.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data78.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... . 418 patterns found. (out of a total of 500 sites) . 72 sites without polymorphism (14.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17310.1352] [GTR parameters ] . ( 1 sec) [ -17055.2843] [Alpha ][ 0.500960] . ( 1 sec) [ -16770.5416] [ 3527] [depth= 8] . ( 1 sec) [ -16212.3322] [ 3435] [depth= 6] . ( 1 sec) [ -16009.1748] [ 3409] [depth= 4] . ( 1 sec) [ -15713.9518] [ 3403] [depth= 7] . ( 1 sec) [ -15385.9564] [ 3333] [depth= 1] . ( 1 sec) [ -15343.4709] [ 3321] [depth= 6] . ( 1 sec) [ -15242.1385] [ 3315] [depth= 1] . ( 1 sec) [ -15231.4665] [ 3312] [depth= 1] . ( 1 sec) [ -15114.3326] [ 3282] [depth= 16] . ( 1 sec) [ -15094.7318] [ 3280] [depth= 2] . ( 1 sec) [ -14902.7996] [ 3232] [depth= 5] . ( 1 sec) [ -14876.0236] [ 3232] [depth= 6] . ( 2 sec) [ -14850.8125] [ 3229] [depth= 2] . ( 2 sec) [ -14845.4074] [ 3206] [depth= 7] . ( 2 sec) [ -14599.6883] [ 3195] [depth= 4] . ( 2 sec) [ -14398.5426] [ 3178] [depth= 12] . ( 2 sec) [ -14336.4538] [ 3151] [depth= 1] . ( 2 sec) [ -14216.1620] [ 3106] [depth= 15] . ( 2 sec) [ -14209.3833] [ 3109] [depth= 1] . ( 2 sec) [ -14032.0762] [ 3070] [depth= 16] . ( 2 sec) [ -14028.2978] [ 3069] [depth= 1] . ( 2 sec) [ -13862.3384] [ 3018] [depth= 1] . ( 2 sec) [ -13711.3938] [ 3003] [depth= 18] . ( 2 sec) [ -13356.2834] [ 2925] [depth= 7] . ( 2 sec) [ -13076.9542] [ 2935] [depth= 3] . ( 2 sec) [ -12823.6517] [ 2898] [depth= 11] . ( 2 sec) [ -12774.8276] [ 2887] [depth= 3] . ( 2 sec) [ -12762.2949] [ 2877] [depth= 1] . ( 2 sec) [ -12571.3418] [ 2738] [depth= 4] . ( 2 sec) [ -12538.2696] [ 2731] [depth= 1] . ( 2 sec) [ -12090.9377] [ 2639] [depth= 2] . ( 2 sec) [ -11585.5932] [ 2642] [depth= 7] . ( 2 sec) [ -11525.7350] [ 2634] [depth= 3] . ( 2 sec) [ -11490.9877] [ 2608] [depth= 1] . ( 3 sec) [ -11483.9445] [ 2609] [depth= 1] . ( 3 sec) [ -10976.9090] [ 2462] [depth= 5] . ( 3 sec) [ -10603.5766] [ 2407] [depth= 4] . ( 3 sec) [ -10431.4671] [ 2336] [depth= 16] . ( 3 sec) [ -10224.6615] [ 2292] [depth= 12] . ( 3 sec) [ -10140.8811] [ 2259] [depth= 1] . ( 3 sec) [ -10045.0826] [ 2230] [depth= 13] . ( 3 sec) [ -10019.6299] [ 2230] [depth= 1] . ( 3 sec) [ -9874.7305] [ 2190] [depth= 6] . ( 3 sec) [ -9616.8915] [ 2123] [depth= 3] . ( 3 sec) [ -9467.1172] [ 2099] [depth= 11] . ( 3 sec) [ -9421.8268] [ 2097] [depth= 2] . ( 3 sec) [ -9383.4919] [ 2083] [depth= 1] . ( 3 sec) [ -9323.3685] [ 2063] [depth= 2] . ( 3 sec) [ -9320.1254] [ 2056] [depth= 4] . ( 3 sec) [ -9175.4942] [ 2023] [depth= 3] . ( 3 sec) [ -9162.5199] [ 2023] [depth= 1] . ( 3 sec) [ -9159.6501] [ 2028] [depth= 1] . ( 4 sec) [ -9144.6773] [ 2009] [depth= 1] . ( 4 sec) [ -9139.9523] [ 2011] [depth= 1] . ( 4 sec) [ -9074.3199] [ 1999] [depth= 1] . ( 4 sec) [ -9071.4629] [ 2001] [depth= 1] . ( 4 sec) [ -9044.8243] [ 1972] [depth= 6] . ( 4 sec) [ -9005.6966] [ 1940] [depth= 6] . ( 4 sec) [ -8990.7297] [ 1914] [depth= 4] . ( 4 sec) [ -8990.1176] [ 1913] [depth= 1] . ( 4 sec) [ -8990.0002] [ 1913] [depth= 1] . ( 4 sec) [ -8957.3326] [ 1913] [depth= 2] . ( 4 sec) [ -8956.5365] [ 1912] [depth= 1] . ( 4 sec) [ -8915.0606] [ 1895] [depth= 3] . ( 4 sec) [ -8909.7684] [ 1897] [depth= 1] . ( 4 sec) [ -8908.8939] [ 1896] [depth= 1] . ( 4 sec) [ -8903.6195] [ 1896] [depth= 1] . ( 4 sec) [ -8902.0627] [ 1900] [depth= 3] . ( 4 sec) [ -8861.9118] [ 1883] [depth= 5] . ( 4 sec) [ -8806.1738] [ 1859] [depth= 1] . ( 4 sec) [ -8787.5509] [ 1851] [depth= 2] . ( 5 sec) [ -8724.3236] [ 1826] [depth= 3] . ( 5 sec) [ -8713.8051] [ 1822] [depth= 1] . ( 5 sec) [ -8707.6316] [ 1821] [depth= 1] . ( 5 sec) [ -8705.3064] [ 1822] [depth= 1] . ( 5 sec) [ -8674.1085] [ 1803] [depth= 3] . ( 5 sec) [ -8667.2205] [ 1802] [depth= 1] . ( 5 sec) [ -8582.0679] [Branch lengths ] . ( 6 sec) [ -8577.2740] [GTR parameters ] . ( 6 sec) [ -8531.4329] [Alpha ][ 1.000243] . ( 6 sec) [ -8493.6410] [ 1785] [depth= 2] . ( 6 sec) [ -8488.8383] [ 1780] [depth= 2] . ( 6 sec) [ -8487.0347] [ 1778] [depth= 1] . ( 6 sec) [ -8478.0148] [ 1772] [depth= 1] . ( 6 sec) [ -8450.5024] [ 1757] [depth= 1] . ( 6 sec) [ -8449.9573] [ 1756] [depth= 1] . ( 6 sec) [ -8449.5371] [ 1758] [depth= 1] . ( 7 sec) [ -8433.4634] [ 1758] [depth= 3] . ( 7 sec) [ -8432.7545] [ 1756] [depth= 1] . ( 7 sec) [ -8428.2061] [ 1750] [depth= 1] . ( 7 sec) [ -8428.0965] [ 1751] [depth= 1] . ( 7 sec) [ -8427.5819] [ 1754] [depth= 1] . ( 7 sec) [ -8426.8381] [ 1753] [depth= 1] . ( 7 sec) [ -8426.8020] [ 1751] [depth= 1] . ( 7 sec) [ -8422.9101] [ 1747] [depth= 1] . ( 7 sec) [ -8422.8836] [ 1748] [depth= 1] . ( 7 sec) [ -8422.2833] [ 1753] [depth= 1] . ( 8 sec) [ -8419.3890] [ 1745] [depth= 2] . ( 8 sec) [ -8415.8823] [ 1744] [depth= 1] . ( 8 sec) [ -8409.3864] [ 1741] [depth= 2] . ( 8 sec) [ -8408.4646] [ 1742] [depth= 3] . ( 8 sec) [ -8408.2794] [ 1741] [depth= 1] . ( 9 sec) [ -8408.2432] [ 1741] [depth= 1] . ( 9 sec) [ -8408.0046] [ 1741] [depth= 2] . ( 9 sec) [ -8401.6886] [ 1738] [depth= 1] . ( 9 sec) [ -8401.5490] [ 1737] [depth= 1] . ( 9 sec) [ -8389.1346] [Branch lengths ] . ( 10 sec) [ -8388.9947] [GTR parameters ] . ( 10 sec) [ -8386.2853] [Alpha ][ 1.218139] . ( 13 sec) [ -8386.2670] [ 1737] [depth= 1] . ( 14 sec) [ -8385.1548] [Branch lengths ] . ( 14 sec) [ -8385.1528] [GTR parameters ] . ( 14 sec) [ -8385.1405] [Alpha ][ 1.234960] . ( 18 sec) [ -8384.9638] [Branch lengths ] . ( 18 sec) [ -8384.4217] [ 1736] [depth= 1] . ( 38 sec) [ -8383.9985] [Branch lengths ] . ( 38 sec) [ -8383.9969] [GTR parameters ] . ( 38 sec) [ -8383.9958] [Alpha ][ 1.239785] . ( 38 sec) [ -8383.9958] [Topology ] . ( 39 sec) [ -8383.9897] [Topology ] . ( 40 sec) [ -8383.9877] [Topology ] . ( 41 sec) [ -8383.9869] [Topology ] . ( 41 sec) [ -8383.9869] [GTR parameters ] . ( 41 sec) [ -8383.9869] [Alpha ][ 1.239785] . ( 41 sec) [ -8383.9869] [Topology ] . ( 42 sec) [ -8383.9865] [Topology ] . ( 42 sec) [ -8383.9865] [GTR parameters ] . ( 42 sec) [ -8383.9865] [Alpha ][ 1.239785] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8383.986479. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16902.7857] [GTR parameters ] . ( 1 sec) [ -16691.7607] [Alpha ][ 0.500960] . ( 1 sec) [ -16489.0283] [ 3418] [depth= 3] . ( 1 sec) [ -15981.6636] [ 3356] [depth= 3] . ( 1 sec) [ -15813.0098] [ 3328] [depth= 4] . ( 1 sec) [ -15773.3273] [ 3326] [depth= 2] . ( 1 sec) [ -15734.3887] [ 3299] [depth= 3] . ( 1 sec) [ -15714.1131] [ 3302] [depth= 4] . ( 1 sec) [ -15695.0783] [ 3297] [depth= 4] . ( 1 sec) [ -15608.3092] [ 3254] [depth= 1] . ( 1 sec) [ -15537.2662] [ 3242] [depth= 4] . ( 1 sec) [ -15434.1863] [ 3224] [depth= 4] . ( 1 sec) [ -15371.6167] [ 3218] [depth= 7] . ( 1 sec) [ -15204.6333] [ 3210] [depth= 2] . ( 2 sec) [ -14987.8179] [ 3141] [depth= 1] . ( 2 sec) [ -14839.3398] [ 3094] [depth= 7] . ( 2 sec) [ -14728.5066] [ 3050] [depth= 1] . ( 2 sec) [ -14723.0258] [ 3043] [depth= 7] . ( 2 sec) [ -14601.7471] [ 3010] [depth= 2] . ( 2 sec) [ -14492.8105] [ 3005] [depth= 1] . ( 2 sec) [ -13674.5285] [ 2976] [depth= 13] . ( 2 sec) [ -13396.5500] [ 2844] [depth= 1] . ( 2 sec) [ -13075.8067] [ 2783] [depth= 12] . ( 2 sec) [ -12824.0776] [ 2725] [depth= 2] . ( 2 sec) [ -12813.7117] [ 2724] [depth= 1] . ( 2 sec) [ -12656.0213] [ 2682] [depth= 13] . ( 2 sec) [ -12550.1437] [ 2667] [depth= 9] . ( 2 sec) [ -12545.2906] [ 2668] [depth= 1] . ( 2 sec) [ -12468.2656] [ 2652] [depth= 9] . ( 2 sec) [ -12305.5854] [ 2641] [depth= 6] . ( 2 sec) [ -11948.8330] [ 2550] [depth= 12] . ( 2 sec) [ -11792.9115] [ 2522] [depth= 7] . ( 2 sec) [ -11681.9203] [ 2483] [depth= 8] . ( 2 sec) [ -11545.3080] [ 2443] [depth= 3] . ( 2 sec) [ -11482.6330] [ 2428] [depth= 4] . ( 3 sec) [ -11481.6162] [ 2428] [depth= 1] . ( 3 sec) [ -11479.5753] [ 2427] [depth= 2] . ( 3 sec) [ -11427.7594] [ 2411] [depth= 2] . ( 3 sec) [ -11372.4667] [ 2407] [depth= 4] . ( 3 sec) [ -11194.0887] [ 2340] [depth= 5] . ( 3 sec) [ -11062.4377] [ 2316] [depth= 4] . ( 3 sec) [ -11026.6953] [ 2312] [depth= 1] . ( 3 sec) [ -10907.9567] [ 2242] [depth= 8] . ( 3 sec) [ -10907.5290] [ 2240] [depth= 1] . ( 3 sec) [ -10712.9845] [ 2235] [depth= 2] . ( 3 sec) [ -10291.8673] [ 2192] [depth= 6] . ( 3 sec) [ -10282.6776] [ 2187] [depth= 1] . ( 3 sec) [ -10207.7942] [ 2183] [depth= 1] . ( 3 sec) [ -10206.2563] [ 2186] [depth= 2] . ( 3 sec) [ -10094.7005] [ 2143] [depth= 1] . ( 3 sec) [ -10082.3008] [ 2145] [depth= 1] . ( 3 sec) [ -10076.2458] [ 2143] [depth= 1] . ( 3 sec) [ -10068.1886] [ 2142] [depth= 1] . ( 3 sec) [ -10051.1276] [ 2122] [depth= 2] . ( 4 sec) [ -10043.0146] [ 2128] [depth= 1] . ( 4 sec) [ -9773.3880] [ 2082] [depth= 3] . ( 4 sec) [ -9770.2149] [ 2064] [depth= 5] . ( 4 sec) [ -9685.4518] [ 2058] [depth= 2] . ( 4 sec) [ -9642.1451] [ 2043] [depth= 1] . ( 4 sec) [ -9634.3487] [ 2045] [depth= 1] . ( 4 sec) [ -9581.4018] [ 2049] [depth= 4] . ( 4 sec) [ -9557.8414] [ 2039] [depth= 1] . ( 4 sec) [ -9557.0367] [ 2039] [depth= 1] . ( 4 sec) [ -9486.1314] [ 2040] [depth= 2] . ( 4 sec) [ -9460.1020] [ 2047] [depth= 2] . ( 4 sec) [ -9420.5281] [ 2032] [depth= 2] . ( 4 sec) [ -9306.8702] [ 2031] [depth= 2] . ( 4 sec) [ -9279.5158] [ 2021] [depth= 2] . ( 4 sec) [ -9196.3190] [ 1994] [depth= 1] . ( 4 sec) [ -9195.7091] [ 1994] [depth= 1] . ( 4 sec) [ -9184.6201] [ 1990] [depth= 1] . ( 4 sec) [ -9182.9037] [ 1986] [depth= 1] . ( 5 sec) [ -9164.2198] [ 1982] [depth= 1] . ( 5 sec) [ -9162.1044] [ 1985] [depth= 3] . ( 5 sec) [ -9147.0034] [ 1965] [depth= 2] . ( 5 sec) [ -9142.3150] [ 1966] [depth= 1] . ( 5 sec) [ -9131.5184] [ 1968] [depth= 1] . ( 5 sec) [ -9121.0353] [ 1964] [depth= 2] . ( 5 sec) [ -9039.1082] [Branch lengths ] . ( 6 sec) [ -9036.6653] [GTR parameters ] . ( 6 sec) [ -8993.0297] [Alpha ][ 1.000086] . ( 6 sec) [ -8983.9366] [ 1959] [depth= 1] . ( 6 sec) [ -8950.1580] [ 1951] [depth= 1] . ( 6 sec) [ -8933.7528] [ 1936] [depth= 1] . ( 6 sec) [ -8565.8183] [ 1783] [depth= 6] . ( 6 sec) [ -8489.9581] [ 1781] [depth= 1] . ( 7 sec) [ -8456.0070] [ 1763] [depth= 2] . ( 7 sec) [ -8455.0752] [ 1759] [depth= 1] . ( 7 sec) [ -8443.8012] [ 1755] [depth= 1] . ( 7 sec) [ -8430.4158] [ 1748] [depth= 1] . ( 7 sec) [ -8430.0266] [ 1749] [depth= 1] . ( 7 sec) [ -8411.4000] [ 1743] [depth= 1] . ( 7 sec) [ -8411.3162] [ 1746] [depth= 1] . ( 7 sec) [ -8410.9852] [ 1747] [depth= 1] . ( 8 sec) [ -8410.5080] [ 1742] [depth= 1] . ( 8 sec) [ -8409.5457] [ 1742] [depth= 1] . ( 8 sec) [ -8408.6096] [ 1734] [depth= 2] . ( 8 sec) [ -8407.1858] [ 1736] [depth= 1] . ( 8 sec) [ -8407.1520] [ 1735] [depth= 1] . ( 9 sec) [ -8407.0707] [ 1736] [depth= 1] . ( 9 sec) [ -8406.7484] [ 1737] [depth= 2] . ( 9 sec) [ -8404.6661] [ 1737] [depth= 1] . ( 9 sec) [ -8404.4828] [ 1738] [depth= 1] . ( 9 sec) [ -8404.0463] [ 1742] [depth= 1] . ( 9 sec) [ -8401.8749] [ 1738] [depth= 2] . ( 10 sec) [ -8388.7999] [Branch lengths ] . ( 10 sec) [ -8388.3661] [GTR parameters ] . ( 10 sec) [ -8385.5494] [Alpha ][ 1.223211] . ( 14 sec) [ -8384.3563] [Branch lengths ] . ( 34 sec) [ -8384.1446] [Branch lengths ] . ( 34 sec) [ -8384.1446] [Topology ] . ( 35 sec) [ -8384.0920] [Topology ] . ( 36 sec) [ -8384.0176] [Topology ] . ( 36 sec) [ -8384.0070] [Topology ] . ( 37 sec) [ -8384.0038] [Topology ] . ( 38 sec) [ -8384.0024] [Topology ] . ( 39 sec) [ -8384.0017] [Topology ] . ( 39 sec) [ -8383.9992] [GTR parameters ] . ( 39 sec) [ -8383.9873] [Alpha ][ 1.239803] . ( 39 sec) [ -8383.9873] [Topology ] . ( 40 sec) [ -8383.9866] [Topology ] . ( 40 sec) [ -8383.9866] [GTR parameters ] . ( 40 sec) [ -8383.9866] [Alpha ][ 1.239803] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8383.986560. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17662.3582] [GTR parameters ] . ( 0 sec) [ -17421.2374] [Alpha ][ 0.500960] . ( 0 sec) [ -17252.8646] [ 3553] [depth= 8] . ( 1 sec) [ -16922.8297] [ 3488] [depth= 8] . ( 1 sec) [ -16854.8656] [ 3482] [depth= 4] . ( 1 sec) [ -16806.2102] [ 3481] [depth= 2] . ( 1 sec) [ -16532.0942] [ 3477] [depth= 8] . ( 1 sec) [ -16494.9280] [ 3475] [depth= 2] . ( 1 sec) [ -15662.5613] [ 3301] [depth= 11] . ( 1 sec) [ -15652.2957] [ 3282] [depth= 5] . ( 1 sec) [ -15300.7485] [ 3181] [depth= 17] . ( 1 sec) [ -15118.9767] [ 3183] [depth= 15] . ( 1 sec) [ -14402.2948] [ 3013] [depth= 7] . ( 1 sec) [ -14282.7332] [ 2968] [depth= 4] . ( 1 sec) [ -14050.0784] [ 2966] [depth= 4] . ( 1 sec) [ -13685.3916] [ 2882] [depth= 10] . ( 1 sec) [ -13656.0785] [ 2879] [depth= 1] . ( 1 sec) [ -13534.1926] [ 2876] [depth= 7] . ( 1 sec) [ -13100.6470] [ 2816] [depth= 7] . ( 1 sec) [ -12737.6763] [ 2773] [depth= 9] . ( 1 sec) [ -12425.2099] [ 2648] [depth= 7] . ( 1 sec) [ -12282.8054] [ 2683] [depth= 6] . ( 1 sec) [ -11968.0200] [ 2630] [depth= 5] . ( 1 sec) [ -11683.3803] [ 2560] [depth= 1] . ( 1 sec) [ -11653.2274] [ 2554] [depth= 8] . ( 1 sec) [ -11579.2559] [ 2574] [depth= 2] . ( 1 sec) [ -11465.7733] [ 2511] [depth= 11] . ( 2 sec) [ -11457.8202] [ 2510] [depth= 1] . ( 2 sec) [ -11447.5903] [ 2516] [depth= 5] . ( 2 sec) [ -11344.8230] [ 2500] [depth= 6] . ( 2 sec) [ -11214.7987] [ 2477] [depth= 7] . ( 2 sec) [ -11094.8884] [ 2421] [depth= 1] . ( 2 sec) [ -11003.2265] [ 2421] [depth= 8] . ( 2 sec) [ -10958.1401] [ 2419] [depth= 2] . ( 2 sec) [ -10770.3496] [ 2339] [depth= 12] . ( 2 sec) [ -10584.1100] [ 2282] [depth= 8] . ( 2 sec) [ -10497.1329] [ 2282] [depth= 7] . ( 2 sec) [ -10486.9928] [ 2277] [depth= 1] . ( 2 sec) [ -10460.4927] [ 2275] [depth= 1] . ( 2 sec) [ -10317.0522] [ 2252] [depth= 4] . ( 2 sec) [ -10173.1821] [ 2211] [depth= 3] . ( 2 sec) [ -10155.9489] [ 2169] [depth= 1] . ( 2 sec) [ -10093.4214] [ 2152] [depth= 3] . ( 2 sec) [ -10011.8602] [ 2134] [depth= 1] . ( 2 sec) [ -9970.2088] [ 2110] [depth= 4] . ( 2 sec) [ -9954.3135] [ 2107] [depth= 1] . ( 2 sec) [ -9931.0263] [ 2108] [depth= 1] . ( 2 sec) [ -9880.5052] [ 2089] [depth= 1] . ( 2 sec) [ -9835.9535] [ 2089] [depth= 1] . ( 3 sec) [ -9807.1944] [ 2087] [depth= 5] . ( 3 sec) [ -9791.2756] [ 2089] [depth= 1] . ( 3 sec) [ -9757.1030] [ 2080] [depth= 6] . ( 3 sec) [ -9672.1005] [ 2053] [depth= 6] . ( 3 sec) [ -9534.7992] [ 2002] [depth= 6] . ( 3 sec) [ -9437.2528] [ 2012] [depth= 1] . ( 3 sec) [ -9358.0316] [ 2004] [depth= 7] . ( 3 sec) [ -9355.7050] [ 2008] [depth= 3] . ( 3 sec) [ -9352.2799] [ 1996] [depth= 1] . ( 3 sec) [ -9350.4121] [ 1991] [depth= 4] . ( 3 sec) [ -9156.0652] [ 1954] [depth= 2] . ( 3 sec) [ -9138.6074] [ 1949] [depth= 2] . ( 3 sec) [ -9121.4253] [ 1942] [depth= 2] . ( 3 sec) [ -9068.8130] [ 1915] [depth= 1] . ( 3 sec) [ -8972.0673] [ 1886] [depth= 2] . ( 3 sec) [ -8966.0754] [ 1885] [depth= 1] . ( 3 sec) [ -8957.8468] [ 1883] [depth= 1] . ( 4 sec) [ -8917.4854] [ 1866] [depth= 1] . ( 4 sec) [ -8908.9884] [ 1866] [depth= 1] . ( 4 sec) [ -8897.7020] [ 1870] [depth= 1] . ( 4 sec) [ -8896.6586] [ 1873] [depth= 2] . ( 4 sec) [ -8832.5761] [ 1873] [depth= 1] . ( 4 sec) [ -8831.6044] [ 1879] [depth= 7] . ( 4 sec) [ -8830.8943] [ 1880] [depth= 1] . ( 4 sec) [ -8775.9668] [ 1862] [depth= 2] . ( 4 sec) [ -8773.2016] [ 1861] [depth= 1] . ( 4 sec) [ -8767.1663] [ 1861] [depth= 1] . ( 4 sec) [ -8721.0776] [ 1837] [depth= 1] . ( 4 sec) [ -8704.0948] [ 1824] [depth= 1] . ( 4 sec) [ -8665.1212] [ 1803] [depth= 4] . ( 4 sec) [ -8662.6004] [ 1803] [depth= 1] . ( 5 sec) [ -8583.8036] [Branch lengths ] . ( 5 sec) [ -8580.6394] [GTR parameters ] . ( 5 sec) [ -8527.7159] [Alpha ][ 1.000490] . ( 5 sec) [ -8527.6428] [ 1802] [depth= 1] . ( 5 sec) [ -8527.0240] [ 1802] [depth= 1] . ( 6 sec) [ -8526.5164] [ 1803] [depth= 1] . ( 6 sec) [ -8525.5339] [ 1800] [depth= 3] . ( 6 sec) [ -8453.4154] [ 1772] [depth= 1] . ( 6 sec) [ -8452.7005] [ 1772] [depth= 1] . ( 6 sec) [ -8419.2385] [ 1756] [depth= 2] . ( 6 sec) [ -8409.1131] [ 1748] [depth= 1] . ( 6 sec) [ -8407.0615] [ 1742] [depth= 3] . ( 7 sec) [ -8406.8826] [ 1744] [depth= 1] . ( 7 sec) [ -8404.5099] [ 1739] [depth= 1] . ( 7 sec) [ -8404.1448] [ 1739] [depth= 2] . ( 7 sec) [ -8401.7443] [ 1734] [depth= 1] . ( 7 sec) [ -8401.6849] [ 1732] [depth= 1] . ( 7 sec) [ -8401.1381] [ 1732] [depth= 1] . ( 8 sec) [ -8400.9664] [ 1733] [depth= 1] . ( 8 sec) [ -8399.4035] [ 1737] [depth= 1] . ( 8 sec) [ -8399.2160] [ 1736] [depth= 1] . ( 9 sec) [ -8391.4677] [Branch lengths ] . ( 9 sec) [ -8391.3684] [GTR parameters ] . ( 9 sec) [ -8388.2392] [Alpha ][ 1.236218] . ( 9 sec) [ -8387.7369] [ 1738] [depth= 1] . ( 9 sec) [ -8387.6588] [ 1739] [depth= 1] . ( 10 sec) [ -8386.7780] [ 1738] [depth= 1] . ( 10 sec) [ -8386.4621] [ 1741] [depth= 1] . ( 11 sec) [ -8385.9992] [ 1740] [depth= 1] . ( 11 sec) [ -8385.8640] [ 1741] [depth= 1] . ( 12 sec) [ -8385.8119] [ 1738] [depth= 1] . ( 13 sec) [ -8384.1842] [Branch lengths ] . ( 13 sec) [ -8384.1743] [GTR parameters ] . ( 13 sec) [ -8384.1742] [Alpha ][ 1.237919] . ( 17 sec) [ -8384.0023] [Branch lengths ] . ( 38 sec) [ -8383.9879] [Branch lengths ] . ( 38 sec) [ -8383.9879] [Topology ] . ( 38 sec) [ -8383.9870] [Topology ] . ( 39 sec) [ -8383.9869] [GTR parameters ] . ( 39 sec) [ -8383.9867] [Alpha ][ 1.239832] . ( 39 sec) [ -8383.9867] [Topology ] . ( 39 sec) [ -8383.9864] [Topology ] . ( 40 sec) [ -8383.9864] [GTR parameters ] . ( 40 sec) [ -8383.9864] [Alpha ][ 1.239832] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8383.986414. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16388.8165] [GTR parameters ] . ( 0 sec) [ -16173.0975] [Alpha ][ 0.500960] . ( 0 sec) [ -15924.2531] [ 3486] [depth= 8] . ( 0 sec) [ -15496.1641] [ 3415] [depth= 9] . ( 1 sec) [ -15340.2952] [ 3393] [depth= 8] . ( 1 sec) [ -15235.4370] [ 3351] [depth= 1] . ( 1 sec) [ -15194.6054] [ 3348] [depth= 6] . ( 1 sec) [ -15181.2579] [ 3339] [depth= 2] . ( 1 sec) [ -15179.7075] [ 3341] [depth= 2] . ( 1 sec) [ -15137.0806] [ 3318] [depth= 1] . ( 1 sec) [ -15031.3463] [ 3309] [depth= 6] . ( 1 sec) [ -14887.7048] [ 3290] [depth= 3] . ( 1 sec) [ -14858.0801] [ 3295] [depth= 5] . ( 1 sec) [ -14688.0272] [ 3254] [depth= 6] . ( 1 sec) [ -14569.6320] [ 3230] [depth= 4] . ( 1 sec) [ -14476.7763] [ 3216] [depth= 7] . ( 1 sec) [ -14293.8211] [ 3187] [depth= 5] . ( 1 sec) [ -14266.5904] [ 3178] [depth= 10] . ( 1 sec) [ -14079.7114] [ 3179] [depth= 1] . ( 1 sec) [ -13826.5009] [ 3139] [depth= 2] . ( 1 sec) [ -13713.6344] [ 3104] [depth= 9] . ( 1 sec) [ -13419.9835] [ 3000] [depth= 4] . ( 1 sec) [ -13263.6200] [ 3006] [depth= 1] . ( 1 sec) [ -13059.4329] [ 2966] [depth= 9] . ( 1 sec) [ -12983.8456] [ 2979] [depth= 1] . ( 1 sec) [ -12639.0026] [ 2919] [depth= 2] . ( 1 sec) [ -12318.0994] [ 2839] [depth= 8] . ( 1 sec) [ -12138.7856] [ 2778] [depth= 12] . ( 2 sec) [ -11954.3030] [ 2720] [depth= 8] . ( 2 sec) [ -11871.2917] [ 2676] [depth= 6] . ( 2 sec) [ -11862.8357] [ 2649] [depth= 12] . ( 2 sec) [ -11689.3893] [ 2608] [depth= 13] . ( 2 sec) [ -11349.1362] [ 2490] [depth= 3] . ( 2 sec) [ -11277.3582] [ 2481] [depth= 6] . ( 2 sec) [ -11274.0532] [ 2479] [depth= 1] . ( 2 sec) [ -11177.0729] [ 2473] [depth= 5] . ( 2 sec) [ -11104.9772] [ 2444] [depth= 1] . ( 2 sec) [ -11059.4649] [ 2438] [depth= 2] . ( 2 sec) [ -11020.0315] [ 2441] [depth= 1] . ( 2 sec) [ -10871.3021] [ 2404] [depth= 1] . ( 2 sec) [ -10773.2028] [ 2337] [depth= 10] . ( 2 sec) [ -10727.0801] [ 2321] [depth= 1] . ( 2 sec) [ -10627.9407] [ 2298] [depth= 11] . ( 2 sec) [ -10605.4906] [ 2282] [depth= 1] . ( 2 sec) [ -10395.8374] [ 2200] [depth= 10] . ( 2 sec) [ -10250.6310] [ 2195] [depth= 2] . ( 2 sec) [ -10147.6340] [ 2175] [depth= 1] . ( 2 sec) [ -10075.8049] [ 2151] [depth= 9] . ( 2 sec) [ -10064.3852] [ 2149] [depth= 1] . ( 2 sec) [ -10061.5830] [ 2150] [depth= 1] . ( 2 sec) [ -9991.3730] [ 2192] [depth= 2] . ( 3 sec) [ -9907.0227] [ 2156] [depth= 9] . ( 3 sec) [ -9898.6681] [ 2148] [depth= 3] . ( 3 sec) [ -9897.4530] [ 2147] [depth= 1] . ( 3 sec) [ -9894.9364] [ 2148] [depth= 1] . ( 3 sec) [ -9877.8779] [ 2145] [depth= 2] . ( 3 sec) [ -9816.1336] [ 2124] [depth= 1] . ( 3 sec) [ -9641.6109] [ 2102] [depth= 1] . ( 3 sec) [ -9633.0433] [ 2096] [depth= 1] . ( 3 sec) [ -9591.3618] [ 2087] [depth= 2] . ( 3 sec) [ -9544.9904] [ 2058] [depth= 4] . ( 3 sec) [ -9397.2868] [ 2051] [depth= 4] . ( 3 sec) [ -9315.9270] [ 2030] [depth= 1] . ( 3 sec) [ -9263.7316] [ 2006] [depth= 1] . ( 3 sec) [ -9034.5484] [ 1893] [depth= 2] . ( 3 sec) [ -8908.6737] [ 1853] [depth= 6] . ( 3 sec) [ -8908.5390] [ 1853] [depth= 1] . ( 3 sec) [ -8838.5293] [ 1824] [depth= 1] . ( 3 sec) [ -8835.5317] [ 1825] [depth= 1] . ( 3 sec) [ -8832.1727] [ 1824] [depth= 1] . ( 3 sec) [ -8820.4416] [ 1820] [depth= 1] . ( 4 sec) [ -8807.2346] [ 1817] [depth= 2] . ( 4 sec) [ -8772.1154] [ 1801] [depth= 1] . ( 4 sec) [ -8760.0804] [ 1800] [depth= 1] . ( 4 sec) [ -8757.8416] [ 1800] [depth= 1] . ( 4 sec) [ -8756.5355] [ 1801] [depth= 2] . ( 4 sec) [ -8713.9302] [ 1820] [depth= 1] . ( 4 sec) [ -8655.8465] [ 1801] [depth= 1] . ( 4 sec) [ -8642.1584] [ 1802] [depth= 1] . ( 4 sec) [ -8641.6949] [ 1805] [depth= 1] . ( 4 sec) [ -8638.1175] [ 1806] [depth= 1] . ( 4 sec) [ -8622.9340] [ 1802] [depth= 1] . ( 5 sec) [ -8573.3166] [Branch lengths ] . ( 5 sec) [ -8571.0461] [GTR parameters ] . ( 5 sec) [ -8521.9115] [Alpha ][ 1.000386] . ( 6 sec) [ -8519.9566] [ 1800] [depth= 1] . ( 6 sec) [ -8470.7999] [ 1784] [depth= 1] . ( 6 sec) [ -8467.5528] [ 1771] [depth= 3] . ( 6 sec) [ -8442.9117] [ 1759] [depth= 3] . ( 6 sec) [ -8438.8600] [ 1756] [depth= 1] . ( 6 sec) [ -8431.0621] [ 1739] [depth= 3] . ( 6 sec) [ -8431.0482] [ 1739] [depth= 1] . ( 6 sec) [ -8428.6172] [ 1732] [depth= 1] . ( 7 sec) [ -8427.8269] [ 1731] [depth= 1] . ( 7 sec) [ -8422.7345] [ 1736] [depth= 1] . ( 7 sec) [ -8421.6620] [ 1732] [depth= 1] . ( 7 sec) [ -8415.3346] [ 1727] [depth= 1] . ( 7 sec) [ -8414.3393] [ 1727] [depth= 1] . ( 7 sec) [ -8411.3896] [ 1725] [depth= 1] . ( 7 sec) [ -8406.9291] [ 1725] [depth= 1] . ( 7 sec) [ -8406.1569] [ 1727] [depth= 1] . ( 7 sec) [ -8402.8045] [ 1727] [depth= 1] . ( 7 sec) [ -8402.7829] [ 1726] [depth= 1] . ( 8 sec) [ -8402.4384] [ 1731] [depth= 1] . ( 8 sec) [ -8402.2463] [ 1731] [depth= 1] . ( 8 sec) [ -8401.9130] [ 1731] [depth= 1] . ( 9 sec) [ -8394.5081] [Branch lengths ] . ( 9 sec) [ -8394.3977] [GTR parameters ] . ( 9 sec) [ -8391.3639] [Alpha ][ 1.232827] . ( 11 sec) [ -8391.3455] [ 1731] [depth= 1] . ( 13 sec) [ -8390.1478] [Branch lengths ] . ( 13 sec) [ -8390.1455] [GTR parameters ] . ( 13 sec) [ -8390.1365] [Alpha ][ 1.247463] . ( 14 sec) [ -8389.9625] [ 1726] [depth= 1] . ( 16 sec) [ -8389.4688] [Branch lengths ] . ( 16 sec) [ -8389.4672] [GTR parameters ] . ( 16 sec) [ -8389.4637] [Alpha ][ 1.256579] . ( 17 sec) [ -8388.5779] [ 1737] [depth= 1] . ( 22 sec) [ -8388.2993] [ 1740] [depth= 1] . ( 23 sec) [ -8387.4363] [ 1741] [depth= 1] . ( 26 sec) [ -8385.9213] [ 1740] [depth= 1] . ( 27 sec) [ -8385.8525] [ 1738] [depth= 1] . ( 28 sec) [ -8385.8332] [ 1739] [depth= 1] . ( 29 sec) [ -8385.2818] [ 1740] [depth= 1] . ( 36 sec) [ -8384.1240] [Branch lengths ] . ( 36 sec) [ -8384.1184] [GTR parameters ] . ( 36 sec) [ -8384.1110] [Alpha ][ 1.242983] . ( 56 sec) [ -8384.0895] [Branch lengths ] . ( 56 sec) [ -8384.0895] [Topology ] . ( 57 sec) [ -8384.0596] [Topology ] . ( 58 sec) [ -8383.9963] [Topology ] . ( 58 sec) [ -8383.9910] [Topology ] . ( 59 sec) [ -8383.9903] [Topology ] . ( 59 sec) [ -8383.9868] [GTR parameters ] . ( 59 sec) [ -8383.9864] [Alpha ][ 1.239758] . ( 59 sec) [ -8383.9864] [Topology ] . ( 60 sec) [ -8383.9863] [Topology ] . ( 60 sec) [ -8383.9862] [GTR parameters ] . ( 60 sec) [ -8383.9862] [Alpha ][ 1.239758] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8383.986249. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17764.5188] [GTR parameters ] . ( 1 sec) [ -17519.2713] [Alpha ][ 0.500960] . ( 1 sec) [ -17301.6904] [ 3538] [depth= 7] . ( 1 sec) [ -16789.1100] [ 3469] [depth= 11] . ( 1 sec) [ -16748.7012] [ 3450] [depth= 4] . ( 1 sec) [ -16721.7094] [ 3447] [depth= 3] . ( 1 sec) [ -16683.9608] [ 3434] [depth= 2] . ( 1 sec) [ -16676.9738] [ 3433] [depth= 3] . ( 1 sec) [ -16674.4287] [ 3424] [depth= 3] . ( 1 sec) [ -16646.0616] [ 3423] [depth= 1] . ( 1 sec) [ -16394.9764] [ 3358] [depth= 8] . ( 1 sec) [ -16314.6726] [ 3341] [depth= 6] . ( 1 sec) [ -16053.6717] [ 3248] [depth= 6] . ( 1 sec) [ -15928.7860] [ 3244] [depth= 7] . ( 1 sec) [ -15642.3645] [ 3183] [depth= 6] . ( 1 sec) [ -15569.4613] [ 3182] [depth= 1] . ( 1 sec) [ -15311.7434] [ 3177] [depth= 4] . ( 1 sec) [ -15297.8223] [ 3171] [depth= 2] . ( 1 sec) [ -15274.1191] [ 3171] [depth= 1] . ( 1 sec) [ -15130.5171] [ 3150] [depth= 9] . ( 1 sec) [ -15082.8309] [ 3149] [depth= 2] . ( 2 sec) [ -14942.7370] [ 3107] [depth= 12] . ( 2 sec) [ -14799.0256] [ 3045] [depth= 1] . ( 2 sec) [ -14611.4801] [ 2996] [depth= 7] . ( 2 sec) [ -14518.9648] [ 2974] [depth= 3] . ( 2 sec) [ -14309.3599] [ 2960] [depth= 9] . ( 2 sec) [ -14269.4902] [ 2961] [depth= 2] . ( 2 sec) [ -14118.3965] [ 2909] [depth= 3] . ( 2 sec) [ -14047.8022] [ 2886] [depth= 8] . ( 2 sec) [ -13868.4757] [ 2850] [depth= 8] . ( 2 sec) [ -13564.0273] [ 2798] [depth= 5] . ( 2 sec) [ -13476.0438] [ 2762] [depth= 1] . ( 2 sec) [ -13374.2689] [ 2756] [depth= 4] . ( 2 sec) [ -13316.5252] [ 2739] [depth= 3] . ( 2 sec) [ -12550.9710] [ 2710] [depth= 2] . ( 2 sec) [ -12069.8124] [ 2566] [depth= 1] . ( 2 sec) [ -12057.8862] [ 2565] [depth= 1] . ( 2 sec) [ -11971.6901] [ 2561] [depth= 1] . ( 2 sec) [ -11920.0665] [ 2531] [depth= 5] . ( 2 sec) [ -11917.4696] [ 2541] [depth= 1] . ( 2 sec) [ -11914.0746] [ 2504] [depth= 3] . ( 2 sec) [ -11637.2500] [ 2446] [depth= 5] . ( 3 sec) [ -11622.5564] [ 2477] [depth= 3] . ( 3 sec) [ -11621.1075] [ 2476] [depth= 1] . ( 3 sec) [ -11455.6500] [ 2404] [depth= 4] . ( 3 sec) [ -11450.6855] [ 2401] [depth= 1] . ( 3 sec) [ -11407.8133] [ 2406] [depth= 3] . ( 3 sec) [ -11385.7242] [ 2399] [depth= 1] . ( 3 sec) [ -11087.7916] [ 2398] [depth= 1] . ( 3 sec) [ -10976.7731] [ 2350] [depth= 4] . ( 3 sec) [ -10844.3760] [ 2314] [depth= 3] . ( 3 sec) [ -10793.5131] [ 2282] [depth= 1] . ( 3 sec) [ -10738.7078] [ 2282] [depth= 1] . ( 3 sec) [ -10527.1955] [ 2284] [depth= 3] . ( 3 sec) [ -9918.6646] [ 2132] [depth= 1] . ( 3 sec) [ -9605.6303] [ 2085] [depth= 3] . ( 3 sec) [ -9604.8845] [ 2086] [depth= 1] . ( 3 sec) [ -9586.7341] [ 2097] [depth= 1] . ( 3 sec) [ -9557.4930] [ 2086] [depth= 1] . ( 3 sec) [ -9439.9218] [ 2054] [depth= 9] . ( 3 sec) [ -9416.7331] [ 2062] [depth= 1] . ( 3 sec) [ -9296.4836] [ 2027] [depth= 4] . ( 4 sec) [ -9285.3140] [ 2027] [depth= 1] . ( 4 sec) [ -9280.8828] [ 2024] [depth= 1] . ( 4 sec) [ -9275.3823] [ 2023] [depth= 1] . ( 4 sec) [ -9235.3326] [ 2010] [depth= 6] . ( 4 sec) [ -9176.8887] [ 1965] [depth= 1] . ( 4 sec) [ -9104.0394] [ 1931] [depth= 8] . ( 4 sec) [ -8951.3802] [ 1882] [depth= 2] . ( 4 sec) [ -8911.6019] [ 1864] [depth= 1] . ( 4 sec) [ -8839.3464] [ 1856] [depth= 1] . ( 4 sec) [ -8828.0348] [ 1858] [depth= 3] . ( 4 sec) [ -8822.1985] [ 1855] [depth= 1] . ( 4 sec) [ -8822.0762] [ 1856] [depth= 1] . ( 5 sec) [ -8815.4926] [ 1850] [depth= 1] . ( 5 sec) [ -8815.4420] [ 1852] [depth= 1] . ( 5 sec) [ -8765.6214] [ 1850] [depth= 1] . ( 5 sec) [ -8651.9211] [ 1827] [depth= 1] . ( 5 sec) [ -8560.9781] [Branch lengths ] . ( 6 sec) [ -8557.9198] [GTR parameters ] . ( 6 sec) [ -8516.2359] [Alpha ][ 1.000115] . ( 6 sec) [ -8515.2131] [ 1819] [depth= 1] . ( 6 sec) [ -8482.3388] [ 1796] [depth= 1] . ( 6 sec) [ -8481.9179] [ 1795] [depth= 1] . ( 6 sec) [ -8480.6344] [ 1793] [depth= 1] . ( 7 sec) [ -8480.1568] [ 1792] [depth= 1] . ( 7 sec) [ -8446.4130] [ 1736] [depth= 8] . ( 7 sec) [ -8445.8902] [ 1736] [depth= 1] . ( 7 sec) [ -8445.8757] [ 1736] [depth= 1] . ( 7 sec) [ -8430.3893] [ 1732] [depth= 2] . ( 7 sec) [ -8412.8551] [ 1736] [depth= 2] . ( 7 sec) [ -8411.1293] [ 1737] [depth= 1] . ( 7 sec) [ -8409.6681] [ 1738] [depth= 2] . ( 7 sec) [ -8409.0367] [ 1738] [depth= 1] . ( 8 sec) [ -8407.3332] [ 1733] [depth= 2] . ( 8 sec) [ -8405.6696] [ 1737] [depth= 1] . ( 8 sec) [ -8404.6221] [ 1735] [depth= 1] . ( 9 sec) [ -8404.5393] [ 1735] [depth= 1] . ( 9 sec) [ -8404.1164] [ 1735] [depth= 2] . ( 9 sec) [ -8393.8164] [Branch lengths ] . ( 10 sec) [ -8393.7383] [GTR parameters ] . ( 10 sec) [ -8390.8796] [Alpha ][ 1.226121] . ( 10 sec) [ -8389.8466] [ 1736] [depth= 1] . ( 10 sec) [ -8389.8287] [ 1736] [depth= 1] . ( 11 sec) [ -8388.7711] [ 1735] [depth= 1] . ( 11 sec) [ -8388.4537] [ 1736] [depth= 1] . ( 12 sec) [ -8388.0370] [ 1737] [depth= 1] . ( 13 sec) [ -8387.9603] [ 1737] [depth= 1] . ( 14 sec) [ -8384.5874] [Branch lengths ] . ( 14 sec) [ -8384.5692] [GTR parameters ] . ( 14 sec) [ -8384.5636] [Alpha ][ 1.237590] . ( 18 sec) [ -8384.1446] [Branch lengths ] . ( 39 sec) [ -8384.0961] [Branch lengths ] . ( 39 sec) [ -8384.0961] [Topology ] . ( 39 sec) [ -8384.0645] [Topology ] . ( 40 sec) [ -8383.9985] [Topology ] . ( 41 sec) [ -8383.9921] [Topology ] . ( 42 sec) [ -8383.9908] [Topology ] . ( 42 sec) [ -8383.9903] [Topology ] . ( 43 sec) [ -8383.9868] [GTR parameters ] . ( 43 sec) [ -8383.9866] [Alpha ][ 1.239776] . ( 43 sec) [ -8383.9866] [Topology ] . ( 43 sec) [ -8383.9864] [Topology ] . ( 43 sec) [ -8383.9863] [GTR parameters ] . ( 44 sec) [ -8383.9863] [Alpha ][ 1.239776] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8383.986337. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8419.296833 . ( 1 sec) [ -8412.2618] [GTR parameters ] . ( 1 sec) [ -8409.5051] [Alpha ][ 1.225301] . ( 1 sec) [ -8409.5051] [Topology ] . ( 2 sec) [ -8391.5520] [Topology ] . ( 3 sec) [ -8388.7643] [Topology ] . ( 4 sec) [ -8387.8745] [Topology ] . ( 4 sec) [ -8387.5222] [Topology ] . ( 5 sec) [ -8387.3734] [Topology ] . ( 6 sec) [ -8387.3068] [Topology ] . ( 7 sec) [ -8387.2763] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -8387.1901] [Topology ] . Before opt ts/t=1.000000 LK=-8387.190119 . ( 12 sec) [ -8387.1746] [GTR parameters ] . ( 12 sec) [ -8387.1528] [Alpha ][ 1.248016] . ( 12 sec) [ -8387.1528] [Topology ] . ( 13 sec) [ -8387.1313] [Topology ] . ( 14 sec) [ -8387.1219] [Topology ] . ( 14 sec) [ -8387.1175] [Topology ] . ( 15 sec) [ -8387.1155] [Topology ] . ( 16 sec) [ -8387.1145] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8387.114542 . ( 21 sec) [ -8387.1145] [GTR parameters ] . ( 21 sec) [ -8387.1145] [Alpha ][ 1.249264] . ( 21 sec) [ -8387.1145] [Topology ] . ( 22 sec) [ -8387.1140] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 33 sec) [ -8412.2618] [GTR parameters ] . ( 33 sec) [ -8409.5051] [Alpha ][ 1.225301] . ( 33 sec) [ -8406.1483] [ 1733] [depth= 1] . ( 33 sec) [ -8405.9203] [ 1734] [depth= 1] . ( 33 sec) [ -8405.6484] [ 1733] [depth= 1] . ( 33 sec) [ -8404.3349] [ 1734] [depth= 1] . ( 34 sec) [ -8403.4439] [ 1736] [depth= 1] . ( 35 sec) [ -8403.2458] [ 1739] [depth= 1] . ( 35 sec) [ -8401.7254] [ 1730] [depth= 1] . ( 35 sec) [ -8401.5850] [ 1735] [depth= 1] . ( 35 sec) [ -8400.8843] [ 1737] [depth= 1] . ( 35 sec) [ -8400.7790] [ 1739] [depth= 1] . ( 35 sec) [ -8400.6341] [ 1740] [depth= 1] . ( 36 sec) [ -8399.3393] [ 1739] [depth= 1] . ( 36 sec) [ -8399.1633] [ 1739] [depth= 1] . ( 36 sec) [ -8399.0180] [ 1739] [depth= 1] . ( 36 sec) [ -8398.1916] [ 1739] [depth= 1] . ( 36 sec) [ -8397.6036] [ 1740] [depth= 2] . ( 36 sec) [ -8390.3666] [Branch lengths ] . ( 36 sec) [ -8390.3456] [GTR parameters ] . ( 37 sec) [ -8390.3307] [Alpha ][ 1.244172] . ( 38 sec) [ -8387.2528] [ 1742] [depth= 2] . ( 38 sec) [ -8386.5270] [ 1741] [depth= 1] . ( 38 sec) [ -8386.0193] [ 1740] [depth= 1] . ( 39 sec) [ -8385.5605] [ 1740] [depth= 2] . ( 40 sec) [ -8384.1866] [Branch lengths ] . ( 40 sec) [ -8384.1727] [GTR parameters ] . ( 40 sec) [ -8384.1706] [Alpha ][ 1.236853] . ( 44 sec) [ -8383.9956] [Branch lengths ] . ( 65 sec) [ -8383.9877] [Branch lengths ] . ( 65 sec) [ -8383.9877] [Topology ] . ( 65 sec) [ -8383.9870] [Topology ] . ( 66 sec) [ -8383.9870] [GTR parameters ] . ( 66 sec) [ -8383.9866] [Alpha ][ 1.239784] . ( 66 sec) [ -8383.9866] [Topology ] . ( 66 sec) [ -8383.9864] [Topology ] . ( 67 sec) [ -8383.9864] [GTR parameters ] . ( 67 sec) [ -8383.9864] [Alpha ][ 1.239784] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8387.114006 . Log likelihood obtained after SPR moves : -8383.986353 . Log likelihood of the current tree: -8383.986353. . Printing the most likely tree in file 'data78.phy_phyml_tree.txt'... . Best log likelihood : -8383.986249 . Time used 0h1m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo