.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2974_56x827_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 : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 330 patterns found. (out of a total of 827 sites) . 592 sites without polymorphism (71.58%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -11975.1507] [GTR parameters ] . ( 2 sec) [ -11648.0606] [Alpha ][ 0.500960] . ( 2 sec) [ -11602.0846] [ 1752] [depth= 8] . ( 2 sec) [ -11535.9236] [ 1740] [depth= 10] . ( 3 sec) [ -11293.3052] [ 1728] [depth= 8] . ( 3 sec) [ -11168.7000] [ 1694] [depth= 1] . ( 3 sec) [ -11069.8571] [ 1685] [depth= 4] . ( 3 sec) [ -11044.6613] [ 1679] [depth= 3] . ( 3 sec) [ -10977.4356] [ 1677] [depth= 3] . ( 3 sec) [ -10897.6900] [ 1642] [depth= 5] . ( 3 sec) [ -10883.8706] [ 1642] [depth= 3] . ( 3 sec) [ -10634.2992] [ 1620] [depth= 4] . ( 3 sec) [ -10608.4097] [ 1619] [depth= 8] . ( 3 sec) [ -10592.5328] [ 1619] [depth= 2] . ( 3 sec) [ -10536.2100] [ 1604] [depth= 11] . ( 3 sec) [ -10459.5080] [ 1603] [depth= 3] . ( 3 sec) [ -10405.3004] [ 1593] [depth= 1] . ( 3 sec) [ -10385.3248] [ 1589] [depth= 1] . ( 3 sec) [ -10339.6931] [ 1586] [depth= 15] . ( 3 sec) [ -10307.5673] [ 1573] [depth= 4] . ( 3 sec) [ -10292.1444] [ 1573] [depth= 2] . ( 3 sec) [ -10170.2373] [ 1574] [depth= 1] . ( 3 sec) [ -10127.3382] [ 1570] [depth= 11] . ( 3 sec) [ -9996.2480] [ 1561] [depth= 2] . ( 3 sec) [ -9936.5825] [ 1548] [depth= 7] . ( 3 sec) [ -9901.4596] [ 1539] [depth= 1] . ( 4 sec) [ -9887.9157] [ 1534] [depth= 2] . ( 4 sec) [ -9747.0083] [ 1549] [depth= 1] . ( 4 sec) [ -9707.8774] [ 1540] [depth= 4] . ( 4 sec) [ -9706.6846] [ 1540] [depth= 1] . ( 4 sec) [ -9404.9815] [ 1523] [depth= 12] . ( 4 sec) [ -9235.2608] [ 1501] [depth= 11] . ( 4 sec) [ -9115.0061] [ 1484] [depth= 12] . ( 4 sec) [ -9072.6384] [ 1474] [depth= 20] . ( 4 sec) [ -8961.8729] [ 1437] [depth= 2] . ( 4 sec) [ -8892.2916] [ 1421] [depth= 8] . ( 4 sec) [ -8612.0531] [ 1409] [depth= 18] . ( 4 sec) [ -8517.0499] [ 1396] [depth= 8] . ( 4 sec) [ -8279.3421] [ 1347] [depth= 8] . ( 4 sec) [ -8213.1347] [ 1342] [depth= 8] . ( 4 sec) [ -8071.8769] [ 1314] [depth= 13] . ( 4 sec) [ -8017.7719] [ 1314] [depth= 1] . ( 4 sec) [ -7805.2808] [ 1309] [depth= 7] . ( 5 sec) [ -7805.2523] [ 1309] [depth= 3] . ( 5 sec) [ -7800.2133] [ 1309] [depth= 1] . ( 5 sec) [ -7777.7303] [ 1302] [depth= 5] . ( 5 sec) [ -7777.5734] [ 1306] [depth= 1] . ( 5 sec) [ -7596.4083] [ 1297] [depth= 7] . ( 5 sec) [ -7576.8950] [ 1301] [depth= 1] . ( 5 sec) [ -7458.7948] [ 1271] [depth= 2] . ( 5 sec) [ -7457.9840] [ 1275] [depth= 1] . ( 5 sec) [ -7453.1027] [ 1271] [depth= 1] . ( 5 sec) [ -7429.5944] [ 1267] [depth= 10] . ( 5 sec) [ -7419.2902] [ 1267] [depth= 4] . ( 5 sec) [ -7269.7021] [ 1247] [depth= 10] . ( 5 sec) [ -7186.4172] [ 1222] [depth= 1] . ( 5 sec) [ -7136.2878] [ 1213] [depth= 3] . ( 5 sec) [ -7132.5213] [ 1208] [depth= 1] . ( 5 sec) [ -7132.4778] [ 1208] [depth= 3] . ( 6 sec) [ -7125.3618] [ 1203] [depth= 8] . ( 6 sec) [ -7065.1057] [ 1176] [depth= 4] . ( 6 sec) [ -6968.5260] [ 1171] [depth= 1] . ( 6 sec) [ -6959.1825] [ 1174] [depth= 2] . ( 6 sec) [ -6921.0048] [ 1159] [depth= 5] . ( 6 sec) [ -6894.8929] [ 1155] [depth= 1] . ( 6 sec) [ -6732.2934] [ 1153] [depth= 1] . ( 6 sec) [ -6685.5500] [ 1162] [depth= 10] . ( 6 sec) [ -6652.7655] [ 1139] [depth= 12] . ( 6 sec) [ -6527.6468] [ 1108] [depth= 10] . ( 6 sec) [ -6475.9563] [ 1107] [depth= 2] . ( 6 sec) [ -6475.8511] [ 1107] [depth= 1] . ( 6 sec) [ -6451.5691] [ 1111] [depth= 1] . ( 6 sec) [ -6425.9584] [ 1104] [depth= 2] . ( 7 sec) [ -6343.7203] [ 1095] [depth= 8] . ( 7 sec) [ -6306.9469] [ 1093] [depth= 1] . ( 7 sec) [ -6306.6609] [ 1094] [depth= 1] . ( 7 sec) [ -6258.7277] [ 1081] [depth= 4] . ( 7 sec) [ -6241.2469] [ 1083] [depth= 5] . ( 7 sec) [ -6232.6719] [ 1081] [depth= 2] . ( 7 sec) [ -6221.6030] [ 1078] [depth= 6] . ( 7 sec) [ -6219.3616] [ 1079] [depth= 1] . ( 7 sec) [ -6211.2521] [ 1076] [depth= 1] . ( 7 sec) [ -6211.1979] [ 1077] [depth= 3] . ( 7 sec) [ -6198.0459] [ 1070] [depth= 8] . ( 7 sec) [ -6194.1784] [ 1069] [depth= 1] . ( 7 sec) [ -6154.8804] [ 1046] [depth= 2] . ( 7 sec) [ -6143.2267] [ 1045] [depth= 1] . ( 7 sec) [ -6138.4188] [ 1044] [depth= 1] . ( 7 sec) [ -6137.3827] [ 1043] [depth= 1] . ( 8 sec) [ -6102.2224] [ 1034] [depth= 9] . ( 8 sec) [ -6098.3054] [ 1032] [depth= 1] . ( 8 sec) [ -6083.8197] [ 1027] [depth= 3] . ( 8 sec) [ -6056.1555] [ 1019] [depth= 3] . ( 8 sec) [ -6049.4890] [ 1015] [depth= 2] . ( 8 sec) [ -5997.0634] [ 1008] [depth= 1] . ( 8 sec) [ -5986.5347] [ 1005] [depth= 3] . ( 8 sec) [ -5984.5043] [ 1005] [depth= 1] . ( 8 sec) [ -5957.0328] [ 997] [depth= 2] . ( 8 sec) [ -5946.2048] [ 999] [depth= 4] . ( 8 sec) [ -5935.5030] [ 993] [depth= 1] . ( 9 sec) [ -5917.5810] [ 993] [depth= 9] . ( 9 sec) [ -5917.3097] [ 993] [depth= 1] . ( 9 sec) [ -5915.1595] [ 993] [depth= 1] . ( 9 sec) [ -5869.7789] [ 981] [depth= 8] . ( 9 sec) [ -5865.0968] [ 991] [depth= 1] . ( 9 sec) [ -5789.6858] [ 962] [depth= 6] . ( 9 sec) [ -5786.3285] [ 951] [depth= 2] . ( 9 sec) [ -5761.0897] [ 938] [depth= 3] . ( 9 sec) [ -5759.9147] [ 935] [depth= 1] . ( 9 sec) [ -5746.8379] [ 933] [depth= 3] . ( 9 sec) [ -5732.5927] [ 926] [depth= 8] . ( 9 sec) [ -5731.3895] [ 927] [depth= 2] . ( 10 sec) [ -5716.3170] [ 924] [depth= 2] . ( 10 sec) [ -5704.7096] [ 913] [depth= 1] . ( 10 sec) [ -5704.2964] [ 911] [depth= 2] . ( 10 sec) [ -5687.5292] [ 923] [depth= 1] . ( 10 sec) [ -5682.3555] [ 911] [depth= 1] . ( 11 sec) [ -5631.3740] [Branch lengths ] . ( 12 sec) [ -5619.9206] [GTR parameters ] . ( 12 sec) [ -5521.5125] [Alpha ][ 0.250961] . ( 13 sec) [ -5488.2916] [ 898] [depth= 1] . ( 13 sec) [ -5471.2346] [ 893] [depth= 1] . ( 13 sec) [ -5456.8717] [ 890] [depth= 1] . ( 13 sec) [ -5452.8435] [ 888] [depth= 1] . ( 13 sec) [ -5450.7460] [ 886] [depth= 2] . ( 13 sec) [ -5450.4768] [ 886] [depth= 1] . ( 14 sec) [ -5450.4372] [ 886] [depth= 1] . ( 14 sec) [ -5448.9830] [ 885] [depth= 1] . ( 14 sec) [ -5448.7417] [ 885] [depth= 1] . ( 14 sec) [ -5448.2371] [ 885] [depth= 1] . ( 15 sec) [ -5448.1894] [ 885] [depth= 1] . ( 15 sec) [ -5443.6201] [ 885] [depth= 2] . ( 16 sec) [ -5442.3723] [ 883] [depth= 1] . ( 17 sec) [ -5442.0535] [ 882] [depth= 1] . ( 17 sec) [ -5435.3946] [ 877] [depth= 4] . ( 17 sec) [ -5430.1033] [ 876] [depth= 2] . ( 18 sec) [ -5417.6482] [ 879] [depth= 9] . ( 18 sec) [ -5416.7031] [ 875] [depth= 1] . ( 19 sec) [ -5416.6182] [ 875] [depth= 1] . ( 19 sec) [ -5415.3863] [ 871] [depth= 2] . ( 19 sec) [ -5415.1392] [ 870] [depth= 1] . ( 19 sec) [ -5414.8035] [ 870] [depth= 1] . ( 20 sec) [ -5412.0355] [ 868] [depth= 3] . ( 21 sec) [ -5398.5187] [Branch lengths ] . ( 22 sec) [ -5398.2600] [GTR parameters ] . ( 22 sec) [ -5384.1954] [Alpha ][ 0.174657] . ( 23 sec) [ -5383.0618] [ 868] [depth= 1] . ( 25 sec) [ -5382.9657] [ 868] [depth= 3] . ( 28 sec) [ -5382.8300] [ 868] [depth= 2] . ( 29 sec) [ -5382.7652] [ 868] [depth= 1] . ( 30 sec) [ -5381.7465] [ 866] [depth= 1] . ( 32 sec) [ -5378.9635] [Branch lengths ] . ( 33 sec) [ -5378.8772] [GTR parameters ] . ( 33 sec) [ -5378.8095] [Alpha ][ 0.170409] . ( 42 sec) [ -5378.6744] [Branch lengths ] . ( 75 sec) [ -5378.6663] [Branch lengths ] . ( 75 sec) [ -5378.6663] [Topology ] . ( 75 sec) [ -5378.6659] [Topology ] . ( 76 sec) [ -5378.6652] [GTR parameters ] . ( 76 sec) [ -5378.6608] [Alpha ][ 0.169271] . ( 76 sec) [ -5378.6608] [Topology ] . ( 77 sec) [ -5378.6602] [Topology ] . ( 77 sec) [ -5378.6600] [GTR parameters ] . ( 77 sec) [ -5378.6600] [Alpha ][ 0.169271] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5378.660044. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -12176.1023] [GTR parameters ] . ( 2 sec) [ -11835.7615] [Alpha ][ 0.500960] . ( 2 sec) [ -11628.0973] [ 1795] [depth= 7] . ( 2 sec) [ -11539.6843] [ 1786] [depth= 5] . ( 2 sec) [ -11474.5557] [ 1777] [depth= 3] . ( 2 sec) [ -11329.8000] [ 1776] [depth= 4] . ( 2 sec) [ -11325.7297] [ 1774] [depth= 1] . ( 2 sec) [ -11292.7436] [ 1772] [depth= 4] . ( 2 sec) [ -11138.2323] [ 1767] [depth= 4] . ( 2 sec) [ -11099.2206] [ 1766] [depth= 2] . ( 2 sec) [ -11045.4805] [ 1736] [depth= 14] . ( 2 sec) [ -10966.0536] [ 1738] [depth= 2] . ( 3 sec) [ -10952.0523] [ 1736] [depth= 3] . ( 3 sec) [ -10849.7374] [ 1709] [depth= 7] . ( 3 sec) [ -10796.4988] [ 1692] [depth= 13] . ( 3 sec) [ -10748.3916] [ 1667] [depth= 1] . ( 3 sec) [ -10702.3344] [ 1666] [depth= 5] . ( 3 sec) [ -10696.8367] [ 1661] [depth= 1] . ( 3 sec) [ -10247.7897] [ 1651] [depth= 4] . ( 3 sec) [ -10101.7936] [ 1620] [depth= 15] . ( 3 sec) [ -10094.9586] [ 1619] [depth= 3] . ( 3 sec) [ -10080.7955] [ 1619] [depth= 1] . ( 3 sec) [ -9949.1688] [ 1579] [depth= 3] . ( 3 sec) [ -9933.5647] [ 1574] [depth= 6] . ( 3 sec) [ -9902.5671] [ 1573] [depth= 2] . ( 3 sec) [ -9848.4404] [ 1567] [depth= 14] . ( 3 sec) [ -9810.3700] [ 1557] [depth= 9] . ( 3 sec) [ -9793.6785] [ 1555] [depth= 1] . ( 3 sec) [ -9745.0786] [ 1549] [depth= 12] . ( 3 sec) [ -9671.1242] [ 1532] [depth= 10] . ( 3 sec) [ -9643.7354] [ 1532] [depth= 4] . ( 3 sec) [ -9633.8018] [ 1536] [depth= 1] . ( 3 sec) [ -9433.6316] [ 1492] [depth= 6] . ( 4 sec) [ -9406.0628] [ 1485] [depth= 1] . ( 4 sec) [ -9295.2505] [ 1479] [depth= 4] . ( 4 sec) [ -9272.5114] [ 1469] [depth= 6] . ( 4 sec) [ -9190.6143] [ 1470] [depth= 1] . ( 4 sec) [ -9128.2287] [ 1460] [depth= 5] . ( 4 sec) [ -9004.0149] [ 1449] [depth= 9] . ( 4 sec) [ -8948.7285] [ 1454] [depth= 1] . ( 4 sec) [ -8902.4268] [ 1444] [depth= 1] . ( 4 sec) [ -8724.5707] [ 1409] [depth= 13] . ( 4 sec) [ -8619.5625] [ 1394] [depth= 6] . ( 4 sec) [ -8523.6367] [ 1375] [depth= 7] . ( 4 sec) [ -8464.4665] [ 1364] [depth= 1] . ( 4 sec) [ -8453.9414] [ 1364] [depth= 9] . ( 4 sec) [ -8453.5649] [ 1364] [depth= 8] . ( 4 sec) [ -8442.0253] [ 1360] [depth= 1] . ( 4 sec) [ -8413.1795] [ 1342] [depth= 9] . ( 4 sec) [ -8395.1062] [ 1336] [depth= 7] . ( 4 sec) [ -8301.1923] [ 1335] [depth= 1] . ( 4 sec) [ -7991.1073] [ 1300] [depth= 14] . ( 4 sec) [ -7792.1772] [ 1277] [depth= 14] . ( 5 sec) [ -7771.5991] [ 1274] [depth= 2] . ( 5 sec) [ -7747.1677] [ 1270] [depth= 5] . ( 5 sec) [ -7642.0914] [ 1253] [depth= 8] . ( 5 sec) [ -7567.8884] [ 1238] [depth= 10] . ( 5 sec) [ -7567.5432] [ 1237] [depth= 1] . ( 5 sec) [ -7565.7700] [ 1240] [depth= 2] . ( 5 sec) [ -7504.9664] [ 1236] [depth= 1] . ( 5 sec) [ -7360.5036] [ 1230] [depth= 5] . ( 5 sec) [ -7304.2199] [ 1230] [depth= 1] . ( 5 sec) [ -7248.7937] [ 1215] [depth= 1] . ( 5 sec) [ -7158.8743] [ 1208] [depth= 3] . ( 5 sec) [ -7039.5121] [ 1182] [depth= 11] . ( 5 sec) [ -7021.5982] [ 1182] [depth= 1] . ( 5 sec) [ -6989.0023] [ 1173] [depth= 1] . ( 5 sec) [ -6966.3597] [ 1167] [depth= 8] . ( 5 sec) [ -6780.1945] [ 1169] [depth= 9] . ( 5 sec) [ -6745.6513] [ 1152] [depth= 4] . ( 5 sec) [ -6740.2429] [ 1149] [depth= 2] . ( 6 sec) [ -6735.5017] [ 1148] [depth= 1] . ( 6 sec) [ -6716.2195] [ 1145] [depth= 3] . ( 6 sec) [ -6709.2323] [ 1145] [depth= 1] . ( 6 sec) [ -6708.8048] [ 1145] [depth= 1] . ( 6 sec) [ -6685.0929] [ 1135] [depth= 6] . ( 6 sec) [ -6612.0254] [ 1127] [depth= 3] . ( 6 sec) [ -6611.7906] [ 1127] [depth= 2] . ( 6 sec) [ -6609.8618] [ 1126] [depth= 4] . ( 6 sec) [ -6609.6150] [ 1128] [depth= 1] . ( 6 sec) [ -6607.7576] [ 1127] [depth= 3] . ( 6 sec) [ -6525.5077] [ 1076] [depth= 5] . ( 6 sec) [ -6521.0850] [ 1077] [depth= 7] . ( 6 sec) [ -6516.1229] [ 1065] [depth= 2] . ( 6 sec) [ -6512.6313] [ 1056] [depth= 10] . ( 6 sec) [ -6510.8327] [ 1056] [depth= 1] . ( 6 sec) [ -6510.7293] [ 1056] [depth= 1] . ( 6 sec) [ -6510.6693] [ 1056] [depth= 2] . ( 6 sec) [ -6504.0440] [ 1051] [depth= 2] . ( 6 sec) [ -6502.4074] [ 1050] [depth= 1] . ( 7 sec) [ -6472.2347] [ 1044] [depth= 2] . ( 7 sec) [ -6434.0842] [ 1036] [depth= 1] . ( 7 sec) [ -6428.9245] [ 1025] [depth= 8] . ( 7 sec) [ -6421.0809] [ 1025] [depth= 1] . ( 7 sec) [ -6412.3612] [ 1025] [depth= 2] . ( 7 sec) [ -6395.4012] [ 1027] [depth= 2] . ( 7 sec) [ -6310.4667] [ 1004] [depth= 2] . ( 7 sec) [ -6288.8030] [ 1003] [depth= 1] . ( 7 sec) [ -6255.3335] [ 997] [depth= 2] . ( 7 sec) [ -6106.2579] [ 968] [depth= 9] . ( 7 sec) [ -6099.2673] [ 961] [depth= 6] . ( 7 sec) [ -6076.7790] [ 948] [depth= 2] . ( 7 sec) [ -6064.1457] [ 941] [depth= 3] . ( 7 sec) [ -6060.2547] [ 939] [depth= 1] . ( 7 sec) [ -5930.8859] [ 942] [depth= 1] . ( 7 sec) [ -5904.3471] [ 934] [depth= 2] . ( 7 sec) [ -5858.1942] [ 923] [depth= 4] . ( 7 sec) [ -5835.1061] [ 923] [depth= 2] . ( 8 sec) [ -5824.0170] [ 914] [depth= 8] . ( 8 sec) [ -5820.8713] [ 913] [depth= 2] . ( 8 sec) [ -5816.5120] [ 916] [depth= 1] . ( 8 sec) [ -5811.2615] [ 913] [depth= 2] . ( 8 sec) [ -5787.1541] [ 907] [depth= 1] . ( 8 sec) [ -5779.4351] [ 906] [depth= 2] . ( 8 sec) [ -5730.4295] [ 903] [depth= 1] . ( 8 sec) [ -5720.8828] [ 905] [depth= 1] . ( 8 sec) [ -5718.9842] [ 905] [depth= 1] . ( 8 sec) [ -5711.9435] [ 907] [depth= 2] . ( 8 sec) [ -5711.7507] [ 907] [depth= 3] . ( 9 sec) [ -5632.3163] [Branch lengths ] . ( 9 sec) [ -5625.2534] [GTR parameters ] . ( 9 sec) [ -5528.2322] [Alpha ][ 0.250961] . ( 9 sec) [ -5528.2188] [ 907] [depth= 2] . ( 9 sec) [ -5527.3502] [ 906] [depth= 1] . ( 10 sec) [ -5524.8855] [ 904] [depth= 2] . ( 10 sec) [ -5523.9757] [ 904] [depth= 1] . ( 10 sec) [ -5480.8052] [ 899] [depth= 4] . ( 10 sec) [ -5476.5492] [ 896] [depth= 2] . ( 10 sec) [ -5476.2682] [ 897] [depth= 1] . ( 10 sec) [ -5474.7654] [ 893] [depth= 4] . ( 11 sec) [ -5472.3247] [ 891] [depth= 2] . ( 11 sec) [ -5451.2169] [ 880] [depth= 1] . ( 11 sec) [ -5443.6991] [ 879] [depth= 4] . ( 11 sec) [ -5437.3201] [ 875] [depth= 1] . ( 11 sec) [ -5434.8833] [ 874] [depth= 3] . ( 11 sec) [ -5433.1003] [ 876] [depth= 1] . ( 11 sec) [ -5424.9741] [ 876] [depth= 1] . ( 11 sec) [ -5424.8833] [ 876] [depth= 1] . ( 12 sec) [ -5419.6148] [ 870] [depth= 1] . ( 12 sec) [ -5419.3570] [ 870] [depth= 1] . ( 12 sec) [ -5418.8109] [ 870] [depth= 1] . ( 12 sec) [ -5418.6909] [ 870] [depth= 1] . ( 13 sec) [ -5417.5349] [ 868] [depth= 1] . ( 13 sec) [ -5417.1556] [ 868] [depth= 1] . ( 13 sec) [ -5415.4159] [ 871] [depth= 1] . ( 13 sec) [ -5415.2654] [ 871] [depth= 1] . ( 14 sec) [ -5415.1893] [ 871] [depth= 1] . ( 14 sec) [ -5413.2799] [ 872] [depth= 2] . ( 14 sec) [ -5412.6877] [ 871] [depth= 1] . ( 14 sec) [ -5412.6674] [ 871] [depth= 3] . ( 15 sec) [ -5411.9994] [ 870] [depth= 1] . ( 15 sec) [ -5411.5672] [ 873] [depth= 1] . ( 16 sec) [ -5411.2163] [ 873] [depth= 1] . ( 16 sec) [ -5409.0694] [ 870] [depth= 3] . ( 17 sec) [ -5402.4176] [Branch lengths ] . ( 18 sec) [ -5401.4935] [GTR parameters ] . ( 18 sec) [ -5386.2792] [Alpha ][ 0.171622] . ( 20 sec) [ -5386.1265] [ 871] [depth= 1] . ( 29 sec) [ -5385.4736] [Branch lengths ] . ( 29 sec) [ -5385.3522] [GTR parameters ] . ( 29 sec) [ -5385.3315] [Alpha ][ 0.169390] . ( 63 sec) [ -5385.1220] [Branch lengths ] . ( 63 sec) [ -5385.1220] [Topology ] . ( 64 sec) [ -5384.5137] [Topology ] . ( 65 sec) [ -5384.3197] [Topology ] . ( 66 sec) [ -5384.2819] [Topology ] . ( 66 sec) [ -5384.2741] [Topology ] . ( 67 sec) [ -5384.2724] [Topology ] . ( 68 sec) [ -5384.2720] [Topology ] . ( 68 sec) [ -5384.2662] [GTR parameters ] . ( 68 sec) [ -5384.2655] [Alpha ][ 0.168908] . ( 68 sec) [ -5384.2655] [Topology ] . ( 69 sec) [ -5384.2651] [Topology ] . ( 69 sec) [ -5384.2651] [GTR parameters ] . ( 69 sec) [ -5384.2651] [Alpha ][ 0.168908] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5384.265080. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13718.9329] [GTR parameters ] . ( 1 sec) [ -13349.5286] [Alpha ][ 0.500960] . ( 1 sec) [ -13289.0346] [ 1888] [depth= 7] . ( 1 sec) [ -13225.0895] [ 1881] [depth= 9] . ( 1 sec) [ -12847.0711] [ 1878] [depth= 8] . ( 1 sec) [ -12598.3389] [ 1877] [depth= 2] . ( 1 sec) [ -12444.2115] [ 1863] [depth= 10] . ( 1 sec) [ -12412.9641] [ 1862] [depth= 1] . ( 1 sec) [ -12178.1475] [ 1857] [depth= 12] . ( 1 sec) [ -12112.4494] [ 1856] [depth= 1] . ( 1 sec) [ -12079.9080] [ 1854] [depth= 2] . ( 1 sec) [ -12060.9361] [ 1851] [depth= 17] . ( 1 sec) [ -11985.7976] [ 1838] [depth= 8] . ( 1 sec) [ -11711.3165] [ 1836] [depth= 1] . ( 1 sec) [ -11513.3165] [ 1809] [depth= 11] . ( 1 sec) [ -11362.1733] [ 1784] [depth= 19] . ( 1 sec) [ -11356.6898] [ 1773] [depth= 11] . ( 1 sec) [ -11306.8974] [ 1773] [depth= 8] . ( 1 sec) [ -11133.8987] [ 1741] [depth= 2] . ( 2 sec) [ -11120.7749] [ 1729] [depth= 3] . ( 2 sec) [ -11062.9178] [ 1729] [depth= 11] . ( 2 sec) [ -10994.7300] [ 1731] [depth= 15] . ( 2 sec) [ -10939.5838] [ 1724] [depth= 3] . ( 2 sec) [ -10823.5973] [ 1706] [depth= 10] . ( 2 sec) [ -10738.7993] [ 1701] [depth= 3] . ( 2 sec) [ -10727.4178] [ 1697] [depth= 1] . ( 2 sec) [ -10542.3968] [ 1669] [depth= 5] . ( 2 sec) [ -10421.4286] [ 1658] [depth= 10] . ( 2 sec) [ -10413.7331] [ 1652] [depth= 7] . ( 2 sec) [ -10362.6968] [ 1636] [depth= 14] . ( 2 sec) [ -10355.4445] [ 1636] [depth= 9] . ( 2 sec) [ -10340.1057] [ 1638] [depth= 1] . ( 2 sec) [ -10326.3397] [ 1637] [depth= 1] . ( 2 sec) [ -10319.5989] [ 1636] [depth= 1] . ( 2 sec) [ -10262.9444] [ 1637] [depth= 2] . ( 2 sec) [ -10217.4211] [ 1631] [depth= 22] . ( 2 sec) [ -10207.3033] [ 1628] [depth= 1] . ( 2 sec) [ -9724.4187] [ 1621] [depth= 17] . ( 2 sec) [ -9474.5839] [ 1596] [depth= 5] . ( 3 sec) [ -9303.0589] [ 1580] [depth= 8] . ( 3 sec) [ -9299.6366] [ 1579] [depth= 1] . ( 3 sec) [ -9135.2658] [ 1535] [depth= 6] . ( 3 sec) [ -9070.9692] [ 1532] [depth= 9] . ( 3 sec) [ -8881.6452] [ 1517] [depth= 10] . ( 3 sec) [ -8798.2989] [ 1498] [depth= 9] . ( 3 sec) [ -8797.7795] [ 1498] [depth= 1] . ( 3 sec) [ -8741.7668] [ 1498] [depth= 16] . ( 3 sec) [ -8732.3265] [ 1498] [depth= 2] . ( 3 sec) [ -8667.5399] [ 1485] [depth= 7] . ( 3 sec) [ -8567.5609] [ 1468] [depth= 10] . ( 3 sec) [ -8543.1266] [ 1476] [depth= 3] . ( 3 sec) [ -8421.8967] [ 1429] [depth= 23] . ( 3 sec) [ -8417.4729] [ 1428] [depth= 1] . ( 3 sec) [ -8341.0858] [ 1434] [depth= 9] . ( 3 sec) [ -8326.4144] [ 1436] [depth= 1] . ( 3 sec) [ -8314.2003] [ 1424] [depth= 6] . ( 3 sec) [ -8218.1271] [ 1381] [depth= 7] . ( 3 sec) [ -8212.9677] [ 1381] [depth= 17] . ( 4 sec) [ -8145.4759] [ 1368] [depth= 5] . ( 4 sec) [ -8035.0648] [ 1354] [depth= 4] . ( 4 sec) [ -7969.0203] [ 1350] [depth= 1] . ( 4 sec) [ -7803.2073] [ 1298] [depth= 15] . ( 4 sec) [ -7709.0618] [ 1271] [depth= 9] . ( 4 sec) [ -7700.0262] [ 1270] [depth= 16] . ( 4 sec) [ -7699.8681] [ 1273] [depth= 2] . ( 4 sec) [ -7687.0431] [ 1276] [depth= 1] . ( 4 sec) [ -7681.2218] [ 1275] [depth= 3] . ( 4 sec) [ -7623.1522] [ 1250] [depth= 1] . ( 4 sec) [ -7544.9895] [ 1246] [depth= 6] . ( 4 sec) [ -7473.2787] [ 1221] [depth= 3] . ( 4 sec) [ -7392.2075] [ 1217] [depth= 11] . ( 4 sec) [ -7224.2295] [ 1165] [depth= 6] . ( 4 sec) [ -7220.0861] [ 1165] [depth= 14] . ( 4 sec) [ -7185.4600] [ 1153] [depth= 3] . ( 4 sec) [ -7183.6056] [ 1154] [depth= 2] . ( 4 sec) [ -7164.7553] [ 1158] [depth= 1] . ( 4 sec) [ -7154.9332] [ 1155] [depth= 2] . ( 4 sec) [ -7129.9643] [ 1143] [depth= 1] . ( 5 sec) [ -7093.6245] [ 1138] [depth= 3] . ( 5 sec) [ -6958.2309] [ 1101] [depth= 6] . ( 5 sec) [ -6954.8435] [ 1101] [depth= 1] . ( 5 sec) [ -6954.6933] [ 1101] [depth= 1] . ( 5 sec) [ -6902.0651] [ 1090] [depth= 9] . ( 5 sec) [ -6867.2484] [ 1090] [depth= 1] . ( 5 sec) [ -6864.3498] [ 1090] [depth= 1] . ( 5 sec) [ -6861.5089] [ 1082] [depth= 15] . ( 5 sec) [ -6812.9285] [ 1080] [depth= 1] . ( 5 sec) [ -6793.1234] [ 1077] [depth= 3] . ( 5 sec) [ -6784.6286] [ 1074] [depth= 3] . ( 5 sec) [ -6782.9816] [ 1074] [depth= 1] . ( 5 sec) [ -6782.9510] [ 1071] [depth= 2] . ( 5 sec) [ -6757.7229] [ 1060] [depth= 4] . ( 5 sec) [ -6736.7437] [ 1054] [depth= 2] . ( 5 sec) [ -6696.8095] [ 1049] [depth= 4] . ( 5 sec) [ -6682.6114] [ 1043] [depth= 1] . ( 5 sec) [ -6674.1281] [ 1037] [depth= 8] . ( 5 sec) [ -6623.0757] [ 1025] [depth= 2] . ( 5 sec) [ -6512.3675] [ 1026] [depth= 1] . ( 6 sec) [ -6504.8096] [ 1025] [depth= 1] . ( 6 sec) [ -6454.1651] [ 993] [depth= 6] . ( 6 sec) [ -6411.6243] [ 996] [depth= 1] . ( 6 sec) [ -6084.0437] [ 976] [depth= 4] . ( 6 sec) [ -6080.4101] [ 974] [depth= 6] . ( 6 sec) [ -6075.7115] [ 972] [depth= 1] . ( 6 sec) [ -6074.9922] [ 972] [depth= 1] . ( 6 sec) [ -5882.9586] [ 954] [depth= 4] . ( 6 sec) [ -5860.0244] [ 951] [depth= 4] . ( 6 sec) [ -5848.2280] [ 950] [depth= 5] . ( 6 sec) [ -5843.4222] [ 950] [depth= 4] . ( 6 sec) [ -5843.4092] [ 950] [depth= 4] . ( 6 sec) [ -5840.1639] [ 951] [depth= 2] . ( 6 sec) [ -5838.3273] [ 951] [depth= 1] . ( 6 sec) [ -5837.6363] [ 951] [depth= 1] . ( 7 sec) [ -5834.4482] [ 951] [depth= 1] . ( 7 sec) [ -5791.3641] [ 934] [depth= 1] . ( 7 sec) [ -5789.2373] [ 933] [depth= 1] . ( 7 sec) [ -5754.7037] [ 922] [depth= 7] . ( 7 sec) [ -5751.5544] [ 920] [depth= 1] . ( 7 sec) [ -5747.6024] [ 918] [depth= 1] . ( 7 sec) [ -5747.4402] [ 919] [depth= 1] . ( 7 sec) [ -5727.0699] [ 928] [depth= 1] . ( 7 sec) [ -5722.7596] [ 919] [depth= 5] . ( 7 sec) [ -5691.2759] [ 910] [depth= 1] . ( 7 sec) [ -5691.0600] [ 910] [depth= 1] . ( 8 sec) [ -5672.4733] [ 906] [depth= 1] . ( 8 sec) [ -5667.7465] [ 906] [depth= 1] . ( 8 sec) [ -5663.9513] [ 905] [depth= 1] . ( 8 sec) [ -5663.7092] [ 905] [depth= 2] . ( 8 sec) [ -5608.0669] [Branch lengths ] . ( 11 sec) [ -5549.7704] [GTR parameters ] . ( 11 sec) [ -5455.5885] [Alpha ][ 0.250961] . ( 11 sec) [ -5455.5742] [ 905] [depth= 1] . ( 12 sec) [ -5455.5532] [ 905] [depth= 1] . ( 13 sec) [ -5453.5339] [ 902] [depth= 1] . ( 13 sec) [ -5452.0992] [ 896] [depth= 2] . ( 13 sec) [ -5430.5789] [ 885] [depth= 1] . ( 13 sec) [ -5429.0448] [ 885] [depth= 2] . ( 14 sec) [ -5428.9513] [ 885] [depth= 1] . ( 14 sec) [ -5428.8025] [ 887] [depth= 1] . ( 15 sec) [ -5428.0242] [ 885] [depth= 1] . ( 15 sec) [ -5424.9266] [ 883] [depth= 1] . ( 16 sec) [ -5424.8147] [ 883] [depth= 1] . ( 16 sec) [ -5424.5990] [ 883] [depth= 1] . ( 16 sec) [ -5424.1495] [ 884] [depth= 1] . ( 16 sec) [ -5419.6133] [ 882] [depth= 5] . ( 16 sec) [ -5419.5328] [ 882] [depth= 1] . ( 17 sec) [ -5418.2370] [ 883] [depth= 3] . ( 17 sec) [ -5414.3762] [ 882] [depth= 1] . ( 18 sec) [ -5413.7501] [ 880] [depth= 1] . ( 18 sec) [ -5413.7213] [ 869] [depth= 1] . ( 19 sec) [ -5413.1901] [ 869] [depth= 1] . ( 20 sec) [ -5409.0130] [Branch lengths ] . ( 21 sec) [ -5408.3950] [GTR parameters ] . ( 21 sec) [ -5394.0743] [Alpha ][ 0.174299] . ( 23 sec) [ -5393.3235] [ 868] [depth= 3] . ( 23 sec) [ -5393.3081] [ 870] [depth= 1] . ( 25 sec) [ -5393.2902] [ 870] [depth= 1] . ( 27 sec) [ -5392.7831] [ 871] [depth= 1] . ( 29 sec) [ -5392.2549] [ 869] [depth= 1] . ( 29 sec) [ -5392.2429] [ 881] [depth= 1] . ( 29 sec) [ -5391.3100] [ 878] [depth= 3] . ( 30 sec) [ -5388.6876] [Branch lengths ] . ( 32 sec) [ -5388.4697] [GTR parameters ] . ( 32 sec) [ -5388.3596] [Alpha ][ 0.168828] . ( 34 sec) [ -5381.6087] [ 866] [depth= 1] . ( 40 sec) [ -5381.0716] [Branch lengths ] . ( 42 sec) [ -5381.0463] [GTR parameters ] . ( 42 sec) [ -5381.0463] [Alpha ][ 0.168828] . ( 50 sec) [ -5381.0284] [Branch lengths ] . ( 84 sec) [ -5380.9934] [Branch lengths ] . ( 84 sec) [ -5380.9934] [Topology ] . ( 85 sec) [ -5380.7676] [Topology ] . ( 85 sec) [ -5379.8401] [Topology ] . ( 86 sec) [ -5378.8286] [Topology ] . ( 87 sec) [ -5378.6649] [Topology ] . ( 88 sec) [ -5378.6334] [Topology ] . ( 88 sec) [ -5378.6273] [Topology ] . ( 89 sec) [ -5378.6272] [GTR parameters ] . ( 89 sec) [ -5378.6268] [Alpha ][ 0.169151] . ( 89 sec) [ -5378.6268] [Topology ] . ( 90 sec) [ -5378.6256] [Topology ] . ( 90 sec) [ -5378.6253] [Topology ] . ( 92 sec) [ -5378.6208] [GTR parameters ] . ( 92 sec) [ -5378.6208] [Alpha ][ 0.169151] . ( 92 sec) [ -5378.6208] [Topology ] . ( 93 sec) [ -5378.6207] [Topology ] . ( 93 sec) [ -5378.6204] [GTR parameters ] . ( 93 sec) [ -5378.6204] [Alpha ][ 0.169151] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5378.620370. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13119.0323] [GTR parameters ] . ( 1 sec) [ -12755.5094] [Alpha ][ 0.500960] . ( 1 sec) [ -12691.9697] [ 1868] [depth= 10] . ( 1 sec) [ -12565.0412] [ 1855] [depth= 13] . ( 1 sec) [ -12524.9146] [ 1857] [depth= 3] . ( 1 sec) [ -12486.9883] [ 1853] [depth= 8] . ( 1 sec) [ -12076.0465] [ 1820] [depth= 3] . ( 1 sec) [ -11985.6608] [ 1818] [depth= 12] . ( 1 sec) [ -11934.0385] [ 1817] [depth= 1] . ( 1 sec) [ -11923.1445] [ 1815] [depth= 5] . ( 1 sec) [ -11922.9476] [ 1814] [depth= 1] . ( 1 sec) [ -11889.7444] [ 1811] [depth= 10] . ( 1 sec) [ -11777.3889] [ 1799] [depth= 5] . ( 1 sec) [ -11728.8043] [ 1798] [depth= 2] . ( 1 sec) [ -11652.5375] [ 1764] [depth= 7] . ( 1 sec) [ -11570.7617] [ 1762] [depth= 6] . ( 1 sec) [ -11563.3910] [ 1756] [depth= 1] . ( 2 sec) [ -11496.6266] [ 1755] [depth= 1] . ( 2 sec) [ -11468.6684] [ 1746] [depth= 10] . ( 2 sec) [ -11252.6057] [ 1740] [depth= 8] . ( 2 sec) [ -10962.7784] [ 1733] [depth= 12] . ( 2 sec) [ -10865.4202] [ 1703] [depth= 8] . ( 2 sec) [ -10772.0544] [ 1705] [depth= 1] . ( 2 sec) [ -10477.7420] [ 1682] [depth= 8] . ( 2 sec) [ -10465.3071] [ 1682] [depth= 1] . ( 2 sec) [ -10266.7843] [ 1630] [depth= 8] . ( 2 sec) [ -9966.3780] [ 1610] [depth= 8] . ( 2 sec) [ -9902.0162] [ 1601] [depth= 2] . ( 2 sec) [ -9884.9008] [ 1598] [depth= 3] . ( 2 sec) [ -9836.0105] [ 1587] [depth= 1] . ( 2 sec) [ -9822.6204] [ 1584] [depth= 5] . ( 2 sec) [ -9603.7626] [ 1570] [depth= 10] . ( 2 sec) [ -9470.9327] [ 1547] [depth= 11] . ( 2 sec) [ -9461.1619] [ 1540] [depth= 6] . ( 2 sec) [ -8854.7550] [ 1486] [depth= 5] . ( 3 sec) [ -8838.2839] [ 1485] [depth= 14] . ( 3 sec) [ -8833.4668] [ 1481] [depth= 1] . ( 3 sec) [ -8826.6747] [ 1480] [depth= 2] . ( 3 sec) [ -8816.7906] [ 1474] [depth= 6] . ( 3 sec) [ -8777.4358] [ 1474] [depth= 1] . ( 3 sec) [ -8776.1220] [ 1474] [depth= 1] . ( 3 sec) [ -8724.0436] [ 1463] [depth= 1] . ( 3 sec) [ -8663.7600] [ 1454] [depth= 13] . ( 3 sec) [ -8160.6767] [ 1410] [depth= 11] . ( 3 sec) [ -8024.1820] [ 1424] [depth= 10] . ( 3 sec) [ -8018.7452] [ 1426] [depth= 2] . ( 3 sec) [ -7997.1249] [ 1421] [depth= 11] . ( 3 sec) [ -7962.5440] [ 1415] [depth= 5] . ( 3 sec) [ -7960.5727] [ 1415] [depth= 15] . ( 3 sec) [ -7939.7622] [ 1404] [depth= 12] . ( 3 sec) [ -7904.1827] [ 1402] [depth= 1] . ( 3 sec) [ -7903.3856] [ 1407] [depth= 11] . ( 3 sec) [ -7896.6027] [ 1408] [depth= 2] . ( 3 sec) [ -7837.1268] [ 1399] [depth= 4] . ( 3 sec) [ -7822.7778] [ 1390] [depth= 1] . ( 4 sec) [ -7791.9442] [ 1389] [depth= 6] . ( 4 sec) [ -7658.5148] [ 1346] [depth= 12] . ( 4 sec) [ -7577.6675] [ 1312] [depth= 7] . ( 4 sec) [ -7360.7571] [ 1283] [depth= 9] . ( 4 sec) [ -7245.4394] [ 1257] [depth= 3] . ( 4 sec) [ -7172.6412] [ 1254] [depth= 3] . ( 4 sec) [ -7172.1045] [ 1254] [depth= 12] . ( 4 sec) [ -7154.5249] [ 1257] [depth= 4] . ( 4 sec) [ -7104.0851] [ 1254] [depth= 1] . ( 4 sec) [ -6991.1447] [ 1219] [depth= 6] . ( 4 sec) [ -6964.7057] [ 1218] [depth= 1] . ( 4 sec) [ -6949.2947] [ 1216] [depth= 6] . ( 4 sec) [ -6936.3844] [ 1214] [depth= 5] . ( 4 sec) [ -6891.9774] [ 1206] [depth= 6] . ( 4 sec) [ -6883.1439] [ 1206] [depth= 7] . ( 5 sec) [ -6859.0667] [ 1201] [depth= 3] . ( 5 sec) [ -6853.4580] [ 1200] [depth= 1] . ( 5 sec) [ -6790.0518] [ 1183] [depth= 5] . ( 5 sec) [ -6781.0009] [ 1177] [depth= 8] . ( 5 sec) [ -6711.9182] [ 1166] [depth= 10] . ( 5 sec) [ -6706.6886] [ 1164] [depth= 2] . ( 5 sec) [ -6703.6756] [ 1155] [depth= 3] . ( 5 sec) [ -6665.9535] [ 1148] [depth= 8] . ( 5 sec) [ -6661.6774] [ 1144] [depth= 1] . ( 5 sec) [ -6637.5639] [ 1145] [depth= 13] . ( 5 sec) [ -6563.2414] [ 1112] [depth= 16] . ( 5 sec) [ -6546.3992] [ 1115] [depth= 1] . ( 5 sec) [ -6431.2287] [ 1079] [depth= 2] . ( 5 sec) [ -6426.9642] [ 1078] [depth= 1] . ( 5 sec) [ -6411.8633] [ 1071] [depth= 12] . ( 5 sec) [ -6402.6239] [ 1073] [depth= 1] . ( 5 sec) [ -6392.8695] [ 1070] [depth= 1] . ( 5 sec) [ -6391.1185] [ 1066] [depth= 3] . ( 6 sec) [ -6384.3031] [ 1065] [depth= 2] . ( 6 sec) [ -6326.7532] [ 1056] [depth= 2] . ( 6 sec) [ -6320.9814] [ 1057] [depth= 1] . ( 6 sec) [ -6315.9511] [ 1056] [depth= 1] . ( 6 sec) [ -6307.8415] [ 1053] [depth= 7] . ( 6 sec) [ -6264.0077] [ 1039] [depth= 1] . ( 6 sec) [ -6263.7851] [ 1039] [depth= 1] . ( 6 sec) [ -6225.4671] [ 1035] [depth= 3] . ( 6 sec) [ -6221.3312] [ 1034] [depth= 8] . ( 6 sec) [ -6221.2918] [ 1037] [depth= 1] . ( 6 sec) [ -6220.0453] [ 1038] [depth= 1] . ( 6 sec) [ -6192.7605] [ 1024] [depth= 4] . ( 6 sec) [ -6148.1111] [ 1025] [depth= 1] . ( 6 sec) [ -6141.2036] [ 1024] [depth= 1] . ( 6 sec) [ -6108.8581] [ 1016] [depth= 6] . ( 7 sec) [ -6087.3029] [ 1007] [depth= 3] . ( 7 sec) [ -6075.9349] [ 1007] [depth= 3] . ( 7 sec) [ -6018.5538] [ 995] [depth= 13] . ( 7 sec) [ -6013.1514] [ 996] [depth= 1] . ( 7 sec) [ -5976.1863] [ 987] [depth= 1] . ( 7 sec) [ -5975.2581] [ 982] [depth= 7] . ( 7 sec) [ -5954.1091] [ 979] [depth= 8] . ( 7 sec) [ -5919.3966] [ 964] [depth= 11] . ( 7 sec) [ -5919.2224] [ 966] [depth= 1] . ( 7 sec) [ -5907.8713] [ 958] [depth= 10] . ( 7 sec) [ -5907.8575] [ 958] [depth= 1] . ( 7 sec) [ -5907.3056] [ 958] [depth= 1] . ( 7 sec) [ -5894.5594] [ 952] [depth= 1] . ( 7 sec) [ -5892.3778] [ 952] [depth= 1] . ( 7 sec) [ -5891.9076] [ 953] [depth= 1] . ( 7 sec) [ -5848.1563] [ 955] [depth= 2] . ( 8 sec) [ -5847.4511] [ 955] [depth= 1] . ( 8 sec) [ -5839.1691] [ 957] [depth= 1] . ( 8 sec) [ -5835.1571] [ 958] [depth= 1] . ( 8 sec) [ -5827.3489] [ 947] [depth= 3] . ( 8 sec) [ -5757.5084] [Branch lengths ] . ( 10 sec) [ -5700.6361] [GTR parameters ] . ( 10 sec) [ -5596.8771] [Alpha ][ 0.250961] . ( 10 sec) [ -5593.2195] [ 948] [depth= 1] . ( 10 sec) [ -5583.9104] [ 941] [depth= 2] . ( 10 sec) [ -5562.1759] [ 933] [depth= 11] . ( 10 sec) [ -5532.4817] [ 918] [depth= 2] . ( 11 sec) [ -5531.2409] [ 914] [depth= 1] . ( 11 sec) [ -5530.9876] [ 913] [depth= 3] . ( 11 sec) [ -5530.7549] [ 913] [depth= 1] . ( 11 sec) [ -5498.1189] [ 901] [depth= 1] . ( 11 sec) [ -5489.7741] [ 899] [depth= 1] . ( 11 sec) [ -5485.7795] [ 898] [depth= 4] . ( 11 sec) [ -5484.3667] [ 895] [depth= 6] . ( 12 sec) [ -5482.9072] [ 896] [depth= 1] . ( 12 sec) [ -5482.3359] [ 901] [depth= 1] . ( 12 sec) [ -5475.6086] [ 894] [depth= 4] . ( 12 sec) [ -5470.8534] [ 893] [depth= 1] . ( 12 sec) [ -5470.6858] [ 893] [depth= 1] . ( 12 sec) [ -5468.3738] [ 891] [depth= 4] . ( 12 sec) [ -5459.2273] [ 887] [depth= 1] . ( 12 sec) [ -5458.2680] [ 888] [depth= 1] . ( 12 sec) [ -5457.5963] [ 887] [depth= 1] . ( 12 sec) [ -5449.2859] [ 884] [depth= 1] . ( 13 sec) [ -5444.8491] [ 882] [depth= 1] . ( 13 sec) [ -5443.7255] [ 885] [depth= 1] . ( 13 sec) [ -5441.9660] [ 884] [depth= 1] . ( 14 sec) [ -5440.8951] [ 883] [depth= 1] . ( 15 sec) [ -5427.1307] [ 878] [depth= 5] . ( 15 sec) [ -5426.6794] [ 881] [depth= 1] . ( 15 sec) [ -5426.4967] [ 884] [depth= 1] . ( 15 sec) [ -5423.5391] [ 879] [depth= 1] . ( 15 sec) [ -5419.6764] [ 877] [depth= 2] . ( 16 sec) [ -5418.1926] [ 877] [depth= 1] . ( 17 sec) [ -5417.8250] [ 877] [depth= 2] . ( 17 sec) [ -5414.6841] [ 874] [depth= 1] . ( 18 sec) [ -5414.0055] [ 874] [depth= 1] . ( 18 sec) [ -5413.7044] [ 874] [depth= 1] . ( 18 sec) [ -5413.6860] [ 874] [depth= 1] . ( 18 sec) [ -5413.3744] [ 873] [depth= 1] . ( 19 sec) [ -5405.8998] [Branch lengths ] . ( 21 sec) [ -5404.9522] [GTR parameters ] . ( 21 sec) [ -5390.4660] [Alpha ][ 0.173777] . ( 22 sec) [ -5387.3444] [ 871] [depth= 2] . ( 23 sec) [ -5386.7508] [ 869] [depth= 1] . ( 23 sec) [ -5385.5198] [ 868] [depth= 2] . ( 23 sec) [ -5383.8656] [ 868] [depth= 1] . ( 23 sec) [ -5383.8546] [ 868] [depth= 1] . ( 25 sec) [ -5383.8325] [ 868] [depth= 2] . ( 29 sec) [ -5383.7786] [ 872] [depth= 1] . ( 29 sec) [ -5383.0522] [ 868] [depth= 1] . ( 30 sec) [ -5380.6314] [Branch lengths ] . ( 32 sec) [ -5380.4721] [GTR parameters ] . ( 32 sec) [ -5380.4312] [Alpha ][ 0.170515] . ( 33 sec) [ -5380.1997] [ 868] [depth= 3] . ( 41 sec) [ -5379.9898] [Branch lengths ] . ( 41 sec) [ -5379.9897] [GTR parameters ] . ( 41 sec) [ -5379.9895] [Alpha ][ 0.170230] . ( 66 sec) [ -5379.9791] [ 868] [depth= 1] . ( 67 sec) [ -5379.9470] [ 868] [depth= 2] . ( 73 sec) [ -5379.6847] [Branch lengths ] . ( 75 sec) [ -5379.6723] [GTR parameters ] . ( 75 sec) [ -5379.6723] [Alpha ][ 0.170230] . ( 75 sec) [ -5379.6723] [Topology ] . ( 76 sec) [ -5379.6654] [Topology ] . ( 77 sec) [ -5379.6638] [Topology ] . ( 77 sec) [ -5379.6633] [Topology ] . ( 78 sec) [ -5379.6633] [GTR parameters ] . ( 78 sec) [ -5379.6632] [Alpha ][ 0.170058] . ( 78 sec) [ -5379.6632] [Topology ] . ( 78 sec) [ -5379.6630] [Topology ] . ( 79 sec) [ -5379.6630] [GTR parameters ] . ( 79 sec) [ -5379.6630] [Alpha ][ 0.170058] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5379.662968. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12964.8708] [GTR parameters ] . ( 0 sec) [ -12606.5194] [Alpha ][ 0.500960] . ( 0 sec) [ -12567.0017] [ 1837] [depth= 6] . ( 1 sec) [ -12288.0292] [ 1830] [depth= 3] . ( 1 sec) [ -12276.9859] [ 1828] [depth= 1] . ( 1 sec) [ -12258.3671] [ 1826] [depth= 2] . ( 1 sec) [ -12242.2972] [ 1822] [depth= 2] . ( 1 sec) [ -12051.7704] [ 1824] [depth= 12] . ( 1 sec) [ -12045.7841] [ 1820] [depth= 5] . ( 1 sec) [ -11948.4923] [ 1818] [depth= 3] . ( 1 sec) [ -11820.4702] [ 1804] [depth= 4] . ( 1 sec) [ -11798.8148] [ 1804] [depth= 3] . ( 1 sec) [ -11602.3365] [ 1797] [depth= 6] . ( 1 sec) [ -11559.2467] [ 1796] [depth= 1] . ( 1 sec) [ -11492.7004] [ 1781] [depth= 11] . ( 1 sec) [ -11379.7705] [ 1766] [depth= 3] . ( 1 sec) [ -11331.8591] [ 1732] [depth= 15] . ( 1 sec) [ -11022.5500] [ 1720] [depth= 9] . ( 1 sec) [ -10907.6655] [ 1715] [depth= 15] . ( 1 sec) [ -10874.6743] [ 1711] [depth= 14] . ( 1 sec) [ -10867.1891] [ 1711] [depth= 12] . ( 1 sec) [ -10867.0935] [ 1711] [depth= 1] . ( 1 sec) [ -10754.4935] [ 1698] [depth= 3] . ( 1 sec) [ -10261.7493] [ 1658] [depth= 10] . ( 2 sec) [ -10221.5266] [ 1653] [depth= 7] . ( 2 sec) [ -10190.3668] [ 1653] [depth= 1] . ( 2 sec) [ -10141.6179] [ 1650] [depth= 2] . ( 2 sec) [ -10113.3509] [ 1651] [depth= 2] . ( 2 sec) [ -10075.0507] [ 1646] [depth= 3] . ( 2 sec) [ -10049.0715] [ 1635] [depth= 6] . ( 2 sec) [ -10049.0473] [ 1635] [depth= 1] . ( 2 sec) [ -9898.3602] [ 1598] [depth= 10] . ( 2 sec) [ -9630.1089] [ 1588] [depth= 9] . ( 2 sec) [ -9598.0524] [ 1582] [depth= 2] . ( 2 sec) [ -9591.2752] [ 1584] [depth= 1] . ( 2 sec) [ -9513.8186] [ 1551] [depth= 12] . ( 2 sec) [ -9438.5783] [ 1531] [depth= 7] . ( 2 sec) [ -9392.1664] [ 1531] [depth= 3] . ( 2 sec) [ -9337.5622] [ 1508] [depth= 2] . ( 2 sec) [ -9191.4680] [ 1498] [depth= 15] . ( 2 sec) [ -9190.4421] [ 1498] [depth= 2] . ( 2 sec) [ -9178.9070] [ 1495] [depth= 6] . ( 2 sec) [ -9170.6091] [ 1501] [depth= 1] . ( 2 sec) [ -9060.0653] [ 1470] [depth= 13] . ( 3 sec) [ -9007.6006] [ 1459] [depth= 12] . ( 3 sec) [ -9004.0437] [ 1459] [depth= 2] . ( 3 sec) [ -8838.9375] [ 1457] [depth= 7] . ( 3 sec) [ -8721.1000] [ 1447] [depth= 4] . ( 3 sec) [ -8518.5160] [ 1429] [depth= 8] . ( 3 sec) [ -8325.3400] [ 1412] [depth= 6] . ( 3 sec) [ -8310.7466] [ 1412] [depth= 2] . ( 3 sec) [ -8061.4020] [ 1370] [depth= 17] . ( 3 sec) [ -8014.4687] [ 1360] [depth= 15] . ( 3 sec) [ -7940.0802] [ 1347] [depth= 4] . ( 3 sec) [ -7701.2045] [ 1310] [depth= 1] . ( 3 sec) [ -7577.6223] [ 1293] [depth= 8] . ( 3 sec) [ -7577.1301] [ 1293] [depth= 1] . ( 3 sec) [ -7519.8833] [ 1283] [depth= 5] . ( 3 sec) [ -7441.8324] [ 1289] [depth= 6] . ( 3 sec) [ -7438.4637] [ 1284] [depth= 1] . ( 3 sec) [ -7398.5645] [ 1273] [depth= 8] . ( 3 sec) [ -7328.0699] [ 1251] [depth= 1] . ( 3 sec) [ -7292.6113] [ 1240] [depth= 5] . ( 3 sec) [ -7280.9810] [ 1232] [depth= 10] . ( 3 sec) [ -7248.8673] [ 1234] [depth= 3] . ( 4 sec) [ -7183.9731] [ 1227] [depth= 2] . ( 4 sec) [ -7147.5454] [ 1226] [depth= 1] . ( 4 sec) [ -7121.2308] [ 1208] [depth= 7] . ( 4 sec) [ -7075.6672] [ 1195] [depth= 11] . ( 4 sec) [ -7073.6016] [ 1195] [depth= 1] . ( 4 sec) [ -6985.7001] [ 1192] [depth= 4] . ( 4 sec) [ -6818.1279] [ 1172] [depth= 2] . ( 4 sec) [ -6795.7570] [ 1163] [depth= 12] . ( 4 sec) [ -6792.6347] [ 1160] [depth= 2] . ( 4 sec) [ -6758.6426] [ 1138] [depth= 5] . ( 4 sec) [ -6724.9557] [ 1121] [depth= 6] . ( 4 sec) [ -6516.5162] [ 1084] [depth= 11] . ( 4 sec) [ -6515.9986] [ 1084] [depth= 1] . ( 4 sec) [ -6464.7472] [ 1075] [depth= 3] . ( 4 sec) [ -6350.7686] [ 1055] [depth= 8] . ( 4 sec) [ -6331.1127] [ 1043] [depth= 2] . ( 5 sec) [ -6294.8624] [ 1037] [depth= 7] . ( 5 sec) [ -6267.1093] [ 1028] [depth= 1] . ( 5 sec) [ -6252.0740] [ 1023] [depth= 1] . ( 5 sec) [ -6247.1394] [ 1025] [depth= 2] . ( 5 sec) [ -6217.7038] [ 1013] [depth= 4] . ( 5 sec) [ -6143.5139] [ 1001] [depth= 3] . ( 5 sec) [ -6143.4658] [ 1001] [depth= 1] . ( 5 sec) [ -6135.9900] [ 1005] [depth= 3] . ( 5 sec) [ -6129.3717] [ 1007] [depth= 2] . ( 5 sec) [ -6097.4301] [ 1005] [depth= 1] . ( 5 sec) [ -6071.2199] [ 999] [depth= 1] . ( 5 sec) [ -6069.2449] [ 997] [depth= 1] . ( 5 sec) [ -6059.5119] [ 994] [depth= 1] . ( 5 sec) [ -6059.0006] [ 994] [depth= 2] . ( 5 sec) [ -6057.1828] [ 994] [depth= 1] . ( 5 sec) [ -6057.0532] [ 994] [depth= 2] . ( 5 sec) [ -6041.7089] [ 986] [depth= 3] . ( 5 sec) [ -6012.3955] [ 968] [depth= 4] . ( 5 sec) [ -6012.0960] [ 968] [depth= 2] . ( 6 sec) [ -6011.8110] [ 968] [depth= 1] . ( 6 sec) [ -5954.9577] [ 957] [depth= 11] . ( 6 sec) [ -5944.6424] [ 955] [depth= 1] . ( 6 sec) [ -5943.8751] [ 952] [depth= 2] . ( 6 sec) [ -5943.5707] [ 951] [depth= 2] . ( 6 sec) [ -5941.6465] [ 951] [depth= 1] . ( 6 sec) [ -5907.3457] [ 942] [depth= 2] . ( 6 sec) [ -5904.5274] [ 942] [depth= 3] . ( 6 sec) [ -5864.2649] [ 934] [depth= 3] . ( 6 sec) [ -5864.0712] [ 934] [depth= 3] . ( 6 sec) [ -5862.6801] [ 933] [depth= 5] . ( 6 sec) [ -5854.0615] [ 926] [depth= 1] . ( 6 sec) [ -5829.8406] [ 925] [depth= 1] . ( 6 sec) [ -5826.6196] [ 924] [depth= 1] . ( 6 sec) [ -5801.1174] [ 922] [depth= 1] . ( 7 sec) [ -5798.8510] [ 919] [depth= 2] . ( 7 sec) [ -5761.5114] [ 906] [depth= 5] . ( 7 sec) [ -5760.4936] [ 905] [depth= 1] . ( 7 sec) [ -5759.9571] [ 905] [depth= 4] . ( 7 sec) [ -5753.6944] [ 906] [depth= 1] . ( 7 sec) [ -5752.1133] [ 907] [depth= 2] . ( 7 sec) [ -5749.7267] [ 900] [depth= 1] . ( 7 sec) [ -5738.1226] [ 898] [depth= 1] . ( 7 sec) [ -5737.9751] [ 900] [depth= 1] . ( 8 sec) [ -5673.1890] [Branch lengths ] . ( 9 sec) [ -5575.1284] [GTR parameters ] . ( 9 sec) [ -5477.8310] [Alpha ][ 0.250961] . ( 9 sec) [ -5477.7910] [ 901] [depth= 1] . ( 9 sec) [ -5476.8230] [ 901] [depth= 1] . ( 9 sec) [ -5450.7340] [ 894] [depth= 1] . ( 9 sec) [ -5449.9424] [ 891] [depth= 1] . ( 9 sec) [ -5448.9892] [ 892] [depth= 1] . ( 10 sec) [ -5448.6475] [ 895] [depth= 1] . ( 10 sec) [ -5447.3873] [ 896] [depth= 2] . ( 10 sec) [ -5447.0618] [ 896] [depth= 4] . ( 10 sec) [ -5444.4978] [ 896] [depth= 2] . ( 10 sec) [ -5442.7710] [ 895] [depth= 1] . ( 11 sec) [ -5442.6808] [ 895] [depth= 1] . ( 11 sec) [ -5441.3965] [ 893] [depth= 1] . ( 11 sec) [ -5439.7781] [ 888] [depth= 5] . ( 11 sec) [ -5439.7102] [ 888] [depth= 1] . ( 11 sec) [ -5439.6888] [ 888] [depth= 1] . ( 11 sec) [ -5439.5315] [ 889] [depth= 1] . ( 11 sec) [ -5432.6198] [ 876] [depth= 6] . ( 11 sec) [ -5429.5488] [ 877] [depth= 1] . ( 12 sec) [ -5427.8260] [ 876] [depth= 1] . ( 12 sec) [ -5424.4169] [ 872] [depth= 1] . ( 12 sec) [ -5424.3671] [ 870] [depth= 3] . ( 12 sec) [ -5424.3194] [ 874] [depth= 2] . ( 13 sec) [ -5422.8763] [ 872] [depth= 1] . ( 13 sec) [ -5421.9734] [ 868] [depth= 1] . ( 13 sec) [ -5418.0237] [ 863] [depth= 1] . ( 14 sec) [ -5418.0073] [ 863] [depth= 4] . ( 15 sec) [ -5417.8184] [ 863] [depth= 1] . ( 16 sec) [ -5401.7228] [Branch lengths ] . ( 17 sec) [ -5401.3379] [GTR parameters ] . ( 17 sec) [ -5387.2974] [Alpha ][ 0.174322] . ( 18 sec) [ -5387.2800] [ 863] [depth= 1] . ( 18 sec) [ -5386.8452] [ 867] [depth= 1] . ( 19 sec) [ -5386.7947] [ 867] [depth= 3] . ( 20 sec) [ -5386.5697] [ 867] [depth= 2] . ( 20 sec) [ -5381.8327] [ 869] [depth= 8] . ( 23 sec) [ -5381.5979] [ 867] [depth= 2] . ( 26 sec) [ -5379.1014] [Branch lengths ] . ( 27 sec) [ -5379.0396] [GTR parameters ] . ( 27 sec) [ -5378.9899] [Alpha ][ 0.170709] . ( 36 sec) [ -5378.7620] [Branch lengths ] . ( 40 sec) [ -5378.7303] [ 866] [depth= 1] . ( 69 sec) [ -5378.6706] [Branch lengths ] . ( 69 sec) [ -5378.6694] [GTR parameters ] . ( 70 sec) [ -5378.6629] [Alpha ][ 0.169337] . ( 70 sec) [ -5378.6629] [Topology ] . ( 70 sec) [ -5378.6605] [Topology ] . ( 71 sec) [ -5378.6599] [Topology ] . ( 71 sec) [ -5378.6599] [GTR parameters ] . ( 71 sec) [ -5378.6599] [Alpha ][ 0.169337] . ( 71 sec) [ -5378.6599] [Topology ] . ( 72 sec) [ -5378.6597] [Topology ] . ( 72 sec) [ -5378.6597] [GTR parameters ] . ( 73 sec) [ -5378.6596] [Alpha ][ 0.169167] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5378.659647. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -5728.9072] [GTR parameters ] . ( 1 sec) [ -5606.6718] [Alpha ][ 0.500960] . ( 1 sec) [ -5606.6718] [Topology ] . ( 2 sec) [ -5510.2825] [Topology ] . ( 3 sec) [ -5499.3079] [Topology ] . ( 4 sec) [ -5491.5808] [Topology ] . ( 4 sec) [ -5489.3486] [Topology ] . ( 5 sec) [ -5488.5977] [Topology ] . ( 6 sec) [ -5488.4658] [Topology ] . ( 7 sec) [ -5488.4264] [Topology ] . ( 7 sec) [ -5488.4137] [Topology ] . ( 8 sec) [ -5488.4094] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -5488.3977] [Topology ] . ( 15 sec) [ -5487.6246] [GTR parameters ] . ( 15 sec) [ -5400.5669] [Alpha ][ 0.250961] . ( 15 sec) [ -5400.5669] [Topology ] . ( 16 sec) [ -5400.1158] [Topology ] . ( 17 sec) [ -5400.0577] [Topology ] . ( 18 sec) [ -5400.0430] [Topology ] . ( 18 sec) [ -5400.0386] [Topology ] . ( 19 sec) [ -5400.0372] [Topology ] . ( 20 sec) [ -5400.0368] [Topology ] . Checking for NNIs, optimizing five branches... . ( 26 sec) [ -5399.3839] [GTR parameters ] . ( 26 sec) [ -5384.6965] [Alpha ][ 0.172277] . ( 26 sec) [ -5384.6965] [Topology ] . ( 27 sec) [ -5384.4114] [Topology ] . ( 28 sec) [ -5384.3536] [Topology ] . ( 28 sec) [ -5384.3367] [Topology ] . ( 29 sec) [ -5384.3312] [Topology ] . ( 30 sec) [ -5384.3293] [Topology ] . ( 31 sec) [ -5384.3287] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -5384.2239] [GTR parameters ] . ( 37 sec) [ -5384.1911] [Alpha ][ 0.169387] . ( 37 sec) [ -5384.1911] [Topology ] . ( 37 sec) [ -5384.1899] [Topology ] . ( 38 sec) [ -5384.1896] [Topology ] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -5384.1893] [GTR parameters ] . ( 44 sec) [ -5384.1892] [Alpha ][ 0.169217] . ( 44 sec) [ -5384.1892] [Topology ] . ( 45 sec) [ -5384.1891] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 57 sec) [ -5728.9072] [GTR parameters ] . ( 57 sec) [ -5606.6718] [Alpha ][ 0.500960] . ( 58 sec) [ -5604.1549] [ 870] [depth= 1] . ( 58 sec) [ -5603.7101] [ 873] [depth= 1] . ( 59 sec) [ -5602.5602] [ 873] [depth= 1] . ( 59 sec) [ -5602.5495] [ 873] [depth= 1] . ( 59 sec) [ -5602.1653] [ 873] [depth= 1] . ( 59 sec) [ -5601.1809] [ 873] [depth= 1] . ( 59 sec) [ -5596.0814] [ 873] [depth= 1] . ( 59 sec) [ -5588.1092] [ 872] [depth= 1] . ( 59 sec) [ -5586.4381] [ 873] [depth= 1] . ( 59 sec) [ -5578.9807] [ 870] [depth= 1] . ( 59 sec) [ -5573.6518] [ 873] [depth= 3] . ( 60 sec) [ -5571.2321] [ 874] [depth= 1] . ( 60 sec) [ -5565.9621] [ 873] [depth= 1] . ( 60 sec) [ -5564.0713] [ 873] [depth= 2] . ( 60 sec) [ -5562.6399] [ 870] [depth= 1] . ( 60 sec) [ -5553.6603] [ 867] [depth= 1] . ( 60 sec) [ -5552.7440] [ 870] [depth= 1] . ( 60 sec) [ -5552.4439] [ 870] [depth= 1] . ( 61 sec) [ -5551.1027] [ 871] [depth= 1] . ( 61 sec) [ -5549.8428] [ 870] [depth= 1] . ( 61 sec) [ -5549.6923] [ 870] [depth= 1] . ( 61 sec) [ -5546.1460] [ 869] [depth= 2] . ( 61 sec) [ -5545.4896] [ 869] [depth= 1] . ( 61 sec) [ -5543.9660] [ 869] [depth= 1] . ( 61 sec) [ -5543.9544] [ 869] [depth= 1] . ( 62 sec) [ -5543.9115] [ 869] [depth= 1] . ( 62 sec) [ -5542.3207] [ 870] [depth= 1] . ( 62 sec) [ -5540.4171] [ 869] [depth= 1] . ( 62 sec) [ -5539.8329] [ 870] [depth= 2] . ( 62 sec) [ -5538.0824] [ 870] [depth= 1] . ( 62 sec) [ -5536.9322] [ 870] [depth= 1] . ( 63 sec) [ -5535.8431] [ 870] [depth= 1] . ( 63 sec) [ -5535.6406] [ 869] [depth= 3] . ( 63 sec) [ -5533.2370] [ 868] [depth= 1] . ( 63 sec) [ -5532.7731] [ 869] [depth= 2] . ( 63 sec) [ -5532.7105] [ 869] [depth= 1] . ( 63 sec) [ -5532.6955] [ 869] [depth= 2] . ( 64 sec) [ -5493.7044] [Branch lengths ] . ( 65 sec) [ -5492.9840] [GTR parameters ] . ( 65 sec) [ -5405.5034] [Alpha ][ 0.250961] . ( 66 sec) [ -5402.9994] [ 866] [depth= 1] . ( 69 sec) [ -5398.3249] [ 868] [depth= 8] . ( 71 sec) [ -5398.3115] [ 868] [depth= 1] . ( 72 sec) [ -5398.0718] [ 868] [depth= 1] . ( 73 sec) [ -5398.0072] [ 868] [depth= 2] . ( 75 sec) [ -5395.1170] [Branch lengths ] . ( 76 sec) [ -5394.6346] [GTR parameters ] . ( 76 sec) [ -5380.1976] [Alpha ][ 0.172872] . ( 80 sec) [ -5380.0177] [ 866] [depth= 2] . ( 84 sec) [ -5379.9978] [ 866] [depth= 4] . ( 85 sec) [ -5378.8965] [Branch lengths ] . ( 86 sec) [ -5378.7548] [GTR parameters ] . ( 86 sec) [ -5378.7207] [Alpha ][ 0.169912] . ( 95 sec) [ -5378.6658] [Branch lengths ] . ( 127 sec) [ -5378.6613] [Branch lengths ] . ( 127 sec) [ -5378.6613] [Topology ] . ( 128 sec) [ -5378.6611] [Topology ] . ( 128 sec) [ -5378.6608] [GTR parameters ] . ( 128 sec) [ -5378.6592] [Alpha ][ 0.169218] . ( 128 sec) [ -5378.6592] [Topology ] . ( 129 sec) [ -5378.6589] [Topology ] . ( 130 sec) [ -5378.6589] [GTR parameters ] . ( 130 sec) [ -5378.6589] [Alpha ][ 0.169218] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5384.189132 . Log likelihood obtained after SPR moves : -5378.658910 . Log likelihood of the current tree: -5378.658910. . Printing the most likely tree in file 'nucleic_M2974_56x827_2006.phy_phyml_tree.txt'... . Best log likelihood : -5378.620370 . Time used 0h2m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 551.44user 0.00system 9:16.74elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps