font_size_max: 20
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
default_node_size: 4
default_node_shape: rectangle
default_node_fill: solid
-taxonomy_colorize_node_shapes: no
#graphics_export_x: 595
#graphics_export_y: 792
pdf_export_line_width: 0.5
color_labels_same_as_branch_length_values: no
display_sequence_relations: no
show_domain_labels: yes
+line_up_renderable_data: no
+right_align_domain_architectures: no
show_seq_annotation_ref_sources: yes
branch_length_value_digits: 3
-confidence_value_digits: 3
+confidence_value_digits: 2
background_gradient: no
allow_editing: yes
ext_descendents_data_to_return_on: window
phylogram: display ?
rollover: display yes
-color_according_to_species: 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_taxonomy_code: display yes
show_taxonomy_scientific_names: display yes
show_taxonomy_common_names: display no
-show_taxonomy_images: display yes
+show_taxonomy_images: display no
show_annotations: display no
write_confidence_values: display ?
+write_branch_length_values: display no
write_events: display ?
-color_branches: display no
+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
click_to: swap 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
display_color: background 0x000000
display_color: background_gradient_bottom 0x0000FF
-display_color: sequence 0xDCDCDC
+display_color: sequence 0xE6E6E6
display_color: taxonomy 0xB4B4B4
-display_color: confidence 0x38B0DE
+display_color: confidence 0xB4B4B4
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: 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: domains 0x7B68EE
+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_button_border_color: 0x000000
-
-# Domain Structure Display Colors
-# -------------------------------
-domain_structure_base_color: 0x202020
-domain_structure_font_color: 0x909090
-
+# 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)
+# 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: 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: 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