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

                . Sequence filename : 				 data28.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

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. Compressing sequences...

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

. 74 sites without polymorphism (14.80%).

. 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=-9517.729777
. (    1 sec) [     -9512.4274] [GTR parameters     ]
. (    1 sec) [     -9512.2160] [Alpha              ][  0.951124]
. (    1 sec) [     -9512.2160] [Topology           ]
. (    2 sec) [     -9481.7224] [Topology           ]
. (    3 sec) [     -9477.1726] [Topology           ]
. (    4 sec) [     -9475.9502] [Topology           ]
. (    5 sec) [     -9475.4351] [Topology           ]
. (    6 sec) [     -9475.1891] [Topology           ]
. (    7 sec) [     -9475.0652] [Topology           ]
. (    8 sec) [     -9475.0016] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9475.001637
. (   17 sec) [     -9474.8908] [GTR parameters     ]
. (   17 sec) [     -9474.5736] [Alpha              ][  1.008942]
. (   17 sec) [     -9474.5736] [Topology           ]
. (   18 sec) [     -9474.5046] [Topology           ]
. (   20 sec) [     -9474.4727] [Topology           ]
. (   21 sec) [     -9474.4565] [Topology           ]
. (   22 sec) [     -9474.4482] [Topology           ]
. (   23 sec) [     -9474.4439] [Topology           ]
. (   24 sec) [     -9474.4417] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9474.441742
. (   33 sec) [     -9474.4413] [GTR parameters     ]
. (   33 sec) [     -9474.4384] [Alpha              ][  1.014807]
. (   33 sec) [     -9474.4384] [Topology           ]
. (   34 sec) [     -9474.4368] [Topology           ]
. (   35 sec) [     -9474.4361] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-9474.436096
. (   43 sec) [     -9474.4361] [GTR parameters     ]
. (   43 sec) [     -9474.4361] [Alpha              ][  1.014807]
. (   43 sec) [     -9474.4361] [Topology           ]
. (   45 sec) [     -9474.4357] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -9474.435707.

. Printing the most likely tree in file 'data28.phy_phyml_tree.txt'...


. Time used 0h1m3s

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