# User Interface Look and Feel # ---------------------------- # Possible values for 'native_ui' # 'yes' to use native (system) "look and feel" # 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below) # '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected, # Archaeopteryx-style "look and feel" otherwise native_ui: ? # Default Values for Options # -------------------------- # Minimal confidence value to be displayed: 'min_confidence_value': # Example: 'min_confidence_value: 50.0' (a commonly used # value for bootstrap support) # Font family name: 'font_family': # Example: 'font_family: Arial,Calibri,Helvetica' # It is advisable to use more than one value for font_family (in # decreasing order of preference). Font family names have to be # comma separated (no spaces). Spaces in font names have to be # replaced by underscores (e.g. 'Times_New_Roman'). # Font size: 'font_size': # Example: 'font_size: 10' # Screen antialias: 'antialias_screen': values: 'yes'/'no' # Show Scale: 'show_scale': values: 'yes'/'no' # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no' # Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no' # Cladogram display type: 'cladogram_type' # Example: 'cladogram_type: ext_node_sum_dep' # The three possible values are: non_lined_up # ext_node_sum_dep # total_node_sum_dep (for "uniform" branch lengths) # Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y': # (Archaeopteryx tries to guess the locale, so setting these is not always necessary) # Example: For A4 (portrait): # 'graphics_export_x: 595' # 'graphics_export_y: 845' # For US Letter (portrait): # 'graphics_export_x: 612' # 'graphics_export_y: 792' # Default line width for PDF export: 'pdf_export_line_wdith': # Example: 'pdf_export_line_width: 0.5' # Show overview: 'show_overview': values: 'yes'/'no' # Phylogeny graphics type: 'phylogeny_graphics_type': # Example: 'phylogeny_graphics_type: euro_style' # The eight possible values are: rectangular # euro_style # rounded # curved # triangular # convex # unrooted # circular # Node label direction for circular and unrooted type: 'node_label_direction': # Example: 'node_label_direction: horizontal' # The two possible values are: horizontal # radial # Show default node shape: 'show_default_node_shapes': values: 'yes'/'no' # Default node shape size: 'default_node_size' # Example: 'default_node_size: 6' # Default node shape type: 'default_node_shape' # Example: 'default_node_shape: ' # Possible values: circle # rectangle # Default node shape fill: 'default_node_fill' # Example: 'default_node_fill: ' # Possible values: solid # gradient # none # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no' # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no' # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no' # Number of fraction digits for branch length values: 'branch_length_value_digits' # Number of fraction digits for confidence values: 'confidence_value_digits' # To turn on/off background color gradient: background_gradient # Example: 'background_gradient: yes' # To allow/not allow editing (cut, copy, and paste): allow_editing # Example: 'allow_editing: yes' # To replace underscores with spaces during NH/NHX/Nexus file parsing (application only): # 'replace_underscores_in_nh_parsing' # To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694') # during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing' # Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only): # 'internal_labels_are_confidence_values' min_confidence_value: 0.0 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans font_size: 10 antialias_screen: yes show_scale: yes show_branch_length_values: no cladogram_type: ext_node_sum_dep phylogeny_graphics_type: rectangular node_label_direction: horizontal show_default_node_shapes: no default_node_size: 6 default_node_shape: circle default_node_fill: gradient taxonomy_colorize_node_shapes: no #graphics_export_x: 595 #graphics_export_y: 792 pdf_export_line_width: 0.5 show_overview: yes overview_width: 120 overview_height: 120 overview_placement_type: upper_left color_labels_same_as_branch_length_values: no display_sequence_relations: no show_domain_labels: yes branch_length_value_digits: 3 confidence_value_digits: 3 background_gradient: no allow_editing: yes # NH/NHX/Nexus file parsing (application only): internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no extract_taxonomy_codes_in_nh_parsing: yes # phyloXML parsing # ---------------- # To ensure compatibility with all current and future # phyloXML applications and to detect malformatted and # possibly erroneous data, it is strongly recommended # to enable validation of all phyloXML files # against the XSD Schema (see: http://www.phyloxml.org/), # with: # 'validate_against_phyloxml_xsd_schema: true' validate_against_phyloxml_xsd_schema: true # Checkbox Display Selection # -------------------------- # This is used to select which checkboxes to display # and what their initial values should be. # Format: 'name: display|nodisplay yes|no' # Note: if an option is not displayed, it will not be enabled # # For the following use '?' to let Archaeopteryx decide (depending on tree): # - 'phylogram' # - 'write_confidence_values' # - 'write_events' phylogram: display ? rollover: display yes color_according_to_species: display yes color_according_to_annotation: display no show_node_names: display yes show_gene_names: display yes show_gene_symbols: display yes show_sequence_acc: display no show_taxonomy_code: display yes show_taxonomy_scientific_names: display yes show_taxonomy_common_names: display no show_taxonomy_images: display yes show_annotations: display no write_confidence_values: display ? write_events: display ? color_branches: display no width_branches: display no show_domain_architectures: display no show_binary_characters: display no show_binary_character_counts: display no display_internal_data: display yes dynamically_hide_data: display yes show_relation_confidence: display no show_properties: display no show_vector_data: display no # Combo-box Display Selection # --------------------------- # Format: 'name: display/nodisplay' click_to: display_node_data display click_to: collapse_uncollapse display click_to: reroot display click_to: subtree display click_to: swap display click_to: sort_descendants display click_to: color_subtree display click_to: open_seq_web display click_to: open_tax_web display click_to: blast display click_to: cut_subtree display click_to: copy_subtree display click_to: paste_subtree display click_to: delete display click_to: add_new_node display click_to: edit_node_data display # Default click-to option (any of the above if set to "display") default_click_to: display_node_data # Default Tree Display Colors # --------------------------- display_color: background 0x000000 display_color: background_gradient_bottom 0x0000FF display_color: sequence 0xDCDCDC display_color: taxonomy 0xB4B4B4 display_color: confidence 0x38B0DE display_color: branch_length 0x8C8C8C display_color: branch 0xFFFFFF display_color: node_box 0xFFFFFF display_color: collapsed 0xFFFF00 display_color: matching_nodes 0x00FF00 display_color: duplication 0xFF0000 display_color: speciation 0x00FF00 display_color: duplication_or_specation 0xFFFF00 display_color: domains 0x7B68EE display_color: binary_domain_combinations 0x4169FF display_color: annotation 0xADFF2F display_color: overview 0x828282 # GUI (graphical user interface) Colors # ------------------------------------- # # These are ignored if native (system) "look and feel" # is being used ('native_ui: yes'). gui_background_color: 0x202020 gui_checkbox_text_color: 0xDCDCDC gui_checkbox_and_button_active_color: 0xFF0000 gui_button_text_color: 0xFFFFFF gui_button_background_color: 0x404040 gui_menu_background_color: 0x000000 gui_menu_text_color: 0xFFFFFF gui_button_border_color: 0x000000 # Domain Structure Display Colors # ------------------------------- domain_structure_base_color: 0x202020 domain_structure_font_color: 0x909090 # Web Links # --------- # Format: web_link: # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB" # is not used at the moment. # corresponds to the element for , # and to the of (see www.phyloxml.org). web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam web_link: http://tolweb.org/ ToL tol web_link: http://www.eol.org/pages/ EOL eol web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID # not working at the moment: web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl # Settings Specific for ArchaeopteryxE # ------------------------------------ # To hide controls and menus: 'hide_controls_and_menus: yes' # To use tabbed display : 'use_tabbed_display: yes' hide_controls_and_menus: no use_tabbed_display: yes # Settings For Phylogenetic Inference # ----------------------------------- # EXPERIMENTAL: DO NOT USE!! default_number_of_bootstrap_resamples: 100 mafft_local: /bin/mafft clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe fastme_local: /bin/fastme raxml_local: /bin/raxml # Application Specific Settings # ----------------------------- # Species colors # -------------- # Format: species_color: speciesname hexcolor species_color: BRAFL 0x00FFFF species_color: SPHGR 0x9620F0 species_color: STRPU 0x9620F0 species_color: CIOIN 0xFF1CAE species_color: CIOSA 0xFF2CAE species_color: BOVIN 0x5C3317 species_color: CANFA 0x8B2323 species_color: HUMAN 0xFF2400 species_color: PANTR 0xCC2400 species_color: MOUSE 0xFF7F00 species_color: RAT 0xFFEF00 species_color: MONDO 0xEE9A49 species_color: ORNAN 0xCD853F species_color: XENLA 0x6BAA23 species_color: XENTR 0x6BAA23 species_color: CHICK 0xFFC125 species_color: FUGRU 0x0000FF species_color: BRARE 0x0000DD species_color: DANRE 0x0000BB species_color: TETNG 0x0000AA species_color: ORYLA 0x000088 species_color: GASAC 0x000066 species_color: CAEEL 0xA0A0A0 species_color: CAEBR 0xB0B0B0 species_color: DROME 0x706F00 species_color: DROPS 0x504F00 species_color: APIME 0x7A7700 species_color: AEDAE 0x8C5900 species_color: TRICA 0x918E00 species_color: NEMVE 0xAABADD species_color: HYDAT 0x7C9BCF species_color: LUBBA 0xF7B5CB species_color: GEOCY 0xF5A0BD species_color: SUBDO 0xC790B9 species_color: MONBE 0xFC0FC0 species_color: DICPU 0x23238E species_color: DICDI 0x4D4DFF species_color: ENTHI 0x5959AB species_color: ARATH 0x00FF00 species_color: POPTR 0x006400 species_color: VITVI 0x00CD00 species_color: GLYMA 0x00FF7F species_color: ORYSA 0x008B00 species_color: ORYSJ 0x008C00 species_color: SORBI 0x00EE76 species_color: SELMO 0x238E23 species_color: PHYPA 0x09F911 species_color: OSTLU 0x7FFF00 species_color: OSTTA 0x7FFF00 species_color: OSTRC 0x7FFF00 species_color: MICPU 0x66CD00 species_color: MIC99 0x66CD00 species_color: CHLRE 0xB3EE3A species_color: VOLCA 0xC0FF3E species_color: CHLSP 0x6B8E23 species_color: CYAME 0xD02090 species_color: YEAST 0xAAAAAA species_color: BACFR 0xFF0000 species_color: BACTN 0xFFFF00 species_color: MYXXD 0x0000FF species_color: STIAU 0x00FFFF species_color: BACOV 0x8C5900 species_color: BACUN 0x66CD00 species_color: PORGI 0x918E00 # rank: Class species_color: Mammalia 0xFF0000 species_color: mammals 0xFF0000 # rank: Phylum species_color: Chordata 0x8470FF species_color: Echinodermata 0x6495ED species_color: Hemichordata 0x7EC0EE species_color: Arthropoda 0x7AC5CD species_color: Nematoda 0x7171C6 species_color: Tardigrada 0x388E8E species_color: Annelida 0xC67171 species_color: Mollusca 0x00F5FF species_color: Ctenophora 0xBBFFFF species_color: Cnidaria 0xFF83FA species_color: Placozoa 0xEED2EE species_color: Porifera 0xFF3E96 species_color: Microsporidia 0x8B8378 species_color: Ascomycota 0xFF6347 species_color: Basidiomycota 0xFFD700 species_color: Chlorophyta 0x00C78C species_color: Streptophyta 0x00C957 # rank: Kingdom species_color: Viridiplantae 0x00FF00 species_color: plants 0x00FF00 species_color: Metazoa 0x0000FF species_color: animals 0x0000FF species_color: Fungi 0xFF9912 # rank: Superkingdom species_color: Viruses 0xFFD700 species_color: Bacteria 0x00FF00 species_color: Archaea 0x0000FF species_color: Eukaryota 0xFF0000 species_color: eukaryotes 0xFF0000 # Domain colors # ------------- domain_color: Cofilin_ADF 0xFC0FC0 domain_color: TIR 0x900000 domain_color: NACHT 0x202020 domain_color: CARD 0xFF0000 domain_color: Peptidase_C14 0x00FF00 domain_color: Death 0x0000FF domain_color: DED 0x00FFFF domain_color: BIR 0xCCFF33 domain_color: PAAD_DAPIN 0x9999CC domain_color: NB-ARC 0x500050 domain_color: WD40 0x888888 domain_color: RVT_1 0x999900 domain_color: NOPS 0x505000 domain_color: RRM_1 0x004400 domain_color: fn3 0xFFCC00 domain_color: Ank 0xCC33FF domain_color: Pkinase 0x339900 domain_color: Pkinase_Tyr 0x336600 domain_color: ig 0x660066 domain_color: zf-C3HC4 0x6699FF domain_color: zf-CCHC 0x6699EE domain_color: zf-C2H2 0x6699CC domain_color: zf-B_box 0x6699DD domain_color: PDZ 0x66FFCC domain_color: SH3_2 0x996600 domain_color: MIRO 0xCCFF00 domain_color: Myb_DNA-binding 0xDDDDDD domain_color: NHL 0x336666 domain_color: PKD_channel 0x336666 domain_color: Ion_trans 0x996666 domain_color: CAP_GLY 0xCC9900 domain_color: LRR_1 0xFFFF99 domain_color: LRR_2 0xFFFF66 domain_color: LRR_3 0xFFFF33 domain_color: LRR_adjacent 0xFFFF00 domain_color: LRRCT 0xFFCC99 domain_color: LRRNT 0xFFCC66 domain_color: LRRNT_2 0xFFCC33 domain_color: Ank 0x990099 domain_color: Sushi 0x004400 domain_color: ZU5 0xFF9999 domain_color: V-set 0x3399FF domain_color: TPR_1 0xFF1493 domain_color: TPR_2 0xFF69B4 domain_color: TPR_3 0xCD6090 domain_color: TPR_4 0xFF6A6A domain_color: TPR_MLP1_2 0x33FF00 domain_color: Collagen 0xFF7F00 domain_color: MIF 0xADD8E6 # Annotation colors # ----------------- annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900 annotation_color: transcription 0xAAAA00 # END