Clone Cross Reference Table

Back to Main Report

Clones for: Bio/Align/AlignInfo.py

Line Range
81-87
90-105
137-143
146-161

Clones for: Bio/Align/Applications/_Clustalw.py

Line Range
27-27
33-33
39-39
64-66
94-94
119-121
125-127
138-140
151-154
158-161
165-168
172-175
187-191
195-198
202-205
209-212
217-217
223-225
229-233
237-240
244-247
251-254
261-264
277-280
284-287
311-311
317-317
323-325
329-331
353-356
360-363
367-370
374-377
381-383
387-389
393-395
399-401
413-415

Clones for: Bio/Align/Applications/_Dialign.py

Line Range
160-161

Clones for: Bio/Align/Applications/_Mafft.py

Line Range
81-84
88-91
94-97
139-142
151-154
158-161
165-168
172-175
179-182
186-189
193-197
202-203

Clones for: Bio/Align/Applications/_Muscle.py

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38-38
41-41
48-48
52-52
57-58
64-65
70-71
78-79
84-85
92-93
102-103
113-114
120-121
128-129
136-137
143-143
149-149
158-162
172-173
179-180
187-188
195-196
203-207
222-223
228-229
237-238
245-246
253-254
260-261
272-273
291-292
314-315

Clones for: Bio/Align/Applications/_Prank.py

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84-88
90-94
96-97
101-102
126-130
145-146
152-153
162-163
167-168
173-174
179-180

Clones for: Bio/Align/Applications/_Probcons.py

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31-32
36-37
41-42
57-57
64-64

Clones for: Bio/Align/Applications/_TCoffee.py

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68-70
74-76

Clones for: Bio/Align/Generic.py

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119-170

Clones for: Bio/AlignAce/Applications.py

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7-37
45-55

Clones for: Bio/AlignAce/Motif.py

Line Range
48-62
89-94
175-180
190-196
218-272

Clones for: Bio/AlignAce/Parser.py

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16-78
91-105

Clones for: Bio/AlignAce/Scanner.py

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9-83

Clones for: Bio/AlignIO/__init__.py

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178-184
312-319
391-401
422-426
431-435
445-462

Clones for: Bio/AlignIO/ClustalIO.py

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142-150
218-226
245-250
342-347
356-361

Clones for: Bio/AlignIO/EmbossIO.py

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169-169
177-177
203-208
582-584
588-590
603-605
612-614

Clones for: Bio/AlignIO/FastaIO.py

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143-148
170-175
184-185
191-192
250-267
270-285

Clones for: Bio/AlignIO/Interfaces.py

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95-98

Clones for: Bio/AlignIO/NexusIO.py

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140-162
163-191

Clones for: Bio/AlignIO/PhylipIO.py

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310-314
316-320
363-367
379-383
395-398

Clones for: Bio/AlignIO/StockholmIO.py

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242-246
256-260
421-426
533-551

Clones for: Bio/Alphabet/Reduced.py

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54-54
79-79
105-105

Clones for: Bio/Application/__init__.py

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37-37

Clones for: Bio/Blast/Applications.py

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18-20
44-44
60-60
98-100
195-195
197-197
199-199
201-201
203-203
233-237
239-239

Clones for: Bio/Blast/NCBIStandalone.py

Line Range
176-178
182-184
194-196
199-201
204-206
209-211
692-694
703-708
713-717
752-765
766-779
1095-1099
1102-1106
1213-1215
1218-1220
1245-1245
1249-1255
1257-1263
1265-1271
1273-1279
1281-1283
1287-1289
1292-1294
1298-1300
1304-1306
1309-1311
1314-1316
1319-1321
1331-1333
1337-1339
1343-1345
1350-1350
1376-1379
1382-1385
1388-1391
1394-1397
1400-1403
1434-1439
1445-1464
1478-1483
1501-1520
1638-1643
1677-1682
1757-1762
1803-1808
1903-1908
1983-1983

Clones for: Bio/Blast/NCBIWWW.py

Line Range
178-182
185-189

Clones for: Bio/Blast/NCBIXML.py

Line Range
420-425
427-432
434-439
571-581
627-630
647-650
660-663

Clones for: Bio/Blast/Record.py

Line Range
168-168
173-173
177-177
185-185
353-357
370-374

Clones for: Bio/Clustalw/__init__.py

Line Range
131-131
497-514

Clones for: Bio/Cluster/__init__.py

Line Range
80-88
90-98
185-187
189-191

Clones for: Bio/Compass/__init__.py

Line Range
176-180
183-187
199-204
212-217
229-233

Clones for: Bio/Crystal/__init__.py

Line Range
171-176
178-183
229-235
237-243

Clones for: Bio/Data/CodonTable.py

Line Range
155-158
162-165
264-264
286-294
303-303
322-322
342-342
363-371
381-381
400-400
417-417
437-437
458-458
478-486
497-505
584-586
587-589
590-592
736-743
751-758
769-769
776-776

Clones for: Bio/Data/IUPACData.py

Line Range
26-38
44-56
62-62
81-81
172-177

Clones for: Bio/DocSQL.py

Line Range
201-207

Clones for: Bio/Emboss/Applications.py

Line Range
215-217
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297-299
347-349
385-387
416-418
453-455
476-478
507-509
547-549
591-593
626-628
665-667
682-707
708-733
739-741
757-759
803-805
825-827
846-848
867-869
883-885

Clones for: Bio/Emboss/Primer3.py

Line Range
77-85
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97-105

Clones for: Bio/Encodings/IUPACEncoding.py

Line Range
14-23
27-36
44-51
54-61
70-73
86-93
96-99
102-105
109-116
119-126

Clones for: Bio/Entrez/__init__.py

Line Range
136-154
157-178
181-196
199-214
217-238
256-260
263-267

Clones for: Bio/Entrez/Parser.py

Line Range
84-89
96-101
238-240
250-252

Clones for: Bio/Enzyme/__init__.py

Line Range
61-85
98-104
171-206

Clones for: Bio/ExPASy/__init__.py

Line Range
26-51
54-76
90-97
109-116

Clones for: Bio/ExPASy/Enzyme.py

Line Range
23-49

Clones for: Bio/ExPASy/Prodoc.py

Line Range
55-85

Clones for: Bio/ExPASy/Prosite.py

Line Range
25-50
53-142
180-211
211-248
252-269

Clones for: Bio/Fasta/__init__.py

Line Range
151-155
183-187

Clones for: Bio/FSSP/__init__.py

Line Range
95-100
102-107

Clones for: Bio/FSSP/FSSPTools.py

Line Range
67-74
85-92

Clones for: Bio/GA/Crossover/Point.py

Line Range
1-28

Clones for: Bio/GA/Crossover/TwoPoint.py

Line Range
1-34

Clones for: Bio/GenBank/__init__.py

Line Range
497-502
774-777
1342-1372

Clones for: Bio/GenBank/LocationParser.py

Line Range
128-132
134-138
149-153
162-166
200-206
209-215

Clones for: Bio/GenBank/Record.py

Line Range
356-362
389-396
547-553
556-562
565-571
574-580
601-607

Clones for: Bio/GenBank/Scanner.py

Line Range
525-529
537-542
747-751
761-766
825-837
849-850
874-887
894-906
917-918
1114-1118
1119-1123
1485-1486
1490-1491
1495-1496
1500-1501
1516-1517

Clones for: Bio/GFF/__init__.py

Line Range
407-413

Clones for: Bio/GFF/binning.py

Line Range
66-72

Clones for: Bio/GFF/easy.py

Line Range
65-69
327-331
586-592

Clones for: Bio/GFF/GenericTools.py

Line Range
151-157

Clones for: Bio/Graphics/BasicChromosome.py

Line Range
115-120
144-151

Clones for: Bio/Graphics/Comparative.py

Line Range
65-70
78-85

Clones for: Bio/Graphics/Distribution.py

Line Range
53-59
75-82

Clones for: Bio/Graphics/GenomeDiagram/_AbstractDrawer.py

Line Range
141-145
178-182
330-332

Clones for: Bio/Graphics/GenomeDiagram/_CircularDrawer.py

Line Range
168-170
221-226
240-253
258-261
281-314
318-336
340-359
443-446
455-458
470-489
505-517
522-526
560-571
607-626
649-664
684-717
750-757
803-812
941-945
957-957
960-960
991-995
1038-1040
1042-1044
1064-1064
1067-1091
1105-1131

Clones for: Bio/Graphics/GenomeDiagram/_Colors.py

Line Range
87-87
89-89
206-209
211-214

Clones for: Bio/Graphics/GenomeDiagram/_Diagram.py

Line Range
151-153
243-246
265-273
276-284
338-348
363-373
452-462

Clones for: Bio/Graphics/GenomeDiagram/_Feature.py

Line Range
169-174
177-182

Clones for: Bio/Graphics/GenomeDiagram/_FeatureSet.py

Line Range
152-155
235-252
286-292

Clones for: Bio/Graphics/GenomeDiagram/_Graph.py

Line Range
117-124
185-187

Clones for: Bio/Graphics/GenomeDiagram/_GraphSet.py

Line Range
115-122
159-169
181-183
187-204

Clones for: Bio/Graphics/GenomeDiagram/_LinearDrawer.py

Line Range
180-182
237-242
267-298
339-352
359-362
375-377
385-387
393-412
442-451
455-457
464-479
483-485
497-530
552-559
562-564
572-574
601-603
616-618
626-645
784-785
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801-808
811-818
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877-881
898-900
903-905
914-934
957-961
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1005-1016
1048-1049
1065-1067

Clones for: Bio/Graphics/GenomeDiagram/_Track.py

Line Range
321-331
334-351
386-391

Clones for: Bio/HMM/DynamicProgramming.py

Line Range
75-83
141-149

Clones for: Bio/HMM/MarkovModel.py

Line Range
49-61
64-76
111-112
116-117
213-222
225-240
245-254
257-272

Clones for: Bio/KDTree/KDTree.py

Line Range
41-45
48-52

Clones for: Bio/KEGG/Compound/__init__.py

Line Range
23-28
88-92
105-109
112-116
143-149
166-177
181-192
194-211

Clones for: Bio/KEGG/Enzyme/__init__.py

Line Range
27-32
142-146
149-153
156-160
163-167
204-210
220-231
264-275
296-313

Clones for: Bio/MarkovModel.py

Line Range
76-79
83-86
101-103
105-107
136-154
184-186
188-190
324-335
340-351
375-393
428-428
440-440
521-521
586-592

Clones for: Bio/MaxEntropy.py

Line Range
225-227
273-286

Clones for: Bio/MEME/Motif.py

Line Range
146-154
182-186
189-193
216-237

Clones for: Bio/MEME/Parser.py

Line Range
13-127
131-171
201-204
207-210
218-451
451-630

Clones for: Bio/Motif/__init__.py

Line Range
122-132
137-154

Clones for: Bio/Motif/_Motif.py

Line Range
65-79
170-175
224-232
263-270
350-355
365-371
612-664
717-719
724-726

Clones for: Bio/Motif/Applications/_AlignAce.py

Line Range
30-60
65-75

Clones for: Bio/Motif/Parsers/AlignAce.py

Line Range
16-78
79-153
166-180

Clones for: Bio/Motif/Parsers/MEME.py

Line Range
47-55
78-99
103-217
221-261
302-535
535-712

Clones for: Bio/NaiveBayes.py

Line Range
128-130
200-213

Clones for: Bio/Ndb/__init__.py

Line Range
64-70
70-77
239-244
246-251

Clones for: Bio/NetCatch.py

Line Range
172-177
186-191
193-206
208-221

Clones for: Bio/NeuralNetwork/BackPropagation/Layer.py

Line Range
74-93
127-142
164-182
193-198
219-235
283-288

Clones for: Bio/NeuralNetwork/Gene/Motif.py

Line Range
196-208

Clones for: Bio/NeuralNetwork/Gene/Schema.py

Line Range
293-300
353-360

Clones for: Bio/NeuralNetwork/Gene/Signature.py

Line Range
202-214

Clones for: Bio/Nexus/Nexus.py

Line Range
727-729
731-733
791-797
909-915
975-999
1019-1042
1223-1223
1229-1229
1439-1444
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Clones for: Bio/Nexus/Trees.py

Line Range
386-388
389-391

Clones for: Bio/NMR/xpktools.py

Line Range
107-109
109-111
111-113
115-121
124-130

Clones for: Bio/pairwise2.py

Line Range
215-218
222-225
325-328
334-337
342-345
408-411
417-421
426-430
501-513
517-529
676-681
685-690
805-811

Clones for: Bio/Parsers/spark.py

Line Range
465-469
489-493

Clones for: Bio/Pathway/Rep/Graph.py

Line Range
37-38
43-57
60-63
67-70
77-78
84-112
116-135

Clones for: Bio/Pathway/Rep/MultiGraph.py

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40-54
57-60
63-66
79-107
111-130
146-154
172-180

Clones for: Bio/PDB/DSSP.py

Line Range
205-211

Clones for: Bio/PDB/HSExposure.py

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77-81
289-292

Clones for: Bio/PDB/NACCESS.py

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76-78
103-105
117-124
147-154
179-183

Clones for: Bio/PDB/parse_pdb_header.py

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160-165
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179-190
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208-213
225-226

Clones for: Bio/PDB/PDBParser.py

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182-186
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200-203
219-222

Clones for: Bio/PDB/Polypeptide.py

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394-398
408-412

Clones for: Bio/PDB/Residue.py

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34-37
125-128

Clones for: Bio/PDB/Vector.py

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42-44
46-48

Clones for: Bio/PopGen/FDist/__init__.py

Line Range
70-81

Clones for: Bio/PopGen/GenePop/__init__.py

Line Range
159-170

Clones for: Bio/PopGen/GenePop/Controller.py

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296-297
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361-369
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529-535
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Clones for: Bio/PopGen/GenePop/EasyController.py

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71-79
82-88

Clones for: Bio/PropertyManager.py

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37-60
63-78

Clones for: Bio/Prosite/__init__.py

Line Range
98-187
228-255
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355-358
388-395
499-530
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Clones for: Bio/Prosite/Pattern.py

Line Range
64-69
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167-173
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Clones for: Bio/Prosite/Prodoc.py

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61-68
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Clones for: Bio/PubMed.py

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62-92

Clones for: Bio/Restriction/_Update/RestrictionCompiler.py

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63-64
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Clones for: Bio/Restriction/_Update/Update.py

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67-71

Clones for: Bio/Restriction/PrintFormat.py

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332-336
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Clones for: Bio/Restriction/Restriction.py

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95-96
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Clones for: Bio/Restriction/Restriction_Dictionary.py

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