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

                . Sequence filename : 				 data5.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...

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

. 48 sites without polymorphism (9.60%).

. 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=-11105.297722
. (    1 sec) [    -11104.8654] [GTR parameters     ]
. (    1 sec) [    -11104.6291] [Alpha              ][  0.951977]
. (    1 sec) [    -11104.6291] [Topology           ]
. (    2 sec) [    -11049.9254] [Topology           ]
. (    3 sec) [    -11041.5184] [Topology           ]
. (    4 sec) [    -11039.1384] [Topology           ]
. (    5 sec) [    -11038.1125] [Topology           ]
. (    6 sec) [    -11037.6114] [Topology           ]
. (    8 sec) [    -11037.3609] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11037.360898
. (   18 sec) [    -11037.3427] [GTR parameters     ]
. (   18 sec) [    -11036.8934] [Alpha              ][  1.016031]
. (   18 sec) [    -11036.8934] [Topology           ]
. (   20 sec) [    -11036.7055] [Topology           ]
. (   22 sec) [    -11036.6169] [Topology           ]
. (   23 sec) [    -11036.5714] [Topology           ]
. (   25 sec) [    -11036.5476] [Topology           ]
. (   26 sec) [    -11036.5352] [Topology           ]
. (   27 sec) [    -11036.5287] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11036.528697
. (   36 sec) [    -11036.5280] [GTR parameters     ]
. (   36 sec) [    -11036.5218] [Alpha              ][  1.023867]
. (   36 sec) [    -11036.5218] [Topology           ]
. (   38 sec) [    -11036.5176] [Topology           ]
. (   39 sec) [    -11036.5155] [Topology           ]
. (   40 sec) [    -11036.5143] [Topology           ]
. (   41 sec) [    -11036.5137] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-11036.513745
. (   52 sec) [    -11036.5137] [GTR parameters     ]
. (   52 sec) [    -11036.5136] [Alpha              ][  1.024891]
. (   52 sec) [    -11036.5136] [Topology           ]
. (   54 sec) [    -11036.5133] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -11036.513298.

. Printing the most likely tree in file 'data5.phy_phyml_tree.txt'...


. Time used 0h1m16s

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