## $Id: MANIFEST,v 1.31.2.5 2001-11-16 14:01:45 jason Exp $
##
## bioperl 0.7.2 manifest listing
##
## This is the file listing for everything that
## comes with the bioperl distribution. The perl
## install procedure uses this file to confirm that
## all necessary files are present.
##
AUTHORS
BUGS
Bio/AlignIO.pm
Bio/AlignIO/bl2seq.pm
Bio/AlignIO/clustalw.pm
Bio/AlignIO/fasta.pm
Bio/AlignIO/mase.pm
Bio/AlignIO/msf.pm
Bio/AlignIO/pfam.pm
Bio/AlignIO/prodom.pm
Bio/AlignIO/selex.pm
Bio/AlignIO/stockholm.pm
Bio/Annotation.pm
Bio/Annotation/Comment.pm
Bio/Annotation/DBLink.pm
Bio/Annotation/Reference.pm
Bio/DB/Ace.pm
Bio/DB/GDB.pm
Bio/DB/GenBank.pm
Bio/DB/GenPept.pm
Bio/DB/NCBIHelper.pm
Bio/DB/RandomAccessI.pm
Bio/DB/SeqI.pm
Bio/DB/SwissProt.pm
Bio/DB/UpdateableSeqI.pm
Bio/DB/WebDBSeqI.pm
Bio/DBLinkContainerI.pm
Bio/Factory/DriverFactory.pm
Bio/Factory/SeqAnalysisParserFactory.pm
Bio/Factory/SeqAnalysisParserFactoryI.pm
Bio/Index/Abstract.pm
Bio/Index/AbstractSeq.pm
Bio/Index/EMBL.pm
Bio/Index/Fasta.pm
Bio/Index/GenBank.pm
Bio/Index/SwissPfam.pm
Bio/Index/Swissprot.pm
Bio/LiveSeq/AARange.pm
Bio/LiveSeq/Chain.pm
Bio/LiveSeq/ChainI.pm
Bio/LiveSeq/DNA.pm
Bio/LiveSeq/Exon.pm
Bio/LiveSeq/Gene.pm
Bio/LiveSeq/IO/BioPerl.pm
Bio/LiveSeq/IO/Loader.pm
Bio/LiveSeq/IO/SRS.pm
Bio/LiveSeq/Intron.pm
Bio/LiveSeq/Mutation.pm
Bio/LiveSeq/Mutator.pm
Bio/LiveSeq/Prim_Transcript.pm
Bio/LiveSeq/Range.pm
Bio/LiveSeq/Repeat_Region.pm
Bio/LiveSeq/Repeat_Unit.pm
Bio/LiveSeq/SeqI.pm
Bio/LiveSeq/Transcript.pm
Bio/LiveSeq/Translation.pm
Bio/LocatableSeq.pm
Bio/Location/AvWithinCoordPolicy.pm
Bio/Location/CoordinatePolicyI.pm
Bio/Location/Fuzzy.pm
Bio/Location/FuzzyLocationI.pm
Bio/Location/NarrowestCoordPolicy.pm
Bio/Location/Simple.pm
Bio/Location/Split.pm
Bio/Location/SplitLocationI.pm
Bio/Location/WidestCoordPolicy.pm
Bio/LocationI.pm
Bio/PrimarySeq.pm
Bio/PrimarySeqI.pm
Bio/Range.pm
Bio/RangeI.pm
Bio/Root/Err.pm
Bio/Root/Global.pm
Bio/Root/IO.pm
Bio/Root/IOManager.pm
Bio/Root/Object.pm
Bio/Root/RootI.pm
Bio/Root/Utilities.pm
Bio/Root/Vector.pm
Bio/Root/Xref.pm
Bio/SearchDist.pm
Bio/Seq.pm
Bio/Seq/LargePrimarySeq.pm
Bio/Seq/LargeSeq.pm
Bio/Seq/RichSeq.pm
Bio/Seq/RichSeqI.pm
Bio/SeqAnalysisParserI.pm
Bio/SeqFeature/FeaturePair.pm
Bio/SeqFeature/Gene/Exon.pm
Bio/SeqFeature/Gene/ExonI.pm
Bio/SeqFeature/Gene/GeneStructure.pm
Bio/SeqFeature/Gene/GeneStructureI.pm
Bio/SeqFeature/Gene/Transcript.pm
Bio/SeqFeature/Gene/TranscriptI.pm
Bio/SeqFeature/Generic.pm
Bio/SeqFeature/Similarity.pm
Bio/SeqFeature/SimilarityPair.pm
Bio/SeqFeatureI.pm
Bio/SeqI.pm
Bio/SeqIO.pm
Bio/SeqIO/FTHelper.pm
Bio/SeqIO/MultiFile.pm
Bio/SeqIO/ace.pm
Bio/SeqIO/embl.pm
Bio/SeqIO/fasta.pm
Bio/SeqIO/game.pm
Bio/SeqIO/game/featureHandler.pm
Bio/SeqIO/game/idHandler.pm
Bio/SeqIO/game/seqHandler.pm
Bio/SeqIO/gcg.pm
Bio/SeqIO/genbank.pm
Bio/SeqIO/largefasta.pm
Bio/SeqIO/raw.pm
Bio/SeqIO/scf.pm
Bio/SeqIO/swiss.pm
Bio/SeqUtils.pm
Bio/SimpleAlign.pm
Bio/Species.pm
Bio/Tools/AlignFactory.pm
Bio/Tools/AnalysisResult.pm
Bio/Tools/BPbl2seq.pm
Bio/Tools/BPlite.pm
Bio/Tools/BPlite/HSP.pm
Bio/Tools/BPlite/Iteration.pm
Bio/Tools/BPlite/Sbjct.pm
Bio/Tools/BPpsilite.pm
Bio/Tools/Blast.pm
Bio/Tools/Blast/CHANGES
Bio/Tools/Blast/HSP.pm
Bio/Tools/Blast/HTML.pm
Bio/Tools/Blast/README
Bio/Tools/Blast/Run/LocalBlast.pm
Bio/Tools/Blast/Run/Webblast.pm
Bio/Tools/Blast/Run/postclient.pl
Bio/Tools/Blast/Sbjct.pm
Bio/Tools/CodonTable.pm
Bio/Tools/ESTScan.pm
Bio/Tools/Fasta.pm
Bio/Tools/GFF.pm
Bio/Tools/Genscan.pm
Bio/Tools/HMMER/Domain.pm
Bio/Tools/HMMER/Results.pm
Bio/Tools/HMMER/Set.pm
Bio/Tools/IUPAC.pm
Bio/Tools/MZEF.pm
Bio/Tools/OddCodes.pm
Bio/Tools/Prediction/Exon.pm
Bio/Tools/Prediction/Gene.pm
Bio/Tools/RestrictionEnzyme.pm
Bio/Tools/Run/Alignment/Clustalw.pm
Bio/Tools/Run/Alignment/TCoffee.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/SeqAnal.pm
Bio/Tools/SeqPattern.pm
Bio/Tools/SeqStats.pm
Bio/Tools/SeqWords.pm
Bio/Tools/Sigcleave.pm
Bio/Tools/Sim4/Exon.pm
Bio/Tools/Sim4/Results.pm
Bio/Tools/WWW.pm
Bio/Tools/pSW.pm
Bio/UnivAln.pm
Bio/Variation/AAChange.pm
Bio/Variation/AAReverseMutate.pm
Bio/Variation/Allele.pm
Bio/Variation/DNAMutation.pm
Bio/Variation/IO.pm
Bio/Variation/IO/flat.pm
Bio/Variation/IO/xml.pm
Bio/Variation/README
Bio/Variation/RNAChange.pm
Bio/Variation/SeqDiff.pm
Bio/Variation/VariantI.pm
Changes
LICENSE
MANIFEST
PLATFORMS
README
bioback.pod
biodesign.pod
bioperl.pod
biostart.pod
bptutorial.pl
examples/blast/blast_config.pl
examples/blast/blast_seq.pl
examples/blast/example.table1
examples/blast/example.table2
examples/blast/html.pl
examples/blast/out/blastn.2.gz
examples/blast/out/blastn.2.wu.gz
examples/blast/out/blastp.1.gcg.gz
examples/blast/out/blastp.1.gz
examples/blast/out/blastp.2.gz
examples/blast/out/blastp.2.nogap.gz
examples/blast/out/blastp.2.wu
examples/blast/out/blastp.205.gz
examples/blast/out/blastp.2a.gz
examples/blast/out/blastp.2b.gz
examples/blast/out/blastp.email.html.gz
examples/blast/out/blastx.2
examples/blast/out/blastx.2.email.gz
examples/blast/out/blastx.208.gz
examples/blast/out/tblastn.206.out.gz
examples/blast/parse_blast.pl
examples/blast/parse_blast2.pl
examples/blast/parse_multi.pl
examples/blast/parse_positions.pl
examples/blast/print_blasts.pl
examples/blast/retrieve_blast.pl
examples/blast/run_blast_remote.pl
examples/blast/seq/acc1.dna.fasta
examples/blast/seq/seqs.fasta
examples/blast/seq/yal011w.dna.fasta
examples/blast/seq/yel009c.fasta
examples/blast/seq/ymr284w.fasta
examples/blosum62.bla
examples/change_gene.pl
examples/clustalw.pl
examples/getGenBank.pl
examples/gon250.bla
examples/gsequence
examples/hitdisplay.pl
examples/psw.pl
examples/restriction.pl
examples/rev_and_trans.pl
examples/root_object/Bar.pm
examples/root_object/Foo.pm
examples/root_object/Outer.pm
examples/root_object/destroy.pl
examples/root_object/error.out
examples/root_object/error.pl
examples/root_object/filehandle.out
examples/root_object/filehandle.pl
examples/root_object/io.out
examples/root_object/io.pl
examples/root_object/read.pl
examples/root_object/read.test
examples/root_object/read.test2
examples/root_object/read.test3
examples/root_object/utilities.pl
examples/root_object/vector/Person.pm
examples/root_object/vector/PersonManager.pm
examples/root_object/vector/vector.out
examples/root_object/vector/vector.pl
examples/seq/id.list
examples/seq/seq.fasta.gz
examples/seq/seq1.fasta
examples/seq/seq2.fasta
examples/seq/seqs1.pl
examples/seq/seqs2.pl
examples/seq/seqs3.pl
examples/seq/seqtools.pl
examples/seq_pattern.pl
examples/simplealign.pl
examples/standaloneblast.pl
examples/test-genscan.pl
scripts/blast_fetch.pl
scripts/bpfetch.pl
scripts/bpindex.pl
scripts/subsequence.cgi
t/AAC12660.fa
t/AAChange.t
t/AAReverseMutate.t
t/AF165282.gb
t/AlignIO.t
t/Allele.t
t/Annotation.t
t/BPbl2seq.t
t/BPlite.t
t/BPpsilite.t
t/Blast.t
t/Chain.t
t/Clustalw.t
t/CodonTable.t
t/DB.t
t/DNAMutation.t
t/GDB.t
t/GFF.t
t/Genpred.t
t/HSP.t
t/HTML.t
t/HUMBETGLOA.fasta
t/HUMBETGLOA.gff
t/HUMBETGLOA.mzef
t/Index.t
t/LiveSeq.t
t/Location.t
t/Mutation.t
t/Mutator.t
t/OddCodes.t
t/PrimarySeq.t
t/RNAChange.t
t/Range.t
t/RangeI.t
t/RestrictionEnzyme.t
t/RootI.t
t/Sbjct.t
t/SearchDist.t
t/Seq.t
t/SeqAnal.t
t/SeqAnalysisParser.t
t/SeqDiff.t
t/SeqFeature.t
t/SeqIO.t
t/SeqPattern.t
t/SeqStats.t
t/SeqUtils.t
t/Sigcleave.t
t/Sim4.t
t/SimilarityPair.t
t/SimpleAlign.t
t/Species.t
t/StandAloneBlast.t
t/TCoffee.t
t/Tempfile.t
t/Test.pm
t/Tools.t
t/UnivAln.t
t/Variation_IO.t
t/WWW.t
t/alnfile.fasta
t/amino.fa
t/ar.embl
t/bl2seq.out
t/blast.report
t/cysprot.fa
t/cysprot.msf
t/cysprot.tblastn
t/cysprot1.fa
t/cysprot1a.fa
t/cysprot1a.msf
t/cysprot1b.fa
t/cysprot1b.msf
t/dna1.fa
t/dna2.fa
t/empty.bl2seq
t/exception.t
t/expected.blast.out
t/factor7.embl
t/game.t
t/genomic-seq.fasta
t/genomic-seq.genscan
t/genomic-seq.mzef
t/hmmer.t
t/hmmpfam.out
t/hmmsearch.out
t/largefasta.t
t/largepseq.t
t/multi_1.fa
t/multi_2.fa
t/multifa.seq
t/multiple_fasta.t
t/mutations.dat
t/mutations.xml
t/phi.out
t/phipsi.out
t/polymorphism.dat
t/polymorphism.xml
t/psiblastreport.out
t/roa1.dat
t/roa1.genbank
t/roa1.swiss
t/seqs.fas
t/sim4.for.for
t/sim4.for.rev
t/sim4.rev
t/swiss.dat
t/swisspfam.data
t/test.ace
t/test.embl
t/test.fasta
t/test.game
t/test.gcg
t/test.genbank
t/test.mase
t/test.pfam
t/test.raw
t/test.txt
t/test_badlf.gcg
t/testaln.fasta
t/testaln.mase
t/testaln.msf
t/testaln.pfam
t/testaln.prodom
t/testaln.selex
t/testaln.stockholm
t/testfuzzy.genbank