JAL-2962 start on help updates

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0104078..5b76d10 100755 (executable)
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -60,15 +60,15 @@
     <em>Calculating PCAs for aligned sequences</em><br />Jalview can
     perform PCA analysis on both proteins and nucleotide sequence
     alignments. In both cases, components are generated by an
-    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>,
     <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.
+      nucleotide substitution matrix</a>, or by sequence percentage identity,
+      or sequence feature similarity. 
   </p>
   <img src="pcaviewer.gif">
   <p>