.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data8.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... . 419 patterns found. (out of a total of 500 sites) . 76 sites without polymorphism (15.20%). . 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=-8988.698459 . ( 1 sec) [ -8984.7515] [GTR parameters ] . ( 1 sec) [ -8984.0081] [Alpha ][ 0.908527] . ( 1 sec) [ -8984.0081] [Topology ] . ( 2 sec) [ -8898.6998] [Topology ] . ( 3 sec) [ -8882.6992] [Topology ] . ( 4 sec) [ -8878.8739] [Topology ] . ( 5 sec) [ -8877.7173] [Topology ] . ( 6 sec) [ -8877.2412] [Topology ] . ( 7 sec) [ -8876.9976] [Topology ] . ( 7 sec) [ -8876.8604] [Topology ] . ( 8 sec) [ -8876.7778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -8876.3657] [Topology ] . Before opt ts/t=1.000000 LK=-8876.365684 . ( 19 sec) [ -8875.9438] [GTR parameters ] . ( 20 sec) [ -8875.8939] [Alpha ][ 0.888108] . ( 20 sec) [ -8875.8939] [Topology ] . ( 21 sec) [ -8875.7268] [Topology ] . ( 22 sec) [ -8875.0780] [Topology ] . ( 23 sec) [ -8874.8683] [Topology ] . ( 24 sec) [ -8874.7383] [Topology ] . ( 25 sec) [ -8874.6503] [Topology ] . ( 26 sec) [ -8874.5883] [Topology ] . ( 26 sec) [ -8874.5429] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.542850 . ( 34 sec) [ -8874.5400] [GTR parameters ] . ( 34 sec) [ -8874.5400] [Alpha ][ 0.888108] . ( 34 sec) [ -8874.5400] [Topology ] . ( 36 sec) [ -8874.5064] [Topology ] . ( 37 sec) [ -8874.4814] [Topology ] . ( 38 sec) [ -8874.4629] [Topology ] . ( 38 sec) [ -8874.4489] [Topology ] . ( 40 sec) [ -8874.4384] [Topology ] . ( 41 sec) [ -8874.4303] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.430347 . ( 51 sec) [ -8874.4303] [GTR parameters ] . ( 51 sec) [ -8874.4303] [Alpha ][ 0.888108] . ( 51 sec) [ -8874.4303] [Topology ] . ( 52 sec) [ -8874.4241] [Topology ] . ( 54 sec) [ -8874.4193] [Topology ] . ( 55 sec) [ -8874.4156] [Topology ] . ( 56 sec) [ -8874.4128] [Topology ] . ( 57 sec) [ -8874.4105] [Topology ] . ( 58 sec) [ -8874.4088] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.408835 . ( 69 sec) [ -8874.4088] [GTR parameters ] . ( 69 sec) [ -8874.4088] [Alpha ][ 0.888108] . ( 69 sec) [ -8874.4088] [Topology ] . ( 70 sec) [ -8874.4075] [Topology ] . ( 71 sec) [ -8874.4065] [Topology ] . ( 72 sec) [ -8874.4057] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.405690 . ( 82 sec) [ -8874.4057] [GTR parameters ] . ( 83 sec) [ -8874.4057] [Alpha ][ 0.888108] . ( 83 sec) [ -8874.4057] [Topology ] . ( 84 sec) [ -8874.4051] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 106 sec) [ -8984.7515] [GTR parameters ] . ( 107 sec) [ -8984.0081] [Alpha ][ 0.908527] . ( 107 sec) [ -8981.9228] [ 1952] [depth= 1] . ( 107 sec) [ -8980.7063] [ 1952] [depth= 1] . ( 107 sec) [ -8980.6844] [ 1952] [depth= 1] . ( 107 sec) [ -8980.6147] [ 1952] [depth= 1] . ( 108 sec) [ -8970.6809] [ 1950] [depth= 1] . ( 108 sec) [ -8968.5819] [ 1950] [depth= 3] . ( 108 sec) [ -8960.8257] [ 1952] [depth= 1] . ( 109 sec) [ -8952.0226] [ 1960] [depth= 1] . ( 109 sec) [ -8948.0852] [ 1973] [depth= 1] . ( 109 sec) [ -8947.8460] [ 1975] [depth= 1] . ( 109 sec) [ -8945.7109] [ 1977] [depth= 1] . ( 109 sec) [ -8944.2047] [ 1975] [depth= 1] . ( 109 sec) [ -8939.4866] [ 1964] [depth= 1] . ( 110 sec) [ -8938.3876] [ 1965] [depth= 1] . ( 110 sec) [ -8937.4598] [ 1964] [depth= 1] . ( 110 sec) [ -8935.9631] [ 1965] [depth= 1] . ( 110 sec) [ -8934.9123] [ 1965] [depth= 1] . ( 110 sec) [ -8934.6651] [ 1965] [depth= 1] . ( 110 sec) [ -8933.9542] [ 1965] [depth= 1] . ( 111 sec) [ -8927.3424] [ 1978] [depth= 2] . ( 111 sec) [ -8925.6618] [ 1977] [depth= 1] . ( 111 sec) [ -8925.3041] [ 1982] [depth= 1] . ( 111 sec) [ -8924.9177] [ 1981] [depth= 1] . ( 111 sec) [ -8921.8065] [ 1989] [depth= 1] . ( 111 sec) [ -8921.6984] [ 1992] [depth= 1] . ( 111 sec) [ -8919.9112] [ 1989] [depth= 1] . ( 111 sec) [ -8919.8347] [ 1978] [depth= 2] . ( 112 sec) [ -8919.5004] [ 1981] [depth= 1] . ( 112 sec) [ -8919.3624] [ 1981] [depth= 1] . ( 113 sec) [ -8892.7533] [Branch lengths ] . ( 113 sec) [ -8892.5878] [GTR parameters ] . ( 113 sec) [ -8892.4633] [Alpha ][ 0.875672] . ( 115 sec) [ -8892.4182] [ 1986] [depth= 1] . ( 115 sec) [ -8884.0682] [ 1979] [depth= 3] . ( 116 sec) [ -8883.9909] [ 1982] [depth= 1] . ( 116 sec) [ -8882.9711] [ 1985] [depth= 1] . ( 116 sec) [ -8880.9338] [ 1964] [depth= 1] . ( 117 sec) [ -8880.8322] [ 1962] [depth= 1] . ( 119 sec) [ -8876.9242] [Branch lengths ] . ( 119 sec) [ -8876.8415] [GTR parameters ] . ( 119 sec) [ -8876.8275] [Alpha ][ 0.886633] . ( 120 sec) [ -8876.7900] [ 1959] [depth= 1] . ( 124 sec) [ -8876.2734] [Branch lengths ] . ( 124 sec) [ -8876.2732] [GTR parameters ] . ( 124 sec) [ -8876.2732] [Alpha ][ 0.886633] . ( 136 sec) [ -8875.9278] [ 1968] [depth= 2] . ( 148 sec) [ -8875.8592] [ 1969] [depth= 1] . ( 149 sec) [ -8875.7478] [ 1970] [depth= 1] . ( 150 sec) [ -8875.7160] [ 1968] [depth= 1] . ( 153 sec) [ -8875.1211] [Branch lengths ] . ( 153 sec) [ -8875.1195] [GTR parameters ] . ( 153 sec) [ -8875.1195] [Alpha ][ 0.886633] . ( 165 sec) [ -8874.8589] [ 1970] [depth= 1] . ( 184 sec) [ -8874.8301] [Branch lengths ] . ( 184 sec) [ -8874.8289] [GTR parameters ] . ( 185 sec) [ -8874.8289] [Alpha ][ 0.885746] . ( 185 sec) [ -8874.8289] [Topology ] . ( 186 sec) [ -8874.8233] [Topology ] . ( 187 sec) [ -8874.8202] [Topology ] . ( 189 sec) [ -8874.8180] [Topology ] . ( 190 sec) [ -8874.8164] [Topology ] . ( 191 sec) [ -8874.8153] [Topology ] . ( 193 sec) [ -8874.8144] [Topology ] . ( 193 sec) [ -8874.8143] [GTR parameters ] . ( 193 sec) [ -8874.8143] [Alpha ][ 0.886632] . ( 193 sec) [ -8874.8143] [Topology ] . ( 195 sec) [ -8874.8135] [Topology ] . ( 195 sec) [ -8874.8135] [GTR parameters ] . ( 195 sec) [ -8874.8135] [Alpha ][ 0.886632] . Checking for NNIs, optimizing five branches... . ( 207 sec) [ -8874.4160] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8874.405073 . Log likelihood obtained after SPR moves : -8874.416035 . Log likelihood of the current tree: -8874.405073. . Printing the most likely tree in file 'data8.phy_phyml_tree.txt'... . Time used 0h3m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo