.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data86.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... . 394 patterns found. (out of a total of 500 sites) . 96 sites without polymorphism (19.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18117.8523] [GTR parameters ] . ( 1 sec) [ -17768.6495] [Alpha ][ 0.500960] . ( 1 sec) [ -17306.1182] [ 3571] [depth= 8] . ( 1 sec) [ -16855.7984] [ 3500] [depth= 6] . ( 1 sec) [ -16749.3853] [ 3480] [depth= 4] . ( 1 sec) [ -16693.7732] [ 3462] [depth= 5] . ( 1 sec) [ -16553.4345] [ 3447] [depth= 3] . ( 1 sec) [ -16475.7433] [ 3438] [depth= 2] . ( 1 sec) [ -16408.0207] [ 3425] [depth= 7] . ( 1 sec) [ -16251.3653] [ 3419] [depth= 1] . ( 1 sec) [ -16230.9772] [ 3417] [depth= 1] . ( 1 sec) [ -15997.9522] [ 3332] [depth= 5] . ( 1 sec) [ -15752.4320] [ 3325] [depth= 12] . ( 1 sec) [ -15732.5896] [ 3311] [depth= 3] . ( 1 sec) [ -15491.0081] [ 3235] [depth= 9] . ( 1 sec) [ -15379.8343] [ 3225] [depth= 1] . ( 1 sec) [ -15293.7817] [ 3222] [depth= 1] . ( 1 sec) [ -15175.2021] [ 3166] [depth= 10] . ( 1 sec) [ -15171.1200] [ 3162] [depth= 3] . ( 1 sec) [ -14758.9845] [ 3137] [depth= 3] . ( 1 sec) [ -14527.8735] [ 3042] [depth= 1] . ( 1 sec) [ -14410.6738] [ 3019] [depth= 7] . ( 1 sec) [ -14250.2410] [ 3041] [depth= 1] . ( 1 sec) [ -14138.5361] [ 3010] [depth= 4] . ( 1 sec) [ -14087.4938] [ 3011] [depth= 1] . ( 2 sec) [ -13676.3308] [ 2957] [depth= 6] . ( 2 sec) [ -13263.0904] [ 2905] [depth= 4] . ( 2 sec) [ -12962.6584] [ 2804] [depth= 8] . ( 2 sec) [ -12842.1309] [ 2772] [depth= 10] . ( 2 sec) [ -12358.1056] [ 2673] [depth= 13] . ( 2 sec) [ -11962.4885] [ 2637] [depth= 3] . ( 2 sec) [ -11883.0092] [ 2647] [depth= 1] . ( 2 sec) [ -11867.5514] [ 2624] [depth= 7] . ( 2 sec) [ -11567.8892] [ 2621] [depth= 13] . ( 2 sec) [ -11557.8329] [ 2610] [depth= 1] . ( 2 sec) [ -11404.7688] [ 2560] [depth= 1] . ( 2 sec) [ -11301.8195] [ 2524] [depth= 10] . ( 2 sec) [ -11027.8775] [ 2473] [depth= 3] . ( 2 sec) [ -10894.2976] [ 2429] [depth= 9] . ( 2 sec) [ -10838.9796] [ 2405] [depth= 9] . ( 2 sec) [ -10783.9332] [ 2403] [depth= 2] . ( 2 sec) [ -10575.1570] [ 2402] [depth= 4] . ( 2 sec) [ -10536.1706] [ 2397] [depth= 1] . ( 2 sec) [ -10387.3686] [ 2382] [depth= 9] . ( 2 sec) [ -10379.5335] [ 2383] [depth= 1] . ( 2 sec) [ -10237.8812] [ 2316] [depth= 1] . ( 2 sec) [ -10094.6457] [ 2274] [depth= 10] . ( 2 sec) [ -10046.0096] [ 2240] [depth= 9] . ( 3 sec) [ -9988.1178] [ 2249] [depth= 1] . ( 3 sec) [ -9941.6753] [ 2235] [depth= 6] . ( 3 sec) [ -9688.5827] [ 2173] [depth= 1] . ( 3 sec) [ -9579.7530] [ 2115] [depth= 3] . ( 3 sec) [ -9571.1986] [ 2116] [depth= 1] . ( 3 sec) [ -9560.0142] [ 2122] [depth= 1] . ( 3 sec) [ -9446.5882] [ 2100] [depth= 8] . ( 3 sec) [ -9419.9845] [ 2114] [depth= 3] . ( 3 sec) [ -9306.4965] [ 2054] [depth= 8] . ( 3 sec) [ -9189.1172] [ 2054] [depth= 2] . ( 3 sec) [ -9178.1064] [ 2027] [depth= 2] . ( 3 sec) [ -9148.0602] [ 2010] [depth= 1] . ( 3 sec) [ -9143.7339] [ 2010] [depth= 1] . ( 3 sec) [ -8974.0333] [ 1922] [depth= 4] . ( 3 sec) [ -8726.3575] [ 1862] [depth= 4] . ( 3 sec) [ -8490.1850] [ 1808] [depth= 4] . ( 3 sec) [ -8489.3132] [ 1810] [depth= 1] . ( 3 sec) [ -8487.3929] [ 1811] [depth= 1] . ( 3 sec) [ -8440.7103] [ 1820] [depth= 1] . ( 3 sec) [ -8420.7480] [ 1814] [depth= 1] . ( 3 sec) [ -8398.9271] [ 1813] [depth= 5] . ( 3 sec) [ -8318.5141] [ 1813] [depth= 1] . ( 4 sec) [ -8316.7369] [ 1803] [depth= 3] . ( 4 sec) [ -8302.2720] [ 1803] [depth= 2] . ( 4 sec) [ -8299.0154] [ 1802] [depth= 2] . ( 4 sec) [ -8295.1006] [ 1802] [depth= 1] . ( 4 sec) [ -8265.2867] [ 1782] [depth= 4] . ( 4 sec) [ -8250.0613] [ 1772] [depth= 3] . ( 4 sec) [ -8227.4907] [ 1763] [depth= 1] . ( 4 sec) [ -8156.4449] [ 1761] [depth= 4] . ( 4 sec) [ -8145.8357] [ 1760] [depth= 1] . ( 4 sec) [ -8143.3894] [ 1755] [depth= 2] . ( 4 sec) [ -8138.9404] [ 1748] [depth= 3] . ( 4 sec) [ -8122.5226] [ 1757] [depth= 1] . ( 4 sec) [ -8108.7547] [ 1719] [depth= 4] . ( 4 sec) [ -8100.0215] [ 1717] [depth= 5] . ( 4 sec) [ -8044.0661] [ 1678] [depth= 2] . ( 4 sec) [ -8041.3532] [ 1678] [depth= 1] . ( 4 sec) [ -8019.3648] [ 1672] [depth= 1] . ( 5 sec) [ -7890.6482] [Branch lengths ] . ( 5 sec) [ -7888.2284] [GTR parameters ] . ( 5 sec) [ -7851.8856] [Alpha ][ 0.963443] . ( 5 sec) [ -7823.1200] [ 1652] [depth= 2] . ( 6 sec) [ -7811.0015] [ 1647] [depth= 1] . ( 6 sec) [ -7809.7509] [ 1648] [depth= 1] . ( 6 sec) [ -7808.9997] [ 1646] [depth= 1] . ( 6 sec) [ -7770.1566] [ 1626] [depth= 2] . ( 6 sec) [ -7762.1188] [ 1624] [depth= 1] . ( 6 sec) [ -7758.1700] [ 1626] [depth= 1] . ( 6 sec) [ -7758.1408] [ 1625] [depth= 2] . ( 6 sec) [ -7750.7412] [ 1616] [depth= 1] . ( 6 sec) [ -7745.4508] [ 1617] [depth= 1] . ( 6 sec) [ -7723.2981] [ 1604] [depth= 1] . ( 6 sec) [ -7721.0125] [ 1602] [depth= 1] . ( 6 sec) [ -7718.0614] [ 1604] [depth= 1] . ( 6 sec) [ -7717.9477] [ 1605] [depth= 1] . ( 6 sec) [ -7702.7119] [ 1600] [depth= 1] . ( 7 sec) [ -7699.2135] [ 1601] [depth= 1] . ( 7 sec) [ -7699.0600] [ 1599] [depth= 1] . ( 7 sec) [ -7664.7876] [ 1584] [depth= 1] . ( 7 sec) [ -7664.0704] [ 1583] [depth= 1] . ( 7 sec) [ -7657.4914] [ 1569] [depth= 1] . ( 7 sec) [ -7653.8708] [ 1567] [depth= 1] . ( 7 sec) [ -7647.9675] [ 1568] [depth= 2] . ( 7 sec) [ -7647.8471] [ 1569] [depth= 1] . ( 7 sec) [ -7638.1277] [ 1560] [depth= 2] . ( 7 sec) [ -7633.5544] [ 1555] [depth= 1] . ( 7 sec) [ -7622.4944] [ 1543] [depth= 2] . ( 8 sec) [ -7621.1896] [ 1541] [depth= 1] . ( 8 sec) [ -7620.1472] [ 1539] [depth= 1] . ( 8 sec) [ -7618.3762] [ 1546] [depth= 1] . ( 8 sec) [ -7617.8059] [ 1548] [depth= 1] . ( 8 sec) [ -7616.8711] [ 1552] [depth= 1] . ( 9 sec) [ -7603.5529] [Branch lengths ] . ( 9 sec) [ -7603.1872] [GTR parameters ] . ( 9 sec) [ -7602.0594] [Alpha ][ 1.092195] . ( 10 sec) [ -7601.9846] [ 1548] [depth= 1] . ( 11 sec) [ -7598.3837] [ 1541] [depth= 1] . ( 12 sec) [ -7598.2951] [ 1539] [depth= 1] . ( 13 sec) [ -7595.2108] [Branch lengths ] . ( 13 sec) [ -7595.1931] [GTR parameters ] . ( 13 sec) [ -7595.1917] [Alpha ][ 1.097228] . ( 16 sec) [ -7594.9719] [Branch lengths ] . ( 35 sec) [ -7594.9505] [Branch lengths ] . ( 35 sec) [ -7594.9505] [Topology ] . ( 36 sec) [ -7594.9487] [Topology ] . ( 37 sec) [ -7594.9482] [Topology ] . ( 37 sec) [ -7594.9471] [GTR parameters ] . ( 37 sec) [ -7594.9463] [Alpha ][ 1.092985] . ( 37 sec) [ -7594.9463] [Topology ] . ( 38 sec) [ -7594.9458] [Topology ] . ( 38 sec) [ -7594.9458] [GTR parameters ] . ( 38 sec) [ -7594.9458] [Alpha ][ 1.092985] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7594.945830. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17149.6725] [GTR parameters ] . ( 0 sec) [ -16828.9798] [Alpha ][ 0.500960] . ( 0 sec) [ -16533.9911] [ 3409] [depth= 3] . ( 0 sec) [ -16095.0869] [ 3315] [depth= 3] . ( 0 sec) [ -16042.9309] [ 3301] [depth= 3] . ( 0 sec) [ -15849.8292] [ 3287] [depth= 2] . ( 0 sec) [ -15613.2608] [ 3175] [depth= 3] . ( 0 sec) [ -15598.6922] [ 3177] [depth= 4] . ( 0 sec) [ -15421.3179] [ 3172] [depth= 4] . ( 1 sec) [ -15214.8109] [ 3086] [depth= 1] . ( 1 sec) [ -15209.5226] [ 3087] [depth= 7] . ( 1 sec) [ -14972.4948] [ 3068] [depth= 3] . ( 1 sec) [ -14876.3624] [ 3062] [depth= 1] . ( 1 sec) [ -14678.8335] [ 3010] [depth= 1] . ( 1 sec) [ -14597.9702] [ 3005] [depth= 4] . ( 1 sec) [ -14560.9692] [ 2965] [depth= 15] . ( 1 sec) [ -14509.4090] [ 2969] [depth= 13] . ( 1 sec) [ -14434.6343] [ 2945] [depth= 12] . ( 1 sec) [ -14311.0258] [ 2941] [depth= 1] . ( 1 sec) [ -13815.4816] [ 2921] [depth= 1] . ( 1 sec) [ -13454.5374] [ 2921] [depth= 1] . ( 1 sec) [ -13063.5851] [ 2880] [depth= 1] . ( 1 sec) [ -12917.8244] [ 2861] [depth= 1] . ( 1 sec) [ -12557.3028] [ 2773] [depth= 16] . ( 1 sec) [ -12204.3795] [ 2679] [depth= 8] . ( 1 sec) [ -12134.8537] [ 2683] [depth= 1] . ( 1 sec) [ -12003.4068] [ 2698] [depth= 1] . ( 1 sec) [ -11868.2579] [ 2701] [depth= 1] . ( 1 sec) [ -11850.0291] [ 2696] [depth= 3] . ( 1 sec) [ -11811.4370] [ 2675] [depth= 1] . ( 1 sec) [ -11760.0044] [ 2653] [depth= 3] . ( 1 sec) [ -11517.0266] [ 2598] [depth= 5] . ( 1 sec) [ -11508.5529] [ 2606] [depth= 2] . ( 1 sec) [ -11420.0867] [ 2555] [depth= 2] . ( 2 sec) [ -11415.2280] [ 2546] [depth= 2] . ( 2 sec) [ -11066.0476] [ 2425] [depth= 11] . ( 2 sec) [ -10914.6037] [ 2400] [depth= 7] . ( 2 sec) [ -10876.8671] [ 2377] [depth= 1] . ( 2 sec) [ -10857.2667] [ 2382] [depth= 2] . ( 2 sec) [ -10809.1806] [ 2370] [depth= 5] . ( 2 sec) [ -10775.5105] [ 2346] [depth= 1] . ( 2 sec) [ -10503.9843] [ 2253] [depth= 4] . ( 2 sec) [ -10391.8536] [ 2225] [depth= 1] . ( 2 sec) [ -10323.4467] [ 2225] [depth= 10] . ( 2 sec) [ -9943.4656] [ 2101] [depth= 11] . ( 2 sec) [ -9872.2504] [ 2105] [depth= 3] . ( 2 sec) [ -9634.5654] [ 2029] [depth= 11] . ( 2 sec) [ -9629.1239] [ 2040] [depth= 1] . ( 2 sec) [ -9597.0837] [ 2039] [depth= 2] . ( 2 sec) [ -9455.1857] [ 2004] [depth= 1] . ( 2 sec) [ -9454.8573] [ 2005] [depth= 1] . ( 2 sec) [ -9422.5105] [ 1992] [depth= 1] . ( 2 sec) [ -9276.7517] [ 1980] [depth= 3] . ( 2 sec) [ -9270.5540] [ 1975] [depth= 3] . ( 2 sec) [ -9244.8864] [ 1978] [depth= 1] . ( 2 sec) [ -9007.2604] [ 1966] [depth= 5] . ( 2 sec) [ -8884.7245] [ 1961] [depth= 1] . ( 3 sec) [ -8878.6646] [ 1963] [depth= 1] . ( 3 sec) [ -8874.6186] [ 1961] [depth= 1] . ( 3 sec) [ -8839.3660] [ 1952] [depth= 2] . ( 3 sec) [ -8821.1999] [ 1946] [depth= 1] . ( 3 sec) [ -8804.2539] [ 1933] [depth= 1] . ( 3 sec) [ -8745.7401] [ 1909] [depth= 3] . ( 3 sec) [ -8603.4994] [ 1831] [depth= 6] . ( 3 sec) [ -8362.6902] [ 1768] [depth= 1] . ( 3 sec) [ -8321.4243] [ 1732] [depth= 2] . ( 3 sec) [ -8310.5187] [ 1734] [depth= 1] . ( 3 sec) [ -8299.4510] [ 1725] [depth= 1] . ( 3 sec) [ -8252.4093] [ 1734] [depth= 1] . ( 3 sec) [ -8251.3696] [ 1736] [depth= 1] . ( 3 sec) [ -8225.7131] [ 1737] [depth= 3] . ( 3 sec) [ -8205.5114] [ 1731] [depth= 1] . ( 3 sec) [ -8201.8172] [ 1732] [depth= 1] . ( 3 sec) [ -8187.3114] [ 1722] [depth= 1] . ( 3 sec) [ -8144.7949] [ 1707] [depth= 1] . ( 3 sec) [ -8123.1930] [ 1697] [depth= 1] . ( 4 sec) [ -8121.1978] [ 1696] [depth= 1] . ( 4 sec) [ -8118.7478] [ 1670] [depth= 3] . ( 4 sec) [ -7839.2433] [ 1596] [depth= 2] . ( 4 sec) [ -7831.5037] [ 1598] [depth= 1] . ( 4 sec) [ -7807.4821] [ 1590] [depth= 2] . ( 4 sec) [ -7805.5341] [ 1593] [depth= 1] . ( 4 sec) [ -7801.7367] [ 1591] [depth= 1] . ( 4 sec) [ -7790.0837] [ 1592] [depth= 1] . ( 4 sec) [ -7747.8019] [Branch lengths ] . ( 5 sec) [ -7745.1069] [GTR parameters ] . ( 5 sec) [ -7712.3714] [Alpha ][ 0.961176] . ( 5 sec) [ -7710.4742] [ 1586] [depth= 1] . ( 5 sec) [ -7615.7570] [ 1544] [depth= 1] . ( 5 sec) [ -7614.4015] [ 1542] [depth= 1] . ( 5 sec) [ -7609.3211] [ 1542] [depth= 1] . ( 6 sec) [ -7609.1815] [ 1542] [depth= 1] . ( 6 sec) [ -7609.1285] [ 1542] [depth= 1] . ( 7 sec) [ -7608.8538] [ 1539] [depth= 1] . ( 7 sec) [ -7608.7929] [ 1542] [depth= 1] . ( 7 sec) [ -7608.7064] [ 1546] [depth= 1] . ( 7 sec) [ -7608.6118] [ 1544] [depth= 1] . ( 8 sec) [ -7597.9875] [Branch lengths ] . ( 9 sec) [ -7597.6546] [GTR parameters ] . ( 9 sec) [ -7596.7432] [Alpha ][ 1.079239] . ( 12 sec) [ -7595.6957] [Branch lengths ] . ( 27 sec) [ -7595.6382] [ 1542] [depth= 1] . ( 31 sec) [ -7595.2691] [Branch lengths ] . ( 31 sec) [ -7595.2671] [GTR parameters ] . ( 31 sec) [ -7595.2535] [Alpha ][ 1.095091] . ( 31 sec) [ -7595.2535] [Topology ] . ( 32 sec) [ -7595.2114] [Topology ] . ( 33 sec) [ -7595.1984] [Topology ] . ( 33 sec) [ -7595.1926] [Topology ] . ( 34 sec) [ -7595.1899] [Topology ] . ( 35 sec) [ -7595.1887] [Topology ] . ( 36 sec) [ -7595.1881] [Topology ] . ( 36 sec) [ -7595.1880] [GTR parameters ] . ( 36 sec) [ -7595.1877] [Alpha ][ 1.097451] . ( 36 sec) [ -7595.1877] [Topology ] . ( 37 sec) [ -7595.1873] [Topology ] . ( 37 sec) [ -7595.1873] [GTR parameters ] . ( 37 sec) [ -7595.1873] [Alpha ][ 1.097451] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -7595.1204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -7595.0599] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7595.059871. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17706.5529] [GTR parameters ] . ( 1 sec) [ -17363.3568] [Alpha ][ 0.500960] . ( 1 sec) [ -17056.5728] [ 3591] [depth= 8] . ( 1 sec) [ -16469.0684] [ 3489] [depth= 8] . ( 1 sec) [ -16456.9975] [ 3489] [depth= 2] . ( 1 sec) [ -16335.8786] [ 3487] [depth= 1] . ( 1 sec) [ -16290.2550] [ 3484] [depth= 5] . ( 1 sec) [ -16233.0281] [ 3483] [depth= 1] . ( 1 sec) [ -15939.5878] [ 3388] [depth= 5] . ( 1 sec) [ -15848.7301] [ 3374] [depth= 5] . ( 1 sec) [ -15254.1775] [ 3229] [depth= 8] . ( 1 sec) [ -15153.3371] [ 3238] [depth= 14] . ( 1 sec) [ -14720.2004] [ 3133] [depth= 3] . ( 1 sec) [ -14366.1303] [ 3054] [depth= 8] . ( 1 sec) [ -14326.7708] [ 3046] [depth= 2] . ( 1 sec) [ -14140.0223] [ 3042] [depth= 1] . ( 1 sec) [ -13942.7352] [ 2984] [depth= 9] . ( 1 sec) [ -13792.5892] [ 2985] [depth= 1] . ( 1 sec) [ -13442.6212] [ 2946] [depth= 6] . ( 1 sec) [ -13197.2259] [ 2901] [depth= 12] . ( 1 sec) [ -12513.2575] [ 2758] [depth= 6] . ( 1 sec) [ -12295.5875] [ 2762] [depth= 12] . ( 1 sec) [ -11954.4342] [ 2627] [depth= 11] . ( 2 sec) [ -11734.2906] [ 2595] [depth= 9] . ( 2 sec) [ -11466.6407] [ 2518] [depth= 8] . ( 2 sec) [ -11321.5826] [ 2510] [depth= 8] . ( 2 sec) [ -10933.7624] [ 2353] [depth= 8] . ( 2 sec) [ -10847.1596] [ 2353] [depth= 9] . ( 2 sec) [ -10654.9618] [ 2301] [depth= 5] . ( 2 sec) [ -10650.2760] [ 2301] [depth= 1] . ( 2 sec) [ -10422.5136] [ 2286] [depth= 2] . ( 2 sec) [ -10396.8800] [ 2289] [depth= 3] . ( 2 sec) [ -10031.9766] [ 2195] [depth= 1] . ( 2 sec) [ -10007.1083] [ 2179] [depth= 1] . ( 2 sec) [ -9981.6611] [ 2112] [depth= 1] . ( 2 sec) [ -9945.8543] [ 2114] [depth= 1] . ( 2 sec) [ -9896.2771] [ 2086] [depth= 4] . ( 2 sec) [ -9887.7954] [ 2083] [depth= 1] . ( 2 sec) [ -9869.0854] [ 2084] [depth= 1] . ( 2 sec) [ -9706.9423] [ 2072] [depth= 3] . ( 2 sec) [ -9687.8513] [ 2033] [depth= 1] . ( 3 sec) [ -9453.9937] [ 2020] [depth= 5] . ( 3 sec) [ -9385.9773] [ 2018] [depth= 1] . ( 3 sec) [ -9368.8373] [ 2015] [depth= 1] . ( 3 sec) [ -9333.8579] [ 1997] [depth= 3] . ( 3 sec) [ -9316.6801] [ 1981] [depth= 2] . ( 3 sec) [ -9254.2500] [ 1977] [depth= 5] . ( 3 sec) [ -9182.5777] [ 1974] [depth= 1] . ( 3 sec) [ -9157.4790] [ 1933] [depth= 3] . ( 3 sec) [ -9091.0238] [ 1899] [depth= 1] . ( 3 sec) [ -9082.8039] [ 1895] [depth= 3] . ( 3 sec) [ -9068.1788] [ 1888] [depth= 1] . ( 3 sec) [ -8865.4549] [ 1816] [depth= 5] . ( 3 sec) [ -8865.1563] [ 1818] [depth= 1] . ( 3 sec) [ -8861.9898] [ 1817] [depth= 1] . ( 3 sec) [ -8657.7495] [ 1766] [depth= 1] . ( 3 sec) [ -8382.9094] [ 1690] [depth= 6] . ( 3 sec) [ -8305.5953] [ 1695] [depth= 1] . ( 3 sec) [ -8303.8163] [ 1695] [depth= 1] . ( 3 sec) [ -8098.6713] [ 1648] [depth= 5] . ( 3 sec) [ -8064.2903] [ 1647] [depth= 1] . ( 3 sec) [ -8048.5164] [ 1662] [depth= 1] . ( 4 sec) [ -8040.0643] [ 1665] [depth= 1] . ( 4 sec) [ -8026.3701] [ 1651] [depth= 1] . ( 4 sec) [ -7989.6473] [ 1632] [depth= 2] . ( 4 sec) [ -7978.5306] [ 1631] [depth= 1] . ( 4 sec) [ -7938.6649] [ 1616] [depth= 2] . ( 4 sec) [ -7926.2583] [ 1610] [depth= 1] . ( 4 sec) [ -7925.0097] [ 1615] [depth= 1] . ( 4 sec) [ -7914.6684] [ 1614] [depth= 1] . ( 4 sec) [ -7883.3468] [ 1606] [depth= 1] . ( 4 sec) [ -7878.5921] [ 1605] [depth= 1] . ( 4 sec) [ -7819.2865] [ 1616] [depth= 1] . ( 4 sec) [ -7757.3064] [Branch lengths ] . ( 5 sec) [ -7755.3616] [GTR parameters ] . ( 5 sec) [ -7721.4865] [Alpha ][ 0.964495] . ( 5 sec) [ -7710.3269] [ 1613] [depth= 1] . ( 5 sec) [ -7708.5954] [ 1611] [depth= 1] . ( 6 sec) [ -7708.2477] [ 1612] [depth= 1] . ( 6 sec) [ -7706.7902] [ 1609] [depth= 1] . ( 6 sec) [ -7702.2764] [ 1603] [depth= 1] . ( 6 sec) [ -7685.7952] [ 1597] [depth= 1] . ( 6 sec) [ -7674.0713] [ 1585] [depth= 1] . ( 6 sec) [ -7634.1209] [ 1563] [depth= 5] . ( 7 sec) [ -7633.8189] [ 1561] [depth= 1] . ( 7 sec) [ -7622.3164] [ 1556] [depth= 1] . ( 7 sec) [ -7620.6713] [ 1557] [depth= 1] . ( 7 sec) [ -7618.8394] [ 1556] [depth= 1] . ( 7 sec) [ -7618.2623] [ 1555] [depth= 1] . ( 7 sec) [ -7609.7824] [ 1544] [depth= 3] . ( 7 sec) [ -7609.5728] [ 1542] [depth= 1] . ( 8 sec) [ -7609.4362] [ 1544] [depth= 1] . ( 8 sec) [ -7608.9578] [ 1547] [depth= 1] . ( 9 sec) [ -7598.9141] [Branch lengths ] . ( 9 sec) [ -7598.7164] [GTR parameters ] . ( 9 sec) [ -7597.9130] [Alpha ][ 1.074761] . ( 10 sec) [ -7596.4046] [ 1546] [depth= 1] . ( 11 sec) [ -7596.3943] [ 1543] [depth= 1] . ( 13 sec) [ -7595.3753] [Branch lengths ] . ( 13 sec) [ -7595.3706] [GTR parameters ] . ( 13 sec) [ -7595.3586] [Alpha ][ 1.089567] . ( 16 sec) [ -7595.2638] [Branch lengths ] . ( 31 sec) [ -7595.1777] [ 1539] [depth= 1] . ( 35 sec) [ -7594.9698] [Branch lengths ] . ( 36 sec) [ -7594.9690] [GTR parameters ] . ( 36 sec) [ -7594.9687] [Alpha ][ 1.091597] . ( 36 sec) [ -7594.9687] [Topology ] . ( 36 sec) [ -7594.9516] [Topology ] . ( 37 sec) [ -7594.9480] [Topology ] . ( 38 sec) [ -7594.9466] [Topology ] . ( 39 sec) [ -7594.9461] [Topology ] . ( 39 sec) [ -7594.9461] [GTR parameters ] . ( 39 sec) [ -7594.9460] [Alpha ][ 1.092688] . ( 39 sec) [ -7594.9460] [Topology ] . ( 40 sec) [ -7594.9457] [Topology ] . ( 40 sec) [ -7594.9457] [GTR parameters ] . ( 40 sec) [ -7594.9457] [Alpha ][ 1.092688] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7594.945719. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17173.8563] [GTR parameters ] . ( 0 sec) [ -16822.6043] [Alpha ][ 0.500960] . ( 0 sec) [ -16504.9973] [ 3495] [depth= 8] . ( 0 sec) [ -15981.2953] [ 3368] [depth= 9] . ( 0 sec) [ -15751.9608] [ 3338] [depth= 2] . ( 0 sec) [ -15582.7576] [ 3248] [depth= 1] . ( 0 sec) [ -15410.8948] [ 3216] [depth= 6] . ( 0 sec) [ -15235.7084] [ 3208] [depth= 3] . ( 0 sec) [ -15206.6020] [ 3198] [depth= 5] . ( 0 sec) [ -15041.6238] [ 3127] [depth= 1] . ( 0 sec) [ -14743.5504] [ 3047] [depth= 7] . ( 0 sec) [ -14645.8187] [ 3012] [depth= 2] . ( 0 sec) [ -14532.9487] [ 3001] [depth= 3] . ( 0 sec) [ -14357.2264] [ 2953] [depth= 4] . ( 0 sec) [ -14190.0492] [ 2947] [depth= 4] . ( 1 sec) [ -14073.0895] [ 2946] [depth= 4] . ( 1 sec) [ -13949.9107] [ 2871] [depth= 5] . ( 1 sec) [ -13901.2566] [ 2864] [depth= 1] . ( 1 sec) [ -13675.7987] [ 2840] [depth= 12] . ( 1 sec) [ -13466.4076] [ 2839] [depth= 1] . ( 1 sec) [ -13370.4283] [ 2772] [depth= 12] . ( 1 sec) [ -13025.1546] [ 2666] [depth= 3] . ( 1 sec) [ -12984.5116] [ 2659] [depth= 2] . ( 1 sec) [ -12933.0804] [ 2665] [depth= 1] . ( 1 sec) [ -12231.9094] [ 2553] [depth= 7] . ( 1 sec) [ -12084.0159] [ 2544] [depth= 16] . ( 1 sec) [ -11969.3997] [ 2555] [depth= 1] . ( 1 sec) [ -11881.8919] [ 2528] [depth= 4] . ( 1 sec) [ -11857.6119] [ 2546] [depth= 1] . ( 1 sec) [ -11476.5241] [ 2392] [depth= 14] . ( 1 sec) [ -11332.7156] [ 2390] [depth= 1] . ( 1 sec) [ -11049.5181] [ 2368] [depth= 12] . ( 1 sec) [ -10953.9875] [ 2315] [depth= 2] . ( 1 sec) [ -10886.3298] [ 2297] [depth= 2] . ( 1 sec) [ -10479.9547] [ 2264] [depth= 9] . ( 1 sec) [ -10475.4536] [ 2273] [depth= 13] . ( 1 sec) [ -10462.9194] [ 2274] [depth= 1] . ( 1 sec) [ -10416.7570] [ 2276] [depth= 9] . ( 1 sec) [ -10102.1696] [ 2137] [depth= 10] . ( 2 sec) [ -9942.7962] [ 2066] [depth= 10] . ( 2 sec) [ -9601.8858] [ 2076] [depth= 11] . ( 2 sec) [ -9476.6562] [ 2047] [depth= 3] . ( 2 sec) [ -9438.4846] [ 2082] [depth= 3] . ( 2 sec) [ -9290.1816] [ 2018] [depth= 7] . ( 2 sec) [ -8975.6945] [ 1926] [depth= 11] . ( 2 sec) [ -8957.5345] [ 1915] [depth= 1] . ( 2 sec) [ -8938.8973] [ 1910] [depth= 3] . ( 2 sec) [ -8935.2183] [ 1909] [depth= 1] . ( 2 sec) [ -8907.0446] [ 1874] [depth= 4] . ( 2 sec) [ -8780.4021] [ 1863] [depth= 1] . ( 2 sec) [ -8713.8796] [ 1849] [depth= 6] . ( 2 sec) [ -8637.3427] [ 1824] [depth= 1] . ( 2 sec) [ -8595.3517] [ 1806] [depth= 4] . ( 2 sec) [ -8576.1530] [ 1798] [depth= 2] . ( 2 sec) [ -8243.7979] [ 1688] [depth= 6] . ( 2 sec) [ -8228.8420] [ 1692] [depth= 2] . ( 2 sec) [ -8203.2311] [ 1689] [depth= 1] . ( 2 sec) [ -8180.6933] [ 1680] [depth= 1] . ( 2 sec) [ -8083.1169] [ 1663] [depth= 3] . ( 3 sec) [ -8081.9735] [ 1662] [depth= 1] . ( 3 sec) [ -8076.6152] [ 1661] [depth= 1] . ( 3 sec) [ -8051.1235] [ 1655] [depth= 2] . ( 3 sec) [ -8048.9588] [ 1658] [depth= 1] . ( 3 sec) [ -8038.1713] [ 1660] [depth= 1] . ( 3 sec) [ -8032.7914] [ 1656] [depth= 1] . ( 3 sec) [ -7976.6662] [ 1622] [depth= 1] . ( 3 sec) [ -7922.3484] [ 1617] [depth= 2] . ( 3 sec) [ -7908.7651] [ 1614] [depth= 1] . ( 3 sec) [ -7905.0268] [ 1611] [depth= 1] . ( 3 sec) [ -7901.3886] [ 1613] [depth= 1] . ( 3 sec) [ -7900.6569] [ 1615] [depth= 1] . ( 3 sec) [ -7893.5550] [ 1607] [depth= 2] . ( 3 sec) [ -7856.8213] [ 1595] [depth= 1] . ( 3 sec) [ -7810.0940] [ 1591] [depth= 2] . ( 3 sec) [ -7807.2842] [ 1589] [depth= 1] . ( 3 sec) [ -7802.1450] [ 1592] [depth= 1] . ( 3 sec) [ -7800.5182] [ 1591] [depth= 1] . ( 3 sec) [ -7779.1733] [ 1594] [depth= 2] . ( 4 sec) [ -7753.3891] [ 1570] [depth= 1] . ( 4 sec) [ -7695.9227] [Branch lengths ] . ( 4 sec) [ -7693.8212] [GTR parameters ] . ( 4 sec) [ -7657.8012] [Alpha ][ 0.994507] . ( 5 sec) [ -7657.2770] [ 1573] [depth= 1] . ( 5 sec) [ -7655.7707] [ 1571] [depth= 1] . ( 5 sec) [ -7650.6170] [ 1562] [depth= 3] . ( 5 sec) [ -7649.5085] [ 1560] [depth= 1] . ( 5 sec) [ -7649.2528] [ 1558] [depth= 1] . ( 5 sec) [ -7643.3365] [ 1552] [depth= 1] . ( 6 sec) [ -7642.9957] [ 1555] [depth= 1] . ( 6 sec) [ -7642.0140] [ 1551] [depth= 1] . ( 6 sec) [ -7640.6379] [ 1549] [depth= 2] . ( 6 sec) [ -7629.8046] [ 1548] [depth= 1] . ( 6 sec) [ -7629.5888] [ 1548] [depth= 1] . ( 6 sec) [ -7624.8392] [ 1547] [depth= 2] . ( 6 sec) [ -7623.0302] [ 1547] [depth= 1] . ( 7 sec) [ -7622.2211] [ 1546] [depth= 1] . ( 7 sec) [ -7620.6189] [ 1539] [depth= 1] . ( 7 sec) [ -7618.2259] [ 1539] [depth= 2] . ( 7 sec) [ -7618.1106] [ 1538] [depth= 1] . ( 7 sec) [ -7617.7209] [ 1538] [depth= 1] . ( 7 sec) [ -7616.9906] [ 1547] [depth= 1] . ( 8 sec) [ -7602.8197] [Branch lengths ] . ( 8 sec) [ -7602.5667] [GTR parameters ] . ( 8 sec) [ -7602.1180] [Alpha ][ 1.078560] . ( 8 sec) [ -7597.3149] [ 1541] [depth= 1] . ( 9 sec) [ -7597.0631] [ 1539] [depth= 1] . ( 9 sec) [ -7596.8085] [ 1541] [depth= 1] . ( 11 sec) [ -7595.3938] [Branch lengths ] . ( 12 sec) [ -7595.3854] [GTR parameters ] . ( 12 sec) [ -7595.3796] [Alpha ][ 1.088826] . ( 15 sec) [ -7595.2669] [Branch lengths ] . ( 20 sec) [ -7595.0179] [ 1539] [depth= 1] . ( 34 sec) [ -7594.9496] [Branch lengths ] . ( 34 sec) [ -7594.9490] [GTR parameters ] . ( 34 sec) [ -7594.9483] [Alpha ][ 1.092335] . ( 34 sec) [ -7594.9483] [Topology ] . ( 35 sec) [ -7594.9464] [Topology ] . ( 35 sec) [ -7594.9459] [Topology ] . ( 36 sec) [ -7594.9458] [GTR parameters ] . ( 36 sec) [ -7594.9458] [Alpha ][ 1.092335] . ( 36 sec) [ -7594.9458] [Topology ] . ( 36 sec) [ -7594.9456] [Topology ] . ( 37 sec) [ -7594.9456] [GTR parameters ] . ( 37 sec) [ -7594.9456] [Alpha ][ 1.092335] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7594.945619. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18230.7185] [GTR parameters ] . ( 1 sec) [ -17875.9528] [Alpha ][ 0.500960] . ( 1 sec) [ -17532.1120] [ 3655] [depth= 6] . ( 1 sec) [ -16958.6888] [ 3554] [depth= 11] . ( 1 sec) [ -16801.0403] [ 3538] [depth= 6] . ( 1 sec) [ -16712.6879] [ 3530] [depth= 5] . ( 1 sec) [ -16635.1394] [ 3466] [depth= 7] . ( 1 sec) [ -16547.6483] [ 3466] [depth= 5] . ( 1 sec) [ -16481.2999] [ 3458] [depth= 12] . ( 1 sec) [ -16332.7521] [ 3467] [depth= 1] . ( 1 sec) [ -16142.9159] [ 3436] [depth= 2] . ( 1 sec) [ -15901.9709] [ 3384] [depth= 13] . ( 1 sec) [ -15768.7059] [ 3340] [depth= 8] . ( 1 sec) [ -15624.1432] [ 3299] [depth= 1] . ( 1 sec) [ -15338.0034] [ 3256] [depth= 5] . ( 1 sec) [ -15281.9692] [ 3252] [depth= 1] . ( 2 sec) [ -15100.1793] [ 3235] [depth= 3] . ( 2 sec) [ -14755.1418] [ 3236] [depth= 1] . ( 2 sec) [ -14371.4793] [ 3226] [depth= 9] . ( 2 sec) [ -14228.1368] [ 3197] [depth= 2] . ( 2 sec) [ -14074.5322] [ 3166] [depth= 8] . ( 2 sec) [ -13864.7586] [ 3144] [depth= 9] . ( 2 sec) [ -13765.9962] [ 3106] [depth= 1] . ( 2 sec) [ -13695.9701] [ 3087] [depth= 1] . ( 2 sec) [ -13381.5427] [ 3035] [depth= 11] . ( 2 sec) [ -13358.8243] [ 3040] [depth= 1] . ( 2 sec) [ -12990.5512] [ 2993] [depth= 7] . ( 2 sec) [ -12876.2706] [ 2995] [depth= 2] . ( 2 sec) [ -12534.8120] [ 2879] [depth= 8] . ( 2 sec) [ -12532.8003] [ 2877] [depth= 1] . ( 2 sec) [ -12510.0055] [ 2872] [depth= 1] . ( 2 sec) [ -12433.5183] [ 2851] [depth= 7] . ( 2 sec) [ -12362.2744] [ 2769] [depth= 5] . ( 2 sec) [ -12343.1374] [ 2767] [depth= 2] . ( 2 sec) [ -12145.6447] [ 2742] [depth= 8] . ( 2 sec) [ -11667.5265] [ 2588] [depth= 5] . ( 2 sec) [ -11434.5296] [ 2581] [depth= 1] . ( 2 sec) [ -11301.5013] [ 2558] [depth= 5] . ( 2 sec) [ -11267.4562] [ 2546] [depth= 1] . ( 3 sec) [ -11156.0638] [ 2547] [depth= 1] . ( 3 sec) [ -11133.8578] [ 2490] [depth= 1] . ( 3 sec) [ -10989.4015] [ 2460] [depth= 8] . ( 3 sec) [ -10970.3707] [ 2453] [depth= 1] . ( 3 sec) [ -10759.3428] [ 2386] [depth= 5] . ( 3 sec) [ -10740.6612] [ 2360] [depth= 4] . ( 3 sec) [ -10203.7406] [ 2213] [depth= 4] . ( 3 sec) [ -10155.8764] [ 2222] [depth= 3] . ( 3 sec) [ -10147.4585] [ 2224] [depth= 1] . ( 3 sec) [ -10120.7541] [ 2213] [depth= 3] . ( 3 sec) [ -9889.3774] [ 2156] [depth= 9] . ( 3 sec) [ -9606.5282] [ 2064] [depth= 2] . ( 3 sec) [ -9468.9164] [ 2029] [depth= 3] . ( 3 sec) [ -9210.5992] [ 2026] [depth= 2] . ( 3 sec) [ -9048.0934] [ 1970] [depth= 1] . ( 3 sec) [ -8964.8367] [ 1963] [depth= 1] . ( 3 sec) [ -8875.1586] [ 1939] [depth= 1] . ( 3 sec) [ -8680.4057] [ 1870] [depth= 6] . ( 3 sec) [ -8675.7281] [ 1870] [depth= 1] . ( 3 sec) [ -8662.0377] [ 1800] [depth= 1] . ( 3 sec) [ -8656.7681] [ 1801] [depth= 1] . ( 3 sec) [ -8602.0632] [ 1798] [depth= 5] . ( 4 sec) [ -8594.4416] [ 1802] [depth= 1] . ( 4 sec) [ -8592.0334] [ 1813] [depth= 7] . ( 4 sec) [ -8590.5656] [ 1813] [depth= 1] . ( 4 sec) [ -8589.8995] [ 1813] [depth= 1] . ( 4 sec) [ -8587.5832] [ 1809] [depth= 1] . ( 4 sec) [ -8539.6050] [ 1808] [depth= 1] . ( 4 sec) [ -8403.9044] [ 1748] [depth= 3] . ( 4 sec) [ -8395.8530] [ 1747] [depth= 3] . ( 4 sec) [ -8388.7854] [ 1746] [depth= 1] . ( 4 sec) [ -8380.7460] [ 1746] [depth= 1] . ( 4 sec) [ -8353.9505] [ 1746] [depth= 2] . ( 4 sec) [ -8343.6563] [ 1748] [depth= 1] . ( 4 sec) [ -8274.7806] [ 1729] [depth= 5] . ( 4 sec) [ -8271.4875] [ 1725] [depth= 4] . ( 4 sec) [ -8266.1074] [ 1724] [depth= 1] . ( 4 sec) [ -8262.4994] [ 1723] [depth= 1] . ( 4 sec) [ -8220.6844] [ 1704] [depth= 3] . ( 4 sec) [ -8199.0643] [ 1705] [depth= 1] . ( 5 sec) [ -8181.4897] [ 1697] [depth= 2] . ( 5 sec) [ -8174.1602] [ 1697] [depth= 1] . ( 5 sec) [ -8172.2041] [ 1694] [depth= 1] . ( 5 sec) [ -8166.6301] [ 1691] [depth= 3] . ( 5 sec) [ -8096.4960] [Branch lengths ] . ( 6 sec) [ -8094.4095] [GTR parameters ] . ( 6 sec) [ -8064.1377] [Alpha ][ 0.909319] . ( 6 sec) [ -8009.2080] [ 1667] [depth= 8] . ( 6 sec) [ -7986.1120] [ 1668] [depth= 1] . ( 6 sec) [ -7985.9824] [ 1671] [depth= 1] . ( 6 sec) [ -7985.4246] [ 1672] [depth= 1] . ( 6 sec) [ -7974.7931] [ 1664] [depth= 2] . ( 6 sec) [ -7910.3857] [ 1662] [depth= 1] . ( 6 sec) [ -7909.9291] [ 1662] [depth= 1] . ( 6 sec) [ -7905.6267] [ 1646] [depth= 6] . ( 6 sec) [ -7899.8906] [ 1637] [depth= 1] . ( 6 sec) [ -7896.2452] [ 1636] [depth= 1] . ( 7 sec) [ -7896.1863] [ 1640] [depth= 1] . ( 7 sec) [ -7830.9101] [ 1594] [depth= 3] . ( 7 sec) [ -7790.1432] [ 1607] [depth= 1] . ( 7 sec) [ -7789.5233] [ 1605] [depth= 1] . ( 7 sec) [ -7789.1807] [ 1605] [depth= 2] . ( 7 sec) [ -7779.3439] [ 1604] [depth= 2] . ( 7 sec) [ -7775.0490] [ 1602] [depth= 1] . ( 7 sec) [ -7758.8798] [ 1596] [depth= 1] . ( 7 sec) [ -7722.5922] [ 1581] [depth= 2] . ( 7 sec) [ -7707.5658] [ 1574] [depth= 2] . ( 7 sec) [ -7701.1266] [ 1574] [depth= 1] . ( 8 sec) [ -7700.6119] [ 1576] [depth= 1] . ( 8 sec) [ -7700.5183] [ 1581] [depth= 1] . ( 8 sec) [ -7654.5376] [ 1549] [depth= 1] . ( 8 sec) [ -7649.2942] [ 1542] [depth= 1] . ( 8 sec) [ -7647.0084] [ 1540] [depth= 1] . ( 8 sec) [ -7646.7756] [ 1538] [depth= 1] . ( 8 sec) [ -7645.4885] [ 1536] [depth= 1] . ( 8 sec) [ -7645.2789] [ 1538] [depth= 1] . ( 8 sec) [ -7644.4400] [ 1541] [depth= 1] . ( 8 sec) [ -7644.1849] [ 1540] [depth= 1] . ( 8 sec) [ -7639.2675] [ 1539] [depth= 1] . ( 8 sec) [ -7638.5253] [ 1537] [depth= 1] . ( 8 sec) [ -7637.8980] [ 1540] [depth= 1] . ( 9 sec) [ -7604.9673] [Branch lengths ] . ( 9 sec) [ -7604.4776] [GTR parameters ] . ( 9 sec) [ -7602.2971] [Alpha ][ 1.085539] . ( 10 sec) [ -7602.2376] [ 1537] [depth= 1] . ( 10 sec) [ -7598.1052] [ 1542] [depth= 2] . ( 10 sec) [ -7596.5459] [ 1539] [depth= 1] . ( 13 sec) [ -7595.0445] [Branch lengths ] . ( 13 sec) [ -7595.0126] [GTR parameters ] . ( 13 sec) [ -7595.0098] [Alpha ][ 1.092654] . ( 16 sec) [ -7594.9481] [Branch lengths ] . ( 35 sec) [ -7594.9457] [Branch lengths ] . ( 35 sec) [ -7594.9457] [Topology ] . ( 36 sec) [ -7594.9456] [Topology ] . ( 36 sec) [ -7594.9455] [GTR parameters ] . ( 36 sec) [ -7594.9455] [Alpha ][ 1.092654] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7594.945509. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7635.534928 . ( 0 sec) [ -7630.7980] [GTR parameters ] . ( 0 sec) [ -7630.6061] [Alpha ][ 1.055716] . ( 0 sec) [ -7630.6061] [Topology ] . ( 1 sec) [ -7600.6305] [Topology ] . ( 2 sec) [ -7596.7981] [Topology ] . ( 3 sec) [ -7595.9117] [Topology ] . ( 3 sec) [ -7595.5834] [Topology ] . ( 4 sec) [ -7595.4422] [Topology ] . ( 5 sec) [ -7595.3780] [Topology ] . ( 6 sec) [ -7595.3480] [Topology ] . Checking for NNIs, optimizing five branches... . ( 11 sec) [ -7595.1140] [Topology ] . Before opt ts/t=1.000000 LK=-7595.114037 . ( 11 sec) [ -7595.0703] [GTR parameters ] . ( 11 sec) [ -7595.0021] [Alpha ][ 1.089690] . ( 11 sec) [ -7595.0021] [Topology ] . ( 12 sec) [ -7594.9687] [Topology ] . ( 13 sec) [ -7594.9564] [Topology ] . ( 14 sec) [ -7594.9510] [Topology ] . ( 14 sec) [ -7594.9484] [Topology ] . ( 15 sec) [ -7594.9472] [Topology ] . ( 16 sec) [ -7594.9466] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7594.946644 . ( 21 sec) [ -7594.9466] [GTR parameters ] . ( 21 sec) [ -7594.9461] [Alpha ][ 1.092464] . ( 21 sec) [ -7594.9461] [Topology ] . ( 22 sec) [ -7594.9458] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 33 sec) [ -7630.7980] [GTR parameters ] . ( 33 sec) [ -7630.6061] [Alpha ][ 1.055716] . ( 34 sec) [ -7628.9628] [ 1539] [depth= 1] . ( 34 sec) [ -7626.5188] [ 1542] [depth= 1] . ( 34 sec) [ -7626.3541] [ 1542] [depth= 1] . ( 34 sec) [ -7625.9825] [ 1539] [depth= 1] . ( 34 sec) [ -7625.2368] [ 1539] [depth= 1] . ( 34 sec) [ -7624.0132] [ 1539] [depth= 1] . ( 34 sec) [ -7623.4564] [ 1540] [depth= 1] . ( 34 sec) [ -7623.4087] [ 1542] [depth= 1] . ( 35 sec) [ -7622.7522] [ 1543] [depth= 1] . ( 35 sec) [ -7622.3383] [ 1541] [depth= 1] . ( 35 sec) [ -7621.4984] [ 1543] [depth= 1] . ( 36 sec) [ -7620.7238] [ 1539] [depth= 1] . ( 36 sec) [ -7620.6113] [ 1537] [depth= 1] . ( 36 sec) [ -7619.5653] [ 1540] [depth= 1] . ( 36 sec) [ -7617.5719] [ 1537] [depth= 1] . ( 36 sec) [ -7609.5343] [ 1539] [depth= 1] . ( 36 sec) [ -7595.7066] [Branch lengths ] . ( 36 sec) [ -7595.6749] [GTR parameters ] . ( 36 sec) [ -7595.6263] [Alpha ][ 1.084265] . ( 40 sec) [ -7595.0052] [Branch lengths ] . ( 59 sec) [ -7594.9571] [Branch lengths ] . ( 59 sec) [ -7594.9571] [Topology ] . ( 59 sec) [ -7594.9532] [Topology ] . ( 60 sec) [ -7594.9519] [Topology ] . ( 61 sec) [ -7594.9514] [Topology ] . ( 61 sec) [ -7594.9501] [GTR parameters ] . ( 61 sec) [ -7594.9464] [Alpha ][ 1.092463] . ( 61 sec) [ -7594.9464] [Topology ] . ( 62 sec) [ -7594.9459] [Topology ] . ( 62 sec) [ -7594.9459] [GTR parameters ] . ( 62 sec) [ -7594.9459] [Alpha ][ 1.092463] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7594.945794 . Log likelihood obtained after SPR moves : -7594.945862 . Log likelihood of the current tree: -7594.945794. . Printing the most likely tree in file 'data86.phy_phyml_tree.txt'... . Best log likelihood : -7594.945509 . Time used 0h1m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo