#  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
