.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data36.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... . 242 patterns found. (out of a total of 500 sites) . 238 sites without polymorphism (47.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -8511.4854] [GTR parameters ] . ( 0 sec) [ -8360.4962] [Alpha ][ 0.500960] . ( 1 sec) [ -8205.3785] [ 1165] [depth= 8] . ( 1 sec) [ -8146.1465] [ 1163] [depth= 6] . ( 1 sec) [ -8046.1380] [ 1158] [depth= 4] . ( 1 sec) [ -8014.3692] [ 1156] [depth= 5] . ( 1 sec) [ -7629.6671] [ 1130] [depth= 4] . ( 1 sec) [ -7590.4563] [ 1130] [depth= 1] . ( 1 sec) [ -7575.3038] [ 1129] [depth= 6] . ( 1 sec) [ -7518.9750] [ 1131] [depth= 1] . ( 1 sec) [ -7518.5902] [ 1131] [depth= 8] . ( 1 sec) [ -7381.5768] [ 1129] [depth= 11] . ( 1 sec) [ -7365.8499] [ 1140] [depth= 1] . ( 1 sec) [ -7223.2374] [ 1091] [depth= 10] . ( 1 sec) [ -7203.0752] [ 1080] [depth= 8] . ( 1 sec) [ -7040.4647] [ 1067] [depth= 10] . ( 1 sec) [ -6939.8599] [ 1063] [depth= 5] . ( 1 sec) [ -6934.1210] [ 1062] [depth= 1] . ( 1 sec) [ -6933.9766] [ 1044] [depth= 6] . ( 1 sec) [ -6876.3144] [ 1044] [depth= 1] . ( 1 sec) [ -6763.4797] [ 1039] [depth= 10] . ( 1 sec) [ -6728.8022] [ 1040] [depth= 2] . ( 1 sec) [ -6666.5605] [ 1014] [depth= 3] . ( 1 sec) [ -6507.6869] [ 984] [depth= 11] . ( 1 sec) [ -6473.2705] [ 984] [depth= 1] . ( 1 sec) [ -6248.2600] [ 973] [depth= 4] . ( 1 sec) [ -6170.5118] [ 975] [depth= 6] . ( 1 sec) [ -6071.5016] [ 964] [depth= 4] . ( 1 sec) [ -6066.6184] [ 964] [depth= 1] . ( 1 sec) [ -6031.1908] [ 958] [depth= 17] . ( 1 sec) [ -5961.2527] [ 951] [depth= 5] . ( 1 sec) [ -5929.9374] [ 943] [depth= 6] . ( 1 sec) [ -5928.7637] [ 943] [depth= 1] . ( 1 sec) [ -5829.4155] [ 932] [depth= 3] . ( 1 sec) [ -5789.9412] [ 933] [depth= 1] . ( 1 sec) [ -5694.1993] [ 931] [depth= 10] . ( 1 sec) [ -5626.9932] [ 909] [depth= 15] . ( 1 sec) [ -5584.5127] [ 886] [depth= 1] . ( 1 sec) [ -5464.9158] [ 867] [depth= 10] . ( 1 sec) [ -5345.9830] [ 855] [depth= 4] . ( 1 sec) [ -5106.7046] [ 818] [depth= 10] . ( 1 sec) [ -5069.2280] [ 813] [depth= 11] . ( 1 sec) [ -4947.1340] [ 810] [depth= 5] . ( 2 sec) [ -4929.4296] [ 809] [depth= 2] . ( 2 sec) [ -4916.8465] [ 812] [depth= 6] . ( 2 sec) [ -4909.9582] [ 812] [depth= 2] . ( 2 sec) [ -4834.0382] [ 801] [depth= 8] . ( 2 sec) [ -4824.8202] [ 801] [depth= 3] . ( 2 sec) [ -4805.5619] [ 797] [depth= 1] . ( 2 sec) [ -4739.4072] [ 797] [depth= 3] . ( 2 sec) [ -4698.5555] [ 785] [depth= 3] . ( 2 sec) [ -4696.6936] [ 785] [depth= 1] . ( 2 sec) [ -4566.7258] [ 748] [depth= 4] . ( 2 sec) [ -4565.2325] [ 748] [depth= 7] . ( 2 sec) [ -4518.4287] [ 743] [depth= 5] . ( 2 sec) [ -4449.7157] [ 736] [depth= 5] . ( 2 sec) [ -4337.5696] [ 731] [depth= 1] . ( 2 sec) [ -4294.6006] [ 702] [depth= 12] . ( 2 sec) [ -4202.1135] [ 687] [depth= 9] . ( 2 sec) [ -4199.9933] [ 685] [depth= 5] . ( 2 sec) [ -4131.1195] [ 671] [depth= 7] . ( 2 sec) [ -4129.9534] [ 671] [depth= 1] . ( 2 sec) [ -4129.6296] [ 652] [depth= 1] . ( 2 sec) [ -4028.3192] [ 642] [depth= 5] . ( 2 sec) [ -4021.7314] [ 641] [depth= 1] . ( 2 sec) [ -3995.4686] [ 635] [depth= 6] . ( 2 sec) [ -3988.2016] [ 635] [depth= 2] . ( 2 sec) [ -3987.5136] [ 635] [depth= 2] . ( 2 sec) [ -3986.8887] [ 632] [depth= 1] . ( 2 sec) [ -3946.4531] [ 623] [depth= 1] . ( 2 sec) [ -3944.6887] [ 623] [depth= 1] . ( 3 sec) [ -3930.2356] [ 619] [depth= 1] . ( 3 sec) [ -3896.8978] [ 606] [depth= 5] . ( 3 sec) [ -3810.1940] [ 588] [depth= 1] . ( 3 sec) [ -3802.6644] [ 585] [depth= 1] . ( 3 sec) [ -3795.3303] [ 580] [depth= 1] . ( 3 sec) [ -3788.1895] [ 579] [depth= 2] . ( 3 sec) [ -3786.9236] [ 579] [depth= 1] . ( 3 sec) [ -3741.0820] [ 565] [depth= 2] . ( 3 sec) [ -3705.0426] [ 557] [depth= 2] . ( 3 sec) [ -3686.0078] [ 549] [depth= 2] . ( 3 sec) [ -3684.7087] [ 549] [depth= 1] . ( 3 sec) [ -3684.6957] [ 549] [depth= 2] . ( 3 sec) [ -3663.6635] [Branch lengths ] . ( 3 sec) [ -3654.2940] [GTR parameters ] . ( 3 sec) [ -3649.9423] [Alpha ][ 0.719490] . ( 4 sec) [ -3626.8711] [ 538] [depth= 4] . ( 4 sec) [ -3626.3824] [ 539] [depth= 1] . ( 4 sec) [ -3624.2057] [ 538] [depth= 1] . ( 5 sec) [ -3613.6246] [ 533] [depth= 2] . ( 5 sec) [ -3611.1909] [ 532] [depth= 1] . ( 5 sec) [ -3606.7916] [ 532] [depth= 1] . ( 6 sec) [ -3606.6769] [ 532] [depth= 1] . ( 7 sec) [ -3606.0948] [Branch lengths ] . ( 7 sec) [ -3605.9956] [GTR parameters ] . ( 7 sec) [ -3605.7646] [Alpha ][ 0.788536] . ( 7 sec) [ -3605.6760] [ 532] [depth= 1] . ( 10 sec) [ -3605.5995] [ 529] [depth= 1] . ( 11 sec) [ -3605.5059] [Branch lengths ] . ( 11 sec) [ -3605.4957] [GTR parameters ] . ( 11 sec) [ -3605.4946] [Alpha ][ 0.793725] . ( 27 sec) [ -3605.4777] [Branch lengths ] . ( 27 sec) [ -3605.4777] [Topology ] . ( 27 sec) [ -3605.4699] [Topology ] . ( 28 sec) [ -3605.4427] [Topology ] . ( 28 sec) [ -3605.2563] [Topology ] . ( 28 sec) [ -3604.0614] [Topology ] . ( 29 sec) [ -3599.8937] [Topology ] . ( 29 sec) [ -3597.0972] [Topology ] . ( 29 sec) [ -3597.0625] [GTR parameters ] . ( 30 sec) [ -3597.0549] [Alpha ][ 0.807881] . ( 30 sec) [ -3597.0549] [Topology ] . ( 30 sec) [ -3596.8292] [Topology ] . ( 30 sec) [ -3596.7958] [Topology ] . ( 31 sec) [ -3596.7876] [Topology ] . ( 31 sec) [ -3596.7846] [Topology ] . ( 32 sec) [ -3596.7831] [Topology ] . ( 32 sec) [ -3596.7822] [Topology ] . ( 32 sec) [ -3596.7815] [GTR parameters ] . ( 32 sec) [ -3596.7814] [Alpha ][ 0.809232] . ( 32 sec) [ -3596.7814] [Topology ] . ( 33 sec) [ -3596.7805] [Topology ] . ( 33 sec) [ -3596.7805] [GTR parameters ] . ( 33 sec) [ -3596.7805] [Alpha ][ 0.809232] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3596.780510. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7882.5926] [GTR parameters ] . ( 1 sec) [ -7744.4177] [Alpha ][ 0.500960] . ( 1 sec) [ -7606.0106] [ 1174] [depth= 3] . ( 1 sec) [ -7449.3937] [ 1148] [depth= 3] . ( 1 sec) [ -7328.9074] [ 1138] [depth= 4] . ( 1 sec) [ -7205.4032] [ 1137] [depth= 5] . ( 1 sec) [ -7184.6449] [ 1129] [depth= 1] . ( 1 sec) [ -7143.8690] [ 1129] [depth= 2] . ( 1 sec) [ -7091.9563] [ 1131] [depth= 1] . ( 1 sec) [ -6946.1847] [ 1128] [depth= 6] . ( 1 sec) [ -6912.1701] [ 1088] [depth= 2] . ( 1 sec) [ -6895.0323] [ 1087] [depth= 6] . ( 1 sec) [ -6820.7844] [ 1065] [depth= 4] . ( 1 sec) [ -6781.4232] [ 1064] [depth= 5] . ( 1 sec) [ -6685.9708] [ 1034] [depth= 14] . ( 1 sec) [ -6596.3640] [ 1034] [depth= 6] . ( 1 sec) [ -6454.3921] [ 999] [depth= 14] . ( 1 sec) [ -6362.1336] [ 985] [depth= 1] . ( 1 sec) [ -6241.1096] [ 972] [depth= 5] . ( 1 sec) [ -6158.3870] [ 970] [depth= 1] . ( 1 sec) [ -6132.5441] [ 969] [depth= 1] . ( 1 sec) [ -6008.1100] [ 952] [depth= 14] . ( 1 sec) [ -5853.8421] [ 918] [depth= 1] . ( 1 sec) [ -5681.2665] [ 905] [depth= 10] . ( 1 sec) [ -5678.6185] [ 905] [depth= 1] . ( 1 sec) [ -5678.2813] [ 911] [depth= 10] . ( 1 sec) [ -5672.6762] [ 912] [depth= 1] . ( 1 sec) [ -5668.5680] [ 907] [depth= 1] . ( 1 sec) [ -5640.7637] [ 904] [depth= 5] . ( 2 sec) [ -5569.4949] [ 882] [depth= 4] . ( 2 sec) [ -5439.6702] [ 859] [depth= 4] . ( 2 sec) [ -5398.7649] [ 852] [depth= 1] . ( 2 sec) [ -5304.3183] [ 837] [depth= 4] . ( 2 sec) [ -5299.4484] [ 836] [depth= 1] . ( 2 sec) [ -5194.1654] [ 826] [depth= 1] . ( 2 sec) [ -5162.5583] [ 820] [depth= 1] . ( 2 sec) [ -5125.4416] [ 798] [depth= 9] . ( 2 sec) [ -5047.7607] [ 792] [depth= 1] . ( 2 sec) [ -4995.5728] [ 789] [depth= 2] . ( 2 sec) [ -4866.2688] [ 790] [depth= 1] . ( 2 sec) [ -4819.9304] [ 774] [depth= 2] . ( 2 sec) [ -4762.2946] [ 761] [depth= 5] . ( 2 sec) [ -4743.1227] [ 756] [depth= 6] . ( 2 sec) [ -4670.8907] [ 758] [depth= 1] . ( 2 sec) [ -4662.8310] [ 752] [depth= 1] . ( 2 sec) [ -4477.3971] [ 709] [depth= 8] . ( 2 sec) [ -4435.7196] [ 702] [depth= 3] . ( 2 sec) [ -4421.4675] [ 704] [depth= 2] . ( 2 sec) [ -4409.7782] [ 700] [depth= 1] . ( 2 sec) [ -4403.5948] [ 700] [depth= 4] . ( 2 sec) [ -4392.3448] [ 700] [depth= 1] . ( 2 sec) [ -4392.3290] [ 700] [depth= 2] . ( 2 sec) [ -4392.2264] [ 700] [depth= 2] . ( 2 sec) [ -4369.5945] [ 699] [depth= 1] . ( 2 sec) [ -4365.6646] [ 699] [depth= 1] . ( 2 sec) [ -4279.0547] [ 683] [depth= 8] . ( 2 sec) [ -4264.9615] [ 684] [depth= 1] . ( 2 sec) [ -4264.5366] [ 684] [depth= 1] . ( 2 sec) [ -4231.1744] [ 684] [depth= 1] . ( 2 sec) [ -4229.6144] [ 680] [depth= 5] . ( 2 sec) [ -4227.0329] [ 678] [depth= 3] . ( 2 sec) [ -4216.1320] [ 674] [depth= 1] . ( 2 sec) [ -4115.0910] [ 666] [depth= 3] . ( 3 sec) [ -4075.5744] [ 655] [depth= 2] . ( 3 sec) [ -4074.0454] [ 654] [depth= 1] . ( 3 sec) [ -4050.3078] [ 645] [depth= 3] . ( 3 sec) [ -4045.4676] [ 643] [depth= 1] . ( 3 sec) [ -4043.0164] [ 642] [depth= 1] . ( 3 sec) [ -4042.8097] [ 641] [depth= 1] . ( 3 sec) [ -4030.8125] [ 637] [depth= 2] . ( 3 sec) [ -4030.5963] [ 638] [depth= 1] . ( 3 sec) [ -4011.1953] [ 633] [depth= 1] . ( 3 sec) [ -4009.8865] [ 631] [depth= 1] . ( 3 sec) [ -3997.7320] [ 627] [depth= 1] . ( 3 sec) [ -3935.4742] [ 602] [depth= 1] . ( 3 sec) [ -3894.3994] [ 600] [depth= 4] . ( 3 sec) [ -3890.8661] [ 604] [depth= 1] . ( 3 sec) [ -3876.7522] [ 604] [depth= 5] . ( 3 sec) [ -3852.5361] [ 597] [depth= 6] . ( 3 sec) [ -3852.5010] [ 597] [depth= 2] . ( 3 sec) [ -3845.0014] [ 594] [depth= 2] . ( 3 sec) [ -3822.4887] [ 588] [depth= 2] . ( 3 sec) [ -3773.0762] [ 572] [depth= 2] . ( 4 sec) [ -3770.2136] [ 565] [depth= 2] . ( 4 sec) [ -3699.9965] [Branch lengths ] . ( 4 sec) [ -3692.6792] [GTR parameters ] . ( 4 sec) [ -3688.1682] [Alpha ][ 0.714721] . ( 4 sec) [ -3683.8113] [ 562] [depth= 1] . ( 4 sec) [ -3678.6109] [ 559] [depth= 1] . ( 4 sec) [ -3633.7793] [ 540] [depth= 1] . ( 4 sec) [ -3631.1911] [ 541] [depth= 2] . ( 4 sec) [ -3625.1328] [ 538] [depth= 1] . ( 4 sec) [ -3624.2460] [ 537] [depth= 1] . ( 5 sec) [ -3621.4576] [ 536] [depth= 1] . ( 5 sec) [ -3620.9894] [ 536] [depth= 1] . ( 5 sec) [ -3618.5735] [ 536] [depth= 1] . ( 5 sec) [ -3611.7613] [ 532] [depth= 1] . ( 5 sec) [ -3611.3804] [ 535] [depth= 1] . ( 5 sec) [ -3611.2085] [ 535] [depth= 1] . ( 6 sec) [ -3604.9355] [ 533] [depth= 1] . ( 6 sec) [ -3604.2568] [ 534] [depth= 1] . ( 6 sec) [ -3604.0352] [ 531] [depth= 1] . ( 6 sec) [ -3602.9290] [ 530] [depth= 1] . ( 6 sec) [ -3600.3373] [ 529] [depth= 1] . ( 7 sec) [ -3597.5561] [Branch lengths ] . ( 7 sec) [ -3597.4590] [GTR parameters ] . ( 7 sec) [ -3597.0342] [Alpha ][ 0.809621] . ( 8 sec) [ -3596.9374] [ 529] [depth= 1] . ( 11 sec) [ -3596.7976] [Branch lengths ] . ( 11 sec) [ -3596.7841] [GTR parameters ] . ( 11 sec) [ -3596.7841] [Alpha ][ 0.809621] . ( 27 sec) [ -3596.7774] [Branch lengths ] . ( 27 sec) [ -3596.7774] [Topology ] . ( 27 sec) [ -3596.7771] [Topology ] . ( 27 sec) [ -3596.7771] [GTR parameters ] . ( 27 sec) [ -3596.7771] [Alpha ][ 0.809621] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3596.777092. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8901.6925] [GTR parameters ] . ( 1 sec) [ -8745.5156] [Alpha ][ 0.500960] . ( 1 sec) [ -8649.5430] [ 1210] [depth= 8] . ( 1 sec) [ -8502.1064] [ 1198] [depth= 8] . ( 1 sec) [ -8493.4292] [ 1197] [depth= 3] . ( 1 sec) [ -8214.9355] [ 1197] [depth= 2] . ( 1 sec) [ -8148.4466] [ 1189] [depth= 7] . ( 1 sec) [ -8121.0037] [ 1189] [depth= 6] . ( 1 sec) [ -7926.9315] [ 1163] [depth= 16] . ( 1 sec) [ -7776.2833] [ 1161] [depth= 15] . ( 1 sec) [ -7707.8938] [ 1158] [depth= 5] . ( 1 sec) [ -7497.1149] [ 1156] [depth= 2] . ( 1 sec) [ -7342.3870] [ 1126] [depth= 9] . ( 1 sec) [ -7150.2290] [ 1123] [depth= 3] . ( 1 sec) [ -7085.1419] [ 1113] [depth= 2] . ( 1 sec) [ -7051.7848] [ 1110] [depth= 11] . ( 1 sec) [ -6969.7167] [ 1084] [depth= 3] . ( 1 sec) [ -6933.5748] [ 1084] [depth= 5] . ( 1 sec) [ -6745.9801] [ 1060] [depth= 1] . ( 1 sec) [ -6494.5971] [ 1048] [depth= 2] . ( 1 sec) [ -6468.0576] [ 1045] [depth= 7] . ( 1 sec) [ -6336.5339] [ 1013] [depth= 6] . ( 1 sec) [ -6261.9465] [ 988] [depth= 1] . ( 1 sec) [ -6118.0683] [ 976] [depth= 14] . ( 1 sec) [ -6042.7445] [ 965] [depth= 2] . ( 2 sec) [ -6027.1899] [ 961] [depth= 1] . ( 2 sec) [ -6024.5351] [ 962] [depth= 13] . ( 2 sec) [ -5976.0829] [ 961] [depth= 1] . ( 2 sec) [ -5937.2529] [ 945] [depth= 6] . ( 2 sec) [ -5937.1756] [ 946] [depth= 1] . ( 2 sec) [ -5930.2114] [ 945] [depth= 1] . ( 2 sec) [ -5892.8627] [ 919] [depth= 8] . ( 2 sec) [ -5803.6125] [ 906] [depth= 12] . ( 2 sec) [ -5647.8096] [ 895] [depth= 13] . ( 2 sec) [ -5445.8822] [ 866] [depth= 6] . ( 2 sec) [ -5401.9336] [ 863] [depth= 6] . ( 2 sec) [ -5300.9001] [ 823] [depth= 9] . ( 2 sec) [ -5149.7820] [ 792] [depth= 3] . ( 2 sec) [ -4967.1000] [ 793] [depth= 8] . ( 2 sec) [ -4938.4134] [ 789] [depth= 1] . ( 2 sec) [ -4885.7231] [ 781] [depth= 5] . ( 2 sec) [ -4796.6641] [ 761] [depth= 6] . ( 2 sec) [ -4776.1786] [ 761] [depth= 4] . ( 2 sec) [ -4680.5197] [ 743] [depth= 5] . ( 2 sec) [ -4676.4384] [ 743] [depth= 1] . ( 2 sec) [ -4671.2013] [ 743] [depth= 3] . ( 2 sec) [ -4670.2828] [ 741] [depth= 2] . ( 2 sec) [ -4647.8526] [ 741] [depth= 1] . ( 2 sec) [ -4636.9353] [ 741] [depth= 1] . ( 2 sec) [ -4636.3699] [ 742] [depth= 1] . ( 2 sec) [ -4617.9352] [ 739] [depth= 1] . ( 2 sec) [ -4616.9440] [ 739] [depth= 1] . ( 2 sec) [ -4598.0005] [ 737] [depth= 2] . ( 2 sec) [ -4480.6273] [ 734] [depth= 6] . ( 2 sec) [ -4458.2791] [ 727] [depth= 1] . ( 2 sec) [ -4457.3192] [ 727] [depth= 1] . ( 2 sec) [ -4429.8230] [ 716] [depth= 1] . ( 2 sec) [ -4404.7247] [ 710] [depth= 5] . ( 3 sec) [ -4399.4253] [ 712] [depth= 1] . ( 3 sec) [ -4362.7793] [ 706] [depth= 2] . ( 3 sec) [ -4361.7549] [ 706] [depth= 2] . ( 3 sec) [ -4291.6037] [ 699] [depth= 2] . ( 3 sec) [ -4271.7495] [ 692] [depth= 1] . ( 3 sec) [ -4223.5235] [ 696] [depth= 8] . ( 3 sec) [ -4204.2092] [ 690] [depth= 4] . ( 3 sec) [ -4204.1504] [ 688] [depth= 1] . ( 3 sec) [ -4189.4886] [ 688] [depth= 2] . ( 3 sec) [ -4140.1074] [ 661] [depth= 8] . ( 3 sec) [ -4091.8442] [ 658] [depth= 1] . ( 3 sec) [ -4075.0061] [ 650] [depth= 1] . ( 3 sec) [ -4061.4663] [ 650] [depth= 1] . ( 3 sec) [ -3998.9774] [ 638] [depth= 4] . ( 3 sec) [ -3989.7094] [ 635] [depth= 1] . ( 3 sec) [ -3984.4067] [ 636] [depth= 1] . ( 3 sec) [ -3948.2400] [ 615] [depth= 2] . ( 3 sec) [ -3904.2454] [ 605] [depth= 8] . ( 3 sec) [ -3872.8937] [ 597] [depth= 7] . ( 3 sec) [ -3869.7539] [ 597] [depth= 2] . ( 3 sec) [ -3780.7910] [ 565] [depth= 6] . ( 3 sec) [ -3755.4360] [ 563] [depth= 1] . ( 3 sec) [ -3746.4658] [ 560] [depth= 1] . ( 3 sec) [ -3736.4936] [ 559] [depth= 2] . ( 3 sec) [ -3736.4811] [ 558] [depth= 1] . ( 4 sec) [ -3720.5618] [Branch lengths ] . ( 4 sec) [ -3711.9735] [GTR parameters ] . ( 4 sec) [ -3708.8984] [Alpha ][ 0.667710] . ( 4 sec) [ -3698.0304] [ 559] [depth= 3] . ( 4 sec) [ -3696.3988] [ 560] [depth= 1] . ( 4 sec) [ -3666.8924] [ 552] [depth= 2] . ( 4 sec) [ -3661.8394] [ 547] [depth= 1] . ( 4 sec) [ -3661.6193] [ 547] [depth= 1] . ( 5 sec) [ -3634.6863] [ 544] [depth= 2] . ( 5 sec) [ -3632.5909] [ 543] [depth= 1] . ( 5 sec) [ -3630.9362] [ 544] [depth= 1] . ( 5 sec) [ -3629.9690] [ 543] [depth= 1] . ( 5 sec) [ -3620.0341] [ 540] [depth= 2] . ( 5 sec) [ -3609.8793] [ 533] [depth= 1] . ( 6 sec) [ -3609.0314] [ 533] [depth= 1] . ( 6 sec) [ -3604.9128] [ 533] [depth= 1] . ( 6 sec) [ -3602.8222] [ 533] [depth= 1] . ( 6 sec) [ -3602.6158] [ 532] [depth= 1] . ( 6 sec) [ -3601.2948] [ 531] [depth= 1] . ( 7 sec) [ -3600.9775] [ 529] [depth= 1] . ( 7 sec) [ -3598.5658] [Branch lengths ] . ( 7 sec) [ -3597.9345] [GTR parameters ] . ( 8 sec) [ -3596.9309] [Alpha ][ 0.807654] . ( 11 sec) [ -3596.7834] [Branch lengths ] . ( 26 sec) [ -3596.7778] [Branch lengths ] . ( 26 sec) [ -3596.7778] [Topology ] . ( 27 sec) [ -3596.7776] [Topology ] . ( 27 sec) [ -3596.7772] [GTR parameters ] . ( 27 sec) [ -3596.7771] [Alpha ][ 0.809208] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3596.777097. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8168.9631] [GTR parameters ] . ( 1 sec) [ -8023.6957] [Alpha ][ 0.500960] . ( 1 sec) [ -7645.0451] [ 1168] [depth= 8] . ( 1 sec) [ -7510.3674] [ 1138] [depth= 8] . ( 1 sec) [ -7301.8740] [ 1118] [depth= 8] . ( 1 sec) [ -7288.5412] [ 1111] [depth= 1] . ( 1 sec) [ -7189.0750] [ 1110] [depth= 6] . ( 1 sec) [ -7184.7930] [ 1109] [depth= 2] . ( 1 sec) [ -7122.5312] [ 1109] [depth= 4] . ( 1 sec) [ -7098.5365] [ 1108] [depth= 2] . ( 1 sec) [ -7063.0016] [ 1108] [depth= 1] . ( 1 sec) [ -6959.7341] [ 1106] [depth= 7] . ( 1 sec) [ -6894.5512] [ 1106] [depth= 5] . ( 1 sec) [ -6676.8332] [ 1092] [depth= 16] . ( 1 sec) [ -6600.8542] [ 1078] [depth= 10] . ( 1 sec) [ -6550.9995] [ 1077] [depth= 1] . ( 1 sec) [ -6365.7524] [ 1050] [depth= 4] . ( 1 sec) [ -6325.4326] [ 1048] [depth= 3] . ( 1 sec) [ -6278.6863] [ 1097] [depth= 1] . ( 1 sec) [ -6095.9667] [ 1040] [depth= 20] . ( 1 sec) [ -5966.7735] [ 1006] [depth= 18] . ( 1 sec) [ -5960.5572] [ 1005] [depth= 14] . ( 1 sec) [ -5799.7636] [ 956] [depth= 14] . ( 1 sec) [ -5720.1202] [ 949] [depth= 8] . ( 1 sec) [ -5631.4078] [ 949] [depth= 1] . ( 1 sec) [ -5592.5191] [ 949] [depth= 3] . ( 2 sec) [ -5371.6240] [ 914] [depth= 11] . ( 2 sec) [ -5369.2938] [ 915] [depth= 1] . ( 2 sec) [ -5328.2544] [ 902] [depth= 10] . ( 2 sec) [ -5327.8131] [ 903] [depth= 1] . ( 2 sec) [ -5295.2014] [ 897] [depth= 2] . ( 2 sec) [ -5173.2799] [ 878] [depth= 3] . ( 2 sec) [ -5173.0119] [ 879] [depth= 1] . ( 2 sec) [ -5148.6499] [ 878] [depth= 3] . ( 2 sec) [ -5020.7113] [ 844] [depth= 10] . ( 2 sec) [ -4990.0958] [ 822] [depth= 2] . ( 2 sec) [ -4945.4197] [ 822] [depth= 3] . ( 2 sec) [ -4883.4028] [ 817] [depth= 12] . ( 2 sec) [ -4766.3405] [ 804] [depth= 6] . ( 2 sec) [ -4762.2928] [ 805] [depth= 1] . ( 2 sec) [ -4757.1857] [ 808] [depth= 2] . ( 2 sec) [ -4729.3965] [ 799] [depth= 11] . ( 2 sec) [ -4626.1364] [ 772] [depth= 5] . ( 2 sec) [ -4605.5786] [ 772] [depth= 1] . ( 2 sec) [ -4584.6828] [ 773] [depth= 2] . ( 2 sec) [ -4485.5872] [ 738] [depth= 4] . ( 2 sec) [ -4466.6604] [ 729] [depth= 9] . ( 2 sec) [ -4456.7619] [ 724] [depth= 5] . ( 2 sec) [ -4455.7122] [ 724] [depth= 1] . ( 2 sec) [ -4348.9768] [ 712] [depth= 6] . ( 2 sec) [ -4313.8453] [ 704] [depth= 8] . ( 2 sec) [ -4299.3706] [ 698] [depth= 3] . ( 2 sec) [ -4243.7448] [ 676] [depth= 5] . ( 2 sec) [ -4180.9683] [ 660] [depth= 5] . ( 2 sec) [ -4113.4087] [ 651] [depth= 6] . ( 2 sec) [ -4098.7916] [ 651] [depth= 2] . ( 3 sec) [ -4098.7135] [ 651] [depth= 2] . ( 3 sec) [ -4087.4384] [ 649] [depth= 2] . ( 3 sec) [ -4073.2398] [ 642] [depth= 2] . ( 3 sec) [ -4058.5017] [ 639] [depth= 8] . ( 3 sec) [ -4049.5505] [ 637] [depth= 1] . ( 3 sec) [ -3942.0661] [ 607] [depth= 5] . ( 3 sec) [ -3930.4868] [ 607] [depth= 4] . ( 3 sec) [ -3890.0610] [ 599] [depth= 3] . ( 3 sec) [ -3889.4827] [ 599] [depth= 2] . ( 3 sec) [ -3882.2472] [ 596] [depth= 1] . ( 3 sec) [ -3877.7460] [ 593] [depth= 4] . ( 3 sec) [ -3846.6181] [ 590] [depth= 1] . ( 3 sec) [ -3842.9051] [ 590] [depth= 1] . ( 3 sec) [ -3836.0311] [ 589] [depth= 1] . ( 3 sec) [ -3829.0783] [ 587] [depth= 1] . ( 3 sec) [ -3829.0132] [ 587] [depth= 1] . ( 3 sec) [ -3817.5074] [ 585] [depth= 1] . ( 3 sec) [ -3805.9813] [ 579] [depth= 1] . ( 3 sec) [ -3782.9677] [ 575] [depth= 7] . ( 3 sec) [ -3767.7695] [ 573] [depth= 1] . ( 3 sec) [ -3757.6230] [ 569] [depth= 1] . ( 3 sec) [ -3756.5782] [ 569] [depth= 1] . ( 4 sec) [ -3742.4184] [ 566] [depth= 2] . ( 4 sec) [ -3736.4543] [ 567] [depth= 2] . ( 4 sec) [ -3701.7928] [Branch lengths ] . ( 4 sec) [ -3696.2354] [GTR parameters ] . ( 4 sec) [ -3692.4998] [Alpha ][ 0.689005] . ( 4 sec) [ -3687.5319] [ 565] [depth= 1] . ( 4 sec) [ -3668.2648] [ 547] [depth= 2] . ( 4 sec) [ -3650.3435] [ 542] [depth= 1] . ( 5 sec) [ -3650.3022] [ 542] [depth= 1] . ( 5 sec) [ -3626.9655] [ 538] [depth= 1] . ( 5 sec) [ -3624.4471] [ 540] [depth= 1] . ( 5 sec) [ -3619.9665] [ 541] [depth= 1] . ( 5 sec) [ -3611.9975] [ 537] [depth= 2] . ( 5 sec) [ -3611.8672] [ 537] [depth= 1] . ( 5 sec) [ -3605.5512] [ 533] [depth= 2] . ( 6 sec) [ -3605.0149] [ 535] [depth= 1] . ( 6 sec) [ -3603.9855] [ 533] [depth= 1] . ( 6 sec) [ -3602.0313] [ 531] [depth= 1] . ( 7 sec) [ -3601.1726] [ 533] [depth= 1] . ( 7 sec) [ -3601.1605] [ 533] [depth= 2] . ( 7 sec) [ -3601.0721] [ 533] [depth= 1] . ( 7 sec) [ -3600.8743] [ 532] [depth= 1] . ( 7 sec) [ -3600.1342] [ 531] [depth= 1] . ( 7 sec) [ -3599.9197] [ 531] [depth= 2] . ( 7 sec) [ -3598.5072] [Branch lengths ] . ( 8 sec) [ -3597.9363] [GTR parameters ] . ( 8 sec) [ -3597.2833] [Alpha ][ 0.803441] . ( 8 sec) [ -3597.0838] [ 529] [depth= 1] . ( 11 sec) [ -3596.9202] [Branch lengths ] . ( 11 sec) [ -3596.9185] [GTR parameters ] . ( 11 sec) [ -3596.9172] [Alpha ][ 0.809178] . ( 27 sec) [ -3596.9099] [Branch lengths ] . ( 27 sec) [ -3596.9099] [Topology ] . ( 27 sec) [ -3596.9025] [Topology ] . ( 28 sec) [ -3596.8778] [Topology ] . ( 28 sec) [ -3596.8582] [Topology ] . ( 29 sec) [ -3596.8436] [Topology ] . ( 29 sec) [ -3596.8323] [Topology ] . ( 30 sec) [ -3596.8234] [Topology ] . ( 30 sec) [ -3596.8207] [GTR parameters ] . ( 30 sec) [ -3596.8207] [Alpha ][ 0.809178] . ( 30 sec) [ -3596.8207] [Topology ] . ( 30 sec) [ -3596.8128] [Topology ] . ( 31 sec) [ -3596.8064] [Topology ] . ( 31 sec) [ -3596.8012] [Topology ] . ( 32 sec) [ -3596.7969] [Topology ] . ( 32 sec) [ -3596.7936] [Topology ] . ( 33 sec) [ -3596.7910] [Topology ] . ( 33 sec) [ -3596.7900] [GTR parameters ] . ( 33 sec) [ -3596.7900] [Alpha ][ 0.809178] . ( 33 sec) [ -3596.7900] [Topology ] . ( 33 sec) [ -3596.7876] [Topology ] . ( 34 sec) [ -3596.7856] [Topology ] . ( 34 sec) [ -3596.7841] [Topology ] . ( 35 sec) [ -3596.7829] [Topology ] . ( 35 sec) [ -3596.7819] [Topology ] . ( 35 sec) [ -3596.7817] [GTR parameters ] . ( 35 sec) [ -3596.7817] [Alpha ][ 0.809178] . ( 36 sec) [ -3596.7817] [Topology ] . ( 36 sec) [ -3596.7809] [Topology ] . ( 36 sec) [ -3596.7808] [GTR parameters ] . ( 36 sec) [ -3596.7808] [Alpha ][ 0.809178] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3596.780845. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8674.3341] [GTR parameters ] . ( 1 sec) [ -8508.2312] [Alpha ][ 0.500960] . ( 1 sec) [ -8323.1633] [ 1185] [depth= 6] . ( 1 sec) [ -8205.7184] [ 1151] [depth= 11] . ( 1 sec) [ -8200.7747] [ 1148] [depth= 2] . ( 1 sec) [ -8128.5784] [ 1148] [depth= 3] . ( 1 sec) [ -8115.0411] [ 1143] [depth= 2] . ( 1 sec) [ -8052.6520] [ 1143] [depth= 4] . ( 1 sec) [ -7632.0038] [ 1138] [depth= 13] . ( 1 sec) [ -7411.8663] [ 1139] [depth= 1] . ( 1 sec) [ -7304.1093] [ 1100] [depth= 9] . ( 1 sec) [ -7194.7175] [ 1090] [depth= 9] . ( 1 sec) [ -6953.0841] [ 1067] [depth= 16] . ( 1 sec) [ -6846.9146] [ 1063] [depth= 1] . ( 1 sec) [ -6775.8750] [ 1039] [depth= 13] . ( 1 sec) [ -6735.2718] [ 1033] [depth= 1] . ( 1 sec) [ -6674.6978] [ 1031] [depth= 4] . ( 1 sec) [ -6645.5777] [ 1028] [depth= 9] . ( 1 sec) [ -6634.0813] [ 1028] [depth= 1] . ( 1 sec) [ -6627.6548] [ 1027] [depth= 2] . ( 1 sec) [ -6626.1023] [ 1027] [depth= 6] . ( 1 sec) [ -6570.3614] [ 1026] [depth= 2] . ( 1 sec) [ -6431.5236] [ 1001] [depth= 20] . ( 1 sec) [ -6363.0439] [ 986] [depth= 6] . ( 1 sec) [ -6357.7798] [ 986] [depth= 2] . ( 1 sec) [ -6342.4927] [ 984] [depth= 1] . ( 1 sec) [ -6282.9188] [ 978] [depth= 16] . ( 1 sec) [ -6067.6904] [ 944] [depth= 8] . ( 1 sec) [ -6039.6386] [ 936] [depth= 4] . ( 1 sec) [ -5826.7730] [ 910] [depth= 11] . ( 1 sec) [ -5577.6892] [ 895] [depth= 5] . ( 1 sec) [ -5573.1860] [ 895] [depth= 3] . ( 1 sec) [ -5466.7386] [ 854] [depth= 7] . ( 1 sec) [ -5406.0943] [ 860] [depth= 5] . ( 1 sec) [ -5362.8599] [ 851] [depth= 9] . ( 1 sec) [ -5191.9688] [ 817] [depth= 10] . ( 1 sec) [ -5176.3360] [ 809] [depth= 2] . ( 1 sec) [ -5095.3840] [ 793] [depth= 8] . ( 2 sec) [ -4942.7878] [ 789] [depth= 6] . ( 2 sec) [ -4942.0314] [ 789] [depth= 8] . ( 2 sec) [ -4845.1354] [ 779] [depth= 1] . ( 2 sec) [ -4796.6760] [ 766] [depth= 4] . ( 2 sec) [ -4794.9719] [ 766] [depth= 2] . ( 2 sec) [ -4727.8419] [ 748] [depth= 5] . ( 2 sec) [ -4627.0030] [ 727] [depth= 4] . ( 2 sec) [ -4621.4630] [ 726] [depth= 1] . ( 2 sec) [ -4541.7155] [ 717] [depth= 5] . ( 2 sec) [ -4537.5409] [ 719] [depth= 1] . ( 2 sec) [ -4487.7864] [ 718] [depth= 2] . ( 2 sec) [ -4425.5146] [ 704] [depth= 3] . ( 2 sec) [ -4382.5061] [ 697] [depth= 3] . ( 2 sec) [ -4365.0456] [ 697] [depth= 3] . ( 2 sec) [ -4360.0068] [ 695] [depth= 1] . ( 2 sec) [ -4292.1587] [ 694] [depth= 1] . ( 2 sec) [ -4267.3440] [ 677] [depth= 2] . ( 2 sec) [ -4198.7652] [ 657] [depth= 2] . ( 2 sec) [ -4172.1680] [ 650] [depth= 1] . ( 2 sec) [ -4157.8717] [ 629] [depth= 4] . ( 2 sec) [ -4092.2207] [ 616] [depth= 8] . ( 2 sec) [ -4081.6002] [ 614] [depth= 1] . ( 2 sec) [ -4063.0858] [ 614] [depth= 1] . ( 2 sec) [ -3961.9132] [ 602] [depth= 3] . ( 2 sec) [ -3896.2279] [ 578] [depth= 2] . ( 2 sec) [ -3872.8574] [ 571] [depth= 2] . ( 2 sec) [ -3763.1871] [ 572] [depth= 1] . ( 2 sec) [ -3737.2954] [ 564] [depth= 4] . ( 2 sec) [ -3725.9307] [ 561] [depth= 1] . ( 2 sec) [ -3722.2915] [ 559] [depth= 2] . ( 2 sec) [ -3699.2118] [ 554] [depth= 3] . ( 3 sec) [ -3694.0437] [ 551] [depth= 2] . ( 3 sec) [ -3693.2354] [ 553] [depth= 1] . ( 3 sec) [ -3692.8704] [ 553] [depth= 2] . ( 3 sec) [ -3692.8518] [ 555] [depth= 1] . ( 3 sec) [ -3689.7955] [ 558] [depth= 1] . ( 3 sec) [ -3652.2891] [ 541] [depth= 4] . ( 3 sec) [ -3644.9012] [ 536] [depth= 1] . ( 3 sec) [ -3631.8282] [Branch lengths ] . ( 4 sec) [ -3618.2841] [GTR parameters ] . ( 4 sec) [ -3612.0868] [Alpha ][ 0.782922] . ( 4 sec) [ -3607.1399] [ 534] [depth= 1] . ( 4 sec) [ -3602.0720] [ 532] [depth= 1] . ( 4 sec) [ -3601.2716] [ 531] [depth= 1] . ( 5 sec) [ -3598.5532] [ 530] [depth= 1] . ( 5 sec) [ -3597.6628] [ 529] [depth= 1] . ( 7 sec) [ -3596.8726] [Branch lengths ] . ( 7 sec) [ -3596.8164] [GTR parameters ] . ( 7 sec) [ -3596.7880] [Alpha ][ 0.809332] . ( 11 sec) [ -3596.7773] [Branch lengths ] . ( 26 sec) [ -3596.7770] [Branch lengths ] . ( 26 sec) [ -3596.7770] [Topology ] . ( 27 sec) [ -3596.7770] [Topology ] . ( 27 sec) [ -3596.7770] [GTR parameters ] . ( 27 sec) [ -3596.7770] [Alpha ][ 0.809332] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3596.776973. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3607.752479 . ( 0 sec) [ -3604.8214] [GTR parameters ] . ( 0 sec) [ -3603.5517] [Alpha ][ 0.788011] . ( 0 sec) [ -3603.5517] [Topology ] . ( 1 sec) [ -3598.3151] [Topology ] . ( 1 sec) [ -3597.5172] [Topology ] . ( 2 sec) [ -3597.3284] [Topology ] . ( 2 sec) [ -3597.2749] [Topology ] . ( 3 sec) [ -3597.2579] [Topology ] . ( 3 sec) [ -3597.2516] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6 sec) [ -3597.1388] [Topology ] . Before opt ts/t=1.000000 LK=-3597.138757 . ( 6 sec) [ -3597.1192] [GTR parameters ] . ( 6 sec) [ -3597.1105] [Alpha ][ 0.802128] . ( 6 sec) [ -3597.1105] [Topology ] . ( 7 sec) [ -3597.0776] [Topology ] . ( 7 sec) [ -3596.9868] [Topology ] . ( 8 sec) [ -3596.8400] [Topology ] . ( 8 sec) [ -3596.7996] [Topology ] . ( 9 sec) [ -3596.7876] [Topology ] . ( 9 sec) [ -3596.7837] [Topology ] . ( 10 sec) [ -3596.7823] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3596.782309 . ( 12 sec) [ -3596.7812] [GTR parameters ] . ( 12 sec) [ -3596.7793] [Alpha ][ 0.809327] . ( 12 sec) [ -3596.7793] [Topology ] . ( 13 sec) [ -3596.7785] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3596.778495 . ( 16 sec) [ -3596.7785] [GTR parameters ] . ( 16 sec) [ -3596.7785] [Alpha ][ 0.809327] . ( 16 sec) [ -3596.7785] [Topology ] . ( 16 sec) [ -3596.7781] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 22 sec) [ -3604.8214] [GTR parameters ] . ( 22 sec) [ -3603.5517] [Alpha ][ 0.788011] . ( 23 sec) [ -3603.4041] [ 531] [depth= 1] . ( 23 sec) [ -3603.2726] [ 531] [depth= 1] . ( 23 sec) [ -3602.5869] [ 529] [depth= 2] . ( 23 sec) [ -3602.0030] [ 532] [depth= 1] . ( 23 sec) [ -3601.9340] [ 532] [depth= 1] . ( 23 sec) [ -3601.3957] [ 532] [depth= 1] . ( 23 sec) [ -3601.3651] [ 532] [depth= 1] . ( 24 sec) [ -3601.3541] [ 533] [depth= 1] . ( 26 sec) [ -3598.0565] [Branch lengths ] . ( 26 sec) [ -3598.0338] [GTR parameters ] . ( 26 sec) [ -3598.0313] [Alpha ][ 0.796029] . ( 27 sec) [ -3598.0175] [ 531] [depth= 1] . ( 27 sec) [ -3597.2328] [ 529] [depth= 1] . ( 29 sec) [ -3596.8196] [Branch lengths ] . ( 29 sec) [ -3596.8034] [GTR parameters ] . ( 29 sec) [ -3596.7973] [Alpha ][ 0.808789] . ( 33 sec) [ -3596.7834] [Branch lengths ] . ( 48 sec) [ -3596.7806] [Branch lengths ] . ( 48 sec) [ -3596.7806] [Topology ] . ( 49 sec) [ -3596.7798] [Topology ] . ( 49 sec) [ -3596.7796] [GTR parameters ] . ( 49 sec) [ -3596.7796] [Alpha ][ 0.809598] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3596.778076 . Log likelihood obtained after SPR moves : -3596.779630 . Log likelihood of the current tree: -3596.778076. . Printing the most likely tree in file 'data36.phy_phyml_tree.txt'... . Best log likelihood : -3596.776973 . Time used 0h0m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo