/usr/local/phylogeny/phyml/phyml-20100824-sm10/src/phyml -i input_files/20130703_152516/input.phy -d aa -b 0 --mechanistic_opt 01000 -o l --mechanistic_params "0.0 -3.5 0.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" -m "custom=/usr/local/phylogeny/phyml/dat/JTT_codon" -f e -c 1 --rate_var_over_sites --output_tree_trace


. Sum=1.000015
. Scaling frequencies...

. The scale_param_b for rate variation over sites has been specified; unreasonable values tend to be estimated for scale and w_0.





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

                . Sequence filename:				 input.phy
                . Data type:					 aa
                . Alphabet size:				 64
                . Sequence format:				 interleaved
                . Number of data sets:				 1
                . Nb of bootstrapped data sets:			 0
                . Model name:					 /usr/local/phylogeny/phyml/dat/JTT_codon
                . Proportion of invariable sites:		 0.000000
                . Number of substitution categs:		 1
                . Amino acid equilibrium frequencies:		 empirical
                . Optimise tree topology:			 no
                . Evaluted tree:				 file "BioNJ"
                . Optimise branch lengths:			 yes
                . Optimise substitution model parameters:	 yes
                . Run ID:					 none
                . Random seed:					 1372832716
                . Subtree patterns aliasing:			 no
                . Version:					 20100824-SM10

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. 1049 sites without polymorphism (94.33%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 2 Mo of memory space.

. (    0 sec) [     -3748.3003] [Branch lengths     ]
. (    0 sec) [     -3748.2958] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.513346 * (1-delta(a,b))] 

. (    1 sec) [     -3748.0032] [Branch lengths     ]
. (    1 sec) [     -3748.0027] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.509833 * (1-delta(a,b))] 

. (    1 sec) [     -3747.8333] [Branch lengths     ]
. (    1 sec) [     -3747.8328] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] 

. (    1 sec) [     -3747.8107] [Branch lengths     ]
. (    1 sec) [     -3747.8107] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] 

. (    2 sec) [     -3747.8106] [Branch lengths     ]
. (    2 sec) [     -3747.8106] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] 

. (    2 sec) [     -3747.8106] [Selective constraints on amino acids ][0.000000 * aa_fitness(a,b) + -3.515531 * (1-delta(a,b))] 

. Log likelihood of the current tree: -3747.810611.

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

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

. Time used 0h0m2s

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