.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2738_53x1538_2006.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... . 762 patterns found. (out of a total of 1538 sites) . 828 sites without polymorphism (53.84%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26600.5262] [GTR parameters ] . ( 2 sec) [ -25963.2683] [Alpha ][ 0.500960] . ( 2 sec) [ -25707.7437] [ 4409] [depth= 7] . ( 2 sec) [ -25647.6853] [ 4403] [depth= 6] . ( 2 sec) [ -25553.5222] [ 4377] [depth= 7] . ( 2 sec) [ -25433.1920] [ 4345] [depth= 1] . ( 2 sec) [ -24914.2012] [ 4333] [depth= 4] . ( 2 sec) [ -24796.1523] [ 4329] [depth= 4] . ( 3 sec) [ -24398.9484] [ 4323] [depth= 3] . ( 3 sec) [ -23858.4329] [ 4272] [depth= 4] . ( 3 sec) [ -23674.1519] [ 4257] [depth= 5] . ( 3 sec) [ -23593.4447] [ 4255] [depth= 4] . ( 3 sec) [ -23303.8123] [ 4216] [depth= 5] . ( 3 sec) [ -23272.6998] [ 4201] [depth= 3] . ( 3 sec) [ -23236.9128] [ 4195] [depth= 4] . ( 3 sec) [ -23084.8203] [ 4166] [depth= 4] . ( 3 sec) [ -23010.5513] [ 4157] [depth= 6] . ( 4 sec) [ -22500.3440] [ 4117] [depth= 4] . ( 4 sec) [ -22441.3280] [ 4089] [depth= 9] . ( 4 sec) [ -22387.4042] [ 4083] [depth= 3] . ( 4 sec) [ -22341.9637] [ 4075] [depth= 1] . ( 4 sec) [ -22278.7772] [ 4064] [depth= 9] . ( 4 sec) [ -22162.8614] [ 4062] [depth= 4] . ( 4 sec) [ -22066.0519] [ 4030] [depth= 6] . ( 4 sec) [ -21943.2938] [ 3992] [depth= 10] . ( 4 sec) [ -21930.4425] [ 3995] [depth= 1] . ( 5 sec) [ -21608.3468] [ 4002] [depth= 13] . ( 5 sec) [ -21485.6032] [ 3962] [depth= 14] . ( 5 sec) [ -21445.6448] [ 3933] [depth= 11] . ( 5 sec) [ -21022.7431] [ 3902] [depth= 17] . ( 5 sec) [ -20909.6980] [ 3889] [depth= 10] . ( 5 sec) [ -20871.9576] [ 3882] [depth= 12] . ( 5 sec) [ -20616.7791] [ 3882] [depth= 1] . ( 6 sec) [ -20572.1319] [ 3879] [depth= 15] . ( 6 sec) [ -20537.4717] [ 3886] [depth= 16] . ( 6 sec) [ -20518.9125] [ 3886] [depth= 2] . ( 6 sec) [ -20305.7350] [ 3824] [depth= 12] . ( 6 sec) [ -20265.3928] [ 3808] [depth= 2] . ( 6 sec) [ -19687.5040] [ 3812] [depth= 7] . ( 6 sec) [ -19440.4318] [ 3762] [depth= 15] . ( 6 sec) [ -19421.3583] [ 3760] [depth= 1] . ( 7 sec) [ -19375.8563] [ 3743] [depth= 1] . ( 7 sec) [ -19356.7084] [ 3739] [depth= 1] . ( 7 sec) [ -19351.8506] [ 3741] [depth= 1] . ( 7 sec) [ -19314.2737] [ 3730] [depth= 2] . ( 7 sec) [ -19180.5929] [ 3720] [depth= 7] . ( 7 sec) [ -18857.7616] [ 3687] [depth= 10] . ( 7 sec) [ -18327.8998] [ 3540] [depth= 7] . ( 8 sec) [ -18326.3597] [ 3554] [depth= 1] . ( 8 sec) [ -18321.8926] [ 3554] [depth= 1] . ( 8 sec) [ -18218.5586] [ 3513] [depth= 12] . ( 8 sec) [ -18103.0569] [ 3504] [depth= 2] . ( 8 sec) [ -18092.7317] [ 3502] [depth= 2] . ( 9 sec) [ -17956.5749] [ 3442] [depth= 3] . ( 9 sec) [ -17887.1761] [ 3441] [depth= 10] . ( 9 sec) [ -17882.3638] [ 3440] [depth= 1] . ( 9 sec) [ -17872.3146] [ 3436] [depth= 2] . ( 9 sec) [ -17854.1316] [ 3437] [depth= 7] . ( 9 sec) [ -17738.0446] [ 3398] [depth= 11] . ( 9 sec) [ -17701.1562] [ 3399] [depth= 2] . ( 9 sec) [ -17636.8803] [ 3372] [depth= 2] . ( 9 sec) [ -17623.9225] [ 3363] [depth= 1] . ( 10 sec) [ -17390.6988] [ 3303] [depth= 8] . ( 10 sec) [ -17307.3471] [ 3232] [depth= 4] . ( 10 sec) [ -16947.6134] [ 3214] [depth= 1] . ( 10 sec) [ -16440.0813] [ 3146] [depth= 8] . ( 10 sec) [ -16326.8084] [ 3140] [depth= 4] . ( 10 sec) [ -16147.9700] [ 3098] [depth= 7] . ( 10 sec) [ -16091.6766] [ 3064] [depth= 9] . ( 10 sec) [ -16088.9336] [ 3063] [depth= 1] . ( 11 sec) [ -16069.2050] [ 3055] [depth= 1] . ( 11 sec) [ -15937.2841] [ 3033] [depth= 1] . ( 11 sec) [ -15917.1026] [ 3042] [depth= 7] . ( 11 sec) [ -15900.7635] [ 3035] [depth= 1] . ( 11 sec) [ -15869.2285] [ 3029] [depth= 5] . ( 11 sec) [ -15811.4134] [ 3028] [depth= 3] . ( 11 sec) [ -15780.3137] [ 3004] [depth= 12] . ( 11 sec) [ -15731.0015] [ 2967] [depth= 2] . ( 11 sec) [ -15597.2932] [ 2905] [depth= 9] . ( 12 sec) [ -15592.9603] [ 2906] [depth= 1] . ( 12 sec) [ -15493.8878] [ 2876] [depth= 3] . ( 12 sec) [ -15432.3410] [ 2862] [depth= 1] . ( 12 sec) [ -15430.4026] [ 2862] [depth= 1] . ( 12 sec) [ -15429.4895] [ 2862] [depth= 1] . ( 12 sec) [ -15360.4258] [ 2836] [depth= 6] . ( 12 sec) [ -15339.8117] [ 2830] [depth= 2] . ( 12 sec) [ -15308.2079] [ 2825] [depth= 3] . ( 13 sec) [ -15300.4997] [ 2826] [depth= 3] . ( 13 sec) [ -15243.4030] [ 2822] [depth= 2] . ( 13 sec) [ -15241.1546] [ 2825] [depth= 2] . ( 13 sec) [ -15163.9875] [ 2810] [depth= 7] . ( 13 sec) [ -15155.2839] [ 2807] [depth= 2] . ( 13 sec) [ -15118.8711] [ 2801] [depth= 1] . ( 13 sec) [ -14962.7978] [ 2753] [depth= 6] . ( 14 sec) [ -14949.6417] [ 2750] [depth= 1] . ( 14 sec) [ -14949.4984] [ 2750] [depth= 1] . ( 14 sec) [ -14947.5706] [ 2751] [depth= 6] . ( 14 sec) [ -14932.8980] [ 2744] [depth= 3] . ( 14 sec) [ -14786.7725] [ 2719] [depth= 2] . ( 15 sec) [ -14633.4370] [ 2686] [depth= 1] . ( 15 sec) [ -14632.0705] [ 2684] [depth= 1] . ( 15 sec) [ -14631.2377] [ 2682] [depth= 1] . ( 15 sec) [ -14627.2715] [ 2683] [depth= 2] . ( 15 sec) [ -14596.5278] [ 2675] [depth= 3] . ( 15 sec) [ -14582.3147] [ 2671] [depth= 1] . ( 15 sec) [ -14578.2821] [ 2676] [depth= 2] . ( 16 sec) [ -14574.8565] [ 2676] [depth= 1] . ( 16 sec) [ -14537.6557] [ 2662] [depth= 1] . ( 17 sec) [ -14368.2696] [Branch lengths ] . ( 21 sec) [ -14067.2293] [GTR parameters ] . ( 22 sec) [ -14006.9210] [Alpha ][ 0.303166] . ( 22 sec) [ -14002.1917] [ 2658] [depth= 2] . ( 22 sec) [ -14001.4469] [ 2658] [depth= 1] . ( 22 sec) [ -14000.8829] [ 2654] [depth= 1] . ( 22 sec) [ -13999.0023] [ 2656] [depth= 1] . ( 22 sec) [ -13998.8687] [ 2653] [depth= 2] . ( 23 sec) [ -13995.0423] [ 2651] [depth= 1] . ( 24 sec) [ -13994.7839] [ 2650] [depth= 1] . ( 25 sec) [ -13994.1427] [ 2652] [depth= 1] . ( 25 sec) [ -13992.4151] [ 2653] [depth= 1] . ( 25 sec) [ -13987.9461] [ 2653] [depth= 1] . ( 26 sec) [ -13985.1881] [ 2651] [depth= 1] . ( 26 sec) [ -13982.8201] [ 2649] [depth= 1] . ( 26 sec) [ -13981.9330] [ 2648] [depth= 1] . ( 27 sec) [ -13934.4256] [ 2599] [depth= 5] . ( 28 sec) [ -13934.4124] [ 2599] [depth= 1] . ( 28 sec) [ -13933.3666] [ 2601] [depth= 1] . ( 29 sec) [ -13933.3481] [ 2603] [depth= 1] . ( 32 sec) [ -13913.4944] [Branch lengths ] . ( 38 sec) [ -13911.5802] [GTR parameters ] . ( 38 sec) [ -13911.5235] [Alpha ][ 0.298829] . ( 51 sec) [ -13910.5898] [Branch lengths ] . ( 87 sec) [ -13909.6634] [ 2611] [depth= 4] . ( 88 sec) [ -13909.3835] [ 2611] [depth= 2] . ( 113 sec) [ -13908.6727] [Branch lengths ] . ( 115 sec) [ -13908.6414] [GTR parameters ] . ( 115 sec) [ -13908.6408] [Alpha ][ 0.298318] . ( 175 sec) [ -13908.5863] [Branch lengths ] . ( 176 sec) [ -13908.5863] [Topology ] . ( 177 sec) [ -13908.5808] [Topology ] . ( 179 sec) [ -13908.5789] [Topology ] . ( 181 sec) [ -13908.5780] [Topology ] . ( 182 sec) [ -13908.5759] [GTR parameters ] . ( 182 sec) [ -13908.5756] [Alpha ][ 0.298616] . ( 183 sec) [ -13908.5756] [Topology ] . ( 184 sec) [ -13908.5747] [Topology ] . ( 185 sec) [ -13908.5747] [GTR parameters ] . ( 185 sec) [ -13908.5747] [Alpha ][ 0.298616] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13908.574667. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -28282.1620] [GTR parameters ] . ( 1 sec) [ -27620.6865] [Alpha ][ 0.500960] . ( 1 sec) [ -27399.3873] [ 4457] [depth= 14] . ( 1 sec) [ -27267.0739] [ 4437] [depth= 9] . ( 1 sec) [ -26902.2775] [ 4426] [depth= 10] . ( 1 sec) [ -26840.5191] [ 4408] [depth= 1] . ( 1 sec) [ -26683.3909] [ 4385] [depth= 7] . ( 2 sec) [ -26592.0811] [ 4376] [depth= 7] . ( 2 sec) [ -26491.2515] [ 4347] [depth= 1] . ( 2 sec) [ -26272.7178] [ 4303] [depth= 7] . ( 2 sec) [ -26238.3736] [ 4297] [depth= 3] . ( 2 sec) [ -26179.2172] [ 4287] [depth= 9] . ( 2 sec) [ -26005.8580] [ 4240] [depth= 4] . ( 2 sec) [ -25843.9508] [ 4228] [depth= 7] . ( 2 sec) [ -25817.2607] [ 4217] [depth= 1] . ( 2 sec) [ -25659.9400] [ 4215] [depth= 2] . ( 2 sec) [ -25579.5601] [ 4193] [depth= 1] . ( 2 sec) [ -25518.8350] [ 4190] [depth= 3] . ( 3 sec) [ -25394.6483] [ 4177] [depth= 2] . ( 3 sec) [ -24985.0863] [ 4171] [depth= 4] . ( 3 sec) [ -24487.3997] [ 4142] [depth= 13] . ( 3 sec) [ -23522.3417] [ 4108] [depth= 4] . ( 3 sec) [ -23522.1492] [ 4107] [depth= 2] . ( 3 sec) [ -23303.4651] [ 4052] [depth= 9] . ( 3 sec) [ -23273.3937] [ 4044] [depth= 1] . ( 3 sec) [ -23178.3905] [ 4034] [depth= 4] . ( 3 sec) [ -23108.0758] [ 4011] [depth= 3] . ( 3 sec) [ -22963.1408] [ 4003] [depth= 1] . ( 4 sec) [ -22937.5931] [ 4007] [depth= 3] . ( 4 sec) [ -22805.7049] [ 3977] [depth= 9] . ( 4 sec) [ -22064.9122] [ 3779] [depth= 11] . ( 4 sec) [ -22005.9842] [ 3756] [depth= 1] . ( 4 sec) [ -21479.7420] [ 3730] [depth= 10] . ( 4 sec) [ -21351.7287] [ 3697] [depth= 13] . ( 4 sec) [ -21253.3194] [ 3684] [depth= 13] . ( 4 sec) [ -21054.3088] [ 3683] [depth= 4] . ( 5 sec) [ -20955.8881] [ 3680] [depth= 11] . ( 5 sec) [ -20840.1461] [ 3655] [depth= 7] . ( 5 sec) [ -20796.6151] [ 3638] [depth= 5] . ( 5 sec) [ -20704.9758] [ 3636] [depth= 1] . ( 5 sec) [ -20704.2462] [ 3634] [depth= 1] . ( 5 sec) [ -20688.5320] [ 3634] [depth= 2] . ( 5 sec) [ -20562.6344] [ 3601] [depth= 5] . ( 5 sec) [ -20533.3008] [ 3597] [depth= 1] . ( 5 sec) [ -20388.8170] [ 3560] [depth= 8] . ( 5 sec) [ -20051.7026] [ 3572] [depth= 1] . ( 6 sec) [ -19871.3788] [ 3647] [depth= 8] . ( 6 sec) [ -19859.7816] [ 3617] [depth= 7] . ( 6 sec) [ -19363.6226] [ 3451] [depth= 9] . ( 6 sec) [ -19232.1726] [ 3428] [depth= 7] . ( 6 sec) [ -19140.2524] [ 3381] [depth= 11] . ( 6 sec) [ -19085.4985] [ 3381] [depth= 1] . ( 6 sec) [ -19018.6918] [ 3365] [depth= 6] . ( 6 sec) [ -18940.2683] [ 3354] [depth= 2] . ( 6 sec) [ -18937.3864] [ 3335] [depth= 7] . ( 6 sec) [ -18661.3779] [ 3329] [depth= 3] . ( 7 sec) [ -18645.6247] [ 3329] [depth= 1] . ( 7 sec) [ -18629.6664] [ 3327] [depth= 1] . ( 7 sec) [ -18325.7208] [ 3275] [depth= 13] . ( 7 sec) [ -18238.3668] [ 3247] [depth= 1] . ( 7 sec) [ -18213.0421] [ 3229] [depth= 5] . ( 7 sec) [ -18178.2299] [ 3222] [depth= 2] . ( 7 sec) [ -17832.1671] [ 3222] [depth= 1] . ( 7 sec) [ -17823.8469] [ 3222] [depth= 1] . ( 7 sec) [ -17759.1030] [ 3197] [depth= 2] . ( 8 sec) [ -17665.6982] [ 3183] [depth= 7] . ( 8 sec) [ -17643.3785] [ 3186] [depth= 2] . ( 8 sec) [ -17575.8969] [ 3184] [depth= 1] . ( 8 sec) [ -17412.9823] [ 3172] [depth= 2] . ( 8 sec) [ -17411.2701] [ 3172] [depth= 5] . ( 8 sec) [ -17334.4639] [ 3140] [depth= 4] . ( 8 sec) [ -17330.2679] [ 3140] [depth= 3] . ( 8 sec) [ -16671.0243] [ 3140] [depth= 3] . ( 8 sec) [ -16503.9784] [ 3082] [depth= 3] . ( 9 sec) [ -16472.0373] [ 3073] [depth= 1] . ( 9 sec) [ -16434.8756] [ 3069] [depth= 2] . ( 9 sec) [ -16380.0187] [ 3059] [depth= 3] . ( 9 sec) [ -16305.1473] [ 3055] [depth= 1] . ( 9 sec) [ -16257.7627] [ 3048] [depth= 10] . ( 9 sec) [ -16228.2647] [ 3035] [depth= 2] . ( 9 sec) [ -16201.2428] [ 3024] [depth= 2] . ( 9 sec) [ -16193.3497] [ 3027] [depth= 2] . ( 9 sec) [ -16191.3372] [ 3030] [depth= 1] . ( 9 sec) [ -16087.2359] [ 2998] [depth= 1] . ( 10 sec) [ -16069.8737] [ 2976] [depth= 6] . ( 10 sec) [ -15770.8103] [ 3005] [depth= 1] . ( 10 sec) [ -15766.2152] [ 2976] [depth= 1] . ( 10 sec) [ -15711.9482] [ 2918] [depth= 1] . ( 10 sec) [ -15684.2032] [ 2909] [depth= 2] . ( 10 sec) [ -15405.5564] [ 2914] [depth= 2] . ( 10 sec) [ -15386.2095] [ 2915] [depth= 1] . ( 10 sec) [ -15365.9274] [ 2913] [depth= 1] . ( 10 sec) [ -15347.8249] [ 2908] [depth= 1] . ( 11 sec) [ -15341.0281] [ 2909] [depth= 1] . ( 11 sec) [ -15335.2160] [ 2911] [depth= 1] . ( 11 sec) [ -15299.5817] [ 2905] [depth= 3] . ( 11 sec) [ -15215.8424] [ 2882] [depth= 2] . ( 11 sec) [ -15210.4330] [ 2882] [depth= 1] . ( 11 sec) [ -15198.9669] [ 2877] [depth= 3] . ( 12 sec) [ -15175.5697] [ 2869] [depth= 5] . ( 12 sec) [ -15170.9285] [ 2870] [depth= 1] . ( 12 sec) [ -15168.3869] [ 2870] [depth= 1] . ( 12 sec) [ -15130.7744] [ 2861] [depth= 3] . ( 12 sec) [ -15124.1421] [ 2862] [depth= 1] . ( 12 sec) [ -15114.1114] [ 2858] [depth= 4] . ( 13 sec) [ -15114.0246] [ 2857] [depth= 1] . ( 13 sec) [ -15101.3456] [ 2817] [depth= 1] . ( 13 sec) [ -15089.7078] [ 2799] [depth= 4] . ( 13 sec) [ -15058.0339] [ 2775] [depth= 11] . ( 13 sec) [ -15035.7709] [ 2773] [depth= 12] . ( 13 sec) [ -15034.1466] [ 2772] [depth= 1] . ( 14 sec) [ -15033.2020] [ 2773] [depth= 1] . ( 14 sec) [ -14869.6881] [Branch lengths ] . ( 17 sec) [ -14369.7667] [GTR parameters ] . ( 18 sec) [ -14294.6956] [Alpha ][ 0.291526] . ( 18 sec) [ -14288.3519] [ 2770] [depth= 1] . ( 18 sec) [ -14284.1348] [ 2771] [depth= 1] . ( 19 sec) [ -14279.1853] [ 2768] [depth= 1] . ( 19 sec) [ -14275.8876] [ 2763] [depth= 1] . ( 19 sec) [ -14275.0584] [ 2762] [depth= 1] . ( 19 sec) [ -14260.5751] [ 2768] [depth= 12] . ( 19 sec) [ -14250.8641] [ 2764] [depth= 2] . ( 20 sec) [ -14250.3127] [ 2765] [depth= 1] . ( 20 sec) [ -14249.3010] [ 2763] [depth= 1] . ( 20 sec) [ -14199.1937] [ 2721] [depth= 11] . ( 21 sec) [ -14198.2152] [ 2722] [depth= 1] . ( 22 sec) [ -14037.1694] [ 2616] [depth= 11] . ( 23 sec) [ -14030.4106] [ 2616] [depth= 1] . ( 24 sec) [ -14029.5441] [ 2622] [depth= 2] . ( 24 sec) [ -14026.8665] [ 2623] [depth= 1] . ( 25 sec) [ -14001.6230] [ 2617] [depth= 2] . ( 25 sec) [ -14001.2730] [ 2617] [depth= 1] . ( 25 sec) [ -13994.3937] [ 2614] [depth= 1] . ( 26 sec) [ -13993.2010] [ 2614] [depth= 1] . ( 26 sec) [ -13992.7114] [ 2616] [depth= 1] . ( 26 sec) [ -13985.8435] [ 2622] [depth= 1] . ( 27 sec) [ -13984.1789] [ 2619] [depth= 1] . ( 27 sec) [ -13983.8824] [ 2618] [depth= 1] . ( 27 sec) [ -13978.6446] [ 2617] [depth= 1] . ( 27 sec) [ -13977.6232] [ 2622] [depth= 1] . ( 28 sec) [ -13976.9827] [ 2623] [depth= 1] . ( 29 sec) [ -13976.7803] [ 2621] [depth= 1] . ( 29 sec) [ -13966.7619] [ 2616] [depth= 1] . ( 30 sec) [ -13964.7485] [ 2617] [depth= 1] . ( 32 sec) [ -13944.9654] [Branch lengths ] . ( 34 sec) [ -13939.1266] [GTR parameters ] . ( 34 sec) [ -13939.0716] [Alpha ][ 0.295855] . ( 36 sec) [ -13938.6978] [ 2616] [depth= 1] . ( 49 sec) [ -13932.8026] [Branch lengths ] . ( 50 sec) [ -13932.7669] [GTR parameters ] . ( 50 sec) [ -13932.7667] [Alpha ][ 0.295539] . ( 64 sec) [ -13915.6552] [Branch lengths ] . ( 124 sec) [ -13908.1434] [Branch lengths ] . ( 124 sec) [ -13908.1434] [Topology ] . ( 126 sec) [ -13907.8616] [Topology ] . ( 128 sec) [ -13907.8225] [Topology ] . ( 130 sec) [ -13907.8144] [Topology ] . ( 131 sec) [ -13907.8124] [Topology ] . ( 133 sec) [ -13907.8118] [Topology ] . ( 134 sec) [ -13907.8010] [GTR parameters ] . ( 134 sec) [ -13907.7786] [Alpha ][ 0.298307] . ( 134 sec) [ -13907.7786] [Topology ] . ( 136 sec) [ -13907.7770] [Topology ] . ( 138 sec) [ -13907.7767] [Topology ] . ( 138 sec) [ -13907.7765] [GTR parameters ] . ( 138 sec) [ -13907.7765] [Alpha ][ 0.298307] . ( 138 sec) [ -13907.7765] [Topology ] . ( 140 sec) [ -13907.7763] [Topology ] . ( 140 sec) [ -13907.7763] [GTR parameters ] . ( 140 sec) [ -13907.7763] [Alpha ][ 0.298307] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13907.776323. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -25131.8600] [GTR parameters ] . ( 4 sec) [ -24528.9390] [Alpha ][ 0.500960] . ( 4 sec) [ -24199.1240] [ 4448] [depth= 13] . ( 4 sec) [ -23668.7003] [ 4441] [depth= 13] . ( 5 sec) [ -23597.5888] [ 4429] [depth= 10] . ( 5 sec) [ -23375.0826] [ 4384] [depth= 1] . ( 5 sec) [ -23272.0274] [ 4370] [depth= 11] . ( 5 sec) [ -23061.4295] [ 4362] [depth= 4] . ( 6 sec) [ -22987.8734] [ 4354] [depth= 6] . ( 6 sec) [ -22839.8786] [ 4336] [depth= 6] . ( 6 sec) [ -22732.9959] [ 4329] [depth= 4] . ( 6 sec) [ -22610.9707] [ 4314] [depth= 5] . ( 6 sec) [ -22511.8606] [ 4280] [depth= 7] . ( 6 sec) [ -22492.9437] [ 4280] [depth= 1] . ( 6 sec) [ -21866.3491] [ 4230] [depth= 9] . ( 6 sec) [ -21830.9509] [ 4227] [depth= 1] . ( 6 sec) [ -21733.3373] [ 4193] [depth= 4] . ( 6 sec) [ -21688.0899] [ 4195] [depth= 2] . ( 7 sec) [ -21567.8402] [ 4146] [depth= 5] . ( 7 sec) [ -21524.9239] [ 4185] [depth= 20] . ( 7 sec) [ -21340.2634] [ 4147] [depth= 18] . ( 7 sec) [ -21191.0716] [ 4134] [depth= 14] . ( 7 sec) [ -21166.0839] [ 4124] [depth= 3] . ( 7 sec) [ -21132.5604] [ 4116] [depth= 6] . ( 7 sec) [ -21009.2564] [ 4074] [depth= 7] . ( 7 sec) [ -20984.3101] [ 4075] [depth= 1] . ( 8 sec) [ -20959.7040] [ 4067] [depth= 1] . ( 8 sec) [ -20609.0237] [ 4038] [depth= 9] . ( 8 sec) [ -20524.4174] [ 4010] [depth= 5] . ( 8 sec) [ -20501.0731] [ 3999] [depth= 14] . ( 8 sec) [ -20481.4018] [ 3995] [depth= 18] . ( 8 sec) [ -20361.0384] [ 3971] [depth= 13] . ( 8 sec) [ -20197.8696] [ 3909] [depth= 16] . ( 8 sec) [ -19474.4135] [ 3877] [depth= 8] . ( 8 sec) [ -19083.7268] [ 3825] [depth= 10] . ( 9 sec) [ -18642.5444] [ 3709] [depth= 4] . ( 9 sec) [ -18484.4311] [ 3647] [depth= 14] . ( 9 sec) [ -18266.4061] [ 3545] [depth= 12] . ( 9 sec) [ -17909.8836] [ 3514] [depth= 2] . ( 9 sec) [ -17848.5551] [ 3517] [depth= 1] . ( 9 sec) [ -17742.0719] [ 3488] [depth= 10] . ( 9 sec) [ -17580.6633] [ 3439] [depth= 13] . ( 9 sec) [ -17489.3166] [ 3419] [depth= 2] . ( 10 sec) [ -17481.6783] [ 3413] [depth= 11] . ( 10 sec) [ -17287.2941] [ 3407] [depth= 1] . ( 10 sec) [ -17193.7175] [ 3380] [depth= 12] . ( 10 sec) [ -17131.9263] [ 3362] [depth= 4] . ( 10 sec) [ -17003.2484] [ 3323] [depth= 4] . ( 10 sec) [ -16872.0617] [ 3308] [depth= 10] . ( 11 sec) [ -16855.8840] [ 3320] [depth= 1] . ( 11 sec) [ -16698.6066] [ 3237] [depth= 6] . ( 11 sec) [ -16651.8537] [ 3229] [depth= 1] . ( 11 sec) [ -16554.7632] [ 3222] [depth= 2] . ( 11 sec) [ -16518.1409] [ 3227] [depth= 1] . ( 11 sec) [ -16314.6373] [ 3178] [depth= 13] . ( 11 sec) [ -16207.2334] [ 3134] [depth= 14] . ( 12 sec) [ -16005.8464] [ 3083] [depth= 3] . ( 12 sec) [ -15999.9785] [ 3082] [depth= 1] . ( 12 sec) [ -15980.1301] [ 3070] [depth= 7] . ( 12 sec) [ -15968.0321] [ 3068] [depth= 1] . ( 12 sec) [ -15940.0487] [ 3060] [depth= 2] . ( 12 sec) [ -15896.8445] [ 3050] [depth= 2] . ( 12 sec) [ -15842.9146] [ 3030] [depth= 6] . ( 12 sec) [ -15810.7531] [ 3030] [depth= 2] . ( 13 sec) [ -15614.5536] [ 2972] [depth= 2] . ( 13 sec) [ -15586.8991] [ 2948] [depth= 12] . ( 13 sec) [ -15552.4344] [ 2947] [depth= 1] . ( 13 sec) [ -15504.3667] [ 2939] [depth= 6] . ( 13 sec) [ -15411.0209] [ 2904] [depth= 3] . ( 13 sec) [ -15368.5025] [ 2892] [depth= 1] . ( 13 sec) [ -15358.6892] [ 2889] [depth= 1] . ( 13 sec) [ -15300.0545] [ 2867] [depth= 3] . ( 14 sec) [ -15288.9907] [ 2860] [depth= 1] . ( 14 sec) [ -15279.5325] [ 2858] [depth= 1] . ( 14 sec) [ -15247.2355] [ 2847] [depth= 11] . ( 14 sec) [ -15229.6247] [ 2841] [depth= 2] . ( 14 sec) [ -15224.1064] [ 2845] [depth= 1] . ( 15 sec) [ -15217.7150] [ 2843] [depth= 1] . ( 15 sec) [ -15066.9286] [ 2793] [depth= 6] . ( 15 sec) [ -15021.1459] [ 2794] [depth= 1] . ( 15 sec) [ -15018.5071] [ 2799] [depth= 1] . ( 15 sec) [ -15012.9509] [ 2794] [depth= 1] . ( 16 sec) [ -15007.7168] [ 2795] [depth= 1] . ( 16 sec) [ -15000.8649] [ 2791] [depth= 1] . ( 16 sec) [ -14994.6521] [ 2795] [depth= 3] . ( 16 sec) [ -14993.4621] [ 2792] [depth= 1] . ( 16 sec) [ -14991.0755] [ 2796] [depth= 2] . ( 16 sec) [ -14986.8644] [ 2797] [depth= 2] . ( 16 sec) [ -14964.4524] [ 2779] [depth= 1] . ( 17 sec) [ -14932.9074] [ 2779] [depth= 1] . ( 17 sec) [ -14879.2965] [ 2781] [depth= 1] . ( 17 sec) [ -14811.3130] [ 2765] [depth= 11] . ( 17 sec) [ -14769.3188] [ 2761] [depth= 1] . ( 17 sec) [ -14738.2743] [ 2754] [depth= 1] . ( 17 sec) [ -14670.5409] [ 2737] [depth= 1] . ( 17 sec) [ -14629.3078] [ 2725] [depth= 4] . ( 17 sec) [ -14617.4441] [ 2728] [depth= 1] . ( 18 sec) [ -14615.0348] [ 2727] [depth= 3] . ( 18 sec) [ -14601.2622] [ 2727] [depth= 1] . ( 18 sec) [ -14594.8151] [ 2727] [depth= 2] . ( 18 sec) [ -14467.1460] [ 2683] [depth= 4] . ( 18 sec) [ -14466.4058] [ 2683] [depth= 1] . ( 18 sec) [ -14457.5121] [ 2682] [depth= 3] . ( 19 sec) [ -14267.2522] [Branch lengths ] . ( 22 sec) [ -14201.6740] [GTR parameters ] . ( 22 sec) [ -14140.2331] [Alpha ][ 0.302829] . ( 23 sec) [ -14139.4770] [ 2685] [depth= 1] . ( 23 sec) [ -14138.1146] [ 2687] [depth= 1] . ( 23 sec) [ -14129.3520] [ 2682] [depth= 1] . ( 24 sec) [ -14116.9937] [ 2678] [depth= 2] . ( 24 sec) [ -14116.8594] [ 2672] [depth= 2] . ( 24 sec) [ -14115.9884] [ 2668] [depth= 2] . ( 24 sec) [ -14074.9045] [ 2655] [depth= 2] . ( 24 sec) [ -14064.1447] [ 2652] [depth= 1] . ( 25 sec) [ -14062.2545] [ 2653] [depth= 1] . ( 25 sec) [ -14046.0788] [ 2648] [depth= 1] . ( 25 sec) [ -14036.6119] [ 2639] [depth= 1] . ( 25 sec) [ -14032.0083] [ 2640] [depth= 1] . ( 26 sec) [ -14031.1369] [ 2642] [depth= 1] . ( 27 sec) [ -14030.9816] [ 2645] [depth= 1] . ( 27 sec) [ -14030.9304] [ 2645] [depth= 1] . ( 27 sec) [ -13968.5839] [ 2620] [depth= 1] . ( 28 sec) [ -13967.5858] [ 2619] [depth= 1] . ( 28 sec) [ -13966.2037] [ 2623] [depth= 1] . ( 28 sec) [ -13965.7195] [ 2627] [depth= 1] . ( 28 sec) [ -13965.7066] [ 2630] [depth= 1] . ( 28 sec) [ -13961.7479] [ 2632] [depth= 2] . ( 28 sec) [ -13960.1787] [ 2631] [depth= 1] . ( 29 sec) [ -13958.6959] [ 2630] [depth= 1] . ( 29 sec) [ -13957.4693] [ 2627] [depth= 1] . ( 30 sec) [ -13956.9859] [ 2625] [depth= 1] . ( 30 sec) [ -13953.4629] [ 2623] [depth= 2] . ( 30 sec) [ -13953.2244] [ 2622] [depth= 1] . ( 31 sec) [ -13952.9315] [ 2622] [depth= 1] . ( 32 sec) [ -13952.4892] [ 2622] [depth= 1] . ( 33 sec) [ -13952.1788] [ 2622] [depth= 1] . ( 34 sec) [ -13950.4565] [ 2621] [depth= 1] . ( 35 sec) [ -13927.6897] [Branch lengths ] . ( 38 sec) [ -13925.2526] [GTR parameters ] . ( 39 sec) [ -13925.2119] [Alpha ][ 0.299227] . ( 44 sec) [ -13924.6184] [ 2614] [depth= 1] . ( 45 sec) [ -13922.8225] [ 2613] [depth= 1] . ( 52 sec) [ -13911.1814] [Branch lengths ] . ( 55 sec) [ -13911.1660] [GTR parameters ] . ( 55 sec) [ -13911.1652] [Alpha ][ 0.298650] . ( 68 sec) [ -13909.9853] [Branch lengths ] . ( 86 sec) [ -13908.9106] [ 2613] [depth= 1] . ( 128 sec) [ -13908.6641] [Branch lengths ] . ( 129 sec) [ -13908.6586] [GTR parameters ] . ( 129 sec) [ -13908.6586] [Alpha ][ 0.298351] . ( 194 sec) [ -13908.6550] [Branch lengths ] . ( 194 sec) [ -13908.6550] [Topology ] . ( 196 sec) [ -13908.5517] [Topology ] . ( 198 sec) [ -13908.5359] [Topology ] . ( 200 sec) [ -13908.5346] [Topology ] . ( 201 sec) [ -13908.5345] [Topology ] . ( 202 sec) [ -13908.5345] [GTR parameters ] . ( 202 sec) [ -13908.5345] [Alpha ][ 0.298351] . ( 202 sec) [ -13908.5345] [Topology ] . ( 204 sec) [ -13908.5345] [Topology ] . ( 204 sec) [ -13908.5345] [GTR parameters ] . ( 204 sec) [ -13908.5345] [Alpha ][ 0.298351] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13908.534451. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -24937.0591] [GTR parameters ] . ( 2 sec) [ -24348.6626] [Alpha ][ 0.500960] . ( 2 sec) [ -24115.3107] [ 4360] [depth= 11] . ( 3 sec) [ -23876.9537] [ 4334] [depth= 8] . ( 3 sec) [ -23352.6613] [ 4314] [depth= 7] . ( 3 sec) [ -23304.6758] [ 4295] [depth= 1] . ( 3 sec) [ -23166.0314] [ 4279] [depth= 9] . ( 3 sec) [ -23124.7202] [ 4269] [depth= 4] . ( 3 sec) [ -23072.2671] [ 4229] [depth= 1] . ( 3 sec) [ -22973.0136] [ 4218] [depth= 9] . ( 3 sec) [ -22955.6918] [ 4211] [depth= 5] . ( 3 sec) [ -22765.2927] [ 4167] [depth= 10] . ( 3 sec) [ -22723.6291] [ 4167] [depth= 9] . ( 4 sec) [ -22684.7936] [ 4159] [depth= 2] . ( 4 sec) [ -22590.7010] [ 4156] [depth= 2] . ( 4 sec) [ -22385.2996] [ 4150] [depth= 11] . ( 4 sec) [ -22337.6543] [ 4144] [depth= 1] . ( 4 sec) [ -22068.1124] [ 4095] [depth= 5] . ( 4 sec) [ -22040.5796] [ 4095] [depth= 1] . ( 4 sec) [ -21972.0351] [ 4070] [depth= 1] . ( 4 sec) [ -21062.6461] [ 3971] [depth= 7] . ( 4 sec) [ -20822.5826] [ 3976] [depth= 1] . ( 4 sec) [ -20539.0964] [ 3880] [depth= 1] . ( 5 sec) [ -20338.9199] [ 3826] [depth= 1] . ( 5 sec) [ -20280.4502] [ 3837] [depth= 1] . ( 5 sec) [ -20266.6638] [ 3826] [depth= 1] . ( 5 sec) [ -19970.7438] [ 3755] [depth= 10] . ( 5 sec) [ -19882.6179] [ 3735] [depth= 4] . ( 5 sec) [ -19875.9373] [ 3743] [depth= 1] . ( 5 sec) [ -19870.4736] [ 3734] [depth= 11] . ( 5 sec) [ -19583.1036] [ 3638] [depth= 12] . ( 5 sec) [ -19506.3218] [ 3604] [depth= 1] . ( 6 sec) [ -19432.3144] [ 3584] [depth= 1] . ( 6 sec) [ -19392.3873] [ 3582] [depth= 4] . ( 6 sec) [ -19249.3961] [ 3573] [depth= 2] . ( 6 sec) [ -19066.6146] [ 3532] [depth= 11] . ( 6 sec) [ -18879.4386] [ 3498] [depth= 10] . ( 6 sec) [ -18317.9541] [ 3469] [depth= 7] . ( 6 sec) [ -18310.4474] [ 3467] [depth= 1] . ( 6 sec) [ -18236.6911] [ 3429] [depth= 8] . ( 6 sec) [ -18061.4933] [ 3387] [depth= 1] . ( 6 sec) [ -17976.3848] [ 3362] [depth= 8] . ( 7 sec) [ -17823.5233] [ 3317] [depth= 1] . ( 7 sec) [ -17763.8840] [ 3291] [depth= 1] . ( 7 sec) [ -17704.5182] [ 3288] [depth= 6] . ( 7 sec) [ -17641.5422] [ 3271] [depth= 2] . ( 7 sec) [ -17323.8125] [ 3198] [depth= 9] . ( 7 sec) [ -17295.7166] [ 3186] [depth= 1] . ( 7 sec) [ -17096.5347] [ 3145] [depth= 7] . ( 7 sec) [ -17034.3036] [ 3122] [depth= 8] . ( 7 sec) [ -17028.9040] [ 3120] [depth= 1] . ( 8 sec) [ -16959.4934] [ 3118] [depth= 9] . ( 8 sec) [ -16896.4189] [ 3102] [depth= 4] . ( 8 sec) [ -16871.3422] [ 3101] [depth= 2] . ( 8 sec) [ -16865.5830] [ 3102] [depth= 1] . ( 8 sec) [ -16855.5258] [ 3102] [depth= 1] . ( 8 sec) [ -16853.8670] [ 3102] [depth= 1] . ( 8 sec) [ -16853.7945] [ 3102] [depth= 1] . ( 8 sec) [ -16738.1812] [ 3068] [depth= 1] . ( 8 sec) [ -16674.1027] [ 3062] [depth= 1] . ( 8 sec) [ -16669.8216] [ 3062] [depth= 1] . ( 9 sec) [ -16558.0901] [ 3018] [depth= 10] . ( 9 sec) [ -16547.1158] [ 3022] [depth= 1] . ( 9 sec) [ -16487.3494] [ 3023] [depth= 5] . ( 9 sec) [ -16436.8425] [ 2977] [depth= 7] . ( 9 sec) [ -16109.6212] [ 2960] [depth= 1] . ( 9 sec) [ -15957.0189] [ 2937] [depth= 4] . ( 9 sec) [ -15581.0180] [ 2937] [depth= 2] . ( 9 sec) [ -15522.4390] [ 2902] [depth= 1] . ( 10 sec) [ -15516.8345] [ 2901] [depth= 1] . ( 10 sec) [ -15498.8516] [ 2885] [depth= 9] . ( 10 sec) [ -15492.5067] [ 2888] [depth= 1] . ( 10 sec) [ -15297.2607] [ 2843] [depth= 3] . ( 10 sec) [ -15202.2336] [ 2822] [depth= 2] . ( 10 sec) [ -15200.9820] [ 2825] [depth= 3] . ( 10 sec) [ -15174.3834] [ 2821] [depth= 2] . ( 10 sec) [ -15139.9384] [ 2815] [depth= 2] . ( 10 sec) [ -15130.0993] [ 2820] [depth= 1] . ( 10 sec) [ -14919.2108] [ 2821] [depth= 6] . ( 11 sec) [ -14859.7036] [ 2811] [depth= 4] . ( 11 sec) [ -14854.4371] [ 2808] [depth= 1] . ( 11 sec) [ -14756.7961] [ 2785] [depth= 5] . ( 11 sec) [ -14678.3040] [ 2758] [depth= 1] . ( 11 sec) [ -14642.0173] [ 2750] [depth= 1] . ( 11 sec) [ -14624.9473] [ 2741] [depth= 1] . ( 11 sec) [ -14620.8747] [ 2740] [depth= 2] . ( 12 sec) [ -14600.0410] [ 2735] [depth= 2] . ( 12 sec) [ -14529.0391] [ 2717] [depth= 1] . ( 12 sec) [ -14528.0919] [ 2714] [depth= 1] . ( 12 sec) [ -14518.8282] [ 2712] [depth= 1] . ( 12 sec) [ -14493.4701] [ 2702] [depth= 2] . ( 13 sec) [ -14405.3133] [ 2670] [depth= 3] . ( 13 sec) [ -14381.9348] [ 2665] [depth= 2] . ( 13 sec) [ -14370.3805] [ 2668] [depth= 1] . ( 13 sec) [ -14340.4813] [ 2663] [depth= 1] . ( 13 sec) [ -14339.5189] [ 2663] [depth= 1] . ( 13 sec) [ -14333.4973] [ 2666] [depth= 1] . ( 13 sec) [ -14324.9929] [ 2662] [depth= 2] . ( 13 sec) [ -14311.8874] [ 2662] [depth= 1] . ( 13 sec) [ -14305.3754] [ 2662] [depth= 1] . ( 14 sec) [ -14305.2120] [ 2660] [depth= 1] . ( 14 sec) [ -14287.9845] [ 2654] [depth= 1] . ( 14 sec) [ -14286.7739] [ 2659] [depth= 1] . ( 15 sec) [ -14130.4547] [Branch lengths ] . ( 17 sec) [ -14074.4779] [GTR parameters ] . ( 18 sec) [ -14012.0928] [Alpha ][ 0.299680] . ( 18 sec) [ -14005.6260] [ 2658] [depth= 1] . ( 18 sec) [ -13995.0158] [ 2644] [depth= 3] . ( 18 sec) [ -13993.1206] [ 2640] [depth= 1] . ( 19 sec) [ -13992.5735] [ 2645] [depth= 3] . ( 19 sec) [ -13985.2051] [ 2640] [depth= 2] . ( 20 sec) [ -13984.7518] [ 2644] [depth= 1] . ( 20 sec) [ -13971.0253] [ 2635] [depth= 2] . ( 21 sec) [ -13969.6246] [ 2633] [depth= 1] . ( 21 sec) [ -13968.9850] [ 2633] [depth= 1] . ( 22 sec) [ -13968.8278] [ 2631] [depth= 1] . ( 22 sec) [ -13962.4190] [ 2632] [depth= 1] . ( 22 sec) [ -13961.9743] [ 2634] [depth= 1] . ( 22 sec) [ -13961.0581] [ 2632] [depth= 1] . ( 23 sec) [ -13957.7968] [ 2631] [depth= 1] . ( 23 sec) [ -13944.7052] [ 2613] [depth= 3] . ( 24 sec) [ -13942.1685] [ 2615] [depth= 1] . ( 25 sec) [ -13938.9774] [ 2614] [depth= 1] . ( 25 sec) [ -13938.0344] [ 2616] [depth= 1] . ( 26 sec) [ -13935.1359] [ 2618] [depth= 1] . ( 26 sec) [ -13935.1084] [ 2616] [depth= 1] . ( 29 sec) [ -13934.8147] [ 2612] [depth= 2] . ( 30 sec) [ -13914.7444] [Branch lengths ] . ( 31 sec) [ -13912.9869] [GTR parameters ] . ( 31 sec) [ -13912.9774] [Alpha ][ 0.297776] . ( 38 sec) [ -13911.9357] [ 2611] [depth= 1] . ( 43 sec) [ -13911.8271] [ 2614] [depth= 1] . ( 46 sec) [ -13908.5250] [Branch lengths ] . ( 47 sec) [ -13908.4838] [GTR parameters ] . ( 47 sec) [ -13908.4838] [Alpha ][ 0.297776] . ( 62 sec) [ -13908.0935] [Branch lengths ] . ( 125 sec) [ -13908.0567] [Branch lengths ] . ( 125 sec) [ -13908.0567] [Topology ] . ( 127 sec) [ -13907.8796] [Topology ] . ( 128 sec) [ -13907.8171] [Topology ] . ( 130 sec) [ -13907.8076] [Topology ] . ( 132 sec) [ -13907.8055] [Topology ] . ( 134 sec) [ -13907.8050] [Topology ] . ( 135 sec) [ -13907.7803] [GTR parameters ] . ( 135 sec) [ -13907.7788] [Alpha ][ 0.298444] . ( 135 sec) [ -13907.7788] [Topology ] . ( 137 sec) [ -13907.7773] [Topology ] . ( 139 sec) [ -13907.7767] [Topology ] . ( 139 sec) [ -13907.7767] [GTR parameters ] . ( 139 sec) [ -13907.7767] [Alpha ][ 0.298444] . ( 139 sec) [ -13907.7767] [Topology ] . ( 141 sec) [ -13907.7764] [Topology ] . ( 141 sec) [ -13907.7764] [GTR parameters ] . ( 141 sec) [ -13907.7764] [Alpha ][ 0.298444] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13907.776406. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -27490.1862] [GTR parameters ] . ( 3 sec) [ -26841.1046] [Alpha ][ 0.500960] . ( 3 sec) [ -26697.5959] [ 4369] [depth= 10] . ( 3 sec) [ -26607.5154] [ 4348] [depth= 9] . ( 3 sec) [ -26598.9673] [ 4347] [depth= 1] . ( 3 sec) [ -26533.9477] [ 4339] [depth= 7] . ( 3 sec) [ -26412.8364] [ 4294] [depth= 2] . ( 4 sec) [ -26385.0016] [ 4290] [depth= 10] . ( 4 sec) [ -26294.6909] [ 4286] [depth= 2] . ( 4 sec) [ -26283.5451] [ 4287] [depth= 4] . ( 4 sec) [ -26022.3600] [ 4243] [depth= 5] . ( 4 sec) [ -25943.9929] [ 4235] [depth= 5] . ( 4 sec) [ -25908.5834] [ 4231] [depth= 1] . ( 4 sec) [ -25370.4407] [ 4215] [depth= 3] . ( 4 sec) [ -25307.6264] [ 4205] [depth= 1] . ( 4 sec) [ -25244.3326] [ 4200] [depth= 13] . ( 4 sec) [ -25166.1694] [ 4197] [depth= 3] . ( 5 sec) [ -24980.2086] [ 4154] [depth= 4] . ( 5 sec) [ -24691.5608] [ 4094] [depth= 16] . ( 5 sec) [ -24540.6100] [ 4092] [depth= 1] . ( 5 sec) [ -24531.9619] [ 4083] [depth= 1] . ( 5 sec) [ -24017.6129] [ 4078] [depth= 1] . ( 5 sec) [ -23933.4965] [ 4075] [depth= 11] . ( 5 sec) [ -23798.6559] [ 4049] [depth= 6] . ( 5 sec) [ -23416.3387] [ 3998] [depth= 10] . ( 5 sec) [ -22557.6789] [ 3982] [depth= 2] . ( 6 sec) [ -22441.1418] [ 3978] [depth= 10] . ( 6 sec) [ -22129.0682] [ 3964] [depth= 8] . ( 6 sec) [ -22122.1115] [ 3966] [depth= 10] . ( 6 sec) [ -22085.8313] [ 3952] [depth= 17] . ( 6 sec) [ -21980.4122] [ 3936] [depth= 1] . ( 6 sec) [ -21805.4432] [ 3935] [depth= 2] . ( 6 sec) [ -21333.4656] [ 3871] [depth= 3] . ( 6 sec) [ -20535.5355] [ 3783] [depth= 8] . ( 6 sec) [ -20456.5826] [ 3756] [depth= 7] . ( 7 sec) [ -20341.0412] [ 3738] [depth= 8] . ( 7 sec) [ -19949.4411] [ 3640] [depth= 7] . ( 7 sec) [ -19641.2673] [ 3557] [depth= 1] . ( 7 sec) [ -19054.5476] [ 3549] [depth= 9] . ( 7 sec) [ -19001.9467] [ 3542] [depth= 8] . ( 7 sec) [ -19000.8379] [ 3545] [depth= 1] . ( 7 sec) [ -18957.9898] [ 3542] [depth= 9] . ( 7 sec) [ -18780.7733] [ 3529] [depth= 10] . ( 8 sec) [ -18731.7663] [ 3516] [depth= 1] . ( 8 sec) [ -18637.5601] [ 3486] [depth= 7] . ( 8 sec) [ -18582.6740] [ 3514] [depth= 7] . ( 8 sec) [ -18456.9044] [ 3496] [depth= 4] . ( 8 sec) [ -18448.9866] [ 3497] [depth= 3] . ( 8 sec) [ -18420.1407] [ 3466] [depth= 3] . ( 8 sec) [ -18408.6413] [ 3466] [depth= 1] . ( 8 sec) [ -18405.7497] [ 3466] [depth= 1] . ( 8 sec) [ -18405.6995] [ 3466] [depth= 1] . ( 8 sec) [ -18312.6126] [ 3460] [depth= 10] . ( 9 sec) [ -18278.4338] [ 3466] [depth= 1] . ( 9 sec) [ -18138.8225] [ 3441] [depth= 12] . ( 9 sec) [ -18128.7329] [ 3445] [depth= 3] . ( 9 sec) [ -17585.5422] [ 3392] [depth= 12] . ( 9 sec) [ -17487.9550] [ 3386] [depth= 3] . ( 9 sec) [ -17481.5404] [ 3379] [depth= 8] . ( 9 sec) [ -17437.7835] [ 3383] [depth= 1] . ( 9 sec) [ -17366.8580] [ 3355] [depth= 3] . ( 9 sec) [ -17219.7224] [ 3339] [depth= 7] . ( 10 sec) [ -17202.8210] [ 3336] [depth= 1] . ( 10 sec) [ -17190.0288] [ 3367] [depth= 9] . ( 10 sec) [ -17087.9993] [ 3325] [depth= 6] . ( 10 sec) [ -16930.6081] [ 3280] [depth= 5] . ( 10 sec) [ -16919.8310] [ 3277] [depth= 1] . ( 10 sec) [ -16786.1133] [ 3254] [depth= 2] . ( 10 sec) [ -16781.9634] [ 3254] [depth= 1] . ( 10 sec) [ -16728.6144] [ 3241] [depth= 5] . ( 10 sec) [ -16727.0126] [ 3240] [depth= 1] . ( 11 sec) [ -16716.4464] [ 3238] [depth= 1] . ( 11 sec) [ -16697.8106] [ 3234] [depth= 2] . ( 11 sec) [ -16690.3487] [ 3233] [depth= 1] . ( 11 sec) [ -16678.0307] [ 3233] [depth= 1] . ( 11 sec) [ -16658.5333] [ 3232] [depth= 1] . ( 11 sec) [ -16611.0789] [ 3222] [depth= 5] . ( 11 sec) [ -16535.2551] [ 3212] [depth= 5] . ( 11 sec) [ -16474.4528] [ 3212] [depth= 2] . ( 11 sec) [ -16464.3775] [ 3208] [depth= 1] . ( 11 sec) [ -16214.5039] [ 3118] [depth= 9] . ( 12 sec) [ -16176.8481] [ 3111] [depth= 3] . ( 12 sec) [ -16168.2853] [ 3111] [depth= 1] . ( 12 sec) [ -15542.5199] [ 3065] [depth= 8] . ( 12 sec) [ -15509.5834] [ 3064] [depth= 2] . ( 12 sec) [ -15450.1036] [ 3058] [depth= 4] . ( 12 sec) [ -15440.0008] [ 3056] [depth= 1] . ( 12 sec) [ -15389.0828] [ 3028] [depth= 2] . ( 12 sec) [ -15269.0574] [ 3007] [depth= 7] . ( 12 sec) [ -15266.3365] [ 2953] [depth= 1] . ( 13 sec) [ -15073.7257] [ 2909] [depth= 10] . ( 13 sec) [ -15056.4142] [ 2904] [depth= 2] . ( 13 sec) [ -15055.0933] [ 2903] [depth= 1] . ( 13 sec) [ -15053.9155] [ 2903] [depth= 1] . ( 13 sec) [ -14931.6315] [ 2865] [depth= 1] . ( 13 sec) [ -14880.9981] [ 2858] [depth= 4] . ( 13 sec) [ -14848.3302] [ 2849] [depth= 4] . ( 14 sec) [ -14822.1558] [ 2844] [depth= 1] . ( 14 sec) [ -14816.4772] [ 2845] [depth= 1] . ( 14 sec) [ -14805.4586] [ 2842] [depth= 2] . ( 14 sec) [ -14802.6637] [ 2842] [depth= 2] . ( 15 sec) [ -14798.5316] [ 2838] [depth= 2] . ( 15 sec) [ -14796.7342] [ 2834] [depth= 1] . ( 15 sec) [ -14782.4819] [ 2836] [depth= 1] . ( 15 sec) [ -14705.9861] [ 2813] [depth= 1] . ( 15 sec) [ -14680.9877] [ 2811] [depth= 1] . ( 15 sec) [ -14656.0621] [ 2809] [depth= 5] . ( 16 sec) [ -14653.1204] [ 2808] [depth= 1] . ( 16 sec) [ -14469.5399] [Branch lengths ] . ( 19 sec) [ -14398.5051] [GTR parameters ] . ( 19 sec) [ -14320.9850] [Alpha ][ 0.289935] . ( 19 sec) [ -14320.8288] [ 2805] [depth= 2] . ( 20 sec) [ -14311.3804] [ 2803] [depth= 1] . ( 20 sec) [ -14307.7441] [ 2800] [depth= 2] . ( 20 sec) [ -14287.3443] [ 2792] [depth= 2] . ( 20 sec) [ -14258.5239] [ 2781] [depth= 1] . ( 20 sec) [ -14253.1165] [ 2781] [depth= 2] . ( 21 sec) [ -14114.2182] [ 2743] [depth= 17] . ( 21 sec) [ -14113.1801] [ 2733] [depth= 1] . ( 21 sec) [ -14109.5759] [ 2730] [depth= 1] . ( 22 sec) [ -14109.2762] [ 2731] [depth= 1] . ( 22 sec) [ -14055.7045] [ 2656] [depth= 15] . ( 22 sec) [ -14046.2414] [ 2648] [depth= 1] . ( 22 sec) [ -14044.6562] [ 2648] [depth= 1] . ( 23 sec) [ -14044.5207] [ 2647] [depth= 1] . ( 23 sec) [ -14041.6536] [ 2652] [depth= 1] . ( 23 sec) [ -14041.1622] [ 2653] [depth= 1] . ( 24 sec) [ -14041.0269] [ 2657] [depth= 1] . ( 24 sec) [ -14035.4078] [ 2652] [depth= 2] . ( 26 sec) [ -14031.7861] [ 2648] [depth= 1] . ( 26 sec) [ -14014.8698] [ 2636] [depth= 1] . ( 28 sec) [ -14014.2923] [ 2641] [depth= 2] . ( 28 sec) [ -14007.5291] [ 2642] [depth= 1] . ( 29 sec) [ -14002.0781] [ 2631] [depth= 8] . ( 29 sec) [ -13986.7779] [ 2627] [depth= 1] . ( 31 sec) [ -13985.9108] [ 2618] [depth= 2] . ( 32 sec) [ -13975.6326] [ 2620] [depth= 2] . ( 32 sec) [ -13974.1190] [ 2624] [depth= 2] . ( 33 sec) [ -13953.9725] [Branch lengths ] . ( 35 sec) [ -13948.8746] [GTR parameters ] . ( 36 sec) [ -13948.7551] [Alpha ][ 0.295969] . ( 36 sec) [ -13947.7211] [ 2618] [depth= 3] . ( 37 sec) [ -13947.3486] [ 2616] [depth= 1] . ( 38 sec) [ -13946.7426] [ 2612] [depth= 1] . ( 41 sec) [ -13945.0429] [ 2617] [depth= 1] . ( 41 sec) [ -13943.9345] [ 2615] [depth= 1] . ( 42 sec) [ -13943.8794] [ 2615] [depth= 1] . ( 44 sec) [ -13943.0580] [ 2611] [depth= 2] . ( 49 sec) [ -13937.6002] [Branch lengths ] . ( 50 sec) [ -13937.5535] [GTR parameters ] . ( 50 sec) [ -13937.5401] [Alpha ][ 0.298083] . ( 51 sec) [ -13937.1330] [ 2614] [depth= 1] . ( 55 sec) [ -13937.1212] [ 2616] [depth= 1] . ( 63 sec) [ -13934.4202] [Branch lengths ] . ( 64 sec) [ -13934.4022] [GTR parameters ] . ( 65 sec) [ -13934.4015] [Alpha ][ 0.297528] . ( 78 sec) [ -13924.6213] [Branch lengths ] . ( 90 sec) [ -13923.6195] [ 2616] [depth= 1] . ( 138 sec) [ -13908.8469] [Branch lengths ] . ( 140 sec) [ -13908.8173] [GTR parameters ] . ( 140 sec) [ -13908.8163] [Alpha ][ 0.298082] . ( 201 sec) [ -13907.8501] [Branch lengths ] . ( 201 sec) [ -13907.8501] [Topology ] . ( 203 sec) [ -13907.7978] [Topology ] . ( 204 sec) [ -13907.7880] [Topology ] . ( 206 sec) [ -13907.7852] [Topology ] . ( 208 sec) [ -13907.7844] [Topology ] . ( 209 sec) [ -13907.7784] [GTR parameters ] . ( 209 sec) [ -13907.7780] [Alpha ][ 0.298408] . ( 209 sec) [ -13907.7780] [Topology ] . ( 211 sec) [ -13907.7771] [Topology ] . ( 212 sec) [ -13907.7770] [GTR parameters ] . ( 212 sec) [ -13907.7770] [Alpha ][ 0.298408] . ( 212 sec) [ -13907.7770] [Topology ] . ( 213 sec) [ -13907.7767] [Topology ] . ( 214 sec) [ -13907.7767] [GTR parameters ] . ( 214 sec) [ -13907.7767] [Alpha ][ 0.298408] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13907.776659. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -14871.4533] [GTR parameters ] . ( 1 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 1 sec) [ -14653.1273] [Topology ] . ( 2 sec) [ -14475.8787] [Topology ] . ( 4 sec) [ -14449.9667] [Topology ] . ( 6 sec) [ -14437.7778] [Topology ] . ( 8 sec) [ -14433.7019] [Topology ] . ( 9 sec) [ -14432.2135] [Topology ] . ( 11 sec) [ -14431.6513] [Topology ] . ( 13 sec) [ -14431.4138] [Topology ] . ( 14 sec) [ -14431.3098] [Topology ] . ( 16 sec) [ -14431.2636] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -13978.0628] [GTR parameters ] . ( 34 sec) [ -13925.0703] [Alpha ][ 0.310835] . ( 34 sec) [ -13925.0703] [Topology ] . ( 36 sec) [ -13913.8490] [Topology ] . ( 38 sec) [ -13912.8086] [Topology ] . ( 39 sec) [ -13912.5969] [Topology ] . ( 41 sec) [ -13912.5496] [Topology ] . ( 43 sec) [ -13912.5342] [Topology ] . ( 45 sec) [ -13912.5281] [Topology ] . ( 46 sec) [ -13912.5254] [Topology ] . ( 48 sec) [ -13912.5242] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -13910.7996] [GTR parameters ] . ( 65 sec) [ -13910.4734] [Alpha ][ 0.299981] . ( 65 sec) [ -13910.4734] [Topology ] . ( 67 sec) [ -13910.3270] [Topology ] . ( 69 sec) [ -13910.3021] [Topology ] . ( 71 sec) [ -13910.2910] [Topology ] . ( 72 sec) [ -13910.2855] [Topology ] . ( 74 sec) [ -13910.2828] [Topology ] . ( 76 sec) [ -13910.2814] [Topology ] . Checking for NNIs, optimizing five branches... . ( 89 sec) [ -13910.2341] [Topology ] . ( 92 sec) [ -13910.1845] [GTR parameters ] . ( 92 sec) [ -13910.1744] [Alpha ][ 0.298017] . ( 92 sec) [ -13910.1744] [Topology ] . ( 94 sec) [ -13910.1474] [Topology ] . ( 96 sec) [ -13910.1430] [Topology ] . ( 97 sec) [ -13910.1416] [Topology ] . ( 99 sec) [ -13910.1410] [Topology ] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -13910.1397] [GTR parameters ] . ( 113 sec) [ -13910.1397] [Alpha ][ 0.298017] . ( 113 sec) [ -13910.1397] [Topology ] . ( 114 sec) [ -13910.1391] [Topology ] . Checking for NNIs, optimizing five branches... . ( 129 sec) [ -13910.1390] [GTR parameters ] . ( 129 sec) [ -13910.1390] [Alpha ][ 0.298017] . ( 129 sec) [ -13910.1390] [Topology ] . ( 131 sec) [ -13910.1388] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 157 sec) [ -14871.4533] [GTR parameters ] . ( 158 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 158 sec) [ -14651.0565] [ 2609] [depth= 1] . ( 158 sec) [ -14639.3400] [ 2603] [depth= 1] . ( 158 sec) [ -14626.0253] [ 2606] [depth= 1] . ( 158 sec) [ -14615.1978] [ 2603] [depth= 1] . ( 159 sec) [ -14605.7753] [ 2606] [depth= 1] . ( 160 sec) [ -14605.6482] [ 2606] [depth= 1] . ( 160 sec) [ -14605.2736] [ 2606] [depth= 1] . ( 160 sec) [ -14602.5720] [ 2606] [depth= 1] . ( 161 sec) [ -14602.5590] [ 2606] [depth= 1] . ( 163 sec) [ -14596.9605] [ 2605] [depth= 1] . ( 163 sec) [ -14588.0827] [ 2606] [depth= 1] . ( 163 sec) [ -14581.4977] [ 2603] [depth= 1] . ( 163 sec) [ -14580.3923] [ 2605] [depth= 1] . ( 163 sec) [ -14576.7139] [ 2611] [depth= 2] . ( 163 sec) [ -14574.3082] [ 2609] [depth= 1] . ( 163 sec) [ -14572.5761] [ 2610] [depth= 1] . ( 164 sec) [ -14572.3718] [ 2611] [depth= 1] . ( 164 sec) [ -14570.4127] [ 2610] [depth= 1] . ( 164 sec) [ -14565.8626] [ 2612] [depth= 2] . ( 165 sec) [ -14559.3115] [ 2614] [depth= 1] . ( 165 sec) [ -14556.0086] [ 2612] [depth= 1] . ( 165 sec) [ -14551.0187] [ 2614] [depth= 1] . ( 165 sec) [ -14545.9264] [ 2611] [depth= 2] . ( 165 sec) [ -14545.7014] [ 2613] [depth= 2] . ( 166 sec) [ -14537.0638] [ 2616] [depth= 1] . ( 166 sec) [ -14532.2768] [ 2616] [depth= 1] . ( 166 sec) [ -14531.0975] [ 2609] [depth= 1] . ( 166 sec) [ -14529.9781] [ 2608] [depth= 1] . ( 166 sec) [ -14528.6283] [ 2609] [depth= 1] . ( 166 sec) [ -14528.1179] [ 2606] [depth= 1] . ( 167 sec) [ -14527.7063] [ 2609] [depth= 1] . ( 168 sec) [ -14527.5902] [ 2609] [depth= 3] . ( 168 sec) [ -14523.2113] [ 2609] [depth= 2] . ( 168 sec) [ -14516.8903] [ 2609] [depth= 3] . ( 168 sec) [ -14513.4038] [ 2610] [depth= 2] . ( 169 sec) [ -14511.7476] [ 2612] [depth= 1] . ( 169 sec) [ -14511.2641] [ 2610] [depth= 1] . ( 169 sec) [ -14504.4392] [ 2607] [depth= 1] . ( 170 sec) [ -14441.3405] [Branch lengths ] . ( 174 sec) [ -13989.7912] [GTR parameters ] . ( 175 sec) [ -13933.4916] [Alpha ][ 0.303968] . ( 179 sec) [ -13931.5205] [ 2606] [depth= 1] . ( 179 sec) [ -13930.9974] [ 2604] [depth= 1] . ( 180 sec) [ -13930.2816] [ 2606] [depth= 1] . ( 182 sec) [ -13928.9740] [ 2606] [depth= 1] . ( 185 sec) [ -13928.3169] [ 2605] [depth= 1] . ( 187 sec) [ -13914.7656] [Branch lengths ] . ( 191 sec) [ -13912.4700] [GTR parameters ] . ( 191 sec) [ -13912.3186] [Alpha ][ 0.296678] . ( 204 sec) [ -13910.6480] [Branch lengths ] . ( 233 sec) [ -13909.9426] [ 2613] [depth= 4] . ( 246 sec) [ -13909.7408] [ 2613] [depth= 2] . ( 265 sec) [ -13908.7738] [Branch lengths ] . ( 270 sec) [ -13908.6859] [GTR parameters ] . ( 270 sec) [ -13908.6781] [Alpha ][ 0.298294] . ( 332 sec) [ -13908.5638] [Branch lengths ] . ( 332 sec) [ -13908.5638] [Topology ] . ( 334 sec) [ -13908.5510] [Topology ] . ( 336 sec) [ -13908.5468] [Topology ] . ( 337 sec) [ -13908.5448] [Topology ] . ( 339 sec) [ -13908.5439] [Topology ] . ( 343 sec) [ -13908.5378] [GTR parameters ] . ( 343 sec) [ -13908.5377] [Alpha ][ 0.298593] . ( 343 sec) [ -13908.5377] [Topology ] . ( 345 sec) [ -13908.5362] [Topology ] . ( 347 sec) [ -13908.5356] [Topology ] . ( 348 sec) [ -13908.5354] [GTR parameters ] . ( 348 sec) [ -13908.5354] [Alpha ][ 0.298593] . ( 348 sec) [ -13908.5354] [Topology ] . ( 350 sec) [ -13908.5350] [Topology ] . ( 351 sec) [ -13908.5350] [GTR parameters ] . ( 351 sec) [ -13908.5350] [Alpha ][ 0.298593] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -13910.138779 . Log likelihood obtained after SPR moves : -13908.535048 . Log likelihood of the current tree: -13908.535048. . Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'... . Best log likelihood : -13907.776323 . Time used 0h6m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1312.99user 0.00system 22:04.13elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps