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

                . Sequence filename : 				 data48.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...

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

. 143 sites without polymorphism (28.60%).

. 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=-5961.452416
. (    1 sec) [     -5958.6771] [GTR parameters     ]
. (    1 sec) [     -5958.5045] [Alpha              ][  1.063482]
. (    1 sec) [     -5958.5045] [Topology           ]
. (    2 sec) [     -5950.2618] [Topology           ]
. (    4 sec) [     -5949.4376] [Topology           ]
. (    5 sec) [     -5949.2690] [Topology           ]
. (    6 sec) [     -5949.2203] [Topology           ]
. (    7 sec) [     -5949.2038] [Topology           ]
. (    8 sec) [     -5949.1978] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5949.197809
. (   14 sec) [     -5949.1898] [GTR parameters     ]
. (   14 sec) [     -5949.1391] [Alpha              ][  1.099532]
. (   14 sec) [     -5949.1391] [Topology           ]
. (   15 sec) [     -5949.1330] [Topology           ]
. (   15 sec) [     -5949.1307] [Topology           ]
. (   16 sec) [     -5949.1298] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5949.129842
. (   23 sec) [     -5949.1298] [GTR parameters     ]
. (   23 sec) [     -5949.1297] [Alpha              ][  1.101246]
. (   23 sec) [     -5949.1297] [Topology           ]
. (   24 sec) [     -5949.1293] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5949.129324.

. Printing the most likely tree in file 'data48.phy_phyml_tree.txt'...


. Time used 0h0m37s

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