.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2708_78x1107_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 . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 1107 sites) . 505 sites without polymorphism (45.62%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 25Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26717.1462] [GTR parameters ] . ( 2 sec) [ -26080.0041] [Alpha ][ 0.500960] . ( 2 sec) [ -25303.6654] [ 3652] [depth= 7] . ( 2 sec) [ -24916.8907] [ 3578] [depth= 14] . ( 2 sec) [ -24581.5576] [ 3547] [depth= 6] . ( 2 sec) [ -24040.5275] [ 3543] [depth= 3] . ( 2 sec) [ -23935.3541] [ 3514] [depth= 11] . ( 2 sec) [ -23641.8972] [ 3511] [depth= 4] . ( 2 sec) [ -22647.3556] [ 3506] [depth= 2] . ( 3 sec) [ -22393.8261] [ 3470] [depth= 8] . ( 3 sec) [ -22280.1650] [ 3468] [depth= 1] . ( 3 sec) [ -21930.4523] [ 3395] [depth= 14] . ( 3 sec) [ -21017.6843] [ 3311] [depth= 3] . ( 3 sec) [ -21004.9094] [ 3311] [depth= 1] . ( 3 sec) [ -20855.6902] [ 3312] [depth= 15] . ( 3 sec) [ -20758.6329] [ 3297] [depth= 1] . ( 3 sec) [ -20671.1657] [ 3278] [depth= 15] . ( 4 sec) [ -20619.2290] [ 3271] [depth= 16] . ( 4 sec) [ -20519.9027] [ 3232] [depth= 8] . ( 4 sec) [ -20327.5334] [ 3230] [depth= 11] . ( 4 sec) [ -20323.8062] [ 3231] [depth= 1] . ( 4 sec) [ -20180.8626] [ 3219] [depth= 3] . ( 4 sec) [ -20091.2239] [ 3219] [depth= 16] . ( 4 sec) [ -19788.6481] [ 3202] [depth= 30] . ( 5 sec) [ -19773.9291] [ 3201] [depth= 11] . ( 5 sec) [ -19753.3538] [ 3195] [depth= 13] . ( 5 sec) [ -19414.9694] [ 3194] [depth= 15] . ( 5 sec) [ -18866.0091] [ 2963] [depth= 17] . ( 5 sec) [ -18574.7503] [ 2930] [depth= 18] . ( 6 sec) [ -18535.1372] [ 2931] [depth= 1] . ( 6 sec) [ -17556.5635] [ 2931] [depth= 4] . ( 6 sec) [ -17528.4617] [ 2927] [depth= 2] . ( 6 sec) [ -17239.5230] [ 2927] [depth= 1] . ( 6 sec) [ -17195.9995] [ 2927] [depth= 1] . ( 6 sec) [ -16991.3061] [ 2927] [depth= 5] . ( 6 sec) [ -16813.9657] [ 2847] [depth= 11] . ( 6 sec) [ -16636.9272] [ 2847] [depth= 2] . ( 7 sec) [ -16600.4396] [ 2790] [depth= 2] . ( 7 sec) [ -16511.1750] [ 2777] [depth= 2] . ( 7 sec) [ -16476.1875] [ 2777] [depth= 16] . ( 7 sec) [ -16473.1877] [ 2774] [depth= 4] . ( 7 sec) [ -16362.1170] [ 2774] [depth= 2] . ( 7 sec) [ -15960.4475] [ 2750] [depth= 13] . ( 7 sec) [ -15779.6363] [ 2729] [depth= 4] . ( 8 sec) [ -15667.3917] [ 2680] [depth= 8] . ( 8 sec) [ -14731.9685] [ 2610] [depth= 12] . ( 8 sec) [ -14358.2865] [ 2609] [depth= 7] . ( 8 sec) [ -14320.6977] [ 2606] [depth= 15] . ( 8 sec) [ -14319.6985] [ 2606] [depth= 5] . ( 8 sec) [ -14315.0951] [ 2599] [depth= 2] . ( 8 sec) [ -14284.6758] [ 2595] [depth= 13] . ( 8 sec) [ -14283.8285] [ 2595] [depth= 1] . ( 9 sec) [ -14272.8742] [ 2593] [depth= 5] . ( 9 sec) [ -14162.7793] [ 2576] [depth= 1] . ( 9 sec) [ -14162.7368] [ 2576] [depth= 12] . ( 9 sec) [ -14162.3281] [ 2576] [depth= 1] . ( 9 sec) [ -14104.2819] [ 2566] [depth= 10] . ( 9 sec) [ -13959.7465] [ 2539] [depth= 7] . ( 9 sec) [ -13957.9494] [ 2539] [depth= 6] . ( 10 sec) [ -13924.5000] [ 2495] [depth= 15] . ( 10 sec) [ -13882.2011] [ 2487] [depth= 12] . ( 10 sec) [ -13850.3401] [ 2489] [depth= 2] . ( 10 sec) [ -13749.2527] [ 2477] [depth= 14] . ( 10 sec) [ -13724.0548] [ 2465] [depth= 9] . ( 10 sec) [ -13645.6171] [ 2465] [depth= 10] . ( 10 sec) [ -13590.1712] [ 2452] [depth= 11] . ( 11 sec) [ -13507.3128] [ 2427] [depth= 11] . ( 11 sec) [ -13397.9511] [ 2418] [depth= 2] . ( 11 sec) [ -13043.5033] [ 2359] [depth= 10] . ( 11 sec) [ -12982.0053] [ 2347] [depth= 2] . ( 11 sec) [ -12926.2005] [ 2349] [depth= 1] . ( 11 sec) [ -12871.3806] [ 2331] [depth= 15] . ( 11 sec) [ -12392.2264] [ 2315] [depth= 16] . ( 11 sec) [ -12348.1583] [ 2311] [depth= 1] . ( 12 sec) [ -12079.9737] [ 2313] [depth= 1] . ( 12 sec) [ -12063.8410] [ 2280] [depth= 7] . ( 12 sec) [ -12028.8171] [ 2278] [depth= 2] . ( 12 sec) [ -12023.5419] [ 2278] [depth= 6] . ( 12 sec) [ -11986.5033] [ 2278] [depth= 9] . ( 12 sec) [ -11960.4851] [ 2277] [depth= 15] . ( 12 sec) [ -11810.4250] [ 2276] [depth= 10] . ( 12 sec) [ -11743.4525] [ 2247] [depth= 1] . ( 13 sec) [ -11717.2599] [ 2236] [depth= 2] . ( 13 sec) [ -11590.6464] [ 2235] [depth= 4] . ( 13 sec) [ -11551.9631] [ 2226] [depth= 18] . ( 13 sec) [ -11510.2447] [ 2221] [depth= 1] . ( 13 sec) [ -11499.0496] [ 2219] [depth= 18] . ( 13 sec) [ -11493.9221] [ 2219] [depth= 1] . ( 14 sec) [ -11481.6151] [ 2219] [depth= 1] . ( 14 sec) [ -11395.1736] [ 2199] [depth= 18] . ( 14 sec) [ -11325.8968] [ 2182] [depth= 8] . ( 14 sec) [ -11305.2402] [ 2177] [depth= 1] . ( 15 sec) [ -11296.1853] [ 2140] [depth= 9] . ( 15 sec) [ -11201.7025] [ 2125] [depth= 1] . ( 15 sec) [ -11191.2118] [ 2126] [depth= 9] . ( 15 sec) [ -11189.4611] [ 2126] [depth= 2] . ( 15 sec) [ -10897.2140] [ 2022] [depth= 11] . ( 15 sec) [ -10800.4156] [ 2019] [depth= 3] . ( 15 sec) [ -10788.1337] [ 2019] [depth= 1] . ( 16 sec) [ -10567.3006] [ 1961] [depth= 12] . ( 16 sec) [ -10154.5284] [ 1950] [depth= 6] . ( 16 sec) [ -10120.6672] [ 1949] [depth= 10] . ( 16 sec) [ -10094.7036] [ 1950] [depth= 1] . ( 16 sec) [ -9977.7138] [ 1891] [depth= 16] . ( 16 sec) [ -9910.2372] [ 1891] [depth= 1] . ( 16 sec) [ -9685.6603] [ 1665] [depth= 11] . ( 17 sec) [ -9682.5535] [ 1666] [depth= 1] . ( 17 sec) [ -9665.8602] [ 1665] [depth= 15] . ( 17 sec) [ -9662.7321] [ 1669] [depth= 1] . ( 17 sec) [ -9662.6959] [ 1669] [depth= 5] . ( 17 sec) [ -9657.5521] [ 1668] [depth= 2] . ( 17 sec) [ -9640.3847] [ 1667] [depth= 1] . ( 17 sec) [ -9620.8988] [ 1667] [depth= 1] . ( 18 sec) [ -9616.9986] [ 1653] [depth= 7] . ( 18 sec) [ -9607.7609] [ 1653] [depth= 1] . ( 18 sec) [ -9595.3709] [ 1650] [depth= 2] . ( 18 sec) [ -9558.3479] [ 1648] [depth= 1] . ( 18 sec) [ -9538.0639] [ 1641] [depth= 8] . ( 18 sec) [ -9158.7821] [ 1641] [depth= 2] . ( 18 sec) [ -9143.6485] [ 1630] [depth= 11] . ( 18 sec) [ -9062.7909] [ 1627] [depth= 6] . ( 19 sec) [ -8997.3247] [ 1623] [depth= 7] . ( 19 sec) [ -8897.7764] [ 1599] [depth= 19] . ( 19 sec) [ -8832.3620] [ 1583] [depth= 5] . ( 19 sec) [ -8830.3368] [ 1583] [depth= 4] . ( 19 sec) [ -8829.6213] [ 1583] [depth= 1] . ( 19 sec) [ -8806.0759] [ 1600] [depth= 1] . ( 20 sec) [ -8487.7670] [ 1594] [depth= 2] . ( 20 sec) [ -8475.5447] [ 1594] [depth= 1] . ( 20 sec) [ -8450.1063] [ 1587] [depth= 5] . ( 20 sec) [ -8143.5156] [ 1592] [depth= 1] . ( 21 sec) [ -8140.7221] [ 1592] [depth= 1] . ( 21 sec) [ -8140.6807] [ 1592] [depth= 1] . ( 21 sec) [ -8140.0385] [ 1587] [depth= 1] . ( 21 sec) [ -8139.3077] [ 1587] [depth= 1] . ( 21 sec) [ -8137.3239] [ 1587] [depth= 1] . ( 21 sec) [ -8133.3160] [ 1589] [depth= 2] . ( 22 sec) [ -8113.5118] [ 1578] [depth= 6] . ( 22 sec) [ -8112.7343] [ 1578] [depth= 1] . ( 22 sec) [ -8112.7228] [ 1578] [depth= 1] . ( 22 sec) [ -8084.0130] [ 1549] [depth= 10] . ( 22 sec) [ -8083.3585] [ 1549] [depth= 2] . ( 22 sec) [ -8075.0599] [ 1551] [depth= 4] . ( 23 sec) [ -8070.8960] [ 1550] [depth= 2] . ( 23 sec) [ -8070.8579] [ 1550] [depth= 1] . ( 23 sec) [ -8069.9416] [ 1550] [depth= 1] . ( 23 sec) [ -8012.0667] [ 1546] [depth= 5] . ( 23 sec) [ -7992.9976] [ 1542] [depth= 1] . ( 23 sec) [ -7986.0398] [ 1543] [depth= 12] . ( 23 sec) [ -7983.2914] [ 1544] [depth= 1] . ( 24 sec) [ -7981.1839] [ 1544] [depth= 2] . ( 24 sec) [ -7975.2311] [ 1541] [depth= 4] . ( 24 sec) [ -7966.3499] [ 1540] [depth= 2] . ( 24 sec) [ -7901.0706] [ 1521] [depth= 1] . ( 24 sec) [ -7884.8334] [ 1520] [depth= 4] . ( 24 sec) [ -7676.9279] [ 1493] [depth= 11] . ( 24 sec) [ -7673.7804] [ 1493] [depth= 1] . ( 25 sec) [ -7672.5483] [ 1493] [depth= 1] . ( 25 sec) [ -7617.7458] [ 1467] [depth= 5] . ( 25 sec) [ -7611.0211] [ 1467] [depth= 2] . ( 25 sec) [ -7610.9544] [ 1467] [depth= 1] . ( 26 sec) [ -7587.2150] [ 1468] [depth= 6] . ( 26 sec) [ -7583.0591] [ 1468] [depth= 6] . ( 26 sec) [ -7550.3821] [ 1467] [depth= 3] . ( 26 sec) [ -7549.0289] [ 1467] [depth= 2] . ( 26 sec) [ -7444.6131] [ 1442] [depth= 18] . ( 26 sec) [ -7417.8205] [ 1443] [depth= 1] . ( 27 sec) [ -7415.9853] [ 1443] [depth= 3] . ( 27 sec) [ -7392.0238] [ 1419] [depth= 11] . ( 27 sec) [ -7327.1493] [ 1409] [depth= 2] . ( 27 sec) [ -7326.1394] [ 1409] [depth= 1] . ( 27 sec) [ -7310.4882] [ 1412] [depth= 1] . ( 27 sec) [ -7310.3919] [ 1418] [depth= 1] . ( 28 sec) [ -7305.1891] [ 1418] [depth= 1] . ( 28 sec) [ -7304.4082] [ 1412] [depth= 3] . ( 28 sec) [ -7293.3853] [ 1410] [depth= 1] . ( 28 sec) [ -7291.3268] [ 1411] [depth= 1] . ( 28 sec) [ -7290.9199] [ 1411] [depth= 4] . ( 29 sec) [ -7279.7882] [ 1409] [depth= 5] . ( 29 sec) [ -7278.0144] [ 1409] [depth= 1] . ( 29 sec) [ -7274.2836] [ 1409] [depth= 5] . ( 29 sec) [ -7254.8193] [ 1401] [depth= 8] . ( 29 sec) [ -7254.7716] [ 1401] [depth= 3] . ( 29 sec) [ -7251.6808] [ 1401] [depth= 1] . ( 29 sec) [ -7250.4978] [ 1401] [depth= 2] . ( 30 sec) [ -7250.4143] [ 1401] [depth= 2] . ( 30 sec) [ -7233.3852] [ 1395] [depth= 2] . ( 30 sec) [ -7233.3397] [ 1395] [depth= 8] . ( 30 sec) [ -7231.5585] [ 1400] [depth= 1] . ( 30 sec) [ -7224.2849] [ 1400] [depth= 2] . ( 30 sec) [ -7222.5634] [ 1400] [depth= 9] . ( 31 sec) [ -7015.1995] [Branch lengths ] . ( 37 sec) [ -6975.5494] [GTR parameters ] . ( 37 sec) [ -6952.7894] [Alpha ][ 0.335129] . ( 37 sec) [ -6951.5677] [ 1399] [depth= 1] . ( 37 sec) [ -6951.0317] [ 1393] [depth= 1] . ( 38 sec) [ -6945.5989] [ 1396] [depth= 3] . ( 39 sec) [ -6944.8119] [ 1395] [depth= 1] . ( 39 sec) [ -6931.9946] [ 1396] [depth= 9] . ( 39 sec) [ -6930.4756] [ 1396] [depth= 1] . ( 40 sec) [ -6928.3697] [ 1397] [depth= 4] . ( 41 sec) [ -6927.6143] [ 1395] [depth= 2] . ( 41 sec) [ -6927.2014] [ 1395] [depth= 1] . ( 42 sec) [ -6861.2755] [ 1365] [depth= 7] . ( 42 sec) [ -6861.2647] [ 1365] [depth= 8] . ( 44 sec) [ -6855.5650] [ 1364] [depth= 2] . ( 44 sec) [ -6853.7418] [ 1363] [depth= 1] . ( 44 sec) [ -6850.4387] [ 1360] [depth= 1] . ( 44 sec) [ -6850.3476] [ 1360] [depth= 1] . ( 45 sec) [ -6808.9543] [ 1343] [depth= 12] . ( 45 sec) [ -6808.9352] [ 1343] [depth= 2] . ( 46 sec) [ -6808.9005] [ 1343] [depth= 8] . ( 46 sec) [ -6808.7805] [ 1344] [depth= 1] . ( 46 sec) [ -6802.1492] [ 1343] [depth= 8] . ( 46 sec) [ -6802.0504] [ 1340] [depth= 2] . ( 47 sec) [ -6797.9949] [ 1341] [depth= 1] . ( 47 sec) [ -6793.0152] [ 1340] [depth= 1] . ( 47 sec) [ -6792.8306] [ 1340] [depth= 1] . ( 48 sec) [ -6792.8038] [ 1340] [depth= 9] . ( 48 sec) [ -6789.7100] [ 1339] [depth= 1] . ( 49 sec) [ -6786.6790] [ 1340] [depth= 1] . ( 49 sec) [ -6786.5922] [ 1340] [depth= 2] . ( 49 sec) [ -6784.4466] [ 1339] [depth= 1] . ( 49 sec) [ -6773.7700] [ 1340] [depth= 1] . ( 50 sec) [ -6767.9857] [ 1339] [depth= 2] . ( 51 sec) [ -6751.5619] [ 1331] [depth= 1] . ( 51 sec) [ -6751.2247] [ 1331] [depth= 1] . ( 51 sec) [ -6751.2084] [ 1326] [depth= 1] . ( 51 sec) [ -6750.8321] [ 1326] [depth= 1] . ( 52 sec) [ -6750.7867] [ 1326] [depth= 1] . ( 52 sec) [ -6738.0166] [ 1327] [depth= 2] . ( 52 sec) [ -6733.9507] [ 1325] [depth= 1] . ( 52 sec) [ -6732.8615] [ 1324] [depth= 5] . ( 53 sec) [ -6721.2354] [ 1323] [depth= 2] . ( 54 sec) [ -6717.7302] [ 1320] [depth= 1] . ( 54 sec) [ -6717.5700] [ 1320] [depth= 2] . ( 55 sec) [ -6712.0059] [ 1317] [depth= 2] . ( 55 sec) [ -6711.8896] [ 1317] [depth= 1] . ( 55 sec) [ -6711.6606] [ 1317] [depth= 1] . ( 55 sec) [ -6706.0203] [ 1316] [depth= 2] . ( 56 sec) [ -6705.7268] [ 1316] [depth= 1] . ( 56 sec) [ -6705.2539] [ 1321] [depth= 1] . ( 58 sec) [ -6704.5177] [ 1309] [depth= 2] . ( 58 sec) [ -6688.8886] [ 1297] [depth= 7] . ( 60 sec) [ -6685.6965] [ 1297] [depth= 1] . ( 61 sec) [ -6685.6585] [ 1297] [depth= 1] . ( 61 sec) [ -6653.8083] [ 1270] [depth= 1] . ( 61 sec) [ -6633.7691] [ 1258] [depth= 9] . ( 61 sec) [ -6633.6691] [ 1258] [depth= 1] . ( 62 sec) [ -6627.0148] [ 1261] [depth= 3] . ( 62 sec) [ -6626.7913] [ 1261] [depth= 1] . ( 64 sec) [ -6623.3410] [ 1261] [depth= 1] . ( 65 sec) [ -6616.6090] [ 1262] [depth= 2] . ( 65 sec) [ -6616.5940] [ 1262] [depth= 3] . ( 65 sec) [ -6616.5344] [ 1262] [depth= 1] . ( 65 sec) [ -6616.0862] [ 1264] [depth= 1] . ( 66 sec) [ -6615.3570] [ 1261] [depth= 1] . ( 67 sec) [ -6615.2741] [ 1261] [depth= 3] . ( 67 sec) [ -6614.9494] [ 1261] [depth= 1] . ( 68 sec) [ -6614.7210] [ 1264] [depth= 1] . ( 68 sec) [ -6614.6565] [ 1264] [depth= 1] . ( 68 sec) [ -6603.3749] [ 1256] [depth= 4] . ( 70 sec) [ -6603.1798] [ 1256] [depth= 9] . ( 70 sec) [ -6601.5589] [ 1256] [depth= 2] . ( 71 sec) [ -6600.9292] [ 1255] [depth= 1] . ( 71 sec) [ -6600.9175] [ 1255] [depth= 1] . ( 71 sec) [ -6600.8079] [ 1256] [depth= 2] . ( 71 sec) [ -6600.7805] [ 1256] [depth= 1] . ( 72 sec) [ -6600.7555] [ 1256] [depth= 7] . ( 73 sec) [ -6584.5578] [Branch lengths ] . ( 78 sec) [ -6584.2832] [GTR parameters ] . ( 78 sec) [ -6584.2827] [Alpha ][ 0.335758] . ( 80 sec) [ -6584.1838] [ 1256] [depth= 3] . ( 80 sec) [ -6580.6778] [ 1255] [depth= 2] . ( 80 sec) [ -6554.5597] [ 1241] [depth= 3] . ( 84 sec) [ -6554.5150] [ 1241] [depth= 1] . ( 89 sec) [ -6552.9551] [ 1240] [depth= 1] . ( 90 sec) [ -6550.2198] [ 1240] [depth= 1] . ( 91 sec) [ -6548.6263] [ 1268] [depth= 2] . ( 94 sec) [ -6548.0185] [ 1269] [depth= 1] . ( 98 sec) [ -6546.6016] [ 1269] [depth= 1] . ( 98 sec) [ -6546.3652] [ 1269] [depth= 1] . ( 99 sec) [ -6546.3387] [ 1269] [depth= 1] . ( 100 sec) [ -6544.1040] [ 1264] [depth= 4] . ( 102 sec) [ -6543.2089] [ 1264] [depth= 1] . ( 106 sec) [ -6541.9190] [ 1265] [depth= 1] . ( 108 sec) [ -6541.4988] [ 1264] [depth= 1] . ( 109 sec) [ -6541.4883] [ 1264] [depth= 1] . ( 113 sec) [ -6541.4762] [ 1264] [depth= 1] . ( 113 sec) [ -6537.2197] [ 1263] [depth= 1] . ( 124 sec) [ -6535.6463] [Branch lengths ] . ( 126 sec) [ -6535.5176] [GTR parameters ] . ( 126 sec) [ -6535.4993] [Alpha ][ 0.339739] . ( 142 sec) [ -6535.3033] [ 1265] [depth= 2] . ( 177 sec) [ -6534.8296] [Branch lengths ] . ( 179 sec) [ -6534.8233] [GTR parameters ] . ( 179 sec) [ -6534.8227] [Alpha ][ 0.340415] . ( 225 sec) [ -6534.6962] [ 1276] [depth= 1] . ( 272 sec) [ -6532.7975] [Branch lengths ] . ( 274 sec) [ -6532.7971] [GTR parameters ] . ( 274 sec) [ -6532.7966] [Alpha ][ 0.341046] . ( 371 sec) [ -6529.9992] [Branch lengths ] . ( 371 sec) [ -6529.9992] [Topology ] . ( 373 sec) [ -6529.5858] [Topology ] . ( 375 sec) [ -6529.5314] [Topology ] . ( 377 sec) [ -6529.5198] [Topology ] . ( 379 sec) [ -6529.5168] [Topology ] . ( 381 sec) [ -6529.5158] [Topology ] . ( 382 sec) [ -6529.5153] [Topology ] . ( 386 sec) [ -6529.5137] [GTR parameters ] . ( 387 sec) [ -6529.5129] [Alpha ][ 0.341876] . ( 387 sec) [ -6529.5129] [Topology ] . ( 388 sec) [ -6529.5121] [Topology ] . ( 389 sec) [ -6529.5121] [GTR parameters ] . ( 389 sec) [ -6529.5120] [Alpha ][ 0.342218] . Checking for NNIs, optimizing five branches... . ( 404 sec) [ -6529.3726] [Topology ] . Checking for NNIs, optimizing five branches... . ( 419 sec) [ -6529.3005] [Topology ] . Checking for NNIs, optimizing five branches... . ( 433 sec) [ -6529.2994] [Topology ] . Checking for NNIs, optimizing five branches... . ( 448 sec) [ -6529.2913] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6529.291297. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -29558.8232] [GTR parameters ] . ( 2 sec) [ -28841.4873] [Alpha ][ 0.500960] . ( 2 sec) [ -27994.5371] [ 3871] [depth= 8] . ( 2 sec) [ -27125.2012] [ 3794] [depth= 11] . ( 3 sec) [ -27037.5315] [ 3794] [depth= 1] . ( 3 sec) [ -26489.2862] [ 3665] [depth= 3] . ( 3 sec) [ -26182.4373] [ 3652] [depth= 1] . ( 3 sec) [ -25956.3269] [ 3499] [depth= 12] . ( 3 sec) [ -24481.5769] [ 3495] [depth= 6] . ( 3 sec) [ -24222.7855] [ 3495] [depth= 2] . ( 3 sec) [ -23238.0911] [ 3435] [depth= 6] . ( 4 sec) [ -23187.0529] [ 3432] [depth= 13] . ( 4 sec) [ -23035.8972] [ 3415] [depth= 2] . ( 4 sec) [ -22961.6257] [ 3415] [depth= 1] . ( 4 sec) [ -22863.3458] [ 3404] [depth= 3] . ( 4 sec) [ -22779.0194] [ 3400] [depth= 2] . ( 4 sec) [ -21914.2227] [ 3353] [depth= 2] . ( 4 sec) [ -21761.0634] [ 3353] [depth= 2] . ( 4 sec) [ -21477.0564] [ 3352] [depth= 2] . ( 4 sec) [ -21412.5150] [ 3353] [depth= 2] . ( 5 sec) [ -21374.6312] [ 3328] [depth= 1] . ( 5 sec) [ -21353.7604] [ 3328] [depth= 1] . ( 5 sec) [ -21293.3158] [ 3319] [depth= 4] . ( 5 sec) [ -21272.0831] [ 3294] [depth= 19] . ( 5 sec) [ -21223.4747] [ 3279] [depth= 1] . ( 5 sec) [ -20847.8405] [ 3172] [depth= 4] . ( 5 sec) [ -20700.6329] [ 3167] [depth= 7] . ( 5 sec) [ -19965.1961] [ 3072] [depth= 19] . ( 6 sec) [ -19653.7041] [ 3025] [depth= 7] . ( 6 sec) [ -19196.4660] [ 2992] [depth= 25] . ( 6 sec) [ -19141.5007] [ 2993] [depth= 1] . ( 6 sec) [ -19122.8430] [ 2992] [depth= 1] . ( 6 sec) [ -19007.1229] [ 2962] [depth= 14] . ( 6 sec) [ -18555.6434] [ 2869] [depth= 5] . ( 7 sec) [ -18268.6534] [ 2825] [depth= 2] . ( 7 sec) [ -17644.8069] [ 2819] [depth= 1] . ( 7 sec) [ -17619.8037] [ 2818] [depth= 1] . ( 7 sec) [ -17408.2456] [ 2769] [depth= 2] . ( 7 sec) [ -17126.6821] [ 2675] [depth= 13] . ( 7 sec) [ -16881.4094] [ 2668] [depth= 5] . ( 7 sec) [ -16528.7517] [ 2648] [depth= 3] . ( 7 sec) [ -16423.3151] [ 2584] [depth= 4] . ( 7 sec) [ -16357.7556] [ 2581] [depth= 1] . ( 8 sec) [ -16344.4235] [ 2574] [depth= 12] . ( 8 sec) [ -16198.6079] [ 2550] [depth= 17] . ( 8 sec) [ -16019.8030] [ 2528] [depth= 11] . ( 8 sec) [ -16014.1177] [ 2529] [depth= 1] . ( 8 sec) [ -15870.9054] [ 2447] [depth= 12] . ( 8 sec) [ -15452.4327] [ 2431] [depth= 1] . ( 8 sec) [ -15404.2877] [ 2404] [depth= 24] . ( 8 sec) [ -15303.4640] [ 2378] [depth= 25] . ( 9 sec) [ -15044.9775] [ 2348] [depth= 7] . ( 9 sec) [ -14949.8565] [ 2366] [depth= 1] . ( 9 sec) [ -14366.7572] [ 2290] [depth= 16] . ( 9 sec) [ -14298.4016] [ 2285] [depth= 5] . ( 9 sec) [ -14179.1242] [ 2283] [depth= 2] . ( 9 sec) [ -14145.7159] [ 2258] [depth= 6] . ( 9 sec) [ -14061.2682] [ 2254] [depth= 9] . ( 9 sec) [ -14045.6214] [ 2253] [depth= 3] . ( 10 sec) [ -13935.5769] [ 2254] [depth= 1] . ( 10 sec) [ -13919.9022] [ 2255] [depth= 1] . ( 10 sec) [ -13590.5252] [ 2255] [depth= 11] . ( 10 sec) [ -13476.4503] [ 2251] [depth= 3] . ( 10 sec) [ -13284.7830] [ 2238] [depth= 8] . ( 10 sec) [ -13277.6634] [ 2238] [depth= 1] . ( 11 sec) [ -13268.0553] [ 2237] [depth= 3] . ( 11 sec) [ -13262.5420] [ 2231] [depth= 9] . ( 11 sec) [ -13086.6433] [ 2215] [depth= 9] . ( 11 sec) [ -12958.0279] [ 2206] [depth= 1] . ( 11 sec) [ -12725.5781] [ 2200] [depth= 4] . ( 11 sec) [ -12717.3498] [ 2200] [depth= 2] . ( 11 sec) [ -12658.0407] [ 2201] [depth= 1] . ( 12 sec) [ -12629.6406] [ 2200] [depth= 3] . ( 12 sec) [ -12586.7356] [ 2182] [depth= 2] . ( 12 sec) [ -12329.7809] [ 2154] [depth= 2] . ( 12 sec) [ -12262.4199] [ 2154] [depth= 1] . ( 12 sec) [ -12130.9553] [ 2139] [depth= 7] . ( 12 sec) [ -12107.0630] [ 2135] [depth= 1] . ( 13 sec) [ -12011.3521] [ 2130] [depth= 16] . ( 13 sec) [ -12000.9224] [ 2130] [depth= 1] . ( 13 sec) [ -11949.3854] [ 2116] [depth= 2] . ( 13 sec) [ -11934.2135] [ 2113] [depth= 1] . ( 13 sec) [ -11913.8423] [ 2113] [depth= 1] . ( 13 sec) [ -11909.1099] [ 2113] [depth= 7] . ( 13 sec) [ -11876.4019] [ 2106] [depth= 16] . ( 14 sec) [ -11742.7521] [ 2074] [depth= 8] . ( 14 sec) [ -11685.1424] [ 2068] [depth= 1] . ( 14 sec) [ -11587.0105] [ 2053] [depth= 6] . ( 14 sec) [ -11585.8016] [ 2053] [depth= 18] . ( 14 sec) [ -11531.6263] [ 2044] [depth= 6] . ( 15 sec) [ -11529.5509] [ 2044] [depth= 1] . ( 15 sec) [ -11523.0945] [ 2029] [depth= 3] . ( 15 sec) [ -11419.2537] [ 2025] [depth= 4] . ( 15 sec) [ -11311.3606] [ 2005] [depth= 24] . ( 15 sec) [ -11306.9119] [ 2005] [depth= 1] . ( 15 sec) [ -11299.9404] [ 2005] [depth= 1] . ( 16 sec) [ -11287.2671] [ 2004] [depth= 1] . ( 16 sec) [ -11285.5886] [ 2004] [depth= 3] . ( 16 sec) [ -11241.6006] [ 2004] [depth= 8] . ( 16 sec) [ -11178.7700] [ 1977] [depth= 3] . ( 16 sec) [ -11111.8349] [ 1952] [depth= 9] . ( 16 sec) [ -11059.1488] [ 1952] [depth= 1] . ( 16 sec) [ -11043.5871] [ 1952] [depth= 2] . ( 16 sec) [ -11042.1125] [ 1951] [depth= 12] . ( 17 sec) [ -10933.6042] [ 1951] [depth= 1] . ( 17 sec) [ -10841.9433] [ 1924] [depth= 11] . ( 17 sec) [ -10836.2303] [ 1924] [depth= 1] . ( 17 sec) [ -10820.7684] [ 1923] [depth= 12] . ( 17 sec) [ -10654.5729] [ 1866] [depth= 3] . ( 17 sec) [ -10469.6756] [ 1854] [depth= 2] . ( 17 sec) [ -10368.0263] [ 1841] [depth= 9] . ( 17 sec) [ -10206.5836] [ 1841] [depth= 1] . ( 18 sec) [ -10141.3429] [ 1841] [depth= 10] . ( 18 sec) [ -10138.1532] [ 1841] [depth= 2] . ( 18 sec) [ -10117.3272] [ 1841] [depth= 2] . ( 18 sec) [ -9866.0186] [ 1824] [depth= 10] . ( 19 sec) [ -9813.3339] [ 1813] [depth= 1] . ( 19 sec) [ -9802.7378] [ 1815] [depth= 1] . ( 19 sec) [ -9774.6432] [ 1814] [depth= 2] . ( 19 sec) [ -9764.4172] [ 1804] [depth= 2] . ( 19 sec) [ -9692.0694] [ 1760] [depth= 3] . ( 19 sec) [ -9688.6791] [ 1759] [depth= 3] . ( 19 sec) [ -9675.8839] [ 1753] [depth= 3] . ( 20 sec) [ -9654.3948] [ 1721] [depth= 4] . ( 20 sec) [ -9436.8491] [ 1702] [depth= 4] . ( 20 sec) [ -9435.2197] [ 1702] [depth= 1] . ( 20 sec) [ -9421.1897] [ 1692] [depth= 2] . ( 20 sec) [ -9408.2222] [ 1692] [depth= 3] . ( 20 sec) [ -9393.7192] [ 1692] [depth= 11] . ( 20 sec) [ -9393.4189] [ 1692] [depth= 2] . ( 21 sec) [ -9260.7826] [ 1686] [depth= 14] . ( 21 sec) [ -9183.1381] [ 1686] [depth= 1] . ( 21 sec) [ -9123.2023] [ 1686] [depth= 13] . ( 22 sec) [ -9108.4750] [ 1686] [depth= 1] . ( 22 sec) [ -9098.4277] [ 1686] [depth= 1] . ( 22 sec) [ -9037.1980] [ 1688] [depth= 2] . ( 22 sec) [ -9036.4734] [ 1688] [depth= 2] . ( 22 sec) [ -9034.5141] [ 1689] [depth= 1] . ( 23 sec) [ -9009.3295] [ 1677] [depth= 1] . ( 23 sec) [ -8994.6940] [ 1680] [depth= 2] . ( 23 sec) [ -8935.4772] [ 1660] [depth= 5] . ( 23 sec) [ -8924.6990] [ 1657] [depth= 9] . ( 23 sec) [ -8908.6805] [ 1640] [depth= 3] . ( 23 sec) [ -8899.5432] [ 1638] [depth= 4] . ( 23 sec) [ -8899.1984] [ 1638] [depth= 1] . ( 23 sec) [ -8894.4072] [ 1637] [depth= 11] . ( 24 sec) [ -8871.8290] [ 1637] [depth= 2] . ( 24 sec) [ -8861.5474] [ 1636] [depth= 2] . ( 24 sec) [ -8713.6377] [ 1630] [depth= 5] . ( 24 sec) [ -8661.8978] [ 1630] [depth= 6] . ( 24 sec) [ -8609.1697] [ 1620] [depth= 10] . ( 24 sec) [ -8607.8218] [ 1620] [depth= 5] . ( 25 sec) [ -8606.7481] [ 1620] [depth= 4] . ( 25 sec) [ -8558.0219] [ 1610] [depth= 3] . ( 25 sec) [ -8491.2274] [ 1585] [depth= 9] . ( 25 sec) [ -8473.0261] [ 1585] [depth= 1] . ( 25 sec) [ -8262.4531] [ 1531] [depth= 1] . ( 25 sec) [ -8259.1589] [ 1531] [depth= 1] . ( 25 sec) [ -8259.1299] [ 1531] [depth= 2] . ( 26 sec) [ -8246.0943] [ 1531] [depth= 3] . ( 26 sec) [ -8244.9022] [ 1531] [depth= 4] . ( 26 sec) [ -8241.8820] [ 1527] [depth= 3] . ( 26 sec) [ -8203.6356] [ 1526] [depth= 1] . ( 26 sec) [ -8127.1744] [ 1495] [depth= 6] . ( 26 sec) [ -8090.0853] [ 1482] [depth= 3] . ( 26 sec) [ -8055.3841] [ 1478] [depth= 3] . ( 26 sec) [ -8046.3058] [ 1477] [depth= 4] . ( 26 sec) [ -8035.6917] [ 1477] [depth= 1] . ( 27 sec) [ -8003.6465] [ 1468] [depth= 11] . ( 27 sec) [ -7986.0954] [ 1468] [depth= 7] . ( 27 sec) [ -7985.7938] [ 1468] [depth= 7] . ( 28 sec) [ -7968.1137] [ 1462] [depth= 1] . ( 28 sec) [ -7929.6294] [ 1453] [depth= 3] . ( 28 sec) [ -7916.5969] [ 1453] [depth= 1] . ( 28 sec) [ -7773.3525] [ 1440] [depth= 3] . ( 28 sec) [ -7773.1477] [ 1440] [depth= 2] . ( 28 sec) [ -7756.2230] [ 1427] [depth= 2] . ( 28 sec) [ -7598.5266] [ 1409] [depth= 6] . ( 28 sec) [ -7592.6121] [ 1409] [depth= 1] . ( 29 sec) [ -7585.1147] [ 1409] [depth= 2] . ( 29 sec) [ -7558.1096] [ 1405] [depth= 1] . ( 30 sec) [ -7540.4678] [ 1405] [depth= 5] . ( 30 sec) [ -7527.1747] [ 1404] [depth= 1] . ( 30 sec) [ -7522.1455] [ 1403] [depth= 1] . ( 30 sec) [ -7488.4445] [ 1391] [depth= 6] . ( 31 sec) [ -7488.1232] [ 1391] [depth= 4] . ( 31 sec) [ -7488.1011] [ 1391] [depth= 2] . ( 31 sec) [ -7480.9969] [ 1392] [depth= 1] . ( 32 sec) [ -7480.8493] [ 1392] [depth= 4] . ( 32 sec) [ -7474.0327] [ 1389] [depth= 4] . ( 32 sec) [ -7469.1000] [ 1389] [depth= 1] . ( 32 sec) [ -7468.8791] [ 1389] [depth= 1] . ( 32 sec) [ -7468.8166] [ 1389] [depth= 1] . ( 32 sec) [ -7207.9222] [ 1363] [depth= 15] . ( 33 sec) [ -7184.7932] [ 1359] [depth= 3] . ( 34 sec) [ -6978.3615] [Branch lengths ] . ( 35 sec) [ -6868.5415] [GTR parameters ] . ( 35 sec) [ -6850.8298] [Alpha ][ 0.351319] . ( 36 sec) [ -6850.8136] [ 1359] [depth= 1] . ( 37 sec) [ -6846.0999] [ 1358] [depth= 1] . ( 37 sec) [ -6819.5769] [ 1339] [depth= 11] . ( 37 sec) [ -6818.4609] [ 1339] [depth= 1] . ( 38 sec) [ -6817.5648] [ 1336] [depth= 7] . ( 38 sec) [ -6815.9698] [ 1335] [depth= 2] . ( 39 sec) [ -6815.9480] [ 1335] [depth= 5] . ( 39 sec) [ -6812.9238] [ 1336] [depth= 1] . ( 39 sec) [ -6812.8030] [ 1336] [depth= 3] . ( 40 sec) [ -6812.3504] [ 1336] [depth= 3] . ( 40 sec) [ -6812.1741] [ 1340] [depth= 1] . ( 40 sec) [ -6812.0425] [ 1341] [depth= 2] . ( 41 sec) [ -6809.6178] [ 1343] [depth= 1] . ( 41 sec) [ -6808.1566] [ 1342] [depth= 1] . ( 42 sec) [ -6804.8782] [ 1345] [depth= 3] . ( 42 sec) [ -6788.7232] [ 1341] [depth= 2] . ( 42 sec) [ -6788.1955] [ 1341] [depth= 1] . ( 42 sec) [ -6783.8477] [ 1339] [depth= 2] . ( 43 sec) [ -6780.0938] [ 1339] [depth= 1] . ( 43 sec) [ -6777.2437] [ 1339] [depth= 1] . ( 43 sec) [ -6776.6104] [ 1339] [depth= 1] . ( 44 sec) [ -6775.1874] [ 1339] [depth= 1] . ( 44 sec) [ -6771.1189] [ 1333] [depth= 18] . ( 45 sec) [ -6754.4600] [ 1330] [depth= 4] . ( 45 sec) [ -6754.4475] [ 1330] [depth= 1] . ( 45 sec) [ -6716.2063] [ 1314] [depth= 6] . ( 45 sec) [ -6714.6912] [ 1314] [depth= 1] . ( 45 sec) [ -6714.5758] [ 1314] [depth= 1] . ( 46 sec) [ -6709.3586] [ 1286] [depth= 3] . ( 46 sec) [ -6704.9891] [ 1287] [depth= 3] . ( 46 sec) [ -6700.2766] [ 1285] [depth= 2] . ( 47 sec) [ -6698.1011] [ 1281] [depth= 1] . ( 47 sec) [ -6694.7206] [ 1281] [depth= 1] . ( 47 sec) [ -6694.7082] [ 1281] [depth= 1] . ( 48 sec) [ -6694.6660] [ 1281] [depth= 1] . ( 48 sec) [ -6694.6337] [ 1281] [depth= 1] . ( 48 sec) [ -6694.5744] [ 1281] [depth= 1] . ( 48 sec) [ -6694.3584] [ 1281] [depth= 2] . ( 49 sec) [ -6693.1918] [ 1283] [depth= 2] . ( 49 sec) [ -6681.5248] [ 1275] [depth= 1] . ( 49 sec) [ -6680.4489] [ 1275] [depth= 3] . ( 50 sec) [ -6680.3167] [ 1275] [depth= 1] . ( 51 sec) [ -6680.2975] [ 1275] [depth= 1] . ( 52 sec) [ -6680.2669] [ 1275] [depth= 1] . ( 55 sec) [ -6674.6941] [ 1275] [depth= 1] . ( 55 sec) [ -6672.0835] [ 1271] [depth= 6] . ( 55 sec) [ -6667.2208] [ 1269] [depth= 4] . ( 55 sec) [ -6667.1860] [ 1269] [depth= 2] . ( 56 sec) [ -6666.7100] [ 1270] [depth= 1] . ( 56 sec) [ -6661.6238] [ 1269] [depth= 1] . ( 56 sec) [ -6661.2990] [ 1269] [depth= 1] . ( 56 sec) [ -6661.1272] [ 1269] [depth= 1] . ( 57 sec) [ -6655.6736] [ 1267] [depth= 2] . ( 57 sec) [ -6655.3239] [ 1267] [depth= 1] . ( 57 sec) [ -6655.2590] [ 1267] [depth= 1] . ( 58 sec) [ -6655.0163] [ 1267] [depth= 2] . ( 59 sec) [ -6650.6802] [ 1267] [depth= 4] . ( 59 sec) [ -6646.9656] [ 1266] [depth= 1] . ( 59 sec) [ -6646.7788] [ 1270] [depth= 1] . ( 59 sec) [ -6646.2331] [ 1266] [depth= 1] . ( 60 sec) [ -6646.1103] [ 1266] [depth= 2] . ( 60 sec) [ -6645.9982] [ 1266] [depth= 1] . ( 61 sec) [ -6638.9633] [ 1264] [depth= 4] . ( 62 sec) [ -6629.7298] [ 1256] [depth= 9] . ( 63 sec) [ -6629.1643] [ 1256] [depth= 6] . ( 63 sec) [ -6625.8130] [ 1256] [depth= 1] . ( 63 sec) [ -6625.7973] [ 1256] [depth= 1] . ( 63 sec) [ -6616.9383] [ 1252] [depth= 1] . ( 63 sec) [ -6615.9921] [ 1252] [depth= 7] . ( 64 sec) [ -6615.9756] [ 1252] [depth= 1] . ( 64 sec) [ -6612.9358] [ 1253] [depth= 3] . ( 65 sec) [ -6612.0184] [ 1252] [depth= 1] . ( 66 sec) [ -6611.9739] [ 1252] [depth= 1] . ( 66 sec) [ -6611.9636] [ 1252] [depth= 7] . ( 66 sec) [ -6609.7471] [ 1249] [depth= 2] . ( 67 sec) [ -6606.7269] [ 1246] [depth= 1] . ( 67 sec) [ -6606.5792] [ 1246] [depth= 1] . ( 68 sec) [ -6606.5339] [ 1246] [depth= 2] . ( 68 sec) [ -6605.4251] [ 1246] [depth= 1] . ( 70 sec) [ -6605.2093] [ 1246] [depth= 4] . ( 71 sec) [ -6604.9271] [ 1246] [depth= 1] . ( 71 sec) [ -6604.9117] [ 1246] [depth= 6] . ( 72 sec) [ -6575.3495] [Branch lengths ] . ( 73 sec) [ -6574.9228] [GTR parameters ] . ( 73 sec) [ -6574.5814] [Alpha ][ 0.334109] . ( 75 sec) [ -6556.4858] [ 1241] [depth= 1] . ( 76 sec) [ -6556.4024] [ 1244] [depth= 1] . ( 77 sec) [ -6556.1964] [ 1244] [depth= 1] . ( 79 sec) [ -6551.7595] [ 1243] [depth= 1] . ( 79 sec) [ -6550.9055] [ 1243] [depth= 2] . ( 80 sec) [ -6550.8860] [ 1243] [depth= 5] . ( 81 sec) [ -6550.6639] [ 1244] [depth= 1] . ( 82 sec) [ -6550.6452] [ 1244] [depth= 1] . ( 82 sec) [ -6549.0867] [ 1243] [depth= 1] . ( 83 sec) [ -6548.5429] [ 1259] [depth= 2] . ( 83 sec) [ -6548.5244] [ 1259] [depth= 1] . ( 86 sec) [ -6547.8221] [ 1259] [depth= 4] . ( 87 sec) [ -6547.2307] [ 1259] [depth= 1] . ( 87 sec) [ -6544.5493] [ 1257] [depth= 1] . ( 90 sec) [ -6544.5195] [ 1257] [depth= 2] . ( 92 sec) [ -6544.4415] [ 1257] [depth= 1] . ( 96 sec) [ -6544.3123] [ 1257] [depth= 5] . ( 97 sec) [ -6544.1900] [ 1257] [depth= 1] . ( 97 sec) [ -6544.1364] [ 1257] [depth= 1] . ( 97 sec) [ -6543.2407] [ 1258] [depth= 2] . ( 100 sec) [ -6542.8621] [ 1258] [depth= 1] . ( 101 sec) [ -6542.7527] [ 1258] [depth= 1] . ( 101 sec) [ -6542.7387] [ 1258] [depth= 4] . ( 103 sec) [ -6542.6119] [ 1258] [depth= 1] . ( 105 sec) [ -6542.5939] [ 1258] [depth= 3] . ( 105 sec) [ -6542.5006] [ 1258] [depth= 1] . ( 108 sec) [ -6542.4508] [ 1258] [depth= 1] . ( 109 sec) [ -6542.2697] [ 1258] [depth= 1] . ( 110 sec) [ -6540.8098] [ 1257] [depth= 1] . ( 114 sec) [ -6534.7975] [Branch lengths ] . ( 115 sec) [ -6534.7267] [GTR parameters ] . ( 115 sec) [ -6534.7209] [Alpha ][ 0.336336] . ( 126 sec) [ -6532.1614] [ 1262] [depth= 4] . ( 143 sec) [ -6532.0744] [ 1262] [depth= 1] . ( 151 sec) [ -6531.9019] [ 1262] [depth= 1] . ( 157 sec) [ -6531.7665] [ 1263] [depth= 1] . ( 158 sec) [ -6531.5819] [ 1263] [depth= 1] . ( 163 sec) [ -6530.6273] [Branch lengths ] . ( 164 sec) [ -6530.6242] [GTR parameters ] . ( 164 sec) [ -6530.6127] [Alpha ][ 0.339495] . ( 191 sec) [ -6530.3479] [ 1262] [depth= 2] . ( 195 sec) [ -6530.3271] [ 1262] [depth= 1] . ( 202 sec) [ -6530.2441] [ 1262] [depth= 1] . ( 207 sec) [ -6530.1523] [ 1262] [depth= 1] . ( 209 sec) [ -6529.2100] [Branch lengths ] . ( 209 sec) [ -6529.1922] [GTR parameters ] . ( 210 sec) [ -6529.1900] [Alpha ][ 0.340876] . ( 254 sec) [ -6529.0391] [Branch lengths ] . ( 275 sec) [ -6528.9410] [ 1273] [depth= 1] . ( 342 sec) [ -6528.7798] [Branch lengths ] . ( 342 sec) [ -6528.7793] [GTR parameters ] . ( 343 sec) [ -6528.7782] [Alpha ][ 0.341882] . ( 343 sec) [ -6528.7782] [Topology ] . ( 345 sec) [ -6528.5444] [Topology ] . ( 347 sec) [ -6528.3084] [Topology ] . ( 348 sec) [ -6528.1070] [Topology ] . ( 350 sec) [ -6527.9810] [Topology ] . ( 352 sec) [ -6527.9491] [Topology ] . ( 354 sec) [ -6527.9340] [Topology ] . ( 356 sec) [ -6527.9257] [Topology ] . ( 358 sec) [ -6527.9209] [Topology ] . ( 360 sec) [ -6527.9182] [Topology ] . ( 361 sec) [ -6527.9142] [GTR parameters ] . ( 362 sec) [ -6527.9131] [Alpha ][ 0.342875] . ( 362 sec) [ -6527.9131] [Topology ] . ( 364 sec) [ -6527.9105] [Topology ] . ( 366 sec) [ -6527.9092] [Topology ] . ( 368 sec) [ -6527.9085] [Topology ] . ( 368 sec) [ -6527.9084] [GTR parameters ] . ( 368 sec) [ -6527.9081] [Alpha ][ 0.343388] . ( 368 sec) [ -6527.9081] [Topology ] . ( 370 sec) [ -6527.9075] [Topology ] . ( 371 sec) [ -6527.9075] [GTR parameters ] . ( 371 sec) [ -6527.9074] [Alpha ][ 0.343731] . Checking for NNIs, optimizing five branches... . ( 386 sec) [ -6527.7069] [Topology ] . Checking for NNIs, optimizing five branches... . ( 402 sec) [ -6527.7064] [Topology ] . Checking for NNIs, optimizing five branches... . ( 417 sec) [ -6527.7063] [Topology ] . Checking for NNIs, optimizing five branches... . ( 433 sec) [ -6527.7054] [Topology ] . Checking for NNIs, optimizing five branches... . ( 449 sec) [ -6527.7051] [Topology ] . Checking for NNIs, optimizing five branches... . ( 464 sec) [ -6527.7050] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.704961. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -30810.4980] [GTR parameters ] . ( 3 sec) [ -30054.0806] [Alpha ][ 0.500960] . ( 4 sec) [ -29423.9671] [ 3893] [depth= 9] . ( 4 sec) [ -29217.3661] [ 3819] [depth= 2] . ( 4 sec) [ -28817.2602] [ 3796] [depth= 9] . ( 4 sec) [ -28748.1575] [ 3789] [depth= 1] . ( 4 sec) [ -28293.3387] [ 3763] [depth= 16] . ( 4 sec) [ -27415.1677] [ 3749] [depth= 6] . ( 4 sec) [ -27259.5380] [ 3746] [depth= 10] . ( 4 sec) [ -27167.6834] [ 3533] [depth= 3] . ( 5 sec) [ -27047.0094] [ 3529] [depth= 9] . ( 5 sec) [ -26861.7412] [ 3523] [depth= 5] . ( 5 sec) [ -25451.7300] [ 3500] [depth= 11] . ( 5 sec) [ -25407.3253] [ 3485] [depth= 4] . ( 5 sec) [ -24753.7252] [ 3481] [depth= 1] . ( 5 sec) [ -24672.0651] [ 3481] [depth= 8] . ( 5 sec) [ -24582.9986] [ 3472] [depth= 7] . ( 6 sec) [ -24524.9523] [ 3470] [depth= 5] . ( 6 sec) [ -24055.6981] [ 3454] [depth= 9] . ( 6 sec) [ -23996.1327] [ 3436] [depth= 1] . ( 6 sec) [ -23616.2294] [ 3370] [depth= 8] . ( 6 sec) [ -23216.8369] [ 3368] [depth= 7] . ( 6 sec) [ -22178.4307] [ 3345] [depth= 2] . ( 6 sec) [ -21532.0727] [ 3370] [depth= 1] . ( 6 sec) [ -21138.0434] [ 3357] [depth= 1] . ( 6 sec) [ -20926.0216] [ 3142] [depth= 19] . ( 7 sec) [ -20618.0600] [ 3129] [depth= 17] . ( 7 sec) [ -20477.7271] [ 3129] [depth= 6] . ( 7 sec) [ -20446.2440] [ 3098] [depth= 2] . ( 7 sec) [ -20440.3926] [ 3098] [depth= 1] . ( 7 sec) [ -20438.0413] [ 3098] [depth= 20] . ( 7 sec) [ -20167.9864] [ 3002] [depth= 2] . ( 7 sec) [ -19721.9334] [ 2996] [depth= 2] . ( 7 sec) [ -19550.2158] [ 2980] [depth= 2] . ( 8 sec) [ -19522.6996] [ 2975] [depth= 9] . ( 8 sec) [ -19486.1216] [ 2975] [depth= 1] . ( 8 sec) [ -19435.9907] [ 2975] [depth= 3] . ( 8 sec) [ -19318.2412] [ 2960] [depth= 7] . ( 8 sec) [ -19208.6979] [ 2937] [depth= 22] . ( 8 sec) [ -19119.6002] [ 2930] [depth= 2] . ( 8 sec) [ -18949.8066] [ 2905] [depth= 16] . ( 8 sec) [ -18946.1492] [ 2905] [depth= 19] . ( 9 sec) [ -18786.9867] [ 2878] [depth= 11] . ( 9 sec) [ -18256.9842] [ 2861] [depth= 8] . ( 9 sec) [ -18245.5797] [ 2861] [depth= 11] . ( 9 sec) [ -18228.6576] [ 2860] [depth= 2] . ( 9 sec) [ -17955.7730] [ 2825] [depth= 15] . ( 9 sec) [ -17954.2543] [ 2825] [depth= 2] . ( 9 sec) [ -17885.8094] [ 2790] [depth= 9] . ( 10 sec) [ -17584.8046] [ 2702] [depth= 16] . ( 10 sec) [ -17552.6075] [ 2702] [depth= 4] . ( 10 sec) [ -17297.2053] [ 2706] [depth= 1] . ( 10 sec) [ -17036.6506] [ 2698] [depth= 11] . ( 10 sec) [ -16567.8939] [ 2659] [depth= 10] . ( 10 sec) [ -16559.4160] [ 2659] [depth= 1] . ( 10 sec) [ -16539.2968] [ 2659] [depth= 2] . ( 10 sec) [ -16147.4045] [ 2658] [depth= 8] . ( 11 sec) [ -15768.3963] [ 2526] [depth= 15] . ( 11 sec) [ -15766.2276] [ 2526] [depth= 10] . ( 11 sec) [ -15749.3467] [ 2525] [depth= 4] . ( 11 sec) [ -15701.3149] [ 2525] [depth= 5] . ( 11 sec) [ -15504.2407] [ 2525] [depth= 2] . ( 11 sec) [ -15501.1421] [ 2525] [depth= 1] . ( 11 sec) [ -15496.0381] [ 2526] [depth= 3] . ( 12 sec) [ -15493.9103] [ 2526] [depth= 1] . ( 12 sec) [ -15491.0510] [ 2526] [depth= 3] . ( 12 sec) [ -15483.0305] [ 2521] [depth= 5] . ( 12 sec) [ -15379.4563] [ 2500] [depth= 4] . ( 12 sec) [ -15379.3218] [ 2500] [depth= 1] . ( 12 sec) [ -15378.2394] [ 2500] [depth= 2] . ( 12 sec) [ -15190.9384] [ 2439] [depth= 12] . ( 12 sec) [ -14900.2552] [ 2431] [depth= 4] . ( 13 sec) [ -14367.1813] [ 2356] [depth= 7] . ( 13 sec) [ -14328.5159] [ 2355] [depth= 15] . ( 13 sec) [ -14195.6472] [ 2334] [depth= 10] . ( 13 sec) [ -14046.3495] [ 2313] [depth= 18] . ( 13 sec) [ -13800.2474] [ 2251] [depth= 12] . ( 13 sec) [ -13679.4652] [ 2237] [depth= 11] . ( 13 sec) [ -13671.3989] [ 2237] [depth= 1] . ( 13 sec) [ -13602.5034] [ 2211] [depth= 2] . ( 14 sec) [ -12979.7994] [ 2162] [depth= 9] . ( 14 sec) [ -12953.5585] [ 2133] [depth= 9] . ( 14 sec) [ -12796.7236] [ 2130] [depth= 3] . ( 14 sec) [ -12635.7397] [ 2083] [depth= 4] . ( 14 sec) [ -12628.5319] [ 2083] [depth= 3] . ( 14 sec) [ -12481.7461] [ 2080] [depth= 2] . ( 14 sec) [ -12458.2079] [ 2035] [depth= 10] . ( 14 sec) [ -12454.4002] [ 2035] [depth= 2] . ( 15 sec) [ -12385.0985] [ 2028] [depth= 14] . ( 15 sec) [ -12289.8503] [ 2020] [depth= 1] . ( 15 sec) [ -12277.4018] [ 2018] [depth= 14] . ( 15 sec) [ -12276.9223] [ 2018] [depth= 1] . ( 15 sec) [ -12224.5491] [ 2013] [depth= 5] . ( 15 sec) [ -11953.3519] [ 1978] [depth= 1] . ( 15 sec) [ -11853.7708] [ 1970] [depth= 14] . ( 15 sec) [ -11814.0506] [ 1975] [depth= 1] . ( 15 sec) [ -11805.0932] [ 1975] [depth= 1] . ( 16 sec) [ -11630.7635] [ 1970] [depth= 10] . ( 16 sec) [ -11404.4638] [ 1947] [depth= 2] . ( 16 sec) [ -10809.6066] [ 1868] [depth= 3] . ( 16 sec) [ -10697.9293] [ 1868] [depth= 1] . ( 16 sec) [ -10623.0624] [ 1868] [depth= 1] . ( 16 sec) [ -10525.8732] [ 1869] [depth= 8] . ( 16 sec) [ -10483.6506] [ 1849] [depth= 10] . ( 16 sec) [ -10477.8970] [ 1849] [depth= 1] . ( 17 sec) [ -10356.2203] [ 1833] [depth= 9] . ( 17 sec) [ -10355.6395] [ 1833] [depth= 1] . ( 17 sec) [ -10355.1154] [ 1835] [depth= 2] . ( 17 sec) [ -10212.2594] [ 1821] [depth= 6] . ( 17 sec) [ -10212.1863] [ 1821] [depth= 1] . ( 17 sec) [ -10211.6857] [ 1821] [depth= 2] . ( 18 sec) [ -10112.3332] [ 1821] [depth= 4] . ( 18 sec) [ -10030.1814] [ 1820] [depth= 4] . ( 18 sec) [ -10025.1269] [ 1825] [depth= 1] . ( 18 sec) [ -9986.2950] [ 1822] [depth= 9] . ( 18 sec) [ -9856.4566] [ 1822] [depth= 1] . ( 18 sec) [ -9802.3024] [ 1815] [depth= 2] . ( 18 sec) [ -9798.7741] [ 1815] [depth= 1] . ( 18 sec) [ -9760.8056] [ 1807] [depth= 1] . ( 18 sec) [ -9758.5620] [ 1807] [depth= 1] . ( 19 sec) [ -9758.2375] [ 1808] [depth= 1] . ( 19 sec) [ -9754.2283] [ 1808] [depth= 2] . ( 19 sec) [ -9596.9224] [ 1780] [depth= 13] . ( 19 sec) [ -9593.1968] [ 1783] [depth= 1] . ( 19 sec) [ -9593.1645] [ 1783] [depth= 4] . ( 19 sec) [ -9593.0559] [ 1783] [depth= 1] . ( 19 sec) [ -9587.6693] [ 1783] [depth= 6] . ( 19 sec) [ -9551.0491] [ 1771] [depth= 8] . ( 20 sec) [ -9257.1829] [ 1754] [depth= 1] . ( 20 sec) [ -9228.1685] [ 1749] [depth= 8] . ( 20 sec) [ -9152.8165] [ 1717] [depth= 11] . ( 20 sec) [ -9055.1118] [ 1699] [depth= 11] . ( 20 sec) [ -8944.3583] [ 1698] [depth= 8] . ( 20 sec) [ -8936.0942] [ 1698] [depth= 2] . ( 20 sec) [ -8876.0046] [ 1686] [depth= 2] . ( 20 sec) [ -8832.7974] [ 1665] [depth= 7] . ( 21 sec) [ -8829.7967] [ 1667] [depth= 1] . ( 21 sec) [ -8827.5278] [ 1667] [depth= 4] . ( 21 sec) [ -8827.2013] [ 1667] [depth= 3] . ( 21 sec) [ -8789.8456] [ 1635] [depth= 2] . ( 21 sec) [ -8661.2909] [ 1625] [depth= 5] . ( 21 sec) [ -8633.4871] [ 1619] [depth= 1] . ( 21 sec) [ -8618.7512] [ 1609] [depth= 3] . ( 21 sec) [ -8607.2828] [ 1608] [depth= 1] . ( 22 sec) [ -8606.7758] [ 1607] [depth= 9] . ( 22 sec) [ -8598.0027] [ 1610] [depth= 8] . ( 22 sec) [ -8313.1260] [ 1535] [depth= 8] . ( 22 sec) [ -8309.5027] [ 1538] [depth= 2] . ( 22 sec) [ -8296.4897] [ 1538] [depth= 1] . ( 23 sec) [ -8289.6672] [ 1537] [depth= 4] . ( 23 sec) [ -8271.8426] [ 1535] [depth= 2] . ( 23 sec) [ -8228.7462] [ 1521] [depth= 5] . ( 23 sec) [ -8225.4563] [ 1521] [depth= 2] . ( 23 sec) [ -8220.8419] [ 1520] [depth= 3] . ( 23 sec) [ -8219.2975] [ 1521] [depth= 2] . ( 23 sec) [ -8198.6215] [ 1507] [depth= 1] . ( 24 sec) [ -8122.3405] [ 1489] [depth= 6] . ( 24 sec) [ -8122.0271] [ 1488] [depth= 3] . ( 24 sec) [ -8121.7168] [ 1488] [depth= 5] . ( 24 sec) [ -8087.2112] [ 1463] [depth= 1] . ( 24 sec) [ -8076.4964] [ 1453] [depth= 2] . ( 24 sec) [ -8073.1860] [ 1453] [depth= 1] . ( 24 sec) [ -7976.1705] [ 1421] [depth= 11] . ( 24 sec) [ -7975.0977] [ 1419] [depth= 2] . ( 25 sec) [ -7971.0925] [ 1419] [depth= 1] . ( 25 sec) [ -7929.6489] [ 1404] [depth= 1] . ( 25 sec) [ -7908.6430] [ 1407] [depth= 3] . ( 25 sec) [ -7906.0008] [ 1387] [depth= 6] . ( 25 sec) [ -7857.8264] [ 1390] [depth= 1] . ( 25 sec) [ -7845.8887] [ 1387] [depth= 1] . ( 25 sec) [ -7818.9107] [ 1383] [depth= 1] . ( 25 sec) [ -7803.5044] [ 1382] [depth= 6] . ( 26 sec) [ -7802.1221] [ 1383] [depth= 1] . ( 26 sec) [ -7795.2670] [ 1383] [depth= 3] . ( 26 sec) [ -7792.3190] [ 1384] [depth= 1] . ( 26 sec) [ -7775.2824] [ 1382] [depth= 3] . ( 26 sec) [ -7699.4897] [ 1382] [depth= 2] . ( 26 sec) [ -7685.5097] [ 1380] [depth= 1] . ( 27 sec) [ -7683.3211] [ 1377] [depth= 2] . ( 27 sec) [ -7682.1349] [ 1376] [depth= 3] . ( 27 sec) [ -7677.4439] [ 1375] [depth= 2] . ( 27 sec) [ -7672.8548] [ 1375] [depth= 1] . ( 27 sec) [ -7612.8864] [ 1351] [depth= 7] . ( 27 sec) [ -7609.8472] [ 1350] [depth= 1] . ( 27 sec) [ -7582.2388] [ 1343] [depth= 7] . ( 28 sec) [ -7581.7207] [ 1343] [depth= 2] . ( 28 sec) [ -7579.0787] [ 1343] [depth= 3] . ( 28 sec) [ -7573.5598] [ 1343] [depth= 2] . ( 28 sec) [ -7572.8823] [ 1343] [depth= 1] . ( 28 sec) [ -7565.6484] [ 1343] [depth= 4] . ( 29 sec) [ -7226.0690] [Branch lengths ] . ( 31 sec) [ -7200.6115] [GTR parameters ] . ( 31 sec) [ -7175.7976] [Alpha ][ 0.332364] . ( 32 sec) [ -7167.1201] [ 1336] [depth= 3] . ( 32 sec) [ -7165.1692] [ 1334] [depth= 2] . ( 32 sec) [ -7165.0238] [ 1334] [depth= 1] . ( 32 sec) [ -7011.5041] [ 1317] [depth= 3] . ( 32 sec) [ -6905.9076] [ 1348] [depth= 1] . ( 32 sec) [ -6904.4081] [ 1345] [depth= 2] . ( 32 sec) [ -6902.2966] [ 1345] [depth= 1] . ( 33 sec) [ -6899.2064] [ 1343] [depth= 2] . ( 34 sec) [ -6889.8092] [ 1337] [depth= 4] . ( 34 sec) [ -6887.6021] [ 1327] [depth= 7] . ( 34 sec) [ -6859.3975] [ 1315] [depth= 1] . ( 34 sec) [ -6845.3010] [ 1311] [depth= 4] . ( 35 sec) [ -6836.7832] [ 1310] [depth= 2] . ( 35 sec) [ -6836.7619] [ 1310] [depth= 2] . ( 35 sec) [ -6832.9910] [ 1310] [depth= 1] . ( 35 sec) [ -6830.4202] [ 1310] [depth= 1] . ( 35 sec) [ -6826.6849] [ 1309] [depth= 2] . ( 35 sec) [ -6825.7758] [ 1285] [depth= 2] . ( 36 sec) [ -6823.0219] [ 1285] [depth= 1] . ( 36 sec) [ -6822.5232] [ 1285] [depth= 1] . ( 37 sec) [ -6780.1329] [ 1279] [depth= 4] . ( 37 sec) [ -6770.3346] [ 1279] [depth= 1] . ( 37 sec) [ -6749.9084] [ 1280] [depth= 1] . ( 38 sec) [ -6747.4477] [ 1280] [depth= 1] . ( 38 sec) [ -6745.0135] [ 1280] [depth= 1] . ( 38 sec) [ -6744.6250] [ 1280] [depth= 1] . ( 39 sec) [ -6744.5468] [ 1280] [depth= 6] . ( 40 sec) [ -6723.1725] [ 1304] [depth= 6] . ( 42 sec) [ -6723.1612] [ 1304] [depth= 5] . ( 44 sec) [ -6688.8436] [ 1289] [depth= 9] . ( 44 sec) [ -6682.7387] [ 1285] [depth= 1] . ( 45 sec) [ -6682.5206] [ 1283] [depth= 2] . ( 46 sec) [ -6682.4898] [ 1283] [depth= 1] . ( 46 sec) [ -6673.3329] [ 1282] [depth= 2] . ( 46 sec) [ -6673.1964] [ 1283] [depth= 1] . ( 46 sec) [ -6649.8165] [ 1276] [depth= 4] . ( 47 sec) [ -6646.0329] [ 1277] [depth= 1] . ( 47 sec) [ -6646.0184] [ 1276] [depth= 2] . ( 47 sec) [ -6645.5381] [ 1276] [depth= 1] . ( 47 sec) [ -6645.5265] [ 1276] [depth= 2] . ( 47 sec) [ -6645.4974] [ 1276] [depth= 1] . ( 49 sec) [ -6625.1938] [ 1275] [depth= 1] . ( 50 sec) [ -6622.9125] [ 1276] [depth= 2] . ( 51 sec) [ -6618.9664] [ 1277] [depth= 1] . ( 51 sec) [ -6617.9242] [ 1276] [depth= 1] . ( 51 sec) [ -6617.0613] [ 1277] [depth= 1] . ( 51 sec) [ -6611.6451] [ 1274] [depth= 1] . ( 51 sec) [ -6611.6110] [ 1274] [depth= 1] . ( 52 sec) [ -6609.5893] [ 1275] [depth= 1] . ( 52 sec) [ -6609.5601] [ 1275] [depth= 1] . ( 52 sec) [ -6609.3550] [ 1275] [depth= 1] . ( 52 sec) [ -6609.3183] [ 1275] [depth= 1] . ( 53 sec) [ -6608.9846] [ 1274] [depth= 1] . ( 54 sec) [ -6604.5988] [ 1273] [depth= 1] . ( 54 sec) [ -6604.4429] [ 1274] [depth= 3] . ( 55 sec) [ -6604.0592] [ 1274] [depth= 2] . ( 56 sec) [ -6603.6167] [ 1274] [depth= 2] . ( 56 sec) [ -6603.5961] [ 1274] [depth= 1] . ( 57 sec) [ -6600.3027] [ 1272] [depth= 1] . ( 57 sec) [ -6599.7416] [ 1274] [depth= 1] . ( 58 sec) [ -6598.7345] [ 1274] [depth= 3] . ( 58 sec) [ -6598.7086] [ 1274] [depth= 1] . ( 60 sec) [ -6596.9926] [ 1276] [depth= 1] . ( 60 sec) [ -6596.3295] [ 1271] [depth= 1] . ( 60 sec) [ -6589.7692] [ 1270] [depth= 2] . ( 60 sec) [ -6589.6288] [ 1270] [depth= 1] . ( 60 sec) [ -6575.6435] [ 1267] [depth= 1] . ( 60 sec) [ -6573.6796] [ 1267] [depth= 1] . ( 61 sec) [ -6573.3524] [ 1267] [depth= 2] . ( 62 sec) [ -6573.1474] [ 1267] [depth= 1] . ( 63 sec) [ -6572.2617] [ 1267] [depth= 1] . ( 63 sec) [ -6571.9939] [ 1266] [depth= 1] . ( 64 sec) [ -6570.4426] [ 1266] [depth= 3] . ( 65 sec) [ -6570.4081] [ 1266] [depth= 1] . ( 65 sec) [ -6564.1679] [ 1266] [depth= 1] . ( 65 sec) [ -6561.1198] [ 1264] [depth= 4] . ( 65 sec) [ -6559.0005] [ 1263] [depth= 1] . ( 67 sec) [ -6558.9350] [ 1263] [depth= 3] . ( 71 sec) [ -6541.9271] [Branch lengths ] . ( 73 sec) [ -6541.7466] [GTR parameters ] . ( 73 sec) [ -6541.7364] [Alpha ][ 0.335279] . ( 76 sec) [ -6541.4723] [ 1264] [depth= 1] . ( 76 sec) [ -6541.4595] [ 1264] [depth= 1] . ( 83 sec) [ -6540.8431] [ 1262] [depth= 2] . ( 89 sec) [ -6537.5356] [ 1261] [depth= 1] . ( 92 sec) [ -6536.0727] [ 1261] [depth= 2] . ( 94 sec) [ -6535.8034] [ 1261] [depth= 1] . ( 95 sec) [ -6535.7636] [ 1261] [depth= 1] . ( 103 sec) [ -6535.7202] [ 1261] [depth= 1] . ( 104 sec) [ -6533.6639] [ 1260] [depth= 4] . ( 113 sec) [ -6533.6515] [ 1260] [depth= 1] . ( 115 sec) [ -6529.8939] [Branch lengths ] . ( 116 sec) [ -6529.8655] [GTR parameters ] . ( 116 sec) [ -6529.8566] [Alpha ][ 0.338042] . ( 164 sec) [ -6529.4727] [Branch lengths ] . ( 179 sec) [ -6529.4312] [ 1259] [depth= 1] . ( 189 sec) [ -6529.3095] [ 1270] [depth= 1] . ( 260 sec) [ -6528.6653] [Branch lengths ] . ( 261 sec) [ -6528.6605] [GTR parameters ] . ( 261 sec) [ -6528.6533] [Alpha ][ 0.340564] . ( 261 sec) [ -6528.6533] [Topology ] . ( 263 sec) [ -6528.5802] [Topology ] . ( 265 sec) [ -6528.5395] [Topology ] . ( 267 sec) [ -6528.5125] [Topology ] . ( 269 sec) [ -6528.4933] [Topology ] . ( 270 sec) [ -6528.4796] [Topology ] . ( 272 sec) [ -6528.4698] [Topology ] . ( 273 sec) [ -6528.4691] [GTR parameters ] . ( 274 sec) [ -6528.4668] [Alpha ][ 0.341984] . ( 274 sec) [ -6528.4668] [Topology ] . ( 276 sec) [ -6528.4586] [Topology ] . ( 277 sec) [ -6528.4532] [Topology ] . ( 279 sec) [ -6528.4495] [Topology ] . ( 281 sec) [ -6528.4468] [Topology ] . ( 283 sec) [ -6528.4448] [Topology ] . ( 285 sec) [ -6528.4434] [Topology ] . ( 285 sec) [ -6528.4434] [GTR parameters ] . ( 285 sec) [ -6528.4428] [Alpha ][ 0.342669] . ( 285 sec) [ -6528.4428] [Topology ] . ( 287 sec) [ -6528.4415] [Topology ] . ( 289 sec) [ -6528.4407] [Topology ] . ( 289 sec) [ -6528.4407] [GTR parameters ] . ( 289 sec) [ -6528.4406] [Alpha ][ 0.343012] . ( 290 sec) [ -6528.4406] [Topology ] . ( 291 sec) [ -6528.4399] [Topology ] . ( 292 sec) [ -6528.4399] [GTR parameters ] . ( 292 sec) [ -6528.4399] [Alpha ][ 0.343012] . Checking for NNIs, optimizing five branches... . ( 307 sec) [ -6528.4390] [Topology ] . Checking for NNIs, optimizing five branches... . ( 323 sec) [ -6528.4389] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6528.438890. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -29388.7135] [GTR parameters ] . ( 3 sec) [ -28686.6752] [Alpha ][ 0.500960] . ( 3 sec) [ -28070.9782] [ 3985] [depth= 13] . ( 4 sec) [ -27370.1689] [ 3912] [depth= 9] . ( 4 sec) [ -26864.5241] [ 3897] [depth= 3] . ( 4 sec) [ -26154.5630] [ 3893] [depth= 4] . ( 4 sec) [ -26019.5405] [ 3814] [depth= 6] . ( 4 sec) [ -26001.9826] [ 3806] [depth= 10] . ( 4 sec) [ -25860.8515] [ 3797] [depth= 1] . ( 4 sec) [ -25701.2942] [ 3768] [depth= 9] . ( 4 sec) [ -25653.6141] [ 3755] [depth= 1] . ( 4 sec) [ -25482.0685] [ 3754] [depth= 4] . ( 5 sec) [ -25431.8068] [ 3754] [depth= 6] . ( 5 sec) [ -25359.5984] [ 3752] [depth= 2] . ( 5 sec) [ -25259.9821] [ 3746] [depth= 2] . ( 5 sec) [ -24961.4460] [ 3743] [depth= 4] . ( 5 sec) [ -24580.7134] [ 3734] [depth= 8] . ( 5 sec) [ -24162.5435] [ 3728] [depth= 1] . ( 5 sec) [ -23772.6192] [ 3714] [depth= 1] . ( 5 sec) [ -23342.4430] [ 3700] [depth= 3] . ( 5 sec) [ -22974.8752] [ 3620] [depth= 2] . ( 6 sec) [ -22713.9707] [ 3606] [depth= 10] . ( 6 sec) [ -22697.3850] [ 3600] [depth= 2] . ( 6 sec) [ -22554.7519] [ 3585] [depth= 13] . ( 6 sec) [ -22401.2351] [ 3563] [depth= 4] . ( 6 sec) [ -22375.5322] [ 3558] [depth= 9] . ( 6 sec) [ -22328.1694] [ 3557] [depth= 1] . ( 6 sec) [ -21957.0998] [ 3469] [depth= 17] . ( 6 sec) [ -21607.1791] [ 3456] [depth= 6] . ( 6 sec) [ -21187.0538] [ 3444] [depth= 2] . ( 7 sec) [ -20964.6283] [ 3365] [depth= 17] . ( 7 sec) [ -20885.6361] [ 3341] [depth= 18] . ( 7 sec) [ -20791.7936] [ 3334] [depth= 4] . ( 7 sec) [ -20718.7501] [ 3330] [depth= 1] . ( 7 sec) [ -20657.8957] [ 3327] [depth= 1] . ( 7 sec) [ -20550.4014] [ 3318] [depth= 1] . ( 7 sec) [ -20479.5082] [ 3304] [depth= 3] . ( 7 sec) [ -20207.1524] [ 3282] [depth= 20] . ( 8 sec) [ -20071.9052] [ 3264] [depth= 19] . ( 8 sec) [ -19985.8296] [ 3240] [depth= 5] . ( 8 sec) [ -19680.4553] [ 3166] [depth= 6] . ( 8 sec) [ -19608.0170] [ 3149] [depth= 4] . ( 8 sec) [ -18961.8854] [ 2945] [depth= 6] . ( 8 sec) [ -18885.0218] [ 2943] [depth= 2] . ( 8 sec) [ -18796.5067] [ 2850] [depth= 16] . ( 8 sec) [ -18754.1713] [ 2839] [depth= 2] . ( 8 sec) [ -18557.1204] [ 2814] [depth= 5] . ( 9 sec) [ -18498.6208] [ 2803] [depth= 8] . ( 9 sec) [ -18496.2114] [ 2809] [depth= 17] . ( 9 sec) [ -18203.5011] [ 2798] [depth= 2] . ( 9 sec) [ -18195.8824] [ 2794] [depth= 3] . ( 9 sec) [ -18141.0480] [ 2791] [depth= 14] . ( 9 sec) [ -16656.7363] [ 2786] [depth= 12] . ( 10 sec) [ -16653.6821] [ 2785] [depth= 1] . ( 10 sec) [ -16652.1651] [ 2784] [depth= 1] . ( 10 sec) [ -16630.7119] [ 2783] [depth= 5] . ( 10 sec) [ -16630.0856] [ 2784] [depth= 2] . ( 10 sec) [ -16408.9400] [ 2784] [depth= 15] . ( 10 sec) [ -16255.9937] [ 2784] [depth= 4] . ( 10 sec) [ -16151.5052] [ 2746] [depth= 20] . ( 10 sec) [ -16115.1521] [ 2746] [depth= 3] . ( 10 sec) [ -16053.7109] [ 2738] [depth= 3] . ( 11 sec) [ -15701.8430] [ 2679] [depth= 17] . ( 11 sec) [ -15574.4908] [ 2647] [depth= 16] . ( 11 sec) [ -15411.7254] [ 2641] [depth= 3] . ( 11 sec) [ -15411.0582] [ 2641] [depth= 9] . ( 11 sec) [ -15382.9290] [ 2642] [depth= 15] . ( 11 sec) [ -15330.7307] [ 2641] [depth= 11] . ( 11 sec) [ -15299.4561] [ 2636] [depth= 14] . ( 12 sec) [ -15269.5974] [ 2635] [depth= 19] . ( 12 sec) [ -15177.4094] [ 2637] [depth= 3] . ( 12 sec) [ -15115.0606] [ 2636] [depth= 4] . ( 12 sec) [ -15095.4228] [ 2607] [depth= 8] . ( 12 sec) [ -15090.4741] [ 2606] [depth= 1] . ( 12 sec) [ -14669.6147] [ 2400] [depth= 10] . ( 12 sec) [ -14668.8803] [ 2405] [depth= 1] . ( 12 sec) [ -14568.9107] [ 2368] [depth= 16] . ( 13 sec) [ -14562.3704] [ 2373] [depth= 4] . ( 13 sec) [ -14561.4365] [ 2373] [depth= 1] . ( 13 sec) [ -14555.7359] [ 2371] [depth= 2] . ( 13 sec) [ -13511.1515] [ 2354] [depth= 3] . ( 13 sec) [ -13406.1530] [ 2350] [depth= 19] . ( 13 sec) [ -13375.7887] [ 2351] [depth= 14] . ( 13 sec) [ -13368.1296] [ 2347] [depth= 6] . ( 13 sec) [ -13362.5967] [ 2347] [depth= 1] . ( 14 sec) [ -12569.8685] [ 2326] [depth= 19] . ( 14 sec) [ -12053.8572] [ 2100] [depth= 8] . ( 14 sec) [ -11949.4548] [ 2093] [depth= 3] . ( 14 sec) [ -11864.9134] [ 2091] [depth= 5] . ( 14 sec) [ -11806.3376] [ 2081] [depth= 2] . ( 14 sec) [ -11716.9152] [ 2077] [depth= 2] . ( 14 sec) [ -11635.1540] [ 2057] [depth= 6] . ( 14 sec) [ -11630.5008] [ 2058] [depth= 2] . ( 15 sec) [ -11618.3549] [ 2051] [depth= 1] . ( 15 sec) [ -11584.6658] [ 2040] [depth= 4] . ( 15 sec) [ -11514.9149] [ 2022] [depth= 22] . ( 15 sec) [ -11168.4482] [ 1911] [depth= 8] . ( 15 sec) [ -11062.1160] [ 1911] [depth= 5] . ( 15 sec) [ -11056.3996] [ 1909] [depth= 3] . ( 15 sec) [ -10924.6941] [ 1896] [depth= 13] . ( 15 sec) [ -10850.8526] [ 1892] [depth= 5] . ( 15 sec) [ -10763.2995] [ 1865] [depth= 13] . ( 16 sec) [ -10715.2460] [ 1857] [depth= 1] . ( 16 sec) [ -10697.2312] [ 1852] [depth= 11] . ( 16 sec) [ -10641.5966] [ 1842] [depth= 12] . ( 16 sec) [ -10602.3871] [ 1836] [depth= 1] . ( 16 sec) [ -10492.7113] [ 1832] [depth= 7] . ( 16 sec) [ -10492.0231] [ 1832] [depth= 1] . ( 16 sec) [ -10432.4656] [ 1810] [depth= 16] . ( 16 sec) [ -10256.6146] [ 1803] [depth= 2] . ( 16 sec) [ -10025.7876] [ 1775] [depth= 3] . ( 17 sec) [ -9848.0483] [ 1751] [depth= 1] . ( 17 sec) [ -9824.5474] [ 1751] [depth= 1] . ( 17 sec) [ -9706.7328] [ 1714] [depth= 3] . ( 17 sec) [ -9539.4779] [ 1688] [depth= 6] . ( 17 sec) [ -9431.7631] [ 1688] [depth= 1] . ( 17 sec) [ -9353.4253] [ 1669] [depth= 4] . ( 17 sec) [ -9316.5697] [ 1669] [depth= 3] . ( 17 sec) [ -9283.8858] [ 1662] [depth= 1] . ( 18 sec) [ -9212.8237] [ 1631] [depth= 5] . ( 18 sec) [ -9118.6670] [ 1624] [depth= 9] . ( 18 sec) [ -9118.5762] [ 1624] [depth= 1] . ( 18 sec) [ -9115.9973] [ 1624] [depth= 1] . ( 18 sec) [ -9101.8521] [ 1624] [depth= 5] . ( 18 sec) [ -9080.2689] [ 1590] [depth= 8] . ( 18 sec) [ -9013.8497] [ 1584] [depth= 3] . ( 18 sec) [ -9013.7067] [ 1584] [depth= 5] . ( 19 sec) [ -8838.9728] [ 1584] [depth= 2] . ( 19 sec) [ -8745.2259] [ 1580] [depth= 1] . ( 19 sec) [ -8513.2805] [ 1579] [depth= 10] . ( 19 sec) [ -8461.7976] [ 1556] [depth= 1] . ( 19 sec) [ -8442.4095] [ 1557] [depth= 1] . ( 19 sec) [ -8430.7497] [ 1556] [depth= 1] . ( 19 sec) [ -8426.2323] [ 1560] [depth= 1] . ( 19 sec) [ -8425.5141] [ 1559] [depth= 3] . ( 20 sec) [ -8330.7846] [ 1531] [depth= 5] . ( 20 sec) [ -8320.3572] [ 1528] [depth= 9] . ( 20 sec) [ -8265.9798] [ 1528] [depth= 2] . ( 20 sec) [ -8258.7262] [ 1528] [depth= 7] . ( 20 sec) [ -8258.0618] [ 1528] [depth= 2] . ( 20 sec) [ -8252.3133] [ 1528] [depth= 1] . ( 20 sec) [ -8187.9145] [ 1518] [depth= 19] . ( 20 sec) [ -8166.0605] [ 1516] [depth= 1] . ( 21 sec) [ -8113.7954] [ 1509] [depth= 4] . ( 21 sec) [ -8112.4277] [ 1509] [depth= 1] . ( 21 sec) [ -8110.6954] [ 1509] [depth= 1] . ( 21 sec) [ -8072.3103] [ 1507] [depth= 1] . ( 21 sec) [ -8008.3710] [ 1493] [depth= 6] . ( 21 sec) [ -7984.2863] [ 1487] [depth= 3] . ( 21 sec) [ -7962.6996] [ 1476] [depth= 1] . ( 21 sec) [ -7936.6133] [ 1475] [depth= 3] . ( 22 sec) [ -7922.8299] [ 1463] [depth= 16] . ( 22 sec) [ -7835.2332] [ 1479] [depth= 1] . ( 22 sec) [ -7812.9339] [ 1477] [depth= 4] . ( 22 sec) [ -7782.3712] [ 1454] [depth= 2] . ( 22 sec) [ -7781.4694] [ 1454] [depth= 1] . ( 22 sec) [ -7779.8393] [ 1479] [depth= 1] . ( 22 sec) [ -7779.2928] [ 1483] [depth= 1] . ( 22 sec) [ -7725.4703] [ 1468] [depth= 3] . ( 23 sec) [ -7691.4694] [ 1455] [depth= 1] . ( 23 sec) [ -7673.6701] [ 1454] [depth= 1] . ( 23 sec) [ -7588.8812] [ 1448] [depth= 1] . ( 23 sec) [ -7586.6588] [ 1452] [depth= 1] . ( 23 sec) [ -7585.9866] [ 1452] [depth= 1] . ( 23 sec) [ -7573.2107] [ 1449] [depth= 1] . ( 23 sec) [ -7570.4121] [ 1450] [depth= 2] . ( 24 sec) [ -7569.7037] [ 1450] [depth= 5] . ( 24 sec) [ -7568.8496] [ 1450] [depth= 1] . ( 24 sec) [ -7567.6428] [ 1449] [depth= 4] . ( 24 sec) [ -7479.4596] [ 1424] [depth= 10] . ( 24 sec) [ -7476.4870] [ 1424] [depth= 1] . ( 24 sec) [ -7475.9763] [ 1424] [depth= 6] . ( 24 sec) [ -7475.2296] [ 1424] [depth= 5] . ( 25 sec) [ -7474.8188] [ 1424] [depth= 3] . ( 25 sec) [ -7470.7363] [ 1424] [depth= 1] . ( 25 sec) [ -7470.5833] [ 1424] [depth= 1] . ( 25 sec) [ -7441.1346] [ 1416] [depth= 5] . ( 25 sec) [ -7316.7591] [ 1416] [depth= 3] . ( 25 sec) [ -7316.7375] [ 1416] [depth= 1] . ( 25 sec) [ -7316.5039] [ 1416] [depth= 1] . ( 26 sec) [ -7316.2346] [ 1416] [depth= 1] . ( 26 sec) [ -7312.4946] [ 1416] [depth= 1] . ( 26 sec) [ -7311.7871] [ 1417] [depth= 2] . ( 26 sec) [ -7311.1020] [ 1417] [depth= 3] . ( 26 sec) [ -7296.0157] [ 1417] [depth= 2] . ( 26 sec) [ -7295.6292] [ 1417] [depth= 1] . ( 26 sec) [ -7287.8462] [ 1416] [depth= 3] . ( 27 sec) [ -7256.1868] [ 1413] [depth= 11] . ( 27 sec) [ -7243.3345] [ 1413] [depth= 1] . ( 27 sec) [ -7231.9650] [ 1413] [depth= 2] . ( 27 sec) [ -7231.7550] [ 1413] [depth= 4] . ( 27 sec) [ -7230.2652] [ 1413] [depth= 2] . ( 27 sec) [ -7220.9043] [ 1413] [depth= 10] . ( 27 sec) [ -7218.6585] [ 1413] [depth= 1] . ( 27 sec) [ -7191.4389] [ 1409] [depth= 1] . ( 28 sec) [ -7186.7779] [ 1409] [depth= 2] . ( 29 sec) [ -6985.1665] [Branch lengths ] . ( 31 sec) [ -6969.7346] [GTR parameters ] . ( 31 sec) [ -6948.8688] [Alpha ][ 0.339750] . ( 31 sec) [ -6947.3275] [ 1409] [depth= 1] . ( 32 sec) [ -6945.6713] [ 1386] [depth= 1] . ( 32 sec) [ -6938.6345] [ 1385] [depth= 3] . ( 32 sec) [ -6934.8772] [ 1385] [depth= 4] . ( 33 sec) [ -6930.2409] [ 1378] [depth= 1] . ( 33 sec) [ -6930.1842] [ 1378] [depth= 2] . ( 34 sec) [ -6926.3987] [ 1377] [depth= 2] . ( 35 sec) [ -6907.4671] [ 1370] [depth= 2] . ( 35 sec) [ -6892.8689] [ 1360] [depth= 5] . ( 35 sec) [ -6880.7718] [ 1354] [depth= 1] . ( 35 sec) [ -6880.7334] [ 1354] [depth= 2] . ( 35 sec) [ -6880.2405] [ 1354] [depth= 1] . ( 36 sec) [ -6880.1118] [ 1354] [depth= 4] . ( 37 sec) [ -6867.8748] [ 1338] [depth= 5] . ( 37 sec) [ -6867.7389] [ 1338] [depth= 1] . ( 37 sec) [ -6867.6958] [ 1339] [depth= 1] . ( 39 sec) [ -6821.5283] [ 1319] [depth= 10] . ( 39 sec) [ -6821.4983] [ 1319] [depth= 1] . ( 39 sec) [ -6785.9174] [ 1303] [depth= 5] . ( 39 sec) [ -6783.5071] [ 1303] [depth= 1] . ( 39 sec) [ -6770.8514] [ 1302] [depth= 2] . ( 39 sec) [ -6760.2831] [ 1302] [depth= 1] . ( 41 sec) [ -6759.2975] [ 1302] [depth= 1] . ( 44 sec) [ -6728.7892] [ 1282] [depth= 16] . ( 44 sec) [ -6727.2978] [ 1282] [depth= 2] . ( 44 sec) [ -6724.2781] [ 1282] [depth= 2] . ( 45 sec) [ -6693.7436] [ 1280] [depth= 3] . ( 46 sec) [ -6693.0509] [ 1280] [depth= 1] . ( 47 sec) [ -6691.0066] [ 1272] [depth= 1] . ( 47 sec) [ -6690.5633] [ 1272] [depth= 1] . ( 48 sec) [ -6687.2103] [ 1273] [depth= 2] . ( 48 sec) [ -6685.9435] [ 1273] [depth= 1] . ( 49 sec) [ -6682.9445] [ 1270] [depth= 4] . ( 49 sec) [ -6679.9587] [ 1270] [depth= 1] . ( 49 sec) [ -6679.7019] [ 1270] [depth= 4] . ( 49 sec) [ -6679.3767] [ 1270] [depth= 1] . ( 49 sec) [ -6679.3664] [ 1270] [depth= 1] . ( 50 sec) [ -6679.3480] [ 1270] [depth= 1] . ( 50 sec) [ -6679.3313] [ 1270] [depth= 2] . ( 50 sec) [ -6674.2148] [ 1270] [depth= 7] . ( 50 sec) [ -6674.1462] [ 1272] [depth= 1] . ( 51 sec) [ -6673.9940] [ 1271] [depth= 1] . ( 52 sec) [ -6660.5196] [ 1263] [depth= 4] . ( 52 sec) [ -6657.2733] [ 1261] [depth= 1] . ( 52 sec) [ -6657.0597] [ 1261] [depth= 3] . ( 52 sec) [ -6651.1568] [ 1261] [depth= 4] . ( 52 sec) [ -6651.0896] [ 1261] [depth= 1] . ( 53 sec) [ -6650.3899] [ 1261] [depth= 1] . ( 53 sec) [ -6647.2403] [ 1263] [depth= 1] . ( 53 sec) [ -6647.1427] [ 1263] [depth= 2] . ( 54 sec) [ -6646.3258] [ 1264] [depth= 1] . ( 54 sec) [ -6646.2768] [ 1264] [depth= 1] . ( 54 sec) [ -6644.2952] [ 1262] [depth= 3] . ( 54 sec) [ -6619.7676] [ 1257] [depth= 5] . ( 56 sec) [ -6619.6847] [ 1257] [depth= 2] . ( 56 sec) [ -6619.6641] [ 1257] [depth= 4] . ( 57 sec) [ -6619.3496] [ 1257] [depth= 1] . ( 58 sec) [ -6612.6688] [ 1255] [depth= 1] . ( 61 sec) [ -6612.5702] [ 1256] [depth= 2] . ( 61 sec) [ -6609.9064] [ 1255] [depth= 2] . ( 61 sec) [ -6609.4715] [ 1257] [depth= 2] . ( 61 sec) [ -6607.6067] [ 1257] [depth= 1] . ( 61 sec) [ -6607.1860] [ 1257] [depth= 2] . ( 62 sec) [ -6605.5515] [ 1277] [depth= 2] . ( 63 sec) [ -6589.9461] [ 1273] [depth= 1] . ( 63 sec) [ -6589.7078] [ 1272] [depth= 1] . ( 63 sec) [ -6589.2672] [ 1271] [depth= 2] . ( 64 sec) [ -6588.5786] [ 1270] [depth= 3] . ( 64 sec) [ -6586.5566] [ 1270] [depth= 1] . ( 65 sec) [ -6585.6423] [ 1270] [depth= 4] . ( 65 sec) [ -6585.6229] [ 1270] [depth= 2] . ( 67 sec) [ -6585.5958] [ 1270] [depth= 3] . ( 70 sec) [ -6580.8686] [ 1269] [depth= 3] . ( 71 sec) [ -6579.0479] [ 1271] [depth= 1] . ( 71 sec) [ -6578.9523] [ 1271] [depth= 1] . ( 71 sec) [ -6578.6696] [ 1271] [depth= 1] . ( 72 sec) [ -6578.6549] [ 1271] [depth= 1] . ( 73 sec) [ -6555.0824] [Branch lengths ] . ( 75 sec) [ -6554.6683] [GTR parameters ] . ( 75 sec) [ -6554.6584] [Alpha ][ 0.336751] . ( 79 sec) [ -6553.0082] [ 1271] [depth= 1] . ( 84 sec) [ -6552.9385] [ 1271] [depth= 1] . ( 84 sec) [ -6552.8887] [ 1271] [depth= 1] . ( 85 sec) [ -6550.2284] [ 1269] [depth= 1] . ( 96 sec) [ -6546.3742] [ 1260] [depth= 5] . ( 96 sec) [ -6546.2983] [ 1260] [depth= 5] . ( 96 sec) [ -6546.2711] [ 1260] [depth= 1] . ( 98 sec) [ -6546.0574] [ 1260] [depth= 1] . ( 99 sec) [ -6546.0033] [ 1260] [depth= 4] . ( 103 sec) [ -6545.9033] [ 1260] [depth= 1] . ( 105 sec) [ -6545.8646] [ 1260] [depth= 4] . ( 106 sec) [ -6545.6797] [ 1260] [depth= 1] . ( 110 sec) [ -6544.1836] [ 1259] [depth= 2] . ( 111 sec) [ -6543.5210] [ 1260] [depth= 1] . ( 113 sec) [ -6543.4738] [ 1262] [depth= 1] . ( 118 sec) [ -6543.4504] [ 1262] [depth= 4] . ( 120 sec) [ -6543.3727] [ 1262] [depth= 2] . ( 122 sec) [ -6543.1786] [ 1262] [depth= 1] . ( 125 sec) [ -6540.3475] [Branch lengths ] . ( 127 sec) [ -6540.3046] [GTR parameters ] . ( 127 sec) [ -6540.2982] [Alpha ][ 0.339100] . ( 143 sec) [ -6540.2792] [ 1262] [depth= 1] . ( 146 sec) [ -6540.2153] [ 1266] [depth= 2] . ( 163 sec) [ -6540.0634] [ 1264] [depth= 1] . ( 174 sec) [ -6539.8509] [Branch lengths ] . ( 175 sec) [ -6539.8423] [GTR parameters ] . ( 175 sec) [ -6539.8423] [Alpha ][ 0.339100] . ( 176 sec) [ -6539.8146] [ 1263] [depth= 1] . ( 176 sec) [ -6539.6956] [ 1264] [depth= 3] . ( 179 sec) [ -6539.6844] [ 1264] [depth= 2] . ( 203 sec) [ -6539.6472] [ 1264] [depth= 3] . ( 212 sec) [ -6539.1873] [ 1270] [depth= 1] . ( 232 sec) [ -6539.1729] [ 1270] [depth= 1] . ( 249 sec) [ -6539.0619] [ 1281] [depth= 1] . ( 256 sec) [ -6539.0425] [ 1275] [depth= 1] . ( 272 sec) [ -6538.6188] [Branch lengths ] . ( 274 sec) [ -6538.6100] [GTR parameters ] . ( 274 sec) [ -6538.6095] [Alpha ][ 0.339714] . ( 349 sec) [ -6538.5646] [ 1274] [depth= 3] . ( 372 sec) [ -6538.2821] [Branch lengths ] . ( 374 sec) [ -6538.2819] [GTR parameters ] . ( 374 sec) [ -6538.2810] [Alpha ][ 0.340610] . ( 374 sec) [ -6538.2810] [Topology ] . ( 376 sec) [ -6538.1592] [Topology ] . ( 377 sec) [ -6537.6567] [Topology ] . ( 379 sec) [ -6535.1369] [Topology ] . ( 381 sec) [ -6529.4574] [Topology ] . ( 383 sec) [ -6527.9616] [Topology ] . ( 385 sec) [ -6527.6902] [Topology ] . ( 386 sec) [ -6527.6804] [GTR parameters ] . ( 387 sec) [ -6527.6784] [Alpha ][ 0.341935] . ( 387 sec) [ -6527.6784] [Topology ] . ( 388 sec) [ -6527.6156] [Topology ] . ( 390 sec) [ -6527.5936] [Topology ] . ( 392 sec) [ -6527.5830] [Topology ] . ( 394 sec) [ -6527.5765] [Topology ] . ( 396 sec) [ -6527.5717] [Topology ] . ( 397 sec) [ -6527.5675] [Topology ] . ( 398 sec) [ -6527.5673] [GTR parameters ] . ( 398 sec) [ -6527.5661] [Alpha ][ 0.342990] . ( 398 sec) [ -6527.5661] [Topology ] . ( 400 sec) [ -6527.5626] [Topology ] . ( 402 sec) [ -6527.5610] [Topology ] . ( 403 sec) [ -6527.5603] [Topology ] . ( 404 sec) [ -6527.5602] [GTR parameters ] . ( 404 sec) [ -6527.5597] [Alpha ][ 0.343642] . ( 404 sec) [ -6527.5597] [Topology ] . ( 406 sec) [ -6527.5590] [Topology ] . ( 407 sec) [ -6527.5590] [GTR parameters ] . ( 407 sec) [ -6527.5590] [Alpha ][ 0.343642] . Checking for NNIs, optimizing five branches... . ( 423 sec) [ -6527.4910] [Topology ] . Checking for NNIs, optimizing five branches... . ( 439 sec) [ -6527.4303] [Topology ] . Checking for NNIs, optimizing five branches... . ( 454 sec) [ -6527.4284] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.428400. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -28133.4591] [GTR parameters ] . ( 5 sec) [ -27393.8260] [Alpha ][ 0.500960] . ( 6 sec) [ -26654.8945] [ 4077] [depth= 11] . ( 6 sec) [ -26274.4913] [ 4001] [depth= 11] . ( 6 sec) [ -25351.1489] [ 3995] [depth= 10] . ( 6 sec) [ -24992.4459] [ 3886] [depth= 1] . ( 6 sec) [ -24692.1792] [ 3880] [depth= 11] . ( 6 sec) [ -24685.8641] [ 3878] [depth= 2] . ( 6 sec) [ -24608.4831] [ 3801] [depth= 7] . ( 6 sec) [ -24101.4714] [ 3786] [depth= 5] . ( 7 sec) [ -23882.3816] [ 3761] [depth= 7] . ( 7 sec) [ -23716.9513] [ 3752] [depth= 6] . ( 7 sec) [ -23713.6485] [ 3752] [depth= 4] . ( 7 sec) [ -23637.3793] [ 3717] [depth= 18] . ( 7 sec) [ -23397.7321] [ 3680] [depth= 10] . ( 7 sec) [ -23357.2922] [ 3680] [depth= 1] . ( 7 sec) [ -21906.8060] [ 3619] [depth= 10] . ( 7 sec) [ -20903.8309] [ 3593] [depth= 6] . ( 8 sec) [ -20504.2285] [ 3574] [depth= 9] . ( 8 sec) [ -20488.9671] [ 3562] [depth= 1] . ( 8 sec) [ -20367.9362] [ 3530] [depth= 10] . ( 8 sec) [ -20145.8228] [ 3422] [depth= 4] . ( 8 sec) [ -19945.6286] [ 3417] [depth= 1] . ( 8 sec) [ -19814.3099] [ 3403] [depth= 1] . ( 8 sec) [ -19661.5685] [ 3327] [depth= 5] . ( 8 sec) [ -19318.9570] [ 3266] [depth= 13] . ( 9 sec) [ -18676.1272] [ 3175] [depth= 8] . ( 9 sec) [ -18513.7685] [ 3175] [depth= 1] . ( 9 sec) [ -18380.7069] [ 2993] [depth= 16] . ( 9 sec) [ -18327.9820] [ 2989] [depth= 2] . ( 9 sec) [ -18282.3566] [ 2941] [depth= 27] . ( 9 sec) [ -18203.2164] [ 2941] [depth= 1] . ( 9 sec) [ -18123.9506] [ 2925] [depth= 22] . ( 9 sec) [ -17768.1174] [ 2910] [depth= 1] . ( 10 sec) [ -17656.1290] [ 2902] [depth= 10] . ( 10 sec) [ -17484.1809] [ 2884] [depth= 5] . ( 10 sec) [ -17465.4671] [ 2883] [depth= 1] . ( 10 sec) [ -17375.2387] [ 2870] [depth= 15] . ( 10 sec) [ -17339.1189] [ 2864] [depth= 2] . ( 10 sec) [ -17337.6549] [ 2864] [depth= 1] . ( 10 sec) [ -17303.7616] [ 2855] [depth= 12] . ( 10 sec) [ -16992.1454] [ 2829] [depth= 8] . ( 11 sec) [ -16975.6347] [ 2829] [depth= 2] . ( 11 sec) [ -16616.4240] [ 2722] [depth= 11] . ( 11 sec) [ -16511.6853] [ 2714] [depth= 14] . ( 11 sec) [ -16401.1467] [ 2710] [depth= 6] . ( 11 sec) [ -16321.0600] [ 2687] [depth= 19] . ( 11 sec) [ -15485.0604] [ 2687] [depth= 11] . ( 11 sec) [ -15419.5550] [ 2670] [depth= 9] . ( 11 sec) [ -15304.5884] [ 2658] [depth= 9] . ( 12 sec) [ -15262.5269] [ 2655] [depth= 2] . ( 12 sec) [ -15216.1467] [ 2652] [depth= 3] . ( 12 sec) [ -15161.0512] [ 2640] [depth= 7] . ( 12 sec) [ -15136.7602] [ 2640] [depth= 1] . ( 12 sec) [ -14713.1646] [ 2622] [depth= 6] . ( 12 sec) [ -14484.9689] [ 2573] [depth= 10] . ( 12 sec) [ -14324.1279] [ 2563] [depth= 1] . ( 12 sec) [ -14300.2142] [ 2565] [depth= 1] . ( 12 sec) [ -14249.9091] [ 2551] [depth= 14] . ( 13 sec) [ -14181.8277] [ 2535] [depth= 15] . ( 13 sec) [ -14116.0522] [ 2531] [depth= 1] . ( 13 sec) [ -14070.0568] [ 2531] [depth= 20] . ( 13 sec) [ -14058.9426] [ 2524] [depth= 2] . ( 13 sec) [ -13981.9660] [ 2526] [depth= 6] . ( 13 sec) [ -13939.8300] [ 2527] [depth= 1] . ( 13 sec) [ -13355.4335] [ 2404] [depth= 9] . ( 13 sec) [ -13290.3566] [ 2387] [depth= 8] . ( 14 sec) [ -13217.1550] [ 2380] [depth= 3] . ( 14 sec) [ -13080.0530] [ 2380] [depth= 1] . ( 14 sec) [ -13065.8220] [ 2379] [depth= 2] . ( 14 sec) [ -12863.4638] [ 2345] [depth= 8] . ( 14 sec) [ -12650.6025] [ 2341] [depth= 2] . ( 14 sec) [ -12583.5214] [ 2334] [depth= 4] . ( 14 sec) [ -12512.4565] [ 2322] [depth= 3] . ( 14 sec) [ -12436.3763] [ 2325] [depth= 1] . ( 15 sec) [ -12330.2713] [ 2310] [depth= 19] . ( 15 sec) [ -12329.8232] [ 2311] [depth= 2] . ( 15 sec) [ -12214.9843] [ 2281] [depth= 13] . ( 15 sec) [ -12137.6058] [ 2272] [depth= 3] . ( 15 sec) [ -12108.4992] [ 2183] [depth= 5] . ( 15 sec) [ -12104.0059] [ 2182] [depth= 13] . ( 15 sec) [ -11998.2446] [ 2153] [depth= 14] . ( 15 sec) [ -11784.4343] [ 2143] [depth= 9] . ( 15 sec) [ -11783.2473] [ 2140] [depth= 1] . ( 16 sec) [ -11762.4756] [ 2137] [depth= 11] . ( 16 sec) [ -11681.3989] [ 2126] [depth= 12] . ( 16 sec) [ -11659.6468] [ 2121] [depth= 16] . ( 16 sec) [ -11641.5444] [ 2112] [depth= 6] . ( 16 sec) [ -11548.3261] [ 2088] [depth= 26] . ( 16 sec) [ -11547.5869] [ 2088] [depth= 2] . ( 16 sec) [ -11512.7399] [ 2088] [depth= 1] . ( 17 sec) [ -11500.1809] [ 2088] [depth= 1] . ( 17 sec) [ -11361.8099] [ 2072] [depth= 25] . ( 17 sec) [ -11324.8415] [ 2072] [depth= 12] . ( 17 sec) [ -11311.3202] [ 2072] [depth= 3] . ( 17 sec) [ -11234.6166] [ 2058] [depth= 9] . ( 17 sec) [ -11215.8438] [ 2058] [depth= 1] . ( 18 sec) [ -11189.0154] [ 2058] [depth= 1] . ( 18 sec) [ -11178.5223] [ 2058] [depth= 15] . ( 18 sec) [ -10797.2838] [ 2058] [depth= 17] . ( 18 sec) [ -10795.1520] [ 2058] [depth= 16] . ( 18 sec) [ -10777.6721] [ 2048] [depth= 17] . ( 19 sec) [ -10678.0053] [ 2015] [depth= 24] . ( 19 sec) [ -10666.5808] [ 2016] [depth= 10] . ( 19 sec) [ -10505.5473] [ 1987] [depth= 14] . ( 19 sec) [ -10500.0854] [ 1987] [depth= 21] . ( 19 sec) [ -10374.1522] [ 1931] [depth= 12] . ( 19 sec) [ -10311.9350] [ 1928] [depth= 1] . ( 19 sec) [ -10244.8979] [ 1912] [depth= 17] . ( 20 sec) [ -10233.9696] [ 1912] [depth= 1] . ( 20 sec) [ -10233.7884] [ 1912] [depth= 1] . ( 20 sec) [ -10194.5569] [ 1898] [depth= 6] . ( 20 sec) [ -10164.9960] [ 1874] [depth= 8] . ( 20 sec) [ -10163.5577] [ 1874] [depth= 3] . ( 20 sec) [ -9864.3269] [ 1810] [depth= 15] . ( 20 sec) [ -9851.0925] [ 1807] [depth= 3] . ( 21 sec) [ -9805.6884] [ 1801] [depth= 2] . ( 21 sec) [ -9739.2899] [ 1788] [depth= 15] . ( 21 sec) [ -9731.9603] [ 1790] [depth= 1] . ( 21 sec) [ -9644.6828] [ 1765] [depth= 4] . ( 21 sec) [ -9615.9551] [ 1737] [depth= 13] . ( 21 sec) [ -9602.2805] [ 1735] [depth= 1] . ( 21 sec) [ -9533.6068] [ 1734] [depth= 2] . ( 21 sec) [ -9530.3739] [ 1648] [depth= 12] . ( 22 sec) [ -9456.1862] [ 1632] [depth= 7] . ( 22 sec) [ -9330.8713] [ 1625] [depth= 4] . ( 22 sec) [ -9282.6281] [ 1628] [depth= 1] . ( 22 sec) [ -9270.7581] [ 1628] [depth= 14] . ( 22 sec) [ -9240.0080] [ 1625] [depth= 1] . ( 22 sec) [ -9229.2817] [ 1625] [depth= 1] . ( 22 sec) [ -9225.6145] [ 1625] [depth= 18] . ( 22 sec) [ -9220.9604] [ 1625] [depth= 14] . ( 23 sec) [ -9153.2872] [ 1621] [depth= 2] . ( 23 sec) [ -9131.9060] [ 1616] [depth= 3] . ( 23 sec) [ -9093.4388] [ 1616] [depth= 1] . ( 23 sec) [ -9069.0566] [ 1616] [depth= 1] . ( 23 sec) [ -9068.5374] [ 1616] [depth= 1] . ( 23 sec) [ -9050.9194] [ 1614] [depth= 1] . ( 23 sec) [ -9029.3746] [ 1615] [depth= 1] . ( 23 sec) [ -9026.4155] [ 1621] [depth= 5] . ( 23 sec) [ -9018.9647] [ 1621] [depth= 2] . ( 24 sec) [ -8938.4381] [ 1598] [depth= 2] . ( 24 sec) [ -8937.0928] [ 1598] [depth= 1] . ( 24 sec) [ -8933.6692] [ 1599] [depth= 3] . ( 24 sec) [ -8933.4501] [ 1599] [depth= 11] . ( 24 sec) [ -8925.5329] [ 1599] [depth= 2] . ( 24 sec) [ -8922.6699] [ 1599] [depth= 3] . ( 24 sec) [ -8921.9529] [ 1599] [depth= 1] . ( 25 sec) [ -8872.2249] [ 1586] [depth= 19] . ( 25 sec) [ -8840.4084] [ 1590] [depth= 2] . ( 25 sec) [ -8767.9989] [ 1588] [depth= 4] . ( 25 sec) [ -8751.7952] [ 1588] [depth= 3] . ( 25 sec) [ -8745.9185] [ 1588] [depth= 6] . ( 25 sec) [ -8738.6290] [ 1588] [depth= 1] . ( 25 sec) [ -8738.5427] [ 1588] [depth= 1] . ( 26 sec) [ -8651.5220] [ 1569] [depth= 11] . ( 26 sec) [ -8550.3724] [ 1547] [depth= 13] . ( 26 sec) [ -8537.7551] [ 1547] [depth= 2] . ( 27 sec) [ -8368.1091] [ 1545] [depth= 2] . ( 27 sec) [ -8367.3648] [ 1541] [depth= 1] . ( 27 sec) [ -8367.2159] [ 1542] [depth= 1] . ( 27 sec) [ -8367.1849] [ 1542] [depth= 1] . ( 27 sec) [ -8367.0782] [ 1546] [depth= 1] . ( 27 sec) [ -8349.1843] [ 1546] [depth= 1] . ( 27 sec) [ -8279.8246] [ 1540] [depth= 4] . ( 28 sec) [ -8102.6733] [ 1512] [depth= 10] . ( 28 sec) [ -8077.2489] [ 1509] [depth= 1] . ( 28 sec) [ -8022.9602] [ 1491] [depth= 1] . ( 28 sec) [ -8004.4059] [ 1487] [depth= 1] . ( 28 sec) [ -7990.7114] [ 1484] [depth= 10] . ( 29 sec) [ -7987.7498] [ 1484] [depth= 1] . ( 29 sec) [ -7982.8362] [ 1486] [depth= 1] . ( 29 sec) [ -7981.0653] [ 1487] [depth= 1] . ( 29 sec) [ -7979.3345] [ 1487] [depth= 1] . ( 29 sec) [ -7977.4218] [ 1488] [depth= 1] . ( 29 sec) [ -7913.7321] [ 1481] [depth= 9] . ( 30 sec) [ -7903.4214] [ 1481] [depth= 10] . ( 30 sec) [ -7846.7275] [ 1458] [depth= 4] . ( 30 sec) [ -7819.6157] [ 1449] [depth= 8] . ( 30 sec) [ -7649.5473] [ 1413] [depth= 8] . ( 30 sec) [ -7643.5492] [ 1413] [depth= 6] . ( 30 sec) [ -7587.1545] [ 1374] [depth= 16] . ( 30 sec) [ -7586.8966] [ 1375] [depth= 1] . ( 31 sec) [ -7557.4087] [ 1368] [depth= 3] . ( 31 sec) [ -7512.8588] [ 1362] [depth= 1] . ( 31 sec) [ -7456.8895] [ 1355] [depth= 19] . ( 31 sec) [ -7455.2458] [ 1355] [depth= 1] . ( 31 sec) [ -7455.1367] [ 1355] [depth= 1] . ( 31 sec) [ -7441.5072] [ 1355] [depth= 2] . ( 31 sec) [ -7441.1652] [ 1355] [depth= 1] . ( 31 sec) [ -7441.1400] [ 1355] [depth= 2] . ( 32 sec) [ -7432.1136] [ 1354] [depth= 5] . ( 33 sec) [ -7012.7462] [Branch lengths ] . ( 35 sec) [ -6994.0914] [GTR parameters ] . ( 35 sec) [ -6964.4893] [Alpha ][ 0.324396] . ( 35 sec) [ -6961.8733] [ 1357] [depth= 1] . ( 35 sec) [ -6960.1686] [ 1353] [depth= 1] . ( 36 sec) [ -6960.1398] [ 1353] [depth= 1] . ( 36 sec) [ -6940.6499] [ 1344] [depth= 15] . ( 36 sec) [ -6940.3830] [ 1344] [depth= 2] . ( 37 sec) [ -6879.7287] [ 1314] [depth= 6] . ( 37 sec) [ -6879.2461] [ 1314] [depth= 1] . ( 38 sec) [ -6877.8421] [ 1314] [depth= 1] . ( 38 sec) [ -6873.1993] [ 1310] [depth= 2] . ( 38 sec) [ -6870.4279] [ 1309] [depth= 2] . ( 39 sec) [ -6869.1545] [ 1309] [depth= 2] . ( 39 sec) [ -6869.0934] [ 1309] [depth= 1] . ( 39 sec) [ -6868.7312] [ 1309] [depth= 1] . ( 39 sec) [ -6868.6257] [ 1309] [depth= 1] . ( 39 sec) [ -6864.4355] [ 1307] [depth= 4] . ( 40 sec) [ -6858.6052] [ 1297] [depth= 5] . ( 40 sec) [ -6767.3045] [ 1321] [depth= 1] . ( 40 sec) [ -6766.4833] [ 1321] [depth= 1] . ( 40 sec) [ -6749.2492] [ 1297] [depth= 2] . ( 42 sec) [ -6748.4011] [ 1297] [depth= 1] . ( 42 sec) [ -6748.3904] [ 1297] [depth= 1] . ( 42 sec) [ -6748.1213] [ 1297] [depth= 2] . ( 42 sec) [ -6744.1867] [ 1297] [depth= 3] . ( 42 sec) [ -6715.9861] [ 1289] [depth= 2] . ( 43 sec) [ -6712.1137] [ 1288] [depth= 1] . ( 44 sec) [ -6712.0920] [ 1288] [depth= 1] . ( 44 sec) [ -6710.1624] [ 1287] [depth= 1] . ( 44 sec) [ -6662.4468] [ 1261] [depth= 11] . ( 44 sec) [ -6660.3433] [ 1261] [depth= 1] . ( 44 sec) [ -6660.2316] [ 1261] [depth= 2] . ( 45 sec) [ -6660.1060] [ 1261] [depth= 1] . ( 45 sec) [ -6645.9410] [ 1258] [depth= 1] . ( 45 sec) [ -6643.5194] [ 1259] [depth= 1] . ( 45 sec) [ -6643.3690] [ 1259] [depth= 1] . ( 46 sec) [ -6641.0638] [ 1258] [depth= 1] . ( 46 sec) [ -6624.8350] [ 1250] [depth= 6] . ( 46 sec) [ -6622.7272] [ 1253] [depth= 1] . ( 46 sec) [ -6622.1384] [ 1253] [depth= 2] . ( 47 sec) [ -6604.7943] [ 1253] [depth= 1] . ( 47 sec) [ -6604.7712] [ 1253] [depth= 1] . ( 48 sec) [ -6603.8479] [ 1253] [depth= 5] . ( 48 sec) [ -6599.7628] [ 1248] [depth= 2] . ( 49 sec) [ -6598.9809] [ 1251] [depth= 2] . ( 50 sec) [ -6595.2266] [ 1252] [depth= 2] . ( 51 sec) [ -6595.2152] [ 1252] [depth= 1] . ( 54 sec) [ -6593.9417] [ 1251] [depth= 1] . ( 54 sec) [ -6593.6642] [ 1250] [depth= 3] . ( 55 sec) [ -6592.6627] [ 1254] [depth= 2] . ( 56 sec) [ -6578.4447] [ 1253] [depth= 1] . ( 56 sec) [ -6578.2734] [ 1253] [depth= 3] . ( 58 sec) [ -6578.2184] [ 1253] [depth= 1] . ( 59 sec) [ -6578.1894] [ 1253] [depth= 1] . ( 61 sec) [ -6575.4323] [ 1254] [depth= 1] . ( 61 sec) [ -6575.4077] [ 1254] [depth= 1] . ( 62 sec) [ -6575.3943] [ 1254] [depth= 1] . ( 65 sec) [ -6574.6691] [ 1253] [depth= 1] . ( 65 sec) [ -6574.6319] [ 1252] [depth= 1] . ( 66 sec) [ -6573.0542] [ 1248] [depth= 4] . ( 67 sec) [ -6572.8582] [ 1253] [depth= 1] . ( 67 sec) [ -6571.5237] [ 1255] [depth= 2] . ( 68 sec) [ -6569.8507] [ 1257] [depth= 1] . ( 69 sec) [ -6567.7730] [ 1257] [depth= 1] . ( 70 sec) [ -6567.6026] [ 1257] [depth= 1] . ( 70 sec) [ -6567.5246] [ 1257] [depth= 1] . ( 72 sec) [ -6565.8506] [ 1255] [depth= 2] . ( 72 sec) [ -6561.5142] [ 1253] [depth= 1] . ( 72 sec) [ -6561.3740] [ 1246] [depth= 1] . ( 72 sec) [ -6560.7410] [ 1242] [depth= 2] . ( 73 sec) [ -6560.2786] [ 1242] [depth= 1] . ( 73 sec) [ -6560.1592] [ 1242] [depth= 2] . ( 74 sec) [ -6560.1415] [ 1242] [depth= 2] . ( 75 sec) [ -6547.7236] [Branch lengths ] . ( 76 sec) [ -6547.5213] [GTR parameters ] . ( 77 sec) [ -6547.4814] [Alpha ][ 0.330022] . ( 77 sec) [ -6545.3852] [ 1264] [depth= 5] . ( 83 sec) [ -6543.4438] [ 1259] [depth= 3] . ( 85 sec) [ -6543.4318] [ 1259] [depth= 4] . ( 86 sec) [ -6542.6030] [ 1259] [depth= 1] . ( 86 sec) [ -6542.5798] [ 1259] [depth= 6] . ( 87 sec) [ -6539.4452] [ 1258] [depth= 1] . ( 93 sec) [ -6538.7835] [ 1259] [depth= 1] . ( 95 sec) [ -6538.7663] [ 1259] [depth= 2] . ( 97 sec) [ -6538.7419] [ 1259] [depth= 2] . ( 98 sec) [ -6538.4455] [ 1259] [depth= 1] . ( 101 sec) [ -6537.8075] [ 1259] [depth= 1] . ( 117 sec) [ -6532.9041] [Branch lengths ] . ( 119 sec) [ -6532.8892] [GTR parameters ] . ( 119 sec) [ -6532.8468] [Alpha ][ 0.336018] . ( 119 sec) [ -6532.7659] [ 1263] [depth= 4] . ( 134 sec) [ -6532.7541] [ 1263] [depth= 1] . ( 144 sec) [ -6532.5686] [ 1263] [depth= 1] . ( 162 sec) [ -6530.6983] [Branch lengths ] . ( 163 sec) [ -6530.6802] [GTR parameters ] . ( 163 sec) [ -6530.6788] [Alpha ][ 0.337097] . ( 211 sec) [ -6530.0046] [Branch lengths ] . ( 211 sec) [ -6529.9747] [ 1261] [depth= 1] . ( 212 sec) [ -6529.4661] [ 1267] [depth= 1] . ( 220 sec) [ -6529.4456] [ 1261] [depth= 1] . ( 226 sec) [ -6529.3473] [ 1272] [depth= 1] . ( 279 sec) [ -6529.2755] [ 1272] [depth= 1] . ( 291 sec) [ -6529.2421] [ 1272] [depth= 1] . ( 307 sec) [ -6528.1251] [Branch lengths ] . ( 308 sec) [ -6528.1139] [GTR parameters ] . ( 308 sec) [ -6528.1033] [Alpha ][ 0.340161] . ( 323 sec) [ -6527.8987] [ 1274] [depth= 2] . ( 323 sec) [ -6527.8302] [ 1273] [depth= 3] . ( 402 sec) [ -6527.6498] [Branch lengths ] . ( 403 sec) [ -6527.6484] [GTR parameters ] . ( 403 sec) [ -6527.6470] [Alpha ][ 0.341229] . ( 403 sec) [ -6527.6470] [Topology ] . ( 405 sec) [ -6527.5811] [Topology ] . ( 407 sec) [ -6527.5436] [Topology ] . ( 409 sec) [ -6527.5165] [Topology ] . ( 410 sec) [ -6527.4960] [Topology ] . ( 412 sec) [ -6527.4795] [Topology ] . ( 414 sec) [ -6527.4659] [Topology ] . ( 414 sec) [ -6527.4656] [GTR parameters ] . ( 415 sec) [ -6527.4630] [Alpha ][ 0.342737] . ( 415 sec) [ -6527.4630] [Topology ] . ( 416 sec) [ -6527.4499] [Topology ] . ( 418 sec) [ -6527.4418] [Topology ] . ( 420 sec) [ -6527.4377] [Topology ] . ( 422 sec) [ -6527.4353] [Topology ] . ( 423 sec) [ -6527.4337] [Topology ] . ( 425 sec) [ -6527.4326] [Topology ] . ( 426 sec) [ -6527.4324] [GTR parameters ] . ( 426 sec) [ -6527.4315] [Alpha ][ 0.343635] . ( 426 sec) [ -6527.4315] [Topology ] . ( 428 sec) [ -6527.4303] [Topology ] . ( 430 sec) [ -6527.4296] [Topology ] . ( 430 sec) [ -6527.4296] [GTR parameters ] . ( 430 sec) [ -6527.4294] [Alpha ][ 0.343992] . ( 430 sec) [ -6527.4294] [Topology ] . ( 432 sec) [ -6527.4288] [Topology ] . ( 432 sec) [ -6527.4288] [GTR parameters ] . ( 433 sec) [ -6527.4288] [Alpha ][ 0.344336] . Checking for NNIs, optimizing five branches... . ( 448 sec) [ -6527.4284] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.428438. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -6941.4211] [GTR parameters ] . ( 3 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 3 sec) [ -6899.8793] [Topology ] . ( 5 sec) [ -6669.7753] [Topology ] . ( 7 sec) [ -6620.7511] [Topology ] . ( 9 sec) [ -6610.4959] [Topology ] . ( 12 sec) [ -6599.3357] [Topology ] . ( 13 sec) [ -6609.3373] [Topology ] . Moving backward . ( 14 sec) [ -6597.4246] [Topology ] . ( 16 sec) [ -6595.4764] [Topology ] . ( 18 sec) [ -6607.0982] [Topology ] . Moving backward . ( 18 sec) [ -6590.6067] [Topology ] . ( 23 sec) [ -6576.6676] [GTR parameters ] . ( 23 sec) [ -6570.7826] [Alpha ][ 0.397913] . ( 23 sec) [ -6570.7826] [Topology ] . ( 25 sec) [ -6564.4184] [Topology ] . ( 27 sec) [ -6560.3072] [Topology ] . ( 29 sec) [ -6558.6608] [Topology ] . ( 30 sec) [ -6554.1380] [Topology ] . ( 32 sec) [ -6555.8576] [Topology ] . Moving backward . ( 32 sec) [ -6547.5431] [Topology ] . ( 34 sec) [ -6546.5753] [Topology ] . ( 36 sec) [ -6545.8661] [Topology ] . ( 38 sec) [ -6545.4234] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -6544.7079] [Topology ] . ( 58 sec) [ -6544.4729] [GTR parameters ] . ( 58 sec) [ -6543.5007] [Alpha ][ 0.364367] . ( 58 sec) [ -6543.5007] [Topology ] . ( 60 sec) [ -6543.0475] [Topology ] . ( 62 sec) [ -6542.9259] [Topology ] . ( 64 sec) [ -6542.8611] [Topology ] . ( 66 sec) [ -6542.8201] [Topology ] . ( 67 sec) [ -6542.7894] [Topology ] . ( 69 sec) [ -6542.7655] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -6542.3276] [Topology ] . ( 87 sec) [ -6542.3035] [GTR parameters ] . ( 87 sec) [ -6542.1103] [Alpha ][ 0.350598] . ( 87 sec) [ -6542.1103] [Topology ] . ( 89 sec) [ -6541.8049] [Topology ] . ( 91 sec) [ -6541.7034] [Topology ] . ( 93 sec) [ -6541.6334] [Topology ] . ( 94 sec) [ -6541.6074] [Topology ] . ( 96 sec) [ -6541.5899] [Topology ] . ( 98 sec) [ -6541.5776] [Topology ] . ( 100 sec) [ -6541.5669] [Topology ] . ( 102 sec) [ -6541.5598] [Topology ] . Checking for NNIs, optimizing five branches... . ( 119 sec) [ -6541.0115] [Topology ] . ( 120 sec) [ -6541.0040] [GTR parameters ] . ( 120 sec) [ -6540.9757] [Alpha ][ 0.345346] . ( 120 sec) [ -6540.9757] [Topology ] . ( 122 sec) [ -6540.9545] [Topology ] . ( 124 sec) [ -6540.9485] [Topology ] . ( 125 sec) [ -6540.9454] [Topology ] . ( 127 sec) [ -6540.9436] [Topology ] . ( 129 sec) [ -6540.9428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 145 sec) [ -6540.7077] [Topology ] . ( 145 sec) [ -6540.7072] [GTR parameters ] . ( 145 sec) [ -6540.7023] [Alpha ][ 0.343170] . ( 146 sec) [ -6540.7023] [Topology ] . ( 147 sec) [ -6540.6981] [Topology ] . ( 149 sec) [ -6540.6973] [Topology ] . Checking for NNIs, optimizing five branches... . ( 164 sec) [ -6540.5640] [Topology ] . ( 165 sec) [ -6540.5638] [GTR parameters ] . ( 165 sec) [ -6540.5634] [Alpha ][ 0.342534] . ( 165 sec) [ -6540.5634] [Topology ] . ( 167 sec) [ -6540.5620] [Topology ] . ( 169 sec) [ -6540.5615] [Topology ] . Checking for NNIs, optimizing five branches... . ( 183 sec) [ -6540.5611] [Topology ] . ( 184 sec) [ -6540.5611] [GTR parameters ] . ( 184 sec) [ -6540.5610] [Alpha ][ 0.342191] . ( 184 sec) [ -6540.5610] [Topology ] . ( 186 sec) [ -6540.5602] [Topology ] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -6540.5596] [Topology ] . ( 201 sec) [ -6540.5596] [GTR parameters ] . ( 201 sec) [ -6540.5594] [Alpha ][ 0.341744] . ( 201 sec) [ -6540.5594] [Topology ] . ( 203 sec) [ -6540.5589] [Topology ] . Checking for NNIs, optimizing five branches... . ( 218 sec) [ -6540.5581] [Topology ] . ( 218 sec) [ -6540.5581] [GTR parameters ] . ( 219 sec) [ -6540.5581] [Alpha ][ 0.342085] . ( 219 sec) [ -6540.5581] [Topology ] . ( 220 sec) [ -6540.5569] [Topology ] . ( 222 sec) [ -6540.5564] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -6540.5564] [GTR parameters ] . ( 237 sec) [ -6540.5564] [Alpha ][ 0.342085] . ( 237 sec) [ -6540.5564] [Topology ] . ( 239 sec) [ -6540.5559] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 270 sec) [ -6941.4211] [GTR parameters ] . ( 271 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 271 sec) [ -6898.9682] [ 1256] [depth= 1] . ( 272 sec) [ -6898.6922] [ 1257] [depth= 1] . ( 272 sec) [ -6862.0853] [ 1254] [depth= 1] . ( 272 sec) [ -6859.2450] [ 1256] [depth= 1] . ( 272 sec) [ -6783.6394] [ 1270] [depth= 1] . ( 272 sec) [ -6781.8295] [ 1267] [depth= 1] . ( 272 sec) [ -6779.1598] [ 1269] [depth= 1] . ( 272 sec) [ -6778.4840] [ 1271] [depth= 1] . ( 273 sec) [ -6776.5967] [ 1271] [depth= 1] . ( 273 sec) [ -6776.3316] [ 1271] [depth= 1] . ( 273 sec) [ -6776.3003] [ 1271] [depth= 1] . ( 273 sec) [ -6773.2248] [ 1271] [depth= 1] . ( 273 sec) [ -6773.1883] [ 1271] [depth= 1] . ( 273 sec) [ -6770.0884] [ 1270] [depth= 4] . ( 273 sec) [ -6751.0122] [ 1268] [depth= 2] . ( 273 sec) [ -6744.9013] [ 1268] [depth= 3] . ( 274 sec) [ -6737.5008] [ 1267] [depth= 1] . ( 274 sec) [ -6735.8779] [ 1268] [depth= 1] . ( 274 sec) [ -6735.8203] [ 1267] [depth= 1] . ( 274 sec) [ -6735.4932] [ 1267] [depth= 1] . ( 274 sec) [ -6735.1440] [ 1267] [depth= 1] . ( 274 sec) [ -6734.9653] [ 1267] [depth= 1] . ( 275 sec) [ -6734.8702] [ 1267] [depth= 3] . ( 275 sec) [ -6734.7178] [ 1267] [depth= 1] . ( 276 sec) [ -6734.0950] [ 1268] [depth= 3] . ( 276 sec) [ -6733.2735] [ 1268] [depth= 3] . ( 277 sec) [ -6713.8518] [ 1266] [depth= 2] . ( 277 sec) [ -6710.1101] [ 1266] [depth= 2] . ( 277 sec) [ -6705.9172] [ 1266] [depth= 4] . ( 277 sec) [ -6705.4473] [ 1266] [depth= 2] . ( 279 sec) [ -6705.2219] [ 1266] [depth= 1] . ( 280 sec) [ -6697.9578] [ 1265] [depth= 2] . ( 280 sec) [ -6697.4188] [ 1265] [depth= 1] . ( 280 sec) [ -6695.8394] [ 1265] [depth= 2] . ( 280 sec) [ -6695.2354] [ 1265] [depth= 1] . ( 280 sec) [ -6695.1205] [ 1262] [depth= 1] . ( 281 sec) [ -6689.8948] [ 1265] [depth= 2] . ( 281 sec) [ -6687.6406] [ 1262] [depth= 1] . ( 281 sec) [ -6687.0497] [ 1265] [depth= 2] . ( 281 sec) [ -6682.7669] [ 1266] [depth= 2] . ( 282 sec) [ -6680.4923] [ 1268] [depth= 1] . ( 282 sec) [ -6678.4931] [ 1266] [depth= 1] . ( 282 sec) [ -6670.3979] [ 1265] [depth= 1] . ( 282 sec) [ -6669.2846] [ 1264] [depth= 1] . ( 282 sec) [ -6663.6149] [ 1259] [depth= 2] . ( 282 sec) [ -6657.6884] [ 1245] [depth= 4] . ( 283 sec) [ -6657.4562] [ 1246] [depth= 1] . ( 283 sec) [ -6655.2062] [ 1246] [depth= 1] . ( 283 sec) [ -6655.1025] [ 1246] [depth= 1] . ( 283 sec) [ -6654.8410] [ 1246] [depth= 1] . ( 284 sec) [ -6653.7394] [ 1246] [depth= 2] . ( 284 sec) [ -6653.4680] [ 1246] [depth= 1] . ( 284 sec) [ -6653.4560] [ 1246] [depth= 1] . ( 285 sec) [ -6651.9113] [ 1246] [depth= 2] . ( 285 sec) [ -6646.1350] [ 1244] [depth= 1] . ( 286 sec) [ -6640.3984] [ 1245] [depth= 2] . ( 287 sec) [ -6640.3662] [ 1245] [depth= 1] . ( 287 sec) [ -6639.7977] [ 1242] [depth= 1] . ( 287 sec) [ -6638.1003] [ 1242] [depth= 2] . ( 287 sec) [ -6635.8135] [ 1241] [depth= 1] . ( 288 sec) [ -6635.3102] [ 1242] [depth= 1] . ( 288 sec) [ -6632.8656] [ 1244] [depth= 2] . ( 288 sec) [ -6628.7609] [ 1245] [depth= 1] . ( 288 sec) [ -6628.2487] [ 1245] [depth= 1] . ( 289 sec) [ -6627.4075] [ 1245] [depth= 1] . ( 289 sec) [ -6621.8047] [ 1244] [depth= 1] . ( 289 sec) [ -6615.9361] [ 1244] [depth= 1] . ( 289 sec) [ -6613.4872] [ 1244] [depth= 1] . ( 289 sec) [ -6613.4705] [ 1244] [depth= 1] . ( 290 sec) [ -6612.8261] [ 1245] [depth= 1] . ( 290 sec) [ -6608.4187] [ 1243] [depth= 1] . ( 290 sec) [ -6608.2166] [ 1243] [depth= 1] . ( 291 sec) [ -6603.3294] [ 1243] [depth= 1] . ( 291 sec) [ -6602.9630] [ 1243] [depth= 2] . ( 291 sec) [ -6602.9450] [ 1243] [depth= 2] . ( 291 sec) [ -6602.6752] [ 1243] [depth= 2] . ( 291 sec) [ -6602.6639] [ 1243] [depth= 2] . ( 292 sec) [ -6602.4765] [ 1243] [depth= 1] . ( 293 sec) [ -6602.2208] [ 1243] [depth= 5] . ( 293 sec) [ -6602.0498] [ 1243] [depth= 1] . ( 293 sec) [ -6601.9435] [ 1243] [depth= 1] . ( 293 sec) [ -6601.8804] [ 1243] [depth= 1] . ( 294 sec) [ -6601.8551] [ 1243] [depth= 3] . ( 294 sec) [ -6601.8432] [ 1243] [depth= 3] . ( 294 sec) [ -6601.5227] [ 1243] [depth= 2] . ( 294 sec) [ -6601.4694] [ 1243] [depth= 3] . ( 294 sec) [ -6601.4555] [ 1243] [depth= 1] . ( 294 sec) [ -6601.3631] [ 1243] [depth= 1] . ( 297 sec) [ -6601.3487] [ 1243] [depth= 4] . ( 298 sec) [ -6601.3128] [ 1243] [depth= 4] . ( 298 sec) [ -6601.2918] [ 1243] [depth= 3] . ( 299 sec) [ -6601.2759] [ 1243] [depth= 4] . ( 301 sec) [ -6575.1063] [Branch lengths ] . ( 303 sec) [ -6567.9357] [GTR parameters ] . ( 303 sec) [ -6563.3657] [Alpha ][ 0.408141] . ( 304 sec) [ -6563.2053] [ 1240] [depth= 1] . ( 304 sec) [ -6557.8033] [ 1263] [depth= 6] . ( 306 sec) [ -6555.4393] [ 1262] [depth= 2] . ( 306 sec) [ -6554.9281] [ 1262] [depth= 1] . ( 306 sec) [ -6554.7742] [ 1262] [depth= 1] . ( 308 sec) [ -6549.2579] [ 1267] [depth= 1] . ( 310 sec) [ -6549.0624] [ 1267] [depth= 4] . ( 313 sec) [ -6548.3324] [ 1267] [depth= 4] . ( 314 sec) [ -6547.7906] [ 1267] [depth= 1] . ( 314 sec) [ -6546.3981] [ 1262] [depth= 6] . ( 315 sec) [ -6544.4423] [ 1263] [depth= 2] . ( 317 sec) [ -6543.0174] [ 1263] [depth= 2] . ( 318 sec) [ -6540.8938] [ 1263] [depth= 1] . ( 318 sec) [ -6540.8699] [ 1263] [depth= 1] . ( 319 sec) [ -6540.3401] [ 1265] [depth= 1] . ( 329 sec) [ -6540.1386] [ 1265] [depth= 1] . ( 330 sec) [ -6540.1026] [ 1265] [depth= 1] . ( 332 sec) [ -6540.0852] [ 1266] [depth= 1] . ( 333 sec) [ -6540.0749] [ 1266] [depth= 5] . ( 341 sec) [ -6540.0588] [ 1266] [depth= 5] . ( 347 sec) [ -6533.1237] [Branch lengths ] . ( 349 sec) [ -6532.5713] [GTR parameters ] . ( 349 sec) [ -6531.6534] [Alpha ][ 0.374202] . ( 351 sec) [ -6531.4907] [ 1267] [depth= 5] . ( 351 sec) [ -6530.9669] [ 1265] [depth= 1] . ( 355 sec) [ -6530.8641] [ 1265] [depth= 5] . ( 365 sec) [ -6530.6974] [ 1264] [depth= 1] . ( 391 sec) [ -6529.1374] [Branch lengths ] . ( 393 sec) [ -6529.0886] [GTR parameters ] . ( 393 sec) [ -6528.8876] [Alpha ][ 0.359592] . ( 395 sec) [ -6528.8344] [ 1264] [depth= 1] . ( 411 sec) [ -6528.8241] [ 1264] [depth= 1] . ( 421 sec) [ -6528.7659] [ 1264] [depth= 1] . ( 422 sec) [ -6528.7502] [ 1264] [depth= 1] . ( 440 sec) [ -6528.2640] [Branch lengths ] . ( 441 sec) [ -6528.2564] [GTR parameters ] . ( 441 sec) [ -6528.2091] [Alpha ][ 0.352922] . ( 445 sec) [ -6528.1898] [ 1264] [depth= 1] . ( 446 sec) [ -6528.0575] [ 1274] [depth= 1] . ( 526 sec) [ -6527.8437] [Branch lengths ] . ( 528 sec) [ -6527.8415] [GTR parameters ] . ( 528 sec) [ -6527.8248] [Alpha ][ 0.348823] . ( 528 sec) [ -6527.8248] [Topology ] . ( 530 sec) [ -6527.7609] [Topology ] . ( 531 sec) [ -6527.7334] [Topology ] . ( 533 sec) [ -6527.7165] [Topology ] . ( 535 sec) [ -6527.7055] [Topology ] . ( 537 sec) [ -6527.6980] [Topology ] . ( 539 sec) [ -6527.6930] [Topology ] . ( 540 sec) [ -6527.6922] [GTR parameters ] . ( 540 sec) [ -6527.6855] [Alpha ][ 0.346244] . ( 540 sec) [ -6527.6855] [Topology ] . ( 542 sec) [ -6527.6787] [Topology ] . ( 544 sec) [ -6527.6756] [Topology ] . ( 546 sec) [ -6527.6736] [Topology ] . ( 548 sec) [ -6527.6722] [Topology ] . ( 550 sec) [ -6527.6713] [Topology ] . ( 550 sec) [ -6527.6711] [GTR parameters ] . ( 550 sec) [ -6527.6696] [Alpha ][ 0.345026] . ( 550 sec) [ -6527.6696] [Topology ] . ( 552 sec) [ -6527.6682] [Topology ] . ( 554 sec) [ -6527.6676] [Topology ] . ( 555 sec) [ -6527.6676] [GTR parameters ] . ( 555 sec) [ -6527.6674] [Alpha ][ 0.344575] . ( 555 sec) [ -6527.6674] [Topology ] . ( 557 sec) [ -6527.6667] [Topology ] . ( 557 sec) [ -6527.6667] [GTR parameters ] . ( 558 sec) [ -6527.6667] [Alpha ][ 0.344575] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6540.555880 . Log likelihood obtained after SPR moves : -6527.666726 . Log likelihood of the current tree: -6527.666726. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Best log likelihood : -6527.428400 . Time used 0h9m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2758.98user 0.00system 46:31.26elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps