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)
18 # Font family name: 'font_family':
19 # Example: 'font_family: Arial,Calibri,Helvetica'
20 # It is advisable to use more than one value for font_family (in
21 # decreasing order of preference). Font family names have to be
22 # comma separated (no spaces). Spaces in font names have to be
23 # replaced by underscores (e.g. 'Times_New_Roman').
24 # Font size: 'font_size':
25 # Example: 'font_size: 10'
26 # Screen antialias: 'antialias_screen': values: 'yes'/'no'
27 # Show Scale: 'show_scale': values: 'yes'/'no'
28 # Show branch length branch values: 'show_branch_length_values': values: 'yes'/'no'
29 # Do/do not line up cladogram display: 'non_lined_up_cladogram': values: 'yes'/'no'
30 # Cladogram display type: 'cladogram_type'
31 # Example: 'cladogram_type: ext_node_sum_dep'
32 # The three possible values are: non_lined_up
34 # total_node_sum_dep (for "uniform" branch lengths)
35 # Default size for graphics export and printing: 'graphics_export_x' and 'graphics_export_y':
36 # (Archaeopteryx tries to guess the locale, so setting these is not always necessary)
37 # Example: For A4 (portrait):
38 # 'graphics_export_x: 595'
39 # 'graphics_export_y: 845'
40 # For US Letter (portrait):
41 # 'graphics_export_x: 612'
42 # 'graphics_export_y: 792'
43 # Default line width for PDF export: 'pdf_export_line_wdith':
44 # Example: 'pdf_export_line_width: 0.5'
45 # 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
56 # Node label direction for circular and unrooted type: 'node_label_direction':
57 # Example: 'node_label_direction: horizontal'
58 # The two possible values are: horizontal
60 # Show default node shape for internal nodes: 'show_default_node_shapes_internal': values: 'yes'/'no'
61 # Show default node shape for external nodes: 'show_default_node_shapes_external': values: 'yes'/'no'
62 # Default node shape size: 'default_node_size'
63 # Example: 'default_node_size: 6'
64 # Default node shape type: 'default_node_shape'
65 # Example: 'default_node_shape: '
66 # Possible values: circle
68 # Default node shape fill: 'default_node_fill'
69 # Example: 'default_node_fill: '
70 # Possible values: solid
74 # To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
75 # Possible values: node_name
79 # sequence_mol_seq_fasta
81 # taxonomy_scientific_name
83 # taxonomy_common_name
86 # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
87 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
88 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
89 # Possible values: window (for output to window and buffer)
90 # console (for output to console and buffer)
91 # buffer_only (for output to buffer only)
93 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
94 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
96 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
97 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
98 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
99 # Number of fraction digits for branch length values: 'branch_length_value_digits'
100 # Number of fraction digits for confidence values: 'confidence_value_digits'
101 # To turn on/off background color gradient: background_gradient
102 # Example: 'background_gradient: yes'
103 # To allow/not allow editing (cut, copy, and paste): allow_editing
104 # Example: 'allow_editing: yes'
106 # NH/NHX/Nexus file parsing
107 # -------------------------
108 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
109 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
111 # To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names)
112 # from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing'
113 # possible values are:
115 # 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453)
116 # 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090)
117 # 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis)
119 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
120 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
126 # To ensure compatibility with all current and future
127 # phyloXML applications and to detect malformatted and
128 # possibly erroneous data, it is strongly recommended
129 # to enable validation of all phyloXML files
130 # against the XSD Schema (see: http://www.phyloxml.org/),
132 # 'validate_against_phyloxml_xsd_schema: true'
134 validate_against_phyloxml_xsd_schema: true
138 min_confidence_value: 0.0
139 font_family: Arial,Helvetica,Verdana,Tahoma,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
143 antialias_screen: yes
145 show_branch_length_values: no
146 cladogram_type: ext_node_sum_dep
147 phylogeny_graphics_type: rectangular
148 node_label_direction: horizontal
149 show_default_node_shapes_internal: no
150 show_default_node_shapes_external: no
152 default_node_shape: rectangle
153 default_node_fill: solid
154 taxonomy_colorize_node_shapes: no
155 #graphics_export_x: 595
156 #graphics_export_y: 792
157 pdf_export_line_width: 0.5
161 overview_placement_type: upper_left
162 color_labels_same_as_branch_length_values: no
163 display_sequence_relations: no
164 show_domain_labels: yes
165 branch_length_value_digits: 3
166 confidence_value_digits: 3
167 background_gradient: no
169 ext_descendents_data_to_return_on: window
170 ext_descendents_data_to_return: user_selected
171 #label_for_get_ext_descendents_data: Get_Node_Data
172 # NH/NHX/Nexus file parsing:
173 internal_labels_are_confidence_values: no
174 replace_underscores_in_nh_parsing: no
175 taxonomy_extraction_in_nh_parsing: no
178 # Checkbox Display Selection
179 # --------------------------
180 # This is used to select which checkboxes to display
181 # and what their initial values should be.
182 # Format: 'name: display|nodisplay yes|no'
183 # Note: if an option is not displayed, it will not be enabled
185 # For the following use '?' to let Archaeopteryx decide (depending on tree):
187 # - 'write_confidence_values'
191 rollover: display yes
192 color_according_to_species: display yes
193 color_according_to_annotation: display no
194 show_node_names: display yes
195 show_gene_names: display yes
196 show_gene_symbols: display yes
197 show_sequence_acc: display no
198 show_taxonomy_code: display yes
199 show_taxonomy_scientific_names: display yes
200 show_taxonomy_common_names: display no
201 show_taxonomy_images: display yes
202 show_annotations: display no
203 write_confidence_values: display ?
204 write_events: display ?
205 color_branches: display no
206 width_branches: display no
207 show_domain_architectures: display no
208 show_binary_characters: display no
209 show_binary_character_counts: display no
210 display_internal_data: display yes
211 dynamically_hide_data: display yes
212 show_relation_confidence: display no
213 show_properties: display no
214 show_vector_data: display no
218 # Combo-box Display Selection
219 # ---------------------------
220 # Format: 'name: display/nodisplay'
221 click_to: display_node_data display
222 click_to: collapse_uncollapse display
223 click_to: reroot display
224 click_to: subtree display
225 click_to: swap display
226 click_to: sort_descendants display
227 click_to: color_subtree display
228 click_to: open_seq_web display
229 click_to: open_tax_web display
230 click_to: blast display
231 click_to: cut_subtree display
232 click_to: copy_subtree display
233 click_to: paste_subtree display
234 click_to: delete display
235 click_to: add_new_node display
236 click_to: edit_node_data display
237 click_to: select_nodes display
238 click_to: get_ext_descendents_data display
240 # Default click-to option (any of the above if set to "display")
241 default_click_to: display_node_data
245 # Default Tree Display Colors
246 # ---------------------------
248 display_color: background 0x000000
249 display_color: background_gradient_bottom 0x0000FF
250 display_color: sequence 0xDCDCDC
251 display_color: taxonomy 0xB4B4B4
252 display_color: confidence 0x38B0DE
253 display_color: branch_length 0x8C8C8C
254 display_color: branch 0xFFFFFF
255 display_color: node_box 0xFFFFFF
256 display_color: collapsed 0xFFFF00
257 display_color: matching_nodes 0x00FF00
258 display_color: duplication 0xFF0000
259 display_color: speciation 0x00FF00
260 display_color: duplication_or_specation 0xFFFF00
261 display_color: domains 0x7B68EE
262 display_color: binary_domain_combinations 0x4169FF
263 display_color: annotation 0xADFF2F
264 display_color: overview 0x828282
268 # GUI (graphical user interface) Colors
269 # -------------------------------------
271 # These are ignored if native (system) "look and feel"
272 # is being used ('native_ui: yes').
274 gui_background_color: 0x202020
275 gui_checkbox_text_color: 0xDCDCDC
276 gui_checkbox_and_button_active_color: 0xFF0000
277 gui_button_text_color: 0xFFFFFF
278 gui_button_background_color: 0x404040
279 gui_menu_background_color: 0x000000
280 gui_menu_text_color: 0xFFFFFF
281 gui_button_border_color: 0x000000
285 # Domain Structure Display Colors
286 # -------------------------------
287 domain_structure_base_color: 0x202020
288 domain_structure_font_color: 0x909090
292 # Settings Specific for Archaeopteryx Applets (E and A)
293 # -----------------------------------------------------
294 # To automatically midpoint reroot trees upon loading: 'midpoint_reroot: yes'
300 # Settings Specific for ArchaeopteryxE Applets
301 # --------------------------------------------
302 # To hide controls and menus: 'hide_controls_and_menus: yes'
303 # To use tabbed display : 'use_tabbed_display: yes'
305 hide_controls_and_menus: no
306 use_tabbed_display: yes
310 # Settings For Phylogenetic Inference
311 # -----------------------------------
312 # EXPERIMENTAL: DO NOT USE!!
314 default_number_of_bootstrap_resamples: 100
315 mafft_local: /bin/mafft
316 fastme_local: /bin/fastme
317 raxml_local: /bin/raxml
323 # Format: species_color: speciesname hexcolor
324 species_color: BRAFL 0x00FFFF
325 species_color: SPHGR 0x9620F0
326 species_color: STRPU 0x9620F0
327 species_color: CIOIN 0xFF1CAE
328 species_color: CIOSA 0xFF2CAE
329 species_color: BOVIN 0x5C3317
330 species_color: CANFA 0x8B2323
331 species_color: HUMAN 0xFF2400
332 species_color: Homo_sapiens 0xFF2400
333 species_color: PANTR 0xCC2400
334 species_color: MOUSE 0xFF7F00
335 species_color: RAT 0xFFEF00
336 species_color: MONDO 0xEE9A49
337 species_color: ORNAN 0xCD853F
338 species_color: XENLA 0x6BAA23
339 species_color: XENTR 0x6BAA23
340 species_color: CHICK 0xFFC125
341 species_color: FUGRU 0x0000FF
342 species_color: BRARE 0x0000DD
343 species_color: DANRE 0x0000BB
344 species_color: TETNG 0x0000AA
345 species_color: ORYLA 0x000088
346 species_color: GASAC 0x000066
347 species_color: CAEEL 0xA0A0A0
348 species_color: CAEBR 0xB0B0B0
349 species_color: DROME 0x706F00
350 species_color: DROPS 0x504F00
351 species_color: APIME 0x7A7700
352 species_color: AEDAE 0x8C5900
353 species_color: TRICA 0x918E00
354 species_color: NEMVE 0xAABADD
355 species_color: HYDAT 0x7C9BCF
356 species_color: LUBBA 0xF7B5CB
357 species_color: GEOCY 0xF5A0BD
358 species_color: SUBDO 0xC790B9
359 species_color: MONBE 0xFC0FC0
360 species_color: DICPU 0x23238E
361 species_color: DICDI 0x4D4DFF
362 species_color: ENTHI 0x5959AB
363 species_color: ARATH 0x00FF00
364 species_color: POPTR 0x006400
365 species_color: VITVI 0x00CD00
366 species_color: GLYMA 0x00FF7F
367 species_color: ORYSA 0x008B00
368 species_color: ORYSJ 0x008C00
369 species_color: SORBI 0x00EE76
370 species_color: SELMO 0x238E23
371 species_color: PHYPA 0x09F911
372 species_color: OSTLU 0x7FFF00
373 species_color: OSTTA 0x7FFF00
374 species_color: OSTRC 0x7FFF00
375 species_color: MICPU 0x66CD00
376 species_color: MIC99 0x66CD00
377 species_color: CHLRE 0xB3EE3A
378 species_color: VOLCA 0xC0FF3E
379 species_color: CHLSP 0x6B8E23
380 species_color: CYAME 0xD02090
381 species_color: YEAST 0xAAAAAA
382 species_color: BACFR 0xFF0000
383 species_color: BACTN 0xFFFF00
384 species_color: MYXXD 0x0000FF
385 species_color: STIAU 0x00FFFF
386 species_color: BACOV 0x8C5900
387 species_color: BACUN 0x66CD00
388 species_color: PORGI 0x918E00
390 species_color: Mammalia 0xFF0000
391 species_color: mammals 0xFF0000
393 species_color: Chordata 0x8470FF
394 species_color: Echinodermata 0x6495ED
395 species_color: Hemichordata 0x7EC0EE
396 species_color: Arthropoda 0x7AC5CD
397 species_color: Nematoda 0x7171C6
398 species_color: Tardigrada 0x388E8E
399 species_color: Annelida 0xC67171
400 species_color: Mollusca 0x00F5FF
401 species_color: Ctenophora 0xBBFFFF
402 species_color: Cnidaria 0xFF83FA
403 species_color: Placozoa 0xEED2EE
404 species_color: Porifera 0xFF3E96
405 species_color: Microsporidia 0x8B8378
406 species_color: Ascomycota 0xFF6347
407 species_color: Basidiomycota 0xFFD700
408 species_color: Chlorophyta 0x00C78C
409 species_color: Streptophyta 0x00C957
411 species_color: Viridiplantae 0x00FF00
412 species_color: plants 0x00FF00
413 species_color: Metazoa 0x0000FF
414 species_color: animals 0x0000FF
415 species_color: Fungi 0xFF9912
417 species_color: Viruses 0xFFD700
418 species_color: Bacteria 0x00FF00
419 species_color: Archaea 0x0000FF
420 species_color: Eukaryota 0xFF0000
421 species_color: eukaryotes 0xFF0000
426 domain_color: Cofilin_ADF 0xFC0FC0
427 domain_color: TIR 0x900000
428 domain_color: NACHT 0x202020
429 domain_color: CARD 0xFF0000
430 domain_color: Peptidase_C14 0x00FF00
431 domain_color: Death 0x0000FF
432 domain_color: DED 0x00FFFF
433 domain_color: BIR 0xCCFF33
434 domain_color: PAAD_DAPIN 0x9999CC
435 domain_color: NB-ARC 0x500050
436 domain_color: WD40 0x888888
437 domain_color: RVT_1 0x999900
444 annotation_color: dehydrogenase 0x0000FF
445 annotation_color: kinase 0xFF00FF
446 annotation_color: protease 0x009900
447 annotation_color: transcription 0xAAAA00