From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 10:54:33 +0000 (+0100)
Subject: JAL-1483 description of the sequence feature based tree calculation
X-Git-Tag: Release_2_10_0~457^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=1dff84dcfc6852d1010626c583a0b5c5f915c7ae;p=jalview.git

JAL-1483 description of the sequence feature based tree calculation
---

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 5ca9fcb..b532aa3 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -48,7 +48,14 @@ between each pair of sequences in the alignment :
 			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>
+    <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>
+  </ul>
 	</p>
 	<p><strong>Tree Construction Methods</strong></p>
 <p>Jalview currently supports two kinds of agglomerative clustering