- <p>
- <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 either with <a href="scorematrices.html#blosum62">BLOSUM62</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.<br />
- Jalview allows two types of PCA calculation. The default <em><strong>Jalview
- PCA Calculation</strong></em> mode (indicated when that option is ticked in the <strong><em>Change
- Parameters</em></strong> menu) of the viewer performs PCA on a matrix where
- elements in the upper diagonal give the sum of scores for mutating in
- one direction, and the lower diagonal is the sum of scores for
- mutating in the other. For protein substitution models like BLOSUM62,
- this gives an asymmetric matrix, and a different PCA to one produced
- with the method described in the paper by G. Casari, C. Sander and A.
- Valencia. Structural Biology volume 2, no. 2, February 1995 (<a
- href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7749921">pubmed</a>)
- and implemented at the SeqSpace server at the EBI. The original method
- preconditions the matrix by multiplying it with its transpose, and
- this mode is enabled by unchecking the <strong><em>Jalview
- PCA Calculation</em></strong> option in the <strong><em>Change
- Parameters</em></strong> menu.
- </p>
-<img src="pcaviewer.gif">
- <p><strong>The PCA Viewer</strong></p>
-<p>This is an interactive display of the sequences positioned 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>
-<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 the up
-and down <strong>arrow keys</strong> (and the roll bar of the mouse if
-present). Labels will be shown for each sequence if the entry in the
-View menu is checked, and the plot background colour changed from the
-View→Background Colour.. dialog box. The File menu allows the view
-to be saved (<strong>File→Save</strong> submenu) as an EPS or PNG
-image or printed, and the original alignment data and matrix resulting
-from its PCA analysis to be retrieved. The coordinates for the whole PCA
-space, or just the current view may also be exported as CSV files for
-visualization in another program or further analysis.<p>
-<p>Options for coordinates export are:</p>
-<ul>
-<li>Output Values - complete dump of analysis (TxT* matrix computed from sum of scores for all pairs of aligned residues from from i->j and j->i, conditioned matrix to be diagonalised, tridiagonal form, major eigenvalues found)</li>
-<li>Output Points - The eigenvector matrix - rows correspond to sequences, columns correspond to each dimension in the PCA</li>
-<li>Transformed Points - The 3D coordinates for each sequence as shown in the PCA plot</li></ul>
+ <p>
+ <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 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>, or by sequence percentage identity,
+ or sequence feature similarity.
+ </p>
+ <img src="pcaviewer.gif">
+ <p>
+ <strong>The PCA Viewer</strong>
+ </p>
+ <p>This is an interactive display of the sequences positioned
+ 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 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
+ the up and down <strong>arrow keys</strong> (and the roll bar of the
+ mouse if present). Labels will be shown for each sequence if the
+ entry in the View menu is checked, and the plot background colour
+ changed from the View→Background Colour.. dialog box. The File
+ menu allows the view to be saved (<strong>File→Save</strong>
+ submenu) as an EPS or PNG image or printed, and the original
+ alignment data and matrix resulting from its PCA analysis to be
+ retrieved. The coordinates for the whole PCA space, or just the
+ current view may also be exported as CSV files for visualization in
+ another program or further analysis.
+ <p>
+ <p>Options for coordinates export are:</p>
+ <ul>
+ <li>Output Values - complete dump of analysis (TxT* matrix
+ computed from sum of scores for all pairs of aligned residues from
+ from i->j and j->i, conditioned matrix to be diagonalised,
+ tridiagonal form, major eigenvalues found)</li>
+ <li>Output Points - The eigenvector matrix - rows correspond to
+ sequences, columns correspond to each dimension in the PCA</li>
+ <li>Transformed Points - The 3D coordinates for each sequence
+ as shown in the PCA plot</li>
+ </ul>