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

                . Sequence filename : 				 data26.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...

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

. 165 sites without polymorphism (33.00%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 7Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-4865.141674
. (    1 sec) [     -4860.9842] [GTR parameters     ]
. (    1 sec) [     -4860.5234] [Alpha              ][  1.125341]
. (    1 sec) [     -4860.5234] [Topology           ]
. (    2 sec) [     -4845.9236] [Topology           ]
. (    3 sec) [     -4844.6195] [Topology           ]
. (    4 sec) [     -4844.4342] [Topology           ]
. (    4 sec) [     -4844.3950] [Topology           ]
. (    5 sec) [     -4844.3845] [Topology           ]
. (    6 sec) [     -4844.3813] [Topology           ]
. (    6 sec) [     -4844.3803] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-4844.380302
. (   10 sec) [     -4844.3571] [GTR parameters     ]
. (   10 sec) [     -4844.3447] [Alpha              ][  1.146930]
. (   10 sec) [     -4844.3447] [Topology           ]
. (   11 sec) [     -4844.3440] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-4844.343980
. (   15 sec) [     -4844.3440] [GTR parameters     ]
. (   15 sec) [     -4844.3439] [Alpha              ][  1.148077]
. (   15 sec) [     -4844.3439] [Topology           ]
. (   15 sec) [     -4844.3437] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -4844.343707.

. Printing the most likely tree in file 'data26.phy_phyml_tree.txt'...


. Time used 0h0m25s

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