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

                . Sequence filename : 				 data88.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...

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

. 94 sites without polymorphism (18.80%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 8Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-7956.615250
. (    2 sec) [     -7955.1854] [GTR parameters     ]
. (    2 sec) [     -7954.9724] [Alpha              ][  1.057884]
. (    2 sec) [     -7954.9724] [Topology           ]
. (    3 sec) [     -7939.3506] [Topology           ]
. (    5 sec) [     -7937.3186] [Topology           ]
. (    6 sec) [     -7936.8134] [Topology           ]
. (    7 sec) [     -7936.6150] [Topology           ]
. (    8 sec) [     -7936.5279] [Topology           ]
. (    9 sec) [     -7936.4882] [Topology           ]
. (   11 sec) [     -7936.4695] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7936.469519
. (   20 sec) [     -7936.4470] [GTR parameters     ]
. (   20 sec) [     -7936.2709] [Alpha              ][  1.112677]
. (   20 sec) [     -7936.2709] [Topology           ]
. (   22 sec) [     -7936.2498] [Topology           ]
. (   23 sec) [     -7936.2412] [Topology           ]
. (   24 sec) [     -7936.2372] [Topology           ]
. (   26 sec) [     -7936.2354] [Topology           ]
. (   28 sec) [     -7936.2346] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7936.234585
. (   36 sec) [     -7936.2345] [GTR parameters     ]
. (   36 sec) [     -7936.2336] [Alpha              ][  1.116587]
. (   36 sec) [     -7936.2336] [Topology           ]
. (   37 sec) [     -7936.2331] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7936.233081
. (   45 sec) [     -7936.2331] [GTR parameters     ]
. (   45 sec) [     -7936.2331] [Alpha              ][  1.116587]
. (   45 sec) [     -7936.2331] [Topology           ]
. (   47 sec) [     -7936.2328] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -7936.232830.

. Printing the most likely tree in file 'data88.phy_phyml_tree.txt'...


. Time used 0h1m2s

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