.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_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 . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . [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)... . ( 1 sec) [ -13837.2695] [GTR parameters ] . ( 1 sec) [ -13540.2473] [Alpha ][ 0.500960] . ( 1 sec) [ -13405.3050] [ 1780] [depth= 4] . ( 1 sec) [ -12687.6458] [ 1770] [depth= 9] . ( 1 sec) [ -12512.6955] [ 1765] [depth= 1] . ( 1 sec) [ -12214.2114] [ 1765] [depth= 11] . ( 1 sec) [ -12128.2619] [ 1694] [depth= 2] . ( 1 sec) [ -12077.3246] [ 1688] [depth= 13] . ( 1 sec) [ -11905.1735] [ 1670] [depth= 9] . ( 1 sec) [ -11600.8831] [ 1588] [depth= 1] . ( 1 sec) [ -11576.4227] [ 1585] [depth= 4] . ( 1 sec) [ -11500.6651] [ 1585] [depth= 3] . ( 1 sec) [ -11451.2116] [ 1584] [depth= 4] . ( 1 sec) [ -11356.6066] [ 1585] [depth= 6] . ( 1 sec) [ -11218.6840] [ 1557] [depth= 12] . ( 1 sec) [ -10943.6625] [ 1580] [depth= 1] . ( 1 sec) [ -10872.5634] [ 1575] [depth= 11] . ( 1 sec) [ -10595.2098] [ 1515] [depth= 20] . ( 2 sec) [ -10488.9519] [ 1487] [depth= 9] . ( 2 sec) [ -10322.4367] [ 1478] [depth= 18] . ( 2 sec) [ -10253.4061] [ 1430] [depth= 18] . ( 2 sec) [ -10207.8278] [ 1430] [depth= 10] . ( 2 sec) [ -10156.6427] [ 1420] [depth= 6] . ( 2 sec) [ -10114.5976] [ 1419] [depth= 3] . ( 2 sec) [ -10063.1767] [ 1418] [depth= 7] . ( 2 sec) [ -10039.2862] [ 1417] [depth= 9] . ( 2 sec) [ -9972.0080] [ 1399] [depth= 4] . ( 2 sec) [ -9918.7777] [ 1397] [depth= 1] . ( 2 sec) [ -9857.7271] [ 1382] [depth= 10] . ( 2 sec) [ -9771.1586] [ 1372] [depth= 8] . ( 2 sec) [ -9745.7982] [ 1359] [depth= 8] . ( 2 sec) [ -9612.3402] [ 1333] [depth= 12] . ( 2 sec) [ -9465.6253] [ 1306] [depth= 8] . ( 2 sec) [ -9464.3941] [ 1307] [depth= 3] . ( 2 sec) [ -9458.8264] [ 1310] [depth= 1] . ( 2 sec) [ -9180.4682] [ 1266] [depth= 14] . ( 2 sec) [ -9115.0533] [ 1253] [depth= 5] . ( 2 sec) [ -9074.3432] [ 1248] [depth= 4] . ( 3 sec) [ -9008.9702] [ 1247] [depth= 2] . ( 3 sec) [ -8874.0219] [ 1243] [depth= 3] . ( 3 sec) [ -8799.5125] [ 1232] [depth= 2] . ( 3 sec) [ -8786.5975] [ 1231] [depth= 3] . ( 3 sec) [ -8762.8345] [ 1225] [depth= 2] . ( 3 sec) [ -8750.4788] [ 1222] [depth= 9] . ( 3 sec) [ -8684.2703] [ 1204] [depth= 15] . ( 3 sec) [ -8654.9763] [ 1195] [depth= 16] . ( 3 sec) [ -8582.5680] [ 1177] [depth= 2] . ( 3 sec) [ -8570.9944] [ 1175] [depth= 2] . ( 3 sec) [ -8533.3770] [ 1172] [depth= 1] . ( 3 sec) [ -8516.4579] [ 1164] [depth= 1] . ( 3 sec) [ -8506.1646] [ 1164] [depth= 1] . ( 3 sec) [ -8501.1390] [ 1162] [depth= 1] . ( 3 sec) [ -8425.8215] [ 1142] [depth= 7] . ( 3 sec) [ -8388.8746] [ 1131] [depth= 1] . ( 3 sec) [ -8358.8072] [ 1131] [depth= 2] . ( 4 sec) [ -8350.1449] [ 1130] [depth= 1] . ( 4 sec) [ -7878.6516] [ 1131] [depth= 3] . ( 4 sec) [ -7712.6218] [ 1107] [depth= 3] . ( 4 sec) [ -7707.7204] [ 1104] [depth= 1] . ( 4 sec) [ -7706.5457] [ 1109] [depth= 1] . ( 4 sec) [ -7671.7443] [ 1102] [depth= 11] . ( 4 sec) [ -7657.8496] [ 1102] [depth= 1] . ( 4 sec) [ -7656.7338] [ 1102] [depth= 1] . ( 4 sec) [ -7656.0954] [ 1097] [depth= 1] . ( 4 sec) [ -7532.6005] [ 1083] [depth= 10] . ( 4 sec) [ -7525.5485] [ 1082] [depth= 1] . ( 4 sec) [ -6754.6405] [ 1015] [depth= 10] . ( 4 sec) [ -6725.9814] [ 999] [depth= 18] . ( 4 sec) [ -6683.9894] [ 985] [depth= 3] . ( 4 sec) [ -6645.0787] [ 979] [depth= 3] . ( 4 sec) [ -6629.4659] [ 975] [depth= 7] . ( 5 sec) [ -6625.6206] [ 974] [depth= 1] . ( 5 sec) [ -6621.3782] [ 978] [depth= 1] . ( 5 sec) [ -6580.3789] [ 970] [depth= 8] . ( 5 sec) [ -6550.5136] [ 959] [depth= 1] . ( 5 sec) [ -6479.3134] [ 958] [depth= 8] . ( 5 sec) [ -6300.2136] [ 963] [depth= 10] . ( 5 sec) [ -6291.4627] [ 960] [depth= 5] . ( 5 sec) [ -6282.2320] [ 958] [depth= 1] . ( 5 sec) [ -6231.7767] [ 952] [depth= 5] . ( 5 sec) [ -6218.7626] [ 951] [depth= 5] . ( 5 sec) [ -6218.7280] [ 951] [depth= 1] . ( 6 sec) [ -6217.9874] [ 950] [depth= 5] . ( 6 sec) [ -6206.0772] [ 950] [depth= 1] . ( 6 sec) [ -6196.1351] [ 956] [depth= 1] . ( 6 sec) [ -6177.9764] [ 943] [depth= 5] . ( 6 sec) [ -6159.0109] [ 939] [depth= 7] . ( 6 sec) [ -6156.5684] [ 939] [depth= 1] . ( 6 sec) [ -6109.5302] [ 930] [depth= 2] . ( 6 sec) [ -6092.8772] [ 931] [depth= 3] . ( 6 sec) [ -6072.1728] [ 927] [depth= 4] . ( 6 sec) [ -6034.4394] [ 905] [depth= 4] . ( 6 sec) [ -6031.2299] [ 905] [depth= 1] . ( 6 sec) [ -6021.0149] [ 904] [depth= 4] . ( 6 sec) [ -6020.0446] [ 904] [depth= 1] . ( 6 sec) [ -6017.6013] [ 902] [depth= 1] . ( 6 sec) [ -5996.0248] [ 900] [depth= 6] . ( 6 sec) [ -5995.9763] [ 900] [depth= 1] . ( 6 sec) [ -5995.3168] [ 901] [depth= 5] . ( 6 sec) [ -5993.3003] [ 899] [depth= 1] . ( 7 sec) [ -5982.8268] [ 897] [depth= 3] . ( 7 sec) [ -5968.9857] [ 895] [depth= 6] . ( 7 sec) [ -5959.8998] [ 892] [depth= 5] . ( 7 sec) [ -5959.6311] [ 892] [depth= 1] . ( 7 sec) [ -5945.1570] [ 893] [depth= 2] . ( 7 sec) [ -5925.3798] [ 889] [depth= 2] . ( 7 sec) [ -5921.2031] [ 888] [depth= 2] . ( 8 sec) [ -5917.1741] [ 887] [depth= 1] . ( 8 sec) [ -5914.0442] [ 886] [depth= 2] . ( 8 sec) [ -5883.6767] [ 877] [depth= 4] . ( 8 sec) [ -5869.7516] [ 879] [depth= 3] . ( 8 sec) [ -5861.8547] [ 880] [depth= 2] . ( 8 sec) [ -5855.7258] [ 875] [depth= 1] . ( 8 sec) [ -5853.2932] [ 875] [depth= 1] . ( 9 sec) [ -5740.8964] [Branch lengths ] . ( 12 sec) [ -5533.6396] [GTR parameters ] . ( 12 sec) [ -5482.8590] [Alpha ][ 0.250961] . ( 13 sec) [ -5482.7482] [ 874] [depth= 2] . ( 13 sec) [ -5477.3669] [ 865] [depth= 1] . ( 13 sec) [ -5465.2212] [ 861] [depth= 3] . ( 14 sec) [ -5465.2003] [ 861] [depth= 1] . ( 14 sec) [ -5464.7981] [ 861] [depth= 1] . ( 14 sec) [ -5428.6548] [ 867] [depth= 1] . ( 14 sec) [ -5428.0172] [ 867] [depth= 1] . ( 14 sec) [ -5427.2839] [ 867] [depth= 1] . ( 14 sec) [ -5426.7961] [ 867] [depth= 1] . ( 15 sec) [ -5426.4164] [ 867] [depth= 1] . ( 15 sec) [ -5423.8494] [ 860] [depth= 2] . ( 15 sec) [ -5423.0238] [ 860] [depth= 2] . ( 16 sec) [ -5422.9211] [ 860] [depth= 3] . ( 16 sec) [ -5422.8398] [ 860] [depth= 1] . ( 16 sec) [ -5418.3427] [ 863] [depth= 2] . ( 16 sec) [ -5417.9418] [ 863] [depth= 1] . ( 17 sec) [ -5416.2042] [ 865] [depth= 1] . ( 18 sec) [ -5411.9898] [ 861] [depth= 1] . ( 18 sec) [ -5411.9375] [ 861] [depth= 1] . ( 18 sec) [ -5411.9196] [ 861] [depth= 1] . ( 18 sec) [ -5411.8958] [ 861] [depth= 1] . ( 19 sec) [ -5406.3635] [ 862] [depth= 1] . ( 20 sec) [ -5406.1235] [ 860] [depth= 1] . ( 20 sec) [ -5401.6479] [ 859] [depth= 2] . ( 20 sec) [ -5401.6133] [ 859] [depth= 1] . ( 20 sec) [ -5401.5207] [ 859] [depth= 1] . ( 20 sec) [ -5401.4953] [ 859] [depth= 1] . ( 22 sec) [ -5401.1568] [ 859] [depth= 1] . ( 22 sec) [ -5400.6092] [ 859] [depth= 1] . ( 22 sec) [ -5400.5791] [ 859] [depth= 1] . ( 24 sec) [ -5400.5164] [ 859] [depth= 1] . ( 24 sec) [ -5399.6581] [ 859] [depth= 1] . ( 26 sec) [ -5392.8041] [Branch lengths ] . ( 28 sec) [ -5392.3132] [GTR parameters ] . ( 28 sec) [ -5391.9071] [Alpha ][ 0.235805] . ( 29 sec) [ -5391.8501] [ 859] [depth= 1] . ( 33 sec) [ -5391.0237] [ 859] [depth= 6] . ( 37 sec) [ -5389.9985] [ 861] [depth= 1] . ( 45 sec) [ -5388.9809] [Branch lengths ] . ( 47 sec) [ -5388.8045] [GTR parameters ] . ( 47 sec) [ -5388.8039] [Alpha ][ 0.235158] . ( 47 sec) [ -5387.8333] [ 854] [depth= 1] . ( 65 sec) [ -5385.6381] [Branch lengths ] . ( 66 sec) [ -5385.6048] [GTR parameters ] . ( 66 sec) [ -5385.5896] [Alpha ][ 0.238050] . ( 83 sec) [ -5382.9061] [Branch lengths ] . ( 119 sec) [ -5382.4729] [Branch lengths ] . ( 119 sec) [ -5382.4729] [Topology ] . ( 120 sec) [ -5382.4160] [Topology ] . ( 121 sec) [ -5382.3934] [Topology ] . ( 122 sec) [ -5382.3819] [Topology ] . ( 123 sec) [ -5382.3755] [Topology ] . ( 123 sec) [ -5382.3721] [Topology ] . ( 124 sec) [ -5382.3701] [Topology ] . ( 125 sec) [ -5382.3667] [GTR parameters ] . ( 125 sec) [ -5382.3651] [Alpha ][ 0.238961] . ( 125 sec) [ -5382.3651] [Topology ] . ( 126 sec) [ -5382.3639] [Topology ] . ( 127 sec) [ -5382.3632] [Topology ] . ( 127 sec) [ -5382.3625] [GTR parameters ] . ( 127 sec) [ -5382.3625] [Alpha ][ 0.238961] . ( 128 sec) [ -5382.3625] [Topology ] . ( 128 sec) [ -5382.3621] [Topology ] . ( 129 sec) [ -5382.3620] [GTR parameters ] . ( 129 sec) [ -5382.3620] [Alpha ][ 0.238961] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.361967. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -11780.1575] [GTR parameters ] . ( 2 sec) [ -11485.2784] [Alpha ][ 0.500960] . ( 2 sec) [ -11375.7516] [ 1871] [depth= 8] . ( 2 sec) [ -11161.3376] [ 1854] [depth= 2] . ( 2 sec) [ -11023.0813] [ 1849] [depth= 1] . ( 2 sec) [ -10932.4674] [ 1844] [depth= 10] . ( 2 sec) [ -10916.0535] [ 1828] [depth= 2] . ( 2 sec) [ -10904.8528] [ 1826] [depth= 4] . ( 2 sec) [ -10618.3387] [ 1823] [depth= 5] . ( 2 sec) [ -10600.6401] [ 1822] [depth= 2] . ( 2 sec) [ -10571.0990] [ 1821] [depth= 4] . ( 2 sec) [ -10272.0818] [ 1826] [depth= 4] . ( 2 sec) [ -9920.6911] [ 1818] [depth= 12] . ( 2 sec) [ -9905.8198] [ 1818] [depth= 1] . ( 2 sec) [ -9888.0877] [ 1816] [depth= 3] . ( 2 sec) [ -9865.1780] [ 1815] [depth= 4] . ( 2 sec) [ -9801.8879] [ 1812] [depth= 10] . ( 3 sec) [ -9766.6740] [ 1805] [depth= 7] . ( 3 sec) [ -9691.6743] [ 1801] [depth= 3] . ( 3 sec) [ -9682.3549] [ 1800] [depth= 2] . ( 3 sec) [ -9647.2230] [ 1789] [depth= 10] . ( 3 sec) [ -9564.1237] [ 1778] [depth= 8] . ( 3 sec) [ -9429.3289] [ 1738] [depth= 16] . ( 3 sec) [ -9410.1445] [ 1721] [depth= 9] . ( 3 sec) [ -9373.7770] [ 1708] [depth= 12] . ( 3 sec) [ -9201.2364] [ 1684] [depth= 14] . ( 3 sec) [ -9196.3613] [ 1684] [depth= 15] . ( 3 sec) [ -9190.2834] [ 1676] [depth= 3] . ( 3 sec) [ -9098.9822] [ 1656] [depth= 1] . ( 3 sec) [ -8995.9729] [ 1645] [depth= 3] . ( 3 sec) [ -8944.9192] [ 1633] [depth= 9] . ( 3 sec) [ -8922.2803] [ 1631] [depth= 8] . ( 3 sec) [ -8832.0599] [ 1623] [depth= 4] . ( 3 sec) [ -8778.1997] [ 1577] [depth= 4] . ( 4 sec) [ -8758.1549] [ 1573] [depth= 1] . ( 4 sec) [ -8753.2384] [ 1573] [depth= 1] . ( 4 sec) [ -8689.5022] [ 1557] [depth= 10] . ( 4 sec) [ -8688.7969] [ 1556] [depth= 1] . ( 4 sec) [ -8607.4510] [ 1555] [depth= 2] . ( 4 sec) [ -8541.5092] [ 1542] [depth= 11] . ( 4 sec) [ -8473.0148] [ 1532] [depth= 6] . ( 4 sec) [ -8472.9527] [ 1536] [depth= 1] . ( 4 sec) [ -8288.3398] [ 1494] [depth= 13] . ( 4 sec) [ -8243.1047] [ 1490] [depth= 1] . ( 4 sec) [ -8208.4732] [ 1486] [depth= 5] . ( 4 sec) [ -8173.7018] [ 1480] [depth= 8] . ( 4 sec) [ -8120.0542] [ 1483] [depth= 1] . ( 4 sec) [ -8095.5771] [ 1476] [depth= 8] . ( 4 sec) [ -8064.0970] [ 1467] [depth= 8] . ( 4 sec) [ -7936.1389] [ 1443] [depth= 10] . ( 4 sec) [ -7933.5162] [ 1443] [depth= 1] . ( 5 sec) [ -7914.7725] [ 1440] [depth= 9] . ( 5 sec) [ -7910.0039] [ 1440] [depth= 1] . ( 5 sec) [ -7906.6094] [ 1442] [depth= 2] . ( 5 sec) [ -7901.4884] [ 1442] [depth= 1] . ( 5 sec) [ -7894.1224] [ 1435] [depth= 1] . ( 5 sec) [ -7891.8889] [ 1435] [depth= 1] . ( 5 sec) [ -7764.9711] [ 1408] [depth= 5] . ( 5 sec) [ -7747.6436] [ 1393] [depth= 1] . ( 5 sec) [ -7730.2543] [ 1392] [depth= 1] . ( 5 sec) [ -7337.5530] [ 1311] [depth= 7] . ( 5 sec) [ -7333.7796] [ 1312] [depth= 2] . ( 5 sec) [ -7090.3443] [ 1297] [depth= 4] . ( 5 sec) [ -7089.8343] [ 1297] [depth= 3] . ( 5 sec) [ -7085.8801] [ 1295] [depth= 2] . ( 6 sec) [ -7064.0848] [ 1276] [depth= 12] . ( 6 sec) [ -7058.4017] [ 1276] [depth= 2] . ( 6 sec) [ -6983.3268] [ 1265] [depth= 1] . ( 6 sec) [ -6977.2489] [ 1262] [depth= 1] . ( 6 sec) [ -6968.0697] [ 1262] [depth= 1] . ( 6 sec) [ -6964.1128] [ 1245] [depth= 1] . ( 6 sec) [ -6955.3686] [ 1240] [depth= 1] . ( 6 sec) [ -6932.7300] [ 1240] [depth= 12] . ( 6 sec) [ -6921.1431] [ 1237] [depth= 1] . ( 6 sec) [ -6847.9614] [ 1227] [depth= 4] . ( 6 sec) [ -6837.0200] [ 1224] [depth= 4] . ( 6 sec) [ -6832.0686] [ 1224] [depth= 3] . ( 6 sec) [ -6747.9897] [ 1208] [depth= 10] . ( 6 sec) [ -6725.3636] [ 1204] [depth= 7] . ( 6 sec) [ -6701.7476] [ 1197] [depth= 1] . ( 6 sec) [ -6693.0175] [ 1196] [depth= 4] . ( 6 sec) [ -6691.4261] [ 1196] [depth= 4] . ( 6 sec) [ -6689.6648] [ 1194] [depth= 3] . ( 7 sec) [ -6635.0709] [ 1197] [depth= 6] . ( 7 sec) [ -6629.4256] [ 1195] [depth= 6] . ( 7 sec) [ -6615.1696] [ 1192] [depth= 8] . ( 7 sec) [ -6614.7393] [ 1191] [depth= 2] . ( 7 sec) [ -6613.6256] [ 1190] [depth= 1] . ( 7 sec) [ -6414.3448] [ 1129] [depth= 1] . ( 7 sec) [ -6380.1751] [ 1109] [depth= 9] . ( 7 sec) [ -6358.9586] [ 1105] [depth= 7] . ( 7 sec) [ -6358.6752] [ 1105] [depth= 1] . ( 8 sec) [ -6330.8666] [ 1087] [depth= 12] . ( 8 sec) [ -6328.5280] [ 1087] [depth= 5] . ( 8 sec) [ -6326.0984] [ 1086] [depth= 4] . ( 8 sec) [ -6316.9312] [ 1080] [depth= 1] . ( 8 sec) [ -6293.7531] [ 1075] [depth= 5] . ( 8 sec) [ -6257.8573] [ 1061] [depth= 4] . ( 9 sec) [ -5996.0983] [ 990] [depth= 13] . ( 9 sec) [ -5995.7028] [ 990] [depth= 3] . ( 10 sec) [ -5989.5443] [ 988] [depth= 1] . ( 10 sec) [ -5983.4051] [ 988] [depth= 1] . ( 10 sec) [ -5980.9344] [ 993] [depth= 1] . ( 10 sec) [ -5942.3027] [ 977] [depth= 8] . ( 10 sec) [ -5917.6347] [ 966] [depth= 1] . ( 10 sec) [ -5915.6398] [ 967] [depth= 2] . ( 10 sec) [ -5907.8702] [ 967] [depth= 1] . ( 10 sec) [ -5905.3745] [ 971] [depth= 1] . ( 10 sec) [ -5851.7672] [ 960] [depth= 7] . ( 10 sec) [ -5851.5293] [ 961] [depth= 1] . ( 10 sec) [ -5849.4719] [ 960] [depth= 1] . ( 10 sec) [ -5838.4833] [ 956] [depth= 1] . ( 10 sec) [ -5828.0833] [ 956] [depth= 2] . ( 10 sec) [ -5823.6097] [ 955] [depth= 2] . ( 11 sec) [ -5818.6644] [ 956] [depth= 2] . ( 11 sec) [ -5775.0649] [ 941] [depth= 2] . ( 11 sec) [ -5700.7792] [ 914] [depth= 9] . ( 11 sec) [ -5700.6727] [ 914] [depth= 2] . ( 11 sec) [ -5700.5951] [ 916] [depth= 3] . ( 11 sec) [ -5646.2195] [Branch lengths ] . ( 12 sec) [ -5639.3902] [GTR parameters ] . ( 12 sec) [ -5584.2342] [Alpha ][ 0.250961] . ( 12 sec) [ -5582.2596] [ 915] [depth= 1] . ( 12 sec) [ -5582.0832] [ 914] [depth= 6] . ( 12 sec) [ -5581.4874] [ 914] [depth= 1] . ( 12 sec) [ -5578.4920] [ 913] [depth= 8] . ( 12 sec) [ -5577.5682] [ 908] [depth= 3] . ( 13 sec) [ -5573.2467] [ 907] [depth= 5] . ( 13 sec) [ -5565.0211] [ 903] [depth= 2] . ( 14 sec) [ -5558.4335] [ 903] [depth= 1] . ( 14 sec) [ -5558.1824] [ 905] [depth= 2] . ( 14 sec) [ -5537.8063] [ 894] [depth= 3] . ( 15 sec) [ -5533.3122] [ 890] [depth= 3] . ( 15 sec) [ -5528.9558] [ 888] [depth= 1] . ( 15 sec) [ -5496.0690] [ 885] [depth= 7] . ( 15 sec) [ -5487.3689] [ 881] [depth= 1] . ( 16 sec) [ -5485.0280] [ 881] [depth= 2] . ( 16 sec) [ -5483.6962] [ 881] [depth= 1] . ( 16 sec) [ -5467.4812] [ 874] [depth= 6] . ( 16 sec) [ -5467.4520] [ 874] [depth= 1] . ( 16 sec) [ -5467.2584] [ 875] [depth= 1] . ( 17 sec) [ -5457.9278] [ 872] [depth= 5] . ( 17 sec) [ -5457.5876] [ 872] [depth= 1] . ( 17 sec) [ -5457.5576] [ 872] [depth= 1] . ( 17 sec) [ -5457.4536] [ 872] [depth= 1] . ( 17 sec) [ -5454.9843] [ 872] [depth= 2] . ( 18 sec) [ -5431.8394] [ 866] [depth= 7] . ( 18 sec) [ -5430.8134] [ 866] [depth= 2] . ( 18 sec) [ -5427.5553] [ 867] [depth= 1] . ( 18 sec) [ -5421.1289] [ 863] [depth= 2] . ( 18 sec) [ -5418.7659] [ 861] [depth= 1] . ( 18 sec) [ -5416.6352] [ 863] [depth= 1] . ( 18 sec) [ -5409.1829] [ 860] [depth= 2] . ( 18 sec) [ -5409.1328] [ 860] [depth= 1] . ( 20 sec) [ -5406.5239] [ 861] [depth= 1] . ( 20 sec) [ -5402.2802] [ 859] [depth= 1] . ( 21 sec) [ -5401.6200] [ 858] [depth= 2] . ( 21 sec) [ -5401.3805] [ 860] [depth= 1] . ( 21 sec) [ -5400.8640] [ 860] [depth= 1] . ( 22 sec) [ -5400.8427] [ 860] [depth= 2] . ( 22 sec) [ -5400.7164] [ 860] [depth= 1] . ( 22 sec) [ -5399.8915] [ 853] [depth= 1] . ( 23 sec) [ -5399.8391] [ 853] [depth= 1] . ( 24 sec) [ -5386.8752] [Branch lengths ] . ( 24 sec) [ -5384.7455] [GTR parameters ] . ( 24 sec) [ -5384.5445] [Alpha ][ 0.240037] . ( 30 sec) [ -5384.4295] [ 853] [depth= 1] . ( 40 sec) [ -5383.9633] [Branch lengths ] . ( 40 sec) [ -5383.9573] [GTR parameters ] . ( 40 sec) [ -5383.9549] [Alpha ][ 0.238806] . ( 76 sec) [ -5383.9333] [Branch lengths ] . ( 76 sec) [ -5383.9333] [Topology ] . ( 77 sec) [ -5383.9322] [Topology ] . ( 78 sec) [ -5383.9318] [Topology ] . ( 78 sec) [ -5383.9317] [GTR parameters ] . ( 78 sec) [ -5383.9317] [Alpha ][ 0.238806] . ( 78 sec) [ -5383.9317] [Topology ] . ( 79 sec) [ -5383.9316] [Topology ] . ( 79 sec) [ -5383.9315] [GTR parameters ] . ( 79 sec) [ -5383.9315] [Alpha ][ 0.238806] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5383.931544. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12808.0924] [GTR parameters ] . ( 2 sec) [ -12503.7674] [Alpha ][ 0.500960] . ( 2 sec) [ -12113.8166] [ 1843] [depth= 12] . ( 2 sec) [ -12034.3302] [ 1822] [depth= 11] . ( 2 sec) [ -11825.5293] [ 1798] [depth= 8] . ( 2 sec) [ -11723.9904] [ 1726] [depth= 1] . ( 2 sec) [ -11549.6311] [ 1709] [depth= 7] . ( 2 sec) [ -11524.0092] [ 1705] [depth= 8] . ( 2 sec) [ -11512.2432] [ 1704] [depth= 1] . ( 2 sec) [ -11449.2069] [ 1700] [depth= 9] . ( 2 sec) [ -11411.4106] [ 1696] [depth= 3] . ( 2 sec) [ -11410.0050] [ 1696] [depth= 1] . ( 2 sec) [ -11338.5053] [ 1692] [depth= 7] . ( 2 sec) [ -11246.8711] [ 1692] [depth= 1] . ( 2 sec) [ -11005.2113] [ 1662] [depth= 13] . ( 2 sec) [ -10966.5756] [ 1660] [depth= 1] . ( 2 sec) [ -10662.5896] [ 1651] [depth= 2] . ( 2 sec) [ -10099.6834] [ 1641] [depth= 4] . ( 2 sec) [ -9974.6934] [ 1606] [depth= 2] . ( 3 sec) [ -9872.4518] [ 1599] [depth= 10] . ( 3 sec) [ -9635.2418] [ 1573] [depth= 7] . ( 3 sec) [ -9619.4672] [ 1564] [depth= 1] . ( 3 sec) [ -9493.6427] [ 1554] [depth= 13] . ( 3 sec) [ -9473.6151] [ 1544] [depth= 12] . ( 3 sec) [ -9418.2452] [ 1522] [depth= 1] . ( 3 sec) [ -9385.1570] [ 1498] [depth= 13] . ( 3 sec) [ -9152.1296] [ 1456] [depth= 15] . ( 3 sec) [ -9119.5580] [ 1459] [depth= 11] . ( 3 sec) [ -9111.8889] [ 1457] [depth= 11] . ( 3 sec) [ -9083.7686] [ 1453] [depth= 2] . ( 3 sec) [ -9012.1695] [ 1452] [depth= 1] . ( 3 sec) [ -8962.1424] [ 1443] [depth= 6] . ( 3 sec) [ -8901.0654] [ 1443] [depth= 1] . ( 3 sec) [ -8857.1788] [ 1440] [depth= 4] . ( 3 sec) [ -8791.7715] [ 1434] [depth= 2] . ( 3 sec) [ -8621.6693] [ 1433] [depth= 3] . ( 3 sec) [ -8283.3858] [ 1433] [depth= 2] . ( 4 sec) [ -8201.6277] [ 1425] [depth= 1] . ( 4 sec) [ -8165.8638] [ 1424] [depth= 5] . ( 4 sec) [ -8054.0905] [ 1394] [depth= 8] . ( 4 sec) [ -8046.7463] [ 1391] [depth= 5] . ( 4 sec) [ -7977.5392] [ 1370] [depth= 2] . ( 4 sec) [ -7968.1640] [ 1372] [depth= 13] . ( 4 sec) [ -7923.8078] [ 1355] [depth= 14] . ( 4 sec) [ -7923.2336] [ 1355] [depth= 4] . ( 4 sec) [ -7911.9092] [ 1354] [depth= 1] . ( 4 sec) [ -7907.8819] [ 1362] [depth= 1] . ( 4 sec) [ -7799.0010] [ 1305] [depth= 8] . ( 4 sec) [ -7774.9788] [ 1303] [depth= 3] . ( 4 sec) [ -7606.0997] [ 1296] [depth= 8] . ( 4 sec) [ -7587.3301] [ 1288] [depth= 1] . ( 5 sec) [ -7575.3746] [ 1286] [depth= 1] . ( 5 sec) [ -7480.1368] [ 1262] [depth= 3] . ( 5 sec) [ -7464.6365] [ 1261] [depth= 2] . ( 5 sec) [ -7424.8251] [ 1253] [depth= 10] . ( 5 sec) [ -7358.6148] [ 1238] [depth= 13] . ( 5 sec) [ -7338.5655] [ 1237] [depth= 1] . ( 5 sec) [ -7250.1551] [ 1214] [depth= 8] . ( 5 sec) [ -7249.0556] [ 1215] [depth= 7] . ( 5 sec) [ -7223.6431] [ 1213] [depth= 13] . ( 5 sec) [ -7185.8328] [ 1209] [depth= 11] . ( 5 sec) [ -7172.7310] [ 1206] [depth= 6] . ( 5 sec) [ -6891.2320] [ 1206] [depth= 1] . ( 5 sec) [ -6879.2325] [ 1205] [depth= 2] . ( 5 sec) [ -6878.1053] [ 1204] [depth= 4] . ( 5 sec) [ -6844.8742] [ 1195] [depth= 1] . ( 5 sec) [ -6763.2628] [ 1169] [depth= 1] . ( 5 sec) [ -6690.7138] [ 1153] [depth= 13] . ( 5 sec) [ -6680.6378] [ 1152] [depth= 2] . ( 6 sec) [ -6680.5506] [ 1152] [depth= 1] . ( 6 sec) [ -6579.2623] [ 1149] [depth= 1] . ( 6 sec) [ -6559.0549] [ 1146] [depth= 2] . ( 6 sec) [ -6552.5224] [ 1143] [depth= 1] . ( 6 sec) [ -6547.8090] [ 1143] [depth= 1] . ( 6 sec) [ -6529.4248] [ 1117] [depth= 1] . ( 6 sec) [ -6494.6402] [ 1112] [depth= 8] . ( 6 sec) [ -6478.3106] [ 1113] [depth= 2] . ( 6 sec) [ -6477.4700] [ 1113] [depth= 1] . ( 6 sec) [ -6424.3072] [ 1100] [depth= 10] . ( 6 sec) [ -6421.7895] [ 1100] [depth= 1] . ( 6 sec) [ -6408.6833] [ 1098] [depth= 8] . ( 6 sec) [ -6408.6555] [ 1098] [depth= 1] . ( 6 sec) [ -6363.5772] [ 1099] [depth= 6] . ( 6 sec) [ -6361.2169] [ 1099] [depth= 1] . ( 6 sec) [ -6343.5243] [ 1096] [depth= 7] . ( 7 sec) [ -6342.7674] [ 1095] [depth= 5] . ( 7 sec) [ -6316.9018] [ 1091] [depth= 6] . ( 7 sec) [ -6287.6505] [ 1094] [depth= 5] . ( 7 sec) [ -6220.3701] [ 1070] [depth= 4] . ( 7 sec) [ -6190.0265] [ 1064] [depth= 1] . ( 7 sec) [ -6185.5277] [ 1065] [depth= 1] . ( 7 sec) [ -6183.5999] [ 1064] [depth= 3] . ( 7 sec) [ -6183.3632] [ 1063] [depth= 1] . ( 7 sec) [ -6012.0447] [ 991] [depth= 8] . ( 7 sec) [ -5996.3063] [ 991] [depth= 2] . ( 7 sec) [ -5992.2183] [ 991] [depth= 1] . ( 7 sec) [ -5992.1794] [ 991] [depth= 1] . ( 7 sec) [ -5991.8638] [ 991] [depth= 5] . ( 7 sec) [ -5983.9958] [ 991] [depth= 6] . ( 8 sec) [ -5981.6284] [ 991] [depth= 1] . ( 8 sec) [ -5964.8996] [ 981] [depth= 1] . ( 8 sec) [ -5960.9278] [ 980] [depth= 2] . ( 8 sec) [ -5959.5562] [ 980] [depth= 4] . ( 8 sec) [ -5889.9483] [ 963] [depth= 1] . ( 8 sec) [ -5887.0198] [ 965] [depth= 1] . ( 9 sec) [ -5865.2526] [ 963] [depth= 1] . ( 9 sec) [ -5831.4235] [ 951] [depth= 1] . ( 9 sec) [ -5830.2991] [ 951] [depth= 1] . ( 9 sec) [ -5812.4571] [ 943] [depth= 4] . ( 9 sec) [ -5785.8701] [ 942] [depth= 1] . ( 9 sec) [ -5785.4286] [ 942] [depth= 9] . ( 9 sec) [ -5759.5811] [ 932] [depth= 16] . ( 10 sec) [ -5754.9744] [ 930] [depth= 2] . ( 10 sec) [ -5749.9919] [ 929] [depth= 1] . ( 10 sec) [ -5749.8846] [ 928] [depth= 3] . ( 10 sec) [ -5711.9298] [ 926] [depth= 1] . ( 10 sec) [ -5652.9995] [Branch lengths ] . ( 11 sec) [ -5644.9077] [GTR parameters ] . ( 11 sec) [ -5588.7330] [Alpha ][ 0.250961] . ( 11 sec) [ -5582.3374] [ 924] [depth= 1] . ( 11 sec) [ -5561.1185] [ 917] [depth= 13] . ( 11 sec) [ -5557.4942] [ 916] [depth= 4] . ( 11 sec) [ -5555.2687] [ 915] [depth= 1] . ( 11 sec) [ -5555.0173] [ 917] [depth= 1] . ( 11 sec) [ -5554.9632] [ 917] [depth= 1] . ( 12 sec) [ -5554.9428] [ 917] [depth= 1] . ( 12 sec) [ -5508.5477] [ 888] [depth= 11] . ( 12 sec) [ -5508.4971] [ 888] [depth= 1] . ( 13 sec) [ -5508.2594] [ 884] [depth= 3] . ( 13 sec) [ -5508.0833] [ 884] [depth= 1] . ( 13 sec) [ -5507.8385] [ 883] [depth= 1] . ( 14 sec) [ -5500.3077] [ 883] [depth= 1] . ( 14 sec) [ -5495.4229] [ 883] [depth= 1] . ( 15 sec) [ -5494.8507] [ 883] [depth= 3] . ( 16 sec) [ -5493.0643] [ 880] [depth= 2] . ( 16 sec) [ -5482.9005] [ 878] [depth= 1] . ( 16 sec) [ -5465.2690] [ 871] [depth= 7] . ( 16 sec) [ -5454.4863] [ 870] [depth= 14] . ( 16 sec) [ -5454.0527] [ 870] [depth= 1] . ( 16 sec) [ -5453.3473] [ 870] [depth= 1] . ( 16 sec) [ -5453.1950] [ 870] [depth= 1] . ( 16 sec) [ -5453.1696] [ 870] [depth= 1] . ( 17 sec) [ -5453.1246] [ 870] [depth= 1] . ( 17 sec) [ -5452.9878] [ 870] [depth= 1] . ( 17 sec) [ -5442.2171] [ 866] [depth= 12] . ( 17 sec) [ -5442.1449] [ 866] [depth= 2] . ( 17 sec) [ -5442.1276] [ 866] [depth= 2] . ( 18 sec) [ -5442.0497] [ 866] [depth= 1] . ( 19 sec) [ -5420.0761] [ 859] [depth= 8] . ( 19 sec) [ -5419.8683] [ 859] [depth= 1] . ( 21 sec) [ -5410.9426] [ 857] [depth= 7] . ( 22 sec) [ -5408.3588] [ 856] [depth= 1] . ( 22 sec) [ -5406.9727] [ 855] [depth= 1] . ( 22 sec) [ -5399.4608] [ 853] [depth= 1] . ( 22 sec) [ -5399.4506] [ 853] [depth= 1] . ( 23 sec) [ -5388.1501] [Branch lengths ] . ( 24 sec) [ -5386.3936] [GTR parameters ] . ( 24 sec) [ -5386.0668] [Alpha ][ 0.237057] . ( 26 sec) [ -5386.0271] [ 856] [depth= 2] . ( 29 sec) [ -5385.9429] [ 855] [depth= 1] . ( 31 sec) [ -5385.0662] [ 855] [depth= 1] . ( 31 sec) [ -5385.0505] [ 855] [depth= 1] . ( 31 sec) [ -5384.9674] [ 855] [depth= 1] . ( 31 sec) [ -5384.7998] [ 855] [depth= 1] . ( 39 sec) [ -5383.7027] [Branch lengths ] . ( 39 sec) [ -5383.6881] [GTR parameters ] . ( 40 sec) [ -5383.6862] [Alpha ][ 0.235954] . ( 55 sec) [ -5382.8603] [Branch lengths ] . ( 91 sec) [ -5382.5686] [Branch lengths ] . ( 91 sec) [ -5382.5686] [Topology ] . ( 92 sec) [ -5382.5269] [Topology ] . ( 92 sec) [ -5382.5094] [Topology ] . ( 93 sec) [ -5382.4998] [Topology ] . ( 94 sec) [ -5382.4943] [Topology ] . ( 95 sec) [ -5382.4912] [Topology ] . ( 96 sec) [ -5382.4894] [Topology ] . ( 96 sec) [ -5382.4868] [GTR parameters ] . ( 96 sec) [ -5382.4835] [Alpha ][ 0.237306] . ( 96 sec) [ -5382.4835] [Topology ] . ( 97 sec) [ -5382.4821] [Topology ] . ( 98 sec) [ -5382.4814] [Topology ] . ( 98 sec) [ -5382.4813] [GTR parameters ] . ( 98 sec) [ -5382.4813] [Alpha ][ 0.237306] . ( 98 sec) [ -5382.4813] [Topology ] . ( 99 sec) [ -5382.4809] [Topology ] . ( 99 sec) [ -5382.4809] [GTR parameters ] . ( 100 sec) [ -5382.4809] [Alpha ][ 0.237306] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.480854. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13583.8929] [GTR parameters ] . ( 1 sec) [ -13281.6272] [Alpha ][ 0.500960] . ( 1 sec) [ -13142.9488] [ 1827] [depth= 12] . ( 1 sec) [ -12963.0577] [ 1804] [depth= 11] . ( 1 sec) [ -12520.9778] [ 1784] [depth= 13] . ( 1 sec) [ -12308.4812] [ 1731] [depth= 1] . ( 1 sec) [ -12091.1973] [ 1728] [depth= 1] . ( 1 sec) [ -12002.6870] [ 1713] [depth= 7] . ( 1 sec) [ -12001.5534] [ 1713] [depth= 1] . ( 1 sec) [ -11919.0675] [ 1704] [depth= 6] . ( 1 sec) [ -11807.5718] [ 1699] [depth= 2] . ( 1 sec) [ -11800.9437] [ 1697] [depth= 4] . ( 1 sec) [ -11783.1994] [ 1684] [depth= 6] . ( 1 sec) [ -11768.2811] [ 1684] [depth= 2] . ( 1 sec) [ -11535.5445] [ 1679] [depth= 4] . ( 1 sec) [ -11530.6305] [ 1679] [depth= 1] . ( 1 sec) [ -11374.2601] [ 1664] [depth= 7] . ( 2 sec) [ -11293.8791] [ 1661] [depth= 15] . ( 2 sec) [ -11211.0109] [ 1660] [depth= 6] . ( 2 sec) [ -11200.9771] [ 1613] [depth= 9] . ( 2 sec) [ -11199.6600] [ 1614] [depth= 3] . ( 2 sec) [ -11167.1511] [ 1611] [depth= 5] . ( 2 sec) [ -11166.5963] [ 1611] [depth= 1] . ( 2 sec) [ -11097.4981] [ 1611] [depth= 2] . ( 2 sec) [ -10955.3919] [ 1608] [depth= 10] . ( 2 sec) [ -10839.0298] [ 1608] [depth= 1] . ( 2 sec) [ -10676.1603] [ 1562] [depth= 10] . ( 2 sec) [ -10622.2775] [ 1558] [depth= 4] . ( 2 sec) [ -10533.0525] [ 1558] [depth= 1] . ( 2 sec) [ -10151.1400] [ 1551] [depth= 5] . ( 2 sec) [ -10147.7066] [ 1553] [depth= 1] . ( 2 sec) [ -10044.6893] [ 1540] [depth= 9] . ( 2 sec) [ -10002.4772] [ 1539] [depth= 1] . ( 2 sec) [ -9973.3422] [ 1528] [depth= 1] . ( 2 sec) [ -9892.4008] [ 1531] [depth= 1] . ( 2 sec) [ -9763.3514] [ 1506] [depth= 17] . ( 2 sec) [ -9714.8998] [ 1501] [depth= 5] . ( 2 sec) [ -9711.1631] [ 1501] [depth= 2] . ( 3 sec) [ -9248.7206] [ 1454] [depth= 8] . ( 3 sec) [ -9245.3287] [ 1452] [depth= 2] . ( 3 sec) [ -8956.1209] [ 1446] [depth= 6] . ( 3 sec) [ -8935.8564] [ 1445] [depth= 2] . ( 3 sec) [ -8892.9987] [ 1441] [depth= 15] . ( 3 sec) [ -8883.5652] [ 1433] [depth= 2] . ( 3 sec) [ -8834.3878] [ 1422] [depth= 11] . ( 3 sec) [ -8823.0539] [ 1419] [depth= 4] . ( 3 sec) [ -8815.4986] [ 1419] [depth= 5] . ( 3 sec) [ -8804.3185] [ 1416] [depth= 1] . ( 3 sec) [ -8776.0556] [ 1415] [depth= 5] . ( 3 sec) [ -8489.4298] [ 1384] [depth= 8] . ( 3 sec) [ -8133.1800] [ 1370] [depth= 15] . ( 3 sec) [ -8125.3498] [ 1368] [depth= 1] . ( 3 sec) [ -8038.4002] [ 1346] [depth= 2] . ( 3 sec) [ -8015.9363] [ 1344] [depth= 6] . ( 3 sec) [ -7967.9954] [ 1300] [depth= 11] . ( 4 sec) [ -7859.3530] [ 1252] [depth= 7] . ( 4 sec) [ -7856.2791] [ 1252] [depth= 2] . ( 4 sec) [ -7852.0587] [ 1252] [depth= 3] . ( 4 sec) [ -6962.3187] [ 1247] [depth= 4] . ( 4 sec) [ -6951.3967] [ 1247] [depth= 1] . ( 4 sec) [ -6822.1929] [ 1220] [depth= 18] . ( 4 sec) [ -6799.3471] [ 1211] [depth= 14] . ( 4 sec) [ -6782.0292] [ 1207] [depth= 1] . ( 4 sec) [ -6619.1083] [ 1158] [depth= 1] . ( 4 sec) [ -6580.2578] [ 1130] [depth= 1] . ( 4 sec) [ -6577.8984] [ 1111] [depth= 14] . ( 4 sec) [ -6517.7035] [ 1115] [depth= 1] . ( 4 sec) [ -6396.4565] [ 1100] [depth= 14] . ( 4 sec) [ -6356.0798] [ 1080] [depth= 1] . ( 4 sec) [ -6355.8202] [ 1081] [depth= 1] . ( 5 sec) [ -6349.4301] [ 1081] [depth= 1] . ( 5 sec) [ -6334.1558] [ 1080] [depth= 1] . ( 5 sec) [ -6285.7619] [ 1038] [depth= 14] . ( 5 sec) [ -6241.8441] [ 1024] [depth= 18] . ( 5 sec) [ -6220.6831] [ 1023] [depth= 1] . ( 5 sec) [ -6219.7688] [ 1024] [depth= 1] . ( 5 sec) [ -6159.5247] [ 1012] [depth= 15] . ( 5 sec) [ -6146.6992] [ 1010] [depth= 1] . ( 5 sec) [ -6123.7751] [ 1007] [depth= 5] . ( 5 sec) [ -6111.9325] [ 1007] [depth= 2] . ( 5 sec) [ -6110.2424] [ 1007] [depth= 1] . ( 5 sec) [ -6094.9018] [ 1007] [depth= 2] . ( 6 sec) [ -6091.5273] [ 1006] [depth= 2] . ( 6 sec) [ -6090.2007] [ 1008] [depth= 1] . ( 6 sec) [ -6072.3606] [ 990] [depth= 4] . ( 6 sec) [ -6071.9278] [ 990] [depth= 2] . ( 6 sec) [ -6056.0920] [ 986] [depth= 1] . ( 6 sec) [ -6043.9224] [ 984] [depth= 2] . ( 6 sec) [ -6041.8290] [ 984] [depth= 1] . ( 6 sec) [ -6041.7354] [ 983] [depth= 2] . ( 6 sec) [ -6041.2085] [ 984] [depth= 2] . ( 6 sec) [ -6001.1354] [ 956] [depth= 1] . ( 6 sec) [ -5982.1756] [ 950] [depth= 5] . ( 7 sec) [ -5981.8027] [ 951] [depth= 2] . ( 7 sec) [ -5970.7660] [ 948] [depth= 2] . ( 7 sec) [ -5905.5213] [ 927] [depth= 4] . ( 7 sec) [ -5901.2007] [ 930] [depth= 1] . ( 7 sec) [ -5901.1769] [ 930] [depth= 1] . ( 7 sec) [ -5900.9232] [ 930] [depth= 1] . ( 7 sec) [ -5900.8833] [ 930] [depth= 2] . ( 7 sec) [ -5872.7528] [ 924] [depth= 9] . ( 7 sec) [ -5871.6385] [ 924] [depth= 1] . ( 7 sec) [ -5871.5356] [ 924] [depth= 2] . ( 7 sec) [ -5871.4926] [ 924] [depth= 2] . ( 7 sec) [ -5871.2688] [ 925] [depth= 1] . ( 7 sec) [ -5869.9181] [ 924] [depth= 3] . ( 7 sec) [ -5865.1277] [ 923] [depth= 1] . ( 7 sec) [ -5841.9996] [ 915] [depth= 2] . ( 8 sec) [ -5829.1765] [ 911] [depth= 4] . ( 8 sec) [ -5828.7240] [ 911] [depth= 2] . ( 9 sec) [ -5826.6222] [ 911] [depth= 1] . ( 9 sec) [ -5818.8331] [ 907] [depth= 2] . ( 9 sec) [ -5812.2373] [ 911] [depth= 2] . ( 9 sec) [ -5779.7023] [ 901] [depth= 7] . ( 9 sec) [ -5770.5529] [ 897] [depth= 1] . ( 9 sec) [ -5727.1252] [Branch lengths ] . ( 11 sec) [ -5555.2168] [GTR parameters ] . ( 11 sec) [ -5504.2671] [Alpha ][ 0.250961] . ( 12 sec) [ -5501.0855] [ 901] [depth= 2] . ( 12 sec) [ -5497.5492] [ 900] [depth= 2] . ( 12 sec) [ -5495.0058] [ 898] [depth= 2] . ( 13 sec) [ -5475.5292] [ 890] [depth= 1] . ( 13 sec) [ -5470.4614] [ 885] [depth= 1] . ( 13 sec) [ -5470.4470] [ 885] [depth= 1] . ( 13 sec) [ -5462.5892] [ 885] [depth= 1] . ( 13 sec) [ -5457.3024] [ 882] [depth= 1] . ( 14 sec) [ -5457.0941] [ 882] [depth= 1] . ( 14 sec) [ -5456.9532] [ 882] [depth= 1] . ( 14 sec) [ -5456.3294] [ 881] [depth= 1] . ( 14 sec) [ -5422.9416] [ 869] [depth= 4] . ( 14 sec) [ -5418.1362] [ 865] [depth= 1] . ( 14 sec) [ -5416.3106] [ 865] [depth= 1] . ( 16 sec) [ -5411.9438] [ 868] [depth= 2] . ( 16 sec) [ -5401.6681] [ 861] [depth= 1] . ( 17 sec) [ -5401.0979] [ 861] [depth= 1] . ( 18 sec) [ -5401.0833] [ 858] [depth= 1] . ( 18 sec) [ -5401.0630] [ 858] [depth= 1] . ( 18 sec) [ -5396.5301] [ 856] [depth= 7] . ( 20 sec) [ -5396.1582] [ 856] [depth= 1] . ( 20 sec) [ -5395.8105] [ 856] [depth= 1] . ( 21 sec) [ -5395.7933] [ 856] [depth= 2] . ( 26 sec) [ -5395.7174] [ 856] [depth= 1] . ( 27 sec) [ -5386.5393] [Branch lengths ] . ( 28 sec) [ -5385.3759] [GTR parameters ] . ( 29 sec) [ -5385.0267] [Alpha ][ 0.236435] . ( 32 sec) [ -5384.9347] [ 855] [depth= 1] . ( 45 sec) [ -5383.8878] [Branch lengths ] . ( 46 sec) [ -5383.8568] [GTR parameters ] . ( 46 sec) [ -5383.8562] [Alpha ][ 0.235817] . ( 63 sec) [ -5383.7458] [Branch lengths ] . ( 99 sec) [ -5383.7300] [Branch lengths ] . ( 99 sec) [ -5383.7300] [Topology ] . ( 99 sec) [ -5383.7284] [Topology ] . ( 100 sec) [ -5383.7266] [Topology ] . ( 101 sec) [ -5383.7155] [Topology ] . ( 102 sec) [ -5383.6362] [Topology ] . ( 103 sec) [ -5383.2360] [Topology ] . ( 104 sec) [ -5382.9472] [Topology ] . ( 105 sec) [ -5382.9427] [GTR parameters ] . ( 105 sec) [ -5382.9402] [Alpha ][ 0.236971] . ( 105 sec) [ -5382.9402] [Topology ] . ( 106 sec) [ -5382.7584] [Topology ] . ( 107 sec) [ -5382.6466] [Topology ] . ( 108 sec) [ -5382.5793] [Topology ] . ( 108 sec) [ -5382.5397] [Topology ] . ( 109 sec) [ -5382.5161] [Topology ] . ( 110 sec) [ -5382.5027] [Topology ] . ( 111 sec) [ -5382.5005] [GTR parameters ] . ( 111 sec) [ -5382.5002] [Alpha ][ 0.237305] . ( 111 sec) [ -5382.5002] [Topology ] . ( 112 sec) [ -5382.4920] [Topology ] . ( 113 sec) [ -5382.4873] [Topology ] . ( 114 sec) [ -5382.4846] [Topology ] . ( 115 sec) [ -5382.4830] [Topology ] . ( 116 sec) [ -5382.4822] [Topology ] . ( 116 sec) [ -5382.4822] [GTR parameters ] . ( 116 sec) [ -5382.4822] [Alpha ][ 0.237305] . ( 116 sec) [ -5382.4822] [Topology ] . ( 117 sec) [ -5382.4817] [Topology ] . ( 117 sec) [ -5382.4817] [GTR parameters ] . ( 117 sec) [ -5382.4817] [Alpha ][ 0.237305] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.481670. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13452.3206] [GTR parameters ] . ( 1 sec) [ -13135.6097] [Alpha ][ 0.500960] . ( 1 sec) [ -13033.9826] [ 1883] [depth= 5] . ( 1 sec) [ -12572.4597] [ 1868] [depth= 9] . ( 1 sec) [ -12528.3006] [ 1867] [depth= 3] . ( 1 sec) [ -12402.8792] [ 1866] [depth= 2] . ( 1 sec) [ -12370.4535] [ 1860] [depth= 7] . ( 1 sec) [ -12205.6944] [ 1859] [depth= 7] . ( 1 sec) [ -12059.0745] [ 1830] [depth= 17] . ( 1 sec) [ -12029.8793] [ 1830] [depth= 1] . ( 1 sec) [ -12028.6736] [ 1835] [depth= 1] . ( 2 sec) [ -11815.0305] [ 1828] [depth= 20] . ( 2 sec) [ -11740.8158] [ 1801] [depth= 1] . ( 2 sec) [ -11679.3073] [ 1796] [depth= 15] . ( 2 sec) [ -11628.2081] [ 1790] [depth= 1] . ( 2 sec) [ -11382.2041] [ 1770] [depth= 12] . ( 2 sec) [ -11123.0657] [ 1759] [depth= 1] . ( 2 sec) [ -9791.7489] [ 1709] [depth= 10] . ( 2 sec) [ -9674.0551] [ 1681] [depth= 10] . ( 2 sec) [ -9393.8404] [ 1680] [depth= 9] . ( 2 sec) [ -9348.2693] [ 1679] [depth= 14] . ( 2 sec) [ -9238.1177] [ 1657] [depth= 2] . ( 2 sec) [ -9208.9232] [ 1654] [depth= 13] . ( 2 sec) [ -9198.5168] [ 1645] [depth= 12] . ( 2 sec) [ -8685.3525] [ 1563] [depth= 13] . ( 2 sec) [ -8666.5864] [ 1557] [depth= 10] . ( 2 sec) [ -8627.0300] [ 1536] [depth= 8] . ( 2 sec) [ -8605.8266] [ 1538] [depth= 1] . ( 3 sec) [ -8578.7046] [ 1528] [depth= 1] . ( 3 sec) [ -8572.4530] [ 1528] [depth= 1] . ( 3 sec) [ -8569.7050] [ 1526] [depth= 1] . ( 3 sec) [ -8464.6053] [ 1503] [depth= 8] . ( 3 sec) [ -8407.4790] [ 1505] [depth= 3] . ( 3 sec) [ -8163.5429] [ 1414] [depth= 12] . ( 3 sec) [ -8118.4077] [ 1407] [depth= 7] . ( 3 sec) [ -8117.3731] [ 1407] [depth= 5] . ( 3 sec) [ -8115.6619] [ 1407] [depth= 11] . ( 3 sec) [ -8083.6870] [ 1401] [depth= 8] . ( 3 sec) [ -8038.4756] [ 1402] [depth= 12] . ( 3 sec) [ -8013.9774] [ 1400] [depth= 11] . ( 3 sec) [ -7997.9602] [ 1388] [depth= 1] . ( 3 sec) [ -7948.9805] [ 1382] [depth= 9] . ( 3 sec) [ -7832.8785] [ 1356] [depth= 4] . ( 3 sec) [ -7832.4980] [ 1356] [depth= 15] . ( 3 sec) [ -7819.5418] [ 1354] [depth= 14] . ( 3 sec) [ -7809.6319] [ 1353] [depth= 2] . ( 4 sec) [ -7808.6165] [ 1352] [depth= 14] . ( 4 sec) [ -7688.6260] [ 1321] [depth= 8] . ( 4 sec) [ -7688.3817] [ 1321] [depth= 1] . ( 4 sec) [ -7680.3565] [ 1320] [depth= 1] . ( 4 sec) [ -7678.4633] [ 1325] [depth= 8] . ( 4 sec) [ -7678.4017] [ 1325] [depth= 1] . ( 4 sec) [ -7676.5385] [ 1324] [depth= 8] . ( 4 sec) [ -7653.5992] [ 1323] [depth= 9] . ( 4 sec) [ -7643.4694] [ 1323] [depth= 1] . ( 4 sec) [ -7638.4087] [ 1323] [depth= 3] . ( 4 sec) [ -7502.1705] [ 1286] [depth= 13] . ( 4 sec) [ -7457.3673] [ 1273] [depth= 8] . ( 5 sec) [ -7448.1564] [ 1265] [depth= 4] . ( 5 sec) [ -7414.4242] [ 1265] [depth= 2] . ( 5 sec) [ -7327.6107] [ 1242] [depth= 8] . ( 5 sec) [ -7303.0019] [ 1233] [depth= 2] . ( 5 sec) [ -7258.8650] [ 1210] [depth= 1] . ( 5 sec) [ -7237.1606] [ 1207] [depth= 3] . ( 5 sec) [ -7228.1319] [ 1209] [depth= 12] . ( 5 sec) [ -7152.4565] [ 1195] [depth= 11] . ( 5 sec) [ -7109.5047] [ 1170] [depth= 5] . ( 5 sec) [ -7082.3898] [ 1170] [depth= 1] . ( 5 sec) [ -7073.0437] [ 1169] [depth= 5] . ( 5 sec) [ -6610.1790] [ 1136] [depth= 10] . ( 5 sec) [ -6522.2660] [ 1142] [depth= 1] . ( 5 sec) [ -6446.7241] [ 1083] [depth= 12] . ( 5 sec) [ -6374.8756] [ 1070] [depth= 9] . ( 5 sec) [ -6364.1836] [ 1067] [depth= 1] . ( 6 sec) [ -6349.7008] [ 1061] [depth= 8] . ( 6 sec) [ -6339.6192] [ 1060] [depth= 3] . ( 6 sec) [ -6336.7666] [ 1060] [depth= 5] . ( 6 sec) [ -6329.8726] [ 1059] [depth= 5] . ( 6 sec) [ -6326.0351] [ 1059] [depth= 1] . ( 6 sec) [ -6314.9009] [ 1055] [depth= 5] . ( 6 sec) [ -6306.0447] [ 1056] [depth= 1] . ( 6 sec) [ -6304.0885] [ 1048] [depth= 6] . ( 6 sec) [ -6112.3402] [ 990] [depth= 2] . ( 6 sec) [ -6112.1513] [ 990] [depth= 1] . ( 6 sec) [ -6111.5090] [ 994] [depth= 1] . ( 6 sec) [ -6105.7264] [ 983] [depth= 11] . ( 6 sec) [ -6066.1473] [ 971] [depth= 3] . ( 6 sec) [ -6018.1553] [ 972] [depth= 1] . ( 6 sec) [ -5983.8443] [ 963] [depth= 5] . ( 6 sec) [ -5980.1205] [ 962] [depth= 1] . ( 6 sec) [ -5932.4824] [ 947] [depth= 4] . ( 7 sec) [ -5932.1146] [ 947] [depth= 1] . ( 7 sec) [ -5931.3272] [ 947] [depth= 1] . ( 7 sec) [ -5929.9752] [ 947] [depth= 2] . ( 8 sec) [ -5891.5453] [ 942] [depth= 6] . ( 8 sec) [ -5868.4125] [ 928] [depth= 1] . ( 8 sec) [ -5861.4873] [ 927] [depth= 2] . ( 8 sec) [ -5860.9890] [ 919] [depth= 1] . ( 8 sec) [ -5804.9332] [ 910] [depth= 1] . ( 8 sec) [ -5804.1802] [ 910] [depth= 1] . ( 8 sec) [ -5766.6249] [ 900] [depth= 7] . ( 8 sec) [ -5737.2083] [ 888] [depth= 5] . ( 8 sec) [ -5736.6707] [ 889] [depth= 1] . ( 8 sec) [ -5735.6008] [ 892] [depth= 1] . ( 8 sec) [ -5731.4673] [ 892] [depth= 1] . ( 8 sec) [ -5709.6495] [ 889] [depth= 1] . ( 8 sec) [ -5705.3562] [ 888] [depth= 1] . ( 8 sec) [ -5705.1660] [ 889] [depth= 1] . ( 9 sec) [ -5675.4537] [ 880] [depth= 4] . ( 9 sec) [ -5670.2672] [ 880] [depth= 2] . ( 9 sec) [ -5666.0862] [ 878] [depth= 1] . ( 9 sec) [ -5623.9603] [ 881] [depth= 1] . ( 9 sec) [ -5619.7658] [ 880] [depth= 1] . ( 9 sec) [ -5615.4776] [ 879] [depth= 2] . ( 9 sec) [ -5554.6065] [Branch lengths ] . ( 10 sec) [ -5545.0376] [GTR parameters ] . ( 10 sec) [ -5498.0985] [Alpha ][ 0.250961] . ( 10 sec) [ -5497.6481] [ 882] [depth= 6] . ( 11 sec) [ -5481.3938] [ 879] [depth= 1] . ( 11 sec) [ -5480.9247] [ 877] [depth= 3] . ( 11 sec) [ -5470.1297] [ 875] [depth= 3] . ( 12 sec) [ -5438.6083] [ 866] [depth= 4] . ( 12 sec) [ -5438.5573] [ 866] [depth= 1] . ( 12 sec) [ -5436.9705] [ 863] [depth= 1] . ( 12 sec) [ -5432.7782] [ 861] [depth= 2] . ( 13 sec) [ -5431.4559] [ 861] [depth= 1] . ( 13 sec) [ -5429.8043] [ 858] [depth= 1] . ( 13 sec) [ -5426.4959] [ 858] [depth= 1] . ( 13 sec) [ -5425.6263] [ 858] [depth= 1] . ( 13 sec) [ -5425.3304] [ 858] [depth= 1] . ( 14 sec) [ -5418.6208] [ 853] [depth= 2] . ( 14 sec) [ -5418.5414] [ 853] [depth= 1] . ( 14 sec) [ -5418.5307] [ 853] [depth= 2] . ( 15 sec) [ -5416.6140] [ 852] [depth= 2] . ( 15 sec) [ -5416.4661] [ 852] [depth= 1] . ( 15 sec) [ -5416.4480] [ 852] [depth= 2] . ( 16 sec) [ -5416.4164] [ 852] [depth= 1] . ( 16 sec) [ -5416.4039] [ 852] [depth= 1] . ( 16 sec) [ -5415.7681] [ 853] [depth= 1] . ( 16 sec) [ -5413.4843] [ 854] [depth= 1] . ( 16 sec) [ -5408.3600] [ 852] [depth= 1] . ( 17 sec) [ -5408.2371] [ 852] [depth= 1] . ( 17 sec) [ -5408.1258] [ 853] [depth= 1] . ( 17 sec) [ -5406.1715] [ 853] [depth= 2] . ( 18 sec) [ -5402.1754] [ 854] [depth= 1] . ( 18 sec) [ -5402.1273] [ 854] [depth= 2] . ( 19 sec) [ -5402.0647] [ 854] [depth= 3] . ( 19 sec) [ -5400.4409] [ 854] [depth= 2] . ( 20 sec) [ -5397.9955] [ 853] [depth= 1] . ( 21 sec) [ -5397.5745] [ 853] [depth= 1] . ( 21 sec) [ -5396.4015] [ 851] [depth= 1] . ( 22 sec) [ -5386.1668] [Branch lengths ] . ( 23 sec) [ -5385.0571] [GTR parameters ] . ( 23 sec) [ -5384.8080] [Alpha ][ 0.238778] . ( 25 sec) [ -5384.6063] [ 854] [depth= 9] . ( 25 sec) [ -5384.5962] [ 854] [depth= 1] . ( 26 sec) [ -5384.3840] [ 854] [depth= 8] . ( 34 sec) [ -5383.6712] [ 854] [depth= 2] . ( 36 sec) [ -5383.5899] [ 854] [depth= 1] . ( 38 sec) [ -5382.4848] [Branch lengths ] . ( 39 sec) [ -5382.4768] [GTR parameters ] . ( 39 sec) [ -5382.4767] [Alpha ][ 0.238537] . ( 56 sec) [ -5382.3711] [Branch lengths ] . ( 92 sec) [ -5382.3631] [Branch lengths ] . ( 92 sec) [ -5382.3631] [Topology ] . ( 93 sec) [ -5382.3624] [Topology ] . ( 93 sec) [ -5382.3622] [GTR parameters ] . ( 93 sec) [ -5382.3620] [Alpha ][ 0.238855] . ( 93 sec) [ -5382.3620] [Topology ] . ( 94 sec) [ -5382.3617] [Topology ] . ( 94 sec) [ -5382.3617] [GTR parameters ] . ( 95 sec) [ -5382.3617] [Alpha ][ 0.238855] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5382.361671. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -5607.7521] [GTR parameters ] . ( 2 sec) [ -5527.3790] [Alpha ][ 0.500960] . ( 2 sec) [ -5527.3790] [Topology ] . ( 3 sec) [ -5448.8222] [Topology ] . ( 4 sec) [ -5438.0985] [Topology ] . ( 5 sec) [ -5434.1096] [Topology ] . ( 5 sec) [ -5433.1507] [Topology ] . ( 6 sec) [ -5432.8467] [Topology ] . ( 7 sec) [ -5432.7452] [Topology ] . ( 8 sec) [ -5432.7100] [Topology ] . ( 9 sec) [ -5432.6977] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -5431.2776] [GTR parameters ] . ( 17 sec) [ -5390.3234] [Alpha ][ 0.250961] . ( 17 sec) [ -5390.3234] [Topology ] . ( 18 sec) [ -5388.8139] [Topology ] . ( 19 sec) [ -5388.5269] [Topology ] . ( 20 sec) [ -5388.2440] [Topology ] . ( 20 sec) [ -5388.1583] [Topology ] . ( 21 sec) [ -5388.0550] [Topology ] . ( 22 sec) [ -5387.7713] [Topology ] . ( 23 sec) [ -5387.7076] [Topology ] . ( 24 sec) [ -5387.6842] [Topology ] . ( 25 sec) [ -5387.6741] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -5386.6889] [GTR parameters ] . ( 33 sec) [ -5386.4426] [Alpha ][ 0.239110] . ( 33 sec) [ -5386.4426] [Topology ] . ( 34 sec) [ -5386.3875] [Topology ] . ( 35 sec) [ -5386.3714] [Topology ] . ( 36 sec) [ -5386.3639] [Topology ] . ( 37 sec) [ -5386.3601] [Topology ] . ( 38 sec) [ -5386.3582] [Topology ] . ( 38 sec) [ -5386.3573] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -5386.3405] [GTR parameters ] . ( 46 sec) [ -5386.3391] [Alpha ][ 0.238200] . ( 46 sec) [ -5386.3391] [Topology ] . ( 47 sec) [ -5386.3364] [Topology ] . ( 47 sec) [ -5386.3353] [Topology ] . ( 48 sec) [ -5386.3348] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -5386.3345] [GTR parameters ] . ( 55 sec) [ -5386.3345] [Alpha ][ 0.238200] . ( 55 sec) [ -5386.3345] [Topology ] . ( 56 sec) [ -5386.3341] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 70 sec) [ -5607.7521] [GTR parameters ] . ( 70 sec) [ -5527.3790] [Alpha ][ 0.500960] . ( 70 sec) [ -5525.4341] [ 850] [depth= 1] . ( 70 sec) [ -5523.1508] [ 853] [depth= 1] . ( 70 sec) [ -5519.7480] [ 850] [depth= 1] . ( 70 sec) [ -5507.5690] [ 851] [depth= 1] . ( 70 sec) [ -5504.6039] [ 850] [depth= 1] . ( 71 sec) [ -5504.2033] [ 851] [depth= 1] . ( 71 sec) [ -5499.4790] [ 853] [depth= 2] . ( 71 sec) [ -5496.3204] [ 853] [depth= 1] . ( 71 sec) [ -5496.1446] [ 854] [depth= 2] . ( 71 sec) [ -5495.3779] [ 853] [depth= 1] . ( 71 sec) [ -5492.1844] [ 853] [depth= 1] . ( 71 sec) [ -5491.9547] [ 854] [depth= 1] . ( 72 sec) [ -5491.1091] [ 854] [depth= 1] . ( 72 sec) [ -5490.9140] [ 853] [depth= 1] . ( 72 sec) [ -5490.8549] [ 854] [depth= 1] . ( 72 sec) [ -5490.6489] [ 854] [depth= 1] . ( 72 sec) [ -5483.4840] [ 850] [depth= 2] . ( 72 sec) [ -5483.1862] [ 855] [depth= 1] . ( 72 sec) [ -5482.9207] [ 853] [depth= 3] . ( 73 sec) [ -5481.9203] [ 853] [depth= 1] . ( 73 sec) [ -5476.1793] [ 854] [depth= 1] . ( 73 sec) [ -5476.1352] [ 855] [depth= 1] . ( 74 sec) [ -5475.2624] [ 854] [depth= 1] . ( 75 sec) [ -5474.3623] [ 856] [depth= 1] . ( 75 sec) [ -5471.7260] [ 854] [depth= 1] . ( 75 sec) [ -5466.7703] [ 855] [depth= 2] . ( 75 sec) [ -5466.6433] [ 856] [depth= 1] . ( 76 sec) [ -5466.5185] [ 856] [depth= 1] . ( 76 sec) [ -5466.2310] [ 856] [depth= 1] . ( 76 sec) [ -5466.1849] [ 856] [depth= 1] . ( 76 sec) [ -5466.1505] [ 856] [depth= 1] . ( 77 sec) [ -5466.0112] [ 856] [depth= 1] . ( 77 sec) [ -5465.5315] [ 855] [depth= 1] . ( 77 sec) [ -5465.1329] [ 855] [depth= 1] . ( 79 sec) [ -5465.0288] [ 855] [depth= 1] . ( 80 sec) [ -5464.9186] [ 855] [depth= 1] . ( 80 sec) [ -5464.4882] [ 855] [depth= 1] . ( 81 sec) [ -5464.3524] [ 855] [depth= 1] . ( 81 sec) [ -5464.3328] [ 855] [depth= 1] . ( 82 sec) [ -5463.9965] [ 855] [depth= 2] . ( 82 sec) [ -5463.9039] [ 855] [depth= 2] . ( 82 sec) [ -5463.8295] [ 855] [depth= 2] . ( 83 sec) [ -5439.6568] [Branch lengths ] . ( 84 sec) [ -5438.5202] [GTR parameters ] . ( 85 sec) [ -5397.9063] [Alpha ][ 0.250961] . ( 85 sec) [ -5397.7295] [ 855] [depth= 1] . ( 85 sec) [ -5396.5947] [ 852] [depth= 1] . ( 85 sec) [ -5395.8082] [ 852] [depth= 1] . ( 85 sec) [ -5392.6402] [ 848] [depth= 2] . ( 101 sec) [ -5388.5981] [Branch lengths ] . ( 102 sec) [ -5387.8347] [GTR parameters ] . ( 102 sec) [ -5387.6991] [Alpha ][ 0.241931] . ( 102 sec) [ -5386.6790] [ 852] [depth= 10] . ( 106 sec) [ -5386.4101] [ 854] [depth= 1] . ( 113 sec) [ -5386.3857] [ 854] [depth= 1] . ( 115 sec) [ -5386.3737] [ 854] [depth= 1] . ( 119 sec) [ -5383.0729] [Branch lengths ] . ( 120 sec) [ -5382.7882] [GTR parameters ] . ( 120 sec) [ -5382.7699] [Alpha ][ 0.238803] . ( 129 sec) [ -5382.7556] [ 854] [depth= 1] . ( 137 sec) [ -5382.4119] [Branch lengths ] . ( 137 sec) [ -5382.4080] [GTR parameters ] . ( 138 sec) [ -5382.4079] [Alpha ][ 0.238551] . ( 174 sec) [ -5382.3690] [Branch lengths ] . ( 174 sec) [ -5382.3690] [Topology ] . ( 175 sec) [ -5382.3649] [Topology ] . ( 176 sec) [ -5382.3635] [Topology ] . ( 177 sec) [ -5382.3629] [Topology ] . ( 177 sec) [ -5382.3622] [GTR parameters ] . ( 177 sec) [ -5382.3619] [Alpha ][ 0.238869] . ( 177 sec) [ -5382.3619] [Topology ] . ( 178 sec) [ -5382.3614] [Topology ] . ( 178 sec) [ -5382.3614] [GTR parameters ] . ( 178 sec) [ -5382.3614] [Alpha ][ 0.238869] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5386.334104 . Log likelihood obtained after SPR moves : -5382.361413 . Log likelihood of the current tree: -5382.361413. . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Best log likelihood : -5382.361413 . Time used 0h3m5s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 738.16user 0.00system 12:23.70elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps