#  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: no



#  Default Values for Phylogeny Display Options
#  --------------------------------------------
#  Minimal confidence value to be displayed ('min_confidence_value'):
#    Example: 'min_confidence_value: 50.0' (a commonly used 
#    values 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'):
#    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'
#  Do/do not line up cladogram display ('non_lined_up_cladogram')
#    Example: 'non_lined_up_cladogram: yes'   
#  Default size for graphics export and printing ('graphics_export_x' and 'graphics_export_y')
#    (ATV 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'
#  Phylogeny graphics type ('phylogeny_graphics_type'):
#    Example: 'phylogeny_graphics_type: euro_style' 
#    The five possible values are: rectangular                    
#                                  euro_style
#                                  curved
#                                  triangular
#                                  convex

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
non_lined_up_cladogram:    no
phylogeny_graphics_type:   rectangular 
#graphics_export_x:        595
#graphics_export_y:        792




#  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 ATV decide (depending on tree):
#  -"phylogram"
#  -"write_confidence_values"
#  -"write_events" 

phylogram:                     display   ?
color_according_to_species:    display   yes
color_according_to_annotation: display   no
show_node_names:               display   yes
show_gene_names                display   yes
show_sequence_acc              display   yes
show_taxonomy_code:            display   yes
show_taxonomy_names:           display   yes
show_annotations               display   no
show_property                  nodisplay no
write_confidence_values:       display   ?
write_events:                  display   ?
color_branches:                display   no
width_branches:                display   no
color_orthologous:             nodisplay no
color_subtree_neighbors:       nodisplay no
color_super_orthologous:       nodisplay 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



#  Combobox 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: color_subtree        display
click_to: open_seq_web         display
click_to: open_tax_web         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: <URL> <description> <source identifier>
#  E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB   UniProtKB"
#  <description> is not used at the moment.
#  <source identifier> corresponds to the <source> element for <sequence> <accession>,
#  and to the <type> of <taxonomy> <id> (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:      yes



#  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


#  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
