- eigenvector decomposition of the matrix formed from the sum of
- substitution matrix scores at each aligned position between each
- pair of sequences - computed with one of the available score
- matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>,