.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data82.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... . 304 patterns found. (out of a total of 500 sites) . 178 sites without polymorphism (35.60%). . [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) [ -18878.9743] [GTR parameters ] . ( 0 sec) [ -18615.8083] [Alpha ][ 0.500960] . ( 0 sec) [ -18344.0015] [ 2140] [depth= 8] . ( 0 sec) [ -18179.9846] [ 2142] [depth= 6] . ( 0 sec) [ -18095.2180] [ 2133] [depth= 3] . ( 0 sec) [ -18076.3477] [ 2127] [depth= 5] . ( 0 sec) [ -16464.2355] [ 2108] [depth= 5] . ( 0 sec) [ -14345.7675] [ 2104] [depth= 8] . ( 0 sec) [ -14339.5975] [ 2100] [depth= 4] . ( 0 sec) [ -14333.2123] [ 2100] [depth= 1] . ( 0 sec) [ -14243.3348] [ 2078] [depth= 1] . ( 0 sec) [ -12485.7118] [ 2079] [depth= 4] . ( 0 sec) [ -12353.3080] [ 2094] [depth= 1] . ( 0 sec) [ -12046.8396] [ 2059] [depth= 10] . ( 0 sec) [ -11783.5797] [ 1979] [depth= 9] . ( 1 sec) [ -11076.6715] [ 1942] [depth= 6] . ( 1 sec) [ -10986.3165] [ 1920] [depth= 3] . ( 1 sec) [ -10820.2923] [ 1919] [depth= 2] . ( 1 sec) [ -10787.3741] [ 1910] [depth= 3] . ( 1 sec) [ -10564.0702] [ 1908] [depth= 1] . ( 1 sec) [ -10482.7853] [ 1898] [depth= 7] . ( 1 sec) [ -10314.4826] [ 1901] [depth= 1] . ( 1 sec) [ -10131.4830] [ 1875] [depth= 12] . ( 1 sec) [ -9831.1844] [ 1827] [depth= 10] . ( 1 sec) [ -9724.9910] [ 1789] [depth= 8] . ( 1 sec) [ -9446.0620] [ 1753] [depth= 16] . ( 1 sec) [ -9431.7820] [ 1751] [depth= 1] . ( 1 sec) [ -9426.1111] [ 1747] [depth= 2] . ( 1 sec) [ -9312.5416] [ 1747] [depth= 3] . ( 1 sec) [ -8620.4731] [ 1618] [depth= 7] . ( 1 sec) [ -8340.7145] [ 1626] [depth= 3] . ( 1 sec) [ -8339.1871] [ 1626] [depth= 1] . ( 1 sec) [ -8283.0892] [ 1589] [depth= 5] . ( 1 sec) [ -7826.0097] [ 1569] [depth= 5] . ( 1 sec) [ -7689.1300] [ 1532] [depth= 2] . ( 1 sec) [ -7634.2038] [ 1530] [depth= 2] . ( 1 sec) [ -7315.5277] [ 1408] [depth= 1] . ( 1 sec) [ -7315.5149] [ 1408] [depth= 1] . ( 1 sec) [ -7307.3436] [ 1399] [depth= 7] . ( 1 sec) [ -7204.0979] [ 1375] [depth= 9] . ( 1 sec) [ -7094.2896] [ 1354] [depth= 1] . ( 1 sec) [ -6892.5066] [ 1309] [depth= 5] . ( 1 sec) [ -6798.3285] [ 1267] [depth= 3] . ( 1 sec) [ -6753.5133] [ 1266] [depth= 3] . ( 1 sec) [ -6534.6657] [ 1261] [depth= 3] . ( 1 sec) [ -6443.7083] [ 1254] [depth= 2] . ( 1 sec) [ -6422.2493] [ 1248] [depth= 1] . ( 2 sec) [ -6398.9875] [ 1242] [depth= 1] . ( 2 sec) [ -6343.8285] [ 1212] [depth= 3] . ( 2 sec) [ -6272.1026] [ 1195] [depth= 1] . ( 2 sec) [ -6213.5014] [ 1175] [depth= 1] . ( 2 sec) [ -6213.1366] [ 1175] [depth= 1] . ( 2 sec) [ -6138.9959] [ 1148] [depth= 1] . ( 2 sec) [ -6117.0034] [ 1139] [depth= 2] . ( 2 sec) [ -6103.4782] [ 1140] [depth= 1] . ( 2 sec) [ -6065.3620] [ 1111] [depth= 1] . ( 2 sec) [ -6053.9667] [ 1094] [depth= 7] . ( 2 sec) [ -5949.4481] [ 1042] [depth= 1] . ( 2 sec) [ -5830.8066] [ 1013] [depth= 4] . ( 2 sec) [ -5632.6941] [ 963] [depth= 8] . ( 2 sec) [ -5410.6097] [ 893] [depth= 7] . ( 2 sec) [ -5387.3630] [ 890] [depth= 4] . ( 2 sec) [ -5328.4299] [ 877] [depth= 4] . ( 2 sec) [ -5227.0012] [ 865] [depth= 3] . ( 2 sec) [ -5164.5414] [ 849] [depth= 2] . ( 2 sec) [ -5161.6356] [ 848] [depth= 1] . ( 2 sec) [ -5161.4597] [ 848] [depth= 1] . ( 2 sec) [ -5153.6748] [ 848] [depth= 2] . ( 2 sec) [ -5126.9491] [ 860] [depth= 1] . ( 2 sec) [ -5109.0557] [ 851] [depth= 1] . ( 2 sec) [ -5084.5904] [ 851] [depth= 1] . ( 2 sec) [ -5084.3928] [ 839] [depth= 1] . ( 2 sec) [ -5049.5448] [ 830] [depth= 1] . ( 3 sec) [ -5038.6539] [ 826] [depth= 2] . ( 3 sec) [ -5037.7836] [ 829] [depth= 1] . ( 3 sec) [ -5037.7694] [ 831] [depth= 1] . ( 3 sec) [ -5031.6504] [ 829] [depth= 1] . ( 3 sec) [ -4967.3889] [ 818] [depth= 1] . ( 3 sec) [ -4956.4249] [ 817] [depth= 1] . ( 3 sec) [ -4929.5807] [ 811] [depth= 1] . ( 3 sec) [ -4916.6318] [ 815] [depth= 1] . ( 3 sec) [ -4912.3716] [ 813] [depth= 1] . ( 3 sec) [ -4842.0607] [Branch lengths ] . ( 4 sec) [ -4836.3683] [GTR parameters ] . ( 4 sec) [ -4816.9520] [Alpha ][ 0.948799] . ( 4 sec) [ -4816.7754] [ 825] [depth= 1] . ( 4 sec) [ -4815.9970] [ 824] [depth= 1] . ( 4 sec) [ -4804.7074] [ 819] [depth= 1] . ( 5 sec) [ -4804.6896] [ 819] [depth= 1] . ( 5 sec) [ -4804.1113] [ 817] [depth= 1] . ( 5 sec) [ -4803.7228] [ 816] [depth= 1] . ( 5 sec) [ -4803.5871] [ 819] [depth= 1] . ( 6 sec) [ -4803.5553] [ 821] [depth= 1] . ( 6 sec) [ -4803.2964] [ 817] [depth= 1] . ( 6 sec) [ -4803.0433] [ 819] [depth= 2] . ( 6 sec) [ -4802.9135] [ 818] [depth= 1] . ( 6 sec) [ -4795.8948] [ 805] [depth= 1] . ( 7 sec) [ -4793.2521] [Branch lengths ] . ( 7 sec) [ -4793.0788] [GTR parameters ] . ( 7 sec) [ -4793.0399] [Alpha ][ 0.979758] . ( 8 sec) [ -4793.0116] [ 804] [depth= 1] . ( 10 sec) [ -4792.9620] [Branch lengths ] . ( 10 sec) [ -4792.9611] [GTR parameters ] . ( 11 sec) [ -4792.9611] [Alpha ][ 0.980737] . ( 27 sec) [ -4792.9596] [Branch lengths ] . ( 27 sec) [ -4792.9596] [Topology ] . ( 27 sec) [ -4792.9595] [Topology ] . ( 27 sec) [ -4792.9595] [GTR parameters ] . ( 28 sec) [ -4792.9595] [Alpha ][ 0.980737] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4792.959475. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16324.4512] [GTR parameters ] . ( 0 sec) [ -16056.7310] [Alpha ][ 0.500960] . ( 0 sec) [ -15762.9770] [ 2144] [depth= 3] . ( 0 sec) [ -15387.3132] [ 2110] [depth= 10] . ( 0 sec) [ -15120.8466] [ 2095] [depth= 3] . ( 0 sec) [ -15093.7812] [ 2093] [depth= 2] . ( 0 sec) [ -15020.8568] [ 2065] [depth= 2] . ( 0 sec) [ -14941.0932] [ 2065] [depth= 6] . ( 1 sec) [ -14914.5345] [ 2060] [depth= 3] . ( 1 sec) [ -14739.3246] [ 2029] [depth= 1] . ( 1 sec) [ -14679.4109] [ 2013] [depth= 8] . ( 1 sec) [ -14493.2918] [ 1976] [depth= 2] . ( 1 sec) [ -14422.8052] [ 1974] [depth= 4] . ( 1 sec) [ -14199.6052] [ 1931] [depth= 15] . ( 1 sec) [ -14047.3102] [ 1928] [depth= 1] . ( 1 sec) [ -13736.7802] [ 1892] [depth= 10] . ( 1 sec) [ -13557.4144] [ 1863] [depth= 20] . ( 1 sec) [ -11348.1083] [ 1834] [depth= 10] . ( 1 sec) [ -11225.9591] [ 1832] [depth= 1] . ( 1 sec) [ -11203.3434] [ 1832] [depth= 1] . ( 1 sec) [ -10828.1369] [ 1822] [depth= 16] . ( 1 sec) [ -10812.4070] [ 1825] [depth= 2] . ( 1 sec) [ -10746.2429] [ 1811] [depth= 1] . ( 1 sec) [ -10589.2234] [ 1764] [depth= 1] . ( 1 sec) [ -10381.0182] [ 1708] [depth= 15] . ( 1 sec) [ -10219.2368] [ 1655] [depth= 17] . ( 1 sec) [ -10188.2933] [ 1653] [depth= 3] . ( 1 sec) [ -10113.8665] [ 1634] [depth= 3] . ( 1 sec) [ -10064.7021] [ 1612] [depth= 1] . ( 1 sec) [ -10003.0506] [ 1597] [depth= 3] . ( 1 sec) [ -10002.2854] [ 1596] [depth= 1] . ( 1 sec) [ -9482.7376] [ 1483] [depth= 2] . ( 1 sec) [ -9466.6002] [ 1462] [depth= 1] . ( 1 sec) [ -9292.2328] [ 1400] [depth= 12] . ( 1 sec) [ -9253.6850] [ 1391] [depth= 3] . ( 1 sec) [ -9199.6717] [ 1392] [depth= 1] . ( 1 sec) [ -8944.2442] [ 1386] [depth= 2] . ( 2 sec) [ -8942.7013] [ 1380] [depth= 1] . ( 2 sec) [ -8936.9668] [ 1380] [depth= 2] . ( 2 sec) [ -8898.6774] [ 1375] [depth= 4] . ( 2 sec) [ -8887.1499] [ 1377] [depth= 1] . ( 2 sec) [ -7567.8545] [ 1358] [depth= 5] . ( 2 sec) [ -7477.3131] [ 1338] [depth= 5] . ( 2 sec) [ -7176.4920] [ 1228] [depth= 7] . ( 2 sec) [ -7164.7874] [ 1227] [depth= 2] . ( 2 sec) [ -7077.7310] [ 1207] [depth= 2] . ( 2 sec) [ -6760.9127] [ 1108] [depth= 2] . ( 2 sec) [ -6692.5137] [ 1093] [depth= 2] . ( 2 sec) [ -6655.4613] [ 1091] [depth= 1] . ( 2 sec) [ -6511.0483] [ 1091] [depth= 4] . ( 2 sec) [ -6230.0728] [ 1047] [depth= 2] . ( 2 sec) [ -6218.5752] [ 1046] [depth= 1] . ( 2 sec) [ -5698.1003] [ 993] [depth= 5] . ( 2 sec) [ -5611.4702] [ 971] [depth= 1] . ( 2 sec) [ -5516.3438] [ 943] [depth= 6] . ( 2 sec) [ -5376.5414] [ 922] [depth= 5] . ( 2 sec) [ -5346.9416] [ 921] [depth= 2] . ( 2 sec) [ -5344.5347] [ 924] [depth= 1] . ( 2 sec) [ -5340.7240] [ 923] [depth= 1] . ( 2 sec) [ -5334.5586] [ 924] [depth= 1] . ( 2 sec) [ -5306.5539] [ 924] [depth= 5] . ( 2 sec) [ -5286.0179] [ 920] [depth= 3] . ( 2 sec) [ -5274.0930] [ 911] [depth= 2] . ( 3 sec) [ -5272.5845] [ 910] [depth= 1] . ( 3 sec) [ -5254.3312] [ 911] [depth= 1] . ( 3 sec) [ -5236.2230] [ 911] [depth= 1] . ( 3 sec) [ -5235.1955] [ 910] [depth= 1] . ( 3 sec) [ -5177.8885] [ 896] [depth= 1] . ( 3 sec) [ -5155.9306] [ 906] [depth= 1] . ( 3 sec) [ -5110.8557] [ 888] [depth= 2] . ( 3 sec) [ -5110.4373] [ 888] [depth= 1] . ( 3 sec) [ -5081.4502] [ 880] [depth= 1] . ( 3 sec) [ -5076.4272] [ 871] [depth= 3] . ( 3 sec) [ -5049.2948] [ 859] [depth= 1] . ( 3 sec) [ -4992.3142] [ 827] [depth= 1] . ( 3 sec) [ -4991.9983] [ 827] [depth= 1] . ( 3 sec) [ -4887.3867] [Branch lengths ] . ( 4 sec) [ -4884.2205] [GTR parameters ] . ( 4 sec) [ -4867.1584] [Alpha ][ 0.908024] . ( 4 sec) [ -4799.7940] [ 806] [depth= 1] . ( 4 sec) [ -4799.6844] [ 807] [depth= 1] . ( 4 sec) [ -4797.3656] [ 806] [depth= 1] . ( 4 sec) [ -4795.8117] [ 805] [depth= 1] . ( 4 sec) [ -4795.7466] [ 804] [depth= 1] . ( 4 sec) [ -4795.6918] [ 804] [depth= 1] . ( 6 sec) [ -4795.6746] [ 806] [depth= 1] . ( 6 sec) [ -4795.6539] [ 806] [depth= 1] . ( 7 sec) [ -4795.0132] [Branch lengths ] . ( 7 sec) [ -4794.9323] [GTR parameters ] . ( 7 sec) [ -4794.7782] [Alpha ][ 0.967059] . ( 11 sec) [ -4794.6870] [Branch lengths ] . ( 13 sec) [ -4794.2640] [ 803] [depth= 1] . ( 26 sec) [ -4793.6975] [Branch lengths ] . ( 27 sec) [ -4793.6933] [GTR parameters ] . ( 27 sec) [ -4793.6913] [Alpha ][ 0.974150] . ( 27 sec) [ -4793.6913] [Topology ] . ( 27 sec) [ -4793.0724] [Topology ] . ( 28 sec) [ -4792.9130] [Topology ] . ( 28 sec) [ -4792.8792] [Topology ] . ( 29 sec) [ -4792.8724] [Topology ] . ( 29 sec) [ -4792.8710] [Topology ] . ( 30 sec) [ -4792.8707] [Topology ] . ( 30 sec) [ -4792.8683] [GTR parameters ] . ( 30 sec) [ -4792.8681] [Alpha ][ 0.976124] . ( 30 sec) [ -4792.8681] [Topology ] . ( 31 sec) [ -4792.8680] [Topology ] . ( 31 sec) [ -4792.8680] [GTR parameters ] . ( 31 sec) [ -4792.8680] [Alpha ][ 0.976124] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4792.868021. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18463.7405] [GTR parameters ] . ( 1 sec) [ -18209.7995] [Alpha ][ 0.500960] . ( 1 sec) [ -17957.9306] [ 2187] [depth= 8] . ( 1 sec) [ -17489.0576] [ 2154] [depth= 8] . ( 1 sec) [ -17455.9149] [ 2150] [depth= 4] . ( 1 sec) [ -15801.6553] [ 2150] [depth= 2] . ( 1 sec) [ -15576.1326] [ 2143] [depth= 8] . ( 1 sec) [ -15469.9750] [ 2144] [depth= 3] . ( 1 sec) [ -15229.6968] [ 2087] [depth= 11] . ( 1 sec) [ -15228.6441] [ 2087] [depth= 1] . ( 1 sec) [ -15180.7802] [ 2087] [depth= 8] . ( 1 sec) [ -15155.3703] [ 2062] [depth= 8] . ( 1 sec) [ -14990.2494] [ 2034] [depth= 7] . ( 1 sec) [ -14680.6571] [ 1964] [depth= 8] . ( 1 sec) [ -14674.5023] [ 1963] [depth= 6] . ( 1 sec) [ -14551.5463] [ 1965] [depth= 4] . ( 1 sec) [ -14538.2892] [ 1963] [depth= 4] . ( 1 sec) [ -14511.2278] [ 1961] [depth= 1] . ( 2 sec) [ -14488.2148] [ 1953] [depth= 1] . ( 2 sec) [ -14303.0958] [ 1952] [depth= 2] . ( 2 sec) [ -14233.3455] [ 1916] [depth= 1] . ( 2 sec) [ -14208.2232] [ 1918] [depth= 1] . ( 2 sec) [ -11568.0389] [ 1871] [depth= 6] . ( 2 sec) [ -9852.9601] [ 1744] [depth= 7] . ( 2 sec) [ -9508.3606] [ 1772] [depth= 7] . ( 2 sec) [ -9480.2026] [ 1771] [depth= 1] . ( 2 sec) [ -9470.9903] [ 1769] [depth= 1] . ( 2 sec) [ -9320.8663] [ 1766] [depth= 6] . ( 2 sec) [ -9316.5893] [ 1768] [depth= 1] . ( 2 sec) [ -9291.7557] [ 1762] [depth= 2] . ( 2 sec) [ -9061.0145] [ 1707] [depth= 10] . ( 2 sec) [ -8944.2342] [ 1679] [depth= 7] . ( 2 sec) [ -8811.7561] [ 1629] [depth= 7] . ( 2 sec) [ -8674.0406] [ 1565] [depth= 3] . ( 2 sec) [ -8590.2924] [ 1550] [depth= 8] . ( 2 sec) [ -8391.9065] [ 1530] [depth= 9] . ( 2 sec) [ -8312.6350] [ 1505] [depth= 7] . ( 2 sec) [ -8299.8563] [ 1505] [depth= 9] . ( 2 sec) [ -8299.0901] [ 1485] [depth= 10] . ( 2 sec) [ -8297.3842] [ 1485] [depth= 1] . ( 2 sec) [ -8158.7685] [ 1445] [depth= 3] . ( 2 sec) [ -7934.7722] [ 1458] [depth= 3] . ( 2 sec) [ -7596.9113] [ 1356] [depth= 10] . ( 2 sec) [ -7592.0966] [ 1356] [depth= 8] . ( 2 sec) [ -7532.8542] [ 1355] [depth= 7] . ( 2 sec) [ -7418.5306] [ 1347] [depth= 8] . ( 2 sec) [ -7298.8394] [ 1310] [depth= 1] . ( 2 sec) [ -7275.4167] [ 1303] [depth= 2] . ( 3 sec) [ -7044.5437] [ 1238] [depth= 8] . ( 3 sec) [ -6983.1009] [ 1225] [depth= 1] . ( 3 sec) [ -6921.4671] [ 1225] [depth= 1] . ( 3 sec) [ -6820.5323] [ 1197] [depth= 6] . ( 3 sec) [ -6724.6992] [ 1195] [depth= 2] . ( 3 sec) [ -6718.3874] [ 1195] [depth= 1] . ( 3 sec) [ -6694.5318] [ 1200] [depth= 6] . ( 3 sec) [ -6665.9908] [ 1200] [depth= 3] . ( 3 sec) [ -6635.1252] [ 1195] [depth= 7] . ( 3 sec) [ -6574.5738] [ 1179] [depth= 5] . ( 3 sec) [ -6562.0788] [ 1179] [depth= 2] . ( 3 sec) [ -6517.2062] [ 1166] [depth= 6] . ( 3 sec) [ -6513.3555] [ 1167] [depth= 4] . ( 3 sec) [ -6452.7884] [ 1166] [depth= 8] . ( 3 sec) [ -6443.0692] [ 1167] [depth= 1] . ( 3 sec) [ -6425.0914] [ 1166] [depth= 1] . ( 3 sec) [ -6418.3406] [ 1169] [depth= 1] . ( 3 sec) [ -6417.4411] [ 1170] [depth= 1] . ( 3 sec) [ -6257.6129] [ 1125] [depth= 5] . ( 3 sec) [ -6204.5217] [ 1087] [depth= 11] . ( 3 sec) [ -6200.5738] [ 1154] [depth= 1] . ( 3 sec) [ -5849.1187] [ 1007] [depth= 3] . ( 3 sec) [ -5799.4539] [ 998] [depth= 3] . ( 3 sec) [ -5769.1309] [ 1007] [depth= 1] . ( 3 sec) [ -5699.5677] [ 1008] [depth= 1] . ( 4 sec) [ -5492.6454] [ 988] [depth= 2] . ( 4 sec) [ -5489.0681] [ 987] [depth= 1] . ( 4 sec) [ -5428.5721] [ 969] [depth= 1] . ( 4 sec) [ -5399.3094] [ 962] [depth= 2] . ( 4 sec) [ -5370.7953] [ 951] [depth= 8] . ( 4 sec) [ -5355.4621] [ 970] [depth= 1] . ( 4 sec) [ -5354.9497] [ 970] [depth= 1] . ( 4 sec) [ -5351.7865] [ 969] [depth= 1] . ( 4 sec) [ -5349.3672] [ 968] [depth= 1] . ( 4 sec) [ -5347.9513] [ 965] [depth= 1] . ( 4 sec) [ -5289.0288] [ 942] [depth= 1] . ( 4 sec) [ -5288.1028] [ 940] [depth= 3] . ( 4 sec) [ -5246.7909] [ 941] [depth= 4] . ( 4 sec) [ -5239.8028] [ 940] [depth= 2] . ( 4 sec) [ -5237.9310] [ 942] [depth= 1] . ( 4 sec) [ -5157.4869] [Branch lengths ] . ( 5 sec) [ -5154.8082] [GTR parameters ] . ( 5 sec) [ -5145.8446] [Alpha ][ 0.739753] . ( 5 sec) [ -5094.6984] [ 930] [depth= 3] . ( 5 sec) [ -5060.0024] [ 920] [depth= 2] . ( 5 sec) [ -5059.0164] [ 918] [depth= 1] . ( 5 sec) [ -5058.9206] [ 918] [depth= 1] . ( 5 sec) [ -4960.7376] [ 884] [depth= 4] . ( 5 sec) [ -4957.4029] [ 881] [depth= 1] . ( 5 sec) [ -4957.2844] [ 880] [depth= 1] . ( 6 sec) [ -4953.1509] [ 877] [depth= 1] . ( 6 sec) [ -4951.0576] [ 861] [depth= 1] . ( 6 sec) [ -4911.5861] [ 852] [depth= 1] . ( 6 sec) [ -4903.0611] [ 851] [depth= 1] . ( 6 sec) [ -4902.3717] [ 851] [depth= 1] . ( 6 sec) [ -4901.6313] [ 851] [depth= 1] . ( 6 sec) [ -4893.0485] [ 849] [depth= 1] . ( 6 sec) [ -4891.2175] [ 849] [depth= 2] . ( 7 sec) [ -4889.9254] [ 850] [depth= 2] . ( 7 sec) [ -4880.9434] [ 834] [depth= 3] . ( 7 sec) [ -4879.6010] [ 835] [depth= 1] . ( 7 sec) [ -4815.2994] [ 805] [depth= 8] . ( 7 sec) [ -4807.2940] [ 804] [depth= 1] . ( 7 sec) [ -4807.2162] [ 805] [depth= 1] . ( 7 sec) [ -4806.8502] [ 804] [depth= 1] . ( 7 sec) [ -4806.0648] [ 803] [depth= 1] . ( 7 sec) [ -4805.8710] [ 806] [depth= 1] . ( 8 sec) [ -4797.9467] [Branch lengths ] . ( 8 sec) [ -4797.5543] [GTR parameters ] . ( 8 sec) [ -4794.4851] [Alpha ][ 0.972953] . ( 8 sec) [ -4793.7819] [ 803] [depth= 1] . ( 9 sec) [ -4793.5261] [ 803] [depth= 1] . ( 10 sec) [ -4793.3356] [ 804] [depth= 1] . ( 11 sec) [ -4792.9059] [Branch lengths ] . ( 11 sec) [ -4792.8908] [GTR parameters ] . ( 11 sec) [ -4792.8907] [Alpha ][ 0.974182] . ( 14 sec) [ -4792.8829] [Branch lengths ] . ( 30 sec) [ -4792.8826] [Branch lengths ] . ( 30 sec) [ -4792.8826] [Topology ] . ( 31 sec) [ -4792.8825] [Topology ] . ( 31 sec) [ -4792.8825] [GTR parameters ] . ( 31 sec) [ -4792.8825] [Alpha ][ 0.975156] . Checking for NNIs, optimizing five branches... . ( 35 sec) [ -4792.8822] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4792.882242. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15666.7393] [GTR parameters ] . ( 1 sec) [ -15422.1223] [Alpha ][ 0.500960] . ( 1 sec) [ -15271.9980] [ 2089] [depth= 8] . ( 1 sec) [ -13599.5157] [ 2014] [depth= 8] . ( 1 sec) [ -13501.8808] [ 2000] [depth= 2] . ( 1 sec) [ -13453.3223] [ 1977] [depth= 1] . ( 1 sec) [ -13313.7203] [ 1960] [depth= 5] . ( 1 sec) [ -13265.3978] [ 1954] [depth= 2] . ( 1 sec) [ -13015.1421] [ 1954] [depth= 4] . ( 1 sec) [ -12887.0790] [ 1911] [depth= 1] . ( 1 sec) [ -12717.3000] [ 1891] [depth= 8] . ( 1 sec) [ -11766.7613] [ 1866] [depth= 2] . ( 1 sec) [ -11680.5310] [ 1866] [depth= 2] . ( 1 sec) [ -11591.3017] [ 1838] [depth= 3] . ( 1 sec) [ -11470.8109] [ 1832] [depth= 2] . ( 1 sec) [ -11408.1030] [ 1831] [depth= 1] . ( 1 sec) [ -11392.8569] [ 1822] [depth= 1] . ( 1 sec) [ -11369.3219] [ 1820] [depth= 2] . ( 1 sec) [ -11280.1912] [ 1818] [depth= 2] . ( 1 sec) [ -11143.0540] [ 1782] [depth= 1] . ( 1 sec) [ -10984.5950] [ 1739] [depth= 9] . ( 1 sec) [ -10960.6972] [ 1736] [depth= 1] . ( 1 sec) [ -10014.9383] [ 1740] [depth= 4] . ( 1 sec) [ -9937.9202] [ 1739] [depth= 1] . ( 1 sec) [ -9934.6561] [ 1740] [depth= 1] . ( 1 sec) [ -9912.9320] [ 1730] [depth= 2] . ( 1 sec) [ -9912.4183] [ 1728] [depth= 2] . ( 1 sec) [ -9878.4218] [ 1694] [depth= 5] . ( 1 sec) [ -9621.2570] [ 1692] [depth= 3] . ( 1 sec) [ -9255.9369] [ 1683] [depth= 14] . ( 2 sec) [ -9157.7088] [ 1698] [depth= 4] . ( 2 sec) [ -9121.8862] [ 1695] [depth= 2] . ( 2 sec) [ -9106.2965] [ 1687] [depth= 2] . ( 2 sec) [ -8705.0547] [ 1617] [depth= 5] . ( 2 sec) [ -8536.9015] [ 1600] [depth= 7] . ( 2 sec) [ -8454.1837] [ 1583] [depth= 1] . ( 2 sec) [ -8429.8331] [ 1562] [depth= 1] . ( 2 sec) [ -8176.7751] [ 1472] [depth= 9] . ( 2 sec) [ -8130.1702] [ 1455] [depth= 1] . ( 2 sec) [ -8017.5692] [ 1439] [depth= 2] . ( 2 sec) [ -8005.9697] [ 1428] [depth= 5] . ( 2 sec) [ -7632.4553] [ 1389] [depth= 2] . ( 2 sec) [ -7532.1096] [ 1372] [depth= 12] . ( 2 sec) [ -7511.5662] [ 1361] [depth= 5] . ( 2 sec) [ -7508.2397] [ 1364] [depth= 1] . ( 2 sec) [ -7502.6237] [ 1361] [depth= 1] . ( 2 sec) [ -7288.9556] [ 1326] [depth= 1] . ( 2 sec) [ -7238.0718] [ 1311] [depth= 3] . ( 2 sec) [ -7218.9848] [ 1311] [depth= 3] . ( 2 sec) [ -7185.8384] [ 1314] [depth= 1] . ( 2 sec) [ -7148.2621] [ 1305] [depth= 4] . ( 2 sec) [ -7011.6269] [ 1272] [depth= 1] . ( 2 sec) [ -6949.3551] [ 1271] [depth= 1] . ( 2 sec) [ -6921.0682] [ 1271] [depth= 1] . ( 2 sec) [ -6459.0108] [ 1175] [depth= 2] . ( 2 sec) [ -6399.8128] [ 1162] [depth= 3] . ( 2 sec) [ -6393.4806] [ 1163] [depth= 1] . ( 2 sec) [ -6391.0143] [ 1162] [depth= 3] . ( 2 sec) [ -6380.3963] [ 1162] [depth= 1] . ( 2 sec) [ -6357.5673] [ 1157] [depth= 1] . ( 3 sec) [ -6311.2963] [ 1152] [depth= 2] . ( 3 sec) [ -6199.2147] [ 1143] [depth= 3] . ( 3 sec) [ -6127.1352] [ 1123] [depth= 2] . ( 3 sec) [ -6002.7081] [ 1088] [depth= 1] . ( 3 sec) [ -5983.4795] [ 1084] [depth= 1] . ( 3 sec) [ -5980.0817] [ 1084] [depth= 1] . ( 3 sec) [ -5973.8368] [ 1084] [depth= 1] . ( 3 sec) [ -5939.7594] [ 1083] [depth= 1] . ( 3 sec) [ -5750.0176] [ 1014] [depth= 3] . ( 3 sec) [ -5540.7957] [ 947] [depth= 3] . ( 3 sec) [ -5510.8070] [ 928] [depth= 2] . ( 3 sec) [ -5479.8957] [ 928] [depth= 1] . ( 3 sec) [ -5430.3916] [ 939] [depth= 1] . ( 3 sec) [ -5423.0797] [ 938] [depth= 2] . ( 3 sec) [ -5353.8001] [ 940] [depth= 1] . ( 3 sec) [ -5325.6042] [ 937] [depth= 2] . ( 3 sec) [ -5323.1872] [ 925] [depth= 1] . ( 3 sec) [ -5211.1733] [ 886] [depth= 8] . ( 3 sec) [ -5211.1519] [ 886] [depth= 1] . ( 4 sec) [ -5070.8011] [Branch lengths ] . ( 4 sec) [ -5064.7343] [GTR parameters ] . ( 4 sec) [ -5049.7408] [Alpha ][ 0.847642] . ( 4 sec) [ -4946.7381] [ 851] [depth= 4] . ( 4 sec) [ -4898.9062] [ 835] [depth= 2] . ( 4 sec) [ -4896.2586] [ 832] [depth= 1] . ( 4 sec) [ -4896.0785] [ 833] [depth= 1] . ( 4 sec) [ -4895.8788] [ 834] [depth= 1] . ( 4 sec) [ -4884.9095] [ 831] [depth= 1] . ( 4 sec) [ -4854.3098] [ 821] [depth= 1] . ( 4 sec) [ -4853.4610] [ 819] [depth= 1] . ( 5 sec) [ -4851.9643] [ 818] [depth= 1] . ( 5 sec) [ -4808.0907] [ 805] [depth= 1] . ( 5 sec) [ -4807.5909] [ 805] [depth= 1] . ( 5 sec) [ -4806.9348] [ 806] [depth= 1] . ( 5 sec) [ -4806.2972] [ 805] [depth= 1] . ( 5 sec) [ -4805.9646] [ 805] [depth= 1] . ( 5 sec) [ -4805.5246] [ 805] [depth= 1] . ( 5 sec) [ -4805.2841] [ 804] [depth= 1] . ( 5 sec) [ -4801.4518] [ 803] [depth= 1] . ( 6 sec) [ -4801.2936] [ 806] [depth= 1] . ( 6 sec) [ -4801.2471] [ 803] [depth= 1] . ( 6 sec) [ -4801.2050] [ 806] [depth= 1] . ( 7 sec) [ -4795.6366] [Branch lengths ] . ( 7 sec) [ -4795.1724] [GTR parameters ] . ( 7 sec) [ -4794.4538] [Alpha ][ 0.969529] . ( 8 sec) [ -4794.3806] [ 803] [depth= 1] . ( 10 sec) [ -4794.0661] [ 804] [depth= 1] . ( 10 sec) [ -4793.7904] [Branch lengths ] . ( 10 sec) [ -4793.7835] [GTR parameters ] . ( 10 sec) [ -4793.7827] [Alpha ][ 0.973979] . ( 26 sec) [ -4793.3735] [Branch lengths ] . ( 26 sec) [ -4793.3735] [Topology ] . ( 27 sec) [ -4792.9636] [Topology ] . ( 27 sec) [ -4792.9020] [Topology ] . ( 28 sec) [ -4792.8894] [Topology ] . ( 29 sec) [ -4792.8869] [Topology ] . ( 29 sec) [ -4792.8863] [Topology ] . ( 29 sec) [ -4792.8828] [GTR parameters ] . ( 29 sec) [ -4792.8827] [Alpha ][ 0.974953] . ( 30 sec) [ -4792.8827] [Topology ] . ( 30 sec) [ -4792.8825] [Topology ] . ( 30 sec) [ -4792.8825] [GTR parameters ] . ( 30 sec) [ -4792.8825] [Alpha ][ 0.974953] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -4792.8823] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4792.882252. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18433.3692] [GTR parameters ] . ( 1 sec) [ -18155.0162] [Alpha ][ 0.500960] . ( 2 sec) [ -17772.3108] [ 2196] [depth= 6] . ( 2 sec) [ -17631.5376] [ 2145] [depth= 11] . ( 2 sec) [ -17541.5605] [ 2135] [depth= 3] . ( 2 sec) [ -17457.0637] [ 2133] [depth= 4] . ( 2 sec) [ -17454.0040] [ 2126] [depth= 8] . ( 2 sec) [ -17365.2645] [ 2125] [depth= 3] . ( 2 sec) [ -17229.5290] [ 2122] [depth= 6] . ( 2 sec) [ -15964.5290] [ 2133] [depth= 1] . ( 2 sec) [ -15358.5586] [ 2092] [depth= 2] . ( 2 sec) [ -15116.0227] [ 2050] [depth= 3] . ( 2 sec) [ -14931.9304] [ 1986] [depth= 17] . ( 2 sec) [ -14805.7450] [ 1967] [depth= 15] . ( 2 sec) [ -14687.0788] [ 1965] [depth= 16] . ( 2 sec) [ -14530.2927] [ 1957] [depth= 1] . ( 2 sec) [ -12598.8167] [ 1948] [depth= 6] . ( 2 sec) [ -12425.1694] [ 1935] [depth= 10] . ( 2 sec) [ -12009.4532] [ 1846] [depth= 1] . ( 2 sec) [ -11873.0330] [ 1831] [depth= 11] . ( 2 sec) [ -11738.0350] [ 1808] [depth= 13] . ( 2 sec) [ -11713.3435] [ 1813] [depth= 1] . ( 2 sec) [ -11658.6896] [ 1802] [depth= 2] . ( 2 sec) [ -11505.0233] [ 1767] [depth= 2] . ( 2 sec) [ -9340.3570] [ 1763] [depth= 1] . ( 2 sec) [ -9310.8173] [ 1758] [depth= 14] . ( 2 sec) [ -9297.5091] [ 1755] [depth= 12] . ( 2 sec) [ -9277.4939] [ 1754] [depth= 1] . ( 2 sec) [ -9241.2120] [ 1745] [depth= 1] . ( 2 sec) [ -9240.1192] [ 1751] [depth= 1] . ( 2 sec) [ -9083.2136] [ 1719] [depth= 5] . ( 2 sec) [ -8956.3713] [ 1701] [depth= 4] . ( 2 sec) [ -8946.6460] [ 1695] [depth= 1] . ( 2 sec) [ -8862.8435] [ 1663] [depth= 1] . ( 2 sec) [ -8819.4605] [ 1659] [depth= 3] . ( 3 sec) [ -8797.8113] [ 1654] [depth= 1] . ( 3 sec) [ -8792.6695] [ 1645] [depth= 6] . ( 3 sec) [ -8039.2064] [ 1531] [depth= 6] . ( 3 sec) [ -7923.0427] [ 1512] [depth= 7] . ( 3 sec) [ -7867.6672] [ 1502] [depth= 3] . ( 3 sec) [ -7866.8092] [ 1502] [depth= 1] . ( 3 sec) [ -7475.6823] [ 1448] [depth= 1] . ( 3 sec) [ -7227.2305] [ 1431] [depth= 9] . ( 3 sec) [ -7214.2454] [ 1430] [depth= 2] . ( 3 sec) [ -7027.2662] [ 1429] [depth= 7] . ( 3 sec) [ -6762.8308] [ 1310] [depth= 8] . ( 3 sec) [ -6644.6726] [ 1330] [depth= 9] . ( 3 sec) [ -6642.4784] [ 1331] [depth= 9] . ( 3 sec) [ -6641.5816] [ 1332] [depth= 2] . ( 3 sec) [ -6631.4819] [ 1332] [depth= 2] . ( 3 sec) [ -6629.8549] [ 1327] [depth= 2] . ( 3 sec) [ -6457.8647] [ 1322] [depth= 2] . ( 3 sec) [ -6380.2162] [ 1309] [depth= 8] . ( 3 sec) [ -6249.5334] [ 1221] [depth= 1] . ( 3 sec) [ -6247.6996] [ 1222] [depth= 1] . ( 3 sec) [ -6247.6122] [ 1222] [depth= 1] . ( 3 sec) [ -6246.4711] [ 1221] [depth= 1] . ( 3 sec) [ -6127.9873] [ 1227] [depth= 1] . ( 3 sec) [ -6086.8773] [ 1230] [depth= 1] . ( 3 sec) [ -6036.4755] [ 1216] [depth= 1] . ( 3 sec) [ -5992.5979] [ 1181] [depth= 1] . ( 4 sec) [ -5984.7721] [ 1180] [depth= 2] . ( 4 sec) [ -5970.8266] [ 1177] [depth= 1] . ( 4 sec) [ -5897.2915] [ 1134] [depth= 3] . ( 4 sec) [ -5888.8529] [ 1120] [depth= 7] . ( 4 sec) [ -5800.1130] [ 1099] [depth= 2] . ( 4 sec) [ -5744.8599] [ 1064] [depth= 1] . ( 4 sec) [ -5679.3720] [ 1042] [depth= 6] . ( 4 sec) [ -5536.3598] [ 1023] [depth= 9] . ( 4 sec) [ -5410.4566] [ 987] [depth= 3] . ( 4 sec) [ -5402.4060] [ 988] [depth= 1] . ( 4 sec) [ -5401.9367] [ 990] [depth= 2] . ( 4 sec) [ -5398.7605] [ 989] [depth= 1] . ( 4 sec) [ -5398.5405] [ 990] [depth= 1] . ( 4 sec) [ -5368.3994] [ 977] [depth= 1] . ( 4 sec) [ -5366.4200] [ 978] [depth= 1] . ( 4 sec) [ -5355.7869] [ 977] [depth= 1] . ( 4 sec) [ -5332.5355] [ 979] [depth= 1] . ( 4 sec) [ -5300.2863] [ 981] [depth= 3] . ( 4 sec) [ -5294.5665] [ 975] [depth= 3] . ( 4 sec) [ -5285.7369] [ 974] [depth= 1] . ( 5 sec) [ -5185.4691] [Branch lengths ] . ( 5 sec) [ -5181.2977] [GTR parameters ] . ( 5 sec) [ -5172.1753] [Alpha ][ 0.737868] . ( 5 sec) [ -5079.5266] [ 937] [depth= 2] . ( 5 sec) [ -5078.9061] [ 938] [depth= 1] . ( 5 sec) [ -5069.2553] [ 933] [depth= 1] . ( 5 sec) [ -5069.1651] [ 937] [depth= 2] . ( 5 sec) [ -5067.6899] [ 936] [depth= 1] . ( 6 sec) [ -5064.9467] [ 935] [depth= 1] . ( 6 sec) [ -5051.3337] [ 923] [depth= 3] . ( 6 sec) [ -5028.3423] [ 921] [depth= 1] . ( 6 sec) [ -4857.5900] [ 832] [depth= 4] . ( 6 sec) [ -4856.0284] [ 832] [depth= 2] . ( 6 sec) [ -4854.1730] [ 831] [depth= 1] . ( 6 sec) [ -4851.2062] [ 831] [depth= 1] . ( 6 sec) [ -4850.7224] [ 829] [depth= 4] . ( 6 sec) [ -4847.3075] [ 826] [depth= 1] . ( 6 sec) [ -4831.1890] [ 818] [depth= 2] . ( 6 sec) [ -4829.2992] [ 818] [depth= 1] . ( 6 sec) [ -4821.3050] [ 816] [depth= 2] . ( 7 sec) [ -4821.2940] [ 816] [depth= 1] . ( 7 sec) [ -4820.9193] [ 815] [depth= 1] . ( 7 sec) [ -4814.7691] [ 812] [depth= 1] . ( 7 sec) [ -4814.4925] [ 813] [depth= 1] . ( 7 sec) [ -4812.5829] [ 824] [depth= 1] . ( 7 sec) [ -4812.2179] [ 821] [depth= 1] . ( 7 sec) [ -4811.0180] [ 825] [depth= 1] . ( 7 sec) [ -4809.4718] [ 824] [depth= 3] . ( 7 sec) [ -4809.1908] [ 825] [depth= 1] . ( 7 sec) [ -4809.0215] [ 825] [depth= 1] . ( 7 sec) [ -4809.0043] [ 824] [depth= 1] . ( 7 sec) [ -4808.9788] [ 813] [depth= 1] . ( 8 sec) [ -4806.2618] [Branch lengths ] . ( 9 sec) [ -4806.1442] [GTR parameters ] . ( 9 sec) [ -4803.2867] [Alpha ][ 0.959348] . ( 9 sec) [ -4803.2534] [ 812] [depth= 1] . ( 11 sec) [ -4803.0852] [ 812] [depth= 2] . ( 12 sec) [ -4802.8843] [Branch lengths ] . ( 12 sec) [ -4802.8642] [GTR parameters ] . ( 12 sec) [ -4802.8579] [Alpha ][ 0.972091] . ( 21 sec) [ -4801.9632] [ 805] [depth= 3] . ( 23 sec) [ -4801.8823] [ 804] [depth= 1] . ( 25 sec) [ -4801.8657] [ 805] [depth= 1] . ( 28 sec) [ -4801.5763] [Branch lengths ] . ( 28 sec) [ -4801.5693] [GTR parameters ] . ( 28 sec) [ -4801.5687] [Alpha ][ 0.967993] . ( 31 sec) [ -4801.5556] [ 804] [depth= 1] . ( 44 sec) [ -4799.6421] [Branch lengths ] . ( 44 sec) [ -4799.6408] [GTR parameters ] . ( 44 sec) [ -4799.6406] [Alpha ][ 0.970318] . ( 60 sec) [ -4794.3010] [Branch lengths ] . ( 60 sec) [ -4794.3010] [Topology ] . ( 61 sec) [ -4793.2055] [Topology ] . ( 61 sec) [ -4793.0314] [Topology ] . ( 62 sec) [ -4792.9870] [Topology ] . ( 63 sec) [ -4792.9749] [Topology ] . ( 63 sec) [ -4792.9713] [Topology ] . ( 64 sec) [ -4792.9702] [Topology ] . ( 64 sec) [ -4792.9640] [GTR parameters ] . ( 64 sec) [ -4792.9602] [Alpha ][ 0.980343] . ( 64 sec) [ -4792.9602] [Topology ] . ( 65 sec) [ -4792.9597] [Topology ] . ( 65 sec) [ -4792.9596] [GTR parameters ] . ( 65 sec) [ -4792.9596] [Alpha ][ 0.980343] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4792.959649. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4811.134925 . ( 0 sec) [ -4808.5288] [GTR parameters ] . ( 0 sec) [ -4808.5204] [Alpha ][ 0.984728] . ( 0 sec) [ -4808.5204] [Topology ] . ( 1 sec) [ -4795.7810] [Topology ] . ( 2 sec) [ -4793.2976] [Topology ] . ( 2 sec) [ -4792.9706] [Topology ] . ( 3 sec) [ -4792.9122] [Topology ] . ( 3 sec) [ -4792.8936] [Topology ] . ( 4 sec) [ -4792.8867] [Topology ] . ( 4 sec) [ -4792.8841] [Topology ] . ( 5 sec) [ -4792.8831] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4792.883097 . ( 9 sec) [ -4792.8710] [GTR parameters ] . ( 9 sec) [ -4792.8681] [Alpha ][ 0.976547] . ( 9 sec) [ -4792.8681] [Topology ] . ( 10 sec) [ -4792.8678] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4792.867818 . ( 14 sec) [ -4792.8678] [GTR parameters ] . ( 14 sec) [ -4792.8678] [Alpha ][ 0.976547] . ( 14 sec) [ -4792.8678] [Topology ] . ( 15 sec) [ -4792.8677] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -4808.5288] [GTR parameters ] . ( 23 sec) [ -4808.5204] [Alpha ][ 0.984728] . ( 23 sec) [ -4808.2950] [ 812] [depth= 1] . ( 24 sec) [ -4806.2962] [ 810] [depth= 1] . ( 24 sec) [ -4805.9249] [ 810] [depth= 1] . ( 24 sec) [ -4805.6271] [ 810] [depth= 1] . ( 24 sec) [ -4805.1660] [ 811] [depth= 2] . ( 24 sec) [ -4804.8692] [ 811] [depth= 1] . ( 25 sec) [ -4803.0042] [ 810] [depth= 1] . ( 25 sec) [ -4802.7890] [ 809] [depth= 1] . ( 25 sec) [ -4801.9850] [ 808] [depth= 1] . ( 25 sec) [ -4800.8108] [ 809] [depth= 1] . ( 25 sec) [ -4800.4726] [ 808] [depth= 1] . ( 25 sec) [ -4800.1933] [ 809] [depth= 2] . ( 25 sec) [ -4799.4029] [ 808] [depth= 2] . ( 25 sec) [ -4799.0610] [ 808] [depth= 1] . ( 25 sec) [ -4799.0508] [ 809] [depth= 1] . ( 26 sec) [ -4798.8624] [ 808] [depth= 1] . ( 26 sec) [ -4794.9716] [Branch lengths ] . ( 26 sec) [ -4794.9555] [GTR parameters ] . ( 26 sec) [ -4794.9507] [Alpha ][ 0.973884] . ( 26 sec) [ -4794.0906] [ 805] [depth= 1] . ( 28 sec) [ -4794.0506] [ 807] [depth= 1] . ( 28 sec) [ -4793.8928] [ 804] [depth= 1] . ( 29 sec) [ -4793.5530] [ 805] [depth= 1] . ( 29 sec) [ -4792.9975] [Branch lengths ] . ( 29 sec) [ -4792.9887] [GTR parameters ] . ( 29 sec) [ -4792.9880] [Alpha ][ 0.977938] . ( 32 sec) [ -4792.9742] [Branch lengths ] . ( 48 sec) [ -4792.9737] [Branch lengths ] . ( 48 sec) [ -4792.9737] [Topology ] . ( 49 sec) [ -4792.9737] [Topology ] . ( 49 sec) [ -4792.9737] [GTR parameters ] . ( 49 sec) [ -4792.9737] [Alpha ][ 0.978916] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -4792.9730] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4792.867666 . Log likelihood obtained after SPR moves : -4792.973018 . Log likelihood of the current tree: -4792.867666. . Printing the most likely tree in file 'data82.phy_phyml_tree.txt'... . Best log likelihood : -4792.867666 . Time used 0h0m57s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo