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

                . Sequence filename : 				 data36.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...

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

. 238 sites without polymorphism (47.60%).

. 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=-3607.752479
. (    0 sec) [     -3604.8214] [GTR parameters     ]
. (    0 sec) [     -3603.5517] [Alpha              ][  0.788011]
. (    0 sec) [     -3603.5517] [Topology           ]
. (    1 sec) [     -3598.3151] [Topology           ]
. (    1 sec) [     -3597.5172] [Topology           ]
. (    2 sec) [     -3597.3284] [Topology           ]
. (    3 sec) [     -3597.2749] [Topology           ]
. (    4 sec) [     -3597.2579] [Topology           ]
. (    5 sec) [     -3597.2516] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (    8 sec) [     -3597.1388] [Topology           ]
. Before opt ts/t=1.000000 LK=-3597.138757
. (    8 sec) [     -3597.1192] [GTR parameters     ]
. (    8 sec) [     -3597.1105] [Alpha              ][  0.802128]
. (    8 sec) [     -3597.1105] [Topology           ]
. (    9 sec) [     -3597.0776] [Topology           ]
. (    9 sec) [     -3596.9868] [Topology           ]
. (   10 sec) [     -3596.8400] [Topology           ]
. (   10 sec) [     -3596.7996] [Topology           ]
. (   11 sec) [     -3596.7876] [Topology           ]
. (   11 sec) [     -3596.7837] [Topology           ]
. (   12 sec) [     -3596.7823] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3596.782309
. (   16 sec) [     -3596.7812] [GTR parameters     ]
. (   16 sec) [     -3596.7793] [Alpha              ][  0.809327]
. (   16 sec) [     -3596.7793] [Topology           ]
. (   17 sec) [     -3596.7785] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-3596.778495
. (   21 sec) [     -3596.7785] [GTR parameters     ]
. (   21 sec) [     -3596.7785] [Alpha              ][  0.809327]
. (   21 sec) [     -3596.7785] [Topology           ]
. (   22 sec) [     -3596.7781] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -3596.778076.

. Printing the most likely tree in file 'data36.phy_phyml_tree.txt'...


. Time used 0h0m30s

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