JAL-1483 description of the sequence feature based tree calculation

[jalview.git] / help / html / calculations / tree.html

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 5ca9fcb..b532aa3 100755 (executable)
--- 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