.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12999.5780] [GTR parameters ] . ( 1 sec) [ -12776.6087] [Alpha ][ 0.500960] . ( 2 sec) [ -12750.5380] [ 1506] [depth= 10] . ( 2 sec) [ -12654.9818] [ 1500] [depth= 4] . ( 2 sec) [ -12649.0819] [ 1499] [depth= 1] . ( 2 sec) [ -12604.8472] [ 1496] [depth= 1] . ( 2 sec) [ -12591.7273] [ 1492] [depth= 5] . ( 2 sec) [ -12446.4608] [ 1488] [depth= 6] . ( 2 sec) [ -12069.5137] [ 1484] [depth= 2] . ( 2 sec) [ -12053.7192] [ 1483] [depth= 3] . ( 2 sec) [ -12042.8891] [ 1481] [depth= 3] . ( 2 sec) [ -11937.6197] [ 1478] [depth= 4] . ( 2 sec) [ -11904.8700] [ 1442] [depth= 5] . ( 2 sec) [ -11885.4522] [ 1441] [depth= 3] . ( 3 sec) [ -11659.5826] [ 1429] [depth= 14] . ( 3 sec) [ -11623.0770] [ 1418] [depth= 1] . ( 3 sec) [ -11604.1410] [ 1414] [depth= 2] . ( 3 sec) [ -11544.3986] [ 1374] [depth= 13] . ( 3 sec) [ -11477.6978] [ 1328] [depth= 13] . ( 3 sec) [ -11308.7947] [ 1304] [depth= 3] . ( 3 sec) [ -11242.7201] [ 1295] [depth= 4] . ( 3 sec) [ -11197.3695] [ 1288] [depth= 1] . ( 3 sec) [ -11181.2594] [ 1283] [depth= 11] . ( 3 sec) [ -11164.8383] [ 1284] [depth= 1] . ( 4 sec) [ -10952.3986] [ 1267] [depth= 9] . ( 4 sec) [ -10940.1897] [ 1265] [depth= 4] . ( 4 sec) [ -10927.3167] [ 1264] [depth= 2] . ( 4 sec) [ -10917.3934] [ 1265] [depth= 7] . ( 4 sec) [ -10898.6305] [ 1265] [depth= 1] . ( 4 sec) [ -10878.4479] [ 1260] [depth= 8] . ( 4 sec) [ -10792.8417] [ 1254] [depth= 10] . ( 4 sec) [ -10743.2711] [ 1242] [depth= 9] . ( 4 sec) [ -10740.1370] [ 1241] [depth= 1] . ( 4 sec) [ -10125.0678] [ 1243] [depth= 1] . ( 5 sec) [ -10092.2290] [ 1237] [depth= 7] . ( 5 sec) [ -10080.4091] [ 1236] [depth= 1] . ( 5 sec) [ -10000.5756] [ 1221] [depth= 4] . ( 5 sec) [ -9962.8287] [ 1219] [depth= 14] . ( 5 sec) [ -9928.0731] [ 1212] [depth= 5] . ( 5 sec) [ -9830.8463] [ 1187] [depth= 1] . ( 5 sec) [ -9805.6991] [ 1180] [depth= 7] . ( 5 sec) [ -9798.4884] [ 1182] [depth= 13] . ( 5 sec) [ -9788.2678] [ 1178] [depth= 1] . ( 5 sec) [ -9766.5881] [ 1178] [depth= 3] . ( 6 sec) [ -9719.0557] [ 1163] [depth= 7] . ( 6 sec) [ -9656.4117] [ 1180] [depth= 1] . ( 6 sec) [ -9501.2162] [ 1151] [depth= 3] . ( 6 sec) [ -9411.9328] [ 1142] [depth= 1] . ( 6 sec) [ -9374.3155] [ 1141] [depth= 2] . ( 6 sec) [ -9357.7023] [ 1141] [depth= 1] . ( 6 sec) [ -9302.5018] [ 1133] [depth= 3] . ( 6 sec) [ -9257.6561] [ 1130] [depth= 11] . ( 6 sec) [ -9257.1495] [ 1131] [depth= 1] . ( 6 sec) [ -9240.4599] [ 1121] [depth= 11] . ( 7 sec) [ -9220.4138] [ 1126] [depth= 2] . ( 7 sec) [ -9180.2528] [ 1121] [depth= 1] . ( 7 sec) [ -9121.8128] [ 1105] [depth= 5] . ( 7 sec) [ -9098.5015] [ 1103] [depth= 4] . ( 7 sec) [ -9079.6990] [ 1102] [depth= 4] . ( 7 sec) [ -9079.0222] [ 1102] [depth= 1] . ( 7 sec) [ -9078.8729] [ 1102] [depth= 2] . ( 7 sec) [ -9050.6054] [ 1095] [depth= 6] . ( 7 sec) [ -8972.0285] [ 1079] [depth= 6] . ( 8 sec) [ -8933.8246] [ 1072] [depth= 3] . ( 8 sec) [ -8930.8653] [ 1072] [depth= 14] . ( 8 sec) [ -8805.5559] [ 1053] [depth= 4] . ( 8 sec) [ -8777.5631] [ 1052] [depth= 2] . ( 8 sec) [ -8742.5276] [ 1046] [depth= 14] . ( 8 sec) [ -8699.3391] [ 1041] [depth= 14] . ( 8 sec) [ -8680.4070] [ 1035] [depth= 1] . ( 8 sec) [ -8663.1186] [ 1033] [depth= 2] . ( 9 sec) [ -8638.4176] [ 1032] [depth= 1] . ( 9 sec) [ -8616.9077] [ 1028] [depth= 1] . ( 9 sec) [ -8609.1407] [ 1026] [depth= 1] . ( 9 sec) [ -8607.3821] [ 1027] [depth= 1] . ( 9 sec) [ -8560.8492] [ 1020] [depth= 1] . ( 9 sec) [ -8515.2394] [ 1012] [depth= 8] . ( 9 sec) [ -8498.7598] [ 1008] [depth= 16] . ( 10 sec) [ -8497.3639] [ 1007] [depth= 3] . ( 10 sec) [ -8495.2408] [ 1008] [depth= 2] . ( 10 sec) [ -8492.5023] [ 1005] [depth= 1] . ( 10 sec) [ -8491.7182] [ 1004] [depth= 1] . ( 10 sec) [ -8484.2927] [ 1001] [depth= 7] . ( 11 sec) [ -8483.6449] [ 1001] [depth= 1] . ( 11 sec) [ -8451.6119] [ 998] [depth= 3] . ( 11 sec) [ -8433.4878] [ 995] [depth= 12] . ( 11 sec) [ -8421.6917] [ 990] [depth= 2] . ( 11 sec) [ -8420.1009] [ 991] [depth= 1] . ( 12 sec) [ -8416.2235] [ 991] [depth= 1] . ( 12 sec) [ -8403.8524] [ 986] [depth= 10] . ( 12 sec) [ -8399.6921] [ 986] [depth= 1] . ( 12 sec) [ -8393.2977] [ 986] [depth= 1] . ( 12 sec) [ -8392.9056] [ 986] [depth= 2] . ( 12 sec) [ -8383.8264] [ 984] [depth= 5] . ( 12 sec) [ -8383.5224] [ 985] [depth= 1] . ( 12 sec) [ -8331.0574] [ 971] [depth= 8] . ( 12 sec) [ -8314.1372] [ 968] [depth= 8] . ( 13 sec) [ -8309.3552] [ 968] [depth= 1] . ( 13 sec) [ -8308.0639] [ 968] [depth= 1] . ( 13 sec) [ -8304.4135] [ 968] [depth= 5] . ( 13 sec) [ -8292.5002] [ 965] [depth= 2] . ( 13 sec) [ -8289.2610] [ 961] [depth= 3] . ( 14 sec) [ -8288.5687] [ 961] [depth= 2] . ( 14 sec) [ -8278.1795] [ 960] [depth= 1] . ( 14 sec) [ -8260.7122] [ 958] [depth= 4] . ( 14 sec) [ -8260.0014] [ 958] [depth= 1] . ( 14 sec) [ -8259.7913] [ 958] [depth= 1] . ( 14 sec) [ -8259.6149] [ 958] [depth= 1] . ( 14 sec) [ -8253.0193] [ 957] [depth= 1] . ( 15 sec) [ -8247.2480] [ 957] [depth= 5] . ( 15 sec) [ -8245.1875] [ 956] [depth= 6] . ( 15 sec) [ -8190.5090] [ 956] [depth= 1] . ( 15 sec) [ -8182.7854] [ 956] [depth= 1] . ( 15 sec) [ -8179.1387] [ 954] [depth= 3] . ( 15 sec) [ -8167.8278] [ 953] [depth= 7] . ( 15 sec) [ -8164.9464] [ 952] [depth= 1] . ( 16 sec) [ -8091.4945] [Branch lengths ] . ( 20 sec) [ -8022.5565] [GTR parameters ] . ( 21 sec) [ -7966.3574] [Alpha ][ 0.250961] . ( 21 sec) [ -7951.3773] [ 947] [depth= 11] . ( 21 sec) [ -7950.6278] [ 946] [depth= 1] . ( 22 sec) [ -7950.1437] [ 949] [depth= 1] . ( 22 sec) [ -7948.3424] [ 947] [depth= 5] . ( 22 sec) [ -7947.8266] [ 947] [depth= 1] . ( 23 sec) [ -7931.3567] [ 937] [depth= 10] . ( 23 sec) [ -7920.3185] [ 934] [depth= 5] . ( 23 sec) [ -7919.2940] [ 931] [depth= 8] . ( 23 sec) [ -7915.8873] [ 929] [depth= 1] . ( 23 sec) [ -7915.1846] [ 931] [depth= 3] . ( 24 sec) [ -7908.9823] [ 931] [depth= 2] . ( 24 sec) [ -7899.8358] [ 929] [depth= 2] . ( 25 sec) [ -7875.4812] [ 921] [depth= 7] . ( 26 sec) [ -7868.4869] [ 921] [depth= 5] . ( 27 sec) [ -7867.9614] [ 921] [depth= 2] . ( 27 sec) [ -7866.8860] [ 921] [depth= 1] . ( 27 sec) [ -7864.6333] [ 919] [depth= 2] . ( 29 sec) [ -7864.4274] [ 919] [depth= 1] . ( 30 sec) [ -7864.0680] [ 919] [depth= 1] . ( 31 sec) [ -7862.4164] [ 919] [depth= 3] . ( 31 sec) [ -7862.2825] [ 919] [depth= 1] . ( 33 sec) [ -7861.9485] [ 920] [depth= 3] . ( 33 sec) [ -7853.3916] [ 917] [depth= 2] . ( 34 sec) [ -7852.5294] [ 918] [depth= 1] . ( 35 sec) [ -7852.2597] [ 918] [depth= 2] . ( 35 sec) [ -7852.2263] [ 918] [depth= 1] . ( 35 sec) [ -7851.7391] [ 916] [depth= 3] . ( 35 sec) [ -7849.3412] [ 916] [depth= 1] . ( 36 sec) [ -7847.9981] [ 916] [depth= 2] . ( 36 sec) [ -7846.7168] [ 916] [depth= 1] . ( 37 sec) [ -7846.3942] [ 916] [depth= 1] . ( 37 sec) [ -7845.5930] [ 916] [depth= 1] . ( 38 sec) [ -7844.6485] [ 916] [depth= 1] . ( 39 sec) [ -7844.4537] [ 916] [depth= 1] . ( 39 sec) [ -7843.9608] [ 916] [depth= 2] . ( 41 sec) [ -7843.5804] [ 916] [depth= 1] . ( 41 sec) [ -7843.4014] [ 916] [depth= 2] . ( 44 sec) [ -7843.2914] [ 916] [depth= 5] . ( 44 sec) [ -7842.7277] [ 916] [depth= 3] . ( 44 sec) [ -7842.3957] [ 916] [depth= 2] . ( 44 sec) [ -7840.9928] [ 916] [depth= 1] . ( 45 sec) [ -7840.0721] [ 916] [depth= 2] . ( 48 sec) [ -7837.8306] [ 917] [depth= 4] . ( 48 sec) [ -7837.7027] [ 917] [depth= 3] . ( 48 sec) [ -7837.6861] [ 917] [depth= 1] . ( 49 sec) [ -7832.6096] [Branch lengths ] . ( 53 sec) [ -7831.4829] [GTR parameters ] . ( 53 sec) [ -7829.4556] [Alpha ][ 0.214415] . ( 56 sec) [ -7829.3048] [ 917] [depth= 2] . ( 63 sec) [ -7825.8082] [ 915] [depth= 2] . ( 86 sec) [ -7824.3947] [ 914] [depth= 5] . ( 93 sec) [ -7824.3506] [ 914] [depth= 3] . ( 94 sec) [ -7824.3318] [ 914] [depth= 4] . ( 102 sec) [ -7823.8747] [Branch lengths ] . ( 103 sec) [ -7823.8546] [GTR parameters ] . ( 103 sec) [ -7823.8539] [Alpha ][ 0.213746] . ( 126 sec) [ -7823.8280] [ 915] [depth= 1] . ( 158 sec) [ -7823.7676] [Branch lengths ] . ( 158 sec) [ -7823.7675] [GTR parameters ] . ( 159 sec) [ -7823.7671] [Alpha ][ 0.213220] . ( 230 sec) [ -7823.7609] [Branch lengths ] . ( 230 sec) [ -7823.7609] [Topology ] . ( 231 sec) [ -7823.7602] [Topology ] . ( 232 sec) [ -7823.7586] [GTR parameters ] . ( 232 sec) [ -7823.7586] [Alpha ][ 0.213220] . ( 232 sec) [ -7823.7586] [Topology ] . ( 234 sec) [ -7823.7581] [Topology ] . ( 234 sec) [ -7823.7581] [GTR parameters ] . ( 234 sec) [ -7823.7581] [Alpha ][ 0.213220] . Checking for NNIs, optimizing five branches... . ( 246 sec) [ -7823.7500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 258 sec) [ -7823.7497] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7823.749704. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12050.1004] [GTR parameters ] . ( 1 sec) [ -11839.8992] [Alpha ][ 0.500960] . ( 1 sec) [ -11813.1294] [ 1466] [depth= 8] . ( 1 sec) [ -11761.3077] [ 1460] [depth= 6] . ( 1 sec) [ -11754.4029] [ 1457] [depth= 3] . ( 1 sec) [ -11753.1033] [ 1454] [depth= 1] . ( 1 sec) [ -11664.7904] [ 1445] [depth= 2] . ( 1 sec) [ -11586.5804] [ 1440] [depth= 5] . ( 1 sec) [ -11580.5257] [ 1437] [depth= 4] . ( 2 sec) [ -11387.4246] [ 1433] [depth= 4] . ( 2 sec) [ -11232.2102] [ 1368] [depth= 3] . ( 2 sec) [ -11210.6677] [ 1366] [depth= 1] . ( 2 sec) [ -11145.9636] [ 1363] [depth= 6] . ( 2 sec) [ -11122.3540] [ 1364] [depth= 1] . ( 2 sec) [ -11055.9573] [ 1359] [depth= 10] . ( 2 sec) [ -10991.6399] [ 1351] [depth= 6] . ( 2 sec) [ -10882.9544] [ 1336] [depth= 11] . ( 2 sec) [ -10865.0708] [ 1332] [depth= 15] . ( 2 sec) [ -10816.7225] [ 1320] [depth= 11] . ( 3 sec) [ -10786.1529] [ 1321] [depth= 17] . ( 3 sec) [ -10786.0279] [ 1321] [depth= 1] . ( 3 sec) [ -10750.8615] [ 1316] [depth= 4] . ( 3 sec) [ -10716.6760] [ 1314] [depth= 3] . ( 3 sec) [ -10683.9815] [ 1309] [depth= 4] . ( 3 sec) [ -10543.0292] [ 1307] [depth= 4] . ( 3 sec) [ -10534.0053] [ 1309] [depth= 1] . ( 3 sec) [ -10532.1895] [ 1309] [depth= 1] . ( 3 sec) [ -10531.7172] [ 1310] [depth= 1] . ( 3 sec) [ -10483.8669] [ 1292] [depth= 2] . ( 3 sec) [ -10462.3949] [ 1285] [depth= 1] . ( 4 sec) [ -10422.1078] [ 1278] [depth= 5] . ( 4 sec) [ -10388.1545] [ 1272] [depth= 18] . ( 4 sec) [ -10332.8743] [ 1264] [depth= 1] . ( 4 sec) [ -10320.7474] [ 1264] [depth= 1] . ( 4 sec) [ -10259.8783] [ 1264] [depth= 4] . ( 4 sec) [ -10226.8504] [ 1261] [depth= 1] . ( 4 sec) [ -10205.1477] [ 1261] [depth= 2] . ( 4 sec) [ -10204.7494] [ 1261] [depth= 2] . ( 4 sec) [ -10201.1650] [ 1261] [depth= 3] . ( 4 sec) [ -10163.8665] [ 1250] [depth= 4] . ( 4 sec) [ -10111.2046] [ 1243] [depth= 3] . ( 5 sec) [ -10056.9326] [ 1236] [depth= 13] . ( 5 sec) [ -10015.0119] [ 1236] [depth= 1] . ( 5 sec) [ -10014.5725] [ 1234] [depth= 11] . ( 5 sec) [ -9917.8247] [ 1212] [depth= 4] . ( 5 sec) [ -9913.0312] [ 1205] [depth= 2] . ( 5 sec) [ -9910.1075] [ 1203] [depth= 2] . ( 6 sec) [ -9887.5391] [ 1208] [depth= 4] . ( 6 sec) [ -9870.3944] [ 1203] [depth= 1] . ( 6 sec) [ -9851.7413] [ 1200] [depth= 17] . ( 6 sec) [ -9845.0165] [ 1199] [depth= 15] . ( 6 sec) [ -9815.8169] [ 1193] [depth= 4] . ( 6 sec) [ -9748.5749] [ 1174] [depth= 20] . ( 6 sec) [ -9747.9826] [ 1176] [depth= 6] . ( 7 sec) [ -9705.4597] [ 1167] [depth= 4] . ( 7 sec) [ -9688.8689] [ 1162] [depth= 1] . ( 7 sec) [ -9660.2141] [ 1159] [depth= 2] . ( 7 sec) [ -9627.5401] [ 1156] [depth= 7] . ( 7 sec) [ -9566.3813] [ 1153] [depth= 8] . ( 7 sec) [ -9536.1214] [ 1143] [depth= 6] . ( 7 sec) [ -9502.3041] [ 1147] [depth= 2] . ( 8 sec) [ -9502.0021] [ 1147] [depth= 1] . ( 8 sec) [ -9496.7987] [ 1147] [depth= 1] . ( 8 sec) [ -9496.4721] [ 1147] [depth= 1] . ( 8 sec) [ -9491.4665] [ 1145] [depth= 2] . ( 8 sec) [ -9490.7346] [ 1145] [depth= 1] . ( 8 sec) [ -9478.3749] [ 1140] [depth= 4] . ( 8 sec) [ -9478.1835] [ 1142] [depth= 1] . ( 8 sec) [ -9412.0475] [ 1135] [depth= 6] . ( 9 sec) [ -9396.0756] [ 1134] [depth= 1] . ( 9 sec) [ -9385.1281] [ 1131] [depth= 2] . ( 9 sec) [ -9382.7019] [ 1131] [depth= 1] . ( 9 sec) [ -9263.7752] [ 1103] [depth= 7] . ( 9 sec) [ -9187.9661] [ 1099] [depth= 3] . ( 9 sec) [ -9179.4788] [ 1095] [depth= 6] . ( 9 sec) [ -9162.7487] [ 1090] [depth= 5] . ( 9 sec) [ -9143.5565] [ 1085] [depth= 1] . ( 9 sec) [ -9134.2282] [ 1084] [depth= 1] . ( 10 sec) [ -9062.6288] [ 1081] [depth= 2] . ( 10 sec) [ -8786.4388] [ 1055] [depth= 2] . ( 10 sec) [ -8784.1405] [ 1054] [depth= 2] . ( 10 sec) [ -8780.2185] [ 1054] [depth= 1] . ( 10 sec) [ -8727.9388] [ 1053] [depth= 2] . ( 10 sec) [ -8695.3219] [ 1048] [depth= 14] . ( 11 sec) [ -8691.7039] [ 1045] [depth= 12] . ( 11 sec) [ -8685.4663] [ 1046] [depth= 7] . ( 11 sec) [ -8671.2839] [ 1043] [depth= 9] . ( 11 sec) [ -8656.9105] [ 1041] [depth= 7] . ( 11 sec) [ -8655.1509] [ 1040] [depth= 1] . ( 11 sec) [ -8647.1599] [ 1037] [depth= 4] . ( 11 sec) [ -8525.1021] [ 996] [depth= 1] . ( 12 sec) [ -8423.7670] [ 992] [depth= 6] . ( 12 sec) [ -8393.9048] [ 988] [depth= 4] . ( 12 sec) [ -8334.0622] [ 978] [depth= 6] . ( 12 sec) [ -8332.2590] [ 978] [depth= 1] . ( 13 sec) [ -8331.9025] [ 980] [depth= 9] . ( 13 sec) [ -8325.8617] [ 980] [depth= 1] . ( 13 sec) [ -8313.5620] [ 975] [depth= 5] . ( 13 sec) [ -8307.2626] [ 971] [depth= 3] . ( 13 sec) [ -8301.6969] [ 969] [depth= 1] . ( 13 sec) [ -8290.2637] [ 966] [depth= 2] . ( 13 sec) [ -8289.1986] [ 966] [depth= 2] . ( 13 sec) [ -8279.5704] [ 964] [depth= 12] . ( 13 sec) [ -8270.6871] [ 960] [depth= 2] . ( 13 sec) [ -8264.8182] [ 957] [depth= 4] . ( 13 sec) [ -8221.3503] [ 946] [depth= 7] . ( 14 sec) [ -8178.5652] [ 945] [depth= 3] . ( 14 sec) [ -8177.1925] [ 946] [depth= 1] . ( 14 sec) [ -8169.1751] [ 945] [depth= 9] . ( 14 sec) [ -8160.2469] [ 945] [depth= 3] . ( 14 sec) [ -8159.9656] [ 947] [depth= 6] . ( 14 sec) [ -8159.5003] [ 946] [depth= 5] . ( 15 sec) [ -8159.2043] [ 946] [depth= 1] . ( 15 sec) [ -8147.8634] [ 943] [depth= 2] . ( 16 sec) [ -8086.2837] [Branch lengths ] . ( 19 sec) [ -8012.1119] [GTR parameters ] . ( 19 sec) [ -7957.7788] [Alpha ][ 0.250961] . ( 20 sec) [ -7943.0952] [ 939] [depth= 13] . ( 20 sec) [ -7941.9424] [ 936] [depth= 1] . ( 20 sec) [ -7941.9176] [ 937] [depth= 1] . ( 21 sec) [ -7941.7901] [ 937] [depth= 1] . ( 21 sec) [ -7935.7079] [ 935] [depth= 5] . ( 24 sec) [ -7933.7358] [ 935] [depth= 2] . ( 25 sec) [ -7932.7502] [ 933] [depth= 5] . ( 27 sec) [ -7897.9592] [ 927] [depth= 5] . ( 27 sec) [ -7894.3441] [ 924] [depth= 4] . ( 29 sec) [ -7888.7855] [ 922] [depth= 2] . ( 29 sec) [ -7888.1339] [ 922] [depth= 1] . ( 32 sec) [ -7888.0141] [ 922] [depth= 1] . ( 34 sec) [ -7884.7435] [ 922] [depth= 2] . ( 35 sec) [ -7884.4750] [ 923] [depth= 2] . ( 35 sec) [ -7883.4459] [ 923] [depth= 2] . ( 37 sec) [ -7882.7946] [ 925] [depth= 1] . ( 37 sec) [ -7877.8991] [ 922] [depth= 1] . ( 38 sec) [ -7877.8823] [ 922] [depth= 1] . ( 38 sec) [ -7876.4642] [ 922] [depth= 1] . ( 38 sec) [ -7875.7908] [ 922] [depth= 1] . ( 38 sec) [ -7864.4160] [ 918] [depth= 7] . ( 41 sec) [ -7862.7136] [ 918] [depth= 1] . ( 41 sec) [ -7859.1106] [ 916] [depth= 1] . ( 45 sec) [ -7857.6763] [ 916] [depth= 1] . ( 48 sec) [ -7856.0987] [ 915] [depth= 2] . ( 48 sec) [ -7856.0744] [ 915] [depth= 1] . ( 48 sec) [ -7856.0640] [ 915] [depth= 1] . ( 50 sec) [ -7856.0437] [ 915] [depth= 1] . ( 59 sec) [ -7851.4117] [ 915] [depth= 2] . ( 62 sec) [ -7842.2729] [Branch lengths ] . ( 65 sec) [ -7841.7970] [GTR parameters ] . ( 65 sec) [ -7839.7645] [Alpha ][ 0.214110] . ( 74 sec) [ -7839.7253] [ 915] [depth= 1] . ( 74 sec) [ -7837.3694] [ 916] [depth= 8] . ( 79 sec) [ -7837.3217] [ 916] [depth= 1] . ( 79 sec) [ -7831.3462] [ 914] [depth= 9] . ( 84 sec) [ -7831.2668] [ 914] [depth= 1] . ( 98 sec) [ -7830.4277] [ 913] [depth= 6] . ( 101 sec) [ -7830.4109] [ 913] [depth= 5] . ( 101 sec) [ -7829.3400] [ 913] [depth= 2] . ( 104 sec) [ -7829.2281] [ 913] [depth= 1] . ( 112 sec) [ -7829.1777] [ 913] [depth= 1] . ( 113 sec) [ -7828.3558] [ 913] [depth= 1] . ( 114 sec) [ -7827.2602] [Branch lengths ] . ( 116 sec) [ -7827.1780] [GTR parameters ] . ( 116 sec) [ -7827.1769] [Alpha ][ 0.213256] . ( 128 sec) [ -7825.0934] [ 915] [depth= 3] . ( 135 sec) [ -7824.9391] [ 915] [depth= 1] . ( 170 sec) [ -7823.8153] [Branch lengths ] . ( 172 sec) [ -7823.7655] [GTR parameters ] . ( 172 sec) [ -7823.7654] [Alpha ][ 0.212957] . ( 211 sec) [ -7823.7543] [ 915] [depth= 1] . ( 225 sec) [ -7823.7312] [Branch lengths ] . ( 226 sec) [ -7823.7312] [GTR parameters ] . ( 226 sec) [ -7823.7312] [Alpha ][ 0.212957] . ( 295 sec) [ -7823.7308] [Branch lengths ] . ( 295 sec) [ -7823.7308] [Topology ] . ( 297 sec) [ -7823.7308] [Topology ] . ( 297 sec) [ -7823.7308] [GTR parameters ] . ( 297 sec) [ -7823.7308] [Alpha ][ 0.213170] . Checking for NNIs, optimizing five branches... . ( 310 sec) [ -7823.7283] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7823.728313. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -12995.2369] [GTR parameters ] . ( 3 sec) [ -12783.6988] [Alpha ][ 0.500960] . ( 3 sec) [ -12755.1739] [ 1497] [depth= 6] . ( 3 sec) [ -12696.8592] [ 1491] [depth= 9] . ( 3 sec) [ -12681.6546] [ 1488] [depth= 3] . ( 3 sec) [ -12678.7406] [ 1487] [depth= 3] . ( 3 sec) [ -12582.5370] [ 1457] [depth= 1] . ( 4 sec) [ -12567.0523] [ 1456] [depth= 1] . ( 4 sec) [ -12473.7732] [ 1454] [depth= 2] . ( 4 sec) [ -12422.6961] [ 1453] [depth= 6] . ( 4 sec) [ -12400.0947] [ 1452] [depth= 8] . ( 4 sec) [ -12370.1697] [ 1455] [depth= 1] . ( 4 sec) [ -12294.0322] [ 1456] [depth= 1] . ( 4 sec) [ -12228.3930] [ 1444] [depth= 3] . ( 4 sec) [ -12193.0713] [ 1436] [depth= 12] . ( 4 sec) [ -12144.5098] [ 1428] [depth= 1] . ( 4 sec) [ -12072.3527] [ 1421] [depth= 8] . ( 4 sec) [ -12064.9324] [ 1420] [depth= 1] . ( 4 sec) [ -11997.3935] [ 1408] [depth= 4] . ( 5 sec) [ -11931.1399] [ 1402] [depth= 10] . ( 5 sec) [ -11579.7679] [ 1365] [depth= 11] . ( 5 sec) [ -11142.7893] [ 1308] [depth= 6] . ( 5 sec) [ -11014.4976] [ 1298] [depth= 12] . ( 5 sec) [ -10985.6582] [ 1290] [depth= 13] . ( 5 sec) [ -10918.9936] [ 1267] [depth= 6] . ( 5 sec) [ -10912.5622] [ 1266] [depth= 1] . ( 5 sec) [ -10844.4468] [ 1266] [depth= 4] . ( 5 sec) [ -10798.0171] [ 1266] [depth= 1] . ( 5 sec) [ -10719.9450] [ 1251] [depth= 2] . ( 5 sec) [ -9895.2005] [ 1239] [depth= 13] . ( 6 sec) [ -9887.6564] [ 1237] [depth= 9] . ( 6 sec) [ -9847.1625] [ 1229] [depth= 6] . ( 6 sec) [ -9819.1440] [ 1223] [depth= 6] . ( 6 sec) [ -9816.2494] [ 1224] [depth= 1] . ( 6 sec) [ -9809.7208] [ 1223] [depth= 1] . ( 6 sec) [ -9749.1816] [ 1206] [depth= 14] . ( 6 sec) [ -9729.5443] [ 1202] [depth= 8] . ( 6 sec) [ -9677.3256] [ 1193] [depth= 1] . ( 6 sec) [ -9645.1967] [ 1193] [depth= 1] . ( 6 sec) [ -9634.4437] [ 1188] [depth= 6] . ( 7 sec) [ -9634.0592] [ 1188] [depth= 2] . ( 7 sec) [ -9538.7999] [ 1181] [depth= 13] . ( 7 sec) [ -9446.2835] [ 1165] [depth= 1] . ( 7 sec) [ -9409.6948] [ 1155] [depth= 4] . ( 7 sec) [ -9406.5484] [ 1154] [depth= 10] . ( 7 sec) [ -9405.8291] [ 1154] [depth= 1] . ( 7 sec) [ -9304.0673] [ 1144] [depth= 10] . ( 7 sec) [ -9170.5730] [ 1136] [depth= 10] . ( 7 sec) [ -9146.6188] [ 1134] [depth= 1] . ( 7 sec) [ -9132.7838] [ 1135] [depth= 1] . ( 8 sec) [ -9125.3875] [ 1134] [depth= 1] . ( 8 sec) [ -9107.9272] [ 1128] [depth= 6] . ( 8 sec) [ -9105.7268] [ 1128] [depth= 2] . ( 8 sec) [ -9100.3915] [ 1127] [depth= 2] . ( 8 sec) [ -9089.9224] [ 1120] [depth= 13] . ( 8 sec) [ -9079.7952] [ 1118] [depth= 5] . ( 8 sec) [ -9029.6359] [ 1115] [depth= 8] . ( 9 sec) [ -9019.9758] [ 1113] [depth= 4] . ( 9 sec) [ -9018.7696] [ 1113] [depth= 2] . ( 9 sec) [ -9003.2250] [ 1110] [depth= 3] . ( 9 sec) [ -9001.4922] [ 1110] [depth= 3] . ( 9 sec) [ -8990.9003] [ 1108] [depth= 5] . ( 9 sec) [ -8990.2569] [ 1108] [depth= 1] . ( 9 sec) [ -8985.5995] [ 1105] [depth= 2] . ( 9 sec) [ -8982.5239] [ 1105] [depth= 2] . ( 9 sec) [ -8981.4883] [ 1105] [depth= 1] . ( 9 sec) [ -8976.7912] [ 1105] [depth= 2] . ( 10 sec) [ -8967.9439] [ 1102] [depth= 4] . ( 10 sec) [ -8961.6967] [ 1089] [depth= 1] . ( 10 sec) [ -8946.3823] [ 1084] [depth= 1] . ( 10 sec) [ -8931.5864] [ 1080] [depth= 1] . ( 10 sec) [ -8888.7018] [ 1074] [depth= 10] . ( 10 sec) [ -8878.9664] [ 1075] [depth= 1] . ( 11 sec) [ -8762.7912] [ 1051] [depth= 13] . ( 11 sec) [ -8532.3641] [ 1000] [depth= 2] . ( 11 sec) [ -8514.3985] [ 998] [depth= 3] . ( 11 sec) [ -8507.3501] [ 996] [depth= 1] . ( 11 sec) [ -8435.2736] [ 992] [depth= 11] . ( 11 sec) [ -8408.6904] [ 981] [depth= 4] . ( 11 sec) [ -8393.5861] [ 979] [depth= 7] . ( 11 sec) [ -8393.1740] [ 979] [depth= 7] . ( 12 sec) [ -8392.2403] [ 979] [depth= 2] . ( 12 sec) [ -8382.9067] [ 977] [depth= 4] . ( 12 sec) [ -8288.9333] [ 971] [depth= 2] . ( 12 sec) [ -8285.9416] [ 971] [depth= 1] . ( 12 sec) [ -8282.2953] [ 970] [depth= 2] . ( 12 sec) [ -8213.2247] [ 952] [depth= 1] . ( 12 sec) [ -8206.2176] [ 949] [depth= 3] . ( 13 sec) [ -8198.3179] [ 948] [depth= 3] . ( 13 sec) [ -8197.7458] [ 948] [depth= 7] . ( 13 sec) [ -8197.5004] [ 949] [depth= 1] . ( 13 sec) [ -8191.3744] [ 947] [depth= 5] . ( 13 sec) [ -8164.5112] [ 942] [depth= 7] . ( 13 sec) [ -8160.3671] [ 940] [depth= 5] . ( 13 sec) [ -8160.3534] [ 940] [depth= 1] . ( 15 sec) [ -8158.5920] [ 940] [depth= 1] . ( 15 sec) [ -8153.4669] [ 940] [depth= 1] . ( 15 sec) [ -8141.8603] [ 938] [depth= 4] . ( 15 sec) [ -8102.6377] [ 938] [depth= 1] . ( 15 sec) [ -8100.3713] [ 943] [depth= 1] . ( 15 sec) [ -8091.4465] [ 942] [depth= 2] . ( 15 sec) [ -8088.8741] [ 941] [depth= 1] . ( 15 sec) [ -8087.3760] [ 940] [depth= 1] . ( 15 sec) [ -8081.3215] [ 939] [depth= 5] . ( 16 sec) [ -8079.4162] [ 938] [depth= 1] . ( 16 sec) [ -8078.4938] [ 939] [depth= 1] . ( 18 sec) [ -8071.2609] [ 938] [depth= 3] . ( 19 sec) [ -8068.9556] [ 937] [depth= 1] . ( 19 sec) [ -8054.9831] [ 934] [depth= 15] . ( 19 sec) [ -8054.0406] [ 934] [depth= 1] . ( 19 sec) [ -8051.4916] [ 934] [depth= 1] . ( 19 sec) [ -8051.0521] [ 935] [depth= 1] . ( 19 sec) [ -8050.5783] [ 934] [depth= 3] . ( 21 sec) [ -7995.5169] [Branch lengths ] . ( 22 sec) [ -7966.8693] [GTR parameters ] . ( 22 sec) [ -7913.5826] [Alpha ][ 0.250961] . ( 22 sec) [ -7897.9058] [ 929] [depth= 7] . ( 23 sec) [ -7896.9512] [ 928] [depth= 1] . ( 23 sec) [ -7893.2413] [ 926] [depth= 1] . ( 23 sec) [ -7893.0348] [ 927] [depth= 1] . ( 23 sec) [ -7892.8626] [ 927] [depth= 1] . ( 23 sec) [ -7892.4161] [ 927] [depth= 1] . ( 23 sec) [ -7892.3305] [ 926] [depth= 1] . ( 26 sec) [ -7891.8958] [ 928] [depth= 6] . ( 26 sec) [ -7880.4205] [ 925] [depth= 3] . ( 26 sec) [ -7874.1241] [ 921] [depth= 1] . ( 27 sec) [ -7866.3627] [ 919] [depth= 1] . ( 30 sec) [ -7865.9911] [ 919] [depth= 1] . ( 30 sec) [ -7865.9434] [ 919] [depth= 1] . ( 30 sec) [ -7865.8183] [ 919] [depth= 1] . ( 31 sec) [ -7865.7007] [ 919] [depth= 1] . ( 33 sec) [ -7865.6828] [ 919] [depth= 1] . ( 33 sec) [ -7865.4949] [ 919] [depth= 1] . ( 33 sec) [ -7858.8587] [ 915] [depth= 3] . ( 35 sec) [ -7858.8150] [ 915] [depth= 2] . ( 35 sec) [ -7858.6314] [ 915] [depth= 1] . ( 35 sec) [ -7858.6022] [ 915] [depth= 1] . ( 36 sec) [ -7858.5851] [ 915] [depth= 1] . ( 40 sec) [ -7858.3578] [ 917] [depth= 1] . ( 40 sec) [ -7856.7856] [ 920] [depth= 1] . ( 40 sec) [ -7854.4733] [ 917] [depth= 1] . ( 41 sec) [ -7854.3699] [ 917] [depth= 1] . ( 42 sec) [ -7854.3267] [ 917] [depth= 2] . ( 42 sec) [ -7854.2273] [ 917] [depth= 2] . ( 44 sec) [ -7853.7733] [ 920] [depth= 3] . ( 44 sec) [ -7853.1882] [ 920] [depth= 2] . ( 44 sec) [ -7853.1769] [ 920] [depth= 2] . ( 45 sec) [ -7851.9843] [ 919] [depth= 1] . ( 45 sec) [ -7851.9438] [ 917] [depth= 1] . ( 45 sec) [ -7851.8274] [ 917] [depth= 1] . ( 47 sec) [ -7851.6648] [ 917] [depth= 1] . ( 47 sec) [ -7851.3850] [ 917] [depth= 1] . ( 49 sec) [ -7850.8235] [ 918] [depth= 1] . ( 49 sec) [ -7850.8090] [ 918] [depth= 1] . ( 49 sec) [ -7850.7963] [ 918] [depth= 1] . ( 49 sec) [ -7849.0600] [ 918] [depth= 9] . ( 51 sec) [ -7840.0277] [Branch lengths ] . ( 52 sec) [ -7839.7402] [GTR parameters ] . ( 52 sec) [ -7837.4787] [Alpha ][ 0.212204] . ( 54 sec) [ -7837.4448] [ 919] [depth= 2] . ( 58 sec) [ -7835.6675] [ 918] [depth= 7] . ( 59 sec) [ -7835.6104] [ 918] [depth= 1] . ( 71 sec) [ -7834.7038] [ 918] [depth= 2] . ( 72 sec) [ -7834.5389] [ 918] [depth= 1] . ( 74 sec) [ -7834.5141] [ 918] [depth= 3] . ( 78 sec) [ -7834.0252] [ 918] [depth= 1] . ( 81 sec) [ -7833.4600] [ 917] [depth= 2] . ( 81 sec) [ -7833.0407] [ 917] [depth= 4] . ( 84 sec) [ -7831.9865] [ 916] [depth= 1] . ( 84 sec) [ -7831.9175] [ 916] [depth= 1] . ( 84 sec) [ -7831.7616] [ 916] [depth= 3] . ( 84 sec) [ -7831.7491] [ 916] [depth= 2] . ( 100 sec) [ -7829.8532] [Branch lengths ] . ( 100 sec) [ -7829.8319] [GTR parameters ] . ( 100 sec) [ -7829.8317] [Alpha ][ 0.212532] . ( 102 sec) [ -7829.8061] [ 915] [depth= 3] . ( 104 sec) [ -7825.1888] [ 914] [depth= 5] . ( 104 sec) [ -7825.1636] [ 914] [depth= 2] . ( 104 sec) [ -7825.1037] [ 914] [depth= 1] . ( 105 sec) [ -7825.0777] [ 914] [depth= 1] . ( 106 sec) [ -7824.8419] [ 914] [depth= 1] . ( 116 sec) [ -7824.7670] [ 914] [depth= 1] . ( 121 sec) [ -7824.3820] [ 914] [depth= 1] . ( 123 sec) [ -7824.3388] [ 914] [depth= 1] . ( 131 sec) [ -7824.3270] [ 914] [depth= 2] . ( 147 sec) [ -7823.8388] [Branch lengths ] . ( 148 sec) [ -7823.8173] [GTR parameters ] . ( 148 sec) [ -7823.8164] [Alpha ][ 0.213240] . ( 201 sec) [ -7823.8082] [Branch lengths ] . ( 269 sec) [ -7823.8065] [Branch lengths ] . ( 269 sec) [ -7823.8065] [Topology ] . ( 271 sec) [ -7823.8056] [Topology ] . ( 271 sec) [ -7823.8056] [GTR parameters ] . ( 271 sec) [ -7823.8056] [Alpha ][ 0.213240] . Checking for NNIs, optimizing five branches... . ( 282 sec) [ -7823.8054] [Topology ] . Checking for NNIs, optimizing five branches... . ( 296 sec) [ -7823.7710] [Topology ] . Checking for NNIs, optimizing five branches... . ( 307 sec) [ -7823.7668] [Topology ] . Checking for NNIs, optimizing five branches... . ( 318 sec) [ -7823.7643] [Topology ] . Checking for NNIs, optimizing five branches... . ( 329 sec) [ -7823.7221] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7823.722093. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12849.0933] [GTR parameters ] . ( 1 sec) [ -12631.6822] [Alpha ][ 0.500960] . ( 2 sec) [ -12539.2215] [ 1520] [depth= 13] . ( 2 sec) [ -12463.7138] [ 1497] [depth= 14] . ( 2 sec) [ -12394.4888] [ 1498] [depth= 1] . ( 2 sec) [ -12094.6607] [ 1448] [depth= 3] . ( 2 sec) [ -12021.5620] [ 1397] [depth= 2] . ( 2 sec) [ -11530.9585] [ 1362] [depth= 7] . ( 2 sec) [ -11495.0836] [ 1358] [depth= 5] . ( 2 sec) [ -11431.7151] [ 1357] [depth= 7] . ( 2 sec) [ -11427.0199] [ 1356] [depth= 1] . ( 2 sec) [ -11412.1579] [ 1355] [depth= 4] . ( 2 sec) [ -11065.2054] [ 1352] [depth= 3] . ( 3 sec) [ -11042.8582] [ 1347] [depth= 5] . ( 3 sec) [ -10781.2639] [ 1346] [depth= 3] . ( 3 sec) [ -10723.8196] [ 1346] [depth= 2] . ( 3 sec) [ -10716.7262] [ 1344] [depth= 4] . ( 3 sec) [ -10596.1415] [ 1342] [depth= 1] . ( 3 sec) [ -10587.4442] [ 1343] [depth= 7] . ( 3 sec) [ -10396.1840] [ 1318] [depth= 8] . ( 3 sec) [ -10388.0310] [ 1316] [depth= 7] . ( 3 sec) [ -10302.5261] [ 1293] [depth= 7] . ( 3 sec) [ -10275.3654] [ 1289] [depth= 1] . ( 3 sec) [ -10247.7753] [ 1283] [depth= 2] . ( 4 sec) [ -10242.5813] [ 1282] [depth= 10] . ( 4 sec) [ -10212.4833] [ 1281] [depth= 1] . ( 4 sec) [ -10147.5708] [ 1269] [depth= 16] . ( 4 sec) [ -10109.3846] [ 1261] [depth= 10] . ( 4 sec) [ -10093.8766] [ 1256] [depth= 13] . ( 4 sec) [ -9999.2110] [ 1251] [depth= 9] . ( 4 sec) [ -9920.3002] [ 1243] [depth= 3] . ( 4 sec) [ -9862.0669] [ 1242] [depth= 6] . ( 4 sec) [ -9860.2298] [ 1243] [depth= 1] . ( 4 sec) [ -9816.2246] [ 1234] [depth= 9] . ( 4 sec) [ -9765.0280] [ 1231] [depth= 2] . ( 4 sec) [ -9750.9555] [ 1230] [depth= 4] . ( 5 sec) [ -9703.2141] [ 1220] [depth= 3] . ( 5 sec) [ -9678.3635] [ 1218] [depth= 1] . ( 5 sec) [ -9664.3390] [ 1217] [depth= 6] . ( 5 sec) [ -9663.3484] [ 1217] [depth= 1] . ( 5 sec) [ -9657.8708] [ 1218] [depth= 6] . ( 5 sec) [ -9634.6584] [ 1215] [depth= 6] . ( 5 sec) [ -9623.5735] [ 1211] [depth= 4] . ( 5 sec) [ -9550.3061] [ 1199] [depth= 4] . ( 6 sec) [ -9536.1173] [ 1196] [depth= 10] . ( 6 sec) [ -9489.9285] [ 1183] [depth= 1] . ( 6 sec) [ -9460.8446] [ 1176] [depth= 11] . ( 6 sec) [ -9408.2819] [ 1158] [depth= 3] . ( 6 sec) [ -9407.3840] [ 1158] [depth= 3] . ( 6 sec) [ -9387.8149] [ 1153] [depth= 12] . ( 6 sec) [ -9382.7945] [ 1153] [depth= 1] . ( 6 sec) [ -9347.5403] [ 1146] [depth= 4] . ( 6 sec) [ -9344.9880] [ 1144] [depth= 3] . ( 6 sec) [ -9305.1767] [ 1138] [depth= 8] . ( 7 sec) [ -9304.6405] [ 1138] [depth= 1] . ( 7 sec) [ -9274.7614] [ 1131] [depth= 6] . ( 7 sec) [ -9235.9948] [ 1128] [depth= 9] . ( 7 sec) [ -9225.6137] [ 1128] [depth= 7] . ( 7 sec) [ -9221.8014] [ 1128] [depth= 1] . ( 7 sec) [ -9209.4581] [ 1125] [depth= 6] . ( 7 sec) [ -9208.8361] [ 1124] [depth= 2] . ( 7 sec) [ -9189.8625] [ 1123] [depth= 6] . ( 8 sec) [ -9176.1367] [ 1121] [depth= 4] . ( 8 sec) [ -9175.9928] [ 1121] [depth= 1] . ( 8 sec) [ -9168.1928] [ 1120] [depth= 2] . ( 8 sec) [ -9159.5112] [ 1118] [depth= 3] . ( 8 sec) [ -9146.8045] [ 1117] [depth= 3] . ( 8 sec) [ -9021.8536] [ 1122] [depth= 4] . ( 9 sec) [ -9008.4570] [ 1126] [depth= 4] . ( 9 sec) [ -8976.5358] [ 1117] [depth= 3] . ( 9 sec) [ -8976.5239] [ 1120] [depth= 3] . ( 9 sec) [ -8960.6845] [ 1114] [depth= 6] . ( 9 sec) [ -8948.3933] [ 1112] [depth= 1] . ( 9 sec) [ -8947.2102] [ 1113] [depth= 1] . ( 9 sec) [ -8941.3959] [ 1111] [depth= 1] . ( 10 sec) [ -8911.6303] [ 1102] [depth= 3] . ( 10 sec) [ -8825.7206] [ 1076] [depth= 2] . ( 10 sec) [ -8774.2899] [ 1068] [depth= 11] . ( 10 sec) [ -8773.3257] [ 1068] [depth= 2] . ( 10 sec) [ -8709.2146] [ 1052] [depth= 12] . ( 11 sec) [ -8700.1880] [ 1052] [depth= 3] . ( 11 sec) [ -8694.7191] [ 1049] [depth= 2] . ( 12 sec) [ -8693.7080] [ 1049] [depth= 2] . ( 12 sec) [ -8644.6204] [ 1034] [depth= 7] . ( 12 sec) [ -8512.4690] [ 988] [depth= 3] . ( 12 sec) [ -8468.1239] [ 976] [depth= 1] . ( 12 sec) [ -8455.5654] [ 975] [depth= 5] . ( 12 sec) [ -8434.7584] [ 970] [depth= 7] . ( 12 sec) [ -8426.9815] [ 969] [depth= 2] . ( 13 sec) [ -8418.3677] [ 966] [depth= 2] . ( 13 sec) [ -8418.1773] [ 966] [depth= 1] . ( 14 sec) [ -8410.6559] [ 964] [depth= 12] . ( 15 sec) [ -8409.5409] [ 965] [depth= 4] . ( 15 sec) [ -8380.2136] [ 956] [depth= 8] . ( 15 sec) [ -8377.3185] [ 955] [depth= 1] . ( 15 sec) [ -8373.0129] [ 955] [depth= 1] . ( 15 sec) [ -8345.4370] [ 949] [depth= 6] . ( 15 sec) [ -8343.1259] [ 951] [depth= 2] . ( 15 sec) [ -8342.6295] [ 951] [depth= 4] . ( 15 sec) [ -8341.1121] [ 949] [depth= 2] . ( 15 sec) [ -8329.5153] [ 947] [depth= 6] . ( 15 sec) [ -8326.1944] [ 946] [depth= 2] . ( 15 sec) [ -8319.9215] [ 942] [depth= 3] . ( 16 sec) [ -8319.8588] [ 942] [depth= 1] . ( 16 sec) [ -8319.5450] [ 942] [depth= 1] . ( 16 sec) [ -8319.4129] [ 941] [depth= 2] . ( 16 sec) [ -8315.4540] [ 941] [depth= 2] . ( 17 sec) [ -8314.8186] [ 941] [depth= 1] . ( 17 sec) [ -8239.6997] [ 937] [depth= 9] . ( 17 sec) [ -8236.2799] [ 939] [depth= 8] . ( 17 sec) [ -8236.0359] [ 939] [depth= 1] . ( 17 sec) [ -8235.6284] [ 938] [depth= 3] . ( 17 sec) [ -8234.3386] [ 938] [depth= 1] . ( 18 sec) [ -8231.9428] [ 938] [depth= 1] . ( 18 sec) [ -8230.9608] [ 938] [depth= 1] . ( 18 sec) [ -8220.6420] [ 937] [depth= 1] . ( 18 sec) [ -8213.3138] [ 936] [depth= 2] . ( 18 sec) [ -8206.8844] [ 935] [depth= 7] . ( 18 sec) [ -8196.1972] [ 933] [depth= 1] . ( 18 sec) [ -8194.8576] [ 945] [depth= 1] . ( 18 sec) [ -8170.1796] [ 948] [depth= 7] . ( 18 sec) [ -8165.8631] [ 947] [depth= 3] . ( 18 sec) [ -8135.5626] [ 940] [depth= 6] . ( 19 sec) [ -8082.2895] [Branch lengths ] . ( 21 sec) [ -7971.6460] [GTR parameters ] . ( 21 sec) [ -7917.2257] [Alpha ][ 0.250961] . ( 21 sec) [ -7898.4717] [ 935] [depth= 9] . ( 22 sec) [ -7898.2829] [ 935] [depth= 1] . ( 27 sec) [ -7897.9905] [ 935] [depth= 1] . ( 28 sec) [ -7897.8801] [ 935] [depth= 1] . ( 28 sec) [ -7897.8317] [ 935] [depth= 1] . ( 28 sec) [ -7896.0928] [ 936] [depth= 2] . ( 28 sec) [ -7895.2557] [ 934] [depth= 3] . ( 28 sec) [ -7895.1682] [ 934] [depth= 1] . ( 29 sec) [ -7884.7751] [ 931] [depth= 5] . ( 32 sec) [ -7884.1835] [ 930] [depth= 1] . ( 34 sec) [ -7884.1668] [ 930] [depth= 1] . ( 38 sec) [ -7883.4126] [ 928] [depth= 4] . ( 39 sec) [ -7871.4635] [ 924] [depth= 8] . ( 45 sec) [ -7860.6133] [ 913] [depth= 1] . ( 47 sec) [ -7859.4897] [ 914] [depth= 1] . ( 50 sec) [ -7859.3098] [ 914] [depth= 1] . ( 53 sec) [ -7856.5339] [ 918] [depth= 3] . ( 54 sec) [ -7856.4784] [ 918] [depth= 3] . ( 56 sec) [ -7856.4623] [ 918] [depth= 1] . ( 56 sec) [ -7856.4501] [ 918] [depth= 1] . ( 60 sec) [ -7856.3503] [ 918] [depth= 1] . ( 65 sec) [ -7855.7682] [ 918] [depth= 2] . ( 66 sec) [ -7844.4696] [Branch lengths ] . ( 67 sec) [ -7844.1392] [GTR parameters ] . ( 67 sec) [ -7842.0779] [Alpha ][ 0.214400] . ( 86 sec) [ -7841.7173] [ 918] [depth= 2] . ( 86 sec) [ -7841.6740] [ 918] [depth= 1] . ( 91 sec) [ -7841.4104] [ 919] [depth= 2] . ( 91 sec) [ -7841.3876] [ 919] [depth= 1] . ( 103 sec) [ -7840.6873] [ 918] [depth= 1] . ( 103 sec) [ -7839.2704] [ 916] [depth= 1] . ( 104 sec) [ -7837.1700] [ 915] [depth= 4] . ( 106 sec) [ -7836.7511] [ 915] [depth= 1] . ( 106 sec) [ -7836.7048] [ 915] [depth= 3] . ( 108 sec) [ -7836.6225] [ 914] [depth= 1] . ( 108 sec) [ -7836.5444] [ 914] [depth= 1] . ( 108 sec) [ -7836.4835] [ 914] [depth= 1] . ( 109 sec) [ -7836.4704] [ 914] [depth= 3] . ( 117 sec) [ -7833.8762] [ 914] [depth= 3] . ( 117 sec) [ -7830.7857] [Branch lengths ] . ( 118 sec) [ -7830.7606] [GTR parameters ] . ( 118 sec) [ -7830.7576] [Alpha ][ 0.213062] . ( 170 sec) [ -7830.7036] [Branch lengths ] . ( 238 sec) [ -7830.6989] [Branch lengths ] . ( 238 sec) [ -7830.6989] [Topology ] . ( 240 sec) [ -7830.6982] [Topology ] . ( 240 sec) [ -7830.6978] [GTR parameters ] . ( 240 sec) [ -7830.6966] [Alpha ][ 0.212205] . ( 240 sec) [ -7830.6966] [Topology ] . ( 242 sec) [ -7830.6960] [Topology ] . ( 242 sec) [ -7830.6959] [GTR parameters ] . ( 242 sec) [ -7830.6959] [Alpha ][ 0.212205] . Checking for NNIs, optimizing five branches... . ( 254 sec) [ -7830.6958] [Topology ] . Checking for NNIs, optimizing five branches... . ( 266 sec) [ -7830.6909] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7830.690883. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12657.8090] [GTR parameters ] . ( 2 sec) [ -12444.1490] [Alpha ][ 0.500960] . ( 2 sec) [ -12058.8993] [ 1504] [depth= 10] . ( 2 sec) [ -11738.5097] [ 1496] [depth= 3] . ( 2 sec) [ -11721.1297] [ 1495] [depth= 7] . ( 2 sec) [ -11701.5052] [ 1492] [depth= 1] . ( 2 sec) [ -11615.0165] [ 1492] [depth= 4] . ( 2 sec) [ -11556.9870] [ 1491] [depth= 1] . ( 3 sec) [ -11449.9141] [ 1483] [depth= 1] . ( 3 sec) [ -11412.8227] [ 1478] [depth= 8] . ( 3 sec) [ -11395.3865] [ 1474] [depth= 3] . ( 3 sec) [ -11352.9892] [ 1473] [depth= 1] . ( 3 sec) [ -11297.1000] [ 1458] [depth= 5] . ( 3 sec) [ -11254.6391] [ 1458] [depth= 2] . ( 3 sec) [ -11190.0917] [ 1457] [depth= 2] . ( 3 sec) [ -11129.8949] [ 1450] [depth= 16] . ( 3 sec) [ -10989.8849] [ 1449] [depth= 14] . ( 3 sec) [ -10986.3442] [ 1450] [depth= 5] . ( 3 sec) [ -10971.2249] [ 1440] [depth= 11] . ( 4 sec) [ -10969.4506] [ 1440] [depth= 1] . ( 4 sec) [ -10913.2442] [ 1429] [depth= 3] . ( 4 sec) [ -10860.1392] [ 1432] [depth= 2] . ( 4 sec) [ -10810.3922] [ 1425] [depth= 11] . ( 4 sec) [ -10731.3440] [ 1410] [depth= 5] . ( 4 sec) [ -10537.1809] [ 1386] [depth= 12] . ( 4 sec) [ -10470.7093] [ 1374] [depth= 5] . ( 4 sec) [ -10397.6058] [ 1366] [depth= 9] . ( 4 sec) [ -10349.3688] [ 1358] [depth= 5] . ( 4 sec) [ -10018.9508] [ 1310] [depth= 5] . ( 4 sec) [ -9858.0191] [ 1280] [depth= 9] . ( 5 sec) [ -9840.3875] [ 1273] [depth= 8] . ( 5 sec) [ -9808.2625] [ 1267] [depth= 10] . ( 5 sec) [ -9804.1491] [ 1267] [depth= 1] . ( 5 sec) [ -9772.7112] [ 1258] [depth= 14] . ( 5 sec) [ -9753.4930] [ 1257] [depth= 3] . ( 5 sec) [ -9727.3000] [ 1249] [depth= 3] . ( 5 sec) [ -9724.4809] [ 1248] [depth= 2] . ( 5 sec) [ -9722.6021] [ 1248] [depth= 1] . ( 6 sec) [ -9717.7030] [ 1245] [depth= 1] . ( 6 sec) [ -9713.3425] [ 1240] [depth= 1] . ( 6 sec) [ -9698.5518] [ 1236] [depth= 1] . ( 6 sec) [ -9682.7859] [ 1231] [depth= 2] . ( 6 sec) [ -9627.0151] [ 1217] [depth= 6] . ( 6 sec) [ -9623.5047] [ 1214] [depth= 1] . ( 6 sec) [ -9576.2057] [ 1196] [depth= 7] . ( 6 sec) [ -9551.5110] [ 1188] [depth= 3] . ( 7 sec) [ -9535.2496] [ 1186] [depth= 1] . ( 7 sec) [ -9451.3699] [ 1168] [depth= 5] . ( 7 sec) [ -9201.3242] [ 1117] [depth= 3] . ( 7 sec) [ -9126.4860] [ 1105] [depth= 14] . ( 7 sec) [ -9113.8038] [ 1103] [depth= 1] . ( 7 sec) [ -9107.9494] [ 1102] [depth= 2] . ( 7 sec) [ -9107.5493] [ 1103] [depth= 2] . ( 8 sec) [ -9107.4237] [ 1102] [depth= 1] . ( 8 sec) [ -9101.1175] [ 1103] [depth= 2] . ( 8 sec) [ -9082.1050] [ 1099] [depth= 2] . ( 8 sec) [ -9082.0274] [ 1101] [depth= 1] . ( 8 sec) [ -9068.1164] [ 1100] [depth= 5] . ( 8 sec) [ -9063.1883] [ 1098] [depth= 1] . ( 8 sec) [ -9051.0196] [ 1097] [depth= 4] . ( 8 sec) [ -9050.5669] [ 1097] [depth= 1] . ( 9 sec) [ -9013.1507] [ 1091] [depth= 11] . ( 9 sec) [ -8988.7415] [ 1091] [depth= 2] . ( 9 sec) [ -8897.5553] [ 1091] [depth= 2] . ( 9 sec) [ -8891.8525] [ 1090] [depth= 3] . ( 9 sec) [ -8887.6370] [ 1090] [depth= 2] . ( 9 sec) [ -8886.9382] [ 1090] [depth= 2] . ( 9 sec) [ -8867.3838] [ 1090] [depth= 1] . ( 9 sec) [ -8851.7163] [ 1084] [depth= 4] . ( 10 sec) [ -8849.5946] [ 1085] [depth= 4] . ( 10 sec) [ -8844.1565] [ 1084] [depth= 1] . ( 10 sec) [ -8843.2889] [ 1076] [depth= 8] . ( 10 sec) [ -8840.4088] [ 1077] [depth= 1] . ( 10 sec) [ -8822.0917] [ 1071] [depth= 11] . ( 10 sec) [ -8813.6134] [ 1071] [depth= 1] . ( 10 sec) [ -8799.0792] [ 1068] [depth= 12] . ( 10 sec) [ -8753.6210] [ 1058] [depth= 8] . ( 10 sec) [ -8660.9555] [ 1034] [depth= 1] . ( 11 sec) [ -8658.7433] [ 1034] [depth= 7] . ( 11 sec) [ -8656.1343] [ 1033] [depth= 1] . ( 11 sec) [ -8650.2343] [ 1028] [depth= 7] . ( 12 sec) [ -8625.6057] [ 1027] [depth= 8] . ( 12 sec) [ -8625.1490] [ 1029] [depth= 1] . ( 12 sec) [ -8605.1103] [ 1029] [depth= 2] . ( 12 sec) [ -8603.2014] [ 1029] [depth= 5] . ( 12 sec) [ -8598.1335] [ 1026] [depth= 9] . ( 12 sec) [ -8586.7452] [ 1024] [depth= 2] . ( 12 sec) [ -8486.9073] [ 1014] [depth= 6] . ( 13 sec) [ -8450.8177] [ 1003] [depth= 10] . ( 13 sec) [ -8445.8585] [ 1001] [depth= 2] . ( 13 sec) [ -8443.2768] [ 1002] [depth= 1] . ( 13 sec) [ -8429.1791] [ 998] [depth= 7] . ( 13 sec) [ -8411.3988] [ 994] [depth= 11] . ( 13 sec) [ -8410.6117] [ 995] [depth= 2] . ( 13 sec) [ -8404.2312] [ 990] [depth= 2] . ( 13 sec) [ -8396.8651] [ 988] [depth= 3] . ( 14 sec) [ -8369.4613] [ 986] [depth= 2] . ( 15 sec) [ -8316.4127] [ 989] [depth= 6] . ( 15 sec) [ -8305.6969] [ 987] [depth= 3] . ( 16 sec) [ -8304.6550] [ 987] [depth= 1] . ( 16 sec) [ -8303.4770] [ 987] [depth= 1] . ( 16 sec) [ -8303.0784] [ 988] [depth= 1] . ( 17 sec) [ -8297.0495] [ 988] [depth= 1] . ( 17 sec) [ -8265.4675] [ 981] [depth= 2] . ( 17 sec) [ -8264.5312] [ 981] [depth= 1] . ( 17 sec) [ -8262.1438] [ 979] [depth= 5] . ( 17 sec) [ -8251.3314] [ 981] [depth= 2] . ( 18 sec) [ -8244.0830] [ 981] [depth= 1] . ( 18 sec) [ -8243.2116] [ 981] [depth= 2] . ( 18 sec) [ -8239.8201] [ 981] [depth= 1] . ( 18 sec) [ -8236.7232] [ 981] [depth= 2] . ( 18 sec) [ -8202.2803] [ 972] [depth= 1] . ( 18 sec) [ -8201.3313] [ 972] [depth= 1] . ( 18 sec) [ -8120.7676] [ 948] [depth= 4] . ( 18 sec) [ -8115.9755] [ 949] [depth= 5] . ( 18 sec) [ -8115.9586] [ 949] [depth= 1] . ( 19 sec) [ -8115.8234] [ 949] [depth= 1] . ( 19 sec) [ -8110.8612] [ 949] [depth= 1] . ( 19 sec) [ -8110.2721] [ 949] [depth= 1] . ( 19 sec) [ -8106.3037] [ 948] [depth= 1] . ( 20 sec) [ -8101.0787] [ 949] [depth= 1] . ( 20 sec) [ -8094.5116] [ 948] [depth= 5] . ( 20 sec) [ -8057.4064] [Branch lengths ] . ( 22 sec) [ -8019.8465] [GTR parameters ] . ( 22 sec) [ -7963.9000] [Alpha ][ 0.250961] . ( 22 sec) [ -7955.0562] [ 946] [depth= 8] . ( 23 sec) [ -7954.3145] [ 945] [depth= 1] . ( 24 sec) [ -7950.2419] [ 944] [depth= 1] . ( 24 sec) [ -7950.2233] [ 944] [depth= 1] . ( 24 sec) [ -7939.1999] [ 941] [depth= 3] . ( 24 sec) [ -7939.0168] [ 941] [depth= 1] . ( 25 sec) [ -7939.0048] [ 941] [depth= 2] . ( 25 sec) [ -7937.7672] [ 941] [depth= 1] . ( 25 sec) [ -7934.6612] [ 937] [depth= 2] . ( 25 sec) [ -7927.6033] [ 936] [depth= 5] . ( 25 sec) [ -7921.9460] [ 936] [depth= 1] . ( 26 sec) [ -7903.4130] [ 923] [depth= 9] . ( 26 sec) [ -7896.9224] [ 923] [depth= 4] . ( 27 sec) [ -7896.7144] [ 925] [depth= 2] . ( 28 sec) [ -7896.0429] [ 925] [depth= 1] . ( 28 sec) [ -7895.8762] [ 924] [depth= 3] . ( 30 sec) [ -7892.4978] [ 923] [depth= 5] . ( 30 sec) [ -7892.4407] [ 923] [depth= 1] . ( 30 sec) [ -7892.2892] [ 923] [depth= 1] . ( 31 sec) [ -7892.0199] [ 924] [depth= 1] . ( 32 sec) [ -7890.7307] [ 925] [depth= 2] . ( 33 sec) [ -7889.2259] [ 927] [depth= 1] . ( 33 sec) [ -7889.0635] [ 926] [depth= 1] . ( 34 sec) [ -7881.5139] [ 924] [depth= 3] . ( 34 sec) [ -7881.4133] [ 925] [depth= 1] . ( 34 sec) [ -7881.0835] [ 925] [depth= 1] . ( 34 sec) [ -7878.0998] [ 925] [depth= 1] . ( 37 sec) [ -7876.0153] [ 926] [depth= 9] . ( 38 sec) [ -7875.8654] [ 926] [depth= 2] . ( 41 sec) [ -7874.9626] [ 926] [depth= 1] . ( 43 sec) [ -7870.2257] [ 922] [depth= 7] . ( 44 sec) [ -7868.9826] [ 922] [depth= 1] . ( 44 sec) [ -7853.7080] [ 918] [depth= 4] . ( 45 sec) [ -7853.5972] [ 921] [depth= 2] . ( 45 sec) [ -7853.2842] [ 919] [depth= 6] . ( 45 sec) [ -7853.1374] [ 918] [depth= 1] . ( 46 sec) [ -7852.7386] [ 919] [depth= 3] . ( 52 sec) [ -7852.6911] [ 919] [depth= 2] . ( 54 sec) [ -7852.0527] [ 919] [depth= 1] . ( 54 sec) [ -7844.8290] [Branch lengths ] . ( 55 sec) [ -7843.9888] [GTR parameters ] . ( 55 sec) [ -7841.8234] [Alpha ][ 0.213026] . ( 61 sec) [ -7841.6575] [ 919] [depth= 1] . ( 65 sec) [ -7841.6303] [ 919] [depth= 4] . ( 67 sec) [ -7841.1413] [ 916] [depth= 3] . ( 68 sec) [ -7841.0742] [ 915] [depth= 1] . ( 68 sec) [ -7841.0575] [ 915] [depth= 1] . ( 68 sec) [ -7840.3040] [ 915] [depth= 1] . ( 72 sec) [ -7840.2304] [ 915] [depth= 1] . ( 73 sec) [ -7837.2329] [ 916] [depth= 2] . ( 76 sec) [ -7836.7168] [ 917] [depth= 2] . ( 81 sec) [ -7836.7053] [ 917] [depth= 2] . ( 86 sec) [ -7833.8950] [ 917] [depth= 5] . ( 87 sec) [ -7833.7687] [ 917] [depth= 1] . ( 90 sec) [ -7832.3482] [ 917] [depth= 2] . ( 91 sec) [ -7832.1524] [ 917] [depth= 1] . ( 94 sec) [ -7831.8516] [ 917] [depth= 2] . ( 96 sec) [ -7831.7974] [ 918] [depth= 1] . ( 96 sec) [ -7831.7779] [ 918] [depth= 1] . ( 102 sec) [ -7829.4993] [Branch lengths ] . ( 102 sec) [ -7829.3633] [GTR parameters ] . ( 103 sec) [ -7829.3633] [Alpha ][ 0.212813] . ( 108 sec) [ -7828.9419] [ 918] [depth= 3] . ( 113 sec) [ -7828.9146] [ 918] [depth= 1] . ( 114 sec) [ -7827.5313] [ 916] [depth= 1] . ( 131 sec) [ -7827.0568] [ 916] [depth= 1] . ( 131 sec) [ -7826.9583] [ 916] [depth= 1] . ( 136 sec) [ -7826.1319] [ 916] [depth= 1] . ( 157 sec) [ -7825.0686] [Branch lengths ] . ( 157 sec) [ -7825.0606] [GTR parameters ] . ( 157 sec) [ -7825.0606] [Alpha ][ 0.213026] . ( 169 sec) [ -7825.0387] [ 915] [depth= 1] . ( 178 sec) [ -7825.0006] [ 915] [depth= 1] . ( 208 sec) [ -7824.9677] [ 915] [depth= 1] . ( 209 sec) [ -7824.8398] [Branch lengths ] . ( 210 sec) [ -7824.8392] [GTR parameters ] . ( 210 sec) [ -7824.8392] [Alpha ][ 0.213026] . ( 283 sec) [ -7824.8346] [Branch lengths ] . ( 283 sec) [ -7824.8346] [Topology ] . ( 284 sec) [ -7824.8340] [Topology ] . ( 285 sec) [ -7824.8340] [GTR parameters ] . ( 285 sec) [ -7824.8340] [Alpha ][ 0.213026] . Checking for NNIs, optimizing five branches... . ( 298 sec) [ -7824.8339] [Topology ] . Checking for NNIs, optimizing five branches... . ( 311 sec) [ -7824.8133] [Topology ] . Checking for NNIs, optimizing five branches... . ( 323 sec) [ -7824.8132] [Topology ] . Checking for NNIs, optimizing five branches... . ( 335 sec) [ -7824.8114] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7824.811436. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -8163.5103] [GTR parameters ] . ( 3 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 3 sec) [ -8080.4464] [Topology ] . ( 5 sec) [ -7998.7983] [Topology ] . ( 7 sec) [ -7955.3559] [Topology ] . ( 8 sec) [ -7942.8529] [Topology ] . ( 10 sec) [ -7938.6627] [Topology ] . ( 12 sec) [ -7938.6180] [Topology ] . ( 13 sec) [ -7936.9159] [Topology ] . ( 15 sec) [ -7937.3880] [Topology ] . Moving backward . ( 15 sec) [ -7936.2310] [Topology ] . ( 17 sec) [ -7935.8656] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -7931.5928] [Topology ] . ( 33 sec) [ -7931.2315] [GTR parameters ] . ( 33 sec) [ -7881.1773] [Alpha ][ 0.250961] . ( 33 sec) [ -7881.1773] [Topology ] . ( 35 sec) [ -7880.5556] [Topology ] . ( 37 sec) [ -7880.3201] [Topology ] . ( 38 sec) [ -7880.2593] [Topology ] . ( 40 sec) [ -7880.2272] [Topology ] . ( 41 sec) [ -7880.2046] [Topology ] . ( 43 sec) [ -7880.1875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7878.0740] [Topology ] . ( 57 sec) [ -7878.0004] [GTR parameters ] . ( 57 sec) [ -7875.6771] [Alpha ][ 0.212336] . ( 57 sec) [ -7875.6771] [Topology ] . ( 58 sec) [ -7875.5666] [Topology ] . ( 60 sec) [ -7875.2585] [Topology ] . ( 61 sec) [ -7873.6080] [Topology ] . ( 63 sec) [ -7869.6012] [Topology ] . ( 65 sec) [ -7868.4627] [Topology ] . ( 66 sec) [ -7868.3538] [Topology ] . ( 68 sec) [ -7868.3402] [Topology ] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -7868.3399] [Topology ] . ( 81 sec) [ -7868.3159] [GTR parameters ] . ( 81 sec) [ -7868.3141] [Alpha ][ 0.211294] . ( 81 sec) [ -7868.3141] [Topology ] . ( 83 sec) [ -7868.3112] [Topology ] . ( 85 sec) [ -7868.3103] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -7868.3029] [Topology ] . ( 97 sec) [ -7868.3029] [GTR parameters ] . ( 97 sec) [ -7868.3029] [Alpha ][ 0.211294] . ( 97 sec) [ -7868.3029] [Topology ] . ( 99 sec) [ -7868.3022] [Topology ] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -7868.3021] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 126 sec) [ -8163.5103] [GTR parameters ] . ( 126 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 126 sec) [ -8077.4988] [ 943] [depth= 1] . ( 127 sec) [ -8074.4226] [ 944] [depth= 1] . ( 127 sec) [ -8069.8592] [ 943] [depth= 1] . ( 128 sec) [ -8065.7549] [ 943] [depth= 2] . ( 128 sec) [ -8035.2996] [ 934] [depth= 12] . ( 128 sec) [ -8035.0145] [ 934] [depth= 1] . ( 128 sec) [ -8033.2509] [ 934] [depth= 1] . ( 128 sec) [ -8032.7544] [ 934] [depth= 1] . ( 128 sec) [ -8032.5127] [ 934] [depth= 2] . ( 128 sec) [ -8031.4073] [ 935] [depth= 1] . ( 129 sec) [ -8030.9440] [ 935] [depth= 2] . ( 129 sec) [ -8018.3883] [ 932] [depth= 3] . ( 130 sec) [ -8013.6878] [ 931] [depth= 1] . ( 134 sec) [ -8004.2182] [ 927] [depth= 3] . ( 134 sec) [ -7995.5703] [ 925] [depth= 3] . ( 134 sec) [ -7993.4724] [ 927] [depth= 3] . ( 136 sec) [ -7993.3462] [ 926] [depth= 1] . ( 136 sec) [ -7992.0605] [ 924] [depth= 1] . ( 136 sec) [ -7985.9831] [ 924] [depth= 3] . ( 136 sec) [ -7975.4984] [ 920] [depth= 1] . ( 137 sec) [ -7973.0920] [ 921] [depth= 1] . ( 138 sec) [ -7962.3801] [ 922] [depth= 2] . ( 138 sec) [ -7955.3368] [ 920] [depth= 1] . ( 138 sec) [ -7946.2442] [ 917] [depth= 6] . ( 139 sec) [ -7945.3685] [ 917] [depth= 1] . ( 140 sec) [ -7945.0053] [ 918] [depth= 1] . ( 140 sec) [ -7943.0299] [ 918] [depth= 2] . ( 140 sec) [ -7940.5241] [ 918] [depth= 3] . ( 140 sec) [ -7936.5351] [ 917] [depth= 2] . ( 141 sec) [ -7936.3747] [ 917] [depth= 2] . ( 142 sec) [ -7936.3609] [ 917] [depth= 2] . ( 142 sec) [ -7935.5532] [ 917] [depth= 1] . ( 142 sec) [ -7935.0894] [ 917] [depth= 2] . ( 143 sec) [ -7934.8823] [ 917] [depth= 4] . ( 143 sec) [ -7931.7450] [ 917] [depth= 5] . ( 144 sec) [ -7930.7373] [ 917] [depth= 1] . ( 144 sec) [ -7928.2193] [ 916] [depth= 1] . ( 144 sec) [ -7927.3382] [ 915] [depth= 8] . ( 145 sec) [ -7925.5620] [ 915] [depth= 1] . ( 146 sec) [ -7923.4738] [ 915] [depth= 4] . ( 146 sec) [ -7919.0905] [ 915] [depth= 1] . ( 146 sec) [ -7916.6878] [ 914] [depth= 2] . ( 147 sec) [ -7916.5886] [ 914] [depth= 1] . ( 147 sec) [ -7913.1575] [ 915] [depth= 10] . ( 151 sec) [ -7912.7043] [ 915] [depth= 1] . ( 151 sec) [ -7912.4281] [ 915] [depth= 1] . ( 152 sec) [ -7912.3920] [ 915] [depth= 1] . ( 152 sec) [ -7912.3295] [ 915] [depth= 1] . ( 155 sec) [ -7888.7799] [Branch lengths ] . ( 157 sec) [ -7888.0247] [GTR parameters ] . ( 157 sec) [ -7840.1979] [Alpha ][ 0.250961] . ( 158 sec) [ -7839.0071] [ 916] [depth= 1] . ( 159 sec) [ -7837.5084] [ 915] [depth= 5] . ( 159 sec) [ -7836.9764] [ 914] [depth= 1] . ( 160 sec) [ -7836.9098] [ 914] [depth= 1] . ( 160 sec) [ -7836.8955] [ 914] [depth= 1] . ( 164 sec) [ -7836.8741] [ 914] [depth= 1] . ( 172 sec) [ -7836.6513] [ 914] [depth= 1] . ( 172 sec) [ -7836.5284] [ 913] [depth= 4] . ( 178 sec) [ -7836.4322] [ 913] [depth= 1] . ( 181 sec) [ -7835.9844] [ 913] [depth= 1] . ( 185 sec) [ -7835.9501] [ 913] [depth= 5] . ( 186 sec) [ -7835.9205] [ 913] [depth= 4] . ( 188 sec) [ -7835.4842] [ 914] [depth= 10] . ( 197 sec) [ -7835.4479] [ 914] [depth= 1] . ( 197 sec) [ -7835.3659] [ 914] [depth= 2] . ( 200 sec) [ -7835.3495] [ 914] [depth= 1] . ( 200 sec) [ -7830.1491] [Branch lengths ] . ( 201 sec) [ -7830.0929] [GTR parameters ] . ( 201 sec) [ -7828.0024] [Alpha ][ 0.213361] . ( 221 sec) [ -7824.4973] [ 915] [depth= 4] . ( 232 sec) [ -7824.3622] [ 915] [depth= 1] . ( 232 sec) [ -7824.3456] [ 915] [depth= 1] . ( 238 sec) [ -7824.2176] [ 915] [depth= 1] . ( 255 sec) [ -7823.7403] [Branch lengths ] . ( 257 sec) [ -7823.7166] [GTR parameters ] . ( 257 sec) [ -7823.7165] [Alpha ][ 0.213039] . ( 312 sec) [ -7823.7128] [Branch lengths ] . ( 382 sec) [ -7823.7126] [Branch lengths ] . ( 382 sec) [ -7823.7126] [Topology ] . ( 384 sec) [ -7823.7126] [Topology ] . ( 384 sec) [ -7823.7126] [GTR parameters ] . ( 384 sec) [ -7823.7126] [Alpha ][ 0.213039] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7868.302081 . Log likelihood obtained after SPR moves : -7823.712571 . Log likelihood of the current tree: -7823.712571. . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Best log likelihood : -7823.712571 . Time used 0h6m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1945.69user 0.00system 32:40.58elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps