#Nexus
Begin data;
dimension ntax=13 nchar=12;
format symbols="0123456789" missing=?;
matrix
H002	112221111122
H010	222212222222
H007	222221111121
H008	112221112112
H014	112221112222
H013	222221122222
H001	112222222222
H003	221122222222
H005	221222222221
H012	222221111112
H009	112221111121
H006	112221111112
H011	222221111122
;
end;
begin assumptions;
ancstates *anc vector = 222222222222;
end;
begin paup;
set nowarnreset autoclose maxtrees = 2000 increase= no [- Auto AutoInc = 100] monitor = no taxlabels = full
root=lundberg warnroot=no opt=deltran [- acctran] ancstates=anc;
hsearch;
savetrees from=1 to=1000 file= test.tree root=yes format=altnexus;
cleartrees nowarn=yes;
gettrees rooted=yes file=test.tree;
log file = test.res.log replace= yes [- no];
describetrees all /plot=cladogram [- phylogram] brlens=yes 
rootmethod=lundberg apolist=yes;
log stop;
end;
quit;
[WARNING, this file is designed for bi-allelic data. If it is not the case, you may have to modify this input file, for example by specifying the ordered option in the typeset command in the assumption block]
