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@ -0,0 +1,502 @@
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# User Interface Look and Feel
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# ----------------------------
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# Possible values for 'native_ui'
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# 'yes' to use native (system) "look and feel"
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# 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
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# '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
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# Archaeopteryx-style "look and feel" otherwise
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native_ui: ?
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# Default Values for Options
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# --------------------------
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# Minimal confidence value to be displayed: 'min_confidence_value':
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# Example: 'min_confidence_value: 50.0' (a commonly used
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# value for bootstrap support)
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#
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# Font family name: 'font_family':
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# Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
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# It is advisable to use more than one value for font_family (in
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# decreasing order of preference). Font family names have to be
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# comma separated (no spaces). Spaces in font names have to be
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# replaced by underscores (e.g. 'Arial_Unicode_MS').
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#
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# Font size: 'font_size':
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# Example: 'font_size: 10'
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#
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# Screen antialias: 'antialias_screen': values: 'yes'/'no'
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#
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# Show Scale: 'show_scale': values: 'yes'/'no'
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#
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# Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
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#
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# Cladogram display type: 'cladogram_type'
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# Example: 'cladogram_type: non_lined_up'
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# The three possible values are: lined_up
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# non_lined_up
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#
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# Default line width for PDF export: 'pdf_export_line_wdith':
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# Example: 'pdf_export_line_width: 0.5'
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#
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# Show overview: 'show_overview': values: 'yes'/'no'
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#
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# Phylogeny graphics type: 'phylogeny_graphics_type':
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# Example: 'phylogeny_graphics_type: euro_style'
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# The eight possible values are: rectangular
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# euro_style
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# rounded
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# curved
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# triangular
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# convex
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# unrooted
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# circular
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#
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# Node label direction for circular and unrooted type: 'node_label_direction':
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# Example: 'node_label_direction: horizontal'
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# The two possible values are: horizontal
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# radial
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#
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# Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
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#
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# Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
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#
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# Default node shape size: 'default_node_size'
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# Example: 'default_node_size: 6'
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#
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# Default node shape type: 'default_node_shape'
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# Example: 'default_node_shape: '
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# Possible values: circle
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# rectangle
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#
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# Default node shape fill: 'default_node_fill'
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# Example: 'default_node_fill: '
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# Possible values: solid
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# gradient
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# none
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#
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# To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
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# Possible values: node_name
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# sequence_name
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# gene_name
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# sequence_acc
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# sequence_mol_seq_fasta
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# sequence_symbol
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# taxonomy_scientific_name
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# taxonomy_code
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# domains
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# domains_collapsed
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# seq_annotations
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# go_term_ids
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# user_selected
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#
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# To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
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# Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
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# classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
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# Possible values: window (for output to window and buffer)
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# console (for output to console and buffer)
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# buffer_only (for output to buffer only)
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#
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# To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
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# Example: 'list_node_data_custom_label: Get_Node_Data'
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#
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# Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
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#
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# Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
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#
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# Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
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#
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# Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
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#
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# Number of fraction digits for branch length values: 'branch_length_value_digits'
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#
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# Number of fraction digits for confidence values: 'confidence_value_digits'
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#
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# To turn on/off background color gradient: background_gradient
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# Example: 'background_gradient: yes'
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#
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# To allow/not allow editing (cut, copy, and paste): allow_editing
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# Example: 'allow_editing: yes'
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#
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# To allow/not allow thicker strokes for very small trees: allow_thick_strokes
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# Example: 'allow_thick_strokes: yes'
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#
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# NH/NHX/Nexus file parsing
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# -------------------------
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# To replace underscores with spaces during NH/NHX/Nexus file parsing:
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# 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
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#
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# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
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# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
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# possible values are:
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# 'no'
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# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
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# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
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# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
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#
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# Internal node labels are confidence values during NH/NHX/Nexus file parsing:
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# 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
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#
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# phyloXML parsing
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# ----------------
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# To ensure compatibility with all current and future
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# phyloXML applications and to detect malformatted and
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# possibly erroneous data, it is strongly recommended
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# to enable validation of all phyloXML files
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# against the XSD Schema (see: http://www.phyloxml.org/),
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# with:
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# 'validate_against_phyloxml_xsd_schema: true'
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min_confidence_value: 0.0
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font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
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font_size: 10
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font_size_min: 2
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font_size_max: 20
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antialias_screen: yes
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show_scale: yes
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cladogram_type: non_lined_up
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phylogeny_graphics_type: rectangular
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node_label_direction: horizontal
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show_default_node_shapes_internal: no
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show_default_node_shapes_external: no
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show_node_shapes_for_nodes_with_vis_data: yes
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default_node_size: 4
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default_node_shape: rectangle
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default_node_fill: solid
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pdf_export_line_width: 0.5
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show_overview: yes
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overview_width: 120
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overview_height: 120
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overview_placement_type: upper_left
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color_labels_same_as_branch_length_values: no
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display_sequence_relations: no
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show_domain_labels: yes
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line_up_renderable_data: yes
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right_align_domain_architectures: no
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show_seq_annotation_ref_sources: yes
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branch_length_value_digits: 3
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confidence_value_digits: 2
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background_gradient: no
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allow_editing: yes
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allow_thick_strokes: no
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list_node_data_in: window
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list_node_data_field: user_selected
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list_node_data_custom_label:
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# NH/NHX/Nexus file parsing:
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internal_labels_are_confidence_values: no
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replace_underscores_in_nh_parsing: no
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taxonomy_extraction_in_nh_parsing: no
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# phyloXML parsing:
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validate_against_phyloxml_xsd_schema: true
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# Checkbox Display Selection
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# --------------------------
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# This is used to select which checkboxes to display
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# and what their initial values should be.
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# Format: 'name: display|nodisplay yes|no'
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# Note: if an option is not displayed, it will not be enabled
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#
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# For the following use '?' to let Archaeopteryx decide (depending on tree):
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# - 'phylogram'
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# - 'write_confidence_values'
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# - 'write_events'
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phylogram: display ?
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rollover: display yes
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color_according_to_sequence: display no
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color_according_to_species: display no
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color_according_to_annotation: display no
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show_node_names: display yes
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show_seq_names: display yes
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show_seq_symbols: display yes
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show_seq_acc: display no
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show_gene_names: display yes
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show_taxonomy_code: display yes
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show_taxonomy_scientific_names: display yes
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show_taxonomy_rank: display no
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show_taxonomy_common_names: display no
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show_taxonomy_images: display no
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show_annotations: display no
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write_confidence_values: display ?
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write_branch_length_values: display no
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write_events: display ?
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use_visual_styles: display no
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width_branches: display no
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show_domain_architectures: display no
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show_msa: display no
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show_binary_characters: display no
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show_binary_character_counts: display no
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display_internal_data: display yes
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dynamically_hide_data: display yes
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show_relation_confidence: display no
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show_properties: display no
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show_vector_data: display no
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# Combo-box Display Selection
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# ---------------------------
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# Format: 'name: display/nodisplay'
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click_to: display_node_data display
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click_to: collapse_uncollapse display
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click_to: uncollapse_all display
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click_to: reroot display
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click_to: subtree display
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click_to: swap display
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click_to: order_subtree display
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click_to: sort_descendants display
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click_to: color_subtree display
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click_to: change_node_font display
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click_to: color_node_font display
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click_to: open_seq_web display
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click_to: open_pdb_web display
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click_to: open_tax_web display
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click_to: blast display
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click_to: cut_subtree display
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click_to: copy_subtree display
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click_to: paste_subtree display
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click_to: delete display
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click_to: add_new_node display
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click_to: edit_node_data display
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click_to: select_nodes display
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click_to: get_ext_descendents_data display
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# Default click-to option (any of the above if set to "display")
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default_click_to: display_node_data
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# Default Tree Display Colors
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# ---------------------------
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display_color: background 0x000000
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display_color: background_gradient_bottom 0x0000FF
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display_color: sequence 0xE6E6E6
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display_color: taxonomy 0xB4B4B4
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display_color: confidence 0xB4B4B4
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display_color: branch_length 0x8C8C8C
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display_color: branch 0xFFFFFF
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display_color: node_box 0xFFFFFF
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display_color: collapsed 0xFFFFFF
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display_color: matching_a 0x00FF00
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display_color: matching_b 0xFF0000
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display_color: matching_a_and_b 0xFFFF00
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display_color: duplication 0xFF0000
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display_color: speciation 0x00FF00
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display_color: duplication_or_specation 0xFFFF00
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display_color: domain_label 0xE6E6E6
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display_color: domain_base 0x646464
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display_color: binary_domain_combinations 0x4169FF
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display_color: annotation 0xADFF2F
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display_color: overview 0x828282
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# GUI (graphical user interface) Colors
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# -------------------------------------
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#
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# These are ignored if native (system) "look and feel"
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# is being used ('native_ui: yes').
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gui_background_color: 0x202020
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gui_checkbox_text_color: 0xDCDCDC
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gui_checkbox_and_button_active_color: 0xFF0000
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gui_button_text_color: 0xFFFFFF
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gui_button_background_color: 0x404040
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gui_menu_background_color: 0x000000
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|
gui_menu_text_color: 0xFFFFFF
|
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|
|
gui_button_border_color: 0x000000
|
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|
# Vector Data Display Colors and Sizes
|
|
|
|
|
# ------------------------------------
|
|
|
|
|
vector_data_min_color: 0x0000FF
|
|
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|
|
vector_data_max_color: 0xFFFF00
|
|
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|
|
vector_data_mean_color: 0x000000
|
|
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|
|
vector_data_width: 120
|
|
|
|
|
vector_data_height: 12
|
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|
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|
|
# Settings Specific for Archaeopteryx Applets (E and A)
|
|
|
|
|
# -----------------------------------------------------
|
|
|
|
|
# To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
|
|
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|
|
|
midpoint_reroot: yes
|
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|
|
|
# Settings Specific for ArchaeopteryxE Applets
|
|
|
|
|
# --------------------------------------------
|
|
|
|
|
# To hide controls and menus: 'hide_controls_and_menus: yes'
|
|
|
|
|
# To use tabbed display : 'use_tabbed_display: yes'
|
|
|
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|
|
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|
|
hide_controls_and_menus: no
|
|
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|
|
use_tabbed_display: yes
|
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|
|
# Settings For Phylogenetic Inference
|
|
|
|
|
# -----------------------------------
|
|
|
|
|
# EXPERIMENTAL: DO NOT USE!!
|
|
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|
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|
|
|
|
default_number_of_bootstrap_resamples: 100
|
|
|
|
|
mafft_local: /bin/mafft
|
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|
|
fastme_local: /bin/fastme
|
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|
|
raxml_local: /bin/raxml
|
|
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|
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|
|
|
|
# Sequence colors
|
|
|
|
|
# ---------------
|
|
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|
|
# Format: species_color: sequencename hexcolor
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|
|
sequence_color: Tubulin-alpha 0xEE0000
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|
|
sequence_color: Tubulin-beta 0x00EE00
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|
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|
|
|
|
|
|
|
|
# Species colors
|
|
|
|
|
# --------------
|
|
|
|
|
# Format: species_color: speciesname hexcolor
|
|
|
|
|
species_color: BRAFL 0x00FFFF
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|
|
|
|
species_color: SPHGR 0x9620F0
|
|
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|
|
species_color: STRPU 0x9620F0
|
|
|
|
|
species_color: CIOIN 0xFF1CAE
|
|
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|
|
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
|
Petar Petrov
