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>
76 <li><strong>Print (Control P)<br> </strong><em>Jalview
77 will print the alignment using the current fonts and colours of
78 your alignment. If the alignment has annotations visible, these
79 will be printed below the alignment. If the alignment is wrapped
80 the number of residues per line of your alignment will depend on
81 the paper width or your alignment window width, whichever is the
84 <li><strong>Export Image</strong> <em><br> Creates an
85 alignment graphic with the current view's annotation, alignment
86 background colours and group colours. If the alignment is <a
87 href="../features/wrap.html">wrapped</a>, the output will also be
88 wrapped and will have the same visible residue width as the open
91 <li><strong>HTML<br> </strong><em>Create a <a
92 href="../io/export.html">web page</a> from your alignment.</em>
94 <li><strong>EPS<br> </strong><em>Create an <a
95 href="../io/export.html">Encapsulated Postscript</a> file from
98 <li><strong>PNG<br> </strong><em>Create a <a
99 href="../io/export.html">Portable Network Graphics</a> file from
103 <li><strong>Export Features</strong><em><br> All
104 features visible on the alignment can be saved to file or
105 displayed in a textbox in either Jalview or GFF format</em>
107 <li><strong>Export Annotations</strong><em><br> All
108 annotations visible on the alignment can be saved to file or
109 displayed in a textbox in Jalview annotations format. </em>
111 <li><strong>Load Associated Tree<br> </strong><em>Jalview
112 can <a href="../calculations/treeviewer.html">view trees</a>
113 stored in the Newick file format, and associate them with the
114 alignment. Note: the ids of the tree file and your alignment MUST
115 be the same.</em></li>
116 <li><strong>Load Features / Annotations<br> </strong><em>Load
117 files describing precalculated <a
118 href="../features/featuresFormat.html">sequence features</a> or <a
119 href="../features/annotationsFormat.html">alignment
120 annotations</a>.</em></li>
121 <li><strong>Close (Control W)</strong><br> <em>Close
122 the alignment window. Make sure you have saved your alignment
123 before you close - either as a Jalview project or by using the <strong>Save
124 As</strong> menu.</em>
127 <li><strong>Edit</strong>
129 <li><strong>Undo (Control Z)</strong><em><br> This
130 will undo any edits you make to the alignment. This applies to
131 insertion or deletion of gaps, cutting residues or sequences from
132 the alignment or pasting sequences to the current alignment or
133 sorting the alignment. <strong>NOTE:</strong> It DOES NOT undo
134 colour changes, adjustments to group sizes, or changes to the
135 annotation panel. </em>
137 <li><strong>Redo (Control Y)<br> </strong><em>Any
138 actions which you undo can be redone using redo. </em>
140 <li><strong>Cut (Control X)<br> </strong><em>This
141 will make a copy of the currently selected residues before
142 removing them from your alignment. Click on a sequence name if you
143 wish to select a whole sequence. <br> Use <CTRL> and X
144 (<APPLE> and X on MacOSX) to cut.</em>
146 <li><strong>Copy (Control C)</strong><br> <em>Copies
147 the currently selected residues to the system clipboard - you can
148 also do this by pressing <CTRL> and C (<APPLE> and C
149 on MacOSX). <br> If you try to paste the clipboard contents
150 to a text editor, you will see the format of the copied residues
152 <li><strong>Paste </strong>
154 <li><strong>To New Alignment (Control Shift V)<br>
155 </strong><em>A new alignment window will be created from sequences
156 previously copied or cut to the system clipboard. <br> Use
157 <CTRL> and <SHIFT> and V(<APPLE> and
158 <SHIFT;> and and V on MacOSX) to paste.</em>
160 <li><strong>Add To This Alignment (Control V)<br>
161 </strong><em>Copied sequences from another alignment window can be
162 added to the current Jalview alignment. </em>
165 <li><strong>Delete (Backspace)<br> </strong><em>This
166 will delete the currently selected residues without copying them
167 to the clipboard. Like the other edit operations, this can be
168 undone with <strong>Undo</strong>.</em>
170 <li><strong>Remove Left (Control L)<br> </strong><em>If
171 the alignment has marked columns, the alignment will be trimmed to
172 the left of the leftmost marked column. To mark a column, mouse
173 click the scale bar above the alignment. Click again to unmark a
174 column, or select "Deselect All" to deselect all
176 <li><strong>Remove Right (Control R)<br> </strong><em>If
177 the alignment has marked columns, the alignment will be trimmed to
178 the left of the leftmost marked column. To mark a column, mouse
179 click the scale bar above the alignment. Click again to unmark a
180 column, or select "Deselect All" to deselect all
182 <li><strong>Remove Empty Columns (Control E)<br>
183 </strong><em>All columns which only contain gap characters
184 ("-", ".") will be deleted.<br> You may
185 set the default gap character in <a
186 href="../features/preferences.html">preferences</a>. </em>
188 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
189 <em>Gap characters ("-", ".") will be
190 deleted from the selected area of the alignment. If no selection
191 is made, ALL the gaps in the alignment will be removed.<br>
192 You may set the default gap character in <a
193 href="../features/preferences.html">preferences</a>. </em>
195 <li><strong>Remove Redundancy (Control D)<br> </strong><em>Selecting
196 this option brings up a window asking you to select a threshold.
197 If the percentage identity between any two sequences (under the
198 current alignment) exceeds this value then one of the sequences
199 (the shorter) is discarded. Press the "Apply" button to
200 remove redundant sequences. The "Undo" button will undo
201 the last redundancy deletion.</em>
203 <li><strong>Pad Gaps<br> </strong><em>When selected,
204 the alignment will be kept at minimal width (so there are no empty
205 columns before or after the first or last aligned residue) and all
206 sequences will be padded with gap characters before and
207 after their terminating residues.<br> This switch is useful
208 when making a tree using unaligned sequences and when working with
209 alignment analysis programs which require 'properly aligned
210 sequences' to be all the same length.<br> You may set the
211 default for <strong>Pad Gaps</strong> in the <a
212 href="../features/preferences.html">preferences</a>. </em>
215 <li><strong>Select</strong>
217 <li><strong><a href="../features/search.html">Find...
218 (Control F)</a> </strong><em><br> Opens the Find dialog box to
219 search for residues, sequence name or residue position within the
220 alignment and create new sequence features from the queries. </em>
222 <li><strong>Select All (Control A)<br> </strong><em>Selects
223 all the sequences and residues in the alignment. <br> Use
224 <CTRL> and A (<APPLE> and A on a MacOSX) to select
226 <li><strong>Deselect All (Escape)<br> </strong><em>Removes
227 the current selection box (red dashed box) from the alignment
228 window. All selected sequences, residues and marked columns will
229 be deselected. </em><em> <br> Use <ESCAPE> to deselect
231 <li><strong>Invert Sequence Selection (Control I)<br>
232 </strong><em>Any sequence ids currently not selected will replace the
233 current selection. </em>
235 <li><strong>Invert Column Selection (Control Alt I)<br>
236 </strong><em>Any columns currently not selected will replace the current
237 column selection. </em>
239 <li><strong>Create Group (Control G)<br></strong>
240 <em>Create a group containing the currently selected sequences.</em></li>
241 <li><strong>Remove Group (Shift Control G)<br></strong>
242 <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
243 <li><strong>Make Groups for selection<br /> </strong> <em>The currently
244 selected groups of the alignment will be subdivided according to
245 the contents of the currently selected region. <br />Use this to
246 subdivide an alignment based on the different combinations of
247 residues observed at specific positions. (new in jalview 2.5)</em>
249 <li><strong>Undefine Groups (Control U)<br> </strong><em>The
250 alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
251 This cannot be undone.</em>
254 <li><strong>View</strong>
256 <li><strong>New View (Control T)</strong><em><br>
257 Creates a new view from the current alignment view. </em>
259 <li><strong>Expand Views (X)</strong><em><br> Display
260 each view associated with the alignment in its own alignment
261 window, allowing several views to be displayed simultaneously. </em>
263 <li><strong>Gather Views (G)</strong><em><br> Each
264 view associated with the alignment will be displayed within its
265 own tab on the current alignment window. </em>
267 <li><strong>Show→(all Columns / Sequences /
268 Sequences and Columns)</strong><em><br> All hidden Columns /
269 Sequences / Sequences and Columns will be revealed. </em>
271 <li><strong>Hide→(all Columns / Sequences /
272 Selected Region / All but Selected Region )</strong><em><br>
273 Hides the all the currently selected Columns / Sequences / Region
274 or everything but the selected Region.</em>
276 <li><strong>Automatic Scrolling<br> </strong><em>When
277 selected, the view will automatically scroll to display the
278 highlighted sequence position corresponding to the position under
279 the mouse pointer in a linked alignment or structure view.</em></li>
280 <li><strong>Show Sequence Features</strong><br> <em>Show
281 or hide sequence features on this alignment.</em>
283 <li><strong><a href="../features/featuresettings.html">Sequence
284 Feature Settings...</a> </strong><em><br> <em>Opens the
285 Sequence Feature Settings dialog box to control the colour and
286 display of sequence features on the alignment, and configure and
287 retrieve features from DAS annotation servers.</em>
289 <li><strong>Sequence ID Tooltip</strong><em> (application
290 only) <br>This submenu's options allow the inclusion or
291 exclusion of non-positional sequence features or database cross
292 references from the tooltip shown when the mouse hovers over the
293 sequence ID panel.</em>
295 <li><strong>Alignment Properties...<br /> </strong><em>Displays
296 some simple statistics computed for the current alignment view and
297 any named properties defined on the whole alignment.</em>
299 <li><strong><a href="../features/overview.html">Overview
300 Window</a><br> </strong><em>A scaled version of the alignment will
301 be displayed in a small window. A red box will indicate the
302 currently visible area of the alignment. Move the visible region
303 using the mouse. </em>
306 <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
308 <li><strong>Show Annotations<br> </strong><em>If this
309 is selected the "Annotation Panel" will be displayed
310 below the alignment. The default setting is to display the
311 conservation calculation, quality calculation and consensus values
314 <li><strong>Show Alignment Related</strong><em><br>
315 Show all annotations that are for the alignment as a whole (for example, Consensus,
316 or secondary structure prediction from alignment).</em></li>
317 <li><strong>Hide Alignment Related</strong><em><br>
318 Hide all annotations that are for the alignment as a whole.</em></li>
319 <li><strong>Show Sequence Related</strong><em><br>
320 Show all annotations that are for individual sequences.</em></li>
321 <li><strong>Hide Sequence Related</strong><em><br>
322 Hide all annotations that are for individual sequences.</em></li>
323 <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
324 or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
325 <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
326 (and within that, by label).</em></li>
327 <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
328 (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
329 allowing you to make a manual ordering of the annotations.</em></li>
330 <li><strong>Autocalculated Annotation<br> </strong><em>Settings
331 for the display of autocalculated annotation.</em>
333 <li><strong>Show first<br></strong><em>
334 Show autocalculated annotations above sequence-specific annotations.
335 Note this also applies to other annotations for the alignment, for example secondary
336 structure prediction from alignment.</em></li>
337 <li><strong>Show last<br></strong><em>
338 Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
339 <li><strong>Apply to all groups<br> </strong><em> When
340 ticked, any modification to the current settings will be applied
341 to all autocalculated annotation.</em></li>
342 <li><strong>Show Consensus Histogram<br> </strong><em>
343 Enable or disable the display of the histogram above the
344 consensus sequence.</em></li>
345 <li><strong>Show Consensus Logo<br> </strong><em> Enable
346 or disable the display of the Consensus Logo above the consensus
348 <li><strong>Normalise Consensus Logo<br>
349 </strong><em>When enabled, scales all logo stacks to the same height,
350 making it easier to compare symbol diversity in highly variable
352 <li><strong>Group Conservation<br> </strong><em> When
353 ticked, display a conservation row for all groups (only available
354 for protein alignments).</em></li>
355 <li><strong>Group Consensus<br> </strong><em> When
356 ticked, display a consensus row for all groups.</em></li>
361 <li><strong>Alignment Window Format Menu</strong>
363 <li><strong>Font...<br> </strong><em>Opens the
364 "Choose Font" dialog box, in order to change the font of
365 the display and enable or disable 'smooth fonts' (anti-aliasing)
366 for faster alignment rendering. </em></li>
367 <li><strong>Wrap<br> </strong><em>When ticked, the
368 alignment display is "<a href="../features/wrap.html">wrapped</a>"
369 to the width of the alignment window. This is useful if your
370 alignment has only a few sequences to view its full width at once.</em><br>
371 Additional options for display of sequence numbering and scales are
372 also visible in wrapped layout mode:<br>
374 <li><strong>Scale Above</strong><br><em> Show the alignment
375 column position scale.</em></li>
376 <li><strong>Scale Left</strong><br><em> Show the sequence
377 position for the first aligned residue in each row in the left
378 column of the alignment.</em></li>
379 <li><strong>Scale Right</strong><br><em> Show the sequence
380 position for the last aligned residue in each row in the
381 right-most column of the alignment.</em></li>
382 <li><strong>Show Sequence Limits<br> </strong><em>If
383 this box is selected the sequence name will have the start and
384 end position of the sequence appended to the name, in the format
387 <li><strong>Right Align Sequence ID<br> </strong><em>If
388 this box is selected then the sequence names displayed in the
389 sequence label area will be aligned against the left-hand edge
390 of the alignment display, rather than the left-hand edge of the
393 <li><strong>Show Hidden Markers<br> </strong><em>When
394 this box is selected, positions in the alignment where rows and
395 columns are hidden will be marked by blue arrows.
397 <li><strong>Boxes</strong><em><br> If this is
398 selected the background of a residue will be coloured using the
399 selected background colour. Useful if used in conjunction with
400 "Colour Text." </em>
402 <li><strong>Text<br> </strong><em>If this is
403 selected the residues will be displayed using the standard 1
404 character amino acid alphabet.</em>
406 <li><strong>Colour Text<br> </strong><em>If this is
407 selected the residues will be coloured according to the
408 background colour associated with that residue. The colour is
409 slightly darker than background so the amino acid symbol remains
412 <li><strong>Show Gaps<br> </strong><em>When this is
413 selected, gap characters will be displayed as "." or
414 "-". If unselected, then gap characters will appear as
415 blank spaces. <br> You may set the default gap character in
416 <a href="../features/preferences.html">preferences</a>.</em>
418 <li><strong>Centre Annotation Labels<br> </strong><em>Select
419 this to center labels along an annotation row relative to their
420 associated column (default is off, i.e. left-justified).</em>
422 <li><strong>Show Unconserved<br> </strong><em>When
423 this is selected, all consensus sequence symbols will be
424 rendered as a '.', highlighting mutations in highly conserved
435 <li><strong>Colour</strong>
437 <li><strong>Apply Colour To All Groups<br> </strong><em>If
438 this is selected, any changes made to the background colour will
439 be applied to all currently defined groups.<br> </em>
441 <li><strong><a href="../colourSchemes/textcolour.html">Colour
442 Text...</a> </strong><em><br> Opens the Colour Text dialog box to
443 set a different text colour for light and dark background, and the
444 intensity threshold for transition between them. </em>
446 <li>Colour Scheme options: <strong>None, ClustalX,
447 Blosum62 Score, Percentage Identity, Zappo, Taylor,
448 Hydrophobicity, Helix Propensity, Strand Propensity, Turn
449 Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
450 <a href="../colourSchemes/index.html">colours</a> for a
451 description of all colour schemes.</em><br></li>
452 <li><strong>By Conservation<br> </strong><em>See <a
453 href="../colourSchemes/conservation.html">Colouring by
454 Conservation</a>.</em><br></li>
455 <li><strong>Modify Conservation Threshold<br> </strong><em>Use
456 this to display the conservation threshold slider window. Useful
457 if the window has been closed, or if the 'by conservation' option
458 appears to be doing nothing!</em><br></li>
459 <li><strong>Above Identity Threshold<br> </strong><em>See
460 <a href="../colourSchemes/abovePID.html">Above Percentage
461 Identity</a> </em><strong>.<br> </strong>
463 <li><strong>Modify Identity Threshold<br> </strong><em>Use
464 this to set the threshold value for colouring above Identity.
465 Useful if the window has been closed.<br> </em>
467 <li><strong>By Annotation</strong><br> <em>Colours
468 the alignment on a per-column value from a specified annotation.
469 See <a href="../colourSchemes/annotationColouring.html">Annotation
470 Colouring</a>.</em><br></li>
471 <li><strong>By RNA Helices</strong><br>
472 <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
473 <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
474 Colouring</a>.</em><br>
477 <li><strong>Calculate</strong>
479 <li><strong>Sort </strong>
481 <li><strong>by ID</strong><em><br> This will sort
482 the sequences according to sequence name. If the sort is
483 repeated, the order of the sorted sequences will be inverted. </em>
485 <li><strong>by Length</strong><em><br> This will
486 sort the sequences according to their length (excluding gap
487 characters). If the sort is repeated, the order of the sorted
488 sequences will be inverted. </em></li>
489 <li><strong>by Group</strong><strong><br> </strong><em>This
490 will sort the sequences according to sequence name. If the sort
491 is repeated, the order of the sorted sequences will be inverted.
492 </em><strong></strong></li>
493 <li><strong>by Pairwise Identity<br> </strong><em>This
494 will sort the selected sequences by their percentage identity to
495 the consensus sequence. The most similar sequence is put at the
497 <li><em>The <a href="../calculations/sorting.html">Sort
498 menu</a> will have some additional options if you have just done a
499 multiple alignment calculation, or opened a tree viewer window.</em><br>
503 <li><strong>Calculate Tree </strong> <br> <em>Functions
504 for calculating trees on the alignment or the currently selected
505 region. See <a href="../calculations/tree.html">calculating
508 <li><strong>Average Distance Using % Identity</strong></li>
509 <li><strong>Neighbour Joining Using % Identity</strong></li>
510 <li><strong>Average Distance Using Blosum62</strong></li>
511 <li><strong>Neighbour Joining Using Blosum62<br>
514 <strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
516 <li><strong>Pairwise Alignments</strong><br> <em>Applies
517 Smith and Waterman algorithm to selected sequences. See <a
518 href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
520 <li><strong>Principal Component Analysis</strong><br> <em>Shows
521 a spatial clustering of the sequences based on similarity scores calculated with
522 the alignment. See <a href="../calculations/pca.html">Principal
523 Component Analysis</a>.</em> <br>
525 <li><strong>Extract Scores ... (optional)</strong><br> <em>This
526 option is only visible if Jalview detects one or more white-space
527 separated values in the description line of the alignment
528 sequences.<br> When selected, these numbers are parsed into
529 sequence associated annotation which can then be used to sort the
530 alignment via the Sort by→Score menu.</em> <br>
532 <li><strong>Autocalculate Consensus</strong><br> <em>For
533 large alignments it can be useful to deselect "Autocalculate
534 Consensus" when editing. This prevents the sometimes lengthy
535 calculations performed after each sequence edit.</em> <br>
537 <li><strong>Sort With New Tree</strong><br> <em>When
538 enabled, Jalview will automatically sort the alignment when a new
539 tree is calculated or loaded onto it.</em> <br></li>
540 <li><strong>Show Flanking Regions</strong><br> <em>Opens
541 a new alignment window showing any additional sequence data either
542 side of the current alignment. Useful in conjunction with 'Fetch
543 Database References' when the 'Trim Retrieved Sequences' option is
544 disabled to retrieve full length sequences for a set of aligned
548 <li><strong>Web Service Menu</strong><br /> <em>This menu
549 is dynamic, and may contain user-defined web service entries in
550 addition to any of the following ones:</em>
552 <li><strong>Fetch DB References</strong><br> <em>This
553 submenu contains options for accessing any of the database services
554 that Jalview is aware of (e.g. DAS sequence servers and the
555 WSDBFetch service provided by the EBI) to verify sequence start/end
556 positions and retrieve all database cross references and PDB ids
557 associated with all or just the selected sequences in the alignment.
559 <li>'Trim Retrieved Sequences' - when checked, Jalview will
560 discard any additional sequence data for accessions associated with
561 sequences in the alignment. <br> <strong>Note: Disabling this
562 could cause out of memory errors when working with genomic
563 sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
565 <li>'Standard Databases' will check sequences against the EBI
566 databases plus any active DAS sequence sources<</li>
567 </ul> Other sub-menus allow you to pick a specific source to query -
568 sources are listed alphabetically according to their nickname.
571 <p>Selecting items from the following submenus will start a
572 remote service on compute facilities at the University of Dundee, or
573 elsewhere. You need a continuous network connection in order to use
574 these services through Jalview.
577 <li><strong>Alignment</strong><br /><em> Align the currently
578 selected sequences or all sequences in the alignment, or re-align
579 unaligned sequences to the aligned sequences. Entries in this menu
580 provide access to the various alignment programs supported by <a
581 href="../webServices/JABAWS.html">JABAWS</a>. See the <a
582 href="../webServices/msaclient.html">Multiple Sequence
583 Alignment webservice client</a> entry for more information.</em></li>
584 <li><strong>Secondary Structure Prediction</strong>
586 <li><strong>JPred Secondary Structure Prediction</strong><br>
587 <em>Secondary structure prediction by network consensus. See
588 the <a href="../webServices/jnet.html">Jpred3</a> client entry for
589 more information. The behaviour of this calculation depends on
590 the current selection:
592 <li>If nothing is selected, and the displayed sequences
593 appear to be aligned, then a JNet prediction will be run for
594 the first sequence in the alignment, using the current
595 alignment. Otherwise the first sequence will be submitted for
597 <li>If just one sequence (or a region on one sequence) has
598 been selected, it will be submitted to the automatic JNet
599 prediction server for homolog detection and prediction.</li>
600 <li>If a set of sequences are selected, and they appear to
601 be aligned, then the alignment will be used for a Jnet
602 prediction on the <strong>first</strong> sequence in the set
603 (that is, the one that appears first in the alignment window).
607 <li><strong>Analysis</strong><br />
609 <li><strong>Multi-Harmony</strong><br> <em>Performs
610 functional residue analysis on a protein family alignment with
611 sub-families defined on it. See the <a
612 href="../webServices/shmr.html">Multi-Harmony service</a> entry for more