- <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
- 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. This method
- preconditions the matrix by multiplying it with its transpose, and
- can be employed in the PCA viewer by unchecking the <strong><em>Jalview
- PCA Calculation</em></strong> option in the <strong><em>Change
- Parameters</em></strong> menu.
- </p>