bioperl-live
Core BioPerl 1.x code
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최종 버전 다운로드 (.zip)- ci.yml
- bp_aacomp
- bp_bioflat_index
- bp_biogetseq
- bp_dbsplit
- bp_extract_feature_seq
- bp_fastam9_to_table
- bp_fetch
- bp_filter_search
- bp_find-blast-matches
- bp_gccalc
- bp_genbank2gff3
- bp_index
- bp_local_taxonomydb_query
- bp_make_mrna_protein
- bp_mask_by_search
- bp_mrtrans
- bp_mutate
- bp_nexus2nh
- bp_nrdb
- bp_oligo_count
- bp_process_gadfly
- bp_process_sgd
- bp_revtrans-motif
- bp_search2alnblocks
- bp_search2gff
- bp_search2table
- bp_search2tribe
- bp_seq_length
- bp_seqconvert
- bp_seqcut
- bp_seqpart
- bp_seqret
- bp_seqretsplit
- bp_split_seq
- bp_sreformat
- bp_taxid4species
- bp_taxonomy2tree
- bp_translate_seq
- bp_tree2pag
- bp_unflatten_seq
- align_on_codons.pl
- aligntutorial.pl
- FastAlign.pl
- simplealign.pl
- load_ucsc.pl
- nmrpdb_parse.pl
- prosite2perl.pl
- rebase2list.pl
- est_tissue_query.pl
- get_seqs.pl
- rfetch.pl
- use_registry.pl
- svgtrace.pl
- exceptions1.pl
- exceptions2.pl
- exceptions3.pl
- exceptions4.pl
- README
- blast_example.pl
- custom_writer.pl
- hitwriter.pl
- hspwriter.pl
- htmlwriter.pl
- psiblast_features.pl
- psiblast_iterations.pl
- rawwriter.pl
- resultwriter.pl
- waba2gff.pl
- waba2gff3.pl
- gsequence.pl
- hitdisplay.pl
- extract_genes.pl
- gb_to_gff.pl
- gff2ps.pl
- parse_codeml.pl
- reverse-translate.pl
- run_genscan.pl
- run_primer3.pl
- seq_pattern.pl
- standaloneblast.pl
- paup2phylip.pl
- classify_hits_kingdom
- generate_random_seq.pl
- longorf.pl
- make_primers.pl
- rev_and_trans.pl
- revcom_dir.pl
- AlignI.pm
- DNAStatistics.pm
- PairwiseStatistics.pm
- ProteinStatistics.pm
- StatisticsI.pm
- Utilities.pm
- GenericAlignHandler.pm
- arp.pm
- bl2seq.pm
- clustalw.pm
- emboss.pm
- fasta.pm
- largemultifasta.pm
- maf.pm
- mase.pm
- mega.pm
- meme.pm
- metafasta.pm
- msf.pm
- nexus.pm
- pfam.pm
- phylip.pm
- po.pm
- proda.pm
- prodom.pm
- psi.pm
- selex.pm
- xmfa.pm
- AnnotationFactory.pm
- Collection.pm
- Comment.pm
- DBLink.pm
- OntologyTerm.pm
- Reference.pm
- Relation.pm
- SimpleValue.pm
- StructuredValue.pm
- TagTree.pm
- Target.pm
- Tree.pm
- TypeManager.pm
- IO.pm
- Table.pm
- FeatureTypeI.pm
- SegmentI.pm
- embl.pm
- fasta.pm
- genbank.pm
- swiss.pm
- BDB.pm
- BinarySearch.pm
- Binning.pm
- Rearrange.pm
- WebQuery.pm
- flatfile.pm
- greengenes.pm
- list.pm
- silva.pm
- DBFetch.pm
- Failover.pm
- Fasta.pm
- FileCache.pm
- Flat.pm
- GenericWebAgent.pm
- IndexedBase.pm
- InMemoryCache.pm
- LocationI.pm
- Qual.pm
- QueryI.pm
- RandomAccessI.pm
- ReferenceI.pm
- Registry.pm
- SeqI.pm
- Taxonomy.pm
- UpdateableSeqI.pm
- WebDBSeqI.pm
- EventGeneratorI.pm
- EventHandlerI.pm
- AnalysisI.pm
- ApplicationFactoryI.pm
- DriverFactory.pm
- FTLocationFactory.pm
- LocationFactoryI.pm
- ObjectBuilderI.pm
- ObjectFactory.pm
- ObjectFactoryI.pm
- SeqAnalysisParserFactory.pm
- SeqAnalysisParserFactoryI.pm
- SequenceFactoryI.pm
- SequenceProcessorI.pm
- SequenceStreamI.pm
- TreeFactoryI.pm
- Abstract.pm
- AbstractSeq.pm
- Blast.pm
- BlastTable.pm
- EMBL.pm
- Fasta.pm
- Fastq.pm
- GenBank.pm
- Qual.pm
- SwissPfam.pm
- Swissprot.pm
- Atomic.pm
- AvWithinCoordPolicy.pm
- CoordinatePolicyI.pm
- Fuzzy.pm
- FuzzyLocationI.pm
- NarrowestCoordPolicy.pm
- Simple.pm
- Split.pm
- SplitLocationI.pm
- WidestCoordPolicy.pm
- mlagan.pm
- phylip.pm
- scoring.pm
- mast.pm
- masta.pm
- meme.pm
- psiblast.pm
- transfac.pm
- InstanceSite.pm
- InstanceSiteI.pm
- IO.pm
- ProtMatrix.pm
- ProtPsm.pm
- Psm.pm
- PsmHeader.pm
- PsmHeaderI.pm
- PsmI.pm
- SiteMatrix.pm
- SiteMatrixI.pm
- Generic.pm
- IO.pm
- MatrixI.pm
- Mlagan.pm
- PhylipDist.pm
- Scoring.pm
- GraphAdaptor.pm
- DocumentRegistry.pm
- GOterm.pm
- InterProTerm.pm
- OBOEngine.pm
- OBOterm.pm
- Ontology.pm
- OntologyEngineI.pm
- OntologyI.pm
- OntologyStore.pm
- Path.pm
- PathI.pm
- Relationship.pm
- RelationshipFactory.pm
- RelationshipI.pm
- RelationshipType.pm
- SimpleOntologyEngine.pm
- Term.pm
- TermFactory.pm
- TermI.pm
- BaseSAXHandler.pm
- InterPro_BioSQL_Handler.pm
- InterProHandler.pm
- dagflat.pm
- goflat.pm
- InterProParser.pm
- obo.pm
- simplehierarchy.pm
- soflat.pm
- Exception.pm
- HTTPget.pm
- IO.pm
- Root.pm
- RootI.pm
- Storable.pm
- Test.pm
- TestObject.pm
- Utilities.pm
- Version.pm
- BlastHit.pm
- BlastPullHit.pm
- Fasta.pm
- GenericHit.pm
- HitFactory.pm
- HitI.pm
- ModelHit.pm
- PsiBlastHit.pm
- PullHitI.pm
- BlastHSP.pm
- BlastPullHSP.pm
- FastaHSP.pm
- GenericHSP.pm
- HSPFactory.pm
- HSPI.pm
- ModelHSP.pm
- PsiBlastHSP.pm
- PSLHSP.pm
- PullHSPI.pm
- WABAHSP.pm
- GenericIteration.pm
- IterationI.pm
- BlastPullResult.pm
- BlastResult.pm
- CrossMatchResult.pm
- GenericResult.pm
- INFERNALResult.pm
- PullResultI.pm
- ResultFactory.pm
- ResultI.pm
- WABAResult.pm
- MapTileUtils.pm
- MapTiling.pm
- TilingI.pm
- BlastStatistics.pm
- BlastUtils.pm
- DatabaseI.pm
- GenericDatabase.pm
- GenericStatistics.pm
- Processor.pm
- SearchUtils.pm
- StatisticsI.pm
- GbrowseGFF.pm
- HitTableWriter.pm
- HSPTableWriter.pm
- HTMLResultWriter.pm
- ResultTableWriter.pm
- TextResultWriter.pm
- axt.pm
- blast.pm
- blast_pull.pm
- blasttable.pm
- cross_match.pm
- erpin.pm
- EventHandlerI.pm
- exonerate.pm
- fasta.pm
- FastHitEventBuilder.pm
- gmap_f9.pm
- infernal.pm
- IteratedSearchResultEventBuilder.pm
- megablast.pm
- psl.pm
- rnamotif.pm
- SearchResultEventBuilder.pm
- SearchWriterI.pm
- sim4.pm
- waba.pm
- wise.pm
- Array.pm
- BaseSeqProcessor.pm
- EncodedSeq.pm
- LargeLocatableSeq.pm
- LargePrimarySeq.pm
- LargeSeq.pm
- LargeSeqI.pm
- Meta.pm
- MetaI.pm
- PrimaryQual.pm
- PrimedSeq.pm
- QualI.pm
- Quality.pm
- RichSeq.pm
- RichSeqI.pm
- SeqBuilder.pm
- SeqFactory.pm
- SeqFastaSpeedFactory.pm
- SequenceTrace.pm
- SimulatedRead.pm
- TraceI.pm
- Exon.pm
- ExonI.pm
- GeneStructure.pm
- GeneStructureI.pm
- Intron.pm
- NC_Feature.pm
- Poly_A_site.pm
- Promoter.pm
- Transcript.pm
- TranscriptI.pm
- UTR.pm
- FeatureNamer.pm
- IDHandler.pm
- TypeMapper.pm
- Unflattener.pm
- Amplicon.pm
- AnnotationAdaptor.pm
- Collection.pm
- CollectionI.pm
- Computation.pm
- FeaturePair.pm
- Generic.pm
- Lite.pm
- PositionProxy.pm
- Primer.pm
- Similarity.pm
- SimilarityPair.pm
- SubSeq.pm
- TypedSeqFeatureI.pm
- GenericRichSeqHandler.pm
- ace.pm
- asciitree.pm
- bsml.pm
- bsml_sax.pm
- embl.pm
- embldriver.pm
- fasta.pm
- fastq.pm
- FTHelper.pm
- gbdriver.pm
- gbxml.pm
- gcg.pm
- genbank.pm
- kegg.pm
- largefasta.pm
- mbsout.pm
- metafasta.pm
- msout.pm
- MultiFile.pm
- phd.pm
- pir.pm
- qual.pm
- raw.pm
- scf.pm
- swiss.pm
- swissdriver.pm
- tab.pm
- table.pm
- tigr.pm
- tigrxml.pm
- Consed.pm
- Trim.pm
- SimpleAnalysisBase.pm
- Palindrome.pm
- Result.pm
- ProtDist.pm
- Gerp.pm
- Molphy.pm
- Exon.pm
- Gene.pm
- Base.pm
- AssessorI.pm
- Feature.pm
- Pair.pm
- PhyloBase.pm
- CommandExts.pm
- Analysis.pm
- AnalysisFactory.pm
- GenericParameters.pm
- ParametersI.pm
- WrapperBase.pm
- Backtranslate.pm
- ExtendedSignalp.pm
- Exon.pm
- Results.pm
- Exon.pm
- Results.pm
- AmpliconSearch.pm
- AnalysisResult.pm
- Blat.pm
- CodonTable.pm
- Coil.pm
- ECnumber.pm
- EPCR.pm
- Eponine.pm
- Est2Genome.pm
- ESTScan.pm
- Fgenesh.pm
- FootPrinter.pm
- Geneid.pm
- Genemark.pm
- Genewise.pm
- Genomewise.pm
- Genscan.pm
- GFF.pm
- Glimmer.pm
- Grail.pm
- GuessSeqFormat.pm
- ipcress.pm
- isPcr.pm
- IUPAC.pm
- Lucy.pm
- Match.pm
- MZEF.pm
- OddCodes.pm
- pICalculator.pm
- Primer3.pm
- Prints.pm
- Profile.pm
- Promoterwise.pm
- PrositeScan.pm
- Pseudowise.pm
- QRNA.pm
- RandomDistFunctions.pm
- RepeatMasker.pm
- Seg.pm
- SeqPattern.pm
- SeqStats.pm
- SeqWords.pm
- Sigcleave.pm
- Signalp.pm
- TandemRepeatsFinder.pm
- TargetP.pm
- Tmhmm.pm
- tRNAscanSE.pm
- AnnotatableNode.pm
- Compatible.pm
- DistanceFactory.pm
- Node.pm
- NodeI.pm
- NodeNHX.pm
- RandomFactory.pm
- Statistics.pm
- Tree.pm
- TreeFunctionsI.pm
- TreeI.pm
- cluster.pm
- lintree.pm
- newick.pm
- NewickParser.pm
- nexus.pm
- nhx.pm
- pag.pm
- tabtree.pm
- TreeEventBuilder.pm
- AlignIO.pm
- AnalysisI.pm
- AnalysisParserI.pm
- AnalysisResultI.pm
- AnnotatableI.pm
- AnnotationCollectionI.pm
- AnnotationI.pm
- DasI.pm
- DBLinkContainerI.pm
- DescribableI.pm
- FeatureHolderI.pm
- HandlerBaseI.pm
- IdCollectionI.pm
- IdentifiableI.pm
- LocatableSeq.pm
- LocationI.pm
- OntologyIO.pm
- ParameterBaseI.pm
- PrimarySeq.pm
- PrimarySeqI.pm
- PullParserI.pm
- Range.pm
- RangeI.pm
- SearchIO.pm
- Seq.pm
- SeqAnalysisParserI.pm
- SeqFeatureI.pm
- SeqI.pm
- SeqIO.pm
- SeqUtils.pm
- SimpleAlign.pm
- SimpleAnalysisI.pm
- Species.pm
- Taxon.pm
- TreeIO.pm
- UpdateableSeqI.pm
- WebAgent.pm
- BioPerl.pm
- AlignStats.t
- AlignUtil.t
- SimpleAlign.t
- TreeBuild.t
- Utilities.t
- AlignIO.t
- arp.t
- bl2seq.t
- clustalw.t
- emboss.t
- fasta.t
- largemultifasta.t
- maf.t
- mase.t
- mega.t
- meme.t
- metafasta.t
- msf.t
- nexus.t
- pfam.t
- phylip.t
- po.t
- prodom.t
- psi.t
- selex.t
- xmfa.t
- Annotation.t
- AnnotationAdaptor.t
- bug3172.fa
- shotdb.fa
- test_project.contigs
- test_project.fasta
- test_project.fasta.log
- test_project.fasta.screen
- test_project.fasta.screen.ace.1
- test_project.fasta.screen.contigs
- test_project.fasta.screen.contigs.qual
- test_project.fasta.screen.log
- test_project.fasta.screen.problems
- test_project.fasta.screen.problems.qual
- test_project.fasta.screen.qual
- test_project.fasta.screen.singlets
- test_project.fasta.screen.view
- test_project.newtags
- test_project.screen.out
- test_project_to_alu.cross
- test_projectNewChromats.fof
- ML4922R.phd.1
- ML4924F.phd.1
- ML4924R.phd.1
- ML4947F.phd.1
- 1.fa
- 2.fa
- 3.fa
- 4.fa
- 5.fa
- 6.fa
- 7.fa
- mixed_alphabet.fasta
- 1.qual
- 2.qual
- 3.qual
- bug2335.fastq
- error_diff_ids.fastq
- error_double_qual.fastq
- error_double_seq.fastq
- error_long_qual.fastq
- error_no_qual.fastq
- error_qual_del.fastq
- error_qual_escape.fastq
- error_qual_null.fastq
- error_qual_space.fastq
- error_qual_tab.fastq
- error_qual_unit_sep.fastq
- error_qual_vtab.fastq
- error_short_qual.fastq
- error_spaces.fastq
- error_tabs.fastq
- error_trunc_at_plus.fastq
- error_trunc_at_qual.fastq
- error_trunc_at_seq.fastq
- error_trunc_in_plus.fastq
- error_trunc_in_qual.fastq
- error_trunc_in_seq.fastq
- error_trunc_in_title.fastq
- evil_wrapping.fastq
- example.fasta
- example.fastq
- example.qual
- illumina_faked.fastq
- RT98876.fastq
- sanger_93.fastq
- sanger_faked.fastq
- solexa_example.fastq
- solexa_faked.fastq
- test1_sanger.fastq
- test2_solexa.fastq
- test3_illumina.fastq
- tricky.fastq
- wrapping_issues.fastq
- zero_qual.fastq
- HEM1-HEM12.fa
- HEM1-HEM12.fa.revcom
- HEM1-HEM12.meme.txt
- HEM1-HEM13.fa
- HEM1-HEM13.meme.txt
- HEM1-HEM14.fa
- HEM1-HEM14.meme.txt
- HEM1-HEM15.fa
- HEM1-HEM15.meme.txt
- HEM1-HEM2.fa
- HEM1-HEM2.fa.revcom
- HEM1-HEM2.meme.txt
- HEM1-HEM3.fa
- HEM1-HEM3.meme.txt
- HEM1-HEM4.fa
- HEM1-HEM4.meme.txt
- HEM1.ups.fa_
- HEM1.ups.fa_.revcom
- HEM12-HEM13.fa
- HEM12-HEM13.meme.txt
- HEM12-HEM14.fa
- HEM12-HEM14.meme.txt
- HEM12-HEM15.fa
- HEM12-HEM15.meme.txt
- HEM12.ups.fa_
- HEM12.ups.fa_.revcom
- HEM13-HEM14.fa
- HEM13-HEM14.meme.txt
- HEM13-HEM15.fa
- HEM13-HEM15.meme.txt
- HEM13.ups.fa_
- HEM13.ups.fa_.revcom
- HEM14-HEM15.fa
- HEM14-HEM15.meme.txt
- HEM14.ups.fa_
- HEM14.ups.fa_.revcom
- HEM15.ups.fa_
- HEM15.ups.fa_.revcom
- HEM2-HEM12.fa
- HEM2-HEM12.meme.txt
