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
57 # and unrooted type: 'node_label_direction':
58 # Example: 'node_label_direction: horizontal'
59 # The two possible values are: horizontal
61 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
62 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
63 # Number of fraction digits for branch length values: 'branch_length_value_digits'
64 # Number of fraction digits for confidence values: 'confidence_value_digits'
65 # To turn on/off background color gradient: background_gradient
66 # Example: 'background_gradient: yes'
67 # To allow/not allow editing (cut, copy, and paste): allow_editing
68 # Example: 'allow_editing: yes'
69 # To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
70 # 'replace_underscores_in_nh_parsing'
71 # To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
72 # during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing'
73 # Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
74 # 'internal_labels_are_confidence_values'
77 min_confidence_value: 0.0
78 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
82 show_branch_length_values: no
83 cladogram_type: ext_node_sum_dep
84 phylogeny_graphics_type: rectangular
85 #graphics_export_x: 595
86 #graphics_export_y: 792
87 pdf_export_line_width: 0.5
91 overview_placement_type: upper_left
92 node_label_direction: horizontal
93 color_labels_same_as_branch_length_values: no
94 show_domain_labels: yes
95 branch_length_value_digits: 3
96 confidence_value_digits: 3
97 background_gradient: no
99 # NH/NHX/Nexus file parsing (application only):
100 internal_labels_are_confidence_values: no
101 replace_underscores_in_nh_parsing: no
102 extract_taxonomy_codes_in_nh_parsing: yes
103 display_sequence_relations: no
108 # To ensure compatibility with all current and future
109 # phyloXML applications and to detect malformatted and
110 # possibly erroneous data, it is strongly recommended
111 # to enable validation of all phyloXML files
112 # against the XSD Schema (see: http://www.phyloxml.org/),
114 # 'validate_against_phyloxml_xsd_schema: true'
116 validate_against_phyloxml_xsd_schema: true
120 # Checkbox Display Selection
121 # --------------------------
122 # This is used to select which checkboxes to display
123 # and what their initial values should be.
124 # Format: 'name: display|nodisplay yes|no'
125 # Note: if an option is not displayed, it will not be enabled
127 # For the following use '?' to let Archaeopteryx decide (depending on tree):
129 # - 'write_confidence_values'
133 rollover: display yes
134 color_according_to_species: display yes
135 color_according_to_annotation: display no
136 show_node_names: display yes
137 show_gene_names: display yes
138 show_gene_symbols: display yes
139 show_sequence_acc: display no
140 show_taxonomy_code: display yes
141 show_taxonomy_scientific_names: display yes
142 show_taxonomy_common_names: display no
143 show_taxonomy_images: display yes
144 show_annotations: display no
145 show_property: nodisplay no
146 write_confidence_values: display ?
147 write_events: display ?
148 color_branches: display no
149 width_branches: display no
150 show_domain_architectures: display no
151 show_binary_characters: display no
152 show_binary_character_counts: display no
153 display_internal_data: display yes
154 dynamically_hide_data: display yes
155 show_relation_confidence: display no
156 show_vector_data: display no
159 # Combo-box Display Selection
160 # ---------------------------
161 # Format: 'name: display/nodisplay'
162 click_to: display_node_data display
163 click_to: collapse_uncollapse display
164 click_to: reroot display
165 click_to: subtree display
166 click_to: swap display
167 click_to: color_subtree display
168 click_to: open_seq_web display
169 click_to: open_tax_web display
170 click_to: cut_subtree display
171 click_to: copy_subtree display
172 click_to: paste_subtree display
173 click_to: delete display
174 click_to: add_new_node display
175 click_to: edit_node_data display
177 # Default click-to option (any of the above if set to "display")
178 default_click_to: display_node_data
182 # Default Tree Display Colors
183 # ---------------------------
185 display_color: background 0x000000
186 display_color: background_gradient_bottom 0x0000FF
187 display_color: sequence 0xDCDCDC
188 display_color: taxonomy 0xB4B4B4
189 display_color: confidence 0x38B0DE
190 display_color: branch_length 0x8C8C8C
191 display_color: branch 0xFFFFFF
192 display_color: node_box 0xFFFFFF
193 display_color: collapsed 0xFFFF00
194 display_color: matching_nodes 0x00FF00
195 display_color: duplication 0xFF0000
196 display_color: speciation 0x00FF00
197 display_color: duplication_or_specation 0xFFFF00
198 display_color: domains 0x7B68EE
199 display_color: binary_domain_combinations 0x4169FF
200 display_color: annotation 0xADFF2F
201 display_color: overview 0x828282
205 # GUI (graphical user interface) Colors
206 # -------------------------------------
208 # These are ignored if native (system) "look and feel"
209 # is being used ('native_ui: yes').
211 gui_background_color: 0x202020
212 gui_checkbox_text_color: 0xDCDCDC
213 gui_checkbox_and_button_active_color: 0xFF0000
214 gui_button_text_color: 0xFFFFFF
215 gui_button_background_color: 0x404040
216 gui_menu_background_color: 0x000000
217 gui_menu_text_color: 0xFFFFFF
218 gui_button_border_color: 0x000000
221 # Domain Structure Display Colors
222 # -------------------------------
223 domain_structure_base_color: 0x202020
224 domain_structure_font_color: 0x909090
230 # Format: web_link: <URL> <description> <source identifier>
231 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
232 # <description> is not used at the moment.
233 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
234 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
236 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
237 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
238 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
239 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
240 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
241 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
242 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
243 web_link: http://tolweb.org/ ToL tol
244 web_link: http://www.eol.org/pages/ EOL eol
245 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
246 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
247 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
248 # not working at the moment:
249 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
253 # Settings Specific for ArchaeopteryxE
254 # ------------------------------------
255 # To hide controls and menus: 'hide_controls_and_menus: yes'
256 # To use tabbed display : 'use_tabbed_display: yes'
258 hide_controls_and_menus: no
259 use_tabbed_display: yes
263 # Settings For Phylogenetic Inference
264 # -----------------------------------
265 # EXPERIMENTAL: DO NOT USE!!
267 default_number_of_bootstrap_resamples: 100
271 # Application Specific Settings
272 # -----------------------------
276 # Format: species_color: speciesname hexcolor
277 species_color: BRAFL 0x00FFFF
278 species_color: SPHGR 0x9620F0
279 species_color: STRPU 0x9620F0
280 species_color: CIOIN 0xFF1CAE
281 species_color: CIOSA 0xFF2CAE
282 species_color: BOVIN 0x5C3317
283 species_color: CANFA 0x8B2323
284 species_color: HUMAN 0xFF2400
285 species_color: PANTR 0xCC2400
286 species_color: MOUSE 0xFF7F00
287 species_color: RAT 0xFFEF00
288 species_color: MONDO 0xEE9A49
289 species_color: ORNAN 0xCD853F
290 species_color: XENLA 0x6BAA23
291 species_color: XENTR 0x6BAA23
292 species_color: CHICK 0xFFC125
293 species_color: FUGRU 0x0000FF
294 species_color: BRARE 0x0000DD
295 species_color: DANRE 0x0000BB
296 species_color: TETNG 0x0000AA
297 species_color: ORYLA 0x000088
298 species_color: GASAC 0x000066
299 species_color: CAEEL 0xA0A0A0
300 species_color: CAEBR 0xB0B0B0
301 species_color: DROME 0x706F00
302 species_color: DROPS 0x504F00
303 species_color: APIME 0x7A7700
304 species_color: AEDAE 0x8C5900
305 species_color: TRICA 0x918E00
306 species_color: NEMVE 0xAABADD
307 species_color: HYDAT 0x7C9BCF
308 species_color: LUBBA 0xF7B5CB
309 species_color: GEOCY 0xF5A0BD
310 species_color: SUBDO 0xC790B9
311 species_color: MONBE 0xFC0FC0
312 species_color: DICPU 0x23238E
313 species_color: DICDI 0x4D4DFF
314 species_color: ENTHI 0x5959AB
315 species_color: ARATH 0x00FF00
316 species_color: POPTR 0x006400
317 species_color: VITVI 0x00CD00
318 species_color: GLYMA 0x00FF7F
319 species_color: ORYSA 0x008B00
320 species_color: ORYSJ 0x008C00
321 species_color: SORBI 0x00EE76
322 species_color: SELMO 0x238E23
323 species_color: PHYPA 0x09F911
324 species_color: OSTLU 0x7FFF00
325 species_color: OSTTA 0x7FFF00
326 species_color: OSTRC 0x7FFF00
327 species_color: MICPU 0x66CD00
328 species_color: MIC99 0x66CD00
329 species_color: CHLRE 0xB3EE3A
330 species_color: VOLCA 0xC0FF3E
331 species_color: CHLSP 0x6B8E23
332 species_color: CYAME 0xD02090
333 species_color: YEAST 0xAAAAAA
334 species_color: BACFR 0xFF0000
335 species_color: BACTN 0xFFFF00
336 species_color: MYXXD 0x0000FF
337 species_color: STIAU 0x00FFFF
338 species_color: BACOV 0x8C5900
339 species_color: BACUN 0x66CD00
340 species_color: PORGI 0x918E00
346 domain_color: Cofilin_ADF 0xFC0FC0
347 domain_color: TIR 0x900000
348 domain_color: NACHT 0x202020
349 domain_color: CARD 0xFF0000
350 domain_color: Peptidase_C14 0x00FF00
351 domain_color: Death 0x0000FF
352 domain_color: DED 0x00FFFF
353 domain_color: BIR 0xCCFF33
354 domain_color: PAAD_DAPIN 0x9999CC
355 domain_color: NB-ARC 0x500050
356 domain_color: WD40 0x888888
357 domain_color: RVT_1 0x999900
358 domain_color: NOPS 0x505000
359 domain_color: RRM_1 0x004400
360 domain_color: fn3 0xFFCC00
361 domain_color: Ank 0xCC33FF
362 domain_color: Pkinase 0x339900
363 domain_color: Pkinase_Tyr 0x336600
364 domain_color: ig 0x660066
365 domain_color: zf-C3HC4 0x6699FF
366 domain_color: zf-CCHC 0x6699EE
367 domain_color: zf-C2H2 0x6699CC
368 domain_color: zf-B_box 0x6699DD
369 domain_color: PDZ 0x66FFCC
370 domain_color: SH3_2 0x996600
371 domain_color: MIRO 0xCCFF00
372 domain_color: Myb_DNA-binding 0xDDDDDD
373 domain_color: NHL 0x336666
374 domain_color: PKD_channel 0x336666
375 domain_color: Ion_trans 0x996666
376 domain_color: CAP_GLY 0xCC9900
377 domain_color: LRR_1 0xFFFF99
378 domain_color: LRR_2 0xFFFF66
379 domain_color: LRR_3 0xFFFF33
380 domain_color: LRR_adjacent 0xFFFF00
381 domain_color: LRRCT 0xFFCC99
382 domain_color: LRRNT 0xFFCC66
383 domain_color: LRRNT_2 0xFFCC33
384 domain_color: Ank 0x990099
385 domain_color: Sushi 0x004400
386 domain_color: ZU5 0xFF9999
387 domain_color: V-set 0x3399FF
388 domain_color: TPR_1 0xFF1493
389 domain_color: TPR_2 0xFF69B4
390 domain_color: TPR_3 0xCD6090
391 domain_color: TPR_4 0xFF6A6A
392 domain_color: TPR_MLP1_2 0x33FF00
393 domain_color: Collagen 0xFF7F00
394 domain_color: MIF 0xADD8E6
400 annotation_color: dehydrogenase 0x0000FF
401 annotation_color: kinase 0xFF00FF
402 annotation_color: protease 0x009900
403 annotation_color: transcription 0xAAAA00