.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2933_99x1634_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 578 patterns found. (out of a total of 1634 sites) . 1151 sites without polymorphism (70.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -7976.1365] [GTR parameters ] . ( 6 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 6 sec) [ -7910.4820] [ 1122] [depth= 3] . ( 6 sec) [ -7910.3003] [ 1122] [depth= 1] . ( 7 sec) [ -7910.2448] [ 1122] [depth= 1] . ( 7 sec) [ -7901.4919] [ 1120] [depth= 2] . ( 8 sec) [ -7901.1456] [ 1120] [depth= 1] . ( 8 sec) [ -7900.8690] [ 1120] [depth= 1] . ( 8 sec) [ -7900.7849] [ 1120] [depth= 1] . ( 8 sec) [ -7900.7743] [ 1120] [depth= 2] . ( 10 sec) [ -7892.3773] [ 1119] [depth= 1] . ( 10 sec) [ -7889.0328] [ 1119] [depth= 1] . ( 11 sec) [ -7887.5374] [ 1119] [depth= 1] . ( 11 sec) [ -7887.1773] [ 1119] [depth= 1] . ( 12 sec) [ -7887.0396] [ 1119] [depth= 2] . ( 12 sec) [ -7879.4261] [ 1117] [depth= 1] . ( 12 sec) [ -7879.3831] [ 1117] [depth= 1] . ( 12 sec) [ -7879.1255] [ 1117] [depth= 1] . ( 13 sec) [ -7875.5196] [ 1117] [depth= 1] . ( 13 sec) [ -7824.9585] [ 1111] [depth= 8] . ( 13 sec) [ -7819.8319] [ 1108] [depth= 1] . ( 14 sec) [ -7818.8319] [ 1108] [depth= 1] . ( 14 sec) [ -7800.3716] [ 1113] [depth= 3] . ( 15 sec) [ -7795.1906] [ 1113] [depth= 3] . ( 15 sec) [ -7791.5418] [ 1111] [depth= 2] . ( 15 sec) [ -7790.9924] [ 1111] [depth= 1] . ( 16 sec) [ -7790.8489] [ 1111] [depth= 1] . ( 16 sec) [ -7790.6995] [ 1111] [depth= 1] . ( 16 sec) [ -7788.5767] [ 1110] [depth= 4] . ( 16 sec) [ -7779.0905] [ 1108] [depth= 4] . ( 17 sec) [ -7778.7667] [ 1108] [depth= 3] . ( 17 sec) [ -7778.7367] [ 1108] [depth= 2] . ( 17 sec) [ -7778.6342] [ 1108] [depth= 1] . ( 17 sec) [ -7778.0860] [ 1108] [depth= 3] . ( 18 sec) [ -7773.3740] [ 1107] [depth= 2] . ( 18 sec) [ -7773.2935] [ 1107] [depth= 1] . ( 18 sec) [ -7773.1310] [ 1107] [depth= 1] . ( 19 sec) [ -7772.1283] [ 1107] [depth= 1] . ( 19 sec) [ -7771.3052] [ 1107] [depth= 2] . ( 19 sec) [ -7767.9333] [ 1106] [depth= 2] . ( 19 sec) [ -7754.6059] [ 1104] [depth= 6] . ( 20 sec) [ -7753.9951] [ 1104] [depth= 1] . ( 20 sec) [ -7753.1934] [ 1104] [depth= 1] . ( 20 sec) [ -7752.5072] [ 1104] [depth= 4] . ( 20 sec) [ -7752.4102] [ 1104] [depth= 2] . ( 20 sec) [ -7752.2367] [ 1104] [depth= 5] . ( 21 sec) [ -7752.0630] [ 1104] [depth= 2] . ( 21 sec) [ -7751.6098] [ 1104] [depth= 1] . ( 21 sec) [ -7751.4651] [ 1104] [depth= 1] . ( 21 sec) [ -7749.3465] [ 1104] [depth= 1] . ( 21 sec) [ -7748.8808] [ 1104] [depth= 2] . ( 21 sec) [ -7748.6488] [ 1104] [depth= 1] . ( 22 sec) [ -7748.6063] [ 1104] [depth= 1] . ( 22 sec) [ -7748.4833] [ 1104] [depth= 1] . ( 22 sec) [ -7748.3381] [ 1104] [depth= 1] . ( 22 sec) [ -7743.5012] [ 1105] [depth= 1] . ( 22 sec) [ -7741.3209] [ 1104] [depth= 2] . ( 23 sec) [ -7738.1186] [ 1103] [depth= 2] . ( 23 sec) [ -7737.8014] [ 1103] [depth= 1] . ( 23 sec) [ -7735.8622] [ 1104] [depth= 2] . ( 23 sec) [ -7733.6203] [ 1103] [depth= 1] . ( 23 sec) [ -7732.8352] [ 1102] [depth= 1] . ( 24 sec) [ -7731.0884] [ 1104] [depth= 2] . ( 24 sec) [ -7729.6590] [ 1096] [depth= 3] . ( 24 sec) [ -7729.6464] [ 1096] [depth= 1] . ( 24 sec) [ -7728.1899] [ 1094] [depth= 5] . ( 25 sec) [ -7726.9109] [ 1094] [depth= 6] . ( 25 sec) [ -7726.1593] [ 1094] [depth= 1] . ( 25 sec) [ -7709.3490] [ 1094] [depth= 4] . ( 25 sec) [ -7706.9059] [ 1091] [depth= 4] . ( 25 sec) [ -7701.7291] [ 1091] [depth= 1] . ( 26 sec) [ -7701.4812] [ 1091] [depth= 1] . ( 26 sec) [ -7701.4661] [ 1091] [depth= 1] . ( 26 sec) [ -7701.2372] [ 1091] [depth= 1] . ( 26 sec) [ -7701.2044] [ 1091] [depth= 2] . ( 26 sec) [ -7701.1511] [ 1091] [depth= 3] . ( 26 sec) [ -7701.1392] [ 1091] [depth= 3] . ( 26 sec) [ -7700.8710] [ 1091] [depth= 1] . ( 27 sec) [ -7699.3408] [ 1091] [depth= 3] . ( 27 sec) [ -7699.1503] [ 1091] [depth= 2] . ( 27 sec) [ -7699.0074] [ 1091] [depth= 1] . ( 28 sec) [ -7698.5749] [ 1091] [depth= 2] . ( 28 sec) [ -7695.2048] [ 1090] [depth= 1] . ( 28 sec) [ -7694.7069] [ 1090] [depth= 1] . ( 29 sec) [ -7694.4599] [ 1090] [depth= 1] . ( 29 sec) [ -7694.2176] [ 1090] [depth= 1] . ( 29 sec) [ -7694.1791] [ 1090] [depth= 1] . ( 30 sec) [ -7694.1290] [ 1090] [depth= 1] . ( 31 sec) [ -7694.1175] [ 1090] [depth= 4] . ( 32 sec) [ -7694.1022] [ 1090] [depth= 1] . ( 36 sec) [ -7649.8923] [Branch lengths ] . ( 42 sec) [ -7648.6111] [GTR parameters ] . ( 42 sec) [ -7646.2990] [Alpha ][ 0.424726] . ( 43 sec) [ -7645.8697] [ 1095] [depth= 2] . ( 43 sec) [ -7645.8592] [ 1095] [depth= 1] . ( 44 sec) [ -7644.1625] [ 1092] [depth= 1] . ( 46 sec) [ -7644.0714] [ 1092] [depth= 2] . ( 47 sec) [ -7644.0542] [ 1092] [depth= 1] . ( 48 sec) [ -7643.3462] [ 1093] [depth= 1] . ( 50 sec) [ -7643.3362] [ 1093] [depth= 2] . ( 50 sec) [ -7643.3222] [ 1093] [depth= 1] . ( 52 sec) [ -7643.2643] [ 1093] [depth= 2] . ( 52 sec) [ -7643.2496] [ 1093] [depth= 1] . ( 54 sec) [ -7642.7634] [ 1093] [depth= 1] . ( 54 sec) [ -7642.6062] [ 1093] [depth= 1] . ( 54 sec) [ -7642.4294] [ 1093] [depth= 3] . ( 55 sec) [ -7642.0067] [ 1093] [depth= 1] . ( 55 sec) [ -7641.9104] [ 1093] [depth= 2] . ( 55 sec) [ -7638.9126] [ 1092] [depth= 1] . ( 56 sec) [ -7638.8015] [ 1092] [depth= 1] . ( 57 sec) [ -7635.5761] [ 1092] [depth= 5] . ( 58 sec) [ -7635.1382] [ 1092] [depth= 1] . ( 59 sec) [ -7635.1167] [ 1092] [depth= 1] . ( 59 sec) [ -7635.1051] [ 1092] [depth= 1] . ( 60 sec) [ -7635.0857] [ 1092] [depth= 1] . ( 60 sec) [ -7635.0622] [ 1092] [depth= 1] . ( 61 sec) [ -7635.0486] [ 1092] [depth= 1] . ( 70 sec) [ -7628.9913] [Branch lengths ] . ( 75 sec) [ -7628.6022] [GTR parameters ] . ( 76 sec) [ -7628.4589] [Alpha ][ 0.408307] . ( 77 sec) [ -7628.3632] [ 1092] [depth= 1] . ( 96 sec) [ -7628.1825] [ 1091] [depth= 4] . ( 131 sec) [ -7626.8879] [Branch lengths ] . ( 137 sec) [ -7626.8794] [GTR parameters ] . ( 138 sec) [ -7626.8698] [Alpha ][ 0.404048] . ( 151 sec) [ -7626.8191] [ 1093] [depth= 1] . ( 152 sec) [ -7626.7243] [ 1093] [depth= 1] . ( 185 sec) [ -7626.3556] [Branch lengths ] . ( 188 sec) [ -7626.3531] [GTR parameters ] . ( 188 sec) [ -7626.3527] [Alpha ][ 0.403226] . ( 193 sec) [ -7626.3391] [ 1094] [depth= 1] . ( 283 sec) [ -7626.2156] [ 1094] [depth= 1] . ( 392 sec) [ -7625.9969] [ 1095] [depth= 8] . ( 393 sec) [ -7625.7823] [ 1095] [depth= 9] . ( 395 sec) [ -7625.2247] [ 1095] [depth= 9] . ( 396 sec) [ -7625.2145] [ 1095] [depth= 2] . ( 410 sec) [ -7624.6800] [Branch lengths ] . ( 414 sec) [ -7624.6486] [GTR parameters ] . ( 414 sec) [ -7624.6473] [Alpha ][ 0.401656] . ( 419 sec) [ -7624.5793] [ 1095] [depth= 2] . ( 484 sec) [ -7624.4292] [ 1095] [depth= 1] . ( 575 sec) [ -7620.7854] [ 1094] [depth= 5] . ( 577 sec) [ -7620.6483] [ 1094] [depth= 1] . ( 577 sec) [ -7620.5340] [ 1094] [depth= 1] . ( 578 sec) [ -7620.4696] [ 1094] [depth= 1] . ( 578 sec) [ -7620.4564] [ 1094] [depth= 3] . ( 579 sec) [ -7620.4444] [ 1094] [depth= 1] . ( 587 sec) [ -7620.4103] [ 1094] [depth= 1] . ( 588 sec) [ -7620.3770] [ 1094] [depth= 3] . ( 590 sec) [ -7620.1160] [ 1094] [depth= 1] . ( 593 sec) [ -7620.1028] [ 1094] [depth= 1] . ( 594 sec) [ -7619.8634] [ 1094] [depth= 1] . ( 596 sec) [ -7619.8142] [ 1094] [depth= 1] . ( 596 sec) [ -7619.2688] [ 1094] [depth= 1] . ( 599 sec) [ -7619.2407] [ 1094] [depth= 1] . ( 623 sec) [ -7618.7744] [Branch lengths ] . ( 627 sec) [ -7618.7615] [GTR parameters ] . ( 627 sec) [ -7618.7610] [Alpha ][ 0.402596] . ( 633 sec) [ -7618.6978] [ 1094] [depth= 1] . ( 786 sec) [ -7618.3381] [ 1094] [depth= 2] . ( 788 sec) [ -7618.3166] [ 1094] [depth= 1] . ( 788 sec) [ -7618.2692] [ 1094] [depth= 1] . ( 796 sec) [ -7618.2491] [ 1094] [depth= 1] . ( 807 sec) [ -7618.2314] [ 1094] [depth= 1] . ( 818 sec) [ -7618.1850] [ 1094] [depth= 3] . ( 820 sec) [ -7618.1670] [ 1094] [depth= 1] . ( 845 sec) [ -7617.9002] [Branch lengths ] . ( 848 sec) [ -7617.8971] [GTR parameters ] . ( 848 sec) [ -7617.8970] [Alpha ][ 0.402071] . ( 849 sec) [ -7617.8970] [Topology ] . ( 852 sec) [ -7617.4728] [Topology ] . ( 855 sec) [ -7617.4404] [Topology ] . ( 858 sec) [ -7617.4358] [Topology ] . ( 862 sec) [ -7617.4346] [Topology ] . ( 865 sec) [ -7617.4341] [Topology ] . ( 867 sec) [ -7617.4320] [GTR parameters ] . ( 867 sec) [ -7617.4320] [Alpha ][ 0.402071] . ( 868 sec) [ -7617.4320] [Topology ] . ( 871 sec) [ -7617.4318] [Topology ] . ( 873 sec) [ -7617.4312] [GTR parameters ] . ( 873 sec) [ -7617.4312] [Alpha ][ 0.402071] . Checking for NNIs, optimizing five branches... . ( 898 sec) [ -7617.3462] [Topology ] . Checking for NNIs, optimizing five branches... . ( 924 sec) [ -7617.3461] [Topology ] . Checking for NNIs, optimizing five branches... . ( 948 sec) [ -7617.3450] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7617.344969. . Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'... . Time used 0h16m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 594.88user 0.00system 16:16.21elapsed 60%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps