.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data10.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... . 293 patterns found. (out of a total of 500 sites) . 199 sites without polymorphism (39.80%). . [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) [ -10301.1892] [GTR parameters ] . ( 0 sec) [ -10103.0831] [Alpha ][ 0.500960] . ( 0 sec) [ -9837.5313] [ 1719] [depth= 8] . ( 0 sec) [ -9779.3290] [ 1722] [depth= 6] . ( 0 sec) [ -9626.4972] [ 1710] [depth= 4] . ( 0 sec) [ -9566.4809] [ 1706] [depth= 6] . ( 1 sec) [ -9513.9165] [ 1688] [depth= 4] . ( 1 sec) [ -9448.1389] [ 1687] [depth= 1] . ( 1 sec) [ -9436.1244] [ 1684] [depth= 4] . ( 1 sec) [ -9432.0305] [ 1684] [depth= 1] . ( 1 sec) [ -9387.4114] [ 1673] [depth= 2] . ( 1 sec) [ -9309.4425] [ 1648] [depth= 1] . ( 1 sec) [ -9032.5922] [ 1605] [depth= 10] . ( 1 sec) [ -8868.3313] [ 1578] [depth= 12] . ( 1 sec) [ -8811.3581] [ 1564] [depth= 1] . ( 1 sec) [ -8721.8108] [ 1558] [depth= 3] . ( 1 sec) [ -8681.8519] [ 1556] [depth= 5] . ( 1 sec) [ -8591.5578] [ 1520] [depth= 1] . ( 1 sec) [ -8404.8534] [ 1519] [depth= 4] . ( 1 sec) [ -8325.0741] [ 1517] [depth= 2] . ( 1 sec) [ -8323.7332] [ 1521] [depth= 2] . ( 1 sec) [ -8202.6914] [ 1492] [depth= 3] . ( 1 sec) [ -8149.5917] [ 1480] [depth= 3] . ( 1 sec) [ -8074.8102] [ 1481] [depth= 1] . ( 1 sec) [ -7894.1677] [ 1448] [depth= 6] . ( 1 sec) [ -7878.6701] [ 1447] [depth= 2] . ( 1 sec) [ -7806.2357] [ 1444] [depth= 4] . ( 1 sec) [ -7789.9219] [ 1445] [depth= 5] . ( 1 sec) [ -7592.8820] [ 1374] [depth= 5] . ( 1 sec) [ -7489.8506] [ 1345] [depth= 6] . ( 1 sec) [ -7282.0539] [ 1330] [depth= 12] . ( 1 sec) [ -7272.1086] [ 1330] [depth= 1] . ( 1 sec) [ -7092.3870] [ 1291] [depth= 10] . ( 1 sec) [ -6986.8589] [ 1293] [depth= 1] . ( 1 sec) [ -6980.1720] [ 1288] [depth= 1] . ( 1 sec) [ -6920.4942] [ 1271] [depth= 1] . ( 1 sec) [ -6798.5132] [ 1230] [depth= 11] . ( 1 sec) [ -6765.8955] [ 1229] [depth= 7] . ( 2 sec) [ -6643.7358] [ 1214] [depth= 5] . ( 2 sec) [ -6617.9718] [ 1202] [depth= 13] . ( 2 sec) [ -6356.2460] [ 1153] [depth= 13] . ( 2 sec) [ -6251.2646] [ 1131] [depth= 6] . ( 2 sec) [ -6250.8452] [ 1124] [depth= 3] . ( 2 sec) [ -6250.3954] [ 1123] [depth= 1] . ( 2 sec) [ -6108.9367] [ 1093] [depth= 5] . ( 2 sec) [ -6092.1420] [ 1088] [depth= 3] . ( 2 sec) [ -6039.0136] [ 1083] [depth= 5] . ( 2 sec) [ -5975.2183] [ 1069] [depth= 6] . ( 2 sec) [ -5967.8355] [ 1068] [depth= 1] . ( 2 sec) [ -5839.5758] [ 1036] [depth= 9] . ( 2 sec) [ -5748.5785] [ 1037] [depth= 1] . ( 2 sec) [ -5697.4962] [ 1037] [depth= 3] . ( 2 sec) [ -5685.3395] [ 1033] [depth= 1] . ( 2 sec) [ -5564.0031] [ 990] [depth= 3] . ( 2 sec) [ -5549.1947] [ 987] [depth= 1] . ( 2 sec) [ -5519.9817] [ 987] [depth= 1] . ( 2 sec) [ -5498.9312] [ 979] [depth= 1] . ( 2 sec) [ -5493.7208] [ 976] [depth= 1] . ( 2 sec) [ -5490.0146] [ 976] [depth= 1] . ( 2 sec) [ -5487.5945] [ 976] [depth= 1] . ( 2 sec) [ -5261.7149] [ 908] [depth= 4] . ( 2 sec) [ -5236.8033] [ 897] [depth= 1] . ( 2 sec) [ -5181.9101] [ 876] [depth= 1] . ( 2 sec) [ -5154.7320] [ 872] [depth= 2] . ( 3 sec) [ -5136.8720] [ 872] [depth= 1] . ( 3 sec) [ -5103.9588] [ 849] [depth= 2] . ( 3 sec) [ -5085.6555] [ 849] [depth= 1] . ( 3 sec) [ -5070.3219] [ 842] [depth= 1] . ( 3 sec) [ -4990.7273] [ 831] [depth= 1] . ( 3 sec) [ -4979.8670] [ 826] [depth= 1] . ( 3 sec) [ -4976.5206] [ 820] [depth= 1] . ( 3 sec) [ -4829.4337] [ 797] [depth= 4] . ( 3 sec) [ -4764.8195] [ 775] [depth= 2] . ( 3 sec) [ -4763.1271] [ 779] [depth= 1] . ( 3 sec) [ -4761.4261] [ 779] [depth= 1] . ( 3 sec) [ -4756.8313] [ 778] [depth= 2] . ( 3 sec) [ -4752.4758] [ 780] [depth= 1] . ( 3 sec) [ -4743.3607] [ 767] [depth= 1] . ( 3 sec) [ -4738.6897] [ 764] [depth= 1] . ( 3 sec) [ -4737.7878] [ 763] [depth= 1] . ( 3 sec) [ -4668.8432] [ 740] [depth= 5] . ( 3 sec) [ -4668.7997] [ 740] [depth= 1] . ( 3 sec) [ -4668.4364] [ 742] [depth= 1] . ( 4 sec) [ -4613.4851] [Branch lengths ] . ( 4 sec) [ -4612.5690] [GTR parameters ] . ( 4 sec) [ -4601.4738] [Alpha ][ 0.844979] . ( 4 sec) [ -4599.3587] [ 744] [depth= 1] . ( 4 sec) [ -4570.9814] [ 734] [depth= 1] . ( 4 sec) [ -4568.8421] [ 732] [depth= 1] . ( 4 sec) [ -4562.7733] [ 729] [depth= 2] . ( 5 sec) [ -4562.6481] [ 729] [depth= 1] . ( 5 sec) [ -4562.5817] [ 729] [depth= 1] . ( 5 sec) [ -4551.9101] [ 722] [depth= 1] . ( 5 sec) [ -4539.2755] [ 715] [depth= 1] . ( 5 sec) [ -4470.3345] [ 684] [depth= 3] . ( 5 sec) [ -4470.3239] [ 684] [depth= 1] . ( 6 sec) [ -4470.3097] [ 684] [depth= 1] . ( 7 sec) [ -4462.6524] [Branch lengths ] . ( 8 sec) [ -4462.4991] [GTR parameters ] . ( 8 sec) [ -4461.4636] [Alpha ][ 1.015592] . ( 11 sec) [ -4461.3232] [Branch lengths ] . ( 27 sec) [ -4461.3142] [Branch lengths ] . ( 27 sec) [ -4461.3142] [Topology ] . ( 28 sec) [ -4461.3137] [Topology ] . ( 28 sec) [ -4461.3105] [GTR parameters ] . ( 28 sec) [ -4461.3079] [Alpha ][ 1.025571] . ( 28 sec) [ -4461.3079] [Topology ] . ( 29 sec) [ -4461.3076] [Topology ] . ( 29 sec) [ -4461.3076] [GTR parameters ] . ( 29 sec) [ -4461.3076] [Alpha ][ 1.025571] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.307603. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10017.6016] [GTR parameters ] . ( 0 sec) [ -9820.9348] [Alpha ][ 0.500960] . ( 0 sec) [ -9509.8972] [ 1690] [depth= 3] . ( 0 sec) [ -9348.6812] [ 1663] [depth= 10] . ( 0 sec) [ -9298.9439] [ 1654] [depth= 3] . ( 0 sec) [ -9275.2070] [ 1647] [depth= 6] . ( 0 sec) [ -9243.6833] [ 1629] [depth= 1] . ( 0 sec) [ -9087.6179] [ 1613] [depth= 10] . ( 0 sec) [ -9054.4597] [ 1617] [depth= 1] . ( 0 sec) [ -9027.9348] [ 1615] [depth= 4] . ( 1 sec) [ -8934.7132] [ 1557] [depth= 2] . ( 1 sec) [ -8900.2173] [ 1555] [depth= 3] . ( 1 sec) [ -8751.2885] [ 1519] [depth= 3] . ( 1 sec) [ -8739.5728] [ 1519] [depth= 2] . ( 1 sec) [ -8736.1214] [ 1519] [depth= 1] . ( 1 sec) [ -8691.5463] [ 1519] [depth= 2] . ( 1 sec) [ -8411.8604] [ 1469] [depth= 10] . ( 1 sec) [ -8349.7832] [ 1459] [depth= 6] . ( 1 sec) [ -8348.0042] [ 1463] [depth= 1] . ( 1 sec) [ -8131.0549] [ 1391] [depth= 8] . ( 1 sec) [ -8073.7669] [ 1377] [depth= 9] . ( 1 sec) [ -7937.8996] [ 1375] [depth= 4] . ( 1 sec) [ -7718.3917] [ 1299] [depth= 5] . ( 1 sec) [ -7393.6945] [ 1298] [depth= 10] . ( 1 sec) [ -7363.0749] [ 1295] [depth= 4] . ( 1 sec) [ -7362.7466] [ 1294] [depth= 1] . ( 1 sec) [ -7347.4909] [ 1297] [depth= 5] . ( 1 sec) [ -7106.1048] [ 1204] [depth= 8] . ( 1 sec) [ -7044.5300] [ 1195] [depth= 6] . ( 1 sec) [ -7016.1262] [ 1160] [depth= 3] . ( 1 sec) [ -7011.1544] [ 1158] [depth= 2] . ( 1 sec) [ -7003.2031] [ 1158] [depth= 2] . ( 1 sec) [ -6988.8896] [ 1158] [depth= 3] . ( 1 sec) [ -6977.8759] [ 1159] [depth= 1] . ( 1 sec) [ -6969.5437] [ 1159] [depth= 1] . ( 1 sec) [ -6928.4024] [ 1150] [depth= 3] . ( 1 sec) [ -6909.1027] [ 1149] [depth= 3] . ( 1 sec) [ -6805.2565] [ 1141] [depth= 9] . ( 1 sec) [ -6787.1520] [ 1138] [depth= 1] . ( 2 sec) [ -6733.2721] [ 1140] [depth= 2] . ( 2 sec) [ -6562.2129] [ 1114] [depth= 6] . ( 2 sec) [ -6336.9440] [ 1113] [depth= 1] . ( 2 sec) [ -6285.9767] [ 1100] [depth= 2] . ( 2 sec) [ -6242.5287] [ 1101] [depth= 1] . ( 2 sec) [ -6064.8339] [ 1096] [depth= 12] . ( 2 sec) [ -5898.1395] [ 1047] [depth= 1] . ( 2 sec) [ -5813.3774] [ 1022] [depth= 10] . ( 2 sec) [ -5807.3197] [ 1019] [depth= 2] . ( 2 sec) [ -5790.9506] [ 1055] [depth= 16] . ( 2 sec) [ -5690.8569] [ 1028] [depth= 7] . ( 2 sec) [ -5686.9276] [ 1029] [depth= 4] . ( 2 sec) [ -5527.7888] [ 983] [depth= 6] . ( 2 sec) [ -5486.9456] [ 976] [depth= 2] . ( 2 sec) [ -5453.0638] [ 961] [depth= 1] . ( 2 sec) [ -5450.0214] [ 961] [depth= 2] . ( 2 sec) [ -5420.0230] [ 958] [depth= 2] . ( 2 sec) [ -5384.7689] [ 942] [depth= 2] . ( 2 sec) [ -5368.0621] [ 942] [depth= 1] . ( 2 sec) [ -5349.6923] [ 941] [depth= 2] . ( 2 sec) [ -5331.0846] [ 937] [depth= 1] . ( 2 sec) [ -5300.5477] [ 932] [depth= 4] . ( 2 sec) [ -5246.7786] [ 929] [depth= 2] . ( 2 sec) [ -5223.6166] [ 922] [depth= 1] . ( 2 sec) [ -5223.1781] [ 923] [depth= 1] . ( 2 sec) [ -5156.2603] [ 892] [depth= 3] . ( 2 sec) [ -5120.3962] [ 876] [depth= 3] . ( 3 sec) [ -5120.1547] [ 853] [depth= 8] . ( 3 sec) [ -5117.4878] [ 852] [depth= 1] . ( 3 sec) [ -5115.7699] [ 851] [depth= 1] . ( 3 sec) [ -5089.6943] [ 852] [depth= 3] . ( 3 sec) [ -5085.9970] [ 850] [depth= 1] . ( 3 sec) [ -5028.1254] [ 847] [depth= 2] . ( 3 sec) [ -4974.0981] [ 824] [depth= 1] . ( 3 sec) [ -4891.6603] [ 805] [depth= 5] . ( 3 sec) [ -4881.3072] [ 798] [depth= 2] . ( 3 sec) [ -4873.1144] [ 793] [depth= 1] . ( 3 sec) [ -4858.9538] [ 783] [depth= 3] . ( 3 sec) [ -4855.1551] [ 782] [depth= 1] . ( 3 sec) [ -4848.6950] [ 780] [depth= 3] . ( 3 sec) [ -4833.7662] [ 774] [depth= 2] . ( 4 sec) [ -4803.1371] [Branch lengths ] . ( 4 sec) [ -4801.8242] [GTR parameters ] . ( 4 sec) [ -4791.3054] [Alpha ][ 0.808033] . ( 4 sec) [ -4751.6831] [ 767] [depth= 2] . ( 4 sec) [ -4724.2271] [ 761] [depth= 3] . ( 4 sec) [ -4723.5493] [ 758] [depth= 2] . ( 4 sec) [ -4705.8937] [ 753] [depth= 1] . ( 4 sec) [ -4705.6923] [ 753] [depth= 1] . ( 4 sec) [ -4698.5004] [ 750] [depth= 1] . ( 4 sec) [ -4697.7780] [ 750] [depth= 1] . ( 4 sec) [ -4640.6657] [ 739] [depth= 2] . ( 4 sec) [ -4638.7330] [ 739] [depth= 1] . ( 5 sec) [ -4638.3643] [ 739] [depth= 1] . ( 5 sec) [ -4558.6261] [ 708] [depth= 1] . ( 5 sec) [ -4558.5884] [ 708] [depth= 1] . ( 5 sec) [ -4558.3778] [ 708] [depth= 1] . ( 5 sec) [ -4492.1859] [ 684] [depth= 1] . ( 7 sec) [ -4466.0377] [Branch lengths ] . ( 7 sec) [ -4465.9743] [GTR parameters ] . ( 7 sec) [ -4464.2250] [Alpha ][ 1.021072] . ( 11 sec) [ -4461.3514] [Branch lengths ] . ( 27 sec) [ -4461.3256] [Branch lengths ] . ( 27 sec) [ -4461.3256] [Topology ] . ( 28 sec) [ -4461.3254] [Topology ] . ( 28 sec) [ -4461.3082] [GTR parameters ] . ( 28 sec) [ -4461.3075] [Alpha ][ 1.026036] . ( 28 sec) [ -4461.3075] [Topology ] . ( 29 sec) [ -4461.3074] [Topology ] . ( 29 sec) [ -4461.3074] [GTR parameters ] . ( 29 sec) [ -4461.3074] [Alpha ][ 1.026036] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.307414. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10914.6366] [GTR parameters ] . ( 0 sec) [ -10684.2648] [Alpha ][ 0.500960] . ( 0 sec) [ -10324.8380] [ 1840] [depth= 8] . ( 0 sec) [ -10076.0174] [ 1815] [depth= 10] . ( 0 sec) [ -10068.0555] [ 1811] [depth= 3] . ( 0 sec) [ -10049.0009] [ 1811] [depth= 1] . ( 0 sec) [ -10048.4919] [ 1811] [depth= 1] . ( 0 sec) [ -10019.5036] [ 1811] [depth= 1] . ( 1 sec) [ -9692.4793] [ 1755] [depth= 10] . ( 1 sec) [ -9510.0766] [ 1747] [depth= 7] . ( 1 sec) [ -9356.5270] [ 1679] [depth= 9] . ( 1 sec) [ -9165.0200] [ 1675] [depth= 9] . ( 1 sec) [ -8994.2748] [ 1632] [depth= 13] . ( 1 sec) [ -8696.7105] [ 1576] [depth= 9] . ( 1 sec) [ -8681.6250] [ 1573] [depth= 3] . ( 1 sec) [ -8650.6089] [ 1573] [depth= 3] . ( 1 sec) [ -8577.4514] [ 1570] [depth= 2] . ( 1 sec) [ -8541.7758] [ 1570] [depth= 1] . ( 1 sec) [ -8382.8208] [ 1554] [depth= 1] . ( 1 sec) [ -8290.2852] [ 1544] [depth= 11] . ( 1 sec) [ -8209.8870] [ 1506] [depth= 4] . ( 1 sec) [ -7865.8470] [ 1427] [depth= 8] . ( 1 sec) [ -7863.5152] [ 1430] [depth= 11] . ( 1 sec) [ -7752.6944] [ 1398] [depth= 2] . ( 1 sec) [ -7640.6614] [ 1362] [depth= 9] . ( 1 sec) [ -7560.4288] [ 1362] [depth= 8] . ( 1 sec) [ -7413.1927] [ 1360] [depth= 8] . ( 1 sec) [ -7193.4810] [ 1360] [depth= 1] . ( 1 sec) [ -6968.6794] [ 1294] [depth= 5] . ( 1 sec) [ -6966.0129] [ 1293] [depth= 1] . ( 1 sec) [ -6909.6462] [ 1289] [depth= 8] . ( 1 sec) [ -6802.1749] [ 1263] [depth= 8] . ( 1 sec) [ -6702.9984] [ 1225] [depth= 10] . ( 1 sec) [ -6698.5774] [ 1231] [depth= 1] . ( 1 sec) [ -6692.0781] [ 1229] [depth= 4] . ( 1 sec) [ -6680.9630] [ 1229] [depth= 2] . ( 1 sec) [ -6674.8532] [ 1227] [depth= 4] . ( 1 sec) [ -6623.6335] [ 1229] [depth= 1] . ( 1 sec) [ -6592.1295] [ 1229] [depth= 6] . ( 2 sec) [ -6433.5977] [ 1197] [depth= 3] . ( 2 sec) [ -6296.7614] [ 1170] [depth= 3] . ( 2 sec) [ -6248.7644] [ 1164] [depth= 6] . ( 2 sec) [ -6129.4872] [ 1130] [depth= 7] . ( 2 sec) [ -6127.9322] [ 1130] [depth= 1] . ( 2 sec) [ -6127.8332] [ 1132] [depth= 1] . ( 2 sec) [ -5977.2949] [ 1093] [depth= 6] . ( 2 sec) [ -5963.1807] [ 1089] [depth= 2] . ( 2 sec) [ -5906.2344] [ 1084] [depth= 5] . ( 2 sec) [ -5879.6129] [ 1084] [depth= 1] . ( 2 sec) [ -5860.0280] [ 1083] [depth= 1] . ( 2 sec) [ -5859.8695] [ 1082] [depth= 1] . ( 2 sec) [ -5838.1275] [ 1081] [depth= 3] . ( 2 sec) [ -5806.1504] [ 1078] [depth= 8] . ( 2 sec) [ -5805.0134] [ 1082] [depth= 1] . ( 2 sec) [ -5804.4299] [ 1082] [depth= 1] . ( 2 sec) [ -5803.9621] [ 1078] [depth= 2] . ( 2 sec) [ -5800.5333] [ 1074] [depth= 5] . ( 2 sec) [ -5783.4526] [ 1054] [depth= 2] . ( 2 sec) [ -5782.8566] [ 1052] [depth= 4] . ( 2 sec) [ -5738.2516] [ 1026] [depth= 4] . ( 2 sec) [ -5545.8559] [ 1004] [depth= 2] . ( 2 sec) [ -5533.0437] [ 985] [depth= 3] . ( 2 sec) [ -5519.9495] [ 962] [depth= 5] . ( 2 sec) [ -5417.7084] [ 932] [depth= 1] . ( 3 sec) [ -5374.0239] [ 928] [depth= 1] . ( 3 sec) [ -5373.9335] [ 929] [depth= 1] . ( 3 sec) [ -5331.0902] [ 920] [depth= 5] . ( 3 sec) [ -5282.9276] [ 916] [depth= 3] . ( 3 sec) [ -5264.5594] [ 907] [depth= 1] . ( 3 sec) [ -5208.5586] [ 893] [depth= 3] . ( 3 sec) [ -5145.2416] [ 883] [depth= 4] . ( 3 sec) [ -5128.8783] [ 878] [depth= 1] . ( 3 sec) [ -5060.4703] [ 863] [depth= 4] . ( 3 sec) [ -5045.7685] [ 858] [depth= 1] . ( 3 sec) [ -5031.5228] [ 855] [depth= 1] . ( 3 sec) [ -5022.9444] [ 841] [depth= 4] . ( 3 sec) [ -5016.7132] [ 841] [depth= 1] . ( 3 sec) [ -4928.7837] [ 820] [depth= 1] . ( 3 sec) [ -4928.4554] [ 820] [depth= 1] . ( 3 sec) [ -4821.3735] [ 789] [depth= 6] . ( 3 sec) [ -4819.7137] [ 788] [depth= 1] . ( 3 sec) [ -4777.8349] [ 778] [depth= 3] . ( 4 sec) [ -4733.7566] [Branch lengths ] . ( 4 sec) [ -4732.3503] [GTR parameters ] . ( 4 sec) [ -4722.7010] [Alpha ][ 0.799654] . ( 4 sec) [ -4606.6642] [ 743] [depth= 2] . ( 4 sec) [ -4546.1680] [ 722] [depth= 2] . ( 4 sec) [ -4533.8363] [ 718] [depth= 1] . ( 4 sec) [ -4509.3497] [ 705] [depth= 2] . ( 5 sec) [ -4500.7182] [ 701] [depth= 1] . ( 5 sec) [ -4500.6924] [ 701] [depth= 1] . ( 5 sec) [ -4487.8177] [ 695] [depth= 1] . ( 6 sec) [ -4482.5334] [ 691] [depth= 1] . ( 6 sec) [ -4482.5202] [ 691] [depth= 1] . ( 6 sec) [ -4466.4450] [ 684] [depth= 1] . ( 8 sec) [ -4463.5787] [Branch lengths ] . ( 8 sec) [ -4463.2155] [GTR parameters ] . ( 8 sec) [ -4461.4382] [Alpha ][ 1.015842] . ( 11 sec) [ -4461.3268] [Branch lengths ] . ( 28 sec) [ -4461.3170] [Branch lengths ] . ( 28 sec) [ -4461.3170] [Topology ] . ( 28 sec) [ -4461.3166] [Topology ] . ( 28 sec) [ -4461.3103] [GTR parameters ] . ( 29 sec) [ -4461.3078] [Alpha ][ 1.025592] . ( 29 sec) [ -4461.3078] [Topology ] . ( 29 sec) [ -4461.3076] [Topology ] . ( 29 sec) [ -4461.3075] [GTR parameters ] . ( 29 sec) [ -4461.3075] [Alpha ][ 1.025592] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.307544. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10812.5007] [GTR parameters ] . ( 1 sec) [ -10600.7181] [Alpha ][ 0.500960] . ( 1 sec) [ -10358.9609] [ 1778] [depth= 8] . ( 1 sec) [ -10251.4465] [ 1748] [depth= 8] . ( 1 sec) [ -10196.8081] [ 1738] [depth= 7] . ( 1 sec) [ -10125.8005] [ 1718] [depth= 1] . ( 1 sec) [ -9987.5408] [ 1704] [depth= 9] . ( 1 sec) [ -9794.7632] [ 1698] [depth= 3] . ( 1 sec) [ -9749.6356] [ 1697] [depth= 2] . ( 1 sec) [ -9678.2797] [ 1696] [depth= 2] . ( 1 sec) [ -9502.1349] [ 1694] [depth= 5] . ( 1 sec) [ -9464.5253] [ 1693] [depth= 6] . ( 1 sec) [ -9328.0661] [ 1692] [depth= 5] . ( 1 sec) [ -9176.1333] [ 1665] [depth= 12] . ( 1 sec) [ -9061.3092] [ 1619] [depth= 5] . ( 1 sec) [ -8996.7426] [ 1616] [depth= 4] . ( 1 sec) [ -8728.5958] [ 1586] [depth= 3] . ( 1 sec) [ -8665.1043] [ 1585] [depth= 7] . ( 1 sec) [ -8503.7285] [ 1527] [depth= 13] . ( 1 sec) [ -8436.8777] [ 1519] [depth= 3] . ( 1 sec) [ -8387.7224] [ 1518] [depth= 5] . ( 1 sec) [ -8381.8032] [ 1518] [depth= 5] . ( 1 sec) [ -8217.3535] [ 1478] [depth= 11] . ( 1 sec) [ -8210.8987] [ 1480] [depth= 1] . ( 1 sec) [ -7971.2818] [ 1466] [depth= 2] . ( 1 sec) [ -7794.4994] [ 1431] [depth= 14] . ( 1 sec) [ -7689.9031] [ 1401] [depth= 16] . ( 1 sec) [ -7551.7514] [ 1362] [depth= 7] . ( 2 sec) [ -7531.1987] [ 1360] [depth= 4] . ( 2 sec) [ -7459.0598] [ 1348] [depth= 1] . ( 2 sec) [ -7445.1149] [ 1345] [depth= 3] . ( 2 sec) [ -7329.6994] [ 1343] [depth= 11] . ( 2 sec) [ -7288.9080] [ 1317] [depth= 1] . ( 2 sec) [ -7261.1095] [ 1304] [depth= 3] . ( 2 sec) [ -7213.9148] [ 1290] [depth= 7] . ( 2 sec) [ -7198.6286] [ 1292] [depth= 1] . ( 2 sec) [ -7122.3622] [ 1268] [depth= 2] . ( 2 sec) [ -7117.9008] [ 1269] [depth= 1] . ( 2 sec) [ -6987.1114] [ 1236] [depth= 2] . ( 2 sec) [ -6906.3654] [ 1218] [depth= 4] . ( 2 sec) [ -6828.6318] [ 1191] [depth= 1] . ( 2 sec) [ -6805.4232] [ 1191] [depth= 1] . ( 2 sec) [ -6686.3726] [ 1150] [depth= 4] . ( 2 sec) [ -6682.0404] [ 1148] [depth= 2] . ( 2 sec) [ -6658.2359] [ 1154] [depth= 5] . ( 2 sec) [ -6486.7626] [ 1154] [depth= 9] . ( 2 sec) [ -6480.1002] [ 1157] [depth= 1] . ( 2 sec) [ -6472.0882] [ 1152] [depth= 1] . ( 2 sec) [ -6387.8888] [ 1149] [depth= 1] . ( 2 sec) [ -6312.9114] [ 1128] [depth= 1] . ( 2 sec) [ -6126.1723] [ 1078] [depth= 1] . ( 2 sec) [ -6095.8975] [ 1075] [depth= 5] . ( 2 sec) [ -6085.6068] [ 1078] [depth= 1] . ( 2 sec) [ -6041.4153] [ 1042] [depth= 3] . ( 2 sec) [ -5953.4980] [ 1032] [depth= 5] . ( 2 sec) [ -5943.9549] [ 1034] [depth= 1] . ( 3 sec) [ -5943.8399] [ 1034] [depth= 1] . ( 3 sec) [ -5928.4063] [ 1029] [depth= 2] . ( 3 sec) [ -5726.6934] [ 989] [depth= 9] . ( 3 sec) [ -5547.9045] [ 934] [depth= 6] . ( 3 sec) [ -5474.6200] [ 922] [depth= 5] . ( 3 sec) [ -5216.9553] [ 889] [depth= 3] . ( 3 sec) [ -5216.6185] [ 890] [depth= 1] . ( 3 sec) [ -5160.8169] [ 863] [depth= 6] . ( 3 sec) [ -5157.9844] [ 863] [depth= 1] . ( 3 sec) [ -5156.3547] [ 863] [depth= 1] . ( 3 sec) [ -5149.6634] [ 857] [depth= 5] . ( 3 sec) [ -5094.2026] [ 853] [depth= 2] . ( 3 sec) [ -5088.6194] [ 855] [depth= 3] . ( 3 sec) [ -4980.4899] [ 827] [depth= 3] . ( 3 sec) [ -4966.9193] [ 825] [depth= 1] . ( 3 sec) [ -4784.2994] [ 752] [depth= 9] . ( 3 sec) [ -4784.2142] [ 752] [depth= 1] . ( 3 sec) [ -4781.3812] [ 751] [depth= 1] . ( 3 sec) [ -4737.9238] [ 740] [depth= 1] . ( 3 sec) [ -4737.2767] [ 738] [depth= 1] . ( 3 sec) [ -4734.3659] [ 738] [depth= 3] . ( 3 sec) [ -4734.1206] [ 738] [depth= 1] . ( 4 sec) [ -4687.4921] [ 729] [depth= 2] . ( 4 sec) [ -4656.7382] [ 725] [depth= 1] . ( 4 sec) [ -4646.8866] [ 722] [depth= 1] . ( 4 sec) [ -4616.9332] [Branch lengths ] . ( 4 sec) [ -4615.8096] [GTR parameters ] . ( 4 sec) [ -4601.6817] [Alpha ][ 0.913318] . ( 4 sec) [ -4601.6411] [ 722] [depth= 1] . ( 4 sec) [ -4549.0847] [ 709] [depth= 1] . ( 4 sec) [ -4538.6419] [ 705] [depth= 1] . ( 5 sec) [ -4531.2118] [ 701] [depth= 1] . ( 5 sec) [ -4504.2674] [ 695] [depth= 3] . ( 5 sec) [ -4504.2549] [ 695] [depth= 1] . ( 5 sec) [ -4504.1363] [ 695] [depth= 1] . ( 5 sec) [ -4490.2536] [ 691] [depth= 2] . ( 6 sec) [ -4467.6093] [ 684] [depth= 1] . ( 8 sec) [ -4462.2330] [Branch lengths ] . ( 8 sec) [ -4461.8137] [GTR parameters ] . ( 8 sec) [ -4461.4523] [Alpha ][ 1.020136] . ( 11 sec) [ -4461.3133] [Branch lengths ] . ( 28 sec) [ -4461.3096] [Branch lengths ] . ( 28 sec) [ -4461.3096] [Topology ] . ( 29 sec) [ -4461.3095] [Topology ] . ( 29 sec) [ -4461.3083] [GTR parameters ] . ( 29 sec) [ -4461.3074] [Alpha ][ 1.025610] . ( 29 sec) [ -4461.3074] [Topology ] . ( 29 sec) [ -4461.3074] [Topology ] . ( 29 sec) [ -4461.3074] [GTR parameters ] . ( 29 sec) [ -4461.3074] [Alpha ][ 1.025610] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.307374. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10692.6005] [GTR parameters ] . ( 1 sec) [ -10476.9568] [Alpha ][ 0.500960] . ( 1 sec) [ -10097.8275] [ 1813] [depth= 6] . ( 1 sec) [ -9968.8494] [ 1786] [depth= 9] . ( 1 sec) [ -9935.0824] [ 1780] [depth= 5] . ( 1 sec) [ -9915.3872] [ 1780] [depth= 1] . ( 1 sec) [ -9896.9803] [ 1774] [depth= 10] . ( 1 sec) [ -9826.6430] [ 1774] [depth= 3] . ( 1 sec) [ -9737.4432] [ 1770] [depth= 10] . ( 1 sec) [ -9671.1064] [ 1771] [depth= 1] . ( 1 sec) [ -9508.5078] [ 1729] [depth= 10] . ( 1 sec) [ -9333.2614] [ 1711] [depth= 9] . ( 1 sec) [ -9262.8097] [ 1705] [depth= 15] . ( 1 sec) [ -9166.3835] [ 1681] [depth= 2] . ( 1 sec) [ -9125.1183] [ 1678] [depth= 14] . ( 1 sec) [ -9037.6729] [ 1672] [depth= 5] . ( 1 sec) [ -9013.6264] [ 1670] [depth= 4] . ( 1 sec) [ -8988.0038] [ 1671] [depth= 1] . ( 1 sec) [ -8942.7551] [ 1670] [depth= 1] . ( 1 sec) [ -8928.2475] [ 1664] [depth= 1] . ( 1 sec) [ -8822.2201] [ 1661] [depth= 8] . ( 1 sec) [ -8752.6302] [ 1655] [depth= 9] . ( 2 sec) [ -8233.9135] [ 1570] [depth= 14] . ( 2 sec) [ -8080.9919] [ 1554] [depth= 3] . ( 2 sec) [ -7999.2878] [ 1521] [depth= 1] . ( 2 sec) [ -7909.4029] [ 1520] [depth= 9] . ( 2 sec) [ -7863.7771] [ 1468] [depth= 8] . ( 2 sec) [ -7773.9237] [ 1467] [depth= 9] . ( 2 sec) [ -7534.6406] [ 1398] [depth= 11] . ( 2 sec) [ -7518.9037] [ 1398] [depth= 3] . ( 2 sec) [ -7460.0144] [ 1388] [depth= 2] . ( 2 sec) [ -7449.8895] [ 1385] [depth= 4] . ( 2 sec) [ -7441.2003] [ 1384] [depth= 1] . ( 2 sec) [ -7422.5078] [ 1384] [depth= 6] . ( 2 sec) [ -7319.5935] [ 1371] [depth= 9] . ( 2 sec) [ -7302.4567] [ 1369] [depth= 2] . ( 2 sec) [ -7052.8284] [ 1393] [depth= 1] . ( 2 sec) [ -6731.3367] [ 1320] [depth= 10] . ( 2 sec) [ -6686.2735] [ 1313] [depth= 5] . ( 2 sec) [ -6566.8820] [ 1268] [depth= 3] . ( 2 sec) [ -6552.7639] [ 1264] [depth= 5] . ( 2 sec) [ -6548.0343] [ 1263] [depth= 5] . ( 2 sec) [ -6510.8784] [ 1255] [depth= 9] . ( 2 sec) [ -6494.1146] [ 1239] [depth= 1] . ( 2 sec) [ -6490.7773] [ 1237] [depth= 2] . ( 2 sec) [ -6489.0392] [ 1238] [depth= 3] . ( 2 sec) [ -6261.7751] [ 1183] [depth= 11] . ( 2 sec) [ -6194.9707] [ 1182] [depth= 2] . ( 2 sec) [ -6158.2369] [ 1180] [depth= 7] . ( 2 sec) [ -6047.0475] [ 1153] [depth= 4] . ( 2 sec) [ -6027.6766] [ 1128] [depth= 6] . ( 3 sec) [ -6002.5142] [ 1127] [depth= 4] . ( 3 sec) [ -5887.0044] [ 1081] [depth= 8] . ( 3 sec) [ -5856.3800] [ 1073] [depth= 8] . ( 3 sec) [ -5713.7550] [ 1031] [depth= 3] . ( 3 sec) [ -5693.4355] [ 1028] [depth= 1] . ( 3 sec) [ -5563.3628] [ 1010] [depth= 3] . ( 3 sec) [ -5544.0915] [ 1010] [depth= 1] . ( 3 sec) [ -5406.6787] [ 966] [depth= 10] . ( 3 sec) [ -5390.4425] [ 945] [depth= 2] . ( 3 sec) [ -5253.4248] [ 914] [depth= 2] . ( 3 sec) [ -5222.4196] [ 899] [depth= 6] . ( 3 sec) [ -5214.7207] [ 897] [depth= 2] . ( 3 sec) [ -5209.0822] [ 894] [depth= 4] . ( 3 sec) [ -5189.0590] [ 893] [depth= 2] . ( 3 sec) [ -5145.1292] [ 894] [depth= 1] . ( 3 sec) [ -5068.4829] [ 860] [depth= 3] . ( 3 sec) [ -5065.2172] [ 860] [depth= 1] . ( 3 sec) [ -5022.1844] [ 848] [depth= 4] . ( 3 sec) [ -5016.3900] [ 847] [depth= 5] . ( 3 sec) [ -4991.1548] [ 843] [depth= 3] . ( 3 sec) [ -4989.6542] [ 843] [depth= 2] . ( 3 sec) [ -4924.1004] [ 816] [depth= 3] . ( 3 sec) [ -4784.2976] [ 771] [depth= 7] . ( 3 sec) [ -4780.2839] [ 774] [depth= 1] . ( 4 sec) [ -4767.7198] [ 770] [depth= 1] . ( 4 sec) [ -4748.9486] [ 761] [depth= 2] . ( 4 sec) [ -4748.7320] [ 762] [depth= 1] . ( 4 sec) [ -4748.5695] [ 762] [depth= 2] . ( 4 sec) [ -4748.2577] [ 762] [depth= 3] . ( 4 sec) [ -4732.8424] [ 755] [depth= 2] . ( 4 sec) [ -4697.0460] [ 751] [depth= 1] . ( 4 sec) [ -4663.9920] [Branch lengths ] . ( 5 sec) [ -4662.6657] [GTR parameters ] . ( 5 sec) [ -4650.1407] [Alpha ][ 0.857851] . ( 5 sec) [ -4634.0300] [ 744] [depth= 2] . ( 5 sec) [ -4633.0839] [ 735] [depth= 4] . ( 5 sec) [ -4631.4580] [ 736] [depth= 1] . ( 5 sec) [ -4631.3644] [ 736] [depth= 1] . ( 5 sec) [ -4628.5136] [ 735] [depth= 2] . ( 5 sec) [ -4505.1367] [ 698] [depth= 9] . ( 5 sec) [ -4501.3819] [ 697] [depth= 2] . ( 5 sec) [ -4501.1110] [ 697] [depth= 1] . ( 6 sec) [ -4501.0261] [ 697] [depth= 1] . ( 6 sec) [ -4499.1513] [ 696] [depth= 1] . ( 6 sec) [ -4499.1277] [ 697] [depth= 1] . ( 6 sec) [ -4497.9737] [ 696] [depth= 1] . ( 6 sec) [ -4497.9599] [ 696] [depth= 1] . ( 6 sec) [ -4489.1228] [ 691] [depth= 1] . ( 6 sec) [ -4469.1056] [ 684] [depth= 2] . ( 7 sec) [ -4469.0692] [ 684] [depth= 1] . ( 8 sec) [ -4462.9907] [Branch lengths ] . ( 8 sec) [ -4462.6885] [GTR parameters ] . ( 8 sec) [ -4461.7576] [Alpha ][ 1.021137] . ( 12 sec) [ -4461.3140] [Branch lengths ] . ( 28 sec) [ -4461.3120] [Branch lengths ] . ( 28 sec) [ -4461.3120] [Topology ] . ( 29 sec) [ -4461.3119] [Topology ] . ( 29 sec) [ -4461.3081] [GTR parameters ] . ( 29 sec) [ -4461.3075] [Alpha ][ 1.025638] . ( 29 sec) [ -4461.3075] [Topology ] . ( 30 sec) [ -4461.3074] [Topology ] . ( 30 sec) [ -4461.3074] [GTR parameters ] . ( 30 sec) [ -4461.3074] [Alpha ][ 1.025638] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4461.307442. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4475.291522 . ( 0 sec) [ -4472.4085] [GTR parameters ] . ( 0 sec) [ -4472.4070] [Alpha ][ 1.007326] . ( 0 sec) [ -4472.4070] [Topology ] . ( 1 sec) [ -4462.4908] [Topology ] . ( 1 sec) [ -4461.5449] [Topology ] . ( 2 sec) [ -4461.3788] [Topology ] . ( 3 sec) [ -4461.3404] [Topology ] . ( 3 sec) [ -4461.3305] [Topology ] . ( 4 sec) [ -4461.3278] [Topology ] . ( 4 sec) [ -4461.3270] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4461.327021 . ( 8 sec) [ -4461.3173] [GTR parameters ] . ( 8 sec) [ -4461.3084] [Alpha ][ 1.024609] . ( 8 sec) [ -4461.3084] [Topology ] . ( 9 sec) [ -4461.3078] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4461.307814 . ( 12 sec) [ -4461.3078] [GTR parameters ] . ( 13 sec) [ -4461.3077] [Alpha ][ 1.025633] . ( 13 sec) [ -4461.3077] [Topology ] . ( 13 sec) [ -4461.3075] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 21 sec) [ -4472.4085] [GTR parameters ] . ( 21 sec) [ -4472.4070] [Alpha ][ 1.007326] . ( 21 sec) [ -4469.8470] [ 684] [depth= 1] . ( 22 sec) [ -4468.0896] [ 684] [depth= 1] . ( 22 sec) [ -4467.9747] [ 684] [depth= 1] . ( 22 sec) [ -4467.6254] [ 684] [depth= 1] . ( 22 sec) [ -4467.5436] [ 684] [depth= 1] . ( 23 sec) [ -4467.5156] [ 684] [depth= 1] . ( 24 sec) [ -4461.4086] [Branch lengths ] . ( 24 sec) [ -4461.3997] [GTR parameters ] . ( 24 sec) [ -4461.3956] [Alpha ][ 1.019776] . ( 28 sec) [ -4461.3124] [Branch lengths ] . ( 44 sec) [ -4461.3085] [Branch lengths ] . ( 44 sec) [ -4461.3085] [Topology ] . ( 45 sec) [ -4461.3084] [Topology ] . ( 45 sec) [ -4461.3084] [GTR parameters ] . ( 45 sec) [ -4461.3074] [Alpha ][ 1.025601] . ( 45 sec) [ -4461.3074] [Topology ] . ( 45 sec) [ -4461.3073] [Topology ] . ( 45 sec) [ -4461.3073] [GTR parameters ] . ( 45 sec) [ -4461.3073] [Alpha ][ 1.025601] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4461.307512 . Log likelihood obtained after SPR moves : -4461.307338 . Log likelihood of the current tree: -4461.307338. . Printing the most likely tree in file 'data10.phy_phyml_tree.txt'... . Best log likelihood : -4461.307338 . Time used 0h0m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo