.......................... 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 ] . ( 5 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 6 sec) [ -7919.7111] [ 1130] [depth= 1] . ( 6 sec) [ -7892.1045] [ 1125] [depth= 1] . ( 6 sec) [ -7886.8255] [ 1122] [depth= 3] . ( 6 sec) [ -7877.2862] [ 1120] [depth= 2] . ( 6 sec) [ -7877.1208] [ 1120] [depth= 1] . ( 7 sec) [ -7877.0627] [ 1125] [depth= 1] . ( 8 sec) [ -7876.7699] [ 1125] [depth= 1] . ( 8 sec) [ -7876.5142] [ 1125] [depth= 1] . ( 8 sec) [ -7876.4680] [ 1125] [depth= 1] . ( 8 sec) [ -7876.4563] [ 1125] [depth= 2] . ( 10 sec) [ -7868.1623] [ 1124] [depth= 1] . ( 11 sec) [ -7864.8399] [ 1124] [depth= 1] . ( 11 sec) [ -7862.7022] [ 1124] [depth= 1] . ( 12 sec) [ -7843.2854] [ 1125] [depth= 2] . ( 12 sec) [ -7842.2243] [ 1124] [depth= 2] . ( 12 sec) [ -7841.6203] [ 1124] [depth= 1] . ( 12 sec) [ -7839.4831] [ 1126] [depth= 1] . ( 13 sec) [ -7839.1417] [ 1126] [depth= 2] . ( 13 sec) [ -7831.6930] [ 1124] [depth= 1] . ( 15 sec) [ -7831.6502] [ 1124] [depth= 1] . ( 15 sec) [ -7831.3547] [ 1124] [depth= 1] . ( 17 sec) [ -7801.4069] [ 1118] [depth= 9] . ( 17 sec) [ -7799.2532] [ 1118] [depth= 1] . ( 18 sec) [ -7798.0461] [ 1116] [depth= 1] . ( 19 sec) [ -7797.4228] [ 1116] [depth= 2] . ( 19 sec) [ -7796.2635] [ 1111] [depth= 1] . ( 19 sec) [ -7796.1892] [ 1111] [depth= 1] . ( 20 sec) [ -7795.6908] [ 1111] [depth= 2] . ( 20 sec) [ -7792.7022] [ 1110] [depth= 1] . ( 21 sec) [ -7790.1238] [ 1106] [depth= 2] . ( 21 sec) [ -7787.0310] [ 1108] [depth= 1] . ( 21 sec) [ -7785.8661] [ 1113] [depth= 2] . ( 21 sec) [ -7782.1952] [ 1111] [depth= 1] . ( 22 sec) [ -7782.0443] [ 1111] [depth= 1] . ( 22 sec) [ -7781.9054] [ 1111] [depth= 1] . ( 22 sec) [ -7779.6357] [ 1110] [depth= 4] . ( 22 sec) [ -7770.4001] [ 1108] [depth= 4] . ( 22 sec) [ -7770.0085] [ 1108] [depth= 3] . ( 22 sec) [ -7769.9503] [ 1108] [depth= 2] . ( 22 sec) [ -7769.8554] [ 1108] [depth= 1] . ( 23 sec) [ -7769.2906] [ 1108] [depth= 3] . ( 25 sec) [ -7764.6244] [ 1107] [depth= 2] . ( 27 sec) [ -7764.4946] [ 1107] [depth= 1] . ( 27 sec) [ -7764.3170] [ 1107] [depth= 1] . ( 27 sec) [ -7763.2778] [ 1107] [depth= 1] . ( 27 sec) [ -7762.1474] [ 1107] [depth= 2] . ( 27 sec) [ -7759.0507] [ 1106] [depth= 2] . ( 27 sec) [ -7745.5066] [ 1104] [depth= 6] . ( 28 sec) [ -7744.8654] [ 1104] [depth= 1] . ( 28 sec) [ -7744.0654] [ 1104] [depth= 1] . ( 28 sec) [ -7743.3889] [ 1104] [depth= 4] . ( 28 sec) [ -7743.2834] [ 1104] [depth= 2] . ( 28 sec) [ -7743.1033] [ 1104] [depth= 5] . ( 28 sec) [ -7742.9132] [ 1104] [depth= 2] . ( 29 sec) [ -7742.4479] [ 1104] [depth= 1] . ( 29 sec) [ -7741.9899] [ 1104] [depth= 2] . ( 29 sec) [ -7740.4884] [ 1104] [depth= 1] . ( 29 sec) [ -7740.0423] [ 1104] [depth= 1] . ( 29 sec) [ -7738.9481] [ 1104] [depth= 5] . ( 29 sec) [ -7738.9046] [ 1104] [depth= 2] . ( 31 sec) [ -7738.4793] [ 1104] [depth= 2] . ( 32 sec) [ -7738.4070] [ 1104] [depth= 2] . ( 32 sec) [ -7735.8995] [ 1103] [depth= 2] . ( 32 sec) [ -7734.5471] [ 1103] [depth= 1] . ( 33 sec) [ -7730.0867] [ 1103] [depth= 1] . ( 33 sec) [ -7725.6454] [ 1102] [depth= 1] . ( 34 sec) [ -7724.4190] [ 1101] [depth= 1] . ( 35 sec) [ -7723.8519] [ 1102] [depth= 1] . ( 35 sec) [ -7722.0237] [ 1103] [depth= 1] . ( 35 sec) [ -7721.5486] [ 1101] [depth= 2] . ( 39 sec) [ -7709.8143] [ 1097] [depth= 5] . ( 41 sec) [ -7708.0280] [ 1097] [depth= 1] . ( 41 sec) [ -7703.9997] [ 1096] [depth= 3] . ( 44 sec) [ -7703.7456] [ 1096] [depth= 3] . ( 44 sec) [ -7702.7360] [ 1096] [depth= 1] . ( 47 sec) [ -7702.5681] [ 1096] [depth= 1] . ( 47 sec) [ -7696.1772] [ 1095] [depth= 5] . ( 47 sec) [ -7695.9060] [ 1095] [depth= 1] . ( 47 sec) [ -7695.8919] [ 1095] [depth= 1] . ( 47 sec) [ -7695.5341] [ 1095] [depth= 1] . ( 47 sec) [ -7695.2087] [ 1095] [depth= 1] . ( 48 sec) [ -7695.0278] [ 1095] [depth= 2] . ( 48 sec) [ -7695.0169] [ 1095] [depth= 1] . ( 49 sec) [ -7694.9789] [ 1095] [depth= 2] . ( 49 sec) [ -7693.2273] [ 1095] [depth= 2] . ( 49 sec) [ -7693.2111] [ 1095] [depth= 1] . ( 49 sec) [ -7691.3352] [ 1095] [depth= 1] . ( 51 sec) [ -7691.2447] [ 1095] [depth= 1] . ( 52 sec) [ -7690.9288] [ 1095] [depth= 2] . ( 52 sec) [ -7690.7531] [ 1096] [depth= 1] . ( 53 sec) [ -7687.7345] [ 1095] [depth= 2] . ( 55 sec) [ -7687.1711] [ 1095] [depth= 1] . ( 55 sec) [ -7686.9963] [ 1095] [depth= 2] . ( 55 sec) [ -7686.2968] [ 1095] [depth= 1] . ( 57 sec) [ -7686.1829] [ 1095] [depth= 1] . ( 57 sec) [ -7686.1314] [ 1095] [depth= 1] . ( 57 sec) [ -7685.9541] [ 1095] [depth= 2] . ( 57 sec) [ -7685.9147] [ 1095] [depth= 1] . ( 58 sec) [ -7685.8379] [ 1095] [depth= 1] . ( 62 sec) [ -7685.8214] [ 1095] [depth= 2] . ( 65 sec) [ -7685.8069] [ 1095] [depth= 1] . ( 76 sec) [ -7649.0667] [Branch lengths ] . ( 80 sec) [ -7647.0248] [GTR parameters ] . ( 81 sec) [ -7644.2475] [Alpha ][ 0.419560] . ( 81 sec) [ -7643.8323] [ 1095] [depth= 2] . ( 81 sec) [ -7641.6625] [ 1091] [depth= 3] . ( 90 sec) [ -7641.5885] [ 1091] [depth= 2] . ( 100 sec) [ -7641.3998] [ 1091] [depth= 1] . ( 113 sec) [ -7641.3198] [ 1090] [depth= 4] . ( 126 sec) [ -7638.4145] [ 1090] [depth= 1] . ( 132 sec) [ -7638.3536] [ 1090] [depth= 1] . ( 133 sec) [ -7635.5466] [ 1090] [depth= 3] . ( 134 sec) [ -7635.4326] [ 1090] [depth= 1] . ( 136 sec) [ -7635.2003] [ 1090] [depth= 1] . ( 139 sec) [ -7635.1537] [ 1090] [depth= 2] . ( 156 sec) [ -7635.1233] [ 1090] [depth= 1] . ( 156 sec) [ -7635.0810] [ 1090] [depth= 1] . ( 173 sec) [ -7634.0090] [ 1091] [depth= 8] . ( 188 sec) [ -7626.2741] [Branch lengths ] . ( 189 sec) [ -7626.0033] [GTR parameters ] . ( 190 sec) [ -7625.8639] [Alpha ][ 0.403674] . ( 190 sec) [ -7625.5301] [ 1090] [depth= 2] . ( 258 sec) [ -7621.7836] [ 1089] [depth= 10] . ( 259 sec) [ -7621.6503] [ 1089] [depth= 2] . ( 260 sec) [ -7621.6189] [ 1089] [depth= 2] . ( 261 sec) [ -7621.3850] [ 1089] [depth= 2] . ( 261 sec) [ -7621.3606] [ 1089] [depth= 1] . ( 277 sec) [ -7620.8571] [ 1089] [depth= 2] . ( 278 sec) [ -7620.7856] [ 1089] [depth= 1] . ( 279 sec) [ -7620.6165] [ 1089] [depth= 2] . ( 279 sec) [ -7620.5806] [ 1089] [depth= 3] . ( 282 sec) [ -7620.5668] [ 1089] [depth= 1] . ( 299 sec) [ -7619.8380] [Branch lengths ] . ( 301 sec) [ -7619.8292] [GTR parameters ] . ( 301 sec) [ -7619.8117] [Alpha ][ 0.398061] . ( 302 sec) [ -7619.0202] [ 1092] [depth= 6] . ( 363 sec) [ -7618.9786] [ 1092] [depth= 4] . ( 366 sec) [ -7618.9589] [ 1092] [depth= 2] . ( 369 sec) [ -7618.9330] [ 1092] [depth= 4] . ( 410 sec) [ -7618.7644] [Branch lengths ] . ( 411 sec) [ -7618.7566] [GTR parameters ] . ( 411 sec) [ -7618.7484] [Alpha ][ 0.401814] . ( 412 sec) [ -7618.6018] [ 1093] [depth= 4] . ( 529 sec) [ -7618.5534] [Branch lengths ] . ( 530 sec) [ -7618.5532] [GTR parameters ] . ( 530 sec) [ -7618.5519] [Alpha ][ 0.403310] . ( 661 sec) [ -7618.5395] [Branch lengths ] . ( 661 sec) [ -7618.5395] [Topology ] . ( 663 sec) [ -7618.5374] [Topology ] . ( 666 sec) [ -7618.5363] [Topology ] . ( 668 sec) [ -7618.5356] [Topology ] . ( 669 sec) [ -7618.5356] [GTR parameters ] . ( 669 sec) [ -7618.5356] [Alpha ][ 0.403713] . ( 669 sec) [ -7618.5356] [Topology ] . ( 671 sec) [ -7618.5351] [Topology ] . ( 673 sec) [ -7618.5350] [GTR parameters ] . ( 673 sec) [ -7618.5350] [Alpha ][ 0.403713] . Checking for NNIs, optimizing five branches... . ( 690 sec) [ -7618.5338] [Topology ] . Checking for NNIs, optimizing five branches... . ( 706 sec) [ -7618.5337] [Topology ] . Checking for NNIs, optimizing five branches... . ( 723 sec) [ -7618.5285] [Topology ] . Checking for NNIs, optimizing five branches... . ( 739 sec) [ -7618.5257] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7618.525716. . Printing the most likely tree in file 'nucleic_M2933_99x1634_2006.phy_phyml_tree.txt'... . Time used 0h12m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 754.90user 0.00system 12:37.96elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps