<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<p>
<strong>Principal Component Analysis</strong>
</p>
+ <p>A principal component analysis can be performed via the
+ <a href="calculations.html">calculations dialog</a> which is accessed by selecting <strong>Calculate→Calculate
+ Tree or PCA...</strong>.</p>
<p>This calculation creates a spatial representation of the
similarities within a selected group, or all of the sequences in an
alignment. After the calculation finishes, a 3D viewer displays the
set of sequences as points in 'similarity space', and similar
sequences tend to lie near each other in the space.</p>
<p>
- <em>Caveats</em><br />The calculation is computationally expensive,
- and may fail for very large sets of sequences - usually because the
- JVM has run out of memory. A future release of Jalview will be able
- to avoid this by executing the calculation via a web service.
+ <em>Caveats</em><br />The calculation can be computationally
+ expensive, and may fail for very large sets of sequences - usually
+ because the JVM has run out of memory. However, the PCA
+ implementation in Jalview 2.10.2 employs more memory efficient
+ matrix storage structures, allowing larger PCAs to be performed.
</p>
<p>
git://source.jalview.org / jalview.git / blobdiff