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

                . Sequence filename : 				 data78.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...

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

. 72 sites without polymorphism (14.40%).

. 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=-8419.296833
. (    1 sec) [     -8412.2618] [GTR parameters     ]
. (    1 sec) [     -8409.5051] [Alpha              ][  1.225301]
. (    1 sec) [     -8409.5051] [Topology           ]
. (    2 sec) [     -8391.5520] [Topology           ]
. (    2 sec) [     -8388.7643] [Topology           ]
. (    3 sec) [     -8387.8745] [Topology           ]
. (    4 sec) [     -8387.5222] [Topology           ]
. (    5 sec) [     -8387.3734] [Topology           ]
. (    6 sec) [     -8387.3068] [Topology           ]
. (    7 sec) [     -8387.2763] [Topology           ]

. Checking for NNIs, optimizing five branches...

. (   12 sec) [     -8387.1901] [Topology           ]
. Before opt ts/t=1.000000 LK=-8387.190119
. (   12 sec) [     -8387.1746] [GTR parameters     ]
. (   12 sec) [     -8387.1528] [Alpha              ][  1.248016]
. (   12 sec) [     -8387.1528] [Topology           ]
. (   13 sec) [     -8387.1313] [Topology           ]
. (   14 sec) [     -8387.1219] [Topology           ]
. (   14 sec) [     -8387.1175] [Topology           ]
. (   15 sec) [     -8387.1155] [Topology           ]
. (   16 sec) [     -8387.1145] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-8387.114542
. (   22 sec) [     -8387.1145] [GTR parameters     ]
. (   22 sec) [     -8387.1145] [Alpha              ][  1.249264]
. (   22 sec) [     -8387.1145] [Topology           ]
. (   23 sec) [     -8387.1140] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Maximizing likelihood (using SPR moves)...

. (   34 sec) [     -8412.2618] [GTR parameters     ]
. (   34 sec) [     -8409.5051] [Alpha              ][  1.225301]
. (   34 sec) [     -8406.1483] [ 1733] [depth=    1]
. (   34 sec) [     -8405.9203] [ 1734] [depth=    1]
. (   34 sec) [     -8405.6484] [ 1733] [depth=    1]
. (   35 sec) [     -8404.3349] [ 1734] [depth=    1]
. (   35 sec) [     -8403.4439] [ 1736] [depth=    1]
. (   36 sec) [     -8403.2458] [ 1739] [depth=    1]
. (   36 sec) [     -8401.7254] [ 1730] [depth=    1]
. (   36 sec) [     -8401.5850] [ 1735] [depth=    1]
. (   36 sec) [     -8400.8843] [ 1737] [depth=    1]
. (   36 sec) [     -8400.7790] [ 1739] [depth=    1]
. (   36 sec) [     -8400.6341] [ 1740] [depth=    1]
. (   37 sec) [     -8399.3393] [ 1739] [depth=    1]
. (   37 sec) [     -8399.1633] [ 1739] [depth=    1]
. (   37 sec) [     -8399.0180] [ 1739] [depth=    1]
. (   37 sec) [     -8398.1916] [ 1739] [depth=    1]
. (   37 sec) [     -8397.6036] [ 1740] [depth=    2]
. (   38 sec) [     -8390.3666] [Branch lengths     ]
. (   38 sec) [     -8390.3456] [GTR parameters     ]
. (   38 sec) [     -8390.3307] [Alpha              ][  1.244172]
. (   40 sec) [     -8387.2528] [ 1742] [depth=    2]
. (   40 sec) [     -8386.5270] [ 1741] [depth=    1]
. (   40 sec) [     -8386.0193] [ 1740] [depth=    1]
. (   41 sec) [     -8385.5605] [ 1740] [depth=    2]
. (   41 sec) [     -8384.1866] [Branch lengths     ]
. (   42 sec) [     -8384.1727] [GTR parameters     ]
. (   42 sec) [     -8384.1706] [Alpha              ][  1.236853]
. (   46 sec) [     -8383.9956] [Branch lengths     ]
. (   66 sec) [     -8383.9877] [Branch lengths     ]
. (   66 sec) [     -8383.9877] [Topology           ]
. (   67 sec) [     -8383.9870] [Topology           ]
. (   67 sec) [     -8383.9870] [GTR parameters     ]
. (   67 sec) [     -8383.9866] [Alpha              ][  1.239784]
. (   67 sec) [     -8383.9866] [Topology           ]
. (   68 sec) [     -8383.9864] [Topology           ]
. (   68 sec) [     -8383.9864] [GTR parameters     ]
. (   68 sec) [     -8383.9864] [Alpha              ][  1.239784]

. Checking for NNIs, optimizing five branches...



. Log likelihood obtained after NNI moves : -8387.114006
. Log likelihood obtained after SPR moves : -8383.986353
. Log likelihood of the current tree: -8383.986353.

. Printing the most likely tree in file 'data78.phy_phyml_tree.txt'...


. Time used 0h1m13s

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