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

                . Sequence filename : 				 data86.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 : 			 Best of NNIs and SPRs
                . Starting tree : 				 BioNJ
                . Add random input tree : 			 no
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

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

. 96 sites without polymorphism (19.20%).

. 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=-7635.534928
. (    1 sec) [     -7630.7980] [GTR parameters     ]
. (    1 sec) [     -7630.6061] [Alpha              ][  1.055716]
. (    1 sec) [     -7630.6061] [Topology           ]
. (    2 sec) [     -7600.6305] [Topology           ]
. (    4 sec) [     -7596.7981] [Topology           ]
. (    5 sec) [     -7595.9117] [Topology           ]
. (    6 sec) [     -7595.5834] [Topology           ]
. (    7 sec) [     -7595.4422] [Topology           ]
. (    8 sec) [     -7595.3780] [Topology           ]
. (    9 sec) [     -7595.3480] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   16 sec) [     -7595.1140] [Topology           ]
. Before opt ts/t=1.000000 LK=-7595.114037
. (   16 sec) [     -7595.0703] [GTR parameters     ]
. (   16 sec) [     -7595.0021] [Alpha              ][  1.089690]
. (   16 sec) [     -7595.0021] [Topology           ]
. (   17 sec) [     -7594.9687] [Topology           ]
. (   18 sec) [     -7594.9564] [Topology           ]
. (   19 sec) [     -7594.9510] [Topology           ]
. (   21 sec) [     -7594.9484] [Topology           ]
. (   22 sec) [     -7594.9472] [Topology           ]
. (   22 sec) [     -7594.9466] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7594.946644
. (   29 sec) [     -7594.9466] [GTR parameters     ]
. (   29 sec) [     -7594.9461] [Alpha              ][  1.092464]
. (   29 sec) [     -7594.9461] [Topology           ]
. (   30 sec) [     -7594.9458] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Maximizing likelihood (using SPR moves)...

. (   43 sec) [     -7630.7980] [GTR parameters     ]
. (   43 sec) [     -7630.6061] [Alpha              ][  1.055716]
. (   44 sec) [     -7628.9628] [ 1539] [depth=    1]
. (   44 sec) [     -7626.5188] [ 1542] [depth=    1]
. (   44 sec) [     -7626.3541] [ 1542] [depth=    1]
. (   44 sec) [     -7625.9825] [ 1539] [depth=    1]
. (   44 sec) [     -7625.2368] [ 1539] [depth=    1]
. (   45 sec) [     -7624.0132] [ 1539] [depth=    1]
. (   45 sec) [     -7623.4564] [ 1540] [depth=    1]
. (   45 sec) [     -7623.4087] [ 1542] [depth=    1]
. (   46 sec) [     -7622.7522] [ 1543] [depth=    1]
. (   46 sec) [     -7622.3383] [ 1541] [depth=    1]
. (   47 sec) [     -7621.4984] [ 1543] [depth=    1]
. (   47 sec) [     -7620.7238] [ 1539] [depth=    1]
. (   47 sec) [     -7620.6113] [ 1537] [depth=    1]
. (   47 sec) [     -7619.5653] [ 1540] [depth=    1]
. (   47 sec) [     -7617.5719] [ 1537] [depth=    1]
. (   47 sec) [     -7609.5343] [ 1539] [depth=    1]
. (   48 sec) [     -7595.7066] [Branch lengths     ]
. (   48 sec) [     -7595.6749] [GTR parameters     ]
. (   48 sec) [     -7595.6263] [Alpha              ][  1.084265]
. (   52 sec) [     -7595.0052] [Branch lengths     ]
. (   76 sec) [     -7594.9571] [Branch lengths     ]
. (   76 sec) [     -7594.9571] [Topology           ]
. (   76 sec) [     -7594.9532] [Topology           ]
. (   77 sec) [     -7594.9519] [Topology           ]
. (   78 sec) [     -7594.9514] [Topology           ]
. (   78 sec) [     -7594.9501] [GTR parameters     ]
. (   78 sec) [     -7594.9464] [Alpha              ][  1.092463]
. (   78 sec) [     -7594.9464] [Topology           ]
. (   79 sec) [     -7594.9459] [Topology           ]
. (   79 sec) [     -7594.9459] [GTR parameters     ]
. (   79 sec) [     -7594.9459] [Alpha              ][  1.092463]

. Checking for NNIs, optimizing five branches...



. Log likelihood obtained after NNI moves : -7594.945794
. Log likelihood obtained after SPR moves : -7594.945862
. Log likelihood of the current tree: -7594.945794.

. Printing the most likely tree in file 'data86.phy_phyml_tree.txt'...


. Time used 0h1m26s

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