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
85 # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
86 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
87 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
88 # Possible values: window (for output to window and buffer)
89 # console (for output to console and buffer)
90 # buffer_only (for output to buffer only)
92 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
93 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
95 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
96 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
97 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
98 # Number of fraction digits for branch length values: 'branch_length_value_digits'
99 # Number of fraction digits for confidence values: 'confidence_value_digits'
100 # To turn on/off background color gradient: background_gradient
101 # Example: 'background_gradient: yes'
102 # To allow/not allow editing (cut, copy, and paste): allow_editing
103 # Example: 'allow_editing: yes'
105 # NH/NHX/Nexus file parsing
106 # -------------------------
107 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
108 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
110 # To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing:
111 # 'taxonomy_extraction_in_nh_parsing',
112 # possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
114 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
115 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
121 # To ensure compatibility with all current and future
122 # phyloXML applications and to detect malformatted and
123 # possibly erroneous data, it is strongly recommended
124 # to enable validation of all phyloXML files
125 # against the XSD Schema (see: http://www.phyloxml.org/),
127 # 'validate_against_phyloxml_xsd_schema: true'
129 validate_against_phyloxml_xsd_schema: true
133 min_confidence_value: 0.0
134 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
138 antialias_screen: yes
140 show_branch_length_values: no
141 cladogram_type: ext_node_sum_dep
142 phylogeny_graphics_type: rectangular
143 node_label_direction: horizontal
144 show_default_node_shapes_internal: no
145 show_default_node_shapes_external: no
147 default_node_shape: circle
148 default_node_fill: gradient
149 taxonomy_colorize_node_shapes: no
150 #graphics_export_x: 595
151 #graphics_export_y: 792
152 pdf_export_line_width: 0.5
156 overview_placement_type: upper_left
157 color_labels_same_as_branch_length_values: no
158 display_sequence_relations: no
159 show_domain_labels: yes
160 branch_length_value_digits: 3
161 confidence_value_digits: 3
162 background_gradient: no
164 ext_descendents_data_to_return_on: window
165 ext_descendents_data_to_return: sequence_mol_seq_fasta
166 #label_for_get_ext_descendents_data: Get_Node_Data
167 # NH/NHX/Nexus file parsing:
168 internal_labels_are_confidence_values: no
169 replace_underscores_in_nh_parsing: no
170 taxonomy_extraction_in_nh_parsing: pfam
173 # Checkbox Display Selection
174 # --------------------------
175 # This is used to select which checkboxes to display
176 # and what their initial values should be.
177 # Format: 'name: display|nodisplay yes|no'
178 # Note: if an option is not displayed, it will not be enabled
180 # For the following use '?' to let Archaeopteryx decide (depending on tree):
182 # - 'write_confidence_values'
186 rollover: display yes
187 color_according_to_species: display yes
188 color_according_to_annotation: display no
189 show_node_names: display yes
190 show_gene_names: display yes
191 show_gene_symbols: display yes
192 show_sequence_acc: display no
193 show_taxonomy_code: display yes
194 show_taxonomy_scientific_names: display yes
195 show_taxonomy_common_names: display no
196 show_taxonomy_images: display yes
197 show_annotations: display no
198 write_confidence_values: display ?
199 write_events: display ?
200 color_branches: display no
201 width_branches: display no
202 show_domain_architectures: display no
203 show_binary_characters: display no
204 show_binary_character_counts: display no
205 display_internal_data: display yes
206 dynamically_hide_data: display yes
207 show_relation_confidence: display no
208 show_properties: display no
209 show_vector_data: display no
213 # Combo-box Display Selection
214 # ---------------------------
215 # Format: 'name: display/nodisplay'
216 click_to: display_node_data display
217 click_to: collapse_uncollapse display
218 click_to: reroot display
219 click_to: subtree display
220 click_to: swap display
221 click_to: sort_descendants display
222 click_to: color_subtree display
223 click_to: open_seq_web display
224 click_to: open_tax_web display
225 click_to: blast display
226 click_to: cut_subtree display
227 click_to: copy_subtree display
228 click_to: paste_subtree display
229 click_to: delete display
230 click_to: add_new_node display
231 click_to: edit_node_data display
232 click_to: select_nodes display
233 click_to: get_ext_descendents_data display
235 # Default click-to option (any of the above if set to "display")
236 default_click_to: display_node_data
240 # Default Tree Display Colors
241 # ---------------------------
243 display_color: background 0x000000
244 display_color: background_gradient_bottom 0x0000FF
245 display_color: sequence 0xDCDCDC
246 display_color: taxonomy 0xB4B4B4
247 display_color: confidence 0x38B0DE
248 display_color: branch_length 0x8C8C8C
249 display_color: branch 0xFFFFFF
250 display_color: node_box 0xFFFFFF
251 display_color: collapsed 0xFFFF00
252 display_color: matching_nodes 0x00FF00
253 display_color: duplication 0xFF0000
254 display_color: speciation 0x00FF00
255 display_color: duplication_or_specation 0xFFFF00
256 display_color: domains 0x7B68EE
257 display_color: binary_domain_combinations 0x4169FF
258 display_color: annotation 0xADFF2F
259 display_color: overview 0x828282
263 # GUI (graphical user interface) Colors
264 # -------------------------------------
266 # These are ignored if native (system) "look and feel"
267 # is being used ('native_ui: yes').
269 gui_background_color: 0x202020
270 gui_checkbox_text_color: 0xDCDCDC
271 gui_checkbox_and_button_active_color: 0xFF0000
272 gui_button_text_color: 0xFFFFFF
273 gui_button_background_color: 0x404040
274 gui_menu_background_color: 0x000000
275 gui_menu_text_color: 0xFFFFFF
276 gui_button_border_color: 0x000000
280 # Domain Structure Display Colors
281 # -------------------------------
282 domain_structure_base_color: 0x202020
283 domain_structure_font_color: 0x909090
289 # Format: web_link: <URL> <description> <source identifier>
290 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
291 # <description> is not used at the moment.
292 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
293 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
295 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
296 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
297 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
298 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
299 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
300 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
301 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
302 web_link: http://tolweb.org/ ToL tol
303 web_link: http://www.eol.org/pages/ EOL eol
304 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
305 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
306 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
307 # not working at the moment:
308 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
312 # Settings Specific for ArchaeopteryxE
313 # ------------------------------------
314 # To hide controls and menus: 'hide_controls_and_menus: yes'
315 # To use tabbed display : 'use_tabbed_display: yes'
317 hide_controls_and_menus: no
318 use_tabbed_display: yes
322 # Settings For Phylogenetic Inference
323 # -----------------------------------
324 # EXPERIMENTAL: DO NOT USE!!
326 default_number_of_bootstrap_resamples: 100
327 mafft_local: /bin/mafft
328 fastme_local: /bin/fastme
329 raxml_local: /bin/raxml
332 # Application Specific Settings
333 # -----------------------------
337 # Format: species_color: speciesname hexcolor
338 species_color: BRAFL 0x00FFFF
339 species_color: SPHGR 0x9620F0
340 species_color: STRPU 0x9620F0
341 species_color: CIOIN 0xFF1CAE
342 species_color: CIOSA 0xFF2CAE
343 species_color: BOVIN 0x5C3317
344 species_color: CANFA 0x8B2323
345 species_color: HUMAN 0xFF2400
346 species_color: PANTR 0xCC2400
347 species_color: MOUSE 0xFF7F00
348 species_color: RAT 0xFFEF00
349 species_color: MONDO 0xEE9A49
350 species_color: ORNAN 0xCD853F
351 species_color: XENLA 0x6BAA23
352 species_color: XENTR 0x6BAA23
353 species_color: CHICK 0xFFC125
354 species_color: FUGRU 0x0000FF
355 species_color: BRARE 0x0000DD
356 species_color: DANRE 0x0000BB
357 species_color: TETNG 0x0000AA
358 species_color: ORYLA 0x000088
359 species_color: GASAC 0x000066
360 species_color: CAEEL 0xA0A0A0
361 species_color: CAEBR 0xB0B0B0
362 species_color: DROME 0x706F00
363 species_color: DROPS 0x504F00
364 species_color: APIME 0x7A7700
365 species_color: AEDAE 0x8C5900
366 species_color: TRICA 0x918E00
367 species_color: NEMVE 0xAABADD
368 species_color: HYDAT 0x7C9BCF
369 species_color: LUBBA 0xF7B5CB
370 species_color: GEOCY 0xF5A0BD
371 species_color: SUBDO 0xC790B9
372 species_color: MONBE 0xFC0FC0
373 species_color: DICPU 0x23238E
374 species_color: DICDI 0x4D4DFF
375 species_color: ENTHI 0x5959AB
376 species_color: ARATH 0x00FF00
377 species_color: POPTR 0x006400
378 species_color: VITVI 0x00CD00
379 species_color: GLYMA 0x00FF7F
380 species_color: ORYSA 0x008B00
381 species_color: ORYSJ 0x008C00
382 species_color: SORBI 0x00EE76
383 species_color: SELMO 0x238E23
384 species_color: PHYPA 0x09F911
385 species_color: OSTLU 0x7FFF00
386 species_color: OSTTA 0x7FFF00
387 species_color: OSTRC 0x7FFF00
388 species_color: MICPU 0x66CD00
389 species_color: MIC99 0x66CD00
390 species_color: CHLRE 0xB3EE3A
391 species_color: VOLCA 0xC0FF3E
392 species_color: CHLSP 0x6B8E23
393 species_color: CYAME 0xD02090
394 species_color: YEAST 0xAAAAAA
395 species_color: BACFR 0xFF0000
396 species_color: BACTN 0xFFFF00
397 species_color: MYXXD 0x0000FF
398 species_color: STIAU 0x00FFFF
399 species_color: BACOV 0x8C5900
400 species_color: BACUN 0x66CD00
401 species_color: PORGI 0x918E00
403 species_color: Mammalia 0xFF0000
404 species_color: mammals 0xFF0000
406 species_color: Chordata 0x8470FF
407 species_color: Echinodermata 0x6495ED
408 species_color: Hemichordata 0x7EC0EE
409 species_color: Arthropoda 0x7AC5CD
410 species_color: Nematoda 0x7171C6
411 species_color: Tardigrada 0x388E8E
412 species_color: Annelida 0xC67171
413 species_color: Mollusca 0x00F5FF
414 species_color: Ctenophora 0xBBFFFF
415 species_color: Cnidaria 0xFF83FA
416 species_color: Placozoa 0xEED2EE
417 species_color: Porifera 0xFF3E96
418 species_color: Microsporidia 0x8B8378
419 species_color: Ascomycota 0xFF6347
420 species_color: Basidiomycota 0xFFD700
421 species_color: Chlorophyta 0x00C78C
422 species_color: Streptophyta 0x00C957
424 species_color: Viridiplantae 0x00FF00
425 species_color: plants 0x00FF00
426 species_color: Metazoa 0x0000FF
427 species_color: animals 0x0000FF
428 species_color: Fungi 0xFF9912
430 species_color: Viruses 0xFFD700
431 species_color: Bacteria 0x00FF00
432 species_color: Archaea 0x0000FF
433 species_color: Eukaryota 0xFF0000
434 species_color: eukaryotes 0xFF0000
439 domain_color: Cofilin_ADF 0xFC0FC0
440 domain_color: TIR 0x900000
441 domain_color: NACHT 0x202020
442 domain_color: CARD 0xFF0000
443 domain_color: Peptidase_C14 0x00FF00
444 domain_color: Death 0x0000FF
445 domain_color: DED 0x00FFFF
446 domain_color: BIR 0xCCFF33
447 domain_color: PAAD_DAPIN 0x9999CC
448 domain_color: NB-ARC 0x500050
449 domain_color: WD40 0x888888
450 domain_color: RVT_1 0x999900
457 annotation_color: dehydrogenase 0x0000FF
458 annotation_color: kinase 0xFF00FF
459 annotation_color: protease 0x009900
460 annotation_color: transcription 0xAAAA00