# 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_Unicode_MS,Dialog,SansSerif,Sans,Arial,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. 'Arial_Unicode_MS'). # # 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' # # Cladogram display type: 'cladogram_type' # Example: 'cladogram_type: non_lined_up' # The three possible values are: lined_up # non_lined_up # # 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 for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no' # # Show default node shape for external nodes: 'show_default_node_shapes_external': 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 # # To determine what data field to return by clicking on "List Node Data": 'list_node_data_field' # Possible values: node_name # sequence_name # gene_name # sequence_acc # sequence_mol_seq_fasta # sequence_symbol # taxonomy_scientific_name # taxonomy_code # domains # domains_collapsed # seq_annotations # go_term_ids # user_selected # # To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in' # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE # Possible values: window (for output to window and buffer) # console (for output to console and buffer) # buffer_only (for output to buffer only) # # To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label' # Example: 'list_node_data_custom_label: Get_Node_Data' # # 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' # # Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': 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 allow/not allow thicker strokes for very small trees: allow_thick_strokes # Example: 'allow_thick_strokes: yes' # # NH/NHX/Nexus file parsing # ------------------------- # To replace underscores with spaces during NH/NHX/Nexus file parsing: # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no' # # To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names) # from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing' # possible values are: # 'no' # 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453) # 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090) # 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis) # # Internal node labels are confidence values during NH/NHX/Nexus file parsing: # 'internal_labels_are_confidence_values', possible values are 'yes', 'no' # # 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' min_confidence_value: 0.0 font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica font_size: 10 font_size_min: 2 font_size_max: 20 antialias_screen: yes show_scale: yes cladogram_type: non_lined_up phylogeny_graphics_type: rectangular node_label_direction: horizontal show_default_node_shapes_internal: no show_default_node_shapes_external: no show_node_shapes_for_nodes_with_vis_data: yes default_node_size: 4 default_node_shape: rectangle default_node_fill: solid 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 line_up_renderable_data: yes right_align_domain_architectures: no show_seq_annotation_ref_sources: yes branch_length_value_digits: 3 confidence_value_digits: 2 background_gradient: no allow_editing: yes allow_thick_strokes: no list_node_data_in: window list_node_data_field: user_selected list_node_data_custom_label: # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no taxonomy_extraction_in_nh_parsing: no # phyloXML parsing: 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_sequence: display no color_according_to_species: display no color_according_to_annotation: display no show_node_names: display yes show_seq_names: display yes show_seq_symbols: display yes show_seq_acc: display no show_gene_names: display yes show_taxonomy_code: display yes show_taxonomy_scientific_names: display yes show_taxonomy_rank: display no show_taxonomy_common_names: display no show_taxonomy_images: display no show_annotations: display no write_confidence_values: display ? write_branch_length_values: display no write_events: display ? use_visual_styles: display no width_branches: display no show_domain_architectures: display no show_msa: 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: uncollapse_all display click_to: reroot display click_to: subtree display click_to: swap display click_to: order_subtree display click_to: sort_descendants display click_to: color_subtree display click_to: change_node_font display click_to: color_node_font display click_to: open_seq_web display click_to: open_pdb_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 click_to: select_nodes display click_to: get_ext_descendents_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 0xE6E6E6 display_color: taxonomy 0xB4B4B4 display_color: confidence 0xB4B4B4 display_color: branch_length 0x8C8C8C display_color: branch 0xFFFFFF display_color: node_box 0xFFFFFF display_color: collapsed 0xFFFFFF display_color: matching_a 0x00FF00 display_color: matching_b 0xFF0000 display_color: matching_a_and_b 0xFFFF00 display_color: duplication 0xFF0000 display_color: speciation 0x00FF00 display_color: duplication_or_specation 0xFFFF00 display_color: domain_label 0xE6E6E6 display_color: domain_base 0x646464 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 # Vector Data Display Colors and Sizes # ------------------------------------ vector_data_min_color: 0x0000FF vector_data_max_color: 0xFFFF00 vector_data_mean_color: 0x000000 vector_data_width: 120 vector_data_height: 12 # Settings Specific for Archaeopteryx Applets (E and A) # ----------------------------------------------------- # To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes' midpoint_reroot: yes # Settings Specific for ArchaeopteryxE Applets # -------------------------------------------- # 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 fastme_local: /bin/fastme raxml_local: /bin/raxml # Sequence colors # --------------- # Format: species_color: sequencename hexcolor sequence_color: Tubulin-alpha 0xEE0000 sequence_color: Tubulin-beta 0x00EE00 # 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 0x666699 species_color: CAEBR 0xB0B0B0 species_color: DROME 0x663366 species_color: DROPS 0x996699 species_color: APIME 0x7A7700 species_color: AEDAE 0x8C5900 species_color: TRICA 0x918E00 species_color: NEMVE 0x0066CC species_color: HYDAT 0x3399FF species_color: HYDVU 0x3399FF species_color: LUBBA 0xF7B5CB species_color: GEOCY 0xF5A0BD species_color: AMPQE 0x009966 species_color: SUBDO 0xC790B9 species_color: MONBE 0xFC0FC0 species_color: DICPU 0xFFCC33 species_color: DICDI 0xFFCC00 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: CBM_48 0xFF0000 domain_color: Alpha-amylase 0x0000FF domain_color: Alpha-amylase_C 0x0080FF domain_color: CBM_48 0xFF0000 domain_color: Alpha-amylase 0x0000FF domain_color: Alpha-amylase_C 0x0080FF domain_color: GDE_N 0x009000 domain_color: GDE_C 0x00FF00 domain_color: hGDE_N 0x990099 domain_color: GDE_N_bis 0x007000 domain_color: hGDE_central 0xFF8000 domain_color: hGDE_amylase 0x0000EE domain_color: hDGE_amylase 0x0000EE # Annotation colors # ----------------- annotation_color: dehydrogenase 0x0000FF annotation_color: kinase 0xFF00FF annotation_color: protease 0x009900 annotation_color: transcription 0xAAAA00 # END