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    • #16848

      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: 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?

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