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" "-n" "--jtt" "-A0.5" "-O"
# Best alpha after branch length optimiziation
1.38169
# The likelihood of the tree
-1035.8
# Best alpha after branch length optimiziation
1.38169
# The likelihood of the tree
-1035.8
# The log likelihood of the tree is:
-1035.8
-1035.8
# The tree
(((Langur:0.083987,Baboon:0.032957):0.018445,Human:0.068531):0.001551,Rat:0.338579,(Cow:0.264533,Horse:0.812056):0.115036);