[Infile for Example 4: Intraspecific Sampling]

begin coal;

  ntax = 4 | nstaxa 4;
  taxa names = A B C D;
  ngtaxa 2 2 1 1;
  gene tree file = ex4_genetrees.tre;
  species tree file = ex4_speciestree.tre;
  intra = yes;
  ngtrees = 1;
  nstrees = 1;
  blstyle = none; [branch lengths read from file]
  logfile = ex4_logfile.log;
  outfile = ex4_output.out / prob;

end;

