

...............
You could use the programs in New Arthur package, they are for clustering
compounds using PCA, KNN and SIMCA methods, he is free.
In order to calculate the phusico-chemical properties you could use WHIM
3D program he is also free and could be found in the inthernet to
download, but has one problem, some parameters do'n't have
physico-chemical significance, they are only mathematical. And you
couldn't use them to derive QSAR models.
You could also, finde COMFA for pc's free in the inthernet.
I don't know any program that could calculate PLS and neural networks, two
other clustering programs, inthe net for free, the are in TSAR package
from Oxford Molecular.
For generate equations, QSAR equations, I thing you could use the Bilin
program, I think he is free too.
I hope that could help you. 
If you're interested, my group here in Brazil has some good experience 
with clustering methods. If I could help more, let me know.
Best Regards

 ___________________________________________________________________
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|Antonio Luiz Oliveira de Noronha   -   [email-masked] |
|Medicinal Chemistry of Organotin Compounds                         |
|NEQUIM - Medicinal Chemistry Group                                 |
|Chemistry Departament - DQ                                         |
|UFMG - Federal University of Minas Gerais - Brazil                 |
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