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<head><title>Tree Calculation</title></head>
<body>
<p><strong>Calculation of trees from alignments</strong></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</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.
git://source.jalview.org / jalview.git / blobdiff