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: 'show_default_node_shapes': values: 'yes'/'no'
61 # Default node shape size: 'default_node_size'
62 # Example: 'default_node_size: 6'
63 # Default node shape type: 'default_node_shape'
64 # Example: 'default_node_shape: '
65 # Possible values: circle
67 # Default node shape fill: 'default_node_fill'
68 # Example: 'default_node_fill: '
69 # Possible values: solid
72 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
73 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
74 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
75 # Number of fraction digits for branch length values: 'branch_length_value_digits'
76 # Number of fraction digits for confidence values: 'confidence_value_digits'
77 # To turn on/off background color gradient: background_gradient
78 # Example: 'background_gradient: yes'
79 # To allow/not allow editing (cut, copy, and paste): allow_editing
80 # Example: 'allow_editing: yes'
81 # To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
82 # 'replace_underscores_in_nh_parsing'
83 # To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
84 # during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing'
85 # Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
86 # 'internal_labels_are_confidence_values'
89 min_confidence_value: 0.0
90 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
94 show_branch_length_values: no
95 cladogram_type: ext_node_sum_dep
96 phylogeny_graphics_type: rectangular
97 node_label_direction: horizontal
98 show_default_node_shapes: no
100 default_node_shape: circle
101 default_node_fill: gradient
102 taxonomy_colorize_node_shapes: no
103 #graphics_export_x: 595
104 #graphics_export_y: 792
105 pdf_export_line_width: 0.5
109 overview_placement_type: upper_left
110 color_labels_same_as_branch_length_values: no
111 show_domain_labels: yes
112 branch_length_value_digits: 3
113 confidence_value_digits: 3
114 background_gradient: no
116 # NH/NHX/Nexus file parsing (application only):
117 internal_labels_are_confidence_values: no
118 replace_underscores_in_nh_parsing: no
119 extract_taxonomy_codes_in_nh_parsing: yes
120 display_sequence_relations: no
125 # To ensure compatibility with all current and future
126 # phyloXML applications and to detect malformatted and
127 # possibly erroneous data, it is strongly recommended
128 # to enable validation of all phyloXML files
129 # against the XSD Schema (see: http://www.phyloxml.org/),
131 # 'validate_against_phyloxml_xsd_schema: true'
133 validate_against_phyloxml_xsd_schema: true
137 # Checkbox Display Selection
138 # --------------------------
139 # This is used to select which checkboxes to display
140 # and what their initial values should be.
141 # Format: 'name: display|nodisplay yes|no'
142 # Note: if an option is not displayed, it will not be enabled
144 # For the following use '?' to let Archaeopteryx decide (depending on tree):
146 # - 'write_confidence_values'
150 rollover: display yes
151 color_according_to_species: display yes
152 color_according_to_annotation: display no
153 show_node_names: display yes
154 show_gene_names: display yes
155 show_gene_symbols: display yes
156 show_sequence_acc: display no
157 show_taxonomy_code: display yes
158 show_taxonomy_scientific_names: display yes
159 show_taxonomy_common_names: display no
160 show_taxonomy_images: display yes
161 show_annotations: display no
162 show_property: nodisplay no
163 write_confidence_values: display ?
164 write_events: display ?
165 color_branches: display no
166 width_branches: display no
167 show_domain_architectures: display no
168 show_binary_characters: display no
169 show_binary_character_counts: display no
170 display_internal_data: display yes
171 dynamically_hide_data: display yes
172 show_relation_confidence: display no
173 show_vector_data: display no
176 # Combo-box Display Selection
177 # ---------------------------
178 # Format: 'name: display/nodisplay'
179 click_to: display_node_data display
180 click_to: collapse_uncollapse display
181 click_to: reroot display
182 click_to: subtree display
183 click_to: swap display
184 click_to: color_subtree display
185 click_to: open_seq_web display
186 click_to: open_tax_web display
187 click_to: cut_subtree display
188 click_to: copy_subtree display
189 click_to: paste_subtree display
190 click_to: delete display
191 click_to: add_new_node display
192 click_to: edit_node_data display
194 # Default click-to option (any of the above if set to "display")
195 default_click_to: display_node_data
199 # Default Tree Display Colors
200 # ---------------------------
202 display_color: background 0x000000
203 display_color: background_gradient_bottom 0x0000FF
204 display_color: sequence 0xDCDCDC
205 display_color: taxonomy 0xB4B4B4
206 display_color: confidence 0x38B0DE
207 display_color: branch_length 0x8C8C8C
208 display_color: branch 0xFFFFFF
209 display_color: node_box 0xFFFFFF
210 display_color: collapsed 0xFFFF00
211 display_color: matching_nodes 0x00FF00
212 display_color: duplication 0xFF0000
213 display_color: speciation 0x00FF00
214 display_color: duplication_or_specation 0xFFFF00
215 display_color: domains 0x7B68EE
216 display_color: binary_domain_combinations 0x4169FF
217 display_color: annotation 0xADFF2F
218 display_color: overview 0x828282
222 # GUI (graphical user interface) Colors
223 # -------------------------------------
225 # These are ignored if native (system) "look and feel"
226 # is being used ('native_ui: yes').
228 gui_background_color: 0x202020
229 gui_checkbox_text_color: 0xDCDCDC
230 gui_checkbox_and_button_active_color: 0xFF0000
231 gui_button_text_color: 0xFFFFFF
232 gui_button_background_color: 0x404040
233 gui_menu_background_color: 0x000000
234 gui_menu_text_color: 0xFFFFFF
235 gui_button_border_color: 0x000000
238 # Domain Structure Display Colors
239 # -------------------------------
240 domain_structure_base_color: 0x202020
241 domain_structure_font_color: 0x909090
247 # Format: web_link: <URL> <description> <source identifier>
248 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
249 # <description> is not used at the moment.
250 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
251 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
253 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
254 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
255 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
256 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
257 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
258 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
259 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
260 web_link: http://tolweb.org/ ToL tol
261 web_link: http://www.eol.org/pages/ EOL eol
262 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
263 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
264 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
265 # not working at the moment:
266 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
270 # Settings Specific for ArchaeopteryxE
271 # ------------------------------------
272 # To hide controls and menus: 'hide_controls_and_menus: yes'
273 # To use tabbed display : 'use_tabbed_display: yes'
275 hide_controls_and_menus: no
276 use_tabbed_display: yes
280 # Settings For Phylogenetic Inference
281 # -----------------------------------
282 # EXPERIMENTAL: DO NOT USE!!
284 default_number_of_bootstrap_resamples: 100
288 # Application Specific Settings
289 # -----------------------------
293 # Format: species_color: speciesname hexcolor
294 species_color: BRAFL 0x00FFFF
295 species_color: SPHGR 0x9620F0
296 species_color: STRPU 0x9620F0
297 species_color: CIOIN 0xFF1CAE
298 species_color: CIOSA 0xFF2CAE
299 species_color: BOVIN 0x5C3317
300 species_color: CANFA 0x8B2323
301 species_color: HUMAN 0xFF2400
302 species_color: PANTR 0xCC2400
303 species_color: MOUSE 0xFF7F00
304 species_color: RAT 0xFFEF00
305 species_color: MONDO 0xEE9A49
306 species_color: ORNAN 0xCD853F
307 species_color: XENLA 0x6BAA23
308 species_color: XENTR 0x6BAA23
309 species_color: CHICK 0xFFC125
310 species_color: FUGRU 0x0000FF
311 species_color: BRARE 0x0000DD
312 species_color: DANRE 0x0000BB
313 species_color: TETNG 0x0000AA
314 species_color: ORYLA 0x000088
315 species_color: GASAC 0x000066
316 species_color: CAEEL 0xA0A0A0
317 species_color: CAEBR 0xB0B0B0
318 species_color: DROME 0x706F00
319 species_color: DROPS 0x504F00
320 species_color: APIME 0x7A7700
321 species_color: AEDAE 0x8C5900
322 species_color: TRICA 0x918E00
323 species_color: NEMVE 0xAABADD
324 species_color: HYDAT 0x7C9BCF
325 species_color: LUBBA 0xF7B5CB
326 species_color: GEOCY 0xF5A0BD
327 species_color: SUBDO 0xC790B9
328 species_color: MONBE 0xFC0FC0
329 species_color: DICPU 0x23238E
330 species_color: DICDI 0x4D4DFF
331 species_color: ENTHI 0x5959AB
332 species_color: ARATH 0x00FF00
333 species_color: POPTR 0x006400
334 species_color: VITVI 0x00CD00
335 species_color: GLYMA 0x00FF7F
336 species_color: ORYSA 0x008B00
337 species_color: ORYSJ 0x008C00
338 species_color: SORBI 0x00EE76
339 species_color: SELMO 0x238E23
340 species_color: PHYPA 0x09F911
341 species_color: OSTLU 0x7FFF00
342 species_color: OSTTA 0x7FFF00
343 species_color: OSTRC 0x7FFF00
344 species_color: MICPU 0x66CD00
345 species_color: MIC99 0x66CD00
346 species_color: CHLRE 0xB3EE3A
347 species_color: VOLCA 0xC0FF3E
348 species_color: CHLSP 0x6B8E23
349 species_color: CYAME 0xD02090
350 species_color: YEAST 0xAAAAAA
351 species_color: BACFR 0xFF0000
352 species_color: BACTN 0xFFFF00
353 species_color: MYXXD 0x0000FF
354 species_color: STIAU 0x00FFFF
355 species_color: BACOV 0x8C5900
356 species_color: BACUN 0x66CD00
357 species_color: PORGI 0x918E00
363 domain_color: Cofilin_ADF 0xFC0FC0
364 domain_color: TIR 0x900000
365 domain_color: NACHT 0x202020
366 domain_color: CARD 0xFF0000
367 domain_color: Peptidase_C14 0x00FF00
368 domain_color: Death 0x0000FF
369 domain_color: DED 0x00FFFF
370 domain_color: BIR 0xCCFF33
371 domain_color: PAAD_DAPIN 0x9999CC
372 domain_color: NB-ARC 0x500050
373 domain_color: WD40 0x888888
374 domain_color: RVT_1 0x999900
375 domain_color: NOPS 0x505000
376 domain_color: RRM_1 0x004400
377 domain_color: fn3 0xFFCC00
378 domain_color: Ank 0xCC33FF
379 domain_color: Pkinase 0x339900
380 domain_color: Pkinase_Tyr 0x336600
381 domain_color: ig 0x660066
382 domain_color: zf-C3HC4 0x6699FF
383 domain_color: zf-CCHC 0x6699EE
384 domain_color: zf-C2H2 0x6699CC
385 domain_color: zf-B_box 0x6699DD
386 domain_color: PDZ 0x66FFCC
387 domain_color: SH3_2 0x996600
388 domain_color: MIRO 0xCCFF00
389 domain_color: Myb_DNA-binding 0xDDDDDD
390 domain_color: NHL 0x336666
391 domain_color: PKD_channel 0x336666
392 domain_color: Ion_trans 0x996666
393 domain_color: CAP_GLY 0xCC9900
394 domain_color: LRR_1 0xFFFF99
395 domain_color: LRR_2 0xFFFF66
396 domain_color: LRR_3 0xFFFF33
397 domain_color: LRR_adjacent 0xFFFF00
398 domain_color: LRRCT 0xFFCC99
399 domain_color: LRRNT 0xFFCC66
400 domain_color: LRRNT_2 0xFFCC33
401 domain_color: Ank 0x990099
402 domain_color: Sushi 0x004400
403 domain_color: ZU5 0xFF9999
404 domain_color: V-set 0x3399FF
405 domain_color: TPR_1 0xFF1493
406 domain_color: TPR_2 0xFF69B4
407 domain_color: TPR_3 0xCD6090
408 domain_color: TPR_4 0xFF6A6A
409 domain_color: TPR_MLP1_2 0x33FF00
410 domain_color: Collagen 0xFF7F00
411 domain_color: MIF 0xADD8E6
417 annotation_color: dehydrogenase 0x0000FF
418 annotation_color: kinase 0xFF00FF
419 annotation_color: protease 0x009900
420 annotation_color: transcription 0xAAAA00