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829 examples/align/FastAlign.pl
830 examples/align/simplealign.pl
831 examples/Bio-DB-GFF/load_ucsc.pl
833 examples/cluster/dbsnp.pl
834 examples/contributed/nmrpdb_parse.pl
835 examples/contributed/prosite2perl.pl
836 examples/contributed/rebase2list.pl
838 examples/db/est_tissue_query.pl
839 examples/db/gb2features.pl
840 examples/db/get_seqs.pl
841 examples/db/getGenBank.pl
842 examples/db/rfetch.pl
843 examples/db/use_registry.pl
844 examples/generate_random_seq.pl
845 examples/liveseq/change_gene.pl
847 examples/make_primers.pl
848 examples/popgen/parse_calc_stats.pl
849 examples/quality/svgtrace.pl
850 examples/rev_and_trans.pl
851 examples/revcom_dir.pl
852 examples/root/exceptions1.pl
853 examples/root/exceptions2.pl
854 examples/root/exceptions3.pl
855 examples/root/exceptions4.pl
857 examples/searchio/blast_example.pl
858 examples/searchio/custom_writer.pl
859 examples/searchio/hitwriter.pl
860 examples/searchio/hspwriter.pl
861 examples/searchio/htmlwriter.pl
862 examples/searchio/psiblast_features.pl
863 examples/searchio/psiblast_iterations.pl
864 examples/searchio/rawwriter.pl
865 examples/searchio/resultwriter.pl
866 examples/searchio/waba2gff.pl
867 examples/searchio/waba2gff3.pl
868 examples/sirna/rnai_finder.cgi
870 examples/structure/structure-io.pl
871 examples/subsequence.cgi
872 examples/tk/gsequence.pl
873 examples/tk/hitdisplay.pl
874 examples/tools/extract_genes.pl
875 examples/tools/gb_to_gff.pl
876 examples/tools/gff2ps.pl
877 examples/tools/parse_codeml.pl
878 examples/tools/psw.pl
879 examples/tools/reverse-translate.pl
880 examples/tools/run_genscan.pl
881 examples/tools/run_primer3.pl
882 examples/tools/seq_pattern.pl
883 examples/tools/standaloneblast.pl
884 examples/tree/paup2phylip.pl
885 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
886 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
887 ide/bioperl-mode/dist/bioperl-mode.tar
888 ide/bioperl-mode/dist/bioperl-mode.tar.md5
889 ide/bioperl-mode/dist/Changes
890 ide/bioperl-mode/dist/package-me
891 ide/bioperl-mode/dist/SKIP
892 ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
893 ide/bioperl-mode/etc/images/bpmode-tool.xpm
894 ide/bioperl-mode/README
895 ide/bioperl-mode/site-lisp/bioperl-init.el
896 ide/bioperl-mode/site-lisp/bioperl-mode.el
897 ide/bioperl-mode/site-lisp/bioperl-skel.el
898 ide/bioperl-mode/site-lisp/pod.el
904 maintenance/authors.pl
905 maintenance/big_split/file_classification.csv
906 maintenance/big_split/rbuels_notes.txt
907 maintenance/check_NAME.pl
908 maintenance/check_URLs.pl
909 maintenance/cvs2cl_by_file.pl
910 maintenance/dependencies.pl
911 maintenance/deprecated.pl
912 maintenance/find_mod_deps.pl
913 maintenance/module_usage.pl
914 maintenance/modules.pl
915 maintenance/ncbi_blast_switches.pl
916 maintenance/perltidy.conf
919 maintenance/symlink_script.pl
920 maintenance/version.pl
921 MANIFEST This list of files
923 models/bio_liveseq_variation.dia
925 models/bio_restriction.dia
927 models/coordinatemapper.dia
928 models/map_proposal.txt
929 models/maps_and_markers.dia
931 models/population_proposal.txt
934 scripts/Bio-DB-GFF/bp_bulk_load_gff.pl
935 scripts/Bio-DB-GFF/bp_fast_load_gff.pl
936 scripts/Bio-DB-GFF/bp_genbank2gff.pl
937 scripts/Bio-DB-GFF/bp_genbank2gff3.pl
938 scripts/Bio-DB-GFF/bp_generate_histogram.pl
939 scripts/Bio-DB-GFF/bp_load_gff.pl
940 scripts/Bio-DB-GFF/bp_meta_gff.pl
941 scripts/Bio-DB-GFF/bp_process_gadfly.pl
942 scripts/Bio-DB-GFF/bp_process_sgd.pl
943 scripts/Bio-DB-GFF/bp_process_wormbase.pl
944 scripts/Bio-DB-GFF/README
945 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_delete.pl
946 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_gff3.pl
947 scripts/Bio-DB-SeqFeature-Store/bp_seqfeature_load.pl
948 scripts/das/bp_das_server.pl
951 scripts/DB-HIV/bp_hivq.pl
952 scripts/DB/bp_biofetch_genbank_proxy.pl
953 scripts/DB/bp_bioflat_index.pl
954 scripts/DB/bp_biogetseq.pl
955 scripts/DB/bp_flanks.pl
957 scripts/index/bp_fetch.pl
958 scripts/index/bp_index.pl
959 scripts/index/bp_seqret.pl
961 scripts/popgen/bp_composite_LD.pl
962 scripts/popgen/bp_heterogeneity_test.pl
964 scripts/searchio/bp_fastam9_to_table.pl
965 scripts/searchio/bp_filter_search.pl
966 scripts/searchio/bp_hmmer_to_table.pl
967 scripts/searchio/bp_parse_hmmsearch.pl
968 scripts/searchio/bp_search2table.pl
969 scripts/searchio/README
971 scripts/seq/bp_extract_feature_seq.pl
972 scripts/seq/bp_make_mrna_protein.pl
973 scripts/seq/bp_seqconvert.pl
974 scripts/seq/bp_seqcut.pl
975 scripts/seq/bp_seqpart.pl
976 scripts/seq/bp_seqretsplit.pl
977 scripts/seq/bp_split_seq.pl
978 scripts/seq/bp_translate_seq.pl
979 scripts/seq/bp_unflatten_seq.pl
981 scripts/seqstats/bp_aacomp.pl
982 scripts/seqstats/bp_chaos_plot.pl
983 scripts/seqstats/bp_gccalc.pl
984 scripts/seqstats/bp_oligo_count.pl
986 scripts/taxa/bp_classify_hits_kingdom.pl
987 scripts/taxa/bp_local_taxonomydb_query.pl
988 scripts/taxa/bp_query_entrez_taxa.pl
989 scripts/taxa/bp_taxid4species.pl
990 scripts/taxa/bp_taxonomy2tree.pl
992 scripts/tree/bp_blast2tree.pl
993 scripts/tree/bp_nexus2nh.pl
994 scripts/tree/bp_tree2pag.pl
996 scripts/utilities/bp_dbsplit.pl
997 scripts/utilities/bp_download_query_genbank.pl
998 scripts/utilities/bp_find-blast-matches.pl
999 scripts/utilities/bp_mask_by_search.pl
1000 scripts/utilities/bp_mrtrans.pl
1001 scripts/utilities/bp_mutate.pl
1002 scripts/utilities/bp_netinstall.pl
1003 scripts/utilities/bp_nrdb.pl
1004 scripts/utilities/bp_pairwise_kaks.pl
1005 scripts/utilities/bp_remote_blast.pl
1006 scripts/utilities/bp_revtrans-motif.pl
1007 scripts/utilities/bp_search2alnblocks.pl
1008 scripts/utilities/bp_search2gff.pl
1009 scripts/utilities/bp_search2tribe.pl
1010 scripts/utilities/bp_seq_length.pl
1011 scripts/utilities/bp_sreformat.pl
1012 scripts/utilities/README
1013 scripts/utilities/TAG
1014 t/Align/AlignStats.t
1017 t/Align/SimpleAlign.t
1023 t/AlignIO/clustalw.t
1026 t/AlignIO/largemultifasta.t
1031 t/AlignIO/metafasta.t
1041 t/AlignIO/stockholm.t
1044 t/Annotation/Annotation.t
1045 t/Annotation/AnnotationAdaptor.t
1046 t/Assembly/ContigSpectrum.t
1048 t/Assembly/IO/bowtie.t
1051 t/ClusterIO/ClusterIO.t
1052 t/ClusterIO/SequenceFamily.t
1053 t/ClusterIO/unigene.t
1055 t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
1056 t/data/02_dogfish_no_taxrefs.xml
1057 t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
1058 t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
1059 t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
1060 t/data/02_mackerel_no_taxrefs.xml
1061 t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
1062 t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
1063 t/data/03_bootstraps.xml
1064 t/data/03_bootstraps_in_tag.xml
1065 t/data/04_labeled_ancestors.xml
1066 t/data/05_ancestral_states.xml
1067 t/data/13-pilE-F.scf
1071 t/data/1ZZ19XR301R-Alignment.tblastn
1072 t/data/2008.blasttable
1073 t/data/27-contig_Newbler.ace
1074 t/data/503384.MEGABLAST.0
1075 t/data/503384.MEGABLAST.2
1076 t/data/5X_1895.FASTXY
1078 t/data/a_thaliana.blastn
1081 t/data/aaml_pairwise.mlc
1083 t/data/acefile.ace.1
1084 t/data/acefile.singlets
1085 t/data/adh.mb_tree.nexus
1086 t/data/AE003528_ecoli.bls
1087 t/data/AE003644_Adh-genomic.gb
1090 t/data/AF222649-rc.gbk
1094 t/data/alnfile.fasta
1096 t/data/amphora.newick
1097 t/data/AnnIX-v003.gbk
1099 t/data/assembly_with_singlets.ace
1103 t/data/AY095303S1.gbk
1108 t/data/bad_dbfa/bug3172.fa
1109 t/data/bad_dbfa/shotdb.fa
1111 t/data/barns-combined.nex
1112 t/data/baseml.pairwise
1113 t/data/baseml.usertree
1114 t/data/basic-bush.nex
1115 t/data/basic-ladder.nex
1117 t/data/BEL16-LTR_AG.embl
1118 t/data/biodbgff/test.gff
1119 t/data/biodbgff/test.gff3
1122 t/data/biorecipe.nhx
1123 t/data/Bird_Ovomucoids.nex
1124 t/data/BK000016-tpa.gbk
1125 t/data/bl2seq+.blastn
1126 t/data/bl2seq.blastn
1127 t/data/bl2seq.blastn.rev
1128 t/data/bl2seq.blastx.out
1129 t/data/bl2seq.bug940.out
1131 t/data/bl2seq.tblastn.out
1132 t/data/bl2seq.tblastx.out
1134 t/data/blast_no_hit_desc.txt
1135 t/data/blast_plus.blastp
1136 t/data/blastp2215.blast
1137 t/data/blat.psLayout3
1140 t/data/BN000066-tpa.embl
1141 t/data/bootstrap.tre
1142 t/data/BOSS_DROME.FASTP_v35_04
1143 t/data/branchSite.mlc
1144 t/data/brassica_ATH.WUBLASTN
1145 t/data/bug1986.blast2
1146 t/data/bug1986.blastp
1148 t/data/bug2246.blast
1149 t/data/bug2391.megablast
1150 t/data/bug2399.tblastn
1152 t/data/bug2473.fasta
1156 t/data/bug2937.fasta
1157 t/data/bug2942.blastx
1163 t/data/c200-vs-yeast.BLASTN
1164 t/data/c200-vs-yeast.BLASTN.m8
1166 t/data/catalase-webblast.BLASTP
1168 t/data/cds_sample.embl
1169 t/data/CG11099.fasaln
1170 t/data/CG2865.fasaln
1172 t/data/char-interleave.nex
1173 t/data/char-matrix-spaces.nex
1174 t/data/characters+trees.nexml.xml
1175 t/data/characters.nexml.old.xml
1176 t/data/cmsearch.multi.out
1177 t/data/cmsearch.nohit.out
1178 t/data/cmsearch_output.txt
1180 t/data/codeml315.mlc
1183 t/data/codeml43_nssites.mlc
1185 t/data/codeml45b.mlc
1186 t/data/codeml_lysozyme/2NG.dN
1187 t/data/codeml_lysozyme/2NG.dS
1188 t/data/codeml_lysozyme/2NG.tt
1189 t/data/codeml_lysozyme/4fold.nuc
1190 t/data/codeml_lysozyme/lnf
1191 t/data/codeml_lysozyme/lysozymeSmall.ctl
1192 t/data/codeml_lysozyme/lysozymeSmall.trees
1193 t/data/codeml_lysozyme/lysozymeSmall.txt
1194 t/data/codeml_lysozyme/mlc
1195 t/data/codeml_lysozyme/rst
1196 t/data/codeml_lysozyme/rst1
1197 t/data/codeml_lysozyme/rub
1198 t/data/codeml_nan.mlc
1199 t/data/codeml_nssites.mlc
1200 t/data/compLD_missingtest.prettybase
1201 t/data/compLD_test.prettybase
1202 t/data/component.ontology.test
1203 t/data/component.ontology.test2
1204 t/data/consed_project/edit_dir/test_project.contigs
1205 t/data/consed_project/edit_dir/test_project.fasta
1206 t/data/consed_project/edit_dir/test_project.fasta.log
1207 t/data/consed_project/edit_dir/test_project.fasta.screen
1208 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
1209 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
1210 t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
1211 t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
1212 t/data/consed_project/edit_dir/test_project.fasta.screen.log
1213 t/data/consed_project/edit_dir/test_project.fasta.screen.problems
1214 t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
1215 t/data/consed_project/edit_dir/test_project.fasta.screen.qual
1216 t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
1217 t/data/consed_project/edit_dir/test_project.fasta.screen.view
1218 t/data/consed_project/edit_dir/test_project.newtags
1219 t/data/consed_project/edit_dir/test_project.phrap.out
1220 t/data/consed_project/edit_dir/test_project.screen.out
1221 t/data/consed_project/edit_dir/test_project_to_alu.cross
1222 t/data/consed_project/edit_dir/test_projectNewChromats.fof
1223 t/data/consed_project/phd_dir/ML4922R.phd.1
1224 t/data/consed_project/phd_dir/ML4924F.phd.1
1225 t/data/consed_project/phd_dir/ML4924R.phd.1
1226 t/data/consed_project/phd_dir/ML4947F.phd.1
1227 t/data/contig-by-hand.wublastp
1228 t/data/contigspectrumtest.tigr
1232 t/data/crypto.sim4-0
1233 t/data/crypto.sim4-3
1234 t/data/crypto.sim4-4
1236 t/data/cys1_dicdi.water
1239 t/data/cysprot.needle
1240 t/data/cysprot.tblastn
1241 t/data/cysprot.water
1243 t/data/cysprot1.FASTA
1245 t/data/cysprot1a.msf
1247 t/data/cysprot1b.hmmsearch
1248 t/data/cysprot1b.msf
1249 t/data/cysprot1b.newick
1250 t/data/cysprot_vs_gadfly.FASTA
1260 t/data/dbfa/mixed_alphabet.fasta
1261 t/data/dbqual/1.qual
1262 t/data/dbqual/2.qual
1263 t/data/dbqual/3.qual
1264 t/data/dcr1_sp.WUBLASTP
1265 t/data/dmel_2Lchunk.gb
1268 t/data/dnaE-bsub-prot.fa
1270 t/data/dnaEbsub_ecoli.wublastx
1271 t/data/dnaEbsub_ecoli.wutblastn
1272 t/data/dnaEbsub_ecoli.wutblastx
1275 t/data/ECAPAH02.embl
1276 t/data/echofilter.wublastn
1277 t/data/ecoli-trna-qrna.out
1278 t/data/ecoli_domains.rpsblast
1281 t/data/ecolitst.noseqs.wublastp
1282 t/data/ecolitst.wublastp
1283 t/data/EG352462.gbxml
1285 t/data/ENr111.mfa.example.elems
1286 t/data/entrezgene.dat
1287 t/data/entrezgene_bug3453.dat
1290 t/data/example.phase
1292 t/data/exonerate.output.dontwork
1293 t/data/exonerate.output.negativescore.works
1294 t/data/exonerate.output.works
1295 t/data/exonerate.whitespace_before_query.works
1296 t/data/expected.blast.out
1297 t/data/exsignalp.out
1299 t/data/Fang_2003.xml
1300 t/data/fastq/bug2335.fastq
1301 t/data/fastq/error_diff_ids.fastq
1302 t/data/fastq/error_double_qual.fastq
1303 t/data/fastq/error_double_seq.fastq
1304 t/data/fastq/error_long_qual.fastq
1305 t/data/fastq/error_no_qual.fastq
1306 t/data/fastq/error_qual_del.fastq
1307 t/data/fastq/error_qual_escape.fastq
1308 t/data/fastq/error_qual_null.fastq
1309 t/data/fastq/error_qual_space.fastq
1310 t/data/fastq/error_qual_tab.fastq
1311 t/data/fastq/error_qual_unit_sep.fastq
1312 t/data/fastq/error_qual_vtab.fastq
1313 t/data/fastq/error_short_qual.fastq
1314 t/data/fastq/error_spaces.fastq
1315 t/data/fastq/error_tabs.fastq
1316 t/data/fastq/error_trunc_at_plus.fastq
1317 t/data/fastq/error_trunc_at_qual.fastq
1318 t/data/fastq/error_trunc_at_seq.fastq
1319 t/data/fastq/error_trunc_in_plus.fastq
1320 t/data/fastq/error_trunc_in_qual.fastq
1321 t/data/fastq/error_trunc_in_seq.fastq
1322 t/data/fastq/error_trunc_in_title.fastq
1323 t/data/fastq/evil_wrapping.fastq
1324 t/data/fastq/example.fasta
1325 t/data/fastq/example.fastq
1326 t/data/fastq/example.qual
1327 t/data/fastq/illumina_faked.fastq
1328 t/data/fastq/sanger_93.fastq
1329 t/data/fastq/sanger_faked.fastq
1330 t/data/fastq/solexa_example.fastq
1331 t/data/fastq/solexa_faked.fastq
1332 t/data/fastq/test1_sanger.fastq
1333 t/data/fastq/test2_solexa.fastq
1334 t/data/fastq/test3_illumina.fastq
1335 t/data/fastq/tricky.fastq
1336 t/data/fastq/wrapping_issues.fastq
1337 t/data/fastq/zero_qual.fastq
1339 t/data/footprinter.out
1340 t/data/forward_primer.fa
1341 t/data/forward_reverse_primers.fa
1342 t/data/frac_problems.blast
1343 t/data/frac_problems2.blast
1344 t/data/frac_problems3.blast
1345 t/data/geneid_1.0.out
1346 t/data/genemark-fragment.out
1349 t/data/genewise_output.paracel_btk
1350 t/data/genomewise.out
1351 t/data/genomic-seq.epcr
1352 t/data/genomic-seq.fasta
1353 t/data/genomic-seq.genscan
1354 t/data/genomic-seq.mzef
1355 t/data/Genscan.FastA
1356 t/data/gf-s71.needle
1358 t/data/glimmer3-fragment.detail
1359 t/data/glimmer3-fragment.predict
1360 t/data/Glimmer3.detail
1361 t/data/Glimmer3.predict
1362 t/data/GlimmerHMM.out
1364 t/data/gmap_f9-multiple_results.txt
1365 t/data/gmap_f9-reverse-strand.txt
1368 t/data/GO.defs.test2
1369 t/data/headerless.psl
1370 t/data/hg16_chroms.gff
1373 t/data/hmmpfam_cs.out
1374 t/data/hmmpfam_fake.out
1375 t/data/hmmpfam_HSPdashline.txt
1376 t/data/hmmpfam_multiresult.out
1378 t/data/hmmscan_multi_domain.out
1379 t/data/hmmscan_qry_stop.txt
1380 t/data/hmmscan_sec_struct.out
1381 t/data/hmmsearch.out
1382 t/data/hmmsearch3.out
1383 t/data/hmmsearch3_multi.out
1384 t/data/hs_est.est2genome
1385 t/data/hs_fugu.newick
1386 t/data/hs_owlmonkey.aln
1387 t/data/hs_owlmonkey.fas
1388 t/data/hs_owlmonkey.fasta
1389 t/data/hsinsulin.blastcl3.blastn
1390 t/data/HUMBETGLOA.fa
1391 t/data/HUMBETGLOA.FASTA
1392 t/data/HUMBETGLOA.gff
1393 t/data/HUMBETGLOA.grail
1394 t/data/HUMBETGLOA.grailexp
1395 t/data/HUMBETGLOA.mzef
1396 t/data/HUMBETGLOA.tblastx
1400 t/data/ids-with-spaces.phy
1402 t/data/insulin.water
1404 t/data/interpro_ebi.xml
1405 t/data/interpro_relationship.xml
1406 t/data/interpro_sample.xml
1407 t/data/interpro_short.xml
1408 t/data/intrablock-comment.nex
1410 t/data/Kingdoms_DNA.nex
1412 t/data/little.largemultifasta
1413 t/data/LittleChrY.dbsnp.xml
1414 t/data/LOAD_Ccd1.dnd
1415 t/data/long-names.nex
1416 t/data/longnames.aln
1417 t/data/longnames.dnd
1422 t/data/lysozyme6.protml
1423 t/data/lysozyme6.simple.protml
1426 t/data/map_hem/HEM1-HEM12.fa
1427 t/data/map_hem/HEM1-HEM12.fa.revcom
1428 t/data/map_hem/HEM1-HEM12.meme.txt
1429 t/data/map_hem/HEM1-HEM13.fa
1430 t/data/map_hem/HEM1-HEM13.meme.txt
1431 t/data/map_hem/HEM1-HEM14.fa
1432 t/data/map_hem/HEM1-HEM14.meme.txt
1433 t/data/map_hem/HEM1-HEM15.fa
1434 t/data/map_hem/HEM1-HEM15.meme.txt
1435 t/data/map_hem/HEM1-HEM2.fa
1436 t/data/map_hem/HEM1-HEM2.fa.revcom
1437 t/data/map_hem/HEM1-HEM2.meme.txt
1438 t/data/map_hem/HEM1-HEM3.fa
1439 t/data/map_hem/HEM1-HEM3.meme.txt
1440 t/data/map_hem/HEM1-HEM4.fa
1441 t/data/map_hem/HEM1-HEM4.meme.txt
1442 t/data/map_hem/HEM1.ups.fa_
1443 t/data/map_hem/HEM1.ups.fa_.revcom
1444 t/data/map_hem/HEM12-HEM13.fa
1445 t/data/map_hem/HEM12-HEM13.meme.txt
1446 t/data/map_hem/HEM12-HEM14.fa
1447 t/data/map_hem/HEM12-HEM14.meme.txt
1448 t/data/map_hem/HEM12-HEM15.fa
1449 t/data/map_hem/HEM12-HEM15.meme.txt
1450 t/data/map_hem/HEM12.ups.fa_
1451 t/data/map_hem/HEM12.ups.fa_.revcom
1452 t/data/map_hem/HEM13-HEM14.fa
1453 t/data/map_hem/HEM13-HEM14.meme.txt
1454 t/data/map_hem/HEM13-HEM15.fa
1455 t/data/map_hem/HEM13-HEM15.meme.txt
1456 t/data/map_hem/HEM13.ups.fa_
1457 t/data/map_hem/HEM13.ups.fa_.revcom
1458 t/data/map_hem/HEM14-HEM15.fa
1459 t/data/map_hem/HEM14-HEM15.meme.txt
1460 t/data/map_hem/HEM14.ups.fa_
1461 t/data/map_hem/HEM14.ups.fa_.revcom
1462 t/data/map_hem/HEM15.ups.fa_
1463 t/data/map_hem/HEM15.ups.fa_.revcom
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1471 t/data/map_hem/HEM2-HEM15.meme.txt
1472 t/data/map_hem/HEM2-HEM3.fa
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1474 t/data/map_hem/HEM2-HEM4.fa
1475 t/data/map_hem/HEM2-HEM4.meme.txt
1476 t/data/map_hem/HEM2.ups.fa_
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1478 t/data/map_hem/HEM3-HEM12.fa
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1482 t/data/map_hem/HEM3-HEM14.fa
1483 t/data/map_hem/HEM3-HEM14.meme.txt
1484 t/data/map_hem/HEM3-HEM15.fa
1485 t/data/map_hem/HEM3-HEM15.meme.txt
1486 t/data/map_hem/HEM3-HEM4.fa
1487 t/data/map_hem/HEM3-HEM4.meme.txt
1488 t/data/map_hem/HEM3.ups.fa_
1489 t/data/map_hem/HEM3.ups.fa_.revcom
1490 t/data/map_hem/HEM4-HEM12.fa
1491 t/data/map_hem/HEM4-HEM12.meme.txt
1492 t/data/map_hem/HEM4-HEM13.fa
1493 t/data/map_hem/HEM4-HEM13.meme.txt
1494 t/data/map_hem/HEM4-HEM14.fa
1495 t/data/map_hem/HEM4-HEM14.meme.txt
1496 t/data/map_hem/HEM4-HEM15.fa
1497 t/data/map_hem/HEM4-HEM15.meme.txt
1498 t/data/map_hem/HEM4.ups.fa_
1499 t/data/map_hem/HEM4.ups.fa_.revcom
1500 t/data/map_hem/yeast.nc.1.freq
1506 t/data/mbsout/mbsout_infile1
1507 t/data/mbsout/mbsout_infile2
1508 t/data/mbsout/mbsout_infile3
1509 t/data/Mcjanrna_rdbII.gbk
1510 t/data/megablast_output.paracel_btk
1512 t/data/mini-AE001405.gb
1513 t/data/mini-align.aln
1514 t/data/mixedmast.dat
1516 t/data/mpath.ontology.test
1518 t/data/msout/bad_msout_infile1
1519 t/data/msout/bad_msout_infile2
1520 t/data/msout/msout_infile1
1521 t/data/msout/msout_infile2
1522 t/data/msout/msout_infile3
1523 t/data/msout/msout_infile4
1524 t/data/multi.blast.m8
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1531 t/data/multifa.seq.qual
1532 t/data/multiline-intrablock-comment.nex
1533 t/data/multiresult_blastn+.bls
1535 t/data/multiseq_tags.phd
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1539 t/data/mutations.xml
1540 t/data/myco_sites.gff
1541 t/data/NC_000007-ribosomal-slippage.gb
1542 t/data/NC_001284.gbk
1543 t/data/NC_002058_multDBLINK_bug3375.gb
1545 t/data/NC_006511-short.gbk
1547 t/data/nei_gojobori_test.aln
1548 t/data/neighbor.dist
1549 t/data/new_blastn.txt
1550 t/data/nexml/characters.nexml.8.xml
1551 t/data/nexml/characters.nexml.xml
1552 t/data/nexml/trees.nexml.8.xml
1553 t/data/nexml/trees.nexml.xml
1554 t/data/nhmmer-3.1.out
1555 t/data/nhx-bacteria.nhx
1557 t/data/no-genes.genscan
1558 t/data/no_cds_example.gb
1560 t/data/no_hsps.blastp
1561 t/data/no_semicolon.newick
1562 t/data/noninterleaved.phy
1563 t/data/NT_021877.gbk
1564 t/data/nucmatrix.txt
1566 t/data/omim_genemap_test
1567 t/data/omim_genemap_test_nolinebreak
1568 t/data/omim_text_test
1569 t/data/ORTHOMCL2345.cluster.aa.fa.aln.aa.phy.txt
1575 t/data/pfam_tests.stk
1576 t/data/pfamOutput-bug3376.out
1580 t/data/phylipdist-36.out
1581 t/data/phylipdist.out
1582 t/data/phyloxml_examples.xml
1584 t/data/polymorphism.dat
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1586 t/data/polymorphism.xml
1587 t/data/popgen_saureus.dat
1588 t/data/popgen_saureus.multidat
1589 t/data/popstats.prettybase
1590 t/data/pre_rel9.swiss
1591 t/data/Primate_mtDNA.nex
1593 t/data/primer3_infile.txt
1594 t/data/primer3_outfile.txt
1595 t/data/primer3_output.txt
1597 t/data/promoterwise.out
1599 t/data/protpars_longid.phy
1600 t/data/pseudowise.out
1602 t/data/psiblastreport.out
1603 t/data/purine_v081.infernal
1607 t/data/qrna-relloc.out
1608 t/data/qualfile.qual
1609 t/data/quoted-strings1.nex
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1611 t/data/Rab1.chaos-xml
1612 t/data/radical-whitespace.nex
1613 t/data/radical-whitespace_02.nex
1614 t/data/rebase.itype2
1615 t/data/rebase.withrefm
1616 t/data/reference_ace.ace
1617 t/data/registry/bdb/seqdatabase.ini
1618 t/data/registry/flat/seqdatabase.ini
1619 t/data/regulation_test.obo
1621 t/data/repeatmasker.fa.out
1622 t/data/revcomp_mrna.gb
1623 t/data/rfam_tests.stk
1624 t/data/ribosome-slippage.gb
1631 t/data/rpsblast_no_hits.bls
1632 t/data/sample_dataset.tigr
1633 t/data/sbay_c127.fas
1634 t/data/sbay_c545-yeast.BLASTZ.PSL
1636 t/data/semicolon.newick
1637 t/data/seqdatabase.ini
1638 t/data/seqfeaturedb/test.gff3
1641 t/data/sequencefamily.dat
1644 t/data/signalp.hmm.short
1645 t/data/signalp.hmm.summary
1646 t/data/signalp.negative.out
1647 t/data/signalp.nn.short
1648 t/data/signalp.nn.summary
1649 t/data/signalp.positive.out
1650 t/data/signalp.short
1651 t/data/signalp.summary
1655 t/data/singleNSsite.mlc
1656 t/data/singlescore.gbk
1657 t/data/singlet_w_CT.ace
1659 t/data/sofa.ontology
1660 t/data/sp_subset.obo
1661 t/data/spaced_fasta.fa
1663 t/data/SPAN_Family4nl.nex
1664 t/data/SPAN_Family7n.nex
1665 t/data/SPAN_Family8a.nex
1666 t/data/sparsealn.needle
1667 t/data/spidey.noalignment
1669 t/data/sprintf.rnamotif
1670 t/data/ssp160.embl.1
1671 t/data/sv40_small.xml
1673 t/data/swisspfam.data
1674 t/data/SwissProt.dat
1679 t/data/tandem_repeats_finder.dat
1680 t/data/tandem_repeats_finder.noresults
1681 t/data/tandem_repeats_finder_no_desc.dat
1683 t/data/taxdump/names.dmp
1684 t/data/taxdump/nodes.dmp
1685 t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt
1686 t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta
1690 t/data/test-1.tab.gb
1691 t/data/test-3.0-1.meme
1692 t/data/test-3.0-2.meme
1693 t/data/test-4.9.meme
1698 t/data/test.cns.fastq
1707 t/data/test.gcgblast
1708 t/data/test.gcgfasta
1710 t/data/test.genbank.noseq
1711 t/data/test.infernal
1712 t/data/test.interpro
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1714 t/data/test.lasergene
1715 t/data/test.locuslink
1717 t/data/test.metafasta
1734 t/data/test1.blasttab3
1735 t/data/test1.wublastp
1736 t/data/test2.infernal
1738 t/data/test_badlf.gcg
1739 t/data/test_clear_range.fastq
1740 t/data/test_data.axt
1741 t/data/test_singlets.cns.fastq
1742 t/data/test_singlets.maq
1743 t/data/test_space.embl
1745 t/data/testaln.clustalw
1746 t/data/testaln.fasta
1747 t/data/testaln.fastq
1751 t/data/testaln.metafasta
1753 t/data/testaln.nexus
1755 t/data/testaln.phylip
1757 t/data/testaln.prodom
1759 t/data/testaln.selex
1760 t/data/testaln.stockholm
1763 t/data/testaln2.fasta
1764 t/data/testdat.exonerate
1765 t/data/testdata.crossmatch
1766 t/data/testdbaccnums.out
1767 t/data/testfile.erpin
1768 t/data/testfuzzy.genbank
1772 t/data/tol-2010-02-18.nhx
1774 t/data/traittree.nexus
1776 t/data/transfac_pro/factor.dat
1777 t/data/transfac_pro/fragment.dat
1778 t/data/transfac_pro/gene.dat
1779 t/data/transfac_pro/matrix.dat
1780 t/data/transfac_pro/readme.txt
1781 t/data/transfac_pro/reference.dat
1782 t/data/transfac_pro/site.dat
1783 t/data/tree_nonewline.nexus
1784 t/data/Treebase-chlamy-dna.nex
1785 t/data/trees.nexml.old.xml
1786 t/data/tricky.wublast
1787 t/data/trna.strict.rnamotif
1790 t/data/U71225.gb.mac
1791 t/data/U71225.gb.unix
1792 t/data/U71225.gb.win
1794 t/data/UnaSmithHIV-both.nex
1796 t/data/urease.tre.nexus
1799 t/data/wellcome_tol.nhx
1801 t/data/worm_fam_2785.cdna
1802 t/data/X98338_Adh-mRNA.gb
1803 t/data/yeast.tRNAscanSE
1806 t/data/YP_007988852.gp
1807 t/data/ZABJ4EA7014.CH878695.1.blast.txt
1812 t/LiveSeq/Mutation.t
1814 t/LocalDB/BioDBGFF.t
1817 t/LocalDB/Index/Blast.t
1818 t/LocalDB/Index/BlastTable.t
1819 t/LocalDB/Index/Index.t
1821 t/LocalDB/Registry.t
1822 t/LocalDB/SeqFeature.t
1823 t/LocalDB/Taxonomy/greengenes.t
1824 t/LocalDB/Taxonomy/silva.t
1825 t/LocalDB/Taxonomy/sqlite.t
1826 t/LocalDB/transfac_pro.t
1831 t/Map/MicrosatelliteMarker.t
1833 t/Matrix/InstanceSite.t
1837 t/Matrix/ProtMatrix.t
1839 t/Matrix/SiteMatrix.t
1842 t/Ontology/GraphAdaptor.t
1844 t/Ontology/IO/interpro.t
1846 t/Ontology/Ontology.t
1847 t/Ontology/OntologyEngine.t
1848 t/Ontology/OntologyStore.t
1849 t/Ontology/Relationship.t
1850 t/Ontology/RelationshipType.t
1853 t/Phenotype/Correlate.t
1854 t/Phenotype/Measure.t
1856 t/Phenotype/MiniMIMentry.t
1857 t/Phenotype/OMIMentry.t
1858 t/Phenotype/OMIMentryAllelicVariant.t
1859 t/Phenotype/OMIMparser.t
1860 t/Phenotype/Phenotype.t
1862 t/PopGen/Coalescent.t
1866 t/PopGen/PopGenSims.t
1867 t/PopGen/TagHaplotype.t
1868 t/RemoteDB/BioFetch.t
1871 t/RemoteDB/EntrezGene.t
1872 t/RemoteDB/GenBank.t
1873 t/RemoteDB/GenPept.t
1874 t/RemoteDB/HIV/HIV.t
1875 t/RemoteDB/HIV/HIVAnnotProcessor.t
1876 t/RemoteDB/HIV/HIVQuery.t
1877 t/RemoteDB/HIV/HIVQueryHelper.t
1879 t/RemoteDB/Query/GenBank.t
1881 t/RemoteDB/SeqRead_fail.t
1882 t/RemoteDB/SeqVersion.t
1883 t/RemoteDB/SwissProt.t
1884 t/RemoteDB/Taxonomy.t
1885 t/Restriction/Analysis-refac.t
1886 t/Restriction/Analysis.t
1899 t/SearchIO/blast_pull.t
1900 t/SearchIO/blasttable.t
1901 t/SearchIO/CigarString.t
1902 t/SearchIO/cross_match.t
1904 t/SearchIO/exonerate.t
1906 t/SearchIO/gmap_f9.t
1908 t/SearchIO/hmmer_pull.t
1909 t/SearchIO/infernal.t
1910 t/SearchIO/megablast.t
1912 t/SearchIO/rnamotif.t
1913 t/SearchIO/SearchIO.t
1915 t/SearchIO/SimilarityPair.t
1919 t/SearchIO/Writer/GbrowseGFF.t
1920 t/SearchIO/Writer/HitTableWriter.t
1921 t/SearchIO/Writer/HSPTableWriter.t
1922 t/SearchIO/Writer/HTMLWriter.t
1923 t/SearchIO/Writer/TextWriter.t
1926 t/Seq/LargeLocatableSeq.t
1928 t/Seq/LocatableSeq.t
1935 t/Seq/SimulatedRead.t
1938 t/SeqFeature/Amplicon.t
1939 t/SeqFeature/Clone.t
1940 t/SeqFeature/Collection.t
1941 t/SeqFeature/Computation.t
1942 t/SeqFeature/FeaturePair.t
1944 t/SeqFeature/Generic.t
1945 t/SeqFeature/Location.t
1946 t/SeqFeature/LocationFactory.t
1947 t/SeqFeature/Primer.t
1948 t/SeqFeature/Range.t
1949 t/SeqFeature/RangeI.t
1950 t/SeqFeature/SeqAnalysisParser.t
1951 t/SeqFeature/SubSeq.t
1952 t/SeqFeature/Unflattener.t
1965 t/SeqIO/entrezgene.t
1970 t/SeqIO/flybase_chadoxml.t
1978 t/SeqIO/largefasta.t
1985 t/SeqIO/Multiple_fasta.t
1993 t/SeqIO/SeqBuilder.t
1996 t/SeqIO/Splicedseq.t
2005 t/SeqTools/Backtranslate.t
2006 t/SeqTools/CodonTable.t
2007 t/SeqTools/ECnumber.t
2008 t/SeqTools/GuessSeqFormat.t
2009 t/SeqTools/OddCodes.t
2010 t/SeqTools/SeqPattern.t
2011 t/SeqTools/SeqStats.t
2012 t/SeqTools/SeqUtils.t
2013 t/SeqTools/SeqWords.t
2016 t/Structure/Structure.t
2019 t/Tools/Alignment/Consed.t
2020 t/Tools/AmpliconSearch.t
2021 t/Tools/Analysis/DNA/ESEfinder.t
2022 t/Tools/Analysis/Protein/Domcut.t
2023 t/Tools/Analysis/Protein/ELM.t
2024 t/Tools/Analysis/Protein/GOR4.t
2025 t/Tools/Analysis/Protein/HNN.t
2026 t/Tools/Analysis/Protein/NetPhos.t
2027 t/Tools/Analysis/Protein/Scansite.t
2028 t/Tools/Analysis/Protein/Sopma.t
2029 t/Tools/EMBOSS/Palindrome.t
2031 t/Tools/Est2Genome.t
2032 t/Tools/FootPrinter.t
2035 t/Tools/Genomewise.t
2042 t/Tools/Phylo/Gerp.t
2043 t/Tools/Phylo/Molphy.t
2044 t/Tools/Phylo/PAML.t
2045 t/Tools/Phylo/Phylip/ProtDist.t
2046 t/Tools/pICalculator.t
2048 t/Tools/Promoterwise.t
2049 t/Tools/Pseudowise.t
2051 t/Tools/RandDistFunctions.t
2052 t/Tools/RepeatMasker.t
2054 t/Tools/Run/RemoteBlast.t
2055 t/Tools/Run/RemoteBlast_rpsblast.t
2059 t/Tools/Signalp/ExtendedSignalp.t
2062 t/Tools/Spidey/Spidey.t
2063 t/Tools/TandemRepeatsFinder.t
2066 t/Tools/tRNAscanSE.t
2069 t/Tree/PhyloNetwork/Factory.t
2070 t/Tree/PhyloNetwork/GraphViz.t
2071 t/Tree/PhyloNetwork/MuVector.t
2072 t/Tree/PhyloNetwork/PhyloNetwork.t
2073 t/Tree/PhyloNetwork/RandomFactory.t
2074 t/Tree/PhyloNetwork/TreeFactory.t
2075 t/Tree/RandomTreeFactory.t
2078 t/Tree/TreeIO/lintree.t
2079 t/Tree/TreeIO/newick.t
2080 t/Tree/TreeIO/nexml.t
2081 t/Tree/TreeIO/nexus.t
2083 t/Tree/TreeIO/phyloxml.t
2084 t/Tree/TreeIO/svggraph.t
2085 t/Tree/TreeIO/tabtree.t
2086 t/Tree/TreeStatistics.t
2087 t/Variation/AAChange.t
2088 t/Variation/AAReverseMutate.t
2089 t/Variation/Allele.t
2090 t/Variation/DNAMutation.t
2091 t/Variation/RNAChange.t
2092 t/Variation/SeqDiff.t
2094 t/Variation/Variation_IO.t
2095 travis_scripts/dependency_installs