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