- 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
+ computed with one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>, <a
+ href="scorematrices.html#pam250">PAM250</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.</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