.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data65.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... . 462 patterns found. (out of a total of 500 sites) . 38 sites without polymorphism (7.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21814.4878] [GTR parameters ] . ( 1 sec) [ -21416.7824] [Alpha ][ 0.500960] . ( 1 sec) [ -21319.2212] [ 5652] [depth= 4] . ( 1 sec) [ -21145.9147] [ 5569] [depth= 6] . ( 1 sec) [ -20874.4532] [ 5552] [depth= 1] . ( 1 sec) [ -20874.3460] [ 5548] [depth= 1] . ( 1 sec) [ -20820.8528] [ 5529] [depth= 5] . ( 1 sec) [ -20694.7972] [ 5498] [depth= 5] . ( 1 sec) [ -20622.5750] [ 5462] [depth= 1] . ( 2 sec) [ -20516.8773] [ 5465] [depth= 4] . ( 2 sec) [ -20086.2537] [ 5436] [depth= 6] . ( 2 sec) [ -19688.1102] [ 5277] [depth= 7] . ( 2 sec) [ -19522.9410] [ 5287] [depth= 12] . ( 2 sec) [ -19364.6355] [ 5172] [depth= 5] . ( 2 sec) [ -19257.4419] [ 5147] [depth= 3] . ( 2 sec) [ -19216.1509] [ 5143] [depth= 3] . ( 2 sec) [ -19048.5022] [ 5111] [depth= 4] . ( 2 sec) [ -18956.0577] [ 5052] [depth= 1] . ( 2 sec) [ -18796.1016] [ 5030] [depth= 12] . ( 2 sec) [ -18495.4139] [ 4954] [depth= 3] . ( 2 sec) [ -18392.2911] [ 4892] [depth= 1] . ( 2 sec) [ -17941.3505] [ 4860] [depth= 8] . ( 2 sec) [ -17632.8118] [ 4881] [depth= 1] . ( 2 sec) [ -17568.9736] [ 4839] [depth= 1] . ( 2 sec) [ -17397.7761] [ 4813] [depth= 11] . ( 2 sec) [ -16966.6703] [ 4720] [depth= 2] . ( 2 sec) [ -16783.0935] [ 4603] [depth= 10] . ( 2 sec) [ -16729.3702] [ 4500] [depth= 8] . ( 2 sec) [ -16708.9316] [ 4491] [depth= 1] . ( 3 sec) [ -16605.3988] [ 4450] [depth= 4] . ( 3 sec) [ -16395.9872] [ 4338] [depth= 4] . ( 3 sec) [ -16361.9468] [ 4363] [depth= 2] . ( 3 sec) [ -16262.1189] [ 4320] [depth= 1] . ( 3 sec) [ -16117.9327] [ 4239] [depth= 8] . ( 3 sec) [ -15921.4879] [ 4198] [depth= 1] . ( 3 sec) [ -15633.5973] [ 4120] [depth= 2] . ( 3 sec) [ -15323.3408] [ 4002] [depth= 8] . ( 3 sec) [ -15304.9292] [ 4010] [depth= 1] . ( 3 sec) [ -15271.8226] [ 3973] [depth= 3] . ( 3 sec) [ -15116.2308] [ 3925] [depth= 1] . ( 3 sec) [ -15086.5988] [ 3911] [depth= 1] . ( 3 sec) [ -15076.4993] [ 3882] [depth= 1] . ( 3 sec) [ -15068.4686] [ 3830] [depth= 10] . ( 3 sec) [ -15006.8962] [ 3801] [depth= 2] . ( 3 sec) [ -14971.4934] [ 3783] [depth= 1] . ( 3 sec) [ -14960.3965] [ 3774] [depth= 2] . ( 3 sec) [ -14868.4772] [ 3770] [depth= 1] . ( 4 sec) [ -14819.7479] [ 3771] [depth= 1] . ( 4 sec) [ -14811.3843] [ 3770] [depth= 1] . ( 4 sec) [ -14803.5385] [ 3768] [depth= 1] . ( 4 sec) [ -14795.1403] [ 3761] [depth= 2] . ( 4 sec) [ -14659.9386] [ 3740] [depth= 8] . ( 4 sec) [ -14569.3959] [ 3767] [depth= 1] . ( 4 sec) [ -14455.0812] [ 3699] [depth= 8] . ( 4 sec) [ -14305.8353] [ 3620] [depth= 5] . ( 4 sec) [ -14131.8478] [ 3548] [depth= 2] . ( 4 sec) [ -13924.0373] [ 3502] [depth= 6] . ( 4 sec) [ -13751.9597] [ 3502] [depth= 2] . ( 4 sec) [ -13707.0419] [ 3459] [depth= 1] . ( 4 sec) [ -13494.1316] [ 3373] [depth= 7] . ( 4 sec) [ -13358.8039] [ 3301] [depth= 9] . ( 4 sec) [ -13301.8321] [ 3295] [depth= 3] . ( 4 sec) [ -13300.4011] [ 3273] [depth= 1] . ( 4 sec) [ -13253.9236] [ 3245] [depth= 1] . ( 4 sec) [ -13125.9679] [ 3182] [depth= 2] . ( 4 sec) [ -13084.8193] [ 3151] [depth= 1] . ( 4 sec) [ -13068.4735] [ 3163] [depth= 1] . ( 4 sec) [ -13065.4674] [ 3151] [depth= 1] . ( 4 sec) [ -12961.8757] [ 3107] [depth= 7] . ( 5 sec) [ -12957.6037] [ 3119] [depth= 1] . ( 5 sec) [ -12951.8990] [ 3130] [depth= 5] . ( 5 sec) [ -12944.5076] [ 3117] [depth= 1] . ( 5 sec) [ -12933.5157] [ 3134] [depth= 1] . ( 5 sec) [ -12819.2880] [ 3090] [depth= 2] . ( 5 sec) [ -12810.4860] [ 3089] [depth= 3] . ( 5 sec) [ -12772.9203] [ 3093] [depth= 3] . ( 5 sec) [ -12771.9313] [ 3096] [depth= 1] . ( 5 sec) [ -12754.7007] [ 3096] [depth= 2] . ( 5 sec) [ -12717.8340] [ 3085] [depth= 1] . ( 5 sec) [ -12657.5117] [ 3059] [depth= 1] . ( 5 sec) [ -12562.8193] [ 3005] [depth= 3] . ( 5 sec) [ -12544.5887] [ 3003] [depth= 2] . ( 5 sec) [ -12539.0253] [ 2988] [depth= 1] . ( 5 sec) [ -12534.9354] [ 2993] [depth= 1] . ( 6 sec) [ -12329.8185] [Branch lengths ] . ( 6 sec) [ -12326.6870] [GTR parameters ] . ( 6 sec) [ -12279.6103] [Alpha ][ 0.948227] . ( 7 sec) [ -12261.7075] [ 2991] [depth= 1] . ( 7 sec) [ -12251.8554] [ 2985] [depth= 2] . ( 7 sec) [ -12251.2705] [ 2984] [depth= 1] . ( 7 sec) [ -12249.1927] [ 2986] [depth= 1] . ( 7 sec) [ -12248.8750] [ 2987] [depth= 1] . ( 7 sec) [ -12239.8495] [ 2965] [depth= 1] . ( 8 sec) [ -12238.2987] [ 2963] [depth= 2] . ( 8 sec) [ -12233.2396] [ 2947] [depth= 1] . ( 8 sec) [ -12231.7849] [ 2946] [depth= 1] . ( 8 sec) [ -12231.3888] [ 2943] [depth= 1] . ( 8 sec) [ -12230.1572] [ 2942] [depth= 1] . ( 8 sec) [ -12230.0591] [ 2943] [depth= 1] . ( 9 sec) [ -12225.6815] [ 2946] [depth= 1] . ( 9 sec) [ -12193.6115] [ 2930] [depth= 2] . ( 9 sec) [ -12189.4192] [ 2933] [depth= 1] . ( 9 sec) [ -12189.3163] [ 2938] [depth= 1] . ( 10 sec) [ -12182.3630] [ 2951] [depth= 1] . ( 10 sec) [ -12152.8494] [Branch lengths ] . ( 11 sec) [ -12152.7942] [GTR parameters ] . ( 11 sec) [ -12152.2981] [Alpha ][ 1.009850] . ( 11 sec) [ -12152.1043] [ 2951] [depth= 1] . ( 11 sec) [ -12149.4437] [ 2937] [depth= 1] . ( 12 sec) [ -12149.2745] [ 2935] [depth= 1] . ( 13 sec) [ -12149.2410] [ 2937] [depth= 1] . ( 14 sec) [ -12141.7988] [Branch lengths ] . ( 15 sec) [ -12141.7955] [GTR parameters ] . ( 15 sec) [ -12141.7955] [Alpha ][ 1.009850] . ( 18 sec) [ -12140.4901] [Branch lengths ] . ( 41 sec) [ -12139.9094] [ 2933] [depth= 1] . ( 42 sec) [ -12139.6785] [Branch lengths ] . ( 42 sec) [ -12139.6766] [GTR parameters ] . ( 42 sec) [ -12139.6717] [Alpha ][ 1.016179] . ( 42 sec) [ -12139.6717] [Topology ] . ( 43 sec) [ -12139.6586] [Topology ] . ( 44 sec) [ -12139.6565] [Topology ] . ( 45 sec) [ -12139.6559] [Topology ] . ( 45 sec) [ -12139.6559] [GTR parameters ] . ( 45 sec) [ -12139.6559] [Alpha ][ 1.016179] . ( 45 sec) [ -12139.6559] [Topology ] . ( 46 sec) [ -12139.6557] [Topology ] . ( 46 sec) [ -12139.6557] [GTR parameters ] . ( 46 sec) [ -12139.6557] [Alpha ][ 1.016179] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.655654. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22018.9699] [GTR parameters ] . ( 1 sec) [ -21622.0139] [Alpha ][ 0.500960] . ( 1 sec) [ -21527.6877] [ 5647] [depth= 11] . ( 1 sec) [ -21067.9160] [ 5586] [depth= 6] . ( 1 sec) [ -21031.1893] [ 5533] [depth= 3] . ( 1 sec) [ -20986.2504] [ 5521] [depth= 3] . ( 1 sec) [ -20916.3846] [ 5488] [depth= 1] . ( 1 sec) [ -20884.8467] [ 5482] [depth= 3] . ( 1 sec) [ -20757.9291] [ 5473] [depth= 3] . ( 2 sec) [ -20593.1137] [ 5466] [depth= 6] . ( 2 sec) [ -20351.7373] [ 5344] [depth= 5] . ( 2 sec) [ -20217.3195] [ 5331] [depth= 3] . ( 2 sec) [ -19478.4740] [ 5207] [depth= 3] . ( 2 sec) [ -19405.4818] [ 5201] [depth= 1] . ( 2 sec) [ -19329.6540] [ 5169] [depth= 1] . ( 2 sec) [ -19266.6807] [ 5165] [depth= 3] . ( 2 sec) [ -18872.2022] [ 4967] [depth= 11] . ( 2 sec) [ -18843.5588] [ 4968] [depth= 1] . ( 2 sec) [ -18841.3436] [ 4948] [depth= 2] . ( 2 sec) [ -18736.0109] [ 4937] [depth= 3] . ( 2 sec) [ -18709.1537] [ 4936] [depth= 6] . ( 2 sec) [ -18600.9089] [ 4859] [depth= 10] . ( 2 sec) [ -18245.4824] [ 4847] [depth= 1] . ( 2 sec) [ -18042.7787] [ 4699] [depth= 12] . ( 2 sec) [ -17918.0047] [ 4675] [depth= 1] . ( 2 sec) [ -17785.9851] [ 4617] [depth= 8] . ( 2 sec) [ -17738.3880] [ 4543] [depth= 1] . ( 2 sec) [ -17727.9959] [ 4531] [depth= 1] . ( 2 sec) [ -17723.7925] [ 4540] [depth= 2] . ( 3 sec) [ -17646.6063] [ 4525] [depth= 3] . ( 3 sec) [ -17497.1228] [ 4463] [depth= 1] . ( 3 sec) [ -17483.0567] [ 4479] [depth= 1] . ( 3 sec) [ -17462.6352] [ 4470] [depth= 1] . ( 3 sec) [ -17352.6307] [ 4450] [depth= 1] . ( 3 sec) [ -17257.3311] [ 4423] [depth= 1] . ( 3 sec) [ -17203.0022] [ 4394] [depth= 1] . ( 3 sec) [ -17182.7700] [ 4399] [depth= 3] . ( 3 sec) [ -17048.2504] [ 4382] [depth= 11] . ( 3 sec) [ -16967.1633] [ 4364] [depth= 4] . ( 3 sec) [ -16820.3123] [ 4334] [depth= 3] . ( 3 sec) [ -16795.0988] [ 4310] [depth= 8] . ( 3 sec) [ -16253.6569] [ 4282] [depth= 8] . ( 3 sec) [ -16218.4987] [ 4254] [depth= 9] . ( 3 sec) [ -16014.7332] [ 4186] [depth= 9] . ( 3 sec) [ -15678.4346] [ 4110] [depth= 2] . ( 4 sec) [ -15677.4404] [ 4112] [depth= 1] . ( 4 sec) [ -15576.9663] [ 4080] [depth= 2] . ( 4 sec) [ -15396.1320] [ 4017] [depth= 2] . ( 4 sec) [ -15040.4169] [ 3951] [depth= 11] . ( 4 sec) [ -14962.0398] [ 3892] [depth= 9] . ( 4 sec) [ -14784.1284] [ 3872] [depth= 1] . ( 4 sec) [ -14680.1542] [ 3868] [depth= 1] . ( 4 sec) [ -14669.1138] [ 3873] [depth= 1] . ( 4 sec) [ -14547.8631] [ 3731] [depth= 13] . ( 4 sec) [ -14546.9656] [ 3717] [depth= 1] . ( 4 sec) [ -14529.0457] [ 3712] [depth= 1] . ( 4 sec) [ -14524.5118] [ 3724] [depth= 1] . ( 4 sec) [ -14446.5550] [ 3723] [depth= 7] . ( 4 sec) [ -14412.6234] [ 3720] [depth= 1] . ( 4 sec) [ -14302.2766] [ 3646] [depth= 8] . ( 4 sec) [ -14288.8660] [ 3633] [depth= 1] . ( 4 sec) [ -14284.6634] [ 3639] [depth= 1] . ( 4 sec) [ -14192.7180] [ 3516] [depth= 5] . ( 4 sec) [ -14123.7935] [ 3512] [depth= 9] . ( 4 sec) [ -14117.8302] [ 3496] [depth= 1] . ( 5 sec) [ -14115.3633] [ 3500] [depth= 1] . ( 5 sec) [ -14085.2585] [ 3464] [depth= 1] . ( 5 sec) [ -14064.0734] [ 3458] [depth= 1] . ( 5 sec) [ -13838.9048] [ 3354] [depth= 10] . ( 5 sec) [ -13819.7959] [ 3352] [depth= 1] . ( 5 sec) [ -13814.6803] [ 3329] [depth= 2] . ( 5 sec) [ -13611.3483] [ 3272] [depth= 2] . ( 5 sec) [ -13555.6886] [ 3264] [depth= 1] . ( 5 sec) [ -13544.6671] [ 3272] [depth= 1] . ( 5 sec) [ -13377.8440] [ 3235] [depth= 7] . ( 5 sec) [ -13217.0157] [ 3158] [depth= 1] . ( 5 sec) [ -13082.2427] [ 3102] [depth= 2] . ( 5 sec) [ -13081.2866] [ 3138] [depth= 1] . ( 5 sec) [ -12885.0194] [ 3140] [depth= 3] . ( 5 sec) [ -12844.6443] [ 3099] [depth= 3] . ( 5 sec) [ -12750.2569] [ 3049] [depth= 5] . ( 6 sec) [ -12356.1397] [Branch lengths ] . ( 6 sec) [ -12352.9154] [GTR parameters ] . ( 6 sec) [ -12309.4405] [Alpha ][ 0.914666] . ( 7 sec) [ -12306.0420] [ 3044] [depth= 3] . ( 7 sec) [ -12295.1002] [ 3039] [depth= 1] . ( 7 sec) [ -12254.1974] [ 3011] [depth= 1] . ( 7 sec) [ -12250.0344] [ 3003] [depth= 1] . ( 7 sec) [ -12245.2312] [ 2995] [depth= 1] . ( 7 sec) [ -12244.0276] [ 2997] [depth= 1] . ( 7 sec) [ -12241.7870] [ 2991] [depth= 1] . ( 8 sec) [ -12218.0537] [ 2959] [depth= 1] . ( 8 sec) [ -12217.9547] [ 2960] [depth= 1] . ( 8 sec) [ -12217.8283] [ 2961] [depth= 1] . ( 8 sec) [ -12215.5306] [ 2957] [depth= 1] . ( 8 sec) [ -12203.0276] [ 2950] [depth= 1] . ( 8 sec) [ -12202.0460] [ 2949] [depth= 1] . ( 8 sec) [ -12200.6667] [ 2963] [depth= 1] . ( 9 sec) [ -12199.0166] [ 2957] [depth= 2] . ( 9 sec) [ -12191.5546] [ 2960] [depth= 1] . ( 9 sec) [ -12186.1469] [ 2944] [depth= 1] . ( 9 sec) [ -12183.2245] [ 2942] [depth= 1] . ( 10 sec) [ -12183.1339] [ 2944] [depth= 1] . ( 10 sec) [ -12182.3036] [ 2943] [depth= 1] . ( 10 sec) [ -12153.6114] [Branch lengths ] . ( 11 sec) [ -12153.4270] [GTR parameters ] . ( 11 sec) [ -12152.3050] [Alpha ][ 1.005874] . ( 11 sec) [ -12151.6276] [ 2944] [depth= 1] . ( 11 sec) [ -12151.5984] [ 2947] [depth= 1] . ( 11 sec) [ -12147.8141] [ 2933] [depth= 1] . ( 14 sec) [ -12147.7361] [ 2938] [depth= 1] . ( 14 sec) [ -12141.2396] [Branch lengths ] . ( 15 sec) [ -12141.2308] [GTR parameters ] . ( 15 sec) [ -12141.2244] [Alpha ][ 1.013136] . ( 18 sec) [ -12140.5785] [Branch lengths ] . ( 25 sec) [ -12139.9833] [ 2934] [depth= 1] . ( 42 sec) [ -12139.7157] [Branch lengths ] . ( 42 sec) [ -12139.7146] [GTR parameters ] . ( 42 sec) [ -12139.7132] [Alpha ][ 1.016597] . ( 43 sec) [ -12139.7132] [Topology ] . ( 43 sec) [ -12139.6698] [Topology ] . ( 44 sec) [ -12139.6620] [Topology ] . ( 45 sec) [ -12139.6588] [Topology ] . ( 46 sec) [ -12139.6573] [Topology ] . ( 47 sec) [ -12139.6565] [Topology ] . ( 47 sec) [ -12139.6565] [GTR parameters ] . ( 47 sec) [ -12139.6565] [Alpha ][ 1.016597] . ( 47 sec) [ -12139.6565] [Topology ] . ( 48 sec) [ -12139.6560] [Topology ] . ( 48 sec) [ -12139.6560] [GTR parameters ] . ( 48 sec) [ -12139.6560] [Alpha ][ 1.016597] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.656020. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22955.3313] [GTR parameters ] . ( 1 sec) [ -22523.1813] [Alpha ][ 0.500960] . ( 1 sec) [ -22410.7861] [ 5767] [depth= 1] . ( 1 sec) [ -22010.4569] [ 5697] [depth= 8] . ( 1 sec) [ -21998.9491] [ 5682] [depth= 3] . ( 1 sec) [ -21921.4441] [ 5672] [depth= 1] . ( 1 sec) [ -21745.3613] [ 5597] [depth= 9] . ( 1 sec) [ -21531.2920] [ 5590] [depth= 2] . ( 1 sec) [ -21325.2911] [ 5498] [depth= 1] . ( 1 sec) [ -21296.7639] [ 5439] [depth= 11] . ( 1 sec) [ -20780.0426] [ 5393] [depth= 1] . ( 2 sec) [ -20375.7795] [ 5206] [depth= 7] . ( 2 sec) [ -20104.1681] [ 5111] [depth= 7] . ( 2 sec) [ -20004.9870] [ 5096] [depth= 3] . ( 2 sec) [ -19688.3250] [ 5028] [depth= 6] . ( 2 sec) [ -19562.3221] [ 5015] [depth= 1] . ( 2 sec) [ -19435.6926] [ 5005] [depth= 1] . ( 2 sec) [ -19096.4902] [ 4897] [depth= 3] . ( 2 sec) [ -19033.0790] [ 4898] [depth= 1] . ( 2 sec) [ -18891.5035] [ 4948] [depth= 4] . ( 2 sec) [ -18761.0596] [ 4914] [depth= 7] . ( 2 sec) [ -18234.7620] [ 4858] [depth= 14] . ( 2 sec) [ -17483.3358] [ 4682] [depth= 6] . ( 2 sec) [ -17285.1413] [ 4600] [depth= 5] . ( 2 sec) [ -17004.9967] [ 4575] [depth= 2] . ( 2 sec) [ -16465.1446] [ 4408] [depth= 17] . ( 2 sec) [ -16298.2187] [ 4330] [depth= 8] . ( 2 sec) [ -16273.8604] [ 4323] [depth= 2] . ( 2 sec) [ -15997.4913] [ 4173] [depth= 15] . ( 3 sec) [ -15838.8506] [ 4019] [depth= 12] . ( 3 sec) [ -15582.7070] [ 3941] [depth= 7] . ( 3 sec) [ -15542.3257] [ 3916] [depth= 3] . ( 3 sec) [ -15372.2868] [ 3808] [depth= 9] . ( 3 sec) [ -15256.1019] [ 3783] [depth= 1] . ( 3 sec) [ -15226.1701] [ 3752] [depth= 2] . ( 3 sec) [ -15180.2206] [ 3715] [depth= 1] . ( 3 sec) [ -15079.2879] [ 3702] [depth= 6] . ( 3 sec) [ -14974.9382] [ 3677] [depth= 1] . ( 3 sec) [ -14730.1509] [ 3619] [depth= 6] . ( 3 sec) [ -14713.0610] [ 3610] [depth= 1] . ( 3 sec) [ -14615.2175] [ 3602] [depth= 1] . ( 3 sec) [ -14547.2082] [ 3556] [depth= 1] . ( 3 sec) [ -14531.1290] [ 3550] [depth= 2] . ( 3 sec) [ -14436.8505] [ 3521] [depth= 2] . ( 3 sec) [ -14307.3770] [ 3504] [depth= 6] . ( 3 sec) [ -14303.6311] [ 3514] [depth= 1] . ( 3 sec) [ -14214.9373] [ 3493] [depth= 1] . ( 4 sec) [ -14200.2783] [ 3486] [depth= 1] . ( 4 sec) [ -13857.1414] [ 3479] [depth= 7] . ( 4 sec) [ -13817.8810] [ 3461] [depth= 1] . ( 4 sec) [ -13662.5184] [ 3407] [depth= 4] . ( 4 sec) [ -13655.9146] [ 3415] [depth= 1] . ( 4 sec) [ -13642.9353] [ 3395] [depth= 1] . ( 4 sec) [ -13544.0965] [ 3406] [depth= 5] . ( 4 sec) [ -13528.4075] [ 3402] [depth= 3] . ( 4 sec) [ -13449.8234] [ 3325] [depth= 7] . ( 4 sec) [ -13391.9587] [ 3304] [depth= 1] . ( 4 sec) [ -13323.7817] [ 3285] [depth= 5] . ( 4 sec) [ -13320.6151] [ 3281] [depth= 1] . ( 4 sec) [ -13191.2197] [ 3271] [depth= 2] . ( 4 sec) [ -13185.1767] [ 3194] [depth= 2] . ( 4 sec) [ -13172.7820] [ 3145] [depth= 5] . ( 4 sec) [ -13168.4297] [ 3138] [depth= 1] . ( 5 sec) [ -13164.1318] [ 3132] [depth= 1] . ( 5 sec) [ -13094.2624] [ 3127] [depth= 3] . ( 5 sec) [ -12995.8268] [ 3076] [depth= 1] . ( 5 sec) [ -12885.2379] [ 3040] [depth= 8] . ( 5 sec) [ -12884.8788] [ 3041] [depth= 1] . ( 5 sec) [ -12842.9169] [ 3038] [depth= 4] . ( 5 sec) [ -12791.5651] [ 3004] [depth= 1] . ( 5 sec) [ -12779.4008] [ 2997] [depth= 1] . ( 5 sec) [ -12767.2675] [ 2988] [depth= 2] . ( 5 sec) [ -12626.2911] [ 2954] [depth= 3] . ( 5 sec) [ -12616.7814] [ 2960] [depth= 1] . ( 5 sec) [ -12612.3887] [ 2974] [depth= 1] . ( 6 sec) [ -12263.0361] [Branch lengths ] . ( 6 sec) [ -12258.3263] [GTR parameters ] . ( 6 sec) [ -12207.2688] [Alpha ][ 0.957710] . ( 6 sec) [ -12199.5656] [ 2974] [depth= 2] . ( 6 sec) [ -12199.2487] [ 2977] [depth= 1] . ( 6 sec) [ -12198.9520] [ 2964] [depth= 1] . ( 7 sec) [ -12198.7702] [ 2959] [depth= 1] . ( 7 sec) [ -12198.2897] [ 2961] [depth= 1] . ( 7 sec) [ -12195.4514] [ 2950] [depth= 1] . ( 7 sec) [ -12195.1422] [ 2953] [depth= 1] . ( 7 sec) [ -12182.1533] [ 2944] [depth= 1] . ( 7 sec) [ -12177.8440] [ 2947] [depth= 1] . ( 8 sec) [ -12177.7399] [ 2946] [depth= 1] . ( 8 sec) [ -12177.6429] [ 2947] [depth= 1] . ( 8 sec) [ -12171.9255] [ 2946] [depth= 2] . ( 8 sec) [ -12167.0979] [ 2942] [depth= 1] . ( 9 sec) [ -12167.0668] [ 2937] [depth= 1] . ( 9 sec) [ -12160.8735] [ 2927] [depth= 1] . ( 9 sec) [ -12160.0181] [ 2928] [depth= 1] . ( 10 sec) [ -12142.4690] [Branch lengths ] . ( 10 sec) [ -12142.4080] [GTR parameters ] . ( 10 sec) [ -12141.9841] [Alpha ][ 1.015068] . ( 12 sec) [ -12141.9531] [ 2929] [depth= 1] . ( 13 sec) [ -12141.9355] [ 2934] [depth= 1] . ( 13 sec) [ -12140.0133] [Branch lengths ] . ( 14 sec) [ -12140.0108] [GTR parameters ] . ( 14 sec) [ -12140.0105] [Alpha ][ 1.016668] . ( 17 sec) [ -12139.7338] [Branch lengths ] . ( 42 sec) [ -12139.6843] [Branch lengths ] . ( 42 sec) [ -12139.6843] [Topology ] . ( 42 sec) [ -12139.6619] [Topology ] . ( 43 sec) [ -12139.6584] [Topology ] . ( 44 sec) [ -12139.6570] [Topology ] . ( 45 sec) [ -12139.6564] [Topology ] . ( 45 sec) [ -12139.6562] [GTR parameters ] . ( 45 sec) [ -12139.6562] [Alpha ][ 1.016668] . ( 45 sec) [ -12139.6562] [Topology ] . ( 46 sec) [ -12139.6559] [Topology ] . ( 46 sec) [ -12139.6559] [GTR parameters ] . ( 46 sec) [ -12139.6559] [Alpha ][ 1.016668] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.655878. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21995.4571] [GTR parameters ] . ( 1 sec) [ -21573.3021] [Alpha ][ 0.500960] . ( 1 sec) [ -21503.2254] [ 5671] [depth= 11] . ( 1 sec) [ -21298.5564] [ 5597] [depth= 9] . ( 1 sec) [ -20759.9010] [ 5521] [depth= 2] . ( 1 sec) [ -20670.3099] [ 5484] [depth= 1] . ( 1 sec) [ -20407.0061] [ 5387] [depth= 6] . ( 1 sec) [ -20309.3001] [ 5370] [depth= 2] . ( 1 sec) [ -20199.1471] [ 5349] [depth= 4] . ( 1 sec) [ -20144.5014] [ 5336] [depth= 1] . ( 1 sec) [ -19934.1214] [ 5295] [depth= 5] . ( 1 sec) [ -19608.1882] [ 5232] [depth= 4] . ( 2 sec) [ -19404.6761] [ 5201] [depth= 2] . ( 2 sec) [ -19258.9572] [ 5133] [depth= 4] . ( 2 sec) [ -19038.8535] [ 5122] [depth= 7] . ( 2 sec) [ -18935.1578] [ 5107] [depth= 2] . ( 2 sec) [ -18635.8280] [ 5002] [depth= 12] . ( 2 sec) [ -18583.8852] [ 5000] [depth= 1] . ( 2 sec) [ -18539.7668] [ 4974] [depth= 1] . ( 2 sec) [ -18464.6407] [ 4959] [depth= 1] . ( 2 sec) [ -18279.6063] [ 4869] [depth= 6] . ( 2 sec) [ -18175.9221] [ 4850] [depth= 1] . ( 2 sec) [ -18153.3777] [ 4830] [depth= 1] . ( 2 sec) [ -18038.9541] [ 4814] [depth= 4] . ( 2 sec) [ -17848.8446] [ 4731] [depth= 1] . ( 2 sec) [ -17493.0845] [ 4598] [depth= 9] . ( 2 sec) [ -17193.2774] [ 4471] [depth= 11] . ( 2 sec) [ -16972.2768] [ 4393] [depth= 5] . ( 2 sec) [ -16760.2175] [ 4301] [depth= 3] . ( 2 sec) [ -16685.0601] [ 4287] [depth= 3] . ( 2 sec) [ -16515.7612] [ 4228] [depth= 15] . ( 3 sec) [ -16363.3881] [ 4217] [depth= 1] . ( 3 sec) [ -16257.8489] [ 4202] [depth= 11] . ( 3 sec) [ -16210.8792] [ 4157] [depth= 1] . ( 3 sec) [ -16097.4378] [ 4105] [depth= 7] . ( 3 sec) [ -15807.7464] [ 4068] [depth= 6] . ( 3 sec) [ -15737.9870] [ 4060] [depth= 2] . ( 3 sec) [ -15697.8305] [ 4012] [depth= 4] . ( 3 sec) [ -15438.0214] [ 3942] [depth= 4] . ( 3 sec) [ -15003.4331] [ 3867] [depth= 7] . ( 3 sec) [ -14942.0114] [ 3859] [depth= 1] . ( 3 sec) [ -14667.1200] [ 3822] [depth= 6] . ( 3 sec) [ -14515.8845] [ 3773] [depth= 1] . ( 3 sec) [ -14401.6848] [ 3747] [depth= 3] . ( 3 sec) [ -14254.5230] [ 3699] [depth= 1] . ( 3 sec) [ -14239.9310] [ 3695] [depth= 2] . ( 3 sec) [ -14197.0763] [ 3663] [depth= 1] . ( 3 sec) [ -14175.2560] [ 3641] [depth= 1] . ( 3 sec) [ -14147.6802] [ 3637] [depth= 1] . ( 4 sec) [ -13785.4370] [ 3529] [depth= 11] . ( 4 sec) [ -13724.2490] [ 3508] [depth= 4] . ( 4 sec) [ -13721.5739] [ 3509] [depth= 1] . ( 4 sec) [ -13695.6678] [ 3503] [depth= 1] . ( 4 sec) [ -13498.0365] [ 3435] [depth= 4] . ( 4 sec) [ -13440.8656] [ 3317] [depth= 2] . ( 4 sec) [ -13399.1674] [ 3302] [depth= 3] . ( 4 sec) [ -13302.8641] [ 3269] [depth= 3] . ( 4 sec) [ -13281.7052] [ 3262] [depth= 1] . ( 4 sec) [ -13181.5597] [ 3275] [depth= 6] . ( 4 sec) [ -13134.0413] [ 3256] [depth= 5] . ( 4 sec) [ -13022.9164] [ 3271] [depth= 1] . ( 4 sec) [ -12943.1082] [ 3196] [depth= 9] . ( 5 sec) [ -12931.6084] [ 3201] [depth= 3] . ( 5 sec) [ -12931.2891] [ 3205] [depth= 1] . ( 5 sec) [ -12925.1867] [ 3209] [depth= 1] . ( 5 sec) [ -12888.2571] [ 3130] [depth= 2] . ( 5 sec) [ -12805.9219] [ 3110] [depth= 2] . ( 5 sec) [ -12768.2887] [ 3100] [depth= 1] . ( 5 sec) [ -12670.9273] [ 3069] [depth= 3] . ( 5 sec) [ -12649.2319] [ 3072] [depth= 1] . ( 5 sec) [ -12642.4265] [ 3070] [depth= 1] . ( 6 sec) [ -12435.1445] [Branch lengths ] . ( 6 sec) [ -12431.9533] [GTR parameters ] . ( 6 sec) [ -12384.6050] [Alpha ][ 0.926029] . ( 6 sec) [ -12383.7718] [ 3071] [depth= 1] . ( 6 sec) [ -12383.6764] [ 3070] [depth= 1] . ( 6 sec) [ -12378.4546] [ 3063] [depth= 1] . ( 6 sec) [ -12369.4010] [ 3061] [depth= 2] . ( 6 sec) [ -12298.8427] [ 3009] [depth= 5] . ( 6 sec) [ -12298.4439] [ 3010] [depth= 1] . ( 7 sec) [ -12297.7800] [ 3008] [depth= 1] . ( 7 sec) [ -12294.2129] [ 3004] [depth= 1] . ( 7 sec) [ -12289.8803] [ 2999] [depth= 2] . ( 7 sec) [ -12264.2548] [ 3001] [depth= 1] . ( 7 sec) [ -12261.5428] [ 2985] [depth= 1] . ( 7 sec) [ -12253.3893] [ 2987] [depth= 1] . ( 7 sec) [ -12251.4536] [ 2992] [depth= 1] . ( 7 sec) [ -12234.8387] [ 2974] [depth= 2] . ( 8 sec) [ -12193.7424] [ 2950] [depth= 1] . ( 8 sec) [ -12191.3012] [ 2948] [depth= 1] . ( 8 sec) [ -12186.4980] [ 2943] [depth= 1] . ( 8 sec) [ -12186.3219] [ 2944] [depth= 1] . ( 8 sec) [ -12185.0807] [ 2932] [depth= 1] . ( 8 sec) [ -12181.8913] [ 2937] [depth= 1] . ( 9 sec) [ -12177.1492] [ 2932] [depth= 1] . ( 9 sec) [ -12177.0607] [ 2937] [depth= 1] . ( 9 sec) [ -12176.9963] [ 2935] [depth= 1] . ( 10 sec) [ -12148.8370] [Branch lengths ] . ( 10 sec) [ -12148.7257] [GTR parameters ] . ( 10 sec) [ -12147.8174] [Alpha ][ 1.007710] . ( 10 sec) [ -12147.2671] [ 2937] [depth= 2] . ( 11 sec) [ -12147.2385] [ 2938] [depth= 1] . ( 11 sec) [ -12146.5171] [ 2933] [depth= 1] . ( 14 sec) [ -12143.3836] [Branch lengths ] . ( 14 sec) [ -12143.3800] [GTR parameters ] . ( 14 sec) [ -12143.3540] [Alpha ][ 1.022560] . ( 18 sec) [ -12142.9572] [Branch lengths ] . ( 22 sec) [ -12142.3532] [ 2929] [depth= 1] . ( 23 sec) [ -12141.8735] [ 2936] [depth= 1] . ( 24 sec) [ -12141.4800] [ 2934] [depth= 1] . ( 41 sec) [ -12139.9671] [Branch lengths ] . ( 42 sec) [ -12139.9599] [GTR parameters ] . ( 42 sec) [ -12139.9559] [Alpha ][ 1.016735] . ( 66 sec) [ -12139.6930] [Branch lengths ] . ( 66 sec) [ -12139.6930] [Topology ] . ( 67 sec) [ -12139.6639] [Topology ] . ( 68 sec) [ -12139.6587] [Topology ] . ( 68 sec) [ -12139.6569] [Topology ] . ( 69 sec) [ -12139.6562] [Topology ] . ( 69 sec) [ -12139.6561] [GTR parameters ] . ( 70 sec) [ -12139.6561] [Alpha ][ 1.016735] . ( 70 sec) [ -12139.6561] [Topology ] . ( 70 sec) [ -12139.6558] [Topology ] . ( 71 sec) [ -12139.6558] [GTR parameters ] . ( 71 sec) [ -12139.6558] [Alpha ][ 1.016735] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.655811. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22687.4551] [GTR parameters ] . ( 0 sec) [ -22249.8876] [Alpha ][ 0.500960] . ( 1 sec) [ -22099.3512] [ 5830] [depth= 7] . ( 1 sec) [ -21624.1189] [ 5738] [depth= 8] . ( 1 sec) [ -21526.7610] [ 5732] [depth= 5] . ( 1 sec) [ -21503.1751] [ 5716] [depth= 4] . ( 1 sec) [ -21432.3879] [ 5620] [depth= 10] . ( 1 sec) [ -21294.7524] [ 5607] [depth= 1] . ( 1 sec) [ -21030.9030] [ 5581] [depth= 6] . ( 1 sec) [ -20568.1152] [ 5499] [depth= 1] . ( 1 sec) [ -20444.8375] [ 5404] [depth= 17] . ( 1 sec) [ -19971.9314] [ 5352] [depth= 17] . ( 1 sec) [ -19929.6112] [ 5349] [depth= 5] . ( 1 sec) [ -19504.1961] [ 5268] [depth= 2] . ( 1 sec) [ -19492.0799] [ 5268] [depth= 1] . ( 1 sec) [ -19323.7946] [ 5238] [depth= 2] . ( 1 sec) [ -19296.5948] [ 5229] [depth= 12] . ( 1 sec) [ -19037.9869] [ 5215] [depth= 2] . ( 1 sec) [ -18707.6783] [ 5137] [depth= 13] . ( 1 sec) [ -18592.0121] [ 5045] [depth= 10] . ( 1 sec) [ -18567.0866] [ 5039] [depth= 1] . ( 1 sec) [ -18422.2350] [ 4946] [depth= 7] . ( 2 sec) [ -18313.8188] [ 4939] [depth= 1] . ( 2 sec) [ -18208.6830] [ 4946] [depth= 1] . ( 2 sec) [ -17961.2696] [ 4863] [depth= 12] . ( 2 sec) [ -17856.2024] [ 4848] [depth= 5] . ( 2 sec) [ -17840.6927] [ 4841] [depth= 1] . ( 2 sec) [ -17603.8356] [ 4795] [depth= 13] . ( 2 sec) [ -17297.4101] [ 4669] [depth= 2] . ( 2 sec) [ -17297.3879] [ 4674] [depth= 1] . ( 2 sec) [ -17187.1494] [ 4669] [depth= 1] . ( 2 sec) [ -16926.0835] [ 4641] [depth= 1] . ( 2 sec) [ -16861.8294] [ 4585] [depth= 1] . ( 2 sec) [ -16821.0666] [ 4575] [depth= 2] . ( 2 sec) [ -16534.3735] [ 4529] [depth= 11] . ( 2 sec) [ -16421.0222] [ 4446] [depth= 1] . ( 2 sec) [ -16345.5830] [ 4417] [depth= 9] . ( 2 sec) [ -16293.5448] [ 4398] [depth= 6] . ( 2 sec) [ -15955.2531] [ 4295] [depth= 7] . ( 2 sec) [ -15797.0151] [ 4219] [depth= 10] . ( 2 sec) [ -15522.6562] [ 4086] [depth= 2] . ( 3 sec) [ -15357.1298] [ 4068] [depth= 11] . ( 3 sec) [ -15334.2235] [ 4079] [depth= 1] . ( 3 sec) [ -15277.9915] [ 4022] [depth= 3] . ( 3 sec) [ -15090.8494] [ 3903] [depth= 5] . ( 3 sec) [ -15047.4871] [ 3893] [depth= 1] . ( 3 sec) [ -15031.7641] [ 3901] [depth= 1] . ( 3 sec) [ -14908.2258] [ 3844] [depth= 3] . ( 3 sec) [ -14817.6339] [ 3822] [depth= 4] . ( 3 sec) [ -14715.2079] [ 3792] [depth= 4] . ( 3 sec) [ -14578.9233] [ 3759] [depth= 6] . ( 3 sec) [ -14314.8532] [ 3669] [depth= 4] . ( 3 sec) [ -14089.9839] [ 3603] [depth= 6] . ( 3 sec) [ -14061.6113] [ 3618] [depth= 6] . ( 3 sec) [ -13871.2726] [ 3546] [depth= 6] . ( 3 sec) [ -13836.1851] [ 3552] [depth= 1] . ( 3 sec) [ -13787.3751] [ 3518] [depth= 2] . ( 3 sec) [ -13760.3584] [ 3509] [depth= 1] . ( 3 sec) [ -13685.7888] [ 3503] [depth= 1] . ( 4 sec) [ -13681.8515] [ 3502] [depth= 1] . ( 4 sec) [ -13672.6123] [ 3491] [depth= 1] . ( 4 sec) [ -13644.8546] [ 3465] [depth= 4] . ( 4 sec) [ -13632.7008] [ 3466] [depth= 1] . ( 4 sec) [ -13565.9374] [ 3459] [depth= 1] . ( 4 sec) [ -13443.0441] [ 3434] [depth= 1] . ( 4 sec) [ -13415.3436] [ 3444] [depth= 1] . ( 4 sec) [ -12970.4672] [ 3259] [depth= 5] . ( 4 sec) [ -12955.7528] [ 3247] [depth= 2] . ( 4 sec) [ -12941.8151] [ 3248] [depth= 5] . ( 4 sec) [ -12933.1094] [ 3243] [depth= 1] . ( 4 sec) [ -12881.8914] [ 3209] [depth= 2] . ( 4 sec) [ -12828.9752] [ 3202] [depth= 2] . ( 4 sec) [ -12769.1075] [ 3178] [depth= 1] . ( 4 sec) [ -12754.1238] [ 3167] [depth= 1] . ( 4 sec) [ -12685.3365] [ 3142] [depth= 2] . ( 4 sec) [ -12684.6737] [ 3145] [depth= 1] . ( 5 sec) [ -12679.3247] [ 3142] [depth= 1] . ( 5 sec) [ -12678.8011] [ 3124] [depth= 2] . ( 5 sec) [ -12660.4664] [ 3123] [depth= 1] . ( 5 sec) [ -12498.0714] [Branch lengths ] . ( 6 sec) [ -12496.7582] [GTR parameters ] . ( 6 sec) [ -12460.0341] [Alpha ][ 0.869162] . ( 6 sec) [ -12459.8430] [ 3107] [depth= 4] . ( 6 sec) [ -12436.5138] [ 3097] [depth= 3] . ( 6 sec) [ -12430.2905] [ 3098] [depth= 1] . ( 6 sec) [ -12413.7486] [ 3083] [depth= 1] . ( 6 sec) [ -12409.7115] [ 3078] [depth= 1] . ( 6 sec) [ -12409.5594] [ 3081] [depth= 1] . ( 6 sec) [ -12408.9345] [ 3077] [depth= 2] . ( 7 sec) [ -12365.0794] [ 3029] [depth= 3] . ( 7 sec) [ -12364.0359] [ 3012] [depth= 1] . ( 7 sec) [ -12358.1801] [ 3017] [depth= 1] . ( 7 sec) [ -12294.9628] [ 2994] [depth= 1] . ( 7 sec) [ -12289.6395] [ 2989] [depth= 2] . ( 7 sec) [ -12284.0868] [ 2992] [depth= 1] . ( 7 sec) [ -12260.6329] [ 2966] [depth= 1] . ( 7 sec) [ -12260.6160] [ 2988] [depth= 1] . ( 8 sec) [ -12258.3504] [ 2993] [depth= 1] . ( 8 sec) [ -12245.0115] [ 2984] [depth= 1] . ( 8 sec) [ -12244.5945] [ 2983] [depth= 1] . ( 8 sec) [ -12241.6077] [ 2987] [depth= 1] . ( 8 sec) [ -12217.3788] [ 2965] [depth= 1] . ( 8 sec) [ -12212.0635] [ 2951] [depth= 1] . ( 8 sec) [ -12200.4831] [ 2935] [depth= 1] . ( 9 sec) [ -12183.3549] [ 2925] [depth= 2] . ( 9 sec) [ -12183.3263] [ 2926] [depth= 1] . ( 9 sec) [ -12149.6220] [Branch lengths ] . ( 10 sec) [ -12149.4085] [GTR parameters ] . ( 10 sec) [ -12146.7244] [Alpha ][ 1.007854] . ( 10 sec) [ -12146.1584] [ 2929] [depth= 1] . ( 12 sec) [ -12145.5698] [ 2934] [depth= 1] . ( 13 sec) [ -12140.2893] [Branch lengths ] . ( 14 sec) [ -12140.2765] [GTR parameters ] . ( 14 sec) [ -12140.2715] [Alpha ][ 1.014253] . ( 17 sec) [ -12139.7647] [Branch lengths ] . ( 41 sec) [ -12139.6886] [Branch lengths ] . ( 41 sec) [ -12139.6886] [Topology ] . ( 42 sec) [ -12139.6634] [Topology ] . ( 43 sec) [ -12139.6593] [Topology ] . ( 44 sec) [ -12139.6577] [Topology ] . ( 45 sec) [ -12139.6569] [Topology ] . ( 45 sec) [ -12139.6569] [GTR parameters ] . ( 45 sec) [ -12139.6564] [Alpha ][ 1.016164] . ( 45 sec) [ -12139.6564] [Topology ] . ( 46 sec) [ -12139.6560] [Topology ] . ( 46 sec) [ -12139.6560] [GTR parameters ] . ( 46 sec) [ -12139.6560] [Alpha ][ 1.016164] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12139.655972. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-12251.477966 . ( 1 sec) [ -12240.5369] [GTR parameters ] . ( 1 sec) [ -12240.5293] [Alpha ][ 0.991383] . ( 1 sec) [ -12240.5293] [Topology ] . ( 2 sec) [ -12159.4656] [Topology ] . ( 3 sec) [ -12146.8006] [Topology ] . ( 3 sec) [ -12143.2282] [Topology ] . ( 4 sec) [ -12141.6547] [Topology ] . ( 5 sec) [ -12140.8761] [Topology ] . ( 6 sec) [ -12140.4867] [Topology ] . ( 7 sec) [ -12140.2849] [Topology ] . ( 8 sec) [ -12140.1779] [Topology ] . ( 9 sec) [ -12140.1204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -12139.8651] [Topology ] . Before opt ts/t=1.000000 LK=-12139.865084 . ( 17 sec) [ -12139.8452] [GTR parameters ] . ( 17 sec) [ -12139.7702] [Alpha ][ 1.016211] . ( 17 sec) [ -12139.7702] [Topology ] . ( 18 sec) [ -12139.7053] [Topology ] . ( 19 sec) [ -12139.6804] [Topology ] . ( 19 sec) [ -12139.6684] [Topology ] . ( 20 sec) [ -12139.6624] [Topology ] . ( 21 sec) [ -12139.6592] [Topology ] . ( 22 sec) [ -12139.6575] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-12139.657526 . ( 29 sec) [ -12139.6575] [GTR parameters ] . ( 29 sec) [ -12139.6575] [Alpha ][ 1.016211] . ( 29 sec) [ -12139.6575] [Topology ] . ( 30 sec) [ -12139.6566] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -12240.5369] [GTR parameters ] . ( 44 sec) [ -12240.5293] [Alpha ][ 0.991383] . ( 45 sec) [ -12237.5201] [ 2943] [depth= 1] . ( 45 sec) [ -12231.2679] [ 2927] [depth= 1] . ( 45 sec) [ -12229.4686] [ 2926] [depth= 1] . ( 45 sec) [ -12228.5852] [ 2929] [depth= 1] . ( 45 sec) [ -12228.4600] [ 2928] [depth= 1] . ( 46 sec) [ -12224.3122] [ 2931] [depth= 1] . ( 46 sec) [ -12222.4618] [ 2932] [depth= 1] . ( 46 sec) [ -12222.1608] [ 2929] [depth= 1] . ( 46 sec) [ -12222.0913] [ 2932] [depth= 1] . ( 46 sec) [ -12214.5512] [ 2931] [depth= 1] . ( 46 sec) [ -12211.7479] [ 2932] [depth= 1] . ( 46 sec) [ -12210.7900] [ 2937] [depth= 1] . ( 46 sec) [ -12210.1804] [ 2955] [depth= 1] . ( 46 sec) [ -12209.7823] [ 2937] [depth= 1] . ( 46 sec) [ -12200.1387] [ 2951] [depth= 1] . ( 46 sec) [ -12195.1253] [ 2937] [depth= 1] . ( 47 sec) [ -12193.2460] [ 2939] [depth= 1] . ( 47 sec) [ -12190.0434] [ 2937] [depth= 1] . ( 47 sec) [ -12189.1867] [ 2933] [depth= 1] . ( 47 sec) [ -12188.4718] [ 2937] [depth= 1] . ( 48 sec) [ -12145.4907] [Branch lengths ] . ( 48 sec) [ -12145.4730] [GTR parameters ] . ( 48 sec) [ -12145.4420] [Alpha ][ 1.007665] . ( 49 sec) [ -12145.4124] [ 2938] [depth= 1] . ( 51 sec) [ -12141.1985] [Branch lengths ] . ( 51 sec) [ -12141.1976] [GTR parameters ] . ( 52 sec) [ -12141.1897] [Alpha ][ 1.015800] . ( 55 sec) [ -12140.5952] [Branch lengths ] . ( 78 sec) [ -12140.0055] [ 2934] [depth= 1] . ( 79 sec) [ -12139.7272] [Branch lengths ] . ( 79 sec) [ -12139.7259] [GTR parameters ] . ( 79 sec) [ -12139.7259] [Alpha ][ 1.015800] . ( 79 sec) [ -12139.7259] [Topology ] . ( 80 sec) [ -12139.6759] [Topology ] . ( 81 sec) [ -12139.6653] [Topology ] . ( 82 sec) [ -12139.6606] [Topology ] . ( 83 sec) [ -12139.6583] [Topology ] . ( 84 sec) [ -12139.6570] [Topology ] . ( 85 sec) [ -12139.6564] [Topology ] . ( 85 sec) [ -12139.6564] [GTR parameters ] . ( 85 sec) [ -12139.6564] [Alpha ][ 1.015800] . ( 85 sec) [ -12139.6564] [Topology ] . ( 86 sec) [ -12139.6560] [Topology ] . ( 86 sec) [ -12139.6560] [GTR parameters ] . ( 86 sec) [ -12139.6560] [Alpha ][ 1.015800] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12139.656578 . Log likelihood obtained after SPR moves : -12139.655976 . Log likelihood of the current tree: -12139.655976. . Printing the most likely tree in file 'data65.phy_phyml_tree.txt'... . Best log likelihood : -12139.655654 . Time used 0h1m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo