.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data48.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... . 353 patterns found. (out of a total of 500 sites) . 143 sites without polymorphism (28.60%). . [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)... . ( 0 sec) [ -13120.2049] [GTR parameters ] . ( 0 sec) [ -12877.2911] [Alpha ][ 0.500960] . ( 0 sec) [ -12609.1117] [ 2456] [depth= 8] . ( 0 sec) [ -12565.8814] [ 2456] [depth= 7] . ( 0 sec) [ -12450.7781] [ 2425] [depth= 1] . ( 0 sec) [ -12403.2897] [ 2417] [depth= 7] . ( 0 sec) [ -12175.6638] [ 2373] [depth= 5] . ( 0 sec) [ -11981.9490] [ 2367] [depth= 3] . ( 0 sec) [ -11957.4152] [ 2355] [depth= 4] . ( 1 sec) [ -11805.7487] [ 2296] [depth= 2] . ( 1 sec) [ -11733.8158] [ 2290] [depth= 12] . ( 1 sec) [ -11674.5505] [ 2278] [depth= 11] . ( 1 sec) [ -11554.6255] [ 2269] [depth= 2] . ( 1 sec) [ -11246.6676] [ 2269] [depth= 5] . ( 1 sec) [ -11220.9066] [ 2268] [depth= 3] . ( 1 sec) [ -11079.0205] [ 2264] [depth= 4] . ( 1 sec) [ -11064.7741] [ 2242] [depth= 4] . ( 1 sec) [ -10870.6852] [ 2241] [depth= 10] . ( 1 sec) [ -10847.4039] [ 2234] [depth= 6] . ( 1 sec) [ -10695.0569] [ 2230] [depth= 2] . ( 1 sec) [ -10580.5277] [ 2185] [depth= 10] . ( 1 sec) [ -10444.0331] [ 2113] [depth= 2] . ( 1 sec) [ -10245.3136] [ 2119] [depth= 1] . ( 1 sec) [ -10038.6344] [ 2058] [depth= 5] . ( 1 sec) [ -10029.8961] [ 2053] [depth= 1] . ( 1 sec) [ -9833.4801] [ 2005] [depth= 1] . ( 1 sec) [ -9809.0529] [ 1973] [depth= 5] . ( 1 sec) [ -9596.3448] [ 1922] [depth= 6] . ( 1 sec) [ -9370.3777] [ 1828] [depth= 2] . ( 1 sec) [ -9366.1774] [ 1828] [depth= 1] . ( 1 sec) [ -9250.7090] [ 1826] [depth= 5] . ( 1 sec) [ -9113.9736] [ 1783] [depth= 1] . ( 1 sec) [ -9066.2024] [ 1777] [depth= 1] . ( 1 sec) [ -9027.6880] [ 1779] [depth= 1] . ( 1 sec) [ -9026.1227] [ 1780] [depth= 1] . ( 1 sec) [ -8805.9262] [ 1730] [depth= 4] . ( 1 sec) [ -8794.4725] [ 1715] [depth= 10] . ( 2 sec) [ -8709.6583] [ 1711] [depth= 2] . ( 2 sec) [ -8630.9066] [ 1702] [depth= 1] . ( 2 sec) [ -8585.3810] [ 1698] [depth= 2] . ( 2 sec) [ -8428.2605] [ 1680] [depth= 7] . ( 2 sec) [ -8102.8924] [ 1592] [depth= 3] . ( 2 sec) [ -8035.3019] [ 1566] [depth= 7] . ( 2 sec) [ -7881.4368] [ 1496] [depth= 4] . ( 2 sec) [ -7863.6764] [ 1480] [depth= 2] . ( 2 sec) [ -7444.8475] [ 1449] [depth= 2] . ( 2 sec) [ -7383.7939] [ 1417] [depth= 7] . ( 2 sec) [ -7338.0895] [ 1413] [depth= 1] . ( 2 sec) [ -7305.1383] [ 1402] [depth= 1] . ( 2 sec) [ -7303.9986] [ 1401] [depth= 1] . ( 2 sec) [ -7278.7698] [ 1389] [depth= 1] . ( 2 sec) [ -7219.7124] [ 1371] [depth= 4] . ( 2 sec) [ -7104.7180] [ 1365] [depth= 2] . ( 2 sec) [ -7017.3524] [ 1321] [depth= 2] . ( 2 sec) [ -6934.5125] [ 1300] [depth= 1] . ( 2 sec) [ -6913.4522] [ 1315] [depth= 1] . ( 2 sec) [ -6881.1832] [ 1311] [depth= 1] . ( 2 sec) [ -6721.2546] [ 1268] [depth= 4] . ( 2 sec) [ -6644.6479] [ 1261] [depth= 4] . ( 2 sec) [ -6634.7406] [ 1259] [depth= 1] . ( 2 sec) [ -6585.1262] [ 1237] [depth= 1] . ( 2 sec) [ -6558.4139] [ 1228] [depth= 2] . ( 3 sec) [ -6505.2989] [ 1224] [depth= 8] . ( 3 sec) [ -6477.6856] [ 1208] [depth= 1] . ( 3 sec) [ -6446.9317] [ 1178] [depth= 1] . ( 3 sec) [ -6433.0631] [ 1174] [depth= 1] . ( 3 sec) [ -6414.4179] [ 1169] [depth= 6] . ( 3 sec) [ -6394.8736] [ 1158] [depth= 1] . ( 3 sec) [ -6391.6195] [ 1156] [depth= 1] . ( 3 sec) [ -6334.1860] [ 1146] [depth= 3] . ( 3 sec) [ -6299.6362] [ 1131] [depth= 3] . ( 3 sec) [ -6294.4073] [ 1128] [depth= 1] . ( 3 sec) [ -6291.2361] [ 1126] [depth= 1] . ( 3 sec) [ -6282.2989] [ 1122] [depth= 1] . ( 3 sec) [ -6281.1355] [ 1122] [depth= 1] . ( 3 sec) [ -6273.6099] [ 1120] [depth= 2] . ( 3 sec) [ -6212.2222] [ 1094] [depth= 1] . ( 3 sec) [ -6210.4105] [ 1096] [depth= 1] . ( 3 sec) [ -6205.9955] [ 1095] [depth= 1] . ( 4 sec) [ -6135.7292] [Branch lengths ] . ( 4 sec) [ -6131.9032] [GTR parameters ] . ( 4 sec) [ -6106.9961] [Alpha ][ 0.956971] . ( 4 sec) [ -6102.7422] [ 1091] [depth= 1] . ( 4 sec) [ -6002.0353] [ 1060] [depth= 2] . ( 4 sec) [ -6001.5161] [ 1057] [depth= 1] . ( 5 sec) [ -5991.7548] [ 1046] [depth= 1] . ( 5 sec) [ -5976.8354] [ 1042] [depth= 2] . ( 5 sec) [ -5974.0340] [ 1042] [depth= 1] . ( 5 sec) [ -5965.8880] [ 1040] [depth= 1] . ( 6 sec) [ -5964.6336] [ 1041] [depth= 1] . ( 6 sec) [ -5964.5421] [ 1041] [depth= 1] . ( 6 sec) [ -5960.3003] [ 1040] [depth= 1] . ( 7 sec) [ -5950.3362] [Branch lengths ] . ( 8 sec) [ -5950.2836] [GTR parameters ] . ( 8 sec) [ -5949.5110] [Alpha ][ 1.087898] . ( 11 sec) [ -5949.1703] [Branch lengths ] . ( 30 sec) [ -5949.1394] [Branch lengths ] . ( 30 sec) [ -5949.1394] [Topology ] . ( 31 sec) [ -5949.1376] [Topology ] . ( 31 sec) [ -5949.1371] [Topology ] . ( 32 sec) [ -5949.1367] [GTR parameters ] . ( 32 sec) [ -5949.1299] [Alpha ][ 1.101552] . ( 32 sec) [ -5949.1299] [Topology ] . ( 32 sec) [ -5949.1294] [Topology ] . ( 33 sec) [ -5949.1294] [GTR parameters ] . ( 33 sec) [ -5949.1294] [Alpha ][ 1.101552] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5949.129373. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13915.8226] [GTR parameters ] . ( 1 sec) [ -13651.7412] [Alpha ][ 0.500960] . ( 1 sec) [ -13406.0850] [ 2519] [depth= 3] . ( 1 sec) [ -13316.7521] [ 2496] [depth= 3] . ( 1 sec) [ -13100.3614] [ 2465] [depth= 4] . ( 1 sec) [ -13048.4121] [ 2462] [depth= 6] . ( 1 sec) [ -12950.3109] [ 2447] [depth= 1] . ( 1 sec) [ -12801.9748] [ 2440] [depth= 9] . ( 1 sec) [ -12749.7621] [ 2434] [depth= 1] . ( 1 sec) [ -12742.7485] [ 2432] [depth= 1] . ( 1 sec) [ -12694.1885] [ 2393] [depth= 2] . ( 1 sec) [ -12590.9839] [ 2392] [depth= 4] . ( 1 sec) [ -12480.1960] [ 2383] [depth= 10] . ( 1 sec) [ -12361.8593] [ 2377] [depth= 1] . ( 1 sec) [ -11873.9286] [ 2326] [depth= 9] . ( 1 sec) [ -11651.4516] [ 2256] [depth= 1] . ( 1 sec) [ -11614.6042] [ 2268] [depth= 11] . ( 1 sec) [ -11472.5265] [ 2253] [depth= 15] . ( 1 sec) [ -11345.8814] [ 2250] [depth= 2] . ( 1 sec) [ -11258.0422] [ 2247] [depth= 3] . ( 1 sec) [ -10918.5683] [ 2249] [depth= 1] . ( 1 sec) [ -10648.3636] [ 2204] [depth= 15] . ( 1 sec) [ -10488.7009] [ 2153] [depth= 5] . ( 1 sec) [ -10311.5299] [ 2100] [depth= 20] . ( 1 sec) [ -10217.7448] [ 2082] [depth= 14] . ( 2 sec) [ -9998.0054] [ 2040] [depth= 5] . ( 2 sec) [ -9985.9630] [ 2038] [depth= 1] . ( 2 sec) [ -9878.9360] [ 1969] [depth= 10] . ( 2 sec) [ -9829.5563] [ 1969] [depth= 2] . ( 2 sec) [ -9726.6572] [ 1930] [depth= 1] . ( 2 sec) [ -9519.1486] [ 1863] [depth= 7] . ( 2 sec) [ -9192.3535] [ 1812] [depth= 8] . ( 2 sec) [ -9005.1054] [ 1751] [depth= 9] . ( 2 sec) [ -8995.9742] [ 1758] [depth= 1] . ( 2 