.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2655_50x872_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 374 patterns found. (out of a total of 872 sites) . 550 sites without polymorphism (63.07%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 10Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17335.2550] [GTR parameters ] . ( 0 sec) [ -16906.0831] [Alpha ][ 0.500960] . ( 0 sec) [ -16427.6917] [ 2540] [depth= 8] . ( 0 sec) [ -16186.3392] [ 2530] [depth= 2] . ( 1 sec) [ -16114.2791] [ 2502] [depth= 5] . ( 1 sec) [ -16063.0610] [ 2502] [depth= 2] . ( 1 sec) [ -16040.8656] [ 2493] [depth= 1] . ( 1 sec) [ -15998.4114] [ 2492] [depth= 1] . ( 1 sec) [ -15620.2960] [ 2445] [depth= 8] . ( 1 sec) [ -15611.2417] [ 2438] [depth= 3] . ( 1 sec) [ -15347.6864] [ 2375] [depth= 13] . ( 1 sec) [ -14954.7423] [ 2374] [depth= 1] . ( 1 sec) [ -13509.9791] [ 2368] [depth= 2] . ( 1 sec) [ -13356.9904] [ 2366] [depth= 1] . ( 1 sec) [ -13253.5962] [ 2361] [depth= 1] . ( 1 sec) [ -13204.3275] [ 2349] [depth= 17] . ( 1 sec) [ -12979.3802] [ 2302] [depth= 1] . ( 1 sec) [ -12975.8761] [ 2306] [depth= 1] . ( 1 sec) [ -12971.1300] [ 2302] [depth= 1] . ( 1 sec) [ -12865.2500] [ 2289] [depth= 19] . ( 1 sec) [ -12451.7993] [ 2215] [depth= 9] . ( 1 sec) [ -12394.5854] [ 2187] [depth= 2] . ( 1 sec) [ -12303.6678] [ 2185] [depth= 14] . ( 1 sec) [ -12276.4786] [ 2188] [depth= 1] . ( 1 sec) [ -12065.3352] [ 2166] [depth= 3] . ( 1 sec) [ -11949.1946] [ 2145] [depth= 19] . ( 2 sec) [ -11873.4548] [ 2138] [depth= 5] . ( 2 sec) [ -11819.5816] [ 2139] [depth= 19] . ( 2 sec) [ -11792.2216] [ 2126] [depth= 11] . ( 2 sec) [ -11776.9635] [ 2123] [depth= 1] . ( 2 sec) [ -11684.8925] [ 2074] [depth= 5] . ( 2 sec) [ -11580.3997] [ 2054] [depth= 1] . ( 2 sec) [ -11304.0553] [ 2013] [depth= 10] . ( 2 sec) [ -11159.1199] [ 1972] [depth= 12] . ( 2 sec) [ -10950.5281] [ 1925] [depth= 1] . ( 2 sec) [ -10918.0428] [ 1926] [depth= 1] . ( 2 sec) [ -10624.6158] [ 1894] [depth= 22] . ( 2 sec) [ -10422.7300] [ 1856] [depth= 4] . ( 2 sec) [ -10230.0837] [ 1836] [depth= 16] . ( 2 sec) [ -10215.0297] [ 1838] [depth= 3] . ( 2 sec) [ -9972.7863] [ 1802] [depth= 4] . ( 2 sec) [ -9815.2490] [ 1759] [depth= 20] . ( 2 sec) [ -9788.9435] [ 1757] [depth= 2] . ( 2 sec) [ -9743.4911] [ 1736] [depth= 19] . ( 2 sec) [ -9638.6893] [ 1711] [depth= 18] . ( 2 sec) [ -9580.0583] [ 1691] [depth= 23] . ( 3 sec) [ -9547.9803] [ 1687] [depth= 1] . ( 3 sec) [ -9494.5323] [ 1686] [depth= 1] . ( 3 sec) [ -9302.6144] [ 1651] [depth= 17] . ( 3 sec) [ -9110.5620] [ 1622] [depth= 16] . ( 3 sec) [ -8985.5402] [ 1583] [depth= 18] . ( 3 sec) [ -8843.0306] [ 1572] [depth= 17] . ( 3 sec) [ -8837.8579] [ 1571] [depth= 1] . ( 3 sec) [ -8837.6376] [ 1575] [depth= 1] . ( 3 sec) [ -8831.1756] [ 1575] [depth= 1] . ( 3 sec) [ -8758.5242] [ 1579] [depth= 1] . ( 3 sec) [ -8755.0856] [ 1581] [depth= 1] . ( 3 sec) [ -8735.4060] [ 1580] [depth= 18] . ( 3 sec) [ -8650.2517] [ 1563] [depth= 7] . ( 3 sec) [ -8649.4950] [ 1567] [depth= 1] . ( 3 sec) [ -8498.2293] [ 1521] [depth= 11] . ( 3 sec) [ -8479.6627] [ 1520] [depth= 1] . ( 3 sec) [ -8471.8947] [ 1524] [depth= 3] . ( 3 sec) [ -8457.2555] [ 1522] [depth= 2] . ( 4 sec) [ -8388.0416] [ 1519] [depth= 2] . ( 4 sec) [ -8280.8545] [ 1519] [depth= 1] . ( 4 sec) [ -8231.3817] [ 1511] [depth= 11] . ( 4 sec) [ -7892.8104] [ 1416] [depth= 12] . ( 4 sec) [ -7792.4095] [ 1377] [depth= 5] . ( 4 sec) [ -7736.9972] [ 1378] [depth= 1] . ( 4 sec) [ -7714.1800] [ 1377] [depth= 1] . ( 4 sec) [ -7487.2696] [ 1303] [depth= 10] . ( 4 sec) [ -7459.7816] [ 1294] [depth= 2] . ( 4 sec) [ -7455.6222] [ 1295] [depth= 1] . ( 4 sec) [ -7444.0787] [ 1294] [depth= 6] . ( 4 sec) [ -7443.4812] [ 1295] [depth= 1] . ( 4 sec) [ -7403.9383] [ 1281] [depth= 4] . ( 4 sec) [ -7398.8322] [ 1282] [depth= 1] . ( 4 sec) [ -7369.2341] [ 1269] [depth= 2] . ( 4 sec) [ -7367.2436] [ 1268] [depth= 1] . ( 5 sec) [ -7333.9044] [ 1257] [depth= 6] . ( 5 sec) [ -7327.7410] [ 1255] [depth= 1] . ( 5 sec) [ -7315.9317] [ 1252] [depth= 3] . ( 5 sec) [ -7301.6531] [ 1249] [depth= 3] . ( 5 sec) [ -7270.3106] [ 1250] [depth= 3] . ( 5 sec) [ -7252.6949] [ 1256] [depth= 2] . ( 5 sec) [ -7242.4938] [ 1250] [depth= 2] . ( 5 sec) [ -7224.0858] [ 1246] [depth= 1] . ( 5 sec) [ -7195.4555] [ 1244] [depth= 2] . ( 5 sec) [ -7183.3859] [ 1246] [depth= 1] . ( 5 sec) [ -7165.2464] [ 1246] [depth= 1] . ( 5 sec) [ -7145.6843] [ 1243] [depth= 3] . ( 5 sec) [ -7140.3597] [ 1243] [depth= 2] . ( 6 sec) [ -7140.1379] [ 1243] [depth= 1] . ( 6 sec) [ -7139.3786] [ 1244] [depth= 2] . ( 6 sec) [ -7089.9503] [ 1209] [depth= 5] . ( 6 sec) [ -7072.0191] [ 1215] [depth= 2] . ( 6 sec) [ -7071.8672] [ 1218] [depth= 1] . ( 6 sec) [ -7066.5368] [ 1215] [depth= 1] . ( 6 sec) [ -7064.8981] [ 1214] [depth= 4] . ( 6 sec) [ -7064.0290] [ 1214] [depth= 1] . ( 6 sec) [ -7062.4206] [ 1214] [depth= 2] . ( 6 sec) [ -7060.2348] [ 1214] [depth= 1] . ( 7 sec) [ -6948.9279] [Branch lengths ] . ( 9 sec) [ -6752.3253] [GTR parameters ] . ( 9 sec) [ -6685.8255] [Alpha ][ 0.250961] . ( 9 sec) [ -6682.7985] [ 1212] [depth= 1] . ( 9 sec) [ -6676.6012] [ 1206] [depth= 1] . ( 9 sec) [ -6672.6407] [ 1202] [depth= 1] . ( 9 sec) [ -6672.2769] [ 1187] [depth= 4] . ( 9 sec) [ -6600.2236] [ 1156] [depth= 8] . ( 9 sec) [ -6599.3928] [ 1155] [depth= 3] . ( 10 sec) [ -6597.6728] [ 1151] [depth= 1] . ( 10 sec) [ -6595.7181] [ 1150] [depth= 2] . ( 10 sec) [ -6595.5831] [ 1152] [depth= 1] . ( 10 sec) [ -6595.5670] [ 1152] [depth= 2] . ( 10 sec) [ -6594.8845] [ 1153] [depth= 1] . ( 11 sec) [ -6592.3442] [ 1146] [depth= 1] . ( 11 sec) [ -6585.4253] [ 1142] [depth= 2] . ( 11 sec) [ -6585.2115] [ 1140] [depth= 2] . ( 11 sec) [ -6583.0063] [ 1140] [depth= 1] . ( 11 sec) [ -6569.5658] [ 1128] [depth= 5] . ( 11 sec) [ -6568.3665] [ 1130] [depth= 1] . ( 11 sec) [ -6566.9999] [ 1128] [depth= 1] . ( 11 sec) [ -6566.9848] [ 1132] [depth= 1] . ( 12 sec) [ -6565.5921] [ 1132] [depth= 1] . ( 12 sec) [ -6557.6364] [ 1129] [depth= 1] . ( 12 sec) [ -6555.6693] [ 1127] [depth= 2] . ( 12 sec) [ -6551.2100] [ 1129] [depth= 1] . ( 13 sec) [ -6549.2227] [ 1132] [depth= 1] . ( 14 sec) [ -6548.7739] [ 1131] [depth= 1] . ( 14 sec) [ -6543.7987] [ 1129] [depth= 1] . ( 14 sec) [ -6533.9887] [ 1125] [depth= 2] . ( 15 sec) [ -6522.1917] [Branch lengths ] . ( 17 sec) [ -6520.8615] [GTR parameters ] . ( 17 sec) [ -6520.4483] [Alpha ][ 0.236850] . ( 18 sec) [ -6516.0391] [ 1122] [depth= 1] . ( 18 sec) [ -6511.2033] [ 1118] [depth= 1] . ( 20 sec) [ -6510.5807] [ 1114] [depth= 1] . ( 20 sec) [ -6510.3343] [ 1112] [depth= 1] . ( 24 sec) [ -6509.3419] [Branch lengths ] . ( 25 sec) [ -6509.3112] [GTR parameters ] . ( 25 sec) [ -6509.3105] [Alpha ][ 0.236221] . ( 31 sec) [ -6509.2438] [Branch lengths ] . ( 61 sec) [ -6509.2396] [Branch lengths ] . ( 61 sec) [ -6509.2396] [Topology ] . ( 62 sec) [ -6509.2394] [Topology ] . ( 63 sec) [ -6509.2390] [GTR parameters ] . ( 63 sec) [ -6509.2384] [Alpha ][ 0.235645] . ( 63 sec) [ -6509.2384] [Topology ] . ( 64 sec) [ -6509.2381] [Topology ] . ( 64 sec) [ -6509.2381] [GTR parameters ] . ( 64 sec) [ -6509.2381] [Alpha ][ 0.235645] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6509.238146. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17880.1010] [GTR parameters ] . ( 1 sec) [ -17368.1295] [Alpha ][ 0.500960] . ( 1 sec) [ -17050.9617] [ 2821] [depth= 6] . ( 1 sec) [ -16925.0170] [ 2806] [depth= 5] . ( 1 sec) [ -16821.7763] [ 2789] [depth= 1] . ( 1 sec) [ -16785.0064] [ 2780] [depth= 9] . ( 1 sec) [ -16555.0752] [ 2724] [depth= 5] . ( 1 sec) [ -16543.4854] [ 2725] [depth= 1] . ( 1 sec) [ -16374.3169] [ 2716] [depth= 1] . ( 2 sec) [ -16138.5341] [ 2711] [depth= 2] . ( 2 sec) [ -15733.0242] [ 2661] [depth= 2] . ( 2 sec) [ -15511.8909] [ 2660] [depth= 10] . ( 2 sec) [ -15370.0607] [ 2626] [depth= 2] . ( 2 sec) [ -15199.2071] [ 2610] [depth= 8] . ( 2 sec) [ -15106.4205] [ 2579] [depth= 1] . ( 2 sec) [ -14869.2606] [ 2582] [depth= 7] . ( 2 sec) [ -14438.5805] [ 2576] [depth= 2] . ( 2 sec) [ -14416.1971] [ 2574] [depth= 4] . ( 2 sec) [ -14211.4598] [ 2538] [depth= 7] . ( 2 sec) [ -14179.9462] [ 2536] [depth= 1] . ( 2 sec) [ -14146.1724] [ 2516] [depth= 13] . ( 2 sec) [ -13991.9935] [ 2519] [depth= 3] . ( 2 sec) [ -13952.1973] [ 2516] [depth= 1] . ( 2 sec) [ -13831.5669] [ 2504] [depth= 1] . ( 2 sec) [ -13810.0229] [ 2491] [depth= 1] . ( 2 sec) [ -13771.1222] [ 2485] [depth= 3] . ( 2 sec) [ -13112.2796] [ 2421] [depth= 13] . ( 2 sec) [ -12604.5751] [ 2337] [depth= 9] . ( 2 sec) [ -12476.2866] [ 2340] [depth= 5] . ( 2 sec) [ -12415.4653] [ 2333] [depth= 8] . ( 3 sec) [ -12365.5179] [ 2333] [depth= 1] . ( 3 sec) [ -12232.8946] [ 2310] [depth= 6] . ( 3 sec) [ -12094.0865] [ 2272] [depth= 1] . ( 3 sec) [ -12090.4618] [ 2256] [depth= 9] . ( 3 sec) [ -11965.7564] [ 2267] [depth= 11] . ( 3 sec) [ -11929.2138] [ 2246] [depth= 2] . ( 3 sec) [ -11899.4024] [ 2244] [depth= 1] . ( 3 sec) [ -11792.6163] [ 2220] [depth= 11] . ( 3 sec) [ -11786.8251] [ 2223] [depth= 2] . ( 3 sec) [ -11752.9750] [ 2222] [depth= 17] . ( 3 sec) [ -11426.6286] [ 2167] [depth= 9] . ( 3 sec) [ -11367.4007] [ 2156] [depth= 1] . ( 3 sec) [ -11339.8301] [ 2153] [depth= 1] . ( 3 sec) [ -11258.0287] [ 2150] [depth= 1] . ( 3 sec) [ -11119.6256] [ 2114] [depth= 1] . ( 3 sec) [ -11117.7385] [ 2110] [depth= 1] . ( 3 sec) [ -10967.5204] [ 2112] [depth= 17] . ( 3 sec) [ -10873.7606] [ 2113] [depth= 3] . ( 3 sec) [ -10868.6759] [ 2109] [depth= 4] . ( 3 sec) [ -10837.5892] [ 2104] [depth= 17] . ( 4 sec) [ -10721.6857] [ 2073] [depth= 15] . ( 4 sec) [ -10503.7429] [ 2039] [depth= 11] . ( 4 sec) [ -10493.3206] [ 2037] [depth= 1] . ( 4 sec) [ -10449.8032] [ 2020] [depth= 1] . ( 4 sec) [ -10426.5720] [ 2020] [depth= 1] . ( 4 sec) [ -10284.3840] [ 2002] [depth= 16] . ( 4 sec) [ -10273.3953] [ 1997] [depth= 1] . ( 4 sec) [ -10253.5404] [ 1994] [depth= 9] . ( 4 sec) [ -10226.8271] [ 1964] [depth= 4] . ( 4 sec) [ -10192.5379] [ 1953] [depth= 8] . ( 4 sec) [ -10070.7741] [ 1953] [depth= 2] . ( 4 sec) [ -9968.9361] [ 1930] [depth= 8] . ( 4 sec) [ -9774.2493] [ 1885] [depth= 4] . ( 4 sec) [ -9743.5112] [ 1872] [depth= 9] . ( 4 sec) [ -9741.0729] [ 1868] [depth= 1] . ( 4 sec) [ -9614.9436] [ 1864] [depth= 6] . ( 4 sec) [ -9544.9486] [ 1861] [depth= 12] . ( 4 sec) [ -9452.9462] [ 1828] [depth= 3] . ( 4 sec) [ -9437.5715] [ 1832] [depth= 3] . ( 4 sec) [ -9397.2266] [ 1842] [depth= 1] . ( 5 sec) [ -9193.1691] [ 1778] [depth= 16] . ( 5 sec) [ -9192.7940] [ 1772] [depth= 3] . ( 5 sec) [ -9156.4352] [ 1750] [depth= 10] . ( 5 sec) [ -9006.7599] [ 1739] [depth= 12] . ( 5 sec) [ -8932.7444] [ 1715] [depth= 1] . ( 5 sec) [ -8780.9444] [ 1651] [depth= 9] . ( 5 sec) [ -8743.2199] [ 1648] [depth= 19] . ( 5 sec) [ -8724.7617] [ 1645] [depth= 1] . ( 5 sec) [ -8670.2063] [ 1627] [depth= 15] . ( 5 sec) [ -8657.6822] [ 1625] [depth= 1] . ( 5 sec) [ -8637.7076] [ 1610] [depth= 17] . ( 5 sec) [ -8636.1718] [ 1605] [depth= 12] . ( 5 sec) [ -8613.1572] [ 1606] [depth= 3] . ( 5 sec) [ -8526.4388] [ 1556] [depth= 4] . ( 5 sec) [ -8504.5398] [ 1548] [depth= 3] . ( 5 sec) [ -8431.1595] [ 1519] [depth= 13] . ( 6 sec) [ -8359.4274] [ 1517] [depth= 1] . ( 6 sec) [ -8332.0465] [ 1514] [depth= 1] . ( 6 sec) [ -8331.7518] [ 1519] [depth= 7] . ( 6 sec) [ -8303.8467] [ 1516] [depth= 1] . ( 6 sec) [ -8190.1737] [ 1482] [depth= 1] . ( 6 sec) [ -8143.4229] [ 1458] [depth= 1] . ( 6 sec) [ -8083.5035] [ 1448] [depth= 2] . ( 6 sec) [ -8035.0120] [ 1424] [depth= 2] . ( 6 sec) [ -8032.3243] [ 1428] [depth= 1] . ( 6 sec) [ -7964.4887] [ 1427] [depth= 2] . ( 6 sec) [ -7909.8258] [ 1397] [depth= 2] . ( 6 sec) [ -7857.0294] [ 1406] [depth= 1] . ( 6 sec) [ -7718.5483] [ 1383] [depth= 2] . ( 6 sec) [ -7717.1356] [ 1387] [depth= 1] . ( 6 sec) [ -7676.1098] [ 1386] [depth= 1] . ( 6 sec) [ -7674.9248] [ 1387] [depth= 1] . ( 6 sec) [ -7673.3257] [ 1387] [depth= 2] . ( 7 sec) [ -7659.8681] [ 1387] [depth= 2] . ( 7 sec) [ -7612.1588] [ 1376] [depth= 1] . ( 7 sec) [ -7597.7436] [ 1367] [depth= 4] . ( 7 sec) [ -7545.6411] [ 1349] [depth= 1] . ( 7 sec) [ -7505.3473] [ 1332] [depth= 2] . ( 7 sec) [ -7497.1599] [ 1331] [depth= 1] . ( 7 sec) [ -7326.5169] [Branch lengths ] . ( 9 sec) [ -7099.5406] [GTR parameters ] . ( 10 sec) [ -7011.3349] [Alpha ][ 0.250961] . ( 10 sec) [ -7001.1310] [ 1306] [depth= 6] . ( 10 sec) [ -6992.8426] [ 1279] [depth= 4] . ( 10 sec) [ -6985.9630] [ 1277] [depth= 1] . ( 10 sec) [ -6909.4491] [ 1244] [depth= 4] . ( 10 sec) [ -6892.8099] [ 1243] [depth= 3] . ( 10 sec) [ -6797.7406] [ 1193] [depth= 9] . ( 10 sec) [ -6796.0654] [ 1194] [depth= 1] . ( 10 sec) [ -6739.1579] [ 1162] [depth= 4] . ( 10 sec) [ -6726.3885] [ 1159] [depth= 1] . ( 10 sec) [ -6724.0853] [ 1160] [depth= 1] . ( 10 sec) [ -6682.9787] [ 1148] [depth= 2] . ( 10 sec) [ -6671.8165] [ 1144] [depth= 2] . ( 11 sec) [ -6655.3971] [ 1142] [depth= 1] . ( 11 sec) [ -6653.6039] [ 1141] [depth= 2] . ( 11 sec) [ -6652.9875] [ 1140] [depth= 2] . ( 11 sec) [ -6633.0678] [ 1135] [depth= 1] . ( 11 sec) [ -6633.0314] [ 1134] [depth= 1] . ( 11 sec) [ -6630.3407] [ 1139] [depth= 1] . ( 11 sec) [ -6611.7495] [ 1133] [depth= 1] . ( 11 sec) [ -6593.8628] [ 1127] [depth= 1] . ( 12 sec) [ -6587.8783] [ 1123] [depth= 1] . ( 12 sec) [ -6587.4413] [ 1125] [depth= 1] . ( 12 sec) [ -6584.6855] [ 1126] [depth= 1] . ( 12 sec) [ -6583.5704] [ 1124] [depth= 1] . ( 13 sec) [ -6576.5845] [ 1120] [depth= 1] . ( 13 sec) [ -6552.8621] [ 1114] [depth= 5] . ( 13 sec) [ -6550.3380] [ 1110] [depth= 1] . ( 13 sec) [ -6548.7276] [ 1109] [depth= 1] . ( 13 sec) [ -6545.9830] [ 1110] [depth= 1] . ( 14 sec) [ -6545.1273] [ 1110] [depth= 1] . ( 14 sec) [ -6545.0222] [ 1110] [depth= 1] . ( 14 sec) [ -6542.1949] [ 1114] [depth= 3] . ( 14 sec) [ -6541.6318] [ 1111] [depth= 1] . ( 14 sec) [ -6537.7331] [ 1114] [depth= 1] . ( 14 sec) [ -6536.9756] [ 1114] [depth= 1] . ( 15 sec) [ -6535.9928] [ 1109] [depth= 1] . ( 15 sec) [ -6535.8677] [ 1110] [depth= 1] . ( 15 sec) [ -6518.7213] [Branch lengths ] . ( 17 sec) [ -6513.9671] [GTR parameters ] . ( 17 sec) [ -6513.3242] [Alpha ][ 0.233561] . ( 23 sec) [ -6512.5385] [Branch lengths ] . ( 26 sec) [ -6512.4955] [ 1112] [depth= 6] . ( 43 sec) [ -6511.6882] [ 1115] [depth= 2] . ( 45 sec) [ -6511.1705] [ 1116] [depth= 1] . ( 51 sec) [ -6508.8511] [Branch lengths ] . ( 53 sec) [ -6508.8119] [GTR parameters ] . ( 53 sec) [ -6508.8000] [Alpha ][ 0.235876] . ( 82 sec) [ -6508.6576] [Branch lengths ] . ( 82 sec) [ -6508.6576] [Topology ] . ( 83 sec) [ -6508.6535] [Topology ] . ( 84 sec) [ -6508.6524] [Topology ] . ( 85 sec) [ -6508.6519] [Topology ] . ( 85 sec) [ -6508.6519] [GTR parameters ] . ( 85 sec) [ -6508.6518] [Alpha ][ 0.235620] . ( 85 sec) [ -6508.6518] [Topology ] . ( 86 sec) [ -6508.6515] [Topology ] . ( 86 sec) [ -6508.6506] [GTR parameters ] . ( 86 sec) [ -6508.6506] [Alpha ][ 0.235620] . ( 86 sec) [ -6508.6506] [Topology ] . ( 87 sec) [ -6508.6504] [Topology ] . ( 88 sec) [ -6508.6504] [GTR parameters ] . ( 88 sec) [ -6508.6504] [Alpha ][ 0.235620] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -6508.5832] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6508.583179. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17025.9545] [GTR parameters ] . ( 1 sec) [ -16550.8930] [Alpha ][ 0.500960] . ( 1 sec) [ -16266.8952] [ 2718] [depth= 10] . ( 1 sec) [ -16109.2045] [ 2713] [depth= 9] . ( 1 sec) [ -15605.1305] [ 2682] [depth= 11] . ( 1 sec) [ -15462.3642] [ 2616] [depth= 1] . ( 1 sec) [ -15322.1741] [ 2570] [depth= 9] . ( 1 sec) [ -14748.3523] [ 2550] [depth= 1] . ( 1 sec) [ -14716.3372] [ 2535] [depth= 6] . ( 1 sec) [ -14617.6529] [ 2453] [depth= 2] . ( 1 sec) [ -14573.1995] [ 2443] [depth= 5] . ( 1 sec) [ -14427.2740] [ 2439] [depth= 3] . ( 1 sec) [ -14412.7645] [ 2432] [depth= 4] . ( 1 sec) [ -14322.5596] [ 2417] [depth= 1] . ( 1 sec) [ -14219.5326] [ 2412] [depth= 8] . ( 1 sec) [ -14107.0165] [ 2407] [depth= 13] . ( 1 sec) [ -14104.7933] [ 2422] [depth= 1] . ( 1 sec) [ -13969.1972] [ 2401] [depth= 16] . ( 1 sec) [ -13743.1470] [ 2363] [depth= 6] . ( 1 sec) [ -13702.1146] [ 2357] [depth= 2] . ( 1 sec) [ -13610.2058] [ 2356] [depth= 7] . ( 1 sec) [ -13440.3336] [ 2313] [depth= 5] . ( 1 sec) [ -13200.9194] [ 2274] [depth= 6] . ( 2 sec) [ -12947.4268] [ 2178] [depth= 7] . ( 2 sec) [ -12911.0979] [ 2175] [depth= 11] . ( 2 sec) [ -12740.7614] [ 2161] [depth= 8] . ( 2 sec) [ -12700.7605] [ 2171] [depth= 1] . ( 2 sec) [ -12560.0982] [ 2132] [depth= 2] . ( 2 sec) [ -12468.2093] [ 2115] [depth= 7] . ( 2 sec) [ -12391.5989] [ 2080] [depth= 6] . ( 2 sec) [ -11971.5301] [ 2077] [depth= 1] . ( 2 sec) [ -11851.2661] [ 2061] [depth= 1] . ( 2 sec) [ -11756.2968] [ 2057] [depth= 2] . ( 2 sec) [ -11683.0727] [ 2059] [depth= 13] . ( 2 sec) [ -11570.2753] [ 2027] [depth= 14] . ( 2 sec) [ -11452.3673] [ 2003] [depth= 7] . ( 2 sec) [ -11442.7534] [ 1988] [depth= 1] . ( 2 sec) [ -11281.1347] [ 1934] [depth= 6] . ( 2 sec) [ -11263.7115] [ 1931] [depth= 2] . ( 2 sec) [ -11069.7355] [ 1891] [depth= 11] . ( 2 sec) [ -11057.5532] [ 1895] [depth= 1] . ( 2 sec) [ -11022.3591] [ 1886] [depth= 1] . ( 3 sec) [ -10894.0853] [ 1838] [depth= 7] . ( 3 sec) [ -10548.6126] [ 1836] [depth= 4] . ( 3 sec) [ -10492.6878] [ 1822] [depth= 1] . ( 3 sec) [ -10455.8996] [ 1816] [depth= 5] . ( 3 sec) [ -10294.0334] [ 1763] [depth= 6] . ( 3 sec) [ -10243.4210] [ 1745] [depth= 1] . ( 3 sec) [ -10125.5544] [ 1738] [depth= 3] . ( 3 sec) [ -10030.8142] [ 1711] [depth= 3] . ( 3 sec) [ -9793.8354] [ 1656] [depth= 9] . ( 3 sec) [ -9779.5519] [ 1656] [depth= 2] . ( 3 sec) [ -9687.0329] [ 1654] [depth= 1] . ( 3 sec) [ -9311.8242] [ 1651] [depth= 8] . ( 3 sec) [ -9232.2592] [ 1622] [depth= 6] . ( 3 sec) [ -9167.3897] [ 1622] [depth= 4] . ( 3 sec) [ -9041.3847] [ 1604] [depth= 4] . ( 3 sec) [ -8899.7828] [ 1602] [depth= 1] . ( 3 sec) [ -8883.4196] [ 1599] [depth= 1] . ( 4 sec) [ -8881.5966] [ 1599] [depth= 1] . ( 4 sec) [ -8852.2570] [ 1597] [depth= 2] . ( 4 sec) [ -8584.8153] [ 1586] [depth= 5] . ( 4 sec) [ -8459.3205] [ 1592] [depth= 1] . ( 4 sec) [ -8239.1849] [ 1502] [depth= 7] . ( 4 sec) [ -8183.4353] [ 1491] [depth= 4] . ( 4 sec) [ -8032.1771] [ 1495] [depth= 1] . ( 4 sec) [ -8025.4552] [ 1491] [depth= 1] . ( 4 sec) [ -8024.1654] [ 1491] [depth= 1] . ( 4 sec) [ -7977.0416] [ 1478] [depth= 5] . ( 4 sec) [ -7935.4895] [ 1483] [depth= 1] . ( 4 sec) [ -7830.8534] [ 1437] [depth= 4] . ( 4 sec) [ -7821.6613] [ 1432] [depth= 3] . ( 4 sec) [ -7818.9040] [ 1436] [depth= 1] . ( 4 sec) [ -7803.6452] [ 1432] [depth= 1] . ( 4 sec) [ -7803.2304] [ 1432] [depth= 1] . ( 4 sec) [ -7768.0982] [ 1420] [depth= 1] . ( 4 sec) [ -7740.4262] [ 1418] [depth= 4] . ( 5 sec) [ -7732.0187] [ 1423] [depth= 3] . ( 5 sec) [ -7727.7432] [ 1427] [depth= 1] . ( 5 sec) [ -7724.9279] [ 1427] [depth= 1] . ( 5 sec) [ -7614.9348] [ 1421] [depth= 3] . ( 5 sec) [ -7455.3432] [ 1363] [depth= 8] . ( 5 sec) [ -7411.9550] [ 1361] [depth= 2] . ( 5 sec) [ -7407.3614] [ 1358] [depth= 1] . ( 5 sec) [ -7405.7642] [ 1354] [depth= 1] . ( 5 sec) [ -7402.5538] [ 1354] [depth= 1] . ( 5 sec) [ -7402.0957] [ 1355] [depth= 1] . ( 5 sec) [ -7308.1878] [ 1331] [depth= 2] . ( 5 sec) [ -7306.5664] [ 1331] [depth= 1] . ( 5 sec) [ -7267.4247] [ 1310] [depth= 6] . ( 5 sec) [ -7266.9697] [ 1314] [depth= 1] . ( 6 sec) [ -7262.1226] [ 1310] [depth= 1] . ( 6 sec) [ -7223.3703] [ 1301] [depth= 7] . ( 6 sec) [ -7221.3759] [ 1306] [depth= 1] . ( 6 sec) [ -7167.3147] [ 1295] [depth= 7] . ( 6 sec) [ -7164.0787] [ 1294] [depth= 1] . ( 6 sec) [ -7139.2162] [ 1287] [depth= 3] . ( 6 sec) [ -7063.6686] [ 1239] [depth= 4] . ( 6 sec) [ -7019.1778] [ 1240] [depth= 1] . ( 6 sec) [ -7009.8418] [ 1238] [depth= 2] . ( 6 sec) [ -6961.1529] [Branch lengths ] . ( 8 sec) [ -6870.9240] [GTR parameters ] . ( 8 sec) [ -6795.2825] [Alpha ][ 0.250961] . ( 8 sec) [ -6764.0730] [ 1211] [depth= 6] . ( 8 sec) [ -6760.8713] [ 1209] [depth= 2] . ( 8 sec) [ -6676.9632] [ 1189] [depth= 12] . ( 8 sec) [ -6674.1604] [ 1186] [depth= 1] . ( 8 sec) [ -6672.3600] [ 1180] [depth= 4] . ( 8 sec) [ -6669.7302] [ 1178] [depth= 2] . ( 8 sec) [ -6666.0673] [ 1175] [depth= 3] . ( 8 sec) [ -6641.0853] [ 1170] [depth= 1] . ( 9 sec) [ -6638.9636] [ 1172] [depth= 6] . ( 9 sec) [ -6638.6276] [ 1170] [depth= 2] . ( 9 sec) [ -6638.3890] [ 1171] [depth= 2] . ( 10 sec) [ -6638.1958] [ 1172] [depth= 1] . ( 10 sec) [ -6595.9811] [ 1146] [depth= 4] . ( 10 sec) [ -6587.5760] [ 1146] [depth= 1] . ( 11 sec) [ -6551.3828] [ 1113] [depth= 7] . ( 11 sec) [ -6551.3643] [ 1114] [depth= 1] . ( 11 sec) [ -6550.9189] [ 1117] [depth= 1] . ( 12 sec) [ -6545.6152] [ 1116] [depth= 1] . ( 12 sec) [ -6545.5954] [ 1115] [depth= 1] . ( 12 sec) [ -6545.2856] [ 1116] [depth= 1] . ( 13 sec) [ -6542.9260] [ 1111] [depth= 5] . ( 13 sec) [ -6542.1247] [ 1112] [depth= 1] . ( 13 sec) [ -6539.4385] [ 1114] [depth= 3] . ( 14 sec) [ -6538.9347] [ 1114] [depth= 1] . ( 14 sec) [ -6538.8635] [ 1114] [depth= 1] . ( 14 sec) [ -6523.9814] [Branch lengths ] . ( 15 sec) [ -6521.3652] [GTR parameters ] . ( 15 sec) [ -6520.8243] [Alpha ][ 0.234951] . ( 16 sec) [ -6520.8072] [ 1113] [depth= 1] . ( 16 sec) [ -6519.4877] [ 1109] [depth= 3] . ( 19 sec) [ -6519.2286] [ 1111] [depth= 1] . ( 21 sec) [ -6518.8884] [ 1114] [depth= 2] . ( 22 sec) [ -6518.6543] [ 1115] [depth= 1] . ( 22 sec) [ -6516.0786] [Branch lengths ] . ( 23 sec) [ -6516.0305] [GTR parameters ] . ( 23 sec) [ -6516.0178] [Alpha ][ 0.232477] . ( 24 sec) [ -6515.4661] [ 1113] [depth= 1] . ( 25 sec) [ -6515.1436] [ 1111] [depth= 1] . ( 26 sec) [ -6514.6758] [ 1112] [depth= 1] . ( 26 sec) [ -6514.6562] [ 1112] [depth= 1] . ( 29 sec) [ -6512.0019] [Branch lengths ] . ( 30 sec) [ -6511.9239] [GTR parameters ] . ( 30 sec) [ -6511.9233] [Alpha ][ 0.232997] . ( 31 sec) [ -6511.8583] [ 1109] [depth= 1] . ( 35 sec) [ -6511.8371] [ 1110] [depth= 1] . ( 37 sec) [ -6511.6285] [Branch lengths ] . ( 37 sec) [ -6511.6283] [GTR parameters ] . ( 37 sec) [ -6511.6281] [Alpha ][ 0.232680] . ( 52 sec) [ -6511.5942] [ 1109] [depth= 1] . ( 67 sec) [ -6511.5276] [Branch lengths ] . ( 67 sec) [ -6511.5273] [GTR parameters ] . ( 67 sec) [ -6511.5273] [Alpha ][ 0.232680] . ( 67 sec) [ -6511.5273] [Topology ] . ( 68 sec) [ -6511.5233] [Topology ] . ( 69 sec) [ -6511.5227] [Topology ] . ( 69 sec) [ -6511.5227] [GTR parameters ] . ( 69 sec) [ -6511.5227] [Alpha ][ 0.232680] . ( 69 sec) [ -6511.5227] [Topology ] . ( 70 sec) [ -6511.5225] [Topology ] . ( 70 sec) [ -6511.5225] [GTR parameters ] . ( 70 sec) [ -6511.5225] [Alpha ][ 0.232680] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6511.522474. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19040.1074] [GTR parameters ] . ( 1 sec) [ -18574.4597] [Alpha ][ 0.500960] . ( 1 sec) [ -18061.7186] [ 2732] [depth= 5] . ( 1 sec) [ -17438.9084] [ 2702] [depth= 8] . ( 1 sec) [ -17207.3521] [ 2694] [depth= 4] . ( 1 sec) [ -17176.7882] [ 2689] [depth= 2] . ( 1 sec) [ -17045.7365] [ 2647] [depth= 4] . ( 1 sec) [ -17041.6033] [ 2646] [depth= 1] . ( 1 sec) [ -16997.3283] [ 2635] [depth= 4] . ( 1 sec) [ -16969.0881] [ 2631] [depth= 4] . ( 1 sec) [ -16753.9847] [ 2583] [depth= 4] . ( 1 sec) [ -16635.8443] [ 2582] [depth= 1] . ( 1 sec) [ -16540.7558] [ 2569] [depth= 13] . ( 1 sec) [ -16286.4751] [ 2575] [depth= 1] . ( 1 sec) [ -16099.5785] [ 2568] [depth= 2] . ( 1 sec) [ -16022.4482] [ 2561] [depth= 10] . ( 1 sec) [ -16005.3282] [ 2559] [depth= 1] . ( 1 sec) [ -15608.1092] [ 2503] [depth= 10] . ( 1 sec) [ -15390.2009] [ 2497] [depth= 12] . ( 2 sec) [ -15339.7112] [ 2495] [depth= 1] . ( 2 sec) [ -15285.5689] [ 2491] [depth= 8] . ( 2 sec) [ -15136.7363] [ 2469] [depth= 3] . ( 2 sec) [ -14936.5998] [ 2460] [depth= 1] . ( 2 sec) [ -14644.6277] [ 2444] [depth= 13] . ( 2 sec) [ -14621.0669] [ 2439] [depth= 5] . ( 2 sec) [ -14263.1699] [ 2311] [depth= 4] . ( 2 sec) [ -14249.1610] [ 2337] [depth= 16] . ( 2 sec) [ -14204.0780] [ 2332] [depth= 3] . ( 2 sec) [ -14132.6138] [ 2332] [depth= 8] . ( 2 sec) [ -14126.6789] [ 2319] [depth= 5] . ( 2 sec) [ -14116.3751] [ 2318] [depth= 3] . ( 2 sec) [ -14019.8111] [ 2290] [depth= 1] . ( 2 sec) [ -13930.0807] [ 2266] [depth= 7] . ( 2 sec) [ -13825.6885] [ 2253] [depth= 8] . ( 2 sec) [ -13213.6699] [ 2141] [depth= 11] . ( 2 sec) [ -13204.5444] [ 2143] [depth= 2] . ( 2 sec) [ -13175.3975] [ 2137] [depth= 1] . ( 2 sec) [ -13161.1809] [ 2122] [depth= 1] . ( 2 sec) [ -13049.5357] [ 2139] [depth= 14] . ( 3 sec) [ -13011.6256] [ 2117] [depth= 1] . ( 3 sec) [ -12930.3218] [ 2093] [depth= 11] . ( 3 sec) [ -12708.1109] [ 2039] [depth= 1] . ( 3 sec) [ -12645.8513] [ 2032] [depth= 12] . ( 3 sec) [ -12611.6348] [ 2023] [depth= 1] . ( 3 sec) [ -12597.0218] [ 2019] [depth= 1] . ( 3 sec) [ -12571.2460] [ 2009] [depth= 2] . ( 3 sec) [ -12440.7508] [ 1970] [depth= 1] . ( 3 sec) [ -12297.5193] [ 1929] [depth= 4] . ( 3 sec) [ -12285.8168] [ 1925] [depth= 4] . ( 3 sec) [ -12205.3844] [ 1913] [depth= 9] . ( 3 sec) [ -10726.4137] [ 1914] [depth= 4] . ( 3 sec) [ -10709.7681] [ 1914] [depth= 10] . ( 3 sec) [ -10702.6159] [ 1912] [depth= 1] . ( 3 sec) [ -10633.2235] [ 1900] [depth= 11] . ( 3 sec) [ -10475.6720] [ 1855] [depth= 8] . ( 3 sec) [ -10433.3296] [ 1850] [depth= 2] . ( 3 sec) [ -10364.2674] [ 1836] [depth= 2] . ( 3 sec) [ -10358.8963] [ 1835] [depth= 1] . ( 4 sec) [ -10297.7014] [ 1819] [depth= 7] . ( 4 sec) [ -10271.8467] [ 1819] [depth= 1] . ( 4 sec) [ -10183.3098] [ 1806] [depth= 8] . ( 4 sec) [ -10172.9983] [ 1804] [depth= 1] . ( 4 sec) [ -10120.6014] [ 1805] [depth= 9] . ( 4 sec) [ -9974.1849] [ 1798] [depth= 9] . ( 4 sec) [ -9960.4526] [ 1777] [depth= 2] . ( 4 sec) [ -9498.1231] [ 1778] [depth= 7] . ( 4 sec) [ -9496.3470] [ 1778] [depth= 1] . ( 4 sec) [ -9474.1194] [ 1768] [depth= 1] . ( 4 sec) [ -9430.7513] [ 1760] [depth= 7] . ( 4 sec) [ -9385.5399] [ 1757] [depth= 1] . ( 4 sec) [ -9369.3145] [ 1751] [depth= 1] . ( 4 sec) [ -9194.0602] [ 1739] [depth= 9] . ( 4 sec) [ -9115.8625] [ 1721] [depth= 2] . ( 5 sec) [ -9037.2127] [ 1694] [depth= 2] . ( 5 sec) [ -9025.3580] [ 1689] [depth= 1] . ( 5 sec) [ -9011.0012] [ 1687] [depth= 1] . ( 5 sec) [ -8929.6438] [ 1675] [depth= 1] . ( 5 sec) [ -8778.6598] [ 1621] [depth= 4] . ( 5 sec) [ -8753.7061] [ 1611] [depth= 2] . ( 5 sec) [ -8513.4077] [ 1567] [depth= 6] . ( 5 sec) [ -8463.8180] [ 1560] [depth= 6] . ( 5 sec) [ -8402.1662] [ 1536] [depth= 1] . ( 5 sec) [ -8398.0279] [ 1541] [depth= 2] . ( 5 sec) [ -8376.6667] [ 1536] [depth= 1] . ( 5 sec) [ -8346.4610] [ 1521] [depth= 1] . ( 5 sec) [ -8344.2353] [ 1521] [depth= 2] . ( 5 sec) [ -8336.1237] [ 1518] [depth= 2] . ( 6 sec) [ -8333.4226] [ 1520] [depth= 1] . ( 6 sec) [ -8120.5495] [ 1501] [depth= 9] . ( 6 sec) [ -8096.1957] [ 1500] [depth= 1] . ( 6 sec) [ -7875.7928] [ 1428] [depth= 3] . ( 6 sec) [ -7859.9872] [ 1426] [depth= 1] . ( 6 sec) [ -7842.9713] [ 1421] [depth= 3] . ( 6 sec) [ -7830.6965] [ 1416] [depth= 3] . ( 6 sec) [ -7829.1726] [ 1417] [depth= 1] . ( 6 sec) [ -7753.4422] [ 1411] [depth= 5] . ( 6 sec) [ -7703.7624] [ 1403] [depth= 1] . ( 6 sec) [ -7660.0560] [ 1386] [depth= 3] . ( 6 sec) [ -7651.3017] [ 1382] [depth= 1] . ( 6 sec) [ -7607.3728] [ 1361] [depth= 1] . ( 6 sec) [ -7566.3984] [ 1336] [depth= 2] . ( 6 sec) [ -7443.6685] [ 1303] [depth= 2] . ( 6 sec) [ -7341.7817] [ 1262] [depth= 3] . ( 7 sec) [ -7241.3867] [ 1230] [depth= 3] . ( 7 sec) [ -7229.5638] [ 1232] [depth= 2] . ( 7 sec) [ -7188.0729] [ 1214] [depth= 1] . ( 7 sec) [ -7128.0660] [ 1217] [depth= 1] . ( 7 sec) [ -7118.5267] [ 1220] [depth= 1] . ( 7 sec) [ -7106.4575] [ 1219] [depth= 2] . ( 7 sec) [ -7106.3849] [ 1219] [depth= 1] . ( 7 sec) [ -7098.1234] [ 1215] [depth= 1] . ( 7 sec) [ -6968.7286] [Branch lengths ] . ( 9 sec) [ -6835.0001] [GTR parameters ] . ( 9 sec) [ -6763.6386] [Alpha ][ 0.250961] . ( 10 sec) [ -6736.8759] [ 1204] [depth= 2] . ( 10 sec) [ -6735.6400] [ 1203] [depth= 2] . ( 10 sec) [ -6735.3015] [ 1202] [depth= 1] . ( 10 sec) [ -6729.3717] [ 1198] [depth= 4] . ( 10 sec) [ -6715.3384] [ 1194] [depth= 2] . ( 10 sec) [ -6709.5149] [ 1190] [depth= 4] . ( 10 sec) [ -6702.4851] [ 1188] [depth= 1] . ( 10 sec) [ -6702.4744] [ 1188] [depth= 1] . ( 10 sec) [ -6665.9153] [ 1176] [depth= 4] . ( 10 sec) [ -6659.8278] [ 1174] [depth= 1] . ( 10 sec) [ -6650.4567] [ 1173] [depth= 1] . ( 11 sec) [ -6643.1129] [ 1163] [depth= 2] . ( 11 sec) [ -6640.5716] [ 1165] [depth= 1] . ( 11 sec) [ -6569.4436] [ 1120] [depth= 4] . ( 11 sec) [ -6569.0009] [ 1118] [depth= 1] . ( 11 sec) [ -6563.1171] [ 1119] [depth= 1] . ( 12 sec) [ -6558.5493] [ 1117] [depth= 2] . ( 12 sec) [ -6549.0022] [ 1110] [depth= 1] . ( 12 sec) [ -6548.0932] [ 1110] [depth= 1] . ( 12 sec) [ -6547.1499] [ 1112] [depth= 1] . ( 12 sec) [ -6545.3571] [ 1111] [depth= 2] . ( 13 sec) [ -6544.2714] [ 1108] [depth= 1] . ( 14 sec) [ -6544.0440] [ 1108] [depth= 1] . ( 14 sec) [ -6543.8696] [ 1108] [depth= 1] . ( 14 sec) [ -6542.1149] [ 1110] [depth= 1] . ( 14 sec) [ -6540.2979] [ 1111] [depth= 1] . ( 15 sec) [ -6539.7817] [ 1109] [depth= 1] . ( 15 sec) [ -6519.6629] [Branch lengths ] . ( 18 sec) [ -6515.9864] [GTR parameters ] . ( 18 sec) [ -6515.4321] [Alpha ][ 0.234647] . ( 22 sec) [ -6515.1201] [ 1107] [depth= 1] . ( 23 sec) [ -6513.9017] [ 1109] [depth= 1] . ( 24 sec) [ -6511.7387] [Branch lengths ] . ( 26 sec) [ -6511.6680] [GTR parameters ] . ( 26 sec) [ -6511.6636] [Alpha ][ 0.233178] . ( 27 sec) [ -6511.6412] [ 1111] [depth= 1] . ( 32 sec) [ -6511.5301] [Branch lengths ] . ( 33 sec) [ -6511.5297] [GTR parameters ] . ( 33 sec) [ -6511.5295] [Alpha ][ 0.232812] . ( 62 sec) [ -6511.5230] [Branch lengths ] . ( 62 sec) [ -6511.5230] [Topology ] . ( 63 sec) [ -6511.5226] [Topology ] . ( 63 sec) [ -6511.5226] [GTR parameters ] . ( 63 sec) [ -6511.5226] [Alpha ][ 0.232812] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6511.522646. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18595.9288] [GTR parameters ] . ( 1 sec) [ -18129.3859] [Alpha ][ 0.500960] . ( 1 sec) [ -17645.6317] [ 2691] [depth= 5] . ( 1 sec) [ -17431.0000] [ 2672] [depth= 10] . ( 1 sec) [ -16335.9418] [ 2607] [depth= 7] . ( 1 sec) [ -16292.2063] [ 2608] [depth= 1] . ( 1 sec) [ -15457.5884] [ 2578] [depth= 14] . ( 1 sec) [ -15445.1030] [ 2573] [depth= 4] . ( 1 sec) [ -15198.7055] [ 2570] [depth= 4] . ( 1 sec) [ -15041.1140] [ 2527] [depth= 7] . ( 1 sec) [ -14996.9456] [ 2523] [depth= 2] . ( 1 sec) [ -13840.8223] [ 2485] [depth= 1] . ( 1 sec) [ -13748.5336] [ 2479] [depth= 2] . ( 1 sec) [ -13669.3332] [ 2466] [depth= 1] . ( 1 sec) [ -13571.8911] [ 2451] [depth= 4] . ( 1 sec) [ -13563.2838] [ 2441] [depth= 7] . ( 1 sec) [ -13521.5827] [ 2438] [depth= 4] . ( 2 sec) [ -13430.1029] [ 2432] [depth= 1] . ( 2 sec) [ -13381.0893] [ 2431] [depth= 1] . ( 2 sec) [ -13208.8886] [ 2416] [depth= 13] . ( 2 sec) [ -13136.5581] [ 2414] [depth= 1] . ( 2 sec) [ -12845.2479] [ 2364] [depth= 17] . ( 2 sec) [ -12610.9781] [ 2350] [depth= 17] . ( 2 sec) [ -12593.6228] [ 2346] [depth= 1] . ( 2 sec) [ -12556.8465] [ 2340] [depth= 2] . ( 2 sec) [ -12514.9148] [ 2327] [depth= 3] . ( 2 sec) [ -12511.7144] [ 2325] [depth= 1] . ( 2 sec) [ -12488.7277] [ 2327] [depth= 1] . ( 2 sec) [ -12438.7338] [ 2317] [depth= 12] . ( 2 sec) [ -12426.6832] [ 2319] [depth= 2] . ( 2 sec) [ -12338.8609] [ 2301] [depth= 10] . ( 2 sec) [ -12203.5159] [ 2250] [depth= 13] . ( 2 sec) [ -12017.4715] [ 2235] [depth= 11] . ( 2 sec) [ -11982.2580] [ 2225] [depth= 1] . ( 2 sec) [ -11919.9799] [ 2216] [depth= 1] . ( 2 sec) [ -11396.4629] [ 2174] [depth= 17] . ( 2 sec) [ -11351.7993] [ 2171] [depth= 8] . ( 2 sec) [ -11330.2478] [ 2168] [depth= 1] . ( 3 sec) [ -11208.6193] [ 2158] [depth= 13] . ( 3 sec) [ -11185.7340] [ 2155] [depth= 2] . ( 3 sec) [ -11042.5813] [ 2130] [depth= 12] . ( 3 sec) [ -10973.1436] [ 2116] [depth= 1] . ( 3 sec) [ -10893.3556] [ 2087] [depth= 8] . ( 3 sec) [ -10874.0299] [ 2088] [depth= 1] . ( 3 sec) [ -10844.3154] [ 2085] [depth= 1] . ( 3 sec) [ -10739.2288] [ 2076] [depth= 6] . ( 3 sec) [ -10723.9766] [ 2074] [depth= 8] . ( 3 sec) [ -10716.6650] [ 2074] [depth= 1] . ( 3 sec) [ -10666.1208] [ 2045] [depth= 6] . ( 3 sec) [ -10633.3684] [ 2048] [depth= 1] . ( 3 sec) [ -10505.7854] [ 2016] [depth= 11] . ( 3 sec) [ -10336.1946] [ 1976] [depth= 7] . ( 3 sec) [ -10227.7333] [ 1955] [depth= 7] . ( 3 sec) [ -10197.8946] [ 1945] [depth= 5] . ( 3 sec) [ -9934.4587] [ 1839] [depth= 8] . ( 3 sec) [ -9843.9707] [ 1806] [depth= 6] . ( 3 sec) [ -9814.8847] [ 1797] [depth= 1] . ( 4 sec) [ -9513.8570] [ 1767] [depth= 5] . ( 4 sec) [ -9487.4113] [ 1747] [depth= 9] . ( 4 sec) [ -9481.4291] [ 1748] [depth= 1] . ( 4 sec) [ -9462.0403] [ 1752] [depth= 1] . ( 4 sec) [ -9265.4627] [ 1726] [depth= 6] . ( 4 sec) [ -9126.4709] [ 1714] [depth= 12] . ( 4 sec) [ -9086.6126] [ 1702] [depth= 5] . ( 4 sec) [ -9073.7641] [ 1719] [depth= 1] . ( 4 sec) [ -8974.2735] [ 1689] [depth= 2] . ( 4 sec) [ -8802.8931] [ 1656] [depth= 6] . ( 4 sec) [ -8725.2203] [ 1651] [depth= 1] . ( 4 sec) [ -8435.1444] [ 1580] [depth= 7] . ( 4 sec) [ -8427.4913] [ 1576] [depth= 1] . ( 4 sec) [ -8363.0387] [ 1577] [depth= 4] . ( 4 sec) [ -8362.7589] [ 1577] [depth= 1] . ( 4 sec) [ -8346.9089] [ 1578] [depth= 5] . ( 4 sec) [ -8324.5531] [ 1581] [depth= 1] . ( 4 sec) [ -8154.0665] [ 1537] [depth= 3] . ( 4 sec) [ -8095.7570] [ 1514] [depth= 7] . ( 4 sec) [ -8075.3185] [ 1502] [depth= 5] . ( 5 sec) [ -7880.9484] [ 1421] [depth= 6] . ( 5 sec) [ -7779.6396] [ 1425] [depth= 1] . ( 5 sec) [ -7660.0987] [ 1390] [depth= 4] . ( 5 sec) [ -7657.5854] [ 1387] [depth= 1] . ( 5 sec) [ -7548.1134] [ 1363] [depth= 10] . ( 5 sec) [ -7510.6877] [ 1333] [depth= 1] . ( 5 sec) [ -7474.7791] [ 1319] [depth= 4] . ( 5 sec) [ -7249.4240] [ 1252] [depth= 4] . ( 5 sec) [ -7246.9103] [ 1249] [depth= 1] . ( 5 sec) [ -7243.3122] [ 1251] [depth= 1] . ( 6 sec) [ -7226.8697] [ 1244] [depth= 1] . ( 6 sec) [ -7200.7050] [ 1235] [depth= 2] . ( 6 sec) [ -7198.7466] [ 1236] [depth= 1] . ( 6 sec) [ -7178.4150] [ 1230] [depth= 1] . ( 6 sec) [ -7173.7818] [ 1230] [depth= 1] . ( 6 sec) [ -7173.4368] [ 1231] [depth= 1] . ( 6 sec) [ -7127.2213] [ 1193] [depth= 1] . ( 6 sec) [ -7103.7000] [ 1183] [depth= 4] . ( 6 sec) [ -7092.5277] [ 1174] [depth= 4] . ( 6 sec) [ -7090.7891] [ 1173] [depth= 1] . ( 6 sec) [ -7070.2769] [ 1173] [depth= 4] . ( 6 sec) [ -7064.0292] [ 1171] [depth= 2] . ( 6 sec) [ -7013.6809] [ 1168] [depth= 1] . ( 6 sec) [ -7009.0173] [ 1167] [depth= 1] . ( 6 sec) [ -6997.4733] [ 1164] [depth= 1] . ( 6 sec) [ -6997.3346] [ 1155] [depth= 7] . ( 6 sec) [ -6990.1000] [ 1155] [depth= 1] . ( 7 sec) [ -6916.1923] [Branch lengths ] . ( 9 sec) [ -6748.8137] [GTR parameters ] . ( 9 sec) [ -6688.0258] [Alpha ][ 0.250961] . ( 9 sec) [ -6686.7506] [ 1158] [depth= 1] . ( 9 sec) [ -6684.9933] [ 1159] [depth= 1] . ( 9 sec) [ -6666.1226] [ 1153] [depth= 1] . ( 9 sec) [ -6666.0444] [ 1153] [depth= 1] . ( 10 sec) [ -6660.6531] [ 1150] [depth= 1] . ( 10 sec) [ -6656.5975] [ 1146] [depth= 1] . ( 10 sec) [ -6615.6799] [ 1121] [depth= 2] . ( 10 sec) [ -6614.8666] [ 1123] [depth= 2] . ( 10 sec) [ -6592.4986] [ 1122] [depth= 1] . ( 10 sec) [ -6588.3865] [ 1121] [depth= 1] . ( 10 sec) [ -6587.0824] [ 1123] [depth= 2] . ( 10 sec) [ -6584.3517] [ 1125] [depth= 1] . ( 10 sec) [ -6583.1934] [ 1126] [depth= 1] . ( 11 sec) [ -6570.2102] [ 1119] [depth= 2] . ( 11 sec) [ -6563.4150] [ 1118] [depth= 1] . ( 11 sec) [ -6553.1284] [ 1120] [depth= 1] . ( 11 sec) [ -6548.4518] [ 1118] [depth= 2] . ( 11 sec) [ -6547.0856] [ 1116] [depth= 1] . ( 11 sec) [ -6545.9298] [ 1116] [depth= 1] . ( 11 sec) [ -6536.8791] [ 1113] [depth= 1] . ( 11 sec) [ -6536.7161] [ 1111] [depth= 1] . ( 12 sec) [ -6536.6940] [ 1114] [depth= 1] . ( 13 sec) [ -6536.4338] [ 1115] [depth= 1] . ( 13 sec) [ -6532.9685] [ 1119] [depth= 1] . ( 14 sec) [ -6532.7655] [ 1117] [depth= 3] . ( 16 sec) [ -6518.1672] [Branch lengths ] . ( 18 sec) [ -6515.0651] [GTR parameters ] . ( 18 sec) [ -6514.3912] [Alpha ][ 0.233047] . ( 18 sec) [ -6513.9635] [ 1114] [depth= 1] . ( 21 sec) [ -6513.9224] [ 1115] [depth= 5] . ( 21 sec) [ -6512.5562] [ 1116] [depth= 1] . ( 24 sec) [ -6508.9685] [Branch lengths ] . ( 26 sec) [ -6508.9182] [GTR parameters ] . ( 26 sec) [ -6508.9057] [Alpha ][ 0.235414] . ( 33 sec) [ -6508.6870] [Branch lengths ] . ( 63 sec) [ -6508.6835] [Branch lengths ] . ( 63 sec) [ -6508.6835] [Topology ] . ( 64 sec) [ -6508.6834] [Topology ] . ( 64 sec) [ -6508.6834] [GTR parameters ] . ( 64 sec) [ -6508.6831] [Alpha ][ 0.235060] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -6508.6829] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6508.682853. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -6841.6794] [GTR parameters ] . ( 1 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 1 sec) [ -6721.7547] [Topology ] . ( 2 sec) [ -6612.7666] [Topology ] . ( 3 sec) [ -6594.7043] [Topology ] . ( 4 sec) [ -6588.9103] [Topology ] . ( 5 sec) [ -6587.3875] [Topology ] . ( 6 sec) [ -6586.8383] [Topology ] . ( 6 sec) [ -6586.3648] [Topology ] . ( 7 sec) [ -6586.2689] [Topology ] . ( 8 sec) [ -6586.2243] [Topology ] . ( 9 sec) [ -6586.1240] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -6584.3212] [Topology ] . ( 17 sec) [ -6582.0995] [GTR parameters ] . ( 17 sec) [ -6525.0173] [Alpha ][ 0.250961] . ( 17 sec) [ -6525.0173] [Topology ] . ( 18 sec) [ -6522.2195] [Topology ] . ( 19 sec) [ -6520.3490] [Topology ] . ( 20 sec) [ -6519.9884] [Topology ] . ( 20 sec) [ -6519.8839] [Topology ] . ( 21 sec) [ -6519.8444] [Topology ] . ( 22 sec) [ -6519.8279] [Topology ] . ( 23 sec) [ -6519.8204] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -6518.8123] [GTR parameters ] . ( 30 sec) [ -6518.2445] [Alpha ][ 0.234545] . ( 30 sec) [ -6518.2445] [Topology ] . ( 31 sec) [ -6518.2141] [Topology ] . ( 32 sec) [ -6518.2079] [Topology ] . ( 33 sec) [ -6518.2054] [Topology ] . ( 34 sec) [ -6518.2043] [Topology ] . ( 35 sec) [ -6518.2038] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -6518.1914] [GTR parameters ] . ( 42 sec) [ -6518.1893] [Alpha ][ 0.233524] . ( 42 sec) [ -6518.1893] [Topology ] . ( 43 sec) [ -6518.1887] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -6518.1886] [GTR parameters ] . ( 49 sec) [ -6518.1886] [Alpha ][ 0.233524] . ( 49 sec) [ -6518.1886] [Topology ] . ( 50 sec) [ -6518.1884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 65 sec) [ -6841.6794] [GTR parameters ] . ( 65 sec) [ -6721.7547] [Alpha ][ 0.500960] . ( 65 sec) [ -6719.2727] [ 1115] [depth= 1] . ( 66 sec) [ -6718.1728] [ 1115] [depth= 1] . ( 66 sec) [ -6713.9543] [ 1115] [depth= 1] . ( 66 sec) [ -6713.8010] [ 1115] [depth= 1] . ( 66 sec) [ -6709.1247] [ 1118] [depth= 1] . ( 66 sec) [ -6708.8321] [ 1121] [depth= 1] . ( 66 sec) [ -6705.1067] [ 1118] [depth= 1] . ( 66 sec) [ -6700.9852] [ 1118] [depth= 1] . ( 67 sec) [ -6699.3761] [ 1116] [depth= 1] . ( 67 sec) [ -6693.9948] [ 1117] [depth= 1] . ( 67 sec) [ -6691.2533] [ 1116] [depth= 1] . ( 67 sec) [ -6691.2330] [ 1117] [depth= 1] . ( 67 sec) [ -6691.1180] [ 1116] [depth= 1] . ( 68 sec) [ -6690.6112] [ 1118] [depth= 1] . ( 68 sec) [ -6686.5190] [ 1116] [depth= 1] . ( 68 sec) [ -6686.3195] [ 1115] [depth= 1] . ( 68 sec) [ -6676.8829] [ 1115] [depth= 1] . ( 68 sec) [ -6674.2944] [ 1114] [depth= 3] . ( 68 sec) [ -6670.7428] [ 1117] [depth= 2] . ( 68 sec) [ -6670.3121] [ 1117] [depth= 1] . ( 68 sec) [ -6666.3950] [ 1115] [depth= 2] . ( 68 sec) [ -6663.4249] [ 1112] [depth= 1] . ( 68 sec) [ -6655.0619] [ 1122] [depth= 1] . ( 68 sec) [ -6653.8756] [ 1126] [depth= 1] . ( 69 sec) [ -6650.9100] [ 1122] [depth= 1] . ( 69 sec) [ -6649.2546] [ 1122] [depth= 3] . ( 69 sec) [ -6648.1506] [ 1124] [depth= 1] . ( 69 sec) [ -6643.1100] [ 1123] [depth= 1] . ( 70 sec) [ -6637.6858] [ 1121] [depth= 1] . ( 71 sec) [ -6636.7553] [ 1120] [depth= 1] . ( 71 sec) [ -6634.2796] [ 1121] [depth= 1] . ( 71 sec) [ -6632.7635] [ 1120] [depth= 1] . ( 71 sec) [ -6591.5811] [Branch lengths ] . ( 73 sec) [ -6589.6343] [GTR parameters ] . ( 73 sec) [ -6531.5745] [Alpha ][ 0.250961] . ( 73 sec) [ -6531.5263] [ 1120] [depth= 1] . ( 73 sec) [ -6530.3439] [ 1112] [depth= 3] . ( 73 sec) [ -6529.3058] [ 1112] [depth= 1] . ( 74 sec) [ -6525.2579] [ 1111] [depth= 2] . ( 74 sec) [ -6523.6616] [ 1113] [depth= 1] . ( 76 sec) [ -6523.5481] [ 1113] [depth= 1] . ( 76 sec) [ -6522.7050] [ 1112] [depth= 2] . ( 76 sec) [ -6518.7362] [ 1111] [depth= 1] . ( 79 sec) [ -6514.0203] [Branch lengths ] . ( 80 sec) [ -6512.7762] [GTR parameters ] . ( 80 sec) [ -6512.1188] [Alpha ][ 0.233131] . ( 80 sec) [ -6512.0400] [ 1111] [depth= 1] . ( 81 sec) [ -6511.9404] [ 1111] [depth= 1] . ( 87 sec) [ -6511.5722] [Branch lengths ] . ( 88 sec) [ -6511.5536] [GTR parameters ] . ( 88 sec) [ -6511.5531] [Alpha ][ 0.232627] . ( 118 sec) [ -6511.5248] [Branch lengths ] . ( 118 sec) [ -6511.5248] [Topology ] . ( 119 sec) [ -6511.5234] [Topology ] . ( 119 sec) [ -6511.5229] [Topology ] . ( 120 sec) [ -6511.5227] [GTR parameters ] . ( 120 sec) [ -6511.5227] [Alpha ][ 0.232627] . ( 120 sec) [ -6511.5227] [Topology ] . ( 121 sec) [ -6511.5225] [Topology ] . ( 121 sec) [ -6511.5225] [GTR parameters ] . ( 121 sec) [ -6511.5225] [Alpha ][ 0.232627] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6518.188398 . Log likelihood obtained after SPR moves : -6511.522478 . Log likelihood of the current tree: -6511.522478. . Printing the most likely tree in file 'nucleic_M2655_50x872_2006.phy_phyml_tree.txt'... . Best log likelihood : -6508.583179 . Time used 0h2m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 518.84user 0.00system 8:44.12elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps