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
34 window, which you can "Copy and Paste" using the pull down
35 menu, or your standard operating system copy and paste keys. The
36 output window also has a <strong>"New Window"</strong>
37 button to import the (possibly edited) text as a new alignment.<br>
38 Select the format of the text by selecting one of the following menu
41 <li><strong>FASTA</strong> <em></em></li>
42 <li><strong>MSF</strong></li>
43 <li><strong>CLUSTAL</strong></li>
44 <li><strong>BLC</strong></li>
45 <li><strong>PIR</strong></li>
46 <li><strong>PFAM</strong></li>
49 <li><strong>Print (Control P)<br>
50 </strong><em>Jalview will print the alignment using the current fonts and
51 colours of your alignment. If the alignment has annotations visible,
52 these will be printed below the alignment. If the alignment is wrapped
53 the number of residues per line of your alignment will depend on the
54 paper width or your alignment window width, whichever is the smaller.
56 <li><strong>Export Image</strong> <em><br>
57 Creates an alignment graphic with the current view's annotation,
58 alignment background colours and group colours. If the alignment is <a
59 href="../features/wrap.html">wrapped</a>, the output will also be
60 wrapped and will have the same visible residue width as the open
64 </strong><em>Create a <a href="../io/export.html">web page</a> from your
67 </strong><em>Create an <a href="../io/export.html">Encapsulated
68 Postscript</a> file from your alignment.</em></li>
70 </strong><em>Create a <a href="../io/export.html">Portable Network
71 Graphics</a> file from your alignment.</em></li>
74 <li><strong>Export Features</strong><em><br>
75 All features visible on the alignment can be saved to file or
76 displayed in a textbox in either Jalview or GFF format</em></li>
77 <li><strong>Export Annotations</strong><em><br>
78 All annotations visible on the alignment can be saved to file or
79 displayed in a textbox in Jalview annotations format. </em></li>
80 <li><strong>Load Associated Tree<br>
81 </strong><em>Jalview can <a href="../calculations/treeviewer.html">view
82 trees</a> stored in the Newick file format, and associate them with the
83 alignment. Note: the ids of the tree file and your alignment MUST be
85 <li><strong>Load Features / Annotations<br>
86 </strong><em>Load files describing precalculated <a
87 href="../features/featuresFormat.html">sequence features</a> or <a
88 href="../features/annotationsFormat.html">alignment annotations</a>.</em></li>
89 <li><strong>Close (Control W)</strong><br>
90 <em>Close the alignment window. Make sure you have saved your
91 alignment before you close - either as a Jalview project or by using
92 the <strong>Save As</strong> menu.</em></li>
95 <li><strong>Edit</strong>
97 <li><strong>Undo (Control Z)</strong><em><br>
98 This will undo any edits you make to the alignment. This applies to
99 insertion or deletion of gaps, cutting residues or sequences from the
100 alignment or pasting sequences to the current alignment or sorting the
101 alignment. <strong>NOTE:</strong> It DOES NOT undo colour changes,
102 adjustments to group sizes, or changes to the annotation panel. </em></li>
103 <li><strong>Redo (Control Y)<br>
104 </strong><em>Any actions which you undo can be redone using redo. </em></li>
105 <li><strong>Cut (Control X)<br>
106 </strong><em>This will make a copy of the currently selected residues
107 before removing them from your alignment. Click on a sequence name if
108 you wish to select a whole sequence. <br>
109 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
110 <li><strong>Copy (Control C)</strong><br>
111 <em>Copies the currently selected residues to the system
112 clipboard - you can also do this by pressing <CTRL> and C
113 (<APPLE> and C on MacOSX). <br>
114 If you try to paste the clipboard contents to a text editor, you will
115 see the format of the copied residues FASTA.</em></li>
116 <li><strong>Paste </strong>
118 <li><strong>To New Alignment (Control Shift V)<br>
119 </strong><em>A new alignment window will be created from sequences
120 previously copied or cut to the system clipboard. <br>
121 Use <CTRL> and <SHIFT> and V(<APPLE> and
122 <SHIFT;> and and V on MacOSX) to paste.</em></li>
123 <li><strong>Add To This Alignment (Control V)<br>
124 </strong><em>Copied sequences from another alignment window can be added
125 to the current Jalview alignment. </em></li>
128 <li><strong>Delete (Backspace)<br>
129 </strong><em>This will delete the currently selected residues without
130 copying them to the clipboard. Like the other edit operations, this
131 can be undone with <strong>Undo</strong>.</em></li>
132 <li><strong>Remove Left (Control L)<br>
133 </strong><em>If the alignment has marked columns, the alignment will be
134 trimmed to the left of the leftmost marked column. To mark a column,
135 mouse click the scale bar above the alignment. Click again to unmark a
136 column, or select "Deselect All" to deselect all columns.</em></li>
137 <li><strong>Remove Right (Control R)<br>
138 </strong><em>If the alignment has marked columns, the alignment will be
139 trimmed to the left of the leftmost marked column. To mark a column,
140 mouse click the scale bar above the alignment. Click again to unmark a
141 column, or select "Deselect All" to deselect all columns.</em></li>
142 <li><strong>Remove Empty Columns (Control E)<br>
143 </strong><em>All columns which only contain gap characters ("-",
144 ".") will be deleted.<br>
145 You may set the default gap character in <a
146 href="../features/preferences.html">preferences</a>. </em></li>
147 <li><strong>Remove All Gaps (Control Shift E)</strong><br>
148 <em>Gap characters ("-", ".") will be deleted
149 from the selected area of the alignment. If no selection is made, ALL
150 the gaps in the alignment will be removed.<br>
151 You may set the default gap character in <a
152 href="../features/preferences.html">preferences</a>. </em></li>
153 <li><strong>Remove Redundancy (Control D)<br>
154 </strong><em>Selecting this option brings up a window asking you to select
155 a threshold. If the percentage identity between any two sequences
156 (under the current alignment) exceeds this value then one of the
157 sequences (the shorter) is discarded. Press the "Apply"
158 button to remove redundant sequences. The "Undo" button will
159 undo the last redundancy deletion.</em></li>
160 <li><strong>Pad Gaps<br>
161 </strong><em>When selected, the alignment will be kept at minimal width
162 (so there no empty columns before or after the first or last aligned
163 residue) and all sequences will be padded with gap characters to the
164 before and after their terminating residues.<br>
165 This switch is useful when making a tree using unaligned sequences and
166 when working with alignment analysis programs which require 'properly
167 aligned sequences' to be all the same length.<br>
168 You may set the default for <strong>Pad Gaps</strong> in the <a
169 href="../features/preferences.html">preferences</a>. </em></li>
172 <li><strong>Select</strong>
174 <li><strong><a href="../features/search.html">Find...
175 (Control F)</a></strong><em><br>
176 Opens the Find dialog box to search for residues, sequence name or
177 residue position within the alignment and create new sequence features
178 from the queries. </em></li>
179 <li><strong>Select All (Control A)<br>
180 </strong><em>Selects all the sequences and residues in the alignment. <br>
181 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select
183 <li><strong>Deselect All (Escape)<br>
184 </strong><em>Removes the current selection box (red dashed box) from the
185 alignment window. All selected sequences, residues and marked columns
186 will be deselected. </em><em> <br>
187 Use <ESCAPE> to deselect all.</em></li>
188 <li><strong>Invert Sequence Selection (Control I)<br>
189 </strong><em>Any sequence ids currently not selected will replace the
190 current selection. </em></li>
191 <li><strong>Invert Column Selection (Control Alt I)<br>
192 </strong><em>Any columns currently not selected will replace the current
193 column selection. </em></li>
194 <li><strong>Undefine Groups (Control U)<br>
195 </strong><em>The alignment will be reset with no defined groups.<br>
196 <strong>WARNING</strong>: This cannot be undone.</em></li>
199 <li><strong>View</strong>
201 <li><strong>New View (Control T)</strong><em><br>
202 Creates a new view from the current alignment view. </em></li>
203 <li><strong>Expand Views (X)</strong><em><br>
204 Display each view associated with the alignment in its own alignment
205 window, allowing several views to be displayed simultaneously. </em></li>
206 <li><strong>Gather Views (G)</strong><em><br>
207 Each view associated with the alignment will be displayed within its
208 own tab on the current alignment window. </em></li>
209 <li><strong>Show→(all Columns / Sequences)</strong><em><br>
210 All hidden Columns / Sequences will be revealed. </em></li>
211 <li><strong>Hide→(all Columns / Sequences)</strong><em><br>
212 Hides the all the currently selected Columns / Sequences</em></li>
213 <li><strong>Show Annotations<br>
214 </strong><em>If this is selected the "Annotation Panel" will be
215 displayed below the alignment. The default setting is to display the
216 conservation calculation, quality calculation and consensus values as
217 bar charts. </em></li>
218 <li><strong>Show Sequence Features</strong><br>
219 <em>Show or hide sequence features on this alignment.</em></li>
220 <li><strong><a href="../features/featuresettings.html">Seqence
221 Feature Settings...</a></strong><em><br>
222 <em>Opens the Sequence Feature Settings dialog box to control the
223 colour and display of sequence features on the alignment, and
224 configure and retrieve features from DAS annotation servers.</em></li>
225 <li><strong><a href="../features/overview.html">Overview
227 </strong><em>A scaled version of the alignment will be displayed in a
228 small window. A red box will indicate the currently visible area of
229 the alignment. Move the visible region using the mouse. </em></li>
232 <li><strong>Alignment Window Format Menu</strong>
234 <li><strong>Font...<br>
235 </strong><em>Opens the "Choose Font" dialog box, in order to
236 change the font of the display and enable or disable 'smooth fonts'
237 (anti-aliasing) for faster alignment rendering. </em></li>
239 </strong><em>When ticked, the alignment display is "<a
240 href="../features/wrap.html">wrapped</a>" to the width of the
241 alignment window. This is useful if your alignment has only a few
242 sequences to view its full width at once.<br>
243 Additional options for display of sequence numbering and scales are
244 also visible in wrapped layout mode:<br>
246 <li><strong>Scale Above</strong><br>
247 Show the alignment column position scale.</li>
248 <li><strong>Scale Left</strong><br>
249 Show the sequence position for the first aligned residue in each row
250 in the left column of the alignment.</li>
251 <li><strong>Scale Right</strong><br>
252 Show the sequence position for the last aligned residue in each row
253 in the right-most column of the alignment.</li>
255 <li><strong>Show Sequence Limits<br>
256 </strong><em>If this box is selected the sequence name will have the start
257 and end position of the sequence appended to the name, in the format
258 NAME/START-END</em></li>
259 <li><strong>Right Align Sequence ID<br>
260 </strong><em>If this box is selected then the sequence names displayed in
261 the sequence label area will be aligned against the left-hand edge of
262 the alignment display, rather than the left-hand edge of the alignment
264 <li><strong>Show Hidden Markers<br>
265 </strong><em>When this box is selected, positions in the alignment where
266 rows and columns are hidden will be marked by blue arrows.</li>
267 <li><strong>Boxes</strong><em><br>
268 If this is selected the background of a residue will be coloured using
269 the selected background colour. Useful if used in conjunction with
270 "Colour Text." </em></li>
272 </strong><em>If this is selected the residues will be displayed using the
273 standard 1 character amino acid alphabet.</em></li>
274 <li><strong>Colour Text<br>
275 </strong><em>If this is selected the residues will be coloured according
276 to the background colour associated with that residue. The colour is
277 slightly darker than background so the amino acid symbol remains
279 <li><strong>Show Gaps<br>
280 </strong><em>When this is selected, gap characters will be displayed as
281 "." or "-". If unselected, then gap characters
282 will appear as blank spaces. <br>
283 You may set the default gap character in <a
284 href="../features/preferences.html">preferences</a>.</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>Autocalculate Consensus</strong><br>
372 <em>For large alignments it can be useful to deselect
373 "Autocalculate Consensus" when editing. This prevents the
374 sometimes lengthy calculations performed after each sequence edit.</em> <br>
378 <li><strong>Web Service<br>
379 </strong> <em>Selecting one of the following menu items starts a remote
380 service on compute facilities at the University of Dundee. You need a
381 continuous network connection in order to use these services through
384 <li><strong>Alignment</strong>
386 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
387 <em> Submits all, or just the currently selected sequences for
388 alignment with clustal W.</em></li>
389 <li><strong>ClustalW Multiple Sequence Alignment
391 <em> Submits the alignment or currently selected region for
392 re-alignment with clustal W. Use this if you have added some new
393 sequences to an existing alignment.</em></li>
394 <li><strong>MAFFT Multiple Sequence Alignment</strong><br>
395 <em>Submits all, or just the currently selected region for
396 alignment with MAFFT. </em></li>
397 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
398 <em> Submits all, or just the currently selected sequences for
399 alignment using Muscle. Do not use this if you are working with
400 nucleic acid sequences.</em></li>
403 <li><strong>Secondary Structure Prediction</strong>
405 <li><strong>JPred Secondary Structure Prediction</strong><br>
406 <em>Secondary structure prediction by network consensus. The
407 behaviour of this calculation depends on the current selection: </em></li>
408 <li><em>If nothing is selected, and the displayed sequences
409 appear to be aligned, then a JNet prediction will be run for the
410 first sequence in the alignment, using the current alignment.
411 Otherwise the first sequence will be submitted for prediction. </em></li>
412 <li><em>If just one sequence (or a region on one sequence)
413 has been selected, it will be submitted to the automatic JNet
414 prediction server for homolog detection and prediction. </em></li>
415 <li><em>If a set of sequences are selected, and they appear
416 to be aligned, then the alignment will be used for a Jnet prediction
417 on the <strong>first</strong> sequence in the set (that is, the one
418 that appears first in the alignment window). </em></li>