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
83 # To determine where to return data selected by user clicking on "Return ...": 'ext_descendents_data_to_return_on'
84 # Contents of buffer can be obtained with method 'getCurrentExternalNodesDataBuffer()' of
85 # classes org.forester.archaeopteryx.MainFrame and org.forester.archaeopteryx.ArchaeopteryxE
86 # Possible values: window (for output to window and buffer)
87 # console (for output to console and buffer)
88 # buffer_only (for output to buffer only)
90 # To override label for menu item to return data of external nodes (default ""Return ..."): 'label_for_get_ext_descendents_data'
91 # Example: 'label_for_get_ext_descendents_data: Get_Node_Data'
93 # Taxonomy colorization of nodes (shapes) instead of labels: 'taxonomy_colorize_node_shapes': values: 'yes'/'no'
94 # Do/not color labels same as branch length values: 'color_labels_same_as_branch_length_values': values: 'yes'/'no'
95 # Do/not show domain labels: 'show_domain_labels': values: 'yes'/'no'
96 # Number of fraction digits for branch length values: 'branch_length_value_digits'
97 # Number of fraction digits for confidence values: 'confidence_value_digits'
98 # To turn on/off background color gradient: background_gradient
99 # Example: 'background_gradient: yes'
100 # To allow/not allow editing (cut, copy, and paste): allow_editing
101 # Example: 'allow_editing: yes'
103 # NH/NHX/Nexus file parsing
104 # -------------------------
105 # To replace underscores with spaces during NH/NHX/Nexus file parsing:
106 # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no'
108 # To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing:
109 # 'taxonomy_extraction_in_nh_parsing',
110 # possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no'
112 # Internal node labels are confidence values during NH/NHX/Nexus file parsing:
113 # 'internal_labels_are_confidence_values', possible values are 'yes', 'no'
119 # To ensure compatibility with all current and future
120 # phyloXML applications and to detect malformatted and
121 # possibly erroneous data, it is strongly recommended
122 # to enable validation of all phyloXML files
123 # against the XSD Schema (see: http://www.phyloxml.org/),
125 # 'validate_against_phyloxml_xsd_schema: true'
127 validate_against_phyloxml_xsd_schema: true
131 min_confidence_value: 0.0
132 font_family: Verdana,Tahoma,Arial,Helvetica,Dialog,Lucida-Sans,SansSerif,Sans-serif,Sans
134 antialias_screen: yes
136 show_branch_length_values: no
137 cladogram_type: ext_node_sum_dep
138 phylogeny_graphics_type: rectangular
139 node_label_direction: horizontal
140 show_default_node_shapes: no
142 default_node_shape: circle
143 default_node_fill: gradient
144 taxonomy_colorize_node_shapes: no
145 #graphics_export_x: 595
146 #graphics_export_y: 792
147 pdf_export_line_width: 0.5
151 overview_placement_type: upper_left
152 color_labels_same_as_branch_length_values: no
153 display_sequence_relations: no
154 show_domain_labels: yes
155 branch_length_value_digits: 3
156 confidence_value_digits: 3
157 background_gradient: no
159 ext_descendents_data_to_return_on: window
160 ext_descendents_data_to_return: user_selected
161 #label_for_get_ext_descendents_data: Get_Node_Data
162 # NH/NHX/Nexus file parsing:
163 internal_labels_are_confidence_values: no
164 replace_underscores_in_nh_parsing: no
165 taxonomy_extraction_in_nh_parsing: pfam
169 # Initial Window Size for Application and ArchaeopteryA applet
170 # ------------------------------------------------------------
171 window_initial_size_x: 800
172 window_initial_size_y: 800
176 # Checkbox Display Selection
177 # --------------------------
178 # This is used to select which checkboxes to display
179 # and what their initial values should be.
180 # Format: 'name: display|nodisplay yes|no'
181 # Note: if an option is not displayed, it will not be enabled
183 # For the following use '?' to let Archaeopteryx decide (depending on tree):
185 # - 'write_confidence_values'
189 rollover: display yes
190 color_according_to_species: display yes
191 color_according_to_annotation: display no
192 show_node_names: display yes
193 show_gene_names: display yes
194 show_gene_symbols: display yes
195 show_sequence_acc: display no
196 show_taxonomy_code: display yes
197 show_taxonomy_scientific_names: display yes
198 show_taxonomy_common_names: display no
199 show_taxonomy_images: display yes
200 show_annotations: display no
201 write_confidence_values: display ?
202 write_events: display ?
203 color_branches: display no
204 width_branches: display no
205 show_domain_architectures: display no
206 show_binary_characters: display no
207 show_binary_character_counts: display no
208 display_internal_data: display yes
209 dynamically_hide_data: display yes
210 show_relation_confidence: nodisplay no
211 show_properties: nodisplay no
212 show_vector_data: nodisplay no
216 # Combo-box Display Selection
217 # ---------------------------
218 # Format: 'name: display/nodisplay'
219 click_to: display_node_data display
220 click_to: collapse_uncollapse display
221 click_to: reroot display
222 click_to: subtree display
223 click_to: swap display
224 click_to: sort_descendants display
225 click_to: color_subtree display
226 click_to: open_seq_web display
227 click_to: open_tax_web display
228 click_to: blast display
229 click_to: cut_subtree display
230 click_to: copy_subtree display
231 click_to: paste_subtree display
232 click_to: delete display
233 click_to: add_new_node display
234 click_to: edit_node_data display
235 click_to: select_nodes display
236 click_to: get_ext_descendents_data display
238 # Default click-to option (any of the above if set to "display")
239 default_click_to: display_node_data
243 # Default Tree Display Colors
244 # ---------------------------
246 display_color: background 0x000000
247 display_color: background_gradient_bottom 0x0000FF
248 display_color: sequence 0xDCDCDC
249 display_color: taxonomy 0xB4B4B4
250 display_color: confidence 0x38B0DE
251 display_color: branch_length 0x8C8C8C
252 display_color: branch 0xFFFFFF
253 display_color: node_box 0xFFFFFF
254 display_color: collapsed 0xFFFF00
255 display_color: matching_nodes 0x00FF00
256 display_color: duplication 0xFF0000
257 display_color: speciation 0x00FF00
258 display_color: duplication_or_specation 0xFFFF00
259 display_color: domains 0x7B68EE
260 display_color: binary_domain_combinations 0x4169FF
261 display_color: annotation 0xADFF2F
262 display_color: overview 0x828282
266 # GUI (graphical user interface) Colors
267 # -------------------------------------
269 # These are ignored if native (system) "look and feel"
270 # is being used ('native_ui: yes').
272 gui_background_color: 0x202020
273 gui_checkbox_text_color: 0xDCDCDC
274 gui_checkbox_and_button_active_color: 0xFF0000
275 gui_button_text_color: 0xFFFFFF
276 gui_button_background_color: 0x404040
277 gui_menu_background_color: 0x000000
278 gui_menu_text_color: 0xFFFFFF
279 gui_button_border_color: 0x000000
283 # Domain Structure Display Colors
284 # -------------------------------
285 domain_structure_base_color: 0x202020
286 domain_structure_font_color: 0x909090
292 # Format: web_link: <URL> <description> <source identifier>
293 # E.g. "http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB"
294 # <description> is not used at the moment.
295 # <source identifier> corresponds to the <source> element for <sequence> <accession>,
296 # and to the <type> of <taxonomy> <id> (see www.phyloxml.org).
298 web_link: http://www.uniprot.org/uniprot/?query= UniProtKB UniProtKB
299 web_link: http://www.uniprot.org/uniprot/?query= SPTREMBL sptrembl
300 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= NCBI GI
301 web_link: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?cmd=Retrieve&val= RefSeq RefSeq
302 web_link: http://www.ebi.ac.uk/interpro/IEntry?ac= InterPro InterPro
303 web_link: http://www.rcsb.org/pdb/explore.do?structureId= PDB PDB
304 web_link: http://pfam.sanger.ac.uk/protein?entry= Pfam pfam
305 web_link: http://tolweb.org/ ToL tol
306 web_link: http://www.eol.org/pages/ EOL eol
307 web_link: http://www.uniprot.org/taxonomy/ UniProt-Taxonomy uniprot
308 web_link: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id= NCBI-Taxonomy ncbi
309 web_link: http://www.ubio.org/browser/details.php?namebankID= uBio namebankID
310 # not working at the moment:
311 web_link: http://www.ensembl.org/Homo_sapiens/Search/Summary?species=all;idx=;q= Ensembl Ensembl
315 # Settings Specific for ArchaeopteryxE
316 # ------------------------------------
317 # To hide controls and menus: 'hide_controls_and_menus: yes'
318 # To use tabbed display : 'use_tabbed_display: yes'
320 hide_controls_and_menus: no
321 use_tabbed_display: yes
325 # Settings For Phylogenetic Inference
326 # -----------------------------------
327 # EXPERIMENTAL: DO NOT USE!!
329 default_number_of_bootstrap_resamples: 100
330 mafft_local: /bin/mafft
331 clustalo_local: C:\Users\zma\SOFTWARE\clustal-omega-1.1.0-win32\clustalo.exe
332 fastme_local: /bin/fastme
333 raxml_local: /bin/raxml
336 # Application Specific Settings
337 # -----------------------------
341 # Format: species_color: speciesname hexcolor
342 species_color: BRAFL 0x00FFFF
343 species_color: SPHGR 0x9620F0
344 species_color: STRPU 0x9620F0
345 species_color: CIOIN 0xFF1CAE
346 species_color: CIOSA 0xFF2CAE
347 species_color: BOVIN 0x5C3317
348 species_color: CANFA 0x8B2323
349 species_color: HUMAN 0xFF2400
350 species_color: PANTR 0xCC2400
351 species_color: MOUSE 0xFF7F00
352 species_color: RAT 0xFFEF00
353 species_color: MONDO 0xEE9A49
354 species_color: ORNAN 0xCD853F
355 species_color: XENLA 0x6BAA23
356 species_color: XENTR 0x6BAA23
357 species_color: CHICK 0xFFC125
358 species_color: FUGRU 0x0000FF
359 species_color: BRARE 0x0000DD
360 species_color: DANRE 0x0000BB
361 species_color: TETNG 0x0000AA
362 species_color: ORYLA 0x000088
363 species_color: GASAC 0x000066
364 species_color: CAEEL 0xA0A0A0
365 species_color: CAEBR 0xB0B0B0
366 species_color: DROME 0x706F00
367 species_color: DROPS 0x504F00
368 species_color: APIME 0x7A7700
369 species_color: AEDAE 0x8C5900
370 species_color: TRICA 0x918E00
371 species_color: NEMVE 0xAABADD
372 species_color: HYDAT 0x7C9BCF
373 species_color: LUBBA 0xF7B5CB
374 species_color: GEOCY 0xF5A0BD
375 species_color: SUBDO 0xC790B9
376 species_color: MONBE 0xFC0FC0
377 species_color: DICPU 0x23238E
378 species_color: DICDI 0x4D4DFF
379 species_color: ENTHI 0x5959AB
380 species_color: ARATH 0x00FF00
381 species_color: POPTR 0x006400
382 species_color: VITVI 0x00CD00
383 species_color: GLYMA 0x00FF7F
384 species_color: ORYSA 0x008B00
385 species_color: ORYSJ 0x008C00
386 species_color: SORBI 0x00EE76
387 species_color: SELMO 0x238E23
388 species_color: PHYPA 0x09F911
389 species_color: OSTLU 0x7FFF00
390 species_color: OSTTA 0x7FFF00
391 species_color: OSTRC 0x7FFF00
392 species_color: MICPU 0x66CD00
393 species_color: MIC99 0x66CD00
394 species_color: CHLRE 0xB3EE3A
395 species_color: VOLCA 0xC0FF3E
396 species_color: CHLSP 0x6B8E23
397 species_color: CYAME 0xD02090
398 species_color: YEAST 0xAAAAAA
399 species_color: BACFR 0xFF0000
400 species_color: BACTN 0xFFFF00
401 species_color: MYXXD 0x0000FF
402 species_color: STIAU 0x00FFFF
403 species_color: BACOV 0x8C5900
404 species_color: BACUN 0x66CD00
405 species_color: PORGI 0x918E00
407 species_color: Mammalia 0xFF0000
408 species_color: mammals 0xFF0000
410 species_color: Chordata 0x8470FF
411 species_color: Echinodermata 0x6495ED
412 species_color: Hemichordata 0x7EC0EE
413 species_color: Arthropoda 0x7AC5CD
414 species_color: Nematoda 0x7171C6
415 species_color: Tardigrada 0x388E8E
416 species_color: Annelida 0xC67171
417 species_color: Mollusca 0x00F5FF
418 species_color: Ctenophora 0xBBFFFF
419 species_color: Cnidaria 0xFF83FA
420 species_color: Placozoa 0xEED2EE
421 species_color: Porifera 0xFF3E96
422 species_color: Microsporidia 0x8B8378
423 species_color: Ascomycota 0xFF6347
424 species_color: Basidiomycota 0xFFD700
425 species_color: Chlorophyta 0x00C78C
426 species_color: Streptophyta 0x00C957
428 species_color: Viridiplantae 0x00FF00
429 species_color: plants 0x00FF00
430 species_color: Metazoa 0x0000FF
431 species_color: animals 0x0000FF
432 species_color: Fungi 0xFF9912
434 species_color: Viruses 0xFFD700
435 species_color: Bacteria 0x00FF00
436 species_color: Archaea 0x0000FF
437 species_color: Eukaryota 0xFF0000
438 species_color: eukaryotes 0xFF0000
443 domain_color: Cofilin_ADF 0xFC0FC0
444 domain_color: TIR 0x900000
445 domain_color: NACHT 0x202020
446 domain_color: CARD 0xFF0000
447 domain_color: Peptidase_C14 0x00FF00
448 domain_color: Death 0x0000FF
449 domain_color: DED 0x00FFFF
450 domain_color: BIR 0xCCFF33
451 domain_color: PAAD_DAPIN 0x9999CC
452 domain_color: NB-ARC 0x500050
453 domain_color: WD40 0x888888
454 domain_color: RVT_1 0x999900
461 annotation_color: dehydrogenase 0x0000FF
462 annotation_color: kinase 0xFF00FF
463 annotation_color: protease 0x009900
464 annotation_color: transcription 0xAAAA00