+ <p>PAE matrix annotation rows behave like any other sequence
+ associated annotation, with the following additional features:</p>
+ <ul>
+ <li>The vertical axis of the PAE heatmap is mapped to positions
+ on the linked 3D structure.
+ <ul>
+ <li>Mousing over the matrix shows a tooltip giving information
+ on the range of values under the mouse.<br />Positions in the
+ associated 3D structure are also highlighted in any linked views.
+ </li>
+ <li>Clicking on positions in the matrix selects columns of the
+ alignment corresponding to the row and column in the matrix.</li>
+ </ul>
+ </li>
+ <li>Rectangular selections (created by Cmd (or Alt)+Click
+ dragging on the matrix) can be created to select multiple ranges of
+ columns at once.</li>
+ <li>Columns corresponding to adjacent regions with similarly low
+ levels of predicted alignment error can be selected by Ctrl+Clicking
+ on a region in the matrix.</li>
+ <li>Columns of an alignment showing a PAE matrix can be grouped
+ and selected by clustering the matrix.</li>
+ </ul>
+ <p>
+ <strong><a name="clustering">Clustering PAE Matrices</a></strong>
+ </p>
+ <p>PAE matrices are useful for identifying regions of 3D structure
+ predictions that are likely to be positioned in space in the same or
+ similar way as shown in the predicted structure data. Regions of low
+ PAE often correlate with high alphafold reliability (PLDDT) scores,
+ but also complement them since they highlight well-folded regions such
+ as domains, and how well those regions have been predicted to be
+ positioned relative to eachother, which is important when evaluating
+ whether domain-domain interactions or other contacts can be trusted.</p>
+ <p>To make it more easy to identify regions of low PAE, Jalview can
+ cluster the PAE matrix, allowing columns of the matrix to be grouped
+ according to their similarity, using an Average Distance (UPGMA) tree
+ algorithm and the sum of differences between each column's PAE values.</p>
+ <p>
+ <strong><em>dist<sub>ij</sub></em> = ∥ <em><u>p</u><sub>i</sub>-<u>p</u><sub>j</sub></em>
+ ∥</strong>
+ </p>
+ <p>
+ To create a PAE matrix tree, right click on a PAE annotation's label
+ to open the annotation popup menu, and select <strong><em>Cluster
+ Matrix</em></strong>. Once the calculation has finished, a tree viewer will open,
+ and columns of the matrix are then partitioned into groups such that
+ the third left-most node from the root is placed in its own group.
+ Colours are randomly assigned to each group, and by default these will
+ also be overlaid on the matrix annotation row.
+ <p>
+ <ul>
+ <li>The PAE matrix tree viewer behaves like other tree views in
+ Jalview, except selecting nodes or groups of nodes in the tree select
+ columns in the alignment rather than sequences, and clicking adjust
+ the matrix's partition.</li>
+ <li>Only one tree and clustering can be defined for a PAE matrix,
+ regardless of whether it is displayed in different views or
+ alignments.</li>
+ <li>Double clicking on a position in the PAE annotation where a
+ clustering has been defined will select both the row and column
+ clusters for the clicked position. This makes it easy to select
+ clusters corresponding to pairs of interacting regions.</li>
+ <li>Cluster colours for a PAE matrix can be used to colour
+ sequences or columns of the alignment via the <strong><em><a
+ href="../colourSchemes/annotationColouring.html">Colour by
+ Annotation.. dialog</a></em></strong>
+ (opened by right-clicking the annotation label
+ and selecting from the popup menu).
+ </li>
+ </ul>