/usr/local/phylogeny/phyml/bin/phyml -i input_files/20110208_105916.phy -d codon -b 0 -f e --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT EI-11" -c 4r -a e --mechanistic_opt 01000 -o lr -a e --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:				 20110208_105916.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:		 4   for rate
                . Gamma distribution parameter:			 estimated
                . 'Middle' of each class:			 mean
                . Codon 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:					 1297130357
                . 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 21 Mo of memory space.

. (    4 sec) [     -6709.4108] [Branch lengths     ]
. (    6 sec) [     -6704.6719] [Alpha              ][  0.507335] [0.034755 0.250000][0.256677 0.250000][0.825533 0.250000][2.883035 0.250000]
. (    7 sec) [     -6654.1532] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.181049] 

. (   11 sec) [     -6653.6912] [Branch lengths     ]
. (   13 sec) [     -6653.6815] [Alpha              ][  0.494351] [0.032346 0.250000][0.248212 0.250000][0.816114 0.250000][2.903328 0.250000]
. (   14 sec) [     -6653.6796] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.189090] 

. (   18 sec) [     -6653.6702] [Branch lengths     ]
. (   20 sec) [     -6653.6701] [Alpha              ][  0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000]
. (   21 sec) [     -6653.6701] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] 

. (   25 sec) [     -6653.6698] [Branch lengths     ]
. (   27 sec) [     -6653.6698] [Alpha              ][  0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000]
. (   28 sec) [     -6653.6698] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] 

. (   30 sec) [     -6653.6698] [Alpha              ][  0.493554] [0.032199 0.250000][0.247687 0.250000][0.815521 0.250000][2.904593 0.250000]
. (   32 sec) [     -6653.6698] [Selective constraints on amino acids ][1.000000 * aa_fitness[i,j] + -1.190369] 

. Log likelihood of the current tree: -6653.669815.

. Printing the most likely tree in file '20110208_105916.phy_phyml_tree.txt'...

. Time used 0h0m32s

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