.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data79.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... . 397 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)... . ( 0 sec) [ -24316.6658] [GTR parameters ] . ( 0 sec) [ -23892.4128] [Alpha ][ 0.500960] . ( 0 sec) [ -19924.9366] [ 4088] [depth= 6] . ( 0 sec) [ -19271.4369] [ 3995] [depth= 13] . ( 0 sec) [ -18888.9242] [ 3964] [depth= 1] . ( 0 sec) [ -18760.5180] [ 3954] [depth= 7] . ( 0 sec) [ -18427.7313] [ 3872] [depth= 5] . ( 0 sec) [ -18372.9698] [ 3872] [depth= 4] . ( 0 sec) [ -18188.3413] [ 3839] [depth= 5] . ( 0 sec) [ -18103.2739] [ 3818] [depth= 1] . ( 0 sec) [ -17833.5208] [ 3710] [depth= 10] . ( 0 sec) [ -17438.2566] [ 3631] [depth= 1] . ( 1 sec) [ -17367.2328] [ 3604] [depth= 15] . ( 1 sec) [ -16637.0924] [ 3608] [depth= 4] . ( 1 sec) [ -16586.7010] [ 3602] [depth= 1] . ( 1 sec) [ -16545.7407] [ 3595] [depth= 1] . ( 1 sec) [ -16398.2066] [ 3545] [depth= 10] . ( 1 sec) [ -16240.3714] [ 3533] [depth= 4] . ( 1 sec) [ -15641.1660] [ 3521] [depth= 2] . ( 1 sec) [ -15619.9057] [ 3527] [depth= 1] . ( 1 sec) [ -15175.4238] [ 3443] [depth= 2] . ( 1 sec) [ -14663.3656] [ 3338] [depth= 5] . ( 1 sec) [ -14382.7551] [ 3274] [depth= 17] . ( 1 sec) [ -14333.6438] [ 3280] [depth= 1] . ( 1 sec) [ -14305.3815] [ 3274] [depth= 1] . ( 1 sec) [ -14081.3372] [ 3150] [depth= 2] . ( 1 sec) [ -14065.9286] [ 3146] [depth= 1] . ( 1 sec) [ -13809.0963] [ 3064] [depth= 8] . ( 1 sec) [ -13107.9221] [ 2937] [depth= 4] . ( 1 sec) [ -12990.5645] [ 2936] [depth= 1] . ( 1 sec) [ -12642.0614] [ 2889] [depth= 4] . ( 1 sec) [ -12546.4496] [ 2873] [depth= 1] . ( 1 sec) [ -12317.2458] [ 2838] [depth= 18] . ( 1 sec) [ -12099.4312] [ 2830] [depth= 1] . ( 1 sec) [ -12088.4439] [ 2836] [depth= 1] . ( 1 sec) [ -11962.4470] [ 2773] [depth= 1] . ( 1 sec) [ -11940.2205] [ 2767] [depth= 1] . ( 1 sec) [ -11883.7508] [ 2762] [depth= 1] . ( 2 sec) [ -11753.5674] [ 2702] [depth= 10] . ( 2 sec) [ -11641.3259] [ 2697] [depth= 1] . ( 2 sec) [ -11637.6864] [ 2701] [depth= 1] . ( 2 sec) [ -11510.8328] [ 2648] [depth= 7] . ( 2 sec) [ -11510.4258] [ 2651] [depth= 2] . ( 2 sec) [ -11474.5498] [ 2654] [depth= 4] . ( 2 sec) [ -11402.9997] [ 2644] [depth= 2] . ( 2 sec) [ -11401.0299] [ 2646] [depth= 1] . ( 2 sec) [ -11355.6810] [ 2629] [depth= 2] . ( 2 sec) [ -11122.6060] [ 2496] [depth= 9] . ( 2 sec) [ -11038.2245] [ 2468] [depth= 1] . ( 2 sec) [ -11021.0932] [ 2466] [depth= 1] . ( 2 sec) [ -10999.9927] [ 2464] [depth= 1] . ( 2 sec) [ -10839.9047] [ 2420] [depth= 10] . ( 2 sec) [ -10825.9803] [ 2412] [depth= 1] . ( 2 sec) [ -10770.3519] [ 2385] [depth= 1] . ( 2 sec) [ -10757.2235] [ 2383] [depth= 1] . ( 2 sec) [ -10479.3611] [ 2379] [depth= 1] . ( 2 sec) [ -10471.2562] [ 2366] [depth= 1] . ( 2 sec) [ -10405.6682] [ 2354] [depth= 6] . ( 2 sec) [ -10388.8039] [ 2327] [depth= 1] . ( 2 sec) [ -10365.0662] [ 2307] [depth= 1] . ( 2 sec) [ -10197.9709] [ 2228] [depth= 1] . ( 2 sec) [ -10122.9675] [ 2214] [depth= 6] . ( 3 sec) [ -10077.7117] [ 2143] [depth= 9] . ( 3 sec) [ -10061.1794] [ 2134] [depth= 2] . ( 3 sec) [ -9920.3535] [ 2135] [depth= 1] . ( 3 sec) [ -9896.6047] [ 2129] [depth= 1] . ( 3 sec) [ -9591.9456] [ 2035] [depth= 4] . ( 3 sec) [ -9548.7889] [ 2032] [depth= 1] . ( 3 sec) [ -9510.0346] [ 2029] [depth= 1] . ( 3 sec) [ -9309.9314] [ 2008] [depth= 1] . ( 3 sec) [ -9299.0054] [ 2010] [depth= 1] . ( 3 sec) [ -9290.3086] [ 2011] [depth= 4] . ( 3 sec) [ -9289.1578] [ 2011] [depth= 1] . ( 3 sec) [ -9262.6856] [ 1997] [depth= 1] . ( 3 sec) [ -9194.4832] [ 1959] [depth= 5] . ( 3 sec) [ -9143.9039] [ 1963] [depth= 1] . ( 3 sec) [ -9137.9875] [ 1959] [depth= 1] . ( 3 sec) [ -9069.6945] [ 1917] [depth= 2] . ( 3 sec) [ -8896.5901] [ 1871] [depth= 2] . ( 3 sec) [ -8812.3361] [ 1849] [depth= 1] . ( 3 sec) [ -8532.2332] [ 1794] [depth= 1] . ( 4 sec) [ -8448.3320] [ 1791] [depth= 2] . ( 4 sec) [ -8277.3129] [ 1733] [depth= 3] . ( 4 sec) [ -8240.2542] [ 1733] [depth= 1] . ( 4 sec) [ -8219.7252] [ 1727] [depth= 2] . ( 4 sec) [ -8206.7039] [ 1700] [depth= 1] . ( 4 sec) [ -8203.4162] [ 1700] [depth= 1] . ( 4 sec) [ -8197.1341] [ 1694] [depth= 1] . ( 4 sec) [ -8192.7412] [ 1690] [depth= 1] . ( 4 sec) [ -8160.0476] [ 1673] [depth= 3] . ( 4 sec) [ -8159.4285] [ 1678] [depth= 1] . ( 4 sec) [ -8083.0823] [Branch lengths ] . ( 5 sec) [ -8080.6318] [GTR parameters ] . ( 5 sec) [ -8046.4958] [Alpha ][ 0.952225] . ( 5 sec) [ -8046.3412] [ 1678] [depth= 1] . ( 5 sec) [ -8026.2604] [ 1672] [depth= 1] . ( 5 sec) [ -7977.5564] [ 1644] [depth= 3] . ( 5 sec) [ -7977.1890] [ 1646] [depth= 1] . ( 6 sec) [ -7976.5933] [ 1646] [depth= 1] . ( 6 sec) [ -7955.6330] [ 1637] [depth= 1] . ( 6 sec) [ -7955.4023] [ 1636] [depth= 1] . ( 6 sec) [ -7955.2908] [ 1635] [depth= 1] . ( 7 sec) [ -7955.1672] [ 1640] [depth= 1] . ( 7 sec) [ -7954.6823] [ 1643] [depth= 1] . ( 7 sec) [ -7954.4428] [ 1638] [depth= 1] . ( 7 sec) [ -7954.2184] [ 1636] [depth= 1] . ( 7 sec) [ -7950.4753] [ 1635] [depth= 1] . ( 8 sec) [ -7950.4585] [ 1636] [depth= 1] . ( 8 sec) [ -7950.4199] [ 1633] [depth= 1] . ( 9 sec) [ -7938.2037] [Branch lengths ] . ( 9 sec) [ -7937.9512] [GTR parameters ] . ( 9 sec) [ -7937.5955] [Alpha ][ 1.020312] . ( 10 sec) [ -7937.5476] [ 1634] [depth= 1] . ( 11 sec) [ -7936.3684] [ 1636] [depth= 1] . ( 11 sec) [ -7936.2741] [ 1636] [depth= 1] . ( 13 sec) [ -7935.4700] [Branch lengths ] . ( 13 sec) [ -7935.4637] [GTR parameters ] . ( 13 sec) [ -7935.4623] [Alpha ][ 1.024771] . ( 16 sec) [ -7935.3533] [Branch lengths ] . ( 35 sec) [ -7935.3359] [Branch lengths ] . ( 35 sec) [ -7935.3359] [Topology ] . ( 36 sec) [ -7935.3349] [Topology ] . ( 37 sec) [ -7935.3345] [Topology ] . ( 37 sec) [ -7935.3344] [GTR parameters ] . ( 37 sec) [ -7935.3339] [Alpha ][ 1.027216] . ( 37 sec) [ -7935.3339] [Topology ] . ( 38 sec) [ -7935.3337] [Topology ] . ( 38 sec) [ -7935.3337] [GTR parameters ] . ( 38 sec) [ -7935.3337] [Alpha ][ 1.027216] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.333705. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22835.4596] [GTR parameters ] . ( 1 sec) [ -22416.6695] [Alpha ][ 0.500960] . ( 1 sec) [ -22181.4923] [ 4137] [depth= 3] . ( 1 sec) [ -21790.2026] [ 4058] [depth= 10] . ( 1 sec) [ -21676.9441] [ 4020] [depth= 4] . ( 1 sec) [ -21653.5458] [ 4004] [depth= 7] . ( 1 sec) [ -20957.8986] [ 3946] [depth= 5] . ( 1 sec) [ -20929.2553] [ 3927] [depth= 8] . ( 1 sec) [ -20929.2046] [ 3915] [depth= 3] . ( 1 sec) [ -20854.4813] [ 3878] [depth= 2] . ( 1 sec) [ -20745.5397] [ 3867] [depth= 5] . ( 1 sec) [ -20674.5374] [ 3855] [depth= 1] . ( 1 sec) [ -20610.5181] [ 3850] [depth= 9] . ( 1 sec) [ -20358.5723] [ 3769] [depth= 5] . ( 1 sec) [ -20340.3959] [ 3767] [depth= 1] . ( 1 sec) [ -20044.8297] [ 3691] [depth= 16] . ( 1 sec) [ -19818.3741] [ 3615] [depth= 9] . ( 1 sec) [ -19700.7107] [ 3616] [depth= 1] . ( 2 sec) [ -19598.9908] [ 3609] [depth= 4] . ( 2 sec) [ -19330.4368] [ 3531] [depth= 2] . ( 2 sec) [ -15438.8618] [ 3533] [depth= 1] . ( 2 sec) [ -14930.4875] [ 3408] [depth= 6] . ( 2 sec) [ -14767.8939] [ 3386] [depth= 7] . ( 2 sec) [ -14436.4394] [ 3342] [depth= 1] . ( 2 sec) [ -14340.9833] [ 3342] [depth= 5] . ( 2 sec) [ -14165.3499] [ 3306] [depth= 13] . ( 2 sec) [ -14097.2802] [ 3301] [depth= 2] . ( 2 sec) [ -13797.6536] [ 3274] [depth= 2] . ( 2 sec) [ -13756.0943] [ 3145] [depth= 1] . ( 2 sec) [ -13421.7276] [ 3141] [depth= 13] . ( 2 sec) [ -13094.2917] [ 3065] [depth= 12] . ( 2 sec) [ -13023.9923] [ 3017] [depth= 1] . ( 2 sec) [ -12841.2962] [ 2932] [depth= 11] . ( 2 sec) [ -12798.7622] [ 2811] [depth= 1] . ( 2 sec) [ -12404.1874] [ 2811] [depth= 1] . ( 2 sec) [ -12337.8929] [ 2722] [depth= 2] . ( 2 sec) [ -12152.5632] [ 2714] [depth= 1] . ( 2 sec) [ -12121.0619] [ 2703] [depth= 1] . ( 2 sec) [ -12120.0158] [ 2703] [depth= 1] . ( 2 sec) [ -12009.9714] [ 2701] [depth= 1] . ( 2 sec) [ -11946.1410] [ 2681] [depth= 4] . ( 2 sec) [ -11845.8241] [ 2661] [depth= 7] . ( 3 sec) [ -11688.2055] [ 2602] [depth= 4] . ( 3 sec) [ -11492.9730] [ 2597] [depth= 1] . ( 3 sec) [ -11487.2104] [ 2597] [depth= 1] . ( 3 sec) [ -11444.3171] [ 2541] [depth= 4] . ( 3 sec) [ -11320.8521] [ 2530] [depth= 4] . ( 3 sec) [ -11294.2401] [ 2531] [depth= 2] . ( 3 sec) [ -11143.1595] [ 2497] [depth= 1] . ( 3 sec) [ -10925.3490] [ 2380] [depth= 6] . ( 3 sec) [ -10796.1529] [ 2352] [depth= 1] . ( 3 sec) [ -10791.4687] [ 2351] [depth= 1] . ( 3 sec) [ -10716.4182] [ 2354] [depth= 1] . ( 3 sec) [ -10712.7568] [ 2357] [depth= 1] . ( 3 sec) [ -10624.6005] [ 2338] [depth= 3] . ( 3 sec) [ -10584.8306] [ 2330] [depth= 2] . ( 3 sec) [ -10429.7310] [ 2336] [depth= 1] . ( 3 sec) [ -10377.8804] [ 2315] [depth= 3] . ( 3 sec) [ -10306.4600] [ 2292] [depth= 3] . ( 3 sec) [ -10298.6261] [ 2290] [depth= 1] . ( 3 sec) [ -10280.1843] [ 2274] [depth= 2] . ( 3 sec) [ -10253.2467] [ 2291] [depth= 2] . ( 4 sec) [ -10121.1830] [ 2269] [depth= 6] . ( 4 sec) [ -10063.0169] [ 2153] [depth= 3] . ( 4 sec) [ -10046.2058] [ 2148] [depth= 1] . ( 4 sec) [ -9799.6763] [ 2075] [depth= 8] . ( 4 sec) [ -9792.1194] [ 2019] [depth= 4] . ( 4 sec) [ -9549.8781] [ 2036] [depth= 2] . ( 4 sec) [ -9546.9833] [ 2036] [depth= 1] . ( 4 sec) [ -9546.7106] [ 2040] [depth= 1] . ( 4 sec) [ -9531.7564] [ 2038] [depth= 1] . ( 4 sec) [ -9513.3554] [ 2040] [depth= 3] . ( 4 sec) [ -9455.8421] [ 2031] [depth= 1] . ( 4 sec) [ -9376.6426] [ 2029] [depth= 1] . ( 4 sec) [ -9330.3652] [ 2031] [depth= 4] . ( 4 sec) [ -9320.8607] [ 2034] [depth= 1] . ( 4 sec) [ -9227.9953] [ 2024] [depth= 7] . ( 4 sec) [ -9225.7949] [ 2030] [depth= 1] . ( 4 sec) [ -9224.2233] [ 2033] [depth= 1] . ( 4 sec) [ -9061.0782] [ 2017] [depth= 2] . ( 4 sec) [ -9060.1131] [ 2018] [depth= 1] . ( 4 sec) [ -9056.4586] [ 2012] [depth= 1] . ( 4 sec) [ -9016.7462] [ 1906] [depth= 2] . ( 4 sec) [ -8897.3784] [ 1912] [depth= 1] . ( 5 sec) [ -8830.5637] [ 1895] [depth= 2] . ( 5 sec) [ -8822.9060] [ 1916] [depth= 1] . ( 5 sec) [ -8822.1172] [ 1918] [depth= 1] . ( 5 sec) [ -8819.5310] [ 1919] [depth= 1] . ( 5 sec) [ -8539.3070] [Branch lengths ] . ( 6 sec) [ -8535.7394] [GTR parameters ] . ( 6 sec) [ -8519.4276] [Alpha ][ 0.765962] . ( 6 sec) [ -8513.5427] [ 1899] [depth= 1] . ( 6 sec) [ -8510.7449] [ 1880] [depth= 2] . ( 6 sec) [ -8509.0832] [ 1791] [depth= 2] . ( 6 sec) [ -8503.4077] [ 1789] [depth= 1] . ( 6 sec) [ -8471.9736] [ 1763] [depth= 2] . ( 6 sec) [ -8469.6583] [ 1772] [depth= 2] . ( 6 sec) [ -8467.7722] [ 1771] [depth= 1] . ( 6 sec) [ -8467.5426] [ 1771] [depth= 1] . ( 6 sec) [ -8466.4687] [ 1773] [depth= 1] . ( 6 sec) [ -8455.1926] [ 1775] [depth= 2] . ( 6 sec) [ -8450.6386] [ 1769] [depth= 1] . ( 6 sec) [ -8450.5854] [ 1769] [depth= 1] . ( 7 sec) [ -8203.3056] [ 1766] [depth= 3] . ( 7 sec) [ -8194.6307] [ 1743] [depth= 1] . ( 7 sec) [ -8145.5098] [ 1723] [depth= 3] . ( 7 sec) [ -8112.7861] [ 1711] [depth= 1] . ( 7 sec) [ -8111.4474] [ 1711] [depth= 1] . ( 7 sec) [ -8110.0582] [ 1711] [depth= 1] . ( 7 sec) [ -8109.8702] [ 1710] [depth= 1] . ( 7 sec) [ -8102.1067] [ 1709] [depth= 2] . ( 7 sec) [ -8099.0217] [ 1711] [depth= 1] . ( 7 sec) [ -8095.2175] [ 1703] [depth= 1] . ( 7 sec) [ -8094.7858] [ 1702] [depth= 1] . ( 8 sec) [ -8088.7184] [ 1697] [depth= 1] . ( 8 sec) [ -8088.3647] [ 1700] [depth= 1] . ( 8 sec) [ -8031.0143] [ 1669] [depth= 1] . ( 8 sec) [ -8025.5053] [ 1671] [depth= 1] . ( 8 sec) [ -7991.4984] [ 1644] [depth= 1] . ( 8 sec) [ -7990.3033] [ 1643] [depth= 1] . ( 8 sec) [ -7977.0569] [ 1641] [depth= 1] . ( 9 sec) [ -7952.9683] [Branch lengths ] . ( 10 sec) [ -7952.2616] [GTR parameters ] . ( 10 sec) [ -7947.4816] [Alpha ][ 0.983096] . ( 10 sec) [ -7943.3696] [ 1636] [depth= 1] . ( 10 sec) [ -7943.1038] [ 1637] [depth= 1] . ( 10 sec) [ -7942.9992] [ 1637] [depth= 1] . ( 11 sec) [ -7942.8243] [ 1639] [depth= 1] . ( 11 sec) [ -7941.1936] [ 1637] [depth= 1] . ( 12 sec) [ -7941.1631] [ 1637] [depth= 1] . ( 12 sec) [ -7940.8587] [ 1634] [depth= 1] . ( 12 sec) [ -7940.7042] [ 1637] [depth= 1] . ( 13 sec) [ -7936.2687] [Branch lengths ] . ( 13 sec) [ -7936.2567] [GTR parameters ] . ( 14 sec) [ -7936.1587] [Alpha ][ 1.019355] . ( 16 sec) [ -7936.0536] [ 1637] [depth= 1] . ( 17 sec) [ -7935.6497] [Branch lengths ] . ( 17 sec) [ -7935.6466] [GTR parameters ] . ( 17 sec) [ -7935.6443] [Alpha ][ 1.025067] . ( 31 sec) [ -7935.5824] [ 1636] [depth= 1] . ( 36 sec) [ -7935.3787] [Branch lengths ] . ( 36 sec) [ -7935.3764] [GTR parameters ] . ( 36 sec) [ -7935.3762] [Alpha ][ 1.026440] . ( 36 sec) [ -7935.3762] [Topology ] . ( 37 sec) [ -7935.3534] [Topology ] . ( 38 sec) [ -7935.3410] [Topology ] . ( 38 sec) [ -7935.3365] [Topology ] . ( 39 sec) [ -7935.3349] [Topology ] . ( 40 sec) [ -7935.3343] [Topology ] . ( 40 sec) [ -7935.3342] [GTR parameters ] . ( 40 sec) [ -7935.3341] [Alpha ][ 1.027466] . ( 40 sec) [ -7935.3341] [Topology ] . ( 41 sec) [ -7935.3338] [Topology ] . ( 41 sec) [ -7935.3338] [GTR parameters ] . ( 41 sec) [ -7935.3338] [Alpha ][ 1.027466] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.333810. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23342.4947] [GTR parameters ] . ( 1 sec) [ -22907.7482] [Alpha ][ 0.500960] . ( 1 sec) [ -22650.1649] [ 4224] [depth= 8] . ( 1 sec) [ -22259.3925] [ 4148] [depth= 8] . ( 1 sec) [ -22167.6834] [ 4134] [depth= 5] . ( 1 sec) [ -22145.9169] [ 4132] [depth= 2] . ( 1 sec) [ -21953.1849] [ 4063] [depth= 9] . ( 1 sec) [ -21880.3818] [ 4062] [depth= 3] . ( 1 sec) [ -21703.2312] [ 4021] [depth= 4] . ( 1 sec) [ -21255.5565] [ 3962] [depth= 9] . ( 1 sec) [ -21156.3576] [ 3958] [depth= 7] . ( 1 sec) [ -21011.2379] [ 3882] [depth= 17] . ( 1 sec) [ -20615.1626] [ 3823] [depth= 6] . ( 1 sec) [ -20385.9546] [ 3755] [depth= 10] . ( 1 sec) [ -20370.9261] [ 3748] [depth= 1] . ( 1 sec) [ -19879.6371] [ 3715] [depth= 11] . ( 2 sec) [ -19786.3537] [ 3701] [depth= 1] . ( 2 sec) [ -19617.4841] [ 3605] [depth= 4] . ( 2 sec) [ -19399.1463] [ 3569] [depth= 15] . ( 2 sec) [ -19369.5690] [ 3595] [depth= 2] . ( 2 sec) [ -18953.2820] [ 3531] [depth= 13] . ( 2 sec) [ -18745.9298] [ 3507] [depth= 6] . ( 2 sec) [ -18605.8593] [ 3440] [depth= 8] . ( 2 sec) [ -18504.9958] [ 3394] [depth= 1] . ( 2 sec) [ -18441.8353] [ 3347] [depth= 3] . ( 2 sec) [ -17929.7322] [ 3287] [depth= 7] . ( 2 sec) [ -17653.5534] [ 3212] [depth= 3] . ( 2 sec) [ -17419.4776] [ 3151] [depth= 5] . ( 2 sec) [ -17175.1408] [ 3007] [depth= 15] . ( 2 sec) [ -17163.4312] [ 3007] [depth= 5] . ( 2 sec) [ -16925.5235] [ 2912] [depth= 9] . ( 2 sec) [ -16773.1456] [ 2848] [depth= 4] . ( 2 sec) [ -16654.9422] [ 2830] [depth= 1] . ( 2 sec) [ -16466.8011] [ 2830] [depth= 1] . ( 2 sec) [ -16400.2605] [ 2817] [depth= 2] . ( 2 sec) [ -16384.1042] [ 2817] [depth= 1] . ( 2 sec) [ -16113.2790] [ 2691] [depth= 11] . ( 2 sec) [ -16058.2228] [ 2667] [depth= 1] . ( 2 sec) [ -16052.2032] [ 2689] [depth= 2] . ( 2 sec) [ -15730.8478] [ 2552] [depth= 8] . ( 2 sec) [ -15666.2243] [ 2574] [depth= 8] . ( 2 sec) [ -15494.3823] [ 2563] [depth= 1] . ( 3 sec) [ -15493.0533] [ 2560] [depth= 10] . ( 3 sec) [ -15453.2273] [ 2541] [depth= 2] . ( 3 sec) [ -11808.1904] [ 2437] [depth= 3] . ( 3 sec) [ -11799.8779] [ 2435] [depth= 1] . ( 3 sec) [ -11612.6015] [ 2343] [depth= 2] . ( 3 sec) [ -11525.9609] [ 2332] [depth= 8] . ( 3 sec) [ -11409.9247] [ 2332] [depth= 1] . ( 3 sec) [ -11303.7241] [ 2302] [depth= 1] . ( 3 sec) [ -11303.4956] [ 2301] [depth= 2] . ( 3 sec) [ -10747.5181] [ 2155] [depth= 6] . ( 3 sec) [ -10701.1203] [ 2152] [depth= 2] . ( 3 sec) [ -10456.3338] [ 2151] [depth= 2] . ( 3 sec) [ -10428.5067] [ 2128] [depth= 1] . ( 3 sec) [ -10313.2286] [ 2122] [depth= 1] . ( 3 sec) [ -10263.4503] [ 2122] [depth= 1] . ( 3 sec) [ -10260.7309] [ 2121] [depth= 2] . ( 3 sec) [ -9976.0577] [ 1989] [depth= 5] . ( 3 sec) [ -9962.6983] [ 1988] [depth= 1] . ( 3 sec) [ -9702.7812] [ 1989] [depth= 1] . ( 3 sec) [ -9624.3337] [ 1959] [depth= 1] . ( 3 sec) [ -9620.2638] [ 1958] [depth= 1] . ( 3 sec) [ -9601.0501] [ 1965] [depth= 1] . ( 4 sec) [ -9595.8982] [ 1963] [depth= 2] . ( 4 sec) [ -9459.2393] [ 1909] [depth= 3] . ( 4 sec) [ -9400.3498] [ 1904] [depth= 2] . ( 4 sec) [ -9291.5683] [ 1875] [depth= 4] . ( 4 sec) [ -9271.2973] [ 1871] [depth= 1] . ( 4 sec) [ -9218.4130] [ 1842] [depth= 1] . ( 4 sec) [ -9069.5972] [ 1817] [depth= 1] . ( 4 sec) [ -9001.3821] [ 1799] [depth= 4] . ( 4 sec) [ -8768.6450] [ 1906] [depth= 1] . ( 4 sec) [ -8350.1600] [ 1750] [depth= 3] . ( 4 sec) [ -8346.3015] [ 1750] [depth= 1] . ( 4 sec) [ -8343.4270] [ 1753] [depth= 1] . ( 4 sec) [ -8343.3747] [ 1752] [depth= 1] . ( 4 sec) [ -8197.8518] [ 1686] [depth= 2] . ( 4 sec) [ -8188.6088] [ 1687] [depth= 1] . ( 4 sec) [ -8188.5375] [ 1683] [depth= 1] . ( 4 sec) [ -8185.1515] [ 1682] [depth= 1] . ( 4 sec) [ -8184.0566] [ 1682] [depth= 1] . ( 4 sec) [ -8174.0066] [ 1679] [depth= 2] . ( 4 sec) [ -8144.6914] [ 1659] [depth= 4] . ( 4 sec) [ -8129.9195] [ 1656] [depth= 1] . ( 4 sec) [ -8128.2251] [ 1657] [depth= 1] . ( 5 sec) [ -8105.4604] [ 1651] [depth= 1] . ( 5 sec) [ -8105.0370] [ 1652] [depth= 1] . ( 5 sec) [ -8043.8198] [Branch lengths ] . ( 6 sec) [ -8041.2432] [GTR parameters ] . ( 6 sec) [ -8012.6390] [Alpha ][ 0.907470] . ( 6 sec) [ -8012.5437] [ 1656] [depth= 1] . ( 6 sec) [ -8010.5979] [ 1656] [depth= 1] . ( 6 sec) [ -7963.1064] [ 1636] [depth= 2] . ( 6 sec) [ -7960.3568] [ 1631] [depth= 1] . ( 7 sec) [ -7960.1724] [ 1631] [depth= 1] . ( 7 sec) [ -7960.0466] [ 1631] [depth= 1] . ( 7 sec) [ -7959.7043] [ 1629] [depth= 1] . ( 7 sec) [ -7956.5909] [ 1627] [depth= 1] . ( 7 sec) [ -7954.8563] [ 1630] [depth= 1] . ( 8 sec) [ -7951.2136] [ 1631] [depth= 1] . ( 8 sec) [ -7951.1907] [ 1634] [depth= 1] . ( 9 sec) [ -7948.5406] [ 1638] [depth= 1] . ( 9 sec) [ -7938.7572] [Branch lengths ] . ( 9 sec) [ -7938.5397] [GTR parameters ] . ( 9 sec) [ -7937.7159] [Alpha ][ 1.008147] . ( 10 sec) [ -7937.4572] [ 1636] [depth= 1] . ( 10 sec) [ -7937.3515] [ 1636] [depth= 1] . ( 11 sec) [ -7937.2595] [ 1637] [depth= 1] . ( 13 sec) [ -7935.8106] [Branch lengths ] . ( 13 sec) [ -7935.8035] [GTR parameters ] . ( 14 sec) [ -7935.7895] [Alpha ][ 1.022411] . ( 17 sec) [ -7935.5544] [Branch lengths ] . ( 21 sec) [ -7935.4526] [ 1636] [depth= 1] . ( 36 sec) [ -7935.3445] [Branch lengths ] . ( 36 sec) [ -7935.3422] [GTR parameters ] . ( 36 sec) [ -7935.3409] [Alpha ][ 1.026712] . ( 36 sec) [ -7935.3409] [Topology ] . ( 37 sec) [ -7935.3363] [Topology ] . ( 38 sec) [ -7935.3348] [Topology ] . ( 38 sec) [ -7935.3342] [Topology ] . ( 38 sec) [ -7935.3342] [GTR parameters ] . ( 38 sec) [ -7935.3342] [Alpha ][ 1.027739] . ( 39 sec) [ -7935.3342] [Topology ] . ( 39 sec) [ -7935.3339] [Topology ] . ( 39 sec) [ -7935.3339] [GTR parameters ] . ( 39 sec) [ -7935.3339] [Alpha ][ 1.027739] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.333860. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24050.6622] [GTR parameters ] . ( 1 sec) [ -23618.0720] [Alpha ][ 0.500960] . ( 1 sec) [ -23505.3317] [ 4285] [depth= 5] . ( 1 sec) [ -23093.3419] [ 4220] [depth= 8] . ( 1 sec) [ -22906.3469] [ 4165] [depth= 8] . ( 1 sec) [ -22857.3288] [ 4051] [depth= 1] . ( 1 sec) [ -22413.1576] [ 3962] [depth= 3] . ( 1 sec) [ -22137.8680] [ 3925] [depth= 2] . ( 1 sec) [ -21984.4987] [ 3920] [depth= 2] . ( 1 sec) [ -21745.7173] [ 3852] [depth= 5] . ( 1 sec) [ -21639.1629] [ 3837] [depth= 5] . ( 1 sec) [ -21621.9986] [ 3830] [depth= 2] . ( 1 sec) [ -21546.8965] [ 3828] [depth= 2] . ( 1 sec) [ -21399.9669] [ 3758] [depth= 4] . ( 1 sec) [ -21113.1548] [ 3693] [depth= 10] . ( 1 sec) [ -21018.0034] [ 3684] [depth= 3] . ( 1 sec) [ -17329.2642] [ 3656] [depth= 9] . ( 2 sec) [ -17107.9513] [ 3638] [depth= 21] . ( 2 sec) [ -16526.8293] [ 3630] [depth= 1] . ( 2 sec) [ -16165.5146] [ 3541] [depth= 2] . ( 2 sec) [ -15791.7907] [ 3452] [depth= 24] . ( 2 sec) [ -15622.2795] [ 3378] [depth= 3] . ( 2 sec) [ -15473.6858] [ 3391] [depth= 15] . ( 2 sec) [ -15434.0047] [ 3352] [depth= 1] . ( 2 sec) [ -15337.6877] [ 3343] [depth= 2] . ( 2 sec) [ -15290.5214] [ 3342] [depth= 1] . ( 2 sec) [ -14864.6078] [ 3250] [depth= 1] . ( 2 sec) [ -14781.8722] [ 3226] [depth= 15] . ( 2 sec) [ -14381.4731] [ 3226] [depth= 1] . ( 2 sec) [ -14056.6452] [ 3229] [depth= 10] . ( 2 sec) [ -13978.2557] [ 3141] [depth= 1] . ( 2 sec) [ -13970.0206] [ 3131] [depth= 1] . ( 2 sec) [ -13262.0020] [ 3059] [depth= 12] . ( 2 sec) [ -13180.8840] [ 2967] [depth= 1] . ( 2 sec) [ -12733.2242] [ 2952] [depth= 1] . ( 2 sec) [ -12694.3604] [ 2943] [depth= 1] . ( 2 sec) [ -12537.5230] [ 2876] [depth= 1] . ( 2 sec) [ -12301.4161] [ 2784] [depth= 16] . ( 2 sec) [ -12208.9218] [ 2802] [depth= 1] . ( 2 sec) [ -12149.1935] [ 2740] [depth= 1] . ( 2 sec) [ -11978.9186] [ 2713] [depth= 8] . ( 2 sec) [ -11892.1813] [ 2719] [depth= 1] . ( 3 sec) [ -11872.1707] [ 2701] [depth= 1] . ( 3 sec) [ -11850.4020] [ 2690] [depth= 3] . ( 3 sec) [ -11716.3764] [ 2596] [depth= 11] . ( 3 sec) [ -11562.2119] [ 2590] [depth= 2] . ( 3 sec) [ -11507.6506] [ 2583] [depth= 2] . ( 3 sec) [ -11499.3892] [ 2565] [depth= 4] . ( 3 sec) [ -10791.6749] [ 2564] [depth= 2] . ( 3 sec) [ -10526.1002] [ 2434] [depth= 9] . ( 3 sec) [ -10433.8945] [ 2435] [depth= 1] . ( 3 sec) [ -10320.7504] [ 2370] [depth= 1] . ( 3 sec) [ -10180.1618] [ 2333] [depth= 10] . ( 3 sec) [ -10164.7382] [ 2332] [depth= 1] . ( 3 sec) [ -10074.9565] [ 2287] [depth= 1] . ( 3 sec) [ -9969.4112] [ 2229] [depth= 4] . ( 3 sec) [ -9798.6586] [ 2211] [depth= 4] . ( 3 sec) [ -9786.1628] [ 2192] [depth= 6] . ( 3 sec) [ -9748.5021] [ 2190] [depth= 3] . ( 3 sec) [ -9740.5217] [ 2181] [depth= 1] . ( 3 sec) [ -9675.7642] [ 2178] [depth= 1] . ( 3 sec) [ -9674.8380] [ 2180] [depth= 1] . ( 3 sec) [ -9415.0913] [ 2139] [depth= 10] . ( 3 sec) [ -9376.4245] [ 2146] [depth= 1] . ( 4 sec) [ -9275.6830] [ 2143] [depth= 1] . ( 4 sec) [ -9268.5306] [ 2136] [depth= 1] . ( 4 sec) [ -9264.6229] [ 2128] [depth= 1] . ( 4 sec) [ -9194.8415] [ 2111] [depth= 2] . ( 4 sec) [ -9190.5981] [ 2110] [depth= 1] . ( 4 sec) [ -9187.9074] [ 2098] [depth= 2] . ( 4 sec) [ -9177.0040] [ 2092] [depth= 1] . ( 4 sec) [ -9102.3349] [ 2091] [depth= 1] . ( 4 sec) [ -9081.6419] [ 2089] [depth= 1] . ( 4 sec) [ -9044.5393] [ 2091] [depth= 1] . ( 4 sec) [ -8921.6482] [ 1987] [depth= 6] . ( 4 sec) [ -8876.3577] [ 1953] [depth= 1] . ( 4 sec) [ -8858.4774] [ 1953] [depth= 1] . ( 4 sec) [ -8845.4712] [ 1951] [depth= 1] . ( 4 sec) [ -8839.2790] [ 1955] [depth= 1] . ( 4 sec) [ -8651.0648] [ 1845] [depth= 5] . ( 4 sec) [ -8601.9434] [ 1849] [depth= 1] . ( 4 sec) [ -8559.1526] [ 1852] [depth= 1] . ( 4 sec) [ -8527.3781] [ 1845] [depth= 5] . ( 4 sec) [ -8527.0330] [ 1846] [depth= 1] . ( 4 sec) [ -8505.0033] [ 1835] [depth= 1] . ( 4 sec) [ -8492.7542] [ 1825] [depth= 2] . ( 5 sec) [ -8489.9745] [ 1824] [depth= 1] . ( 5 sec) [ -8483.6064] [ 1818] [depth= 1] . ( 5 sec) [ -8479.7608] [ 1820] [depth= 1] . ( 5 sec) [ -8464.6299] [ 1818] [depth= 1] . ( 5 sec) [ -8460.0464] [ 1818] [depth= 1] . ( 5 sec) [ -8342.4158] [Branch lengths ] . ( 6 sec) [ -8339.6419] [GTR parameters ] . ( 6 sec) [ -8309.2656] [Alpha ][ 0.883999] . ( 6 sec) [ -8299.3451] [ 1812] [depth= 4] . ( 6 sec) [ -8296.2805] [ 1808] [depth= 2] . ( 6 sec) [ -8295.2935] [ 1812] [depth= 2] . ( 6 sec) [ -8167.1651] [ 1752] [depth= 1] . ( 6 sec) [ -8151.7506] [ 1755] [depth= 1] . ( 6 sec) [ -8150.3942] [ 1753] [depth= 1] . ( 6 sec) [ -8150.2655] [ 1755] [depth= 1] . ( 7 sec) [ -8135.8469] [ 1757] [depth= 1] . ( 7 sec) [ -8135.2728] [ 1760] [depth= 1] . ( 7 sec) [ -8134.8626] [ 1751] [depth= 1] . ( 7 sec) [ -8102.7006] [ 1719] [depth= 3] . ( 7 sec) [ -8102.5309] [ 1720] [depth= 1] . ( 7 sec) [ -8101.5727] [ 1718] [depth= 1] . ( 8 sec) [ -7979.4272] [ 1640] [depth= 2] . ( 8 sec) [ -7977.5000] [ 1643] [depth= 1] . ( 8 sec) [ -7974.3270] [ 1643] [depth= 1] . ( 8 sec) [ -7973.7943] [ 1641] [depth= 1] . ( 8 sec) [ -7973.6594] [ 1641] [depth= 1] . ( 8 sec) [ -7973.6486] [ 1638] [depth= 1] . ( 9 sec) [ -7949.1998] [ 1632] [depth= 1] . ( 9 sec) [ -7948.8129] [ 1634] [depth= 1] . ( 9 sec) [ -7948.4835] [ 1635] [depth= 1] . ( 9 sec) [ -7942.0389] [Branch lengths ] . ( 10 sec) [ -7941.4277] [GTR parameters ] . ( 10 sec) [ -7939.9471] [Alpha ][ 1.015652] . ( 10 sec) [ -7939.8060] [ 1637] [depth= 1] . ( 11 sec) [ -7938.6526] [ 1634] [depth= 1] . ( 13 sec) [ -7937.5273] [Branch lengths ] . ( 14 sec) [ -7937.5181] [GTR parameters ] . ( 14 sec) [ -7937.5153] [Alpha ][ 1.021948] . ( 14 sec) [ -7937.3958] [ 1634] [depth= 1] . ( 17 sec) [ -7935.9348] [Branch lengths ] . ( 17 sec) [ -7935.9316] [GTR parameters ] . ( 17 sec) [ -7935.9309] [Alpha ][ 1.025043] . ( 21 sec) [ -7935.8661] [Branch lengths ] . ( 26 sec) [ -7935.7257] [ 1634] [depth= 1] . ( 39 sec) [ -7935.6304] [Branch lengths ] . ( 39 sec) [ -7935.6295] [GTR parameters ] . ( 39 sec) [ -7935.6294] [Alpha ][ 1.026068] . ( 39 sec) [ -7935.6294] [Topology ] . ( 40 sec) [ -7935.6187] [Topology ] . ( 41 sec) [ -7935.6168] [Topology ] . ( 42 sec) [ -7935.6162] [Topology ] . ( 42 sec) [ -7935.6161] [GTR parameters ] . ( 42 sec) [ -7935.6161] [Alpha ][ 1.026068] . ( 42 sec) [ -7935.6161] [Topology ] . ( 43 sec) [ -7935.6159] [Topology ] . ( 43 sec) [ -7935.6159] [GTR parameters ] . ( 43 sec) [ -7935.6159] [Alpha ][ 1.026068] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -7935.5267] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -7935.3665] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.366518. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22892.4785] [GTR parameters ] . ( 0 sec) [ -22423.6730] [Alpha ][ 0.500960] . ( 0 sec) [ -22300.9114] [ 4323] [depth= 3] . ( 0 sec) [ -22027.2102] [ 4264] [depth= 7] . ( 0 sec) [ -21893.8997] [ 4253] [depth= 4] . ( 0 sec) [ -21884.0295] [ 4254] [depth= 2] . ( 0 sec) [ -21773.7336] [ 4247] [depth= 4] . ( 0 sec) [ -21724.6728] [ 4241] [depth= 3] . ( 0 sec) [ -19744.4801] [ 4225] [depth= 6] . ( 0 sec) [ -19444.5712] [ 4258] [depth= 1] . ( 0 sec) [ -18891.8988] [ 4175] [depth= 2] . ( 1 sec) [ -18605.7183] [ 4090] [depth= 8] . ( 1 sec) [ -18243.6158] [ 3962] [depth= 8] . ( 1 sec) [ -17669.1276] [ 3845] [depth= 8] . ( 1 sec) [ -17650.6022] [ 3791] [depth= 10] . ( 1 sec) [ -17544.8391] [ 3792] [depth= 4] . ( 1 sec) [ -17291.2286] [ 3675] [depth= 17] . ( 1 sec) [ -17196.0004] [ 3651] [depth= 14] . ( 1 sec) [ -17087.1593] [ 3575] [depth= 3] . ( 1 sec) [ -16839.0118] [ 3573] [depth= 14] . ( 1 sec) [ -16770.4758] [ 3549] [depth= 12] . ( 1 sec) [ -16635.1519] [ 3549] [depth= 2] . ( 1 sec) [ -16557.7481] [ 3507] [depth= 2] . ( 1 sec) [ -16441.4119] [ 3444] [depth= 7] . ( 1 sec) [ -16316.0733] [ 3388] [depth= 2] . ( 1 sec) [ -15367.2277] [ 3374] [depth= 9] . ( 1 sec) [ -14590.3792] [ 3262] [depth= 9] . ( 1 sec) [ -13813.5017] [ 3156] [depth= 5] . ( 1 sec) [ -13511.1869] [ 3112] [depth= 9] . ( 1 sec) [ -13448.4343] [ 3111] [depth= 11] . ( 1 sec) [ -13438.6327] [ 3113] [depth= 1] . ( 1 sec) [ -13386.0696] [ 3108] [depth= 4] . ( 1 sec) [ -13360.2951] [ 3106] [depth= 1] . ( 1 sec) [ -13019.6471] [ 3106] [depth= 1] . ( 1 sec) [ -13013.9546] [ 3002] [depth= 4] . ( 1 sec) [ -12895.2797] [ 3000] [depth= 10] . ( 2 sec) [ -12678.3764] [ 2967] [depth= 6] . ( 2 sec) [ -12425.9491] [ 2851] [depth= 10] . ( 2 sec) [ -12414.8078] [ 2855] [depth= 1] . ( 2 sec) [ -12113.1287] [ 2861] [depth= 2] . ( 2 sec) [ -11857.3085] [ 2804] [depth= 4] . ( 2 sec) [ -11827.4506] [ 2803] [depth= 1] . ( 2 sec) [ -11826.0801] [ 2802] [depth= 1] . ( 2 sec) [ -11816.5982] [ 2777] [depth= 7] . ( 2 sec) [ -11752.8375] [ 2769] [depth= 3] . ( 2 sec) [ -11640.9164] [ 2711] [depth= 1] . ( 2 sec) [ -11573.4612] [ 2673] [depth= 12] . ( 2 sec) [ -11525.9357] [ 2681] [depth= 1] . ( 2 sec) [ -11357.0237] [ 2612] [depth= 3] . ( 2 sec) [ -11156.2371] [ 2532] [depth= 13] . ( 2 sec) [ -11110.4750] [ 2513] [depth= 1] . ( 2 sec) [ -10869.0013] [ 2439] [depth= 7] . ( 2 sec) [ -10476.2438] [ 2332] [depth= 4] . ( 2 sec) [ -10353.9022] [ 2319] [depth= 2] . ( 2 sec) [ -10258.9538] [ 2314] [depth= 1] . ( 3 sec) [ -10198.4983] [ 2319] [depth= 3] . ( 3 sec) [ -10189.1438] [ 2317] [depth= 1] . ( 3 sec) [ -9938.1671] [ 2264] [depth= 11] . ( 3 sec) [ -9857.5931] [ 2265] [depth= 1] . ( 3 sec) [ -9857.2893] [ 2265] [depth= 1] . ( 3 sec) [ -9807.5716] [ 2250] [depth= 4] . ( 3 sec) [ -9758.0811] [ 2218] [depth= 1] . ( 3 sec) [ -9688.3006] [ 2206] [depth= 3] . ( 3 sec) [ -9651.0724] [ 2191] [depth= 2] . ( 3 sec) [ -9590.7288] [ 2146] [depth= 2] . ( 3 sec) [ -9431.7841] [ 2093] [depth= 8] . ( 3 sec) [ -9427.5416] [ 2095] [depth= 1] . ( 3 sec) [ -9421.0036] [ 2093] [depth= 1] . ( 3 sec) [ -9338.8706] [ 2065] [depth= 1] . ( 3 sec) [ -9326.0443] [ 2069] [depth= 1] . ( 3 sec) [ -9296.3478] [ 2069] [depth= 1] . ( 3 sec) [ -9253.5260] [ 2061] [depth= 1] . ( 3 sec) [ -9242.5800] [ 2029] [depth= 1] . ( 3 sec) [ -9201.5264] [ 2009] [depth= 1] . ( 3 sec) [ -9046.1743] [ 1951] [depth= 2] . ( 3 sec) [ -9010.9069] [ 1949] [depth= 2] . ( 3 sec) [ -8995.1745] [ 1948] [depth= 6] . ( 3 sec) [ -8990.3339] [ 1947] [depth= 1] . ( 3 sec) [ -8988.8635] [ 1948] [depth= 1] . ( 4 sec) [ -8962.3671] [ 1923] [depth= 1] . ( 4 sec) [ -8766.3606] [ 1842] [depth= 4] . ( 4 sec) [ -8637.4293] [ 1771] [depth= 3] . ( 4 sec) [ -8630.2180] [ 1776] [depth= 1] . ( 4 sec) [ -8627.3060] [ 1777] [depth= 1] . ( 4 sec) [ -8623.7027] [ 1777] [depth= 1] . ( 4 sec) [ -8620.9502] [ 1780] [depth= 1] . ( 4 sec) [ -8447.1884] [ 1741] [depth= 5] . ( 4 sec) [ -8419.2529] [ 1747] [depth= 1] . ( 4 sec) [ -8416.2447] [ 1749] [depth= 1] . ( 4 sec) [ -8390.3972] [ 1750] [depth= 3] . ( 4 sec) [ -8124.0657] [Branch lengths ] . ( 5 sec) [ -8122.0894] [GTR parameters ] . ( 5 sec) [ -8090.9888] [Alpha ][ 0.901774] . ( 5 sec) [ -8051.5370] [ 1737] [depth= 1] . ( 5 sec) [ -8042.9646] [ 1732] [depth= 1] . ( 5 sec) [ -8035.8889] [ 1730] [depth= 1] . ( 5 sec) [ -8032.1009] [ 1721] [depth= 2] . ( 5 sec) [ -8030.9311] [ 1723] [depth= 2] . ( 5 sec) [ -8030.1043] [ 1721] [depth= 1] . ( 5 sec) [ -8028.2758] [ 1720] [depth= 1] . ( 6 sec) [ -7990.9740] [ 1679] [depth= 4] . ( 6 sec) [ -7974.7507] [ 1651] [depth= 3] . ( 6 sec) [ -7974.7167] [ 1654] [depth= 1] . ( 6 sec) [ -7972.3340] [ 1650] [depth= 1] . ( 6 sec) [ -7972.1986] [ 1650] [depth= 1] . ( 6 sec) [ -7962.9944] [ 1640] [depth= 1] . ( 6 sec) [ -7962.4332] [ 1644] [depth= 1] . ( 7 sec) [ -7961.7827] [ 1645] [depth= 1] . ( 7 sec) [ -7961.6279] [ 1647] [depth= 1] . ( 7 sec) [ -7960.0569] [ 1642] [depth= 1] . ( 7 sec) [ -7950.4210] [ 1637] [depth= 1] . ( 7 sec) [ -7948.2689] [ 1638] [depth= 1] . ( 8 sec) [ -7947.9853] [ 1635] [depth= 1] . ( 8 sec) [ -7946.9232] [ 1639] [depth= 1] . ( 9 sec) [ -7939.7007] [Branch lengths ] . ( 9 sec) [ -7939.1073] [GTR parameters ] . ( 9 sec) [ -7938.0412] [Alpha ][ 1.014969] . ( 10 sec) [ -7937.7461] [ 1637] [depth= 1] . ( 12 sec) [ -7937.7054] [ 1637] [depth= 1] . ( 13 sec) [ -7935.7857] [Branch lengths ] . ( 13 sec) [ -7935.7801] [GTR parameters ] . ( 13 sec) [ -7935.7729] [Alpha ][ 1.025132] . ( 17 sec) [ -7935.5998] [Branch lengths ] . ( 26 sec) [ -7935.5202] [ 1636] [depth= 1] . ( 36 sec) [ -7935.3394] [Branch lengths ] . ( 36 sec) [ -7935.3377] [GTR parameters ] . ( 36 sec) [ -7935.3374] [Alpha ][ 1.027177] . ( 36 sec) [ -7935.3374] [Topology ] . ( 37 sec) [ -7935.3347] [Topology ] . ( 37 sec) [ -7935.3341] [Topology ] . ( 38 sec) [ -7935.3341] [GTR parameters ] . ( 38 sec) [ -7935.3341] [Alpha ][ 1.027177] . ( 38 sec) [ -7935.3341] [Topology ] . ( 38 sec) [ -7935.3339] [Topology ] . ( 38 sec) [ -7935.3339] [GTR parameters ] . ( 39 sec) [ -7935.3339] [Alpha ][ 1.027177] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7935.333886. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7990.949843 . ( 1 sec) [ -7988.1958] [GTR parameters ] . ( 1 sec) [ -7988.1956] [Alpha ][ 0.998171] . ( 1 sec) [ -7988.1956] [Topology ] . ( 1 sec) [ -7946.8898] [Topology ] . ( 2 sec) [ -7942.5047] [Topology ] . ( 3 sec) [ -7940.3008] [Topology ] . ( 4 sec) [ -7939.1196] [Topology ] . ( 4 sec) [ -7938.8803] [Topology ] . ( 5 sec) [ -7938.7734] [Topology ] . ( 6 sec) [ -7938.7010] [Topology ] . ( 7 sec) [ -7938.5453] [Topology ] . ( 7 sec) [ -7936.6980] [Topology ] . Before opt ts/t=1.000000 LK=-7935.798149 . ( 9 sec) [ -7935.7576] [GTR parameters ] . ( 9 sec) [ -7935.6997] [Alpha ][ 1.026029] . ( 9 sec) [ -7935.6997] [Topology ] . ( 9 sec) [ -7935.4675] [Topology ] . ( 10 sec) [ -7935.3702] [Topology ] . ( 11 sec) [ -7935.3500] [Topology ] . ( 12 sec) [ -7935.3422] [Topology ] . ( 12 sec) [ -7935.3386] [Topology ] . ( 13 sec) [ -7935.3369] [Topology ] . ( 14 sec) [ -7935.3360] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.336011 . ( 19 sec) [ -7935.3345] [GTR parameters ] . ( 19 sec) [ -7935.3344] [Alpha ][ 1.027305] . ( 19 sec) [ -7935.3344] [Topology ] . ( 20 sec) [ -7935.3339] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7935.333949 . ( 25 sec) [ -7935.3339] [GTR parameters ] . ( 25 sec) [ -7935.3339] [Alpha ][ 1.027305] . ( 25 sec) [ -7935.3339] [Topology ] . ( 26 sec) [ -7935.3337] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 37 sec) [ -7988.1958] [GTR parameters ] . ( 37 sec) [ -7988.1956] [Alpha ][ 0.998171] . ( 37 sec) [ -7988.1635] [ 1628] [depth= 1] . ( 37 sec) [ -7987.6224] [ 1628] [depth= 1] . ( 37 sec) [ -7987.3773] [ 1628] [depth= 1] . ( 37 sec) [ -7984.4829] [ 1628] [depth= 1] . ( 37 sec) [ -7984.0566] [ 1630] [depth= 1] . ( 38 sec) [ -7982.7212] [ 1630] [depth= 1] . ( 38 sec) [ -7981.1481] [ 1628] [depth= 1] . ( 38 sec) [ -7979.5774] [ 1632] [depth= 1] . ( 38 sec) [ -7976.7897] [ 1633] [depth= 1] . ( 38 sec) [ -7968.0716] [ 1638] [depth= 1] . ( 38 sec) [ -7966.7634] [ 1640] [depth= 1] . ( 38 sec) [ -7966.1916] [ 1638] [depth= 1] . ( 38 sec) [ -7964.7461] [ 1640] [depth= 1] . ( 38 sec) [ -7963.2952] [ 1641] [depth= 1] . ( 38 sec) [ -7963.1830] [ 1642] [depth= 1] . ( 38 sec) [ -7962.0833] [ 1639] [depth= 1] . ( 39 sec) [ -7961.4020] [ 1643] [depth= 1] . ( 40 sec) [ -7961.3089] [ 1645] [depth= 1] . ( 40 sec) [ -7961.2720] [ 1641] [depth= 1] . ( 40 sec) [ -7959.8943] [ 1641] [depth= 1] . ( 40 sec) [ -7939.1251] [Branch lengths ] . ( 41 sec) [ -7939.0429] [GTR parameters ] . ( 41 sec) [ -7939.0243] [Alpha ][ 1.014460] . ( 41 sec) [ -7939.0007] [ 1641] [depth= 1] . ( 41 sec) [ -7938.2809] [ 1639] [depth= 1] . ( 42 sec) [ -7937.1521] [ 1635] [depth= 1] . ( 44 sec) [ -7935.7476] [Branch lengths ] . ( 44 sec) [ -7935.7387] [GTR parameters ] . ( 44 sec) [ -7935.7299] [Alpha ][ 1.025762] . ( 48 sec) [ -7935.6495] [Branch lengths ] . ( 53 sec) [ -7935.5950] [ 1636] [depth= 1] . ( 66 sec) [ -7935.5171] [Branch lengths ] . ( 67 sec) [ -7935.5169] [GTR parameters ] . ( 67 sec) [ -7935.5167] [Alpha ][ 1.026997] . ( 67 sec) [ -7935.5167] [Topology ] . ( 67 sec) [ -7935.5149] [Topology ] . ( 68 sec) [ -7935.5144] [Topology ] . ( 68 sec) [ -7935.5144] [GTR parameters ] . ( 68 sec) [ -7935.5144] [Alpha ][ 1.026997] . ( 68 sec) [ -7935.5144] [Topology ] . ( 69 sec) [ -7935.5141] [Topology ] . ( 69 sec) [ -7935.5141] [GTR parameters ] . ( 69 sec) [ -7935.5141] [Alpha ][ 1.026997] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7935.333689 . Log likelihood obtained after SPR moves : -7935.514145 . Log likelihood of the current tree: -7935.333689. . Printing the most likely tree in file 'data79.phy_phyml_tree.txt'... . Best log likelihood : -7935.333689 . Time used 0h1m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo