2 <head><title>Alignment Window Menus</title></head>
\r
5 <p><strong>Alignment Window Menus</strong></p>
\r
7 <li><strong>File</strong>
\r
9 <li><strong>Add Sequences</strong><em><br>
\r
10 Add sequences to the visible alignment from file, URL, or cut & paste
\r
12 <li><strong>Fetch Sequence</strong><br>
\r
13 <em>Shows a dialog window in which you can select known ids from Uniprot,
\r
14 EMBL, EMBLCDS or PDB database using Web Services provided by the European
\r
15 Bioinformatics Institute. See <a href="../features/seqfetch.html">Sequence
\r
16 Fetcher</a></em>.</li>
\r
17 <li><strong>Save As<br>
\r
18 </strong><em>Save the alignment to local file. A file selection window
\r
19 will open, use the "Files of type:" selection box to determine
\r
20 which <a href="../io/index.html">alignment format</a> to save as.</em></li>
\r
21 <li><strong>Export</strong> <em><br>
\r
22 Creates an alignment graphic with the current annotation, alignment background
\r
23 colours and group colours. If the alignment is <a
\r
24 href="../features/wrap.html">wrapped</a>, the output will also be wrapped
\r
25 and will have the same visible residue width as the open alignment. </em>
\r
27 <li><strong>HTML<br>
\r
28 </strong><em>Create a <a href="../io/export.html">web page</a> from
\r
29 your alignment.</em></li>
\r
31 </strong><em>Create an <a href="../io/export.html">Encapsulated Postscript</a>
\r
32 file from your alignment.</em></li>
\r
34 </strong><em>Create a <a href="../io/export.html">Portable Network
\r
35 Graphics</a> file from your alignment.</em></li>
\r
38 <li><strong>Output to Textbox<br>
\r
39 </strong><em>The alignment will be displayed in plain text in a new window
\r
40 which you can "Copy and Paste" using the pull down menu, or
\r
41 your standard operating system copy and paste keys. <br>
\r
42 Select the format of the text by selecting one of the following menu items.</em>
\r
44 <li><strong>FASTA</strong> <em></em></li>
\r
45 <li><strong>MSF</strong></li>
\r
46 <li><strong>CLUSTAL</strong></li>
\r
47 <li><strong>BLC</strong></li>
\r
48 <li><strong>PIR</strong></li>
\r
49 <li><strong>PFAM</strong></li>
\r
52 <li><strong>Print<br>
\r
53 </strong><em>Jalview will print the alignment using the current fonts
\r
54 and colours of your alignment. If the alignment has annotations visible,
\r
55 these will be printed below the alignment. If the alignment is wrapped
\r
56 the number of residues per line of your alignment will depend on the paper
\r
57 width or your alignment window width, whichever is the smaller. </em></li>
\r
58 <li><strong>Export Features</strong><em><br>
\r
59 All features visible on the alignment can be saved to file or displayed
\r
60 in a textbox in either Jalview or GFF format</em></li>
\r
61 <li><strong>Export Annotations</strong><em><br>
\r
62 All annotations visible on the alignment can be saved to file or displayed
\r
63 in a textbox in Jalview annotations format. </em></li>
\r
64 <li><strong>Load Associated Tree<br>
\r
65 </strong><em>Jalview can <a
\r
66 href="../calculations/treeviewer.html">view trees</a> stored in the Newick
\r
67 file format, and associate them with the alignment. Note: the ids of the
\r
68 tree file and your alignment MUST be the same.</em></li>
\r
69 <li><strong>Load Features / Annotations<br>
\r
70 </strong><em>Load files describing precalculated <a href="../features/featuresFormat.html">sequence
\r
71 features</a> or <a href="../features/annotationsFormat.html">alignment
\r
72 annotations</a>.</em></li>
\r
73 <li><strong>Close</strong><br>
\r
74 <em>Close the alignment window. Make sure you have saved your alignment
\r
75 before you close - either as a Jalview project or by using the <strong>Save
\r
76 As</strong> menu.<br>
\r
80 <li><strong>Edit</strong>
\r
82 <li><strong>Undo</strong><em><br>
\r
83 This will undo any edits you make to the alignment. This applies to insertion
\r
84 or deletion of gaps, cutting residues or sequences from the alignment
\r
85 or pasting sequences to the current alignment or sorting the alignment.
\r
86 <strong>NOTE:</strong> It DOES NOT undo colour changes, adjustments to
\r
87 group sizes, or changes to the annotation panel. </em></li>
\r
88 <li><strong>Redo<br>
\r
89 </strong><em>Any actions which you undo can be redone using redo. </em></li>
\r
91 </strong><em>This will make a copy of the currently selected residues
\r
92 before removing them from your alignment. Click on a sequence name if
\r
93 you wish to select a whole sequence. <br>
\r
94 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.</em></li>
\r
95 <li><strong>Copy</strong><br>
\r
96 <em>Copies the currently selected residues to the system clipboard - you
\r
97 can also do this by pressing <CTRL> and C (<APPLE> and C on
\r
99 If you try to paste the clipboard contents to a text editor, you will
\r
100 see the format of the copied residues FASTA.</em></li>
\r
101 <li><strong>Paste </strong>
\r
103 <li><strong>To New Alignment<br>
\r
104 </strong><em>A new alignment window will be created from sequences
\r
105 previously copied or cut to the system clipboard. <br>
\r
106 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
\r
107 <li><strong>Add To This Alignment<br>
\r
108 </strong><em>Copied sequences from another alignment window can be
\r
109 added to the current Jalview alignment. </em></li>
\r
112 <li><strong>Delete<br>
\r
113 </strong><em>This will delete the currently selected residues without
\r
114 copying them to the clipboard. Like the other edit operations, this can
\r
115 be undone with <strong>Undo</strong>.</em></li>
\r
116 <li><strong>Select All<br>
\r
117 </strong><em>Selects all the sequences and residues in the alignment.
\r
119 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.</em></li>
\r
120 <li><strong>Deselect All<br>
\r
121 </strong><em>Removes the current selection box (red dashed box) from the
\r
122 alignment window. All selected sequences, residues and marked columns
\r
123 will be deselected. </em><em> <br>
\r
124 Use <ESCAPE> to deselect all.</em></li>
\r
125 <li><strong>Invert Sequence Selection<br>
\r
126 </strong><em>Any sequence ids currently not selected will replace the
\r
127 current selection. </em></li>
\r
128 <li><strong>Invert Column Selection<br>
\r
129 </strong><em>Any columns currently not selected will replace the current
\r
130 column selection. </em></li>
\r
131 <li><strong>Undefine Groups<br>
\r
132 </strong><em>The alignment will be reset with no defined groups.<br>
\r
133 <strong>WARNING</strong>: This cannot be undone.</em></li>
\r
134 <li><strong>Remove Left<br>
\r
135 </strong><em>If the alignment has marked columns, the alignment will be
\r
136 trimmed to the left of the leftmost marked column. To mark a column, mouse
\r
137 click the scale bar above the alignment. Click again to unmark a column,
\r
138 or select "Deselect All" to deselect all columns.</em></li>
\r
139 <li><strong>Remove Right<br>
\r
140 </strong><em>If the alignment has marked columns, the alignment will be
\r
141 trimmed to the left of the leftmost marked column. To mark a column, mouse
\r
142 click the scale bar above the alignment. Click again to unmark a column,
\r
143 or select "Deselect All" to deselect all columns.</em></li>
\r
144 <li><strong>Remove Empty Columns<br>
\r
145 </strong><em>All columns which only contain gap characters ("-",
\r
146 ".") will be deleted.<br>
\r
147 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
149 <li><strong>Remove All Gaps</strong><br>
\r
150 <em>Gap characters ("-", ".") will be deleted from
\r
151 the selected area of the alignment. If no selection is made, ALL the gaps
\r
152 in the alignment will be removed.<br>
\r
153 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
155 <li><strong>Remove Redundancy<br>
\r
156 </strong><em>Selecting this option brings up a window asking you to select
\r
157 a threshold. If the percentage identity between any two sequences (under
\r
158 the current alignment) exceeds this value then one of the sequences (the
\r
159 shorter) is discarded. Press the "Apply" button to remove redundant
\r
160 sequences. The "Undo" button will undo the last redundancy deletion.</em></li>
\r
161 <li><strong>Pad Gaps<br>
\r
162 </strong><em>When selected, the alignment will be kept at minimal width
\r
163 (so there no empty columns before or after the first or last aligned residue)
\r
164 and all sequences will be padded with gap characters to the before and
\r
165 after their terminating residues.<br>
\r
166 This switch is useful when making a tree using unaligned sequences and
\r
167 when working with alignment analysis programs which require 'properly
\r
168 aligned sequences' to be all the same length.<br>
\r
169 You may set the default for <strong>Pad Gaps</strong> in the <a href="../features/preferences.html">preferences</a>.
\r
174 <li><strong>Search</strong>
\r
176 <li><strong>Find<br>
\r
177 </strong><em>Select this to <a href="../features/search.html">search</a>
\r
178 for residues, sequence name or residue position within the alignment and
\r
179 create new sequence features from the queries. <br>
\r
183 <li><strong>View</strong>
\r
185 <li><strong>Font<br>
\r
186 </strong><em>Change the font of the display from the "Choose Font"
\r
187 dialog box, which is shown when this item is selected. </em></li>
\r
188 <li><strong>Smooth Fonts</strong><em><br>
\r
189 If selected, the alignment will be drawn with anti-aliasing on which looks
\r
190 better, but performace is reduced. </em></li>
\r
191 <li><strong>Show (all Columns / Sequences)</strong><em><br>
\r
192 All hidden Columns / Sequences will be revealed. </em></li>
\r
193 <li><strong>Hide (all Columns / Sequences)</strong><em><br>
\r
194 Hides the all the currently selected Columns / Sequences</em></li>
\r
195 <li><strong>Wrap<br>
\r
196 </strong><em>When ticked, the alignment display is "<a href="../features/wrap.html">wrapped</a>"
\r
197 to the width of the alignment window. This is useful if your alignment
\r
198 has only a few sequences to view its full width at once.<br>
\r
199 Options are available to show the residue numbering at the start and/or
\r
200 end of an alignment as well as showing the alignment position above each
\r
202 <strong>NOTE</strong>: When in wrapped alignment view, the alignment cannot
\r
203 be edited or have regions selected on it. </em></li>
\r
204 <li><strong>Show Full Sequence ID<br>
\r
205 </strong><em>If this box is selected the sequence name will have the start
\r
206 and end position of the sequence appended to the name, in the format NAME/START-END</em></li>
\r
207 <li><strong>Boxes</strong><em><br>
\r
208 If this is selected the background of a residue will be coloured using
\r
209 the selected background colour. Useful if used in conjunction with "Colour
\r
210 Text." </em></li>
\r
211 <li><strong>Text<br>
\r
212 </strong><em>If this is selected the residues will be displayed using
\r
213 the standard 1 character amino acid alphabet.</em></li>
\r
214 <li><strong>Colour Text<br>
\r
215 </strong><em>If this is selected the residues will be coloured according
\r
216 to the background colour associated with that residue. The colour is slightly
\r
217 darker than background so the amino acid symbol remains visible. </em></li>
\r
218 <li><strong>Show Gaps<br>
\r
219 </strong><em>When this is selected, gap characters will be displayed as
\r
220 "." or "-". If unselected, then gap characters will
\r
221 appear as blank spaces. <br>
\r
222 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.</em></li>
\r
223 <li><strong>Show Annotations<br>
\r
224 </strong><em>If this is selected the "Annotation Panel" will
\r
225 be displayed below the alignment. The default setting is to display the
\r
226 conservation calculation, quality calculation and consensus values as
\r
227 bar charts. </em></li>
\r
228 <li><strong>Fetch Sequence Features<br>
\r
229 </strong><em>If the sequence names are Swissprot entries Jalview will
\r
230 use the names to retrieve <a href="../features/seqfeatures.html">sequence
\r
231 features</a> from the EBI. Features which are 1 residue in length are
\r
232 coloured red, sequences longer than 1 residue are coloured blue. Move
\r
233 the mouse over a coloured feature to display the details of the feature.
\r
235 Note: The retrieved information will update the sequence start and end
\r
236 labels if they are incorrect. </em></li>
\r
237 <li><strong>Show Sequence Features</strong><br>
\r
238 <em>Show or hide sequence features on this alignment.</em></li>
\r
239 <li><strong>Seqence Feature Settings...</strong><em><br>
\r
240 <em>Control the colour and display of sequence features on the alignment.
\r
242 href="../features/featuresettings.html">Sequence Feature Settings</a>.</em></em></li>
\r
243 <li><strong><a href="../features/overview.html">Overview Window</a><br>
\r
244 </strong><em>A scaled version of the alignment will be displayed in a
\r
245 small window. A red box will indicate the currently visible area of the
\r
246 alignment. Move the visible region using the mouse. </em><strong> </strong></li>
\r
249 <li><strong>Colour</strong>
\r
251 <li><strong>Apply Colour To All Groups<br>
\r
252 </strong><em>If this is selected, any changes made to the background colour
\r
253 will be applied to all currently defined groups.</em></li>
\r
254 <li>Colour Scheme options: <strong>None, ClustalX, Blosum62 Score, Percentage
\r
255 Identity, Zappo, Taylor, Hydrophobicity, Helix Propensity, Strand Propensity,
\r
256 Turn Propensity, Buried Index, Nucleotide, User Defined<br>
\r
257 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
\r
258 a description of all colour schemes.</em></li>
\r
259 <li><strong>By Conservation<br>
\r
260 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
\r
261 by Conservation</a>.</em></li>
\r
262 <li><strong>Modify Conservation Threshold<br>
\r
263 </strong><em>Use this to display the conservation threshold slider window.
\r
264 Useful if the window has been closed, or if the 'by conservation' option
\r
265 appears to be doing nothing!</em></li>
\r
266 <li><strong>Above Identity Threshold<br>
\r
267 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
\r
268 Identity</a></em><strong>.</strong></li>
\r
269 <li><strong>Modify Identity Threshold<br>
\r
270 </strong><em>Use this to set the threshold value for colouring above Identity.
\r
271 Useful if the window has been closed. </em></li>
\r
272 <li><strong>By Annotation</strong><br>
\r
273 <em>Colours the alignment on a per-column value from a specified annotation.
\r
274 See <a href="../colourSchemes/annotationColouring.html">Annotation Colouring</a>.</em><br>
\r
278 <li><strong>Calculate</strong>
\r
282 <li><strong>by ID</strong><em><br>
\r
283 This will sort the sequences according to sequence name. If the sort
\r
284 is repeated, the order of the sorted sequences will be inverted. </em></li>
\r
285 <li><strong>by Group</strong><strong><br>
\r
286 </strong><em>This will sort the sequences according to sequence name.
\r
287 If the sort is repeated, the order of the sorted sequences will be
\r
288 inverted. </em><strong></strong></li>
\r
289 <li><strong>by Pairwise Identity<br>
\r
290 </strong><em>This will sort the selected sequences by their percentage
\r
291 identity to the consensus sequence. The most similar sequence is put
\r
292 at the top. </em></li>
\r
293 <li><em>The <a href="../calculations/sorting.html">Sort menu</a> will
\r
294 have some additional options if you have just done a multiple alignment
\r
295 calculation, or opened a tree viewer window.</em></li>
\r
298 <li><strong>Calculate Tree </strong> <br>
\r
299 <em>Functions for calculating trees on the alignment or the currently
\r
300 selected region. See <a
\r
301 href="../calculations/tree.html">calculating trees</a>.</em>
\r
303 <li><strong>Average Distance Using % Identity</strong></li>
\r
304 <li><strong>Neighbour Joining Using % Identity</strong></li>
\r
305 <li><strong>Average Distance Using Blosum62</strong></li>
\r
306 <li><strong>Neighbour Joining Using Blosum62</strong></li>
\r
309 <li><strong>Pairwise Alignments</strong><br>
\r
310 <em>Applies Smith and Waterman algorithm to selected sequences. See <a href="../calculations/pairwise.html">pairwise
\r
311 alignments</a>.</em></li>
\r
312 <li><strong>Principal Component Analysis</strong><br>
\r
313 <em>Shows a spatial clustering of the sequences based on the BLOSUM62
\r
314 scores in the alignment. See <a href="../calculations/pca.html">Principal
\r
315 Component Analysis</a>.</em> </li>
\r
316 <li><strong>Translate cDNA</strong><br>
\r
317 <em>If you are viewing a cDNA alignment a very simple translation service
\r
318 is available. The translation ignores all gaps in the cDNA sequences.
\r
323 <li><strong>Web Service<br>
\r
324 </strong> <em>Selecting one of the following menu items starts a remote service
\r
325 on compute facilities at the University of Dundee. You need a continuous network
\r
326 connection in order to use these services through Jalview. </em>
\r
328 <li><strong>Alignment </strong>
\r
330 <li><strong>ClustalW Multiple Sequence Alignment</strong><br>
\r
331 <em> Submits all, or just the currently selected sequences for alignment
\r
332 with clustal W.</em></li>
\r
333 <li><strong>ClustalW Multiple Sequence Alignment Realign</strong><br>
\r
334 <em> Submits the alignment or currently selected region for re-alignment
\r
335 with clustal W. Use this if you have added some new sequences to an
\r
336 existing alignment.</em></li>
\r
337 <li><strong>Muscle Multiple Protein Sequence Alignment</strong><br>
\r
338 <em> Submits all, or jut the currently selected sequences for alignment
\r
339 using Muscle. Do not use this if you are working with nucleic acid
\r
340 sequences.</em></li>
\r
343 <li><strong>Secondary Structure Prediction</strong>
\r
345 <li><strong>JPred Secondary Structure Prediction</strong><br>
\r
346 <em>Secondary structure prediction by network consensus. The behaviour
\r
347 of this calculation depends on the current selection: </em></li>
\r
348 <li><em>If nothing is selected, and the displayed sequences appear to
\r
349 be aligned, then a JNet prediction will be run for the first sequence
\r
350 in the alignment, using the current alignment. Otherwise the first
\r
351 sequence will be submitted for prediction. </em></li>
\r
352 <li><em>If just one sequence (or a region on one sequence) has been
\r
353 selected, it will be submitted to the automatic JNet prediction server
\r
354 for homolog detection and prediction. </em></li>
\r
355 <li><em>If a set of sequences are selected, and they appear to be aligned,
\r
356 then the alignment will be used for a Jnet prediction on the <strong>first</strong>
\r
357 sequence selected in the set (that is, the one that was first clicked
\r