.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data12.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... . 349 patterns found. (out of a total of 500 sites) . 135 sites without polymorphism (27.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15872.4460] [GTR parameters ] . ( 0 sec) [ -15596.3231] [Alpha ][ 0.500960] . ( 1 sec) [ -15414.8006] [ 2629] [depth= 4] . ( 1 sec) [ -15191.7190] [ 2574] [depth= 6] . ( 1 sec) [ -14854.5504] [ 2540] [depth= 1] . ( 1 sec) [ -14643.3770] [ 2530] [depth= 7] . ( 1 sec) [ -12787.1071] [ 2486] [depth= 5] . ( 1 sec) [ -12698.7759] [ 2486] [depth= 1] . ( 1 sec) [ -12693.1759] [ 2485] [depth= 1] . ( 1 sec) [ -12692.0077] [ 2486] [depth= 1] . ( 1 sec) [ -12500.8600] [ 2417] [depth= 9] . ( 1 sec) [ -12417.7435] [ 2403] [depth= 1] . ( 1 sec) [ -12376.9155] [ 2405] [depth= 3] . ( 1 sec) [ -12350.9391] [ 2401] [depth= 2] . ( 1 sec) [ -12337.8067] [ 2395] [depth= 1] . ( 1 sec) [ -12244.7174] [ 2391] [depth= 1] . ( 1 sec) [ -12148.8087] [ 2357] [depth= 9] . ( 1 sec) [ -12002.5473] [ 2350] [depth= 3] . ( 1 sec) [ -11932.2479] [ 2343] [depth= 2] . ( 1 sec) [ -11813.3854] [ 2303] [depth= 1] . ( 1 sec) [ -11743.3392] [ 2285] [depth= 14] . ( 1 sec) [ -11610.7460] [ 2282] [depth= 1] . ( 1 sec) [ -11461.5757] [ 2270] [depth= 16] . ( 1 sec) [ -11196.2373] [ 2148] [depth= 10] . ( 1 sec) [ -10931.1680] [ 2135] [depth= 15] . ( 1 sec) [ -10810.5802] [ 2109] [depth= 1] . ( 1 sec) [ -10708.6407] [ 2098] [depth= 10] . ( 1 sec) [ -10649.6983] [ 2090] [depth= 2] . ( 1 sec) [ -10467.9057] [ 2013] [depth= 10] . ( 2 sec) [ -10333.9757] [ 1973] [depth= 3] . ( 2 sec) [ -10248.3191] [ 1964] [depth= 3] . ( 2 sec) [ -10050.2236] [ 1925] [depth= 13] . ( 2 sec) [ -10004.7892] [ 1929] [depth= 1] . ( 2 sec) [ -9990.9641] [ 1932] [depth= 1] . ( 2 sec) [ -9793.1107] [ 1894] [depth= 1] . ( 2 sec) [ -9733.7970] [ 1885] [depth= 3] . ( 2 sec) [ -9582.7317] [ 1853] [depth= 4] . ( 2 sec) [ -9472.2370] [ 1799] [depth= 6] . ( 2 sec) [ -9027.8158] [ 1791] [depth= 11] . ( 2 sec) [ -8995.7840] [ 1785] [depth= 1] . ( 2 sec) [ -8849.2886] [ 1740] [depth= 7] . ( 2 sec) [ -8718.0144] [ 1682] [depth= 3] . ( 2 sec) [ -8698.7075] [ 1684] [depth= 1] . ( 2 sec) [ -8550.5093] [ 1652] [depth= 3] . ( 2 sec) [ -8542.0509] [ 1665] [depth= 1] . ( 2 sec) [ -8414.7719] [ 1641] [depth= 10] . ( 2 sec) [ -8403.7096] [ 1628] [depth= 1] . ( 2 sec) [ -8381.2739] [ 1629] [depth= 1] . ( 2 sec) [ -8333.2375] [ 1592] [depth= 6] . ( 2 sec) [ -7871.9460] [ 1586] [depth= 12] . ( 2 sec) [ -7865.3182] [ 1581] [depth= 1] . ( 2 sec) [ -7765.2078] [ 1575] [depth= 1] . ( 2 sec) [ -7759.5297] [ 1573] [depth= 1] . ( 2 sec) [ -7428.6664] [ 1468] [depth= 13] . ( 2 sec) [ -7415.3509] [ 1461] [depth= 1] . ( 2 sec) [ -7298.7174] [ 1420] [depth= 1] . ( 3 sec) [ -7292.3700] [ 1422] [depth= 1] . ( 3 sec) [ -7278.1984] [ 1415] [depth= 5] . ( 3 sec) [ -7074.3119] [ 1400] [depth= 1] . ( 3 sec) [ -6983.2722] [ 1359] [depth= 5] . ( 3 sec) [ -6971.3744] [ 1361] [depth= 2] . ( 3 sec) [ -6966.5338] [ 1360] [depth= 2] . ( 3 sec) [ -6913.8193] [ 1346] [depth= 1] . ( 3 sec) [ -6903.1609] [ 1364] [depth= 3] . ( 3 sec) [ -6842.9536] [ 1329] [depth= 4] . ( 3 sec) [ -6780.6008] [ 1300] [depth= 2] . ( 3 sec) [ -6749.7234] [ 1296] [depth= 1] . ( 3 sec) [ -6651.6068] [ 1296] [depth= 1] . ( 3 sec) [ -6634.7702] [ 1293] [depth= 1] . ( 3 sec) [ -6531.3061] [ 1243] [depth= 6] . ( 3 sec) [ -6505.5805] [ 1232] [depth= 2] . ( 3 sec) [ -6495.9514] [ 1229] [depth= 1] . ( 3 sec) [ -6490.3626] [ 1232] [depth= 1] . ( 3 sec) [ -6488.3746] [ 1232] [depth= 1] . ( 3 sec) [ -6488.0711] [ 1232] [depth= 1] . ( 3 sec) [ -6478.0613] [ 1230] [depth= 1] . ( 3 sec) [ -6385.5244] [ 1214] [depth= 3] . ( 3 sec) [ -6361.2264] [ 1212] [depth= 2] . ( 4 sec) [ -6320.9069] [ 1193] [depth= 1] . ( 4 sec) [ -6318.9252] [ 1193] [depth= 1] . ( 4 sec) [ -6315.0994] [ 1191] [depth= 2] . ( 4 sec) [ -6314.6323] [ 1191] [depth= 1] . ( 4 sec) [ -6267.0623] [Branch lengths ] . ( 5 sec) [ -6265.5278] [GTR parameters ] . ( 5 sec) [ -6247.8413] [Alpha ][ 0.842204] . ( 5 sec) [ -6247.3386] [ 1189] [depth= 1] . ( 5 sec) [ -6215.3844] [ 1173] [depth= 1] . ( 5 sec) [ -6214.9947] [ 1175] [depth= 1] . ( 5 sec) [ -6209.4338] [ 1170] [depth= 1] . ( 5 sec) [ -6200.1066] [ 1166] [depth= 1] . ( 5 sec) [ -6199.2992] [ 1165] [depth= 1] . ( 5 sec) [ -6194.8899] [ 1151] [depth= 5] . ( 5 sec) [ -6179.2381] [ 1142] [depth= 1] . ( 5 sec) [ -6178.4727] [ 1141] [depth= 3] . ( 5 sec) [ -6177.6085] [ 1140] [depth= 1] . ( 6 sec) [ -6125.3549] [ 1122] [depth= 1] . ( 6 sec) [ -6122.1405] [ 1120] [depth= 1] . ( 6 sec) [ -6119.3319] [ 1116] [depth= 1] . ( 6 sec) [ -6118.9294] [ 1112] [depth= 1] . ( 7 sec) [ -6118.3498] [ 1115] [depth= 1] . ( 7 sec) [ -6040.9022] [ 1084] [depth= 4] . ( 7 sec) [ -6039.3862] [ 1081] [depth= 1] . ( 8 sec) [ -6033.9750] [Branch lengths ] . ( 8 sec) [ -6033.7723] [GTR parameters ] . ( 8 sec) [ -6032.4545] [Alpha ][ 0.987092] . ( 11 sec) [ -6031.9638] [Branch lengths ] . ( 27 sec) [ -6031.9144] [Branch lengths ] . ( 27 sec) [ -6031.9144] [Topology ] . ( 28 sec) [ -6031.9114] [Topology ] . ( 29 sec) [ -6031.9105] [Topology ] . ( 29 sec) [ -6031.9093] [GTR parameters ] . ( 29 sec) [ -6031.8971] [Alpha ][ 1.002837] . ( 29 sec) [ -6031.8971] [Topology ] . ( 30 sec) [ -6031.8961] [Topology ] . ( 30 sec) [ -6031.8961] [GTR parameters ] . ( 30 sec) [ -6031.8961] [Alpha ][ 1.002837] . ( 30 sec) [ -6031.8961] [Topology ] . ( 30 sec) [ -6031.8957] [Topology ] . ( 31 sec) [ -6031.8957] [GTR parameters ] . ( 31 sec) [ -6031.8957] [Alpha ][ 1.002837] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895694. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16258.5365] [GTR parameters ] . ( 1 sec) [ -16002.2238] [Alpha ][ 0.500960] . ( 1 sec) [ -15815.5665] [ 2627] [depth= 4] . ( 1 sec) [ -15610.0462] [ 2577] [depth= 3] . ( 1 sec) [ -13336.5234] [ 2510] [depth= 4] . ( 1 sec) [ -13069.8962] [ 2506] [depth= 6] . ( 1 sec) [ -12848.8149] [ 2506] [depth= 1] . ( 1 sec) [ -12692.9830] [ 2478] [depth= 9] . ( 1 sec) [ -12535.9801] [ 2466] [depth= 1] . ( 1 sec) [ -12428.9744] [ 2460] [depth= 4] . ( 1 sec) [ -12393.3119] [ 2387] [depth= 2] . ( 1 sec) [ -12115.5302] [ 2388] [depth= 1] . ( 1 sec) [ -11922.3199] [ 2348] [depth= 11] . ( 1 sec) [ -11811.4479] [ 2338] [depth= 5] . ( 1 sec) [ -11552.5880] [ 2304] [depth= 4] . ( 1 sec) [ -11351.8356] [ 2298] [depth= 4] . ( 1 sec) [ -10918.1421] [ 2208] [depth= 10] . ( 1 sec) [ -10697.4140] [ 2132] [depth= 17] . ( 2 sec) [ -10279.4626] [ 2051] [depth= 11] . ( 2 sec) [ -10130.2942] [ 2020] [depth= 1] . ( 2 sec) [ -9838.3044] [ 2021] [depth= 1] . ( 2 sec) [ -9812.4344] [ 1976] [depth= 1] . ( 2 sec) [ -9774.1687] [ 1973] [depth= 1] . ( 2 sec) [ -9358.1218] [ 1901] [depth= 17] . ( 2 sec) [ -9267.7283] [ 1908] [depth= 8] . ( 2 sec) [ -9134.5901] [ 1890] [depth= 6] . ( 2 sec) [ -9086.0174] [ 1871] [depth= 1] . ( 2 sec) [ -8829.2603] [ 1853] [depth= 13] . ( 2 sec) [ -8782.9806] [ 1848] [depth= 1] . ( 2 sec) [ -8746.1090] [ 1831] [depth= 7] . ( 2 sec) [ -8678.7214] [ 1810] [depth= 1] . ( 2 sec) [ -8650.1251] [ 1781] [depth= 1] . ( 2 sec) [ -8558.1556] [ 1712] [depth= 13] . ( 2 sec) [ -8337.8053] [ 1649] [depth= 2] . ( 2 sec) [ -8313.7476] [ 1630] [depth= 2] . ( 2 sec) [ -8303.1300] [ 1635] [depth= 5] . ( 2 sec) [ -8187.6723] [ 1600] [depth= 6] . ( 2 sec) [ -8064.4561] [ 1597] [depth= 5] . ( 2 sec) [ -8043.4591] [ 1590] [depth= 1] . ( 2 sec) [ -7963.7962] [ 1594] [depth= 3] . ( 2 sec) [ -7913.3967] [ 1575] [depth= 5] . ( 2 sec) [ -7899.2720] [ 1572] [depth= 3] . ( 3 sec) [ -7771.2499] [ 1493] [depth= 5] . ( 3 sec) [ -7668.1991] [ 1490] [depth= 1] . ( 3 sec) [ -7436.6552] [ 1443] [depth= 3] . ( 3 sec) [ -7401.3362] [ 1443] [depth= 4] . ( 3 sec) [ -7360.6728] [ 1432] [depth= 2] . ( 3 sec) [ -7328.3488] [ 1413] [depth= 8] . ( 3 sec) [ -7139.9782] [ 1408] [depth= 2] . ( 3 sec) [ -7105.5647] [ 1408] [depth= 1] . ( 3 sec) [ -7104.3405] [ 1413] [depth= 1] . ( 3 sec) [ -7091.5751] [ 1406] [depth= 1] . ( 3 sec) [ -7083.5758] [ 1401] [depth= 1] . ( 3 sec) [ -7083.4345] [ 1401] [depth= 1] . ( 3 sec) [ -7081.1236] [ 1406] [depth= 2] . ( 3 sec) [ -7079.8729] [ 1406] [depth= 1] . ( 3 sec) [ -7036.8257] [ 1406] [depth= 1] . ( 3 sec) [ -7029.8996] [ 1406] [depth= 3] . ( 3 sec) [ -6933.4788] [ 1379] [depth= 2] . ( 3 sec) [ -6929.2282] [ 1378] [depth= 1] . ( 3 sec) [ -6897.9425] [ 1363] [depth= 1] . ( 3 sec) [ -6821.1401] [ 1350] [depth= 6] . ( 4 sec) [ -6808.3426] [ 1349] [depth= 2] . ( 4 sec) [ -6804.0116] [ 1353] [depth= 3] . ( 4 sec) [ -6796.7406] [ 1352] [depth= 2] . ( 4 sec) [ -6775.2236] [ 1331] [depth= 4] . ( 4 sec) [ -6696.3935] [ 1308] [depth= 2] . ( 4 sec) [ -6668.9534] [ 1294] [depth= 3] . ( 4 sec) [ -6657.9398] [ 1286] [depth= 1] . ( 4 sec) [ -6644.5236] [ 1265] [depth= 10] . ( 4 sec) [ -6644.3612] [ 1265] [depth= 2] . ( 4 sec) [ -6636.5881] [ 1266] [depth= 1] . ( 4 sec) [ -6616.7205] [ 1260] [depth= 1] . ( 4 sec) [ -6606.9770] [ 1258] [depth= 1] . ( 4 sec) [ -6592.0138] [ 1254] [depth= 1] . ( 4 sec) [ -6590.1313] [ 1255] [depth= 1] . ( 4 sec) [ -6523.5538] [Branch lengths ] . ( 5 sec) [ -6521.6988] [GTR parameters ] . ( 5 sec) [ -6503.5202] [Alpha ][ 0.835538] . ( 5 sec) [ -6487.2027] [ 1251] [depth= 2] . ( 5 sec) [ -6481.5082] [ 1249] [depth= 1] . ( 5 sec) [ -6480.7972] [ 1251] [depth= 1] . ( 5 sec) [ -6480.1808] [ 1259] [depth= 2] . ( 5 sec) [ -6442.4534] [ 1249] [depth= 7] . ( 5 sec) [ -6315.9910] [ 1206] [depth= 3] . ( 5 sec) [ -6315.1052] [ 1205] [depth= 1] . ( 6 sec) [ -6312.1372] [ 1207] [depth= 1] . ( 6 sec) [ -6277.9440] [ 1190] [depth= 1] . ( 6 sec) [ -6274.9824] [ 1185] [depth= 1] . ( 6 sec) [ -6170.1753] [ 1135] [depth= 4] . ( 6 sec) [ -6169.0549] [ 1132] [depth= 1] . ( 6 sec) [ -6121.4081] [ 1115] [depth= 1] . ( 6 sec) [ -6119.8887] [ 1114] [depth= 1] . ( 6 sec) [ -6111.7483] [ 1110] [depth= 1] . ( 7 sec) [ -6101.1143] [ 1110] [depth= 2] . ( 7 sec) [ -6100.6094] [ 1110] [depth= 1] . ( 7 sec) [ -6100.4562] [ 1111] [depth= 1] . ( 7 sec) [ -6053.6484] [ 1086] [depth= 1] . ( 8 sec) [ -6046.0555] [ 1085] [depth= 1] . ( 8 sec) [ -6044.0111] [ 1086] [depth= 1] . ( 8 sec) [ -6042.7361] [ 1086] [depth= 1] . ( 8 sec) [ -6034.3391] [Branch lengths ] . ( 9 sec) [ -6033.7583] [GTR parameters ] . ( 9 sec) [ -6032.1535] [Alpha ][ 0.993981] . ( 12 sec) [ -6032.0323] [Branch lengths ] . ( 23 sec) [ -6031.9547] [ 1082] [depth= 1] . ( 28 sec) [ -6031.9041] [Branch lengths ] . ( 28 sec) [ -6031.9012] [GTR parameters ] . ( 28 sec) [ -6031.8974] [Alpha ][ 1.002699] . ( 28 sec) [ -6031.8974] [Topology ] . ( 29 sec) [ -6031.8958] [Topology ] . ( 30 sec) [ -6031.8955] [Topology ] . ( 30 sec) [ -6031.8955] [GTR parameters ] . ( 30 sec) [ -6031.8955] [Alpha ][ 1.002699] . ( 30 sec) [ -6031.8955] [Topology ] . ( 30 sec) [ -6031.8954] [Topology ] . ( 30 sec) [ -6031.8954] [GTR parameters ] . ( 31 sec) [ -6031.8954] [Alpha ][ 1.002699] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895383. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16215.4428] [GTR parameters ] . ( 1 sec) [ -15929.7369] [Alpha ][ 0.500960] . ( 1 sec) [ -15714.1992] [ 2759] [depth= 1] . ( 1 sec) [ -15432.8454] [ 2700] [depth= 8] . ( 1 sec) [ -15405.0798] [ 2682] [depth= 2] . ( 1 sec) [ -15403.3051] [ 2679] [depth= 2] . ( 1 sec) [ -15349.2816] [ 2662] [depth= 2] . ( 1 sec) [ -15268.7324] [ 2654] [depth= 1] . ( 1 sec) [ -15012.7560] [ 2591] [depth= 1] . ( 1 sec) [ -14965.8465] [ 2577] [depth= 8] . ( 1 sec) [ -14890.8124] [ 2576] [depth= 6] . ( 2 sec) [ -14780.0920] [ 2556] [depth= 2] . ( 2 sec) [ -14681.5608] [ 2525] [depth= 10] . ( 2 sec) [ -13038.1354] [ 2477] [depth= 4] . ( 2 sec) [ -12974.6676] [ 2477] [depth= 1] . ( 2 sec) [ -12883.3175] [ 2466] [depth= 6] . ( 2 sec) [ -12807.8988] [ 2452] [depth= 4] . ( 2 sec) [ -12415.1923] [ 2450] [depth= 11] . ( 2 sec) [ -12242.7866] [ 2401] [depth= 5] . ( 2 sec) [ -12113.8373] [ 2401] [depth= 7] . ( 2 sec) [ -11941.7024] [ 2385] [depth= 1] . ( 2 sec) [ -11894.8952] [ 2374] [depth= 11] . ( 2 sec) [ -11816.2645] [ 2324] [depth= 2] . ( 2 sec) [ -11728.0524] [ 2290] [depth= 5] . ( 2 sec) [ -11607.2149] [ 2269] [depth= 2] . ( 2 sec) [ -11210.3137] [ 2223] [depth= 1] . ( 2 sec) [ -11207.7100] [ 2220] [depth= 1] . ( 2 sec) [ -10943.2409] [ 2167] [depth= 9] . ( 2 sec) [ -10772.3154] [ 2129] [depth= 2] . ( 2 sec) [ -10362.7583] [ 2058] [depth= 6] . ( 2 sec) [ -10268.8933] [ 2034] [depth= 1] . ( 2 sec) [ -10012.3059] [ 1965] [depth= 8] . ( 2 sec) [ -9676.5879] [ 1878] [depth= 12] . ( 2 sec) [ -9460.7678] [ 1828] [depth= 15] . ( 2 sec) [ -9259.3177] [ 1824] [depth= 8] . ( 2 sec) [ -9074.1254] [ 1767] [depth= 5] . ( 2 sec) [ -8764.3324] [ 1759] [depth= 7] . ( 3 sec) [ -8704.3552] [ 1762] [depth= 2] . ( 3 sec) [ -8515.5313] [ 1684] [depth= 9] . ( 3 sec) [ -8387.8294] [ 1687] [depth= 1] . ( 3 sec) [ -8384.1809] [ 1688] [depth= 1] . ( 3 sec) [ -8321.6643] [ 1663] [depth= 1] . ( 3 sec) [ -8318.8474] [ 1665] [depth= 1] . ( 3 sec) [ -8196.3343] [ 1638] [depth= 6] . ( 3 sec) [ -7984.4935] [ 1620] [depth= 10] . ( 3 sec) [ -7870.7630] [ 1625] [depth= 10] . ( 3 sec) [ -7860.5470] [ 1601] [depth= 1] . ( 3 sec) [ -7851.8944] [ 1589] [depth= 7] . ( 3 sec) [ -7826.0483] [ 1585] [depth= 1] . ( 3 sec) [ -7819.4764] [ 1585] [depth= 1] . ( 3 sec) [ -7813.6353] [ 1562] [depth= 4] . ( 3 sec) [ -7805.0983] [ 1560] [depth= 3] . ( 3 sec) [ -7790.1018] [ 1552] [depth= 1] . ( 3 sec) [ -7762.2547] [ 1545] [depth= 4] . ( 3 sec) [ -7676.7245] [ 1535] [depth= 2] . ( 3 sec) [ -7676.6717] [ 1517] [depth= 1] . ( 3 sec) [ -7652.0892] [ 1507] [depth= 2] . ( 3 sec) [ -7635.2171] [ 1507] [depth= 2] . ( 3 sec) [ -7584.9817] [ 1509] [depth= 2] . ( 3 sec) [ -7436.6621] [ 1493] [depth= 3] . ( 3 sec) [ -7180.8717] [ 1455] [depth= 2] . ( 3 sec) [ -7165.4864] [ 1451] [depth= 1] . ( 3 sec) [ -7164.3099] [ 1455] [depth= 1] . ( 4 sec) [ -7107.8972] [ 1446] [depth= 2] . ( 4 sec) [ -7098.9365] [ 1444] [depth= 2] . ( 4 sec) [ -7054.6139] [ 1433] [depth= 5] . ( 4 sec) [ -6946.8441] [ 1432] [depth= 2] . ( 4 sec) [ -6940.1798] [ 1428] [depth= 1] . ( 4 sec) [ -6917.4615] [ 1403] [depth= 1] . ( 4 sec) [ -6912.8677] [ 1401] [depth= 1] . ( 4 sec) [ -6909.1259] [ 1397] [depth= 1] . ( 4 sec) [ -6909.0007] [ 1392] [depth= 2] . ( 4 sec) [ -6900.8773] [ 1392] [depth= 2] . ( 4 sec) [ -6896.3253] [ 1392] [depth= 1] . ( 4 sec) [ -6845.6406] [ 1374] [depth= 4] . ( 4 sec) [ -6844.2331] [ 1375] [depth= 1] . ( 4 sec) [ -6831.5637] [ 1376] [depth= 1] . ( 4 sec) [ -6831.4498] [ 1382] [depth= 2] . ( 4 sec) [ -6829.6810] [ 1386] [depth= 1] . ( 4 sec) [ -6773.1057] [ 1351] [depth= 1] . ( 4 sec) [ -6695.4492] [ 1302] [depth= 1] . ( 4 sec) [ -6687.7698] [ 1297] [depth= 1] . ( 4 sec) [ -6649.5417] [ 1280] [depth= 3] . ( 4 sec) [ -6625.2444] [ 1253] [depth= 1] . ( 4 sec) [ -6609.3669] [ 1255] [depth= 1] . ( 4 sec) [ -6601.7401] [ 1250] [depth= 1] . ( 4 sec) [ -6425.5265] [ 1195] [depth= 1] . ( 5 sec) [ -6423.4475] [ 1195] [depth= 1] . ( 5 sec) [ -6400.6563] [ 1195] [depth= 2] . ( 5 sec) [ -6395.1333] [ 1192] [depth= 1] . ( 5 sec) [ -6301.9903] [Branch lengths ] . ( 5 sec) [ -6300.5243] [GTR parameters ] . ( 5 sec) [ -6281.0922] [Alpha ][ 0.856696] . ( 6 sec) [ -6280.6754] [ 1189] [depth= 1] . ( 6 sec) [ -6265.9483] [ 1185] [depth= 2] . ( 6 sec) [ -6263.8238] [ 1182] [depth= 1] . ( 6 sec) [ -6204.1553] [ 1158] [depth= 6] . ( 6 sec) [ -6140.9767] [ 1122] [depth= 4] . ( 6 sec) [ -6140.9586] [ 1122] [depth= 1] . ( 6 sec) [ -6140.9245] [ 1118] [depth= 1] . ( 6 sec) [ -6140.0645] [ 1117] [depth= 1] . ( 6 sec) [ -6081.7820] [ 1103] [depth= 1] . ( 6 sec) [ -6080.5150] [ 1109] [depth= 1] . ( 6 sec) [ -6080.4435] [ 1110] [depth= 1] . ( 7 sec) [ -6080.0801] [ 1107] [depth= 1] . ( 7 sec) [ -6080.0665] [ 1111] [depth= 1] . ( 7 sec) [ -6079.7467] [ 1110] [depth= 1] . ( 7 sec) [ -6077.7371] [ 1104] [depth= 1] . ( 7 sec) [ -6077.1259] [ 1106] [depth= 1] . ( 7 sec) [ -6055.6821] [ 1090] [depth= 1] . ( 7 sec) [ -6054.6646] [ 1093] [depth= 1] . ( 7 sec) [ -6053.8652] [ 1090] [depth= 2] . ( 8 sec) [ -6049.5113] [ 1086] [depth= 1] . ( 8 sec) [ -6048.4576] [ 1089] [depth= 1] . ( 8 sec) [ -6041.9918] [ 1089] [depth= 1] . ( 9 sec) [ -6040.4209] [ 1086] [depth= 1] . ( 9 sec) [ -6033.4777] [Branch lengths ] . ( 9 sec) [ -6033.3560] [GTR parameters ] . ( 9 sec) [ -6032.1158] [Alpha ][ 0.997931] . ( 13 sec) [ -6032.0228] [Branch lengths ] . ( 21 sec) [ -6031.9615] [ 1082] [depth= 1] . ( 29 sec) [ -6031.9003] [Branch lengths ] . ( 29 sec) [ -6031.8979] [GTR parameters ] . ( 29 sec) [ -6031.8967] [Alpha ][ 1.002883] . ( 29 sec) [ -6031.8967] [Topology ] . ( 30 sec) [ -6031.8955] [Topology ] . ( 30 sec) [ -6031.8953] [Topology ] . ( 31 sec) [ -6031.8953] [GTR parameters ] . ( 31 sec) [ -6031.8953] [Alpha ][ 1.002883] . ( 31 sec) [ -6031.8953] [Topology ] . ( 31 sec) [ -6031.8953] [Topology ] . ( 31 sec) [ -6031.8953] [GTR parameters ] . ( 31 sec) [ -6031.8953] [Alpha ][ 1.002883] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895264. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16415.6596] [GTR parameters ] . ( 1 sec) [ -16131.3590] [Alpha ][ 0.500960] . ( 1 sec) [ -15975.8338] [ 2730] [depth= 8] . ( 1 sec) [ -14166.8301] [ 2663] [depth= 9] . ( 1 sec) [ -13890.6071] [ 2641] [depth= 8] . ( 1 sec) [ -13701.6632] [ 2596] [depth= 1] . ( 1 sec) [ -13411.2220] [ 2557] [depth= 9] . ( 1 sec) [ -13314.8773] [ 2534] [depth= 1] . ( 1 sec) [ -12949.7835] [ 2531] [depth= 5] . ( 1 sec) [ -12689.6639] [ 2465] [depth= 3] . ( 1 sec) [ -12657.2499] [ 2459] [depth= 4] . ( 1 sec) [ -12551.5314] [ 2450] [depth= 3] . ( 1 sec) [ -12496.2540] [ 2451] [depth= 1] . ( 1 sec) [ -12302.8459] [ 2408] [depth= 8] . ( 1 sec) [ -12288.0492] [ 2408] [depth= 1] . ( 1 sec) [ -12249.2727] [ 2406] [depth= 4] . ( 1 sec) [ -12193.5199] [ 2405] [depth= 1] . ( 2 sec) [ -12100.5494] [ 2366] [depth= 7] . ( 2 sec) [ -12068.4533] [ 2365] [depth= 1] . ( 2 sec) [ -11976.4462] [ 2326] [depth= 7] . ( 2 sec) [ -11905.4788] [ 2298] [depth= 8] . ( 2 sec) [ -11727.8744] [ 2255] [depth= 15] . ( 2 sec) [ -11581.0022] [ 2202] [depth= 8] . ( 2 sec) [ -11417.0662] [ 2170] [depth= 6] . ( 2 sec) [ -11406.1443] [ 2170] [depth= 2] . ( 2 sec) [ -11292.2920] [ 2125] [depth= 1] . ( 2 sec) [ -11150.6691] [ 2083] [depth= 8] . ( 2 sec) [ -11059.8455] [ 2086] [depth= 1] . ( 2 sec) [ -10667.5114] [ 2100] [depth= 17] . ( 2 sec) [ -10553.4916] [ 2062] [depth= 12] . ( 2 sec) [ -10549.9265] [ 2060] [depth= 3] . ( 2 sec) [ -10247.7875] [ 2002] [depth= 15] . ( 2 sec) [ -9950.0966] [ 1996] [depth= 1] . ( 2 sec) [ -9920.0190] [ 1989] [depth= 1] . ( 2 sec) [ -9604.2775] [ 1990] [depth= 15] . ( 2 sec) [ -9555.5855] [ 1932] [depth= 2] . ( 2 sec) [ -9478.0675] [ 1908] [depth= 2] . ( 2 sec) [ -9330.4556] [ 1898] [depth= 3] . ( 2 sec) [ -9157.3988] [ 1890] [depth= 1] . ( 2 sec) [ -9052.7337] [ 1888] [depth= 1] . ( 2 sec) [ -8912.7508] [ 1881] [depth= 3] . ( 2 sec) [ -8847.4326] [ 1858] [depth= 1] . ( 2 sec) [ -8644.5320] [ 1776] [depth= 11] . ( 2 sec) [ -8570.5115] [ 1742] [depth= 1] . ( 2 sec) [ -8536.9127] [ 1742] [depth= 16] . ( 3 sec) [ -8289.4179] [ 1676] [depth= 3] . ( 3 sec) [ -8262.0129] [ 1670] [depth= 12] . ( 3 sec) [ -8260.3173] [ 1670] [depth= 1] . ( 3 sec) [ -8131.6539] [ 1673] [depth= 2] . ( 3 sec) [ -8065.8748] [ 1634] [depth= 4] . ( 3 sec) [ -8052.4749] [ 1632] [depth= 2] . ( 3 sec) [ -8046.0708] [ 1632] [depth= 1] . ( 3 sec) [ -8035.0684] [ 1629] [depth= 1] . ( 3 sec) [ -8029.2915] [ 1629] [depth= 1] . ( 3 sec) [ -7897.3188] [ 1545] [depth= 4] . ( 3 sec) [ -7770.6183] [ 1527] [depth= 2] . ( 3 sec) [ -7705.7328] [ 1505] [depth= 3] . ( 3 sec) [ -7670.8234] [ 1495] [depth= 13] . ( 3 sec) [ -7670.6824] [ 1497] [depth= 1] . ( 3 sec) [ -7594.4482] [ 1465] [depth= 2] . ( 3 sec) [ -7526.0447] [ 1444] [depth= 3] . ( 3 sec) [ -7517.1829] [ 1440] [depth= 2] . ( 3 sec) [ -7474.8281] [ 1455] [depth= 14] . ( 3 sec) [ -7455.3357] [ 1456] [depth= 1] . ( 3 sec) [ -7426.5422] [ 1450] [depth= 15] . ( 3 sec) [ -7415.7917] [ 1435] [depth= 2] . ( 3 sec) [ -7295.0398] [ 1409] [depth= 3] . ( 3 sec) [ -7149.8219] [ 1366] [depth= 1] . ( 3 sec) [ -7144.9707] [ 1368] [depth= 1] . ( 4 sec) [ -7117.3933] [ 1351] [depth= 2] . ( 4 sec) [ -6885.9583] [ 1317] [depth= 8] . ( 4 sec) [ -6737.4250] [ 1264] [depth= 4] . ( 4 sec) [ -6586.8891] [ 1257] [depth= 2] . ( 4 sec) [ -6586.0030] [ 1263] [depth= 1] . ( 4 sec) [ -6584.2735] [ 1257] [depth= 1] . ( 4 sec) [ -6572.2951] [ 1249] [depth= 1] . ( 4 sec) [ -6563.4677] [ 1246] [depth= 1] . ( 4 sec) [ -6556.9841] [ 1245] [depth= 2] . ( 4 sec) [ -6494.2837] [ 1225] [depth= 3] . ( 4 sec) [ -6488.6197] [ 1232] [depth= 1] . ( 4 sec) [ -6488.5602] [ 1232] [depth= 1] . ( 4 sec) [ -6425.2794] [ 1204] [depth= 1] . ( 4 sec) [ -6399.8804] [ 1200] [depth= 1] . ( 4 sec) [ -6388.5396] [ 1198] [depth= 2] . ( 4 sec) [ -6323.7387] [ 1167] [depth= 3] . ( 4 sec) [ -6323.0400] [ 1164] [depth= 1] . ( 4 sec) [ -6319.2678] [ 1163] [depth= 1] . ( 4 sec) [ -6306.4938] [ 1163] [depth= 1] . ( 5 sec) [ -6257.3003] [Branch lengths ] . ( 5 sec) [ -6256.4286] [GTR parameters ] . ( 5 sec) [ -6236.6773] [Alpha ][ 0.876902] . ( 6 sec) [ -6234.4455] [ 1162] [depth= 1] . ( 6 sec) [ -6143.5215] [ 1128] [depth= 5] . ( 6 sec) [ -6143.3362] [ 1127] [depth= 1] . ( 6 sec) [ -6135.4298] [ 1122] [depth= 1] . ( 6 sec) [ -6131.0003] [ 1119] [depth= 2] . ( 6 sec) [ -6130.1179] [ 1120] [depth= 1] . ( 6 sec) [ -6128.0251] [ 1120] [depth= 1] . ( 6 sec) [ -6048.0261] [ 1084] [depth= 1] . ( 6 sec) [ -6047.5688] [ 1089] [depth= 1] . ( 6 sec) [ -6038.7749] [ 1084] [depth= 1] . ( 6 sec) [ -6038.6683] [ 1086] [depth= 1] . ( 7 sec) [ -6038.5659] [ 1086] [depth= 1] . ( 7 sec) [ -6037.9534] [ 1086] [depth= 1] . ( 8 sec) [ -6037.8419] [ 1086] [depth= 1] . ( 8 sec) [ -6037.6069] [ 1086] [depth= 1] . ( 8 sec) [ -6037.5879] [ 1086] [depth= 1] . ( 8 sec) [ -6037.2533] [ 1086] [depth= 1] . ( 8 sec) [ -6033.0382] [Branch lengths ] . ( 9 sec) [ -6032.9936] [GTR parameters ] . ( 9 sec) [ -6032.1397] [Alpha ][ 0.995853] . ( 12 sec) [ -6032.0348] [Branch lengths ] . ( 17 sec) [ -6031.9558] [ 1082] [depth= 1] . ( 28 sec) [ -6031.9018] [Branch lengths ] . ( 28 sec) [ -6031.8999] [GTR parameters ] . ( 28 sec) [ -6031.8975] [Alpha ][ 1.002657] . ( 28 sec) [ -6031.8975] [Topology ] . ( 29 sec) [ -6031.8958] [Topology ] . ( 30 sec) [ -6031.8955] [Topology ] . ( 30 sec) [ -6031.8955] [GTR parameters ] . ( 30 sec) [ -6031.8955] [Alpha ][ 1.002657] . ( 30 sec) [ -6031.8955] [Topology ] . ( 31 sec) [ -6031.8954] [Topology ] . ( 31 sec) [ -6031.8954] [GTR parameters ] . ( 31 sec) [ -6031.8954] [Alpha ][ 1.002657] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895388. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15029.8948] [GTR parameters ] . ( 0 sec) [ -14723.6587] [Alpha ][ 0.500960] . ( 1 sec) [ -14420.2788] [ 2805] [depth= 6] . ( 1 sec) [ -14184.3612] [ 2742] [depth= 11] . ( 1 sec) [ -14136.6311] [ 2726] [depth= 3] . ( 1 sec) [ -13992.2256] [ 2724] [depth= 3] . ( 1 sec) [ -13813.0037] [ 2679] [depth= 8] . ( 1 sec) [ -13738.8830] [ 2678] [depth= 4] . ( 1 sec) [ -13694.5929] [ 2669] [depth= 2] . ( 1 sec) [ -13607.3797] [ 2672] [depth= 1] . ( 1 sec) [ -13463.5050] [ 2625] [depth= 7] . ( 1 sec) [ -13393.4138] [ 2626] [depth= 16] . ( 1 sec) [ -13288.5120] [ 2587] [depth= 3] . ( 1 sec) [ -13086.2518] [ 2534] [depth= 15] . ( 1 sec) [ -12881.1979] [ 2467] [depth= 16] . ( 1 sec) [ -12745.4208] [ 2457] [depth= 1] . ( 1 sec) [ -12711.3004] [ 2451] [depth= 4] . ( 1 sec) [ -12687.4561] [ 2443] [depth= 1] . ( 1 sec) [ -12508.2244] [ 2420] [depth= 10] . ( 1 sec) [ -12429.0778] [ 2385] [depth= 2] . ( 1 sec) [ -12402.7607] [ 2385] [depth= 3] . ( 1 sec) [ -12202.4694] [ 2372] [depth= 15] . ( 1 sec) [ -11716.1189] [ 2286] [depth= 9] . ( 1 sec) [ -11443.9994] [ 2239] [depth= 12] . ( 1 sec) [ -10792.7777] [ 2206] [depth= 8] . ( 1 sec) [ -10787.6733] [ 2196] [depth= 14] . ( 1 sec) [ -10585.7993] [ 2149] [depth= 1] . ( 1 sec) [ -10540.4503] [ 2094] [depth= 2] . ( 1 sec) [ -10533.8216] [ 2101] [depth= 1] . ( 2 sec) [ -10493.8946] [ 2081] [depth= 11] . ( 2 sec) [ -10457.1630] [ 2083] [depth= 1] . ( 2 sec) [ -10444.6404] [ 2074] [depth= 1] . ( 2 sec) [ -10442.2300] [ 2076] [depth= 1] . ( 2 sec) [ -10258.3113] [ 2061] [depth= 6] . ( 2 sec) [ -10062.7616] [ 2023] [depth= 13] . ( 2 sec) [ -9706.9652] [ 1979] [depth= 2] . ( 2 sec) [ -9261.7882] [ 1924] [depth= 1] . ( 2 sec) [ -9029.6932] [ 1866] [depth= 12] . ( 2 sec) [ -8750.7643] [ 1852] [depth= 11] . ( 2 sec) [ -8741.3404] [ 1849] [depth= 1] . ( 2 sec) [ -8659.3369] [ 1806] [depth= 2] . ( 2 sec) [ -8545.3981] [ 1767] [depth= 8] . ( 2 sec) [ -8404.2889] [ 1688] [depth= 12] . ( 2 sec) [ -8395.6725] [ 1688] [depth= 3] . ( 2 sec) [ -8367.6463] [ 1687] [depth= 1] . ( 2 sec) [ -8352.6537] [ 1684] [depth= 1] . ( 2 sec) [ -8298.2522] [ 1682] [depth= 1] . ( 2 sec) [ -8284.3769] [ 1682] [depth= 1] . ( 2 sec) [ -8281.2385] [ 1678] [depth= 3] . ( 2 sec) [ -8065.3556] [ 1629] [depth= 3] . ( 2 sec) [ -7929.6900] [ 1608] [depth= 11] . ( 2 sec) [ -7899.1066] [ 1604] [depth= 1] . ( 2 sec) [ -7791.6980] [ 1576] [depth= 6] . ( 2 sec) [ -7704.1931] [ 1534] [depth= 6] . ( 3 sec) [ -7693.9764] [ 1525] [depth= 3] . ( 3 sec) [ -7650.6722] [ 1498] [depth= 1] . ( 3 sec) [ -7599.6587] [ 1501] [depth= 4] . ( 3 sec) [ -7318.1569] [ 1420] [depth= 13] . ( 3 sec) [ -7091.1395] [ 1376] [depth= 4] . ( 3 sec) [ -7019.2290] [ 1356] [depth= 7] . ( 3 sec) [ -7006.6506] [ 1354] [depth= 2] . ( 3 sec) [ -6928.4388] [ 1334] [depth= 3] . ( 3 sec) [ -6892.8348] [ 1330] [depth= 3] . ( 3 sec) [ -6890.8302] [ 1329] [depth= 1] . ( 3 sec) [ -6785.1152] [ 1295] [depth= 2] . ( 3 sec) [ -6773.1968] [ 1292] [depth= 3] . ( 3 sec) [ -6730.5466] [ 1288] [depth= 1] . ( 3 sec) [ -6709.4284] [ 1285] [depth= 2] . ( 3 sec) [ -6651.9702] [ 1262] [depth= 1] . ( 3 sec) [ -6638.1796] [ 1262] [depth= 8] . ( 3 sec) [ -6601.9052] [ 1239] [depth= 1] . ( 3 sec) [ -6601.4121] [ 1239] [depth= 1] . ( 3 sec) [ -6601.2549] [ 1244] [depth= 1] . ( 4 sec) [ -6570.3334] [ 1230] [depth= 2] . ( 4 sec) [ -6550.8492] [ 1234] [depth= 1] . ( 4 sec) [ -6535.0220] [ 1230] [depth= 1] . ( 4 sec) [ -6534.7566] [ 1230] [depth= 1] . ( 4 sec) [ -6462.9725] [ 1191] [depth= 1] . ( 4 sec) [ -6429.4014] [ 1182] [depth= 4] . ( 4 sec) [ -6428.2194] [ 1185] [depth= 1] . ( 4 sec) [ -6401.4725] [ 1191] [depth= 1] . ( 4 sec) [ -6327.3104] [Branch lengths ] . ( 5 sec) [ -6325.1519] [GTR parameters ] . ( 5 sec) [ -6306.9107] [Alpha ][ 0.852638] . ( 5 sec) [ -6275.3036] [ 1178] [depth= 1] . ( 5 sec) [ -6275.0698] [ 1180] [depth= 1] . ( 5 sec) [ -6275.0309] [ 1179] [depth= 1] . ( 5 sec) [ -6266.7483] [ 1174] [depth= 1] . ( 5 sec) [ -6261.4879] [ 1171] [depth= 1] . ( 5 sec) [ -6177.3098] [ 1116] [depth= 3] . ( 5 sec) [ -6174.6371] [ 1113] [depth= 1] . ( 6 sec) [ -6174.3025] [ 1113] [depth= 1] . ( 6 sec) [ -6108.7347] [ 1117] [depth= 3] . ( 6 sec) [ -6103.5368] [ 1110] [depth= 2] . ( 6 sec) [ -6051.2355] [ 1088] [depth= 1] . ( 6 sec) [ -6050.8424] [ 1088] [depth= 1] . ( 6 sec) [ -6041.2002] [ 1087] [depth= 1] . ( 7 sec) [ -6040.5752] [ 1083] [depth= 1] . ( 7 sec) [ -6039.6936] [ 1086] [depth= 1] . ( 7 sec) [ -6038.5251] [ 1086] [depth= 1] . ( 8 sec) [ -6038.1101] [ 1086] [depth= 1] . ( 8 sec) [ -6033.5705] [Branch lengths ] . ( 8 sec) [ -6033.5273] [GTR parameters ] . ( 9 sec) [ -6032.3980] [Alpha ][ 0.987124] . ( 12 sec) [ -6032.0601] [Branch lengths ] . ( 26 sec) [ -6032.0103] [ 1082] [depth= 1] . ( 28 sec) [ -6031.9164] [Branch lengths ] . ( 28 sec) [ -6031.9146] [GTR parameters ] . ( 28 sec) [ -6031.9039] [Alpha ][ 1.001831] . ( 28 sec) [ -6031.9039] [Topology ] . ( 29 sec) [ -6031.8985] [Topology ] . ( 29 sec) [ -6031.8967] [Topology ] . ( 30 sec) [ -6031.8960] [Topology ] . ( 30 sec) [ -6031.8960] [GTR parameters ] . ( 30 sec) [ -6031.8960] [Alpha ][ 1.002833] . ( 30 sec) [ -6031.8960] [Topology ] . ( 31 sec) [ -6031.8957] [Topology ] . ( 31 sec) [ -6031.8957] [GTR parameters ] . ( 31 sec) [ -6031.8957] [Alpha ][ 1.002833] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.895684. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6050.947914 . ( 0 sec) [ -6049.3553] [GTR parameters ] . ( 0 sec) [ -6049.3232] [Alpha ][ 0.974396] . ( 1 sec) [ -6049.3232] [Topology ] . ( 1 sec) [ -6034.4456] [Topology ] . ( 2 sec) [ -6032.8652] [Topology ] . ( 3 sec) [ -6032.4749] [Topology ] . ( 3 sec) [ -6032.3420] [Topology ] . ( 4 sec) [ -6032.2915] [Topology ] . ( 5 sec) [ -6032.2714] [Topology ] . ( 5 sec) [ -6032.2632] [Topology ] . Checking for NNIs, optimizing five branches... . ( 10 sec) [ -6031.9929] [Topology ] . Before opt ts/t=1.000000 LK=-6031.992854 . ( 10 sec) [ -6031.9701] [GTR parameters ] . ( 10 sec) [ -6031.9311] [Alpha ][ 1.001414] . ( 10 sec) [ -6031.9311] [Topology ] . ( 11 sec) [ -6031.9038] [Topology ] . ( 12 sec) [ -6031.8983] [Topology ] . ( 12 sec) [ -6031.8966] [Topology ] . ( 13 sec) [ -6031.8959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6031.895930 . ( 17 sec) [ -6031.8959] [GTR parameters ] . ( 17 sec) [ -6031.8958] [Alpha ][ 1.002853] . ( 18 sec) [ -6031.8958] [Topology ] . ( 18 sec) [ -6031.8955] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 27 sec) [ -6049.3553] [GTR parameters ] . ( 28 sec) [ -6049.3232] [Alpha ][ 0.974396] . ( 28 sec) [ -6047.0883] [ 1080] [depth= 1] . ( 28 sec) [ -6046.1418] [ 1082] [depth= 1] . ( 29 sec) [ -6044.5745] [ 1085] [depth= 1] . ( 29 sec) [ -6042.5194] [ 1085] [depth= 1] . ( 29 sec) [ -6041.2747] [ 1086] [depth= 1] . ( 29 sec) [ -6041.0408] [ 1086] [depth= 1] . ( 29 sec) [ -6040.0915] [ 1086] [depth= 1] . ( 30 sec) [ -6039.8905] [ 1086] [depth= 1] . ( 30 sec) [ -6039.6897] [ 1086] [depth= 1] . ( 30 sec) [ -6039.1390] [ 1086] [depth= 1] . ( 30 sec) [ -6039.1261] [ 1086] [depth= 1] . ( 31 sec) [ -6032.3997] [Branch lengths ] . ( 31 sec) [ -6032.3737] [GTR parameters ] . ( 31 sec) [ -6032.3571] [Alpha ][ 0.992661] . ( 34 sec) [ -6032.0587] [Branch lengths ] . ( 41 sec) [ -6031.9778] [ 1082] [depth= 1] . ( 50 sec) [ -6031.9068] [Branch lengths ] . ( 51 sec) [ -6031.9063] [GTR parameters ] . ( 51 sec) [ -6031.9017] [Alpha ][ 1.002262] . ( 51 sec) [ -6031.9017] [Topology ] . ( 51 sec) [ -6031.8970] [Topology ] . ( 52 sec) [ -6031.8960] [Topology ] . ( 53 sec) [ -6031.8956] [Topology ] . ( 53 sec) [ -6031.8955] [GTR parameters ] . ( 53 sec) [ -6031.8955] [Alpha ][ 1.003264] . ( 53 sec) [ -6031.8955] [Topology ] . ( 53 sec) [ -6031.8953] [Topology ] . ( 54 sec) [ -6031.8953] [GTR parameters ] . ( 54 sec) [ -6031.8953] [Alpha ][ 1.003264] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6031.895482 . Log likelihood obtained after SPR moves : -6031.895324 . Log likelihood of the current tree: -6031.895324. . Printing the most likely tree in file 'data12.phy_phyml_tree.txt'... . Best log likelihood : -6031.895264 . Time used 0h0m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo