.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data32.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... . 364 patterns found. (out of a total of 500 sites) . 126 sites without polymorphism (25.20%). . [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) [ -13230.6417] [GTR parameters ] . ( 1 sec) [ -13029.2778] [Alpha ][ 0.500960] . ( 1 sec) [ -12681.9946] [ 2295] [depth= 4] . ( 1 sec) [ -12409.9809] [ 2213] [depth= 6] . ( 1 sec) [ -12232.1011] [ 2194] [depth= 4] . ( 1 sec) [ -12221.8442] [ 2190] [depth= 6] . ( 1 sec) [ -12159.4873] [ 2175] [depth= 1] . ( 1 sec) [ -12156.0941] [ 2175] [depth= 2] . ( 1 sec) [ -12140.7501] [ 2174] [depth= 1] . ( 2 sec) [ -12137.3634] [ 2239] [depth= 4] . ( 2 sec) [ -12083.4656] [ 2228] [depth= 5] . ( 2 sec) [ -11939.6635] [ 2210] [depth= 5] . ( 2 sec) [ -11769.3349] [ 2165] [depth= 1] . ( 2 sec) [ -11591.4534] [ 2126] [depth= 12] . ( 2 sec) [ -11213.2818] [ 2071] [depth= 9] . ( 2 sec) [ -11071.9668] [ 2065] [depth= 3] . ( 2 sec) [ -11062.1726] [ 2061] [depth= 2] . ( 2 sec) [ -10994.6865] [ 2026] [depth= 2] . ( 2 sec) [ -10858.3633] [ 2015] [depth= 5] . ( 2 sec) [ -10740.3460] [ 2015] [depth= 1] . ( 2 sec) [ -10709.4357] [ 2014] [depth= 1] . ( 2 sec) [ -10592.6327] [ 1988] [depth= 3] . ( 2 sec) [ -10471.3024] [ 1971] [depth= 3] . ( 2 sec) [ -10317.8772] [ 1957] [depth= 8] . ( 2 sec) [ -9851.9621] [ 1863] [depth= 5] . ( 3 sec) [ -9831.4937] [ 1862] [depth= 2] . ( 3 sec) [ -9788.7565] [ 1854] [depth= 6] . ( 3 sec) [ -9277.9582] [ 1778] [depth= 10] . ( 3 sec) [ -9159.9062] [ 1751] [depth= 6] . ( 3 sec) [ -9008.6199] [ 1731] [depth= 7] . ( 3 sec) [ -8718.0399] [ 1724] [depth= 1] . ( 3 sec) [ -8585.7745] [ 1690] [depth= 5] . ( 3 sec) [ -8536.7260] [ 1684] [depth= 4] . ( 3 sec) [ -8502.4535] [ 1680] [depth= 1] . ( 3 sec) [ -8483.5206] [ 1649] [depth= 4] . ( 3 sec) [ -8465.4877] [ 1635] [depth= 3] . ( 3 sec) [ -8457.8019] [ 1630] [depth= 1] . ( 3 sec) [ -8444.3134] [ 1609] [depth= 1] . ( 3 sec) [ -8415.2389] [ 1613] [depth= 1] . ( 3 sec) [ -8043.1148] [ 1536] [depth= 10] . ( 3 sec) [ -7850.5730] [ 1475] [depth= 11] . ( 3 sec) [ -7771.0391] [ 1473] [depth= 3] . ( 3 sec) [ -7678.7394] [ 1470] [depth= 5] . ( 3 sec) [ -7672.2865] [ 1470] [depth= 1] . ( 3 sec) [ -7671.8613] [ 1470] [depth= 1] . ( 3 sec) [ -7634.1531] [ 1457] [depth= 5] . ( 4 sec) [ -7452.3779] [ 1417] [depth= 2] . ( 4 sec) [ -7421.8773] [ 1416] [depth= 1] . ( 4 sec) [ -7217.7341] [ 1373] [depth= 4] . ( 4 sec) [ -7169.6761] [ 1364] [depth= 2] . ( 4 sec) [ -7122.4430] [ 1366] [depth= 1] . ( 4 sec) [ -7105.7759] [ 1370] [depth= 8] . ( 4 sec) [ -7105.6447] [ 1369] [depth= 1] . ( 4 sec) [ -7100.4960] [ 1359] [depth= 1] . ( 4 sec) [ -7089.3163] [ 1361] [depth= 7] . ( 4 sec) [ -7053.9903] [ 1355] [depth= 1] . ( 4 sec) [ -7049.5550] [ 1356] [depth= 1] . ( 4 sec) [ -7049.1878] [ 1356] [depth= 1] . ( 4 sec) [ -6943.6921] [ 1318] [depth= 8] . ( 4 sec) [ -6942.9209] [ 1319] [depth= 11] . ( 5 sec) [ -6942.8564] [ 1321] [depth= 1] . ( 5 sec) [ -6812.5059] [ 1287] [depth= 6] . ( 5 sec) [ -6775.6283] [ 1280] [depth= 1] . ( 5 sec) [ -6730.6994] [ 1262] [depth= 1] . ( 5 sec) [ -6699.5412] [ 1252] [depth= 4] . ( 5 sec) [ -6694.9004] [ 1251] [depth= 2] . ( 5 sec) [ -6693.5700] [ 1253] [depth= 2] . ( 5 sec) [ -6689.1824] [ 1251] [depth= 2] . ( 5 sec) [ -6688.7606] [ 1252] [depth= 1] . ( 5 sec) [ -6660.4794] [ 1260] [depth= 2] . ( 5 sec) [ -6619.2355] [ 1251] [depth= 4] . ( 5 sec) [ -6537.8476] [ 1237] [depth= 3] . ( 5 sec) [ -6530.8340] [ 1233] [depth= 1] . ( 5 sec) [ -6499.4646] [ 1232] [depth= 1] . ( 5 sec) [ -6483.3028] [ 1227] [depth= 2] . ( 5 sec) [ -6483.0331] [ 1228] [depth= 1] . ( 5 sec) [ -6482.2812] [ 1227] [depth= 1] . ( 5 sec) [ -6463.4193] [ 1217] [depth= 1] . ( 5 sec) [ -6462.8746] [ 1215] [depth= 2] . ( 5 sec) [ -6462.7864] [ 1217] [depth= 1] . ( 6 sec) [ -6460.3585] [ 1216] [depth= 2] . ( 6 sec) [ -6414.5771] [Branch lengths ] . ( 6 sec) [ -6412.7480] [GTR parameters ] . ( 6 sec) [ -6386.9370] [Alpha ][ 0.950768] . ( 6 sec) [ -6299.7589] [ 1198] [depth= 7] . ( 7 sec) [ -6298.7536] [ 1196] [depth= 1] . ( 7 sec) [ -6296.8460] [ 1195] [depth= 1] . ( 7 sec) [ -6190.6485] [ 1154] [depth= 5] . ( 7 sec) [ -6171.3738] [ 1153] [depth= 1] . ( 7 sec) [ -6104.9505] [ 1118] [depth= 1] . ( 7 sec) [ -6072.1071] [ 1101] [depth= 4] . ( 7 sec) [ -6069.8350] [ 1101] [depth= 2] . ( 7 sec) [ -6069.7958] [ 1101] [depth= 1] . ( 7 sec) [ -6069.6138] [ 1102] [depth= 1] . ( 8 sec) [ -6052.8850] [ 1095] [depth= 1] . ( 8 sec) [ -6042.6404] [ 1094] [depth= 1] . ( 8 sec) [ -6042.5793] [ 1094] [depth= 1] . ( 9 sec) [ -6041.6952] [ 1097] [depth= 1] . ( 9 sec) [ -6041.6531] [ 1097] [depth= 1] . ( 10 sec) [ -6041.6382] [ 1096] [depth= 2] . ( 10 sec) [ -6041.5557] [ 1096] [depth= 1] . ( 11 sec) [ -6041.5350] [ 1096] [depth= 1] . ( 11 sec) [ -6033.8204] [Branch lengths ] . ( 12 sec) [ -6033.6596] [GTR parameters ] . ( 12 sec) [ -6031.8217] [Alpha ][ 1.156651] . ( 12 sec) [ -6031.8071] [ 1096] [depth= 1] . ( 13 sec) [ -6031.7747] [ 1097] [depth= 2] . ( 13 sec) [ -6031.7553] [ 1096] [depth= 1] . ( 15 sec) [ -6031.7313] [ 1097] [depth= 1] . ( 16 sec) [ -6031.7177] [ 1097] [depth= 1] . ( 16 sec) [ -6031.2578] [Branch lengths ] . ( 16 sec) [ -6031.2576] [GTR parameters ] . ( 17 sec) [ -6031.2475] [Alpha ][ 1.174384] . ( 19 sec) [ -6031.2214] [ 1095] [depth= 1] . ( 45 sec) [ -6031.0954] [Branch lengths ] . ( 45 sec) [ -6031.0949] [GTR parameters ] . ( 45 sec) [ -6031.0943] [Alpha ][ 1.178472] . ( 46 sec) [ -6031.0943] [Topology ] . ( 46 sec) [ -6031.0900] [Topology ] . ( 48 sec) [ -6031.0890] [Topology ] . ( 49 sec) [ -6031.0886] [Topology ] . ( 49 sec) [ -6031.0885] [GTR parameters ] . ( 49 sec) [ -6031.0885] [Alpha ][ 1.179650] . ( 49 sec) [ -6031.0885] [Topology ] . ( 51 sec) [ -6031.0883] [Topology ] . ( 51 sec) [ -6031.0883] [GTR parameters ] . ( 51 sec) [ -6031.0883] [Alpha ][ 1.179650] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -6031.0882] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.088215. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13320.8843] [GTR parameters ] . ( 1 sec) [ -13102.8034] [Alpha ][ 0.500960] . ( 1 sec) [ -12597.3262] [ 2393] [depth= 9] . ( 1 sec) [ -12290.7197] [ 2308] [depth= 11] . ( 1 sec) [ -12193.2718] [ 2289] [depth= 4] . ( 1 sec) [ -12193.0969] [ 2283] [depth= 6] . ( 1 sec) [ -12083.5233] [ 2253] [depth= 1] . ( 1 sec) [ -11993.7053] [ 2245] [depth= 3] . ( 2 sec) [ -11929.2487] [ 2248] [depth= 1] . ( 2 sec) [ -11765.3001] [ 2243] [depth= 3] . ( 2 sec) [ -11720.5425] [ 2229] [depth= 1] . ( 2 sec) [ -11648.6854] [ 2223] [depth= 2] . ( 2 sec) [ -11533.0444] [ 2208] [depth= 4] . ( 2 sec) [ -11412.2665] [ 2207] [depth= 1] . ( 2 sec) [ -11219.7120] [ 2163] [depth= 3] . ( 2 sec) [ -11201.5378] [ 2163] [depth= 4] . ( 2 sec) [ -11141.8076] [ 2163] [depth= 4] . ( 2 sec) [ -11041.1171] [ 2129] [depth= 5] . ( 2 sec) [ -11000.3611] [ 2105] [depth= 10] . ( 2 sec) [ -10860.2769] [ 2110] [depth= 3] . ( 2 sec) [ -10837.3557] [ 2107] [depth= 1] . ( 2 sec) [ -10828.0659] [ 2104] [depth= 2] . ( 2 sec) [ -10779.6193] [ 2083] [depth= 9] . ( 3 sec) [ -10585.5848] [ 2031] [depth= 6] . ( 3 sec) [ -10565.2988] [ 2029] [depth= 7] . ( 3 sec) [ -10353.4947] [ 1985] [depth= 4] . ( 3 sec) [ -10217.1273] [ 1975] [depth= 4] . ( 3 sec) [ -10185.3752] [ 1967] [depth= 1] . ( 3 sec) [ -9835.8133] [ 1895] [depth= 4] . ( 3 sec) [ -9809.9298] [ 1894] [depth= 1] . ( 3 sec) [ -9619.6580] [ 1886] [depth= 11] . ( 3 sec) [ -9365.7610] [ 1802] [depth= 8] . ( 3 sec) [ -9272.6888] [ 1745] [depth= 5] . ( 3 sec) [ -9053.5659] [ 1707] [depth= 7] . ( 3 sec) [ -8914.9422] [ 1695] [depth= 10] . ( 4 sec) [ -8905.7416] [ 1697] [depth= 1] . ( 4 sec) [ -8754.0108] [ 1676] [depth= 2] . ( 4 sec) [ -8725.9703] [ 1677] [depth= 1] . ( 4 sec) [ -8701.9539] [ 1673] [depth= 1] . ( 4 sec) [ -8609.1214] [ 1642] [depth= 11] . ( 4 sec) [ -8578.2451] [ 