First example, using the ade4 library and showing how to do a coinertia analysis :
Here is the example showing how you can search sequence data banks for gene sequences, compute the codon frequences for these genes, and perform a correspondence analysis (CA) of the frequencies table. This example makes the CA of the codon frequencies in the coding sequences of Mycoplasma genitalium. The web page explaining this example is here.
Here is a code example showing how an external data set can be used. You must use one of the three data entry methods to provide data table X, and the PCA of this table will be computed.
If you don't know how to program in R, here is a short code snippet that shows you a little bit about what R can do.