.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data61.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... . 443 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . [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)... . ( 0 sec) [ -21421.9541] [GTR parameters ] . ( 0 sec) [ -21005.8999] [Alpha ][ 0.500960] . ( 1 sec) [ -20437.6921] [ 4838] [depth= 8] . ( 1 sec) [ -20290.1006] [ 4824] [depth= 6] . ( 1 sec) [ -20131.3041] [ 4802] [depth= 1] . ( 1 sec) [ -20031.4291] [ 4785] [depth= 7] . ( 1 sec) [ -19706.2655] [ 4702] [depth= 6] . ( 1 sec) [ -19474.6581] [ 4675] [depth= 6] . ( 1 sec) [ -19351.7128] [ 4665] [depth= 3] . ( 1 sec) [ -19244.4709] [ 4670] [depth= 9] . ( 1 sec) [ -19107.1690] [ 4569] [depth= 16] . ( 1 sec) [ -18766.3150] [ 4438] [depth= 14] . ( 1 sec) [ -18743.7324] [ 4438] [depth= 2] . ( 1 sec) [ -18733.7378] [ 4477] [depth= 1] . ( 1 sec) [ -18444.7033] [ 4389] [depth= 7] . ( 1 sec) [ -18424.7862] [ 4385] [depth= 1] . ( 1 sec) [ -18113.0981] [ 4376] [depth= 4] . ( 1 sec) [ -17869.9201] [ 4346] [depth= 2] . ( 1 sec) [ -17833.7868] [ 4346] [depth= 3] . ( 1 sec) [ -17543.9217] [ 4309] [depth= 2] . ( 1 sec) [ -17483.9343] [ 4234] [depth= 1] . ( 1 sec) [ -17372.9403] [ 4230] [depth= 1] . ( 1 sec) [ -17227.9988] [ 4219] [depth= 1] . ( 1 sec) [ -17017.3524] [ 4200] [depth= 11] . ( 1 sec) [ -16798.6803] [ 4201] [depth= 2] . ( 2 sec) [ -16693.9129] [ 4140] [depth= 1] . ( 2 sec) [ -16550.4927] [ 4057] [depth= 6] . ( 2 sec) [ -16376.5367] [ 3979] [depth= 4] . ( 2 sec) [ -16269.5885] [ 3969] [depth= 2] . ( 2 sec) [ -16113.1796] [ 3892] [depth= 16] . ( 2 sec) [ -15873.3789] [ 3819] [depth= 14] . ( 2 sec) [ -15660.6151] [ 3710] [depth= 4] . ( 2 sec) [ -15515.8197] [ 3684] [depth= 14] . ( 2 sec) [ -15480.5225] [ 3677] [depth= 1] . ( 2 sec) [ -15477.7163] [ 3700] [depth= 1] . ( 2 sec) [ -15130.2459] [ 3593] [depth= 6] . ( 2 sec) [ -14698.1663] [ 3520] [depth= 16] . ( 2 sec) [ -14656.2683] [ 3515] [depth= 1] . ( 2 sec) [ -14591.3913] [ 3455] [depth= 19] . ( 2 sec) [ -14585.7337] [ 3455] [depth= 1] . ( 2 sec) [ -14321.7005] [ 3351] [depth= 11] . ( 2 sec) [ -14174.0183] [ 3326] [depth= 2] . ( 2 sec) [ -14051.8235] [ 3326] [depth= 1] . ( 2 sec) [ -13942.5277] [ 3290] [depth= 15] . ( 2 sec) [ -13892.4391] [ 3277] [depth= 1] . ( 2 sec) [ -13820.8404] [ 3282] [depth= 1] . ( 3 sec) [ -13705.1377] [ 3189] [depth= 7] . ( 3 sec) [ -13699.6658] [ 3190] [depth= 1] . ( 3 sec) [ -13688.4747] [ 3190] [depth= 1] . ( 3 sec) [ -13686.0864] [ 3189] [depth= 1] . ( 3 sec) [ -13621.9232] [ 3159] [depth= 1] . ( 3 sec) [ -13578.1533] [ 3156] [depth= 5] . ( 3 sec) [ -13575.4127] [ 3154] [depth= 1] . ( 3 sec) [ -13448.3005] [ 3127] [depth= 3] . ( 3 sec) [ -13386.2773] [ 3099] [depth= 1] . ( 3 sec) [ -13376.6521] [ 3087] [depth= 2] . ( 3 sec) [ -13146.3398] [ 3019] [depth= 4] . ( 3 sec) [ -13118.3181] [ 3019] [depth= 2] . ( 3 sec) [ -13116.5718] [ 3021] [depth= 1] . ( 3 sec) [ -13062.3117] [ 3016] [depth= 3] . ( 3 sec) [ -13039.3259] [ 2989] [depth= 1] . ( 3 sec) [ -12982.1101] [ 2949] [depth= 2] . ( 3 sec) [ -12624.8416] [ 2884] [depth= 4] . ( 3 sec) [ -12581.5426] [ 2841] [depth= 1] . ( 3 sec) [ -12577.6110] [ 2841] [depth= 1] . ( 3 sec) [ -12533.9508] [ 2827] [depth= 3] . ( 3 sec) [ -12438.4513] [ 2783] [depth= 4] . ( 4 sec) [ -12426.7973] [ 2789] [depth= 2] . ( 4 sec) [ -12424.7619] [ 2788] [depth= 1] . ( 4 sec) [ -12419.3292] [ 2782] [depth= 1] . ( 4 sec) [ -12418.7845] [ 2777] [depth= 1] . ( 4 sec) [ -12404.2410] [ 2783] [depth= 1] . ( 4 sec) [ -12370.9330] [ 2762] [depth= 1] . ( 4 sec) [ -12342.9254] [ 2756] [depth= 1] . ( 4 sec) [ -12340.9350] [ 2759] [depth= 1] . ( 4 sec) [ -12340.5718] [ 2762] [depth= 1] . ( 4 sec) [ -12336.5763] [ 2767] [depth= 2] . ( 4 sec) [ -12085.2460] [ 2745] [depth= 1] . ( 4 sec) [ -11909.2021] [ 2719] [depth= 1] . ( 4 sec) [ -11882.3250] [ 2718] [depth= 3] . ( 4 sec) [ -11638.2531] [ 2696] [depth= 1] . ( 4 sec) [ -11588.4806] [ 2681] [depth= 1] . ( 4 sec) [ -11173.4141] [ 2669] [depth= 3] . ( 4 sec) [ -11167.8897] [ 2672] [depth= 2] . ( 4 sec) [ -11110.2308] [ 2594] [depth= 7] . ( 5 sec) [ -11062.8608] [ 2592] [depth= 1] . ( 5 sec) [ -10970.0909] [ 2552] [depth= 3] . ( 5 sec) [ -10969.5464] [ 2550] [depth= 1] . ( 5 sec) [ -10779.3294] [Branch lengths ] . ( 6 sec) [ -10776.9348] [GTR parameters ] . ( 6 sec) [ -10743.1185] [Alpha ][ 0.874529] . ( 6 sec) [ -10718.2640] [ 2539] [depth= 1] . ( 6 sec) [ -10716.4589] [ 2544] [depth= 1] . ( 6 sec) [ -10675.5536] [ 2501] [depth= 3] . ( 6 sec) [ -10674.6130] [ 2500] [depth= 1] . ( 6 sec) [ -10674.2085] [ 2500] [depth= 1] . ( 6 sec) [ -10660.7917] [ 2491] [depth= 1] . ( 6 sec) [ -10660.5036] [ 2487] [depth= 2] . ( 6 sec) [ -10659.0708] [ 2489] [depth= 1] . ( 7 sec) [ -10630.3320] [ 2476] [depth= 1] . ( 7 sec) [ -10629.8277] [ 2473] [depth= 1] . ( 7 sec) [ -10613.5793] [ 2476] [depth= 1] . ( 7 sec) [ -10613.3771] [ 2477] [depth= 1] . ( 7 sec) [ -10613.3630] [ 2476] [depth= 1] . ( 7 sec) [ -10613.2516] [ 2473] [depth= 1] . ( 7 sec) [ -10610.4448] [ 2470] [depth= 1] . ( 8 sec) [ -10610.3906] [ 2473] [depth= 1] . ( 8 sec) [ -10609.6114] [ 2475] [depth= 1] . ( 8 sec) [ -10608.7626] [ 2472] [depth= 1] . ( 8 sec) [ -10605.7388] [ 2475] [depth= 1] . ( 9 sec) [ -10605.5618] [ 2473] [depth= 1] . ( 9 sec) [ -10589.4182] [Branch lengths ] . ( 9 sec) [ -10589.3556] [GTR parameters ] . ( 9 sec) [ -10588.3518] [Alpha ][ 0.964517] . ( 10 sec) [ -10588.2984] [ 2477] [depth= 1] . ( 13 sec) [ -10586.9604] [Branch lengths ] . ( 13 sec) [ -10586.9595] [GTR parameters ] . ( 13 sec) [ -10586.9542] [Alpha ][ 0.971521] . ( 16 sec) [ -10586.8073] [Branch lengths ] . ( 38 sec) [ -10586.7862] [Branch lengths ] . ( 38 sec) [ -10586.7862] [Topology ] . ( 38 sec) [ -10586.6701] [Topology ] . ( 39 sec) [ -10586.5605] [Topology ] . ( 40 sec) [ -10586.5403] [Topology ] . ( 41 sec) [ -10586.5327] [Topology ] . ( 42 sec) [ -10586.5296] [Topology ] . ( 43 sec) [ -10586.5283] [Topology ] . ( 43 sec) [ -10586.5278] [Topology ] . ( 44 sec) [ -10586.5264] [GTR parameters ] . ( 44 sec) [ -10586.5264] [Alpha ][ 0.971521] . ( 44 sec) [ -10586.5264] [Topology ] . ( 44 sec) [ -10586.5262] [Topology ] . ( 45 sec) [ -10586.5261] [GTR parameters ] . ( 45 sec) [ -10586.5261] [Alpha ][ 0.971521] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -10585.2591] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.259103. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22013.8349] [GTR parameters ] . ( 1 sec) [ -21573.9204] [Alpha ][ 0.500960] . ( 1 sec) [ -21227.5755] [ 4992] [depth= 3] . ( 1 sec) [ -20680.9730] [ 4908] [depth= 3] . ( 1 sec) [ -20606.1107] [ 4879] [depth= 3] . ( 1 sec) [ -20367.8549] [ 4857] [depth= 2] . ( 2 sec) [ -20058.6525] [ 4739] [depth= 3] . ( 2 sec) [ -19993.0033] [ 4733] [depth= 6] . ( 2 sec) [ -19818.7570] [ 4688] [depth= 5] . ( 2 sec) [ -19808.4757] [ 4664] [depth= 1] . ( 2 sec) [ -19686.8600] [ 4645] [depth= 1] . ( 2 sec) [ -19588.5365] [ 4601] [depth= 3] . ( 2 sec) [ -19426.9202] [ 4589] [depth= 2] . ( 2 sec) [ -19283.3683] [ 4556] [depth= 13] . ( 2 sec) [ -18971.8287] [ 4547] [depth= 3] . ( 2 sec) [ -18298.8106] [ 4402] [depth= 14] . ( 2 sec) [ -18089.4756] [ 4369] [depth= 8] . ( 2 sec) [ -17520.5631] [ 4206] [depth= 10] . ( 2 sec) [ -17491.5399] [ 4146] [depth= 13] . ( 2 sec) [ -17162.2800] [ 4123] [depth= 4] . ( 2 sec) [ -17124.0541] [ 4122] [depth= 1] . ( 2 sec) [ -16638.3819] [ 4064] [depth= 2] . ( 2 sec) [ -16293.3774] [ 3945] [depth= 17] . ( 2 sec) [ -16240.8304] [ 3946] [depth= 1] . ( 2 sec) [ -15948.0641] [ 3863] [depth= 3] . ( 2 sec) [ -15734.2309] [ 3821] [depth= 3] . ( 2 sec) [ -15699.1835] [ 3821] [depth= 1] . ( 2 sec) [ -15368.4503] [ 3748] [depth= 8] . ( 3 sec) [ -15239.1850] [ 3750] [depth= 1] . ( 3 sec) [ -15106.1576] [ 3654] [depth= 6] . ( 3 sec) [ -14203.1184] [ 3503] [depth= 9] . ( 3 sec) [ -14188.7801] [ 3498] [depth= 1] . ( 3 sec) [ -13775.9506] [ 3346] [depth= 6] . ( 3 sec) [ -13770.9988] [ 3346] [depth= 1] . ( 3 sec) [ -13768.2652] [ 3348] [depth= 1] . ( 3 sec) [ -13523.9366] [ 3329] [depth= 1] . ( 3 sec) [ -13404.5708] [ 3296] [depth= 1] . ( 3 sec) [ -13256.1915] [ 3226] [depth= 7] . ( 3 sec) [ -13198.1234] [ 3216] [depth= 2] . ( 3 sec) [ -12865.8143] [ 3092] [depth= 7] . ( 3 sec) [ -12855.8185] [ 3096] [depth= 1] . ( 3 sec) [ -12822.3220] [ 3090] [depth= 2] . ( 3 sec) [ -12809.3761] [ 3089] [depth= 1] . ( 3 sec) [ -12770.4343] [ 3091] [depth= 1] . ( 3 sec) [ -12765.6017] [ 3095] [depth= 1] . ( 3 sec) [ -12744.7998] [ 3109] [depth= 1] . ( 3 sec) [ -12734.4472] [ 3106] [depth= 2] . ( 3 sec) [ -12724.3350] [ 3111] [depth= 2] . ( 4 sec) [ -12724.3178] [ 3111] [depth= 1] . ( 4 sec) [ -12698.5939] [ 3092] [depth= 2] . ( 4 sec) [ -12526.2499] [ 3097] [depth= 1] . ( 4 sec) [ -12337.3146] [ 3094] [depth= 1] . ( 4 sec) [ -12233.1621] [ 3011] [depth= 2] . ( 4 sec) [ -12093.7800] [ 2999] [depth= 2] . ( 4 sec) [ -11896.2866] [ 2937] [depth= 2] . ( 4 sec) [ -11875.2306] [ 2937] [depth= 2] . ( 4 sec) [ -11832.9263] [ 2936] [depth= 2] . ( 4 sec) [ -11828.1282] [ 2935] [depth= 1] . ( 4 sec) [ -11724.6273] [ 2869] [depth= 7] . ( 4 sec) [ -11720.4763] [ 2870] [depth= 1] . ( 4 sec) [ -11647.2622] [ 2840] [depth= 6] . ( 4 sec) [ -11541.9361] [ 2777] [depth= 2] . ( 4 sec) [ -11539.8470] [ 2781] [depth= 1] . ( 4 sec) [ -11505.0517] [ 2742] [depth= 1] . ( 4 sec) [ -11495.6806] [ 2741] [depth= 1] . ( 5 sec) [ -11478.0352] [ 2723] [depth= 2] . ( 5 sec) [ -11435.7210] [ 2703] [depth= 6] . ( 5 sec) [ -11403.4966] [ 2698] [depth= 5] . ( 5 sec) [ -11389.4564] [ 2697] [depth= 1] . ( 5 sec) [ -11380.4334] [ 2691] [depth= 1] . ( 5 sec) [ -11342.3137] [ 2673] [depth= 1] . ( 5 sec) [ -11206.8388] [ 2676] [depth= 8] . ( 5 sec) [ -11183.1539] [ 2677] [depth= 1] . ( 5 sec) [ -11168.4603] [ 2661] [depth= 1] . ( 6 sec) [ -10992.6049] [Branch lengths ] . ( 6 sec) [ -10988.3968] [GTR parameters ] . ( 6 sec) [ -10957.6215] [Alpha ][ 0.855350] . ( 6 sec) [ -10734.2500] [ 2551] [depth= 7] . ( 6 sec) [ -10722.3333] [ 2531] [depth= 1] . ( 6 sec) [ -10685.6413] [ 2503] [depth= 1] . ( 6 sec) [ -10656.1329] [ 2486] [depth= 1] . ( 7 sec) [ -10655.8936] [ 2484] [depth= 1] . ( 7 sec) [ -10655.8554] [ 2486] [depth= 1] . ( 7 sec) [ -10652.5922] [ 2483] [depth= 1] . ( 7 sec) [ -10647.9555] [ 2482] [depth= 1] . ( 7 sec) [ -10646.1394] [ 2483] [depth= 1] . ( 7 sec) [ -10644.5973] [ 2486] [depth= 1] . ( 7 sec) [ -10643.7514] [ 2481] [depth= 1] . ( 8 sec) [ -10636.7984] [ 2473] [depth= 1] . ( 8 sec) [ -10633.8379] [ 2471] [depth= 1] . ( 8 sec) [ -10632.3967] [ 2474] [depth= 1] . ( 8 sec) [ -10631.9781] [ 2476] [depth= 1] . ( 8 sec) [ -10629.9457] [ 2478] [depth= 1] . ( 8 sec) [ -10629.1060] [ 2474] [depth= 2] . ( 8 sec) [ -10620.8841] [ 2467] [depth= 2] . ( 8 sec) [ -10620.5874] [ 2466] [depth= 1] . ( 9 sec) [ -10620.4133] [ 2465] [depth= 1] . ( 9 sec) [ -10619.9002] [ 2461] [depth= 1] . ( 9 sec) [ -10618.9926] [ 2462] [depth= 1] . ( 9 sec) [ -10589.5658] [Branch lengths ] . ( 10 sec) [ -10589.3949] [GTR parameters ] . ( 10 sec) [ -10587.9039] [Alpha ][ 0.964718] . ( 10 sec) [ -10587.8513] [ 2463] [depth= 1] . ( 11 sec) [ -10587.7250] [ 2467] [depth= 1] . ( 13 sec) [ -10585.6954] [Branch lengths ] . ( 13 sec) [ -10585.6933] [GTR parameters ] . ( 13 sec) [ -10585.6867] [Alpha ][ 0.972566] . ( 17 sec) [ -10585.3810] [Branch lengths ] . ( 38 sec) [ -10585.3150] [Branch lengths ] . ( 38 sec) [ -10585.3150] [Topology ] . ( 39 sec) [ -10585.2773] [Topology ] . ( 40 sec) [ -10585.2582] [Topology ] . ( 40 sec) [ -10585.2534] [Topology ] . ( 41 sec) [ -10585.2514] [Topology ] . ( 42 sec) [ -10585.2505] [Topology ] . ( 42 sec) [ -10585.2497] [GTR parameters ] . ( 42 sec) [ -10585.2497] [Alpha ][ 0.972566] . ( 42 sec) [ -10585.2497] [Topology ] . ( 43 sec) [ -10585.2493] [Topology ] . ( 43 sec) [ -10585.2492] [GTR parameters ] . ( 43 sec) [ -10585.2492] [Alpha ][ 0.972566] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.249235. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22216.6927] [GTR parameters ] . ( 1 sec) [ -21785.2628] [Alpha ][ 0.500960] . ( 1 sec) [ -21104.3346] [ 5073] [depth= 8] . ( 1 sec) [ -20847.4755] [ 5025] [depth= 8] . ( 1 sec) [ -20637.7826] [ 5008] [depth= 4] . ( 1 sec) [ -20556.4196] [ 4992] [depth= 1] . ( 1 sec) [ -20364.0539] [ 4902] [depth= 7] . ( 1 sec) [ -20180.5496] [ 4881] [depth= 7] . ( 1 sec) [ -20136.0281] [ 4835] [depth= 2] . ( 1 sec) [ -19659.5448] [ 4747] [depth= 1] . ( 1 sec) [ -19594.2773] [ 4710] [depth= 9] . ( 1 sec) [ -19152.7251] [ 4591] [depth= 5] . ( 1 sec) [ -19032.9172] [ 4571] [depth= 6] . ( 1 sec) [ -18769.3441] [ 4558] [depth= 9] . ( 1 sec) [ -18571.2298] [ 4535] [depth= 3] . ( 1 sec) [ -18428.6943] [ 4525] [depth= 2] . ( 1 sec) [ -18394.8640] [ 4493] [depth= 1] . ( 1 sec) [ -18284.4931] [ 4478] [depth= 1] . ( 1 sec) [ -18197.7199] [ 4443] [depth= 1] . ( 1 sec) [ -17568.7791] [ 4413] [depth= 2] . ( 1 sec) [ -17336.3651] [ 4371] [depth= 4] . ( 1 sec) [ -16730.6867] [ 4168] [depth= 6] . ( 2 sec) [ -16533.9269] [ 4077] [depth= 9] . ( 2 sec) [ -16523.8406] [ 4083] [depth= 1] . ( 2 sec) [ -16133.3242] [ 4010] [depth= 4] . ( 2 sec) [ -15835.6581] [ 3908] [depth= 11] . ( 2 sec) [ -15564.3698] [ 3895] [depth= 1] . ( 2 sec) [ -15539.5360] [ 3889] [depth= 1] . ( 2 sec) [ -15537.2943] [ 3895] [depth= 1] . ( 2 sec) [ -15144.6667] [ 3773] [depth= 5] . ( 2 sec) [ -14927.8678] [ 3710] [depth= 14] . ( 2 sec) [ -14903.4784] [ 3708] [depth= 2] . ( 2 sec) [ -14641.9637] [ 3592] [depth= 5] . ( 2 sec) [ -14552.9740] [ 3567] [depth= 1] . ( 2 sec) [ -14489.1865] [ 3502] [depth= 1] . ( 2 sec) [ -14308.5061] [ 3422] [depth= 5] . ( 2 sec) [ -14220.6553] [ 3422] [depth= 8] . ( 2 sec) [ -14187.3795] [ 3409] [depth= 6] . ( 2 sec) [ -14121.9205] [ 3373] [depth= 2] . ( 2 sec) [ -14062.4251] [ 3311] [depth= 1] . ( 3 sec) [ -13804.6289] [ 3301] [depth= 5] . ( 3 sec) [ -13734.0580] [ 3277] [depth= 2] . ( 3 sec) [ -13726.7901] [ 3261] [depth= 4] . ( 3 sec) [ -13554.5878] [ 3204] [depth= 2] . ( 3 sec) [ -13513.6797] [ 3204] [depth= 1] . ( 3 sec) [ -13456.6742] [ 3190] [depth= 10] . ( 3 sec) [ -13372.0351] [ 3219] [depth= 1] . ( 3 sec) [ -13360.4214] [ 3190] [depth= 1] . ( 3 sec) [ -13217.7716] [ 3089] [depth= 10] . ( 3 sec) [ -12906.7215] [ 3050] [depth= 4] . ( 3 sec) [ -12810.7734] [ 3013] [depth= 1] . ( 3 sec) [ -12698.7363] [ 2969] [depth= 2] . ( 3 sec) [ -12680.9974] [ 2967] [depth= 2] . ( 3 sec) [ -12673.1818] [ 2983] [depth= 7] . ( 3 sec) [ -12630.1843] [ 2961] [depth= 4] . ( 3 sec) [ -12470.4985] [ 2952] [depth= 3] . ( 3 sec) [ -12460.6399] [ 2952] [depth= 1] . ( 3 sec) [ -12438.8138] [ 2967] [depth= 1] . ( 3 sec) [ -12435.1128] [ 2967] [depth= 1] . ( 3 sec) [ -12427.4392] [ 2987] [depth= 8] . ( 3 sec) [ -12400.0396] [ 2983] [depth= 2] . ( 3 sec) [ -12352.7851] [ 2980] [depth= 1] . ( 4 sec) [ -12265.3111] [ 2917] [depth= 5] . ( 4 sec) [ -12156.8637] [ 2868] [depth= 1] . ( 4 sec) [ -12098.8145] [ 2856] [depth= 4] . ( 4 sec) [ -12050.7527] [ 2858] [depth= 1] . ( 4 sec) [ -12038.3529] [ 2851] [depth= 2] . ( 4 sec) [ -11888.1102] [ 2845] [depth= 1] . ( 4 sec) [ -11759.1139] [ 2834] [depth= 2] . ( 4 sec) [ -11553.5594] [ 2810] [depth= 2] . ( 4 sec) [ -11501.7958] [ 2798] [depth= 1] . ( 4 sec) [ -11471.1532] [ 2792] [depth= 1] . ( 4 sec) [ -11416.1317] [ 2761] [depth= 1] . ( 4 sec) [ -11386.5932] [ 2750] [depth= 1] . ( 4 sec) [ -11381.2303] [ 2748] [depth= 1] . ( 4 sec) [ -11378.9672] [ 2749] [depth= 1] . ( 4 sec) [ -11372.9417] [ 2729] [depth= 1] . ( 4 sec) [ -11359.9880] [ 2731] [depth= 1] . ( 4 sec) [ -11281.7076] [ 2718] [depth= 1] . ( 4 sec) [ -11276.4466] [ 2726] [depth= 1] . ( 5 sec) [ -11271.3991] [ 2713] [depth= 2] . ( 5 sec) [ -11245.3870] [ 2710] [depth= 1] . ( 5 sec) [ -11080.7337] [Branch lengths ] . ( 5 sec) [ -11078.6003] [GTR parameters ] . ( 5 sec) [ -11043.6159] [Alpha ][ 0.866938] . ( 6 sec) [ -11040.5611] [ 2699] [depth= 1] . ( 6 sec) [ -11020.9231] [ 2669] [depth= 1] . ( 6 sec) [ -11018.1885] [ 2667] [depth= 1] . ( 6 sec) [ -10988.3264] [ 2639] [depth= 2] . ( 6 sec) [ -10983.3883] [ 2681] [depth= 1] . ( 6 sec) [ -10960.5660] [ 2639] [depth= 1] . ( 6 sec) [ -10958.9246] [ 2637] [depth= 1] . ( 6 sec) [ -10881.3293] [ 2640] [depth= 1] . ( 6 sec) [ -10876.4439] [ 2638] [depth= 1] . ( 7 sec) [ -10802.5361] [ 2600] [depth= 1] . ( 7 sec) [ -10714.0739] [ 2530] [depth= 7] . ( 7 sec) [ -10655.0089] [ 2506] [depth= 1] . ( 7 sec) [ -10638.9089] [ 2493] [depth= 1] . ( 7 sec) [ -10636.3757] [ 2484] [depth= 1] . ( 7 sec) [ -10635.6850] [ 2487] [depth= 1] . ( 7 sec) [ -10632.4785] [ 2489] [depth= 1] . ( 7 sec) [ -10632.2439] [ 2488] [depth= 1] . ( 8 sec) [ -10631.5662] [ 2489] [depth= 1] . ( 8 sec) [ -10627.5590] [ 2492] [depth= 1] . ( 8 sec) [ -10614.2743] [ 2477] [depth= 1] . ( 8 sec) [ -10612.9220] [ 2478] [depth= 1] . ( 8 sec) [ -10612.6591] [ 2475] [depth= 1] . ( 9 sec) [ -10612.6083] [ 2478] [depth= 1] . ( 9 sec) [ -10612.5753] [ 2474] [depth= 1] . ( 9 sec) [ -10590.8765] [Branch lengths ] . ( 9 sec) [ -10590.5454] [GTR parameters ] . ( 9 sec) [ -10589.2528] [Alpha ][ 0.967909] . ( 10 sec) [ -10588.8942] [ 2474] [depth= 1] . ( 10 sec) [ -10588.6566] [ 2478] [depth= 1] . ( 13 sec) [ -10587.4716] [Branch lengths ] . ( 13 sec) [ -10587.4664] [GTR parameters ] . ( 13 sec) [ -10587.4637] [Alpha ][ 0.972904] . ( 16 sec) [ -10587.4184] [Branch lengths ] . ( 24 sec) [ -10587.0263] [ 2474] [depth= 1] . ( 37 sec) [ -10586.9778] [Branch lengths ] . ( 37 sec) [ -10586.9769] [GTR parameters ] . ( 37 sec) [ -10586.9769] [Alpha ][ 0.972904] . ( 37 sec) [ -10586.9769] [Topology ] . ( 38 sec) [ -10586.7767] [Topology ] . ( 39 sec) [ -10586.5761] [Topology ] . ( 40 sec) [ -10586.5448] [Topology ] . ( 41 sec) [ -10586.5352] [Topology ] . ( 42 sec) [ -10586.5317] [Topology ] . ( 42 sec) [ -10586.5304] [Topology ] . ( 43 sec) [ -10586.5299] [Topology ] . ( 43 sec) [ -10586.5265] [GTR parameters ] . ( 43 sec) [ -10586.5264] [Alpha ][ 0.971645] . ( 44 sec) [ -10586.5264] [Topology ] . ( 44 sec) [ -10586.5261] [Topology ] . ( 44 sec) [ -10586.5261] [GTR parameters ] . ( 45 sec) [ -10586.5261] [Alpha ][ 0.971645] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -10585.2596] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -10585.2591] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.259143. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21828.1190] [GTR parameters ] . ( 0 sec) [ -21455.5874] [Alpha ][ 0.500960] . ( 1 sec) [ -21208.0618] [ 4967] [depth= 8] . ( 1 sec) [ -20973.8173] [ 4884] [depth= 9] . ( 1 sec) [ -20376.1689] [ 4813] [depth= 2] . ( 1 sec) [ -20296.3818] [ 4754] [depth= 1] . ( 1 sec) [ -19993.8517] [ 4664] [depth= 6] . ( 1 sec) [ -19816.1007] [ 4659] [depth= 2] . ( 1 sec) [ -19590.5700] [ 4645] [depth= 4] . ( 1 sec) [ -19386.4177] [ 4592] [depth= 1] . ( 1 sec) [ -19261.1795] [ 4586] [depth= 8] . ( 1 sec) [ -18976.1576] [ 4496] [depth= 1] . ( 1 sec) [ -18869.7525] [ 4491] [depth= 1] . ( 1 sec) [ -18585.9374] [ 4417] [depth= 4] . ( 1 sec) [ -18566.8808] [ 4361] [depth= 2] . ( 1 sec) [ -18504.2949] [ 4359] [depth= 4] . ( 1 sec) [ -18322.7479] [ 4309] [depth= 5] . ( 1 sec) [ -18245.1261] [ 4312] [depth= 6] . ( 1 sec) [ -18027.3072] [ 4287] [depth= 17] . ( 1 sec) [ -17962.7319] [ 4317] [depth= 1] . ( 1 sec) [ -17517.3869] [ 4219] [depth= 2] . ( 1 sec) [ -17164.8546] [ 4089] [depth= 15] . ( 1 sec) [ -17099.5409] [ 4054] [depth= 7] . ( 1 sec) [ -16898.5549] [ 4040] [depth= 1] . ( 2 sec) [ -16780.1920] [ 4025] [depth= 1] . ( 2 sec) [ -16622.2560] [ 3988] [depth= 3] . ( 2 sec) [ -16487.1954] [ 3975] [depth= 7] . ( 2 sec) [ -16315.4208] [ 3920] [depth= 3] . ( 2 sec) [ -16284.9917] [ 3912] [depth= 2] . ( 2 sec) [ -16282.0793] [ 3913] [depth= 1] . ( 2 sec) [ -15955.0140] [ 3786] [depth= 6] . ( 2 sec) [ -15731.6100] [ 3720] [depth= 6] . ( 2 sec) [ -15713.1205] [ 3724] [depth= 1] . ( 2 sec) [ -15599.7942] [ 3660] [depth= 5] . ( 2 sec) [ -15581.6990] [ 3663] [depth= 8] . ( 2 sec) [ -15238.0749] [ 3566] [depth= 10] . ( 2 sec) [ -14953.4352] [ 3519] [depth= 5] . ( 2 sec) [ -14773.4992] [ 3432] [depth= 1] . ( 2 sec) [ -14690.9064] [ 3421] [depth= 4] . ( 2 sec) [ -14578.8334] [ 3416] [depth= 2] . ( 2 sec) [ -14510.7767] [ 3387] [depth= 4] . ( 2 sec) [ -14351.0381] [ 3365] [depth= 3] . ( 2 sec) [ -14269.8840] [ 3358] [depth= 4] . ( 3 sec) [ -14014.1708] [ 3308] [depth= 7] . ( 3 sec) [ -13987.1955] [ 3310] [depth= 1] . ( 3 sec) [ -13977.9529] [ 3307] [depth= 1] . ( 3 sec) [ -13935.6425] [ 3306] [depth= 1] . ( 3 sec) [ -13934.5157] [ 3308] [depth= 1] . ( 3 sec) [ -13933.3320] [ 3307] [depth= 2] . ( 3 sec) [ -13874.6394] [ 3240] [depth= 3] . ( 3 sec) [ -13832.6600] [ 3203] [depth= 5] . ( 3 sec) [ -13582.6139] [ 3188] [depth= 2] . ( 3 sec) [ -13575.6457] [ 3208] [depth= 2] . ( 3 sec) [ -13546.7112] [ 3133] [depth= 2] . ( 3 sec) [ -13272.4792] [ 3061] [depth= 2] . ( 3 sec) [ -13211.9202] [ 3034] [depth= 3] . ( 3 sec) [ -13181.8411] [ 3030] [depth= 2] . ( 3 sec) [ -12953.2503] [ 2970] [depth= 4] . ( 3 sec) [ -12910.0417] [ 2937] [depth= 1] . ( 3 sec) [ -12865.0220] [ 2939] [depth= 1] . ( 3 sec) [ -12800.6393] [ 2911] [depth= 6] . ( 3 sec) [ -12758.8319] [ 2891] [depth= 4] . ( 3 sec) [ -12052.4525] [ 2825] [depth= 5] . ( 3 sec) [ -11981.6695] [ 2828] [depth= 1] . ( 3 sec) [ -11871.3767] [ 2793] [depth= 5] . ( 4 sec) [ -11840.0812] [ 2777] [depth= 1] . ( 4 sec) [ -11804.4143] [ 2736] [depth= 1] . ( 4 sec) [ -11715.1857] [ 2735] [depth= 1] . ( 4 sec) [ -11708.0973] [ 2732] [depth= 1] . ( 4 sec) [ -11691.1145] [ 2713] [depth= 4] . ( 4 sec) [ -11404.1228] [ 2660] [depth= 2] . ( 4 sec) [ -11377.9793] [ 2662] [depth= 1] . ( 4 sec) [ -11301.2731] [ 2621] [depth= 1] . ( 4 sec) [ -11140.4326] [ 2562] [depth= 6] . ( 4 sec) [ -11129.4222] [ 2559] [depth= 1] . ( 4 sec) [ -11097.8676] [ 2536] [depth= 1] . ( 4 sec) [ -11074.8969] [ 2528] [depth= 1] . ( 4 sec) [ -11067.5475] [ 2527] [depth= 1] . ( 4 sec) [ -11058.4981] [ 2531] [depth= 2] . ( 4 sec) [ -11055.0107] [ 2536] [depth= 1] . ( 4 sec) [ -11053.4698] [ 2534] [depth= 1] . ( 5 sec) [ -11036.4673] [ 2491] [depth= 5] . ( 5 sec) [ -11028.2722] [ 2491] [depth= 1] . ( 5 sec) [ -10757.3261] [Branch lengths ] . ( 6 sec) [ -10754.6928] [GTR parameters ] . ( 6 sec) [ -10715.5406] [Alpha ][ 0.928049] . ( 6 sec) [ -10693.9729] [ 2481] [depth= 1] . ( 6 sec) [ -10689.9991] [ 2479] [depth= 1] . ( 6 sec) [ -10687.6487] [ 2476] [depth= 1] . ( 6 sec) [ -10678.7520] [ 2474] [depth= 1] . ( 6 sec) [ -10678.4022] [ 2474] [depth= 1] . ( 6 sec) [ -10678.3743] [ 2472] [depth= 1] . ( 6 sec) [ -10678.2852] [ 2469] [depth= 1] . ( 6 sec) [ -10675.3851] [ 2466] [depth= 1] . ( 7 sec) [ -10673.8933] [ 2468] [depth= 1] . ( 7 sec) [ -10673.0559] [ 2471] [depth= 1] . ( 7 sec) [ -10671.9910] [ 2473] [depth= 1] . ( 7 sec) [ -10670.2503] [ 2475] [depth= 1] . ( 7 sec) [ -10668.6878] [ 2468] [depth= 2] . ( 7 sec) [ -10666.7406] [ 2469] [depth= 1] . ( 7 sec) [ -10655.3831] [ 2473] [depth= 1] . ( 8 sec) [ -10631.1746] [ 2472] [depth= 2] . ( 8 sec) [ -10629.4469] [ 2470] [depth= 1] . ( 8 sec) [ -10629.3730] [ 2476] [depth= 1] . ( 8 sec) [ -10629.0298] [ 2474] [depth= 1] . ( 8 sec) [ -10627.3525] [ 2477] [depth= 1] . ( 8 sec) [ -10618.7919] [ 2468] [depth= 2] . ( 8 sec) [ -10618.6887] [ 2471] [depth= 1] . ( 8 sec) [ -10618.2513] [ 2466] [depth= 1] . ( 8 sec) [ -10617.9135] [ 2465] [depth= 1] . ( 8 sec) [ -10615.7792] [ 2463] [depth= 1] . ( 9 sec) [ -10615.6965] [ 2464] [depth= 1] . ( 9 sec) [ -10614.1994] [ 2463] [depth= 1] . ( 9 sec) [ -10587.6710] [Branch lengths ] . ( 10 sec) [ -10587.5920] [GTR parameters ] . ( 10 sec) [ -10587.3869] [Alpha ][ 0.970565] . ( 11 sec) [ -10587.0600] [ 2467] [depth= 1] . ( 12 sec) [ -10586.9600] [ 2464] [depth= 1] . ( 13 sec) [ -10586.9445] [ 2467] [depth= 1] . ( 13 sec) [ -10585.4478] [Branch lengths ] . ( 13 sec) [ -10585.4438] [GTR parameters ] . ( 13 sec) [ -10585.4434] [Alpha ][ 0.972501] . ( 16 sec) [ -10585.3166] [Branch lengths ] . ( 37 sec) [ -10585.3008] [Branch lengths ] . ( 38 sec) [ -10585.3008] [Topology ] . ( 38 sec) [ -10585.2700] [Topology ] . ( 39 sec) [ -10585.2543] [Topology ] . ( 40 sec) [ -10585.2511] [Topology ] . ( 41 sec) [ -10585.2499] [Topology ] . ( 42 sec) [ -10585.2494] [Topology ] . ( 42 sec) [ -10585.2492] [GTR parameters ] . ( 42 sec) [ -10585.2492] [Alpha ][ 0.972501] . ( 42 sec) [ -10585.2492] [Topology ] . ( 43 sec) [ -10585.2490] [Topology ] . ( 43 sec) [ -10585.2489] [GTR parameters ] . ( 43 sec) [ -10585.2489] [Alpha ][ 0.972501] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.248925. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22611.3267] [GTR parameters ] . ( 1 sec) [ -22145.2029] [Alpha ][ 0.500960] . ( 1 sec) [ -21435.4825] [ 5121] [depth= 6] . ( 1 sec) [ -21098.8072] [ 5041] [depth= 11] . ( 1 sec) [ -20940.4374] [ 4990] [depth= 3] . ( 1 sec) [ -20909.1525] [ 4986] [depth= 6] . ( 1 sec) [ -20366.5363] [ 4908] [depth= 7] . ( 2 sec) [ -20291.1952] [ 4887] [depth= 4] . ( 2 sec) [ -20171.8612] [ 4879] [depth= 1] . ( 2 sec) [ -20045.0006] [ 4808] [depth= 17] . ( 2 sec) [ -19403.1465] [ 4769] [depth= 13] . ( 2 sec) [ -19187.7255] [ 4679] [depth= 15] . ( 2 sec) [ -18996.4843] [ 4679] [depth= 16] . ( 2 sec) [ -18603.9525] [ 4561] [depth= 15] . ( 2 sec) [ -18521.3934] [ 4550] [depth= 1] . ( 2 sec) [ -18434.7036] [ 4544] [depth= 10] . ( 2 sec) [ -18328.8135] [ 4546] [depth= 1] . ( 2 sec) [ -18117.3162] [ 4521] [depth= 8] . ( 2 sec) [ -17979.4506] [ 4468] [depth= 2] . ( 2 sec) [ -17627.5661] [ 4439] [depth= 8] . ( 2 sec) [ -17595.8847] [ 4413] [depth= 13] . ( 2 sec) [ -17400.8167] [ 4414] [depth= 1] . ( 2 sec) [ -17261.3438] [ 4314] [depth= 9] . ( 2 sec) [ -17256.9169] [ 4315] [depth= 1] . ( 2 sec) [ -17199.0574] [ 4281] [depth= 1] . ( 2 sec) [ -17040.9034] [ 4243] [depth= 7] . ( 2 sec) [ -16836.1157] [ 4201] [depth= 7] . ( 2 sec) [ -16123.2986] [ 4028] [depth= 11] . ( 2 sec) [ -16088.9918] [ 4035] [depth= 8] . ( 3 sec) [ -15837.9139] [ 3963] [depth= 7] . ( 3 sec) [ -15502.7059] [ 3884] [depth= 6] . ( 3 sec) [ -15370.6074] [ 3862] [depth= 14] . ( 3 sec) [ -15208.1064] [ 3814] [depth= 8] . ( 3 sec) [ -14815.3126] [ 3607] [depth= 11] . ( 3 sec) [ -14436.9218] [ 3585] [depth= 9] . ( 3 sec) [ -14427.9343] [ 3586] [depth= 1] . ( 3 sec) [ -14228.2267] [ 3495] [depth= 2] . ( 3 sec) [ -14225.1512] [ 3493] [depth= 1] . ( 3 sec) [ -13954.9245] [ 3381] [depth= 3] . ( 3 sec) [ -13940.3801] [ 3387] [depth= 1] . ( 3 sec) [ -13852.1435] [ 3366] [depth= 1] . ( 3 sec) [ -13818.0542] [ 3361] [depth= 1] . ( 3 sec) [ -13790.4282] [ 3350] [depth= 1] . ( 3 sec) [ -13779.8174] [ 3353] [depth= 1] . ( 3 sec) [ -13647.0320] [ 3337] [depth= 6] . ( 3 sec) [ -13482.6695] [ 3314] [depth= 2] . ( 3 sec) [ -13288.7259] [ 3214] [depth= 5] . ( 3 sec) [ -13181.9262] [ 3207] [depth= 1] . ( 4 sec) [ -13177.0453] [ 3209] [depth= 2] . ( 4 sec) [ -13176.5296] [ 3213] [depth= 1] . ( 4 sec) [ -13054.7391] [ 3212] [depth= 3] . ( 4 sec) [ -12897.5243] [ 3146] [depth= 7] . ( 4 sec) [ -12822.6560] [ 3133] [depth= 1] . ( 4 sec) [ -12704.4494] [ 3105] [depth= 3] . ( 4 sec) [ -12411.2555] [ 3070] [depth= 1] . ( 4 sec) [ -12160.7794] [ 2941] [depth= 12] . ( 4 sec) [ -12159.8423] [ 2946] [depth= 1] . ( 4 sec) [ -12053.7639] [ 2913] [depth= 3] . ( 4 sec) [ -12044.6992] [ 2909] [depth= 1] . ( 4 sec) [ -11967.4720] [ 2871] [depth= 4] . ( 4 sec) [ -11965.1632] [ 2873] [depth= 1] . ( 4 sec) [ -11951.9526] [ 2868] [depth= 1] . ( 4 sec) [ -11942.9049] [ 2861] [depth= 3] . ( 4 sec) [ -11875.0358] [ 2792] [depth= 4] . ( 4 sec) [ -11766.6759] [ 2768] [depth= 3] . ( 4 sec) [ -11722.6496] [ 2746] [depth= 1] . ( 4 sec) [ -11715.9184] [ 2746] [depth= 1] . ( 5 sec) [ -11662.3545] [ 2747] [depth= 3] . ( 5 sec) [ -11439.8864] [ 2712] [depth= 4] . ( 5 sec) [ -11436.9814] [ 2708] [depth= 1] . ( 5 sec) [ -11288.9581] [ 2661] [depth= 1] . ( 5 sec) [ -11225.9559] [ 2655] [depth= 1] . ( 5 sec) [ -11222.2024] [ 2659] [depth= 1] . ( 5 sec) [ -11209.2306] [ 2655] [depth= 1] . ( 5 sec) [ -11141.8851] [ 2655] [depth= 2] . ( 5 sec) [ -11053.7501] [ 2605] [depth= 1] . ( 5 sec) [ -11048.2018] [ 2605] [depth= 1] . ( 5 sec) [ -11047.3835] [ 2608] [depth= 1] . ( 6 sec) [ -10882.6353] [Branch lengths ] . ( 6 sec) [ -10879.9915] [GTR parameters ] . ( 7 sec) [ -10846.6448] [Alpha ][ 0.864550] . ( 7 sec) [ -10845.6748] [ 2612] [depth= 1] . ( 7 sec) [ -10845.5001] [ 2608] [depth= 1] . ( 7 sec) [ -10844.3465] [ 2605] [depth= 1] . ( 7 sec) [ -10812.1648] [ 2605] [depth= 4] . ( 7 sec) [ -10809.1642] [ 2583] [depth= 1] . ( 7 sec) [ -10762.1798] [ 2568] [depth= 1] . ( 7 sec) [ -10758.4367] [ 2572] [depth= 1] . ( 7 sec) [ -10710.2680] [ 2513] [depth= 5] . ( 7 sec) [ -10710.1285] [ 2518] [depth= 1] . ( 7 sec) [ -10706.9374] [ 2518] [depth= 1] . ( 7 sec) [ -10684.0148] [ 2497] [depth= 1] . ( 8 sec) [ -10683.0763] [ 2501] [depth= 2] . ( 8 sec) [ -10682.7424] [ 2506] [depth= 1] . ( 8 sec) [ -10681.7537] [ 2510] [depth= 1] . ( 8 sec) [ -10677.0778] [ 2506] [depth= 1] . ( 8 sec) [ -10677.0452] [ 2501] [depth= 1] . ( 8 sec) [ -10673.4730] [ 2501] [depth= 1] . ( 8 sec) [ -10665.0052] [ 2502] [depth= 1] . ( 8 sec) [ -10664.7123] [ 2502] [depth= 1] . ( 9 sec) [ -10631.5625] [ 2477] [depth= 3] . ( 9 sec) [ -10627.3368] [ 2480] [depth= 1] . ( 9 sec) [ -10624.4579] [ 2478] [depth= 1] . ( 9 sec) [ -10611.6272] [ 2476] [depth= 1] . ( 9 sec) [ -10611.3104] [ 2478] [depth= 1] . ( 9 sec) [ -10608.0104] [ 2477] [depth= 1] . ( 9 sec) [ -10607.2901] [ 2476] [depth= 1] . ( 10 sec) [ -10605.9116] [ 2478] [depth= 1] . ( 10 sec) [ -10605.8859] [ 2480] [depth= 1] . ( 10 sec) [ -10593.1325] [Branch lengths ] . ( 11 sec) [ -10593.0330] [GTR parameters ] . ( 11 sec) [ -10591.7867] [Alpha ][ 0.964043] . ( 11 sec) [ -10591.3089] [ 2479] [depth= 1] . ( 11 sec) [ -10591.2931] [ 2478] [depth= 1] . ( 11 sec) [ -10590.5479] [ 2478] [depth= 1] . ( 11 sec) [ -10590.1528] [ 2478] [depth= 1] . ( 12 sec) [ -10588.9125] [ 2481] [depth= 1] . ( 14 sec) [ -10587.4224] [Branch lengths ] . ( 14 sec) [ -10587.4133] [GTR parameters ] . ( 14 sec) [ -10587.4070] [Alpha ][ 0.971674] . ( 18 sec) [ -10587.2662] [Branch lengths ] . ( 21 sec) [ -10587.0778] [ 2474] [depth= 1] . ( 31 sec) [ -10587.0186] [ 2470] [depth= 1] . ( 36 sec) [ -10586.8597] [ 2466] [depth= 1] . ( 39 sec) [ -10586.5648] [Branch lengths ] . ( 39 sec) [ -10586.5635] [GTR parameters ] . ( 39 sec) [ -10586.5635] [Alpha ][ 0.971674] . ( 39 sec) [ -10586.5635] [Topology ] . ( 40 sec) [ -10586.5367] [Topology ] . ( 41 sec) [ -10586.5300] [Topology ] . ( 41 sec) [ -10586.5277] [Topology ] . ( 42 sec) [ -10586.5268] [Topology ] . ( 42 sec) [ -10586.5267] [GTR parameters ] . ( 42 sec) [ -10586.5267] [Alpha ][ 0.971674] . ( 42 sec) [ -10586.5267] [Topology ] . ( 43 sec) [ -10586.5263] [Topology ] . ( 43 sec) [ -10586.5263] [GTR parameters ] . ( 43 sec) [ -10586.5263] [Alpha ][ 0.971674] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -10585.2603] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10585.260317. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10669.048113 . ( 1 sec) [ -10666.4815] [GTR parameters ] . ( 1 sec) [ -10666.1551] [Alpha ][ 0.942575] . ( 1 sec) [ -10666.1551] [Topology ] . ( 1 sec) [ -10601.6847] [Topology ] . ( 2 sec) [ -10591.0335] [Topology ] . ( 3 sec) [ -10588.0682] [Topology ] . ( 4 sec) [ -10586.8013] [Topology ] . ( 5 sec) [ -10586.1775] [Topology ] . ( 6 sec) [ -10585.8506] [Topology ] . ( 6 sec) [ -10585.6740] [Topology ] . ( 7 sec) [ -10585.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.576851 . ( 14 sec) [ -10585.4824] [GTR parameters ] . ( 14 sec) [ -10585.3893] [Alpha ][ 0.970827] . ( 14 sec) [ -10585.3893] [Topology ] . ( 15 sec) [ -10585.3253] [Topology ] . ( 16 sec) [ -10585.2917] [Topology ] . ( 17 sec) [ -10585.2731] [Topology ] . ( 17 sec) [ -10585.2627] [Topology ] . ( 18 sec) [ -10585.2568] [Topology ] . ( 19 sec) [ -10585.2535] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.253512 . ( 25 sec) [ -10585.2534] [GTR parameters ] . ( 26 sec) [ -10585.2530] [Alpha ][ 0.972592] . ( 26 sec) [ -10585.2530] [Topology ] . ( 26 sec) [ -10585.2511] [Topology ] . ( 27 sec) [ -10585.2501] [Topology ] . ( 28 sec) [ -10585.2495] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10585.249466 . ( 34 sec) [ -10585.2495] [GTR parameters ] . ( 35 sec) [ -10585.2495] [Alpha ][ 0.972592] . ( 35 sec) [ -10585.2495] [Topology ] . ( 35 sec) [ -10585.2491] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -10666.4815] [GTR parameters ] . ( 49 sec) [ -10666.1551] [Alpha ][ 0.942575] . ( 49 sec) [ -10666.0635] [ 2475] [depth= 1] . ( 49 sec) [ -10663.6758] [ 2475] [depth= 1] . ( 50 sec) [ -10663.2245] [ 2475] [depth= 1] . ( 50 sec) [ -10660.6480] [ 2476] [depth= 1] . ( 50 sec) [ -10660.5665] [ 2479] [depth= 1] . ( 50 sec) [ -10659.2284] [ 2473] [depth= 1] . ( 50 sec) [ -10652.4409] [ 2471] [depth= 1] . ( 50 sec) [ -10651.1805] [ 2470] [depth= 1] . ( 50 sec) [ -10649.2389] [ 2471] [depth= 1] . ( 50 sec) [ -10647.9733] [ 2472] [depth= 1] . ( 50 sec) [ -10644.8117] [ 2471] [depth= 1] . ( 50 sec) [ -10643.6844] [ 2473] [depth= 1] . ( 50 sec) [ -10640.8768] [ 2474] [depth= 1] . ( 51 sec) [ -10640.3771] [ 2473] [depth= 1] . ( 51 sec) [ -10632.6432] [ 2475] [depth= 1] . ( 51 sec) [ -10627.7592] [ 2473] [depth= 1] . ( 51 sec) [ -10622.9803] [ 2470] [depth= 1] . ( 52 sec) [ -10591.0249] [Branch lengths ] . ( 52 sec) [ -10590.9426] [GTR parameters ] . ( 52 sec) [ -10590.8769] [Alpha ][ 0.966371] . ( 53 sec) [ -10589.6656] [ 2471] [depth= 1] . ( 54 sec) [ -10589.6458] [ 2476] [depth= 1] . ( 54 sec) [ -10589.2784] [ 2477] [depth= 1] . ( 56 sec) [ -10587.1672] [Branch lengths ] . ( 56 sec) [ -10587.1644] [GTR parameters ] . ( 56 sec) [ -10587.1612] [Alpha ][ 0.971819] . ( 59 sec) [ -10586.8564] [Branch lengths ] . ( 80 sec) [ -10586.7962] [Branch lengths ] . ( 80 sec) [ -10586.7962] [Topology ] . ( 81 sec) [ -10586.6851] [Topology ] . ( 82 sec) [ -10586.5647] [Topology ] . ( 83 sec) [ -10586.5423] [Topology ] . ( 84 sec) [ -10586.5337] [Topology ] . ( 84 sec) [ -10586.5301] [Topology ] . ( 85 sec) [ -10586.5286] [Topology ] . ( 86 sec) [ -10586.5279] [Topology ] . ( 86 sec) [ -10586.5265] [GTR parameters ] . ( 86 sec) [ -10586.5265] [Alpha ][ 0.971819] . ( 86 sec) [ -10586.5265] [Topology ] . ( 87 sec) [ -10586.5262] [Topology ] . ( 87 sec) [ -10586.5262] [GTR parameters ] . ( 87 sec) [ -10586.5262] [Alpha ][ 0.971819] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -10585.2593] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10585.249115 . Log likelihood obtained after SPR moves : -10585.259349 . Log likelihood of the current tree: -10585.249115. . Printing the most likely tree in file 'data61.phy_phyml_tree.txt'... . Best log likelihood : -10585.248925 . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo