.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data54.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... . 272 patterns found. (out of a total of 500 sites) . 217 sites without polymorphism (43.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12687.3840] [GTR parameters ] . ( 0 sec) [ -12486.4943] [Alpha ][ 0.500960] . ( 0 sec) [ -12358.5272] [ 1641] [depth= 8] . ( 0 sec) [ -12269.5512] [ 1642] [depth= 6] . ( 0 sec) [ -10905.9353] [ 1636] [depth= 6] . ( 0 sec) [ -10720.0403] [ 1635] [depth= 5] . ( 0 sec) [ -10572.6523] [ 1618] [depth= 1] . ( 0 sec) [ -10552.2562] [ 1618] [depth= 1] . ( 0 sec) [ -10536.8179] [ 1611] [depth= 4] . ( 0 sec) [ -10524.6608] [ 1611] [depth= 2] . ( 1 sec) [ -10496.5736] [ 1606] [depth= 3] . ( 1 sec) [ -10485.8729] [ 1607] [depth= 1] . ( 1 sec) [ -10445.5618] [ 1611] [depth= 1] . ( 1 sec) [ -10197.1825] [ 1571] [depth= 10] . ( 1 sec) [ -9761.2046] [ 1490] [depth= 17] . ( 1 sec) [ -9756.1154] [ 1489] [depth= 1] . ( 1 sec) [ -9736.4662] [ 1476] [depth= 10] . ( 1 sec) [ -9693.7190] [ 1475] [depth= 3] . ( 1 sec) [ -9684.4880] [ 1474] [depth= 4] . ( 1 sec) [ -8415.2256] [ 1446] [depth= 6] . ( 1 sec) [ -8369.3494] [ 1442] [depth= 3] . ( 1 sec) [ -8306.0727] [ 1443] [depth= 2] . ( 1 sec) [ -8156.2664] [ 1405] [depth= 3] . ( 1 sec) [ -7978.5696] [ 1386] [depth= 10] . ( 1 sec) [ -7936.7608] [ 1386] [depth= 6] . ( 1 sec) [ -7791.9288] [ 1342] [depth= 7] . ( 1 sec) [ -7735.7042] [ 1343] [depth= 1] . ( 1 sec) [ -7661.0422] [ 1315] [depth= 1] . ( 1 sec) [ -7511.2105] [ 1263] [depth= 8] . ( 1 sec) [ -7458.1914] [ 1265] [depth= 14] . ( 1 sec) [ -7309.5401] [ 1228] [depth= 11] . ( 1 sec) [ -7253.9326] [ 1213] [depth= 10] . ( 1 sec) [ -7143.7944] [ 1190] [depth= 13] . ( 1 sec) [ -7063.1374] [ 1179] [depth= 2] . ( 1 sec) [ -6894.7990] [ 1131] [depth= 14] . ( 1 sec) [ -6857.3220] [ 1125] [depth= 1] . ( 1 sec) [ -6833.6465] [ 1116] [depth= 1] . ( 1 sec) [ -6430.1651] [ 1080] [depth= 9] . ( 1 sec) [ -6420.1881] [ 1093] [depth= 1] . ( 1 sec) [ -6386.9406] [ 1079] [depth= 2] . ( 1 sec) [ -6376.5966] [ 1079] [depth= 3] . ( 1 sec) [ -6280.9974] [ 1052] [depth= 4] . ( 1 sec) [ -6063.9678] [ 1019] [depth= 4] . ( 1 sec) [ -5973.2154] [ 990] [depth= 4] . ( 2 sec) [ -5954.9521] [ 987] [depth= 1] . ( 2 sec) [ -5953.9367] [ 992] [depth= 12] . ( 2 sec) [ -5796.9695] [ 975] [depth= 6] . ( 2 sec) [ -5708.3243] [ 983] [depth= 1] . ( 2 sec) [ -5654.7281] [ 953] [depth= 1] . ( 2 sec) [ -5554.5637] [ 940] [depth= 2] . ( 2 sec) [ -5450.2173] [ 939] [depth= 1] . ( 2 sec) [ -5384.0923] [ 918] [depth= 2] . ( 2 sec) [ -5310.5392] [ 894] [depth= 5] . ( 2 sec) [ -5288.1864] [ 895] [depth= 1] . ( 2 sec) [ -5283.8958] [ 893] [depth= 2] . ( 2 sec) [ -5281.4116] [ 892] [depth= 5] . ( 2 sec) [ -5273.6311] [ 885] [depth= 1] . ( 2 sec) [ -5246.8349] [ 870] [depth= 1] . ( 2 sec) [ -5198.2212] [ 864] [depth= 1] . ( 2 sec) [ -5111.1524] [ 843] [depth= 1] . ( 2 sec) [ -4939.3148] [ 795] [depth= 4] . ( 2 sec) [ -4920.2246] [ 794] [depth= 3] . ( 2 sec) [ -4919.1126] [ 795] [depth= 1] . ( 2 sec) [ -4886.5761] [ 772] [depth= 4] . ( 2 sec) [ -4885.1645] [ 772] [depth= 1] . ( 2 sec) [ -4823.7699] [ 756] [depth= 3] . ( 2 sec) [ -4823.3746] [ 760] [depth= 4] . ( 2 sec) [ -4818.0093] [ 758] [depth= 4] . ( 2 sec) [ -4716.6679] [ 745] [depth= 2] . ( 2 sec) [ -4699.0576] [ 743] [depth= 1] . ( 2 sec) [ -4652.3408] [ 732] [depth= 3] . ( 2 sec) [ -4648.3934] [ 730] [depth= 1] . ( 3 sec) [ -4628.3939] [ 719] [depth= 1] . ( 3 sec) [ -4592.6058] [ 710] [depth= 1] . ( 3 sec) [ -4557.4677] [ 699] [depth= 2] . ( 3 sec) [ -4557.0949] [ 700] [depth= 2] . ( 3 sec) [ -4542.3894] [ 705] [depth= 1] . ( 3 sec) [ -4541.1762] [ 708] [depth= 1] . ( 3 sec) [ -4504.3147] [ 708] [depth= 1] . ( 3 sec) [ -4502.8830] [ 707] [depth= 3] . ( 3 sec) [ -4479.3095] [ 696] [depth= 3] . ( 3 sec) [ -4479.2624] [ 695] [depth= 1] . ( 3 sec) [ -4468.5749] [ 691] [depth= 1] . ( 3 sec) [ -4451.6779] [Branch lengths ] . ( 3 sec) [ -4450.3074] [GTR parameters ] . ( 3 sec) [ -4444.5272] [Alpha ][ 0.729137] . ( 4 sec) [ -4440.1050] [ 689] [depth= 1] . ( 4 sec) [ -4439.5106] [ 690] [depth= 2] . ( 4 sec) [ -4439.4232] [ 691] [depth= 1] . ( 4 sec) [ -4438.8014] [ 691] [depth= 1] . ( 4 sec) [ -4435.9349] [ 691] [depth= 1] . ( 4 sec) [ -4426.7636] [ 686] [depth= 1] . ( 4 sec) [ -4426.7458] [ 686] [depth= 1] . ( 5 sec) [ -4426.7037] [ 685] [depth= 1] . ( 5 sec) [ -4426.6317] [ 685] [depth= 1] . ( 5 sec) [ -4426.2695] [ 683] [depth= 1] . ( 6 sec) [ -4425.1471] [Branch lengths ] . ( 6 sec) [ -4425.1227] [GTR parameters ] . ( 6 sec) [ -4425.0609] [Alpha ][ 0.759678] . ( 9 sec) [ -4424.9891] [Branch lengths ] . ( 24 sec) [ -4424.9822] [Branch lengths ] . ( 24 sec) [ -4424.9822] [Topology ] . ( 24 sec) [ -4424.9817] [Topology ] . ( 24 sec) [ -4424.9817] [GTR parameters ] . ( 24 sec) [ -4424.9800] [Alpha ][ 0.764958] . ( 24 sec) [ -4424.9800] [Topology ] . ( 25 sec) [ -4424.9797] [Topology ] . ( 25 sec) [ -4424.9797] [GTR parameters ] . ( 25 sec) [ -4424.9797] [Alpha ][ 0.764958] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -4424.7914] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4424.791410. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11862.1888] [GTR parameters ] . ( 1 sec) [ -11666.7970] [Alpha ][ 0.500960] . ( 1 sec) [ -11559.8787] [ 1619] [depth= 3] . ( 1 sec) [ -11337.5502] [ 1589] [depth= 3] . ( 1 sec) [ -11263.1968] [ 1581] [depth= 3] . ( 1 sec) [ -11126.5375] [ 1579] [depth= 2] . ( 1 sec) [ -10990.6201] [ 1541] [depth= 3] . ( 1 sec) [ -10931.6639] [ 1541] [depth= 6] . ( 1 sec) [ -10836.0170] [ 1537] [depth= 3] . ( 1 sec) [ -10738.2650] [ 1499] [depth= 1] . ( 1 sec) [ -10657.2729] [ 1494] [depth= 3] . ( 1 sec) [ -10616.7063] [ 1481] [depth= 10] . ( 1 sec) [ -10320.4143] [ 1480] [depth= 3] . ( 1 sec) [ -10048.0228] [ 1458] [depth= 4] . ( 1 sec) [ -9903.2621] [ 1456] [depth= 1] . ( 1 sec) [ -9657.5455] [ 1412] [depth= 3] . ( 1 sec) [ -9520.0493] [ 1379] [depth= 15] . ( 1 sec) [ -9188.0132] [ 1304] [depth= 9] . ( 1 sec) [ -9013.3335] [ 1304] [depth= 2] . ( 1 sec) [ -7349.1248] [ 1305] [depth= 1] . ( 1 sec) [ -7338.0171] [ 1275] [depth= 3] . ( 1 sec) [ -7280.6020] [ 1274] [depth= 4] . ( 1 sec) [ -7086.2395] [ 1231] [depth= 8] . ( 1 sec) [ -7072.8100] [ 1232] [depth= 3] . ( 1 sec) [ -6939.7405] [ 1198] [depth= 13] . ( 1 sec) [ -6874.5190] [ 1175] [depth= 4] . ( 1 sec) [ -6810.8414] [ 1156] [depth= 1] . ( 2 sec) [ -6796.3241] [ 1153] [depth= 1] . ( 2 sec) [ -6771.8801] [ 1150] [depth= 11] . ( 2 sec) [ -6706.5939] [ 1126] [depth= 9] . ( 2 sec) [ -6610.7983] [ 1107] [depth= 1] . ( 2 sec) [ -6466.4890] [ 1107] [depth= 2] . ( 2 sec) [ -6255.5066] [ 1081] [depth= 10] . ( 2 sec) [ -6250.5753] [ 1081] [depth= 2] . ( 2 sec) [ -6234.7829] [ 1078] [depth= 1] . ( 2 sec) [ -6160.8674] [ 1075] [depth= 2] . ( 2 sec) [ -6160.5380] [ 1074] [depth= 1] . ( 2 sec) [ -6123.5147] [ 1063] [depth= 2] . ( 2 sec) [ -6120.8342] [ 1060] [depth= 1] . ( 2 sec) [ -6060.2689] [ 1055] [depth= 7] . ( 2 sec) [ -5961.8671] [ 1045] [depth= 7] . ( 2 sec) [ -5836.8066] [ 1026] [depth= 2] . ( 2 sec) [ -5771.8869] [ 1023] [depth= 8] . ( 2 sec) [ -5584.0487] [ 974] [depth= 5] . ( 2 sec) [ -5566.8036] [ 974] [depth= 2] . ( 2 sec) [ -5516.9668] [ 954] [depth= 1] . ( 2 sec) [ -5516.5153] [ 955] [depth= 1] . ( 2 sec) [ -5390.5711] [ 941] [depth= 2] . ( 2 sec) [ -5382.9939] [ 938] [depth= 1] . ( 2 sec) [ -5281.4054] [ 895] [depth= 3] . ( 2 sec) [ -5219.8483] [ 871] [depth= 3] . ( 2 sec) [ -5205.9595] [ 868] [depth= 4] . ( 2 sec) [ -5178.1488] [ 869] [depth= 2] . ( 2 sec) [ -5039.1265] [ 840] [depth= 9] . ( 2 sec) [ -4986.9022] [ 827] [depth= 1] . ( 3 sec) [ -4972.8142] [ 827] [depth= 1] . ( 3 sec) [ -4971.7996] [ 829] [depth= 1] . ( 3 sec) [ -4918.6239] [ 812] [depth= 3] . ( 3 sec) [ -4908.2016] [ 810] [depth= 1] . ( 3 sec) [ -4870.7459] [ 791] [depth= 3] . ( 3 sec) [ -4859.4527] [ 792] [depth= 1] . ( 3 sec) [ -4816.4538] [ 780] [depth= 7] . ( 3 sec) [ -4783.1061] [ 769] [depth= 1] . ( 3 sec) [ -4780.4604] [ 769] [depth= 1] . ( 3 sec) [ -4758.0971] [ 764] [depth= 1] . ( 3 sec) [ -4756.4687] [ 766] [depth= 1] . ( 3 sec) [ -4739.0901] [ 758] [depth= 3] . ( 3 sec) [ -4732.6747] [ 755] [depth= 1] . ( 3 sec) [ -4730.0263] [ 752] [depth= 2] . ( 3 sec) [ -4707.8893] [ 742] [depth= 3] . ( 3 sec) [ -4656.5343] [ 722] [depth= 1] . ( 3 sec) [ -4649.8296] [ 720] [depth= 1] . ( 3 sec) [ -4647.8407] [ 719] [depth= 1] . ( 4 sec) [ -4572.9565] [Branch lengths ] . ( 4 sec) [ -4571.2620] [GTR parameters ] . ( 4 sec) [ -4566.7224] [Alpha ][ 0.680353] . ( 4 sec) [ -4549.7164] [ 710] [depth= 1] . ( 4 sec) [ -4548.8907] [ 707] [depth= 1] . ( 4 sec) [ -4545.7921] [ 707] [depth= 1] . ( 4 sec) [ -4545.6631] [ 707] [depth= 1] . ( 5 sec) [ -4505.7299] [ 693] [depth= 2] . ( 5 sec) [ -4505.6989] [ 693] [depth= 1] . ( 5 sec) [ -4478.1618] [ 683] [depth= 2] . ( 5 sec) [ -4431.7391] [ 685] [depth= 1] . ( 6 sec) [ -4431.5780] [ 685] [depth= 1] . ( 6 sec) [ -4430.9766] [ 683] [depth= 1] . ( 6 sec) [ -4430.7619] [ 683] [depth= 1] . ( 6 sec) [ -4430.5918] [ 683] [depth= 1] . ( 7 sec) [ -4428.3602] [Branch lengths ] . ( 7 sec) [ -4428.3282] [GTR parameters ] . ( 7 sec) [ -4427.7930] [Alpha ][ 0.765307] . ( 9 sec) [ -4426.8635] [Branch lengths ] . ( 24 sec) [ -4424.9825] [Branch lengths ] . ( 24 sec) [ -4424.9825] [Topology ] . ( 25 sec) [ -4424.8008] [Topology ] . ( 26 sec) [ -4424.7923] [Topology ] . ( 26 sec) [ -4424.7920] [Topology ] . ( 26 sec) [ -4424.7904] [GTR parameters ] . ( 26 sec) [ -4424.7904] [Alpha ][ 0.766211] . ( 26 sec) [ -4424.7904] [Topology ] . ( 27 sec) [ -4424.7903] [Topology ] . ( 27 sec) [ -4424.7903] [GTR parameters ] . ( 27 sec) [ -4424.7903] [Alpha ][ 0.766211] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4424.790328. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13237.2411] [GTR parameters ] . ( 1 sec) [ -13032.1618] [Alpha ][ 0.500960] . ( 1 sec) [ -12920.2359] [ 1686] [depth= 1] . ( 1 sec) [ -12718.0078] [ 1657] [depth= 8] . ( 1 sec) [ -12676.4960] [ 1655] [depth= 5] . ( 1 sec) [ -12599.4822] [ 1654] [depth= 2] . ( 1 sec) [ -12521.8627] [ 1621] [depth= 7] . ( 1 sec) [ -12467.0988] [ 1619] [depth= 4] . ( 1 sec) [ -12346.1550] [ 1592] [depth= 10] . ( 1 sec) [ -12327.8529] [ 1575] [depth= 7] . ( 1 sec) [ -12275.5647] [ 1573] [depth= 2] . ( 1 sec) [ -12064.2491] [ 1537] [depth= 1] . ( 1 sec) [ -11986.1047] [ 1537] [depth= 9] . ( 1 sec) [ -11773.5487] [ 1515] [depth= 8] . ( 1 sec) [ -11638.4009] [ 1470] [depth= 11] . ( 1 sec) [ -11561.3875] [ 1478] [depth= 1] . ( 1 sec) [ -9990.8139] [ 1443] [depth= 5] . ( 1 sec) [ -8852.2903] [ 1438] [depth= 9] . ( 1 sec) [ -8742.6265] [ 1441] [depth= 3] . ( 1 sec) [ -8599.0504] [ 1414] [depth= 9] . ( 1 sec) [ -8531.2775] [ 1394] [depth= 12] . ( 1 sec) [ -8176.5743] [ 1318] [depth= 8] . ( 1 sec) [ -8162.8030] [ 1324] [depth= 12] . ( 1 sec) [ -8020.9875] [ 1302] [depth= 11] . ( 1 sec) [ -7723.5374] [ 1250] [depth= 11] . ( 1 sec) [ -7364.0628] [ 1216] [depth= 6] . ( 1 sec) [ -7170.8286] [ 1173] [depth= 12] . ( 1 sec) [ -7169.2478] [ 1174] [depth= 1] . ( 1 sec) [ -6929.8854] [ 1168] [depth= 6] . ( 1 sec) [ -6748.3210] [ 1166] [depth= 1] . ( 1 sec) [ -6683.8180] [ 1166] [depth= 1] . ( 2 sec) [ -6677.3373] [ 1165] [depth= 2] . ( 2 sec) [ -6663.7540] [ 1161] [depth= 1] . ( 2 sec) [ -6587.6995] [ 1134] [depth= 5] . ( 2 sec) [ -6581.4573] [ 1125] [depth= 1] . ( 2 sec) [ -6549.9677] [ 1109] [depth= 4] . ( 2 sec) [ -6441.8771] [ 1088] [depth= 1] . ( 2 sec) [ -6433.1929] [ 1083] [depth= 1] . ( 2 sec) [ -6377.0038] [ 1081] [depth= 5] . ( 2 sec) [ -6374.7237] [ 1083] [depth= 2] . ( 2 sec) [ -6372.3043] [ 1082] [depth= 1] . ( 2 sec) [ -6361.0752] [ 1078] [depth= 1] . ( 2 sec) [ -6350.3921] [ 1077] [depth= 1] . ( 2 sec) [ -6290.2244] [ 1077] [depth= 2] . ( 2 sec) [ -6119.0752] [ 1008] [depth= 4] . ( 2 sec) [ -5973.1104] [ 974] [depth= 6] . ( 2 sec) [ -5935.2265] [ 973] [depth= 1] . ( 2 sec) [ -5929.6485] [ 973] [depth= 1] . ( 2 sec) [ -5927.1999] [ 971] [depth= 1] . ( 2 sec) [ -5890.2080] [ 973] [depth= 1] . ( 2 sec) [ -5888.1578] [ 970] [depth= 1] . ( 2 sec) [ -5818.8399] [ 948] [depth= 5] . ( 2 sec) [ -5701.9936] [ 917] [depth= 5] . ( 2 sec) [ -5569.7230] [ 911] [depth= 3] . ( 2 sec) [ -5568.7415] [ 911] [depth= 1] . ( 2 sec) [ -5437.5332] [ 906] [depth= 5] . ( 2 sec) [ -5316.4341] [ 871] [depth= 2] . ( 2 sec) [ -5316.3833] [ 872] [depth= 1] . ( 2 sec) [ -5315.5673] [ 869] [depth= 2] . ( 2 sec) [ -5313.6980] [ 869] [depth= 1] . ( 2 sec) [ -5270.6317] [ 832] [depth= 6] . ( 3 sec) [ -5162.9750] [ 825] [depth= 10] . ( 3 sec) [ -5061.1532] [ 823] [depth= 1] . ( 3 sec) [ -5060.6043] [ 824] [depth= 1] . ( 3 sec) [ -5053.1693] [ 825] [depth= 1] . ( 3 sec) [ -4997.1887] [ 827] [depth= 2] . ( 3 sec) [ -4981.5680] [ 827] [depth= 1] . ( 3 sec) [ -4977.7923] [ 829] [depth= 1] . ( 3 sec) [ -4930.5031] [ 838] [depth= 1] . ( 3 sec) [ -4926.9932] [ 837] [depth= 2] . ( 3 sec) [ -4890.3072] [ 826] [depth= 1] . ( 3 sec) [ -4886.6576] [ 824] [depth= 1] . ( 3 sec) [ -4767.6831] [ 781] [depth= 5] . ( 3 sec) [ -4747.0162] [ 776] [depth= 11] . ( 3 sec) [ -4682.5461] [ 756] [depth= 10] . ( 3 sec) [ -4680.9370] [ 757] [depth= 1] . ( 3 sec) [ -4676.4175] [ 758] [depth= 1] . ( 3 sec) [ -4647.3200] [ 755] [depth= 8] . ( 3 sec) [ -4623.5879] [ 745] [depth= 1] . ( 3 sec) [ -4623.0219] [ 744] [depth= 1] . ( 4 sec) [ -4582.5310] [Branch lengths ] . ( 4 sec) [ -4580.8797] [GTR parameters ] . ( 4 sec) [ -4577.3553] [Alpha ][ 0.656730] . ( 4 sec) [ -4574.7825] [ 743] [depth= 1] . ( 4 sec) [ -4550.6016] [ 732] [depth= 1] . ( 4 sec) [ -4547.9705] [ 730] [depth= 1] . ( 4 sec) [ -4539.3287] [ 725] [depth= 1] . ( 5 sec) [ -4525.1464] [ 716] [depth= 2] . ( 5 sec) [ -4431.8947] [ 683] [depth= 6] . ( 5 sec) [ -4431.5975] [ 683] [depth= 1] . ( 5 sec) [ -4431.2420] [ 684] [depth= 1] . ( 5 sec) [ -4430.2739] [ 683] [depth= 1] . ( 5 sec) [ -4429.8936] [ 683] [depth= 1] . ( 5 sec) [ -4429.7443] [ 685] [depth= 1] . ( 5 sec) [ -4429.6401] [ 685] [depth= 1] . ( 6 sec) [ -4429.3389] [ 683] [depth= 1] . ( 6 sec) [ -4427.9683] [ 683] [depth= 1] . ( 7 sec) [ -4425.8424] [Branch lengths ] . ( 7 sec) [ -4425.6850] [GTR parameters ] . ( 7 sec) [ -4424.8226] [Alpha ][ 0.762837] . ( 9 sec) [ -4424.7944] [Branch lengths ] . ( 25 sec) [ -4424.7929] [Branch lengths ] . ( 25 sec) [ -4424.7929] [Topology ] . ( 25 sec) [ -4424.7927] [Topology ] . ( 25 sec) [ -4424.7913] [GTR parameters ] . ( 25 sec) [ -4424.7906] [Alpha ][ 0.766145] . ( 25 sec) [ -4424.7906] [Topology ] . ( 26 sec) [ -4424.7905] [Topology ] . ( 26 sec) [ -4424.7905] [GTR parameters ] . ( 26 sec) [ -4424.7905] [Alpha ][ 0.766145] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4424.790547. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11013.6464] [GTR parameters ] . ( 0 sec) [ -10802.8197] [Alpha ][ 0.500960] . ( 0 sec) [ -10711.1664] [ 1636] [depth= 8] . ( 0 sec) [ -10574.9723] [ 1603] [depth= 9] . ( 0 sec) [ -10499.8214] [ 1587] [depth= 7] . ( 0 sec) [ -10226.9221] [ 1560] [depth= 1] . ( 0 sec) [ -10009.3165] [ 1539] [depth= 8] . ( 0 sec) [ -9976.0812] [ 1537] [depth= 3] . ( 0 sec) [ -9913.5897] [ 1537] [depth= 5] . ( 0 sec) [ -9723.8810] [ 1472] [depth= 3] . ( 0 sec) [ -9658.4405] [ 1461] [depth= 7] . ( 0 sec) [ -9653.3439] [ 1460] [depth= 4] . ( 0 sec) [ -9607.8109] [ 1460] [depth= 6] . ( 0 sec) [ -9436.5739] [ 1413] [depth= 10] . ( 0 sec) [ -9383.6641] [ 1379] [depth= 3] . ( 1 sec) [ -9379.0387] [ 1379] [depth= 6] . ( 1 sec) [ -9181.8537] [ 1342] [depth= 4] . ( 1 sec) [ -9121.0560] [ 1340] [depth= 2] . ( 1 sec) [ -8622.9407] [ 1340] [depth= 3] . ( 1 sec) [ -8546.8973] [ 1311] [depth= 2] . ( 1 sec) [ -8364.5028] [ 1279] [depth= 4] . ( 1 sec) [ -8347.8016] [ 1276] [depth= 1] . ( 1 sec) [ -8324.6924] [ 1280] [depth= 3] . ( 1 sec) [ -8252.1815] [ 1274] [depth= 4] . ( 1 sec) [ -8232.6818] [ 1273] [depth= 2] . ( 1 sec) [ -8148.3685] [ 1250] [depth= 6] . ( 1 sec) [ -7894.8283] [ 1248] [depth= 10] . ( 1 sec) [ -7874.8131] [ 1248] [depth= 1] . ( 1 sec) [ -7802.2666] [ 1211] [depth= 16] . ( 1 sec) [ -6989.4080] [ 1176] [depth= 10] . ( 1 sec) [ -6964.9259] [ 1175] [depth= 1] . ( 1 sec) [ -6819.8260] [ 1144] [depth= 1] . ( 1 sec) [ -6753.1509] [ 1134] [depth= 13] . ( 1 sec) [ -6704.5510] [ 1114] [depth= 1] . ( 1 sec) [ -6639.1271] [ 1112] [depth= 13] . ( 1 sec) [ -6478.8926] [ 1073] [depth= 5] . ( 1 sec) [ -6406.1863] [ 1058] [depth= 1] . ( 1 sec) [ -6393.1090] [ 1053] [depth= 1] . ( 1 sec) [ -6347.9577] [ 1048] [depth= 10] . ( 1 sec) [ -6242.3515] [ 1020] [depth= 4] . ( 1 sec) [ -6049.1706] [ 979] [depth= 9] . ( 1 sec) [ -6023.6691] [ 982] [depth= 1] . ( 1 sec) [ -5982.5516] [ 968] [depth= 4] . ( 1 sec) [ -5981.9620] [ 970] [depth= 1] . ( 1 sec) [ -5901.5256] [ 968] [depth= 6] . ( 1 sec) [ -5844.8356] [ 968] [depth= 8] . ( 1 sec) [ -5840.2320] [ 971] [depth= 1] . ( 2 sec) [ -5819.0093] [ 950] [depth= 9] . ( 2 sec) [ -5566.6917] [ 922] [depth= 2] . ( 2 sec) [ -5565.9418] [ 922] [depth= 1] . ( 2 sec) [ -5542.6166] [ 917] [depth= 1] . ( 2 sec) [ -5521.4908] [ 892] [depth= 2] . ( 2 sec) [ -5517.4965] [ 890] [depth= 4] . ( 2 sec) [ -5388.0735] [ 862] [depth= 5] . ( 2 sec) [ -5381.1011] [ 856] [depth= 1] . ( 2 sec) [ -5306.5430] [ 846] [depth= 1] . ( 2 sec) [ -5292.6563] [ 843] [depth= 1] . ( 2 sec) [ -5289.8153] [ 842] [depth= 1] . ( 2 sec) [ -5282.5105] [ 839] [depth= 1] . ( 2 sec) [ -5260.7765] [ 817] [depth= 3] . ( 2 sec) [ -5223.1243] [ 810] [depth= 1] . ( 2 sec) [ -5203.6925] [ 810] [depth= 7] . ( 2 sec) [ -5191.6471] [ 830] [depth= 5] . ( 2 sec) [ -5188.6716] [ 831] [depth= 1] . ( 2 sec) [ -5129.6323] [ 814] [depth= 8] . ( 2 sec) [ -5029.1996] [ 793] [depth= 3] . ( 2 sec) [ -4990.6041] [ 788] [depth= 1] . ( 2 sec) [ -4958.5090] [ 780] [depth= 3] . ( 2 sec) [ -4953.9351] [ 779] [depth= 1] . ( 2 sec) [ -4940.8000] [ 779] [depth= 1] . ( 2 sec) [ -4838.0785] [ 781] [depth= 1] . ( 2 sec) [ -4827.5762] [ 788] [depth= 1] . ( 2 sec) [ -4827.1902] [ 788] [depth= 1] . ( 2 sec) [ -4811.8295] [ 782] [depth= 6] . ( 2 sec) [ -4770.1585] [ 781] [depth= 4] . ( 3 sec) [ -4768.4775] [ 783] [depth= 1] . ( 3 sec) [ -4762.0007] [ 780] [depth= 2] . ( 3 sec) [ -4760.9409] [ 780] [depth= 1] . ( 3 sec) [ -4760.8847] [ 778] [depth= 2] . ( 3 sec) [ -4674.5377] [Branch lengths ] . ( 3 sec) [ -4673.3951] [GTR parameters ] . ( 3 sec) [ -4670.9384] [Alpha ][ 0.622449] . ( 3 sec) [ -4670.1781] [ 778] [depth= 1] . ( 3 sec) [ -4669.1245] [ 768] [depth= 2] . ( 4 sec) [ -4636.2925] [ 745] [depth= 4] . ( 4 sec) [ -4633.5066] [ 746] [depth= 2] . ( 4 sec) [ -4620.3416] [ 759] [depth= 1] . ( 4 sec) [ -4620.1656] [ 761] [depth= 1] . ( 4 sec) [ -4607.6345] [ 753] [depth= 1] . ( 4 sec) [ -4607.5244] [ 753] [depth= 1] . ( 4 sec) [ -4604.0375] [ 756] [depth= 2] . ( 4 sec) [ -4586.9085] [ 747] [depth= 3] . ( 4 sec) [ -4561.3513] [ 737] [depth= 3] . ( 4 sec) [ -4519.9826] [ 722] [depth= 3] . ( 4 sec) [ -4519.9268] [ 709] [depth= 1] . ( 5 sec) [ -4519.2776] [ 708] [depth= 2] . ( 5 sec) [ -4493.9916] [ 701] [depth= 1] . ( 5 sec) [ -4492.4340] [ 690] [depth= 2] . ( 5 sec) [ -4490.6986] [ 690] [depth= 1] . ( 5 sec) [ -4468.8462] [ 685] [depth= 2] . ( 5 sec) [ -4468.7959] [ 699] [depth= 1] . ( 5 sec) [ -4468.6414] [ 699] [depth= 1] . ( 5 sec) [ -4453.2232] [ 685] [depth= 1] . ( 5 sec) [ -4452.4818] [ 685] [depth= 1] . ( 5 sec) [ -4450.5161] [ 688] [depth= 1] . ( 5 sec) [ -4445.4766] [ 685] [depth= 1] . ( 6 sec) [ -4445.3508] [ 685] [depth= 1] . ( 6 sec) [ -4445.3394] [ 685] [depth= 1] . ( 6 sec) [ -4442.6540] [ 683] [depth= 1] . ( 6 sec) [ -4427.4504] [Branch lengths ] . ( 6 sec) [ -4427.0513] [GTR parameters ] . ( 7 sec) [ -4425.3342] [Alpha ][ 0.766883] . ( 9 sec) [ -4425.0083] [Branch lengths ] . ( 24 sec) [ -4424.9831] [Branch lengths ] . ( 24 sec) [ -4424.9831] [Topology ] . ( 25 sec) [ -4424.9826] [Topology ] . ( 25 sec) [ -4424.9800] [GTR parameters ] . ( 25 sec) [ -4424.9799] [Alpha ][ 0.765465] . ( 25 sec) [ -4424.9799] [Topology ] . ( 25 sec) [ -4424.9796] [Topology ] . ( 25 sec) [ -4424.9796] [GTR parameters ] . ( 25 sec) [ -4424.9796] [Alpha ][ 0.765465] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -4424.7912] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4424.791193. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11362.5784] [GTR parameters ] . ( 0 sec) [ -11144.6614] [Alpha ][ 0.500960] . ( 0 sec) [ -10983.9646] [ 1675] [depth= 6] . ( 0 sec) [ -10805.7177] [ 1639] [depth= 11] . ( 0 sec) [ -10628.9160] [ 1636] [depth= 5] . ( 0 sec) [ -10554.1482] [ 1635] [depth= 3] . ( 0 sec) [ -10374.0993] [ 1595] [depth= 5] . ( 0 sec) [ -10366.7883] [ 1595] [depth= 1] . ( 0 sec) [ -10291.8953] [ 1594] [depth= 6] . ( 0 sec) [ -10186.0608] [ 1572] [depth= 11] . ( 0 sec) [ -10090.5215] [ 1548] [depth= 7] . ( 1 sec) [ -9884.9400] [ 1509] [depth= 8] . ( 1 sec) [ -9860.5809] [ 1512] [depth= 13] . ( 1 sec) [ -9697.4792] [ 1476] [depth= 12] . ( 1 sec) [ -9634.0639] [ 1465] [depth= 2] . ( 1 sec) [ -9604.3148] [ 1465] [depth= 2] . ( 1 sec) [ -9525.8765] [ 1462] [depth= 10] . ( 1 sec) [ -9425.7536] [ 1451] [depth= 2] . ( 1 sec) [ -9411.8499] [ 1448] [depth= 1] . ( 1 sec) [ -9288.0321] [ 1442] [depth= 7] . ( 1 sec) [ -8225.3109] [ 1392] [depth= 3] . ( 1 sec) [ -8144.4222] [ 1405] [depth= 1] . ( 1 sec) [ -8077.7286] [ 1399] [depth= 7] . ( 1 sec) [ -7830.2061] [ 1359] [depth= 1] . ( 1 sec) [ -7594.8417] [ 1311] [depth= 6] . ( 1 sec) [ -7488.3848] [ 1275] [depth= 6] . ( 1 sec) [ -7312.2216] [ 1246] [depth= 8] . ( 1 sec) [ -7272.2722] [ 1251] [depth= 9] . ( 1 sec) [ -7140.8087] [ 1250] [depth= 8] . ( 1 sec) [ -7091.2338] [ 1241] [depth= 7] . ( 1 sec) [ -7071.5346] [ 1232] [depth= 5] . ( 1 sec) [ -6794.6588] [ 1158] [depth= 7] . ( 1 sec) [ -6767.0651] [ 1157] [depth= 6] . ( 1 sec) [ -6541.2444] [ 1140] [depth= 2] . ( 1 sec) [ -6470.2386] [ 1135] [depth= 11] . ( 1 sec) [ -6463.2311] [ 1139] [depth= 1] . ( 1 sec) [ -6365.0213] [ 1116] [depth= 1] . ( 1 sec) [ -6268.5754] [ 1100] [depth= 1] . ( 1 sec) [ -6144.1163] [ 1065] [depth= 10] . ( 1 sec) [ -6091.3352] [ 1049] [depth= 1] . ( 1 sec) [ -6075.9331] [ 1039] [depth= 4] . ( 1 sec) [ -6067.9278] [ 1027] [depth= 1] . ( 2 sec) [ -5994.7851] [ 1002] [depth= 4] . ( 2 sec) [ -5935.3576] [ 997] [depth= 2] . ( 2 sec) [ -5902.0647] [ 977] [depth= 1] . ( 2 sec) [ -5893.5419] [ 972] [depth= 1] . ( 2 sec) [ -5800.4823] [ 961] [depth= 6] . ( 2 sec) [ -5787.8371] [ 962] [depth= 2] . ( 2 sec) [ -5694.6311] [ 955] [depth= 9] . ( 2 sec) [ -5664.6024] [ 951] [depth= 2] . ( 2 sec) [ -5664.4082] [ 950] [depth= 1] . ( 2 sec) [ -5559.9147] [ 951] [depth= 1] . ( 2 sec) [ -5467.3607] [ 932] [depth= 10] . ( 2 sec) [ -5396.1049] [ 910] [depth= 2] . ( 2 sec) [ -5353.6963] [ 894] [depth= 2] . ( 2 sec) [ -5327.5988] [ 881] [depth= 4] . ( 2 sec) [ -5256.8127] [ 852] [depth= 9] . ( 2 sec) [ -5256.6271] [ 853] [depth= 1] . ( 2 sec) [ -5241.1054] [ 845] [depth= 1] . ( 2 sec) [ -5230.1284] [ 845] [depth= 2] . ( 2 sec) [ -5213.9763] [ 845] [depth= 2] . ( 2 sec) [ -5204.2867] [ 845] [depth= 3] . ( 2 sec) [ -5155.8440] [ 842] [depth= 1] . ( 2 sec) [ -5109.2726] [ 840] [depth= 1] . ( 2 sec) [ -5054.3813] [ 840] [depth= 7] . ( 2 sec) [ -5040.0874] [ 838] [depth= 6] . ( 2 sec) [ -4990.1118] [ 813] [depth= 7] . ( 2 sec) [ -4965.5614] [ 803] [depth= 2] . ( 2 sec) [ -4951.0150] [ 803] [depth= 1] . ( 3 sec) [ -4841.8568] [ 800] [depth= 5] . ( 3 sec) [ -4834.9029] [ 796] [depth= 1] . ( 3 sec) [ -4762.0060] [ 766] [depth= 4] . ( 3 sec) [ -4761.8748] [ 766] [depth= 1] . ( 3 sec) [ -4761.4127] [ 771] [depth= 1] . ( 3 sec) [ -4686.2612] [Branch lengths ] . ( 3 sec) [ -4685.2718] [GTR parameters ] . ( 3 sec) [ -4682.3434] [Alpha ][ 0.636662] . ( 3 sec) [ -4671.3339] [ 766] [depth= 1] . ( 3 sec) [ -4671.2554] [ 767] [depth= 1] . ( 4 sec) [ -4607.2728] [ 742] [depth= 2] . ( 4 sec) [ -4607.1089] [ 742] [depth= 1] . ( 4 sec) [ -4597.2568] [ 738] [depth= 1] . ( 4 sec) [ -4583.1365] [ 731] [depth= 1] . ( 4 sec) [ -4578.0802] [ 730] [depth= 1] . ( 4 sec) [ -4563.9173] [ 723] [depth= 1] . ( 4 sec) [ -4563.4247] [ 722] [depth= 1] . ( 4 sec) [ -4563.0511] [ 723] [depth= 2] . ( 4 sec) [ -4562.1397] [ 724] [depth= 2] . ( 5 sec) [ -4561.7994] [ 724] [depth= 1] . ( 5 sec) [ -4527.8296] [ 713] [depth= 1] . ( 5 sec) [ -4526.3710] [ 713] [depth= 1] . ( 5 sec) [ -4525.0195] [ 710] [depth= 2] . ( 5 sec) [ -4504.9255] [ 704] [depth= 2] . ( 5 sec) [ -4469.7130] [ 684] [depth= 1] . ( 5 sec) [ -4466.8925] [ 684] [depth= 1] . ( 5 sec) [ -4465.2306] [ 686] [depth= 1] . ( 5 sec) [ -4454.3686] [ 686] [depth= 1] . ( 5 sec) [ -4447.2938] [ 684] [depth= 1] . ( 5 sec) [ -4445.0263] [ 685] [depth= 1] . ( 5 sec) [ -4444.3250] [ 687] [depth= 1] . ( 6 sec) [ -4444.2566] [ 686] [depth= 1] . ( 6 sec) [ -4442.7833] [ 685] [depth= 1] . ( 6 sec) [ -4439.8635] [Branch lengths ] . ( 6 sec) [ -4439.6348] [GTR parameters ] . ( 6 sec) [ -4438.7146] [Alpha ][ 0.741177] . ( 9 sec) [ -4436.0765] [Branch lengths ] . ( 10 sec) [ -4436.0358] [ 683] [depth= 1] . ( 23 sec) [ -4426.4290] [Branch lengths ] . ( 24 sec) [ -4426.4224] [GTR parameters ] . ( 24 sec) [ -4426.3892] [Alpha ][ 0.763663] . ( 39 sec) [ -4424.9838] [Branch lengths ] . ( 39 sec) [ -4424.9838] [Topology ] . ( 39 sec) [ -4424.9807] [Topology ] . ( 40 sec) [ -4424.9805] [Topology ] . ( 40 sec) [ -4424.9799] [GTR parameters ] . ( 40 sec) [ -4424.9797] [Alpha ][ 0.765177] . ( 40 sec) [ -4424.9797] [Topology ] . ( 41 sec) [ -4424.9797] [Topology ] . ( 41 sec) [ -4424.9796] [GTR parameters ] . ( 41 sec) [ -4424.9796] [Alpha ][ 0.765177] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -4424.7913] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4424.791281. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4435.128913 . ( 0 sec) [ -4434.0770] [GTR parameters ] . ( 1 sec) [ -4431.3121] [Alpha ][ 0.745784] . ( 1 sec) [ -4431.3121] [Topology ] . ( 1 sec) [ -4425.7334] [Topology ] . ( 2 sec) [ -4425.1425] [Topology ] . ( 2 sec) [ -4424.9939] [Topology ] . ( 3 sec) [ -4424.9398] [Topology ] . ( 3 sec) [ -4424.9144] [Topology ] . ( 4 sec) [ -4424.8984] [Topology ] . ( 4 sec) [ -4424.8861] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4424.886111 . ( 8 sec) [ -4424.8579] [GTR parameters ] . ( 8 sec) [ -4424.8340] [Alpha ][ 0.764840] . ( 8 sec) [ -4424.8340] [Topology ] . ( 9 sec) [ -4424.8188] [Topology ] . ( 9 sec) [ -4424.8065] [Topology ] . ( 10 sec) [ -4424.7967] [Topology ] . ( 10 sec) [ -4424.7921] [Topology ] . ( 11 sec) [ -4424.7910] [Topology ] . ( 11 sec) [ -4424.7907] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4424.790725 . ( 15 sec) [ -4424.7904] [GTR parameters ] . ( 15 sec) [ -4424.7902] [Alpha ][ 0.766147] . ( 15 sec) [ -4424.7902] [Topology ] . ( 16 sec) [ -4424.7901] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -4434.0770] [GTR parameters ] . ( 23 sec) [ -4431.3121] [Alpha ][ 0.745784] . ( 24 sec) [ -4430.8322] [ 683] [depth= 1] . ( 24 sec) [ -4430.6063] [ 684] [depth= 1] . ( 24 sec) [ -4429.0542] [ 684] [depth= 1] . ( 24 sec) [ -4429.0222] [ 683] [depth= 1] . ( 25 sec) [ -4429.0106] [ 683] [depth= 1] . ( 25 sec) [ -4428.7210] [ 685] [depth= 1] . ( 25 sec) [ -4428.6819] [ 683] [depth= 1] . ( 25 sec) [ -4425.8767] [Branch lengths ] . ( 26 sec) [ -4425.8604] [GTR parameters ] . ( 26 sec) [ -4425.8410] [Alpha ][ 0.762873] . ( 27 sec) [ -4425.7080] [ 683] [depth= 1] . ( 28 sec) [ -4425.0740] [Branch lengths ] . ( 28 sec) [ -4425.0712] [GTR parameters ] . ( 28 sec) [ -4425.0708] [Alpha ][ 0.765193] . ( 43 sec) [ -4425.0308] [Branch lengths ] . ( 43 sec) [ -4425.0308] [Topology ] . ( 44 sec) [ -4425.0143] [Topology ] . ( 44 sec) [ -4425.0024] [Topology ] . ( 45 sec) [ -4424.9908] [Topology ] . ( 45 sec) [ -4424.9836] [Topology ] . ( 46 sec) [ -4424.9815] [Topology ] . ( 47 sec) [ -4424.9810] [Topology ] . ( 47 sec) [ -4424.9796] [GTR parameters ] . ( 47 sec) [ -4424.9796] [Alpha ][ 0.765193] . ( 47 sec) [ -4424.9796] [Topology ] . ( 47 sec) [ -4424.9795] [Topology ] . ( 47 sec) [ -4424.9795] [GTR parameters ] . ( 47 sec) [ -4424.9795] [Alpha ][ 0.765193] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -4424.7911] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4424.790112 . Log likelihood obtained after SPR moves : -4424.791060 . Log likelihood of the current tree: -4424.790112. . Printing the most likely tree in file 'data54.phy_phyml_tree.txt'... . Best log likelihood : -4424.790112 . Time used 0h0m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo