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

                . Sequence filename : 				 data75.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...

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

. 45 sites without polymorphism (9.00%).

. 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=-11926.345408
. (    1 sec) [    -11920.9976] [GTR parameters     ]
. (    1 sec) [    -11920.2947] [Alpha              ][  0.921942]
. (    1 sec) [    -11920.2947] [Topology           ]
. (    2 sec) [    -11833.5228] [Topology           ]
. (    3 sec) [    -11820.3464] [Topology           ]
. (    3 sec) [    -11817.2226] [Topology           ]
. (    4 sec) [    -11815.9974] [Topology           ]
. (    5 sec) [    -11815.4346] [Topology           ]
. (    6 sec) [    -11815.1196] [Topology           ]
. (    7 sec) [    -11814.7511] [Topology           ]
. (    8 sec) [    -11814.6249] [Topology           ]
. (    9 sec) [    -11814.5406] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11814.427333
. (   17 sec) [    -11814.3787] [GTR parameters     ]
. (   17 sec) [    -11814.1596] [Alpha              ][  0.962056]
. (   17 sec) [    -11814.1596] [Topology           ]
. (   18 sec) [    -11814.1196] [Topology           ]
. (   18 sec) [    -11814.1055] [Topology           ]
. (   19 sec) [    -11814.0985] [Topology           ]
. (   20 sec) [    -11814.0949] [Topology           ]
. (   21 sec) [    -11814.0930] [Topology           ]
. (   22 sec) [    -11814.0919] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11814.091919
. (   29 sec) [    -11814.0918] [GTR parameters     ]
. (   29 sec) [    -11814.0911] [Alpha              ][  0.964293]
. (   29 sec) [    -11814.0911] [Topology           ]
. (   30 sec) [    -11814.0905] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11814.090495
. (   37 sec) [    -11814.0905] [GTR parameters     ]
. (   37 sec) [    -11814.0905] [Alpha              ][  0.964293]
. (   37 sec) [    -11814.0905] [Topology           ]
. (   38 sec) [    -11814.0902] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -11814.090161.

. Printing the most likely tree in file 'data75.phy_phyml_tree.txt'...


. Time used 0h0m52s

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