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+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
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+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
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+<head>
+<title>The Alignment Calculations Dialog</title>
+</head>
+<body>
+ <p>
+ <strong>The Alignment Calculations Dialog</strong>
+ </p>
+ <img
+ alt="Alignment Calculations dialog box - opened via Calculations->Tree or PCA..."
+ 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>
+ 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
+ sequence similarity score model that will be used to perform the
+ analysis.
+ </p>
+ <p>
+ <strong>Adding additional score models</strong><br />Jalview can
+ import substitution matrices in both <a
+ href="http://www.genome.jp/aaindex/aaindex_help.html">AAindex</a>
+ and NCBI format (see e.g. <a
+ href="http://ftp.ncbi.nlm.nih.gov/blast/matrices/">ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/</a>).
+ In Jalview 2.10.2, the easiest way to import new models is to drag
+ the score model file onto any alignment window. See the <a
+ href="scorematrices.html">Substitution Matrices Documentation</a>
+ for more information.
+ </p>
+</body>
+</html>