.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data43.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... . 428 patterns found. (out of a total of 500 sites) . 67 sites without polymorphism (13.40%). . [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) [ -17243.0097] [GTR parameters ] . ( 1 sec) [ -16987.1106] [Alpha ][ 0.500960] . ( 1 sec) [ -16912.0334] [ 3981] [depth= 8] . ( 1 sec) [ -16738.3210] [ 3941] [depth= 6] . ( 1 sec) [ -16480.4465] [ 3910] [depth= 1] . ( 1 sec) [ -16300.9857] [ 3904] [depth= 3] . ( 1 sec) [ -16240.5059] [ 3883] [depth= 6] . ( 1 sec) [ -16103.4653] [ 3886] [depth= 8] . ( 1 sec) [ -15979.3195] [ 3846] [depth= 6] . ( 1 sec) [ -15824.0229] [ 3790] [depth= 1] . ( 1 sec) [ -15764.3176] [ 3774] [depth= 3] . ( 1 sec) [ -15636.8288] [ 3737] [depth= 9] . ( 1 sec) [ -15515.7132] [ 3684] [depth= 1] . ( 1 sec) [ -15281.3302] [ 3667] [depth= 6] . ( 1 sec) [ -15127.1092] [ 3648] [depth= 10] . ( 2 sec) [ -15113.6286] [ 3638] [depth= 1] . ( 2 sec) [ -15033.8535] [ 3630] [depth= 4] . ( 2 sec) [ -15001.3716] [ 3591] [depth= 1] . ( 2 sec) [ -14970.8720] [ 3575] [depth= 12] . ( 2 sec) [ -14824.8035] [ 3551] [depth= 3] . ( 2 sec) [ -14692.2218] [ 3511] [depth= 1] . ( 2 sec) [ -14547.9659] [ 3490] [depth= 16] . ( 2 sec) [ -14510.1529] [ 3492] [depth= 1] . ( 2 sec) [ -14492.2031] [ 3480] [depth= 1] . ( 2 sec) [ -14446.7254] [ 3461] [depth= 4] . ( 2 sec) [ -14296.1523] [ 3418] [depth= 16] . ( 2 sec) [ -14061.4874] [ 3352] [depth= 2] . ( 2 sec) [ -14030.2381] [ 3326] [depth= 1] . ( 2 sec) [ -13948.0212] [ 3307] [depth= 11] . ( 2 sec) [ -13829.5245] [ 3288] [depth= 3] . ( 2 sec) [ -13463.6191] [ 3204] [depth= 12] . ( 2 sec) [ -13272.3578] [ 3146] [depth= 6] . ( 2 sec) [ -13197.4702] [ 3091] [depth= 1] . ( 2 sec) [ -13085.0325] [ 3064] [depth= 8] . ( 2 sec) [ -12991.6698] [ 3061] [depth= 2] . ( 2 sec) [ -12988.4126] [ 3064] [depth= 1] . ( 3 sec) [ -12905.3597] [ 3027] [depth= 3] . ( 3 sec) [ -12881.5179] [ 3010] [depth= 1] . ( 3 sec) [ -12763.8578] [ 2960] [depth= 9] . ( 3 sec) [ -12715.1375] [ 2952] [depth= 5] . ( 3 sec) [ -12627.1425] [ 2930] [depth= 2] . ( 3 sec) [ -12599.7850] [ 2918] [depth= 3] . ( 3 sec) [ -12578.7626] [ 2910] [depth= 2] . ( 3 sec) [ -12504.0046] [ 2848] [depth= 3] . ( 3 sec) [ -12438.9291] [ 2822] [depth= 3] . ( 3 sec) [ -12414.0510] [ 2821] [depth= 2] . ( 3 sec) [ -12410.2959] [ 2812] [depth= 1] . ( 3 sec) [ -12256.1560] [ 2721] [depth= 13] . ( 3 sec) [ -12235.6093] [ 2721] [depth= 1] . ( 3 sec) [ -12229.4051] [ 2721] [depth= 2] . ( 3 sec) [ -12158.8856] [ 2698] [depth= 1] . ( 3 sec) [ -12155.7083] [ 2696] [depth= 1] . ( 3 sec) [ -12049.0956] [ 2659] [depth= 2] . ( 3 sec) [ -11997.0522] [ 2644] [depth= 1] . ( 3 sec) [ -11905.1191] [ 2673] [depth= 1] . ( 3 sec) [ -11851.7844] [ 2663] [depth= 1] . ( 3 sec) [ -11777.1755] [ 2623] [depth= 9] . ( 4 sec) [ -11712.0332] [ 2604] [depth= 1] . ( 4 sec) [ -11686.5961] [ 2590] [depth= 2] . ( 4 sec) [ -11651.9953] [ 2580] [depth= 1] . ( 4 sec) [ -11590.5356] [ 2533] [depth= 4] . ( 4 sec) [ -11587.4330] [ 2544] [depth= 1] . ( 4 sec) [ -11576.3363] [ 2521] [depth= 1] . ( 4 sec) [ -11412.2257] [ 2503] [depth= 3] . ( 4 sec) [ -11411.8013] [ 2508] [depth= 1] . ( 4 sec) [ -11411.2143] [ 2509] [depth= 2] . ( 4 sec) [ -11238.1680] [ 2497] [depth= 3] . ( 4 sec) [ -11222.0546] [ 2508] [depth= 1] . ( 4 sec) [ -10939.3269] [ 2476] [depth= 2] . ( 4 sec) [ -10939.2718] [ 2477] [depth= 1] . ( 4 sec) [ -10931.6900] [ 2454] [depth= 3] . ( 4 sec) [ -10863.9952] [ 2416] [depth= 3] . ( 4 sec) [ -10607.0955] [ 2350] [depth= 1] . ( 5 sec) [ -10556.8212] [ 2333] [depth= 1] . ( 5 sec) [ -10531.1756] [ 2318] [depth= 1] . ( 5 sec) [ -10529.3281] [ 2322] [depth= 1] . ( 5 sec) [ -10518.0642] [ 2313] [depth= 2] . ( 5 sec) [ -10396.6845] [Branch lengths ] . ( 6 sec) [ -10394.7741] [GTR parameters ] . ( 6 sec) [ -10355.1478] [Alpha ][ 0.921592] . ( 6 sec) [ -10344.6371] [ 2302] [depth= 1] . ( 6 sec) [ -10333.1426] [ 2280] [depth= 2] . ( 6 sec) [ -10332.2844] [ 2282] [depth= 1] . ( 6 sec) [ -10330.5217] [ 2280] [depth= 2] . ( 6 sec) [ -10330.2537] [ 2279] [depth= 1] . ( 6 sec) [ -10313.1455] [ 2271] [depth= 1] . ( 7 sec) [ -10306.8777] [ 2267] [depth= 1] . ( 7 sec) [ -10306.6189] [ 2268] [depth= 1] . ( 7 sec) [ -10305.9341] [ 2267] [depth= 1] . ( 7 sec) [ -10305.5560] [ 2269] [depth= 1] . ( 7 sec) [ -10304.7084] [ 2267] [depth= 2] . ( 7 sec) [ -10303.7099] [ 2268] [depth= 1] . ( 8 sec) [ -10299.5728] [ 2265] [depth= 1] . ( 8 sec) [ -10297.9436] [ 2265] [depth= 1] . ( 8 sec) [ -10297.2934] [ 2265] [depth= 1] . ( 8 sec) [ -10295.8734] [ 2269] [depth= 1] . ( 8 sec) [ -10293.5995] [ 2264] [depth= 1] . ( 9 sec) [ -10290.1793] [ 2266] [depth= 1] . ( 9 sec) [ -10273.6442] [Branch lengths ] . ( 9 sec) [ -10273.5938] [GTR parameters ] . ( 9 sec) [ -10273.2446] [Alpha ][ 0.977460] . ( 9 sec) [ -10272.4317] [ 2266] [depth= 1] . ( 9 sec) [ -10268.1557] [ 2260] [depth= 2] . ( 10 sec) [ -10267.5051] [ 2264] [depth= 1] . ( 10 sec) [ -10267.0483] [ 2264] [depth= 1] . ( 11 sec) [ -10266.0381] [ 2265] [depth= 1] . ( 12 sec) [ -10265.9337] [ 2266] [depth= 1] . ( 12 sec) [ -10264.9731] [ 2269] [depth= 1] . ( 13 sec) [ -10263.0483] [Branch lengths ] . ( 13 sec) [ -10263.0428] [GTR parameters ] . ( 13 sec) [ -10263.0304] [Alpha ][ 0.988585] . ( 13 sec) [ -10262.4534] [ 2266] [depth= 1] . ( 13 sec) [ -10262.2080] [ 2265] [depth= 1] . ( 16 sec) [ -10261.6011] [Branch lengths ] . ( 16 sec) [ -10261.5986] [GTR parameters ] . ( 16 sec) [ -10261.5985] [Alpha ][ 0.989668] . ( 20 sec) [ -10261.5647] [Branch lengths ] . ( 43 sec) [ -10261.5592] [Branch lengths ] . ( 43 sec) [ -10261.5592] [Topology ] . ( 43 sec) [ -10261.5586] [Topology ] . ( 44 sec) [ -10261.5586] [GTR parameters ] . ( 44 sec) [ -10261.5580] [Alpha ][ 0.992060] . ( 44 sec) [ -10261.5580] [Topology ] . ( 44 sec) [ -10261.5577] [Topology ] . ( 45 sec) [ -10261.5577] [GTR parameters ] . ( 45 sec) [ -10261.5577] [Alpha ][ 0.992060] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557657. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17773.6908] [GTR parameters ] . ( 1 sec) [ -17508.5167] [Alpha ][ 0.500960] . ( 1 sec) [ -17505.6640] [ 4048] [depth= 3] . ( 1 sec) [ -17290.2304] [ 3986] [depth= 3] . ( 1 sec) [ -17120.4976] [ 3940] [depth= 4] . ( 1 sec) [ -16816.6314] [ 3930] [depth= 4] . ( 1 sec) [ -16754.5752] [ 3885] [depth= 1] . ( 1 sec) [ -16628.2147] [ 3878] [depth= 7] . ( 1 sec) [ -16622.5925] [ 3877] [depth= 1] . ( 1 sec) [ -16608.8547] [ 3869] [depth= 3] . ( 1 sec) [ -16607.4238] [ 3852] [depth= 1] . ( 1 sec) [ -16575.5310] [ 3848] [depth= 2] . ( 1 sec) [ -16398.1712] [ 3826] [depth= 9] . ( 1 sec) [ -16266.9424] [ 3826] [depth= 1] . ( 1 sec) [ -16123.3766] [ 3790] [depth= 1] . ( 1 sec) [ -15958.3588] [ 3792] [depth= 5] . ( 1 sec) [ -15804.1285] [ 3730] [depth= 14] . ( 1 sec) [ -15632.9559] [ 3680] [depth= 10] . ( 1 sec) [ -15356.1412] [ 3622] [depth= 8] . ( 1 sec) [ -15205.0392] [ 3612] [depth= 1] . ( 1 sec) [ -14960.5429] [ 3602] [depth= 1] . ( 2 sec) [ -14421.7757] [ 3597] [depth= 1] . ( 2 sec) [ -14397.2534] [ 3489] [depth= 3] . ( 2 sec) [ -14366.2168] [ 3484] [depth= 3] . ( 2 sec) [ -14162.7828] [ 3482] [depth= 15] . ( 2 sec) [ -14160.5816] [ 3480] [depth= 2] . ( 2 sec) [ -13845.7261] [ 3374] [depth= 4] . ( 2 sec) [ -13828.6167] [ 3350] [depth= 2] . ( 2 sec) [ -13810.8128] [ 3334] [depth= 11] . ( 2 sec) [ -13719.8231] [ 3265] [depth= 6] . ( 2 sec) [ -13659.1437] [ 3197] [depth= 9] . ( 2 sec) [ -13523.1714] [ 3139] [depth= 1] . ( 2 sec) [ -13193.2119] [ 3068] [depth= 12] . ( 2 sec) [ -13083.0861] [ 3045] [depth= 3] . ( 2 sec) [ -13078.8879] [ 3041] [depth= 1] . ( 3 sec) [ -12840.8076] [ 3032] [depth= 2] . ( 3 sec) [ -12682.6061] [ 2967] [depth= 1] . ( 3 sec) [ -12581.9858] [ 2943] [depth= 4] . ( 3 sec) [ -12555.0174] [ 2945] [depth= 1] . ( 3 sec) [ -12442.9460] [ 2902] [depth= 11] . ( 3 sec) [ -12422.1996] [ 2901] [depth= 1] . ( 3 sec) [ -12404.3642] [ 2907] [depth= 2] . ( 3 sec) [ -12346.2598] [ 2899] [depth= 1] . ( 3 sec) [ -12323.8584] [ 2851] [depth= 7] . ( 3 sec) [ -12317.7543] [ 2849] [depth= 2] . ( 3 sec) [ -12091.3516] [ 2756] [depth= 14] . ( 3 sec) [ -12073.8136] [ 2751] [depth= 1] . ( 3 sec) [ -12058.2406] [ 2747] [depth= 6] . ( 3 sec) [ -12050.2509] [ 2751] [depth= 2] . ( 3 sec) [ -12039.8829] [ 2730] [depth= 4] . ( 3 sec) [ -12000.6467] [ 2693] [depth= 5] . ( 3 sec) [ -11937.3698] [ 2695] [depth= 1] . ( 3 sec) [ -11932.1908] [ 2698] [depth= 1] . ( 3 sec) [ -11804.6893] [ 2648] [depth= 5] . ( 3 sec) [ -11635.2889] [ 2622] [depth= 1] . ( 4 sec) [ -11601.3404] [ 2609] [depth= 5] . ( 4 sec) [ -11599.5483] [ 2607] [depth= 1] . ( 4 sec) [ -11590.4642] [ 2605] [depth= 2] . ( 4 sec) [ -11471.7656] [ 2568] [depth= 4] . ( 4 sec) [ -11471.6166] [ 2557] [depth= 5] . ( 4 sec) [ -11470.2501] [ 2557] [depth= 1] . ( 4 sec) [ -11316.1413] [ 2531] [depth= 1] . ( 4 sec) [ -11306.7550] [ 2529] [depth= 2] . ( 4 sec) [ -11257.7174] [ 2496] [depth= 5] . ( 4 sec) [ -11131.3218] [ 2449] [depth= 2] . ( 4 sec) [ -11103.8995] [ 2451] [depth= 1] . ( 4 sec) [ -11100.6461] [ 2451] [depth= 2] . ( 4 sec) [ -10928.3479] [ 2447] [depth= 2] . ( 4 sec) [ -10906.3256] [ 2432] [depth= 2] . ( 4 sec) [ -10879.0466] [ 2423] [depth= 3] . ( 4 sec) [ -10834.7031] [ 2408] [depth= 1] . ( 4 sec) [ -10811.1049] [ 2399] [depth= 2] . ( 4 sec) [ -10790.4619] [ 2383] [depth= 1] . ( 5 sec) [ -10760.5222] [ 2369] [depth= 1] . ( 5 sec) [ -10734.0686] [ 2352] [depth= 1] . ( 5 sec) [ -10631.7826] [ 2306] [depth= 2] . ( 5 sec) [ -10627.3229] [ 2305] [depth= 1] . ( 5 sec) [ -10434.6667] [Branch lengths ] . ( 6 sec) [ -10430.3520] [GTR parameters ] . ( 6 sec) [ -10387.5075] [Alpha ][ 0.942156] . ( 6 sec) [ -10357.1658] [ 2295] [depth= 2] . ( 6 sec) [ -10311.0987] [ 2284] [depth= 2] . ( 6 sec) [ -10310.6315] [ 2285] [depth= 1] . ( 6 sec) [ -10310.5622] [ 2284] [depth= 1] . ( 6 sec) [ -10310.5444] [ 2283] [depth= 1] . ( 7 sec) [ -10310.2429] [ 2285] [depth= 1] . ( 7 sec) [ -10307.2762] [ 2287] [depth= 1] . ( 7 sec) [ -10299.7455] [ 2281] [depth= 2] . ( 7 sec) [ -10299.3177] [ 2280] [depth= 1] . ( 7 sec) [ -10298.4972] [ 2280] [depth= 1] . ( 7 sec) [ -10297.7046] [ 2283] [depth= 1] . ( 7 sec) [ -10296.0031] [ 2286] [depth= 1] . ( 7 sec) [ -10294.6166] [ 2281] [depth= 1] . ( 7 sec) [ -10281.1732] [ 2264] [depth= 2] . ( 8 sec) [ -10281.1307] [ 2266] [depth= 1] . ( 8 sec) [ -10281.0674] [ 2271] [depth= 1] . ( 8 sec) [ -10280.8327] [ 2270] [depth= 1] . ( 8 sec) [ -10280.6066] [ 2268] [depth= 1] . ( 8 sec) [ -10279.9619] [ 2269] [depth= 1] . ( 8 sec) [ -10277.6356] [ 2270] [depth= 1] . ( 9 sec) [ -10277.6053] [ 2271] [depth= 1] . ( 9 sec) [ -10264.8872] [Branch lengths ] . ( 10 sec) [ -10264.8292] [GTR parameters ] . ( 10 sec) [ -10264.6744] [Alpha ][ 0.980032] . ( 10 sec) [ -10264.4925] [ 2268] [depth= 2] . ( 11 sec) [ -10263.9830] [ 2265] [depth= 1] . ( 12 sec) [ -10263.3603] [ 2266] [depth= 1] . ( 13 sec) [ -10262.4168] [Branch lengths ] . ( 14 sec) [ -10262.4164] [GTR parameters ] . ( 14 sec) [ -10262.4091] [Alpha ][ 0.988570] . ( 14 sec) [ -10262.2928] [ 2265] [depth= 1] . ( 17 sec) [ -10262.0841] [Branch lengths ] . ( 18 sec) [ -10262.0832] [GTR parameters ] . ( 18 sec) [ -10262.0824] [Alpha ][ 0.991345] . ( 40 sec) [ -10262.0550] [Branch lengths ] . ( 40 sec) [ -10262.0550] [Topology ] . ( 41 sec) [ -10261.5725] [Topology ] . ( 42 sec) [ -10261.5613] [Topology ] . ( 43 sec) [ -10261.5596] [Topology ] . ( 44 sec) [ -10261.5592] [Topology ] . ( 44 sec) [ -10261.5578] [GTR parameters ] . ( 44 sec) [ -10261.5577] [Alpha ][ 0.992337] . ( 44 sec) [ -10261.5577] [Topology ] . ( 45 sec) [ -10261.5575] [Topology ] . ( 45 sec) [ -10261.5575] [GTR parameters ] . ( 45 sec) [ -10261.5575] [Alpha ][ 0.992337] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557512. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18163.1021] [GTR parameters ] . ( 0 sec) [ -17877.0157] [Alpha ][ 0.500960] . ( 0 sec) [ -17718.2939] [ 4131] [depth= 1] . ( 0 sec) [ -17313.0894] [ 4069] [depth= 8] . ( 0 sec) [ -17262.6845] [ 4064] [depth= 3] . ( 1 sec) [ -17206.5699] [ 4066] [depth= 1] . ( 1 sec) [ -17190.2849] [ 4061] [depth= 6] . ( 1 sec) [ -17160.6801] [ 4059] [depth= 1] . ( 1 sec) [ -16516.1107] [ 3933] [depth= 10] . ( 1 sec) [ -16366.6184] [ 3905] [depth= 4] . ( 1 sec) [ -16062.8774] [ 3806] [depth= 8] . ( 1 sec) [ -16040.4735] [ 3800] [depth= 8] . ( 1 sec) [ -15824.6522] [ 3713] [depth= 7] . ( 1 sec) [ -15824.6066] [ 3697] [depth= 7] . ( 1 sec) [ -15653.7171] [ 3690] [depth= 1] . ( 1 sec) [ -15229.1033] [ 3600] [depth= 5] . ( 1 sec) [ -15151.4361] [ 3596] [depth= 4] . ( 1 sec) [ -15000.1318] [ 3566] [depth= 11] . ( 1 sec) [ -14889.7593] [ 3555] [depth= 7] . ( 1 sec) [ -14487.2586] [ 3428] [depth= 6] . ( 1 sec) [ -14373.7259] [ 3402] [depth= 9] . ( 1 sec) [ -14365.6323] [ 3385] [depth= 1] . ( 1 sec) [ -14219.1870] [ 3339] [depth= 7] . ( 1 sec) [ -13911.7803] [ 3234] [depth= 10] . ( 1 sec) [ -13769.2079] [ 3196] [depth= 8] . ( 1 sec) [ -13677.4793] [ 3146] [depth= 3] . ( 2 sec) [ -13658.2313] [ 3140] [depth= 6] . ( 2 sec) [ -13476.6326] [ 3139] [depth= 9] . ( 2 sec) [ -13422.5664] [ 3141] [depth= 1] . ( 2 sec) [ -13403.7982] [ 3137] [depth= 4] . ( 2 sec) [ -13332.3503] [ 3104] [depth= 6] . ( 2 sec) [ -13120.8778] [ 3061] [depth= 5] . ( 2 sec) [ -13081.0103] [ 3031] [depth= 9] . ( 2 sec) [ -12847.3120] [ 3031] [depth= 1] . ( 2 sec) [ -12754.4054] [ 3016] [depth= 2] . ( 2 sec) [ -12696.9259] [ 3008] [depth= 8] . ( 2 sec) [ -12590.6885] [ 2944] [depth= 1] . ( 2 sec) [ -12532.0723] [ 2934] [depth= 8] . ( 2 sec) [ -12517.9956] [ 2915] [depth= 6] . ( 2 sec) [ -12457.8675] [ 2909] [depth= 3] . ( 2 sec) [ -12371.7842] [ 2881] [depth= 10] . ( 2 sec) [ -12274.6200] [ 2859] [depth= 2] . ( 2 sec) [ -12262.1454] [ 2855] [depth= 1] . ( 2 sec) [ -12253.8164] [ 2830] [depth= 4] . ( 2 sec) [ -12181.2228] [ 2822] [depth= 1] . ( 2 sec) [ -12072.3209] [ 2788] [depth= 1] . ( 3 sec) [ -11932.2259] [ 2740] [depth= 1] . ( 3 sec) [ -11845.9873] [ 2705] [depth= 5] . ( 3 sec) [ -11726.5076] [ 2661] [depth= 6] . ( 3 sec) [ -11613.7921] [ 2662] [depth= 1] . ( 3 sec) [ -11548.9837] [ 2661] [depth= 1] . ( 3 sec) [ -11486.6944] [ 2621] [depth= 6] . ( 3 sec) [ -11331.0809] [ 2616] [depth= 1] . ( 3 sec) [ -11328.6386] [ 2611] [depth= 9] . ( 3 sec) [ -11314.8016] [ 2614] [depth= 2] . ( 3 sec) [ -11314.4514] [ 2619] [depth= 1] . ( 3 sec) [ -11214.0643] [ 2598] [depth= 8] . ( 3 sec) [ -11201.7665] [ 2592] [depth= 1] . ( 3 sec) [ -11168.6559] [ 2591] [depth= 2] . ( 3 sec) [ -11163.3469] [ 2580] [depth= 1] . ( 3 sec) [ -11134.8081] [ 2557] [depth= 1] . ( 3 sec) [ -11129.6397] [ 2540] [depth= 2] . ( 4 sec) [ -11062.3696] [ 2492] [depth= 1] . ( 4 sec) [ -10953.0524] [ 2490] [depth= 6] . ( 4 sec) [ -10952.0329] [ 2490] [depth= 1] . ( 4 sec) [ -10914.9224] [ 2472] [depth= 5] . ( 4 sec) [ -10896.0363] [ 2472] [depth= 1] . ( 4 sec) [ -10860.7874] [ 2451] [depth= 3] . ( 4 sec) [ -10859.4743] [ 2454] [depth= 1] . ( 4 sec) [ -10858.9489] [ 2459] [depth= 1] . ( 4 sec) [ -10850.7767] [ 2459] [depth= 1] . ( 5 sec) [ -10685.1041] [Branch lengths ] . ( 5 sec) [ -10681.5323] [GTR parameters ] . ( 5 sec) [ -10647.2018] [Alpha ][ 0.867577] . ( 6 sec) [ -10646.8696] [ 2460] [depth= 1] . ( 6 sec) [ -10596.4945] [ 2436] [depth= 6] . ( 6 sec) [ -10596.2374] [ 2441] [depth= 2] . ( 6 sec) [ -10472.1983] [ 2362] [depth= 5] . ( 6 sec) [ -10467.6368] [ 2358] [depth= 1] . ( 6 sec) [ -10467.3286] [ 2361] [depth= 1] . ( 6 sec) [ -10463.6911] [ 2357] [depth= 1] . ( 6 sec) [ -10444.2289] [ 2346] [depth= 1] . ( 6 sec) [ -10436.8064] [ 2346] [depth= 2] . ( 7 sec) [ -10431.7716] [ 2334] [depth= 2] . ( 7 sec) [ -10430.9101] [ 2336] [depth= 1] . ( 7 sec) [ -10428.0806] [ 2337] [depth= 1] . ( 7 sec) [ -10408.6887] [ 2325] [depth= 3] . ( 7 sec) [ -10407.7934] [ 2328] [depth= 1] . ( 7 sec) [ -10378.1159] [ 2319] [depth= 1] . ( 7 sec) [ -10334.1549] [ 2293] [depth= 4] . ( 7 sec) [ -10320.1446] [ 2287] [depth= 1] . ( 7 sec) [ -10319.9555] [ 2283] [depth= 1] . ( 8 sec) [ -10305.9710] [ 2271] [depth= 1] . ( 8 sec) [ -10305.8518] [ 2276] [depth= 1] . ( 8 sec) [ -10305.1751] [ 2278] [depth= 1] . ( 8 sec) [ -10304.3159] [ 2279] [depth= 1] . ( 8 sec) [ -10303.9837] [ 2280] [depth= 1] . ( 9 sec) [ -10303.4489] [ 2278] [depth= 2] . ( 9 sec) [ -10283.3961] [Branch lengths ] . ( 9 sec) [ -10283.1498] [GTR parameters ] . ( 10 sec) [ -10281.9866] [Alpha ][ 0.965502] . ( 10 sec) [ -10281.2409] [ 2277] [depth= 1] . ( 10 sec) [ -10266.6975] [ 2265] [depth= 1] . ( 11 sec) [ -10264.8594] [ 2264] [depth= 1] . ( 13 sec) [ -10262.4536] [Branch lengths ] . ( 13 sec) [ -10262.4480] [GTR parameters ] . ( 13 sec) [ -10262.4047] [Alpha ][ 0.986170] . ( 14 sec) [ -10261.9457] [ 2265] [depth= 1] . ( 16 sec) [ -10261.6022] [Branch lengths ] . ( 17 sec) [ -10261.6013] [GTR parameters ] . ( 17 sec) [ -10261.5996] [Alpha ][ 0.990196] . ( 39 sec) [ -10261.5641] [Branch lengths ] . ( 39 sec) [ -10261.5641] [Topology ] . ( 40 sec) [ -10261.5604] [Topology ] . ( 41 sec) [ -10261.5591] [Topology ] . ( 42 sec) [ -10261.5585] [Topology ] . ( 42 sec) [ -10261.5585] [GTR parameters ] . ( 42 sec) [ -10261.5581] [Alpha ][ 0.992021] . ( 42 sec) [ -10261.5581] [Topology ] . ( 43 sec) [ -10261.5578] [Topology ] . ( 43 sec) [ -10261.5578] [GTR parameters ] . ( 43 sec) [ -10261.5578] [Alpha ][ 0.992021] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557752. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17383.5744] [GTR parameters ] . ( 1 sec) [ -17104.8623] [Alpha ][ 0.500960] . ( 1 sec) [ -16975.7479] [ 4103] [depth= 11] . ( 1 sec) [ -16695.4811] [ 4044] [depth= 9] . ( 1 sec) [ -16552.3977] [ 4012] [depth= 8] . ( 1 sec) [ -16425.6598] [ 3958] [depth= 1] . ( 1 sec) [ -16388.2858] [ 3958] [depth= 9] . ( 1 sec) [ -16231.6482] [ 3926] [depth= 2] . ( 1 sec) [ -16001.8714] [ 3923] [depth= 2] . ( 1 sec) [ -15919.1870] [ 3903] [depth= 1] . ( 1 sec) [ -15877.3166] [ 3901] [depth= 1] . ( 1 sec) [ -15871.3221] [ 3898] [depth= 3] . ( 2 sec) [ -15828.5191] [ 3898] [depth= 4] . ( 2 sec) [ -15629.9380] [ 3844] [depth= 7] . ( 2 sec) [ -15487.7631] [ 3809] [depth= 6] . ( 2 sec) [ -15463.3898] [ 3811] [depth= 5] . ( 2 sec) [ -15402.5552] [ 3800] [depth= 5] . ( 2 sec) [ -15171.4467] [ 3776] [depth= 9] . ( 2 sec) [ -15052.8432] [ 3721] [depth= 1] . ( 2 sec) [ -14873.6067] [ 3634] [depth= 13] . ( 2 sec) [ -14773.8539] [ 3598] [depth= 5] . ( 2 sec) [ -14719.4916] [ 3583] [depth= 1] . ( 2 sec) [ -14463.7642] [ 3546] [depth= 10] . ( 2 sec) [ -14347.4139] [ 3555] [depth= 1] . ( 2 sec) [ -14040.6156] [ 3507] [depth= 2] . ( 2 sec) [ -13843.9230] [ 3502] [depth= 10] . ( 2 sec) [ -13779.4976] [ 3455] [depth= 10] . ( 2 sec) [ -13296.4719] [ 3358] [depth= 8] . ( 2 sec) [ -13135.8718] [ 3297] [depth= 5] . ( 2 sec) [ -13092.7952] [ 3323] [depth= 1] . ( 2 sec) [ -12953.3505] [ 3237] [depth= 4] . ( 2 sec) [ -12705.1254] [ 3168] [depth= 9] . ( 2 sec) [ -12689.8862] [ 3156] [depth= 1] . ( 2 sec) [ -12662.2707] [ 3138] [depth= 8] . ( 2 sec) [ -12541.3302] [ 3077] [depth= 1] . ( 3 sec) [ -12361.1383] [ 3013] [depth= 7] . ( 3 sec) [ -12338.8977] [ 3008] [depth= 4] . ( 3 sec) [ -12288.2078] [ 2977] [depth= 1] . ( 3 sec) [ -12277.5734] [ 2970] [depth= 1] . ( 3 sec) [ -12217.9358] [ 2939] [depth= 14] . ( 3 sec) [ -12201.0150] [ 2941] [depth= 2] . ( 3 sec) [ -12200.4233] [ 2943] [depth= 1] . ( 3 sec) [ -12190.6270] [ 2927] [depth= 3] . ( 3 sec) [ -12062.6164] [ 2882] [depth= 7] . ( 3 sec) [ -12047.9578] [ 2857] [depth= 1] . ( 3 sec) [ -12041.6315] [ 2853] [depth= 1] . ( 3 sec) [ -12019.7204] [ 2847] [depth= 1] . ( 3 sec) [ -11983.6771] [ 2840] [depth= 2] . ( 3 sec) [ -11982.5707] [ 2838] [depth= 1] . ( 3 sec) [ -11953.0539] [ 2811] [depth= 5] . ( 3 sec) [ -11812.1719] [ 2773] [depth= 3] . ( 3 sec) [ -11787.3733] [ 2770] [depth= 1] . ( 3 sec) [ -11753.2689] [ 2758] [depth= 1] . ( 3 sec) [ -11752.7127] [ 2761] [depth= 1] . ( 3 sec) [ -11726.3617] [ 2745] [depth= 1] . ( 3 sec) [ -11713.0122] [ 2743] [depth= 3] . ( 4 sec) [ -11503.1743] [ 2659] [depth= 5] . ( 4 sec) [ -11502.2257] [ 2657] [depth= 2] . ( 4 sec) [ -11314.2008] [ 2614] [depth= 6] . ( 4 sec) [ -11311.4703] [ 2612] [depth= 1] . ( 4 sec) [ -11287.5626] [ 2594] [depth= 4] . ( 4 sec) [ -11261.9041] [ 2576] [depth= 1] . ( 4 sec) [ -11140.9147] [ 2521] [depth= 4] . ( 4 sec) [ -11023.5456] [ 2486] [depth= 1] . ( 4 sec) [ -10991.9821] [ 2476] [depth= 1] . ( 4 sec) [ -10941.9595] [ 2443] [depth= 3] . ( 4 sec) [ -10937.8957] [ 2446] [depth= 1] . ( 4 sec) [ -10937.0273] [ 2458] [depth= 1] . ( 4 sec) [ -10722.9865] [ 2369] [depth= 4] . ( 4 sec) [ -10722.7578] [ 2371] [depth= 1] . ( 4 sec) [ -10720.6903] [ 2370] [depth= 2] . ( 4 sec) [ -10662.0506] [ 2335] [depth= 2] . ( 4 sec) [ -10658.3912] [ 2333] [depth= 1] . ( 5 sec) [ -10655.6007] [ 2334] [depth= 1] . ( 5 sec) [ -10620.8301] [ 2321] [depth= 1] . ( 5 sec) [ -10557.6209] [ 2297] [depth= 4] . ( 5 sec) [ -10536.1187] [ 2303] [depth= 1] . ( 5 sec) [ -10533.7503] [ 2302] [depth= 1] . ( 5 sec) [ -10499.7646] [ 2297] [depth= 2] . ( 5 sec) [ -10480.4685] [ 2285] [depth= 2] . ( 5 sec) [ -10372.7043] [Branch lengths ] . ( 6 sec) [ -10370.1490] [GTR parameters ] . ( 6 sec) [ -10333.3325] [Alpha ][ 0.908382] . ( 6 sec) [ -10333.0655] [ 2286] [depth= 1] . ( 6 sec) [ -10316.3692] [ 2282] [depth= 1] . ( 6 sec) [ -10316.2077] [ 2281] [depth= 1] . ( 7 sec) [ -10311.1806] [ 2276] [depth= 1] . ( 7 sec) [ -10310.6745] [ 2277] [depth= 1] . ( 7 sec) [ -10310.5740] [ 2279] [depth= 1] . ( 7 sec) [ -10310.4154] [ 2279] [depth= 2] . ( 7 sec) [ -10288.1665] [ 2271] [depth= 1] . ( 7 sec) [ -10281.7446] [ 2266] [depth= 1] . ( 7 sec) [ -10280.5117] [ 2264] [depth= 1] . ( 8 sec) [ -10279.1501] [ 2266] [depth= 1] . ( 8 sec) [ -10278.6016] [ 2267] [depth= 1] . ( 8 sec) [ -10278.0263] [ 2264] [depth= 1] . ( 9 sec) [ -10277.9422] [ 2266] [depth= 1] . ( 9 sec) [ -10265.9096] [Branch lengths ] . ( 10 sec) [ -10265.7924] [GTR parameters ] . ( 10 sec) [ -10265.4062] [Alpha ][ 0.966684] . ( 10 sec) [ -10265.2087] [ 2265] [depth= 2] . ( 10 sec) [ -10264.3773] [ 2265] [depth= 1] . ( 13 sec) [ -10262.0261] [Branch lengths ] . ( 13 sec) [ -10262.0237] [GTR parameters ] . ( 13 sec) [ -10261.9939] [Alpha ][ 0.983867] . ( 17 sec) [ -10261.6285] [Branch lengths ] . ( 39 sec) [ -10261.5742] [Branch lengths ] . ( 39 sec) [ -10261.5742] [Topology ] . ( 40 sec) [ -10261.5689] [Topology ] . ( 41 sec) [ -10261.5670] [Topology ] . ( 42 sec) [ -10261.5661] [Topology ] . ( 42 sec) [ -10261.5658] [GTR parameters ] . ( 42 sec) [ -10261.5594] [Alpha ][ 0.991855] . ( 42 sec) [ -10261.5594] [Topology ] . ( 43 sec) [ -10261.5584] [Topology ] . ( 44 sec) [ -10261.5579] [Topology ] . ( 44 sec) [ -10261.5579] [GTR parameters ] . ( 44 sec) [ -10261.5579] [Alpha ][ 0.991855] . ( 44 sec) [ -10261.5579] [Topology ] . ( 45 sec) [ -10261.5576] [Topology ] . ( 45 sec) [ -10261.5576] [GTR parameters ] . ( 45 sec) [ -10261.5576] [Alpha ][ 0.991855] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557639. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18139.1215] [GTR parameters ] . ( 1 sec) [ -17856.9958] [Alpha ][ 0.500960] . ( 1 sec) [ -17583.6272] [ 4154] [depth= 6] . ( 1 sec) [ -17176.3109] [ 4077] [depth= 11] . ( 1 sec) [ -17095.2036] [ 4052] [depth= 5] . ( 1 sec) [ -17083.5451] [ 4047] [depth= 2] . ( 1 sec) [ -16995.4204] [ 4004] [depth= 2] . ( 1 sec) [ -16953.0289] [ 3996] [depth= 6] . ( 1 sec) [ -16929.3426] [ 3985] [depth= 2] . ( 2 sec) [ -16842.9471] [ 3973] [depth= 1] . ( 2 sec) [ -16786.0114] [ 3963] [depth= 2] . ( 2 sec) [ -16711.6675] [ 3940] [depth= 17] . ( 2 sec) [ -16375.9601] [ 3854] [depth= 7] . ( 2 sec) [ -16203.6526] [ 3816] [depth= 11] . ( 2 sec) [ -16200.0489] [ 3811] [depth= 1] . ( 2 sec) [ -16114.3954] [ 3801] [depth= 13] . ( 2 sec) [ -16074.7024] [ 3803] [depth= 1] . ( 2 sec) [ -15782.1320] [ 3791] [depth= 7] . ( 2 sec) [ -15736.8469] [ 3766] [depth= 2] . ( 2 sec) [ -15682.1471] [ 3756] [depth= 5] . ( 2 sec) [ -15292.0050] [ 3738] [depth= 13] . ( 2 sec) [ -14751.0409] [ 3648] [depth= 7] . ( 2 sec) [ -14653.2627] [ 3638] [depth= 10] . ( 2 sec) [ -14424.7289] [ 3564] [depth= 9] . ( 2 sec) [ -14385.7998] [ 3559] [depth= 1] . ( 2 sec) [ -14349.1367] [ 3556] [depth= 11] . ( 2 sec) [ -14296.7716] [ 3538] [depth= 2] . ( 2 sec) [ -14271.4785] [ 3531] [depth= 2] . ( 2 sec) [ -14130.5008] [ 3493] [depth= 1] . ( 2 sec) [ -14044.7795] [ 3460] [depth= 9] . ( 2 sec) [ -13830.2532] [ 3406] [depth= 2] . ( 3 sec) [ -13470.7414] [ 3287] [depth= 6] . ( 3 sec) [ -13398.3132] [ 3275] [depth= 6] . ( 3 sec) [ -13294.3423] [ 3225] [depth= 1] . ( 3 sec) [ -13272.0134] [ 3207] [depth= 2] . ( 3 sec) [ -13226.9926] [ 3195] [depth= 3] . ( 3 sec) [ -13194.3540] [ 3184] [depth= 1] . ( 3 sec) [ -13119.5149] [ 3152] [depth= 1] . ( 3 sec) [ -12980.3891] [ 3092] [depth= 1] . ( 3 sec) [ -12908.0262] [ 3060] [depth= 5] . ( 3 sec) [ -12607.6772] [ 3007] [depth= 1] . ( 3 sec) [ -12513.0531] [ 2960] [depth= 5] . ( 3 sec) [ -12350.4886] [ 2923] [depth= 6] . ( 3 sec) [ -12300.4419] [ 2910] [depth= 1] . ( 3 sec) [ -12042.1885] [ 2895] [depth= 10] . ( 3 sec) [ -12023.5892] [ 2845] [depth= 1] . ( 3 sec) [ -11986.0520] [ 2830] [depth= 9] . ( 3 sec) [ -11948.1714] [ 2806] [depth= 1] . ( 3 sec) [ -11936.2424] [ 2798] [depth= 1] . ( 3 sec) [ -11852.5639] [ 2759] [depth= 10] . ( 3 sec) [ -11667.7220] [ 2680] [depth= 3] . ( 3 sec) [ -11556.0366] [ 2673] [depth= 3] . ( 4 sec) [ -11547.9282] [ 2651] [depth= 3] . ( 4 sec) [ -11506.9446] [ 2642] [depth= 2] . ( 4 sec) [ -11505.4850] [ 2645] [depth= 1] . ( 4 sec) [ -11416.1277] [ 2638] [depth= 11] . ( 4 sec) [ -11397.8830] [ 2632] [depth= 2] . ( 4 sec) [ -11375.9274] [ 2620] [depth= 4] . ( 4 sec) [ -11373.0875] [ 2622] [depth= 1] . ( 4 sec) [ -11372.9363] [ 2625] [depth= 1] . ( 4 sec) [ -11297.3866] [ 2599] [depth= 9] . ( 4 sec) [ -11296.9659] [ 2598] [depth= 1] . ( 4 sec) [ -11166.9875] [ 2532] [depth= 9] . ( 4 sec) [ -11164.6529] [ 2564] [depth= 3] . ( 4 sec) [ -11093.4262] [ 2523] [depth= 3] . ( 4 sec) [ -11035.3187] [ 2497] [depth= 7] . ( 4 sec) [ -11033.0914] [ 2499] [depth= 2] . ( 5 sec) [ -10970.7887] [ 2478] [depth= 6] . ( 5 sec) [ -10956.7757] [ 2502] [depth= 11] . ( 5 sec) [ -10902.9027] [ 2485] [depth= 1] . ( 5 sec) [ -10900.3590] [ 2476] [depth= 1] . ( 5 sec) [ -10887.0202] [ 2462] [depth= 1] . ( 5 sec) [ -10798.7253] [ 2427] [depth= 2] . ( 5 sec) [ -10789.8124] [ 2434] [depth= 1] . ( 5 sec) [ -10712.0168] [ 2392] [depth= 2] . ( 5 sec) [ -10685.0783] [ 2378] [depth= 4] . ( 5 sec) [ -10684.6254] [ 2376] [depth= 1] . ( 5 sec) [ -10540.6496] [Branch lengths ] . ( 6 sec) [ -10536.2929] [GTR parameters ] . ( 6 sec) [ -10499.9971] [Alpha ][ 0.894371] . ( 6 sec) [ -10479.2503] [ 2369] [depth= 1] . ( 6 sec) [ -10472.6195] [ 2363] [depth= 1] . ( 6 sec) [ -10471.2932] [ 2364] [depth= 1] . ( 6 sec) [ -10470.7798] [ 2367] [depth= 1] . ( 6 sec) [ -10468.1250] [ 2364] [depth= 1] . ( 6 sec) [ -10468.0736] [ 2362] [depth= 1] . ( 7 sec) [ -10468.0440] [ 2366] [depth= 2] . ( 7 sec) [ -10467.2207] [ 2363] [depth= 1] . ( 7 sec) [ -10461.0275] [ 2367] [depth= 1] . ( 7 sec) [ -10403.3514] [ 2348] [depth= 5] . ( 7 sec) [ -10402.2083] [ 2353] [depth= 1] . ( 7 sec) [ -10401.3249] [ 2353] [depth= 1] . ( 7 sec) [ -10397.0552] [ 2331] [depth= 1] . ( 7 sec) [ -10389.5276] [ 2325] [depth= 1] . ( 7 sec) [ -10388.7297] [ 2324] [depth= 1] . ( 7 sec) [ -10388.2929] [ 2325] [depth= 1] . ( 8 sec) [ -10335.7571] [ 2299] [depth= 4] . ( 8 sec) [ -10332.4939] [ 2302] [depth= 1] . ( 8 sec) [ -10292.4703] [ 2273] [depth= 4] . ( 8 sec) [ -10291.9289] [ 2271] [depth= 1] . ( 8 sec) [ -10290.8391] [ 2272] [depth= 1] . ( 8 sec) [ -10290.1501] [ 2269] [depth= 1] . ( 8 sec) [ -10289.3479] [ 2266] [depth= 1] . ( 8 sec) [ -10288.9961] [ 2265] [depth= 1] . ( 9 sec) [ -10288.8628] [ 2263] [depth= 1] . ( 9 sec) [ -10288.5650] [ 2265] [depth= 1] . ( 10 sec) [ -10265.7977] [Branch lengths ] . ( 10 sec) [ -10265.7293] [GTR parameters ] . ( 10 sec) [ -10265.0828] [Alpha ][ 0.969049] . ( 10 sec) [ -10264.8760] [ 2264] [depth= 1] . ( 13 sec) [ -10264.0234] [ 2265] [depth= 1] . ( 13 sec) [ -10262.4222] [Branch lengths ] . ( 14 sec) [ -10262.4210] [GTR parameters ] . ( 14 sec) [ -10262.3920] [Alpha ][ 0.986021] . ( 17 sec) [ -10262.1042] [Branch lengths ] . ( 40 sec) [ -10262.0634] [Branch lengths ] . ( 40 sec) [ -10262.0634] [Topology ] . ( 41 sec) [ -10261.5787] [Topology ] . ( 41 sec) [ -10261.5669] [Topology ] . ( 42 sec) [ -10261.5650] [Topology ] . ( 43 sec) [ -10261.5644] [Topology ] . ( 43 sec) [ -10261.5620] [GTR parameters ] . ( 43 sec) [ -10261.5584] [Alpha ][ 0.992014] . ( 43 sec) [ -10261.5584] [Topology ] . ( 44 sec) [ -10261.5578] [Topology ] . ( 44 sec) [ -10261.5578] [GTR parameters ] . ( 44 sec) [ -10261.5578] [Alpha ][ 0.992014] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10261.557847. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10318.994783 . ( 0 sec) [ -10312.0688] [GTR parameters ] . ( 0 sec) [ -10311.6492] [Alpha ][ 0.935381] . ( 1 sec) [ -10311.6492] [Topology ] . ( 1 sec) [ -10271.7364] [Topology ] . ( 2 sec) [ -10265.0575] [Topology ] . ( 3 sec) [ -10263.2794] [Topology ] . ( 4 sec) [ -10262.6090] [Topology ] . ( 5 sec) [ -10262.2889] [Topology ] . ( 5 sec) [ -10262.1288] [Topology ] . ( 6 sec) [ -10262.0472] [Topology ] . ( 7 sec) [ -10262.0051] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10262.005059 . ( 13 sec) [ -10261.9510] [GTR parameters ] . ( 13 sec) [ -10261.6619] [Alpha ][ 0.986600] . ( 13 sec) [ -10261.6619] [Topology ] . ( 14 sec) [ -10261.6104] [Topology ] . ( 15 sec) [ -10261.5863] [Topology ] . ( 16 sec) [ -10261.5740] [Topology ] . ( 17 sec) [ -10261.5677] [Topology ] . ( 18 sec) [ -10261.5644] [Topology ] . ( 18 sec) [ -10261.5627] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.562735 . ( 24 sec) [ -10261.5626] [GTR parameters ] . ( 24 sec) [ -10261.5600] [Alpha ][ 0.991703] . ( 24 sec) [ -10261.5600] [Topology ] . ( 25 sec) [ -10261.5587] [Topology ] . ( 26 sec) [ -10261.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10261.558104 . ( 32 sec) [ -10261.5581] [GTR parameters ] . ( 32 sec) [ -10261.5581] [Alpha ][ 0.991703] . ( 32 sec) [ -10261.5581] [Topology ] . ( 33 sec) [ -10261.5578] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -10312.0688] [GTR parameters ] . ( 45 sec) [ -10311.6492] [Alpha ][ 0.935381] . ( 46 sec) [ -10311.0174] [ 2257] [depth= 2] . ( 46 sec) [ -10310.7489] [ 2254] [depth= 2] . ( 46 sec) [ -10309.0195] [ 2255] [depth= 1] . ( 46 sec) [ -10308.5527] [ 2254] [depth= 1] . ( 46 sec) [ -10307.1233] [ 2255] [depth= 1] . ( 46 sec) [ -10305.9064] [ 2257] [depth= 1] . ( 47 sec) [ -10304.3128] [ 2258] [depth= 1] . ( 47 sec) [ -10303.9779] [ 2257] [depth= 1] . ( 47 sec) [ -10302.5236] [ 2260] [depth= 1] . ( 47 sec) [ -10301.9731] [ 2260] [depth= 1] . ( 47 sec) [ -10298.1291] [ 2258] [depth= 1] . ( 47 sec) [ -10295.3385] [ 2260] [depth= 1] . ( 47 sec) [ -10291.7170] [ 2261] [depth= 1] . ( 47 sec) [ -10291.0106] [ 2260] [depth= 1] . ( 47 sec) [ -10290.8519] [ 2264] [depth= 1] . ( 47 sec) [ -10288.3332] [ 2266] [depth= 1] . ( 48 sec) [ -10288.0158] [ 2264] [depth= 1] . ( 48 sec) [ -10287.9646] [ 2266] [depth= 1] . ( 48 sec) [ -10287.1933] [ 2265] [depth= 1] . ( 49 sec) [ -10263.9806] [Branch lengths ] . ( 49 sec) [ -10263.9422] [GTR parameters ] . ( 49 sec) [ -10263.7825] [Alpha ][ 0.973650] . ( 52 sec) [ -10262.3031] [Branch lengths ] . ( 75 sec) [ -10262.1239] [Branch lengths ] . ( 75 sec) [ -10262.1239] [Topology ] . ( 76 sec) [ -10261.6218] [Topology ] . ( 77 sec) [ -10261.6051] [Topology ] . ( 78 sec) [ -10261.6009] [Topology ] . ( 79 sec) [ -10261.5991] [Topology ] . ( 79 sec) [ -10261.5983] [Topology ] . ( 80 sec) [ -10261.5944] [GTR parameters ] . ( 80 sec) [ -10261.5616] [Alpha ][ 0.991689] . ( 80 sec) [ -10261.5616] [Topology ] . ( 80 sec) [ -10261.5593] [Topology ] . ( 81 sec) [ -10261.5584] [Topology ] . ( 81 sec) [ -10261.5584] [GTR parameters ] . ( 82 sec) [ -10261.5584] [Alpha ][ 0.991689] . ( 82 sec) [ -10261.5584] [Topology ] . ( 82 sec) [ -10261.5579] [Topology ] . ( 83 sec) [ -10261.5579] [GTR parameters ] . ( 83 sec) [ -10261.5579] [Alpha ][ 0.991689] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10261.557766 . Log likelihood obtained after SPR moves : -10261.557897 . Log likelihood of the current tree: -10261.557766. . Printing the most likely tree in file 'data43.phy_phyml_tree.txt'... . Best log likelihood : -10261.557512 . Time used 0h1m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo