full semphy, with gamma and alpha optimiziation
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# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference  #
# for information, please send email to semphy@cs.huji.ac.il    #
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 ============== final tree and likelihoods ================== 
likelihood after semphy: -1035.81
Best trees under semphy (gam)
(((Rat:0.338849,(Cow:0.265162,Horse:0.815433):0.114742):0.002137,Human:0.068640):0.018396,Baboon:0.033009,Langur:0.084048);
# Best alpha (for fixed branch lengths)
1.38228
# The likelihood of the tree
-1035.81
# Best alpha (for fixed branch lengths)
1.38228
# The likelihood of the tree
-1035.81
# The log likelihood of the tree is:
-1035.81
-1035.81
# The tree
(((Rat:0.338849,(Cow:0.265162,Horse:0.815433):0.114742):0.00213733,Human:0.0686395):0.0183963,Baboon:0.0330087,Langur:0.0840479);