/usr/local/phylogeny/phyml/bin/phyml-codon.sh JTT-ML91+-4-E-F input_files/20130704_123827/input.phy  --mechanistic_params "-9.0 -1.5 0.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0"
is translated to
/usr/local/phylogeny/phyml/src/phyml -i input_files/20130704_123827/input.phy -d codon -b 0 --mechanistic_opt 11020 -o l --mechanistic_params "-9.0 -1.5 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0" --mechanistic "/usr/local/phylogeny/phyml/dat/Wmatrix_with_EI-11_JTT JTT-ML91+mod-0" -f e -c 1 --rate_var_over_sites --output_tree_trace --mechanistic_params "-9.0 -1.5 0.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0 -9.0"


. Sum=1.000003
. 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:					 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 JTT-ML91+mod-0
                . 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:	 yes
                . Run ID:					 none
                . Random seed:					 1372909107
                . Subtree patterns aliasing:			 no
                . Version:					 20100824-SM10

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



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

. 832 sites without polymorphism (74.82%).

. Computing pairwise distances...

. Building BioNJ tree...

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

. (    0 sec) [     -6667.7596] [Branch lengths     ]
. (    0 sec) [     -6667.5046] [Selective constraints on amino acids ][0.993877 * aa_fitness(a,b) + -1.591102 * (1-delta(a,b))] 
. (    1 sec) [     -6642.7513] [GTR parameters     ][rr_val: 0.110174 2.316070 1.137439 0.728588 0.940053 1.188633]

. (    1 sec) [     -6642.6860] [Branch lengths     ]
. (    1 sec) [     -6636.6685] [Selective constraints on amino acids ][0.679947 * aa_fitness(a,b) + -1.591102 * (1-delta(a,b))] 
. (    2 sec) [     -6635.9130] [GTR parameters     ][rr_val: 0.068061 2.444146 1.137439 0.728588 0.940053 1.188633]

. (    2 sec) [     -6635.9119] [Branch lengths     ]
. (    2 sec) [     -6635.8430] [Selective constraints on amino acids ][0.648685 * aa_fitness(a,b) + -1.585650 * (1-delta(a,b))] 
. (    2 sec) [     -6635.8320] [GTR parameters     ][rr_val: 0.063756 2.460498 1.137439 0.728588 0.940053 1.188633]

. (    3 sec) [     -6635.8320] [Branch lengths     ]
. (    3 sec) [     -6635.8311] [Selective constraints on amino acids ][0.648685 * aa_fitness(a,b) + -1.580657 * (1-delta(a,b))] 
. (    3 sec) [     -6635.8310] [GTR parameters     ][rr_val: 0.063387 2.460498 1.137439 0.728588 0.940053 1.188633]

. (    4 sec) [     -6635.8303] [Selective constraints on amino acids ][0.650952 * aa_fitness(a,b) + -1.577442 * (1-delta(a,b))] 
. (    4 sec) [     -6635.8303] [GTR parameters     ][rr_val: 0.063387 2.460498 1.137439 0.728588 0.940053 1.188633]

. Log likelihood of the current tree: -6635.830291.

. 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 0h0m4s

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