Hi,
I'm not exactly sure what tool to use, but I want to make a phylo tree using my own PSSM I generated off some structural constraints. Anyway, clustal says it has the option to use user defined matrices rather than the hard-coded ones. It says this needs to be in blast format. I was wondering if anyone could tell me the easiest way to get my pssm into "blast" format. I have tried downloading the ASN.1 files and they are pretty convuluted. Is there any documentation explaining on how these matrices should go?
I have tried to generate some psiblast output using
psiblast -db somedatabse -in_msa input.fasta -out_ascii_pssm pssm.txt
However, when I try and put this pssm back into clustal it says "too many entries"
I'm not dead set on using clustal, I just want to use my matrix. Does anyone have any suggestions?