.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data69.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... . 454 patterns found. (out of a total of 500 sites) . 46 sites without polymorphism (9.20%). . [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) [ -20850.8129] [GTR parameters ] . ( 1 sec) [ -20518.0760] [Alpha ][ 0.500960] . ( 1 sec) [ -20148.7040] [ 4658] [depth= 8] . ( 1 sec) [ -19420.2563] [ 4657] [depth= 6] . ( 1 sec) [ -19213.3324] [ 4622] [depth= 4] . ( 1 sec) [ -19207.6602] [ 4610] [depth= 6] . ( 2 sec) [ -19152.6785] [ 4580] [depth= 1] . ( 2 sec) [ -19036.0049] [ 4570] [depth= 3] . ( 2 sec) [ -18991.5498] [ 4537] [depth= 4] . ( 2 sec) [ -18937.9934] [ 4539] [depth= 1] . ( 2 sec) [ -18909.7311] [ 4543] [depth= 1] . ( 2 sec) [ -18869.7960] [ 4518] [depth= 5] . ( 2 sec) [ -17933.0842] [ 4439] [depth= 9] . ( 2 sec) [ -17536.5396] [ 4316] [depth= 10] . ( 2 sec) [ -17118.3730] [ 4262] [depth= 5] . ( 2 sec) [ -17112.3719] [ 4252] [depth= 1] . ( 2 sec) [ -16910.9733] [ 4249] [depth= 1] . ( 2 sec) [ -16788.5325] [ 4213] [depth= 4] . ( 2 sec) [ -16727.0674] [ 4204] [depth= 3] . ( 2 sec) [ -16638.4843] [ 4187] [depth= 6] . ( 2 sec) [ -16580.6224] [ 4184] [depth= 1] . ( 2 sec) [ -16524.4018] [ 4173] [depth= 1] . ( 2 sec) [ -16367.7733] [ 4142] [depth= 4] . ( 2 sec) [ -16259.0612] [ 4091] [depth= 7] . ( 2 sec) [ -15989.2609] [ 4018] [depth= 8] . ( 2 sec) [ -15940.4634] [ 3999] [depth= 1] . ( 2 sec) [ -15801.3419] [ 3964] [depth= 1] . ( 2 sec) [ -15577.4131] [ 3879] [depth= 1] . ( 3 sec) [ -15366.2650] [ 3832] [depth= 4] . ( 3 sec) [ -15055.9523] [ 3739] [depth= 8] . ( 3 sec) [ -14811.0402] [ 3692] [depth= 10] . ( 3 sec) [ -14584.5588] [ 3628] [depth= 10] . ( 3 sec) [ -14480.7218] [ 3626] [depth= 1] . ( 3 sec) [ -14462.3960] [ 3608] [depth= 1] . ( 3 sec) [ -14356.6439] [ 3586] [depth= 4] . ( 3 sec) [ -14248.3274] [ 3565] [depth= 1] . ( 3 sec) [ -14162.4590] [ 3504] [depth= 4] . ( 3 sec) [ -14136.8303] [ 3497] [depth= 3] . ( 3 sec) [ -14105.9540] [ 3467] [depth= 1] . ( 3 sec) [ -14017.2570] [ 3441] [depth= 3] . ( 3 sec) [ -13994.4006] [ 3436] [depth= 3] . ( 3 sec) [ -13934.3185] [ 3426] [depth= 2] . ( 3 sec) [ -13886.7968] [ 3420] [depth= 4] . ( 3 sec) [ -13570.9514] [ 3315] [depth= 12] . ( 3 sec) [ -13436.1914] [ 3282] [depth= 1] . ( 4 sec) [ -13341.8855] [ 3236] [depth= 2] . ( 4 sec) [ -13310.3444] [ 3229] [depth= 1] . ( 4 sec) [ -13300.7716] [ 3226] [depth= 2] . ( 4 sec) [ -13255.6078] [ 3223] [depth= 2] . ( 4 sec) [ -13023.2462] [ 3166] [depth= 1] . ( 4 sec) [ -12614.7488] [ 3003] [depth= 5] . ( 4 sec) [ -12581.9311] [ 2992] [depth= 1] . ( 4 sec) [ -12549.8219] [ 2988] [depth= 9] . ( 4 sec) [ -12542.1020] [ 2982] [depth= 1] . ( 4 sec) [ -12308.0684] [ 2931] [depth= 7] . ( 4 sec) [ -12307.8339] [ 2941] [depth= 1] . ( 4 sec) [ -12277.5179] [ 2929] [depth= 1] . ( 4 sec) [ -12263.8547] [ 2928] [depth= 1] . ( 4 sec) [ -12165.3595] [ 2921] [depth= 1] . ( 4 sec) [ -12134.3016] [ 2920] [depth= 1] . ( 4 sec) [ -12133.6387] [ 2921] [depth= 1] . ( 4 sec) [ -12010.1559] [ 2870] [depth= 10] . ( 4 sec) [ -12007.1050] [ 2870] [depth= 1] . ( 5 sec) [ -11874.3695] [ 2847] [depth= 1] . ( 5 sec) [ -11822.1319] [ 2800] [depth= 5] . ( 5 sec) [ -11819.3498] [ 2790] [depth= 3] . ( 5 sec) [ -11809.0068] [ 2791] [depth= 1] . ( 5 sec) [ -11786.9703] [ 2775] [depth= 1] . ( 5 sec) [ -11704.2839] [ 2779] [depth= 3] . ( 5 sec) [ -11679.0102] [ 2758] [depth= 7] . ( 5 sec) [ -11672.2985] [ 2758] [depth= 1] . ( 5 sec) [ -11589.0306] [ 2735] [depth= 1] . ( 5 sec) [ -11587.5420] [ 2735] [depth= 1] . ( 5 sec) [ -11578.2224] [ 2733] [depth= 1] . ( 5 sec) [ -11501.5822] [ 2728] [depth= 1] . ( 5 sec) [ -11493.0222] [ 2725] [depth= 2] . ( 6 sec) [ -11233.0397] [Branch lengths ] . ( 6 sec) [ -11231.6223] [GTR parameters ] . ( 6 sec) [ -11193.1998] [Alpha ][ 0.906552] . ( 7 sec) [ -11192.6602] [ 2715] [depth= 1] . ( 7 sec) [ -11184.5528] [ 2698] [depth= 1] . ( 7 sec) [ -11183.1555] [ 2700] [depth= 1] . ( 7 sec) [ -11181.3754] [ 2701] [depth= 1] . ( 7 sec) [ -11174.2553] [ 2693] [depth= 1] . ( 7 sec) [ -11148.7404] [ 2672] [depth= 2] . ( 7 sec) [ -11142.2014] [ 2672] [depth= 1] . ( 7 sec) [ -11137.0071] [ 2672] [depth= 1] . ( 7 sec) [ -11135.4733] [ 2670] [depth= 1] . ( 7 sec) [ -11070.5075] [ 2646] [depth= 1] . ( 8 sec) [ -11066.4067] [ 2646] [depth= 1] . ( 8 sec) [ -11066.2346] [ 2645] [depth= 1] . ( 8 sec) [ -11062.2764] [ 2649] [depth= 1] . ( 9 sec) [ -11062.2105] [ 2649] [depth= 1] . ( 9 sec) [ -11062.0920] [ 2654] [depth= 1] . ( 9 sec) [ -11061.6215] [ 2651] [depth= 1] . ( 9 sec) [ -11061.0114] [ 2654] [depth= 1] . ( 10 sec) [ -11041.8305] [Branch lengths ] . ( 11 sec) [ -11041.6437] [GTR parameters ] . ( 11 sec) [ -11041.2469] [Alpha ][ 0.961771] . ( 15 sec) [ -11040.0735] [Branch lengths ] . ( 39 sec) [ -11039.9286] [Branch lengths ] . ( 39 sec) [ -11039.9286] [Topology ] . ( 40 sec) [ -11039.9095] [Topology ] . ( 41 sec) [ -11039.9012] [Topology ] . ( 41 sec) [ -11039.8966] [Topology ] . ( 42 sec) [ -11039.8939] [Topology ] . ( 43 sec) [ -11039.8923] [Topology ] . ( 44 sec) [ -11039.8914] [Topology ] . ( 44 sec) [ -11039.8912] [GTR parameters ] . ( 44 sec) [ -11039.8857] [Alpha ][ 0.968511] . ( 44 sec) [ -11039.8857] [Topology ] . ( 45 sec) [ -11039.8846] [Topology ] . ( 46 sec) [ -11039.8842] [Topology ] . ( 46 sec) [ -11039.8842] [GTR parameters ] . ( 46 sec) [ -11039.8842] [Alpha ][ 0.968511] . ( 46 sec) [ -11039.8842] [Topology ] . ( 47 sec) [ -11039.8839] [Topology ] . ( 47 sec) [ -11039.8839] [GTR parameters ] . ( 47 sec) [ -11039.8839] [Alpha ][ 0.968511] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -11039.5140] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11039.514014. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21579.2199] [GTR parameters ] . ( 1 sec) [ -21279.8175] [Alpha ][ 0.500960] . ( 1 sec) [ -20816.0833] [ 4723] [depth= 3] . ( 1 sec) [ -20337.4500] [ 4618] [depth= 10] . ( 2 sec) [ -20228.3345] [ 4608] [depth= 4] . ( 2 sec) [ -20020.8206] [ 4583] [depth= 4] . ( 2 sec) [ -19989.9275] [ 4557] [depth= 1] . ( 2 sec) [ -19945.0233] [ 4545] [depth= 5] . ( 2 sec) [ -19862.1293] [ 4536] [depth= 1] . ( 2 sec) [ -19685.8586] [ 4510] [depth= 4] . ( 2 sec) [ -19461.0948] [ 4418] [depth= 2] . ( 2 sec) [ -19348.0370] [ 4407] [depth= 2] . ( 2 sec) [ -19103.2706] [ 4373] [depth= 4] . ( 2 sec) [ -18962.9856] [ 4362] [depth= 3] . ( 2 sec) [ -18758.0761] [ 4309] [depth= 1] . ( 2 sec) [ -18482.3256] [ 4288] [depth= 5] . ( 2 sec) [ -18349.7472] [ 4251] [depth= 3] . ( 2 sec) [ -18024.4919] [ 4121] [depth= 10] . ( 2 sec) [ -17267.5236] [ 4109] [depth= 5] . ( 2 sec) [ -17078.1278] [ 4097] [depth= 2] . ( 2 sec) [ -16962.6873] [ 4083] [depth= 1] . ( 2 sec) [ -16853.3309] [ 4068] [depth= 1] . ( 2 sec) [ -16817.4559] [ 4046] [depth= 1] . ( 2 sec) [ -16771.9310] [ 4039] [depth= 1] . ( 2 sec) [ -16507.3497] [ 3968] [depth= 1] . ( 2 sec) [ -16249.3698] [ 3840] [depth= 4] . ( 3 sec) [ -15859.2695] [ 3769] [depth= 1] . ( 3 sec) [ -15698.8708] [ 3722] [depth= 2] . ( 3 sec) [ -15636.0314] [ 3693] [depth= 1] . ( 3 sec) [ -15503.0058] [ 3700] [depth= 1] . ( 3 sec) [ -15316.7756] [ 3648] [depth= 7] . ( 3 sec) [ -15028.9964] [ 3617] [depth= 6] . ( 3 sec) [ -15003.1250] [ 3611] [depth= 1] . ( 3 sec) [ -14855.0345] [ 3532] [depth= 1] . ( 3 sec) [ -14685.8525] [ 3531] [depth= 4] . ( 3 sec) [ -14651.8621] [ 3530] [depth= 1] . ( 3 sec) [ -14354.8574] [ 3477] [depth= 4] . ( 3 sec) [ -14211.5381] [ 3472] [depth= 3] . ( 3 sec) [ -14115.8497] [ 3464] [depth= 2] . ( 3 sec) [ -14080.6873] [ 3428] [depth= 3] . ( 3 sec) [ -14047.1848] [ 3428] [depth= 1] . ( 3 sec) [ -13977.9647] [ 3403] [depth= 12] . ( 3 sec) [ -13767.3934] [ 3379] [depth= 9] . ( 3 sec) [ -13575.2042] [ 3260] [depth= 13] . ( 3 sec) [ -13403.7040] [ 3175] [depth= 8] . ( 4 sec) [ -13380.9282] [ 3165] [depth= 7] . ( 4 sec) [ -13363.7614] [ 3145] [depth= 2] . ( 4 sec) [ -13303.8947] [ 3129] [depth= 5] . ( 4 sec) [ -13164.2036] [ 3081] [depth= 5] . ( 4 sec) [ -12901.7910] [ 2999] [depth= 2] . ( 4 sec) [ -12722.8576] [ 2991] [depth= 1] . ( 4 sec) [ -12656.8051] [ 2986] [depth= 2] . ( 4 sec) [ -12521.0129] [ 2960] [depth= 1] . ( 4 sec) [ -12472.3040] [ 2951] [depth= 11] . ( 4 sec) [ -12442.2382] [ 2951] [depth= 4] . ( 4 sec) [ -12420.4015] [ 2941] [depth= 1] . ( 4 sec) [ -12419.0785] [ 2937] [depth= 1] . ( 4 sec) [ -12407.5870] [ 2972] [depth= 1] . ( 4 sec) [ -12392.8609] [ 2975] [depth= 3] . ( 4 sec) [ -12342.9126] [ 2954] [depth= 2] . ( 4 sec) [ -12286.8373] [ 2929] [depth= 1] . ( 4 sec) [ -12281.5609] [ 2927] [depth= 7] . ( 4 sec) [ -12108.3605] [ 2871] [depth= 6] . ( 4 sec) [ -12088.6361] [ 2861] [depth= 2] . ( 5 sec) [ -12066.6583] [ 2862] [depth= 1] . ( 5 sec) [ -11954.7921] [ 2857] [depth= 2] . ( 5 sec) [ -11915.8571] [ 2839] [depth= 1] . ( 5 sec) [ -11869.2934] [ 2810] [depth= 2] . ( 5 sec) [ -11776.5561] [ 2736] [depth= 4] . ( 5 sec) [ -11753.8618] [ 2721] [depth= 1] . ( 5 sec) [ -11670.9470] [ 2715] [depth= 2] . ( 5 sec) [ -11595.3451] [ 2717] [depth= 1] . ( 5 sec) [ -11550.4918] [ 2724] [depth= 3] . ( 5 sec) [ -11497.3370] [ 2699] [depth= 1] . ( 5 sec) [ -11428.9851] [ 2697] [depth= 1] . ( 5 sec) [ -11428.4758] [ 2696] [depth= 1] . ( 5 sec) [ -11411.5000] [ 2696] [depth= 1] . ( 5 sec) [ -11411.4384] [ 2690] [depth= 2] . ( 5 sec) [ -11380.9862] [ 2693] [depth= 1] . ( 5 sec) [ -11360.7958] [ 2696] [depth= 1] . ( 5 sec) [ -11354.8493] [ 2689] [depth= 1] . ( 5 sec) [ -11341.2465] [ 2684] [depth= 2] . ( 6 sec) [ -11339.4391] [ 2682] [depth= 1] . ( 6 sec) [ -11330.0849] [ 2677] [depth= 1] . ( 6 sec) [ -11270.1286] [ 2661] [depth= 1] . ( 6 sec) [ -11135.4459] [Branch lengths ] . ( 6 sec) [ -11134.0066] [GTR parameters ] . ( 6 sec) [ -11097.7430] [Alpha ][ 0.890650] . ( 6 sec) [ -11097.4459] [ 2666] [depth= 1] . ( 7 sec) [ -11095.9073] [ 2665] [depth= 1] . ( 7 sec) [ -11095.4554] [ 2666] [depth= 1] . ( 7 sec) [ -11094.5991] [ 2660] [depth= 1] . ( 7 sec) [ -11093.7339] [ 2650] [depth= 4] . ( 8 sec) [ -11082.7381] [ 2649] [depth= 2] . ( 8 sec) [ -11081.3684] [ 2648] [depth= 1] . ( 8 sec) [ -11072.6258] [ 2642] [depth= 1] . ( 8 sec) [ -11071.7458] [ 2641] [depth= 1] . ( 8 sec) [ -11070.5008] [ 2638] [depth= 1] . ( 8 sec) [ -11070.3998] [ 2642] [depth= 1] . ( 9 sec) [ -11070.2406] [ 2644] [depth= 1] . ( 9 sec) [ -11069.7550] [ 2642] [depth= 1] . ( 9 sec) [ -11067.6714] [ 2648] [depth= 1] . ( 9 sec) [ -11067.3840] [ 2645] [depth= 1] . ( 10 sec) [ -11065.7899] [ 2646] [depth= 1] . ( 10 sec) [ -11052.1912] [Branch lengths ] . ( 10 sec) [ -11051.9879] [GTR parameters ] . ( 10 sec) [ -11051.4391] [Alpha ][ 0.955278] . ( 10 sec) [ -11051.2565] [ 2648] [depth= 1] . ( 11 sec) [ -11051.0733] [ 2646] [depth= 1] . ( 11 sec) [ -11049.3723] [ 2650] [depth= 1] . ( 11 sec) [ -11047.3227] [ 2647] [depth= 1] . ( 12 sec) [ -11047.2985] [ 2651] [depth= 1] . ( 13 sec) [ -11045.1921] [ 2653] [depth= 2] . ( 14 sec) [ -11044.5598] [ 2655] [depth= 1] . ( 14 sec) [ -11044.4336] [ 2654] [depth= 1] . ( 14 sec) [ -11040.9136] [Branch lengths ] . ( 15 sec) [ -11040.8945] [GTR parameters ] . ( 15 sec) [ -11040.8747] [Alpha ][ 0.968145] . ( 19 sec) [ -11040.3770] [Branch lengths ] . ( 39 sec) [ -11040.3226] [ 2653] [depth= 2] . ( 43 sec) [ -11039.8682] [Branch lengths ] . ( 43 sec) [ -11039.8477] [GTR parameters ] . ( 43 sec) [ -11039.8477] [Alpha ][ 0.968145] . ( 43 sec) [ -11039.8477] [Topology ] . ( 44 sec) [ -11039.7112] [Topology ] . ( 45 sec) [ -11039.6463] [Topology ] . ( 46 sec) [ -11039.6092] [Topology ] . ( 47 sec) [ -11039.5859] [Topology ] . ( 47 sec) [ -11039.5712] [Topology ] . ( 48 sec) [ -11039.5618] [Topology ] . ( 48 sec) [ -11039.5617] [GTR parameters ] . ( 48 sec) [ -11039.5614] [Alpha ][ 0.969656] . ( 49 sec) [ -11039.5614] [Topology ] . ( 49 sec) [ -11039.5553] [Topology ] . ( 50 sec) [ -11039.5514] [Topology ] . ( 51 sec) [ -11039.5490] [Topology ] . ( 52 sec) [ -11039.5474] [Topology ] . ( 53 sec) [ -11039.5464] [Topology ] . ( 54 sec) [ -11039.5457] [Topology ] . ( 54 sec) [ -11039.5457] [GTR parameters ] . ( 54 sec) [ -11039.5457] [Alpha ][ 0.969656] . ( 54 sec) [ -11039.5457] [Topology ] . ( 55 sec) [ -11039.5453] [Topology ] . ( 55 sec) [ -11039.5453] [GTR parameters ] . ( 55 sec) [ -11039.5453] [Alpha ][ 0.969656] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -11039.5366] [Topology ] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -11039.5357] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11039.535702. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20173.0671] [GTR parameters ] . ( 1 sec) [ -19866.3689] [Alpha ][ 0.500960] . ( 1 sec) [ -19260.8634] [ 4809] [depth= 8] . ( 1 sec) [ -18843.6513] [ 4695] [depth= 8] . ( 1 sec) [ -18780.9074] [ 4690] [depth= 4] . ( 1 sec) [ -18680.8911] [ 4679] [depth= 1] . ( 1 sec) [ -18631.8249] [ 4602] [depth= 9] . ( 1 sec) [ -18594.6390] [ 4600] [depth= 1] . ( 1 sec) [ -18578.9138] [ 4630] [depth= 8] . ( 1 sec) [ -18478.5794] [ 4610] [depth= 2] . ( 1 sec) [ -18085.9632] [ 4520] [depth= 1] . ( 1 sec) [ -17946.4636] [ 4473] [depth= 12] . ( 1 sec) [ -17667.7591] [ 4420] [depth= 15] . ( 1 sec) [ -17601.1348] [ 4411] [depth= 6] . ( 1 sec) [ -17467.4467] [ 4395] [depth= 2] . ( 1 sec) [ -17396.3359] [ 4393] [depth= 1] . ( 1 sec) [ -17198.7940] [ 4378] [depth= 10] . ( 1 sec) [ -17148.0008] [ 4341] [depth= 2] . ( 2 sec) [ -17094.7827] [ 4326] [depth= 5] . ( 2 sec) [ -16950.1270] [ 4291] [depth= 7] . ( 2 sec) [ -16820.1535] [ 4277] [depth= 3] . ( 2 sec) [ -16689.5011] [ 4257] [depth= 9] . ( 2 sec) [ -16564.1218] [ 4165] [depth= 9] . ( 2 sec) [ -16416.6441] [ 4163] [depth= 1] . ( 2 sec) [ -16411.7585] [ 4161] [depth= 1] . ( 2 sec) [ -16156.2376] [ 4066] [depth= 9] . ( 2 sec) [ -15925.5420] [ 4000] [depth= 1] . ( 2 sec) [ -15807.1538] [ 3926] [depth= 10] . ( 2 sec) [ -15726.7917] [ 3915] [depth= 5] . ( 2 sec) [ -15533.0329] [ 3869] [depth= 1] . ( 2 sec) [ -15480.6938] [ 3858] [depth= 7] . ( 2 sec) [ -15463.2754] [ 3876] [depth= 9] . ( 2 sec) [ -15429.5406] [ 3854] [depth= 1] . ( 2 sec) [ -15428.4680] [ 3844] [depth= 1] . ( 2 sec) [ -15143.6313] [ 3793] [depth= 3] . ( 2 sec) [ -15090.0357] [ 3796] [depth= 1] . ( 2 sec) [ -14854.0664] [ 3780] [depth= 5] . ( 2 sec) [ -14848.5623] [ 3820] [depth= 1] . ( 3 sec) [ -14776.7071] [ 3804] [depth= 6] . ( 3 sec) [ -14690.7183] [ 3756] [depth= 10] . ( 3 sec) [ -14666.4796] [ 3757] [depth= 1] . ( 3 sec) [ -14465.2884] [ 3644] [depth= 5] . ( 3 sec) [ -14443.7375] [ 3656] [depth= 1] . ( 3 sec) [ -14357.4520] [ 3596] [depth= 3] . ( 3 sec) [ -14336.5701] [ 3582] [depth= 7] . ( 3 sec) [ -14252.7287] [ 3561] [depth= 5] . ( 3 sec) [ -14075.4535] [ 3402] [depth= 10] . ( 3 sec) [ -13835.3765] [ 3339] [depth= 5] . ( 3 sec) [ -13686.0755] [ 3322] [depth= 2] . ( 3 sec) [ -13671.2294] [ 3317] [depth= 3] . ( 3 sec) [ -13306.0558] [ 3293] [depth= 4] . ( 3 sec) [ -13242.8613] [ 3278] [depth= 2] . ( 3 sec) [ -13229.0505] [ 3287] [depth= 8] . ( 3 sec) [ -13218.8652] [ 3281] [depth= 2] . ( 3 sec) [ -13125.0188] [ 3256] [depth= 5] . ( 3 sec) [ -13011.1082] [ 3214] [depth= 1] . ( 3 sec) [ -12675.4713] [ 3139] [depth= 3] . ( 4 sec) [ -12486.3917] [ 3020] [depth= 5] . ( 4 sec) [ -12388.6327] [ 2991] [depth= 3] . ( 4 sec) [ -12311.8983] [ 2967] [depth= 1] . ( 4 sec) [ -12311.0914] [ 2961] [depth= 2] . ( 4 sec) [ -12280.3950] [ 2973] [depth= 1] . ( 4 sec) [ -12259.2480] [ 2957] [depth= 3] . ( 4 sec) [ -12058.3143] [ 2899] [depth= 5] . ( 4 sec) [ -12051.2869] [ 2915] [depth= 1] . ( 4 sec) [ -12045.2283] [ 2909] [depth= 4] . ( 4 sec) [ -12028.5787] [ 2894] [depth= 1] . ( 4 sec) [ -12022.1384] [ 2883] [depth= 1] . ( 4 sec) [ -12010.0488] [ 2882] [depth= 1] . ( 4 sec) [ -11975.0553] [ 2880] [depth= 2] . ( 4 sec) [ -11853.0463] [ 2871] [depth= 3] . ( 4 sec) [ -11794.8423] [ 2853] [depth= 2] . ( 4 sec) [ -11712.6742] [ 2823] [depth= 2] . ( 4 sec) [ -11681.1254] [ 2804] [depth= 1] . ( 4 sec) [ -11585.6423] [ 2765] [depth= 6] . ( 5 sec) [ -11500.6286] [ 2809] [depth= 1] . ( 5 sec) [ -11488.2681] [ 2819] [depth= 6] . ( 5 sec) [ -11487.1312] [ 2821] [depth= 1] . ( 5 sec) [ -11470.0526] [ 2802] [depth= 1] . ( 5 sec) [ -11440.0532] [ 2794] [depth= 2] . ( 5 sec) [ -11433.1319] [ 2796] [depth= 1] . ( 5 sec) [ -11316.8485] [Branch lengths ] . ( 6 sec) [ -11315.9721] [GTR parameters ] . ( 6 sec) [ -11284.8278] [Alpha ][ 0.843516] . ( 6 sec) [ -11284.7947] [ 2798] [depth= 1] . ( 6 sec) [ -11282.7330] [ 2794] [depth= 2] . ( 6 sec) [ -11282.7171] [ 2791] [depth= 1] . ( 6 sec) [ -11282.0779] [ 2788] [depth= 1] . ( 6 sec) [ -11268.3581] [ 2788] [depth= 6] . ( 7 sec) [ -11263.8080] [ 2783] [depth= 1] . ( 7 sec) [ -11245.2788] [ 2751] [depth= 6] . ( 7 sec) [ -11215.7832] [ 2702] [depth= 2] . ( 7 sec) [ -11210.2730] [ 2691] [depth= 4] . ( 7 sec) [ -11181.3635] [ 2677] [depth= 5] . ( 7 sec) [ -11181.0359] [ 2674] [depth= 1] . ( 8 sec) [ -11180.6061] [ 2674] [depth= 1] . ( 8 sec) [ -11180.5565] [ 2677] [depth= 1] . ( 8 sec) [ -11163.9320] [ 2674] [depth= 3] . ( 8 sec) [ -11163.1348] [ 2673] [depth= 2] . ( 8 sec) [ -11155.4892] [ 2671] [depth= 1] . ( 8 sec) [ -11154.7267] [ 2672] [depth= 2] . ( 8 sec) [ -11103.7701] [ 2646] [depth= 1] . ( 8 sec) [ -11090.9196] [ 2638] [depth= 3] . ( 8 sec) [ -11088.1620] [ 2638] [depth= 1] . ( 9 sec) [ -11076.6453] [ 2642] [depth= 1] . ( 9 sec) [ -11076.3014] [ 2642] [depth= 1] . ( 9 sec) [ -11050.0666] [Branch lengths ] . ( 10 sec) [ -11049.5717] [GTR parameters ] . ( 10 sec) [ -11048.0689] [Alpha ][ 0.947653] . ( 11 sec) [ -11047.4682] [ 2638] [depth= 1] . ( 11 sec) [ -11047.3530] [ 2642] [depth= 1] . ( 13 sec) [ -11047.2964] [ 2642] [depth= 1] . ( 14 sec) [ -11043.1426] [Branch lengths ] . ( 14 sec) [ -11043.1399] [GTR parameters ] . ( 14 sec) [ -11043.1129] [Alpha ][ 0.962614] . ( 15 sec) [ -11042.6358] [ 2640] [depth= 1] . ( 17 sec) [ -11042.4715] [ 2648] [depth= 1] . ( 18 sec) [ -11040.8318] [Branch lengths ] . ( 18 sec) [ -11040.8269] [GTR parameters ] . ( 18 sec) [ -11040.8234] [Alpha ][ 0.967941] . ( 19 sec) [ -11040.5628] [ 2649] [depth= 2] . ( 22 sec) [ -11039.9072] [Branch lengths ] . ( 22 sec) [ -11039.8827] [GTR parameters ] . ( 22 sec) [ -11039.8827] [Alpha ][ 0.967941] . ( 46 sec) [ -11039.6786] [Branch lengths ] . ( 46 sec) [ -11039.6786] [Topology ] . ( 47 sec) [ -11039.6047] [Topology ] . ( 48 sec) [ -11039.5682] [Topology ] . ( 49 sec) [ -11039.5472] [Topology ] . ( 49 sec) [ -11039.5342] [Topology ] . ( 50 sec) [ -11039.5260] [Topology ] . ( 51 sec) [ -11039.5209] [Topology ] . ( 51 sec) [ -11039.5207] [GTR parameters ] . ( 51 sec) [ -11039.5201] [Alpha ][ 0.969962] . ( 51 sec) [ -11039.5201] [Topology ] . ( 52 sec) [ -11039.5168] [Topology ] . ( 53 sec) [ -11039.5147] [Topology ] . ( 54 sec) [ -11039.5133] [Topology ] . ( 55 sec) [ -11039.5125] [Topology ] . ( 55 sec) [ -11039.5124] [GTR parameters ] . ( 55 sec) [ -11039.5124] [Alpha ][ 0.969962] . ( 55 sec) [ -11039.5124] [Topology ] . ( 56 sec) [ -11039.5119] [Topology ] . ( 56 sec) [ -11039.5119] [GTR parameters ] . ( 56 sec) [ -11039.5119] [Alpha ][ 0.969962] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11039.511897. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19899.5758] [GTR parameters ] . ( 0 sec) [ -19607.5437] [Alpha ][ 0.500960] . ( 0 sec) [ -19008.8511] [ 4720] [depth= 8] . ( 0 sec) [ -18519.3694] [ 4583] [depth= 9] . ( 0 sec) [ -18318.3820] [ 4547] [depth= 7] . ( 0 sec) [ -18286.4987] [ 4455] [depth= 1] . ( 1 sec) [ -17931.6078] [ 4408] [depth= 9] . ( 1 sec) [ -17853.0046] [ 4399] [depth= 2] . ( 1 sec) [ -17788.1998] [ 4391] [depth= 5] . ( 1 sec) [ -17546.1825] [ 4333] [depth= 3] . ( 1 sec) [ -17339.0511] [ 4321] [depth= 8] . ( 1 sec) [ -17101.9464] [ 4304] [depth= 7] . ( 1 sec) [ -16824.1654] [ 4296] [depth= 2] . ( 1 sec) [ -16711.0331] [ 4232] [depth= 13] . ( 1 sec) [ -16582.8463] [ 4110] [depth= 2] . ( 1 sec) [ -16524.5484] [ 4100] [depth= 3] . ( 1 sec) [ -16284.5643] [ 4038] [depth= 3] . ( 1 sec) [ -15994.1754] [ 3939] [depth= 4] . ( 1 sec) [ -15952.1136] [ 3935] [depth= 7] . ( 1 sec) [ -15855.1764] [ 3877] [depth= 2] . ( 1 sec) [ -15849.6812] [ 3878] [depth= 2] . ( 1 sec) [ -15651.4189] [ 3843] [depth= 3] . ( 1 sec) [ -15609.9567] [ 3826] [depth= 2] . ( 1 sec) [ -15509.9545] [ 3807] [depth= 3] . ( 1 sec) [ -15501.5771] [ 3812] [depth= 2] . ( 1 sec) [ -15369.2755] [ 3776] [depth= 9] . ( 1 sec) [ -15305.6586] [ 3802] [depth= 15] . ( 2 sec) [ -15301.2256] [ 3797] [depth= 1] . ( 2 sec) [ -14884.5333] [ 3714] [depth= 3] . ( 2 sec) [ -14881.7667] [ 3714] [depth= 1] . ( 2 sec) [ -14879.9224] [ 3716] [depth= 2] . ( 2 sec) [ -14790.2912] [ 3691] [depth= 1] . ( 2 sec) [ -14635.7429] [ 3639] [depth= 11] . ( 2 sec) [ -14497.4955] [ 3568] [depth= 3] . ( 2 sec) [ -14464.5579] [ 3564] [depth= 1] . ( 2 sec) [ -14373.3566] [ 3529] [depth= 11] . ( 2 sec) [ -14232.8314] [ 3494] [depth= 10] . ( 2 sec) [ -13915.0775] [ 3285] [depth= 8] . ( 2 sec) [ -13549.8185] [ 3242] [depth= 1] . ( 2 sec) [ -13291.2749] [ 3263] [depth= 6] . ( 2 sec) [ -12925.3047] [ 3138] [depth= 5] . ( 2 sec) [ -12838.2364] [ 3120] [depth= 2] . ( 2 sec) [ -12825.1195] [ 3108] [depth= 2] . ( 2 sec) [ -12802.1966] [ 3115] [depth= 2] . ( 2 sec) [ -12797.5321] [ 3116] [depth= 1] . ( 2 sec) [ -12783.3015] [ 3106] [depth= 6] . ( 2 sec) [ -12733.8324] [ 3097] [depth= 1] . ( 3 sec) [ -12617.7816] [ 3064] [depth= 1] . ( 3 sec) [ -12555.1540] [ 3030] [depth= 5] . ( 3 sec) [ -12519.3175] [ 3022] [depth= 1] . ( 3 sec) [ -12410.3502] [ 2945] [depth= 11] . ( 3 sec) [ -12400.9107] [ 2941] [depth= 1] . ( 3 sec) [ -12269.9826] [ 2932] [depth= 2] . ( 3 sec) [ -12239.1043] [ 2919] [depth= 1] . ( 3 sec) [ -12233.8278] [ 2918] [depth= 3] . ( 3 sec) [ -12230.1168] [ 2922] [depth= 1] . ( 3 sec) [ -12193.4694] [ 2924] [depth= 1] . ( 3 sec) [ -12153.3256] [ 2907] [depth= 1] . ( 3 sec) [ -12034.3254] [ 2900] [depth= 1] . ( 3 sec) [ -11984.1472] [ 2895] [depth= 1] . ( 3 sec) [ -11955.6769] [ 2851] [depth= 13] . ( 3 sec) [ -11921.4939] [ 2835] [depth= 1] . ( 3 sec) [ -11864.0795] [ 2807] [depth= 6] . ( 3 sec) [ -11857.8611] [ 2809] [depth= 1] . ( 3 sec) [ -11857.3829] [ 2810] [depth= 1] . ( 3 sec) [ -11854.9983] [ 2811] [depth= 1] . ( 3 sec) [ -11806.6869] [ 2782] [depth= 2] . ( 4 sec) [ -11790.1298] [ 2771] [depth= 6] . ( 4 sec) [ -11789.2653] [ 2768] [depth= 1] . ( 4 sec) [ -11785.2401] [ 2786] [depth= 1] . ( 4 sec) [ -11759.7528] [ 2774] [depth= 1] . ( 4 sec) [ -11687.5176] [ 2773] [depth= 1] . ( 4 sec) [ -11653.3877] [ 2764] [depth= 2] . ( 4 sec) [ -11594.2846] [ 2753] [depth= 1] . ( 4 sec) [ -11568.6830] [ 2754] [depth= 1] . ( 4 sec) [ -11565.5124] [ 2759] [depth= 1] . ( 4 sec) [ -11557.8982] [ 2754] [depth= 1] . ( 4 sec) [ -11532.9042] [ 2752] [depth= 2] . ( 4 sec) [ -11522.1740] [ 2744] [depth= 3] . ( 4 sec) [ -11505.3409] [ 2745] [depth= 1] . ( 4 sec) [ -11464.9815] [ 2717] [depth= 1] . ( 4 sec) [ -11453.2686] [ 2717] [depth= 1] . ( 4 sec) [ -11421.8130] [ 2699] [depth= 1] . ( 4 sec) [ -11418.5563] [ 2693] [depth= 1] . ( 4 sec) [ -11415.0586] [ 2696] [depth= 1] . ( 5 sec) [ -11397.2190] [ 2693] [depth= 1] . ( 5 sec) [ -11152.0236] [Branch lengths ] . ( 5 sec) [ -11150.5585] [GTR parameters ] . ( 6 sec) [ -11106.8652] [Alpha ][ 0.927647] . ( 6 sec) [ -11103.8909] [ 2697] [depth= 1] . ( 6 sec) [ -11100.6858] [ 2693] [depth= 1] . ( 6 sec) [ -11073.5817] [ 2674] [depth= 1] . ( 6 sec) [ -11072.5960] [ 2674] [depth= 1] . ( 7 sec) [ -11072.3404] [ 2658] [depth= 1] . ( 7 sec) [ -11069.4685] [ 2647] [depth= 7] . ( 8 sec) [ -11066.0132] [ 2649] [depth= 1] . ( 8 sec) [ -11065.1102] [ 2647] [depth= 2] . ( 8 sec) [ -11064.4535] [ 2649] [depth= 1] . ( 8 sec) [ -11064.2399] [ 2648] [depth= 1] . ( 8 sec) [ -11060.4859] [ 2644] [depth= 1] . ( 8 sec) [ -11060.4139] [ 2643] [depth= 1] . ( 9 sec) [ -11059.1122] [ 2647] [depth= 1] . ( 9 sec) [ -11058.6644] [ 2647] [depth= 1] . ( 9 sec) [ -11058.6374] [ 2649] [depth= 1] . ( 10 sec) [ -11049.0412] [Branch lengths ] . ( 10 sec) [ -11048.7883] [GTR parameters ] . ( 10 sec) [ -11048.6322] [Alpha ][ 0.961989] . ( 11 sec) [ -11045.7243] [ 2650] [depth= 2] . ( 11 sec) [ -11045.4609] [ 2645] [depth= 1] . ( 11 sec) [ -11045.4334] [ 2650] [depth= 1] . ( 12 sec) [ -11045.4209] [ 2652] [depth= 1] . ( 12 sec) [ -11044.9909] [ 2649] [depth= 1] . ( 12 sec) [ -11044.5787] [ 2651] [depth= 1] . ( 14 sec) [ -11044.3715] [ 2655] [depth= 1] . ( 14 sec) [ -11044.3293] [ 2652] [depth= 1] . ( 14 sec) [ -11042.3199] [Branch lengths ] . ( 15 sec) [ -11042.3013] [GTR parameters ] . ( 15 sec) [ -11042.2959] [Alpha ][ 0.968657] . ( 15 sec) [ -11041.2742] [ 2648] [depth= 1] . ( 16 sec) [ -11041.0606] [ 2647] [depth= 1] . ( 17 sec) [ -11040.9547] [ 2649] [depth= 2] . ( 18 sec) [ -11040.0033] [Branch lengths ] . ( 19 sec) [ -11039.9892] [GTR parameters ] . ( 19 sec) [ -11039.9890] [Alpha ][ 0.967245] . ( 23 sec) [ -11039.6349] [Branch lengths ] . ( 46 sec) [ -11039.5483] [Branch lengths ] . ( 46 sec) [ -11039.5483] [Topology ] . ( 47 sec) [ -11039.5358] [Topology ] . ( 48 sec) [ -11039.5300] [Topology ] . ( 49 sec) [ -11039.5266] [Topology ] . ( 50 sec) [ -11039.5244] [Topology ] . ( 51 sec) [ -11039.5231] [Topology ] . ( 51 sec) [ -11039.5223] [Topology ] . ( 52 sec) [ -11039.5220] [GTR parameters ] . ( 52 sec) [ -11039.5210] [Alpha ][ 0.970003] . ( 52 sec) [ -11039.5210] [Topology ] . ( 52 sec) [ -11039.5204] [Topology ] . ( 53 sec) [ -11039.5204] [GTR parameters ] . ( 53 sec) [ -11039.5204] [Alpha ][ 0.970003] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -11039.5118] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11039.511827. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20927.9872] [GTR parameters ] . ( 1 sec) [ -20584.7278] [Alpha ][ 0.500960] . ( 1 sec) [ -20157.5797] [ 4764] [depth= 6] . ( 1 sec) [ -19863.1151] [ 4650] [depth= 12] . ( 1 sec) [ -19834.4688] [ 4625] [depth= 6] . ( 1 sec) [ -19708.0238] [ 4613] [depth= 1] . ( 1 sec) [ -19425.8379] [ 4512] [depth= 3] . ( 1 sec) [ -19008.4446] [ 4497] [depth= 7] . ( 1 sec) [ -18962.3559] [ 4486] [depth= 8] . ( 1 sec) [ -18922.5204] [ 4493] [depth= 1] . ( 1 sec) [ -18539.6570] [ 4424] [depth= 4] . ( 1 sec) [ -18445.4737] [ 4448] [depth= 3] . ( 1 sec) [ -18234.0162] [ 4399] [depth= 1] . ( 1 sec) [ -17794.7787] [ 4181] [depth= 10] . ( 1 sec) [ -17569.9208] [ 4114] [depth= 2] . ( 1 sec) [ -17440.0659] [ 4045] [depth= 4] . ( 1 sec) [ -17368.5424] [ 4040] [depth= 1] . ( 1 sec) [ -17200.5376] [ 4015] [depth= 13] . ( 1 sec) [ -17155.4499] [ 4010] [depth= 1] . ( 1 sec) [ -16979.7185] [ 3974] [depth= 14] . ( 2 sec) [ -16929.7650] [ 3965] [depth= 1] . ( 2 sec) [ -16857.4636] [ 3951] [depth= 6] . ( 2 sec) [ -16727.1176] [ 3919] [depth= 14] . ( 2 sec) [ -16525.3402] [ 3894] [depth= 1] . ( 2 sec) [ -16410.8067] [ 3865] [depth= 10] . ( 2 sec) [ -16364.7231] [ 3845] [depth= 1] . ( 2 sec) [ -16128.1614] [ 3808] [depth= 2] . ( 2 sec) [ -16009.9206] [ 3828] [depth= 1] . ( 2 sec) [ -15811.6856] [ 3716] [depth= 12] . ( 2 sec) [ -15782.4671] [ 3732] [depth= 1] . ( 2 sec) [ -15592.6685] [ 3642] [depth= 8] . ( 2 sec) [ -15531.3874] [ 3634] [depth= 2] . ( 2 sec) [ -15494.5053] [ 3617] [depth= 2] . ( 2 sec) [ -15474.9396] [ 3594] [depth= 2] . ( 2 sec) [ -15451.1955] [ 3533] [depth= 4] . ( 2 sec) [ -15414.7404] [ 3505] [depth= 1] . ( 2 sec) [ -15068.6339] [ 3464] [depth= 1] . ( 2 sec) [ -14876.4821] [ 3436] [depth= 1] . ( 2 sec) [ -14648.1676] [ 3419] [depth= 3] . ( 2 sec) [ -14569.1255] [ 3384] [depth= 10] . ( 3 sec) [ -13767.2547] [ 3300] [depth= 3] . ( 3 sec) [ -13678.9869] [ 3290] [depth= 6] . ( 3 sec) [ -13662.8129] [ 3284] [depth= 2] . ( 3 sec) [ -13486.6380] [ 3200] [depth= 5] . ( 3 sec) [ -13456.3949] [ 3189] [depth= 1] . ( 3 sec) [ -13275.0243] [ 3079] [depth= 6] . ( 3 sec) [ -13221.4495] [ 3099] [depth= 1] . ( 3 sec) [ -13185.0002] [ 3079] [depth= 1] . ( 3 sec) [ -13085.6367] [ 3033] [depth= 7] . ( 3 sec) [ -12977.9542] [ 3019] [depth= 4] . ( 3 sec) [ -12926.7157] [ 3015] [depth= 1] . ( 3 sec) [ -12820.8335] [ 2986] [depth= 1] . ( 3 sec) [ -12798.4315] [ 2975] [depth= 3] . ( 3 sec) [ -12773.5561] [ 2970] [depth= 1] . ( 3 sec) [ -12675.1985] [ 2925] [depth= 5] . ( 3 sec) [ -12622.9106] [ 2898] [depth= 3] . ( 3 sec) [ -12575.6032] [ 2890] [depth= 4] . ( 4 sec) [ -12561.1820] [ 2906] [depth= 1] . ( 4 sec) [ -12481.6893] [ 2868] [depth= 1] . ( 4 sec) [ -12386.4080] [ 2868] [depth= 3] . ( 4 sec) [ -12376.7578] [ 2857] [depth= 1] . ( 4 sec) [ -12264.8190] [ 2828] [depth= 2] . ( 4 sec) [ -12047.8185] [ 2841] [depth= 1] . ( 4 sec) [ -11748.3408] [ 2751] [depth= 6] . ( 4 sec) [ -11654.3133] [ 2739] [depth= 3] . ( 4 sec) [ -11648.2215] [ 2733] [depth= 1] . ( 4 sec) [ -11641.9090] [ 2724] [depth= 1] . ( 4 sec) [ -11582.3676] [ 2713] [depth= 1] . ( 4 sec) [ -11575.9218] [ 2695] [depth= 4] . ( 4 sec) [ -11573.5288] [ 2709] [depth= 1] . ( 4 sec) [ -11568.2828] [ 2705] [depth= 1] . ( 4 sec) [ -11549.8639] [ 2709] [depth= 1] . ( 4 sec) [ -11545.1200] [ 2712] [depth= 1] . ( 4 sec) [ -11542.8672] [ 2697] [depth= 1] . ( 5 sec) [ -11525.3936] [ 2677] [depth= 1] . ( 5 sec) [ -11517.7211] [ 2686] [depth= 1] . ( 5 sec) [ -11512.6160] [ 2689] [depth= 1] . ( 5 sec) [ -11503.5951] [ 2677] [depth= 4] . ( 5 sec) [ -11457.9798] [ 2680] [depth= 1] . ( 5 sec) [ -11405.3763] [ 2677] [depth= 1] . ( 5 sec) [ -11395.9348] [ 2675] [depth= 1] . ( 5 sec) [ -11161.5751] [Branch lengths ] . ( 6 sec) [ -11160.8093] [GTR parameters ] . ( 6 sec) [ -11121.2196] [Alpha ][ 0.915351] . ( 6 sec) [ -11105.2615] [ 2667] [depth= 1] . ( 6 sec) [ -11095.5629] [ 2669] [depth= 1] . ( 6 sec) [ -11091.3970] [ 2657] [depth= 2] . ( 6 sec) [ -11086.4285] [ 2661] [depth= 3] . ( 6 sec) [ -11068.1940] [ 2656] [depth= 3] . ( 6 sec) [ -11067.6467] [ 2658] [depth= 1] . ( 7 sec) [ -11066.0785] [ 2654] [depth= 1] . ( 7 sec) [ -11064.4951] [ 2651] [depth= 1] . ( 7 sec) [ -11063.5200] [ 2648] [depth= 1] . ( 8 sec) [ -11063.0600] [ 2647] [depth= 1] . ( 8 sec) [ -11061.3016] [ 2649] [depth= 1] . ( 8 sec) [ -11060.7213] [ 2647] [depth= 1] . ( 8 sec) [ -11059.3552] [ 2647] [depth= 1] . ( 10 sec) [ -11042.0580] [Branch lengths ] . ( 10 sec) [ -11041.9539] [GTR parameters ] . ( 10 sec) [ -11041.6454] [Alpha ][ 0.965388] . ( 14 sec) [ -11040.5130] [Branch lengths ] . ( 38 sec) [ -11040.2933] [Branch lengths ] . ( 38 sec) [ -11040.2933] [Topology ] . ( 39 sec) [ -11040.2097] [Topology ] . ( 40 sec) [ -11040.1729] [Topology ] . ( 41 sec) [ -11040.1529] [Topology ] . ( 42 sec) [ -11040.1414] [Topology ] . ( 42 sec) [ -11040.1346] [Topology ] . ( 43 sec) [ -11040.1306] [Topology ] . ( 43 sec) [ -11040.1281] [GTR parameters ] . ( 43 sec) [ -11040.1228] [Alpha ][ 0.971976] . ( 43 sec) [ -11040.1228] [Topology ] . ( 44 sec) [ -11040.1198] [Topology ] . ( 45 sec) [ -11040.1181] [Topology ] . ( 46 sec) [ -11040.1171] [Topology ] . ( 47 sec) [ -11040.1164] [Topology ] . ( 47 sec) [ -11040.1164] [GTR parameters ] . ( 47 sec) [ -11040.1164] [Alpha ][ 0.972948] . ( 47 sec) [ -11040.1164] [Topology ] . ( 48 sec) [ -11040.1160] [Topology ] . ( 48 sec) [ -11040.1160] [GTR parameters ] . ( 48 sec) [ -11040.1160] [Alpha ][ 0.972948] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -11040.1144] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11040.114399. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11173.737666 . ( 1 sec) [ -11168.5712] [GTR parameters ] . ( 1 sec) [ -11168.2821] [Alpha ][ 0.947402] . ( 1 sec) [ -11168.2821] [Topology ] . ( 2 sec) [ -11068.6753] [Topology ] . ( 3 sec) [ -11049.7537] [Topology ] . ( 3 sec) [ -11045.0305] [Topology ] . ( 4 sec) [ -11043.0991] [Topology ] . ( 5 sec) [ -11042.2218] [Topology ] . ( 6 sec) [ -11041.7763] [Topology ] . ( 7 sec) [ -11041.5398] [Topology ] . ( 8 sec) [ -11041.3785] [Topology ] . ( 8 sec) [ -11040.7455] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -11040.4333] [Topology ] . Before opt ts/t=1.000000 LK=-11040.433323 . ( 16 sec) [ -11040.2647] [GTR parameters ] . ( 16 sec) [ -11040.2022] [Alpha ][ 0.970113] . ( 16 sec) [ -11040.2022] [Topology ] . ( 17 sec) [ -11040.1562] [Topology ] . ( 18 sec) [ -11040.1377] [Topology ] . ( 19 sec) [ -11040.1280] [Topology ] . ( 20 sec) [ -11040.1225] [Topology ] . ( 20 sec) [ -11040.1193] [Topology ] . ( 21 sec) [ -11040.1175] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11040.117474 . ( 28 sec) [ -11040.1173] [GTR parameters ] . ( 28 sec) [ -11040.1167] [Alpha ][ 0.972223] . ( 28 sec) [ -11040.1167] [Topology ] . ( 29 sec) [ -11040.1155] [Topology ] . ( 30 sec) [ -11040.1148] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11040.114800 . ( 36 sec) [ -11040.1148] [GTR parameters ] . ( 36 sec) [ -11040.1148] [Alpha ][ 0.972223] . ( 36 sec) [ -11040.1148] [Topology ] . ( 37 sec) [ -11040.1144] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 51 sec) [ -11168.5712] [GTR parameters ] . ( 51 sec) [ -11168.2821] [Alpha ][ 0.947402] . ( 51 sec) [ -11150.9127] [ 2657] [depth= 1] . ( 51 sec) [ -11140.4319] [ 2664] [depth= 1] . ( 51 sec) [ -11134.8617] [ 2657] [depth= 1] . ( 51 sec) [ -11125.6557] [ 2647] [depth= 2] . ( 51 sec) [ -11119.7433] [ 2649] [depth= 1] . ( 51 sec) [ -11116.6405] [ 2655] [depth= 1] . ( 52 sec) [ -11116.0627] [ 2664] [depth= 1] . ( 52 sec) [ -11110.9528] [ 2665] [depth= 1] . ( 52 sec) [ -11110.8532] [ 2665] [depth= 1] . ( 53 sec) [ -11110.2055] [ 2667] [depth= 1] . ( 53 sec) [ -11107.6092] [ 2665] [depth= 1] . ( 53 sec) [ -11107.2589] [ 2667] [depth= 1] . ( 53 sec) [ -11106.9879] [ 2665] [depth= 1] . ( 53 sec) [ -11097.5526] [ 2662] [depth= 1] . ( 53 sec) [ -11094.4013] [ 2659] [depth= 1] . ( 53 sec) [ -11093.9512] [ 2654] [depth= 1] . ( 53 sec) [ -11093.3383] [ 2657] [depth= 1] . ( 53 sec) [ -11090.9693] [ 2654] [depth= 1] . ( 54 sec) [ -11089.9107] [ 2653] [depth= 1] . ( 54 sec) [ -11088.6537] [ 2654] [depth= 1] . ( 54 sec) [ -11088.5041] [ 2655] [depth= 3] . ( 54 sec) [ -11088.4910] [ 2659] [depth= 1] . ( 55 sec) [ -11052.7122] [Branch lengths ] . ( 55 sec) [ -11052.4786] [GTR parameters ] . ( 55 sec) [ -11052.4652] [Alpha ][ 0.957957] . ( 56 sec) [ -11052.1142] [ 2661] [depth= 2] . ( 56 sec) [ -11049.1972] [ 2652] [depth= 1] . ( 57 sec) [ -11049.1329] [ 2652] [depth= 1] . ( 58 sec) [ -11049.1015] [ 2652] [depth= 2] . ( 58 sec) [ -11048.7299] [ 2649] [depth= 1] . ( 58 sec) [ -11048.2700] [ 2650] [depth= 2] . ( 58 sec) [ -11046.2905] [ 2646] [depth= 1] . ( 59 sec) [ -11040.4434] [Branch lengths ] . ( 59 sec) [ -11040.4147] [GTR parameters ] . ( 59 sec) [ -11040.4073] [Alpha ][ 0.965838] . ( 63 sec) [ -11039.6810] [Branch lengths ] . ( 87 sec) [ -11039.5589] [Branch lengths ] . ( 87 sec) [ -11039.5589] [Topology ] . ( 88 sec) [ -11039.5416] [Topology ] . ( 89 sec) [ -11039.5340] [Topology ] . ( 89 sec) [ -11039.5296] [Topology ] . ( 90 sec) [ -11039.5270] [Topology ] . ( 91 sec) [ -11039.5254] [Topology ] . ( 92 sec) [ -11039.5244] [Topology ] . ( 92 sec) [ -11039.5235] [GTR parameters ] . ( 92 sec) [ -11039.5215] [Alpha ][ 0.969868] . ( 92 sec) [ -11039.5215] [Topology ] . ( 93 sec) [ -11039.5207] [Topology ] . ( 93 sec) [ -11039.5206] [GTR parameters ] . ( 93 sec) [ -11039.5206] [Alpha ][ 0.969868] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -11039.5203] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11040.114360 . Log likelihood obtained after SPR moves : -11039.520309 . Log likelihood of the current tree: -11039.520309. . Printing the most likely tree in file 'data69.phy_phyml_tree.txt'... . Best log likelihood : -11039.511827 . Time used 0h1m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo