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
Changes
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/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/Handler/GenericAlignHandler.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/dagflat.pm
lib/FAST/Bio/OntologyIO/goflat.pm
lib/FAST/Bio/OntologyIO/Handlers/BaseSAXHandler.pm
lib/FAST/Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm
lib/FAST/Bio/OntologyIO/Handlers/InterProHandler.pm
lib/FAST/Bio/OntologyIO/InterProParser.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/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/HSP/BlastPullHSP.pm
lib/FAST/Bio/Search/HSP/GenericHSP.pm
lib/FAST/Bio/Search/HSP/HmmpfamHSP.pm
lib/FAST/Bio/Search/HSP/HSPFactory.pm
lib/FAST/Bio/Search/HSP/HSPI.pm
lib/FAST/Bio/Search/HSP/PullHSPI.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/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/EventHandlerI.pm
lib/FAST/Bio/SearchIO/exonerate.pm
lib/FAST/Bio/SearchIO/fasta.pm
lib/FAST/Bio/SearchIO/FastHitEventBuilder.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/IteratedSearchResultEventBuilder.pm
lib/FAST/Bio/SearchIO/megablast.pm
lib/FAST/Bio/SearchIO/psl.pm
lib/FAST/Bio/SearchIO/rnamotif.pm
lib/FAST/Bio/SearchIO/SearchResultEventBuilder.pm
lib/FAST/Bio/SearchIO/SearchWriterI.pm
lib/FAST/Bio/SearchIO/sim4.pm
lib/FAST/Bio/SearchIO/waba.pm
lib/FAST/Bio/SearchIO/wise.pm
lib/FAST/Bio/SearchIO/Writer/BSMLResultWriter.pm
lib/FAST/Bio/SearchIO/Writer/GbrowseGFF.pm
lib/FAST/Bio/SearchIO/Writer/HitTableWriter.pm
lib/FAST/Bio/SearchIO/Writer/HSPTableWriter.pm
lib/FAST/Bio/SearchIO/Writer/HTMLResultWriter.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/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/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/FTHelper.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/Handler/GenericRichSeqHandler.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/MultiFile.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/Genewise.pm
lib/FAST/Bio/Tools/Genomewise.pm
lib/FAST/Bio/Tools/GFF.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
Makefile.PL
MANIFEST			This list of files
README
INSTALL
README.md
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/chr01.fsa
t/data/Dros.fas
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/P450.clustalw2.aln
t/data/P450.clustalw2.fas
t/data/P450.fas
t/data/test.fq
t/data/tRNAdb-CE.sample2000.fas
t/lib/Test/Cmd.pm
t/lib/Test/Cmd/Common.pm
t/pod.t
META.yml                                 Module YAML meta-data (added by MakeMaker)
META.json                                Module JSON meta-data (added by MakeMaker)