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JAL-1483 description of the sequence feature based tree calculation
author
Jim Procter
<jprocter@issues.jalview.org>
Wed, 9 Sep 2015 10:54:33 +0000
(11:54 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Wed, 9 Sep 2015 11:25:36 +0000
(12:25 +0100)
help/html/calculations/tree.html
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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>
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
</p>
<p><strong>Tree Construction Methods</strong></p>
<p>Jalview currently supports two kinds of agglomerative clustering