.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2707_115x1677_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... . 759 patterns found. (out of a total of 1677 sites) . 924 sites without polymorphism (55.10%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 46Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -11652.5156] [GTR parameters ] . ( 6 sec) [ -11452.6188] [Alpha ][ 0.500960] . ( 6 sec) [ -11452.6188] [Topology ] . ( 10 sec) [ -10365.2625] [Topology ] . ( 14 sec) [ -10031.8375] [Topology ] . ( 18 sec) [ -10010.6258] [Topology ] . ( 22 sec) [ -10000.4939] [Topology ] . ( 26 sec) [ -10078.8663] [Topology ] . Moving backward . ( 26 sec) [ -9998.0838] [Topology ] . ( 30 sec) [ -9978.6205] [Topology ] . ( 34 sec) [ -10082.5053] [Topology ] . Moving backward . ( 34 sec) [ -9970.6332] [Topology ] . ( 43 sec) [ -9952.5716] [GTR parameters ] . ( 43 sec) [ -9875.4361] [Alpha ][ 0.259706] . ( 43 sec) [ -9875.4361] [Topology ] . ( 47 sec) [ -9932.2170] [Topology ] . Moving backward . ( 47 sec) [ -9874.3108] [Topology ] . ( 51 sec) [ -9863.8641] [Topology ] . ( 54 sec) [ -9930.4278] [Topology ] . Moving backward . ( 55 sec) [ -9853.3092] [Topology ] . ( 58 sec) [ -9848.7910] [Topology ] . ( 62 sec) [ -9895.9855] [Topology ] . Moving backward . ( 62 sec) [ -9846.4683] [Topology ] . ( 66 sec) [ -9842.2614] [Topology ] . ( 73 sec) [ -9850.4471] [GTR parameters ] . ( 73 sec) [ -9850.3708] [Alpha ][ 0.255177] . ( 73 sec) [ -9850.3708] [Topology ] . ( 77 sec) [ -9839.3721] [Topology ] . ( 80 sec) [ -9894.3038] [Topology ] . Moving backward . ( 81 sec) [ -9832.5169] [Topology ] . ( 84 sec) [ -9828.9871] [Topology ] . ( 87 sec) [ -9848.9864] [Topology ] . Moving backward . ( 88 sec) [ -9828.5015] [Topology ] . ( 91 sec) [ -9828.1237] [Topology ] . ( 94 sec) [ -9853.2397] [Topology ] . Moving backward . ( 95 sec) [ -9823.8735] [Topology ] . Checking for NNIs, optimizing five branches... . ( 126 sec) [ -9822.3410] [Topology ] . ( 129 sec) [ -9822.1675] [GTR parameters ] . ( 130 sec) [ -9819.7744] [Alpha ][ 0.231992] . ( 130 sec) [ -9819.7744] [Topology ] . ( 133 sec) [ -9824.8512] [Topology ] . Moving backward . ( 133 sec) [ -9817.6700] [Topology ] . ( 137 sec) [ -9817.3750] [Topology ] . ( 140 sec) [ -9824.1131] [Topology ] . Moving backward . ( 140 sec) [ -9816.1565] [Topology ] . ( 144 sec) [ -9816.4149] [Topology ] . Moving backward . ( 144 sec) [ -9814.5736] [Topology ] . ( 147 sec) [ -9814.0199] [Topology ] . ( 150 sec) [ -9813.6959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 180 sec) [ -9812.9284] [Topology ] . ( 183 sec) [ -9812.4685] [GTR parameters ] . ( 184 sec) [ -9812.0924] [Alpha ][ 0.223570] . ( 184 sec) [ -9812.0924] [Topology ] . ( 187 sec) [ -9811.0097] [Topology ] . ( 191 sec) [ -9810.6491] [Topology ] . ( 194 sec) [ -9810.6447] [Topology ] . ( 197 sec) [ -9814.1610] [Topology ] . Moving backward . ( 197 sec) [ -9809.4865] [Topology ] . ( 201 sec) [ -9809.4931] [Topology ] . Moving backward . ( 201 sec) [ -9808.5732] [Topology ] . ( 204 sec) [ -9808.0614] [Topology ] . Checking for NNIs, optimizing five branches... . ( 230 sec) [ -9807.9271] [Topology ] . ( 234 sec) [ -9807.8015] [GTR parameters ] . ( 234 sec) [ -9807.3598] [Alpha ][ 0.214946] . ( 235 sec) [ -9807.3598] [Topology ] . ( 238 sec) [ -9806.6399] [Topology ] . ( 241 sec) [ -9806.2793] [Topology ] . ( 244 sec) [ -9806.1576] [Topology ] . ( 248 sec) [ -9807.5394] [Topology ] . Moving backward . ( 248 sec) [ -9805.4493] [Topology ] . ( 251 sec) [ -9805.3474] [Topology ] . ( 254 sec) [ -9805.9623] [Topology ] . Checking for NNIs, optimizing five branches... . ( 281 sec) [ -9805.1128] [Topology ] . ( 284 sec) [ -9805.0099] [GTR parameters ] . ( 285 sec) [ -9804.6287] [Alpha ][ 0.207349] . ( 285 sec) [ -9804.6287] [Topology ] . ( 288 sec) [ -9802.2333] [Topology ] . ( 291 sec) [ -9802.9608] [Topology ] . Moving backward . ( 292 sec) [ -9801.3804] [Topology ] . ( 295 sec) [ -9800.7142] [Topology ] . ( 298 sec) [ -9800.3920] [Topology ] . ( 301 sec) [ -9800.4421] [Topology ] . Moving backward . ( 302 sec) [ -9799.3829] [Topology ] . ( 305 sec) [ -9799.1803] [Topology ] . ( 308 sec) [ -9799.0856] [Topology ] . Checking for NNIs, optimizing five branches... . ( 335 sec) [ -9799.0828] [Topology ] . ( 338 sec) [ -9799.0160] [GTR parameters ] . ( 338 sec) [ -9798.6946] [Alpha ][ 0.200634] . ( 338 sec) [ -9798.6946] [Topology ] . ( 342 sec) [ -9798.4749] [Topology ] . ( 345 sec) [ -9798.3588] [Topology ] . ( 348 sec) [ -9798.2947] [Topology ] . ( 351 sec) [ -9798.2596] [Topology ] . ( 355 sec) [ -9798.2430] [Topology ] . ( 358 sec) [ -9798.2384] [Topology ] . Checking for NNIs, optimizing five branches... . ( 384 sec) [ -9798.2256] [Topology ] . ( 387 sec) [ -9798.1963] [GTR parameters ] . ( 387 sec) [ -9798.0724] [Alpha ][ 0.196577] . ( 387 sec) [ -9798.0724] [Topology ] . ( 391 sec) [ -9798.0224] [Topology ] . ( 394 sec) [ -9798.0187] [Topology ] . ( 397 sec) [ -9798.0873] [Topology ] . Moving backward . ( 397 sec) [ -9797.9429] [Topology ] . ( 401 sec) [ -9797.9340] [Topology ] . ( 404 sec) [ -9797.9378] [Topology ] . Moving backward . ( 404 sec) [ -9797.9210] [Topology ] . ( 407 sec) [ -9797.9162] [Topology ] . Checking for NNIs, optimizing five branches... . ( 433 sec) [ -9797.9151] [Topology ] . ( 436 sec) [ -9797.9040] [GTR parameters ] . ( 437 sec) [ -9797.8693] [Alpha ][ 0.194506] . ( 437 sec) [ -9797.8693] [Topology ] . ( 440 sec) [ -9797.8490] [Topology ] . ( 443 sec) [ -9797.8406] [Topology ] . ( 446 sec) [ -9797.8393] [Topology ] . ( 450 sec) [ -9797.8428] [Topology ] . Moving backward . ( 450 sec) [ -9797.8300] [Topology ] . ( 453 sec) [ -9797.8281] [Topology ] . ( 456 sec) [ -9797.8274] [Topology ] . Checking for NNIs, optimizing five branches... . ( 483 sec) [ -9797.8245] [GTR parameters ] . ( 484 sec) [ -9797.8118] [Alpha ][ 0.193307] . ( 484 sec) [ -9797.8118] [Topology ] . ( 487 sec) [ -9797.8064] [Topology ] . ( 490 sec) [ -9797.8047] [Topology ] . ( 493 sec) [ -9797.8056] [Topology ] . Checking for NNIs, optimizing five branches... . ( 519 sec) [ -9797.8044] [GTR parameters ] . ( 520 sec) [ -9797.8022] [Alpha ][ 0.192686] . ( 520 sec) [ -9797.8022] [Topology ] . ( 523 sec) [ -9797.8030] [Topology ] . Checking for NNIs, optimizing five branches... . ( 550 sec) [ -9797.8029] [GTR parameters ] . ( 550 sec) [ -9797.8027] [Alpha ][ 0.192434] . ( 550 sec) [ -9797.8027] [Topology ] . ( 553 sec) [ -9797.8092] [Topology ] . Moving backward . ( 553 sec) [ -9797.7933] [Topology ] . ( 557 sec) [ -9797.7920] [Topology ] . ( 560 sec) [ -9797.7919] [Topology ] . Checking for NNIs, optimizing five branches... . ( 586 sec) [ -9797.7913] [GTR parameters ] . ( 587 sec) [ -9797.7912] [Alpha ][ 0.192235] . ( 587 sec) [ -9797.7912] [Topology ] . ( 590 sec) [ -9797.7912] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 645 sec) [ -11652.5156] [GTR parameters ] . ( 646 sec) [ -11452.6188] [Alpha ][ 0.500960] . ( 647 sec) [ -11452.0929] [ 1804] [depth= 1] . ( 648 sec) [ -11450.2527] [ 1804] [depth= 1] . ( 648 sec) [ -11449.6563] [ 1804] [depth= 1] . ( 648 sec) [ -11449.6408] [ 1804] [depth= 1] . ( 649 sec) [ -11449.1939] [ 1804] [depth= 2] . ( 651 sec) [ -11448.9557] [ 1804] [depth= 2] . ( 651 sec) [ -11444.7108] [ 1803] [depth= 2] . ( 652 sec) [ -11443.9941] [ 1803] [depth= 1] . ( 652 sec) [ -11443.6221] [ 1803] [depth= 1] . ( 652 sec) [ -11442.0931] [ 1803] [depth= 3] . ( 656 sec) [ -11439.9495] [ 1818] [depth= 1] . ( 656 sec) [ -11431.1045] [ 1815] [depth= 1] . ( 661 sec) [ -11430.6152] [ 1815] [depth= 1] . ( 661 sec) [ -11430.4390] [ 1815] [depth= 1] . ( 662 sec) [ -11430.2673] [ 1815] [depth= 1] . ( 663 sec) [ -11428.8043] [ 1818] [depth= 1] . ( 663 sec) [ -11425.3632] [ 1815] [depth= 1] . ( 663 sec) [ -11405.3575] [ 1814] [depth= 3] . ( 664 sec) [ -11379.2932] [ 1815] [depth= 1] . ( 665 sec) [ -11376.8116] [ 1814] [depth= 1] . ( 665 sec) [ -11260.5507] [ 1815] [depth= 1] . ( 665 sec) [ -11211.7209] [ 1818] [depth= 5] . ( 666 sec) [ -10932.8505] [ 1816] [depth= 5] . ( 666 sec) [ -10928.3357] [ 1818] [depth= 1] . ( 667 sec) [ -10928.0609] [ 1817] [depth= 1] . ( 667 sec) [ -10862.3752] [ 1822] [depth= 1] . ( 667 sec) [ -10682.0570] [ 1817] [depth= 1] . ( 668 sec) [ -10506.1219] [ 1822] [depth= 1] . ( 668 sec) [ -10506.0163] [ 1824] [depth= 1] . ( 668 sec) [ -10486.0299] [ 1811] [depth= 16] . ( 669 sec) [ -10485.6073] [ 1811] [depth= 1] . ( 669 sec) [ -10481.9317] [ 1811] [depth= 2] . ( 669 sec) [ -10480.5685] [ 1811] [depth= 2] . ( 669 sec) [ -10480.5001] [ 1811] [depth= 2] . ( 670 sec) [ -10479.9902] [ 1811] [depth= 2] . ( 670 sec) [ -10478.6706] [ 1812] [depth= 5] . ( 672 sec) [ -10345.4997] [ 1812] [depth= 1] . ( 672 sec) [ -10344.8115] [ 1812] [depth= 1] . ( 672 sec) [ -10343.9147] [ 1812] [depth= 1] . ( 672 sec) [ -10343.6896] [ 1812] [depth= 1] . ( 672 sec) [ -10342.7771] [ 1812] [depth= 1] . ( 673 sec) [ -10342.7585] [ 1812] [depth= 3] . ( 673 sec) [ -10342.6410] [ 1812] [depth= 1] . ( 673 sec) [ -10341.2968] [ 1812] [depth= 2] . ( 673 sec) [ -10341.2713] [ 1812] [depth= 1] . ( 674 sec) [ -10341.2601] [ 1812] [depth= 3] . ( 674 sec) [ -10341.0839] [ 1812] [depth= 1] . ( 675 sec) [ -10339.4682] [ 1812] [depth= 1] . ( 675 sec) [ -10339.2280] [ 1812] [depth= 1] . ( 675 sec) [ -10330.8042] [ 1813] [depth= 1] . ( 675 sec) [ -10330.4004] [ 1813] [depth= 2] . ( 676 sec) [ -10306.4524] [ 1813] [depth= 8] . ( 676 sec) [ -10305.0688] [ 1813] [depth= 3] . ( 676 sec) [ -10305.0362] [ 1813] [depth= 2] . ( 677 sec) [ -10290.7678] [ 1818] [depth= 4] . ( 677 sec) [ -10275.7196] [ 1815] [depth= 4] . ( 677 sec) [ -10275.6396] [ 1815] [depth= 1] . ( 678 sec) [ -10275.6051] [ 1815] [depth= 1] . ( 678 sec) [ -10275.5351] [ 1815] [depth= 2] . ( 678 sec) [ -10274.7962] [ 1815] [depth= 3] . ( 678 sec) [ -10274.7424] [ 1815] [depth= 1] . ( 679 sec) [ -10274.7241] [ 1815] [depth= 1] . ( 679 sec) [ -10269.5965] [ 1814] [depth= 1] . ( 679 sec) [ -10269.5806] [ 1814] [depth= 2] . ( 680 sec) [ -10269.5653] [ 1814] [depth= 1] . ( 681 sec) [ -10269.5203] [ 1814] [depth= 2] . ( 682 sec) [ -10267.5626] [ 1814] [depth= 1] . ( 683 sec) [ -10267.3426] [ 1814] [depth= 3] . ( 683 sec) [ -10260.5144] [ 1814] [depth= 1] . ( 684 sec) [ -10259.3318] [ 1814] [depth= 7] . ( 684 sec) [ -10259.3152] [ 1814] [depth= 1] . ( 685 sec) [ -10258.6743] [ 1814] [depth= 1] . ( 686 sec) [ -10258.5015] [ 1814] [depth= 2] . ( 686 sec) [ -10258.4641] [ 1814] [depth= 2] . ( 686 sec) [ -10257.5676] [ 1814] [depth= 2] . ( 687 sec) [ -10257.4190] [ 1814] [depth= 3] . ( 688 sec) [ -10232.7877] [ 1819] [depth= 5] . ( 689 sec) [ -10228.8684] [ 1819] [depth= 2] . ( 689 sec) [ -10228.2124] [ 1819] [depth= 1] . ( 689 sec) [ -10227.3146] [ 1819] [depth= 3] . ( 690 sec) [ -10226.9743] [ 1819] [depth= 3] . ( 690 sec) [ -10226.4122] [ 1819] [depth= 3] . ( 691 sec) [ -10226.3557] [ 1819] [depth= 1] . ( 691 sec) [ -10226.3196] [ 1819] [depth= 2] . ( 692 sec) [ -10222.9446] [ 1821] [depth= 1] . ( 694 sec) [ -10221.1931] [ 1817] [depth= 2] . ( 695 sec) [ -10220.1763] [ 1817] [depth= 2] . ( 696 sec) [ -10218.8665] [ 1812] [depth= 1] . ( 697 sec) [ -10218.5340] [ 1812] [depth= 1] . ( 700 sec) [ -10218.1278] [ 1812] [depth= 1] . ( 700 sec) [ -10217.9908] [ 1812] [depth= 1] . ( 700 sec) [ -10217.9197] [ 1812] [depth= 1] . ( 701 sec) [ -10217.8218] [ 1812] [depth= 2] . ( 704 sec) [ -10216.2169] [ 1812] [depth= 4] . ( 704 sec) [ -10215.6185] [ 1812] [depth= 4] . ( 705 sec) [ -10215.0826] [ 1812] [depth= 1] . ( 705 sec) [ -10213.9255] [ 1812] [depth= 3] . ( 709 sec) [ -10210.9828] [ 1812] [depth= 4] . ( 709 sec) [ -10209.1256] [ 1811] [depth= 2] . ( 710 sec) [ -10209.0368] [ 1813] [depth= 1] . ( 710 sec) [ -10203.1643] [ 1812] [depth= 3] . ( 711 sec) [ -10202.7814] [ 1811] [depth= 2] . ( 711 sec) [ -10202.3141] [ 1809] [depth= 1] . ( 711 sec) [ -10201.0728] [ 1809] [depth= 1] . ( 711 sec) [ -10196.3600] [ 1811] [depth= 1] . ( 712 sec) [ -10193.7246] [ 1809] [depth= 1] . ( 712 sec) [ -10180.4249] [ 1809] [depth= 2] . ( 712 sec) [ -10178.5417] [ 1804] [depth= 2] . ( 712 sec) [ -10175.1988] [ 1804] [depth= 1] . ( 712 sec) [ -10161.7998] [ 1803] [depth= 2] . ( 713 sec) [ -10155.9310] [ 1802] [depth= 2] . ( 713 sec) [ -10155.8624] [ 1802] [depth= 1] . ( 714 sec) [ -10148.1001] [ 1806] [depth= 6] . ( 715 sec) [ -10147.9870] [ 1806] [depth= 1] . ( 715 sec) [ -10147.4608] [ 1806] [depth= 3] . ( 715 sec) [ -10127.8867] [ 1807] [depth= 2] . ( 715 sec) [ -10126.4583] [ 1807] [depth= 2] . ( 716 sec) [ -10120.9671] [ 1804] [depth= 3] . ( 716 sec) [ -10116.5433] [ 1803] [depth= 8] . ( 716 sec) [ -10113.3981] [ 1803] [depth= 2] . ( 717 sec) [ -10109.3047] [ 1802] [depth= 3] . ( 717 sec) [ -10108.0795] [ 1802] [depth= 1] . ( 719 sec) [ -10107.9814] [ 1802] [depth= 1] . ( 720 sec) [ -10107.5590] [ 1802] [depth= 1] . ( 720 sec) [ -10106.8627] [ 1802] [depth= 1] . ( 720 sec) [ -10106.7735] [ 1802] [depth= 1] . ( 721 sec) [ -10105.8981] [ 1801] [depth= 6] . ( 730 sec) [ -10105.7823] [ 1801] [depth= 2] . ( 731 sec) [ -10105.0299] [ 1801] [depth= 1] . ( 732 sec) [ -10104.8888] [ 1801] [depth= 1] . ( 734 sec) [ -10104.0647] [ 1801] [depth= 1] . ( 734 sec) [ -10104.0379] [ 1801] [depth= 2] . ( 735 sec) [ -10103.8436] [ 1801] [depth= 4] . ( 735 sec) [ -10103.8001] [ 1801] [depth= 2] . ( 735 sec) [ -10103.4647] [ 1801] [depth= 3] . ( 737 sec) [ -10103.3643] [ 1801] [depth= 2] . ( 738 sec) [ -10103.2997] [ 1801] [depth= 2] . ( 738 sec) [ -10102.5848] [ 1801] [depth= 3] . ( 740 sec) [ -10101.9438] [ 1801] [depth= 1] . ( 740 sec) [ -10101.8763] [ 1801] [depth= 4] . ( 741 sec) [ -10101.8585] [ 1801] [depth= 1] . ( 741 sec) [ -10101.8157] [ 1801] [depth= 1] . ( 741 sec) [ -10101.7736] [ 1801] [depth= 1] . ( 741 sec) [ -10101.7615] [ 1801] [depth= 3] . ( 755 sec) [ -9953.1794] [Branch lengths ] . ( 760 sec) [ -9941.6140] [GTR parameters ] . ( 760 sec) [ -9881.3484] [Alpha ][ 0.271001] . ( 762 sec) [ -9881.2692] [ 1801] [depth= 1] . ( 762 sec) [ -9881.1741] [ 1801] [depth= 1] . ( 762 sec) [ -9881.1510] [ 1801] [depth= 1] . ( 763 sec) [ -9881.0101] [ 1801] [depth= 3] . ( 763 sec) [ -9880.9907] [ 1801] [depth= 3] . ( 767 sec) [ -9880.9311] [ 1801] [depth= 1] . ( 767 sec) [ -9880.8473] [ 1801] [depth= 1] . ( 769 sec) [ -9878.1579] [ 1788] [depth= 1] . ( 770 sec) [ -9873.2427] [ 1801] [depth= 1] . ( 774 sec) [ -9872.8832] [ 1801] [depth= 1] . ( 774 sec) [ -9872.6139] [ 1801] [depth= 1] . ( 777 sec) [ -9872.4297] [ 1801] [depth= 1] . ( 779 sec) [ -9872.4004] [ 1802] [depth= 2] . ( 779 sec) [ -9862.4614] [ 1799] [depth= 5] . ( 779 sec) [ -9861.9306] [ 1797] [depth= 1] . ( 780 sec) [ -9861.8916] [ 1797] [depth= 1] . ( 780 sec) [ -9861.7102] [ 1797] [depth= 4] . ( 780 sec) [ -9861.6852] [ 1797] [depth= 1] . ( 781 sec) [ -9861.6545] [ 1797] [depth= 3] . ( 784 sec) [ -9860.3191] [ 1792] [depth= 2] . ( 785 sec) [ -9860.2976] [ 1792] [depth= 1] . ( 786 sec) [ -9860.1987] [ 1792] [depth= 2] . ( 789 sec) [ -9860.1795] [ 1792] [depth= 1] . ( 790 sec) [ -9860.1642] [ 1792] [depth= 2] . ( 790 sec) [ -9860.1193] [ 1792] [depth= 1] . ( 795 sec) [ -9859.9091] [ 1792] [depth= 1] . ( 799 sec) [ -9859.8069] [ 1792] [depth= 3] . ( 802 sec) [ -9859.2012] [ 1792] [depth= 1] . ( 805 sec) [ -9847.2649] [ 1790] [depth= 5] . ( 805 sec) [ -9846.9679] [ 1790] [depth= 1] . ( 806 sec) [ -9844.7968] [ 1790] [depth= 3] . ( 806 sec) [ -9844.5218] [ 1790] [depth= 3] . ( 808 sec) [ -9844.4750] [ 1790] [depth= 3] . ( 808 sec) [ -9844.2455] [ 1790] [depth= 3] . ( 809 sec) [ -9844.2291] [ 1790] [depth= 1] . ( 811 sec) [ -9843.6004] [ 1791] [depth= 2] . ( 812 sec) [ -9842.2061] [ 1795] [depth= 1] . ( 813 sec) [ -9841.3029] [ 1794] [depth= 1] . ( 814 sec) [ -9836.1393] [ 1792] [depth= 1] . ( 818 sec) [ -9836.0983] [ 1792] [depth= 2] . ( 818 sec) [ -9835.7542] [ 1792] [depth= 4] . ( 819 sec) [ -9835.6089] [ 1792] [depth= 1] . ( 822 sec) [ -9835.5737] [ 1792] [depth= 2] . ( 826 sec) [ -9835.5561] [ 1792] [depth= 3] . ( 836 sec) [ -9835.5391] [ 1792] [depth= 5] . ( 842 sec) [ -9834.6284] [ 1791] [depth= 7] . ( 844 sec) [ -9834.5055] [ 1791] [depth= 1] . ( 844 sec) [ -9834.4278] [ 1791] [depth= 1] . ( 844 sec) [ -9834.3327] [ 1791] [depth= 5] . ( 848 sec) [ -9834.2188] [ 1791] [depth= 2] . ( 853 sec) [ -9834.2047] [ 1791] [depth= 4] . ( 853 sec) [ -9834.1833] [ 1791] [depth= 1] . ( 861 sec) [ -9834.1377] [ 1791] [depth= 2] . ( 863 sec) [ -9834.1029] [ 1791] [depth= 1] . ( 863 sec) [ -9834.0909] [ 1791] [depth= 2] . ( 865 sec) [ -9834.0328] [ 1791] [depth= 1] . ( 865 sec) [ -9833.9698] [ 1791] [depth= 3] . ( 866 sec) [ -9833.6468] [ 1791] [depth= 2] . ( 866 sec) [ -9833.6321] [ 1791] [depth= 3] . ( 867 sec) [ -9833.5122] [ 1791] [depth= 2] . ( 867 sec) [ -9833.4785] [ 1791] [depth= 3] . ( 872 sec) [ -9833.4450] [ 1791] [depth= 5] . ( 875 sec) [ -9833.2978] [ 1791] [depth= 5] . ( 875 sec) [ -9833.2720] [ 1791] [depth= 2] . ( 891 sec) [ -9803.7671] [Branch lengths ] . ( 895 sec) [ -9800.3513] [GTR parameters ] . ( 896 sec) [ -9799.7017] [Alpha ][ 0.256544] . ( 897 sec) [ -9799.6585] [ 1791] [depth= 3] . ( 897 sec) [ -9799.6427] [ 1791] [depth= 1] . ( 899 sec) [ -9799.6110] [ 1791] [depth= 2] . ( 901 sec) [ -9799.5992] [ 1791] [depth= 2] . ( 905 sec) [ -9799.0196] [ 1775] [depth= 1] . ( 913 sec) [ -9798.7283] [ 1775] [depth= 2] . ( 913 sec) [ -9798.5514] [ 1774] [depth= 1] . ( 919 sec) [ -9798.0360] [ 1776] [depth= 1] . ( 926 sec) [ -9795.6130] [ 1781] [depth= 2] . ( 926 sec) [ -9795.5867] [ 1781] [depth= 3] . ( 926 sec) [ -9795.5644] [ 1781] [depth= 3] . ( 926 sec) [ -9795.4940] [ 1781] [depth= 1] . ( 927 sec) [ -9795.4829] [ 1781] [depth= 1] . ( 928 sec) [ -9795.1437] [ 1781] [depth= 1] . ( 930 sec) [ -9794.6439] [ 1781] [depth= 2] . ( 947 sec) [ -9794.6310] [ 1781] [depth= 3] . ( 949 sec) [ -9794.6001] [ 1776] [depth= 1] . ( 950 sec) [ -9794.5703] [ 1776] [depth= 3] . ( 970 sec) [ -9794.5218] [ 1776] [depth= 1] . ( 994 sec) [ -9793.3703] [ 1776] [depth= 1] . ( 1008 sec) [ -9793.3389] [ 1776] [depth= 1] . ( 1014 sec) [ -9793.3157] [ 1776] [depth= 2] . ( 1026 sec) [ -9793.2296] [ 1776] [depth= 4] . ( 1058 sec) [ -9772.2670] [Branch lengths ] . ( 1062 sec) [ -9771.3043] [GTR parameters ] . ( 1062 sec) [ -9770.5418] [Alpha ][ 0.242539] . ( 1064 sec) [ -9770.5201] [ 1776] [depth= 3] . ( 1064 sec) [ -9770.4923] [ 1776] [depth= 1] . ( 1064 sec) [ -9770.4729] [ 1776] [depth= 1] . ( 1064 sec) [ -9770.4143] [ 1776] [depth= 1] . ( 1080 sec) [ -9770.3980] [ 1776] [depth= 1] . ( 1082 sec) [ -9770.0808] [ 1775] [depth= 1] . ( 1083 sec) [ -9769.1841] [ 1772] [depth= 1] . ( 1087 sec) [ -9769.1155] [ 1772] [depth= 2] . ( 1095 sec) [ -9769.0782] [ 1772] [depth= 1] . ( 1097 sec) [ -9768.8525] [ 1772] [depth= 4] . ( 1106 sec) [ -9768.8053] [ 1772] [depth= 2] . ( 1113 sec) [ -9768.6990] [ 1772] [depth= 1] . ( 1118 sec) [ -9768.4987] [ 1772] [depth= 2] . ( 1119 sec) [ -9768.4545] [ 1772] [depth= 2] . ( 1135 sec) [ -9768.3774] [ 1772] [depth= 3] . ( 1136 sec) [ -9768.3491] [ 1772] [depth= 2] . ( 1141 sec) [ -9767.9802] [ 1772] [depth= 1] . ( 1224 sec) [ -9755.7875] [Branch lengths ] . ( 1227 sec) [ -9755.6310] [GTR parameters ] . ( 1227 sec) [ -9755.1136] [Alpha ][ 0.232004] . ( 1228 sec) [ -9755.0893] [ 1772] [depth= 2] . ( 1230 sec) [ -9755.0692] [ 1772] [depth= 1] . ( 1230 sec) [ -9755.0389] [ 1772] [depth= 2] . ( 1232 sec) [ -9755.0012] [ 1772] [depth= 2] . ( 1234 sec) [ -9754.9835] [ 1772] [depth= 1] . ( 1249 sec) [ -9754.9662] [ 1772] [depth= 1] . ( 1250 sec) [ -9754.6012] [ 1773] [depth= 1] . ( 1262 sec) [ -9754.5902] [ 1773] [depth= 3] . ( 1266 sec) [ -9754.5709] [ 1773] [depth= 1] . ( 1398 sec) [ -9745.7989] [Branch lengths ] . ( 1401 sec) [ -9745.6503] [GTR parameters ] . ( 1402 sec) [ -9745.0591] [Alpha ][ 0.221561] . ( 1404 sec) [ -9745.0394] [ 1773] [depth= 2] . ( 1405 sec) [ -9744.9778] [ 1773] [depth= 3] . ( 1408 sec) [ -9744.8273] [ 1773] [depth= 1] . ( 1424 sec) [ -9744.7975] [ 1773] [depth= 1] . ( 1426 sec) [ -9744.7786] [ 1772] [depth= 1] . ( 1522 sec) [ -9744.7681] [ 1772] [depth= 2] . ( 1572 sec) [ -9738.4495] [Branch lengths ] . ( 1575 sec) [ -9738.3435] [GTR parameters ] . ( 1576 sec) [ -9737.7858] [Alpha ][ 0.211998] . ( 1578 sec) [ -9737.7480] [ 1772] [depth= 3] . ( 1581 sec) [ -9737.7294] [ 1772] [depth= 2] . ( 1594 sec) [ -9737.6210] [ 1773] [depth= 1] . ( 1598 sec) [ -9737.5690] [ 1774] [depth= 1] . ( 1612 sec) [ -9737.5563] [ 1775] [depth= 2] . ( 1612 sec) [ -9737.5456] [ 1775] [depth= 1] . ( 1744 sec) [ -9730.2258] [Branch lengths ] . ( 1747 sec) [ -9730.0041] [GTR parameters ] . ( 1748 sec) [ -9729.4555] [Alpha ][ 0.203008] . ( 1749 sec) [ -9729.4367] [ 1775] [depth= 2] . ( 1920 sec) [ -9725.8229] [Branch lengths ] . ( 1924 sec) [ -9725.7603] [GTR parameters ] . ( 1924 sec) [ -9725.4276] [Alpha ][ 0.196247] . ( 1927 sec) [ -9725.4155] [ 1775] [depth= 2] . ( 1952 sec) [ -9725.3902] [ 1775] [depth= 3] . ( 2093 sec) [ -9722.1618] [Branch lengths ] . ( 2095 sec) [ -9722.1311] [GTR parameters ] . ( 2095 sec) [ -9721.9653] [Alpha ][ 0.191592] . ( 2255 sec) [ -9721.3562] [Branch lengths ] . ( 2305 sec) [ -9721.2129] [ 1773] [depth= 1] . ( 2319 sec) [ -9721.0153] [ 1772] [depth= 2] . ( 2419 sec) [ -9721.0000] [ 1772] [depth= 1] . ( 2431 sec) [ -9720.6734] [Branch lengths ] . ( 2434 sec) [ -9720.6482] [GTR parameters ] . ( 2434 sec) [ -9720.5001] [Alpha ][ 0.187220] . ( 2434 sec) [ -9720.5001] [Topology ] . ( 2438 sec) [ -9720.3292] [Topology ] . ( 2441 sec) [ -9720.2420] [Topology ] . ( 2444 sec) [ -9720.1868] [Topology ] . ( 2448 sec) [ -9720.1510] [Topology ] . ( 2451 sec) [ -9720.1275] [Topology ] . ( 2454 sec) [ -9720.1120] [Topology ] . ( 2455 sec) [ -9720.0959] [GTR parameters ] . ( 2456 sec) [ -9719.9999] [Alpha ][ 0.183753] . ( 2456 sec) [ -9719.9999] [Topology ] . ( 2459 sec) [ -9719.9431] [Topology ] . ( 2462 sec) [ -9719.9109] [Topology ] . ( 2466 sec) [ -9719.8905] [Topology ] . ( 2469 sec) [ -9719.8773] [Topology ] . ( 2472 sec) [ -9719.8685] [Topology ] . ( 2475 sec) [ -9719.8626] [Topology ] . ( 2477 sec) [ -9719.8556] [GTR parameters ] . ( 2477 sec) [ -9719.8198] [Alpha ][ 0.181671] . ( 2477 sec) [ -9719.8198] [Topology ] . ( 2481 sec) [ -9719.7981] [Topology ] . ( 2484 sec) [ -9719.7856] [Topology ] . ( 2487 sec) [ -9719.7775] [Topology ] . ( 2490 sec) [ -9719.7727] [Topology ] . ( 2494 sec) [ -9719.7699] [Topology ] . ( 2497 sec) [ -9719.7681] [Topology ] . ( 2499 sec) [ -9719.7655] [GTR parameters ] . ( 2499 sec) [ -9719.7521] [Alpha ][ 0.180440] . ( 2499 sec) [ -9719.7521] [Topology ] . ( 2502 sec) [ -9719.7447] [Topology ] . ( 2506 sec) [ -9719.7407] [Topology ] . ( 2509 sec) [ -9719.7382] [Topology ] . ( 2512 sec) [ -9719.7367] [Topology ] . ( 2515 sec) [ -9719.7358] [Topology ] . ( 2516 sec) [ -9719.7350] [GTR parameters ] . ( 2517 sec) [ -9719.7303] [Alpha ][ 0.179746] . ( 2517 sec) [ -9719.7303] [Topology ] . ( 2520 sec) [ -9719.7274] [Topology ] . ( 2523 sec) [ -9719.7258] [Topology ] . ( 2527 sec) [ -9719.7248] [Topology ] . ( 2527 sec) [ -9719.7246] [GTR parameters ] . ( 2528 sec) [ -9719.7233] [Alpha ][ 0.179429] . ( 2528 sec) [ -9719.7233] [Topology ] . ( 2531 sec) [ -9719.7219] [Topology ] . ( 2534 sec) [ -9719.7210] [Topology ] . ( 2535 sec) [ -9719.7209] [GTR parameters ] . ( 2536 sec) [ -9719.7205] [Alpha ][ 0.179077] . ( 2536 sec) [ -9719.7205] [Topology ] . ( 2539 sec) [ -9719.7191] [Topology ] . ( 2542 sec) [ -9719.7183] [Topology ] . ( 2543 sec) [ -9719.7182] [GTR parameters ] . ( 2543 sec) [ -9719.7182] [Alpha ][ 0.179077] . ( 2543 sec) [ -9719.7182] [Topology ] . ( 2547 sec) [ -9719.7177] [Topology ] . ( 2548 sec) [ -9719.7177] [GTR parameters ] . ( 2548 sec) [ -9719.7176] [Alpha ][ 0.178845] . Checking for NNIs, optimizing five branches... . ( 2573 sec) [ -9719.7166] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9797.791236 . Log likelihood obtained after SPR moves : -9719.716553 . Log likelihood of the current tree: -9719.716553. . Printing the most likely tree in file 'nucleic_M2707_115x1677_2006.phy_phyml_tree.txt'... . Time used 0h43m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2595.38user 0.00system 43:21.23elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps