X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;h=7ffb1602ae383c6319f561e57b20938cce04fcfa;hb=80ac7d84002118186a11658f38abfa5c4fe3d8da;hp=c38d9ac812f81b944c1909a63935924f5d418988;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index c38d9ac..7ffb160 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -26,16 +26,20 @@
Principal Component Analysis
+A principal component analysis can be performed via the + calculations dialog which is accessed by selecting Calculate→Calculate + Tree or PCA....
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.
- Caveats
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.
+ Caveats
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.