From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 3 Jun 2014 13:26:22 +0000 (+0100)
Subject: JAL-1503 document updated PCA interface
X-Git-Tag: Release_2_8_1~4^2~5^2~9
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2ff5639e0ba863bf19212971977524f0a3c955be;p=jalview.git

JAL-1503 document updated PCA interface
---

diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html
index 0d6e85e..49019a7 100755
--- a/help/html/calculations/pca.html
+++ b/help/html/calculations/pca.html
@@ -46,25 +46,30 @@ of variation in the data set.</p>
 		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 either with <a href="scorematrices.html#blosum62">BLOSUM62</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.<br />
-		Jalview allows two types of PCA calculation. The default <em><strong>Jalview
-				PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
-				Parameters</em></strong> menu) of the viewer performs 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 one 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
+		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 Parameters</em></strong> menu.<br /> Jalview allows
+		two types of PCA calculation. The default
+		<em><strong>Jalview PCA Calculation</strong></em> mode (indicated when
+		that option is ticked in the
+		<strong><em>Change Parameters</em></strong> menu) of the viewer
+		performs 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 one 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. The original method
 		preconditions the matrix by multiplying it with its transpose, and
-		this mode is enabled by unchecking the <strong><em>Jalview
-				PCA Calculation</em></strong> option in the <strong><em>Change
-				Parameters</em></strong> menu.
+		this mode is enabled by unchecking the
+		<strong><em>Jalview PCA Calculation</em></strong> option in the
+		<strong><em>Change Parameters</em></strong> menu.
 	</p>
 <img src="pcaviewer.gif">
 	<p><strong>The PCA Viewer</strong></p>
@@ -106,5 +111,6 @@ located below the 3d display. The <strong><em>Reset</em></strong> button will re
 <p>
 <em>The output of points and transformed point coordinates was added to the Jalview desktop in v2.7.</em>
 <em>The Reset button and Change Parameters menu were added in Jalview 2.8.</em>
+<em>Support for PAM250 based PCA was added in Jalview 2.8.1.</em>
 </body>
 </html>
diff --git a/help/html/calculations/pcaviewer.gif b/help/html/calculations/pcaviewer.gif
index 215ceaf..78c82f2 100644
Binary files a/help/html/calculations/pcaviewer.gif and b/help/html/calculations/pcaviewer.gif differ