[Biojava-l] BioJava Question - Evolutionary Rate Calculation

[JP]

Hi there at Biojava,

I have a number of orthologue protein (sequences) from different species - I
would like to calculate the distance (score) between each of these
(programatically) based on the sequence.

Can anyone suggest a way to do this (I'd rather use an existing bit of
software than having to reinvent the wheel) ?  Surely this software must
exist...(hopefully in biojava).

Many Thanks
Jean-Paul Ebejer, Malta