[Bio-software] "state-of-the-art" software for calculating distances

[Jan Kosinski]

Hi,

I am looking for a best (fast but robust, incorporating wide spectrum of 
models and parameters ) software
for calculating distances between protein sequences. To this end I was
using vanilla and its v_mldist. However, it does not allow to use
proportion of invariable sites parameter in the substitution model.
Could you recommend me anything?

Best regards,
Jan Kosinski