.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data47.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... . 292 patterns found. (out of a total of 500 sites) . 197 sites without polymorphism (39.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10405.8488] [GTR parameters ] . ( 0 sec) [ -10202.1519] [Alpha ][ 0.500960] . ( 0 sec) [ -9971.9030] [ 1720] [depth= 4] . ( 0 sec) [ -9848.5231] [ 1706] [depth= 5] . ( 1 sec) [ -9790.5804] [ 1705] [depth= 1] . ( 1 sec) [ -9738.6298] [ 1704] [depth= 7] . ( 1 sec) [ -9676.3943] [ 1682] [depth= 4] . ( 1 sec) [ -9666.1965] [ 1682] [depth= 1] . ( 1 sec) [ -9604.1805] [ 1664] [depth= 1] . ( 1 sec) [ -9462.6400] [ 1648] [depth= 3] . ( 1 sec) [ -9439.4618] [ 1646] [depth= 1] . ( 1 sec) [ -9332.1184] [ 1642] [depth= 12] . ( 1 sec) [ -8994.8884] [ 1568] [depth= 13] . ( 1 sec) [ -8858.0944] [ 1558] [depth= 6] . ( 1 sec) [ -8841.9885] [ 1558] [depth= 1] . ( 1 sec) [ -8748.6853] [ 1557] [depth= 4] . ( 1 sec) [ -8494.0219] [ 1502] [depth= 3] . ( 1 sec) [ -8478.2795] [ 1502] [depth= 11] . ( 1 sec) [ -8405.8964] [ 1467] [depth= 2] . ( 1 sec) [ -8295.8670] [ 1451] [depth= 6] . ( 1 sec) [ -8261.1644] [ 1444] [depth= 15] . ( 2 sec) [ -8123.5376] [ 1413] [depth= 4] . ( 2 sec) [ -8112.0477] [ 1413] [depth= 4] . ( 2 sec) [ -8050.0681] [ 1403] [depth= 3] . ( 2 sec) [ -7949.4702] [ 1375] [depth= 5] . ( 2 sec) [ -7866.3080] [ 1362] [depth= 11] . ( 2 sec) [ -7661.7773] [ 1354] [depth= 8] . ( 2 sec) [ -7380.4392] [ 1345] [depth= 7] . ( 2 sec) [ -7216.0266] [ 1288] [depth= 9] . ( 2 sec) [ -7212.4398] [ 1289] [depth= 11] . ( 2 sec) [ -7095.5764] [ 1285] [depth= 4] . ( 2 sec) [ -7087.4688] [ 1285] [depth= 2] . ( 2 sec) [ -7087.3351] [ 1283] [depth= 3] . ( 2 sec) [ -7008.9207] [ 1281] [depth= 2] . ( 2 sec) [ -6823.2298] [ 1232] [depth= 4] . ( 2 sec) [ -6738.8090] [ 1222] [depth= 3] . ( 2 sec) [ -6692.6108] [ 1222] [depth= 2] . ( 3 sec) [ -6670.6397] [ 1195] [depth= 13] . ( 3 sec) [ -6249.9811] [ 1133] [depth= 15] . ( 3 sec) [ -6245.9924] [ 1132] [depth= 1] . ( 3 sec) [ -6215.6216] [ 1105] [depth= 2] . ( 3 sec) [ -6201.7199] [ 1103] [depth= 1] . ( 3 sec) [ -6126.8488] [ 1094] [depth= 2] . ( 3 sec) [ -5972.9625] [ 1074] [depth= 8] . ( 3 sec) [ -5849.5872] [ 1051] [depth= 6] . ( 3 sec) [ -5817.7851] [ 1051] [depth= 1] . ( 3 sec) [ -5817.6452] [ 1051] [depth= 1] . ( 3 sec) [ -5814.6989] [ 1051] [depth= 1] . ( 3 sec) [ -5777.7658] [ 1032] [depth= 3] . ( 3 sec) [ -5738.4208] [ 979] [depth= 3] . ( 3 sec) [ -5686.9762] [ 974] [depth= 1] . ( 3 sec) [ -5608.0870] [ 975] [depth= 1] . ( 3 sec) [ -5604.0002] [ 978] [depth= 3] . ( 3 sec) [ -5554.9950] [ 958] [depth= 5] . ( 3 sec) [ -5484.4054] [ 966] [depth= 1] . ( 3 sec) [ -5482.2636] [ 964] [depth= 1] . ( 3 sec) [ -5403.1395] [ 952] [depth= 1] . ( 3 sec) [ -5334.8548] [ 946] [depth= 2] . ( 4 sec) [ -5252.3829] [ 942] [depth= 1] . ( 4 sec) [ -5252.2627] [ 941] [depth= 2] . ( 4 sec) [ -5206.3298] [ 940] [depth= 1] . ( 4 sec) [ -5177.7255] [ 931] [depth= 1] . ( 4 sec) [ -5172.0339] [ 891] [depth= 2] . ( 4 sec) [ -5170.9693] [ 892] [depth= 1] . ( 4 sec) [ -5169.7300] [ 892] [depth= 1] . ( 4 sec) [ -5156.5415] [ 888] [depth= 1] . ( 4 sec) [ -5024.1704] [ 865] [depth= 2] . ( 4 sec) [ -4985.1192] [ 850] [depth= 2] . ( 4 sec) [ -4980.0132] [ 853] [depth= 2] . ( 4 sec) [ -4959.7702] [ 853] [depth= 1] . ( 4 sec) [ -4835.6256] [ 827] [depth= 4] . ( 4 sec) [ -4828.9309] [ 826] [depth= 2] . ( 4 sec) [ -4828.8661] [ 826] [depth= 1] . ( 4 sec) [ -4782.9183] [ 794] [depth= 3] . ( 4 sec) [ -4746.5913] [ 789] [depth= 1] . ( 4 sec) [ -4739.9598] [ 793] [depth= 1] . ( 4 sec) [ -4705.0873] [ 790] [depth= 9] . ( 5 sec) [ -4691.3620] [ 786] [depth= 1] . ( 5 sec) [ -4679.1712] [ 775] [depth= 4] . ( 5 sec) [ -4647.7684] [ 775] [depth= 4] . ( 5 sec) [ -4614.6922] [Branch lengths ] . ( 5 sec) [ -4613.1053] [GTR parameters ] . ( 5 sec) [ -4604.8200] [Alpha ][ 0.772880] . ( 5 sec) [ -4563.5230] [ 755] [depth= 1] . ( 5 sec) [ -4563.4794] [ 755] [depth= 1] . ( 6 sec) [ -4551.9638] [ 744] [depth= 1] . ( 6 sec) [ -4528.6404] [ 729] [depth= 5] . ( 6 sec) [ -4437.8913] [ 706] [depth= 1] . ( 6 sec) [ -4425.1310] [ 702] [depth= 2] . ( 6 sec) [ -4422.5610] [ 700] [depth= 1] . ( 6 sec) [ -4418.3030] [ 699] [depth= 1] . ( 6 sec) [ -4391.7022] [ 687] [depth= 1] . ( 6 sec) [ -4390.9545] [ 686] [depth= 1] . ( 6 sec) [ -4390.0745] [ 685] [depth= 1] . ( 6 sec) [ -4389.5644] [ 684] [depth= 2] . ( 6 sec) [ -4384.3729] [ 682] [depth= 1] . ( 8 sec) [ -4380.9612] [Branch lengths ] . ( 9 sec) [ -4380.8052] [GTR parameters ] . ( 9 sec) [ -4378.0924] [Alpha ][ 1.040762] . ( 9 sec) [ -4352.1160] [ 671] [depth= 1] . ( 11 sec) [ -4352.1023] [ 671] [depth= 1] . ( 12 sec) [ -4351.7428] [Branch lengths ] . ( 12 sec) [ -4351.6410] [GTR parameters ] . ( 12 sec) [ -4351.6032] [Alpha ][ 1.080649] . ( 16 sec) [ -4351.5782] [Branch lengths ] . ( 38 sec) [ -4351.5768] [Branch lengths ] . ( 38 sec) [ -4351.5768] [Topology ] . ( 38 sec) [ -4351.5768] [Topology ] . ( 39 sec) [ -4351.5767] [GTR parameters ] . ( 39 sec) [ -4351.5763] [Alpha ][ 1.084729] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4351.576327. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -10816.5713] [GTR parameters ] . ( 2 sec) [ -10597.8940] [Alpha ][ 0.500960] . ( 2 sec) [ -10512.6503] [ 1782] [depth= 4] . ( 2 sec) [ -10341.6894] [ 1767] [depth= 11] . ( 2 sec) [ -10275.7518] [ 1760] [depth= 4] . ( 2 sec) [ -10255.8106] [ 1762] [depth= 7] . ( 2 sec) [ -10197.2366] [ 1726] [depth= 3] . ( 2 sec) [ -10069.4568] [ 1725] [depth= 1] . ( 2 sec) [ -9811.1669] [ 1723] [depth= 1] . ( 2 sec) [ -9769.9017] [ 1721] [depth= 6] . ( 2 sec) [ -9659.8655] [ 1677] [depth= 2] . ( 2 sec) [ -9642.1201] [ 1676] [depth= 2] . ( 2 sec) [ -9453.4899] [ 1648] [depth= 12] . ( 2 sec) [ -9345.1458] [ 1647] [depth= 1] . ( 2 sec) [ -9261.2986] [ 1639] [depth= 6] . ( 2 sec) [ -9195.9594] [ 1641] [depth= 3] . ( 2 sec) [ -9103.4549] [ 1615] [depth= 6] . ( 2 sec) [ -8830.5914] [ 1567] [depth= 3] . ( 2 sec) [ -8724.8950] [ 1540] [depth= 6] . ( 2 sec) [ -8713.8088] [ 1540] [depth= 4] . ( 2 sec) [ -8649.8166] [ 1522] [depth= 5] . ( 2 sec) [ -8522.7793] [ 1521] [depth= 1] . ( 2 sec) [ -8329.5282] [ 1484] [depth= 5] . ( 2 sec) [ -8220.4801] [ 1476] [depth= 5] . ( 2 sec) [ -8205.3931] [ 1450] [depth= 1] . ( 2 sec) [ -8110.3631] [ 1404] [depth= 6] . ( 2 sec) [ -7776.3799] [ 1394] [depth= 2] . ( 2 sec) [ -7721.7481] [ 1391] [depth= 1] . ( 2 sec) [ -7720.2823] [ 1391] [depth= 2] . ( 2 sec) [ -7675.1857] [ 1372] [depth= 4] . ( 3 sec) [ -7554.5154] [ 1345] [depth= 16] . ( 3 sec) [ -7497.9736] [ 1330] [depth= 3] . ( 3 sec) [ -7386.4103] [ 1298] [depth= 4] . ( 3 sec) [ -7263.5181] [ 1288] [depth= 16] . ( 3 sec) [ -7148.1068] [ 1248] [depth= 15] . ( 3 sec) [ -7144.9232] [ 1245] [depth= 5] . ( 3 sec) [ -7113.3928] [ 1242] [depth= 2] . ( 3 sec) [ -7082.9217] [ 1241] [depth= 7] . ( 3 sec) [ -6988.6614] [ 1213] [depth= 8] . ( 3 sec) [ -6735.1771] [ 1212] [depth= 1] . ( 3 sec) [ -6604.7929] [ 1178] [depth= 3] . ( 3 sec) [ -6568.4185] [ 1161] [depth= 5] . ( 3 sec) [ -6534.5312] [ 1157] [depth= 1] . ( 3 sec) [ -6384.4556] [ 1110] [depth= 4] . ( 3 sec) [ -6049.6920] [ 1086] [depth= 13] . ( 3 sec) [ -5922.7471] [ 1035] [depth= 11] . ( 3 sec) [ -5913.3522] [ 1042] [depth= 1] . ( 3 sec) [ -5901.6606] [ 1035] [depth= 1] . ( 3 sec) [ -5824.6131] [ 1020] [depth= 2] . ( 3 sec) [ -5811.9875] [ 1016] [depth= 3] . ( 3 sec) [ -5779.1343] [ 1014] [depth= 3] . ( 3 sec) [ -5604.7094] [ 1014] [depth= 1] . ( 3 sec) [ -5539.3029] [ 1004] [depth= 6] . ( 3 sec) [ -5511.9339] [ 992] [depth= 1] . ( 3 sec) [ -5497.4811] [ 992] [depth= 2] . ( 3 sec) [ -5293.9646] [ 920] [depth= 10] . ( 3 sec) [ -5290.2787] [ 920] [depth= 1] . ( 4 sec) [ -5176.3166] [ 863] [depth= 7] . ( 4 sec) [ -5175.0475] [ 861] [depth= 2] . ( 4 sec) [ -5171.0121] [ 861] [depth= 1] . ( 4 sec) [ -5163.3031] [ 861] [depth= 2] . ( 4 sec) [ -5132.7145] [ 855] [depth= 4] . ( 4 sec) [ -5125.8001] [ 855] [depth= 1] . ( 4 sec) [ -5113.1236] [ 853] [depth= 1] . ( 4 sec) [ -4900.3368] [ 799] [depth= 8] . ( 4 sec) [ -4858.9650] [ 786] [depth= 1] . ( 4 sec) [ -4696.8845] [ 748] [depth= 2] . ( 4 sec) [ -4696.6705] [ 748] [depth= 2] . ( 4 sec) [ -4642.9963] [ 734] [depth= 1] . ( 4 sec) [ -4626.0727] [ 728] [depth= 1] . ( 4 sec) [ -4625.1499] [ 727] [depth= 1] . ( 4 sec) [ -4613.7356] [ 726] [depth= 1] . ( 4 sec) [ -4603.2985] [ 724] [depth= 1] . ( 4 sec) [ -4602.8201] [ 724] [depth= 1] . ( 4 sec) [ -4554.1916] [ 712] [depth= 2] . ( 4 sec) [ -4517.6751] [ 714] [depth= 1] . ( 4 sec) [ -4510.3496] [ 711] [depth= 2] . ( 5 sec) [ -4509.8992] [ 712] [depth= 1] . ( 5 sec) [ -4501.1276] [ 705] [depth= 1] . ( 5 sec) [ -4488.8581] [ 697] [depth= 1] . ( 5 sec) [ -4488.4388] [ 697] [depth= 1] . ( 5 sec) [ -4454.1192] [Branch lengths ] . ( 5 sec) [ -4452.7318] [GTR parameters ] . ( 5 sec) [ -4437.2037] [Alpha ][ 0.958160] . ( 5 sec) [ -4359.4069] [ 674] [depth= 2] . ( 6 sec) [ -4358.9836] [ 674] [depth= 1] . ( 6 sec) [ -4354.0479] [ 671] [depth= 1] . ( 6 sec) [ -4354.0311] [ 671] [depth= 1] . ( 6 sec) [ -4353.9471] [ 671] [depth= 1] . ( 7 sec) [ -4353.9358] [ 671] [depth= 1] . ( 7 sec) [ -4353.9246] [ 671] [depth= 1] . ( 8 sec) [ -4352.0851] [Branch lengths ] . ( 9 sec) [ -4352.0259] [GTR parameters ] . ( 9 sec) [ -4351.6458] [Alpha ][ 1.077792] . ( 11 sec) [ -4351.5821] [Branch lengths ] . ( 29 sec) [ -4351.5781] [Branch lengths ] . ( 29 sec) [ -4351.5781] [Topology ] . ( 30 sec) [ -4351.5780] [Topology ] . ( 30 sec) [ -4351.5774] [GTR parameters ] . ( 30 sec) [ -4351.5763] [Alpha ][ 1.084715] . ( 30 sec) [ -4351.5763] [Topology ] . ( 31 sec) [ -4351.5762] [Topology ] . ( 31 sec) [ -4351.5762] [GTR parameters ] . ( 31 sec) [ -4351.5762] [Alpha ][ 1.084715] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4351.576225. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10945.2915] [GTR parameters ] . ( 1 sec) [ -10725.9040] [Alpha ][ 0.500960] . ( 1 sec) [ -10621.1641] [ 1817] [depth= 1] . ( 1 sec) [ -10567.9674] [ 1804] [depth= 4] . ( 1 sec) [ -10487.5108] [ 1801] [depth= 4] . ( 1 sec) [ -10419.7358] [ 1800] [depth= 2] . ( 1 sec) [ -10371.0477] [ 1785] [depth= 5] . ( 1 sec) [ -10249.6093] [ 1783] [depth= 4] . ( 1 sec) [ -10052.2557] [ 1744] [depth= 15] . ( 2 sec) [ -9972.6249] [ 1743] [depth= 14] . ( 2 sec) [ -9349.2846] [ 1653] [depth= 15] . ( 2 sec) [ -9192.4746] [ 1654] [depth= 12] . ( 2 sec) [ -8893.7628] [ 1621] [depth= 6] . ( 2 sec) [ -8882.7913] [ 1616] [depth= 2] . ( 2 sec) [ -8841.9837] [ 1615] [depth= 1] . ( 2 sec) [ -8759.4741] [ 1612] [depth= 5] . ( 2 sec) [ -8726.3752] [ 1611] [depth= 3] . ( 2 sec) [ -8624.5446] [ 1601] [depth= 2] . ( 2 sec) [ -8546.9148] [ 1601] [depth= 2] . ( 2 sec) [ -8321.4782] [ 1552] [depth= 1] . ( 2 sec) [ -8181.3683] [ 1549] [depth= 6] . ( 2 sec) [ -8114.6457] [ 1526] [depth= 1] . ( 2 sec) [ -8019.8046] [ 1522] [depth= 7] . ( 2 sec) [ -7800.6940] [ 1468] [depth= 7] . ( 2 sec) [ -7746.0459] [ 1450] [depth= 1] . ( 2 sec) [ -7615.9775] [ 1409] [depth= 6] . ( 2 sec) [ -7480.9905] [ 1397] [depth= 8] . ( 3 sec) [ -7475.5103] [ 1393] [depth= 1] . ( 3 sec) [ -7446.3412] [ 1391] [depth= 5] . ( 3 sec) [ -7395.7311] [ 1388] [depth= 1] . ( 3 sec) [ -7221.7129] [ 1347] [depth= 7] . ( 3 sec) [ -7200.2899] [ 1350] [depth= 1] . ( 3 sec) [ -7090.6954] [ 1311] [depth= 3] . ( 3 sec) [ -7072.1820] [ 1305] [depth= 1] . ( 3 sec) [ -7064.5829] [ 1296] [depth= 8] . ( 3 sec) [ -7049.9032] [ 1252] [depth= 4] . ( 3 sec) [ -7040.6442] [ 1257] [depth= 1] . ( 3 sec) [ -7005.6675] [ 1254] [depth= 1] . ( 3 sec) [ -6949.8441] [ 1246] [depth= 7] . ( 3 sec) [ -6805.5702] [ 1219] [depth= 2] . ( 3 sec) [ -6735.2610] [ 1216] [depth= 2] . ( 3 sec) [ -6734.5965] [ 1216] [depth= 9] . ( 3 sec) [ -6621.0668] [ 1202] [depth= 7] . ( 3 sec) [ -6555.5351] [ 1167] [depth= 5] . ( 4 sec) [ -6554.3538] [ 1129] [depth= 1] . ( 4 sec) [ -6368.6381] [ 1095] [depth= 8] . ( 4 sec) [ -6318.8565] [ 1086] [depth= 9] . ( 4 sec) [ -6241.0185] [ 1081] [depth= 1] . ( 4 sec) [ -6161.3902] [ 1080] [depth= 9] . ( 4 sec) [ -6114.5813] [ 1080] [depth= 2] . ( 4 sec) [ -6043.6335] [ 1078] [depth= 1] . ( 4 sec) [ -5928.3990] [ 1043] [depth= 1] . ( 4 sec) [ -5922.5665] [ 1041] [depth= 10] . ( 4 sec) [ -5919.3957] [ 1039] [depth= 1] . ( 4 sec) [ -5801.6043] [ 1019] [depth= 6] . ( 4 sec) [ -5793.5885] [ 1018] [depth= 1] . ( 4 sec) [ -5756.2032] [ 997] [depth= 2] . ( 4 sec) [ -5738.9008] [ 994] [depth= 2] . ( 4 sec) [ -5699.2240] [ 979] [depth= 1] . ( 4 sec) [ -5675.6043] [ 977] [depth= 1] . ( 4 sec) [ -5594.0803] [ 966] [depth= 14] . ( 4 sec) [ -5568.2560] [ 964] [depth= 1] . ( 5 sec) [ -5564.4434] [ 966] [depth= 1] . ( 5 sec) [ -5562.2121] [ 966] [depth= 1] . ( 5 sec) [ -5519.7975] [ 950] [depth= 1] . ( 5 sec) [ -5514.0768] [ 946] [depth= 6] . ( 5 sec) [ -5437.0231] [ 917] [depth= 2] . ( 5 sec) [ -5301.6976] [ 916] [depth= 1] . ( 5 sec) [ -5298.5623] [ 914] [depth= 1] . ( 5 sec) [ -5293.8150] [ 912] [depth= 1] . ( 5 sec) [ -5247.3978] [ 902] [depth= 1] . ( 5 sec) [ -5144.3098] [ 877] [depth= 1] . ( 5 sec) [ -5115.1526] [ 875] [depth= 5] . ( 5 sec) [ -5111.5473] [ 874] [depth= 2] . ( 5 sec) [ -5043.1202] [ 854] [depth= 2] . ( 5 sec) [ -4966.2621] [ 819] [depth= 2] . ( 5 sec) [ -4965.3275] [ 819] [depth= 1] . ( 5 sec) [ -4964.0744] [ 819] [depth= 1] . ( 5 sec) [ -4931.5957] [ 820] [depth= 3] . ( 6 sec) [ -4931.4432] [ 820] [depth= 1] . ( 6 sec) [ -4845.3601] [ 813] [depth= 3] . ( 6 sec) [ -4797.4266] [ 802] [depth= 1] . ( 6 sec) [ -4785.5979] [ 793] [depth= 1] . ( 6 sec) [ -4756.6599] [ 772] [depth= 2] . ( 6 sec) [ -4731.7624] [ 757] [depth= 1] . ( 6 sec) [ -4730.5633] [ 759] [depth= 1] . ( 6 sec) [ -4685.0601] [ 747] [depth= 3] . ( 6 sec) [ -4685.0288] [ 747] [depth= 1] . ( 6 sec) [ -4657.5251] [ 727] [depth= 1] . ( 6 sec) [ -4632.7445] [ 720] [depth= 2] . ( 6 sec) [ -4632.5895] [ 720] [depth= 3] . ( 6 sec) [ -4631.5724] [ 722] [depth= 1] . ( 7 sec) [ -4534.7795] [Branch lengths ] . ( 7 sec) [ -4534.5189] [GTR parameters ] . ( 7 sec) [ -4517.2475] [Alpha ][ 0.949452] . ( 7 sec) [ -4507.5073] [ 720] [depth= 1] . ( 7 sec) [ -4449.6810] [ 708] [depth= 2] . ( 8 sec) [ -4449.5260] [ 708] [depth= 1] . ( 8 sec) [ -4435.3137] [ 703] [depth= 2] . ( 8 sec) [ -4406.5394] [ 693] [depth= 1] . ( 8 sec) [ -4358.2995] [ 672] [depth= 5] . ( 9 sec) [ -4358.1963] [ 672] [depth= 1] . ( 9 sec) [ -4358.1358] [ 672] [depth= 1] . ( 9 sec) [ -4357.7065] [ 671] [depth= 1] . ( 9 sec) [ -4357.6721] [ 672] [depth= 1] . ( 10 sec) [ -4357.6520] [ 672] [depth= 1] . ( 11 sec) [ -4353.0955] [Branch lengths ] . ( 12 sec) [ -4352.9585] [GTR parameters ] . ( 12 sec) [ -4352.4501] [Alpha ][ 1.084704] . ( 12 sec) [ -4351.7592] [ 671] [depth= 1] . ( 14 sec) [ -4351.7483] [ 671] [depth= 1] . ( 15 sec) [ -4351.5819] [Branch lengths ] . ( 15 sec) [ -4351.5798] [GTR parameters ] . ( 16 sec) [ -4351.5798] [Alpha ][ 1.085808] . ( 32 sec) [ -4351.5764] [Branch lengths ] . ( 32 sec) [ -4351.5764] [Topology ] . ( 33 sec) [ -4351.5763] [Topology ] . ( 33 sec) [ -4351.5763] [GTR parameters ] . ( 33 sec) [ -4351.5763] [Alpha ][ 1.084722] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4351.576305. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11004.9636] [GTR parameters ] . ( 0 sec) [ -10777.6341] [Alpha ][ 0.500960] . ( 0 sec) [ -10573.5516] [ 1835] [depth= 11] . ( 0 sec) [ -10300.3556] [ 1820] [depth= 3] . ( 1 sec) [ -10265.8475] [ 1808] [depth= 6] . ( 1 sec) [ -10197.7875] [ 1787] [depth= 1] . ( 1 sec) [ -10098.5869] [ 1763] [depth= 9] . ( 1 sec) [ -9933.3302] [ 1742] [depth= 3] . ( 1 sec) [ -9715.5749] [ 1742] [depth= 5] . ( 1 sec) [ -9526.5335] [ 1674] [depth= 3] . ( 1 sec) [ -9481.2679] [ 1674] [depth= 1] . ( 1 sec) [ -9402.1849] [ 1672] [depth= 4] . ( 1 sec) [ -9373.6677] [ 1672] [depth= 2] . ( 1 sec) [ -9210.8221] [ 1639] [depth= 16] . ( 1 sec) [ -9144.6346] [ 1618] [depth= 5] . ( 1 sec) [ -9055.0468] [ 1616] [depth= 2] . ( 1 sec) [ -8877.3561] [ 1566] [depth= 13] . ( 1 sec) [ -8848.0647] [ 1552] [depth= 14] . ( 1 sec) [ -8628.3087] [ 1551] [depth= 1] . ( 1 sec) [ -8361.6678] [ 1497] [depth= 3] . ( 1 sec) [ -8120.5346] [ 1448] [depth= 14] . ( 1 sec) [ -8034.7765] [ 1416] [depth= 6] . ( 1 sec) [ -7940.8121] [ 1426] [depth= 13] . ( 2 sec) [ -7868.7968] [ 1403] [depth= 1] . ( 2 sec) [ -7849.9583] [ 1401] [depth= 1] . ( 2 sec) [ -7761.1193] [ 1386] [depth= 1] . ( 2 sec) [ -7678.3092] [ 1387] [depth= 10] . ( 2 sec) [ -7670.7051] [ 1385] [depth= 2] . ( 2 sec) [ -7481.2864] [ 1384] [depth= 8] . ( 2 sec) [ -7478.8222] [ 1365] [depth= 3] . ( 2 sec) [ -7174.3263] [ 1313] [depth= 7] . ( 2 sec) [ -7101.0924] [ 1294] [depth= 1] . ( 2 sec) [ -7064.5782] [ 1298] [depth= 3] . ( 2 sec) [ -6814.3734] [ 1275] [depth= 12] . ( 2 sec) [ -6637.3483] [ 1247] [depth= 7] . ( 2 sec) [ -6529.7599] [ 1222] [depth= 1] . ( 2 sec) [ -6502.0479] [ 1222] [depth= 1] . ( 2 sec) [ -6494.4748] [ 1199] [depth= 1] . ( 2 sec) [ -6445.6455] [ 1181] [depth= 2] . ( 2 sec) [ -6399.1188] [ 1176] [depth= 5] . ( 2 sec) [ -6313.5370] [ 1166] [depth= 11] . ( 3 sec) [ -6285.7559] [ 1160] [depth= 1] . ( 3 sec) [ -6264.3129] [ 1162] [depth= 2] . ( 3 sec) [ -6181.3038] [ 1141] [depth= 3] . ( 3 sec) [ -6042.4435] [ 1118] [depth= 11] . ( 3 sec) [ -6007.8550] [ 1119] [depth= 7] . ( 3 sec) [ -5983.8331] [ 1117] [depth= 2] . ( 3 sec) [ -5957.3201] [ 1114] [depth= 1] . ( 3 sec) [ -5948.3829] [ 1115] [depth= 13] . ( 3 sec) [ -5844.7224] [ 1086] [depth= 9] . ( 3 sec) [ -5838.7802] [ 1085] [depth= 1] . ( 3 sec) [ -5826.6223] [ 1079] [depth= 1] . ( 3 sec) [ -5773.0535] [ 1051] [depth= 1] . ( 3 sec) [ -5695.4779] [ 1019] [depth= 5] . ( 3 sec) [ -5688.8705] [ 1007] [depth= 1] . ( 4 sec) [ -5652.4140] [ 1006] [depth= 1] . ( 4 sec) [ -5651.9449] [ 1008] [depth= 3] . ( 4 sec) [ -5643.6546] [ 1006] [depth= 1] . ( 4 sec) [ -5540.2264] [ 988] [depth= 3] . ( 4 sec) [ -5518.6360] [ 956] [depth= 12] . ( 4 sec) [ -5503.1881] [ 949] [depth= 1] . ( 4 sec) [ -5486.6217] [ 954] [depth= 2] . ( 4 sec) [ -5368.3400] [ 944] [depth= 1] . ( 4 sec) [ -5363.2914] [ 948] [depth= 12] . ( 4 sec) [ -5358.0727] [ 943] [depth= 6] . ( 4 sec) [ -5354.4734] [ 943] [depth= 2] . ( 4 sec) [ -5302.4455] [ 928] [depth= 2] . ( 5 sec) [ -5287.0454] [ 925] [depth= 2] . ( 5 sec) [ -5251.0160] [ 921] [depth= 2] . ( 5 sec) [ -5226.8947] [ 923] [depth= 3] . ( 5 sec) [ -5226.7954] [ 923] [depth= 1] . ( 5 sec) [ -5226.7038] [ 923] [depth= 1] . ( 5 sec) [ -5204.9480] [ 911] [depth= 4] . ( 5 sec) [ -5204.3561] [ 911] [depth= 2] . ( 5 sec) [ -5154.7674] [ 894] [depth= 1] . ( 6 sec) [ -5148.0816] [ 894] [depth= 2] . ( 6 sec) [ -5144.4640] [ 894] [depth= 2] . ( 6 sec) [ -4982.8947] [ 846] [depth= 7] . ( 6 sec) [ -4977.4440] [ 843] [depth= 2] . ( 6 sec) [ -4971.5634] [ 839] [depth= 2] . ( 6 sec) [ -4955.0059] [ 839] [depth= 1] . ( 6 sec) [ -4953.9918] [ 839] [depth= 1] . ( 7 sec) [ -4953.4717] [ 839] [depth= 1] . ( 7 sec) [ -4953.4160] [ 838] [depth= 1] . ( 7 sec) [ -4951.7890] [ 837] [depth= 1] . ( 7 sec) [ -4850.9223] [ 802] [depth= 1] . ( 7 sec) [ -4850.8917] [ 802] [depth= 1] . ( 7 sec) [ -4687.9524] [ 750] [depth= 10] . ( 7 sec) [ -4551.0367] [Branch lengths ] . ( 8 sec) [ -4550.6040] [GTR parameters ] . ( 8 sec) [ -4536.9677] [Alpha ][ 0.860759] . ( 8 sec) [ -4536.1244] [ 750] [depth= 2] . ( 8 sec) [ -4536.0886] [ 750] [depth= 1] . ( 8 sec) [ -4525.6662] [ 745] [depth= 1] . ( 8 sec) [ -4522.7505] [ 745] [depth= 3] . ( 8 sec) [ -4515.3722] [ 742] [depth= 3] . ( 8 sec) [ -4505.6814] [ 738] [depth= 1] . ( 9 sec) [ -4501.1912] [ 735] [depth= 1] . ( 9 sec) [ -4496.6000] [ 732] [depth= 1] . ( 9 sec) [ -4495.0075] [ 729] [depth= 1] . ( 9 sec) [ -4478.5443] [ 720] [depth= 2] . ( 9 sec) [ -4463.5389] [ 708] [depth= 1] . ( 9 sec) [ -4463.4231] [ 708] [depth= 1] . ( 10 sec) [ -4428.3952] [ 695] [depth= 2] . ( 10 sec) [ -4389.7719] [ 682] [depth= 1] . ( 10 sec) [ -4389.7379] [ 682] [depth= 1] . ( 11 sec) [ -4389.5146] [ 682] [depth= 1] . ( 11 sec) [ -4382.1302] [ 680] [depth= 1] . ( 11 sec) [ -4382.1138] [ 680] [depth= 1] . ( 12 sec) [ -4367.0814] [Branch lengths ] . ( 12 sec) [ -4366.9030] [GTR parameters ] . ( 13 sec) [ -4365.7272] [Alpha ][ 1.046531] . ( 13 sec) [ -4352.5531] [ 671] [depth= 1] . ( 15 sec) [ -4352.5412] [ 671] [depth= 1] . ( 17 sec) [ -4351.6554] [Branch lengths ] . ( 17 sec) [ -4351.6358] [GTR parameters ] . ( 17 sec) [ -4351.5952] [Alpha ][ 1.087945] . ( 20 sec) [ -4351.5774] [Branch lengths ] . ( 38 sec) [ -4351.5767] [Branch lengths ] . ( 38 sec) [ -4351.5767] [Topology ] . ( 38 sec) [ -4351.5766] [Topology ] . ( 38 sec) [ -4351.5766] [GTR parameters ] . ( 38 sec) [ -4351.5764] [Alpha ][ 1.084718] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4351.576380. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11181.2044] [GTR parameters ] . ( 0 sec) [ -10939.8717] [Alpha ][ 0.500960] . ( 0 sec) [ -10864.9409] [ 1854] [depth= 6] . ( 1 sec) [ -10668.7602] [ 1837] [depth= 11] . ( 1 sec) [ -10490.7546] [ 1836] [depth= 3] . ( 1 sec) [ -10425.2858] [ 1836] [depth= 3] . ( 1 sec) [ -9999.9231] [ 1828] [depth= 7] . ( 1 sec) [ -9834.7379] [ 1828] [depth= 4] . ( 1 sec) [ -9825.6274] [ 1809] [depth= 13] . ( 1 sec) [ -9710.7065] [ 1806] [depth= 1] . ( 1 sec) [ -9536.9067] [ 1787] [depth= 18] . ( 1 sec) [ -9186.8522] [ 1758] [depth= 12] . ( 1 sec) [ -9101.9158] [ 1728] [depth= 12] . ( 1 sec) [ -8913.5003] [ 1679] [depth= 9] . ( 1 sec) [ -8776.5408] [ 1636] [depth= 12] . ( 1 sec) [ -8707.3777] [ 1631] [depth= 1] . ( 1 sec) [ -8648.7268] [ 1623] [depth= 2] . ( 1 sec) [ -8580.0750] [ 1614] [depth= 12] . ( 1 sec) [ -8508.7699] [ 1612] [depth= 2] . ( 1 sec) [ -8438.4533] [ 1595] [depth= 2] . ( 2 sec) [ -8377.1941] [ 1599] [depth= 3] . ( 2 sec) [ -8272.3314] [ 1577] [depth= 8] . ( 2 sec) [ -8247.7868] [ 1581] [depth= 4] . ( 2 sec) [ -8104.9781] [ 1536] [depth= 11] . ( 2 sec) [ -7951.3909] [ 1521] [depth= 5] . ( 2 sec) [ -7831.6248] [ 1503] [depth= 7] . ( 2 sec) [ -7752.0344] [ 1492] [depth= 1] . ( 2 sec) [ -7429.6289] [ 1485] [depth= 8] . ( 2 sec) [ -7426.4822] [ 1481] [depth= 4] . ( 2 sec) [ -7401.6860] [ 1460] [depth= 8] . ( 2 sec) [ -7373.8685] [ 1459] [depth= 1] . ( 2 sec) [ -7226.6643] [ 1414] [depth= 12] . ( 2 sec) [ -7161.4919] [ 1396] [depth= 6] . ( 2 sec) [ -7090.2091] [ 1373] [depth= 1] . ( 2 sec) [ -7085.2043] [ 1371] [depth= 8] . ( 2 sec) [ -6974.5806] [ 1346] [depth= 11] . ( 2 sec) [ -6658.3989] [ 1312] [depth= 1] . ( 2 sec) [ -6481.7672] [ 1273] [depth= 8] . ( 3 sec) [ -6384.1382] [ 1236] [depth= 4] . ( 3 sec) [ -6213.9461] [ 1210] [depth= 8] . ( 3 sec) [ -6212.8304] [ 1212] [depth= 2] . ( 3 sec) [ -6141.2436] [ 1164] [depth= 5] . ( 3 sec) [ -5961.8686] [ 1118] [depth= 6] . ( 3 sec) [ -5893.0753] [ 1093] [depth= 5] . ( 3 sec) [ -5891.5390] [ 1098] [depth= 1] . ( 3 sec) [ -5882.7019] [ 1093] [depth= 4] . ( 3 sec) [ -5844.4033] [ 1079] [depth= 1] . ( 3 sec) [ -5829.7350] [ 1064] [depth= 4] . ( 3 sec) [ -5814.6012] [ 1058] [depth= 1] . ( 3 sec) [ -5771.1309] [ 1042] [depth= 2] . ( 3 sec) [ -5758.3019] [ 1037] [depth= 1] . ( 3 sec) [ -5740.2163] [ 1032] [depth= 1] . ( 3 sec) [ -5739.4024] [ 1031] [depth= 2] . ( 4 sec) [ -5524.4449] [ 974] [depth= 9] . ( 4 sec) [ -5497.8054] [ 973] [depth= 2] . ( 4 sec) [ -5491.8772] [ 969] [depth= 1] . ( 4 sec) [ -5488.0090] [ 970] [depth= 2] . ( 4 sec) [ -5459.6920] [ 963] [depth= 1] . ( 4 sec) [ -5459.2452] [ 963] [depth= 1] . ( 4 sec) [ -5459.2308] [ 963] [depth= 1] . ( 4 sec) [ -5400.6594] [ 935] [depth= 8] . ( 4 sec) [ -5350.7234] [ 934] [depth= 4] . ( 4 sec) [ -5350.0444] [ 934] [depth= 1] . ( 4 sec) [ -5133.5765] [ 854] [depth= 5] . ( 4 sec) [ -5028.1933] [ 849] [depth= 3] . ( 4 sec) [ -5024.4674] [ 851] [depth= 2] . ( 5 sec) [ -5019.2210] [ 853] [depth= 2] . ( 5 sec) [ -5002.6129] [ 839] [depth= 2] . ( 5 sec) [ -4996.0649] [ 836] [depth= 2] . ( 5 sec) [ -4995.1732] [ 836] [depth= 1] . ( 5 sec) [ -4995.1386] [ 836] [depth= 1] . ( 5 sec) [ -4920.3851] [ 822] [depth= 7] . ( 5 sec) [ -4910.5791] [ 824] [depth= 1] . ( 5 sec) [ -4857.7973] [ 804] [depth= 2] . ( 5 sec) [ -4723.9926] [ 792] [depth= 5] . ( 5 sec) [ -4711.8850] [ 789] [depth= 2] . ( 5 sec) [ -4711.2180] [ 788] [depth= 2] . ( 5 sec) [ -4702.9873] [ 784] [depth= 3] . ( 5 sec) [ -4702.8346] [ 784] [depth= 1] . ( 5 sec) [ -4702.7847] [ 784] [depth= 1] . ( 5 sec) [ -4700.1280] [ 781] [depth= 3] . ( 6 sec) [ -4694.2900] [ 778] [depth= 3] . ( 6 sec) [ -4623.6716] [Branch lengths ] . ( 7 sec) [ -4622.6893] [GTR parameters ] . ( 7 sec) [ -4613.2723] [Alpha ][ 0.781599] . ( 7 sec) [ -4558.1767] [ 758] [depth= 1] . ( 7 sec) [ -4557.9995] [ 746] [depth= 1] . ( 7 sec) [ -4555.8522] [ 744] [depth= 1] . ( 7 sec) [ -4536.7782] [ 723] [depth= 1] . ( 7 sec) [ -4531.3130] [ 722] [depth= 2] . ( 8 sec) [ -4527.1812] [ 720] [depth= 1] . ( 8 sec) [ -4520.5680] [ 718] [depth= 1] . ( 8 sec) [ -4507.4916] [ 721] [depth= 7] . ( 9 sec) [ -4453.8789] [ 708] [depth= 1] . ( 9 sec) [ -4433.4318] [ 701] [depth= 3] . ( 9 sec) [ -4410.1647] [ 693] [depth= 1] . ( 9 sec) [ -4409.2610] [ 688] [depth= 4] . ( 9 sec) [ -4408.6469] [ 687] [depth= 1] . ( 10 sec) [ -4408.6221] [ 687] [depth= 1] . ( 10 sec) [ -4408.5367] [ 687] [depth= 1] . ( 10 sec) [ -4390.7542] [ 682] [depth= 5] . ( 10 sec) [ -4385.2370] [ 679] [depth= 1] . ( 11 sec) [ -4362.8684] [ 671] [depth= 3] . ( 11 sec) [ -4355.1717] [Branch lengths ] . ( 12 sec) [ -4354.9426] [GTR parameters ] . ( 12 sec) [ -4351.6837] [Alpha ][ 1.085057] . ( 15 sec) [ -4351.5831] [Branch lengths ] . ( 36 sec) [ -4351.5823] [Branch lengths ] . ( 36 sec) [ -4351.5823] [Topology ] . ( 36 sec) [ -4351.5822] [Topology ] . ( 37 sec) [ -4351.5763] [GTR parameters ] . ( 37 sec) [ -4351.5763] [Alpha ][ 1.085057] . ( 37 sec) [ -4351.5763] [Topology ] . ( 37 sec) [ -4351.5763] [Topology ] . ( 38 sec) [ -4351.5763] [GTR parameters ] . ( 38 sec) [ -4351.5763] [Alpha ][ 1.085057] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4351.576323. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4367.043375 . ( 1 sec) [ -4364.7703] [GTR parameters ] . ( 1 sec) [ -4364.6848] [Alpha ][ 1.057958] . ( 1 sec) [ -4364.6848] [Topology ] . ( 1 sec) [ -4355.6395] [Topology ] . ( 2 sec) [ -4354.4887] [Topology ] . ( 2 sec) [ -4354.2756] [Topology ] . ( 3 sec) [ -4354.2280] [Topology ] . ( 4 sec) [ -4354.2139] [Topology ] . ( 4 sec) [ -4354.1917] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4354.191669 . ( 8 sec) [ -4354.1882] [GTR parameters ] . ( 8 sec) [ -4354.1779] [Alpha ][ 1.078429] . ( 8 sec) [ -4354.1779] [Topology ] . ( 9 sec) [ -4354.0381] [Topology ] . ( 10 sec) [ -4353.3434] [Topology ] . ( 11 sec) [ -4351.9441] [Topology ] . ( 12 sec) [ -4351.5987] [Topology ] . ( 12 sec) [ -4351.5811] [Topology ] . ( 13 sec) [ -4351.5801] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4351.580143 . ( 18 sec) [ -4351.5775] [GTR parameters ] . ( 18 sec) [ -4351.5766] [Alpha ][ 1.084915] . ( 18 sec) [ -4351.5766] [Topology ] . ( 18 sec) [ -4351.5765] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4351.576504 . ( 23 sec) [ -4351.5765] [GTR parameters ] . ( 23 sec) [ -4351.5765] [Alpha ][ 1.084915] . ( 23 sec) [ -4351.5765] [Topology ] . ( 23 sec) [ -4351.5765] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 34 sec) [ -4364.7703] [GTR parameters ] . ( 34 sec) [ -4364.6848] [Alpha ][ 1.057958] . ( 34 sec) [ -4364.2236] [ 671] [depth= 1] . ( 36 sec) [ -4363.9512] [ 671] [depth= 1] . ( 36 sec) [ -4363.8216] [ 671] [depth= 1] . ( 36 sec) [ -4363.4315] [ 671] [depth= 1] . ( 38 sec) [ -4362.9586] [ 671] [depth= 1] . ( 38 sec) [ -4362.9267] [ 671] [depth= 1] . ( 38 sec) [ -4362.9021] [ 671] [depth= 1] . ( 38 sec) [ -4362.8881] [ 671] [depth= 1] . ( 38 sec) [ -4354.3031] [Branch lengths ] . ( 38 sec) [ -4354.3000] [GTR parameters ] . ( 39 sec) [ -4354.2933] [Alpha ][ 1.075314] . ( 42 sec) [ -4354.2015] [Branch lengths ] . ( 61 sec) [ -4354.1985] [Branch lengths ] . ( 61 sec) [ -4354.1985] [Topology ] . ( 61 sec) [ -4354.1977] [Topology ] . ( 61 sec) [ -4354.1976] [GTR parameters ] . ( 61 sec) [ -4354.1972] [Alpha ][ 1.079401] . ( 62 sec) [ -4354.1972] [Topology ] . ( 62 sec) [ -4354.1918] [Topology ] . ( 63 sec) [ -4354.1515] [Topology ] . ( 64 sec) [ -4353.8833] [Topology ] . ( 65 sec) [ -4352.8552] [Topology ] . ( 65 sec) [ -4351.6429] [Topology ] . ( 66 sec) [ -4351.5846] [Topology ] . ( 66 sec) [ -4351.5818] [GTR parameters ] . ( 66 sec) [ -4351.5811] [Alpha ][ 1.085094] . ( 66 sec) [ -4351.5811] [Topology ] . ( 67 sec) [ -4351.5766] [Topology ] . ( 68 sec) [ -4351.5763] [Topology ] . ( 68 sec) [ -4351.5763] [GTR parameters ] . ( 68 sec) [ -4351.5763] [Alpha ][ 1.085094] . ( 68 sec) [ -4351.5763] [Topology ] . ( 69 sec) [ -4351.5763] [Topology ] . ( 69 sec) [ -4351.5763] [GTR parameters ] . ( 69 sec) [ -4351.5763] [Alpha ][ 1.085094] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4351.576496 . Log likelihood obtained after SPR moves : -4351.576275 . Log likelihood of the current tree: -4351.576275. . Printing the most likely tree in file 'data47.phy_phyml_tree.txt'... . Best log likelihood : -4351.576225 . Time used 0h1m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo