#NEXUS

BEGIN NETWORKS;
Network net = %s
END;

Begin DATA;
   dimensions ntax=%s nchar=%s;
        format datatype=dna symbols="ACTG" missing=? gap=-;
        matrix
%s
;
END;

BEGIN PHYLONET;

HmmCommand net -allelemap %s -treefile "treefile" -outputdirectory "foo" -numberofruns 1 %s;

END;
