[med-svn] [Git][med-team/arb][master] 7 commits: d/watch: version=5

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / arb


Commits:
b97de473 by Andreas Tille at 2026-10-23T07:24:37+02:00
d/watch: version=5

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b299b7ce by Andreas Tille at 2026-10-23T07:24:51+02:00
New upstream version

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8b70311b by Andreas Tille at 2026-10-23T07:24:52+02:00
New upstream version 7.0
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32b9e3a3 by Andreas Tille at 2026-10-23T07:26:05+02:00
Update upstream source from tag 'upstream/7.0'

Update to upstream version '7.0'
with Debian dir 45f07260fb3467cf62c1c47a3463522fe7058043
- - - - -
33e42555 by Andreas Tille at 2026-10-23T07:27:06+02:00
Changes made by cme

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f0effdb3 by Andreas Tille at 2026-10-23T06:27:14+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/10_upstream_r12793__show_db_load_progress]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/20_upstream_r12794__socket_permissions]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/30_upstream_r12814__desktop_keywords]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/40_upstream_r12815__lintian_spelling]
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/70_skip_compler_version_check.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html

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07e9e04b by Andreas Tille at 2026-10-23T07:27:18+02:00
debputy lint --auto-fix (routine-update)

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2000 changed files:

- AISC/Makefile
- AISC/aisc.c
- − AISC/aisc.h
- AISC/aisc_commands.c
- AISC/aisc_def.h
- AISC/aisc_eval.c
- AISC/aisc_eval.h
- AISC/aisc_inline.h
- AISC/aisc_interpreter.h
- AISC/aisc_location.h
- AISC/aisc_mix.c
- AISC/aisc_parser.c
- AISC/aisc_parser.h
- AISC/aisc_token.h
- AISC/aisc_var_ref.c
- AISC_COM/AISC/Makefile
- AISC_COM/AISC/aisc_global.pa
- AISC_COM/AISC/aisc_server.pa
- AISC_COM/AISC/keys.README
- AISC_COM/C/Makefile
- AISC_COM/C/aisc_extern.c
- AISC_COM/C/aisc_global.h
- AISC_COM/C/client.c
- − AISC_COM/C/common.c
- − AISC_COM/C/common.h
- AISC_COM/C/server.c
- AISC_COM/C/server.h
- AISC_COM/C/struct_man.c
- AISC_COM/C/trace.h
- AISC_MKPTPS/Makefile
- AISC_MKPTPS/mkptypes.cxx
- ARBDB/Makefile
- SL/ROOTED_TREE/RootedTree.cxx → ARBDB/TreeNode.cxx
- + ARBDB/TreeNode.h
- ARBDB/adChangeKey.cxx
- ARBDB/adGene.cxx
- ARBDB/adGene.h
- ARBDB/adRevCompl.cxx
- ARBDB/adTest.cxx
- + ARBDB/ad_cb.cxx
- ARBDB/ad_cb_prot.h
- + ARBDB/ad_colorset.cxx
- + ARBDB/ad_colorset.h
- ARBDB/ad_config.cxx
- ARBDB/ad_config.h
- ARBDB/ad_core.cxx
- ARBDB/ad_hcb.h
- ARBDB/ad_io_inline.h
- ARBDB/ad_load.cxx
- ARBDB/ad_p_prot.h
- ARBDB/ad_prot.h
- ARBDB/ad_remote.h
- ARBDB/ad_save_load.cxx
- ARBDB/ad_t_prot.h
- ARBDB/adali.cxx
- ARBDB/adcache.cxx
- ARBDB/adcomm.cxx
- ARBDB/adcompr.cxx
- ARBDB/adfile.cxx
- ARBDB/adhash.cxx
- ARBDB/adhashtools.cxx
- ARBDB/adindex.cxx
- ARBDB/aditem.cxx
- ARBDB/adlang1.cxx
- − ARBDB/adlink.cxx
- ARBDB/admalloc.cxx
- ARBDB/admap.cxx
- ARBDB/admatch.cxx
- ARBDB/admath.cxx
- ARBDB/adname.cxx
- ARBDB/adoptimize.cxx
- ARBDB/adperl.cxx
- ARBDB/adperl.h
- ARBDB/adquery.cxx
- ARBDB/adseqcompr.cxx
- ARBDB/adsocket.cxx
- ARBDB/adstring.cxx
- ARBDB/adsystem.cxx
- − ARBDB/adtables.cxx
- ARBDB/adtcp.cxx
- ARBDB/adtools.cxx
- ARBDB/adtree.cxx
- ARBDB/arbdb.cxx
- ARBDB/arbdb.h
- ARBDB/arbdb_base.h
- ARBDB/arbdbpp.cxx
- ARBDB/arbdbt.h
- + ARBDB/gb_aci.cxx
- ARBDB/gb_aci.h
- + ARBDB/gb_aci_impl.h
- ARBDB/gb_cb.h
- ARBDB/gb_data.h
- ARBDB/gb_header.h
- ARBDB/gb_index.h
- ARBDB/gb_key.h
- ARBDB/gb_localdata.h
- ARBDB/gb_main.h
- ARBDB/gb_map.h
- ARBDB/gb_memory.h
- ARBDB/gb_prot.h
- ARBDB/gb_storage.h
- ARBDB/gb_ts.h
- ARB_GDE/GDE.cxx
- ARB_GDE/GDE_FileIO.cxx
- ARB_GDE/GDE_Genbank.cxx
- ARB_GDE/GDE_HGLfile.cxx
- ARB_GDE/GDE_ParseMenu.cxx
- ARB_GDE/GDE_arbdb_io.cxx
- ARB_GDE/GDE_awars.h
- ARB_GDE/GDE_def.h
- ARB_GDE/GDE_event.cxx
- ARB_GDE/GDE_global.cxx
- ARB_GDE/GDE_menu.h
- ARB_GDE/GDE_proto.h
- ARB_GDE/Makefile
- ARB_GDE/gde.hxx
- AWT/AWT_TreeAwars.cxx
- AWT/AWT_asciiprint.cxx
- − AWT/AWT_attributes.cxx
- AWT/AWT_canio.cxx
- AWT/AWT_canvas.cxx
- AWT/AWT_config_manager.cxx
- AWT/AWT_db_browser.cxx
- AWT/AWT_hexdump.cxx
- AWT/AWT_input_mask.cxx
- AWT/AWT_map_key.cxx
- + AWT/AWT_misc.cxx
- AWT/AWT_modules.cxx
- + AWT/AWT_prompt.cxx
- AWT/AWT_sel_boxes.cxx
- − AWT/AWT_tables.cxx
- AWT/AWT_www.cxx
- AWT/Makefile
- AWT/awt.hxx
- − AWT/awt_attributes.hxx
- AWT/awt_canvas.hxx
- AWT/awt_config_manager.hxx
- AWT/awt_hexdump.hxx
- AWT/awt_hotkeys.hxx
- AWT/awt_input_mask_internal.hxx
- AWT/awt_map_key.hxx
- + AWT/awt_misc.hxx
- AWT/awt_modules.hxx
- + AWT/awt_prompt.hxx
- AWT/awt_sel_boxes.hxx
- − AWT/awt_seq_colors.hxx
- AWT/awt_www.hxx
- − AWT/awtlocal.hxx
- AWTC/AWTC_next_neighbours.cxx
- AWTC/AWTC_submission.cxx
- AWTC/Makefile
- AWTC/awtc_next_neighbours.hxx
- + AWTI/AWTI_edit.cxx
- AWTI/AWTI_export.cxx
- AWTI/AWTI_import.cxx
- AWTI/Makefile
- PARSIMONY/PARS_debug.cxx → AWTI/awti_edit.hxx
- + AWTI/awti_exp_local.hxx
- AWTI/awti_imp_local.hxx
- AWTI/awti_import.hxx
- AWTI/needs_libs
- + BINDEP/README
- + BINDEP/needs_libs.arb_2_ascii
- BINDEP/needs_libs.arb_notify → BINDEP/needs_libs.arb_2_bin
- + BINDEP/needs_libs.arb_calc_pvp
- + BINDEP/needs_libs.arb_export_newick
- + BINDEP/needs_libs.arb_export_seq_filtered
- + BINDEP/needs_libs.arb_export_sequences
- + BINDEP/needs_libs.arb_flush_mem
- + BINDEP/needs_libs.arb_probe_match
- + BINDEP/needs_libs.arb_proto_2_xsub
- + BINDEP/needs_libs.arb_replace
- + BINDEP/needs_libs.arb_sub2ascii
- + BINDEP/needs_libs.arb_write_tree_comment
- BUGEX/bugex.h
- + CONSENSUS_TREE/CT_common.hxx
- CONSENSUS_TREE/CT_ctree.cxx
- CONSENSUS_TREE/CT_ctree.hxx
- CONSENSUS_TREE/CT_def.hxx
- CONSENSUS_TREE/CT_dtree.cxx
- CONSENSUS_TREE/CT_hash.cxx
- CONSENSUS_TREE/CT_hash.hxx
- − CONSENSUS_TREE/CT_mem.cxx
- CONSENSUS_TREE/CT_ntree.cxx
- CONSENSUS_TREE/CT_part.cxx
- CONSENSUS_TREE/CT_part.hxx
- CONSENSUS_TREE/CT_rbtree.cxx
- CONSENSUS_TREE/Makefile
- + CONSENSUS_TREE/SyncRoot.cxx
- + CONSENSUS_TREE/SyncRoot.hxx
- CONSENSUS_TREE/needs_libs
- CONVERTALN/Makefile
- CONVERTALN/convert.cxx
- CONVERTALN/date.cxx
- CONVERTALN/embl.cxx
- CONVERTALN/embl.h
- CONVERTALN/fconv.cxx
- CONVERTALN/fun.h
- CONVERTALN/gcg.cxx
- CONVERTALN/genbank.cxx
- CONVERTALN/genbank.h
- CONVERTALN/global.h
- CONVERTALN/input_format.h
- CONVERTALN/macke.cxx
- CONVERTALN/macke.h
- CONVERTALN/main.cxx
- CONVERTALN/mg.cxx
- CONVERTALN/paup.cxx
- CONVERTALN/printable.cxx
- CONVERTALN/prototypes.h
- CONVERTALN/rdp_info.h
- CONVERTALN/reader.cxx
- CONVERTALN/reader.h
- CONVERTALN/refs.h
- CONVERTALN/seq.h
- CONVERTALN/util.cxx
- CONVERTALN/wrap.cxx
- CONVERTALN/wrap.h
- CORE/BufferedFileReader.cxx
- CORE/BufferedFileReader.h
- + CORE/ConfigMapping.cxx
- + CORE/ConfigMapping.h
- CORE/FileContent.cxx
- CORE/FileContent.h
- CORE/Makefile
- CORE/MultiFileReader.cxx
- CORE/MultiFileReader.h
- + CORE/StrUniquifier.h
- CORE/arb_assert.h
- CORE/arb_core.h
- CORE/arb_cs.cxx
- CORE/arb_cs.h
- CORE/arb_diff.cxx
- CORE/arb_diff.h
- CORE/arb_file.cxx
- CORE/arb_file.h
- CORE/arb_handlers.cxx
- CORE/arb_handlers.h
- CORE/arb_match.cxx
- + CORE/arb_mem.cxx
- + CORE/arb_mem.h
- CORE/arb_misc.cxx
- CORE/arb_misc.h
- CORE/arb_msg.cxx
- CORE/arb_msg.h
- + CORE/arb_pattern.cxx
- + CORE/arb_pattern.h
- CORE/arb_progress.cxx
- CORE/arb_progress.h
- CORE/arb_signal.cxx
- CORE/arb_signal.h
- CORE/arb_sort.cxx
- + CORE/arb_stdstring.h
- CORE/arb_strarray.cxx
- CORE/arb_strarray.h
- CORE/arb_strbuf.cxx
- CORE/arb_strbuf.h
- CORE/arb_string.cxx
- CORE/arb_string.h
- + CORE/arb_zfile.cxx
- + CORE/arb_zfile.h
- CORE/pos_range.cxx
- CORE/pos_range.h
- DBSERVER/Makefile
- DBSERVER/db_server.cxx
- DIST/DI_clusters.cxx
- DIST/DI_clustertree.cxx
- DIST/DI_compress_matrix.cxx
- DIST/DI_foundclusters.cxx
- DIST/DI_main.cxx
- DIST/DI_matr.cxx
- DIST/DI_protdist.cxx
- DIST/DI_save_matr.cxx
- DIST/DI_view_matrix.cxx
- DIST/Makefile
- DIST/di_clustertree.hxx
- DIST/di_foundclusters.hxx
- DIST/di_matr.hxx
- DIST/di_protdist.hxx
- DIST/di_view_matrix.hxx
- DIST/distanalyse.cxx
- Doxyfile
- EDIT4/ED4_ProteinViewer.cxx
- EDIT4/ED4_base.cxx
- EDIT4/ED4_block.cxx
- EDIT4/ED4_colStat.cxx
- + EDIT4/ED4_consensus.cxx
- EDIT4/ED4_members.cxx → EDIT4/ED4_container.cxx
- EDIT4/ED4_cursor.cxx
- EDIT4/ED4_dots.cxx
- EDIT4/ED4_dump.cxx
- EDIT4/ED4_edit_string.cxx
- + EDIT4/ED4_flags.cxx
- EDIT4/ED4_main.cxx
- EDIT4/ED4_manager.cxx
- EDIT4/ED4_naligner.cxx
- EDIT4/ED4_nds.cxx
- EDIT4/ED4_no_class.cxx
- EDIT4/ED4_objspec.cxx
- EDIT4/ED4_plugins.cxx
- EDIT4/ED4_protein_2nd_structure.cxx
- EDIT4/ED4_root.cxx
- EDIT4/ED4_search.cxx
- AWT/AWT_seq_colors.cxx → EDIT4/ED4_seq_colors.cxx
- EDIT4/ED4_terminal.cxx
- EDIT4/ED4_text_terminals.cxx
- EDIT4/ED4_tools.cxx
- EDIT4/ED4_visualizeSAI.cxx
- EDIT4/ED4_window.cxx
- EDIT4/EDB_root_bact.cxx
- EDIT4/Makefile
- − EDIT4/config_beschr.txt
- EDIT4/ed4_awars.hxx
- EDIT4/ed4_block.hxx
- EDIT4/ed4_class.hxx
- EDIT4/ed4_colStat.hxx
- EDIT4/ed4_defs.hxx
- EDIT4/ed4_dots.hxx
- EDIT4/ed4_edit_string.hxx
- EDIT4/ed4_extern.hxx
- + EDIT4/ed4_flags.hxx
- EDIT4/ed4_list.hxx
- EDIT4/ed4_naligner.hxx
- EDIT4/ed4_nds.hxx
- EDIT4/ed4_plugins.hxx
- EDIT4/ed4_protein_2nd_structure.hxx
- EDIT4/ed4_search.hxx
- + EDIT4/ed4_seq_colors.hxx
- EDIT4/ed4_tools.hxx
- EDIT4/ed4_visualizeSAI.hxx
- EDIT4/graph_aligner_gui.cxx
- EDIT4/graph_aligner_gui.hxx
- EDIT4/needs_libs
- EISPACK/Makefile
- GDE/AxML/axml.c
- GDE/CLUSTAL/Makefile
- GDE/CLUSTAL/amenu.c
- GDE/CLUSTAL/clustalv.h
- GDE/CLUSTAL/gcgcheck.c
- GDE/CLUSTAL/general.h
- GDE/CLUSTAL/matrices.h
- GDE/CLUSTAL/myers.c
- GDE/CLUSTAL/sequence.c
- GDE/CLUSTAL/showpair.c
- GDE/CLUSTAL/trees.c
- GDE/CLUSTAL/upgma.c
- GDE/CLUSTAL/util.c
- GDE/CLUSTALW/Makefile
- GDE/CLUSTALW/clustalw.doc
- GDE/CLUSTALW/clustalw.ms
- GDE/CLUSTALW/globin.pep
- GDE/CLUSTALW/interface.c
- GDE/FASTDNAML/Makefile
- GDE/FASTDNAML/fastDNAml.c
- GDE/MAFFT/Makefile
- + GDE/MAFFT/mafft-7.055-with-extensions/.gitignore
- + GDE/MAFFT/mafft-7.055-with-extensions/core/.gitignore
- + GDE/MAFFT/mafft-7.055-with-extensions/extensions/.gitignore
- GDE/MUSCLE/src/subfams.cpp
- GDE/MUSCLE/src/typetostr.cpp
- GDE/Makefile
- GDE/MrBAYES/mrbayes_3.2.1/gpl.txt
- GDE/PHYLIP/Makefile
- GDE/PHYLIP/dnaml.c
- GDE/PHYLIP/dnamlk.c
- GDE/PHYML20130708/Makefile
- GDE/PHYML20130708/phyml/configure.fallback
- GDE/PHYML20130708/phyml/src/mpi_boot.c
- GDE/PHYML20130708/phyml/src/utilities.c
- GDE/PROBCONS/Makefile
- GDE/RAxML/ancestralStates.c
- GDE/RAxML/avxLikelihood.c
- GDE/RAxML/axml.c
- GDE/RAxML/classify.c
- GDE/RAxML/compiler.h
- GDE/RAxML/evaluateGenericSpecial.c
- GDE/RAxML/evaluatePartialGenericSpecial.c
- GDE/RAxML/fastDNAparsimony.c
- GDE/RAxML/fastSearch.c
- GDE/RAxML/gcc.h
- GDE/RAxML/leaveDropping.c
- GDE/RAxML/ll_alloc.c
- GDE/RAxML/ll_asm.h
- GDE/RAxML/ll_list.h
- GDE/RAxML/makenewzGenericSpecial.c
- GDE/RAxML/mem_alloc.c
- GDE/RAxML/ming.h
- GDE/RAxML/newviewGenericSpecial.c
- GDE/RAxML/rogueEPA.c
- + GDE/RAxML8/Makefile
- + GDE/RAxML8/arb_raxml8.sh
- + GDE/RAxML8/raxml8.menu
- + GDE/RAxML8/standard-RAxML-8.2.8.tar.gz
- GDE/README
- + GDE/SATIVA/Makefile
- + GDE/SATIVA/arb_raxml8_sativa.sh
- + GDE/SATIVA/arb_sativa.pl
- + GDE/SATIVA/sativa-RAxML-8.2.3.tar.gz
- + GDE/SATIVA/sativa.menu
- + GDE/SATIVA/sativa/epa_trainer.py
- + GDE/SATIVA/sativa/epac.cfg.sativa
- + GDE/SATIVA/sativa/epac/__init__.py
- + GDE/SATIVA/sativa/epac/argparse/__init__.py
- + GDE/SATIVA/sativa/epac/argparse/argparse.py
- + GDE/SATIVA/sativa/epac/classify_util.py
- + GDE/SATIVA/sativa/epac/config.py
- + GDE/SATIVA/sativa/epac/erlang.py
- + GDE/SATIVA/sativa/epac/ete2/__init__.py
- + GDE/SATIVA/sativa/epac/ete2/arraytable.py
- + GDE/SATIVA/sativa/epac/ete2/fasta.py
- + GDE/SATIVA/sativa/epac/ete2/newick.py
- + GDE/SATIVA/sativa/epac/ete2/paml.py
- + GDE/SATIVA/sativa/epac/ete2/phylip.py
- + GDE/SATIVA/sativa/epac/ete2/seqgroup.py
- + GDE/SATIVA/sativa/epac/ete2/text_arraytable.py
- + GDE/SATIVA/sativa/epac/ete2/tree.py
- + GDE/SATIVA/sativa/epac/json_util.py
- + GDE/SATIVA/sativa/epac/msa.py
- + GDE/SATIVA/sativa/epac/raxml_util.py
- + GDE/SATIVA/sativa/epac/taxonomy_util.py
- + GDE/SATIVA/sativa/epac/version.py
- + GDE/SATIVA/sativa/gpl-3.0.txt
- + GDE/SATIVA/sativa/sativa.py
- − GDE/SUPPORT/CAP2.c
- GDE/SUPPORT/Makefile
- GDE/SUPPORT/Zuk_to_gen.c
- GDE/TREEPUZZLE/Makefile
- GDEHELP/ARB_GDEmenus.source
- − GDEHELP/HELP_PLAIN/CAP2.help
- GDEHELP/HELP_WRITTEN/MrBayes.help
- GDEHELP/HELP_WRITTEN/raxml.help
- + GDEHELP/HELP_WRITTEN/raxml8.help
- + GDEHELP/HELP_WRITTEN/sativa.help
- GDEHELP/MENUS/align.menu
- GDEHELP/MENUS/desoete.menu
- GDEHELP/MENUS/phylip_dist.menu
- GDEHELP/MENUS/phylip_help.menu
- GDEHELP/MENUS/phylip_ml.menu
- GDEHELP/MENUS/phylip_pars.menu
- GDEHELP/MENUS/phyml.menu
- GDEHELP/MENUS/phyml_20130708.menu
- GDEHELP/MENUS/pretty_print.menu
- GDEHELP/MENUS/puzzle.menu
- GDEHELP/MENUS/raxml.menu
- GDEHELP/MENUS/start_arb.menu
- GDEHELP/Makefile
- GDEHELP/Makefile.helpfiles
- GENOM/EXP.hxx
- GENOM/EXP_interface.cxx
- GENOM/EXP_local.hxx
- GENOM/EXP_main.cxx
- GENOM/GEN.hxx
- GENOM/GEN_gene.cxx
- GENOM/GEN_gene.hxx
- GENOM/GEN_graphic.cxx
- GENOM/GEN_graphic.hxx
- GENOM/GEN_interface.cxx
- GENOM/GEN_local.hxx
- GENOM/GEN_map.cxx
- GENOM/GEN_nds.cxx
- GENOM/GEN_nds.hxx
- GENOM/GEN_translations.cxx
- GENOM/Makefile
- GENOM_IMPORT/DBwriter.cxx
- GENOM_IMPORT/DBwriter.h
- GENOM_IMPORT/Feature.cxx
- GENOM_IMPORT/GenomeImport.cxx
- GENOM_IMPORT/Importer.cxx
- GENOM_IMPORT/Importer.h
- GENOM_IMPORT/Makefile
- GENOM_IMPORT/MetaInfo.cxx
- GENOM_IMPORT/MetaInfo.h
- GENOM_IMPORT/MetaTag.h
- GENOM_IMPORT/SequenceBuffer.cxx
- GENOM_IMPORT/SequenceBuffer.h
- GENOM_IMPORT/tools.h
- + GFX/arb_db.png
- + GFX/arb_db.svg
- GL/glAW/AW_window_ogl.cxx
- GL/glAW/Makefile
- GL/glpng/Makefile
- GL/glpng/glpng.c
- HEADERLIBS/Makefile
- HELP_SOURCE/Makefile
- HELP_SOURCE/arb_help2xml.cxx
- HELP_SOURCE/generate_index.pl
- HELP_SOURCE/genhelp/Makefile
- HELP_SOURCE/oldhelp/FAQS.hlp
- HELP_SOURCE/oldhelp/FORM.hlp
- + HELP_SOURCE/oldhelp/aaali.hlp
- + HELP_SOURCE/oldhelp/accessibility_sai.hlp
- HELP_SOURCE/oldhelp/aci.hlp
- HELP_SOURCE/oldhelp/acisrt.hlp
- HELP_SOURCE/oldhelp/ad_align.hlp
- HELP_SOURCE/oldhelp/ad_extended.hlp
- + HELP_SOURCE/oldhelp/advice.hlp
- HELP_SOURCE/oldhelp/alignment.hlp
- HELP_SOURCE/oldhelp/ap_stack.hlp
- HELP_SOURCE/oldhelp/arb.hlp
- HELP_SOURCE/oldhelp/arb_commands.hlp
- HELP_SOURCE/oldhelp/arb_edit4.hlp
- HELP_SOURCE/oldhelp/arb_envar.hlp
- HELP_SOURCE/oldhelp/arb_export.hlp
- HELP_SOURCE/oldhelp/arb_export_nds.hlp
- HELP_SOURCE/oldhelp/arb_import.hlp
- HELP_SOURCE/oldhelp/arb_intro.hlp
- HELP_SOURCE/oldhelp/arb_merge_workflow.hlp
- HELP_SOURCE/oldhelp/arb_pars.hlp
- HELP_SOURCE/oldhelp/bonds.hlp
- HELP_SOURCE/oldhelp/branch_analysis.hlp
- HELP_SOURCE/oldhelp/checkfield.hlp
- HELP_SOURCE/oldhelp/chimera_check.hlp
- HELP_SOURCE/oldhelp/color.hlp
- + HELP_SOURCE/oldhelp/color_loadsave.hlp
- HELP_SOURCE/oldhelp/color_props.hlp
- HELP_SOURCE/oldhelp/color_props_groups.hlp
- + HELP_SOURCE/oldhelp/color_ranges.hlp
- HELP_SOURCE/oldhelp/colorize.hlp
- + HELP_SOURCE/oldhelp/compare_taxonomy.hlp
- HELP_SOURCE/oldhelp/tree_diff.hlp → HELP_SOURCE/oldhelp/compare_topo.hlp
- HELP_SOURCE/oldhelp/concatenate.hlp
- − HELP_SOURCE/oldhelp/configuration.hlp
- HELP_SOURCE/oldhelp/consense_algo.hlp
- − HELP_SOURCE/oldhelp/consensus.ps.gz
- HELP_SOURCE/oldhelp/consensus_def.hlp
- + HELP_SOURCE/oldhelp/console.hlp
- + HELP_SOURCE/oldhelp/copyNpaste.hlp
- HELP_SOURCE/oldhelp/del_list.hlp
- HELP_SOURCE/oldhelp/di_clusters.hlp
- + HELP_SOURCE/oldhelp/displayField.hlp
- HELP_SOURCE/oldhelp/dist.hlp
- HELP_SOURCE/oldhelp/e4.hlp
- + HELP_SOURCE/oldhelp/e4_background_priority.hlp
- HELP_SOURCE/oldhelp/e4_block.hlp
- + HELP_SOURCE/oldhelp/e4_defaults.hlp
- + HELP_SOURCE/oldhelp/e4_get_species.hlp
- + HELP_SOURCE/oldhelp/e4_mode.hlp
- HELP_SOURCE/oldhelp/e4_modsai.hlp
- HELP_SOURCE/oldhelp/e4_options.hlp
- HELP_SOURCE/oldhelp/e4_replace.hlp
- HELP_SOURCE/oldhelp/e4_search.hlp
- HELP_SOURCE/oldhelp/ecoliref.hlp
- + HELP_SOURCE/oldhelp/ed4_flags.hlp
- HELP_SOURCE/oldhelp/exec_bug.hlp
- + HELP_SOURCE/oldhelp/experiment_info.hlp
- HELP_SOURCE/oldhelp/nt_props_data.hlp → HELP_SOURCE/oldhelp/experiment_search.hlp
- HELP_SOURCE/oldhelp/export_format.hlp
- + HELP_SOURCE/oldhelp/export_test.hlp
- HELP_SOURCE/oldhelp/faligner.hlp
- HELP_SOURCE/oldhelp/gene_options.hlp → HELP_SOURCE/oldhelp/field_sel_new.hlp
- + HELP_SOURCE/oldhelp/field_shader.hlp
- HELP_SOURCE/oldhelp/gde_menus.hlp
- HELP_SOURCE/oldhelp/markcolor.hlp → HELP_SOURCE/oldhelp/gen_disp_style.hlp
- + HELP_SOURCE/oldhelp/gen_jump.hlp
- + HELP_SOURCE/oldhelp/gen_mode.hlp
- + HELP_SOURCE/oldhelp/gen_new_view.hlp
- + HELP_SOURCE/oldhelp/gen_options.hlp
- HELP_SOURCE/oldhelp/gene_extract.hlp
- HELP_SOURCE/oldhelp/gene_hide.hlp
- HELP_SOURCE/oldhelp/gene_info.hlp
- HELP_SOURCE/oldhelp/gene_mark.hlp
- HELP_SOURCE/oldhelp/gene_search.hlp
- HELP_SOURCE/oldhelp/gene_species.hlp
- HELP_SOURCE/oldhelp/gene_species_mark.hlp
- HELP_SOURCE/oldhelp/genes.hlp
- HELP_SOURCE/oldhelp/glossary.hlp
- + HELP_SOURCE/oldhelp/group_by_field.hlp
- + HELP_SOURCE/oldhelp/group_rename.hlp
- + HELP_SOURCE/oldhelp/group_search.hlp
- HELP_SOURCE/oldhelp/rdp_ift.hlp → HELP_SOURCE/oldhelp/group_trees.hlp
- HELP_SOURCE/oldhelp/help.hlp
- + HELP_SOURCE/oldhelp/import_test.hlp
- HELP_SOURCE/oldhelp/importift.hlp
- HELP_SOURCE/oldhelp/insdel.hlp
- HELP_SOURCE/oldhelp/insdel_sai.hlp
- HELP_SOURCE/oldhelp/islandhopping.hlp
- HELP_SOURCE/oldhelp/iupac-codes.hlp
- + HELP_SOURCE/oldhelp/keeled_groups.hlp
- + HELP_SOURCE/oldhelp/kernlin.hlp
- HELP_SOURCE/oldhelp/macro.hlp
- + HELP_SOURCE/oldhelp/manage_test.hlp
- HELP_SOURCE/oldhelp/mark.hlp
- HELP_SOURCE/oldhelp/mark_duplicates.hlp
- HELP_SOURCE/oldhelp/mark_genes.hlp
- HELP_SOURCE/oldhelp/mark_list.hlp
- HELP_SOURCE/oldhelp/markbyref.hlp
- HELP_SOURCE/oldhelp/max_freq.hlp
- HELP_SOURCE/oldhelp/merge_species.hlp
- + HELP_SOURCE/oldhelp/mergetaggedfield.hlp
- HELP_SOURCE/oldhelp/mg_names.hlp
- HELP_SOURCE/oldhelp/mg_species.hlp
- HELP_SOURCE/oldhelp/mg_configs.hlp → HELP_SOURCE/oldhelp/mg_species_configs.hlp
- HELP_SOURCE/oldhelp/mg_spec_sel_field.hlp → HELP_SOURCE/oldhelp/mg_xfer_field_of_listed.hlp
- + HELP_SOURCE/oldhelp/mg_xfer_field_of_sel.hlp
- HELP_SOURCE/oldhelp/mod_field_list.hlp
- HELP_SOURCE/oldhelp/mode_group.hlp
- HELP_SOURCE/oldhelp/mode_info.hlp
- HELP_SOURCE/oldhelp/mode_kernlin.hlp
- HELP_SOURCE/oldhelp/mode_move.hlp
- HELP_SOURCE/oldhelp/mode_nni.hlp
- HELP_SOURCE/oldhelp/mode_optimize.hlp
- HELP_SOURCE/oldhelp/mode_setroot.hlp
- + HELP_SOURCE/oldhelp/move_groups.hlp
- HELP_SOURCE/oldhelp/mp_params.hlp
- HELP_SOURCE/oldhelp/multifurcate.hlp
- HELP_SOURCE/oldhelp/multiprobe.hlp
- HELP_SOURCE/oldhelp/multiproberesults.hlp
- HELP_SOURCE/oldhelp/namesadmin.hlp
- HELP_SOURCE/oldhelp/nekey_map.hlp
- HELP_SOURCE/oldhelp/newwindow.hlp
- HELP_SOURCE/oldhelp/next_neighbours.hlp
- HELP_SOURCE/oldhelp/next_neighbours_listed.hlp
- + HELP_SOURCE/oldhelp/nni.hlp
- HELP_SOURCE/oldhelp/nt_keys.hlp
- + HELP_SOURCE/oldhelp/nt_tree_marker_settings.hlp
- HELP_SOURCE/oldhelp/nt_tree_settings.hlp
- + HELP_SOURCE/oldhelp/nt_tree_settings_bootstrap.hlp
- + HELP_SOURCE/oldhelp/nt_tree_settings_expert.hlp
- HELP_SOURCE/oldhelp/optimize.hlp
- HELP_SOURCE/oldhelp/pa_add.hlp
- − HELP_SOURCE/oldhelp/pa_add_sel.hlp
- HELP_SOURCE/oldhelp/pa_bootstrap.hlp
- HELP_SOURCE/oldhelp/pa_branchlengths.hlp
- + HELP_SOURCE/oldhelp/pa_globopti.hlp
- + HELP_SOURCE/oldhelp/pa_kernlin.hlp
- + HELP_SOURCE/oldhelp/pa_locopti.hlp
- + HELP_SOURCE/oldhelp/pa_mixtree.hlp
- HELP_SOURCE/oldhelp/pa_optimizer.hlp
- HELP_SOURCE/oldhelp/pa_partial.hlp
- HELP_SOURCE/oldhelp/pa_quick.hlp
- − HELP_SOURCE/oldhelp/pa_quick_sel.hlp
- + HELP_SOURCE/oldhelp/pa_reset.hlp
- + HELP_SOURCE/oldhelp/pa_value.hlp
- HELP_SOURCE/oldhelp/pars.hlp
- HELP_SOURCE/oldhelp/partial_sequences.hlp
- + HELP_SOURCE/oldhelp/pd_match_iupac.hlp
- HELP_SOURCE/oldhelp/pfold.hlp
- HELP_SOURCE/oldhelp/pfold_sai.hlp
- HELP_SOURCE/oldhelp/phyl.hlp
- HELP_SOURCE/oldhelp/phylo.hlp
- HELP_SOURCE/oldhelp/pm_spec_param.hlp
- HELP_SOURCE/oldhelp/pos_var_pars.hlp
- HELP_SOURCE/oldhelp/primer_new.hlp
- − HELP_SOURCE/oldhelp/primer_parameters.hlp
- + HELP_SOURCE/oldhelp/primer_result.hlp
- HELP_SOURCE/oldhelp/probe_param.hlp
- HELP_SOURCE/oldhelp/probeadmin.hlp
- HELP_SOURCE/oldhelp/probedesign.hlp
- HELP_SOURCE/oldhelp/probedesignresult.hlp
- HELP_SOURCE/oldhelp/probematch.hlp
- + HELP_SOURCE/oldhelp/probespec.hlp
- HELP_SOURCE/oldhelp/configurations.hlp → HELP_SOURCE/oldhelp/prop_configs.hlp
- + HELP_SOURCE/oldhelp/prop_configs_edit.hlp
- HELP_SOURCE/oldhelp/props_frame.hlp
- HELP_SOURCE/oldhelp/props_nds.hlp
- HELP_SOURCE/oldhelp/props_www.hlp
- HELP_SOURCE/oldhelp/proteinViewer.hlp
- HELP_SOURCE/oldhelp/pt_server.hlp
- + HELP_SOURCE/oldhelp/questions.hlp
- HELP_SOURCE/oldhelp/realign_dna.hlp
- HELP_SOURCE/oldhelp/reg.hlp
- HELP_SOURCE/oldhelp/rename.hlp
- + HELP_SOURCE/oldhelp/rerepair.hlp
- HELP_SOURCE/oldhelp/tgroupcolor.hlp → HELP_SOURCE/oldhelp/reset_win_layout.hlp
- HELP_SOURCE/oldhelp/resorttree.hlp
- HELP_SOURCE/oldhelp/tungroupall.hlp → HELP_SOURCE/oldhelp/rna3d_changeMolecule.hlp
- HELP_SOURCE/oldhelp/rna3d_dispMolecule.hlp
- HELP_SOURCE/oldhelp/saiProbeHelp.hlp → HELP_SOURCE/oldhelp/saiProbe.hlp
- + HELP_SOURCE/oldhelp/saicalc.hlp
- HELP_SOURCE/oldhelp/save.hlp
- − HELP_SOURCE/oldhelp/saveas.hlp
- HELP_SOURCE/oldhelp/savedef.hlp
- HELP_SOURCE/oldhelp/scandb.hlp
- HELP_SOURCE/oldhelp/search_duplicates.hlp
- HELP_SOURCE/oldhelp/searching.hlp
- HELP_SOURCE/oldhelp/sel_spec.hlp → HELP_SOURCE/oldhelp/sec_bonddef.hlp
- HELP_SOURCE/oldhelp/sec_display.hlp
- + HELP_SOURCE/oldhelp/sec_imexport.hlp
- HELP_SOURCE/oldhelp/sel_box.hlp
- HELP_SOURCE/oldhelp/sel_fil.hlp
- HELP_SOURCE/oldhelp/selected.hlp
- HELP_SOURCE/oldhelp/selected_gene.hlp
- HELP_SOURCE/oldhelp/set_color_of_listed.hlp
- + HELP_SOURCE/oldhelp/sp_IDs.hlp
- HELP_SOURCE/oldhelp/sp_info.hlp
- HELP_SOURCE/oldhelp/sp_info_locked.hlp
- − HELP_SOURCE/oldhelp/sp_rename.hlp
- HELP_SOURCE/oldhelp/sp_search.hlp
- HELP_SOURCE/oldhelp/sp_sort_fld.hlp
- HELP_SOURCE/oldhelp/sp_sort_phyl.hlp
- HELP_SOURCE/oldhelp/sp_sp_2_ext.hlp
- HELP_SOURCE/oldhelp/spa_copy.hlp
- HELP_SOURCE/oldhelp/spa_create.hlp
- HELP_SOURCE/oldhelp/spa_delete.hlp
- HELP_SOURCE/oldhelp/spa_rename.hlp
- HELP_SOURCE/oldhelp/spaf_create.hlp
- HELP_SOURCE/oldhelp/spaf_delete.hlp
- HELP_SOURCE/oldhelp/spaf_reorder.hlp
- HELP_SOURCE/oldhelp/species.hlp
- + HELP_SOURCE/oldhelp/species_configs.hlp
- + HELP_SOURCE/oldhelp/species_configs_highlight.hlp
- + HELP_SOURCE/oldhelp/species_configs_saveload.hlp
- HELP_SOURCE/oldhelp/species_join.hlp
- HELP_SOURCE/oldhelp/srt.hlp
- HELP_SOURCE/oldhelp/st_ml.hlp
- HELP_SOURCE/oldhelp/ebi_ift.hlp → HELP_SOURCE/oldhelp/sync_colors.hlp
- + HELP_SOURCE/oldhelp/syncroots.hlp
- + HELP_SOURCE/oldhelp/syncscroll.hlp
- HELP_SOURCE/oldhelp/tags.hlp
- HELP_SOURCE/oldhelp/fasta_ift.hlp → HELP_SOURCE/oldhelp/ted_boot.hlp
- − HELP_SOURCE/oldhelp/tgroupnmrkd.hlp
- HELP_SOURCE/oldhelp/tkeep_mrkd.hlp
- + HELP_SOURCE/oldhelp/topology_shader.hlp
- HELP_SOURCE/oldhelp/tr_export.hlp
- HELP_SOURCE/oldhelp/tr_import.hlp
- HELP_SOURCE/oldhelp/tr_jump.hlp
- + HELP_SOURCE/oldhelp/transl_table.hlp
- HELP_SOURCE/oldhelp/translate_dna_2_pro.hlp
- HELP_SOURCE/oldhelp/tree2file.hlp
- − HELP_SOURCE/oldhelp/tree_cmp.hlp
- + HELP_SOURCE/oldhelp/tree_group.hlp
- HELP_SOURCE/oldhelp/tgroupall.hlp → HELP_SOURCE/oldhelp/tree_pseudo.hlp
- + HELP_SOURCE/oldhelp/tree_shading.hlp
- HELP_SOURCE/oldhelp/treeadm.hlp
- HELP_SOURCE/oldhelp/trm_boot.hlp
- HELP_SOURCE/oldhelp/trm_del.hlp
- HELP_SOURCE/oldhelp/undo.hlp
- HELP_SOURCE/oldhelp/unmark_list.hlp
- HELP_SOURCE/oldhelp/user_matrix.hlp
- + HELP_SOURCE/oldhelp/viewdiff.hlp
- HELP_SOURCE/oldhelp/visualizeSAI.hlp
- HELP_SOURCE/oldhelp/vn_search.hlp
- HELP_SOURCE/oldhelp/write_field_list.hlp
- + HELP_SOURCE/oldhelp/xferset.hlp
- + HELP_SOURCE/oldhelp/xterm.hlp
- HELP_SOURCE/to_help.xsl
- + HELP_SOURCE/xml_2_depends.pl
- − HELP_SOURCE/xml_2_depends.sh
- ISLAND_HOPPING/Makefile
- ISLAND_HOPPING/align.cxx
- ISLAND_HOPPING/i-hopper.cxx
- ISLAND_HOPPING/island_hopping.cxx
- ISLAND_HOPPING/island_hopping.h
- ISLAND_HOPPING/mem.cxx
- MERGE/MG_adapt_ali.cxx
- MERGE/MG_adapt_ali.hxx
- MERGE/MG_alignment.cxx
- MERGE/MG_checkfield.cxx
- MERGE/MG_configs.cxx
- MERGE/MG_extendeds.cxx
- MERGE/MG_gene_species.cxx
- MERGE/MG_main.cxx
- MERGE/MG_names.cxx
- MERGE/MG_preserves.cxx
- MERGE/MG_species.cxx
- MERGE/MG_trees.cxx
- MERGE/Makefile
- MERGE/merge.hxx
- MERGE/needs_libs
- MULTI_PROBE/MP_Generation.cxx
- MULTI_PROBE/MP_GenerationDuplicates.cxx
- MULTI_PROBE/MP_Window.cxx
- MULTI_PROBE/MP_externs.hxx
- MULTI_PROBE/MP_main.cxx
- MULTI_PROBE/MP_mo_liste.cxx
- MULTI_PROBE/MP_noclass.cxx
- MULTI_PROBE/MP_permute.cxx
- MULTI_PROBE/MP_probe.cxx
- MULTI_PROBE/MP_probe.hxx
- MULTI_PROBE/MP_probe_combi_statistic.cxx
- MULTI_PROBE/MP_probe_tabs.cxx
- MULTI_PROBE/MP_sonde.cxx
- MULTI_PROBE/MP_sondentopf.cxx
- MULTI_PROBE/Makefile
- MULTI_PROBE/MultiProbe.hxx
- MULTI_PROBE/SoTl.hxx
- MULTI_PROBE/mp_proto.hxx
- MULTI_PROBE/mpdefs.h
- MULTI_PROBE/multi_probe.hxx
- Makefile
- NALIGNER/Makefile
- NALIGNER/ali_aligner.cxx
- NALIGNER/ali_aligner.hxx
- NALIGNER/ali_arbdb.cxx
- NALIGNER/ali_arbdb.hxx
- NALIGNER/ali_global.cxx
- NALIGNER/ali_main.cxx
- NALIGNER/ali_misc.hxx
- NALIGNER/ali_pathmap.cxx
- NALIGNER/ali_pathmap.hxx
- NALIGNER/ali_prealigner.cxx
- NALIGNER/ali_prealigner.hxx
- NALIGNER/ali_profile.cxx
- NALIGNER/ali_profile.hxx
- NALIGNER/ali_pt.cxx
- NALIGNER/ali_sequence.cxx
- NALIGNER/ali_sequence.hxx
- NALIGNER/ali_solution.cxx
- NALIGNER/ali_tarray.hxx
- NALIGNER/ali_tlist.hxx
- NAMES/Makefile
- NAMES/names.cxx
- NAMES_COM/Makefile
- NAMES_COM/names_extern.c
- NTREE/AP_consensus.cxx
- − NTREE/AP_conservProfile2Gnuplot.cxx
- NTREE/AP_pos_var_pars.cxx
- NTREE/ColumnStat_2_gnuplot.cxx
- NTREE/Makefile
- NTREE/NT_branchAnalysis.cxx
- NTREE/NT_cb.cxx
- − NTREE/NT_cb.h
- NTREE/NT_concatenate.cxx
- NTREE/NT_dbrepair.cxx
- NTREE/NT_edconf.cxx
- NTREE/NT_extern.cxx
- + NTREE/NT_group_search.cxx
- EDIT4/ed4_known_plugins.hxx → NTREE/NT_group_search.h
- NTREE/NT_import.cxx
- NTREE/NT_ins_col.cxx
- NTREE/NT_join.cxx
- NTREE/NT_local.h
- NTREE/NT_local_proto.h
- NTREE/NT_main.cxx
- + NTREE/NT_shadeTree.cxx
- NTREE/NT_sort.cxx
- NTREE/NT_species_set.h
- + NTREE/NT_sync_scroll.cxx
- + NTREE/NT_sync_scroll.h
- + NTREE/NT_syncroot.cxx
- + NTREE/NT_taxonomy.cxx
- NTREE/NT_trackAliChanges.cxx
- NTREE/NT_tree_cmp.cxx
- NTREE/NT_tree_cmp.h
- NTREE/NT_userland_fixes.cxx
- NTREE/NT_validManual.cxx
- NTREE/NT_validNameParser.cxx
- NTREE/NT_validNameParser.h
- NTREE/NT_validNames.cxx
- + NTREE/ScrollSynchronizer.cxx
- + NTREE/ScrollSynchronizer.h
- − NTREE/ad_ali.cxx
- NTREE/ad_ext.cxx
- NTREE/ad_spec.cxx
- NTREE/ad_transpro.cxx
- NTREE/ad_trees.cxx
- NTREE/ad_trees.h
- NTREE/needs_libs
- + NTREE/tree_position.h
- PARSIMONY/AP_buffer.cxx
- PARSIMONY/AP_buffer.hxx
- − PARSIMONY/AP_error.hxx
- PARSIMONY/AP_main.cxx
- PARSIMONY/AP_tree_edge.cxx
- PARSIMONY/AP_tree_nlen.cxx
- − PARSIMONY/GA_genetic.cxx
- − PARSIMONY/GA_genetic.hxx
- − PARSIMONY/GA_main.cxx
- − PARSIMONY/GA_window.cxx
- PARSIMONY/Makefile
- PARSIMONY/PARS_dtree.cxx
- PARSIMONY/PARS_klprops.cxx
- PARSIMONY/PARS_main.cxx
- + PARSIMONY/PerfMeter.h
- PARSIMONY/ap_main.hxx
- + PARSIMONY/ap_main_type.hxx
- PARSIMONY/ap_tree_nlen.hxx
- + PARSIMONY/pars_awars.h
- − PARSIMONY/pars_debug.hxx
- PARSIMONY/pars_dtree.hxx
- PARSIMONY/pars_klprops.hxx
- PARSIMONY/pars_main.hxx
- + PARSIMONY/test_env.h
- PERL2ARB/ARB.default.xs
- PERL2ARB/ARB.pm
- PERL2ARB/DOC.html
- PERL2ARB/Makefile.main
- PERL2ARB/make_arbperl_makefile.pl
- PERL2ARB/perlmain_source.c
- PERL2ARB/typemap
- PERLTOOLS/Makefile
- PERLTOOLS/arb_proto_2_xsub.cxx
- + PERL_SCRIPTS/ACI/sortListNumeric.pl
- + PERL_SCRIPTS/ARBTOOLS/IFTHELP/README
- + PERL_SCRIPTS/ARBTOOLS/TESTS/README
- + PERL_SCRIPTS/ARBTOOLS/TESTS/automatic.pl
- + PERL_SCRIPTS/ARBTOOLS/TESTS/manual.pl
- PERL_SCRIPTS/ARBTOOLS/import_from_table.pl
- PERL_SCRIPTS/ARBTOOLS/raxml2arb.pl
- PERL_SCRIPTS/GENOME/GI.pm
- PERL_SCRIPTS/GENOME/collect_gene_info.pl
- PERL_SCRIPTS/MACROS/with_all_marked.pl
- PERL_SCRIPTS/SAI/SAI_demo.pl
- + PERL_SCRIPTS/SPECIES/clone_taxonomy.pl
- PERL_SCRIPTS/SPECIES/markSpecies.pl
- + PERL_SCRIPTS/SPECIES/useFieldAsID.pl
- + PERL_SCRIPTS/lib/ali_dnapro.pm
- PERL_SCRIPTS/test/Makefile
- PERL_SCRIPTS/test/testScripts.pl
- PHYLO/Makefile
- PHYLO/PH_data.cxx
- PHYLO/PH_display.cxx
- PHYLO/PH_display.hxx
- PHYLO/PH_filt.cxx
- PHYLO/PH_filter.hxx
- PHYLO/PH_main.cxx
- PHYLO/PH_root.cxx
- PHYLO/needs_libs
- PHYLO/phylo.hxx
- PRIMER_DESIGN/Makefile
- PRIMER_DESIGN/PRD_Design.cxx
- PRIMER_DESIGN/PRD_Globals.hxx
- PRIMER_DESIGN/PRD_Item.cxx
- PRIMER_DESIGN/PRD_Node.cxx
- PRIMER_DESIGN/PRD_Node.hxx
- PRIMER_DESIGN/PRD_Pair.cxx
- PRIMER_DESIGN/PRD_Range.cxx
- PRIMER_DESIGN/PRD_SearchFIFO.cxx
- PRIMER_DESIGN/PRD_SequenceIterator.cxx
- PRIMER_DESIGN/primer_design.cxx
- PROBE/Makefile
- PROBE/PT_buildtree.cxx
- PROBE/PT_compress.h
- PROBE/PT_debug.cxx
- PROBE/PT_etc.cxx
- PROBE/PT_family.cxx
- PROBE/PT_findEx.cxx
- PROBE/PT_io.cxx
- PROBE/PT_main.cxx
- PROBE/PT_match.cxx
- PROBE/PT_mem.h
- PROBE/PT_new_design.cxx
- PROBE/PT_partition.h
- PROBE/PT_prefixIter.h
- PROBE/PT_prefixtree.cxx
- PROBE/PT_rangeCheck.h
- PROBE/PT_tools.h
- PROBE/probe.h
- PROBE/probe_tree.h
- PROBE/pt_prototypes.h
- PROBE/pt_split.h
- PROBE_COM/Makefile
- PROBE_COM/PT.aisc
- PROBE_COM/PT_extern.c
- PROBE_COM/needs_libs.client_a
- − PROBE_COM/needs_libs.common_a
- PROBE_DESIGN/Makefile
- PROBE_DESIGN/SaiProbeVisualization.cxx
- PROBE_DESIGN/SaiProbeVisualization.hxx
- PROBE_DESIGN/needs_libs
- + PROBE_DESIGN/probe_collection.cxx
- + PROBE_DESIGN/probe_collection.hxx
- PROBE_DESIGN/probe_design.cxx
- PROBE_DESIGN/probe_design.hxx → PROBE_DESIGN/probe_gui.hxx
- NTREE/AP_conservProfile2Gnuplot.h → PROBE_DESIGN/probe_local.hxx
- PROBE_DESIGN/probe_match_parser.cxx
- PROBE_DESIGN/probe_match_parser.hxx
- PROBE_SET/Makefile
- PROBE_SET/fb_test.cxx
- + PROBE_SET/needs_libs.fb_test_o
- + PROBE_SET/needs_libs.ps_filebuffer_o
- PROBE_SET/ps_arb2asciipaths.cxx
- PROBE_SET/ps_bitmap.hxx
- PROBE_SET/ps_bitset.hxx
- PROBE_SET/ps_candidate.hxx
- PROBE_SET/ps_convert_db.cxx
- PROBE_SET/ps_database.cxx
- PROBE_SET/ps_database.hxx
- PROBE_SET/ps_detect_weak_differences.cxx
- PROBE_SET/ps_eval_candidates.cxx
- PROBE_SET/ps_filebuffer.cxx
- PROBE_SET/ps_filebuffer.hxx
- PROBE_SET/ps_find_probes.cxx
- PROBE_SET/ps_get_probes.cxx
- PROBE_SET/ps_make_sample_db.cxx
- PROBE_SET/ps_my2asciipaths.cxx
- PROBE_SET/ps_node.cxx
- PROBE_SET/ps_node.hxx
- PROBE_SET/ps_pg_specmap.hxx
- PROBE_SET/ps_show_result.cxx
- PROBE_SET/ps_tools.hxx
- READSEQ/Formats
- READSEQ/Makefile
- RNA3D/Makefile
- RNA3D/RNA3D_Global.hxx
- RNA3D/RNA3D_GlobalHeader.hxx
- RNA3D/RNA3D_Graphics.cxx
- RNA3D/RNA3D_Graphics.hxx
- RNA3D/RNA3D_Interface.cxx
- RNA3D/RNA3D_OpenGLEngine.cxx
- RNA3D/RNA3D_OpenGLEngine.hxx
- RNA3D/RNA3D_OpenGLGraphics.cxx
- RNA3D/RNA3D_Renderer.cxx
- RNA3D/RNA3D_Renderer.hxx
- RNA3D/RNA3D_StructureData.cxx
- RNA3D/RNA3D_StructureData.hxx
- RNA3D/RNA3D_Textures.cxx
- RNACMA/AlignedSequenceLoader.cxx
- RNACMA/AlignedSequenceLoader.h
- RNACMA/Analyser.cxx
- RNACMA/Analyser.h
- RNACMA/Cma.cxx
- RNACMA/Cma.h
- RNACMA/Makefile
- RNACMA/needs_libs
- SECEDIT/Makefile
- SECEDIT/SEC_abspos.cxx
- SECEDIT/SEC_bonddef.cxx
- SECEDIT/SEC_db.cxx
- SECEDIT/SEC_db.hxx
- SECEDIT/SEC_drawn_pos.hxx
- SECEDIT/SEC_graphic.cxx
- SECEDIT/SEC_graphic.hxx
- SECEDIT/SEC_helix.cxx
- SECEDIT/SEC_io.cxx
- SECEDIT/SEC_iter.hxx
- SECEDIT/SEC_layout.cxx
- SECEDIT/SEC_main.cxx
- SECEDIT/SEC_paint.cxx
- SECEDIT/SEC_read.cxx
- SECEDIT/SEC_root.hxx
- SECEDIT/SEC_split.cxx
- SECEDIT/SEC_structure.cxx
- SECEDIT/SEC_toggle.cxx
- SEQ_QUALITY/Makefile
- SEQ_QUALITY/SQ_GroupData.cxx
- SEQ_QUALITY/SQ_GroupData.h
- SEQ_QUALITY/SQ_ambiguities.h
- SEQ_QUALITY/SQ_functions.cxx
- SEQ_QUALITY/SQ_functions.h
- SEQ_QUALITY/SQ_helix.h
- SEQ_QUALITY/SQ_main.cxx
- SERVERCNTRL/Makefile
- SERVERCNTRL/servercntrl.cxx
- SERVERCNTRL/servercntrl.h
- SH/README
- SH/arb
- SH/arb_clean
- SH/arb_installubuntu4arb.sh
- SH/arb_launcher
- − SH/arb_ludwig
- + SH/arb_macro_compatibility.sh
- + SH/arb_show_log.pl
- SH/arb_textedit
- SH/arb_wait
- SH/dszmconnect.pl
- + SL/ALILINK/AdminGui.cxx
- + SL/ALILINK/AliAdmin.cxx
- + SL/ALILINK/AliAdmin.h
- + SL/ALILINK/Makefile
- + SL/ALILINK/TranslateRealign.cxx
- RNACMA/dbconn.cxx → SL/ALILINK/TranslateRealign.h
- + SL/ALILINK/needs_libs
- SL/ALIVIEW/AliView.cxx
- SL/ALIVIEW/AliView.hxx
- SL/ALIVIEW/Makefile
- SL/AP_TREE/AP_Tree.cxx
- SL/AP_TREE/AP_Tree.hxx
- + SL/AP_TREE/AP_TreeColors.hxx
- + SL/AP_TREE/AP_TreeSet.cxx
- + SL/AP_TREE/AP_TreeSet.hxx
- + SL/AP_TREE/AP_TreeShader.hxx
- SL/AP_TREE/Makefile
- SL/ARB_TREE/ARB_Tree.cxx
- SL/ARB_TREE/ARB_Tree.hxx
- SL/ARB_TREE/Makefile
- SL/ARB_TREE/needs_libs
- SL/AW_HELIX/AW_helix.cxx
- SL/AW_HELIX/AW_helix.hxx
- SL/AW_HELIX/Makefile
- SL/AW_NAME/AW_names_admin.cxx
- SL/AW_NAME/AW_rename.cxx
- SL/AW_NAME/AW_rename.hxx
- SL/AW_NAME/Makefile
- SL/CB/Makefile
- SL/CB/cb.cxx
- SL/CB/cb.h
- SL/CB/cbtypes.h
- SL/CB/needs_libs
- SL/ROOTED_TREE/Makefile → SL/CONSENSUS/Makefile
- EDIT4/ED4_mini_classes.cxx → SL/CONSENSUS/chartable.cxx
- + SL/CONSENSUS/chartable.h
- + SL/CONSENSUS/consensus.h
- + SL/CONSENSUS/consensus_config.h
- + SL/CONSENSUS/needs_libs
- SL/DB_QUERY/Makefile
- SL/DB_QUERY/db_query.cxx
- SL/DB_QUERY/db_query.h
- SL/DB_QUERY/db_query_local.h
- SL/DB_QUERY/needs_libs
- SL/DB_SCANNER/Makefile
- SL/DB_SCANNER/db_scanner.cxx
- SL/DB_SCANNER/db_scanner.hxx
- SL/DB_UI/Makefile
- SL/DB_UI/dbui.h
- SL/DB_UI/info_window.cxx
- SL/DB_UI/info_window.h
- SL/DB_UI/ui_species.cxx
- SL/FAST_ALIGNER/ClustalV.cxx
- SL/FAST_ALIGNER/Makefile
- SL/FAST_ALIGNER/fast_aligner.cxx
- SL/FAST_ALIGNER/fast_aligner.hxx
- SL/FAST_ALIGNER/seq_search.cxx
- SL/FAST_ALIGNER/seq_search.hxx
- SL/FILTER/AP_filter.cxx
- SL/FILTER/AP_filter.hxx
- SL/FILTER/Makefile
- SL/FILTER/RangeList.cxx
- + SL/FILTSEQEXP/FilteredExport.cxx
- + SL/FILTSEQEXP/FilteredExport.h
- + SL/FILTSEQEXP/Makefile
- + SL/FILTSEQEXP/needs_libs
- + SL/GROUP_SEARCH/Makefile
- + SL/GROUP_SEARCH/group_search.cxx
- + SL/GROUP_SEARCH/group_search.h
- + SL/GROUP_SEARCH/needs_libs
- SL/GUI_ALIVIEW/AWT_filter.cxx
- SL/GUI_ALIVIEW/ColumnStat.cxx
- SL/GUI_ALIVIEW/ColumnStat.hxx
- SL/GUI_ALIVIEW/GUI_aliview.cxx
- SL/GUI_ALIVIEW/Makefile
- SL/GUI_ALIVIEW/awt_filter.hxx
- SL/HELIX/BI_basepos.cxx
- SL/HELIX/BI_basepos.hxx
- SL/HELIX/BI_helix.cxx
- SL/HELIX/BI_helix.hxx
- SL/HELIX/Makefile
- SL/INSDEL/Makefile
- SL/INSDEL/insdel.cxx
- SL/ITEMS/Makefile
- SL/ITEMS/changekey.cxx
- SL/ITEMS/item_sel_list.cxx
- SL/ITEMS/item_sel_list.h
- + SL/ITEMS/items.cxx
- SL/ITEMS/items.h
- + SL/ITEMS/itemtools.cxx
- SL/ITEMS/species.cxx
- + SL/ITEM_SHADER/Makefile
- + SL/ITEM_SHADER/ValueTuple.cxx
- + SL/ITEM_SHADER/field_shader.cxx
- + SL/ITEM_SHADER/field_shader.h
- + SL/ITEM_SHADER/item_shader.cxx
- + SL/ITEM_SHADER/item_shader.h
- + SL/ITEM_SHADER/needs_libs
- SL/LOCATION/Location.cxx
- SL/LOCATION/Makefile
- SL/MACROS/Makefile
- SL/MACROS/dbserver.cxx
- SL/MACROS/macro_gui.cxx
- SL/MACROS/recmac.cxx
- SL/MACROS/trackers.cxx
- SL/MACROS/trackers.hxx
- SL/MATRIX/AP_matrix.cxx
- SL/MATRIX/AP_matrix.hxx
- SL/MATRIX/Makefile
- SL/Makefile
- SL/NDS/Makefile
- SL/NDS/nds.cxx
- SL/NDS/nds.h
- SL/NEIGHBOURJOIN/Makefile
- SL/NEIGHBOURJOIN/NJ.cxx
- SL/NEIGHBOURJOIN/NJ.hxx
- SL/NEIGHBOURJOIN/neighbourjoin.hxx
- SL/PRONUC/AP_codon_table.cxx
- SL/PRONUC/AP_codon_table.hxx
- SL/PRONUC/AP_pro_a_nucs.cxx
- SL/PRONUC/AP_pro_a_nucs.hxx
- SL/PRONUC/Makefile
- SL/PRONUC/iupac.cxx
- SL/PRONUC/iupac.h
- SL/PTCLEAN/Makefile
- SL/PTCLEAN/ptclean.cxx
- SL/PTCLEAN/ptclean.h
- + SL/PVP/AP_pos_var.cxx
- NTREE/AP_pos_var_pars.h → SL/PVP/AP_pos_var.h
- + SL/PVP/Makefile
- + SL/PVP/needs_libs
- + SL/PVP/pvp.cxx
- CONSENSUS_TREE/CT_mem.hxx → SL/PVP/pvp.h
- + SL/QUERY/Makefile
- + SL/QUERY/needs_libs
- + SL/QUERY/query_expr.cxx
- + SL/QUERY/query_expr.h
- SL/README
- SL/REFENTRIES/Makefile
- SL/REFENTRIES/refentries.cxx
- SL/REFENTRIES/refentries.h
- SL/REGEXPR/Makefile
- SL/REGEXPR/RegExpr.cxx
- SL/REGEXPR/RegExpr.hxx
- − SL/ROOTED_TREE/RootedTree.h
- − SL/ROOTED_TREE/needs_libs
- + SL/SAICALC/Makefile
- + SL/SAICALC/calculator.cxx
- + SL/SAICALC/calculator.h
- + SL/SAICALC/needs_libs
- + SL/SAICALC/saicalc.cxx
- + SL/SAICALC/saicalc.h
- + SL/SAICALC/saiop.cxx
- + SL/SAICALC/saiop.h
- SL/SEQIO/Makefile
- SL/SEQIO/needs_libs
- SL/SEQIO/seq_export.cxx
- SL/SEQIO/seqio.cxx
- SL/SEQIO/seqio.hxx
- − SL/SEQUENCE/AP_parsimony_defaults.hxx
- SL/SEQUENCE/AP_seq_dna.cxx
- SL/SEQUENCE/AP_seq_dna.hxx
- SL/SEQUENCE/AP_seq_protein.cxx
- SL/SEQUENCE/AP_seq_protein.hxx
- SL/SEQUENCE/AP_seq_simple_pro.cxx
- SL/SEQUENCE/AP_seq_simple_pro.hxx
- SL/SEQUENCE/AP_sequence.cxx
- SL/SEQUENCE/AP_sequence.hxx
- SL/SEQUENCE/Makefile
- SL/TRANSLATE/Makefile
- SL/TRANSLATE/Translate.cxx
- SL/TRANSLATE/Translate.hxx
- + SL/TREEDISP/Group.cxx
- + SL/TREEDISP/Group.hxx
- + SL/TREEDISP/GroupIterator.hxx
- SL/TREEDISP/Makefile
- SL/TREEDISP/TreeCallbacks.cxx
- SL/TREEDISP/TreeCallbacks.hxx
- SL/TREEDISP/TreeDisplay.cxx
- SL/TREEDISP/TreeDisplay.hxx
- SL/TREEDISP/irstree_display.cxx
- SL/TREE_ADMIN/Makefile
- SL/TREE_ADMIN/TreeAdmin.cxx
- SL/TREE_READ/Makefile
- SL/TREE_READ/TreeRead.cxx
- SL/TREE_READ/TreeRead.h
- SL/TREE_READ/TreeTools.cxx
- SL/TREE_WRITE/Makefile
- SL/TREE_WRITE/TreeWrite.cxx
- SL/TREE_WRITE/TreeWrite.h
- + SL/XFERGUI/Makefile
- + SL/XFERGUI/needs_libs
- + SL/XFERGUI/xfergui.cxx
- + SL/XFERGUI/xfergui.h
- + SL/XFERSET/Makefile
- + SL/XFERSET/needs_libs
- + SL/XFERSET/xferset.cxx
- + SL/XFERSET/xferset.h
- SOURCE_TOOLS/COMPILE_COMPAT/Makefile
- SOURCE_TOOLS/Makefile
- + SOURCE_TOOLS/arb.leaksan.supp
- + SOURCE_TOOLS/arb.supp
- + SOURCE_TOOLS/arb_build_common.pm
- SOURCE_TOOLS/arb_cleanup_patches.pl
- SOURCE_TOOLS/arb_compiler_version.pl
- SOURCE_TOOLS/arb_create_patch.sh
- + SOURCE_TOOLS/arb_gtk.supp
- SOURCE_TOOLS/arb_main.h
- + SOURCE_TOOLS/arb_motif.supp
- SOURCE_TOOLS/arb_valgrind
- + SOURCE_TOOLS/asan2msg.pl
- SOURCE_TOOLS/binuptodate.pl
- SOURCE_TOOLS/build_info.pl
- + SOURCE_TOOLS/check_bin_dependencies.pl
- SOURCE_TOOLS/check_dirs_equal.sh
- SOURCE_TOOLS/check_ressources.pl → SOURCE_TOOLS/check_resources.pl
- + SOURCE_TOOLS/clean_checked_vectorizations.sh
- SOURCE_TOOLS/deadcode.pl
- SOURCE_TOOLS/dep.4dummy
- SOURCE_TOOLS/dep.alltargets
- SOURCE_TOOLS/dep.libtargets
- SOURCE_TOOLS/dependency_graphs.pl
- SOURCE_TOOLS/diff2grep.pl
- + SOURCE_TOOLS/etags_ignore.lst
- SOURCE_TOOLS/export2sub
- SOURCE_TOOLS/find_newest_source.pl
- SOURCE_TOOLS/generate_all_links.sh
- SOURCE_TOOLS/needed_libs.pl
- SOURCE_TOOLS/parent_make.txt
- SOURCE_TOOLS/postcompile.pl
- + SOURCE_TOOLS/refactor/v1.cxx
- + SOURCE_TOOLS/refactor/v2.cxx
- SOURCE_TOOLS/release/HOWTO.release
- SOURCE_TOOLS/release/release_tool.pl
- SOURCE_TOOLS/remake_after_change.pl
- − SOURCE_TOOLS/requireVersion.pl
- + SOURCE_TOOLS/sortfig.pl
- SOURCE_TOOLS/svn_apply_ignores.pl
- SOURCE_TOOLS/svn_undo_depends.pl
- SOURCE_TOOLS/tabBrake.pl
- + SOURCE_TOOLS/uniqueID.sh
- SOURCE_TOOLS/update_config_makefile.pl
- SOURCE_TOOLS/valgrind2grep
- + SOURCE_TOOLS/vectorize.README
- + SOURCE_TOOLS/vectorized.source
- SOURCE_TOOLS/version_info
- STAT/Makefile
- STAT/MostLikelySeq.hxx
- STAT/ST_ml.cxx
- STAT/ST_quality.cxx
- STAT/ST_window.cxx
- STAT/st_ml.hxx
- STAT/st_quality.hxx
- STAT/st_window.hxx
- TEMPLATES/ChecksumCollector.h
- + TEMPLATES/ErrorOrType.h
- + TEMPLATES/FileWatch.h
- DIST/dist.hxx → TEMPLATES/Keeper.h
- TEMPLATES/SuppressOutput.h
- TEMPLATES/arb_algo.h
- TEMPLATES/arb_backtrace.h
- TEMPLATES/arb_defs.h
- TEMPLATES/arb_error.h
- TEMPLATES/arb_global_defs.h
- TEMPLATES/arb_simple_assert.h
- TEMPLATES/arb_sleep.h
- TEMPLATES/arb_stdstr.h
- TEMPLATES/arb_str.h
- TEMPLATES/arb_unit_test.h
- TEMPLATES/arbtools.h
- TEMPLATES/attributes.h
- TEMPLATES/cache.h
- TEMPLATES/command_output.h
- TEMPLATES/config_parser.h
- TEMPLATES/cxxforward.h
- TEMPLATES/downcast.h
- TEMPLATES/dupstr.h
- TEMPLATES/gccver.h
- + TEMPLATES/lazy.h
- + TEMPLATES/matrix.h
- + TEMPLATES/mod_rlimit.h
- TEMPLATES/mode_text.h
- TEMPLATES/output.h
- TEMPLATES/perf_timer.h
- + TEMPLATES/sized_cstr.h
- TEMPLATES/smartptr.h
- TEMPLATES/static_assert.h
- TEMPLATES/svn_revision.h
- TEMPLATES/ut_valgrinded.h
- TOOLS/Makefile
- TOOLS/arb_2_ascii.cxx
- TOOLS/arb_2_bin.cxx
- TOOLS/arb_a2ps.c
- + TOOLS/arb_calc_pvp.cxx
- TOOLS/arb_consensus_tree.cxx
- TOOLS/arb_dnarates.cxx
- + TOOLS/arb_export_newick.cxx
- TOOLS/arb_export_rates.cxx
- + TOOLS/arb_export_seq_filtered.cxx
- + TOOLS/arb_export_sequences.cxx
- TOOLS/arb_export_tree.cxx
- TOOLS/arb_gene_probe.cxx
- TOOLS/arb_message.cxx
- − TOOLS/arb_notify.cxx
- TOOLS/arb_perf_test.cxx
- TOOLS/arb_primer.cxx
- TOOLS/arb_probe.cxx
- + TOOLS/arb_probe_match.cxx
- TOOLS/arb_read_tree.cxx
- TOOLS/arb_replace.cxx
- + TOOLS/arb_sub2ascii.cxx
- TOOLS/arb_test.cxx
- + TOOLS/arb_write_tree_comment.cxx
- TREEGEN/Makefile
- TREEGEN/base.c
- TREEGEN/defines.c
- TREEGEN/frand.c
- TREEGEN/frand.h
- TREEGEN/readcfg.c
- TREEGEN/readcfg.h
- TREEGEN/rns.c
- TREEGEN/rns.h
- TREEGEN/simcfg.c
- TREEGEN/spreadin.c
- TREEGEN/spreadin.h
- UNIT_TESTER/Makefile
- UNIT_TESTER/Makefile.setup.template
- UNIT_TESTER/Makefile.suite
- UNIT_TESTER/Makefile.test
- UNIT_TESTER/README.txt
- UNIT_TESTER/TestEnvironment.cxx
- UNIT_TESTER/UnitTester.cxx
- UNIT_TESTER/UnitTester.hxx
- + UNIT_TESTER/dumpTestLocations.pl
- + UNIT_TESTER/dupsymwarn.pl
- + UNIT_TESTER/list_undefined_units.pl
- UNIT_TESTER/log_result.pl
- UNIT_TESTER/make_symlist.sh
- UNIT_TESTER/reporter.pl
- UNIT_TESTER/run/AB735678_expected.arb
- + UNIT_TESTER/run/TEST_aci.arb
- UNIT_TESTER/run/TEST_arbdbserver_save_expected.arb
- + UNIT_TESTER/run/TEST_calcSAI_expectd.arb
- + UNIT_TESTER/run/TEST_copy.arb
- + UNIT_TESTER/run/TEST_copy_noProtect.arb
- + UNIT_TESTER/run/TEST_fields_ascii.arb
- + UNIT_TESTER/run/TEST_fields_cloned_expected.arb
- + UNIT_TESTER/run/TEST_fields_xferred_expected.arb
- UNIT_TESTER/run/TEST_gpt.arb.expected
- UNIT_TESTER/run/TEST_gpt_src.arb
- UNIT_TESTER/run/TEST_loadsave.arb
- UNIT_TESTER/run/TEST_loadsave_ascii.arb
- UNIT_TESTER/run/TEST_loadsave_quick.a00
- UNIT_TESTER/run/TEST_nuc.arb
- UNIT_TESTER/run/TEST_nuc_seqcompr_exp.arb
- + UNIT_TESTER/run/TEST_nuc_short.arb
- UNIT_TESTER/run/TEST_opti_ascii_in.arb
- UNIT_TESTER/run/TEST_opti_ascii_renamed_expected.arb
- UNIT_TESTER/run/TEST_opti_expected.arb
- UNIT_TESTER/run/TEST_prot.arb
- + UNIT_TESTER/run/TEST_prot_tiny.arb
- UNIT_TESTER/run/TEST_pt.arb.pt.expected
- UNIT_TESTER/run/TEST_pt_cleaned_expected.arb
- UNIT_TESTER/run/TEST_pt_src.arb
- + UNIT_TESTER/run/TEST_realign.arb
- UNIT_TESTER/run/TEST_trees.arb
- UNIT_TESTER/run/diff/base.input
- UNIT_TESTER/run/diff/date_changed.input
- UNIT_TESTER/run/diff/date_swapped.input
- UNIT_TESTER/run/diff/swapped.input
- UNIT_TESTER/run/display/dendro_CH.fig
- + UNIT_TESTER/run/display/dendro_CH_centered.fig
- + UNIT_TESTER/run/display/dendro_CH_centered_diagonal.fig
- + UNIT_TESTER/run/display/dendro_CH_diagonal.fig
- UNIT_TESTER/run/display/dendro_CN.fig
- + UNIT_TESTER/run/display/dendro_CN_diagonal.fig
- + UNIT_TESTER/run/display/dendro_CN_shortSmall.fig
- UNIT_TESTER/run/display/dendro_MH.fig
- + UNIT_TESTER/run/display/dendro_MH_diagonal.fig
- + UNIT_TESTER/run/display/dendro_MH_long.fig
- UNIT_TESTER/run/display/dendro_MN.fig
- + UNIT_TESTER/run/display/dendro_MN_diagonal.fig
- UNIT_TESTER/run/display/irs_CH.fig
- UNIT_TESTER/run/display/irs_CN.fig
- UNIT_TESTER/run/display/irs_MH.fig
- UNIT_TESTER/run/display/irs_MN.fig
- UNIT_TESTER/run/display/nds_CH.fig
- UNIT_TESTER/run/display/nds_CN.fig
- UNIT_TESTER/run/display/nds_MH.fig
- UNIT_TESTER/run/display/nds_MN.fig
- UNIT_TESTER/run/display/radial_CH.fig
- UNIT_TESTER/run/display/radial_CN.fig
- UNIT_TESTER/run/display/radial_MH.fig
- UNIT_TESTER/run/display/radial_MN.fig
- + UNIT_TESTER/run/distance/matrix.dna.phylipComp.expected
- + UNIT_TESTER/run/distance/matrix.dna.readable.expected
- + UNIT_TESTER/run/distance/matrix.dna.tabbed.expected
- + UNIT_TESTER/run/distance/matrix.pro.phylipComp.expected
- + UNIT_TESTER/run/distance/matrix.pro.readable.expected
- + UNIT_TESTER/run/distance/matrix.pro.tabbed.expected
- + UNIT_TESTER/run/distance/matrix.rna.phylipComp.expected
- + UNIT_TESTER/run/distance/matrix.rna.readable.expected
- + UNIT_TESTER/run/distance/matrix.rna.tabbed.expected
- + UNIT_TESTER/run/group_xfer_11.log.expected
- + UNIT_TESTER/run/group_xfer_21.log.expected
- + UNIT_TESTER/run/group_xfer_32.log.expected
- + UNIT_TESTER/run/group_xfer_32_li.log.expected
- + UNIT_TESTER/run/group_xfer_32_rc.log.expected
- + UNIT_TESTER/run/group_xfer_32_rel.log.expected
- UNIT_TESTER/run/help/unittest.hlp
- UNIT_TESTER/run/impexp/embl.eft.exported
- + UNIT_TESTER/run/impexp/ruleset.fts
- UNIT_TESTER/run/impexp/xml.eft.exported
- UNIT_TESTER/run/index_pt.dump.expected
- + UNIT_TESTER/run/pars/nucl-add-NNI.tree.expected
- + UNIT_TESTER/run/pars/nucl-add-quick.tree.expected
- + UNIT_TESTER/run/pars/nucl-addPart-CloButyP.tree.expected
- + UNIT_TESTER/run/pars/nucl-addPart-CorGlutP-CloButyP.tree.expected
- + UNIT_TESTER/run/pars/nucl-addPart-CorGlutP.tree.expected
- + UNIT_TESTER/run/pars/nucl-addPart-bug609.tree.expected
- + UNIT_TESTER/run/pars/nucl-addPartialAsFull-CorGlutP.tree.expected
- + UNIT_TESTER/run/pars/nucl-calclength.tree.expected
- + UNIT_TESTER/run/pars/nucl-initial.tree.expected
- + UNIT_TESTER/run/pars/nucl-opti-NNI.tree.expected
- + UNIT_TESTER/run/pars/nucl-opti-all-NNI.tree.expected
- + UNIT_TESTER/run/pars/nucl-opti-global.tree.expected
- + UNIT_TESTER/run/pars/nucl-opti-marked-global.tree.expected
- + UNIT_TESTER/run/pars/nucl-opti-visible-global.tree.expected
- + UNIT_TESTER/run/pars/nucl-readdall-NNI.tree.expected
- + UNIT_TESTER/run/pars/nucl-readdall-quick.tree.expected
- + UNIT_TESTER/run/pars/nucl-removed.tree.expected
- + UNIT_TESTER/run/pars/prot-add-NNI.tree.expected
- + UNIT_TESTER/run/pars/prot-add-quick.tree.expected
- + UNIT_TESTER/run/pars/prot-addPart-MucRaceP-StrCoelP.tree.expected
- + UNIT_TESTER/run/pars/prot-addPart-MucRaceP.tree.expected
- + UNIT_TESTER/run/pars/prot-addPart-StrCoelP.tree.expected
- + UNIT_TESTER/run/pars/prot-addPart-bug609.tree.expected
- + UNIT_TESTER/run/pars/prot-addPartialAsFull-MucRaceP.tree.expected
- + UNIT_TESTER/run/pars/prot-calclength.tree.expected
- + UNIT_TESTER/run/pars/prot-initial.tree.expected
- + UNIT_TESTER/run/pars/prot-mixed.tree.expected
- + UNIT_TESTER/run/pars/prot-opti-NNI.tree.expected
- + UNIT_TESTER/run/pars/prot-opti-all-NNI.tree.expected
- + UNIT_TESTER/run/pars/prot-opti-global.tree.expected
- + UNIT_TESTER/run/pars/prot-opti-marked-global.tree.expected
- + UNIT_TESTER/run/pars/prot-removed.tree.expected
- + UNIT_TESTER/run/pvp/custom.dump.expected
- + UNIT_TESTER/run/pvp/flippedTreeImported.dump.expected
- + UNIT_TESTER/run/pvp/gottree.dump.expected
- + UNIT_TESTER/run/pvp/notree.dump.expected
- + UNIT_TESTER/run/pvp/standard.dump.expected
- + UNIT_TESTER/run/syncroot/1/disjunct.tree
- + UNIT_TESTER/run/syncroot/1/overlap.tree
- + UNIT_TESTER/run/syncroot/1/overlap_A.tree
- + UNIT_TESTER/run/syncroot/1/ref.tree
- + UNIT_TESTER/run/syncroot/1/tosync.tree
- + UNIT_TESTER/run/tools/acc.list
- UNIT_TESTER/run/tools/dnarates_expected.arb
- + UNIT_TESTER/run/tools/exflt_AMI_mf.fasta.expected
- + UNIT_TESTER/run/tools/exflt_AMI_skipShort.fasta.expected
- + UNIT_TESTER/run/tools/exflt_AMI_unfiltered.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_mf.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_mfpvp.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_partial.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_pvp.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_pvp_g05.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_pvp_gaps.fasta.expected
- + UNIT_TESTER/run/tools/exflt_DNA_unfiltered.fasta.expected
- + UNIT_TESTER/run/tools/exflt_empty.fasta.expected
- + UNIT_TESTER/run/tools/export_newick.arb
- + UNIT_TESTER/run/tools/exseq.fasta.expected
- + UNIT_TESTER/run/tools/exseq_ascii.arb.expected
- + UNIT_TESTER/run/tools/exseq_via_eft.fasta.expected
- + UNIT_TESTER/run/tools/min_template.arb
- + UNIT_TESTER/run/tools/probeset.data.expected
- + UNIT_TESTER/run/tools/probeset.out.expected
- UNIT_TESTER/run/tools/read_tree_out_expected.arb
- + UNIT_TESTER/run/trees/nuc_flipped.tree
- − UNIT_TESTER/sockets/README
- + UNIT_TESTER/sok/README
- UNIT_TESTER/sym2testcode.pl
- UNIT_TESTER/test_global.h
- + UNIT_TESTER/test_runtool.h
- UNIT_TESTER/test_unit.h
- WETC/Makefile
- WETC/WETC_main.cxx
- WINDOW/AW_Xm.cxx
- WINDOW/AW_advice.cxx
- WINDOW/AW_at.cxx
- WINDOW/AW_awar.cxx
- WINDOW/AW_button.cxx
- WINDOW/AW_cb_struct.cxx
- WINDOW/AW_clipable.cxx
- WINDOW/AW_device.cxx
- WINDOW/AW_device_click.cxx
- WINDOW/AW_device_size.cxx
- WINDOW/AW_edit.cxx
- WINDOW/AW_file.cxx
- WINDOW/AW_font_group.cxx
- WINDOW/AW_global_awars.cxx
- WINDOW/AW_help.cxx
- + WINDOW/AW_inotify.cxx
- WINDOW/AW_modal.cxx
- + WINDOW/AW_option_toggle.cxx
- WINDOW/AW_position.cxx
- WINDOW/AW_preset.cxx
- WINDOW/AW_print.cxx
- WINDOW/AW_question.cxx
- + WINDOW/AW_rgb.cxx
- WINDOW/AW_root.cxx
- WINDOW/AW_root_debug.cxx
- WINDOW/AW_select.cxx
- WINDOW/AW_status.cxx
- WINDOW/AW_window.cxx
- WINDOW/AW_window_Xm_interface.cxx
- WINDOW/AW_xfig.cxx
- WINDOW/AW_xfont.cxx
- WINDOW/AW_xkey.cxx
- WINDOW/Makefile
- WINDOW/aw_Xm.hxx
- WINDOW/aw_advice.hxx
- WINDOW/aw_at.hxx
- WINDOW/aw_awar.hxx
- WINDOW/aw_awar_defs.hxx
- WINDOW/aw_base.hxx
- WINDOW/aw_color_groups.hxx
- WINDOW/aw_common.hxx
- WINDOW/aw_common_xm.hxx
- WINDOW/aw_def.hxx
- WINDOW/aw_device.hxx
- WINDOW/aw_device_click.hxx
- WINDOW/aw_edit.hxx
- WINDOW/aw_font_group.hxx
- + WINDOW/aw_font_limits.hxx
- + WINDOW/aw_inotify.hxx
- WINDOW/aw_keysym.hxx
- RNACMA/dbconn.h → WINDOW/aw_localdef.hxx
- WINDOW/aw_nawar.hxx
- WINDOW/aw_position.hxx
- WINDOW/aw_preset.hxx
- WINDOW/aw_question.hxx
- + WINDOW/aw_rgb.hxx
- WINDOW/aw_root.hxx
- WINDOW/aw_scalar.cxx
- WINDOW/aw_scalar.hxx
- WINDOW/aw_select.hxx
- WINDOW/aw_status.hxx
- + WINDOW/aw_varupdate.hxx
- WINDOW/aw_window.hxx
- WINDOW/aw_window_Xm.hxx
- WINDOW/aw_xfig.hxx
- WINDOW/aw_xfont.hxx
- XML/Makefile
- XML/xml.cxx
- XML/xml.hxx
- − XML_IMPORT/IMP_TREE/Makefile
- − XML_IMPORT/IMP_TREE/MySAXHandler.cxx
- − XML_IMPORT/IMP_TREE/MySAXHandler.hxx
- − XML_IMPORT/IMP_TREE/sax2Handler.cxx
- − XML_IMPORT/IMP_TREE/sax2Handler.hxx
- − XML_IMPORT/IMP_TREE/testParser.cxx
- − XML_IMPORT/IMP_TREE/testParser.hxx
- − XML_IMPORT/IMP_TREE/xmlParser.cxx
- − XML_IMPORT/IMP_TREE/xmlParser.hxx
- − XML_IMPORT/Makefile
- − XML_IMPORT/needs_libs
- arb_CHANGES.txt
- arb_INSTALL.txt
- arb_LICENSE.txt
- arb_OS_X.txt
- + arb_PUBLIB_LICENSE.txt
- arb_README.txt
- arb_UBUNTU.txt
- arb_install.sh
- arbsrc_README_gcc.txt
- bin/Makefile
- config.makefile.template
- debian/changelog
- debian/control
- debian/patches/10_upstream_r12793__show_db_load_progress
- debian/patches/20_upstream_r12794__socket_permissions
- debian/patches/30_upstream_r12814__desktop_keywords
- debian/patches/40_upstream_r12815__lintian_spelling
- debian/patches/70_skip_compler_version_check.patch
- debian/watch
- demo.arb
- − lib/arb_default/phyl.arb
- lib/arb_default/status.arb
- lib/arb_tcp_org.dat
- lib/desktop/arb.desktop
- lib/export/embl.eft
- lib/export/fasta_wacc.eft
- lib/gde/README
- lib/import/fasta.ift
- lib/import/fasta_wacc_wgap.ift
- lib/import/fasta_wgap.ift
- lib/import/rdp.ift
- lib/import/universal_dna.ift
- lib/macros/ARB/SEQ_DATA/dashes2dots_at_sequenceends_of_marked.amc
- + lib/macros/demo__mark_species_named_a.amc
- lib/macros/xopen.amc → lib/macros/demo__open_windows.amc
- lib/macros/toggle_color.amc → lib/macros/demo__toggle_color.amc
- − lib/macros/replamb.amc
- − lib/macros/test.amc
- − lib/macros/testwl.amc
- lib/motifHack/Makefile
- lib/motifHack/convert_xpm.pl
- lib/pictures/RNA3D_ChangeMolecule.fig
- lib/pictures/RNA3D_DisplayBases.fig
- lib/pictures/RNA3D_DisplayHelices.fig
- lib/pictures/RNA3D_DisplayOptions.fig
- − lib/pictures/RNA3D_Help.fig
- lib/pictures/RNA3D_SeqMapping.fig
- − lib/pictures/ad_al_si.fig
- lib/pictures/ad_align.fig
- lib/pictures/ad_branch.fig
- lib/pictures/ad_cons_tree.fig
- lib/pictures/ad_conv.fig
- lib/pictures/ad_delof.fig
- lib/pictures/ad_ext.fig
- + lib/pictures/ad_ext_group.fig
- lib/pictures/ad_fcrea.fig
- lib/pictures/ad_gen_create.fig
- lib/pictures/ad_kreo.fig
- − lib/pictures/ad_mset.fig
- lib/pictures/ad_one_tree.fig
- lib/pictures/ad_query.fig
- lib/pictures/ad_selManNam.fig
- lib/pictures/ad_spec.fig
- lib/pictures/ad_spec_nn.fig
- lib/pictures/ad_spec_nnm.fig
- − lib/pictures/ad_table_admin.fig
- − lib/pictures/ad_table_fields.fig
- lib/pictures/ad_tree.fig
- − lib/pictures/ad_two_trees.fig
- lib/pictures/arb_intro.fig
- lib/pictures/awt/align.fig
- lib/pictures/awt/ascii_print.fig
- lib/pictures/awt/col_statistic.fig
- + lib/pictures/awt/edit_config.fig
- lib/pictures/awt/export.fig
- lib/pictures/awt/export_db.fig
- + lib/pictures/awt/export_test.fig
- lib/pictures/gene_options.fig → lib/pictures/awt/field_sel.fig
- + lib/pictures/awt/field_sel_new.fig
- lib/pictures/awt/filter.fig
- lib/pictures/awt/import_db.fig
- + lib/pictures/awt/import_test.fig
- + lib/pictures/awt/manage_config.fig
- lib/pictures/awt/nds.fig
- − lib/pictures/awt/nds_sel.fig
- − lib/pictures/awt/parser.fig
- lib/pictures/awt/print.fig
- lib/pictures/awt/secExport.fig
- − lib/pictures/awt/set_protection.fig
- lib/pictures/awt/srt_select.fig
- lib/pictures/awt/tree_settings.fig
- lib/pictures/awt/www.fig
- lib/pictures/awtc/autoren.fig
- lib/pictures/awtc/names_admin.fig
- lib/pictures/calltexe.fig
- lib/pictures/chimera_check.fig
- − lib/pictures/color_loadsave.fig
- + lib/pictures/compare_taxonomy.fig
- + lib/pictures/compare_topo.fig
- lib/pictures/concatenate.fig
- lib/pictures/consensus/expert.fig
- − lib/pictures/consensus/groups.fig
- lib/pictures/consensus/max_freq.fig
- − lib/pictures/conservProfile2Gnuplot.fig
- lib/pictures/cpro/csp_2_gnuplot.fig
- lib/pictures/cpro/parsimony.fig
- lib/pictures/dbbrowser.fig
- lib/pictures/di_cancel.fig
- lib/pictures/di_clusters.fig
- lib/pictures/di_ge_ma.fig
- lib/pictures/displayField.fig
- lib/pictures/ed_al_ex.fig
- lib/pictures/ed_al_sp.fig
- lib/pictures/ed_key.fig
- − lib/pictures/edit4/choose_field.fig
- lib/pictures/edit4/consensus.fig
- lib/pictures/edit4/create_seq.fig
- lib/pictures/edit4/create_seq_fc.fig
- lib/pictures/edit4/editmenu.fig
- + lib/pictures/edit4/load_config.fig
- + lib/pictures/edit4/load_sai.fig
- lib/pictures/edit4/message.fig
- lib/pictures/edit4/missbase.fig
- lib/pictures/edit4/modsai.fig
- lib/pictures/edit4/nds.fig
- lib/pictures/edit4/options.fig
- lib/pictures/edit4/replace.fig
- lib/pictures/edit4/save_config.fig
- lib/pictures/edit4/save_search.fig
- lib/pictures/edit4/search.fig
- + lib/pictures/edit4/viewdiff.fig
- lib/pictures/faligner/faligner.fig
- lib/pictures/faligner/family_settings.fig
- lib/pictures/faligner/islandhopping.fig
- lib/pictures/fileselect.fig
- + lib/pictures/fts_ruledef.fig
- + lib/pictures/fts_select.fig
- lib/pictures/gde3item.fig
- lib/pictures/gdeitem.fig
- lib/pictures/gdeitem_simple.fig
- + lib/pictures/gen_options.fig
- − lib/pictures/gene_layout.fig
- + lib/pictures/group_search.fig
- + lib/pictures/group_trees.fig
- lib/pictures/help.fig
- lib/pictures/insdel.fig
- lib/pictures/insdel_sai.fig
- + lib/pictures/item_shader_cfg.fig
- + lib/pictures/iupac.fig
- lib/pictures/join_species.fig
- lib/pictures/load_box.fig
- lib/pictures/macro_select.fig
- + lib/pictures/mark_configs.fig
- − lib/pictures/merge/ad_align.fig
- lib/pictures/merge/alignment.fig
- lib/pictures/merge/configs.fig
- lib/pictures/merge/extended.fig
- lib/pictures/merge/main.fig
- lib/pictures/merge/mg_def_gene_species_fields.fig
- lib/pictures/merge/mg_mergetaggedfield.fig
- − lib/pictures/merge/mg_movefield.fig
- lib/pictures/merge/mg_transfield.fig
- lib/pictures/merge/names.fig
- lib/pictures/merge/preserves.fig
- lib/pictures/merge/seqcheck.fig
- lib/pictures/merge/species.fig
- lib/pictures/merge/trees.fig
- lib/pictures/merge_species.fig
- lib/pictures/message.fig
- + lib/pictures/move_groups.fig
- lib/pictures/mp_results.fig
- lib/pictures/multiprobe.fig
- lib/pictures/nt_selection.fig
- lib/pictures/nt_sort.fig
- lib/pictures/optimize.fig
- lib/pictures/pars/init.fig
- lib/pictures/pars/kernlin.fig
- + lib/pictures/pars/tree_opti.fig
- lib/pictures/pd_admin.fig
- lib/pictures/pd_main.fig
- lib/pictures/pd_match.fig
- lib/pictures/pd_match_iupac.fig
- + lib/pictures/pd_match_probe_collection.fig
- + lib/pictures/pd_match_with_specificity.fig
- lib/pictures/pd_reslt.fig
- lib/pictures/pd_spec.fig
- − lib/pictures/pg_select.fig
- lib/pictures/phylo/filter.fig
- lib/pictures/phylo/save_markerline.fig
- lib/pictures/phylo/select_ali.fig
- lib/pictures/pm_spec.fig
- lib/pictures/prd_main.fig
- lib/pictures/probeSaiColors.fig
- lib/pictures/proteinViewer.fig
- + lib/pictures/query/color_loadsave.fig
- lib/pictures/colorize.fig → lib/pictures/query/colorize.fig
- + lib/pictures/query/modify_fields.fig
- + lib/pictures/query/set_protection.fig
- + lib/pictures/query/write_fields.fig
- + lib/pictures/realign_dna.fig
- lib/pictures/saiColorRange.fig
- + lib/pictures/saiaci.fig
- + lib/pictures/saicalc.fig
- + lib/pictures/saichain.fig
- + lib/pictures/saimatrix.fig
- + lib/pictures/saitrans.fig
- lib/pictures/save_as.fig
- lib/pictures/sec_bonddef.fig
- lib/pictures/sec_display.fig
- lib/pictures/sec_imexport.fig
- lib/pictures/sel_box.fig
- lib/pictures/sel_box_nds.fig
- lib/pictures/sel_box_tree.fig
- lib/pictures/sel_box_user.fig
- − lib/pictures/sel_box_user2.fig
- − lib/pictures/sel_box_user3.fig
- lib/pictures/select_simple.fig
- lib/pictures/seq_quality.fig
- lib/pictures/sl_l_box.fig
- lib/pictures/sl_s_box.fig
- lib/pictures/stat_main.fig
- lib/pictures/status.fig
- lib/pictures/submiss.fig
- + lib/pictures/syncroot.fig
- + lib/pictures/syncscroll.fig
- lib/pictures/trackali.fig
- − lib/pictures/transdna.fig
- lib/pictures/transpro.fig
- + lib/pictures/tree_export.fig
- − lib/pictures/unused/RNA3D_MapSAI.fig
- − lib/pictures/unused/RNA3D_MapSpeciesOptions.fig
- − lib/pictures/unused/demo/demo.fig
- − lib/pictures/unused/demo/demo1.fig
- − lib/pictures/unused/demo/demo2.fig
- − lib/pictures/unused/demo/demo3.fig
- − lib/pictures/unused/demo/demo_buttons_2.fig
- − lib/pictures/unused/demo/demo_buttons_3.fig
- − lib/pictures/unused/demo/demo_input.fig
- − lib/pictures/unused/demo/demo_input_2.fig
- − lib/pictures/unused/demo/demo_input_3.fig
- − lib/pictures/unused/demo/demo_label.fig
- − lib/pictures/unused/demo/demo_label_2.fig
- − lib/pictures/unused/demo/demo_label_3.fig
- − lib/pictures/unused/demo/demo_options.fig
- − lib/pictures/unused/demo/demo_options_2.fig
- − lib/pictures/unused/demo/demo_pictures.fig
- − lib/pictures/unused/demo/demo_pictures_2.fig
- − lib/pictures/unused/demo/demo_selections.fig
- − lib/pictures/unused/demo/demo_selections_2.fig
- − lib/pictures/unused/demo/demo_selections_3.fig
- − lib/pictures/unused/demo/demo_string.fig
- − lib/pictures/unused/demo/demo_string_2.fig
- − lib/pictures/unused/demo/demo_text.fig
- − lib/pictures/unused/demo/demo_text_2.fig
- − lib/pictures/unused/demo/demo_text_3.fig
- − lib/pictures/unused/demo/demo_toggles.fig
- − lib/pictures/unused/demo/demo_toggles_2.fig
- − lib/pictures/unused/demo/dm.fig
- − lib/pictures/unused/duplicates.fig
- − lib/pictures/unused/ed_align.fig
- − lib/pictures/unused/findcorr/bc_bgprocess.fig
- − lib/pictures/unused/findcorr/bc_ccheck.fig
- − lib/pictures/unused/findcorr/bc_fa.fig
- − lib/pictures/unused/findcorr/bc_fat.fig
- − lib/pictures/unused/findcorr/bc_hydro.fig
- − lib/pictures/unused/findcorr/bc_noise.fig
- − lib/pictures/unused/findcorr/bc_overview.fig
- − lib/pictures/unused/findcorr/bc_ovrview.fig
- − lib/pictures/unused/findcorr/bc_plot.fig
- − lib/pictures/unused/findcorr/bc_rank.fig
- − lib/pictures/unused/findcorr/bc_rank66.fig
- − lib/pictures/unused/findcorr/bc_start.fig
- − lib/pictures/unused/findcorr/bc_surface.fig
- − lib/pictures/unused/findcorr/bc_verb.fig
- − lib/pictures/unused/findcorr/bc_verb2.fig
- − lib/pictures/unused/findcorr/bc_window.fig
- − lib/pictures/unused/findcorr/pca_comp.fig
- − lib/pictures/unused/findcorr/pca_text.fig
- − lib/pictures/unused/findcorr/sel_box.fig
- − lib/pictures/unused/logo.fig
- lib/pictures/visualizeSAI.fig
- lib/pictures/window/advice.fig
- − lib/pixmaps/bases.xpm
- − lib/pixmaps/edit/unused/3to5.xpm
- − lib/pixmaps/edit/unused/5to3.xpm
- − lib/pixmaps/edit/unused/align.xpm
- − lib/pixmaps/edit/unused/edit_sec.xpm
- − lib/pixmaps/edit/unused/folded.xpm
- − lib/pixmaps/edit/unused/insert.xpm
- − lib/pixmaps/edit/unused/noalign.xpm
- − lib/pixmaps/edit/unused/probeInfo.xpm
- − lib/pixmaps/edit/unused/replace.xpm
- − lib/pixmaps/edit/unused/rna3D.xpm
- − lib/pixmaps/edit/unused/stop.xpm
- − lib/pixmaps/edit/unused/stretch.xpm
- − lib/pixmaps/edit/unused/unfolded.xpm
- lib/pixmaps/editor.xpm
- + lib/pixmaps/editor_small.xpm
- − lib/pixmaps/helix.xpm
- − lib/pixmaps/icons/unused/ARB_EDIT.xpm
- − lib/pixmaps/icons/unused/ARB_NT.xpm
- − lib/pixmaps/icons/unused/ARB_PARSIMONY.xpm
- − lib/pixmaps/icons/unused/NEIGHBOR_JOINING.xpm
- − lib/pixmaps/icons/unused/SAVE_ARB_DB.xpm
- − lib/pixmaps/icons/unused/SAVE_CHANGES_TO.xpm
- − lib/pixmaps/icons/unused/default.xpm
- − lib/pixmaps/icons/unused/message.xpm
- − lib/pixmaps/print/unused/clipScreenStr.xpm
- − lib/pixmaps/print/unused/potrait.xpm
- − lib/pixmaps/unused/Close.xpm
- − lib/pixmaps/unused/arb_edit.xpm
- − lib/pixmaps/unused/arrow.xpm
- − lib/pixmaps/unused/compress.xpm
- − lib/pixmaps/unused/cppast.xpm
- − lib/pixmaps/unused/dendro.xpm
- − lib/pixmaps/unused/dendroIrs.xpm
- − lib/pixmaps/unused/disk.xpm
- − lib/pixmaps/unused/edit.xpm
- − lib/pixmaps/unused/exit.xpm
- − lib/pixmaps/unused/gen_map.xpm
- − lib/pixmaps/unused/jm1.xpm
- − lib/pixmaps/unused/jm2.xpm
- − lib/pixmaps/unused/jm3.xpm
- − lib/pixmaps/unused/jm4.xpm
- − lib/pixmaps/unused/jm5.xpm
- − lib/pixmaps/unused/jm6.xpm
- − lib/pixmaps/unused/kill.xpm
- − lib/pixmaps/unused/less.xpm
- − lib/pixmaps/unused/ljump.xpm
- − lib/pixmaps/unused/logo.xpm
- − lib/pixmaps/unused/lzoom_sec.xpm
- − lib/pixmaps/unused/matches.xpm
- − lib/pixmaps/unused/minus.xpm
- − lib/pixmaps/unused/mol.xpm
- − lib/pixmaps/unused/more.xpm
- − lib/pixmaps/unused/move2.xpm
- − lib/pixmaps/unused/moveleft.xpm
- − lib/pixmaps/unused/ndstree.xpm
- − lib/pixmaps/unused/not.xpm
- − lib/pixmaps/unused/pdown.xpm
- − lib/pixmaps/unused/plus.xpm
- − lib/pixmaps/unused/pup.xpm
- − lib/pixmaps/unused/quitText.xpm
- − lib/pixmaps/unused/redo.xpm
- − lib/pixmaps/unused/refreshText.xpm
- − lib/pixmaps/unused/search.xpm
- − lib/pixmaps/unused/separator.xpm
- − lib/pixmaps/unused/stop.xpm
- − lib/pixmaps/unused/tselect.xpm
- − lib/pixmaps/unused/undo.xpm
- − lib/pixmaps/unused/www.xpm
- + lib/probe_match_collection_demo.xpc
- + lib/revision_info.txt
- lib/rna3d/images/Circle.png
- lib/rna3d/images/ConeDown.png
- lib/rna3d/images/ConeUp.png
- lib/rna3d/images/Cross.png
- lib/rna3d/images/Danger.png
- lib/rna3d/images/Diamond.png
- − lib/rna3d/images/FreeForm_1.png
- lib/rna3d/images/Hexagon.png
- lib/rna3d/images/LetterA.png
- lib/rna3d/images/LetterC.png
- lib/rna3d/images/LetterG.png
- lib/rna3d/images/LetterU.png
- − lib/rna3d/images/Letter_A.png
- − lib/rna3d/images/Letter_C.png
- − lib/rna3d/images/Letter_G.png
- − lib/rna3d/images/Letter_U.png
- lib/rna3d/images/Polygon.png
- lib/rna3d/images/Question.png
- lib/rna3d/images/Rectangle.png
- lib/rna3d/images/RectangleRound.png
- lib/rna3d/images/Star.png
- lib/rna3d/images/StarSmooth.png
- lib/sellists/srt_aci.sellst
- lib/sellists/srt_aci_cosmetic.sellst
- lib/sellists/srt_aci_gc.sellst
- − ptpan/Makefile
- − ptpan/PTP_main.cxx
- − ptpan/needs_libs.PROBE_a
- − ptpan/ptpan_info.txt
- util/arb_check_build_env.pl
- util/arb_compile.sh
- util/arb_fig
- util/arb_srclst.pl
- util/jenkins_build.sh
- + util/usecores.pl


The diff was not included because it is too large.


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