| blob | e79f1447dfa0c394412e596ce99bb6034ac58ea9 |
1 AUTHORS
2 Bio/Align/AlignI.pm
3 Bio/Align/DNAStatistics.pm
4 Bio/Align/Graphics.pm
5 Bio/Align/PairwiseStatistics.pm
6 Bio/Align/ProteinStatistics.pm
7 Bio/Align/StatisticsI.pm
8 Bio/Align/Utilities.pm
9 Bio/AlignIO.pm
10 Bio/AlignIO/arp.pm
11 Bio/AlignIO/bl2seq.pm
12 Bio/AlignIO/clustalw.pm
13 Bio/AlignIO/emboss.pm
14 Bio/AlignIO/fasta.pm
15 Bio/AlignIO/Handler/GenericAlignHandler.pm
16 Bio/AlignIO/largemultifasta.pm
17 Bio/AlignIO/maf.pm
18 Bio/AlignIO/mase.pm
19 Bio/AlignIO/mega.pm
20 Bio/AlignIO/meme.pm
21 Bio/AlignIO/metafasta.pm
22 Bio/AlignIO/msf.pm
23 Bio/AlignIO/nexml.pm
24 Bio/AlignIO/nexus.pm
25 Bio/AlignIO/pfam.pm
26 Bio/AlignIO/phylip.pm
27 Bio/AlignIO/po.pm
28 Bio/AlignIO/proda.pm
29 Bio/AlignIO/prodom.pm
30 Bio/AlignIO/psi.pm
31 Bio/AlignIO/selex.pm
32 Bio/AlignIO/stockholm.pm
33 Bio/AlignIO/xmfa.pm
34 Bio/AnalysisI.pm
35 Bio/AnalysisParserI.pm
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38 Bio/Annotation/AnnotationFactory.pm
39 Bio/Annotation/Collection.pm
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50 Bio/Annotation/TypeManager.pm
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66 Bio/Biblio.pm
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206 Bio/DB/Query/HIVQuery.pm
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226 Bio/DB/SeqFeature/Store/FeatureFileLoader.pm
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299 Bio/LiveSeq/IO/README
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618 Bio/SeqFeature/Similarity.pm
619 Bio/SeqFeature/SimilarityPair.pm
620 Bio/SeqFeature/SiRNA/Oligo.pm
621 Bio/SeqFeature/SiRNA/Pair.pm
622 Bio/SeqFeature/Tools/FeatureNamer.pm
623 Bio/SeqFeature/Tools/IDHandler.pm
624 Bio/SeqFeature/Tools/TypeMapper.pm
625 Bio/SeqFeature/Tools/Unflattener.pm
626 Bio/SeqFeature/TypedSeqFeatureI.pm
627 Bio/SeqFeatureI.pm
628 Bio/SeqI.pm
629 Bio/SeqIO.pm
630 Bio/SeqIO/abi.pm
631 Bio/SeqIO/ace.pm
632 Bio/SeqIO/agave.pm
633 Bio/SeqIO/alf.pm
634 Bio/SeqIO/asciitree.pm
635 Bio/SeqIO/bsml.pm
636 Bio/SeqIO/bsml_sax.pm
637 Bio/SeqIO/chadoxml.pm
638 Bio/SeqIO/chaos.pm
639 Bio/SeqIO/chaosxml.pm
640 Bio/SeqIO/ctf.pm
641 Bio/SeqIO/embl.pm
642 Bio/SeqIO/embldriver.pm
643 Bio/SeqIO/entrezgene.pm
644 Bio/SeqIO/excel.pm
645 Bio/SeqIO/exp.pm
646 Bio/SeqIO/fasta.pm
647 Bio/SeqIO/fastq.pm
648 Bio/SeqIO/flybase_chadoxml.pm
649 Bio/SeqIO/FTHelper.pm
650 Bio/SeqIO/game.pm
651 Bio/SeqIO/game/featHandler.pm
652 Bio/SeqIO/game/gameHandler.pm
653 Bio/SeqIO/game/gameSubs.pm
654 Bio/SeqIO/game/gameWriter.pm
655 Bio/SeqIO/game/seqHandler.pm
656 Bio/SeqIO/gbdriver.pm
657 Bio/SeqIO/gbxml.pm
658 Bio/SeqIO/gcg.pm
659 Bio/SeqIO/genbank.pm
660 Bio/SeqIO/Handler/GenericRichSeqHandler.pm
661 Bio/SeqIO/interpro.pm
662 Bio/SeqIO/kegg.pm
663 Bio/SeqIO/largefasta.pm
664 Bio/SeqIO/lasergene.pm
665 Bio/SeqIO/locuslink.pm
666 Bio/SeqIO/mbsout.pm
667 Bio/SeqIO/metafasta.pm
668 Bio/SeqIO/msout.pm
669 Bio/SeqIO/MultiFile.pm
670 Bio/SeqIO/nexml.pm
671 Bio/SeqIO/phd.pm
672 Bio/SeqIO/pir.pm
673 Bio/SeqIO/pln.pm
674 Bio/SeqIO/qual.pm
675 Bio/SeqIO/raw.pm
676 Bio/SeqIO/scf.pm
677 Bio/SeqIO/seqxml.pm
678 Bio/SeqIO/strider.pm
679 Bio/SeqIO/swiss.pm
680 Bio/SeqIO/swissdriver.pm
681 Bio/SeqIO/tab.pm
682 Bio/SeqIO/table.pm
683 Bio/SeqIO/tigr.pm
684 Bio/SeqIO/tigrxml.pm
685 Bio/SeqIO/tinyseq.pm
686 Bio/SeqIO/tinyseq/tinyseqHandler.pm
687 Bio/SeqIO/ztr.pm
688 Bio/SeqUtils.pm
689 Bio/SimpleAlign.pm
690 Bio/SimpleAnalysisI.pm
691 Bio/Species.pm
692 Bio/Structure/Atom.pm
693 Bio/Structure/Chain.pm
694 Bio/Structure/Entry.pm
695 Bio/Structure/IO.pm
696 Bio/Structure/IO/pdb.pm
697 Bio/Structure/Model.pm
698 Bio/Structure/Residue.pm
699 Bio/Structure/SecStr/DSSP/Res.pm
700 Bio/Structure/SecStr/STRIDE/Res.pm
701 Bio/Structure/StructureI.pm
702 Bio/Symbol/Alphabet.pm
703 Bio/Symbol/AlphabetI.pm
704 Bio/Symbol/DNAAlphabet.pm
705 Bio/Symbol/ProteinAlphabet.pm
706 Bio/Symbol/README.Symbol
707 Bio/Symbol/Symbol.pm
708 Bio/Symbol/SymbolI.pm
709 Bio/Taxon.pm
710 Bio/Taxonomy.pm
711 Bio/Taxonomy/FactoryI.pm
712 Bio/Taxonomy/Node.pm
713 Bio/Taxonomy/Taxon.pm
714 Bio/Taxonomy/Tree.pm
715 Bio/Tools/AlignFactory.pm
716 Bio/Tools/Alignment/Consed.pm
717 Bio/Tools/Alignment/Trim.pm
718 Bio/Tools/Analysis/DNA/ESEfinder.pm
719 Bio/Tools/Analysis/Protein/Domcut.pm
720 Bio/Tools/Analysis/Protein/ELM.pm
721 Bio/Tools/Analysis/Protein/GOR4.pm
722 Bio/Tools/Analysis/Protein/HNN.pm
723 Bio/Tools/Analysis/Protein/Mitoprot.pm
724 Bio/Tools/Analysis/Protein/NetPhos.pm
725 Bio/Tools/Analysis/Protein/Scansite.pm
726 Bio/Tools/Analysis/Protein/Sopma.pm
727 Bio/Tools/Analysis/SimpleAnalysisBase.pm
728 Bio/Tools/AnalysisResult.pm
729 Bio/Tools/Blat.pm
730 Bio/Tools/CodonTable.pm
731 Bio/Tools/Coil.pm
732 Bio/Tools/dpAlign.pm
733 Bio/Tools/ECnumber.pm
734 Bio/Tools/EMBOSS/Palindrome.pm
735 Bio/Tools/EPCR.pm
736 Bio/Tools/Eponine.pm
737 Bio/Tools/ERPIN.pm
738 Bio/Tools/Est2Genome.pm
739 Bio/Tools/ESTScan.pm
740 Bio/Tools/EUtilities.pm
741 Bio/Tools/EUtilities/EUtilDataI.pm
742 Bio/Tools/EUtilities/EUtilParameters.pm
743 Bio/Tools/EUtilities/History.pm
744 Bio/Tools/EUtilities/HistoryI.pm
745 Bio/Tools/EUtilities/Info.pm
746 Bio/Tools/EUtilities/Info/FieldInfo.pm
747 Bio/Tools/EUtilities/Info/LinkInfo.pm
748 Bio/Tools/EUtilities/Link.pm
749 Bio/Tools/EUtilities/Link/LinkSet.pm
750 Bio/Tools/EUtilities/Link/UrlLink.pm
751 Bio/Tools/EUtilities/Query.pm
752 Bio/Tools/EUtilities/Query/GlobalQuery.pm
753 Bio/Tools/EUtilities/Summary.pm
754 Bio/Tools/EUtilities/Summary/DocSum.pm
755 Bio/Tools/EUtilities/Summary/Item.pm
756 Bio/Tools/EUtilities/Summary/ItemContainerI.pm
757 Bio/Tools/Fgenesh.pm
758 Bio/Tools/FootPrinter.pm
759 Bio/Tools/Gel.pm
760 Bio/Tools/Geneid.pm
761 Bio/Tools/Genemark.pm
762 Bio/Tools/Genewise.pm
763 Bio/Tools/Genomewise.pm
764 Bio/Tools/Genscan.pm
765 Bio/Tools/GFF.pm
766 Bio/Tools/Glimmer.pm
767 Bio/Tools/Grail.pm
768 Bio/Tools/GuessSeqFormat.pm
769 Bio/Tools/HMMER/Domain.pm
770 Bio/Tools/HMMER/Results.pm
771 Bio/Tools/HMMER/Set.pm
772 Bio/Tools/Hmmpfam.pm
773 Bio/Tools/Infernal.pm
774 Bio/Tools/ipcress.pm
775 Bio/Tools/isPcr.pm
776 Bio/Tools/IUPAC.pm
777 Bio/Tools/Lucy.pm
778 Bio/Tools/Match.pm
779 Bio/Tools/MZEF.pm
780 Bio/Tools/OddCodes.pm
781 Bio/Tools/Phylo/Gerp.pm
782 Bio/Tools/Phylo/Gumby.pm
783 Bio/Tools/Phylo/Molphy.pm
784 Bio/Tools/Phylo/Molphy/Result.pm
785 Bio/Tools/Phylo/PAML.pm
786 Bio/Tools/Phylo/PAML/Codeml.pm
787 Bio/Tools/Phylo/PAML/ModelResult.pm
788 Bio/Tools/Phylo/PAML/Result.pm
789 Bio/Tools/Phylo/Phylip/ProtDist.pm
790 Bio/Tools/pICalculator.pm
791 Bio/Tools/Prediction/Exon.pm
792 Bio/Tools/Prediction/Gene.pm
793 Bio/Tools/Primer/Assessor/Base.pm
794 Bio/Tools/Primer/AssessorI.pm
795 Bio/Tools/Primer/Feature.pm
796 Bio/Tools/Primer/Pair.pm
797 Bio/Tools/Primer3.pm
798 Bio/Tools/Prints.pm
799 Bio/Tools/Profile.pm
800 Bio/Tools/Promoterwise.pm
801 Bio/Tools/PrositeScan.pm
802 Bio/Tools/Protparam.pm
803 Bio/Tools/Pseudowise.pm
804 Bio/Tools/pSW.pm
805 Bio/Tools/QRNA.pm
806 Bio/Tools/RandomDistFunctions.pm
807 Bio/Tools/RepeatMasker.pm
808 Bio/Tools/RNAMotif.pm
809 Bio/Tools/Run/GenericParameters.pm
810 Bio/Tools/Run/hmmer3.pm
811 Bio/Tools/Run/ParametersI.pm
812 Bio/Tools/Run/README
813 Bio/Tools/Run/RemoteBlast.pm
814 Bio/Tools/Run/StandAloneBlast.pm
815 Bio/Tools/Run/StandAloneNCBIBlast.pm
816 Bio/Tools/Run/StandAloneWUBlast.pm
817 Bio/Tools/Run/WrapperBase.pm
818 Bio/Tools/Run/WrapperBase/CommandExts.pm
819 Bio/Tools/Seg.pm
820 Bio/Tools/SeqPattern.pm
821 Bio/Tools/SeqPattern/Backtranslate.pm
822 Bio/Tools/SeqStats.pm
823 Bio/Tools/SeqWords.pm
824 Bio/Tools/Sigcleave.pm
825 Bio/Tools/Signalp.pm
826 Bio/Tools/Signalp/ExtendedSignalp.pm
827 Bio/Tools/Sim4/Exon.pm
828 Bio/Tools/Sim4/Results.pm
829 Bio/Tools/SiRNA.pm
830 Bio/Tools/SiRNA/Ruleset/saigo.pm
831 Bio/Tools/SiRNA/Ruleset/tuschl.pm
832 Bio/Tools/Spidey/Exon.pm
833 Bio/Tools/Spidey/Results.pm
834 Bio/Tools/TandemRepeatsFinder.pm
835 Bio/Tools/TargetP.pm
836 Bio/Tools/Tmhmm.pm
837 Bio/Tools/tRNAscanSE.pm
838 Bio/Tree/AlleleNode.pm
839 Bio/Tree/AnnotatableNode.pm
840 Bio/Tree/Compatible.pm
841 Bio/Tree/DistanceFactory.pm
842 Bio/Tree/Draw/Cladogram.pm
843 Bio/Tree/Node.pm
844 Bio/Tree/NodeI.pm
845 Bio/Tree/NodeNHX.pm
846 Bio/Tree/RandomFactory.pm
847 Bio/Tree/Statistics.pm
848 Bio/Tree/Tree.pm
849 Bio/Tree/TreeFunctionsI.pm
850 Bio/Tree/TreeI.pm
851 Bio/TreeIO.pm
852 Bio/TreeIO/cluster.pm
853 Bio/TreeIO/lintree.pm
854 Bio/TreeIO/newick.pm
855 Bio/TreeIO/NewickParser.pm
856 Bio/TreeIO/nexml.pm
857 Bio/TreeIO/nexus.pm
858 Bio/TreeIO/nhx.pm
859 Bio/TreeIO/pag.pm
860 Bio/TreeIO/phyloxml.pm
861 Bio/TreeIO/svggraph.pm
862 Bio/TreeIO/tabtree.pm
863 Bio/TreeIO/TreeEventBuilder.pm
864 Bio/UpdateableSeqI.pm
865 Bio/Variation/AAChange.pm
866 Bio/Variation/AAReverseMutate.pm
867 Bio/Variation/Allele.pm
868 Bio/Variation/DNAMutation.pm
869 Bio/Variation/IO.pm
870 Bio/Variation/IO/flat.pm
871 Bio/Variation/IO/xml.pm
872 Bio/Variation/README
873 Bio/Variation/RNAChange.pm
874 Bio/Variation/SeqDiff.pm
875 Bio/Variation/SNP.pm
876 Bio/Variation/VariantI.pm
877 Bio/WebAgent.pm
878 BioPerl.pm
879 BUGS
880 Build.PL
881 Changes
882 DEPENDENCIES
883 DEPRECATED
884 doc/Deobfuscator/bin/deob_index.pl
