# 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,Calibri,Helvetica'
+# 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. 'Times_New_Roman').
+# 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'
+#
# Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no'
+#
# Cladogram display type: 'cladogram_type'
# Example: 'cladogram_type: ext_node_sum_dep'
# The three possible values are: non_lined_up
# ext_node_sum_dep
# total_node_sum_dep (for "uniform" branch lengths)
+#
# Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y':
# (Archaeopteryx tries to guess the locale, so setting these is not always necessary)
# Example: For A4 (portrait):
# For US Letter (portrait):
# 'graphics_export_x: 612'
# 'graphics_export_y: 792'
+#
# 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
# 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 "Return ...": 'ext_descendents_data_to_return'
+# 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
# 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 "Return ...": 'ext_descendents_data_to_return_on'
+# 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 ""Return ..."): 'label_for_get_ext_descendents_data'
-# Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
+# 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) from node names during NH/NHX/Nexus file parsing:
-# 'taxonomy_extraction_in_nh_parsing',
-# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), '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
# with:
# 'validate_against_phyloxml_xsd_schema: true'
-validate_against_phyloxml_xsd_schema: true
-
-
min_confidence_value: 0.0
-font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
+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
-show_branch_length_values: no
cladogram_type: ext_node_sum_dep
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
-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: yes
+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
-ext_descendents_data_to_return: sequence_mol_seq_fasta
-#label_for_get_ext_descendents_data: Get_Node_Data
+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: yes
+taxonomy_extraction_in_nh_parsing: no
+validate_against_phyloxml_xsd_schema: true
# Checkbox Display Selection
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_seq_symbols: display yes
+show_seq_acc: display no
show_gene_names: display yes
-show_gene_symbols: display yes
-show_sequence_acc: display no
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
+# 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
-# Domain Structure Display Colors
-# -------------------------------
-domain_structure_base_color: 0x202020
-domain_structure_font_color: 0x909090
+# 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
-# ------------------------------------
+
+
+# Settings Specific for ArchaeopteryxE Applets
+# --------------------------------------------
# To hide controls and menus: 'hide_controls_and_menus: yes'
# To use tabbed display : 'use_tabbed_display: yes'
raxml_local: /bin/raxml
-# Application Specific Settings
-# -----------------------------
+
+# 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 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
+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
species_color: Chordata 0x8470FF
species_color: Echinodermata 0x6495ED
species_color: Hemichordata 0x7EC0EE
-species_color: Arthropoda 0x7AC5CD
+species_color: Arthropoda 0x7AC5CD
species_color: Nematoda 0x7171C6
species_color: Tardigrada 0x388E8E
species_color: Annelida 0xC67171
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
git://source.jalview.org / jalview.git / blobdiff