1 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
4 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
5 * Copyright (C) 2014 The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Alignment Window Menus</title>
\r
27 <p> <strong>Alignment Window Menus x</strong> </p>
\r
31 <li><strong>File</strong>
\r
33 <li><strong>Fetch Sequence</strong><br>
\r
34 <em>Shows a dialog window in which you can retrieve known ids
\r
35 from Uniprot, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web
\r
36 Services provided by the European Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
\r
37 <li><strong>Add Sequences</strong><em><br>
\r
38 Add sequences to the visible alignment from file, URL, or cut &
\r
39 paste window </em> </li>
\r
40 <li><strong>Reload</strong><em><br>
\r
41 Reloads the alignment from the original file, if available.<br>
\r
42 <strong>Warning: This will delete any edits, analyses and
\r
43 colourings applied since the alignment was last saved, and cannot be
\r
44 undone.</strong> </em> </li>
\r
45 <li><strong>Save (Control S)</strong><em><br>
\r
46 Saves the alignment to the file it was loaded from (if available), in
\r
47 the same format, updating the original in place. </em> </li>
\r
48 <li><strong>Save As (Control Shift S)<br>
\r
49 </strong><em>Save the alignment to local file. A file selection
\r
50 window will open, use the "Files of type:" selection box to determine
\r
51 which <a href="../io/index.html">alignment format</a> to save as.</em>
\r
53 <li><strong>Output to Textbox<br>
\r
54 </strong><em>The alignment will be displayed in plain text in a
\r
55 new window, which you can "Copy and Paste" using the pull down menu, or
\r
56 your standard operating system copy and paste keys. The output window
\r
57 also has a <strong>"New Window"</strong> button to import the
\r
58 (possibly edited) text as a new alignment.<br>
\r
59 Select the format of the text by selecting one of the following menu
\r
62 <#list format_adapters as format_adapter>
63 <li><strong>${format_adapter}</strong> </li>
66 <!--<li><strong>FASTA</strong> <em></em> </li>
\r
67 <li><strong>MSF</strong> </li>
\r
68 <li><strong>CLUSTAL</strong> </li>
\r
69 <li><strong>BLC</strong> </li>
\r
70 <li><strong>PIR</strong> </li>
\r
71 <li><strong>PFAM</strong> </li> -->
\r
74 <li><strong>Print (Control P)<br>
\r
75 </strong><em>Jalview will print the alignment using the current
\r
76 fonts and colours of your alignment. If the alignment has annotations
\r
77 visible, these will be printed below the alignment. If the alignment is
\r
78 wrapped the number of residues per line of your alignment will depend
\r
79 on the paper width or your alignment window width, whichever is the
\r
80 smaller. </em> </li>
\r
81 <li><strong>Export Image</strong> <em><br>
\r
82 Creates an alignment graphic with the current view's annotation,
\r
83 alignment background colours and group colours. If the alignment is <a href="../features/wrap.html">wrapped</a>, the output will also be
\r
84 wrapped and will have the same visible residue width as the open
\r
87 <li><strong>HTML<br>
\r
88 </strong><em>Create a <a href="../io/export.html">web page</a>
\r
89 from your alignment.</em> </li>
\r
91 </strong><em>Create an <a href="../io/export.html">Encapsulated
\r
92 Postscript</a> file from your alignment.</em> </li>
\r
94 </strong><em>Create a <a href="../io/export.html">Portable
\r
95 Network Graphics</a> file from your alignment.</em> </li>
\r
98 <li><strong>Export Features</strong><em><br>
\r
99 All features visible on the alignment can be saved to file or displayed
\r
100 in a textbox in either Jalview or GFF format</em> </li>
\r
101 <li><strong>Export Annotations</strong><em><br>
\r
102 All annotations visible on the alignment can be saved to file or
\r
103 displayed in a textbox in Jalview annotations format. </em> </li>
\r
104 <li><strong>Load Associated Tree<br>
\r
105 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view trees</a> stored in the
\r
106 Newick file format, and associate them with the alignment. Note: the
\r
107 ids of the tree file and your alignment MUST be the same.</em></li>
\r
108 <li><strong>Load Features / Annotations<br>
\r
109 </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence features</a> or <a href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
\r
110 <li><strong>Close (Control W)</strong><br>
\r
111 <em>Close the alignment window. Make sure you have saved your
\r
112 alignment before you close - either as a Jalview project or by using
\r
113 the <strong>Save As</strong> menu.</em> </li>
\r
116 <li><strong>Edit</strong>
\r
118 <li><strong>Undo (Control Z)</strong><em><br>
\r
119 This will undo any edits you make to the alignment. This applies to
\r
120 insertion or deletion of gaps, cutting residues or sequences from the
\r
121 alignment or pasting sequences to the current alignment or sorting the
\r
122 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
\r
123 adjustments to group sizes, or changes to the annotation panel. </em> </li>
\r
124 <li><strong>Redo (Control Y)<br>
\r
125 </strong><em>Any actions which you undo can be redone using
\r
127 <li><strong>Cut (Control X)<br>
\r
128 </strong><em>This will make a copy of the currently selected
\r
129 residues before removing them from your alignment. Click on a sequence
\r
130 name if you wish to select a whole sequence. <br>
\r
131 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em> </li>
\r
132 <li><strong>Copy (Control C)</strong><br>
\r
133 <em>Copies the currently selected residues to the system
\r
134 clipboard - you can also do this by pressing <CTRL> and C
\r
135 (<APPLE> and C on MacOSX). <br>
\r
136 If you try to paste the clipboard contents to a text editor, you will
\r
137 see the format of the copied residues FASTA.</em></li>
\r
138 <li><strong>Paste </strong>
\r
140 <li><strong>To New Alignment (Control Shift V)<br>
\r
141 </strong><em>A new alignment window will be created from
\r
142 sequences previously copied or cut to the system clipboard. <br>
\r
143 Use <CTRL> and <SHIFT> and V(<APPLE> and
\r
144 <SHIFT;> and and V on MacOSX) to paste.</em> </li>
\r
145 <li><strong>Add To This Alignment (Control V)<br>
\r
146 </strong><em>Copied sequences from another alignment window
\r
147 can be added to the current Jalview alignment. </em> </li>
\r
150 <li><strong>Delete (Backspace)<br>
\r
151 </strong><em>This will delete the currently selected residues
\r
152 without copying them to the clipboard. Like the other edit operations,
\r
153 this can be undone with <strong>Undo</strong>.</em> </li>
\r
154 <li><strong>Remove Left (Control L)<br>
\r
155 </strong><em>If the alignment has marked columns, the alignment
\r
156 will be trimmed to the left of the leftmost marked column. To mark a
\r
157 column, mouse click the scale bar above the alignment. Click again to
\r
158 unmark a column, or select "Deselect All" to deselect all columns.</em></li>
\r
159 <li><strong>Remove Right (Control R)<br>
\r
160 </strong><em>If the alignment has marked columns, the alignment
\r
161 will be trimmed to the left of the leftmost marked column. To mark a
\r
162 column, mouse click the scale bar above the alignment. Click again to
\r
163 unmark a column, or select "Deselect All" to deselect all columns.</em></li>
\r
164 <li><strong>Remove Empty Columns (Control E)<br>
\r
165 </strong><em>All columns which only contain gap characters
\r
166 ("-", ".") will be deleted.<br>
\r
167 You may set the default gap character in <a href="../features/preferences.html">preferences</a>. </em> </li>
\r
168 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
\r
169 <em>Gap characters ("-", ".") will be deleted from the selected
\r
170 area of the alignment. If no selection is made, ALL the gaps in the
\r
171 alignment will be removed.<br>
\r
172 You may set the default gap character in <a href="../features/preferences.html">preferences</a>. </em> </li>
\r
173 <li><strong>Remove Redundancy (Control D)<br>
\r
174 </strong><em>Selecting this option brings up a window asking
\r
175 you to select a threshold. If the percentage identity between any two
\r
176 sequences (under the current alignment) exceeds this value then one of
\r
177 the sequences (the shorter) is discarded. Press the "Apply" button to
\r
178 remove redundant sequences. The "Undo" button will undo the last
\r
179 redundancy deletion.</em> </li>
\r
180 <li><strong>Pad Gaps<br>
\r
181 </strong><em>When selected, the alignment will be kept at
\r
182 minimal width (so there no empty columns before or after the first or
\r
183 last aligned residue) and all sequences will be padded with gap
\r
184 characters to the before and after their terminating residues.<br>
\r
185 This switch is useful when making a tree using unaligned sequences and
\r
186 when working with alignment analysis programs which require 'properly
\r
187 aligned sequences' to be all the same length.<br>
\r
188 You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>. </em> </li>
\r
191 <li><strong>Select</strong>
\r
193 <li><strong><a href="../features/search.html">Find... (Control F)</a>
\r
195 Opens the Find dialog box to search for residues, sequence name or
\r
196 residue position within the alignment and create new sequence features
\r
197 from the queries. </em> </li>
\r
198 <li><strong>Select All (Control A)<br>
\r
199 </strong><em>Selects all the sequences and residues in the
\r
201 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
\r
202 <li><strong>Deselect All (Escape)<br>
\r
203 </strong><em>Removes the current selection box (red dashed box)
\r
204 from the alignment window. All selected sequences, residues and marked
\r
205 columns will be deselected. </em><em> <br>
\r
206 Use <ESCAPE> to deselect all.</em></li>
\r
207 <li><strong>Invert Sequence Selection (Control I)<br>
\r
208 </strong><em>Any sequence ids currently not selected will
\r
209 replace the current selection. </em> </li>
\r
210 <li><strong>Invert Column Selection (Control Alt I)<br>
\r
211 </strong><em>Any columns currently not selected will replace
\r
212 the current column selection. </em> </li>
\r
213 <li><strong>Create Group (Control G)<br>
\r
214 </strong> <em>Create a group containing the currently selected
\r
215 sequences.</em></li>
\r
216 <li><strong>Remove Group (Shift Control G)<br>
\r
217 </strong> <em>Ungroup the currently selected sequence group.
\r
218 (Create/Remove group new in Jalview 2.8.1)</em></li>
\r
219 <li><strong>Make Groups for selection<br>
\r
220 </strong> <em>The currently selected groups of the alignment
\r
221 will be subdivided according to the contents of the currently selected
\r
223 Use this to subdivide an alignment based on the different combinations
\r
224 of residues observed at specific positions. (new in jalview 2.5)</em> </li>
\r
225 <li><strong>Undefine Groups (Control U)<br>
\r
226 </strong><em>The alignment will be reset with no defined groups.<br>
\r
227 <strong>WARNING</strong>: This cannot be undone.</em> </li>
\r
230 <li><strong>View</strong>
\r
232 <li><strong>New View (Control T)</strong><em><br>
\r
233 Creates a new view from the current alignment view. </em> </li>
\r
234 <li><strong>Expand Views (X)</strong><em><br>
\r
235 Display each view associated with the alignment in its own alignment
\r
236 window, allowing several views to be displayed simultaneously. </em> </li>
\r
237 <li><strong>Gather Views (G)</strong><em><br>
\r
238 Each view associated with the alignment will be displayed within its
\r
239 own tab on the current alignment window. </em> </li>
\r
240 <li><strong>Show→(all Columns / Sequences / Sequences and Columns)</strong><em><br>
\r
241 All hidden Columns / Sequences / Sequences and Columns will be
\r
242 revealed. </em> </li>
\r
243 <li><strong>Hide→(all Columns / Sequences / Selected Region / All
\r
244 but Selected Region )</strong><em><br>
\r
245 Hides the all the currently selected Columns / Sequences / Region or
\r
246 everything but the selected Region.</em> </li>
\r
247 <li><strong>Automatic Scrolling<br>
\r
248 </strong><em>When selected, the view will automatically scroll
\r
249 to display the highlighted sequence position corresponding to the
\r
250 position under the mouse pointer in a linked alignment or structure
\r
252 <li><strong>Show Annotations<br>
\r
253 </strong><em>If this is selected the "Annotation Panel" will be
\r
254 displayed below the alignment. The default setting is to display the
\r
255 conservation calculation, quality calculation and consensus values as
\r
256 bar charts. </em> </li>
\r
257 <li><strong>Autocalculated Annotation<br>
\r
258 </strong><em>Settings for the display of autocalculated
\r
261 <li><strong>Apply to all groups<br>
\r
262 </strong><em> When ticked, any modification to the current
\r
263 settings will be applied to all autocalculated annotation.</em></li>
\r
264 <li><strong>Show Consensus Histogram<br>
\r
265 </strong><em> Enable or disable the display of the
\r
266 histogram above the consensus sequence.</em></li>
\r
267 <li><strong>Show Consensus Logo<br>
\r
268 </strong><em> Enable or disable the display of the
\r
269 Consensus Logo above the consensus sequence.</em></li>
\r
270 <li><strong>Normalise Consensus Logo<br>
\r
271 </strong><em>When enabled, scales all logo stacks to the
\r
272 same height, making it easier to compare symbol diversity in highly
\r
273 variable regions.</em></li>
\r
274 <li><strong>Group Conservation<br>
\r
275 </strong><em> When ticked, display a conservation row for
\r
276 all groups (only available for protein alignments).</em></li>
\r
277 <li><strong>Apply to all groups<br>
\r
278 </strong><em> When ticked, display a consensus row for all
\r
282 <li><strong>Show Sequence Features</strong><br>
\r
283 <em>Show or hide sequence features on this alignment.</em> </li>
\r
284 <li><strong><a href="../features/featuresettings.html">Seqence
\r
285 Feature Settings...</a> </strong><em><br>
\r
286 <em>Opens the Sequence Feature Settings dialog box to control
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287 the colour and display of sequence features on the alignment, and
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288 configure and retrieve features from DAS annotation servers.</em> </em></li>
\r
290 <li><em><strong>Sequence ID Tooltip</strong><em> (application
\r
292 This submenu's options allow the inclusion or exclusion of
\r
293 non-positional sequence features or database cross references from the
\r
294 tooltip shown when the mouse hovers over the sequence ID panel.</em> </em></li>
\r
296 <li><em><strong>Alignment Properties...<br>
\r
297 </strong><em>Displays some simple statistics computed for the
\r
298 current alignment view and any named properties defined on the whole
\r
299 alignment.</em> </em></li>
\r
301 <li><em><strong><a href="../features/overview.html">Overview
\r
303 </strong><em>A scaled version of the alignment will be
\r
304 displayed in a small window. A red box will indicate the currently
\r
305 visible area of the alignment. Move the visible region using the mouse.
\r
311 <li><em><strong>Alignment Window Format Menu</strong> </em>
\r
314 <li><em><strong>Font...<br>
\r
315 </strong><em>Opens the "Choose Font" dialog box, in order to
\r
316 change the font of the display and enable or disable 'smooth fonts'
\r
317 (anti-aliasing) for faster alignment rendering. </em></em></li>
\r
319 <li><em><strong>Wrap<br>
\r
320 </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>" to the width of the
\r
321 alignment window. This is useful if your alignment has only a few
\r
322 sequences to view its full width at once.</em><br>
\r
323 Additional options for display of sequence numbering and scales are
\r
324 also visible in wrapped layout mode:<br>
\r
328 <li><em><strong>Scale Above</strong><br>
\r
329 <em> Show the alignment column position scale.</em></em></li>
\r
331 <li><em><strong>Scale Left</strong><br>
\r
332 <em> Show the sequence position for the first aligned
\r
333 residue in each row in the left column of the alignment.</em></em></li>
\r
335 <li><em><strong>Scale Right</strong><br>
\r
336 <em> Show the sequence position for the last aligned
\r
337 residue in each row in the right-most column of the alignment.</em></em></li>
\r
339 <li><em><strong>Show Sequence Limits<br>
\r
340 </strong><em>If this box is selected the sequence name will
\r
341 have the start and end position of the sequence appended to the name,
\r
342 in the format NAME/START-END</em> </em></li>
\r
344 <li><em><strong>Right Align Sequence ID<br>
\r
345 </strong><em>If this box is selected then the sequence
\r
346 names displayed in the sequence label area will be aligned against the
\r
347 left-hand edge of the alignment display, rather than the left-hand edge
\r
348 of the alignment window. </em></em></li>
\r
349 <em><em> </em></em>
\r
350 <li><em><em><strong>Show Hidden Markers<br>
\r
351 </strong><em>When this box is selected, positions in the
\r
352 alignment where rows and columns are hidden will be marked by blue
\r
353 arrows. </em></em></em></li>
\r
354 <em><em><em> </em></em></em>
\r
355 <li><em><em><em><strong>Boxes</strong><em><br>
\r
356 If this is selected the background of a residue will be coloured using
\r
357 the selected background colour. Useful if used in conjunction with
\r
358 "Colour Text." </em> </em></em></em></li>
\r
359 <em><em><em> </em></em></em>
\r
360 <li><em><em><em><strong>Text<br>
\r
361 </strong><em>If this is selected the residues will be
\r
362 displayed using the standard 1 character amino acid alphabet.</em> </em></em></em></li>
\r
363 <em><em><em> </em></em></em>
\r
364 <li><em><em><em><strong>Colour Text<br>
\r
365 </strong><em>If this is selected the residues will be
\r
366 coloured according to the background colour associated with that
\r
367 residue. The colour is slightly darker than background so the amino
\r
368 acid symbol remains visible. </em> </em></em></em></li>
\r
369 <em><em><em> </em></em></em>
\r
370 <li><em><em><em><strong>Show Gaps<br>
\r
371 </strong><em>When this is selected, gap characters will be
\r
372 displayed as "." or "-". If unselected, then gap characters will appear
\r
373 as blank spaces. <br>
\r
374 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em> </em></em></em></li>
\r
375 <em><em><em> </em></em></em>
\r
376 <li><em><em><em><strong>Centre Annotation Labels<br>
\r
377 </strong><em>Select this to center labels along an
\r
378 annotation row relative to their associated column (default is off,
\r
379 i.e. left-justified).</em> </em></em></em></li>
\r
380 <em><em><em> </em></em></em>
\r
381 <li><em><em><em><strong>Show Unconserved<br>
\r
382 </strong><em>When this is selected, all consensus sequence
\r
383 symbols will be rendered as a '.', highlighting mutations in highly
\r
384 conserved alignments. </em> </em></em></em></li>
\r
385 <em><em><em> </em></em></em>
\r
388 <em><em><em> </em></em></em>
\r
390 <em><em><em> </em></em></em></li>
\r
391 <em><em><em> </em></em></em>
\r
394 <em><em><em> </em></em></em>
\r
395 <li><em><em><em><strong>Colour</strong> </em></em></em>
\r
397 <em><em><em> </em></em></em>
\r
398 <li><em><em><em><strong>Apply Colour To All Groups<br>
\r
399 </strong><em>If this is selected, any changes made to the
\r
400 background colour will be applied to all currently defined groups.<br>
\r
401 </em> </em></em></em></li>
\r
402 <em><em><em> </em></em></em>
\r
403 <li><em><em><em><strong><a href="../colourSchemes/textcolour.html">Colour
\r
404 Text...</a> </strong><em><br>
\r
405 Opens the Colour Text dialog box to set a different text colour for
\r
406 light and dark background, and the intensity threshold for transition
\r
407 between them. </em> </em></em></em></li>
\r
408 <em><em><em> </em></em></em>
\r
409 <li><em><em><em>Colour Scheme options: <strong>None, ClustalX,
\r
410 Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
\r
411 Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
\r
412 Nucleotide, Purine/Pyrimidine, User Defined<br>
\r
413 </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
\r
414 for a description of all colour schemes.</em><br>
\r
415 </em></em></em></li>
\r
416 <em><em><em> </em></em></em>
\r
417 <li><em><em><em><strong>By Conservation<br>
\r
418 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
\r
419 by Conservation</a>.</em><br>
\r
420 </em></em></em></li>
\r
421 <em><em><em> </em></em></em>
\r
422 <li><em><em><em><strong>Modify Conservation Threshold<br>
\r
423 </strong><em>Use this to display the conservation threshold
\r
424 slider window. Useful if the window has been closed, or if the 'by
\r
425 conservation' option appears to be doing nothing!</em><br>
\r
426 </em></em></em></li>
\r
427 <em><em><em> </em></em></em>
\r
428 <li><em><em><em><strong>Above Identity Threshold<br>
\r
429 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
\r
430 Percentage Identity</a> </em><strong>.<br>
\r
431 </strong> </em></em></em></li>
\r
432 <em><em><em> </em></em></em>
\r
433 <li><em><em><em><strong>Modify Identity Threshold<br>
\r
434 </strong><em>Use this to set the threshold value for colouring
\r
435 above Identity. Useful if the window has been closed.<br>
\r
436 </em> </em></em></em></li>
\r
437 <em><em><em> </em></em></em>
\r
438 <li><em><em><em><strong>By Annotation</strong><br>
\r
439 <em>Colours the alignment on a per-column value from a specified
\r
440 annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
\r
441 Colouring</a>.</em><br>
\r
442 </em></em></em></li>
\r
443 <em><em><em> </em></em></em>
\r
444 <li><em><em><em><strong>By RNA Helices</strong><br>
\r
445 <em>Colours the helices of an RNA alignment loaded from a
\r
446 Stockholm file. See <a href="../colourSchemes/rnahelicesColouring.html">RNA
\r
447 Helices Colouring</a>.</em><br>
\r
448 </em></em></em></li>
\r
449 <em><em><em> </em></em></em>
\r
453 <em><em><em> </em></em></em>
\r
454 <li><em><em><em><strong>Calculate</strong> </em></em></em>
\r
456 <em><em><em> </em></em></em>
\r
457 <li><em><em><em><strong>Sort </strong> </em></em></em>
\r
459 <em><em><em> </em></em></em>
\r
460 <li><em><em><em><strong>by ID</strong><em><br>
\r
461 This will sort the sequences according to sequence name. If the sort is
\r
462 repeated, the order of the sorted sequences will be inverted. </em> </em></em></em></li>
\r
463 <em><em><em> </em></em></em>
\r
464 <li><em><em><em><strong>by Length</strong><em><br>
\r
465 This will sort the sequences according to their length (excluding gap
\r
466 characters). If the sort is repeated, the order of the sorted sequences
\r
467 will be inverted. </em></em></em></em></li>
\r
468 <em><em><em> </em></em></em>
\r
469 <li><em><em><em><strong>by Group</strong><strong><br>
\r
470 </strong><em>This will sort the sequences according to
\r
471 sequence name. If the sort is repeated, the order of the sorted
\r
472 sequences will be inverted. </em><strong></strong></em></em></em></li>
\r
473 <em><em><em> </em></em></em>
\r
474 <li><em><em><em><strong>by Pairwise Identity<br>
\r
475 </strong><em>This will sort the selected sequences by their
\r
476 percentage identity to the consensus sequence. The most similar
\r
477 sequence is put at the top. </em></em></em></em></li>
\r
478 <em><em><em> </em></em></em>
\r
479 <li><em><em><em><em>The <a href="../calculations/sorting.html">Sort
\r
480 menu</a> will have some additional options if you have just done a
\r
481 multiple alignment calculation, or opened a tree viewer window.</em><br>
\r
482 </em></em></em></li>
\r
483 <em><em><em> </em></em></em>
\r
485 <em><em><em> </em></em></em></li>
\r
486 <em><em><em> </em></em></em>
\r
487 <li><em><em><em><strong>Calculate Tree </strong> <br>
\r
488 <em>Functions for calculating trees on the alignment or the
\r
489 currently selected region. See <a href="../calculations/tree.html">calculating
\r
490 trees</a>.</em> </em></em></em>
\r
492 <em><em><em> </em></em></em>
\r
493 <li><em><em><em><strong>Average Distance Using % Identity</strong></em></em></em></li>
\r
494 <em><em><em> </em></em></em>
\r
495 <li><em><em><em><strong>Neighbour Joining Using % Identity</strong></em></em></em></li>
\r
496 <em><em><em> </em></em></em>
\r
497 <li><em><em><em><strong>Average Distance Using Blosum62</strong></em></em></em></li>
\r
498 <em><em><em> </em></em></em>
\r
499 <li><em><em><em><strong>Neighbour Joining Using Blosum62<br>
\r
500 </strong></em></em></em></li>
\r
501 <em><em><em> </em></em></em>
\r
503 <em><em><em> <strong>Note: Since Version 2.8.1, a number of
\r
504 additional similarity measures for tree calculation are provided in
\r
505 this menu.</strong> </em></em></em></li>
\r
506 <em><em><em> </em></em></em>
\r
507 <li><em><em><em><strong>Pairwise Alignments</strong><br>
\r
508 <em>Applies Smith and Waterman algorithm to selected sequences.
\r
509 See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
\r
510 </em></em></em></li>
\r
511 <em><em><em> </em></em></em>
\r
512 <li><em><em><em><strong>Principal Component Analysis</strong><br>
\r
513 <em>Shows a spatial clustering of the sequences based on
\r
514 similarity scores calculated with the alignment. See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>
\r
516 </em></em></em></li>
\r
517 <em><em><em> </em></em></em>
\r
518 <li><em><em><em><strong>Extract Scores ... (optional)</strong><br>
\r
519 <em>This option is only visible if Jalview detects one or more
\r
520 white-space separated values in the description line of the alignment
\r
522 When selected, these numbers are parsed into sequence associated
\r
523 annotation which can then be used to sort the alignment via the Sort
\r
524 by→Score menu.</em> <br>
\r
525 </em></em></em></li>
\r
526 <em><em><em> </em></em></em>
\r
527 <li><em><em><em><strong>Autocalculate Consensus</strong><br>
\r
528 <em>For large alignments it can be useful to deselect
\r
529 "Autocalculate Consensus" when editing. This prevents the sometimes
\r
530 lengthy calculations performed after each sequence edit.</em> <br>
\r
531 </em></em></em></li>
\r
532 <em><em><em> </em></em></em>
\r
533 <li><em><em><em><strong>Sort With New Tree</strong><br>
\r
534 <em>When enabled, Jalview will automatically sort the alignment
\r
535 when a new tree is calculated or loaded onto it.</em> <br>
\r
536 </em></em></em></li>
\r
537 <em><em><em> </em></em></em>
\r
538 <li><em><em><em><strong>Show Flanking Regions</strong><br>
\r
539 <em>Opens a new alignment window showing any additional sequence
\r
540 data either side of the current alignment. Useful in conjunction with
\r
541 'Fetch Database References' when the 'Trim Retrieved Sequences' option
\r
542 is disabled to retrieve full length sequences for a set of aligned
\r
543 peptides. </em></em></em></em></li>
\r
544 <em><em><em> </em></em></em>
\r
548 <em><em><em> </em></em></em>
\r
549 <li><em><em><em><strong>Web Service Menu</strong><br>
\r
550 <em>This menu is dynamic, and may contain user-defined web service
\r
551 entries in addition to any of the following ones:</em> </em></em></em>
\r
553 <em><em><em> </em></em></em>
\r
554 <li><em><em><em><strong>Fetch DB References</strong><br>
\r
555 <em>This submenu contains options for accessing any of the
\r
556 database services that Jalview is aware of (e.g. DAS sequence servers
\r
557 and the WSDBFetch service provided by the EBI) to verify sequence
\r
558 start/end positions and retrieve all database cross references and PDB
\r
559 ids associated with all or just the selected sequences in the
\r
560 alignment. </em></em></em></em>
\r
562 <em><em><em><em> </em></em></em></em>
\r
563 <li><em><em><em><em>'Trim Retrieved Sequences' - when checked,
\r
564 Jalview will discard any additional sequence data for accessions
\r
565 associated with sequences in the alignment. <br>
\r
566 <strong>Note: Disabling this could cause out of memory errors
\r
567 when working with genomic sequence records !</strong><br>
\r
568 <strong>Added in Jalview 2.8.1</strong> </em></em></em></em></li>
\r
569 <em><em><em><em> </em></em></em></em>
\r
570 <li><em><em><em><em>'Standard Databases' will check sequences
\r
571 against the EBI databases plus any active DAS sequence sources<</em></em></em></em></li>
\r
572 <em><em><em><em> </em></em></em></em>
\r
574 <em><em><em><em> Other sub-menus allow you to pick a specific
\r
575 source to query - sources are listed alphabetically according to their
\r
576 nickname. </em><br>
\r
577 </em></em></em></li>
\r
578 <em><em><em> </em></em></em>
\r
580 <em><em><em> </em></em></em>
\r
581 <p><em><em><em>Selecting items from the following submenus will start
\r
582 a remote service on compute facilities at the University of Dundee, or
\r
583 elsewhere. You need a continuous network connection in order to use
\r
584 these services through Jalview. </em></em></em></p>
\r
585 <em><em><em> </em></em></em>
\r
587 <em><em><em> </em></em></em>
\r
588 <li><em><em><em><strong>Alignment</strong><br>
\r
589 <em> Align the currently selected sequences or all sequences in
\r
590 the alignment, or re-align unaligned sequences to the aligned
\r
591 sequences. Entries in this menu provide access to the various alignment
\r
592 programs supported by <a href="../webServices/JABAWS.html">JABAWS</a>.
\r
593 See the <a href="../webServices/msaclient.html">Multiple Sequence
\r
594 Alignment webservice client</a> entry for more information.</em></em></em></em></li>
\r
595 <em><em><em> </em></em></em>
\r
596 <li><em><em><em><strong>Secondary Structure Prediction</strong> </em></em></em>
\r
598 <em><em><em> </em></em></em>
\r
599 <li><em><em><em><strong>JPred Secondary Structure Prediction</strong><br>
\r
600 <em>Secondary structure prediction by network consensus. See
\r
601 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
\r
602 more information. The behaviour of this calculation depends on the
\r
603 current selection: </em></em></em></em>
\r
605 <em><em><em><em> </em></em></em></em>
\r
606 <li><em><em><em><em>If nothing is selected, and the
\r
607 displayed sequences appear to be aligned, then a JNet prediction will
\r
608 be run for the first sequence in the alignment, using the current
\r
609 alignment. Otherwise the first sequence will be submitted for
\r
610 prediction.</em></em></em></em></li>
\r
611 <em><em><em><em> </em></em></em></em>
\r
612 <li><em><em><em><em>If just one sequence (or a region on
\r
613 one sequence) has been selected, it will be submitted to the automatic
\r
614 JNet prediction server for homolog detection and prediction.</em></em></em></em></li>
\r
615 <em><em><em><em> </em></em></em></em>
\r
616 <li><em><em><em><em>If a set of sequences are selected, and
\r
617 they appear to be aligned, then the alignment will be used for a Jnet
\r
618 prediction on the <strong>first</strong> sequence in the set (that is,
\r
619 the one that appears first in the alignment window). </em></em></em></em></li>
\r
620 <em><em><em><em> </em></em></em></em>
\r
622 <em><em><em><em> </em> </em></em></em></li>
\r
625 <em><em><em> </em></em></em>
\r
626 <li><em><em><em><strong>Analysis</strong><br>
\r
629 <em><em><em> </em></em></em>
\r
630 <li><em><em><em><strong>Multi-Harmony</strong><br>
\r
631 <em>Performs functional residue analysis on a protein family
\r
632 alignment with sub-families defined on it. See the <a href="../webServices/shmr.html">Multi-Harmony service</a> entry for
\r
633 more information.</em> </em></em></em></li>
\r
634 <em><em><em> </em></em></em>
\r
637 <em><em><em> </em></em></em>
\r
641 <em><em><em> </em></em></em>
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git://source.jalview.org / jalview.git / blob