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

                . Sequence filename : 				 proteic_M2304_31x429_2005.phy
                . Data type :             			 aa
                . Sequence format : 				 interleaved
                . Number of data sets : 			 1
                . Nb of bootstrapped data sets : 		 0
                . Model name : 					 WAG
                . Proportion of invariable sites :		 0.000000
                . Number of subst. rate categs : 		 4
                . Gamma distribution parameter : 		 estimated
                . 'Middle' of each rate class  : 		 mean
                . Amino acid equilibrium frequencies : 		 model
                . Optimise tree topology : 			 yes
                . Tree topology search : 			 SPRs
                . Starting tree : 				 BioNJ
                . Add random input tree : 			 no
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. 35 sites are made from completely undetermined states ('X', '-', '?')...

. Compressing sequences...

. 305 patterns found. (out of a total of 429 sites) 

. 122 sites without polymorphism (28.44%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 23Mo of memory space.

. Maximizing likelihood (using SPR moves)...

. (    0 sec) [     -5525.2178] [Alpha              ][  1.019870]
. (    2 sec) [     -5523.7723] [  799] [depth=    1]
. (    3 sec) [     -5518.4228] [  794] [depth=    1]
. (    5 sec) [     -5517.8227] [  795] [depth=    1]
. (    6 sec) [     -5517.6086] [  794] [depth=    1]
. (    7 sec) [     -5517.0146] [  794] [depth=    1]
. (    8 sec) [     -5516.7583] [  794] [depth=    1]
. (    8 sec) [     -5514.9515] [  794] [depth=    1]
. (   17 sec) [     -5514.9117] [  794] [depth=    1]
. (   20 sec) [     -5514.7584] [  794] [depth=    1]
. (   52 sec) [     -5514.1524] [  794] [depth=    1]
. (   53 sec) [     -5513.7654] [  794] [depth=    1]
. (   55 sec) [     -5513.6489] [  794] [depth=    2]
. (   57 sec) [     -5513.5736] [  794] [depth=    1]
. (   62 sec) [     -5513.3028] [  794] [depth=    1]
. (   63 sec) [     -5512.9288] [  794] [depth=    1]
. (   65 sec) [     -5512.9169] [  794] [depth=    2]
. (   65 sec) [     -5507.5579] [Branch lengths     ]
. (   66 sec) [     -5507.5577] [Alpha              ][  1.017255]
. (   70 sec) [     -5506.6049] [  795] [depth=    1]
. (  151 sec) [     -5506.0668] [Branch lengths     ]
. (  151 sec) [     -5506.0668] [Alpha              ][  1.018272]
. (  241 sec) [     -5506.0415] [Branch lengths     ]
. (  241 sec) [     -5506.0415] [Topology           ]
. (  244 sec) [     -5506.0411] [Topology           ]
. (  244 sec) [     -5506.0410] [Alpha              ][  1.016884]

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5506.041042.

. Printing the most likely tree in file 'proteic_M2304_31x429_2005.phy_phyml_tree.txt'...


. Time used 0h4m23s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
249.54user 0.00system 4:23.59elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps