.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data15.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... . 424 patterns found. (out of a total of 500 sites) . 69 sites without polymorphism (13.80%). . 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=-9232.261190 . ( 1 sec) [ -9223.1516] [GTR parameters ] . ( 1 sec) [ -9221.6649] [Alpha ][ 0.876656] . ( 1 sec) [ -9221.6649] [Topology ] . ( 2 sec) [ -9163.9155] [Topology ] . ( 2 sec) [ -9152.7065] [Topology ] . ( 3 sec) [ -9149.0056] [Topology ] . ( 4 sec) [ -9147.2834] [Topology ] . ( 5 sec) [ -9146.3846] [Topology ] . ( 6 sec) [ -9145.8961] [Topology ] . ( 7 sec) [ -9145.6216] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.621608 . ( 13 sec) [ -9145.5746] [GTR parameters ] . ( 13 sec) [ -9145.5006] [Alpha ][ 0.900803] . ( 13 sec) [ -9145.5006] [Topology ] . ( 14 sec) [ -9145.3417] [Topology ] . ( 15 sec) [ -9145.2518] [Topology ] . ( 16 sec) [ -9145.2001] [Topology ] . ( 17 sec) [ -9145.1700] [Topology ] . ( 17 sec) [ -9145.1523] [Topology ] . ( 18 sec) [ -9145.1419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.141931 . ( 25 sec) [ -9145.1415] [GTR parameters ] . ( 25 sec) [ -9145.1414] [Alpha ][ 0.899898] . ( 25 sec) [ -9145.1414] [Topology ] . ( 26 sec) [ -9145.1352] [Topology ] . ( 27 sec) [ -9145.1314] [Topology ] . ( 28 sec) [ -9145.1292] [Topology ] . ( 29 sec) [ -9145.1279] [Topology ] . ( 29 sec) [ -9145.1272] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9145.127155 . ( 36 sec) [ -9145.1272] [GTR parameters ] . ( 36 sec) [ -9145.1271] [Alpha ][ 0.898998] . ( 36 sec) [ -9145.1271] [Topology ] . ( 36 sec) [ -9145.1266] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -9223.1516] [GTR parameters ] . ( 50 sec) [ -9221.6649] [Alpha ][ 0.876656] . ( 50 sec) [ -9214.3897] [ 2046] [depth= 1] . ( 50 sec) [ -9212.3115] [ 2046] [depth= 1] . ( 50 sec) [ -9212.0305] [ 2046] [depth= 1] . ( 50 sec) [ -9211.9235] [ 2046] [depth= 1] . ( 50 sec) [ -9211.8882] [ 2046] [depth= 1] . ( 50 sec) [ -9211.1258] [ 2045] [depth= 1] . ( 51 sec) [ -9210.5856] [ 2050] [depth= 1] . ( 51 sec) [ -9210.4695] [ 2045] [depth= 1] . ( 51 sec) [ -9208.4230] [ 2048] [depth= 1] . ( 51 sec) [ -9200.4094] [ 2054] [depth= 1] . ( 51 sec) [ -9194.9303] [ 2057] [depth= 1] . ( 51 sec) [ -9194.8775] [ 2057] [depth= 4] . ( 51 sec) [ -9191.4959] [ 2059] [depth= 1] . ( 51 sec) [ -9190.8781] [ 2058] [depth= 1] . ( 51 sec) [ -9190.0593] [ 2061] [depth= 1] . ( 51 sec) [ -9189.6955] [ 2060] [depth= 1] . ( 52 sec) [ -9187.7893] [ 2065] [depth= 1] . ( 52 sec) [ -9187.5841] [ 2066] [depth= 1] . ( 52 sec) [ -9186.7844] [ 2071] [depth= 1] . ( 53 sec) [ -9159.8013] [Branch lengths ] . ( 53 sec) [ -9159.7196] [GTR parameters ] . ( 53 sec) [ -9159.7175] [Alpha ][ 0.880815] . ( 54 sec) [ -9159.7012] [ 2071] [depth= 1] . ( 54 sec) [ -9154.4040] [ 2068] [depth= 4] . ( 55 sec) [ -9153.6993] [ 2066] [depth= 1] . ( 55 sec) [ -9150.7759] [ 2070] [depth= 2] . ( 55 sec) [ -9150.0219] [ 2068] [depth= 2] . ( 55 sec) [ -9149.8851] [ 2064] [depth= 1] . ( 55 sec) [ -9149.7144] [ 2067] [depth= 1] . ( 55 sec) [ -9148.7675] [ 2070] [depth= 1] . ( 55 sec) [ -9147.4543] [ 2062] [depth= 1] . ( 56 sec) [ -9146.1291] [ 2056] [depth= 1] . ( 56 sec) [ -9139.5273] [Branch lengths ] . ( 57 sec) [ -9139.5110] [GTR parameters ] . ( 57 sec) [ -9139.4912] [Alpha ][ 0.893707] . ( 57 sec) [ -9138.7577] [ 2053] [depth= 1] . ( 58 sec) [ -9138.7451] [ 2048] [depth= 1] . ( 60 sec) [ -9135.5791] [Branch lengths ] . ( 60 sec) [ -9135.5657] [GTR parameters ] . ( 60 sec) [ -9135.5657] [Alpha ][ 0.893707] . ( 63 sec) [ -9135.2588] [Branch lengths ] . ( 85 sec) [ -9135.2299] [Branch lengths ] . ( 85 sec) [ -9135.2299] [Topology ] . ( 86 sec) [ -9135.2267] [Topology ] . ( 86 sec) [ -9135.2255] [Topology ] . ( 87 sec) [ -9135.2249] [Topology ] . ( 87 sec) [ -9135.2248] [GTR parameters ] . ( 87 sec) [ -9135.2248] [Alpha ][ 0.892814] . ( 87 sec) [ -9135.2248] [Topology ] . ( 88 sec) [ -9135.2244] [Topology ] . ( 88 sec) [ -9135.2244] [GTR parameters ] . ( 88 sec) [ -9135.2244] [Alpha ][ 0.892814] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9145.126630 . Log likelihood obtained after SPR moves : -9135.224424 . Log likelihood of the current tree: -9135.224424. . Printing the most likely tree in file 'data15.phy_phyml_tree.txt'... . Time used 0h1m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo