3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Alignment Window Menus</title>
25 <strong>Alignment Window Menus</strong>
28 <li><strong>File</strong>
30 <li><strong>Fetch Sequence</strong><br> <em>Shows a
31 dialog window in which you can retrieve known ids from Uniprot,
32 EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
33 European Bioinformatics Institute. See <a
34 href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
35 <li><strong>Add Sequences</strong><em><br> Add
36 sequences to the visible alignment from file, URL, or cut &
39 <li><strong>Reload</strong><em><br> Reloads the
40 alignment from the original file, if available.<br> <strong>Warning:
41 This will delete any edits, analyses and colourings applied since
42 the alignment was last saved, and cannot be undone.</strong> </em>
44 <li><strong>Save (Control S)</strong><em><br> Saves
45 the alignment to the file it was loaded from (if available), in
46 the same format, updating the original in place. </em>
48 <li><strong>Save As (Control Shift S)<br> </strong><em>Save
49 the alignment to local file. A file selection window will open,
50 use the "Files of type:" selection box to determine
51 which <a href="../io/index.html">alignment format</a> to save as.</em>
53 <li><strong>Output to Textbox<br> </strong><em>The
54 alignment will be displayed in plain text in a new window, which
55 you can "Copy and Paste" using the pull down menu, or
56 your standard operating system copy and paste keys. The output
57 window also has a <strong>"New Window"</strong> button
58 to import the (possibly edited) text as a new alignment.<br>
59 Select the format of the text by selecting one of the following
62 <li><strong>FASTA</strong> <em></em>
64 <li><strong>MSF</strong>
66 <li><strong>CLUSTAL</strong>
68 <li><strong>BLC</strong>
70 <li><strong>PIR</strong>
72 <li><strong>PFAM</strong>
75 <li><strong>Print (Control P)<br> </strong><em>Jalview
76 will print the alignment using the current fonts and colours of
77 your alignment. If the alignment has annotations visible, these
78 will be printed below the alignment. If the alignment is wrapped
79 the number of residues per line of your alignment will depend on
80 the paper width or your alignment window width, whichever is the
83 <li><strong>Export Image</strong> <em><br> Creates an
84 alignment graphic with the current view's annotation, alignment
85 background colours and group colours. If the alignment is <a
86 href="../features/wrap.html">wrapped</a>, the output will also be
87 wrapped and will have the same visible residue width as the open
90 <li><strong>HTML<br> </strong><em>Create a <a
91 href="../io/export.html">web page</a> from your alignment.</em>
93 <li><strong>EPS<br> </strong><em>Create an <a
94 href="../io/export.html">Encapsulated Postscript</a> file from
97 <li><strong>PNG<br> </strong><em>Create a <a
98 href="../io/export.html">Portable Network Graphics</a> file from
102 <li><strong>Export Features</strong><em><br> All
103 features visible on the alignment can be saved to file or
104 displayed in a textbox in either Jalview or GFF format</em>
106 <li><strong>Export Annotations</strong><em><br> All
107 annotations visible on the alignment can be saved to file or
108 displayed in a textbox in Jalview annotations format. </em>
110 <li><strong>Load Associated Tree<br> </strong><em>Jalview
111 can <a href="../calculations/treeviewer.html">view trees</a>
112 stored in the Newick file format, and associate them with the
113 alignment. Note: the ids of the tree file and your alignment MUST
114 be the same.</em></li>
115 <li><strong>Load Features / Annotations<br> </strong><em>Load
116 files describing precalculated <a
117 href="../features/featuresFormat.html">sequence features</a> or <a
118 href="../features/annotationsFormat.html">alignment
119 annotations</a>.</em></li>
120 <li><strong>Close (Control W)</strong><br> <em>Close
121 the alignment window. Make sure you have saved your alignment
122 before you close - either as a Jalview project or by using the <strong>Save
123 As</strong> menu.</em>
126 <li><strong>Edit</strong>
128 <li><strong>Undo (Control Z)</strong><em><br> This
129 will undo any edits you make to the alignment. This applies to
130 insertion or deletion of gaps, cutting residues or sequences from
131 the alignment or pasting sequences to the current alignment or
132 sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
133 colour changes, adjustments to group sizes, or changes to the
134 annotation panel. </em>
136 <li><strong>Redo (Control Y)<br> </strong><em>Any
137 actions which you undo can be redone using redo. </em>
139 <li><strong>Cut (Control X)<br> </strong><em>This
140 will make a copy of the currently selected residues before
141 removing them from your alignment. Click on a sequence name if you
142 wish to select a whole sequence. <br> Use <CTRL> and X
143 (<APPLE> and X on MacOSX) to cut.</em>
145 <li><strong>Copy (Control C)</strong><br> <em>Copies
146 the currently selected residues to the system clipboard - you can
147 also do this by pressing <CTRL> and C (<APPLE> and C
148 on MacOSX). <br> If you try to paste the clipboard contents
149 to a text editor, you will see the format of the copied residues
151 <li><strong>Paste </strong>
153 <li><strong>To New Alignment (Control Shift V)<br>
154 </strong><em>A new alignment window will be created from sequences
155 previously copied or cut to the system clipboard. <br> Use
156 <CTRL> and <SHIFT> and V(<APPLE> and
157 <SHIFT;> and and V on MacOSX) to paste.</em>
159 <li><strong>Add To This Alignment (Control V)<br>
160 </strong><em>Copied sequences from another alignment window can be
161 added to the current Jalview alignment. </em>
164 <li><strong>Delete (Backspace)<br> </strong><em>This
165 will delete the currently selected residues without copying them
166 to the clipboard. Like the other edit operations, this can be
167 undone with <strong>Undo</strong>.</em>
169 <li><strong>Remove Left (Control L)<br> </strong><em>If
170 the alignment has marked columns, the alignment will be trimmed to
171 the left of the leftmost marked column. To mark a column, mouse
172 click the scale bar above the alignment. Click again to unmark a
173 column, or select "Deselect All" to deselect all
175 <li><strong>Remove Right (Control R)<br> </strong><em>If
176 the alignment has marked columns, the alignment will be trimmed to
177 the left of the leftmost marked column. To mark a column, mouse
178 click the scale bar above the alignment. Click again to unmark a
179 column, or select "Deselect All" to deselect all
181 <li><strong>Remove Empty Columns (Control E)<br>
182 </strong><em>All columns which only contain gap characters
183 ("-", ".") will be deleted.<br> You may
184 set the default gap character in <a
185 href="../features/preferences.html">preferences</a>. </em>
187 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
188 <em>Gap characters ("-", ".") will be
189 deleted from the selected area of the alignment. If no selection
190 is made, ALL the gaps in the alignment will be removed.<br>
191 You may set the default gap character in <a
192 href="../features/preferences.html">preferences</a>. </em>
194 <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
195 this option brings up a window asking you to select a threshold.
196 If the percentage identity between any two sequences (under the
197 current alignment) exceeds this value then one of the sequences
198 (the shorter) is discarded. Press the "Apply" button to
199 remove redundant sequences. The "Undo" button will undo
200 the last redundancy deletion.</em>
202 <li><strong>Pad Gaps<br> </strong><em>When selected,
203 the alignment will be kept at minimal width (so there no empty
204 columns before or after the first or last aligned residue) and all
205 sequences will be padded with gap characters to the before and
206 after their terminating residues.<br> This switch is useful
207 when making a tree using unaligned sequences and when working with
208 alignment analysis programs which require 'properly aligned
209 sequences' to be all the same length.<br> You may set the
210 default for <strong>Pad Gaps</strong> in the <a
211 href="../features/preferences.html">preferences</a>. </em>
214 <li><strong>Select</strong>
216 <li><strong><a href="../features/search.html">Find...
217 (Control F)</a> </strong><em><br> Opens the Find dialog box to
218 search for residues, sequence name or residue position within the
219 alignment and create new sequence features from the queries. </em>
221 <li><strong>Select All (Control A)<br> </strong><em>Selects
222 all the sequences and residues in the alignment. <br> Use
223 <CTRL> and A (<APPLE> and A on a MacOSX) to select
225 <li><strong>Deselect All (Escape)<br> </strong><em>Removes
226 the current selection box (red dashed box) from the alignment
227 window. All selected sequences, residues and marked columns will
228 be deselected. </em><em> <br> Use <ESCAPE> to deselect
230 <li><strong>Invert Sequence Selection (Control I)<br>
231 </strong><em>Any sequence ids currently not selected will replace the
232 current selection. </em>
234 <li><strong>Invert Column Selection (Control Alt I)<br>
235 </strong><em>Any columns currently not selected will replace the current
236 column selection. </em>
238 <li><strong>Create Group (Control G)<br></strong>
239 <em>Create a group containing the currently selected sequences.</em></li>
240 <li><strong>Remove Group (Shift Control G)<br></strong>
241 <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
242 <li><strong>Make Groups for selection<br /> </strong> <em>The currently
243 selected groups of the alignment will be subdivided according to
244 the contents of the currently selected region. <br />Use this to
245 subdivide an alignment based on the different combinations of
246 residues observed at specific positions. (new in jalview 2.5)</em>
248 <li><strong>Undefine Groups (Control U)<br> </strong><em>The
249 alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
250 This cannot be undone.</em>
253 <li><strong>View</strong>
255 <li><strong>New View (Control T)</strong><em><br>
256 Creates a new view from the current alignment view. </em>
258 <li><strong>Expand Views (X)</strong><em><br> Display
259 each view associated with the alignment in its own alignment
260 window, allowing several views to be displayed simultaneously. </em>
262 <li><strong>Gather Views (G)</strong><em><br> Each
263 view associated with the alignment will be displayed within its
264 own tab on the current alignment window. </em>
266 <li><strong>Show→(all Columns / Sequences /
267 Sequences and Columns)</strong><em><br> All hidden Columns /
268 Sequences / Sequences and Columns will be revealed. </em>
270 <li><strong>Hide→(all Columns / Sequences /
271 Selected Region / All but Selected Region )</strong><em><br>
272 Hides the all the currently selected Columns / Sequences / Region
273 or everything but the selected Region.</em>
275 <li><strong>Automatic Scrolling<br> </strong><em>When
276 selected, the view will automatically scroll to display the
277 highlighted sequence position corresponding to the position under
278 the mouse pointer in a linked alignment or structure view.</em></li>
279 <li><strong>Show Annotations<br> </strong><em>If this
280 is selected the "Annotation Panel" will be displayed
281 below the alignment. The default setting is to display the
282 conservation calculation, quality calculation and consensus values
285 <li><strong>Autocalculated Annotation<br> </strong><em>Settings
286 for the display of autocalculated annotation.</em>
288 <li><strong>Apply to all groups<br> </strong><em> When
289 ticked, any modification to the current settings will be applied
290 to all autocalculated annotation.</em></li>
291 <li><strong>Show Consensus Histogram<br> </strong><em>
292 Enable or disable the display of the histogram above the
293 consensus sequence.</em></li>
294 <li><strong>Show Consensus Logo<br> </strong><em> Enable
295 or disable the display of the Consensus Logo above the consensus
297 <li><strong>Normalise Consensus Logo<br>
298 </strong><em>When enabled, scales all logo stacks to the same height,
299 making it easier to compare symbol diversity in highly variable
301 <li><strong>Group Conservation<br> </strong><em> When
302 ticked, display a conservation row for all groups (only available
303 for protein alignments).</em></li>
304 <li><strong>Apply to all groups<br> </strong><em> When
305 ticked, display a consensus row for all groups.</em></li>
307 <li><strong>Show Sequence Features</strong><br> <em>Show
308 or hide sequence features on this alignment.</em>
310 <li><strong><a href="../features/featuresettings.html">Seqence
311 Feature Settings...</a> </strong><em><br> <em>Opens the
312 Sequence Feature Settings dialog box to control the colour and
313 display of sequence features on the alignment, and configure and
314 retrieve features from DAS annotation servers.</em>
316 <li><strong>Sequence ID Tooltip</strong><em> (application
317 only) <br>This submenu's options allow the inclusion or
318 exclusion of non-positional sequence features or database cross
319 references from the tooltip shown when the mouse hovers over the
320 sequence ID panel.</em>
322 <li><strong>Alignment Properties...<br /> </strong><em>Displays
323 some simple statistics computed for the current alignment view and
324 any named properties defined on the whole alignment.</em>
326 <li><strong><a href="../features/overview.html">Overview
327 Window</a><br> </strong><em>A scaled version of the alignment will
328 be displayed in a small window. A red box will indicate the
329 currently visible area of the alignment. Move the visible region
330 using the mouse. </em>
333 <li><strong>Alignment Window Format Menu</strong>
335 <li><strong>Font...<br> </strong><em>Opens the
336 "Choose Font" dialog box, in order to change the font of
337 the display and enable or disable 'smooth fonts' (anti-aliasing)
338 for faster alignment rendering. </em></li>
339 <li><strong>Wrap<br> </strong><em>When ticked, the
340 alignment display is "<a href="../features/wrap.html">wrapped</a>"
341 to the width of the alignment window. This is useful if your
342 alignment has only a few sequences to view its full width at once.</em><br>
343 Additional options for display of sequence numbering and scales are
344 also visible in wrapped layout mode:<br>
346 <li><strong>Scale Above</strong><br><em> Show the alignment
347 column position scale.</em></li>
348 <li><strong>Scale Left</strong><br><em> Show the sequence
349 position for the first aligned residue in each row in the left
350 column of the alignment.</em></li>
351 <li><strong>Scale Right</strong><br><em> Show the sequence
352 position for the last aligned residue in each row in the
353 right-most column of the alignment.</em></li>
354 <li><strong>Show Sequence Limits<br> </strong><em>If
355 this box is selected the sequence name will have the start and
356 end position of the sequence appended to the name, in the format
359 <li><strong>Right Align Sequence ID<br> </strong><em>If
360 this box is selected then the sequence names displayed in the
361 sequence label area will be aligned against the left-hand edge
362 of the alignment display, rather than the left-hand edge of the
365 <li><strong>Show Hidden Markers<br> </strong><em>When
366 this box is selected, positions in the alignment where rows and
367 columns are hidden will be marked by blue arrows.
369 <li><strong>Boxes</strong><em><br> If this is
370 selected the background of a residue will be coloured using the
371 selected background colour. Useful if used in conjunction with
372 "Colour Text." </em>
374 <li><strong>Text<br> </strong><em>If this is
375 selected the residues will be displayed using the standard 1
376 character amino acid alphabet.</em>
378 <li><strong>Colour Text<br> </strong><em>If this is
379 selected the residues will be coloured according to the
380 background colour associated with that residue. The colour is
381 slightly darker than background so the amino acid symbol remains
384 <li><strong>Show Gaps<br> </strong><em>When this is
385 selected, gap characters will be displayed as "." or
386 "-". If unselected, then gap characters will appear as
387 blank spaces. <br> You may set the default gap character in
388 <a href="../features/preferences.html">preferences</a>.</em>
390 <li><strong>Centre Annotation Labels<br> </strong><em>Select
391 this to center labels along an annotation row relative to their
392 associated column (default is off, i.e. left-justified).</em>
394 <li><strong>Show Unconserved<br> </strong><em>When
395 this is selected, all consensus sequence symbols will be
396 rendered as a '.', highlighting mutations in highly conserved
407 <li><strong>Colour</strong>
409 <li><strong>Apply Colour To All Groups<br> </strong><em>If
410 this is selected, any changes made to the background colour will
411 be applied to all currently defined groups.<br> </em>
413 <li><strong><a href="../colourSchemes/textcolour.html">Colour
414 Text...</a> </strong><em><br> Opens the Colour Text dialog box to
415 set a different text colour for light and dark background, and the
416 intensity threshold for transition between them. </em>
418 <li>Colour Scheme options: <strong>None, ClustalX,
419 Blosum62 Score, Percentage Identity, Zappo, Taylor,
420 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
421 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
422 <a href="../colourSchemes/index.html">colours</a> for a
423 description of all colour schemes.</em><br></li>
424 <li><strong>By Conservation<br> </strong><em>See <a
425 href="../colourSchemes/conservation.html">Colouring by
426 Conservation</a>.</em><br></li>
427 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
428 this to display the conservation threshold slider window. Useful
429 if the window has been closed, or if the 'by conservation' option
430 appears to be doing nothing!</em><br></li>
431 <li><strong>Above Identity Threshold<br> </strong><em>See
432 <a href="../colourSchemes/abovePID.html">Above Percentage
433 Identity</a> </em><strong>.<br> </strong>
435 <li><strong>Modify Identity Threshold<br> </strong><em>Use
436 this to set the threshold value for colouring above Identity.
437 Useful if the window has been closed.<br> </em>
439 <li><strong>By Annotation</strong><br> <em>Colours
440 the alignment on a per-column value from a specified annotation.
441 See <a href="../colourSchemes/annotationColouring.html">Annotation
442 Colouring</a>.</em><br></li>
443 <li><strong>By RNA Helices</strong><br>
444 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
445 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
446 Colouring</a>.</em><br>
449 <li><strong>Calculate</strong>
451 <li><strong>Sort </strong>
453 <li><strong>by ID</strong><em><br> This will sort
454 the sequences according to sequence name. If the sort is
455 repeated, the order of the sorted sequences will be inverted. </em>
457 <li><strong>by Length</strong><em><br> This will
458 sort the sequences according to their length (excluding gap
459 characters). If the sort is repeated, the order of the sorted
460 sequences will be inverted. </em></li>
461 <li><strong>by Group</strong><strong><br> </strong><em>This
462 will sort the sequences according to sequence name. If the sort
463 is repeated, the order of the sorted sequences will be inverted.
464 </em><strong></strong></li>
465 <li><strong>by Pairwise Identity<br> </strong><em>This
466 will sort the selected sequences by their percentage identity to
467 the consensus sequence. The most similar sequence is put at the
469 <li><em>The <a href="../calculations/sorting.html">Sort
470 menu</a> will have some additional options if you have just done a
471 multiple alignment calculation, or opened a tree viewer window.</em><br>
475 <li><strong>Calculate Tree </strong> <br> <em>Functions
476 for calculating trees on the alignment or the currently selected
477 region. See <a href="../calculations/tree.html">calculating
480 <li><strong>Average Distance Using % Identity</strong></li>
481 <li><strong>Neighbour Joining Using % Identity</strong></li>
482 <li><strong>Average Distance Using Blosum62</strong></li>
483 <li><strong>Neighbour Joining Using Blosum62<br>
487 <li><strong>Pairwise Alignments</strong><br> <em>Applies
488 Smith and Waterman algorithm to selected sequences. See <a
489 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
491 <li><strong>Principal Component Analysis</strong><br> <em>Shows
492 a spatial clustering of the sequences based on the BLOSUM62 scores
493 in the alignment. See <a href="../calculations/pca.html">Principal
494 Component Analysis</a>.</em> <br>
496 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
497 option is only visible if Jalview detects one or more white-space
498 separated values in the description line of the alignment
499 sequences.<br> When selected, these numbers are parsed into
500 sequence associated annotation which can then be used to sort the
501 alignment via the Sort by→Score menu.</em> <br>
503 <li><strong>Autocalculate Consensus</strong><br> <em>For
504 large alignments it can be useful to deselect "Autocalculate
505 Consensus" when editing. This prevents the sometimes lengthy
506 calculations performed after each sequence edit.</em> <br>
508 <li><strong>Sort With New Tree</strong><br> <em>When
509 enabled, Jalview will automatically sort the alignment when a new
510 tree is calculated or loaded onto it.</em> <br></li>
513 <li><strong>Web Service Menu</strong><br /> <em>This menu
514 is dynamic, and may contain user-defined web service entries in
515 addition to any of the following ones:</em>
517 <li><strong>Fetch DB References</strong><br> <em>This
518 will use any of the database services that Jalview is aware of
519 (e.g. DAS sequence servers and the WSDBFetch service provided by
520 the EBI) to verify the sequence and retrieve all database cross
521 references and PDB ids associated with all or just the selected
522 sequences in the alignment. <br />'Standard Databases' will check
523 sequences against the EBI databases plus any active DAS sequence
524 sources, or you can verify against a specific source from one of
525 the sub-menus.</em><br></li>
526 <li><strong>Envision2 Services</strong><br /><em> Submits one or
527 more sequences, sequence IDs or database references to analysis
528 workflows provided by the <a
529 href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
530 application</a>. This allows Jalview users to easily access the EnCore
531 network of databases and analysis services developed by members of
532 <a href="http://www.enfin.org">ENFIN</a></em>.</li>
534 <p>Selecting items from the following submenus will start a
535 remote service on compute facilities at the University of Dundee, or
536 elsewhere. You need a continuous network connection in order to use
537 these services through Jalview.
540 <li><strong>Alignment</strong><br /><em> Align the currently
541 selected sequences or all sequences in the alignment, or re-align
542 unaligned sequences to the aligned sequences. Entries in this menu
543 provide access to the various alignment programs supported by <a
544 href="../webServices/JABAWS.html">JABAWS</a>. See the <a
545 href="../webServices/msaclient.html">Multiple Sequence
546 Alignment webservice client</a> entry for more information.</em></li>
547 <li><strong>Secondary Structure Prediction</strong>
549 <li><strong>JPred Secondary Structure Prediction</strong><br>
550 <em>Secondary structure prediction by network consensus. See
551 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
552 more information. The behaviour of this calculation depends on
553 the current selection:
555 <li>If nothing is selected, and the displayed sequences
556 appear to be aligned, then a JNet prediction will be run for
557 the first sequence in the alignment, using the current
558 alignment. Otherwise the first sequence will be submitted for
560 <li>If just one sequence (or a region on one sequence) has
561 been selected, it will be submitted to the automatic JNet
562 prediction server for homolog detection and prediction.</li>
563 <li>If a set of sequences are selected, and they appear to
564 be aligned, then the alignment will be used for a Jnet
565 prediction on the <strong>first</strong> sequence in the set
566 (that is, the one that appears first in the alignment window).
570 <li><strong>Analysis</strong><br />
572 <li><strong>Multi-Harmony</strong><br> <em>Performs
573 functional residue analysis on a protein family alignment with
574 sub-families defined on it. See the <a
575 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more