<em>Calculating PCAs for aligned sequences</em><br />Jalview can
perform PCA analysis on both proteins and nucleotide sequence
alignments. In both cases, components are generated by an
- eigenvector decomposition of the matrix formed from the sum of
- substitution matrix scores at each aligned position between each
- pair of sequences - computed with one of the available score
- matrices, such as <a href="scorematrices.html#blosum62">BLOSUM62</a>,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the <a href="calculations.html">calculations dialog</a>, and
+ may use one of the available score matrices, such as
+ <a href="scorematrices.html#blosum62">BLOSUM62</a>,
<a href="scorematrices.html#pam250">PAM250</a>, or the <a
href="scorematrices.html#simplenucleotide">simple single
- nucleotide substitution matrix</a>. The options available for
- calculation are given in the <strong><em>Change
- Parameters</em></strong> menu.
+ nucleotide substitution matrix</a>, or by sequence percentage identity,
+ or sequence feature similarity.
</p>
<img src="pcaviewer.gif">
<p>
within the similarity space, as points in a rotateable 3D
scatterplot. The colour of each sequence point is the same as the
sequence group colours, white if no colour has been defined for the
- sequence, and green if the sequence is part of a the currently
- selected group.</p>
+ sequence, and grey if the sequence is part of the currently selected
+ group. The viewer also employs depth cueing, so points appear darker
+ the farther away they are, and become brighter as they are rotated
+ towards the front of the view.</p>
<p>
The 3d view can be rotated by dragging the mouse with the <strong>left
mouse button</strong> pressed. The view can also be zoomed in and out with
git://source.jalview.org / jalview.git / blobdiff