-<p><strong>Calculation of trees from alignments</strong></p>
-<p>Trees are calculated on either the complete alignment, or just the
-currently selected group of sequences, using the functions in the
-<strong>Calculate→Calculate tree</strong> submenu.
-Once calculated, trees are displayed in a new <a
-href="../calculations/treeviewer.html">tree viewing window</a>. There are
-four different calculations, using one of two distance measures and
-constructing the tree from one of two algorithms :
-</p>
-<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>
+ <p>
+ <strong>Calculation of trees from alignments</strong>
+ </p>
+ <p>
+ Trees are calculated on either the complete alignment, or just the
+ currently selected group of sequences, via the <a href="calculations.html">calculations dialog</a> opened from the <strong>Calculate→Calculate
+ Tree or PCA...</strong> menu entry. Once calculated, trees are displayed in a new <a
+ href="../calculations/treeviewer.html">tree viewing
+ window</a>. There are four different calculations, using one of two
+ distance measures and constructing the tree from one of two
+ algorithms :
+ </p>
+ <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.
+ <ul>
+ <li>For details about each model, see the <a
+ href="scorematrices.html">list of built-in score
+ matrices</a>.
+ </li>
+ </ul></li>