3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>Undefine Groups (Control U)<br> </strong><em>The
239 alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
240 This cannot be undone.</em>
242 <li><strong>Make Groups<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>
249 <li><strong>View</strong>
251 <li><strong>New View (Control T)</strong><em><br>
252 Creates a new view from the current alignment view. </em>
254 <li><strong>Expand Views (X)</strong><em><br> Display
255 each view associated with the alignment in its own alignment
256 window, allowing several views to be displayed simultaneously. </em>
258 <li><strong>Gather Views (G)</strong><em><br> Each
259 view associated with the alignment will be displayed within its
260 own tab on the current alignment window. </em>
262 <li><strong>Show→(all Columns / Sequences /
263 Sequences and Columns)</strong><em><br> All hidden Columns /
264 Sequences / Sequences and Columns will be revealed. </em>
266 <li><strong>Hide→(all Columns / Sequences /
267 Selected Region / All but Selected Region )</strong><em><br>
268 Hides the all the currently selected Columns / Sequences / Region
269 or everything but the selected Region.</em>
271 <li><strong>Automatic Scrolling<br> </strong><em>When
272 selected, the view will automatically scroll to display the
273 highlighted sequence position corresponding to the position under
274 the mouse pointer in a linked alignment or structure view.</em></li>
275 <li><strong>Show Annotations<br> </strong><em>If this
276 is selected the "Annotation Panel" will be displayed
277 below the alignment. The default setting is to display the
278 conservation calculation, quality calculation and consensus values
281 <li><strong>Autocalculated Annotation<br> </strong><em>Settings
282 for the display of autocalculated annotation.</em>
284 <li><strong>Apply to all groups<br> </strong><em> When
285 ticked, any modification to the current settings will be applied
286 to all autocalculated annotation.</em></li>
287 <li><strong>Show Consensus Histogram<br> </strong><em>
288 Enable or disable the display of the histogram above the
289 consensus sequence.</em></li>
290 <li><strong>Show Consensus Logo<br> </strong><em> Enable
291 or disable the display of the Consensus Logo above the consensus
293 <li><strong>Normalise Consensus Logo<br>
294 </strong><em>When enabled, scales all logo stacks to the same height,
295 making it easier to compare symbol diversity in highly variable
297 <li><strong>Group Conservation<br> </strong><em> When
298 ticked, display a conservation row for all groups (only available
299 for protein alignments).</em></li>
300 <li><strong>Apply to all groups<br> </strong><em> When
301 ticked, display a consensus row for all groups.</em></li>
303 <li><strong>Show Sequence Features</strong><br> <em>Show
304 or hide sequence features on this alignment.</em>
306 <li><strong><a href="../features/featuresettings.html">Seqence
307 Feature Settings...</a> </strong><em><br> <em>Opens the
308 Sequence Feature Settings dialog box to control the colour and
309 display of sequence features on the alignment, and configure and
310 retrieve features from DAS annotation servers.</em>
312 <li><strong>Sequence ID Tooltip</strong><em> (application
313 only) <br>This submenu's options allow the inclusion or
314 exclusion of non-positional sequence features or database cross
315 references from the tooltip shown when the mouse hovers over the
316 sequence ID panel.</em>
318 <li><strong>Alignment Properties...<br /> </strong><em>Displays
319 some simple statistics computed for the current alignment view and
320 any named properties defined on the whole alignment.</em>
322 <li><strong><a href="../features/overview.html">Overview
323 Window</a><br> </strong><em>A scaled version of the alignment will
324 be displayed in a small window. A red box will indicate the
325 currently visible area of the alignment. Move the visible region
326 using the mouse. </em>
329 <li><strong>Alignment Window Format Menu</strong>
331 <li><strong>Font...<br> </strong><em>Opens the
332 "Choose Font" dialog box, in order to change the font of
333 the display and enable or disable 'smooth fonts' (anti-aliasing)
334 for faster alignment rendering. </em></li>
335 <li><strong>Wrap<br> </strong><em>When ticked, the
336 alignment display is "<a href="../features/wrap.html">wrapped</a>"
337 to the width of the alignment window. This is useful if your
338 alignment has only a few sequences to view its full width at once.</em><br>
339 Additional options for display of sequence numbering and scales are
340 also visible in wrapped layout mode:<br>
342 <li><strong>Scale Above</strong><br><em> Show the alignment
343 column position scale.</em></li>
344 <li><strong>Scale Left</strong><br><em> Show the sequence
345 position for the first aligned residue in each row in the left
346 column of the alignment.</em></li>
347 <li><strong>Scale Right</strong><br><em> Show the sequence
348 position for the last aligned residue in each row in the
349 right-most column of the alignment.</em></li>
350 <li><strong>Show Sequence Limits<br> </strong><em>If
351 this box is selected the sequence name will have the start and
352 end position of the sequence appended to the name, in the format
355 <li><strong>Right Align Sequence ID<br> </strong><em>If
356 this box is selected then the sequence names displayed in the
357 sequence label area will be aligned against the left-hand edge
358 of the alignment display, rather than the left-hand edge of the
361 <li><strong>Show Hidden Markers<br> </strong><em>When
362 this box is selected, positions in the alignment where rows and
363 columns are hidden will be marked by blue arrows.
365 <li><strong>Boxes</strong><em><br> If this is
366 selected the background of a residue will be coloured using the
367 selected background colour. Useful if used in conjunction with
368 "Colour Text." </em>
370 <li><strong>Text<br> </strong><em>If this is
371 selected the residues will be displayed using the standard 1
372 character amino acid alphabet.</em>
374 <li><strong>Colour Text<br> </strong><em>If this is
375 selected the residues will be coloured according to the
376 background colour associated with that residue. The colour is
377 slightly darker than background so the amino acid symbol remains
380 <li><strong>Show Gaps<br> </strong><em>When this is
381 selected, gap characters will be displayed as "." or
382 "-". If unselected, then gap characters will appear as
383 blank spaces. <br> You may set the default gap character in
384 <a href="../features/preferences.html">preferences</a>.</em>
386 <li><strong>Centre Annotation Labels<br> </strong><em>Select
387 this to center labels along an annotation row relative to their
388 associated column (default is off, i.e. left-justified).</em>
390 <li><strong>Show Unconserved<br> </strong><em>When
391 this is selected, all consensus sequence symbols will be
392 rendered as a '.', highlighting mutations in highly conserved
403 <li><strong>Colour</strong>
405 <li><strong>Apply Colour To All Groups<br> </strong><em>If
406 this is selected, any changes made to the background colour will
407 be applied to all currently defined groups.<br> </em>
409 <li><strong><a href="../colourSchemes/textcolour.html">Colour
410 Text...</a> </strong><em><br> Opens the Colour Text dialog box to
411 set a different text colour for light and dark background, and the
412 intensity threshold for transition between them. </em>
414 <li>Colour Scheme options: <strong>None, ClustalX,
415 Blosum62 Score, Percentage Identity, Zappo, Taylor,
416 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
417 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
418 <a href="../colourSchemes/index.html">colours</a> for a
419 description of all colour schemes.</em><br></li>
420 <li><strong>By Conservation<br> </strong><em>See <a
421 href="../colourSchemes/conservation.html">Colouring by
422 Conservation</a>.</em><br></li>
423 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
424 this to display the conservation threshold slider window. Useful
425 if the window has been closed, or if the 'by conservation' option
426 appears to be doing nothing!</em><br></li>
427 <li><strong>Above Identity Threshold<br> </strong><em>See
428 <a href="../colourSchemes/abovePID.html">Above Percentage
429 Identity</a> </em><strong>.<br> </strong>
431 <li><strong>Modify Identity Threshold<br> </strong><em>Use
432 this to set the threshold value for colouring above Identity.
433 Useful if the window has been closed.<br> </em>
435 <li><strong>By Annotation</strong><br> <em>Colours
436 the alignment on a per-column value from a specified annotation.
437 See <a href="../colourSchemes/annotationColouring.html">Annotation
438 Colouring</a>.</em><br></li>
439 <li><strong>By RNA Helices</strong><br>
440 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
441 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
442 Colouring</a>.</em><br>
445 <li><strong>Calculate</strong>
447 <li><strong>Sort </strong>
449 <li><strong>by ID</strong><em><br> This will sort
450 the sequences according to sequence name. If the sort is
451 repeated, the order of the sorted sequences will be inverted. </em>
453 <li><strong>by Length</strong><em><br> This will
454 sort the sequences according to their length (excluding gap
455 characters). If the sort is repeated, the order of the sorted
456 sequences will be inverted. </em></li>
457 <li><strong>by Group</strong><strong><br> </strong><em>This
458 will sort the sequences according to sequence name. If the sort
459 is repeated, the order of the sorted sequences will be inverted.
460 </em><strong></strong></li>
461 <li><strong>by Pairwise Identity<br> </strong><em>This
462 will sort the selected sequences by their percentage identity to
463 the consensus sequence. The most similar sequence is put at the
465 <li><em>The <a href="../calculations/sorting.html">Sort
466 menu</a> will have some additional options if you have just done a
467 multiple alignment calculation, or opened a tree viewer window.</em><br>
471 <li><strong>Calculate Tree </strong> <br> <em>Functions
472 for calculating trees on the alignment or the currently selected
473 region. See <a href="../calculations/tree.html">calculating
476 <li><strong>Average Distance Using % Identity</strong></li>
477 <li><strong>Neighbour Joining Using % Identity</strong></li>
478 <li><strong>Average Distance Using Blosum62</strong></li>
479 <li><strong>Neighbour Joining Using Blosum62<br>
483 <li><strong>Pairwise Alignments</strong><br> <em>Applies
484 Smith and Waterman algorithm to selected sequences. See <a
485 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
487 <li><strong>Principal Component Analysis</strong><br> <em>Shows
488 a spatial clustering of the sequences based on the BLOSUM62 scores
489 in the alignment. See <a href="../calculations/pca.html">Principal
490 Component Analysis</a>.</em> <br>
492 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
493 option is only visible if Jalview detects one or more white-space
494 separated values in the description line of the alignment
495 sequences.<br> When selected, these numbers are parsed into
496 sequence associated annotation which can then be used to sort the
497 alignment via the Sort by→Score menu.</em> <br>
499 <li><strong>Autocalculate Consensus</strong><br> <em>For
500 large alignments it can be useful to deselect "Autocalculate
501 Consensus" when editing. This prevents the sometimes lengthy
502 calculations performed after each sequence edit.</em> <br>
504 <li><strong>Sort With New Tree</strong><br> <em>When
505 enabled, Jalview will automatically sort the alignment when a new
506 tree is calculated or loaded onto it.</em> <br></li>
509 <li><strong>Web Service Menu</strong><br /> <em>This menu
510 is dynamic, and may contain user-defined web service entries in
511 addition to any of the following ones:</em>
513 <li><strong>Fetch DB References</strong><br> <em>This
514 will use any of the database services that Jalview is aware of
515 (e.g. DAS sequence servers and the WSDBFetch service provided by
516 the EBI) to verify the sequence and retrieve all database cross
517 references and PDB ids associated with all or just the selected
518 sequences in the alignment. <br />'Standard Databases' will check
519 sequences against the EBI databases plus any active DAS sequence
520 sources, or you can verify against a specific source from one of
521 the sub-menus.</em><br></li>
522 <li><strong>Envision2 Services</strong><br /><em> Submits one or
523 more sequences, sequence IDs or database references to analysis
524 workflows provided by the <a
525 href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
526 application</a>. This allows Jalview users to easily access the EnCore
527 network of databases and analysis services developed by members of
528 <a href="http://www.enfin.org">ENFIN</a></em>.</li>
530 <p>Selecting items from the following submenus will start a
531 remote service on compute facilities at the University of Dundee, or
532 elsewhere. You need a continuous network connection in order to use
533 these services through Jalview.
536 <li><strong>Alignment</strong><br /><em> Align the currently
537 selected sequences or all sequences in the alignment, or re-align
538 unaligned sequences to the aligned sequences. Entries in this menu
539 provide access to the various alignment programs supported by <a
540 href="../webServices/JABAWS.html">JABAWS</a>. See the <a
541 href="../webServices/msaclient.html">Multiple Sequence
542 Alignment webservice client</a> entry for more information.</em></li>
543 <li><strong>Secondary Structure Prediction</strong>
545 <li><strong>JPred Secondary Structure Prediction</strong><br>
546 <em>Secondary structure prediction by network consensus. See
547 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
548 more information. The behaviour of this calculation depends on
549 the current selection:
551 <li>If nothing is selected, and the displayed sequences
552 appear to be aligned, then a JNet prediction will be run for
553 the first sequence in the alignment, using the current
554 alignment. Otherwise the first sequence will be submitted for
556 <li>If just one sequence (or a region on one sequence) has
557 been selected, it will be submitted to the automatic JNet
558 prediction server for homolog detection and prediction.</li>
559 <li>If a set of sequences are selected, and they appear to
560 be aligned, then the alignment will be used for a Jnet
561 prediction on the <strong>first</strong> sequence in the set
562 (that is, the one that appears first in the alignment window).
566 <li><strong>Analysis</strong><br />
568 <li><strong>Multi-Harmony</strong><br> <em>Performs
569 functional residue analysis on a protein family alignment with
570 sub-families defined on it. See the <a
571 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more