<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<head>
<title>Alignment Window Menus</title>
<li><strong>File</strong>
<ul>
<li><strong>Fetch Sequence</strong><br> <em>Shows a
- dialog window in which you can select known ids from Uniprot,
- EMBL, EMBLCDS or PDB database using Web Services provided by the
+ dialog window in which you can retrieve known ids from Uniprot,
+ EMBL, EMBLCDS, PFAM, Rfam, or PDB database using Web Services provided by the
European Bioinformatics Institute. See <a
href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
<li><strong>Add Sequences</strong><em><br> Add
</strong><em>Any columns currently not selected will replace the current
column selection. </em>
</li>
- <li><strong>Undefine Groups (Control U)<br> </strong><em>The
- alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
- This cannot be undone.</em>
- </li>
- <li><strong>Make Groups<br /> </strong> <em>The currently
+ <li><strong>Create Group (Control G)<br></strong>
+ <em>Create a group containing the currently selected sequences.</em></li>
+ <li><strong>Remove Group (Shift Control G)<br></strong>
+ <em>Ungroup the currently selected sequence group. (Create/Remove group new in Jalview 2.8.1)</em></li>
+ <li><strong>Make Groups for selection<br /> </strong> <em>The currently
selected groups of the alignment will be subdivided according to
the contents of the currently selected region. <br />Use this to
subdivide an alignment based on the different combinations of
residues observed at specific positions. (new in jalview 2.5)</em>
</li>
- </ul></li>
+ <li><strong>Undefine Groups (Control U)<br> </strong><em>The
+ alignment will be reset with no defined groups.<br> <strong>WARNING</strong>:
+ This cannot be undone.</em>
+ </li>
+ </ul></li>
<li><strong>View</strong>
<ul>
<li><strong>New View (Control T)</strong><em><br>
<li><strong>Show Consensus Histogram<br> </strong><em>
Enable or disable the display of the histogram above the
consensus sequence.</em></li>
- <li><strong>Show Consensus Profile<br> </strong><em> Enable
- or disable the display of the sequence logo above the consensus
+ <li><strong>Show Consensus Logo<br> </strong><em> Enable
+ or disable the display of the Consensus Logo above the consensus
sequence.</em></li>
+ <li><strong>Normalise Consensus Logo<br>
+ </strong><em>When enabled, scales all logo stacks to the same height,
+ making it easier to compare symbol diversity in highly variable
+ regions.</em></li>
<li><strong>Group Conservation<br> </strong><em> When
ticked, display a conservation row for all groups (only available
for protein alignments).</em></li>
</ul></li>
</ul>
+ </li>
+
+ </ul>
</li>
<li><strong>Colour</strong>
<li>Colour Scheme options: <strong>None, ClustalX,
Blosum62 Score, Percentage Identity, Zappo, Taylor,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, User Defined<br> </strong> <em>See
+ Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User Defined<br> </strong> <em>See
<a href="../colourSchemes/index.html">colours</a> for a
description of all colour schemes.</em><br></li>
<li><strong>By Conservation<br> </strong><em>See <a
the alignment on a per-column value from a specified annotation.
See <a href="../colourSchemes/annotationColouring.html">Annotation
Colouring</a>.</em><br></li>
+ <li><strong>By RNA Helices</strong><br>
+ <em>Colours the helices of an RNA alignment loaded from a Stockholm file. See
+ <a href="../colourSchemes/rnahelicesColouring.html">RNA Helices
+ Colouring</a>.</em><br>
+ </li>
</ul></li>
<li><strong>Calculate</strong>
<ul>
git://source.jalview.org / jalview.git / blobdiff