# User Interface Look and Feel # ---------------------------- # Set to "yes" to use native (system) "look and feel" (user interface style) # (if Mac OS X is detected, native look and feel is always used): native_ui: ? # Default Values for Phylogeny Display Options # -------------------------------------------- # 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'): # Example: 'antialias_screen: yes' # Show Scale ('show_scale') # Example: 'show_scale: yes' # Show branch length branch values ('show_branch_length_values') # Example: 'show_branch_length_values: no' # Default size for graphics export and printing ('graphics_export_x' and 'graphics_export_y') # Example: 'graphics_export_x: 610' # 'graphics_export_y: 790' # Show overview ('show_overview'): not implemented yet # Phylogeny display type ('phylogeny_display_type'): not implemented yet font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans font_size: 9 antialias_screen: yes show_scale: no show_branch_length_values: no show_overview: no phylogeny_graphics_type: rounded graphics_export_x: 610 graphics_export_y: 790 show_overview: yes allow_editing: yes # 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 # -"phylogram" (synonym: "use_real_br_lengths"), # -"write_support_values" (synonym "write_bootstrap_values"), and # -"write_dup_spec" # use "?" to let ATV decide (depending on tree) # phylogram: display ? color_according_to_species: display no color_according_to_annotation: nodisplay no show_node_names: nodisplay no show_gene_names nodisplay no show_sequence_acc nodisplay no show_taxonomy_code: nodisplay no show_taxonomy_names: display yes show_annotations nodisplay no show_property nodisplay no write_confidence_values: display yes write_events: nodisplay no color_branches: display no width_branches: nodisplay no show_domain_architectures: nodisplay no show_binary_characters nodisplay no show_binary_character_counts nodisplay no display_internal_data display yes dynamically_hide_data display yes # Combobox Display Selection # -------------------------- # Format: 'name: display/nodisplay' click_to: display_node_data display click_to: collapse_uncollapse display click_to: reroot nodisplay click_to: subtree display click_to: swap display click_to: color_subtree display click_to: open_seq_web nodisplay click_to: open_tax_web display click_to: open_seq_web display click_to: open_tax_web 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: 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 0x00EE00 display_color: duplication_or_specation 0xFFFF00 display_color: domains 0x7B68EE display_color: binary_domain_combinations 0x4169FF display_color: annotation 0xADFF2F # 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://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 # not working at the moment: web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl # Settings Specific for ATVe # -------------------------- # 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: no # 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 0x0000BB species_color: DANRE 0x000099 species_color: TETNG 0x000077 species_color: ORYLA 0x000066 species_color: GASAC 0x000044 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 # END