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

                . Sequence filename : 				 nucleic_M2572_191x990_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...

. 285 patterns found. (out of a total of 990 sites) 

. 729 sites without polymorphism (73.64%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 29Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. (    4 sec) [     -3531.0072] [GTR parameters     ]
. (    4 sec) [     -3527.8965] [Alpha              ][  0.577459]
. (    4 sec) [     -3527.8965] [Topology           ]
. (    7 sec) [     -3510.2444] [Topology           ]
. (    9 sec) [     -3508.5708] [Topology           ]
. (   11 sec) [     -3508.2867] [Topology           ]
. (   13 sec) [     -3508.2234] [Topology           ]
. (   16 sec) [     -3508.2072] [Topology           ]
. (   18 sec) [     -3508.2027] [Topology           ]
. (   20 sec) [     -3508.2013] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   31 sec) [     -3508.0718] [GTR parameters     ]
. (   31 sec) [     -3508.0712] [Alpha              ][  0.573895]
. (   31 sec) [     -3508.0712] [Topology           ]
. (   33 sec) [     -3508.0703] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   43 sec) [     -3508.0703] [GTR parameters     ]
. (   43 sec) [     -3508.0703] [Alpha              ][  0.573191]
. (   44 sec) [     -3508.0703] [Topology           ]
. (   46 sec) [     -3508.0702] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -3508.070176.

. Printing the most likely tree in file 'nucleic_M2572_191x990_2006.phy_phyml_tree.txt'...


. Time used 0h1m5s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
65.16user 0.00system 1:06.41elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps