3 <title>Alignment Window Menus</title>
7 <p><strong>Alignment Window Menus</strong></p>
8 <li><strong>File</strong>
10 <li><strong>Fetch Sequence</strong><br>
11 <em>Shows a dialog window in which you can select known ids from
12 Uniprot, EMBL, EMBLCDS or PDB database using Web Services provided by
13 the European Bioinformatics Institute. See <a
14 href="../features/seqfetch.html">Sequence Fetcher</a></em>.</li>
15 <li><strong>Add Sequences</strong><em><br>
16 Add sequences to the visible alignment from file, URL, or cut &
17 paste window </em></li>
18 <li><strong>Reload</strong><em><br>
19 Reloads the alignment from the original file, if available.<br>
20 <strong>Warning: This will delete any edits, analyses and
21 colourings applied since the alignment was last saved, and cannot be
22 undone.</strong></em></li>
23 <li><strong>Save (Control S)</strong><em><br>
24 Saves the alignment to the file it was loaded from (if available), in
25 the same format, updating the original in place. </em></li>
26 <li><strong>Save As (Control Shift S)<br>
27 </strong><em>Save the alignment to local file. A file selection window
28 will open, use the "Files of type:" selection box to
29 determine which <a href="../io/index.html">alignment format</a> to
31 <li><strong>Output to Textbox<br>
32 </strong><em>The alignment will be displayed in plain text in a new
33 window, which you can "Copy and Paste" using the pull down
34 menu, or your standard operating system copy and paste keys. The
35 output window also has a <strong>"New Window"</strong>
36 button to import the (possibly edited) text as a new alignment.<br>
37 Select the format of the text by selecting one of the following menu
40 <li><strong>FASTA</strong> <em></em></li>
41 <li><strong>MSF</strong></li>
42 <li><strong>CLUSTAL</strong></li>
43 <li><strong>BLC</strong></li>
44 <li><strong>PIR</strong></li>
45 <li><strong>PFAM</strong></li>
48 <li><strong>Print (Control P)<br>
49 </strong><em>Jalview will print the alignment using the current fonts and
50 colours of your alignment. If the alignment has annotations visible,
51 these will be printed below the alignment. If the alignment is wrapped
52 the number of residues per line of your alignment will depend on the
53 paper width or your alignment window width, whichever is the smaller.
55 <li><strong>Export Image</strong> <em><br>
56 Creates an alignment graphic with the current view's annotation,
57 alignment background colours and group colours. If the alignment is <a
58 href="../features/wrap.html">wrapped</a>, the output will also be
59 wrapped and will have the same visible residue width as the open
63 </strong><em>Create a <a href="../io/export.html">web page</a> from your
66 </strong><em>Create an <a href="../io/export.html">Encapsulated
67 Postscript</a> file from your alignment.</em></li>
69 </strong><em>Create a <a href="../io/export.html">Portable Network
70 Graphics</a> file from your alignment.</em></li>
73 <li><strong>Export Features</strong><em><br>
74 All features visible on the alignment can be saved to file or
75 displayed in a textbox in either Jalview or GFF format</em></li>
76 <li><strong>Export Annotations</strong><em><br>
77 All annotations visible on the alignment can be saved to file or
78 displayed in a textbox in Jalview annotations format. </em></li>
79 <li><strong>Load Associated Tree<br>
80 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
81 trees</a> stored in the Newick file format, and associate them with the
82 alignment. Note: the ids of the tree file and your alignment MUST be
84 <li><strong>Load Features / Annotations<br>
85 </strong><em>Load files describing precalculated <a
86 href="../features/featuresFormat.html">sequence features</a> or <a
87 href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
88 <li><strong>Close (Control W)</strong><br>
89 <em>Close the alignment window. Make sure you have saved your
90 alignment before you close - either as a Jalview project or by using
91 the <strong>Save As</strong> menu.</em></li>
94 <li><strong>Edit</strong>
96 <li><strong>Undo (Control Z)</strong><em><br>
97 This will undo any edits you make to the alignment. This applies to
98 insertion or deletion of gaps, cutting residues or sequences from the
99 alignment or pasting sequences to the current alignment or sorting the
100 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
101 adjustments to group sizes, or changes to the annotation panel. </em></li>
102 <li><strong>Redo (Control Y)<br>
103 </strong><em>Any actions which you undo can be redone using redo. </em></li>
104 <li><strong>Cut (Control X)<br>
105 </strong><em>This will make a copy of the currently selected residues
106 before removing them from your alignment. Click on a sequence name if
107 you wish to select a whole sequence. <br>
108 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
109 <li><strong>Copy (Control C)</strong><br>
110 <em>Copies the currently selected residues to the system
111 clipboard - you can also do this by pressing <CTRL> and C
112 (<APPLE> and C on MacOSX). <br>
113 If you try to paste the clipboard contents to a text editor, you will
114 see the format of the copied residues FASTA.</em></li>
115 <li><strong>Paste </strong>
117 <li><strong>To New Alignment (Control Shift V)<br>
118 </strong><em>A new alignment window will be created from sequences
119 previously copied or cut to the system clipboard. <br>
120 Use <CTRL> and <SHIFT> and V(<APPLE> and
121 <SHIFT;> and and V on MacOSX) to paste.</em></li>
122 <li><strong>Add To This Alignment (Control V)<br>
123 </strong><em>Copied sequences from another alignment window can be added
124 to the current Jalview alignment. </em></li>
127 <li><strong>Delete (Backspace)<br>
128 </strong><em>This will delete the currently selected residues without
129 copying them to the clipboard. Like the other edit operations, this
130 can be undone with <strong>Undo</strong>.</em></li>
131 <li><strong>Remove Left (Control L)<br>
132 </strong><em>If the alignment has marked columns, the alignment will be
133 trimmed to the left of the leftmost marked column. To mark a column,
134 mouse click the scale bar above the alignment. Click again to unmark a
135 column, or select "Deselect All" to deselect all columns.</em></li>
136 <li><strong>Remove Right (Control R)<br>
137 </strong><em>If the alignment has marked columns, the alignment will be
138 trimmed to the left of the leftmost marked column. To mark a column,
139 mouse click the scale bar above the alignment. Click again to unmark a
140 column, or select "Deselect All" to deselect all columns.</em></li>
141 <li><strong>Remove Empty Columns (Control E)<br>
142 </strong><em>All columns which only contain gap characters ("-",
143 ".") will be deleted.<br>
144 You may set the default gap character in <a
145 href="../features/preferences.html">preferences</a>. </em></li>
146 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
147 <em>Gap characters ("-", ".") will be deleted
148 from the selected area of the alignment. If no selection is made, ALL
149 the gaps in the alignment will be removed.<br>
150 You may set the default gap character in <a
151 href="../features/preferences.html">preferences</a>. </em></li>
152 <li><strong>Remove Redundancy (Control D)<br>
153 </strong><em>Selecting this option brings up a window asking you to select
154 a threshold. If the percentage identity between any two sequences
155 (under the current alignment) exceeds this value then one of the
156 sequences (the shorter) is discarded. Press the "Apply"
157 button to remove redundant sequences. The "Undo" button will
158 undo the last redundancy deletion.</em></li>
159 <li><strong>Pad Gaps<br>
160 </strong><em>When selected, the alignment will be kept at minimal width
161 (so there no empty columns before or after the first or last aligned
162 residue) and all sequences will be padded with gap characters to the
163 before and after their terminating residues.<br>
164 This switch is useful when making a tree using unaligned sequences and
165 when working with alignment analysis programs which require 'properly
166 aligned sequences' to be all the same length.<br>
167 You may set the default for <strong>Pad Gaps</strong> in the <a
168 href="../features/preferences.html">preferences</a>. </em></li>
171 <li><strong>Select</strong>
173 <li><strong><a href="../features/search.html">Find...
174 (Control F)</a></strong><em><br>
175 Opens the Find dialog box to search for residues, sequence name or
176 residue position within the alignment and create new sequence features
177 from the queries. </em></li>
178 <li><strong>Select All (Control A)<br>
179 </strong><em>Selects all the sequences and residues in the alignment. <br>
180 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
182 <li><strong>Deselect All (Escape)<br>
183 </strong><em>Removes the current selection box (red dashed box) from the
184 alignment window. All selected sequences, residues and marked columns
185 will be deselected. </em><em> <br>
186 Use <ESCAPE> to deselect all.</em></li>
187 <li><strong>Invert Sequence Selection (Control I)<br>
188 </strong><em>Any sequence ids currently not selected will replace the
189 current selection. </em></li>
190 <li><strong>Invert Column Selection (Control Alt I)<br>
191 </strong><em>Any columns currently not selected will replace the current
192 column selection. </em></li>
193 <li><strong>Undefine Groups (Control U)<br>
194 </strong><em>The alignment will be reset with no defined groups.<br>
195 <strong>WARNING</strong>: This cannot be undone.</em></li>
198 <li><strong>View</strong>
200 <li><strong>New View (Control T)</strong><em><br>
201 Creates a new view from the current alignment view. </em></li>
202 <li><strong>Expand Views (X)</strong><em><br>
203 Display each view associated with the alignment in its own alignment
204 window, allowing several views to be displayed simultaneously. </em></li>
205 <li><strong>Gather Views (G)</strong><em><br>
206 Each view associated with the alignment will be displayed within its
207 own tab on the current alignment window. </em></li>
208 <li><strong>Show→(all Columns / Sequences)</strong><em><br>
209 All hidden Columns / Sequences will be revealed. </em></li>
210 <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
211 Hides the all the currently selected Columns / Sequences</em></li>
212 <li><strong>Show Annotations<br>
213 </strong><em>If this is selected the "Annotation Panel" will be
214 displayed below the alignment. The default setting is to display the
215 conservation calculation, quality calculation and consensus values as
216 bar charts. </em></li>
217 <li><strong>Show Sequence Features</strong><br>
218 <em>Show or hide sequence features on this alignment.</em></li>
219 <li><strong><a href="../features/featuresettings.html">Seqence
220 Feature Settings...</a></strong><em><br>
221 <em>Opens the Sequence Feature Settings dialog box to control the
222 colour and display of sequence features on the alignment, and
223 configure and retrieve features from DAS annotation servers.</em></li>
224 <li><strong><a href="../features/overview.html">Overview
226 </strong><em>A scaled version of the alignment will be displayed in a
227 small window. A red box will indicate the currently visible area of
228 the alignment. Move the visible region using the mouse. </em></li>
231 <li><strong>Alignment Window Format Menu</strong>
233 <li><strong>Font...<br>
234 </strong><em>Opens the "Choose Font" dialog box, in order to
235 change the font of the display and enable or disable 'smooth fonts'
236 (anti-aliasing) for faster alignment rendering. </em></li>
238 </strong><em>When ticked, the alignment display is "<a
239 href="../features/wrap.html">wrapped</a>" to the width of the
240 alignment window. This is useful if your alignment has only a few
241 sequences to view its full width at once.<br>
242 Additional options for display of sequence numbering and scales are
243 also visible in wrapped layout mode:<br>
245 <li><strong>Scale Above</strong><br>
246 Show the alignment column position scale.</li>
247 <li><strong>Scale Left</strong><br>
248 Show the sequence position for the first aligned residue in each row
249 in the left column of the alignment.</li>
250 <li><strong>Scale Right</strong><br>
251 Show the sequence position for the last aligned residue in each row
252 in the right-most column of the alignment.</li>
253 <li><strong>Show Sequence Limits<br>
254 </strong><em>If this box is selected the sequence name will have the start
255 and end position of the sequence appended to the name, in the format
256 NAME/START-END</em></li>
257 <li><strong>Right Align Sequence ID<br>
258 </strong><em>If this box is selected then the sequence names displayed in
259 the sequence label area will be aligned against the left-hand edge of
260 the alignment display, rather than the left-hand edge of the alignment
262 <li><strong>Show Hidden Markers<br>
263 </strong><em>When this box is selected, positions in the alignment where
264 rows and columns are hidden will be marked by blue arrows.</li>
265 <li><strong>Boxes</strong><em><br>
266 If this is selected the background of a residue will be coloured using
267 the selected background colour. Useful if used in conjunction with
268 "Colour Text." </em></li>
270 </strong><em>If this is selected the residues will be displayed using the
271 standard 1 character amino acid alphabet.</em></li>
272 <li><strong>Colour Text<br>
273 </strong><em>If this is selected the residues will be coloured according
274 to the background colour associated with that residue. The colour is
275 slightly darker than background so the amino acid symbol remains
277 <li><strong>Show Gaps<br>
278 </strong><em>When this is selected, gap characters will be displayed as
279 "." or "-". If unselected, then gap characters
280 will appear as blank spaces. <br>
281 You may set the default gap character in <a
282 href="../features/preferences.html">preferences</a>.</em></li>
283 <li><strong>Centre Annotation Labels<br>
284 </strong><em>Select this to center labels along an annotation row
285 relative to their associated column (default is off, i.e. left-justified).</em></li>
287 <li><strong>Colour</strong>
289 <li><strong>Apply Colour To All Groups<br>
290 </strong><em>If this is selected, any changes made to the background
291 colour will be applied to all currently defined groups.<br>
293 <li><strong><a href="../colourSchemes/textcolour.html">Colour
294 Text...</a></strong><em><br>
295 Opens the Colour Text dialog box to set a different text colour for
296 light and dark background, and the intensity threshold for transition
297 between them. </em></li>
298 <li>Colour Scheme options: <strong>None, ClustalX,
299 Blosum62 Score, Percentage Identity, Zappo, Taylor, Hydrophobicity,
300 Helix Propensity, Strand Propensity, Turn Propensity, Buried Index,
301 Nucleotide, User Defined<br>
302 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for a
303 description of all colour schemes.</em><br>
305 <li><strong>By Conservation<br>
306 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
307 by Conservation</a>.</em><br>
309 <li><strong>Modify Conservation Threshold<br>
310 </strong><em>Use this to display the conservation threshold slider window.
311 Useful if the window has been closed, or if the 'by conservation'
312 option appears to be doing nothing!</em><br>
314 <li><strong>Above Identity Threshold<br>
315 </strong><em>See <a href="../colourSchemes/abovePID.html">Above
316 Percentage Identity</a></em><strong>.<br>
318 <li><strong>Modify Identity Threshold<br>
319 </strong><em>Use this to set the threshold value for colouring above
320 Identity. Useful if the window has been closed.<br>
322 <li><strong>By Annotation</strong><br>
323 <em>Colours the alignment on a per-column value from a specified
324 annotation. See <a href="../colourSchemes/annotationColouring.html">Annotation
325 Colouring</a>.</em><br>
329 <li><strong>Calculate</strong>
331 <li><strong>Sort </strong>
333 <li><strong>by ID</strong><em><br>
334 This will sort the sequences according to sequence name. If the sort
335 is repeated, the order of the sorted sequences will be inverted. </em></li>
336 <li><strong>by Group</strong><strong><br>
337 </strong><em>This will sort the sequences according to sequence name. If
338 the sort is repeated, the order of the sorted sequences will be
339 inverted. </em><strong></strong></li>
340 <li><strong>by Pairwise Identity<br>
341 </strong><em>This will sort the selected sequences by their percentage
342 identity to the consensus sequence. The most similar sequence is put
343 at the top. </em></li>
344 <li><em>The <a href="../calculations/sorting.html">Sort
345 menu</a> will have some additional options if you have just done a
346 multiple alignment calculation, or opened a tree viewer window.</em><br>
350 <li><strong>Calculate Tree </strong> <br>
351 <em>Functions for calculating trees on the alignment or the
352 currently selected region. See <a href="../calculations/tree.html">calculating
355 <li><strong>Average Distance Using % Identity</strong></li>
356 <li><strong>Neighbour Joining Using % Identity</strong></li>
357 <li><strong>Average Distance Using Blosum62</strong></li>
358 <li><strong>Neighbour Joining Using Blosum62<br>
362 <li><strong>Pairwise Alignments</strong><br>
363 <em>Applies Smith and Waterman algorithm to selected sequences.
364 See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
366 <li><strong>Principal Component Analysis</strong><br>
367 <em>Shows a spatial clustering of the sequences based on the
368 BLOSUM62 scores in the alignment. See <a
369 href="../calculations/pca.html">Principal Component Analysis</a>.</em> <br>
371 <li><strong>Extract Scores ... (optional)</strong><br>
372 <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>
373 When selected, these numbers are parsed into sequence associated annotation which can
374 then be used to sort the alignment via the Sort by→Score menu.</em> <br>
376 <li><strong>Autocalculate Consensus</strong><br>
377 <em>For large alignments it can be useful to deselect
378 "Autocalculate Consensus" when editing. This prevents the
379 sometimes lengthy calculations performed after each sequence edit.</em> <br>
383 <li><strong>Web Service<br>
385 <ul><li><strong>Fetch DB References</strong><br>
386 <em>This will use any of the database services that Jalview is aware
387 of (e.g. DAS sequence servers and the WSDBFetch service provided by the EBI)
388 to verify the sequence and retrieve all database cross references and PDB ids
389 associated with all or just the selected sequences in the alignment.</em><br>
392 <em>Selecting one of the following menu items starts a remote
393 service on compute facilities at the University of Dundee. You need a
394 continuous network connection in order to use these services through
397 <li><strong>Alignment</strong>
399 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
400 <em> Submits all, or just the currently selected sequences for
401 alignment with clustal W.</em></li>
402 <li><strong>ClustalW Multiple Sequence Alignment
404 <em> Submits the alignment or currently selected region for
405 re-alignment with clustal W. Use this if you have added some new
406 sequences to an existing alignment.</em></li>
407 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
408 <em>Submits all, or just the currently selected region for
409 alignment with MAFFT. </em></li>
410 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
411 <em> Submits all, or just the currently selected sequences for
412 alignment using Muscle. Do not use this if you are working with
413 nucleic acid sequences.</em></li>
416 <li><strong>Secondary Structure Prediction</strong>
418 <li><strong>JPred Secondary Structure Prediction</strong><br>
419 <em>Secondary structure prediction by network consensus. The
420 behaviour of this calculation depends on the current selection: </em></li>
421 <li><em>If nothing is selected, and the displayed sequences
422 appear to be aligned, then a JNet prediction will be run for the
423 first sequence in the alignment, using the current alignment.
424 Otherwise the first sequence will be submitted for prediction. </em></li>
425 <li><em>If just one sequence (or a region on one sequence)
426 has been selected, it will be submitted to the automatic JNet
427 prediction server for homolog detection and prediction. </em></li>
428 <li><em>If a set of sequences are selected, and they appear
429 to be aligned, then the alignment will be used for a Jnet prediction
430 on the <strong>first</strong> sequence in the set (that is, the one
431 that appears first in the alignment window). </em></li>