2 <head><title>Menus</title></head>
\r
5 <p><strong>Alignment Menu</strong></p>
\r
7 <li><strong>File</strong></li>
\r
9 <li><strong>Save As<br>
\r
10 </strong><em>Save the alignment to local file. A file selection window will
\r
11 open, use the "Files of type:" selection box to determine which
\r
12 <a href="../io/index.html">alignment format</a> to save as.<br>
\r
14 <li><strong>Export</strong> <em><br>
\r
15 Creates an alignment output maintaining the alignment background colours
\r
16 and group colours. If the alignment is wrapped, the output will also be
\r
17 wrapped and will have the same visible residue width as the open alignment.
\r
20 <li><strong>HTML<br>
\r
21 </strong><em>Create a <a href="../io/index.html#export">web page</a>
\r
22 from your alignment.</em></li>
\r
24 </strong><em>Create an <a href="../io/index.html#export">Encapsulated
\r
25 Postscript</a> file from your alignment.</em></li>
\r
27 </strong><em>Create a <a href="../io/index.html#export">Portable Network
\r
28 Graphics</a> file from your alignment.<br>
\r
32 <li><strong>Output to Textbox<br>
\r
33 </strong><em>The alignment will be displayed in plain text in a new window
\r
34 which you can "Copy and Paste" using the pull down menu, or your
\r
35 standard operating system copy and paste keys. <br>
\r
36 Select the format of the text by selecting one of the following menu items.</em>
\r
38 <li><strong>FASTA</strong> <em></em></li>
\r
39 <li><strong>MSF</strong></li>
\r
40 <li><strong>CLUSTAL</strong></li>
\r
41 <li><strong>BLC</strong></li>
\r
42 <li><strong>PIR</strong></li>
\r
43 <li><strong>PFAM<br>
\r
47 <li><strong>Print<br>
\r
48 </strong><em>Jalview will print the alignment using the current fonts and
\r
49 colours of your alignment. If the alignment has annotations visible, these
\r
50 will be printed below the alignment. If the alignment is wrapped the number
\r
51 of residues per line of your alignment will depend on the paper width or
\r
52 your alignment window width, whichever is the smaller. <br>
\r
54 <li><strong>Load Associated Tree<br>
\r
55 </strong><em>Jalview can load in trees which are in the Newick file format
\r
56 and associate them with a particular alignment. Note: the ids of the tree
\r
57 file and your alignment MUST be the same.<br>
\r
59 <li><strong>Close<br>
\r
60 </strong><em>Close the alignment window. Be aware that changes to your alignment
\r
61 will not be save unless specifically actioned from the "Save As"
\r
65 <li><strong>Edit</strong></li>
\r
69 <li><strong>Undo</strong><em><br>
\r
70 This will undo any edits you make to the alignment. This applies to insertion
\r
71 or deletion of gaps, cutting residues or sequences from the alignment or
\r
72 pasting sequences to the current alignment or sorting the alignment. It
\r
73 DOES NOT undo colour changes or adjustments to group sizes affect the annotation
\r
76 <li><strong>Redo<br>
\r
77 </strong><em>Any actions which you undo can be redone using redo. <br>
\r
80 </strong><em>This will make a copy of the currently selected residues before
\r
81 removing them from your alignment. Click on a sequence name if you wish
\r
82 to select a whole sequence. <br>
\r
83 Use <CTRL> and X (<APPLE> and X on MacOSX) to cut.<br>
\r
85 <li><strong>Copy</strong><br>
\r
86 <em>Copies the currently selected residues to the system clipboard. The
\r
87 format of copied residues is NAME<tab>START_RES<tab>END_RES<tab>SEQUENCE
\r
89 Use <CTRL> and C (<APPLE> and C on MacOSX) to copy.<br>
\r
91 <li><strong>Paste </strong>
\r
93 <li><strong>To New Alignment<br>
\r
94 </strong><em>A new alignment window will be created from sequences previously
\r
95 copied or cut to the system clipboard. <br>
\r
96 Use <CTRL> and V(<APPLE> and V on MacOSX) to paste.</em></li>
\r
97 <li><strong>Add To This Alignment<br>
\r
98 </strong><em>Copied sequences from another alignment window can be added
\r
99 to the current Jalview alignment. <br>
\r
100 </em><strong> </strong></li>
\r
103 <li><strong>Delete<br>
\r
104 </strong><em>This will delete the currently selected residues without making
\r
105 a copy of them first.<br>
\r
107 <li><strong>Select All<br>
\r
108 </strong><em>Selects all the sequences and residues in the alignment. <br>
\r
109 Use <CTRL> and A (<APPLE> and A on a MacOSX) to select all.<br>
\r
111 <li><strong>Deselect All<br>
\r
112 </strong><em>Removes the current selection box (red dashed box) from the
\r
113 alignment window. All selected sequences, residues and marked columns will
\r
114 be deselected. </em><em> <br>
\r
115 Use <ESCAPE> to deselect all.<br>
\r
117 <li><strong>Invert Selection<br>
\r
118 </strong><em>Any sequence ids currently not selected will replace the current
\r
120 </em><strong> </strong></li>
\r
121 <li><strong>Undefine Groups<br>
\r
122 </strong><em>The alignment will be reset with no defined groups. WARNING:
\r
123 This cannot be undone.<br>
\r
125 <li><strong>Remove Left<br>
\r
126 </strong><em>If the alignment has marked columns, the alignment will be
\r
127 trimmed to the left of the leftmost marked column. To mark a column, mouse
\r
128 click the scale bar above the alignment. Click again to unmark a column,
\r
129 or select "Deselect All" to deselect all columns.<br>
\r
131 <li><strong>Remove Right<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, mouse
\r
134 click the scale bar above the alignment. Click again to unmark a column,
\r
135 or select "Deselect All" to deselect all columns.<br>
\r
137 <li><strong>Remove Empty Columns<br>
\r
138 </strong><em>All columns which contain purely gap characters ("-",
\r
139 ".") will be deleted.<br>
\r
140 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
143 <li><strong>Remove All Gaps</strong><br>
\r
144 <em>All gap characters ("-", ".") will be deleted from
\r
146 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
149 <li><strong>Remove Redundancy<br>
\r
150 </strong><em>Selecting this option brings up a window asking you to select
\r
151 a threshold. If the percentage identity between two sequences exceeds this
\r
152 value one of the sequences (the shorter) is discarded. Press the "Apply"
\r
153 button to remove redundant sequences.<br>
\r
155 <li><strong>Pad Gaps<br>
\r
156 </strong><em>If the sequences in an alignment window are not all the same
\r
157 length they can all be set to the length of the longest sequence by selecting
\r
158 "Pad Gaps." Any sequences which are shorter than the longest sequence
\r
159 in an alignment will have gap characters ("-" or ".")
\r
160 appended to the beginning or end to make them equal length. <br>
\r
161 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.
\r
166 <li><strong>Search</strong></li>
\r
170 <li><strong>Find<br>
\r
171 </strong><em>Select this to <a href="../features/search.html">search</a>
\r
172 for residues, sequence name or residue position within the alignment. </em></li>
\r
176 <li><strong>View</strong></li>
\r
180 <li><strong>Font<br>
\r
181 </strong><em>Change the font of the display. The default font can be set
\r
182 from the "Choose Font" window, which is shown when the "Font
\r
183 Menu" is selected. <br>
\r
185 <li><strong>Wrap<br>
\r
186 </strong><em>The default alignment display shows sequences in a single horizontal
\r
187 row. If your alignment has only a few sequences you may wish to "Wrap"
\r
188 the alignment so that the sequences are shown on multiple horizontal rows.
\r
189 Options are available to show the residue numbering at the start and/or
\r
190 end of an alignment as well as showing the alignment position above each
\r
192 NOTE: In the current version the wrap alignment should be used for viewing,
\r
194 </em><strong> </strong></li>
\r
195 <li><strong>Show Full Sequence ID<br>
\r
196 </strong><em>If this box is selected the sequence name will have the start
\r
197 and end position of the sequence appended to the name, in the format NAME/START-END<br>
\r
199 <li><strong>Boxes</strong><em><br>
\r
200 If this is selected the background of a residue will be coloured using the
\r
201 selected background colour. Useful if used in conjunction with "Colour
\r
204 <li><strong>Text<br>
\r
205 </strong><em>If this is selected the residues will be displayed using the
\r
206 standard 1 character amino acid alphabet.<br>
\r
208 <li><strong>Colour Text<br>
\r
209 </strong><em>If this is selected the residues will be coloured according
\r
210 to the background colour associated with that residue. The colour is slightly
\r
211 darker than background to enable the residue to be read. <br>
\r
213 <li><strong>Show Gaps<br>
\r
214 </strong><em>If this is selected gap characters will be displayed as "."
\r
215 or "-". If unselected gap characters will appear as blank spaces.
\r
217 You may set the default gap character in <a href="../features/preferences.html">preferences</a>.<br>
\r
219 <li><strong>Show Annotations<br>
\r
220 </strong><em>If this is selected the "Annotation Panel" will be
\r
221 displayed below the alignment. The default setting is to display the conservation
\r
222 calculation, quality calculation and consensus values as bar charts. </em><br>
\r
224 <li><strong>Sequence Features<br>
\r
225 </strong><em>If the sequence names are Swissprot entries Jalview will use
\r
226 the names to retrieve sequence features from the EBI. Features which are
\r
227 1 residue in length are coloured red, sequences longer than 1 residue are
\r
228 coloured blue. Move the mouse over a coloured feature to display the details
\r
229 of the feature. <br>
\r
230 Note: The retrieved information will update the sequence start and end labels
\r
231 if they are incorrect. <br>
\r
233 <li><strong>Overview Window<br>
\r
234 </strong><em>A scaled version of the alignment will be displayed in a small
\r
235 window. A red box will indicate the currently visible area of the alignment.
\r
236 Move the visible region using the mouse. </em><strong> </strong></li>
\r
240 <li><strong>Colour</strong></li>
\r
244 <li><strong>Apply Colour To All Groups<br>
\r
245 </strong><em>If this is selected, any changes made to the background colour
\r
246 will be applied to all currently defined groups.<br>
\r
248 <li><strong>None, ClustalX, Blosum62 Score, Percentage Identity, Zappo, Taylor,
\r
249 Hydrophobicity, Helix Propensity, Strand Propensity, Turn Propensity, Buried
\r
250 Index, Nucleotide, User Defined<br>
\r
251 </strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
\r
252 a description of all colour schemes.</em><br>
\r
254 <li><strong>By Conservation<br>
\r
255 </strong><em>See <a href="../colourSchemes/conservation.html">Colouring
\r
256 by Conservation</a>.</em><br>
\r
258 <li><strong>Modify Conservation Threshold<br>
\r
259 </strong><em>Use this to display the conservation threshold slider window.
\r
260 Useful if the window has been closed. </em></li>
\r
261 <li><strong>Above Identity Threshold<br>
\r
262 </strong><em>See <a href="../colourSchemes/abovePID.html">Above Percentage
\r
263 Identity</a></em><strong>.<br>
\r
265 <li><strong>Modify Identity Threshold<br>
\r
266 </strong><em>Use this to set the threshold value for colouring above Identity.
\r
267 Useful if the window has been closed. </em></li>
\r
271 <li><strong>Calculate</strong></li>
\r
275 <li><strong>Sort </strong>
\r
277 <li><strong>by ID<br>
\r
278 </strong><em>This will sort the sequences according to sequence name.
\r
279 If the sort is repeated, the order of the sorted sequences will be inverted.
\r
282 <li><strong>by Group</strong><strong><br>
\r
283 </strong><em>This will sort the sequences according to sequence name.
\r
284 If the sort is repeated, the order of the sorted sequences will be inverted.
\r
285 </em><strong></strong><strong><br>
\r
287 <li><strong>by Pairwise Identity<br>
\r
288 </strong><em>This will sort the selected sequences by their percentage
\r
289 identity to the consensus sequence. The most similar sequence is put
\r
290 at the top. </em><strong><br>
\r
294 <li><strong>Calculate Tree </strong>
\r
296 <li><strong>Average Distance Using % Identity</strong></li>
\r
297 <li><strong>Neighbour Joining Using % Identity</strong></li>
\r
298 <li><strong>Average Distance Using Blosum62</strong></li>
\r
299 <li><strong>Neighbour Joining Using Blosum62<br>
\r
300 </strong><em>See <a href="../calculations/tree.html">calculating trees</a>.</em><strong>
\r
305 <li><strong>Pairwise Alignments</strong><br>
\r
306 <em>See <a href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
\r
308 <li><strong>Principal Component Analysis</strong><br>
\r
309 <em>See <a href="../calculations/pca.html">Principal Component Analysis</a>.</em>
\r
312 <li><strong>Web Service <br>
\r
315 <em>Selecting one of the following menu items will start a remote service
\r
316 on the high powered computing facility at the University of Dundee. You
\r
317 will need a continuous network connection in order to use these services.
\r
319 <li><strong>Clustal Alignment</strong></li>
\r
320 <li><strong>Clustal Realign</strong></li>
\r
321 <li><strong>JPred</strong></li>
\r
322 <li><strong>Muscle Alignment</strong></li>
\r
git://source.jalview.org / jalview.git / blob