We used the Bayesian method described in the following article: 

Deforche K, Silander T, Camacho R, Grossman Z, Soares M, et al. (2006) Analysis
of hiv-1 pol sequences using bayesian networks: implications for drug resistance.
Bioinformatics 22: 2975–2979.

The software is available in: https://code.google.com/p/bright/

