.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2921_54x966_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... . 397 patterns found. (out of a total of 966 sites) . 643 sites without polymorphism (66.56%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16247.4795] [GTR parameters ] . ( 0 sec) [ -15840.0807] [Alpha ][ 0.500960] . ( 0 sec) [ -15763.5555] [ 2281] [depth= 9] . ( 0 sec) [ -15627.8238] [ 2271] [depth= 1] . ( 0 sec) [ -14475.5810] [ 2265] [depth= 1] . ( 1 sec) [ -14418.9631] [ 2262] [depth= 7] . ( 1 sec) [ -14351.5022] [ 2250] [depth= 1] . ( 1 sec) [ -14322.7690] [ 2248] [depth= 4] . ( 1 sec) [ -13991.0441] [ 2249] [depth= 1] . ( 1 sec) [ -13989.8460] [ 2242] [depth= 6] . ( 1 sec) [ -13858.1251] [ 2229] [depth= 3] . ( 1 sec) [ -13851.3327] [ 2229] [depth= 3] . ( 1 sec) [ -13768.8658] [ 2217] [depth= 3] . ( 1 sec) [ -13722.6929] [ 2198] [depth= 5] . ( 1 sec) [ -13710.8139] [ 2199] [depth= 5] . ( 1 sec) [ -13264.3435] [ 2182] [depth= 4] . ( 1 sec) [ -13198.0245] [ 2180] [depth= 1] . ( 1 sec) [ -13160.4028] [ 2177] [depth= 1] . ( 1 sec) [ -13082.5139] [ 2171] [depth= 11] . ( 1 sec) [ -12914.8237] [ 2130] [depth= 1] . ( 1 sec) [ -12802.8298] [ 2125] [depth= 4] . ( 1 sec) [ -12773.4434] [ 2125] [depth= 1] . ( 1 sec) [ -12645.0137] [ 2092] [depth= 2] . ( 2 sec) [ -12609.4080] [ 2092] [depth= 1] . ( 2 sec) [ -12555.9847] [ 2078] [depth= 4] . ( 2 sec) [ -12535.3868] [ 2078] [depth= 2] . ( 2 sec) [ -12489.0717] [ 2070] [depth= 2] . ( 2 sec) [ -12410.4092] [ 2048] [depth= 2] . ( 2 sec) [ -12393.5436] [ 2049] [depth= 5] . ( 2 sec) [ -12268.4821] [ 2041] [depth= 17] . ( 2 sec) [ -12180.8736] [ 2016] [depth= 12] . ( 2 sec) [ -12171.0604] [ 2016] [depth= 16] . ( 2 sec) [ -12064.5333] [ 1995] [depth= 15] . ( 2 sec) [ -11933.4771] [ 1994] [depth= 15] . ( 2 sec) [ -11438.0467] [ 1959] [depth= 16] . ( 2 sec) [ -11253.9300] [ 1954] [depth= 9] . ( 2 sec) [ -11099.8735] [ 1912] [depth= 6] . ( 2 sec) [ -11061.4571] [ 1903] [depth= 8] . ( 2 sec) [ -10788.6603] [ 1855] [depth= 11] . ( 2 sec) [ -10760.9944] [ 1836] [depth= 11] . ( 2 sec) [ -10743.2084] [ 1839] [depth= 1] . ( 3 sec) [ -10737.2489] [ 1831] [depth= 1] . ( 3 sec) [ -10718.4275] [ 1823] [depth= 1] . ( 3 sec) [ -10641.7394] [ 1809] [depth= 3] . ( 3 sec) [ -10542.3934] [ 1805] [depth= 1] . ( 3 sec) [ -10418.1834] [ 1769] [depth= 8] . ( 3 sec) [ -10374.5040] [ 1768] [depth= 2] . ( 3 sec) [ -10275.2135] [ 1765] [depth= 4] . ( 3 sec) [ -10219.2713] [ 1741] [depth= 5] . ( 3 sec) [ -10027.0680] [ 1691] [depth= 8] . ( 3 sec) [ -9891.5579] [ 1662] [depth= 12] . ( 3 sec) [ -9887.2705] [ 1659] [depth= 1] . ( 3 sec) [ -9812.9137] [ 1660] [depth= 1] . ( 3 sec) [ -9758.4019] [ 1662] [depth= 2] . ( 3 sec) [ -9634.3105] [ 1650] [depth= 9] . ( 3 sec) [ -9540.5644] [ 1616] [depth= 1] . ( 4 sec) [ -9488.1185] [ 1600] [depth= 3] . ( 4 sec) [ -9479.8145] [ 1599] [depth= 1] . ( 4 sec) [ -9396.7891] [ 1578] [depth= 1] . ( 4 sec) [ -9367.7725] [ 1574] [depth= 7] . ( 4 sec) [ -9322.3867] [ 1567] [depth= 3] . ( 4 sec) [ -9321.9208] [ 1568] [depth= 11] . ( 4 sec) [ -9223.6710] [ 1539] [depth= 16] . ( 4 sec) [ -9221.8910] [ 1542] [depth= 1] . ( 4 sec) [ -9218.5658] [ 1548] [depth= 1] . ( 4 sec) [ -9145.8886] [ 1523] [depth= 3] . ( 4 sec) [ -9128.3179] [ 1518] [depth= 1] . ( 4 sec) [ -9075.6909] [ 1507] [depth= 15] . ( 4 sec) [ -9060.3070] [ 1503] [depth= 5] . ( 5 sec) [ -9025.0187] [ 1493] [depth= 1] . ( 5 sec) [ -9008.4557] [ 1492] [depth= 1] . ( 5 sec) [ -8933.8711] [ 1495] [depth= 1] . ( 5 sec) [ -8931.7392] [ 1495] [depth= 1] . ( 5 sec) [ -8919.9154] [ 1492] [depth= 1] . ( 5 sec) [ -8906.8749] [ 1486] [depth= 3] . ( 5 sec) [ -8886.8223] [ 1482] [depth= 1] . ( 5 sec) [ -8879.6613] [ 1487] [depth= 9] . ( 5 sec) [ -8838.3211] [ 1482] [depth= 2] . ( 5 sec) [ -8687.4726] [ 1476] [depth= 3] . ( 5 sec) [ -8611.4121] [ 1446] [depth= 1] . ( 5 sec) [ -8599.6071] [ 1442] [depth= 6] . ( 5 sec) [ -8596.0867] [ 1441] [depth= 3] . ( 5 sec) [ -8555.7367] [ 1427] [depth= 1] . ( 5 sec) [ -8553.2288] [ 1425] [depth= 2] . ( 5 sec) [ -8516.8055] [ 1412] [depth= 7] . ( 6 sec) [ -8452.2649] [ 1393] [depth= 1] . ( 6 sec) [ -8336.6273] [ 1381] [depth= 7] . ( 6 sec) [ -8298.4921] [ 1368] [depth= 7] . ( 6 sec) [ -8256.1229] [ 1359] [depth= 6] . ( 6 sec) [ -8013.8377] [ 1319] [depth= 2] . ( 6 sec) [ -8012.2846] [ 1316] [depth= 1] . ( 6 sec) [ -7943.3393] [ 1301] [depth= 4] . ( 6 sec) [ -7940.3854] [ 1299] [depth= 1] . ( 6 sec) [ -7884.2380] [ 1302] [depth= 2] . ( 6 sec) [ -7851.7890] [ 1294] [depth= 2] . ( 6 sec) [ -7829.1255] [ 1288] [depth= 1] . ( 6 sec) [ -7823.8451] [ 1290] [depth= 3] . ( 6 sec) [ -7802.0922] [ 1289] [depth= 1] . ( 7 sec) [ -7771.7439] [ 1278] [depth= 6] . ( 7 sec) [ -7757.1790] [ 1277] [depth= 1] . ( 7 sec) [ -7749.4536] [ 1274] [depth= 2] . ( 7 sec) [ -7735.4881] [ 1276] [depth= 1] . ( 7 sec) [ -7716.7621] [ 1269] [depth= 5] . ( 7 sec) [ -7609.6998] [ 1245] [depth= 15] . ( 7 sec) [ -7573.0157] [ 1235] [depth= 3] . ( 7 sec) [ -7520.8604] [ 1226] [depth= 4] . ( 7 sec) [ -7520.2949] [ 1220] [depth= 3] . ( 7 sec) [ -7504.1667] [ 1220] [depth= 1] . ( 7 sec) [ -7483.0796] [ 1201] [depth= 1] . ( 7 sec) [ -7444.7354] [ 1188] [depth= 1] . ( 7 sec) [ -7307.6303] [ 1155] [depth= 8] . ( 7 sec) [ -7281.6269] [ 1159] [depth= 2] . ( 7 sec) [ -7278.0210] [ 1173] [depth= 2] . ( 7 sec) [ -7235.1123] [ 1171] [depth= 8] . ( 8 sec) [ -7222.7579] [ 1171] [depth= 1] . ( 8 sec) [ -7222.4751] [ 1171] [depth= 1] . ( 8 sec) [ -7212.7813] [ 1162] [depth= 3] . ( 8 sec) [ -7203.1675] [ 1155] [depth= 2] . ( 8 sec) [ -7193.2408] [ 1156] [depth= 1] . ( 8 sec) [ -7182.3714] [ 1153] [depth= 1] . ( 8 sec) [ -7172.1396] [ 1148] [depth= 2] . ( 8 sec) [ -7141.0735] [ 1150] [depth= 1] . ( 8 sec) [ -7066.9494] [Branch lengths ] . ( 11 sec) [ -6863.7281] [GTR parameters ] . ( 11 sec) [ -6782.7018] [Alpha ][ 0.250961] . ( 11 sec) [ -6779.4910] [ 1148] [depth= 1] . ( 11 sec) [ -6776.2089] [ 1151] [depth= 3] . ( 12 sec) [ -6767.7412] [ 1146] [depth= 1] . ( 12 sec) [ -6759.1015] [ 1144] [depth= 2] . ( 12 sec) [ -6751.0993] [ 1130] [depth= 5] . ( 12 sec) [ -6748.9463] [ 1135] [depth= 1] . ( 12 sec) [ -6728.1479] [ 1119] [depth= 1] . ( 12 sec) [ -6673.1757] [ 1098] [depth= 1] . ( 13 sec) [ -6603.8177] [ 1061] [depth= 10] . ( 13 sec) [ -6602.7247] [ 1061] [depth= 1] . ( 13 sec) [ -6602.6549] [ 1062] [depth= 1] . ( 13 sec) [ -6598.3391] [ 1052] [depth= 4] . ( 13 sec) [ -6583.7091] [ 1050] [depth= 2] . ( 14 sec) [ -6582.7487] [ 1048] [depth= 1] . ( 14 sec) [ -6575.8774] [ 1044] [depth= 1] . ( 14 sec) [ -6547.5387] [ 1037] [depth= 5] . ( 14 sec) [ -6543.7491] [ 1035] [depth= 1] . ( 14 sec) [ -6537.6168] [ 1032] [depth= 1] . ( 14 sec) [ -6529.0976] [ 1025] [depth= 1] . ( 14 sec) [ -6526.7968] [ 1022] [depth= 1] . ( 15 sec) [ -6521.3142] [ 1024] [depth= 2] . ( 15 sec) [ -6519.7431] [ 1024] [depth= 1] . ( 16 sec) [ -6517.5191] [ 1028] [depth= 1] . ( 16 sec) [ -6514.5357] [ 1029] [depth= 1] . ( 16 sec) [ -6514.5173] [ 1029] [depth= 1] . ( 17 sec) [ -6512.9317] [ 1029] [depth= 1] . ( 17 sec) [ -6512.0507] [ 1029] [depth= 1] . ( 17 sec) [ -6508.8224] [ 1028] [depth= 1] . ( 17 sec) [ -6507.1993] [ 1032] [depth= 2] . ( 18 sec) [ -6477.4471] [ 1019] [depth= 1] . ( 18 sec) [ -6477.2466] [ 1019] [depth= 1] . ( 18 sec) [ -6469.6512] [ 1016] [depth= 5] . ( 19 sec) [ -6468.6281] [ 1015] [depth= 2] . ( 19 sec) [ -6465.7724] [ 1015] [depth= 1] . ( 19 sec) [ -6464.1779] [ 1015] [depth= 1] . ( 19 sec) [ -6463.0423] [ 1015] [depth= 1] . ( 19 sec) [ -6461.6940] [ 1015] [depth= 1] . ( 20 sec) [ -6461.6150] [ 1015] [depth= 1] . ( 20 sec) [ -6459.7291] [ 1013] [depth= 1] . ( 21 sec) [ -6443.4870] [Branch lengths ] . ( 22 sec) [ -6442.5184] [GTR parameters ] . ( 23 sec) [ -6441.3882] [Alpha ][ 0.227124] . ( 24 sec) [ -6441.3581] [ 1013] [depth= 1] . ( 25 sec) [ -6441.3231] [ 1013] [depth= 1] . ( 28 sec) [ -6441.2257] [ 1012] [depth= 1] . ( 31 sec) [ -6439.5715] [Branch lengths ] . ( 32 sec) [ -6439.5712] [GTR parameters ] . ( 32 sec) [ -6439.5393] [Alpha ][ 0.223399] . ( 33 sec) [ -6439.5158] [ 1012] [depth= 1] . ( 41 sec) [ -6438.8509] [Branch lengths ] . ( 42 sec) [ -6438.7929] [GTR parameters ] . ( 42 sec) [ -6438.7830] [Alpha ][ 0.221193] . ( 80 sec) [ -6438.6937] [Branch lengths ] . ( 80 sec) [ -6438.6937] [Topology ] . ( 81 sec) [ -6438.6866] [Topology ] . ( 82 sec) [ -6438.6846] [Topology ] . ( 83 sec) [ -6438.6839] [Topology ] . ( 85 sec) [ -6438.6626] [GTR parameters ] . ( 85 sec) [ -6438.6583] [Alpha ][ 0.219743] . ( 85 sec) [ -6438.6583] [Topology ] . ( 86 sec) [ -6438.6566] [Topology ] . ( 87 sec) [ -6438.6559] [Topology ] . ( 87 sec) [ -6438.6558] [GTR parameters ] . ( 87 sec) [ -6438.6558] [Alpha ][ 0.219743] . ( 87 sec) [ -6438.6558] [Topology ] . ( 88 sec) [ -6438.6556] [Topology ] . ( 88 sec) [ -6438.6556] [GTR parameters ] . ( 88 sec) [ -6438.6556] [Alpha ][ 0.219523] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -6438.5546] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6438.554550. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -15603.1189] [GTR parameters ] . ( 2 sec) [ -15226.7392] [Alpha ][ 0.500960] . ( 2 sec) [ -15195.1014] [ 2249] [depth= 1] . ( 2 sec) [ -15041.3698] [ 2227] [depth= 11] . ( 2 sec) [ -14877.2517] [ 2219] [depth= 4] . ( 2 sec) [ -14809.4248] [ 2188] [depth= 1] . ( 2 sec) [ -14682.5153] [ 2174] [depth= 5] . ( 2 sec) [ -14671.7538] [ 2175] [depth= 3] . ( 2 sec) [ -14542.4469] [ 2168] [depth= 8] . ( 2 sec) [ -14403.2320] [ 2124] [depth= 5] . ( 2 sec) [ -14166.2338] [ 2117] [depth= 9] . ( 3 sec) [ -14122.2899] [ 2106] [depth= 8] . ( 3 sec) [ -14021.1195] [ 2100] [depth= 1] . ( 3 sec) [ -13941.2504] [ 2057] [depth= 8] . ( 3 sec) [ -13877.4035] [ 2051] [depth= 6] . ( 3 sec) [ -13760.2232] [ 2043] [depth= 13] . ( 3 sec) [ -13425.3873] [ 2038] [depth= 4] . ( 3 sec) [ -13231.8955] [ 2004] [depth= 8] . ( 3 sec) [ -13134.1691] [ 1992] [depth= 5] . ( 3 sec) [ -13113.0310] [ 1987] [depth= 4] . ( 3 sec) [ -13064.2595] [ 1987] [depth= 1] . ( 3 sec) [ -12954.9211] [ 1957] [depth= 11] . ( 3 sec) [ -12940.5393] [ 1952] [depth= 2] . ( 3 sec) [ -11934.1078] [ 1923] [depth= 8] . ( 3 sec) [ -11915.2146] [ 1906] [depth= 6] . ( 3 sec) [ -11768.1004] [ 1906] [depth= 2] . ( 3 sec) [ -11620.5389] [ 1895] [depth= 9] . ( 3 sec) [ -11612.1688] [ 1902] [depth= 6] . ( 3 sec) [ -11542.0549] [ 1884] [depth= 5] . ( 4 sec) [ -11226.8883] [ 1825] [depth= 8] . ( 4 sec) [ -11219.1060] [ 1817] [depth= 1] . ( 4 sec) [ -10988.2263] [ 1806] [depth= 5] . ( 4 sec) [ -10982.4129] [ 1800] [depth= 9] . ( 4 sec) [ -10717.4789] [ 1746] [depth= 10] . ( 4 sec) [ -10588.8473] [ 1738] [depth= 7] . ( 4 sec) [ -10571.9947] [ 1734] [depth= 6] . ( 4 sec) [ -10516.7925] [ 1738] [depth= 1] . ( 4 sec) [ -10477.2959] [ 1737] [depth= 1] . ( 4 sec) [ -10253.7323] [ 1691] [depth= 7] . ( 4 sec) [ -10235.1932] [ 1687] [depth= 1] . ( 4 sec) [ -10112.3191] [ 1655] [depth= 5] . ( 4 sec) [ -9927.1678] [ 1615] [depth= 3] . ( 4 sec) [ -9915.7550] [ 1611] [depth= 1] . ( 4 sec) [ -9690.3493] [ 1614] [depth= 1] . ( 4 sec) [ -9631.4855] [ 1630] [depth= 1] . ( 4 sec) [ -9599.7551] [ 1617] [depth= 9] . ( 5 sec) [ -9595.9521] [ 1610] [depth= 1] . ( 5 sec) [ -9574.3278] [ 1589] [depth= 1] . ( 5 sec) [ -9461.0082] [ 1577] [depth= 7] . ( 5 sec) [ -9337.8975] [ 1571] [depth= 4] . ( 5 sec) [ -9295.8699] [ 1564] [depth= 2] . ( 5 sec) [ -9260.5572] [ 1556] [depth= 1] . ( 5 sec) [ -9234.5711] [ 1545] [depth= 13] . ( 5 sec) [ -9185.4398] [ 1538] [depth= 7] . ( 5 sec) [ -9168.4382] [ 1529] [depth= 3] . ( 5 sec) [ -9163.0696] [ 1530] [depth= 2] . ( 5 sec) [ -9046.0526] [ 1529] [depth= 1] . ( 5 sec) [ -8951.8053] [ 1495] [depth= 13] . ( 5 sec) [ -8911.0691] [ 1483] [depth= 1] . ( 5 sec) [ -8838.9812] [ 1447] [depth= 14] . ( 6 sec) [ -8836.2196] [ 1446] [depth= 1] . ( 6 sec) [ -8637.5393] [ 1416] [depth= 12] . ( 6 sec) [ -8340.6135] [ 1361] [depth= 8] . ( 6 sec) [ -8295.9606] [ 1338] [depth= 1] . ( 6 sec) [ -8175.2803] [ 1332] [depth= 10] . ( 6 sec) [ -8099.9372] [ 1313] [depth= 7] . ( 6 sec) [ -7886.8152] [ 1281] [depth= 2] . ( 6 sec) [ -7883.6939] [ 1280] [depth= 1] . ( 6 sec) [ -7867.0841] [ 1274] [depth= 1] . ( 6 sec) [ -7857.5490] [ 1275] [depth= 1] . ( 6 sec) [ -7803.7757] [ 1245] [depth= 4] . ( 6 sec) [ -7771.0629] [ 1240] [depth= 1] . ( 6 sec) [ -7766.1173] [ 1238] [depth= 2] . ( 7 sec) [ -7735.7315] [ 1238] [depth= 1] . ( 7 sec) [ -7734.1636] [ 1239] [depth= 1] . ( 7 sec) [ -7643.8283] [ 1209] [depth= 2] . ( 7 sec) [ -7590.6874] [ 1209] [depth= 1] . ( 7 sec) [ -7590.3309] [ 1209] [depth= 1] . ( 7 sec) [ -7563.8985] [ 1201] [depth= 1] . ( 7 sec) [ -7519.8231] [ 1195] [depth= 7] . ( 7 sec) [ -7514.1167] [ 1194] [depth= 1] . ( 7 sec) [ -7486.5418] [ 1178] [depth= 1] . ( 7 sec) [ -7483.6988] [ 1177] [depth= 4] . ( 7 sec) [ -7432.6166] [ 1177] [depth= 4] . ( 7 sec) [ -7411.6555] [ 1165] [depth= 5] . ( 7 sec) [ -7327.8937] [ 1178] [depth= 5] . ( 7 sec) [ -7326.6721] [ 1180] [depth= 1] . ( 7 sec) [ -7319.1263] [ 1173] [depth= 4] . ( 7 sec) [ -7316.8445] [ 1170] [depth= 4] . ( 8 sec) [ -7315.7462] [ 1170] [depth= 1] . ( 8 sec) [ -7271.3563] [ 1151] [depth= 1] . ( 8 sec) [ -7253.5971] [ 1145] [depth= 2] . ( 8 sec) [ -7249.0809] [ 1143] [depth= 1] . ( 8 sec) [ -7242.9589] [ 1141] [depth= 2] . ( 8 sec) [ -7234.3358] [ 1138] [depth= 3] . ( 8 sec) [ -7227.0198] [ 1138] [depth= 1] . ( 8 sec) [ -7226.3089] [ 1138] [depth= 1] . ( 8 sec) [ -7209.2579] [ 1139] [depth= 1] . ( 8 sec) [ -7202.3108] [ 1138] [depth= 1] . ( 8 sec) [ -7186.1789] [ 1138] [depth= 1] . ( 8 sec) [ -7183.6109] [ 1141] [depth= 2] . ( 8 sec) [ -7181.3905] [ 1140] [depth= 2] . ( 9 sec) [ -7174.1278] [ 1139] [depth= 1] . ( 9 sec) [ -7169.6529] [ 1139] [depth= 4] . ( 9 sec) [ -7164.1777] [ 1139] [depth= 1] . ( 9 sec) [ -7150.6164] [ 1145] [depth= 2] . ( 9 sec) [ -7139.4899] [ 1145] [depth= 5] . ( 9 sec) [ -7132.1698] [ 1143] [depth= 1] . ( 9 sec) [ -7122.6821] [ 1133] [depth= 6] . ( 9 sec) [ -7083.6575] [ 1118] [depth= 4] . ( 9 sec) [ -7083.3023] [ 1120] [depth= 2] . ( 9 sec) [ -7060.9117] [ 1105] [depth= 3] . ( 9 sec) [ -7037.1522] [ 1099] [depth= 2] . ( 9 sec) [ -6991.3928] [ 1087] [depth= 1] . ( 9 sec) [ -6988.5515] [ 1088] [depth= 6] . ( 9 sec) [ -6977.3584] [ 1084] [depth= 1] . ( 10 sec) [ -6976.6275] [ 1084] [depth= 1] . ( 10 sec) [ -6973.9233] [ 1089] [depth= 1] . ( 10 sec) [ -6964.3315] [ 1084] [depth= 1] . ( 10 sec) [ -6946.6140] [ 1087] [depth= 1] . ( 10 sec) [ -6887.7069] [Branch lengths ] . ( 13 sec) [ -6747.8407] [GTR parameters ] . ( 13 sec) [ -6675.5635] [Alpha ][ 0.250961] . ( 13 sec) [ -6674.1416] [ 1085] [depth= 1] . ( 13 sec) [ -6593.4786] [ 1042] [depth= 7] . ( 13 sec) [ -6592.9790] [ 1042] [depth= 2] . ( 13 sec) [ -6578.6095] [ 1038] [depth= 2] . ( 13 sec) [ -6576.0359] [ 1037] [depth= 1] . ( 14 sec) [ -6560.7562] [ 1037] [depth= 1] . ( 14 sec) [ -6538.3647] [ 1038] [depth= 1] . ( 14 sec) [ -6537.4178] [ 1035] [depth= 1] . ( 14 sec) [ -6531.7646] [ 1031] [depth= 2] . ( 14 sec) [ -6523.5365] [ 1030] [depth= 1] . ( 14 sec) [ -6519.4925] [ 1030] [depth= 2] . ( 14 sec) [ -6518.9895] [ 1033] [depth= 1] . ( 15 sec) [ -6512.0060] [ 1029] [depth= 1] . ( 15 sec) [ -6510.7850] [ 1029] [depth= 1] . ( 15 sec) [ -6507.4709] [ 1027] [depth= 1] . ( 15 sec) [ -6504.6993] [ 1028] [depth= 5] . ( 15 sec) [ -6504.2728] [ 1030] [depth= 1] . ( 15 sec) [ -6503.1724] [ 1029] [depth= 1] . ( 15 sec) [ -6502.5387] [ 1029] [depth= 1] . ( 16 sec) [ -6484.2845] [ 1023] [depth= 2] . ( 17 sec) [ -6483.6545] [ 1022] [depth= 1] . ( 17 sec) [ -6483.6439] [ 1025] [depth= 1] . ( 17 sec) [ -6481.9169] [ 1024] [depth= 1] . ( 19 sec) [ -6479.4191] [ 1025] [depth= 1] . ( 20 sec) [ -6479.3971] [ 1027] [depth= 1] . ( 20 sec) [ -6479.3783] [ 1027] [depth= 1] . ( 20 sec) [ -6476.6410] [ 1028] [depth= 4] . ( 20 sec) [ -6468.8834] [ 1026] [depth= 3] . ( 20 sec) [ -6461.4862] [ 1022] [depth= 1] . ( 20 sec) [ -6461.1382] [ 1020] [depth= 1] . ( 20 sec) [ -6456.6954] [ 1019] [depth= 1] . ( 23 sec) [ -6447.9550] [Branch lengths ] . ( 25 sec) [ -6446.8925] [GTR parameters ] . ( 25 sec) [ -6445.4707] [Alpha ][ 0.224137] . ( 27 sec) [ -6442.1010] [ 1018] [depth= 3] . ( 30 sec) [ -6442.0848] [ 1018] [depth= 1] . ( 35 sec) [ -6441.1051] [Branch lengths ] . ( 36 sec) [ -6441.0509] [GTR parameters ] . ( 36 sec) [ -6441.0402] [Alpha ][ 0.221868] . ( 37 sec) [ -6440.1297] [ 1017] [depth= 2] . ( 47 sec) [ -6439.7386] [Branch lengths ] . ( 49 sec) [ -6439.7288] [GTR parameters ] . ( 49 sec) [ -6439.7276] [Alpha ][ 0.221108] . ( 59 sec) [ -6439.7137] [Branch lengths ] . ( 97 sec) [ -6439.7125] [Branch lengths ] . ( 97 sec) [ -6439.7125] [Topology ] . ( 98 sec) [ -6439.7124] [Topology ] . ( 98 sec) [ -6439.7124] [GTR parameters ] . ( 98 sec) [ -6439.7120] [Alpha ][ 0.220636] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6439.711967. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16327.3155] [GTR parameters ] . ( 0 sec) [ -15914.2631] [Alpha ][ 0.500960] . ( 0 sec) [ -15772.0249] [ 2284] [depth= 5] . ( 0 sec) [ -15664.5504] [ 2270] [depth= 8] . ( 0 sec) [ -15274.5747] [ 2250] [depth= 4] . ( 1 sec) [ -15273.0589] [ 2249] [depth= 1] . ( 1 sec) [ -15148.2962] [ 2245] [depth= 1] . ( 1 sec) [ -15137.0173] [ 2243] [depth= 2] . ( 1 sec) [ -14936.0414] [ 2228] [depth= 8] . ( 1 sec) [ -14866.8647] [ 2228] [depth= 3] . ( 1 sec) [ -14743.3468] [ 2220] [depth= 3] . ( 1 sec) [ -14580.7181] [ 2217] [depth= 15] . ( 1 sec) [ -14553.1038] [ 2210] [depth= 1] . ( 1 sec) [ -14408.2406] [ 2209] [depth= 2] . ( 1 sec) [ -14301.3769] [ 2195] [depth= 14] . ( 1 sec) [ -13968.0120] [ 2153] [depth= 12] . ( 1 sec) [ -13817.7385] [ 2127] [depth= 4] . ( 1 sec) [ -13799.0312] [ 2122] [depth= 2] . ( 1 sec) [ -13564.0005] [ 2098] [depth= 6] . ( 1 sec) [ -13507.2737] [ 2098] [depth= 17] . ( 1 sec) [ -13357.4354] [ 2070] [depth= 6] . ( 1 sec) [ -13323.0133] [ 2067] [depth= 4] . ( 1 sec) [ -13173.3389] [ 2054] [depth= 2] . ( 2 sec) [ -13150.0276] [ 2057] [depth= 21] . ( 2 sec) [ -12871.4957] [ 2026] [depth= 9] . ( 2 sec) [ -12848.0781] [ 2027] [depth= 3] . ( 2 sec) [ -12737.0761] [ 2003] [depth= 12] . ( 2 sec) [ -12561.2047] [ 1994] [depth= 11] . ( 2 sec) [ -12460.4575] [ 1954] [depth= 12] . ( 2 sec) [ -12404.1347] [ 1948] [depth= 3] . ( 2 sec) [ -12283.4757] [ 1916] [depth= 1] . ( 2 sec) [ -12228.0616] [ 1894] [depth= 7] . ( 2 sec) [ -12003.1368] [ 1823] [depth= 7] . ( 2 sec) [ -11942.0820] [ 1822] [depth= 1] . ( 2 sec) [ -11572.6004] [ 1821] [depth= 13] . ( 2 sec) [ -11564.6365] [ 1816] [depth= 1] . ( 2 sec) [ -11553.5055] [ 1811] [depth= 2] . ( 2 sec) [ -11461.7499] [ 1774] [depth= 1] . ( 2 sec) [ -11421.8175] [ 1779] [depth= 2] . ( 2 sec) [ -11396.5544] [ 1782] [depth= 16] . ( 3 sec) [ -11384.2701] [ 1781] [depth= 1] . ( 3 sec) [ -11339.9744] [ 1772] [depth= 15] . ( 3 sec) [ -11203.6853] [ 1755] [depth= 8] . ( 3 sec) [ -11196.4975] [ 1757] [depth= 6] . ( 3 sec) [ -11001.6636] [ 1703] [depth= 11] . ( 3 sec) [ -10988.7925] [ 1694] [depth= 17] . ( 3 sec) [ -10965.6391] [ 1683] [depth= 14] . ( 3 sec) [ -10612.1602] [ 1649] [depth= 1] . ( 3 sec) [ -10528.4678] [ 1644] [depth= 3] . ( 3 sec) [ -10415.6397] [ 1612] [depth= 2] . ( 3 sec) [ -10381.8613] [ 1627] [depth= 8] . ( 3 sec) [ -10236.5334] [ 1593] [depth= 8] . ( 3 sec) [ -10228.5220] [ 1593] [depth= 1] . ( 3 sec) [ -10036.6774] [ 1571] [depth= 13] . ( 3 sec) [ -9956.0334] [ 1550] [depth= 12] . ( 3 sec) [ -9943.1604] [ 1553] [depth= 1] . ( 3 sec) [ -9906.7856] [ 1549] [depth= 5] . ( 4 sec) [ -9812.7261] [ 1511] [depth= 9] . ( 4 sec) [ -9787.4908] [ 1505] [depth= 1] . ( 4 sec) [ -9780.1001] [ 1508] [depth= 1] . ( 4 sec) [ -9774.5448] [ 1503] [depth= 3] . ( 4 sec) [ -9749.1809] [ 1498] [depth= 2] . ( 4 sec) [ -9743.8932] [ 1498] [depth= 1] . ( 4 sec) [ -9698.6913] [ 1470] [depth= 1] . ( 4 sec) [ -9656.4609] [ 1467] [depth= 2] . ( 4 sec) [ -8566.1857] [ 1444] [depth= 2] . ( 4 sec) [ -8525.3293] [ 1441] [depth= 3] . ( 4 sec) [ -8421.9823] [ 1414] [depth= 9] . ( 4 sec) [ -8394.4927] [ 1413] [depth= 1] . ( 4 sec) [ -8337.4532] [ 1392] [depth= 11] . ( 4 sec) [ -8279.8843] [ 1390] [depth= 1] . ( 4 sec) [ -8279.5454] [ 1391] [depth= 1] . ( 4 sec) [ -8218.3953] [ 1384] [depth= 1] . ( 5 sec) [ -8201.5818] [ 1379] [depth= 5] . ( 5 sec) [ -8186.6432] [ 1380] [depth= 1] . ( 5 sec) [ -8177.2243] [ 1381] [depth= 5] . ( 5 sec) [ -8176.7494] [ 1382] [depth= 1] . ( 5 sec) [ -8139.8586] [ 1382] [depth= 10] . ( 5 sec) [ -7878.7029] [ 1332] [depth= 9] . ( 5 sec) [ -7875.8674] [ 1331] [depth= 1] . ( 5 sec) [ -7874.0153] [ 1329] [depth= 4] . ( 5 sec) [ -7830.0400] [ 1314] [depth= 3] . ( 5 sec) [ -7827.4416] [ 1316] [depth= 3] . ( 5 sec) [ -7820.5348] [ 1314] [depth= 1] . ( 5 sec) [ -7813.5031] [ 1315] [depth= 1] . ( 5 sec) [ -7811.4775] [ 1315] [depth= 1] . ( 6 sec) [ -7761.1479] [ 1307] [depth= 1] . ( 6 sec) [ -7716.9639] [ 1285] [depth= 9] . ( 6 sec) [ -7716.4703] [ 1284] [depth= 2] . ( 6 sec) [ -7710.5233] [ 1279] [depth= 1] . ( 6 sec) [ -7710.4574] [ 1273] [depth= 3] . ( 6 sec) [ -7708.0902] [ 1274] [depth= 1] . ( 6 sec) [ -7703.7959] [ 1273] [depth= 1] . ( 6 sec) [ -7608.2458] [ 1240] [depth= 1] . ( 6 sec) [ -7606.6132] [ 1233] [depth= 1] . ( 7 sec) [ -7587.7834] [ 1232] [depth= 2] . ( 7 sec) [ -7582.9896] [ 1232] [depth= 1] . ( 7 sec) [ -7482.6470] [ 1220] [depth= 7] . ( 7 sec) [ -7468.3679] [ 1220] [depth= 1] . ( 7 sec) [ -7464.3437] [ 1220] [depth= 1] . ( 7 sec) [ -7447.9438] [ 1219] [depth= 8] . ( 7 sec) [ -7429.7019] [ 1211] [depth= 2] . ( 7 sec) [ -7425.5183] [ 1212] [depth= 1] . ( 7 sec) [ -7423.8877] [ 1210] [depth= 3] . ( 7 sec) [ -7414.9458] [ 1209] [depth= 1] . ( 7 sec) [ -7365.6817] [ 1189] [depth= 3] . ( 7 sec) [ -7296.4848] [ 1165] [depth= 2] . ( 7 sec) [ -7193.3320] [ 1139] [depth= 4] . ( 8 sec) [ -7185.2890] [ 1138] [depth= 2] . ( 8 sec) [ -7176.5906] [ 1101] [depth= 2] . ( 8 sec) [ -7175.6880] [ 1101] [depth= 1] . ( 8 sec) [ -7170.8100] [ 1100] [depth= 1] . ( 8 sec) [ -7169.9475] [ 1100] [depth= 1] . ( 8 sec) [ -7137.3232] [ 1111] [depth= 6] . ( 8 sec) [ -7117.0919] [ 1104] [depth= 2] . ( 8 sec) [ -7115.4640] [ 1105] [depth= 3] . ( 8 sec) [ -6940.0788] [ 1076] [depth= 5] . ( 8 sec) [ -6916.9527] [ 1071] [depth= 2] . ( 9 sec) [ -6823.1790] [Branch lengths ] . ( 12 sec) [ -6655.0924] [GTR parameters ] . ( 12 sec) [ -6585.2965] [Alpha ][ 0.250961] . ( 13 sec) [ -6579.2816] [ 1066] [depth= 2] . ( 13 sec) [ -6577.6290] [ 1069] [depth= 1] . ( 13 sec) [ -6573.9287] [ 1067] [depth= 1] . ( 13 sec) [ -6557.7695] [ 1060] [depth= 6] . ( 13 sec) [ -6544.2532] [ 1051] [depth= 2] . ( 13 sec) [ -6542.2793] [ 1052] [depth= 1] . ( 14 sec) [ -6542.0742] [ 1054] [depth= 2] . ( 14 sec) [ -6528.5427] [ 1045] [depth= 7] . ( 14 sec) [ -6525.6615] [ 1044] [depth= 1] . ( 14 sec) [ -6522.1108] [ 1043] [depth= 1] . ( 15 sec) [ -6518.8935] [ 1040] [depth= 2] . ( 15 sec) [ -6517.8128] [ 1040] [depth= 1] . ( 15 sec) [ -6516.9877] [ 1040] [depth= 1] . ( 15 sec) [ -6515.2593] [ 1041] [depth= 1] . ( 15 sec) [ -6509.6987] [ 1039] [depth= 1] . ( 16 sec) [ -6504.3630] [ 1035] [depth= 2] . ( 16 sec) [ -6495.0820] [ 1031] [depth= 1] . ( 16 sec) [ -6493.9320] [ 1036] [depth= 2] . ( 16 sec) [ -6491.5910] [ 1035] [depth= 3] . ( 17 sec) [ -6489.8141] [ 1034] [depth= 2] . ( 17 sec) [ -6489.3808] [ 1033] [depth= 1] . ( 17 sec) [ -6483.0189] [ 1026] [depth= 5] . ( 18 sec) [ -6468.5712] [ 1017] [depth= 2] . ( 18 sec) [ -6466.7523] [ 1016] [depth= 2] . ( 19 sec) [ -6464.8259] [ 1015] [depth= 2] . ( 19 sec) [ -6464.7813] [ 1015] [depth= 1] . ( 19 sec) [ -6461.8675] [ 1013] [depth= 1] . ( 20 sec) [ -6461.5931] [ 1013] [depth= 1] . ( 21 sec) [ -6448.1711] [Branch lengths ] . ( 23 sec) [ -6446.9277] [GTR parameters ] . ( 23 sec) [ -6445.4487] [Alpha ][ 0.223777] . ( 24 sec) [ -6444.9175] [ 1014] [depth= 2] . ( 25 sec) [ -6444.7939] [ 1012] [depth= 1] . ( 26 sec) [ -6444.4372] [ 1011] [depth= 1] . ( 29 sec) [ -6444.3995] [ 1012] [depth= 1] . ( 30 sec) [ -6444.1728] [ 1011] [depth= 1] . ( 30 sec) [ -6441.9659] [ 1013] [depth= 4] . ( 32 sec) [ -6438.4346] [Branch lengths ] . ( 32 sec) [ -6438.4344] [GTR parameters ] . ( 32 sec) [ -6438.4127] [Alpha ][ 0.220735] . ( 33 sec) [ -6438.2773] [ 1012] [depth= 1] . ( 42 sec) [ -6437.7464] [Branch lengths ] . ( 43 sec) [ -6437.7124] [GTR parameters ] . ( 43 sec) [ -6437.7107] [Alpha ][ 0.219803] . ( 82 sec) [ -6437.6785] [Branch lengths ] . ( 82 sec) [ -6437.6785] [Topology ] . ( 83 sec) [ -6437.6767] [Topology ] . ( 84 sec) [ -6437.6763] [Topology ] . ( 84 sec) [ -6437.6696] [GTR parameters ] . ( 84 sec) [ -6437.6688] [Alpha ][ 0.219169] . ( 84 sec) [ -6437.6688] [Topology ] . ( 85 sec) [ -6437.6684] [Topology ] . ( 86 sec) [ -6437.6667] [GTR parameters ] . ( 86 sec) [ -6437.6667] [Alpha ][ 0.219169] . ( 86 sec) [ -6437.6667] [Topology ] . ( 87 sec) [ -6437.6666] [Topology ] . ( 88 sec) [ -6437.6666] [GTR parameters ] . ( 88 sec) [ -6437.6666] [Alpha ][ 0.219169] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6437.666633. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16835.7015] [GTR parameters ] . ( 1 sec) [ -16417.6851] [Alpha ][ 0.500960] . ( 1 sec) [ -16388.9543] [ 2302] [depth= 7] . ( 1 sec) [ -16308.5472] [ 2287] [depth= 5] . ( 1 sec) [ -15977.3875] [ 2272] [depth= 9] . ( 2 sec) [ -15916.3474] [ 2251] [depth= 1] . ( 2 sec) [ -15835.0325] [ 2229] [depth= 9] . ( 2 sec) [ -15803.5058] [ 2218] [depth= 1] . ( 2 sec) [ -15742.0248] [ 2214] [depth= 7] . ( 2 sec) [ -15730.3729] [ 2209] [depth= 2] . ( 2 sec) [ -15692.0087] [ 2205] [depth= 2] . ( 2 sec) [ -15661.2626] [ 2208] [depth= 1] . ( 2 sec) [ -15620.5245] [ 2201] [depth= 6] . ( 2 sec) [ -15331.9741] [ 2191] [depth= 14] . ( 2 sec) [ -15237.4289] [ 2158] [depth= 2] . ( 2 sec) [ -15211.2410] [ 2154] [depth= 6] . ( 2 sec) [ -14946.2062] [ 2145] [depth= 6] . ( 2 sec) [ -14918.9913] [ 2146] [depth= 1] . ( 2 sec) [ -14701.9066] [ 2130] [depth= 10] . ( 2 sec) [ -14559.7651] [ 2125] [depth= 11] . ( 2 sec) [ -14438.1923] [ 2083] [depth= 14] . ( 3 sec) [ -14314.8219] [ 2076] [depth= 12] . ( 3 sec) [ -14266.5034] [ 2076] [depth= 8] . ( 3 sec) [ -14142.8738] [ 2056] [depth= 9] . ( 3 sec) [ -14050.3727] [ 2042] [depth= 5] . ( 3 sec) [ -14029.3457] [ 2042] [depth= 1] . ( 3 sec) [ -13971.5823] [ 2032] [depth= 7] . ( 3 sec) [ -13556.8523] [ 2006] [depth= 1] . ( 3 sec) [ -13279.7434] [ 1967] [depth= 7] . ( 3 sec) [ -11786.2083] [ 1888] [depth= 9] . ( 3 sec) [ -11642.1047] [ 1888] [depth= 1] . ( 3 sec) [ -11583.1876] [ 1892] [depth= 7] . ( 3 sec) [ -11368.2611] [ 1891] [depth= 2] . ( 3 sec) [ -11136.7749] [ 1864] [depth= 13] . ( 3 sec) [ -11101.6683] [ 1863] [depth= 1] . ( 3 sec) [ -10960.6328] [ 1839] [depth= 6] . ( 3 sec) [ -10585.2684] [ 1800] [depth= 9] . ( 4 sec) [ -10519.0013] [ 1749] [depth= 2] . ( 4 sec) [ -10508.0265] [ 1746] [depth= 2] . ( 4 sec) [ -10440.6515] [ 1738] [depth= 4] . ( 4 sec) [ -10439.5137] [ 1739] [depth= 1] . ( 4 sec) [ -10384.8540] [ 1722] [depth= 7] . ( 4 sec) [ -10126.8628] [ 1721] [depth= 1] . ( 4 sec) [ -10008.3808] [ 1702] [depth= 12] . ( 4 sec) [ -9998.5149] [ 1706] [depth= 1] . ( 4 sec) [ -9848.4525] [ 1668] [depth= 6] . ( 4 sec) [ -9847.0006] [ 1668] [depth= 1] . ( 4 sec) [ -9800.8201] [ 1666] [depth= 5] . ( 4 sec) [ -9673.2574] [ 1624] [depth= 13] . ( 4 sec) [ -9664.6803] [ 1624] [depth= 6] . ( 4 sec) [ -9454.9644] [ 1633] [depth= 10] . ( 4 sec) [ -9380.8215] [ 1590] [depth= 8] . ( 4 sec) [ -9260.0223] [ 1567] [depth= 9] . ( 5 sec) [ -9219.9739] [ 1561] [depth= 2] . ( 5 sec) [ -8650.6450] [ 1559] [depth= 1] . ( 5 sec) [ -8648.8890] [ 1558] [depth= 1] . ( 5 sec) [ -8486.3631] [ 1510] [depth= 13] . ( 5 sec) [ -8453.4127] [ 1513] [depth= 8] . ( 5 sec) [ -8435.7025] [ 1511] [depth= 2] . ( 5 sec) [ -8398.0093] [ 1522] [depth= 1] . ( 5 sec) [ -8358.8981] [ 1506] [depth= 1] . ( 5 sec) [ -8344.1270] [ 1497] [depth= 2] . ( 5 sec) [ -8335.2896] [ 1494] [depth= 1] . ( 5 sec) [ -8301.2975] [ 1486] [depth= 9] . ( 5 sec) [ -8295.8456] [ 1479] [depth= 9] . ( 5 sec) [ -8202.4658] [ 1465] [depth= 9] . ( 5 sec) [ -8080.7423] [ 1428] [depth= 9] . ( 5 sec) [ -8059.1636] [ 1427] [depth= 6] . ( 5 sec) [ -8054.9731] [ 1427] [depth= 1] . ( 5 sec) [ -8053.9226] [ 1428] [depth= 1] . ( 5 sec) [ -7913.3167] [ 1380] [depth= 3] . ( 6 sec) [ -7870.8318] [ 1357] [depth= 5] . ( 6 sec) [ -7849.9177] [ 1347] [depth= 6] . ( 6 sec) [ -7846.9491] [ 1347] [depth= 1] . ( 6 sec) [ -7846.7529] [ 1350] [depth= 6] . ( 6 sec) [ -7844.0708] [ 1351] [depth= 1] . ( 6 sec) [ -7825.6641] [ 1346] [depth= 7] . ( 6 sec) [ -7786.2717] [ 1324] [depth= 6] . ( 6 sec) [ -7728.8429] [ 1318] [depth= 1] . ( 6 sec) [ -7654.7112] [ 1286] [depth= 7] . ( 6 sec) [ -7645.7919] [ 1282] [depth= 4] . ( 6 sec) [ -7546.9130] [ 1279] [depth= 2] . ( 6 sec) [ -7516.8236] [ 1267] [depth= 15] . ( 6 sec) [ -7510.7043] [ 1264] [depth= 1] . ( 6 sec) [ -7500.4355] [ 1263] [depth= 1] . ( 6 sec) [ -7482.5453] [ 1258] [depth= 8] . ( 7 sec) [ -7397.4035] [ 1235] [depth= 5] . ( 7 sec) [ -7396.6170] [ 1239] [depth= 2] . ( 7 sec) [ -7393.8690] [ 1238] [depth= 1] . ( 7 sec) [ -7386.7109] [ 1232] [depth= 10] . ( 7 sec) [ -7372.2232] [ 1233] [depth= 1] . ( 7 sec) [ -7366.6980] [ 1233] [depth= 2] . ( 7 sec) [ -7364.2537] [ 1233] [depth= 1] . ( 7 sec) [ -7359.9988] [ 1227] [depth= 5] . ( 7 sec) [ -7344.9911] [ 1220] [depth= 2] . ( 7 sec) [ -7276.4719] [ 1194] [depth= 1] . ( 7 sec) [ -7255.8080] [ 1190] [depth= 8] . ( 7 sec) [ -7246.6094] [ 1197] [depth= 1] . ( 7 sec) [ -7141.7694] [ 1163] [depth= 5] . ( 7 sec) [ -7058.9291] [ 1139] [depth= 2] . ( 7 sec) [ -7052.9787] [ 1131] [depth= 6] . ( 8 sec) [ -6987.8642] [ 1105] [depth= 5] . ( 8 sec) [ -6987.4975] [ 1103] [depth= 3] . ( 8 sec) [ -6979.1827] [ 1102] [depth= 4] . ( 8 sec) [ -6955.2523] [ 1099] [depth= 2] . ( 8 sec) [ -6951.8600] [ 1100] [depth= 3] . ( 8 sec) [ -6951.1457] [ 1100] [depth= 1] . ( 8 sec) [ -6930.2676] [ 1100] [depth= 1] . ( 8 sec) [ -6926.3806] [ 1098] [depth= 1] . ( 8 sec) [ -6914.1819] [ 1097] [depth= 1] . ( 9 sec) [ -6901.1885] [ 1093] [depth= 1] . ( 9 sec) [ -6900.4394] [ 1097] [depth= 4] . ( 9 sec) [ -6877.5174] [ 1091] [depth= 6] . ( 9 sec) [ -6875.6082] [ 1091] [depth= 1] . ( 9 sec) [ -6864.7771] [ 1087] [depth= 1] . ( 9 sec) [ -6785.1078] [Branch lengths ] . ( 13 sec) [ -6731.7898] [GTR parameters ] . ( 13 sec) [ -6658.3007] [Alpha ][ 0.250961] . ( 13 sec) [ -6645.2808] [ 1085] [depth= 3] . ( 14 sec) [ -6643.3006] [ 1085] [depth= 1] . ( 14 sec) [ -6586.6332] [ 1064] [depth= 1] . ( 14 sec) [ -6580.1825] [ 1059] [depth= 7] . ( 15 sec) [ -6579.4235] [ 1058] [depth= 1] . ( 15 sec) [ -6535.6218] [ 1040] [depth= 4] . ( 15 sec) [ -6532.8247] [ 1036] [depth= 1] . ( 15 sec) [ -6532.7651] [ 1039] [depth= 1] . ( 15 sec) [ -6532.6736] [ 1038] [depth= 1] . ( 15 sec) [ -6532.4816] [ 1037] [depth= 1] . ( 16 sec) [ -6516.2962] [ 1032] [depth= 6] . ( 16 sec) [ -6513.3915] [ 1031] [depth= 2] . ( 16 sec) [ -6477.5749] [ 1020] [depth= 1] . ( 16 sec) [ -6473.9735] [ 1018] [depth= 1] . ( 16 sec) [ -6472.6963] [ 1019] [depth= 2] . ( 17 sec) [ -6472.6051] [ 1018] [depth= 1] . ( 17 sec) [ -6468.7380] [ 1017] [depth= 1] . ( 17 sec) [ -6468.3644] [ 1017] [depth= 1] . ( 17 sec) [ -6463.5998] [ 1015] [depth= 1] . ( 17 sec) [ -6463.3108] [ 1017] [depth= 1] . ( 18 sec) [ -6463.0842] [ 1016] [depth= 1] . ( 18 sec) [ -6461.9884] [ 1016] [depth= 1] . ( 19 sec) [ -6461.8782] [ 1017] [depth= 1] . ( 19 sec) [ -6459.9693] [ 1016] [depth= 1] . ( 19 sec) [ -6459.9490] [ 1016] [depth= 1] . ( 19 sec) [ -6457.4083] [ 1014] [depth= 1] . ( 20 sec) [ -6456.6484] [ 1016] [depth= 1] . ( 20 sec) [ -6456.5919] [ 1016] [depth= 1] . ( 20 sec) [ -6455.5427] [ 1016] [depth= 1] . ( 21 sec) [ -6455.4668] [ 1016] [depth= 1] . ( 22 sec) [ -6455.1956] [ 1014] [depth= 1] . ( 22 sec) [ -6454.6881] [ 1014] [depth= 1] . ( 22 sec) [ -6444.8861] [Branch lengths ] . ( 24 sec) [ -6444.6405] [GTR parameters ] . ( 24 sec) [ -6443.1365] [Alpha ][ 0.223556] . ( 25 sec) [ -6442.8969] [ 1013] [depth= 1] . ( 25 sec) [ -6442.4171] [ 1012] [depth= 1] . ( 29 sec) [ -6442.0775] [ 1012] [depth= 1] . ( 31 sec) [ -6441.8640] [ 1011] [depth= 1] . ( 34 sec) [ -6440.1996] [Branch lengths ] . ( 36 sec) [ -6440.1373] [GTR parameters ] . ( 36 sec) [ -6440.1321] [Alpha ][ 0.221961] . ( 39 sec) [ -6439.9987] [ 1011] [depth= 1] . ( 46 sec) [ -6439.1425] [Branch lengths ] . ( 46 sec) [ -6439.1275] [GTR parameters ] . ( 46 sec) [ -6439.1269] [Alpha ][ 0.221377] . ( 57 sec) [ -6439.0594] [Branch lengths ] . ( 96 sec) [ -6439.0547] [Branch lengths ] . ( 96 sec) [ -6439.0547] [Topology ] . ( 97 sec) [ -6439.0544] [Topology ] . ( 99 sec) [ -6439.0517] [GTR parameters ] . ( 99 sec) [ -6439.0503] [Alpha ][ 0.220541] . ( 99 sec) [ -6439.0503] [Topology ] . ( 100 sec) [ -6439.0499] [Topology ] . ( 100 sec) [ -6439.0499] [GTR parameters ] . ( 100 sec) [ -6439.0499] [Alpha ][ 0.220541] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -6438.9146] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6438.914650. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16273.1305] [GTR parameters ] . ( 1 sec) [ -15848.5846] [Alpha ][ 0.500960] . ( 1 sec) [ -15723.9335] [ 2329] [depth= 11] . ( 1 sec) [ -15637.5807] [ 2311] [depth= 5] . ( 1 sec) [ -15426.0581] [ 2299] [depth= 9] . ( 1 sec) [ -15402.3545] [ 2290] [depth= 1] . ( 1 sec) [ -15370.2340] [ 2287] [depth= 9] . ( 1 sec) [ -15210.6635] [ 2274] [depth= 5] . ( 1 sec) [ -15201.0164] [ 2258] [depth= 1] . ( 1 sec) [ -15141.5609] [ 2254] [depth= 9] . ( 1 sec) [ -15113.4055] [ 2249] [depth= 3] . ( 1 sec) [ -15103.7065] [ 2246] [depth= 5] . ( 1 sec) [ -15102.2201] [ 2245] [depth= 1] . ( 1 sec) [ -15091.4889] [ 2245] [depth= 1] . ( 1 sec) [ -15002.1129] [ 2243] [depth= 3] . ( 1 sec) [ -14949.3728] [ 2241] [depth= 2] . ( 1 sec) [ -14902.2696] [ 2239] [depth= 1] . ( 2 sec) [ -14890.4960] [ 2238] [depth= 1] . ( 2 sec) [ -14838.9269] [ 2236] [depth= 6] . ( 2 sec) [ -14619.3038] [ 2199] [depth= 6] . ( 2 sec) [ -14577.2004] [ 2196] [depth= 9] . ( 2 sec) [ -14525.7321] [ 2180] [depth= 3] . ( 2 sec) [ -14500.4455] [ 2176] [depth= 1] . ( 2 sec) [ -14500.1368] [ 2180] [depth= 1] . ( 2 sec) [ -14494.8655] [ 2171] [depth= 5] . ( 2 sec) [ -14476.5049] [ 2171] [depth= 1] . ( 2 sec) [ -14228.3471] [ 2145] [depth= 10] . ( 2 sec) [ -14137.1160] [ 2121] [depth= 10] . ( 2 sec) [ -13806.8076] [ 2073] [depth= 8] . ( 2 sec) [ -13803.1659] [ 2074] [depth= 1] . ( 2 sec) [ -13622.7007] [ 2034] [depth= 4] . ( 2 sec) [ -13156.7490] [ 2026] [depth= 2] . ( 2 sec) [ -12212.4107] [ 1976] [depth= 13] . ( 3 sec) [ -12134.5578] [ 1974] [depth= 1] . ( 3 sec) [ -12070.2481] [ 1940] [depth= 16] . ( 3 sec) [ -12057.6000] [ 1939] [depth= 2] . ( 3 sec) [ -12029.7586] [ 1959] [depth= 1] . ( 3 sec) [ -11968.4821] [ 1948] [depth= 1] . ( 3 sec) [ -11861.3166] [ 1907] [depth= 11] . ( 3 sec) [ -11802.7750] [ 1908] [depth= 1] . ( 3 sec) [ -11795.0054] [ 1907] [depth= 1] . ( 3 sec) [ -11324.9382] [ 1862] [depth= 7] . ( 3 sec) [ -11285.0610] [ 1846] [depth= 6] . ( 3 sec) [ -11177.9743] [ 1839] [depth= 2] . ( 3 sec) [ -11120.8881] [ 1830] [depth= 3] . ( 3 sec) [ -10941.6285] [ 1827] [depth= 4] . ( 3 sec) [ -10792.1648] [ 1824] [depth= 1] . ( 3 sec) [ -10731.0996] [ 1790] [depth= 1] . ( 3 sec) [ -10553.2447] [ 1787] [depth= 9] . ( 3 sec) [ -10492.9247] [ 1779] [depth= 2] . ( 3 sec) [ -10420.0710] [ 1750] [depth= 1] . ( 4 sec) [ -10228.3472] [ 1747] [depth= 6] . ( 4 sec) [ -9974.1425] [ 1730] [depth= 19] . ( 4 sec) [ -9917.6721] [ 1704] [depth= 7] . ( 4 sec) [ -9775.9763] [ 1677] [depth= 10] . ( 4 sec) [ -9761.6129] [ 1674] [depth= 2] . ( 4 sec) [ -9676.4121] [ 1667] [depth= 3] . ( 4 sec) [ -9613.9951] [ 1665] [depth= 1] . ( 4 sec) [ -9479.3527] [ 1625] [depth= 9] . ( 4 sec) [ -9449.2159] [ 1620] [depth= 1] . ( 4 sec) [ -9349.7205] [ 1614] [depth= 9] . ( 4 sec) [ -9334.2236] [ 1613] [depth= 9] . ( 4 sec) [ -9303.8831] [ 1594] [depth= 1] . ( 4 sec) [ -9232.2190] [ 1549] [depth= 7] . ( 4 sec) [ -9212.5469] [ 1549] [depth= 1] . ( 4 sec) [ -9194.8271] [ 1549] [depth= 1] . ( 4 sec) [ -9084.3990] [ 1540] [depth= 2] . ( 5 sec) [ -9073.3138] [ 1541] [depth= 1] . ( 5 sec) [ -8883.4681] [ 1534] [depth= 2] . ( 5 sec) [ -8730.7373] [ 1495] [depth= 13] . ( 5 sec) [ -8626.4276] [ 1461] [depth= 9] . ( 5 sec) [ -8622.2605] [ 1458] [depth= 1] . ( 5 sec) [ -8496.7496] [ 1418] [depth= 6] . ( 5 sec) [ -8490.5925] [ 1410] [depth= 2] . ( 5 sec) [ -8489.3514] [ 1411] [depth= 1] . ( 5 sec) [ -8484.9160] [ 1403] [depth= 6] . ( 5 sec) [ -8466.9655] [ 1401] [depth= 1] . ( 5 sec) [ -8453.5219] [ 1394] [depth= 1] . ( 5 sec) [ -8425.6935] [ 1389] [depth= 5] . ( 5 sec) [ -8422.8233] [ 1385] [depth= 1] . ( 5 sec) [ -8352.7583] [ 1360] [depth= 4] . ( 5 sec) [ -8329.0953] [ 1358] [depth= 3] . ( 6 sec) [ -8324.7754] [ 1361] [depth= 7] . ( 6 sec) [ -8311.2189] [ 1358] [depth= 1] . ( 6 sec) [ -8309.6809] [ 1360] [depth= 1] . ( 6 sec) [ -8297.2388] [ 1359] [depth= 1] . ( 6 sec) [ -8295.6835] [ 1357] [depth= 2] . ( 6 sec) [ -8294.0413] [ 1359] [depth= 2] . ( 6 sec) [ -8293.9626] [ 1353] [depth= 3] . ( 6 sec) [ -8287.9743] [ 1350] [depth= 2] . ( 6 sec) [ -8283.9011] [ 1349] [depth= 1] . ( 6 sec) [ -8270.6918] [ 1350] [depth= 1] . ( 6 sec) [ -8268.7637] [ 1350] [depth= 4] . ( 6 sec) [ -8123.3051] [ 1319] [depth= 4] . ( 6 sec) [ -8023.5015] [ 1290] [depth= 2] . ( 6 sec) [ -8017.7445] [ 1291] [depth= 15] . ( 6 sec) [ -7937.0759] [ 1257] [depth= 6] . ( 7 sec) [ -7925.9844] [ 1253] [depth= 3] . ( 7 sec) [ -7860.5768] [ 1240] [depth= 8] . ( 7 sec) [ -7854.5050] [ 1239] [depth= 5] . ( 7 sec) [ -7852.0354] [ 1237] [depth= 1] . ( 7 sec) [ -7733.2352] [ 1193] [depth= 15] . ( 7 sec) [ -7732.3095] [ 1198] [depth= 3] . ( 7 sec) [ -7732.0379] [ 1193] [depth= 5] . ( 7 sec) [ -7731.5872] [ 1194] [depth= 1] . ( 7 sec) [ -7731.1593] [ 1193] [depth= 2] . ( 7 sec) [ -7729.5420] [ 1197] [depth= 1] . ( 7 sec) [ -7417.9673] [ 1199] [depth= 1] . ( 7 sec) [ -7365.1221] [ 1172] [depth= 7] . ( 7 sec) [ -7354.4042] [ 1171] [depth= 1] . ( 8 sec) [ -7320.4543] [ 1165] [depth= 2] . ( 8 sec) [ -7307.9130] [ 1164] [depth= 1] . ( 8 sec) [ -7289.8431] [ 1158] [depth= 2] . ( 8 sec) [ -7287.7443] [ 1160] [depth= 1] . ( 8 sec) [ -7202.3750] [ 1166] [depth= 7] . ( 8 sec) [ -7193.0665] [ 1164] [depth= 3] . ( 8 sec) [ -7173.3110] [ 1167] [depth= 2] . ( 8 sec) [ -7124.2246] [ 1167] [depth= 1] . ( 8 sec) [ -7059.0096] [ 1147] [depth= 5] . ( 8 sec) [ -7058.8183] [ 1148] [depth= 1] . ( 8 sec) [ -7053.9144] [ 1148] [depth= 1] . ( 9 sec) [ -7048.4305] [ 1145] [depth= 2] . ( 9 sec) [ -6950.9995] [Branch lengths ] . ( 11 sec) [ -6885.9780] [GTR parameters ] . ( 11 sec) [ -6800.7204] [Alpha ][ 0.250961] . ( 11 sec) [ -6787.4506] [ 1137] [depth= 4] . ( 11 sec) [ -6786.2509] [ 1138] [depth= 8] . ( 12 sec) [ -6772.6447] [ 1133] [depth= 2] . ( 12 sec) [ -6759.5191] [ 1132] [depth= 3] . ( 12 sec) [ -6686.9408] [ 1111] [depth= 7] . ( 12 sec) [ -6675.1836] [ 1106] [depth= 1] . ( 12 sec) [ -6663.4458] [ 1105] [depth= 3] . ( 12 sec) [ -6662.8582] [ 1104] [depth= 2] . ( 12 sec) [ -6662.5711] [ 1103] [depth= 1] . ( 12 sec) [ -6661.0673] [ 1101] [depth= 3] . ( 12 sec) [ -6659.3994] [ 1098] [depth= 2] . ( 13 sec) [ -6635.6030] [ 1092] [depth= 8] . ( 13 sec) [ -6635.5707] [ 1091] [depth= 1] . ( 13 sec) [ -6631.0826] [ 1087] [depth= 3] . ( 14 sec) [ -6627.2246] [ 1081] [depth= 1] . ( 14 sec) [ -6625.5713] [ 1079] [depth= 3] . ( 14 sec) [ -6625.5529] [ 1079] [depth= 1] . ( 15 sec) [ -6622.4615] [ 1082] [depth= 1] . ( 15 sec) [ -6618.6505] [ 1079] [depth= 1] . ( 15 sec) [ -6555.3909] [ 1048] [depth= 3] . ( 15 sec) [ -6550.8579] [ 1046] [depth= 1] . ( 15 sec) [ -6550.6403] [ 1045] [depth= 1] . ( 15 sec) [ -6548.4649] [ 1045] [depth= 1] . ( 15 sec) [ -6541.5270] [ 1041] [depth= 1] . ( 15 sec) [ -6541.2660] [ 1045] [depth= 1] . ( 15 sec) [ -6540.2014] [ 1048] [depth= 3] . ( 15 sec) [ -6529.9727] [ 1045] [depth= 2] . ( 16 sec) [ -6528.8112] [ 1042] [depth= 1] . ( 16 sec) [ -6523.5932] [ 1034] [depth= 3] . ( 16 sec) [ -6519.8447] [ 1031] [depth= 2] . ( 16 sec) [ -6519.8128] [ 1031] [depth= 1] . ( 16 sec) [ -6519.7456] [ 1031] [depth= 1] . ( 17 sec) [ -6519.6660] [ 1031] [depth= 1] . ( 17 sec) [ -6515.1477] [ 1027] [depth= 2] . ( 17 sec) [ -6515.0669] [ 1027] [depth= 1] . ( 18 sec) [ -6512.4212] [ 1028] [depth= 1] . ( 19 sec) [ -6512.1898] [ 1027] [depth= 2] . ( 20 sec) [ -6511.9034] [ 1026] [depth= 2] . ( 20 sec) [ -6507.3867] [ 1025] [depth= 1] . ( 21 sec) [ -6506.6844] [ 1024] [depth= 1] . ( 21 sec) [ -6502.9434] [ 1025] [depth= 1] . ( 21 sec) [ -6502.1311] [ 1026] [depth= 1] . ( 21 sec) [ -6489.0505] [ 1016] [depth= 1] . ( 21 sec) [ -6474.1389] [ 1014] [depth= 3] . ( 21 sec) [ -6472.9242] [ 1014] [depth= 1] . ( 22 sec) [ -6455.2229] [Branch lengths ] . ( 23 sec) [ -6454.5870] [GTR parameters ] . ( 23 sec) [ -6453.3877] [Alpha ][ 0.226605] . ( 25 sec) [ -6453.3253] [ 1014] [depth= 1] . ( 26 sec) [ -6451.1398] [ 1012] [depth= 1] . ( 27 sec) [ -6447.9171] [ 1010] [depth= 1] . ( 27 sec) [ -6447.4167] [ 1012] [depth= 1] . ( 27 sec) [ -6445.7467] [ 1011] [depth= 2] . ( 28 sec) [ -6445.3671] [ 1011] [depth= 1] . ( 29 sec) [ -6445.2709] [ 1009] [depth= 1] . ( 31 sec) [ -6445.1072] [ 1009] [depth= 1] . ( 33 sec) [ -6445.0023] [ 1014] [depth= 2] . ( 34 sec) [ -6441.1491] [Branch lengths ] . ( 36 sec) [ -6440.8883] [GTR parameters ] . ( 36 sec) [ -6440.8580] [Alpha ][ 0.222977] . ( 37 sec) [ -6440.7656] [ 1013] [depth= 1] . ( 37 sec) [ -6439.2310] [ 1012] [depth= 2] . ( 46 sec) [ -6438.1064] [Branch lengths ] . ( 47 sec) [ -6438.0915] [GTR parameters ] . ( 48 sec) [ -6438.0823] [Alpha ][ 0.220853] . ( 57 sec) [ -6438.0048] [Branch lengths ] . ( 97 sec) [ -6437.9955] [Branch lengths ] . ( 97 sec) [ -6437.9955] [Topology ] . ( 98 sec) [ -6437.9950] [Topology ] . ( 99 sec) [ -6437.9942] [GTR parameters ] . ( 99 sec) [ -6437.9914] [Alpha ][ 0.219670] . ( 99 sec) [ -6437.9914] [Topology ] . ( 100 sec) [ -6437.9908] [Topology ] . ( 100 sec) [ -6437.9899] [GTR parameters ] . ( 101 sec) [ -6437.9899] [Alpha ][ 0.219670] . ( 101 sec) [ -6437.9899] [Topology ] . ( 102 sec) [ -6437.9896] [Topology ] . ( 102 sec) [ -6437.9896] [GTR parameters ] . ( 102 sec) [ -6437.9896] [Alpha ][ 0.219451] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -6437.7415] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6437.741491. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -6773.7497] [GTR parameters ] . ( 3 sec) [ -6662.0020] [Alpha ][ 0.500960] . ( 3 sec) [ -6662.0020] [Topology ] . ( 4 sec) [ -6547.3809] [Topology ] . ( 5 sec) [ -6525.6674] [Topology ] . ( 6 sec) [ -6520.6991] [Topology ] . ( 7 sec) [ -6516.7996] [Topology ] . ( 8 sec) [ -6514.1314] [Topology ] . ( 8 sec) [ -6511.5506] [Topology ] . ( 9 sec) [ -6509.4561] [Topology ] . ( 10 sec) [ -6508.1008] [Topology ] . ( 11 sec) [ -6508.0602] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -6507.6199] [Topology ] . ( 21 sec) [ -6506.3544] [GTR parameters ] . ( 21 sec) [ -6446.9494] [Alpha ][ 0.250961] . ( 21 sec) [ -6446.9494] [Topology ] . ( 22 sec) [ -6446.1760] [Topology ] . ( 23 sec) [ -6445.3926] [Topology ] . ( 24 sec) [ -6444.6345] [Topology ] . ( 24 sec) [ -6444.4249] [Topology ] . ( 25 sec) [ -6444.3550] [Topology ] . ( 26 sec) [ -6444.3291] [Topology ] . ( 27 sec) [ -6444.3194] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -6443.4624] [Topology ] . ( 36 sec) [ -6442.6721] [GTR parameters ] . ( 36 sec) [ -6441.0623] [Alpha ][ 0.222185] . ( 36 sec) [ -6441.0623] [Topology ] . ( 37 sec) [ -6440.9592] [Topology ] . ( 38 sec) [ -6440.9275] [Topology ] . ( 39 sec) [ -6440.9151] [Topology ] . ( 39 sec) [ -6440.9100] [Topology ] . ( 40 sec) [ -6440.9079] [Topology ] . ( 41 sec) [ -6440.9070] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -6440.8713] [GTR parameters ] . ( 49 sec) [ -6440.8583] [Alpha ][ 0.219892] . ( 49 sec) [ -6440.8583] [Topology ] . ( 50 sec) [ -6440.8564] [Topology ] . ( 51 sec) [ -6440.8556] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -6440.8552] [GTR parameters ] . ( 58 sec) [ -6440.8550] [Alpha ][ 0.219505] . ( 58 sec) [ -6440.8550] [Topology ] . ( 59 sec) [ -6440.8545] [Topology ] . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -6440.8545] [GTR parameters ] . ( 66 sec) [ -6440.8545] [Alpha ][ 0.219505] . ( 66 sec) [ -6440.8545] [Topology ] . ( 67 sec) [ -6440.8544] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 82 sec) [ -6773.7497] [GTR parameters ] . ( 82 sec) [ -6662.0020] [Alpha ][ 0.500960] . ( 83 sec) [ -6661.2176] [ 1015] [depth= 1] . ( 83 sec) [ -6657.6560] [ 1017] [depth= 1] . ( 83 sec) [ -6643.6053] [ 1021] [depth= 3] . ( 83 sec) [ -6641.0309] [ 1021] [depth= 1] . ( 83 sec) [ -6638.5305] [ 1021] [depth= 1] . ( 83 sec) [ -6633.4998] [ 1021] [depth= 1] . ( 84 sec) [ -6630.8745] [ 1021] [depth= 1] . ( 84 sec) [ -6629.9916] [ 1021] [depth= 1] . ( 84 sec) [ -6622.7123] [ 1018] [depth= 2] . ( 84 sec) [ -6621.7876] [ 1019] [depth= 1] . ( 84 sec) [ -6617.7013] [ 1018] [depth= 1] . ( 84 sec) [ -6608.9048] [ 1016] [depth= 1] . ( 84 sec) [ -6601.3592] [ 1014] [depth= 1] . ( 85 sec) [ -6601.1610] [ 1016] [depth= 1] . ( 85 sec) [ -6598.7269] [ 1016] [depth= 1] . ( 85 sec) [ -6592.3337] [ 1016] [depth= 1] . ( 86 sec) [ -6591.8220] [ 1016] [depth= 1] . ( 86 sec) [ -6590.0681] [ 1016] [depth= 1] . ( 86 sec) [ -6588.2294] [ 1016] [depth= 1] . ( 86 sec) [ -6588.1324] [ 1016] [depth= 1] . ( 86 sec) [ -6586.6852] [ 1016] [depth= 1] . ( 86 sec) [ -6586.5950] [ 1020] [depth= 2] . ( 86 sec) [ -6582.2061] [ 1020] [depth= 2] . ( 86 sec) [ -6581.5121] [ 1020] [depth= 1] . ( 86 sec) [ -6580.0273] [ 1020] [depth= 1] . ( 86 sec) [ -6579.5942] [ 1019] [depth= 1] . ( 87 sec) [ -6577.0371] [ 1018] [depth= 1] . ( 87 sec) [ -6576.6929] [ 1018] [depth= 1] . ( 87 sec) [ -6575.7276] [ 1020] [depth= 1] . ( 87 sec) [ -6574.3250] [ 1020] [depth= 1] . ( 88 sec) [ -6572.4235] [ 1022] [depth= 1] . ( 88 sec) [ -6572.3127] [ 1022] [depth= 1] . ( 88 sec) [ -6572.1131] [ 1022] [depth= 1] . ( 88 sec) [ -6570.5866] [ 1020] [depth= 1] . ( 89 sec) [ -6569.8711] [ 1022] [depth= 2] . ( 89 sec) [ -6563.0274] [ 1018] [depth= 1] . ( 89 sec) [ -6560.2201] [ 1019] [depth= 1] . ( 89 sec) [ -6554.7428] [ 1015] [depth= 3] . ( 90 sec) [ -6551.7431] [ 1015] [depth= 1] . ( 90 sec) [ -6547.0640] [ 1015] [depth= 1] . ( 90 sec) [ -6547.0264] [ 1015] [depth= 1] . ( 90 sec) [ -6545.5836] [ 1015] [depth= 1] . ( 91 sec) [ -6509.9789] [Branch lengths ] . ( 93 sec) [ -6508.8959] [GTR parameters ] . ( 93 sec) [ -6448.6182] [Alpha ][ 0.250961] . ( 94 sec) [ -6448.5987] [ 1015] [depth= 1] . ( 95 sec) [ -6448.2173] [ 1016] [depth= 1] . ( 95 sec) [ -6443.9611] [ 1013] [depth= 2] . ( 97 sec) [ -6443.8114] [ 1012] [depth= 1] . ( 97 sec) [ -6443.5939] [ 1012] [depth= 1] . ( 102 sec) [ -6440.4312] [Branch lengths ] . ( 103 sec) [ -6439.6497] [GTR parameters ] . ( 103 sec) [ -6437.8273] [Alpha ][ 0.220074] . ( 113 sec) [ -6437.7151] [Branch lengths ] . ( 150 sec) [ -6437.7093] [Branch lengths ] . ( 150 sec) [ -6437.7093] [Topology ] . ( 151 sec) [ -6437.7091] [Topology ] . ( 152 sec) [ -6437.6682] [GTR parameters ] . ( 152 sec) [ -6437.6661] [Alpha ][ 0.219041] . ( 152 sec) [ -6437.6661] [Topology ] . ( 153 sec) [ -6437.6657] [Topology ] . ( 153 sec) [ -6437.6656] [GTR parameters ] . ( 153 sec) [ -6437.6656] [Alpha ][ 0.219041] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6440.854359 . Log likelihood obtained after SPR moves : -6437.665605 . Log likelihood of the current tree: -6437.665605. . Printing the most likely tree in file 'nucleic_M2921_54x966_2006.phy_phyml_tree.txt'... . Best log likelihood : -6437.665605 . Time used 0h2m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 689.58user 0.00system 11:35.41elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps