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