JAL-1503 additional tree score functions

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index ba3582b..11b79ae 100755 (executable)
--- 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.