X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Ftree.html;h=b532aa3aa4c771e69d461c0ff471ef2595314443;hb=1dff84dcfc6852d1010626c583a0b5c5f915c7ae;hp=5ca9fcbd2dd78a09ea704d49a497a69fe91635f4;hpb=9cf2285dee92b3e12e818261503a575d45f02cc2;p=jalview.git

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