.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data34.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... . 357 patterns found. (out of a total of 500 sites) . 130 sites without polymorphism (26.00%). . [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) [ -16702.1397] [GTR parameters ] . ( 1 sec) [ -16386.0518] [Alpha ][ 0.500960] . ( 1 sec) [ -16253.7354] [ 2747] [depth= 7] . ( 1 sec) [ -16223.9093] [ 2750] [depth= 1] . ( 1 sec) [ -15853.0484] [ 2700] [depth= 3] . ( 1 sec) [ -15549.3037] [ 2670] [depth= 4] . ( 1 sec) [ -15498.0708] [ 2668] [depth= 6] . ( 1 sec) [ -15382.8104] [ 2633] [depth= 1] . ( 1 sec) [ -15248.5196] [ 2629] [depth= 7] . ( 1 sec) [ -15003.0566] [ 2604] [depth= 6] . ( 1 sec) [ -14992.0720] [ 2602] [depth= 1] . ( 1 sec) [ -14784.7750] [ 2532] [depth= 10] . ( 1 sec) [ -14560.7814] [ 2507] [depth= 1] . ( 1 sec) [ -14165.7501] [ 2456] [depth= 13] . ( 1 sec) [ -14137.7871] [ 2459] [depth= 2] . ( 1 sec) [ -14034.3069] [ 2459] [depth= 1] . ( 1 sec) [ -14029.0702] [ 2454] [depth= 2] . ( 2 sec) [ -13975.7298] [ 2410] [depth= 4] . ( 2 sec) [ -13863.2787] [ 2406] [depth= 6] . ( 2 sec) [ -13713.4166] [ 2405] [depth= 3] . ( 2 sec) [ -13327.0070] [ 2405] [depth= 12] . ( 2 sec) [ -12957.5085] [ 2289] [depth= 13] . ( 2 sec) [ -12500.1120] [ 2176] [depth= 4] . ( 2 sec) [ -12336.3005] [ 2153] [depth= 9] . ( 2 sec) [ -12139.6293] [ 2144] [depth= 7] . ( 2 sec) [ -11899.5064] [ 2061] [depth= 5] . ( 2 sec) [ -11837.7628] [ 2028] [depth= 2] . ( 2 sec) [ -9939.0593] [ 2001] [depth= 1] . ( 2 sec) [ -9701.3032] [ 1949] [depth= 9] . ( 2 sec) [ -9577.7894] [ 1936] [depth= 3] . ( 2 sec) [ -9529.7911] [ 1932] [depth= 2] . ( 2 sec) [ -9497.2821] [ 1934] [depth= 13] . ( 2 sec) [ -9478.6511] [ 1932] [depth= 3] . ( 3 sec) [ -9462.9778] [ 1930] [depth= 1] . ( 3 sec) [ -9428.1993] [ 1932] [depth= 1] . ( 3 sec) [ -9400.1980] [ 1931] [depth= 13] . ( 3 sec) [ -9362.7601] [ 1892] [depth= 7] . ( 3 sec) [ -9104.4351] [ 1894] [depth= 1] . ( 3 sec) [ -8957.7930] [ 1777] [depth= 10] . ( 3 sec) [ -8939.6950] [ 1779] [depth= 1] . ( 3 sec) [ -8873.7022] [ 1780] [depth= 2] . ( 3 sec) [ -8414.7957] [ 1698] [depth= 5] . ( 3 sec) [ -8303.3901] [ 1657] [depth= 7] . ( 3 sec) [ -8300.7139] [ 1655] [depth= 1] . ( 3 sec) [ -8139.2957] [ 1588] [depth= 11] . ( 3 sec) [ -8095.3617] [ 1588] [depth= 1] . ( 3 sec) [ -8053.2634] [ 1590] [depth= 1] . ( 3 sec) [ -7980.5162] [ 1577] [depth= 5] . ( 3 sec) [ -7977.3891] [ 1576] [depth= 1] . ( 3 sec) [ -7899.8266] [ 1540] [depth= 4] . ( 3 sec) [ -7804.7369] [ 1548] [depth= 3] . ( 3 sec) [ -7768.6922] [ 1544] [depth= 4] . ( 3 sec) [ -7655.5748] [ 1521] [depth= 5] . ( 3 sec) [ -7651.7279] [ 1519] [depth= 1] . ( 4 sec) [ -7498.3225] [ 1477] [depth= 7] . ( 4 sec) [ -7441.8232] [ 1465] [depth= 1] . ( 4 sec) [ -7441.5901] [ 1466] [depth= 1] . ( 4 sec) [ -7396.0137] [ 1461] [depth= 2] . ( 4 sec) [ -7393.2687] [ 1460] [depth= 1] . ( 4 sec) [ -7388.9676] [ 1462] [depth= 1] . ( 4 sec) [ -7233.9156] [ 1426] [depth= 5] . ( 4 sec) [ -7018.2926] [ 1404] [depth= 6] . ( 4 sec) [ -6897.3913] [ 1384] [depth= 3] . ( 4 sec) [ -6889.4734] [ 1384] [depth= 1] . ( 4 sec) [ -6881.8766] [ 1388] [depth= 3] . ( 4 sec) [ -6809.0970] [ 1339] [depth= 4] . ( 4 sec) [ -6806.6615] [ 1338] [depth= 1] . ( 4 sec) [ -6798.0177] [ 1336] [depth= 1] . ( 4 sec) [ -6778.4470] [ 1331] [depth= 2] . ( 5 sec) [ -6778.3227] [ 1331] [depth= 1] . ( 5 sec) [ -6769.9758] [ 1327] [depth= 2] . ( 5 sec) [ -6567.4929] [ 1292] [depth= 5] . ( 5 sec) [ -6527.1413] [ 1262] [depth= 4] . ( 5 sec) [ -6462.7043] [ 1233] [depth= 2] . ( 5 sec) [ -6457.4501] [ 1226] [depth= 1] . ( 5 sec) [ -6180.5542] [ 1194] [depth= 5] . ( 5 sec) [ -6174.2911] [ 1193] [depth= 1] . ( 5 sec) [ -6173.4470] [ 1188] [depth= 1] . ( 5 sec) [ -6166.6176] [ 1189] [depth= 1] . ( 5 sec) [ -6091.7017] [ 1160] [depth= 2] . ( 5 sec) [ -6089.1671] [ 1159] [depth= 1] . ( 5 sec) [ -6056.8581] [ 1160] [depth= 2] . ( 5 sec) [ -6056.5529] [ 1160] [depth= 1] . ( 5 sec) [ -6035.8668] [ 1150] [depth= 1] . ( 5 sec) [ -6034.2044] [ 1150] [depth= 2] . ( 6 sec) [ -5988.0652] [Branch lengths ] . ( 6 sec) [ -5986.2570] [GTR parameters ] . ( 6 sec) [ -5963.2000] [Alpha ][ 0.927872] . ( 6 sec) [ -5962.0635] [ 1154] [depth= 2] . ( 6 sec) [ -5962.0213] [ 1154] [depth= 1] . ( 7 sec) [ -5947.8924] [ 1131] [depth= 1] . ( 7 sec) [ -5939.9014] [ 1118] [depth= 1] . ( 7 sec) [ -5913.1593] [ 1111] [depth= 1] . ( 7 sec) [ -5911.9398] [ 1118] [depth= 1] . ( 7 sec) [ -5911.9131] [ 1118] [depth= 1] . ( 7 sec) [ -5910.5382] [ 1107] [depth= 1] . ( 8 sec) [ -5910.3996] [ 1105] [depth= 1] . ( 8 sec) [ -5910.3798] [ 1105] [depth= 1] . ( 8 sec) [ -5909.8540] [ 1107] [depth= 1] . ( 8 sec) [ -5909.8048] [ 1107] [depth= 1] . ( 8 sec) [ -5888.5261] [ 1094] [depth= 2] . ( 8 sec) [ -5887.4575] [ 1093] [depth= 1] . ( 8 sec) [ -5887.4158] [ 1093] [depth= 2] . ( 8 sec) [ -5887.3181] [ 1093] [depth= 1] . ( 8 sec) [ -5884.0600] [ 1089] [depth= 1] . ( 10 sec) [ -5883.9076] [ 1089] [depth= 1] . ( 10 sec) [ -5880.1215] [Branch lengths ] . ( 10 sec) [ -5879.7613] [GTR parameters ] . ( 10 sec) [ -5878.7119] [Alpha ][ 1.072247] . ( 15 sec) [ -5878.3651] [Branch lengths ] . ( 36 sec) [ -5878.3470] [Branch lengths ] . ( 36 sec) [ -5878.3470] [Topology ] . ( 37 sec) [ -5878.3462] [Topology ] . ( 37 sec) [ -5878.3452] [GTR parameters ] . ( 37 sec) [ -5878.3399] [Alpha ][ 1.083739] . ( 37 sec) [ -5878.3399] [Topology ] . ( 38 sec) [ -5878.3395] [Topology ] . ( 38 sec) [ -5878.3395] [GTR parameters ] . ( 38 sec) [ -5878.3395] [Alpha ][ 1.083739] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -5878.3323] [Topology ] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -5878.2922] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.292187. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14295.4773] [GTR parameters ] . ( 1 sec) [ -13997.1392] [Alpha ][ 0.500960] . ( 1 sec) [ -13762.3177] [ 2679] [depth= 3] . ( 1 sec) [ -13512.9478] [ 2633] [depth= 3] . ( 1 sec) [ -13338.1857] [ 2614] [depth= 4] . ( 1 sec) [ -13264.3517] [ 2604] [depth= 3] . ( 1 sec) [ -13090.4146] [ 2572] [depth= 1] . ( 1 sec) [ -13052.4958] [ 2552] [depth= 7] . ( 1 sec) [ -12989.1228] [ 2554] [depth= 1] . ( 1 sec) [ -12933.3259] [ 2550] [depth= 2] . ( 1 sec) [ -12862.7496] [ 2537] [depth= 2] . ( 1 sec) [ -12838.6307] [ 2536] [depth= 4] . ( 1 sec) [ -12535.2659] [ 2487] [depth= 8] . ( 1 sec) [ -12379.5228] [ 2478] [depth= 3] . ( 1 sec) [ -12069.6714] [ 2421] [depth= 9] . ( 2 sec) [ -11934.6258] [ 2412] [depth= 4] . ( 2 sec) [ -11404.0001] [ 2359] [depth= 16] . ( 2 sec) [ -11115.5919] [ 2235] [depth= 11] . ( 2 sec) [ -11101.5733] [ 2232] [depth= 1] . ( 2 sec) [ -10827.1659] [ 2233] [depth= 1] . ( 2 sec) [ -10656.2267] [ 2221] [depth= 9] . ( 2 sec) [ -10555.6653] [ 2201] [depth= 1] . ( 2 sec) [ -10323.9979] [ 2150] [depth= 18] . ( 2 sec) [ -10249.6956] [ 2150] [depth= 8] . ( 2 sec) [ -9856.4043] [ 2047] [depth= 13] . ( 2 sec) [ -9802.3927] [ 2031] [depth= 9] . ( 2 sec) [ -9712.0719] [ 1995] [depth= 7] . ( 2 sec) [ -9527.5610] [ 1954] [depth= 3] . ( 2 sec) [ -9420.4392] [ 1940] [depth= 5] . ( 2 sec) [ -9219.9215] [ 1939] [depth= 9] . ( 2 sec) [ -8959.9388] [ 1853] [depth= 9] . ( 2 sec) [ -8888.7608] [ 1862] [depth= 10] . ( 2 sec) [ -8874.5138] [ 1847] [depth= 4] . ( 2 sec) [ -8650.3798] [ 1841] [depth= 7] . ( 2 sec) [ -8631.2656] [ 1843] [depth= 1] . ( 2 sec) [ -8627.8786] [ 1843] [depth= 1] . ( 2 sec) [ -8606.7839] [ 1841] [depth= 1] . ( 2 sec) [ -8601.5042] [ 1840] [depth= 3] . ( 2 sec) [ -8523.2591] [ 1823] [depth= 4] . ( 2 sec) [ -8324.8607] [ 1752] [depth= 3] . ( 2 sec) [ -8162.8259] [ 1752] [depth= 1] . ( 2 sec) [ -8112.9440] [ 1713] [depth= 4] . ( 3 sec) [ -8095.0213] [ 1707] [depth= 1] . ( 3 sec) [ -8056.5708] [ 1675] [depth= 1] . ( 3 sec) [ -8024.9176] [ 1672] [depth= 2] . ( 3 sec) [ -8007.4272] [ 1678] [depth= 1] . ( 3 sec) [ -7985.7401] [ 1651] [depth= 5] . ( 3 sec) [ -7810.8701] [ 1601] [depth= 5] . ( 3 sec) [ -7798.7619] [ 1601] [depth= 1] . ( 3 sec) [ -7798.0847] [ 1602] [depth= 1] . ( 3 sec) [ -7791.3405] [ 1600] [depth= 2] . ( 3 sec) [ -7767.0275] [ 1569] [depth= 1] . ( 3 sec) [ -7764.2259] [ 1571] [depth= 1] . ( 3 sec) [ -7760.5283] [ 1569] [depth= 1] . ( 3 sec) [ -7751.1430] [ 1574] [depth= 2] . ( 3 sec) [ -7744.6556] [ 1572] [depth= 1] . ( 3 sec) [ -7354.5362] [ 1508] [depth= 12] . ( 3 sec) [ -7354.1933] [ 1508] [depth= 1] . ( 3 sec) [ -7334.5299] [ 1500] [depth= 2] . ( 3 sec) [ -7306.7650] [ 1499] [depth= 2] . ( 3 sec) [ -7194.9941] [ 1501] [depth= 1] . ( 3 sec) [ -7186.1776] [ 1499] [depth= 1] . ( 3 sec) [ -7182.6908] [ 1474] [depth= 2] . ( 3 sec) [ -7074.9087] [ 1433] [depth= 8] . ( 3 sec) [ -7067.6353] [ 1432] [depth= 1] . ( 3 sec) [ -7059.2998] [ 1429] [depth= 1] . ( 3 sec) [ -7057.9719] [ 1430] [depth= 1] . ( 4 sec) [ -6824.1288] [ 1345] [depth= 5] . ( 4 sec) [ -6818.7278] [ 1346] [depth= 1] . ( 4 sec) [ -6817.7740] [ 1347] [depth= 2] . ( 4 sec) [ -6407.6905] [ 1254] [depth= 5] . ( 4 sec) [ -6407.3564] [ 1254] [depth= 1] . ( 4 sec) [ -6405.8902] [ 1254] [depth= 1] . ( 4 sec) [ -6363.1515] [ 1245] [depth= 3] . ( 4 sec) [ -6346.1230] [ 1222] [depth= 4] . ( 4 sec) [ -6344.7928] [ 1222] [depth= 1] . ( 4 sec) [ -6342.2254] [ 1221] [depth= 1] . ( 4 sec) [ -6342.1807] [ 1221] [depth= 1] . ( 4 sec) [ -6241.1924] [ 1194] [depth= 2] . ( 4 sec) [ -6235.5517] [ 1193] [depth= 1] . ( 4 sec) [ -6222.2436] [ 1181] [depth= 1] . ( 4 sec) [ -6141.5553] [ 1143] [depth= 3] . ( 4 sec) [ -6066.6207] [ 1121] [depth= 2] . ( 4 sec) [ -6038.5485] [ 1119] [depth= 1] . ( 4 sec) [ -6026.2001] [ 1113] [depth= 1] . ( 4 sec) [ -6018.5963] [ 1112] [depth= 4] . ( 4 sec) [ -6007.7608] [ 1110] [depth= 1] . ( 5 sec) [ -6004.3601] [ 1108] [depth= 2] . ( 5 sec) [ -5995.6300] [ 1106] [depth= 1] . ( 5 sec) [ -5943.1180] [Branch lengths ] . ( 6 sec) [ -5940.8441] [GTR parameters ] . ( 6 sec) [ -5914.1122] [Alpha ][ 0.989506] . ( 6 sec) [ -5914.0936] [ 1109] [depth= 1] . ( 6 sec) [ -5909.0782] [ 1096] [depth= 1] . ( 6 sec) [ -5909.0086] [ 1096] [depth= 1] . ( 6 sec) [ -5890.9392] [ 1090] [depth= 2] . ( 6 sec) [ -5889.9655] [ 1089] [depth= 1] . ( 7 sec) [ -5889.9002] [ 1089] [depth= 1] . ( 7 sec) [ -5885.9120] [ 1087] [depth= 1] . ( 7 sec) [ -5885.8738] [ 1087] [depth= 1] . ( 7 sec) [ -5885.8524] [ 1087] [depth= 1] . ( 8 sec) [ -5885.6837] [ 1087] [depth= 2] . ( 8 sec) [ -5885.6116] [ 1087] [depth= 1] . ( 8 sec) [ -5885.5838] [ 1087] [depth= 2] . ( 8 sec) [ -5885.3172] [ 1087] [depth= 1] . ( 8 sec) [ -5885.2598] [ 1087] [depth= 1] . ( 9 sec) [ -5879.2219] [Branch lengths ] . ( 10 sec) [ -5879.1384] [GTR parameters ] . ( 10 sec) [ -5878.7904] [Alpha ][ 1.076085] . ( 13 sec) [ -5878.7800] [ 1087] [depth= 2] . ( 13 sec) [ -5878.3758] [Branch lengths ] . ( 14 sec) [ -5878.3757] [GTR parameters ] . ( 14 sec) [ -5878.3740] [Alpha ][ 1.082452] . ( 33 sec) [ -5878.3546] [Branch lengths ] . ( 33 sec) [ -5878.3546] [Topology ] . ( 33 sec) [ -5878.3537] [Topology ] . ( 33 sec) [ -5878.3537] [GTR parameters ] . ( 33 sec) [ -5878.3537] [Alpha ][ 1.083534] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5878.3530] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.352995. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17137.1759] [GTR parameters ] . ( 1 sec) [ -16815.1242] [Alpha ][ 0.500960] . ( 1 sec) [ -16652.9372] [ 2819] [depth= 8] . ( 1 sec) [ -16448.3313] [ 2767] [depth= 8] . ( 1 sec) [ -16262.7868] [ 2763] [depth= 5] . ( 1 sec) [ -16242.2231] [ 2763] [depth= 1] . ( 1 sec) [ -16212.8125] [ 2756] [depth= 6] . ( 1 sec) [ -15963.6626] [ 2752] [depth= 5] . ( 1 sec) [ -15503.4313] [ 2676] [depth= 5] . ( 1 sec) [ -15200.9556] [ 2663] [depth= 12] . ( 1 sec) [ -15165.7498] [ 2635] [depth= 1] . ( 1 sec) [ -15059.7165] [ 2618] [depth= 12] . ( 1 sec) [ -14909.9948] [ 2596] [depth= 2] . ( 1 sec) [ -14897.7851] [ 2598] [depth= 1] . ( 1 sec) [ -14861.0617] [ 2597] [depth= 1] . ( 1 sec) [ -14578.2731] [ 2578] [depth= 2] . ( 1 sec) [ -14385.5952] [ 2563] [depth= 13] . ( 1 sec) [ -14148.6060] [ 2480] [depth= 1] . ( 2 sec) [ -14013.3410] [ 2474] [depth= 10] . ( 2 sec) [ -13677.1312] [ 2445] [depth= 1] . ( 2 sec) [ -13577.6676] [ 2440] [depth= 11] . ( 2 sec) [ -13392.0045] [ 2407] [depth= 1] . ( 2 sec) [ -13142.8872] [ 2397] [depth= 11] . ( 2 sec) [ -13024.4139] [ 2353] [depth= 4] . ( 2 sec) [ -13023.8206] [ 2322] [depth= 7] . ( 2 sec) [ -12888.0026] [ 2307] [depth= 7] . ( 2 sec) [ -12887.2865] [ 2308] [depth= 2] . ( 2 sec) [ -12775.9664] [ 2256] [depth= 3] . ( 2 sec) [ -12661.3219] [ 2251] [depth= 8] . ( 2 sec) [ -12528.5924] [ 2211] [depth= 10] . ( 2 sec) [ -12389.5307] [ 2143] [depth= 8] . ( 2 sec) [ -12358.8080] [ 2156] [depth= 1] . ( 2 sec) [ -12317.0191] [ 2139] [depth= 2] . ( 2 sec) [ -12051.0729] [ 2048] [depth= 11] . ( 2 sec) [ -12017.8847] [ 2048] [depth= 1] . ( 2 sec) [ -12000.5209] [ 2058] [depth= 3] . ( 2 sec) [ -11953.5322] [ 2052] [depth= 1] . ( 2 sec) [ -11785.6627] [ 1971] [depth= 4] . ( 2 sec) [ -11766.7648] [ 1970] [depth= 1] . ( 2 sec) [ -11620.2583] [ 1926] [depth= 7] . ( 2 sec) [ -11605.7991] [ 1922] [depth= 1] . ( 2 sec) [ -11587.5886] [ 1879] [depth= 1] . ( 2 sec) [ -11581.3299] [ 1881] [depth= 1] . ( 3 sec) [ -11531.4255] [ 1875] [depth= 4] . ( 3 sec) [ -9263.9288] [ 1827] [depth= 6] . ( 3 sec) [ -9107.9181] [ 1795] [depth= 4] . ( 3 sec) [ -9102.7755] [ 1793] [depth= 2] . ( 3 sec) [ -8717.3085] [ 1760] [depth= 6] . ( 3 sec) [ -8652.5484] [ 1758] [depth= 2] . ( 3 sec) [ -8557.2480] [ 1755] [depth= 1] . ( 3 sec) [ -8510.0914] [ 1704] [depth= 4] . ( 3 sec) [ -8504.3759] [ 1703] [depth= 2] . ( 3 sec) [ -8416.1887] [ 1701] [depth= 2] . ( 3 sec) [ -8406.9257] [ 1703] [depth= 2] . ( 3 sec) [ -8218.6977] [ 1629] [depth= 7] . ( 3 sec) [ -8046.5239] [ 1586] [depth= 2] . ( 3 sec) [ -7865.1967] [ 1581] [depth= 1] . ( 3 sec) [ -7797.8264] [ 1576] [depth= 3] . ( 3 sec) [ -7512.9563] [ 1549] [depth= 3] . ( 3 sec) [ -7413.2716] [ 1524] [depth= 2] . ( 3 sec) [ -7413.1566] [ 1526] [depth= 1] . ( 3 sec) [ -7339.0433] [ 1482] [depth= 4] . ( 3 sec) [ -7329.0111] [ 1481] [depth= 1] . ( 3 sec) [ -7325.9580] [ 1483] [depth= 1] . ( 3 sec) [ -7320.5276] [ 1488] [depth= 3] . ( 3 sec) [ -7254.7077] [ 1476] [depth= 4] . ( 3 sec) [ -7170.2337] [ 1454] [depth= 3] . ( 3 sec) [ -7169.7091] [ 1454] [depth= 1] . ( 4 sec) [ -6911.1838] [ 1398] [depth= 7] . ( 4 sec) [ -6823.0828] [ 1388] [depth= 1] . ( 4 sec) [ -6820.7862] [ 1388] [depth= 1] . ( 4 sec) [ -6609.0289] [ 1327] [depth= 1] . ( 4 sec) [ -6608.9866] [ 1327] [depth= 2] . ( 4 sec) [ -6587.9762] [ 1318] [depth= 2] . ( 4 sec) [ -6525.1386] [ 1287] [depth= 2] . ( 4 sec) [ -6494.0978] [ 1285] [depth= 1] . ( 4 sec) [ -6473.8969] [ 1279] [depth= 1] . ( 4 sec) [ -6472.6532] [ 1279] [depth= 1] . ( 4 sec) [ -6465.0444] [ 1275] [depth= 1] . ( 4 sec) [ -6453.5664] [ 1269] [depth= 1] . ( 4 sec) [ -6380.8537] [ 1248] [depth= 4] . ( 4 sec) [ -6377.0374] [ 1249] [depth= 1] . ( 4 sec) [ -6373.8437] [ 1249] [depth= 1] . ( 4 sec) [ -6311.7370] [ 1225] [depth= 2] . ( 4 sec) [ -6299.6162] [ 1220] [depth= 2] . ( 4 sec) [ -6299.4960] [ 1220] [depth= 1] . ( 4 sec) [ -6287.9470] [ 1218] [depth= 1] . ( 4 sec) [ -6283.5075] [ 1217] [depth= 1] . ( 4 sec) [ -6232.6178] [ 1204] [depth= 2] . ( 4 sec) [ -6182.2493] [ 1185] [depth= 1] . ( 4 sec) [ -6033.3106] [ 1107] [depth= 2] . ( 5 sec) [ -5975.3394] [Branch lengths ] . ( 5 sec) [ -5971.3000] [GTR parameters ] . ( 5 sec) [ -5945.1926] [Alpha ][ 0.982399] . ( 5 sec) [ -5933.6413] [ 1103] [depth= 4] . ( 6 sec) [ -5922.1197] [ 1099] [depth= 2] . ( 6 sec) [ -5917.9630] [ 1097] [depth= 1] . ( 6 sec) [ -5907.9523] [ 1094] [depth= 1] . ( 6 sec) [ -5887.0381] [ 1084] [depth= 3] . ( 6 sec) [ -5886.8136] [ 1086] [depth= 1] . ( 6 sec) [ -5886.7784] [ 1084] [depth= 1] . ( 7 sec) [ -5885.5510] [ 1085] [depth= 1] . ( 7 sec) [ -5885.3090] [ 1087] [depth= 1] . ( 7 sec) [ -5884.0620] [ 1085] [depth= 1] . ( 7 sec) [ -5884.0497] [ 1085] [depth= 2] . ( 7 sec) [ -5884.0236] [ 1085] [depth= 1] . ( 7 sec) [ -5883.9585] [ 1085] [depth= 1] . ( 8 sec) [ -5883.9438] [ 1085] [depth= 1] . ( 8 sec) [ -5883.9229] [ 1085] [depth= 1] . ( 8 sec) [ -5883.8609] [ 1087] [depth= 1] . ( 8 sec) [ -5883.8428] [ 1087] [depth= 1] . ( 9 sec) [ -5879.2499] [Branch lengths ] . ( 9 sec) [ -5879.1713] [GTR parameters ] . ( 9 sec) [ -5878.7949] [Alpha ][ 1.072187] . ( 13 sec) [ -5878.4033] [Branch lengths ] . ( 31 sec) [ -5878.3633] [Branch lengths ] . ( 31 sec) [ -5878.3633] [Topology ] . ( 32 sec) [ -5878.3606] [Topology ] . ( 32 sec) [ -5878.3598] [Topology ] . ( 33 sec) [ -5878.3593] [GTR parameters ] . ( 33 sec) [ -5878.3542] [Alpha ][ 1.083359] . ( 33 sec) [ -5878.3542] [Topology ] . ( 33 sec) [ -5878.3537] [Topology ] . ( 33 sec) [ -5878.3537] [GTR parameters ] . ( 33 sec) [ -5878.3537] [Alpha ][ 1.083359] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5878.2804] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.280447. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17791.1653] [GTR parameters ] . ( 0 sec) [ -17469.5009] [Alpha ][ 0.500960] . ( 0 sec) [ -17160.3075] [ 2795] [depth= 8] . ( 0 sec) [ -16832.4869] [ 2735] [depth= 9] . ( 0 sec) [ -14340.2378] [ 2713] [depth= 8] . ( 0 sec) [ -13473.5471] [ 2620] [depth= 1] . ( 0 sec) [ -13178.3633] [ 2608] [depth= 6] . ( 0 sec) [ -13075.7481] [ 2588] [depth= 2] . ( 0 sec) [ -12985.5682] [ 2588] [depth= 5] . ( 0 sec) [ -12783.8309] [ 2555] [depth= 5] . ( 1 sec) [ -12620.6571] [ 2544] [depth= 4] . ( 1 sec) [ -12434.1327] [ 2536] [depth= 4] . ( 1 sec) [ -12412.6677] [ 2534] [depth= 3] . ( 1 sec) [ -12218.6341] [ 2479] [depth= 5] . ( 1 sec) [ -12066.0526] [ 2431] [depth= 6] . ( 1 sec) [ -12055.8466] [ 2429] [depth= 2] . ( 1 sec) [ -11620.2415] [ 2379] [depth= 5] . ( 1 sec) [ -11582.7624] [ 2371] [depth= 7] . ( 1 sec) [ -11490.5909] [ 2379] [depth= 1] . ( 1 sec) [ -11296.7174] [ 2288] [depth= 10] . ( 1 sec) [ -11144.4995] [ 2246] [depth= 16] . ( 1 sec) [ -10895.4175] [ 2248] [depth= 9] . ( 1 sec) [ -10804.6794] [ 2235] [depth= 9] . ( 1 sec) [ -10666.0544] [ 2202] [depth= 3] . ( 1 sec) [ -10544.6125] [ 2198] [depth= 1] . ( 1 sec) [ -10344.9074] [ 2192] [depth= 8] . ( 1 sec) [ -10160.0341] [ 2175] [depth= 3] . ( 1 sec) [ -10045.2890] [ 2096] [depth= 3] . ( 1 sec) [ -9955.1165] [ 2110] [depth= 7] . ( 1 sec) [ -9835.9203] [ 2106] [depth= 13] . ( 1 sec) [ -9713.2811] [ 2101] [depth= 5] . ( 1 sec) [ -9702.6323] [ 2104] [depth= 1] . ( 1 sec) [ -9565.5977] [ 2095] [depth= 6] . ( 1 sec) [ -9264.5363] [ 2043] [depth= 9] . ( 2 sec) [ -9232.8365] [ 2019] [depth= 6] . ( 2 sec) [ -9102.7303] [ 2005] [depth= 2] . ( 2 sec) [ -9084.1379] [ 2001] [depth= 1] . ( 2 sec) [ -8976.7301] [ 1921] [depth= 1] . ( 2 sec) [ -8781.1792] [ 1909] [depth= 2] . ( 2 sec) [ -8638.4539] [ 1911] [depth= 1] . ( 2 sec) [ -8624.3848] [ 1924] [depth= 9] . ( 2 sec) [ -8530.0858] [ 1918] [depth= 4] . ( 2 sec) [ -8495.5125] [ 1909] [depth= 1] . ( 2 sec) [ -8315.0372] [ 1856] [depth= 2] . ( 2 sec) [ -8275.2883] [ 1845] [depth= 3] . ( 2 sec) [ -8240.3112] [ 1841] [depth= 1] . ( 2 sec) [ -8185.8039] [ 1815] [depth= 7] . ( 2 sec) [ -8120.8063] [ 1835] [depth= 2] . ( 2 sec) [ -7890.0849] [ 1733] [depth= 1] . ( 2 sec) [ -7830.6712] [ 1734] [depth= 2] . ( 2 sec) [ -7752.3108] [ 1723] [depth= 3] . ( 2 sec) [ -7733.8968] [ 1724] [depth= 2] . ( 2 sec) [ -7721.6894] [ 1724] [depth= 2] . ( 2 sec) [ -7612.1404] [ 1662] [depth= 1] . ( 2 sec) [ -7552.9409] [ 1661] [depth= 2] . ( 3 sec) [ -7547.0475] [ 1660] [depth= 1] . ( 3 sec) [ -7538.7317] [ 1644] [depth= 1] . ( 3 sec) [ -7505.8180] [ 1651] [depth= 1] . ( 3 sec) [ -7452.0508] [ 1641] [depth= 9] . ( 3 sec) [ -7381.8687] [ 1610] [depth= 4] . ( 3 sec) [ -7336.0815] [ 1584] [depth= 1] . ( 3 sec) [ -7331.9485] [ 1584] [depth= 1] . ( 3 sec) [ -7326.8267] [ 1582] [depth= 1] . ( 3 sec) [ -7293.2553] [ 1558] [depth= 3] . ( 3 sec) [ -7275.6695] [ 1550] [depth= 1] . ( 3 sec) [ -7273.8790] [ 1550] [depth= 1] . ( 3 sec) [ -7267.3413] [ 1544] [depth= 3] . ( 3 sec) [ -7248.9780] [ 1537] [depth= 6] . ( 3 sec) [ -7227.6351] [ 1537] [depth= 8] . ( 3 sec) [ -7216.2174] [ 1515] [depth= 3] . ( 3 sec) [ -7033.9871] [ 1463] [depth= 3] . ( 3 sec) [ -7013.6361] [ 1463] [depth= 1] . ( 3 sec) [ -7012.0920] [ 1463] [depth= 1] . ( 3 sec) [ -7009.5531] [ 1464] [depth= 2] . ( 3 sec) [ -7009.1040] [ 1464] [depth= 1] . ( 3 sec) [ -7002.5780] [ 1462] [depth= 1] . ( 4 sec) [ -6946.5507] [ 1457] [depth= 2] . ( 4 sec) [ -6891.6789] [ 1458] [depth= 1] . ( 4 sec) [ -6884.8983] [ 1447] [depth= 1] . ( 4 sec) [ -6876.8162] [ 1443] [depth= 2] . ( 4 sec) [ -6862.5476] [ 1401] [depth= 4] . ( 4 sec) [ -6638.1606] [ 1400] [depth= 2] . ( 4 sec) [ -6563.5809] [ 1336] [depth= 3] . ( 4 sec) [ -6563.5579] [ 1336] [depth= 1] . ( 4 sec) [ -6562.8347] [ 1336] [depth= 1] . ( 4 sec) [ -6535.4582] [ 1317] [depth= 1] . ( 4 sec) [ -6535.4106] [ 1317] [depth= 1] . ( 4 sec) [ -6523.1699] [ 1317] [depth= 1] . ( 4 sec) [ -6515.7176] [ 1315] [depth= 1] . ( 4 sec) [ -6427.0362] [ 1291] [depth= 12] . ( 4 sec) [ -6342.8404] [ 1261] [depth= 1] . ( 4 sec) [ -6304.2935] [ 1252] [depth= 3] . ( 4 sec) [ -6084.2894] [ 1146] [depth= 3] . ( 4 sec) [ -6053.8365] [ 1133] [depth= 1] . ( 5 sec) [ -5993.2363] [Branch lengths ] . ( 5 sec) [ -5989.4625] [GTR parameters ] . ( 5 sec) [ -5965.4023] [Alpha ][ 0.934885] . ( 5 sec) [ -5965.3624] [ 1134] [depth= 1] . ( 5 sec) [ -5950.8370] [ 1119] [depth= 2] . ( 6 sec) [ -5947.8499] [ 1111] [depth= 1] . ( 6 sec) [ -5947.2178] [ 1110] [depth= 2] . ( 6 sec) [ -5947.2007] [ 1111] [depth= 1] . ( 6 sec) [ -5931.0447] [ 1106] [depth= 3] . ( 6 sec) [ -5928.1517] [ 1102] [depth= 1] . ( 7 sec) [ -5918.1386] [ 1096] [depth= 1] . ( 7 sec) [ -5918.1198] [ 1097] [depth= 1] . ( 7 sec) [ -5918.0098] [ 1097] [depth= 1] . ( 7 sec) [ -5897.0830] [ 1088] [depth= 1] . ( 7 sec) [ -5896.8262] [ 1088] [depth= 2] . ( 7 sec) [ -5896.7951] [ 1088] [depth= 2] . ( 8 sec) [ -5892.6886] [ 1086] [depth= 1] . ( 8 sec) [ -5890.3344] [ 1085] [depth= 1] . ( 8 sec) [ -5889.5764] [ 1085] [depth= 2] . ( 8 sec) [ -5889.5226] [ 1085] [depth= 1] . ( 8 sec) [ -5889.4972] [ 1085] [depth= 1] . ( 9 sec) [ -5889.3448] [ 1087] [depth= 1] . ( 9 sec) [ -5889.3191] [ 1087] [depth= 1] . ( 9 sec) [ -5880.6690] [Branch lengths ] . ( 9 sec) [ -5880.3045] [GTR parameters ] . ( 9 sec) [ -5879.3020] [Alpha ][ 1.076335] . ( 13 sec) [ -5878.3977] [Branch lengths ] . ( 31 sec) [ -5878.3301] [ 1086] [depth= 1] . ( 31 sec) [ -5878.2860] [Branch lengths ] . ( 32 sec) [ -5878.2819] [GTR parameters ] . ( 32 sec) [ -5878.2790] [Alpha ][ 1.084853] . ( 32 sec) [ -5878.2790] [Topology ] . ( 32 sec) [ -5878.2775] [Topology ] . ( 33 sec) [ -5878.2773] [Topology ] . ( 33 sec) [ -5878.2773] [GTR parameters ] . ( 33 sec) [ -5878.2773] [Alpha ][ 1.084853] . ( 33 sec) [ -5878.2773] [Topology ] . ( 34 sec) [ -5878.2773] [Topology ] . ( 34 sec) [ -5878.2773] [GTR parameters ] . ( 34 sec) [ -5878.2773] [Alpha ][ 1.084853] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.277258. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17681.5491] [GTR parameters ] . ( 0 sec) [ -17350.9687] [Alpha ][ 0.500960] . ( 0 sec) [ -17144.0262] [ 2839] [depth= 6] . ( 0 sec) [ -16896.0395] [ 2789] [depth= 11] . ( 0 sec) [ -16865.2267] [ 2774] [depth= 4] . ( 1 sec) [ -16688.5926] [ 2773] [depth= 5] . ( 1 sec) [ -16658.3520] [ 2760] [depth= 5] . ( 1 sec) [ -16638.3264] [ 2759] [depth= 3] . ( 1 sec) [ -16394.4177] [ 2742] [depth= 14] . ( 1 sec) [ -14001.2253] [ 2746] [depth= 1] . ( 1 sec) [ -13529.3916] [ 2694] [depth= 19] . ( 1 sec) [ -13141.6745] [ 2634] [depth= 17] . ( 1 sec) [ -12747.0509] [ 2547] [depth= 16] . ( 1 sec) [ -12317.0329] [ 2471] [depth= 10] . ( 1 sec) [ -12312.8970] [ 2471] [depth= 1] . ( 1 sec) [ -12046.4193] [ 2413] [depth= 8] . ( 1 sec) [ -11964.8699] [ 2406] [depth= 1] . ( 1 sec) [ -11903.1462] [ 2396] [depth= 3] . ( 1 sec) [ -11536.0407] [ 2395] [depth= 7] . ( 1 sec) [ -11462.2253] [ 2390] [depth= 2] . ( 1 sec) [ -11305.4411] [ 2342] [depth= 2] . ( 1 sec) [ -11291.0041] [ 2341] [depth= 2] . ( 1 sec) [ -11202.2167] [ 2294] [depth= 2] . ( 1 sec) [ -11120.3941] [ 2292] [depth= 1] . ( 1 sec) [ -11046.5066] [ 2286] [depth= 1] . ( 1 sec) [ -10984.6085] [ 2265] [depth= 3] . ( 1 sec) [ -10825.0175] [ 2217] [depth= 9] . ( 1 sec) [ -10786.7926] [ 2212] [depth= 2] . ( 1 sec) [ -10447.9640] [ 2106] [depth= 4] . ( 1 sec) [ -10426.0586] [ 2090] [depth= 1] . ( 2 sec) [ -10416.9629] [ 2090] [depth= 1] . ( 2 sec) [ -10380.8025] [ 2074] [depth= 1] . ( 2 sec) [ -10005.5943] [ 2035] [depth= 11] . ( 2 sec) [ -9852.9357] [ 2024] [depth= 2] . ( 2 sec) [ -9626.1460] [ 2002] [depth= 10] . ( 2 sec) [ -9608.4324] [ 2006] [depth= 1] . ( 2 sec) [ -9466.4368] [ 1961] [depth= 5] . ( 2 sec) [ -9423.9453] [ 1956] [depth= 10] . ( 2 sec) [ -9339.8836] [ 1907] [depth= 8] . ( 2 sec) [ -9154.1947] [ 1898] [depth= 7] . ( 2 sec) [ -9149.4248] [ 1896] [depth= 1] . ( 2 sec) [ -9137.9687] [ 1894] [depth= 1] . ( 2 sec) [ -9135.9513] [ 1891] [depth= 1] . ( 2 sec) [ -8974.0674] [ 1884] [depth= 10] . ( 2 sec) [ -8963.8217] [ 1886] [depth= 1] . ( 2 sec) [ -8949.1377] [ 1870] [depth= 1] . ( 2 sec) [ -8935.6801] [ 1867] [depth= 1] . ( 2 sec) [ -8706.3301] [ 1776] [depth= 13] . ( 2 sec) [ -8699.7874] [ 1778] [depth= 1] . ( 2 sec) [ -8490.7886] [ 1730] [depth= 8] . ( 2 sec) [ -8313.9348] [ 1697] [depth= 8] . ( 2 sec) [ -8153.4159] [ 1642] [depth= 4] . ( 2 sec) [ -8148.3653] [ 1642] [depth= 1] . ( 3 sec) [ -8074.0593] [ 1621] [depth= 3] . ( 3 sec) [ -8032.1471] [ 1613] [depth= 5] . ( 3 sec) [ -7879.7014] [ 1577] [depth= 4] . ( 3 sec) [ -7865.3144] [ 1577] [depth= 2] . ( 3 sec) [ -7624.7879] [ 1566] [depth= 11] . ( 3 sec) [ -7542.3100] [ 1533] [depth= 1] . ( 3 sec) [ -7541.7596] [ 1534] [depth= 1] . ( 3 sec) [ -7532.9275] [ 1538] [depth= 1] . ( 3 sec) [ -7383.0639] [ 1485] [depth= 12] . ( 3 sec) [ -7138.8841] [ 1426] [depth= 3] . ( 3 sec) [ -7090.4578] [ 1411] [depth= 3] . ( 3 sec) [ -7089.0052] [ 1411] [depth= 1] . ( 3 sec) [ -7083.7020] [ 1417] [depth= 1] . ( 3 sec) [ -7044.5415] [ 1412] [depth= 3] . ( 3 sec) [ -7042.1742] [ 1412] [depth= 1] . ( 3 sec) [ -7036.5272] [ 1405] [depth= 1] . ( 3 sec) [ -7007.7586] [ 1393] [depth= 2] . ( 3 sec) [ -6932.0219] [ 1392] [depth= 2] . ( 3 sec) [ -6899.5273] [ 1392] [depth= 1] . ( 3 sec) [ -6879.3950] [ 1391] [depth= 1] . ( 3 sec) [ -6651.2995] [ 1317] [depth= 2] . ( 3 sec) [ -6643.2483] [ 1316] [depth= 1] . ( 3 sec) [ -6629.2905] [ 1313] [depth= 1] . ( 3 sec) [ -6462.1263] [ 1274] [depth= 8] . ( 4 sec) [ -6376.4388] [ 1240] [depth= 2] . ( 4 sec) [ -6328.0891] [ 1204] [depth= 7] . ( 4 sec) [ -6192.8904] [ 1180] [depth= 1] . ( 4 sec) [ -6192.5551] [ 1180] [depth= 2] . ( 4 sec) [ -6189.4389] [ 1181] [depth= 1] . ( 4 sec) [ -6188.5252] [ 1180] [depth= 1] . ( 4 sec) [ -6185.8244] [ 1179] [depth= 1] . ( 4 sec) [ -6181.6460] [ 1177] [depth= 1] . ( 5 sec) [ -6112.1518] [Branch lengths ] . ( 5 sec) [ -6107.5074] [GTR parameters ] . ( 5 sec) [ -6084.8600] [Alpha ][ 0.907471] . ( 5 sec) [ -6084.0561] [ 1176] [depth= 1] . ( 5 sec) [ -6083.6501] [ 1189] [depth= 1] . ( 5 sec) [ -5909.8776] [ 1104] [depth= 3] . ( 5 sec) [ -5909.4199] [ 1104] [depth= 1] . ( 6 sec) [ -5909.3789] [ 1104] [depth= 2] . ( 6 sec) [ -5905.2897] [ 1102] [depth= 1] . ( 6 sec) [ -5905.2386] [ 1102] [depth= 1] . ( 6 sec) [ -5903.5981] [ 1114] [depth= 2] . ( 6 sec) [ -5903.3610] [ 1115] [depth= 1] . ( 6 sec) [ -5903.1349] [ 1115] [depth= 1] . ( 6 sec) [ -5902.9598] [ 1114] [depth= 1] . ( 6 sec) [ -5892.9251] [ 1103] [depth= 1] . ( 7 sec) [ -5890.7124] [ 1103] [depth= 1] . ( 7 sec) [ -5890.6754] [ 1103] [depth= 2] . ( 7 sec) [ -5885.0398] [ 1099] [depth= 1] . ( 7 sec) [ -5885.0295] [ 1099] [depth= 1] . ( 7 sec) [ -5885.0135] [ 1099] [depth= 1] . ( 7 sec) [ -5884.4600] [ 1100] [depth= 1] . ( 9 sec) [ -5881.1533] [Branch lengths ] . ( 9 sec) [ -5881.0129] [GTR parameters ] . ( 9 sec) [ -5879.6002] [Alpha ][ 1.071809] . ( 13 sec) [ -5879.4731] [Branch lengths ] . ( 17 sec) [ -5878.9433] [ 1089] [depth= 2] . ( 17 sec) [ -5878.8979] [ 1087] [depth= 1] . ( 19 sec) [ -5878.8395] [ 1089] [depth= 1] . ( 20 sec) [ -5878.5930] [ 1089] [depth= 1] . ( 26 sec) [ -5878.5747] [ 1087] [depth= 1] . ( 31 sec) [ -5878.3704] [Branch lengths ] . ( 32 sec) [ -5878.3674] [GTR parameters ] . ( 32 sec) [ -5878.3625] [Alpha ][ 1.082860] . ( 50 sec) [ -5878.3542] [Branch lengths ] . ( 50 sec) [ -5878.3542] [Topology ] . ( 51 sec) [ -5878.3535] [Topology ] . ( 51 sec) [ -5878.3535] [GTR parameters ] . ( 51 sec) [ -5878.3535] [Alpha ][ 1.082860] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -5878.3530] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -5878.2922] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5878.292249. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5915.368272 . ( 0 sec) [ -5914.3337] [GTR parameters ] . ( 0 sec) [ -5914.2453] [Alpha ][ 1.044120] . ( 0 sec) [ -5914.2453] [Topology ] . ( 1 sec) [ -5884.5145] [Topology ] . ( 1 sec) [ -5879.8822] [Topology ] . ( 2 sec) [ -5878.8229] [Topology ] . ( 3 sec) [ -5878.5145] [Topology ] . ( 4 sec) [ -5878.4132] [Topology ] . ( 4 sec) [ -5878.3768] [Topology ] . ( 5 sec) [ -5878.3628] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.362839 . ( 9 sec) [ -5878.3580] [GTR parameters ] . ( 10 sec) [ -5878.2915] [Alpha ][ 1.083518] . ( 10 sec) [ -5878.2915] [Topology ] . ( 10 sec) [ -5878.2828] [Topology ] . ( 11 sec) [ -5878.2795] [Topology ] . ( 12 sec) [ -5878.2782] [Topology ] . ( 12 sec) [ -5878.2777] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5878.277650 . ( 17 sec) [ -5878.2776] [GTR parameters ] . ( 17 sec) [ -5878.2775] [Alpha ][ 1.084814] . ( 17 sec) [ -5878.2775] [Topology ] . ( 17 sec) [ -5878.2772] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 26 sec) [ -5914.3337] [GTR parameters ] . ( 26 sec) [ -5914.2453] [Alpha ][ 1.044120] . ( 27 sec) [ -5913.8418] [ 1089] [depth= 1] . ( 27 sec) [ -5913.7836] [ 1089] [depth= 1] . ( 27 sec) [ -5913.0286] [ 1089] [depth= 1] . ( 27 sec) [ -5908.3687] [ 1089] [depth= 1] . ( 27 sec) [ -5907.6441] [ 1089] [depth= 1] . ( 27 sec) [ -5907.4454] [ 1089] [depth= 1] . ( 27 sec) [ -5907.3233] [ 1089] [depth= 1] . ( 27 sec) [ -5907.3116] [ 1089] [depth= 2] . ( 27 sec) [ -5907.2691] [ 1089] [depth= 1] . ( 28 sec) [ -5906.9424] [ 1090] [depth= 1] . ( 28 sec) [ -5905.2974] [ 1094] [depth= 1] . ( 28 sec) [ -5904.4479] [ 1094] [depth= 1] . ( 28 sec) [ -5904.4147] [ 1094] [depth= 1] . ( 28 sec) [ -5904.3980] [ 1094] [depth= 1] . ( 29 sec) [ -5898.4707] [ 1091] [depth= 1] . ( 30 sec) [ -5882.9331] [Branch lengths ] . ( 30 sec) [ -5882.8961] [GTR parameters ] . ( 30 sec) [ -5882.8629] [Alpha ][ 1.071721] . ( 31 sec) [ -5879.8435] [ 1087] [depth= 1] . ( 32 sec) [ -5879.1989] [ 1086] [depth= 1] . ( 32 sec) [ -5879.1357] [ 1089] [depth= 1] . ( 33 sec) [ -5879.1199] [ 1089] [depth= 1] . ( 34 sec) [ -5878.4015] [Branch lengths ] . ( 34 sec) [ -5878.3863] [GTR parameters ] . ( 34 sec) [ -5878.3822] [Alpha ][ 1.081915] . ( 38 sec) [ -5878.3427] [Branch lengths ] . ( 56 sec) [ -5878.3397] [Branch lengths ] . ( 56 sec) [ -5878.3397] [Topology ] . ( 57 sec) [ -5878.3395] [Topology ] . ( 57 sec) [ -5878.3395] [GTR parameters ] . ( 57 sec) [ -5878.3393] [Alpha ][ 1.083706] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -5878.3321] [Topology ] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -5878.2923] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5878.277241 . Log likelihood obtained after SPR moves : -5878.292255 . Log likelihood of the current tree: -5878.277241. . Printing the most likely tree in file 'data34.phy_phyml_tree.txt'... . Best log likelihood : -5878.277241 . Time used 0h1m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo