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MANIFEST
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MANIFEST
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bin/auto_install_databases.pl
bin/bed2gff3.pl
bin/bp_load_gff.pl
bin/gbrowse_attach_slaves.pl
bin/gbrowse_change_passwd.pl
bin/gbrowse_clean.pl
bin/gbrowse_create_account.pl
bin/gbrowse_metadb_config.pl
bin/gbrowse_netinstall.pl
bin/gbrowse_netinstall2.pl
bin/gbrowse_set_admin_passwd.pl
bin/gbrowse_slave
bin/gbrowse_syn_load_alignment_database.pl
bin/gbrowse_syn_load_alignments_msa.pl
bin/gtf2gff3.pl
bin/load_genbank.pl
bin/make_das_conf.pl
bin/process_bamfiles.pl
bin/process_gadfly.pl
bin/process_ncbi_human.pl
bin/process_sgd.pl
bin/report_missing_language_tags.pl
bin/scan_gbrowse.pl
bin/ucsc_genes2gff.pl
bin/wiggle2gff3.pl
Build.PL
cgi-bin/das
cgi-bin/gbgff
cgi-bin/gbrowse
cgi-bin/gbrowse_details
cgi-bin/gbrowse_gmap
cgi-bin/gbrowse_img
cgi-bin/gbrowse_key_img
cgi-bin/gbrowse_login
cgi-bin/gbrowse_syn
Changes
conf/detail_select_menu.conf
conf/enzymes.txt
conf/GBrowse.conf
conf/languages/de.pm
conf/languages/en.pm
conf/languages/es.pm
conf/languages/fr.pm
conf/languages/is.pm
conf/languages/it.pm
conf/languages/ja.pm
conf/languages/ko.pm
conf/languages/nl.pm
conf/languages/pl.pm
conf/languages/POSIX.pm
conf/languages/ru.pm
conf/languages/zh.pm
conf/languages/zh_cn.pm
conf/log4perl.conf
conf/MobyServices/b64_encoded_gif_renderer.pm
conf/MobyServices/b64_encoded_jpeg_renderer.pm
conf/MobyServices/GbrowseServices.pm
conf/MobyServices/GbrowseServices.PMS
conf/MobyServices/moby.conf
conf/MobyServices/text_formatted_renderer.pm
conf/MobyServices/text_html_renderer.pm
conf/MobyServices/text_plain_renderer.pm
conf/MobyServices/text_xml_renderer.pm
conf/plugins/Aligner.pm
conf/plugins/AlignTwoSequences.pm
conf/plugins/AttributeHiliter.pm
conf/plugins/BatchDumper.pm
conf/plugins/Blat.pm
conf/plugins/CMapDumper.pm
conf/plugins/CreateBlastDB.pm
conf/plugins/FastaDumper.pm
conf/plugins/FBTableDumper.pm
conf/plugins/FilterTest.pm
conf/plugins/GeneFinder.pm
conf/plugins/LDAPAuthenticate.pm
conf/plugins/OligoFinder.pm
conf/plugins/PamAuthenticate.pm
conf/plugins/PrimerDesigner.pm
conf/plugins/ProteinDumper.pm
conf/plugins/RandomGene.pm
conf/plugins/RestrictionAnnotator.pm
conf/plugins/SequenceDumper.pm
conf/plugins/SimpleTrackFinder.pm
conf/plugins/SinWave.pm
conf/plugins/SourceTrackFinder.pm
conf/plugins/Spectrogram.pm
conf/plugins/Submitter.pm
conf/plugins/test.pm
conf/plugins/TestAuthenticator.pm
conf/plugins/TestFinder.pm
conf/plugins/TrackDumper.pm
conf/plugins/TrackFinder.pm
conf/pop_demo.conf
conf/slave_preload.conf
conf/submitter_plugin.conf
conf/synteny/oryza.synconf.disabled
conf/synteny/rice_synteny.conf
conf/synteny/wild_rice_synteny.conf
conf/themes/solid_gray_colors
conf/themes/transparent_colors
conf/themes/warm_colors
conf/volvox.conf
conf/yeast_chr1+2.conf
conf/yeast_renderfarm.conf
conf/yeast_simple.conf
contrib/ace2gff.pl
contrib/AxtPairwise_convert/axt2phy.pl
contrib/blast2gff.pl
contrib/conf_files/01.yeast.conf
contrib/conf_files/02.wormbase.conf
contrib/conf_files/03.fly.conf
contrib/conf_files/04.human.conf
contrib/conf_files/05.embl_proxy.conf
contrib/conf_files/06.biosql.conf
contrib/conf_files/07.chado.conf
contrib/conf_files/08.genbank.conf
contrib/conf_files/09.human_karyotype.conf
contrib/conf_files/index.html
contrib/conf_files/wormbase.syn
contrib/Coverage/INSTALL
contrib/Coverage/plugin/Coverage.pm
contrib/Coverage/README
contrib/gdump.pl
contrib/GeneFinder/genefinder/gfcode.c
contrib/GeneFinder/genefinder/README
contrib/GeneFinder/genefinder/readseq.c
contrib/GeneFinder/genefinder/readseq.h
contrib/GeneFinder/nematode_gftables/cds.hex
contrib/GeneFinder/nematode_gftables/gftables
contrib/GeneFinder/nematode_gftables/newnem.atg
contrib/GeneFinder/nematode_gftables/newnem.codon
contrib/GeneFinder/nematode_gftables/newnem.gene
contrib/GeneFinder/nematode_gftables/newnem.intron3
contrib/GeneFinder/nematode_gftables/newnem.intron5
contrib/GeneFinder/nematode_gftables/ref.hist
contrib/GeneFinder/nematode_gftables/zk637.atg
contrib/GeneFinder/nematode_gftables/zk637.intron3
contrib/GeneFinder/nematode_gftables/zk637.intron5
contrib/GeneFinder/nematode_gftables/zk637.trinuc
contrib/import_ncbi_mv_hs.pl
contrib/install_macosx/BuildConfig.pm
contrib/install_macosx/README.html
contrib/install_macosx/README.pod
contrib/install_macosx/scripts/build-gbrowse.pl
contrib/install_macosx/scripts/build-libraries.pl
contrib/README
contrib/SynView/cgi-lib/DAS/GUS.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment.pm
contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm
contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm
contrib/SynView/gbrowse.conf/plasmodb.conf
contrib/SynView/gbrowse.conf/plasmodb.xml
contrib/SynView/MAL11/MAL11.conf
contrib/SynView/MAL11/MAL11.fa
contrib/SynView/MAL11/MAL11.gff3
contrib/SynView/README
contrib/TextDumper/README
contrib/TextDumper/TextDumper.pm
DISCLAIMER
docs/developer_notes/README.rearchitecture
docs/developer_notes/README.sharing_tracks
docs/example_remote_configs/volvox_local.conf
docs/example_remote_configs/volvox_remote.conf
docs/example_remote_configs/volvox_slave.conf
docs/Gbrowse_Color_Palette.pdf
docs/login.sql
docs/pod/BIOSQL_ADAPTER_HOWTO.pod
docs/pod/CONFIGURE_HOWTO.pod
docs/pod/CONTROLLER.pod
docs/pod/DAS_HOWTO.pod
docs/pod/FAQ.pod
docs/pod/GBROWSE_IMG.pod
docs/pod/GENBANK_HOWTO.pod
docs/pod/INSTALL.MacOSX.pod
docs/pod/INSTALL.pod
docs/pod/MAKE_IMAGES_HOWTO.pod
docs/pod/ORACLE_AND_POSTGRESQL.pod
docs/pod/PLUGINS_HOWTO.pod
docs/pod/README-berkeley-gadfly.pod
docs/pod/README-chado.pod
docs/pod/README-gff-files.pod
docs/pod/README-lucegene.pod
docs/README.AWS
docs/README.tutorial
etc/default/gbrowse-slave
etc/init.d/gbrowse-slave
htdocs/annotation_help.html
htdocs/css/dropdown/default_theme.css
htdocs/css/dropdown/dropdown.css
htdocs/css/dropdown/helper.css
htdocs/css/dropdown/images/favicon.ico
htdocs/css/dropdown/images/icon.png
htdocs/css/dropdown/images/nav-arrow-down-on.png
htdocs/css/dropdown/images/nav-arrow-down-open.png
htdocs/css/dropdown/images/nav-arrow-down.png
htdocs/css/dropdown/images/nav-arrow-left-on.png
htdocs/css/dropdown/images/nav-arrow-left-open.png
htdocs/css/dropdown/images/nav-arrow-left.png
htdocs/css/dropdown/images/nav-arrow-right-on.png
htdocs/css/dropdown/images/nav-arrow-right-open.png
htdocs/css/dropdown/images/nav-arrow-right.png
htdocs/css/dropdown/images/nav-arrow-up-on.png
htdocs/css/dropdown/images/nav-arrow-up-open.png
htdocs/css/dropdown/images/nav-arrow-up.png
htdocs/css/dropdown/images/pattern1.png
htdocs/css/dropdown/images/pattern2.png
htdocs/css/dropdown/images/pattern3.png
htdocs/css/gbrowse.css
htdocs/css/gbrowse_autocomplete.css
htdocs/css/gbrowse_elements.css
htdocs/css/gbrowse_solid.css
htdocs/css/gbrowse_transparent.css
htdocs/css/gbrowse_warm.css
htdocs/css/karyotype.css
htdocs/css/menulink.png
htdocs/css/menulink_active.png
htdocs/css/snapshots.css
htdocs/css/subtracktable.css
htdocs/css/titlebar-default.css
htdocs/css/titlebar-safari.css
htdocs/css/tracks.css
htdocs/example_scripts/gbrowse_get_sessionid.pl
htdocs/example_scripts/gbrowse_new_sessionid.pl
htdocs/example_scripts/gbrowse_upload_data.pl
htdocs/example_scripts/gbrowse_upload_file.pl
htdocs/example_scripts/index.html
htdocs/example_scripts/README
htdocs/example_scripts/test_file.bed
htdocs/gbrowse_karyotype_help.html
htdocs/gbrowse_syn_help.html
htdocs/general_help.html
htdocs/general_help.html.zh
htdocs/gmod_cog.jpeg
htdocs/images/backgrounds/cloud.jpg
htdocs/images/backgrounds/lrock005.jpg
htdocs/images/backgrounds/steel.jpg
htdocs/images/balloons/GBubble/balloon.png
htdocs/images/balloons/GBubble/balloon_ie.png
htdocs/images/balloons/GBubble/close.png
htdocs/images/balloons/GBubble/down_left.png
htdocs/images/balloons/GBubble/down_right.png
htdocs/images/balloons/GBubble/up_left.png
htdocs/images/balloons/GBubble/up_right.png
htdocs/images/balloons/GPlain/balloon.png
htdocs/images/balloons/GPlain/close.png
htdocs/images/balloons/GPlain/down_left.png
htdocs/images/balloons/GPlain/down_right.png
htdocs/images/balloons/GPlain/up_left.png
htdocs/images/balloons/GPlain/up_right.png
htdocs/images/buttons/ajax-loader.gif
htdocs/images/buttons/blue_peaks.png
htdocs/images/buttons/check.png
htdocs/images/buttons/cursor-ewmove.ico
htdocs/images/buttons/dark_0.4_pixel.png
htdocs/images/buttons/download.png
htdocs/images/buttons/empty.png
htdocs/images/buttons/ex.png
htdocs/images/buttons/ficon.png
htdocs/images/buttons/ficon_2.png
htdocs/images/buttons/fmini.png
htdocs/images/buttons/fmini_2.png
htdocs/images/buttons/green.gif
htdocs/images/buttons/green1.gif
htdocs/images/buttons/green2.gif
htdocs/images/buttons/green3.gif
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htdocs/images/buttons/green_l1.gif
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htdocs/images/buttons/green_r1.gif
htdocs/images/buttons/green_r2.gif
htdocs/images/buttons/grey.png
htdocs/images/buttons/grey_0.4_pixel.png
htdocs/images/buttons/menu.png
htdocs/images/buttons/minus.gif
htdocs/images/buttons/minus.png
htdocs/images/buttons/minus12.png
htdocs/images/buttons/mminus.png
htdocs/images/buttons/mplus.gif
htdocs/images/buttons/mplus.png
htdocs/images/buttons/opacity_thumb.png
htdocs/images/buttons/open_open.png
htdocs/images/buttons/panleft.png
htdocs/images/buttons/panleft2.png
htdocs/images/buttons/panright.png
htdocs/images/buttons/panright2.png
htdocs/images/buttons/plus.gif
htdocs/images/buttons/plus.png
htdocs/images/buttons/query.png
htdocs/images/buttons/red.gif
htdocs/images/buttons/red1.gif
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htdocs/images/buttons/red_peaks.png
htdocs/images/buttons/ruler-icon.png
htdocs/images/buttons/ruler.png
htdocs/images/buttons/share.png
htdocs/images/buttons/snap_check.png
htdocs/images/buttons/snap_down.png
htdocs/images/buttons/snap_ex.png
htdocs/images/buttons/snap_mail.png
htdocs/images/buttons/snap_share.png
htdocs/images/buttons/snap_trash.png
htdocs/images/buttons/sortable.gif
htdocs/images/buttons/sorted_down.gif
htdocs/images/buttons/sorted_up.gif
htdocs/images/buttons/spinner.gif
htdocs/images/buttons/square.png
htdocs/images/buttons/square.xpm
htdocs/images/buttons/tools.png
htdocs/images/buttons/trash.gif
htdocs/images/buttons/trash.png
htdocs/images/help/detail.gif
htdocs/images/help/detail.png
htdocs/images/help/detail_scale.gif
htdocs/images/help/detail_scale.png
htdocs/images/help/landmark.gif
htdocs/images/help/landmark.png
htdocs/images/help/multiple_hits.png
htdocs/images/help/navbar.gif
htdocs/images/help/navbar.png
htdocs/images/help/numeric+data.gif
htdocs/images/help/overview+detail.gif
htdocs/images/help/overview+detail.png
htdocs/images/help/overview.gif
htdocs/images/help/remote.png
htdocs/images/help/search+settings.gif
htdocs/images/help/track+settings.gif
htdocs/images/help/upload+edit.gif
htdocs/images/help/upload+remote.gif
htdocs/images/help/upload.gif
htdocs/images/help/upload.png
htdocs/images/help/upload_field.png
htdocs/images/help/upload_list.png
htdocs/images/help/worm_exons_spec.png
htdocs/images/help/worm_telomeric_spec.png
htdocs/images/help/yeast_I_genes_spec.png
htdocs/images/openid/aim-logo.png
htdocs/images/openid/blogspot-logo.png
htdocs/images/openid/google-logo.gif
htdocs/images/openid/livejournal-logo.png
htdocs/images/openid/myopenid-logo.png
htdocs/images/openid/openid-logo.gif
htdocs/images/openid/yahoo-logo.png
htdocs/index.html
htdocs/js/ajax_upload.js
htdocs/js/autocomplete.js
htdocs/js/balloon.config.js
htdocs/js/balloon.js
htdocs/js/box.js
htdocs/js/builder.js
htdocs/js/buttons.js
htdocs/js/controller.js
htdocs/js/controls.js
htdocs/js/detailSelect.js
htdocs/js/dragdrop.js
htdocs/js/effects.js
htdocs/js/GBox.js
htdocs/js/karyotype.js
htdocs/js/login.js
htdocs/js/menu.js
htdocs/js/overviewSelect.js
htdocs/js/prototype.js
htdocs/js/regionSelect.js
htdocs/js/rubber.js
htdocs/js/ruler.js
htdocs/js/scriptaculous.js
htdocs/js/scrollfix.js
htdocs/js/slider.js
htdocs/js/snapshotManager.js
htdocs/js/sound.js
htdocs/js/subtracktable.css
htdocs/js/subtracktable.js
htdocs/js/tabs.js
htdocs/js/track.js
htdocs/js/track_configure.js
htdocs/js/track_pan.js
htdocs/js/trackFavorites.js
htdocs/js/unittest.js
htdocs/js/x_cook.js
htdocs/tutorial/bin/expression_levels.pl
htdocs/tutorial/bin/make_exon.pl
htdocs/tutorial/bin/random_dna.pl
htdocs/tutorial/bin/random_feature.pl
htdocs/tutorial/bin/random_segments.pl
htdocs/tutorial/bin/reformat.pl
htdocs/tutorial/conf_files/elegans_core.conf
htdocs/tutorial/conf_files/elegans_extra.conf
htdocs/tutorial/conf_files/HEADER.html
htdocs/tutorial/conf_files/volvox.conf
htdocs/tutorial/conf_files/volvox_final.conf
htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
htdocs/tutorial/conf_files/volvox_halfway.conf
htdocs/tutorial/conf_files/volvox_Phylo.conf
htdocs/tutorial/conf_files/volvox_quarter.conf
htdocs/tutorial/conf_files/volvox_refactored.conf
htdocs/tutorial/data_files/dog1_1700.wig
htdocs/tutorial/data_files/elegans.fa
htdocs/tutorial/data_files/elegans_acceptor.gff3
htdocs/tutorial/data_files/elegans_core.gff3
htdocs/tutorial/data_files/elegans_deletion.gff3
htdocs/tutorial/data_files/elegans_expression.gff3
htdocs/tutorial/data_files/elegans_extra.gff3
htdocs/tutorial/data_files/elegans_repeats.gff3
htdocs/tutorial/data_files/elegans_sts.gff3
htdocs/tutorial/data_files/ests.fa
htdocs/tutorial/data_files/HEADER.html
htdocs/tutorial/data_files/species.tre
htdocs/tutorial/data_files/volvox.fa
htdocs/tutorial/data_files/volvox.gff3
htdocs/tutorial/data_files/volvox_all.fa
htdocs/tutorial/data_files/volvox_all.gff3
htdocs/tutorial/data_files/volvox_array.gff3
htdocs/tutorial/data_files/volvox_bacs.gff3
htdocs/tutorial/data_files/volvox_domains.gff3
htdocs/tutorial/data_files/volvox_est.gff3
htdocs/tutorial/data_files/volvox_est_targets.gff3
htdocs/tutorial/data_files/volvox_geneproducts.gff3
htdocs/tutorial/data_files/volvox_genes.gff3
htdocs/tutorial/data_files/volvox_genes_simple.gff3
htdocs/tutorial/data_files/volvox_matches.gff3
htdocs/tutorial/data_files/volvox_microarray.gff3
htdocs/tutorial/data_files/volvox_microarray.wig
htdocs/tutorial/data_files/volvox_phyloalign.fa
htdocs/tutorial/data_files/volvox_phyloalign.gff3
htdocs/tutorial/data_files/volvox_phyloalign_wigentries.gff3
htdocs/tutorial/data_files/volvox_remarks.gff3
htdocs/tutorial/data_files/volvox_trace.gff3
htdocs/tutorial/data_files/volvox_trace.scf
htdocs/tutorial/dbgff/data_files/elegans_acceptor.gff
htdocs/tutorial/dbgff/data_files/elegans_core.gff
htdocs/tutorial/dbgff/data_files/elegans_deletion.gff
htdocs/tutorial/dbgff/data_files/elegans_expression.gff
htdocs/tutorial/dbgff/data_files/elegans_extra.gff
htdocs/tutorial/dbgff/data_files/elegans_repeats.gff
htdocs/tutorial/dbgff/data_files/elegans_sts.gff
htdocs/tutorial/dbgff/data_files/volvox1.gff
htdocs/tutorial/dbgff/data_files/volvox2.gff
htdocs/tutorial/dbgff/data_files/volvox3.gff
htdocs/tutorial/dbgff/data_files/volvox4.gff
htdocs/tutorial/dbgff/data_files/volvox4a.gff
htdocs/tutorial/dbgff/data_files/volvox4b.gff
htdocs/tutorial/dbgff/data_files/volvox5.gff
htdocs/tutorial/dbgff/data_files/volvox6.gff
htdocs/tutorial/dbgff/data_files/volvox7.gff
htdocs/tutorial/dbgff/data_files/volvox8.gff
htdocs/tutorial/dbgff/data_files/volvox9.gff
htdocs/tutorial/dbgff/data_files/volvox_all.gff
htdocs/tutorial/figures/adding_dna_to_alignments1.gif
htdocs/tutorial/figures/aliases.gif
htdocs/tutorial/figures/basic_conf1.gif
htdocs/tutorial/figures/basic_conf2.gif
htdocs/tutorial/figures/basics1.gif
htdocs/tutorial/figures/canonical_gene1.gif
htdocs/tutorial/figures/canonical_gene2.gif
htdocs/tutorial/figures/canonical_gene3.gif
htdocs/tutorial/figures/categorytable.png
htdocs/tutorial/figures/cds1.gif
htdocs/tutorial/figures/config_editing.png
htdocs/tutorial/figures/custom_aggregators1.gif
htdocs/tutorial/figures/DAS1.gif
htdocs/tutorial/figures/descriptions1.gif
htdocs/tutorial/figures/dna1.gif
htdocs/tutorial/figures/dna1.png
htdocs/tutorial/figures/dna2.gif
htdocs/tutorial/figures/dna2.png
htdocs/tutorial/figures/enhancements1.gif
htdocs/tutorial/figures/enhancements2.gif
htdocs/tutorial/figures/enhancements3.gif
htdocs/tutorial/figures/figure1.gif
htdocs/tutorial/figures/figure10.gif
htdocs/tutorial/figures/figure11.gif
htdocs/tutorial/figures/figure12.gif
htdocs/tutorial/figures/figure13a.gif
htdocs/tutorial/figures/figure13b.gif
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htdocs/tutorial/figures/figure7a.gif
htdocs/tutorial/figures/figure7b.gif
htdocs/tutorial/figures/figure8.gif
htdocs/tutorial/figures/figure9.gif
htdocs/tutorial/figures/graph1.gif
htdocs/tutorial/figures/multiple_alignments1.gif
htdocs/tutorial/figures/multiple_alignments2.gif
htdocs/tutorial/figures/multiple_alignments3.gif
htdocs/tutorial/figures/overview1.gif
htdocs/tutorial/figures/phylo_align1.gif
htdocs/tutorial/figures/phylo_align2.gif
htdocs/tutorial/figures/phylo_align3.gif
htdocs/tutorial/figures/plugins1.gif
htdocs/tutorial/figures/plugins2.gif
htdocs/tutorial/figures/predicted_genes.gif
htdocs/tutorial/figures/segmented_features1.gif
htdocs/tutorial/figures/segmented_features2.gif
htdocs/tutorial/figures/semantic_zooming1.gif
htdocs/tutorial/figures/setting_popup.png
htdocs/tutorial/figures/third_party1.gif
htdocs/tutorial/figures/third_party2.gif
htdocs/tutorial/figures/third_party3.gif
htdocs/tutorial/figures/third_party4.gif
htdocs/tutorial/figures/third_party5.gif
htdocs/tutorial/figures/trace1.png
htdocs/tutorial/figures/trace2.png
htdocs/tutorial/figures/wiggle_density.gif
htdocs/tutorial/figures/wiggle_density.png
htdocs/tutorial/tutorial.css
htdocs/tutorial/tutorial.html
htdocs/tutorial/tutorial.phyTreeEdit.html
INSTALL
install_util/cgi_install.pl
install_util/conf_install.pl
install_util/gbrowse_ppm_install.pl
install_util/GBrowseGuessDirectories.pm
install_util/GBrowseInstall.pm
install_util/htdocs_install.pl
install_util/InstallUtil.pm
install_util/make_clean_add.pl
install_util/pod2docs.pl
install_util/sync-bioperl.sh
install_util/tag.pl
lib/Bio/DB/GFF/Aggregator/match_gap.pm
lib/Bio/DB/GFF/Aggregator/reftranscript.pm
lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
lib/Bio/DB/SeqFeature/Store/BedLoader.pm
lib/Bio/DB/Tagger.pm
lib/Bio/DB/Tagger/mysql.pm
lib/Bio/DB/Tagger/Tag.pm
lib/Bio/Graphics/Browser2.pm
lib/Bio/Graphics/Browser2/Action.pm
lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
lib/Bio/Graphics/Browser2/CachedTrack.pm
lib/Bio/Graphics/Browser2/CAlign.pm
lib/Bio/Graphics/Browser2/CAlign.xs
lib/Bio/Graphics/Browser2/DataBase.pm
lib/Bio/Graphics/Browser2/DataLoader.pm
lib/Bio/Graphics/Browser2/DataLoader/bam.pm
lib/Bio/Graphics/Browser2/DataLoader/bed.pm
lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
lib/Bio/Graphics/Browser2/DataLoader/generic.pm
lib/Bio/Graphics/Browser2/DataLoader/gff.pm
lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
lib/Bio/Graphics/Browser2/DataLoader/sam.pm
lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
lib/Bio/Graphics/Browser2/DataSource.pm
lib/Bio/Graphics/Browser2/ExternalData.pm
lib/Bio/Graphics/Browser2/GFFhelper.pm
lib/Bio/Graphics/Browser2/I18n.pm
lib/Bio/Graphics/Browser2/Markup.pm
lib/Bio/Graphics/Browser2/OptionPick.pm
lib/Bio/Graphics/Browser2/PadAlignment.pm
lib/Bio/Graphics/Browser2/Plugin.pm
lib/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm
lib/Bio/Graphics/Browser2/PluginSet.pm
lib/Bio/Graphics/Browser2/Realign.pm
lib/Bio/Graphics/Browser2/Region.pm
lib/Bio/Graphics/Browser2/RegionSearch.pm
lib/Bio/Graphics/Browser2/RemoteSet.pm
lib/Bio/Graphics/Browser2/Render.pm
lib/Bio/Graphics/Browser2/Render/HTML.pm
lib/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm
lib/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm
lib/Bio/Graphics/Browser2/Render/Login.pm
lib/Bio/Graphics/Browser2/Render/Slave.pm
lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
lib/Bio/Graphics/Browser2/Render/SnapshotManager.pm
lib/Bio/Graphics/Browser2/Render/TrackConfig.pm
lib/Bio/Graphics/Browser2/RenderPanels.pm
lib/Bio/Graphics/Browser2/SendMail.pm
lib/Bio/Graphics/Browser2/Session.pm
lib/Bio/Graphics/Browser2/Shellwords.pm
lib/Bio/Graphics/Browser2/SubtrackTable.pm
lib/Bio/Graphics/Browser2/TrackDumper.pm
lib/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm
lib/Bio/Graphics/Browser2/UserDB.pm
lib/Bio/Graphics/Browser2/UserTracks.pm
lib/Bio/Graphics/Browser2/UserTracks/Database.pm
lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
lib/Bio/Graphics/Browser2/Util.pm
lib/Bio/Graphics/GBrowseFeature.pm
lib/Bio/Graphics/Karyotype.pm
lib/CGI/Toggle.pm
lib/Legacy/DB/SyntenyBlock.pm
lib/Legacy/DB/SyntenyIO.pm
lib/Legacy/Graphics/Browser.pm
lib/Legacy/Graphics/Browser/I18n.pm
lib/Legacy/Graphics/Browser/PageSettings.pm
lib/Legacy/Graphics/Browser/Synteny.pm
lib/Legacy/Graphics/Browser/Util.pm
libalign/CAlign.pm
libalign/CAlign.xs
libalign/Changes
libalign/README
libalign/realign.h
LICENSE
Makefile.PL
MANIFEST
README
README.fedora_and_selinux
README.gff3
README.IF.GBROWSE.ISNT.WORKING
sample_data/admin_uploads/README
sample_data/gbrowse_syn/alignments/rice.aln.gz
sample_data/gbrowse_syn/rice/rice.gff3
sample_data/gbrowse_syn/wild_rice/wild_rice.gff3
sample_data/ideograms/human_cytobands.gff
sample_data/ideograms/mouse_cytobands.gff
sample_data/ideograms/rat_cytobands.gff
sample_data/pop_demo/pop_demo.gff3
sample_data/yeast_chr1+2/yeast_chr1+2.gff3
sample_data/yeast_scaffolds/chr1.fa
sample_data/yeast_scaffolds/chr2.fa
sample_data/yeast_scaffolds/chromosomes.gff3
t/00.compile.t
t/01.yeast.t
t/02.rearchitecture.t
t/03.render.t
t/04.remoteserver.t
t/05.deferredrendering.t
t/06.featuresearch.t
t/07.karyotype.t
t/08.calign.t
t/Test.pm
t/testdata/conf/enzymes.txt
t/testdata/conf/GBrowse.conf
t/testdata/conf/languages/fr.pm
t/testdata/conf/languages/POSIX.pm
t/testdata/conf/templates/volvox_final.conf
t/testdata/conf/templates/yeast_chr1.conf
t/testdata/conf/WHERE_ARE_THE_CONF_FILES.txt
t/testdata/data/volvox/volvox.gff
t/testdata/data/volvox2/volvox2.gff
t/testdata/data/volvox3/volvox3.gff
t/testdata/data/volvox4/volvox4.gff
t/testdata/phylo_align/phyloalign.fa
t/testdata/phylo_align/readme.txt
t/testdata/phylo_align/species.tre
t/testdata/phylo_align/volvox_alignment.conf
t/testdata/phylo_align/volvox_phyloalign.gff
t/testdata/TemplateCopy.pm