..........................                                      
 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]
. (    4 sec) [     -5524.7398] [  795] [depth=    1]
. (    6 sec) [     -5524.1501] [  795] [depth=    1]
. (    7 sec) [     -5523.9136] [  795] [depth=    1]
. (    7 sec) [     -5523.7500] [  794] [depth=    1]
. (    8 sec) [     -5520.9466] [  795] [depth=    1]
. (   10 sec) [     -5520.8772] [  795] [depth=    1]
. (   11 sec) [     -5520.7248] [  795] [depth=    1]
. (   12 sec) [     -5520.6627] [  795] [depth=    1]
. (   14 sec) [     -5520.0020] [  795] [depth=    1]
. (   15 sec) [     -5519.5821] [  795] [depth=    1]
. (   15 sec) [     -5519.5135] [  795] [depth=    2]
. (   16 sec) [     -5519.4361] [  795] [depth=    1]
. (   17 sec) [     -5519.1592] [  795] [depth=    1]
. (   17 sec) [     -5518.8061] [  795] [depth=    1]
. (   18 sec) [     -5518.7681] [  795] [depth=    2]
. (   18 sec) [     -5507.0259] [Branch lengths     ]
. (   19 sec) [     -5507.0249] [Alpha              ][  1.014277]
. (   24 sec) [     -5506.8604] [  795] [depth=    1]
. (   38 sec) [     -5506.0787] [Branch lengths     ]
. (   39 sec) [     -5506.0784] [Alpha              ][  1.016933]
. (   39 sec) [     -5506.0784] [Topology           ]
. (   41 sec) [     -5506.0527] [Topology           ]
. (   44 sec) [     -5506.0456] [Topology           ]
. (   46 sec) [     -5506.0428] [Topology           ]
. (   48 sec) [     -5506.0417] [Topology           ]
. (   51 sec) [     -5506.0412] [Topology           ]
. (   51 sec) [     -5506.0412] [Alpha              ][  1.016933]
. (   51 sec) [     -5506.0412] [Topology           ]
. (   54 sec) [     -5506.0410] [Topology           ]
. (   54 sec) [     -5506.0410] [Alpha              ][  1.016933]

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5506.041009.

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


. Time used 0h1m10s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
67.68user 0.00system 1:11.58elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps