.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data27.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 349 patterns found. (out of a total of 500 sites) . 141 sites without polymorphism (28.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14579.9045] [GTR parameters ] . ( 1 sec) [ -14321.0714] [Alpha ][ 0.500960] . ( 1 sec) [ -12711.9390] [ 2503] [depth= 8] . ( 1 sec) [ -12486.3166] [ 2499] [depth= 4] . ( 1 sec) [ -12263.5328] [ 2449] [depth= 1] . ( 1 sec) [ -12157.9596] [ 2447] [depth= 7] . ( 1 sec) [ -12040.8234] [ 2392] [depth= 1] . ( 1 sec) [ -11686.9611] [ 2387] [depth= 2] . ( 1 sec) [ -11639.3833] [ 2353] [depth= 4] . ( 1 sec) [ -11515.2782] [ 2375] [depth= 1] . ( 1 sec) [ -11283.2519] [ 2257] [depth= 2] . ( 1 sec) [ -11039.3160] [ 2139] [depth= 5] . ( 1 sec) [ -10938.7825] [ 2123] [depth= 8] . ( 1 sec) [ -10712.6880] [ 2090] [depth= 17] . ( 1 sec) [ -10690.2523] [ 2092] [depth= 1] . ( 1 sec) [ -10621.4950] [ 2082] [depth= 1] . ( 1 sec) [ -10457.9333] [ 2080] [depth= 1] . ( 2 sec) [ -10383.8760] [ 2030] [depth= 1] . ( 2 sec) [ -10165.3086] [ 2022] [depth= 3] . ( 2 sec) [ -10152.1197] [ 2019] [depth= 2] . ( 2 sec) [ -10053.6865] [ 2016] [depth= 2] . ( 2 sec) [ -9906.2132] [ 1947] [depth= 7] . ( 2 sec) [ -9830.6957] [ 1920] [depth= 3] . ( 2 sec) [ -9687.8645] [ 1906] [depth= 1] . ( 2 sec) [ -9633.4491] [ 1907] [depth= 2] . ( 2 sec) [ -9528.1890] [ 1896] [depth= 5] . ( 2 sec) [ -9389.9065] [ 1843] [depth= 4] . ( 2 sec) [ -9336.0160] [ 1838] [depth= 5] . ( 2 sec) [ -9245.6940] [ 1842] [depth= 3] . ( 2 sec) [ -9200.0703] [ 1826] [depth= 11] . ( 2 sec) [ -9170.1385] [ 1757] [depth= 1] . ( 2 sec) [ -9134.1426] [ 1756] [depth= 1] . ( 2 sec) [ -8865.9544] [ 1667] [depth= 4] . ( 2 sec) [ -8769.3077] [ 1663] [depth= 5] . ( 2 sec) [ -8764.7813] [ 1661] [depth= 1] . ( 2 sec) [ -8697.1316] [ 1655] [depth= 2] . ( 2 sec) [ -8660.6260] [ 1648] [depth= 5] . ( 2 sec) [ -8655.7991] [ 1646] [depth= 7] . ( 2 sec) [ -8640.0064] [ 1646] [depth= 4] . ( 2 sec) [ -8622.8489] [ 1638] [depth= 5] . ( 2 sec) [ -8620.5365] [ 1640] [depth= 1] . ( 2 sec) [ -8445.5169] [ 1610] [depth= 9] . ( 2 sec) [ -8369.8886] [ 1615] [depth= 9] . ( 3 sec) [ -8350.4116] [ 1610] [depth= 4] . ( 3 sec) [ -8302.6123] [ 1612] [depth= 2] . ( 3 sec) [ -7827.5471] [ 1599] [depth= 13] . ( 3 sec) [ -7559.3193] [ 1564] [depth= 12] . ( 3 sec) [ -7504.5655] [ 1514] [depth= 5] . ( 3 sec) [ -7455.4511] [ 1516] [depth= 4] . ( 3 sec) [ -7450.6758] [ 1495] [depth= 5] . ( 3 sec) [ -7449.6009] [ 1496] [depth= 1] . ( 3 sec) [ -7393.3197] [ 1488] [depth= 7] . ( 3 sec) [ -7176.2103] [ 1434] [depth= 21] . ( 3 sec) [ -7160.5790] [ 1433] [depth= 1] . ( 3 sec) [ -7134.8281] [ 1427] [depth= 1] . ( 3 sec) [ -7129.1455] [ 1426] [depth= 2] . ( 3 sec) [ -7065.8958] [ 1343] [depth= 11] . ( 3 sec) [ -6946.1514] [ 1342] [depth= 2] . ( 3 sec) [ -6938.2416] [ 1333] [depth= 1] . ( 3 sec) [ -6626.4072] [ 1320] [depth= 3] . ( 3 sec) [ -6616.8115] [ 1318] [depth= 2] . ( 3 sec) [ -6600.7087] [ 1282] [depth= 13] . ( 3 sec) [ -6562.6145] [ 1277] [depth= 1] . ( 3 sec) [ -6559.8549] [ 1276] [depth= 3] . ( 3 sec) [ -6552.8172] [ 1274] [depth= 2] . ( 3 sec) [ -6464.5061] [ 1208] [depth= 16] . ( 4 sec) [ -6429.5358] [ 1199] [depth= 9] . ( 4 sec) [ -6425.5921] [ 1203] [depth= 5] . ( 4 sec) [ -6399.8062] [ 1207] [depth= 1] . ( 4 sec) [ -6397.5796] [ 1208] [depth= 3] . ( 4 sec) [ -6366.5480] [ 1201] [depth= 6] . ( 4 sec) [ -6288.4262] [ 1185] [depth= 3] . ( 4 sec) [ -6255.4535] [ 1181] [depth= 1] . ( 4 sec) [ -6254.8720] [ 1182] [depth= 2] . ( 4 sec) [ -6252.6809] [ 1179] [depth= 2] . ( 4 sec) [ -6247.6032] [ 1171] [depth= 4] . ( 4 sec) [ -6226.7360] [ 1166] [depth= 1] . ( 4 sec) [ -6214.7793] [ 1155] [depth= 2] . ( 4 sec) [ -6214.7582] [ 1155] [depth= 2] . ( 5 sec) [ -6145.4443] [Branch lengths ] . ( 5 sec) [ -6142.8211] [GTR parameters ] . ( 5 sec) [ -6119.5097] [Alpha ][ 0.900326] . ( 5 sec) [ -6119.2682] [ 1156] [depth= 1] . ( 5 sec) [ -6118.4972] [ 1159] [depth= 1] . ( 5 sec) [ -6081.7223] [ 1139] [depth= 3] . ( 5 sec) [ -6081.4639] [ 1140] [depth= 1] . ( 6 sec) [ -6064.0085] [ 1135] [depth= 1] . ( 6 sec) [ -6062.7944] [ 1134] [depth= 1] . ( 6 sec) [ -6062.0426] [ 1135] [depth= 1] . ( 6 sec) [ -6059.2836] [ 1130] [depth= 1] . ( 6 sec) [ -6055.8542] [ 1129] [depth= 2] . ( 6 sec) [ -6048.6343] [ 1127] [depth= 1] . ( 6 sec) [ -6047.1571] [ 1124] [depth= 1] . ( 7 sec) [ -6011.5841] [ 1093] [depth= 2] . ( 7 sec) [ -6011.5223] [ 1093] [depth= 1] . ( 8 sec) [ -6008.5439] [ 1095] [depth= 1] . ( 8 sec) [ -6008.5308] [ 1095] [depth= 1] . ( 8 sec) [ -6003.7272] [ 1093] [depth= 1] . ( 9 sec) [ -6003.6913] [ 1094] [depth= 1] . ( 9 sec) [ -6003.4825] [ 1097] [depth= 1] . ( 9 sec) [ -5978.3649] [ 1084] [depth= 1] . ( 10 sec) [ -5968.2601] [Branch lengths ] . ( 10 sec) [ -5968.2206] [GTR parameters ] . ( 10 sec) [ -5967.5519] [Alpha ][ 1.007003] . ( 11 sec) [ -5967.2833] [ 1083] [depth= 1] . ( 15 sec) [ -5966.1668] [Branch lengths ] . ( 15 sec) [ -5966.1632] [GTR parameters ] . ( 15 sec) [ -5966.1630] [Alpha ][ 1.004718] . ( 20 sec) [ -5966.1199] [Branch lengths ] . ( 41 sec) [ -5966.1163] [Branch lengths ] . ( 41 sec) [ -5966.1163] [Topology ] . ( 42 sec) [ -5966.1161] [Topology ] . ( 42 sec) [ -5966.1160] [GTR parameters ] . ( 42 sec) [ -5966.1158] [Alpha ][ 1.002489] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5966.115811. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16435.1341] [GTR parameters ] . ( 0 sec) [ -16143.8941] [Alpha ][ 0.500960] . ( 0 sec) [ -15827.7663] [ 2656] [depth= 3] . ( 0 sec) [ -15610.0460] [ 2577] [depth= 10] . ( 0 sec) [ -15128.4476] [ 2506] [depth= 4] . ( 0 sec) [ -12417.8175] [ 2503] [depth= 6] . ( 0 sec) [ -12226.0796] [ 2428] [depth= 1] . ( 0 sec) [ -11996.8370] [ 2421] [depth= 9] . ( 0 sec) [ -11981.4402] [ 2431] [depth= 1] . ( 0 sec) [ -11901.3362] [ 2420] [depth= 4] . ( 0 sec) [ -11854.7660] [ 2409] [depth= 2] . ( 0 sec) [ -11789.2666] [ 2406] [depth= 6] . ( 0 sec) [ -11664.3082] [ 2355] [depth= 12] . ( 0 sec) [ -11515.1804] [ 2349] [depth= 3] . ( 0 sec) [ -11211.7932] [ 2293] [depth= 11] . ( 1 sec) [ -11090.5655] [ 2287] [depth= 3] . ( 1 sec) [ -10755.5699] [ 2213] [depth= 5] . ( 1 sec) [ -10684.4239] [ 2190] [depth= 1] . ( 1 sec) [ -10119.3244] [ 2118] [depth= 14] . ( 1 sec) [ -10093.9834] [ 2118] [depth= 1] . ( 1 sec) [ -9827.8748] [ 2045] [depth= 13] . ( 1 sec) [ -9527.4436] [ 1942] [depth= 1] . ( 1 sec) [ -9459.6953] [ 1940] [depth= 4] . ( 1 sec) [ -9434.2272] [ 1944] [depth= 7] . ( 1 sec) [ -9354.2117] [ 1938] [depth= 2] . ( 1 sec) [ -9212.0921] [ 1919] [depth= 1] . ( 1 sec) [ -9105.7525] [ 1890] [depth= 20] . ( 1 sec) [ -8915.6653] [ 1804] [depth= 19] . ( 1 sec) [ -8766.6003] [ 1760] [depth= 6] . ( 1 sec) [ -8716.2097] [ 1745] [depth= 1] . ( 1 sec) [ -8694.6039] [ 1747] [depth= 1] . ( 1 sec) [ -8644.2607] [ 1731] [depth= 2] . ( 1 sec) [ -8634.6180] [ 1728] [depth= 1] . ( 1 sec) [ -8629.7305] [ 1727] [depth= 1] . ( 1 sec) [ -8534.8435] [ 1722] [depth= 1] . ( 1 sec) [ -8191.9819] [ 1719] [depth= 2] . ( 2 sec) [ -8146.8282] [ 1712] [depth= 1] . ( 2 sec) [ -8143.3304] [ 1709] [depth= 2] . ( 2 sec) [ -8139.7519] [ 1707] [depth= 2] . ( 2 sec) [ -8125.5889] [ 1696] [depth= 1] . ( 2 sec) [ -8105.6326] [ 1682] [depth= 6] . ( 2 sec) [ -8029.9650] [ 1667] [depth= 6] . ( 2 sec) [ -7996.3035] [ 1613] [depth= 2] . ( 2 sec) [ -7703.3683] [ 1545] [depth= 7] . ( 2 sec) [ -7688.2029] [ 1551] [depth= 3] . ( 2 sec) [ -7680.5782] [ 1545] [depth= 13] . ( 2 sec) [ -7591.1714] [ 1493] [depth= 8] . ( 2 sec) [ -7512.1444] [ 1472] [depth= 1] . ( 2 sec) [ -7496.2795] [ 1473] [depth= 4] . ( 2 sec) [ -7478.2918] [ 1472] [depth= 1] . ( 2 sec) [ -7450.5507] [ 1469] [depth= 2] . ( 2 sec) [ -7441.2617] [ 1481] [depth= 1] . ( 2 sec) [ -7415.7779] [ 1458] [depth= 3] . ( 2 sec) [ -7414.9765] [ 1458] [depth= 4] . ( 2 sec) [ -7361.1857] [ 1459] [depth= 5] . ( 2 sec) [ -7355.9513] [ 1458] [depth= 5] . ( 2 sec) [ -7347.7894] [ 1453] [depth= 1] . ( 2 sec) [ -7301.2684] [ 1451] [depth= 9] . ( 2 sec) [ -7246.0499] [ 1431] [depth= 1] . ( 2 sec) [ -7239.5417] [ 1429] [depth= 2] . ( 2 sec) [ -7239.0731] [ 1429] [depth= 1] . ( 3 sec) [ -7111.6305] [ 1352] [depth= 7] . ( 3 sec) [ -7085.2356] [ 1355] [depth= 5] . ( 3 sec) [ -6925.1561] [ 1328] [depth= 4] . ( 3 sec) [ -6918.5079] [ 1326] [depth= 3] . ( 3 sec) [ -6805.9177] [ 1305] [depth= 5] . ( 3 sec) [ -6791.1026] [ 1292] [depth= 13] . ( 3 sec) [ -6786.6515] [ 1291] [depth= 1] . ( 3 sec) [ -6763.4749] [ 1286] [depth= 2] . ( 3 sec) [ -6619.7956] [ 1282] [depth= 2] . ( 3 sec) [ -6613.6629] [ 1283] [depth= 1] . ( 3 sec) [ -6611.8187] [ 1281] [depth= 1] . ( 3 sec) [ -6581.8211] [ 1272] [depth= 3] . ( 3 sec) [ -6539.3754] [ 1235] [depth= 1] . ( 3 sec) [ -6532.1647] [ 1225] [depth= 2] . ( 3 sec) [ -6478.6128] [ 1225] [depth= 3] . ( 3 sec) [ -6352.1195] [ 1198] [depth= 4] . ( 3 sec) [ -6341.6551] [ 1196] [depth= 1] . ( 3 sec) [ -6275.1864] [ 1180] [depth= 2] . ( 3 sec) [ -6268.6901] [ 1178] [depth= 1] . ( 4 sec) [ -6223.8262] [Branch lengths ] . ( 4 sec) [ -6221.0174] [GTR parameters ] . ( 4 sec) [ -6201.4952] [Alpha ][ 0.867256] . ( 4 sec) [ -6200.9329] [ 1179] [depth= 1] . ( 4 sec) [ -6167.2617] [ 1165] [depth= 5] . ( 4 sec) [ -6117.2264] [ 1135] [depth= 2] . ( 4 sec) [ -6116.0632] [ 1134] [depth= 1] . ( 5 sec) [ -6109.7186] [ 1132] [depth= 1] . ( 5 sec) [ -6091.1307] [ 1132] [depth= 1] . ( 5 sec) [ -6027.2033] [ 1108] [depth= 1] . ( 5 sec) [ -6023.6073] [ 1103] [depth= 1] . ( 5 sec) [ -5990.0211] [ 1085] [depth= 2] . ( 5 sec) [ -5985.4436] [ 1084] [depth= 1] . ( 6 sec) [ -5984.7529] [ 1084] [depth= 1] . ( 6 sec) [ -5980.9133] [ 1083] [depth= 2] . ( 6 sec) [ -5978.9353] [ 1087] [depth= 1] . ( 6 sec) [ -5972.9455] [ 1087] [depth= 1] . ( 6 sec) [ -5972.9014] [ 1087] [depth= 1] . ( 7 sec) [ -5972.0066] [ 1084] [depth= 1] . ( 7 sec) [ -5971.9937] [ 1084] [depth= 1] . ( 7 sec) [ -5971.9564] [ 1082] [depth= 1] . ( 7 sec) [ -5971.7604] [ 1084] [depth= 1] . ( 8 sec) [ -5971.4218] [ 1085] [depth= 1] . ( 8 sec) [ -5967.4834] [Branch lengths ] . ( 9 sec) [ -5967.3751] [GTR parameters ] . ( 9 sec) [ -5966.5027] [Alpha ][ 0.987278] . ( 14 sec) [ -5966.2235] [Branch lengths ] . ( 35 sec) [ -5966.1852] [Branch lengths ] . ( 35 sec) [ -5966.1852] [Topology ] . ( 35 sec) [ -5966.1827] [Topology ] . ( 36 sec) [ -5966.1820] [Topology ] . ( 36 sec) [ -5966.1805] [GTR parameters ] . ( 36 sec) [ -5966.1736] [Alpha ][ 0.999125] . ( 36 sec) [ -5966.1736] [Topology ] . ( 37 sec) [ -5966.1729] [Topology ] . ( 37 sec) [ -5966.1729] [GTR parameters ] . ( 37 sec) [ -5966.1729] [Alpha ][ 0.999125] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -5966.1200] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -5966.1199] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5966.119860. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14201.7198] [GTR parameters ] . ( 1 sec) [ -13907.2886] [Alpha ][ 0.500960] . ( 1 sec) [ -13636.2249] [ 2716] [depth= 8] . ( 1 sec) [ -13298.8115] [ 2646] [depth= 8] . ( 1 sec) [ -13268.2047] [ 2630] [depth= 3] . ( 1 sec) [ -13253.4388] [ 2627] [depth= 3] . ( 1 sec) [ -13214.4816] [ 2603] [depth= 2] . ( 1 sec) [ -13187.9945] [ 2603] [depth= 1] . ( 1 sec) [ -12739.1034] [ 2513] [depth= 14] . ( 1 sec) [ -12562.7779] [ 2490] [depth= 13] . ( 1 sec) [ -12493.0434] [ 2473] [depth= 1] . ( 1 sec) [ -12341.0021] [ 2446] [depth= 18] . ( 1 sec) [ -12064.8639] [ 2359] [depth= 6] . ( 1 sec) [ -11896.4709] [ 2295] [depth= 17] . ( 1 sec) [ -11836.1337] [ 2294] [depth= 1] . ( 1 sec) [ -11771.9578] [ 2290] [depth= 4] . ( 1 sec) [ -11767.1252] [ 2276] [depth= 13] . ( 1 sec) [ -11759.2969] [ 2277] [depth= 2] . ( 2 sec) [ -11650.4730] [ 2267] [depth= 1] . ( 2 sec) [ -11503.6353] [ 2262] [depth= 7] . ( 2 sec) [ -11445.0146] [ 2257] [depth= 5] . ( 2 sec) [ -11068.3545] [ 2167] [depth= 6] . ( 2 sec) [ -10814.2765] [ 2132] [depth= 10] . ( 2 sec) [ -10636.6423] [ 2066] [depth= 1] . ( 2 sec) [ -10381.3785] [ 2046] [depth= 6] . ( 2 sec) [ -10255.5618] [ 1977] [depth= 14] . ( 2 sec) [ -10171.5078] [ 1956] [depth= 5] . ( 2 sec) [ -10161.7461] [ 1958] [depth= 1] . ( 2 sec) [ -10120.0687] [ 1953] [depth= 15] . ( 2 sec) [ -10117.0914] [ 1951] [depth= 1] . ( 2 sec) [ -10034.4318] [ 1928] [depth= 2] . ( 2 sec) [ -9968.5646] [ 1906] [depth= 13] . ( 2 sec) [ -9858.7617] [ 1897] [depth= 6] . ( 2 sec) [ -9818.8150] [ 1875] [depth= 10] . ( 2 sec) [ -9601.3607] [ 1874] [depth= 1] . ( 2 sec) [ -8898.2436] [ 1871] [depth= 2] . ( 2 sec) [ -8864.8113] [ 1852] [depth= 3] . ( 2 sec) [ -8805.6396] [ 1823] [depth= 7] . ( 2 sec) [ -8803.3523] [ 1823] [depth= 1] . ( 2 sec) [ -8802.2795] [ 1823] [depth= 1] . ( 2 sec) [ -8770.6056] [ 1821] [depth= 1] . ( 2 sec) [ -8445.7218] [ 1728] [depth= 3] . ( 2 sec) [ -8416.7654] [ 1714] [depth= 1] . ( 2 sec) [ -8286.7624] [ 1692] [depth= 10] . ( 3 sec) [ -8283.1244] [ 1684] [depth= 2] . ( 3 sec) [ -8178.9555] [ 1658] [depth= 4] . ( 3 sec) [ -7914.1714] [ 1650] [depth= 8] . ( 3 sec) [ -7875.3607] [ 1647] [depth= 1] . ( 3 sec) [ -7775.4129] [ 1645] [depth= 2] . ( 3 sec) [ -7756.7790] [ 1610] [depth= 1] . ( 3 sec) [ -7749.7096] [ 1609] [depth= 2] . ( 3 sec) [ -7747.0268] [ 1609] [depth= 1] . ( 3 sec) [ -7744.6215] [ 1615] [depth= 1] . ( 3 sec) [ -7740.0438] [ 1609] [depth= 1] . ( 3 sec) [ -7596.1577] [ 1631] [depth= 6] . ( 3 sec) [ -7587.3455] [ 1576] [depth= 1] . ( 3 sec) [ -7570.6475] [ 1573] [depth= 1] . ( 3 sec) [ -7471.2267] [ 1564] [depth= 3] . ( 3 sec) [ -7379.8629] [ 1555] [depth= 1] . ( 3 sec) [ -7215.6732] [ 1500] [depth= 3] . ( 3 sec) [ -7100.9719] [ 1478] [depth= 4] . ( 3 sec) [ -6854.4969] [ 1414] [depth= 3] . ( 3 sec) [ -6829.8317] [ 1411] [depth= 1] . ( 3 sec) [ -6826.3965] [ 1410] [depth= 1] . ( 3 sec) [ -6815.3684] [ 1408] [depth= 1] . ( 3 sec) [ -6813.5375] [ 1408] [depth= 3] . ( 4 sec) [ -6803.8811] [ 1407] [depth= 1] . ( 4 sec) [ -6779.0744] [ 1401] [depth= 3] . ( 4 sec) [ -6675.6673] [ 1393] [depth= 1] . ( 4 sec) [ -6653.1423] [ 1385] [depth= 1] . ( 4 sec) [ -6487.0749] [ 1301] [depth= 3] . ( 4 sec) [ -6448.8746] [ 1301] [depth= 1] . ( 4 sec) [ -6448.8565] [ 1301] [depth= 1] . ( 4 sec) [ -6443.1609] [ 1299] [depth= 3] . ( 4 sec) [ -6407.6586] [ 1246] [depth= 6] . ( 4 sec) [ -6380.8520] [ 1237] [depth= 2] . ( 4 sec) [ -6372.6775] [ 1241] [depth= 1] . ( 4 sec) [ -6361.3930] [ 1241] [depth= 2] . ( 4 sec) [ -6352.5893] [ 1238] [depth= 1] . ( 4 sec) [ -6347.5198] [ 1236] [depth= 1] . ( 5 sec) [ -6288.2513] [Branch lengths ] . ( 5 sec) [ -6285.1597] [GTR parameters ] . ( 5 sec) [ -6271.9475] [Alpha ][ 0.774784] . ( 5 sec) [ -6262.5225] [ 1222] [depth= 1] . ( 5 sec) [ -6260.5171] [ 1224] [depth= 1] . ( 5 sec) [ -6234.2811] [ 1210] [depth= 3] . ( 6 sec) [ -6162.3747] [ 1162] [depth= 8] . ( 6 sec) [ -6050.2227] [ 1132] [depth= 4] . ( 6 sec) [ -6050.2020] [ 1132] [depth= 1] . ( 6 sec) [ -6045.7116] [ 1130] [depth= 1] . ( 7 sec) [ -6045.5988] [ 1127] [depth= 3] . ( 7 sec) [ -6045.3836] [ 1128] [depth= 1] . ( 7 sec) [ -6045.3540] [ 1127] [depth= 1] . ( 7 sec) [ -6043.4853] [ 1123] [depth= 1] . ( 7 sec) [ -6039.9767] [ 1112] [depth= 3] . ( 7 sec) [ -5997.2989] [ 1084] [depth= 1] . ( 8 sec) [ -5992.9254] [ 1083] [depth= 1] . ( 8 sec) [ -5988.8072] [ 1083] [depth= 1] . ( 8 sec) [ -5983.2511] [ 1081] [depth= 1] . ( 8 sec) [ -5982.5805] [ 1080] [depth= 1] . ( 9 sec) [ -5980.5059] [ 1080] [depth= 1] . ( 9 sec) [ -5979.4840] [ 1083] [depth= 1] . ( 10 sec) [ -5970.0914] [Branch lengths ] . ( 10 sec) [ -5969.8343] [GTR parameters ] . ( 10 sec) [ -5966.6614] [Alpha ][ 0.989141] . ( 15 sec) [ -5966.3560] [Branch lengths ] . ( 35 sec) [ -5966.3204] [Branch lengths ] . ( 35 sec) [ -5966.3204] [Topology ] . ( 36 sec) [ -5966.3177] [Topology ] . ( 37 sec) [ -5966.3169] [Topology ] . ( 37 sec) [ -5966.3113] [GTR parameters ] . ( 37 sec) [ -5966.3054] [Alpha ][ 1.000125] . ( 37 sec) [ -5966.3054] [Topology ] . ( 38 sec) [ -5966.3047] [Topology ] . ( 38 sec) [ -5966.3047] [GTR parameters ] . ( 38 sec) [ -5966.3047] [Alpha ][ 1.000125] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -5966.1951] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -5966.1279] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5966.127870. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -17122.4834] [GTR parameters ] . ( 2 sec) [ -16811.4898] [Alpha ][ 0.500960] . ( 2 sec) [ -16390.0219] [ 2721] [depth= 10] . ( 2 sec) [ -15456.0216] [ 2633] [depth= 3] . ( 2 sec) [ -15316.1771] [ 2617] [depth= 8] . ( 2 sec) [ -15269.9215] [ 2604] [depth= 1] . ( 2 sec) [ -15137.7209] [ 2570] [depth= 5] . ( 2 sec) [ -14846.7505] [ 2509] [depth= 3] . ( 2 sec) [ -14759.8204] [ 2501] [depth= 6] . ( 2 sec) [ -14489.3688] [ 2395] [depth= 5] . ( 2 sec) [ -14330.4944] [ 2389] [depth= 8] . ( 2 sec) [ -14305.4257] [ 2386] [depth= 3] . ( 2 sec) [ -14301.4349] [ 2386] [depth= 2] . ( 2 sec) [ -14204.2636] [ 2355] [depth= 8] . ( 2 sec) [ -13992.2011] [ 2308] [depth= 4] . ( 2 sec) [ -13820.1366] [ 2306] [depth= 3] . ( 2 sec) [ -13574.4096] [ 2256] [depth= 15] . ( 2 sec) [ -13510.4133] [ 2237] [depth= 5] . ( 2 sec) [ -13397.3264] [ 2237] [depth= 1] . ( 2 sec) [ -13156.7464] [ 2190] [depth= 11] . ( 2 sec) [ -13031.7783] [ 2158] [depth= 14] . ( 2 sec) [ -12991.0653] [ 2144] [depth= 1] . ( 2 sec) [ -12893.0889] [ 2136] [depth= 8] . ( 2 sec) [ -12819.5888] [ 2127] [depth= 11] . ( 3 sec) [ -12766.1614] [ 2111] [depth= 1] . ( 3 sec) [ -12661.1005] [ 2031] [depth= 4] . ( 3 sec) [ -12583.9811] [ 2036] [depth= 8] . ( 3 sec) [ -12473.2823] [ 2033] [depth= 1] . ( 3 sec) [ -12161.2640] [ 2034] [depth= 3] . ( 3 sec) [ -12059.7801] [ 2033] [depth= 10] . ( 3 sec) [ -11994.4731] [ 1960] [depth= 3] . ( 3 sec) [ -11980.2917] [ 1960] [depth= 2] . ( 3 sec) [ -11805.7854] [ 1949] [depth= 3] . ( 3 sec) [ -11703.2163] [ 1883] [depth= 6] . ( 3 sec) [ -11482.8178] [ 1881] [depth= 1] . ( 3 sec) [ -11480.2086] [ 1865] [depth= 1] . ( 3 sec) [ -11476.5102] [ 1817] [depth= 1] . ( 3 sec) [ -11450.2726] [ 1811] [depth= 4] . ( 3 sec) [ -8248.6834] [ 1809] [depth= 1] . ( 3 sec) [ -8228.0134] [ 1802] [depth= 5] . ( 3 sec) [ -8159.0674] [ 1788] [depth= 8] . ( 3 sec) [ -8115.8327] [ 1783] [depth= 5] . ( 3 sec) [ -8107.7679] [ 1771] [depth= 2] . ( 3 sec) [ -7980.0395] [ 1764] [depth= 4] . ( 3 sec) [ -7947.3395] [ 1757] [depth= 1] . ( 3 sec) [ -7899.9144] [ 1754] [depth= 4] . ( 3 sec) [ -7693.4018] [ 1637] [depth= 6] . ( 3 sec) [ -7683.3008] [ 1632] [depth= 3] . ( 3 sec) [ -7675.9993] [ 1639] [depth= 1] . ( 4 sec) [ -7518.7513] [ 1596] [depth= 1] . ( 4 sec) [ -7423.0711] [ 1582] [depth= 1] . ( 4 sec) [ -7395.5774] [ 1574] [depth= 2] . ( 4 sec) [ -7393.4840] [ 1575] [depth= 2] . ( 4 sec) [ -7208.2646] [ 1532] [depth= 11] . ( 4 sec) [ -7089.9135] [ 1463] [depth= 11] . ( 4 sec) [ -7079.4156] [ 1459] [depth= 1] . ( 4 sec) [ -6930.2428] [ 1458] [depth= 4] . ( 4 sec) [ -6927.7417] [ 1449] [depth= 4] . ( 4 sec) [ -6917.4623] [ 1446] [depth= 1] . ( 4 sec) [ -6735.3769] [ 1353] [depth= 9] . ( 4 sec) [ -6728.7959] [ 1345] [depth= 1] . ( 4 sec) [ -6718.5501] [ 1342] [depth= 1] . ( 4 sec) [ -6713.4338] [ 1343] [depth= 4] . ( 4 sec) [ -6708.7340] [ 1343] [depth= 1] . ( 4 sec) [ -6699.3497] [ 1342] [depth= 2] . ( 4 sec) [ -6692.3283] [ 1313] [depth= 6] . ( 4 sec) [ -6621.0678] [ 1281] [depth= 6] . ( 5 sec) [ -6477.9106] [ 1265] [depth= 2] . ( 5 sec) [ -6460.3043] [ 1273] [depth= 4] . ( 5 sec) [ -6441.9841] [ 1248] [depth= 5] . ( 5 sec) [ -6355.5598] [ 1194] [depth= 5] . ( 5 sec) [ -6335.2909] [ 1184] [depth= 1] . ( 5 sec) [ -6292.6062] [ 1185] [depth= 1] . ( 5 sec) [ -6267.6838] [ 1176] [depth= 2] . ( 5 sec) [ -6265.9130] [ 1175] [depth= 1] . ( 5 sec) [ -6261.9428] [ 1177] [depth= 2] . ( 6 sec) [ -6203.5668] [Branch lengths ] . ( 6 sec) [ -6195.0331] [GTR parameters ] . ( 6 sec) [ -6176.4215] [Alpha ][ 0.855574] . ( 6 sec) [ -6140.2384] [ 1142] [depth= 8] . ( 6 sec) [ -6132.7351] [ 1142] [depth= 1] . ( 6 sec) [ -6128.7921] [ 1140] [depth= 2] . ( 6 sec) [ -6095.9945] [ 1113] [depth= 2] . ( 7 sec) [ -6093.2277] [ 1113] [depth= 1] . ( 7 sec) [ -6093.2155] [ 1112] [depth= 2] . ( 7 sec) [ -6093.2023] [ 1113] [depth= 2] . ( 7 sec) [ -6081.5707] [ 1109] [depth= 5] . ( 7 sec) [ -6080.5567] [ 1110] [depth= 1] . ( 7 sec) [ -6080.5188] [ 1110] [depth= 2] . ( 7 sec) [ -6080.4739] [ 1110] [depth= 1] . ( 8 sec) [ -6080.4557] [ 1110] [depth= 1] . ( 8 sec) [ -6047.6101] [ 1100] [depth= 1] . ( 8 sec) [ -6046.0637] [ 1100] [depth= 1] . ( 8 sec) [ -6031.5581] [ 1096] [depth= 2] . ( 8 sec) [ -6031.3643] [ 1094] [depth= 1] . ( 8 sec) [ -6030.5569] [ 1096] [depth= 1] . ( 8 sec) [ -5987.8333] [ 1085] [depth= 1] . ( 9 sec) [ -5986.9445] [ 1084] [depth= 1] . ( 9 sec) [ -5986.9134] [ 1083] [depth= 1] . ( 9 sec) [ -5983.1276] [ 1080] [depth= 1] . ( 9 sec) [ -5977.3754] [ 1082] [depth= 1] . ( 9 sec) [ -5976.8041] [ 1084] [depth= 1] . ( 10 sec) [ -5969.0218] [Branch lengths ] . ( 11 sec) [ -5968.8931] [GTR parameters ] . ( 11 sec) [ -5967.7622] [Alpha ][ 0.991083] . ( 12 sec) [ -5967.1944] [ 1084] [depth= 1] . ( 12 sec) [ -5966.7028] [ 1084] [depth= 1] . ( 12 sec) [ -5966.6504] [ 1084] [depth= 1] . ( 14 sec) [ -5966.5349] [ 1084] [depth= 1] . ( 15 sec) [ -5966.2016] [Branch lengths ] . ( 15 sec) [ -5966.1963] [GTR parameters ] . ( 15 sec) [ -5966.1940] [Alpha ][ 0.997951] . ( 20 sec) [ -5966.1738] [Branch lengths ] . ( 41 sec) [ -5966.1726] [Branch lengths ] . ( 41 sec) [ -5966.1726] [Topology ] . ( 41 sec) [ -5966.1725] [Topology ] . ( 41 sec) [ -5966.1725] [GTR parameters ] . ( 41 sec) [ -5966.1724] [Alpha ][ 0.999367] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -5966.1194] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5966.119382. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16375.9674] [GTR parameters ] . ( 1 sec) [ -16073.2084] [Alpha ][ 0.500960] . ( 1 sec) [ -15704.3821] [ 2748] [depth= 6] . ( 1 sec) [ -15213.7815] [ 2646] [depth= 9] . ( 1 sec) [ -15207.3320] [ 2634] [depth= 5] . ( 1 sec) [ -15181.0290] [ 2634] [depth= 1] . ( 1 sec) [ -15085.8197] [ 2628] [depth= 6] . ( 1 sec) [ -15074.7998] [ 2628] [depth= 1] . ( 1 sec) [ -14969.2491] [ 2619] [depth= 17] . ( 1 sec) [ -14852.0505] [ 2590] [depth= 1] . ( 1 sec) [ -14478.2793] [ 2580] [depth= 7] . ( 1 sec) [ -14278.1478] [ 2552] [depth= 2] . ( 1 sec) [ -14135.7947] [ 2439] [depth= 16] . ( 1 sec) [ -14063.0081] [ 2431] [depth= 8] . ( 1 sec) [ -11517.3210] [ 2424] [depth= 5] . ( 1 sec) [ -11429.5251] [ 2423] [depth= 3] . ( 1 sec) [ -11309.5201] [ 2400] [depth= 1] . ( 1 sec) [ -11141.4831] [ 2394] [depth= 2] . ( 1 sec) [ -11113.9621] [ 2361] [depth= 1] . ( 1 sec) [ -10934.9820] [ 2347] [depth= 11] . ( 1 sec) [ -10883.7866] [ 2337] [depth= 1] . ( 1 sec) [ -10872.2066] [ 2333] [depth= 4] . ( 1 sec) [ -10812.3054] [ 2320] [depth= 1] . ( 1 sec) [ -10729.4401] [ 2309] [depth= 9] . ( 2 sec) [ -10707.4471] [ 2295] [depth= 4] . ( 2 sec) [ -10655.7379] [ 2293] [depth= 2] . ( 2 sec) [ -10609.1895] [ 2286] [depth= 1] . ( 2 sec) [ -10454.9662] [ 2232] [depth= 12] . ( 2 sec) [ -10302.8679] [ 2208] [depth= 4] . ( 2 sec) [ -10133.6366] [ 2157] [depth= 4] . ( 2 sec) [ -9959.5358] [ 2112] [depth= 11] . ( 2 sec) [ -9872.8817] [ 2104] [depth= 8] . ( 2 sec) [ -9796.3769] [ 2094] [depth= 6] . ( 2 sec) [ -9754.8426] [ 2095] [depth= 8] . ( 2 sec) [ -9484.2366] [ 2063] [depth= 9] . ( 2 sec) [ -9315.6478] [ 1983] [depth= 10] . ( 2 sec) [ -9287.7009] [ 1956] [depth= 1] . ( 2 sec) [ -9202.2881] [ 1953] [depth= 4] . ( 2 sec) [ -9146.9061] [ 1952] [depth= 1] . ( 2 sec) [ -9045.7539] [ 1928] [depth= 3] . ( 2 sec) [ -9021.5173] [ 1879] [depth= 5] . ( 2 sec) [ -8932.9165] [ 1856] [depth= 1] . ( 2 sec) [ -8741.9674] [ 1831] [depth= 4] . ( 2 sec) [ -8703.5482] [ 1835] [depth= 2] . ( 2 sec) [ -8670.7011] [ 1840] [depth= 1] . ( 2 sec) [ -8533.5203] [ 1836] [depth= 4] . ( 2 sec) [ -8390.0811] [ 1723] [depth= 10] . ( 2 sec) [ -8175.3220] [ 1701] [depth= 1] . ( 2 sec) [ -8170.2731] [ 1682] [depth= 7] . ( 3 sec) [ -8029.6916] [ 1637] [depth= 2] . ( 3 sec) [ -8009.4543] [ 1630] [depth= 1] . ( 3 sec) [ -7984.4660] [ 1631] [depth= 2] . ( 3 sec) [ -7951.2711] [ 1621] [depth= 5] . ( 3 sec) [ -7932.2378] [ 1620] [depth= 1] . ( 3 sec) [ -7920.6937] [ 1620] [depth= 1] . ( 3 sec) [ -7879.4314] [ 1620] [depth= 1] . ( 3 sec) [ -7674.4456] [ 1603] [depth= 10] . ( 3 sec) [ -7634.9526] [ 1603] [depth= 1] . ( 3 sec) [ -7581.0128] [ 1607] [depth= 1] . ( 3 sec) [ -7569.8299] [ 1603] [depth= 2] . ( 3 sec) [ -7569.2261] [ 1604] [depth= 2] . ( 3 sec) [ -7526.2211] [ 1585] [depth= 6] . ( 3 sec) [ -7421.5806] [ 1559] [depth= 1] . ( 3 sec) [ -7421.2573] [ 1560] [depth= 1] . ( 4 sec) [ -7391.6775] [ 1556] [depth= 2] . ( 4 sec) [ -7353.6938] [ 1476] [depth= 3] . ( 4 sec) [ -7347.8037] [ 1477] [depth= 1] . ( 4 sec) [ -7346.5324] [ 1474] [depth= 1] . ( 4 sec) [ -7341.1181] [ 1468] [depth= 1] . ( 4 sec) [ -7320.8925] [ 1473] [depth= 9] . ( 4 sec) [ -7208.8278] [ 1429] [depth= 6] . ( 4 sec) [ -7201.6757] [ 1420] [depth= 5] . ( 4 sec) [ -7039.3632] [ 1422] [depth= 1] . ( 4 sec) [ -7030.8646] [ 1419] [depth= 1] . ( 4 sec) [ -7015.9578] [ 1413] [depth= 5] . ( 4 sec) [ -7013.6766] [ 1410] [depth= 4] . ( 4 sec) [ -7000.0051] [ 1409] [depth= 1] . ( 4 sec) [ -6868.8741] [ 1414] [depth= 1] . ( 4 sec) [ -6867.5691] [ 1395] [depth= 1] . ( 5 sec) [ -6858.8097] [ 1390] [depth= 1] . ( 5 sec) [ -6834.4572] [ 1384] [depth= 1] . ( 5 sec) [ -6761.2894] [Branch lengths ] . ( 5 sec) [ -6755.8089] [GTR parameters ] . ( 5 sec) [ -6750.4514] [Alpha ][ 0.644864] . ( 6 sec) [ -6735.6746] [ 1362] [depth= 3] . ( 6 sec) [ -6728.4323] [ 1359] [depth= 3] . ( 6 sec) [ -6653.3933] [ 1342] [depth= 6] . ( 6 sec) [ -6651.7592] [ 1340] [depth= 2] . ( 6 sec) [ -6645.1071] [ 1334] [depth= 3] . ( 6 sec) [ -6640.3495] [ 1332] [depth= 1] . ( 6 sec) [ -6511.3535] [ 1266] [depth= 1] . ( 6 sec) [ -6469.5328] [ 1246] [depth= 2] . ( 6 sec) [ -6458.2849] [ 1247] [depth= 2] . ( 6 sec) [ -6457.9420] [ 1252] [depth= 1] . ( 6 sec) [ -6192.2317] [ 1180] [depth= 2] . ( 6 sec) [ -6175.7185] [ 1179] [depth= 1] . ( 6 sec) [ -6170.2420] [ 1179] [depth= 5] . ( 6 sec) [ -6168.4918] [ 1178] [depth= 1] . ( 6 sec) [ -6137.1502] [ 1149] [depth= 2] . ( 7 sec) [ -6124.2128] [ 1145] [depth= 4] . ( 7 sec) [ -6118.0936] [ 1142] [depth= 1] . ( 7 sec) [ -6108.9080] [ 1137] [depth= 1] . ( 7 sec) [ -6106.0595] [ 1140] [depth= 1] . ( 7 sec) [ -6096.1241] [ 1129] [depth= 1] . ( 8 sec) [ -6092.3814] [ 1128] [depth= 2] . ( 8 sec) [ -6092.3702] [ 1128] [depth= 1] . ( 8 sec) [ -6086.1003] [ 1125] [depth= 1] . ( 8 sec) [ -6064.4315] [ 1116] [depth= 1] . ( 8 sec) [ -6058.8094] [ 1102] [depth= 4] . ( 9 sec) [ -6058.3545] [ 1101] [depth= 1] . ( 9 sec) [ -6057.6933] [ 1101] [depth= 1] . ( 9 sec) [ -6057.2820] [ 1102] [depth= 1] . ( 9 sec) [ -6054.0162] [ 1108] [depth= 1] . ( 9 sec) [ -6034.0978] [ 1099] [depth= 3] . ( 10 sec) [ -6020.3147] [Branch lengths ] . ( 10 sec) [ -6019.6466] [GTR parameters ] . ( 10 sec) [ -6010.6051] [Alpha ][ 0.958899] . ( 11 sec) [ -6004.6285] [ 1096] [depth= 2] . ( 11 sec) [ -5992.3709] [ 1084] [depth= 1] . ( 12 sec) [ -5991.3776] [ 1086] [depth= 1] . ( 12 sec) [ -5990.8515] [ 1084] [depth= 1] . ( 15 sec) [ -5988.2005] [Branch lengths ] . ( 15 sec) [ -5988.1781] [GTR parameters ] . ( 15 sec) [ -5988.1348] [Alpha ][ 0.987031] . ( 20 sec) [ -5988.0598] [Branch lengths ] . ( 41 sec) [ -5988.0465] [Branch lengths ] . ( 41 sec) [ -5988.0465] [Topology ] . ( 41 sec) [ -5987.9817] [Topology ] . ( 42 sec) [ -5987.5015] [Topology ] . ( 43 sec) [ -5984.5756] [Topology ] . ( 43 sec) [ -5974.9837] [Topology ] . ( 44 sec) [ -5967.0276] [Topology ] . ( 45 sec) [ -5966.3910] [Topology ] . ( 45 sec) [ -5966.3787] [GTR parameters ] . ( 45 sec) [ -5966.3686] [Alpha ][ 1.001438] . ( 45 sec) [ -5966.3686] [Topology ] . ( 46 sec) [ -5966.3099] [Topology ] . ( 46 sec) [ -5966.3049] [Topology ] . ( 47 sec) [ -5966.3044] [Topology ] . ( 47 sec) [ -5966.3044] [GTR parameters ] . ( 47 sec) [ -5966.3044] [Alpha ][ 1.000436] . ( 47 sec) [ -5966.3044] [Topology ] . ( 48 sec) [ -5966.3043] [Topology ] . ( 48 sec) [ -5966.3043] [GTR parameters ] . ( 48 sec) [ -5966.3043] [Alpha ][ 1.000436] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -5966.1942] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -5966.1270] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5966.126973. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5986.650611 . ( 1 sec) [ -5984.4472] [GTR parameters ] . ( 1 sec) [ -5984.4385] [Alpha ][ 0.986858] . ( 1 sec) [ -5984.4385] [Topology ] . ( 1 sec) [ -5969.4084] [Topology ] . ( 2 sec) [ -5967.7631] [Topology ] . ( 3 sec) [ -5967.0781] [Topology ] . Moving backward . ( 4 sec) [ -5966.5799] [Topology ] . ( 4 sec) [ -5966.2404] [Topology ] . ( 5 sec) [ -5966.1746] [Topology ] . ( 6 sec) [ -5966.1529] [Topology ] . ( 6 sec) [ -5966.1448] [Topology ] . ( 7 sec) [ -5966.1417] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5966.140439 . ( 12 sec) [ -5966.1288] [GTR parameters ] . ( 12 sec) [ -5966.1175] [Alpha ][ 1.002142] . ( 12 sec) [ -5966.1175] [Topology ] . ( 13 sec) [ -5966.1163] [Topology ] . ( 14 sec) [ -5966.1159] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5966.115860 . ( 18 sec) [ -5966.1159] [GTR parameters ] . ( 18 sec) [ -5966.1159] [Alpha ][ 1.002142] . ( 18 sec) [ -5966.1159] [Topology ] . ( 19 sec) [ -5966.1157] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 28 sec) [ -5984.4472] [GTR parameters ] . ( 28 sec) [ -5984.4385] [Alpha ][ 0.986858] . ( 28 sec) [ -5983.9445] [ 1080] [depth= 1] . ( 28 sec) [ -5983.5588] [ 1078] [depth= 1] . ( 28 sec) [ -5979.7326] [ 1080] [depth= 1] . ( 28 sec) [ -5977.6685] [ 1084] [depth= 1] . ( 30 sec) [ -5977.3826] [ 1082] [depth= 1] . ( 30 sec) [ -5975.1296] [ 1084] [depth= 1] . ( 30 sec) [ -5974.8690] [ 1087] [depth= 1] . ( 30 sec) [ -5974.4485] [ 1087] [depth= 1] . ( 30 sec) [ -5974.4308] [ 1087] [depth= 1] . ( 32 sec) [ -5973.9120] [ 1087] [depth= 1] . ( 32 sec) [ -5973.9017] [ 1087] [depth= 1] . ( 32 sec) [ -5966.6691] [Branch lengths ] . ( 33 sec) [ -5966.6477] [GTR parameters ] . ( 33 sec) [ -5966.6434] [Alpha ][ 0.996132] . ( 37 sec) [ -5966.4650] [Branch lengths ] . ( 58 sec) [ -5966.4548] [Branch lengths ] . ( 58 sec) [ -5966.4548] [Topology ] . ( 59 sec) [ -5966.4543] [Topology ] . ( 59 sec) [ -5966.4541] [GTR parameters ] . ( 59 sec) [ -5966.4538] [Alpha ][ 0.998225] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -5966.1738] [Topology ] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -5966.1185] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5966.115680 . Log likelihood obtained after SPR moves : -5966.118526 . Log likelihood of the current tree: -5966.115680. . Printing the most likely tree in file 'data27.phy_phyml_tree.txt'... . Best log likelihood : -5966.115680 . Time used 0h1m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo