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

                . Sequence filename : 				 nucleic_M2599_66x1137_2006.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 : 			 SPRs
                . Starting tree : 				 BioNJ
                . Add random input tree : 			 no
                . Optimise branch lengths : 			 yes
                . Optimise substitution model parameters : 	 yes
                . Run ID : 					 none

 oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo



. Compressing sequences...

. 131 patterns found. (out of a total of 1137 sites) 

. 1062 sites without polymorphism (93.40%).

. Computing pairwise distances...

. Building BioNJ tree...

. This analysis requires at least 5Mo of memory space.

. Maximizing likelihood (using SPR moves)...

. (    0 sec) [     -2167.7777] [GTR parameters     ]
. (    0 sec) [     -2167.7484] [Alpha              ][  0.762192]
. (    0 sec) [     -2167.5690] [   80] [depth=    5]
. (    0 sec) [     -2167.5255] [   80] [depth=    1]
. (    0 sec) [     -2167.4612] [   80] [depth=    1]
. (    0 sec) [     -2167.4301] [   80] [depth=    2]
. (    0 sec) [     -2167.3835] [   80] [depth=    2]
. (    0 sec) [     -2167.2964] [   80] [depth=    1]
. (    0 sec) [     -2167.2521] [   80] [depth=    1]
. (    1 sec) [     -2167.2139] [   80] [depth=    3]
. (    1 sec) [     -2167.1975] [   80] [depth=    3]
. (    1 sec) [     -2167.1458] [   80] [depth=    1]
. (    1 sec) [     -2166.6462] [   80] [depth=    5]
. (    1 sec) [     -2166.6336] [   80] [depth=    5]
. (    1 sec) [     -2166.5335] [   80] [depth=    3]
. (    1 sec) [     -2166.5235] [   80] [depth=    3]
. (    1 sec) [     -2166.5082] [   80] [depth=    1]
. (    1 sec) [     -2166.4108] [   80] [depth=    2]
. (    2 sec) [     -2165.9948] [   80] [depth=    2]
. (    2 sec) [     -2165.9793] [   80] [depth=    1]
. (    2 sec) [     -2165.8827] [   80] [depth=    3]
. (    2 sec) [     -2165.7892] [   80] [depth=    4]
. (    2 sec) [     -2165.6397] [   80] [depth=    4]
. (    2 sec) [     -2165.6014] [   80] [depth=    4]
. (    2 sec) [     -2165.5608] [   80] [depth=    3]
. (    2 sec) [     -2165.5485] [   80] [depth=    5]
. (    2 sec) [     -2165.5263] [   80] [depth=    1]
. (    2 sec) [     -2165.4871] [   80] [depth=    2]
. (    2 sec) [     -2165.4203] [   80] [depth=    2]
. (    2 sec) [     -2165.3554] [   80] [depth=    1]
. (    3 sec) [     -2165.3401] [   80] [depth=    1]
. (    3 sec) [     -2164.9097] [   80] [depth=    1]
. (    3 sec) [     -2164.8711] [   80] [depth=    3]
. (    3 sec) [     -2164.8555] [   80] [depth=    2]
. (    3 sec) [     -2164.8322] [   80] [depth=    3]
. (    3 sec) [     -2164.7953] [   80] [depth=    1]
. (    3 sec) [     -2164.7507] [   80] [depth=    2]
. (    3 sec) [     -2164.7201] [   80] [depth=    1]
. (    3 sec) [     -2164.6756] [   80] [depth=    4]
. (    3 sec) [     -2164.5015] [   80] [depth=    5]
. (    3 sec) [     -2164.4504] [   80] [depth=    6]
. (    3 sec) [     -2164.3594] [   80] [depth=    2]
. (    3 sec) [     -2164.1632] [   80] [depth=    1]
. (    3 sec) [     -2164.0895] [   80] [depth=    1]
. (    4 sec) [     -2163.8452] [   80] [depth=    1]
. (    5 sec) [     -2163.7936] [   80] [depth=    6]
. (    5 sec) [     -2163.7456] [   80] [depth=    5]
. (    6 sec) [     -2163.4890] [Branch lengths     ]
. (    6 sec) [     -2163.4889] [GTR parameters     ]
. (    7 sec) [     -2163.4888] [Alpha              ][  0.759420]
. (   13 sec) [     -2163.4873] [Branch lengths     ]
. (   32 sec) [     -2163.4873] [Branch lengths     ]
. (   32 sec) [     -2163.4873] [Topology           ]
. (   32 sec) [     -2163.4873] [Topology           ]
. (   32 sec) [     -2163.4873] [Topology           ]
. (   33 sec) [     -2163.4873] [Topology           ]
. (   33 sec) [     -2163.4873] [Topology           ]
. (   33 sec) [     -2163.4873] [Topology           ]
. (   33 sec) [     -2163.4873] [Topology           ]
. (   33 sec) [     -2163.4873] [GTR parameters     ]
. (   33 sec) [     -2163.4873] [Alpha              ][  0.759420]

. Checking for NNIs, optimizing five branches...


. Log likelihood of the current tree: -2163.487251.

. Printing the most likely tree in file 'nucleic_M2599_66x1137_2006.phy_phyml_tree.txt'...


. Time used 0h0m35s

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34.32user 0.00system 0:35.91elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (0major+0minor)pagefaults 0swaps