SEMPHY with Constraints from given tree
lys_test0.ctree
(Langur,Human,Horse,Cow,Baboon,Rat);
Running "../semphy -H -s lys6.seq  -t lys6.tree --jtt -c lys_test0.ctree -v5 -S"

START OF LOG FILE
Using uniform rates
#################################################################
# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference  #
# for information, please send email to semphy@cs.huji.ac.il    #
#################################################################

argv = "../semphy" "-H" "-s" "lys6.seq" "-t" "lys6.tree" "--jtt" "-c" "lys_test0.ctree" "-v5" "-S"
semphy iteration: 0
starting semhy step by bbl...starting likelihood = -1043.99
ENTERTING COMPUTE DISTANCES() 
likelihood after semphy step is: -1043.99
sep best trees under semphy (gam)
(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106429):0.009939,Human:0.064584):0.020854,Baboon:0.033403,Langur:0.081619);
 ============== final tree and likelihoods ================== 
 ============== final tree and likelihoods ================== 
likelihood after semphy: -1043.99
likelihood after semphy: -1043.99
Best trees under semphy (gam)
Best trees under semphy (gam)
(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
# The log likelihood of the tree is:
-1043.99
# The log likelihood of the tree is:
-1043.99
# The tree
(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
# The tree
(((Rat:0.289108,(Cow:0.241165,Horse:0.633556):0.106536):0.0099173,Human:0.0645835):0.0208539,Baboon:0.0334025,Langur:0.0816193);
END OF LOG FILE


lys_test1-2.ctree
(Langur,Horse,(Human:0.017860,Cow:0.279822):0.072072,Baboon,Rat);
Running "../semphy -H -s lys6.seq  -t lys6.tree --jtt -c lys_test1-2.ctree -v5 -S"

START OF LOG FILE
Using uniform rates
#################################################################
# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference  #
# for information, please send email to semphy@cs.huji.ac.il    #
#################################################################

Input tree does not fit constraints!
(Cow,Human)

Please enter a starting tree that fits the constraints

Please enter a starting tree that fits the constraints
semphy: errorMsg.cpp:39: static void errorMsg::reportError(const std::string&, int): Assertion `0' failed.
Abort


lys_test1.ctree
((Human,Cow),Langur,(Rat:0.1,Baboon:0.2),Horse);

Running "../semphy -H -s lys6.seq  -t lys6.tree --jtt -c lys_test1.ctree -v5 -S"

START OF LOG FILE
Using uniform rates
#################################################################
# SEMPHY: A Structural EM Algorithm for Phylogenetic Inference  #
# for information, please send email to semphy@cs.huji.ac.il    #
#################################################################

Input tree does not fit constraints!
(Baboon,Horse,Langur,Rat)
(Baboon,Rat)

Please enter a starting tree that fits the constraints

Please enter a starting tree that fits the constraints
semphy: errorMsg.cpp:39: static void errorMsg::reportError(const std::string&, int): Assertion `0' failed.
Abort