3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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11 * of the License, or (at your option) any later version.
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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.
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23 <title>Alignment Window Menus</title>
27 <!-- NOTE: THIS PAGE COLLECTS TOGETHER THE INDIVIDUAL ALIGNMENT WINDOW MENU PAGES - DON"T EDIT INDIVIDUAL ENTRIES HERE! -->
29 <strong>Alignment Window Menus</strong>
32 <li><strong>File</strong>
34 <li><strong>Fetch Sequence</strong><br> <em>Shows
35 a dialog window in which you can retrieve known ids from
36 UniProt, EMBL, EMBLCDS, PFAM, Rfam, or PDB database using
37 Web Services provided by the European Bioinformatics
38 Institute. See <a href="../features/seqfetch.html">Sequence
41 <li><strong>Add Sequences</strong><em><br> Add
42 sequences to the visible alignment from file, URL, or cut
43 & paste window </em></li>
44 <li><strong>Reload</strong><em><br> Reloads the
45 alignment from the original file, if available.<br> <strong>Warning:
46 This will delete any edits, analyses and colourings
47 applied since the alignment was last saved, and cannot be
48 undone.</strong> </em></li>
49 <li><strong>Save (Control S)</strong><em><br>
50 Saves the alignment to the file it was loaded from (if
51 available), in the same format, updating the original in
53 <li><strong>Save As (Control Shift S)<br>
54 </strong><em>Save the alignment to local file. A file selection
55 window will open, use the "Files of type:"
56 selection box to determine which <a href="../io/index.html">alignment
57 format</a> to save as.
59 <li><strong>Output to Textbox<br>
60 </strong><em>The alignment will be displayed in plain text in a new
61 window, which you can "Copy and Paste" using the
62 pull down menu, or your standard operating system copy and
63 paste keys. The output window also has a <strong>"New
64 Window"</strong> button to import the (possibly edited) text
65 as a new alignment.<br> Select the format of the text
66 by selecting one of the following menu items.
69 <li><strong>FASTA</strong></li>
70 <li><strong>MSF</strong></li>
71 <li><strong>CLUSTAL</strong></li>
72 <li><strong>BLC</strong></li>
73 <li><strong>PIR</strong></li>
74 <li><strong>PFAM</strong></li>
75 <li><strong>PileUp</strong></li>
76 <li><strong>AMSA</strong></li>
77 <li><strong>STH</strong></li>
78 <li><strong>Phylip</strong></li>
79 <li><strong>JSON</strong></li>
81 <li><strong>Page Setup ...</strong><br> <em>Open
82 the printing system's Page Setup dialog box, to control page
83 size, layout and orientation.</em></li>
84 <li><strong>Print (Control P)<br>
85 </strong><em>Jalview will print the alignment using the current
86 fonts and colours of your alignment. If the alignment has
87 annotations visible, these will be printed below the
88 alignment. If the alignment is wrapped the number of
89 residues per line of your alignment will depend on the paper
90 width or your alignment window width, whichever is the
92 <li><strong>Export Image</strong> <em><br>
93 Creates an alignment graphic with the current view's
94 annotation, alignment background colours and group colours.
95 If the alignment is <a href="../features/wrap.html">wrapped</a>,
96 the output will also be wrapped and will have the same
97 visible residue width as the open alignment. </em>
100 </strong><em>Create a <a href="../io/export.html">web page</a>
104 </strong><em>Create an <a href="../io/export.html">Encapsulated
105 Postscript</a> file from your alignment.
108 </strong><em>Create a <a href="../io/export.html">Portable
109 Network Graphics</a> file from your alignment.
112 </strong><em>Create a <a href="../io/export.html">Scalable
113 Vector Graphics</a> file from your alignment for embedding
116 <li><strong>BioJS<br>
117 </strong><em>Create a <a href="../io/export.html">BioJS MSA
118 Viewer HTML </a> file from your alignment.
121 <li><strong>Export Features</strong><em><br> All
122 features visible on the alignment can be saved to file or
123 displayed in a textbox in either Jalview or GFF format</em></li>
124 <li><strong>Export Annotations</strong><em><br>
125 All annotations visible on the alignment can be saved to
126 file or displayed in a textbox in Jalview annotations
128 <li><strong>Load Associated Tree<br>
129 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
130 trees</a> stored in the Newick file format, and associate them
131 with the alignment. Note: the ids of the tree file and your
132 alignment MUST be the same.
134 <li><strong>Load Features / Annotations<br>
135 </strong><em>Load files describing precalculated <a
136 href="../features/featuresFormat.html">sequence
137 features</a> or <a href="../features/annotationsFormat.html">alignment
140 <li><strong>Close (Control W)</strong><br> <em>Close
141 the alignment window. Make sure you have saved your
142 alignment before you close - either from the Desktop's <strong>Save
143 Project</strong> File menu option, or by using the <strong>Save
147 <li><strong>Edit</strong>
149 <li><strong>Undo (Control Z)</strong><em><br>
150 This will undo any edits you make to the alignment. This
151 applies to insertion or deletion of gaps, cutting residues
152 or sequences from the alignment or pasting sequences to the
153 current alignment or sorting the alignment. <strong>NOTE:</strong>
154 It DOES NOT undo colour changes, adjustments to group sizes,
155 or changes to the annotation panel. </em></li>
156 <li><strong>Redo (Control Y)<br>
157 </strong><em>Any actions which you undo can be redone using redo. </em></li>
158 <li><strong>Cut (Control X)<br>
159 </strong><em>This will make a copy of the currently selected
160 residues before removing them from your alignment. Click on
161 a sequence name if you wish to select a whole sequence. <br>
162 Use <CTRL> and X (<APPLE> and X on MacOSX) to
165 <li><strong>Copy (Control C)</strong><br> <em>Copies
166 the currently selected residues to the system clipboard -
167 you can also do this by pressing <CTRL> and C
168 (<APPLE> and C on MacOSX). <br> If you try to
169 paste the clipboard contents to a text editor, you will see
170 the format of the copied residues FASTA.
172 <li><strong>Copy Highlighted region (Control Shift
173 C)</strong><br> <em>Copies each stretch of highlighted
174 residues as a new sequence on the system clipboard - you can
175 also do this by pressing <CTRL> <SHIFT> and C
176 (<APPLE> <SHIFT> and C on MacOSX). <br>Use
177 this when you want to extract sequence regions highlighted
178 as a result of a Find operation, or due to mouseovers or
179 selections made in other views such as an assocated 3D
182 <li><strong>Paste </strong>
184 <li><strong>To New Alignment (Control Shift V)<br>
185 </strong><em>A new alignment window will be created from
186 sequences previously copied or cut to the system
187 clipboard. <br> Use <CTRL> and <SHIFT>
188 and V(<APPLE> and <SHIFT;> and and V on
191 <li><strong>Add To This Alignment (Control V)<br>
192 </strong><em>Copied sequences from another alignment window can
193 be added to the current Jalview alignment. </em></li>
195 <li><strong>Delete (Backspace)<br>
196 </strong><em>This will delete the currently selected residues
197 without copying them to the clipboard. Like the other edit
198 operations, this can be undone with <strong>Undo</strong>.
200 <li><strong>Remove Left (Control L)<br>
201 </strong><em>If the alignment has marked columns, the alignment will
202 be trimmed to the left of the leftmost marked column. To
203 mark a column, mouse click the scale bar above the
204 alignment. Click again to unmark a column, or select
205 "Deselect All" to deselect all columns.</em></li>
206 <li><strong>Remove Right (Control R)<br>
207 </strong><em>If the alignment has marked columns, the alignment will
208 be trimmed to the right of the rightmost marked column. To
209 mark a column, mouse click the scale bar above the
210 alignment. Click again to unmark a column, or select
211 "Deselect All" to deselect all columns.</em></li>
212 <li><strong>Remove Empty Columns (Control E)<br>
213 </strong><em>All columns which only contain gap characters
214 ("-", ".") will be deleted.<br> You
215 may set the default gap character in <a
216 href="../features/preferences.html">preferences</a>.
218 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
219 <em>Gap characters ("-", ".") will be
220 deleted from the selected area of the alignment. If no
221 selection is made, ALL the gaps in the alignment will be
222 removed.<br> You may set the default gap character in <a
223 href="../features/preferences.html">preferences</a>.
225 <li><strong>Remove Redundancy (Control D)<br>
226 </strong><em>Selecting this option brings up a window asking you to
227 select a threshold. If the percentage identity between any
228 two sequences (under the current alignment) exceeds this
229 value then one of the sequences (the shorter) is discarded.
230 Press the "Apply" button to remove redundant
231 sequences. The "Undo" button will undo the last
232 redundancy deletion.</em></li>
233 <li><strong>Pad Gaps<br>
234 </strong><em>When selected, the alignment will be kept at minimal
235 width (so there are no empty columns before or after the
236 first or last aligned residue) and all sequences will be
237 padded with gap characters before and after their
238 terminating residues.<br> This switch is useful when
239 making a tree using unaligned sequences and when working
240 with alignment analysis programs which require 'properly
241 aligned sequences' to be all the same length.<br> You
242 may set the default for <strong>Pad Gaps</strong> in the <a
243 href="../features/preferences.html">preferences</a>.
246 <li><strong>Select</strong>
248 <li><a href="../features/search.html"><strong>Find...
249 (Control F)</strong></a><br> <em>Opens the Find dialog box to
250 search for residues, sequence name or residue position
251 within the alignment and create new sequence features from
253 <li><strong>Select All (Control A)</strong><strong><br>
254 </strong><em>Selects all the sequences and residues in the
255 alignment. <br> Use <CTRL> and A (<APPLE>
256 and A on a MacOSX) to select all.
258 <li><strong>Deselect All (Escape)<br>
259 </strong><em>Removes the current selection box (red dashed box) from
260 the alignment window. All selected sequences, residues and
261 marked columns will be deselected. </em><em> <br> Use
262 <ESCAPE> to deselect all.
264 <li><strong>Invert Sequence Selection (Control I)<br>
265 </strong><em>Any sequence ids currently not selected will replace
266 the current selection. </em></li>
267 <li><strong>Invert Column Selection (Control Alt
269 </strong><em>Any columns currently not selected will replace the
270 current column selection. </em></li>
271 <li><strong>Create Group (Control G)<br></strong> <em>Create
272 a group containing the currently selected sequences.</em></li>
273 <li><strong>Remove Group (Shift Control G)<br></strong>
274 <em>Ungroup the currently selected sequence group.</em></li>
275 <li><strong>Make Groups for selection<br /></strong> <em>The
276 currently selected groups of the alignment will be
277 subdivided according to the contents of the currently
278 selected region. <br />Use this to subdivide an alignment
279 based on the different combinations of residues at marked
282 <li><strong>Undefine Groups (Control U)<br>
283 </strong><em>The alignment will be reset with no defined groups.<br>
284 <strong>WARNING</strong>: This cannot be undone.
287 href="../features/columnFilterByAnnotation.html">Select/Hide
288 Columns by Annotation</a></strong> <br /> <em>Select or Hide
289 columns in the alignment according to secondary structure,
290 labels and values shown in alignment annotation rows. </em></li>
291 <li><strong>Select Highlighted Columns</strong> <br /> <em>Selects
292 the columns currently highlighted as a result of a find, mouse
293 over, or selection event from a linked structure viewer or other
294 application. Modifiers will work on some platforms: ALT will add
295 all but the highlighted set to the column selection, and CTRL
296 (or META) will toggle the selection. </em></li>
298 <li><strong>View</strong>
300 <li><strong>New View (Control T)</strong><em><br>
301 Creates a new view from the current alignment view. </em></li>
302 <li><strong>Expand Views (X)</strong><em><br>
303 Display each view associated with the alignment in its own
304 alignment window, allowing several views to be displayed
305 simultaneously. </em></li>
306 <li><strong>Gather Views (G)</strong><em><br>
307 Each view associated with the alignment will be displayed
308 within its own tab on the current alignment window. </em></li>
309 <li><strong>Show→(all Columns / Sequences /
310 Sequences and Columns)</strong><em><br> All hidden Columns
311 / Sequences / Sequences and Columns will be revealed. </em></li>
312 <li><strong>Hide→(all Columns / Sequences /
313 Selected Region / All but Selected Region )</strong><em><br>
314 Hides the all the currently selected Columns / Sequences /
315 Region or everything but the selected Region.</em></li>
316 <li><strong>Automatic Scrolling<br>
317 </strong><em>When selected, the view will automatically scroll to
318 display the highlighted sequence position corresponding to
319 the position under the mouse pointer in a linked alignment
320 or structure view.</em></li>
321 <li><strong>Show Sequence Features</strong><br> <em>Show
322 or hide sequence features on this alignment.</em></li>
324 href="../features/featuresettings.html">Sequence
325 Feature Settings...</a> </strong><br> <em>Opens the
326 Sequence Feature Settings dialog box to control the colour
327 and display of sequence features on the alignment.</em></li>
328 <li><strong>Sequence ID Tooltip</strong><em>
329 (application only) <br>This submenu's options allow the
330 inclusion or exclusion of non-positional sequence features
331 or database cross references from the tooltip shown when the
332 mouse hovers over the sequence ID panel.
334 <li><strong>Alignment Properties...<br />
335 </strong><em>Displays some simple statistics computed for the
336 current alignment view and any named properties defined on
337 the whole alignment.</em></li>
338 <li><strong><a href="../features/overview.html">Overview
339 Window</a><br> </strong><em>A scaled version of the alignment
340 will be displayed in a small window. A red box will indicate
341 the currently visible area of the alignment. Move the
342 visible region using the mouse. </em></li>
344 <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
346 <li><strong>Show Annotations<br>
347 </strong><em>If this is selected the "Annotation Panel"
348 will be displayed below the alignment. The default setting
349 is to display the conservation calculation, quality
350 calculation and consensus values as bar charts. </em></li>
351 <li><strong>Show Alignment Related</strong><em><br>
352 Show all annotations that are for the alignment as a whole
353 (for example, Consensus, or secondary structure prediction
354 from alignment).</em></li>
355 <li><strong>Hide Alignment Related</strong><em><br>
356 Hide all annotations that are for the alignment as a whole.</em></li>
357 <li><strong>Show Sequence Related</strong><em><br>
358 Show all annotations that are for individual sequences.</em></li>
359 <li><strong>Hide Sequence Related</strong><em><br>
360 Hide all annotations that are for individual sequences.</em></li>
361 <li><em>You can also selectively show or hide
362 annotations from the <a href="./popupMenu.html">Popup</a> or
363 <a href="../features/annotation.html">Annotation</a> menus.
365 <li><strong>Sort by Sequence</strong><em><br>Sort
366 sequence-specific annotations by sequence order in the
367 alignment (and within that, by label).</em></li>
368 <li><strong>Sort by Label</strong><em><br>Sort
369 sequence-specific annotations by label (and within that, by
370 sequence order). If neither sort order is selected, no
371 sorting is applied, allowing you to make a manual ordering
372 of the annotations.</em></li>
373 <li><strong>Autocalculated Annotation<br>
374 </strong><em>Settings for the display of autocalculated annotation.</em>
376 <li><strong>Show first<br></strong><em> Show
377 autocalculated annotations above sequence-specific
378 annotations. Note this also applies to other annotations
379 for the alignment, for example secondary structure
380 prediction from alignment.</em></li>
381 <li><strong>Show last<br></strong><em> Show
382 autocalculated / alignment annotations below
383 sequence-specific annotations.</em></li>
384 <li><strong>Apply to all groups<br>
385 </strong><em> When ticked, any modification to the current
386 settings will be applied to all autocalculated
387 annotation.</em></li>
388 <li><strong>Show Consensus Histogram<br>
389 </strong><em> Enable or disable the display of the histogram
390 above the consensus sequence.</em></li>
391 <li><strong>Show Consensus Logo<br>
392 </strong><em> Enable or disable the display of the Consensus
393 Logo above the consensus sequence.</em></li>
394 <li><strong>Normalise Consensus Logo<br>
395 </strong><em>When enabled, scales all logo stacks to the same
396 height, making it easier to compare symbol diversity in
397 highly variable regions.</em></li>
398 <li><strong>Group Conservation<br>
399 </strong><em> When ticked, display a conservation row for all
400 groups (only available for protein alignments).</em></li>
401 <li><strong>Group Consensus<br>
402 </strong><em> When ticked, display a consensus row for all
406 <li><strong>Alignment Window Format Menu</strong>
408 <li><strong>Font...<br>
409 </strong><em>Opens the "Choose Font" dialog box, in order
410 to change the font of the display and enable or disable
411 'smooth fonts' (anti-aliasing) for faster alignment
412 rendering. </em></li>
414 </strong><em>When ticked, the alignment display is "<a
415 href="../features/wrap.html">wrapped</a>" to
416 the width of the alignment window. This is useful if your
417 alignment has only a few sequences to view its full width at
419 </em><br> Additional options for display of sequence numbering
420 and scales are also visible in wrapped layout mode:<br>
422 <li><strong>Scale Above</strong><br> <em>
423 Show the alignment column position scale.</em></li>
424 <li><strong>Scale Left</strong><br> <em> Show
425 the sequence position for the first aligned residue in
426 each row in the left column of the alignment.</em></li>
427 <li><strong>Scale Right</strong><br> <em>
428 Show the sequence position for the last aligned residue
429 in each row in the right-most column of the alignment.</em></li>
430 <li><strong>Show Sequence Limits<br>
431 </strong><em>If this box is selected the sequence name will have
432 the start and end position of the sequence appended to
433 the name, in the format NAME/START-END</em></li>
434 <li><strong>Right Align Sequence ID<br>
435 </strong><em>If this box is selected then the sequence names
436 displayed in the sequence label area will be aligned
437 against the left-hand edge of the alignment display,
438 rather than the left-hand edge of the alignment window.</em>
440 <li><strong>Show Hidden Markers<br>
441 </strong><em>When this box is selected, positions in the
442 alignment where rows and columns are hidden will be
443 marked by blue arrows. </em></li>
444 <li><strong>Boxes</strong><em><br> If this is
445 selected the background of a residue will be coloured
446 using the selected background colour. Useful if used in
447 conjunction with "Colour Text." </em></li>
449 </strong><em>If this is selected the residues will be displayed
450 using the standard 1 character amino acid alphabet.</em></li>
451 <li><strong>Colour Text<br>
452 </strong><em>If this is selected the residues will be coloured
453 according to the background colour associated with that
454 residue. The colour is slightly darker than background
455 so the amino acid symbol remains visible. </em></li>
456 <li><strong>Show Gaps<br>
457 </strong><em>When this is selected, gap characters will be
458 displayed as "." or "-". If
459 unselected, then gap characters will appear as blank
460 spaces. <br> You may set the default gap character
461 in <a href="../features/preferences.html">preferences</a>.
463 <li><strong>Centre Annotation Labels<br>
464 </strong><em>Select this to center labels along an annotation
465 row relative to their associated column (default is off,
466 i.e. left-justified).</em></li>
467 <li><strong>Show Unconserved<br>
468 </strong><em>When this is selected, all consensus sequence
469 symbols will be rendered as a '.', highlighting
470 mutations in highly conserved alignments. </em></li>
477 <li><strong>Colour</strong>
479 <li><strong>Apply Colour To All Groups<br>
480 </strong><em>If this is selected, any changes made to the background
481 colour will be applied to all currently defined groups.<br>
484 href="../colourSchemes/textcolour.html">Colour
485 Text...</a> </strong><em><br> Opens the Colour Text dialog box
486 to set a different text colour for light and dark background,
487 and the intensity threshold for transition between them. </em></li>
488 <li>Colour Scheme options: <strong>None, ClustalX,
489 Blosum62 Score, Percentage Identity, Zappo, Taylor,
490 gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
491 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
492 Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
494 </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
495 for a description of all colour schemes.
497 <li><strong>Sequence ID<br></strong><em>Shades
498 sequences using their Sequence ID colour. Useful when
500 href="../calculations/treeviewer.html#partitioning">tree
501 based subfamily analysis</a>.
503 <li><strong>By Conservation<br>
504 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
507 <li><strong>Modify Conservation Threshold<br>
508 </strong><em>Use this to display the conservation threshold slider
509 window. Useful if the window has been closed, or if the 'by
510 conservation' option appears to be doing nothing!</em><br></li>
511 <li><strong>Above Identity Threshold<br>
512 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
513 Percentage Identity</a>
516 <li><strong>Modify Identity Threshold<br>
517 </strong><em>Use this to set the threshold value for colouring above
518 Identity. Useful if the window has been closed.<br>
520 <li><strong>By Annotation</strong><br> <em>Colours
521 the alignment on a per-column value from a specified
523 href="../colourSchemes/annotationColouring.html">Annotation
526 <li><strong>By RNA Helices</strong><br> <em>Colours
527 the helices of an RNA alignment loaded from a Stockholm file.
528 See <a href="../colourSchemes/rnahelicesColouring.html">RNA
529 Helices Colouring</a>.
532 <li><strong>Calculate</strong>
534 <li><strong>Sort </strong>
536 <li><strong>by ID</strong><em><br> This will
537 sort the sequences according to sequence name. If the sort
538 is repeated, the order of the sorted sequences will be
540 <li><strong>by Length</strong><em><br> This
541 will sort the sequences according to their length
542 (excluding gap characters). If the sort is repeated, the
543 order of the sorted sequences will be inverted. </em></li>
544 <li><strong>by Group</strong><strong><br> </strong><em>This
545 will sort the sequences according to sequence name. If the
546 sort is repeated, the order of the sorted sequences will
547 be inverted. </em><strong></strong></li>
548 <li><strong>by Pairwise Identity<br>
549 </strong><em>This will sort the selected sequences by their
550 percentage identity to the consensus sequence. The most
551 similar sequence is put at the top. </em></li>
552 <li><em>The <a href="../calculations/sorting.html">Sort
553 menu</a> will have some additional options if you have just
554 done a multiple alignment calculation, or opened a tree
558 <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
559 <a href="../calculations/calculations.html">calculations dialog</a> for
560 for calculating <a href="../calculations/tree.html">trees</a> or
561 <a href="../calculations/pca.html">principal component analysis
562 plots</a> on the alignment or the currently selected
565 <li><strong>Pairwise Alignments</strong><br> <em>Applies
566 Smith and Waterman algorithm to selected sequences. See <a
567 href="../calculations/pairwise.html">pairwise
570 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
571 option is only visible if Jalview detects one or more
572 white-space separated values in the description line of the
573 alignment sequences.<br> When selected, these numbers are
574 parsed into sequence associated annotation which can then be
575 used to sort the alignment via the Sort by→Score menu.
577 <li><strong>Autocalculate Consensus</strong><br> <em>For
578 large alignments it can be useful to deselect
579 "Autocalculate Consensus" when editing. This
580 prevents the sometimes lengthy calculations performed after
581 each sequence edit.</em> <br></li>
582 <li><strong>Sort With New Tree</strong><br> <em>When
583 enabled, Jalview will automatically sort the alignment when a
584 new tree is calculated or loaded onto it.</em> <br></li>
585 <li><strong>Show Flanking Regions</strong><br> <em>Opens
586 a new alignment window showing any additional sequence data
587 either side of the current alignment. Useful in conjunction
588 with 'Fetch Database References' when the 'Trim Retrieved
589 Sequences' option is disabled to retrieve full length
590 sequences for a set of aligned peptides. </em></li>
593 <li><strong>Web Service Menu</strong><br /> <em>This menu
594 is dynamic, and may contain user-defined web service entries in
595 addition to any of the following ones:</em>
597 <li><strong>Fetch DB References</strong><br> <em>This
598 submenu contains options for accessing any of the database
599 services that Jalview is aware of (e.g. those provided by
600 EMBL-EBI) to verify sequence start/end positions and retrieve all
601 database cross references and PDB ids associated with all or just
602 the selected sequences in the alignment.
604 <li>'Trim Retrieved Sequences' - when checked, Jalview will
605 discard any additional sequence data for accessions associated
606 with sequences in the alignment. <br> <strong>Note:
607 Disabling this could cause out of memory errors when working
608 with genomic sequence records !</strong><br> <strong>Added
609 in Jalview 2.8.1</strong>
611 <li>'Standard Databases' will check sequences against the
613 </ul> Other sub-menus allow you to pick a specific source to query -
614 sources are listed alphabetically according to their nickname.
617 <p>Selecting items from the following submenus will start a
618 remote service on compute facilities at the University of Dundee,
619 or elsewhere. You need a continuous network connection in order to
620 use these services through Jalview.</p>
622 <li><strong>Alignment</strong><br /> <em> Align the
623 currently selected sequences or all sequences in the
624 alignment, or re-align unaligned sequences to the aligned
625 sequences. Entries in this menu provide access to the various
626 alignment programs supported by <a
627 href="../webServices/JABAWS.html">JABAWS</a>. See the
628 <a href="../webServices/msaclient.html">Multiple Sequence
629 Alignment webservice client</a> entry for more information.
631 <li><strong>Secondary Structure Prediction</strong>
633 <li><strong>JPred Secondary Structure Prediction</strong><br>
634 <em>Secondary structure prediction by network
635 consensus. See the <a href="../webServices/jnet.html">Jpred</a>
636 client entry for more information. The behaviour of this
637 calculation depends on the current selection:
639 <li>If nothing is selected, and the displayed
640 sequences appear to be aligned, then a JPred prediction
641 will be run for the first sequence in the alignment,
642 using the current alignment. Otherwise the first
643 sequence will be submitted for prediction.</li>
644 <li>If just one sequence (or a region on one
645 sequence) has been selected, it will be submitted to
646 the automatic JPred prediction server for homolog
647 detection and prediction.</li>
648 <li>If a set of sequences are selected, and they
649 appear to be aligned, then the alignment will be used
650 for a JPred prediction on the <strong>first</strong>
651 sequence in the set (that is, the one that appears
652 first in the alignment window).
657 <li><strong>Analysis</strong><br />
659 <li><strong>Multi-Harmony</strong><br> <em>Performs
660 functional residue analysis on a protein family alignment
661 with sub-families defined on it. See the <a
662 href="../webServices/shmr.html">Multi-Harmony
663 service</a> entry for more information.