-<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 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>
-
-<p><strong>The PCA Viewer</strong></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 the sum of substitution matrix
+ scores at each aligned position between each pair of sequences -
+ computed either with <a href="scorematrices.html#blosum62">BLOSUM62</a> or the <a
+ href="scorematrices.html#simplenucleotide">simple single nucleotide
+ substitution matrix</a>. The options available for calculation are given
+ in the <strong><em>Change Parameters</em></strong> menu.<br />
+ Jalview allows two types of PCA calculation. The default <em><strong>Jalview
+ PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
+ Parameters</em></strong> menu) of the viewer performs PCA on a matrix where
+ 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. For protein substitution models like BLOSUM62,
+ this gives an asymmetric matrix, and a different PCA to one 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. The original method
+ preconditions the matrix by multiplying it with its transpose, and
+ this mode is enabled by unchecking the <strong><em>Jalview
+ PCA Calculation</em></strong> option in the <strong><em>Change
+ Parameters</em></strong> menu.
+ </p>
+<img src="pcaviewer.gif">
+ <p><strong>The PCA Viewer</strong></p>