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

                . Sequence filename : 				 data17.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...

. 394 patterns found. (out of a total of 500 sites) 

. 90 sites without polymorphism (18.00%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 8Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-7947.170164
. (    1 sec) [     -7944.4534] [GTR parameters     ]
. (    1 sec) [     -7943.8676] [Alpha              ][  0.913664]
. (    1 sec) [     -7943.8676] [Topology           ]
. (    2 sec) [     -7907.6242] [Topology           ]
. (    3 sec) [     -7899.5631] [Topology           ]
. (    4 sec) [     -7895.5710] [Topology           ]
. (    5 sec) [     -7894.5882] [Topology           ]
. (    6 sec) [     -7894.2081] [Topology           ]
. (    6 sec) [     -7894.0524] [Topology           ]
. (    7 sec) [     -7893.9831] [Topology           ]
. (    8 sec) [     -7893.9520] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   13 sec) [     -7893.8894] [Topology           ]
. Before opt ts/t=1.000000 LK=-7893.889429
. (   13 sec) [     -7893.8379] [GTR parameters     ]
. (   14 sec) [     -7893.5614] [Alpha              ][  0.969457]
. (   14 sec) [     -7893.5614] [Topology           ]
. (   14 sec) [     -7893.5239] [Topology           ]
. (   15 sec) [     -7893.5111] [Topology           ]
. (   16 sec) [     -7893.5055] [Topology           ]
. (   16 sec) [     -7893.5029] [Topology           ]
. (   17 sec) [     -7893.5016] [Topology           ]
. (   18 sec) [     -7893.5010] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7893.501048
. (   24 sec) [     -7893.5008] [GTR parameters     ]
. (   24 sec) [     -7893.4986] [Alpha              ][  0.974705]
. (   24 sec) [     -7893.4986] [Topology           ]
. (   25 sec) [     -7893.4980] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7893.498049
. (   34 sec) [     -7893.4980] [GTR parameters     ]
. (   35 sec) [     -7893.4980] [Alpha              ][  0.974705]
. (   35 sec) [     -7893.4980] [Topology           ]
. (   36 sec) [     -7893.4978] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -7893.497825.

. Printing the most likely tree in file 'data17.phy_phyml_tree.txt'...


. Time used 0h0m53s

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