.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data42.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... . 279 patterns found. (out of a total of 500 sites) . 203 sites without polymorphism (40.60%). . [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) [ -12846.4291] [GTR parameters ] . ( 0 sec) [ -12603.1458] [Alpha ][ 0.500960] . ( 0 sec) [ -12224.1137] [ 1674] [depth= 8] . ( 0 sec) [ -12082.7245] [ 1670] [depth= 6] . ( 0 sec) [ -11989.9763] [ 1656] [depth= 4] . ( 0 sec) [ -11959.3939] [ 1653] [depth= 6] . ( 0 sec) [ -11826.8142] [ 1638] [depth= 4] . ( 1 sec) [ -11801.1970] [ 1637] [depth= 6] . ( 1 sec) [ -11410.9817] [ 1630] [depth= 4] . ( 1 sec) [ -11382.3405] [ 1631] [depth= 1] . ( 1 sec) [ -10113.0853] [ 1607] [depth= 7] . ( 1 sec) [ -9998.1480] [ 1590] [depth= 10] . ( 1 sec) [ -9939.7640] [ 1563] [depth= 1] . ( 1 sec) [ -9747.0334] [ 1546] [depth= 11] . ( 1 sec) [ -9379.2333] [ 1512] [depth= 9] . ( 1 sec) [ -9278.3040] [ 1505] [depth= 1] . ( 1 sec) [ -8737.5758] [ 1504] [depth= 3] . ( 1 sec) [ -8411.0580] [ 1453] [depth= 1] . ( 1 sec) [ -8288.8558] [ 1451] [depth= 1] . ( 1 sec) [ -8264.7239] [ 1450] [depth= 1] . ( 1 sec) [ -8234.5170] [ 1451] [depth= 1] . ( 1 sec) [ -8095.3417] [ 1428] [depth= 9] . ( 1 sec) [ -8056.7079] [ 1426] [depth= 4] . ( 1 sec) [ -7929.8949] [ 1421] [depth= 3] . ( 1 sec) [ -7885.8682] [ 1421] [depth= 1] . ( 1 sec) [ -7853.5734] [ 1416] [depth= 9] . ( 1 sec) [ -7814.2604] [ 1388] [depth= 5] . ( 1 sec) [ -7785.4488] [ 1380] [depth= 5] . ( 1 sec) [ -7520.5331] [ 1331] [depth= 9] . ( 1 sec) [ -7468.6056] [ 1331] [depth= 5] . ( 1 sec) [ -7284.8641] [ 1301] [depth= 5] . ( 1 sec) [ -7278.9686] [ 1291] [depth= 1] . ( 1 sec) [ -7224.7600] [ 1288] [depth= 7] . ( 1 sec) [ -6718.0677] [ 1287] [depth= 11] . ( 1 sec) [ -6700.0242] [ 1288] [depth= 1] . ( 1 sec) [ -6520.1270] [ 1266] [depth= 12] . ( 1 sec) [ -6439.5378] [ 1250] [depth= 1] . ( 1 sec) [ -6424.4442] [ 1246] [depth= 2] . ( 1 sec) [ -6423.6520] [ 1246] [depth= 1] . ( 1 sec) [ -6421.2278] [ 1246] [depth= 1] . ( 1 sec) [ -6349.2854] [ 1218] [depth= 11] . ( 1 sec) [ -6159.2817] [ 1190] [depth= 6] . ( 2 sec) [ -6008.8274] [ 1153] [depth= 4] . ( 2 sec) [ -5958.4456] [ 1154] [depth= 7] . ( 2 sec) [ -5892.2768] [ 1153] [depth= 1] . ( 2 sec) [ -5791.8316] [ 1135] [depth= 3] . ( 2 sec) [ -5788.4829] [ 1136] [depth= 1] . ( 2 sec) [ -5787.9901] [ 1137] [depth= 1] . ( 2 sec) [ -5773.7088] [ 1135] [depth= 2] . ( 2 sec) [ -5770.1444] [ 1134] [depth= 1] . ( 2 sec) [ -5643.0177] [ 1092] [depth= 7] . ( 2 sec) [ -5590.6068] [ 1063] [depth= 2] . ( 2 sec) [ -5420.5565] [ 1006] [depth= 2] . ( 2 sec) [ -5420.2389] [ 1006] [depth= 2] . ( 2 sec) [ -5416.2257] [ 1007] [depth= 2] . ( 2 sec) [ -5411.6048] [ 1005] [depth= 2] . ( 2 sec) [ -5410.6543] [ 1006] [depth= 1] . ( 2 sec) [ -5335.9013] [ 1005] [depth= 3] . ( 2 sec) [ -5334.3003] [ 1005] [depth= 1] . ( 2 sec) [ -5330.0990] [ 1002] [depth= 6] . ( 2 sec) [ -5298.8350] [ 978] [depth= 1] . ( 2 sec) [ -5257.1418] [ 970] [depth= 4] . ( 2 sec) [ -5255.9656] [ 969] [depth= 1] . ( 2 sec) [ -5225.0453] [ 964] [depth= 14] . ( 2 sec) [ -5223.1979] [ 964] [depth= 4] . ( 2 sec) [ -5177.0124] [ 955] [depth= 4] . ( 2 sec) [ -5161.7915] [ 955] [depth= 1] . ( 2 sec) [ -5117.2586] [ 938] [depth= 7] . ( 2 sec) [ -5115.4749] [ 938] [depth= 1] . ( 2 sec) [ -5101.5484] [ 923] [depth= 3] . ( 3 sec) [ -4982.5962] [ 897] [depth= 5] . ( 3 sec) [ -4977.2254] [ 894] [depth= 1] . ( 3 sec) [ -4941.2243] [ 881] [depth= 1] . ( 3 sec) [ -4935.6922] [ 880] [depth= 1] . ( 3 sec) [ -4914.7124] [ 881] [depth= 1] . ( 3 sec) [ -4908.3555] [ 880] [depth= 1] . ( 3 sec) [ -4825.4184] [ 856] [depth= 2] . ( 3 sec) [ -4825.3155] [ 856] [depth= 1] . ( 3 sec) [ -4824.8525] [ 859] [depth= 7] . ( 3 sec) [ -4812.5793] [ 853] [depth= 1] . ( 3 sec) [ -4807.1878] [ 851] [depth= 11] . ( 3 sec) [ -4620.6250] [ 795] [depth= 7] . ( 3 sec) [ -4613.0358] [ 793] [depth= 2] . ( 3 sec) [ -4604.2414] [ 793] [depth= 2] . ( 3 sec) [ -4593.4524] [ 796] [depth= 1] . ( 3 sec) [ -4591.9377] [ 796] [depth= 1] . ( 4 sec) [ -4557.5054] [Branch lengths ] . ( 4 sec) [ -4555.5422] [GTR parameters ] . ( 4 sec) [ -4552.1008] [Alpha ][ 0.648724] . ( 4 sec) [ -4505.5780] [ 769] [depth= 3] . ( 4 sec) [ -4472.5847] [ 749] [depth= 7] . ( 4 sec) [ -4472.1518] [ 749] [depth= 1] . ( 4 sec) [ -4458.0005] [ 741] [depth= 1] . ( 4 sec) [ -4438.3685] [ 731] [depth= 3] . ( 4 sec) [ -4437.0114] [ 732] [depth= 1] . ( 5 sec) [ -4436.7912] [ 729] [depth= 1] . ( 5 sec) [ -4431.6320] [ 726] [depth= 1] . ( 5 sec) [ -4427.6393] [ 725] [depth= 1] . ( 5 sec) [ -4427.1849] [ 725] [depth= 1] . ( 5 sec) [ -4427.1634] [ 725] [depth= 1] . ( 5 sec) [ -4419.2107] [ 722] [depth= 7] . ( 5 sec) [ -4408.8443] [ 729] [depth= 8] . ( 5 sec) [ -4350.9788] [ 703] [depth= 6] . ( 5 sec) [ -4339.9642] [ 700] [depth= 1] . ( 5 sec) [ -4339.8511] [ 700] [depth= 2] . ( 5 sec) [ -4339.5640] [ 700] [depth= 1] . ( 6 sec) [ -4329.7288] [ 694] [depth= 1] . ( 6 sec) [ -4298.9088] [ 676] [depth= 5] . ( 6 sec) [ -4253.8106] [ 659] [depth= 3] . ( 6 sec) [ -4253.5608] [ 659] [depth= 1] . ( 6 sec) [ -4235.0305] [ 651] [depth= 4] . ( 6 sec) [ -4229.9444] [ 648] [depth= 1] . ( 6 sec) [ -4229.9304] [ 648] [depth= 1] . ( 7 sec) [ -4229.8675] [ 648] [depth= 1] . ( 7 sec) [ -4229.7946] [ 647] [depth= 1] . ( 8 sec) [ -4221.0456] [Branch lengths ] . ( 8 sec) [ -4220.2484] [GTR parameters ] . ( 8 sec) [ -4214.8149] [Alpha ][ 0.972454] . ( 8 sec) [ -4214.7441] [ 647] [depth= 1] . ( 12 sec) [ -4214.5625] [Branch lengths ] . ( 12 sec) [ -4214.5583] [GTR parameters ] . ( 12 sec) [ -4214.5578] [Alpha ][ 0.976149] . ( 26 sec) [ -4214.5549] [Branch lengths ] . ( 26 sec) [ -4214.5549] [Topology ] . ( 27 sec) [ -4214.5548] [Topology ] . ( 27 sec) [ -4214.5548] [GTR parameters ] . ( 27 sec) [ -4214.5548] [Alpha ][ 0.977125] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.554824. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11705.9983] [GTR parameters ] . ( 0 sec) [ -11471.1518] [Alpha ][ 0.500960] . ( 0 sec) [ -11062.4181] [ 1771] [depth= 3] . ( 0 sec) [ -10957.3885] [ 1758] [depth= 10] . ( 0 sec) [ -10776.3973] [ 1742] [depth= 3] . ( 0 sec) [ -10730.9536] [ 1739] [depth= 7] . ( 0 sec) [ -10572.9607] [ 1739] [depth= 5] . ( 0 sec) [ -10417.5492] [ 1738] [depth= 4] . ( 0 sec) [ -10347.9748] [ 1730] [depth= 1] . ( 0 sec) [ -10342.8238] [ 1727] [depth= 4] . ( 0 sec) [ -10284.4303] [ 1697] [depth= 2] . ( 0 sec) [ -10253.1215] [ 1697] [depth= 1] . ( 0 sec) [ -10059.4882] [ 1675] [depth= 4] . ( 0 sec) [ -10035.0240] [ 1675] [depth= 2] . ( 0 sec) [ -9909.5863] [ 1615] [depth= 8] . ( 0 sec) [ -9821.1843] [ 1614] [depth= 3] . ( 0 sec) [ -9505.9183] [ 1543] [depth= 14] . ( 0 sec) [ -9370.2924] [ 1513] [depth= 5] . ( 0 sec) [ -9265.9425] [ 1512] [depth= 15] . ( 0 sec) [ -9113.6753] [ 1486] [depth= 9] . ( 0 sec) [ -8938.8688] [ 1477] [depth= 3] . ( 0 sec) [ -8802.1132] [ 1477] [depth= 3] . ( 1 sec) [ -8583.3459] [ 1390] [depth= 5] . ( 1 sec) [ -8568.3786] [ 1388] [depth= 1] . ( 1 sec) [ -8459.5017] [ 1361] [depth= 9] . ( 1 sec) [ -8458.2113] [ 1357] [depth= 7] . ( 1 sec) [ -8457.3035] [ 1357] [depth= 1] . ( 1 sec) [ -8304.5614] [ 1299] [depth= 9] . ( 1 sec) [ -8280.6372] [ 1299] [depth= 6] . ( 1 sec) [ -8166.2158] [ 1279] [depth= 7] . ( 1 sec) [ -8087.2773] [ 1268] [depth= 5] . ( 1 sec) [ -7968.5072] [ 1226] [depth= 13] . ( 1 sec) [ -7900.2667] [ 1222] [depth= 9] . ( 1 sec) [ -7870.5523] [ 1223] [depth= 4] . ( 1 sec) [ -7800.0743] [ 1221] [depth= 3] . ( 1 sec) [ -7690.5917] [ 1182] [depth= 9] . ( 1 sec) [ -7533.8992] [ 1170] [depth= 7] . ( 1 sec) [ -7343.7223] [ 1112] [depth= 3] . ( 1 sec) [ -7303.4271] [ 1110] [depth= 2] . ( 1 sec) [ -7226.4455] [ 1116] [depth= 2] . ( 1 sec) [ -7096.6613] [ 1080] [depth= 3] . ( 1 sec) [ -6945.7639] [ 1058] [depth= 11] . ( 1 sec) [ -6944.7707] [ 1058] [depth= 1] . ( 1 sec) [ -6831.9936] [ 1033] [depth= 7] . ( 1 sec) [ -6815.8156] [ 1033] [depth= 1] . ( 1 sec) [ -6759.7828] [ 1001] [depth= 7] . ( 1 sec) [ -6759.6855] [ 1001] [depth= 1] . ( 1 sec) [ -6759.0702] [ 1001] [depth= 1] . ( 1 sec) [ -6750.6193] [ 1001] [depth= 1] . ( 1 sec) [ -6743.1833] [ 998] [depth= 1] . ( 1 sec) [ -6563.3443] [ 983] [depth= 2] . ( 1 sec) [ -6547.4611] [ 984] [depth= 1] . ( 1 sec) [ -5794.6208] [ 972] [depth= 6] . ( 2 sec) [ -5609.8713] [ 953] [depth= 4] . ( 2 sec) [ -5589.1131] [ 945] [depth= 1] . ( 2 sec) [ -5518.7044] [ 921] [depth= 2] . ( 2 sec) [ -5492.7979] [ 914] [depth= 2] . ( 2 sec) [ -5405.2362] [ 914] [depth= 1] . ( 2 sec) [ -5313.7498] [ 914] [depth= 1] . ( 2 sec) [ -5295.7265] [ 907] [depth= 1] . ( 2 sec) [ -5283.9997] [ 904] [depth= 1] . ( 2 sec) [ -5214.4412] [ 887] [depth= 2] . ( 2 sec) [ -5210.1676] [ 886] [depth= 1] . ( 2 sec) [ -5193.3178] [ 887] [depth= 9] . ( 2 sec) [ -5189.3987] [ 884] [depth= 6] . ( 2 sec) [ -5146.5531] [ 884] [depth= 1] . ( 2 sec) [ -4976.1018] [ 868] [depth= 7] . ( 2 sec) [ -4976.0239] [ 869] [depth= 1] . ( 2 sec) [ -4784.9290] [ 788] [depth= 8] . ( 2 sec) [ -4626.9038] [ 757] [depth= 6] . ( 2 sec) [ -4626.6356] [ 757] [depth= 1] . ( 2 sec) [ -4625.2695] [ 756] [depth= 3] . ( 2 sec) [ -4619.7495] [ 749] [depth= 4] . ( 2 sec) [ -4597.1173] [ 748] [depth= 1] . ( 2 sec) [ -4530.9972] [ 732] [depth= 1] . ( 2 sec) [ -4530.9588] [ 732] [depth= 1] . ( 2 sec) [ -4529.4866] [ 738] [depth= 2] . ( 2 sec) [ -4529.0483] [ 739] [depth= 1] . ( 3 sec) [ -4460.9518] [ 706] [depth= 2] . ( 3 sec) [ -4460.8362] [ 706] [depth= 1] . ( 3 sec) [ -4363.8378] [ 689] [depth= 1] . ( 3 sec) [ -4363.3659] [ 688] [depth= 1] . ( 3 sec) [ -4363.0288] [ 688] [depth= 1] . ( 3 sec) [ -4321.1782] [Branch lengths ] . ( 3 sec) [ -4319.4375] [GTR parameters ] . ( 3 sec) [ -4308.1411] [Alpha ][ 0.856824] . ( 4 sec) [ -4292.3624] [ 678] [depth= 1] . ( 4 sec) [ -4292.3259] [ 678] [depth= 1] . ( 4 sec) [ -4291.9453] [ 677] [depth= 1] . ( 4 sec) [ -4290.4615] [ 677] [depth= 1] . ( 4 sec) [ -4286.8361] [ 685] [depth= 3] . ( 4 sec) [ -4286.6774] [ 684] [depth= 1] . ( 4 sec) [ -4235.7761] [ 660] [depth= 2] . ( 5 sec) [ -4235.7575] [ 660] [depth= 1] . ( 5 sec) [ -4235.2963] [ 657] [depth= 1] . ( 6 sec) [ -4235.2092] [ 656] [depth= 1] . ( 6 sec) [ -4217.6497] [ 647] [depth= 1] . ( 7 sec) [ -4215.1917] [Branch lengths ] . ( 7 sec) [ -4215.1243] [GTR parameters ] . ( 7 sec) [ -4214.6337] [Alpha ][ 0.973487] . ( 11 sec) [ -4214.5673] [Branch lengths ] . ( 26 sec) [ -4214.5604] [Branch lengths ] . ( 26 sec) [ -4214.5604] [Topology ] . ( 26 sec) [ -4214.5591] [Topology ] . ( 27 sec) [ -4214.5584] [Topology ] . ( 27 sec) [ -4214.5582] [GTR parameters ] . ( 27 sec) [ -4214.5578] [Alpha ][ 0.976652] . ( 27 sec) [ -4214.5578] [Topology ] . ( 27 sec) [ -4214.5572] [Topology ] . ( 28 sec) [ -4214.5572] [GTR parameters ] . ( 28 sec) [ -4214.5572] [Alpha ][ 0.976652] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.557155. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13404.3333] [GTR parameters ] . ( 1 sec) [ -13148.5074] [Alpha ][ 0.500960] . ( 1 sec) [ -12571.2268] [ 1822] [depth= 8] . ( 1 sec) [ -12328.5986] [ 1812] [depth= 8] . ( 1 sec) [ -12111.3908] [ 1810] [depth= 4] . ( 1 sec) [ -12009.1561] [ 1809] [depth= 2] . ( 1 sec) [ -11873.3384] [ 1777] [depth= 8] . ( 1 sec) [ -11868.4244] [ 1775] [depth= 2] . ( 1 sec) [ -11568.4798] [ 1711] [depth= 11] . ( 1 sec) [ -11460.1049] [ 1693] [depth= 11] . ( 1 sec) [ -11351.7267] [ 1689] [depth= 1] . ( 1 sec) [ -11183.0660] [ 1656] [depth= 15] . ( 1 sec) [ -10710.9592] [ 1586] [depth= 8] . ( 1 sec) [ -10384.6628] [ 1560] [depth= 13] . ( 1 sec) [ -10352.8066] [ 1556] [depth= 3] . ( 1 sec) [ -10303.8359] [ 1555] [depth= 1] . ( 1 sec) [ -10076.1281] [ 1506] [depth= 12] . ( 1 sec) [ -10069.9526] [ 1506] [depth= 2] . ( 1 sec) [ -10006.9061] [ 1459] [depth= 15] . ( 2 sec) [ -9949.7542] [ 1458] [depth= 1] . ( 2 sec) [ -9896.2689] [ 1442] [depth= 1] . ( 2 sec) [ -9764.3035] [ 1433] [depth= 5] . ( 2 sec) [ -9749.1225] [ 1435] [depth= 1] . ( 2 sec) [ -9529.2925] [ 1381] [depth= 17] . ( 2 sec) [ -9438.5006] [ 1347] [depth= 5] . ( 2 sec) [ -9359.7708] [ 1344] [depth= 1] . ( 2 sec) [ -9246.7381] [ 1337] [depth= 14] . ( 2 sec) [ -7790.4709] [ 1329] [depth= 11] . ( 2 sec) [ -7675.3984] [ 1319] [depth= 7] . ( 2 sec) [ -7421.0319] [ 1318] [depth= 10] . ( 2 sec) [ -7120.7107] [ 1319] [depth= 1] . ( 2 sec) [ -6718.4598] [ 1292] [depth= 8] . ( 2 sec) [ -6666.8233] [ 1270] [depth= 1] . ( 2 sec) [ -6495.8425] [ 1203] [depth= 10] . ( 2 sec) [ -6431.9170] [ 1187] [depth= 7] . ( 2 sec) [ -6339.9405] [ 1162] [depth= 2] . ( 2 sec) [ -6291.6699] [ 1157] [depth= 6] . ( 2 sec) [ -6163.0610] [ 1151] [depth= 8] . ( 2 sec) [ -6152.0520] [ 1136] [depth= 1] . ( 2 sec) [ -6001.7867] [ 1104] [depth= 5] . ( 2 sec) [ -5950.7855] [ 1106] [depth= 7] . ( 2 sec) [ -5867.7346] [ 1098] [depth= 4] . ( 2 sec) [ -5865.3800] [ 1098] [depth= 1] . ( 2 sec) [ -5761.2320] [ 1071] [depth= 4] . ( 2 sec) [ -5751.9435] [ 1070] [depth= 1] . ( 2 sec) [ -5577.4364] [ 996] [depth= 6] . ( 2 sec) [ -5559.6047] [ 995] [depth= 2] . ( 2 sec) [ -5555.6360] [ 995] [depth= 1] . ( 2 sec) [ -5536.8415] [ 985] [depth= 3] . ( 3 sec) [ -5534.2761] [ 988] [depth= 3] . ( 3 sec) [ -5418.5630] [ 983] [depth= 2] . ( 3 sec) [ -5409.7197] [ 982] [depth= 6] . ( 3 sec) [ -5405.0915] [ 979] [depth= 1] . ( 3 sec) [ -5402.6005] [ 978] [depth= 1] . ( 3 sec) [ -5373.5580] [ 975] [depth= 8] . ( 3 sec) [ -5336.3550] [ 960] [depth= 1] . ( 3 sec) [ -5177.8773] [ 944] [depth= 5] . ( 3 sec) [ -5165.1764] [ 934] [depth= 1] . ( 3 sec) [ -5107.8674] [ 908] [depth= 5] . ( 3 sec) [ -4989.7566] [ 888] [depth= 6] . ( 3 sec) [ -4761.7430] [ 807] [depth= 5] . ( 3 sec) [ -4751.2646] [ 812] [depth= 1] . ( 3 sec) [ -4739.6306] [ 807] [depth= 1] . ( 3 sec) [ -4722.2463] [ 799] [depth= 1] . ( 3 sec) [ -4705.7531] [ 786] [depth= 1] . ( 3 sec) [ -4690.0093] [ 791] [depth= 3] . ( 3 sec) [ -4656.0261] [ 791] [depth= 2] . ( 3 sec) [ -4649.9348] [ 787] [depth= 1] . ( 3 sec) [ -4641.4364] [ 786] [depth= 1] . ( 3 sec) [ -4640.4676] [ 786] [depth= 1] . ( 3 sec) [ -4635.2187] [ 786] [depth= 1] . ( 3 sec) [ -4632.0753] [ 786] [depth= 1] . ( 3 sec) [ -4622.5288] [ 786] [depth= 1] . ( 3 sec) [ -4622.4862] [ 786] [depth= 1] . ( 3 sec) [ -4599.7053] [ 779] [depth= 4] . ( 3 sec) [ -4556.2844] [ 755] [depth= 5] . ( 4 sec) [ -4508.4582] [ 738] [depth= 4] . ( 4 sec) [ -4500.2944] [ 735] [depth= 1] . ( 4 sec) [ -4500.0543] [ 735] [depth= 1] . ( 4 sec) [ -4497.5915] [ 735] [depth= 1] . ( 4 sec) [ -4496.7570] [ 735] [depth= 1] . ( 4 sec) [ -4496.1456] [ 738] [depth= 1] . ( 4 sec) [ -4435.2894] [ 723] [depth= 1] . ( 4 sec) [ -4435.1817] [ 723] [depth= 1] . ( 4 sec) [ -4406.9338] [Branch lengths ] . ( 5 sec) [ -4405.0411] [GTR parameters ] . ( 5 sec) [ -4395.8871] [Alpha ][ 0.790537] . ( 5 sec) [ -4370.3822] [ 695] [depth= 2] . ( 5 sec) [ -4340.0157] [ 688] [depth= 1] . ( 5 sec) [ -4319.8864] [ 687] [depth= 2] . ( 6 sec) [ -4248.8099] [ 662] [depth= 1] . ( 6 sec) [ -4248.5484] [ 662] [depth= 1] . ( 6 sec) [ -4248.4208] [ 662] [depth= 1] . ( 6 sec) [ -4233.0538] [ 655] [depth= 1] . ( 6 sec) [ -4230.6842] [ 654] [depth= 1] . ( 6 sec) [ -4229.8710] [ 654] [depth= 2] . ( 6 sec) [ -4226.9692] [ 651] [depth= 1] . ( 6 sec) [ -4226.8238] [ 652] [depth= 1] . ( 6 sec) [ -4226.7011] [ 652] [depth= 1] . ( 6 sec) [ -4226.0652] [ 651] [depth= 2] . ( 7 sec) [ -4225.7770] [ 650] [depth= 1] . ( 7 sec) [ -4225.7446] [ 650] [depth= 1] . ( 7 sec) [ -4225.7318] [ 650] [depth= 1] . ( 8 sec) [ -4221.1842] [ 648] [depth= 2] . ( 8 sec) [ -4221.0084] [ 648] [depth= 1] . ( 8 sec) [ -4216.4283] [Branch lengths ] . ( 8 sec) [ -4216.1959] [GTR parameters ] . ( 8 sec) [ -4214.8605] [Alpha ][ 0.972003] . ( 9 sec) [ -4214.7493] [ 647] [depth= 1] . ( 12 sec) [ -4214.5807] [Branch lengths ] . ( 12 sec) [ -4214.5773] [GTR parameters ] . ( 12 sec) [ -4214.5766] [Alpha ][ 0.976906] . ( 27 sec) [ -4214.5660] [Branch lengths ] . ( 27 sec) [ -4214.5660] [Topology ] . ( 27 sec) [ -4214.5633] [Topology ] . ( 28 sec) [ -4214.5617] [Topology ] . ( 28 sec) [ -4214.5605] [Topology ] . ( 29 sec) [ -4214.5595] [Topology ] . ( 29 sec) [ -4214.5591] [GTR parameters ] . ( 29 sec) [ -4214.5591] [Alpha ][ 0.976906] . ( 29 sec) [ -4214.5591] [Topology ] . ( 29 sec) [ -4214.5582] [Topology ] . ( 29 sec) [ -4214.5582] [GTR parameters ] . ( 30 sec) [ -4214.5582] [Alpha ][ 0.976906] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.558237. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13602.3047] [GTR parameters ] . ( 1 sec) [ -13346.5801] [Alpha ][ 0.500960] . ( 1 sec) [ -12870.6108] [ 1823] [depth= 8] . ( 1 sec) [ -12723.5270] [ 1765] [depth= 9] . ( 1 sec) [ -12618.1221] [ 1757] [depth= 8] . ( 1 sec) [ -12583.1365] [ 1718] [depth= 1] . ( 1 sec) [ -12508.3179] [ 1714] [depth= 3] . ( 1 sec) [ -12218.9580] [ 1677] [depth= 3] . ( 1 sec) [ -12132.6978] [ 1676] [depth= 7] . ( 1 sec) [ -12066.3688] [ 1664] [depth= 1] . ( 1 sec) [ -11336.9724] [ 1664] [depth= 4] . ( 1 sec) [ -11201.3006] [ 1659] [depth= 4] . ( 1 sec) [ -11180.9254] [ 1660] [depth= 3] . ( 1 sec) [ -11041.0554] [ 1640] [depth= 9] . ( 1 sec) [ -11015.2985] [ 1628] [depth= 6] . ( 2 sec) [ -10960.1335] [ 1626] [depth= 4] . ( 2 sec) [ -10784.7848] [ 1605] [depth= 5] . ( 2 sec) [ -10767.0675] [ 1591] [depth= 9] . ( 2 sec) [ -10632.1220] [ 1588] [depth= 2] . ( 2 sec) [ -10499.0054] [ 1564] [depth= 4] . ( 2 sec) [ -10495.1073] [ 1560] [depth= 1] . ( 2 sec) [ -10238.5462] [ 1493] [depth= 9] . ( 2 sec) [ -10209.7260] [ 1493] [depth= 4] . ( 2 sec) [ -10130.0828] [ 1473] [depth= 3] . ( 2 sec) [ -10025.2039] [ 1457] [depth= 1] . ( 2 sec) [ -9891.5448] [ 1426] [depth= 11] . ( 2 sec) [ -9851.3279] [ 1441] [depth= 4] . ( 2 sec) [ -9840.8269] [ 1443] [depth= 1] . ( 2 sec) [ -9718.1062] [ 1433] [depth= 3] . ( 2 sec) [ -9637.8706] [ 1422] [depth= 1] . ( 2 sec) [ -9600.6048] [ 1420] [depth= 9] . ( 2 sec) [ -9556.4522] [ 1405] [depth= 1] . ( 2 sec) [ -9456.0473] [ 1402] [depth= 2] . ( 2 sec) [ -9255.8207] [ 1346] [depth= 4] . ( 2 sec) [ -9138.1798] [ 1319] [depth= 10] . ( 2 sec) [ -9065.1316] [ 1316] [depth= 1] . ( 2 sec) [ -9059.0656] [ 1314] [depth= 1] . ( 2 sec) [ -9029.1006] [ 1314] [depth= 1] . ( 2 sec) [ -8939.4127] [ 1311] [depth= 5] . ( 2 sec) [ -8906.9291] [ 1311] [depth= 5] . ( 2 sec) [ -8896.6819] [ 1311] [depth= 1] . ( 2 sec) [ -7168.2667] [ 1282] [depth= 7] . ( 2 sec) [ -7082.5546] [ 1269] [depth= 5] . ( 2 sec) [ -7080.9978] [ 1270] [depth= 1] . ( 2 sec) [ -7080.7905] [ 1267] [depth= 2] . ( 2 sec) [ -7059.8643] [ 1264] [depth= 5] . ( 2 sec) [ -7005.3465] [ 1263] [depth= 1] . ( 2 sec) [ -6872.9943] [ 1239] [depth= 3] . ( 2 sec) [ -6707.9964] [ 1227] [depth= 7] . ( 2 sec) [ -6682.8422] [ 1225] [depth= 1] . ( 3 sec) [ -6678.4176] [ 1225] [depth= 1] . ( 3 sec) [ -6599.4846] [ 1202] [depth= 3] . ( 3 sec) [ -6525.4117] [ 1202] [depth= 11] . ( 3 sec) [ -6512.2328] [ 1198] [depth= 4] . ( 3 sec) [ -6512.0571] [ 1198] [depth= 1] . ( 3 sec) [ -6500.2359] [ 1194] [depth= 2] . ( 3 sec) [ -6385.3156] [ 1180] [depth= 1] . ( 3 sec) [ -6267.6074] [ 1119] [depth= 10] . ( 3 sec) [ -6265.0060] [ 1125] [depth= 1] . ( 3 sec) [ -6234.2971] [ 1111] [depth= 1] . ( 3 sec) [ -6197.8025] [ 1097] [depth= 1] . ( 3 sec) [ -6134.7871] [ 1086] [depth= 10] . ( 3 sec) [ -6088.4790] [ 1079] [depth= 8] . ( 3 sec) [ -5915.2955] [ 1074] [depth= 13] . ( 3 sec) [ -5724.5800] [ 1010] [depth= 5] . ( 3 sec) [ -5681.1187] [ 1011] [depth= 1] . ( 3 sec) [ -5592.5021] [ 1005] [depth= 2] . ( 3 sec) [ -5279.0514] [ 918] [depth= 6] . ( 3 sec) [ -5182.0308] [ 917] [depth= 1] . ( 3 sec) [ -5154.6024] [ 918] [depth= 1] . ( 3 sec) [ -5154.3827] [ 916] [depth= 1] . ( 3 sec) [ -4955.1241] [ 854] [depth= 2] . ( 3 sec) [ -4906.1222] [ 837] [depth= 3] . ( 4 sec) [ -4903.5372] [ 836] [depth= 1] . ( 4 sec) [ -4903.4612] [ 836] [depth= 1] . ( 4 sec) [ -4884.6939] [ 834] [depth= 3] . ( 4 sec) [ -4881.4958] [ 834] [depth= 2] . ( 4 sec) [ -4836.6910] [ 832] [depth= 4] . ( 4 sec) [ -4833.3549] [ 825] [depth= 2] . ( 4 sec) [ -4832.8309] [ 825] [depth= 1] . ( 4 sec) [ -4831.8084] [ 824] [depth= 1] . ( 4 sec) [ -4831.3739] [ 823] [depth= 1] . ( 4 sec) [ -4822.8754] [ 823] [depth= 1] . ( 4 sec) [ -4817.6877] [ 822] [depth= 2] . ( 4 sec) [ -4762.0555] [Branch lengths ] . ( 5 sec) [ -4757.1255] [GTR parameters ] . ( 5 sec) [ -4754.6894] [Alpha ][ 0.618524] . ( 5 sec) [ -4723.5207] [ 805] [depth= 5] . ( 5 sec) [ -4609.0098] [ 778] [depth= 6] . ( 5 sec) [ -4608.3015] [ 777] [depth= 1] . ( 5 sec) [ -4522.4958] [ 753] [depth= 2] . ( 5 sec) [ -4519.4484] [ 755] [depth= 2] . ( 5 sec) [ -4518.4723] [ 753] [depth= 2] . ( 5 sec) [ -4516.5176] [ 748] [depth= 3] . ( 5 sec) [ -4516.1624] [ 759] [depth= 2] . ( 5 sec) [ -4470.5234] [ 740] [depth= 1] . ( 5 sec) [ -4466.2920] [ 718] [depth= 1] . ( 5 sec) [ -4408.6906] [ 689] [depth= 2] . ( 6 sec) [ -4397.1091] [ 689] [depth= 1] . ( 6 sec) [ -4396.8659] [ 688] [depth= 1] . ( 6 sec) [ -4308.7362] [ 657] [depth= 4] . ( 6 sec) [ -4308.2152] [ 662] [depth= 1] . ( 6 sec) [ -4304.6639] [ 657] [depth= 1] . ( 6 sec) [ -4298.2688] [ 660] [depth= 1] . ( 6 sec) [ -4294.3956] [ 657] [depth= 1] . ( 6 sec) [ -4293.6895] [ 657] [depth= 1] . ( 7 sec) [ -4293.2487] [ 657] [depth= 1] . ( 7 sec) [ -4292.1274] [ 661] [depth= 1] . ( 7 sec) [ -4243.0746] [ 652] [depth= 1] . ( 7 sec) [ -4243.0394] [ 651] [depth= 1] . ( 7 sec) [ -4242.2208] [ 656] [depth= 1] . ( 7 sec) [ -4242.1814] [ 656] [depth= 1] . ( 8 sec) [ -4241.9874] [ 656] [depth= 1] . ( 8 sec) [ -4239.7304] [ 651] [depth= 1] . ( 8 sec) [ -4225.5743] [Branch lengths ] . ( 8 sec) [ -4223.8633] [GTR parameters ] . ( 8 sec) [ -4217.3020] [Alpha ][ 0.957440] . ( 10 sec) [ -4214.9937] [ 647] [depth= 1] . ( 12 sec) [ -4214.5870] [Branch lengths ] . ( 12 sec) [ -4214.5714] [GTR parameters ] . ( 12 sec) [ -4214.5599] [Alpha ][ 0.976366] . ( 16 sec) [ -4214.5549] [Branch lengths ] . ( 30 sec) [ -4214.5548] [Branch lengths ] . ( 30 sec) [ -4214.5548] [Topology ] . ( 31 sec) [ -4214.5548] [Topology ] . ( 31 sec) [ -4214.5548] [GTR parameters ] . ( 31 sec) [ -4214.5548] [Alpha ][ 0.976366] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.554764. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14778.8284] [GTR parameters ] . ( 0 sec) [ -14531.3261] [Alpha ][ 0.500960] . ( 0 sec) [ -14060.2937] [ 1876] [depth= 6] . ( 0 sec) [ -13912.9141] [ 1851] [depth= 11] . ( 0 sec) [ -13855.2858] [ 1841] [depth= 4] . ( 0 sec) [ -13775.7304] [ 1840] [depth= 1] . ( 0 sec) [ -12589.8402] [ 1821] [depth= 10] . ( 0 sec) [ -12398.9573] [ 1821] [depth= 3] . ( 0 sec) [ -12285.4101] [ 1820] [depth= 6] . ( 0 sec) [ -12189.8401] [ 1820] [depth= 14] . ( 0 sec) [ -11919.8412] [ 1770] [depth= 18] . ( 0 sec) [ -11847.1754] [ 1744] [depth= 7] . ( 0 sec) [ -11399.5836] [ 1744] [depth= 6] . ( 0 sec) [ -11246.4978] [ 1689] [depth= 21] . ( 1 sec) [ -10791.8125] [ 1688] [depth= 18] . ( 1 sec) [ -10558.5946] [ 1662] [depth= 2] . ( 1 sec) [ -9017.4697] [ 1652] [depth= 1] . ( 1 sec) [ -8911.1197] [ 1648] [depth= 2] . ( 1 sec) [ -8891.0312] [ 1648] [depth= 1] . ( 1 sec) [ -8855.5642] [ 1644] [depth= 13] . ( 1 sec) [ -8779.5010] [ 1638] [depth= 2] . ( 1 sec) [ -8779.2652] [ 1638] [depth= 6] . ( 1 sec) [ -8664.6719] [ 1632] [depth= 7] . ( 1 sec) [ -8512.2672] [ 1600] [depth= 5] . ( 1 sec) [ -8374.6439] [ 1571] [depth= 5] . ( 1 sec) [ -8292.7199] [ 1558] [depth= 14] . ( 1 sec) [ -8281.7654] [ 1559] [depth= 2] . ( 1 sec) [ -8068.1354] [ 1498] [depth= 12] . ( 1 sec) [ -8022.7523] [ 1501] [depth= 3] . ( 1 sec) [ -8016.3539] [ 1501] [depth= 2] . ( 1 sec) [ -7970.4812] [ 1500] [depth= 10] . ( 1 sec) [ -7967.6979] [ 1499] [depth= 3] . ( 1 sec) [ -7963.9533] [ 1495] [depth= 3] . ( 1 sec) [ -7719.8293] [ 1470] [depth= 3] . ( 1 sec) [ -7512.1573] [ 1434] [depth= 1] . ( 1 sec) [ -7512.0308] [ 1431] [depth= 1] . ( 1 sec) [ -7436.2482] [ 1424] [depth= 4] . ( 1 sec) [ -7138.8328] [ 1367] [depth= 10] . ( 1 sec) [ -6957.8304] [ 1334] [depth= 11] . ( 1 sec) [ -6895.0412] [ 1329] [depth= 5] . ( 1 sec) [ -6822.9122] [ 1343] [depth= 1] . ( 1 sec) [ -6822.4537] [ 1341] [depth= 4] . ( 1 sec) [ -6819.9341] [ 1341] [depth= 1] . ( 1 sec) [ -6676.8879] [ 1304] [depth= 6] . ( 1 sec) [ -6604.5193] [ 1286] [depth= 8] . ( 1 sec) [ -6579.9869] [ 1256] [depth= 1] . ( 1 sec) [ -6429.7483] [ 1201] [depth= 2] . ( 2 sec) [ -6192.3171] [ 1171] [depth= 9] . ( 2 sec) [ -6191.1961] [ 1173] [depth= 1] . ( 2 sec) [ -6068.1877] [ 1144] [depth= 3] . ( 2 sec) [ -6059.4569] [ 1144] [depth= 1] . ( 2 sec) [ -6049.8439] [ 1144] [depth= 1] . ( 2 sec) [ -6048.7995] [ 1143] [depth= 1] . ( 2 sec) [ -5997.8847] [ 1138] [depth= 4] . ( 2 sec) [ -5947.3923] [ 1106] [depth= 7] . ( 2 sec) [ -5786.5831] [ 1065] [depth= 5] . ( 2 sec) [ -5775.1759] [ 1066] [depth= 1] . ( 2 sec) [ -5772.1421] [ 1064] [depth= 2] . ( 2 sec) [ -5737.9364] [ 1035] [depth= 2] . ( 2 sec) [ -5737.8733] [ 1035] [depth= 1] . ( 2 sec) [ -5699.3910] [ 1030] [depth= 7] . ( 2 sec) [ -5696.2367] [ 1022] [depth= 5] . ( 2 sec) [ -5553.0690] [ 1027] [depth= 2] . ( 2 sec) [ -5392.6737] [ 944] [depth= 5] . ( 2 sec) [ -5384.5640] [ 944] [depth= 1] . ( 2 sec) [ -5359.8141] [ 944] [depth= 3] . ( 2 sec) [ -5356.3948] [ 945] [depth= 1] . ( 2 sec) [ -5342.4501] [ 938] [depth= 4] . ( 2 sec) [ -5319.1193] [ 938] [depth= 1] . ( 2 sec) [ -5311.4398] [ 938] [depth= 1] . ( 2 sec) [ -5283.7194] [ 929] [depth= 2] . ( 2 sec) [ -5159.8801] [ 912] [depth= 1] . ( 2 sec) [ -5087.9512] [ 887] [depth= 1] . ( 3 sec) [ -5087.7490] [ 884] [depth= 1] . ( 3 sec) [ -5063.7484] [ 886] [depth= 2] . ( 3 sec) [ -5005.5807] [ 851] [depth= 1] . ( 3 sec) [ -4992.1887] [ 843] [depth= 2] . ( 3 sec) [ -4830.5015] [ 814] [depth= 3] . ( 3 sec) [ -4788.4863] [ 797] [depth= 4] . ( 3 sec) [ -4592.1686] [ 738] [depth= 4] . ( 3 sec) [ -4566.8457] [ 739] [depth= 1] . ( 3 sec) [ -4551.3602] [ 733] [depth= 3] . ( 3 sec) [ -4551.0782] [ 736] [depth= 1] . ( 3 sec) [ -4547.4101] [ 736] [depth= 2] . ( 3 sec) [ -4547.3575] [ 734] [depth= 1] . ( 3 sec) [ -4422.4991] [ 705] [depth= 2] . ( 3 sec) [ -4366.6816] [Branch lengths ] . ( 4 sec) [ -4364.1878] [GTR parameters ] . ( 4 sec) [ -4353.2657] [Alpha ][ 0.839511] . ( 4 sec) [ -4319.3375] [ 691] [depth= 1] . ( 4 sec) [ -4318.7880] [ 690] [depth= 1] . ( 4 sec) [ -4287.0568] [ 678] [depth= 1] . ( 4 sec) [ -4281.3811] [ 674] [depth= 2] . ( 4 sec) [ -4267.9339] [ 664] [depth= 1] . ( 4 sec) [ -4267.8397] [ 664] [depth= 1] . ( 4 sec) [ -4267.1059] [ 665] [depth= 1] . ( 5 sec) [ -4263.7315] [ 662] [depth= 1] . ( 5 sec) [ -4261.0161] [ 661] [depth= 1] . ( 5 sec) [ -4251.9544] [ 658] [depth= 2] . ( 5 sec) [ -4250.3907] [ 657] [depth= 1] . ( 5 sec) [ -4221.5957] [ 649] [depth= 1] . ( 5 sec) [ -4220.2932] [ 648] [depth= 1] . ( 5 sec) [ -4220.1252] [ 648] [depth= 1] . ( 5 sec) [ -4219.9421] [ 648] [depth= 1] . ( 5 sec) [ -4219.7107] [ 648] [depth= 1] . ( 5 sec) [ -4218.9065] [ 648] [depth= 2] . ( 5 sec) [ -4218.7948] [ 648] [depth= 1] . ( 6 sec) [ -4218.5040] [ 647] [depth= 1] . ( 7 sec) [ -4215.4349] [Branch lengths ] . ( 7 sec) [ -4215.2884] [GTR parameters ] . ( 7 sec) [ -4214.6075] [Alpha ][ 0.974679] . ( 11 sec) [ -4214.5559] [Branch lengths ] . ( 25 sec) [ -4214.5555] [Branch lengths ] . ( 25 sec) [ -4214.5555] [Topology ] . ( 26 sec) [ -4214.5555] [Topology ] . ( 26 sec) [ -4214.5550] [GTR parameters ] . ( 26 sec) [ -4214.5549] [Alpha ][ 0.976601] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4214.554873. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4232.026270 . ( 0 sec) [ -4230.2548] [GTR parameters ] . ( 0 sec) [ -4230.1853] [Alpha ][ 0.950604] . ( 0 sec) [ -4230.1853] [Topology ] . ( 1 sec) [ -4215.8559] [Topology ] . ( 1 sec) [ -4214.8475] [Topology ] . ( 2 sec) [ -4214.6692] [Topology ] . ( 2 sec) [ -4214.6239] [Topology ] . ( 3 sec) [ -4214.6092] [Topology ] . ( 3 sec) [ -4214.6031] [Topology ] . ( 4 sec) [ -4214.5999] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.599937 . ( 7 sec) [ -4214.5866] [GTR parameters ] . ( 7 sec) [ -4214.5662] [Alpha ][ 0.976114] . ( 7 sec) [ -4214.5662] [Topology ] . ( 8 sec) [ -4214.5632] [Topology ] . ( 9 sec) [ -4214.5614] [Topology ] . ( 9 sec) [ -4214.5600] [Topology ] . ( 10 sec) [ -4214.5589] [Topology ] . ( 10 sec) [ -4214.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.558087 . ( 14 sec) [ -4214.5580] [GTR parameters ] . ( 14 sec) [ -4214.5580] [Alpha ][ 0.977090] . ( 14 sec) [ -4214.5580] [Topology ] . ( 14 sec) [ -4214.5572] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 21 sec) [ -4230.2548] [GTR parameters ] . ( 21 sec) [ -4230.1853] [Alpha ][ 0.950604] . ( 22 sec) [ -4224.0623] [ 648] [depth= 2] . ( 22 sec) [ -4223.5846] [ 648] [depth= 1] . ( 22 sec) [ -4222.3690] [ 648] [depth= 1] . ( 23 sec) [ -4222.2615] [ 648] [depth= 1] . ( 23 sec) [ -4222.1229] [ 648] [depth= 1] . ( 24 sec) [ -4222.0692] [ 648] [depth= 1] . ( 24 sec) [ -4221.9858] [ 648] [depth= 1] . ( 24 sec) [ -4221.0501] [ 647] [depth= 1] . ( 25 sec) [ -4214.7012] [Branch lengths ] . ( 25 sec) [ -4214.6884] [GTR parameters ] . ( 25 sec) [ -4214.6700] [Alpha ][ 0.974743] . ( 25 sec) [ -4214.6599] [ 647] [depth= 1] . ( 29 sec) [ -4214.5723] [Branch lengths ] . ( 29 sec) [ -4214.5722] [GTR parameters ] . ( 29 sec) [ -4214.5721] [Alpha ][ 0.976356] . ( 43 sec) [ -4214.5623] [Branch lengths ] . ( 43 sec) [ -4214.5623] [Topology ] . ( 44 sec) [ -4214.5604] [Topology ] . ( 44 sec) [ -4214.5592] [Topology ] . ( 45 sec) [ -4214.5583] [Topology ] . ( 45 sec) [ -4214.5581] [GTR parameters ] . ( 45 sec) [ -4214.5581] [Alpha ][ 0.976356] . ( 45 sec) [ -4214.5581] [Topology ] . ( 46 sec) [ -4214.5573] [Topology ] . ( 46 sec) [ -4214.5573] [GTR parameters ] . ( 46 sec) [ -4214.5573] [Alpha ][ 0.976356] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4214.557221 . Log likelihood obtained after SPR moves : -4214.557326 . Log likelihood of the current tree: -4214.557221. . Printing the most likely tree in file 'data42.phy_phyml_tree.txt'... . Best log likelihood : -4214.554764 . Time used 0h0m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo