3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Alignment Window Menus</title>
24 <p><strong>Alignment Window Menus</strong></p>
25 <li><strong>File</strong>
27 <li><strong>Fetch Sequence</strong><br>
28 <em>Shows a dialog window in which you can select known ids from
29 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
30 the European Bioinformatics Institute. See <a
31 href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
32 <li><strong>Add Sequences</strong><em><br>
33 Add sequences to the visible alignment from file, URL, or cut &
34 paste window </em></li>
35 <li><strong>Reload</strong><em><br>
36 Reloads the alignment from the original file, if available.<br>
37 <strong>Warning: This will delete any edits, analyses and
38 colourings applied since the alignment was last saved, and cannot be
39 undone.</strong></em></li>
40 <li><strong>Save (Control S)</strong><em><br>
41 Saves the alignment to the file it was loaded from (if available), in
42 the same format, updating the original in place. </em></li>
43 <li><strong>Save As (Control Shift S)<br>
44 </strong><em>Save the alignment to local file. A file selection window
45 will open, use the "Files of type:" selection box to
46 determine which <a href="../io/index.html">alignment format</a> to
48 <li><strong>Output to Textbox<br>
49 </strong><em>The alignment will be displayed in plain text in a new
50 window, which you can "Copy and Paste" using the pull down
51 menu, or your standard operating system copy and paste keys. The
52 output window also has a <strong>"New Window"</strong>
53 button to import the (possibly edited) text as a new alignment.<br>
54 Select the format of the text by selecting one of the following menu
57 <li><strong>FASTA</strong> <em></em></li>
58 <li><strong>MSF</strong></li>
59 <li><strong>CLUSTAL</strong></li>
60 <li><strong>BLC</strong></li>
61 <li><strong>PIR</strong></li>
62 <li><strong>PFAM</strong></li>
65 <li><strong>Print (Control P)<br>
66 </strong><em>Jalview will print the alignment using the current fonts and
67 colours of your alignment. If the alignment has annotations visible,
68 these will be printed below the alignment. If the alignment is wrapped
69 the number of residues per line of your alignment will depend on the
70 paper width or your alignment window width, whichever is the smaller.
72 <li><strong>Export Image</strong> <em><br>
73 Creates an alignment graphic with the current view's annotation,
74 alignment background colours and group colours. If the alignment is <a
75 href="../features/wrap.html">wrapped</a>, the output will also be
76 wrapped and will have the same visible residue width as the open
80 </strong><em>Create a <a href="../io/export.html">web page</a> from your
83 </strong><em>Create an <a href="../io/export.html">Encapsulated
84 Postscript</a> file from your alignment.</em></li>
86 </strong><em>Create a <a href="../io/export.html">Portable Network
87 Graphics</a> file from your alignment.</em></li>
90 <li><strong>Export Features</strong><em><br>
91 All features visible on the alignment can be saved to file or
92 displayed in a textbox in either Jalview or GFF format</em></li>
93 <li><strong>Export Annotations</strong><em><br>
94 All annotations visible on the alignment can be saved to file or
95 displayed in a textbox in Jalview annotations format. </em></li>
96 <li><strong>Load Associated Tree<br>
97 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
98 trees</a> stored in the Newick file format, and associate them with the
99 alignment. Note: the ids of the tree file and your alignment MUST be
101 <li><strong>Load Features / Annotations<br>
102 </strong><em>Load files describing precalculated <a
103 href="../features/featuresFormat.html">sequence features</a> or <a
104 href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
105 <li><strong>Close (Control W)</strong><br>
106 <em>Close the alignment window. Make sure you have saved your
107 alignment before you close - either as a Jalview project or by using
108 the <strong>Save As</strong> menu.</em></li>
111 <li><strong>Edit</strong>
113 <li><strong>Undo (Control Z)</strong><em><br>
114 This will undo any edits you make to the alignment. This applies to
115 insertion or deletion of gaps, cutting residues or sequences from the
116 alignment or pasting sequences to the current alignment or sorting the
117 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
118 adjustments to group sizes, or changes to the annotation panel. </em></li>
119 <li><strong>Redo (Control Y)<br>
120 </strong><em>Any actions which you undo can be redone using redo. </em></li>
121 <li><strong>Cut (Control X)<br>
122 </strong><em>This will make a copy of the currently selected residues
123 before removing them from your alignment. Click on a sequence name if
124 you wish to select a whole sequence. <br>
125 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
126 <li><strong>Copy (Control C)</strong><br>
127 <em>Copies the currently selected residues to the system
128 clipboard - you can also do this by pressing <CTRL> and C
129 (<APPLE> and C on MacOSX). <br>
130 If you try to paste the clipboard contents to a text editor, you will
131 see the format of the copied residues FASTA.</em></li>
132 <li><strong>Paste </strong>
134 <li><strong>To New Alignment (Control Shift V)<br>
135 </strong><em>A new alignment window will be created from sequences
136 previously copied or cut to the system clipboard. <br>
137 Use <CTRL> and <SHIFT> and V(<APPLE> and
138 <SHIFT;> and and V on MacOSX) to paste.</em></li>
139 <li><strong>Add To This Alignment (Control V)<br>
140 </strong><em>Copied sequences from another alignment window can be added
141 to the current Jalview alignment. </em></li>
144 <li><strong>Delete (Backspace)<br>
145 </strong><em>This will delete the currently selected residues without
146 copying them to the clipboard. Like the other edit operations, this
147 can be undone with <strong>Undo</strong>.</em></li>
148 <li><strong>Remove Left (Control L)<br>
149 </strong><em>If the alignment has marked columns, the alignment will be
150 trimmed to the left of the leftmost marked column. To mark a column,
151 mouse click the scale bar above the alignment. Click again to unmark a
152 column, or select "Deselect All" to deselect all columns.</em></li>
153 <li><strong>Remove Right (Control R)<br>
154 </strong><em>If the alignment has marked columns, the alignment will be
155 trimmed to the left of the leftmost marked column. To mark a column,
156 mouse click the scale bar above the alignment. Click again to unmark a
157 column, or select "Deselect All" to deselect all columns.</em></li>
158 <li><strong>Remove Empty Columns (Control E)<br>
159 </strong><em>All columns which only contain gap characters ("-",
160 ".") will be deleted.<br>
161 You may set the default gap character in <a
162 href="../features/preferences.html">preferences</a>. </em></li>
163 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
164 <em>Gap characters ("-", ".") will be deleted
165 from the selected area of the alignment. If no selection is made, ALL
166 the gaps in the alignment will be removed.<br>
167 You may set the default gap character in <a
168 href="../features/preferences.html">preferences</a>. </em></li>
169 <li><strong>Remove Redundancy (Control D)<br>
170 </strong><em>Selecting this option brings up a window asking you to select
171 a threshold. If the percentage identity between any two sequences
172 (under the current alignment) exceeds this value then one of the
173 sequences (the shorter) is discarded. Press the "Apply"
174 button to remove redundant sequences. The "Undo" button will
175 undo the last redundancy deletion.</em></li>
176 <li><strong>Pad Gaps<br>
177 </strong><em>When selected, the alignment will be kept at minimal width
178 (so there no empty columns before or after the first or last aligned
179 residue) and all sequences will be padded with gap characters to the
180 before and after their terminating residues.<br>
181 This switch is useful when making a tree using unaligned sequences and
182 when working with alignment analysis programs which require 'properly
183 aligned sequences' to be all the same length.<br>
184 You may set the default for <strong>Pad Gaps</strong> in the <a
185 href="../features/preferences.html">preferences</a>. </em></li>
188 <li><strong>Select</strong>
190 <li><strong><a href="../features/search.html">Find...
191 (Control F)</a></strong><em><br>
192 Opens the Find dialog box to search for residues, sequence name or
193 residue position within the alignment and create new sequence features
194 from the queries. </em></li>
195 <li><strong>Select All (Control A)<br>
196 </strong><em>Selects all the sequences and residues in the alignment. <br>
197 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
199 <li><strong>Deselect All (Escape)<br>
200 </strong><em>Removes the current selection box (red dashed box) from the
201 alignment window. All selected sequences, residues and marked columns
202 will be deselected. </em><em> <br>
203 Use <ESCAPE> to deselect all.</em></li>
204 <li><strong>Invert Sequence Selection (Control I)<br>
205 </strong><em>Any sequence ids currently not selected will replace the
206 current selection. </em></li>
207 <li><strong>Invert Column Selection (Control Alt I)<br>
208 </strong><em>Any columns currently not selected will replace the current
209 column selection. </em></li>
210 <li><strong>Undefine Groups (Control U)<br>
211 </strong><em>The alignment will be reset with no defined groups.<br>
212 <strong>WARNING</strong>: This cannot be undone.</em></li>
213 <li><strong>Make Groups<br/></strong>
214 <em>The currently selected groups of the alignment will be
215 subdivided according to the contents of the currently selected region.
216 <br/>Use this to subdivide an alignment based on the
217 different combinations of residues observed at specific
218 positions. (new in jalview 2.5)</em></li>
221 <li><strong>View</strong>
223 <li><strong>New View (Control T)</strong><em><br>
224 Creates a new view from the current alignment view. </em></li>
225 <li><strong>Expand Views (X)</strong><em><br>
226 Display each view associated with the alignment in its own alignment
227 window, allowing several views to be displayed simultaneously. </em></li>
228 <li><strong>Gather Views (G)</strong><em><br>
229 Each view associated with the alignment will be displayed within its
230 own tab on the current alignment window. </em></li>
231 <li><strong>Show→(all Columns / Sequences / Sequences and Columns)</strong><em><br>
232 All hidden Columns / Sequences / Sequences and Columns will be revealed. </em></li>
233 <li><strong>Hide→(all Columns / Sequences / Selected Region / All but Selected Region )</strong><em><br>
234 Hides the all the currently selected Columns / Sequences / Region or everything but the selected Region.</em></li>
235 <li><strong>Automatic Scrolling<br>
236 </strong><em>When selected, the view will automatically scroll to display the
237 highlighted sequence position corresponding to the position under the mouse
238 pointer in a linked alignment or structure view.</em>
240 <li><strong>Show Annotations<br>
241 </strong><em>If this is selected the "Annotation Panel" will be
242 displayed below the alignment. The default setting is to display the
243 conservation calculation, quality calculation and consensus values as
244 bar charts. </em></li>
245 <li><strong>Autocalculated Annotation<br></strong>Settings for the display of autocalculated annotation.
247 <strong>Apply to all groups<br></strong>
248 When ticked, any modification to the current settings will be applied to all autocalculated annotation.
251 <strong>Show Consensus Histogram<br></strong>
252 Enable or disable the display of the histogram above the consensus sequence.
255 <strong>Show Consensus Profile<br></strong>
256 Enable or disable the display of the sequence logo above the consensus sequence.
259 <strong>Group Conservation<br></strong>
260 When ticked, display a conservation row for all groups (only available for protein alignments).
263 <strong>Apply to all groups<br></strong>
264 When ticked, display a consensus row for all groups.
268 <li><strong>Show Sequence Features</strong><br>
269 <em>Show or hide sequence features on this alignment.</em></li>
270 <li><strong><a href="../features/featuresettings.html">Seqence
271 Feature Settings...</a></strong><em><br>
272 <em>Opens the Sequence Feature Settings dialog box to control the
273 colour and display of sequence features on the alignment, and
274 configure and retrieve features from DAS annotation servers.</em></li>
275 <li><strong>Sequence ID Tooltip</strong><em> (application only)
276 <br>This submenu's options allow the inclusion or exclusion of
277 non-positional sequence features or database cross references
278 from the tooltip shown when the mouse hovers over the sequence ID panel.</em></li>
279 <li><strong>Alignment Properties...<br/>
280 </strong><em>Displays some simple statistics computed for the
281 current alignment view and any named properties defined on the
282 whole alignment.</em></li>
283 <li><strong><a href="../features/overview.html">Overview
285 </strong><em>A scaled version of the alignment will be displayed in a
286 small window. A red box will indicate the currently visible area of
287 the alignment. Move the visible region using the mouse. </em></li>
290 <li><strong>Alignment Window Format Menu</strong>
292 <li><strong>Font...<br>
293 </strong><em>Opens the "Choose Font" dialog box, in order to
294 change the font of the display and enable or disable 'smooth fonts'
295 (anti-aliasing) for faster alignment rendering. </em></li>
297 </strong><em>When ticked, the alignment display is "<a
298 href="../features/wrap.html">wrapped</a>" to the width of the
299 alignment window. This is useful if your alignment has only a few
300 sequences to view its full width at once.<br>
301 Additional options for display of sequence numbering and scales are
302 also visible in wrapped layout mode:<br>
304 <li><strong>Scale Above</strong><br>
305 Show the alignment column position scale.</li>
306 <li><strong>Scale Left</strong><br>
307 Show the sequence position for the first aligned residue in each row
308 in the left column of the alignment.</li>
309 <li><strong>Scale Right</strong><br>
310 Show the sequence position for the last aligned residue in each row
311 in the right-most column of the alignment.</li>
312 <li><strong>Show Sequence Limits<br>
313 </strong><em>If this box is selected the sequence name will have the start
314 and end position of the sequence appended to the name, in the format
315 NAME/START-END</em></li>
316 <li><strong>Right Align Sequence ID<br>
317 </strong><em>If this box is selected then the sequence names displayed in
318 the sequence label area will be aligned against the left-hand edge of
319 the alignment display, rather than the left-hand edge of the alignment
321 <li><strong>Show Hidden Markers<br>
322 </strong><em>When this box is selected, positions in the alignment where
323 rows and columns are hidden will be marked by blue arrows.</li>
324 <li><strong>Boxes</strong><em><br>
325 If this is selected the background of a residue will be coloured using
326 the selected background colour. Useful if used in conjunction with
327 "Colour Text." </em></li>
329 </strong><em>If this is selected the residues will be displayed using the
330 standard 1 character amino acid alphabet.</em></li>
331 <li><strong>Colour Text<br>
332 </strong><em>If this is selected the residues will be coloured according
333 to the background colour associated with that residue. The colour is
334 slightly darker than background so the amino acid symbol remains
336 <li><strong>Show Gaps<br>
337 </strong><em>When this is selected, gap characters will be displayed as
338 "." or "-". If unselected, then gap characters
339 will appear as blank spaces. <br>
340 You may set the default gap character in <a
341 href="../features/preferences.html">preferences</a>.</em></li>
342 <li><strong>Centre Annotation Labels<br>
343 </strong><em>Select this to center labels along an annotation row
344 relative to their associated column (default is off, i.e. left-justified).</em></li>
345 <li><strong>Show Unconserved<br>
346 </strong><em>When this is selected, all consensus sequence symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.
350 <li><strong>Colour</strong>
352 <li><strong>Apply Colour To All Groups<br>
353 </strong><em>If this is selected, any changes made to the background
354 colour will be applied to all currently defined groups.<br>
356 <li><strong><a href="../colourSchemes/textcolour.html">Colour
357 Text...</a></strong><em><br>
358 Opens the Colour Text dialog box to set a different text colour for
359 light and dark background, and the intensity threshold for transition
360 between them. </em></li>
361 <li>Colour Scheme options: <strong>None, ClustalX,
362 Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
363 Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
364 Nucleotide, User Defined<br>
365 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a
366 description of all colour schemes.</em><br>
368 <li><strong>By Conservation<br>
369 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
370 by Conservation</a>.</em><br>
372 <li><strong>Modify Conservation Threshold<br>
373 </strong><em>Use this to display the conservation threshold slider window.
374 Useful if the window has been closed, or if the 'by conservation'
375 option appears to be doing nothing!</em><br>
377 <li><strong>Above Identity Threshold<br>
378 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
379 Percentage Identity</a></em><strong>.<br>
381 <li><strong>Modify Identity Threshold<br>
382 </strong><em>Use this to set the threshold value for colouring above
383 Identity. Useful if the window has been closed.<br>
385 <li><strong>By Annotation</strong><br>
386 <em>Colours the alignment on a per-column value from a specified
387 annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
388 Colouring</a>.</em><br>
392 <li><strong>Calculate</strong>
394 <li><strong>Sort </strong>
396 <li><strong>by ID</strong><em><br>
397 This will sort the sequences according to sequence name. If the sort
398 is repeated, the order of the sorted sequences will be inverted. </em></li>
399 <li><strong>by Length</strong><em><br>
400 This will sort the sequences according to their length (excluding gap characters). If the sort is
401 repeated, the order of the sorted sequences will be inverted. </em></li>
402 <li><strong>by Group</strong><strong><br>
403 </strong><em>This will sort the sequences according to sequence name. If
404 the sort is repeated, the order of the sorted sequences will be
405 inverted. </em><strong></strong></li>
406 <li><strong>by Pairwise Identity<br>
407 </strong><em>This will sort the selected sequences by their percentage
408 identity to the consensus sequence. The most similar sequence is put
409 at the top. </em></li>
410 <li><em>The <a href="../calculations/sorting.html">Sort
411 menu</a> will have some additional options if you have just done a
412 multiple alignment calculation, or opened a tree viewer window.</em><br>
416 <li><strong>Calculate Tree </strong> <br>
417 <em>Functions for calculating trees on the alignment or the
418 currently selected region. See <a href="../calculations/tree.html">calculating
421 <li><strong>Average Distance Using % Identity</strong></li>
422 <li><strong>Neighbour Joining Using % Identity</strong></li>
423 <li><strong>Average Distance Using Blosum62</strong></li>
424 <li><strong>Neighbour Joining Using Blosum62<br>
428 <li><strong>Pairwise Alignments</strong><br>
429 <em>Applies Smith and Waterman algorithm to selected sequences.
430 See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
432 <li><strong>Principal Component Analysis</strong><br>
433 <em>Shows a spatial clustering of the sequences based on the
434 BLOSUM62 scores in the alignment. See <a
435 href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>
437 <li><strong>Extract Scores ... (optional)</strong><br>
438 <em>This option is only visible if Jalview detects one or more white-space separated values in the description line of the alignment sequences.<br>
439 When selected, these numbers are parsed into sequence associated annotation which can
440 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
442 <li><strong>Autocalculate Consensus</strong><br>
443 <em>For large alignments it can be useful to deselect
444 "Autocalculate Consensus" when editing. This prevents the
445 sometimes lengthy calculations performed after each sequence edit.</em> <br>
449 <li><strong>Web Service<br>
451 <ul><li><strong>Fetch DB References</strong><br>
452 <em>This will use any of the database services that Jalview is aware
453 of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
454 to verify the sequence and retrieve all database cross references and PDB ids
455 associated with all or just the selected sequences in the alignment.</em><br>
458 <em>Selecting one of the following menu items starts a remote
459 service on compute facilities at the University of Dundee. You need a
460 continuous network connection in order to use these services through
463 <li><strong>Alignment</strong>
465 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
466 <em> Submits all, or just the currently selected sequences for
467 alignment with clustal W.</em></li>
468 <li><strong>ClustalW Multiple Sequence Alignment
470 <em> Submits the alignment or currently selected region for
471 re-alignment with clustal W. Use this if you have added some new
472 sequences to an existing alignment.</em></li>
473 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
474 <em>Submits all, or just the currently selected region for
475 alignment with MAFFT. </em></li>
476 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
477 <em> Submits all, or just the currently selected sequences for
478 alignment using Muscle. Do not use this if you are working with
479 nucleic acid sequences.</em></li>
482 <li><strong>Secondary Structure Prediction</strong>
484 <li><strong>JPred Secondary Structure Prediction</strong><br>
485 <em>Secondary structure prediction by network consensus. The
486 behaviour of this calculation depends on the current selection: </em></li>
487 <li><em>If nothing is selected, and the displayed sequences
488 appear to be aligned, then a JNet prediction will be run for the
489 first sequence in the alignment, using the current alignment.
490 Otherwise the first sequence will be submitted for prediction. </em></li>
491 <li><em>If just one sequence (or a region on one sequence)
492 has been selected, it will be submitted to the automatic JNet
493 prediction server for homolog detection and prediction. </em></li>
494 <li><em>If a set of sequences are selected, and they appear
495 to be aligned, then the alignment will be used for a Jnet prediction
496 on the <strong>first</strong> sequence in the set (that is, the one
497 that appears first in the alignment window). </em></li>