.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data31.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... . 380 patterns found. (out of a total of 500 sites) . 109 sites without polymorphism (21.80%). . [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) [ -16329.2976] [GTR parameters ] . ( 1 sec) [ -16004.5238] [Alpha ][ 0.500960] . ( 1 sec) [ -15930.5726] [ 3245] [depth= 8] . ( 1 sec) [ -15609.3766] [ 3187] [depth= 7] . ( 1 sec) [ -15095.2813] [ 3173] [depth= 4] . ( 1 sec) [ -14875.8274] [ 3164] [depth= 7] . ( 1 sec) [ -14858.4823] [ 3078] [depth= 5] . ( 1 sec) [ -14829.3061] [ 3082] [depth= 8] . ( 1 sec) [ -14583.5860] [ 3063] [depth= 3] . ( 1 sec) [ -14376.6012] [ 3066] [depth= 9] . ( 1 sec) [ -14093.7722] [ 2954] [depth= 15] . ( 1 sec) [ -13617.3235] [ 2866] [depth= 9] . ( 1 sec) [ -13556.0360] [ 2863] [depth= 2] . ( 1 sec) [ -13401.5875] [ 2797] [depth= 6] . ( 1 sec) [ -13151.0491] [ 2744] [depth= 1] . ( 1 sec) [ -12745.0103] [ 2642] [depth= 10] . ( 1 sec) [ -12678.4451] [ 2640] [depth= 3] . ( 1 sec) [ -12413.5822] [ 2636] [depth= 2] . ( 1 sec) [ -12222.8556] [ 2537] [depth= 4] . ( 1 sec) [ -12217.3289] [ 2537] [depth= 1] . ( 1 sec) [ -12129.5953] [ 2521] [depth= 3] . ( 1 sec) [ -12087.5516] [ 2524] [depth= 4] . ( 2 sec) [ -12001.4227] [ 2482] [depth= 6] . ( 2 sec) [ -11814.8356] [ 2416] [depth= 5] . ( 2 sec) [ -11757.1498] [ 2384] [depth= 1] . ( 2 sec) [ -11537.4340] [ 2318] [depth= 10] . ( 2 sec) [ -11401.9363] [ 2286] [depth= 4] . ( 2 sec) [ -11049.5785] [ 2203] [depth= 10] . ( 2 sec) [ -10968.9245] [ 2196] [depth= 13] . ( 2 sec) [ -10918.2795] [ 2176] [depth= 4] . ( 2 sec) [ -10895.3992] [ 2173] [depth= 1] . ( 2 sec) [ -10804.3510] [ 2170] [depth= 2] . ( 2 sec) [ -10712.3597] [ 2165] [depth= 6] . ( 2 sec) [ -10599.4190] [ 2163] [depth= 4] . ( 2 sec) [ -10515.2386] [ 2151] [depth= 5] . ( 2 sec) [ -10358.6680] [ 2122] [depth= 5] . ( 2 sec) [ -10240.4689] [ 2062] [depth= 10] . ( 2 sec) [ -10230.1439] [ 2063] [depth= 2] . ( 2 sec) [ -10179.0815] [ 2051] [depth= 1] . ( 2 sec) [ -9573.7441] [ 1938] [depth= 10] . ( 2 sec) [ -9248.6249] [ 1838] [depth= 5] . ( 2 sec) [ -9233.0951] [ 1834] [depth= 1] . ( 2 sec) [ -9152.2657] [ 1828] [depth= 1] . ( 2 sec) [ -9112.1780] [ 1812] [depth= 1] . ( 3 sec) [ -9010.9988] [ 1786] [depth= 1] . ( 3 sec) [ -8967.1970] [ 1759] [depth= 4] . ( 3 sec) [ -8918.8964] [ 1760] [depth= 4] . ( 3 sec) [ -8643.6326] [ 1753] [depth= 8] . ( 3 sec) [ -8631.5050] [ 1754] [depth= 1] . ( 3 sec) [ -8623.9266] [ 1753] [depth= 2] . ( 3 sec) [ -8623.8831] [ 1756] [depth= 2] . ( 3 sec) [ -8597.5527] [ 1752] [depth= 3] . ( 3 sec) [ -8587.0216] [ 1746] [depth= 1] . ( 3 sec) [ -8552.6448] [ 1744] [depth= 1] . ( 3 sec) [ -8465.4668] [ 1715] [depth= 1] . ( 3 sec) [ -8421.2127] [ 1702] [depth= 4] . ( 3 sec) [ -8273.9259] [ 1612] [depth= 3] . ( 3 sec) [ -8225.1464] [ 1610] [depth= 4] . ( 3 sec) [ -8129.4792] [ 1610] [depth= 2] . ( 3 sec) [ -8119.5415] [ 1609] [depth= 1] . ( 3 sec) [ -8107.7691] [ 1608] [depth= 1] . ( 3 sec) [ -8107.3459] [ 1609] [depth= 1] . ( 4 sec) [ -8102.5441] [ 1605] [depth= 1] . ( 4 sec) [ -7964.5948] [ 1593] [depth= 7] . ( 4 sec) [ -7961.0830] [ 1593] [depth= 2] . ( 4 sec) [ -7951.5219] [ 1592] [depth= 6] . ( 4 sec) [ -7950.7364] [ 1594] [depth= 1] . ( 4 sec) [ -7754.0475] [ 1585] [depth= 4] . ( 4 sec) [ -7744.8381] [ 1579] [depth= 3] . ( 4 sec) [ -7681.6364] [ 1576] [depth= 3] . ( 4 sec) [ -7676.2822] [ 1569] [depth= 1] . ( 4 sec) [ -7667.5167] [ 1565] [depth= 1] . ( 4 sec) [ -7586.0075] [ 1546] [depth= 1] . ( 4 sec) [ -7585.9717] [ 1546] [depth= 1] . ( 4 sec) [ -7585.8085] [ 1547] [depth= 1] . ( 4 sec) [ -7581.8418] [ 1547] [depth= 2] . ( 4 sec) [ -7545.7542] [ 1549] [depth= 2] . ( 4 sec) [ -7531.9693] [ 1546] [depth= 1] . ( 5 sec) [ -7526.1548] [ 1547] [depth= 1] . ( 5 sec) [ -7507.1453] [ 1542] [depth= 2] . ( 5 sec) [ -7383.3080] [Branch lengths ] . ( 5 sec) [ -7381.9711] [GTR parameters ] . ( 5 sec) [ -7361.8854] [Alpha ][ 0.827550] . ( 5 sec) [ -7337.9700] [ 1500] [depth= 4] . ( 5 sec) [ -7337.1701] [ 1500] [depth= 1] . ( 6 sec) [ -7325.6106] [ 1496] [depth= 1] . ( 6 sec) [ -7325.0368] [ 1498] [depth= 3] . ( 6 sec) [ -7324.6837] [ 1498] [depth= 1] . ( 6 sec) [ -7304.8181] [ 1489] [depth= 1] . ( 6 sec) [ -7299.3007] [ 1490] [depth= 4] . ( 6 sec) [ -7278.6309] [ 1477] [depth= 1] . ( 6 sec) [ -7277.0928] [ 1476] [depth= 2] . ( 6 sec) [ -7273.8645] [ 1475] [depth= 2] . ( 6 sec) [ -7273.8105] [ 1475] [depth= 2] . ( 6 sec) [ -7268.5949] [ 1471] [depth= 2] . ( 6 sec) [ -7268.5010] [ 1470] [depth= 1] . ( 6 sec) [ -7268.2696] [ 1468] [depth= 1] . ( 7 sec) [ -7267.0569] [ 1464] [depth= 3] . ( 7 sec) [ -7265.2229] [ 1465] [depth= 1] . ( 7 sec) [ -7263.6562] [ 1469] [depth= 1] . ( 7 sec) [ -7263.6276] [ 1471] [depth= 1] . ( 7 sec) [ -7246.1483] [ 1466] [depth= 1] . ( 7 sec) [ -7244.7508] [ 1466] [depth= 1] . ( 7 sec) [ -7244.7009] [ 1467] [depth= 1] . ( 8 sec) [ -7244.1590] [ 1466] [depth= 1] . ( 8 sec) [ -7230.2780] [ 1457] [depth= 2] . ( 8 sec) [ -7223.6272] [ 1458] [depth= 4] . ( 8 sec) [ -7223.2718] [ 1458] [depth= 2] . ( 8 sec) [ -7223.2209] [ 1457] [depth= 1] . ( 8 sec) [ -7208.6904] [ 1446] [depth= 5] . ( 8 sec) [ -7197.3581] [ 1448] [depth= 1] . ( 8 sec) [ -7197.3178] [ 1448] [depth= 1] . ( 8 sec) [ -7195.0412] [ 1447] [depth= 1] . ( 8 sec) [ -7194.5275] [ 1450] [depth= 1] . ( 8 sec) [ -7192.8310] [ 1450] [depth= 2] . ( 8 sec) [ -7190.9808] [ 1448] [depth= 1] . ( 8 sec) [ -7189.5330] [ 1445] [depth= 1] . ( 9 sec) [ -7188.8790] [ 1443] [depth= 1] . ( 9 sec) [ -7181.5111] [Branch lengths ] . ( 10 sec) [ -7181.3891] [GTR parameters ] . ( 10 sec) [ -7180.4583] [Alpha ][ 0.927975] . ( 14 sec) [ -7179.8834] [Branch lengths ] . ( 27 sec) [ -7179.8657] [ 1443] [depth= 4] . ( 35 sec) [ -7179.6575] [Branch lengths ] . ( 36 sec) [ -7179.5986] [GTR parameters ] . ( 36 sec) [ -7179.5912] [Alpha ][ 0.937693] . ( 36 sec) [ -7179.5912] [Topology ] . ( 37 sec) [ -7179.5756] [Topology ] . ( 37 sec) [ -7179.5709] [Topology ] . ( 38 sec) [ -7179.5689] [Topology ] . ( 39 sec) [ -7179.5680] [Topology ] . ( 39 sec) [ -7179.5680] [GTR parameters ] . ( 39 sec) [ -7179.5677] [Alpha ][ 0.939386] . ( 39 sec) [ -7179.5677] [Topology ] . ( 40 sec) [ -7179.5672] [Topology ] . ( 40 sec) [ -7179.5672] [GTR parameters ] . ( 40 sec) [ -7179.5672] [Alpha ][ 0.939386] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.567243. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16725.1704] [GTR parameters ] . ( 0 sec) [ -16376.5548] [Alpha ][ 0.500960] . ( 0 sec) [ -16281.8676] [ 3345] [depth= 9] . ( 0 sec) [ -16003.0949] [ 3275] [depth= 11] . ( 0 sec) [ -15820.1230] [ 3241] [depth= 2] . ( 0 sec) [ -15748.2899] [ 3230] [depth= 2] . ( 0 sec) [ -15548.1261] [ 3156] [depth= 1] . ( 0 sec) [ -15463.0975] [ 3140] [depth= 3] . ( 1 sec) [ -15366.2400] [ 3137] [depth= 2] . ( 1 sec) [ -15344.8598] [ 3116] [depth= 1] . ( 1 sec) [ -15193.8616] [ 3109] [depth= 2] . ( 1 sec) [ -14944.9460] [ 3025] [depth= 6] . ( 1 sec) [ -14862.1455] [ 3022] [depth= 2] . ( 1 sec) [ -14853.5118] [ 3021] [depth= 1] . ( 1 sec) [ -14847.8791] [ 3020] [depth= 2] . ( 1 sec) [ -14400.4281] [ 2897] [depth= 14] . ( 1 sec) [ -13988.7485] [ 2864] [depth= 13] . ( 1 sec) [ -13806.1545] [ 2820] [depth= 3] . ( 1 sec) [ -13439.6025] [ 2708] [depth= 11] . ( 1 sec) [ -13298.8998] [ 2705] [depth= 17] . ( 1 sec) [ -12592.8537] [ 2559] [depth= 19] . ( 1 sec) [ -12485.3028] [ 2562] [depth= 4] . ( 1 sec) [ -11939.2321] [ 2500] [depth= 13] . ( 1 sec) [ -11626.9419] [ 2496] [depth= 2] . ( 1 sec) [ -11417.1916] [ 2496] [depth= 2] . ( 1 sec) [ -11410.6977] [ 2500] [depth= 7] . ( 1 sec) [ -11362.9219] [ 2408] [depth= 3] . ( 1 sec) [ -11097.3880] [ 2351] [depth= 11] . ( 1 sec) [ -11082.7290] [ 2353] [depth= 7] . ( 1 sec) [ -10664.6957] [ 2260] [depth= 6] . ( 1 sec) [ -10624.4764] [ 2257] [depth= 5] . ( 1 sec) [ -10018.0762] [ 2133] [depth= 8] . ( 2 sec) [ -10002.0946] [ 2134] [depth= 3] . ( 2 sec) [ -9959.6993] [ 2120] [depth= 5] . ( 2 sec) [ -9880.0560] [ 2126] [depth= 2] . ( 2 sec) [ -9622.6939] [ 2051] [depth= 3] . ( 2 sec) [ -9608.6738] [ 2032] [depth= 1] . ( 2 sec) [ -9608.6406] [ 2034] [depth= 1] . ( 2 sec) [ -9577.2255] [ 2037] [depth= 1] . ( 2 sec) [ -9501.8520] [ 2011] [depth= 7] . ( 2 sec) [ -9421.0423] [ 2004] [depth= 7] . ( 2 sec) [ -9387.9229] [ 1997] [depth= 1] . ( 2 sec) [ -9186.5548] [ 1889] [depth= 7] . ( 2 sec) [ -9091.4620] [ 1869] [depth= 1] . ( 2 sec) [ -8933.5130] [ 1793] [depth= 2] . ( 2 sec) [ -8863.9551] [ 1793] [depth= 1] . ( 2 sec) [ -8816.5519] [ 1807] [depth= 6] . ( 2 sec) [ -8739.0431] [ 1794] [depth= 2] . ( 2 sec) [ -8738.2292] [ 1791] [depth= 1] . ( 2 sec) [ -8573.4559] [ 1795] [depth= 2] . ( 2 sec) [ -8564.6404] [ 1798] [depth= 1] . ( 2 sec) [ -8556.6629] [ 1785] [depth= 2] . ( 2 sec) [ -8549.1608] [ 1785] [depth= 1] . ( 3 sec) [ -8495.9326] [ 1763] [depth= 9] . ( 3 sec) [ -8494.9290] [ 1767] [depth= 1] . ( 3 sec) [ -8477.2966] [ 1769] [depth= 1] . ( 3 sec) [ -8310.8029] [ 1767] [depth= 3] . ( 3 sec) [ -8310.5430] [ 1769] [depth= 1] . ( 3 sec) [ -8290.1415] [ 1767] [depth= 1] . ( 3 sec) [ -8288.0029] [ 1766] [depth= 1] . ( 3 sec) [ -8208.4417] [ 1745] [depth= 8] . ( 3 sec) [ -8207.3733] [ 1745] [depth= 1] . ( 3 sec) [ -8207.1195] [ 1747] [depth= 1] . ( 3 sec) [ -8167.5143] [ 1745] [depth= 3] . ( 3 sec) [ -8164.0305] [ 1745] [depth= 1] . ( 3 sec) [ -8162.5397] [ 1741] [depth= 3] . ( 3 sec) [ -8119.1639] [ 1737] [depth= 1] . ( 3 sec) [ -8110.7606] [ 1738] [depth= 1] . ( 3 sec) [ -8110.3323] [ 1740] [depth= 1] . ( 3 sec) [ -8107.4054] [ 1740] [depth= 1] . ( 3 sec) [ -8035.0313] [ 1664] [depth= 4] . ( 3 sec) [ -7864.3817] [ 1686] [depth= 1] . ( 3 sec) [ -7736.5861] [ 1632] [depth= 8] . ( 4 sec) [ -7721.4270] [ 1630] [depth= 1] . ( 4 sec) [ -7718.8753] [ 1628] [depth= 2] . ( 4 sec) [ -7468.8034] [ 1523] [depth= 4] . ( 4 sec) [ -7467.2330] [ 1523] [depth= 2] . ( 4 sec) [ -7467.1528] [ 1522] [depth= 1] . ( 4 sec) [ -7427.2535] [ 1507] [depth= 6] . ( 4 sec) [ -7426.9063] [ 1505] [depth= 2] . ( 4 sec) [ -7425.8733] [ 1505] [depth= 1] . ( 4 sec) [ -7315.3725] [Branch lengths ] . ( 5 sec) [ -7313.8482] [GTR parameters ] . ( 5 sec) [ -7291.9655] [Alpha ][ 0.844759] . ( 5 sec) [ -7265.5187] [ 1469] [depth= 2] . ( 5 sec) [ -7265.4774] [ 1469] [depth= 1] . ( 5 sec) [ -7258.4007] [ 1468] [depth= 3] . ( 5 sec) [ -7257.4403] [ 1465] [depth= 1] . ( 5 sec) [ -7256.9437] [ 1463] [depth= 1] . ( 5 sec) [ -7223.8060] [ 1456] [depth= 1] . ( 5 sec) [ -7221.2739] [ 1453] [depth= 1] . ( 6 sec) [ -7219.8111] [ 1452] [depth= 1] . ( 6 sec) [ -7205.9522] [ 1447] [depth= 1] . ( 6 sec) [ -7205.7910] [ 1446] [depth= 1] . ( 6 sec) [ -7205.7184] [ 1449] [depth= 1] . ( 6 sec) [ -7204.6922] [ 1447] [depth= 1] . ( 6 sec) [ -7204.3693] [ 1445] [depth= 1] . ( 7 sec) [ -7203.5052] [ 1446] [depth= 1] . ( 7 sec) [ -7201.2836] [ 1445] [depth= 3] . ( 7 sec) [ -7199.4748] [ 1449] [depth= 3] . ( 7 sec) [ -7198.7699] [ 1449] [depth= 1] . ( 8 sec) [ -7198.5438] [ 1451] [depth= 1] . ( 8 sec) [ -7198.1404] [ 1449] [depth= 1] . ( 9 sec) [ -7185.8265] [Branch lengths ] . ( 10 sec) [ -7185.6553] [GTR parameters ] . ( 10 sec) [ -7185.0858] [Alpha ][ 0.922949] . ( 10 sec) [ -7183.3454] [ 1449] [depth= 1] . ( 11 sec) [ -7183.1594] [ 1446] [depth= 1] . ( 12 sec) [ -7182.8892] [ 1446] [depth= 1] . ( 12 sec) [ -7181.8167] [ 1448] [depth= 2] . ( 13 sec) [ -7181.7073] [ 1449] [depth= 1] . ( 13 sec) [ -7181.3265] [ 1447] [depth= 1] . ( 15 sec) [ -7179.7970] [Branch lengths ] . ( 15 sec) [ -7179.7873] [GTR parameters ] . ( 15 sec) [ -7179.7661] [Alpha ][ 0.939422] . ( 21 sec) [ -7179.7180] [Branch lengths ] . ( 43 sec) [ -7179.7169] [Branch lengths ] . ( 43 sec) [ -7179.7169] [Topology ] . ( 44 sec) [ -7179.5777] [Topology ] . ( 44 sec) [ -7179.5686] [Topology ] . ( 45 sec) [ -7179.5675] [Topology ] . ( 46 sec) [ -7179.5673] [Topology ] . ( 46 sec) [ -7179.5669] [GTR parameters ] . ( 46 sec) [ -7179.5669] [Alpha ][ 0.940362] . ( 46 sec) [ -7179.5669] [Topology ] . ( 47 sec) [ -7179.5668] [Topology ] . ( 47 sec) [ -7179.5668] [GTR parameters ] . ( 47 sec) [ -7179.5668] [Alpha ][ 0.940362] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.566810. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16698.5263] [GTR parameters ] . ( 1 sec) [ -16372.4744] [Alpha ][ 0.500960] . ( 1 sec) [ -16143.9910] [ 3303] [depth= 8] . ( 1 sec) [ -15902.1975] [ 3249] [depth= 13] . ( 1 sec) [ -15802.5337] [ 3243] [depth= 4] . ( 1 sec) [ -15749.5324] [ 3241] [depth= 1] . ( 1 sec) [ -15576.8068] [ 3177] [depth= 2] . ( 1 sec) [ -15492.0376] [ 3170] [depth= 3] . ( 1 sec) [ -15446.0401] [ 3190] [depth= 8] . ( 1 sec) [ -15078.7274] [ 3129] [depth= 2] . ( 1 sec) [ -14910.1631] [ 3081] [depth= 1] . ( 1 sec) [ -14814.3486] [ 3080] [depth= 12] . ( 1 sec) [ -14632.7233] [ 3026] [depth= 9] . ( 1 sec) [ -14565.9832] [ 3022] [depth= 3] . ( 1 sec) [ -14313.2258] [ 3009] [depth= 6] . ( 1 sec) [ -14189.3486] [ 2993] [depth= 1] . ( 2 sec) [ -13912.8665] [ 2990] [depth= 9] . ( 2 sec) [ -13703.1379] [ 2902] [depth= 2] . ( 2 sec) [ -13436.2950] [ 2886] [depth= 3] . ( 2 sec) [ -13119.1790] [ 2786] [depth= 7] . ( 2 sec) [ -13017.1205] [ 2787] [depth= 1] . ( 2 sec) [ -12776.6826] [ 2783] [depth= 1] . ( 2 sec) [ -12748.9768] [ 2776] [depth= 2] . ( 2 sec) [ -12682.0168] [ 2753] [depth= 9] . ( 2 sec) [ -12647.3146] [ 2744] [depth= 6] . ( 2 sec) [ -12394.6175] [ 2714] [depth= 5] . ( 2 sec) [ -12103.5368] [ 2661] [depth= 6] . ( 2 sec) [ -11730.9424] [ 2623] [depth= 7] . ( 2 sec) [ -11462.6720] [ 2503] [depth= 8] . ( 2 sec) [ -11371.3199] [ 2486] [depth= 1] . ( 2 sec) [ -11355.9371] [ 2486] [depth= 7] . ( 2 sec) [ -11348.7399] [ 2488] [depth= 1] . ( 2 sec) [ -11228.0014] [ 2471] [depth= 7] . ( 2 sec) [ -11167.5366] [ 2472] [depth= 4] . ( 2 sec) [ -11153.5573] [ 2472] [depth= 1] . ( 2 sec) [ -11148.3838] [ 2468] [depth= 1] . ( 2 sec) [ -11114.6141] [ 2468] [depth= 1] . ( 2 sec) [ -11035.2356] [ 2451] [depth= 3] . ( 2 sec) [ -10897.3377] [ 2438] [depth= 4] . ( 2 sec) [ -10870.9829] [ 2437] [depth= 1] . ( 3 sec) [ -10757.2025] [ 2410] [depth= 6] . ( 3 sec) [ -10626.5740] [ 2381] [depth= 1] . ( 3 sec) [ -10581.3063] [ 2378] [depth= 10] . ( 3 sec) [ -10456.0796] [ 2348] [depth= 7] . ( 3 sec) [ -10350.9531] [ 2344] [depth= 1] . ( 3 sec) [ -10348.1763] [ 2341] [depth= 3] . ( 3 sec) [ -10296.6989] [ 2292] [depth= 2] . ( 3 sec) [ -10288.1279] [ 2286] [depth= 2] . ( 3 sec) [ -10253.2651] [ 2286] [depth= 1] . ( 3 sec) [ -10251.0252] [ 2283] [depth= 1] . ( 3 sec) [ -10235.7053] [ 2283] [depth= 1] . ( 3 sec) [ -10231.7706] [ 2283] [depth= 1] . ( 3 sec) [ -9889.8036] [ 2233] [depth= 2] . ( 3 sec) [ -9615.4960] [ 2161] [depth= 3] . ( 3 sec) [ -9584.6903] [ 2146] [depth= 1] . ( 3 sec) [ -9448.0913] [ 2105] [depth= 5] . ( 3 sec) [ -9232.8149] [ 1989] [depth= 6] . ( 3 sec) [ -9212.3217] [ 1985] [depth= 1] . ( 3 sec) [ -9199.7354] [ 1987] [depth= 1] . ( 3 sec) [ -8878.0241] [ 1956] [depth= 4] . ( 3 sec) [ -8874.2296] [ 1952] [depth= 1] . ( 4 sec) [ -8845.4687] [ 1924] [depth= 1] . ( 4 sec) [ -8835.2872] [ 1924] [depth= 1] . ( 4 sec) [ -8350.4687] [ 1877] [depth= 4] . ( 4 sec) [ -8222.9375] [ 1799] [depth= 3] . ( 4 sec) [ -8209.2168] [ 1797] [depth= 3] . ( 4 sec) [ -8039.4426] [ 1769] [depth= 5] . ( 4 sec) [ -7921.5510] [ 1705] [depth= 8] . ( 4 sec) [ -7866.3616] [ 1684] [depth= 3] . ( 4 sec) [ -7861.8807] [ 1684] [depth= 2] . ( 4 sec) [ -7855.4683] [ 1685] [depth= 1] . ( 4 sec) [ -7849.7074] [ 1684] [depth= 1] . ( 4 sec) [ -7838.5001] [ 1679] [depth= 2] . ( 4 sec) [ -7837.8208] [ 1678] [depth= 2] . ( 4 sec) [ -7831.3094] [ 1679] [depth= 2] . ( 4 sec) [ -7815.7702] [ 1682] [depth= 2] . ( 4 sec) [ -7809.8095] [ 1679] [depth= 1] . ( 4 sec) [ -7805.1757] [ 1681] [depth= 1] . ( 4 sec) [ -7801.9489] [ 1681] [depth= 2] . ( 4 sec) [ -7801.7838] [ 1681] [depth= 1] . ( 4 sec) [ -7712.6421] [ 1597] [depth= 4] . ( 4 sec) [ -7712.3622] [ 1597] [depth= 2] . ( 5 sec) [ -7614.1117] [Branch lengths ] . ( 5 sec) [ -7613.5332] [GTR parameters ] . ( 5 sec) [ -7594.9210] [Alpha ][ 0.805786] . ( 5 sec) [ -7559.5116] [ 1572] [depth= 3] . ( 5 sec) [ -7554.9589] [ 1571] [depth= 1] . ( 5 sec) [ -7526.5582] [ 1559] [depth= 3] . ( 5 sec) [ -7526.0579] [ 1561] [depth= 1] . ( 6 sec) [ -7388.2962] [ 1515] [depth= 1] . ( 6 sec) [ -7387.3128] [ 1510] [depth= 1] . ( 6 sec) [ -7386.6670] [ 1506] [depth= 1] . ( 6 sec) [ -7376.5561] [ 1502] [depth= 1] . ( 6 sec) [ -7375.5351] [ 1509] [depth= 1] . ( 6 sec) [ -7327.6964] [ 1474] [depth= 1] . ( 6 sec) [ -7327.3956] [ 1475] [depth= 1] . ( 6 sec) [ -7324.0473] [ 1478] [depth= 1] . ( 6 sec) [ -7321.0785] [ 1456] [depth= 1] . ( 6 sec) [ -7318.6862] [ 1455] [depth= 1] . ( 6 sec) [ -7315.3059] [ 1455] [depth= 1] . ( 6 sec) [ -7274.3831] [ 1454] [depth= 1] . ( 6 sec) [ -7273.8107] [ 1454] [depth= 1] . ( 6 sec) [ -7273.7511] [ 1454] [depth= 2] . ( 7 sec) [ -7265.6570] [ 1451] [depth= 1] . ( 7 sec) [ -7249.6773] [ 1454] [depth= 1] . ( 7 sec) [ -7246.0800] [ 1453] [depth= 2] . ( 7 sec) [ -7210.3861] [ 1444] [depth= 3] . ( 7 sec) [ -7209.9757] [ 1445] [depth= 1] . ( 7 sec) [ -7209.5312] [ 1446] [depth= 1] . ( 7 sec) [ -7209.3307] [ 1444] [depth= 1] . ( 7 sec) [ -7209.0784] [ 1445] [depth= 1] . ( 7 sec) [ -7208.5599] [ 1444] [depth= 1] . ( 8 sec) [ -7204.9207] [ 1444] [depth= 1] . ( 8 sec) [ -7204.8026] [ 1444] [depth= 1] . ( 9 sec) [ -7202.9645] [ 1443] [depth= 1] . ( 9 sec) [ -7202.9509] [ 1443] [depth= 1] . ( 9 sec) [ -7202.8753] [ 1443] [depth= 1] . ( 9 sec) [ -7202.8559] [ 1443] [depth= 1] . ( 9 sec) [ -7195.5849] [Branch lengths ] . ( 10 sec) [ -7195.2784] [GTR parameters ] . ( 10 sec) [ -7194.2346] [Alpha ][ 0.908774] . ( 10 sec) [ -7193.9376] [ 1445] [depth= 1] . ( 10 sec) [ -7188.7302] [ 1447] [depth= 4] . ( 10 sec) [ -7187.2118] [ 1449] [depth= 1] . ( 10 sec) [ -7187.1888] [ 1450] [depth= 1] . ( 10 sec) [ -7184.5843] [ 1449] [depth= 1] . ( 11 sec) [ -7184.3469] [ 1448] [depth= 1] . ( 11 sec) [ -7184.2430] [ 1447] [depth= 1] . ( 11 sec) [ -7183.8283] [ 1448] [depth= 1] . ( 12 sec) [ -7183.7980] [ 1447] [depth= 1] . ( 12 sec) [ -7183.7372] [ 1446] [depth= 1] . ( 12 sec) [ -7183.1132] [ 1448] [depth= 1] . ( 12 sec) [ -7181.9199] [ 1447] [depth= 1] . ( 14 sec) [ -7179.9756] [Branch lengths ] . ( 15 sec) [ -7179.9475] [GTR parameters ] . ( 15 sec) [ -7179.8882] [Alpha ][ 0.935279] . ( 20 sec) [ -7179.7393] [Branch lengths ] . ( 42 sec) [ -7179.7210] [Branch lengths ] . ( 42 sec) [ -7179.7210] [Topology ] . ( 43 sec) [ -7179.5789] [Topology ] . ( 43 sec) [ -7179.5700] [Topology ] . ( 44 sec) [ -7179.5689] [Topology ] . ( 45 sec) [ -7179.5687] [Topology ] . ( 45 sec) [ -7179.5685] [GTR parameters ] . ( 45 sec) [ -7179.5669] [Alpha ][ 0.939790] . ( 45 sec) [ -7179.5669] [Topology ] . ( 46 sec) [ -7179.5668] [Topology ] . ( 46 sec) [ -7179.5668] [GTR parameters ] . ( 46 sec) [ -7179.5668] [Alpha ][ 0.939790] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.566814. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16314.9895] [GTR parameters ] . ( 1 sec) [ -15991.9711] [Alpha ][ 0.500960] . ( 1 sec) [ -15983.3247] [ 3196] [depth= 8] . ( 1 sec) [ -15636.5434] [ 3122] [depth= 8] . ( 1 sec) [ -15431.2513] [ 3036] [depth= 8] . ( 1 sec) [ -15222.9350] [ 3024] [depth= 4] . ( 1 sec) [ -15205.6064] [ 3025] [depth= 1] . ( 1 sec) [ -14945.4496] [ 3005] [depth= 2] . ( 1 sec) [ -14747.9324] [ 3003] [depth= 3] . ( 1 sec) [ -14693.6944] [ 2973] [depth= 1] . ( 1 sec) [ -14669.7711] [ 2965] [depth= 1] . ( 1 sec) [ -14505.3319] [ 2903] [depth= 3] . ( 1 sec) [ -14255.6308] [ 2901] [depth= 4] . ( 1 sec) [ -13912.0114] [ 2864] [depth= 10] . ( 1 sec) [ -13894.5346] [ 2827] [depth= 3] . ( 1 sec) [ -13888.6184] [ 2826] [depth= 3] . ( 1 sec) [ -13415.3905] [ 2707] [depth= 9] . ( 2 sec) [ -13175.5480] [ 2697] [depth= 2] . ( 2 sec) [ -13050.3378] [ 2721] [depth= 1] . ( 2 sec) [ -12650.9192] [ 2621] [depth= 2] . ( 2 sec) [ -12383.6649] [ 2513] [depth= 10] . ( 2 sec) [ -12113.0984] [ 2436] [depth= 15] . ( 2 sec) [ -11727.4656] [ 2384] [depth= 13] . ( 2 sec) [ -11555.8932] [ 2355] [depth= 13] . ( 2 sec) [ -11313.9900] [ 2326] [depth= 7] . ( 2 sec) [ -11133.5434] [ 2312] [depth= 4] . ( 2 sec) [ -11129.0702] [ 2320] [depth= 1] . ( 2 sec) [ -11034.7921] [ 2331] [depth= 15] . ( 2 sec) [ -10932.2442] [ 2286] [depth= 8] . ( 2 sec) [ -10454.6554] [ 2162] [depth= 13] . ( 2 sec) [ -10427.9402] [ 2159] [depth= 3] . ( 2 sec) [ -10338.9385] [ 2159] [depth= 1] . ( 2 sec) [ -10214.5053] [ 2127] [depth= 5] . ( 2 sec) [ -10129.8114] [ 2112] [depth= 5] . ( 2 sec) [ -10125.4772] [ 2112] [depth= 1] . ( 2 sec) [ -10122.0525] [ 2114] [depth= 1] . ( 2 sec) [ -10121.2635] [ 2113] [depth= 2] . ( 2 sec) [ -10108.9126] [ 2112] [depth= 2] . ( 2 sec) [ -10071.9364] [ 2100] [depth= 5] . ( 2 sec) [ -10070.1378] [ 2099] [depth= 1] . ( 2 sec) [ -10049.9172] [ 2094] [depth= 2] . ( 2 sec) [ -9854.6590] [ 1984] [depth= 14] . ( 2 sec) [ -9419.4544] [ 1890] [depth= 5] . ( 3 sec) [ -9344.5395] [ 1890] [depth= 1] . ( 3 sec) [ -9328.0763] [ 1889] [depth= 2] . ( 3 sec) [ -9287.5374] [ 1882] [depth= 5] . ( 3 sec) [ -9229.9821] [ 1891] [depth= 1] . ( 3 sec) [ -9211.3776] [ 1887] [depth= 2] . ( 3 sec) [ -9210.0627] [ 1887] [depth= 1] . ( 3 sec) [ -9166.2574] [ 1857] [depth= 1] . ( 3 sec) [ -9154.7880] [ 1854] [depth= 1] . ( 3 sec) [ -9145.1952] [ 1853] [depth= 1] . ( 3 sec) [ -8916.2241] [ 1811] [depth= 3] . ( 3 sec) [ -8897.6734] [ 1800] [depth= 1] . ( 3 sec) [ -8895.0297] [ 1799] [depth= 3] . ( 3 sec) [ -8884.4876] [ 1793] [depth= 2] . ( 3 sec) [ -8449.6414] [ 1788] [depth= 2] . ( 3 sec) [ -8320.9655] [ 1778] [depth= 6] . ( 3 sec) [ -8236.5587] [ 1773] [depth= 4] . ( 3 sec) [ -8188.6581] [ 1774] [depth= 1] . ( 3 sec) [ -8179.3172] [ 1770] [depth= 2] . ( 3 sec) [ -8173.4254] [ 1770] [depth= 1] . ( 4 sec) [ -8103.0119] [ 1667] [depth= 1] . ( 4 sec) [ -7796.4045] [ 1632] [depth= 2] . ( 4 sec) [ -7795.8150] [ 1633] [depth= 1] . ( 4 sec) [ -7729.7876] [ 1604] [depth= 1] . ( 4 sec) [ -7678.0356] [ 1603] [depth= 1] . ( 4 sec) [ -7674.4757] [ 1601] [depth= 1] . ( 4 sec) [ -7674.4339] [ 1603] [depth= 1] . ( 4 sec) [ -7588.5134] [ 1572] [depth= 8] . ( 4 sec) [ -7586.7826] [ 1572] [depth= 1] . ( 4 sec) [ -7548.5505] [ 1562] [depth= 4] . ( 4 sec) [ -7458.4038] [ 1556] [depth= 2] . ( 4 sec) [ -7457.1139] [ 1554] [depth= 1] . ( 4 sec) [ -7439.6998] [ 1540] [depth= 1] . ( 4 sec) [ -7424.6010] [ 1533] [depth= 1] . ( 4 sec) [ -7424.4724] [ 1530] [depth= 3] . ( 4 sec) [ -7423.5755] [ 1527] [depth= 1] . ( 4 sec) [ -7421.6877] [ 1528] [depth= 2] . ( 5 sec) [ -7414.9122] [ 1523] [depth= 2] . ( 5 sec) [ -7343.2621] [ 1501] [depth= 1] . ( 5 sec) [ -7342.7248] [ 1503] [depth= 1] . ( 5 sec) [ -7342.1583] [ 1503] [depth= 1] . ( 5 sec) [ -7277.2039] [Branch lengths ] . ( 6 sec) [ -7276.4713] [GTR parameters ] . ( 6 sec) [ -7255.4075] [Alpha ][ 0.841980] . ( 6 sec) [ -7235.3556] [ 1459] [depth= 3] . ( 6 sec) [ -7233.4090] [ 1457] [depth= 1] . ( 6 sec) [ -7228.7257] [ 1455] [depth= 1] . ( 6 sec) [ -7228.6456] [ 1455] [depth= 1] . ( 6 sec) [ -7219.2019] [ 1453] [depth= 1] . ( 7 sec) [ -7219.1848] [ 1453] [depth= 1] . ( 7 sec) [ -7216.8789] [ 1454] [depth= 1] . ( 7 sec) [ -7215.1547] [ 1452] [depth= 2] . ( 7 sec) [ -7206.9475] [ 1445] [depth= 6] . ( 7 sec) [ -7204.6327] [ 1447] [depth= 1] . ( 7 sec) [ -7204.1446] [ 1450] [depth= 1] . ( 7 sec) [ -7203.9831] [ 1452] [depth= 1] . ( 7 sec) [ -7203.8034] [ 1452] [depth= 4] . ( 7 sec) [ -7203.4960] [ 1453] [depth= 1] . ( 8 sec) [ -7203.4803] [ 1453] [depth= 1] . ( 8 sec) [ -7202.5843] [ 1450] [depth= 1] . ( 8 sec) [ -7201.8355] [ 1454] [depth= 1] . ( 8 sec) [ -7195.7612] [ 1452] [depth= 1] . ( 8 sec) [ -7194.4907] [ 1447] [depth= 2] . ( 8 sec) [ -7194.1705] [ 1446] [depth= 1] . ( 8 sec) [ -7193.2786] [ 1446] [depth= 1] . ( 9 sec) [ -7190.6255] [ 1446] [depth= 2] . ( 9 sec) [ -7190.6143] [ 1444] [depth= 1] . ( 9 sec) [ -7190.2135] [ 1448] [depth= 1] . ( 9 sec) [ -7190.1712] [ 1448] [depth= 1] . ( 10 sec) [ -7186.1373] [Branch lengths ] . ( 10 sec) [ -7186.0346] [GTR parameters ] . ( 10 sec) [ -7185.3248] [Alpha ][ 0.930280] . ( 12 sec) [ -7185.2944] [ 1448] [depth= 2] . ( 13 sec) [ -7184.3977] [ 1450] [depth= 1] . ( 14 sec) [ -7183.9518] [ 1448] [depth= 1] . ( 15 sec) [ -7183.2100] [Branch lengths ] . ( 16 sec) [ -7183.1636] [GTR parameters ] . ( 16 sec) [ -7183.1608] [Alpha ][ 0.936228] . ( 21 sec) [ -7182.0015] [Branch lengths ] . ( 43 sec) [ -7179.8219] [Branch lengths ] . ( 43 sec) [ -7179.8219] [Topology ] . ( 44 sec) [ -7179.6008] [Topology ] . ( 44 sec) [ -7179.5787] [Topology ] . ( 45 sec) [ -7179.5740] [Topology ] . ( 46 sec) [ -7179.5727] [Topology ] . ( 47 sec) [ -7179.5723] [Topology ] . ( 47 sec) [ -7179.5681] [GTR parameters ] . ( 47 sec) [ -7179.5671] [Alpha ][ 0.939758] . ( 47 sec) [ -7179.5671] [Topology ] . ( 48 sec) [ -7179.5669] [Topology ] . ( 48 sec) [ -7179.5669] [GTR parameters ] . ( 48 sec) [ -7179.5669] [Alpha ][ 0.939758] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.566919. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16591.6979] [GTR parameters ] . ( 1 sec) [ -16269.8066] [Alpha ][ 0.500960] . ( 1 sec) [ -16183.5085] [ 3280] [depth= 5] . ( 1 sec) [ -16081.1173] [ 3248] [depth= 2] . ( 1 sec) [ -15948.6036] [ 3221] [depth= 3] . ( 1 sec) [ -15859.1154] [ 3214] [depth= 3] . ( 1 sec) [ -15749.7614] [ 3210] [depth= 4] . ( 1 sec) [ -15535.4043] [ 3117] [depth= 7] . ( 1 sec) [ -15516.0306] [ 3114] [depth= 3] . ( 1 sec) [ -15408.0249] [ 3099] [depth= 12] . ( 1 sec) [ -15148.0507] [ 3101] [depth= 1] . ( 1 sec) [ -14954.4544] [ 3008] [depth= 14] . ( 2 sec) [ -14757.2770] [ 2996] [depth= 4] . ( 2 sec) [ -14540.2663] [ 2979] [depth= 11] . ( 2 sec) [ -14247.7258] [ 2972] [depth= 6] . ( 2 sec) [ -13823.3715] [ 2869] [depth= 9] . ( 2 sec) [ -13679.4336] [ 2870] [depth= 1] . ( 2 sec) [ -13620.6115] [ 2865] [depth= 4] . ( 2 sec) [ -13495.4185] [ 2835] [depth= 2] . ( 2 sec) [ -13468.1070] [ 2834] [depth= 1] . ( 2 sec) [ -13324.3050] [ 2829] [depth= 4] . ( 2 sec) [ -13298.9146] [ 2829] [depth= 1] . ( 2 sec) [ -13242.5523] [ 2817] [depth= 3] . ( 2 sec) [ -12997.6066] [ 2754] [depth= 1] . ( 2 sec) [ -12926.0814] [ 2723] [depth= 1] . ( 2 sec) [ -12921.6783] [ 2727] [depth= 1] . ( 2 sec) [ -12784.6610] [ 2711] [depth= 5] . ( 2 sec) [ -12529.7517] [ 2682] [depth= 12] . ( 2 sec) [ -11793.6638] [ 2522] [depth= 12] . ( 2 sec) [ -11713.9568] [ 2500] [depth= 4] . ( 2 sec) [ -11255.6863] [ 2463] [depth= 11] . ( 2 sec) [ -11250.4623] [ 2462] [depth= 2] . ( 2 sec) [ -11187.3111] [ 2461] [depth= 11] . ( 2 sec) [ -11162.3484] [ 2461] [depth= 2] . ( 2 sec) [ -10765.9155] [ 2410] [depth= 13] . ( 2 sec) [ -10599.3316] [ 2290] [depth= 2] . ( 3 sec) [ -10594.7102] [ 2294] [depth= 10] . ( 3 sec) [ -10581.6817] [ 2281] [depth= 2] . ( 3 sec) [ -10461.1000] [ 2280] [depth= 7] . ( 3 sec) [ -10434.2540] [ 2271] [depth= 5] . ( 3 sec) [ -10390.8915] [ 2270] [depth= 3] . ( 3 sec) [ -10319.0539] [ 2224] [depth= 5] . ( 3 sec) [ -10314.3064] [ 2226] [depth= 1] . ( 3 sec) [ -10305.8894] [ 2220] [depth= 11] . ( 3 sec) [ -10268.9031] [ 2222] [depth= 6] . ( 3 sec) [ -10193.0538] [ 2191] [depth= 4] . ( 3 sec) [ -10140.2050] [ 2181] [depth= 2] . ( 3 sec) [ -9886.0025] [ 2063] [depth= 9] . ( 3 sec) [ -9884.9595] [ 2064] [depth= 2] . ( 3 sec) [ -9849.0302] [ 2046] [depth= 5] . ( 3 sec) [ -9795.2412] [ 2025] [depth= 3] . ( 3 sec) [ -9761.5120] [ 2024] [depth= 1] . ( 3 sec) [ -9760.8076] [ 2023] [depth= 2] . ( 3 sec) [ -9455.0723] [ 1994] [depth= 4] . ( 3 sec) [ -9367.7607] [ 1971] [depth= 4] . ( 3 sec) [ -9367.6276] [ 1971] [depth= 2] . ( 3 sec) [ -9367.2773] [ 1971] [depth= 1] . ( 3 sec) [ -9258.3572] [ 1951] [depth= 4] . ( 4 sec) [ -9217.1195] [ 1947] [depth= 6] . ( 4 sec) [ -9145.6827] [ 1952] [depth= 1] . ( 4 sec) [ -9140.7405] [ 1950] [depth= 2] . ( 4 sec) [ -9102.6752] [ 1943] [depth= 1] . ( 4 sec) [ -9069.4810] [ 1943] [depth= 9] . ( 4 sec) [ -9058.2792] [ 1947] [depth= 1] . ( 4 sec) [ -8835.5309] [ 1912] [depth= 5] . ( 4 sec) [ -8816.7000] [ 1851] [depth= 4] . ( 4 sec) [ -8784.1130] [ 1840] [depth= 2] . ( 4 sec) [ -8719.7936] [ 1840] [depth= 2] . ( 4 sec) [ -8707.0587] [ 1839] [depth= 2] . ( 4 sec) [ -8665.4566] [ 1830] [depth= 3] . ( 4 sec) [ -8357.4329] [ 1698] [depth= 6] . ( 4 sec) [ -8354.3831] [ 1697] [depth= 2] . ( 4 sec) [ -8341.8186] [ 1695] [depth= 1] . ( 4 sec) [ -8281.0260] [ 1686] [depth= 1] . ( 4 sec) [ -8000.5450] [ 1678] [depth= 3] . ( 4 sec) [ -7969.4337] [ 1665] [depth= 1] . ( 4 sec) [ -7969.0903] [ 1667] [depth= 1] . ( 4 sec) [ -7961.3032] [ 1678] [depth= 1] . ( 4 sec) [ -7900.2162] [ 1651] [depth= 3] . ( 5 sec) [ -7642.6357] [ 1538] [depth= 9] . ( 5 sec) [ -7630.3809] [ 1534] [depth= 1] . ( 5 sec) [ -7619.8804] [ 1529] [depth= 1] . ( 5 sec) [ -7607.3341] [ 1527] [depth= 1] . ( 5 sec) [ -7599.6897] [ 1527] [depth= 1] . ( 5 sec) [ -7597.7973] [ 1531] [depth= 1] . ( 5 sec) [ -7331.3586] [Branch lengths ] . ( 5 sec) [ -7329.5301] [GTR parameters ] . ( 5 sec) [ -7305.7714] [Alpha ][ 0.861069] . ( 6 sec) [ -7292.9952] [ 1493] [depth= 4] . ( 6 sec) [ -7272.7683] [ 1471] [depth= 6] . ( 6 sec) [ -7270.3214] [ 1469] [depth= 1] . ( 6 sec) [ -7257.5545] [ 1466] [depth= 1] . ( 6 sec) [ -7255.2411] [ 1465] [depth= 1] . ( 6 sec) [ -7239.9011] [ 1459] [depth= 2] . ( 6 sec) [ -7239.8679] [ 1459] [depth= 1] . ( 6 sec) [ -7236.7323] [ 1458] [depth= 1] . ( 6 sec) [ -7235.2086] [ 1458] [depth= 1] . ( 6 sec) [ -7224.2801] [ 1458] [depth= 1] . ( 7 sec) [ -7223.2549] [ 1462] [depth= 3] . ( 7 sec) [ -7200.8163] [ 1450] [depth= 1] . ( 7 sec) [ -7199.7756] [ 1449] [depth= 3] . ( 7 sec) [ -7199.1089] [ 1451] [depth= 1] . ( 8 sec) [ -7199.0537] [ 1449] [depth= 1] . ( 8 sec) [ -7198.8714] [ 1449] [depth= 1] . ( 8 sec) [ -7198.8327] [ 1449] [depth= 1] . ( 8 sec) [ -7194.3547] [ 1451] [depth= 2] . ( 8 sec) [ -7191.1775] [ 1447] [depth= 1] . ( 8 sec) [ -7190.7545] [ 1449] [depth= 1] . ( 8 sec) [ -7190.6411] [ 1451] [depth= 1] . ( 9 sec) [ -7190.2947] [ 1449] [depth= 1] . ( 9 sec) [ -7183.8087] [Branch lengths ] . ( 10 sec) [ -7183.4961] [GTR parameters ] . ( 10 sec) [ -7183.1283] [Alpha ][ 0.924790] . ( 10 sec) [ -7181.5569] [ 1447] [depth= 3] . ( 11 sec) [ -7181.5140] [ 1448] [depth= 2] . ( 11 sec) [ -7181.5004] [ 1448] [depth= 1] . ( 11 sec) [ -7181.2387] [ 1450] [depth= 1] . ( 13 sec) [ -7181.0443] [ 1450] [depth= 1] . ( 14 sec) [ -7181.0248] [ 1449] [depth= 3] . ( 15 sec) [ -7180.2314] [Branch lengths ] . ( 16 sec) [ -7180.1278] [GTR parameters ] . ( 16 sec) [ -7180.1167] [Alpha ][ 0.936694] . ( 16 sec) [ -7179.8699] [ 1447] [depth= 1] . ( 21 sec) [ -7179.7289] [Branch lengths ] . ( 21 sec) [ -7179.7282] [GTR parameters ] . ( 21 sec) [ -7179.7277] [Alpha ][ 0.939115] . ( 43 sec) [ -7179.7173] [Branch lengths ] . ( 43 sec) [ -7179.7173] [Topology ] . ( 44 sec) [ -7179.5778] [Topology ] . ( 44 sec) [ -7179.5687] [Topology ] . ( 45 sec) [ -7179.5675] [Topology ] . ( 46 sec) [ -7179.5673] [Topology ] . ( 46 sec) [ -7179.5670] [GTR parameters ] . ( 46 sec) [ -7179.5669] [Alpha ][ 0.940054] . ( 46 sec) [ -7179.5669] [Topology ] . ( 47 sec) [ -7179.5669] [Topology ] . ( 47 sec) [ -7179.5668] [GTR parameters ] . ( 47 sec) [ -7179.5668] [Alpha ][ 0.940054] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7179.566844. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7232.842533 . ( 1 sec) [ -7230.4040] [GTR parameters ] . ( 1 sec) [ -7229.6204] [Alpha ][ 0.896021] . ( 1 sec) [ -7229.6204] [Topology ] . ( 2 sec) [ -7192.0939] [Topology ] . ( 2 sec) [ -7187.0334] [Topology ] . ( 3 sec) [ -7185.9593] [Topology ] . ( 4 sec) [ -7185.6067] [Topology ] . ( 5 sec) [ -7185.4697] [Topology ] . ( 5 sec) [ -7185.4114] [Topology ] . ( 6 sec) [ -7185.3852] [Topology ] . ( 7 sec) [ -7185.3059] [Topology ] . ( 7 sec) [ -7182.8083] [Topology ] . Before opt ts/t=1.000000 LK=-7182.649243 . ( 9 sec) [ -7182.5732] [GTR parameters ] . ( 9 sec) [ -7182.4728] [Alpha ][ 0.929875] . ( 9 sec) [ -7182.4728] [Topology ] . ( 9 sec) [ -7181.7891] [Topology ] . ( 10 sec) [ -7179.9913] [Topology ] . ( 11 sec) [ -7179.6157] [Topology ] . ( 12 sec) [ -7179.5869] [Topology ] . ( 12 sec) [ -7179.5798] [Topology ] . ( 13 sec) [ -7179.5776] [Topology ] . ( 14 sec) [ -7179.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.576932 . ( 19 sec) [ -7179.5752] [GTR parameters ] . ( 19 sec) [ -7179.5673] [Alpha ][ 0.939938] . ( 19 sec) [ -7179.5673] [Topology ] . ( 20 sec) [ -7179.5669] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.566930 . ( 25 sec) [ -7179.5669] [GTR parameters ] . ( 25 sec) [ -7179.5669] [Alpha ][ 0.939938] . ( 25 sec) [ -7179.5669] [Topology ] . ( 26 sec) [ -7179.5668] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -7230.4040] [GTR parameters ] . ( 36 sec) [ -7229.6204] [Alpha ][ 0.896021] . ( 36 sec) [ -7229.5500] [ 1446] [depth= 1] . ( 36 sec) [ -7228.5236] [ 1445] [depth= 1] . ( 37 sec) [ -7227.7082] [ 1447] [depth= 1] . ( 37 sec) [ -7224.8975] [ 1445] [depth= 1] . ( 37 sec) [ -7224.7264] [ 1445] [depth= 1] . ( 37 sec) [ -7224.2540] [ 1445] [depth= 1] . ( 37 sec) [ -7224.0131] [ 1445] [depth= 1] . ( 37 sec) [ -7223.9768] [ 1445] [depth= 1] . ( 37 sec) [ -7222.4071] [ 1445] [depth= 1] . ( 37 sec) [ -7222.3622] [ 1445] [depth= 1] . ( 37 sec) [ -7221.8243] [ 1446] [depth= 1] . ( 37 sec) [ -7221.2932] [ 1445] [depth= 1] . ( 38 sec) [ -7220.3057] [ 1446] [depth= 1] . ( 39 sec) [ -7215.1876] [ 1445] [depth= 1] . ( 39 sec) [ -7210.9794] [ 1444] [depth= 1] . ( 39 sec) [ -7207.7011] [ 1445] [depth= 1] . ( 39 sec) [ -7206.6468] [ 1444] [depth= 1] . ( 39 sec) [ -7206.3219] [ 1444] [depth= 1] . ( 39 sec) [ -7206.1998] [ 1446] [depth= 2] . ( 39 sec) [ -7204.7896] [ 1449] [depth= 2] . ( 40 sec) [ -7200.3620] [ 1450] [depth= 1] . ( 40 sec) [ -7186.3168] [Branch lengths ] . ( 41 sec) [ -7186.2890] [GTR parameters ] . ( 41 sec) [ -7186.2249] [Alpha ][ 0.923339] . ( 43 sec) [ -7186.2014] [ 1448] [depth= 1] . ( 44 sec) [ -7185.5295] [ 1452] [depth= 1] . ( 44 sec) [ -7183.5661] [ 1447] [depth= 2] . ( 45 sec) [ -7182.8653] [ 1450] [depth= 1] . ( 46 sec) [ -7180.9195] [ 1448] [depth= 1] . ( 46 sec) [ -7179.8380] [Branch lengths ] . ( 46 sec) [ -7179.8137] [GTR parameters ] . ( 46 sec) [ -7179.8012] [Alpha ][ 0.935945] . ( 52 sec) [ -7179.7267] [Branch lengths ] . ( 74 sec) [ -7179.7190] [Branch lengths ] . ( 74 sec) [ -7179.7190] [Topology ] . ( 74 sec) [ -7179.5787] [Topology ] . ( 75 sec) [ -7179.5698] [Topology ] . ( 76 sec) [ -7179.5687] [Topology ] . ( 76 sec) [ -7179.5685] [Topology ] . ( 77 sec) [ -7179.5682] [GTR parameters ] . ( 77 sec) [ -7179.5670] [Alpha ][ 0.939863] . ( 77 sec) [ -7179.5670] [Topology ] . ( 77 sec) [ -7179.5669] [Topology ] . ( 78 sec) [ -7179.5669] [GTR parameters ] . ( 78 sec) [ -7179.5669] [Alpha ][ 0.939863] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7179.566849 . Log likelihood obtained after SPR moves : -7179.566904 . Log likelihood of the current tree: -7179.566849. . Printing the most likely tree in file 'data31.phy_phyml_tree.txt'... . Best log likelihood : -7179.566810 . Time used 0h1m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo