.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2627_54x1915_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 . Compressing sequences... . 1299 patterns found. (out of a total of 1915 sites) . 625 sites without polymorphism (32.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -36710.7724] [GTR parameters ] . ( 2 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 2 sec) [ -36466.0989] [Topology ] . ( 5 sec) [ -36209.2967] [Topology ] . ( 8 sec) [ -36187.4972] [Topology ] . ( 10 sec) [ -36183.6050] [Topology ] . ( 13 sec) [ -36182.2546] [Topology ] . ( 16 sec) [ -36181.6395] [Topology ] . ( 19 sec) [ -36181.3321] [Topology ] . ( 22 sec) [ -36181.1727] [Topology ] . ( 24 sec) [ -36181.0882] [Topology ] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -36180.6868] [Topology ] . ( 55 sec) [ -35322.5824] [GTR parameters ] . ( 55 sec) [ -35320.2697] [Alpha ][ 0.467463] . ( 56 sec) [ -35320.2697] [Topology ] . ( 58 sec) [ -35294.8290] [Topology ] . ( 61 sec) [ -35286.3497] [Topology ] . ( 64 sec) [ -35282.3406] [Topology ] . ( 67 sec) [ -35280.0868] [Topology ] . ( 70 sec) [ -35278.7376] [Topology ] . ( 73 sec) [ -35277.8949] [Topology ] . ( 76 sec) [ -35277.3529] [Topology ] . Checking for NNIs, optimizing five branches... . ( 104 sec) [ -35269.7035] [GTR parameters ] . ( 104 sec) [ -35268.4270] [Alpha ][ 0.491109] . ( 104 sec) [ -35268.4270] [Topology ] . ( 107 sec) [ -35265.7908] [Topology ] . ( 110 sec) [ -35264.1797] [Topology ] . ( 113 sec) [ -35263.1137] [Topology ] . ( 116 sec) [ -35262.3863] [Topology ] . ( 119 sec) [ -35261.8806] [Topology ] . ( 121 sec) [ -35261.5229] [Topology ] . Checking for NNIs, optimizing five branches... . ( 149 sec) [ -35260.9682] [GTR parameters ] . ( 150 sec) [ -35260.8456] [Alpha ][ 0.498712] . ( 150 sec) [ -35260.8456] [Topology ] . ( 153 sec) [ -35260.2677] [Topology ] . ( 155 sec) [ -35259.8627] [Topology ] . ( 158 sec) [ -35259.5713] [Topology ] . ( 161 sec) [ -35259.3594] [Topology ] . ( 164 sec) [ -35259.2041] [Topology ] . ( 167 sec) [ -35259.0888] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -35258.9334] [GTR parameters ] . ( 195 sec) [ -35258.9280] [Alpha ][ 0.500271] . ( 195 sec) [ -35258.9280] [Topology ] . ( 198 sec) [ -35258.7614] [Topology ] . ( 201 sec) [ -35258.6406] [Topology ] . ( 204 sec) [ -35258.5508] [Topology ] . ( 206 sec) [ -35258.4836] [Topology ] . ( 209 sec) [ -35258.4333] [Topology ] . ( 212 sec) [ -35258.3953] [Topology ] . Checking for NNIs, optimizing five branches... . ( 238 sec) [ -35258.3366] [GTR parameters ] . ( 238 sec) [ -35258.3366] [Alpha ][ 0.500271] . ( 238 sec) [ -35258.3366] [Topology ] . ( 241 sec) [ -35258.2807] [Topology ] . ( 244 sec) [ -35258.2399] [Topology ] . ( 247 sec) [ -35258.2092] [Topology ] . ( 250 sec) [ -35258.1859] [Topology ] . ( 253 sec) [ -35258.1682] [Topology ] . ( 256 sec) [ -35258.1547] [Topology ] . Checking for NNIs, optimizing five branches... . ( 280 sec) [ -35258.1319] [GTR parameters ] . ( 280 sec) [ -35258.1319] [Alpha ][ 0.500271] . ( 280 sec) [ -35258.1319] [Topology ] . ( 283 sec) [ -35258.1114] [Topology ] . ( 286 sec) [ -35258.0963] [Topology ] . ( 289 sec) [ -35258.0849] [Topology ] . ( 292 sec) [ -35258.0762] [Topology ] . ( 295 sec) [ -35258.0695] [Topology ] . ( 298 sec) [ -35258.0644] [Topology ] . Checking for NNIs, optimizing five branches... . ( 322 sec) [ -35258.0563] [GTR parameters ] . ( 322 sec) [ -35258.0563] [Alpha ][ 0.500271] . ( 322 sec) [ -35258.0563] [Topology ] . ( 325 sec) [ -35258.0487] [Topology ] . ( 328 sec) [ -35258.0431] [Topology ] . ( 331 sec) [ -35258.0389] [Topology ] . ( 333 sec) [ -35258.0356] [Topology ] . ( 336 sec) [ -35258.0331] [Topology ] . ( 339 sec) [ -35258.0312] [Topology ] . Checking for NNIs, optimizing five branches... . ( 364 sec) [ -35258.0280] [GTR parameters ] . ( 364 sec) [ -35258.0277] [Alpha ][ 0.499771] . ( 364 sec) [ -35258.0277] [Topology ] . ( 367 sec) [ -35258.0248] [Topology ] . ( 370 sec) [ -35258.0228] [Topology ] . ( 373 sec) [ -35258.0212] [Topology ] . ( 375 sec) [ -35258.0200] [Topology ] . ( 378 sec) [ -35258.0190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 404 sec) [ -35258.0177] [GTR parameters ] . ( 404 sec) [ -35258.0177] [Alpha ][ 0.499771] . ( 404 sec) [ -35258.0177] [Topology ] . ( 407 sec) [ -35258.0164] [Topology ] . ( 410 sec) [ -35258.0154] [Topology ] . Checking for NNIs, optimizing five branches... . ( 434 sec) [ -35258.0153] [GTR parameters ] . ( 434 sec) [ -35258.0153] [Alpha ][ 0.499771] . ( 434 sec) [ -35258.0153] [Topology ] . ( 437 sec) [ -35258.0145] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 485 sec) [ -36710.7724] [GTR parameters ] . ( 486 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 490 sec) [ -36464.9677] [ 8258] [depth= 1] . ( 491 sec) [ -36460.8603] [ 8291] [depth= 2] . ( 491 sec) [ -36413.8896] [ 8255] [depth= 2] . ( 491 sec) [ -36411.3454] [ 8249] [depth= 1] . ( 491 sec) [ -36397.3331] [ 8254] [depth= 1] . ( 492 sec) [ -36396.4495] [ 8264] [depth= 1] . ( 492 sec) [ -36396.4283] [ 8268] [depth= 1] . ( 493 sec) [ -36393.2290] [ 8263] [depth= 2] . ( 493 sec) [ -36391.5326] [ 8259] [depth= 1] . ( 493 sec) [ -36388.9751] [ 8260] [depth= 1] . ( 493 sec) [ -36362.6353] [ 8249] [depth= 5] . ( 494 sec) [ -36359.1347] [ 8255] [depth= 1] . ( 494 sec) [ -36350.2260] [ 8249] [depth= 1] . ( 495 sec) [ -36349.7371] [ 8242] [depth= 1] . ( 495 sec) [ -36349.4200] [ 8246] [depth= 1] . ( 496 sec) [ -36343.2807] [ 8241] [depth= 1] . ( 496 sec) [ -36329.9012] [ 8240] [depth= 1] . ( 500 sec) [ -36327.9565] [ 8239] [depth= 1] . ( 502 sec) [ -36197.4375] [Branch lengths ] . ( 509 sec) [ -35337.0661] [GTR parameters ] . ( 509 sec) [ -35334.1525] [Alpha ][ 0.463557] . ( 513 sec) [ -35331.7797] [ 8231] [depth= 1] . ( 515 sec) [ -35326.9401] [ 8235] [depth= 1] . ( 515 sec) [ -35323.2659] [ 8231] [depth= 1] . ( 523 sec) [ -35284.2968] [Branch lengths ] . ( 527 sec) [ -35280.5360] [GTR parameters ] . ( 528 sec) [ -35279.7293] [Alpha ][ 0.482446] . ( 541 sec) [ -35265.7588] [Branch lengths ] . ( 623 sec) [ -35261.5709] [Branch lengths ] . ( 623 sec) [ -35261.5709] [Topology ] . ( 625 sec) [ -35260.7430] [Topology ] . ( 628 sec) [ -35260.3509] [Topology ] . ( 631 sec) [ -35260.0876] [Topology ] . ( 634 sec) [ -35259.9043] [Topology ] . ( 637 sec) [ -35259.7739] [Topology ] . ( 640 sec) [ -35259.6805] [Topology ] . ( 643 sec) [ -35256.7278] [GTR parameters ] . ( 643 sec) [ -35256.1861] [Alpha ][ 0.497802] . ( 643 sec) [ -35256.1861] [Topology ] . ( 646 sec) [ -35255.4758] [Topology ] . ( 649 sec) [ -35255.0131] [Topology ] . ( 652 sec) [ -35254.6866] [Topology ] . ( 655 sec) [ -35254.4527] [Topology ] . ( 658 sec) [ -35254.2838] [Topology ] . ( 660 sec) [ -35254.1601] [Topology ] . ( 662 sec) [ -35254.0202] [GTR parameters ] . ( 662 sec) [ -35254.0124] [Alpha ][ 0.499682] . ( 662 sec) [ -35254.0124] [Topology ] . ( 665 sec) [ -35253.8451] [Topology ] . ( 668 sec) [ -35253.7249] [Topology ] . ( 671 sec) [ -35253.6364] [Topology ] . ( 674 sec) [ -35253.5712] [Topology ] . ( 677 sec) [ -35253.5228] [Topology ] . ( 680 sec) [ -35253.4868] [Topology ] . ( 681 sec) [ -35253.4261] [GTR parameters ] . ( 681 sec) [ -35253.4261] [Alpha ][ 0.499682] . ( 681 sec) [ -35253.4261] [Topology ] . ( 684 sec) [ -35253.3725] [Topology ] . ( 687 sec) [ -35253.3340] [Topology ] . ( 690 sec) [ -35253.3053] [Topology ] . ( 693 sec) [ -35253.2838] [Topology ] . ( 696 sec) [ -35253.2676] [Topology ] . ( 699 sec) [ -35253.2554] [Topology ] . ( 699 sec) [ -35253.2326] [GTR parameters ] . ( 700 sec) [ -35253.2326] [Alpha ][ 0.499682] . ( 700 sec) [ -35253.2326] [Topology ] . ( 703 sec) [ -35253.2134] [Topology ] . ( 705 sec) [ -35253.1996] [Topology ] . ( 708 sec) [ -35253.1893] [Topology ] . ( 711 sec) [ -35253.1815] [Topology ] . ( 714 sec) [ -35253.1756] [Topology ] . ( 717 sec) [ -35253.1711] [Topology ] . ( 719 sec) [ -35253.1631] [GTR parameters ] . ( 719 sec) [ -35253.1629] [Alpha ][ 0.499183] . ( 719 sec) [ -35253.1629] [Topology ] . ( 722 sec) [ -35253.1561] [Topology ] . ( 725 sec) [ -35253.1513] [Topology ] . ( 728 sec) [ -35253.1476] [Topology ] . ( 731 sec) [ -35253.1448] [Topology ] . ( 733 sec) [ -35253.1427] [Topology ] . ( 736 sec) [ -35253.1412] [Topology ] . ( 738 sec) [ -35253.1379] [GTR parameters ] . ( 738 sec) [ -35253.1379] [Alpha ][ 0.499183] . ( 738 sec) [ -35253.1379] [Topology ] . ( 741 sec) [ -35253.1354] [Topology ] . ( 744 sec) [ -35253.1335] [Topology ] . ( 747 sec) [ -35253.1321] [Topology ] . ( 750 sec) [ -35253.1311] [Topology ] . ( 753 sec) [ -35253.1302] [Topology ] . ( 754 sec) [ -35253.1295] [GTR parameters ] . ( 754 sec) [ -35253.1295] [Alpha ][ 0.499183] . ( 754 sec) [ -35253.1295] [Topology ] . ( 757 sec) [ -35253.1285] [Topology ] . ( 758 sec) [ -35253.1284] [GTR parameters ] . ( 758 sec) [ -35253.1284] [Alpha ][ 0.499183] . ( 758 sec) [ -35253.1284] [Topology ] . ( 761 sec) [ -35253.1275] [Topology ] . ( 762 sec) [ -35253.1274] [GTR parameters ] . ( 763 sec) [ -35253.1274] [Alpha ][ 0.499183] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -35258.014465 . Log likelihood obtained after SPR moves : -35253.127376 . Log likelihood of the current tree: -35253.127376. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 0h13m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 783.93user 0.00system 13:07.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps