.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data13.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... . 440 patterns found. (out of a total of 500 sites) . 60 sites without polymorphism (12.00%). . 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=-10546.845838 . ( 1 sec) [ -10543.7747] [GTR parameters ] . ( 1 sec) [ -10542.3913] [Alpha ][ 0.887695] . ( 1 sec) [ -10542.3913] [Topology ] . ( 2 sec) [ -10460.0048] [Topology ] . ( 3 sec) [ -10440.8259] [Topology ] . ( 4 sec) [ -10432.6380] [Topology ] . ( 5 sec) [ -10421.9951] [Topology ] . ( 6 sec) [ -10416.4032] [Topology ] . ( 7 sec) [ -10414.6769] [Topology ] . ( 7 sec) [ -10413.9441] [Topology ] . ( 8 sec) [ -10413.6686] [Topology ] . ( 9 sec) [ -10413.5911] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -10413.3990] [Topology ] . Before opt ts/t=1.000000 LK=-10413.399007 . ( 18 sec) [ -10413.2633] [GTR parameters ] . ( 18 sec) [ -10413.2633] [Alpha ][ 0.887695] . ( 18 sec) [ -10413.2633] [Topology ] . ( 19 sec) [ -10413.2479] [Topology ] . ( 20 sec) [ -10413.2403] [Topology ] . ( 20 sec) [ -10413.2362] [Topology ] . ( 21 sec) [ -10413.2340] [Topology ] . ( 22 sec) [ -10413.2326] [Topology ] . ( 23 sec) [ -10413.2319] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10413.231925 . ( 30 sec) [ -10413.2319] [GTR parameters ] . ( 30 sec) [ -10413.2316] [Alpha ][ 0.889193] . ( 30 sec) [ -10413.2316] [Topology ] . ( 31 sec) [ -10413.2311] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -10543.7747] [GTR parameters ] . ( 47 sec) [ -10542.3913] [Alpha ][ 0.887695] . ( 48 sec) [ -10536.5809] [ 2504] [depth= 1] . ( 48 sec) [ -10526.7558] [ 2500] [depth= 1] . ( 48 sec) [ -10515.3687] [ 2509] [depth= 1] . ( 49 sec) [ -10511.6005] [ 2510] [depth= 1] . ( 49 sec) [ -10507.5594] [ 2509] [depth= 1] . ( 49 sec) [ -10502.9401] [ 2510] [depth= 1] . ( 49 sec) [ -10501.8837] [ 2503] [depth= 1] . ( 50 sec) [ -10500.3942] [ 2504] [depth= 2] . ( 50 sec) [ -10494.6069] [ 2504] [depth= 1] . ( 50 sec) [ -10483.0385] [ 2503] [depth= 2] . ( 50 sec) [ -10474.6558] [ 2512] [depth= 3] . ( 50 sec) [ -10472.9685] [ 2513] [depth= 1] . ( 50 sec) [ -10472.7260] [ 2519] [depth= 1] . ( 50 sec) [ -10471.6765] [ 2521] [depth= 1] . ( 51 sec) [ -10457.5637] [ 2507] [depth= 2] . ( 51 sec) [ -10455.6164] [ 2511] [depth= 1] . ( 52 sec) [ -10455.4959] [ 2507] [depth= 2] . ( 52 sec) [ -10452.3761] [ 2507] [depth= 1] . ( 52 sec) [ -10452.3631] [ 2509] [depth= 1] . ( 52 sec) [ -10417.5918] [Branch lengths ] . ( 53 sec) [ -10417.4853] [GTR parameters ] . ( 53 sec) [ -10417.4849] [Alpha ][ 0.885927] . ( 53 sec) [ -10417.3977] [ 2514] [depth= 2] . ( 54 sec) [ -10417.1800] [ 2515] [depth= 1] . ( 54 sec) [ -10416.6037] [ 2513] [depth= 1] . ( 56 sec) [ -10414.5094] [Branch lengths ] . ( 56 sec) [ -10414.5051] [GTR parameters ] . ( 57 sec) [ -10414.5048] [Alpha ][ 0.887345] . ( 57 sec) [ -10414.4790] [ 2513] [depth= 1] . ( 60 sec) [ -10414.1965] [Branch lengths ] . ( 61 sec) [ -10414.1963] [GTR parameters ] . ( 61 sec) [ -10414.1962] [Alpha ][ 0.888232] . ( 75 sec) [ -10413.9349] [ 2522] [depth= 1] . ( 82 sec) [ -10413.8585] [Branch lengths ] . ( 82 sec) [ -10413.8570] [GTR parameters ] . ( 82 sec) [ -10413.8570] [Alpha ][ 0.888232] . ( 82 sec) [ -10413.8570] [Topology ] . ( 83 sec) [ -10413.8240] [Topology ] . ( 83 sec) [ -10413.7969] [Topology ] . ( 84 sec) [ -10413.7736] [Topology ] . ( 85 sec) [ -10413.6336] [Topology ] . ( 86 sec) [ -10413.2913] [Topology ] . ( 86 sec) [ -10413.2507] [Topology ] . ( 87 sec) [ -10413.2387] [Topology ] . ( 88 sec) [ -10413.2346] [Topology ] . ( 89 sec) [ -10413.2331] [Topology ] . ( 90 sec) [ -10413.2310] [GTR parameters ] . ( 90 sec) [ -10413.2308] [Alpha ][ 0.889464] . ( 90 sec) [ -10413.2308] [Topology ] . ( 91 sec) [ -10413.2305] [Topology ] . ( 91 sec) [ -10413.2305] [GTR parameters ] . ( 91 sec) [ -10413.2305] [Alpha ][ 0.889464] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10413.231081 . Log likelihood obtained after SPR moves : -10413.230492 . Log likelihood of the current tree: -10413.230492. . Printing the most likely tree in file 'data13.phy_phyml_tree.txt'... . Time used 0h1m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo