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

                . Sequence filename : 				 data59.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...

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

. 69 sites without polymorphism (13.80%).

. 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=-10186.540847
. (    0 sec) [    -10185.4470] [GTR parameters     ]
. (    1 sec) [    -10184.2698] [Alpha              ][  0.894321]
. (    1 sec) [    -10184.2698] [Topology           ]
. (    2 sec) [    -10117.0407] [Topology           ]
. (    4 sec) [    -10103.8503] [Topology           ]
. (    5 sec) [    -10100.4331] [Topology           ]
. (    6 sec) [    -10098.0463] [Topology           ]

. Moving backward

. (    7 sec) [    -10096.1225] [Topology           ]
. (    8 sec) [    -10095.2812] [Topology           ]

. Moving backward

. (    9 sec) [    -10094.3631] [Topology           ]
. (   11 sec) [    -10093.8820] [Topology           ]
. (   12 sec) [    -10093.6541] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-10093.529204
. (   22 sec) [    -10093.4996] [GTR parameters     ]
. (   22 sec) [    -10093.4945] [Alpha              ][  0.900666]
. (   22 sec) [    -10093.4945] [Topology           ]
. (   23 sec) [    -10093.4231] [Topology           ]
. (   24 sec) [    -10093.3824] [Topology           ]
. (   25 sec) [    -10093.3592] [Topology           ]
. (   26 sec) [    -10093.3458] [Topology           ]
. (   27 sec) [    -10093.3379] [Topology           ]
. (   29 sec) [    -10093.3334] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-10093.333388
. (   40 sec) [    -10093.3333] [GTR parameters     ]
. (   40 sec) [    -10093.3329] [Alpha              ][  0.898930]
. (   40 sec) [    -10093.3329] [Topology           ]
. (   41 sec) [    -10093.3301] [Topology           ]
. (   43 sec) [    -10093.3285] [Topology           ]
. (   44 sec) [    -10093.3276] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-10093.327553
. (   53 sec) [    -10093.3275] [GTR parameters     ]
. (   53 sec) [    -10093.3275] [Alpha              ][  0.898930]
. (   53 sec) [    -10093.3275] [Topology           ]
. (   54 sec) [    -10093.3269] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -10093.326949.

. Printing the most likely tree in file 'data59.phy_phyml_tree.txt'...


. Time used 0h1m14s

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