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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/TreeIO/tabtree.pm
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Bio/TreeIO/TreeEventBuilder.pm
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doc/Deobfuscator/cgi-bin/deob_help.html
867
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doc/Deobfuscator/cgi-bin/deob_interface.cgi
868
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doc/Deobfuscator/Changes
 
869
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869
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doc/Deobfuscator/lib/Deobfuscator.pm
870
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doc/Deobfuscator/LICENSE
871
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doc/Deobfuscator/Makefile.PL
884
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examples/biblio/biblio-soap-example.pl
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examples/biblio/biblio_soap.pl
886
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examples/Bio-DB-GFF/load_ucsc.pl
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examples/biographics/all_glyphs.pl
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examples/biographics/dynamic_glyphs.pl
889
 
examples/biographics/feature_data.gff
890
 
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891
 
examples/biographics/lots_of_glyphs.pl
892
 
examples/biographics/render_sequence.pl
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examples/bioperl.pl
894
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examples/cluster/dbsnp.pl
895
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examples/contributed/nmrpdb_parse.pl
907
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examples/longorf.pl
908
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examples/make_primers.pl
909
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examples/popgen/parse_calc_stats.pl
 
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910
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examples/rev_and_trans.pl
911
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examples/revcom_dir.pl
912
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examples/root/exceptions1.pl
942
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943
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944
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examples/tools/psw.pl
 
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945
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946
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947
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maintenance/dependencies.pl
 
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961
 
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962
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963
 
Makefile.PL
964
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MANIFEST                        This list of files
965
 
META.yml
966
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models/biblio.dia
967
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models/bio_liveseq_variation.dia
968
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models/bio_map.dia
974
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975
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976
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977
 
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978
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PLATFORMS
979
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README
980
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981
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982
 
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983
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984
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1009
 
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1010
 
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1011
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1012
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1025
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1026
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1027
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1028
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1029
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1030
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1049
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1050
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1041
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1051
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1052
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1053
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1067
 
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1068
 
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1069
 
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1057
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1058
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1075
 
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1077
 
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1078
 
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1079
 
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1080
 
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1081
 
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1082
 
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1083
 
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1084
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1086
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1087
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1088
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1089
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1090
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1143
 
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1144
 
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1288
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1281
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1295
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1283
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1284
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t/data/eutils/esearch2.xml
 
1305
t/data/eutils/espell.xml
 
1306
t/data/eutils/esummary1.xml
 
1307
t/data/eutils/esummary2.xml
1296
1308
t/data/example.hap
1297
1309
t/data/example.phase
1298
1310
t/data/expected.blast.out
 
1311
t/data/exsignalp.out
1299
1312
t/data/factor7.embl
 
1313
t/data/fgenesh.out
1300
1314
t/data/footprinter.out
1301
1315
t/data/frac_problems.blast
 
1316
t/data/frac_problems2.blast
 
1317
t/data/frac_problems3.blast
1302
1318
t/data/geneid_1.0.out
 
1319
t/data/genemark-fragment.out
1303
1320
t/data/genemark.out
1304
1321
t/data/genewise.out
1305
1322
t/data/genewise_output.paracel_btk
1310
1327
t/data/genomic-seq.mzef
1311
1328
t/data/Genscan.FastA
1312
1329
t/data/gf-s71.needle
1313
 
t/data/glimmer.out
1314
1330
t/data/Glimmer2.out
 
1331
t/data/glimmer3-fragment.detail
 
1332
t/data/glimmer3-fragment.predict
1315
1333
t/data/Glimmer3.detail
1316
1334
t/data/Glimmer3.predict
1317
1335
t/data/GlimmerHMM.out
1321
1339
t/data/hemoglobinA.meg
1322
1340
t/data/hg16_chroms.gff
1323
1341
t/data/hmmpfam.out
 
1342
t/data/hmmpfam_cs.out
1324
1343
t/data/hmmpfam_fake.out
1325
1344
t/data/hmmsearch.out
1326
1345
t/data/hs_est.est2genome
1344
1363
t/data/interpro_ebi.xml
1345
1364
t/data/interpro_short.xml
1346
1365
t/data/intrablock-comment.nex
1347
 
t/data/kinases.tsv
1348
 
t/data/kinases.xls
1349
1366
t/data/Kingdoms_DNA.nex
1350
1367
t/data/knownGene.gff3
1351
1368
t/data/L77119.hmmer
1352
1369
t/data/little.largemultifasta
1353
1370
t/data/LittleChrY.dbsnp.xml
1354
 
t/data/LL-sample.seq
1355
1371
t/data/LOAD_Ccd1.dnd
1356
1372
t/data/long-names.nex
 
1373
t/data/longnames.aln
 
1374
t/data/longnames.dnd
1357
1375
t/data/lucy.info
1358
1376
t/data/lucy.qual
1359
1377
t/data/lucy.seq
1361
1379
t/data/lysozyme6.protml
1362
1380
t/data/lysozyme6.simple.protml
1363
1381
t/data/M0.mlc
 
1382
t/data/M12730.gb
 
1383
t/data/map_hem/HEM1-HEM12.fa
 
1384
t/data/map_hem/HEM1-HEM12.fa.revcom
 
1385
t/data/map_hem/HEM1-HEM12.meme.txt
 
1386
t/data/map_hem/HEM1-HEM13.fa
 
1387
t/data/map_hem/HEM1-HEM13.meme.txt
 
1388
t/data/map_hem/HEM1-HEM14.fa
 
1389
t/data/map_hem/HEM1-HEM14.meme.txt
 
1390
t/data/map_hem/HEM1-HEM15.fa
 
1391
t/data/map_hem/HEM1-HEM15.meme.txt
 
1392
t/data/map_hem/HEM1-HEM2.fa
 
1393
t/data/map_hem/HEM1-HEM2.fa.revcom
 
1394
t/data/map_hem/HEM1-HEM2.meme.txt
 
1395
t/data/map_hem/HEM1-HEM3.fa
 
1396
t/data/map_hem/HEM1-HEM3.meme.txt
 
1397
t/data/map_hem/HEM1-HEM4.fa
 
1398
t/data/map_hem/HEM1-HEM4.meme.txt
 
1399
t/data/map_hem/HEM1.ups.fa_
 
1400
t/data/map_hem/HEM1.ups.fa_.revcom
 
1401
t/data/map_hem/HEM12-HEM13.fa
 
1402
t/data/map_hem/HEM12-HEM13.meme.txt
 
1403
t/data/map_hem/HEM12-HEM14.fa
 
1404
t/data/map_hem/HEM12-HEM14.meme.txt
 
1405
t/data/map_hem/HEM12-HEM15.fa
 
1406
t/data/map_hem/HEM12-HEM15.meme.txt
 
1407
t/data/map_hem/HEM12.ups.fa_
 
1408
t/data/map_hem/HEM12.ups.fa_.revcom
 
1409
t/data/map_hem/HEM13-HEM14.fa
 
1410
t/data/map_hem/HEM13-HEM14.meme.txt
 
1411
t/data/map_hem/HEM13-HEM15.fa
 
1412
t/data/map_hem/HEM13-HEM15.meme.txt
 
1413
t/data/map_hem/HEM13.ups.fa_
 
1414
t/data/map_hem/HEM13.ups.fa_.revcom
 
1415
t/data/map_hem/HEM14-HEM15.fa
 
1416
t/data/map_hem/HEM14-HEM15.meme.txt
 
1417
t/data/map_hem/HEM14.ups.fa_
 
1418
t/data/map_hem/HEM14.ups.fa_.revcom
 
1419
t/data/map_hem/HEM15.ups.fa_
 
1420
t/data/map_hem/HEM15.ups.fa_.revcom
 
1421
t/data/map_hem/HEM2-HEM12.fa
 
1422
t/data/map_hem/HEM2-HEM12.meme.txt
 
1423
t/data/map_hem/HEM2-HEM13.fa
 
1424
t/data/map_hem/HEM2-HEM13.meme.txt
 
1425
t/data/map_hem/HEM2-HEM14.fa
 
1426
t/data/map_hem/HEM2-HEM14.meme.txt
 
1427
t/data/map_hem/HEM2-HEM15.fa
 
1428
t/data/map_hem/HEM2-HEM15.meme.txt
 
1429
t/data/map_hem/HEM2-HEM3.fa
 
1430
t/data/map_hem/HEM2-HEM3.meme.txt
 
1431
t/data/map_hem/HEM2-HEM4.fa
 
1432
t/data/map_hem/HEM2-HEM4.meme.txt
 
1433
t/data/map_hem/HEM2.ups.fa_
 
1434
t/data/map_hem/HEM2.ups.fa_.revcom
 
1435
t/data/map_hem/HEM3-HEM12.fa
 
1436
t/data/map_hem/HEM3-HEM12.meme.txt
 
1437
t/data/map_hem/HEM3-HEM13.fa
 
1438
t/data/map_hem/HEM3-HEM13.meme.txt
 
1439
t/data/map_hem/HEM3-HEM14.fa
 
1440
t/data/map_hem/HEM3-HEM14.meme.txt
 
1441
t/data/map_hem/HEM3-HEM15.fa
 
1442
t/data/map_hem/HEM3-HEM15.meme.txt
 
1443
t/data/map_hem/HEM3-HEM4.fa
 
1444
t/data/map_hem/HEM3-HEM4.meme.txt
 
1445
t/data/map_hem/HEM3.ups.fa_
 
1446
t/data/map_hem/HEM3.ups.fa_.revcom
 
1447
t/data/map_hem/HEM4-HEM12.fa
 
1448
t/data/map_hem/HEM4-HEM12.meme.txt
 
1449
t/data/map_hem/HEM4-HEM13.fa
 
1450
t/data/map_hem/HEM4-HEM13.meme.txt
 
1451
t/data/map_hem/HEM4-HEM14.fa
 
1452
t/data/map_hem/HEM4-HEM14.meme.txt
 
1453
t/data/map_hem/HEM4-HEM15.fa
 
1454
t/data/map_hem/HEM4-HEM15.meme.txt
 
1455
t/data/map_hem/HEM4.ups.fa_
 
1456
t/data/map_hem/HEM4.ups.fa_.revcom
 
1457
t/data/map_hem/yeast.nc.1.freq
1364
1458
t/data/mapmaker.out
1365
1459
t/data/mapmaker.txt
1366
1460
t/data/mast.dat
1367
1461
t/data/masta.dat
 
1462
t/data/match.output
1368
1463
t/data/Mcjanrna_rdbII.gbk
1369
1464
t/data/megablast_output.paracel_btk
1370
1465
t/data/meme.dat
1374
1469
t/data/MmCT
1375
1470
t/data/mpath.ontology.test
1376
1471
t/data/MSGEFTUA.gb
 
1472
t/data/multi.phd
1377
1473
t/data/multi_1.fa
1378
1474
t/data/multi_2.fa
1379
1475
t/data/multi_blast.bls
1390
1486
t/data/NC_001284.gbk
1391
1487
t/data/NC_006346.gb
1392
1488
t/data/NC_006511-short.gbk
 
1489
t/data/NC_008536.gb
1393
1490
t/data/nei_gojobori_test.aln
1394
1491
t/data/neighbor.dist
1395
1492
t/data/new_blastn.txt
1396
 
t/data/newformat.swiss
1397
 
t/data/NM_002253.tseq
 
1493
t/data/newblast.xml
1398
1494
t/data/NM_002254.gb
1399
1495
t/data/no-genes.genscan
1400
1496
t/data/no_cds_example.gb
1402
1498
t/data/no_hsps.blastp
1403
1499
t/data/noninterleaved.phy
1404
1500
t/data/NT_021877.gbk
 
1501
t/data/nucmatrix.txt
1405
1502
t/data/O_sat.wgs
1406
1503
t/data/omim_genemap_test
 
1504
t/data/omim_genemap_test_nolinebreak
1407
1505
t/data/omim_text_test
1408
1506
t/data/P33897
1409
1507
t/data/P35527.gb
1412
1510
t/data/pfam_tests.stk
1413
1511
t/data/phi.out
1414
1512
t/data/phipsi.out
1415
 
t/data/phredfile.phd
1416
1513
t/data/phylipdist-36.out
1417
1514
t/data/phylipdist.out
 
1515
t/data/phyloxml_examples.xml
1418
1516
t/data/pictogram.fa
1419
1517
t/data/plague_yeast.bls.xml
1420
1518
t/data/polymorphism.dat
1432
1530
t/data/prints.out
1433
1531
t/data/promoterwise.out
1434
1532
t/data/protpars.phy
 
1533
t/data/protpars_longid.phy
1435
1534
t/data/pseudowise.out
1436
1535
t/data/psi_xml.dat
 
1536
t/data/psiblast.xml
1437
1537
t/data/psiblastreport.out
 
1538
t/data/purine_v081.infernal
1438
1539
t/data/puzzle.tre
 
1540
t/data/Q8GBD3.swiss
1439
1541
t/data/qrna-relloc.out
1440
1542
t/data/qualfile.qual
1441
1543
t/data/quoted-strings1.nex
1443
1545
t/data/Rab1.chaos-xml
1444
1546
t/data/radical-whitespace.nex
1445
1547
t/data/radical-whitespace_02.nex
1446
 
t/data/readtest.abi
1447
 
t/data/readtest.ctf
1448
 
t/data/readtest.exp
1449
 
t/data/readtest.pln
1450
 
t/data/readtest.ztr
1451
1548
t/data/rebase.itype2
1452
1549
t/data/rebase.withrefm
1453
1550
t/data/registry/bdb/seqdatabase.ini
1454
1551
t/data/registry/flat/seqdatabase.ini
 
1552
t/data/regulation_test.obo
1455
1553
t/data/rel9.swiss
1456
1554
t/data/repeatmasker.fa.out
 
1555
t/data/ReseqChip_ExampleData.fasta
 
1556
t/data/ReseqChip_mtDNA_design_annotation_file_FINAL.xls
 
1557
t/data/ReseqChip_RefSeq.fasta
1457
1558
t/data/revcomp_mrna.gb
1458
1559
t/data/rfam_tests.stk
1459
1560
t/data/roa1.dat
1460
1561
t/data/roa1.genbank
1461
1562
t/data/roa1.swiss
1462
1563
t/data/roa1_v2.dat
 
1564
t/data/rpsblast.bls
 
1565
t/data/sample_dataset.tasm
 
1566
t/data/sbay_c127.fas
1463
1567
t/data/sbay_c545-yeast.BLASTZ.PSL
1464
1568
t/data/seg.out
1465
1569
t/data/seqdatabase.ini
1468
1572
t/data/seqs.fas
1469
1573
t/data/sequencefamily.dat
1470
1574
t/data/short.blx
 
1575
t/data/signalp.hmm.short
 
1576
t/data/signalp.hmm.summary
1471
1577
t/data/signalp.negative.out
 
1578
t/data/signalp.nn.short
 
1579
t/data/signalp.nn.summary
1472
1580
t/data/signalp.positive.out
 
1581
t/data/signalp.short
 
1582
t/data/signalp.summary
1473
1583
t/data/sim4.for.for
1474
1584
t/data/sim4.for.rev
1475
1585
t/data/sim4.rev
1476
1586
t/data/singleNSsite.mlc
1477
1587
t/data/so.obo
1478
1588
t/data/sofa.ontology
 
1589
t/data/spaces.nex
1479
1590
t/data/SPAN_Family4nl.nex
1480
1591
t/data/SPAN_Family7n.nex
1481
1592
t/data/SPAN_Family8a.nex
1494
1605
t/data/tab1part.mif
1495
1606
t/data/tab2part.mif
1496
1607
t/data/tab3part.mif
 
1608
t/data/tandem_repeats_finder.dat
 
1609
t/data/tandem_repeats_finder.noresults
 
1610
t/data/targetp.out
1497
1611
t/data/taxdump/names.dmp
1498
1612
t/data/taxdump/nodes.dmp
1499
1613
t/data/tblastn.out
 
1614
t/data/test.abi
1500
1615
t/data/test.ace
 
1616
t/data/test.ctf
1501
1617
t/data/test.embl
1502
1618
t/data/test.embl2sq
 
1619
t/data/test.exp
1503
1620
t/data/test.fasta
1504
1621
t/data/test.game
1505
1622
t/data/test.gcg
1507
1624
t/data/test.gcgfasta
1508
1625
t/data/test.genbank
1509
1626
t/data/test.genbank.noseq
 
1627
t/data/test.infernal
1510
1628
t/data/test.interpro
 
1629
t/data/test.interpro-go.xml
1511
1630
t/data/test.lasergene
 
1631
t/data/test.locuslink
1512
1632
t/data/test.mase
1513
1633
t/data/test.meme
1514
1634
t/data/test.meme2
1516
1636
t/data/test.nh
1517
1637
t/data/test.nhx
1518
1638
t/data/test.pfam
 
1639
t/data/test.phd
1519
1640
t/data/test.pir
 
1641
t/data/test.pln
1520
1642
t/data/test.ptt
1521
1643
t/data/test.raw
1522
1644
t/data/test.swiss
1523
1645
t/data/test.tab
1524
1646
t/data/test.tigrxml
 
1647
t/data/test.tseq
 
1648
t/data/test.tsv
1525
1649
t/data/test.txt
1526
1650
t/data/test.waba
 
1651
t/data/test.xls
 
1652
t/data/test.ztr
 
1653
t/data/test1.blasttab3
 
1654
t/data/test1.wublastp
1527
1655
t/data/test_badlf.gcg
1528
1656
t/data/testaln.aln
 
1657
t/data/testaln.arp
1529
1658
t/data/testaln.fasta
 
1659
t/data/testaln.list
1530
1660
t/data/testaln.mase
1531
1661
t/data/testaln.metafasta
1532
1662
t/data/testaln.msf
1538
1668
t/data/testaln.psi
1539
1669
t/data/testaln.selex
1540
1670
t/data/testaln.stockholm
 
1671
t/data/testaln.xmfa
 
1672
t/data/testaln2.arp
1541
1673
t/data/testaln2.fasta
1542
1674
t/data/testdat.exonerate
 
1675
t/data/testdata.crossmatch
1543
1676
t/data/testdbaccnums.out
1544
1677
t/data/testfile.erpin
1545
1678
t/data/testfuzzy.genbank
1546
1679
t/data/tmhmm.out
 
1680
t/data/tmp.fst
 
1681
t/data/traits.tab
 
1682
t/data/traittree.nexus
1547
1683
t/data/transfac.dat
 
1684
t/data/transfac_pro/factor.dat
 
1685
t/data/transfac_pro/fragment.dat
 
1686
t/data/transfac_pro/gene.dat
 
1687
t/data/transfac_pro/matrix.dat
 
1688
t/data/transfac_pro/readme.txt
 
1689
t/data/transfac_pro/reference.dat
 
1690
t/data/transfac_pro/site.dat
1548
1691
t/data/tree_nonewline.nexus
1549
1692
t/data/Treebase-chlamy-dna.nex
1550
1693
t/data/tricky.wublast
1555
1698
t/data/UnaSmithHIV-both.nex
1556
1699
t/data/unigene.data
1557
1700
t/data/urease.tre.nexus
 
1701
t/data/vecscreen_simple.test_output
1558
1702
t/data/version2.scf
1559
1703
t/data/version3.scf
1560
1704
t/data/worm_fam_2785.cdna
1561
1705
t/data/X98338_Adh-mRNA.gb
1562
1706
t/data/yeast.tRNAscanSE
1563
1707
t/data/yn00.mlc
1564
 
