.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data21.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... . 451 patterns found. (out of a total of 500 sites) . 45 sites without polymorphism (9.00%). . [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) [ -20615.8235] [GTR parameters ] . ( 1 sec) [ -20213.7014] [Alpha ][ 0.500960] . ( 1 sec) [ -20023.3685] [ 4932] [depth= 8] . ( 1 sec) [ -19794.9291] [ 4938] [depth= 6] . ( 1 sec) [ -19197.8674] [ 4879] [depth= 4] . ( 1 sec) [ -18940.3221] [ 4855] [depth= 5] . ( 1 sec) [ -18767.2425] [ 4728] [depth= 2] . ( 1 sec) [ -18734.0663] [ 4729] [depth= 1] . ( 1 sec) [ -18707.9878] [ 4693] [depth= 5] . ( 1 sec) [ -18510.2157] [ 4685] [depth= 1] . ( 1 sec) [ -18388.0030] [ 4635] [depth= 1] . ( 1 sec) [ -18341.1797] [ 4629] [depth= 5] . ( 1 sec) [ -17958.2879] [ 4610] [depth= 1] . ( 2 sec) [ -17493.9141] [ 4520] [depth= 10] . ( 2 sec) [ -17320.4547] [ 4461] [depth= 7] . ( 2 sec) [ -17240.8673] [ 4387] [depth= 9] . ( 2 sec) [ -17213.4519] [ 4382] [depth= 2] . ( 2 sec) [ -17041.4426] [ 4375] [depth= 3] . ( 2 sec) [ -16892.0360] [ 4300] [depth= 2] . ( 2 sec) [ -16728.3634] [ 4287] [depth= 3] . ( 2 sec) [ -16529.5105] [ 4248] [depth= 3] . ( 2 sec) [ -16476.8840] [ 4215] [depth= 1] . ( 2 sec) [ -16303.0122] [ 4188] [depth= 18] . ( 2 sec) [ -16154.0837] [ 4171] [depth= 1] . ( 2 sec) [ -16064.1644] [ 4139] [depth= 4] . ( 2 sec) [ -15955.4501] [ 4098] [depth= 1] . ( 2 sec) [ -15638.4287] [ 3970] [depth= 6] . ( 2 sec) [ -15571.8956] [ 3938] [depth= 1] . ( 2 sec) [ -15521.9787] [ 3917] [depth= 15] . ( 2 sec) [ -15295.4119] [ 3851] [depth= 12] . ( 2 sec) [ -15044.3723] [ 3852] [depth= 1] . ( 2 sec) [ -14842.3122] [ 3740] [depth= 3] . ( 2 sec) [ -14584.0059] [ 3661] [depth= 10] . ( 2 sec) [ -14434.1753] [ 3606] [depth= 2] . ( 2 sec) [ -14170.2995] [ 3520] [depth= 11] . ( 3 sec) [ -13990.2196] [ 3411] [depth= 9] . ( 3 sec) [ -13972.0347] [ 3415] [depth= 1] . ( 3 sec) [ -13829.5875] [ 3408] [depth= 1] . ( 3 sec) [ -13716.8447] [ 3387] [depth= 9] . ( 3 sec) [ -13511.0892] [ 3355] [depth= 1] . ( 3 sec) [ -13423.5497] [ 3310] [depth= 4] . ( 3 sec) [ -13097.5033] [ 3239] [depth= 11] . ( 3 sec) [ -13081.1195] [ 3216] [depth= 1] . ( 3 sec) [ -13055.4845] [ 3221] [depth= 2] . ( 3 sec) [ -13024.4786] [ 3213] [depth= 5] . ( 3 sec) [ -12958.5685] [ 3205] [depth= 4] . ( 3 sec) [ -12813.2926] [ 3198] [depth= 10] . ( 3 sec) [ -12807.2400] [ 3199] [depth= 1] . ( 3 sec) [ -12761.3456] [ 3179] [depth= 1] . ( 3 sec) [ -12657.4252] [ 3099] [depth= 8] . ( 3 sec) [ -12472.9459] [ 3040] [depth= 2] . ( 3 sec) [ -12382.3404] [ 3036] [depth= 1] . ( 3 sec) [ -12093.6464] [ 2983] [depth= 1] . ( 4 sec) [ -11894.1156] [ 2884] [depth= 6] . ( 4 sec) [ -11742.6233] [ 2853] [depth= 8] . ( 4 sec) [ -11708.2784] [ 2850] [depth= 1] . ( 4 sec) [ -11638.8126] [ 2843] [depth= 1] . ( 4 sec) [ -11613.4874] [ 2844] [depth= 6] . ( 4 sec) [ -11602.4173] [ 2843] [depth= 1] . ( 4 sec) [ -11577.9450] [ 2841] [depth= 1] . ( 4 sec) [ -11440.1081] [ 2814] [depth= 5] . ( 4 sec) [ -11437.8081] [ 2810] [depth= 2] . ( 4 sec) [ -11437.1745] [ 2814] [depth= 1] . ( 4 sec) [ -11205.5952] [ 2758] [depth= 1] . ( 4 sec) [ -11043.8168] [ 2695] [depth= 4] . ( 4 sec) [ -11035.9343] [ 2697] [depth= 1] . ( 5 sec) [ -11009.4894] [ 2670] [depth= 4] . ( 5 sec) [ -10974.0583] [ 2620] [depth= 1] . ( 5 sec) [ -10961.0949] [ 2617] [depth= 1] . ( 5 sec) [ -10923.8134] [ 2607] [depth= 3] . ( 5 sec) [ -10767.8717] [ 2557] [depth= 5] . ( 5 sec) [ -10759.0973] [ 2543] [depth= 3] . ( 5 sec) [ -10745.7128] [ 2538] [depth= 1] . ( 5 sec) [ -10568.7880] [Branch lengths ] . ( 6 sec) [ -10566.9233] [GTR parameters ] . ( 6 sec) [ -10530.6284] [Alpha ][ 0.895066] . ( 6 sec) [ -10525.5768] [ 2523] [depth= 1] . ( 6 sec) [ -10518.7635] [ 2494] [depth= 2] . ( 7 sec) [ -10517.4616] [ 2497] [depth= 1] . ( 7 sec) [ -10481.5506] [ 2482] [depth= 2] . ( 7 sec) [ -10480.7822] [ 2480] [depth= 1] . ( 7 sec) [ -10451.3157] [ 2446] [depth= 4] . ( 7 sec) [ -10450.3740] [ 2447] [depth= 3] . ( 7 sec) [ -10450.0904] [ 2450] [depth= 1] . ( 7 sec) [ -10450.0266] [ 2447] [depth= 1] . ( 8 sec) [ -10449.6552] [ 2451] [depth= 1] . ( 8 sec) [ -10435.4038] [ 2425] [depth= 3] . ( 8 sec) [ -10432.5159] [ 2396] [depth= 2] . ( 8 sec) [ -10414.9848] [ 2394] [depth= 1] . ( 8 sec) [ -10414.5079] [ 2393] [depth= 1] . ( 8 sec) [ -10414.3959] [ 2394] [depth= 1] . ( 8 sec) [ -10413.4945] [ 2393] [depth= 1] . ( 9 sec) [ -10412.3928] [ 2398] [depth= 1] . ( 9 sec) [ -10412.2528] [ 2396] [depth= 1] . ( 10 sec) [ -10366.9014] [Branch lengths ] . ( 10 sec) [ -10366.7753] [GTR parameters ] . ( 10 sec) [ -10365.3504] [Alpha ][ 1.005033] . ( 11 sec) [ -10364.8507] [ 2397] [depth= 1] . ( 12 sec) [ -10364.6658] [ 2395] [depth= 1] . ( 12 sec) [ -10364.6507] [ 2397] [depth= 1] . ( 13 sec) [ -10361.2849] [Branch lengths ] . ( 14 sec) [ -10361.2828] [GTR parameters ] . ( 14 sec) [ -10361.2607] [Alpha ][ 1.019885] . ( 17 sec) [ -10361.0939] [Branch lengths ] . ( 38 sec) [ -10361.0785] [Branch lengths ] . ( 38 sec) [ -10361.0785] [Topology ] . ( 39 sec) [ -10361.0769] [Topology ] . ( 40 sec) [ -10361.0763] [Topology ] . ( 40 sec) [ -10361.0763] [GTR parameters ] . ( 40 sec) [ -10361.0762] [Alpha ][ 1.020905] . ( 40 sec) [ -10361.0762] [Topology ] . ( 41 sec) [ -10361.0759] [Topology ] . ( 41 sec) [ -10361.0759] [GTR parameters ] . ( 41 sec) [ -10361.0759] [Alpha ][ 1.020905] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -10361.0735] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -10361.0731] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10361.073131. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22121.8427] [GTR parameters ] . ( 1 sec) [ -21710.3830] [Alpha ][ 0.500960] . ( 1 sec) [ -21551.6248] [ 4959] [depth= 4] . ( 1 sec) [ -21069.7359] [ 4896] [depth= 11] . ( 1 sec) [ -20895.7164] [ 4880] [depth= 4] . ( 1 sec) [ -20797.9273] [ 4864] [depth= 4] . ( 1 sec) [ -20691.5927] [ 4835] [depth= 1] . ( 2 sec) [ -20657.8274] [ 4836] [depth= 4] . ( 2 sec) [ -20486.7265] [ 4832] [depth= 1] . ( 2 sec) [ -20334.7055] [ 4813] [depth= 8] . ( 2 sec) [ -20330.0921] [ 4764] [depth= 2] . ( 2 sec) [ -20204.5153] [ 4733] [depth= 10] . ( 2 sec) [ -20110.0038] [ 4710] [depth= 10] . ( 2 sec) [ -19666.1134] [ 4700] [depth= 3] . ( 2 sec) [ -19414.6894] [ 4642] [depth= 4] . ( 2 sec) [ -19210.2250] [ 4615] [depth= 3] . ( 2 sec) [ -18889.7230] [ 4483] [depth= 3] . ( 2 sec) [ -18526.7589] [ 4415] [depth= 14] . ( 2 sec) [ -18440.4449] [ 4415] [depth= 15] . ( 2 sec) [ -17965.4337] [ 4364] [depth= 4] . ( 2 sec) [ -17706.6296] [ 4365] [depth= 1] . ( 2 sec) [ -17702.1542] [ 4334] [depth= 1] . ( 2 sec) [ -17681.9509] [ 4327] [depth= 1] . ( 2 sec) [ -17249.4063] [ 4161] [depth= 22] . ( 2 sec) [ -16408.9102] [ 4088] [depth= 10] . ( 2 sec) [ -16379.0913] [ 4087] [depth= 1] . ( 2 sec) [ -16266.0390] [ 4054] [depth= 1] . ( 2 sec) [ -16264.2940] [ 4048] [depth= 1] . ( 3 sec) [ -16094.2379] [ 3976] [depth= 13] . ( 3 sec) [ -15801.2180] [ 3779] [depth= 5] . ( 3 sec) [ -15788.4268] [ 3774] [depth= 1] . ( 3 sec) [ -15542.4184] [ 3701] [depth= 14] . ( 3 sec) [ -15450.5611] [ 3674] [depth= 7] . ( 3 sec) [ -15415.0170] [ 3674] [depth= 1] . ( 3 sec) [ -15203.5566] [ 3574] [depth= 5] . ( 3 sec) [ -15176.5327] [ 3574] [depth= 1] . ( 3 sec) [ -14982.8110] [ 3518] [depth= 2] . ( 3 sec) [ -14905.9705] [ 3491] [depth= 1] . ( 3 sec) [ -14864.1214] [ 3484] [depth= 7] . ( 3 sec) [ -14781.3919] [ 3423] [depth= 2] . ( 3 sec) [ -14756.9505] [ 3421] [depth= 1] . ( 3 sec) [ -14190.6826] [ 3370] [depth= 1] . ( 3 sec) [ -14164.8912] [ 3345] [depth= 3] . ( 3 sec) [ -14157.4416] [ 3349] [depth= 1] . ( 3 sec) [ -14065.2706] [ 3348] [depth= 1] . ( 3 sec) [ -14051.2239] [ 3338] [depth= 2] . ( 3 sec) [ -13955.1354] [ 3339] [depth= 10] . ( 3 sec) [ -13743.6918] [ 3304] [depth= 5] . ( 4 sec) [ -13648.1492] [ 3291] [depth= 5] . ( 4 sec) [ -13491.7193] [ 3328] [depth= 13] . ( 4 sec) [ -13472.7684] [ 3343] [depth= 1] . ( 4 sec) [ -13333.4544] [ 3285] [depth= 12] . ( 4 sec) [ -13286.4532] [ 3253] [depth= 1] . ( 4 sec) [ -13220.3450] [ 3253] [depth= 1] . ( 4 sec) [ -12941.7701] [ 3130] [depth= 9] . ( 4 sec) [ -12926.2590] [ 3132] [depth= 1] . ( 4 sec) [ -12400.7440] [ 3041] [depth= 1] . ( 4 sec) [ -12292.8128] [ 3033] [depth= 2] . ( 4 sec) [ -12286.9723] [ 3031] [depth= 1] . ( 4 sec) [ -12129.2995] [ 2975] [depth= 2] . ( 4 sec) [ -11955.5837] [ 2889] [depth= 1] . ( 4 sec) [ -11782.5566] [ 2856] [depth= 4] . ( 4 sec) [ -11718.1139] [ 2837] [depth= 1] . ( 4 sec) [ -11644.3622] [ 2772] [depth= 7] . ( 4 sec) [ -11632.1013] [ 2776] [depth= 1] . ( 4 sec) [ -11624.5947] [ 2779] [depth= 1] . ( 4 sec) [ -11560.1702] [ 2752] [depth= 1] . ( 4 sec) [ -11539.7166] [ 2733] [depth= 2] . ( 5 sec) [ -11418.4461] [ 2659] [depth= 8] . ( 5 sec) [ -11280.9035] [ 2685] [depth= 1] . ( 5 sec) [ -11279.7673] [ 2689] [depth= 2] . ( 5 sec) [ -11233.0254] [ 2666] [depth= 5] . ( 5 sec) [ -11063.5627] [ 2657] [depth= 3] . ( 5 sec) [ -10985.5832] [ 2599] [depth= 5] . ( 5 sec) [ -10977.9537] [ 2618] [depth= 4] . ( 5 sec) [ -10975.0926] [ 2597] [depth= 1] . ( 5 sec) [ -10841.5650] [ 2558] [depth= 3] . ( 5 sec) [ -10838.9744] [ 2563] [depth= 1] . ( 5 sec) [ -10790.6275] [ 2530] [depth= 5] . ( 5 sec) [ -10780.0025] [ 2530] [depth= 1] . ( 5 sec) [ -10779.2463] [ 2530] [depth= 1] . ( 6 sec) [ -10627.9023] [Branch lengths ] . ( 6 sec) [ -10624.8570] [GTR parameters ] . ( 6 sec) [ -10581.4695] [Alpha ][ 0.928206] . ( 7 sec) [ -10574.5571] [ 2527] [depth= 1] . ( 7 sec) [ -10543.6002] [ 2516] [depth= 2] . ( 7 sec) [ -10535.9129] [ 2494] [depth= 1] . ( 7 sec) [ -10510.8152] [ 2470] [depth= 2] . ( 7 sec) [ -10506.3277] [ 2471] [depth= 1] . ( 7 sec) [ -10505.8102] [ 2468] [depth= 1] . ( 7 sec) [ -10505.4004] [ 2465] [depth= 1] . ( 7 sec) [ -10504.8241] [ 2465] [depth= 1] . ( 8 sec) [ -10499.9648] [ 2461] [depth= 3] . ( 8 sec) [ -10499.7222] [ 2460] [depth= 1] . ( 8 sec) [ -10471.6370] [ 2440] [depth= 1] . ( 8 sec) [ -10470.2927] [ 2439] [depth= 1] . ( 8 sec) [ -10469.6543] [ 2443] [depth= 1] . ( 8 sec) [ -10404.1964] [ 2403] [depth= 2] . ( 8 sec) [ -10399.4594] [ 2401] [depth= 1] . ( 9 sec) [ -10394.8180] [ 2397] [depth= 1] . ( 9 sec) [ -10394.6910] [ 2395] [depth= 1] . ( 10 sec) [ -10394.2676] [ 2396] [depth= 1] . ( 10 sec) [ -10364.7576] [Branch lengths ] . ( 10 sec) [ -10364.7132] [GTR parameters ] . ( 10 sec) [ -10363.8836] [Alpha ][ 1.012369] . ( 13 sec) [ -10361.3380] [Branch lengths ] . ( 35 sec) [ -10361.1374] [Branch lengths ] . ( 35 sec) [ -10361.1374] [Topology ] . ( 36 sec) [ -10361.1124] [Topology ] . ( 36 sec) [ -10361.1019] [Topology ] . ( 37 sec) [ -10361.0964] [Topology ] . ( 38 sec) [ -10361.0933] [Topology ] . ( 39 sec) [ -10361.0915] [Topology ] . ( 40 sec) [ -10361.0905] [Topology ] . ( 40 sec) [ -10361.0844] [GTR parameters ] . ( 40 sec) [ -10361.0783] [Alpha ][ 1.020089] . ( 40 sec) [ -10361.0783] [Topology ] . ( 41 sec) [ -10361.0772] [Topology ] . ( 42 sec) [ -10361.0768] [Topology ] . ( 42 sec) [ -10361.0767] [GTR parameters ] . ( 42 sec) [ -10361.0767] [Alpha ][ 1.020089] . ( 42 sec) [ -10361.0767] [Topology ] . ( 43 sec) [ -10361.0765] [Topology ] . ( 43 sec) [ -10361.0765] [GTR parameters ] . ( 43 sec) [ -10361.0765] [Alpha ][ 1.020089] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -10361.0429] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -10361.0421] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10361.042142. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21423.5409] [GTR parameters ] . ( 0 sec) [ -21018.4838] [Alpha ][ 0.500960] . ( 0 sec) [ -20911.0274] [ 5073] [depth= 8] . ( 0 sec) [ -20775.9291] [ 5038] [depth= 8] . ( 1 sec) [ -20720.4242] [ 5028] [depth= 4] . ( 1 sec) [ -20698.8343] [ 5028] [depth= 1] . ( 1 sec) [ -20681.2981] [ 5013] [depth= 6] . ( 1 sec) [ -20581.4415] [ 5003] [depth= 1] . ( 1 sec) [ -20225.4244] [ 4865] [depth= 1] . ( 1 sec) [ -20038.7881] [ 4825] [depth= 8] . ( 1 sec) [ -19294.6722] [ 4719] [depth= 12] . ( 1 sec) [ -19151.8828] [ 4723] [depth= 14] . ( 1 sec) [ -18837.3926] [ 4649] [depth= 13] . ( 1 sec) [ -18737.5208] [ 4635] [depth= 7] . ( 1 sec) [ -18601.4024] [ 4628] [depth= 1] . ( 1 sec) [ -18564.8693] [ 4615] [depth= 11] . ( 1 sec) [ -18401.4525] [ 4599] [depth= 1] . ( 1 sec) [ -18092.1802] [ 4497] [depth= 12] . ( 1 sec) [ -18048.9601] [ 4497] [depth= 1] . ( 1 sec) [ -17632.5122] [ 4492] [depth= 12] . ( 1 sec) [ -17511.1217] [ 4479] [depth= 1] . ( 1 sec) [ -17063.1648] [ 4430] [depth= 11] . ( 1 sec) [ -16861.5484] [ 4389] [depth= 1] . ( 1 sec) [ -16542.0773] [ 4320] [depth= 6] . ( 1 sec) [ -16352.1664] [ 4196] [depth= 9] . ( 1 sec) [ -16332.1380] [ 4194] [depth= 1] . ( 2 sec) [ -15867.8142] [ 4045] [depth= 9] . ( 2 sec) [ -15845.9993] [ 4045] [depth= 1] . ( 2 sec) [ -15402.2530] [ 3937] [depth= 9] . ( 2 sec) [ -15247.1719] [ 3912] [depth= 12] . ( 2 sec) [ -15243.6588] [ 3915] [depth= 1] . ( 2 sec) [ -15239.9346] [ 3915] [depth= 11] . ( 2 sec) [ -15083.2379] [ 3883] [depth= 6] . ( 2 sec) [ -15027.2995] [ 3895] [depth= 4] . ( 2 sec) [ -15009.8457] [ 3894] [depth= 2] . ( 2 sec) [ -14287.3506] [ 3759] [depth= 3] . ( 2 sec) [ -13933.2301] [ 3628] [depth= 3] . ( 2 sec) [ -13922.5889] [ 3627] [depth= 11] . ( 2 sec) [ -13888.9786] [ 3613] [depth= 1] . ( 2 sec) [ -13835.6724] [ 3565] [depth= 12] . ( 2 sec) [ -13819.6605] [ 3579] [depth= 1] . ( 2 sec) [ -13419.3444] [ 3498] [depth= 3] . ( 2 sec) [ -13417.7436] [ 3513] [depth= 2] . ( 2 sec) [ -13400.1856] [ 3509] [depth= 11] . ( 2 sec) [ -13370.6034] [ 3496] [depth= 1] . ( 2 sec) [ -13274.3536] [ 3476] [depth= 3] . ( 3 sec) [ -13235.0745] [ 3405] [depth= 1] . ( 3 sec) [ -13228.4519] [ 3395] [depth= 1] . ( 3 sec) [ -13049.5554] [ 3370] [depth= 6] . ( 3 sec) [ -12967.3831] [ 3361] [depth= 2] . ( 3 sec) [ -12880.4647] [ 3347] [depth= 1] . ( 3 sec) [ -12734.8101] [ 3245] [depth= 9] . ( 3 sec) [ -12699.4384] [ 3236] [depth= 1] . ( 3 sec) [ -12658.2546] [ 3215] [depth= 1] . ( 3 sec) [ -12346.0185] [ 3116] [depth= 9] . ( 3 sec) [ -12342.2402] [ 3122] [depth= 1] . ( 3 sec) [ -12297.4305] [ 3087] [depth= 1] . ( 3 sec) [ -12234.2184] [ 3089] [depth= 1] . ( 3 sec) [ -12123.5370] [ 3055] [depth= 10] . ( 3 sec) [ -11929.4494] [ 2981] [depth= 2] . ( 3 sec) [ -11917.0597] [ 2978] [depth= 2] . ( 3 sec) [ -11839.8146] [ 2962] [depth= 1] . ( 3 sec) [ -11773.2323] [ 2935] [depth= 10] . ( 4 sec) [ -11772.5529] [ 2932] [depth= 1] . ( 4 sec) [ -11508.7745] [ 2851] [depth= 2] . ( 4 sec) [ -11467.4984] [ 2853] [depth= 1] . ( 4 sec) [ -11422.3693] [ 2826] [depth= 1] . ( 4 sec) [ -11300.0567] [ 2775] [depth= 1] . ( 4 sec) [ -11299.8473] [ 2773] [depth= 1] . ( 4 sec) [ -11259.0495] [ 2768] [depth= 1] . ( 4 sec) [ -11100.3150] [ 2697] [depth= 6] . ( 4 sec) [ -11100.2489] [ 2697] [depth= 2] . ( 4 sec) [ -11056.3207] [ 2662] [depth= 4] . ( 4 sec) [ -11050.2617] [ 2660] [depth= 2] . ( 4 sec) [ -10984.8565] [ 2650] [depth= 1] . ( 4 sec) [ -10983.0629] [ 2652] [depth= 1] . ( 4 sec) [ -10923.5715] [ 2618] [depth= 1] . ( 4 sec) [ -10905.6977] [ 2575] [depth= 4] . ( 4 sec) [ -10902.5623] [ 2577] [depth= 2] . ( 4 sec) [ -10879.8677] [ 2571] [depth= 2] . ( 5 sec) [ -10874.2157] [ 2568] [depth= 1] . ( 5 sec) [ -10722.3873] [Branch lengths ] . ( 5 sec) [ -10719.9495] [GTR parameters ] . ( 6 sec) [ -10690.7626] [Alpha ][ 0.853311] . ( 6 sec) [ -10688.2030] [ 2566] [depth= 1] . ( 6 sec) [ -10668.2774] [ 2550] [depth= 7] . ( 6 sec) [ -10666.5464] [ 2550] [depth= 1] . ( 6 sec) [ -10665.9351] [ 2549] [depth= 1] . ( 6 sec) [ -10543.0628] [ 2474] [depth= 5] . ( 6 sec) [ -10493.5290] [ 2437] [depth= 4] . ( 7 sec) [ -10493.0217] [ 2435] [depth= 1] . ( 7 sec) [ -10486.4271] [ 2428] [depth= 1] . ( 7 sec) [ -10485.7940] [ 2429] [depth= 1] . ( 7 sec) [ -10481.9180] [ 2421] [depth= 1] . ( 7 sec) [ -10479.8789] [ 2417] [depth= 1] . ( 7 sec) [ -10450.5820] [ 2412] [depth= 1] . ( 7 sec) [ -10450.1019] [ 2415] [depth= 1] . ( 7 sec) [ -10412.6719] [ 2401] [depth= 1] . ( 8 sec) [ -10406.4951] [ 2397] [depth= 1] . ( 8 sec) [ -10406.0835] [ 2400] [depth= 1] . ( 8 sec) [ -10405.1779] [ 2397] [depth= 1] . ( 8 sec) [ -10405.0671] [ 2400] [depth= 1] . ( 8 sec) [ -10404.5536] [ 2397] [depth= 1] . ( 8 sec) [ -10402.8469] [ 2402] [depth= 1] . ( 8 sec) [ -10402.5161] [ 2402] [depth= 1] . ( 9 sec) [ -10402.2204] [ 2401] [depth= 1] . ( 9 sec) [ -10368.3946] [Branch lengths ] . ( 10 sec) [ -10368.0881] [GTR parameters ] . ( 10 sec) [ -10365.2464] [Alpha ][ 1.007041] . ( 11 sec) [ -10365.2049] [ 2402] [depth= 1] . ( 11 sec) [ -10365.1126] [ 2401] [depth= 1] . ( 13 sec) [ -10361.8553] [Branch lengths ] . ( 13 sec) [ -10361.8491] [GTR parameters ] . ( 13 sec) [ -10361.8323] [Alpha ][ 1.020035] . ( 16 sec) [ -10361.5081] [Branch lengths ] . ( 37 sec) [ -10361.4662] [Branch lengths ] . ( 37 sec) [ -10361.4662] [Topology ] . ( 38 sec) [ -10361.4616] [Topology ] . ( 39 sec) [ -10361.4599] [Topology ] . ( 40 sec) [ -10361.4591] [Topology ] . ( 40 sec) [ -10361.4584] [GTR parameters ] . ( 40 sec) [ -10361.4582] [Alpha ][ 1.018511] . ( 40 sec) [ -10361.4582] [Topology ] . ( 41 sec) [ -10361.4577] [Topology ] . ( 41 sec) [ -10361.4577] [GTR parameters ] . ( 41 sec) [ -10361.4577] [Alpha ][ 1.018511] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -10361.0770] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -10361.0766] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10361.076605. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20850.1557] [GTR parameters ] . ( 1 sec) [ -20443.1884] [Alpha ][ 0.500960] . ( 1 sec) [ -20391.3632] [ 5031] [depth= 8] . ( 1 sec) [ -20128.7238] [ 4975] [depth= 9] . ( 1 sec) [ -19854.1333] [ 4946] [depth= 8] . ( 1 sec) [ -19681.1163] [ 4890] [depth= 1] . ( 1 sec) [ -19419.5427] [ 4851] [depth= 9] . ( 1 sec) [ -19360.6394] [ 4839] [depth= 2] . ( 1 sec) [ -19238.0987] [ 4830] [depth= 2] . ( 1 sec) [ -18828.1249] [ 4792] [depth= 5] . ( 1 sec) [ -18524.2283] [ 4772] [depth= 6] . ( 1 sec) [ -18316.4843] [ 4736] [depth= 3] . ( 1 sec) [ -18085.2845] [ 4657] [depth= 1] . ( 1 sec) [ -18032.9756] [ 4647] [depth= 3] . ( 1 sec) [ -17956.4832] [ 4640] [depth= 3] . ( 1 sec) [ -17886.4961] [ 4614] [depth= 6] . ( 1 sec) [ -17865.6040] [ 4617] [depth= 3] . ( 2 sec) [ -17767.5914] [ 4594] [depth= 5] . ( 2 sec) [ -17533.6735] [ 4522] [depth= 7] . ( 2 sec) [ -17189.4940] [ 4442] [depth= 15] . ( 2 sec) [ -17126.7188] [ 4425] [depth= 1] . ( 2 sec) [ -16959.3052] [ 4400] [depth= 20] . ( 2 sec) [ -16705.4179] [ 4373] [depth= 3] . ( 2 sec) [ -16081.8902] [ 4223] [depth= 13] . ( 2 sec) [ -15982.3513] [ 4166] [depth= 2] . ( 2 sec) [ -15845.2387] [ 4153] [depth= 2] . ( 2 sec) [ -15719.2435] [ 4159] [depth= 1] . ( 2 sec) [ -15408.6356] [ 4077] [depth= 17] . ( 2 sec) [ -15258.6398] [ 4034] [depth= 6] . ( 2 sec) [ -15013.9294] [ 4011] [depth= 2] . ( 2 sec) [ -14883.6093] [ 3880] [depth= 9] . ( 2 sec) [ -14797.6603] [ 3876] [depth= 4] . ( 2 sec) [ -14685.1268] [ 3835] [depth= 5] . ( 2 sec) [ -14578.5659] [ 3809] [depth= 1] . ( 2 sec) [ -14555.6538] [ 3796] [depth= 1] . ( 3 sec) [ -14458.6771] [ 3743] [depth= 10] . ( 3 sec) [ -14449.1909] [ 3735] [depth= 1] . ( 3 sec) [ -14422.3221] [ 3725] [depth= 1] . ( 3 sec) [ -14408.3490] [ 3725] [depth= 10] . ( 3 sec) [ -14405.3470] [ 3735] [depth= 2] . ( 3 sec) [ -14280.6160] [ 3690] [depth= 7] . ( 3 sec) [ -14105.7853] [ 3631] [depth= 10] . ( 3 sec) [ -14051.1926] [ 3594] [depth= 5] . ( 3 sec) [ -14042.6330] [ 3588] [depth= 1] . ( 3 sec) [ -13827.8297] [ 3472] [depth= 7] . ( 3 sec) [ -13821.7959] [ 3466] [depth= 1] . ( 3 sec) [ -13771.4501] [ 3405] [depth= 1] . ( 3 sec) [ -13325.2854] [ 3402] [depth= 3] . ( 3 sec) [ -13164.3781] [ 3396] [depth= 4] . ( 3 sec) [ -13113.2083] [ 3406] [depth= 9] . ( 3 sec) [ -13094.5683] [ 3370] [depth= 4] . ( 3 sec) [ -13024.9284] [ 3349] [depth= 1] . ( 3 sec) [ -12918.9439] [ 3281] [depth= 9] . ( 3 sec) [ -12846.2084] [ 3224] [depth= 6] . ( 3 sec) [ -12827.0021] [ 3228] [depth= 6] . ( 3 sec) [ -12823.8040] [ 3226] [depth= 1] . ( 4 sec) [ -12821.6244] [ 3231] [depth= 1] . ( 4 sec) [ -12734.7175] [ 3234] [depth= 3] . ( 4 sec) [ -12600.8255] [ 3171] [depth= 6] . ( 4 sec) [ -12287.9510] [ 3048] [depth= 3] . ( 4 sec) [ -12285.2690] [ 3046] [depth= 3] . ( 4 sec) [ -12033.7530] [ 2919] [depth= 4] . ( 4 sec) [ -11960.5873] [ 2914] [depth= 1] . ( 4 sec) [ -11959.5028] [ 2912] [depth= 1] . ( 4 sec) [ -11940.5452] [ 2905] [depth= 1] . ( 4 sec) [ -11931.1936] [ 2902] [depth= 1] . ( 4 sec) [ -11797.3852] [ 2883] [depth= 3] . ( 4 sec) [ -11735.1175] [ 2840] [depth= 7] . ( 4 sec) [ -11713.6437] [ 2841] [depth= 1] . ( 4 sec) [ -11708.3339] [ 2836] [depth= 1] . ( 4 sec) [ -11670.5688] [ 2828] [depth= 3] . ( 4 sec) [ -11659.2973] [ 2821] [depth= 2] . ( 5 sec) [ -11615.2620] [ 2828] [depth= 1] . ( 5 sec) [ -11613.2184] [ 2825] [depth= 1] . ( 5 sec) [ -11528.9322] [ 2779] [depth= 6] . ( 5 sec) [ -11469.0281] [ 2757] [depth= 1] . ( 5 sec) [ -11208.3922] [ 2677] [depth= 4] . ( 5 sec) [ -11161.5409] [ 2671] [depth= 3] . ( 5 sec) [ -11119.7606] [ 2653] [depth= 5] . ( 5 sec) [ -11113.7475] [ 2649] [depth= 1] . ( 5 sec) [ -11110.8330] [ 2646] [depth= 1] . ( 5 sec) [ -10928.2597] [Branch lengths ] . ( 6 sec) [ -10925.4398] [GTR parameters ] . ( 6 sec) [ -10893.8598] [Alpha ][ 0.848703] . ( 6 sec) [ -10883.9919] [ 2632] [depth= 1] . ( 6 sec) [ -10870.8228] [ 2613] [depth= 4] . ( 6 sec) [ -10858.0713] [ 2587] [depth= 2] . ( 6 sec) [ -10743.0425] [ 2551] [depth= 3] . ( 6 sec) [ -10666.9594] [ 2548] [depth= 1] . ( 6 sec) [ -10639.9119] [ 2519] [depth= 2] . ( 6 sec) [ -10587.7454] [ 2497] [depth= 1] . ( 7 sec) [ -10558.6585] [ 2471] [depth= 1] . ( 7 sec) [ -10551.4181] [ 2475] [depth= 1] . ( 7 sec) [ -10533.9517] [ 2469] [depth= 1] . ( 7 sec) [ -10507.1823] [ 2455] [depth= 2] . ( 7 sec) [ -10505.0670] [ 2462] [depth= 1] . ( 7 sec) [ -10504.0035] [ 2463] [depth= 1] . ( 7 sec) [ -10500.2221] [ 2462] [depth= 1] . ( 7 sec) [ -10427.1969] [ 2399] [depth= 1] . ( 7 sec) [ -10425.4179] [ 2402] [depth= 1] . ( 8 sec) [ -10424.2902] [ 2399] [depth= 1] . ( 8 sec) [ -10419.2243] [ 2397] [depth= 1] . ( 8 sec) [ -10418.9896] [ 2398] [depth= 1] . ( 8 sec) [ -10418.4014] [ 2402] [depth= 1] . ( 8 sec) [ -10418.2427] [ 2401] [depth= 1] . ( 8 sec) [ -10416.9348] [ 2405] [depth= 1] . ( 8 sec) [ -10416.8149] [ 2404] [depth= 1] . ( 8 sec) [ -10416.1300] [ 2405] [depth= 1] . ( 9 sec) [ -10414.7173] [ 2401] [depth= 1] . ( 9 sec) [ -10414.5027] [ 2400] [depth= 1] . ( 9 sec) [ -10367.5083] [Branch lengths ] . ( 10 sec) [ -10366.7098] [GTR parameters ] . ( 10 sec) [ -10363.6833] [Alpha ][ 1.004659] . ( 10 sec) [ -10363.5204] [ 2402] [depth= 1] . ( 13 sec) [ -10361.6093] [Branch lengths ] . ( 13 sec) [ -10361.6073] [GTR parameters ] . ( 13 sec) [ -10361.5842] [Alpha ][ 1.019817] . ( 17 sec) [ -10361.4742] [Branch lengths ] . ( 38 sec) [ -10361.4603] [Branch lengths ] . ( 38 sec) [ -10361.4603] [Topology ] . ( 39 sec) [ -10361.4589] [Topology ] . ( 39 sec) [ -10361.4584] [Topology ] . ( 39 sec) [ -10361.4582] [GTR parameters ] . ( 40 sec) [ -10361.4580] [Alpha ][ 1.018397] . ( 40 sec) [ -10361.4580] [Topology ] . ( 40 sec) [ -10361.4578] [Topology ] . ( 40 sec) [ -10361.4578] [GTR parameters ] . ( 41 sec) [ -10361.4578] [Alpha ][ 1.018397] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -10361.0790] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -10361.0752] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -10361.0748] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10361.074775. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21442.7197] [GTR parameters ] . ( 1 sec) [ -21044.4055] [Alpha ][ 0.500960] . ( 1 sec) [ -20900.5712] [ 5108] [depth= 6] . ( 1 sec) [ -20478.2184] [ 5062] [depth= 11] . ( 1 sec) [ -20450.0734] [ 5058] [depth= 1] . ( 1 sec) [ -20181.5358] [ 5036] [depth= 7] . ( 1 sec) [ -19666.1723] [ 4931] [depth= 7] . ( 1 sec) [ -19519.2211] [ 4913] [depth= 4] . ( 2 sec) [ -19479.7130] [ 4904] [depth= 1] . ( 2 sec) [ -19187.9924] [ 4809] [depth= 5] . ( 2 sec) [ -18638.9944] [ 4724] [depth= 5] . ( 2 sec) [ -18402.4545] [ 4635] [depth= 2] . ( 2 sec) [ -18358.0323] [ 4618] [depth= 15] . ( 2 sec) [ -18283.4421] [ 4592] [depth= 5] . ( 2 sec) [ -18190.1496] [ 4586] [depth= 1] . ( 2 sec) [ -18153.2595] [ 4565] [depth= 11] . ( 2 sec) [ -18148.8277] [ 4566] [depth= 1] . ( 2 sec) [ -17968.4045] [ 4528] [depth= 10] . ( 2 sec) [ -17931.7728] [ 4510] [depth= 1] . ( 2 sec) [ -17792.0264] [ 4516] [depth= 9] . ( 2 sec) [ -17636.0677] [ 4475] [depth= 5] . ( 2 sec) [ -17597.5914] [ 4462] [depth= 1] . ( 2 sec) [ -17277.3930] [ 4370] [depth= 8] . ( 2 sec) [ -17151.0707] [ 4385] [depth= 1] . ( 2 sec) [ -17058.6135] [ 4362] [depth= 2] . ( 2 sec) [ -17015.5771] [ 4333] [depth= 7] . ( 2 sec) [ -16713.3897] [ 4324] [depth= 1] . ( 2 sec) [ -16611.6070] [ 4281] [depth= 1] . ( 2 sec) [ -16188.5440] [ 4216] [depth= 8] . ( 2 sec) [ -16148.4214] [ 4188] [depth= 3] . ( 3 sec) [ -15991.8575] [ 4152] [depth= 8] . ( 3 sec) [ -15931.9381] [ 4144] [depth= 3] . ( 3 sec) [ -15868.0521] [ 4092] [depth= 2] . ( 3 sec) [ -15587.8747] [ 4028] [depth= 8] . ( 3 sec) [ -15509.6721] [ 4045] [depth= 1] . ( 3 sec) [ -15081.1441] [ 3989] [depth= 2] . ( 3 sec) [ -14928.4480] [ 3968] [depth= 12] . ( 3 sec) [ -14606.2159] [ 3829] [depth= 9] . ( 3 sec) [ -14167.7164] [ 3733] [depth= 17] . ( 3 sec) [ -13893.9365] [ 3577] [depth= 10] . ( 3 sec) [ -13814.4681] [ 3559] [depth= 1] . ( 3 sec) [ -13771.4841] [ 3548] [depth= 1] . ( 3 sec) [ -13759.3471] [ 3550] [depth= 1] . ( 3 sec) [ -13756.2260] [ 3557] [depth= 1] . ( 3 sec) [ -13748.2231] [ 3551] [depth= 1] . ( 3 sec) [ -13545.8803] [ 3535] [depth= 5] . ( 3 sec) [ -13351.0708] [ 3486] [depth= 2] . ( 4 sec) [ -13330.8303] [ 3480] [depth= 1] . ( 4 sec) [ -13148.7751] [ 3432] [depth= 2] . ( 4 sec) [ -13096.8391] [ 3391] [depth= 5] . ( 4 sec) [ -13023.5020] [ 3372] [depth= 3] . ( 4 sec) [ -12726.1605] [ 3292] [depth= 6] . ( 4 sec) [ -12371.1758] [ 3140] [depth= 10] . ( 4 sec) [ -12262.4666] [ 3138] [depth= 1] . ( 4 sec) [ -12255.4269] [ 3134] [depth= 1] . ( 4 sec) [ -12245.4015] [ 3136] [depth= 1] . ( 4 sec) [ -12119.5921] [ 3091] [depth= 1] . ( 4 sec) [ -12096.0225] [ 3077] [depth= 3] . ( 4 sec) [ -11948.6907] [ 3074] [depth= 1] . ( 4 sec) [ -11928.6777] [ 3072] [depth= 1] . ( 4 sec) [ -11756.3407] [ 3027] [depth= 2] . ( 5 sec) [ -11751.3970] [ 3010] [depth= 2] . ( 5 sec) [ -11550.2056] [ 2960] [depth= 1] . ( 5 sec) [ -11518.9653] [ 2959] [depth= 1] . ( 5 sec) [ -11499.5024] [ 2932] [depth= 1] . ( 5 sec) [ -11491.4312] [ 2921] [depth= 1] . ( 5 sec) [ -11480.5780] [ 2925] [depth= 1] . ( 5 sec) [ -11455.3684] [ 2874] [depth= 1] . ( 5 sec) [ -11425.6226] [ 2866] [depth= 2] . ( 5 sec) [ -11385.8707] [ 2848] [depth= 2] . ( 5 sec) [ -11359.4201] [ 2823] [depth= 4] . ( 5 sec) [ -11357.2036] [ 2815] [depth= 1] . ( 5 sec) [ -11119.4811] [ 2744] [depth= 1] . ( 5 sec) [ -11008.9472] [ 2679] [depth= 4] . ( 5 sec) [ -11005.4687] [ 2704] [depth= 1] . ( 5 sec) [ -10994.7085] [ 2705] [depth= 1] . ( 5 sec) [ -10994.6509] [ 2706] [depth= 1] . ( 6 sec) [ -10987.6080] [ 2699] [depth= 1] . ( 6 sec) [ -10987.0163] [ 2701] [depth= 1] . ( 6 sec) [ -10833.9615] [Branch lengths ] . ( 7 sec) [ -10830.6728] [GTR parameters ] . ( 7 sec) [ -10798.7234] [Alpha ][ 0.840568] . ( 7 sec) [ -10793.3611] [ 2700] [depth= 1] . ( 7 sec) [ -10787.1751] [ 2648] [depth= 3] . ( 7 sec) [ -10784.0918] [ 2643] [depth= 1] . ( 7 sec) [ -10647.1851] [ 2602] [depth= 4] . ( 7 sec) [ -10629.7181] [ 2593] [depth= 5] . ( 7 sec) [ -10624.7730] [ 2588] [depth= 2] . ( 7 sec) [ -10619.4906] [ 2584] [depth= 1] . ( 7 sec) [ -10613.2531] [ 2571] [depth= 1] . ( 8 sec) [ -10572.1453] [ 2534] [depth= 1] . ( 8 sec) [ -10558.5340] [ 2515] [depth= 1] . ( 8 sec) [ -10527.0971] [ 2469] [depth= 4] . ( 8 sec) [ -10504.4924] [ 2447] [depth= 1] . ( 8 sec) [ -10486.4198] [ 2450] [depth= 1] . ( 8 sec) [ -10485.4082] [ 2448] [depth= 1] . ( 8 sec) [ -10485.3543] [ 2449] [depth= 1] . ( 8 sec) [ -10471.4194] [ 2422] [depth= 1] . ( 8 sec) [ -10454.0976] [ 2412] [depth= 1] . ( 8 sec) [ -10425.0936] [ 2394] [depth= 1] . ( 9 sec) [ -10420.8627] [ 2393] [depth= 1] . ( 9 sec) [ -10420.4789] [ 2392] [depth= 1] . ( 9 sec) [ -10419.2520] [ 2394] [depth= 1] . ( 9 sec) [ -10418.4535] [ 2392] [depth= 1] . ( 9 sec) [ -10418.3583] [ 2395] [depth= 1] . ( 10 sec) [ -10417.7039] [ 2395] [depth= 1] . ( 10 sec) [ -10372.8639] [Branch lengths ] . ( 10 sec) [ -10372.7924] [GTR parameters ] . ( 11 sec) [ -10369.2246] [Alpha ][ 1.008194] . ( 11 sec) [ -10369.0911] [ 2397] [depth= 1] . ( 11 sec) [ -10368.8918] [ 2394] [depth= 1] . ( 13 sec) [ -10368.6871] [ 2393] [depth= 1] . ( 13 sec) [ -10368.6066] [ 2397] [depth= 1] . ( 13 sec) [ -10368.0055] [ 2395] [depth= 1] . ( 14 sec) [ -10362.0235] [Branch lengths ] . ( 14 sec) [ -10361.9941] [GTR parameters ] . ( 14 sec) [ -10361.9783] [Alpha ][ 1.020640] . ( 18 sec) [ -10361.2582] [Branch lengths ] . ( 39 sec) [ -10361.1169] [Branch lengths ] . ( 39 sec) [ -10361.1169] [Topology ] . ( 40 sec) [ -10361.0961] [Topology ] . ( 41 sec) [ -10361.0872] [Topology ] . ( 42 sec) [ -10361.0822] [Topology ] . ( 43 sec) [ -10361.0794] [Topology ] . ( 43 sec) [ -10361.0777] [Topology ] . ( 44 sec) [ -10361.0768] [Topology ] . ( 44 sec) [ -10361.0746] [GTR parameters ] . ( 45 sec) [ -10361.0746] [Alpha ][ 1.020640] . ( 45 sec) [ -10361.0746] [Topology ] . ( 45 sec) [ -10361.0740] [Topology ] . ( 45 sec) [ -10361.0740] [GTR parameters ] . ( 46 sec) [ -10361.0740] [Alpha ][ 1.020640] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -10361.0732] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10361.073203. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10442.050381 . ( 1 sec) [ -10438.0065] [GTR parameters ] . ( 1 sec) [ -10437.9885] [Alpha ][ 1.014348] . ( 1 sec) [ -10437.9885] [Topology ] . ( 2 sec) [ -10372.8235] [Topology ] . ( 3 sec) [ -10365.3616] [Topology ] . ( 4 sec) [ -10363.0571] [Topology ] . ( 4 sec) [ -10362.0626] [Topology ] . ( 5 sec) [ -10361.5856] [Topology ] . ( 6 sec) [ -10361.3468] [Topology ] . ( 7 sec) [ -10361.2242] [Topology ] . ( 8 sec) [ -10361.1605] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10361.160492 . ( 15 sec) [ -10361.1203] [GTR parameters ] . ( 15 sec) [ -10361.1152] [Alpha ][ 1.021447] . ( 15 sec) [ -10361.1152] [Topology ] . ( 16 sec) [ -10361.0795] [Topology ] . ( 17 sec) [ -10361.0607] [Topology ] . ( 18 sec) [ -10361.0508] [Topology ] . ( 18 sec) [ -10361.0455] [Topology ] . ( 19 sec) [ -10361.0427] [Topology ] . ( 20 sec) [ -10361.0412] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10361.041191 . ( 27 sec) [ -10361.0410] [GTR parameters ] . ( 27 sec) [ -10361.0410] [Alpha ][ 1.021447] . ( 27 sec) [ -10361.0410] [Topology ] . ( 28 sec) [ -10361.0402] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -10438.0065] [GTR parameters ] . ( 43 sec) [ -10437.9885] [Alpha ][ 1.014348] . ( 43 sec) [ -10437.7956] [ 2397] [depth= 1] . ( 43 sec) [ -10436.3584] [ 2398] [depth= 1] . ( 43 sec) [ -10434.9893] [ 2397] [depth= 1] . ( 43 sec) [ -10434.7881] [ 2401] [depth= 1] . ( 44 sec) [ -10433.6224] [ 2400] [depth= 1] . ( 44 sec) [ -10432.3945] [ 2405] [depth= 1] . ( 44 sec) [ -10428.9415] [ 2400] [depth= 1] . ( 44 sec) [ -10427.0585] [ 2399] [depth= 1] . ( 44 sec) [ -10413.7179] [ 2405] [depth= 1] . ( 44 sec) [ -10410.1481] [ 2407] [depth= 1] . ( 45 sec) [ -10405.9416] [ 2399] [depth= 1] . ( 45 sec) [ -10404.2320] [ 2400] [depth= 1] . ( 45 sec) [ -10403.5151] [ 2399] [depth= 1] . ( 46 sec) [ -10367.2144] [Branch lengths ] . ( 46 sec) [ -10367.1608] [GTR parameters ] . ( 46 sec) [ -10367.1597] [Alpha ][ 1.017659] . ( 46 sec) [ -10366.2503] [ 2396] [depth= 1] . ( 47 sec) [ -10366.0461] [ 2393] [depth= 1] . ( 47 sec) [ -10365.0204] [ 2395] [depth= 1] . ( 49 sec) [ -10361.6255] [Branch lengths ] . ( 50 sec) [ -10361.6165] [GTR parameters ] . ( 50 sec) [ -10361.6157] [Alpha ][ 1.020418] . ( 53 sec) [ -10361.1462] [Branch lengths ] . ( 74 sec) [ -10361.0869] [Branch lengths ] . ( 74 sec) [ -10361.0869] [Topology ] . ( 75 sec) [ -10361.0811] [Topology ] . ( 76 sec) [ -10361.0790] [Topology ] . ( 76 sec) [ -10361.0779] [Topology ] . ( 77 sec) [ -10361.0774] [Topology ] . ( 77 sec) [ -10361.0763] [GTR parameters ] . ( 77 sec) [ -10361.0763] [Alpha ][ 1.020418] . ( 78 sec) [ -10361.0763] [Topology ] . ( 78 sec) [ -10361.0759] [Topology ] . ( 78 sec) [ -10361.0759] [GTR parameters ] . ( 79 sec) [ -10361.0759] [Alpha ][ 1.020418] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -10361.0736] [Topology ] . Checking for NNIs, optimizing five branches... . ( 92 sec) [ -10361.0731] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10361.040201 . Log likelihood obtained after SPR moves : -10361.073061 . Log likelihood of the current tree: -10361.040201. . Printing the most likely tree in file 'data21.phy_phyml_tree.txt'... . Best log likelihood : -10361.040201 . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo