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25 lines
1010 B
Plaintext
25 lines
1010 B
Plaintext
full semphy, with gamma and alpha optimiziation
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#################################################################
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# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference #
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# for information, please send email to semphy@cs.huji.ac.il #
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#################################################################
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argv = "../semphy" "-s" "lys6.seq" "-t" "lys6.tree" "--jtt" "-A0.5" "-O" "-S"
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============== final tree and likelihoods ==================
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likelihood after semphy: -1035.81
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Best trees under semphy (gam)
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(((Rat:0.338849,(Cow:0.265162,Horse:0.815433):0.114742):0.002137,Human:0.068640):0.018396,Baboon:0.033009,Langur:0.084048);
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# Best alpha (for fixed branch lengths)
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1.38228
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# The likelihood of the tree
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-1035.81
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# Best alpha (for fixed branch lengths)
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1.38228
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# The likelihood of the tree
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-1035.81
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# The log likelihood of the tree is:
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-1035.81
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-1035.81
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# The tree
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(((Rat:0.338849,(Cow:0.265162,Horse:0.815433):0.114742):0.00213733,Human:0.0686395):0.0183963,Baboon:0.0330087,Langur:0.0840479);
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