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+<head>
+<title>Supported Formats for Predicted Alignment Error Matrices</title>
+</head>
+
+<body>
+ <p>
+ <strong>Supported Formats for Predicted Alignment Error
+ Matrices</strong>
+ </p>
+ <p>
+ Predicted Alignment Error matrices are square matrices produced as
+ part of deep-learning based 3D-structure prediction pipelines such as
+ AlphaFold. They can be imported via <a
+ href="../features/structurechooser.html">Jalview's structure
+ chooser</a> GUI and the <a href="../features/clarguments-basic.html">Command
+ Line Interface</a>. See <a href="../features/paematrices.html">Working
+ with PAE Matrices</a> for information on how they are visualised and
+ analysed in Jalview.
+ </p>
+ <p>
+ <strong>Supported Formats</strong>
+ </p>
+ <p>Jalview supports import of PAE matrix data as provided by the
+ EBI-AlphaFold database. This resource provides PAE matrices as a JSON
+ files structured in one of the following ways:</p>
+ <pre>
+ # Version 1 format PAE file - deprecated 28th July 2022
+ {
+ residue1:[1,1,... total number of residues]
+ residue2:[1,2,... total number of residues]
+ distance:[0.1,0.3,... list of PAE matrix elements as doubles]
+ }
+ </pre>
+ <pre>
+ # Version 2 format PAE file - see https://alphafold.ebi.ac.uk/faq
+ {
+ max_predicted_alignment_error: 4.0, # may also be max_pae
+ predicted_alignment_error: [[1,2,0,0,3,...],...] # may also be pae
+ }
+ </pre>
+ <p>
+ Variants of the version 2 format include using 'pae' instead of
+ 'predicted_alignment_error' in the names of keys. Jalview copes both.<br />
+ Once imported, Jalview stores PAE matrices as float arrays along with
+ any associated tree and partition set resultant from clustering the
+ matrix. <br/><br/><em>PAE Matrix import support was added in Jalview 2.11.3
+ </em>
+ </p>
+</body>
+</html>
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