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

                . Sequence filename : 				 data27.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...

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

. 141 sites without polymorphism (28.20%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 7Mo of memory space.

. Maximizing likelihood (using NNI moves)...

. Before opt ts/t=1.000000 LK=-5986.650611
. (    0 sec) [     -5984.4472] [GTR parameters     ]
. (    0 sec) [     -5984.4385] [Alpha              ][  0.986858]
. (    0 sec) [     -5984.4385] [Topology           ]
. (    1 sec) [     -5969.4084] [Topology           ]
. (    2 sec) [     -5967.7631] [Topology           ]
. (    3 sec) [     -5967.0781] [Topology           ]

. Moving backward

. (    4 sec) [     -5966.5799] [Topology           ]
. (    5 sec) [     -5966.2404] [Topology           ]
. (    6 sec) [     -5966.1746] [Topology           ]
. (    6 sec) [     -5966.1529] [Topology           ]
. (    7 sec) [     -5966.1448] [Topology           ]
. (    8 sec) [     -5966.1417] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5966.140439
. (   15 sec) [     -5966.1288] [GTR parameters     ]
. (   15 sec) [     -5966.1175] [Alpha              ][  1.002142]
. (   15 sec) [     -5966.1175] [Topology           ]
. (   16 sec) [     -5966.1163] [Topology           ]
. (   17 sec) [     -5966.1159] [Topology           ]

. Checking for NNIs, optimizing five branches...

. Before opt ts/t=1.000000 LK=-5966.115860
. (   24 sec) [     -5966.1159] [GTR parameters     ]
. (   24 sec) [     -5966.1159] [Alpha              ][  1.002142]
. (   24 sec) [     -5966.1159] [Topology           ]
. (   25 sec) [     -5966.1157] [Topology           ]

. Checking for NNIs, optimizing five branches...


. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -5966.115680.

. Printing the most likely tree in file 'data27.phy_phyml_tree.txt'...


. Time used 0h0m39s

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