#NEXUS

BEGIN NETWORKS;
Network net = ((A:3,ANC#H1:2.25):2,((B:.75)ANC#H1:0,C:.75):4.25);
END;

Begin DATA;
   dimensions ntax=3 nchar=6;
        format datatype=dna symbols="ACTG" missing=? gap=-;
        matrix
1   AGGTGG
2   AACCTT
3   ACCTGT
;
END;

BEGIN PHYLONET;
HmmCommand net -allelemap <A:1; B:2; C:3>  -treefile "treefile" -outputdirectory "foo" -threads 4 -iterations 300;
END;