.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2770_86x1628_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 . Compressing sequences... . 571 patterns found. (out of a total of 1628 sites) . 1267 sites without polymorphism (77.83%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -15595.1783] [GTR parameters ] . ( 6 sec) [ -15316.3240] [Alpha ][ 0.500960] . ( 6 sec) [ -15032.5607] [ 1816] [depth= 11] . ( 6 sec) [ -14953.1024] [ 1808] [depth= 6] . ( 6 sec) [ -14878.6165] [ 1807] [depth= 10] . ( 6 sec) [ -14845.9654] [ 1799] [depth= 1] . ( 6 sec) [ -14793.4669] [ 1798] [depth= 16] . ( 6 sec) [ -14590.3137] [ 1798] [depth= 3] . ( 6 sec) [ -14566.4928] [ 1798] [depth= 1] . ( 6 sec) [ -14553.6876] [ 1775] [depth= 2] . ( 7 sec) [ -14458.1007] [ 1775] [depth= 4] . ( 7 sec) [ -14434.2983] [ 1767] [depth= 7] . ( 7 sec) [ -14386.2964] [ 1767] [depth= 5] . ( 7 sec) [ -14189.4963] [ 1738] [depth= 4] . ( 7 sec) [ -14128.5734] [ 1734] [depth= 4] . ( 7 sec) [ -14081.7139] [ 1734] [depth= 9] . ( 7 sec) [ -13874.5930] [ 1700] [depth= 14] . ( 7 sec) [ -13775.4414] [ 1689] [depth= 9] . ( 7 sec) [ -13618.1263] [ 1682] [depth= 6] . ( 8 sec) [ -13611.9836] [ 1682] [depth= 1] . ( 8 sec) [ -13472.3927] [ 1646] [depth= 8] . ( 8 sec) [ -13425.8423] [ 1645] [depth= 1] . ( 8 sec) [ -13414.1603] [ 1644] [depth= 12] . ( 8 sec) [ -13388.1146] [ 1640] [depth= 13] . ( 8 sec) [ -13322.8911] [ 1644] [depth= 9] . ( 9 sec) [ -13205.7101] [ 1633] [depth= 15] . ( 9 sec) [ -13197.4522] [ 1628] [depth= 4] . ( 9 sec) [ -13104.0128] [ 1622] [depth= 1] . ( 9 sec) [ -12758.3676] [ 1621] [depth= 6] . ( 9 sec) [ -12739.2208] [ 1598] [depth= 9] . ( 9 sec) [ -12630.2577] [ 1594] [depth= 19] . ( 9 sec) [ -12609.1659] [ 1592] [depth= 20] . ( 9 sec) [ -12481.4078] [ 1591] [depth= 12] . ( 10 sec) [ -12323.7121] [ 1551] [depth= 10] . ( 10 sec) [ -12253.2730] [ 1544] [depth= 27] . ( 10 sec) [ -12186.8143] [ 1548] [depth= 22] . ( 10 sec) [ -12134.5094] [ 1544] [depth= 22] . ( 10 sec) [ -12077.6653] [ 1543] [depth= 10] . ( 10 sec) [ -11948.9537] [ 1539] [depth= 8] . ( 10 sec) [ -11899.2581] [ 1534] [depth= 3] . ( 10 sec) [ -11830.0411] [ 1534] [depth= 3] . ( 11 sec) [ -11776.1972] [ 1525] [depth= 8] . ( 11 sec) [ -11772.5888] [ 1525] [depth= 1] . ( 11 sec) [ -11713.9795] [ 1523] [depth= 2] . ( 11 sec) [ -11600.2858] [ 1504] [depth= 4] . ( 11 sec) [ -11588.1849] [ 1503] [depth= 8] . ( 11 sec) [ -11583.7793] [ 1503] [depth= 8] . ( 11 sec) [ -11573.7670] [ 1504] [depth= 7] . ( 11 sec) [ -11540.2578] [ 1503] [depth= 4] . ( 11 sec) [ -11537.5622] [ 1503] [depth= 1] . ( 12 sec) [ -11523.7592] [ 1499] [depth= 6] . ( 12 sec) [ -11468.7245] [ 1489] [depth= 16] . ( 12 sec) [ -11413.9714] [ 1480] [depth= 9] . ( 12 sec) [ -11293.4017] [ 1480] [depth= 1] . ( 12 sec) [ -11287.5442] [ 1480] [depth= 1] . ( 12 sec) [ -11244.1290] [ 1472] [depth= 6] . ( 12 sec) [ -11119.9371] [ 1434] [depth= 11] . ( 13 sec) [ -11107.7420] [ 1433] [depth= 2] . ( 13 sec) [ -11023.3969] [ 1421] [depth= 5] . ( 13 sec) [ -10985.7329] [ 1414] [depth= 12] . ( 13 sec) [ -10955.8988] [ 1409] [depth= 8] . ( 13 sec) [ -10909.6736] [ 1408] [depth= 12] . ( 13 sec) [ -10785.8333] [ 1368] [depth= 10] . ( 13 sec) [ -10777.1577] [ 1368] [depth= 2] . ( 13 sec) [ -10765.3546] [ 1369] [depth= 1] . ( 13 sec) [ -10710.0213] [ 1359] [depth= 17] . ( 13 sec) [ -10686.1874] [ 1356] [depth= 7] . ( 14 sec) [ -10660.3840] [ 1361] [depth= 1] . ( 14 sec) [ -10604.0088] [ 1349] [depth= 6] . ( 14 sec) [ -10575.6359] [ 1344] [depth= 1] . ( 14 sec) [ -10529.5980] [ 1334] [depth= 5] . ( 14 sec) [ -10523.5849] [ 1335] [depth= 3] . ( 14 sec) [ -10516.7072] [ 1334] [depth= 23] . ( 14 sec) [ -10514.6222] [ 1334] [depth= 1] . ( 15 sec) [ -10474.1599] [ 1328] [depth= 19] . ( 15 sec) [ -10433.3560] [ 1328] [depth= 11] . ( 15 sec) [ -10360.9146] [ 1321] [depth= 9] . ( 15 sec) [ -10278.2870] [ 1320] [depth= 6] . ( 15 sec) [ -10151.5179] [ 1288] [depth= 6] . ( 15 sec) [ -10120.6597] [ 1283] [depth= 9] . ( 15 sec) [ -9943.8488] [ 1259] [depth= 7] . ( 15 sec) [ -9931.7330] [ 1258] [depth= 5] . ( 16 sec) [ -9834.6851] [ 1228] [depth= 16] . ( 16 sec) [ -9806.1685] [ 1229] [depth= 1] . ( 16 sec) [ -9662.9732] [ 1190] [depth= 6] . ( 16 sec) [ -9648.3129] [ 1189] [depth= 2] . ( 16 sec) [ -9520.4368] [ 1163] [depth= 2] . ( 16 sec) [ -9520.1754] [ 1163] [depth= 1] . ( 16 sec) [ -9491.2533] [ 1152] [depth= 8] . ( 16 sec) [ -9481.3466] [ 1155] [depth= 2] . ( 17 sec) [ -9443.5875] [ 1151] [depth= 9] . ( 17 sec) [ -9434.9267] [ 1150] [depth= 5] . ( 17 sec) [ -9396.5521] [ 1152] [depth= 2] . ( 17 sec) [ -9359.4284] [ 1143] [depth= 4] . ( 17 sec) [ -9278.2047] [ 1131] [depth= 9] . ( 18 sec) [ -9252.8605] [ 1130] [depth= 16] . ( 18 sec) [ -9162.9353] [ 1098] [depth= 2] . ( 18 sec) [ -9135.5152] [ 1096] [depth= 2] . ( 18 sec) [ -9119.9133] [ 1093] [depth= 1] . ( 18 sec) [ -9087.0495] [ 1091] [depth= 3] . ( 18 sec) [ -9074.0550] [ 1093] [depth= 15] . ( 19 sec) [ -9044.2291] [ 1089] [depth= 2] . ( 19 sec) [ -9001.7664] [ 1080] [depth= 14] . ( 19 sec) [ -8848.0811] [ 1053] [depth= 8] . ( 19 sec) [ -8821.0161] [ 1051] [depth= 6] . ( 19 sec) [ -8564.8528] [ 1011] [depth= 12] . ( 20 sec) [ -8551.8545] [ 1010] [depth= 14] . ( 20 sec) [ -8550.0340] [ 1010] [depth= 1] . ( 20 sec) [ -8497.5064] [ 1003] [depth= 11] . ( 20 sec) [ -8429.5634] [ 1003] [depth= 14] . ( 20 sec) [ -8425.0029] [ 1001] [depth= 13] . ( 20 sec) [ -8398.8748] [ 994] [depth= 1] . ( 20 sec) [ -8380.8175] [ 990] [depth= 5] . ( 21 sec) [ -8349.1037] [ 985] [depth= 12] . ( 21 sec) [ -8221.0535] [ 952] [depth= 11] . ( 21 sec) [ -8211.5432] [ 952] [depth= 2] . ( 21 sec) [ -8196.3647] [ 950] [depth= 11] . ( 21 sec) [ -8188.5377] [ 950] [depth= 1] . ( 21 sec) [ -8036.2108] [ 949] [depth= 4] . ( 21 sec) [ -8021.9877] [ 945] [depth= 12] . ( 21 sec) [ -8002.3330] [ 940] [depth= 1] . ( 21 sec) [ -7837.4068] [ 899] [depth= 11] . ( 22 sec) [ -7835.9143] [ 899] [depth= 10] . ( 22 sec) [ -7831.3822] [ 899] [depth= 1] . ( 22 sec) [ -7788.5146] [ 894] [depth= 8] . ( 22 sec) [ -7786.3934] [ 894] [depth= 2] . ( 22 sec) [ -7785.4651] [ 894] [depth= 16] . ( 22 sec) [ -7729.3153] [ 881] [depth= 17] . ( 22 sec) [ -7722.9141] [ 881] [depth= 1] . ( 22 sec) [ -7717.0299] [ 880] [depth= 5] . ( 23 sec) [ -7716.3088] [ 885] [depth= 12] . ( 23 sec) [ -7698.0366] [ 885] [depth= 7] . ( 23 sec) [ -7697.8100] [ 886] [depth= 1] . ( 23 sec) [ -7680.6012] [ 884] [depth= 6] . ( 24 sec) [ -7673.2717] [ 881] [depth= 4] . ( 24 sec) [ -7659.9090] [ 879] [depth= 7] . ( 24 sec) [ -7640.5351] [ 874] [depth= 6] . ( 24 sec) [ -7639.2507] [ 874] [depth= 1] . ( 24 sec) [ -7633.9603] [ 873] [depth= 3] . ( 24 sec) [ -7596.6676] [ 863] [depth= 6] . ( 24 sec) [ -7522.9133] [ 842] [depth= 3] . ( 24 sec) [ -7521.3531] [ 842] [depth= 1] . ( 25 sec) [ -7471.4269] [ 835] [depth= 4] . ( 25 sec) [ -7460.2149] [ 833] [depth= 11] . ( 25 sec) [ -7459.9849] [ 833] [depth= 1] . ( 25 sec) [ -7409.3372] [ 818] [depth= 7] . ( 25 sec) [ -7393.0217] [ 813] [depth= 9] . ( 25 sec) [ -7286.9548] [ 798] [depth= 9] . ( 26 sec) [ -7208.7268] [ 786] [depth= 9] . ( 26 sec) [ -7169.4653] [ 779] [depth= 1] . ( 26 sec) [ -7156.1603] [ 763] [depth= 5] . ( 26 sec) [ -7079.0116] [ 750] [depth= 10] . ( 26 sec) [ -7076.5828] [ 751] [depth= 1] . ( 26 sec) [ -7073.7270] [ 751] [depth= 2] . ( 26 sec) [ -7073.5297] [ 751] [depth= 8] . ( 27 sec) [ -7042.0071] [ 737] [depth= 1] . ( 27 sec) [ -7033.0107] [ 737] [depth= 1] . ( 27 sec) [ -6980.0064] [ 711] [depth= 4] . ( 27 sec) [ -6978.0498] [ 711] [depth= 1] . ( 27 sec) [ -6972.9956] [ 710] [depth= 2] . ( 27 sec) [ -6968.5641] [ 710] [depth= 1] . ( 28 sec) [ -6952.1861] [ 698] [depth= 2] . ( 28 sec) [ -6925.4718] [ 694] [depth= 3] . ( 28 sec) [ -6922.2822] [ 689] [depth= 8] . ( 28 sec) [ -6806.3648] [ 663] [depth= 8] . ( 28 sec) [ -6796.9494] [ 661] [depth= 2] . ( 28 sec) [ -6790.8911] [ 660] [depth= 7] . ( 28 sec) [ -6782.4147] [ 660] [depth= 3] . ( 28 sec) [ -6722.5103] [ 650] [depth= 4] . ( 29 sec) [ -6662.7248] [ 648] [depth= 5] . ( 29 sec) [ -6658.0396] [ 647] [depth= 1] . ( 29 sec) [ -6651.0169] [ 647] [depth= 2] . ( 29 sec) [ -6650.6643] [ 647] [depth= 2] . ( 29 sec) [ -6646.6356] [ 647] [depth= 1] . ( 29 sec) [ -6631.5410] [ 646] [depth= 4] . ( 30 sec) [ -6616.3874] [ 645] [depth= 3] . ( 30 sec) [ -6561.8526] [ 637] [depth= 3] . ( 30 sec) [ -6550.8438] [ 636] [depth= 1] . ( 30 sec) [ -6543.4604] [ 635] [depth= 4] . ( 30 sec) [ -6540.5881] [ 635] [depth= 1] . ( 30 sec) [ -6539.2202] [ 635] [depth= 1] . ( 30 sec) [ -6513.1442] [ 630] [depth= 8] . ( 30 sec) [ -6449.3087] [ 604] [depth= 6] . ( 31 sec) [ -6442.5555] [ 603] [depth= 1] . ( 31 sec) [ -6440.0104] [ 603] [depth= 2] . ( 32 sec) [ -6438.2208] [ 603] [depth= 2] . ( 32 sec) [ -6437.7817] [ 603] [depth= 2] . ( 32 sec) [ -6397.7856] [ 609] [depth= 2] . ( 32 sec) [ -6272.2328] [ 582] [depth= 1] . ( 33 sec) [ -6266.5645] [ 582] [depth= 6] . ( 33 sec) [ -6254.5755] [ 581] [depth= 10] . ( 33 sec) [ -6254.2462] [ 581] [depth= 1] . ( 33 sec) [ -6253.2934] [ 581] [depth= 3] . ( 33 sec) [ -6252.4951] [ 581] [depth= 1] . ( 35 sec) [ -6142.2500] [Branch lengths ] . ( 37 sec) [ -6137.4412] [GTR parameters ] . ( 37 sec) [ -6135.8437] [Alpha ][ 0.632080] . ( 38 sec) [ -6134.5369] [ 580] [depth= 1] . ( 38 sec) [ -6121.9144] [ 576] [depth= 2] . ( 38 sec) [ -6111.6699] [ 568] [depth= 9] . ( 39 sec) [ -6111.5815] [ 568] [depth= 1] . ( 40 sec) [ -6111.3247] [ 568] [depth= 4] . ( 40 sec) [ -6084.5190] [ 562] [depth= 1] . ( 40 sec) [ -6067.2843] [ 559] [depth= 3] . ( 41 sec) [ -6066.5571] [ 559] [depth= 1] . ( 42 sec) [ -6063.4270] [ 558] [depth= 2] . ( 43 sec) [ -6053.2922] [ 556] [depth= 4] . ( 43 sec) [ -6031.7736] [ 554] [depth= 5] . ( 44 sec) [ -6024.5456] [ 550] [depth= 8] . ( 45 sec) [ -6009.7343] [ 547] [depth= 3] . ( 45 sec) [ -6006.7781] [ 546] [depth= 2] . ( 45 sec) [ -6006.2380] [ 546] [depth= 1] . ( 46 sec) [ -5998.8306] [ 544] [depth= 1] . ( 46 sec) [ -5994.5799] [ 542] [depth= 2] . ( 46 sec) [ -5994.5629] [ 542] [depth= 1] . ( 46 sec) [ -5994.4470] [ 542] [depth= 1] . ( 47 sec) [ -5991.8847] [ 542] [depth= 5] . ( 47 sec) [ -5991.8638] [ 542] [depth= 1] . ( 47 sec) [ -5986.5693] [ 541] [depth= 3] . ( 47 sec) [ -5981.0148] [ 540] [depth= 1] . ( 48 sec) [ -5980.1163] [ 540] [depth= 1] . ( 48 sec) [ -5973.7348] [ 540] [depth= 3] . ( 48 sec) [ -5973.6758] [ 540] [depth= 2] . ( 49 sec) [ -5926.2791] [ 531] [depth= 10] . ( 49 sec) [ -5926.2198] [ 531] [depth= 1] . ( 50 sec) [ -5926.2051] [ 531] [depth= 1] . ( 50 sec) [ -5926.0907] [ 531] [depth= 1] . ( 51 sec) [ -5926.0634] [ 531] [depth= 1] . ( 52 sec) [ -5925.9627] [ 531] [depth= 1] . ( 53 sec) [ -5925.8214] [ 531] [depth= 2] . ( 54 sec) [ -5913.1268] [ 527] [depth= 1] . ( 55 sec) [ -5913.1027] [ 527] [depth= 1] . ( 56 sec) [ -5913.0848] [ 527] [depth= 1] . ( 57 sec) [ -5910.5943] [ 527] [depth= 2] . ( 57 sec) [ -5896.9785] [ 524] [depth= 3] . ( 58 sec) [ -5896.8190] [ 524] [depth= 1] . ( 58 sec) [ -5896.0418] [ 524] [depth= 1] . ( 58 sec) [ -5869.3043] [ 517] [depth= 3] . ( 59 sec) [ -5869.2897] [ 517] [depth= 1] . ( 60 sec) [ -5855.8426] [ 513] [depth= 3] . ( 62 sec) [ -5855.8143] [ 513] [depth= 1] . ( 62 sec) [ -5855.7962] [ 513] [depth= 1] . ( 63 sec) [ -5854.5976] [ 512] [depth= 5] . ( 63 sec) [ -5854.5528] [ 512] [depth= 1] . ( 64 sec) [ -5851.0107] [ 511] [depth= 1] . ( 64 sec) [ -5850.8721] [ 511] [depth= 1] . ( 66 sec) [ -5850.7293] [ 511] [depth= 1] . ( 66 sec) [ -5850.7162] [ 511] [depth= 3] . ( 66 sec) [ -5850.5685] [ 511] [depth= 1] . ( 70 sec) [ -5850.1137] [ 511] [depth= 1] . ( 70 sec) [ -5849.8279] [ 511] [depth= 1] . ( 71 sec) [ -5849.7829] [ 511] [depth= 1] . ( 74 sec) [ -5849.7346] [ 511] [depth= 1] . ( 74 sec) [ -5848.5624] [ 511] [depth= 1] . ( 75 sec) [ -5848.1959] [ 511] [depth= 2] . ( 75 sec) [ -5848.1452] [ 511] [depth= 2] . ( 76 sec) [ -5843.4073] [ 510] [depth= 1] . ( 79 sec) [ -5843.3039] [ 510] [depth= 1] . ( 80 sec) [ -5838.6292] [ 509] [depth= 2] . ( 81 sec) [ -5837.9690] [ 509] [depth= 2] . ( 81 sec) [ -5837.9551] [ 509] [depth= 2] . ( 82 sec) [ -5837.7025] [ 509] [depth= 1] . ( 84 sec) [ -5837.6427] [ 509] [depth= 1] . ( 84 sec) [ -5836.8282] [ 509] [depth= 1] . ( 87 sec) [ -5836.7889] [ 509] [depth= 1] . ( 88 sec) [ -5836.7165] [ 509] [depth= 1] . ( 90 sec) [ -5824.3939] [Branch lengths ] . ( 91 sec) [ -5823.7398] [GTR parameters ] . ( 91 sec) [ -5817.9422] [Alpha ][ 1.171286] . ( 93 sec) [ -5817.8501] [ 509] [depth= 1] . ( 97 sec) [ -5817.6352] [ 509] [depth= 1] . ( 100 sec) [ -5815.6486] [ 508] [depth= 3] . ( 103 sec) [ -5815.6085] [ 508] [depth= 1] . ( 108 sec) [ -5814.2152] [ 508] [depth= 1] . ( 119 sec) [ -5814.0948] [ 508] [depth= 1] . ( 120 sec) [ -5814.0793] [ 508] [depth= 1] . ( 128 sec) [ -5813.9170] [ 508] [depth= 1] . ( 136 sec) [ -5813.8935] [ 508] [depth= 1] . ( 138 sec) [ -5813.8800] [ 508] [depth= 1] . ( 140 sec) [ -5813.4238] [ 508] [depth= 2] . ( 146 sec) [ -5813.4109] [ 508] [depth= 1] . ( 147 sec) [ -5813.3519] [ 508] [depth= 2] . ( 156 sec) [ -5812.3321] [Branch lengths ] . ( 157 sec) [ -5812.3191] [GTR parameters ] . ( 157 sec) [ -5812.3098] [Alpha ][ 1.205806] . ( 162 sec) [ -5811.7553] [ 508] [depth= 2] . ( 187 sec) [ -5811.7250] [ 508] [depth= 1] . ( 193 sec) [ -5811.6625] [ 508] [depth= 1] . ( 204 sec) [ -5809.7085] [ 507] [depth= 1] . ( 206 sec) [ -5808.6899] [ 507] [depth= 1] . ( 224 sec) [ -5807.9900] [Branch lengths ] . ( 225 sec) [ -5807.9460] [GTR parameters ] . ( 225 sec) [ -5807.9416] [Alpha ][ 1.230085] . ( 296 sec) [ -5807.9377] [Branch lengths ] . ( 402 sec) [ -5807.9370] [Branch lengths ] . ( 402 sec) [ -5807.9370] [Topology ] . ( 404 sec) [ -5807.9369] [Topology ] . ( 405 sec) [ -5807.9369] [GTR parameters ] . ( 405 sec) [ -5807.9369] [Alpha ][ 1.230085] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5807.936902. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -15516.1326] [GTR parameters ] . ( 3 sec) [ -15236.1147] [Alpha ][ 0.500960] . ( 3 sec) [ -15171.3528] [ 1802] [depth= 14] . ( 3 sec) [ -15147.9801] [ 1798] [depth= 14] . ( 4 sec) [ -15092.5046] [ 1796] [depth= 2] . ( 4 sec) [ -15046.0046] [ 1796] [depth= 3] . ( 4 sec) [ -15024.6290] [ 1794] [depth= 1] . ( 4 sec) [ -14949.6718] [ 1794] [depth= 2] . ( 4 sec) [ -14935.2931] [ 1792] [depth= 4] . ( 4 sec) [ -14845.3583] [ 1791] [depth= 6] . ( 4 sec) [ -14843.2887] [ 1791] [depth= 1] . ( 4 sec) [ -14829.7478] [ 1791] [depth= 1] . ( 4 sec) [ -14805.0654] [ 1789] [depth= 3] . ( 5 sec) [ -14700.6238] [ 1789] [depth= 4] . ( 5 sec) [ -14493.7855] [ 1764] [depth= 6] . ( 5 sec) [ -14462.9254] [ 1764] [depth= 1] . ( 5 sec) [ -14256.7449] [ 1725] [depth= 14] . ( 5 sec) [ -14182.3922] [ 1715] [depth= 16] . ( 5 sec) [ -14142.5713] [ 1706] [depth= 4] . ( 5 sec) [ -13986.0808] [ 1669] [depth= 11] . ( 5 sec) [ -13965.9516] [ 1669] [depth= 1] . ( 6 sec) [ -13940.2951] [ 1666] [depth= 11] . ( 6 sec) [ -13937.9748] [ 1665] [depth= 3] . ( 6 sec) [ -13719.1827] [ 1625] [depth= 16] . ( 6 sec) [ -13691.6527] [ 1620] [depth= 13] . ( 6 sec) [ -13676.4126] [ 1619] [depth= 3] . ( 6 sec) [ -13675.6148] [ 1619] [depth= 1] . ( 6 sec) [ -13552.4550] [ 1602] [depth= 12] . ( 6 sec) [ -13440.3319] [ 1597] [depth= 10] . ( 6 sec) [ -13436.3989] [ 1597] [depth= 1] . ( 7 sec) [ -13372.6679] [ 1598] [depth= 1] . ( 7 sec) [ -13334.4480] [ 1596] [depth= 6] . ( 7 sec) [ -13083.7093] [ 1552] [depth= 3] . ( 7 sec) [ -13031.2792] [ 1548] [depth= 14] . ( 7 sec) [ -12958.9377] [ 1545] [depth= 5] . ( 7 sec) [ -12880.3577] [ 1530] [depth= 18] . ( 7 sec) [ -12637.0916] [ 1495] [depth= 5] . ( 7 sec) [ -12522.9568] [ 1488] [depth= 8] . ( 8 sec) [ -12384.9497] [ 1456] [depth= 5] . ( 8 sec) [ -12269.0462] [ 1452] [depth= 14] . ( 8 sec) [ -12229.7168] [ 1435] [depth= 9] . ( 8 sec) [ -12181.8388] [ 1428] [depth= 11] . ( 8 sec) [ -12110.5512] [ 1425] [depth= 7] . ( 8 sec) [ -12066.6035] [ 1424] [depth= 1] . ( 8 sec) [ -12058.0812] [ 1424] [depth= 1] . ( 8 sec) [ -11915.1944] [ 1385] [depth= 9] . ( 8 sec) [ -11901.7537] [ 1381] [depth= 13] . ( 9 sec) [ -11898.3877] [ 1381] [depth= 1] . ( 9 sec) [ -11837.0435] [ 1373] [depth= 12] . ( 9 sec) [ -11776.0590] [ 1358] [depth= 7] . ( 9 sec) [ -11769.1296] [ 1358] [depth= 2] . ( 9 sec) [ -11757.2210] [ 1358] [depth= 5] . ( 9 sec) [ -11752.6708] [ 1358] [depth= 1] . ( 9 sec) [ -11701.7872] [ 1356] [depth= 10] . ( 9 sec) [ -11698.2946] [ 1356] [depth= 1] . ( 9 sec) [ -11569.0613] [ 1356] [depth= 1] . ( 10 sec) [ -11562.1486] [ 1356] [depth= 1] . ( 10 sec) [ -11548.7584] [ 1355] [depth= 12] . ( 10 sec) [ -11490.2953] [ 1356] [depth= 1] . ( 10 sec) [ -11382.2370] [ 1327] [depth= 11] . ( 10 sec) [ -11363.2438] [ 1328] [depth= 1] . ( 10 sec) [ -11312.9944] [ 1314] [depth= 14] . ( 10 sec) [ -11193.5468] [ 1306] [depth= 11] . ( 10 sec) [ -11135.3317] [ 1298] [depth= 13] . ( 10 sec) [ -11099.0597] [ 1290] [depth= 11] . ( 11 sec) [ -10949.1793] [ 1286] [depth= 13] . ( 11 sec) [ -10896.0129] [ 1279] [depth= 18] . ( 11 sec) [ -10878.2683] [ 1280] [depth= 15] . ( 11 sec) [ -10866.0806] [ 1279] [depth= 4] . ( 11 sec) [ -10798.6936] [ 1280] [depth= 3] . ( 11 sec) [ -10708.3657] [ 1277] [depth= 17] . ( 11 sec) [ -10537.3073] [ 1248] [depth= 15] . ( 11 sec) [ -10467.0393] [ 1247] [depth= 12] . ( 12 sec) [ -10441.8371] [ 1247] [depth= 4] . ( 12 sec) [ -10397.7237] [ 1244] [depth= 15] . ( 12 sec) [ -10306.1142] [ 1212] [depth= 8] . ( 12 sec) [ -10187.1593] [ 1201] [depth= 2] . ( 12 sec) [ -10170.2794] [ 1198] [depth= 3] . ( 12 sec) [ -10148.5081] [ 1198] [depth= 1] . ( 12 sec) [ -10071.6044] [ 1188] [depth= 16] . ( 12 sec) [ -10039.7146] [ 1187] [depth= 14] . ( 13 sec) [ -10010.0986] [ 1182] [depth= 7] . ( 13 sec) [ -10006.8748] [ 1182] [depth= 1] . ( 13 sec) [ -9899.9673] [ 1167] [depth= 11] . ( 13 sec) [ -9874.5148] [ 1163] [depth= 1] . ( 13 sec) [ -9738.6664] [ 1158] [depth= 13] . ( 13 sec) [ -9735.5342] [ 1158] [depth= 1] . ( 13 sec) [ -9734.3687] [ 1158] [depth= 1] . ( 13 sec) [ -9580.4807] [ 1123] [depth= 13] . ( 13 sec) [ -9576.0691] [ 1122] [depth= 2] . ( 14 sec) [ -9557.2475] [ 1121] [depth= 11] . ( 14 sec) [ -9544.3006] [ 1118] [depth= 7] . ( 15 sec) [ -9542.2906] [ 1120] [depth= 2] . ( 15 sec) [ -9325.8792] [ 1110] [depth= 11] . ( 15 sec) [ -9324.1709] [ 1110] [depth= 6] . ( 15 sec) [ -9206.0462] [ 1111] [depth= 2] . ( 15 sec) [ -9009.7308] [ 1075] [depth= 17] . ( 15 sec) [ -8984.2246] [ 1070] [depth= 10] . ( 16 sec) [ -8964.5564] [ 1069] [depth= 1] . ( 16 sec) [ -8961.3481] [ 1072] [depth= 1] . ( 16 sec) [ -8827.4730] [ 1039] [depth= 9] . ( 16 sec) [ -8801.6412] [ 1031] [depth= 8] . ( 16 sec) [ -8792.0025] [ 1033] [depth= 1] . ( 16 sec) [ -8788.5170] [ 1030] [depth= 13] . ( 16 sec) [ -8658.5087] [ 993] [depth= 10] . ( 16 sec) [ -8636.3311] [ 990] [depth= 1] . ( 17 sec) [ -8629.0778] [ 990] [depth= 5] . ( 17 sec) [ -8627.9613] [ 991] [depth= 8] . ( 17 sec) [ -8624.5174] [ 990] [depth= 1] . ( 18 sec) [ -8585.2055] [ 960] [depth= 9] . ( 18 sec) [ -8577.1353] [ 960] [depth= 1] . ( 18 sec) [ -8555.5226] [ 959] [depth= 1] . ( 18 sec) [ -8552.5384] [ 959] [depth= 2] . ( 18 sec) [ -8410.9334] [ 911] [depth= 8] . ( 18 sec) [ -8360.6929] [ 900] [depth= 12] . ( 18 sec) [ -8360.1660] [ 900] [depth= 1] . ( 19 sec) [ -8359.7503] [ 900] [depth= 1] . ( 19 sec) [ -8359.4561] [ 900] [depth= 1] . ( 19 sec) [ -8205.4651] [ 858] [depth= 11] . ( 19 sec) [ -8166.4583] [ 848] [depth= 6] . ( 20 sec) [ -8147.8228] [ 845] [depth= 2] . ( 20 sec) [ -8127.8922] [ 839] [depth= 1] . ( 20 sec) [ -8123.1517] [ 839] [depth= 1] . ( 20 sec) [ -8005.4465] [ 819] [depth= 4] . ( 20 sec) [ -7984.5658] [ 818] [depth= 6] . ( 20 sec) [ -7976.2746] [ 815] [depth= 15] . ( 21 sec) [ -7879.2756] [ 804] [depth= 5] . ( 21 sec) [ -7877.8837] [ 806] [depth= 2] . ( 21 sec) [ -7863.3656] [ 807] [depth= 2] . ( 21 sec) [ -7862.1195] [ 807] [depth= 1] . ( 21 sec) [ -7837.7654] [ 804] [depth= 11] . ( 22 sec) [ -7799.7655] [ 806] [depth= 13] . ( 22 sec) [ -7789.5700] [ 805] [depth= 10] . ( 22 sec) [ -7788.7217] [ 805] [depth= 1] . ( 22 sec) [ -7744.0197] [ 798] [depth= 3] . ( 22 sec) [ -7421.2425] [ 792] [depth= 6] . ( 22 sec) [ -7261.6853] [ 749] [depth= 5] . ( 23 sec) [ -7177.5332] [ 739] [depth= 8] . ( 23 sec) [ -7170.2065] [ 739] [depth= 2] . ( 23 sec) [ -7163.6565] [ 737] [depth= 14] . ( 23 sec) [ -7158.5450] [ 738] [depth= 1] . ( 23 sec) [ -7151.4068] [ 737] [depth= 1] . ( 23 sec) [ -7144.9513] [ 736] [depth= 12] . ( 24 sec) [ -7110.5284] [ 733] [depth= 13] . ( 24 sec) [ -7109.2349] [ 733] [depth= 1] . ( 24 sec) [ -7102.6284] [ 730] [depth= 1] . ( 24 sec) [ -7040.3554] [ 724] [depth= 9] . ( 24 sec) [ -6975.6631] [ 714] [depth= 7] . ( 24 sec) [ -6973.2999] [ 716] [depth= 5] . ( 25 sec) [ -6967.7097] [ 719] [depth= 1] . ( 25 sec) [ -6945.1205] [ 715] [depth= 1] . ( 25 sec) [ -6917.6885] [ 708] [depth= 6] . ( 25 sec) [ -6796.6311] [ 678] [depth= 12] . ( 25 sec) [ -6794.8835] [ 674] [depth= 8] . ( 25 sec) [ -6794.3193] [ 673] [depth= 1] . ( 26 sec) [ -6758.4388] [ 664] [depth= 3] . ( 26 sec) [ -6730.2891] [ 662] [depth= 3] . ( 26 sec) [ -6728.4047] [ 661] [depth= 1] . ( 26 sec) [ -6722.4775] [ 660] [depth= 4] . ( 26 sec) [ -6689.7109] [ 651] [depth= 5] . ( 27 sec) [ -6674.9613] [ 651] [depth= 5] . ( 27 sec) [ -6654.5804] [ 650] [depth= 3] . ( 27 sec) [ -6623.4404] [ 650] [depth= 4] . ( 27 sec) [ -6621.2566] [ 650] [depth= 1] . ( 27 sec) [ -6618.4045] [ 649] [depth= 1] . ( 27 sec) [ -6607.3232] [ 649] [depth= 10] . ( 27 sec) [ -6606.2355] [ 649] [depth= 1] . ( 28 sec) [ -6597.3675] [ 649] [depth= 2] . ( 28 sec) [ -6597.1967] [ 644] [depth= 2] . ( 28 sec) [ -6581.0852] [ 644] [depth= 1] . ( 28 sec) [ -6574.5194] [ 644] [depth= 1] . ( 28 sec) [ -6573.7146] [ 643] [depth= 2] . ( 29 sec) [ -6528.2201] [ 643] [depth= 4] . ( 29 sec) [ -6523.6107] [ 642] [depth= 1] . ( 29 sec) [ -6522.8952] [ 642] [depth= 3] . ( 29 sec) [ -6520.9619] [ 642] [depth= 6] . ( 30 sec) [ -6430.4165] [ 622] [depth= 4] . ( 30 sec) [ -6411.0777] [ 618] [depth= 2] . ( 31 sec) [ -6404.4253] [ 617] [depth= 2] . ( 32 sec) [ -6399.5774] [ 616] [depth= 2] . ( 32 sec) [ -6396.3371] [ 615] [depth= 1] . ( 32 sec) [ -6387.7885] [ 613] [depth= 1] . ( 32 sec) [ -6386.2849] [ 612] [depth= 2] . ( 32 sec) [ -6385.8736] [ 612] [depth= 1] . ( 32 sec) [ -6381.0626] [ 612] [depth= 1] . ( 33 sec) [ -6346.7418] [ 605] [depth= 2] . ( 33 sec) [ -6346.2059] [ 605] [depth= 1] . ( 34 sec) [ -6345.7640] [ 605] [depth= 2] . ( 34 sec) [ -6345.4502] [ 605] [depth= 1] . ( 34 sec) [ -6327.8554] [ 601] [depth= 4] . ( 35 sec) [ -6326.4271] [ 601] [depth= 2] . ( 35 sec) [ -6318.6656] [ 599] [depth= 3] . ( 35 sec) [ -6310.0122] [ 598] [depth= 3] . ( 36 sec) [ -6220.5843] [Branch lengths ] . ( 38 sec) [ -6215.2696] [GTR parameters ] . ( 38 sec) [ -6214.7841] [Alpha ][ 0.567472] . ( 44 sec) [ -6211.3857] [ 597] [depth= 3] . ( 45 sec) [ -6210.8607] [ 597] [depth= 4] . ( 45 sec) [ -6207.3434] [ 596] [depth= 3] . ( 45 sec) [ -6207.0160] [ 595] [depth= 1] . ( 45 sec) [ -6196.0236] [ 593] [depth= 2] . ( 46 sec) [ -6183.5006] [ 591] [depth= 4] . ( 46 sec) [ -6124.8956] [ 571] [depth= 11] . ( 46 sec) [ -6120.0883] [ 571] [depth= 1] . ( 47 sec) [ -6119.9687] [ 571] [depth= 2] . ( 48 sec) [ -6118.5903] [ 570] [depth= 1] . ( 48 sec) [ -6117.9297] [ 570] [depth= 3] . ( 49 sec) [ -6117.3442] [ 571] [depth= 1] . ( 50 sec) [ -6111.8489] [ 571] [depth= 3] . ( 50 sec) [ -6101.6730] [ 569] [depth= 2] . ( 51 sec) [ -6098.5924] [ 566] [depth= 3] . ( 51 sec) [ -6096.4996] [ 565] [depth= 1] . ( 52 sec) [ -6079.6496] [ 559] [depth= 1] . ( 52 sec) [ -6079.1030] [ 559] [depth= 2] . ( 52 sec) [ -6076.6736] [ 558] [depth= 2] . ( 52 sec) [ -5995.6058] [ 539] [depth= 3] . ( 53 sec) [ -5994.0398] [ 542] [depth= 1] . ( 53 sec) [ -5993.6650] [ 542] [depth= 2] . ( 54 sec) [ -5986.5642] [ 540] [depth= 2] . ( 54 sec) [ -5975.5276] [ 542] [depth= 1] . ( 57 sec) [ -5971.4873] [ 539] [depth= 11] . ( 57 sec) [ -5971.2661] [ 539] [depth= 2] . ( 57 sec) [ -5964.7181] [ 538] [depth= 2] . ( 57 sec) [ -5964.3121] [ 538] [depth= 1] . ( 58 sec) [ -5961.1474] [ 538] [depth= 1] . ( 58 sec) [ -5961.0316] [ 538] [depth= 1] . ( 59 sec) [ -5954.7342] [ 537] [depth= 3] . ( 59 sec) [ -5953.7993] [ 536] [depth= 2] . ( 59 sec) [ -5952.7485] [ 535] [depth= 3] . ( 59 sec) [ -5948.2078] [ 534] [depth= 1] . ( 60 sec) [ -5942.6370] [ 533] [depth= 2] . ( 62 sec) [ -5942.5800] [ 533] [depth= 1] . ( 62 sec) [ -5941.3915] [ 533] [depth= 1] . ( 62 sec) [ -5941.3738] [ 533] [depth= 1] . ( 63 sec) [ -5940.1010] [ 533] [depth= 2] . ( 63 sec) [ -5935.7788] [ 532] [depth= 4] . ( 64 sec) [ -5935.5053] [ 532] [depth= 1] . ( 64 sec) [ -5931.6916] [ 531] [depth= 2] . ( 65 sec) [ -5931.6425] [ 531] [depth= 1] . ( 65 sec) [ -5898.6401] [ 525] [depth= 2] . ( 65 sec) [ -5898.5781] [ 525] [depth= 1] . ( 66 sec) [ -5888.5528] [ 523] [depth= 1] . ( 66 sec) [ -5887.9339] [ 523] [depth= 1] . ( 67 sec) [ -5887.8671] [ 523] [depth= 2] . ( 68 sec) [ -5886.4699] [ 523] [depth= 1] . ( 68 sec) [ -5886.0288] [ 523] [depth= 1] . ( 68 sec) [ -5885.6202] [ 523] [depth= 1] . ( 68 sec) [ -5885.5220] [ 523] [depth= 1] . ( 69 sec) [ -5885.4347] [ 523] [depth= 1] . ( 70 sec) [ -5884.8176] [ 523] [depth= 3] . ( 71 sec) [ -5884.7173] [ 523] [depth= 2] . ( 74 sec) [ -5877.3167] [ 520] [depth= 2] . ( 74 sec) [ -5863.6300] [ 515] [depth= 2] . ( 74 sec) [ -5856.2651] [ 512] [depth= 1] . ( 74 sec) [ -5856.1409] [ 512] [depth= 1] . ( 76 sec) [ -5850.7330] [ 512] [depth= 1] . ( 77 sec) [ -5845.3194] [ 511] [depth= 1] . ( 78 sec) [ -5845.2848] [ 511] [depth= 1] . ( 79 sec) [ -5845.1068] [ 511] [depth= 2] . ( 80 sec) [ -5845.0297] [ 511] [depth= 1] . ( 81 sec) [ -5844.8768] [ 511] [depth= 1] . ( 82 sec) [ -5844.8040] [ 511] [depth= 1] . ( 87 sec) [ -5840.7724] [ 509] [depth= 1] . ( 90 sec) [ -5840.7036] [ 509] [depth= 1] . ( 91 sec) [ -5824.6603] [Branch lengths ] . ( 92 sec) [ -5824.5214] [GTR parameters ] . ( 93 sec) [ -5816.1438] [Alpha ][ 1.133097] . ( 95 sec) [ -5814.0253] [ 508] [depth= 1] . ( 99 sec) [ -5811.6769] [ 507] [depth= 4] . ( 100 sec) [ -5810.9627] [ 507] [depth= 1] . ( 103 sec) [ -5810.8775] [ 507] [depth= 1] . ( 124 sec) [ -5810.7447] [ 507] [depth= 1] . ( 133 sec) [ -5810.2340] [ 507] [depth= 1] . ( 148 sec) [ -5809.4446] [ 507] [depth= 1] . ( 150 sec) [ -5809.4207] [ 507] [depth= 1] . ( 160 sec) [ -5808.1573] [Branch lengths ] . ( 161 sec) [ -5808.0552] [GTR parameters ] . ( 162 sec) [ -5807.9819] [Alpha ][ 1.230588] . ( 235 sec) [ -5807.9397] [Branch lengths ] . ( 345 sec) [ -5807.9375] [Branch lengths ] . ( 345 sec) [ -5807.9375] [Topology ] . ( 348 sec) [ -5807.9373] [Topology ] . ( 348 sec) [ -5807.9373] [GTR parameters ] . ( 348 sec) [ -5807.9373] [Alpha ][ 1.230588] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5807.937281. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -16023.2689] [GTR parameters ] . ( 3 sec) [ -15726.0494] [Alpha ][ 0.500960] . ( 3 sec) [ -15679.4186] [ 1930] [depth= 6] . ( 3 sec) [ -15610.5201] [ 1923] [depth= 12] . ( 4 sec) [ -15554.1605] [ 1922] [depth= 5] . ( 4 sec) [ -15522.5610] [ 1919] [depth= 10] . ( 4 sec) [ -15432.7259] [ 1916] [depth= 6] . ( 4 sec) [ -15378.6591] [ 1916] [depth= 1] . ( 4 sec) [ -15096.7411] [ 1915] [depth= 3] . ( 4 sec) [ -15094.7552] [ 1915] [depth= 1] . ( 4 sec) [ -14975.4625] [ 1915] [depth= 6] . ( 5 sec) [ -14863.9223] [ 1915] [depth= 9] . ( 5 sec) [ -14775.6287] [ 1912] [depth= 9] . ( 5 sec) [ -14743.6257] [ 1912] [depth= 2] . ( 5 sec) [ -14703.8100] [ 1899] [depth= 7] . ( 5 sec) [ -14674.3911] [ 1899] [depth= 4] . ( 5 sec) [ -14537.1960] [ 1899] [depth= 10] . ( 5 sec) [ -14470.2640] [ 1884] [depth= 12] . ( 5 sec) [ -14347.9929] [ 1870] [depth= 19] . ( 6 sec) [ -14257.4483] [ 1860] [depth= 17] . ( 6 sec) [ -13964.8780] [ 1828] [depth= 16] . ( 6 sec) [ -13908.9231] [ 1810] [depth= 8] . ( 6 sec) [ -13744.7087] [ 1793] [depth= 17] . ( 6 sec) [ -13507.7052] [ 1760] [depth= 3] . ( 6 sec) [ -13491.2470] [ 1758] [depth= 10] . ( 6 sec) [ -13400.0674] [ 1748] [depth= 8] . ( 7 sec) [ -13333.7481] [ 1743] [depth= 4] . ( 7 sec) [ -13309.8842] [ 1742] [depth= 1] . ( 7 sec) [ -13258.8894] [ 1740] [depth= 6] . ( 7 sec) [ -13210.9192] [ 1733] [depth= 19] . ( 7 sec) [ -13083.5827] [ 1724] [depth= 5] . ( 7 sec) [ -13006.7518] [ 1719] [depth= 1] . ( 7 sec) [ -12873.5594] [ 1714] [depth= 4] . ( 7 sec) [ -12847.8011] [ 1712] [depth= 14] . ( 8 sec) [ -12714.6083] [ 1676] [depth= 18] . ( 8 sec) [ -12687.8254] [ 1654] [depth= 4] . ( 8 sec) [ -12651.7369] [ 1654] [depth= 2] . ( 8 sec) [ -12528.1045] [ 1627] [depth= 14] . ( 8 sec) [ -12427.1480] [ 1624] [depth= 1] . ( 8 sec) [ -12388.9614] [ 1624] [depth= 2] . ( 8 sec) [ -12317.5608] [ 1594] [depth= 2] . ( 8 sec) [ -12306.3852] [ 1594] [depth= 1] . ( 8 sec) [ -12292.0241] [ 1593] [depth= 4] . ( 8 sec) [ -12278.6941] [ 1593] [depth= 2] . ( 9 sec) [ -12159.6415] [ 1561] [depth= 2] . ( 9 sec) [ -11999.7699] [ 1560] [depth= 7] . ( 9 sec) [ -11966.2938] [ 1559] [depth= 2] . ( 9 sec) [ -11879.6088] [ 1560] [depth= 19] . ( 9 sec) [ -11792.7160] [ 1546] [depth= 12] . ( 9 sec) [ -11690.8620] [ 1514] [depth= 12] . ( 9 sec) [ -11624.5034] [ 1504] [depth= 13] . ( 10 sec) [ -11613.1842] [ 1504] [depth= 11] . ( 10 sec) [ -11401.2663] [ 1501] [depth= 26] . ( 10 sec) [ -11334.0879] [ 1497] [depth= 14] . ( 10 sec) [ -11208.7718] [ 1463] [depth= 1] . ( 10 sec) [ -11203.2540] [ 1462] [depth= 23] . ( 10 sec) [ -11168.5836] [ 1448] [depth= 8] . ( 10 sec) [ -11094.9538] [ 1413] [depth= 21] . ( 10 sec) [ -10986.0171] [ 1377] [depth= 17] . ( 10 sec) [ -10823.3556] [ 1370] [depth= 4] . ( 11 sec) [ -10822.7211] [ 1370] [depth= 1] . ( 11 sec) [ -10795.7428] [ 1366] [depth= 2] . ( 11 sec) [ -10792.9925] [ 1366] [depth= 1] . ( 11 sec) [ -10604.7782] [ 1364] [depth= 8] . ( 11 sec) [ -10395.0839] [ 1365] [depth= 1] . ( 11 sec) [ -10227.3332] [ 1354] [depth= 3] . ( 11 sec) [ -10113.3760] [ 1315] [depth= 1] . ( 11 sec) [ -10045.7407] [ 1307] [depth= 9] . ( 12 sec) [ -10024.4034] [ 1305] [depth= 9] . ( 12 sec) [ -9919.5171] [ 1287] [depth= 11] . ( 12 sec) [ -9705.7284] [ 1245] [depth= 9] . ( 12 sec) [ -9647.3128] [ 1232] [depth= 18] . ( 12 sec) [ -9643.2647] [ 1232] [depth= 19] . ( 12 sec) [ -9638.1172] [ 1231] [depth= 18] . ( 13 sec) [ -9581.6673] [ 1223] [depth= 15] . ( 13 sec) [ -9522.2376] [ 1212] [depth= 8] . ( 13 sec) [ -9501.5033] [ 1208] [depth= 3] . ( 13 sec) [ -9499.7846] [ 1210] [depth= 1] . ( 13 sec) [ -9356.1935] [ 1174] [depth= 7] . ( 13 sec) [ -9297.2715] [ 1168] [depth= 21] . ( 13 sec) [ -9257.6109] [ 1167] [depth= 13] . ( 14 sec) [ -9206.0133] [ 1160] [depth= 4] . ( 14 sec) [ -9203.1692] [ 1160] [depth= 1] . ( 14 sec) [ -9200.2872] [ 1159] [depth= 1] . ( 14 sec) [ -9191.5160] [ 1158] [depth= 2] . ( 14 sec) [ -9145.6121] [ 1147] [depth= 8] . ( 14 sec) [ -9125.6369] [ 1147] [depth= 1] . ( 14 sec) [ -9116.9789] [ 1148] [depth= 1] . ( 14 sec) [ -9097.6603] [ 1145] [depth= 18] . ( 14 sec) [ -9091.9802] [ 1145] [depth= 4] . ( 15 sec) [ -9022.5204] [ 1142] [depth= 5] . ( 15 sec) [ -8895.6087] [ 1107] [depth= 4] . ( 15 sec) [ -8836.1948] [ 1098] [depth= 13] . ( 15 sec) [ -8833.4643] [ 1100] [depth= 8] . ( 15 sec) [ -8828.1069] [ 1099] [depth= 1] . ( 15 sec) [ -8765.4307] [ 1097] [depth= 7] . ( 15 sec) [ -8717.9188] [ 1092] [depth= 4] . ( 16 sec) [ -8698.5396] [ 1092] [depth= 1] . ( 16 sec) [ -8698.4305] [ 1092] [depth= 1] . ( 16 sec) [ -8670.9007] [ 1089] [depth= 5] . ( 16 sec) [ -8652.0033] [ 1088] [depth= 18] . ( 16 sec) [ -8644.0918] [ 1087] [depth= 1] . ( 16 sec) [ -8628.1739] [ 1083] [depth= 18] . ( 16 sec) [ -8615.1251] [ 1081] [depth= 3] . ( 17 sec) [ -8613.8956] [ 1083] [depth= 1] . ( 17 sec) [ -8582.4552] [ 1078] [depth= 5] . ( 17 sec) [ -8581.9920] [ 1079] [depth= 19] . ( 17 sec) [ -8569.9349] [ 1080] [depth= 10] . ( 17 sec) [ -8551.7860] [ 1081] [depth= 10] . ( 17 sec) [ -8547.4658] [ 1077] [depth= 14] . ( 18 sec) [ -8445.5273] [ 1046] [depth= 12] . ( 18 sec) [ -8428.6286] [ 1042] [depth= 3] . ( 18 sec) [ -8334.0785] [ 1003] [depth= 16] . ( 18 sec) [ -8239.8228] [ 1004] [depth= 1] . ( 18 sec) [ -8225.5802] [ 1003] [depth= 1] . ( 18 sec) [ -8189.3452] [ 999] [depth= 23] . ( 18 sec) [ -8185.7521] [ 999] [depth= 1] . ( 18 sec) [ -8185.6221] [ 999] [depth= 1] . ( 19 sec) [ -8169.4889] [ 996] [depth= 1] . ( 19 sec) [ -8110.1010] [ 984] [depth= 14] . ( 19 sec) [ -7990.4440] [ 942] [depth= 22] . ( 19 sec) [ -7964.9466] [ 940] [depth= 15] . ( 20 sec) [ -7964.6415] [ 940] [depth= 1] . ( 20 sec) [ -7954.8583] [ 935] [depth= 4] . ( 20 sec) [ -7932.5323] [ 932] [depth= 12] . ( 20 sec) [ -7853.1323] [ 934] [depth= 4] . ( 20 sec) [ -7849.2193] [ 934] [depth= 3] . ( 21 sec) [ -7707.2837] [ 886] [depth= 14] . ( 21 sec) [ -7697.6464] [ 885] [depth= 1] . ( 21 sec) [ -7679.1225] [ 886] [depth= 1] . ( 21 sec) [ -7676.3935] [ 886] [depth= 1] . ( 21 sec) [ -7653.7911] [ 878] [depth= 8] . ( 21 sec) [ -7631.9232] [ 881] [depth= 5] . ( 21 sec) [ -7551.9370] [ 849] [depth= 1] . ( 22 sec) [ -7526.0514] [ 848] [depth= 5] . ( 22 sec) [ -7524.4828] [ 847] [depth= 2] . ( 22 sec) [ -7476.8847] [ 838] [depth= 6] . ( 22 sec) [ -7365.7257] [ 808] [depth= 11] . ( 22 sec) [ -7358.2608] [ 807] [depth= 3] . ( 23 sec) [ -7345.9161] [ 807] [depth= 5] . ( 23 sec) [ -7332.1756] [ 803] [depth= 9] . ( 23 sec) [ -7331.1925] [ 803] [depth= 5] . ( 23 sec) [ -7327.9753] [ 802] [depth= 1] . ( 24 sec) [ -7272.5820] [ 789] [depth= 5] . ( 24 sec) [ -7258.2437] [ 787] [depth= 8] . ( 24 sec) [ -7258.1210] [ 792] [depth= 1] . ( 24 sec) [ -7224.0961] [ 785] [depth= 5] . ( 24 sec) [ -7211.6692] [ 784] [depth= 4] . ( 24 sec) [ -7186.7048] [ 781] [depth= 4] . ( 24 sec) [ -7149.9504] [ 774] [depth= 7] . ( 24 sec) [ -7136.9105] [ 773] [depth= 13] . ( 25 sec) [ -7135.6923] [ 773] [depth= 1] . ( 25 sec) [ -7133.6558] [ 773] [depth= 2] . ( 25 sec) [ -7125.4706] [ 776] [depth= 2] . ( 25 sec) [ -7121.2564] [ 775] [depth= 4] . ( 25 sec) [ -7109.5856] [ 775] [depth= 2] . ( 26 sec) [ -7104.1434] [ 773] [depth= 6] . ( 26 sec) [ -7060.5105] [ 744] [depth= 4] . ( 27 sec) [ -7053.4959] [ 744] [depth= 1] . ( 27 sec) [ -6922.7890] [ 707] [depth= 11] . ( 27 sec) [ -6915.2835] [ 707] [depth= 2] . ( 27 sec) [ -6909.3501] [ 707] [depth= 1] . ( 27 sec) [ -6906.8302] [ 707] [depth= 6] . ( 27 sec) [ -6818.1352] [ 700] [depth= 6] . ( 28 sec) [ -6810.5005] [ 698] [depth= 1] . ( 28 sec) [ -6794.9996] [ 695] [depth= 1] . ( 29 sec) [ -6794.5670] [ 696] [depth= 1] . ( 29 sec) [ -6788.8631] [ 697] [depth= 3] . ( 29 sec) [ -6785.5416] [ 696] [depth= 3] . ( 31 sec) [ -6777.8590] [ 693] [depth= 7] . ( 31 sec) [ -6670.8415] [ 666] [depth= 2] . ( 31 sec) [ -6665.8940] [ 666] [depth= 10] . ( 31 sec) [ -6664.5796] [ 667] [depth= 1] . ( 31 sec) [ -6661.0969] [ 666] [depth= 1] . ( 32 sec) [ -6660.7827] [ 668] [depth= 1] . ( 32 sec) [ -6647.2352] [ 664] [depth= 5] . ( 32 sec) [ -6642.3503] [ 663] [depth= 3] . ( 32 sec) [ -6639.2077] [ 663] [depth= 1] . ( 32 sec) [ -6590.1381] [ 657] [depth= 8] . ( 32 sec) [ -6590.0594] [ 657] [depth= 2] . ( 33 sec) [ -6589.0592] [ 657] [depth= 1] . ( 33 sec) [ -6583.3129] [ 656] [depth= 1] . ( 33 sec) [ -6582.1876] [ 656] [depth= 1] . ( 34 sec) [ -6579.7789] [ 656] [depth= 1] . ( 34 sec) [ -6578.6904] [ 656] [depth= 1] . ( 34 sec) [ -6574.7535] [ 656] [depth= 1] . ( 34 sec) [ -6574.5461] [ 656] [depth= 1] . ( 34 sec) [ -6573.7582] [ 656] [depth= 2] . ( 34 sec) [ -6571.5631] [ 656] [depth= 1] . ( 36 sec) [ -6442.5323] [Branch lengths ] . ( 38 sec) [ -6439.2038] [GTR parameters ] . ( 38 sec) [ -6438.3211] [Alpha ][ 0.433685] . ( 38 sec) [ -6438.2881] [ 656] [depth= 1] . ( 39 sec) [ -6438.2750] [ 656] [depth= 1] . ( 39 sec) [ -6436.7546] [ 654] [depth= 1] . ( 41 sec) [ -6434.1960] [ 653] [depth= 1] . ( 42 sec) [ -6432.9693] [ 653] [depth= 5] . ( 43 sec) [ -6384.7432] [ 642] [depth= 10] . ( 43 sec) [ -6381.8675] [ 642] [depth= 1] . ( 45 sec) [ -6366.1618] [ 639] [depth= 3] . ( 45 sec) [ -6356.9458] [ 637] [depth= 1] . ( 45 sec) [ -6356.5087] [ 637] [depth= 1] . ( 45 sec) [ -6351.2606] [ 636] [depth= 2] . ( 48 sec) [ -6310.5401] [ 614] [depth= 11] . ( 48 sec) [ -6306.9396] [ 613] [depth= 1] . ( 48 sec) [ -6300.2447] [ 612] [depth= 6] . ( 48 sec) [ -6298.0878] [ 610] [depth= 1] . ( 48 sec) [ -6293.1203] [ 608] [depth= 9] . ( 49 sec) [ -6292.6371] [ 608] [depth= 3] . ( 49 sec) [ -6292.6233] [ 608] [depth= 2] . ( 51 sec) [ -6264.5397] [ 607] [depth= 8] . ( 53 sec) [ -6144.2182] [ 583] [depth= 11] . ( 53 sec) [ -6144.1960] [ 583] [depth= 2] . ( 53 sec) [ -6143.4852] [ 583] [depth= 1] . ( 53 sec) [ -6142.3415] [ 583] [depth= 1] . ( 53 sec) [ -6128.6706] [ 583] [depth= 5] . ( 53 sec) [ -6127.2906] [ 583] [depth= 1] . ( 55 sec) [ -6124.2120] [ 582] [depth= 1] . ( 55 sec) [ -6124.0568] [ 582] [depth= 1] . ( 56 sec) [ -6121.7875] [ 576] [depth= 3] . ( 57 sec) [ -6120.6295] [ 576] [depth= 1] . ( 57 sec) [ -6108.9885] [ 574] [depth= 2] . ( 57 sec) [ -6108.9343] [ 574] [depth= 1] . ( 57 sec) [ -6108.4984] [ 574] [depth= 1] . ( 58 sec) [ -6108.4714] [ 574] [depth= 1] . ( 58 sec) [ -6108.4481] [ 574] [depth= 2] . ( 58 sec) [ -5999.9682] [ 548] [depth= 1] . ( 58 sec) [ -5995.5159] [ 548] [depth= 5] . ( 58 sec) [ -5987.4311] [ 546] [depth= 2] . ( 59 sec) [ -5987.1764] [ 546] [depth= 2] . ( 60 sec) [ -5987.0294] [ 546] [depth= 1] . ( 60 sec) [ -5980.8185] [ 544] [depth= 2] . ( 60 sec) [ -5980.4556] [ 544] [depth= 1] . ( 60 sec) [ -5974.8066] [ 543] [depth= 1] . ( 60 sec) [ -5974.0561] [ 543] [depth= 1] . ( 61 sec) [ -5966.1108] [ 541] [depth= 8] . ( 61 sec) [ -5963.2038] [ 540] [depth= 1] . ( 61 sec) [ -5959.6523] [ 539] [depth= 2] . ( 61 sec) [ -5949.6200] [ 535] [depth= 1] . ( 61 sec) [ -5948.3348] [ 535] [depth= 4] . ( 62 sec) [ -5941.8747] [ 533] [depth= 1] . ( 62 sec) [ -5941.7717] [ 533] [depth= 1] . ( 64 sec) [ -5941.7284] [ 533] [depth= 2] . ( 64 sec) [ -5909.5499] [ 527] [depth= 3] . ( 65 sec) [ -5908.3773] [ 527] [depth= 1] . ( 67 sec) [ -5908.0758] [ 527] [depth= 1] . ( 69 sec) [ -5908.0548] [ 527] [depth= 1] . ( 69 sec) [ -5908.0423] [ 527] [depth= 1] . ( 70 sec) [ -5907.7496] [ 527] [depth= 1] . ( 70 sec) [ -5907.6839] [ 527] [depth= 3] . ( 71 sec) [ -5907.6297] [ 527] [depth= 1] . ( 71 sec) [ -5907.6183] [ 527] [depth= 1] . ( 71 sec) [ -5882.2909] [ 517] [depth= 4] . ( 72 sec) [ -5869.8638] [ 515] [depth= 7] . ( 72 sec) [ -5869.3830] [ 515] [depth= 1] . ( 72 sec) [ -5865.9130] [ 513] [depth= 1] . ( 73 sec) [ -5862.7540] [ 512] [depth= 1] . ( 77 sec) [ -5859.0531] [ 511] [depth= 1] . ( 78 sec) [ -5858.8128] [ 511] [depth= 1] . ( 78 sec) [ -5854.8571] [ 510] [depth= 1] . ( 78 sec) [ -5854.6311] [ 510] [depth= 1] . ( 78 sec) [ -5854.6203] [ 510] [depth= 1] . ( 78 sec) [ -5854.6091] [ 510] [depth= 1] . ( 79 sec) [ -5854.5684] [ 510] [depth= 1] . ( 79 sec) [ -5853.1423] [ 509] [depth= 1] . ( 81 sec) [ -5853.0731] [ 509] [depth= 2] . ( 82 sec) [ -5852.7935] [ 509] [depth= 1] . ( 83 sec) [ -5848.1767] [ 509] [depth= 3] . ( 83 sec) [ -5848.1095] [ 509] [depth= 1] . ( 85 sec) [ -5846.8054] [ 508] [depth= 1] . ( 87 sec) [ -5846.7214] [ 508] [depth= 1] . ( 88 sec) [ -5846.7086] [ 508] [depth= 1] . ( 90 sec) [ -5846.6740] [ 508] [depth= 1] . ( 91 sec) [ -5846.4854] [ 508] [depth= 1] . ( 91 sec) [ -5846.4614] [ 508] [depth= 1] . ( 91 sec) [ -5846.4499] [ 508] [depth= 1] . ( 93 sec) [ -5831.5746] [Branch lengths ] . ( 94 sec) [ -5831.0097] [GTR parameters ] . ( 95 sec) [ -5814.6286] [Alpha ][ 0.866380] . ( 97 sec) [ -5810.8894] [ 507] [depth= 1] . ( 106 sec) [ -5810.2942] [ 507] [depth= 2] . ( 146 sec) [ -5810.2225] [ 507] [depth= 1] . ( 163 sec) [ -5809.7779] [Branch lengths ] . ( 164 sec) [ -5809.6817] [GTR parameters ] . ( 164 sec) [ -5808.1693] [Alpha ][ 1.228091] . ( 234 sec) [ -5808.1573] [Branch lengths ] . ( 339 sec) [ -5808.1571] [Branch lengths ] . ( 339 sec) [ -5808.1571] [Topology ] . ( 341 sec) [ -5808.1571] [Topology ] . ( 342 sec) [ -5808.1558] [GTR parameters ] . ( 342 sec) [ -5808.1557] [Alpha ][ 1.229695] . ( 342 sec) [ -5808.1557] [Topology ] . ( 345 sec) [ -5808.1557] [Topology ] . ( 345 sec) [ -5808.1557] [GTR parameters ] . ( 345 sec) [ -5808.1557] [Alpha ][ 1.229695] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5808.155736. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15961.3156] [GTR parameters ] . ( 2 sec) [ -15672.4702] [Alpha ][ 0.500960] . ( 2 sec) [ -15586.3318] [ 1892] [depth= 15] . ( 2 sec) [ -15522.9460] [ 1885] [depth= 8] . ( 3 sec) [ -15514.8041] [ 1884] [depth= 1] . ( 3 sec) [ -15506.8962] [ 1884] [depth= 1] . ( 3 sec) [ -15484.0657] [ 1882] [depth= 2] . ( 3 sec) [ -15460.7576] [ 1882] [depth= 1] . ( 3 sec) [ -15457.5147] [ 1881] [depth= 3] . ( 3 sec) [ -15417.3634] [ 1881] [depth= 3] . ( 3 sec) [ -15317.1370] [ 1857] [depth= 5] . ( 3 sec) [ -15274.6404] [ 1856] [depth= 7] . ( 3 sec) [ -15212.4692] [ 1855] [depth= 1] . ( 3 sec) [ -15198.7761] [ 1855] [depth= 3] . ( 4 sec) [ -15168.3935] [ 1828] [depth= 13] . ( 4 sec) [ -15123.1927] [ 1828] [depth= 1] . ( 4 sec) [ -15086.3276] [ 1827] [depth= 14] . ( 4 sec) [ -14853.5400] [ 1827] [depth= 1] . ( 4 sec) [ -14840.4888] [ 1824] [depth= 13] . ( 4 sec) [ -14755.5093] [ 1824] [depth= 2] . ( 4 sec) [ -14629.1695] [ 1795] [depth= 15] . ( 4 sec) [ -14622.3110] [ 1795] [depth= 3] . ( 4 sec) [ -14557.7779] [ 1793] [depth= 7] . ( 4 sec) [ -14485.2624] [ 1793] [depth= 4] . ( 5 sec) [ -14460.3049] [ 1790] [depth= 18] . ( 5 sec) [ -14407.4631] [ 1790] [depth= 1] . ( 5 sec) [ -14281.8328] [ 1789] [depth= 6] . ( 5 sec) [ -14253.9974] [ 1790] [depth= 1] . ( 5 sec) [ -14251.4305] [ 1790] [depth= 1] . ( 5 sec) [ -14210.7256] [ 1783] [depth= 10] . ( 5 sec) [ -14186.7115] [ 1783] [depth= 6] . ( 5 sec) [ -14135.7761] [ 1773] [depth= 11] . ( 6 sec) [ -14087.2669] [ 1736] [depth= 30] . ( 6 sec) [ -14060.0716] [ 1734] [depth= 12] . ( 6 sec) [ -13861.4527] [ 1733] [depth= 2] . ( 6 sec) [ -13739.3663] [ 1731] [depth= 9] . ( 6 sec) [ -13711.3335] [ 1725] [depth= 7] . ( 6 sec) [ -13424.4814] [ 1688] [depth= 3] . ( 6 sec) [ -13411.3302] [ 1685] [depth= 10] . ( 6 sec) [ -13255.9231] [ 1673] [depth= 22] . ( 7 sec) [ -12934.5525] [ 1630] [depth= 22] . ( 7 sec) [ -12854.3027] [ 1629] [depth= 17] . ( 7 sec) [ -12797.2276] [ 1622] [depth= 11] . ( 7 sec) [ -12607.4351] [ 1612] [depth= 29] . ( 7 sec) [ -12456.1827] [ 1576] [depth= 16] . ( 7 sec) [ -12378.4520] [ 1568] [depth= 15] . ( 7 sec) [ -12257.1889] [ 1533] [depth= 6] . ( 7 sec) [ -12239.6406] [ 1528] [depth= 7] . ( 8 sec) [ -12206.3364] [ 1523] [depth= 16] . ( 8 sec) [ -12185.0105] [ 1520] [depth= 4] . ( 8 sec) [ -12180.5182] [ 1519] [depth= 3] . ( 8 sec) [ -11977.2196] [ 1519] [depth= 3] . ( 8 sec) [ -11842.3746] [ 1484] [depth= 3] . ( 8 sec) [ -11834.0203] [ 1484] [depth= 1] . ( 8 sec) [ -11830.8431] [ 1484] [depth= 2] . ( 8 sec) [ -11829.5363] [ 1484] [depth= 1] . ( 8 sec) [ -11667.6345] [ 1495] [depth= 25] . ( 9 sec) [ -11539.5708] [ 1479] [depth= 4] . ( 9 sec) [ -11536.1167] [ 1477] [depth= 30] . ( 9 sec) [ -11511.1498] [ 1474] [depth= 4] . ( 9 sec) [ -11454.8820] [ 1466] [depth= 23] . ( 9 sec) [ -11337.5052] [ 1471] [depth= 26] . ( 9 sec) [ -11297.5016] [ 1442] [depth= 3] . ( 10 sec) [ -11293.8397] [ 1442] [depth= 25] . ( 10 sec) [ -11232.0750] [ 1433] [depth= 19] . ( 10 sec) [ -11124.4633] [ 1419] [depth= 22] . ( 10 sec) [ -10922.8303] [ 1382] [depth= 10] . ( 10 sec) [ -10868.4992] [ 1375] [depth= 19] . ( 10 sec) [ -10773.6756] [ 1365] [depth= 28] . ( 11 sec) [ -10639.1097] [ 1323] [depth= 3] . ( 11 sec) [ -10635.8430] [ 1323] [depth= 1] . ( 11 sec) [ -10492.7058] [ 1315] [depth= 23] . ( 11 sec) [ -10424.4402] [ 1307] [depth= 12] . ( 11 sec) [ -10296.6892] [ 1271] [depth= 19] . ( 11 sec) [ -10270.7815] [ 1265] [depth= 2] . ( 11 sec) [ -10013.4132] [ 1237] [depth= 10] . ( 12 sec) [ -9812.2805] [ 1201] [depth= 14] . ( 12 sec) [ -9794.6630] [ 1199] [depth= 12] . ( 12 sec) [ -9793.4277] [ 1198] [depth= 10] . ( 12 sec) [ -9781.7594] [ 1197] [depth= 1] . ( 12 sec) [ -9765.3171] [ 1196] [depth= 9] . ( 12 sec) [ -9704.1673] [ 1198] [depth= 8] . ( 13 sec) [ -9655.1958] [ 1184] [depth= 21] . ( 13 sec) [ -9612.6005] [ 1174] [depth= 1] . ( 13 sec) [ -9595.1895] [ 1171] [depth= 4] . ( 13 sec) [ -9544.3577] [ 1163] [depth= 19] . ( 13 sec) [ -9502.6665] [ 1157] [depth= 15] . ( 14 sec) [ -9388.7996] [ 1152] [depth= 3] . ( 14 sec) [ -9373.6911] [ 1152] [depth= 1] . ( 14 sec) [ -9319.6087] [ 1141] [depth= 6] . ( 14 sec) [ -9316.5053] [ 1140] [depth= 1] . ( 14 sec) [ -9298.0470] [ 1142] [depth= 16] . ( 14 sec) [ -9266.4856] [ 1137] [depth= 14] . ( 14 sec) [ -9250.4906] [ 1134] [depth= 1] . ( 15 sec) [ -9206.0594] [ 1120] [depth= 23] . ( 15 sec) [ -9195.7649] [ 1117] [depth= 8] . ( 15 sec) [ -9195.6987] [ 1118] [depth= 9] . ( 15 sec) [ -9191.1869] [ 1117] [depth= 1] . ( 15 sec) [ -9155.2976] [ 1109] [depth= 20] . ( 15 sec) [ -9109.3096] [ 1101] [depth= 9] . ( 15 sec) [ -9096.3674] [ 1100] [depth= 1] . ( 16 sec) [ -9038.4528] [ 1090] [depth= 12] . ( 16 sec) [ -9036.0965] [ 1089] [depth= 1] . ( 16 sec) [ -9004.2626] [ 1086] [depth= 4] . ( 16 sec) [ -8954.2293] [ 1080] [depth= 14] . ( 16 sec) [ -8952.1865] [ 1081] [depth= 2] . ( 16 sec) [ -8923.3761] [ 1050] [depth= 3] . ( 16 sec) [ -8921.0571] [ 1050] [depth= 1] . ( 17 sec) [ -8909.5853] [ 1049] [depth= 20] . ( 17 sec) [ -8908.6845] [ 1049] [depth= 1] . ( 18 sec) [ -8906.5076] [ 1049] [depth= 1] . ( 18 sec) [ -8869.1162] [ 1043] [depth= 13] . ( 18 sec) [ -8745.3524] [ 1029] [depth= 3] . ( 18 sec) [ -8745.1725] [ 1029] [depth= 2] . ( 18 sec) [ -8742.3690] [ 1004] [depth= 1] . ( 18 sec) [ -8707.1994] [ 1004] [depth= 1] . ( 18 sec) [ -8633.3383] [ 996] [depth= 1] . ( 18 sec) [ -8627.7247] [ 993] [depth= 11] . ( 19 sec) [ -8560.7495] [ 958] [depth= 2] . ( 19 sec) [ -8539.7036] [ 954] [depth= 9] . ( 19 sec) [ -8533.7874] [ 955] [depth= 7] . ( 19 sec) [ -8436.7483] [ 934] [depth= 1] . ( 19 sec) [ -8425.6394] [ 934] [depth= 2] . ( 19 sec) [ -8390.2982] [ 934] [depth= 5] . ( 19 sec) [ -8339.1132] [ 924] [depth= 9] . ( 20 sec) [ -8287.7639] [ 923] [depth= 2] . ( 20 sec) [ -8230.4167] [ 916] [depth= 14] . ( 20 sec) [ -8080.5896] [ 918] [depth= 2] . ( 20 sec) [ -8080.4646] [ 918] [depth= 1] . ( 20 sec) [ -8076.4007] [ 918] [depth= 5] . ( 20 sec) [ -7988.3155] [ 896] [depth= 14] . ( 20 sec) [ -7962.9004] [ 893] [depth= 12] . ( 20 sec) [ -7953.2504] [ 892] [depth= 1] . ( 20 sec) [ -7940.6839] [ 890] [depth= 2] . ( 21 sec) [ -7937.0436] [ 890] [depth= 17] . ( 21 sec) [ -7697.0007] [ 853] [depth= 5] . ( 21 sec) [ -7664.6493] [ 846] [depth= 16] . ( 21 sec) [ -7640.5258] [ 842] [depth= 12] . ( 21 sec) [ -7639.0127] [ 842] [depth= 1] . ( 22 sec) [ -7635.5964] [ 847] [depth= 13] . ( 22 sec) [ -7633.0504] [ 847] [depth= 1] . ( 22 sec) [ -7601.0231] [ 844] [depth= 13] . ( 22 sec) [ -7600.7003] [ 844] [depth= 1] . ( 23 sec) [ -7597.4449] [ 844] [depth= 1] . ( 23 sec) [ -7587.6014] [ 843] [depth= 1] . ( 23 sec) [ -7361.0744] [ 798] [depth= 10] . ( 23 sec) [ -7359.1783] [ 798] [depth= 2] . ( 23 sec) [ -7358.8636] [ 798] [depth= 1] . ( 23 sec) [ -7302.8098] [ 785] [depth= 11] . ( 23 sec) [ -7296.7037] [ 784] [depth= 1] . ( 23 sec) [ -7294.4653] [ 785] [depth= 1] . ( 23 sec) [ -7293.3935] [ 785] [depth= 3] . ( 24 sec) [ -7286.1198] [ 785] [depth= 2] . ( 24 sec) [ -7272.4848] [ 782] [depth= 8] . ( 24 sec) [ -7267.5601] [ 781] [depth= 1] . ( 24 sec) [ -7266.9897] [ 781] [depth= 1] . ( 24 sec) [ -7261.2074] [ 781] [depth= 16] . ( 25 sec) [ -7249.6405] [ 778] [depth= 17] . ( 25 sec) [ -7114.9360] [ 748] [depth= 8] . ( 25 sec) [ -7105.8071] [ 748] [depth= 1] . ( 25 sec) [ -7096.5800] [ 751] [depth= 2] . ( 25 sec) [ -7079.9911] [ 748] [depth= 2] . ( 25 sec) [ -7059.6394] [ 745] [depth= 13] . ( 26 sec) [ -7058.6309] [ 745] [depth= 1] . ( 26 sec) [ -7052.2030] [ 743] [depth= 1] . ( 26 sec) [ -7051.3097] [ 743] [depth= 15] . ( 26 sec) [ -7048.2724] [ 745] [depth= 1] . ( 26 sec) [ -6953.8287] [ 728] [depth= 12] . ( 26 sec) [ -6949.6612] [ 727] [depth= 2] . ( 26 sec) [ -6940.9011] [ 726] [depth= 1] . ( 26 sec) [ -6926.0176] [ 725] [depth= 1] . ( 27 sec) [ -6925.8210] [ 725] [depth= 1] . ( 27 sec) [ -6920.6437] [ 726] [depth= 2] . ( 27 sec) [ -6920.0979] [ 726] [depth= 1] . ( 27 sec) [ -6872.9234] [ 702] [depth= 6] . ( 27 sec) [ -6872.7129] [ 702] [depth= 2] . ( 27 sec) [ -6872.6651] [ 702] [depth= 1] . ( 27 sec) [ -6788.8155] [ 694] [depth= 7] . ( 28 sec) [ -6784.2761] [ 696] [depth= 1] . ( 28 sec) [ -6721.5489] [ 684] [depth= 4] . ( 29 sec) [ -6615.5817] [ 658] [depth= 3] . ( 29 sec) [ -6606.7425] [ 658] [depth= 3] . ( 29 sec) [ -6597.6827] [ 655] [depth= 1] . ( 29 sec) [ -6595.8658] [ 654] [depth= 2] . ( 29 sec) [ -6589.3467] [ 652] [depth= 2] . ( 29 sec) [ -6587.6730] [ 652] [depth= 1] . ( 29 sec) [ -6505.2723] [ 639] [depth= 5] . ( 30 sec) [ -6494.3168] [ 636] [depth= 3] . ( 30 sec) [ -6494.2197] [ 636] [depth= 1] . ( 30 sec) [ -6494.1057] [ 636] [depth= 3] . ( 31 sec) [ -6489.6130] [ 635] [depth= 1] . ( 31 sec) [ -6488.7690] [ 635] [depth= 1] . ( 32 sec) [ -6460.2302] [ 628] [depth= 2] . ( 32 sec) [ -6459.7508] [ 628] [depth= 1] . ( 32 sec) [ -6454.7138] [ 626] [depth= 3] . ( 33 sec) [ -6366.4616] [Branch lengths ] . ( 36 sec) [ -6334.9215] [GTR parameters ] . ( 36 sec) [ -6334.9214] [Alpha ][ 0.501461] . ( 36 sec) [ -6331.1923] [ 625] [depth= 2] . ( 36 sec) [ -6328.5845] [ 624] [depth= 2] . ( 37 sec) [ -6327.6440] [ 619] [depth= 3] . ( 37 sec) [ -6317.2090] [ 617] [depth= 3] . ( 37 sec) [ -6317.1754] [ 617] [depth= 1] . ( 38 sec) [ -6312.4596] [ 616] [depth= 1] . ( 39 sec) [ -6309.0774] [ 615] [depth= 1] . ( 39 sec) [ -6309.0559] [ 615] [depth= 2] . ( 39 sec) [ -6304.1996] [ 614] [depth= 1] . ( 39 sec) [ -6297.2051] [ 614] [depth= 1] . ( 39 sec) [ -6287.7404] [ 612] [depth= 1] . ( 39 sec) [ -6263.1816] [ 609] [depth= 12] . ( 40 sec) [ -6263.0499] [ 609] [depth= 1] . ( 40 sec) [ -6248.3061] [ 605] [depth= 2] . ( 40 sec) [ -6248.1097] [ 605] [depth= 3] . ( 40 sec) [ -6240.1514] [ 602] [depth= 1] . ( 40 sec) [ -6240.1356] [ 602] [depth= 1] . ( 41 sec) [ -6231.2031] [ 595] [depth= 3] . ( 42 sec) [ -6231.0306] [ 595] [depth= 1] . ( 43 sec) [ -6170.6013] [ 583] [depth= 1] . ( 45 sec) [ -6170.5888] [ 583] [depth= 1] . ( 45 sec) [ -6141.3161] [ 581] [depth= 8] . ( 47 sec) [ -6132.7189] [ 579] [depth= 1] . ( 47 sec) [ -6132.4628] [ 579] [depth= 1] . ( 50 sec) [ -6128.4154] [ 578] [depth= 1] . ( 50 sec) [ -6125.8800] [ 578] [depth= 2] . ( 53 sec) [ -6110.8976] [ 574] [depth= 1] . ( 54 sec) [ -6110.8184] [ 574] [depth= 2] . ( 54 sec) [ -6100.5591] [ 571] [depth= 1] . ( 54 sec) [ -6098.4868] [ 571] [depth= 3] . ( 54 sec) [ -6090.9147] [ 573] [depth= 1] . ( 54 sec) [ -6079.8209] [ 571] [depth= 3] . ( 57 sec) [ -6062.2526] [ 565] [depth= 9] . ( 58 sec) [ -6061.0496] [ 565] [depth= 1] . ( 58 sec) [ -6058.1804] [ 565] [depth= 1] . ( 59 sec) [ -6057.9796] [ 565] [depth= 1] . ( 60 sec) [ -6057.9452] [ 565] [depth= 1] . ( 60 sec) [ -6055.8894] [ 564] [depth= 1] . ( 60 sec) [ -6055.6986] [ 564] [depth= 2] . ( 60 sec) [ -6055.1566] [ 564] [depth= 1] . ( 61 sec) [ -6052.7904] [ 565] [depth= 1] . ( 61 sec) [ -6052.5256] [ 565] [depth= 3] . ( 61 sec) [ -6040.4356] [ 563] [depth= 4] . ( 62 sec) [ -6032.7991] [ 561] [depth= 2] . ( 63 sec) [ -6031.5114] [ 561] [depth= 1] . ( 64 sec) [ -6031.2323] [ 561] [depth= 2] . ( 66 sec) [ -6031.0943] [ 561] [depth= 1] . ( 68 sec) [ -6031.0085] [ 561] [depth= 1] . ( 69 sec) [ -6030.8486] [ 561] [depth= 1] . ( 69 sec) [ -6028.4363] [ 561] [depth= 4] . ( 70 sec) [ -6021.7312] [ 560] [depth= 3] . ( 71 sec) [ -6021.0283] [ 560] [depth= 1] . ( 71 sec) [ -6021.0149] [ 560] [depth= 1] . ( 71 sec) [ -6020.9856] [ 560] [depth= 1] . ( 72 sec) [ -6020.9428] [ 560] [depth= 1] . ( 73 sec) [ -6020.8790] [ 560] [depth= 1] . ( 73 sec) [ -6019.8367] [ 558] [depth= 2] . ( 73 sec) [ -6019.8058] [ 558] [depth= 1] . ( 73 sec) [ -5939.0953] [ 535] [depth= 1] . ( 73 sec) [ -5925.1054] [ 529] [depth= 1] . ( 74 sec) [ -5925.0840] [ 529] [depth= 2] . ( 75 sec) [ -5923.4772] [ 527] [depth= 1] . ( 75 sec) [ -5913.0563] [ 529] [depth= 1] . ( 75 sec) [ -5910.2826] [ 527] [depth= 2] . ( 76 sec) [ -5910.1026] [ 527] [depth= 1] . ( 76 sec) [ -5910.0906] [ 527] [depth= 1] . ( 78 sec) [ -5909.9053] [ 527] [depth= 1] . ( 79 sec) [ -5909.6933] [ 527] [depth= 1] . ( 79 sec) [ -5908.3072] [ 526] [depth= 1] . ( 82 sec) [ -5908.2931] [ 526] [depth= 1] . ( 84 sec) [ -5907.8855] [ 526] [depth= 1] . ( 84 sec) [ -5907.5178] [ 526] [depth= 1] . ( 84 sec) [ -5907.4823] [ 526] [depth= 1] . ( 84 sec) [ -5875.9815] [ 515] [depth= 1] . ( 88 sec) [ -5872.6637] [ 515] [depth= 1] . ( 88 sec) [ -5872.5269] [ 515] [depth= 1] . ( 89 sec) [ -5872.0349] [ 515] [depth= 3] . ( 89 sec) [ -5871.5610] [ 515] [depth= 1] . ( 94 sec) [ -5847.6853] [Branch lengths ] . ( 96 sec) [ -5847.1572] [GTR parameters ] . ( 96 sec) [ -5836.5435] [Alpha ][ 1.001096] . ( 96 sec) [ -5825.1522] [ 512] [depth= 1] . ( 104 sec) [ -5816.0828] [ 508] [depth= 2] . ( 105 sec) [ -5816.0351] [ 508] [depth= 2] . ( 126 sec) [ -5812.7050] [ 507] [depth= 3] . ( 129 sec) [ -5812.6899] [ 507] [depth= 2] . ( 166 sec) [ -5808.5318] [Branch lengths ] . ( 167 sec) [ -5808.4360] [GTR parameters ] . ( 167 sec) [ -5807.9456] [Alpha ][ 1.229560] . ( 243 sec) [ -5807.9376] [Branch lengths ] . ( 352 sec) [ -5807.9375] [Branch lengths ] . ( 352 sec) [ -5807.9375] [Topology ] . ( 354 sec) [ -5807.9374] [Topology ] . ( 355 sec) [ -5807.9370] [GTR parameters ] . ( 355 sec) [ -5807.9370] [Alpha ][ 1.230789] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5807.937041. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -16194.7503] [GTR parameters ] . ( 3 sec) [ -15895.8250] [Alpha ][ 0.500960] . ( 4 sec) [ -15860.5782] [ 1906] [depth= 5] . ( 4 sec) [ -15787.4550] [ 1898] [depth= 6] . ( 4 sec) [ -15749.1218] [ 1898] [depth= 1] . ( 4 sec) [ -15723.4290] [ 1896] [depth= 3] . ( 4 sec) [ -15578.6519] [ 1889] [depth= 3] . ( 4 sec) [ -15515.1711] [ 1888] [depth= 11] . ( 4 sec) [ -15427.8607] [ 1886] [depth= 4] . ( 4 sec) [ -15427.1062] [ 1886] [depth= 4] . ( 4 sec) [ -15424.6499] [ 1886] [depth= 2] . ( 5 sec) [ -15419.2778] [ 1886] [depth= 8] . ( 5 sec) [ -15192.3647] [ 1884] [depth= 4] . ( 5 sec) [ -15184.6183] [ 1883] [depth= 3] . ( 5 sec) [ -15148.5810] [ 1882] [depth= 1] . ( 5 sec) [ -15066.4681] [ 1881] [depth= 8] . ( 5 sec) [ -14976.7581] [ 1880] [depth= 2] . ( 5 sec) [ -14960.0299] [ 1880] [depth= 2] . ( 5 sec) [ -14946.7109] [ 1880] [depth= 2] . ( 5 sec) [ -14930.7637] [ 1880] [depth= 1] . ( 5 sec) [ -14858.9254] [ 1878] [depth= 14] . ( 6 sec) [ -14814.5847] [ 1879] [depth= 1] . ( 6 sec) [ -14795.4940] [ 1874] [depth= 1] . ( 6 sec) [ -14628.7985] [ 1832] [depth= 22] . ( 6 sec) [ -14563.1274] [ 1828] [depth= 10] . ( 6 sec) [ -14545.2921] [ 1829] [depth= 9] . ( 6 sec) [ -14456.8808] [ 1800] [depth= 17] . ( 6 sec) [ -14430.5303] [ 1800] [depth= 1] . ( 6 sec) [ -14377.7510] [ 1789] [depth= 3] . ( 6 sec) [ -14332.1569] [ 1789] [depth= 1] . ( 7 sec) [ -14268.9873] [ 1760] [depth= 4] . ( 7 sec) [ -14134.7354] [ 1760] [depth= 23] . ( 7 sec) [ -13982.9733] [ 1751] [depth= 5] . ( 7 sec) [ -13936.8751] [ 1737] [depth= 22] . ( 7 sec) [ -13861.2649] [ 1726] [depth= 2] . ( 7 sec) [ -13722.4016] [ 1689] [depth= 8] . ( 7 sec) [ -13703.2645] [ 1689] [depth= 21] . ( 7 sec) [ -13533.8167] [ 1677] [depth= 13] . ( 8 sec) [ -13492.5862] [ 1677] [depth= 1] . ( 8 sec) [ -13490.5757] [ 1677] [depth= 12] . ( 8 sec) [ -13426.0368] [ 1668] [depth= 4] . ( 8 sec) [ -13387.0786] [ 1647] [depth= 10] . ( 8 sec) [ -13165.8280] [ 1620] [depth= 8] . ( 8 sec) [ -12930.6154] [ 1585] [depth= 6] . ( 8 sec) [ -12739.1886] [ 1585] [depth= 1] . ( 8 sec) [ -12726.4648] [ 1585] [depth= 2] . ( 8 sec) [ -12632.1173] [ 1552] [depth= 4] . ( 9 sec) [ -12579.4032] [ 1545] [depth= 1] . ( 9 sec) [ -12159.6995] [ 1507] [depth= 14] . ( 9 sec) [ -11860.4898] [ 1460] [depth= 20] . ( 9 sec) [ -11801.3000] [ 1448] [depth= 11] . ( 9 sec) [ -11624.5660] [ 1443] [depth= 14] . ( 9 sec) [ -11588.0478] [ 1437] [depth= 14] . ( 9 sec) [ -11540.7149] [ 1447] [depth= 1] . ( 9 sec) [ -11424.3367] [ 1409] [depth= 2] . ( 9 sec) [ -11302.5969] [ 1378] [depth= 14] . ( 10 sec) [ -11299.8022] [ 1378] [depth= 11] . ( 10 sec) [ -11238.1943] [ 1365] [depth= 11] . ( 10 sec) [ -11202.7243] [ 1362] [depth= 9] . ( 10 sec) [ -11140.1428] [ 1350] [depth= 8] . ( 10 sec) [ -11125.1658] [ 1349] [depth= 17] . ( 10 sec) [ -11102.4945] [ 1350] [depth= 1] . ( 10 sec) [ -11054.5152] [ 1346] [depth= 10] . ( 11 sec) [ -11036.7146] [ 1342] [depth= 12] . ( 11 sec) [ -10939.2606] [ 1332] [depth= 5] . ( 11 sec) [ -10803.2875] [ 1303] [depth= 6] . ( 11 sec) [ -10785.9944] [ 1303] [depth= 13] . ( 11 sec) [ -10673.2305] [ 1303] [depth= 3] . ( 11 sec) [ -10635.2877] [ 1303] [depth= 1] . ( 11 sec) [ -10611.5463] [ 1301] [depth= 3] . ( 11 sec) [ -10607.8685] [ 1301] [depth= 1] . ( 11 sec) [ -10527.1670] [ 1285] [depth= 4] . ( 12 sec) [ -10450.6241] [ 1277] [depth= 12] . ( 12 sec) [ -10431.8316] [ 1275] [depth= 1] . ( 12 sec) [ -10427.3308] [ 1274] [depth= 1] . ( 12 sec) [ -10418.4919] [ 1273] [depth= 15] . ( 12 sec) [ -10295.9955] [ 1271] [depth= 11] . ( 12 sec) [ -10236.2965] [ 1271] [depth= 2] . ( 12 sec) [ -10089.6896] [ 1236] [depth= 19] . ( 12 sec) [ -10057.7564] [ 1232] [depth= 20] . ( 12 sec) [ -9884.8557] [ 1228] [depth= 12] . ( 13 sec) [ -9880.2012] [ 1228] [depth= 2] . ( 13 sec) [ -9877.7060] [ 1228] [depth= 1] . ( 13 sec) [ -9876.2684] [ 1228] [depth= 3] . ( 13 sec) [ -9675.9285] [ 1185] [depth= 21] . ( 13 sec) [ -9633.0229] [ 1187] [depth= 20] . ( 13 sec) [ -9590.7714] [ 1179] [depth= 9] . ( 13 sec) [ -9510.0807] [ 1170] [depth= 13] . ( 14 sec) [ -9497.7873] [ 1170] [depth= 5] . ( 14 sec) [ -9396.8156] [ 1170] [depth= 2] . ( 14 sec) [ -9387.5151] [ 1167] [depth= 8] . ( 14 sec) [ -9380.5114] [ 1167] [depth= 1] . ( 14 sec) [ -9296.8798] [ 1153] [depth= 4] . ( 14 sec) [ -9288.8410] [ 1149] [depth= 4] . ( 14 sec) [ -9284.3016] [ 1150] [depth= 2] . ( 14 sec) [ -9282.7886] [ 1150] [depth= 1] . ( 14 sec) [ -9278.3211] [ 1148] [depth= 3] . ( 15 sec) [ -9278.1974] [ 1150] [depth= 2] . ( 15 sec) [ -9262.5813] [ 1153] [depth= 1] . ( 15 sec) [ -9155.0479] [ 1117] [depth= 10] . ( 15 sec) [ -9146.5105] [ 1115] [depth= 1] . ( 15 sec) [ -9090.8997] [ 1093] [depth= 6] . ( 15 sec) [ -8987.3586] [ 1093] [depth= 1] . ( 16 sec) [ -8919.9078] [ 1066] [depth= 1] . ( 16 sec) [ -8901.8319] [ 1066] [depth= 1] . ( 16 sec) [ -8901.2800] [ 1066] [depth= 3] . ( 16 sec) [ -8766.7978] [ 1069] [depth= 1] . ( 16 sec) [ -8613.0993] [ 1022] [depth= 4] . ( 16 sec) [ -8611.4228] [ 1022] [depth= 1] . ( 16 sec) [ -8601.8643] [ 1021] [depth= 4] . ( 16 sec) [ -8599.1911] [ 1020] [depth= 1] . ( 16 sec) [ -8589.5553] [ 1018] [depth= 1] . ( 17 sec) [ -8580.2680] [ 1016] [depth= 2] . ( 17 sec) [ -8554.9705] [ 1014] [depth= 4] . ( 17 sec) [ -8544.9496] [ 1011] [depth= 10] . ( 17 sec) [ -8544.2685] [ 1011] [depth= 11] . ( 17 sec) [ -8426.6930] [ 972] [depth= 7] . ( 17 sec) [ -8401.6338] [ 966] [depth= 14] . ( 18 sec) [ -8349.5875] [ 959] [depth= 11] . ( 18 sec) [ -8348.8350] [ 959] [depth= 2] . ( 18 sec) [ -8307.4423] [ 956] [depth= 10] . ( 18 sec) [ -8173.6797] [ 956] [depth= 1] . ( 18 sec) [ -8163.2912] [ 954] [depth= 1] . ( 18 sec) [ -8162.4956] [ 954] [depth= 2] . ( 18 sec) [ -8154.5397] [ 920] [depth= 1] . ( 18 sec) [ -8116.3238] [ 918] [depth= 1] . ( 19 sec) [ -7936.3746] [ 883] [depth= 10] . ( 19 sec) [ -7878.6192] [ 883] [depth= 2] . ( 19 sec) [ -7863.4177] [ 882] [depth= 11] . ( 19 sec) [ -7858.6644] [ 882] [depth= 2] . ( 19 sec) [ -7822.0506] [ 879] [depth= 9] . ( 20 sec) [ -7821.9092] [ 879] [depth= 2] . ( 20 sec) [ -7815.5343] [ 878] [depth= 1] . ( 20 sec) [ -7801.3413] [ 877] [depth= 12] . ( 20 sec) [ -7792.1955] [ 875] [depth= 2] . ( 20 sec) [ -7790.2470] [ 875] [depth= 1] . ( 20 sec) [ -7724.5090] [ 862] [depth= 9] . ( 21 sec) [ -7694.9836] [ 858] [depth= 12] . ( 21 sec) [ -7677.1947] [ 856] [depth= 11] . ( 21 sec) [ -7655.6340] [ 853] [depth= 7] . ( 21 sec) [ -7625.6784] [ 851] [depth= 2] . ( 22 sec) [ -7621.5689] [ 848] [depth= 6] . ( 22 sec) [ -7611.8506] [ 848] [depth= 1] . ( 22 sec) [ -7600.2443] [ 845] [depth= 16] . ( 22 sec) [ -7584.7244] [ 841] [depth= 10] . ( 22 sec) [ -7579.3928] [ 842] [depth= 1] . ( 22 sec) [ -7572.7183] [ 841] [depth= 1] . ( 23 sec) [ -7563.5998] [ 840] [depth= 10] . ( 23 sec) [ -7559.8162] [ 840] [depth= 1] . ( 23 sec) [ -7556.4782] [ 840] [depth= 8] . ( 23 sec) [ -7554.4341] [ 838] [depth= 4] . ( 23 sec) [ -7554.0625] [ 837] [depth= 2] . ( 23 sec) [ -7553.9592] [ 838] [depth= 1] . ( 23 sec) [ -7449.7338] [ 809] [depth= 5] . ( 23 sec) [ -7447.9515] [ 809] [depth= 3] . ( 24 sec) [ -7436.7583] [ 808] [depth= 13] . ( 24 sec) [ -7427.6775] [ 808] [depth= 7] . ( 24 sec) [ -7427.3646] [ 808] [depth= 3] . ( 24 sec) [ -7399.3189] [ 797] [depth= 2] . ( 25 sec) [ -7397.2237] [ 797] [depth= 1] . ( 25 sec) [ -7392.6644] [ 796] [depth= 3] . ( 25 sec) [ -7387.7509] [ 795] [depth= 1] . ( 25 sec) [ -7384.6509] [ 795] [depth= 1] . ( 25 sec) [ -7381.0669] [ 795] [depth= 1] . ( 25 sec) [ -7380.8573] [ 795] [depth= 1] . ( 25 sec) [ -7379.7337] [ 795] [depth= 1] . ( 25 sec) [ -7375.3200] [ 794] [depth= 2] . ( 26 sec) [ -7374.6873] [ 794] [depth= 2] . ( 26 sec) [ -7371.9881] [ 793] [depth= 6] . ( 26 sec) [ -7358.0218] [ 793] [depth= 1] . ( 26 sec) [ -7356.5656] [ 792] [depth= 6] . ( 26 sec) [ -7346.2318] [ 784] [depth= 1] . ( 26 sec) [ -7109.5433] [ 753] [depth= 8] . ( 27 sec) [ -7105.5485] [ 751] [depth= 5] . ( 27 sec) [ -7103.6435] [ 753] [depth= 1] . ( 28 sec) [ -7016.8209] [ 722] [depth= 9] . ( 28 sec) [ -7005.1250] [ 713] [depth= 3] . ( 28 sec) [ -7000.8215] [ 714] [depth= 5] . ( 28 sec) [ -6998.2491] [ 716] [depth= 6] . ( 28 sec) [ -6971.5460] [ 713] [depth= 2] . ( 28 sec) [ -6969.2374] [ 712] [depth= 1] . ( 28 sec) [ -6950.9309] [ 712] [depth= 2] . ( 29 sec) [ -6948.3402] [ 712] [depth= 1] . ( 30 sec) [ -6948.3296] [ 712] [depth= 1] . ( 30 sec) [ -6909.4079] [ 701] [depth= 7] . ( 30 sec) [ -6892.5597] [ 698] [depth= 1] . ( 30 sec) [ -6864.9952] [ 691] [depth= 2] . ( 30 sec) [ -6857.2054] [ 689] [depth= 3] . ( 30 sec) [ -6856.2571] [ 689] [depth= 2] . ( 30 sec) [ -6847.4954] [ 688] [depth= 3] . ( 31 sec) [ -6845.7098] [ 690] [depth= 1] . ( 31 sec) [ -6845.1923] [ 690] [depth= 1] . ( 31 sec) [ -6797.0427] [ 673] [depth= 5] . ( 31 sec) [ -6791.2122] [ 672] [depth= 3] . ( 31 sec) [ -6748.2089] [ 667] [depth= 13] . ( 31 sec) [ -6608.3327] [ 644] [depth= 9] . ( 32 sec) [ -6586.6954] [ 641] [depth= 4] . ( 32 sec) [ -6581.3670] [ 640] [depth= 1] . ( 32 sec) [ -6581.1683] [ 640] [depth= 1] . ( 33 sec) [ -6399.1740] [Branch lengths ] . ( 35 sec) [ -6395.8101] [GTR parameters ] . ( 35 sec) [ -6395.5771] [Alpha ][ 0.463821] . ( 36 sec) [ -6389.9614] [ 638] [depth= 1] . ( 36 sec) [ -6346.5720] [ 627] [depth= 2] . ( 37 sec) [ -6337.0382] [ 625] [depth= 5] . ( 39 sec) [ -6336.8224] [ 625] [depth= 1] . ( 39 sec) [ -6332.6372] [ 624] [depth= 1] . ( 39 sec) [ -6330.6685] [ 623] [depth= 1] . ( 40 sec) [ -6282.0764] [ 615] [depth= 6] . ( 40 sec) [ -6281.1790] [ 615] [depth= 1] . ( 41 sec) [ -6280.5038] [ 614] [depth= 1] . ( 41 sec) [ -6264.8288] [ 613] [depth= 4] . ( 41 sec) [ -6264.7573] [ 613] [depth= 2] . ( 41 sec) [ -6257.7267] [ 612] [depth= 4] . ( 41 sec) [ -6257.7088] [ 612] [depth= 2] . ( 41 sec) [ -6257.6809] [ 612] [depth= 1] . ( 42 sec) [ -6257.6605] [ 612] [depth= 1] . ( 42 sec) [ -6257.5744] [ 612] [depth= 2] . ( 43 sec) [ -6257.5287] [ 612] [depth= 1] . ( 43 sec) [ -6257.5129] [ 612] [depth= 1] . ( 44 sec) [ -6257.4981] [ 612] [depth= 1] . ( 45 sec) [ -6249.9369] [ 610] [depth= 1] . ( 45 sec) [ -6227.3698] [ 604] [depth= 1] . ( 47 sec) [ -6224.3148] [ 603] [depth= 3] . ( 47 sec) [ -6198.8736] [ 597] [depth= 2] . ( 49 sec) [ -6195.9265] [ 596] [depth= 1] . ( 50 sec) [ -6191.9994] [ 594] [depth= 2] . ( 50 sec) [ -6178.9539] [ 590] [depth= 3] . ( 50 sec) [ -6175.4989] [ 590] [depth= 3] . ( 50 sec) [ -6175.4735] [ 590] [depth= 1] . ( 51 sec) [ -6090.1785] [ 567] [depth= 4] . ( 51 sec) [ -5988.8448] [ 543] [depth= 4] . ( 51 sec) [ -5988.3318] [ 542] [depth= 2] . ( 51 sec) [ -5985.3090] [ 542] [depth= 1] . ( 51 sec) [ -5984.9737] [ 542] [depth= 2] . ( 51 sec) [ -5978.5081] [ 542] [depth= 1] . ( 52 sec) [ -5977.7195] [ 542] [depth= 2] . ( 52 sec) [ -5975.1495] [ 542] [depth= 1] . ( 52 sec) [ -5958.2352] [ 538] [depth= 3] . ( 52 sec) [ -5954.4992] [ 538] [depth= 2] . ( 53 sec) [ -5944.7754] [ 536] [depth= 5] . ( 53 sec) [ -5940.1907] [ 537] [depth= 2] . ( 55 sec) [ -5939.5084] [ 537] [depth= 1] . ( 56 sec) [ -5939.4599] [ 537] [depth= 1] . ( 56 sec) [ -5935.8480] [ 536] [depth= 1] . ( 58 sec) [ -5931.4009] [ 536] [depth= 3] . ( 59 sec) [ -5930.4514] [ 536] [depth= 1] . ( 60 sec) [ -5930.3977] [ 536] [depth= 1] . ( 60 sec) [ -5928.7581] [ 535] [depth= 4] . ( 60 sec) [ -5928.6936] [ 535] [depth= 2] . ( 61 sec) [ -5928.3280] [ 535] [depth= 1] . ( 61 sec) [ -5928.2622] [ 535] [depth= 1] . ( 62 sec) [ -5923.4344] [ 534] [depth= 2] . ( 62 sec) [ -5923.4040] [ 534] [depth= 1] . ( 62 sec) [ -5922.0041] [ 535] [depth= 1] . ( 63 sec) [ -5914.6361] [ 529] [depth= 1] . ( 64 sec) [ -5914.6255] [ 529] [depth= 1] . ( 67 sec) [ -5914.6115] [ 529] [depth= 1] . ( 68 sec) [ -5891.3610] [ 524] [depth= 2] . ( 69 sec) [ -5891.2408] [ 524] [depth= 2] . ( 69 sec) [ -5890.6771] [ 524] [depth= 1] . ( 71 sec) [ -5890.6619] [ 524] [depth= 1] . ( 73 sec) [ -5888.2929] [ 523] [depth= 1] . ( 74 sec) [ -5888.1690] [ 523] [depth= 1] . ( 76 sec) [ -5887.3723] [ 522] [depth= 1] . ( 79 sec) [ -5886.9961] [ 522] [depth= 1] . ( 80 sec) [ -5885.7938] [ 521] [depth= 1] . ( 81 sec) [ -5884.0642] [ 521] [depth= 1] . ( 81 sec) [ -5848.8959] [ 508] [depth= 1] . ( 85 sec) [ -5847.5714] [ 510] [depth= 1] . ( 85 sec) [ -5842.6808] [ 509] [depth= 1] . ( 89 sec) [ -5842.6609] [ 509] [depth= 1] . ( 90 sec) [ -5842.3386] [ 509] [depth= 1] . ( 90 sec) [ -5842.3129] [ 509] [depth= 1] . ( 92 sec) [ -5842.0662] [ 509] [depth= 1] . ( 93 sec) [ -5836.7812] [ 507] [depth= 1] . ( 94 sec) [ -5824.4413] [Branch lengths ] . ( 96 sec) [ -5823.5971] [GTR parameters ] . ( 96 sec) [ -5809.0203] [Alpha ][ 0.926428] . ( 165 sec) [ -5808.9203] [Branch lengths ] . ( 270 sec) [ -5808.9185] [Branch lengths ] . ( 270 sec) [ -5808.9185] [Topology ] . ( 272 sec) [ -5808.9184] [Topology ] . ( 273 sec) [ -5808.9040] [GTR parameters ] . ( 274 sec) [ -5807.9403] [Alpha ][ 1.229418] . ( 274 sec) [ -5807.9403] [Topology ] . ( 276 sec) [ -5807.9379] [Topology ] . ( 278 sec) [ -5807.9375] [Topology ] . ( 279 sec) [ -5807.9368] [GTR parameters ] . ( 279 sec) [ -5807.9368] [Alpha ][ 1.230647] . ( 279 sec) [ -5807.9368] [Topology ] . ( 282 sec) [ -5807.9367] [Topology ] . ( 282 sec) [ -5807.9367] [GTR parameters ] . ( 282 sec) [ -5807.9367] [Alpha ][ 1.230647] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5807.936714. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -5881.3955] [GTR parameters ] . ( 3 sec) [ -5881.3763] [Alpha ][ 1.039147] . ( 3 sec) [ -5881.3763] [Topology ] . ( 6 sec) [ -5840.5187] [Topology ] . ( 8 sec) [ -5831.9227] [Topology ] . ( 11 sec) [ -5825.2712] [Topology ] . ( 13 sec) [ -5824.3381] [Topology ] . ( 16 sec) [ -5824.2227] [Topology ] . ( 18 sec) [ -5824.2058] [Topology ] . ( 20 sec) [ -5824.2023] [Topology ] . ( 23 sec) [ -5824.2014] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -5824.0941] [GTR parameters ] . ( 39 sec) [ -5823.9485] [Alpha ][ 1.159997] . ( 39 sec) [ -5823.9485] [Topology ] . ( 42 sec) [ -5823.9480] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -5823.9479] [GTR parameters ] . ( 57 sec) [ -5823.9479] [Alpha ][ 1.159997] . ( 57 sec) [ -5823.9479] [Topology ] . ( 59 sec) [ -5823.9478] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 92 sec) [ -5881.3955] [GTR parameters ] . ( 92 sec) [ -5881.3763] [Alpha ][ 1.039147] . ( 92 sec) [ -5880.5971] [ 518] [depth= 1] . ( 92 sec) [ -5880.0235] [ 518] [depth= 1] . ( 93 sec) [ -5879.6552] [ 518] [depth= 1] . ( 93 sec) [ -5879.6115] [ 518] [depth= 1] . ( 93 sec) [ -5873.8661] [ 517] [depth= 1] . ( 93 sec) [ -5873.4203] [ 517] [depth= 1] . ( 94 sec) [ -5873.1945] [ 517] [depth= 1] . ( 94 sec) [ -5871.1004] [ 517] [depth= 2] . ( 94 sec) [ -5870.9911] [ 517] [depth= 2] . ( 96 sec) [ -5870.9400] [ 517] [depth= 1] . ( 96 sec) [ -5870.9271] [ 517] [depth= 2] . ( 96 sec) [ -5870.9154] [ 517] [depth= 1] . ( 96 sec) [ -5869.2789] [ 517] [depth= 1] . ( 97 sec) [ -5868.9431] [ 517] [depth= 1] . ( 97 sec) [ -5868.7479] [ 517] [depth= 1] . ( 97 sec) [ -5868.0867] [ 517] [depth= 3] . ( 97 sec) [ -5868.0291] [ 517] [depth= 1] . ( 98 sec) [ -5867.9488] [ 517] [depth= 1] . ( 101 sec) [ -5856.0675] [ 515] [depth= 4] . ( 102 sec) [ -5855.4154] [ 515] [depth= 1] . ( 103 sec) [ -5854.9416] [ 515] [depth= 1] . ( 103 sec) [ -5848.7736] [ 513] [depth= 1] . ( 104 sec) [ -5844.2807] [ 512] [depth= 2] . ( 105 sec) [ -5844.0683] [ 512] [depth= 1] . ( 107 sec) [ -5844.0464] [ 512] [depth= 1] . ( 112 sec) [ -5843.9813] [ 512] [depth= 1] . ( 112 sec) [ -5843.8187] [ 512] [depth= 1] . ( 112 sec) [ -5843.8039] [ 512] [depth= 1] . ( 114 sec) [ -5843.7888] [ 512] [depth= 1] . ( 116 sec) [ -5843.1350] [ 512] [depth= 1] . ( 116 sec) [ -5842.5610] [ 512] [depth= 1] . ( 120 sec) [ -5842.3305] [ 512] [depth= 2] . ( 120 sec) [ -5842.1627] [ 512] [depth= 2] . ( 120 sec) [ -5841.8969] [ 512] [depth= 1] . ( 120 sec) [ -5841.8809] [ 512] [depth= 2] . ( 120 sec) [ -5841.8298] [ 512] [depth= 1] . ( 122 sec) [ -5841.4085] [ 512] [depth= 1] . ( 122 sec) [ -5841.3910] [ 512] [depth= 1] . ( 127 sec) [ -5839.2863] [ 510] [depth= 1] . ( 131 sec) [ -5837.6801] [ 510] [depth= 5] . ( 136 sec) [ -5836.9725] [ 510] [depth= 1] . ( 136 sec) [ -5834.5589] [ 510] [depth= 2] . ( 137 sec) [ -5831.0691] [ 509] [depth= 1] . ( 137 sec) [ -5830.3719] [ 509] [depth= 1] . ( 139 sec) [ -5829.7456] [ 509] [depth= 2] . ( 144 sec) [ -5829.0950] [ 509] [depth= 2] . ( 144 sec) [ -5825.3656] [ 508] [depth= 2] . ( 145 sec) [ -5824.6950] [ 508] [depth= 1] . ( 145 sec) [ -5824.4269] [ 508] [depth= 1] . ( 147 sec) [ -5824.2963] [ 508] [depth= 1] . ( 149 sec) [ -5824.2545] [ 508] [depth= 1] . ( 150 sec) [ -5822.5161] [ 508] [depth= 1] . ( 150 sec) [ -5822.3249] [ 508] [depth= 1] . ( 151 sec) [ -5822.3077] [ 508] [depth= 1] . ( 154 sec) [ -5811.0309] [Branch lengths ] . ( 156 sec) [ -5810.7118] [GTR parameters ] . ( 156 sec) [ -5810.4587] [Alpha ][ 1.204117] . ( 166 sec) [ -5810.3495] [ 508] [depth= 2] . ( 169 sec) [ -5810.3213] [ 508] [depth= 2] . ( 170 sec) [ -5810.3024] [ 508] [depth= 1] . ( 171 sec) [ -5810.2764] [ 508] [depth= 1] . ( 200 sec) [ -5810.2647] [ 508] [depth= 1] . ( 227 sec) [ -5809.8864] [Branch lengths ] . ( 229 sec) [ -5809.8704] [GTR parameters ] . ( 229 sec) [ -5809.8703] [Alpha ][ 1.207420] . ( 259 sec) [ -5809.8574] [ 508] [depth= 1] . ( 336 sec) [ -5809.6359] [Branch lengths ] . ( 336 sec) [ -5809.6359] [GTR parameters ] . ( 337 sec) [ -5809.6359] [Alpha ][ 1.207420] . ( 337 sec) [ -5809.6359] [Topology ] . ( 339 sec) [ -5809.6325] [Topology ] . ( 341 sec) [ -5809.6319] [Topology ] . ( 342 sec) [ -5809.6319] [GTR parameters ] . ( 342 sec) [ -5809.6319] [Alpha ][ 1.207420] . ( 342 sec) [ -5809.6319] [Topology ] . ( 344 sec) [ -5809.6318] [Topology ] . ( 345 sec) [ -5809.6318] [GTR parameters ] . ( 345 sec) [ -5809.6318] [Alpha ][ 1.207420] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5823.947839 . Log likelihood obtained after SPR moves : -5809.631777 . Log likelihood of the current tree: -5809.631777. . Printing the most likely tree in file 'nucleic_M2770_86x1628_2006.phy_phyml_tree.txt'... . Best log likelihood : -5807.936714 . Time used 0h6m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2139.19user 0.00system 36:19.11elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps