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+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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<head>
<title>Principal Component Analysis</title>
</head>
<p>In this case, the components are generated by an eigenvector
decomposition of the matrix formed from the sum of BLOSUM scores at each
-aligned position between each pair of sequences. The basic method is
-described in the paper by G. Casari, C. Sander and A. Valencia.
-Structural Biology volume 2, no. 2, February 1995 (<a
+aligned position between each pair of sequences. The matrix is not
+symmetric - elements in the upper diagonal give the sum of scores for
+mutating in one direction, and the lower diagonal is the sum of scores
+for mutating in the other. This is a refinement of 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.</p>
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>Associate
+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
git://source.jalview.org / jalview.git / blobdiff