Full SEMPHY, gamma=0.742
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# 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" "--jtt" "-A0.742" "-S"
 ============== final tree and likelihoods ================== 
likelihood after semphy: -1037.97
Best trees under semphy (gam)
(((Rat:0.355144,(Cow:0.273323,Horse:0.931360):0.116299):0.001292,Human:0.069344):0.016700,Baboon:0.032468,Langur:0.083116);
# The log likelihood of the tree is:
-1037.97
-1037.97
# The tree
(((Rat:0.355144,(Cow:0.273323,Horse:0.93136):0.116299):0.00129223,Human:0.0693439):0.0167004,Baboon:0.0324676,Langur:0.0831164);