gameWriter.pm": { … - "FAST::Bio::SeqIO::game::gameWriter": "undef"
},+
"lib/FAST/Bio/SeqIO/game/seqHandler.pm": { … - "FAST::Bio::SeqIO::game::seqHandler": "undef"
},+
"lib/FAST/Bio/SeqIO/gbdriver.pm": { … - "FAST::Bio::SeqIO::gbdriver": "undef"
},+
"lib/FAST/Bio/SeqIO/gbxml.pm": { … - "FAST::Bio::SeqIO::gbxml": "undef"
},+
"lib/FAST/Bio/SeqIO/gcg.pm": { … - "FAST::Bio::SeqIO::gcg": "undef"
},+
"lib/FAST/Bio/SeqIO/genbank.pm": { … - "FAST::Bio::SeqIO::genbank": "undef"
},+
"lib/FAST/Bio/SeqIO/interpro.pm": { … - "FAST::Bio::SeqIO::interpro": "undef"
},+
"lib/FAST/Bio/SeqIO/kegg.pm": { … - "FAST::Bio::SeqIO::kegg": "undef"
},+
"lib/FAST/Bio/SeqIO/largefasta.pm": { … - "FAST::Bio::SeqIO::largefasta": "undef"
},+
"lib/FAST/Bio/SeqIO/lasergene.pm": { … - "FAST::Bio::SeqIO::lasergene": "undef"
},+
"lib/FAST/Bio/SeqIO/locuslink.pm": { … - "FAST::Bio::SeqIO::locuslink": "undef"
},+
"lib/FAST/Bio/SeqIO/mbsout.pm": { … - "FAST::Bio::SeqIO::mbsout": "undef"
},+
"lib/FAST/Bio/SeqIO/metafasta.pm": { … - "FAST::Bio::SeqIO::metafasta": "undef"
},+
"lib/FAST/Bio/SeqIO/msout.pm": { … - "FAST::Bio::SeqIO::msout": "undef"
},+
"lib/FAST/Bio/SeqIO/nexml.pm": { … - "FAST::Bio::SeqIO::nexml": "undef"
},+
"lib/FAST/Bio/SeqIO/phd.pm": { … - "FAST::Bio::SeqIO::phd": "undef"
},+
"lib/FAST/Bio/SeqIO/pir.pm": { … - "FAST::Bio::SeqIO::pir": "undef"
},+
"lib/FAST/Bio/SeqIO/pln.pm": { … - "FAST::Bio::SeqIO::pln": "undef"
},+
"lib/FAST/Bio/SeqIO/qual.pm": { … - "FAST::Bio::SeqIO::qual": "undef"
},+
"lib/FAST/Bio/SeqIO/raw.pm": { … - "FAST::Bio::SeqIO::raw": "undef"
},+
"lib/FAST/Bio/SeqIO/scf.pm": { … - "FAST::Bio::SeqIO::scf": "undef"
},+
"lib/FAST/Bio/SeqIO/seqxml.pm": { … - "FAST::Bio::SeqIO::seqxml": "undef"
},+
"lib/FAST/Bio/SeqIO/strider.pm": { … - "FAST::Bio::SeqIO::strider": "undef"
},+
"lib/FAST/Bio/SeqIO/swiss.pm": { … - "FAST::Bio::SeqIO::swiss": "undef"
},+
"lib/FAST/Bio/SeqIO/swissdriver.pm": { … - "FAST::Bio::SeqIO::swissdriver": "undef"
},+
"lib/FAST/Bio/SeqIO/tab.pm": { … - "FAST::Bio::SeqIO::tab": "undef"
},+
"lib/FAST/Bio/SeqIO/table.pm": { … - "FAST::Bio::SeqIO::table": "undef"
},+
"lib/FAST/Bio/SeqIO/tigr.pm": { … - "FAST::Bio::SeqIO::tigr": "undef"
},+
"lib/FAST/Bio/SeqIO/tigrxml.pm": { … - "FAST::Bio::SeqIO::tigrxml": "undef"
},+
"lib/FAST/Bio/SeqIO/tinyseq.pm": { … - "FAST::Bio::SeqIO::tinyseq": "undef"
},+
"lib/FAST/Bio/SeqIO/tinyseq/tinyseqHandler.pm": { … - "FAST::Bio::SeqIO::tinyseq::tinyseqHandler": "undef"
},+
"lib/FAST/Bio/SeqIO/ztr.pm": { … - "FAST::Bio::SeqIO::ztr": "undef"
},+
"lib/FAST/Bio/SeqUtils.pm": { … - "FAST::Bio::SeqUtils": "undef"
},+
"lib/FAST/Bio/SimpleAlign.pm": { … - "FAST::Bio::SimpleAlign": "undef"
},+
"lib/FAST/Bio/Species.pm": { … - "FAST::Bio::Species": "undef"
},+
"lib/FAST/Bio/Taxon.pm": { … - "FAST::Bio::Taxon": "undef"
},+
"lib/FAST/Bio/Tools/AnalysisResult.pm": { … - "FAST::Bio::Tools::AnalysisResult": "undef"
},+
"lib/FAST/Bio/Tools/CodonTable.pm": { … - "FAST::Bio::Tools::CodonTable": "undef"
},+
"lib/FAST/Bio/Tools/GFF.pm": { … - "FAST::Bio::Tools::GFF": "undef"
},+
"lib/FAST/Bio/Tools/Genewise.pm": { … - "FAST::Bio::Tools::Genewise": "undef"
},+
"lib/FAST/Bio/Tools/Genomewise.pm": { … - "FAST::Bio::Tools::Genomewise": "undef"
},+
"lib/FAST/Bio/Tools/GuessSeqFormat.pm": { … - "FAST::Bio::Tools::GuessSeqFormat": "undef"
},+
"lib/FAST/Bio/Tools/IUPAC.pm": { … - "FAST::Bio::Tools::IUPAC": "undef"
},+
"lib/FAST/Bio/Tools/MySeqStats.pm": { … - "FAST::Bio::Tools::MySeqStats": "undef"
},+
"lib/FAST/Bio/Tools/Run/GenericParameters.pm": { … - "FAST::Bio::Tools::Run::GenericParameters": "undef"
},+
"lib/FAST/Bio/Tools/Run/ParametersI.pm": { … - "FAST::Bio::Tools::Run::ParametersI": "undef"
},+
"lib/FAST/Bio/Tools/SeqPattern.pm": { … - "FAST::Bio::Tools::SeqPattern": "undef"
},+
"lib/FAST/Bio/Tools/SeqPattern/Backtranslate.pm": { … - "FAST::Bio::Tools::SeqPattern::Backtranslate": "undef"
},+
"lib/FAST/Bio/Tools/SeqStats.pm": { … - "FAST::Bio::Tools::SeqStats": "undef"
},+
"lib/FAST/Bio/Tree/Node.pm": { … - "FAST::Bio::Tree::Node": "undef"
},+
"lib/FAST/Bio/Tree/NodeI.pm": { … - "FAST::Bio::Tree::NodeI": "undef"
},+
"lib/FAST/Bio/Tree/Tree.pm": { … - "FAST::Bio::Tree::Tree": "undef"
},+
"lib/FAST/Bio/Tree/TreeFunctionsI.pm": { … - "FAST::Bio::Tree::TreeFunctionsI": "undef"
},+
"lib/FAST/Bio/Tree/TreeI.pm": { … - "FAST::Bio::Tree::TreeI": "undef"
},+
"lib/FAST/Bio/UnivAln.pm": { … - "FAST::Bio::UnivAln": "1.01"
},+
"lib/FAST/Bio/WebAgent.pm": { … - "FAST::Bio::WebAgent": "undef"
},+
"lib/FAST/List/Gen.pm": { … - "FAST::List::Gen": "0.974"
},+
"lib/FAST/List/Gen/Benchmark.pm": { … - "FAST::List::Gen::Benchmark": "undef"
},+
"lib/FAST/List/Gen/Cookbook.pm": { … - "FAST::List::Gen::Cookbook": "undef"
},+
"lib/FAST/List/Gen/Haskell.pm": { … - "FAST::List::Gen::Haskell": "undef"
},+
"lib/FAST/List/Gen/Lazy.pm": { … - "FAST::List::Gen::Lazy": "undef"
},+
"lib/FAST/List/Gen/Lazy/Builtins.pm": { … - "FAST::List::Gen::Lazy::Builtins": "undef"
},+
"lib/FAST/List/Gen/Lazy/Ops.pm": { … - "FAST::List::Gen::Lazy::Ops": "undef"
},+
"lib/FAST/List/Gen/Perl6.pm": { … - "FAST::List::Gen::Perl6": "undef"
},+
"lib/FAST/List/Generator.pm": { … - "FAST::List::Generator": "undef"
}
},- "vname": "FAST-1.01"
}