t/DB.t
1565
 
t/DBCUTG.t
1566
 
t/DBFasta.t
1567
 
t/DNAMutation.t
1568
 
t/Domcut.t
1569
 
t/ECnumber.t
1570
 
t/ELM.t
1571
 
t/embl.t
1572
 
t/EMBL_DB.t
1573
 
t/EMBOSS_Tools.t
1574
 
t/EncodedSeq.t
1575
 
t/entrezgene.t
1576
 
t/ePCR.t
1577
 
t/ESEfinder.t
1578
 
t/est2genome.t
1579
 
t/EUtilities.t
1580
 
t/Exception.t
1581
 
t/Exonerate.t
1582
 
t/exp.t
1583
 
t/fasta.t
1584
 
t/FeatureHolder.x
1585
 
t/FeatureIO.t
1586
 
t/flat.t
1587
 
t/FootPrinter.t
1588
 
t/game.t
1589
 
t/GbrowseGFF.t
1590
 
t/gcg.t
1591
 
t/GDB.t
1592
 
t/Gel.t
1593
 
t/genbank.t
1594
 
t/GeneCoordinateMapper.t
1595
 
t/Geneid.t
1596
 
t/Genewise.t
1597
 
t/Genomewise.t
1598
 
t/Genpred.t
1599
 
t/GFF.t
1600
 
t/GOR4.t
1601
 
t/GOterm.t
1602
 
t/GraphAdaptor.t
1603
 
t/GuessSeqFormat.t
1604
 
t/hmmer.t
1605
 
t/hmmer_pull.t
1606
 
t/HNN.t
1607
 
t/HtSNP.t
1608
 
t/Index.t
1609
 
t/InstanceSite.t
1610
 
t/interpro.t
1611
 
t/InterProParser.t
1612
 
t/IUPAC.t
1613
 
t/kegg.t
1614
 
t/largefasta.t
1615
 
t/LargeLocatableSeq.t
1616
 
t/largepseq.t
1617
 
t/lasergene.t
 
1708
t/lib/Array/Compare.pm
1618
1709
t/lib/Error.pm
 
1710
t/lib/Sub/Uplevel.pm
1619
1711
t/lib/Test/Builder.pm
1620
1712
t/lib/Test/Builder/Module.pm
1621
1713
t/lib/Test/Builder/Tester.pm
1622
1714
t/lib/Test/Builder/Tester/Color.pm
 
1715
t/lib/Test/Exception.pm
 
1716
t/lib/Test/Harness.pm
 
1717
t/lib/Test/Harness/Assert.pm
 
1718
t/lib/Test/Harness/Iterator.pm
 
1719
t/lib/Test/Harness/Point.pm
 
1720
t/lib/Test/Harness/Results.pm
 
1721
t/lib/Test/Harness/Straps.pm
 
1722
t/lib/Test/Harness/TAP.pod
 
1723
t/lib/Test/Harness/Util.pm
1623
1724
t/lib/Test/More.pm
1624
1725
t/lib/Test/Simple.pm
1625
1726
t/lib/Test/Tutorial.pod
1626
 
t/LinkageMap.t
1627
 
t/LiveSeq.t
1628
 
t/LocatableSeq.t
1629
 
t/Location.t
1630
 
t/LocationFactory.t
1631
 
t/LocusLink.t
1632
 
t/lucy.t
1633
 
t/Map.t
1634
 
t/MapIO.t
1635
 
t/masta.t
1636
 
t/Matrix.t
1637
 
t/Measure.t
1638
 
t/MeSH.t
1639
 
t/metafasta.t
1640
 
t/MetaSeq.t
1641
 
t/MicrosatelliteMarker.t
1642
 
t/MiniMIMentry.t
1643
 
t/MitoProt.t
1644
 
t/Molphy.t
1645
 
t/MultiFile.t
1646
 
t/multiple_fasta.t
1647
 
t/Mutation.t
1648
 
t/Mutator.t
1649
 
t/NetPhos.t
1650
 
t/Node.t
1651
 
t/obo_parser.t
1652
 
t/OddCodes.t
1653
 
t/OMIMentry.t
1654
 
t/OMIMentryAllelicVariant.t
1655
 
t/OMIMparser.t
1656
 
t/Ontology.t
1657
 
t/OntologyEngine.t
1658
 
t/OntologyStore.t
1659
 
t/PAML.t
 
1727
t/lib/Test/Warn.pm
 
1728
t/lib/Tree/DAG_Node.pm
 
1729
t/LiveSeq/Chain.t
 
1730
t/LiveSeq/LiveSeq.t
 
1731
t/LiveSeq/Mutation.t
 
1732
t/LiveSeq/Mutator.t
 
1733
t/LocalDB/BioDBGFF.t
 
1734
t/LocalDB/BlastIndex.t
 
1735
t/LocalDB/DBFasta.t
 
1736
t/LocalDB/DBQual.t
 
1737
t/LocalDB/Flat.t
 
1738
t/LocalDB/Index.t
 
1739
t/LocalDB/Registry.t
 
1740
t/LocalDB/SeqFeature.t
 
1741
t/LocalDB/transfac_pro.t
 
1742
t/Map/Cyto.t
 
1743
t/Map/Linkage.t
 
1744
t/Map/Map.t
 
1745
t/Map/MapIO.t
 
1746
t/Map/MicrosatelliteMarker.t
 
1747
t/Map/Physical.t
 
1748
t/Matrix/InstanceSite.t
 
1749
t/Matrix/IO/masta.t
 
1750
t/Matrix/IO/psm.t
 
1751
t/Matrix/Matrix.t
 
1752
t/Matrix/ProtMatrix.t
 
1753
t/Matrix/ProtPsm.t
 
1754
t/Matrix/SiteMatrix.t
 
1755
t/Ontology/GOterm.t
 
1756
t/Ontology/GraphAdaptor.t
 
1757
t/Ontology/IO/go.t
 
1758
t/Ontology/IO/interpro.t
 
1759
t/Ontology/IO/obo.t
 
1760
t/Ontology/Ontology.t
 
1761
t/Ontology/OntologyEngine.t
 
1762
t/Ontology/OntologyStore.t
 
1763
t/Ontology/Relationship.t
 
1764
t/Ontology/RelationshipType.t
 
1765
t/Ontology/Term.t
1660
1766
t/Perl.t
1661
 
t/phd.t
1662
 
t/Phenotype.t
1663
 
t/PhylipDist.t
1664
 
t/PhysicalMap.t
1665
 
t/pICalculator.t
1666
 
t/Pictogram.t
1667
 
t/pir.t
1668
 
t/pln.t
1669
 
t/PopGen.t
1670
 
t/PopGenSims.t
1671
 
t/primaryqual.t
1672
 
t/PrimarySeq.t
1673
 
t/primedseq.t
1674
 
t/Primer.t
1675
 
t/primer3.t
1676
 
t/Promoterwise.t
1677
 
t/ProtDist.t
1678
 
t/protgraph.t
1679
 
t/ProtMatrix.t
1680
 
t/ProtPsm.t
1681
 
t/Pseudowise.t
1682
 
t/psm.t
1683
 
t/QRNA.t
1684
 
t/qual.t
1685
 
t/RandDistFunctions.t
1686
 
t/RandomTreeFactory.t
1687
 
t/Range.t
1688
 
t/RangeI.t
1689
 
t/raw.t
1690
 
t/RefSeq.t
1691
 
t/Registry.t
1692
 
t/Relationship.t
1693
 
t/RelationshipType.t
1694
 
t/RemoteBlast.t
1695
 
t/RepeatMasker.t
1696
 
t/RestrictionAnalysis.t
1697
 
t/RestrictionIO.t
1698
 
t/RNAChange.t
1699
 
t/rnamotif.t
1700
 
t/RootI.t
1701
 
t/RootIO.t
1702
 
t/RootStorable.t
1703
 
t/Scansite.t
1704
 
t/scf.t
 
1767
t/Phenotype/Correlate.t
 
1768
t/Phenotype/Measure.t
 
1769
t/Phenotype/MeSH.t
 
1770
t/Phenotype/MiniMIMentry.t
 
1771
t/Phenotype/OMIMentry.t
 
1772
t/Phenotype/OMIMentryAllelicVariant.t
 
1773
t/Phenotype/OMIMparser.t
 
1774
t/Phenotype/Phenotype.t
 
1775
t/PodSyntax.t
 
1776
t/PopGen/Coalescent.t
 
1777
t/PopGen/HtSNP.t
 
1778
t/PopGen/MK.t
 
1779
t/PopGen/PopGen.t
 
1780
t/PopGen/PopGenSims.t
 
1781
t/PopGen/TagHaplotype.t
 
1782
t/RemoteDB/BioFetch.t
 
1783
t/RemoteDB/CUTG.t
 
1784
t/RemoteDB/DB.t
 
1785
t/RemoteDB/EMBL.t
 
1786
t/RemoteDB/EUtilities.t
 
1787
t/RemoteDB/HIV/HIV.t
 
1788
t/RemoteDB/HIV/HIVAnnotProcessor.t
 
1789
t/RemoteDB/HIV/HIVQuery.t
 
1790
t/RemoteDB/HIV/HIVQueryHelper.t
 
1791
t/RemoteDB/RefSeq.t
 
1792
t/RemoteDB/SeqHound.t
 
1793
t/RemoteDB/SeqRead_fail.t
 
1794
t/RemoteDB/SeqVersion.t
 
1795
t/RemoteDB/Taxonomy.t
 
1796
t/Restriction/Analysis.t
 
1797
t/Restriction/Gel.t
 
1798
t/Restriction/IO.t
 
1799
t/Root/Exception.t
 
1800
t/Root/RootI.t
 
1801
t/Root/RootIO.t
 
1802
t/Root/Storable.t
 
1803
t/Root/Tempfile.t
 
1804
t/Root/Utilities.t
1705
1805
t/SearchDist.t
1706
 
t/SearchIO.t
1707
 
t/Seg.t
1708
 
t/Seq.t
1709
 
t/seq_quality.t
1710
 
t/SeqAnalysisParser.t
1711
 
t/SeqBuilder.t
1712
 
t/SeqDiff.t
1713
 
t/SeqFeatCollection.t
1714
 
t/SeqFeature.t
1715
 
t/seqfeaturePrimer.t
1716
 
t/SeqHound_DB.t
 
1806
t/SearchIO/blast.t
 
1807
t/SearchIO/blast_pull.t
 
1808
t/SearchIO/blasttable.t
 
1809
t/SearchIO/blastxml.t
 
1810
t/SearchIO/CigarString.t
 
1811
t/SearchIO/cross_match.t
 
1812
t/SearchIO/erpin.t
 
1813
t/SearchIO/exonerate.t
 
1814
t/SearchIO/fasta.t
 
1815
t/SearchIO/GbrowseGFF.t
 
1816
t/SearchIO/hmmer.t
 
1817
t/SearchIO/hmmer_pull.t
 
1818
t/SearchIO/infernal.t
 
1819
t/SearchIO/megablast.t
 
1820
t/SearchIO/psl.t
 
1821
t/SearchIO/rnamotif.t
 
1822
t/SearchIO/SearchIO.t
 
1823
t/SearchIO/sim4.t
 
1824
t/SearchIO/SimilarityPair.t
 
1825
t/SearchIO/waba.t
 
1826
t/SearchIO/wise.t
 
1827
t/SearchIO/Writer/HitTableWriter.t
 
1828
t/SearchIO/Writer/HTMLWriter.t
 
1829
t/Seq/DBLink.t
 
1830
t/Seq/EncodedSeq.t
 
1831
t/Seq/LargeLocatableSeq.t
 
1832
t/Seq/LargePSeq.t
 
1833
t/Seq/LocatableSeq.t
 
1834
t/Seq/MetaSeq.t
 
1835
t/Seq/PrimaryQual.t
 
1836
t/Seq/PrimarySeq.t
 
1837
t/Seq/PrimedSeq.t
 
1838
t/Seq/Quality.t
 
1839
t/Seq/Seq.t
 
1840
t/Seq/WithQuality.t
 
1841
t/SeqEvolution.t
 
1842
t/SeqFeature/FeatureIO.t
 
1843
t/SeqFeature/Location.t
 
1844
t/SeqFeature/LocationFactory.t
 
1845
t/SeqFeature/Primer.t
 
1846
t/SeqFeature/Range.t
 
1847
t/SeqFeature/RangeI.t
 
1848
t/SeqFeature/SeqAnalysisParser.t
 
1849
t/SeqFeature/SeqFeatAnnotated.t
 
1850
t/SeqFeature/SeqFeatCollection.t
 
1851
t/SeqFeature/SeqFeature.t
 
1852
t/SeqFeature/SeqFeaturePrimer.t
 
1853
t/SeqFeature/Unflattener.t
 
1854
t/SeqFeature/Unflattener2.t
1717
1855
t/SeqIO.t
1718
 
t/SeqPattern.t
1719
 
t/seqread_fail.t
1720
 
t/SeqStats.t
1721
 
t/SequenceFamily.t
1722
 
t/sequencetrace.t
1723
 
t/SeqUtils.t
1724
 
t/SeqVersion.t
1725
 
t/seqwithquality.t
1726
 
t/SeqWords.t
1727
 
t/Sigcleave.t
1728
 
t/Signalp.t
1729
 
t/Sim4.t
1730
 
t/SimilarityPair.t
1731
 
t/SimpleAlign.t
1732
 
t/simpleGOparser.t
1733
 
t/singlet.t
1734
 
t/sirna.t
1735
 
t/SiteMatrix.t
1736
 
t/SNP.t
1737
 
t/Sopma.t
 
1856
t/SeqIO/abi.t
 
1857
t/SeqIO/ace.t
 
1858
t/SeqIO/agave.t
 
1859
t/SeqIO/alf.t
 
1860
t/SeqIO/asciitree.t
 
1861
t/SeqIO/bsml.t
 
1862
t/SeqIO/bsml_sax.t
 
1863
t/SeqIO/chadoxml.t
 
1864
t/SeqIO/chaos.t
 
1865
t/SeqIO/chaosxml.t
 
1866
t/SeqIO/ctf.t
 
1867
t/SeqIO/embl.t
 
1868
t/SeqIO/entrezgene.t
 
1869
t/SeqIO/excel.t
 
1870
t/SeqIO/exp.t
 
1871
t/SeqIO/fasta.t
 
1872
t/SeqIO/fastq.t
 
1873
t/SeqIO/flybase_chadoxml.t
 
1874
t/SeqIO/game.t
 
1875
t/SeqIO/gcg.t
 
1876
t/SeqIO/genbank.t
 
1877
t/SeqIO/Handler.t
 
1878
t/SeqIO/interpro.t
 
1879
t/SeqIO/kegg.t
 
1880
t/SeqIO/largefasta.t
 
1881
t/SeqIO/lasergene.t
 
1882
t/SeqIO/locuslink.t
 
1883
t/SeqIO/metafasta.t
 
1884
t/SeqIO/MultiFile.t
 
1885
t/SeqIO/Multiple_fasta.t
 
1886
t/SeqIO/phd.t
 
1887
t/SeqIO/pir.t
 
1888
t/SeqIO/pln.t
 
1889
t/SeqIO/qual.t
 
1890
t/SeqIO/raw.t
 
1891
t/SeqIO/scf.t
 
1892
t/SeqIO/SeqBuilder.t
 
1893
t/SeqIO/Splicedseq.t
 
1894
t/SeqIO/strider.t
 
1895
t/SeqIO/swiss.t
 
1896
t/SeqIO/tab.t
 
1897
t/SeqIO/table.t
 
1898
t/SeqIO/tigr.t
 
1899
t/SeqIO/tigrxml.t
 
1900
t/SeqIO/tinyseq.t
 
1901
t/SeqIO/ztr.t
 
1902
t/SeqTools/CodonTable.t
 
1903
t/SeqTools/ECnumber.t
 
1904
t/SeqTools/GuessSeqFormat.t
 
1905
t/SeqTools/OddCodes.t
 
1906
t/SeqTools/SeqPattern.t
 
1907
t/SeqTools/SeqStats.t
 
1908
t/SeqTools/SeqUtils.t
 
1909
t/SeqTools/SeqWords.t
1738
1910
t/Species.t
1739
 
t/Spidey.t
1740
 
t/splicedseq.t
1741
 
t/StandAloneBlast.t
1742
 
t/StructIO.t
1743
 
t/Structure.t
1744
 
t/swiss.t
 
1911
t/Structure/IO.t
 
1912
t/Structure/Structure.t
1745
1913
t/Symbol.t
1746
 
t/tab.t
1747
 
t/table.t
1748
 
t/TagHaplotype.t
1749
 
t/Taxonomy.t
1750
1914
t/TaxonTree.t
1751
 
t/Tempfile.t
1752
 
t/Term.t
1753
 
t/Test.pm
1754
 
t/testformats.pl
1755
 
t/tigrxml.t
1756
 
t/tinyseq.t
1757
 
t/Tmhmm.t
1758
 
t/Tools.t
1759
 
t/Tree.t
1760
 
t/TreeBuild.t
1761
 
t/TreeIO.t
1762
 
t/trim.t
1763
 
t/tRNAscanSE.t
1764
 
t/UCSCParsers.t
1765
 
t/Unflattener.t
1766
 
t/Unflattener2.t
1767
 
t/UniGene.t
1768
 
t/Variation_IO.t
1769
 
t/WABA.t
1770
 
t/XEMBL_DB.t
1771
 
t/ztr.t
 
1915
t/Tools/Alignment/Consed.t
 
1916
t/Tools/Analysis/DNA/ESEfinder.t
 
1917
t/Tools/Analysis/Protein/Domcut.t
 
1918
t/Tools/Analysis/Protein/ELM.t
 
1919
t/Tools/Analysis/Protein/GOR4.t
 
1920
t/Tools/Analysis/Protein/HNN.t
 
1921
t/Tools/Analysis/Protein/Mitoprot.t
 
1922
t/Tools/Analysis/Protein/NetPhos.t
 
1923
t/Tools/Analysis/Protein/Scansite.t
 
1924
t/Tools/Analysis/Protein/Sopma.t
 
1925
t/Tools/EMBOSS/Palindrome.t
 
1926
t/Tools/ePCR.t
 
1927
t/Tools/Est2Genome.t
 
1928
t/Tools/EUtilities/egquery.t
 
1929
t/Tools/EUtilities/einfo.t
 
1930
t/Tools/EUtilities/elink_acheck.t
 
1931
t/Tools/EUtilities/elink_lcheck.t
 
1932
t/Tools/EUtilities/elink_llinks.t
 
1933
t/Tools/EUtilities/elink_ncheck.t
 
1934
t/Tools/EUtilities/elink_neighbor.t
 
1935
t/Tools/EUtilities/elink_neighbor_history.t
 
1936
t/Tools/EUtilities/elink_scores.t
 
1937
t/Tools/EUtilities/epost.t
 
1938
t/Tools/EUtilities/esearch.t
 
1939
t/Tools/EUtilities/espell.t
 
1940
t/Tools/EUtilities/esummary.t
 
1941
t/Tools/EUtilities/EUtilParameters.t
 
1942
t/Tools/FootPrinter.t
 
1943
t/Tools/Geneid.t
 
1944
t/Tools/Genewise.t
 
1945
t/Tools/Genomewise.t
 
1946
t/Tools/Genpred.t
 
1947
t/Tools/GFF.t
 
1948
t/Tools/Hmmer.t
 
1949
t/Tools/IUPAC.t
 
1950
t/Tools/Lucy.t
 
1951
t/Tools/Match.t
 
1952
t/Tools/Phylo/Gerp.t
 
1953
t/Tools/Phylo/Molphy.t
 
1954
t/Tools/Phylo/PAML.t
 
1955
t/Tools/Phylo/Phylip/ProtDist.t
 
1956
t/Tools/pICalculator.t
 
1957
t/Tools/Primer3.t
 
1958
t/Tools/Promoterwise.t
 
1959
t/Tools/Pseudowise.t
 
1960
t/Tools/QRNA.t
 
1961
t/Tools/RandDistFunctions.t
 
1962
t/Tools/RepeatMasker.t
 
1963
t/Tools/rnamotif.t
 
1964
t/Tools/Run/RemoteBlast.t
 
1965
t/Tools/Run/StandAloneBlast.t
 
1966
t/Tools/Run/WrapperBase.t
 
1967
t/Tools/Seg.t
 
1968
t/Tools/Sigcleave.t
 
1969
t/Tools/Signalp.t
 
1970
t/Tools/Signalp/ExtendedSignalp.t
 
1971
t/Tools/Sim4.t
 
1972
t/Tools/SiRNA.t
 
1973
t/Tools/Spidey/Spidey.t
 
1974
t/Tools/TandemRepeatsFinder.t
 
1975
t/Tools/TargetP.t
 
1976
t/Tools/Tmhmm.t
 
1977
t/Tools/tRNAscanSE.t
 
1978
t/Tree/Compatible.t
 
1979
t/Tree/Node.t
 
1980
t/Tree/PhyloNetwork/Factory.t
 
1981
t/Tree/PhyloNetwork/GraphViz.t
 
1982
t/Tree/PhyloNetwork/MuVector.t
 
1983
t/Tree/PhyloNetwork/PhyloNetwork.t
 
1984
t/Tree/PhyloNetwork/RandomFactory.t
 
1985
t/Tree/PhyloNetwork/TreeFactory.t
 
1986
t/Tree/RandomTreeFactory.t
 
1987
t/Tree/Tree.t
 
1988
t/Tree/TreeIO.t
 
1989
t/Tree/TreeIO/lintree.t
 
1990
t/Tree/TreeIO/newick.t
 
1991
t/Tree/TreeIO/nexus.t
 
1992
t/Tree/TreeIO/nhx.t
 
1993
t/Tree/TreeIO/phyloxml.t
 
1994
t/Tree/TreeIO/svggraph.t
 
1995
t/Tree/TreeIO/tabtree.t
 
1996
t/Tree/TreeStatistics.t
 
1997
t/Variation/AAChange.t
 
1998
t/Variation/AAReverseMutate.t
 
1999
t/Variation/Allele.t
 
2000
t/Variation/DNAMutation.t
 
2001
t/Variation/RNAChange.t
 
2002
t/Variation/SeqDiff.t
 
2003
t/Variation/SNP.t
 
2004
t/Variation/Variation_IO.t
 
2005
Makefile.PL
 
2006
META.yml