sec) [ -8789.1522] [ 1692] [depth= 15] . ( 2 sec) [ -8764.3939] [ 1691] [depth= 2] . ( 2 sec) [ -8726.5655] [ 1677] [depth= 2] . ( 2 sec) [ -8723.5368] [ 1681] [depth= 1] . ( 2 sec) [ -8677.8904] [ 1673] [depth= 2] . ( 2 sec) [ -8660.6707] [ 1669] [depth= 3] . ( 2 sec) [ -8632.0257] [ 1641] [depth= 4] . ( 2 sec) [ -8467.8618] [ 1637] [depth= 1] . ( 2 sec) [ -8454.0997] [ 1630] [depth= 2] . ( 2 sec) [ -8320.8676] [ 1592] [depth= 9] . ( 2 sec) [ -8235.9936] [ 1551] [depth= 1] . ( 2 sec) [ -8049.6937] [ 1499] [depth= 5] . ( 2 sec) [ -7996.4852] [ 1492] [depth= 5] . ( 2 sec) [ -7970.3961] [ 1493] [depth= 1] . ( 2 sec) [ -7953.1736] [ 1494] [depth= 1] . ( 2 sec) [ -7917.2412] [ 1482] [depth= 1] . ( 2 sec) [ -7847.0681] [ 1455] [depth= 8] . ( 2 sec) [ -7762.8802] [ 1423] [depth= 8] . ( 3 sec) [ -7713.4023] [ 1386] [depth= 1] . ( 3 sec) [ -7381.1287] [ 1383] [depth= 3] . ( 3 sec) [ -7371.9381] [ 1375] [depth= 1] . ( 3 sec) [ -7370.0793] [ 1370] [depth= 3] . ( 3 sec) [ -7274.9290] [ 1338] [depth= 5] . ( 3 sec) [ -7270.6887] [ 1340] [depth= 1] . ( 3 sec) [ -7136.8282] [ 1332] [depth= 7] . ( 3 sec) [ -7107.9082] [ 1289] [depth= 4] . ( 3 sec) [ -6906.1411] [ 1252] [depth= 8] . ( 3 sec) [ -6900.9108] [ 1253] [depth= 1] . ( 3 sec) [ -6890.2177] [ 1241] [depth= 1] . ( 3 sec) [ -6692.5810] [ 1161] [depth= 7] . ( 3 sec) [ -6672.8933] [ 1154] [depth= 1] . ( 3 sec) [ -6640.3394] [ 1150] [depth= 2] . ( 3 sec) [ -6640.2148] [ 1151] [depth= 1] . ( 3 sec) [ -6606.5562] [ 1142] [depth= 2] . ( 3 sec) [ -6544.5215] [ 1141] [depth= 1] . ( 3 sec) [ -6544.4432] [ 1143] [depth= 2] . ( 4 sec) [ -6530.8485] [ 1135] [depth= 2] . ( 4 sec) [ -6407.6661] [ 1128] [depth= 1] . ( 4 sec) [ -6405.9513] [ 1127] [depth= 1] . ( 4 sec) [ -6358.7796] [ 1113] [depth= 1] . ( 4 sec) [ -6355.9054] [ 1112] [depth= 1] . ( 4 sec) [ -6355.3152] [ 1112] [depth= 2] . ( 4 sec) [ -6331.2657] [ 1099] [depth= 1] . ( 4 sec) [ -6161.7295] [ 1054] [depth= 3] . ( 4 sec) [ -6099.5384] [ 1046] [depth= 2] . ( 4 sec) [ -6095.9485] [ 1045] [depth= 2] . ( 4 sec) [ -6000.8889] [Branch lengths ] . ( 5 sec) [ -5997.1989] [GTR parameters ] . ( 5 sec) [ -5968.2227] [Alpha ][ 1.000069] . ( 5 sec) [ -5960.9777] [ 1043] [depth= 1] . ( 5 sec) [ -5960.0631] [ 1042] [depth= 2] . ( 5 sec) [ -5958.9932] [ 1040] [depth= 1] . ( 5 sec) [ -5957.7727] [ 1040] [depth= 1] . ( 6 sec) [ -5953.8749] [ 1039] [depth= 1] . ( 7 sec) [ -5953.7582] [ 1041] [depth= 1] . ( 8 sec) [ -5950.2903] [Branch lengths ] . ( 9 sec) [ -5950.2270] [GTR parameters ] . ( 9 sec) [ -5949.8982] [Alpha ][ 1.087923] . ( 12 sec) [ -5949.5794] [Branch lengths ] . ( 31 sec) [ -5949.5453] [Branch lengths ] . ( 31 sec) [ -5949.5453] [Topology ] . ( 32 sec) [ -5949.5434] [Topology ] . ( 32 sec) [ -5949.5428] [Topology ] . ( 33 sec) [ -5949.5425] [GTR parameters ] . ( 33 sec) [ -5949.5338] [Alpha ][ 1.103417] . ( 33 sec) [ -5949.5338] [Topology ] . ( 33 sec) [ -5949.5331] [Topology ] . ( 33 sec) [ -5949.5331] [GTR parameters ] . ( 34 sec) [ -5949.5331] [Alpha ][ 1.103417] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -5949.1306] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5949.130614. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13971.8591] [GTR parameters ] . ( 1 sec) [ -13704.5405] [Alpha ][ 0.500960] . ( 1 sec) [ -13439.8748] [ 2583] [depth= 8] . ( 1 sec) [ -13211.7613] [ 2571] [depth= 11] . ( 1 sec) [ -13136.9112] [ 2567] [depth= 3] . ( 1 sec) [ -13045.5284] [ 2567] [depth= 4] . ( 1 sec) [ -12739.7008] [ 2546] [depth= 8] . ( 1 sec) [ -12690.8839] [ 2545] [depth= 2] . ( 1 sec) [ -12286.9974] [ 2481] [depth= 15] . ( 1 sec) [ -12195.0049] [ 2440] [depth= 12] . ( 1 sec) [ -12109.0231] [ 2410] [depth= 1] . ( 1 sec) [ -11917.8176] [ 2364] [depth= 8] . ( 1 sec) [ -11814.5188] [ 2334] [depth= 8] . ( 1 sec) [ -11707.3173] [ 2285] [depth= 12] . ( 1 sec) [ -11578.2538] [ 2271] [depth= 1] . ( 1 sec) [ -11462.2585] [ 2268] [depth= 3] . ( 1 sec) [ -11346.0194] [ 2221] [depth= 1] . ( 1 sec) [ -11275.5200] [ 2208] [depth= 2] . ( 1 sec) [ -11060.5796] [ 2147] [depth= 8] . ( 1 sec) [ -11016.9685] [ 2147] [depth= 1] . ( 1 sec) [ -10700.5129] [ 2143] [depth= 1] . ( 1 sec) [ -10696.9768] [ 2143] [depth= 1] . ( 1 sec) [ -10602.6052] [ 2108] [depth= 1] . ( 1 sec) [ -10340.2723] [ 2054] [depth= 3] . ( 1 sec) [ -10070.3738] [ 2015] [depth= 11] . ( 1 sec) [ -9636.0466] [ 1931] [depth= 3] . ( 2 sec) [ -9463.7136] [ 1900] [depth= 7] . ( 2 sec) [ -9190.6324] [ 1794] [depth= 9] . ( 2 sec) [ -9153.8140] [ 1793] [depth= 1] . ( 2 sec) [ -9151.9194] [ 1796] [depth= 1] . ( 2 sec) [ -8865.7839] [ 1733] [depth= 7] . ( 2 sec) [ -8805.5106] [ 1727] [depth= 6] . ( 2 sec) [ -8671.2977] [ 1700] [depth= 10] . ( 2 sec) [ -8538.8251] [ 1648] [depth= 9] . ( 2 sec) [ -8524.7691] [ 1649] [depth= 1] . ( 2 sec) [ -8470.0335] [ 1614] [depth= 1] . ( 2 sec) [ -8452.8976] [ 1612] [depth= 1] . ( 2 sec) [ -8428.8764] [ 1599] [depth= 1] . ( 2 sec) [ -8291.2751] [ 1583] [depth= 6] . ( 2 sec) [ -8288.6572] [ 1586] [depth= 1] . ( 2 sec) [ -8163.2973] [ 1538] [depth= 7] . ( 2 sec) [ -8095.3734] [ 1519] [depth= 2] . ( 2 sec) [ -8091.4527] [ 1517] [depth= 1] . ( 2 sec) [ -7910.5740] [ 1513] [depth= 2] . ( 2 sec) [ -7875.6843] [ 1511] [depth= 1] . ( 2 sec) [ -7809.9425] [ 1469] [depth= 3] . ( 2 sec) [ -7761.4324] [ 1468] [depth= 3] . ( 2 sec) [ -7735.1354] [ 1465] [depth= 1] . ( 3 sec) [ -7607.9046] [ 1425] [depth= 3] . ( 3 sec) [ -7574.2569] [ 1418] [depth= 2] . ( 3 sec) [ -7482.9897] [ 1399] [depth= 4] . ( 3 sec) [ -7428.8680] [ 1397] [depth= 1] . ( 3 sec) [ -7402.7688] [ 1392] [depth= 1] . ( 3 sec) [ -7202.4770] [ 1354] [depth= 2] . ( 3 sec) [ -7128.8132] [ 1341] [depth= 1] . ( 3 sec) [ -7106.8437] [ 1345] [depth= 6] . ( 3 sec) [ -7103.6948] [ 1342] [depth= 1] . ( 3 sec) [ -7099.0736] [ 1341] [depth= 6] . ( 3 sec) [ -6836.1343] [ 1301] [depth= 5] . ( 3 sec) [ -6820.6513] [ 1290] [depth= 1] . ( 3 sec) [ -6794.0142] [ 1280] [depth= 2] . ( 3 sec) [ -6614.9882] [ 1230] [depth= 3] . ( 3 sec) [ -6605.0893] [ 1222] [depth= 1] . ( 3 sec) [ -6515.0424] [ 1192] [depth= 1] . ( 3 sec) [ -6444.7017] [ 1177] [depth= 5] . ( 3 sec) [ -6433.2075] [ 1179] [depth= 3] . ( 3 sec) [ -6427.3640] [ 1166] [depth= 2] . ( 3 sec) [ -6398.0424] [ 1158] [depth= 1] . ( 3 sec) [ -6357.1862] [ 1148] [depth= 5] . ( 4 sec) [ -6333.2750] [ 1147] [depth= 1] . ( 4 sec) [ -6244.0392] [ 1120] [depth= 2] . ( 4 sec) [ -6197.4671] [ 1109] [depth= 2] . ( 4 sec) [ -6195.9646] [ 1109] [depth= 1] . ( 4 sec) [ -6139.1217] [ 1080] [depth= 3] . ( 4 sec) [ -6139.0167] [ 1087] [depth= 1] . ( 4 sec) [ -6074.1079] [Branch lengths ] . ( 5 sec) [ -6072.1201] [GTR parameters ] . ( 5 sec) [ -6045.5902] [Alpha ][ 0.986996] . ( 5 sec) [ -6020.9316] [ 1078] [depth= 1] . ( 5 sec) [ -5994.9703] [ 1063] [depth= 1] . ( 5 sec) [ -5990.3063] [ 1060] [depth= 1] . ( 5 sec) [ -5989.3585] [ 1063] [depth= 1] . ( 5 sec) [ -5988.1228] [ 1060] [depth= 2] . ( 5 sec) [ -5988.0756] [ 1057] [depth= 1] . ( 6 sec) [ -5979.0528] [ 1050] [depth= 2] . ( 6 sec) [ -5978.9043] [ 1052] [depth= 1] . ( 6 sec) [ -5976.6366] [ 1050] [depth= 3] . ( 6 sec) [ -5973.3822] [ 1048] [depth= 1] . ( 6 sec) [ -5971.6148] [ 1047] [depth= 1] . ( 7 sec) [ -5959.8161] [ 1041] [depth= 1] . ( 8 sec) [ -5957.5057] [ 1043] [depth= 1] . ( 8 sec) [ -5951.0428] [Branch lengths ] . ( 9 sec) [ -5950.9055] [GTR parameters ] . ( 9 sec) [ -5950.4401] [Alpha ][ 1.090367] . ( 11 sec) [ -5949.9066] [ 1041] [depth= 1] . ( 12 sec) [ -5949.5631] [Branch lengths ] . ( 13 sec) [ -5949.5615] [GTR parameters ] . ( 13 sec) [ -5949.5572] [Alpha ][ 1.101223] . ( 32 sec) [ -5949.5349] [Branch lengths ] . ( 32 sec) [ -5949.5349] [Topology ] . ( 32 sec) [ -5949.5335] [Topology ] . ( 33 sec) [ -5949.5331] [Topology ] . ( 33 sec) [ -5949.5331] [GTR parameters ] . ( 33 sec) [ -5949.5329] [Alpha ][ 1.103344] . ( 33 sec) [ -5949.5329] [Topology ] . ( 34 sec) [ -5949.5328] [Topology ] . ( 34 sec) [ -5949.5328] [GTR parameters ] . ( 34 sec) [ -5949.5328] [Alpha ][ 1.103344] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -5949.1301] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5949.130145. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13084.0526] [GTR parameters ] . ( 1 sec) [ -12843.9995] [Alpha ][ 0.500960] . ( 1 sec) [ -12569.8120] [ 2434] [depth= 8] . ( 1 sec) [ -12396.9588] [ 2406] [depth= 7] . ( 1 sec) [ -12259.0119] [ 2361] [depth= 8] . ( 1 sec) [ -12228.2110] [ 2348] [depth= 1] . ( 1 sec) [ -12038.9029] [ 2297] [depth= 4] . ( 1 sec) [ -12017.7676] [ 2291] [depth= 2] . ( 1 sec) [ -11932.4503] [ 2289] [depth= 4] . ( 1 sec) [ -11730.4366] [ 2286] [depth= 2] . ( 1 sec) [ -11644.7691] [ 2284] [depth= 1] . ( 1 sec) [ -11640.3617] [ 2279] [depth= 4] . ( 1 sec) [ -11423.4503] [ 2280] [depth= 5] . ( 1 sec) [ -11221.0784] [ 2222] [depth= 12] . ( 1 sec) [ -11059.1581] [ 2201] [depth= 5] . ( 1 sec) [ -11015.7253] [ 2202] [depth= 3] . ( 1 sec) [ -10831.5793] [ 2157] [depth= 1] . ( 1 sec) [ -10761.8154] [ 2146] [depth= 11] . ( 2 sec) [ -10671.7071] [ 2143] [depth= 1] . ( 2 sec) [ -10610.2399] [ 2122] [depth= 2] . ( 2 sec) [ -10261.5957] [ 2055] [depth= 15] . ( 2 sec) [ -10235.2812] [ 2045] [depth= 1] . ( 2 sec) [ -10203.2315] [ 2039] [depth= 9] . ( 2 sec) [ -9946.3036] [ 1956] [depth= 9] . ( 2 sec) [ -9777.7458] [ 1924] [depth= 5] . ( 2 sec) [ -9753.2006] [ 1922] [depth= 1] . ( 2 sec) [ -9747.0117] [ 1926] [depth= 3] . ( 2 sec) [ -9564.1577] [ 1866] [depth= 7] . ( 2 sec) [ -9477.1678] [ 1854] [depth= 1] . ( 2 sec) [ -9311.3006] [ 1846] [depth= 9] . ( 2 sec) [ -9159.3044] [ 1808] [depth= 1] . ( 2 sec) [ -9042.8606] [ 1769] [depth= 5] . ( 2 sec) [ -9037.6529] [ 1767] [depth= 1] . ( 2 sec) [ -8870.5447] [ 1710] [depth= 6] . ( 2 sec) [ -8534.5610] [ 1626] [depth= 12] . ( 2 sec) [ -8445.4785] [ 1625] [depth= 12] . ( 2 sec) [ -8284.3347] [ 1597] [depth= 2] . ( 2 sec) [ -8225.5376] [ 1596] [depth= 3] . ( 2 sec) [ -8217.1338] [ 1590] [depth= 3] . ( 2 sec) [ -8190.1390] [ 1592] [depth= 3] . ( 2 sec) [ -8186.7389] [ 1595] [depth= 5] . ( 3 sec) [ -8055.7641] [ 1549] [depth= 4] . ( 3 sec) [ -8023.4329] [ 1546] [depth= 1] . ( 3 sec) [ -8010.3430] [ 1545] [depth= 1] . ( 3 sec) [ -8002.2779] [ 1537] [depth= 2] . ( 3 sec) [ -8001.3402] [ 1536] [depth= 1] . ( 3 sec) [ -7948.2716] [ 1508] [depth= 1] . ( 3 sec) [ -7858.7457] [ 1497] [depth= 1] . ( 3 sec) [ -7844.0167] [ 1492] [depth= 1] . ( 3 sec) [ -7817.2418] [ 1480] [depth= 1] . ( 3 sec) [ -7629.1253] [ 1432] [depth= 9] . ( 3 sec) [ -7483.6718] [ 1407] [depth= 6] . ( 3 sec) [ -7474.3666] [ 1409] [depth= 1] . ( 3 sec) [ -7469.1063] [ 1407] [depth= 1] . ( 3 sec) [ -7207.1312] [ 1371] [depth= 4] . ( 3 sec) [ -7205.1795] [ 1371] [depth= 1] . ( 3 sec) [ -7129.7714] [ 1353] [depth= 1] . ( 3 sec) [ -6997.8803] [ 1323] [depth= 4] . ( 3 sec) [ -6877.4984] [ 1283] [depth= 1] . ( 3 sec) [ -6855.0106] [ 1272] [depth= 1] . ( 3 sec) [ -6824.1295] [ 1259] [depth= 1] . ( 4 sec) [ -6820.7840] [ 1258] [depth= 1] . ( 4 sec) [ -6637.7083] [ 1182] [depth= 8] . ( 4 sec) [ -6620.4862] [ 1185] [depth= 1] . ( 4 sec) [ -6599.6772] [ 1180] [depth= 4] . ( 4 sec) [ -6520.4352] [ 1153] [depth= 1] . ( 4 sec) [ -6489.0833] [ 1142] [depth= 3] . ( 4 sec) [ -6427.6793] [ 1131] [depth= 1] . ( 4 sec) [ -6404.1122] [ 1126] [depth= 1] . ( 4 sec) [ -6344.4703] [ 1149] [depth= 1] . ( 4 sec) [ -6273.0930] [ 1118] [depth= 4] . ( 4 sec) [ -6260.0506] [ 1111] [depth= 2] . ( 4 sec) [ -6246.2957] [ 1106] [depth= 1] . ( 4 sec) [ -6243.7419] [ 1107] [depth= 1] . ( 4 sec) [ -6241.2351] [ 1106] [depth= 1] . ( 4 sec) [ -6187.3480] [ 1093] [depth= 3] . ( 4 sec) [ -6141.3418] [ 1059] [depth= 3] . ( 4 sec) [ -6140.1353] [ 1059] [depth= 1] . ( 4 sec) [ -6076.8707] [ 1047] [depth= 1] . ( 5 sec) [ -5989.8015] [Branch lengths ] . ( 5 sec) [ -5986.4214] [GTR parameters ] . ( 5 sec) [ -5958.7245] [Alpha ][ 1.000038] . ( 5 sec) [ -5953.7533] [ 1042] [depth= 1] . ( 6 sec) [ -5953.3371] [ 1040] [depth= 1] . ( 9 sec) [ -5949.9277] [Branch lengths ] . ( 10 sec) [ -5949.9171] [GTR parameters ] . ( 10 sec) [ -5949.6184] [Alpha ][ 1.083687] . ( 14 sec) [ -5949.1856] [Branch lengths ] . ( 33 sec) [ -5949.1451] [Branch lengths ] . ( 33 sec) [ -5949.1451] [Topology ] . ( 33 sec) [ -5949.1428] [Topology ] . ( 34 sec) [ -5949.1422] [Topology ] . ( 34 sec) [ -5949.1419] [GTR parameters ] . ( 35 sec) [ -5949.1304] [Alpha ][ 1.101536] . ( 35 sec) [ -5949.1304] [Topology ] . ( 36 sec) [ -5949.1295] [Topology ] . ( 36 sec) [ -5949.1295] [GTR parameters ] . ( 36 sec) [ -5949.1295] [Alpha ][ 1.101536] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5949.129537. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13876.0915] [GTR parameters ] . ( 0 sec) [ -13625.4431] [Alpha ][ 0.500960] . ( 0 sec) [ -13405.7512] [ 2528] [depth= 6] . ( 0 sec) [ -13164.6628] [ 2499] [depth= 12] . ( 0 sec) [ -13136.2609] [ 2493] [depth= 3] . ( 0 sec) [ -13130.9948] [ 2490] [depth= 2] . ( 0 sec) [ -13069.5038] [ 2487] [depth= 8] . ( 0 sec) [ -13056.7085] [ 2486] [depth= 3] . ( 0 sec) [ -13024.8580] [ 2479] [depth= 3] . ( 0 sec) [ -12910.6532] [ 2480] [depth= 1] . ( 1 sec) [ -12694.7703] [ 2419] [depth= 9] . ( 1 sec) [ -12403.8788] [ 2390] [depth= 7] . ( 1 sec) [ -12280.7620] [ 2332] [depth= 9] . ( 1 sec) [ -12223.4644] [ 2338] [depth= 17] . ( 1 sec) [ -12178.4758] [ 2329] [depth= 5] . ( 1 sec) [ -12155.8144] [ 2331] [depth= 3] . ( 1 sec) [ -11961.8355] [ 2283] [depth= 16] . ( 1 sec) [ -11769.7935] [ 2272] [depth= 1] . ( 1 sec) [ -11724.2219] [ 2269] [depth= 1] . ( 1 sec) [ -11589.6131] [ 2224] [depth= 1] . ( 1 sec) [ -11526.9421] [ 2220] [depth= 8] . ( 1 sec) [ -11450.9566] [ 2198] [depth= 1] . ( 1 sec) [ -11434.3684] [ 2196] [depth= 9] . ( 1 sec) [ -10925.4789] [ 2096] [depth= 16] . ( 1 sec) [ -10887.7263] [ 2086] [depth= 9] . ( 1 sec) [ -10777.1222] [ 2078] [depth= 1] . ( 1 sec) [ -10692.0845] [ 2048] [depth= 11] . ( 1 sec) [ -10431.5361] [ 1996] [depth= 11] . ( 1 sec) [ -10303.4134] [ 1984] [depth= 13] . ( 1 sec) [ -10181.5656] [ 1949] [depth= 1] . ( 1 sec) [ -10083.0079] [ 1950] [depth= 3] . ( 1 sec) [ -9773.2823] [ 1903] [depth= 9] . ( 1 sec) [ -9686.9715] [ 1899] [depth= 8] . ( 1 sec) [ -9528.6629] [ 1898] [depth= 1] . ( 1 sec) [ -9527.9872] [ 1895] [depth= 1] . ( 1 sec) [ -9362.0372] [ 1852] [depth= 1] . ( 2 sec) [ -9176.8676] [ 1837] [depth= 1] . ( 2 sec) [ -9136.5852] [ 1818] [depth= 10] . ( 2 sec) [ -9001.0512] [ 1774] [depth= 12] . ( 2 sec) [ -9000.0365] [ 1775] [depth= 1] . ( 2 sec) [ -8667.0328] [ 1774] [depth= 6] . ( 2 sec) [ -8608.1607] [ 1759] [depth= 9] . ( 2 sec) [ -8569.7514] [ 1759] [depth= 1] . ( 2 sec) [ -8313.3865] [ 1675] [depth= 4] . ( 2 sec) [ -8230.9508] [ 1656] [depth= 9] . ( 2 sec) [ -8194.7207] [ 1656] [depth= 1] . ( 2 sec) [ -8110.0977] [ 1643] [depth= 14] . ( 2 sec) [ -8104.4691] [ 1600] [depth= 6] . ( 2 sec) [ -8072.5122] [ 1593] [depth= 3] . ( 2 sec) [ -7975.3829] [ 1592] [depth= 2] . ( 2 sec) [ -7907.6824] [ 1546] [depth= 1] . ( 2 sec) [ -7827.4669] [ 1543] [depth= 1] . ( 2 sec) [ -7801.9976] [ 1543] [depth= 2] . ( 2 sec) [ -7801.5595] [ 1543] [depth= 1] . ( 2 sec) [ -7583.6278] [ 1489] [depth= 3] . ( 2 sec) [ -7583.1406] [ 1489] [depth= 1] . ( 2 sec) [ -7395.3561] [ 1464] [depth= 6] . ( 3 sec) [ -7298.0661] [ 1423] [depth= 1] . ( 3 sec) [ -7221.4158] [ 1398] [depth= 11] . ( 3 sec) [ -7211.9540] [ 1397] [depth= 1] . ( 3 sec) [ -7101.1709] [ 1350] [depth= 4] . ( 3 sec) [ -7090.0022] [ 1348] [depth= 3] . ( 3 sec) [ -7023.8679] [ 1312] [depth= 5] . ( 3 sec) [ -6962.7450] [ 1295] [depth= 3] . ( 3 sec) [ -6948.9725] [ 1304] [depth= 3] . ( 3 sec) [ -6910.2249] [ 1295] [depth= 2] . ( 3 sec) [ -6856.0013] [ 1269] [depth= 4] . ( 3 sec) [ -6817.3946] [ 1259] [depth= 1] . ( 3 sec) [ -6796.3303] [ 1257] [depth= 2] . ( 3 sec) [ -6776.7258] [ 1261] [depth= 2] . ( 3 sec) [ -6695.4715] [ 1220] [depth= 2] . ( 3 sec) [ -6496.5787] [ 1170] [depth= 4] . ( 3 sec) [ -6495.2088] [ 1170] [depth= 1] . ( 3 sec) [ -6491.6236] [ 1169] [depth= 1] . ( 3 sec) [ -6473.1246] [ 1174] [depth= 3] . ( 3 sec) [ -6458.6089] [ 1175] [depth= 1] . ( 3 sec) [ -6457.3795] [ 1176] [depth= 1] . ( 3 sec) [ -6365.5078] [ 1129] [depth= 3] . ( 4 sec) [ -6265.1975] [ 1114] [depth= 3] . ( 4 sec) [ -6261.8477] [ 1117] [depth= 1] . ( 4 sec) [ -6260.9562] [ 1120] [depth= 1] . ( 4 sec) [ -6194.0121] [Branch lengths ] . ( 4 sec) [ -6192.7226] [GTR parameters ] . ( 4 sec) [ -6166.6133] [Alpha ][ 0.973708] . ( 5 sec) [ -6166.6003] [ 1123] [depth= 1] . ( 5 sec) [ -6162.8962] [ 1120] [depth= 1] . ( 5 sec) [ -6161.8361] [ 1110] [depth= 1] . ( 5 sec) [ -6158.7195] [ 1101] [depth= 3] . ( 5 sec) [ -6142.2947] [ 1096] [depth= 1] . ( 5 sec) [ -6141.9438] [ 1095] [depth= 1] . ( 5 sec) [ -6124.8768] [ 1091] [depth= 1] . ( 5 sec) [ -6053.7577] [ 1067] [depth= 1] . ( 5 sec) [ -6053.0739] [ 1068] [depth= 1] . ( 5 sec) [ -6037.8283] [ 1060] [depth= 2] . ( 6 sec) [ -6033.0635] [ 1065] [depth= 1] . ( 6 sec) [ -5988.2381] [ 1051] [depth= 1] . ( 6 sec) [ -5986.2174] [ 1049] [depth= 1] . ( 6 sec) [ -5985.7523] [ 1049] [depth= 1] . ( 6 sec) [ -5985.4408] [ 1053] [depth= 1] . ( 6 sec) [ -5982.2287] [ 1052] [depth= 1] . ( 7 sec) [ -5959.2611] [ 1043] [depth= 2] . ( 7 sec) [ -5956.3623] [ 1040] [depth= 1] . ( 8 sec) [ -5950.2874] [Branch lengths ] . ( 9 sec) [ -5950.0508] [GTR parameters ] . ( 9 sec) [ -5949.4847] [Alpha ][ 1.086920] . ( 12 sec) [ -5949.1706] [Branch lengths ] . ( 32 sec) [ -5949.1405] [Branch lengths ] . ( 32 sec) [ -5949.1405] [Topology ] . ( 33 sec) [ -5949.1387] [Topology ] . ( 34 sec) [ -5949.1382] [Topology ] . ( 34 sec) [ -5949.1378] [GTR parameters ] . ( 34 sec) [ -5949.1300] [Alpha ][ 1.101546] . ( 34 sec) [ -5949.1300] [Topology ] . ( 34 sec) [ -5949.1294] [Topology ] . ( 35 sec) [ -5949.1294] [GTR parameters ] . ( 35 sec) [ -5949.1294] [Alpha ][ 1.101546] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5949.129391. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5961.452416 . ( 0 sec) [ -5958.6771] [GTR parameters ] . ( 0 sec) [ -5958.5045] [Alpha ][ 1.063482] . ( 0 sec) [ -5958.5045] [Topology ] . ( 1 sec) [ -5950.2618] [Topology ] . ( 2 sec) [ -5949.4376] [Topology ] . ( 2 sec) [ -5949.2690] [Topology ] . ( 3 sec) [ -5949.2203] [Topology ] . ( 4 sec) [ -5949.2038] [Topology ] . ( 4 sec) [ -5949.1978] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5949.197809 . ( 9 sec) [ -5949.1898] [GTR parameters ] . ( 9 sec) [ -5949.1391] [Alpha ][ 1.099532] . ( 9 sec) [ -5949.1391] [Topology ] . ( 10 sec) [ -5949.1330] [Topology ] . ( 11 sec) [ -5949.1307] [Topology ] . ( 11 sec) [ -5949.1298] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5949.129842 . ( 16 sec) [ -5949.1298] [GTR parameters ] . ( 16 sec) [ -5949.1297] [Alpha ][ 1.101246] . ( 16 sec) [ -5949.1297] [Topology ] . ( 16 sec) [ -5949.1293] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 25 sec) [ -5958.6771] [GTR parameters ] . ( 25 sec) [ -5958.5045] [Alpha ][ 1.063482] . ( 27 sec) [ -5958.3948] [ 1042] [depth= 1] . ( 27 sec) [ -5957.3988] [ 1040] [depth= 1] . ( 29 sec) [ -5949.3394] [Branch lengths ] . ( 29 sec) [ -5949.3325] [GTR parameters ] . ( 30 sec) [ -5949.2950] [Alpha ][ 1.094354] . ( 33 sec) [ -5949.1401] [Branch lengths ] . ( 52 sec) [ -5949.1318] [Branch lengths ] . ( 52 sec) [ -5949.1318] [Topology ] . ( 53 sec) [ -5949.1314] [Topology ] . ( 53 sec) [ -5949.1313] [GTR parameters ] . ( 53 sec) [ -5949.1294] [Alpha ][ 1.101598] . ( 53 sec) [ -5949.1294] [Topology ] . ( 54 sec) [ -5949.1292] [Topology ] . ( 54 sec) [ -5949.1292] [GTR parameters ] . ( 54 sec) [ -5949.1292] [Alpha ][ 1.101598] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5949.129324 . Log likelihood obtained after SPR moves : -5949.129175 . Log likelihood of the current tree: -5949.129175. . Printing the most likely tree in file 'data48.phy_phyml_tree.txt'... . Best log likelihood : -5949.129175 . Time used 0h0m59s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo