msf sequence identity

michael.baron at michael.baron at
Mon Nov 23 04:21:38 EST 1998

Per Kallblad wrote:
> Hi,
> 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

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