Files Analyzed for Clones

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Common Path Prefix: S:/SourceCodeBases/Python/v2_6/BioPython/Source/biopython-1.52/


Total number of files: 346

File
Number
Clone
Ratio
Source
Lines
File Name
10.0%352setup.py
20.0%35Bio/distance.py
33.38%207Bio/DocSQL.py
40.0%78Bio/EZRetrieve.py
50.0%188Bio/File.py
60.0%158Bio/FilteredReader.py
70.0%77Bio/HotRand.py
80.0%142Bio/Index.py
90.0%128Bio/kNN.py
100.0%158Bio/listfns.py
110.0%136Bio/LogisticRegression.py
1216.6%591Bio/MarkovModel.py
130.0%100Bio/mathfns.py
148.67%323Bio/MaxEntropy.py
1512.2%230Bio/NaiveBayes.py
1617.9%223Bio/NetCatch.py
1712.0%811Bio/pairwise2.py
180.0%426Bio/ParserSupport.py
1948.2%83Bio/PropertyManager.py
209.58%313Bio/PubMed.py
210.0%153Bio/Search.py
2227.1%1704Bio/Seq.py
2325.2%493Bio/SeqFeature.py
247.36%693Bio/SeqRecord.py
250.0%90Bio/stringfns.py
260.0%44Bio/Transcribe.py
2711.2%143Bio/Translate.py
280.0%92Bio/triefind.py
2934.4%163Bio/utils.py
300.0%17Bio/__init__.py
310.0%269Bio/Affy/CelFile.py
320.0%2Bio/Affy/__init__.py
336.72%744Bio/Align/AlignInfo.py
340.0%65Bio/Align/FormatConvert.py
3512.3%422Bio/Align/Generic.py
360.0%2Bio/Align/__init__.py
3756.8%438Bio/Align/Applications/_Clustalw.py
382.92%171Bio/Align/Applications/_Dialign.py
3917.3%283Bio/Align/Applications/_Mafft.py
4034.1%440Bio/Align/Applications/_Muscle.py
4127.2%195Bio/Align/Applications/_Prank.py
4232.9%76Bio/Align/Applications/_Probcons.py
4313.6%88Bio/Align/Applications/_TCoffee.py
440.0%12Bio/Align/Applications/__init__.py
450.0%69Bio/AlignAce/AlignAceStandalone.py
4674.6%59Bio/AlignAce/Applications.py
470.0%43Bio/AlignAce/CompareAceStandalone.py
4832.1%274Bio/AlignAce/Motif.py
4973.1%104Bio/AlignAce/Parser.py
5090.2%82Bio/AlignAce/Scanner.py
510.0%26Bio/AlignAce/__init__.py
527.36%462Bio/AlignIO/ClustalIO.py
533.24%618Bio/AlignIO/EmbossIO.py
547.21%721Bio/AlignIO/FastaIO.py
552.04%147Bio/AlignIO/Interfaces.py
5625.1%207Bio/AlignIO/NexusIO.py
575.93%405Bio/AlignIO/PhylipIO.py
587.25%552Bio/AlignIO/StockholmIO.py
5913.0%463Bio/AlignIO/__init__.py
600.0%127Bio/Alphabet/IUPAC.py
6133.1%181Bio/Alphabet/Reduced.py
620.0%255Bio/Alphabet/__init__.py
630.965%518Bio/Application/__init__.py
6412.1%247Bio/Blast/Applications.py
6513.6%2089Bio/Blast/NCBIStandalone.py
664.59%218Bio/Blast/NCBIWWW.py
676.35%709Bio/Blast/NCBIXML.py
680.0%103Bio/Blast/ParseBlastTable.py
696.95%374Bio/Blast/Record.py
700.0%6Bio/Blast/__init__.py
710.0%119Bio/CAPS/__init__.py
724.66%515Bio/Clustalw/__init__.py
734.40%636Bio/Cluster/__init__.py
7411.9%260Bio/Compass/__init__.py
759.42%276Bio/Crystal/__init__.py
7628.8%805Bio/Data/CodonTable.py
7731.6%209Bio/Data/IUPACData.py
780.0%3Bio/Data/__init__.py
7913.5%949Bio/Emboss/Applications.py
8026.8%112Bio/Emboss/Primer3.py
810.0%69Bio/Emboss/PrimerSearch.py
820.0%2Bio/Emboss/__init__.py
8359.5%126Bio/Encodings/IUPACEncoding.py
840.0%3Bio/Encodings/__init__.py
855.87%341Bio/Entrez/Parser.py
8630.7%358Bio/Entrez/__init__.py
8728.3%251Bio/Enzyme/__init__.py
8818.9%148Bio/ExPASy/Enzyme.py
8917.5%171Bio/ExPASy/Prodoc.py
9070.5%292Bio/ExPASy/Prosite.py
910.0%111Bio/ExPASy/ScanProsite.py
9246.9%143Bio/ExPASy/__init__.py
930.0%85Bio/Fasta/FastaAlign.py
944.93%203Bio/Fasta/__init__.py
9517.2%93Bio/FSSP/FSSPTools.py
960.0%34Bio/FSSP/fssp_rec.py
975.24%267Bio/FSSP/__init__.py
980.0%71Bio/GA/Evolver.py
990.0%144Bio/GA/Organism.py
1000.0%2Bio/GA/__init__.py
1010.0%60Bio/GA/Crossover/General.py
1020.0%177Bio/GA/Crossover/GeneralPoint.py
103100.0%27Bio/GA/Crossover/Point.py
104100.0%33Bio/GA/Crossover/TwoPoint.py
1050.0%59Bio/GA/Crossover/Uniform.py
1060.0%1Bio/GA/Crossover/__init__.py
1070.0%44Bio/GA/Mutation/General.py
1080.0%88Bio/GA/Mutation/Simple.py
1090.0%1Bio/GA/Mutation/__init__.py
1100.0%59Bio/GA/Repair/Stabilizing.py
1110.0%1Bio/GA/Repair/__init__.py
1120.0%59Bio/GA/Selection/Abstract.py
1130.0%98Bio/GA/Selection/Diversity.py
1140.0%125Bio/GA/Selection/RouletteWheel.py
1150.0%82Bio/GA/Selection/Tournament.py
1160.0%1Bio/GA/Selection/__init__.py
11712.4%322Bio/GenBank/LocationParser.py
1188.77%650Bio/GenBank/Record.py
1196.25%1519Bio/GenBank/Scanner.py
1200.0%48Bio/GenBank/utils.py
1212.81%1458Bio/GenBank/__init__.py
1220.0%89Bio/Geo/Record.py
1230.0%59Bio/Geo/__init__.py
1249.72%72Bio/GFF/binning.py
1253.21%592Bio/GFF/easy.py
1264.46%157Bio/GFF/GenericTools.py
1271.69%413Bio/GFF/__init__.py
1283.27%459Bio/Graphics/BasicChromosome.py
1299.15%164Bio/Graphics/Comparative.py
1300.0%184Bio/Graphics/DisplayRepresentation.py
1316.53%245Bio/Graphics/Distribution.py
1320.0%79Bio/Graphics/__init__.py
1333.01%498Bio/Graphics/GenomeDiagram/_AbstractDrawer.py
13430.4%1132Bio/Graphics/GenomeDiagram/_CircularDrawer.py
1355.50%218Bio/Graphics/GenomeDiagram/_Colors.py
13612.2%485Bio/Graphics/GenomeDiagram/_Diagram.py
1375.58%251Bio/Graphics/GenomeDiagram/_Feature.py
1389.15%306Bio/Graphics/GenomeDiagram/_FeatureSet.py
1394.27%281Bio/Graphics/GenomeDiagram/_Graph.py
14015.8%247Bio/Graphics/GenomeDiagram/_GraphSet.py
14131.3%1091Bio/Graphics/GenomeDiagram/_LinearDrawer.py
1427.91%417Bio/Graphics/GenomeDiagram/_Track.py
1430.0%23Bio/Graphics/GenomeDiagram/__init__.py
1446.1%328Bio/HMM/DynamicProgramming.py
14518.6%484Bio/HMM/MarkovModel.py
1460.0%429Bio/HMM/Trainer.py
1470.0%58Bio/HMM/Utilities.py
1480.0%2Bio/HMM/__init__.py
1490.0%269Bio/InterPro/__init__.py
1504.55%264Bio/KDTree/KDTree.py
1510.0%10Bio/KDTree/__init__.py
1520.0%82Bio/KEGG/__init__.py
15336.3%212Bio/KEGG/Compound/__init__.py
15426.8%314Bio/KEGG/Enzyme/__init__.py
1550.0%48Bio/KEGG/Map/__init__.py
1560.0%223Bio/Medline/__init__.py
15715.9%264Bio/MEME/Motif.py
15891.6%629Bio/MEME/Parser.py
1590.0%22Bio/MEME/__init__.py
1600.0%92Bio/Motif/Thresholds.py
16114.1%774Bio/Motif/_Motif.py
16220.5%156Bio/Motif/__init__.py
16357.9%76Bio/Motif/Applications/_AlignAce.py
1640.0%8Bio/Motif/Applications/__init__.py
16583.8%179Bio/Motif/Parsers/AlignAce.py
16683.8%711Bio/Motif/Parsers/MEME.py
1670.0%0Bio/Motif/Parsers/__init__.py
1688.11%296Bio/Ndb/__init__.py
1690.0%70Bio/NeuralNetwork/StopTraining.py
1700.0%89Bio/NeuralNetwork/Training.py
1710.0%1Bio/NeuralNetwork/__init__.py
17227.7%325Bio/NeuralNetwork/BackPropagation/Layer.py
1730.0%111Bio/NeuralNetwork/BackPropagation/Network.py
1740.0%1Bio/NeuralNetwork/BackPropagation/__init__.py
1756.60%212Bio/NeuralNetwork/Gene/Motif.py
1760.0%253Bio/NeuralNetwork/Gene/Pattern.py
1772.5%721Bio/NeuralNetwork/Gene/Schema.py
1786.42%218Bio/NeuralNetwork/Gene/Signature.py
1790.0%1Bio/NeuralNetwork/Gene/__init__.py
1805.14%1732Bio/Nexus/Nexus.py
1810.0%172Bio/Nexus/Nodes.py
1820.708%848Bio/Nexus/Trees.py
1830.0%5Bio/Nexus/__init__.py
1840.0%72Bio/NMR/NOEtools.py
1859.40%234Bio/NMR/xpktools.py
1860.0%6Bio/NMR/__init__.py
1872.12%565Bio/Parsers/spark.py
1880.0%2Bio/Parsers/__init__.py
1890.0%309Bio/Pathway/__init__.py
19052.7%146Bio/Pathway/Rep/Graph.py
1910.0%99Bio/Pathway/Rep/HashSet.py
19247.6%191Bio/Pathway/Rep/MultiGraph.py
1930.0%8Bio/Pathway/Rep/__init__.py
1940.0%113Bio/PDB/AbstractPropertyMap.py
1950.0%278Bio/PDB/Atom.py
1960.0%122Bio/PDB/Chain.py
1970.0%80Bio/PDB/Dice.py
1983.56%225Bio/PDB/DSSP.py
1990.0%231Bio/PDB/Entity.py
2000.0%323Bio/PDB/FragmentMapper.py
2013.21%343Bio/PDB/HSExposure.py
2020.0%151Bio/PDB/MMCIF2Dict.py
2030.0%147Bio/PDB/MMCIFParser.py
2040.0%67Bio/PDB/Model.py
20515.0%187Bio/PDB/NACCESS.py
2060.0%144Bio/PDB/NeighborSearch.py
20716.6%271Bio/PDB/parse_pdb_header.py
2080.0%18Bio/PDB/PDBExceptions.py
2090.0%188Bio/PDB/PDBIO.py
2100.0%376Bio/PDB/PDBList.py
2118.24%279Bio/PDB/PDBParser.py
2122.88%416Bio/PDB/Polypeptide.py
2130.0%94Bio/PDB/PSEA.py
2145.99%167Bio/PDB/Residue.py
2150.0%166Bio/PDB/ResidueDepth.py
2160.0%78Bio/PDB/Selection.py
2170.0%57Bio/PDB/Structure.py
2180.0%133Bio/PDB/StructureAlignment.py
2190.0%257Bio/PDB/StructureBuilder.py
2200.0%88Bio/PDB/Superimposer.py
2212.11%379Bio/PDB/Vector.py
2220.0%74Bio/PDB/__init__.py
2230.0%0Bio/PDB/mmCIF/__init__.py
2240.0%8Bio/PopGen/__init__.py
2250.0%66Bio/PopGen/Async/Local.py
2260.0%113Bio/PopGen/Async/__init__.py
2270.0%168Bio/PopGen/FDist/Async.py
2280.0%246Bio/PopGen/FDist/Controller.py
2290.0%69Bio/PopGen/FDist/Utils.py
2307.33%150Bio/PopGen/FDist/__init__.py
23117.7%891Bio/PopGen/GenePop/Controller.py
23210.4%173Bio/PopGen/GenePop/EasyController.py
2330.0%18Bio/PopGen/GenePop/Utils.py
2343.75%293Bio/PopGen/GenePop/__init__.py
2350.0%36Bio/PopGen/SimCoal/Async.py
2360.0%90Bio/PopGen/SimCoal/Cache.py
2370.0%61Bio/PopGen/SimCoal/Controller.py
2380.0%221Bio/PopGen/SimCoal/Template.py
2390.0%19Bio/PopGen/SimCoal/__init__.py
2407.69%494Bio/Prosite/Pattern.py
24134.1%331Bio/Prosite/Prodoc.py
24240.1%738Bio/Prosite/__init__.py
2435.33%413Bio/Restriction/PrintFormat.py
2440.0%86Bio/Restriction/RanaConfig.py
24528.9%2376Bio/Restriction/Restriction.py
24647.4%14498Bio/Restriction/Restriction_Dictionary.py
2470.0%195Bio/Restriction/__init__.py
2484.35%942Bio/Restriction/_Update/RestrictionCompiler.py
2494.31%116Bio/Restriction/_Update/Update.py
2500.0%0Bio/Restriction/_Update/__init__.py
2519.38%128Bio/SCOP/Cla.py
2528.99%89Bio/SCOP/Des.py
2530.0%122Bio/SCOP/Dom.py
2540.0%74Bio/SCOP/FileIndex.py
2550.0%101Bio/SCOP/Hie.py
2565.62%356Bio/SCOP/Raf.py
2570.0%95Bio/SCOP/Residues.py
2585.60%910Bio/SCOP/__init__.py
25915.5%129Bio/SeqIO/AceIO.py
26034.8%210Bio/SeqIO/FastaIO.py
2610.0%97Bio/SeqIO/IgIO.py
2628.33%612Bio/SeqIO/InsdcIO.py
2631.1%273Bio/SeqIO/Interfaces.py
26411.8%169Bio/SeqIO/PhdIO.py
2650.0%182Bio/SeqIO/PirIO.py
26616.5%1763Bio/SeqIO/QualityIO.py
2670.0%111Bio/SeqIO/SwissIO.py
2680.0%109Bio/SeqIO/TabIO.py
26934.8%299Bio/SeqIO/_convert.py
2709.76%461Bio/SeqIO/_index.py
2715.72%874Bio/SeqIO/__init__.py
27211.0%517Bio/Sequencing/Ace.py
2730.0%139Bio/Sequencing/Phd.py
2740.0%6Bio/Sequencing/__init__.py
27556.4%156Bio/Sequencing/Applications/_Novoalign.py
2760.0%3Bio/Sequencing/Applications/__init__.py
2770.0%124Bio/SeqUtils/CheckSum.py
2780.0%153Bio/SeqUtils/CodonUsage.py
2790.0%14Bio/SeqUtils/CodonUsageIndices.py
2807.02%114Bio/SeqUtils/IsoelectricPoint.py
28150.0%162Bio/SeqUtils/lcc.py
28233.3%156Bio/SeqUtils/MeltingTemp.py
2830.0%251Bio/SeqUtils/ProtParam.py
28414.0%565Bio/SeqUtils/__init__.py
2850.0%102Bio/Statistics/lowess.py
2860.0%1Bio/Statistics/__init__.py
2870.0%94Bio/SubsMat/FreqTable.py
28823.3%2624Bio/SubsMat/MatrixInfo.py
2891.96%715Bio/SubsMat/__init__.py
2900.0%160Bio/SVDSuperimposer/SVDSuperimposer.py
2910.0%8Bio/SVDSuperimposer/__init__.py
2920.0%72Bio/SwissProt/KeyWList.py
29332.6%1227Bio/SwissProt/SProt.py
29436.0%553Bio/SwissProt/__init__.py
29523.7%619Bio/UniGene/__init__.py
2966.11%131Bio/Wise/dnal.py
2975.67%141Bio/Wise/psw.py
2986.15%130Bio/Wise/__init__.py
2990.0%32Bio/WWW/__init__.py
3000.962%520BioSQL/BioSeq.py
30113.9%505BioSQL/BioSeqDatabase.py
30228.4%109BioSQL/DBUtils.py
3035.73%1064BioSQL/Loader.py
3040.0%15BioSQL/__init__.py
3050.0%63Doc/examples/clustal_run.py
30614.5%55Doc/examples/fasta_dictionary.py
3070.0%60Doc/examples/fasta_iterator.py
30824.6%268Doc/examples/getgene.py
3095.77%52Doc/examples/local_blast.py
3100.0%32Doc/examples/make_subsmat.py
3110.0%25Doc/examples/pubmed_search.py
3120.0%34Doc/examples/query_entrez.py
3130.0%20Doc/examples/swissprot.py
3145.66%53Doc/examples/www_blast.py
3150.0%169Doc/examples/nmr/simplepredict.py
3160.0%77Scripts/query_pubmed.py
3170.0%178Scripts/scop_pdb.py
3182.04%245Scripts/debug/debug_blast_parser.py
3196.67%75Scripts/debug/test_db_registry.py
3200.0%87Scripts/GenBank/check_output.py
3219.09%55Scripts/GenBank/check_output_simple.py
3228.62%58Scripts/GenBank/find_parser_problems.py
3230.0%45Scripts/Index/indexing_ex.py
32414.3%84Scripts/Performance/biocorba_performance_client.py
3250.0%68Scripts/Performance/biocorba_sql_server.py
3260.0%33Scripts/Performance/biosql_performanace_load.py
32726.7%45Scripts/Performance/biosql_performance_read.py
32865.4%26Scripts/Registry/biocorba_db_ex.py
32954.8%31Scripts/Registry/biosql_db_ex.py
33065.4%26Scripts/Registry/indexed_db_ex.py
3310.0%27Scripts/Registry/register_db_ex.py
3320.0%20Scripts/Registry/use_cgi_db.py
33325.0%48Scripts/Restriction/ranacompiler.py
33435.1%37Scripts/Restriction/rebase_update.py
33537.1%275Scripts/SeqGui/SeqGui.py
33613.0%285Scripts/xbbtools/nextorf.py
3370.0%28Scripts/xbbtools/xbbtools.py
3386.21%161Scripts/xbbtools/xbb_blast.py
3390.0%88Scripts/xbbtools/xbb_blastbg.py
34014.7%68Scripts/xbbtools/xbb_help.py
3410.0%33Scripts/xbbtools/xbb_io.py
3420.0%171Scripts/xbbtools/xbb_search.py
3430.0%21Scripts/xbbtools/xbb_sequence.py
34416.0%125Scripts/xbbtools/xbb_translations.py
3450.0%40Scripts/xbbtools/xbb_utils.py
34613.7%512Scripts/xbbtools/xbb_widget.py