James O. McInerney (j.mcinerney at nhm.ac.uk) wrote:
>You can get some of the programs of the PHYLIP package to do this, but as for
>the best way of doing it, I don't know. I would like to hear other people's
>opinions on this.
The best method I've found for ancestral sequence reconstruction is PAML.
You can download it from http://mw511.biol.berkeley.edu/ziheng/paml.html (it's