Files

• 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
• doc/org2html
• doc/org2pdf
• lib/FAST.pm
• lib/FAST/Bio/Align/AlignI.pm
• lib/FAST/Bio/AlignIO.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/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.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/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.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/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
• lib/FAST/Bio/Search/HSP/HSPFactory.pm
• lib/FAST/Bio/Search/HSP/HSPI.pm
• lib/FAST/Bio/Search/HSP/HmmpfamHSP.pm
• lib/FAST/Bio/Search/HSP/PullHSPI.pm
• lib/FAST/Bio/Search/Hit/BlastPullHit.pm
• lib/FAST/Bio/Search/Hit/GenericHit.pm
• lib/FAST/Bio/Search/Hit/HitFactory.pm
• lib/FAST/Bio/Search/Hit/HitI.pm
• lib/FAST/Bio/Search/Hit/HmmpfamHit.pm
• lib/FAST/Bio/Search/Hit/PullHitI.pm
• lib/FAST/Bio/Search/Result/BlastPullResult.pm
• lib/FAST/Bio/Search/Result/CrossMatchResult.pm
• lib/FAST/Bio/Search/Result/GenericResult.pm
• lib/FAST/Bio/Search/Result/HmmpfamResult.pm
• lib/FAST/Bio/Search/Result/PullResultI.pm
• lib/FAST/Bio/Search/Result/ResultFactory.pm
• lib/FAST/Bio/Search/Result/ResultI.pm
• lib/FAST/Bio/Search/SearchUtils.pm
• lib/FAST/Bio/Search/StatisticsI.pm
• lib/FAST/Bio/SearchIO.pm
• lib/FAST/Bio/SearchIO/EventHandlerI.pm
• lib/FAST/Bio/SearchIO/FastHitEventBuilder.pm
• lib/FAST/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
• lib/FAST/Bio/SearchIO/SearchResultEventBuilder.pm
• lib/FAST/Bio/SearchIO/SearchWriterI.pm
• lib/FAST/Bio/SearchIO/Writer/BSMLResultWriter.pm
• lib/FAST/Bio/SearchIO/Writer/GbrowseGFF.pm
• lib/FAST/Bio/SearchIO/Writer/HSPTableWriter.pm
• lib/FAST/Bio/SearchIO/Writer/HTMLResultWriter.pm
• lib/FAST/Bio/SearchIO/Writer/HitTableWriter.pm
• lib/FAST/Bio/SearchIO/Writer/ResultTableWriter.pm
• lib/FAST/Bio/SearchIO/Writer/TextResultWriter.pm
• lib/FAST/Bio/SearchIO/XML/BlastHandler.pm
• lib/FAST/Bio/SearchIO/XML/PsiBlastHandler.pm
• lib/FAST/Bio/SearchIO/axt.pm
• lib/FAST/Bio/SearchIO/blast.pm
• lib/FAST/Bio/SearchIO/blast_pull.pm
• lib/FAST/Bio/SearchIO/blasttable.pm
• lib/FAST/Bio/SearchIO/blastxml.pm
• lib/FAST/Bio/SearchIO/cross_match.pm
• lib/FAST/Bio/SearchIO/erpin.pm
• lib/FAST/Bio/SearchIO/exonerate.pm
• lib/FAST/Bio/SearchIO/fasta.pm
• lib/FAST/Bio/SearchIO/gmap_f9.pm
• lib/FAST/Bio/SearchIO/hmmer.pm
• lib/FAST/Bio/SearchIO/hmmer2.pm
• lib/FAST/Bio/SearchIO/hmmer3.pm
• lib/FAST/Bio/SearchIO/hmmer_pull.pm
• lib/FAST/Bio/SearchIO/infernal.pm
• lib/FAST/Bio/SearchIO/megablast.pm
• lib/FAST/Bio/SearchIO/psl.pm
• lib/FAST/Bio/SearchIO/rnamotif.pm
• lib/FAST/Bio/SearchIO/sim4.pm
• lib/FAST/Bio/SearchIO/waba.pm
• lib/FAST/Bio/SearchIO/wise.pm
• lib/FAST/Bio/Seq.pm
• lib/FAST/Bio/Seq/LargeLocatableSeq.pm
• lib/FAST/Bio/Seq/LargePrimarySeq.pm
• lib/FAST/Bio/Seq/LargeSeqI.pm
• lib/FAST/Bio/Seq/Meta.pm
• lib/FAST/Bio/Seq/Meta/Array.pm
• lib/FAST/Bio/Seq/MetaI.pm
• lib/FAST/Bio/Seq/PrimaryQual.pm
• lib/FAST/Bio/Seq/QualI.pm
• lib/FAST/Bio/Seq/Quality.pm
• lib/FAST/Bio/Seq/RichSeq.pm
• lib/FAST/Bio/Seq/RichSeqI.pm
• lib/FAST/Bio/Seq/SeqBuilder.pm
• lib/FAST/Bio/Seq/SeqFactory.pm
• lib/FAST/Bio/Seq/SeqFastaSpeedFactory.pm
• lib/FAST/Bio/Seq/SequenceTrace.pm
• lib/FAST/Bio/Seq/TraceI.pm
• lib/FAST/Bio/SeqAnalysisParserI.pm
• lib/FAST/Bio/SeqFeature/FeaturePair.pm
• lib/FAST/Bio/SeqFeature/Gene/Exon.pm
• lib/FAST/Bio/SeqFeature/Gene/ExonI.pm
• lib/FAST/Bio/SeqFeature/Gene/GeneStructure.pm
• lib/FAST/Bio/SeqFeature/Gene/GeneStructureI.pm
• lib/FAST/Bio/SeqFeature/Gene/Intron.pm
• lib/FAST/Bio/SeqFeature/Gene/NC_Feature.pm
• lib/FAST/Bio/SeqFeature/Gene/Poly_A_site.pm
• lib/FAST/Bio/SeqFeature/Gene/Promoter.pm
• lib/FAST/Bio/SeqFeature/Gene/Transcript.pm
• lib/FAST/Bio/SeqFeature/Gene/TranscriptI.pm
• lib/FAST/Bio/SeqFeature/Gene/UTR.pm
• lib/FAST/Bio/SeqFeature/Generic.pm
• lib/FAST/Bio/SeqFeature/Similarity.pm
• lib/FAST/Bio/SeqFeature/SimilarityPair.pm
• lib/FAST/Bio/SeqFeature/Tools/FeatureNamer.pm
• lib/FAST/Bio/SeqFeature/Tools/IDHandler.pm
• lib/FAST/Bio/SeqFeature/Tools/TypeMapper.pm
• lib/FAST/Bio/SeqFeature/Tools/Unflattener.pm
• lib/FAST/Bio/SeqFeatureI.pm
• lib/FAST/Bio/SeqI.pm
• lib/FAST/Bio/SeqIO.pm
• lib/FAST/Bio/SeqIO/FTHelper.pm
• lib/FAST/Bio/SeqIO/Handler/GenericRichSeqHandler.pm
• lib/FAST/Bio/SeqIO/MultiFile.pm
• lib/FAST/Bio/SeqIO/abi.pm
• lib/FAST/Bio/SeqIO/ace.pm
• lib/FAST/Bio/SeqIO/agave.pm
• lib/FAST/Bio/SeqIO/alf.pm
• lib/FAST/Bio/SeqIO/asciitree.pm
• lib/FAST/Bio/SeqIO/bsml.pm
• lib/FAST/Bio/SeqIO/bsml_sax.pm
• lib/FAST/Bio/SeqIO/chadoxml.pm
• lib/FAST/Bio/SeqIO/chaos.pm
• lib/FAST/Bio/SeqIO/chaosxml.pm
• lib/FAST/Bio/SeqIO/ctf.pm
• lib/FAST/Bio/SeqIO/embl.pm
• lib/FAST/Bio/SeqIO/embldriver.pm
• lib/FAST/Bio/SeqIO/entrezgene.pm
• lib/FAST/Bio/SeqIO/excel.pm
• lib/FAST/Bio/SeqIO/exp.pm
• lib/FAST/Bio/SeqIO/fasta.pm
• lib/FAST/Bio/SeqIO/fastq.pm
• lib/FAST/Bio/SeqIO/flybase_chadoxml.pm
• lib/FAST/Bio/SeqIO/game.pm
• lib/FAST/Bio/SeqIO/game/featHandler.pm
• lib/FAST/Bio/SeqIO/game/gameHandler.pm
• lib/FAST/Bio/SeqIO/game/gameSubs.pm
• lib/FAST/Bio/SeqIO/game/gameWriter.pm
• lib/FAST/Bio/SeqIO/game/seqHandler.pm
• lib/FAST/Bio/SeqIO/gbdriver.pm
• lib/FAST/Bio/SeqIO/gbxml.pm
• lib/FAST/Bio/SeqIO/gcg.pm
• lib/FAST/Bio/SeqIO/genbank.pm
• lib/FAST/Bio/SeqIO/interpro.pm
• lib/FAST/Bio/SeqIO/kegg.pm
• lib/FAST/Bio/SeqIO/largefasta.pm
• lib/FAST/Bio/SeqIO/lasergene.pm
• lib/FAST/Bio/SeqIO/locuslink.pm
• lib/FAST/Bio/SeqIO/mbsout.pm
• lib/FAST/Bio/SeqIO/metafasta.pm
• lib/FAST/Bio/SeqIO/msout.pm
• lib/FAST/Bio/SeqIO/nexml.pm
• lib/FAST/Bio/SeqIO/phd.pm
• lib/FAST/Bio/SeqIO/pir.pm
• lib/FAST/Bio/SeqIO/pln.pm
• lib/FAST/Bio/SeqIO/qual.pm
• lib/FAST/Bio/SeqIO/raw.pm
• lib/FAST/Bio/SeqIO/scf.pm
• lib/FAST/Bio/SeqIO/seqxml.pm
• lib/FAST/Bio/SeqIO/strider.pm
• lib/FAST/Bio/SeqIO/swiss.pm
• lib/FAST/Bio/SeqIO/swissdriver.pm
• lib/FAST/Bio/SeqIO/tab.pm
• lib/FAST/Bio/SeqIO/table.pm
• lib/FAST/Bio/SeqIO/tigr.pm
• lib/FAST/Bio/SeqIO/tigrxml.pm
• lib/FAST/Bio/SeqIO/tinyseq.pm
• lib/FAST/Bio/SeqIO/tinyseq/tinyseqHandler.pm
• lib/FAST/Bio/SeqIO/ztr.pm
• lib/FAST/Bio/SeqUtils.pm
• lib/FAST/Bio/SimpleAlign.pm
• lib/FAST/Bio/Species.pm
• lib/FAST/Bio/Taxon.pm
• lib/FAST/Bio/Tools/AnalysisResult.pm
• lib/FAST/Bio/Tools/CodonTable.pm
• lib/FAST/Bio/Tools/GFF.pm
• lib/FAST/Bio/Tools/Genewise.pm
• lib/FAST/Bio/Tools/Genomewise.pm
• lib/FAST/Bio/Tools/GuessSeqFormat.pm
• lib/FAST/Bio/Tools/IUPAC.pm
• lib/FAST/Bio/Tools/MySeqStats.pm
• lib/FAST/Bio/Tools/Run/GenericParameters.pm
• lib/FAST/Bio/Tools/Run/ParametersI.pm
• lib/FAST/Bio/Tools/SeqPattern.pm
• lib/FAST/Bio/Tools/SeqPattern/Backtranslate.pm
• lib/FAST/Bio/Tools/SeqStats.pm
• lib/FAST/Bio/Tree/Node.pm
• lib/FAST/Bio/Tree/NodeI.pm
• lib/FAST/Bio/Tree/Tree.pm
• lib/FAST/Bio/Tree/TreeFunctionsI.pm
• lib/FAST/Bio/Tree/TreeI.pm
• lib/FAST/Bio/UnivAln.pm
• lib/FAST/Bio/WebAgent.pm
• lib/FAST/List/Gen.pm
• lib/FAST/List/Gen/Benchmark.pm
• lib/FAST/List/Gen/Cookbook.pm
• lib/FAST/List/Gen/Haskell.pm
• lib/FAST/List/Gen/Lazy.pm
• lib/FAST/List/Gen/Lazy/Builtins.pm
• lib/FAST/List/Gen/Lazy/Ops.pm
• lib/FAST/List/Gen/Perl6.pm
• lib/FAST/List/Generator.pm
• t/00-load.t
• t/boilerplate.t
• t/data/AF194338.1.gb
• t/data/ArdellEtAl03_ncbi_popset_32329588.aln
• t/data/ArdellEtAl03_ncbi_popset_32329588.fas
• t/data/ArdellEtAl03_ncbi_popset_32329588.nexus
• t/data/ArdellEtAl03_ncbi_popset_32329588.phylip
• t/data/Dros.fas
• t/data/P450.clustalw2.aln
• t/data/P450.clustalw2.fas
• t/data/P450.fas
• t/data/chr01.fsa
• t/data/fascodon_test.fas
• t/data/fascodon_test.output.txt
• t/data/fasfilter_test.fas
• t/data/fashead_tail_test1.fas
• t/data/faslen_test1.fas
• t/data/faspaste_test.fas
• t/data/faspaste_test2.fas
• t/data/fasrc_test.fas
• t/data/fastr_test.fas
• t/data/fasuniq_test1.fas
• t/data/fasuniq_test2.fas
• t/data/fasuniq_test3.fas
• t/data/fasuniq_test4.fas
• t/data/fasuniq_test5.fas
• t/data/fasuniq_test6.fas
• t/data/fasxl_test.fas
• t/data/fasxl_test2.fas
• t/data/fasxl_test3.fas
• t/data/fasxl_test4.fas
• t/data/fasxl_test5.fas
• t/data/flybase_fasta_100_cds.fas
• t/data/gbfcut_test.fas
• t/data/mito-ascaris.gb
• t/data/popset_32329688.fas
• t/data/tRNAdb-CE.sample2000.fas
• t/data/test.fq
• t/lib/Test/Cmd.pm
• t/lib/Test/Cmd/Common.pm
• t/pod.t