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