- <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
+ <strong><em>Change Parameters</em></strong> menu.</p>
+ <p>
+ <em>PCA Calculation modes</em><br/>
+ The default Jalview calculation mode
+ (indicated when <em><strong>Jalview PCA Calculation</strong></em> is
+ ticked in the <strong><em>Change Parameters</em></strong> menu) is to
+ perform a 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 a matrix 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