.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M4058_406x6016_2008.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 . 71 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 5231 patterns found. (out of a total of 6016 sites) . 919 sites without polymorphism (15.28%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis requires at least 1133Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 135 sec) [ -490006.6934] [GTR parameters ] . ( 147 sec) [ -489279.9174] [Alpha ][ 0.667175] . ( 207 sec) [ -489227.7592] [125926] [depth= 2] . ( 212 sec) [ -489127.4282] [125872] [depth= 2] . ( 218 sec) [ -489028.7135] [125843] [depth= 2] . ( 235 sec) [ -489010.0936] [125819] [depth= 2] . ( 241 sec) [ -488959.2680] [125775] [depth= 2] . ( 268 sec) [ -488957.6376] [125783] [depth= 1] . ( 273 sec) [ -488907.7615] [125760] [depth= 3] . ( 301 sec) [ -488873.1332] [125762] [depth= 1] . ( 316 sec) [ -488738.9605] [125692] [depth= 4] . ( 334 sec) [ -488720.8224] [125693] [depth= 1] . ( 339 sec) [ -488695.8571] [125692] [depth= 1] . ( 355 sec) [ -488693.3603] [125664] [depth= 1] . ( 360 sec) [ -488676.8418] [125656] [depth= 1] . ( 370 sec) [ -488658.8944] [125685] [depth= 3] . ( 389 sec) [ -488641.9768] [125673] [depth= 2] . ( 394 sec) [ -488638.5719] [125678] [depth= 1] . ( 400 sec) [ -488637.5022] [125677] [depth= 1] . ( 406 sec) [ -488415.2943] [125566] [depth= 106] . ( 429 sec) [ -488409.0933] [125565] [depth= 1] . ( 435 sec) [ -488275.2003] [125529] [depth= 102] . ( 441 sec) [ -488252.1138] [125545] [depth= 1] . ( 446 sec) [ -488229.6187] [125527] [depth= 3] . ( 452 sec) [ -487913.4805] [125314] [depth= 98] . ( 462 sec) [ -487875.5753] [125289] [depth= 3] . ( 470 sec) [ -487861.9700] [125294] [depth= 4] . ( 476 sec) [ -487814.7566] [125253] [depth= 19] . ( 481 sec) [ -487757.5798] [125246] [depth= 17] . ( 487 sec) [ -487707.9969] [125217] [depth= 16] . ( 497 sec) [ -487694.2473] [125210] [depth= 4] . ( 505 sec) [ -487646.1882] [125176] [depth= 2] . ( 519 sec) [ -487616.7850] [125181] [depth= 10] . ( 544 sec) [ -487616.1660] [125162] [depth= 2] . ( 551 sec) [ -487508.2379] [125106] [depth= 1] . ( 559 sec) [ -487501.0407] [125101] [depth= 1] . ( 567 sec) [ -487499.2362] [125105] [depth= 1] . ( 575 sec) [ -487492.2867] [125107] [depth= 1] . ( 580 sec) [ -487490.5178] [125098] [depth= 1] . ( 598 sec) [ -487488.3696] [125096] [depth= 1] . ( 604 sec) [ -487450.7987] [125076] [depth= 2] . ( 616 sec) [ -487388.3671] [125022] [depth= 10] . ( 622 sec) [ -487369.2025] [125023] [depth= 4] . ( 628 sec) [ -487355.4881] [125020] [depth= 3] . ( 633 sec) [ -487340.7742] [125000] [depth= 2] . ( 639 sec) [ -487317.7584] [124994] [depth= 8] . ( 644 sec) [ -487304.8252] [124988] [depth= 6] . ( 648 sec) [ -487259.3809] [124980] [depth= 1] . ( 653 sec) [ -487136.6298] [124956] [depth= 1] . ( 658 sec) [ -487121.5538] [124930] [depth= 7] . ( 668 sec) [ -487098.9500] [124934] [depth= 4] . ( 680 sec) [ -487082.7926] [124929] [depth= 1] . ( 686 sec) [ -487076.4145] [124918] [depth= 1] . ( 704 sec) [ -487064.4193] [124914] [depth= 1] . ( 711 sec) [ -487028.8819] [124868] [depth= 4] . ( 717 sec) [ -487020.3401] [124865] [depth= 1] . ( 727 sec) [ -486976.5135] [124841] [depth= 4] . ( 733 sec) [ -486969.4525] [124841] [depth= 1] . ( 738 sec) [ -486968.0724] [124843] [depth= 2] . ( 747 sec) [ -486743.8251] [124737] [depth= 26] . ( 768 sec) [ -486577.8569] [124707] [depth= 2] . ( 773 sec) [ -486566.3275] [124688] [depth= 1] . ( 779 sec) [ -486528.1630] [124650] [depth= 1] . ( 796 sec) [ -486512.2609] [124654] [depth= 2] . ( 808 sec) [ -486507.5751] [124654] [depth= 2] . ( 817 sec) [ -486471.3268] [124673] [depth= 1] . ( 830 sec) [ -486403.1745] [124659] [depth= 20] . ( 836 sec) [ -486395.2185] [124639] [depth= 4] . ( 845 sec) [ -486371.2952] [124629] [depth= 1] . ( 860 sec) [ -486369.2412] [124598] [depth= 4] . ( 870 sec) [ -486219.5918] [124540] [depth= 12] . ( 875 sec) [ -486180.8795] [124503] [depth= 1] . ( 883 sec) [ -486093.3329] [124504] [depth= 19] . ( 892 sec) [ -486089.0049] [124506] [depth= 1] . ( 906 sec) [ -486071.8601] [124501] [depth= 7] . ( 930 sec) [ -486056.5261] [124505] [depth= 1] . ( 935 sec) [ -486046.1516] [124501] [depth= 1] . ( 941 sec) [ -485875.0057] [124437] [depth= 5] . ( 947 sec) [ -485797.9122] [124404] [depth= 1] . ( 952 sec) [ -485506.3017] [124355] [depth= 9] . ( 958 sec) [ -485427.9141] [124318] [depth= 7] . ( 961 sec) [ -485339.3703] [124294] [depth= 2] . ( 967 sec) [ -485322.4823] [124299] [depth= 2] . ( 972 sec) [ -485123.1675] [124180] [depth= 18] . ( 983 sec) [ -485121.2323] [124169] [depth= 2] . ( 988 sec) [ -485107.9749] [124149] [depth= 1] . ( 999 sec) [ -485098.1118] [124149] [depth= 1] . ( 1006 sec) [ -485094.4681] [124142] [depth= 1] . ( 1012 sec) [ -485092.4114] [124119] [depth= 1] . ( 1017 sec) [ -485046.6026] [124105] [depth= 2] . ( 1039 sec) [ -484896.5868] [123996] [depth= 4] . ( 1042 sec) [ -484869.8869] [123975] [depth= 1] . ( 1050 sec) [ -484833.8188] [123965] [depth= 6] . ( 1056 sec) [ -484769.5164] [123929] [depth= 6] . ( 1064 sec) [ -484678.9082] [123910] [depth= 1] . ( 1072 sec) [ -484640.8278] [123895] [depth= 1] . ( 1082 sec) [ -484621.8960] [123886] [depth= 1] . ( 1088 sec) [ -484617.1750] [123877] [depth= 8] . ( 1094 sec) [ -484613.6669] [123867] [depth= 4] . ( 1099 sec) [ -484576.2312] [123850] [depth= 5] . ( 1107 sec) [ -484574.9737] [123852] [depth= 1] . ( 1110 sec) [ -484574.0689] [123853] [depth= 1] . ( 1116 sec) [ -484563.0918] [123858] [depth= 1] . ( 1121 sec) [ -484453.3991] [123797] [depth= 12] . ( 1132 sec) [ -484442.4814] [123777] [depth= 3] . ( 1138 sec) [ -484440.5266] [123775] [depth= 1] . ( 1144 sec) [ -484435.2111] [123748] [depth= 1] . ( 1150 sec) [ -484380.7810] [123714] [depth= 6] . ( 1158 sec) [ -484373.8068] [123720] [depth= 2] . ( 1165 sec) [ -484326.1269] [123761] [depth= 1] . ( 1170 sec) [ -484290.2440] [123747] [depth= 11] . ( 1179 sec) [ -484289.1679] [123744] [depth= 6] . ( 1184 sec) [ -484272.1345] [123747] [depth= 1] . ( 1190 sec) [ -484208.1089] [123743] [depth= 7] . ( 1198 sec) [ -484159.0930] [123709] [depth= 2] . ( 1206 sec) [ -484157.5692] [123702] [depth= 9] . ( 1216 sec) [ -484064.8846] [123658] [depth= 3] . ( 1222 sec) [ -483998.9743] [123635] [depth= 4] . ( 1227 sec) [ -483944.1741] [123650] [depth= 1] . ( 1235 sec) [ -483901.0449] [123625] [depth= 3] . ( 1243 sec) [ -483853.7862] [123590] [depth= 2] . ( 1248 sec) [ -483818.0394] [123557] [depth= 2] . ( 1257 sec) [ -483802.4183] [123542] [depth= 1] . ( 1265 sec) [ -483711.7513] [123505] [depth= 1] . ( 1273 sec) [ -483671.1079] [123487] [depth= 3] . ( 1286 sec) [ -483659.1242] [123476] [depth= 2] . ( 1292 sec) [ -483614.0984] [123442] [depth= 1] . ( 1297 sec) [ -483527.0140] [123408] [depth= 2] . ( 1303 sec) [ -483502.9353] [123413] [depth= 1] . ( 1313 sec) [ -483478.8950] [123411] [depth= 1] . ( 1322 sec) [ -483458.8940] [123416] [depth= 1] . ( 1340 sec) [ -483440.6798] [123415] [depth= 1] . ( 1348 sec) [ -483439.3673] [123403] [depth= 2] . ( 1353 sec) [ -483394.1805] [123379] [depth= 1] . ( 1363 sec) [ -483381.2833] [123346] [depth= 11] . ( 1369 sec) [ -483274.9950] [123289] [depth= 10] . ( 1377 sec) [ -483244.6241] [123275] [depth= 2] . ( 1380 sec) [ -483242.7629] [123270] [depth= 1] . ( 1388 sec) [ -483236.1125] [123269] [depth= 1] . ( 1393 sec) [ -483223.5613] [123262] [depth= 1] . ( 1406 sec) [ -483192.9419] [123248] [depth= 1] . ( 1410 sec) [ -483178.5189] [123249] [depth= 1] . ( 1415 sec) [ -483104.1430] [123121] [depth= 43] . ( 1423 sec) [ -483103.4215] [123127] [depth= 1] . ( 1428 sec) [ -483062.5401] [123133] [depth= 1] . ( 1437 sec) [ -483031.7309] [123127] [depth= 1] . ( 1442 sec) [ -482780.3675] [123037] [depth= 5] . ( 1450 sec) [ -482763.5534] [123023] [depth= 1] . ( 1470 sec) [ -482758.0727] [123031] [depth= 1] . ( 1483 sec) [ -482739.5416] [123020] [depth= 5] . ( 1492 sec) [ -482636.4986] [122981] [depth= 5] . ( 1502 sec) [ -482604.6825] [122940] [depth= 7] . ( 1507 sec) [ -482575.7553] [122915] [depth= 3] . ( 1513 sec) [ -482560.1088] [122913] [depth= 1] . ( 1518 sec) [ -482549.2087] [122911] [depth= 3] . ( 1529 sec) [ -482473.7291] [122906] [depth= 2] . ( 1534 sec) [ -482470.4897] [122906] [depth= 2] . ( 1544 sec) [ -482460.5078] [122905] [depth= 1] . ( 1551 sec) [ -482453.4382] [122898] [depth= 1] . ( 1560 sec) [ -482450.8540] [122904] [depth= 1] . ( 1564 sec) [ -482450.4402] [122905] [depth= 1] . ( 1570 sec) [ -482391.7461] [122874] [depth= 5] . ( 1575 sec) [ -482386.9379] [122864] [depth= 2] . ( 1581 sec) [ -482354.1977] [122847] [depth= 2] . ( 1591 sec) [ -482341.9002] [122850] [depth= 2] . ( 1602 sec) [ -482328.1449] [122853] [depth= 2] . ( 1620 sec) [ -482242.8181] [122818] [depth= 8] . ( 1625 sec) [ -481958.3050] [122680] [depth= 22] . ( 1630 sec) [ -481953.7843] [122684] [depth= 1] . ( 1643 sec) [ -481915.1388] [122681] [depth= 5] . ( 1650 sec) [ -481912.1029] [122671] [depth= 2] . ( 1655 sec) [ -481910.9552] [122675] [depth= 1] . ( 1662 sec) [ -481907.5512] [122675] [depth= 2] . ( 1668 sec) [ -481903.1477] [122664] [depth= 4] . ( 1676 sec) [ -481795.4096] [122613] [depth= 4] . ( 1691 sec) [ -481789.1581] [122609] [depth= 1] . ( 1696 sec) [ -481782.7688] [122600] [depth= 2] . ( 1710 sec) [ -481777.5874] [122592] [depth= 1] . ( 1715 sec) [ -481757.9276] [122596] [depth= 1] . ( 1721 sec) [ -481722.6251] [122595] [depth= 1] . ( 1729 sec) [ -481718.3684] [122597] [depth= 1] . ( 1747 sec) [ -481717.3973] [122597] [depth= 2] . ( 1755 sec) [ -481678.6289] [122576] [depth= 1] . ( 1760 sec) [ -481670.1080] [122576] [depth= 1] . ( 1779 sec) [ -481669.2964] [122579] [depth= 1] . ( 1784 sec) [ -481667.7979] [122589] [depth= 1] . ( 1801 sec) [ -481634.3350] [122554] [depth= 2] . ( 1810 sec) [ -481621.1394] [122533] [depth= 1] . ( 1818 sec) [ -481608.8089] [122526] [depth= 1] . ( 1831 sec) [ -481596.7736] [122517] [depth= 1] . ( 1844 sec) [ -481593.9244] [122515] [depth= 1] . ( 1850 sec) [ -481580.5533] [122519] [depth= 1] . ( 1854 sec) [ -481577.4253] [122516] [depth= 1] . ( 1864 sec) [ -481566.4308] [122518] [depth= 3] . ( 1869 sec) [ -481522.9172] [122483] [depth= 8] . ( 1877 sec) [ -481368.2958] [122398] [depth= 12] . ( 1892 sec) [ -481363.9800] [122398] [depth= 2] . ( 1899 sec) [ -481357.4403] [122375] [depth= 3] . ( 1904 sec) [ -481186.2331] [122332] [depth= 47] . ( 1914 sec) [ -481158.9934] [122321] [depth= 4] . ( 1919 sec) [ -481134.0895] [122312] [depth= 1] . ( 1925 sec) [ -481078.6997] [122309] [depth= 1] . ( 1935 sec) [ -481071.3372] [122310] [depth= 1] . ( 1952 sec) [ -481059.3065] [122304] [depth= 5] . ( 1956 sec) [ -481054.0005] [122304] [depth= 1] . ( 1961 sec) [ -481006.7162] [122280] [depth= 2] . ( 1966 sec) [ -480994.2008] [122266] [depth= 3] . ( 1972 sec) [ -480989.1701] [122262] [depth= 2] . ( 1980 sec) [ -480970.9126] [122263] [depth= 1] . ( 1986 sec) [ -480939.7562] [122232] [depth= 6] . ( 1991 sec) [ -480868.2582] [122192] [depth= 2] . ( 1997 sec) [ -480857.8194] [122189] [depth= 1] . ( 2007 sec) [ -480856.7621] [122177] [depth= 2] . ( 2019 sec) [ -480849.1203] [122173] [depth= 1] . ( 2024 sec) [ -480848.1404] [122179] [depth= 3] . ( 2028 sec) [ -480838.1159] [122164] [depth= 1] . ( 2042 sec) [ -480792.9540] [122123] [depth= 6] . ( 2046 sec) [ -480760.1193] [122111] [depth= 1] . ( 2051 sec) [ -480752.6336] [122106] [depth= 3] . ( 2056 sec) [ -480500.4403] [121999] [depth= 8] . ( 2061 sec) [ -480482.9398] [121993] [depth= 3] . ( 2075 sec) [ -480455.8340] [121995] [depth= 2] . ( 2088 sec) [ -480451.4605] [121985] [depth= 2] . ( 2099 sec) [ -480447.0624] [121980] [depth= 2] . ( 2105 sec) [ -480439.9996] [121976] [depth= 1] . ( 2111 sec) [ -480410.8568] [121979] [depth= 1] . ( 2138 sec) [ -480404.2705] [121983] [depth= 3] . ( 2147 sec) [ -480388.3121] [121973] [depth= 2] . ( 2154 sec) [ -480380.3405] [121966] [depth= 1] . ( 2160 sec) [ -480374.5341] [121974] [depth= 1] . ( 2168 sec) [ -480306.4985] [121950] [depth= 2] . ( 2173 sec) [ -480298.0348] [121936] [depth= 1] . ( 2184 sec) [ -480273.3683] [121915] [depth= 3] . ( 2192 sec) [ -480268.1650] [121904] [depth= 3] . ( 2197 sec) [ -480204.2040] [121844] [depth= 4] . ( 2207 sec) [ -480200.2674] [121828] [depth= 3] . ( 2229 sec) [ -480126.7977] [121799] [depth= 6] . ( 2235 sec) [ -480118.8430] [121777] [depth= 2] . ( 2240 sec) [ -480116.0112] [121772] [depth= 1] . ( 2251 sec) [ -480113.4549] [121772] [depth= 1] . ( 2259 sec) [ -480092.0612] [121772] [depth= 1] . ( 2268 sec) [ -480072.1129] [121818] [depth= 1] . ( 2275 sec) [ -480033.2778] [121807] [depth= 1] . ( 2279 sec) [ -479957.7906] [121806] [depth= 1] . ( 2285 sec) [ -479952.6789] [121794] [depth= 4] . ( 2301 sec) [ -479885.3551] [121782] [depth= 1] . ( 2317 sec) [ -479885.2790] [121777] [depth= 1] . ( 2324 sec) [ -479877.4156] [121782] [depth= 1] . ( 2343 sec) [ -479860.0633] [121757] [depth= 4] . ( 2359 sec) [ -479854.2517] [121758] [depth= 1] . ( 2364 sec) [ -479832.3244] [121757] [depth= 1] . ( 2375 sec) [ -479806.1859] [121758] [depth= 3] . ( 2381 sec) [ -479804.3824] [121747] [depth= 2] . ( 2386 sec) [ -479771.5194] [121744] [depth= 2] . ( 2392 sec) [ -479757.0884] [121744] [depth= 3] . ( 2398 sec) [ -479732.1744] [121729] [depth= 3] . ( 2403 sec) [ -479729.1180] [121732] [depth= 1] . ( 2418 sec) [ -479688.7282] [121715] [depth= 2] . ( 2422 sec) [ -479631.7035] [121723] [depth= 1] . ( 2427 sec) [ -479552.4247] [121666] [depth= 2] . ( 2433 sec) [ -479497.0332] [121662] [depth= 3] . ( 2438 sec) [ -479479.3548] [121664] [depth= 1] . ( 2446 sec) [ -479475.8895] [121659] [depth= 2] . ( 2463 sec) [ -479469.0647] [121664] [depth= 1] . ( 2469 sec) [ -479441.6344] [121670] [depth= 1] . ( 2491 sec) [ -479441.3028] [121666] [depth= 1] . ( 2508 sec) [ -479435.6238] [121670] [depth= 1] . ( 2525 sec) [ -479434.3808] [121680] [depth= 1] . ( 2530 sec) [ -479395.1928] [121683] [depth= 1] . ( 2555 sec) [ -479359.8497] [121683] [depth= 1] . ( 2560 sec) [ -479350.8764] [121683] [depth= 1] . ( 2580 sec) [ -479316.7737] [121672] [depth= 2] . ( 2588 sec) [ -479307.7873] [121672] [depth= 1] . ( 2594 sec) [ -479303.2198] [121672] [depth= 1] . ( 2608 sec) [ -479278.3818] [121662] [depth= 1] . ( 2614 sec) [ -479267.0712] [121660] [depth= 1] . ( 2624 sec) [ -479230.4591] [121648] [depth= 1] . ( 2636 sec) [ -479220.9886] [121652] [depth= 1] . ( 2644 sec) [ -479218.2413] [121655] [depth= 1] . ( 2650 sec) [ -479189.8406] [121647] [depth= 4] . ( 2655 sec) [ -479181.3812] [121625] [depth= 2] . ( 2661 sec) [ -479178.1910] [121628] [depth= 2] . ( 2668 sec) [ -479146.3511] [121612] [depth= 1] . ( 2676 sec) [ -479052.3689] [121603] [depth= 1] . ( 2682 sec) [ -478983.7286] [121608] [depth= 1] . ( 2692 sec) [ -478973.7457] [121617] [depth= 1] . ( 2698 sec) [ -478959.8940] [121620] [depth= 1] . ( 2703 sec) [ -478951.2169] [121615] [depth= 1] . ( 2707 sec) [ -478932.5566] [121620] [depth= 2] . ( 2713 sec) [ -478767.9739] [121600] [depth= 1] . ( 2722 sec) [ -478747.2288] [121597] [depth= 1] . ( 2728 sec) [ -478727.5041] [121588] [depth= 1] . ( 2735 sec) [ -478727.4410] [121589] [depth= 1] . ( 2748 sec) [ -478720.7379] [121578] [depth= 2] . ( 2756 sec) [ -478705.2195] [121581] [depth= 1] . ( 2761 sec) [ -478700.2049] [121578] [depth= 1] . ( 2771 sec) [ -478697.2454] [121580] [depth= 2] . ( 2784 sec) [ -478694.5966] [121584] [depth= 1] . ( 2789 sec) [ -478676.1793] [121580] [depth= 1] . ( 2795 sec) [ -478669.3419] [121573] [depth= 3] . ( 2800 sec) [ -478587.3110] [121563] [depth= 2] . ( 2816 sec) [ -478587.2186] [121558] [depth= 1] . ( 2822 sec) [ -478574.8061] [121556] [depth= 2] . ( 2834 sec) [ -478559.2957] [121565] [depth= 2] . ( 2840 sec) [ -478529.6328] [121565] [depth= 1] . ( 2853 sec) [ -478526.5702] [121560] [depth= 1] . ( 2863 sec) [ -478520.6856] [121563] [depth= 1] . ( 2871 sec) [ -478516.1970] [121562] [depth= 5] . ( 2877 sec) [ -478497.4539] [121559] [depth= 1] . ( 2887 sec) [ -478475.3640] [121562] [depth= 1] . ( 2902 sec) [ -478471.0957] [121565] [depth= 1] . ( 2909 sec) [ -478317.5261] [121572] [depth= 1] . ( 2914 sec) [ -478317.4843] [121576] [depth= 1] . ( 2920 sec) [ -478316.8047] [121581] [depth= 1] . ( 2925 sec) [ -478313.5100] [121576] [depth= 1] . ( 2933 sec) [ -478303.2147] [121584] [depth= 1] . ( 2936 sec) [ -478300.6156] [121587] [depth= 2] . ( 2944 sec) [ -478251.1658] [121570] [depth= 1] . ( 2950 sec) [ -478247.8145] [121566] [depth= 1] . ( 2957 sec) [ -478235.3978] [121570] [depth= 1] . ( 2962 sec) [ -478224.7325] [121571] [depth= 1] . ( 2968 sec) [ -478191.9363] [121570] [depth= 1] . ( 2973 sec) [ -478188.0548] [121567] [depth= 1] . ( 2987 sec) [ -478187.3912] [121571] [depth= 1] . ( 2992 sec) [ -478186.4012] [121574] [depth= 2] . ( 3000 sec) [ -477974.3298] [121553] [depth= 1] . ( 3006 sec) [ -477973.2111] [121556] [depth= 1] . ( 3021 sec) [ -477950.0679] [121556] [depth= 1] . ( 3026 sec) [ -477917.9484] [121550] [depth= 1] . ( 3032 sec) [ -477906.9591] [121539] [depth= 1] . ( 3043 sec) [ -477904.4938] [121543] [depth= 1] . ( 3049 sec) [ -477902.7198] [121535] [depth= 1] . ( 3057 sec) [ -477872.8362] [121537] [depth= 1] . ( 3065 sec) [ -477848.6753] [121541] [depth= 2] . ( 3071 sec) [ -477843.5189] [121534] [depth= 2] . ( 3080 sec) [ -477838.8498] [121535] [depth= 1] . ( 3084 sec) [ -477832.4787] [121550] [depth= 1] . ( 3089 sec) [ -477827.4401] [121560] [depth= 1] . ( 3099 sec) [ -477822.0396] [121559] [depth= 2] . ( 3106 sec) [ -477818.5057] [121553] [depth= 1] . ( 3112 sec) [ -477779.3774] [121556] [depth= 1] . ( 3118 sec) [ -477773.8819] [121553] [depth= 1] . ( 3129 sec) [ -477745.5094] [121538] [depth= 6] . ( 3137 sec) [ -477733.2083] [121533] [depth= 1] . ( 3146 sec) [ -477729.2974] [121532] [depth= 1] . ( 3165 sec) [ -477724.8737] [121538] [depth= 1] . ( 3173 sec) [ -477714.6674] [121529] [depth= 1] . ( 3178 sec) [ -477698.2133] [121524] [depth= 1] . ( 3195 sec) [ -477692.5041] [121517] [depth= 1] . ( 3201 sec) [ -477685.1798] [121521] [depth= 1] . ( 3207 sec) [ -477685.0820] [121525] [depth= 1] . ( 3215 sec) [ -477685.0007] [121520] [depth= 1] . ( 3225 sec) [ -477660.8987] [121527] [depth= 1] . ( 3237 sec) [ -477653.9060] [121525] [depth= 1] . ( 3242 sec) [ -477642.8772] [121519] [depth= 2] . ( 3247 sec) [ -477640.7782] [121506] [depth= 1] . ( 3259 sec) [ -477634.9438] [121501] [depth= 1] . ( 3265 sec) [ -477597.9473] [121506] [depth= 1] . ( 3275 sec) [ -477595.8156] [121509] [depth= 1] . ( 3280 sec) [ -477595.1268] [121506] [depth= 1] . ( 3286 sec) [ -477584.5598] [121509] [depth= 2] . ( 3296 sec) [ -477582.3689] [121526] [depth= 1] . ( 3307 sec) [ -477575.1653] [121529] [depth= 1] . ( 3319 sec) [ -477568.2479] [121528] [depth= 1] . ( 3324 sec) [ -477557.9836] [121525] [depth= 2] . ( 3332 sec) [ -477545.0679] [121522] [depth= 2] . ( 3340 sec) [ -477541.9524] [121534] [depth= 1] . ( 3346 sec) [ -477539.8715] [121532] [depth= 2] . ( 3362 sec) [ -477527.2608] [121524] [depth= 4] . ( 3369 sec) [ -477508.2154] [121509] [depth= 2] . ( 3373 sec) [ -477506.2213] [121510] [depth= 1] . ( 3386 sec) [ -477485.8517] [121534] [depth= 1] . ( 3392 sec) [ -477429.8695] [121537] [depth= 1] . ( 3397 sec) [ -477368.7640] [121533] [depth= 1] . ( 3403 sec) [ -477362.9159] [121536] [depth= 3] . ( 3409 sec) [ -477332.7923] [121538] [depth= 2] . ( 3416 sec) [ -477306.3550] [121536] [depth= 1] . ( 3422 sec) [ -477303.1630] [121536] [depth= 1] . ( 3428 sec) [ -477303.1442] [121529] [depth= 3] . ( 3436 sec) [ -477292.4171] [121517] [depth= 3] . ( 3439 sec) [ -477282.8780] [121518] [depth= 1] . ( 3445 sec) [ -477275.4131] [121522] [depth= 2] . ( 3456 sec) [ -477270.1098] [121524] [depth= 1] . ( 3462 sec) [ -477232.4264] [121526] [depth= 2] . ( 3467 sec) [ -477227.0112] [121526] [depth= 2] . ( 3474 sec) [ -477190.0737] [121518] [depth= 1] . ( 3480 sec) [ -477182.6550] [121523] [depth= 1] . ( 3492 sec) [ -477179.2687] [121523] [depth= 1] . ( 3506 sec) [ -477149.5494] [121506] [depth= 3] . ( 3528 sec) [ -477103.0383] [121489] [depth= 2] . ( 3574 sec) [ -473646.7105] [Branch lengths ] . ( 3671 sec) [ -473551.5584] [GTR parameters ] . ( 3681 sec) [ -473223.1221] [Alpha ][ 0.863908] . ( 3764 sec) [ -473222.5357] [121485] [depth= 1] . ( 3816 sec) [ -473219.5882] [121489] [depth= 1] . ( 3863 sec) [ -473204.1461] [121470] [depth= 2] . ( 3868 sec) [ -473193.1457] [121466] [depth= 1] . ( 3927 sec) [ -473155.7619] [121462] [depth= 30] . ( 3952 sec) [ -473149.3034] [121460] [depth= 1] . ( 3962 sec) [ -473138.1278] [121458] [depth= 3] . ( 3980 sec) [ -473137.1305] [121462] [depth= 1] . ( 4018 sec) [ -473136.6897] [121466] [depth= 2] . ( 4024 sec) [ -473119.7194] [121468] [depth= 2] . ( 4029 sec) [ -473117.4631] [121462] [depth= 1] . ( 4071 sec) [ -473116.1275] [121467] [depth= 1] . ( 4082 sec) [ -473104.4986] [121448] [depth= 2] . ( 4098 sec) [ -473097.6206] [121441] [depth= 2] . ( 4126 sec) [ -473097.4356] [121444] [depth= 1] . ( 4150 sec) [ -473089.4879] [121439] [depth= 1] . ( 4181 sec) [ -473086.1782] [121443] [depth= 2] . ( 4210 sec) [ -473024.4015] [121419] [depth= 7] . ( 4229 sec) [ -473002.7275] [121396] [depth= 1] . ( 4243 sec) [ -472976.1670] [121386] [depth= 2] . ( 4251 sec) [ -472946.3019] [121362] [depth= 8] . ( 4267 sec) [ -472938.6981] [121352] [depth= 1] . ( 4310 sec) [ -472934.7500] [121350] [depth= 1] . ( 4318 sec) [ -472918.3843] [121342] [depth= 1] . ( 4324 sec) [ -472909.8544] [121328] [depth= 1] . ( 4331 sec) [ -472906.8589] [121324] [depth= 1] . ( 4354 sec) [ -472854.8908] [121308] [depth= 8] . ( 4366 sec) [ -472848.7201] [121303] [depth= 1] . ( 4403 sec) [ -472846.6388] [121308] [depth= 1] . ( 4411 sec) [ -472828.1900] [121311] [depth= 1] . ( 4416 sec) [ -472798.1313] [121295] [depth= 4] . ( 4436 sec) [ -472795.8601] [121299] [depth= 1] . ( 4463 sec) [ -472515.3417] [121233] [depth= 3] . ( 4486 sec) [ -472437.8816] [121206] [depth= 1] . ( 4530 sec) [ -472399.2838] [121188] [depth= 1] . ( 4561 sec) [ -472398.6878] [121188] [depth= 2] . ( 4571 sec) [ -472391.0383] [121181] [depth= 1] . ( 4654 sec) [ -472390.9352] [121179] [depth= 1] . ( 4660 sec) [ -472382.4331] [121178] [depth= 1] . ( 4665 sec) [ -472380.7664] [121179] [depth= 1] . ( 4677 sec) [ -472380.5920] [121178] [depth= 2] . ( 4690 sec) [ -472370.2500] [121172] [depth= 2] . ( 4697 sec) [ -472368.9605] [121167] [depth= 1] . ( 4712 sec) [ -472367.6187] [121165] [depth= 1] . ( 4721 sec) [ -472363.9082] [121160] [depth= 1] . ( 4738 sec) [ -472363.1827] [121161] [depth= 1] . ( 4770 sec) [ -472360.5622] [121158] [depth= 1] . ( 4776 sec) [ -472360.1175] [121163] [depth= 1] . ( 4816 sec) [ -472350.6265] [121168] [depth= 1] . ( 4833 sec) [ -472336.6935] [121159] [depth= 1] . ( 4852 sec) [ -472329.1425] [121154] [depth= 1] . ( 4880 sec) [ -472322.0520] [121148] [depth= 1] . ( 4890 sec) [ -472317.4883] [121153] [depth= 1] . ( 4925 sec) [ -472315.2557] [121153] [depth= 1] . ( 4957 sec) [ -472312.1916] [121144] [depth= 1] . ( 4979 sec) [ -472297.9140] [121136] [depth= 1] . ( 4987 sec) [ -472290.1771] [121131] [depth= 46] . ( 5039 sec) [ -472272.7888] [121128] [depth= 1] . ( 5051 sec) [ -472271.4768] [121133] [depth= 1] . ( 5060 sec) [ -472257.8576] [121129] [depth= 2] . ( 5066 sec) [ -472255.3070] [121134] [depth= 1] . ( 5078 sec) [ -472252.3263] [121124] [depth= 1] . ( 5088 sec) [ -472251.0639] [121122] [depth= 1] . ( 5159 sec) [ -472249.0795] [121121] [depth= 1] . ( 5202 sec) [ -472240.6412] [121120] [depth= 1] . ( 5290 sec) [ -472238.1640] [121119] [depth= 1] . ( 5308 sec) [ -472236.8621] [121119] [depth= 1] . ( 5334 sec) [ -472232.1743] [121121] [depth= 1] . ( 5350 sec) [ -472230.4462] [121114] [depth= 1] . ( 5387 sec) [ -472229.7456] [121117] [depth= 1] . ( 5407 sec) [ -472217.7931] [121117] [depth= 1] . ( 5447 sec) [ -472217.2530] [121112] [depth= 1] . ( 5486 sec) [ -472215.1974] [121117] [depth= 1] . ( 5491 sec) [ -472213.9664] [121111] [depth= 2] . ( 5509 sec) [ -472211.2138] [121110] [depth= 4] . ( 5532 sec) [ -472200.6210] [121108] [depth= 3] . ( 5560 sec) [ -472200.4054] [121100] [depth= 1] . ( 5566 sec) [ -472199.7510] [121101] [depth= 3] . ( 5571 sec) [ -472196.6718] [121096] [depth= 1] . ( 5598 sec) [ -472195.2744] [121084] [depth= 1] . ( 5612 sec) [ -472194.5956] [121089] [depth= 2] . ( 5617 sec) [ -472187.8979] [121082] [depth= 3] . ( 5625 sec) [ -472186.8525] [121075] [depth= 1] . ( 5635 sec) [ -472185.5234] [121060] [depth= 1] . ( 5641 sec) [ -472182.2325] [121056] [depth= 1] . ( 5667 sec) [ -472178.5895] [121051] [depth= 1] . ( 5688 sec) [ -472178.0461] [121052] [depth= 1] . ( 5694 sec) [ -472177.9336] [121060] [depth= 1] . ( 5704 sec) [ -472174.2747] [121063] [depth= 1] . ( 5709 sec) [ -472173.2708] [121052] [depth= 1] . ( 5719 sec) [ -472170.8122] [121053] [depth= 1] . ( 5747 sec) [ -472168.8981] [121046] [depth= 2] . ( 5752 sec) [ -472168.4413] [121044] [depth= 1] . ( 5758 sec) [ -472167.2698] [121050] [depth= 3] . ( 5820 sec) [ -472165.9005] [121052] [depth= 1] . ( 5825 sec) [ -472164.5627] [121047] [depth= 1] . ( 5851 sec) [ -472163.0455] [121050] [depth= 1] . ( 5862 sec) [ -472161.9640] [121047] [depth= 1] . ( 5874 sec) [ -472159.0569] [121050] [depth= 2] . ( 5892 sec) [ -472154.5981] [121043] [depth= 1] . ( 5900 sec) [ -472137.7559] [121037] [depth= 2] . ( 5960 sec) [ -472137.5799] [121041] [depth= 3] . ( 5966 sec) [ -472134.5346] [121038] [depth= 1] . ( 6002 sec) [ -472132.0233] [121037] [depth= 1] . ( 6041 sec) [ -472129.8585] [121038] [depth= 1] . ( 6057 sec) [ -472129.8137] [121033] [depth= 1] . ( 6062 sec) [ -472126.9223] [121035] [depth= 2] . ( 6094 sec) [ -472114.4178] [121039] [depth= 9] . ( 6175 sec) [ -471293.7940] [Branch lengths ] . ( 6237 sec) [ -471293.5060] [GTR parameters ] . ( 6246 sec) [ -471285.9129] [Alpha ][ 0.897438] . ( 6478 sec) [ -471284.6109] [121031] [depth= 1] . ( 6506 sec) [ -471280.7719] [121023] [depth= 1] . ( 6540 sec) [ -471279.6046] [121027] [depth= 2] . ( 6592 sec) [ -471269.4339] [121014] [depth= 1] . ( 6653 sec) [ -471267.8379] [121016] [depth= 1] . ( 6702 sec) [ -471266.4320] [121017] [depth= 3] . ( 6730 sec) [ -471241.8117] [121008] [depth= 1] . ( 6760 sec) [ -471241.7340] [121004] [depth= 1] . ( 7202 sec) [ -471241.0871] [121004] [depth= 2] . ( 7217 sec) [ -471240.6270] [120998] [depth= 1] . ( 7329 sec) [ -471240.2110] [120993] [depth= 1] . ( 7389 sec) [ -471238.0152] [120991] [depth= 1] . ( 7452 sec) [ -471234.2939] [120993] [depth= 2] . ( 7738 sec) [ -471233.0202] [120989] [depth= 1] . ( 7844 sec) [ -471232.9060] [120988] [depth= 1] . ( 7850 sec) [ -471231.2148] [120989] [depth= 1] . ( 7912 sec) [ -471229.6553] [120989] [depth= 1] . ( 8033 sec) [ -471224.5520] [120984] [depth= 1] . ( 8067 sec) [ -471216.9313] [120979] [depth= 1] . ( 8125 sec) [ -471215.4771] [120971] [depth= 2] . ( 8169 sec) [ -471211.4575] [120976] [depth= 1] . ( 8191 sec) [ -471200.9123] [120979] [depth= 1] . ( 8211 sec) [ -471197.4374] [120984] [depth= 2] . ( 8268 sec) [ -471196.2933] [120989] [depth= 1] . ( 8307 sec) [ -471196.0939] [120983] [depth= 1] . ( 8318 sec) [ -471194.9205] [120980] [depth= 1] . ( 8325 sec) [ -471168.2244] [120976] [depth= 3] . ( 8373 sec) [ -471165.2639] [120975] [depth= 2] . ( 8543 sec) [ -470886.2605] [Branch lengths ] . ( 8605 sec) [ -470885.5488] [GTR parameters ] . ( 8614 sec) [ -470884.6191] [Alpha ][ 0.909399] . ( 8931 sec) [ -470884.4405] [120972] [depth= 1] . (10376 sec) [ -470883.4948] [120977] [depth= 2] . (10460 sec) [ -470883.4548] [120975] [depth= 1] . (10497 sec) [ -470881.7767] [120975] [depth= 1] . (10949 sec) [ -470772.7794] [Branch lengths ] . (11020 sec) [ -470772.2218] [GTR parameters ] . (11028 sec) [ -470772.2218] [Alpha ][ 0.909399] . (12882 sec) [ -470771.5530] [120976] [depth= 1] . (13155 sec) [ -470770.9058] [120973] [depth= 3] . (13334 sec) [ -470711.9295] [Branch lengths ] . (13405 sec) [ -470711.6254] [GTR parameters ] . (13416 sec) [ -470711.5547] [Alpha ][ 0.906198] . (13941 sec) [ -470711.2171] [120960] [depth= 14] . (15472 sec) [ -470671.6462] [Branch lengths ] . (15534 sec) [ -470671.3848] [GTR parameters ] . (15544 sec) [ -470671.3126] [Alpha ][ 0.903015] . (17897 sec) [ -470660.2792] [Branch lengths ] . (19319 sec) [ -470659.9759] [120967] [depth= 1] . (20199 sec) [ -470658.4492] [120950] [depth= 1] . (20449 sec) [ -470658.0939] [120955] [depth= 2] . (20564 sec) [ -470655.2736] [120959] [depth= 1] . (20814 sec) [ -470655.1696] [120968] [depth= 2] . (21936 sec) [ -470653.8922] [120997] [depth= 2] . (22271 sec) [ -470652.2071] [120984] [depth= 1] . (22901 sec) [ -470652.1629] [120972] [depth= 1] . (23564 sec) [ -470651.6967] [120978] [depth= 1] . (23811 sec) [ -470648.6399] [120979] [depth= 1] . (24061 sec) [ -470647.5958] [120988] [depth= 2] . (24630 sec) [ -470619.2224] [Branch lengths ] . (24675 sec) [ -470619.0561] [GTR parameters ] . (24684 sec) [ -470618.9412] [Alpha ][ 0.899084] . (29917 sec) [ -470618.8922] [120986] [depth= 1] . (30118 sec) [ -470618.7212] [120981] [depth= 1] . (30354 sec) [ -470615.9156] [120976] [depth= 4] . (30854 sec) [ -470604.8075] [Branch lengths ] . (30901 sec) [ -470604.7712] [GTR parameters ] . (30911 sec) [ -470604.6806] [Alpha ][ 0.895640] . (31826 sec) [ -470604.6370] [120975] [depth= 1] . (35929 sec) [ -470604.4161] [120975] [depth= 1] . (36373 sec) [ -470603.0700] [120975] [depth= 1] . (37114 sec) [ -470593.4385] [Branch lengths ] . (37185 sec) [ -470593.4119] [GTR parameters ] . (37195 sec) [ -470593.3318] [Alpha ][ 0.892451] . (43785 sec) [ -470588.6634] [Branch lengths ] . (43788 sec) [ -470588.6634] [Topology ] . (43883 sec) [ -470586.1878] [Topology ] . (43978 sec) [ -470584.2932] [Topology ] . (44073 sec) [ -470583.4872] [Topology ] . (44168 sec) [ -470582.9423] [Topology ] . (44263 sec) [ -470582.5402] [Topology ] . (44358 sec) [ -470582.2365] [Topology ] . (44452 sec) [ -470582.0060] [Topology ] . (44522 sec) [ -470581.8987] [GTR parameters ] . (44532 sec) [ -470581.2493] [Alpha ][ 0.883674] . (44535 sec) [ -470581.2493] [Topology ] . (44630 sec) [ -470580.8943] [Topology ] . (44725 sec) [ -470580.6281] [Topology ] . (44820 sec) [ -470580.4266] [Topology ] . (44915 sec) [ -470580.2742] [Topology ] . (45010 sec) [ -470580.1592] [Topology ] . (45104 sec) [ -470580.0726] [Topology ] . (45192 sec) [ -470580.0472] [GTR parameters ] . (45203 sec) [ -470579.9813] [Alpha ][ 0.880896] . (45206 sec) [ -470579.9813] [Topology ] . (45301 sec) [ -470579.8806] [Topology ] . (45395 sec) [ -470579.8053] [Topology ] . (45490 sec) [ -470579.7486] [Topology ] . (45585 sec) [ -470579.7059] [Topology ] . (45680 sec) [ -470579.6737] [Topology ] . (45775 sec) [ -470579.6495] [Topology ] . (45818 sec) [ -470579.6467] [GTR parameters ] . (45827 sec) [ -470579.6279] [Alpha ][ 0.879398] . (45830 sec) [ -470579.6279] [Topology ] . (45925 sec) [ -470579.6004] [Topology ] . (46020 sec) [ -470579.5799] [Topology ] . (46115 sec) [ -470579.5644] [Topology ] . (46210 sec) [ -470579.5527] [Topology ] . (46304 sec) [ -470579.5439] [Topology ] . (46399 sec) [ -470579.5372] [Topology ] . (46426 sec) [ -470579.5359] [GTR parameters ] . (46434 sec) [ -470579.5308] [Alpha ][ 0.878518] . (46437 sec) [ -470579.5308] [Topology ] . (46532 sec) [ -470579.5225] [Topology ] . (46627 sec) [ -470579.5163] [Topology ] . (46722 sec) [ -470579.5116] [Topology ] . (46817 sec) [ -470579.5080] [Topology ] . (46912 sec) [ -470579.5053] [Topology ] . (47007 sec) [ -470579.5033] [Topology ] . (47034 sec) [ -470579.5026] [GTR parameters ] . (47043 sec) [ -470579.5026] [Alpha ][ 0.878518] . (47046 sec) [ -470579.5026] [Topology ] . (47141 sec) [ -470579.5010] [Topology ] . (47236 sec) [ -470579.4999] [Topology ] . (47331 sec) [ -470579.4990] [Topology ] . (47349 sec) [ -470579.4988] [GTR parameters ] . (47357 sec) [ -470579.4988] [Alpha ][ 0.878518] . (47360 sec) [ -470579.4988] [Topology ] . (47455 sec) [ -470579.4982] [Topology ] . (47473 sec) [ -470579.4981] [GTR parameters ] . (47482 sec) [ -470579.4980] [Alpha ][ 0.877640] . Checking for NNIs, optimizing five branches... . (48314 sec) [ -470579.4720] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -470579.471966. . Printing the most likely tree in file 'nucleic_M4058_406x6016_2008.phy_phyml_tree.txt'... . Time used 13h39m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 49211.84user 0.00system 13:40:26elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps