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JAL-1620 version bump and release notes
[jalview.git] / help / html / menus / alignmentMenu.html
diff --git a/help/html/menus/alignmentMenu.html b/help/html/menus/alignmentMenu.html
index ff74139..966c005 100755 (executable)
--- a/help/html/menus/alignmentMenu.html
+++ b/help/html/menus/alignmentMenu.html
@@ -1,21 +1,24 @@
 <html>
 <!--
 <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 
  * 
  * 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.
  * 
  * 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>
 <head>
 <title>Alignment Window Menus</title>
 </head>
@@ -28,8 +31,8 @@
                <li><strong>File</strong>
                        <ul>
                                <li><strong>Fetch Sequence</strong><br> <em>Shows a
                <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
                                                European Bioinformatics Institute. See <a
                                                href="../features/seqfetch.html">Sequence Fetcher</a> </em>.</li>
                                <li><strong>Add Sequences</strong><em><br> Add
@@ -59,18 +62,16 @@
                                                Select the format of the text by selecting one of the following
                                                menu items.</em>
                                        <ul>
                                                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
                                        </ul></li>
                                <li><strong>Print (Control P)<br> </strong><em>Jalview
                                                will print the alignment using the current fonts and colours of
@@ -109,7 +110,7 @@
                                </li>
                                <li><strong>Load Associated Tree<br> </strong><em>Jalview
                                                can <a href="../calculations/treeviewer.html">view trees</a>
                                </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
                                                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
@@ -200,9 +201,9 @@
                                                the last redundancy deletion.</em>
                                </li>
                                <li><strong>Pad Gaps<br> </strong><em>When selected,
                                                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
                                                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
                                                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
@@ -235,17 +236,21 @@
                                </strong><em>Any columns currently not selected will replace the current
                                                column selection. </em>
                                </li>
                                </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>
                                                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>View</strong>
                        <ul>
                                <li><strong>New View (Control T)</strong><em><br>
@@ -272,34 +277,10 @@
                                                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>
                                                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 &quot;Annotation Panel&quot; 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>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
                                                        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
@@ -322,6 +303,61 @@
                                                using the mouse. </em>
                                </li>
                        </ul></li>
                                                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 &quot;Annotation Panel&quot; 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
                <li><strong>Alignment Window Format Menu</strong>
                        <ul>
                                <li><strong>Font...<br> </strong><em>Opens the
@@ -391,6 +427,9 @@
 
                                        </ul></li>
                        </ul>
 
                                        </ul></li>
                        </ul>
+       </li>
+
+               </ul>
                </li>
 
                <li><strong>Colour</strong>
                </li>
 
                <li><strong>Colour</strong>
@@ -407,7 +446,7 @@
                                <li>Colour Scheme options: <strong>None, ClustalX,
                                                Blosum62 Score, Percentage Identity, Zappo, Taylor,
                                                Hydrophobicity, Helix Propensity, Strand Propensity, Turn
                                <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
                                                <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
@@ -429,6 +468,11 @@
                                                the alignment on a per-column value from a specified annotation.
                                                See <a href="../colourSchemes/annotationColouring.html">Annotation
                                                        Colouring</a>.</em><br></li>
                                                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>
                        </ul></li>
                <li><strong>Calculate</strong>
                        <ul>
@@ -467,14 +511,15 @@
                                                <li><strong>Neighbour Joining Using Blosum62<br>
                                                </strong></li>
                                        </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
                                </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
                                                        Component Analysis</a>.</em> <br>
                                </li>
                                <li><strong>Extract Scores ... (optional)</strong><br> <em>This
@@ -492,28 +537,36 @@
                                <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>
                                <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
 
                <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
                        </ul>
                        <p>Selecting items from the following submenus will start a
                                remote service on compute facilities at the University of Dundee, or