.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data7.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... . 288 patterns found. (out of a total of 500 sites) . 188 sites without polymorphism (37.60%). . [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)... . ( 1 sec) [ -11487.2818] [GTR parameters ] . ( 1 sec) [ -11356.0338] [Alpha ][ 0.500960] . ( 1 sec) [ -11209.2277] [ 1365] [depth= 4] . ( 1 sec) [ -9991.5285] [ 1331] [depth= 6] . ( 1 sec) [ -9273.9428] [ 1321] [depth= 4] . ( 1 sec) [ -9244.1761] [ 1321] [depth= 1] . ( 1 sec) [ -9224.6742] [ 1320] [depth= 2] . ( 1 sec) [ -9204.5896] [ 1319] [depth= 4] . ( 1 sec) [ -9062.9086] [ 1315] [depth= 1] . ( 2 sec) [ -8778.3530] [ 1308] [depth= 4] . ( 2 sec) [ -8676.2551] [ 1303] [depth= 10] . ( 2 sec) [ -8445.8314] [ 1251] [depth= 16] . ( 2 sec) [ -8303.3015] [ 1224] [depth= 13] . ( 2 sec) [ -8283.0037] [ 1221] [depth= 4] . ( 2 sec) [ -8281.8260] [ 1221] [depth= 2] . ( 2 sec) [ -8275.4111] [ 1208] [depth= 2] . ( 2 sec) [ -8270.3744] [ 1208] [depth= 2] . ( 2 sec) [ -8210.1020] [ 1206] [depth= 12] . ( 2 sec) [ -8093.7732] [ 1206] [depth= 2] . ( 2 sec) [ -7851.5326] [ 1170] [depth= 12] . ( 2 sec) [ -7797.9756] [ 1137] [depth= 13] . ( 2 sec) [ -7756.7046] [ 1137] [depth= 1] . ( 2 sec) [ -6868.4896] [ 1121] [depth= 16] . ( 2 sec) [ -6804.0431] [ 1119] [depth= 2] . ( 2 sec) [ -6756.0068] [ 1111] [depth= 3] . ( 2 sec) [ -6708.0213] [ 1107] [depth= 11] . ( 2 sec) [ -6544.7595] [ 1066] [depth= 8] . ( 2 sec) [ -6449.7507] [ 1064] [depth= 2] . ( 2 sec) [ -6382.2708] [ 1035] [depth= 1] . ( 2 sec) [ -6347.6116] [ 1032] [depth= 9] . ( 2 sec) [ -6335.1927] [ 1031] [depth= 1] . ( 2 sec) [ -6314.0952] [ 1023] [depth= 1] . ( 2 sec) [ -6253.2854] [ 1015] [depth= 7] . ( 2 sec) [ -6206.5790] [ 1009] [depth= 5] . ( 2 sec) [ -6097.0624] [ 985] [depth= 12] . ( 2 sec) [ -5982.0083] [ 963] [depth= 1] . ( 3 sec) [ -5785.9014] [ 935] [depth= 10] . ( 3 sec) [ -5688.3411] [ 928] [depth= 8] . ( 3 sec) [ -5687.5814] [ 927] [depth= 2] . ( 3 sec) [ -5656.6470] [ 925] [depth= 8] . ( 3 sec) [ -5555.9219] [ 904] [depth= 5] . ( 3 sec) [ -5552.8295] [ 905] [depth= 7] . ( 3 sec) [ -5533.1008] [ 895] [depth= 1] . ( 3 sec) [ -5479.9296] [ 888] [depth= 3] . ( 3 sec) [ -5450.2687] [ 889] [depth= 1] . ( 3 sec) [ -5287.8591] [ 853] [depth= 5] . ( 3 sec) [ -5230.3963] [ 885] [depth= 7] . ( 3 sec) [ -5229.3395] [ 882] [depth= 7] . ( 3 sec) [ -5204.0620] [ 879] [depth= 3] . ( 3 sec) [ -5185.4839] [ 869] [depth= 8] . ( 3 sec) [ -5131.7015] [ 852] [depth= 1] . ( 3 sec) [ -5111.6829] [ 849] [depth= 4] . ( 3 sec) [ -5034.4889] [ 818] [depth= 1] . ( 3 sec) [ -5027.1506] [ 815] [depth= 3] . ( 3 sec) [ -4991.7775] [ 806] [depth= 3] . ( 3 sec) [ -4952.2428] [ 801] [depth= 8] . ( 3 sec) [ -4932.1435] [ 796] [depth= 1] . ( 3 sec) [ -4906.3293] [ 792] [depth= 1] . ( 3 sec) [ -4855.9044] [ 785] [depth= 2] . ( 3 sec) [ -4766.7942] [ 762] [depth= 1] . ( 3 sec) [ -4747.9250] [ 761] [depth= 3] . ( 3 sec) [ -4702.9646] [ 758] [depth= 1] . ( 4 sec) [ -4682.3448] [ 752] [depth= 2] . ( 4 sec) [ -4672.5872] [ 750] [depth= 1] . ( 4 sec) [ -4650.5088] [ 739] [depth= 4] . ( 4 sec) [ -4640.0108] [ 734] [depth= 4] . ( 4 sec) [ -4638.7301] [ 734] [depth= 1] . ( 4 sec) [ -4618.0183] [ 736] [depth= 2] . ( 4 sec) [ -4616.5069] [ 736] [depth= 2] . ( 4 sec) [ -4616.0080] [ 736] [depth= 1] . ( 4 sec) [ -4609.9888] [ 733] [depth= 2] . ( 4 sec) [ -4600.4053] [ 732] [depth= 1] . ( 4 sec) [ -4594.3151] [ 730] [depth= 1] . ( 4 sec) [ -4594.1654] [ 731] [depth= 1] . ( 5 sec) [ -4532.6533] [Branch lengths ] . ( 5 sec) [ -4531.9904] [GTR parameters ] . ( 5 sec) [ -4518.9808] [Alpha ][ 0.854041] . ( 5 sec) [ -4423.2299] [ 736] [depth= 1] . ( 5 sec) [ -4422.5093] [ 735] [depth= 1] . ( 5 sec) [ -4397.4080] [ 733] [depth= 2] . ( 5 sec) [ -4392.7855] [ 728] [depth= 1] . ( 5 sec) [ -4386.4377] [ 726] [depth= 1] . ( 5 sec) [ -4359.4438] [ 720] [depth= 2] . ( 6 sec) [ -4354.9822] [ 718] [depth= 1] . ( 6 sec) [ -4338.2288] [ 709] [depth= 1] . ( 6 sec) [ -4336.7729] [ 709] [depth= 1] . ( 6 sec) [ -4333.3350] [ 707] [depth= 1] . ( 6 sec) [ -4332.0422] [ 706] [depth= 2] . ( 6 sec) [ -4326.4815] [ 704] [depth= 1] . ( 6 sec) [ -4325.2868] [ 704] [depth= 1] . ( 7 sec) [ -4318.2866] [ 701] [depth= 2] . ( 7 sec) [ -4317.0569] [ 701] [depth= 1] . ( 7 sec) [ -4316.8598] [ 703] [depth= 4] . ( 8 sec) [ -4316.8071] [ 704] [depth= 1] . ( 9 sec) [ -4316.5516] [ 703] [depth= 2] . ( 9 sec) [ -4312.9979] [Branch lengths ] . ( 9 sec) [ -4312.1677] [GTR parameters ] . ( 9 sec) [ -4310.9266] [Alpha ][ 1.039357] . ( 9 sec) [ -4310.7557] [ 703] [depth= 1] . ( 10 sec) [ -4310.0079] [ 705] [depth= 2] . ( 10 sec) [ -4309.4665] [ 705] [depth= 1] . ( 10 sec) [ -4308.9138] [ 705] [depth= 1] . ( 10 sec) [ -4308.4917] [ 703] [depth= 1] . ( 14 sec) [ -4308.3700] [ 703] [depth= 1] . ( 14 sec) [ -4307.8681] [Branch lengths ] . ( 14 sec) [ -4307.8353] [GTR parameters ] . ( 14 sec) [ -4307.8336] [Alpha ][ 1.047455] . ( 20 sec) [ -4307.8001] [Branch lengths ] . ( 38 sec) [ -4307.7985] [Branch lengths ] . ( 38 sec) [ -4307.7985] [Topology ] . ( 38 sec) [ -4307.7984] [Topology ] . ( 39 sec) [ -4307.7983] [GTR parameters ] . ( 39 sec) [ -4307.7983] [Alpha ][ 1.047455] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4307.798287. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11228.2803] [GTR parameters ] . ( 1 sec) [ -11110.8017] [Alpha ][ 0.500960] . ( 1 sec) [ -10911.8212] [ 1342] [depth= 3] . ( 1 sec) [ -10622.1295] [ 1308] [depth= 3] . ( 1 sec) [ -10590.3840] [ 1305] [depth= 1] . ( 1 sec) [ -10316.1267] [ 1303] [depth= 5] . ( 1 sec) [ -10294.6118] [ 1299] [depth= 2] . ( 1 sec) [ -10292.7889] [ 1299] [depth= 2] . ( 1 sec) [ -10263.3649] [ 1293] [depth= 1] . ( 1 sec) [ -10224.6715] [ 1291] [depth= 5] . ( 1 sec) [ -10102.4270] [ 1256] [depth= 1] . ( 1 sec) [ -10090.8168] [ 1255] [depth= 1] . ( 1 sec) [ -9986.6147] [ 1232] [depth= 3] . ( 1 sec) [ -9955.8487] [ 1232] [depth= 2] . ( 1 sec) [ -9955.0941] [ 1231] [depth= 1] . ( 2 sec) [ -9938.3247] [ 1231] [depth= 3] . ( 2 sec) [ -8826.6285] [ 1181] [depth= 20] . ( 2 sec) [ -8816.6052] [ 1176] [depth= 5] . ( 2 sec) [ -8437.4573] [ 1149] [depth= 10] . ( 2 sec) [ -8375.2243] [ 1131] [depth= 2] . ( 2 sec) [ -8351.3368] [ 1130] [depth= 6] . ( 2 sec) [ -8231.4528] [ 1101] [depth= 1] . ( 2 sec) [ -8164.9863] [ 1084] [depth= 10] . ( 2 sec) [ -8063.8111] [ 1072] [depth= 3] . ( 2 sec) [ -8048.6752] [ 1052] [depth= 2] . ( 2 sec) [ -7984.2453] [ 1052] [depth= 1] . ( 2 sec) [ -7961.9404] [ 1049] [depth= 4] . ( 2 sec) [ -7934.0648] [ 1044] [depth= 2] . ( 2 sec) [ -7915.4285] [ 1040] [depth= 1] . ( 2 sec) [ -7770.5495] [ 994] [depth= 9] . ( 2 sec) [ -7258.3496] [ 981] [depth= 6] . ( 2 sec) [ -7080.0665] [ 973] [depth= 5] . ( 2 sec) [ -6931.4298] [ 962] [depth= 8] . ( 2 sec) [ -6891.8033] [ 962] [depth= 5] . ( 2 sec) [ -6889.4612] [ 965] [depth= 1] . ( 2 sec) [ -6813.5299] [ 948] [depth= 2] . ( 2 sec) [ -6745.6442] [ 933] [depth= 7] . ( 2 sec) [ -6681.9114] [ 932] [depth= 5] . ( 2 sec) [ -5696.0436] [ 931] [depth= 1] . ( 2 sec) [ -5685.4811] [ 935] [depth= 1] . ( 2 sec) [ -5415.2541] [ 931] [depth= 3] . ( 2 sec) [ -5284.0731] [ 898] [depth= 8] . ( 3 sec) [ -5200.0489] [ 875] [depth= 6] . ( 3 sec) [ -5096.6769] [ 850] [depth= 4] . ( 3 sec) [ -5021.6268] [ 848] [depth= 5] . ( 3 sec) [ -4972.2143] [ 834] [depth= 7] . ( 3 sec) [ -4962.0953] [ 832] [depth= 1] . ( 3 sec) [ -4919.0569] [ 834] [depth= 1] . ( 3 sec) [ -4899.5027] [ 828] [depth= 1] . ( 3 sec) [ -4894.0233] [ 820] [depth= 6] . ( 3 sec) [ -4855.6696] [ 812] [depth= 5] . ( 3 sec) [ -4852.7125] [ 811] [depth= 1] . ( 3 sec) [ -4819.6102] [ 798] [depth= 3] . ( 3 sec) [ -4815.2226] [ 798] [depth= 2] . ( 3 sec) [ -4810.9127] [ 796] [depth= 4] . ( 3 sec) [ -4780.0233] [ 790] [depth= 1] . ( 3 sec) [ -4766.6077] [ 775] [depth= 5] . ( 3 sec) [ -4766.5970] [ 775] [depth= 2] . ( 3 sec) [ -4730.2495] [ 763] [depth= 3] . ( 3 sec) [ -4729.6357] [ 763] [depth= 2] . ( 3 sec) [ -4727.8087] [ 763] [depth= 1] . ( 3 sec) [ -4654.4524] [ 761] [depth= 3] . ( 3 sec) [ -4642.4354] [ 758] [depth= 3] . ( 4 sec) [ -4635.9123] [ 758] [depth= 1] . ( 4 sec) [ -4635.4044] [ 757] [depth= 2] . ( 4 sec) [ -4564.6465] [ 757] [depth= 1] . ( 4 sec) [ -4563.7353] [ 758] [depth= 1] . ( 4 sec) [ -4563.5198] [ 762] [depth= 1] . ( 4 sec) [ -4563.4857] [ 762] [depth= 2] . ( 4 sec) [ -4563.0265] [ 764] [depth= 1] . ( 4 sec) [ -4559.6927] [ 763] [depth= 1] . ( 4 sec) [ -4452.1745] [ 725] [depth= 2] . ( 4 sec) [ -4450.5053] [ 725] [depth= 2] . ( 4 sec) [ -4444.1610] [ 721] [depth= 1] . ( 4 sec) [ -4443.9140] [ 724] [depth= 2] . ( 4 sec) [ -4429.5449] [ 715] [depth= 6] . ( 4 sec) [ -4429.1677] [ 716] [depth= 1] . ( 5 sec) [ -4385.2202] [Branch lengths ] . ( 5 sec) [ -4384.9382] [GTR parameters ] . ( 5 sec) [ -4369.3577] [Alpha ][ 0.937176] . ( 5 sec) [ -4367.7486] [ 715] [depth= 2] . ( 5 sec) [ -4359.6354] [ 719] [depth= 2] . ( 5 sec) [ -4359.6108] [ 719] [depth= 1] . ( 5 sec) [ -4359.5523] [ 719] [depth= 1] . ( 5 sec) [ -4352.2948] [ 715] [depth= 1] . ( 6 sec) [ -4341.4413] [ 716] [depth= 1] . ( 6 sec) [ -4340.7295] [ 715] [depth= 1] . ( 6 sec) [ -4330.9778] [ 713] [depth= 1] . ( 7 sec) [ -4329.6291] [ 713] [depth= 2] . ( 7 sec) [ -4328.6082] [ 706] [depth= 5] . ( 7 sec) [ -4321.2081] [ 707] [depth= 5] . ( 8 sec) [ -4313.0637] [ 704] [depth= 1] . ( 8 sec) [ -4310.3288] [ 703] [depth= 1] . ( 8 sec) [ -4310.2208] [ 703] [depth= 1] . ( 9 sec) [ -4309.1770] [Branch lengths ] . ( 9 sec) [ -4308.8467] [GTR parameters ] . ( 9 sec) [ -4308.5039] [Alpha ][ 1.041600] . ( 15 sec) [ -4308.4811] [Branch lengths ] . ( 34 sec) [ -4308.3837] [Branch lengths ] . ( 34 sec) [ -4308.3837] [Topology ] . ( 34 sec) [ -4307.9941] [Topology ] . ( 35 sec) [ -4307.8659] [Topology ] . ( 36 sec) [ -4307.8230] [Topology ] . ( 36 sec) [ -4307.8091] [Topology ] . ( 37 sec) [ -4307.8044] [Topology ] . ( 37 sec) [ -4307.8029] [Topology ] . ( 37 sec) [ -4307.8003] [GTR parameters ] . ( 38 sec) [ -4307.7993] [Alpha ][ 1.047704] . ( 38 sec) [ -4307.7993] [Topology ] . ( 38 sec) [ -4307.7987] [Topology ] . ( 38 sec) [ -4307.7987] [GTR parameters ] . ( 38 sec) [ -4307.7987] [Alpha ][ 1.047704] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4307.798689. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12297.6957] [GTR parameters ] . ( 1 sec) [ -12173.2580] [Alpha ][ 0.500960] . ( 1 sec) [ -11920.5051] [ 1363] [depth= 1] . ( 1 sec) [ -11712.6970] [ 1325] [depth= 8] . ( 1 sec) [ -11190.8635] [ 1325] [depth= 3] . ( 1 sec) [ -11106.0254] [ 1324] [depth= 2] . ( 1 sec) [ -10941.6310] [ 1318] [depth= 8] . ( 1 sec) [ -10843.9601] [ 1318] [depth= 6] . ( 1 sec) [ -10701.0967] [ 1307] [depth= 15] . ( 1 sec) [ -10663.1088] [ 1306] [depth= 8] . ( 1 sec) [ -10545.3398] [ 1273] [depth= 1] . ( 1 sec) [ -10418.7985] [ 1256] [depth= 8] . ( 1 sec) [ -10359.0733] [ 1250] [depth= 11] . ( 1 sec) [ -10296.0021] [ 1227] [depth= 6] . ( 1 sec) [ -10212.3494] [ 1225] [depth= 2] . ( 1 sec) [ -9744.1329] [ 1210] [depth= 12] . ( 1 sec) [ -9706.7260] [ 1206] [depth= 2] . ( 1 sec) [ -9590.6328] [ 1206] [depth= 2] . ( 1 sec) [ -9399.5273] [ 1189] [depth= 1] . ( 1 sec) [ -8698.8066] [ 1177] [depth= 2] . ( 1 sec) [ -8662.6047] [ 1176] [depth= 7] . ( 1 sec) [ -8659.5943] [ 1181] [depth= 1] . ( 1 sec) [ -8561.8965] [ 1159] [depth= 6] . ( 1 sec) [ -8519.3476] [ 1159] [depth= 11] . ( 1 sec) [ -8279.2135] [ 1141] [depth= 1] . ( 1 sec) [ -8213.8330] [ 1134] [depth= 8] . ( 1 sec) [ -8122.4591] [ 1111] [depth= 2] . ( 1 sec) [ -8112.6181] [ 1094] [depth= 1] . ( 1 sec) [ -8062.6295] [ 1087] [depth= 5] . ( 1 sec) [ -8010.0586] [ 1085] [depth= 1] . ( 1 sec) [ -7956.7995] [ 1069] [depth= 11] . ( 1 sec) [ -7928.6474] [ 1070] [depth= 1] . ( 2 sec) [ -6268.8637] [ 1043] [depth= 5] . ( 2 sec) [ -6235.3168] [ 1037] [depth= 1] . ( 2 sec) [ -6028.7269] [ 1024] [depth= 7] . ( 2 sec) [ -6027.7043] [ 1022] [depth= 1] . ( 2 sec) [ -5992.0323] [ 1009] [depth= 11] . ( 2 sec) [ -5990.7750] [ 1008] [depth= 2] . ( 2 sec) [ -5858.6725] [ 1002] [depth= 3] . ( 2 sec) [ -5853.5432] [ 1002] [depth= 1] . ( 2 sec) [ -5817.1822] [ 986] [depth= 3] . ( 2 sec) [ -5815.4917] [ 989] [depth= 1] . ( 2 sec) [ -5809.1591] [ 985] [depth= 1] . ( 2 sec) [ -5745.1819] [ 961] [depth= 2] . ( 2 sec) [ -5549.1062] [ 927] [depth= 5] . ( 2 sec) [ -5536.3347] [ 922] [depth= 5] . ( 2 sec) [ -5499.1880] [ 922] [depth= 4] . ( 2 sec) [ -5270.2009] [ 887] [depth= 8] . ( 2 sec) [ -5270.1126] [ 887] [depth= 2] . ( 2 sec) [ -5229.4563] [ 879] [depth= 4] . ( 2 sec) [ -5221.9670] [ 879] [depth= 1] . ( 2 sec) [ -5212.1582] [ 879] [depth= 2] . ( 2 sec) [ -5207.2857] [ 876] [depth= 3] . ( 2 sec) [ -5202.3229] [ 875] [depth= 1] . ( 2 sec) [ -5184.6653] [ 875] [depth= 3] . ( 2 sec) [ -5059.1436] [ 859] [depth= 4] . ( 2 sec) [ -5055.5020] [ 859] [depth= 5] . ( 2 sec) [ -4973.2962] [ 836] [depth= 8] . ( 3 sec) [ -4972.0948] [ 835] [depth= 5] . ( 3 sec) [ -4925.7758] [ 840] [depth= 1] . ( 3 sec) [ -4893.9129] [ 825] [depth= 5] . ( 3 sec) [ -4872.5679] [ 820] [depth= 4] . ( 3 sec) [ -4848.8127] [ 810] [depth= 1] . ( 3 sec) [ -4848.5772] [ 810] [depth= 1] . ( 3 sec) [ -4834.1893] [ 814] [depth= 9] . ( 3 sec) [ -4832.4308] [ 811] [depth= 1] . ( 3 sec) [ -4776.0989] [ 808] [depth= 6] . ( 3 sec) [ -4759.6112] [ 808] [depth= 1] . ( 3 sec) [ -4739.2586] [ 801] [depth= 3] . ( 3 sec) [ -4697.5133] [ 795] [depth= 9] . ( 3 sec) [ -4692.2636] [ 793] [depth= 1] . ( 4 sec) [ -4692.0996] [ 793] [depth= 2] . ( 4 sec) [ -4666.3669] [ 786] [depth= 1] . ( 4 sec) [ -4664.1548] [ 786] [depth= 1] . ( 4 sec) [ -4658.5274] [ 785] [depth= 1] . ( 4 sec) [ -4658.1237] [ 785] [depth= 2] . ( 4 sec) [ -4627.6545] [ 776] [depth= 1] . ( 4 sec) [ -4623.7484] [ 773] [depth= 1] . ( 4 sec) [ -4623.0348] [ 771] [depth= 1] . ( 4 sec) [ -4622.3312] [ 769] [depth= 1] . ( 4 sec) [ -4607.6869] [Branch lengths ] . ( 5 sec) [ -4606.6611] [GTR parameters ] . ( 5 sec) [ -4597.7429] [Alpha ][ 0.778943] . ( 5 sec) [ -4563.1077] [ 769] [depth= 6] . ( 5 sec) [ -4556.5657] [ 767] [depth= 2] . ( 5 sec) [ -4541.3710] [ 761] [depth= 4] . ( 5 sec) [ -4501.7731] [ 743] [depth= 1] . ( 5 sec) [ -4485.8235] [ 743] [depth= 1] . ( 5 sec) [ -4485.5626] [ 744] [depth= 3] . ( 5 sec) [ -4477.3216] [ 748] [depth= 2] . ( 6 sec) [ -4470.5336] [ 747] [depth= 2] . ( 6 sec) [ -4469.2548] [ 746] [depth= 2] . ( 6 sec) [ -4458.2099] [ 743] [depth= 2] . ( 6 sec) [ -4458.1924] [ 743] [depth= 1] . ( 6 sec) [ -4434.1830] [ 733] [depth= 1] . ( 6 sec) [ -4429.6250] [ 730] [depth= 2] . ( 6 sec) [ -4422.5426] [ 728] [depth= 1] . ( 6 sec) [ -4420.2047] [ 730] [depth= 2] . ( 6 sec) [ -4419.2979] [ 730] [depth= 1] . ( 6 sec) [ -4418.3266] [ 728] [depth= 2] . ( 7 sec) [ -4416.8745] [ 728] [depth= 1] . ( 7 sec) [ -4334.1478] [ 714] [depth= 2] . ( 7 sec) [ -4326.7804] [ 701] [depth= 1] . ( 7 sec) [ -4325.9454] [ 703] [depth= 2] . ( 8 sec) [ -4325.8639] [ 705] [depth= 1] . ( 8 sec) [ -4320.1488] [Branch lengths ] . ( 9 sec) [ -4320.0283] [GTR parameters ] . ( 9 sec) [ -4317.4770] [Alpha ][ 1.029298] . ( 9 sec) [ -4317.2896] [ 702] [depth= 1] . ( 10 sec) [ -4314.3617] [ 700] [depth= 1] . ( 10 sec) [ -4313.8074] [ 703] [depth= 4] . ( 14 sec) [ -4310.2553] [Branch lengths ] . ( 14 sec) [ -4310.2243] [GTR parameters ] . ( 14 sec) [ -4310.2180] [Alpha ][ 1.044909] . ( 19 sec) [ -4308.2783] [Branch lengths ] . ( 23 sec) [ -4308.0511] [ 703] [depth= 1] . ( 27 sec) [ -4307.8981] [ 703] [depth= 1] . ( 37 sec) [ -4307.8048] [Branch lengths ] . ( 38 sec) [ -4307.7989] [GTR parameters ] . ( 38 sec) [ -4307.7987] [Alpha ][ 1.047625] . ( 38 sec) [ -4307.7987] [Topology ] . ( 39 sec) [ -4307.7984] [Topology ] . ( 39 sec) [ -4307.7984] [GTR parameters ] . ( 39 sec) [ -4307.7984] [Alpha ][ 1.047625] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4307.798373. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12480.0194] [GTR parameters ] . ( 1 sec) [ -12348.0626] [Alpha ][ 0.500960] . ( 1 sec) [ -12033.9643] [ 1345] [depth= 8] . ( 1 sec) [ -11069.2811] [ 1310] [depth= 9] . ( 1 sec) [ -9737.8159] [ 1302] [depth= 7] . ( 1 sec) [ -9536.8325] [ 1274] [depth= 1] . ( 1 sec) [ -8981.0856] [ 1268] [depth= 9] . ( 1 sec) [ -8948.1299] [ 1266] [depth= 3] . ( 1 sec) [ -8944.1033] [ 1266] [depth= 3] . ( 1 sec) [ -8910.8870] [ 1266] [depth= 2] . ( 1 sec) [ -8894.1526] [ 1266] [depth= 6] . ( 1 sec) [ -8892.7176] [ 1264] [depth= 10] . ( 1 sec) [ -8840.5847] [ 1264] [depth= 2] . ( 1 sec) [ -8586.0813] [ 1231] [depth= 3] . ( 1 sec) [ -8534.7034] [ 1225] [depth= 4] . ( 1 sec) [ -8526.6792] [ 1225] [depth= 1] . ( 1 sec) [ -8382.1186] [ 1195] [depth= 9] . ( 1 sec) [ -8287.3144] [ 1194] [depth= 2] . ( 2 sec) [ -8189.9429] [ 1163] [depth= 1] . ( 2 sec) [ -8073.0752] [ 1141] [depth= 11] . ( 2 sec) [ -8007.7569] [ 1135] [depth= 10] . ( 2 sec) [ -8002.8286] [ 1136] [depth= 4] . ( 2 sec) [ -7966.6521] [ 1129] [depth= 7] . ( 2 sec) [ -7950.9858] [ 1129] [depth= 1] . ( 2 sec) [ -7884.3683] [ 1123] [depth= 16] . ( 2 sec) [ -7751.6132] [ 1084] [depth= 7] . ( 2 sec) [ -7687.0190] [ 1075] [depth= 9] . ( 2 sec) [ -7373.1024] [ 1057] [depth= 7] . ( 2 sec) [ -7350.1142] [ 1048] [depth= 13] . ( 2 sec) [ -7331.3657] [ 1041] [depth= 10] . ( 2 sec) [ -6385.0076] [ 1028] [depth= 13] . ( 2 sec) [ -6384.3641] [ 1031] [depth= 12] . ( 2 sec) [ -6331.0533] [ 1027] [depth= 1] . ( 2 sec) [ -6324.7256] [ 1028] [depth= 1] . ( 2 sec) [ -6206.7155] [ 1027] [depth= 4] . ( 2 sec) [ -6191.6450] [ 1026] [depth= 2] . ( 2 sec) [ -6060.0916] [ 977] [depth= 1] . ( 2 sec) [ -6023.4127] [ 973] [depth= 1] . ( 2 sec) [ -5925.8010] [ 946] [depth= 6] . ( 2 sec) [ -5887.0722] [ 931] [depth= 2] . ( 2 sec) [ -5845.5700] [ 927] [depth= 8] . ( 2 sec) [ -5799.4357] [ 916] [depth= 7] . ( 3 sec) [ -5730.6749] [ 919] [depth= 2] . ( 3 sec) [ -5721.9247] [ 929] [depth= 3] . ( 3 sec) [ -5535.0508] [ 938] [depth= 9] . ( 3 sec) [ -5441.8969] [ 910] [depth= 6] . ( 3 sec) [ -5415.5978] [ 888] [depth= 9] . ( 3 sec) [ -5245.1850] [ 867] [depth= 2] . ( 3 sec) [ -5212.7121] [ 863] [depth= 7] . ( 3 sec) [ -5165.3410] [ 844] [depth= 8] . ( 3 sec) [ -5119.9488] [ 835] [depth= 3] . ( 3 sec) [ -5055.0828] [ 819] [depth= 7] . ( 3 sec) [ -5003.9291] [ 820] [depth= 3] . ( 3 sec) [ -5000.5133] [ 819] [depth= 1] . ( 3 sec) [ -4917.5297] [ 821] [depth= 3] . ( 3 sec) [ -4870.3751] [ 808] [depth= 3] . ( 3 sec) [ -4866.5550] [ 806] [depth= 1] . ( 3 sec) [ -4849.0460] [ 805] [depth= 4] . ( 3 sec) [ -4843.4638] [ 806] [depth= 3] . ( 3 sec) [ -4814.4686] [ 801] [depth= 2] . ( 3 sec) [ -4806.8753] [ 799] [depth= 2] . ( 3 sec) [ -4802.5154] [ 789] [depth= 7] . ( 3 sec) [ -4787.7693] [ 788] [depth= 1] . ( 3 sec) [ -4784.6873] [ 788] [depth= 1] . ( 3 sec) [ -4775.9767] [ 787] [depth= 4] . ( 4 sec) [ -4736.8558] [ 769] [depth= 4] . ( 4 sec) [ -4718.6107] [ 767] [depth= 1] . ( 4 sec) [ -4699.3339] [ 764] [depth= 1] . ( 4 sec) [ -4679.1283] [ 762] [depth= 1] . ( 4 sec) [ -4658.7758] [ 760] [depth= 4] . ( 4 sec) [ -4656.6741] [ 761] [depth= 1] . ( 4 sec) [ -4656.1577] [ 761] [depth= 1] . ( 4 sec) [ -4651.1215] [ 760] [depth= 3] . ( 4 sec) [ -4613.5638] [ 751] [depth= 3] . ( 4 sec) [ -4597.8975] [ 755] [depth= 2] . ( 4 sec) [ -4595.0218] [ 764] [depth= 3] . ( 4 sec) [ -4516.4127] [ 751] [depth= 3] . ( 4 sec) [ -4481.7653] [Branch lengths ] . ( 5 sec) [ -4481.1945] [GTR parameters ] . ( 5 sec) [ -4467.5687] [Alpha ][ 0.881912] . ( 5 sec) [ -4414.7788] [ 730] [depth= 3] . ( 5 sec) [ -4361.5417] [ 718] [depth= 1] . ( 5 sec) [ -4353.5705] [ 717] [depth= 1] . ( 5 sec) [ -4351.7853] [ 716] [depth= 1] . ( 6 sec) [ -4327.8757] [ 708] [depth= 1] . ( 6 sec) [ -4327.3453] [ 709] [depth= 1] . ( 6 sec) [ -4327.0354] [ 709] [depth= 1] . ( 6 sec) [ -4325.5306] [ 706] [depth= 1] . ( 6 sec) [ -4318.4460] [ 702] [depth= 1] . ( 7 sec) [ -4318.2854] [ 699] [depth= 1] . ( 8 sec) [ -4317.9429] [ 701] [depth= 1] . ( 9 sec) [ -4317.3621] [ 700] [depth= 1] . ( 9 sec) [ -4310.8878] [Branch lengths ] . ( 9 sec) [ -4310.2824] [GTR parameters ] . ( 9 sec) [ -4309.2863] [Alpha ][ 1.054866] . ( 13 sec) [ -4308.8054] [ 703] [depth= 4] . ( 14 sec) [ -4308.1571] [Branch lengths ] . ( 14 sec) [ -4308.1364] [GTR parameters ] . ( 14 sec) [ -4308.1353] [Alpha ][ 1.048987] . ( 17 sec) [ -4308.0910] [ 703] [depth= 1] . ( 18 sec) [ -4308.0763] [ 703] [depth= 1] . ( 19 sec) [ -4308.0365] [ 703] [depth= 1] . ( 20 sec) [ -4307.9469] [Branch lengths ] . ( 20 sec) [ -4307.9450] [GTR parameters ] . ( 20 sec) [ -4307.9450] [Alpha ][ 1.047289] . ( 21 sec) [ -4307.8610] [ 703] [depth= 1] . ( 38 sec) [ -4307.8024] [Branch lengths ] . ( 38 sec) [ -4307.8005] [GTR parameters ] . ( 38 sec) [ -4307.8005] [Alpha ][ 1.047289] . ( 38 sec) [ -4307.8005] [Topology ] . ( 38 sec) [ -4307.7985] [Topology ] . ( 39 sec) [ -4307.7984] [Topology ] . ( 39 sec) [ -4307.7984] [GTR parameters ] . ( 39 sec) [ -4307.7984] [Alpha ][ 1.047289] . ( 39 sec) [ -4307.7984] [Topology ] . ( 40 sec) [ -4307.7984] [Topology ] . ( 40 sec) [ -4307.7984] [GTR parameters ] . ( 40 sec) [ -4307.7984] [Alpha ][ 1.047289] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4307.798375. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11809.4258] [GTR parameters ] . ( 0 sec) [ -11684.0048] [Alpha ][ 0.500960] . ( 0 sec) [ -11330.6952] [ 1366] [depth= 6] . ( 0 sec) [ -11180.6872] [ 1329] [depth= 11] . ( 0 sec) [ -11150.8355] [ 1329] [depth= 2] . ( 0 sec) [ -11150.4486] [ 1329] [depth= 1] . ( 0 sec) [ -11078.3028] [ 1327] [depth= 4] . ( 0 sec) [ -10956.2227] [ 1327] [depth= 3] . ( 0 sec) [ -10869.7942] [ 1323] [depth= 6] . ( 0 sec) [ -10798.2778] [ 1328] [depth= 1] . ( 1 sec) [ -10611.0577] [ 1288] [depth= 2] . ( 1 sec) [ -10471.2356] [ 1257] [depth= 3] . ( 1 sec) [ -9586.3849] [ 1235] [depth= 6] . ( 1 sec) [ -9360.0886] [ 1201] [depth= 13] . ( 1 sec) [ -8931.0774] [ 1172] [depth= 12] . ( 1 sec) [ -8916.7301] [ 1167] [depth= 5] . ( 1 sec) [ -8865.8490] [ 1167] [depth= 1] . ( 1 sec) [ -8769.2765] [ 1167] [depth= 1] . ( 1 sec) [ -8758.9970] [ 1167] [depth= 2] . ( 1 sec) [ -8753.8578] [ 1165] [depth= 6] . ( 1 sec) [ -8703.4232] [ 1165] [depth= 1] . ( 1 sec) [ -8693.1882] [ 1163] [depth= 3] . ( 1 sec) [ -8669.6844] [ 1163] [depth= 8] . ( 1 sec) [ -8549.3101] [ 1138] [depth= 2] . ( 1 sec) [ -8446.2144] [ 1110] [depth= 7] . ( 1 sec) [ -8424.2709] [ 1104] [depth= 3] . ( 1 sec) [ -8409.0872] [ 1101] [depth= 6] . ( 1 sec) [ -8403.7368] [ 1091] [depth= 6] . ( 1 sec) [ -8223.7587] [ 1059] [depth= 4] . ( 1 sec) [ -8187.7768] [ 1058] [depth= 2] . ( 1 sec) [ -7836.8602] [ 1026] [depth= 13] . ( 1 sec) [ -7823.1705] [ 1024] [depth= 5] . ( 1 sec) [ -7749.8002] [ 1010] [depth= 5] . ( 1 sec) [ -7708.2916] [ 1003] [depth= 1] . ( 1 sec) [ -7589.9579] [ 983] [depth= 7] . ( 1 sec) [ -6929.7059] [ 969] [depth= 7] . ( 1 sec) [ -6896.8244] [ 982] [depth= 1] . ( 1 sec) [ -6822.0451] [ 968] [depth= 1] . ( 1 sec) [ -6818.7847] [ 966] [depth= 3] . ( 1 sec) [ -6809.4871] [ 961] [depth= 1] . ( 1 sec) [ -6752.6692] [ 947] [depth= 6] . ( 2 sec) [ -6734.7391] [ 943] [depth= 1] . ( 2 sec) [ -6601.5413] [ 914] [depth= 10] . ( 2 sec) [ -6560.0303] [ 913] [depth= 3] . ( 2 sec) [ -6476.3501] [ 884] [depth= 5] . ( 2 sec) [ -6469.1487] [ 884] [depth= 1] . ( 2 sec) [ -6462.1535] [ 886] [depth= 1] . ( 2 sec) [ -6423.8348] [ 881] [depth= 4] . ( 2 sec) [ -6298.6562] [ 851] [depth= 4] . ( 2 sec) [ -6268.9361] [ 840] [depth= 2] . ( 2 sec) [ -5032.3240] [ 840] [depth= 3] . ( 2 sec) [ -5009.7934] [ 840] [depth= 1] . ( 2 sec) [ -4971.5723] [ 840] [depth= 2] . ( 2 sec) [ -4946.7109] [ 847] [depth= 1] . ( 2 sec) [ -4911.8395] [ 858] [depth= 6] . ( 2 sec) [ -4894.2632] [ 848] [depth= 2] . ( 2 sec) [ -4856.4106] [ 840] [depth= 4] . ( 2 sec) [ -4839.7176] [ 833] [depth= 4] . ( 2 sec) [ -4812.7879] [ 816] [depth= 8] . ( 2 sec) [ -4807.3414] [ 816] [depth= 1] . ( 2 sec) [ -4794.4516] [ 815] [depth= 2] . ( 2 sec) [ -4777.6184] [ 812] [depth= 7] . ( 2 sec) [ -4679.6990] [ 786] [depth= 4] . ( 3 sec) [ -4665.9701] [ 781] [depth= 1] . ( 3 sec) [ -4664.4810] [ 779] [depth= 2] . ( 3 sec) [ -4582.1463] [ 753] [depth= 4] . ( 3 sec) [ -4579.3950] [ 753] [depth= 1] . ( 3 sec) [ -4554.0669] [ 753] [depth= 4] . ( 3 sec) [ -4551.1543] [ 753] [depth= 6] . ( 3 sec) [ -4511.7463] [ 743] [depth= 2] . ( 3 sec) [ -4506.2933] [ 741] [depth= 1] . ( 3 sec) [ -4504.8335] [ 740] [depth= 1] . ( 3 sec) [ -4500.7567] [ 740] [depth= 4] . ( 3 sec) [ -4500.4878] [ 739] [depth= 2] . ( 3 sec) [ -4499.4617] [ 737] [depth= 2] . ( 3 sec) [ -4495.6974] [ 737] [depth= 1] . ( 3 sec) [ -4492.2591] [ 737] [depth= 1] . ( 3 sec) [ -4486.9423] [ 734] [depth= 1] . ( 3 sec) [ -4454.6664] [ 729] [depth= 3] . ( 3 sec) [ -4452.4651] [ 729] [depth= 1] . ( 3 sec) [ -4444.1806] [ 726] [depth= 4] . ( 4 sec) [ -4397.5220] [Branch lengths ] . ( 4 sec) [ -4396.7208] [GTR parameters ] . ( 4 sec) [ -4381.6868] [Alpha ][ 0.919719] . ( 4 sec) [ -4380.7621] [ 726] [depth= 1] . ( 5 sec) [ -4368.0339] [ 721] [depth= 2] . ( 5 sec) [ -4368.0156] [ 721] [depth= 1] . ( 5 sec) [ -4361.5919] [ 719] [depth= 3] . ( 5 sec) [ -4358.4526] [ 712] [depth= 2] . ( 5 sec) [ -4356.8059] [ 710] [depth= 2] . ( 6 sec) [ -4349.0974] [ 711] [depth= 2] . ( 6 sec) [ -4329.0635] [ 706] [depth= 3] . ( 6 sec) [ -4325.6363] [ 704] [depth= 1] . ( 6 sec) [ -4323.9155] [ 704] [depth= 1] . ( 6 sec) [ -4317.0160] [ 703] [depth= 1] . ( 6 sec) [ -4314.8606] [ 701] [depth= 1] . ( 6 sec) [ -4314.5444] [ 701] [depth= 1] . ( 7 sec) [ -4314.4874] [ 706] [depth= 2] . ( 7 sec) [ -4313.5881] [ 704] [depth= 1] . ( 7 sec) [ -4310.9803] [ 703] [depth= 2] . ( 8 sec) [ -4308.8424] [Branch lengths ] . ( 9 sec) [ -4308.3550] [GTR parameters ] . ( 9 sec) [ -4307.8517] [Alpha ][ 1.045013] . ( 14 sec) [ -4307.8012] [Branch lengths ] . ( 32 sec) [ -4307.8009] [Branch lengths ] . ( 32 sec) [ -4307.8009] [Topology ] . ( 33 sec) [ -4307.8009] [Topology ] . ( 33 sec) [ -4307.7987] [GTR parameters ] . ( 33 sec) [ -4307.7985] [Alpha ][ 1.047625] . ( 33 sec) [ -4307.7985] [Topology ] . ( 33 sec) [ -4307.7985] [Topology ] . ( 33 sec) [ -4307.7985] [GTR parameters ] . ( 33 sec) [ -4307.7985] [Alpha ][ 1.047625] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4307.798512. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4321.356122 . ( 1 sec) [ -4317.7470] [GTR parameters ] . ( 1 sec) [ -4317.7006] [Alpha ][ 1.041435] . ( 1 sec) [ -4317.7006] [Topology ] . ( 1 sec) [ -4310.8662] [Topology ] . ( 2 sec) [ -4310.0336] [Topology ] . ( 3 sec) [ -4309.9103] [Topology ] . ( 3 sec) [ -4309.8799] [Topology ] . ( 4 sec) [ -4309.8710] [Topology ] . ( 4 sec) [ -4309.8682] [Topology ] . ( 5 sec) [ -4309.8671] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4309.867116 . ( 9 sec) [ -4309.8394] [GTR parameters ] . ( 9 sec) [ -4309.8274] [Alpha ][ 1.062573] . ( 9 sec) [ -4309.8274] [Topology ] . ( 9 sec) [ -4309.8264] [Topology ] . ( 10 sec) [ -4309.8261] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4309.826070 . ( 13 sec) [ -4309.8260] [GTR parameters ] . ( 13 sec) [ -4309.8260] [Alpha ][ 1.063635] . ( 13 sec) [ -4309.8260] [Topology ] . ( 14 sec) [ -4309.8259] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 21 sec) [ -4317.7470] [GTR parameters ] . ( 21 sec) [ -4317.7006] [Alpha ][ 1.041435] . ( 22 sec) [ -4316.8262] [ 700] [depth= 1] . ( 23 sec) [ -4316.1976] [ 700] [depth= 1] . ( 23 sec) [ -4315.9168] [ 700] [depth= 1] . ( 23 sec) [ -4315.8543] [ 700] [depth= 1] . ( 23 sec) [ -4314.4693] [ 703] [depth= 2] . ( 24 sec) [ -4313.5571] [ 704] [depth= 2] . ( 24 sec) [ -4313.3107] [ 704] [depth= 1] . ( 24 sec) [ -4313.1471] [ 704] [depth= 1] . ( 24 sec) [ -4311.8275] [ 703] [depth= 3] . ( 25 sec) [ -4308.0539] [Branch lengths ] . ( 26 sec) [ -4308.0027] [GTR parameters ] . ( 26 sec) [ -4308.0025] [Alpha ][ 1.043809] . ( 29 sec) [ -4307.9155] [ 703] [depth= 1] . ( 31 sec) [ -4307.8029] [Branch lengths ] . ( 31 sec) [ -4307.7999] [GTR parameters ] . ( 31 sec) [ -4307.7996] [Alpha ][ 1.047006] . ( 49 sec) [ -4307.7979] [Branch lengths ] . ( 49 sec) [ -4307.7979] [Topology ] . ( 50 sec) [ -4307.7978] [Topology ] . ( 50 sec) [ -4307.7978] [GTR parameters ] . ( 50 sec) [ -4307.7978] [Alpha ][ 1.048053] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4309.825920 . Log likelihood obtained after SPR moves : -4307.797803 . Log likelihood of the current tree: -4307.797803. . Printing the most likely tree in file 'data7.phy_phyml_tree.txt'... . Best log likelihood : -4307.797803 . Time used 0h0m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo