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

                . Sequence filename : 				 data81.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...

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

. 167 sites without polymorphism (33.40%).

. 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=-5112.589783
. (    0 sec) [     -5111.9426] [GTR parameters     ]
. (    0 sec) [     -5111.9419] [Alpha              ][  1.004062]
. (    0 sec) [     -5111.9419] [Topology           ]
. (    2 sec) [     -5099.1697] [Topology           ]
. (    3 sec) [     -5097.6528] [Topology           ]
. (    5 sec) [     -5097.3802] [Topology           ]
. (    5 sec) [     -5097.3097] [Topology           ]
. (    6 sec) [     -5097.2897] [Topology           ]
. (    7 sec) [     -5097.2835] [Topology           ]
. (    8 sec) [     -5097.2815] [Topology           ]
. (    9 sec) [     -5097.2806] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5097.280569
. (   15 sec) [     -5097.2553] [GTR parameters     ]
. (   15 sec) [     -5097.2534] [Alpha              ][  1.011239]
. (   15 sec) [     -5097.2534] [Topology           ]
. (   16 sec) [     -5097.2527] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5097.252714
. (   22 sec) [     -5097.2527] [GTR parameters     ]
. (   22 sec) [     -5097.2527] [Alpha              ][  1.011239]
. (   22 sec) [     -5097.2527] [Topology           ]
. (   23 sec) [     -5097.2525] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5097.252494.

. Printing the most likely tree in file 'data81.phy_phyml_tree.txt'...


. Time used 0h0m33s

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