X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpca.html;fp=help%2Fhtml%2Fcalculations%2Fpca.html;h=5b76d109f29cb9c03024a5b6a9aa572932579ff6;hb=904d2d844982ac214ff989516b10d3e4ea01a842;hp=0104078be6e66707cb67fe623f80be11858d150f;hpb=cf6ec9416dae77d30b5be628c1112a609ed088fe;p=jalview.git
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Calculating PCAs for aligned sequences
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 BLOSUM62,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the calculations dialog, and
+ may use one of the available score matrices, such as
+ BLOSUM62,
PAM250, or the simple single
- nucleotide substitution matrix. The options available for
- calculation are given in the Change
- Parameters menu.
+ nucleotide substitution matrix, or by sequence percentage identity,
+ or sequence feature similarity.