- HEM2-HEM13.fa
- HEM2-HEM13.meme.txt
- HEM2-HEM14.fa
- HEM2-HEM14.meme.txt
- HEM2-HEM15.fa
- HEM2-HEM15.meme.txt
- HEM2-HEM3.fa
- HEM2-HEM3.meme.txt
- HEM2-HEM4.fa
- HEM2-HEM4.meme.txt
- HEM2.ups.fa_
- HEM2.ups.fa_.revcom
- HEM3-HEM12.fa
- HEM3-HEM12.meme.txt
- HEM3-HEM13.fa
- HEM3-HEM13.meme.txt
- HEM3-HEM14.fa
- HEM3-HEM14.meme.txt
- HEM3-HEM15.fa
- HEM3-HEM15.meme.txt
- HEM3-HEM4.fa
- HEM3-HEM4.meme.txt
- HEM3.ups.fa_
- HEM3.ups.fa_.revcom
- HEM4-HEM12.fa
- HEM4-HEM12.meme.txt
- HEM4-HEM13.fa
- HEM4-HEM13.meme.txt
- HEM4-HEM14.fa
- HEM4-HEM14.meme.txt
- HEM4-HEM15.fa
- HEM4-HEM15.meme.txt
- HEM4.ups.fa_
- HEM4.ups.fa_.revcom
- yeast.nc.1.freq
- mbsout_infile1
- mbsout_infile2
- mbsout_infile3
- bad_msout_infile1
- bad_msout_infile2
- msout_infile1
- msout_infile2
- msout_infile3
- msout_infile4
- out.PrositeScan
- seqdatabase.ini
- seqdatabase.ini
- test.gff3
- names.dmp
- nodes.dmp
- greengenes_taxonomy_16S_candiv_gg_2011_1.txt
- silva_SSURef_108_tax_silva_trunc.fasta
- 13-pilE-F.scf
- 1ZZ19XR301R-Alignment.tblastn
- 2008.blasttable
- 503384.MEGABLAST.0
- 503384.MEGABLAST.2
- 5X_1895.FASTXY
- a_thaliana.blastn
- AAC12660.fa
- AB077698.gb
- acefile.ace.1
- acefile.singlets
- adh.mb_tree.nexus
- AE003528_ecoli.bls
- AE003644_Adh-genomic.gb
- AF032047.gbk
- AF165282.gb
- AF222649-rc.gbk
- AF305198.gb
- AHCYL1.kegg
- alleles.fas
- alnfile.fasta
- amino.fa
- amphora.newick
- AnnIX-v003.gbk
- ATF14F8.gbk
- atp1.matrix
- ay007676.gb
- AY095303S1.gbk
- ay116458.gb
- ay149291.gb
- AY763288.gb
- BAB68554.gb
- badfasta.fa
- barns-combined.nex
- basic-bush.nex
- basic-ladder.nex
- BC000007.gbk
- BEL16-LTR_AG.embl
- biorecipe.nhx
- Bird_Ovomucoids.nex
- BK000016-tpa.gbk
- bl2seq+.blastn
- bl2seq.blastn
- bl2seq.blastn.rev
- bl2seq.blastx.out
- bl2seq.bug940.out
- bl2seq.out
- bl2seq.tblastn.out
- bl2seq.tblastx.out
- blast.report
- blast_no_hit_desc.txt
- blast_plus.blastp
- blastp2215.blast
- blat.psLayout3
- BLOSUM50
- blosum62.bla
- BN000066-tpa.embl
- bootstrap.tre
- BOSS_DROME.FASTP_v35_04
- brassica_ATH.WUBLASTN
- bug1986.blast2
- bug1986.blastp
- bug2120.phd
- bug2246.blast
- bug2391.megablast
- bug2399.tblastn
- bug2453.maf
- bug2473.fasta
- bug2862.pmr
- bug2869.tree
- bug2901.fa
- bug2937.fasta
- bug2942.blastx
- bug2982.embl
- bug2982.gb
- bug3021.gmap
- bug3086.embl
- c200-vs-yeast.BLASTN
- c200-vs-yeast.BLASTN.m8
- calm.swiss
- catalase-webblast.BLASTP
- cds-266.fas
- cds_sample.embl
- chad100.scf
- char-interleave.nex
- char-matrix-spaces.nex
- cmsearch.multi.out
- cmsearch.nohit.out
- cmsearch_output.txt
- codeml45b.mlc
- component.ontology.test
- component.ontology.test2
- contig-by-hand.wublastp
- crab.dat.cn
- crab.nj
- crab.njb
- crypto.sim4-0
- crypto.sim4-3
- crypto.sim4-4
- cys1_dicdi.water
- cysprot.fa
- cysprot.msf
- cysprot.needle
- cysprot.tblastn
- cysprot.water
- cysprot1.fa
- cysprot1.FASTA
- cysprot1a.fa
- cysprot1a.msf
- cysprot1b.fa
- cysprot1b.msf
- cysprot1b.newick
- cysprot_vs_gadfly.FASTA
- D10483.gbk
- D12555.gbk
- dcr1_sp.WUBLASTP
- dmel_2Lchunk.gb
- dna2.fa
- dnaE-bsub-prot.fa
- dnaE-bsub.fa
- dnaEbsub_ecoli.wublastx
- dnaEbsub_ecoli.wutblastn
- dnaEbsub_ecoli.wutblastx
- DQ018368.gb
- dq519393.gb
- ECAPAH02.embl
- echofilter.wublastn
- ecoli-trna-qrna.out
- ecoli_domains.rpsblast
- ecolitst.bls
- ecolitst.noseqs.wublastp
- ecolitst.wublastp
- EG352462.gbxml
- empty.bl2seq
- ENr111.mfa.example.elems
- ex1.nucl.nhx
- example.vcf
- exonerate.output.dontwork
- exonerate.output.negativescore.works
- exonerate.output.works
- exonerate.whitespace_before_query.works
- expected.blast.out
- exsignalp.out
- fgenesh.out
- footprinter.out
- forward_primer.fa
- forward_reverse_primers.fa
- frac_problems.blast
- frac_problems2.blast
- frac_problems3.blast
- geneid_1.0.out
- genemark-fragment.out
- genemark.out
- genewise.out
- genewise_output.paracel_btk
- genomewise.out
- genomic-seq.epcr
- genomic-seq.fasta
- genomic-seq.genscan
- genomic-seq.mzef
- Genscan.FastA
- gf-s71.needle
- Glimmer2.out
- glimmer3-fragment.detail
- glimmer3-fragment.predict
- Glimmer3.detail
- Glimmer3.predict
- GlimmerHMM.out
- GlimmerM.out
- gmap_f9-multiple_results.txt
- gmap_f9-reverse-strand.txt
- gmap_f9.txt
- GO.defs.test
- GO.defs.test2
- headerless.psl
- hg16_chroms.gff
- HM138502.gbk
- hmmpfam.out
- hs_est.est2genome
- hs_fugu.newick
- hs_owlmonkey.aln
- hs_owlmonkey.fas
- hs_owlmonkey.fasta
- hsinsulin.blastcl3.blastn
- HUMBETGLOA.FASTA
- HUMBETGLOA.gff
- HUMBETGLOA.grail
- HUMBETGLOA.grailexp
- HUMBETGLOA.mzef
- HUMBETGLOA.tblastx
- humor.maf
- humts1.pal
- hybrid2.gff3
- ids-with-spaces.phy
- in.fasta
- insulin.water
- interpro.xml
- interpro_relationship.xml
- interpro_sample.xml
- interpro_short.xml
- intrablock-comment.nex
- issue255_ssearch.fasta
- KF527485.gbk
- Kingdoms_DNA.nex
- little.largemultifasta
- LOAD_Ccd1.dnd
- long-names.nex
- longnames.aln
- longnames.dnd
- lucy.info
- lucy.qual
- lucy.seq
- lucy.stderr
- lysozyme6.protml
- lysozyme6.simple.protml
- M12730.gb
- mast.dat
- masta.dat
- match.output
- Mcjanrna_rdbII.gbk
- megablast_output.paracel_btk
- meme.dat
- mini-AE001405.gb
- mini-align.aln
- mixedmast.dat
- MmCT
- mpath.ontology.test
- MSGEFTUA.gb
- multi.blast.m8
- multi.blast.m9
- multi.phd
- multi_1.fa
- multi_2.fa
- multi_blast.bls
- multifa.seq
- multifa.seq.qual
- multiline-intrablock-comment.nex
- multiresult_blastn+.bls
- multiseq.bls
- multiseq_tags.phd
- myco_sites.gff
- NC_000007-ribosomal-slippage.gb
- NC_001284.gbk
- NC_002058_multDBLINK_bug3375.gb
- NC_006346.gb
- NC_006511-short.gbk
- NC_008536.gb
- nei_gojobori_test.aln
- neighbor.dist
- new_blastn.txt
- nhx-bacteria.nhx
