Which utility package (preferably web-based) is available to generate PCA plots based on nucleotide word frequency (k-mer)?

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Chayan Roy

(http://gos.jcvi.org/openAccess/scatterPlotViewer.html)

This one from the JCVI is not currently available, any alternate source of this???

Oliver Sampson

I don't know specifically about "nucleotide word frequency", but if you might want to give KNIME a try. If the data isn't already in the format you need (finding the frequencies) there are some (free) bio/chem plugins available that might do that for you.

http://www.knime.org