<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 2.8.2b1)
+ * 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.
- *
+ * 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/>.
--->
+ * 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>
</head>
<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
Select the format of the text by selecting one of the following
menu items.</em>
<ul>
- <li><strong>FASTA</strong> <em></em>
- </li>
- <li><strong>MSF</strong>
- </li>
- <li><strong>CLUSTAL</strong>
- </li>
- <li><strong>BLC</strong>
- </li>
- <li><strong>PIR</strong>
- </li>
- <li><strong>PFAM</strong>
- </li>
+ <li><strong>FASTA</strong> </li>
+ <li><strong>MSF</strong></li>
+ <li><strong>CLUSTAL</strong></li>
+ <li><strong>BLC</strong></li>
+ <li><strong>PIR</strong></li>
+ <li><strong>PFAM</strong></li>
+ <li><strong>PileUp</strong></li>
+ <li><strong>AMSA</strong></li>
+ <li><strong>STH</strong></li>
+ <li><strong>Phylip</strong></li>
</ul></li>
<li><strong>Print (Control P)<br> </strong><em>Jalview
will print the alignment using the current fonts and colours of
</li>
<li><strong>Load Associated Tree<br> </strong><em>Jalview
can <a href="../calculations/treeviewer.html">view trees</a>
- stored in the Newick file format, and associate them with the
+ stored in the Newick file format, and associate them with the
alignment. Note: the ids of the tree file and your alignment MUST
be the same.</em></li>
<li><strong>Load Features / Annotations<br> </strong><em>Load
the last redundancy deletion.</em>
</li>
<li><strong>Pad Gaps<br> </strong><em>When selected,
- the alignment will be kept at minimal width (so there no empty
+ the alignment will be kept at minimal width (so there are no empty
columns before or after the first or last aligned residue) and all
- sequences will be padded with gap characters to the before and
+ sequences will be padded with gap characters before and
after their terminating residues.<br> This switch is useful
when making a tree using unaligned sequences and when working with
alignment analysis programs which require 'properly aligned
</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>
selected, the view will automatically scroll to display the
highlighted sequence position corresponding to the position under
the mouse pointer in a linked alignment or structure view.</em></li>
- <li><strong>Show Annotations<br> </strong><em>If this
- is selected the "Annotation Panel" will be displayed
- below the alignment. The default setting is to display the
- conservation calculation, quality calculation and consensus values
- as bar charts. </em>
- </li>
- <li><strong>Autocalculated Annotation<br> </strong><em>Settings
- for the display of autocalculated annotation.</em>
- <ul>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, any modification to the current settings will be applied
- to all autocalculated annotation.</em></li>
- <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
- sequence.</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>
- <li><strong>Apply to all groups<br> </strong><em> When
- ticked, display a consensus row for all groups.</em></li>
- </ul></li>
<li><strong>Show Sequence Features</strong><br> <em>Show
or hide sequence features on this alignment.</em>
</li>
- <li><strong><a href="../features/featuresettings.html">Seqence
+ <li><strong><a href="../features/featuresettings.html">Sequence
Feature Settings...</a> </strong><em><br> <em>Opens the
Sequence Feature Settings dialog box to control the colour and
display of sequence features on the alignment, and configure and
using the mouse. </em>
</li>
</ul></li>
+ <li><strong>Annotations</strong><em> (Since Jalview 2.8.2)</em>
+ <ul>
+ <li><strong>Show Annotations<br> </strong><em>If this
+ is selected the "Annotation Panel" will be displayed
+ below the alignment. The default setting is to display the
+ conservation calculation, quality calculation and consensus values
+ as bar charts. </em>
+ </li>
+ <li><strong>Show Alignment Related</strong><em><br>
+ Show all annotations that are for the alignment as a whole (for example, Consensus,
+ or secondary structure prediction from alignment).</em></li>
+ <li><strong>Hide Alignment Related</strong><em><br>
+ Hide all annotations that are for the alignment as a whole.</em></li>
+ <li><strong>Show Sequence Related</strong><em><br>
+ Show all annotations that are for individual sequences.</em></li>
+ <li><strong>Hide Sequence Related</strong><em><br>
+ Hide all annotations that are for individual sequences.</em></li>
+ <li><em>You can also selectively show or hide annotations from the <a href="./popupMenu.html">Popup</a>
+ or <a href="../features/annotation.html">Annotation</a> menus.</em></li>
+ <li><strong>Sort by Sequence</strong><em><br>Sort sequence-specific annotations by sequence order in the alignment
+ (and within that, by label).</em></li>
+ <li><strong>Sort by Label</strong><em><br>Sort sequence-specific annotations by label
+ (and within that, by sequence order). If neither sort order is selected, no sorting is applied,
+ allowing you to make a manual ordering of the annotations.</em></li>
+ <li><strong>Autocalculated Annotation<br> </strong><em>Settings
+ for the display of autocalculated annotation.</em>
+ <ul>
+ <li><strong>Show first<br></strong><em>
+ Show autocalculated annotations above sequence-specific annotations.
+ Note this also applies to other annotations for the alignment, for example secondary
+ structure prediction from alignment.</em></li>
+ <li><strong>Show last<br></strong><em>
+ Show autocalculated / alignment annotations below sequence-specific annotations.</em></li>
+ <li><strong>Apply to all groups<br> </strong><em> When
+ ticked, any modification to the current settings will be applied
+ to all autocalculated annotation.</em></li>
+ <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 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>
+ <li><strong>Group Consensus<br> </strong><em> When
+ ticked, display a consensus row for all groups.</em></li>
+ </ul>
+ </li>
+ </ul>
+ </li>
<li><strong>Alignment Window Format Menu</strong>
<ul>
<li><strong>Font...<br> </strong><em>Opens the
</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>
<li><strong>Neighbour Joining Using Blosum62<br>
</strong></li>
</ul>
+ <strong>Note: Since Version 2.8.1, a number of additional similarity measures for tree calculation are provided in this menu.</strong>
</li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
href="../calculations/pairwise.html">pairwise alignments</a>.</em><br>
</li>
<li><strong>Principal Component Analysis</strong><br> <em>Shows
- a spatial clustering of the sequences based on the BLOSUM62 scores
- in the alignment. See <a href="../calculations/pca.html">Principal
+ a spatial clustering of the sequences based on similarity scores calculated with
+ the alignment. See <a href="../calculations/pca.html">Principal
Component Analysis</a>.</em> <br>
</li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
<li><strong>Sort With New Tree</strong><br> <em>When
enabled, Jalview will automatically sort the alignment when a new
tree is calculated or loaded onto it.</em> <br></li>
- </ul></li>
+ <li><strong>Show Flanking Regions</strong><br> <em>Opens
+ a new alignment window showing any additional sequence data either
+ side of the current alignment. Useful in conjunction with 'Fetch
+ Database References' when the 'Trim Retrieved Sequences' option is
+ disabled to retrieve full length sequences for a set of aligned
+ peptides. </em></li>
+ </ul></li>
<li><strong>Web Service Menu</strong><br /> <em>This menu
is dynamic, and may contain user-defined web service entries in
addition to any of the following ones:</em>
<ul>
<li><strong>Fetch DB References</strong><br> <em>This
- will use any of the database services that Jalview is aware of
- (e.g. DAS sequence servers and the WSDBFetch service provided by
- the EBI) to verify the sequence and retrieve all database cross
- references and PDB ids associated with all or just the selected
- sequences in the alignment. <br />'Standard Databases' will check
- sequences against the EBI databases plus any active DAS sequence
- sources, or you can verify against a specific source from one of
- the sub-menus.</em><br></li>
- <li><strong>Envision2 Services</strong><br /><em> Submits one or
- more sequences, sequence IDs or database references to analysis
- workflows provided by the <a
- href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
- application</a>. This allows Jalview users to easily access the EnCore
- network of databases and analysis services developed by members of
- <a href="http://www.enfin.org">ENFIN</a></em>.</li>
+ submenu contains options for accessing any of the database services
+ that Jalview is aware of (e.g. DAS sequence servers and the
+ WSDBFetch service provided by the EBI) to verify sequence start/end
+ positions and retrieve all database cross references and PDB ids
+ associated with all or just the selected sequences in the alignment.
+ <ul>
+ <li>'Trim Retrieved Sequences' - when checked, Jalview will
+ discard any additional sequence data for accessions associated with
+ sequences in the alignment. <br> <strong>Note: Disabling this
+ could cause out of memory errors when working with genomic
+ sequence records !</strong><br> <strong>Added in Jalview 2.8.1</strong>
+ </li>
+ <li>'Standard Databases' will check sequences against the EBI
+ databases plus any active DAS sequence sources<</li>
+ </ul> Other sub-menus allow you to pick a specific source to query -
+ sources are listed alphabetically according to their nickname.
+ </em><br></li>
</ul>
<p>Selecting items from the following submenus will start a
remote service on compute facilities at the University of Dundee, or
git://source.jalview.org / jalview.git / blobdiff