#NEXUS
BEGIN TAXA;
    dimensions ntax=4;
    taxlabels A B C D;  
END;
BEGIN CHARACTERS;
    dimensions nchar=6;
    format
        datatype=protein missing=? gap=- ;
    matrix
	[change: in taxon 'A', second char is changes from 'M' to 'Q']
        A   -QQG-?
        B   ---G--
        C   -MGG--
        D   -MGTGQ
        ;
END;
BEGIN TREES;
	[change: ... ]
    tree 'basic bush' = ((A:1,B:1):1,(C:1,D:1):1);
END;