likelihood computation only, with gamma and alpha optimiziation
#################################################################
# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference  #
# for information, please send email to semphy@cs.huji.ac.il    #
#################################################################

argv = "../semphy" "-s" "lys6.seq" "-t" "lys6.tree" "-L" "--jtt" "-A0.5" "-O"
# Best alpha (for fixed branch lengths)
1.48489
# The likelihood of the tree
-1037.11
# Best alpha (for fixed branch lengths)
1.48489
# The likelihood of the tree
-1037.11
# The log likelihood of the tree is:
-1037.11
-1037.11
# The tree
(((Langur:0.081000,Baboon:0.033000):0.021000,Human:0.064000):0.010000,Rat:0.288000,(Cow:0.240000,Horse:0.630000):0.106000);