3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
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6 * This file is part of Jalview.
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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"
137 >sequence features</a> or <a
138 href="../features/annotationsFormat.html"
139 >alignment annotations</a>.
141 <li><strong>Close (Control W)</strong><br> <em>Close
142 the alignment window. Make sure you have saved your
143 alignment before you close - either from the Desktop's <strong>Save
144 Project</strong> File menu option, or by using the <strong>Save
148 <li><strong>Edit</strong>
150 <li><strong>Undo (Control Z)</strong><em><br>
151 This will undo any edits you make to the alignment. This
152 applies to insertion or deletion of gaps, cutting residues
153 or sequences from the alignment or pasting sequences to the
154 current alignment or sorting the alignment. <strong>NOTE:</strong>
155 It DOES NOT undo colour changes, adjustments to group sizes,
156 or changes to the annotation panel. </em></li>
157 <li><strong>Redo (Control Y)<br>
158 </strong><em>Any actions which you undo can be redone using redo. </em></li>
159 <li><strong>Cut (Control X)<br>
160 </strong><em>This will make a copy of the currently selected
161 residues before removing them from your alignment. Click on
162 a sequence name if you wish to select a whole sequence. <br>
163 Use <CTRL> and X (<APPLE> and X on MacOSX) to
166 <li><strong>Copy (Control C)</strong><br> <em>Copies
167 the currently selected residues to the system clipboard -
168 you can also do this by pressing <CTRL> and C
169 (<APPLE> and C on MacOSX). <br> If you try to
170 paste the clipboard contents to a text editor, you will see
171 the format of the copied residues FASTA.
173 <li><strong>Paste </strong>
175 <li><strong>To New Alignment (Control Shift V)<br>
176 </strong><em>A new alignment window will be created from
177 sequences previously copied or cut to the system
178 clipboard. <br> Use <CTRL> and <SHIFT>
179 and V(<APPLE> and <SHIFT;> and and V on
182 <li><strong>Add To This Alignment (Control V)<br>
183 </strong><em>Copied sequences from another alignment window can
184 be added to the current Jalview alignment. </em></li>
186 <li><strong>Delete (Backspace)<br>
187 </strong><em>This will delete the currently selected residues
188 without copying them to the clipboard. Like the other edit
189 operations, this can be undone with <strong>Undo</strong>.
191 <li><strong>Remove Left (Control L)<br>
192 </strong><em>If the alignment has marked columns, the alignment will
193 be trimmed to the left of the leftmost marked column. To
194 mark a column, mouse click the scale bar above the
195 alignment. Click again to unmark a column, or select
196 "Deselect All" to deselect all columns.</em></li>
197 <li><strong>Remove Right (Control R)<br>
198 </strong><em>If the alignment has marked columns, the alignment will
199 be trimmed to the left of the leftmost marked column. To
200 mark a column, mouse click the scale bar above the
201 alignment. Click again to unmark a column, or select
202 "Deselect All" to deselect all columns.</em></li>
203 <li><strong>Remove Empty Columns (Control E)<br>
204 </strong><em>All columns which only contain gap characters
205 ("-", ".") will be deleted.<br> You
206 may set the default gap character in <a
207 href="../features/preferences.html"
210 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
211 <em>Gap characters ("-", ".") will be
212 deleted from the selected area of the alignment. If no
213 selection is made, ALL the gaps in the alignment will be
214 removed.<br> You may set the default gap character in <a
215 href="../features/preferences.html"
218 <li><strong>Remove Redundancy (Control D)<br>
219 </strong><em>Selecting this option brings up a window asking you to
220 select a threshold. If the percentage identity between any
221 two sequences (under the current alignment) exceeds this
222 value then one of the sequences (the shorter) is discarded.
223 Press the "Apply" button to remove redundant
224 sequences. The "Undo" button will undo the last
225 redundancy deletion.</em></li>
226 <li><strong>Pad Gaps<br>
227 </strong><em>When selected, the alignment will be kept at minimal
228 width (so there are no empty columns before or after the
229 first or last aligned residue) and all sequences will be
230 padded with gap characters before and after their
231 terminating residues.<br> This switch is useful when
232 making a tree using unaligned sequences and when working
233 with alignment analysis programs which require 'properly
234 aligned sequences' to be all the same length.<br> You
235 may set the default for <strong>Pad Gaps</strong> in the <a
236 href="../features/preferences.html"
240 <li><strong>Select</strong>
242 <li><a href="../features/search.html"><strong>Find...
243 (Control F)</strong></a><br> <em>Opens the Find dialog box to
244 search for residues, sequence name or residue position
245 within the alignment and create new sequence features from
247 <li><strong>Select All (Control A)</strong><strong><br>
248 </strong><em>Selects all the sequences and residues in the
249 alignment. <br> Use <CTRL> and A (<APPLE>
250 and A on a MacOSX) to select all.
252 <li><strong>Deselect All (Escape)<br>
253 </strong><em>Removes the current selection box (red dashed box) from
254 the alignment window. All selected sequences, residues and
255 marked columns will be deselected. </em><em> <br> Use
256 <ESCAPE> to deselect all.
258 <li><strong>Invert Sequence Selection (Control I)<br>
259 </strong><em>Any sequence ids currently not selected will replace
260 the current selection. </em></li>
261 <li><strong>Invert Column Selection (Control Alt
263 </strong><em>Any columns currently not selected will replace the
264 current column selection. </em></li>
265 <li><strong>Create Group (Control G)<br></strong> <em>Create
266 a group containing the currently selected sequences.</em></li>
267 <li><strong>Remove Group (Shift Control G)<br></strong>
268 <em>Ungroup the currently selected sequence group.</em></li>
269 <li><strong>Make Groups for selection<br /></strong> <em>The
270 currently selected groups of the alignment will be
271 subdivided according to the contents of the currently
272 selected region. <br />Use this to subdivide an alignment
273 based on the different combinations of residues at marked
276 <li><strong>Undefine Groups (Control U)<br>
277 </strong><em>The alignment will be reset with no defined groups.<br>
278 <strong>WARNING</strong>: This cannot be undone.
281 href="../features/columnFilterByAnnotation.html"
282 >Select/Hide Columns by Annotation</a></strong> <br /> <em>Select
283 or Hide columns in the alignment according to secondary
284 structure, labels and values shown in alignment annotation
287 <li><strong>View</strong>
289 <li><strong>New View (Control T)</strong><em><br>
290 Creates a new view from the current alignment view. </em></li>
291 <li><strong>Expand Views (X)</strong><em><br>
292 Display each view associated with the alignment in its own
293 alignment window, allowing several views to be displayed
294 simultaneously. </em></li>
295 <li><strong>Gather Views (G)</strong><em><br>
296 Each view associated with the alignment will be displayed
297 within its own tab on the current alignment window. </em></li>
298 <li><strong>Show→(all Columns / Sequences /
299 Sequences and Columns)</strong><em><br> All hidden Columns
300 / Sequences / Sequences and Columns will be revealed. </em></li>
301 <li><strong>Hide→(all Columns / Sequences /
302 Selected Region / All but Selected Region )</strong><em><br>
303 Hides the all the currently selected Columns / Sequences /
304 Region or everything but the selected Region.</em></li>
305 <li><strong>Automatic Scrolling<br>
306 </strong><em>When selected, the view will automatically scroll to
307 display the highlighted sequence position corresponding to
308 the position under the mouse pointer in a linked alignment
309 or structure view.</em></li>
310 <li><strong>Show Sequence Features</strong><br> <em>Show
311 or hide sequence features on this alignment.</em></li>
313 href="../features/featuresettings.html"
314 >Sequence Feature Settings...</a> </strong><em><br> <em>Opens
315 the Sequence Feature Settings dialog box to control the
316 colour and display of sequence features on the alignment,
317 and configure and retrieve features from DAS annotation
319 <li><strong>Sequence ID Tooltip</strong><em>
320 (application only) <br>This submenu's options allow the
321 inclusion or exclusion of non-positional sequence features
322 or database cross references from the tooltip shown when the
323 mouse hovers over the sequence ID panel.
325 <li><strong>Alignment Properties...<br />
326 </strong><em>Displays some simple statistics computed for the
327 current alignment view and any named properties defined on
328 the whole alignment.</em></li>
329 <li><strong><a href="../features/overview.html">Overview
330 Window</a><br> </strong><em>A scaled version of the alignment
331 will be displayed in a small window. A red box will indicate
332 the currently visible area of the alignment. Move the
333 visible region using the mouse. </em></li>
335 <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
337 <li><strong>Show Annotations<br>
338 </strong><em>If this is selected the "Annotation Panel"
339 will be displayed below the alignment. The default setting
340 is to display the conservation calculation, quality
341 calculation and consensus values as bar charts. </em></li>
342 <li><strong>Show Alignment Related</strong><em><br>
343 Show all annotations that are for the alignment as a whole
344 (for example, Consensus, or secondary structure prediction
345 from alignment).</em></li>
346 <li><strong>Hide Alignment Related</strong><em><br>
347 Hide all annotations that are for the alignment as a whole.</em></li>
348 <li><strong>Show Sequence Related</strong><em><br>
349 Show all annotations that are for individual sequences.</em></li>
350 <li><strong>Hide Sequence Related</strong><em><br>
351 Hide all annotations that are for individual sequences.</em></li>
352 <li><em>You can also selectively show or hide
353 annotations from the <a href="./popupMenu.html">Popup</a> or
354 <a href="../features/annotation.html">Annotation</a> menus.
356 <li><strong>Sort by Sequence</strong><em><br>Sort
357 sequence-specific annotations by sequence order in the
358 alignment (and within that, by label).</em></li>
359 <li><strong>Sort by Label</strong><em><br>Sort
360 sequence-specific annotations by label (and within that, by
361 sequence order). If neither sort order is selected, no
362 sorting is applied, allowing you to make a manual ordering
363 of the annotations.</em></li>
364 <li><strong>Autocalculated Annotation<br>
365 </strong><em>Settings for the display of autocalculated annotation.</em>
367 <li><strong>Show first<br></strong><em> Show
368 autocalculated annotations above sequence-specific
369 annotations. Note this also applies to other annotations
370 for the alignment, for example secondary structure
371 prediction from alignment.</em></li>
372 <li><strong>Show last<br></strong><em> Show
373 autocalculated / alignment annotations below
374 sequence-specific annotations.</em></li>
375 <li><strong>Apply to all groups<br>
376 </strong><em> When ticked, any modification to the current
377 settings will be applied to all autocalculated
378 annotation.</em></li>
379 <li><strong>Show Consensus Histogram<br>
380 </strong><em> Enable or disable the display of the histogram
381 above the consensus sequence.</em></li>
382 <li><strong>Show Consensus Logo<br>
383 </strong><em> Enable or disable the display of the Consensus
384 Logo above the consensus sequence.</em></li>
385 <li><strong>Normalise Consensus Logo<br>
386 </strong><em>When enabled, scales all logo stacks to the same
387 height, making it easier to compare symbol diversity in
388 highly variable regions.</em></li>
389 <li><strong>Group Conservation<br>
390 </strong><em> When ticked, display a conservation row for all
391 groups (only available for protein alignments).</em></li>
392 <li><strong>Group Consensus<br>
393 </strong><em> When ticked, display a consensus row for all
397 <li><strong>Alignment Window Format Menu</strong>
399 <li><strong>Font...<br>
400 </strong><em>Opens the "Choose Font" dialog box, in order
401 to change the font of the display and enable or disable
402 'smooth fonts' (anti-aliasing) for faster alignment
403 rendering. </em></li>
405 </strong><em>When ticked, the alignment display is "<a
406 href="../features/wrap.html"
407 >wrapped</a>" to the width of the alignment window. This is
408 useful if your alignment has only a few sequences to view
409 its full width at once.
410 </em><br> Additional options for display of sequence numbering
411 and scales are also visible in wrapped layout mode:<br>
413 <li><strong>Scale Above</strong><br>
414 <em> Show the alignment column position scale.</em></li>
415 <li><strong>Scale Left</strong><br>
416 <em> Show the sequence position for the first aligned
417 residue in each row in the left column of the alignment.</em></li>
418 <li><strong>Scale Right</strong><br>
419 <em> Show the sequence position for the last aligned
420 residue in each row in the right-most column of the
422 <li><strong>Show Sequence Limits<br>
423 </strong><em>If this box is selected the sequence name will have
424 the start and end position of the sequence appended to
425 the name, in the format NAME/START-END</em></li>
426 <li><strong>Right Align Sequence ID<br>
427 </strong><em>If this box is selected then the sequence names
428 displayed in the sequence label area will be aligned
429 against the left-hand edge of the alignment display,
430 rather than the left-hand edge of the alignment window.
432 <li><strong>Show Hidden Markers<br>
433 </strong><em>When this box is selected, positions in the
434 alignment where rows and columns are hidden will be
435 marked by blue arrows. </li>
436 <li><strong>Boxes</strong><em><br> If this is
437 selected the background of a residue will be coloured
438 using the selected background colour. Useful if used in
439 conjunction with "Colour Text." </em></li>
441 </strong><em>If this is selected the residues will be displayed
442 using the standard 1 character amino acid alphabet.</em></li>
443 <li><strong>Colour Text<br>
444 </strong><em>If this is selected the residues will be coloured
445 according to the background colour associated with that
446 residue. The colour is slightly darker than background
447 so the amino acid symbol remains visible. </em></li>
448 <li><strong>Show Gaps<br>
449 </strong><em>When this is selected, gap characters will be
450 displayed as "." or "-". If
451 unselected, then gap characters will appear as blank
452 spaces. <br> You may set the default gap character
453 in <a href="../features/preferences.html">preferences</a>.
455 <li><strong>Centre Annotation Labels<br>
456 </strong><em>Select this to center labels along an annotation
457 row relative to their associated column (default is off,
458 i.e. left-justified).</em></li>
459 <li><strong>Show Unconserved<br>
460 </strong><em>When this is selected, all consensus sequence
461 symbols will be rendered as a '.', highlighting
462 mutations in highly conserved alignments. </em></li>
470 <li><strong>Colour</strong>
472 <li><strong>Apply Colour To All Groups<br>
473 </strong><em>If this is selected, any changes made to the background
474 colour will be applied to all currently defined groups.<br>
477 href="../colourSchemes/textcolour.html"
478 >Colour Text...</a> </strong><em><br> Opens the Colour Text
479 dialog box to set a different text colour for light and dark
480 background, and the intensity threshold for transition between
482 <li>Colour Scheme options: <strong>None, ClustalX,
483 Blosum62 Score, Percentage Identity, Zappo, Taylor,
484 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
485 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
487 </strong> <em>See <a href="../colourSchemes/index.html">colours</a>
488 for a description of all colour schemes.
490 <li><strong>By Conservation<br>
491 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
494 <li><strong>Modify Conservation Threshold<br>
495 </strong><em>Use this to display the conservation threshold slider
496 window. Useful if the window has been closed, or if the 'by
497 conservation' option appears to be doing nothing!</em><br></li>
498 <li><strong>Above Identity Threshold<br>
499 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
500 Percentage Identity</a>
503 <li><strong>Modify Identity Threshold<br>
504 </strong><em>Use this to set the threshold value for colouring above
505 Identity. Useful if the window has been closed.<br>
507 <li><strong>By Annotation</strong><br> <em>Colours
508 the alignment on a per-column value from a specified
510 href="../colourSchemes/annotationColouring.html"
511 >Annotation Colouring</a>.
513 <li><strong>By RNA Helices</strong><br> <em>Colours
514 the helices of an RNA alignment loaded from a Stockholm file.
515 See <a href="../colourSchemes/rnahelicesColouring.html">RNA
516 Helices Colouring</a>.
519 <li><strong>Calculate</strong>
521 <li><strong>Sort </strong>
523 <li><strong>by ID</strong><em><br> This will
524 sort the sequences according to sequence name. If the sort
525 is repeated, the order of the sorted sequences will be
527 <li><strong>by Length</strong><em><br> This
528 will sort the sequences according to their length
529 (excluding gap characters). If the sort is repeated, the
530 order of the sorted sequences will be inverted. </em></li>
531 <li><strong>by Group</strong><strong><br> </strong><em>This
532 will sort the sequences according to sequence name. If the
533 sort is repeated, the order of the sorted sequences will
534 be inverted. </em><strong></strong></li>
535 <li><strong>by Pairwise Identity<br>
536 </strong><em>This will sort the selected sequences by their
537 percentage identity to the consensus sequence. The most
538 similar sequence is put at the top. </em></li>
539 <li><em>The <a href="../calculations/sorting.html">Sort
540 menu</a> will have some additional options if you have just
541 done a multiple alignment calculation, or opened a tree
545 <li><strong>Calculate Tree </strong> <br> <em>Functions
546 for calculating trees on the alignment or the currently
547 selected region. See <a href="../calculations/tree.html">calculating
551 <li><strong>Neighbour Joining Using PAM250 </strong></li>
552 <li><strong>Neighbour Joining Using Sequence
553 Feature Similarity</strong></li>
554 <li><strong>Neighbour Joining Using Blosum62 </strong></li>
555 <li><strong>Neighbour Joining Using % Identity</strong></li>
556 <li><strong>Average Distance Using PAM250 </strong></li>
557 <li><strong>Average Distance Using Sequence
558 Feature Similarity</strong></li>
559 <li><strong>Average Distance Using Blosum62</strong></li>
560 <li><strong>Average Distance Using % Identity</strong></li>
561 </ul> <strong>Note: Since Version 2.8.1, a number of
562 additional similarity measures for tree calculation are
563 provided in this menu.</strong></li>
564 <li><strong>Pairwise Alignments</strong><br> <em>Applies
565 Smith and Waterman algorithm to selected sequences. See <a
566 href="../calculations/pairwise.html"
567 >pairwise alignments</a>.
569 <li><strong>Principal Component Analysis</strong><br> <em>Shows
570 a spatial clustering of the sequences based on similarity
571 scores calculated with the alignment. See <a
572 href="../calculations/pca.html"
573 >Principal Component Analysis</a>.
575 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
576 option is only visible if Jalview detects one or more
577 white-space separated values in the description line of the
578 alignment sequences.<br> When selected, these numbers are
579 parsed into sequence associated annotation which can then be
580 used to sort the alignment via the Sort by→Score menu.
582 <li><strong>Autocalculate Consensus</strong><br> <em>For
583 large alignments it can be useful to deselect
584 "Autocalculate Consensus" when editing. This
585 prevents the sometimes lengthy calculations performed after
586 each sequence edit.</em> <br></li>
587 <li><strong>Sort With New Tree</strong><br> <em>When
588 enabled, Jalview will automatically sort the alignment when a
589 new tree is calculated or loaded onto it.</em> <br></li>
590 <li><strong>Show Flanking Regions</strong><br> <em>Opens
591 a new alignment window showing any additional sequence data
592 either side of the current alignment. Useful in conjunction
593 with 'Fetch Database References' when the 'Trim Retrieved
594 Sequences' option is disabled to retrieve full length
595 sequences for a set of aligned peptides. </em></li>
598 <li><strong>Web Service Menu</strong><br /> <em>This menu
599 is dynamic, and may contain user-defined web service entries in
600 addition to any of the following ones:</em>
602 <li><strong>Fetch DB References</strong><br> <em>This
603 submenu contains options for accessing any of the database
604 services that Jalview is aware of (e.g. DAS sequence servers
605 and the WSDBFetch service provided by the EBI) to verify
606 sequence start/end positions and retrieve all database cross
607 references and PDB ids associated with all or just the
608 selected sequences in the alignment.
610 <li>'Trim Retrieved Sequences' - when checked, Jalview
611 will discard any additional sequence data for accessions
612 associated with sequences in the alignment. <br> <strong>Note:
613 Disabling this could cause out of memory errors when
614 working with genomic sequence records !</strong><br> <strong>Added
615 in Jalview 2.8.1</strong>
617 <li>'Standard Databases' will check sequences against
618 the EBI databases plus any active DAS sequence sources<</li>
619 </ul> Other sub-menus allow you to pick a specific source to query
620 - sources are listed alphabetically according to their
624 <p>Selecting items from the following submenus will start a
625 remote service on compute facilities at the University of Dundee,
626 or elsewhere. You need a continuous network connection in order to
627 use these services through Jalview.</p>
629 <li><strong>Alignment</strong><br />
630 <em> Align the currently selected sequences or all sequences
631 in the alignment, or re-align unaligned sequences to the
632 aligned sequences. Entries in this menu provide access to the
633 various alignment programs supported by <a
634 href="../webServices/JABAWS.html"
635 >JABAWS</a>. See the <a href="../webServices/msaclient.html">Multiple
636 Sequence Alignment webservice client</a> entry for more
639 <li><strong>Secondary Structure Prediction</strong>
641 <li><strong>JPred Secondary Structure Prediction</strong><br>
642 <em>Secondary structure prediction by network
643 consensus. See the <a href="../webServices/jnet.html">Jpred3</a>
644 client entry for more information. The behaviour of this
645 calculation depends on the current selection:
647 <li>If nothing is selected, and the displayed
648 sequences appear to be aligned, then a JNet prediction
649 will be run for the first sequence in the alignment,
650 using the current alignment. Otherwise the first
651 sequence will be submitted for prediction.</li>
652 <li>If just one sequence (or a region on one
653 sequence) has been selected, it will be submitted to
654 the automatic JNet prediction server for homolog
655 detection and prediction.</li>
656 <li>If a set of sequences are selected, and they
657 appear to be aligned, then the alignment will be used
658 for a Jnet prediction on the <strong>first</strong>
659 sequence in the set (that is, the one that appears
660 first in the alignment window).
665 <li><strong>Analysis</strong><br />
667 <li><strong>Multi-Harmony</strong><br> <em>Performs
668 functional residue analysis on a protein family alignment
669 with sub-families defined on it. See the <a
670 href="../webServices/shmr.html"
671 >Multi-Harmony service</a> entry for more information.