1 # User Interface Look and Feel
2 # ----------------------------
3 # Possible values for 'native_ui'
4 # 'yes' to use native (system) "look and feel"
5 # 'no' to use Archaeopteryx-style "look and feel", can set GUI colors via this file (see below)
6 # '?' to use native (system) "look and feel" if Mac OS X with Java 1.5 is detected,
7 # Archaeopteryx-style "look and feel" otherwise
13 # Default Values for Options
14 # --------------------------
15 # Minimal confidence value to be displayed: 'min_confidence_value':
16 # Example: 'min_confidence_value: 50.0' (a commonly used
17 # value for bootstrap support)
19 # Font family name: 'font_family':
20 # Example: 'font_family: Arial,Calibri,Helvetica'
21 # It is advisable to use more than one value for font_family (in
22 # decreasing order of preference). Font family names have to be
23 # comma separated (no spaces). Spaces in font names have to be
24 # replaced by underscores (e.g. 'Times_New_Roman').
26 # Font size: 'font_size':
27 # Example: 'font_size: 10'
29 # Screen antialias: 'antialias_screen': values: 'yes'/'no'
31 # Show Scale: 'show_scale': values: 'yes'/'no'
33 # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
35 # Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no'
37 # Cladogram display type: 'cladogram_type'
38 # Example: 'cladogram_type: ext_node_sum_dep'
39 # The three possible values are: non_lined_up
41 # total_node_sum_dep (for "uniform" branch lengths)
43 # Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y':
44 # (Archaeopteryx tries to guess the locale, so setting these is not always necessary)
45 # Example: For A4 (portrait):
46 # 'graphics_export_x: 595'
47 # 'graphics_export_y: 845'
48 # For US Letter (portrait):
49 # 'graphics_export_x: 612'
50 # 'graphics_export_y: 792'
52 # Default line width for PDF export: 'pdf_export_line_wdith':
53 # Example: 'pdf_export_line_width: 0.5'
55 # Show overview: 'show_overview': values: 'yes'/'no'
57 # Phylogeny graphics type: 'phylogeny_graphics_type':
58 # Example: 'phylogeny_graphics_type: euro_style'
59 # The eight possible values are: rectangular
68 # Node label direction for circular and unrooted type: 'node_label_direction':
69 # Example: 'node_label_direction: horizontal'
70 # The two possible values are: horizontal
73 # Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
75 # Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
77 # Default node shape size: 'default_node_size'
78 # Example: 'default_node_size: 6'
80 # Default node shape type: 'default_node_shape'
81 # Example: 'default_node_shape: '
82 # Possible values: circle
85 # Default node shape fill: 'default_node_fill'
86 # Example: 'default_node_fill: '
87 # Possible values: solid
91 # To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
92 # Possible values: node_name
97 # sequence_mol_seq_fasta
99 # taxonomy_scientific_name
101 # taxonomy_common_name
104 # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
105 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
106 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
107 # Possible values: window (for output to window and buffer)
108 # console (for output to console and buffer)
109 # buffer_only (for output to buffer only)
111 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
112 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
114 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
116 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
118 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
120 # Do/not show reference sources for sequence annotation: 'show_seq_annotation_ref_sources': values: 'yes'/'no'
122 # Number of fraction digits for branch length values: 'branch_length_value_digits'
124 # Number of fraction digits for confidence values: 'confidence_value_digits'
126 # To turn on/off background color gradient: background_gradient
127 # Example: 'background_gradient: yes'
129 # To allow/not allow editing (cut, copy, and paste): allow_editing
130 # Example: 'allow_editing: yes'
132 # NH/NHX/Nexus file parsing
133 # -------------------------
134 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
135 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
137 # To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
138 # from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
139 # possible values are:
141 # 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
142 # 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
143 # 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
145 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
146 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
150 # To ensure compatibility with all current and future
151 # phyloXML applications and to detect malformatted and
152 # possibly erroneous data, it is strongly recommended
153 # to enable validation of all phyloXML files
154 # against the XSD Schema (see: http://www.phyloxml.org/),
156 # 'validate_against_phyloxml_xsd_schema: true'
159 min_confidence_value: 0.0
160 font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
164 antialias_screen: yes
166 cladogram_type: ext_node_sum_dep
167 phylogeny_graphics_type: rectangular
168 node_label_direction: horizontal
169 show_default_node_shapes_internal: no
170 show_default_node_shapes_external: no
172 default_node_shape: rectangle
173 default_node_fill: solid
174 #graphics_export_x: 595
175 #graphics_export_y: 792
176 pdf_export_line_width: 0.5
180 overview_placement_type: upper_left
181 color_labels_same_as_branch_length_values: no
182 display_sequence_relations: no
183 show_domain_labels: yes
184 line_up_renderable_data: no
185 right_align_domain_architectures: no
186 show_seq_annotation_ref_sources: yes
187 branch_length_value_digits: 3
188 confidence_value_digits: 2
189 background_gradient: no
191 ext_descendents_data_to_return_on: window
192 ext_descendents_data_to_return: user_selected
193 #label_for_get_ext_descendents_data: Return_Node_Data
194 # NH/NHX/Nexus file parsing:
195 internal_labels_are_confidence_values: no
196 replace_underscores_in_nh_parsing: no
197 taxonomy_extraction_in_nh_parsing: no
198 validate_against_phyloxml_xsd_schema: true
201 # Checkbox Display Selection
202 # --------------------------
203 # This is used to select which checkboxes to display
204 # and what their initial values should be.
205 # Format: 'name: display|nodisplay yes|no'
206 # Note: if an option is not displayed, it will not be enabled
208 # For the following use '?' to let Archaeopteryx decide (depending on tree):
210 # - 'write_confidence_values'
214 rollover: display yes
215 color_according_to_sequence: display no
216 color_according_to_species: display no
217 color_according_to_annotation: display no
218 show_node_names: display yes
219 show_seq_names: display yes
220 show_seq_symbols: display yes
221 show_seq_acc: display no
222 show_gene_names: display yes
223 show_taxonomy_code: display yes
224 show_taxonomy_scientific_names: display yes
225 show_taxonomy_common_names: display no
226 show_taxonomy_images: display no
227 show_annotations: display no
228 write_confidence_values: display ?
229 write_branch_length_values: display no
230 write_events: display ?
231 use_visual_styles: display no
232 width_branches: display no
233 show_domain_architectures: display no
235 show_binary_characters: display no
236 show_binary_character_counts: display no
237 display_internal_data: display yes
238 dynamically_hide_data: display yes
239 show_relation_confidence: display no
240 show_properties: display no
241 show_vector_data: display no
245 # Combo-box Display Selection
246 # ---------------------------
247 # Format: 'name: display/nodisplay'
248 click_to: display_node_data display
249 click_to: collapse_uncollapse display
250 click_to: reroot display
251 click_to: subtree display
252 click_to: swap display
253 click_to: sort_descendants display
254 click_to: color_subtree display
255 click_to: change_node_font display
256 click_to: color_node_font display
257 click_to: open_seq_web display
258 click_to: open_pdb_web display
259 click_to: open_tax_web display
260 click_to: blast display
261 click_to: cut_subtree display
262 click_to: copy_subtree display
263 click_to: paste_subtree display
264 click_to: delete display
265 click_to: add_new_node display
266 click_to: edit_node_data display
267 click_to: select_nodes display
268 click_to: get_ext_descendents_data display
270 # Default click-to option (any of the above if set to "display")
271 default_click_to: display_node_data
275 # Default Tree Display Colors
276 # ---------------------------
278 display_color: background 0x000000
279 display_color: background_gradient_bottom 0x0000FF
280 display_color: sequence 0xE6E6E6
281 display_color: taxonomy 0xB4B4B4
282 display_color: confidence 0xB4B4B4
283 display_color: branch_length 0x8C8C8C
284 display_color: branch 0xFFFFFF
285 display_color: node_box 0xFFFFFF
286 display_color: collapsed 0xFFFFFF
287 display_color: matching_a 0x00FF00
288 display_color: matching_b 0xFF0000
289 display_color: matching_a_and_b 0xFFFF00
290 display_color: duplication 0xFF0000
291 display_color: speciation 0x00FF00
292 display_color: duplication_or_specation 0xFFFF00
293 display_color: domain_label 0xE6E6E6
294 display_color: domain_base 0x646464
295 display_color: binary_domain_combinations 0x4169FF
296 display_color: annotation 0xADFF2F
297 display_color: overview 0x828282
301 # GUI (graphical user interface) Colors
302 # -------------------------------------
304 # These are ignored if native (system) "look and feel"
305 # is being used ('native_ui: yes').
307 gui_background_color: 0x202020
308 gui_checkbox_text_color: 0xDCDCDC
309 gui_checkbox_and_button_active_color: 0xFF0000
310 gui_button_text_color: 0xFFFFFF
311 gui_button_background_color: 0x404040
312 gui_menu_background_color: 0x000000
313 gui_menu_text_color: 0xFFFFFF
314 gui_button_border_color: 0x000000
317 # Vector Data Display Colors and Sizes
318 # ------------------------------------
319 vector_data_min_color: 0x0000FF
320 vector_data_max_color: 0xFFFF00
321 vector_data_mean_color: 0x000000
322 vector_data_width: 120
323 vector_data_height: 12
326 # Settings Specific for Archaeopteryx Applets (E and A)
327 # -----------------------------------------------------
328 # To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
334 # Settings Specific for ArchaeopteryxE Applets
335 # --------------------------------------------
336 # To hide controls and menus: 'hide_controls_and_menus: yes'
337 # To use tabbed display : 'use_tabbed_display: yes'
339 hide_controls_and_menus: no
340 use_tabbed_display: yes
344 # Settings For Phylogenetic Inference
345 # -----------------------------------
346 # EXPERIMENTAL: DO NOT USE!!
348 default_number_of_bootstrap_resamples: 100
349 mafft_local: /bin/mafft
350 fastme_local: /bin/fastme
351 raxml_local: /bin/raxml
357 # Format: species_color: sequencename hexcolor
358 sequence_color: Tubulin-alpha 0xEE0000
359 sequence_color: Tubulin-beta 0x00EE00
364 # Format: species_color: speciesname hexcolor
365 species_color: BRAFL 0x00FFFF
366 species_color: SPHGR 0x9620F0
367 species_color: STRPU 0x9620F0
368 species_color: CIOIN 0xFF1CAE
369 species_color: CIOSA 0xFF2CAE
370 species_color: BOVIN 0x5C3317
371 species_color: CANFA 0x8B2323
372 species_color: HUMAN 0xFF2400
373 species_color: Homo_sapiens 0xFF2400
374 species_color: PANTR 0xCC2400
375 species_color: MOUSE 0xFF7F00
376 species_color: RAT 0xFFEF00
377 species_color: MONDO 0xEE9A49
378 species_color: ORNAN 0xCD853F
379 species_color: XENLA 0x6BAA23
380 species_color: XENTR 0x6BAA23
381 species_color: CHICK 0xFFC125
382 species_color: FUGRU 0x0000FF
383 species_color: BRARE 0x0000DD
384 species_color: DANRE 0x0000BB
385 species_color: TETNG 0x0000AA
386 species_color: ORYLA 0x000088
387 species_color: GASAC 0x000066
388 species_color: CAEEL 0x666666
389 species_color: CAEBR 0xB0B0B0
390 species_color: DROME 0x706F00
391 species_color: DROPS 0x504F00
392 species_color: APIME 0x7A7700
393 species_color: AEDAE 0x8C5900
394 species_color: TRICA 0x918E00
395 species_color: NEMVE 0x0066CC
396 species_color: HYDAT 0x3399FF
397 species_color: HYDVU 0x3399FF
398 species_color: LUBBA 0xF7B5CB
399 species_color: GEOCY 0xF5A0BD
400 species_color: AMPQE 0x0099FF
401 species_color: SUBDO 0xC790B9
402 species_color: MONBE 0xFC0FC0
403 species_color: DICPU 0xFFCC33
404 species_color: DICDI 0xFFCC00
405 species_color: ENTHI 0x5959AB
406 species_color: ARATH 0x00FF00
407 species_color: POPTR 0x006400
408 species_color: VITVI 0x00CD00
409 species_color: GLYMA 0x00FF7F
410 species_color: ORYSA 0x008B00
411 species_color: ORYSJ 0x008C00
412 species_color: SORBI 0x00EE76
413 species_color: SELMO 0x238E23
414 species_color: PHYPA 0x09F911
415 species_color: OSTLU 0x7FFF00
416 species_color: OSTTA 0x7FFF00
417 species_color: OSTRC 0x7FFF00
418 species_color: MICPU 0x66CD00
419 species_color: MIC99 0x66CD00
420 species_color: CHLRE 0xB3EE3A
421 species_color: VOLCA 0xC0FF3E
422 species_color: CHLSP 0x6B8E23
423 species_color: CYAME 0xD02090
424 species_color: YEAST 0xAAAAAA
425 species_color: BACFR 0xFF0000
426 species_color: BACTN 0xFFFF00
427 species_color: MYXXD 0x0000FF
428 species_color: STIAU 0x00FFFF
429 species_color: BACOV 0x8C5900
430 species_color: BACUN 0x66CD00
431 species_color: PORGI 0x918E00
433 species_color: Mammalia 0xFF0000
434 species_color: mammals 0xFF0000
436 species_color: Chordata 0x8470FF
437 species_color: Echinodermata 0x6495ED
438 species_color: Hemichordata 0x7EC0EE
439 species_color: Arthropoda 0x7AC5CD
440 species_color: Nematoda 0x7171C6
441 species_color: Tardigrada 0x388E8E
442 species_color: Annelida 0xC67171
443 species_color: Mollusca 0x00F5FF
444 species_color: Ctenophora 0xBBFFFF
445 species_color: Cnidaria 0xFF83FA
446 species_color: Placozoa 0xEED2EE
447 species_color: Porifera 0xFF3E96
448 species_color: Microsporidia 0x8B8378
449 species_color: Ascomycota 0xFF6347
450 species_color: Basidiomycota 0xFFD700
451 species_color: Chlorophyta 0x00C78C
452 species_color: Streptophyta 0x00C957
454 species_color: Viridiplantae 0x00FF00
455 species_color: plants 0x00FF00
456 species_color: Metazoa 0x0000FF
457 species_color: animals 0x0000FF
458 species_color: Fungi 0xFF9912
460 species_color: Viruses 0xFFD700
461 species_color: Bacteria 0x00FF00
462 species_color: Archaea 0x0000FF
463 species_color: Eukaryota 0xFF0000
464 species_color: eukaryotes 0xFF0000
470 domain_color: Cofilin_ADF 0xFC0FC0
471 domain_color: TIR 0x900000
472 domain_color: NACHT 0x202020
473 domain_color: CARD 0xFF0000
474 domain_color: Peptidase_C14 0x00FF00
475 domain_color: Death 0x0000FF
476 domain_color: DED 0x00FFFF
477 domain_color: BIR 0xCCFF33
478 domain_color: PAAD_DAPIN 0x9999CC
479 domain_color: NB-ARC 0x500050
480 domain_color: WD40 0x888888
481 domain_color: RVT_1 0x999900
482 domain_color: CBM_48 0xFF0000
483 domain_color: Alpha-amylase 0x0000FF
484 domain_color: Alpha-amylase_C 0x0080FF
485 domain_color: CBM_48 0xFF0000
486 domain_color: Alpha-amylase 0x0000FF
487 domain_color: Alpha-amylase_C 0x0080FF
488 domain_color: GDE_N 0x009000
489 domain_color: GDE_C 0x00FF00
490 domain_color: hGDE_N 0x990099
491 domain_color: GDE_N_bis 0x007000
492 domain_color: hGDE_central 0xFF8000
493 domain_color: hGDE_amylase 0x0000EE
494 domain_color: hDGE_amylase 0x0000EE
500 annotation_color: dehydrogenase 0x0000FF
501 annotation_color: kinase 0xFF00FF
502 annotation_color: protease 0x009900
503 annotation_color: transcription 0xAAAA00