2 # User Interface Look and Feel
3 # ----------------------------
4 # Possible values for 'native_ui'
5 # 'yes' to use native (system) "look and feel"
6 # 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
7 # '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
8 # Archaeopteryx-style "look and feel" otherwise
14 # Default Values for Options
15 # --------------------------
16 # Minimal confidence value to be displayed: 'min_confidence_value':
17 # Example: 'min_confidence_value: 50.0' (a commonly used
18 # value for bootstrap support)
20 # Font family name: 'font_family':
21 # Example: 'font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica'
22 # It is advisable to use more than one value for font_family (in
23 # decreasing order of preference). Font family names have to be
24 # comma separated (no spaces). Spaces in font names have to be
25 # replaced by underscores (e.g. 'Arial_Unicode_MS').
27 # Font size: 'font_size':
28 # Example: 'font_size: 10'
30 # Screen antialias: 'antialias_screen': values: 'yes'/'no'
32 # Show Scale: 'show_scale': values: 'yes'/'no'
34 # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
36 # Cladogram display type: 'cladogram_type'
37 # Example: 'cladogram_type: non_lined_up'
38 # The three possible values are: lined_up
41 # Default line width for PDF export: 'pdf_export_line_wdith':
42 # Example: 'pdf_export_line_width: 0.5'
44 # Show overview: 'show_overview': values: 'yes'/'no'
46 # Phylogeny graphics type: 'phylogeny_graphics_type':
47 # Example: 'phylogeny_graphics_type: euro_style'
48 # The eight possible values are: rectangular
57 # Node label direction for circular and unrooted type: 'node_label_direction':
58 # Example: 'node_label_direction: horizontal'
59 # The two possible values are: horizontal
62 # Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
64 # Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
66 # Default node shape size: 'default_node_size'
67 # Example: 'default_node_size: 6'
69 # Default node shape type: 'default_node_shape'
70 # Example: 'default_node_shape: '
71 # Possible values: circle
74 # Default node shape fill: 'default_node_fill'
75 # Example: 'default_node_fill: '
76 # Possible values: solid
80 # To determine what data field to return by clicking on "List Node Data": 'list_node_data_field'
81 # Possible values: node_name
85 # sequence_mol_seq_fasta
87 # taxonomy_scientific_name
95 # To determine where to return data selected by user clicking on "List Node Data": 'list_node_data_in'
96 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
97 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
98 # Possible values: window (for output to window and buffer)
99 # console (for output to console and buffer)
100 # buffer_only (for output to buffer only)
102 # To override label for menu item to return data of external nodes (default "List Node Data"): 'list_node_data_custom_label'
103 # Example: 'list_node_data_custom_label: Get_Node_Data'
105 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
107 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
109 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
111 # Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
113 # Number of fraction digits for branch length values: 'branch_length_value_digits'
115 # Number of fraction digits for confidence values: 'confidence_value_digits'
117 # To turn on/off background color gradient: background_gradient
118 # Example: 'background_gradient: yes'
120 # To allow/not allow editing (cut, copy, and paste): allow_editing
121 # Example: 'allow_editing: yes'
123 # To allow/not allow thicker strokes for very small trees: allow_thick_strokes
124 # Example: 'allow_thick_strokes: yes'
126 # NH/NHX/Nexus file parsing
127 # -------------------------
128 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
129 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
131 # To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
132 # from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
133 # possible values are:
135 # 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
136 # 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
137 # 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
139 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
140 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
144 # To ensure compatibility with all current and future
145 # phyloXML applications and to detect malformatted and
146 # possibly erroneous data, it is strongly recommended
147 # to enable validation of all phyloXML files
148 # against the XSD Schema (see: http://www.phyloxml.org/),
150 # 'validate_against_phyloxml_xsd_schema: true'
153 min_confidence_value: 0.0
154 font_family: Arial_Unicode_MS,Dialog,SansSerif,Sans,Arial,Helvetica
158 antialias_screen: yes
160 cladogram_type: lined_up
161 phylogeny_graphics_type: rectangular
162 node_label_direction: horizontal
163 show_default_node_shapes_internal: yes
164 show_default_node_shapes_external: yes
165 show_node_shapes_for_nodes_with_vis_data: yes
167 default_node_shape: rectangle
168 default_node_fill: solid
169 pdf_export_line_width: 0.5
173 overview_placement_type: upper_right
174 color_labels_same_as_branch_length_values: no
175 display_sequence_relations: no
176 show_domain_labels: yes
177 line_up_renderable_data: yes
178 right_align_domain_architectures: no
179 show_seq_annotation_ref_sources: yes
180 branch_length_value_digits: 3
181 confidence_value_digits: 2
182 background_gradient: no
184 allow_thick_strokes: no
185 list_node_data_in: window
186 list_node_data_field: user_selected
187 list_node_data_custom_label:
188 # NH/NHX/Nexus file parsing:
189 internal_labels_are_confidence_values: no
190 replace_underscores_in_nh_parsing: no
191 taxonomy_extraction_in_nh_parsing: no
193 validate_against_phyloxml_xsd_schema: true
196 # Checkbox Display Selection
197 # --------------------------
198 # This is used to select which checkboxes to display
199 # and what their initial values should be.
200 # Format: 'name: display|nodisplay yes|no'
201 # Note: if an option is not displayed, it will not be enabled
203 # For the following use '?' to let Archaeopteryx decide (depending on tree):
205 # - 'write_confidence_values'
209 rollover: display yes
210 color_according_to_sequence: display no
211 color_according_to_species: display no
212 color_according_to_annotation: display no
213 show_node_names: display yes
214 show_seq_names: display yes
215 show_seq_symbols: display yes
216 show_seq_acc: display no
217 show_gene_names: display yes
218 show_taxonomy_code: display yes
219 show_taxonomy_scientific_names: display yes
220 show_taxonomy_rank: display no
221 show_taxonomy_common_names: display no
222 show_taxonomy_images: display no
223 show_annotations: display no
224 write_confidence_values: display ?
225 write_branch_length_values: display yes
226 write_events: display ?
227 use_visual_styles: display yes
228 width_branches: display no
229 show_domain_architectures: display no
231 show_binary_characters: display no
232 show_binary_character_counts: display no
233 display_internal_data: display yes
234 dynamically_hide_data: display yes
235 show_relation_confidence: display no
236 show_properties: display no
237 show_vector_data: display no
241 # Combo-box Display Selection
242 # ---------------------------
243 # Format: 'name: display/nodisplay'
244 click_to: display_node_data display
245 click_to: collapse_uncollapse display
246 click_to: uncollapse_all display
247 click_to: reroot display
248 click_to: subtree display
249 click_to: swap display
250 click_to: order_subtree display
251 click_to: sort_descendants display
252 click_to: color_subtree display
253 click_to: change_node_font display
254 click_to: color_node_font display
255 click_to: open_seq_web display
256 click_to: open_pdb_web display
257 click_to: open_tax_web display
258 click_to: blast display
259 click_to: cut_subtree display
260 click_to: copy_subtree display
261 click_to: paste_subtree display
262 click_to: delete display
263 click_to: add_new_node display
264 click_to: edit_node_data display
265 click_to: select_nodes display
266 click_to: get_ext_descendents_data display
268 # Default click-to option (any of the above if set to "display")
269 default_click_to: select_nodes
273 # Default Tree Display Colors
274 # ---------------------------
276 display_color: background 0xFFFFFF
277 display_color: background_gradient_bottom 0xFFFFFF
278 display_color: sequence 0x111111
279 display_color: taxonomy 0x8D8D8D
280 display_color: confidence 0xAEAEAE
281 display_color: branch_length 0x3A3A3A
282 display_color: branch 0x000000
283 display_color: node_box 0x000000
284 display_color: collapsed 0x000000
285 display_color: matching_a 0xCC6600
286 display_color: matching_b 0xCC70CC
287 display_color: matching_a_and_b 0x0000CC
288 display_color: duplication 0xFF00FF
289 display_color: speciation 0xFFFF00
290 display_color: duplication_or_specation 0xFFAA20
291 display_color: domain_label 0x939393
292 display_color: domain_base 0x505050
293 display_color: binary_domain_combinations 0x4169FF
294 display_color: annotation 0xFFCC00
295 display_color: overview 0x828282
299 # GUI (graphical user interface) Colors
300 # -------------------------------------
302 # These are ignored if native (system) "look and feel"
303 # is being used ('native_ui: yes').
305 gui_background_color: 0x202020
306 gui_checkbox_text_color: 0xDCDCDC
307 gui_checkbox_and_button_active_color: 0xFF0000
308 gui_button_text_color: 0xFFFFFF
309 gui_button_background_color: 0x404040
310 gui_menu_background_color: 0x000000
311 gui_menu_text_color: 0xFFFFFF
312 gui_button_border_color: 0x000000
315 # Vector Data Display Colors and Sizes
316 # ------------------------------------
317 vector_data_min_color: 0x0000FF
318 vector_data_max_color: 0xFFFF00
319 vector_data_mean_color: 0x000000
320 vector_data_width: 120
321 vector_data_height: 12
324 # Settings Specific for Archaeopteryx Applets (E and A)
325 # -----------------------------------------------------
326 # To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
332 # Settings Specific for ArchaeopteryxE Applets
333 # --------------------------------------------
334 # To hide controls and menus: 'hide_controls_and_menus: yes'
335 # To use tabbed display : 'use_tabbed_display: yes'
337 hide_controls_and_menus: no
338 use_tabbed_display: yes
342 # Settings For Phylogenetic Inference
343 # -----------------------------------
344 # EXPERIMENTAL: DO NOT USE!!
346 default_number_of_bootstrap_resamples: 100
347 mafft_local: /bin/mafft
348 fastme_local: /bin/fastme
349 raxml_local: /bin/raxml
355 # Format: species_color: sequencename hexcolor
356 sequence_color: Tubulin-alpha 0xEE0000
357 sequence_color: Tubulin-beta 0x00EE00
362 # Format: species_color: speciesname hexcolor
363 species_color: BRAFL 0x00FFFF
364 species_color: SPHGR 0x9620F0
365 species_color: STRPU 0x9620F0
366 species_color: CIOIN 0xFF1CAE
367 species_color: CIOSA 0xFF2CAE
368 species_color: BOVIN 0x5C3317
369 species_color: CANFA 0x8B2323
370 species_color: HUMAN 0xFF2400
371 species_color: PANTR 0xCC2400
372 species_color: MOUSE 0xFF7F00
373 species_color: RAT 0xFFEF00
374 species_color: MONDO 0xEE9A49
375 species_color: ORNAN 0xCD853F
376 species_color: XENLA 0x6BAA23
377 species_color: XENTR 0x6BAA23
378 species_color: CHICK 0xFFC125
379 species_color: FUGRU 0x0000FF
380 species_color: BRARE 0x0000DD
381 species_color: DANRE 0x0000BB
382 species_color: TETNG 0x0000AA
383 species_color: ORYLA 0x000088
384 species_color: GASAC 0x000066
385 species_color: CAEEL 0x666699
386 species_color: CAEBR 0xB0B0B0
387 species_color: DROME 0x663366
388 species_color: DROPS 0x996699
389 species_color: APIME 0x7A7700
390 species_color: AEDAE 0x8C5900
391 species_color: TRICA 0x918E00
392 species_color: NEMVE 0x0066CC
393 species_color: HYDAT 0x3399FF
394 species_color: HYDVU 0x3399FF
395 species_color: LUBBA 0xF7B5CB
396 species_color: GEOCY 0xF5A0BD
397 species_color: AMPQE 0x009966
398 species_color: SUBDO 0xC790B9
399 species_color: MONBE 0xFC0FC0
400 species_color: DICPU 0xFFCC33
401 species_color: DICDI 0xFFCC00
402 species_color: ENTHI 0x5959AB
403 species_color: ARATH 0x00FF00
404 species_color: POPTR 0x006400
405 species_color: VITVI 0x00CD00
406 species_color: GLYMA 0x00FF7F
407 species_color: ORYSA 0x008B00
408 species_color: ORYSJ 0x008C00
409 species_color: SORBI 0x00EE76
410 species_color: SELMO 0x238E23
411 species_color: PHYPA 0x09F911
412 species_color: OSTLU 0x7FFF00
413 species_color: OSTTA 0x7FFF00
414 species_color: OSTRC 0x7FFF00
415 species_color: MICPU 0x66CD00
416 species_color: MIC99 0x66CD00
417 species_color: CHLRE 0xB3EE3A
418 species_color: VOLCA 0xC0FF3E
419 species_color: CHLSP 0x6B8E23
420 species_color: CYAME 0xD02090
421 species_color: YEAST 0xAAAAAA
422 species_color: BACFR 0xFF0000
423 species_color: BACTN 0xFFFF00
424 species_color: MYXXD 0x0000FF
425 species_color: STIAU 0x00FFFF
426 species_color: BACOV 0x8C5900
427 species_color: BACUN 0x66CD00
428 species_color: PORGI 0x918E00
430 species_color: Mammalia 0xFF0000
431 species_color: mammals 0xFF0000
433 species_color: Chordata 0x8470FF
434 species_color: Echinodermata 0x6495ED
435 species_color: Hemichordata 0x7EC0EE
436 species_color: Arthropoda 0x7AC5CD
437 species_color: Nematoda 0x7171C6
438 species_color: Tardigrada 0x388E8E
439 species_color: Annelida 0xC67171
440 species_color: Mollusca 0x00F5FF
441 species_color: Ctenophora 0xBBFFFF
442 species_color: Cnidaria 0xFF83FA
443 species_color: Placozoa 0xEED2EE
444 species_color: Porifera 0xFF3E96
445 species_color: Microsporidia 0x8B8378
446 species_color: Ascomycota 0xFF6347
447 species_color: Basidiomycota 0xFFD700
448 species_color: Chlorophyta 0x00C78C
449 species_color: Streptophyta 0x00C957
451 species_color: Viridiplantae 0x00FF00
452 species_color: plants 0x00FF00
453 species_color: Metazoa 0x0000FF
454 species_color: animals 0x0000FF
455 species_color: Fungi 0xFF9912
457 species_color: Viruses 0xFFD700
458 species_color: Bacteria 0x00FF00
459 species_color: Archaea 0x0000FF
460 species_color: Eukaryota 0xFF0000
461 species_color: eukaryotes 0xFF0000
467 domain_color: Cofilin_ADF 0xFC0FC0
468 domain_color: TIR 0x900000
469 domain_color: NACHT 0x202020
470 domain_color: CARD 0xFF0000
471 domain_color: Peptidase_C14 0x00FF00
472 domain_color: Death 0x0000FF
473 domain_color: DED 0x00FFFF
474 domain_color: BIR 0xCCFF33
475 domain_color: PAAD_DAPIN 0x9999CC
476 domain_color: NB-ARC 0x500050
477 domain_color: WD40 0x888888
478 domain_color: RVT_1 0x999900
479 domain_color: CBM_48 0xFF0000
480 domain_color: Alpha-amylase 0x0000FF
481 domain_color: Alpha-amylase_C 0x0080FF
482 domain_color: CBM_48 0xFF0000
483 domain_color: Alpha-amylase 0x0000FF
484 domain_color: Alpha-amylase_C 0x0080FF
485 domain_color: GDE_N 0x009000
486 domain_color: GDE_C 0x00FF00
487 domain_color: hGDE_N 0x990099
488 domain_color: GDE_N_bis 0x007000
489 domain_color: hGDE_central 0xFF8000
490 domain_color: hGDE_amylase 0x0000EE
491 domain_color: hDGE_amylase 0x0000EE
497 annotation_color: dehydrogenase 0x0000FF
498 annotation_color: kinase 0xFF00FF
499 annotation_color: protease 0x009900
500 annotation_color: transcription 0xAAAA00