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

                . Sequence filename : 				 data16.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...

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

. 238 sites without polymorphism (47.60%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 5Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-3809.279994
. (    1 sec) [     -3808.5219] [GTR parameters     ]
. (    1 sec) [     -3807.9062] [Alpha              ][  0.847346]
. (    1 sec) [     -3807.9062] [Topology           ]
. (    2 sec) [     -3796.9317] [Topology           ]
. (    2 sec) [     -3795.7445] [Topology           ]
. (    3 sec) [     -3795.4946] [Topology           ]
. (    3 sec) [     -3795.4363] [Topology           ]
. (    4 sec) [     -3795.4223] [Topology           ]
. (    5 sec) [     -3795.4188] [Topology           ]
. (    5 sec) [     -3795.4177] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3795.417742
. (    9 sec) [     -3795.4124] [GTR parameters     ]
. (    9 sec) [     -3795.3950] [Alpha              ][  0.870219]
. (    9 sec) [     -3795.3950] [Topology           ]
. (   10 sec) [     -3795.3941] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3795.394058
. (   14 sec) [     -3795.3940] [GTR parameters     ]
. (   14 sec) [     -3795.3940] [Alpha              ][  0.871089]
. (   14 sec) [     -3795.3940] [Topology           ]
. (   15 sec) [     -3795.3938] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -3795.393804.

. Printing the most likely tree in file 'data16.phy_phyml_tree.txt'...


. Time used 0h0m22s

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