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