- no-genes.genscan
- no_cds_example.gb
- no_FH.embl
- no_hsps.blastp
- no_semicolon.newick
- noninterleaved.phy
- NT_021877.gbk
- nucmatrix.txt
- O_sat.wgs
- ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt
- P33897
- P35527.gb
- P39765.gb
- PAM250
- pep-266.aln
- phi.out
- phipsi.out
- phylipdist-36.out
- phylipdist.out
- pre_rel9.swiss
- Primate_mtDNA.nex
- primedseq.fa
- primer3_infile.txt
- primer3_outfile.txt
- primer3_output.txt
- prints.out
- promoterwise.out
- protpars.phy
- protpars_longid.phy
- pseudowise.out
- psi_xml.dat
- psiblastreport.out
- purine_v081.infernal
- puzzle.tre
- PX1CG.gb
- Q8GBD3.swiss
- qrna-relloc.out
- qualfile.qual
- quoted-strings1.nex
- quoted-strings2.nex
- Rab1.chaos-xml
- radical-whitespace.nex
- radical-whitespace_02.nex
- regulation_test.obo
- rel9.swiss
- repeatmasker.fa.out
- revcomp_mrna.gb
- ribosome-slippage.gb
- roa1.dat
- roa1.gbxml
- roa1.genbank
- roa1.swiss
- roa1_v2.dat
- rpsblast.bls
- rpsblast_no_hits.bls
- sbay_c127.fas
- sbay_c545-yeast.BLASTZ.PSL
- seg.out
- semicolon.newick
- seqdatabase.ini
- seqfile-no-desc.pir
- seqfile.pir
- seqs.fas
- short.blx
- signalp.hmm.short
- signalp.hmm.summary
- signalp.negative.out
- signalp.nn.short
- signalp.nn.summary
- signalp.positive.out
- signalp.short
- signalp.summary
- sim4.for.for
- sim4.for.rev
- sim4.rev
- singlescore.gbk
- so.obo
- sofa.ontology
- sp_subset.obo
- spaced_fasta.fa
- spaces.nex
- SPAN_Family4nl.nex
- SPAN_Family7n.nex
- SPAN_Family8a.nex
- sparsealn.needle
- spidey.noalignment
- spidey.test1
- sprintf.rnamotif
- sv40_small.xml
- swiss.dat
- swisspfam.data
- SwissProt.dat
- tab1part.mif
- tab2part.mif
- tab3part.mif
- tandem_repeats_finder.dat
- tandem_repeats_finder.noresults
- tandem_repeats_finder_no_desc.dat
- targetp.out
- tblastn.out
- test 2.txt
- test-1.tab
- test-1.tab.gb
- test-3.0-1.meme
- test-3.0-2.meme
- test-4.9.meme
- test.ace
- test.embl
- test.embl2sq
- test.fasta
- test.fastq
- test.gcg
- test.gcgblast
- test.gcgfasta
- test.genbank
- test.genbank.noseq
- test.infernal
- test.metafasta
- test.nh
- test.nhx
- test.phd
- test.pir
- test.raw
- test.swiss
- test.tab
- test.tigrxml
- test.tsv
- test.txt
- test.waba
- test1.blasttab3
- test1.wublastp
- test2.infernal
- test2.raw
- test_badlf.gcg
- test_clear_range.fastq
- test_data.axt
- test_space.embl
- testaln.arp
- testaln.clustalw
- testaln.fasta
- testaln.fastq
- testaln.list
- testaln.mase
- testaln.mega
- testaln.metafasta
- testaln.msf
- testaln.nexus
- testaln.pfam
- testaln.phylip
- testaln.po
- testaln.prodom
- testaln.psi
- testaln.selex
- testaln.stockholm
- testaln.xmfa
- testaln2.arp
- testaln2.fasta
- testdat.exonerate
- testdata.crossmatch
- testdbaccnums.out
- testfile.erpin
- testfuzzy.genbank
- tmhmm.out
- tmp.fst
- tol-2010-02-18.nhx
- traits.tab
- traittree.nexus
- transfac.dat
- tree_nonewline.nexus
- Treebase-chlamy-dna.nex
- tricky.wublast
- trna.strict.rnamotif
- U58726.gb
- U71225.gb
- U71225.gb.mac
- U71225.gb.unix
- U71225.gb.win
- U83300.bsml
- UnaSmithHIV-both.nex
- urease.tre.nexus
- version2.scf
- version3.scf
- wellcome_tol.nhx
- worm_fam_2785.cdna
- X98338_Adh-mRNA.gb
- yeast.tRNAscanSE
- YP_007988852.gp
- ZABJ4EA7014.CH878695.1.blast.txt
- Blast.t
- BlastTable.t
- Index.t
- greengenes.t
- silva.t
- Fasta.t
- Flat.t
- Qual.t
- Registry.t
- masta.t
- psm.t
- InstanceSite.t
- Matrix.t
- ProtMatrix.t
- ProtPsm.t
- SiteMatrix.t
- go.t
- interpro.t
- obo.t
- GOterm.t
- GraphAdaptor.t
- Ontology.t
- OntologyEngine.t
- OntologyStore.t
- Relationship.t
- RelationshipType.t
- Term.t
- SeqRead_fail.t
- Taxonomy.t
- Exception.t
- HTTPget.t
- IO.t
- RootI.t
- RootIO.t
- Storable.t
- Utilities.t
- GbrowseGFF.t
- HitTableWriter.t
- HSPTableWriter.t
- HTMLWriter.t
- TextWriter.t
- axt.t
- blast.t
- blast_pull.t
- blasttable.t
- CigarString.t
- cross_match.t
- erpin.t
- exonerate.t
- fasta.t
- gmap_f9.t
- infernal.t
- megablast.t
- psl.t
- rnamotif.t
- SearchIO.t
- sim4.t
- SimilarityPair.t
- Tiling.t
- waba.t
- wise.t
- DBLink.t
- EncodedSeq.t
- LargeLocatableSeq.t
- LargePSeq.t
- LocatableSeq.t
- MetaSeq.t
- PrimaryQual.t
- PrimarySeq.t
- PrimedSeq.t
- Quality.t
- Seq.t
- SimulatedRead.t
- Amplicon.t
- Clone.t
- Collection.t
- Computation.t
- FeaturePair.t
- Gene.t
- Generic.t
- Location.t
- LocationFactory.t
- Primer.t
- Range.t
- RangeI.t
- SeqAnalysisParser.t
- SubSeq.t
- Unflattener.t
- ace.t
- asciitree.t
- bsml.t
- bsml_sax.t
- embl.t
- fasta.t
- fastq.t
- gbxml.t
- gcg.t
- genbank.t
- Handler.t
- kegg.t
- largefasta.t
- mbsout.t
- metafasta.t
- msout.t
- MultiFile.t
- Multiple_fasta.t
- phd.t
- pir.t
- qual.t
- raw.t
- scf.t
- SeqBuilder.t
- SeqIO.t
- Splicedseq.t
- swiss.t
- tab.t
- table.t
- tigr.t
- tigrxml.t
- Backtranslate.t
- CodonTable.t
- ECnumber.t
- GuessSeqFormat.t
- OddCodes.t
- SeqPattern.t
- SeqStats.t
- SeqUtils.t
- SeqWords.t
- Consed.t
- Palindrome.t
- ProtDist.t
- Gerp.t
- Molphy.t
- ExtendedSignalp.t
- Spidey.t
- AmpliconSearch.t
- ePCR.t
- Est2Genome.t
- FootPrinter.t
- Geneid.t
- Genewise.t
- Genomewise.t
- Genpred.t
- GFF.t
- IUPAC.t
- Lucy.t
- Match.t
- pICalculator.t
- Primer3.t
- Promoterwise.t
- PrositeScan.t
- Pseudowise.t
- QRNA.t
- RandDistFunctions.t
- RepeatMasker.t
- Seg.t
- Sigcleave.t
- Signalp.t
- Sim4.t
- TandemRepeatsFinder.t
- TargetP.t
- Tmhmm.t
- tRNAscanSE.t
- lintree.t
- newick.t
- nexus.t
- nhx.t
- tabtree.t
- Compatible.t
- Node.t
- RandomTreeFactory.t
- Tree.t
- TreeIO.t
- TreeStatistics.t
- Species.t
- .gitignore
- AUTHORS
- Changes
- CODE_OF_CONDUCT.md
- dist.ini
- HACKING.md
- README.md
// repository documentation
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