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