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Anyone know of a good factors analysis library for R?

Steven Lembark 
Trying to separatey correlate the regions of HIV-1's gp120 
with neutralization data. I have comparison matrixes for 
the sequences and cross-clade neutralization data. My guess
is that analyzing in the individual regions will give us
better correlation with the neutralization data, but at 
this point cannot find a good package for analyzing the 
similarity matrixes. 

The inputs inlcude a square matrixes of comparisons between
each clade for each region and cross-clade antibody responses.

What I need is a level of correlation between the neutralization
data and the similarity matrixes. 

Searching CRAN for "factors analysis", "cross clade", and
"corretion model" in various combinations hadn't gotten me
anything that looks relevant.

Any advice would be appreciated.

thanx