# 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'
# 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': 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
# sequence_symbol
# taxonomy_scientific_name
# taxonomy_code
+# taxonomy_common_name
# user_selected
#
# To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
# Example: 'label_for_get_ext_descendents_data: 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 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,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
font_size: 10
font_size_min: 2
font_size_max: 20
color_labels_same_as_branch_length_values: no
display_sequence_relations: no
show_domain_labels: yes
+show_seq_annotation_ref_sources: yes
branch_length_value_digits: 3
confidence_value_digits: 3
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
+ext_descendents_data_to_return: user_selected
+#label_for_get_ext_descendents_data: Return_Node_Data
# 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
raxml_local: /bin/raxml
-# 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 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: Homo_sapiens 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
# rank: Class
species_color: Mammalia 0xFF0000
species_color: mammals 0xFF0000