pair of sequences - 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
+ 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
+ <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
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
+ 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>