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

                . Sequence filename : 				 data83.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...

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

. 100 sites without polymorphism (20.00%).

. 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=-7561.691620
. (    1 sec) [     -7552.1318] [GTR parameters     ]
. (    1 sec) [     -7552.1260] [Alpha              ][  0.990008]
. (    1 sec) [     -7552.1260] [Topology           ]
. (    2 sec) [     -7524.8516] [Topology           ]
. (    3 sec) [     -7518.9915] [Topology           ]
. (    3 sec) [     -7516.0097] [Topology           ]
. (    4 sec) [     -7515.2027] [Topology           ]
. (    5 sec) [     -7514.9296] [Topology           ]
. (    6 sec) [     -7514.8573] [Topology           ]
. (    6 sec) [     -7514.8285] [Topology           ]
. (    7 sec) [     -7514.8156] [Topology           ]
. (    8 sec) [     -7514.8095] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7514.806675
. (   15 sec) [     -7514.7032] [GTR parameters     ]
. (   15 sec) [     -7514.5454] [Alpha              ][  1.039178]
. (   15 sec) [     -7514.5454] [Topology           ]
. (   15 sec) [     -7514.5374] [Topology           ]
. (   16 sec) [     -7514.5347] [Topology           ]
. (   17 sec) [     -7514.5335] [Topology           ]
. (   18 sec) [     -7514.5329] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-7514.532913
. (   23 sec) [     -7514.5327] [GTR parameters     ]
. (   23 sec) [     -7514.5325] [Alpha              ][  1.040837]
. (   23 sec) [     -7514.5325] [Topology           ]
. (   24 sec) [     -7514.5323] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Maximizing likelihood (using SPR moves)...

. (   36 sec) [     -7552.1318] [GTR parameters     ]
. (   36 sec) [     -7552.1260] [Alpha              ][  0.990008]
. (   37 sec) [     -7549.9773] [ 1498] [depth=    1]
. (   37 sec) [     -7548.8446] [ 1498] [depth=    1]
. (   37 sec) [     -7547.7971] [ 1496] [depth=    1]
. (   37 sec) [     -7547.5127] [ 1498] [depth=    1]
. (   37 sec) [     -7545.4285] [ 1496] [depth=    1]
. (   38 sec) [     -7543.5265] [ 1495] [depth=    1]
. (   38 sec) [     -7542.9340] [ 1496] [depth=    1]
. (   38 sec) [     -7541.6378] [ 1498] [depth=    2]
. (   38 sec) [     -7541.3508] [ 1498] [depth=    1]
. (   38 sec) [     -7541.1682] [ 1497] [depth=    1]
. (   39 sec) [     -7540.5468] [ 1497] [depth=    3]
. (   39 sec) [     -7539.6281] [ 1496] [depth=    2]
. (   39 sec) [     -7538.9150] [ 1496] [depth=    1]
. (   39 sec) [     -7533.4348] [ 1494] [depth=    3]
. (   40 sec) [     -7516.1541] [Branch lengths     ]
. (   40 sec) [     -7516.0673] [GTR parameters     ]
. (   40 sec) [     -7515.9652] [Alpha              ][  1.029534]
. (   44 sec) [     -7514.6971] [Branch lengths     ]
. (   65 sec) [     -7514.5614] [Branch lengths     ]
. (   65 sec) [     -7514.5614] [Topology           ]
. (   66 sec) [     -7514.5491] [Topology           ]
. (   67 sec) [     -7514.5450] [Topology           ]
. (   68 sec) [     -7514.5431] [Topology           ]
. (   68 sec) [     -7514.5422] [Topology           ]
. (   69 sec) [     -7514.5411] [GTR parameters     ]
. (   69 sec) [     -7514.5334] [Alpha              ][  1.040890]
. (   69 sec) [     -7514.5334] [Topology           ]
. (   69 sec) [     -7514.5326] [Topology           ]
. (   70 sec) [     -7514.5326] [GTR parameters     ]
. (   70 sec) [     -7514.5326] [Alpha              ][  1.040890]

. Checking for NNIs, optimizing five branches...



. Log likelihood obtained after NNI moves : -7514.532262
. Log likelihood obtained after SPR moves : -7514.532624
. Log likelihood of the current tree: -7514.532262.

. Printing the most likely tree in file 'data83.phy_phyml_tree.txt'...


. Time used 0h1m15s

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