.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2902_51x908_2006.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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 467 patterns found. (out of a total of 908 sites) . 480 sites without polymorphism (52.86%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21620.0158] [GTR parameters ] . ( 1 sec) [ -21167.1721] [Alpha ][ 0.500960] . ( 1 sec) [ -20576.3005] [ 2912] [depth= 9] . ( 2 sec) [ -19922.2376] [ 2856] [depth= 17] . ( 2 sec) [ -17272.2281] [ 2826] [depth= 14] . ( 2 sec) [ -16864.4078] [ 2793] [depth= 1] . ( 2 sec) [ -16706.5473] [ 2777] [depth= 5] . ( 2 sec) [ -16564.3632] [ 2766] [depth= 2] . ( 2 sec) [ -15353.0641] [ 2759] [depth= 10] . ( 2 sec) [ -14558.9519] [ 2720] [depth= 5] . ( 2 sec) [ -14336.1702] [ 2710] [depth= 3] . ( 2 sec) [ -14255.7017] [ 2708] [depth= 3] . ( 2 sec) [ -14168.4638] [ 2697] [depth= 3] . ( 2 sec) [ -14087.0708] [ 2656] [depth= 4] . ( 2 sec) [ -14079.4984] [ 2657] [depth= 1] . ( 2 sec) [ -13983.5126] [ 2627] [depth= 2] . ( 2 sec) [ -13899.6939] [ 2611] [depth= 5] . ( 2 sec) [ -13684.4642] [ 2600] [depth= 1] . ( 2 sec) [ -13219.1091] [ 2596] [depth= 6] . ( 2 sec) [ -13074.1040] [ 2567] [depth= 3] . ( 2 sec) [ -12944.2375] [ 2562] [depth= 5] . ( 2 sec) [ -12605.1231] [ 2552] [depth= 4] . ( 3 sec) [ -12371.6230] [ 2520] [depth= 6] . ( 3 sec) [ -12030.8166] [ 2470] [depth= 1] . ( 3 sec) [ -11909.7873] [ 2453] [depth= 5] . ( 3 sec) [ -11893.3882] [ 2453] [depth= 1] . ( 3 sec) [ -11876.0709] [ 2445] [depth= 2] . ( 3 sec) [ -11852.2929] [ 2441] [depth= 2] . ( 3 sec) [ -11818.1518] [ 2389] [depth= 23] . ( 3 sec) [ -11784.0917] [ 2364] [depth= 13] . ( 3 sec) [ -11707.9498] [ 2360] [depth= 1] . ( 3 sec) [ -11431.8607] [ 2326] [depth= 7] . ( 3 sec) [ -11408.7610] [ 2326] [depth= 4] . ( 3 sec) [ -11275.3662] [ 2291] [depth= 1] . ( 3 sec) [ -11270.4550] [ 2284] [depth= 2] . ( 3 sec) [ -11167.6825] [ 2224] [depth= 12] . ( 3 sec) [ -11137.3437] [ 2224] [depth= 16] . ( 3 sec) [ -11136.5047] [ 2221] [depth= 1] . ( 3 sec) [ -11136.4592] [ 2221] [depth= 2] . ( 4 sec) [ -11134.7106] [ 2221] [depth= 2] . ( 4 sec) [ -11073.8076] [ 2204] [depth= 17] . ( 4 sec) [ -11005.7760] [ 2199] [depth= 1] . ( 4 sec) [ -11005.7554] [ 2199] [depth= 2] . ( 4 sec) [ -11005.7251] [ 2199] [depth= 2] . ( 4 sec) [ -10944.2537] [ 2197] [depth= 9] . ( 4 sec) [ -10902.6472] [ 2200] [depth= 1] . ( 4 sec) [ -10816.9668] [ 2207] [depth= 20] . ( 4 sec) [ -10678.7220] [ 2138] [depth= 18] . ( 4 sec) [ -10608.8380] [ 2121] [depth= 6] . ( 4 sec) [ -10555.7337] [ 2115] [depth= 7] . ( 4 sec) [ -10516.0625] [ 2093] [depth= 6] . ( 4 sec) [ -10478.0838] [ 2081] [depth= 2] . ( 4 sec) [ -10414.4072] [ 2065] [depth= 7] . ( 5 sec) [ -10402.6815] [ 2064] [depth= 1] . ( 5 sec) [ -10391.4304] [ 2056] [depth= 1] . ( 5 sec) [ -10328.0231] [ 2041] [depth= 13] . ( 5 sec) [ -10291.7261] [ 2029] [depth= 2] . ( 5 sec) [ -10236.8541] [ 2013] [depth= 1] . ( 5 sec) [ -10226.9134] [ 2015] [depth= 1] . ( 5 sec) [ -10153.0127] [ 1984] [depth= 8] . ( 5 sec) [ -10150.7019] [ 1982] [depth= 1] . ( 5 sec) [ -10006.6096] [ 1943] [depth= 14] . ( 5 sec) [ -9940.0219] [ 1943] [depth= 2] . ( 5 sec) [ -9919.6879] [ 1936] [depth= 4] . ( 5 sec) [ -9913.1726] [ 1938] [depth= 1] . ( 5 sec) [ -9902.6344] [ 1945] [depth= 1] . ( 5 sec) [ -9770.0440] [ 1906] [depth= 11] . ( 5 sec) [ -9716.8180] [ 1883] [depth= 4] . ( 5 sec) [ -9681.8685] [ 1888] [depth= 3] . ( 6 sec) [ -9563.7798] [ 1824] [depth= 7] . ( 6 sec) [ -9563.2483] [ 1825] [depth= 1] . ( 6 sec) [ -9520.4597] [ 1818] [depth= 2] . ( 6 sec) [ -9514.0913] [ 1814] [depth= 2] . ( 6 sec) [ -9443.9830] [ 1816] [depth= 3] . ( 6 sec) [ -9357.6111] [ 1790] [depth= 4] . ( 6 sec) [ -9354.1527] [ 1791] [depth= 1] . ( 6 sec) [ -9289.3539] [ 1795] [depth= 1] . ( 6 sec) [ -9162.0051] [ 1748] [depth= 3] . ( 6 sec) [ -9160.3342] [ 1747] [depth= 1] . ( 6 sec) [ -9156.1619] [ 1744] [depth= 1] . ( 6 sec) [ -9145.2869] [ 1743] [depth= 1] . ( 6 sec) [ -9130.5379] [ 1746] [depth= 2] . ( 6 sec) [ -9118.9069] [ 1742] [depth= 3] . ( 6 sec) [ -9068.2927] [ 1743] [depth= 1] . ( 7 sec) [ -9068.2162] [ 1747] [depth= 1] . ( 7 sec) [ -9046.6008] [ 1743] [depth= 1] . ( 7 sec) [ -9044.1468] [ 1746] [depth= 1] . ( 7 sec) [ -9034.8087] [ 1745] [depth= 11] . ( 7 sec) [ -9034.4197] [ 1750] [depth= 1] . ( 7 sec) [ -9030.8535] [ 1750] [depth= 1] . ( 7 sec) [ -9030.0426] [ 1750] [depth= 1] . ( 7 sec) [ -9029.6503] [ 1751] [depth= 1] . ( 7 sec) [ -9026.2806] [ 1752] [depth= 2] . ( 7 sec) [ -8884.2249] [ 1699] [depth= 4] . ( 7 sec) [ -8835.1620] [ 1687] [depth= 1] . ( 7 sec) [ -8722.2826] [ 1640] [depth= 4] . ( 7 sec) [ -8684.2327] [ 1627] [depth= 4] . ( 7 sec) [ -8678.9111] [ 1628] [depth= 1] . ( 7 sec) [ -8671.9213] [ 1621] [depth= 3] . ( 7 sec) [ -8597.7606] [ 1602] [depth= 13] . ( 8 sec) [ -8577.8556] [ 1598] [depth= 1] . ( 8 sec) [ -8564.6287] [ 1596] [depth= 1] . ( 8 sec) [ -8559.0402] [ 1596] [depth= 1] . ( 8 sec) [ -8558.4040] [ 1595] [depth= 1] . ( 8 sec) [ -8558.3449] [ 1595] [depth= 2] . ( 8 sec) [ -8483.8816] [ 1580] [depth= 15] . ( 8 sec) [ -8483.8219] [ 1572] [depth= 6] . ( 9 sec) [ -8454.8822] [ 1560] [depth= 9] . ( 9 sec) [ -8446.4371] [ 1564] [depth= 2] . ( 9 sec) [ -8423.6431] [ 1559] [depth= 1] . ( 9 sec) [ -8423.5992] [ 1553] [depth= 6] . ( 9 sec) [ -8400.7333] [ 1552] [depth= 1] . ( 9 sec) [ -8171.0095] [ 1460] [depth= 17] . ( 9 sec) [ -8170.9674] [ 1459] [depth= 1] . ( 9 sec) [ -8165.8265] [ 1460] [depth= 2] . ( 9 sec) [ -8165.7711] [ 1460] [depth= 1] . ( 10 sec) [ -8164.5671] [ 1456] [depth= 1] . ( 10 sec) [ -8164.5040] [ 1456] [depth= 2] . ( 10 sec) [ -8163.7915] [ 1454] [depth= 1] . ( 10 sec) [ -8020.3901] [Branch lengths ] . ( 11 sec) [ -7884.3311] [GTR parameters ] . ( 11 sec) [ -7874.9247] [Alpha ][ 0.374320] . ( 11 sec) [ -7874.8105] [ 1449] [depth= 2] . ( 11 sec) [ -7866.5422] [ 1446] [depth= 1] . ( 12 sec) [ -7865.8437] [ 1447] [depth= 2] . ( 13 sec) [ -7789.6189] [ 1420] [depth= 6] . ( 14 sec) [ -7740.2726] [ 1407] [depth= 5] . ( 14 sec) [ -7724.5422] [ 1405] [depth= 4] . ( 14 sec) [ -7720.9379] [ 1402] [depth= 2] . ( 14 sec) [ -7719.3109] [ 1401] [depth= 1] . ( 14 sec) [ -7717.9779] [ 1401] [depth= 1] . ( 14 sec) [ -7713.6314] [ 1401] [depth= 1] . ( 15 sec) [ -7711.6162] [ 1394] [depth= 2] . ( 16 sec) [ -7709.7722] [ 1384] [depth= 5] . ( 16 sec) [ -7704.1581] [ 1383] [depth= 4] . ( 16 sec) [ -7704.0835] [ 1385] [depth= 3] . ( 17 sec) [ -7701.9428] [ 1387] [depth= 1] . ( 17 sec) [ -7698.6135] [ 1387] [depth= 2] . ( 17 sec) [ -7697.3721] [ 1391] [depth= 1] . ( 18 sec) [ -7631.8835] [ 1369] [depth= 4] . ( 18 sec) [ -7625.9282] [ 1365] [depth= 1] . ( 18 sec) [ -7625.2436] [ 1364] [depth= 1] . ( 18 sec) [ -7624.7715] [ 1364] [depth= 1] . ( 19 sec) [ -7616.1047] [ 1366] [depth= 1] . ( 19 sec) [ -7612.5039] [ 1366] [depth= 9] . ( 19 sec) [ -7605.6030] [ 1360] [depth= 4] . ( 19 sec) [ -7605.2774] [ 1360] [depth= 1] . ( 20 sec) [ -7604.1983] [ 1362] [depth= 1] . ( 20 sec) [ -7598.4888] [ 1359] [depth= 1] . ( 21 sec) [ -7598.0574] [ 1361] [depth= 1] . ( 21 sec) [ -7596.6461] [ 1357] [depth= 5] . ( 21 sec) [ -7592.1086] [ 1357] [depth= 1] . ( 22 sec) [ -7590.0613] [ 1362] [depth= 1] . ( 22 sec) [ -7587.3608] [ 1361] [depth= 3] . ( 23 sec) [ -7576.8876] [Branch lengths ] . ( 24 sec) [ -7576.2661] [GTR parameters ] . ( 24 sec) [ -7576.1911] [Alpha ][ 0.384033] . ( 25 sec) [ -7575.8684] [ 1359] [depth= 1] . ( 26 sec) [ -7574.5501] [ 1359] [depth= 2] . ( 28 sec) [ -7574.0504] [ 1359] [depth= 1] . ( 30 sec) [ -7573.8502] [ 1361] [depth= 1] . ( 35 sec) [ -7573.3763] [ 1352] [depth= 2] . ( 39 sec) [ -7570.4002] [Branch lengths ] . ( 40 sec) [ -7570.3627] [GTR parameters ] . ( 40 sec) [ -7570.3623] [Alpha ][ 0.384697] . ( 47 sec) [ -7570.2869] [ 1351] [depth= 1] . ( 54 sec) [ -7570.0926] [Branch lengths ] . ( 55 sec) [ -7570.0911] [GTR parameters ] . ( 55 sec) [ -7570.0910] [Alpha ][ 0.385082] . ( 95 sec) [ -7569.9770] [Branch lengths ] . ( 95 sec) [ -7569.9770] [Topology ] . ( 96 sec) [ -7569.9710] [Topology ] . ( 97 sec) [ -7569.9702] [Topology ] . ( 97 sec) [ -7569.9700] [GTR parameters ] . ( 98 sec) [ -7569.9700] [Alpha ][ 0.385082] . ( 98 sec) [ -7569.9700] [Topology ] . ( 99 sec) [ -7569.9698] [Topology ] . ( 99 sec) [ -7569.9698] [GTR parameters ] . ( 99 sec) [ -7569.9698] [Alpha ][ 0.385082] . Checking for NNIs, optimizing five branches... . ( 106 sec) [ -7569.8671] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7569.867090. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19370.3820] [GTR parameters ] . ( 1 sec) [ -18943.4625] [Alpha ][ 0.500960] . ( 1 sec) [ -15860.8814] [ 2712] [depth= 3] . ( 1 sec) [ -15769.4434] [ 2701] [depth= 13] . ( 1 sec) [ -15718.8598] [ 2701] [depth= 1] . ( 1 sec) [ -15609.7126] [ 2692] [depth= 11] . ( 1 sec) [ -15525.1564] [ 2658] [depth= 2] . ( 1 sec) [ -15480.6350] [ 2654] [depth= 5] . ( 1 sec) [ -15294.7728] [ 2587] [depth= 3] . ( 1 sec) [ -15275.6518] [ 2583] [depth= 8] . ( 1 sec) [ -15274.5314] [ 2544] [depth= 3] . ( 1 sec) [ -15096.3266] [ 2526] [depth= 8] . ( 1 sec) [ -15066.9720] [ 2529] [depth= 1] . ( 2 sec) [ -14957.2727] [ 2517] [depth= 3] . ( 2 sec) [ -14877.2356] [ 2497] [depth= 5] . ( 2 sec) [ -14780.4796] [ 2478] [depth= 12] . ( 2 sec) [ -14595.6554] [ 2449] [depth= 10] . ( 2 sec) [ -14527.5530] [ 2416] [depth= 1] . ( 2 sec) [ -14479.2378] [ 2407] [depth= 3] . ( 2 sec) [ -14428.1630] [ 2394] [depth= 1] . ( 2 sec) [ -14417.3794] [ 2394] [depth= 21] . ( 2 sec) [ -14409.2306] [ 2394] [depth= 21] . ( 2 sec) [ -14313.8489] [ 2399] [depth= 2] . ( 2 sec) [ -14158.2965] [ 2356] [depth= 6] . ( 2 sec) [ -14116.4253] [ 2341] [depth= 9] . ( 2 sec) [ -13636.8711] [ 2332] [depth= 5] . ( 2 sec) [ -13568.4706] [ 2331] [depth= 1] . ( 2 sec) [ -13497.4038] [ 2330] [depth= 1] . ( 3 sec) [ -13385.7020] [ 2319] [depth= 15] . ( 3 sec) [ -13165.9356] [ 2229] [depth= 1] . ( 3 sec) [ -13137.8046] [ 2216] [depth= 6] . ( 3 sec) [ -13107.2861] [ 2210] [depth= 1] . ( 3 sec) [ -12957.5191] [ 2197] [depth= 17] . ( 3 sec) [ -12941.3621] [ 2196] [depth= 8] . ( 3 sec) [ -12808.0354] [ 2144] [depth= 11] . ( 3 sec) [ -12805.4218] [ 2144] [depth= 1] . ( 3 sec) [ -12749.0533] [ 2130] [depth= 2] . ( 3 sec) [ -12518.0555] [ 2129] [depth= 7] . ( 4 sec) [ -12282.7146] [ 2098] [depth= 4] . ( 4 sec) [ -12240.5154] [ 2088] [depth= 8] . ( 4 sec) [ -12078.8631] [ 2067] [depth= 8] . ( 4 sec) [ -12064.8021] [ 2065] [depth= 5] . ( 4 sec) [ -12053.0735] [ 2064] [depth= 12] . ( 4 sec) [ -12047.0351] [ 2062] [depth= 6] . ( 4 sec) [ -12004.3768] [ 2060] [depth= 4] . ( 4 sec) [ -11687.4342] [ 2058] [depth= 2] . ( 4 sec) [ -11087.9807] [ 2040] [depth= 16] . ( 4 sec) [ -10999.7374] [ 2036] [depth= 1] . ( 4 sec) [ -10994.4114] [ 1990] [depth= 1] . ( 4 sec) [ -10985.5090] [ 1990] [depth= 2] . ( 4 sec) [ -10914.6510] [ 1983] [depth= 14] . ( 4 sec) [ -10682.3832] [ 1990] [depth= 1] . ( 4 sec) [ -10652.2882] [ 1985] [depth= 3] . ( 5 sec) [ -10646.1194] [ 1983] [depth= 1] . ( 5 sec) [ -10615.2834] [ 1976] [depth= 6] . ( 5 sec) [ -10612.4413] [ 1978] [depth= 1] . ( 5 sec) [ -10600.0612] [ 1977] [depth= 2] . ( 5 sec) [ -10584.6055] [ 1968] [depth= 2] . ( 5 sec) [ -10437.0840] [ 1943] [depth= 17] . ( 5 sec) [ -10288.1558] [ 1894] [depth= 5] . ( 5 sec) [ -10047.5086] [ 1847] [depth= 4] . ( 5 sec) [ -9889.5639] [ 1831] [depth= 1] . ( 5 sec) [ -9832.1271] [ 1801] [depth= 1] . ( 6 sec) [ -9765.0175] [ 1779] [depth= 3] . ( 6 sec) [ -9676.5770] [ 1789] [depth= 3] . ( 6 sec) [ -9653.3060] [ 1784] [depth= 2] . ( 6 sec) [ -9623.4224] [ 1778] [depth= 1] . ( 6 sec) [ -9608.0473] [ 1775] [depth= 3] . ( 6 sec) [ -9526.5129] [ 1735] [depth= 12] . ( 6 sec) [ -9493.0584] [ 1725] [depth= 4] . ( 6 sec) [ -9298.9155] [ 1738] [depth= 1] . ( 6 sec) [ -9267.3046] [ 1726] [depth= 4] . ( 6 sec) [ -9262.4075] [ 1727] [depth= 2] . ( 6 sec) [ -9210.1073] [ 1720] [depth= 1] . ( 6 sec) [ -9205.3007] [ 1721] [depth= 1] . ( 6 sec) [ -9196.4723] [ 1722] [depth= 2] . ( 7 sec) [ -9182.2420] [ 1720] [depth= 1] . ( 7 sec) [ -9176.0051] [ 1735] [depth= 1] . ( 7 sec) [ -8991.6460] [ 1654] [depth= 16] . ( 7 sec) [ -8963.8041] [ 1634] [depth= 5] . ( 7 sec) [ -8952.8269] [ 1632] [depth= 2] . ( 7 sec) [ -8949.4434] [ 1633] [depth= 1] . ( 7 sec) [ -8934.2271] [ 1636] [depth= 1] . ( 7 sec) [ -8931.5724] [ 1636] [depth= 3] . ( 7 sec) [ -8886.2258] [ 1630] [depth= 12] . ( 7 sec) [ -8876.5908] [ 1630] [depth= 1] . ( 7 sec) [ -8868.4379] [ 1629] [depth= 1] . ( 8 sec) [ -8769.2393] [ 1603] [depth= 11] . ( 8 sec) [ -8765.1008] [ 1606] [depth= 5] . ( 8 sec) [ -8675.7088] [ 1590] [depth= 1] . ( 8 sec) [ -8537.1870] [ 1584] [depth= 19] . ( 8 sec) [ -8536.2535] [ 1584] [depth= 1] . ( 8 sec) [ -8535.6887] [ 1584] [depth= 1] . ( 8 sec) [ -8535.1069] [ 1584] [depth= 1] . ( 8 sec) [ -8533.5032] [ 1583] [depth= 2] . ( 8 sec) [ -8444.5347] [ 1584] [depth= 1] . ( 8 sec) [ -8410.1598] [ 1583] [depth= 2] . ( 8 sec) [ -8363.6193] [ 1553] [depth= 5] . ( 8 sec) [ -8349.3195] [ 1550] [depth= 1] . ( 8 sec) [ -8299.1262] [ 1544] [depth= 11] . ( 8 sec) [ -8286.2323] [ 1534] [depth= 2] . ( 8 sec) [ -8282.6780] [ 1540] [depth= 1] . ( 9 sec) [ -8266.3352] [ 1531] [depth= 4] . ( 9 sec) [ -8264.4187] [ 1531] [depth= 2] . ( 9 sec) [ -8152.4176] [ 1491] [depth= 2] . ( 9 sec) [ -8121.7837] [ 1470] [depth= 8] . ( 9 sec) [ -8091.6493] [ 1461] [depth= 2] . ( 9 sec) [ -8088.0672] [ 1466] [depth= 1] . ( 9 sec) [ -8082.4006] [ 1461] [depth= 1] . ( 9 sec) [ -8064.8636] [ 1455] [depth= 1] . ( 9 sec) [ -8063.0837] [ 1450] [depth= 1] . ( 9 sec) [ -8042.0441] [ 1450] [depth= 1] . ( 9 sec) [ -8039.2115] [ 1452] [depth= 1] . ( 10 sec) [ -8038.6920] [ 1452] [depth= 1] . ( 10 sec) [ -8035.9883] [ 1456] [depth= 1] . ( 10 sec) [ -7916.1752] [Branch lengths ] . ( 12 sec) [ -7816.8295] [GTR parameters ] . ( 12 sec) [ -7806.7205] [Alpha ][ 0.374209] . ( 12 sec) [ -7806.0678] [ 1456] [depth= 1] . ( 13 sec) [ -7804.9708] [ 1455] [depth= 2] . ( 13 sec) [ -7803.4101] [ 1454] [depth= 1] . ( 13 sec) [ -7713.2443] [ 1402] [depth= 8] . ( 13 sec) [ -7713.1414] [ 1404] [depth= 2] . ( 14 sec) [ -7653.5265] [ 1373] [depth= 4] . ( 14 sec) [ -7653.4977] [ 1373] [depth= 3] . ( 14 sec) [ -7647.7808] [ 1371] [depth= 1] . ( 14 sec) [ -7647.7629] [ 1371] [depth= 1] . ( 14 sec) [ -7647.7110] [ 1371] [depth= 3] . ( 14 sec) [ -7646.8934] [ 1372] [depth= 1] . ( 14 sec) [ -7646.8600] [ 1372] [depth= 1] . ( 15 sec) [ -7644.2636] [ 1369] [depth= 6] . ( 15 sec) [ -7640.6608] [ 1371] [depth= 1] . ( 16 sec) [ -7636.2454] [ 1371] [depth= 2] . ( 16 sec) [ -7635.1647] [ 1370] [depth= 2] . ( 16 sec) [ -7633.5047] [ 1368] [depth= 1] . ( 16 sec) [ -7630.7752] [ 1366] [depth= 1] . ( 16 sec) [ -7630.2951] [ 1365] [depth= 1] . ( 16 sec) [ -7629.5407] [ 1365] [depth= 1] . ( 16 sec) [ -7628.2417] [ 1366] [depth= 1] . ( 17 sec) [ -7627.7758] [ 1364] [depth= 2] . ( 18 sec) [ -7627.3978] [ 1363] [depth= 1] . ( 18 sec) [ -7624.5389] [ 1363] [depth= 2] . ( 18 sec) [ -7619.5647] [ 1361] [depth= 1] . ( 19 sec) [ -7605.1733] [ 1360] [depth= 5] . ( 20 sec) [ -7604.9437] [ 1358] [depth= 1] . ( 20 sec) [ -7601.0900] [ 1361] [depth= 1] . ( 20 sec) [ -7600.9897] [ 1362] [depth= 1] . ( 21 sec) [ -7600.9501] [ 1362] [depth= 1] . ( 21 sec) [ -7600.9285] [ 1362] [depth= 2] . ( 21 sec) [ -7600.7344] [ 1358] [depth= 1] . ( 22 sec) [ -7600.5721] [ 1356] [depth= 1] . ( 22 sec) [ -7600.3159] [ 1357] [depth= 1] . ( 22 sec) [ -7599.8097] [ 1351] [depth= 1] . ( 23 sec) [ -7599.6402] [ 1351] [depth= 1] . ( 23 sec) [ -7599.2489] [ 1351] [depth= 1] . ( 24 sec) [ -7585.9747] [Branch lengths ] . ( 25 sec) [ -7585.5412] [GTR parameters ] . ( 25 sec) [ -7585.4262] [Alpha ][ 0.386084] . ( 28 sec) [ -7585.3783] [ 1351] [depth= 1] . ( 28 sec) [ -7584.9825] [ 1353] [depth= 1] . ( 30 sec) [ -7584.8098] [ 1353] [depth= 1] . ( 30 sec) [ -7584.7861] [ 1353] [depth= 1] . ( 31 sec) [ -7584.7498] [ 1353] [depth= 3] . ( 33 sec) [ -7583.2552] [ 1354] [depth= 2] . ( 35 sec) [ -7583.0554] [ 1353] [depth= 3] . ( 36 sec) [ -7582.6538] [ 1358] [depth= 1] . ( 39 sec) [ -7580.9885] [Branch lengths ] . ( 39 sec) [ -7580.9679] [GTR parameters ] . ( 40 sec) [ -7580.9328] [Alpha ][ 0.379475] . ( 45 sec) [ -7580.8282] [ 1358] [depth= 1] . ( 55 sec) [ -7578.8730] [Branch lengths ] . ( 55 sec) [ -7578.8718] [GTR parameters ] . ( 55 sec) [ -7578.8716] [Alpha ][ 0.378895] . ( 70 sec) [ -7578.1366] [Branch lengths ] . ( 81 sec) [ -7577.8961] [ 1357] [depth= 1] . ( 110 sec) [ -7577.7950] [Branch lengths ] . ( 111 sec) [ -7577.7918] [GTR parameters ] . ( 111 sec) [ -7577.7918] [Alpha ][ 0.378895] . ( 111 sec) [ -7577.7918] [Topology ] . ( 112 sec) [ -7577.7861] [Topology ] . ( 113 sec) [ -7577.7855] [Topology ] . ( 113 sec) [ -7577.7855] [GTR parameters ] . ( 113 sec) [ -7577.7855] [Alpha ][ 0.378895] . ( 113 sec) [ -7577.7855] [Topology ] . ( 114 sec) [ -7577.7854] [Topology ] . ( 115 sec) [ -7577.7854] [GTR parameters ] . ( 115 sec) [ -7577.7854] [Alpha ][ 0.378895] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -7577.6457] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7577.645747. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18742.6514] [GTR parameters ] . ( 1 sec) [ -18333.8487] [Alpha ][ 0.500960] . ( 1 sec) [ -18141.1315] [ 2855] [depth= 4] . ( 1 sec) [ -17598.8684] [ 2845] [depth= 8] . ( 1 sec) [ -17496.6574] [ 2805] [depth= 9] . ( 1 sec) [ -17418.8110] [ 2785] [depth= 1] . ( 1 sec) [ -17248.7617] [ 2718] [depth= 10] . ( 1 sec) [ -17047.9356] [ 2692] [depth= 9] . ( 1 sec) [ -17024.8537] [ 2682] [depth= 1] . ( 1 sec) [ -16906.2424] [ 2643] [depth= 11] . ( 1 sec) [ -16868.9030] [ 2626] [depth= 6] . ( 1 sec) [ -16466.1320] [ 2596] [depth= 1] . ( 1 sec) [ -16411.4945] [ 2594] [depth= 9] . ( 2 sec) [ -16288.8977] [ 2588] [depth= 4] . ( 2 sec) [ -16285.4820] [ 2587] [depth= 7] . ( 2 sec) [ -16230.4117] [ 2572] [depth= 14] . ( 2 sec) [ -15965.6156] [ 2572] [depth= 2] . ( 2 sec) [ -15944.6881] [ 2558] [depth= 9] . ( 2 sec) [ -15885.4476] [ 2556] [depth= 2] . ( 2 sec) [ -15720.4499] [ 2543] [depth= 8] . ( 2 sec) [ -15685.0540] [ 2510] [depth= 1] . ( 2 sec) [ -15531.3898] [ 2471] [depth= 10] . ( 2 sec) [ -15066.8698] [ 2378] [depth= 9] . ( 2 sec) [ -14300.1291] [ 2363] [depth= 11] . ( 2 sec) [ -14281.0941] [ 2362] [depth= 11] . ( 2 sec) [ -14227.9205] [ 2349] [depth= 1] . ( 2 sec) [ -14150.9833] [ 2339] [depth= 13] . ( 2 sec) [ -14044.6351] [ 2300] [depth= 14] . ( 2 sec) [ -13879.1336] [ 2242] [depth= 8] . ( 3 sec) [ -13843.4293] [ 2242] [depth= 5] . ( 3 sec) [ -13826.2171] [ 2241] [depth= 1] . ( 3 sec) [ -13743.9656] [ 2223] [depth= 11] . ( 3 sec) [ -13591.8849] [ 2184] [depth= 6] . ( 3 sec) [ -13551.6065] [ 2180] [depth= 4] . ( 3 sec) [ -13303.6916] [ 2161] [depth= 3] . ( 3 sec) [ -13198.8371] [ 2160] [depth= 2] . ( 3 sec) [ -13187.8515] [ 2157] [depth= 1] . ( 3 sec) [ -13070.7635] [ 2138] [depth= 13] . ( 3 sec) [ -12945.6027] [ 2091] [depth= 17] . ( 3 sec) [ -12846.9615] [ 2087] [depth= 2] . ( 3 sec) [ -12721.9738] [ 2064] [depth= 7] . ( 3 sec) [ -12611.1324] [ 2031] [depth= 18] . ( 3 sec) [ -12554.3094] [ 2025] [depth= 3] . ( 3 sec) [ -12488.0606] [ 2030] [depth= 2] . ( 3 sec) [ -12164.3801] [ 1961] [depth= 11] . ( 4 sec) [ -12159.4632] [ 1961] [depth= 1] . ( 4 sec) [ -12058.4908] [ 1944] [depth= 8] . ( 4 sec) [ -12056.9975] [ 1938] [depth= 3] . ( 4 sec) [ -12019.3757] [ 1924] [depth= 15] . ( 4 sec) [ -11986.9071] [ 1924] [depth= 1] . ( 4 sec) [ -10850.3729] [ 1908] [depth= 16] . ( 4 sec) [ -10832.8264] [ 1909] [depth= 1] . ( 4 sec) [ -10823.3754] [ 1898] [depth= 2] . ( 4 sec) [ -10815.0502] [ 1892] [depth= 1] . ( 4 sec) [ -10730.0506] [ 1878] [depth= 8] . ( 4 sec) [ -10728.7685] [ 1881] [depth= 1] . ( 4 sec) [ -10521.2216] [ 1814] [depth= 18] . ( 4 sec) [ -10414.7123] [ 1814] [depth= 2] . ( 4 sec) [ -10261.6081] [ 1740] [depth= 7] . ( 5 sec) [ -10234.6119] [ 1733] [depth= 3] . ( 5 sec) [ -10094.7786] [ 1690] [depth= 3] . ( 5 sec) [ -10042.1881] [ 1686] [depth= 4] . ( 5 sec) [ -9950.3293] [ 1677] [depth= 2] . ( 5 sec) [ -9447.3893] [ 1684] [depth= 2] . ( 5 sec) [ -9036.8664] [ 1658] [depth= 10] . ( 5 sec) [ -8979.8193] [ 1656] [depth= 1] . ( 5 sec) [ -8971.3583] [ 1652] [depth= 2] . ( 5 sec) [ -8942.7747] [ 1647] [depth= 4] . ( 5 sec) [ -8922.8746] [ 1647] [depth= 3] . ( 5 sec) [ -8922.0991] [ 1650] [depth= 2] . ( 5 sec) [ -8790.5847] [ 1581] [depth= 10] . ( 5 sec) [ -8738.3596] [ 1567] [depth= 8] . ( 5 sec) [ -8736.8980] [ 1566] [depth= 5] . ( 6 sec) [ -8714.8423] [ 1560] [depth= 7] . ( 6 sec) [ -8714.4401] [ 1560] [depth= 1] . ( 6 sec) [ -8703.0089] [ 1559] [depth= 7] . ( 6 sec) [ -8586.9682] [ 1522] [depth= 6] . ( 6 sec) [ -8582.1211] [ 1525] [depth= 3] . ( 6 sec) [ -8553.5517] [ 1521] [depth= 6] . ( 6 sec) [ -8546.2844] [ 1520] [depth= 4] . ( 6 sec) [ -8492.1289] [ 1501] [depth= 4] . ( 6 sec) [ -8485.5429] [ 1500] [depth= 4] . ( 6 sec) [ -8475.7162] [ 1496] [depth= 2] . ( 6 sec) [ -8468.9563] [ 1494] [depth= 3] . ( 6 sec) [ -8468.7709] [ 1493] [depth= 2] . ( 6 sec) [ -8462.5538] [ 1491] [depth= 1] . ( 6 sec) [ -8440.7690] [ 1492] [depth= 3] . ( 7 sec) [ -8438.7549] [ 1492] [depth= 2] . ( 7 sec) [ -8437.3578] [ 1495] [depth= 2] . ( 7 sec) [ -8436.8116] [ 1498] [depth= 4] . ( 7 sec) [ -8436.7676] [ 1500] [depth= 1] . ( 7 sec) [ -8427.2912] [ 1499] [depth= 1] . ( 7 sec) [ -8415.9565] [ 1484] [depth= 10] . ( 7 sec) [ -8415.3724] [ 1484] [depth= 2] . ( 7 sec) [ -8308.4943] [ 1449] [depth= 5] . ( 7 sec) [ -8270.8284] [ 1436] [depth= 3] . ( 7 sec) [ -8270.7442] [ 1436] [depth= 1] . ( 8 sec) [ -8265.9633] [ 1436] [depth= 2] . ( 8 sec) [ -8127.6891] [ 1416] [depth= 3] . ( 8 sec) [ -8123.2828] [ 1410] [depth= 4] . ( 8 sec) [ -8118.0668] [ 1411] [depth= 4] . ( 8 sec) [ -8039.8198] [ 1402] [depth= 1] . ( 8 sec) [ -8039.7522] [ 1406] [depth= 4] . ( 8 sec) [ -8036.8896] [ 1407] [depth= 1] . ( 8 sec) [ -7970.4883] [ 1386] [depth= 1] . ( 8 sec) [ -7965.6922] [ 1386] [depth= 1] . ( 8 sec) [ -7950.0910] [ 1387] [depth= 2] . ( 9 sec) [ -7942.6569] [ 1384] [depth= 5] . ( 9 sec) [ -7821.2745] [Branch lengths ] . ( 12 sec) [ -7683.1413] [GTR parameters ] . ( 12 sec) [ -7675.3774] [Alpha ][ 0.383455] . ( 12 sec) [ -7665.1973] [ 1378] [depth= 2] . ( 12 sec) [ -7660.9844] [ 1374] [depth= 1] . ( 12 sec) [ -7658.2044] [ 1372] [depth= 1] . ( 12 sec) [ -7656.8252] [ 1371] [depth= 1] . ( 12 sec) [ -7656.5570] [ 1375] [depth= 2] . ( 12 sec) [ -7656.2254] [ 1378] [depth= 1] . ( 13 sec) [ -7650.5607] [ 1374] [depth= 2] . ( 13 sec) [ -7649.8018] [ 1373] [depth= 1] . ( 13 sec) [ -7649.0024] [ 1375] [depth= 1] . ( 13 sec) [ -7648.7193] [ 1374] [depth= 1] . ( 13 sec) [ -7637.2009] [ 1369] [depth= 2] . ( 14 sec) [ -7634.7948] [ 1371] [depth= 3] . ( 14 sec) [ -7634.0786] [ 1373] [depth= 1] . ( 15 sec) [ -7623.8328] [ 1367] [depth= 1] . ( 15 sec) [ -7623.3128] [ 1365] [depth= 1] . ( 16 sec) [ -7620.4426] [ 1365] [depth= 1] . ( 16 sec) [ -7613.3111] [ 1360] [depth= 1] . ( 16 sec) [ -7612.3064] [ 1359] [depth= 1] . ( 16 sec) [ -7606.3087] [ 1354] [depth= 2] . ( 17 sec) [ -7606.2139] [ 1354] [depth= 3] . ( 17 sec) [ -7604.1533] [ 1346] [depth= 2] . ( 18 sec) [ -7603.4069] [ 1347] [depth= 1] . ( 18 sec) [ -7603.1661] [ 1346] [depth= 1] . ( 18 sec) [ -7601.6830] [ 1350] [depth= 2] . ( 18 sec) [ -7601.0104] [ 1353] [depth= 1] . ( 19 sec) [ -7596.6939] [ 1354] [depth= 2] . ( 20 sec) [ -7595.3581] [ 1356] [depth= 1] . ( 20 sec) [ -7594.5991] [ 1355] [depth= 1] . ( 20 sec) [ -7590.2864] [ 1345] [depth= 2] . ( 22 sec) [ -7589.9664] [ 1342] [depth= 1] . ( 22 sec) [ -7589.8377] [ 1345] [depth= 1] . ( 22 sec) [ -7589.3779] [ 1347] [depth= 1] . ( 23 sec) [ -7588.9924] [ 1346] [depth= 3] . ( 23 sec) [ -7573.4047] [Branch lengths ] . ( 25 sec) [ -7572.9677] [GTR parameters ] . ( 25 sec) [ -7572.9673] [Alpha ][ 0.384100] . ( 26 sec) [ -7572.8603] [ 1346] [depth= 1] . ( 34 sec) [ -7571.5438] [ 1347] [depth= 2] . ( 37 sec) [ -7570.9423] [Branch lengths ] . ( 38 sec) [ -7570.9341] [GTR parameters ] . ( 38 sec) [ -7570.9296] [Alpha ][ 0.381530] . ( 47 sec) [ -7570.8556] [ 1346] [depth= 2] . ( 50 sec) [ -7570.7183] [Branch lengths ] . ( 51 sec) [ -7570.7183] [GTR parameters ] . ( 51 sec) [ -7570.7182] [Alpha ][ 0.381912] . ( 92 sec) [ -7570.6108] [Branch lengths ] . ( 92 sec) [ -7570.6108] [Topology ] . ( 93 sec) [ -7570.6050] [Topology ] . ( 94 sec) [ -7570.6041] [Topology ] . ( 94 sec) [ -7570.6024] [GTR parameters ] . ( 95 sec) [ -7570.6024] [Alpha ][ 0.381912] . ( 95 sec) [ -7570.6024] [Topology ] . ( 96 sec) [ -7570.6021] [Topology ] . ( 96 sec) [ -7570.6020] [GTR parameters ] . ( 96 sec) [ -7570.6020] [Alpha ][ 0.381912] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7570.602015. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20096.4404] [GTR parameters ] . ( 1 sec) [ -19652.1717] [Alpha ][ 0.500960] . ( 1 sec) [ -18881.6631] [ 2861] [depth= 10] . ( 2 sec) [ -18812.7802] [ 2854] [depth= 13] . ( 2 sec) [ -18761.5078] [ 2848] [depth= 3] . ( 2 sec) [ -18606.1241] [ 2839] [depth= 10] . ( 2 sec) [ -18425.1213] [ 2785] [depth= 7] . ( 2 sec) [ -18420.0565] [ 2783] [depth= 2] . ( 2 sec) [ -18240.0292] [ 2778] [depth= 2] . ( 2 sec) [ -18235.1881] [ 2766] [depth= 5] . ( 2 sec) [ -17955.6442] [ 2746] [depth= 3] . ( 2 sec) [ -17323.1979] [ 2737] [depth= 2] . ( 2 sec) [ -17263.8327] [ 2713] [depth= 13] . ( 2 sec) [ -17150.9512] [ 2704] [depth= 3] . ( 2 sec) [ -17105.4648] [ 2696] [depth= 17] . ( 2 sec) [ -17010.8482] [ 2673] [depth= 16] . ( 2 sec) [ -15268.3874] [ 2664] [depth= 3] . ( 2 sec) [ -15086.3738] [ 2627] [depth= 21] . ( 2 sec) [ -15022.8624] [ 2589] [depth= 4] . ( 2 sec) [ -14601.2305] [ 2538] [depth= 7] . ( 3 sec) [ -14358.5902] [ 2536] [depth= 3] . ( 3 sec) [ -14205.6869] [ 2536] [depth= 7] . ( 3 sec) [ -14060.4995] [ 2544] [depth= 1] . ( 3 sec) [ -13924.1373] [ 2500] [depth= 2] . ( 3 sec) [ -13696.1161] [ 2479] [depth= 5] . ( 3 sec) [ -13687.4428] [ 2479] [depth= 1] . ( 3 sec) [ -12785.2537] [ 2468] [depth= 7] . ( 3 sec) [ -12723.3877] [ 2468] [depth= 4] . ( 3 sec) [ -12593.9430] [ 2431] [depth= 10] . ( 3 sec) [ -12485.8120] [ 2419] [depth= 7] . ( 3 sec) [ -12403.6824] [ 2415] [depth= 1] . ( 3 sec) [ -12340.0746] [ 2409] [depth= 8] . ( 3 sec) [ -12311.3358] [ 2408] [depth= 19] . ( 3 sec) [ -12253.8818] [ 2391] [depth= 18] . ( 3 sec) [ -12217.1986] [ 2379] [depth= 1] . ( 3 sec) [ -12156.9955] [ 2343] [depth= 9] . ( 3 sec) [ -12095.8877] [ 2328] [depth= 14] . ( 4 sec) [ -11974.9987] [ 2321] [depth= 2] . ( 4 sec) [ -11898.9177] [ 2322] [depth= 1] . ( 4 sec) [ -11850.6871] [ 2295] [depth= 10] . ( 4 sec) [ -11834.8356] [ 2289] [depth= 1] . ( 4 sec) [ -11584.8341] [ 2240] [depth= 6] . ( 4 sec) [ -11400.7380] [ 2169] [depth= 10] . ( 4 sec) [ -11352.0742] [ 2155] [depth= 1] . ( 4 sec) [ -11228.2701] [ 2105] [depth= 5] . ( 4 sec) [ -11174.1221] [ 2095] [depth= 1] . ( 4 sec) [ -10998.4378] [ 2004] [depth= 10] . ( 4 sec) [ -10982.1446] [ 2001] [depth= 1] . ( 4 sec) [ -10858.9875] [ 1976] [depth= 8] . ( 4 sec) [ -10587.0899] [ 1940] [depth= 16] . ( 4 sec) [ -10586.3967] [ 1957] [depth= 1] . ( 4 sec) [ -10554.6931] [ 1960] [depth= 9] . ( 5 sec) [ -10470.1719] [ 1939] [depth= 8] . ( 5 sec) [ -10460.3996] [ 1922] [depth= 3] . ( 5 sec) [ -10459.9319] [ 1912] [depth= 6] . ( 5 sec) [ -10295.3344] [ 1855] [depth= 4] . ( 5 sec) [ -10288.7664] [ 1853] [depth= 7] . ( 5 sec) [ -10249.0255] [ 1849] [depth= 1] . ( 5 sec) [ -10165.4611] [ 1850] [depth= 6] . ( 5 sec) [ -9976.6344] [ 1790] [depth= 6] . ( 5 sec) [ -9955.7417] [ 1786] [depth= 1] . ( 5 sec) [ -9941.5020] [ 1781] [depth= 7] . ( 5 sec) [ -9933.8871] [ 1770] [depth= 8] . ( 5 sec) [ -9887.7483] [ 1759] [depth= 8] . ( 5 sec) [ -9782.1077] [ 1762] [depth= 1] . ( 5 sec) [ -9762.3106] [ 1753] [depth= 2] . ( 5 sec) [ -9755.8326] [ 1750] [depth= 1] . ( 5 sec) [ -9635.0717] [ 1747] [depth= 5] . ( 6 sec) [ -9626.0382] [ 1748] [depth= 4] . ( 6 sec) [ -9621.6533] [ 1746] [depth= 1] . ( 6 sec) [ -9608.8241] [ 1748] [depth= 1] . ( 6 sec) [ -9600.0780] [ 1747] [depth= 1] . ( 6 sec) [ -9592.4480] [ 1742] [depth= 3] . ( 6 sec) [ -9582.4582] [ 1742] [depth= 1] . ( 6 sec) [ -9562.5624] [ 1735] [depth= 9] . ( 6 sec) [ -9401.8253] [ 1676] [depth= 3] . ( 6 sec) [ -9342.0099] [ 1668] [depth= 14] . ( 6 sec) [ -9335.4243] [ 1668] [depth= 5] . ( 6 sec) [ -9322.4099] [ 1659] [depth= 5] . ( 6 sec) [ -9321.9855] [ 1664] [depth= 3] . ( 6 sec) [ -9319.8770] [ 1664] [depth= 1] . ( 6 sec) [ -9311.3773] [ 1664] [depth= 3] . ( 6 sec) [ -9310.4537] [ 1665] [depth= 2] . ( 7 sec) [ -9282.9794] [ 1666] [depth= 3] . ( 7 sec) [ -9278.7593] [ 1664] [depth= 3] . ( 7 sec) [ -9278.2367] [ 1666] [depth= 1] . ( 7 sec) [ -9269.8201] [ 1663] [depth= 2] . ( 7 sec) [ -9182.0242] [ 1646] [depth= 1] . ( 7 sec) [ -9002.9407] [ 1607] [depth= 8] . ( 7 sec) [ -8990.0732] [ 1602] [depth= 3] . ( 7 sec) [ -8972.6971] [ 1600] [depth= 1] . ( 7 sec) [ -8972.2035] [ 1600] [depth= 1] . ( 7 sec) [ -8971.5242] [ 1600] [depth= 2] . ( 7 sec) [ -8948.2810] [ 1598] [depth= 3] . ( 7 sec) [ -8945.9636] [ 1598] [depth= 4] . ( 8 sec) [ -8934.9385] [ 1592] [depth= 3] . ( 8 sec) [ -8908.3031] [ 1584] [depth= 3] . ( 8 sec) [ -8769.6559] [ 1544] [depth= 6] . ( 8 sec) [ -8769.1973] [ 1544] [depth= 1] . ( 8 sec) [ -8769.1463] [ 1543] [depth= 2] . ( 8 sec) [ -8761.8045] [ 1539] [depth= 7] . ( 8 sec) [ -8761.7815] [ 1539] [depth= 1] . ( 8 sec) [ -8709.3606] [ 1528] [depth= 5] . ( 8 sec) [ -8414.4604] [ 1517] [depth= 10] . ( 8 sec) [ -8294.7034] [ 1471] [depth= 7] . ( 8 sec) [ -8247.5531] [ 1471] [depth= 4] . ( 8 sec) [ -8187.4368] [ 1464] [depth= 1] . ( 8 sec) [ -8177.7825] [ 1463] [depth= 2] . ( 8 sec) [ -8177.4630] [ 1462] [depth= 1] . ( 9 sec) [ -8132.2822] [ 1448] [depth= 14] . ( 9 sec) [ -8131.5906] [ 1448] [depth= 1] . ( 9 sec) [ -8131.4437] [ 1448] [depth= 1] . ( 9 sec) [ -8125.7619] [ 1446] [depth= 1] . ( 9 sec) [ -8119.8354] [ 1440] [depth= 1] . ( 9 sec) [ -8106.6940] [ 1438] [depth= 7] . ( 9 sec) [ -8104.5576] [ 1442] [depth= 4] . ( 9 sec) [ -8104.5369] [ 1442] [depth= 1] . ( 9 sec) [ -8100.4628] [ 1442] [depth= 2] . ( 9 sec) [ -7947.2755] [Branch lengths ] . ( 12 sec) [ -7873.0181] [GTR parameters ] . ( 12 sec) [ -7863.7914] [Alpha ][ 0.376653] . ( 12 sec) [ -7840.5694] [ 1428] [depth= 5] . ( 12 sec) [ -7836.8494] [ 1424] [depth= 2] . ( 12 sec) [ -7828.5285] [ 1420] [depth= 3] . ( 12 sec) [ -7800.5476] [ 1407] [depth= 1] . ( 12 sec) [ -7797.6647] [ 1406] [depth= 1] . ( 13 sec) [ -7796.9567] [ 1408] [depth= 1] . ( 13 sec) [ -7791.9921] [ 1404] [depth= 1] . ( 13 sec) [ -7791.9618] [ 1404] [depth= 2] . ( 13 sec) [ -7788.6820] [ 1402] [depth= 2] . ( 13 sec) [ -7786.4273] [ 1402] [depth= 1] . ( 13 sec) [ -7781.2122] [ 1402] [depth= 1] . ( 13 sec) [ -7777.9568] [ 1404] [depth= 1] . ( 14 sec) [ -7777.9229] [ 1404] [depth= 3] . ( 14 sec) [ -7777.5176] [ 1405] [depth= 1] . ( 15 sec) [ -7777.2031] [ 1408] [depth= 1] . ( 15 sec) [ -7756.3337] [ 1399] [depth= 4] . ( 15 sec) [ -7750.8080] [ 1404] [depth= 3] . ( 15 sec) [ -7750.4087] [ 1401] [depth= 3] . ( 15 sec) [ -7749.7389] [ 1402] [depth= 1] . ( 15 sec) [ -7709.8693] [ 1384] [depth= 4] . ( 15 sec) [ -7706.9264] [ 1383] [depth= 2] . ( 16 sec) [ -7704.4081] [ 1387] [depth= 2] . ( 16 sec) [ -7703.1095] [ 1387] [depth= 1] . ( 16 sec) [ -7703.0638] [ 1387] [depth= 3] . ( 16 sec) [ -7698.7922] [ 1384] [depth= 2] . ( 16 sec) [ -7697.4865] [ 1383] [depth= 1] . ( 16 sec) [ -7640.7666] [ 1367] [depth= 3] . ( 16 sec) [ -7639.6401] [ 1368] [depth= 1] . ( 16 sec) [ -7638.7596] [ 1368] [depth= 1] . ( 16 sec) [ -7637.2947] [ 1366] [depth= 1] . ( 17 sec) [ -7637.2589] [ 1366] [depth= 2] . ( 18 sec) [ -7630.3543] [ 1366] [depth= 8] . ( 18 sec) [ -7625.6439] [ 1355] [depth= 3] . ( 18 sec) [ -7622.8743] [ 1355] [depth= 1] . ( 20 sec) [ -7622.0326] [ 1357] [depth= 1] . ( 20 sec) [ -7621.8898] [ 1357] [depth= 1] . ( 22 sec) [ -7587.0879] [Branch lengths ] . ( 23 sec) [ -7586.7843] [GTR parameters ] . ( 23 sec) [ -7586.7389] [Alpha ][ 0.384521] . ( 23 sec) [ -7581.2171] [ 1355] [depth= 1] . ( 24 sec) [ -7579.2367] [ 1350] [depth= 2] . ( 24 sec) [ -7579.1645] [ 1350] [depth= 1] . ( 24 sec) [ -7578.3773] [ 1351] [depth= 2] . ( 24 sec) [ -7577.9373] [ 1352] [depth= 1] . ( 25 sec) [ -7577.2074] [ 1352] [depth= 1] . ( 26 sec) [ -7576.4972] [ 1351] [depth= 1] . ( 27 sec) [ -7576.4728] [ 1349] [depth= 1] . ( 28 sec) [ -7575.5748] [ 1345] [depth= 2] . ( 29 sec) [ -7573.1038] [ 1346] [depth= 1] . ( 30 sec) [ -7572.8283] [ 1346] [depth= 2] . ( 30 sec) [ -7572.8165] [ 1346] [depth= 2] . ( 36 sec) [ -7568.0361] [Branch lengths ] . ( 37 sec) [ -7568.0239] [GTR parameters ] . ( 37 sec) [ -7568.0239] [Alpha ][ 0.384905] . ( 45 sec) [ -7568.0072] [ 1350] [depth= 1] . ( 51 sec) [ -7567.8216] [Branch lengths ] . ( 51 sec) [ -7567.8210] [GTR parameters ] . ( 51 sec) [ -7567.8207] [Alpha ][ 0.384254] . ( 61 sec) [ -7567.6570] [ 1350] [depth= 1] . ( 93 sec) [ -7567.5701] [Branch lengths ] . ( 93 sec) [ -7567.5699] [GTR parameters ] . ( 93 sec) [ -7567.5699] [Alpha ][ 0.384254] . ( 93 sec) [ -7567.5699] [Topology ] . ( 94 sec) [ -7567.5656] [Topology ] . ( 95 sec) [ -7567.5651] [Topology ] . ( 95 sec) [ -7567.5651] [GTR parameters ] . ( 95 sec) [ -7567.5651] [Alpha ][ 0.384254] . ( 95 sec) [ -7567.5651] [Topology ] . ( 96 sec) [ -7567.5650] [Topology ] . ( 96 sec) [ -7567.5650] [GTR parameters ] . ( 96 sec) [ -7567.5650] [Alpha ][ 0.384254] . Checking for NNIs, optimizing five branches... . ( 104 sec) [ -7567.4654] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7567.465356. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17989.9834] [GTR parameters ] . ( 1 sec) [ -17526.4359] [Alpha ][ 0.500960] . ( 1 sec) [ -16874.6996] [ 2972] [depth= 5] . ( 1 sec) [ -16697.0169] [ 2912] [depth= 6] . ( 1 sec) [ -16447.8005] [ 2906] [depth= 3] . ( 1 sec) [ -16394.6445] [ 2909] [depth= 5] . ( 1 sec) [ -16325.8644] [ 2896] [depth= 1] . ( 1 sec) [ -16265.5784] [ 2886] [depth= 4] . ( 1 sec) [ -16144.8926] [ 2886] [depth= 4] . ( 1 sec) [ -16027.8684] [ 2877] [depth= 5] . ( 1 sec) [ -15988.0376] [ 2846] [depth= 1] . ( 1 sec) [ -15893.9749] [ 2837] [depth= 3] . ( 1 sec) [ -15837.6750] [ 2838] [depth= 1] . ( 2 sec) [ -15582.8614] [ 2787] [depth= 14] . ( 2 sec) [ -15389.0188] [ 2778] [depth= 1] . ( 2 sec) [ -15364.1442] [ 2771] [depth= 6] . ( 2 sec) [ -15143.0139] [ 2765] [depth= 3] . ( 2 sec) [ -15013.4094] [ 2768] [depth= 1] . ( 2 sec) [ -14974.7562] [ 2720] [depth= 2] . ( 2 sec) [ -14396.3257] [ 2697] [depth= 13] . ( 2 sec) [ -14215.5384] [ 2681] [depth= 11] . ( 2 sec) [ -14209.7136] [ 2681] [depth= 2] . ( 2 sec) [ -13990.5499] [ 2628] [depth= 5] . ( 2 sec) [ -13884.9004] [ 2625] [depth= 5] . ( 2 sec) [ -13299.1184] [ 2566] [depth= 11] . ( 2 sec) [ -12842.6333] [ 2533] [depth= 9] . ( 2 sec) [ -12273.0482] [ 2525] [depth= 7] . ( 2 sec) [ -12221.5746] [ 2518] [depth= 4] . ( 2 sec) [ -12209.3046] [ 2513] [depth= 3] . ( 3 sec) [ -12180.5923] [ 2497] [depth= 12] . ( 3 sec) [ -12115.3772] [ 2495] [depth= 1] . ( 3 sec) [ -11944.7180] [ 2433] [depth= 2] . ( 3 sec) [ -11883.0639] [ 2395] [depth= 22] . ( 3 sec) [ -11856.1095] [ 2385] [depth= 27] . ( 3 sec) [ -11738.2271] [ 2358] [depth= 11] . ( 3 sec) [ -11680.3448] [ 2339] [depth= 6] . ( 3 sec) [ -11679.7289] [ 2340] [depth= 1] . ( 3 sec) [ -11614.2587] [ 2319] [depth= 23] . ( 3 sec) [ -11546.7199] [ 2304] [depth= 3] . ( 3 sec) [ -11542.6774] [ 2295] [depth= 5] . ( 3 sec) [ -11540.6876] [ 2295] [depth= 1] . ( 3 sec) [ -11489.1305] [ 2268] [depth= 1] . ( 3 sec) [ -11450.8172] [ 2256] [depth= 2] . ( 3 sec) [ -11411.4130] [ 2255] [depth= 8] . ( 4 sec) [ -11320.9360] [ 2237] [depth= 3] . ( 4 sec) [ -11227.0521] [ 2229] [depth= 5] . ( 4 sec) [ -11192.6636] [ 2220] [depth= 4] . ( 4 sec) [ -11056.0622] [ 2218] [depth= 1] . ( 4 sec) [ -10859.0330] [ 2174] [depth= 4] . ( 4 sec) [ -10840.2198] [ 2164] [depth= 1] . ( 4 sec) [ -10567.4068] [ 2097] [depth= 11] . ( 4 sec) [ -10552.5030] [ 2103] [depth= 1] . ( 4 sec) [ -10393.8304] [ 2067] [depth= 8] . ( 4 sec) [ -10361.8592] [ 2056] [depth= 6] . ( 4 sec) [ -10349.1448] [ 2061] [depth= 1] . ( 4 sec) [ -10310.1470] [ 2052] [depth= 3] . ( 4 sec) [ -10282.4232] [ 2047] [depth= 4] . ( 4 sec) [ -10279.5746] [ 2047] [depth= 1] . ( 4 sec) [ -10278.4012] [ 2051] [depth= 1] . ( 4 sec) [ -10227.9568] [ 2042] [depth= 7] . ( 4 sec) [ -10151.8244] [ 2021] [depth= 6] . ( 5 sec) [ -10044.2617] [ 1994] [depth= 9] . ( 5 sec) [ -9984.5251] [ 1990] [depth= 7] . ( 5 sec) [ -9950.9048] [ 1977] [depth= 1] . ( 5 sec) [ -9905.9551] [ 1966] [depth= 7] . ( 5 sec) [ -9884.5297] [ 1970] [depth= 5] . ( 5 sec) [ -9856.2998] [ 1938] [depth= 5] . ( 5 sec) [ -9695.4543] [ 1900] [depth= 12] . ( 5 sec) [ -9642.8187] [ 1874] [depth= 10] . ( 5 sec) [ -9592.6852] [ 1853] [depth= 3] . ( 5 sec) [ -9579.4599] [ 1853] [depth= 2] . ( 5 sec) [ -9576.1449] [ 1853] [depth= 3] . ( 5 sec) [ -9568.2053] [ 1856] [depth= 1] . ( 5 sec) [ -9559.2922] [ 1851] [depth= 2] . ( 6 sec) [ -9557.1402] [ 1851] [depth= 3] . ( 6 sec) [ -9460.5203] [ 1796] [depth= 11] . ( 6 sec) [ -9449.8936] [ 1792] [depth= 1] . ( 6 sec) [ -9333.4849] [ 1781] [depth= 3] . ( 6 sec) [ -9323.0489] [ 1780] [depth= 2] . ( 6 sec) [ -9206.4868] [ 1741] [depth= 2] . ( 6 sec) [ -9166.3813] [ 1728] [depth= 2] . ( 6 sec) [ -9075.0530] [ 1691] [depth= 1] . ( 6 sec) [ -9066.2823] [ 1686] [depth= 5] . ( 6 sec) [ -9065.4172] [ 1686] [depth= 2] . ( 6 sec) [ -9007.1249] [ 1691] [depth= 2] . ( 6 sec) [ -9006.4251] [ 1692] [depth= 1] . ( 6 sec) [ -8928.6584] [ 1672] [depth= 1] . ( 7 sec) [ -8848.4922] [ 1637] [depth= 7] . ( 7 sec) [ -8833.8084] [ 1637] [depth= 2] . ( 7 sec) [ -8833.6879] [ 1641] [depth= 1] . ( 7 sec) [ -8833.2931] [ 1638] [depth= 1] . ( 7 sec) [ -8776.6801] [ 1609] [depth= 11] . ( 7 sec) [ -8774.8171] [ 1608] [depth= 1] . ( 7 sec) [ -8767.9470] [ 1606] [depth= 1] . ( 7 sec) [ -8743.2909] [ 1598] [depth= 1] . ( 7 sec) [ -8696.9388] [ 1575] [depth= 3] . ( 7 sec) [ -8680.1370] [ 1578] [depth= 1] . ( 7 sec) [ -8663.8745] [ 1574] [depth= 4] . ( 7 sec) [ -8643.0672] [ 1562] [depth= 3] . ( 7 sec) [ -8632.5469] [ 1562] [depth= 2] . ( 7 sec) [ -8630.6674] [ 1574] [depth= 1] . ( 7 sec) [ -8623.9656] [ 1571] [depth= 4] . ( 8 sec) [ -8622.7150] [ 1572] [depth= 1] . ( 8 sec) [ -8596.0393] [ 1561] [depth= 1] . ( 8 sec) [ -8595.3613] [ 1565] [depth= 1] . ( 8 sec) [ -8591.5250] [ 1564] [depth= 4] . ( 8 sec) [ -8575.7048] [ 1561] [depth= 2] . ( 8 sec) [ -8556.3034] [ 1561] [depth= 3] . ( 8 sec) [ -8554.1818] [ 1565] [depth= 1] . ( 9 sec) [ -8553.9225] [ 1566] [depth= 1] . ( 9 sec) [ -8551.2189] [ 1566] [depth= 2] . ( 9 sec) [ -8550.6551] [ 1566] [depth= 1] . ( 9 sec) [ -8549.6381] [ 1566] [depth= 1] . ( 9 sec) [ -8157.8692] [ 1501] [depth= 9] . ( 9 sec) [ -8153.3033] [ 1498] [depth= 1] . ( 9 sec) [ -8153.1671] [ 1498] [depth= 3] . ( 9 sec) [ -8140.5780] [ 1486] [depth= 7] . ( 10 sec) [ -8010.7221] [Branch lengths ] . ( 12 sec) [ -7976.8979] [GTR parameters ] . ( 13 sec) [ -7961.4025] [Alpha ][ 0.352491] . ( 13 sec) [ -7956.8447] [ 1489] [depth= 1] . ( 13 sec) [ -7955.0639] [ 1493] [depth= 1] . ( 13 sec) [ -7951.8822] [ 1488] [depth= 2] . ( 13 sec) [ -7951.6178] [ 1488] [depth= 2] . ( 13 sec) [ -7950.7273] [ 1488] [depth= 3] . ( 13 sec) [ -7947.3267] [ 1491] [depth= 1] . ( 13 sec) [ -7946.9816] [ 1485] [depth= 1] . ( 13 sec) [ -7945.7662] [ 1481] [depth= 2] . ( 14 sec) [ -7945.4617] [ 1478] [depth= 1] . ( 14 sec) [ -7945.3507] [ 1478] [depth= 2] . ( 14 sec) [ -7940.8507] [ 1463] [depth= 4] . ( 14 sec) [ -7940.6084] [ 1464] [depth= 2] . ( 14 sec) [ -7922.0909] [ 1467] [depth= 1] . ( 14 sec) [ -7914.8843] [ 1464] [depth= 1] . ( 14 sec) [ -7912.2973] [ 1467] [depth= 1] . ( 15 sec) [ -7911.9907] [ 1468] [depth= 1] . ( 15 sec) [ -7890.1091] [ 1461] [depth= 2] . ( 15 sec) [ -7866.5086] [ 1459] [depth= 9] . ( 15 sec) [ -7861.1700] [ 1453] [depth= 3] . ( 15 sec) [ -7861.0929] [ 1453] [depth= 1] . ( 15 sec) [ -7824.9477] [ 1434] [depth= 1] . ( 15 sec) [ -7813.7840] [ 1433] [depth= 1] . ( 15 sec) [ -7812.4017] [ 1436] [depth= 1] . ( 15 sec) [ -7812.3708] [ 1436] [depth= 2] . ( 16 sec) [ -7812.1923] [ 1431] [depth= 1] . ( 16 sec) [ -7787.7448] [ 1415] [depth= 7] . ( 16 sec) [ -7787.5367] [ 1415] [depth= 2] . ( 16 sec) [ -7787.0462] [ 1415] [depth= 1] . ( 16 sec) [ -7740.5002] [ 1401] [depth= 1] . ( 16 sec) [ -7719.5266] [ 1393] [depth= 4] . ( 16 sec) [ -7719.4976] [ 1393] [depth= 1] . ( 17 sec) [ -7718.2317] [ 1392] [depth= 2] . ( 17 sec) [ -7717.6818] [ 1392] [depth= 1] . ( 17 sec) [ -7717.5591] [ 1392] [depth= 1] . ( 18 sec) [ -7717.3891] [ 1391] [depth= 1] . ( 18 sec) [ -7717.3689] [ 1391] [depth= 1] . ( 18 sec) [ -7716.9230] [ 1391] [depth= 2] . ( 18 sec) [ -7716.8096] [ 1390] [depth= 1] . ( 19 sec) [ -7656.6802] [ 1364] [depth= 8] . ( 19 sec) [ -7656.6677] [ 1364] [depth= 2] . ( 19 sec) [ -7656.2395] [ 1364] [depth= 2] . ( 20 sec) [ -7650.8887] [ 1358] [depth= 2] . ( 20 sec) [ -7649.3960] [ 1358] [depth= 1] . ( 20 sec) [ -7649.1201] [ 1363] [depth= 1] . ( 20 sec) [ -7644.4284] [ 1355] [depth= 7] . ( 20 sec) [ -7642.8497] [ 1354] [depth= 2] . ( 21 sec) [ -7639.9927] [ 1352] [depth= 1] . ( 21 sec) [ -7638.9323] [ 1353] [depth= 1] . ( 21 sec) [ -7638.3320] [ 1353] [depth= 2] . ( 22 sec) [ -7595.2643] [Branch lengths ] . ( 24 sec) [ -7594.8067] [GTR parameters ] . ( 24 sec) [ -7593.7625] [Alpha ][ 0.387476] . ( 26 sec) [ -7593.3109] [ 1354] [depth= 1] . ( 26 sec) [ -7592.6205] [ 1354] [depth= 1] . ( 27 sec) [ -7587.4168] [ 1350] [depth= 6] . ( 27 sec) [ -7587.3172] [ 1350] [depth= 1] . ( 29 sec) [ -7583.8202] [ 1349] [depth= 1] . ( 33 sec) [ -7583.6006] [ 1351] [depth= 1] . ( 33 sec) [ -7583.4199] [ 1356] [depth= 1] . ( 34 sec) [ -7582.3632] [ 1356] [depth= 1] . ( 34 sec) [ -7581.1230] [ 1350] [depth= 1] . ( 34 sec) [ -7580.9354] [ 1351] [depth= 1] . ( 34 sec) [ -7580.8450] [ 1350] [depth= 1] . ( 36 sec) [ -7575.3680] [Branch lengths ] . ( 38 sec) [ -7575.2929] [GTR parameters ] . ( 38 sec) [ -7575.2925] [Alpha ][ 0.386655] . ( 39 sec) [ -7574.7590] [ 1352] [depth= 1] . ( 39 sec) [ -7573.3146] [ 1353] [depth= 2] . ( 39 sec) [ -7573.3024] [ 1353] [depth= 2] . ( 44 sec) [ -7573.0446] [ 1355] [depth= 1] . ( 49 sec) [ -7572.8934] [ 1348] [depth= 1] . ( 49 sec) [ -7572.1423] [ 1352] [depth= 1] . ( 52 sec) [ -7570.3470] [Branch lengths ] . ( 54 sec) [ -7570.3221] [GTR parameters ] . ( 54 sec) [ -7570.3205] [Alpha ][ 0.385049] . ( 58 sec) [ -7570.2411] [ 1351] [depth= 2] . ( 64 sec) [ -7570.1602] [ 1350] [depth= 1] . ( 68 sec) [ -7569.9881] [Branch lengths ] . ( 69 sec) [ -7569.9860] [GTR parameters ] . ( 69 sec) [ -7569.9858] [Alpha ][ 0.385435] . ( 109 sec) [ -7569.8720] [Branch lengths ] . ( 109 sec) [ -7569.8720] [Topology ] . ( 110 sec) [ -7569.8661] [Topology ] . ( 111 sec) [ -7569.8651] [Topology ] . ( 112 sec) [ -7569.8649] [GTR parameters ] . ( 112 sec) [ -7569.8649] [Alpha ][ 0.385435] . ( 112 sec) [ -7569.8649] [Topology ] . ( 113 sec) [ -7569.8646] [Topology ] . ( 113 sec) [ -7569.8646] [GTR parameters ] . ( 113 sec) [ -7569.8646] [Alpha ][ 0.385435] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7569.864569. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7873.6472] [GTR parameters ] . ( 2 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 2 sec) [ -7790.9479] [Topology ] . ( 3 sec) [ -7695.8151] [Topology ] . ( 4 sec) [ -7654.2234] [Topology ] . ( 5 sec) [ -7635.8857] [Topology ] . ( 6 sec) [ -7621.9400] [Topology ] . ( 7 sec) [ -7616.0972] [Topology ] . ( 8 sec) [ -7614.9800] [Topology ] . ( 9 sec) [ -7614.7148] [Topology ] . ( 10 sec) [ -7614.5517] [Topology ] . ( 11 sec) [ -7613.9240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -7608.2048] [GTR parameters ] . ( 20 sec) [ -7600.3742] [Alpha ][ 0.381413] . ( 20 sec) [ -7600.3742] [Topology ] . ( 21 sec) [ -7595.2839] [Topology ] . ( 22 sec) [ -7593.6950] [Topology ] . ( 23 sec) [ -7593.3087] [Topology ] . ( 23 sec) [ -7593.2116] [Topology ] . ( 24 sec) [ -7593.1863] [Topology ] . ( 25 sec) [ -7593.1793] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -7593.1100] [GTR parameters ] . ( 33 sec) [ -7593.1097] [Alpha ][ 0.382068] . ( 33 sec) [ -7593.1097] [Topology ] . ( 34 sec) [ -7593.1069] [Topology ] . ( 35 sec) [ -7593.1060] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -7593.1060] [GTR parameters ] . ( 42 sec) [ -7593.1060] [Alpha ][ 0.382068] . ( 42 sec) [ -7593.1060] [Topology ] . ( 43 sec) [ -7593.1057] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 59 sec) [ -7873.6472] [GTR parameters ] . ( 59 sec) [ -7790.9479] [Alpha ][ 0.500960] . ( 60 sec) [ -7790.3934] [ 1390] [depth= 1] . ( 60 sec) [ -7780.7630] [ 1392] [depth= 1] . ( 60 sec) [ -7772.7156] [ 1390] [depth= 1] . ( 60 sec) [ -7770.5775] [ 1388] [depth= 1] . ( 60 sec) [ -7767.6349] [ 1390] [depth= 1] . ( 60 sec) [ -7762.5253] [ 1389] [depth= 1] . ( 61 sec) [ -7753.2366] [ 1384] [depth= 1] . ( 61 sec) [ -7751.6072] [ 1383] [depth= 1] . ( 61 sec) [ -7750.3527] [ 1384] [depth= 1] . ( 61 sec) [ -7750.1659] [ 1384] [depth= 1] . ( 61 sec) [ -7749.7937] [ 1380] [depth= 2] . ( 61 sec) [ -7746.6235] [ 1379] [depth= 1] . ( 61 sec) [ -7727.1260] [ 1379] [depth= 2] . ( 61 sec) [ -7725.1616] [ 1378] [depth= 2] . ( 61 sec) [ -7724.9374] [ 1375] [depth= 2] . ( 61 sec) [ -7721.9866] [ 1373] [depth= 1] . ( 62 sec) [ -7718.0482] [ 1371] [depth= 1] . ( 62 sec) [ -7716.0328] [ 1372] [depth= 2] . ( 62 sec) [ -7714.6230] [ 1374] [depth= 1] . ( 62 sec) [ -7712.6430] [ 1372] [depth= 1] . ( 62 sec) [ -7710.0737] [ 1370] [depth= 3] . ( 62 sec) [ -7706.1817] [ 1365] [depth= 1] . ( 62 sec) [ -7705.6485] [ 1366] [depth= 1] . ( 63 sec) [ -7692.6834] [ 1371] [depth= 1] . ( 63 sec) [ -7692.3938] [ 1371] [depth= 1] . ( 63 sec) [ -7691.9334] [ 1371] [depth= 1] . ( 63 sec) [ -7691.4335] [ 1371] [depth= 1] . ( 63 sec) [ -7691.4091] [ 1371] [depth= 3] . ( 63 sec) [ -7691.3212] [ 1371] [depth= 3] . ( 63 sec) [ -7690.8156] [ 1371] [depth= 1] . ( 63 sec) [ -7684.8985] [ 1366] [depth= 1] . ( 64 sec) [ -7682.6111] [ 1368] [depth= 2] . ( 64 sec) [ -7681.0068] [ 1366] [depth= 1] . ( 64 sec) [ -7672.1283] [ 1367] [depth= 4] . ( 64 sec) [ -7669.8978] [ 1366] [depth= 1] . ( 64 sec) [ -7665.4158] [ 1364] [depth= 1] . ( 64 sec) [ -7657.0635] [ 1363] [depth= 2] . ( 64 sec) [ -7652.0370] [ 1364] [depth= 4] . ( 65 sec) [ -7651.3717] [ 1364] [depth= 1] . ( 66 sec) [ -7650.4078] [ 1361] [depth= 2] . ( 67 sec) [ -7650.2644] [ 1360] [depth= 2] . ( 67 sec) [ -7649.2167] [ 1364] [depth= 1] . ( 70 sec) [ -7614.2902] [Branch lengths ] . ( 70 sec) [ -7612.3626] [GTR parameters ] . ( 70 sec) [ -7604.6228] [Alpha ][ 0.379693] . ( 70 sec) [ -7603.5880] [ 1360] [depth= 1] . ( 71 sec) [ -7602.9717] [ 1350] [depth= 4] . ( 71 sec) [ -7601.7044] [ 1349] [depth= 2] . ( 72 sec) [ -7601.3500] [ 1348] [depth= 1] . ( 72 sec) [ -7601.2784] [ 1350] [depth= 1] . ( 72 sec) [ -7590.8202] [ 1349] [depth= 7] . ( 72 sec) [ -7590.3864] [ 1350] [depth= 1] . ( 73 sec) [ -7590.3461] [ 1351] [depth= 1] . ( 75 sec) [ -7589.4481] [ 1349] [depth= 1] . ( 75 sec) [ -7589.1696] [ 1348] [depth= 1] . ( 75 sec) [ -7587.5993] [ 1348] [depth= 1] . ( 76 sec) [ -7587.5770] [ 1350] [depth= 1] . ( 76 sec) [ -7583.8405] [ 1351] [depth= 1] . ( 76 sec) [ -7582.9821] [ 1350] [depth= 2] . ( 76 sec) [ -7581.4845] [ 1349] [depth= 1] . ( 77 sec) [ -7581.1903] [ 1352] [depth= 1] . ( 81 sec) [ -7572.8917] [Branch lengths ] . ( 82 sec) [ -7572.5328] [GTR parameters ] . ( 82 sec) [ -7572.5008] [Alpha ][ 0.386412] . ( 85 sec) [ -7572.4363] [ 1355] [depth= 1] . ( 90 sec) [ -7572.3025] [ 1351] [depth= 1] . ( 91 sec) [ -7571.0906] [ 1352] [depth= 2] . ( 96 sec) [ -7570.2470] [Branch lengths ] . ( 96 sec) [ -7570.2305] [GTR parameters ] . ( 97 sec) [ -7570.2288] [Alpha ][ 0.384822] . ( 103 sec) [ -7570.1497] [ 1351] [depth= 2] . ( 112 sec) [ -7569.9900] [Branch lengths ] . ( 112 sec) [ -7569.9889] [GTR parameters ] . ( 112 sec) [ -7569.9887] [Alpha ][ 0.385219] . ( 154 sec) [ -7569.8696] [Branch lengths ] . ( 154 sec) [ -7569.8696] [Topology ] . ( 155 sec) [ -7569.8648] [Topology ] . ( 156 sec) [ -7569.8640] [Topology ] . ( 156 sec) [ -7569.8639] [GTR parameters ] . ( 156 sec) [ -7569.8639] [Alpha ][ 0.385219] . ( 156 sec) [ -7569.8639] [Topology ] . ( 157 sec) [ -7569.8637] [Topology ] . ( 157 sec) [ -7569.8637] [GTR parameters ] . ( 157 sec) [ -7569.8637] [Alpha ][ 0.385219] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7593.105691 . Log likelihood obtained after SPR moves : -7569.863686 . Log likelihood of the current tree: -7569.863686. . Printing the most likely tree in file 'nucleic_M2902_51x908_2006.phy_phyml_tree.txt'... . Best log likelihood : -7567.465356 . Time used 0h2m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 743.01user 0.00system 12:28.54elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps