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

                . Sequence filename : 				 data49.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...

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

. 240 sites without polymorphism (48.00%).

. 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=-3491.381768
. (    1 sec) [     -3490.8884] [GTR parameters     ]
. (    1 sec) [     -3490.7282] [Alpha              ][  1.104161]
. (    1 sec) [     -3490.7282] [Topology           ]
. (    1 sec) [     -3485.5616] [Topology           ]
. (    2 sec) [     -3485.0246] [Topology           ]
. (    2 sec) [     -3484.9129] [Topology           ]
. (    3 sec) [     -3484.8770] [Topology           ]

. Moving backward

. (    3 sec) [     -3484.8327] [Topology           ]
. (    3 sec) [     -3484.8068] [Topology           ]
. (    4 sec) [     -3484.8045] [Topology           ]
. (    4 sec) [     -3484.8042] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3484.804156
. (    7 sec) [     -3484.7990] [GTR parameters     ]
. (    7 sec) [     -3484.7928] [Alpha              ][  1.125754]
. (    7 sec) [     -3484.7928] [Topology           ]
. (    8 sec) [     -3484.7926] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3484.792586
. (   11 sec) [     -3484.7926] [GTR parameters     ]
. (   11 sec) [     -3484.7926] [Alpha              ][  1.126879]
. (   11 sec) [     -3484.7926] [Topology           ]
. (   11 sec) [     -3484.7925] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -3484.792537.

. Printing the most likely tree in file 'data49.phy_phyml_tree.txt'...


. Time used 0h0m17s

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo