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

                . Sequence filename : 				 proteic_M1990_35x153_2004.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



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

. Compressing sequences...

. 104 patterns found. (out of a total of 153 sites) 

. 83 sites without polymorphism (54.25%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 9Mo of memory space.

. Maximizing likelihood (using SPR moves)...

. (    0 sec) [     -1475.6886] [Alpha              ][  0.500960]
. (    1 sec) [     -1475.5479] [  181] [depth=    1]
. (    1 sec) [     -1474.1794] [  180] [depth=    2]
. (    2 sec) [     -1473.3210] [  180] [depth=    2]
. (    2 sec) [     -1468.9409] [  183] [depth=    1]
. (    3 sec) [     -1466.3719] [  180] [depth=    1]
. (    3 sec) [     -1466.1893] [  180] [depth=    2]
. (    3 sec) [     -1465.7909] [  180] [depth=    2]
. (    5 sec) [     -1465.7130] [  180] [depth=    1]
. (    8 sec) [     -1464.2475] [  180] [depth=    1]
. (    8 sec) [     -1464.2100] [  180] [depth=    1]
. (    9 sec) [     -1463.9596] [  180] [depth=    1]
. (    9 sec) [     -1463.3145] [  180] [depth=    1]
. (   10 sec) [     -1458.0908] [Branch lengths     ]
. (   11 sec) [     -1457.8997] [Alpha              ][  0.446191]
. (   12 sec) [     -1457.8794] [  180] [depth=    2]
. (   14 sec) [     -1457.8499] [  180] [depth=    2]
. (   15 sec) [     -1457.3129] [  180] [depth=    1]
. (   16 sec) [     -1457.1661] [  180] [depth=    1]
. (   25 sec) [     -1454.5921] [Branch lengths     ]
. (   25 sec) [     -1454.5493] [Alpha              ][  0.423062]
. (   43 sec) [     -1454.4390] [Branch lengths     ]
. (   44 sec) [     -1454.4390] [Topology           ]
. (   46 sec) [     -1454.4340] [Topology           ]
. (   47 sec) [     -1454.4331] [Topology           ]
. (   48 sec) [     -1454.4313] [Alpha              ][  0.418363]
. (   48 sec) [     -1454.4313] [Topology           ]
. (   50 sec) [     -1454.4306] [Topology           ]
. (   50 sec) [     -1454.4306] [Alpha              ][  0.417590]

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -1454.430570.

. Printing the most likely tree in file 'proteic_M1990_35x153_2004.phy_phyml_tree.txt'...


. Time used 0h1m5s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
39.40user 0.00system 1:05.81elapsed 59%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps