You should be able to use MEGA for this,
Thorsten Burmester wrote in message <85d7ia$ro0$1 at mercury.hgmp.mrc.ac.uk>...
>James McInerney wrote:
>>>> One of the programs in the molphy package calculates amino acid distance
>> There is a reference ot it on Joe Felsenstein's webpage:
>>>>http://evolution.genetics.washington.edu/>>Thanks. I have MOLPHY. However, the program PROTST.EXE does not estimate
>distances but plain aa composition. I would like to estimate distances
>based on the aa compositions of the different proteins.
>>> I can send you a macintosh version of my program GCUA that will do this,
>> although it needs fasta-formatted protein-coding DNA sequences as input
>> (it converts to proteins and then calculates a distance matrix).
>>Unfortunately, I don't have a Mac. UNIX or DOS are always welcome.