X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=d9b4b45010475cf3b3192fc47c39dfa7a21a7518;hb=b76d0ffcb6effa94954f75e030d1d67c890134eb;hp=8cbf0ca8cb41a30a475ca090485865c28076285a;hpb=96b6991703b70a1bbb0491f9946d397c9fcf5a38;p=jalview.git

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 8cbf0ca..d9b4b45 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -1,4 +1,21 @@
 <html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+-->
 <head>
 <title>Principal Component Analysis</title>
 </head>
@@ -23,9 +40,12 @@ of variation in the data set.</p>
 
 <p>In this case, the components are generated by an eigenvector
 decomposition of the matrix formed from the sum of BLOSUM scores at each
-aligned position between each pair of sequences. The basic method is
-described in the paper by G. Casari, C. Sander and A. Valencia.
-Structural Biology volume 2, no. 2, February 1995 (<a
+aligned position between each pair of sequences. The matrix is not
+symmetric - 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. This is a refinement of 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.</p>
 
@@ -50,7 +70,7 @@ sequence in the associated alignment window views. Rectangular region
 based selection is also possible, by holding the 'S' key whilst
 left-clicking and dragging the mouse over the display. By default,
 points are only associated with the alignment view from which the PCA
-was calculated, but this may be changed via the <strong>Associate
+was calculated, but this may be changed via the <strong>View&#8594;Associate
 Nodes</strong> sub-menu.</p>
 <p>Initially, the display shows the first three components of the
 similarity space, but any eigenvector can be used by changing the
