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

                . Sequence filename : 				 nucleic_M2770_86x1628_2006.phy
                . Data type :             			 dna
                . Sequence format : 				 interleaved
                . Number of data sets : 			 1
                . Nb of bootstrapped data sets : 		 0
                . Model name : 					 GTR
                . Proportion of invariable sites :		 0.000000
                . Number of subst. rate categs : 		 4
                . Gamma distribution parameter : 		 estimated
                . 'Middle' of each rate class  : 		 mean
                . Nucleotide equilibrium frequencies : 		 empirical
                . Optimise tree topology : 			 yes
                . Tree topology search : 			 NNIs
                . Starting tree : 				 BioNJ
                . Add random input tree : 			 no
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 571 patterns found. (out of a total of 1628 sites) 

. 1267 sites without polymorphism (77.83%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 26Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. (    3 sec) [     -5881.3955] [GTR parameters     ]
. (    3 sec) [     -5881.3763] [Alpha              ][  1.039147]
. (    3 sec) [     -5881.3763] [Topology           ]
. (    5 sec) [     -5840.5187] [Topology           ]
. (    8 sec) [     -5831.9227] [Topology           ]
. (   10 sec) [     -5825.2712] [Topology           ]
. (   13 sec) [     -5824.3381] [Topology           ]
. (   15 sec) [     -5824.2227] [Topology           ]
. (   17 sec) [     -5824.2058] [Topology           ]
. (   20 sec) [     -5824.2023] [Topology           ]
. (   22 sec) [     -5824.2014] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   38 sec) [     -5824.0941] [GTR parameters     ]
. (   38 sec) [     -5823.9485] [Alpha              ][  1.159997]
. (   38 sec) [     -5823.9485] [Topology           ]
. (   40 sec) [     -5823.9480] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   55 sec) [     -5823.9479] [GTR parameters     ]
. (   55 sec) [     -5823.9479] [Alpha              ][  1.159997]
. (   56 sec) [     -5823.9479] [Topology           ]
. (   58 sec) [     -5823.9478] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5823.947839.

. Printing the most likely tree in file 'nucleic_M2770_86x1628_2006.phy_phyml_tree.txt'...


. Time used 0h1m27s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
86.76user 0.00system 1:27.05elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps