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

                . Sequence filename : 				 data64.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

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. Compressing sequences...

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

. 61 sites without polymorphism (12.20%).

. Computing pairwise distances...

. Building BioNJ tree...

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

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-9633.594476
. (    1 sec) [     -9633.1925] [GTR parameters     ]
. (    1 sec) [     -9631.5367] [Alpha              ][  1.149448]
. (    1 sec) [     -9631.5367] [Topology           ]
. (    2 sec) [     -9584.1716] [Topology           ]
. (    3 sec) [     -9574.1907] [Topology           ]
. (    4 sec) [     -9571.8821] [Topology           ]
. (    6 sec) [     -9571.1460] [Topology           ]
. (    7 sec) [     -9570.8312] [Topology           ]
. (    8 sec) [     -9570.6829] [Topology           ]
. (    9 sec) [     -9570.6084] [Topology           ]
. (   10 sec) [     -9570.5694] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9570.569422
. (   18 sec) [     -9570.5359] [GTR parameters     ]
. (   18 sec) [     -9570.5256] [Alpha              ][  1.162201]
. (   18 sec) [     -9570.5256] [Topology           ]
. (   19 sec) [     -9570.5023] [Topology           ]
. (   20 sec) [     -9570.4906] [Topology           ]
. (   22 sec) [     -9570.4847] [Topology           ]
. (   23 sec) [     -9570.4816] [Topology           ]
. (   24 sec) [     -9570.4800] [Topology           ]
. (   25 sec) [     -9570.4792] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9570.479199
. (   34 sec) [     -9570.4792] [GTR parameters     ]
. (   34 sec) [     -9570.4787] [Alpha              ][  1.164851]
. (   34 sec) [     -9570.4787] [Topology           ]
. (   35 sec) [     -9570.4782] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9570.478181
. (   44 sec) [     -9570.4782] [GTR parameters     ]
. (   44 sec) [     -9570.4782] [Alpha              ][  1.164851]
. (   44 sec) [     -9570.4782] [Topology           ]
. (   45 sec) [     -9570.4779] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -9570.477914.

. Printing the most likely tree in file 'data64.phy_phyml_tree.txt'...


. Time used 0h1m5s

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