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 # To determine what data field to return by clicking on "return external descendents data":
73 # 'ext_descendents_data_to_return'
74 # Possible values: node_name
79 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
80 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
81 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
82 # Number of fraction digits for branch length values: 'branch_length_value_digits'
83 # Number of fraction digits for confidence values: 'confidence_value_digits'
84 # To turn on/off background color gradient: background_gradient
85 # Example: 'background_gradient: yes'
86 # To allow/not allow editing (cut, copy, and paste): allow_editing
87 # Example: 'allow_editing: yes'
88 # To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
89 # 'replace_underscores_in_nh_parsing'
90 # To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
91 # during NH/NHX/Nexus file parsing (application only): 'extract_pfam_tax_codes_in_nh_parsing'
92 # Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
93 # 'internal_labels_are_confidence_values'
97 min_confidence_value: 0.0
98 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
100 antialias_screen: yes
102 show_branch_length_values: no
103 cladogram_type: ext_node_sum_dep
104 phylogeny_graphics_type: rectangular
105 node_label_direction: horizontal
106 show_default_node_shapes: no
108 default_node_shape: circle
109 default_node_fill: gradient
110 taxonomy_colorize_node_shapes: no
111 #graphics_export_x: 595
112 #graphics_export_y: 792
113 pdf_export_line_width: 0.5
117 overview_placement_type: upper_left
118 color_labels_same_as_branch_length_values: no
119 display_sequence_relations: no
120 show_domain_labels: yes
121 branch_length_value_digits: 3
122 confidence_value_digits: 3
123 background_gradient: no
125 # NH/NHX/Nexus file parsing (application only):
126 internal_labels_are_confidence_values: no
127 replace_underscores_in_nh_parsing: no
128 extract_taxonomy_codes_in_nh_parsing: yes
129 ext_descendents_data_to_return: sequence_mol_seq
134 # To ensure compatibility with all current and future
135 # phyloXML applications and to detect malformatted and
136 # possibly erroneous data, it is strongly recommended
137 # to enable validation of all phyloXML files
138 # against the XSD Schema (see: http://www.phyloxml.org/),
140 # 'validate_against_phyloxml_xsd_schema: true'
142 validate_against_phyloxml_xsd_schema: true
146 # Checkbox Display Selection
147 # --------------------------
148 # This is used to select which checkboxes to display
149 # and what their initial values should be.
150 # Format: 'name: display|nodisplay yes|no'
151 # Note: if an option is not displayed, it will not be enabled
153 # For the following use '?' to let Archaeopteryx decide (depending on tree):
155 # - 'write_confidence_values'
159 rollover: display yes
160 color_according_to_species: display yes
161 color_according_to_annotation: display no
162 show_node_names: display yes
163 show_gene_names: display yes
164 show_gene_symbols: display yes
165 show_sequence_acc: display no
166 show_taxonomy_code: display yes
167 show_taxonomy_scientific_names: display yes
168 show_taxonomy_common_names: display no
169 show_taxonomy_images: display yes
170 show_annotations: display no
171 write_confidence_values: display ?
172 write_events: display ?
173 color_branches: display no
174 width_branches: display no
175 show_domain_architectures: display no
176 show_binary_characters: display no
177 show_binary_character_counts: display no
178 display_internal_data: display yes
179 dynamically_hide_data: display yes
180 show_relation_confidence: display no
181 show_properties: display no
182 show_vector_data: display no
185 # Combo-box Display Selection
186 # ---------------------------
187 # Format: 'name: display/nodisplay'
188 click_to: display_node_data display
189 click_to: collapse_uncollapse display
190 click_to: reroot display
191 click_to: subtree display
192 click_to: swap display
193 click_to: sort_descendants display
194 click_to: color_subtree display
195 click_to: open_seq_web display
196 click_to: open_tax_web display
197 click_to: blast display
198 click_to: cut_subtree display
199 click_to: copy_subtree display
200 click_to: paste_subtree display
201 click_to: delete display
202 click_to: add_new_node display
203 click_to: edit_node_data display
204 click_to: get_ext_descendents_data display
206 # Default click-to option (any of the above if set to "display")
207 default_click_to: display_node_data
211 # Default Tree Display Colors
212 # ---------------------------
214 display_color: background 0x000000
215 display_color: background_gradient_bottom 0x0000FF
216 display_color: sequence 0xDCDCDC
217 display_color: taxonomy 0xB4B4B4
218 display_color: confidence 0x38B0DE
219 display_color: branch_length 0x8C8C8C
220 display_color: branch 0xFFFFFF
221 display_color: node_box 0xFFFFFF
222 display_color: collapsed 0xFFFF00
223 display_color: matching_nodes 0x00FF00
224 display_color: duplication 0xFF0000
225 display_color: speciation 0x00FF00
226 display_color: duplication_or_specation 0xFFFF00
227 display_color: domains 0x7B68EE
228 display_color: binary_domain_combinations 0x4169FF
229 display_color: annotation 0xADFF2F
230 display_color: overview 0x828282
234 # GUI (graphical user interface) Colors
235 # -------------------------------------
237 # These are ignored if native (system) "look and feel"
238 # is being used ('native_ui: yes').
240 gui_background_color: 0x202020
241 gui_checkbox_text_color: 0xDCDCDC
242 gui_checkbox_and_button_active_color: 0xFF0000
243 gui_button_text_color: 0xFFFFFF
244 gui_button_background_color: 0x404040
245 gui_menu_background_color: 0x000000
246 gui_menu_text_color: 0xFFFFFF
247 gui_button_border_color: 0x000000
250 # Domain Structure Display Colors
251 # -------------------------------
252 domain_structure_base_color: 0x202020
253 domain_structure_font_color: 0x909090
259 # Format: web_link: <URL> <description> <source identifier>
260 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
261 # <description> is not used at the moment.
262 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
263 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
265 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
266 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
267 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
268 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
269 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
270 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
271 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
272 web_link: http://tolweb.org/ ToL tol
273 web_link: http://www.eol.org/pages/ EOL eol
274 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
275 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
276 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
277 # not working at the moment:
278 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
282 # Settings Specific for ArchaeopteryxE
283 # ------------------------------------
284 # To hide controls and menus: 'hide_controls_and_menus: yes'
285 # To use tabbed display : 'use_tabbed_display: yes'
287 hide_controls_and_menus: no
288 use_tabbed_display: yes
292 # Settings For Phylogenetic Inference
293 # -----------------------------------
294 # EXPERIMENTAL: DO NOT USE!!
296 default_number_of_bootstrap_resamples: 100
297 mafft_local: /bin/mafft
298 clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
299 fastme_local: /bin/fastme
300 raxml_local: /bin/raxml
303 # Application Specific Settings
304 # -----------------------------
308 # Format: species_color: speciesname hexcolor
309 species_color: BRAFL 0x00FFFF
310 species_color: SPHGR 0x9620F0
311 species_color: STRPU 0x9620F0
312 species_color: CIOIN 0xFF1CAE
313 species_color: CIOSA 0xFF2CAE
314 species_color: BOVIN 0x5C3317
315 species_color: CANFA 0x8B2323
316 species_color: HUMAN 0xFF2400
317 species_color: PANTR 0xCC2400
318 species_color: MOUSE 0xFF7F00
319 species_color: RAT 0xFFEF00
320 species_color: MONDO 0xEE9A49
321 species_color: ORNAN 0xCD853F
322 species_color: XENLA 0x6BAA23
323 species_color: XENTR 0x6BAA23
324 species_color: CHICK 0xFFC125
325 species_color: FUGRU 0x0000FF
326 species_color: BRARE 0x0000DD
327 species_color: DANRE 0x0000BB
328 species_color: TETNG 0x0000AA
329 species_color: ORYLA 0x000088
330 species_color: GASAC 0x000066
331 species_color: CAEEL 0xA0A0A0
332 species_color: CAEBR 0xB0B0B0
333 species_color: DROME 0x706F00
334 species_color: DROPS 0x504F00
335 species_color: APIME 0x7A7700
336 species_color: AEDAE 0x8C5900
337 species_color: TRICA 0x918E00
338 species_color: NEMVE 0xAABADD
339 species_color: HYDAT 0x7C9BCF
340 species_color: LUBBA 0xF7B5CB
341 species_color: GEOCY 0xF5A0BD
342 species_color: SUBDO 0xC790B9
343 species_color: MONBE 0xFC0FC0
344 species_color: DICPU 0x23238E
345 species_color: DICDI 0x4D4DFF
346 species_color: ENTHI 0x5959AB
347 species_color: ARATH 0x00FF00
348 species_color: POPTR 0x006400
349 species_color: VITVI 0x00CD00
350 species_color: GLYMA 0x00FF7F
351 species_color: ORYSA 0x008B00
352 species_color: ORYSJ 0x008C00
353 species_color: SORBI 0x00EE76
354 species_color: SELMO 0x238E23
355 species_color: PHYPA 0x09F911
356 species_color: OSTLU 0x7FFF00
357 species_color: OSTTA 0x7FFF00
358 species_color: OSTRC 0x7FFF00
359 species_color: MICPU 0x66CD00
360 species_color: MIC99 0x66CD00
361 species_color: CHLRE 0xB3EE3A
362 species_color: VOLCA 0xC0FF3E
363 species_color: CHLSP 0x6B8E23
364 species_color: CYAME 0xD02090
365 species_color: YEAST 0xAAAAAA
366 species_color: BACFR 0xFF0000
367 species_color: BACTN 0xFFFF00
368 species_color: MYXXD 0x0000FF
369 species_color: STIAU 0x00FFFF
370 species_color: BACOV 0x8C5900
371 species_color: BACUN 0x66CD00
372 species_color: PORGI 0x918E00
374 species_color: Mammalia 0xFF0000
375 species_color: mammals 0xFF0000
377 species_color: Chordata 0x8470FF
378 species_color: Echinodermata 0x6495ED
379 species_color: Hemichordata 0x7EC0EE
380 species_color: Arthropoda 0x7AC5CD
381 species_color: Nematoda 0x7171C6
382 species_color: Tardigrada 0x388E8E
383 species_color: Annelida 0xC67171
384 species_color: Mollusca 0x00F5FF
385 species_color: Ctenophora 0xBBFFFF
386 species_color: Cnidaria 0xFF83FA
387 species_color: Placozoa 0xEED2EE
388 species_color: Porifera 0xFF3E96
389 species_color: Microsporidia 0x8B8378
390 species_color: Ascomycota 0xFF6347
391 species_color: Basidiomycota 0xFFD700
392 species_color: Chlorophyta 0x00C78C
393 species_color: Streptophyta 0x00C957
395 species_color: Viridiplantae 0x00FF00
396 species_color: plants 0x00FF00
397 species_color: Metazoa 0x0000FF
398 species_color: animals 0x0000FF
399 species_color: Fungi 0xFF9912
401 species_color: Viruses 0xFFD700
402 species_color: Bacteria 0x00FF00
403 species_color: Archaea 0x0000FF
404 species_color: Eukaryota 0xFF0000
405 species_color: eukaryotes 0xFF0000
410 domain_color: Cofilin_ADF 0xFC0FC0
411 domain_color: TIR 0x900000
412 domain_color: NACHT 0x202020
413 domain_color: CARD 0xFF0000
414 domain_color: Peptidase_C14 0x00FF00
415 domain_color: Death 0x0000FF
416 domain_color: DED 0x00FFFF
417 domain_color: BIR 0xCCFF33
418 domain_color: PAAD_DAPIN 0x9999CC
419 domain_color: NB-ARC 0x500050
420 domain_color: WD40 0x888888
421 domain_color: RVT_1 0x999900
422 domain_color: NOPS 0x505000
423 domain_color: RRM_1 0x004400
424 domain_color: fn3 0xFFCC00
425 domain_color: Ank 0xCC33FF
426 domain_color: Pkinase 0x339900
427 domain_color: Pkinase_Tyr 0x336600
428 domain_color: ig 0x660066
429 domain_color: zf-C3HC4 0x6699FF
430 domain_color: zf-CCHC 0x6699EE
431 domain_color: zf-C2H2 0x6699CC
432 domain_color: zf-B_box 0x6699DD
433 domain_color: PDZ 0x66FFCC
434 domain_color: SH3_2 0x996600
435 domain_color: MIRO 0xCCFF00
436 domain_color: Myb_DNA-binding 0xDDDDDD
437 domain_color: NHL 0x336666
438 domain_color: PKD_channel 0x336666
439 domain_color: Ion_trans 0x996666
440 domain_color: CAP_GLY 0xCC9900
441 domain_color: LRR_1 0xFFFF99
442 domain_color: LRR_2 0xFFFF66
443 domain_color: LRR_3 0xFFFF33
444 domain_color: LRR_adjacent 0xFFFF00
445 domain_color: LRRCT 0xFFCC99
446 domain_color: LRRNT 0xFFCC66
447 domain_color: LRRNT_2 0xFFCC33
448 domain_color: Ank 0x990099
449 domain_color: Sushi 0x004400
450 domain_color: ZU5 0xFF9999
451 domain_color: V-set 0x3399FF
452 domain_color: TPR_1 0xFF1493
453 domain_color: TPR_2 0xFF69B4
454 domain_color: TPR_3 0xCD6090
455 domain_color: TPR_4 0xFF6A6A
456 domain_color: TPR_MLP1_2 0x33FF00
457 domain_color: Collagen 0xFF7F00
458 domain_color: MIF 0xADD8E6
464 annotation_color: dehydrogenase 0x0000FF
465 annotation_color: kinase 0xFF00FF
466 annotation_color: protease 0x009900
467 annotation_color: transcription 0xAAAA00