.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2564_142x1130_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... . 780 patterns found. (out of a total of 1130 sites) . 486 sites without polymorphism (43.01%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 7 sec) [ -21575.3354] [GTR parameters ] . ( 8 sec) [ -21206.7214] [Alpha ][ 0.500960] . ( 8 sec) [ -21206.7214] [Topology ] . ( 13 sec) [ -20737.3169] [Topology ] . ( 18 sec) [ -20622.9577] [Topology ] . ( 24 sec) [ -20586.6538] [Topology ] . ( 29 sec) [ -20570.9427] [Topology ] . ( 35 sec) [ -20566.3417] [Topology ] . ( 40 sec) [ -20561.9455] [Topology ] . ( 45 sec) [ -20559.4520] [Topology ] . ( 50 sec) [ -20551.4915] [Topology ] . ( 55 sec) [ -20546.5863] [Topology ] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -20541.1422] [Topology ] . ( 104 sec) [ -20529.9550] [GTR parameters ] . ( 105 sec) [ -20478.5225] [Alpha ][ 0.348656] . ( 105 sec) [ -20478.5225] [Topology ] . ( 110 sec) [ -20471.3446] [Topology ] . ( 115 sec) [ -20470.4270] [Topology ] . ( 121 sec) [ -20469.8076] [Topology ] . ( 126 sec) [ -20469.2380] [Topology ] . ( 131 sec) [ -20469.1369] [Topology ] . ( 136 sec) [ -20469.1145] [Topology ] . ( 141 sec) [ -20469.1090] [Topology ] . ( 146 sec) [ -20469.1075] [Topology ] . ( 152 sec) [ -20469.1071] [Topology ] . Checking for NNIs, optimizing five branches... . ( 188 sec) [ -20468.5217] [Topology ] . ( 192 sec) [ -20468.0511] [GTR parameters ] . ( 192 sec) [ -20467.8627] [Alpha ][ 0.341568] . ( 193 sec) [ -20467.8627] [Topology ] . ( 198 sec) [ -20467.5304] [Topology ] . ( 203 sec) [ -20467.1917] [Topology ] . ( 208 sec) [ -20465.9457] [Topology ] . ( 213 sec) [ -20465.8018] [Topology ] . ( 218 sec) [ -20465.7725] [Topology ] . ( 223 sec) [ -20465.7638] [Topology ] . ( 228 sec) [ -20465.7610] [Topology ] . ( 234 sec) [ -20465.7599] [Topology ] . Checking for NNIs, optimizing five branches... . ( 271 sec) [ -20465.2554] [Topology ] . ( 273 sec) [ -20465.2491] [GTR parameters ] . ( 273 sec) [ -20465.2471] [Alpha ][ 0.340728] . ( 273 sec) [ -20465.2471] [Topology ] . ( 278 sec) [ -20465.2386] [Topology ] . ( 283 sec) [ -20465.2368] [Topology ] . ( 289 sec) [ -20465.2364] [Topology ] . Checking for NNIs, optimizing five branches... . ( 326 sec) [ -20464.7322] [Topology ] . ( 328 sec) [ -20464.7257] [GTR parameters ] . ( 328 sec) [ -20464.7251] [Alpha ][ 0.341069] . ( 328 sec) [ -20464.7251] [Topology ] . ( 333 sec) [ -20464.6624] [Topology ] . ( 338 sec) [ -20464.6484] [Topology ] . ( 344 sec) [ -20464.6430] [Topology ] . ( 349 sec) [ -20464.6405] [Topology ] . ( 354 sec) [ -20464.6392] [Topology ] . ( 359 sec) [ -20464.6386] [Topology ] . Checking for NNIs, optimizing five branches... . ( 396 sec) [ -20464.6349] [Topology ] . ( 397 sec) [ -20464.6341] [GTR parameters ] . ( 397 sec) [ -20464.6335] [Alpha ][ 0.341410] . ( 398 sec) [ -20464.6335] [Topology ] . ( 403 sec) [ -20464.6329] [Topology ] . Checking for NNIs, optimizing five branches... . ( 440 sec) [ -20464.6329] [GTR parameters ] . ( 441 sec) [ -20464.6329] [Alpha ][ 0.341410] . ( 441 sec) [ -20464.6329] [Topology ] . ( 446 sec) [ -20464.6326] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 526 sec) [ -21575.3354] [GTR parameters ] . ( 527 sec) [ -21206.7214] [Alpha ][ 0.500960] . ( 528 sec) [ -21206.1411] [ 4073] [depth= 1] . ( 528 sec) [ -21199.5150] [ 4077] [depth= 1] . ( 528 sec) [ -21185.9218] [ 4073] [depth= 1] . ( 529 sec) [ -21171.3223] [ 4059] [depth= 1] . ( 529 sec) [ -21169.7149] [ 4065] [depth= 1] . ( 530 sec) [ -21169.1018] [ 4076] [depth= 1] . ( 530 sec) [ -21148.9782] [ 4065] [depth= 1] . ( 531 sec) [ -21148.1301] [ 4070] [depth= 1] . ( 531 sec) [ -21138.2511] [ 4065] [depth= 1] . ( 532 sec) [ -21132.9040] [ 4069] [depth= 1] . ( 533 sec) [ -21118.3850] [ 4065] [depth= 1] . ( 533 sec) [ -21116.7828] [ 4067] [depth= 1] . ( 533 sec) [ -21107.9046] [ 4065] [depth= 1] . ( 534 sec) [ -21107.6878] [ 4069] [depth= 1] . ( 534 sec) [ -21102.5459] [ 4081] [depth= 1] . ( 535 sec) [ -21073.5167] [ 4069] [depth= 1] . ( 535 sec) [ -21067.2112] [ 4065] [depth= 1] . ( 536 sec) [ -21042.3328] [ 4074] [depth= 4] . ( 536 sec) [ -21031.7104] [ 4078] [depth= 1] . ( 537 sec) [ -21031.5153] [ 4074] [depth= 1] . ( 538 sec) [ -21031.0870] [ 4070] [depth= 1] . ( 538 sec) [ -21030.5398] [ 4070] [depth= 2] . ( 538 sec) [ -21030.4456] [ 4074] [depth= 1] . ( 538 sec) [ -21029.3591] [ 4077] [depth= 1] . ( 539 sec) [ -21028.4497] [ 4078] [depth= 1] . ( 539 sec) [ -21027.1816] [ 4074] [depth= 1] . ( 539 sec) [ -21026.3218] [ 4077] [depth= 1] . ( 540 sec) [ -21024.7836] [ 4074] [depth= 1] . ( 540 sec) [ -21024.5493] [ 4078] [depth= 1] . ( 541 sec) [ -21016.1002] [ 4080] [depth= 1] . ( 541 sec) [ -21012.7409] [ 4079] [depth= 1] . ( 542 sec) [ -21008.0453] [ 4080] [depth= 1] . ( 542 sec) [ -20998.6533] [ 4077] [depth= 1] . ( 543 sec) [ -20997.7683] [ 4078] [depth= 1] . ( 543 sec) [ -20996.9510] [ 4077] [depth= 1] . ( 543 sec) [ -20991.8876] [ 4076] [depth= 1] . ( 543 sec) [ -20986.3212] [ 4077] [depth= 1] . ( 544 sec) [ -20982.1182] [ 4078] [depth= 1] . ( 546 sec) [ -20981.9009] [ 4079] [depth= 1] . ( 547 sec) [ -20981.6467] [ 4078] [depth= 3] . ( 547 sec) [ -20981.1407] [ 4079] [depth= 1] . ( 547 sec) [ -20953.4563] [ 4073] [depth= 4] . ( 547 sec) [ -20947.8959] [ 4071] [depth= 2] . ( 549 sec) [ -20946.9900] [ 4073] [depth= 1] . ( 549 sec) [ -20944.4483] [ 4071] [depth= 1] . ( 550 sec) [ -20943.7214] [ 4071] [depth= 1] . ( 550 sec) [ -20943.4590] [ 4072] [depth= 1] . ( 551 sec) [ -20941.0003] [ 4068] [depth= 12] . ( 552 sec) [ -20932.6285] [ 4067] [depth= 6] . ( 552 sec) [ -20924.4043] [ 4066] [depth= 2] . ( 552 sec) [ -20920.8819] [ 4064] [depth= 7] . ( 553 sec) [ -20919.2612] [ 4064] [depth= 2] . ( 553 sec) [ -20918.2796] [ 4064] [depth= 1] . ( 553 sec) [ -20897.8781] [ 4063] [depth= 2] . ( 554 sec) [ -20892.2793] [ 4056] [depth= 5] . ( 554 sec) [ -20890.2083] [ 4056] [depth= 2] . ( 554 sec) [ -20889.8978] [ 4056] [depth= 1] . ( 554 sec) [ -20889.7377] [ 4056] [depth= 1] . ( 556 sec) [ -20885.1230] [ 4057] [depth= 2] . ( 556 sec) [ -20883.7516] [ 4057] [depth= 1] . ( 557 sec) [ -20883.6787] [ 4062] [depth= 1] . ( 557 sec) [ -20877.6561] [ 4063] [depth= 1] . ( 558 sec) [ -20877.1934] [ 4062] [depth= 1] . ( 558 sec) [ -20876.0042] [ 4062] [depth= 1] . ( 558 sec) [ -20875.3066] [ 4062] [depth= 1] . ( 558 sec) [ -20874.4625] [ 4062] [depth= 1] . ( 559 sec) [ -20867.5433] [ 4061] [depth= 6] . ( 559 sec) [ -20867.5068] [ 4061] [depth= 1] . ( 559 sec) [ -20866.3044] [ 4060] [depth= 1] . ( 561 sec) [ -20864.0107] [ 4059] [depth= 2] . ( 562 sec) [ -20863.9519] [ 4063] [depth= 1] . ( 562 sec) [ -20863.1543] [ 4059] [depth= 1] . ( 563 sec) [ -20861.3639] [ 4060] [depth= 1] . ( 565 sec) [ -20861.1209] [ 4061] [depth= 2] . ( 566 sec) [ -20859.3721] [ 4061] [depth= 2] . ( 567 sec) [ -20858.6604] [ 4061] [depth= 1] . ( 568 sec) [ -20857.7099] [ 4061] [depth= 1] . ( 569 sec) [ -20857.4707] [ 4061] [depth= 1] . ( 570 sec) [ -20857.4052] [ 4061] [depth= 1] . ( 571 sec) [ -20856.7512] [ 4062] [depth= 1] . ( 571 sec) [ -20856.3820] [ 4062] [depth= 1] . ( 572 sec) [ -20855.4101] [ 4062] [depth= 1] . ( 572 sec) [ -20853.0166] [ 4062] [depth= 1] . ( 573 sec) [ -20851.1565] [ 4064] [depth= 1] . ( 573 sec) [ -20844.2644] [ 4062] [depth= 1] . ( 574 sec) [ -20844.2112] [ 4062] [depth= 1] . ( 574 sec) [ -20844.0141] [ 4062] [depth= 1] . ( 575 sec) [ -20843.7250] [ 4062] [depth= 1] . ( 575 sec) [ -20843.2067] [ 4062] [depth= 2] . ( 575 sec) [ -20837.7391] [ 4061] [depth= 1] . ( 576 sec) [ -20832.8016] [ 4060] [depth= 1] . ( 576 sec) [ -20832.0503] [ 4059] [depth= 1] . ( 577 sec) [ -20828.0222] [ 4059] [depth= 1] . ( 578 sec) [ -20827.5277] [ 4060] [depth= 1] . ( 580 sec) [ -20815.1555] [ 4055] [depth= 7] . ( 580 sec) [ -20809.7885] [ 4055] [depth= 1] . ( 581 sec) [ -20807.5134] [ 4055] [depth= 1] . ( 582 sec) [ -20804.0305] [ 4054] [depth= 1] . ( 582 sec) [ -20800.0927] [ 4054] [depth= 1] . ( 584 sec) [ -20799.8763] [ 4057] [depth= 1] . ( 586 sec) [ -20796.6724] [ 4057] [depth= 1] . ( 586 sec) [ -20793.7520] [ 4056] [depth= 1] . ( 589 sec) [ -20789.9325] [ 4060] [depth= 4] . ( 590 sec) [ -20787.1378] [ 4056] [depth= 4] . ( 590 sec) [ -20775.3477] [ 4053] [depth= 7] . ( 590 sec) [ -20773.9425] [ 4053] [depth= 1] . ( 591 sec) [ -20772.5686] [ 4054] [depth= 2] . ( 591 sec) [ -20770.5859] [ 4053] [depth= 1] . ( 592 sec) [ -20770.2396] [ 4055] [depth= 8] . ( 593 sec) [ -20769.4393] [ 4053] [depth= 6] . ( 597 sec) [ -20766.0015] [ 4052] [depth= 2] . ( 598 sec) [ -20765.5721] [ 4051] [depth= 1] . ( 598 sec) [ -20760.5993] [ 4048] [depth= 1] . ( 603 sec) [ -20760.3302] [ 4051] [depth= 2] . ( 604 sec) [ -20758.9319] [ 4050] [depth= 3] . ( 604 sec) [ -20757.6391] [ 4050] [depth= 2] . ( 605 sec) [ -20745.2456] [ 4045] [depth= 3] . ( 605 sec) [ -20745.0911] [ 4047] [depth= 2] . ( 605 sec) [ -20743.1663] [ 4045] [depth= 2] . ( 605 sec) [ -20742.9972] [ 4046] [depth= 1] . ( 606 sec) [ -20742.6183] [ 4045] [depth= 1] . ( 606 sec) [ -20742.5467] [ 4045] [depth= 1] . ( 608 sec) [ -20741.4109] [ 4045] [depth= 1] . ( 609 sec) [ -20741.2551] [ 4045] [depth= 1] . ( 609 sec) [ -20739.1957] [ 4045] [depth= 1] . ( 609 sec) [ -20738.7493] [ 4045] [depth= 1] . ( 611 sec) [ -20738.3673] [ 4045] [depth= 1] . ( 612 sec) [ -20737.1109] [ 4044] [depth= 4] . ( 612 sec) [ -20737.0004] [ 4044] [depth= 2] . ( 612 sec) [ -20735.0054] [ 4044] [depth= 1] . ( 618 sec) [ -20734.8551] [ 4045] [depth= 1] . ( 619 sec) [ -20732.5964] [ 4045] [depth= 1] . ( 620 sec) [ -20730.3801] [ 4045] [depth= 2] . ( 621 sec) [ -20730.1478] [ 4045] [depth= 1] . ( 623 sec) [ -20729.3912] [ 4045] [depth= 1] . ( 623 sec) [ -20728.9981] [ 4046] [depth= 1] . ( 626 sec) [ -20727.1255] [ 4044] [depth= 1] . ( 628 sec) [ -20553.4281] [Branch lengths ] . ( 633 sec) [ -20545.2582] [GTR parameters ] . ( 634 sec) [ -20488.8294] [Alpha ][ 0.339831] . ( 634 sec) [ -20486.0947] [ 4044] [depth= 1] . ( 636 sec) [ -20484.0219] [ 4050] [depth= 1] . ( 642 sec) [ -20480.7496] [ 4052] [depth= 5] . ( 643 sec) [ -20480.3805] [ 4052] [depth= 1] . ( 644 sec) [ -20480.0668] [ 4049] [depth= 1] . ( 645 sec) [ -20473.9225] [ 4043] [depth= 1] . ( 646 sec) [ -20473.0011] [ 4047] [depth= 1] . ( 654 sec) [ -20472.8530] [ 4047] [depth= 1] . ( 663 sec) [ -20472.6913] [ 4048] [depth= 1] . ( 665 sec) [ -20472.6650] [ 4048] [depth= 1] . ( 669 sec) [ -20472.6147] [ 4049] [depth= 1] . ( 669 sec) [ -20472.5287] [ 4048] [depth= 1] . ( 676 sec) [ -20472.4525] [ 4048] [depth= 1] . ( 678 sec) [ -20472.4280] [ 4048] [depth= 1] . ( 682 sec) [ -20470.0690] [ 4047] [depth= 2] . ( 685 sec) [ -20469.0941] [ 4047] [depth= 1] . ( 687 sec) [ -20468.9624] [ 4047] [depth= 1] . ( 688 sec) [ -20462.6495] [ 4044] [depth= 1] . ( 688 sec) [ -20461.8610] [ 4044] [depth= 1] . ( 699 sec) [ -20460.6745] [ 4045] [depth= 3] . ( 703 sec) [ -20459.6244] [ 4046] [depth= 7] . ( 708 sec) [ -20457.3936] [ 4046] [depth= 1] . ( 709 sec) [ -20457.0632] [ 4046] [depth= 1] . ( 709 sec) [ -20455.9182] [ 4046] [depth= 1] . ( 709 sec) [ -20455.6620] [ 4046] [depth= 1] . ( 719 sec) [ -20455.4574] [ 4047] [depth= 2] . ( 724 sec) [ -20454.6221] [ 4049] [depth= 7] . ( 725 sec) [ -20454.2434] [ 4048] [depth= 1] . ( 727 sec) [ -20454.2287] [ 4048] [depth= 1] . ( 729 sec) [ -20454.1110] [ 4048] [depth= 1] . ( 730 sec) [ -20453.6661] [ 4049] [depth= 1] . ( 730 sec) [ -20453.0362] [ 4047] [depth= 1] . ( 741 sec) [ -20452.7598] [ 4051] [depth= 7] . ( 742 sec) [ -20451.9105] [ 4050] [depth= 1] . ( 742 sec) [ -20451.6577] [ 4052] [depth= 1] . ( 742 sec) [ -20450.5604] [ 4049] [depth= 2] . ( 747 sec) [ -20422.2990] [Branch lengths ] . ( 750 sec) [ -20421.1370] [GTR parameters ] . ( 751 sec) [ -20421.1312] [Alpha ][ 0.338476] . ( 757 sec) [ -20420.7962] [ 4053] [depth= 1] . ( 760 sec) [ -20419.2140] [ 4053] [depth= 1] . ( 774 sec) [ -20418.8796] [ 4057] [depth= 15] . ( 777 sec) [ -20418.8638] [ 4057] [depth= 1] . ( 778 sec) [ -20418.8467] [ 4057] [depth= 1] . ( 789 sec) [ -20418.7989] [ 4058] [depth= 1] . ( 818 sec) [ -20417.8336] [ 4057] [depth= 1] . ( 860 sec) [ -20417.6036] [ 4057] [depth= 1] . ( 894 sec) [ -20413.7598] [Branch lengths ] . ( 898 sec) [ -20413.6812] [GTR parameters ] . ( 898 sec) [ -20413.6753] [Alpha ][ 0.339677] . ( 907 sec) [ -20413.0862] [ 4059] [depth= 3] . ( 924 sec) [ -20413.0575] [ 4061] [depth= 2] . ( 929 sec) [ -20411.9624] [ 4059] [depth= 3] . ( 931 sec) [ -20410.8771] [ 4061] [depth= 1] . ( 932 sec) [ -20410.8539] [ 4062] [depth= 1] . ( 932 sec) [ -20410.3091] [ 4062] [depth= 1] . ( 938 sec) [ -20410.2517] [ 4061] [depth= 1] . ( 1046 sec) [ -20409.0614] [Branch lengths ] . ( 1049 sec) [ -20409.0349] [GTR parameters ] . ( 1049 sec) [ -20409.0349] [Alpha ][ 0.339677] . ( 1070 sec) [ -20408.8730] [ 4062] [depth= 1] . ( 1199 sec) [ -20408.0815] [Branch lengths ] . ( 1200 sec) [ -20408.0784] [GTR parameters ] . ( 1200 sec) [ -20408.0780] [Alpha ][ 0.340017] . ( 1407 sec) [ -20408.0531] [ 4061] [depth= 1] . ( 1452 sec) [ -20406.7347] [Branch lengths ] . ( 1453 sec) [ -20406.7334] [GTR parameters ] . ( 1453 sec) [ -20406.7334] [Alpha ][ 0.340017] . ( 1707 sec) [ -20404.3797] [Branch lengths ] . ( 1707 sec) [ -20404.3797] [Topology ] . ( 1712 sec) [ -20401.7950] [Topology ] . ( 1717 sec) [ -20398.3187] [Topology ] . ( 1722 sec) [ -20397.5064] [Topology ] . ( 1728 sec) [ -20397.3467] [Topology ] . ( 1733 sec) [ -20397.3155] [Topology ] . ( 1738 sec) [ -20397.3090] [Topology ] . ( 1739 sec) [ -20397.3079] [GTR parameters ] . ( 1740 sec) [ -20397.3077] [Alpha ][ 0.340357] . ( 1740 sec) [ -20397.3077] [Topology ] . ( 1745 sec) [ -20397.3062] [Topology ] . ( 1750 sec) [ -20397.3057] [Topology ] . ( 1751 sec) [ -20397.3057] [GTR parameters ] . ( 1751 sec) [ -20397.3057] [Alpha ][ 0.340357] . ( 1752 sec) [ -20397.3057] [Topology ] . ( 1757 sec) [ -20397.3056] [Topology ] . ( 1758 sec) [ -20397.3056] [GTR parameters ] . ( 1758 sec) [ -20397.3056] [Alpha ][ 0.340357] . Checking for NNIs, optimizing five branches... . ( 1794 sec) [ -20397.2961] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1830 sec) [ -20397.2949] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -20464.632592 . Log likelihood obtained after SPR moves : -20397.294920 . Log likelihood of the current tree: -20397.294920. . Printing the most likely tree in file 'nucleic_M2564_142x1130_2006.phy_phyml_tree.txt'... . Time used 0h31m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1860.72user 0.00system 31:09.98elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps