.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data76.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... . 391 patterns found. (out of a total of 500 sites) . 102 sites without polymorphism (20.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14435.6877] [GTR parameters ] . ( 1 sec) [ -14201.3260] [Alpha ][ 0.500960] . ( 1 sec) [ -13739.2713] [ 2799] [depth= 8] . ( 1 sec) [ -13483.3526] [ 2741] [depth= 6] . ( 1 sec) [ -13336.9249] [ 2732] [depth= 1] . ( 1 sec) [ -13314.0584] [ 2730] [depth= 1] . ( 1 sec) [ -13245.0023] [ 2694] [depth= 1] . ( 1 sec) [ -13227.6535] [ 2689] [depth= 5] . ( 1 sec) [ -13140.7780] [ 2679] [depth= 5] . ( 1 sec) [ -13070.5472] [ 2682] [depth= 1] . ( 1 sec) [ -13069.9110] [ 2691] [depth= 1] . ( 1 sec) [ -12912.1436] [ 2677] [depth= 10] . ( 2 sec) [ -12759.2145] [ 2647] [depth= 10] . ( 2 sec) [ -12666.7921] [ 2606] [depth= 10] . ( 2 sec) [ -12431.4037] [ 2566] [depth= 10] . ( 2 sec) [ -12406.8309] [ 2564] [depth= 1] . ( 2 sec) [ -12367.6275] [ 2563] [depth= 3] . ( 2 sec) [ -12078.3246] [ 2536] [depth= 13] . ( 2 sec) [ -11807.2182] [ 2522] [depth= 4] . ( 2 sec) [ -11452.8170] [ 2446] [depth= 1] . ( 2 sec) [ -11414.5013] [ 2438] [depth= 6] . ( 2 sec) [ -11248.0838] [ 2405] [depth= 3] . ( 2 sec) [ -11242.0767] [ 2405] [depth= 1] . ( 2 sec) [ -11200.7845] [ 2377] [depth= 5] . ( 2 sec) [ -11126.2394] [ 2370] [depth= 4] . ( 2 sec) [ -10924.5430] [ 2275] [depth= 5] . ( 2 sec) [ -10736.9316] [ 2274] [depth= 8] . ( 2 sec) [ -10644.0673] [ 2210] [depth= 10] . ( 2 sec) [ -10472.6494] [ 2173] [depth= 3] . ( 2 sec) [ -10428.1487] [ 2145] [depth= 8] . ( 2 sec) [ -10404.4376] [ 2138] [depth= 1] . ( 2 sec) [ -10397.1394] [ 2142] [depth= 1] . ( 2 sec) [ -10341.3306] [ 2132] [depth= 5] . ( 2 sec) [ -10203.5150] [ 2086] [depth= 2] . ( 3 sec) [ -10149.4959] [ 2061] [depth= 5] . ( 3 sec) [ -10144.2079] [ 2066] [depth= 5] . ( 3 sec) [ -10029.7326] [ 2051] [depth= 5] . ( 3 sec) [ -9820.6003] [ 2012] [depth= 2] . ( 3 sec) [ -9809.2546] [ 2006] [depth= 2] . ( 3 sec) [ -9758.3891] [ 1999] [depth= 3] . ( 3 sec) [ -9711.6542] [ 1966] [depth= 6] . ( 3 sec) [ -9669.9122] [ 1962] [depth= 1] . ( 3 sec) [ -9562.0766] [ 1912] [depth= 1] . ( 3 sec) [ -9549.5427] [ 1909] [depth= 1] . ( 3 sec) [ -9533.5456] [ 1909] [depth= 2] . ( 3 sec) [ -9507.3014] [ 1898] [depth= 1] . ( 3 sec) [ -9507.0208] [ 1894] [depth= 2] . ( 3 sec) [ -9416.7244] [ 1889] [depth= 10] . ( 3 sec) [ -9344.1180] [ 1869] [depth= 1] . ( 3 sec) [ -9334.6570] [ 1873] [depth= 7] . ( 3 sec) [ -9305.2300] [ 1869] [depth= 2] . ( 3 sec) [ -9252.6128] [ 1853] [depth= 2] . ( 3 sec) [ -8850.3157] [ 1851] [depth= 1] . ( 3 sec) [ -8746.3058] [ 1776] [depth= 13] . ( 3 sec) [ -8728.0697] [ 1766] [depth= 8] . ( 3 sec) [ -8622.2646] [ 1725] [depth= 1] . ( 3 sec) [ -8577.4121] [ 1722] [depth= 2] . ( 4 sec) [ -8461.0133] [ 1684] [depth= 8] . ( 4 sec) [ -8452.7782] [ 1674] [depth= 1] . ( 4 sec) [ -8313.9950] [ 1626] [depth= 6] . ( 4 sec) [ -8152.2928] [ 1631] [depth= 8] . ( 4 sec) [ -7976.2091] [ 1589] [depth= 5] . ( 4 sec) [ -7882.9765] [ 1549] [depth= 2] . ( 4 sec) [ -7881.2225] [ 1549] [depth= 1] . ( 4 sec) [ -7869.7441] [ 1543] [depth= 1] . ( 4 sec) [ -7862.1734] [ 1540] [depth= 1] . ( 4 sec) [ -7856.0786] [ 1540] [depth= 1] . ( 4 sec) [ -7808.7743] [ 1518] [depth= 5] . ( 4 sec) [ -7797.8547] [ 1513] [depth= 1] . ( 4 sec) [ -7761.3828] [ 1499] [depth= 1] . ( 4 sec) [ -7722.8555] [ 1486] [depth= 2] . ( 4 sec) [ -7716.1382] [ 1486] [depth= 1] . ( 4 sec) [ -7711.2847] [ 1482] [depth= 1] . ( 4 sec) [ -7690.6878] [ 1465] [depth= 1] . ( 5 sec) [ -7610.0136] [ 1437] [depth= 3] . ( 5 sec) [ -7602.6988] [ 1433] [depth= 1] . ( 5 sec) [ -7524.1666] [Branch lengths ] . ( 5 sec) [ -7521.2402] [GTR parameters ] . ( 6 sec) [ -7486.1583] [Alpha ][ 1.000087] . ( 6 sec) [ -7430.0759] [ 1408] [depth= 1] . ( 6 sec) [ -7427.7518] [ 1408] [depth= 1] . ( 7 sec) [ -7427.2962] [ 1411] [depth= 1] . ( 9 sec) [ -7427.1149] [ 1411] [depth= 1] . ( 9 sec) [ -7417.9065] [Branch lengths ] . ( 9 sec) [ -7417.7747] [GTR parameters ] . ( 9 sec) [ -7417.5067] [Alpha ][ 1.067517] . ( 10 sec) [ -7417.3809] [ 1411] [depth= 1] . ( 13 sec) [ -7417.3550] [ 1411] [depth= 1] . ( 13 sec) [ -7416.1227] [Branch lengths ] . ( 13 sec) [ -7416.1224] [GTR parameters ] . ( 13 sec) [ -7416.1019] [Alpha ][ 1.087493] . ( 17 sec) [ -7415.9258] [Branch lengths ] . ( 28 sec) [ -7415.8925] [ 1408] [depth= 1] . ( 37 sec) [ -7415.8649] [Branch lengths ] . ( 37 sec) [ -7415.8645] [GTR parameters ] . ( 37 sec) [ -7415.8627] [Alpha ][ 1.093323] . ( 37 sec) [ -7415.8627] [Topology ] . ( 38 sec) [ -7415.8600] [Topology ] . ( 39 sec) [ -7415.8591] [Topology ] . ( 39 sec) [ -7415.8591] [GTR parameters ] . ( 39 sec) [ -7415.8591] [Alpha ][ 1.094416] . ( 39 sec) [ -7415.8591] [Topology ] . ( 40 sec) [ -7415.8587] [Topology ] . ( 40 sec) [ -7415.8587] [GTR parameters ] . ( 40 sec) [ -7415.8587] [Alpha ][ 1.094416] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7415.858665. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13899.4768] [GTR parameters ] . ( 1 sec) [ -13678.0888] [Alpha ][ 0.500960] . ( 1 sec) [ -13332.6692] [ 2772] [depth= 3] . ( 1 sec) [ -12944.8108] [ 2702] [depth= 3] . ( 1 sec) [ -12895.7013] [ 2693] [depth= 4] . ( 1 sec) [ -12861.4200] [ 2689] [depth= 7] . ( 1 sec) [ -12726.1585] [ 2640] [depth= 5] . ( 1 sec) [ -12640.4221] [ 2639] [depth= 9] . ( 1 sec) [ -12627.9152] [ 2635] [depth= 3] . ( 1 sec) [ -12627.1801] [ 2609] [depth= 1] . ( 2 sec) [ -12483.3246] [ 2605] [depth= 1] . ( 2 sec) [ -12186.0605] [ 2561] [depth= 9] . ( 2 sec) [ -11969.2674] [ 2558] [depth= 5] . ( 2 sec) [ -11713.7407] [ 2508] [depth= 13] . ( 2 sec) [ -11679.2973] [ 2508] [depth= 1] . ( 2 sec) [ -11380.6733] [ 2422] [depth= 14] . ( 2 sec) [ -11302.6158] [ 2396] [depth= 3] . ( 2 sec) [ -11051.5242] [ 2352] [depth= 10] . ( 2 sec) [ -11029.6248] [ 2351] [depth= 2] . ( 2 sec) [ -10860.1812] [ 2350] [depth= 1] . ( 2 sec) [ -10830.6568] [ 2318] [depth= 3] . ( 2 sec) [ -10808.7266] [ 2314] [depth= 1] . ( 2 sec) [ -10679.5067] [ 2282] [depth= 3] . ( 2 sec) [ -10644.4322] [ 2265] [depth= 2] . ( 2 sec) [ -10578.9681] [ 2250] [depth= 2] . ( 2 sec) [ -10578.6216] [ 2253] [depth= 1] . ( 2 sec) [ -10568.8260] [ 2245] [depth= 1] . ( 2 sec) [ -10537.0924] [ 2207] [depth= 13] . ( 2 sec) [ -10382.3307] [ 2156] [depth= 6] . ( 2 sec) [ -10224.9918] [ 2095] [depth= 13] . ( 2 sec) [ -10090.7910] [ 2064] [depth= 3] . ( 2 sec) [ -10062.9585] [ 2055] [depth= 1] . ( 2 sec) [ -9958.5986] [ 2025] [depth= 8] . ( 3 sec) [ -9611.4504] [ 1956] [depth= 12] . ( 3 sec) [ -9605.3874] [ 1954] [depth= 1] . ( 3 sec) [ -9532.8041] [ 1946] [depth= 2] . ( 3 sec) [ -9510.9782] [ 1948] [depth= 1] . ( 3 sec) [ -9428.1930] [ 1919] [depth= 5] . ( 3 sec) [ -9204.7602] [ 1894] [depth= 7] . ( 3 sec) [ -9174.9278] [ 1897] [depth= 2] . ( 3 sec) [ -9072.9686] [ 1876] [depth= 5] . ( 3 sec) [ -9066.5932] [ 1875] [depth= 1] . ( 3 sec) [ -9055.7539] [ 1868] [depth= 1] . ( 3 sec) [ -9049.8938] [ 1865] [depth= 2] . ( 3 sec) [ -8956.3046] [ 1847] [depth= 2] . ( 3 sec) [ -8808.2985] [ 1802] [depth= 1] . ( 3 sec) [ -8805.2055] [ 1797] [depth= 2] . ( 3 sec) [ -8789.7100] [ 1774] [depth= 2] . ( 3 sec) [ -8720.9627] [ 1759] [depth= 2] . ( 3 sec) [ -8695.3413] [ 1751] [depth= 3] . ( 3 sec) [ -8645.0444] [ 1750] [depth= 1] . ( 3 sec) [ -8569.8684] [ 1707] [depth= 12] . ( 3 sec) [ -8566.6191] [ 1706] [depth= 1] . ( 4 sec) [ -8498.1614] [ 1679] [depth= 1] . ( 4 sec) [ -8319.9985] [ 1639] [depth= 3] . ( 4 sec) [ -8295.4797] [ 1605] [depth= 1] . ( 4 sec) [ -8192.1925] [ 1597] [depth= 2] . ( 4 sec) [ -8183.2452] [ 1591] [depth= 2] . ( 4 sec) [ -8154.0536] [ 1584] [depth= 2] . ( 4 sec) [ -8147.6324] [ 1581] [depth= 1] . ( 4 sec) [ -8051.0431] [ 1558] [depth= 3] . ( 4 sec) [ -8049.2090] [ 1559] [depth= 1] . ( 4 sec) [ -8039.9649] [ 1556] [depth= 1] . ( 4 sec) [ -8038.3477] [ 1555] [depth= 1] . ( 4 sec) [ -7775.9648] [ 1494] [depth= 3] . ( 4 sec) [ -7773.5638] [ 1493] [depth= 1] . ( 4 sec) [ -7737.7881] [ 1467] [depth= 5] . ( 4 sec) [ -7726.1609] [ 1464] [depth= 1] . ( 4 sec) [ -7670.6054] [ 1445] [depth= 2] . ( 4 sec) [ -7641.3219] [ 1441] [depth= 2] . ( 4 sec) [ -7636.3472] [ 1440] [depth= 1] . ( 4 sec) [ -7636.1874] [ 1442] [depth= 1] . ( 5 sec) [ -7633.2339] [ 1445] [depth= 1] . ( 5 sec) [ -7631.1555] [ 1448] [depth= 1] . ( 5 sec) [ -7586.4727] [ 1433] [depth= 1] . ( 5 sec) [ -7565.6567] [ 1428] [depth= 1] . ( 5 sec) [ -7562.0069] [ 1431] [depth= 2] . ( 5 sec) [ -7500.8472] [Branch lengths ] . ( 5 sec) [ -7496.0552] [GTR parameters ] . ( 6 sec) [ -7461.0251] [Alpha ][ 1.000684] . ( 7 sec) [ -7458.6702] [ 1426] [depth= 2] . ( 7 sec) [ -7432.3025] [ 1412] [depth= 1] . ( 7 sec) [ -7429.7504] [ 1408] [depth= 2] . ( 8 sec) [ -7428.8683] [ 1411] [depth= 1] . ( 8 sec) [ -7428.7378] [ 1414] [depth= 1] . ( 8 sec) [ -7428.1926] [ 1411] [depth= 1] . ( 9 sec) [ -7417.4261] [Branch lengths ] . ( 9 sec) [ -7417.3938] [GTR parameters ] . ( 9 sec) [ -7417.0693] [Alpha ][ 1.074993] . ( 10 sec) [ -7416.9152] [ 1411] [depth= 1] . ( 13 sec) [ -7416.0315] [Branch lengths ] . ( 13 sec) [ -7416.0307] [GTR parameters ] . ( 13 sec) [ -7416.0215] [Alpha ][ 1.088404] . ( 17 sec) [ -7415.9167] [Branch lengths ] . ( 37 sec) [ -7415.9022] [Branch lengths ] . ( 37 sec) [ -7415.9022] [Topology ] . ( 38 sec) [ -7415.9010] [Topology ] . ( 38 sec) [ -7415.9006] [Topology ] . ( 38 sec) [ -7415.9005] [GTR parameters ] . ( 38 sec) [ -7415.8989] [Alpha ][ 1.093901] . ( 39 sec) [ -7415.8989] [Topology ] . ( 39 sec) [ -7415.8986] [Topology ] . ( 39 sec) [ -7415.8986] [GTR parameters ] . ( 39 sec) [ -7415.8986] [Alpha ][ 1.093901] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -7415.8974] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7415.897373. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14082.9177] [GTR parameters ] . ( 1 sec) [ -13865.2855] [Alpha ][ 0.500960] . ( 1 sec) [ -13746.7744] [ 2835] [depth= 8] . ( 1 sec) [ -13228.8894] [ 2775] [depth= 8] . ( 1 sec) [ -13125.1956] [ 2771] [depth= 4] . ( 1 sec) [ -13117.1658] [ 2768] [depth= 2] . ( 1 sec) [ -13077.6530] [ 2729] [depth= 8] . ( 1 sec) [ -12913.9997] [ 2730] [depth= 6] . ( 1 sec) [ -12688.3042] [ 2675] [depth= 6] . ( 1 sec) [ -12638.8817] [ 2665] [depth= 2] . ( 1 sec) [ -12582.7836] [ 2626] [depth= 1] . ( 1 sec) [ -12334.1588] [ 2570] [depth= 7] . ( 1 sec) [ -12091.2600] [ 2523] [depth= 4] . ( 1 sec) [ -11985.2893] [ 2512] [depth= 9] . ( 1 sec) [ -11968.8882] [ 2497] [depth= 1] . ( 1 sec) [ -11893.7303] [ 2484] [depth= 9] . ( 1 sec) [ -11875.6567] [ 2468] [depth= 1] . ( 1 sec) [ -11847.9291] [ 2467] [depth= 5] . ( 1 sec) [ -11319.2820] [ 2436] [depth= 1] . ( 1 sec) [ -11134.1886] [ 2424] [depth= 4] . ( 1 sec) [ -11026.3438] [ 2378] [depth= 1] . ( 1 sec) [ -10971.4032] [ 2363] [depth= 4] . ( 2 sec) [ -10878.3667] [ 2333] [depth= 6] . ( 2 sec) [ -10858.8869] [ 2326] [depth= 1] . ( 2 sec) [ -10762.3908] [ 2309] [depth= 6] . ( 2 sec) [ -10693.4155] [ 2281] [depth= 1] . ( 2 sec) [ -10606.4078] [ 2270] [depth= 7] . ( 2 sec) [ -10411.3595] [ 2200] [depth= 3] . ( 2 sec) [ -10363.5338] [ 2207] [depth= 1] . ( 2 sec) [ -10339.6728] [ 2191] [depth= 2] . ( 2 sec) [ -10267.9391] [ 2168] [depth= 10] . ( 2 sec) [ -10181.2461] [ 2166] [depth= 8] . ( 2 sec) [ -10167.6145] [ 2171] [depth= 1] . ( 2 sec) [ -10153.8315] [ 2166] [depth= 1] . ( 2 sec) [ -10028.7827] [ 2132] [depth= 7] . ( 2 sec) [ -9897.2392] [ 2082] [depth= 1] . ( 2 sec) [ -9853.8514] [ 2062] [depth= 1] . ( 2 sec) [ -9792.9534] [ 2071] [depth= 1] . ( 2 sec) [ -9783.6431] [ 2056] [depth= 3] . ( 2 sec) [ -9768.6229] [ 2045] [depth= 1] . ( 2 sec) [ -9650.3678] [ 2008] [depth= 8] . ( 2 sec) [ -9482.0118] [ 1962] [depth= 6] . ( 2 sec) [ -9344.5273] [ 1900] [depth= 7] . ( 2 sec) [ -9264.0662] [ 1897] [depth= 6] . ( 3 sec) [ -8966.6719] [ 1841] [depth= 5] . ( 3 sec) [ -8955.9295] [ 1838] [depth= 2] . ( 3 sec) [ -8953.8601] [ 1838] [depth= 1] . ( 3 sec) [ -8951.0609] [ 1839] [depth= 1] . ( 3 sec) [ -8942.1579] [ 1836] [depth= 1] . ( 3 sec) [ -8871.8326] [ 1798] [depth= 9] . ( 3 sec) [ -8823.2817] [ 1794] [depth= 2] . ( 3 sec) [ -8718.6566] [ 1768] [depth= 1] . ( 3 sec) [ -8685.3649] [ 1766] [depth= 1] . ( 3 sec) [ -8489.5761] [ 1720] [depth= 7] . ( 3 sec) [ -8350.9858] [ 1684] [depth= 7] . ( 3 sec) [ -8346.4825] [ 1687] [depth= 1] . ( 3 sec) [ -8300.1164] [ 1686] [depth= 3] . ( 3 sec) [ -8292.9373] [ 1686] [depth= 1] . ( 3 sec) [ -8228.2811] [ 1662] [depth= 2] . ( 3 sec) [ -8208.2560] [ 1652] [depth= 5] . ( 3 sec) [ -8202.9848] [ 1653] [depth= 1] . ( 3 sec) [ -8198.3608] [ 1645] [depth= 2] . ( 3 sec) [ -8190.4950] [ 1653] [depth= 1] . ( 3 sec) [ -8140.7048] [ 1640] [depth= 2] . ( 4 sec) [ -8140.2406] [ 1643] [depth= 2] . ( 4 sec) [ -8036.5150] [ 1594] [depth= 3] . ( 4 sec) [ -8023.3088] [ 1588] [depth= 2] . ( 4 sec) [ -7936.3949] [ 1558] [depth= 1] . ( 4 sec) [ -7842.5323] [ 1530] [depth= 5] . ( 4 sec) [ -7792.4149] [ 1526] [depth= 1] . ( 4 sec) [ -7792.3181] [ 1527] [depth= 1] . ( 4 sec) [ -7779.8207] [ 1525] [depth= 1] . ( 4 sec) [ -7717.6697] [ 1504] [depth= 1] . ( 4 sec) [ -7715.2805] [ 1499] [depth= 6] . ( 4 sec) [ -7715.1795] [ 1500] [depth= 1] . ( 4 sec) [ -7706.9505] [ 1496] [depth= 1] . ( 4 sec) [ -7681.9080] [ 1474] [depth= 5] . ( 4 sec) [ -7659.1273] [ 1463] [depth= 2] . ( 4 sec) [ -7579.1939] [ 1445] [depth= 1] . ( 4 sec) [ -7568.3877] [ 1439] [depth= 3] . ( 4 sec) [ -7567.9841] [ 1447] [depth= 2] . ( 5 sec) [ -7506.8349] [Branch lengths ] . ( 5 sec) [ -7502.2360] [GTR parameters ] . ( 5 sec) [ -7470.2286] [Alpha ][ 0.974189] . ( 5 sec) [ -7465.0799] [ 1444] [depth= 1] . ( 6 sec) [ -7464.3947] [ 1443] [depth= 1] . ( 6 sec) [ -7456.3613] [ 1436] [depth= 1] . ( 6 sec) [ -7455.3723] [ 1435] [depth= 1] . ( 6 sec) [ -7455.0501] [ 1428] [depth= 1] . ( 6 sec) [ -7439.5311] [ 1421] [depth= 2] . ( 6 sec) [ -7434.8403] [ 1417] [depth= 1] . ( 6 sec) [ -7433.0728] [ 1414] [depth= 1] . ( 7 sec) [ -7430.2899] [ 1411] [depth= 1] . ( 7 sec) [ -7429.3852] [ 1408] [depth= 1] . ( 8 sec) [ -7429.2448] [ 1410] [depth= 1] . ( 8 sec) [ -7429.0346] [ 1408] [depth= 1] . ( 9 sec) [ -7417.5049] [Branch lengths ] . ( 9 sec) [ -7417.4146] [GTR parameters ] . ( 9 sec) [ -7416.7971] [Alpha ][ 1.075135] . ( 10 sec) [ -7416.7723] [ 1411] [depth= 1] . ( 13 sec) [ -7416.0207] [Branch lengths ] . ( 13 sec) [ -7416.0200] [GTR parameters ] . ( 13 sec) [ -7416.0097] [Alpha ][ 1.089321] . ( 16 sec) [ -7415.9726] [ 1408] [depth= 1] . ( 33 sec) [ -7415.8735] [Branch lengths ] . ( 33 sec) [ -7415.8733] [GTR parameters ] . ( 34 sec) [ -7415.8727] [Alpha ][ 1.092615] . ( 34 sec) [ -7415.8727] [Topology ] . ( 34 sec) [ -7415.8638] [Topology ] . ( 35 sec) [ -7415.8608] [Topology ] . ( 36 sec) [ -7415.8596] [Topology ] . ( 37 sec) [ -7415.8590] [Topology ] . ( 37 sec) [ -7415.8590] [GTR parameters ] . ( 37 sec) [ -7415.8589] [Alpha ][ 1.093853] . ( 37 sec) [ -7415.8589] [Topology ] . ( 38 sec) [ -7415.8586] [Topology ] . ( 38 sec) [ -7415.8586] [GTR parameters ] . ( 38 sec) [ -7415.8586] [Alpha ][ 1.093853] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7415.858560. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14274.4046] [GTR parameters ] . ( 1 sec) [ -14042.0597] [Alpha ][ 0.500960] . ( 1 sec) [ -13650.1314] [ 2790] [depth= 8] . ( 1 sec) [ -13280.8991] [ 2717] [depth= 9] . ( 1 sec) [ -12961.7548] [ 2683] [depth= 2] . ( 1 sec) [ -12781.6322] [ 2622] [depth= 1] . ( 1 sec) [ -12662.9105] [ 2588] [depth= 6] . ( 1 sec) [ -12635.7421] [ 2584] [depth= 2] . ( 1 sec) [ -12583.6294] [ 2581] [depth= 1] . ( 1 sec) [ -12571.2982] [ 2576] [depth= 1] . ( 1 sec) [ -12436.4259] [ 2575] [depth= 5] . ( 1 sec) [ -12337.7311] [ 2547] [depth= 2] . ( 1 sec) [ -12318.6065] [ 2545] [depth= 2] . ( 1 sec) [ -12159.7689] [ 2526] [depth= 1] . ( 1 sec) [ -12037.5812] [ 2524] [depth= 3] . ( 1 sec) [ -11946.1177] [ 2516] [depth= 4] . ( 2 sec) [ -11908.7918] [ 2475] [depth= 5] . ( 2 sec) [ -11874.5896] [ 2474] [depth= 2] . ( 2 sec) [ -11829.2678] [ 2463] [depth= 4] . ( 2 sec) [ -11740.5251] [ 2468] [depth= 1] . ( 2 sec) [ -11616.2153] [ 2421] [depth= 3] . ( 2 sec) [ -11449.3494] [ 2390] [depth= 6] . ( 2 sec) [ -11378.8475] [ 2351] [depth= 6] . ( 2 sec) [ -11278.3667] [ 2314] [depth= 11] . ( 2 sec) [ -11139.1519] [ 2305] [depth= 5] . ( 2 sec) [ -11003.2113] [ 2267] [depth= 1] . ( 2 sec) [ -10973.8252] [ 2253] [depth= 5] . ( 2 sec) [ -10871.2709] [ 2206] [depth= 6] . ( 2 sec) [ -10753.4413] [ 2176] [depth= 6] . ( 2 sec) [ -10689.9258] [ 2171] [depth= 10] . ( 2 sec) [ -10684.6561] [ 2164] [depth= 1] . ( 2 sec) [ -10657.0421] [ 2162] [depth= 2] . ( 2 sec) [ -10651.6875] [ 2146] [depth= 2] . ( 2 sec) [ -10468.8731] [ 2107] [depth= 7] . ( 2 sec) [ -10408.4277] [ 2100] [depth= 3] . ( 2 sec) [ -10287.9640] [ 2097] [depth= 12] . ( 2 sec) [ -10264.0936] [ 2080] [depth= 1] . ( 2 sec) [ -10144.0759] [ 2037] [depth= 5] . ( 2 sec) [ -10041.5073] [ 1987] [depth= 4] . ( 3 sec) [ -10032.6975] [ 1985] [depth= 15] . ( 3 sec) [ -9876.1624] [ 1957] [depth= 8] . ( 3 sec) [ -9646.2854] [ 1921] [depth= 9] . ( 3 sec) [ -9608.5391] [ 1907] [depth= 7] . ( 3 sec) [ -9594.1112] [ 1902] [depth= 2] . ( 3 sec) [ -9540.2731] [ 1879] [depth= 6] . ( 3 sec) [ -9427.0639] [ 1876] [depth= 1] . ( 3 sec) [ -9312.9231] [ 1868] [depth= 4] . ( 3 sec) [ -9235.4611] [ 1838] [depth= 4] . ( 3 sec) [ -9003.9673] [ 1771] [depth= 7] . ( 3 sec) [ -8938.9860] [ 1751] [depth= 8] . ( 3 sec) [ -8925.7503] [ 1751] [depth= 1] . ( 3 sec) [ -8746.8643] [ 1707] [depth= 9] . ( 3 sec) [ -8715.2310] [ 1710] [depth= 4] . ( 3 sec) [ -8617.1427] [ 1666] [depth= 3] . ( 3 sec) [ -8510.8514] [ 1639] [depth= 3] . ( 3 sec) [ -8510.5629] [ 1644] [depth= 1] . ( 3 sec) [ -8505.2793] [ 1644] [depth= 1] . ( 3 sec) [ -8504.2793] [ 1644] [depth= 1] . ( 3 sec) [ -8319.6885] [ 1613] [depth= 6] . ( 3 sec) [ -8236.8904] [ 1588] [depth= 1] . ( 3 sec) [ -8235.6115] [ 1589] [depth= 1] . ( 3 sec) [ -8213.3948] [ 1587] [depth= 1] . ( 4 sec) [ -8157.8177] [ 1587] [depth= 2] . ( 4 sec) [ -8070.5746] [ 1567] [depth= 4] . ( 4 sec) [ -8002.0283] [ 1542] [depth= 1] . ( 4 sec) [ -7973.1027] [ 1542] [depth= 1] . ( 4 sec) [ -7950.1911] [ 1534] [depth= 1] . ( 4 sec) [ -7944.6227] [ 1532] [depth= 1] . ( 4 sec) [ -7943.5844] [ 1536] [depth= 2] . ( 4 sec) [ -7886.1757] [ 1537] [depth= 2] . ( 4 sec) [ -7779.3908] [ 1505] [depth= 6] . ( 4 sec) [ -7770.0071] [ 1500] [depth= 2] . ( 4 sec) [ -7741.1691] [ 1494] [depth= 1] . ( 4 sec) [ -7739.7158] [ 1497] [depth= 1] . ( 4 sec) [ -7709.9966] [ 1496] [depth= 1] . ( 4 sec) [ -7693.9190] [ 1494] [depth= 2] . ( 4 sec) [ -7683.3810] [ 1490] [depth= 1] . ( 4 sec) [ -7649.5805] [ 1477] [depth= 1] . ( 4 sec) [ -7614.0678] [ 1457] [depth= 1] . ( 5 sec) [ -7607.8303] [ 1460] [depth= 1] . ( 5 sec) [ -7565.7545] [Branch lengths ] . ( 5 sec) [ -7561.7461] [GTR parameters ] . ( 5 sec) [ -7531.3983] [Alpha ][ 0.953724] . ( 6 sec) [ -7507.8124] [ 1450] [depth= 4] . ( 6 sec) [ -7506.4884] [ 1448] [depth= 1] . ( 6 sec) [ -7506.4302] [ 1445] [depth= 1] . ( 6 sec) [ -7488.6991] [ 1441] [depth= 2] . ( 6 sec) [ -7483.4496] [ 1438] [depth= 1] . ( 6 sec) [ -7464.9847] [ 1430] [depth= 1] . ( 6 sec) [ -7464.2337] [ 1429] [depth= 1] . ( 6 sec) [ -7464.0972] [ 1431] [depth= 1] . ( 6 sec) [ -7464.0064] [ 1433] [depth= 1] . ( 7 sec) [ -7438.4824] [ 1420] [depth= 1] . ( 7 sec) [ -7432.5536] [ 1416] [depth= 1] . ( 7 sec) [ -7432.2184] [ 1416] [depth= 1] . ( 8 sec) [ -7430.0208] [ 1411] [depth= 2] . ( 8 sec) [ -7429.7665] [ 1408] [depth= 1] . ( 9 sec) [ -7417.8161] [Branch lengths ] . ( 9 sec) [ -7417.5767] [GTR parameters ] . ( 9 sec) [ -7416.6002] [Alpha ][ 1.079139] . ( 13 sec) [ -7415.9496] [Branch lengths ] . ( 33 sec) [ -7415.8817] [Branch lengths ] . ( 33 sec) [ -7415.8817] [Topology ] . ( 34 sec) [ -7415.8759] [Topology ] . ( 35 sec) [ -7415.8739] [Topology ] . ( 35 sec) [ -7415.8731] [Topology ] . ( 36 sec) [ -7415.8712] [GTR parameters ] . ( 36 sec) [ -7415.8601] [Alpha ][ 1.093840] . ( 36 sec) [ -7415.8601] [Topology ] . ( 36 sec) [ -7415.8591] [Topology ] . ( 37 sec) [ -7415.8591] [GTR parameters ] . ( 37 sec) [ -7415.8591] [Alpha ][ 1.093840] . ( 37 sec) [ -7415.8591] [Topology ] . ( 37 sec) [ -7415.8587] [Topology ] . ( 37 sec) [ -7415.8587] [GTR parameters ] . ( 38 sec) [ -7415.8587] [Alpha ][ 1.093840] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7415.858659. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14086.5652] [GTR parameters ] . ( 1 sec) [ -13863.5925] [Alpha ][ 0.500960] . ( 1 sec) [ -13309.7133] [ 2828] [depth= 6] . ( 1 sec) [ -13034.9727] [ 2751] [depth= 11] . ( 1 sec) [ -12968.2209] [ 2740] [depth= 4] . ( 1 sec) [ -12959.2991] [ 2740] [depth= 1] . ( 1 sec) [ -12876.9033] [ 2691] [depth= 5] . ( 1 sec) [ -12874.5046] [ 2694] [depth= 1] . ( 1 sec) [ -12783.1890] [ 2681] [depth= 7] . ( 1 sec) [ -12542.6474] [ 2628] [depth= 1] . ( 1 sec) [ -12318.9151] [ 2568] [depth= 13] . ( 1 sec) [ -12271.8933] [ 2563] [depth= 13] . ( 1 sec) [ -12114.9696] [ 2554] [depth= 8] . ( 1 sec) [ -11981.2194] [ 2476] [depth= 5] . ( 1 sec) [ -11935.6568] [ 2475] [depth= 1] . ( 1 sec) [ -11882.8725] [ 2463] [depth= 10] . ( 1 sec) [ -11878.7416] [ 2463] [depth= 1] . ( 1 sec) [ -11840.0328] [ 2446] [depth= 5] . ( 1 sec) [ -11789.7051] [ 2446] [depth= 1] . ( 1 sec) [ -11734.8954] [ 2439] [depth= 9] . ( 1 sec) [ -11660.6083] [ 2440] [depth= 1] . ( 1 sec) [ -11644.7136] [ 2433] [depth= 10] . ( 1 sec) [ -11552.8160] [ 2403] [depth= 10] . ( 1 sec) [ -11511.5317] [ 2400] [depth= 4] . ( 1 sec) [ -11370.8039] [ 2356] [depth= 12] . ( 1 sec) [ -11332.6497] [ 2356] [depth= 1] . ( 2 sec) [ -11320.2530] [ 2376] [depth= 1] . ( 2 sec) [ -11222.6435] [ 2375] [depth= 1] . ( 2 sec) [ -11065.8166] [ 2288] [depth= 5] . ( 2 sec) [ -11061.8367] [ 2286] [depth= 1] . ( 2 sec) [ -10763.7837] [ 2173] [depth= 7] . ( 2 sec) [ -10698.5777] [ 2166] [depth= 8] . ( 2 sec) [ -10651.1591] [ 2164] [depth= 2] . ( 2 sec) [ -10631.5097] [ 2155] [depth= 5] . ( 2 sec) [ -10444.1383] [ 2091] [depth= 5] . ( 2 sec) [ -10430.2025] [ 2093] [depth= 1] . ( 2 sec) [ -10357.8766] [ 2071] [depth= 1] . ( 2 sec) [ -10327.9621] [ 2068] [depth= 1] . ( 2 sec) [ -9949.0481] [ 2032] [depth= 13] . ( 2 sec) [ -9890.3985] [ 2039] [depth= 1] . ( 2 sec) [ -9776.2144] [ 1984] [depth= 1] . ( 2 sec) [ -9735.0975] [ 1961] [depth= 10] . ( 2 sec) [ -9477.1306] [ 1889] [depth= 13] . ( 2 sec) [ -9377.4308] [ 1876] [depth= 8] . ( 2 sec) [ -9206.9290] [ 1832] [depth= 8] . ( 2 sec) [ -9159.4889] [ 1833] [depth= 2] . ( 2 sec) [ -9157.1614] [ 1831] [depth= 10] . ( 3 sec) [ -8988.1016] [ 1824] [depth= 5] . ( 3 sec) [ -8962.1287] [ 1836] [depth= 13] . ( 3 sec) [ -8937.2427] [ 1826] [depth= 3] . ( 3 sec) [ -8874.2505] [ 1812] [depth= 12] . ( 3 sec) [ -8859.6763] [ 1805] [depth= 2] . ( 3 sec) [ -8818.3652] [ 1806] [depth= 1] . ( 3 sec) [ -8734.0591] [ 1804] [depth= 2] . ( 3 sec) [ -8724.0178] [ 1794] [depth= 5] . ( 3 sec) [ -8633.6157] [ 1752] [depth= 4] . ( 3 sec) [ -8537.3189] [ 1724] [depth= 3] . ( 3 sec) [ -8514.4368] [ 1722] [depth= 1] . ( 3 sec) [ -8459.8275] [ 1699] [depth= 3] . ( 3 sec) [ -8435.7587] [ 1694] [depth= 1] . ( 3 sec) [ -8424.5330] [ 1688] [depth= 1] . ( 3 sec) [ -8416.4463] [ 1679] [depth= 1] . ( 3 sec) [ -8391.6410] [ 1667] [depth= 3] . ( 3 sec) [ -8210.7906] [ 1640] [depth= 2] . ( 3 sec) [ -8200.5602] [ 1640] [depth= 1] . ( 4 sec) [ -8111.3448] [ 1613] [depth= 1] . ( 4 sec) [ -8110.5363] [ 1614] [depth= 1] . ( 4 sec) [ -8026.3590] [ 1593] [depth= 6] . ( 4 sec) [ -7999.3533] [ 1584] [depth= 2] . ( 4 sec) [ -7930.3019] [ 1561] [depth= 3] . ( 4 sec) [ -7861.6159] [ 1538] [depth= 2] . ( 4 sec) [ -7844.2648] [ 1536] [depth= 6] . ( 4 sec) [ -7834.3506] [ 1536] [depth= 1] . ( 4 sec) [ -7825.7307] [ 1532] [depth= 2] . ( 4 sec) [ -7824.9431] [ 1533] [depth= 1] . ( 4 sec) [ -7817.5358] [ 1524] [depth= 1] . ( 4 sec) [ -7763.1412] [ 1508] [depth= 1] . ( 4 sec) [ -7751.5235] [ 1509] [depth= 1] . ( 4 sec) [ -7737.4964] [ 1506] [depth= 1] . ( 4 sec) [ -7648.6652] [ 1454] [depth= 4] . ( 5 sec) [ -7550.9064] [Branch lengths ] . ( 5 sec) [ -7546.8400] [GTR parameters ] . ( 5 sec) [ -7514.0445] [Alpha ][ 0.978888] . ( 5 sec) [ -7475.0253] [ 1431] [depth= 4] . ( 5 sec) [ -7474.7857] [ 1434] [depth= 1] . ( 6 sec) [ -7473.5136] [ 1431] [depth= 1] . ( 6 sec) [ -7472.7687] [ 1430] [depth= 1] . ( 6 sec) [ -7459.1570] [ 1421] [depth= 1] . ( 6 sec) [ -7439.0508] [ 1411] [depth= 1] . ( 6 sec) [ -7433.7635] [ 1408] [depth= 1] . ( 7 sec) [ -7433.6433] [ 1408] [depth= 1] . ( 7 sec) [ -7430.6812] [ 1411] [depth= 1] . ( 7 sec) [ -7429.9684] [ 1408] [depth= 1] . ( 9 sec) [ -7418.1675] [Branch lengths ] . ( 9 sec) [ -7418.1072] [GTR parameters ] . ( 9 sec) [ -7417.6102] [Alpha ][ 1.069807] . ( 12 sec) [ -7416.0937] [Branch lengths ] . ( 33 sec) [ -7415.9143] [Branch lengths ] . ( 33 sec) [ -7415.9143] [Topology ] . ( 34 sec) [ -7415.9000] [Topology ] . ( 34 sec) [ -7415.8954] [Topology ] . ( 35 sec) [ -7415.8934] [Topology ] . ( 36 sec) [ -7415.8924] [Topology ] . ( 36 sec) [ -7415.8910] [GTR parameters ] . ( 36 sec) [ -7415.8613] [Alpha ][ 1.092739] . ( 36 sec) [ -7415.8613] [Topology ] . ( 37 sec) [ -7415.8597] [Topology ] . ( 38 sec) [ -7415.8591] [Topology ] . ( 38 sec) [ -7415.8590] [GTR parameters ] . ( 38 sec) [ -7415.8589] [Alpha ][ 1.093832] . ( 38 sec) [ -7415.8589] [Topology ] . ( 39 sec) [ -7415.8586] [Topology ] . ( 39 sec) [ -7415.8586] [GTR parameters ] . ( 39 sec) [ -7415.8586] [Alpha ][ 1.093832] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7415.858589. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7436.387967 . ( 0 sec) [ -7433.1227] [GTR parameters ] . ( 0 sec) [ -7432.9847] [Alpha ][ 1.048573] . ( 0 sec) [ -7432.9847] [Topology ] . ( 1 sec) [ -7418.7794] [Topology ] . ( 2 sec) [ -7416.8646] [Topology ] . ( 2 sec) [ -7416.3286] [Topology ] . ( 3 sec) [ -7416.1296] [Topology ] . ( 4 sec) [ -7416.0462] [Topology ] . ( 5 sec) [ -7416.0093] [Topology ] . ( 5 sec) [ -7415.9925] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.992527 . ( 11 sec) [ -7415.9864] [GTR parameters ] . ( 11 sec) [ -7415.8865] [Alpha ][ 1.090665] . ( 11 sec) [ -7415.8865] [Topology ] . ( 12 sec) [ -7415.8713] [Topology ] . ( 13 sec) [ -7415.8647] [Topology ] . ( 13 sec) [ -7415.8617] [Topology ] . ( 14 sec) [ -7415.8603] [Topology ] . ( 15 sec) [ -7415.8597] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.859668 . ( 20 sec) [ -7415.8596] [GTR parameters ] . ( 20 sec) [ -7415.8590] [Alpha ][ 1.093839] . ( 20 sec) [ -7415.8590] [Topology ] . ( 21 sec) [ -7415.8586] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7415.858641 . ( 26 sec) [ -7415.8586] [GTR parameters ] . ( 26 sec) [ -7415.8586] [Alpha ][ 1.093839] . ( 26 sec) [ -7415.8586] [Topology ] . ( 27 sec) [ -7415.8585] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 37 sec) [ -7433.1227] [GTR parameters ] . ( 37 sec) [ -7432.9847] [Alpha ][ 1.048573] . ( 39 sec) [ -7432.6038] [ 1416] [depth= 2] . ( 39 sec) [ -7432.4633] [ 1415] [depth= 1] . ( 40 sec) [ -7431.5506] [ 1418] [depth= 1] . ( 40 sec) [ -7431.4944] [ 1417] [depth= 1] . ( 41 sec) [ -7431.3212] [ 1418] [depth= 1] . ( 41 sec) [ -7431.0753] [ 1417] [depth= 1] . ( 41 sec) [ -7420.2776] [Branch lengths ] . ( 41 sec) [ -7420.2627] [GTR parameters ] . ( 41 sec) [ -7420.2281] [Alpha ][ 1.073037] . ( 43 sec) [ -7418.6845] [ 1414] [depth= 2] . ( 43 sec) [ -7417.6300] [ 1408] [depth= 1] . ( 45 sec) [ -7415.9768] [Branch lengths ] . ( 45 sec) [ -7415.9709] [GTR parameters ] . ( 45 sec) [ -7415.9536] [Alpha ][ 1.091420] . ( 49 sec) [ -7415.8670] [Branch lengths ] . ( 69 sec) [ -7415.8598] [Branch lengths ] . ( 69 sec) [ -7415.8598] [Topology ] . ( 70 sec) [ -7415.8592] [Topology ] . ( 70 sec) [ -7415.8591] [GTR parameters ] . ( 70 sec) [ -7415.8587] [Alpha ][ 1.093940] . ( 70 sec) [ -7415.8587] [Topology ] . ( 71 sec) [ -7415.8585] [Topology ] . ( 71 sec) [ -7415.8585] [GTR parameters ] . ( 71 sec) [ -7415.8585] [Alpha ][ 1.093940] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7415.858458 . Log likelihood obtained after SPR moves : -7415.858484 . Log likelihood of the current tree: -7415.858458. . Printing the most likely tree in file 'data76.phy_phyml_tree.txt'... . Best log likelihood : -7415.858458 . Time used 0h1m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo