.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data9.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... . 316 patterns found. (out of a total of 500 sites) . 164 sites without polymorphism (32.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16539.0938] [GTR parameters ] . ( 1 sec) [ -16156.6532] [Alpha ][ 0.500960] . ( 1 sec) [ -15917.0130] [ 2664] [depth= 8] . ( 1 sec) [ -13521.4221] [ 2654] [depth= 6] . ( 1 sec) [ -13413.6434] [ 2649] [depth= 1] . ( 1 sec) [ -13312.6237] [ 2646] [depth= 7] . ( 1 sec) [ -13001.3046] [ 2540] [depth= 5] . ( 1 sec) [ -12726.6063] [ 2536] [depth= 9] . ( 1 sec) [ -12598.1336] [ 2532] [depth= 5] . ( 1 sec) [ -12550.5755] [ 2533] [depth= 1] . ( 1 sec) [ -12120.0310] [ 2531] [depth= 1] . ( 1 sec) [ -12066.1624] [ 2525] [depth= 2] . ( 1 sec) [ -11945.3158] [ 2419] [depth= 3] . ( 1 sec) [ -11896.8505] [ 2410] [depth= 7] . ( 1 sec) [ -11703.3978] [ 2382] [depth= 6] . ( 1 sec) [ -11683.4109] [ 2379] [depth= 1] . ( 1 sec) [ -11675.8032] [ 2377] [depth= 2] . ( 2 sec) [ -11482.0049] [ 2348] [depth= 5] . ( 2 sec) [ -11306.2419] [ 2347] [depth= 5] . ( 2 sec) [ -11044.7279] [ 2347] [depth= 2] . ( 2 sec) [ -10865.6332] [ 2358] [depth= 2] . ( 2 sec) [ -10546.6141] [ 2233] [depth= 3] . ( 2 sec) [ -10301.0347] [ 2120] [depth= 13] . ( 2 sec) [ -10278.4758] [ 2120] [depth= 1] . ( 2 sec) [ -10214.1876] [ 2103] [depth= 1] . ( 2 sec) [ -10208.1634] [ 2101] [depth= 1] . ( 2 sec) [ -10089.7607] [ 2070] [depth= 3] . ( 2 sec) [ -9962.7291] [ 2044] [depth= 6] . ( 2 sec) [ -9952.1143] [ 2043] [depth= 9] . ( 2 sec) [ -9524.7829] [ 2018] [depth= 8] . ( 2 sec) [ -9515.0156] [ 2019] [depth= 1] . ( 2 sec) [ -9291.9441] [ 1929] [depth= 2] . ( 2 sec) [ -9193.7788] [ 1831] [depth= 8] . ( 2 sec) [ -9169.0580] [ 1827] [depth= 8] . ( 2 sec) [ -9046.8501] [ 1813] [depth= 8] . ( 2 sec) [ -9037.7269] [ 1811] [depth= 1] . ( 2 sec) [ -8991.0172] [ 1800] [depth= 7] . ( 3 sec) [ -8983.6936] [ 1800] [depth= 1] . ( 3 sec) [ -8935.5469] [ 1797] [depth= 2] . ( 3 sec) [ -8864.5740] [ 1787] [depth= 1] . ( 3 sec) [ -8863.9242] [ 1785] [depth= 1] . ( 3 sec) [ -8650.9650] [ 1776] [depth= 11] . ( 3 sec) [ -8466.2042] [ 1648] [depth= 8] . ( 3 sec) [ -8445.0453] [ 1645] [depth= 6] . ( 3 sec) [ -8411.2570] [ 1640] [depth= 1] . ( 3 sec) [ -8402.0822] [ 1636] [depth= 1] . ( 3 sec) [ -8371.9028] [ 1627] [depth= 1] . ( 3 sec) [ -8343.2099] [ 1628] [depth= 2] . ( 3 sec) [ -8311.9963] [ 1625] [depth= 3] . ( 3 sec) [ -8292.8730] [ 1612] [depth= 1] . ( 3 sec) [ -8044.1019] [ 1515] [depth= 12] . ( 3 sec) [ -7831.3009] [ 1509] [depth= 1] . ( 3 sec) [ -7724.7623] [ 1490] [depth= 2] . ( 3 sec) [ -7682.4412] [ 1486] [depth= 3] . ( 3 sec) [ -7671.5705] [ 1607] [depth= 1] . ( 3 sec) [ -7368.7349] [ 1475] [depth= 2] . ( 3 sec) [ -7331.2228] [ 1460] [depth= 2] . ( 3 sec) [ -7242.3759] [ 1451] [depth= 4] . ( 3 sec) [ -6887.4887] [ 1343] [depth= 5] . ( 3 sec) [ -6762.2072] [ 1327] [depth= 1] . ( 3 sec) [ -6725.4931] [ 1322] [depth= 5] . ( 3 sec) [ -6724.2050] [ 1338] [depth= 1] . ( 3 sec) [ -6485.5394] [ 1231] [depth= 9] . ( 3 sec) [ -6354.1512] [ 1129] [depth= 8] . ( 4 sec) [ -6353.2932] [ 1131] [depth= 1] . ( 4 sec) [ -6341.5080] [ 1128] [depth= 2] . ( 4 sec) [ -6316.4170] [ 1131] [depth= 1] . ( 4 sec) [ -6237.1748] [ 1117] [depth= 1] . ( 4 sec) [ -5740.9503] [ 1004] [depth= 15] . ( 4 sec) [ -5713.3928] [ 994] [depth= 2] . ( 4 sec) [ -5701.5346] [ 992] [depth= 3] . ( 4 sec) [ -5641.9741] [ 971] [depth= 4] . ( 4 sec) [ -5637.6391] [ 970] [depth= 1] . ( 4 sec) [ -5596.0297] [ 961] [depth= 1] . ( 4 sec) [ -5590.1489] [ 962] [depth= 2] . ( 4 sec) [ -5531.0272] [ 958] [depth= 1] . ( 4 sec) [ -5526.9997] [ 954] [depth= 1] . ( 4 sec) [ -5525.2969] [ 949] [depth= 2] . ( 4 sec) [ -5495.8204] [ 950] [depth= 1] . ( 4 sec) [ -5492.4860] [ 948] [depth= 3] . ( 4 sec) [ -5409.9221] [ 929] [depth= 5] . ( 4 sec) [ -5407.1368] [ 931] [depth= 1] . ( 4 sec) [ -5380.7886] [ 916] [depth= 1] . ( 4 sec) [ -5335.0055] [ 905] [depth= 3] . ( 5 sec) [ -5286.1231] [Branch lengths ] . ( 5 sec) [ -5284.9137] [GTR parameters ] . ( 5 sec) [ -5267.8023] [Alpha ][ 0.909661] . ( 6 sec) [ -5267.7678] [ 905] [depth= 1] . ( 6 sec) [ -5189.0279] [ 884] [depth= 2] . ( 6 sec) [ -5187.1466] [ 884] [depth= 1] . ( 6 sec) [ -5182.1536] [ 883] [depth= 1] . ( 6 sec) [ -5182.1377] [ 881] [depth= 1] . ( 6 sec) [ -5181.7773] [ 882] [depth= 2] . ( 7 sec) [ -5181.7151] [ 883] [depth= 1] . ( 7 sec) [ -5181.7036] [ 883] [depth= 1] . ( 7 sec) [ -5178.2819] [ 882] [depth= 1] . ( 7 sec) [ -5178.0179] [ 881] [depth= 1] . ( 7 sec) [ -5177.8617] [ 884] [depth= 1] . ( 7 sec) [ -5170.7242] [ 880] [depth= 1] . ( 8 sec) [ -5167.0407] [ 875] [depth= 2] . ( 8 sec) [ -5164.8233] [ 874] [depth= 1] . ( 8 sec) [ -5164.1156] [ 873] [depth= 2] . ( 8 sec) [ -5164.0735] [ 873] [depth= 1] . ( 8 sec) [ -5163.2209] [ 872] [depth= 1] . ( 9 sec) [ -5162.1518] [ 873] [depth= 1] . ( 9 sec) [ -5156.4785] [Branch lengths ] . ( 9 sec) [ -5156.2340] [GTR parameters ] . ( 10 sec) [ -5155.8596] [Alpha ][ 1.001745] . ( 10 sec) [ -5155.8494] [ 873] [depth= 1] . ( 14 sec) [ -5155.4591] [Branch lengths ] . ( 14 sec) [ -5155.4590] [GTR parameters ] . ( 14 sec) [ -5155.4546] [Alpha ][ 1.012617] . ( 35 sec) [ -5155.4056] [Branch lengths ] . ( 35 sec) [ -5155.4056] [Topology ] . ( 35 sec) [ -5155.4022] [Topology ] . ( 36 sec) [ -5155.4012] [Topology ] . ( 36 sec) [ -5155.4012] [GTR parameters ] . ( 36 sec) [ -5155.4008] [Alpha ][ 1.015707] . ( 36 sec) [ -5155.4008] [Topology ] . ( 37 sec) [ -5155.4004] [Topology ] . ( 37 sec) [ -5155.4004] [GTR parameters ] . ( 37 sec) [ -5155.4004] [Alpha ][ 1.015707] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5155.400370. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18228.7691] [GTR parameters ] . ( 1 sec) [ -17847.5583] [Alpha ][ 0.500960] . ( 1 sec) [ -17527.9917] [ 2821] [depth= 4] . ( 1 sec) [ -17106.1296] [ 2729] [depth= 3] . ( 1 sec) [ -17036.2980] [ 2711] [depth= 4] . ( 1 sec) [ -13782.6986] [ 2710] [depth= 2] . ( 1 sec) [ -13515.5571] [ 2691] [depth= 6] . ( 1 sec) [ -13472.4905] [ 2680] [depth= 4] . ( 1 sec) [ -13424.6695] [ 2679] [depth= 1] . ( 1 sec) [ -13379.2109] [ 2661] [depth= 6] . ( 1 sec) [ -12894.3737] [ 2580] [depth= 3] . ( 1 sec) [ -12838.5672] [ 2579] [depth= 1] . ( 2 sec) [ -12642.5625] [ 2540] [depth= 9] . ( 2 sec) [ -12327.5230] [ 2541] [depth= 3] . ( 2 sec) [ -12028.9810] [ 2426] [depth= 4] . ( 2 sec) [ -11756.0281] [ 2315] [depth= 5] . ( 2 sec) [ -11611.3403] [ 2309] [depth= 2] . ( 2 sec) [ -11568.9214] [ 2299] [depth= 3] . ( 2 sec) [ -11511.2462] [ 2298] [depth= 10] . ( 2 sec) [ -11459.8429] [ 2278] [depth= 14] . ( 2 sec) [ -10761.5424] [ 2265] [depth= 1] . ( 2 sec) [ -10592.1520] [ 2159] [depth= 17] . ( 2 sec) [ -10507.0430] [ 2140] [depth= 10] . ( 2 sec) [ -10393.9817] [ 2129] [depth= 7] . ( 2 sec) [ -9979.5753] [ 2055] [depth= 13] . ( 2 sec) [ -9907.4788] [ 2057] [depth= 1] . ( 2 sec) [ -9726.8513] [ 2070] [depth= 1] . ( 2 sec) [ -9692.6633] [ 2057] [depth= 1] . ( 2 sec) [ -9487.5525] [ 1961] [depth= 15] . ( 2 sec) [ -9406.1275] [ 1934] [depth= 6] . ( 2 sec) [ -9405.2578] [ 1939] [depth= 1] . ( 2 sec) [ -9277.8866] [ 1930] [depth= 8] . ( 2 sec) [ -9269.4312] [ 1928] [depth= 1] . ( 2 sec) [ -9076.0589] [ 1846] [depth= 8] . ( 2 sec) [ -8422.4535] [ 1797] [depth= 10] . ( 2 sec) [ -8365.0655] [ 1798] [depth= 5] . ( 2 sec) [ -8219.0342] [ 1796] [depth= 3] . ( 2 sec) [ -8146.1038] [ 1789] [depth= 2] . ( 2 sec) [ -8084.0319] [ 1756] [depth= 6] . ( 2 sec) [ -8045.3440] [ 1755] [depth= 1] . ( 2 sec) [ -8028.9051] [ 1735] [depth= 4] . ( 3 sec) [ -7861.5690] [ 1631] [depth= 7] . ( 3 sec) [ -7859.8816] [ 1628] [depth= 1] . ( 3 sec) [ -7833.9464] [ 1636] [depth= 1] . ( 3 sec) [ -7827.9744] [ 1634] [depth= 2] . ( 3 sec) [ -7726.9846] [ 1612] [depth= 8] . ( 3 sec) [ -7717.8655] [ 1615] [depth= 2] . ( 3 sec) [ -7715.5016] [ 1613] [depth= 1] . ( 3 sec) [ -7629.8148] [ 1592] [depth= 11] . ( 3 sec) [ -7538.6311] [ 1573] [depth= 6] . ( 3 sec) [ -7476.4971] [ 1524] [depth= 7] . ( 3 sec) [ -7451.9566] [ 1436] [depth= 3] . ( 3 sec) [ -7354.2413] [ 1419] [depth= 6] . ( 3 sec) [ -7301.3583] [ 1410] [depth= 1] . ( 3 sec) [ -7248.5097] [ 1406] [depth= 9] . ( 3 sec) [ -7226.6979] [ 1320] [depth= 1] . ( 3 sec) [ -7109.1133] [ 1307] [depth= 1] . ( 3 sec) [ -7106.3707] [ 1307] [depth= 1] . ( 3 sec) [ -7104.5497] [ 1307] [depth= 1] . ( 3 sec) [ -7064.9555] [ 1300] [depth= 4] . ( 3 sec) [ -7024.5438] [ 1311] [depth= 9] . ( 3 sec) [ -6846.1648] [ 1227] [depth= 1] . ( 3 sec) [ -6644.2110] [ 1212] [depth= 2] . ( 3 sec) [ -6641.3827] [ 1217] [depth= 2] . ( 3 sec) [ -6543.1256] [ 1110] [depth= 1] . ( 3 sec) [ -6530.6447] [ 1105] [depth= 1] . ( 3 sec) [ -6513.1274] [ 1087] [depth= 6] . ( 4 sec) [ -6509.3560] [ 1084] [depth= 1] . ( 4 sec) [ -6442.5618] [ 1089] [depth= 1] . ( 4 sec) [ -6308.8675] [ 1109] [depth= 11] . ( 4 sec) [ -6302.8833] [ 1111] [depth= 3] . ( 4 sec) [ -6279.1610] [ 1108] [depth= 2] . ( 4 sec) [ -6277.5235] [ 1107] [depth= 2] . ( 4 sec) [ -6176.6848] [ 1101] [depth= 1] . ( 4 sec) [ -6174.5065] [ 1102] [depth= 1] . ( 4 sec) [ -6126.5879] [ 1090] [depth= 1] . ( 4 sec) [ -5957.6733] [ 1068] [depth= 2] . ( 4 sec) [ -5949.0666] [ 1069] [depth= 1] . ( 4 sec) [ -5938.0960] [ 1065] [depth= 1] . ( 4 sec) [ -5932.5035] [ 1065] [depth= 2] . ( 4 sec) [ -5930.3683] [ 1064] [depth= 1] . ( 4 sec) [ -5904.9982] [ 1059] [depth= 1] . ( 4 sec) [ -5895.7707] [ 1059] [depth= 2] . ( 4 sec) [ -5876.4350] [ 1052] [depth= 1] . ( 4 sec) [ -5868.3902] [ 1049] [depth= 7] . ( 4 sec) [ -5853.8780] [ 1044] [depth= 1] . ( 4 sec) [ -5760.6143] [ 1029] [depth= 5] . ( 5 sec) [ -5753.4584] [ 1033] [depth= 1] . ( 5 sec) [ -5747.1284] [ 1029] [depth= 1] . ( 5 sec) [ -5588.0789] [Branch lengths ] . ( 5 sec) [ -5586.5455] [GTR parameters ] . ( 5 sec) [ -5572.4608] [Alpha ][ 0.803762] . ( 6 sec) [ -5560.0482] [ 1027] [depth= 3] . ( 6 sec) [ -5558.4767] [ 926] [depth= 5] . ( 6 sec) [ -5558.3961] [ 926] [depth= 1] . ( 6 sec) [ -5546.1236] [ 925] [depth= 2] . ( 6 sec) [ -5544.9166] [ 925] [depth= 1] . ( 6 sec) [ -5537.4198] [ 919] [depth= 2] . ( 6 sec) [ -5532.0802] [ 915] [depth= 1] . ( 6 sec) [ -5532.0128] [ 915] [depth= 1] . ( 6 sec) [ -5527.6317] [ 915] [depth= 3] . ( 6 sec) [ -5527.5455] [ 919] [depth= 1] . ( 6 sec) [ -5510.7994] [ 911] [depth= 4] . ( 7 sec) [ -5502.4676] [ 911] [depth= 1] . ( 7 sec) [ -5498.4710] [ 909] [depth= 2] . ( 7 sec) [ -5496.1559] [ 909] [depth= 3] . ( 7 sec) [ -5495.3932] [ 909] [depth= 1] . ( 7 sec) [ -5481.8241] [ 890] [depth= 2] . ( 7 sec) [ -5211.7587] [ 896] [depth= 1] . ( 7 sec) [ -5205.1817] [ 893] [depth= 1] . ( 7 sec) [ -5197.1080] [ 887] [depth= 1] . ( 7 sec) [ -5197.0332] [ 887] [depth= 1] . ( 7 sec) [ -5196.0590] [ 887] [depth= 1] . ( 7 sec) [ -5188.8807] [ 883] [depth= 1] . ( 7 sec) [ -5188.8617] [ 883] [depth= 1] . ( 7 sec) [ -5182.0797] [ 881] [depth= 1] . ( 7 sec) [ -5170.1346] [ 874] [depth= 4] . ( 8 sec) [ -5170.0076] [ 874] [depth= 1] . ( 8 sec) [ -5169.8445] [ 874] [depth= 1] . ( 8 sec) [ -5168.5830] [ 875] [depth= 1] . ( 8 sec) [ -5168.5558] [ 875] [depth= 1] . ( 8 sec) [ -5168.5442] [ 875] [depth= 1] . ( 8 sec) [ -5168.3855] [ 874] [depth= 1] . ( 9 sec) [ -5166.6667] [ 873] [depth= 1] . ( 9 sec) [ -5158.3672] [Branch lengths ] . ( 10 sec) [ -5157.9644] [GTR parameters ] . ( 10 sec) [ -5155.6129] [Alpha ][ 1.016768] . ( 11 sec) [ -5155.6016] [ 873] [depth= 1] . ( 14 sec) [ -5155.4055] [Branch lengths ] . ( 15 sec) [ -5155.4042] [GTR parameters ] . ( 15 sec) [ -5155.4042] [Alpha ][ 1.016768] . ( 34 sec) [ -5155.4002] [Branch lengths ] . ( 34 sec) [ -5155.4002] [Topology ] . ( 35 sec) [ -5155.4001] [Topology ] . ( 35 sec) [ -5155.4001] [GTR parameters ] . ( 35 sec) [ -5155.4001] [Alpha ][ 1.016768] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5155.400115. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17391.3919] [GTR parameters ] . ( 0 sec) [ -17009.9203] [Alpha ][ 0.500960] . ( 0 sec) [ -16614.8056] [ 2769] [depth= 1] . ( 0 sec) [ -16337.6158] [ 2669] [depth= 8] . ( 0 sec) [ -16024.4887] [ 2655] [depth= 4] . ( 0 sec) [ -15991.9377] [ 2655] [depth= 1] . ( 0 sec) [ -15981.6291] [ 2645] [depth= 2] . ( 0 sec) [ -15956.4896] [ 2644] [depth= 1] . ( 0 sec) [ -15884.5767] [ 2627] [depth= 1] . ( 0 sec) [ -15719.1004] [ 2625] [depth= 3] . ( 0 sec) [ -12491.1072] [ 2497] [depth= 12] . ( 0 sec) [ -12228.7406] [ 2491] [depth= 4] . ( 0 sec) [ -11769.1206] [ 2477] [depth= 12] . ( 1 sec) [ -11319.0014] [ 2459] [depth= 7] . ( 1 sec) [ -11311.3736] [ 2458] [depth= 2] . ( 1 sec) [ -10942.7325] [ 2463] [depth= 3] . ( 1 sec) [ -10923.2569] [ 2456] [depth= 12] . ( 1 sec) [ -10883.5353] [ 2431] [depth= 4] . ( 1 sec) [ -10850.2352] [ 2422] [depth= 9] . ( 1 sec) [ -10291.5166] [ 2341] [depth= 9] . ( 1 sec) [ -10282.3677] [ 2341] [depth= 1] . ( 1 sec) [ -10213.8757] [ 2327] [depth= 8] . ( 1 sec) [ -10196.4385] [ 2326] [depth= 1] . ( 1 sec) [ -10149.0306] [ 2330] [depth= 14] . ( 1 sec) [ -10127.6664] [ 2333] [depth= 14] . ( 1 sec) [ -9970.7616] [ 2213] [depth= 8] . ( 1 sec) [ -9938.1099] [ 2203] [depth= 1] . ( 1 sec) [ -9711.0854] [ 2081] [depth= 12] . ( 1 sec) [ -9444.5385] [ 2049] [depth= 9] . ( 1 sec) [ -9154.7412] [ 2026] [depth= 10] . ( 1 sec) [ -8964.9306] [ 1929] [depth= 6] . ( 1 sec) [ -8843.4543] [ 1899] [depth= 7] . ( 1 sec) [ -8618.5076] [ 1799] [depth= 11] . ( 1 sec) [ -8565.9373] [ 1659] [depth= 4] . ( 1 sec) [ -8548.5992] [ 1659] [depth= 1] . ( 1 sec) [ -8528.2051] [ 1660] [depth= 1] . ( 1 sec) [ -8424.0385] [ 1646] [depth= 11] . ( 1 sec) [ -8419.4946] [ 1656] [depth= 2] . ( 1 sec) [ -8401.9111] [ 1649] [depth= 1] . ( 2 sec) [ -8098.2147] [ 1633] [depth= 2] . ( 2 sec) [ -8097.7019] [ 1635] [depth= 1] . ( 2 sec) [ -7780.1248] [ 1630] [depth= 3] . ( 2 sec) [ -7707.1236] [ 1616] [depth= 4] . ( 2 sec) [ -7469.1173] [ 1601] [depth= 6] . ( 2 sec) [ -7284.2994] [ 1509] [depth= 1] . ( 2 sec) [ -7194.6015] [ 1506] [depth= 2] . ( 2 sec) [ -7156.3231] [ 1504] [depth= 1] . ( 2 sec) [ -7152.1554] [ 1504] [depth= 1] . ( 2 sec) [ -7145.8318] [ 1504] [depth= 4] . ( 2 sec) [ -7114.8913] [ 1507] [depth= 1] . ( 2 sec) [ -7107.4914] [ 1499] [depth= 10] . ( 2 sec) [ -6971.0103] [ 1469] [depth= 9] . ( 2 sec) [ -6801.6872] [ 1435] [depth= 6] . ( 2 sec) [ -6775.4828] [ 1437] [depth= 1] . ( 2 sec) [ -6734.2244] [ 1433] [depth= 2] . ( 2 sec) [ -6655.1591] [ 1418] [depth= 6] . ( 2 sec) [ -6650.3155] [ 1403] [depth= 1] . ( 2 sec) [ -6648.6012] [ 1407] [depth= 1] . ( 2 sec) [ -6438.3413] [ 1300] [depth= 7] . ( 2 sec) [ -6434.5692] [ 1304] [depth= 2] . ( 2 sec) [ -6426.8770] [ 1304] [depth= 3] . ( 2 sec) [ -6414.7391] [ 1296] [depth= 5] . ( 2 sec) [ -6398.7326] [ 1293] [depth= 3] . ( 2 sec) [ -6385.3598] [ 1291] [depth= 3] . ( 2 sec) [ -6354.7070] [ 1289] [depth= 3] . ( 3 sec) [ -6263.7066] [ 1282] [depth= 3] . ( 3 sec) [ -6259.9592] [ 1272] [depth= 1] . ( 3 sec) [ -6193.7221] [ 1263] [depth= 3] . ( 3 sec) [ -6192.0265] [ 1263] [depth= 1] . ( 3 sec) [ -5944.9451] [ 1143] [depth= 7] . ( 3 sec) [ -5940.4589] [ 1141] [depth= 3] . ( 3 sec) [ -5894.3928] [ 1143] [depth= 2] . ( 3 sec) [ -5630.0872] [ 1019] [depth= 8] . ( 3 sec) [ -5628.2702] [ 1018] [depth= 1] . ( 3 sec) [ -5611.7136] [ 1007] [depth= 3] . ( 3 sec) [ -5599.4393] [ 1002] [depth= 1] . ( 3 sec) [ -5596.9375] [ 1006] [depth= 1] . ( 4 sec) [ -5511.8927] [Branch lengths ] . ( 4 sec) [ -5504.0078] [GTR parameters ] . ( 4 sec) [ -5493.1586] [Alpha ][ 0.770050] . ( 4 sec) [ -5491.2849] [ 1007] [depth= 1] . ( 4 sec) [ -5485.1279] [ 1003] [depth= 3] . ( 4 sec) [ -5484.9539] [ 1004] [depth= 2] . ( 5 sec) [ -5484.9251] [ 1004] [depth= 1] . ( 5 sec) [ -5474.5979] [ 999] [depth= 1] . ( 5 sec) [ -5474.0549] [ 1000] [depth= 2] . ( 5 sec) [ -5473.7853] [ 1001] [depth= 1] . ( 5 sec) [ -5462.1280] [ 996] [depth= 1] . ( 5 sec) [ -5462.1112] [ 998] [depth= 1] . ( 5 sec) [ -5460.5554] [ 1000] [depth= 1] . ( 6 sec) [ -5287.5773] [ 902] [depth= 9] . ( 6 sec) [ -5249.2341] [ 895] [depth= 2] . ( 6 sec) [ -5218.4979] [ 894] [depth= 1] . ( 6 sec) [ -5215.0423] [ 894] [depth= 1] . ( 6 sec) [ -5180.2546] [ 873] [depth= 6] . ( 6 sec) [ -5180.1891] [ 873] [depth= 1] . ( 6 sec) [ -5179.9591] [ 873] [depth= 1] . ( 6 sec) [ -5179.6129] [ 874] [depth= 3] . ( 7 sec) [ -5179.5969] [ 874] [depth= 1] . ( 7 sec) [ -5179.3876] [ 874] [depth= 1] . ( 8 sec) [ -5178.9303] [ 874] [depth= 1] . ( 8 sec) [ -5178.7608] [ 873] [depth= 1] . ( 9 sec) [ -5173.1478] [Branch lengths ] . ( 9 sec) [ -5172.9461] [GTR parameters ] . ( 9 sec) [ -5170.3265] [Alpha ][ 0.986475] . ( 10 sec) [ -5170.2583] [ 872] [depth= 1] . ( 12 sec) [ -5170.2479] [ 872] [depth= 1] . ( 14 sec) [ -5169.7815] [Branch lengths ] . ( 15 sec) [ -5169.7809] [GTR parameters ] . ( 15 sec) [ -5169.7700] [Alpha ][ 1.003370] . ( 36 sec) [ -5168.8889] [Branch lengths ] . ( 36 sec) [ -5168.8889] [Topology ] . ( 37 sec) [ -5164.9916] [Topology ] . ( 37 sec) [ -5157.1359] [Topology ] . ( 38 sec) [ -5155.5576] [Topology ] . ( 39 sec) [ -5155.4456] [Topology ] . ( 39 sec) [ -5155.4373] [Topology ] . ( 40 sec) [ -5155.4366] [Topology ] . ( 40 sec) [ -5155.4066] [GTR parameters ] . ( 40 sec) [ -5155.4003] [Alpha ][ 1.016380] . ( 40 sec) [ -5155.4003] [Topology ] . ( 41 sec) [ -5155.4001] [Topology ] . ( 41 sec) [ -5155.4001] [GTR parameters ] . ( 41 sec) [ -5155.4001] [Alpha ][ 1.016380] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5155.400133. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14544.7033] [GTR parameters ] . ( 1 sec) [ -14164.1714] [Alpha ][ 0.500960] . ( 1 sec) [ -14124.8298] [ 2700] [depth= 11] . ( 1 sec) [ -13823.0770] [ 2607] [depth= 9] . ( 1 sec) [ -13038.3027] [ 2515] [depth= 2] . ( 1 sec) [ -13003.3087] [ 2495] [depth= 1] . ( 1 sec) [ -12705.5995] [ 2392] [depth= 6] . ( 1 sec) [ -12689.4949] [ 2390] [depth= 2] . ( 1 sec) [ -12687.5356] [ 2389] [depth= 1] . ( 1 sec) [ -12565.4231] [ 2359] [depth= 1] . ( 1 sec) [ -12244.2018] [ 2352] [depth= 5] . ( 1 sec) [ -12153.4982] [ 2327] [depth= 3] . ( 1 sec) [ -12125.7055] [ 2327] [depth= 2] . ( 1 sec) [ -11978.0391] [ 2309] [depth= 1] . ( 1 sec) [ -11753.9941] [ 2305] [depth= 3] . ( 1 sec) [ -11731.2118] [ 2303] [depth= 2] . ( 1 sec) [ -11702.5070] [ 2191] [depth= 6] . ( 1 sec) [ -11638.3368] [ 2190] [depth= 1] . ( 1 sec) [ -11544.2481] [ 2188] [depth= 9] . ( 1 sec) [ -11287.0152] [ 2198] [depth= 1] . ( 1 sec) [ -11017.1659] [ 2076] [depth= 13] . ( 1 sec) [ -10778.5062] [ 1983] [depth= 1] . ( 1 sec) [ -10601.0254] [ 1953] [depth= 3] . ( 1 sec) [ -10417.7124] [ 1939] [depth= 6] . ( 1 sec) [ -10128.4341] [ 1926] [depth= 6] . ( 1 sec) [ -10113.2649] [ 1929] [depth= 2] . ( 1 sec) [ -10107.1267] [ 1927] [depth= 1] . ( 1 sec) [ -9689.6074] [ 1927] [depth= 4] . ( 1 sec) [ -9684.5422] [ 1927] [depth= 1] . ( 2 sec) [ -9532.4163] [ 1832] [depth= 10] . ( 2 sec) [ -9246.7302] [ 1827] [depth= 9] . ( 2 sec) [ -9221.1206] [ 1823] [depth= 5] . ( 2 sec) [ -9218.8614] [ 1822] [depth= 2] . ( 2 sec) [ -9209.1515] [ 1813] [depth= 2] . ( 2 sec) [ -8848.3291] [ 1814] [depth= 2] . ( 2 sec) [ -8729.5872] [ 1774] [depth= 9] . ( 2 sec) [ -8720.3939] [ 1770] [depth= 1] . ( 2 sec) [ -8494.4122] [ 1670] [depth= 8] . ( 2 sec) [ -8487.7428] [ 1669] [depth= 5] . ( 2 sec) [ -8202.2263] [ 1648] [depth= 8] . ( 2 sec) [ -8180.5852] [ 1646] [depth= 1] . ( 2 sec) [ -7972.5861] [ 1667] [depth= 13] . ( 2 sec) [ -7912.1885] [ 1652] [depth= 8] . ( 2 sec) [ -7881.4016] [ 1652] [depth= 2] . ( 2 sec) [ -7643.3050] [ 1542] [depth= 3] . ( 2 sec) [ -7578.1595] [ 1539] [depth= 3] . ( 2 sec) [ -7529.4511] [ 1538] [depth= 2] . ( 2 sec) [ -7521.5573] [ 1446] [depth= 5] . ( 2 sec) [ -7371.7429] [ 1443] [depth= 1] . ( 2 sec) [ -7160.3526] [ 1418] [depth= 5] . ( 2 sec) [ -7145.3346] [ 1415] [depth= 1] . ( 2 sec) [ -6853.6269] [ 1294] [depth= 6] . ( 2 sec) [ -6745.2969] [ 1276] [depth= 5] . ( 2 sec) [ -6644.6816] [ 1252] [depth= 5] . ( 2 sec) [ -6610.8071] [ 1251] [depth= 2] . ( 3 sec) [ -6556.7422] [ 1243] [depth= 1] . ( 3 sec) [ -6545.7147] [ 1240] [depth= 1] . ( 3 sec) [ -6532.8310] [ 1241] [depth= 1] . ( 3 sec) [ -6527.6630] [ 1241] [depth= 1] . ( 3 sec) [ -6426.2820] [ 1225] [depth= 1] . ( 3 sec) [ -6386.1615] [ 1220] [depth= 5] . ( 3 sec) [ -6306.8204] [ 1217] [depth= 2] . ( 3 sec) [ -6306.8016] [ 1216] [depth= 1] . ( 3 sec) [ -6236.7687] [ 1194] [depth= 2] . ( 3 sec) [ -6224.3445] [ 1191] [depth= 1] . ( 3 sec) [ -6216.9386] [ 1190] [depth= 3] . ( 3 sec) [ -6164.9497] [ 1187] [depth= 2] . ( 3 sec) [ -6151.0098] [ 1182] [depth= 6] . ( 3 sec) [ -6142.1387] [ 1180] [depth= 4] . ( 3 sec) [ -6124.4517] [ 1164] [depth= 2] . ( 3 sec) [ -5770.8947] [ 1027] [depth= 6] . ( 3 sec) [ -5768.7154] [ 1027] [depth= 1] . ( 3 sec) [ -5768.0101] [ 1029] [depth= 2] . ( 4 sec) [ -5680.9441] [ 1015] [depth= 2] . ( 4 sec) [ -5667.7922] [ 1012] [depth= 2] . ( 4 sec) [ -5662.4834] [ 1008] [depth= 1] . ( 4 sec) [ -5661.8403] [ 1008] [depth= 1] . ( 4 sec) [ -5610.7572] [ 995] [depth= 3] . ( 4 sec) [ -5581.3586] [ 990] [depth= 2] . ( 4 sec) [ -5546.7662] [ 983] [depth= 5] . ( 4 sec) [ -5501.4180] [Branch lengths ] . ( 5 sec) [ -5499.7159] [GTR parameters ] . ( 5 sec) [ -5487.2213] [Alpha ][ 0.805736] . ( 5 sec) [ -5413.8948] [ 975] [depth= 3] . ( 5 sec) [ -5413.8595] [ 976] [depth= 1] . ( 5 sec) [ -5413.8428] [ 976] [depth= 1] . ( 5 sec) [ -5413.8034] [ 972] [depth= 1] . ( 5 sec) [ -5174.0584] [ 876] [depth= 3] . ( 6 sec) [ -5173.9439] [ 876] [depth= 1] . ( 6 sec) [ -5172.6167] [ 875] [depth= 2] . ( 6 sec) [ -5171.9065] [ 874] [depth= 2] . ( 6 sec) [ -5171.2569] [ 874] [depth= 1] . ( 6 sec) [ -5171.2178] [ 874] [depth= 1] . ( 7 sec) [ -5171.1483] [ 874] [depth= 1] . ( 7 sec) [ -5170.5111] [ 877] [depth= 1] . ( 8 sec) [ -5170.3564] [ 878] [depth= 1] . ( 8 sec) [ -5170.2618] [ 878] [depth= 1] . ( 8 sec) [ -5161.3936] [ 875] [depth= 1] . ( 9 sec) [ -5159.2201] [Branch lengths ] . ( 9 sec) [ -5159.0811] [GTR parameters ] . ( 9 sec) [ -5157.2709] [Alpha ][ 0.992274] . ( 10 sec) [ -5155.9442] [ 874] [depth= 1] . ( 14 sec) [ -5155.5821] [Branch lengths ] . ( 14 sec) [ -5155.5769] [GTR parameters ] . ( 14 sec) [ -5155.5665] [Alpha ][ 1.008929] . ( 19 sec) [ -5155.5258] [Branch lengths ] . ( 33 sec) [ -5155.4894] [ 873] [depth= 1] . ( 39 sec) [ -5155.4062] [Branch lengths ] . ( 39 sec) [ -5155.4057] [GTR parameters ] . ( 39 sec) [ -5155.4037] [Alpha ][ 1.016329] . ( 39 sec) [ -5155.4037] [Topology ] . ( 39 sec) [ -5155.4012] [Topology ] . ( 40 sec) [ -5155.4005] [Topology ] . ( 40 sec) [ -5155.4005] [GTR parameters ] . ( 40 sec) [ -5155.4005] [Alpha ][ 1.016329] . ( 40 sec) [ -5155.4005] [Topology ] . ( 41 sec) [ -5155.4003] [Topology ] . ( 41 sec) [ -5155.4003] [GTR parameters ] . ( 41 sec) [ -5155.4003] [Alpha ][ 1.016329] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5155.400262. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14678.3770] [GTR parameters ] . ( 1 sec) [ -14294.0184] [Alpha ][ 0.500960] . ( 1 sec) [ -13980.1069] [ 2746] [depth= 7] . ( 1 sec) [ -13556.0007] [ 2740] [depth= 11] . ( 1 sec) [ -13490.3442] [ 2736] [depth= 5] . ( 1 sec) [ -13379.1154] [ 2735] [depth= 1] . ( 1 sec) [ -13271.5254] [ 2641] [depth= 3] . ( 1 sec) [ -13029.9240] [ 2644] [depth= 7] . ( 1 sec) [ -12418.6829] [ 2633] [depth= 5] . ( 1 sec) [ -12254.7020] [ 2633] [depth= 1] . ( 1 sec) [ -11987.8373] [ 2512] [depth= 8] . ( 1 sec) [ -11714.3412] [ 2492] [depth= 2] . ( 1 sec) [ -11632.1936] [ 2474] [depth= 1] . ( 1 sec) [ -11241.9224] [ 2434] [depth= 13] . ( 1 sec) [ -10944.3333] [ 2330] [depth= 11] . ( 1 sec) [ -10938.0001] [ 2333] [depth= 1] . ( 1 sec) [ -10885.1423] [ 2327] [depth= 2] . ( 1 sec) [ -10781.0749] [ 2323] [depth= 1] . ( 1 sec) [ -10781.0638] [ 2324] [depth= 1] . ( 1 sec) [ -10780.5930] [ 2312] [depth= 1] . ( 1 sec) [ -10712.9636] [ 2312] [depth= 1] . ( 2 sec) [ -10607.5764] [ 2300] [depth= 9] . ( 2 sec) [ -10214.1416] [ 2268] [depth= 9] . ( 2 sec) [ -10158.7341] [ 2260] [depth= 2] . ( 2 sec) [ -10133.4850] [ 2256] [depth= 5] . ( 2 sec) [ -10108.2225] [ 2235] [depth= 3] . ( 2 sec) [ -10072.1274] [ 2131] [depth= 5] . ( 2 sec) [ -9924.5273] [ 2130] [depth= 4] . ( 2 sec) [ -9704.0839] [ 2083] [depth= 5] . ( 2 sec) [ -9701.0164] [ 2082] [depth= 4] . ( 2 sec) [ -9562.7627] [ 1992] [depth= 4] . ( 2 sec) [ -9401.6811] [ 1961] [depth= 2] . ( 2 sec) [ -9400.7427] [ 1964] [depth= 1] . ( 2 sec) [ -9253.1251] [ 1951] [depth= 10] . ( 2 sec) [ -9236.3677] [ 1950] [depth= 2] . ( 2 sec) [ -9020.9333] [ 1871] [depth= 5] . ( 2 sec) [ -9010.1442] [ 1871] [depth= 8] . ( 2 sec) [ -8996.2033] [ 1867] [depth= 2] . ( 2 sec) [ -8947.5787] [ 1855] [depth= 7] . ( 2 sec) [ -8870.7505] [ 1852] [depth= 2] . ( 2 sec) [ -8685.0005] [ 1759] [depth= 5] . ( 2 sec) [ -8657.9442] [ 1752] [depth= 1] . ( 2 sec) [ -8478.3787] [ 1726] [depth= 4] . ( 2 sec) [ -8471.2107] [ 1723] [depth= 1] . ( 2 sec) [ -8438.6393] [ 1723] [depth= 2] . ( 2 sec) [ -8330.0860] [ 1603] [depth= 3] . ( 2 sec) [ -8123.4702] [ 1591] [depth= 11] . ( 2 sec) [ -8114.1057] [ 1590] [depth= 1] . ( 3 sec) [ -8101.3791] [ 1592] [depth= 2] . ( 3 sec) [ -8096.1653] [ 1590] [depth= 2] . ( 3 sec) [ -8087.8950] [ 1588] [depth= 2] . ( 3 sec) [ -7994.3108] [ 1574] [depth= 13] . ( 3 sec) [ -7702.1517] [ 1470] [depth= 10] . ( 3 sec) [ -7460.6307] [ 1378] [depth= 5] . ( 3 sec) [ -7096.0762] [ 1373] [depth= 2] . ( 3 sec) [ -7026.8276] [ 1280] [depth= 6] . ( 3 sec) [ -6972.3347] [ 1267] [depth= 1] . ( 3 sec) [ -6963.6000] [ 1265] [depth= 1] . ( 3 sec) [ -6737.5117] [ 1226] [depth= 5] . ( 3 sec) [ -6676.0260] [ 1211] [depth= 5] . ( 3 sec) [ -6578.2043] [ 1219] [depth= 1] . ( 3 sec) [ -6355.5056] [ 1119] [depth= 3] . ( 3 sec) [ -6308.1606] [ 1107] [depth= 7] . ( 3 sec) [ -6179.7671] [ 1076] [depth= 10] . ( 3 sec) [ -6179.7374] [ 1077] [depth= 1] . ( 3 sec) [ -6057.5683] [ 1040] [depth= 5] . ( 3 sec) [ -5952.4113] [ 1021] [depth= 10] . ( 3 sec) [ -5942.1920] [ 1019] [depth= 3] . ( 3 sec) [ -5852.2016] [ 1025] [depth= 2] . ( 3 sec) [ -5626.1860] [ 930] [depth= 3] . ( 3 sec) [ -5530.2343] [ 913] [depth= 7] . ( 3 sec) [ -5506.8730] [ 909] [depth= 3] . ( 4 sec) [ -5425.3691] [ 909] [depth= 2] . ( 4 sec) [ -5356.5692] [ 913] [depth= 1] . ( 4 sec) [ -5346.7696] [ 911] [depth= 2] . ( 4 sec) [ -5342.2231] [ 910] [depth= 1] . ( 4 sec) [ -5330.6041] [ 911] [depth= 1] . ( 4 sec) [ -5325.6384] [ 911] [depth= 1] . ( 4 sec) [ -5322.9915] [ 910] [depth= 1] . ( 4 sec) [ -5322.7276] [ 910] [depth= 1] . ( 4 sec) [ -5269.8526] [ 893] [depth= 2] . ( 4 sec) [ -5261.6271] [ 889] [depth= 1] . ( 4 sec) [ -5256.5776] [ 886] [depth= 1] . ( 5 sec) [ -5206.3987] [Branch lengths ] . ( 5 sec) [ -5204.4958] [GTR parameters ] . ( 5 sec) [ -5182.2042] [Alpha ][ 0.983869] . ( 5 sec) [ -5180.8629] [ 885] [depth= 1] . ( 6 sec) [ -5180.3930] [ 886] [depth= 2] . ( 6 sec) [ -5168.6180] [ 879] [depth= 3] . ( 6 sec) [ -5167.9204] [ 877] [depth= 2] . ( 6 sec) [ -5159.2538] [ 873] [depth= 1] . ( 6 sec) [ -5159.1308] [ 873] [depth= 1] . ( 6 sec) [ -5159.0642] [ 874] [depth= 1] . ( 7 sec) [ -5158.6367] [ 873] [depth= 2] . ( 7 sec) [ -5158.5719] [ 874] [depth= 1] . ( 8 sec) [ -5157.8166] [ 874] [depth= 1] . ( 8 sec) [ -5157.7010] [ 873] [depth= 1] . ( 9 sec) [ -5157.6690] [ 873] [depth= 1] . ( 9 sec) [ -5155.5813] [Branch lengths ] . ( 9 sec) [ -5155.4734] [GTR parameters ] . ( 10 sec) [ -5155.4386] [Alpha ][ 1.013353] . ( 14 sec) [ -5155.4022] [Branch lengths ] . ( 33 sec) [ -5155.4006] [Branch lengths ] . ( 33 sec) [ -5155.4006] [Topology ] . ( 34 sec) [ -5155.4005] [Topology ] . ( 34 sec) [ -5155.4005] [GTR parameters ] . ( 34 sec) [ -5155.4002] [Alpha ][ 1.015998] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5155.400198. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5188.828666 . ( 1 sec) [ -5182.3636] [GTR parameters ] . ( 1 sec) [ -5182.3635] [Alpha ][ 0.998896] . ( 1 sec) [ -5182.3635] [Topology ] . ( 1 sec) [ -5158.5937] [Topology ] . ( 2 sec) [ -5155.9177] [Topology ] . ( 3 sec) [ -5155.5437] [Topology ] . ( 3 sec) [ -5155.4587] [Topology ] . ( 4 sec) [ -5155.4345] [Topology ] . ( 4 sec) [ -5155.4267] [Topology ] . ( 5 sec) [ -5155.4241] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5155.424069 . ( 9 sec) [ -5155.4131] [GTR parameters ] . ( 9 sec) [ -5155.4028] [Alpha ][ 1.015610] . ( 9 sec) [ -5155.4028] [Topology ] . ( 10 sec) [ -5155.4010] [Topology ] . ( 10 sec) [ -5155.4004] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5155.400408 . ( 14 sec) [ -5155.4004] [GTR parameters ] . ( 14 sec) [ -5155.4004] [Alpha ][ 1.015610] . ( 14 sec) [ -5155.4004] [Topology ] . ( 15 sec) [ -5155.4002] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -5182.3636] [GTR parameters ] . ( 23 sec) [ -5182.3635] [Alpha ][ 0.998896] . ( 24 sec) [ -5182.3360] [ 876] [depth= 1] . ( 24 sec) [ -5181.5259] [ 877] [depth= 1] . ( 24 sec) [ -5179.9695] [ 876] [depth= 1] . ( 24 sec) [ -5179.3411] [ 875] [depth= 1] . ( 24 sec) [ -5176.9973] [ 876] [depth= 1] . ( 24 sec) [ -5176.8402] [ 876] [depth= 1] . ( 24 sec) [ -5174.7927] [ 874] [depth= 1] . ( 24 sec) [ -5174.6594] [ 873] [depth= 1] . ( 25 sec) [ -5174.5811] [ 874] [depth= 1] . ( 25 sec) [ -5174.1271] [ 874] [depth= 2] . ( 25 sec) [ -5173.9853] [ 874] [depth= 1] . ( 26 sec) [ -5173.8692] [ 874] [depth= 1] . ( 26 sec) [ -5173.2085] [ 874] [depth= 1] . ( 26 sec) [ -5172.5776] [ 873] [depth= 1] . ( 26 sec) [ -5172.1389] [ 874] [depth= 1] . ( 26 sec) [ -5172.0627] [ 874] [depth= 1] . ( 26 sec) [ -5172.0309] [ 874] [depth= 1] . ( 26 sec) [ -5170.7349] [ 874] [depth= 1] . ( 26 sec) [ -5170.6631] [ 874] [depth= 1] . ( 26 sec) [ -5170.6383] [ 874] [depth= 1] . ( 26 sec) [ -5170.5211] [ 874] [depth= 1] . ( 27 sec) [ -5170.3762] [ 874] [depth= 1] . ( 27 sec) [ -5158.1596] [Branch lengths ] . ( 27 sec) [ -5158.1513] [GTR parameters ] . ( 27 sec) [ -5158.1471] [Alpha ][ 1.009460] . ( 27 sec) [ -5155.7878] [ 873] [depth= 1] . ( 32 sec) [ -5155.4065] [Branch lengths ] . ( 32 sec) [ -5155.4055] [GTR parameters ] . ( 32 sec) [ -5155.4040] [Alpha ][ 1.015682] . ( 37 sec) [ -5155.4004] [Branch lengths ] . ( 56 sec) [ -5155.4000] [Branch lengths ] . ( 56 sec) [ -5155.4000] [Topology ] . ( 56 sec) [ -5155.4000] [Topology ] . ( 56 sec) [ -5155.4000] [GTR parameters ] . ( 56 sec) [ -5155.4000] [Alpha ][ 1.016698] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5155.400193 . Log likelihood obtained after SPR moves : -5155.400010 . Log likelihood of the current tree: -5155.400010. . Printing the most likely tree in file 'data9.phy_phyml_tree.txt'... . Best log likelihood : -5155.400010 . Time used 0h1m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo