.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data81.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 322 patterns found. (out of a total of 500 sites) . 167 sites without polymorphism (33.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9595.6428] [GTR parameters ] . ( 1 sec) [ -9472.4817] [Alpha ][ 0.500960] . ( 1 sec) [ -9294.3227] [ 1611] [depth= 9] . ( 1 sec) [ -9243.5216] [ 1608] [depth= 2] . ( 1 sec) [ -9073.6780] [ 1604] [depth= 6] . ( 1 sec) [ -8990.2505] [ 1602] [depth= 5] . ( 1 sec) [ -8982.8695] [ 1598] [depth= 1] . ( 1 sec) [ -8950.0172] [ 1597] [depth= 5] . ( 1 sec) [ -8868.0022] [ 1595] [depth= 5] . ( 1 sec) [ -8684.5526] [ 1582] [depth= 2] . ( 1 sec) [ -8553.1930] [ 1544] [depth= 14] . ( 1 sec) [ -8516.4133] [ 1536] [depth= 11] . ( 1 sec) [ -8503.7338] [ 1536] [depth= 10] . ( 1 sec) [ -8447.9467] [ 1527] [depth= 10] . ( 1 sec) [ -8400.3535] [ 1525] [depth= 1] . ( 1 sec) [ -8325.1185] [ 1524] [depth= 4] . ( 1 sec) [ -8317.7684] [ 1510] [depth= 4] . ( 1 sec) [ -8307.5203] [ 1514] [depth= 13] . ( 1 sec) [ -8277.2285] [ 1513] [depth= 1] . ( 1 sec) [ -8211.3857] [ 1511] [depth= 1] . ( 1 sec) [ -8069.0297] [ 1462] [depth= 5] . ( 1 sec) [ -8065.8905] [ 1461] [depth= 2] . ( 1 sec) [ -8049.7329] [ 1460] [depth= 6] . ( 1 sec) [ -8004.6456] [ 1457] [depth= 10] . ( 1 sec) [ -7845.9004] [ 1409] [depth= 9] . ( 1 sec) [ -7823.4649] [ 1409] [depth= 4] . ( 1 sec) [ -7812.0819] [ 1396] [depth= 2] . ( 1 sec) [ -7784.5341] [ 1391] [depth= 1] . ( 2 sec) [ -7701.7567] [ 1395] [depth= 16] . ( 2 sec) [ -7325.7128] [ 1357] [depth= 3] . ( 2 sec) [ -7189.8604] [ 1318] [depth= 3] . ( 2 sec) [ -7183.4757] [ 1311] [depth= 8] . ( 2 sec) [ -7121.3526] [ 1302] [depth= 2] . ( 2 sec) [ -7114.9978] [ 1300] [depth= 1] . ( 2 sec) [ -7056.1639] [ 1296] [depth= 2] . ( 2 sec) [ -6974.5243] [ 1277] [depth= 1] . ( 2 sec) [ -6901.2859] [ 1257] [depth= 4] . ( 2 sec) [ -6856.9846] [ 1253] [depth= 11] . ( 2 sec) [ -6798.8192] [ 1223] [depth= 2] . ( 2 sec) [ -6795.9310] [ 1223] [depth= 1] . ( 2 sec) [ -6706.0055] [ 1181] [depth= 14] . ( 2 sec) [ -6677.6750] [ 1181] [depth= 1] . ( 2 sec) [ -6666.8532] [ 1180] [depth= 2] . ( 2 sec) [ -6535.5009] [ 1154] [depth= 14] . ( 2 sec) [ -6506.0555] [ 1152] [depth= 15] . ( 2 sec) [ -6505.9312] [ 1153] [depth= 1] . ( 2 sec) [ -6504.8223] [ 1154] [depth= 1] . ( 2 sec) [ -6485.2967] [ 1154] [depth= 1] . ( 2 sec) [ -6448.5183] [ 1158] [depth= 13] . ( 2 sec) [ -6435.5786] [ 1155] [depth= 3] . ( 2 sec) [ -6428.0775] [ 1146] [depth= 11] . ( 2 sec) [ -6285.6235] [ 1154] [depth= 3] . ( 2 sec) [ -6226.9969] [ 1139] [depth= 15] . ( 3 sec) [ -6195.6803] [ 1136] [depth= 11] . ( 3 sec) [ -6168.9647] [ 1133] [depth= 2] . ( 3 sec) [ -6088.2026] [ 1098] [depth= 13] . ( 3 sec) [ -6052.0787] [ 1087] [depth= 1] . ( 3 sec) [ -6029.5883] [ 1079] [depth= 1] . ( 3 sec) [ -5978.9260] [ 1072] [depth= 8] . ( 3 sec) [ -5899.2567] [ 1069] [depth= 6] . ( 3 sec) [ -5885.3624] [ 1072] [depth= 1] . ( 3 sec) [ -5849.9264] [ 1058] [depth= 6] . ( 3 sec) [ -5804.5458] [ 1045] [depth= 5] . ( 3 sec) [ -5797.0482] [ 1045] [depth= 1] . ( 3 sec) [ -5793.7630] [ 1044] [depth= 1] . ( 3 sec) [ -5779.3004] [ 1033] [depth= 1] . ( 3 sec) [ -5628.4767] [ 988] [depth= 8] . ( 3 sec) [ -5624.1680] [ 984] [depth= 1] . ( 3 sec) [ -5598.6572] [ 973] [depth= 6] . ( 3 sec) [ -5576.0790] [ 978] [depth= 1] . ( 3 sec) [ -5500.6166] [ 958] [depth= 2] . ( 3 sec) [ -5499.8179] [ 958] [depth= 1] . ( 3 sec) [ -5457.4870] [ 949] [depth= 1] . ( 3 sec) [ -5456.2664] [ 948] [depth= 4] . ( 3 sec) [ -5445.6381] [ 948] [depth= 1] . ( 3 sec) [ -5444.9561] [ 948] [depth= 1] . ( 3 sec) [ -5443.5683] [ 951] [depth= 1] . ( 3 sec) [ -5438.8667] [ 949] [depth= 2] . ( 3 sec) [ -5438.8391] [ 949] [depth= 1] . ( 3 sec) [ -5437.8610] [ 949] [depth= 1] . ( 3 sec) [ -5401.5994] [ 951] [depth= 2] . ( 4 sec) [ -5396.0180] [ 949] [depth= 3] . ( 4 sec) [ -5395.9689] [ 950] [depth= 1] . ( 4 sec) [ -5368.5212] [ 939] [depth= 2] . ( 4 sec) [ -5368.4706] [ 939] [depth= 2] . ( 4 sec) [ -5367.9927] [ 939] [depth= 1] . ( 4 sec) [ -5367.9518] [ 939] [depth= 3] . ( 4 sec) [ -5367.8506] [ 939] [depth= 1] . ( 4 sec) [ -5367.8317] [ 939] [depth= 1] . ( 4 sec) [ -5367.8105] [ 937] [depth= 1] . ( 4 sec) [ -5308.6828] [Branch lengths ] . ( 5 sec) [ -5305.8397] [GTR parameters ] . ( 5 sec) [ -5288.5158] [Alpha ][ 0.893269] . ( 5 sec) [ -5285.0660] [ 929] [depth= 5] . ( 5 sec) [ -5284.2440] [ 934] [depth= 7] . ( 5 sec) [ -5266.3259] [ 928] [depth= 8] . ( 5 sec) [ -5263.7080] [ 929] [depth= 1] . ( 5 sec) [ -5263.6830] [ 929] [depth= 1] . ( 5 sec) [ -5255.3939] [ 927] [depth= 2] . ( 5 sec) [ -5255.3288] [ 927] [depth= 1] . ( 5 sec) [ -5255.2084] [ 927] [depth= 2] . ( 5 sec) [ -5222.3706] [ 915] [depth= 6] . ( 6 sec) [ -5181.2547] [ 902] [depth= 2] . ( 6 sec) [ -5179.1653] [ 901] [depth= 1] . ( 6 sec) [ -5145.9103] [ 889] [depth= 1] . ( 6 sec) [ -5135.5698] [ 888] [depth= 4] . ( 6 sec) [ -5131.0348] [ 887] [depth= 1] . ( 6 sec) [ -5130.9760] [ 887] [depth= 1] . ( 6 sec) [ -5130.9319] [ 887] [depth= 1] . ( 6 sec) [ -5118.8356] [ 884] [depth= 2] . ( 6 sec) [ -5116.4852] [ 883] [depth= 1] . ( 6 sec) [ -5116.1716] [ 883] [depth= 1] . ( 6 sec) [ -5114.9063] [ 881] [depth= 2] . ( 6 sec) [ -5114.8898] [ 881] [depth= 1] . ( 6 sec) [ -5114.1913] [ 881] [depth= 3] . ( 7 sec) [ -5114.1153] [ 881] [depth= 1] . ( 7 sec) [ -5112.1801] [ 881] [depth= 1] . ( 7 sec) [ -5111.4179] [ 879] [depth= 1] . ( 8 sec) [ -5106.0170] [ 877] [depth= 1] . ( 8 sec) [ -5105.3997] [ 877] [depth= 1] . ( 9 sec) [ -5104.7625] [ 875] [depth= 1] . ( 10 sec) [ -5101.6022] [Branch lengths ] . ( 10 sec) [ -5101.2763] [GTR parameters ] . ( 10 sec) [ -5100.7963] [Alpha ][ 0.995309] . ( 16 sec) [ -5100.1781] [Branch lengths ] . ( 36 sec) [ -5097.9724] [Branch lengths ] . ( 36 sec) [ -5097.9724] [Topology ] . ( 36 sec) [ -5097.4036] [Topology ] . ( 37 sec) [ -5097.3017] [Topology ] . ( 38 sec) [ -5097.2844] [Topology ] . ( 38 sec) [ -5097.2814] [Topology ] . ( 39 sec) [ -5097.2808] [Topology ] . ( 39 sec) [ -5097.2716] [GTR parameters ] . ( 39 sec) [ -5097.2619] [Alpha ][ 1.011520] . ( 39 sec) [ -5097.2619] [Topology ] . ( 40 sec) [ -5097.2616] [Topology ] . ( 40 sec) [ -5097.2615] [GTR parameters ] . ( 40 sec) [ -5097.2615] [Alpha ][ 1.011520] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -5097.2524] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5097.252433. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9795.7474] [GTR parameters ] . ( 1 sec) [ -9664.3339] [Alpha ][ 0.500960] . ( 1 sec) [ -9396.9792] [ 1628] [depth= 9] . ( 1 sec) [ -9302.5895] [ 1615] [depth= 9] . ( 1 sec) [ -9197.9929] [ 1602] [depth= 4] . ( 1 sec) [ -9169.7277] [ 1599] [depth= 6] . ( 1 sec) [ -9059.2208] [ 1568] [depth= 1] . ( 1 sec) [ -9041.8155] [ 1568] [depth= 3] . ( 1 sec) [ -9038.6439] [ 1567] [depth= 1] . ( 1 sec) [ -8913.1245] [ 1567] [depth= 5] . ( 1 sec) [ -8851.7485] [ 1545] [depth= 1] . ( 2 sec) [ -8632.0560] [ 1536] [depth= 8] . ( 2 sec) [ -8617.1664] [ 1504] [depth= 4] . ( 2 sec) [ -8505.1941] [ 1503] [depth= 3] . ( 2 sec) [ -8458.1883] [ 1470] [depth= 1] . ( 2 sec) [ -8424.2862] [ 1466] [depth= 4] . ( 2 sec) [ -8297.0269] [ 1440] [depth= 4] . ( 2 sec) [ -8251.4664] [ 1421] [depth= 4] . ( 2 sec) [ -8056.9424] [ 1385] [depth= 10] . ( 2 sec) [ -8054.6738] [ 1393] [depth= 1] . ( 2 sec) [ -7933.0833] [ 1388] [depth= 1] . ( 2 sec) [ -7881.6631] [ 1365] [depth= 2] . ( 2 sec) [ -7863.1259] [ 1359] [depth= 1] . ( 2 sec) [ -7734.1394] [ 1317] [depth= 4] . ( 2 sec) [ -7731.4471] [ 1318] [depth= 1] . ( 2 sec) [ -7501.4932] [ 1302] [depth= 14] . ( 2 sec) [ -7422.6238] [ 1301] [depth= 1] . ( 2 sec) [ -7330.2346] [ 1273] [depth= 1] . ( 2 sec) [ -7265.6440] [ 1269] [depth= 7] . ( 2 sec) [ -7264.9947] [ 1277] [depth= 1] . ( 2 sec) [ -7253.9510] [ 1266] [depth= 1] . ( 2 sec) [ -7074.5613] [ 1221] [depth= 16] . ( 2 sec) [ -7069.8163] [ 1222] [depth= 1] . ( 2 sec) [ -7016.1052] [ 1213] [depth= 6] . ( 2 sec) [ -6970.4500] [ 1206] [depth= 2] . ( 2 sec) [ -6957.1136] [ 1204] [depth= 2] . ( 2 sec) [ -6929.3827] [ 1197] [depth= 3] . ( 3 sec) [ -6913.2114] [ 1190] [depth= 4] . ( 3 sec) [ -6900.6935] [ 1192] [depth= 2] . ( 3 sec) [ -6873.3816] [ 1194] [depth= 2] . ( 3 sec) [ -6764.9086] [ 1186] [depth= 2] . ( 3 sec) [ -6723.1660] [ 1186] [depth= 6] . ( 3 sec) [ -6610.5292] [ 1195] [depth= 15] . ( 3 sec) [ -6606.0378] [ 1184] [depth= 2] . ( 3 sec) [ -6548.7368] [ 1175] [depth= 6] . ( 3 sec) [ -6540.4162] [ 1175] [depth= 1] . ( 3 sec) [ -6484.4979] [ 1157] [depth= 2] . ( 3 sec) [ -6411.7069] [ 1149] [depth= 3] . ( 3 sec) [ -6379.2518] [ 1140] [depth= 1] . ( 3 sec) [ -6304.1909] [ 1121] [depth= 4] . ( 3 sec) [ -6271.2269] [ 1115] [depth= 4] . ( 3 sec) [ -6270.7449] [ 1117] [depth= 1] . ( 3 sec) [ -6264.3129] [ 1112] [depth= 7] . ( 3 sec) [ -6261.7465] [ 1100] [depth= 4] . ( 3 sec) [ -6159.6664] [ 1093] [depth= 4] . ( 3 sec) [ -6103.7907] [ 1081] [depth= 1] . ( 3 sec) [ -6103.0283] [ 1079] [depth= 1] . ( 4 sec) [ -6077.7383] [ 1080] [depth= 4] . ( 4 sec) [ -6077.6566] [ 1081] [depth= 1] . ( 4 sec) [ -6077.4014] [ 1081] [depth= 1] . ( 4 sec) [ -6076.9615] [ 1081] [depth= 1] . ( 4 sec) [ -6028.9764] [ 1077] [depth= 10] . ( 4 sec) [ -6020.7117] [ 1079] [depth= 1] . ( 4 sec) [ -6019.6637] [ 1079] [depth= 1] . ( 4 sec) [ -5957.7621] [ 1063] [depth= 8] . ( 4 sec) [ -5956.6282] [ 1062] [depth= 1] . ( 4 sec) [ -5956.5142] [ 1063] [depth= 1] . ( 4 sec) [ -5951.1035] [ 1061] [depth= 1] . ( 4 sec) [ -5950.9869] [ 1061] [depth= 1] . ( 4 sec) [ -5950.3567] [ 1059] [depth= 2] . ( 4 sec) [ -5914.2898] [ 1058] [depth= 1] . ( 4 sec) [ -5895.6569] [ 1057] [depth= 1] . ( 4 sec) [ -5713.0728] [ 1017] [depth= 3] . ( 4 sec) [ -5689.5599] [ 1017] [depth= 1] . ( 4 sec) [ -5550.0114] [ 1000] [depth= 13] . ( 4 sec) [ -5380.5368] [ 935] [depth= 4] . ( 4 sec) [ -5377.6241] [ 934] [depth= 1] . ( 4 sec) [ -5377.4034] [ 934] [depth= 2] . ( 4 sec) [ -5256.5736] [ 916] [depth= 5] . ( 5 sec) [ -5256.1518] [ 916] [depth= 2] . ( 5 sec) [ -5223.4590] [ 898] [depth= 4] . ( 5 sec) [ -5165.4445] [Branch lengths ] . ( 5 sec) [ -5162.3115] [GTR parameters ] . ( 5 sec) [ -5144.1512] [Alpha ][ 0.922403] . ( 6 sec) [ -5142.0572] [ 897] [depth= 1] . ( 6 sec) [ -5139.3434] [ 896] [depth= 1] . ( 6 sec) [ -5139.2918] [ 896] [depth= 1] . ( 6 sec) [ -5139.2756] [ 898] [depth= 1] . ( 6 sec) [ -5137.9644] [ 897] [depth= 1] . ( 6 sec) [ -5120.4743] [ 893] [depth= 3] . ( 6 sec) [ -5118.4698] [ 893] [depth= 1] . ( 7 sec) [ -5118.0724] [ 893] [depth= 1] . ( 7 sec) [ -5118.0437] [ 893] [depth= 1] . ( 7 sec) [ -5111.9472] [ 889] [depth= 2] . ( 7 sec) [ -5111.7898] [ 889] [depth= 2] . ( 8 sec) [ -5111.7771] [ 889] [depth= 1] . ( 8 sec) [ -5101.4048] [ 878] [depth= 2] . ( 8 sec) [ -5101.0291] [ 878] [depth= 1] . ( 9 sec) [ -5100.2525] [ 876] [depth= 1] . ( 10 sec) [ -5100.2119] [ 876] [depth= 1] . ( 10 sec) [ -5100.1851] [ 875] [depth= 1] . ( 11 sec) [ -5098.4465] [Branch lengths ] . ( 11 sec) [ -5098.3586] [GTR parameters ] . ( 11 sec) [ -5098.0948] [Alpha ][ 1.000021] . ( 17 sec) [ -5097.9161] [Branch lengths ] . ( 37 sec) [ -5097.4915] [Branch lengths ] . ( 37 sec) [ -5097.4915] [Topology ] . ( 37 sec) [ -5097.2808] [Topology ] . ( 38 sec) [ -5097.2626] [Topology ] . ( 38 sec) [ -5097.2605] [Topology ] . ( 39 sec) [ -5097.2602] [Topology ] . ( 39 sec) [ -5097.2577] [GTR parameters ] . ( 39 sec) [ -5097.2527] [Alpha ][ 1.011636] . ( 39 sec) [ -5097.2527] [Topology ] . ( 40 sec) [ -5097.2525] [Topology ] . ( 40 sec) [ -5097.2524] [GTR parameters ] . ( 40 sec) [ -5097.2524] [Alpha ][ 1.011636] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5097.252447. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10064.0856] [GTR parameters ] . ( 1 sec) [ -9927.9373] [Alpha ][ 0.500960] . ( 1 sec) [ -9555.5559] [ 1679] [depth= 8] . ( 1 sec) [ -9459.0564] [ 1674] [depth= 2] . ( 1 sec) [ -9437.5743] [ 1673] [depth= 3] . ( 1 sec) [ -9392.2983] [ 1673] [depth= 2] . ( 1 sec) [ -9339.7130] [ 1634] [depth= 4] . ( 1 sec) [ -9307.8933] [ 1637] [depth= 6] . ( 1 sec) [ -9250.2051] [ 1623] [depth= 4] . ( 1 sec) [ -9146.2659] [ 1611] [depth= 4] . ( 1 sec) [ -9080.9161] [ 1591] [depth= 4] . ( 1 sec) [ -8966.1900] [ 1592] [depth= 17] . ( 1 sec) [ -8815.3217] [ 1574] [depth= 12] . ( 1 sec) [ -8622.5141] [ 1551] [depth= 16] . ( 1 sec) [ -8573.2381] [ 1527] [depth= 3] . ( 1 sec) [ -8497.7351] [ 1513] [depth= 9] . ( 2 sec) [ -8357.2979] [ 1474] [depth= 4] . ( 2 sec) [ -8329.2886] [ 1474] [depth= 2] . ( 2 sec) [ -8194.4180] [ 1435] [depth= 8] . ( 2 sec) [ -7954.3123] [ 1435] [depth= 1] . ( 2 sec) [ -7887.6295] [ 1432] [depth= 6] . ( 2 sec) [ -7817.0942] [ 1408] [depth= 8] . ( 2 sec) [ -7721.5677] [ 1391] [depth= 8] . ( 2 sec) [ -7705.0883] [ 1387] [depth= 1] . ( 2 sec) [ -7517.0047] [ 1388] [depth= 8] . ( 2 sec) [ -7390.9154] [ 1379] [depth= 6] . ( 2 sec) [ -7351.1162] [ 1372] [depth= 3] . ( 2 sec) [ -7224.2933] [ 1333] [depth= 8] . ( 2 sec) [ -7211.8677] [ 1325] [depth= 4] . ( 2 sec) [ -7206.5095] [ 1327] [depth= 3] . ( 2 sec) [ -7205.2459] [ 1327] [depth= 1] . ( 2 sec) [ -6893.0971] [ 1309] [depth= 6] . ( 2 sec) [ -6826.3825] [ 1293] [depth= 10] . ( 2 sec) [ -6759.5688] [ 1282] [depth= 10] . ( 2 sec) [ -6682.1131] [ 1257] [depth= 10] . ( 2 sec) [ -6554.8287] [ 1225] [depth= 7] . ( 2 sec) [ -6548.5204] [ 1225] [depth= 7] . ( 2 sec) [ -6546.6014] [ 1227] [depth= 1] . ( 2 sec) [ -6497.3124] [ 1218] [depth= 8] . ( 2 sec) [ -6488.7585] [ 1217] [depth= 2] . ( 2 sec) [ -6483.0194] [ 1213] [depth= 1] . ( 2 sec) [ -6453.6418] [ 1214] [depth= 2] . ( 2 sec) [ -6434.0857] [ 1218] [depth= 4] . ( 2 sec) [ -6268.6011] [ 1172] [depth= 8] . ( 2 sec) [ -6251.5358] [ 1165] [depth= 1] . ( 3 sec) [ -6247.2552] [ 1164] [depth= 1] . ( 3 sec) [ -6151.1166] [ 1135] [depth= 10] . ( 3 sec) [ -6118.0635] [ 1121] [depth= 6] . ( 3 sec) [ -6107.6892] [ 1121] [depth= 2] . ( 3 sec) [ -6105.1586] [ 1120] [depth= 3] . ( 3 sec) [ -6068.7290] [ 1115] [depth= 4] . ( 3 sec) [ -6045.6707] [ 1116] [depth= 1] . ( 3 sec) [ -5997.6608] [ 1115] [depth= 3] . ( 3 sec) [ -5993.1293] [ 1114] [depth= 1] . ( 3 sec) [ -5938.6459] [ 1106] [depth= 4] . ( 3 sec) [ -5900.4575] [ 1103] [depth= 6] . ( 3 sec) [ -5868.7700] [ 1098] [depth= 1] . ( 3 sec) [ -5864.9542] [ 1095] [depth= 5] . ( 3 sec) [ -5789.3041] [ 1082] [depth= 7] . ( 3 sec) [ -5785.1795] [ 1082] [depth= 2] . ( 3 sec) [ -5773.1334] [ 1079] [depth= 2] . ( 3 sec) [ -5741.7129] [ 1067] [depth= 3] . ( 3 sec) [ -5728.6833] [ 1060] [depth= 6] . ( 3 sec) [ -5712.7952] [ 1057] [depth= 4] . ( 3 sec) [ -5702.4904] [ 1038] [depth= 4] . ( 3 sec) [ -5694.5615] [ 1038] [depth= 1] . ( 3 sec) [ -5694.5293] [ 1038] [depth= 1] . ( 3 sec) [ -5694.4375] [ 1038] [depth= 1] . ( 3 sec) [ -5645.2922] [ 1019] [depth= 2] . ( 3 sec) [ -5637.9176] [ 1019] [depth= 1] . ( 4 sec) [ -5635.0897] [ 1018] [depth= 4] . ( 4 sec) [ -5634.9526] [ 1020] [depth= 2] . ( 4 sec) [ -5602.7201] [ 1004] [depth= 4] . ( 4 sec) [ -5515.2002] [ 986] [depth= 1] . ( 4 sec) [ -5508.9542] [ 986] [depth= 1] . ( 4 sec) [ -5508.5019] [ 986] [depth= 1] . ( 4 sec) [ -5502.5450] [ 986] [depth= 6] . ( 4 sec) [ -5494.8998] [ 973] [depth= 3] . ( 4 sec) [ -5471.2947] [ 970] [depth= 2] . ( 4 sec) [ -5471.2458] [ 970] [depth= 1] . ( 4 sec) [ -5437.2159] [ 967] [depth= 1] . ( 4 sec) [ -5435.1345] [ 966] [depth= 1] . ( 4 sec) [ -5403.5296] [ 963] [depth= 8] . ( 4 sec) [ -5382.6994] [ 952] [depth= 1] . ( 4 sec) [ -5381.6320] [ 945] [depth= 4] . ( 5 sec) [ -5318.2230] [Branch lengths ] . ( 5 sec) [ -5315.0880] [GTR parameters ] . ( 5 sec) [ -5298.3439] [Alpha ][ 0.872848] . ( 5 sec) [ -5293.1385] [ 932] [depth= 6] . ( 5 sec) [ -5293.1057] [ 932] [depth= 2] . ( 5 sec) [ -5291.5938] [ 931] [depth= 3] . ( 5 sec) [ -5291.5805] [ 931] [depth= 1] . ( 6 sec) [ -5290.9090] [ 930] [depth= 3] . ( 6 sec) [ -5277.3837] [ 930] [depth= 2] . ( 6 sec) [ -5191.1698] [ 905] [depth= 5] . ( 6 sec) [ -5187.7790] [ 903] [depth= 2] . ( 6 sec) [ -5186.2420] [ 903] [depth= 1] . ( 7 sec) [ -5186.2108] [ 903] [depth= 1] . ( 7 sec) [ -5186.0766] [ 902] [depth= 1] . ( 7 sec) [ -5185.4811] [ 901] [depth= 1] . ( 7 sec) [ -5158.7662] [ 898] [depth= 1] . ( 7 sec) [ -5156.1090] [ 890] [depth= 2] . ( 7 sec) [ -5155.9179] [ 889] [depth= 3] . ( 7 sec) [ -5141.5105] [ 883] [depth= 4] . ( 8 sec) [ -5140.8364] [ 891] [depth= 1] . ( 8 sec) [ -5140.2614] [ 890] [depth= 1] . ( 8 sec) [ -5121.8926] [ 878] [depth= 2] . ( 8 sec) [ -5120.1728] [ 879] [depth= 2] . ( 8 sec) [ -5115.9226] [ 877] [depth= 1] . ( 8 sec) [ -5115.9070] [ 877] [depth= 1] . ( 9 sec) [ -5115.2935] [ 878] [depth= 1] . ( 9 sec) [ -5115.1170] [ 877] [depth= 1] . ( 10 sec) [ -5105.0665] [ 879] [depth= 1] . ( 10 sec) [ -5103.5855] [ 877] [depth= 1] . ( 10 sec) [ -5103.2308] [ 878] [depth= 1] . ( 11 sec) [ -5100.8356] [Branch lengths ] . ( 11 sec) [ -5100.7429] [GTR parameters ] . ( 11 sec) [ -5099.9353] [Alpha ][ 1.004014] . ( 12 sec) [ -5098.2461] [ 877] [depth= 1] . ( 13 sec) [ -5097.4826] [ 875] [depth= 1] . ( 17 sec) [ -5097.2614] [Branch lengths ] . ( 17 sec) [ -5097.2591] [GTR parameters ] . ( 17 sec) [ -5097.2574] [Alpha ][ 1.010740] . ( 23 sec) [ -5097.2529] [Branch lengths ] . ( 43 sec) [ -5097.2525] [Branch lengths ] . ( 43 sec) [ -5097.2525] [Topology ] . ( 44 sec) [ -5097.2525] [Topology ] . ( 44 sec) [ -5097.2525] [GTR parameters ] . ( 44 sec) [ -5097.2524] [Alpha ][ 1.011751] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5097.252449. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9917.7672] [GTR parameters ] . ( 1 sec) [ -9783.7096] [Alpha ][ 0.500960] . ( 1 sec) [ -9388.6601] [ 1653] [depth= 8] . ( 1 sec) [ -9360.1402] [ 1649] [depth= 9] . ( 1 sec) [ -9188.1190] [ 1634] [depth= 7] . ( 1 sec) [ -9059.0741] [ 1587] [depth= 1] . ( 1 sec) [ -8851.7298] [ 1587] [depth= 5] . ( 1 sec) [ -8782.3947] [ 1574] [depth= 3] . ( 2 sec) [ -8689.2822] [ 1571] [depth= 7] . ( 2 sec) [ -8609.7813] [ 1545] [depth= 2] . ( 2 sec) [ -8559.6996] [ 1544] [depth= 2] . ( 2 sec) [ -8545.5271] [ 1542] [depth= 7] . ( 2 sec) [ -8509.7656] [ 1542] [depth= 1] . ( 2 sec) [ -8220.9153] [ 1498] [depth= 10] . ( 2 sec) [ -8011.1499] [ 1486] [depth= 7] . ( 2 sec) [ -8008.9091] [ 1483] [depth= 1] . ( 2 sec) [ -7984.9600] [ 1480] [depth= 2] . ( 2 sec) [ -7861.9742] [ 1437] [depth= 10] . ( 2 sec) [ -7830.1550] [ 1432] [depth= 1] . ( 2 sec) [ -7729.7280] [ 1393] [depth= 14] . ( 2 sec) [ -7553.4183] [ 1358] [depth= 9] . ( 2 sec) [ -7508.3018] [ 1349] [depth= 1] . ( 2 sec) [ -7455.5437] [ 1320] [depth= 12] . ( 2 sec) [ -7367.2856] [ 1301] [depth= 10] . ( 2 sec) [ -7353.7763] [ 1307] [depth= 1] . ( 2 sec) [ -7278.7284] [ 1284] [depth= 3] . ( 2 sec) [ -7177.0658] [ 1275] [depth= 6] . ( 2 sec) [ -7148.7330] [ 1274] [depth= 9] . ( 2 sec) [ -7142.6929] [ 1273] [depth= 2] . ( 2 sec) [ -7109.9436] [ 1260] [depth= 13] . ( 2 sec) [ -6989.6111] [ 1233] [depth= 5] . ( 2 sec) [ -6949.9486] [ 1207] [depth= 1] . ( 2 sec) [ -6907.8317] [ 1192] [depth= 10] . ( 2 sec) [ -6898.3856] [ 1196] [depth= 8] . ( 2 sec) [ -6774.8519] [ 1163] [depth= 1] . ( 2 sec) [ -6663.1904] [ 1137] [depth= 2] . ( 3 sec) [ -6617.5279] [ 1136] [depth= 1] . ( 3 sec) [ -6339.7721] [ 1143] [depth= 6] . ( 3 sec) [ -6246.0294] [ 1120] [depth= 7] . ( 3 sec) [ -6225.3130] [ 1116] [depth= 3] . ( 3 sec) [ -6195.6772] [ 1115] [depth= 1] . ( 3 sec) [ -6194.0765] [ 1113] [depth= 1] . ( 3 sec) [ -6151.8254] [ 1103] [depth= 4] . ( 3 sec) [ -6096.8630] [ 1095] [depth= 6] . ( 3 sec) [ -6095.6054] [ 1095] [depth= 2] . ( 3 sec) [ -6077.4815] [ 1090] [depth= 4] . ( 3 sec) [ -6063.5165] [ 1089] [depth= 2] . ( 3 sec) [ -5996.0192] [ 1056] [depth= 4] . ( 3 sec) [ -5903.5818] [ 1032] [depth= 4] . ( 3 sec) [ -5896.2919] [ 1028] [depth= 2] . ( 3 sec) [ -5892.3786] [ 1028] [depth= 1] . ( 3 sec) [ -5798.3628] [ 1028] [depth= 1] . ( 3 sec) [ -5787.1306] [ 1028] [depth= 3] . ( 3 sec) [ -5699.9301] [ 1008] [depth= 3] . ( 3 sec) [ -5697.6481] [ 1006] [depth= 3] . ( 3 sec) [ -5645.4780] [ 1007] [depth= 4] . ( 3 sec) [ -5644.2467] [ 1005] [depth= 5] . ( 3 sec) [ -5644.0175] [ 1005] [depth= 1] . ( 3 sec) [ -5635.2240] [ 1000] [depth= 2] . ( 3 sec) [ -5628.2701] [ 1000] [depth= 1] . ( 3 sec) [ -5593.5144] [ 988] [depth= 6] . ( 3 sec) [ -5583.5993] [ 984] [depth= 1] . ( 3 sec) [ -5575.3851] [ 983] [depth= 1] . ( 4 sec) [ -5549.0122] [ 971] [depth= 4] . ( 4 sec) [ -5546.4523] [ 971] [depth= 3] . ( 4 sec) [ -5516.1168] [ 963] [depth= 1] . ( 4 sec) [ -5491.1311] [ 955] [depth= 1] . ( 4 sec) [ -5491.0497] [ 956] [depth= 3] . ( 4 sec) [ -5430.9447] [ 955] [depth= 2] . ( 4 sec) [ -5428.8251] [ 955] [depth= 1] . ( 4 sec) [ -5428.1233] [ 959] [depth= 2] . ( 4 sec) [ -5411.2215] [ 954] [depth= 1] . ( 4 sec) [ -5407.1889] [ 952] [depth= 1] . ( 4 sec) [ -5377.2618] [ 951] [depth= 6] . ( 4 sec) [ -5377.1856] [ 951] [depth= 1] . ( 4 sec) [ -5372.7314] [ 951] [depth= 3] . ( 4 sec) [ -5364.8946] [ 951] [depth= 2] . ( 4 sec) [ -5362.5568] [ 948] [depth= 2] . ( 4 sec) [ -5349.2048] [ 941] [depth= 1] . ( 4 sec) [ -5346.5348] [ 940] [depth= 1] . ( 5 sec) [ -5344.9550] [ 940] [depth= 2] . ( 5 sec) [ -5334.5774] [ 938] [depth= 1] . ( 5 sec) [ -5316.2715] [ 937] [depth= 1] . ( 5 sec) [ -5304.0499] [ 935] [depth= 1] . ( 5 sec) [ -5281.1260] [ 923] [depth= 3] . ( 5 sec) [ -5246.2341] [ 913] [depth= 2] . ( 5 sec) [ -5198.2065] [Branch lengths ] . ( 5 sec) [ -5195.1643] [GTR parameters ] . ( 5 sec) [ -5178.2755] [Alpha ][ 0.898987] . ( 5 sec) [ -5175.3203] [ 905] [depth= 2] . ( 5 sec) [ -5174.5664] [ 904] [depth= 3] . ( 6 sec) [ -5146.9751] [ 890] [depth= 2] . ( 6 sec) [ -5140.3260] [ 889] [depth= 1] . ( 6 sec) [ -5123.6946] [ 886] [depth= 4] . ( 6 sec) [ -5119.2280] [ 884] [depth= 1] . ( 6 sec) [ -5118.7287] [ 884] [depth= 1] . ( 6 sec) [ -5116.0877] [ 882] [depth= 3] . ( 6 sec) [ -5103.0157] [ 877] [depth= 1] . ( 6 sec) [ -5102.1761] [ 876] [depth= 1] . ( 8 sec) [ -5102.1447] [ 876] [depth= 1] . ( 8 sec) [ -5102.0587] [ 876] [depth= 1] . ( 10 sec) [ -5102.0379] [ 876] [depth= 1] . ( 10 sec) [ -5101.9461] [ 875] [depth= 1] . ( 10 sec) [ -5101.9155] [ 875] [depth= 2] . ( 11 sec) [ -5098.0113] [Branch lengths ] . ( 11 sec) [ -5097.9076] [GTR parameters ] . ( 11 sec) [ -5097.4463] [Alpha ][ 1.000250] . ( 17 sec) [ -5097.2869] [Branch lengths ] . ( 37 sec) [ -5097.2688] [Branch lengths ] . ( 37 sec) [ -5097.2688] [Topology ] . ( 38 sec) [ -5097.2677] [Topology ] . ( 38 sec) [ -5097.2674] [Topology ] . ( 39 sec) [ -5097.2665] [GTR parameters ] . ( 39 sec) [ -5097.2622] [Alpha ][ 1.010987] . ( 39 sec) [ -5097.2622] [Topology ] . ( 39 sec) [ -5097.2618] [Topology ] . ( 40 sec) [ -5097.2618] [GTR parameters ] . ( 40 sec) [ -5097.2618] [Alpha ][ 1.010987] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -5097.2527] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5097.252733. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10159.4915] [GTR parameters ] . ( 1 sec) [ -10022.3390] [Alpha ][ 0.500960] . ( 1 sec) [ -9750.2806] [ 1678] [depth= 5] . ( 1 sec) [ -9711.5647] [ 1674] [depth= 6] . ( 1 sec) [ -9659.7847] [ 1671] [depth= 5] . ( 1 sec) [ -9654.0558] [ 1671] [depth= 2] . ( 1 sec) [ -9637.4862] [ 1667] [depth= 3] . ( 1 sec) [ -9627.5848] [ 1667] [depth= 2] . ( 1 sec) [ -9464.3450] [ 1663] [depth= 11] . ( 1 sec) [ -9462.5058] [ 1664] [depth= 1] . ( 1 sec) [ -9353.3905] [ 1645] [depth= 3] . ( 1 sec) [ -9291.5361] [ 1632] [depth= 15] . ( 1 sec) [ -9038.2172] [ 1561] [depth= 14] . ( 1 sec) [ -9021.6893] [ 1555] [depth= 1] . ( 1 sec) [ -8960.3759] [ 1555] [depth= 3] . ( 1 sec) [ -8907.3947] [ 1548] [depth= 9] . ( 1 sec) [ -8813.1206] [ 1543] [depth= 1] . ( 1 sec) [ -8802.6691] [ 1542] [depth= 4] . ( 1 sec) [ -8762.1736] [ 1527] [depth= 1] . ( 1 sec) [ -8751.4903] [ 1525] [depth= 3] . ( 1 sec) [ -8676.3612] [ 1523] [depth= 3] . ( 1 sec) [ -8513.1784] [ 1475] [depth= 8] . ( 1 sec) [ -8512.9805] [ 1475] [depth= 1] . ( 1 sec) [ -8495.7448] [ 1479] [depth= 13] . ( 1 sec) [ -8427.2975] [ 1473] [depth= 3] . ( 1 sec) [ -7695.7435] [ 1413] [depth= 11] . ( 1 sec) [ -7671.2178] [ 1412] [depth= 7] . ( 1 sec) [ -7602.2878] [ 1397] [depth= 7] . ( 1 sec) [ -7520.3707] [ 1372] [depth= 10] . ( 2 sec) [ -7519.9549] [ 1373] [depth= 1] . ( 2 sec) [ -7514.4663] [ 1372] [depth= 2] . ( 2 sec) [ -7441.5062] [ 1351] [depth= 4] . ( 2 sec) [ -7403.8896] [ 1348] [depth= 5] . ( 2 sec) [ -7355.7432] [ 1336] [depth= 1] . ( 2 sec) [ -7294.6503] [ 1327] [depth= 4] . ( 2 sec) [ -7286.9586] [ 1332] [depth= 2] . ( 2 sec) [ -7189.3921] [ 1327] [depth= 7] . ( 2 sec) [ -7102.9604] [ 1326] [depth= 3] . ( 2 sec) [ -7052.9714] [ 1295] [depth= 1] . ( 2 sec) [ -6884.6866] [ 1261] [depth= 9] . ( 2 sec) [ -6871.5317] [ 1259] [depth= 1] . ( 2 sec) [ -6870.9465] [ 1260] [depth= 1] . ( 2 sec) [ -6823.7714] [ 1251] [depth= 3] . ( 2 sec) [ -6747.8240] [ 1227] [depth= 11] . ( 2 sec) [ -6741.4182] [ 1225] [depth= 7] . ( 2 sec) [ -6683.9502] [ 1211] [depth= 10] . ( 2 sec) [ -6606.1525] [ 1175] [depth= 5] . ( 2 sec) [ -6455.1996] [ 1172] [depth= 7] . ( 2 sec) [ -6374.4274] [ 1163] [depth= 2] . ( 2 sec) [ -6275.9791] [ 1161] [depth= 2] . ( 3 sec) [ -6239.4566] [ 1149] [depth= 3] . ( 3 sec) [ -6229.0828] [ 1149] [depth= 1] . ( 3 sec) [ -6168.9912] [ 1132] [depth= 6] . ( 3 sec) [ -6167.7634] [ 1130] [depth= 3] . ( 3 sec) [ -6150.9330] [ 1127] [depth= 1] . ( 3 sec) [ -6045.9319] [ 1102] [depth= 1] . ( 3 sec) [ -6019.9352] [ 1091] [depth= 4] . ( 3 sec) [ -5997.7194] [ 1093] [depth= 2] . ( 3 sec) [ -5946.4787] [ 1059] [depth= 8] . ( 3 sec) [ -5917.3846] [ 1060] [depth= 7] . ( 3 sec) [ -5905.6089] [ 1055] [depth= 1] . ( 3 sec) [ -5904.1716] [ 1055] [depth= 1] . ( 3 sec) [ -5842.1156] [ 1043] [depth= 3] . ( 3 sec) [ -5838.4010] [ 1043] [depth= 2] . ( 3 sec) [ -5797.1573] [ 1042] [depth= 1] . ( 3 sec) [ -5794.5286] [ 1042] [depth= 2] . ( 3 sec) [ -5787.1955] [ 1045] [depth= 7] . ( 4 sec) [ -5756.2643] [ 1031] [depth= 4] . ( 4 sec) [ -5718.1851] [ 1031] [depth= 1] . ( 4 sec) [ -5688.5224] [ 1017] [depth= 5] . ( 4 sec) [ -5508.3441] [ 966] [depth= 5] . ( 4 sec) [ -5508.0273] [ 966] [depth= 2] . ( 4 sec) [ -5500.6296] [ 964] [depth= 3] . ( 4 sec) [ -5465.2903] [ 943] [depth= 5] . ( 4 sec) [ -5464.8333] [ 943] [depth= 1] . ( 4 sec) [ -5464.7397] [ 944] [depth= 1] . ( 4 sec) [ -5464.6892] [ 944] [depth= 1] . ( 4 sec) [ -5434.7349] [ 943] [depth= 3] . ( 4 sec) [ -5426.5860] [ 940] [depth= 1] . ( 4 sec) [ -5424.0409] [ 941] [depth= 1] . ( 4 sec) [ -5419.3553] [ 941] [depth= 4] . ( 4 sec) [ -5348.5989] [Branch lengths ] . ( 5 sec) [ -5345.2917] [GTR parameters ] . ( 5 sec) [ -5330.0082] [Alpha ][ 0.857536] . ( 5 sec) [ -5302.0947] [ 927] [depth= 2] . ( 5 sec) [ -5246.1379] [ 915] [depth= 1] . ( 6 sec) [ -5185.7236] [ 893] [depth= 1] . ( 6 sec) [ -5184.8437] [ 892] [depth= 1] . ( 6 sec) [ -5176.3541] [ 892] [depth= 1] . ( 6 sec) [ -5176.3159] [ 892] [depth= 1] . ( 6 sec) [ -5170.0921] [ 890] [depth= 1] . ( 6 sec) [ -5158.4594] [ 885] [depth= 1] . ( 6 sec) [ -5156.2796] [ 884] [depth= 1] . ( 6 sec) [ -5156.2105] [ 884] [depth= 1] . ( 6 sec) [ -5147.4490] [ 880] [depth= 2] . ( 6 sec) [ -5145.5073] [ 879] [depth= 1] . ( 6 sec) [ -5144.8037] [ 879] [depth= 2] . ( 6 sec) [ -5144.7587] [ 879] [depth= 1] . ( 6 sec) [ -5144.3111] [ 879] [depth= 3] . ( 7 sec) [ -5125.2838] [ 875] [depth= 1] . ( 7 sec) [ -5125.2219] [ 875] [depth= 1] . ( 7 sec) [ -5125.1294] [ 875] [depth= 1] . ( 8 sec) [ -5125.0930] [ 875] [depth= 1] . ( 8 sec) [ -5125.0807] [ 875] [depth= 2] . ( 8 sec) [ -5124.9757] [ 876] [depth= 1] . ( 9 sec) [ -5124.9422] [ 876] [depth= 1] . ( 9 sec) [ -5123.7705] [ 876] [depth= 1] . ( 9 sec) [ -5123.7427] [ 876] [depth= 1] . ( 10 sec) [ -5098.6220] [Branch lengths ] . ( 10 sec) [ -5098.5766] [GTR parameters ] . ( 10 sec) [ -5097.4083] [Alpha ][ 1.013527] . ( 16 sec) [ -5097.2774] [Branch lengths ] . ( 36 sec) [ -5097.2687] [Branch lengths ] . ( 36 sec) [ -5097.2687] [Topology ] . ( 37 sec) [ -5097.2681] [Topology ] . ( 37 sec) [ -5097.2621] [GTR parameters ] . ( 37 sec) [ -5097.2620] [Alpha ][ 1.011698] . ( 37 sec) [ -5097.2620] [Topology ] . ( 38 sec) [ -5097.2617] [Topology ] . ( 38 sec) [ -5097.2617] [GTR parameters ] . ( 38 sec) [ -5097.2617] [Alpha ][ 1.011698] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -5097.2614] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5097.261404. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5112.589783 . ( 0 sec) [ -5111.9426] [GTR parameters ] . ( 0 sec) [ -5111.9419] [Alpha ][ 1.004062] . ( 0 sec) [ -5111.9419] [Topology ] . ( 1 sec) [ -5099.1697] [Topology ] . ( 1 sec) [ -5097.6528] [Topology ] . ( 2 sec) [ -5097.3802] [Topology ] . ( 3 sec) [ -5097.3097] [Topology ] . ( 3 sec) [ -5097.2897] [Topology ] . ( 4 sec) [ -5097.2835] [Topology ] . ( 4 sec) [ -5097.2815] [Topology ] . ( 5 sec) [ -5097.2806] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5097.280569 . ( 9 sec) [ -5097.2553] [GTR parameters ] . ( 9 sec) [ -5097.2534] [Alpha ][ 1.011239] . ( 9 sec) [ -5097.2534] [Topology ] . ( 10 sec) [ -5097.2527] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5097.252714 . ( 14 sec) [ -5097.2527] [GTR parameters ] . ( 14 sec) [ -5097.2527] [Alpha ][ 1.011239] . ( 14 sec) [ -5097.2527] [Topology ] . ( 15 sec) [ -5097.2525] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 22 sec) [ -5111.9426] [GTR parameters ] . ( 23 sec) [ -5111.9419] [Alpha ][ 1.004062] . ( 23 sec) [ -5110.8380] [ 877] [depth= 1] . ( 23 sec) [ -5110.6570] [ 876] [depth= 1] . ( 23 sec) [ -5109.6050] [ 877] [depth= 1] . ( 23 sec) [ -5109.3363] [ 876] [depth= 1] . ( 23 sec) [ -5108.8254] [ 876] [depth= 1] . ( 24 sec) [ -5108.7209] [ 876] [depth= 1] . ( 24 sec) [ -5108.6451] [ 876] [depth= 1] . ( 24 sec) [ -5108.2606] [ 876] [depth= 1] . ( 24 sec) [ -5108.2137] [ 876] [depth= 1] . ( 24 sec) [ -5108.0193] [ 876] [depth= 1] . ( 24 sec) [ -5107.4271] [ 876] [depth= 1] . ( 24 sec) [ -5107.4005] [ 876] [depth= 1] . ( 24 sec) [ -5107.2415] [ 876] [depth= 1] . ( 24 sec) [ -5106.8456] [ 876] [depth= 1] . ( 24 sec) [ -5106.8008] [ 876] [depth= 1] . ( 24 sec) [ -5106.7321] [ 876] [depth= 1] . ( 24 sec) [ -5106.7009] [ 876] [depth= 1] . ( 26 sec) [ -5103.9016] [ 875] [depth= 1] . ( 27 sec) [ -5102.1506] [ 875] [depth= 1] . ( 28 sec) [ -5097.3507] [Branch lengths ] . ( 28 sec) [ -5097.3285] [GTR parameters ] . ( 28 sec) [ -5097.3277] [Alpha ][ 1.008490] . ( 34 sec) [ -5097.2653] [Branch lengths ] . ( 54 sec) [ -5097.2621] [Branch lengths ] . ( 54 sec) [ -5097.2621] [Topology ] . ( 54 sec) [ -5097.2619] [Topology ] . ( 55 sec) [ -5097.2618] [GTR parameters ] . ( 55 sec) [ -5097.2615] [Alpha ][ 1.011143] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -5097.2524] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5097.252494 . Log likelihood obtained after SPR moves : -5097.252441 . Log likelihood of the current tree: -5097.252441. . Printing the most likely tree in file 'data81.phy_phyml_tree.txt'... . Best log likelihood : -5097.252433 . Time used 0h1m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo