Good question. I think you can do this, but I have a few questions about exactly what you want to do:
(1) Do you think the main difference between transmembrane spans is
just which amino acids are common? In that case, you could use two
instances of the (for example) the LG matrix with different amino
bali-phy amino-acids.fasta -S mixture[models=[lg08+f,lg08+f],rates=[1,1]]
I don't know if its clear from the command line above, but each +f model gets its own set of frequencies.
This would really divide the sequence into two frequency classes,
which I presume would correspond to the transmembrane regions, but
I am not sure.
(2) Alternatively, you could divide the sequence into a sequence
of partitions a priori, where every other partition is a
transmembrane partition. This prohibits sequences in one
partition from aligning to sequences in another partition. Do you
want to do that instead?
(3) To load your own exchangeability matrix, you can do
empirical[file]+f. You need a file that describe the transition
matrix, though. It should look like this:
Does that make sense?
I would like to use two substitution matrices on two different regions of a protein I am evaluating - one for the transmembrane spans, and one for the solvent-exposes areas of the protein. This paper describes the methodology. I'm not sure how to use two separate matrices in Bali-Phy, and I don't know how to use custom matrices such as the one described in the paper. Any help you could give would be appreciated!James
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