.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2696_50x1472_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1472 sites) . 982 sites without polymorphism (66.71%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -12697.4073] [GTR parameters ] . ( 3 sec) [ -12566.5270] [Alpha ][ 0.500960] . ( 3 sec) [ -12359.1762] [ 1184] [depth= 9] . ( 3 sec) [ -11970.9363] [ 1168] [depth= 10] . ( 3 sec) [ -11965.4050] [ 1168] [depth= 1] . ( 3 sec) [ -11925.6028] [ 1168] [depth= 3] . ( 3 sec) [ -11878.3407] [ 1161] [depth= 3] . ( 3 sec) [ -11867.9295] [ 1161] [depth= 1] . ( 3 sec) [ -11809.2716] [ 1161] [depth= 6] . ( 3 sec) [ -11805.5162] [ 1161] [depth= 5] . ( 4 sec) [ -11770.7006] [ 1145] [depth= 12] . ( 4 sec) [ -11738.5875] [ 1145] [depth= 2] . ( 4 sec) [ -11712.9357] [ 1141] [depth= 10] . ( 4 sec) [ -11493.7415] [ 1141] [depth= 3] . ( 4 sec) [ -11488.0722] [ 1139] [depth= 3] . ( 4 sec) [ -11455.1513] [ 1139] [depth= 6] . ( 4 sec) [ -10526.4416] [ 1113] [depth= 3] . ( 4 sec) [ -10443.2966] [ 1113] [depth= 2] . ( 4 sec) [ -10441.5701] [ 1113] [depth= 2] . ( 4 sec) [ -10435.0634] [ 1110] [depth= 3] . ( 4 sec) [ -10421.5016] [ 1110] [depth= 7] . ( 4 sec) [ -10399.8040] [ 1108] [depth= 9] . ( 5 sec) [ -10378.5085] [ 1102] [depth= 6] . ( 5 sec) [ -10265.6108] [ 1101] [depth= 7] . ( 5 sec) [ -10226.4192] [ 1098] [depth= 10] . ( 5 sec) [ -10138.4891] [ 1084] [depth= 12] . ( 5 sec) [ -9888.8392] [ 1059] [depth= 16] . ( 5 sec) [ -9879.9214] [ 1058] [depth= 6] . ( 5 sec) [ -9879.4231] [ 1067] [depth= 16] . ( 5 sec) [ -9876.8372] [ 1067] [depth= 1] . ( 5 sec) [ -9876.6977] [ 1067] [depth= 3] . ( 5 sec) [ -9870.1638] [ 1067] [depth= 6] . ( 5 sec) [ -9869.5061] [ 1067] [depth= 2] . ( 5 sec) [ -9776.6109] [ 1032] [depth= 5] . ( 6 sec) [ -9768.9225] [ 1030] [depth= 2] . ( 6 sec) [ -9727.6105] [ 1024] [depth= 17] . ( 6 sec) [ -9712.5114] [ 1021] [depth= 5] . ( 6 sec) [ -9665.6422] [ 1015] [depth= 7] . ( 6 sec) [ -9665.6197] [ 1015] [depth= 1] . ( 6 sec) [ -9661.8051] [ 1011] [depth= 9] . ( 6 sec) [ -8845.1572] [ 1014] [depth= 9] . ( 7 sec) [ -8817.7935] [ 1006] [depth= 2] . ( 7 sec) [ -8796.5883] [ 1001] [depth= 3] . ( 7 sec) [ -8787.4561] [ 999] [depth= 2] . ( 7 sec) [ -8749.0727] [ 991] [depth= 16] . ( 7 sec) [ -8662.3631] [ 986] [depth= 5] . ( 7 sec) [ -8647.5779] [ 985] [depth= 1] . ( 7 sec) [ -8647.5368] [ 985] [depth= 1] . ( 8 sec) [ -8602.3788] [ 979] [depth= 4] . ( 8 sec) [ -8548.2827] [ 975] [depth= 11] . ( 8 sec) [ -8495.0790] [ 971] [depth= 2] . ( 8 sec) [ -8494.9298] [ 971] [depth= 1] . ( 8 sec) [ -8485.4144] [ 968] [depth= 4] . ( 8 sec) [ -8484.8577] [ 969] [depth= 1] . ( 8 sec) [ -8474.7920] [ 968] [depth= 15] . ( 9 sec) [ -8474.2139] [ 971] [depth= 15] . ( 9 sec) [ -8440.4127] [ 967] [depth= 14] . ( 9 sec) [ -8366.4804] [ 970] [depth= 10] . ( 9 sec) [ -8331.5104] [ 962] [depth= 9] . ( 9 sec) [ -8329.7690] [ 962] [depth= 4] . ( 10 sec) [ -8251.7498] [ 941] [depth= 10] . ( 10 sec) [ -8180.7923] [ 927] [depth= 13] . ( 10 sec) [ -8136.6803] [ 921] [depth= 11] . ( 10 sec) [ -8135.9793] [ 922] [depth= 1] . ( 10 sec) [ -8110.6405] [ 919] [depth= 7] . ( 10 sec) [ -8100.4042] [ 919] [depth= 6] . ( 10 sec) [ -8080.3004] [ 919] [depth= 1] . ( 10 sec) [ -8044.4591] [ 911] [depth= 12] . ( 10 sec) [ -8026.8488] [ 912] [depth= 1] . ( 10 sec) [ -7743.9995] [ 911] [depth= 5] . ( 10 sec) [ -7305.5730] [ 918] [depth= 1] . ( 10 sec) [ -7280.1761] [ 894] [depth= 10] . ( 10 sec) [ -7271.2495] [ 893] [depth= 14] . ( 11 sec) [ -7267.3992] [ 892] [depth= 1] . ( 11 sec) [ -7226.2773] [ 881] [depth= 6] . ( 11 sec) [ -7213.6891] [ 887] [depth= 2] . ( 11 sec) [ -7165.8648] [ 879] [depth= 12] . ( 11 sec) [ -7159.1570] [ 880] [depth= 3] . ( 11 sec) [ -7079.7467] [ 866] [depth= 2] . ( 11 sec) [ -7078.8982] [ 866] [depth= 2] . ( 11 sec) [ -7072.7288] [ 866] [depth= 4] . ( 11 sec) [ -7000.8987] [ 858] [depth= 4] . ( 11 sec) [ -6992.5102] [ 857] [depth= 5] . ( 11 sec) [ -6989.8136] [ 857] [depth= 3] . ( 12 sec) [ -6982.7253] [ 857] [depth= 1] . ( 12 sec) [ -6961.5196] [ 853] [depth= 3] . ( 12 sec) [ -6959.4336] [ 853] [depth= 1] . ( 12 sec) [ -6959.1032] [ 853] [depth= 5] . ( 12 sec) [ -6947.0453] [ 853] [depth= 8] . ( 12 sec) [ -6946.9009] [ 853] [depth= 1] . ( 12 sec) [ -6946.8808] [ 853] [depth= 2] . ( 12 sec) [ -6946.8701] [ 853] [depth= 1] . ( 12 sec) [ -6937.5590] [ 839] [depth= 7] . ( 12 sec) [ -6903.5147] [ 839] [depth= 2] . ( 13 sec) [ -6902.6307] [ 839] [depth= 1] . ( 13 sec) [ -6883.3841] [ 836] [depth= 2] . ( 13 sec) [ -6831.6398] [ 824] [depth= 2] . ( 13 sec) [ -6797.5516] [ 815] [depth= 2] . ( 13 sec) [ -6793.7897] [ 817] [depth= 3] . ( 13 sec) [ -6664.7417] [ 790] [depth= 4] . ( 13 sec) [ -6656.5469] [ 787] [depth= 1] . ( 13 sec) [ -6640.0284] [ 775] [depth= 14] . ( 13 sec) [ -6595.7429] [ 772] [depth= 7] . ( 13 sec) [ -6568.9751] [ 766] [depth= 3] . ( 13 sec) [ -6567.6254] [ 766] [depth= 2] . ( 13 sec) [ -6553.1575] [ 763] [depth= 4] . ( 14 sec) [ -6553.0923] [ 763] [depth= 1] . ( 14 sec) [ -6552.9189] [ 763] [depth= 1] . ( 14 sec) [ -6552.8415] [ 763] [depth= 5] . ( 14 sec) [ -6549.2232] [ 762] [depth= 2] . ( 14 sec) [ -6522.3410] [ 762] [depth= 2] . ( 14 sec) [ -6464.6638] [ 750] [depth= 2] . ( 14 sec) [ -6464.1564] [ 750] [depth= 1] . ( 14 sec) [ -6463.6407] [ 750] [depth= 1] . ( 14 sec) [ -6463.5607] [ 750] [depth= 1] . ( 14 sec) [ -6447.0783] [ 746] [depth= 2] . ( 14 sec) [ -6435.4685] [ 743] [depth= 6] . ( 15 sec) [ -6430.2589] [ 743] [depth= 2] . ( 15 sec) [ -6425.3075] [ 742] [depth= 1] . ( 15 sec) [ -6425.1995] [ 742] [depth= 4] . ( 15 sec) [ -6414.2399] [ 740] [depth= 3] . ( 16 sec) [ -6412.2213] [ 740] [depth= 1] . ( 16 sec) [ -6379.5273] [Branch lengths ] . ( 18 sec) [ -6350.5551] [GTR parameters ] . ( 18 sec) [ -6348.2012] [Alpha ][ 0.655255] . ( 19 sec) [ -6341.4887] [ 739] [depth= 1] . ( 19 sec) [ -6340.5567] [ 737] [depth= 2] . ( 19 sec) [ -6335.5931] [ 735] [depth= 2] . ( 19 sec) [ -6307.6102] [ 728] [depth= 4] . ( 20 sec) [ -6304.1125] [ 729] [depth= 3] . ( 20 sec) [ -6260.1772] [ 715] [depth= 1] . ( 20 sec) [ -6231.5243] [ 700] [depth= 4] . ( 22 sec) [ -6226.9163] [ 698] [depth= 3] . ( 23 sec) [ -6226.9036] [ 698] [depth= 1] . ( 25 sec) [ -6214.2689] [ 696] [depth= 1] . ( 25 sec) [ -6213.5164] [ 698] [depth= 1] . ( 26 sec) [ -6213.5039] [ 698] [depth= 1] . ( 26 sec) [ -6207.9355] [ 697] [depth= 1] . ( 26 sec) [ -6193.1774] [ 695] [depth= 1] . ( 27 sec) [ -6190.0881] [ 696] [depth= 1] . ( 27 sec) [ -6190.0731] [ 696] [depth= 1] . ( 28 sec) [ -6185.2410] [ 695] [depth= 2] . ( 31 sec) [ -6175.6415] [ 693] [depth= 1] . ( 33 sec) [ -6174.6037] [ 693] [depth= 1] . ( 33 sec) [ -6174.5829] [ 693] [depth= 1] . ( 34 sec) [ -6174.4560] [ 693] [depth= 2] . ( 35 sec) [ -6172.6174] [ 692] [depth= 2] . ( 36 sec) [ -6172.6007] [ 692] [depth= 3] . ( 37 sec) [ -6171.1163] [ 691] [depth= 1] . ( 38 sec) [ -6170.9469] [ 687] [depth= 1] . ( 39 sec) [ -6170.9124] [ 687] [depth= 1] . ( 44 sec) [ -6170.8691] [ 687] [depth= 1] . ( 51 sec) [ -6168.3219] [Branch lengths ] . ( 52 sec) [ -6168.1803] [GTR parameters ] . ( 52 sec) [ -6165.4763] [Alpha ][ 0.932462] . ( 89 sec) [ -6165.3972] [Branch lengths ] . ( 141 sec) [ -6165.3963] [Branch lengths ] . ( 141 sec) [ -6165.3963] [Topology ] . ( 142 sec) [ -6165.3963] [Topology ] . ( 143 sec) [ -6165.3866] [GTR parameters ] . ( 143 sec) [ -6165.3857] [Alpha ][ 0.938822] . ( 143 sec) [ -6165.3857] [Topology ] . ( 144 sec) [ -6165.3857] [Topology ] . ( 144 sec) [ -6165.3857] [GTR parameters ] . ( 144 sec) [ -6165.3857] [Alpha ][ 0.938822] . Checking for NNIs, optimizing five branches... . ( 153 sec) [ -6165.3856] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.385592. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12572.1975] [GTR parameters ] . ( 1 sec) [ -12448.5383] [Alpha ][ 0.500960] . ( 1 sec) [ -12272.3832] [ 1183] [depth= 15] . ( 1 sec) [ -12099.5897] [ 1148] [depth= 7] . ( 1 sec) [ -12092.8519] [ 1154] [depth= 1] . ( 1 sec) [ -12047.3001] [ 1148] [depth= 7] . ( 2 sec) [ -12013.6976] [ 1142] [depth= 2] . ( 2 sec) [ -12011.7257] [ 1142] [depth= 2] . ( 2 sec) [ -11424.7548] [ 1140] [depth= 7] . ( 2 sec) [ -11414.3575] [ 1138] [depth= 1] . ( 2 sec) [ -11400.5566] [ 1135] [depth= 7] . ( 2 sec) [ -10149.3979] [ 1117] [depth= 1] . ( 2 sec) [ -10130.5485] [ 1112] [depth= 7] . ( 2 sec) [ -10129.9618] [ 1111] [depth= 3] . ( 2 sec) [ -10120.5775] [ 1111] [depth= 1] . ( 2 sec) [ -9487.3503] [ 1111] [depth= 1] . ( 2 sec) [ -9260.3962] [ 1111] [depth= 1] . ( 3 sec) [ -9252.3074] [ 1109] [depth= 5] . ( 3 sec) [ -9189.7855] [ 1109] [depth= 4] . ( 3 sec) [ -9186.4027] [ 1076] [depth= 10] . ( 3 sec) [ -9158.5867] [ 1072] [depth= 4] . ( 3 sec) [ -9119.5758] [ 1066] [depth= 15] . ( 3 sec) [ -9107.1075] [ 1066] [depth= 1] . ( 3 sec) [ -9077.1055] [ 1065] [depth= 14] . ( 3 sec) [ -9067.7166] [ 1065] [depth= 7] . ( 3 sec) [ -9046.9274] [ 1065] [depth= 4] . ( 3 sec) [ -8996.7422] [ 1065] [depth= 1] . ( 3 sec) [ -8990.8976] [ 1063] [depth= 8] . ( 3 sec) [ -8985.9215] [ 1063] [depth= 1] . ( 3 sec) [ -8954.8725] [ 1059] [depth= 12] . ( 4 sec) [ -8894.8763] [ 1051] [depth= 10] . ( 4 sec) [ -8758.6346] [ 1024] [depth= 14] . ( 4 sec) [ -8719.2211] [ 1018] [depth= 7] . ( 4 sec) [ -8695.6423] [ 1016] [depth= 5] . ( 4 sec) [ -8661.2609] [ 1009] [depth= 2] . ( 4 sec) [ -8630.6618] [ 1005] [depth= 3] . ( 4 sec) [ -8526.1271] [ 985] [depth= 13] . ( 4 sec) [ -8522.3662] [ 984] [depth= 1] . ( 4 sec) [ -8457.6359] [ 975] [depth= 3] . ( 4 sec) [ -8452.3903] [ 974] [depth= 13] . ( 4 sec) [ -8428.8301] [ 974] [depth= 9] . ( 4 sec) [ -8042.3180] [ 974] [depth= 2] . ( 4 sec) [ -7994.3010] [ 963] [depth= 8] . ( 5 sec) [ -7993.8557] [ 963] [depth= 1] . ( 5 sec) [ -7976.8547] [ 963] [depth= 1] . ( 5 sec) [ -7899.1504] [ 953] [depth= 2] . ( 5 sec) [ -7873.5384] [ 956] [depth= 11] . ( 5 sec) [ -7819.7877] [ 936] [depth= 14] . ( 5 sec) [ -7753.6126] [ 919] [depth= 3] . ( 5 sec) [ -7597.1456] [ 920] [depth= 1] . ( 5 sec) [ -7570.5446] [ 913] [depth= 12] . ( 5 sec) [ -7563.3269] [ 909] [depth= 1] . ( 6 sec) [ -7560.1800] [ 906] [depth= 1] . ( 6 sec) [ -7542.4020] [ 902] [depth= 5] . ( 6 sec) [ -7515.4423] [ 903] [depth= 14] . ( 6 sec) [ -7443.2491] [ 890] [depth= 10] . ( 6 sec) [ -7433.0341] [ 888] [depth= 3] . ( 6 sec) [ -7351.2315] [ 870] [depth= 6] . ( 6 sec) [ -7340.2659] [ 869] [depth= 6] . ( 6 sec) [ -7290.0214] [ 861] [depth= 3] . ( 6 sec) [ -7212.8979] [ 852] [depth= 9] . ( 7 sec) [ -7178.4830] [ 845] [depth= 8] . ( 7 sec) [ -7156.3770] [ 837] [depth= 8] . ( 7 sec) [ -7053.3466] [ 820] [depth= 6] . ( 7 sec) [ -7014.2670] [ 818] [depth= 8] . ( 7 sec) [ -7012.7357] [ 818] [depth= 1] . ( 7 sec) [ -6969.6918] [ 812] [depth= 8] . ( 7 sec) [ -6963.6558] [ 812] [depth= 1] . ( 7 sec) [ -6951.5191] [ 812] [depth= 1] . ( 7 sec) [ -6950.2041] [ 812] [depth= 1] . ( 8 sec) [ -6950.1041] [ 812] [depth= 1] . ( 8 sec) [ -6950.0724] [ 812] [depth= 4] . ( 8 sec) [ -6949.2390] [ 812] [depth= 1] . ( 8 sec) [ -6949.1551] [ 812] [depth= 1] . ( 8 sec) [ -6908.9242] [ 805] [depth= 12] . ( 9 sec) [ -6908.8909] [ 805] [depth= 3] . ( 9 sec) [ -6864.5899] [ 798] [depth= 4] . ( 9 sec) [ -6861.6875] [ 798] [depth= 4] . ( 9 sec) [ -6843.5430] [ 794] [depth= 1] . ( 9 sec) [ -6816.2755] [ 792] [depth= 6] . ( 9 sec) [ -6779.0412] [ 784] [depth= 4] . ( 9 sec) [ -6778.1307] [ 784] [depth= 1] . ( 9 sec) [ -6719.3776] [ 773] [depth= 4] . ( 9 sec) [ -6713.2184] [ 772] [depth= 4] . ( 9 sec) [ -6705.0793] [ 772] [depth= 11] . ( 9 sec) [ -6685.8217] [ 770] [depth= 10] . ( 10 sec) [ -6683.8032] [ 770] [depth= 1] . ( 10 sec) [ -6683.7894] [ 770] [depth= 3] . ( 12 sec) [ -6647.2950] [ 764] [depth= 6] . ( 12 sec) [ -6646.3078] [ 764] [depth= 2] . ( 12 sec) [ -6639.9715] [ 763] [depth= 1] . ( 12 sec) [ -6606.2951] [ 756] [depth= 1] . ( 12 sec) [ -6606.2017] [ 756] [depth= 2] . ( 12 sec) [ -6604.2841] [ 756] [depth= 1] . ( 12 sec) [ -6602.7142] [ 756] [depth= 3] . ( 12 sec) [ -6596.1886] [ 755] [depth= 1] . ( 12 sec) [ -6590.0294] [ 755] [depth= 5] . ( 13 sec) [ -6589.6803] [ 756] [depth= 3] . ( 13 sec) [ -6589.5694] [ 756] [depth= 1] . ( 13 sec) [ -6525.4312] [ 733] [depth= 6] . ( 13 sec) [ -6517.3111] [ 731] [depth= 2] . ( 13 sec) [ -6469.5616] [ 727] [depth= 1] . ( 13 sec) [ -6467.5976] [ 728] [depth= 1] . ( 13 sec) [ -6466.7406] [ 728] [depth= 1] . ( 13 sec) [ -6466.7166] [ 728] [depth= 1] . ( 13 sec) [ -6457.8555] [ 725] [depth= 4] . ( 13 sec) [ -6457.7758] [ 725] [depth= 1] . ( 14 sec) [ -6453.3183] [ 726] [depth= 4] . ( 14 sec) [ -6453.0299] [ 726] [depth= 1] . ( 15 sec) [ -6436.2563] [Branch lengths ] . ( 16 sec) [ -6416.3635] [GTR parameters ] . ( 16 sec) [ -6415.2113] [Alpha ][ 0.600371] . ( 16 sec) [ -6413.5497] [ 725] [depth= 2] . ( 17 sec) [ -6401.7713] [ 723] [depth= 6] . ( 18 sec) [ -6398.1777] [ 722] [depth= 1] . ( 18 sec) [ -6397.7713] [ 721] [depth= 1] . ( 19 sec) [ -6392.6021] [ 718] [depth= 1] . ( 19 sec) [ -6379.7417] [ 716] [depth= 1] . ( 19 sec) [ -6305.0817] [ 724] [depth= 1] . ( 19 sec) [ -6303.8853] [ 724] [depth= 1] . ( 19 sec) [ -6299.0088] [ 723] [depth= 1] . ( 20 sec) [ -6293.5330] [ 722] [depth= 5] . ( 20 sec) [ -6293.5126] [ 722] [depth= 2] . ( 24 sec) [ -6279.4606] [ 720] [depth= 2] . ( 25 sec) [ -6233.8696] [ 705] [depth= 5] . ( 25 sec) [ -6233.8382] [ 705] [depth= 3] . ( 26 sec) [ -6229.9387] [ 705] [depth= 3] . ( 26 sec) [ -6227.2919] [ 704] [depth= 1] . ( 27 sec) [ -6226.7587] [ 704] [depth= 1] . ( 37 sec) [ -6226.7281] [ 704] [depth= 2] . ( 38 sec) [ -6217.2129] [ 703] [depth= 4] . ( 38 sec) [ -6216.4998] [ 703] [depth= 1] . ( 39 sec) [ -6215.1626] [ 702] [depth= 3] . ( 39 sec) [ -6196.2676] [ 695] [depth= 2] . ( 44 sec) [ -6192.4569] [ 698] [depth= 1] . ( 46 sec) [ -6183.8508] [ 694] [depth= 1] . ( 47 sec) [ -6182.5310] [ 695] [depth= 1] . ( 51 sec) [ -6178.8860] [Branch lengths ] . ( 52 sec) [ -6178.6029] [GTR parameters ] . ( 52 sec) [ -6174.8932] [Alpha ][ 0.893934] . ( 55 sec) [ -6174.1929] [ 694] [depth= 1] . ( 55 sec) [ -6173.9549] [ 694] [depth= 1] . ( 55 sec) [ -6166.9858] [ 691] [depth= 1] . ( 85 sec) [ -6166.6588] [ 687] [depth= 1] . ( 89 sec) [ -6165.8561] [Branch lengths ] . ( 90 sec) [ -6165.8280] [GTR parameters ] . ( 90 sec) [ -6165.7827] [Alpha ][ 0.939182] . ( 127 sec) [ -6165.7702] [Branch lengths ] . ( 179 sec) [ -6165.7701] [Branch lengths ] . ( 179 sec) [ -6165.7701] [Topology ] . ( 180 sec) [ -6165.7701] [Topology ] . ( 181 sec) [ -6165.7699] [GTR parameters ] . ( 181 sec) [ -6165.7699] [Alpha ][ 0.940732] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.769880. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11537.5211] [GTR parameters ] . ( 1 sec) [ -11416.7448] [Alpha ][ 0.500960] . ( 1 sec) [ -11246.3698] [ 1192] [depth= 8] . ( 1 sec) [ -11092.5716] [ 1161] [depth= 8] . ( 1 sec) [ -11091.9731] [ 1162] [depth= 1] . ( 1 sec) [ -11060.6511] [ 1152] [depth= 2] . ( 2 sec) [ -11030.9640] [ 1143] [depth= 4] . ( 2 sec) [ -10849.4486] [ 1130] [depth= 6] . ( 2 sec) [ -10614.5254] [ 1127] [depth= 6] . ( 2 sec) [ -10203.2886] [ 1124] [depth= 1] . ( 2 sec) [ -10055.2985] [ 1102] [depth= 8] . ( 2 sec) [ -9979.8352] [ 1094] [depth= 1] . ( 2 sec) [ -9903.8505] [ 1087] [depth= 7] . ( 2 sec) [ -9900.1015] [ 1087] [depth= 1] . ( 2 sec) [ -9861.1140] [ 1082] [depth= 15] . ( 2 sec) [ -9817.4383] [ 1081] [depth= 8] . ( 2 sec) [ -9790.8283] [ 1079] [depth= 11] . ( 2 sec) [ -9263.6555] [ 1078] [depth= 9] . ( 3 sec) [ -9044.2389] [ 1077] [depth= 5] . ( 3 sec) [ -8535.6231] [ 1069] [depth= 6] . ( 3 sec) [ -8515.3239] [ 1068] [depth= 6] . ( 3 sec) [ -8507.7258] [ 1068] [depth= 5] . ( 3 sec) [ -8487.9336] [ 1062] [depth= 1] . ( 3 sec) [ -8441.4027] [ 1058] [depth= 12] . ( 3 sec) [ -8382.9627] [ 1055] [depth= 4] . ( 3 sec) [ -8325.9189] [ 1044] [depth= 8] . ( 3 sec) [ -8325.6631] [ 1044] [depth= 1] . ( 3 sec) [ -8324.2153] [ 1044] [depth= 2] . ( 3 sec) [ -8320.1517] [ 1046] [depth= 10] . ( 3 sec) [ -8308.6897] [ 1044] [depth= 11] . ( 3 sec) [ -8203.9828] [ 1026] [depth= 9] . ( 4 sec) [ -8203.8144] [ 1026] [depth= 1] . ( 4 sec) [ -8203.7022] [ 1026] [depth= 1] . ( 4 sec) [ -7877.5166] [ 1018] [depth= 8] . ( 4 sec) [ -7833.7394] [ 1017] [depth= 1] . ( 4 sec) [ -7796.9112] [ 1017] [depth= 2] . ( 4 sec) [ -7693.5670] [ 1017] [depth= 6] . ( 4 sec) [ -7682.0005] [ 1021] [depth= 2] . ( 4 sec) [ -7669.1294] [ 1021] [depth= 1] . ( 4 sec) [ -7654.3098] [ 1021] [depth= 8] . ( 4 sec) [ -7597.6417] [ 1005] [depth= 4] . ( 5 sec) [ -7589.4422] [ 1003] [depth= 10] . ( 5 sec) [ -7589.1175] [ 1002] [depth= 2] . ( 5 sec) [ -7572.8061] [ 1000] [depth= 6] . ( 5 sec) [ -7541.3804] [ 1001] [depth= 3] . ( 5 sec) [ -7531.1163] [ 998] [depth= 4] . ( 5 sec) [ -7454.9437] [ 958] [depth= 14] . ( 5 sec) [ -7406.4880] [ 947] [depth= 6] . ( 5 sec) [ -7364.3020] [ 939] [depth= 6] . ( 5 sec) [ -7301.8516] [ 929] [depth= 6] . ( 5 sec) [ -7189.1039] [ 890] [depth= 14] . ( 6 sec) [ -7188.7453] [ 890] [depth= 2] . ( 6 sec) [ -7183.4575] [ 890] [depth= 5] . ( 6 sec) [ -7180.6306] [ 890] [depth= 2] . ( 6 sec) [ -7176.4018] [ 880] [depth= 6] . ( 6 sec) [ -7169.0489] [ 879] [depth= 2] . ( 6 sec) [ -7143.2807] [ 877] [depth= 3] . ( 7 sec) [ -7116.7556] [ 856] [depth= 11] . ( 7 sec) [ -7104.2660] [ 856] [depth= 1] . ( 7 sec) [ -7086.8877] [ 853] [depth= 2] . ( 7 sec) [ -7073.4885] [ 853] [depth= 1] . ( 7 sec) [ -6988.3960] [ 840] [depth= 10] . ( 7 sec) [ -6929.9223] [ 828] [depth= 5] . ( 7 sec) [ -6898.0682] [ 824] [depth= 4] . ( 7 sec) [ -6892.7270] [ 824] [depth= 3] . ( 8 sec) [ -6878.3501] [ 821] [depth= 4] . ( 8 sec) [ -6878.3149] [ 821] [depth= 2] . ( 8 sec) [ -6873.1820] [ 815] [depth= 4] . ( 9 sec) [ -6786.3322] [ 794] [depth= 3] . ( 9 sec) [ -6781.3675] [ 791] [depth= 2] . ( 9 sec) [ -6708.9528] [ 778] [depth= 2] . ( 9 sec) [ -6701.4602] [ 779] [depth= 1] . ( 9 sec) [ -6654.8611] [ 770] [depth= 3] . ( 9 sec) [ -6648.6861] [ 767] [depth= 7] . ( 9 sec) [ -6634.3878] [ 764] [depth= 2] . ( 9 sec) [ -6628.5312] [ 763] [depth= 6] . ( 9 sec) [ -6600.3863] [ 759] [depth= 4] . ( 10 sec) [ -6600.3193] [ 759] [depth= 1] . ( 10 sec) [ -6600.2609] [ 759] [depth= 1] . ( 10 sec) [ -6538.0506] [ 748] [depth= 6] . ( 11 sec) [ -6537.9900] [ 748] [depth= 2] . ( 12 sec) [ -6537.6719] [ 748] [depth= 1] . ( 12 sec) [ -6536.0566] [ 748] [depth= 1] . ( 12 sec) [ -6488.4929] [ 741] [depth= 13] . ( 12 sec) [ -6488.2163] [ 741] [depth= 1] . ( 12 sec) [ -6473.2933] [ 738] [depth= 1] . ( 12 sec) [ -6464.6078] [ 738] [depth= 1] . ( 12 sec) [ -6456.3832] [ 737] [depth= 2] . ( 12 sec) [ -6441.4133] [ 733] [depth= 2] . ( 12 sec) [ -6426.5383] [ 730] [depth= 10] . ( 12 sec) [ -6369.5698] [ 720] [depth= 2] . ( 12 sec) [ -6368.6819] [ 720] [depth= 1] . ( 12 sec) [ -6358.3275] [ 717] [depth= 2] . ( 12 sec) [ -6356.5839] [ 716] [depth= 1] . ( 13 sec) [ -6351.8472] [ 715] [depth= 2] . ( 14 sec) [ -6351.7845] [ 715] [depth= 1] . ( 14 sec) [ -6351.7707] [ 715] [depth= 1] . ( 14 sec) [ -6297.9924] [ 706] [depth= 5] . ( 15 sec) [ -6297.8561] [ 710] [depth= 1] . ( 15 sec) [ -6288.2450] [ 710] [depth= 1] . ( 16 sec) [ -6265.6772] [ 706] [depth= 1] . ( 16 sec) [ -6265.6487] [ 707] [depth= 2] . ( 16 sec) [ -6265.4354] [ 707] [depth= 1] . ( 16 sec) [ -6265.4135] [ 707] [depth= 1] . ( 17 sec) [ -6242.9929] [Branch lengths ] . ( 18 sec) [ -6232.1892] [GTR parameters ] . ( 18 sec) [ -6225.4595] [Alpha ][ 0.823648] . ( 18 sec) [ -6215.4166] [ 705] [depth= 2] . ( 19 sec) [ -6212.0672] [ 704] [depth= 2] . ( 19 sec) [ -6212.0079] [ 701] [depth= 1] . ( 19 sec) [ -6208.9513] [ 696] [depth= 2] . ( 21 sec) [ -6208.2438] [ 696] [depth= 4] . ( 21 sec) [ -6208.2068] [ 696] [depth= 4] . ( 23 sec) [ -6198.0536] [ 694] [depth= 1] . ( 23 sec) [ -6198.0261] [ 694] [depth= 4] . ( 24 sec) [ -6197.9756] [ 694] [depth= 3] . ( 28 sec) [ -6195.7448] [ 694] [depth= 4] . ( 28 sec) [ -6188.6830] [ 692] [depth= 1] . ( 28 sec) [ -6186.9891] [ 692] [depth= 1] . ( 29 sec) [ -6184.3720] [ 692] [depth= 4] . ( 30 sec) [ -6184.3606] [ 692] [depth= 1] . ( 31 sec) [ -6175.3358] [ 691] [depth= 1] . ( 32 sec) [ -6174.5122] [ 691] [depth= 1] . ( 33 sec) [ -6174.0981] [ 691] [depth= 1] . ( 34 sec) [ -6173.9531] [ 691] [depth= 1] . ( 36 sec) [ -6173.4378] [ 691] [depth= 1] . ( 41 sec) [ -6173.3306] [ 690] [depth= 1] . ( 42 sec) [ -6172.4986] [ 690] [depth= 2] . ( 42 sec) [ -6171.4006] [ 690] [depth= 1] . ( 42 sec) [ -6171.3051] [ 690] [depth= 1] . ( 43 sec) [ -6171.2280] [ 690] [depth= 1] . ( 44 sec) [ -6170.9244] [ 690] [depth= 1] . ( 45 sec) [ -6170.9044] [ 690] [depth= 1] . ( 46 sec) [ -6170.8411] [ 692] [depth= 1] . ( 47 sec) [ -6170.8224] [ 692] [depth= 1] . ( 47 sec) [ -6170.5908] [ 692] [depth= 1] . ( 49 sec) [ -6167.8994] [Branch lengths ] . ( 50 sec) [ -6167.5823] [GTR parameters ] . ( 50 sec) [ -6167.3699] [Alpha ][ 0.913426] . ( 51 sec) [ -6166.7892] [ 692] [depth= 1] . ( 53 sec) [ -6166.0916] [ 691] [depth= 1] . ( 60 sec) [ -6165.8908] [ 687] [depth= 1] . ( 68 sec) [ -6165.6432] [ 691] [depth= 1] . ( 88 sec) [ -6165.4707] [Branch lengths ] . ( 88 sec) [ -6165.4686] [GTR parameters ] . ( 89 sec) [ -6165.4645] [Alpha ][ 0.927509] . ( 128 sec) [ -6165.4632] [Branch lengths ] . ( 182 sec) [ -6165.4632] [Branch lengths ] . ( 182 sec) [ -6165.4632] [Topology ] . ( 183 sec) [ -6165.4632] [Topology ] . ( 183 sec) [ -6165.4632] [GTR parameters ] . ( 184 sec) [ -6165.4632] [Alpha ][ 0.927509] . Checking for NNIs, optimizing five branches... . ( 192 sec) [ -6165.3967] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.396711. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -10806.4389] [GTR parameters ] . ( 2 sec) [ -10691.1485] [Alpha ][ 0.500960] . ( 2 sec) [ -10577.1163] [ 1222] [depth= 10] . ( 2 sec) [ -10452.8069] [ 1193] [depth= 6] . ( 2 sec) [ -10372.7071] [ 1183] [depth= 1] . ( 2 sec) [ -10348.3532] [ 1176] [depth= 1] . ( 2 sec) [ -10234.4769] [ 1166] [depth= 6] . ( 2 sec) [ -10190.0218] [ 1166] [depth= 6] . ( 2 sec) [ -10189.3038] [ 1165] [depth= 1] . ( 2 sec) [ -10116.5592] [ 1146] [depth= 5] . ( 2 sec) [ -10091.5341] [ 1146] [depth= 5] . ( 2 sec) [ -9751.0677] [ 1146] [depth= 3] . ( 3 sec) [ -9750.9736] [ 1145] [depth= 4] . ( 3 sec) [ -9705.0277] [ 1145] [depth= 3] . ( 3 sec) [ -9688.9400] [ 1145] [depth= 1] . ( 3 sec) [ -9620.8963] [ 1145] [depth= 3] . ( 3 sec) [ -9566.5865] [ 1143] [depth= 2] . ( 3 sec) [ -9521.8872] [ 1143] [depth= 2] . ( 3 sec) [ -9471.2838] [ 1130] [depth= 4] . ( 3 sec) [ -9436.3041] [ 1130] [depth= 2] . ( 3 sec) [ -9391.7654] [ 1126] [depth= 5] . ( 3 sec) [ -9348.3530] [ 1126] [depth= 1] . ( 3 sec) [ -9280.6002] [ 1121] [depth= 5] . ( 4 sec) [ -9272.7497] [ 1124] [depth= 9] . ( 4 sec) [ -9243.4099] [ 1117] [depth= 7] . ( 4 sec) [ -9241.6646] [ 1116] [depth= 4] . ( 4 sec) [ -9213.2348] [ 1113] [depth= 12] . ( 4 sec) [ -9168.3896] [ 1105] [depth= 3] . ( 4 sec) [ -9119.3099] [ 1097] [depth= 16] . ( 4 sec) [ -9105.0759] [ 1089] [depth= 13] . ( 4 sec) [ -9006.1050] [ 1082] [depth= 3] . ( 4 sec) [ -9001.5033] [ 1082] [depth= 5] . ( 4 sec) [ -8984.2764] [ 1081] [depth= 3] . ( 4 sec) [ -8968.9135] [ 1080] [depth= 1] . ( 5 sec) [ -8964.5690] [ 1080] [depth= 1] . ( 5 sec) [ -8945.6913] [ 1080] [depth= 12] . ( 5 sec) [ -8868.8649] [ 1069] [depth= 12] . ( 5 sec) [ -8781.1654] [ 1044] [depth= 20] . ( 5 sec) [ -8778.9067] [ 1043] [depth= 6] . ( 5 sec) [ -8770.8086] [ 1044] [depth= 1] . ( 5 sec) [ -8764.9979] [ 1042] [depth= 6] . ( 5 sec) [ -8757.9351] [ 1041] [depth= 1] . ( 5 sec) [ -8339.3646] [ 1038] [depth= 12] . ( 5 sec) [ -8121.3883] [ 999] [depth= 1] . ( 6 sec) [ -7970.0852] [ 997] [depth= 13] . ( 6 sec) [ -7519.9539] [ 979] [depth= 15] . ( 6 sec) [ -7519.8076] [ 981] [depth= 1] . ( 7 sec) [ -7517.9080] [ 986] [depth= 6] . ( 7 sec) [ -7446.5230] [ 977] [depth= 14] . ( 7 sec) [ -7442.7910] [ 980] [depth= 2] . ( 7 sec) [ -7402.1909] [ 953] [depth= 18] . ( 7 sec) [ -7329.7522] [ 946] [depth= 17] . ( 8 sec) [ -7308.7107] [ 942] [depth= 3] . ( 8 sec) [ -7260.4022] [ 935] [depth= 1] . ( 8 sec) [ -7249.1285] [ 933] [depth= 5] . ( 8 sec) [ -7207.4800] [ 903] [depth= 15] . ( 8 sec) [ -7177.2491] [ 903] [depth= 2] . ( 8 sec) [ -7149.8809] [ 903] [depth= 15] . ( 8 sec) [ -7077.1688] [ 886] [depth= 7] . ( 9 sec) [ -7072.2230] [ 876] [depth= 2] . ( 9 sec) [ -7037.2200] [ 871] [depth= 5] . ( 9 sec) [ -7036.0780] [ 871] [depth= 2] . ( 9 sec) [ -7033.0599] [ 871] [depth= 3] . ( 9 sec) [ -7031.8641] [ 871] [depth= 1] . ( 9 sec) [ -7025.2370] [ 871] [depth= 1] . ( 9 sec) [ -7022.3374] [ 871] [depth= 1] . ( 9 sec) [ -6989.7647] [ 865] [depth= 11] . ( 9 sec) [ -6989.2569] [ 865] [depth= 3] . ( 10 sec) [ -6989.1534] [ 865] [depth= 5] . ( 10 sec) [ -6982.2942] [ 863] [depth= 10] . ( 10 sec) [ -6976.6303] [ 862] [depth= 4] . ( 10 sec) [ -6963.1823] [ 866] [depth= 1] . ( 10 sec) [ -6904.7333] [ 855] [depth= 5] . ( 10 sec) [ -6903.5191] [ 855] [depth= 11] . ( 10 sec) [ -6902.8223] [ 855] [depth= 1] . ( 11 sec) [ -6885.9279] [ 862] [depth= 1] . ( 12 sec) [ -6885.0144] [ 864] [depth= 1] . ( 12 sec) [ -6879.2088] [ 862] [depth= 1] . ( 12 sec) [ -6877.9174] [ 862] [depth= 13] . ( 12 sec) [ -6874.2815] [ 862] [depth= 1] . ( 12 sec) [ -6815.6528] [ 850] [depth= 3] . ( 12 sec) [ -6815.3091] [ 850] [depth= 1] . ( 12 sec) [ -6813.4714] [ 850] [depth= 12] . ( 12 sec) [ -6795.3273] [ 846] [depth= 7] . ( 12 sec) [ -6746.7816] [ 823] [depth= 6] . ( 12 sec) [ -6728.6066] [ 819] [depth= 4] . ( 12 sec) [ -6718.1509] [ 816] [depth= 5] . ( 12 sec) [ -6712.6142] [ 815] [depth= 1] . ( 13 sec) [ -6694.9030] [ 813] [depth= 3] . ( 13 sec) [ -6686.4200] [ 813] [depth= 1] . ( 13 sec) [ -6669.6050] [ 812] [depth= 3] . ( 13 sec) [ -6651.4705] [ 808] [depth= 7] . ( 13 sec) [ -6649.3764] [ 808] [depth= 1] . ( 13 sec) [ -6643.9825] [ 806] [depth= 1] . ( 13 sec) [ -6641.7773] [ 806] [depth= 1] . ( 13 sec) [ -6641.7406] [ 806] [depth= 1] . ( 14 sec) [ -6626.9945] [ 806] [depth= 7] . ( 14 sec) [ -6621.3525] [ 806] [depth= 2] . ( 14 sec) [ -6621.2230] [ 806] [depth= 3] . ( 14 sec) [ -6621.1010] [ 806] [depth= 2] . ( 14 sec) [ -6595.9820] [ 802] [depth= 4] . ( 14 sec) [ -6594.3879] [ 801] [depth= 7] . ( 14 sec) [ -6594.2944] [ 801] [depth= 2] . ( 14 sec) [ -6576.6710] [ 799] [depth= 9] . ( 15 sec) [ -6565.0117] [ 796] [depth= 8] . ( 15 sec) [ -6548.7457] [ 795] [depth= 4] . ( 15 sec) [ -6520.8422] [ 788] [depth= 3] . ( 15 sec) [ -6517.9093] [ 788] [depth= 1] . ( 15 sec) [ -6512.3101] [ 787] [depth= 3] . ( 15 sec) [ -6473.9747] [ 782] [depth= 5] . ( 15 sec) [ -6466.0845] [ 780] [depth= 5] . ( 16 sec) [ -6453.5151] [ 778] [depth= 2] . ( 16 sec) [ -6447.6418] [ 777] [depth= 2] . ( 16 sec) [ -6447.6038] [ 777] [depth= 1] . ( 17 sec) [ -6447.0339] [ 777] [depth= 1] . ( 18 sec) [ -6432.7124] [Branch lengths ] . ( 18 sec) [ -6430.3969] [GTR parameters ] . ( 18 sec) [ -6430.1431] [Alpha ][ 0.542264] . ( 19 sec) [ -6427.4915] [ 775] [depth= 1] . ( 19 sec) [ -6403.8089] [ 758] [depth= 8] . ( 19 sec) [ -6403.7805] [ 758] [depth= 4] . ( 20 sec) [ -6403.6791] [ 758] [depth= 1] . ( 20 sec) [ -6391.3094] [ 756] [depth= 2] . ( 21 sec) [ -6387.6203] [ 755] [depth= 4] . ( 21 sec) [ -6387.5663] [ 755] [depth= 5] . ( 21 sec) [ -6386.6537] [ 755] [depth= 1] . ( 22 sec) [ -6377.1887] [ 755] [depth= 5] . ( 23 sec) [ -6368.3109] [ 751] [depth= 5] . ( 25 sec) [ -6355.8544] [ 749] [depth= 3] . ( 25 sec) [ -6355.8295] [ 749] [depth= 4] . ( 26 sec) [ -6337.6152] [ 745] [depth= 2] . ( 28 sec) [ -6327.2769] [ 738] [depth= 2] . ( 28 sec) [ -6276.1688] [ 724] [depth= 10] . ( 28 sec) [ -6235.3146] [ 698] [depth= 8] . ( 29 sec) [ -6230.1170] [ 699] [depth= 1] . ( 31 sec) [ -6223.2474] [ 697] [depth= 1] . ( 31 sec) [ -6213.7477] [ 695] [depth= 6] . ( 31 sec) [ -6209.7446] [ 694] [depth= 1] . ( 33 sec) [ -6207.7352] [ 694] [depth= 2] . ( 33 sec) [ -6207.6559] [ 694] [depth= 4] . ( 33 sec) [ -6207.4638] [ 694] [depth= 1] . ( 33 sec) [ -6200.2967] [ 691] [depth= 2] . ( 33 sec) [ -6199.3443] [ 691] [depth= 2] . ( 34 sec) [ -6199.3055] [ 691] [depth= 3] . ( 34 sec) [ -6198.0742] [ 695] [depth= 2] . ( 35 sec) [ -6196.0191] [ 695] [depth= 1] . ( 35 sec) [ -6196.0017] [ 695] [depth= 4] . ( 38 sec) [ -6195.5917] [ 695] [depth= 1] . ( 41 sec) [ -6189.0686] [ 693] [depth= 3] . ( 41 sec) [ -6178.8803] [ 691] [depth= 1] . ( 44 sec) [ -6178.3582] [ 691] [depth= 1] . ( 44 sec) [ -6178.2708] [ 691] [depth= 1] . ( 48 sec) [ -6174.6540] [Branch lengths ] . ( 49 sec) [ -6172.6539] [GTR parameters ] . ( 49 sec) [ -6166.0098] [Alpha ][ 0.917635] . ( 49 sec) [ -6165.6587] [ 691] [depth= 1] . ( 86 sec) [ -6165.4825] [Branch lengths ] . ( 87 sec) [ -6165.4655] [GTR parameters ] . ( 87 sec) [ -6165.4636] [Alpha ][ 0.927313] . ( 140 sec) [ -6165.4626] [Branch lengths ] . ( 140 sec) [ -6165.4626] [Topology ] . ( 141 sec) [ -6165.4626] [Topology ] . ( 142 sec) [ -6165.4626] [GTR parameters ] . ( 142 sec) [ -6165.4626] [Alpha ][ 0.927313] . Checking for NNIs, optimizing five branches... . ( 150 sec) [ -6165.3961] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.396150. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -12385.5698] [GTR parameters ] . ( 3 sec) [ -12249.0066] [Alpha ][ 0.500960] . ( 3 sec) [ -11811.0956] [ 1219] [depth= 7] . ( 3 sec) [ -11462.1632] [ 1183] [depth= 11] . ( 3 sec) [ -11447.6672] [ 1179] [depth= 5] . ( 3 sec) [ -11439.9463] [ 1179] [depth= 1] . ( 3 sec) [ -11432.3824] [ 1179] [depth= 1] . ( 3 sec) [ -11428.6568] [ 1179] [depth= 1] . ( 4 sec) [ -11379.9240] [ 1173] [depth= 10] . ( 4 sec) [ -11371.4104] [ 1173] [depth= 1] . ( 4 sec) [ -11367.3726] [ 1172] [depth= 5] . ( 4 sec) [ -11343.5118] [ 1172] [depth= 1] . ( 4 sec) [ -11263.7311] [ 1153] [depth= 13] . ( 4 sec) [ -11254.7457] [ 1151] [depth= 1] . ( 4 sec) [ -11236.8652] [ 1150] [depth= 15] . ( 4 sec) [ -11198.1398] [ 1136] [depth= 16] . ( 4 sec) [ -10755.2506] [ 1136] [depth= 1] . ( 4 sec) [ -10702.7947] [ 1127] [depth= 4] . ( 4 sec) [ -10664.2620] [ 1128] [depth= 1] . ( 4 sec) [ -10631.9814] [ 1117] [depth= 3] . ( 4 sec) [ -10594.0029] [ 1111] [depth= 14] . ( 5 sec) [ -10525.3743] [ 1107] [depth= 9] . ( 5 sec) [ -10200.7643] [ 1104] [depth= 6] . ( 5 sec) [ -9989.8728] [ 1082] [depth= 10] . ( 5 sec) [ -9960.8713] [ 1078] [depth= 1] . ( 5 sec) [ -9952.6699] [ 1078] [depth= 1] . ( 5 sec) [ -9827.0502] [ 1053] [depth= 11] . ( 5 sec) [ -9822.3519] [ 1053] [depth= 12] . ( 5 sec) [ -9728.1348] [ 1054] [depth= 1] . ( 5 sec) [ -9616.6864] [ 1045] [depth= 14] . ( 5 sec) [ -9613.2122] [ 1045] [depth= 3] . ( 5 sec) [ -9550.8240] [ 1035] [depth= 13] . ( 5 sec) [ -9482.0561] [ 1024] [depth= 9] . ( 5 sec) [ -9482.0095] [ 1024] [depth= 1] . ( 6 sec) [ -9435.3579] [ 1019] [depth= 2] . ( 6 sec) [ -9435.1401] [ 1021] [depth= 13] . ( 6 sec) [ -9420.2783] [ 1018] [depth= 10] . ( 6 sec) [ -9416.9440] [ 1018] [depth= 1] . ( 6 sec) [ -9416.8818] [ 1018] [depth= 1] . ( 6 sec) [ -9413.7767] [ 1020] [depth= 15] . ( 6 sec) [ -9124.2402] [ 990] [depth= 10] . ( 7 sec) [ -9117.3508] [ 988] [depth= 2] . ( 7 sec) [ -9083.2321] [ 986] [depth= 6] . ( 7 sec) [ -9033.2626] [ 959] [depth= 4] . ( 7 sec) [ -9020.4976] [ 958] [depth= 3] . ( 7 sec) [ -8965.1558] [ 958] [depth= 2] . ( 7 sec) [ -8915.3587] [ 952] [depth= 6] . ( 7 sec) [ -8787.7809] [ 935] [depth= 5] . ( 7 sec) [ -8778.4229] [ 935] [depth= 4] . ( 7 sec) [ -8602.9276] [ 935] [depth= 5] . ( 7 sec) [ -7861.4587] [ 935] [depth= 1] . ( 8 sec) [ -7805.5286] [ 913] [depth= 6] . ( 8 sec) [ -7709.0797] [ 914] [depth= 3] . ( 8 sec) [ -7708.6206] [ 914] [depth= 6] . ( 8 sec) [ -7706.1640] [ 914] [depth= 1] . ( 8 sec) [ -7675.2093] [ 911] [depth= 8] . ( 8 sec) [ -7671.9582] [ 910] [depth= 2] . ( 8 sec) [ -7623.6541] [ 902] [depth= 2] . ( 8 sec) [ -7603.9217] [ 896] [depth= 4] . ( 8 sec) [ -7601.1456] [ 897] [depth= 4] . ( 8 sec) [ -7481.7380] [ 867] [depth= 5] . ( 8 sec) [ -7463.9472] [ 868] [depth= 3] . ( 8 sec) [ -7444.6847] [ 867] [depth= 1] . ( 9 sec) [ -7433.9965] [ 866] [depth= 1] . ( 9 sec) [ -7425.9558] [ 865] [depth= 5] . ( 9 sec) [ -7403.7520] [ 856] [depth= 1] . ( 9 sec) [ -7400.4968] [ 857] [depth= 1] . ( 9 sec) [ -7395.0193] [ 856] [depth= 2] . ( 9 sec) [ -7388.6274] [ 856] [depth= 1] . ( 9 sec) [ -7361.2403] [ 858] [depth= 9] . ( 9 sec) [ -7348.5583] [ 853] [depth= 2] . ( 10 sec) [ -7029.3462] [ 857] [depth= 9] . ( 10 sec) [ -6993.2938] [ 853] [depth= 7] . ( 10 sec) [ -6991.8571] [ 852] [depth= 1] . ( 10 sec) [ -6983.3571] [ 852] [depth= 2] . ( 10 sec) [ -6974.4167] [ 829] [depth= 13] . ( 10 sec) [ -6965.1541] [ 826] [depth= 4] . ( 10 sec) [ -6951.9215] [ 824] [depth= 1] . ( 10 sec) [ -6949.3414] [ 823] [depth= 2] . ( 11 sec) [ -6942.2454] [ 828] [depth= 9] . ( 12 sec) [ -6910.0465] [ 821] [depth= 1] . ( 12 sec) [ -6851.8924] [ 809] [depth= 11] . ( 12 sec) [ -6851.2622] [ 809] [depth= 1] . ( 12 sec) [ -6826.0918] [ 804] [depth= 2] . ( 13 sec) [ -6820.1662] [ 802] [depth= 1] . ( 13 sec) [ -6819.9723] [ 802] [depth= 1] . ( 13 sec) [ -6778.8834] [ 797] [depth= 7] . ( 13 sec) [ -6760.3706] [ 796] [depth= 1] . ( 13 sec) [ -6737.8742] [ 793] [depth= 2] . ( 13 sec) [ -6668.1215] [ 779] [depth= 5] . ( 13 sec) [ -6662.1934] [ 779] [depth= 1] . ( 14 sec) [ -6646.7827] [ 778] [depth= 4] . ( 14 sec) [ -6591.7562] [ 769] [depth= 7] . ( 14 sec) [ -6586.4628] [ 769] [depth= 1] . ( 14 sec) [ -6537.9661] [ 761] [depth= 9] . ( 15 sec) [ -6537.9267] [ 761] [depth= 1] . ( 15 sec) [ -6526.5035] [ 761] [depth= 1] . ( 15 sec) [ -6512.5341] [ 758] [depth= 4] . ( 15 sec) [ -6511.8426] [ 758] [depth= 1] . ( 15 sec) [ -6502.6370] [ 754] [depth= 4] . ( 15 sec) [ -6499.2528] [ 751] [depth= 4] . ( 15 sec) [ -6489.8192] [ 749] [depth= 3] . ( 16 sec) [ -6466.7100] [ 749] [depth= 11] . ( 16 sec) [ -6466.5011] [ 749] [depth= 3] . ( 16 sec) [ -6455.5342] [ 747] [depth= 3] . ( 16 sec) [ -6396.4782] [ 733] [depth= 1] . ( 16 sec) [ -6393.7432] [ 735] [depth= 1] . ( 16 sec) [ -6385.3986] [ 734] [depth= 1] . ( 16 sec) [ -6384.8405] [ 734] [depth= 1] . ( 17 sec) [ -6384.2853] [ 734] [depth= 1] . ( 17 sec) [ -6360.9564] [ 729] [depth= 9] . ( 17 sec) [ -6355.9477] [ 728] [depth= 4] . ( 17 sec) [ -6354.0992] [ 728] [depth= 2] . ( 18 sec) [ -6333.5190] [Branch lengths ] . ( 19 sec) [ -6327.3320] [GTR parameters ] . ( 19 sec) [ -6323.9188] [Alpha ][ 0.697186] . ( 19 sec) [ -6301.7867] [ 721] [depth= 1] . ( 19 sec) [ -6300.3607] [ 720] [depth= 2] . ( 20 sec) [ -6297.9213] [ 718] [depth= 1] . ( 22 sec) [ -6288.2644] [ 714] [depth= 2] . ( 23 sec) [ -6288.1912] [ 714] [depth= 1] . ( 26 sec) [ -6285.8085] [ 715] [depth= 2] . ( 27 sec) [ -6285.4446] [ 715] [depth= 1] . ( 28 sec) [ -6282.4339] [ 714] [depth= 3] . ( 29 sec) [ -6276.6913] [ 713] [depth= 2] . ( 31 sec) [ -6276.6042] [ 713] [depth= 1] . ( 32 sec) [ -6275.0670] [ 713] [depth= 3] . ( 34 sec) [ -6274.7306] [ 717] [depth= 1] . ( 34 sec) [ -6274.7135] [ 717] [depth= 1] . ( 35 sec) [ -6270.3068] [ 716] [depth= 2] . ( 35 sec) [ -6233.5984] [ 709] [depth= 2] . ( 35 sec) [ -6182.5648] [ 695] [depth= 1] . ( 36 sec) [ -6174.6814] [ 692] [depth= 1] . ( 36 sec) [ -6174.4884] [ 692] [depth= 1] . ( 39 sec) [ -6173.9328] [ 692] [depth= 1] . ( 39 sec) [ -6173.8796] [ 695] [depth= 3] . ( 40 sec) [ -6173.8052] [ 695] [depth= 1] . ( 43 sec) [ -6171.8933] [ 694] [depth= 1] . ( 43 sec) [ -6171.5741] [ 693] [depth= 2] . ( 46 sec) [ -6171.3907] [ 693] [depth= 1] . ( 50 sec) [ -6170.6385] [ 692] [depth= 1] . ( 51 sec) [ -6170.5846] [ 692] [depth= 1] . ( 53 sec) [ -6169.1800] [Branch lengths ] . ( 54 sec) [ -6169.1561] [GTR parameters ] . ( 54 sec) [ -6167.6517] [Alpha ][ 0.907403] . ( 55 sec) [ -6166.8865] [ 691] [depth= 1] . ( 71 sec) [ -6166.6311] [ 691] [depth= 1] . ( 74 sec) [ -6166.5461] [ 687] [depth= 1] . ( 92 sec) [ -6165.9957] [Branch lengths ] . ( 92 sec) [ -6165.9872] [GTR parameters ] . ( 93 sec) [ -6165.9750] [Alpha ][ 0.930795] . ( 130 sec) [ -6165.9664] [Branch lengths ] . ( 181 sec) [ -6165.9663] [Branch lengths ] . ( 181 sec) [ -6165.9663] [Topology ] . ( 183 sec) [ -6165.9663] [Topology ] . ( 183 sec) [ -6165.9662] [GTR parameters ] . ( 183 sec) [ -6165.9662] [Alpha ][ 0.932032] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6165.966179. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -6200.7052] [GTR parameters ] . ( 2 sec) [ -6200.4585] [Alpha ][ 0.888648] . ( 2 sec) [ -6200.4585] [Topology ] . ( 3 sec) [ -6182.7216] [Topology ] . ( 5 sec) [ -6179.1097] [Topology ] . ( 6 sec) [ -6177.1327] [Topology ] . ( 7 sec) [ -6176.7462] [Topology ] . ( 9 sec) [ -6176.4431] [Topology ] . ( 10 sec) [ -6175.2148] [Topology ] . ( 11 sec) [ -6172.8305] [Topology ] . ( 13 sec) [ -6171.2354] [Topology ] . ( 14 sec) [ -6171.1404] [Topology ] . Checking for NNIs, optimizing five branches... . ( 23 sec) [ -6170.6119] [Topology ] . ( 24 sec) [ -6170.5804] [GTR parameters ] . ( 24 sec) [ -6170.5599] [Alpha ][ 0.918247] . ( 24 sec) [ -6170.5599] [Topology ] . ( 25 sec) [ -6170.5479] [Topology ] . ( 27 sec) [ -6170.5456] [Topology ] . ( 28 sec) [ -6170.5450] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -6170.4837] [Topology ] . ( 37 sec) [ -6170.4754] [GTR parameters ] . ( 37 sec) [ -6170.4727] [Alpha ][ 0.929672] . ( 37 sec) [ -6170.4727] [Topology ] . ( 38 sec) [ -6170.4723] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -6170.4723] [GTR parameters ] . ( 48 sec) [ -6170.4723] [Alpha ][ 0.929672] . ( 48 sec) [ -6170.4723] [Topology ] . ( 49 sec) [ -6170.4722] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 68 sec) [ -6200.7052] [GTR parameters ] . ( 68 sec) [ -6200.4585] [Alpha ][ 0.888648] . ( 69 sec) [ -6195.9714] [ 694] [depth= 1] . ( 69 sec) [ -6194.9058] [ 694] [depth= 2] . ( 69 sec) [ -6194.2719] [ 694] [depth= 1] . ( 69 sec) [ -6191.7026] [ 689] [depth= 2] . ( 70 sec) [ -6191.6456] [ 689] [depth= 1] . ( 70 sec) [ -6191.1332] [ 689] [depth= 1] . ( 71 sec) [ -6187.2019] [ 688] [depth= 1] . ( 71 sec) [ -6186.5973] [ 688] [depth= 1] . ( 71 sec) [ -6186.5564] [ 688] [depth= 1] . ( 71 sec) [ -6186.4915] [ 688] [depth= 1] . ( 72 sec) [ -6186.4566] [ 688] [depth= 1] . ( 72 sec) [ -6186.2611] [ 688] [depth= 1] . ( 73 sec) [ -6186.0197] [ 688] [depth= 1] . ( 73 sec) [ -6186.0009] [ 688] [depth= 1] . ( 75 sec) [ -6185.2512] [ 688] [depth= 1] . ( 75 sec) [ -6185.2308] [ 688] [depth= 1] . ( 75 sec) [ -6185.2025] [ 688] [depth= 1] . ( 76 sec) [ -6185.1748] [ 688] [depth= 1] . ( 76 sec) [ -6185.0588] [ 688] [depth= 1] . ( 76 sec) [ -6184.9805] [ 688] [depth= 1] . ( 76 sec) [ -6183.1945] [ 688] [depth= 1] . ( 77 sec) [ -6182.9011] [ 688] [depth= 1] . ( 77 sec) [ -6179.7585] [ 688] [depth= 1] . ( 78 sec) [ -6178.7250] [ 688] [depth= 1] . ( 78 sec) [ -6178.6783] [ 688] [depth= 1] . ( 81 sec) [ -6178.6440] [ 688] [depth= 1] . ( 88 sec) [ -6178.6081] [ 688] [depth= 1] . ( 88 sec) [ -6177.9620] [ 688] [depth= 1] . ( 88 sec) [ -6177.8896] [ 688] [depth= 1] . ( 88 sec) [ -6177.2200] [ 688] [depth= 1] . ( 88 sec) [ -6171.3743] [ 687] [depth= 2] . ( 89 sec) [ -6171.0396] [ 687] [depth= 3] . ( 89 sec) [ -6170.9276] [ 687] [depth= 3] . ( 89 sec) [ -6170.9170] [ 687] [depth= 2] . ( 90 sec) [ -6170.8169] [ 687] [depth= 3] . ( 90 sec) [ -6170.7633] [ 687] [depth= 2] . ( 91 sec) [ -6170.7197] [ 687] [depth= 1] . ( 91 sec) [ -6170.6773] [ 687] [depth= 2] . ( 95 sec) [ -6165.5609] [Branch lengths ] . ( 96 sec) [ -6165.5176] [GTR parameters ] . ( 96 sec) [ -6165.4624] [Alpha ][ 0.937895] . ( 132 sec) [ -6165.3852] [Branch lengths ] . ( 184 sec) [ -6165.3848] [Branch lengths ] . ( 184 sec) [ -6165.3848] [Topology ] . ( 185 sec) [ -6165.3848] [Topology ] . ( 186 sec) [ -6165.3846] [GTR parameters ] . ( 186 sec) [ -6165.3846] [Alpha ][ 0.938833] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6170.472231 . Log likelihood obtained after SPR moves : -6165.384557 . Log likelihood of the current tree: -6165.384557. . Printing the most likely tree in file 'nucleic_M2696_50x1472_2006.phy_phyml_tree.txt'... . Best log likelihood : -6165.384557 . Time used 0h3m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1097.06user 0.00system 18:25.22elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps