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83 lines
3.2 KiB
Plaintext
83 lines
3.2 KiB
Plaintext
SEMPHY with Constraints from given tree
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lys_test0.ctree
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(Langur,Human,Horse,Cow,Baboon,Rat);
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Running "../semphy -H -s lys6.seq -t lys6.tree --jtt -c lys_test0.ctree -v5 -S"
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START OF LOG FILE
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Using uniform rates
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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" "-H" "-s" "lys6.seq" "-t" "lys6.tree" "--jtt" "-c" "lys_test0.ctree" "-v5" "-S"
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semphy iteration: 0
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starting semhy step by bbl...starting likelihood = -1043.99
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ENTERTING COMPUTE DISTANCES()
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likelihood after semphy step is: -1043.99
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sep best trees under semphy (gam)
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(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106429):0.009939,Human:0.064584):0.020854,Baboon:0.033403,Langur:0.081619);
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============== final tree and likelihoods ==================
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============== final tree and likelihoods ==================
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likelihood after semphy: -1043.99
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likelihood after semphy: -1043.99
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Best trees under semphy (gam)
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Best trees under semphy (gam)
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(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
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(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
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# The log likelihood of the tree is:
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-1043.99
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# The log likelihood of the tree is:
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-1043.99
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# The tree
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(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
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# The tree
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(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
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END OF LOG FILE
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lys_test1-2.ctree
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(Langur,Horse,(Human:0.017860,Cow:0.279822):0.072072,Baboon,Rat);
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Running "../semphy -H -s lys6.seq -t lys6.tree --jtt -c lys_test1-2.ctree -v5 -S"
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START OF LOG FILE
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Using uniform rates
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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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Input tree does not fit constraints!
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(Cow,Human)
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Please enter a starting tree that fits the constraints
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Please enter a starting tree that fits the constraints
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semphy: errorMsg.cpp:39: static void errorMsg::reportError(const std::string&, int): Assertion `0' failed.
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Abort
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lys_test1.ctree
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((Human,Cow),Langur,(Rat:0.1,Baboon:0.2),Horse);
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Running "../semphy -H -s lys6.seq -t lys6.tree --jtt -c lys_test1.ctree -v5 -S"
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START OF LOG FILE
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Using uniform rates
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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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Input tree does not fit constraints!
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(Baboon,Horse,Langur,Rat)
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(Baboon,Rat)
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Please enter a starting tree that fits the constraints
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Please enter a starting tree that fits the constraints
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semphy: errorMsg.cpp:39: static void errorMsg::reportError(const std::string&, int): Assertion `0' failed.
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Abort
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