1622] [depth= 1] . ( 4 sec) [ -8571.8854] [ 1623] [depth= 1] . ( 4 sec) [ -8513.9746] [ 1596] [depth= 7] . ( 4 sec) [ -8500.1113] [ 1595] [depth= 1] . ( 4 sec) [ -8457.1243] [ 1592] [depth= 1] . ( 4 sec) [ -8412.3885] [ 1583] [depth= 1] . ( 4 sec) [ -8406.3889] [ 1579] [depth= 9] . ( 5 sec) [ -8274.4666] [ 1551] [depth= 3] . ( 5 sec) [ -8207.6910] [ 1520] [depth= 3] . ( 5 sec) [ -8201.4464] [ 1517] [depth= 1] . ( 5 sec) [ -8008.9548] [ 1473] [depth= 7] . ( 5 sec) [ -7907.2861] [ 1420] [depth= 2] . ( 5 sec) [ -7842.9063] [ 1420] [depth= 1] . ( 5 sec) [ -7798.5533] [ 1415] [depth= 4] . ( 5 sec) [ -7793.6556] [ 1413] [depth= 2] . ( 5 sec) [ -7753.1007] [ 1413] [depth= 1] . ( 5 sec) [ -7751.2618] [ 1413] [depth= 1] . ( 5 sec) [ -7750.3933] [ 1412] [depth= 2] . ( 5 sec) [ -7719.6357] [ 1403] [depth= 1] . ( 5 sec) [ -7718.1778] [ 1404] [depth= 1] . ( 6 sec) [ -7686.7245] [ 1390] [depth= 1] . ( 6 sec) [ -7671.7196] [ 1388] [depth= 1] . ( 6 sec) [ -7668.9672] [ 1385] [depth= 1] . ( 6 sec) [ -7668.9328] [ 1386] [depth= 2] . ( 6 sec) [ -7665.2084] [ 1384] [depth= 1] . ( 6 sec) [ -7600.2979] [ 1356] [depth= 9] . ( 6 sec) [ -7526.1683] [ 1322] [depth= 7] . ( 6 sec) [ -7238.3297] [ 1309] [depth= 1] . ( 6 sec) [ -7056.4000] [ 1310] [depth= 5] . ( 6 sec) [ -7056.2037] [ 1310] [depth= 1] . ( 6 sec) [ -7051.9551] [ 1308] [depth= 2] . ( 7 sec) [ -6979.7842] [ 1284] [depth= 5] . ( 7 sec) [ -6940.9461] [ 1281] [depth= 2] . ( 7 sec) [ -6897.1531] [ 1279] [depth= 1] . ( 7 sec) [ -6880.1217] [ 1271] [depth= 1] . ( 7 sec) [ -6879.4393] [ 1272] [depth= 1] . ( 7 sec) [ -6743.2258] [ 1263] [depth= 2] . ( 7 sec) [ -6718.0248] [ 1280] [depth= 2] . ( 7 sec) [ -6694.1540] [ 1277] [depth= 2] . ( 7 sec) [ -6608.2649] [ 1238] [depth= 3] . ( 7 sec) [ -6531.4219] [ 1223] [depth= 5] . ( 8 sec) [ -6506.2578] [ 1214] [depth= 1] . ( 8 sec) [ -6489.3276] [ 1212] [depth= 5] . ( 8 sec) [ -6485.1790] [ 1215] [depth= 1] . ( 8 sec) [ -6413.5005] [Branch lengths ] . ( 9 sec) [ -6410.6307] [GTR parameters ] . ( 9 sec) [ -6384.4607] [Alpha ][ 0.955454] . ( 9 sec) [ -6383.6372] [ 1215] [depth= 1] . ( 10 sec) [ -6383.4710] [ 1215] [depth= 1] . ( 10 sec) [ -6327.0654] [ 1192] [depth= 1] . ( 10 sec) [ -6319.4897] [ 1191] [depth= 2] . ( 10 sec) [ -6303.8657] [ 1185] [depth= 1] . ( 10 sec) [ -6295.1863] [ 1182] [depth= 1] . ( 10 sec) [ -6253.2293] [ 1150] [depth= 1] . ( 11 sec) [ -6237.7266] [ 1141] [depth= 2] . ( 11 sec) [ -6228.8027] [ 1136] [depth= 2] . ( 11 sec) [ -6136.9767] [ 1118] [depth= 1] . ( 11 sec) [ -6101.8914] [ 1116] [depth= 1] . ( 11 sec) [ -6100.1517] [ 1114] [depth= 1] . ( 11 sec) [ -6071.5658] [ 1103] [depth= 1] . ( 11 sec) [ -6069.4688] [ 1103] [depth= 1] . ( 12 sec) [ -6052.8735] [ 1093] [depth= 1] . ( 12 sec) [ -6052.8181] [ 1093] [depth= 1] . ( 13 sec) [ -6052.1802] [ 1095] [depth= 1] . ( 13 sec) [ -6052.1111] [ 1095] [depth= 1] . ( 13 sec) [ -6050.6093] [ 1094] [depth= 1] . ( 13 sec) [ -6050.5607] [ 1094] [depth= 1] . ( 13 sec) [ -6048.4598] [ 1093] [depth= 1] . ( 14 sec) [ -6047.2883] [ 1093] [depth= 2] . ( 14 sec) [ -6034.0659] [Branch lengths ] . ( 15 sec) [ -6033.7122] [GTR parameters ] . ( 15 sec) [ -6031.9157] [Alpha ][ 1.160115] . ( 20 sec) [ -6031.1834] [Branch lengths ] . ( 50 sec) [ -6031.1087] [Branch lengths ] . ( 50 sec) [ -6031.1087] [Topology ] . ( 51 sec) [ -6031.1038] [Topology ] . ( 52 sec) [ -6031.1024] [Topology ] . ( 53 sec) [ -6031.1019] [Topology ] . ( 54 sec) [ -6031.1012] [GTR parameters ] . ( 54 sec) [ -6031.0893] [Alpha ][ 1.179512] . ( 54 sec) [ -6031.0893] [Topology ] . ( 55 sec) [ -6031.0886] [Topology ] . ( 55 sec) [ -6031.0886] [GTR parameters ] . ( 55 sec) [ -6031.0886] [Alpha ][ 1.179512] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -6031.0885] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.088471. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13955.0500] [GTR parameters ] . ( 1 sec) [ -13729.3235] [Alpha ][ 0.500960] . ( 1 sec) [ -13301.3289] [ 2463] [depth= 1] . ( 1 sec) [ -12943.7379] [ 2379] [depth= 4] . ( 1 sec) [ -12877.1496] [ 2376] [depth= 4] . ( 1 sec) [ -12619.5975] [ 2374] [depth= 2] . ( 1 sec) [ -12519.8428] [ 2319] [depth= 7] . ( 1 sec) [ -12289.4340] [ 2318] [depth= 3] . ( 1 sec) [ -11846.1783] [ 2297] [depth= 7] . ( 1 sec) [ -11761.3441] [ 2286] [depth= 5] . ( 1 sec) [ -11497.3290] [ 2214] [depth= 11] . ( 1 sec) [ -11447.1306] [ 2213] [depth= 10] . ( 1 sec) [ -11231.3811] [ 2186] [depth= 9] . ( 1 sec) [ -11044.2250] [ 2144] [depth= 10] . ( 2 sec) [ -11013.9348] [ 2143] [depth= 4] . ( 2 sec) [ -10964.7906] [ 2141] [depth= 1] . ( 2 sec) [ -10888.2717] [ 2088] [depth= 5] . ( 2 sec) [ -10810.8760] [ 2092] [depth= 3] . ( 2 sec) [ -10802.3615] [ 2085] [depth= 3] . ( 2 sec) [ -10675.9119] [ 2078] [depth= 10] . ( 2 sec) [ -10547.0887] [ 2043] [depth= 6] . ( 2 sec) [ -10273.1440] [ 1980] [depth= 11] . ( 2 sec) [ -10178.6171] [ 1939] [depth= 1] . ( 2 sec) [ -10052.4280] [ 1928] [depth= 9] . ( 2 sec) [ -9998.9311] [ 1897] [depth= 1] . ( 2 sec) [ -9993.7840] [ 1897] [depth= 1] . ( 2 sec) [ -9805.1600] [ 1868] [depth= 5] . ( 2 sec) [ -9750.0983] [ 1846] [depth= 1] . ( 3 sec) [ -9748.8057] [ 1846] [depth= 1] . ( 3 sec) [ -9624.8640] [ 1842] [depth= 6] . ( 3 sec) [ -9385.0436] [ 1827] [depth= 10] . ( 3 sec) [ -9100.6017] [ 1770] [depth= 7] . ( 3 sec) [ -8922.2033] [ 1727] [depth= 2] . ( 3 sec) [ -8900.1237] [ 1725] [depth= 1] . ( 3 sec) [ -8803.5888] [ 1686] [depth= 9] . ( 3 sec) [ -8796.7331] [ 1685] [depth= 1] . ( 3 sec) [ -8633.1742] [ 1631] [depth= 1] . ( 3 sec) [ -8613.4913] [ 1630] [depth= 1] . ( 3 sec) [ -8610.9812] [ 1630] [depth= 1] . ( 3 sec) [ -8465.0692] [ 1578] [depth= 1] . ( 4 sec) [ -8407.0433] [ 1586] [depth= 7] . ( 4 sec) [ -8220.8499] [ 1536] [depth= 1] . ( 4 sec) [ -8186.8079] [ 1555] [depth= 6] . ( 4 sec) [ -8110.1579] [ 1542] [depth= 5] . ( 4 sec) [ -8008.3947] [ 1539] [depth= 2] . ( 4 sec) [ -7945.7186] [ 1539] [depth= 1] . ( 4 sec) [ -7863.3495] [ 1529] [depth= 4] . ( 4 sec) [ -7743.2550] [ 1527] [depth= 2] . ( 4 sec) [ -7742.9771] [ 1523] [depth= 8] . ( 4 sec) [ -7706.9739] [ 1509] [depth= 1] . ( 4 sec) [ -7449.8340] [ 1462] [depth= 7] . ( 4 sec) [ -7372.3638] [ 1459] [depth= 2] . ( 5 sec) [ -7329.9056] [ 1413] [depth= 3] . ( 5 sec) [ -7303.0270] [ 1412] [depth= 1] . ( 5 sec) [ -7156.3560] [ 1385] [depth= 9] . ( 5 sec) [ -7143.9068] [ 1384] [depth= 1] . ( 5 sec) [ -7143.6155] [ 1386] [depth= 1] . ( 5 sec) [ -7108.6717] [ 1370] [depth= 4] . ( 5 sec) [ -7105.1223] [ 1366] [depth= 3] . ( 5 sec) [ -7038.3026] [ 1363] [depth= 1] . ( 5 sec) [ -6945.6579] [ 1310] [depth= 6] . ( 5 sec) [ -6856.2545] [ 1290] [depth= 3] . ( 5 sec) [ -6836.1505] [ 1290] [depth= 1] . ( 6 sec) [ -6761.5989] [ 1288] [depth= 2] . ( 6 sec) [ -6745.2269] [ 1298] [depth= 1] . ( 6 sec) [ -6731.8346] [ 1292] [depth= 1] . ( 6 sec) [ -6730.5453] [ 1292] [depth= 1] . ( 6 sec) [ -6669.6798] [ 1288] [depth= 2] . ( 6 sec) [ -6666.4498] [ 1289] [depth= 2] . ( 6 sec) [ -6658.4536] [ 1285] [depth= 1] . ( 6 sec) [ -6606.0494] [ 1282] [depth= 3] . ( 6 sec) [ -6604.2049] [ 1284] [depth= 1] . ( 7 sec) [ -6556.8741] [ 1260] [depth= 7] . ( 7 sec) [ -6556.5640] [ 1259] [depth= 1] . ( 7 sec) [ -6539.3170] [ 1259] [depth= 4] . ( 7 sec) [ -6513.6347] [ 1249] [depth= 1] . ( 7 sec) [ -6512.8481] [ 1249] [depth= 1] . ( 7 sec) [ -6508.4131] [ 1248] [depth= 1] . ( 8 sec) [ -6420.3102] [Branch lengths ] . ( 8 sec) [ -6418.8526] [GTR parameters ] . ( 9 sec) [ -6391.1007] [Alpha ][ 0.959007] . ( 9 sec) [ -6373.2387] [ 1238] [depth= 1] . ( 9 sec) [ -6370.5174] [ 1240] [depth= 1] . ( 9 sec) [ -6354.9153] [ 1230] [depth= 1] . ( 9 sec) [ -6354.9049] [ 1230] [depth= 2] . ( 9 sec) [ -6286.1043] [ 1184] [depth= 8] . ( 9 sec) [ -6259.1507] [ 1165] [depth= 4] . ( 9 sec) [ -6259.1262] [ 1165] [depth= 1] . ( 10 sec) [ -6259.0383] [ 1166] [depth= 2] . ( 10 sec) [ -6257.8108] [ 1166] [depth= 1] . ( 10 sec) [ -6257.6284] [ 1170] [depth= 1] . ( 10 sec) [ -6239.5068] [ 1156] [depth= 2] . ( 11 sec) [ -6239.4895] [ 1156] [depth= 1] . ( 11 sec) [ -6202.2483] [ 1138] [depth= 2] . ( 11 sec) [ -6202.1373] [ 1153] [depth= 1] . ( 11 sec) [ -6151.1996] [ 1129] [depth= 3] . ( 11 sec) [ -6123.4353] [ 1118] [depth= 1] . ( 11 sec) [ -6106.2195] [ 1116] [depth= 2] . ( 12 sec) [ -6106.2067] [ 1117] [depth= 1] . ( 12 sec) [ -6067.8442] [ 1105] [depth= 1] . ( 12 sec) [ -6048.5847] [ 1095] [depth= 1] . ( 12 sec) [ -6048.5589] [ 1094] [depth= 1] . ( 14 sec) [ -6033.8201] [Branch lengths ] . ( 15 sec) [ -6033.3068] [GTR parameters ] . ( 15 sec) [ -6031.2220] [Alpha ][ 1.179089] . ( 19 sec) [ -6031.0942] [Branch lengths ] . ( 44 sec) [ -6031.0890] [Branch lengths ] . ( 44 sec) [ -6031.0890] [Topology ] . ( 46 sec) [ -6031.0889] [Topology ] . ( 46 sec) [ -6031.0882] [GTR parameters ] . ( 46 sec) [ -6031.0882] [Alpha ][ 1.180269] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.088210. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14025.4813] [GTR parameters ] . ( 1 sec) [ -13786.8994] [Alpha ][ 0.500960] . ( 2 sec) [ -13137.6935] [ 2468] [depth= 10] . ( 2 sec) [ -12626.1380] [ 2389] [depth= 3] . ( 2 sec) [ -12542.3522] [ 2377] [depth= 7] . ( 2 sec) [ -12503.3211] [ 2354] [depth= 1] . ( 2 sec) [ -12379.9581] [ 2339] [depth= 5] . ( 2 sec) [ -12225.2050] [ 2324] [depth= 3] . ( 2 sec) [ -12143.1792] [ 2324] [depth= 5] . ( 2 sec) [ -11946.0272] [ 2306] [depth= 7] . ( 2 sec) [ -11903.9009] [ 2305] [depth= 1] . ( 2 sec) [ -11780.0512] [ 2299] [depth= 4] . ( 2 sec) [ -11661.1541] [ 2268] [depth= 1] . ( 2 sec) [ -11573.2474] [ 2251] [depth= 10] . ( 2 sec) [ -11498.3067] [ 2251] [depth= 1] . ( 3 sec) [ -11451.6955] [ 2212] [depth= 3] . ( 3 sec) [ -11442.6395] [ 2212] [depth= 1] . ( 3 sec) [ -11326.6889] [ 2206] [depth= 3] . ( 3 sec) [ -11242.9572] [ 2179] [depth= 1] . ( 3 sec) [ -11069.8888] [ 2142] [depth= 3] . ( 3 sec) [ -10879.7877] [ 2097] [depth= 4] . ( 3 sec) [ -10756.9493] [ 2076] [depth= 8] . ( 3 sec) [ -10720.3801] [ 2055] [depth= 1] . ( 3 sec) [ -10667.7607] [ 2051] [depth= 6] . ( 3 sec) [ -10536.1930] [ 2012] [depth= 1] . ( 3 sec) [ -10491.9566] [ 2001] [depth= 1] . ( 3 sec) [ -10420.2249] [ 1980] [depth= 5] . ( 4 sec) [ -10330.7870] [ 1960] [depth= 4] . ( 4 sec) [ -10071.3579] [ 1957] [depth= 11] . ( 4 sec) [ -9980.9604] [ 1905] [depth= 1] . ( 4 sec) [ -9709.2871] [ 1888] [depth= 4] . ( 4 sec) [ -9694.3213] [ 1890] [depth= 1] . ( 4 sec) [ -9424.8586] [ 1765] [depth= 11] . ( 4 sec) [ -9411.8180] [ 1765] [depth= 1] . ( 4 sec) [ -9360.9863] [ 1759] [depth= 1] . ( 4 sec) [ -9279.0900] [ 1748] [depth= 1] . ( 4 sec) [ -9148.2462] [ 1738] [depth= 5] . ( 4 sec) [ -8972.6413] [ 1724] [depth= 5] . ( 4 sec) [ -8894.6924] [ 1721] [depth= 1] . ( 4 sec) [ -8655.2524] [ 1703] [depth= 9] . ( 5 sec) [ -8648.7236] [ 1703] [depth= 1] . ( 5 sec) [ -8645.1591] [ 1704] [depth= 3] . ( 5 sec) [ -8344.2648] [ 1678] [depth= 3] . ( 5 sec) [ -8326.5266] [ 1678] [depth= 1] . ( 5 sec) [ -8118.5865] [ 1631] [depth= 3] . ( 5 sec) [ -8117.9588] [ 1631] [depth= 1] . ( 5 sec) [ -8108.5139] [ 1630] [depth= 1] . ( 5 sec) [ -8101.7057] [ 1625] [depth= 1] . ( 5 sec) [ -7980.8252] [ 1626] [depth= 4] . ( 5 sec) [ -7815.9870] [ 1546] [depth= 6] . ( 5 sec) [ -7795.8722] [ 1541] [depth= 1] . ( 5 sec) [ -7763.4807] [ 1542] [depth= 1] . ( 5 sec) [ -7741.9829] [ 1537] [depth= 2] . ( 5 sec) [ -7532.5270] [ 1494] [depth= 4] . ( 5 sec) [ -7393.2586] [ 1456] [depth= 8] . ( 6 sec) [ -7355.3066] [ 1457] [depth= 6] . ( 6 sec) [ -7347.0231] [ 1454] [depth= 1] . ( 6 sec) [ -7339.8507] [ 1458] [depth= 1] . ( 6 sec) [ -7336.9372] [ 1457] [depth= 1] . ( 6 sec) [ -7333.3364] [ 1441] [depth= 5] . ( 6 sec) [ -7266.5761] [ 1425] [depth= 6] . ( 6 sec) [ -7167.2715] [ 1427] [depth= 3] . ( 6 sec) [ -7076.6165] [ 1375] [depth= 10] . ( 6 sec) [ -6979.7478] [ 1354] [depth= 7] . ( 6 sec) [ -6895.9099] [ 1335] [depth= 8] . ( 7 sec) [ -6890.3307] [ 1334] [depth= 1] . ( 7 sec) [ -6881.2218] [ 1332] [depth= 1] . ( 7 sec) [ -6875.9835] [ 1305] [depth= 1] . ( 7 sec) [ -6875.7124] [ 1303] [depth= 2] . ( 7 sec) [ -6693.2229] [ 1272] [depth= 4] . ( 7 sec) [ -6670.5941] [ 1275] [depth= 2] . ( 7 sec) [ -6668.4090] [ 1275] [depth= 2] . ( 7 sec) [ -6581.0934] [ 1245] [depth= 3] . ( 7 sec) [ -6575.7811] [ 1242] [depth= 1] . ( 7 sec) [ -6572.1880] [ 1241] [depth= 3] . ( 8 sec) [ -6536.9274] [ 1238] [depth= 4] . ( 8 sec) [ -6492.6303] [ 1225] [depth= 2] . ( 8 sec) [ -6483.5061] [ 1220] [depth= 1] . ( 8 sec) [ -6366.0263] [Branch lengths ] . ( 9 sec) [ -6364.2090] [GTR parameters ] . ( 9 sec) [ -6340.9143] [Alpha ][ 0.920907] . ( 9 sec) [ -6337.2506] [ 1218] [depth= 1] . ( 9 sec) [ -6333.5827] [ 1215] [depth= 2] . ( 9 sec) [ -6313.3770] [ 1205] [depth= 1] . ( 9 sec) [ -6311.9581] [ 1203] [depth= 2] . ( 9 sec) [ -6311.6188] [ 1203] [depth= 1] . ( 10 sec) [ -6276.1376] [ 1200] [depth= 2] . ( 10 sec) [ -6250.8530] [ 1188] [depth= 1] . ( 10 sec) [ -6247.8327] [ 1187] [depth= 1] . ( 10 sec) [ -6227.9339] [ 1158] [depth= 1] . ( 10 sec) [ -6199.4163] [ 1150] [depth= 1] . ( 10 sec) [ -6160.7522] [ 1144] [depth= 1] . ( 10 sec) [ -6160.5997] [ 1145] [depth= 1] . ( 10 sec) [ -6160.5519] [ 1145] [depth= 1] . ( 11 sec) [ -6160.3268] [ 1147] [depth= 1] . ( 11 sec) [ -6153.7222] [ 1147] [depth= 1] . ( 11 sec) [ -6117.9559] [ 1131] [depth= 4] . ( 11 sec) [ -6112.7779] [ 1128] [depth= 1] . ( 11 sec) [ -6104.7807] [ 1122] [depth= 2] . ( 11 sec) [ -6104.1830] [ 1121] [depth= 1] . ( 11 sec) [ -6104.1133] [ 1122] [depth= 1] . ( 12 sec) [ -6103.9406] [ 1122] [depth= 1] . ( 12 sec) [ -6064.4236] [ 1104] [depth= 4] . ( 12 sec) [ -6063.2477] [ 1105] [depth= 1] . ( 12 sec) [ -6062.8405] [ 1109] [depth= 2] . ( 12 sec) [ -6060.6910] [ 1109] [depth= 1] . ( 12 sec) [ -6060.5825] [ 1109] [depth= 1] . ( 13 sec) [ -6060.5356] [ 1109] [depth= 1] . ( 13 sec) [ -6060.0341] [ 1109] [depth= 1] . ( 13 sec) [ -6045.3719] [ 1101] [depth= 1] . ( 13 sec) [ -6045.0148] [ 1101] [depth= 1] . ( 13 sec) [ -6044.9842] [ 1101] [depth= 1] . ( 13 sec) [ -6042.7355] [ 1100] [depth= 1] . ( 14 sec) [ -6037.5792] [Branch lengths ] . ( 15 sec) [ -6036.5281] [GTR parameters ] . ( 15 sec) [ -6034.1726] [Alpha ][ 1.148132] . ( 15 sec) [ -6034.1076] [ 1095] [depth= 1] . ( 16 sec) [ -6034.0822] [ 1095] [depth= 1] . ( 17 sec) [ -6034.0672] [ 1096] [depth= 1] . ( 17 sec) [ -6034.0448] [ 1096] [depth= 1] . ( 18 sec) [ -6033.1094] [ 1097] [depth= 2] . ( 18 sec) [ -6032.5240] [ 1096] [depth= 1] . ( 18 sec) [ -6032.4602] [ 1095] [depth= 1] . ( 20 sec) [ -6031.3993] [Branch lengths ] . ( 20 sec) [ -6031.3955] [GTR parameters ] . ( 20 sec) [ -6031.3726] [Alpha ][ 1.173724] . ( 25 sec) [ -6031.2053] [Branch lengths ] . ( 44 sec) [ -6031.1167] [ 1093] [depth= 1] . ( 52 sec) [ -6031.0915] [Branch lengths ] . ( 53 sec) [ -6031.0909] [GTR parameters ] . ( 53 sec) [ -6031.0898] [Alpha ][ 1.179396] . ( 53 sec) [ -6031.0898] [Topology ] . ( 54 sec) [ -6031.0885] [Topology ] . ( 55 sec) [ -6031.0882] [Topology ] . ( 55 sec) [ -6031.0882] [GTR parameters ] . ( 55 sec) [ -6031.0882] [Alpha ][ 1.179396] . ( 55 sec) [ -6031.0882] [Topology ] . ( 56 sec) [ -6031.0881] [Topology ] . ( 56 sec) [ -6031.0881] [GTR parameters ] . ( 56 sec) [ -6031.0881] [Alpha ][ 1.179396] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.088126. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14111.7516] [GTR parameters ] . ( 1 sec) [ -13892.4314] [Alpha ][ 0.500960] . ( 1 sec) [ -13441.0922] [ 2474] [depth= 7] . ( 1 sec) [ -12922.2376] [ 2394] [depth= 6] . ( 1 sec) [ -12891.1577] [ 2390] [depth= 6] . ( 1 sec) [ -12751.7508] [ 2389] [depth= 6] . ( 1 sec) [ -12546.4300] [ 2331] [depth= 2] . ( 1 sec) [ -12446.9931] [ 2330] [depth= 3] . ( 1 sec) [ -12210.4667] [ 2315] [depth= 10] . ( 1 sec) [ -12099.8599] [ 2310] [depth= 1] . ( 1 sec) [ -11952.5302] [ 2276] [depth= 9] . ( 1 sec) [ -11675.6511] [ 2191] [depth= 1] . ( 1 sec) [ -11609.9626] [ 2190] [depth= 1] . ( 1 sec) [ -11607.8781] [ 2191] [depth= 1] . ( 2 sec) [ -11465.6238] [ 2156] [depth= 6] . ( 2 sec) [ -11441.8722] [ 2144] [depth= 2] . ( 2 sec) [ -11327.8857] [ 2114] [depth= 9] . ( 2 sec) [ -11115.5477] [ 2109] [depth= 1] . ( 2 sec) [ -11061.9380] [ 2103] [depth= 10] . ( 2 sec) [ -10957.5123] [ 2096] [depth= 1] . ( 2 sec) [ -10901.0827] [ 2095] [depth= 11] . ( 2 sec) [ -10837.2295] [ 2043] [depth= 2] . ( 2 sec) [ -10730.0825] [ 2020] [depth= 8] . ( 2 sec) [ -10596.7960] [ 1988] [depth= 6] . ( 2 sec) [ -10590.6366] [ 1989] [depth= 2] . ( 2 sec) [ -10334.8939] [ 1921] [depth= 6] . ( 2 sec) [ -10298.2977] [ 1926] [depth= 8] . ( 3 sec) [ -10262.8019] [ 1940] [depth= 10] . ( 3 sec) [ -9898.4214] [ 1919] [depth= 7] . ( 3 sec) [ -9738.8588] [ 1881] [depth= 1] . ( 3 sec) [ -9652.3578] [ 1855] [depth= 4] . ( 3 sec) [ -9583.5167] [ 1839] [depth= 3] . ( 3 sec) [ -9534.1501] [ 1825] [depth= 1] . ( 3 sec) [ -9488.6521] [ 1816] [depth= 6] . ( 3 sec) [ -9461.7360] [ 1822] [depth= 3] . ( 3 sec) [ -9396.5367] [ 1792] [depth= 12] . ( 3 sec) [ -9257.3485] [ 1747] [depth= 4] . ( 3 sec) [ -9187.4796] [ 1747] [depth= 1] . ( 3 sec) [ -9166.2664] [ 1743] [depth= 2] . ( 3 sec) [ -9161.9660] [ 1767] [depth= 6] . ( 4 sec) [ -9066.8359] [ 1722] [depth= 4] . ( 4 sec) [ -9053.5224] [ 1722] [depth= 1] . ( 4 sec) [ -8947.2290] [ 1699] [depth= 5] . ( 4 sec) [ -8944.7433] [ 1698] [depth= 1] . ( 4 sec) [ -8865.0222] [ 1679] [depth= 2] . ( 4 sec) [ -8860.4147] [ 1680] [depth= 1] . ( 4 sec) [ -8789.8281] [ 1662] [depth= 6] . ( 4 sec) [ -8786.5348] [ 1663] [depth= 2] . ( 4 sec) [ -8605.4784] [ 1625] [depth= 9] . ( 5 sec) [ -8555.6416] [ 1604] [depth= 1] . ( 5 sec) [ -8531.4102] [ 1603] [depth= 9] . ( 5 sec) [ -8317.2427] [ 1541] [depth= 7] . ( 5 sec) [ -8234.5156] [ 1528] [depth= 2] . ( 5 sec) [ -8191.1841] [ 1518] [depth= 1] . ( 5 sec) [ -8112.8263] [ 1506] [depth= 3] . ( 5 sec) [ -8035.4505] [ 1496] [depth= 3] . ( 5 sec) [ -8035.3044] [ 1496] [depth= 1] . ( 5 sec) [ -7932.4704] [ 1479] [depth= 1] . ( 5 sec) [ -7858.5058] [ 1466] [depth= 6] . ( 6 sec) [ -7544.9743] [ 1413] [depth= 1] . ( 6 sec) [ -7480.1987] [ 1396] [depth= 5] . ( 6 sec) [ -7353.1137] [ 1367] [depth= 7] . ( 6 sec) [ -7347.3767] [ 1367] [depth= 1] . ( 6 sec) [ -7342.1916] [ 1367] [depth= 2] . ( 6 sec) [ -7306.5132] [ 1363] [depth= 6] . ( 6 sec) [ -7175.2542] [ 1324] [depth= 1] . ( 6 sec) [ -7154.8494] [ 1320] [depth= 4] . ( 6 sec) [ -6756.4285] [ 1285] [depth= 12] . ( 7 sec) [ -6710.6696] [ 1263] [depth= 5] . ( 7 sec) [ -6641.0004] [ 1265] [depth= 1] . ( 7 sec) [ -6629.4869] [ 1261] [depth= 1] . ( 7 sec) [ -6585.4775] [ 1247] [depth= 1] . ( 7 sec) [ -6569.7094] [ 1241] [depth= 1] . ( 7 sec) [ -6497.7253] [ 1217] [depth= 2] . ( 7 sec) [ -6493.7949] [ 1217] [depth= 1] . ( 7 sec) [ -6487.3436] [ 1216] [depth= 1] . ( 8 sec) [ -6476.0257] [ 1214] [depth= 1] . ( 8 sec) [ -6459.0674] [ 1209] [depth= 2] . ( 8 sec) [ -6447.0118] [ 1201] [depth= 1] . ( 8 sec) [ -6407.7608] [ 1199] [depth= 1] . ( 8 sec) [ -6404.2329] [ 1198] [depth= 3] . ( 9 sec) [ -6327.6011] [Branch lengths ] . ( 9 sec) [ -6324.7370] [GTR parameters ] . ( 10 sec) [ -6297.4202] [Alpha ][ 0.966732] . ( 10 sec) [ -6264.5128] [ 1188] [depth= 3] . ( 10 sec) [ -6263.9017] [ 1188] [depth= 1] . ( 10 sec) [ -6253.7900] [ 1185] [depth= 1] . ( 11 sec) [ -6223.2257] [ 1165] [depth= 6] . ( 11 sec) [ -6222.8347] [ 1167] [depth= 1] . ( 11 sec) [ -6220.0933] [ 1163] [depth= 1] . ( 11 sec) [ -6213.7314] [ 1159] [depth= 2] . ( 11 sec) [ -6210.3347] [ 1169] [depth= 2] . ( 11 sec) [ -6183.4874] [ 1153] [depth= 3] . ( 11 sec) [ -6178.4333] [ 1151] [depth= 1] . ( 11 sec) [ -6143.7548] [ 1140] [depth= 1] . ( 12 sec) [ -6110.7163] [ 1126] [depth= 1] . ( 12 sec) [ -6110.5474] [ 1124] [depth= 1] . ( 12 sec) [ -6106.3315] [ 1123] [depth= 1] . ( 12 sec) [ -6104.6053] [ 1123] [depth= 2] . ( 12 sec) [ -6087.3245] [ 1115] [depth= 2] . ( 12 sec) [ -6087.2868] [ 1115] [depth= 1] . ( 13 sec) [ -6086.9731] [ 1116] [depth= 2] . ( 13 sec) [ -6060.5536] [ 1105] [depth= 1] . ( 14 sec) [ -6055.4990] [ 1104] [depth= 1] . ( 14 sec) [ -6055.4491] [ 1104] [depth= 1] . ( 14 sec) [ -6055.4176] [ 1106] [depth= 1] . ( 15 sec) [ -6054.7066] [ 1109] [depth= 1] . ( 15 sec) [ -6051.2121] [Branch lengths ] . ( 16 sec) [ -6050.6943] [GTR parameters ] . ( 16 sec) [ -6049.2732] [Alpha ][ 1.146241] . ( 16 sec) [ -6036.6312] [ 1101] [depth= 2] . ( 16 sec) [ -6033.1993] [ 1100] [depth= 1] . ( 16 sec) [ -6032.7573] [ 1098] [depth= 1] . ( 19 sec) [ -6032.7449] [ 1098] [depth= 1] . ( 20 sec) [ -6032.6868] [ 1097] [depth= 1] . ( 21 sec) [ -6031.2664] [Branch lengths ] . ( 21 sec) [ -6031.2544] [GTR parameters ] . ( 21 sec) [ -6031.2270] [Alpha ][ 1.174271] . ( 26 sec) [ -6031.1960] [Branch lengths ] . ( 45 sec) [ -6031.0974] [ 1095] [depth= 1] . ( 52 sec) [ -6031.0899] [Branch lengths ] . ( 53 sec) [ -6031.0893] [GTR parameters ] . ( 53 sec) [ -6031.0884] [Alpha ][ 1.179445] . ( 53 sec) [ -6031.0884] [Topology ] . ( 54 sec) [ -6031.0882] [Topology ] . ( 54 sec) [ -6031.0882] [GTR parameters ] . ( 54 sec) [ -6031.0882] [Alpha ][ 1.179445] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6031.088220. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6050.767439 . ( 1 sec) [ -6049.9424] [GTR parameters ] . ( 1 sec) [ -6049.0215] [Alpha ][ 1.151920] . ( 1 sec) [ -6049.0215] [Topology ] . ( 2 sec) [ -6033.2685] [Topology ] . ( 3 sec) [ -6031.6348] [Topology ] . ( 4 sec) [ -6031.2775] [Topology ] . ( 5 sec) [ -6031.1739] [Topology ] . ( 6 sec) [ -6031.1396] [Topology ] . ( 7 sec) [ -6031.1271] [Topology ] . ( 7 sec) [ -6031.1224] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6031.122354 . ( 13 sec) [ -6031.1169] [GTR parameters ] . ( 13 sec) [ -6031.0936] [Alpha ][ 1.177729] . ( 13 sec) [ -6031.0936] [Topology ] . ( 14 sec) [ -6031.0902] [Topology ] . ( 15 sec) [ -6031.0890] [Topology ] . ( 16 sec) [ -6031.0885] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6031.088514 . ( 21 sec) [ -6031.0885] [GTR parameters ] . ( 21 sec) [ -6031.0884] [Alpha ][ 1.179251] . ( 21 sec) [ -6031.0884] [Topology ] . ( 22 sec) [ -6031.0882] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -6049.9424] [GTR parameters ] . ( 36 sec) [ -6049.0215] [Alpha ][ 1.151920] . ( 36 sec) [ -6045.8023] [ 1094] [depth= 1] . ( 37 sec) [ -6044.8063] [ 1094] [depth= 1] . ( 38 sec) [ -6044.6454] [ 1094] [depth= 1] . ( 38 sec) [ -6044.3978] [ 1096] [depth= 2] . ( 38 sec) [ -6042.5937] [ 1097] [depth= 2] . ( 38 sec) [ -6041.7103] [ 1096] [depth= 1] . ( 39 sec) [ -6041.4186] [ 1097] [depth= 1] . ( 39 sec) [ -6041.3359] [ 1096] [depth= 1] . ( 39 sec) [ -6040.3112] [ 1094] [depth= 1] . ( 39 sec) [ -6040.1278] [ 1095] [depth= 1] . ( 40 sec) [ -6040.0503] [ 1095] [depth= 1] . ( 40 sec) [ -6040.0016] [ 1095] [depth= 1] . ( 40 sec) [ -6031.5047] [Branch lengths ] . ( 40 sec) [ -6031.4968] [GTR parameters ] . ( 41 sec) [ -6031.4805] [Alpha ][ 1.173367] . ( 45 sec) [ -6031.2116] [Branch lengths ] . ( 68 sec) [ -6031.1242] [ 1093] [depth= 1] . ( 73 sec) [ -6031.0926] [Branch lengths ] . ( 73 sec) [ -6031.0917] [GTR parameters ] . ( 73 sec) [ -6031.0906] [Alpha ][ 1.179291] . ( 73 sec) [ -6031.0906] [Topology ] . ( 75 sec) [ -6031.0888] [Topology ] . ( 76 sec) [ -6031.0884] [Topology ] . ( 76 sec) [ -6031.0884] [GTR parameters ] . ( 76 sec) [ -6031.0884] [Alpha ][ 1.179291] . ( 76 sec) [ -6031.0884] [Topology ] . ( 77 sec) [ -6031.0883] [Topology ] . ( 77 sec) [ -6031.0883] [GTR parameters ] . ( 77 sec) [ -6031.0883] [Alpha ][ 1.179291] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6031.088198 . Log likelihood obtained after SPR moves : -6031.088274 . Log likelihood of the current tree: -6031.088198. . Printing the most likely tree in file 'data32.phy_phyml_tree.txt'... . Best log likelihood : -6031.088126 . Time used 0h1m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo