I’m using MUSCLE to construct a multiple sequence alignment. Problem is, I have no idea what amino acid substitution matrix MUSCLE uses (I’m using the online version of MUSCLE, here: http://www.ebi.ac.uk/Tools/msa/muscle/). In short, I don’t see anyplace that I can change the parameters or select an amino acid matrix. I’ve searched the web and haven’t found much info on this.
My question therefore is: what aa substitution matrix does MUSCLE use?