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
73 # To determine what data field to return by clicking on "Return ...": 'ext_descendents_data_to_return'
74 # Possible values: node_name
79 # taxonomy_scientific_name
82 # To determine where to return data by clicking on "Return ...": 'ext_descendents_data_to_return_on'
83 # Possible values: window
85 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
86 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
88 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
89 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
90 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
91 # Number of fraction digits for branch length values: 'branch_length_value_digits'
92 # Number of fraction digits for confidence values: 'confidence_value_digits'
93 # To turn on/off background color gradient: background_gradient
94 # Example: 'background_gradient: yes'
95 # To allow/not allow editing (cut, copy, and paste): allow_editing
96 # Example: 'allow_editing: yes'
98 # NH/NHX/Nexus file parsing
99 # -------------------------
100 # To replace underscores with spaces during NH/NHX/Nexus file parsing (application only):
101 # 'replace_underscores_in_nh_parsing'
102 # To extract taxonomy codes from Pfam-style sequence labels (e.g. 'QW231_HUMAN/129-694')
103 # during NH/NHX/Nexus file parsing (application only): 'taxonomy_extraction_in_nh_parsing'
104 # Internal node labels are confidence values during NH/NHX/Nexus file parsing (application only):
105 # 'internal_labels_are_confidence_values'
111 # To ensure compatibility with all current and future
112 # phyloXML applications and to detect malformatted and
113 # possibly erroneous data, it is strongly recommended
114 # to enable validation of all phyloXML files
115 # against the XSD Schema (see: http://www.phyloxml.org/),
117 # 'validate_against_phyloxml_xsd_schema: true'
119 validate_against_phyloxml_xsd_schema: true
123 min_confidence_value: 0.0
124 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
126 antialias_screen: yes
128 show_branch_length_values: no
129 cladogram_type: ext_node_sum_dep
130 phylogeny_graphics_type: rectangular
131 node_label_direction: horizontal
132 show_default_node_shapes: no
134 default_node_shape: circle
135 default_node_fill: gradient
136 taxonomy_colorize_node_shapes: no
137 #graphics_export_x: 595
138 #graphics_export_y: 792
139 pdf_export_line_width: 0.5
143 overview_placement_type: upper_left
144 color_labels_same_as_branch_length_values: no
145 display_sequence_relations: no
146 show_domain_labels: yes
147 branch_length_value_digits: 3
148 confidence_value_digits: 3
149 background_gradient: no
151 # NH/NHX/Nexus file parsing (application only):
152 internal_labels_are_confidence_values: no
153 replace_underscores_in_nh_parsing: no
154 taxonomy_extraction_in_nh_parsing: pfam
155 ext_descendents_data_to_return_on: window
156 ext_descendents_data_to_return: user_selected
157 #label_for_get_ext_descendents_data: Get_Node_Data
161 # Checkbox Display Selection
162 # --------------------------
163 # This is used to select which checkboxes to display
164 # and what their initial values should be.
165 # Format: 'name: display|nodisplay yes|no'
166 # Note: if an option is not displayed, it will not be enabled
168 # For the following use '?' to let Archaeopteryx decide (depending on tree):
170 # - 'write_confidence_values'
174 rollover: display yes
175 color_according_to_species: display yes
176 color_according_to_annotation: display no
177 show_node_names: display yes
178 show_gene_names: display yes
179 show_gene_symbols: display yes
180 show_sequence_acc: display no
181 show_taxonomy_code: display yes
182 show_taxonomy_scientific_names: display yes
183 show_taxonomy_common_names: display no
184 show_taxonomy_images: display yes
185 show_annotations: display no
186 write_confidence_values: display ?
187 write_events: display ?
188 color_branches: display no
189 width_branches: display no
190 show_domain_architectures: display no
191 show_binary_characters: display no
192 show_binary_character_counts: display no
193 display_internal_data: display yes
194 dynamically_hide_data: display yes
195 show_relation_confidence: display no
196 show_properties: display no
197 show_vector_data: display no
201 # Combo-box Display Selection
202 # ---------------------------
203 # Format: 'name: display/nodisplay'
204 click_to: display_node_data display
205 click_to: collapse_uncollapse display
206 click_to: reroot display
207 click_to: subtree display
208 click_to: swap display
209 click_to: sort_descendants display
210 click_to: color_subtree display
211 click_to: open_seq_web display
212 click_to: open_tax_web display
213 click_to: blast display
214 click_to: cut_subtree display
215 click_to: copy_subtree display
216 click_to: paste_subtree display
217 click_to: delete display
218 click_to: add_new_node display
219 click_to: edit_node_data display
220 click_to: select_nodes display
221 click_to: get_ext_descendents_data display
223 # Default click-to option (any of the above if set to "display")
224 default_click_to: display_node_data
228 # Default Tree Display Colors
229 # ---------------------------
231 display_color: background 0x000000
232 display_color: background_gradient_bottom 0x0000FF
233 display_color: sequence 0xDCDCDC
234 display_color: taxonomy 0xB4B4B4
235 display_color: confidence 0x38B0DE
236 display_color: branch_length 0x8C8C8C
237 display_color: branch 0xFFFFFF
238 display_color: node_box 0xFFFFFF
239 display_color: collapsed 0xFFFF00
240 display_color: matching_nodes 0x00FF00
241 display_color: duplication 0xFF0000
242 display_color: speciation 0x00FF00
243 display_color: duplication_or_specation 0xFFFF00
244 display_color: domains 0x7B68EE
245 display_color: binary_domain_combinations 0x4169FF
246 display_color: annotation 0xADFF2F
247 display_color: overview 0x828282
251 # GUI (graphical user interface) Colors
252 # -------------------------------------
254 # These are ignored if native (system) "look and feel"
255 # is being used ('native_ui: yes').
257 gui_background_color: 0x202020
258 gui_checkbox_text_color: 0xDCDCDC
259 gui_checkbox_and_button_active_color: 0xFF0000
260 gui_button_text_color: 0xFFFFFF
261 gui_button_background_color: 0x404040
262 gui_menu_background_color: 0x000000
263 gui_menu_text_color: 0xFFFFFF
264 gui_button_border_color: 0x000000
268 # Domain Structure Display Colors
269 # -------------------------------
270 domain_structure_base_color: 0x202020
271 domain_structure_font_color: 0x909090
277 # Format: web_link: <URL> <description> <source identifier>
278 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
279 # <description> is not used at the moment.
280 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
281 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
283 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
284 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
285 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
286 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
287 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
288 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
289 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
290 web_link: http://tolweb.org/ ToL tol
291 web_link: http://www.eol.org/pages/ EOL eol
292 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
293 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
294 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
295 # not working at the moment:
296 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
300 # Settings Specific for ArchaeopteryxE
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 clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
317 fastme_local: /bin/fastme
318 raxml_local: /bin/raxml
321 # Application Specific Settings
322 # -----------------------------
326 # Format: species_color: speciesname hexcolor
327 species_color: BRAFL 0x00FFFF
328 species_color: SPHGR 0x9620F0
329 species_color: STRPU 0x9620F0
330 species_color: CIOIN 0xFF1CAE
331 species_color: CIOSA 0xFF2CAE
332 species_color: BOVIN 0x5C3317
333 species_color: CANFA 0x8B2323
334 species_color: HUMAN 0xFF2400
335 species_color: PANTR 0xCC2400
336 species_color: MOUSE 0xFF7F00
337 species_color: RAT 0xFFEF00
338 species_color: MONDO 0xEE9A49
339 species_color: ORNAN 0xCD853F
340 species_color: XENLA 0x6BAA23
341 species_color: XENTR 0x6BAA23
342 species_color: CHICK 0xFFC125
343 species_color: FUGRU 0x0000FF
344 species_color: BRARE 0x0000DD
345 species_color: DANRE 0x0000BB
346 species_color: TETNG 0x0000AA
347 species_color: ORYLA 0x000088
348 species_color: GASAC 0x000066
349 species_color: CAEEL 0xA0A0A0
350 species_color: CAEBR 0xB0B0B0
351 species_color: DROME 0x706F00
352 species_color: DROPS 0x504F00
353 species_color: APIME 0x7A7700
354 species_color: AEDAE 0x8C5900
355 species_color: TRICA 0x918E00
356 species_color: NEMVE 0xAABADD
357 species_color: HYDAT 0x7C9BCF
358 species_color: LUBBA 0xF7B5CB
359 species_color: GEOCY 0xF5A0BD
360 species_color: SUBDO 0xC790B9
361 species_color: MONBE 0xFC0FC0
362 species_color: DICPU 0x23238E
363 species_color: DICDI 0x4D4DFF
364 species_color: ENTHI 0x5959AB
365 species_color: ARATH 0x00FF00
366 species_color: POPTR 0x006400
367 species_color: VITVI 0x00CD00
368 species_color: GLYMA 0x00FF7F
369 species_color: ORYSA 0x008B00
370 species_color: ORYSJ 0x008C00
371 species_color: SORBI 0x00EE76
372 species_color: SELMO 0x238E23
373 species_color: PHYPA 0x09F911
374 species_color: OSTLU 0x7FFF00
375 species_color: OSTTA 0x7FFF00
376 species_color: OSTRC 0x7FFF00
377 species_color: MICPU 0x66CD00
378 species_color: MIC99 0x66CD00
379 species_color: CHLRE 0xB3EE3A
380 species_color: VOLCA 0xC0FF3E
381 species_color: CHLSP 0x6B8E23
382 species_color: CYAME 0xD02090
383 species_color: YEAST 0xAAAAAA
384 species_color: BACFR 0xFF0000
385 species_color: BACTN 0xFFFF00
386 species_color: MYXXD 0x0000FF
387 species_color: STIAU 0x00FFFF
388 species_color: BACOV 0x8C5900
389 species_color: BACUN 0x66CD00
390 species_color: PORGI 0x918E00
392 species_color: Mammalia 0xFF0000
393 species_color: mammals 0xFF0000
395 species_color: Chordata 0x8470FF
396 species_color: Echinodermata 0x6495ED
397 species_color: Hemichordata 0x7EC0EE
398 species_color: Arthropoda 0x7AC5CD
399 species_color: Nematoda 0x7171C6
400 species_color: Tardigrada 0x388E8E
401 species_color: Annelida 0xC67171
402 species_color: Mollusca 0x00F5FF
403 species_color: Ctenophora 0xBBFFFF
404 species_color: Cnidaria 0xFF83FA
405 species_color: Placozoa 0xEED2EE
406 species_color: Porifera 0xFF3E96
407 species_color: Microsporidia 0x8B8378
408 species_color: Ascomycota 0xFF6347
409 species_color: Basidiomycota 0xFFD700
410 species_color: Chlorophyta 0x00C78C
411 species_color: Streptophyta 0x00C957
413 species_color: Viridiplantae 0x00FF00
414 species_color: plants 0x00FF00
415 species_color: Metazoa 0x0000FF
416 species_color: animals 0x0000FF
417 species_color: Fungi 0xFF9912
419 species_color: Viruses 0xFFD700
420 species_color: Bacteria 0x00FF00
421 species_color: Archaea 0x0000FF
422 species_color: Eukaryota 0xFF0000
423 species_color: eukaryotes 0xFF0000
428 domain_color: Cofilin_ADF 0xFC0FC0
429 domain_color: TIR 0x900000
430 domain_color: NACHT 0x202020
431 domain_color: CARD 0xFF0000
432 domain_color: Peptidase_C14 0x00FF00
433 domain_color: Death 0x0000FF
434 domain_color: DED 0x00FFFF
435 domain_color: BIR 0xCCFF33
436 domain_color: PAAD_DAPIN 0x9999CC
437 domain_color: NB-ARC 0x500050
438 domain_color: WD40 0x888888
439 domain_color: RVT_1 0x999900
446 annotation_color: dehydrogenase 0x0000FF
447 annotation_color: kinase 0xFF00FF
448 annotation_color: protease 0x009900
449 annotation_color: transcription 0xAAAA00