From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Sep 2015 11:21:22 +0000 (+0100)
Subject: JAL-1645 formatting tree distance docs
X-Git-Tag: Release_2_10_0~457^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cd33c321daf37cdd0d67e9745fc699aa9e7fc103;hp=e1f1933f8038dd46960bf5c564e37de8211732ae;p=jalview.git

JAL-1645 formatting tree distance docs
---

diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index b223b0b..6a31403 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -33,21 +33,26 @@ 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, 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>
+    <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.
+      <ul><li>For details about each model, see the 
+      <a href="scorematrices.html">list of built-in score matrices</a>.
+        </li>
+        </ul></li>
     <li><strong>Sequence Feature Similarity</strong><br>Trees
       are constructed from a distance matrix formed from Jaccard
       distances between sequence features observed at each column of the
@@ -68,7 +73,6 @@ between each pair of sequences in the alignment :
       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>
 <p>Jalview currently supports two kinds of agglomerative clustering
 methods. These are not intended to substitute for rigorous
@@ -89,7 +93,6 @@ phylogenetic tree construction, and may fail on very large alignments.
   expensive than UPGMA.
 </li>
 </ul>
-</p>
 <p>A newly calculated tree will be displayed in a new <a
 href="../calculations/treeviewer.html">tree viewing window</a>. In
 addition, a new entry with the same tree viewer window name will be added in the Sort