From 8fb68bdd03fd4be2a8dd536e547c9b1d59b60734 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 3 Jun 2014 14:27:21 +0100
Subject: [PATCH] JAL-1503 additional tree score functions

---
 help/html/calculations/tree.html |   29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index ba3582b..11b79ae 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -31,17 +31,24 @@ constructing the tree from one of two algorithms :
 <p><strong>Distance Measures</strong></p>
 <p>Trees are calculated on the basis of a measure of similarity
 between each pair of sequences in the alignment :
-<ul>
-<li><strong>PID</strong><br>The percentage identity between the two
-sequences at each aligned position.<ul><li>PID = Number of equivalent
-aligned non-gap symbols * 100 / Smallest number of non-gap positions
-in either of both sequences<br><em>This is essentially the 'number of
-identical bases (or residues) per 100 base pairs (or residues)'.</em></li></ul>
-<li><strong>BLOSUM62</strong><br>The sum of BLOSUM62 scores for the
-residue pair at each aligned position.
-</ul>
-</p>
-<p><strong>Tree Construction Methods</strong></p>
+	<ul>
+		<li><strong>PID</strong><br>The percentage identity between
+			the two sequences at each aligned position.
+			<ul>
+				<li>PID = Number of equivalent aligned non-gap symbols * 100 /
+					Smallest number of non-gap positions in either of both sequences<br>
+				<em>This is essentially the 'number of identical bases (or
+						residues) per 100 base pairs (or residues)'.</em>
+				</li>
+			</ul>
+		<li><strong>BLOSUM62, PAM250, DNA</strong><br>These options
+			use one of the available substitution matrices to compute a sum of
+			scores for the residue pairs at each aligned position. For details
+			about each model, see the <a href="scorematrices.html">list of
+				built-in score matrices.</a></li>
+	</ul>
+	</p>
+	<p><strong>Tree Construction Methods</strong></p>
 <p>Jalview currently supports two kinds of agglomerative clustering
 methods. These are not intended to substitute for rigorous
 phylogenetic tree construction, and may fail on very large alignments.
-- 
1.7.10.2