<mapID target="trees" url="html/calculations/tree.html"/>
<mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
<mapID target="sorting" url="html/calculations/sorting.html"/>
+ <mapID target="pasimap" url="html/calculations/pasimap.html"/>
+ <mapID target="proteinss" url="html/calculations/protssconsensus.html"/>
+ <mapID target="proteinssanaly" url="html/calculations/tree.html#ssim"/>
<mapID target="pca" url="html/calculations/pca.html"/>
<mapID target="pairwise" url="html/calculations/pairwise.html"/>
<mapID target="redundancy" url="html/calculations/redundancy.html"/>
<tocitem text="Jalview Documentation" target="home" expand="true">
<tocitem text="What's new" target="new" expand="true">
<tocitem text="Latest Release Notes" target="release"/>
- <tocitem text="Next Generation Command Line Interface" target="clarguments" />
- <tocitem text="AlphaFold PAE Matrices" target="workingwithpae" />
- <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
+ <tocitem text="PaSiMap Sequence Similarity Plots" target="pasimap" />
+ <tocitem text="Secondary Structure Trees and PCAs" target="proteinsssim" />
+ <tocitem text="Secondary Structure Consensus" target="proteinss" />
</tocitem>
<tocitem text="Editing Alignments" target="edit" />
<tocitem text="Calculations" expand="false">
<tocitem text="Sorting alignments" target="sorting" />
- <tocitem text="Trees and PCA" target="calcs.dialog" expand="false">
+ <tocitem text="Trees, PCA and PaSiMap" target="calcs.dialog" expand="false">
<tocitem text="Calculating trees" target="trees" />
<tocitem text="Principal Component Analysis" target="pca" />
+ <tocitem text="Principal Component Analysis" target="pasimap" />
</tocitem>
<tocitem text="Tree/PCA Input Data" target="recoverInputdata" />
<tocitem text="Pairwise Alignments" target="pairwise" />
<strong>The Alignment Calculations Dialog</strong>
</p>
<img
- alt="Alignment Calculations dialog box - opened via Calculations->Tree or PCA..."
+ alt="Alignment Calculations dialog box - opened via Calculations->Tree, PCA, or PaSiMap..."
src="calculatedialog.png" width="350" height="241">
<p>
The <strong>Calculations Dialog</strong> (shown above) is opened via
- the <strong>Calculations→Calculate Tree or PCA...</strong>
+ the <strong>Calculations→Calculate Tree, PCA or PaSiMap...</strong>
menu entry.
</p>
<p>
- It allows you to select the type of alignment analysis calculation (<a
- href="pca.html">PCA</a> or <a href="tree.html">Tree</a>), and the
+ It allows you to select the type of analysis (<a
+ href="pca.html">PCA</a>, <a href="tree.html">Tree</a>, <a href="pasimap.html">PaSiMap</a> or <a href="pairwise.html">Pairwise Alignment</a>), and below, the
sequence similarity score model that will be used to perform the
analysis.
</p>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>PaSiMap Sequence Similarity Analysis</title>
+</head>
+<body>
+ <p>
+ <strong>PaSiMap Sequence Similarity Analysis</strong>
+ </p>
+ <p>
+ PaSiMap analyses are performed via the <a
+ href="calculations.html">calculations dialog</a>, accessed
+ by selecting <strong>Calculate→Calculate Tree,
+ PCA or PaSiMap...</strong>.
+ </p>
+ <p>Like the <a href="pca.html">PCA<a> function in Jalview, PaSiMap
+ analysis creates a spatial representation of
+ how similar sequences are within a selected group, or all of the sequences in an
+ alignment. After the calculation finishes, a 3D viewer displays the
+ set of sequences as points in 'similarity space', and similar
+ sequences tend to lie near each other in the space.</p>
+ <p>Similarities in the PaSiMap calculation are calculated from
+ pairwise alignments of all pairs of input sequences. Since this can be
+ very time consuming, the maximum number sequences that can be used to
+ calculate a PaSiMap is limited by available time. Jalview will provide
+ an estimate of how long the calculation will take, and a 'Cancel' button
+ allows it to be stopped if desired.
+ </p>
+ <p>
+ <strong>About PaSiMap</strong>
+ </p>
+ <p>
+
+ Principal components analysis is a technique for examining the
+ structure of complex data sets. The components are a set of
+ dimensions formed from the measured values in the data set, and the
+ principal component is the one with the greatest magnitude, or
+ length. The sets of measurements that differ the most should lie at
+ either end of this principal axis, and the other axes correspond to
+ less extreme patterns of variation in the data set.</p>
+
+ <p>
+ <em>Calculating PCAs for aligned sequences</em><br />Jalview can
+ perform PCA analysis on both proteins and nucleotide sequence
+ alignments. In both cases, components are generated by an
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ <a href="scorematrices.html#pam250">PAM250</a>, or the <a
+ href="scorematrices.html#simplenucleotide">simple single
+ nucleotide substitution matrix</a>, or by sequence percentage identity,
+ or sequence feature similarity.
+ </p>
+ <img src="pcaviewer.png">
+ <p>
+ <strong>The PCA Viewer</strong>
+ </p>
+ <p>This is an interactive display of the sequences positioned
+ within the similarity space, as points in a rotateable 3D
+ scatterplot. The colour of each sequence point is the same as the
+ sequence group colours, white if no colour has been defined for the
+ sequence, and grey if the sequence is part of the currently selected
+ group. The viewer also employs depth cueing, so points appear darker
+ the farther away they are, and become brighter as they are rotated
+ towards the front of the view.</p>
+ <p>
+ The 3d view can be rotated by dragging the mouse with the <strong>left
+ mouse button</strong> pressed, or with the <strong>arrow
+ keys</strong> when <strong>SHIFT</strong> is pressed. The
+ view can also be zoomed in and out with
+ the up and down <strong>arrow keys</strong> (and the roll bar of the
+ mouse if present). Labels will be shown for each sequence if the
+ entry in the View menu is checked, and the plot background colour
+ changed from the View→Background Colour.. dialog box. The File
+ menu allows the view to be saved (<strong>File→Save</strong>
+ submenu) as an EPS or PNG image or printed, and the original
+ alignment data and matrix resulting from its PCA analysis to be
+ retrieved. The coordinates for the whole PCA space, or just the
+ current view may also be exported as CSV files for visualization in
+ another program or further analysis.
+ <p>
+ <p>Options for coordinates export are:</p>
+ <ul>
+ <li>Output Values - complete dump of analysis (TxT* matrix
+ computed from sum of scores for all pairs of aligned residues from
+ from i->j and j->i, conditioned matrix to be diagonalised,
+ tridiagonal form, major eigenvalues found)</li>
+ <li>Output Points - The eigenvector matrix - rows correspond to
+ sequences, columns correspond to each dimension in the PCA</li>
+ <li>Transformed Points - The 3D coordinates for each sequence
+ as shown in the PCA plot</li>
+ </ul>
+
+ <p>
+ A tool tip gives the sequence ID corresponding to a point in the
+ space, and clicking a point toggles the selection of the
+ corresponding sequence in the associated alignment window views.
+ <!-- Rectangular region
+based selection is also possible, by holding the 'S' key whilst
+left-clicking and dragging the mouse over the display. -->
+ By default, points are only associated with the alignment view from
+ which the PCA was calculated, but this may be changed via the <strong>View→Associate
+ Nodes</strong> sub-menu.
+ </p>
+ <p>
+ Initially, the display shows the first three components of the
+ similarity space, but any eigenvector can be used by changing the
+ selected dimension for the x, y, or z axis through each one's menu
+ located below the 3d display. The <strong><em>Reset</em></strong>
+ button will reset axis and rotation settings to their defaults.
+ </p>
+ <p>
+ <p>
+ <em>The output of points and transformed point coordinates was
+ added to the Jalview desktop in v2.7.</em> <em>The Reset button
+ and Change Parameters menu were added in Jalview 2.8.</em> <em>Support
+ for PAM250 based PCA was added in Jalview 2.8.1.</em><em>In Jalview 2.11, support for saving and restoring PCAs in Project files was added, and the Change parameters menu removed.</em>
+ </p>
+ <p>
+ <strong>Reproducing PCA calculations performed with older
+ Jalview releases</strong> Jalview 2.10.2 included a revised PCA
+ implementation which treated Gaps and non-standard residues in the
+ same way as a matrix produced with the method described in the paper
+ by G. Casari, C. Sander and A. Valencia. Structural Biology volume
+ 2, no. 2, February 1995 (<a
+ href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
+ and implemented at the SeqSpace server at the EBI. To reproduce
+ calculations performed with earlier Jalview releases it is necessary
+ to execute the following Groovy script:
+ <pre>
+ jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
+ jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
+ </pre>
+ This script enables the legacy PCA mode where gaps were treated as
+ 'X', and to modify the BLOSUM62 matrix so it is asymmetric for
+ mutations between C to R (this was a typo in the original Jalview
+ BLOSUM62 matrix which was fixed in 2.10.2).
+ </p>
+</body>
+</html>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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>Protein Secondary Structure Consensus Annotation</title>
+</head>
+<body>
+ <p>
+ <strong>Protein Secondary Structure Consensus Annotation</strong>
+ </p>
+
+ <p>Since version 2.11.4.0, Jalview can automatically calculate consensus
+ secondary structure for an alignment of protein sequences where one or
+ more sequences have secondary structure annotation, in the same way
+ as is done with the <a href="consensus.html">sequence consensus</a>.</p>
+ <p>
+ <em>Sources of secondary structure data</em></p>
+ <p>Sequences can have several different secondary structure
+ annotations, including those provided by
+ <a href="../features/xsspannotation.html">observed or computationally
+ determined 3D structures</a>, or predicted by
+ <a href="../webServices/jnet.html">JPred</a>. Sequence associated
+ secondary structure annotations can also be imported as
+ <a href="../features/annotationsFormat.html">Jalview Annotation
+ files</a>. Secondary structure annotations for a particular source can
+ be shown or hidden via <strong>Annotations→Show Secondary
+ Structure</strong> menu option in the alignment window.</p>
+ <p><strong>Consensus Secondary Structure</strong></p>
+ <p>The secondary structure consensus can be shown as a histogram,
+ reflecting the proportion of the most frequent conformation observed
+ in a column, optionally overlaid with a logo to reflect the
+ distribution of observed structure. The Alignment window's
+ <strong>Annotations→Autocalculated Annotation</strong> includes
+ options for controlling the appearance of the secondary structure
+ consensus row, and whether rows should be shown for groups defined
+ on the alignment.
+ </p>
+</body>
+</html>
same type will be grouped together in trees computed with this
metric. <em>This measure was introduced in Jalview 2.9</em></li>
- <li><strong>Secondary Structure Similarity</strong><br>Trees are
+ <li><strong><a name="sssim">Secondary Structure Similarity</strong><br>Trees are
generated using a distance matrix, which is constructed from Jaccard
- distances that specifically consider the secondary structure features
+ distances that specifically consider the secondary structure annotation
observed at each column of the alignment.
<ul>
<li>For secondary structure similarity analysis, at any given column
Press the "Apply" button to remove redundant
sequences. The "Undo" button will undo the last
redundancy deletion.</em></li>
+ <li><strong>Left Justify</strong> and <strong>Right
+ Justify<br></strong><em>Moves all gaps to either right or
+ left of the sequences in the alignment or the currently
+ selected region.</em></li>
<li><strong>Pad Gaps<br>
</strong><em>When selected, the alignment will be kept at minimal
width (so there are no empty columns before or after the
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>Show Secondary Structure</strong> (since 2.11.4.0)<em>
+ <br><strong><em>All</em></strong> and <strong><em>None</em></strong> control display of secondary structure annotations on the alignment.
+ Additional options allow just a specific source of protein secondary structure to be shown.</li>
<li><strong>Autocalculated Annotation<br>
</strong><em>Settings for the display of autocalculated annotation.</em>
<ul>
<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>Show SS Consensus Histogram<br>
+ </strong><em> Enable or disable the display of histogram for Secondary Structure Consensus.</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
</strong><em>Select this to center labels along an annotation
row relative to their associated column (default is off,
i.e. left-justified).</em></li>
- <li><strong>Show Unconserved<br>
+ <li><strong>Show Nonconserved<br>
</strong><em>When this is selected, all consensus sequence
symbols will be rendered as a '.', highlighting
mutations in highly conserved alignments. </em></li>
+ <li><strong>Copy format from<br>
+ </strong><em>When available, the submenu allows
+ the format and layout from one of the listed alignment views
+ to be copied to the current view.
+ </em></li>
</ul></li>
colour will be applied to all currently defined groups.<br>
</em></li>
<li><strong><a
- href="../colourSchemes/textcolour.html">Colour
- Text...</a> </strong><em><br> Opens the Colour Text dialog box
+ href="../colourSchemes/textcolour.html">Text
+ Colour...</a> </strong><em><br> Opens the foreground text colour dialog box
to set a different text colour for light and dark background,
and the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
viewer window.
</em><br></li>
</ul></li>
- <li><strong>Calculate Tree or PCA ...</strong><em> <br> Opens the
- <a href="../calculations/calculations.html">calculations dialog</a> for
- for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principal component analysis
- plots</a> on the alignment or the currently selected
- region.
+ <li><strong>Calculate Tree, PCA or PaSiMap...</strong><em> <br> Opens the
+ <a href="../calculations/calculations.html">calculations dialog</a> which allows calculation of<ul>
+ <li><a href="../calculations/tree.html">trees</a></li><li><a href="../calculations/pca.html">principal component analysis
+ plots</a></li><li><a href="../calculations/pasimap.html">PaSiMap plots</li></ul>
</em><br></li>
<li><strong>Pairwise Alignments</strong><br> <em>Applies
Smith and Waterman algorithm to selected sequences. See <a
</ul>
</em>
</ul></li>
+ <li><strong>Protein Disorder Prediction</strong><br/><em>
+ Allows access to a range of <a href="../webServices/proteinDisorder.html">protein disorder predictors</a>
+ provided by <a href="../webServices/JABAWS.html">JABAWS 2.2</a>.
+ </em></li>
<li><strong>Analysis</strong><br />
<ul>
<li><strong>Multi-Harmony</strong><br> <em>Performs
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>Show Secondary Structure</strong> (since 2.11.4.0)<em>
+ <br><strong><em>All</em></strong> and <strong><em>None</em></strong> control display of secondary structure annotations on the alignment.
+ Additional options allow just a specific source of <a href="../calculations/protssconsensus.html">Protein secondary structure</a> to be shown.</li>
<li><strong>Autocalculated Annotation<br>
</strong><em>Settings for the display of autocalculated annotation.</em>
<ul>
<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>Show SS Consensus Histogram<br>
+ </strong><em> Enable or disable the display of histogram for Secondary Structure Consensus.</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
(numerical or otherwise) at each position in the row. This
is useful to export alignment quality measurements for
further analysis.</em></li>
+ <li><strong>Colour by Annotation</strong> <br>
+ <em>Open's the <a href="../colourSchemes/annotationColouring.html">
+ Colour by Annotation</a> dialog, already configured
+ for this annotation row.</em>
+ <br>
+ <strong>Colour by Annotation (Per-Sequence)</strong> may also be
+ available for sequence associated annotations, such as secondary structure
+ or AlphaFold PLDDT score annotation tracks.
+ </li>
+ <li><strong>Select/Hide columns by annotation...</strong> <br>
+ <em>Open's the <a href="../features/columnFilterByAnnotation.html">
+ select/hide by annotation</a> dialog, already configured
+ for this annotation row.</em>
+ </li>
</ul> <em>The following additional entries are available when the
popup menu is opened on a consensus sequence annotation row:</em>
<ul>
format, to allow the consensus sequence to be added to an
alignment. Note the copied sequence is not accessible to other
programs if Jalview is running as an applet in a web page.</li>
- </ul></li>
+ </ul>
+
+ <strong>Predicted Alignment Error</strong> annotation
+ tracks have the following additional options (see
+ <a href="../features/paematrices.html">working with
+ PAE Matrices</a> for full details):
+ <ul>
+ <li><strong>Show Groups on Matrix</strong><br/><em>When ticked,
+ colour the columns of the matrix by the clusters on it tree.</em></li>
+ <li><strong>Cluster Matrix</strong><br/><em>Select this to calculate
+ a tree for the PAE matrix, allowing identification of reliably
+ positioned regions of structure.</em></li>
+ <li><strong>Show Matrix</strong> or <strong>Show Tree for
+ Matrix</strong><br/><em>Select this to either calculate
+ or show the tree calculated for the PAE matrix, allowing columns
+ of the alignment to be clustered in order to identify reliably
+ positioned regions of structure.</em></li>
+ </ul>
+ </li>
<li><strong>Annotation Popup Menu<br>
</strong><em>This menu is opened when right-clicking on the selected
positions of an annotation.</em>
window.
</em><br></li>
</ul></li>
- <li><strong>Calculate Tree or PCA ...</strong> <br> <em>Opens the
- <a href="../calculations/calculations.html">calculations dialog</a> for
- for calculating <a href="../calculations/tree.html">trees</a> or
- <a href="../calculations/pca.html">principal component analysis
- plots</a> on the alignment or the currently selected
- region.
- </em><br>
- </li>
+ <li><strong>Calculate Tree, PCA or PaSiMap...</strong><em> <br> Opens the
+ <a href="../calculations/calculations.html">Calculations dialog</a> which allows calculation of<ul>
+ <li><a href="../calculations/tree.html">trees</a></li><li><a href="../calculations/pca.html">principal component analysis
+ plots</a></li><li><a href="../calculations/pasimap.html">PaSiMap plots</li></ul>
+ </em><br></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>.
+ alignments</a>. Also available via the
+ <a href="../calculations/calculations.html">Calculations dialog</a>.
</em><br></li>
<li><strong>Extract Scores ... (optional)</strong><br> <em>This
option is only visible if Jalview detects one or more
</strong><em>If this is selected, any changes made to the background
colour will be applied to all currently defined groups.<br>
</em></li>
- <li><strong><a href="../colourSchemes/textcolour.html">Colour
- Text ...</a></strong><em><br> Opens the Colour Text dialog box to
+ <li><strong><a href="../colourSchemes/textcolour.html">Text
+ Colour...</a></strong><em><br> Opens the foreground text colour dialog box to
set a different text colour for light and dark background, and
the intensity threshold for transition between them. </em></li>
<li>Colour Scheme options: <strong>None, ClustalX,
<li><strong>Centre Column Labels<br>
</strong><em>When this is selected, the text labels within each annotation
row will be centred on the column that they are associated with. </em></li>
- <li><strong>Show Unconserved<br>
+ <li><strong>Show Nonconserved<br>
</strong><em>When this is selected, all consensus sequence symbols will be
rendered as a '.', highlighting mutations in highly conserved
alignments. </em></li>
-
+ <li><strong>Copy format from<br>
+ </strong><em>When available, the submenu allows
+ the format and layout from one of the listed alignment views
+ to be copied to the current view.
+ </em></li>
</ul>
</body>
</html>
<li><strong>Load Project</strong><br> <em>Loads
Jalview archives <strong>only</strong>.
</em></li>
- <li><strong>Quit</strong><br> <em>Close Jalview.
- <br> <strong>Note - any annotation you have
+ <li><strong>Quit</strong><br> <em>Close Jalview.</em>
+ <br> <em>Under the Jalview dropdown on Macs</em>
+ <br>
+ <strong>Jalview will try to check if you have any unsaved
+ data and warn you, but please remember that any annotation you have
made on alignments will be lost unless you Save your work
before quitting.</strong>
- </em><br></li>
+ <br></li>
</ul></li>
<li><strong>Tools</strong>
<ul>
<li><strong><a href="../features/preferences.html">Preferences<br>
- </a></strong><em>Change the default visual settings for opening new
+ </a></strong><em>Under the Jalview menu on OSX</em><br><em>Change the default visual settings for opening new
alignment windows.</em></li>
<li><strong>Show Memory Usage<br></strong> <em>When
ticked, the currently available memory will be displayed in
the <a href="../features/groovy.html">Groovy Console</a> for
interactive scripting.
</em><strong><br></strong></li>
- <!-- <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em> -->
+ <strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em>
</ul></li>
<li><strong>Help </strong>
information.
</em></li>
<li><strong>Secondary Structure Prediction</strong>
+ <br><em>Provides access to protein and RNA secondary structure prediction tools.
<ul>
<li><strong>JPred Secondary Structure Prediction</strong><br>
<em>Secondary structure prediction by network consensus.
</li>
</ul>
</em>
+ </li><strong>RNAAliFold Prediction</strong><br>Submit the
+ alignment to the
+ <a href="../webServices/RNAalifold.html">JABAWS RNAAliFold
+ service</a> for consensus RNA base pair prediction. The
+ prediction will be updated if the alignment is edited.</li>
</ul></li>
+ <li><strong>Protein Disorder Prediction</strong><br/><em>
+ Allows access to a range of <a href="../webServices/proteinDisorder.html">protein disorder predictors</a>
+ provided by <a href="../webServices/JABAWS.html">JABAWS 2.2</a>.
+ </em></li>
<li><strong>Analysis</strong><br />
<ul>
<li><strong>Multi-Harmony</strong><br> <em>Performs
The 2.11.4 series is the fourth in the minor-release trilogy planned for Jalview's 2.11 series.
-This release adds new capabilities for consensus and clustering of protein secondary structure, along with enhanced control of the display and analysis of secondary structure from different sources of 3D structure and prediction, and also features a new implementation of the PASiMap method for sequence clustering ([Su et al. 2022 <i>Comp. Struc. Biotech.</i>](https://doi.org/10.1016/j.csbj.2022.09.034)).
+This release adds new capabilities for visualisation and clustering of protein secondary structure annotations,
+along with enhanced control of the display and analysis of secondary structure from different
+sources of 3D structure and prediction.
+The Calculations dialog has also been revised to accommodate a new implementation of
+the spatial clustering method PASiMap
+([Su et al. 2022 <i>Comp. Struc. Biotech.</i>](https://doi.org/10.1016/j.csbj.2022.09.034))
+which was added to Jalview by Thomas Morrell and Jen Christianson.
+Jalview 2.11.4 also has new installers and command line scripts that bring several
+minor improvements, and also makes it easier for IT admins to manage Jalview installations
+on computers used by many different people. New installations of Jalview will by default
+store updates in user's home directories, Automatic updates can also be disabled, and
+updates instead carried out using a new jalview_admin command line tool.
+
+
+## Experimental features
+
+This release includes experimental support (enabled in the Tools menu) for
+handling drag'n'drop of alignment, tree, annotations and feature file(s)
+onto the Jalview Desktop. They can also be dragged onto the Jalview icon.
+
+
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git://source.jalview.org / jalview.git / commitdiff