.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data93.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... . 402 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . [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)... . ( 1 sec) [ -18157.8439] [GTR parameters ] . ( 1 sec) [ -17835.7590] [Alpha ][ 0.500960] . ( 1 sec) [ -17545.2536] [ 3718] [depth= 8] . ( 1 sec) [ -16786.0689] [ 3671] [depth= 6] . ( 1 sec) [ -16707.2056] [ 3663] [depth= 1] . ( 1 sec) [ -16696.3504] [ 3665] [depth= 6] . ( 1 sec) [ -16568.4176] [ 3635] [depth= 5] . ( 1 sec) [ -16498.4909] [ 3619] [depth= 2] . ( 1 sec) [ -16400.2251] [ 3592] [depth= 10] . ( 1 sec) [ -16284.2532] [ 3581] [depth= 1] . ( 1 sec) [ -16231.1917] [ 3568] [depth= 1] . ( 1 sec) [ -15942.2062] [ 3503] [depth= 3] . ( 1 sec) [ -15777.6957] [ 3475] [depth= 11] . ( 1 sec) [ -15762.2918] [ 3519] [depth= 1] . ( 2 sec) [ -15327.0890] [ 3524] [depth= 11] . ( 2 sec) [ -15147.2212] [ 3487] [depth= 3] . ( 2 sec) [ -15066.4323] [ 3482] [depth= 3] . ( 2 sec) [ -14988.9148] [ 3428] [depth= 5] . ( 2 sec) [ -14925.4854] [ 3429] [depth= 9] . ( 2 sec) [ -14682.6055] [ 3420] [depth= 18] . ( 2 sec) [ -14655.7642] [ 3451] [depth= 1] . ( 2 sec) [ -14453.6856] [ 3414] [depth= 3] . ( 2 sec) [ -14274.1396] [ 3417] [depth= 1] . ( 2 sec) [ -14190.6665] [ 3402] [depth= 1] . ( 2 sec) [ -14000.2944] [ 3386] [depth= 20] . ( 2 sec) [ -13732.2372] [ 3345] [depth= 10] . ( 2 sec) [ -13684.4240] [ 3315] [depth= 1] . ( 2 sec) [ -13563.1584] [ 3224] [depth= 22] . ( 2 sec) [ -13146.4616] [ 3100] [depth= 6] . ( 2 sec) [ -13100.1584] [ 3105] [depth= 2] . ( 2 sec) [ -12819.9051] [ 2992] [depth= 1] . ( 2 sec) [ -12711.9656] [ 2943] [depth= 3] . ( 2 sec) [ -12658.7471] [ 2941] [depth= 3] . ( 2 sec) [ -12636.7614] [ 2925] [depth= 2] . ( 2 sec) [ -12509.1745] [ 2926] [depth= 7] . ( 2 sec) [ -12337.3562] [ 2883] [depth= 9] . ( 2 sec) [ -12023.5459] [ 2794] [depth= 7] . ( 2 sec) [ -12011.0445] [ 2791] [depth= 2] . ( 2 sec) [ -11958.5314] [ 2783] [depth= 2] . ( 3 sec) [ -11855.5187] [ 2758] [depth= 6] . ( 3 sec) [ -11821.7933] [ 2752] [depth= 16] . ( 3 sec) [ -11799.1437] [ 2748] [depth= 4] . ( 3 sec) [ -11731.1513] [ 2728] [depth= 2] . ( 3 sec) [ -11645.5057] [ 2702] [depth= 9] . ( 3 sec) [ -11620.3922] [ 2697] [depth= 1] . ( 3 sec) [ -11532.7237] [ 2667] [depth= 8] . ( 3 sec) [ -11513.8389] [ 2618] [depth= 1] . ( 3 sec) [ -11511.6796] [ 2619] [depth= 1] . ( 3 sec) [ -11397.2049] [ 2609] [depth= 9] . ( 3 sec) [ -11300.4096] [ 2608] [depth= 1] . ( 3 sec) [ -11215.6988] [ 2562] [depth= 1] . ( 3 sec) [ -11142.8921] [ 2528] [depth= 2] . ( 3 sec) [ -11019.8789] [ 2493] [depth= 7] . ( 3 sec) [ -10992.2869] [ 2491] [depth= 2] . ( 3 sec) [ -10350.5871] [ 2336] [depth= 5] . ( 3 sec) [ -10333.2588] [ 2325] [depth= 1] . ( 3 sec) [ -10283.1394] [ 2310] [depth= 9] . ( 3 sec) [ -10273.7756] [ 2291] [depth= 2] . ( 3 sec) [ -10154.6032] [ 2262] [depth= 12] . ( 3 sec) [ -10014.8203] [ 2208] [depth= 4] . ( 4 sec) [ -10010.2633] [ 2206] [depth= 1] . ( 4 sec) [ -9952.1936] [ 2197] [depth= 2] . ( 4 sec) [ -9946.7056] [ 2192] [depth= 1] . ( 4 sec) [ -9936.2030] [ 2204] [depth= 1] . ( 4 sec) [ -9908.1412] [ 2192] [depth= 1] . ( 4 sec) [ -9907.7825] [ 2197] [depth= 1] . ( 4 sec) [ -9852.3239] [ 2185] [depth= 1] . ( 4 sec) [ -9826.8536] [ 2101] [depth= 1] . ( 4 sec) [ -9774.6507] [ 2083] [depth= 1] . ( 4 sec) [ -9737.5734] [ 2076] [depth= 2] . ( 4 sec) [ -9735.5924] [ 2075] [depth= 1] . ( 4 sec) [ -9624.6271] [ 2064] [depth= 5] . ( 4 sec) [ -9620.5925] [ 2065] [depth= 8] . ( 4 sec) [ -9515.5737] [ 2004] [depth= 2] . ( 4 sec) [ -9422.2546] [ 2005] [depth= 1] . ( 4 sec) [ -9301.9779] [ 2013] [depth= 2] . ( 4 sec) [ -9293.5721] [ 2011] [depth= 1] . ( 4 sec) [ -9122.8502] [ 1977] [depth= 1] . ( 5 sec) [ -9120.2713] [ 1978] [depth= 1] . ( 5 sec) [ -9071.7526] [ 1971] [depth= 6] . ( 5 sec) [ -9061.9255] [ 1966] [depth= 1] . ( 5 sec) [ -8940.9501] [Branch lengths ] . ( 5 sec) [ -8939.5862] [GTR parameters ] . ( 6 sec) [ -8918.0083] [Alpha ][ 0.804061] . ( 6 sec) [ -8805.6806] [ 1931] [depth= 7] . ( 6 sec) [ -8800.5227] [ 1927] [depth= 1] . ( 6 sec) [ -8799.8186] [ 1924] [depth= 1] . ( 6 sec) [ -8755.5194] [ 1873] [depth= 3] . ( 6 sec) [ -8718.4580] [ 1847] [depth= 1] . ( 6 sec) [ -8716.3326] [ 1850] [depth= 1] . ( 6 sec) [ -8670.1444] [ 1832] [depth= 1] . ( 6 sec) [ -8624.9014] [ 1814] [depth= 1] . ( 6 sec) [ -8619.7766] [ 1814] [depth= 1] . ( 6 sec) [ -8616.0333] [ 1807] [depth= 1] . ( 6 sec) [ -8608.4055] [ 1801] [depth= 1] . ( 6 sec) [ -8603.2733] [ 1795] [depth= 2] . ( 7 sec) [ -8590.2848] [ 1787] [depth= 1] . ( 7 sec) [ -8561.9664] [ 1782] [depth= 2] . ( 7 sec) [ -8559.0481] [ 1786] [depth= 1] . ( 7 sec) [ -8559.0224] [ 1787] [depth= 2] . ( 7 sec) [ -8500.3986] [ 1770] [depth= 3] . ( 7 sec) [ -8492.9152] [ 1772] [depth= 2] . ( 7 sec) [ -8490.9512] [ 1772] [depth= 1] . ( 7 sec) [ -8474.5268] [ 1756] [depth= 2] . ( 8 sec) [ -8473.8891] [ 1753] [depth= 1] . ( 8 sec) [ -8471.9570] [ 1755] [depth= 2] . ( 8 sec) [ -8462.1094] [ 1753] [depth= 2] . ( 8 sec) [ -8461.4326] [ 1756] [depth= 1] . ( 8 sec) [ -8451.3313] [ 1750] [depth= 1] . ( 8 sec) [ -8450.5642] [ 1749] [depth= 1] . ( 9 sec) [ -8445.0072] [ 1743] [depth= 2] . ( 9 sec) [ -8426.7923] [Branch lengths ] . ( 9 sec) [ -8426.3253] [GTR parameters ] . ( 9 sec) [ -8424.2517] [Alpha ][ 0.941550] . ( 10 sec) [ -8419.8856] [ 1743] [depth= 1] . ( 12 sec) [ -8418.6881] [Branch lengths ] . ( 13 sec) [ -8418.6809] [GTR parameters ] . ( 13 sec) [ -8418.6755] [Alpha ][ 0.949340] . ( 15 sec) [ -8418.5863] [Branch lengths ] . ( 19 sec) [ -8418.5299] [ 1741] [depth= 1] . ( 35 sec) [ -8418.4736] [Branch lengths ] . ( 35 sec) [ -8418.4732] [GTR parameters ] . ( 35 sec) [ -8418.4722] [Alpha ][ 0.952660] . ( 35 sec) [ -8418.4722] [Topology ] . ( 36 sec) [ -8418.4703] [Topology ] . ( 36 sec) [ -8418.4696] [Topology ] . ( 36 sec) [ -8418.4696] [GTR parameters ] . ( 37 sec) [ -8418.4696] [Alpha ][ 0.952660] . ( 37 sec) [ -8418.4696] [Topology ] . ( 37 sec) [ -8418.4693] [Topology ] . ( 37 sec) [ -8418.4692] [GTR parameters ] . ( 37 sec) [ -8418.4692] [Alpha ][ 0.952660] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -8418.4685] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.468549. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17351.5750] [GTR parameters ] . ( 0 sec) [ -17026.4418] [Alpha ][ 0.500960] . ( 0 sec) [ -16707.4172] [ 3573] [depth= 3] . ( 0 sec) [ -16029.7879] [ 3463] [depth= 3] . ( 0 sec) [ -15927.1614] [ 3434] [depth= 3] . ( 1 sec) [ -15823.5045] [ 3425] [depth= 7] . ( 1 sec) [ -15692.7486] [ 3356] [depth= 3] . ( 1 sec) [ -15679.6583] [ 3359] [depth= 8] . ( 1 sec) [ -15495.8456] [ 3350] [depth= 1] . ( 1 sec) [ -15362.4152] [ 3332] [depth= 4] . ( 1 sec) [ -15143.1590] [ 3278] [depth= 1] . ( 1 sec) [ -15132.3021] [ 3276] [depth= 2] . ( 1 sec) [ -15111.1238] [ 3270] [depth= 3] . ( 1 sec) [ -14971.3301] [ 3259] [depth= 3] . ( 1 sec) [ -14897.2185] [ 3227] [depth= 3] . ( 1 sec) [ -14859.6106] [ 3216] [depth= 2] . ( 1 sec) [ -14635.9873] [ 3158] [depth= 7] . ( 1 sec) [ -14398.4317] [ 3082] [depth= 11] . ( 1 sec) [ -14304.3472] [ 3072] [depth= 9] . ( 1 sec) [ -14051.0028] [ 3006] [depth= 2] . ( 1 sec) [ -14047.8977] [ 3004] [depth= 1] . ( 1 sec) [ -13837.2842] [ 2978] [depth= 12] . ( 1 sec) [ -13719.8235] [ 2978] [depth= 3] . ( 1 sec) [ -13505.5080] [ 2936] [depth= 1] . ( 1 sec) [ -13279.1385] [ 2815] [depth= 11] . ( 1 sec) [ -12878.6599] [ 2713] [depth= 3] . ( 1 sec) [ -12676.4912] [ 2706] [depth= 4] . ( 1 sec) [ -12485.2705] [ 2685] [depth= 9] . ( 2 sec) [ -12156.8410] [ 2671] [depth= 1] . ( 2 sec) [ -12062.6882] [ 2597] [depth= 10] . ( 2 sec) [ -11766.4776] [ 2462] [depth= 6] . ( 2 sec) [ -11694.8658] [ 2466] [depth= 1] . ( 2 sec) [ -11622.1648] [ 2489] [depth= 3] . ( 2 sec) [ -11346.6482] [ 2430] [depth= 5] . ( 2 sec) [ -11271.5953] [ 2433] [depth= 1] . ( 2 sec) [ -11078.8758] [ 2398] [depth= 2] . ( 2 sec) [ -10843.4304] [ 2350] [depth= 1] . ( 2 sec) [ -10806.2407] [ 2334] [depth= 6] . ( 2 sec) [ -10717.4036] [ 2330] [depth= 1] . ( 2 sec) [ -10606.9042] [ 2309] [depth= 5] . ( 2 sec) [ -10596.1104] [ 2296] [depth= 1] . ( 2 sec) [ -10549.9676] [ 2301] [depth= 1] . ( 2 sec) [ -10346.2421] [ 2295] [depth= 4] . ( 2 sec) [ -10339.1426] [ 2291] [depth= 1] . ( 2 sec) [ -10287.9759] [ 2276] [depth= 1] . ( 2 sec) [ -10246.1846] [ 2262] [depth= 1] . ( 2 sec) [ -10162.0426] [ 2232] [depth= 4] . ( 2 sec) [ -10104.4307] [ 2235] [depth= 1] . ( 3 sec) [ -10086.2088] [ 2225] [depth= 2] . ( 3 sec) [ -9957.8144] [ 2176] [depth= 2] . ( 3 sec) [ -9895.0221] [ 2153] [depth= 1] . ( 3 sec) [ -9891.6112] [ 2155] [depth= 1] . ( 3 sec) [ -9880.8032] [ 2157] [depth= 2] . ( 3 sec) [ -9879.4722] [ 2173] [depth= 1] . ( 3 sec) [ -9799.8888] [ 2157] [depth= 3] . ( 3 sec) [ -9736.1809] [ 2124] [depth= 2] . ( 3 sec) [ -9707.9424] [ 2111] [depth= 1] . ( 3 sec) [ -9676.7558] [ 2096] [depth= 2] . ( 3 sec) [ -9675.6365] [ 2101] [depth= 1] . ( 3 sec) [ -9575.6940] [ 2058] [depth= 2] . ( 3 sec) [ -9484.9213] [ 2047] [depth= 2] . ( 3 sec) [ -9482.5068] [ 2041] [depth= 1] . ( 3 sec) [ -9308.2022] [ 2003] [depth= 6] . ( 3 sec) [ -9287.2402] [ 1995] [depth= 1] . ( 3 sec) [ -9075.8529] [ 1967] [depth= 2] . ( 3 sec) [ -9072.0640] [ 1964] [depth= 2] . ( 3 sec) [ -9052.6269] [ 1964] [depth= 1] . ( 3 sec) [ -8986.8357] [ 1898] [depth= 4] . ( 4 sec) [ -8981.8098] [ 1897] [depth= 2] . ( 4 sec) [ -8979.1913] [ 1897] [depth= 1] . ( 4 sec) [ -8977.3471] [ 1895] [depth= 1] . ( 4 sec) [ -8926.2269] [ 1876] [depth= 1] . ( 4 sec) [ -8915.9752] [ 1872] [depth= 2] . ( 4 sec) [ -8863.3342] [ 1860] [depth= 4] . ( 4 sec) [ -8861.5018] [ 1862] [depth= 1] . ( 4 sec) [ -8772.0934] [ 1825] [depth= 1] . ( 4 sec) [ -8738.0645] [ 1817] [depth= 1] . ( 4 sec) [ -8665.4933] [ 1787] [depth= 2] . ( 4 sec) [ -8539.5782] [Branch lengths ] . ( 5 sec) [ -8538.2589] [GTR parameters ] . ( 5 sec) [ -8510.8726] [Alpha ][ 0.873577] . ( 5 sec) [ -8485.8209] [ 1776] [depth= 4] . ( 5 sec) [ -8477.6894] [ 1769] [depth= 2] . ( 5 sec) [ -8476.2890] [ 1767] [depth= 1] . ( 5 sec) [ -8475.1736] [ 1768] [depth= 1] . ( 6 sec) [ -8469.4356] [ 1766] [depth= 1] . ( 6 sec) [ -8467.1012] [ 1763] [depth= 1] . ( 6 sec) [ -8458.7922] [ 1754] [depth= 1] . ( 6 sec) [ -8456.9387] [ 1755] [depth= 1] . ( 6 sec) [ -8455.8298] [ 1754] [depth= 1] . ( 6 sec) [ -8453.9854] [ 1752] [depth= 1] . ( 6 sec) [ -8443.5582] [ 1746] [depth= 1] . ( 6 sec) [ -8436.8070] [ 1739] [depth= 2] . ( 6 sec) [ -8436.6979] [ 1740] [depth= 1] . ( 6 sec) [ -8433.6703] [ 1741] [depth= 1] . ( 7 sec) [ -8433.3894] [ 1740] [depth= 1] . ( 8 sec) [ -8421.2922] [Branch lengths ] . ( 8 sec) [ -8421.1879] [GTR parameters ] . ( 9 sec) [ -8420.7267] [Alpha ][ 0.941587] . ( 10 sec) [ -8420.7069] [ 1741] [depth= 1] . ( 10 sec) [ -8420.6777] [ 1740] [depth= 1] . ( 11 sec) [ -8419.8525] [Branch lengths ] . ( 12 sec) [ -8419.8521] [GTR parameters ] . ( 12 sec) [ -8419.8466] [Alpha ][ 0.949455] . ( 31 sec) [ -8418.8899] [Branch lengths ] . ( 31 sec) [ -8418.8899] [Topology ] . ( 32 sec) [ -8418.5030] [Topology ] . ( 33 sec) [ -8418.4771] [Topology ] . ( 34 sec) [ -8418.4731] [Topology ] . ( 34 sec) [ -8418.4718] [Topology ] . ( 35 sec) [ -8418.4713] [Topology ] . ( 35 sec) [ -8418.4705] [GTR parameters ] . ( 35 sec) [ -8418.4695] [Alpha ][ 0.952793] . ( 35 sec) [ -8418.4695] [Topology ] . ( 36 sec) [ -8418.4691] [Topology ] . ( 36 sec) [ -8418.4691] [GTR parameters ] . ( 36 sec) [ -8418.4691] [Alpha ][ 0.952793] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -8418.4687] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.468689. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18686.1767] [GTR parameters ] . ( 1 sec) [ -18333.9997] [Alpha ][ 0.500960] . ( 1 sec) [ -17801.8022] [ 3875] [depth= 8] . ( 1 sec) [ -17233.6426] [ 3763] [depth= 8] . ( 1 sec) [ -17092.0408] [ 3754] [depth= 4] . ( 1 sec) [ -17035.6130] [ 3752] [depth= 1] . ( 1 sec) [ -16965.8273] [ 3686] [depth= 3] . ( 1 sec) [ -16960.3249] [ 3687] [depth= 1] . ( 1 sec) [ -16653.4403] [ 3664] [depth= 8] . ( 1 sec) [ -16486.3736] [ 3644] [depth= 4] . ( 1 sec) [ -16072.8425] [ 3595] [depth= 1] . ( 1 sec) [ -15766.8165] [ 3515] [depth= 10] . ( 1 sec) [ -15682.3726] [ 3489] [depth= 5] . ( 1 sec) [ -15669.6555] [ 3472] [depth= 8] . ( 1 sec) [ -15626.7875] [ 3461] [depth= 3] . ( 1 sec) [ -15546.6534] [ 3450] [depth= 11] . ( 1 sec) [ -15470.0163] [ 3448] [depth= 1] . ( 1 sec) [ -15064.6035] [ 3390] [depth= 4] . ( 2 sec) [ -14768.6744] [ 3385] [depth= 4] . ( 2 sec) [ -14538.4259] [ 3356] [depth= 12] . ( 2 sec) [ -14337.3462] [ 3323] [depth= 11] . ( 2 sec) [ -14098.9668] [ 3270] [depth= 1] . ( 2 sec) [ -13856.2630] [ 3201] [depth= 5] . ( 2 sec) [ -13828.3840] [ 3158] [depth= 1] . ( 2 sec) [ -13779.7840] [ 3141] [depth= 9] . ( 2 sec) [ -13527.6995] [ 3071] [depth= 13] . ( 2 sec) [ -13318.1051] [ 3017] [depth= 5] . ( 2 sec) [ -13176.7863] [ 2922] [depth= 1] . ( 2 sec) [ -13029.6391] [ 2888] [depth= 13] . ( 2 sec) [ -12959.8227] [ 2898] [depth= 1] . ( 2 sec) [ -12634.9289] [ 2746] [depth= 17] . ( 2 sec) [ -12573.1979] [ 2751] [depth= 7] . ( 2 sec) [ -12518.9649] [ 2698] [depth= 1] . ( 2 sec) [ -12489.2777] [ 2692] [depth= 2] . ( 2 sec) [ -12463.2515] [ 2689] [depth= 7] . ( 2 sec) [ -12460.0789] [ 2686] [depth= 1] . ( 2 sec) [ -12426.6166] [ 2672] [depth= 1] . ( 2 sec) [ -12210.9954] [ 2591] [depth= 3] . ( 2 sec) [ -12175.4431] [ 2568] [depth= 5] . ( 3 sec) [ -12148.2442] [ 2519] [depth= 2] . ( 3 sec) [ -11262.5460] [ 2499] [depth= 7] . ( 3 sec) [ -11163.9078] [ 2335] [depth= 2] . ( 3 sec) [ -11163.6557] [ 2340] [depth= 1] . ( 3 sec) [ -10986.7178] [ 2279] [depth= 6] . ( 3 sec) [ -10952.7036] [ 2275] [depth= 1] . ( 3 sec) [ -10886.0962] [ 2268] [depth= 4] . ( 3 sec) [ -10873.6753] [ 2225] [depth= 6] . ( 3 sec) [ -10754.2287] [ 2228] [depth= 2] . ( 3 sec) [ -10740.8717] [ 2220] [depth= 10] . ( 3 sec) [ -10719.6038] [ 2249] [depth= 1] . ( 3 sec) [ -10700.2407] [ 2220] [depth= 1] . ( 3 sec) [ -10432.2884] [ 2146] [depth= 12] . ( 3 sec) [ -10125.6188] [ 2117] [depth= 8] . ( 3 sec) [ -10053.6091] [ 2085] [depth= 11] . ( 3 sec) [ -9922.5682] [ 2084] [depth= 1] . ( 3 sec) [ -9874.9085] [ 2079] [depth= 1] . ( 3 sec) [ -9716.5763] [ 2028] [depth= 1] . ( 3 sec) [ -9657.5718] [ 2032] [depth= 2] . ( 3 sec) [ -9649.2520] [ 2045] [depth= 1] . ( 3 sec) [ -9531.8511] [ 1985] [depth= 11] . ( 3 sec) [ -9519.5001] [ 1983] [depth= 1] . ( 3 sec) [ -9511.9200] [ 1988] [depth= 1] . ( 3 sec) [ -9469.3312] [ 1976] [depth= 1] . ( 4 sec) [ -9413.5816] [ 1961] [depth= 9] . ( 4 sec) [ -9341.0832] [ 1959] [depth= 1] . ( 4 sec) [ -9323.0958] [ 1947] [depth= 1] . ( 4 sec) [ -9303.7910] [ 1946] [depth= 3] . ( 4 sec) [ -9293.7328] [ 1944] [depth= 2] . ( 4 sec) [ -9206.9211] [ 1947] [depth= 1] . ( 4 sec) [ -9187.2651] [ 1943] [depth= 1] . ( 4 sec) [ -9178.7279] [ 1934] [depth= 1] . ( 4 sec) [ -9163.1724] [ 1927] [depth= 1] . ( 4 sec) [ -9079.8224] [ 1854] [depth= 2] . ( 4 sec) [ -9073.9093] [ 1872] [depth= 1] . ( 4 sec) [ -9049.4275] [ 1869] [depth= 1] . ( 4 sec) [ -8925.6258] [ 1861] [depth= 1] . ( 4 sec) [ -8914.1427] [ 1859] [depth= 1] . ( 4 sec) [ -8799.3998] [ 1823] [depth= 3] . ( 5 sec) [ -8758.1137] [ 1806] [depth= 3] . ( 5 sec) [ -8752.8611] [ 1805] [depth= 1] . ( 5 sec) [ -8611.1553] [Branch lengths ] . ( 5 sec) [ -8608.7000] [GTR parameters ] . ( 6 sec) [ -8576.5799] [Alpha ][ 0.904362] . ( 6 sec) [ -8572.7690] [ 1788] [depth= 1] . ( 6 sec) [ -8569.3238] [ 1789] [depth= 1] . ( 6 sec) [ -8550.4032] [ 1777] [depth= 3] . ( 6 sec) [ -8548.4501] [ 1780] [depth= 1] . ( 6 sec) [ -8529.6506] [ 1778] [depth= 2] . ( 6 sec) [ -8523.1468] [ 1773] [depth= 1] . ( 6 sec) [ -8452.9183] [ 1743] [depth= 1] . ( 6 sec) [ -8449.3552] [ 1741] [depth= 1] . ( 6 sec) [ -8446.3345] [ 1741] [depth= 1] . ( 7 sec) [ -8446.0465] [ 1741] [depth= 1] . ( 7 sec) [ -8444.7157] [ 1743] [depth= 1] . ( 7 sec) [ -8435.5685] [ 1744] [depth= 1] . ( 8 sec) [ -8420.8780] [Branch lengths ] . ( 9 sec) [ -8420.5823] [GTR parameters ] . ( 9 sec) [ -8420.3779] [Alpha ][ 0.950260] . ( 12 sec) [ -8419.7861] [Branch lengths ] . ( 19 sec) [ -8419.7272] [ 1740] [depth= 1] . ( 31 sec) [ -8419.4130] [Branch lengths ] . ( 31 sec) [ -8419.4121] [GTR parameters ] . ( 31 sec) [ -8419.4119] [Alpha ][ 0.951408] . ( 31 sec) [ -8419.4119] [Topology ] . ( 32 sec) [ -8418.6689] [Topology ] . ( 33 sec) [ -8418.5059] [Topology ] . ( 34 sec) [ -8418.4763] [Topology ] . ( 34 sec) [ -8418.4710] [Topology ] . ( 35 sec) [ -8418.4698] [Topology ] . ( 36 sec) [ -8418.4695] [Topology ] . ( 36 sec) [ -8418.4681] [GTR parameters ] . ( 36 sec) [ -8418.4678] [Alpha ][ 0.953380] . ( 36 sec) [ -8418.4678] [Topology ] . ( 37 sec) [ -8418.4676] [Topology ] . ( 37 sec) [ -8418.4676] [GTR parameters ] . ( 37 sec) [ -8418.4676] [Alpha ][ 0.953380] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.467603. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18169.3683] [GTR parameters ] . ( 0 sec) [ -17818.7935] [Alpha ][ 0.500960] . ( 1 sec) [ -17477.4434] [ 3860] [depth= 8] . ( 1 sec) [ -17066.7115] [ 3738] [depth= 9] . ( 1 sec) [ -16928.3613] [ 3709] [depth= 7] . ( 1 sec) [ -16902.3245] [ 3594] [depth= 1] . ( 1 sec) [ -16299.8626] [ 3571] [depth= 3] . ( 1 sec) [ -16233.4580] [ 3567] [depth= 2] . ( 1 sec) [ -16088.4498] [ 3565] [depth= 3] . ( 1 sec) [ -15901.6031] [ 3545] [depth= 4] . ( 1 sec) [ -15791.1981] [ 3536] [depth= 1] . ( 1 sec) [ -15790.0307] [ 3529] [depth= 4] . ( 1 sec) [ -15732.8281] [ 3528] [depth= 1] . ( 1 sec) [ -15695.0407] [ 3519] [depth= 7] . ( 1 sec) [ -15561.2015] [ 3521] [depth= 1] . ( 1 sec) [ -15466.9129] [ 3500] [depth= 6] . ( 1 sec) [ -15367.0359] [ 3475] [depth= 3] . ( 1 sec) [ -15252.5386] [ 3474] [depth= 1] . ( 1 sec) [ -15111.7777] [ 3354] [depth= 1] . ( 1 sec) [ -14790.6759] [ 3334] [depth= 10] . ( 1 sec) [ -14378.3407] [ 3334] [depth= 1] . ( 1 sec) [ -14248.5145] [ 3270] [depth= 9] . ( 1 sec) [ -14133.4548] [ 3218] [depth= 6] . ( 1 sec) [ -13968.2300] [ 3178] [depth= 1] . ( 1 sec) [ -13749.6336] [ 3139] [depth= 8] . ( 1 sec) [ -13563.3138] [ 3104] [depth= 9] . ( 1 sec) [ -13226.7265] [ 2992] [depth= 1] . ( 2 sec) [ -12959.3380] [ 2984] [depth= 8] . ( 2 sec) [ -12915.6209] [ 2988] [depth= 1] . ( 2 sec) [ -12853.9613] [ 2991] [depth= 10] . ( 2 sec) [ -12846.6100] [ 2987] [depth= 1] . ( 2 sec) [ -12831.5411] [ 2952] [depth= 11] . ( 2 sec) [ -12805.7782] [ 2949] [depth= 1] . ( 2 sec) [ -12802.9462] [ 2924] [depth= 6] . ( 2 sec) [ -12722.3803] [ 2905] [depth= 13] . ( 2 sec) [ -12715.3446] [ 2848] [depth= 3] . ( 2 sec) [ -12695.4601] [ 2834] [depth= 1] . ( 2 sec) [ -12608.2742] [ 2815] [depth= 3] . ( 2 sec) [ -12509.3937] [ 2800] [depth= 2] . ( 2 sec) [ -12344.6360] [ 2754] [depth= 4] . ( 2 sec) [ -12248.0019] [ 2753] [depth= 2] . ( 2 sec) [ -12043.0414] [ 2628] [depth= 9] . ( 2 sec) [ -12035.8134] [ 2632] [depth= 1] . ( 2 sec) [ -11761.4606] [ 2535] [depth= 10] . ( 2 sec) [ -11703.9985] [ 2533] [depth= 6] . ( 2 sec) [ -11616.0250] [ 2520] [depth= 2] . ( 2 sec) [ -11557.1073] [ 2517] [depth= 3] . ( 2 sec) [ -11451.2495] [ 2492] [depth= 14] . ( 2 sec) [ -11392.7340] [ 2461] [depth= 1] . ( 2 sec) [ -11306.1976] [ 2442] [depth= 13] . ( 3 sec) [ -11292.0797] [ 2444] [depth= 1] . ( 3 sec) [ -11104.1903] [ 2381] [depth= 2] . ( 3 sec) [ -11049.5548] [ 2349] [depth= 7] . ( 3 sec) [ -10902.6767] [ 2340] [depth= 1] . ( 3 sec) [ -10850.3069] [ 2326] [depth= 2] . ( 3 sec) [ -10621.7740] [ 2294] [depth= 1] . ( 3 sec) [ -10575.1150] [ 2259] [depth= 12] . ( 3 sec) [ -10513.2249] [ 2287] [depth= 1] . ( 3 sec) [ -10253.6905] [ 2244] [depth= 12] . ( 3 sec) [ -10128.8469] [ 2214] [depth= 2] . ( 3 sec) [ -9994.7230] [ 2184] [depth= 10] . ( 3 sec) [ -9938.4917] [ 2189] [depth= 2] . ( 3 sec) [ -9850.1198] [ 2167] [depth= 3] . ( 3 sec) [ -9760.0029] [ 2168] [depth= 1] . ( 3 sec) [ -9663.1696] [ 2135] [depth= 1] . ( 3 sec) [ -9599.8190] [ 2090] [depth= 1] . ( 3 sec) [ -9488.9999] [ 2080] [depth= 7] . ( 3 sec) [ -9436.1009] [ 2043] [depth= 2] . ( 3 sec) [ -9271.4409] [ 2018] [depth= 6] . ( 3 sec) [ -9225.4161] [ 1988] [depth= 2] . ( 4 sec) [ -9220.6449] [ 1999] [depth= 1] . ( 4 sec) [ -9211.0883] [ 1990] [depth= 1] . ( 4 sec) [ -9117.3111] [ 1953] [depth= 4] . ( 4 sec) [ -9098.3087] [ 1953] [depth= 1] . ( 4 sec) [ -8993.2951] [ 1928] [depth= 1] . ( 4 sec) [ -8986.0626] [ 1926] [depth= 1] . ( 4 sec) [ -8981.8045] [ 1925] [depth= 2] . ( 4 sec) [ -8965.6477] [ 1913] [depth= 3] . ( 4 sec) [ -8935.8944] [ 1909] [depth= 1] . ( 4 sec) [ -8914.3683] [ 1883] [depth= 1] . ( 4 sec) [ -8849.7349] [ 1859] [depth= 1] . ( 4 sec) [ -8845.7390] [ 1862] [depth= 1] . ( 4 sec) [ -8827.9588] [ 1860] [depth= 1] . ( 4 sec) [ -8788.0386] [ 1840] [depth= 1] . ( 5 sec) [ -8775.9876] [ 1835] [depth= 1] . ( 5 sec) [ -8647.5668] [Branch lengths ] . ( 5 sec) [ -8646.5551] [GTR parameters ] . ( 5 sec) [ -8617.0985] [Alpha ][ 0.884087] . ( 6 sec) [ -8616.0211] [ 1833] [depth= 1] . ( 6 sec) [ -8614.9263] [ 1835] [depth= 3] . ( 6 sec) [ -8568.1204] [ 1805] [depth= 1] . ( 6 sec) [ -8567.5554] [ 1807] [depth= 1] . ( 6 sec) [ -8566.8693] [ 1798] [depth= 3] . ( 6 sec) [ -8516.4829] [ 1786] [depth= 2] . ( 6 sec) [ -8496.1566] [ 1779] [depth= 1] . ( 6 sec) [ -8468.8701] [ 1759] [depth= 3] . ( 6 sec) [ -8468.8492] [ 1760] [depth= 1] . ( 7 sec) [ -8463.0685] [ 1759] [depth= 1] . ( 7 sec) [ -8455.6026] [ 1754] [depth= 2] . ( 7 sec) [ -8442.6397] [ 1749] [depth= 2] . ( 8 sec) [ -8440.9287] [ 1749] [depth= 1] . ( 8 sec) [ -8440.3191] [ 1748] [depth= 1] . ( 8 sec) [ -8439.6861] [ 1750] [depth= 1] . ( 8 sec) [ -8434.5581] [ 1746] [depth= 1] . ( 8 sec) [ -8430.9595] [ 1743] [depth= 1] . ( 8 sec) [ -8430.0934] [ 1746] [depth= 1] . ( 8 sec) [ -8427.5389] [ 1743] [depth= 1] . ( 9 sec) [ -8419.4088] [Branch lengths ] . ( 9 sec) [ -8419.2236] [GTR parameters ] . ( 9 sec) [ -8418.8368] [Alpha ][ 0.946598] . ( 12 sec) [ -8418.5987] [Branch lengths ] . ( 20 sec) [ -8418.5072] [ 1741] [depth= 1] . ( 32 sec) [ -8418.4771] [Branch lengths ] . ( 32 sec) [ -8418.4766] [GTR parameters ] . ( 32 sec) [ -8418.4735] [Alpha ][ 0.952485] . ( 32 sec) [ -8418.4735] [Topology ] . ( 33 sec) [ -8418.4708] [Topology ] . ( 33 sec) [ -8418.4698] [Topology ] . ( 34 sec) [ -8418.4694] [Topology ] . ( 34 sec) [ -8418.4694] [GTR parameters ] . ( 34 sec) [ -8418.4694] [Alpha ][ 0.952485] . ( 34 sec) [ -8418.4694] [Topology ] . ( 35 sec) [ -8418.4691] [Topology ] . ( 35 sec) [ -8418.4691] [GTR parameters ] . ( 35 sec) [ -8418.4691] [Alpha ][ 0.953438] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -8418.4686] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.468568. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18694.6973] [GTR parameters ] . ( 0 sec) [ -18335.4699] [Alpha ][ 0.500960] . ( 0 sec) [ -17720.5851] [ 3864] [depth= 6] . ( 0 sec) [ -17015.7814] [ 3743] [depth= 11] . ( 1 sec) [ -16902.2369] [ 3715] [depth= 6] . ( 1 sec) [ -16826.5890] [ 3709] [depth= 1] . ( 1 sec) [ -16748.2226] [ 3662] [depth= 10] . ( 1 sec) [ -16594.5076] [ 3657] [depth= 6] . ( 1 sec) [ -16128.9265] [ 3630] [depth= 6] . ( 1 sec) [ -15795.5592] [ 3576] [depth= 1] . ( 1 sec) [ -15577.5146] [ 3547] [depth= 1] . ( 1 sec) [ -15013.1505] [ 3447] [depth= 7] . ( 1 sec) [ -14657.0281] [ 3395] [depth= 3] . ( 1 sec) [ -14523.2664] [ 3374] [depth= 13] . ( 1 sec) [ -14504.1529] [ 3360] [depth= 1] . ( 1 sec) [ -14379.5930] [ 3350] [depth= 14] . ( 1 sec) [ -14367.4447] [ 3352] [depth= 1] . ( 1 sec) [ -14360.2362] [ 3343] [depth= 2] . ( 1 sec) [ -14275.9025] [ 3280] [depth= 3] . ( 1 sec) [ -14211.8844] [ 3258] [depth= 6] . ( 1 sec) [ -14174.0475] [ 3258] [depth= 1] . ( 1 sec) [ -13898.2661] [ 3256] [depth= 3] . ( 1 sec) [ -13749.6866] [ 3209] [depth= 3] . ( 1 sec) [ -13729.8956] [ 3194] [depth= 12] . ( 1 sec) [ -13621.8192] [ 3168] [depth= 1] . ( 1 sec) [ -13609.9562] [ 3164] [depth= 3] . ( 1 sec) [ -13505.4862] [ 3141] [depth= 8] . ( 1 sec) [ -13199.2373] [ 3065] [depth= 11] . ( 2 sec) [ -13116.4309] [ 3045] [depth= 7] . ( 2 sec) [ -13113.0945] [ 3043] [depth= 1] . ( 2 sec) [ -13077.0254] [ 3032] [depth= 1] . ( 2 sec) [ -12983.0869] [ 3000] [depth= 1] . ( 2 sec) [ -12852.2575] [ 2932] [depth= 9] . ( 2 sec) [ -12628.2048] [ 2882] [depth= 1] . ( 2 sec) [ -12354.9733] [ 2829] [depth= 4] . ( 2 sec) [ -12249.4651] [ 2791] [depth= 1] . ( 2 sec) [ -12062.3577] [ 2798] [depth= 11] . ( 2 sec) [ -11996.7483] [ 2772] [depth= 3] . ( 2 sec) [ -11910.6530] [ 2761] [depth= 9] . ( 2 sec) [ -11600.1879] [ 2725] [depth= 10] . ( 2 sec) [ -11588.6726] [ 2711] [depth= 1] . ( 2 sec) [ -11521.5964] [ 2677] [depth= 1] . ( 2 sec) [ -11138.5716] [ 2534] [depth= 5] . ( 2 sec) [ -11137.2752] [ 2543] [depth= 1] . ( 2 sec) [ -11013.4473] [ 2480] [depth= 5] . ( 2 sec) [ -10905.5813] [ 2439] [depth= 8] . ( 2 sec) [ -10850.7267] [ 2431] [depth= 5] . ( 2 sec) [ -10742.2709] [ 2430] [depth= 5] . ( 3 sec) [ -10702.5430] [ 2408] [depth= 2] . ( 3 sec) [ -10650.2076] [ 2388] [depth= 11] . ( 3 sec) [ -10430.4664] [ 2337] [depth= 7] . ( 3 sec) [ -10406.0725] [ 2335] [depth= 3] . ( 3 sec) [ -10264.2258] [ 2297] [depth= 3] . ( 3 sec) [ -10183.0433] [ 2270] [depth= 10] . ( 3 sec) [ -9830.5443] [ 2253] [depth= 1] . ( 3 sec) [ -9756.7176] [ 2199] [depth= 13] . ( 3 sec) [ -9673.9871] [ 2164] [depth= 1] . ( 3 sec) [ -9515.0923] [ 2123] [depth= 5] . ( 3 sec) [ -9509.5615] [ 2122] [depth= 2] . ( 3 sec) [ -9502.9622] [ 2110] [depth= 1] . ( 3 sec) [ -9492.5477] [ 2109] [depth= 1] . ( 3 sec) [ -9470.7344] [ 2087] [depth= 1] . ( 3 sec) [ -9429.9017] [ 2083] [depth= 3] . ( 3 sec) [ -9357.9172] [ 2072] [depth= 1] . ( 3 sec) [ -9332.5422] [ 2035] [depth= 1] . ( 3 sec) [ -9275.8307] [ 2036] [depth= 1] . ( 3 sec) [ -9258.3128] [ 2030] [depth= 1] . ( 3 sec) [ -9219.4545] [ 2025] [depth= 1] . ( 4 sec) [ -9201.6943] [ 2021] [depth= 1] . ( 4 sec) [ -9196.2244] [ 2019] [depth= 1] . ( 4 sec) [ -9088.1190] [ 2000] [depth= 8] . ( 4 sec) [ -9014.0117] [ 1925] [depth= 4] . ( 4 sec) [ -9006.0350] [ 1913] [depth= 1] . ( 4 sec) [ -8980.1833] [ 1903] [depth= 1] . ( 4 sec) [ -8961.6955] [ 1894] [depth= 2] . ( 4 sec) [ -8940.1993] [ 1852] [depth= 1] . ( 4 sec) [ -8706.7432] [Branch lengths ] . ( 5 sec) [ -8705.8355] [GTR parameters ] . ( 5 sec) [ -8675.9026] [Alpha ][ 0.886328] . ( 5 sec) [ -8667.2398] [ 1843] [depth= 2] . ( 5 sec) [ -8663.4181] [ 1834] [depth= 1] . ( 5 sec) [ -8646.5506] [ 1837] [depth= 1] . ( 5 sec) [ -8626.2382] [ 1829] [depth= 2] . ( 5 sec) [ -8608.4355] [ 1822] [depth= 2] . ( 6 sec) [ -8596.9381] [ 1803] [depth= 2] . ( 6 sec) [ -8460.9859] [ 1741] [depth= 1] . ( 6 sec) [ -8449.0691] [ 1746] [depth= 1] . ( 6 sec) [ -8449.0496] [ 1747] [depth= 1] . ( 6 sec) [ -8446.6332] [ 1745] [depth= 1] . ( 6 sec) [ -8446.2869] [ 1747] [depth= 1] . ( 6 sec) [ -8446.2375] [ 1749] [depth= 1] . ( 7 sec) [ -8431.1419] [ 1745] [depth= 1] . ( 8 sec) [ -8419.9880] [Branch lengths ] . ( 8 sec) [ -8419.6514] [GTR parameters ] . ( 8 sec) [ -8419.3076] [Alpha ][ 0.945370] . ( 9 sec) [ -8418.9489] [ 1745] [depth= 1] . ( 11 sec) [ -8418.6159] [Branch lengths ] . ( 11 sec) [ -8418.6156] [GTR parameters ] . ( 11 sec) [ -8418.6131] [Alpha ][ 0.950632] . ( 22 sec) [ -8418.5214] [ 1742] [depth= 1] . ( 31 sec) [ -8418.4769] [Branch lengths ] . ( 32 sec) [ -8418.4766] [GTR parameters ] . ( 32 sec) [ -8418.4763] [Alpha ][ 0.952253] . ( 32 sec) [ -8418.4763] [Topology ] . ( 32 sec) [ -8418.4719] [Topology ] . ( 33 sec) [ -8418.4704] [Topology ] . ( 34 sec) [ -8418.4697] [Topology ] . ( 34 sec) [ -8418.4697] [GTR parameters ] . ( 34 sec) [ -8418.4696] [Alpha ][ 0.953205] . ( 34 sec) [ -8418.4696] [Topology ] . ( 35 sec) [ -8418.4693] [Topology ] . ( 35 sec) [ -8418.4693] [GTR parameters ] . ( 35 sec) [ -8418.4693] [Alpha ][ 0.953205] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -8418.4691] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8418.469142. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8471.601432 . ( 1 sec) [ -8466.7709] [GTR parameters ] . ( 1 sec) [ -8465.8651] [Alpha ][ 0.896372] . ( 1 sec) [ -8465.8651] [Topology ] . ( 2 sec) [ -8427.9263] [Topology ] . ( 3 sec) [ -8421.9128] [Topology ] . ( 4 sec) [ -8420.1616] [Topology ] . ( 4 sec) [ -8419.4102] [Topology ] . ( 5 sec) [ -8419.0903] [Topology ] . ( 6 sec) [ -8418.9520] [Topology ] . ( 7 sec) [ -8418.8875] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.887512 . ( 13 sec) [ -8418.8409] [GTR parameters ] . ( 13 sec) [ -8418.5825] [Alpha ][ 0.947946] . ( 13 sec) [ -8418.5825] [Topology ] . ( 13 sec) [ -8418.5235] [Topology ] . ( 14 sec) [ -8418.4968] [Topology ] . ( 15 sec) [ -8418.4836] [Topology ] . ( 16 sec) [ -8418.4771] [Topology ] . ( 16 sec) [ -8418.4738] [Topology ] . ( 17 sec) [ -8418.4721] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.472118 . ( 23 sec) [ -8418.4720] [GTR parameters ] . ( 23 sec) [ -8418.4699] [Alpha ][ 0.952739] . ( 23 sec) [ -8418.4699] [Topology ] . ( 24 sec) [ -8418.4688] [Topology ] . ( 24 sec) [ -8418.4683] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.468264 . ( 30 sec) [ -8418.4683] [GTR parameters ] . ( 30 sec) [ -8418.4683] [Alpha ][ 0.952739] . ( 30 sec) [ -8418.4683] [Topology ] . ( 31 sec) [ -8418.4680] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -8466.7709] [GTR parameters ] . ( 43 sec) [ -8465.8651] [Alpha ][ 0.896372] . ( 43 sec) [ -8465.4448] [ 1745] [depth= 1] . ( 43 sec) [ -8462.7015] [ 1743] [depth= 1] . ( 43 sec) [ -8453.4460] [ 1739] [depth= 1] . ( 43 sec) [ -8453.2703] [ 1740] [depth= 1] . ( 44 sec) [ -8453.1350] [ 1739] [depth= 1] . ( 44 sec) [ -8452.6541] [ 1743] [depth= 1] . ( 44 sec) [ -8452.2686] [ 1739] [depth= 1] . ( 45 sec) [ -8449.0090] [ 1743] [depth= 1] . ( 45 sec) [ -8443.6588] [ 1739] [depth= 1] . ( 46 sec) [ -8443.6409] [ 1740] [depth= 1] . ( 46 sec) [ -8441.7570] [ 1739] [depth= 1] . ( 46 sec) [ -8441.5495] [ 1743] [depth= 1] . ( 46 sec) [ -8440.3955] [ 1746] [depth= 1] . ( 46 sec) [ -8421.2535] [Branch lengths ] . ( 46 sec) [ -8421.2189] [GTR parameters ] . ( 47 sec) [ -8421.0096] [Alpha ][ 0.942826] . ( 47 sec) [ -8420.6643] [ 1747] [depth= 1] . ( 48 sec) [ -8420.1888] [ 1742] [depth= 1] . ( 49 sec) [ -8419.9111] [ 1741] [depth= 1] . ( 49 sec) [ -8419.8582] [ 1742] [depth= 1] . ( 49 sec) [ -8418.5925] [Branch lengths ] . ( 50 sec) [ -8418.5910] [GTR parameters ] . ( 50 sec) [ -8418.5874] [Alpha ][ 0.949201] . ( 52 sec) [ -8418.4908] [Branch lengths ] . ( 72 sec) [ -8418.4736] [Branch lengths ] . ( 72 sec) [ -8418.4736] [Topology ] . ( 73 sec) [ -8418.4718] [Topology ] . ( 74 sec) [ -8418.4711] [Topology ] . ( 74 sec) [ -8418.4708] [GTR parameters ] . ( 74 sec) [ -8418.4697] [Alpha ][ 0.952781] . ( 74 sec) [ -8418.4697] [Topology ] . ( 75 sec) [ -8418.4692] [Topology ] . ( 75 sec) [ -8418.4692] [GTR parameters ] . ( 75 sec) [ -8418.4692] [Alpha ][ 0.952781] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -8418.4690] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8418.467977 . Log likelihood obtained after SPR moves : -8418.468999 . Log likelihood of the current tree: -8418.467977. . Printing the most likely tree in file 'data93.phy_phyml_tree.txt'... . Best log likelihood : -8418.467603 . Time used 0h1m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo