AUTHORS
Bio/Align/AlignI.pm
Bio/Align/DNAStatistics.pm
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Bio/AlignIO.pm
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Bio/SeqIO/tigrxml.pm
Bio/SeqIO/tinyseq.pm
Bio/SeqIO/tinyseq/tinyseqHandler.pm
Bio/SeqIO/ztr.pm
Bio/SeqUtils.pm
Bio/SimpleAlign.pm
Bio/SimpleAnalysisI.pm
Bio/Species.pm
Bio/Structure/Atom.pm
Bio/Structure/Chain.pm
Bio/Structure/Entry.pm
Bio/Structure/IO.pm
Bio/Structure/IO/pdb.pm
Bio/Structure/Model.pm
Bio/Structure/Residue.pm
Bio/Structure/SecStr/DSSP/Res.pm
Bio/Structure/SecStr/STRIDE/Res.pm
Bio/Structure/StructureI.pm
Bio/Symbol/Alphabet.pm
Bio/Symbol/AlphabetI.pm
Bio/Symbol/DNAAlphabet.pm
Bio/Symbol/ProteinAlphabet.pm
Bio/Symbol/README.Symbol
Bio/Symbol/Symbol.pm
Bio/Symbol/SymbolI.pm
Bio/Taxon.pm
Bio/Taxonomy.pm
Bio/Taxonomy/FactoryI.pm
Bio/Taxonomy/Node.pm
Bio/Taxonomy/Taxon.pm
Bio/Taxonomy/Tree.pm
Bio/Tools/AlignFactory.pm
Bio/Tools/Alignment/Consed.pm
Bio/Tools/Alignment/Trim.pm
Bio/Tools/Analysis/DNA/ESEfinder.pm
Bio/Tools/Analysis/Protein/Domcut.pm
Bio/Tools/Analysis/Protein/ELM.pm
Bio/Tools/Analysis/Protein/GOR4.pm
Bio/Tools/Analysis/Protein/HNN.pm
Bio/Tools/Analysis/Protein/Mitoprot.pm
Bio/Tools/Analysis/Protein/NetPhos.pm
Bio/Tools/Analysis/Protein/Scansite.pm
Bio/Tools/Analysis/Protein/Sopma.pm
Bio/Tools/Analysis/SimpleAnalysisBase.pm
Bio/Tools/AnalysisResult.pm
Bio/Tools/Blat.pm
Bio/Tools/CodonTable.pm
Bio/Tools/Coil.pm
Bio/Tools/dpAlign.pm
Bio/Tools/ECnumber.pm
Bio/Tools/EMBOSS/Palindrome.pm
Bio/Tools/EPCR.pm
Bio/Tools/Eponine.pm
Bio/Tools/ERPIN.pm
Bio/Tools/Est2Genome.pm
Bio/Tools/ESTScan.pm
Bio/Tools/EUtilities.pm
Bio/Tools/EUtilities/Cookie.pm
Bio/Tools/EUtilities/EUtilDataI.pm
Bio/Tools/EUtilities/EUtilParameters.pm
Bio/Tools/EUtilities/History.pm
Bio/Tools/EUtilities/HistoryI.pm
Bio/Tools/EUtilities/Info.pm
Bio/Tools/EUtilities/Info/FieldInfo.pm
Bio/Tools/EUtilities/Info/LinkInfo.pm
Bio/Tools/EUtilities/Link.pm
Bio/Tools/EUtilities/Link/LinkSet.pm
Bio/Tools/EUtilities/Link/UrlLink.pm
Bio/Tools/EUtilities/Query.pm
Bio/Tools/EUtilities/Query/GlobalQuery.pm
Bio/Tools/EUtilities/Summary.pm
Bio/Tools/EUtilities/Summary/DocSum.pm
Bio/Tools/EUtilities/Summary/Item.pm
Bio/Tools/EUtilities/Summary/ItemContainerI.pm
Bio/Tools/Fgenesh.pm
Bio/Tools/FootPrinter.pm
Bio/Tools/Gel.pm
Bio/Tools/Geneid.pm
Bio/Tools/Genemark.pm
Bio/Tools/Genewise.pm
Bio/Tools/Genomewise.pm
Bio/Tools/Genscan.pm
Bio/Tools/GFF.pm
Bio/Tools/Glimmer.pm
Bio/Tools/Grail.pm
Bio/Tools/GuessSeqFormat.pm
Bio/Tools/HMMER/Domain.pm
Bio/Tools/HMMER/Results.pm
Bio/Tools/HMMER/Set.pm
Bio/Tools/Hmmpfam.pm
Bio/Tools/Infernal.pm
Bio/Tools/ipcress.pm
Bio/Tools/isPcr.pm
Bio/Tools/IUPAC.pm
Bio/Tools/Lucy.pm
Bio/Tools/Match.pm
Bio/Tools/MZEF.pm
Bio/Tools/OddCodes.pm
Bio/Tools/Phylo/Gerp.pm
Bio/Tools/Phylo/Gumby.pm
Bio/Tools/Phylo/Molphy.pm
Bio/Tools/Phylo/Molphy/Result.pm
Bio/Tools/Phylo/PAML.pm
Bio/Tools/Phylo/PAML/ModelResult.pm
Bio/Tools/Phylo/PAML/Result.pm
Bio/Tools/Phylo/Phylip/ProtDist.pm
Bio/Tools/pICalculator.pm
Bio/Tools/Prediction/Exon.pm
Bio/Tools/Prediction/Gene.pm
Bio/Tools/Primer/Assessor/Base.pm
Bio/Tools/Primer/AssessorI.pm
Bio/Tools/Primer/Feature.pm
Bio/Tools/Primer/Pair.pm
Bio/Tools/Primer3.pm
Bio/Tools/Prints.pm
Bio/Tools/Profile.pm
Bio/Tools/Promoterwise.pm
Bio/Tools/PrositeScan.pm
Bio/Tools/Protparam.pm
Bio/Tools/Pseudowise.pm
Bio/Tools/pSW.pm
Bio/Tools/QRNA.pm
Bio/Tools/RandomDistFunctions.pm
Bio/Tools/RepeatMasker.pm
Bio/Tools/RNAMotif.pm
Bio/Tools/Run/GenericParameters.pm
Bio/Tools/Run/ParametersI.pm
Bio/Tools/Run/README
Bio/Tools/Run/RemoteBlast.pm
Bio/Tools/Run/StandAloneBlast.pm
Bio/Tools/Run/StandAloneNCBIBlast.pm
Bio/Tools/Run/StandAloneWUBlast.pm
Bio/Tools/Run/WrapperBase.pm
Bio/Tools/Seg.pm
Bio/Tools/SeqPattern.pm
Bio/Tools/SeqPattern/Backtranslate.pm
Bio/Tools/SeqStats.pm
Bio/Tools/SeqWords.pm
Bio/Tools/Sigcleave.pm
Bio/Tools/Signalp.pm
Bio/Tools/Signalp/ExtendedSignalp.pm
Bio/Tools/Sim4/Exon.pm
Bio/Tools/Sim4/Results.pm
Bio/Tools/SiRNA.pm
Bio/Tools/SiRNA/Ruleset/saigo.pm
Bio/Tools/SiRNA/Ruleset/tuschl.pm
Bio/Tools/Spidey/Exon.pm
Bio/Tools/Spidey/Results.pm
Bio/Tools/TandemRepeatsFinder.pm
Bio/Tools/TargetP.pm
Bio/Tools/Tmhmm.pm
Bio/Tools/tRNAscanSE.pm
Bio/Tree/AlleleNode.pm
Bio/Tree/AnnotatableNode.pm
Bio/Tree/Compatible.pm
Bio/Tree/DistanceFactory.pm
Bio/Tree/Draw/Cladogram.pm
Bio/Tree/Node.pm
Bio/Tree/NodeI.pm
Bio/Tree/NodeNHX.pm
Bio/Tree/RandomFactory.pm
Bio/Tree/Statistics.pm
Bio/Tree/Tree.pm
Bio/Tree/TreeFunctionsI.pm
Bio/Tree/TreeI.pm
Bio/TreeIO.pm
Bio/TreeIO/cluster.pm
Bio/TreeIO/lintree.pm
Bio/TreeIO/newick.pm
Bio/TreeIO/nexus.pm
Bio/TreeIO/nhx.pm
Bio/TreeIO/pag.pm
Bio/TreeIO/phyloxml.pm
Bio/TreeIO/svggraph.pm
Bio/TreeIO/tabtree.pm
Bio/TreeIO/TreeEventBuilder.pm
Bio/UpdateableSeqI.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/SNP.pm
Bio/Variation/VariantI.pm
Bio/WebAgent.pm
BioPerl.pm
BUGS
Build.PL
Changes
DEPENDENCIES
DEPRECATED
doc/Deobfuscator/bin/deob_index.pl
doc/Deobfuscator/Build.PL
doc/Deobfuscator/cgi-bin/deob_detail.cgi
doc/Deobfuscator/cgi-bin/deob_flowchart.png
doc/Deobfuscator/cgi-bin/deob_help.html
doc/Deobfuscator/cgi-bin/deob_interface.cgi
doc/Deobfuscator/Changes
doc/Deobfuscator/excluded_modules.txt
doc/Deobfuscator/lib/Deobfuscator.pm
doc/Deobfuscator/LICENSE
doc/Deobfuscator/Makefile.PL
doc/Deobfuscator/MANIFEST
doc/Deobfuscator/META.yml
doc/Deobfuscator/README
doc/Deobfuscator/t/00.load.t
doc/Deobfuscator/t/pod.t
doc/makedoc.PL
doc/README
examples/align/align_on_codons.pl
examples/align/aligntutorial.pl
examples/align/clustalw.pl
examples/align/simplealign.pl
examples/biblio/biblio-eutils-example.pl
examples/biblio/biblio-soap-example.pl
examples/biblio/biblio_soap.pl
examples/Bio-DB-GFF/load_ucsc.pl
examples/bioperl.pl
examples/cluster/dbsnp.pl
examples/contributed/nmrpdb_parse.pl
examples/contributed/prosite2perl.pl
examples/contributed/rebase2list.pl
examples/db/dbfetch
examples/db/est_tissue_query.pl
examples/db/gb2features.pl
examples/db/get_seqs.pl
examples/db/getGenBank.pl
examples/db/rfetch.pl
examples/db/use_registry.pl
examples/generate_random_seq.pl
examples/liveseq/change_gene.pl
examples/longorf.pl
examples/make_primers.pl
examples/popgen/parse_calc_stats.pl
examples/quality/svgtrace.pl
examples/rev_and_trans.pl
examples/revcom_dir.pl
examples/root/exceptions1.pl
examples/root/exceptions2.pl
examples/root/exceptions3.pl
examples/root/exceptions4.pl
examples/root/lib/Bio/PrimarySeq.pm
examples/root/lib/Bio/PrimarySeqI.pm
examples/root/lib/Bio/Seq.pm
examples/root/lib/Bio/SeqI.pm
examples/root/lib/TestInterface.pm
examples/root/lib/TestObject.pm
examples/root/README
examples/searchio/blast_example.pl
examples/searchio/custom_writer.pl
examples/searchio/hitwriter.pl
examples/searchio/hspwriter.pl
examples/searchio/htmlwriter.pl
examples/searchio/psiblast_features.pl
examples/searchio/psiblast_iterations.pl
examples/searchio/rawwriter.pl
examples/searchio/resultwriter.pl
examples/searchio/waba2gff.pl
examples/searchio/waba2gff3.pl
examples/sirna/rnai_finder.cgi
examples/sirna/TAG
examples/structure/structure-io.pl
examples/subsequence.cgi
examples/tk/gsequence.pl
examples/tk/hitdisplay.pl
examples/tools/extract_genes.pl
examples/tools/gb_to_gff.pl
examples/tools/gff2ps.pl
examples/tools/parse_codeml.pl
examples/tools/psw.pl
examples/tools/reverse-translate.pl
examples/tools/run_genscan.pl
examples/tools/run_primer3.pl
examples/tools/seq_pattern.pl
examples/tools/standaloneblast.pl
examples/tree/paup2phylip.pl
ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
ide/bioperl-mode/dist/bioperl-mode.tar
ide/bioperl-mode/dist/bioperl-mode.tar.md5
ide/bioperl-mode/dist/package-me
ide/bioperl-mode/dist/SKIP
ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
ide/bioperl-mode/etc/images/bpmode-tool.xpm
ide/bioperl-mode/README
ide/bioperl-mode/site-lisp/bioperl-init.el
ide/bioperl-mode/site-lisp/bioperl-mode.el
ide/bioperl-mode/site-lisp/bioperl-skel.el
ide/bioperl-mode/site-lisp/pod.el
ide/bioperl.komodo
INSTALL
INSTALL.SKIP
INSTALL.WIN
LICENSE
maintenance/authors.pl
maintenance/check_NAME.pl
maintenance/check_URLs.pl
maintenance/cvs2cl_by_file.pl
maintenance/dependencies.pl
maintenance/deprecated.pl
maintenance/module_usage.pl
maintenance/modules.pl
maintenance/ncbi_blast_switches.pl
maintenance/perltidy.conf
maintenance/pod.pl
maintenance/README
maintenance/symlink_script.pl
maintenance/version.pl
MANIFEST			This list of files
MANIFEST.SKIP
models/biblio.dia
models/bio_liveseq_variation.dia
models/bio_map.dia
models/bio_restriction.dia
models/bioperl.dia
models/coordinatemapper.dia
models/map_proposal.txt
models/maps_and_markers.dia
models/popgen.dia
models/population_proposal.txt
models/README
README
scripts/biblio/biblio.PLS
scripts/biblio/TAG
scripts/Bio-DB-EUtilities/einfo.PLS
scripts/Bio-DB-GFF/bulk_load_gff.PLS
scripts/Bio-DB-GFF/fast_load_gff.PLS
scripts/Bio-DB-GFF/genbank2gff.PLS
scripts/Bio-DB-GFF/genbank2gff3.PLS
scripts/Bio-DB-GFF/generate_histogram.PLS
scripts/Bio-DB-GFF/load_gff.PLS
scripts/Bio-DB-GFF/meta_gff.PLS
scripts/Bio-DB-GFF/process_gadfly.PLS
scripts/Bio-DB-GFF/process_sgd.PLS
scripts/Bio-DB-GFF/process_wormbase.PLS
scripts/Bio-DB-GFF/README
scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
scripts/das/README
scripts/das/TAG
scripts/DB-HIV/hivq.PLS
scripts/DB/biofetch_genbank_proxy.PLS
scripts/DB/bioflat_index.PLS
scripts/DB/biogetseq.PLS
scripts/DB/flanks.PLS
scripts/DB/TAG
scripts/index/bp_fetch.PLS
scripts/index/bp_index.PLS
scripts/index/bp_seqret.PLS
scripts/index/TAG
scripts/popgen/composite_LD.PLS
scripts/popgen/heterogeneity_test.PLS
scripts/README
scripts/searchio/fastam9_to_table.PLS
scripts/searchio/filter_search.PLS
scripts/searchio/hmmer_to_table.PLS
scripts/searchio/parse_hmmsearch.PLS
scripts/searchio/README
scripts/searchio/search2table.PLS
scripts/searchio/TAG
scripts/seq/extract_feature_seq.PLS
scripts/seq/make_mrna_protein.PLS
scripts/seq/seqconvert.PLS
scripts/seq/seqretsplit.PLS
scripts/seq/split_seq.PLS
scripts/seq/TAG
scripts/seq/translate_seq.PLS
scripts/seq/unflatten_seq.PLS
scripts/seqstats/aacomp.PLS
scripts/seqstats/chaos_plot.PLS
scripts/seqstats/gccalc.PLS
scripts/seqstats/oligo_count.PLS
scripts/seqstats/TAG
scripts/taxa/classify_hits_kingdom.PLS
scripts/taxa/local_taxonomydb_query.PLS
scripts/taxa/query_entrez_taxa.PLS
scripts/taxa/TAG
scripts/taxa/taxid4species.PLS
scripts/taxa/taxonomy2tree.PLS
scripts/tree/blast2tree.PLS
scripts/tree/nexus2nh.PLS
scripts/tree/TAG
scripts/tree/tree2pag.PLS
scripts/utilities/bp_mrtrans.PLS
scripts/utilities/bp_nrdb.PLS
scripts/utilities/bp_sreformat.PLS
scripts/utilities/dbsplit.PLS
scripts/utilities/download_query_genbank.PLS
scripts/utilities/mask_by_search.PLS
scripts/utilities/mutate.PLS
scripts/utilities/pairwise_kaks.PLS
scripts/utilities/README
scripts/utilities/remote_blast.PLS
scripts/utilities/revtrans-motif.PLS
scripts/utilities/search2alnblocks.PLS
scripts/utilities/search2BSML.PLS
scripts/utilities/search2gff.PLS
scripts/utilities/search2tribe.PLS
scripts/utilities/seq_length.PLS
scripts/utilities/TAG
t/Align/AlignStats.t
t/Align/AlignUtil.t
t/Align/SimpleAlign.t
t/Align/TreeBuild.t
t/Align/Utilities.t
t/AlignIO/AlignIO.t
t/AlignIO/arp.t
t/AlignIO/bl2seq.t
t/AlignIO/clustalw.t
t/AlignIO/emboss.t
t/AlignIO/fasta.t
t/AlignIO/largemultifasta.t
t/AlignIO/maf.t
t/AlignIO/mase.t
t/AlignIO/mega.t
t/AlignIO/meme.t
t/AlignIO/metafasta.t
t/AlignIO/msf.t
t/AlignIO/nexus.t
t/AlignIO/pfam.t
t/AlignIO/phylip.t
t/AlignIO/po.t
t/AlignIO/prodom.t
t/AlignIO/psi.t
t/AlignIO/selex.t
t/AlignIO/stockholm.t
t/AlignIO/xmfa.t
t/Alphabet.t
t/Annotation/Annotation.t
t/Annotation/AnnotationAdaptor.t
t/Assembly/Assembly.t
t/Assembly/ContigSpectrum.t
t/Biblio/Biblio.t
t/Biblio/biofetch.t
t/Biblio/eutils.t
t/Biblio/References.t
t/ClusterIO/ClusterIO.t
t/ClusterIO/SequenceFamily.t
t/ClusterIO/unigene.t
t/Coordinate/CoordinateGraph.t
t/Coordinate/CoordinateMapper.t
t/Coordinate/GeneCoordinateMapper.t
t/data/13-pilE-F.scf
t/data/1A11.pdb
t/data/1A3I.pdb
t/data/1BPT.pdb
t/data/1ZZ19XR301R-Alignment.tblastn
t/data/2008.blasttable
t/data/503384.MEGABLAST.0
t/data/503384.MEGABLAST.2
t/data/5X_1895.FASTXY
t/data/8HVP.pdb
t/data/a_thaliana.blastn
t/data/AAC12660.fa
t/data/aaml.mlc
t/data/aaml_pairwise.mlc
t/data/AB077698.gb
t/data/acefile.ace.1
t/data/acefile.singlets
t/data/adh.mb_tree.nexus
t/data/AE003528_ecoli.bls
t/data/AE003644_Adh-genomic.gb
t/data/AF032047.gbk
t/data/AF165282.gb
t/data/AF305198.gb
t/data/AHCYL1.kegg
t/data/alleles.fas
t/data/alnfile.fasta
t/data/amino.fa
t/data/AnnIX-v003.gbk
t/data/ar.embl
t/data/assembly_with_singlets.ace
t/data/ATF14F8.gbk
t/data/atp1.matrix
t/data/ay007676.gb
t/data/AY095303S1.gbk
t/data/ay116458.gb
t/data/ay149291.gb
t/data/AY763288.gb
t/data/BAB68554.gb
t/data/barns-combined.nex
t/data/baseml.pairwise
t/data/baseml.usertree
t/data/basic-bush.nex
t/data/basic-ladder.nex
t/data/BC000007.gbk
t/data/BEL16-LTR_AG.embl
t/data/biodbgff/test.gff
t/data/biodbgff/test.gff3
t/data/biofpc.cor
t/data/biofpc.fpc
t/data/Bird_Ovomucoids.nex
t/data/BK000016-tpa.gbk
t/data/bl2seq.blastn
t/data/bl2seq.blastn.rev
t/data/bl2seq.blastx.out
t/data/bl2seq.bug940.out
t/data/bl2seq.out
t/data/bl2seq.tblastx.out
t/data/blast.report
t/data/blast_no_hit_desc.txt
t/data/blastp2215.blast
t/data/blat.psLayout3
t/data/BLOSUM50
t/data/blosum62.bla
t/data/BN000066-tpa.embl
t/data/bootstrap.tre
t/data/BOSS_DROME.FASTP_v35_04
t/data/branchSite.mlc
t/data/brassica_ATH.WUBLASTN
t/data/bug1986.blast2
t/data/bug1986.blastp
t/data/bug2120.phd
t/data/bug2246.blast
t/data/bug2391.megablast
t/data/bug2399.tblastn
t/data/bug2453.maf
t/data/bug2473.fasta
t/data/bug2862.pmr
t/data/c200-vs-yeast.BLASTN
t/data/c200-vs-yeast.BLASTN.m8
t/data/calm.swiss
t/data/catalase-webblast.BLASTP
t/data/cds-266.fas
t/data/cds_sample.embl
t/data/CG11099.fasaln
t/data/CG2865.fasaln
t/data/chad100.scf
t/data/char-interleave.nex
t/data/char-matrix-spaces.nex
t/data/codeml.mlc
t/data/codeml315.mlc
t/data/codeml4.mlc
t/data/codeml_lysozyme/2NG.dN
t/data/codeml_lysozyme/2NG.dS
t/data/codeml_lysozyme/2NG.tt
t/data/codeml_lysozyme/4fold.nuc
t/data/codeml_lysozyme/lnf
t/data/codeml_lysozyme/lysozymeSmall.ctl
t/data/codeml_lysozyme/lysozymeSmall.trees
t/data/codeml_lysozyme/lysozymeSmall.txt
t/data/codeml_lysozyme/mlc
t/data/codeml_lysozyme/rst
t/data/codeml_lysozyme/rst1
t/data/codeml_lysozyme/rub
t/data/codeml_nssites.mlc
t/data/compLD_missingtest.prettybase
t/data/compLD_test.prettybase
t/data/component.ontology.test
t/data/component.ontology.test2
t/data/consed_project/edit_dir/test_project.contigs
t/data/consed_project/edit_dir/test_project.fasta
t/data/consed_project/edit_dir/test_project.fasta.log
t/data/consed_project/edit_dir/test_project.fasta.screen
t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.log
t/data/consed_project/edit_dir/test_project.fasta.screen.problems
t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.qual
t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
t/data/consed_project/edit_dir/test_project.fasta.screen.view
t/data/consed_project/edit_dir/test_project.newtags
t/data/consed_project/edit_dir/test_project.phrap.out
t/data/consed_project/edit_dir/test_project.screen.out
t/data/consed_project/edit_dir/test_project_to_alu.cross
t/data/consed_project/edit_dir/test_projectNewChromats.fof
t/data/consed_project/phd_dir/ML4922R.phd.1
t/data/consed_project/phd_dir/ML4924F.phd.1
t/data/consed_project/phd_dir/ML4924R.phd.1
t/data/consed_project/phd_dir/ML4947F.phd.1
t/data/contig-by-hand.wublastp
t/data/contigspectrumtest.asm
t/data/crab.dat.cn
t/data/crab.nj
t/data/crab.njb
t/data/crypto.sim4-0
t/data/crypto.sim4-3
t/data/crypto.sim4-4
t/data/ctgdemo.fpc
t/data/cys1_dicdi.water
t/data/cysprot.fa
t/data/cysprot.msf
t/data/cysprot.needle
t/data/cysprot.tblastn
t/data/cysprot.water
t/data/cysprot1.fa
t/data/cysprot1.FASTA
t/data/cysprot1a.fa
t/data/cysprot1a.msf
t/data/cysprot1b.fa
t/data/cysprot1b.hmmsearch
t/data/cysprot1b.msf
t/data/cysprot1b.newick
t/data/cysprot_vs_gadfly.FASTA
t/data/D10483.gbk
t/data/D12555.gbk
t/data/dbfa/1.fa
t/data/dbfa/2.fa
t/data/dbfa/3.fa
t/data/dbfa/4.fa
t/data/dbfa/5.fa
t/data/dbfa/6.fa
t/data/dbfa/7.fa
t/data/dbqual/1.qual
t/data/dbqual/2.qual
t/data/dbqual/3.qual
t/data/dcr1_sp.WUBLASTP
t/data/directives.gff3
t/data/dmel_2Lchunk.gb
t/data/dna1.fa
t/data/dna2.fa
t/data/dnaE-bsub-prot.fa
t/data/dnaE-bsub.fa
t/data/dnaEbsub_ecoli.wublastx
t/data/dnaEbsub_ecoli.wutblastn
t/data/dnaEbsub_ecoli.wutblastx
t/data/DQ018368.gb
t/data/dq519393.gb
t/data/ECAPAH02.embl
t/data/echofilter.wublastn
t/data/ecoli-trna-qrna.out
t/data/ecoli_domains.rps.xml
t/data/ecoli_domains.rpsblast
t/data/ecolitst.bls
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t/SearchIO/SimilarityPair.t
t/SearchIO/Tiling.t
t/SearchIO/waba.t
t/SearchIO/wise.t
t/SearchIO/Writer/GbrowseGFF.t
t/SearchIO/Writer/HitTableWriter.t
t/SearchIO/Writer/HSPTableWriter.t
t/SearchIO/Writer/HTMLWriter.t
t/Seq/DBLink.t
t/Seq/EncodedSeq.t
t/Seq/LargeLocatableSeq.t
t/Seq/LargePSeq.t
t/Seq/LocatableSeq.t
t/Seq/MetaSeq.t
t/Seq/PrimaryQual.t
t/Seq/PrimarySeq.t
t/Seq/PrimedSeq.t
t/Seq/Quality.t
t/Seq/Seq.t
t/Seq/WithQuality.t
t/SeqEvolution.t
t/SeqFeature/FeatureIO.t
t/SeqFeature/Location.t
t/SeqFeature/LocationFactory.t
t/SeqFeature/Primer.t
t/SeqFeature/Range.t
t/SeqFeature/RangeI.t
t/SeqFeature/SeqAnalysisParser.t
t/SeqFeature/SeqFeatAnnotated.t
t/SeqFeature/SeqFeatCollection.t
t/SeqFeature/SeqFeature.t
t/SeqFeature/SeqFeaturePrimer.t
t/SeqFeature/Unflattener.t
t/SeqFeature/Unflattener2.t
t/SeqIO.t
t/SeqIO/abi.t
t/SeqIO/ace.t
t/SeqIO/agave.t
t/SeqIO/alf.t
t/SeqIO/asciitree.t
t/SeqIO/bsml.t
t/SeqIO/bsml_sax.t
t/SeqIO/chadoxml.t
t/SeqIO/chaos.t
t/SeqIO/chaosxml.t
t/SeqIO/ctf.t
t/SeqIO/embl.t
t/SeqIO/entrezgene.t
t/SeqIO/excel.t
t/SeqIO/exp.t
t/SeqIO/fasta.t
t/SeqIO/fastq.t
t/SeqIO/flybase_chadoxml.t
t/SeqIO/game.t
t/SeqIO/gcg.t
t/SeqIO/genbank.t
t/SeqIO/Handler.t
t/SeqIO/interpro.t
t/SeqIO/kegg.t
t/SeqIO/largefasta.t
t/SeqIO/lasergene.t
t/SeqIO/locuslink.t
t/SeqIO/metafasta.t
t/SeqIO/MultiFile.t
t/SeqIO/Multiple_fasta.t
t/SeqIO/phd.t
t/SeqIO/pir.t
t/SeqIO/pln.t
t/SeqIO/qual.t
t/SeqIO/raw.t
t/SeqIO/scf.t
t/SeqIO/SeqBuilder.t
t/SeqIO/Splicedseq.t
t/SeqIO/strider.t
t/SeqIO/swiss.t
t/SeqIO/tab.t
t/SeqIO/table.t
t/SeqIO/tigr.t
t/SeqIO/tigrxml.t
t/SeqIO/tinyseq.t
t/SeqIO/ztr.t
t/SeqTools/Backtranslate.t
t/SeqTools/CodonTable.t
t/SeqTools/ECnumber.t
t/SeqTools/GuessSeqFormat.t
t/SeqTools/OddCodes.t
t/SeqTools/SeqPattern.t
t/SeqTools/SeqStats.t
t/SeqTools/SeqUtils.t
t/SeqTools/SeqWords.t
t/Species.t
t/Structure/IO.t
t/Structure/Structure.t
t/Symbol.t
t/TaxonTree.t
t/Tools/Alignment/Consed.t
t/Tools/Analysis/DNA/ESEfinder.t
t/Tools/Analysis/Protein/Domcut.t
t/Tools/Analysis/Protein/ELM.t
t/Tools/Analysis/Protein/GOR4.t
t/Tools/Analysis/Protein/HNN.t
t/Tools/Analysis/Protein/Mitoprot.t
t/Tools/Analysis/Protein/NetPhos.t
t/Tools/Analysis/Protein/Scansite.t
t/Tools/Analysis/Protein/Sopma.t
t/Tools/EMBOSS/Palindrome.t
t/Tools/ePCR.t
t/Tools/Est2Genome.t
t/Tools/EUtilities/egquery.t
t/Tools/EUtilities/einfo.t
t/Tools/EUtilities/elink_acheck.t
t/Tools/EUtilities/elink_lcheck.t
t/Tools/EUtilities/elink_llinks.t
t/Tools/EUtilities/elink_ncheck.t
t/Tools/EUtilities/elink_neighbor.t
t/Tools/EUtilities/elink_neighbor_history.t
t/Tools/EUtilities/elink_scores.t
t/Tools/EUtilities/epost.t
t/Tools/EUtilities/esearch.t
t/Tools/EUtilities/espell.t
t/Tools/EUtilities/esummary.t
t/Tools/EUtilities/EUtilParameters.t
t/Tools/FootPrinter.t
t/Tools/Geneid.t
t/Tools/Genewise.t
t/Tools/Genomewise.t
t/Tools/Genpred.t
t/Tools/GFF.t
t/Tools/Hmmer.t
t/Tools/IUPAC.t
t/Tools/Lucy.t
t/Tools/Match.t
t/Tools/Phylo/Gerp.t
t/Tools/Phylo/Molphy.t
t/Tools/Phylo/PAML.t
t/Tools/Phylo/Phylip/ProtDist.t
t/Tools/pICalculator.t
t/Tools/Primer3.t
t/Tools/Promoterwise.t
t/Tools/Pseudowise.t
t/Tools/QRNA.t
t/Tools/RandDistFunctions.t
t/Tools/RepeatMasker.t
t/Tools/rnamotif.t
t/Tools/Run/RemoteBlast.t
t/Tools/Run/RemoteBlast_rpsblast.t
t/Tools/Run/StandAloneBlast.t
t/Tools/Run/WrapperBase.t
t/Tools/Seg.t
t/Tools/Sigcleave.t
t/Tools/Signalp.t
t/Tools/Signalp/ExtendedSignalp.t
t/Tools/Sim4.t
t/Tools/SiRNA.t
t/Tools/Spidey/Spidey.t
t/Tools/TandemRepeatsFinder.t
t/Tools/TargetP.t
t/Tools/Tmhmm.t
t/Tools/tRNAscanSE.t
t/Tree/Compatible.t
t/Tree/Node.t
t/Tree/PhyloNetwork/Factory.t
t/Tree/PhyloNetwork/GraphViz.t
t/Tree/PhyloNetwork/MuVector.t
t/Tree/PhyloNetwork/PhyloNetwork.t
t/Tree/PhyloNetwork/RandomFactory.t
t/Tree/PhyloNetwork/TreeFactory.t
t/Tree/RandomTreeFactory.t
t/Tree/Tree.t
t/Tree/TreeIO.t
t/Tree/TreeIO/lintree.t
t/Tree/TreeIO/newick.t
t/Tree/TreeIO/nexus.t
t/Tree/TreeIO/nhx.t
t/Tree/TreeIO/phyloxml.t
t/Tree/TreeIO/svggraph.t
t/Tree/TreeIO/tabtree.t
t/Tree/TreeStatistics.t
t/Variation/AAChange.t
t/Variation/AAReverseMutate.t
t/Variation/Allele.t
t/Variation/DNAMutation.t
t/Variation/RNAChange.t
t/Variation/SeqDiff.t
t/Variation/SNP.t
t/Variation/Variation_IO.t
Makefile.PL
META.yml
