.......................... 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 : 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 . 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 NNI moves)... . ( 5 sec) [ -7976.1365] [GTR parameters ] . ( 5 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 5 sec) [ -7938.7269] [Topology ] . ( 8 sec) [ -7771.5480] [Topology ] . ( 11 sec) [ -7728.7608] [Topology ] . ( 13 sec) [ -7700.1450] [Topology ] . ( 16 sec) [ -7680.7802] [Topology ] . ( 18 sec) [ -7678.2991] [Topology ] . ( 21 sec) [ -7676.5846] [Topology ] . ( 23 sec) [ -7674.6303] [Topology ] . ( 25 sec) [ -7667.7629] [Topology ] . ( 28 sec) [ -7667.4228] [Topology ] . ( 34 sec) [ -7664.6970] [GTR parameters ] . ( 35 sec) [ -7661.5225] [Alpha ][ 0.415125] . ( 35 sec) [ -7661.5225] [Topology ] . ( 37 sec) [ -7661.1540] [Topology ] . ( 40 sec) [ -7660.4607] [Topology ] . ( 42 sec) [ -7661.0734] [Topology ] . Moving backward . ( 42 sec) [ -7660.1118] [Topology ] . ( 45 sec) [ -7660.4785] [Topology ] . Moving backward . ( 45 sec) [ -7659.9803] [Topology ] . ( 48 sec) [ -7659.9438] [Topology ] . ( 50 sec) [ -7660.2313] [Topology ] . Moving backward . ( 50 sec) [ -7659.9080] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -7659.7717] [Topology ] . ( 72 sec) [ -7659.7392] [GTR parameters ] . ( 72 sec) [ -7659.5438] [Alpha ][ 0.396820] . ( 73 sec) [ -7659.5438] [Topology ] . ( 75 sec) [ -7659.7614] [Topology ] . Moving backward . ( 75 sec) [ -7659.4154] [Topology ] . ( 77 sec) [ -7659.3894] [Topology ] . ( 80 sec) [ -7659.7340] [Topology ] . Moving backward . ( 80 sec) [ -7659.3474] [Topology ] . ( 82 sec) [ -7659.3732] [Topology ] . Moving backward . ( 82 sec) [ -7659.3316] [Topology ] . ( 85 sec) [ -7659.3403] [Topology ] . Moving backward . ( 85 sec) [ -7659.3246] [Topology ] . Checking for NNIs, optimizing five branches... . ( 103 sec) [ -7659.2657] [Topology ] . ( 105 sec) [ -7659.2579] [GTR parameters ] . ( 105 sec) [ -7659.2400] [Alpha ][ 0.391325] . ( 105 sec) [ -7659.2400] [Topology ] . ( 108 sec) [ -7659.2530] [Topology ] . Moving backward . ( 108 sec) [ -7659.2325] [Topology ] . ( 110 sec) [ -7659.2332] [Topology ] . Checking for NNIs, optimizing five branches... . ( 127 sec) [ -7657.6420] [Topology ] . ( 129 sec) [ -7657.6412] [GTR parameters ] . ( 129 sec) [ -7657.6385] [Alpha ][ 0.393389] . ( 129 sec) [ -7657.6385] [Topology ] . ( 132 sec) [ -7657.6576] [Topology ] . Moving backward . ( 132 sec) [ -7657.6330] [Topology ] . ( 134 sec) [ -7657.6358] [Topology ] . Moving backward . ( 134 sec) [ -7657.6308] [Topology ] . ( 136 sec) [ -7657.6310] [Topology ] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -7657.6300] [Topology ] . ( 155 sec) [ -7657.6295] [GTR parameters ] . ( 155 sec) [ -7657.6294] [Alpha ][ 0.393782] . ( 155 sec) [ -7657.6294] [Topology ] . ( 157 sec) [ -7657.6331] [Topology ] . Moving backward . ( 157 sec) [ -7657.6281] [Topology ] . ( 160 sec) [ -7657.6289] [Topology ] . Checking for NNIs, optimizing five branches... . ( 176 sec) [ -7655.6257] [Topology ] . ( 178 sec) [ -7655.6247] [GTR parameters ] . ( 178 sec) [ -7655.6246] [Alpha ][ 0.394176] . ( 178 sec) [ -7655.6246] [Topology ] . ( 181 sec) [ -7655.6246] [Topology ] . Checking for NNIs, optimizing five branches... . ( 198 sec) [ -7655.6241] [Topology ] . ( 198 sec) [ -7655.6240] [GTR parameters ] . ( 198 sec) [ -7655.6240] [Alpha ][ 0.394176] . ( 198 sec) [ -7655.6240] [Topology ] . ( 201 sec) [ -7655.6365] [Topology ] . Moving backward . ( 201 sec) [ -7655.6196] [Topology ] . ( 203 sec) [ -7655.6137] [Topology ] . ( 205 sec) [ -7655.6234] [Topology ] . Moving backward . ( 205 sec) [ -7655.6064] [Topology ] . ( 208 sec) [ -7655.6022] [Topology ] . ( 210 sec) [ -7655.6164] [Topology ] . Moving backward . ( 210 sec) [ -7655.5950] [Topology ] . ( 213 sec) [ -7655.5924] [Topology ] . Checking for NNIs, optimizing five branches... . ( 229 sec) [ -7655.5921] [Topology ] . ( 230 sec) [ -7655.5921] [GTR parameters ] . ( 230 sec) [ -7655.5921] [Alpha ][ 0.394176] . ( 230 sec) [ -7655.5921] [Topology ] . ( 232 sec) [ -7655.6091] [Topology ] . Moving backward . ( 232 sec) [ -7655.5843] [Topology ] . ( 235 sec) [ -7655.5781] [Topology ] . ( 237 sec) [ -7655.6019] [Topology ] . Moving backward . ( 237 sec) [ -7655.5687] [Topology ] . ( 239 sec) [ -7655.5646] [Topology ] . ( 242 sec) [ -7655.0309] [Topology ] . ( 244 sec) [ -7653.2849] [Topology ] . ( 246 sec) [ -7652.7476] [Topology ] . Checking for NNIs, optimizing five branches... . ( 266 sec) [ -7652.7052] [Topology ] . ( 269 sec) [ -7652.6955] [GTR parameters ] . ( 269 sec) [ -7652.6930] [Alpha ][ 0.396188] . ( 269 sec) [ -7652.6930] [Topology ] . ( 271 sec) [ -7652.1134] [Topology ] . ( 274 sec) [ -7652.3556] [Topology ] . Moving backward . ( 274 sec) [ -7652.0414] [Topology ] . ( 276 sec) [ -7652.3909] [Topology ] . Moving backward . ( 276 sec) [ -7651.9902] [Topology ] . ( 279 sec) [ -7652.0309] [Topology ] . Moving backward . ( 279 sec) [ -7651.9729] [Topology ] . ( 281 sec) [ -7652.0462] [Topology ] . Moving backward . ( 281 sec) [ -7651.9610] [Topology ] . Checking for NNIs, optimizing five branches... . ( 300 sec) [ -7651.9756] [Topology ] . ( 301 sec) [ -7651.9756] [GTR parameters ] . ( 301 sec) [ -7651.9756] [Alpha ][ 0.396584] . ( 301 sec) [ -7651.9756] [Topology ] . ( 303 sec) [ -7652.3305] [Topology ] . Moving backward . ( 303 sec) [ -7651.9232] [Topology ] . ( 306 sec) [ -7651.9725] [Topology ] . Moving backward . ( 306 sec) [ -7651.9121] [Topology ] . ( 308 sec) [ -7651.9917] [Topology ] . Moving backward . ( 308 sec) [ -7651.9069] [Topology ] . ( 311 sec) [ -7651.9446] [Topology ] . Moving backward . ( 311 sec) [ -7651.9018] [Topology ] . ( 313 sec) [ -7651.9575] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 330 sec) [ -7651.8985] [Topology ] . ( 331 sec) [ -7651.8984] [GTR parameters ] . ( 331 sec) [ -7651.8984] [Alpha ][ 0.396584] . ( 331 sec) [ -7651.8984] [Topology ] . ( 333 sec) [ -7651.9250] [Topology ] . Moving backward . ( 333 sec) [ -7651.8946] [Topology ] . ( 336 sec) [ -7651.9260] [Topology ] . Moving backward . ( 336 sec) [ -7651.8920] [Topology ] . ( 338 sec) [ -7651.9111] [Topology ] . Moving backward . ( 338 sec) [ -7651.8902] [Topology ] . ( 341 sec) [ -7651.9102] [Topology ] . Moving backward . ( 341 sec) [ -7651.8880] [Topology ] . ( 343 sec) [ -7651.8988] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 360 sec) [ -7651.8863] [Topology ] . ( 361 sec) [ -7651.8863] [GTR parameters ] . ( 361 sec) [ -7651.8863] [Alpha ][ 0.396584] . ( 361 sec) [ -7651.8863] [Topology ] . ( 363 sec) [ -7651.8959] [Topology ] . Moving backward . ( 363 sec) [ -7651.8848] [Topology ] . ( 366 sec) [ -7651.8900] [Topology ] . Moving backward . ( 366 sec) [ -7651.8836] [Topology ] . ( 368 sec) [ -7651.8880] [Topology ] . Moving backward . ( 368 sec) [ -7651.8825] [Topology ] . ( 371 sec) [ -7651.8849] [Topology ] . Moving backward . ( 371 sec) [ -7651.8816] [Topology ] . Checking for NNIs, optimizing five branches... . ( 387 sec) [ -7650.2293] [Topology ] . ( 389 sec) [ -7650.2177] [GTR parameters ] . ( 389 sec) [ -7650.2175] [Alpha ][ 0.397081] . ( 389 sec) [ -7650.2175] [Topology ] . ( 391 sec) [ -7649.5030] [Topology ] . ( 393 sec) [ -7649.4525] [Topology ] . ( 396 sec) [ -7649.3903] [Topology ] . ( 398 sec) [ -7649.5926] [Topology ] . Moving backward . ( 398 sec) [ -7649.3115] [Topology ] . ( 401 sec) [ -7649.2912] [Topology ] . ( 403 sec) [ -7649.4242] [Topology ] . Checking for NNIs, optimizing five branches... . ( 420 sec) [ -7649.0423] [Topology ] . ( 422 sec) [ -7649.0379] [GTR parameters ] . ( 423 sec) [ -7649.0379] [Alpha ][ 0.397081] . ( 423 sec) [ -7649.0379] [Topology ] . ( 425 sec) [ -7648.9056] [Topology ] . ( 427 sec) [ -7648.8291] [Topology ] . ( 430 sec) [ -7648.7451] [Topology ] . ( 432 sec) [ -7648.6669] [Topology ] . ( 435 sec) [ -7648.6457] [Topology ] . ( 437 sec) [ -7648.6412] [Topology ] . Checking for NNIs, optimizing five branches... . ( 454 sec) [ -7648.6407] [Topology ] . ( 454 sec) [ -7648.6407] [GTR parameters ] . ( 454 sec) [ -7648.6407] [Alpha ][ 0.397081] . ( 454 sec) [ -7648.6407] [Topology ] . ( 457 sec) [ -7648.6396] [Topology ] . ( 459 sec) [ -7648.6389] [Topology ] . Checking for NNIs, optimizing five branches... . ( 476 sec) [ -7648.6296] [Topology ] . ( 477 sec) [ -7648.6295] [GTR parameters ] . ( 477 sec) [ -7648.6295] [Alpha ][ 0.397081] . ( 477 sec) [ -7648.6295] [Topology ] . ( 479 sec) [ -7648.6290] [Topology ] . Checking for NNIs, optimizing five branches... . ( 496 sec) [ -7648.6239] [Topology ] . ( 496 sec) [ -7648.6239] [GTR parameters ] . ( 496 sec) [ -7648.6239] [Alpha ][ 0.397081] . ( 496 sec) [ -7648.6239] [Topology ] . ( 499 sec) [ -7648.6235] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 536 sec) [ -7976.1365] [GTR parameters ] . ( 537 sec) [ -7938.7269] [Alpha ][ 0.500960] . ( 537 sec) [ -7919.7111] [ 1130] [depth= 1] . ( 538 sec) [ -7892.1045] [ 1125] [depth= 1] . ( 538 sec) [ -7886.8255] [ 1122] [depth= 3] . ( 538 sec) [ -7877.2862] [ 1120] [depth= 2] . ( 538 sec) [ -7877.1208] [ 1120] [depth= 1] . ( 539 sec) [ -7877.0627] [ 1125] [depth= 1] . ( 539 sec) [ -7876.7699] [ 1125] [depth= 1] . ( 540 sec) [ -7876.5142] [ 1125] [depth= 1] . ( 540 sec) [ -7876.4680] [ 1125] [depth= 1] . ( 540 sec) [ -7876.4563] [ 1125] [depth= 2] . ( 542 sec) [ -7868.1623] [ 1124] [depth= 1] . ( 543 sec) [ -7864.8399] [ 1124] [depth= 1] . ( 543 sec) [ -7862.7022] [ 1124] [depth= 1] . ( 544 sec) [ -7843.2854] [ 1125] [depth= 2] . ( 544 sec) [ -7842.2243] [ 1124] [depth= 2] . ( 544 sec) [ -7841.6203] [ 1124] [depth= 1] . ( 544 sec) [ -7839.4831] [ 1126] [depth= 1] . ( 545 sec) [ -7839.1417] [ 1126] [depth= 2] . ( 545 sec) [ -7831.6930] [ 1124] [depth= 1] . ( 547 sec) [ -7831.6502] [ 1124] [depth= 1] . ( 547 sec) [ -7831.3547] [ 1124] [depth= 1] . ( 549 sec) [ -7801.4069] [ 1118] [depth= 9] . ( 549 sec) [ -7799.2532] [ 1118] [depth= 1] . ( 550 sec) [ -7798.0461] [ 1116] [depth= 1] . ( 551 sec) [ -7797.4228] [ 1116] [depth= 2] . ( 551 sec) [ -7796.2635] [ 1111] [depth= 1] . ( 551 sec) [ -7796.1892] [ 1111] [depth= 1] . ( 552 sec) [ -7795.6908] [ 1111] [depth= 2] . ( 552 sec) [ -7792.7022] [ 1110] [depth= 1] . ( 552 sec) [ -7790.1238] [ 1106] [depth= 2] . ( 553 sec) [ -7787.0310] [ 1108] [depth= 1] . ( 553 sec) [ -7785.8661] [ 1113] [depth= 2] . ( 553 sec) [ -7782.1952] [ 1111] [depth= 1] . ( 553 sec) [ -7782.0443] [ 1111] [depth= 1] . ( 553 sec) [ -7781.9054] [ 1111] [depth= 1] . ( 554 sec) [ -7779.6357] [ 1110] [depth= 4] . ( 554 sec) [ -7770.4001] [ 1108] [depth= 4] . ( 554 sec) [ -7770.0085] [ 1108] [depth= 3] . ( 554 sec) [ -7769.9503] [ 1108] [depth= 2] . ( 554 sec) [ -7769.8554] [ 1108] [depth= 1] . ( 554 sec) [ -7769.2906] [ 1108] [depth= 3] . ( 557 sec) [ -7764.6244] [ 1107] [depth= 2] . ( 558 sec) [ -7764.4946] [ 1107] [depth= 1] . ( 559 sec) [ -7764.3170] [ 1107] [depth= 1] . ( 559 sec) [ -7763.2778] [ 1107] [depth= 1] . ( 559 sec) [ -7762.1474] [ 1107] [depth= 2] . ( 559 sec) [ -7759.0507] [ 1106] [depth= 2] . ( 559 sec) [ -7745.5066] [ 1104] [depth= 6] . ( 559 sec) [ -7744.8654] [ 1104] [depth= 1] . ( 560 sec) [ -7744.0654] [ 1104] [depth= 1] . ( 560 sec) [ -7743.3889] [ 1104] [depth= 4] . ( 560 sec) [ -7743.2834] [ 1104] [depth= 2] . ( 560 sec) [ -7743.1033] [ 1104] [depth= 5] . ( 560 sec) [ -7742.9132] [ 1104] [depth= 2] . ( 560 sec) [ -7742.4479] [ 1104] [depth= 1] . ( 561 sec) [ -7741.9899] [ 1104] [depth= 2] . ( 561 sec) [ -7740.4884] [ 1104] [depth= 1] . ( 561 sec) [ -7740.0423] [ 1104] [depth= 1] . ( 561 sec) [ -7738.9481] [ 1104] [depth= 5] . ( 561 sec) [ -7738.9046] [ 1104] [depth= 2] . ( 563 sec) [ -7738.4793] [ 1104] [depth= 2] . ( 563 sec) [ -7738.4070] [ 1104] [depth= 2] . ( 564 sec) [ -7735.8995] [ 1103] [depth= 2] . ( 564 sec) [ -7734.5471] [ 1103] [depth= 1] . ( 565 sec) [ -7730.0867] [ 1103] [depth= 1] . ( 565 sec) [ -7725.6454] [ 1102] [depth= 1] . ( 566 sec) [ -7724.4190] [ 1101] [depth= 1] . ( 567 sec) [ -7723.8519] [ 1102] [depth= 1] . ( 567 sec) [ -7722.0237] [ 1103] [depth= 1] . ( 567 sec) [ -7721.5486] [ 1101] [depth= 2] . ( 571 sec) [ -7709.8143] [ 1097] [depth= 5] . ( 573 sec) [ -7708.0280] [ 1097] [depth= 1] . ( 573 sec) [ -7703.9997] [ 1096] [depth= 3] . ( 576 sec) [ -7703.7456] [ 1096] [depth= 3] . ( 576 sec) [ -7702.7360] [ 1096] [depth= 1] . ( 579 sec) [ -7702.5681] [ 1096] [depth= 1] . ( 579 sec) [ -7696.1772] [ 1095] [depth= 5] . ( 579 sec) [ -7695.9060] [ 1095] [depth= 1] . ( 579 sec) [ -7695.8919] [ 1095] [depth= 1] . ( 579 sec) [ -7695.5341] [ 1095] [depth= 1] . ( 579 sec) [ -7695.2087] [ 1095] [depth= 1] . ( 580 sec) [ -7695.0278] [ 1095] [depth= 2] . ( 580 sec) [ -7695.0169] [ 1095] [depth= 1] . ( 581 sec) [ -7694.9789] [ 1095] [depth= 2] . ( 581 sec) [ -7693.2273] [ 1095] [depth= 2] . ( 581 sec) [ -7693.2111] [ 1095] [depth= 1] . ( 582 sec) [ -7691.3352] [ 1095] [depth= 1] . ( 583 sec) [ -7691.2447] [ 1095] [depth= 1] . ( 584 sec) [ -7690.9288] [ 1095] [depth= 2] . ( 584 sec) [ -7690.7531] [ 1096] [depth= 1] . ( 585 sec) [ -7687.7345] [ 1095] [depth= 2] . ( 587 sec) [ -7687.1711] [ 1095] [depth= 1] . ( 587 sec) [ -7686.9963] [ 1095] [depth= 2] . ( 587 sec) [ -7686.2968] [ 1095] [depth= 1] . ( 588 sec) [ -7686.1829] [ 1095] [depth= 1] . ( 588 sec) [ -7686.1314] [ 1095] [depth= 1] . ( 589 sec) [ -7685.9541] [ 1095] [depth= 2] . ( 589 sec) [ -7685.9147] [ 1095] [depth= 1] . ( 590 sec) [ -7685.8379] [ 1095] [depth= 1] . ( 593 sec) [ -7685.8214] [ 1095] [depth= 2] . ( 597 sec) [ -7685.8069] [ 1095] [depth= 1] . ( 608 sec) [ -7649.0667] [Branch lengths ] . ( 612 sec) [ -7647.0248] [GTR parameters ] . ( 612 sec) [ -7644.2475] [Alpha ][ 0.419560] . ( 613 sec) [ -7643.8323] [ 1095] [depth= 2] . ( 613 sec) [ -7641.6625] [ 1091] [depth= 3] . ( 621 sec) [ -7641.5885] [ 1091] [depth= 2] . ( 632 sec) [ -7641.3998] [ 1091] [depth= 1] . ( 645 sec) [ -7641.3198] [ 1090] [depth= 4] . ( 658 sec) [ -7638.4145] [ 1090] [depth= 1] . ( 664 sec) [ -7638.3536] [ 1090] [depth= 1] . ( 664 sec) [ -7635.5466] [ 1090] [depth= 3] . ( 666 sec) [ -7635.4326] [ 1090] [depth= 1] . ( 667 sec) [ -7635.2003] [ 1090] [depth= 1] . ( 670 sec) [ -7635.1537] [ 1090] [depth= 2] . ( 687 sec) [ -7635.1233] [ 1090] [depth= 1] . ( 688 sec) [ -7635.0810] [ 1090] [depth= 1] . ( 705 sec) [ -7634.0090] [ 1091] [depth= 8] . ( 719 sec) [ -7626.2741] [Branch lengths ] . ( 721 sec) [ -7626.0033] [GTR parameters ] . ( 721 sec) [ -7625.8639] [Alpha ][ 0.403674] . ( 722 sec) [ -7625.5301] [ 1090] [depth= 2] . ( 789 sec) [ -7621.7836] [ 1089] [depth= 10] . ( 790 sec) [ -7621.6503] [ 1089] [depth= 2] . ( 792 sec) [ -7621.6189] [ 1089] [depth= 2] . ( 792 sec) [ -7621.3850] [ 1089] [depth= 2] . ( 792 sec) [ -7621.3606] [ 1089] [depth= 1] . ( 808 sec) [ -7620.8571] [ 1089] [depth= 2] . ( 809 sec) [ -7620.7856] [ 1089] [depth= 1] . ( 810 sec) [ -7620.6165] [ 1089] [depth= 2] . ( 810 sec) [ -7620.5806] [ 1089] [depth= 3] . ( 813 sec) [ -7620.5668] [ 1089] [depth= 1] . ( 830 sec) [ -7619.8380] [Branch lengths ] . ( 832 sec) [ -7619.8292] [GTR parameters ] . ( 832 sec) [ -7619.8117] [Alpha ][ 0.398061] . ( 833 sec) [ -7619.0202] [ 1092] [depth= 6] . ( 894 sec) [ -7618.9786] [ 1092] [depth= 4] . ( 897 sec) [ -7618.9589] [ 1092] [depth= 2] . ( 900 sec) [ -7618.9330] [ 1092] [depth= 4] . ( 941 sec) [ -7618.7644] [Branch lengths ] . ( 942 sec) [ -7618.7566] [GTR parameters ] . ( 942 sec) [ -7618.7484] [Alpha ][ 0.401814] . ( 943 sec) [ -7618.6018] [ 1093] [depth= 4] . ( 1060 sec) [ -7618.5534] [Branch lengths ] . ( 1061 sec) [ -7618.5532] [GTR parameters ] . ( 1061 sec) [ -7618.5519] [Alpha ][ 0.403310] . ( 1192 sec) [ -7618.5395] [Branch lengths ] . ( 1192 sec) [ -7618.5395] [Topology ] . ( 1194 sec) [ -7618.5374] [Topology ] . ( 1197 sec) [ -7618.5363] [Topology ] . ( 1199 sec) [ -7618.5356] [Topology ] . ( 1200 sec) [ -7618.5356] [GTR parameters ] . ( 1200 sec) [ -7618.5356] [Alpha ][ 0.403713] . ( 1200 sec) [ -7618.5356] [Topology ] . ( 1203 sec) [ -7618.5351] [Topology ] . ( 1204 sec) [ -7618.5350] [GTR parameters ] . ( 1205 sec) [ -7618.5350] [Alpha ][ 0.403713] . Checking for NNIs, optimizing five branches... . ( 1221 sec) [ -7618.5338] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1238 sec) [ -7618.5337] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1255 sec) [ -7618.5285] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1271 sec) [ -7618.5257] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7648.623540 . Log likelihood obtained after SPR moves : -7618.525716 . 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 0h21m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1283.42user 0.00system 21:29.88elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps