.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data65.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... . 462 patterns found. (out of a total of 500 sites) . 38 sites without polymorphism (7.60%). . 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=-12251.477966 . ( 1 sec) [ -12240.5369] [GTR parameters ] . ( 1 sec) [ -12240.5293] [Alpha ][ 0.991383] . ( 1 sec) [ -12240.5293] [Topology ] . ( 2 sec) [ -12159.4656] [Topology ] . ( 3 sec) [ -12146.8006] [Topology ] . ( 5 sec) [ -12143.2282] [Topology ] . ( 6 sec) [ -12141.6547] [Topology ] . ( 7 sec) [ -12140.8761] [Topology ] . ( 8 sec) [ -12140.4867] [Topology ] . ( 8 sec) [ -12140.2849] [Topology ] . ( 9 sec) [ -12140.1779] [Topology ] . ( 10 sec) [ -12140.1204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -12139.8651] [Topology ] . Before opt ts/t=1.000000 LK=-12139.865084 . ( 21 sec) [ -12139.8452] [GTR parameters ] . ( 21 sec) [ -12139.7702] [Alpha ][ 1.016211] . ( 21 sec) [ -12139.7702] [Topology ] . ( 22 sec) [ -12139.7053] [Topology ] . ( 23 sec) [ -12139.6804] [Topology ] . ( 24 sec) [ -12139.6684] [Topology ] . ( 25 sec) [ -12139.6624] [Topology ] . ( 26 sec) [ -12139.6592] [Topology ] . ( 27 sec) [ -12139.6575] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-12139.657526 . ( 36 sec) [ -12139.6575] [GTR parameters ] . ( 36 sec) [ -12139.6575] [Alpha ][ 1.016211] . ( 36 sec) [ -12139.6575] [Topology ] . ( 37 sec) [ -12139.6566] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -12240.5369] [GTR parameters ] . ( 52 sec) [ -12240.5293] [Alpha ][ 0.991383] . ( 53 sec) [ -12237.5201] [ 2943] [depth= 1] . ( 53 sec) [ -12231.2679] [ 2927] [depth= 1] . ( 53 sec) [ -12229.4686] [ 2926] [depth= 1] . ( 53 sec) [ -12228.5852] [ 2929] [depth= 1] . ( 53 sec) [ -12228.4600] [ 2928] [depth= 1] . ( 54 sec) [ -12224.3122] [ 2931] [depth= 1] . ( 54 sec) [ -12222.4618] [ 2932] [depth= 1] . ( 54 sec) [ -12222.1608] [ 2929] [depth= 1] . ( 54 sec) [ -12222.0913] [ 2932] [depth= 1] . ( 54 sec) [ -12214.5512] [ 2931] [depth= 1] . ( 54 sec) [ -12211.7479] [ 2932] [depth= 1] . ( 54 sec) [ -12210.7900] [ 2937] [depth= 1] . ( 54 sec) [ -12210.1804] [ 2955] [depth= 1] . ( 54 sec) [ -12209.7823] [ 2937] [depth= 1] . ( 54 sec) [ -12200.1387] [ 2951] [depth= 1] . ( 55 sec) [ -12195.1253] [ 2937] [depth= 1] . ( 55 sec) [ -12193.2460] [ 2939] [depth= 1] . ( 55 sec) [ -12190.0434] [ 2937] [depth= 1] . ( 56 sec) [ -12189.1867] [ 2933] [depth= 1] . ( 56 sec) [ -12188.4718] [ 2937] [depth= 1] . ( 56 sec) [ -12145.4907] [Branch lengths ] . ( 56 sec) [ -12145.4730] [GTR parameters ] . ( 57 sec) [ -12145.4420] [Alpha ][ 1.007665] . ( 58 sec) [ -12145.4124] [ 2938] [depth= 1] . ( 61 sec) [ -12141.1985] [Branch lengths ] . ( 61 sec) [ -12141.1976] [GTR parameters ] . ( 61 sec) [ -12141.1897] [Alpha ][ 1.015800] . ( 66 sec) [ -12140.5952] [Branch lengths ] . ( 95 sec) [ -12140.0055] [ 2934] [depth= 1] . ( 97 sec) [ -12139.7272] [Branch lengths ] . ( 97 sec) [ -12139.7259] [GTR parameters ] . ( 97 sec) [ -12139.7259] [Alpha ][ 1.015800] . ( 98 sec) [ -12139.7259] [Topology ] . ( 98 sec) [ -12139.6759] [Topology ] . ( 99 sec) [ -12139.6653] [Topology ] . ( 100 sec) [ -12139.6606] [Topology ] . ( 101 sec) [ -12139.6583] [Topology ] . ( 102 sec) [ -12139.6570] [Topology ] . ( 103 sec) [ -12139.6564] [Topology ] . ( 103 sec) [ -12139.6564] [GTR parameters ] . ( 104 sec) [ -12139.6564] [Alpha ][ 1.015800] . ( 104 sec) [ -12139.6564] [Topology ] . ( 105 sec) [ -12139.6560] [Topology ] . ( 105 sec) [ -12139.6560] [GTR parameters ] . ( 105 sec) [ -12139.6560] [Alpha ][ 1.015800] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12139.656578 . Log likelihood obtained after SPR moves : -12139.655976 . Log likelihood of the current tree: -12139.655976. . Printing the most likely tree in file 'data65.phy_phyml_tree.txt'... . Time used 0h1m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo