.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2567_64x1044_2006.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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 408 patterns found. (out of a total of 1044 sites) . 678 sites without polymorphism (64.94%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -19092.8346] [GTR parameters ] . ( 2 sec) [ -18711.7135] [Alpha ][ 0.500960] . ( 2 sec) [ -18502.6527] [ 2291] [depth= 7] . ( 2 sec) [ -18448.4172] [ 2282] [depth= 6] . ( 2 sec) [ -18439.7115] [ 2282] [depth= 1] . ( 2 sec) [ -18439.0784] [ 2282] [depth= 1] . ( 2 sec) [ -18433.5283] [ 2282] [depth= 2] . ( 2 sec) [ -18419.4087] [ 2280] [depth= 7] . ( 2 sec) [ -18317.9443] [ 2281] [depth= 4] . ( 2 sec) [ -18220.6048] [ 2272] [depth= 8] . ( 3 sec) [ -18202.7059] [ 2272] [depth= 1] . ( 3 sec) [ -17544.9509] [ 2268] [depth= 10] . ( 3 sec) [ -17460.0166] [ 2268] [depth= 2] . ( 3 sec) [ -17399.4568] [ 2267] [depth= 2] . ( 3 sec) [ -17377.4508] [ 2267] [depth= 1] . ( 3 sec) [ -17234.9549] [ 2244] [depth= 2] . ( 3 sec) [ -17082.1779] [ 2211] [depth= 7] . ( 3 sec) [ -16991.9787] [ 2209] [depth= 5] . ( 3 sec) [ -16828.5231] [ 2164] [depth= 12] . ( 3 sec) [ -16760.8911] [ 2158] [depth= 20] . ( 3 sec) [ -16718.5396] [ 2149] [depth= 1] . ( 3 sec) [ -16297.9222] [ 2130] [depth= 9] . ( 3 sec) [ -16064.5087] [ 2129] [depth= 18] . ( 3 sec) [ -16000.9522] [ 2129] [depth= 2] . ( 3 sec) [ -15833.5116] [ 2106] [depth= 11] . ( 3 sec) [ -15751.9534] [ 2107] [depth= 1] . ( 3 sec) [ -15718.2514] [ 2099] [depth= 1] . ( 4 sec) [ -15242.9836] [ 2084] [depth= 12] . ( 4 sec) [ -15075.1820] [ 2047] [depth= 15] . ( 4 sec) [ -14974.8437] [ 2027] [depth= 17] . ( 4 sec) [ -14944.9767] [ 2030] [depth= 14] . ( 4 sec) [ -14690.8979] [ 2015] [depth= 7] . ( 4 sec) [ -14582.8828] [ 2007] [depth= 9] . ( 4 sec) [ -14549.5333] [ 2000] [depth= 3] . ( 4 sec) [ -14321.6056] [ 1970] [depth= 2] . ( 4 sec) [ -14177.2421] [ 1968] [depth= 1] . ( 4 sec) [ -14159.1307] [ 1966] [depth= 6] . ( 4 sec) [ -14151.5929] [ 1965] [depth= 2] . ( 4 sec) [ -13866.1735] [ 1960] [depth= 7] . ( 4 sec) [ -13865.0083] [ 1962] [depth= 1] . ( 4 sec) [ -13804.5033] [ 1950] [depth= 9] . ( 4 sec) [ -13674.4029] [ 1927] [depth= 13] . ( 4 sec) [ -13602.9859] [ 1927] [depth= 1] . ( 5 sec) [ -13492.2705] [ 1904] [depth= 5] . ( 5 sec) [ -13468.4310] [ 1905] [depth= 1] . ( 5 sec) [ -11766.4359] [ 1883] [depth= 17] . ( 5 sec) [ -11755.2139] [ 1885] [depth= 5] . ( 5 sec) [ -11750.8493] [ 1881] [depth= 2] . ( 5 sec) [ -11658.6601] [ 1862] [depth= 3] . ( 5 sec) [ -11649.1257] [ 1861] [depth= 10] . ( 5 sec) [ -11626.4532] [ 1859] [depth= 11] . ( 5 sec) [ -11517.6197] [ 1845] [depth= 16] . ( 5 sec) [ -11444.3068] [ 1822] [depth= 10] . ( 5 sec) [ -11283.1499] [ 1791] [depth= 18] . ( 5 sec) [ -11188.6304] [ 1771] [depth= 1] . ( 5 sec) [ -11064.3790] [ 1761] [depth= 6] . ( 6 sec) [ -11057.3427] [ 1761] [depth= 1] . ( 6 sec) [ -11039.4213] [ 1759] [depth= 6] . ( 6 sec) [ -10971.0483] [ 1738] [depth= 8] . ( 6 sec) [ -10908.4019] [ 1736] [depth= 1] . ( 6 sec) [ -10897.1716] [ 1733] [depth= 1] . ( 6 sec) [ -10896.3747] [ 1743] [depth= 1] . ( 6 sec) [ -10858.4705] [ 1733] [depth= 1] . ( 6 sec) [ -10858.1017] [ 1736] [depth= 1] . ( 6 sec) [ -10856.2354] [ 1736] [depth= 2] . ( 6 sec) [ -10760.1978] [ 1710] [depth= 9] . ( 6 sec) [ -10596.3437] [ 1708] [depth= 11] . ( 6 sec) [ -10535.6279] [ 1689] [depth= 1] . ( 6 sec) [ -10427.7053] [ 1689] [depth= 1] . ( 7 sec) [ -10400.4977] [ 1676] [depth= 1] . ( 7 sec) [ -10393.1815] [ 1673] [depth= 2] . ( 7 sec) [ -10364.8814] [ 1658] [depth= 17] . ( 7 sec) [ -10354.1741] [ 1656] [depth= 1] . ( 7 sec) [ -10288.6197] [ 1637] [depth= 1] . ( 7 sec) [ -10248.9830] [ 1626] [depth= 12] . ( 7 sec) [ -10131.1764] [ 1602] [depth= 9] . ( 7 sec) [ -10123.8519] [ 1599] [depth= 2] . ( 7 sec) [ -9841.9007] [ 1553] [depth= 17] . ( 7 sec) [ -9522.2760] [ 1535] [depth= 5] . ( 7 sec) [ -9502.9033] [ 1531] [depth= 1] . ( 7 sec) [ -9479.8092] [ 1521] [depth= 11] . ( 7 sec) [ -9475.3088] [ 1519] [depth= 1] . ( 7 sec) [ -9372.5402] [ 1490] [depth= 13] . ( 8 sec) [ -9343.9752] [ 1484] [depth= 1] . ( 8 sec) [ -9332.9548] [ 1480] [depth= 1] . ( 8 sec) [ -9282.1697] [ 1470] [depth= 5] . ( 8 sec) [ -9195.9030] [ 1456] [depth= 9] . ( 8 sec) [ -9182.7392] [ 1451] [depth= 3] . ( 8 sec) [ -9099.4992] [ 1424] [depth= 6] . ( 8 sec) [ -9094.5976] [ 1424] [depth= 1] . ( 8 sec) [ -9021.8004] [ 1403] [depth= 6] . ( 8 sec) [ -9015.2987] [ 1399] [depth= 4] . ( 8 sec) [ -8997.5992] [ 1395] [depth= 4] . ( 8 sec) [ -8996.1105] [ 1395] [depth= 2] . ( 8 sec) [ -8988.5977] [ 1393] [depth= 15] . ( 8 sec) [ -8981.7345] [ 1395] [depth= 3] . ( 8 sec) [ -8981.3021] [ 1397] [depth= 1] . ( 9 sec) [ -8968.6763] [ 1392] [depth= 6] . ( 9 sec) [ -8940.6404] [ 1385] [depth= 3] . ( 9 sec) [ -8931.4079] [ 1365] [depth= 12] . ( 9 sec) [ -8893.6203] [ 1347] [depth= 12] . ( 9 sec) [ -8893.2756] [ 1347] [depth= 2] . ( 9 sec) [ -8702.6799] [ 1299] [depth= 7] . ( 9 sec) [ -8663.9484] [ 1296] [depth= 5] . ( 9 sec) [ -8487.7938] [ 1283] [depth= 9] . ( 9 sec) [ -8487.4964] [ 1283] [depth= 1] . ( 9 sec) [ -8481.8794] [ 1296] [depth= 7] . ( 9 sec) [ -8420.2572] [ 1272] [depth= 7] . ( 9 sec) [ -8268.9575] [ 1280] [depth= 1] . ( 9 sec) [ -8197.6775] [ 1238] [depth= 10] . ( 9 sec) [ -8146.9184] [ 1245] [depth= 1] . ( 9 sec) [ -8144.5654] [ 1245] [depth= 9] . ( 10 sec) [ -8003.3864] [ 1210] [depth= 1] . ( 10 sec) [ -7992.2719] [ 1210] [depth= 1] . ( 10 sec) [ -7990.8947] [ 1210] [depth= 1] . ( 10 sec) [ -7990.4054] [ 1210] [depth= 2] . ( 10 sec) [ -7986.6187] [ 1209] [depth= 2] . ( 10 sec) [ -7961.1512] [ 1206] [depth= 3] . ( 10 sec) [ -7961.1001] [ 1206] [depth= 2] . ( 10 sec) [ -7944.7743] [ 1201] [depth= 2] . ( 10 sec) [ -7943.2126] [ 1201] [depth= 1] . ( 10 sec) [ -7932.2868] [ 1200] [depth= 8] . ( 10 sec) [ -7921.3333] [ 1191] [depth= 5] . ( 11 sec) [ -7914.9972] [ 1191] [depth= 1] . ( 11 sec) [ -7897.9328] [ 1188] [depth= 4] . ( 11 sec) [ -7897.7285] [ 1188] [depth= 1] . ( 11 sec) [ -7896.2306] [ 1187] [depth= 2] . ( 11 sec) [ -7883.8501] [ 1183] [depth= 1] . ( 11 sec) [ -7874.8347] [ 1157] [depth= 2] . ( 11 sec) [ -7838.7289] [ 1149] [depth= 4] . ( 11 sec) [ -7792.8016] [ 1153] [depth= 1] . ( 11 sec) [ -7747.8507] [ 1143] [depth= 1] . ( 11 sec) [ -7747.6898] [ 1143] [depth= 1] . ( 11 sec) [ -7737.4703] [ 1145] [depth= 9] . ( 12 sec) [ -7721.2312] [ 1138] [depth= 3] . ( 12 sec) [ -7630.5237] [ 1122] [depth= 2] . ( 12 sec) [ -7619.3599] [ 1116] [depth= 2] . ( 12 sec) [ -7617.5612] [ 1116] [depth= 1] . ( 12 sec) [ -7611.4147] [ 1116] [depth= 3] . ( 12 sec) [ -7602.9717] [ 1114] [depth= 2] . ( 12 sec) [ -7561.2938] [ 1101] [depth= 1] . ( 12 sec) [ -7549.4212] [ 1104] [depth= 1] . ( 13 sec) [ -7523.4564] [ 1105] [depth= 3] . ( 13 sec) [ -7445.8112] [Branch lengths ] . ( 14 sec) [ -7375.9252] [GTR parameters ] . ( 15 sec) [ -7324.9574] [Alpha ][ 0.256479] . ( 15 sec) [ -7295.7888] [ 1095] [depth= 7] . ( 15 sec) [ -7276.8965] [ 1090] [depth= 2] . ( 15 sec) [ -7252.8742] [ 1089] [depth= 1] . ( 15 sec) [ -7249.9507] [ 1088] [depth= 3] . ( 15 sec) [ -7246.8822] [ 1088] [depth= 2] . ( 15 sec) [ -7171.7417] [ 1068] [depth= 10] . ( 15 sec) [ -7170.8051] [ 1068] [depth= 1] . ( 16 sec) [ -7170.6955] [ 1068] [depth= 1] . ( 16 sec) [ -7167.8040] [ 1068] [depth= 2] . ( 16 sec) [ -7053.5855] [ 1038] [depth= 6] . ( 16 sec) [ -7027.9346] [ 1030] [depth= 2] . ( 16 sec) [ -7024.8554] [ 1030] [depth= 2] . ( 16 sec) [ -6961.4238] [ 1011] [depth= 1] . ( 16 sec) [ -6959.1391] [ 1011] [depth= 1] . ( 16 sec) [ -6957.7056] [ 1012] [depth= 1] . ( 17 sec) [ -6957.5488] [ 1011] [depth= 2] . ( 17 sec) [ -6949.5791] [ 1016] [depth= 1] . ( 17 sec) [ -6942.3650] [ 1012] [depth= 1] . ( 17 sec) [ -6942.3427] [ 1012] [depth= 1] . ( 17 sec) [ -6941.2861] [ 1012] [depth= 1] . ( 18 sec) [ -6941.2329] [ 1012] [depth= 1] . ( 18 sec) [ -6929.4723] [ 1006] [depth= 2] . ( 18 sec) [ -6927.1245] [ 1004] [depth= 1] . ( 18 sec) [ -6926.7336] [ 1004] [depth= 1] . ( 18 sec) [ -6926.5719] [ 1002] [depth= 2] . ( 19 sec) [ -6926.1910] [ 1003] [depth= 3] . ( 19 sec) [ -6925.8759] [ 1003] [depth= 1] . ( 19 sec) [ -6922.0734] [ 999] [depth= 1] . ( 19 sec) [ -6922.0574] [ 999] [depth= 1] . ( 19 sec) [ -6920.8448] [ 998] [depth= 1] . ( 20 sec) [ -6910.0934] [ 990] [depth= 3] . ( 20 sec) [ -6909.9964] [ 990] [depth= 1] . ( 20 sec) [ -6897.1244] [ 987] [depth= 2] . ( 20 sec) [ -6897.0944] [ 981] [depth= 1] . ( 21 sec) [ -6894.9205] [ 980] [depth= 1] . ( 22 sec) [ -6894.8452] [ 981] [depth= 1] . ( 22 sec) [ -6894.2230] [ 978] [depth= 3] . ( 22 sec) [ -6878.8538] [ 974] [depth= 1] . ( 23 sec) [ -6878.4754] [ 976] [depth= 1] . ( 23 sec) [ -6871.4157] [ 973] [depth= 1] . ( 24 sec) [ -6871.3979] [ 973] [depth= 2] . ( 24 sec) [ -6871.3801] [ 973] [depth= 1] . ( 24 sec) [ -6822.6688] [ 962] [depth= 2] . ( 24 sec) [ -6820.8797] [ 962] [depth= 1] . ( 25 sec) [ -6820.8628] [ 962] [depth= 1] . ( 25 sec) [ -6819.4305] [ 964] [depth= 2] . ( 25 sec) [ -6819.1682] [ 964] [depth= 1] . ( 26 sec) [ -6819.1272] [ 964] [depth= 1] . ( 26 sec) [ -6815.2635] [ 961] [depth= 1] . ( 26 sec) [ -6814.9429] [ 961] [depth= 1] . ( 27 sec) [ -6814.6731] [ 961] [depth= 2] . ( 27 sec) [ -6813.3958] [ 958] [depth= 2] . ( 27 sec) [ -6813.3572] [ 958] [depth= 2] . ( 27 sec) [ -6805.5385] [Branch lengths ] . ( 28 sec) [ -6805.3064] [GTR parameters ] . ( 28 sec) [ -6804.7547] [Alpha ][ 0.275057] . ( 32 sec) [ -6804.0561] [ 957] [depth= 1] . ( 33 sec) [ -6804.0097] [ 957] [depth= 1] . ( 39 sec) [ -6803.9468] [ 957] [depth= 1] . ( 42 sec) [ -6802.3927] [Branch lengths ] . ( 42 sec) [ -6802.3659] [GTR parameters ] . ( 42 sec) [ -6802.3633] [Alpha ][ 0.276409] . ( 43 sec) [ -6802.0368] [ 957] [depth= 1] . ( 45 sec) [ -6802.0096] [ 957] [depth= 1] . ( 47 sec) [ -6801.9796] [ 957] [depth= 1] . ( 53 sec) [ -6801.5720] [ 958] [depth= 1] . ( 57 sec) [ -6797.2618] [Branch lengths ] . ( 57 sec) [ -6797.2469] [GTR parameters ] . ( 57 sec) [ -6797.2469] [Alpha ][ 0.276409] . ( 71 sec) [ -6797.0520] [ 958] [depth= 1] . ( 72 sec) [ -6792.1390] [Branch lengths ] . ( 72 sec) [ -6792.1383] [GTR parameters ] . ( 72 sec) [ -6792.1378] [Alpha ][ 0.277010] . ( 87 sec) [ -6791.9582] [Branch lengths ] . ( 131 sec) [ -6791.9563] [Branch lengths ] . ( 131 sec) [ -6791.9563] [Topology ] . ( 132 sec) [ -6791.9560] [Topology ] . ( 132 sec) [ -6791.9560] [GTR parameters ] . ( 133 sec) [ -6791.9560] [Alpha ][ 0.277010] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.955982. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19319.8473] [GTR parameters ] . ( 1 sec) [ -18931.2841] [Alpha ][ 0.500960] . ( 1 sec) [ -17997.1761] [ 2342] [depth= 14] . ( 1 sec) [ -17712.1477] [ 2324] [depth= 14] . ( 1 sec) [ -17539.0390] [ 2309] [depth= 1] . ( 1 sec) [ -17436.9043] [ 2304] [depth= 9] . ( 1 sec) [ -17326.6110] [ 2268] [depth= 1] . ( 1 sec) [ -17136.0609] [ 2262] [depth= 6] . ( 1 sec) [ -17114.4075] [ 2261] [depth= 1] . ( 1 sec) [ -17104.6193] [ 2259] [depth= 4] . ( 1 sec) [ -17094.5993] [ 2259] [depth= 1] . ( 1 sec) [ -17064.0156] [ 2259] [depth= 4] . ( 1 sec) [ -17056.6618] [ 2261] [depth= 1] . ( 1 sec) [ -16891.1362] [ 2255] [depth= 9] . ( 2 sec) [ -16852.8597] [ 2239] [depth= 2] . ( 2 sec) [ -16796.0947] [ 2241] [depth= 11] . ( 2 sec) [ -16560.7033] [ 2216] [depth= 9] . ( 2 sec) [ -15695.3581] [ 2216] [depth= 2] . ( 2 sec) [ -15634.5255] [ 2181] [depth= 17] . ( 2 sec) [ -15541.7315] [ 2181] [depth= 1] . ( 2 sec) [ -15274.7453] [ 2154] [depth= 20] . ( 2 sec) [ -15174.2254] [ 2125] [depth= 4] . ( 2 sec) [ -15119.9546] [ 2118] [depth= 13] . ( 2 sec) [ -15093.3327] [ 2110] [depth= 3] . ( 2 sec) [ -15085.6641] [ 2106] [depth= 1] . ( 2 sec) [ -15017.2760] [ 2100] [depth= 3] . ( 2 sec) [ -14975.1405] [ 2097] [depth= 18] . ( 2 sec) [ -14231.1845] [ 2023] [depth= 9] . ( 2 sec) [ -14219.1230] [ 2022] [depth= 18] . ( 3 sec) [ -14172.0847] [ 2016] [depth= 16] . ( 3 sec) [ -14106.1018] [ 2004] [depth= 16] . ( 3 sec) [ -14093.2619] [ 2003] [depth= 1] . ( 3 sec) [ -14062.7891] [ 1979] [depth= 7] . ( 3 sec) [ -14038.7639] [ 1978] [depth= 7] . ( 3 sec) [ -14015.7246] [ 1974] [depth= 1] . ( 3 sec) [ -14006.5372] [ 1973] [depth= 20] . ( 3 sec) [ -13954.2028] [ 1954] [depth= 16] . ( 3 sec) [ -13928.5121] [ 1952] [depth= 3] . ( 3 sec) [ -13304.7058] [ 1950] [depth= 1] . ( 3 sec) [ -13221.2044] [ 1950] [depth= 1] . ( 3 sec) [ -13144.5133] [ 1950] [depth= 1] . ( 3 sec) [ -12843.3876] [ 1895] [depth= 25] . ( 3 sec) [ -12786.8977] [ 1900] [depth= 17] . ( 3 sec) [ -12691.1773] [ 1895] [depth= 17] . ( 3 sec) [ -12655.6373] [ 1890] [depth= 14] . ( 4 sec) [ -12622.6640] [ 1891] [depth= 2] . ( 4 sec) [ -12403.9887] [ 1888] [depth= 18] . ( 4 sec) [ -12230.9345] [ 1891] [depth= 1] . ( 4 sec) [ -12023.0054] [ 1852] [depth= 26] . ( 4 sec) [ -11941.5006] [ 1851] [depth= 1] . ( 4 sec) [ -11900.6590] [ 1851] [depth= 1] . ( 4 sec) [ -11900.5517] [ 1851] [depth= 1] . ( 4 sec) [ -11896.6881] [ 1850] [depth= 1] . ( 4 sec) [ -11881.4138] [ 1852] [depth= 1] . ( 4 sec) [ -11851.0989] [ 1843] [depth= 13] . ( 4 sec) [ -11810.4789] [ 1834] [depth= 18] . ( 4 sec) [ -11803.4321] [ 1835] [depth= 1] . ( 4 sec) [ -11619.4089] [ 1804] [depth= 16] . ( 4 sec) [ -11593.3787] [ 1802] [depth= 14] . ( 5 sec) [ -11502.4900] [ 1784] [depth= 1] . ( 5 sec) [ -11457.6769] [ 1781] [depth= 4] . ( 5 sec) [ -11225.8514] [ 1718] [depth= 15] . ( 5 sec) [ -11127.2074] [ 1706] [depth= 8] . ( 5 sec) [ -11046.0139] [ 1695] [depth= 2] . ( 5 sec) [ -11026.9315] [ 1693] [depth= 6] . ( 5 sec) [ -10922.5696] [ 1642] [depth= 11] . ( 5 sec) [ -10894.5971] [ 1644] [depth= 3] . ( 5 sec) [ -10890.8492] [ 1642] [depth= 20] . ( 5 sec) [ -10775.7488] [ 1624] [depth= 19] . ( 5 sec) [ -10708.3728] [ 1628] [depth= 14] . ( 5 sec) [ -10611.1358] [ 1598] [depth= 13] . ( 6 sec) [ -10597.2415] [ 1597] [depth= 1] . ( 6 sec) [ -10581.9598] [ 1599] [depth= 1] . ( 6 sec) [ -10378.7410] [ 1564] [depth= 22] . ( 6 sec) [ -10208.5788] [ 1553] [depth= 12] . ( 6 sec) [ -10089.0763] [ 1528] [depth= 19] . ( 6 sec) [ -9986.3514] [ 1498] [depth= 11] . ( 6 sec) [ -9935.9319] [ 1489] [depth= 13] . ( 6 sec) [ -9902.4189] [ 1482] [depth= 5] . ( 6 sec) [ -9879.7499] [ 1477] [depth= 8] . ( 7 sec) [ -9818.2731] [ 1477] [depth= 19] . ( 7 sec) [ -9664.2423] [ 1455] [depth= 18] . ( 7 sec) [ -9611.6429] [ 1460] [depth= 13] . ( 7 sec) [ -9563.2727] [ 1471] [depth= 1] . ( 7 sec) [ -9444.1437] [ 1452] [depth= 9] . ( 7 sec) [ -9321.0306] [ 1425] [depth= 3] . ( 7 sec) [ -9205.9370] [ 1395] [depth= 11] . ( 7 sec) [ -9123.7493] [ 1364] [depth= 16] . ( 7 sec) [ -8933.0639] [ 1330] [depth= 14] . ( 7 sec) [ -8926.4613] [ 1332] [depth= 1] . ( 7 sec) [ -8830.1137] [ 1305] [depth= 7] . ( 7 sec) [ -8825.7417] [ 1305] [depth= 2] . ( 8 sec) [ -8813.6238] [ 1302] [depth= 1] . ( 8 sec) [ -8711.1284] [ 1303] [depth= 2] . ( 8 sec) [ -8685.0033] [ 1299] [depth= 5] . ( 8 sec) [ -8679.5022] [ 1298] [depth= 1] . ( 8 sec) [ -8659.0591] [ 1297] [depth= 2] . ( 8 sec) [ -8617.8735] [ 1257] [depth= 3] . ( 8 sec) [ -8564.2713] [ 1253] [depth= 1] . ( 8 sec) [ -8381.4987] [ 1258] [depth= 1] . ( 8 sec) [ -8220.6689] [ 1234] [depth= 11] . ( 8 sec) [ -8220.3172] [ 1233] [depth= 2] . ( 8 sec) [ -8209.2237] [ 1244] [depth= 1] . ( 8 sec) [ -8171.0485] [ 1237] [depth= 2] . ( 8 sec) [ -8141.6257] [ 1229] [depth= 1] . ( 8 sec) [ -8124.7682] [ 1229] [depth= 1] . ( 9 sec) [ -8106.1623] [ 1230] [depth= 3] . ( 9 sec) [ -8106.1247] [ 1230] [depth= 2] . ( 9 sec) [ -8101.5965] [ 1227] [depth= 2] . ( 9 sec) [ -8100.7142] [ 1230] [depth= 2] . ( 9 sec) [ -8098.0758] [ 1231] [depth= 1] . ( 9 sec) [ -8064.6565] [ 1235] [depth= 2] . ( 9 sec) [ -8055.8514] [ 1231] [depth= 2] . ( 9 sec) [ -7998.2752] [ 1223] [depth= 1] . ( 9 sec) [ -7973.6952] [ 1214] [depth= 2] . ( 9 sec) [ -7964.5230] [ 1200] [depth= 4] . ( 9 sec) [ -7941.2548] [ 1197] [depth= 2] . ( 10 sec) [ -7893.1744] [ 1186] [depth= 8] . ( 10 sec) [ -7875.4351] [ 1182] [depth= 2] . ( 10 sec) [ -7856.9257] [ 1179] [depth= 2] . ( 10 sec) [ -7855.2733] [ 1179] [depth= 1] . ( 10 sec) [ -7854.0887] [ 1179] [depth= 1] . ( 10 sec) [ -7854.0119] [ 1179] [depth= 2] . ( 10 sec) [ -7849.1703] [ 1178] [depth= 2] . ( 10 sec) [ -7845.0689] [ 1178] [depth= 1] . ( 10 sec) [ -7845.0394] [ 1178] [depth= 1] . ( 11 sec) [ -7844.7465] [ 1178] [depth= 4] . ( 11 sec) [ -7842.1784] [ 1178] [depth= 1] . ( 11 sec) [ -7839.6299] [ 1178] [depth= 1] . ( 11 sec) [ -7836.4591] [ 1176] [depth= 1] . ( 11 sec) [ -7681.5333] [ 1131] [depth= 12] . ( 11 sec) [ -7680.5031] [ 1133] [depth= 1] . ( 11 sec) [ -7673.3028] [ 1131] [depth= 2] . ( 11 sec) [ -7665.7073] [ 1132] [depth= 1] . ( 11 sec) [ -7574.4523] [ 1110] [depth= 11] . ( 11 sec) [ -7562.4842] [ 1107] [depth= 2] . ( 11 sec) [ -7510.0962] [ 1089] [depth= 2] . ( 11 sec) [ -7504.0552] [ 1088] [depth= 3] . ( 11 sec) [ -7503.1989] [ 1088] [depth= 1] . ( 11 sec) [ -7447.4778] [ 1071] [depth= 10] . ( 12 sec) [ -7414.8444] [ 1071] [depth= 2] . ( 12 sec) [ -7355.6444] [ 1049] [depth= 6] . ( 12 sec) [ -7289.3314] [ 1036] [depth= 5] . ( 12 sec) [ -7274.3696] [ 1016] [depth= 3] . ( 12 sec) [ -7268.4638] [ 1014] [depth= 1] . ( 12 sec) [ -7183.8050] [Branch lengths ] . ( 15 sec) [ -7046.3734] [GTR parameters ] . ( 15 sec) [ -7006.0057] [Alpha ][ 0.265033] . ( 15 sec) [ -7005.7218] [ 1014] [depth= 1] . ( 15 sec) [ -6927.0255] [ 990] [depth= 2] . ( 16 sec) [ -6919.9566] [ 987] [depth= 1] . ( 16 sec) [ -6893.2653] [ 980] [depth= 1] . ( 16 sec) [ -6891.9554] [ 979] [depth= 2] . ( 17 sec) [ -6890.2799] [ 979] [depth= 1] . ( 17 sec) [ -6890.2699] [ 979] [depth= 1] . ( 17 sec) [ -6889.7718] [ 978] [depth= 1] . ( 17 sec) [ -6889.2341] [ 979] [depth= 1] . ( 18 sec) [ -6860.0555] [ 973] [depth= 2] . ( 19 sec) [ -6859.6940] [ 973] [depth= 1] . ( 19 sec) [ -6854.8711] [ 968] [depth= 2] . ( 20 sec) [ -6854.4353] [ 968] [depth= 1] . ( 20 sec) [ -6854.3037] [ 968] [depth= 3] . ( 20 sec) [ -6854.0156] [ 968] [depth= 1] . ( 20 sec) [ -6851.9505] [ 968] [depth= 1] . ( 20 sec) [ -6851.5625] [ 968] [depth= 1] . ( 21 sec) [ -6850.6695] [ 968] [depth= 1] . ( 21 sec) [ -6850.6537] [ 968] [depth= 1] . ( 21 sec) [ -6850.3707] [ 968] [depth= 1] . ( 22 sec) [ -6850.3535] [ 968] [depth= 1] . ( 22 sec) [ -6814.6836] [ 956] [depth= 1] . ( 23 sec) [ -6814.2823] [ 957] [depth= 1] . ( 23 sec) [ -6814.2511] [ 957] [depth= 1] . ( 23 sec) [ -6813.2932] [ 958] [depth= 2] . ( 23 sec) [ -6813.2602] [ 959] [depth= 1] . ( 23 sec) [ -6813.2437] [ 959] [depth= 1] . ( 23 sec) [ -6812.0030] [ 958] [depth= 1] . ( 24 sec) [ -6811.9346] [ 958] [depth= 1] . ( 25 sec) [ -6811.7604] [ 958] [depth= 2] . ( 26 sec) [ -6811.2640] [ 958] [depth= 1] . ( 26 sec) [ -6810.9140] [ 958] [depth= 1] . ( 27 sec) [ -6810.0568] [ 959] [depth= 1] . ( 28 sec) [ -6793.0290] [Branch lengths ] . ( 28 sec) [ -6792.8307] [GTR parameters ] . ( 28 sec) [ -6792.6312] [Alpha ][ 0.276413] . ( 31 sec) [ -6792.5566] [ 959] [depth= 1] . ( 39 sec) [ -6792.4029] [ 959] [depth= 1] . ( 42 sec) [ -6792.3278] [ 959] [depth= 1] . ( 43 sec) [ -6791.9702] [Branch lengths ] . ( 43 sec) [ -6791.9674] [GTR parameters ] . ( 43 sec) [ -6791.9671] [Alpha ][ 0.276797] . ( 88 sec) [ -6791.9573] [Branch lengths ] . ( 89 sec) [ -6791.9573] [Topology ] . ( 90 sec) [ -6791.9567] [Topology ] . ( 90 sec) [ -6791.9567] [GTR parameters ] . ( 90 sec) [ -6791.9567] [Alpha ][ 0.276797] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.956657. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -19210.7261] [GTR parameters ] . ( 2 sec) [ -18812.6652] [Alpha ][ 0.500960] . ( 2 sec) [ -18719.4893] [ 2341] [depth= 7] . ( 2 sec) [ -18621.4335] [ 2329] [depth= 10] . ( 2 sec) [ -18451.1737] [ 2308] [depth= 2] . ( 3 sec) [ -18397.5193] [ 2307] [depth= 5] . ( 3 sec) [ -18362.4198] [ 2297] [depth= 1] . ( 3 sec) [ -18219.6633] [ 2293] [depth= 4] . ( 3 sec) [ -18216.4864] [ 2288] [depth= 1] . ( 3 sec) [ -18162.9520] [ 2287] [depth= 5] . ( 3 sec) [ -18155.8430] [ 2274] [depth= 3] . ( 3 sec) [ -18153.6835] [ 2273] [depth= 1] . ( 3 sec) [ -18103.1165] [ 2269] [depth= 12] . ( 3 sec) [ -18056.0359] [ 2269] [depth= 1] . ( 3 sec) [ -17987.0659] [ 2267] [depth= 3] . ( 3 sec) [ -17808.4731] [ 2268] [depth= 13] . ( 3 sec) [ -17561.6317] [ 2214] [depth= 10] . ( 3 sec) [ -17401.7781] [ 2211] [depth= 1] . ( 3 sec) [ -17335.0692] [ 2208] [depth= 6] . ( 3 sec) [ -16357.8131] [ 2188] [depth= 3] . ( 4 sec) [ -15958.2959] [ 2174] [depth= 2] . ( 4 sec) [ -15427.7235] [ 2172] [depth= 5] . ( 4 sec) [ -15390.1445] [ 2172] [depth= 2] . ( 4 sec) [ -15120.1995] [ 2142] [depth= 7] . ( 4 sec) [ -15024.1517] [ 2128] [depth= 5] . ( 4 sec) [ -14812.0340] [ 2116] [depth= 18] . ( 4 sec) [ -14741.6361] [ 2098] [depth= 16] . ( 4 sec) [ -14705.3925] [ 2098] [depth= 1] . ( 4 sec) [ -14549.4067] [ 2083] [depth= 10] . ( 4 sec) [ -14543.7398] [ 2083] [depth= 1] . ( 4 sec) [ -14521.3821] [ 2066] [depth= 1] . ( 4 sec) [ -14251.1610] [ 2011] [depth= 11] . ( 4 sec) [ -14208.6334] [ 1995] [depth= 1] . ( 4 sec) [ -13995.9370] [ 1984] [depth= 11] . ( 4 sec) [ -13929.7166] [ 1982] [depth= 11] . ( 5 sec) [ -13777.1247] [ 1961] [depth= 2] . ( 5 sec) [ -13734.2950] [ 1944] [depth= 9] . ( 5 sec) [ -13598.0375] [ 1932] [depth= 13] . ( 5 sec) [ -13527.2274] [ 1910] [depth= 1] . ( 5 sec) [ -13093.9695] [ 1901] [depth= 18] . ( 5 sec) [ -12991.8322] [ 1864] [depth= 17] . ( 5 sec) [ -12907.9236] [ 1856] [depth= 1] . ( 5 sec) [ -12903.1463] [ 1855] [depth= 1] . ( 5 sec) [ -12738.8908] [ 1826] [depth= 3] . ( 5 sec) [ -12556.0031] [ 1791] [depth= 17] . ( 5 sec) [ -12320.2095] [ 1781] [depth= 7] . ( 5 sec) [ -11507.5017] [ 1722] [depth= 5] . ( 5 sec) [ -11491.1663] [ 1718] [depth= 6] . ( 5 sec) [ -11184.5518] [ 1694] [depth= 14] . ( 5 sec) [ -11183.1288] [ 1694] [depth= 1] . ( 6 sec) [ -11178.6502] [ 1698] [depth= 1] . ( 6 sec) [ -11125.0363] [ 1680] [depth= 1] . ( 6 sec) [ -11083.5259] [ 1679] [depth= 8] . ( 6 sec) [ -10824.5062] [ 1671] [depth= 10] . ( 6 sec) [ -10781.9238] [ 1682] [depth= 1] . ( 6 sec) [ -10781.4859] [ 1682] [depth= 1] . ( 6 sec) [ -10780.1635] [ 1682] [depth= 1] . ( 6 sec) [ -10780.1397] [ 1682] [depth= 1] . ( 6 sec) [ -10579.3337] [ 1632] [depth= 5] . ( 6 sec) [ -10562.1246] [ 1631] [depth= 7] . ( 6 sec) [ -10521.6442] [ 1616] [depth= 7] . ( 6 sec) [ -10420.7112] [ 1591] [depth= 11] . ( 6 sec) [ -10307.2309] [ 1573] [depth= 3] . ( 6 sec) [ -10304.3010] [ 1572] [depth= 1] . ( 6 sec) [ -10303.5634] [ 1572] [depth= 1] . ( 6 sec) [ -10143.0137] [ 1539] [depth= 3] . ( 7 sec) [ -10038.8207] [ 1532] [depth= 1] . ( 7 sec) [ -10038.7291] [ 1533] [depth= 1] . ( 7 sec) [ -10034.6928] [ 1516] [depth= 6] . ( 7 sec) [ -9983.8574] [ 1514] [depth= 2] . ( 7 sec) [ -9900.0027] [ 1498] [depth= 3] . ( 7 sec) [ -9852.4674] [ 1489] [depth= 11] . ( 7 sec) [ -9849.4581] [ 1489] [depth= 1] . ( 7 sec) [ -9772.1128] [ 1470] [depth= 9] . ( 7 sec) [ -9704.5976] [ 1452] [depth= 3] . ( 7 sec) [ -9656.8619] [ 1449] [depth= 1] . ( 7 sec) [ -9604.2044] [ 1441] [depth= 5] . ( 7 sec) [ -9384.1722] [ 1438] [depth= 2] . ( 8 sec) [ -9272.2413] [ 1417] [depth= 1] . ( 8 sec) [ -9173.6825] [ 1391] [depth= 2] . ( 8 sec) [ -9049.6425] [ 1380] [depth= 1] . ( 8 sec) [ -8980.1791] [ 1374] [depth= 2] . ( 8 sec) [ -8923.5701] [ 1375] [depth= 8] . ( 8 sec) [ -8906.3373] [ 1369] [depth= 13] . ( 8 sec) [ -8830.5056] [ 1369] [depth= 1] . ( 8 sec) [ -8801.2677] [ 1374] [depth= 1] . ( 8 sec) [ -8757.3896] [ 1366] [depth= 10] . ( 8 sec) [ -8756.2332] [ 1366] [depth= 1] . ( 8 sec) [ -8743.3324] [ 1366] [depth= 7] . ( 8 sec) [ -8632.2505] [ 1340] [depth= 15] . ( 8 sec) [ -8627.0320] [ 1340] [depth= 1] . ( 8 sec) [ -8624.4086] [ 1340] [depth= 1] . ( 8 sec) [ -8567.9784] [ 1323] [depth= 4] . ( 8 sec) [ -8534.7125] [ 1316] [depth= 4] . ( 9 sec) [ -8479.3189] [ 1310] [depth= 1] . ( 9 sec) [ -8478.8742] [ 1310] [depth= 1] . ( 9 sec) [ -8474.8694] [ 1309] [depth= 1] . ( 9 sec) [ -8473.7388] [ 1309] [depth= 1] . ( 9 sec) [ -8379.2746] [ 1258] [depth= 7] . ( 9 sec) [ -8326.9775] [ 1250] [depth= 9] . ( 9 sec) [ -8321.2534] [ 1248] [depth= 2] . ( 9 sec) [ -8313.1156] [ 1247] [depth= 2] . ( 9 sec) [ -8312.2449] [ 1247] [depth= 2] . ( 9 sec) [ -8198.5498] [ 1215] [depth= 8] . ( 9 sec) [ -8196.0310] [ 1213] [depth= 2] . ( 9 sec) [ -8179.7719] [ 1208] [depth= 1] . ( 10 sec) [ -8175.0775] [ 1207] [depth= 1] . ( 10 sec) [ -8126.8332] [ 1191] [depth= 14] . ( 10 sec) [ -8109.2604] [ 1188] [depth= 5] . ( 10 sec) [ -8102.8990] [ 1189] [depth= 1] . ( 10 sec) [ -8017.1353] [ 1165] [depth= 3] . ( 10 sec) [ -7887.1591] [ 1129] [depth= 5] . ( 10 sec) [ -7866.5032] [ 1123] [depth= 1] . ( 10 sec) [ -7831.8154] [ 1117] [depth= 4] . ( 10 sec) [ -7810.0093] [ 1115] [depth= 3] . ( 10 sec) [ -7809.0677] [ 1117] [depth= 1] . ( 10 sec) [ -7773.5656] [ 1117] [depth= 1] . ( 11 sec) [ -7703.3952] [ 1092] [depth= 7] . ( 11 sec) [ -7685.6122] [ 1094] [depth= 1] . ( 11 sec) [ -7675.6326] [ 1096] [depth= 11] . ( 11 sec) [ -7665.7408] [ 1094] [depth= 1] . ( 11 sec) [ -7659.2013] [ 1093] [depth= 1] . ( 11 sec) [ -7619.7097] [ 1085] [depth= 3] . ( 11 sec) [ -7584.9264] [ 1084] [depth= 2] . ( 11 sec) [ -7577.2621] [ 1084] [depth= 1] . ( 11 sec) [ -7539.5178] [ 1089] [depth= 4] . ( 11 sec) [ -7538.3506] [ 1088] [depth= 1] . ( 11 sec) [ -7522.4390] [ 1084] [depth= 5] . ( 11 sec) [ -7517.9494] [ 1086] [depth= 11] . ( 11 sec) [ -7483.6752] [ 1085] [depth= 2] . ( 11 sec) [ -7483.6543] [ 1085] [depth= 1] . ( 12 sec) [ -7483.5171] [ 1085] [depth= 2] . ( 12 sec) [ -7453.4961] [ 1076] [depth= 4] . ( 12 sec) [ -7453.4847] [ 1076] [depth= 2] . ( 12 sec) [ -7433.9473] [ 1073] [depth= 2] . ( 12 sec) [ -7432.6341] [ 1073] [depth= 1] . ( 12 sec) [ -7431.4003] [ 1073] [depth= 1] . ( 12 sec) [ -7422.8288] [ 1073] [depth= 1] . ( 13 sec) [ -7411.7975] [ 1072] [depth= 3] . ( 13 sec) [ -7405.9201] [ 1071] [depth= 2] . ( 13 sec) [ -7334.0315] [Branch lengths ] . ( 15 sec) [ -7237.6388] [GTR parameters ] . ( 15 sec) [ -7189.5094] [Alpha ][ 0.259304] . ( 15 sec) [ -7175.4059] [ 1064] [depth= 3] . ( 15 sec) [ -7169.8076] [ 1063] [depth= 2] . ( 15 sec) [ -7165.9252] [ 1061] [depth= 1] . ( 15 sec) [ -7159.9674] [ 1059] [depth= 2] . ( 15 sec) [ -7159.8541] [ 1061] [depth= 1] . ( 15 sec) [ -7158.0828] [ 1060] [depth= 1] . ( 16 sec) [ -7153.9773] [ 1057] [depth= 1] . ( 16 sec) [ -7139.2816] [ 1053] [depth= 2] . ( 16 sec) [ -7137.8199] [ 1053] [depth= 1] . ( 16 sec) [ -7136.1952] [ 1052] [depth= 1] . ( 16 sec) [ -7122.3548] [ 1046] [depth= 1] . ( 17 sec) [ -7116.0714] [ 1044] [depth= 1] . ( 17 sec) [ -7073.1915] [ 1029] [depth= 4] . ( 17 sec) [ -7068.6550] [ 1030] [depth= 2] . ( 18 sec) [ -7006.9088] [ 1019] [depth= 9] . ( 18 sec) [ -7005.9083] [ 1019] [depth= 1] . ( 19 sec) [ -7005.0605] [ 1019] [depth= 1] . ( 19 sec) [ -7000.1682] [ 1016] [depth= 1] . ( 19 sec) [ -6997.8190] [ 1014] [depth= 1] . ( 20 sec) [ -6997.8013] [ 1014] [depth= 1] . ( 20 sec) [ -6997.6985] [ 1014] [depth= 1] . ( 20 sec) [ -6977.4699] [ 1006] [depth= 1] . ( 20 sec) [ -6943.0718] [ 998] [depth= 2] . ( 20 sec) [ -6942.9439] [ 998] [depth= 1] . ( 22 sec) [ -6920.7718] [ 991] [depth= 2] . ( 22 sec) [ -6920.7171] [ 992] [depth= 1] . ( 22 sec) [ -6881.0624] [ 978] [depth= 4] . ( 23 sec) [ -6880.6012] [ 977] [depth= 2] . ( 24 sec) [ -6880.2267] [ 977] [depth= 1] . ( 24 sec) [ -6857.6269] [ 971] [depth= 1] . ( 24 sec) [ -6845.0798] [ 969] [depth= 2] . ( 24 sec) [ -6843.6027] [ 967] [depth= 1] . ( 25 sec) [ -6820.0105] [ 960] [depth= 1] . ( 25 sec) [ -6814.9999] [ 958] [depth= 3] . ( 26 sec) [ -6814.9574] [ 958] [depth= 1] . ( 26 sec) [ -6811.3248] [ 958] [depth= 1] . ( 27 sec) [ -6807.7599] [ 960] [depth= 1] . ( 27 sec) [ -6807.0900] [ 960] [depth= 1] . ( 28 sec) [ -6805.1355] [ 960] [depth= 1] . ( 28 sec) [ -6804.8647] [ 960] [depth= 1] . ( 29 sec) [ -6799.2040] [Branch lengths ] . ( 30 sec) [ -6798.9396] [GTR parameters ] . ( 30 sec) [ -6798.4496] [Alpha ][ 0.277024] . ( 30 sec) [ -6797.7310] [ 960] [depth= 1] . ( 33 sec) [ -6792.9624] [ 958] [depth= 1] . ( 39 sec) [ -6792.6734] [ 959] [depth= 2] . ( 43 sec) [ -6792.0190] [Branch lengths ] . ( 44 sec) [ -6791.9669] [GTR parameters ] . ( 44 sec) [ -6791.9669] [Alpha ][ 0.277024] . ( 58 sec) [ -6791.9561] [Branch lengths ] . ( 101 sec) [ -6791.9559] [Branch lengths ] . ( 101 sec) [ -6791.9559] [Topology ] . ( 102 sec) [ -6791.9559] [Topology ] . ( 103 sec) [ -6791.9559] [GTR parameters ] . ( 103 sec) [ -6791.9559] [Alpha ][ 0.277024] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.955855. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18294.4836] [GTR parameters ] . ( 1 sec) [ -17918.1770] [Alpha ][ 0.500960] . ( 1 sec) [ -17814.9606] [ 2362] [depth= 5] . ( 1 sec) [ -17689.4582] [ 2344] [depth= 10] . ( 1 sec) [ -16766.5150] [ 2351] [depth= 1] . ( 1 sec) [ -16633.6087] [ 2344] [depth= 3] . ( 1 sec) [ -16562.4480] [ 2326] [depth= 2] . ( 1 sec) [ -16436.7256] [ 2321] [depth= 5] . ( 2 sec) [ -16430.5128] [ 2317] [depth= 4] . ( 2 sec) [ -16345.5959] [ 2317] [depth= 1] . ( 2 sec) [ -16165.9642] [ 2285] [depth= 9] . ( 2 sec) [ -16063.1756] [ 2282] [depth= 3] . ( 2 sec) [ -15916.4090] [ 2278] [depth= 12] . ( 2 sec) [ -15886.6117] [ 2274] [depth= 2] . ( 2 sec) [ -15861.4627] [ 2273] [depth= 2] . ( 2 sec) [ -15709.9661] [ 2263] [depth= 1] . ( 2 sec) [ -15700.7151] [ 2264] [depth= 1] . ( 2 sec) [ -15539.0397] [ 2247] [depth= 18] . ( 2 sec) [ -15385.4960] [ 2220] [depth= 8] . ( 2 sec) [ -15256.6617] [ 2191] [depth= 7] . ( 2 sec) [ -15209.7594] [ 2190] [depth= 17] . ( 2 sec) [ -15148.1005] [ 2178] [depth= 14] . ( 2 sec) [ -14974.0729] [ 2149] [depth= 12] . ( 2 sec) [ -14897.7009] [ 2147] [depth= 5] . ( 3 sec) [ -14781.8763] [ 2134] [depth= 2] . ( 3 sec) [ -14779.1176] [ 2135] [depth= 2] . ( 3 sec) [ -14660.7687] [ 2110] [depth= 1] . ( 3 sec) [ -14616.2156] [ 2105] [depth= 16] . ( 3 sec) [ -14582.5068] [ 2102] [depth= 13] . ( 3 sec) [ -14554.7510] [ 2092] [depth= 1] . ( 3 sec) [ -14541.3558] [ 2091] [depth= 6] . ( 3 sec) [ -14521.6929] [ 2083] [depth= 12] . ( 3 sec) [ -14446.3912] [ 2082] [depth= 1] . ( 3 sec) [ -14398.1454] [ 2069] [depth= 4] . ( 3 sec) [ -14099.5902] [ 2060] [depth= 2] . ( 3 sec) [ -14072.0024] [ 2049] [depth= 7] . ( 3 sec) [ -13809.1175] [ 2011] [depth= 12] . ( 3 sec) [ -13717.1100] [ 1984] [depth= 14] . ( 3 sec) [ -13712.4761] [ 1976] [depth= 2] . ( 4 sec) [ -13204.1258] [ 1953] [depth= 1] . ( 4 sec) [ -13102.5022] [ 1932] [depth= 5] . ( 4 sec) [ -12502.2728] [ 1909] [depth= 13] . ( 4 sec) [ -12499.9110] [ 1909] [depth= 1] . ( 4 sec) [ -12498.3788] [ 1909] [depth= 1] . ( 4 sec) [ -12319.1229] [ 1897] [depth= 6] . ( 4 sec) [ -12303.2018] [ 1895] [depth= 7] . ( 4 sec) [ -12291.8373] [ 1892] [depth= 1] . ( 4 sec) [ -12134.6557] [ 1838] [depth= 8] . ( 4 sec) [ -11872.1182] [ 1839] [depth= 4] . ( 4 sec) [ -11860.2968] [ 1836] [depth= 13] . ( 4 sec) [ -11700.2638] [ 1841] [depth= 20] . ( 4 sec) [ -11610.7281] [ 1838] [depth= 4] . ( 4 sec) [ -11560.0240] [ 1838] [depth= 1] . ( 5 sec) [ -11505.8032] [ 1838] [depth= 3] . ( 5 sec) [ -11468.2995] [ 1838] [depth= 10] . ( 5 sec) [ -11286.8150] [ 1791] [depth= 13] . ( 5 sec) [ -11273.0158] [ 1790] [depth= 14] . ( 5 sec) [ -11197.9554] [ 1789] [depth= 9] . ( 5 sec) [ -11127.7162] [ 1769] [depth= 3] . ( 5 sec) [ -10999.7279] [ 1743] [depth= 3] . ( 5 sec) [ -10995.3067] [ 1743] [depth= 1] . ( 5 sec) [ -10953.7770] [ 1736] [depth= 2] . ( 5 sec) [ -10916.2181] [ 1733] [depth= 8] . ( 5 sec) [ -10899.0940] [ 1729] [depth= 3] . ( 5 sec) [ -10862.7214] [ 1727] [depth= 8] . ( 5 sec) [ -10831.4875] [ 1718] [depth= 7] . ( 5 sec) [ -10817.9499] [ 1718] [depth= 1] . ( 5 sec) [ -10771.4800] [ 1718] [depth= 1] . ( 5 sec) [ -10748.1013] [ 1713] [depth= 9] . ( 6 sec) [ -10735.3473] [ 1714] [depth= 18] . ( 6 sec) [ -10716.1716] [ 1707] [depth= 10] . ( 6 sec) [ -10666.2802] [ 1700] [depth= 1] . ( 6 sec) [ -10591.6632] [ 1675] [depth= 5] . ( 6 sec) [ -10554.5935] [ 1689] [depth= 1] . ( 6 sec) [ -10444.8285] [ 1672] [depth= 6] . ( 6 sec) [ -10418.6940] [ 1659] [depth= 2] . ( 6 sec) [ -10363.3542] [ 1655] [depth= 8] . ( 6 sec) [ -10164.1804] [ 1641] [depth= 2] . ( 6 sec) [ -10139.2951] [ 1636] [depth= 11] . ( 6 sec) [ -10120.5465] [ 1634] [depth= 1] . ( 6 sec) [ -10007.8679] [ 1597] [depth= 14] . ( 6 sec) [ -9991.5539] [ 1577] [depth= 16] . ( 6 sec) [ -9918.5872] [ 1558] [depth= 9] . ( 6 sec) [ -9871.6064] [ 1544] [depth= 2] . ( 7 sec) [ -9796.2786] [ 1529] [depth= 9] . ( 7 sec) [ -9743.6629] [ 1524] [depth= 2] . ( 7 sec) [ -9491.4192] [ 1524] [depth= 2] . ( 7 sec) [ -9389.2470] [ 1461] [depth= 13] . ( 7 sec) [ -9389.1621] [ 1461] [depth= 1] . ( 7 sec) [ -9388.6275] [ 1461] [depth= 2] . ( 7 sec) [ -9333.3556] [ 1440] [depth= 7] . ( 7 sec) [ -9321.2397] [ 1437] [depth= 1] . ( 7 sec) [ -9315.7508] [ 1436] [depth= 11] . ( 7 sec) [ -9310.1450] [ 1436] [depth= 2] . ( 7 sec) [ -9264.9242] [ 1412] [depth= 4] . ( 7 sec) [ -8872.9303] [ 1372] [depth= 9] . ( 7 sec) [ -8850.0489] [ 1388] [depth= 9] . ( 7 sec) [ -8756.5754] [ 1364] [depth= 6] . ( 8 sec) [ -8740.8806] [ 1364] [depth= 2] . ( 8 sec) [ -8730.8813] [ 1362] [depth= 3] . ( 8 sec) [ -8673.6969] [ 1347] [depth= 2] . ( 8 sec) [ -8666.9709] [ 1346] [depth= 7] . ( 8 sec) [ -8658.7698] [ 1345] [depth= 2] . ( 8 sec) [ -8616.7159] [ 1337] [depth= 6] . ( 8 sec) [ -8589.7675] [ 1333] [depth= 8] . ( 8 sec) [ -8548.3763] [ 1333] [depth= 1] . ( 8 sec) [ -8528.3652] [ 1338] [depth= 1] . ( 8 sec) [ -8408.5785] [ 1305] [depth= 6] . ( 8 sec) [ -8406.4660] [ 1308] [depth= 1] . ( 8 sec) [ -8389.0291] [ 1311] [depth= 2] . ( 9 sec) [ -8329.0228] [ 1291] [depth= 6] . ( 9 sec) [ -8263.4705] [ 1278] [depth= 4] . ( 9 sec) [ -8210.7291] [ 1263] [depth= 3] . ( 9 sec) [ -8129.9795] [ 1237] [depth= 1] . ( 9 sec) [ -8118.4960] [ 1233] [depth= 3] . ( 9 sec) [ -8035.7856] [ 1220] [depth= 8] . ( 9 sec) [ -8025.2381] [ 1212] [depth= 3] . ( 9 sec) [ -8023.2134] [ 1211] [depth= 4] . ( 9 sec) [ -8000.4989] [ 1211] [depth= 1] . ( 9 sec) [ -7984.0757] [ 1208] [depth= 1] . ( 10 sec) [ -7947.2166] [ 1198] [depth= 1] . ( 10 sec) [ -7884.0947] [ 1156] [depth= 6] . ( 10 sec) [ -7868.4776] [ 1154] [depth= 1] . ( 10 sec) [ -7863.1529] [ 1153] [depth= 1] . ( 10 sec) [ -7759.2937] [ 1155] [depth= 2] . ( 10 sec) [ -7758.0274] [ 1157] [depth= 1] . ( 10 sec) [ -7740.1535] [ 1152] [depth= 1] . ( 10 sec) [ -7739.5607] [ 1148] [depth= 3] . ( 10 sec) [ -7683.5229] [ 1138] [depth= 2] . ( 11 sec) [ -7618.0058] [ 1116] [depth= 3] . ( 11 sec) [ -7599.2864] [ 1114] [depth= 3] . ( 11 sec) [ -7578.3301] [ 1114] [depth= 2] . ( 11 sec) [ -7519.5382] [ 1106] [depth= 4] . ( 11 sec) [ -7518.0330] [ 1106] [depth= 1] . ( 11 sec) [ -7517.1696] [ 1106] [depth= 2] . ( 11 sec) [ -7493.3913] [ 1099] [depth= 2] . ( 12 sec) [ -7449.5606] [ 1093] [depth= 4] . ( 12 sec) [ -7409.6508] [ 1096] [depth= 5] . ( 12 sec) [ -7405.4422] [ 1095] [depth= 1] . ( 12 sec) [ -7323.1839] [Branch lengths ] . ( 13 sec) [ -7311.8833] [GTR parameters ] . ( 13 sec) [ -7256.5788] [Alpha ][ 0.250961] . ( 14 sec) [ -7251.7691] [ 1087] [depth= 2] . ( 14 sec) [ -7247.6630] [ 1088] [depth= 1] . ( 14 sec) [ -7218.0407] [ 1070] [depth= 3] . ( 14 sec) [ -7217.9363] [ 1070] [depth= 2] . ( 14 sec) [ -7187.2291] [ 1061] [depth= 3] . ( 14 sec) [ -7186.9583] [ 1060] [depth= 4] . ( 14 sec) [ -7185.5776] [ 1060] [depth= 6] . ( 14 sec) [ -7181.1120] [ 1059] [depth= 2] . ( 14 sec) [ -7177.0901] [ 1057] [depth= 2] . ( 15 sec) [ -7115.9778] [ 1040] [depth= 1] . ( 15 sec) [ -7086.0448] [ 1034] [depth= 5] . ( 15 sec) [ -7083.5392] [ 1033] [depth= 1] . ( 15 sec) [ -7071.9141] [ 1031] [depth= 2] . ( 15 sec) [ -7067.1189] [ 1028] [depth= 4] . ( 15 sec) [ -7062.5737] [ 1024] [depth= 1] . ( 15 sec) [ -7059.8921] [ 1026] [depth= 1] . ( 16 sec) [ -7037.7901] [ 1021] [depth= 1] . ( 16 sec) [ -7037.6630] [ 1022] [depth= 1] . ( 16 sec) [ -7007.3716] [ 1014] [depth= 1] . ( 17 sec) [ -6996.5642] [ 1008] [depth= 2] . ( 17 sec) [ -6996.4678] [ 1008] [depth= 1] . ( 17 sec) [ -6987.3587] [ 1008] [depth= 1] . ( 17 sec) [ -6979.8386] [ 1004] [depth= 3] . ( 17 sec) [ -6961.0144] [ 1001] [depth= 2] . ( 17 sec) [ -6960.2399] [ 1001] [depth= 1] . ( 17 sec) [ -6960.0429] [ 1001] [depth= 4] . ( 17 sec) [ -6959.9958] [ 1001] [depth= 2] . ( 18 sec) [ -6959.9141] [ 1001] [depth= 1] . ( 18 sec) [ -6959.8498] [ 1001] [depth= 1] . ( 18 sec) [ -6917.5783] [ 988] [depth= 5] . ( 18 sec) [ -6856.5519] [ 975] [depth= 1] . ( 18 sec) [ -6846.7935] [ 973] [depth= 1] . ( 19 sec) [ -6836.7703] [ 970] [depth= 1] . ( 19 sec) [ -6831.9025] [ 968] [depth= 1] . ( 19 sec) [ -6830.4989] [ 966] [depth= 1] . ( 20 sec) [ -6830.4225] [ 966] [depth= 1] . ( 20 sec) [ -6830.3876] [ 966] [depth= 1] . ( 20 sec) [ -6829.3140] [ 966] [depth= 1] . ( 20 sec) [ -6829.2487] [ 968] [depth= 1] . ( 21 sec) [ -6826.5553] [ 968] [depth= 1] . ( 21 sec) [ -6826.3960] [ 968] [depth= 1] . ( 21 sec) [ -6826.0462] [ 968] [depth= 1] . ( 21 sec) [ -6826.0267] [ 968] [depth= 1] . ( 21 sec) [ -6825.0474] [ 968] [depth= 1] . ( 21 sec) [ -6823.6168] [ 966] [depth= 1] . ( 22 sec) [ -6823.4695] [ 967] [depth= 1] . ( 22 sec) [ -6823.3249] [ 967] [depth= 1] . ( 23 sec) [ -6823.3074] [ 967] [depth= 1] . ( 23 sec) [ -6816.1509] [ 965] [depth= 1] . ( 24 sec) [ -6813.5626] [ 965] [depth= 1] . ( 24 sec) [ -6813.5461] [ 965] [depth= 1] . ( 25 sec) [ -6812.6219] [ 965] [depth= 1] . ( 25 sec) [ -6806.7517] [ 962] [depth= 1] . ( 26 sec) [ -6800.5110] [Branch lengths ] . ( 27 sec) [ -6800.0529] [GTR parameters ] . ( 27 sec) [ -6799.0534] [Alpha ][ 0.275370] . ( 28 sec) [ -6797.7650] [ 960] [depth= 1] . ( 28 sec) [ -6794.5065] [ 960] [depth= 1] . ( 30 sec) [ -6793.6160] [ 958] [depth= 1] . ( 31 sec) [ -6793.5106] [ 958] [depth= 1] . ( 36 sec) [ -6793.3378] [ 958] [depth= 1] . ( 37 sec) [ -6793.3178] [ 958] [depth= 1] . ( 37 sec) [ -6793.2617] [ 958] [depth= 1] . ( 41 sec) [ -6792.0045] [Branch lengths ] . ( 42 sec) [ -6791.9927] [GTR parameters ] . ( 42 sec) [ -6791.9890] [Alpha ][ 0.276982] . ( 57 sec) [ -6791.9586] [Branch lengths ] . ( 101 sec) [ -6791.9564] [Branch lengths ] . ( 101 sec) [ -6791.9564] [Topology ] . ( 102 sec) [ -6791.9562] [Topology ] . ( 103 sec) [ -6791.9560] [GTR parameters ] . ( 103 sec) [ -6791.9560] [Alpha ][ 0.276982] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.956036. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19619.4409] [GTR parameters ] . ( 1 sec) [ -19219.9874] [Alpha ][ 0.500960] . ( 1 sec) [ -19117.0437] [ 2376] [depth= 4] . ( 1 sec) [ -19059.1858] [ 2352] [depth= 6] . ( 2 sec) [ -18685.1288] [ 2323] [depth= 8] . ( 2 sec) [ -18668.4572] [ 2325] [depth= 1] . ( 2 sec) [ -18533.5682] [ 2313] [depth= 14] . ( 2 sec) [ -18323.5674] [ 2273] [depth= 12] . ( 2 sec) [ -18028.5966] [ 2231] [depth= 14] . ( 2 sec) [ -17879.8637] [ 2223] [depth= 13] . ( 2 sec) [ -17862.9273] [ 2221] [depth= 6] . ( 2 sec) [ -17800.2850] [ 2223] [depth= 5] . ( 2 sec) [ -17624.4203] [ 2191] [depth= 13] . ( 2 sec) [ -17579.8523] [ 2179] [depth= 7] . ( 2 sec) [ -17480.8549] [ 2174] [depth= 2] . ( 2 sec) [ -16691.9986] [ 2155] [depth= 19] . ( 2 sec) [ -16560.3068] [ 2135] [depth= 3] . ( 2 sec) [ -16435.5763] [ 2106] [depth= 14] . ( 2 sec) [ -15485.5672] [ 2081] [depth= 4] . ( 2 sec) [ -15197.9662] [ 2066] [depth= 6] . ( 3 sec) [ -15155.9042] [ 2053] [depth= 1] . ( 3 sec) [ -15047.9817] [ 2054] [depth= 5] . ( 3 sec) [ -14961.8376] [ 2019] [depth= 2] . ( 3 sec) [ -14754.9535] [ 1986] [depth= 10] . ( 3 sec) [ -14674.5109] [ 1971] [depth= 1] . ( 3 sec) [ -14384.9386] [ 1966] [depth= 10] . ( 3 sec) [ -14310.2834] [ 1964] [depth= 13] . ( 3 sec) [ -14220.0763] [ 1949] [depth= 6] . ( 3 sec) [ -14204.9766] [ 1948] [depth= 1] . ( 3 sec) [ -14200.7796] [ 1948] [depth= 7] . ( 3 sec) [ -14021.6200] [ 1896] [depth= 12] . ( 3 sec) [ -13906.5070] [ 1865] [depth= 3] . ( 3 sec) [ -13902.4268] [ 1865] [depth= 1] . ( 3 sec) [ -13901.8826] [ 1865] [depth= 1] . ( 3 sec) [ -13441.6975] [ 1814] [depth= 11] . ( 3 sec) [ -13426.8793] [ 1813] [depth= 8] . ( 4 sec) [ -13425.1966] [ 1813] [depth= 1] . ( 4 sec) [ -13389.8837] [ 1808] [depth= 5] . ( 4 sec) [ -13384.5275] [ 1808] [depth= 1] . ( 4 sec) [ -12912.2103] [ 1793] [depth= 3] . ( 4 sec) [ -12832.7188] [ 1793] [depth= 1] . ( 4 sec) [ -12831.3358] [ 1793] [depth= 2] . ( 4 sec) [ -12821.1684] [ 1784] [depth= 11] . ( 4 sec) [ -12787.5739] [ 1780] [depth= 1] . ( 4 sec) [ -12701.2702] [ 1771] [depth= 1] . ( 4 sec) [ -12517.7923] [ 1763] [depth= 1] . ( 4 sec) [ -12307.2196] [ 1764] [depth= 3] . ( 4 sec) [ -12220.7718] [ 1758] [depth= 6] . ( 4 sec) [ -12078.4600] [ 1731] [depth= 10] . ( 4 sec) [ -11869.0220] [ 1711] [depth= 9] . ( 4 sec) [ -11537.7720] [ 1694] [depth= 11] . ( 4 sec) [ -11466.4447] [ 1680] [depth= 11] . ( 5 sec) [ -11244.5578] [ 1615] [depth= 16] . ( 5 sec) [ -11158.4574] [ 1615] [depth= 8] . ( 5 sec) [ -11144.4986] [ 1611] [depth= 1] . ( 5 sec) [ -11000.7059] [ 1591] [depth= 11] . ( 5 sec) [ -10779.3631] [ 1583] [depth= 4] . ( 5 sec) [ -10698.6180] [ 1583] [depth= 3] . ( 5 sec) [ -10661.6730] [ 1576] [depth= 2] . ( 5 sec) [ -10650.2794] [ 1575] [depth= 2] . ( 5 sec) [ -10525.1957] [ 1535] [depth= 5] . ( 5 sec) [ -10513.1071] [ 1533] [depth= 1] . ( 5 sec) [ -10469.2616] [ 1523] [depth= 1] . ( 5 sec) [ -10347.3307] [ 1519] [depth= 11] . ( 5 sec) [ -10329.3275] [ 1517] [depth= 8] . ( 5 sec) [ -10328.7111] [ 1517] [depth= 1] . ( 5 sec) [ -10288.1873] [ 1516] [depth= 1] . ( 6 sec) [ -10270.7221] [ 1505] [depth= 5] . ( 6 sec) [ -10094.8985] [ 1438] [depth= 13] . ( 6 sec) [ -10007.0964] [ 1408] [depth= 8] . ( 6 sec) [ -10006.3069] [ 1410] [depth= 1] . ( 6 sec) [ -10006.2297] [ 1402] [depth= 1] . ( 6 sec) [ -9979.1313] [ 1399] [depth= 5] . ( 6 sec) [ -9978.7384] [ 1399] [depth= 1] . ( 6 sec) [ -9932.1209] [ 1403] [depth= 9] . ( 6 sec) [ -9917.4926] [ 1405] [depth= 1] . ( 6 sec) [ -9790.9764] [ 1375] [depth= 11] . ( 6 sec) [ -9790.6396] [ 1376] [depth= 8] . ( 6 sec) [ -9667.6406] [ 1342] [depth= 9] . ( 6 sec) [ -9412.4305] [ 1331] [depth= 5] . ( 6 sec) [ -9329.3807] [ 1340] [depth= 2] . ( 7 sec) [ -9095.9813] [ 1311] [depth= 3] . ( 7 sec) [ -8790.6928] [ 1266] [depth= 15] . ( 7 sec) [ -8752.3954] [ 1227] [depth= 7] . ( 7 sec) [ -8749.7809] [ 1226] [depth= 1] . ( 7 sec) [ -8696.8166] [ 1219] [depth= 11] . ( 7 sec) [ -8684.2093] [ 1216] [depth= 1] . ( 7 sec) [ -8586.0002] [ 1195] [depth= 7] . ( 7 sec) [ -8585.9516] [ 1195] [depth= 2] . ( 7 sec) [ -8582.3139] [ 1195] [depth= 1] . ( 7 sec) [ -8565.5970] [ 1193] [depth= 2] . ( 7 sec) [ -8555.1422] [ 1191] [depth= 2] . ( 7 sec) [ -8519.2441] [ 1183] [depth= 2] . ( 7 sec) [ -8508.1513] [ 1180] [depth= 1] . ( 7 sec) [ -8467.4429] [ 1168] [depth= 4] . ( 7 sec) [ -8417.5377] [ 1169] [depth= 7] . ( 7 sec) [ -8374.8576] [ 1164] [depth= 1] . ( 8 sec) [ -7993.1554] [ 1199] [depth= 1] . ( 8 sec) [ -7853.9897] [ 1164] [depth= 1] . ( 8 sec) [ -7805.3808] [ 1153] [depth= 1] . ( 8 sec) [ -7781.2135] [ 1145] [depth= 5] . ( 8 sec) [ -7695.3142] [ 1125] [depth= 5] . ( 8 sec) [ -7687.9056] [ 1125] [depth= 6] . ( 8 sec) [ -7603.3091] [ 1105] [depth= 8] . ( 8 sec) [ -7602.9110] [ 1105] [depth= 1] . ( 8 sec) [ -7599.3172] [ 1105] [depth= 2] . ( 8 sec) [ -7597.7290] [ 1104] [depth= 3] . ( 8 sec) [ -7582.3029] [ 1102] [depth= 2] . ( 8 sec) [ -7569.1461] [ 1100] [depth= 2] . ( 8 sec) [ -7507.6872] [ 1089] [depth= 8] . ( 8 sec) [ -7506.0253] [ 1089] [depth= 1] . ( 9 sec) [ -7505.4229] [ 1089] [depth= 1] . ( 9 sec) [ -7504.9793] [ 1089] [depth= 1] . ( 9 sec) [ -7500.9110] [ 1090] [depth= 2] . ( 9 sec) [ -7490.0368] [ 1088] [depth= 2] . ( 9 sec) [ -7472.8115] [ 1081] [depth= 3] . ( 9 sec) [ -7460.2878] [ 1076] [depth= 1] . ( 9 sec) [ -7460.2030] [ 1074] [depth= 2] . ( 9 sec) [ -7400.7045] [ 1057] [depth= 4] . ( 9 sec) [ -7400.5046] [ 1059] [depth= 2] . ( 9 sec) [ -7398.7134] [ 1060] [depth= 1] . ( 9 sec) [ -7390.2221] [ 1058] [depth= 1] . ( 10 sec) [ -7389.2798] [ 1057] [depth= 1] . ( 10 sec) [ -7388.1353] [ 1057] [depth= 1] . ( 10 sec) [ -7385.7978] [ 1057] [depth= 1] . ( 10 sec) [ -7380.1129] [ 1054] [depth= 1] . ( 11 sec) [ -7367.5408] [ 1054] [depth= 2] . ( 11 sec) [ -7367.1958] [ 1053] [depth= 2] . ( 11 sec) [ -7366.6336] [ 1053] [depth= 2] . ( 11 sec) [ -7363.3337] [ 1055] [depth= 1] . ( 11 sec) [ -7356.3760] [ 1051] [depth= 2] . ( 11 sec) [ -7355.8070] [ 1051] [depth= 1] . ( 11 sec) [ -7344.2441] [ 1050] [depth= 2] . ( 12 sec) [ -7279.7730] [ 1036] [depth= 2] . ( 12 sec) [ -7263.9368] [ 1035] [depth= 1] . ( 12 sec) [ -7259.5265] [ 1034] [depth= 1] . ( 12 sec) [ -7259.1197] [ 1034] [depth= 2] . ( 12 sec) [ -7255.4204] [ 1033] [depth= 1] . ( 12 sec) [ -7176.6450] [Branch lengths ] . ( 14 sec) [ -7103.0574] [GTR parameters ] . ( 14 sec) [ -7059.5837] [Alpha ][ 0.263766] . ( 14 sec) [ -7015.8081] [ 1025] [depth= 2] . ( 15 sec) [ -7015.3374] [ 1025] [depth= 1] . ( 15 sec) [ -6960.0534] [ 1007] [depth= 2] . ( 16 sec) [ -6945.8026] [ 999] [depth= 2] . ( 16 sec) [ -6938.0477] [ 994] [depth= 2] . ( 16 sec) [ -6937.7926] [ 994] [depth= 1] . ( 16 sec) [ -6936.8229] [ 990] [depth= 2] . ( 17 sec) [ -6930.9135] [ 990] [depth= 1] . ( 17 sec) [ -6917.7355] [ 982] [depth= 2] . ( 17 sec) [ -6917.2570] [ 981] [depth= 1] . ( 17 sec) [ -6915.1163] [ 980] [depth= 1] . ( 18 sec) [ -6908.7690] [ 978] [depth= 1] . ( 18 sec) [ -6904.5792] [ 979] [depth= 1] . ( 19 sec) [ -6904.5591] [ 980] [depth= 3] . ( 19 sec) [ -6868.9562] [ 972] [depth= 1] . ( 19 sec) [ -6868.9384] [ 972] [depth= 1] . ( 19 sec) [ -6868.7854] [ 972] [depth= 1] . ( 20 sec) [ -6868.7617] [ 972] [depth= 1] . ( 21 sec) [ -6865.6254] [ 972] [depth= 1] . ( 21 sec) [ -6864.9949] [ 972] [depth= 1] . ( 22 sec) [ -6864.4379] [ 973] [depth= 1] . ( 23 sec) [ -6864.3403] [ 973] [depth= 1] . ( 25 sec) [ -6863.6888] [ 972] [depth= 1] . ( 27 sec) [ -6818.5502] [ 958] [depth= 4] . ( 27 sec) [ -6818.5116] [ 958] [depth= 1] . ( 27 sec) [ -6818.5012] [ 958] [depth= 1] . ( 28 sec) [ -6795.6970] [Branch lengths ] . ( 29 sec) [ -6795.3033] [GTR parameters ] . ( 29 sec) [ -6795.1105] [Alpha ][ 0.274722] . ( 41 sec) [ -6795.0304] [ 958] [depth= 1] . ( 44 sec) [ -6792.3211] [Branch lengths ] . ( 44 sec) [ -6792.3141] [GTR parameters ] . ( 44 sec) [ -6792.3060] [Alpha ][ 0.277102] . ( 59 sec) [ -6791.9778] [Branch lengths ] . ( 103 sec) [ -6791.9595] [Branch lengths ] . ( 103 sec) [ -6791.9595] [Topology ] . ( 104 sec) [ -6791.9580] [Topology ] . ( 105 sec) [ -6791.9575] [Topology ] . ( 106 sec) [ -6791.9567] [GTR parameters ] . ( 106 sec) [ -6791.9567] [Alpha ][ 0.276825] . ( 106 sec) [ -6791.9567] [Topology ] . ( 107 sec) [ -6791.9563] [Topology ] . ( 107 sec) [ -6791.9563] [GTR parameters ] . ( 107 sec) [ -6791.9563] [Alpha ][ 0.276825] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6791.956344. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7007.3560] [GTR parameters ] . ( 2 sec) [ -6925.4087] [Alpha ][ 0.500960] . ( 2 sec) [ -6925.4087] [Topology ] . ( 3 sec) [ -6848.6098] [Topology ] . ( 4 sec) [ -6831.2831] [Topology ] . ( 6 sec) [ -6827.5568] [Topology ] . ( 7 sec) [ -6826.0300] [Topology ] . ( 8 sec) [ -6825.4490] [Topology ] . ( 9 sec) [ -6825.2395] [Topology ] . ( 10 sec) [ -6825.1698] [Topology ] . ( 11 sec) [ -6825.1447] [Topology ] . ( 13 sec) [ -6825.1351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 21 sec) [ -6824.9189] [Topology ] . ( 22 sec) [ -6824.8588] [GTR parameters ] . ( 22 sec) [ -6793.4815] [Alpha ][ 0.278369] . ( 22 sec) [ -6793.4815] [Topology ] . ( 23 sec) [ -6793.2337] [Topology ] . ( 24 sec) [ -6793.1641] [Topology ] . ( 25 sec) [ -6793.1308] [Topology ] . ( 27 sec) [ -6793.1140] [Topology ] . ( 28 sec) [ -6793.1054] [Topology ] . ( 29 sec) [ -6793.1011] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -6792.9534] [Topology ] . ( 38 sec) [ -6792.7485] [GTR parameters ] . ( 38 sec) [ -6792.7442] [Alpha ][ 0.276515] . ( 38 sec) [ -6792.7442] [Topology ] . ( 39 sec) [ -6792.6671] [Topology ] . ( 40 sec) [ -6792.6469] [Topology ] . ( 42 sec) [ -6792.6391] [Topology ] . ( 43 sec) [ -6792.6357] [Topology ] . ( 44 sec) [ -6792.6341] [Topology ] . ( 45 sec) [ -6792.6333] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -6792.5556] [Topology ] . ( 54 sec) [ -6792.5462] [GTR parameters ] . ( 54 sec) [ -6792.5460] [Alpha ][ 0.276824] . ( 54 sec) [ -6792.5460] [Topology ] . ( 55 sec) [ -6792.0186] [Topology ] . ( 56 sec) [ -6791.9663] [Topology ] . ( 57 sec) [ -6791.9610] [Topology ] . ( 59 sec) [ -6791.9601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -6791.9559] [GTR parameters ] . ( 68 sec) [ -6791.9559] [Alpha ][ 0.276824] . ( 68 sec) [ -6791.9559] [Topology ] . ( 69 sec) [ -6791.9557] [Topology ] . Checking for NNIs, optimizing five branches... . ( 77 sec) [ -6791.9556] [GTR parameters ] . ( 78 sec) [ -6791.9556] [Alpha ][ 0.276824] . ( 78 sec) [ -6791.9556] [Topology ] . ( 79 sec) [ -6791.9556] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 97 sec) [ -7007.3560] [GTR parameters ] . ( 97 sec) [ -6925.4087] [Alpha ][ 0.500960] . ( 97 sec) [ -6925.3545] [ 965] [depth= 1] . ( 97 sec) [ -6925.3355] [ 965] [depth= 1] . ( 97 sec) [ -6925.3142] [ 965] [depth= 1] . ( 97 sec) [ -6922.0750] [ 965] [depth= 2] . ( 98 sec) [ -6922.0117] [ 965] [depth= 1] . ( 98 sec) [ -6921.6923] [ 965] [depth= 1] . ( 98 sec) [ -6921.4604] [ 965] [depth= 1] . ( 98 sec) [ -6921.4480] [ 965] [depth= 1] . ( 99 sec) [ -6920.0256] [ 965] [depth= 1] . ( 99 sec) [ -6919.4940] [ 965] [depth= 1] . ( 99 sec) [ -6918.9738] [ 965] [depth= 3] . ( 99 sec) [ -6917.6880] [ 965] [depth= 1] . ( 99 sec) [ -6917.3110] [ 965] [depth= 1] . ( 99 sec) [ -6908.0135] [ 966] [depth= 1] . ( 99 sec) [ -6906.1612] [ 968] [depth= 1] . ( 99 sec) [ -6904.1512] [ 966] [depth= 1] . ( 99 sec) [ -6902.8193] [ 966] [depth= 1] . ( 99 sec) [ -6901.8640] [ 966] [depth= 1] . ( 102 sec) [ -6894.5646] [ 964] [depth= 2] . ( 102 sec) [ -6891.9879] [ 962] [depth= 1] . ( 103 sec) [ -6887.2451] [ 962] [depth= 1] . ( 103 sec) [ -6887.1358] [ 962] [depth= 1] . ( 103 sec) [ -6887.0553] [ 963] [depth= 1] . ( 104 sec) [ -6884.1030] [ 962] [depth= 1] . ( 104 sec) [ -6875.8546] [ 959] [depth= 1] . ( 106 sec) [ -6875.7013] [ 961] [depth= 1] . ( 106 sec) [ -6868.8417] [ 959] [depth= 1] . ( 107 sec) [ -6868.2051] [ 959] [depth= 1] . ( 107 sec) [ -6866.2390] [ 959] [depth= 1] . ( 107 sec) [ -6862.1974] [ 958] [depth= 1] . ( 108 sec) [ -6861.9667] [ 958] [depth= 1] . ( 108 sec) [ -6861.8849] [ 958] [depth= 1] . ( 108 sec) [ -6861.8248] [ 958] [depth= 1] . ( 108 sec) [ -6861.1538] [ 958] [depth= 1] . ( 108 sec) [ -6861.1391] [ 958] [depth= 1] . ( 109 sec) [ -6861.1256] [ 958] [depth= 1] . ( 109 sec) [ -6861.1092] [ 958] [depth= 1] . ( 109 sec) [ -6861.0913] [ 958] [depth= 1] . ( 110 sec) [ -6827.2596] [Branch lengths ] . ( 111 sec) [ -6827.2170] [GTR parameters ] . ( 111 sec) [ -6796.4574] [Alpha ][ 0.275898] . ( 113 sec) [ -6796.3034] [ 957] [depth= 1] . ( 115 sec) [ -6795.4649] [ 957] [depth= 1] . ( 125 sec) [ -6792.9270] [Branch lengths ] . ( 126 sec) [ -6792.7223] [GTR parameters ] . ( 126 sec) [ -6792.7202] [Alpha ][ 0.277144] . ( 136 sec) [ -6792.6824] [ 958] [depth= 1] . ( 140 sec) [ -6792.1049] [Branch lengths ] . ( 141 sec) [ -6792.0766] [GTR parameters ] . ( 141 sec) [ -6792.0763] [Alpha ][ 0.276627] . ( 187 sec) [ -6791.9760] [Branch lengths ] . ( 187 sec) [ -6791.9760] [Topology ] . ( 188 sec) [ -6791.9648] [Topology ] . ( 189 sec) [ -6791.9607] [Topology ] . ( 191 sec) [ -6791.9586] [Topology ] . ( 192 sec) [ -6791.9575] [Topology ] . ( 193 sec) [ -6791.9570] [Topology ] . ( 193 sec) [ -6791.9565] [GTR parameters ] . ( 193 sec) [ -6791.9564] [Alpha ][ 0.276904] . ( 193 sec) [ -6791.9564] [Topology ] . ( 194 sec) [ -6791.9561] [Topology ] . ( 195 sec) [ -6791.9561] [GTR parameters ] . ( 195 sec) [ -6791.9561] [Alpha ][ 0.276904] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6791.955578 . Log likelihood obtained after SPR moves : -6791.956055 . Log likelihood of the current tree: -6791.955578. . Printing the most likely tree in file 'nucleic_M2567_64x1044_2006.phy_phyml_tree.txt'... . Best log likelihood : -6791.955578 . Time used 0h3m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 778.17user 0.00system 13:04.71elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps