/usr/local/phylogeny/phyml/bin/phyml -i input_files/20110225_042637/input.phy -d codon -b 0 -f e --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11" -c 1 --mechanistic_opt 01000 -o lr --mechanistic_params "1.0 0.0 0.0 0.0 1.0 1.0 1.0 1.0 1.0 0.25 0.25 0.25"


. Sum=1.000003
. Scaling frequencies...





                                 ..........................                                      
 ooooooooooooooooooooooooooooo        CURRENT SETTINGS        ooooooooooooooooooooooooooooooooooo
                                 ..........................                                      

                . Sequence filename:				 input.phy
                . Data type:					 codon
                . Alphabet size:				 64
                . Sequence format:				 interleaved
                . Number of data sets:				 1
                . Nb of bootstrapped data sets:			 0
                . Model name:					 /usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11
                . Proportion of invariable sites:		 0.000000
                . Number of substitution categs:		 1
                . Codon equilibrium frequencies : 		 empirical
                . Optimise tree topology:			 no
                . Evaluted tree:				 file "BioNJ"
                . Optimise branch lengths:			 yes
                . Optimise substitution model parameters:	 no
                . Run ID:					 none
                . Random seed:					 1298575597
                . Subtree patterns aliasing:			 no
                . Version:					 20100824-SM04.101103

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. 318 patterns found (out of a total of 1112 sites). 

. 0 sites without polymorphism (0.00%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 7 Mo of memory space.

. (    1 sec) [     -6740.0267] [Branch lengths     ]
. (    2 sec) [     -6690.5991] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.140274] 

. (    3 sec) [     -6690.5357] [Branch lengths     ]
. (    3 sec) [     -6690.5357] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.141468] 

. (    4 sec) [     -6690.5351] [Branch lengths     ]
. (    5 sec) [     -6690.5351] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.141468] 

. (    5 sec) [     -6690.5351] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.141468] 

. Log likelihood of the current tree: -6690.535065.

. Printing the most likely tree in file 'input.phy_phyml_tree.txt'...

. Time used 0h0m5s

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