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

                . Sequence filename : 				 data13.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...

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

. 60 sites without polymorphism (12.00%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 9Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-10546.845838
. (    1 sec) [    -10543.7747] [GTR parameters     ]
. (    2 sec) [    -10542.3913] [Alpha              ][  0.887695]
. (    2 sec) [    -10542.3913] [Topology           ]
. (    3 sec) [    -10460.0048] [Topology           ]
. (    4 sec) [    -10440.8259] [Topology           ]
. (    5 sec) [    -10432.6380] [Topology           ]
. (    6 sec) [    -10421.9951] [Topology           ]
. (    7 sec) [    -10416.4032] [Topology           ]
. (    8 sec) [    -10414.6769] [Topology           ]
. (    9 sec) [    -10413.9441] [Topology           ]
. (   10 sec) [    -10413.6686] [Topology           ]
. (   11 sec) [    -10413.5911] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   19 sec) [    -10413.3990] [Topology           ]
. Before opt ts/t=1.000000 LK=-10413.399007
. (   20 sec) [    -10413.2633] [GTR parameters     ]
. (   20 sec) [    -10413.2633] [Alpha              ][  0.887695]
. (   20 sec) [    -10413.2633] [Topology           ]
. (   21 sec) [    -10413.2479] [Topology           ]
. (   22 sec) [    -10413.2403] [Topology           ]
. (   23 sec) [    -10413.2362] [Topology           ]
. (   24 sec) [    -10413.2340] [Topology           ]
. (   26 sec) [    -10413.2326] [Topology           ]
. (   27 sec) [    -10413.2319] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-10413.231925
. (   39 sec) [    -10413.2319] [GTR parameters     ]
. (   39 sec) [    -10413.2316] [Alpha              ][  0.889193]
. (   39 sec) [    -10413.2316] [Topology           ]
. (   40 sec) [    -10413.2311] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -10413.231081.

. Printing the most likely tree in file 'data13.phy_phyml_tree.txt'...


. Time used 0h1m2s

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