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

                . Sequence filename : 				 nucleic_M2599_66x1137_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...

. 131 patterns found. (out of a total of 1137 sites) 

. 1062 sites without polymorphism (93.40%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 5Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. (    1 sec) [     -2167.7777] [GTR parameters     ]
. (    1 sec) [     -2167.7484] [Alpha              ][  0.762192]
. (    1 sec) [     -2167.7484] [Topology           ]
. (    1 sec) [     -2164.8151] [Topology           ]
. (    2 sec) [     -2164.1354] [Topology           ]
. (    2 sec) [     -2163.7186] [Topology           ]
. (    2 sec) [     -2163.5431] [Topology           ]
. (    2 sec) [     -2163.5011] [Topology           ]
. (    3 sec) [     -2163.4908] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (    4 sec) [     -2163.4906] [GTR parameters     ]
. (    4 sec) [     -2163.4906] [Alpha              ][  0.759129]
. (    4 sec) [     -2163.4906] [Topology           ]
. (    5 sec) [     -2163.4878] [Topology           ]
. (    5 sec) [     -2163.4872] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (    7 sec) [     -2163.4872] [GTR parameters     ]
. (    7 sec) [     -2163.4872] [Alpha              ][  0.759129]
. (    7 sec) [     -2163.4872] [Topology           ]
. (    7 sec) [     -2163.4870] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -2163.487012.

. Printing the most likely tree in file 'nucleic_M2599_66x1137_2006.phy_phyml_tree.txt'...


. Time used 0h0m10s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
9.65user 0.00system 0:09.88elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps