From e1f1933f8038dd46960bf5c564e37de8211732ae Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 12:20:48 +0100
Subject: [PATCH] JAL-1483 more explicit description of feature similarity
 calculation

---
 help/html/calculations/tree.html |   24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index b532aa3..b223b0b 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -49,12 +49,24 @@ between each pair of sequences in the alignment :
 			about each model, see the <a href="scorematrices.html">list of
 				built-in score matrices.</a></li>
     <li><strong>Sequence Feature Similarity</strong><br>Trees
-      are constructed from a distance matrix formed from the normalised
-      hamming distance between the sequence features observed in each column of
-      the alignment.<br> <br>Distances are computed based on
-      the currently displayed feature types. Sequences with similar
-      distributions of features of the same type will be grouped
-      together in trees computed with this metric.</li>
+      are constructed from a distance matrix formed from Jaccard
+      distances between sequence features observed at each column of the
+      alignment.
+      <ul>
+        <li>Similarity at column <em>i</em> = (Total number of
+          features displayed - Sum of number of features in common at <em>i</em>)
+          <br />Similarities are summed over all columns and divided by
+          the number of columns. <br />Since the total number of
+          feature types is constant over all columns of the alignment,
+          we do not scale the matrix, so tree distances can be
+          interpreted as the average number of features that differ over
+          all sites in the aligned region.
+        </li>
+
+      </ul> Distances are computed based on the currently displayed feature
+      types. Sequences with similar distributions of features of the
+      same type will be grouped together in trees computed with this
+      metric. <em>This measure was introduced in Jalview 2.9</em></li>
   </ul>
 	</p>
 	<p><strong>Tree Construction Methods</strong></p>
-- 
1.7.10.2