885 doc/Deobfuscator/Build.PL
886 doc/Deobfuscator/cgi-bin/deob_detail.cgi
887 doc/Deobfuscator/cgi-bin/deob_flowchart.png
888 doc/Deobfuscator/cgi-bin/deob_help.html
889 doc/Deobfuscator/cgi-bin/deob_interface.cgi
890 doc/Deobfuscator/Changes
891 doc/Deobfuscator/excluded_modules.txt
892 doc/Deobfuscator/lib/Deobfuscator.pm
893 doc/Deobfuscator/LICENSE
894 doc/Deobfuscator/Makefile.PL
895 doc/Deobfuscator/MANIFEST
896 doc/Deobfuscator/META.yml
897 doc/Deobfuscator/README
898 doc/Deobfuscator/t/00.load.t
899 doc/Deobfuscator/t/pod.t
900 doc/makedoc.PL
901 doc/README
902 examples/align/align_on_codons.pl
903 examples/align/aligntutorial.pl
904 examples/align/clustalw.pl
905 examples/align/simplealign.pl
906 examples/biblio/biblio-eutils-example.pl
907 examples/biblio/biblio-soap-example.pl
908 examples/biblio/biblio_soap.pl
909 examples/Bio-DB-GFF/load_ucsc.pl
910 examples/bioperl.pl
911 examples/cluster/dbsnp.pl
912 examples/contributed/nmrpdb_parse.pl
913 examples/contributed/prosite2perl.pl
914 examples/contributed/rebase2list.pl
915 examples/db/dbfetch
916 examples/db/est_tissue_query.pl
917 examples/db/gb2features.pl
918 examples/db/get_seqs.pl
919 examples/db/getGenBank.pl
920 examples/db/rfetch.pl
921 examples/db/use_registry.pl
922 examples/generate_random_seq.pl
923 examples/liveseq/change_gene.pl
924 examples/longorf.pl
925 examples/make_primers.pl
926 examples/popgen/parse_calc_stats.pl
927 examples/quality/svgtrace.pl
928 examples/rev_and_trans.pl
929 examples/revcom_dir.pl
930 examples/root/exceptions1.pl
931 examples/root/exceptions2.pl
932 examples/root/exceptions3.pl
933 examples/root/exceptions4.pl
934 examples/root/lib/TestInterface.pm
935 examples/root/lib/TestObject.pm
936 examples/root/README
937 examples/searchio/blast_example.pl
938 examples/searchio/custom_writer.pl
939 examples/searchio/hitwriter.pl
940 examples/searchio/hspwriter.pl
941 examples/searchio/htmlwriter.pl
942 examples/searchio/psiblast_features.pl
943 examples/searchio/psiblast_iterations.pl
944 examples/searchio/rawwriter.pl
945 examples/searchio/resultwriter.pl
946 examples/searchio/waba2gff.pl
947 examples/searchio/waba2gff3.pl
948 examples/sirna/rnai_finder.cgi
949 examples/sirna/TAG
950 examples/structure/structure-io.pl
951 examples/subsequence.cgi
952 examples/tk/gsequence.pl
953 examples/tk/hitdisplay.pl
954 examples/tools/extract_genes.pl
955 examples/tools/gb_to_gff.pl
956 examples/tools/gff2ps.pl
957 examples/tools/parse_codeml.pl
958 examples/tools/psw.pl
959 examples/tools/reverse-translate.pl
960 examples/tools/run_genscan.pl
961 examples/tools/run_primer3.pl
962 examples/tools/seq_pattern.pl
963 examples/tools/standaloneblast.pl
964 examples/tree/paup2phylip.pl
965 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar
966 ide/bioperl-mode/dist/bioperl-mode-xemacs.tar.md5
967 ide/bioperl-mode/dist/bioperl-mode.tar
968 ide/bioperl-mode/dist/bioperl-mode.tar.md5
969 ide/bioperl-mode/dist/Changes
970 ide/bioperl-mode/dist/package-me
971 ide/bioperl-mode/dist/SKIP
972 ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
973 ide/bioperl-mode/etc/images/bpmode-tool.xpm
974 ide/bioperl-mode/README
975 ide/bioperl-mode/site-lisp/bioperl-init.el
976 ide/bioperl-mode/site-lisp/bioperl-mode.el
977 ide/bioperl-mode/site-lisp/bioperl-skel.el
978 ide/bioperl-mode/site-lisp/pod.el
979 ide/bioperl.komodo
980 INSTALL
981 INSTALL.SKIP
982 INSTALL.WIN
983 LICENSE
984 maintenance/authors.pl
985 maintenance/big_split/file_classification.csv
986 maintenance/big_split/rbuels_notes.txt
987 maintenance/check_NAME.pl
988 maintenance/check_URLs.pl
989 maintenance/cvs2cl_by_file.pl
990 maintenance/dependencies.pl
991 maintenance/deprecated.pl
992 maintenance/module_usage.pl
993 maintenance/modules.pl
994 maintenance/ncbi_blast_switches.pl
995 maintenance/perltidy.conf
996 maintenance/pod.pl
997 maintenance/README
998 maintenance/symlink_script.pl
999 maintenance/version.pl
1000 MANIFEST This list of files
1001 models/biblio.dia
1002 models/bio_liveseq_variation.dia
1003 models/bio_map.dia
1004 models/bio_restriction.dia
1005 models/bioperl.dia
1006 models/coordinatemapper.dia
1007 models/map_proposal.txt
1008 models/maps_and_markers.dia
1009 models/popgen.dia
1010 models/population_proposal.txt
1011 models/README
1012 README
1013 scripts/biblio/biblio.PLS
1014 scripts/biblio/TAG
1015 scripts/Bio-DB-EUtilities/einfo.PLS
1016 scripts/Bio-DB-GFF/bulk_load_gff.PLS
1017 scripts/Bio-DB-GFF/fast_load_gff.PLS
1018 scripts/Bio-DB-GFF/genbank2gff.PLS
1019 scripts/Bio-DB-GFF/genbank2gff3.PLS
1020 scripts/Bio-DB-GFF/generate_histogram.PLS
1021 scripts/Bio-DB-GFF/load_gff.PLS
1022 scripts/Bio-DB-GFF/meta_gff.PLS
1023 scripts/Bio-DB-GFF/process_gadfly.PLS
1024 scripts/Bio-DB-GFF/process_sgd.PLS
1025 scripts/Bio-DB-GFF/process_wormbase.PLS
1026 scripts/Bio-DB-GFF/README
1027 scripts/Bio-SeqFeature-Store/bp_seqfeature_delete.PLS
1028 scripts/Bio-SeqFeature-Store/bp_seqfeature_gff3.PLS
1029 scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
1030 scripts/bioperl_netinstall.pl
1031 scripts/das/das_server.pl
1032 scripts/das/README
1033 scripts/das/TAG
1034 scripts/DB-HIV/hivq.PLS
1035 scripts/DB/biofetch_genbank_proxy.PLS
1036 scripts/DB/bioflat_index.PLS
1037 scripts/DB/biogetseq.PLS
1038 scripts/DB/flanks.PLS
1039 scripts/DB/TAG
1040 scripts/index/bp_fetch.PLS
1041 scripts/index/bp_index.PLS
1042 scripts/index/bp_seqret.PLS
1043 scripts/index/TAG
1044 scripts/popgen/composite_LD.PLS
1045 scripts/popgen/heterogeneity_test.PLS
1046 scripts/README
1047 scripts/searchio/fastam9_to_table.PLS
1048 scripts/searchio/filter_search.PLS
1049 scripts/searchio/hmmer_to_table.PLS
1050 scripts/searchio/parse_hmmsearch.PLS
1051 scripts/searchio/README
1052 scripts/searchio/search2table.PLS
1053 scripts/searchio/TAG
1054 scripts/seq/extract_feature_seq.PLS
1055 scripts/seq/make_mrna_protein.PLS
1056 scripts/seq/seqconvert.PLS
1057 scripts/seq/seqretsplit.PLS
1058 scripts/seq/split_seq.PLS
1059 scripts/seq/TAG
1060 scripts/seq/translate_seq.PLS
1061 scripts/seq/unflatten_seq.PLS
1062 scripts/seqstats/aacomp.PLS
1063 scripts/seqstats/chaos_plot.PLS
1064 scripts/seqstats/gccalc.PLS
1065 scripts/seqstats/oligo_count.PLS
1066 scripts/seqstats/TAG
1067 scripts/taxa/classify_hits_kingdom.PLS
1068 scripts/taxa/local_taxonomydb_query.PLS
1069 scripts/taxa/query_entrez_taxa.PLS
1070 scripts/taxa/TAG
1071 scripts/taxa/taxid4species.PLS
1072 scripts/taxa/taxonomy2tree.PLS
1073 scripts/tree/blast2tree.PLS
1074 scripts/tree/nexus2nh.PLS
1075 scripts/tree/TAG
1076 scripts/tree/tree2pag.PLS
1077 scripts/utilities/bp_mrtrans.PLS
1078 scripts/utilities/bp_nrdb.PLS
1079 scripts/utilities/bp_sreformat.PLS
1080 scripts/utilities/dbsplit.PLS
1081 scripts/utilities/download_query_genbank.PLS
1082 scripts/utilities/mask_by_search.PLS
1083 scripts/utilities/mutate.PLS
1084 scripts/utilities/pairwise_kaks.PLS
1085 scripts/utilities/README
1086 scripts/utilities/remote_blast.PLS
1087 scripts/utilities/revtrans-motif.PLS
1088 scripts/utilities/search2alnblocks.PLS
1089 scripts/utilities/search2BSML.PLS
1090 scripts/utilities/search2gff.PLS
1091 scripts/utilities/search2tribe.PLS
1092 scripts/utilities/seq_length.PLS
1093 scripts/utilities/TAG
1094 t/Align/AlignStats.t
1095 t/Align/AlignUtil.t
1096 t/Align/Graphics.t
1097 t/Align/SimpleAlign.t
1098 t/Align/TreeBuild.t
1099 t/Align/Utilities.t
1100 t/AlignIO/AlignIO.t
1101 t/AlignIO/arp.t
1102 t/AlignIO/bl2seq.t
1103 t/AlignIO/clustalw.t
1104 t/AlignIO/emboss.t
1105 t/AlignIO/fasta.t
1106 t/AlignIO/largemultifasta.t
1107 t/AlignIO/maf.t
1108 t/AlignIO/mase.t
1109 t/AlignIO/mega.t
1110 t/AlignIO/meme.t
1111 t/AlignIO/metafasta.t
1112 t/AlignIO/msf.t
1113 t/AlignIO/nexml.t
1114 t/AlignIO/nexus.t
1115 t/AlignIO/pfam.t
1116 t/AlignIO/phylip.t
1117 t/AlignIO/po.t
1118 t/AlignIO/prodom.t
1119 t/AlignIO/psi.t
1120 t/AlignIO/selex.t
1121 t/AlignIO/stockholm.t
1122 t/AlignIO/xmfa.t
1123 t/Alphabet.t
1124 t/Annotation/Annotation.t
1125 t/Annotation/AnnotationAdaptor.t
1126 t/Assembly/ContigSpectrum.t
1127 t/Assembly/core.t
1128 t/Assembly/IO/bowtie.t
1129 t/Assembly/IO/sam.t
1130 t/Biblio/Biblio.t
1131 t/Biblio/biofetch.t
1132 t/Biblio/eutils.t
1133 t/Biblio/References.t
1134 t/ClusterIO/ClusterIO.t
1135 t/ClusterIO/SequenceFamily.t
1136 t/ClusterIO/unigene.t
1137 t/Coordinate/CoordinateGraph.t
1138 t/Coordinate/CoordinateMapper.t
1139 t/Coordinate/GeneCoordinateMapper.t
1140 t/data/01_basic.xml
1141 t/data/02_dogfish_dict_cdao_lsid_taxrefs.xml
1142 t/data/02_dogfish_no_taxrefs.xml
1143 t/data/02_dogfish_rdfa_2_cdao_lsid_taxrefs.xml
1144 t/data/02_dogfish_rdfa_tdwg_lsid_taxrefs.xml
1145 t/data/02_mackerel_dict_cdao_lsid_taxrefs.xml
1146 t/data/02_mackerel_no_taxrefs.xml
1147 t/data/02_mackerel_rdfa_2_cdao_lsid_taxrefs.xml
1148 t/data/02_mackerel_rdfa_tdwg_lsid_taxrefs.xml
1149 t/data/03_bootstraps.xml
1150 t/data/03_bootstraps_in_tag.xml
1151 t/data/04_labeled_ancestors.xml
1152 t/data/05_ancestral_states.xml
1153 t/data/1.bed
1154 t/data/13-pilE-F.scf
1155 t/data/1A11.pdb
1156 t/data/1A3I.pdb
1157 t/data/1BPT.pdb
1158 t/data/1ZZ19XR301R-Alignment.tblastn
1159 t/data/2008.blasttable
1160 t/data/27-contig_Newbler.ace
1161 t/data/503384.MEGABLAST.0
1162 t/data/503384.MEGABLAST.2
1163 t/data/5X_1895.FASTXY
1164 t/data/8HVP.pdb
1165 t/data/9K_v4.psl
1166 t/data/a_thaliana.blastn
1167 t/data/AAC12660.fa
1168 t/data/aaml.mlc
1169 t/data/aaml_pairwise.mlc
1170 t/data/AB077698.gb
1171 t/data/acefile.ace.1
1172 t/data/acefile.singlets
1173 t/data/adh.mb_tree.nexus
1174 t/data/AE003528_ecoli.bls
1175 t/data/AE003644_Adh-genomic.gb
1176 t/data/AF032047.gbk
1177 t/data/AF165282.gb
1178 t/data/AF305198.gb
1179 t/data/AHCYL1.kegg
1180 t/data/alleles.fas
1181 t/data/alnfile.fasta
1182 t/data/amino.fa
1183 t/data/AnnIX-v003.gbk
1184 t/data/ar.embl
1185 t/data/assembly_with_singlets.ace
1186 t/data/ATF14F8.gbk
1187 t/data/atp1.matrix
1188 t/data/ay007676.gb
1189 t/data/AY095303S1.gbk
1190 t/data/ay116458.gb
1191 t/data/ay149291.gb
1192 t/data/AY763288.gb
1193 t/data/BAB68554.gb
1194 t/data/barns-combined.nex
1195 t/data/baseml.pairwise
1196 t/data/baseml.usertree
1197 t/data/basic-bush.nex
1198 t/data/basic-ladder.nex
1199 t/data/BC000007.gbk
1200 t/data/BEL16-LTR_AG.embl
1201 t/data/biodbgff/test.gff
1202 t/data/biodbgff/test.gff3
1203 t/data/biofpc.cor
1204 t/data/biofpc.fpc
1205 t/data/biorecipe.nhx
1206 t/data/Bird_Ovomucoids.nex
1207 t/data/BK000016-tpa.gbk
1208 t/data/bl2seq.blastn
1209 t/data/bl2seq.blastn.rev
1210 t/data/bl2seq.blastx.out
1211 t/data/bl2seq.bug940.out
1212 t/data/bl2seq.out
1213 t/data/bl2seq.tblastx.out
1214 t/data/blast.report
1215 t/data/blast_no_hit_desc.txt
1216 t/data/blast_plus.blastp
1217 t/data/blastp2215.blast
1218 t/data/blat.psLayout3
1219 t/data/BLOSUM50
1220 t/data/blosum62.bla
1221 t/data/BN000066-tpa.embl
1222 t/data/bootstrap.tre
1223 t/data/BOSS_DROME.FASTP_v35_04
1224 t/data/branchSite.mlc
1225 t/data/brassica_ATH.WUBLASTN
1226 t/data/bug1986.blast2
1227 t/data/bug1986.blastp
1228 t/data/bug2120.phd
1229 t/data/bug2246.blast
1230 t/data/bug2391.megablast
1231 t/data/bug2399.tblastn
1232 t/data/bug2453.maf
1233 t/data/bug2473.fasta
1234 t/data/bug2862.pmr
1235 t/data/bug2869.tree
1236 t/data/bug2901.fa
1237 t/data/bug2937.fasta
1238 t/data/bug2942.blastx
1239 t/data/bug2982.embl
1240 t/data/bug2982.gb
1241 t/data/bug3021.gmap
1242 t/data/bug3086.embl
1243 t/data/c200-vs-yeast.BLASTN
1244 t/data/c200-vs-yeast.BLASTN.m8
1245 t/data/calm.swiss
1246 t/data/catalase-webblast.BLASTP
1247 t/data/cds-266.fas
1248 t/data/cds_sample.embl
1249 t/data/CG11099.fasaln
1250 t/data/CG2865.fasaln
1251 t/data/chad100.scf
1252 t/data/char-interleave.nex
1253 t/data/char-matrix-spaces.nex
1254 t/data/characters+trees.nexml.xml
1255 t/data/characters.nexml.old.xml
1256 t/data/characters.nexml.xml
1257 t/data/codeml.mlc
1258 t/data/codeml315.mlc
1259 t/data/codeml4.mlc
1260 t/data/codeml43.mlc
1261 t/data/codeml43_nssites.mlc
1262 t/data/codeml_lysozyme/2NG.dN
1263 t/data/codeml_lysozyme/2NG.dS
1264 t/data/codeml_lysozyme/2NG.tt
1265 t/data/codeml_lysozyme/4fold.nuc
1266 t/data/codeml_lysozyme/lnf
1267 t/data/codeml_lysozyme/lysozymeSmall.ctl
1268 t/data/codeml_lysozyme/lysozymeSmall.trees
1269 t/data/codeml_lysozyme/lysozymeSmall.txt
1270 t/data/codeml_lysozyme/mlc
1271 t/data/codeml_lysozyme/rst
1272 t/data/codeml_lysozyme/rst1
1273 t/data/codeml_lysozyme/rub
1274 t/data/codeml_nan.mlc
1275 t/data/codeml_nssites.mlc
1276 t/data/compLD_missingtest.prettybase
1277 t/data/compLD_test.prettybase
1278 t/data/component.ontology.test
1279 t/data/component.ontology.test2
1280 t/data/consed_project/edit_dir/test_project.contigs
1281 t/data/consed_project/edit_dir/test_project.fasta
1282 t/data/consed_project/edit_dir/test_project.fasta.log
1283 t/data/consed_project/edit_dir/test_project.fasta.screen
1284 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.1
1285 t/data/consed_project/edit_dir/test_project.fasta.screen.ace.2
1286 t/data/consed_project/edit_dir/test_project.fasta.screen.contigs
1287 t/data/consed_project/edit_dir/test_project.fasta.screen.contigs.qual
1288 t/data/consed_project/edit_dir/test_project.fasta.screen.log
1289 t/data/consed_project/edit_dir/test_project.fasta.screen.problems
1290 t/data/consed_project/edit_dir/test_project.fasta.screen.problems.qual
1291 t/data/consed_project/edit_dir/test_project.fasta.screen.qual
1292 t/data/consed_project/edit_dir/test_project.fasta.screen.singlets
1293 t/data/consed_project/edit_dir/test_project.fasta.screen.view
1294 t/data/consed_project/edit_dir/test_project.newtags
1295 t/data/consed_project/edit_dir/test_project.phrap.out
1296 t/data/consed_project/edit_dir/test_project.screen.out
1297 t/data/consed_project/edit_dir/test_project_to_alu.cross
1298 t/data/consed_project/edit_dir/test_projectNewChromats.fof
1299 t/data/consed_project/phd_dir/ML4922R.phd.1
1300 t/data/consed_project/phd_dir/ML4924F.phd.1
1301 t/data/consed_project/phd_dir/ML4924R.phd.1
1302 t/data/consed_project/phd_dir/ML4947F.phd.1
1303 t/data/contig-by-hand.wublastp
1304 t/data/contigspectrumtest.tigr
1305 t/data/crab.dat.cn
1306 t/data/crab.nj
1307 t/data/crab.njb
1308 t/data/crypto.sim4-0
1309 t/data/crypto.sim4-3
1310 t/data/crypto.sim4-4
1311 t/data/ctgdemo.fpc
1312 t/data/cys1_dicdi.water
1313 t/data/cysprot.fa
1314 t/data/cysprot.msf
1315 t/data/cysprot.needle
1316 t/data/cysprot.tblastn
1317 t/data/cysprot.water
1318 t/data/cysprot1.fa
1319 t/data/cysprot1.FASTA
1320 t/data/cysprot1a.fa
1321 t/data/cysprot1a.msf
1322 t/data/cysprot1b.fa
1323 t/data/cysprot1b.hmmsearch
1324 t/data/cysprot1b.msf
1325 t/data/cysprot1b.newick
1326 t/data/cysprot_vs_gadfly.FASTA
1327 t/data/D10483.gbk
1328 t/data/D12555.gbk
1329 t/data/dbfa/1.fa
1330 t/data/dbfa/2.fa
1331 t/data/dbfa/3.fa
1332 t/data/dbfa/4.fa
1333 t/data/dbfa/5.fa
1334 t/data/dbfa/6.fa
1335 t/data/dbfa/7.fa
1336 t/data/dbqual/1.qual
1337 t/data/dbqual/2.qual
1338 t/data/dbqual/3.qual
1339 t/data/dcr1_sp.WUBLASTP
1340 t/data/directives.gff3
1341 t/data/dmel_2Lchunk.gb
1342 t/data/dna1.fa
1343 t/data/dna2.fa
1344 t/data/dnaE-bsub-prot.fa
1345 t/data/dnaE-bsub.fa
1346 t/data/dnaEbsub_ecoli.wublastx
1347 t/data/dnaEbsub_ecoli.wutblastn
1348 t/data/dnaEbsub_ecoli.wutblastx
1349 t/data/DQ018368.gb
1350 t/data/dq519393.gb
1351 t/data/ECAPAH02.embl
1352 t/data/echofilter.wublastn
1353 t/data/ecoli-trna-qrna.out
1354 t/data/ecoli_domains.rps.xml
1355 t/data/ecoli_domains.rpsblast
1356 t/data/ecolitst.bls
1357 t/data/ecolitst.fa
1358 t/data/ecolitst.noseqs.wublastp
1359 t/data/ecolitst.wublastp
1360 t/data/EG352462.gbxml
1361 t/data/empty.bl2seq
1362 t/data/ENr111.mfa.example.elems
1363 t/data/entrezgene.dat
1364 t/data/eutils/egquery.xml
1365 t/data/eutils/einfo.xml
1366 t/data/eutils/einfo_dbs.xml
1367 t/data/eutils/elink_acheck.xml
1368 t/data/eutils/elink_acheck_corr.xml
1369 t/data/eutils/elink_dball.xml
1370 t/data/eutils/elink_lcheck.xml
1371 t/data/eutils/elink_lcheck_corr.xml
1372 t/data/eutils/elink_llinks.xml
1373 t/data/eutils/elink_llinks_corr.xml
1374 t/data/eutils/elink_multidb.xml
1375 t/data/eutils/elink_multidb_corr.xml
1376 t/data/eutils/elink_ncheck.xml
1377 t/data/eutils/elink_ncheck_corr.xml
1378 t/data/eutils/elink_neighbor.xml
1379 t/data/eutils/elink_neighbor_corr.xml
1380 t/data/eutils/elink_nhist.xml
1381 t/data/eutils/elink_nhist_corr.xml
1382 t/data/eutils/elink_scores.xml
1383 t/data/eutils/epost.xml
1384 t/data/eutils/esearch1.xml
1385 t/data/eutils/esearch2.xml
1386 t/data/eutils/espell.xml
1387 t/data/eutils/esummary1.xml
1388 t/data/eutils/esummary2.xml
1389 t/data/ex1.nucl.nhx
1390 t/data/example.hap
1391 t/data/example.phase
1392 t/data/exonerate.output.dontwork
1393 t/data/exonerate.output.works
1394 t/data/exonerate.whitespace_before_query.works
1395 t/data/expected.blast.out
1396 t/data/exsignalp.out
1397 t/data/factor7.embl
1398 t/data/Fang_2003.xml
1399 t/data/fastq/bug2335.fastq
1400 t/data/fastq/error_diff_ids.fastq
1401 t/data/fastq/error_double_qual.fastq
1402 t/data/fastq/error_double_seq.fastq
1403 t/data/fastq/error_long_qual.fastq
1404 t/data/fastq/error_no_qual.fastq
1405 t/data/fastq/error_qual_del.fastq
1406 t/data/fastq/error_qual_escape.fastq
1407 t/data/fastq/error_qual_null.fastq
1408 t/data/fastq/error_qual_space.fastq
1409 t/data/fastq/error_qual_tab.fastq
1410 t/data/fastq/error_qual_unit_sep.fastq
1411 t/data/fastq/error_qual_vtab.fastq
1412 t/data/fastq/error_short_qual.fastq
1413 t/data/fastq/error_spaces.fastq
1414 t/data/fastq/error_tabs.fastq
1415 t/data/fastq/error_trunc_at_plus.fastq
1416 t/data/fastq/error_trunc_at_qual.fastq
1417 t/data/fastq/error_trunc_at_seq.fastq
1418 t/data/fastq/error_trunc_in_plus.fastq
1419 t/data/fastq/error_trunc_in_qual.fastq
1420 t/data/fastq/error_trunc_in_seq.fastq
1421 t/data/fastq/error_trunc_in_title.fastq
1422 t/data/fastq/evil_wrapping.fastq
1423 t/data/fastq/example.fasta
1424 t/data/fastq/example.fastq
1425 t/data/fastq/example.qual
1426 t/data/fastq/illumina_faked.fastq
1427 t/data/fastq/sanger_93.fastq
1428 t/data/fastq/sanger_faked.fastq
1429 t/data/fastq/solexa_example.fastq
1430 t/data/fastq/solexa_faked.fastq
1431 t/data/fastq/test1_sanger.fastq
1432 t/data/fastq/test2_solexa.fastq
1433 t/data/fastq/test3_illumina.fastq
1434 t/data/fastq/tricky.fastq
1435 t/data/fastq/wrapping_issues.fastq
1436 t/data/fgenesh.out
1437 t/data/fishBlats.txt
1438 t/data/fishBlats_UCSC.psl
1439 t/data/footprinter.out
1440 t/data/frac_problems.blast
1441 t/data/frac_problems2.blast
1442 t/data/frac_problems3.blast
1443 t/data/geneid_1.0.out
1444 t/data/genemark-fragment.out
1445 t/data/genemark.out
1446 t/data/genewise.out
1447 t/data/genewise_output.paracel_btk
1448 t/data/genomewise.out
1449 t/data/genomic-seq.epcr
1450 t/data/genomic-seq.fasta
1451 t/data/genomic-seq.genscan
1452 t/data/genomic-seq.mzef
1453 t/data/Genscan.FastA
1454 t/data/gf-s71.needle
1455 t/data/Glimmer2.out
1456 t/data/glimmer3-fragment.detail
1457 t/data/glimmer3-fragment.predict
1458 t/data/Glimmer3.detail
1459 t/data/Glimmer3.predict
1460 t/data/GlimmerHMM.out
1461 t/data/GlimmerM.out
1462 t/data/gmap_f9-multiple_results.txt
1463 t/data/gmap_f9-reverse-strand.txt
1464 t/data/gmap_f9.txt
1465 t/data/GO.defs.test
1466 t/data/GO.defs.test2
1467 t/data/headerless.psl
1468 t/data/hemoglobinA.meg
1469 t/data/hg16_chroms.gff
1470 t/data/hmmpfam.out
1471 t/data/hmmpfam_cs.out
1472 t/data/hmmpfam_fake.out
1473 t/data/hmmscan.out
1474 t/data/hmmscan_multi_domain.out
1475 t/data/hmmscan_sec_struct.out
1476 t/data/hmmsearch.out
1477 t/data/hmmsearch3.out
1478 t/data/hs_est.est2genome
1479 t/data/hs_fugu.newick
1480 t/data/hs_owlmonkey.aln
1481 t/data/hs_owlmonkey.fas
1482 t/data/hs_owlmonkey.fasta
1483 t/data/hsinsulin.blastcl3.blastn
1484 t/data/HUMBETGLOA.fa
1485 t/data/HUMBETGLOA.FASTA
1486 t/data/HUMBETGLOA.gff
1487 t/data/HUMBETGLOA.grail
1488 t/data/HUMBETGLOA.grailexp
1489 t/data/HUMBETGLOA.mzef
1490 t/data/HUMBETGLOA.tblastx
1491 t/data/humor.maf
1492 t/data/humts1.pal
1493 t/data/hybrid1.gff3
1494 t/data/hybrid2.gff3
1495 t/data/in.fasta
1496 t/data/insulin.water
1497 t/data/interpro.xml
1498 t/data/interpro_ebi.xml
1499 t/data/interpro_relationship.xml
1500 t/data/interpro_sample.xml
1501 t/data/interpro_short.xml
1502 t/data/intrablock-comment.nex
1503 t/data/Kingdoms_DNA.nex
1504 t/data/knownGene.gff3
1505 t/data/L77119.hmmer
1506 t/data/little.largemultifasta
1507 t/data/LittleChrY.dbsnp.xml
1508 t/data/LOAD_Ccd1.dnd
1509 t/data/long-names.nex
1510 t/data/longnames.aln
1511 t/data/longnames.dnd
1512 t/data/lucy.info
1513 t/data/lucy.qual
1514 t/data/lucy.seq
1515 t/data/lucy.stderr
1516 t/data/lysozyme6.protml
1517 t/data/lysozyme6.simple.protml
1518 t/data/M0.mlc
1519 t/data/M12730.gb
1520 t/data/map_hem/HEM1-HEM12.fa
1521 t/data/map_hem/HEM1-HEM12.fa.revcom
1522 t/data/map_hem/HEM1-HEM12.meme.txt
1523 t/data/map_hem/HEM1-HEM13.fa
1524 t/data/map_hem/HEM1-HEM13.meme.txt
1525 t/data/map_hem/HEM1-HEM14.fa
1526 t/data/map_hem/HEM1-HEM14.meme.txt
1527 t/data/map_hem/HEM1-HEM15.fa
1528 t/data/map_hem/HEM1-HEM15.meme.txt
1529 t/data/map_hem/HEM1-HEM2.fa
1530 t/data/map_hem/HEM1-HEM2.fa.revcom
1531 t/data/map_hem/HEM1-HEM2.meme.txt
1532 t/data/map_hem/HEM1-HEM3.fa
1533 t/data/map_hem/HEM1-HEM3.meme.txt
1534 t/data/map_hem/HEM1-HEM4.fa
1535 t/data/map_hem/HEM1-HEM4.meme.txt
1536 t/data/map_hem/HEM1.ups.fa_
1537 t/data/map_hem/HEM1.ups.fa_.revcom
1538 t/data/map_hem/HEM12-HEM13.fa
1539 t/data/map_hem/HEM12-HEM13.meme.txt
1540 t/data/map_hem/HEM12-HEM14.fa
1541 t/data/map_hem/HEM12-HEM14.meme.txt
1542 t/data/map_hem/HEM12-HEM15.fa
1543 t/data/map_hem/HEM12-HEM15.meme.txt
1544 t/data/map_hem/HEM12.ups.fa_
1545 t/data/map_hem/HEM12.ups.fa_.revcom
1546 t/data/map_hem/HEM13-HEM14.fa
1547 t/data/map_hem/HEM13-HEM14.meme.txt
1548 t/data/map_hem/HEM13-HEM15.fa
1549 t/data/map_hem/HEM13-HEM15.meme.txt
1550 t/data/map_hem/HEM13.ups.fa_
1551 t/data/map_hem/HEM13.ups.fa_.revcom
1552 t/data/map_hem/HEM14-HEM15.fa
1553 t/data/map_hem/HEM14-HEM15.meme.txt
1554 t/data/map_hem/HEM14.ups.fa_
1555 t/data/map_hem/HEM14.ups.fa_.revcom
1556 t/data/map_hem/HEM15.ups.fa_
1557 t/data/map_hem/HEM15.ups.fa_.revcom
1558 t/data/map_hem/HEM2-HEM12.fa
1559 t/data/map_hem/HEM2-HEM12.meme.txt
1560 t/data/map_hem/HEM2-HEM13.fa
1561 t/data/map_hem/HEM2-HEM13.meme.txt
1562 t/data/map_hem/HEM2-HEM14.fa
1563 t/data/map_hem/HEM2-HEM14.meme.txt
1564 t/data/map_hem/HEM2-HEM15.fa
1565 t/data/map_hem/HEM2-HEM15.meme.txt
1566 t/data/map_hem/HEM2-HEM3.fa
1567 t/data/map_hem/HEM2-HEM3.meme.txt
1568 t/data/map_hem/HEM2-HEM4.fa
1569 t/data/map_hem/HEM2-HEM4.meme.txt
1570 t/data/map_hem/HEM2.ups.fa_
1571 t/data/map_hem/HEM2.ups.fa_.revcom
1572 t/data/map_hem/HEM3-HEM12.fa
1573 t/data/map_hem/HEM3-HEM12.meme.txt
1574 t/data/map_hem/HEM3-HEM13.fa
1575 t/data/map_hem/HEM3-HEM13.meme.txt
1576 t/data/map_hem/HEM3-HEM14.fa
1577 t/data/map_hem/HEM3-HEM14.meme.txt
1578 t/data/map_hem/HEM3-HEM15.fa
1579 t/data/map_hem/HEM3-HEM15.meme.txt
1580 t/data/map_hem/HEM3-HEM4.fa
1581 t/data/map_hem/HEM3-HEM4.meme.txt
1582 t/data/map_hem/HEM3.ups.fa_
1583 t/data/map_hem/HEM3.ups.fa_.revcom
1584 t/data/map_hem/HEM4-HEM12.fa
1585 t/data/map_hem/HEM4-HEM12.meme.txt
1586 t/data/map_hem/HEM4-HEM13.fa
1587 t/data/map_hem/HEM4-HEM13.meme.txt
1588 t/data/map_hem/HEM4-HEM14.fa
1589 t/data/map_hem/HEM4-HEM14.meme.txt
1590 t/data/map_hem/HEM4-HEM15.fa
1591 t/data/map_hem/HEM4-HEM15.meme.txt
1592 t/data/map_hem/HEM4.ups.fa_
1593 t/data/map_hem/HEM4.ups.fa_.revcom
1594 t/data/map_hem/yeast.nc.1.freq
1595 t/data/mapmaker.out
1596 t/data/mapmaker.txt
1597 t/data/mast.dat
1598 t/data/masta.dat
1599 t/data/match.output
1600 t/data/mbsout/mbsout_infile1
1601 t/data/mbsout/mbsout_infile2
1602 t/data/mbsout/mbsout_infile3
1603 t/data/Mcjanrna_rdbII.gbk
1604 t/data/megablast_output.paracel_btk
1605 t/data/meme.dat
1606 t/data/mini-AE001405.gb
1607 t/data/mini-align.aln
1608 t/data/mixedmast.dat
1609 t/data/MmCT
1610 t/data/mpath.ontology.test
1611 t/data/MSGEFTUA.gb
1612 t/data/msout_infile1
1613 t/data/msout_infile1.gz
1614 t/data/msout_infile2
1615 t/data/msout_infile2.gz
1616 t/data/multi.blast.m8
1617 t/data/multi.blast.m9
1618 t/data/multi.phd
1619 t/data/multi_1.fa
1620 t/data/multi_2.fa
1621 t/data/multi_blast.bls
1622 t/data/multifa.seq
1623 t/data/multifa.seq.qual
1624 t/data/multiline-intrablock-comment.nex
1625 t/data/multiseq.bls
1626 t/data/multiseq_tags.phd
1627 t/data/mus.bls.xml
1628 t/data/mutations.dat
1629 t/data/mutations.old.dat
1630 t/data/mutations.old.xml
1631 t/data/mutations.xml
1632 t/data/myco_sites.gff
1633 t/data/NC_001284.gbk
1634 t/data/NC_006346.gb
1635 t/data/NC_006511-short.gbk
1636 t/data/NC_008536.gb
1637 t/data/nei_gojobori_test.aln
1638 t/data/neighbor.dist
1639 t/data/new_blastn.txt
1640 t/data/newblast.xml
1641 t/data/nhx-bacteria.nhx
1642 t/data/NM_002254.gb
1643 t/data/no-genes.genscan
1644 t/data/no_cds_example.gb
1645 t/data/no_FH.embl
1646 t/data/no_hsps.blastp
1647 t/data/no_semicolon.newick
1648 t/data/noninterleaved.phy
1649 t/data/NT_021877.gbk
1650 t/data/nucmatrix.txt
1651 t/data/O_sat.wgs
1652 t/data/O_ZNF496.blast
1653 t/data/O_ZNF496.psl
1654 t/data/omim_genemap_test
1655 t/data/omim_genemap_test_nolinebreak
1656 t/data/omim_text_test
1657 t/data/P33897
1658 t/data/P35527.gb
1659 t/data/P39765.gb
1660 t/data/PAM250
1661 t/data/pep-266.aln
1662 t/data/pfam_tests.stk
1663 t/data/phi.out
1664 t/data/phipsi.out
1665 t/data/phylipdist-36.out
1666 t/data/phylipdist.out
1667 t/data/phyloxml_examples.xml
1668 t/data/pictogram.fa
1669 t/data/plague_yeast.bls.xml
1670 t/data/polymorphism.dat
1671 t/data/polymorphism.old.xml
1672 t/data/polymorphism.xml
1673 t/data/popgen_saureus.dat
1674 t/data/popgen_saureus.multidat
1675 t/data/popstats.prettybase
1676 t/data/pre_rel9.swiss
1677 t/data/Primate_mtDNA.nex
1678 t/data/primedseq.fa
1679 t/data/primer3_infile.txt
1680 t/data/primer3_outfile.txt
1681 t/data/primer3_output.txt
1682 t/data/prints.out
1683 t/data/promoterwise.out
1684 t/data/protpars.phy
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1933 t/Matrix/IO/psm.t
1934 t/Matrix/Matrix.t
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1956 t/Phenotype/OMIMentryAllelicVariant.t
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1975 t/RemoteDB/HIV/HIVQuery.t
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1981 t/RemoteDB/SeqRead_fail.t
1982 t/RemoteDB/SeqVersion.t
1983 t/RemoteDB/SwissProt.t
1984 t/RemoteDB/Taxonomy.t
1985 t/Restriction/Analysis-refac.t
1986 t/Restriction/Analysis.t
1987 t/Restriction/Gel.t
1988 t/Restriction/IO.t
1989 t/Root/Exception.t
1990 t/Root/HTTPget.t
1991 t/Root/RootI.t
1992 t/Root/RootIO.t
1993 t/Root/Storable.t
1994 t/Root/Tempfile.t
1995 t/Root/Utilities.t
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1998 t/SearchIO/blast.t
1999 t/SearchIO/blast_pull.t
2000 t/SearchIO/blasttable.t
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2002 t/SearchIO/CigarString.t
2003 t/SearchIO/cross_match.t
2004 t/SearchIO/erpin.t
2005 t/SearchIO/exonerate.t
2006 t/SearchIO/fasta.t
2007 t/SearchIO/gmap_f9.t
2008 t/SearchIO/hmmer.t
2009 t/SearchIO/hmmer_pull.t
2010 t/SearchIO/infernal.t
2011 t/SearchIO/megablast.t
2012 t/SearchIO/psl.t
2013 t/SearchIO/rnamotif.t
2014 t/SearchIO/SearchIO.t
2015 t/SearchIO/sim4.t
2016 t/SearchIO/SimilarityPair.t
2017 t/SearchIO/Tiling.t
2018 t/SearchIO/waba.t
2019 t/SearchIO/wise.t
2020 t/SearchIO/Writer/GbrowseGFF.t
2021 t/SearchIO/Writer/HitTableWriter.t
2022 t/SearchIO/Writer/HSPTableWriter.t
2023 t/SearchIO/Writer/HTMLWriter.t
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