Per Kallblad wrote:
>> I would be greatful if someone could point me towards a program that
> calculates the percent amino acid identity between all sequence pairs in a
> multiple sequence alignment?
The program MACBOXSHADE (v2.1)will provide such output, if you are using
the mac platform. There is a windows compiled version of BOXSHADE (a
command-line driven program) at the same site which also has the
matrix-of-identities/similarities option (I think that is version 3.2,
but the numbering of the two programs is quite independent).
michael.baron at bbsrc.ac.uk