.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data41.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... . 348 patterns found. (out of a total of 500 sites) . 135 sites without polymorphism (27.00%). . [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) [ -15558.2854] [GTR parameters ] . ( 0 sec) [ -15203.9743] [Alpha ][ 0.500960] . ( 0 sec) [ -14680.2561] [ 2940] [depth= 8] . ( 0 sec) [ -14026.7196] [ 2938] [depth= 6] . ( 0 sec) [ -14002.5488] [ 2931] [depth= 1] . ( 0 sec) [ -13983.7079] [ 2929] [depth= 7] . ( 1 sec) [ -13849.5055] [ 2909] [depth= 5] . ( 1 sec) [ -13539.6375] [ 2906] [depth= 8] . ( 1 sec) [ -13510.6307] [ 2901] [depth= 3] . ( 1 sec) [ -13509.1779] [ 2910] [depth= 1] . ( 1 sec) [ -13491.2180] [ 2909] [depth= 1] . ( 1 sec) [ -13349.9669] [ 2899] [depth= 9] . ( 1 sec) [ -13182.1383] [ 2864] [depth= 7] . ( 1 sec) [ -13175.6851] [ 2846] [depth= 1] . ( 1 sec) [ -12966.8138] [ 2830] [depth= 5] . ( 1 sec) [ -12922.7558] [ 2825] [depth= 7] . ( 1 sec) [ -12832.8787] [ 2823] [depth= 3] . ( 1 sec) [ -12821.1473] [ 2786] [depth= 3] . ( 1 sec) [ -12791.3296] [ 2791] [depth= 1] . ( 1 sec) [ -12406.4655] [ 2758] [depth= 4] . ( 1 sec) [ -12350.3209] [ 2673] [depth= 1] . ( 1 sec) [ -12191.7394] [ 2642] [depth= 9] . ( 1 sec) [ -12080.9350] [ 2639] [depth= 3] . ( 1 sec) [ -12025.0434] [ 2634] [depth= 17] . ( 1 sec) [ -12024.8650] [ 2645] [depth= 1] . ( 1 sec) [ -11948.9739] [ 2625] [depth= 1] . ( 1 sec) [ -11737.8451] [ 2550] [depth= 2] . ( 1 sec) [ -11618.6395] [ 2542] [depth= 2] . ( 1 sec) [ -11294.5897] [ 2467] [depth= 12] . ( 1 sec) [ -10992.0249] [ 2447] [depth= 6] . ( 1 sec) [ -10929.8418] [ 2449] [depth= 5] . ( 1 sec) [ -10912.0477] [ 2443] [depth= 4] . ( 1 sec) [ -10604.4057] [ 2350] [depth= 5] . ( 2 sec) [ -10546.7201] [ 2353] [depth= 11] . ( 2 sec) [ -10538.7823] [ 2357] [depth= 1] . ( 2 sec) [ -10444.7858] [ 2295] [depth= 6] . ( 2 sec) [ -10375.5473] [ 2278] [depth= 2] . ( 2 sec) [ -10184.9259] [ 2179] [depth= 6] . ( 2 sec) [ -10158.9067] [ 2168] [depth= 1] . ( 2 sec) [ -10154.8787] [ 2167] [depth= 17] . ( 2 sec) [ -10151.1701] [ 2168] [depth= 2] . ( 2 sec) [ -9894.5920] [ 2109] [depth= 5] . ( 2 sec) [ -9794.2449] [ 2102] [depth= 5] . ( 2 sec) [ -9752.2201] [ 2066] [depth= 3] . ( 2 sec) [ -9735.9622] [ 2064] [depth= 1] . ( 2 sec) [ -9658.8213] [ 2052] [depth= 7] . ( 2 sec) [ -9634.7311] [ 2049] [depth= 1] . ( 2 sec) [ -8863.9092] [ 1919] [depth= 8] . ( 2 sec) [ -8563.6975] [ 1814] [depth= 3] . ( 2 sec) [ -8547.3835] [ 1810] [depth= 1] . ( 2 sec) [ -8512.3374] [ 1800] [depth= 1] . ( 2 sec) [ -8239.4064] [ 1820] [depth= 11] . ( 2 sec) [ -8198.6145] [ 1800] [depth= 1] . ( 2 sec) [ -8164.3479] [ 1769] [depth= 1] . ( 3 sec) [ -7944.0692] [ 1710] [depth= 11] . ( 3 sec) [ -7728.9788] [ 1647] [depth= 1] . ( 3 sec) [ -7717.3797] [ 1635] [depth= 3] . ( 3 sec) [ -7716.8191] [ 1635] [depth= 1] . ( 3 sec) [ -7457.8052] [ 1544] [depth= 7] . ( 3 sec) [ -7434.5671] [ 1541] [depth= 1] . ( 3 sec) [ -7434.4605] [ 1541] [depth= 1] . ( 3 sec) [ -6951.2660] [ 1423] [depth= 13] . ( 3 sec) [ -6949.5136] [ 1423] [depth= 1] . ( 3 sec) [ -6906.9226] [ 1424] [depth= 1] . ( 3 sec) [ -6898.2464] [ 1422] [depth= 1] . ( 3 sec) [ -6891.2057] [ 1419] [depth= 3] . ( 3 sec) [ -6867.9542] [ 1415] [depth= 2] . ( 3 sec) [ -6856.1649] [ 1418] [depth= 1] . ( 3 sec) [ -6814.8570] [ 1420] [depth= 2] . ( 3 sec) [ -6813.6278] [ 1422] [depth= 1] . ( 3 sec) [ -6777.2041] [ 1377] [depth= 3] . ( 3 sec) [ -6731.3809] [ 1350] [depth= 2] . ( 3 sec) [ -6539.0231] [ 1310] [depth= 2] . ( 3 sec) [ -6518.1096] [ 1326] [depth= 1] . ( 3 sec) [ -6310.5569] [ 1270] [depth= 2] . ( 3 sec) [ -6237.7884] [ 1234] [depth= 1] . ( 3 sec) [ -6227.3394] [ 1226] [depth= 4] . ( 4 sec) [ -6106.2622] [ 1188] [depth= 2] . ( 4 sec) [ -6057.6538] [ 1177] [depth= 1] . ( 4 sec) [ -5991.5145] [ 1104] [depth= 6] . ( 4 sec) [ -5953.5418] [ 1088] [depth= 3] . ( 4 sec) [ -5832.3818] [ 1052] [depth= 8] . ( 4 sec) [ -5831.7277] [ 1054] [depth= 1] . ( 4 sec) [ -5701.4912] [Branch lengths ] . ( 4 sec) [ -5699.0127] [GTR parameters ] . ( 5 sec) [ -5675.0798] [Alpha ][ 0.955061] . ( 5 sec) [ -5674.4439] [ 1055] [depth= 1] . ( 5 sec) [ -5673.5025] [ 1054] [depth= 1] . ( 5 sec) [ -5648.0466] [ 1014] [depth= 8] . ( 5 sec) [ -5647.4600] [ 1015] [depth= 1] . ( 5 sec) [ -5643.7426] [ 1014] [depth= 1] . ( 5 sec) [ -5642.0062] [ 1014] [depth= 1] . ( 5 sec) [ -5627.9750] [ 1012] [depth= 1] . ( 5 sec) [ -5606.0592] [ 1000] [depth= 3] . ( 5 sec) [ -5605.4355] [ 1003] [depth= 1] . ( 5 sec) [ -5604.6697] [ 1003] [depth= 1] . ( 5 sec) [ -5600.5816] [ 1000] [depth= 1] . ( 5 sec) [ -5592.1338] [ 997] [depth= 1] . ( 6 sec) [ -5578.9919] [ 991] [depth= 3] . ( 6 sec) [ -5577.2242] [ 989] [depth= 1] . ( 6 sec) [ -5576.7210] [ 989] [depth= 1] . ( 6 sec) [ -5575.8953] [ 990] [depth= 1] . ( 6 sec) [ -5574.9496] [ 989] [depth= 1] . ( 7 sec) [ -5574.6749] [ 988] [depth= 1] . ( 7 sec) [ -5574.5497] [ 988] [depth= 1] . ( 7 sec) [ -5574.5128] [ 988] [depth= 1] . ( 8 sec) [ -5569.0805] [Branch lengths ] . ( 9 sec) [ -5569.0327] [GTR parameters ] . ( 9 sec) [ -5567.7460] [Alpha ][ 1.131715] . ( 13 sec) [ -5567.6159] [Branch lengths ] . ( 31 sec) [ -5567.6148] [Branch lengths ] . ( 31 sec) [ -5567.6148] [Topology ] . ( 32 sec) [ -5567.6148] [Topology ] . ( 32 sec) [ -5567.6143] [GTR parameters ] . ( 32 sec) [ -5567.6136] [Alpha ][ 1.136310] . ( 32 sec) [ -5567.6136] [Topology ] . ( 33 sec) [ -5567.6136] [Topology ] . ( 33 sec) [ -5567.6136] [GTR parameters ] . ( 33 sec) [ -5567.6136] [Alpha ][ 1.136310] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.613562. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16548.8773] [GTR parameters ] . ( 1 sec) [ -16148.0143] [Alpha ][ 0.500960] . ( 1 sec) [ -15624.0077] [ 3077] [depth= 4] . ( 1 sec) [ -15168.8456] [ 2952] [depth= 3] . ( 1 sec) [ -15084.2750] [ 2944] [depth= 4] . ( 1 sec) [ -15077.6146] [ 2943] [depth= 5] . ( 1 sec) [ -14788.0032] [ 2938] [depth= 3] . ( 1 sec) [ -14781.1469] [ 2937] [depth= 3] . ( 1 sec) [ -14506.7008] [ 2937] [depth= 1] . ( 1 sec) [ -14494.4564] [ 2931] [depth= 6] . ( 1 sec) [ -14447.5783] [ 2788] [depth= 2] . ( 1 sec) [ -14416.1298] [ 2785] [depth= 4] . ( 1 sec) [ -14234.7287] [ 2754] [depth= 9] . ( 1 sec) [ -13930.5954] [ 2746] [depth= 3] . ( 1 sec) [ -13835.8753] [ 2662] [depth= 6] . ( 1 sec) [ -13378.1673] [ 2655] [depth= 3] . ( 1 sec) [ -13259.6347] [ 2636] [depth= 1] . ( 1 sec) [ -13097.5994] [ 2538] [depth= 10] . ( 1 sec) [ -13025.9092] [ 2532] [depth= 5] . ( 2 sec) [ -12693.0777] [ 2519] [depth= 3] . ( 2 sec) [ -12690.2335] [ 2399] [depth= 1] . ( 2 sec) [ -12124.2559] [ 2396] [depth= 1] . ( 2 sec) [ -12057.9684] [ 2264] [depth= 1] . ( 2 sec) [ -11979.4381] [ 2252] [depth= 1] . ( 2 sec) [ -11078.6480] [ 2228] [depth= 14] . ( 2 sec) [ -11078.0823] [ 2239] [depth= 1] . ( 2 sec) [ -10620.3365] [ 2217] [depth= 13] . ( 2 sec) [ -10394.4329] [ 2169] [depth= 8] . ( 2 sec) [ -10274.3303] [ 2168] [depth= 2] . ( 2 sec) [ -9889.1357] [ 2152] [depth= 14] . ( 2 sec) [ -9542.2980] [ 2027] [depth= 6] . ( 2 sec) [ -9443.7046] [ 2009] [depth= 1] . ( 2 sec) [ -9218.2710] [ 2009] [depth= 3] . ( 2 sec) [ -9150.0109] [ 1998] [depth= 9] . ( 2 sec) [ -9125.4172] [ 2024] [depth= 1] . ( 2 sec) [ -9117.7261] [ 2014] [depth= 1] . ( 2 sec) [ -8783.3047] [ 2005] [depth= 2] . ( 2 sec) [ -8668.2407] [ 2004] [depth= 3] . ( 2 sec) [ -8390.1204] [ 1894] [depth= 9] . ( 2 sec) [ -8350.0351] [ 1885] [depth= 6] . ( 2 sec) [ -7826.3089] [ 1836] [depth= 5] . ( 2 sec) [ -7739.0308] [ 1816] [depth= 4] . ( 2 sec) [ -7735.7562] [ 1814] [depth= 8] . ( 2 sec) [ -7656.4797] [ 1797] [depth= 9] . ( 3 sec) [ -7597.0488] [ 1779] [depth= 1] . ( 3 sec) [ -7588.9562] [ 1781] [depth= 7] . ( 3 sec) [ -7498.7757] [ 1756] [depth= 5] . ( 3 sec) [ -7479.7371] [ 1752] [depth= 1] . ( 3 sec) [ -7472.0416] [ 1744] [depth= 7] . ( 3 sec) [ -7442.2937] [ 1731] [depth= 3] . ( 3 sec) [ -7428.3948] [ 1739] [depth= 3] . ( 3 sec) [ -7414.9975] [ 1733] [depth= 1] . ( 3 sec) [ -7343.7334] [ 1641] [depth= 5] . ( 3 sec) [ -7121.3321] [ 1493] [depth= 4] . ( 3 sec) [ -6852.1308] [ 1363] [depth= 5] . ( 3 sec) [ -6777.8943] [ 1365] [depth= 1] . ( 3 sec) [ -6689.0577] [ 1343] [depth= 4] . ( 3 sec) [ -6673.3119] [ 1341] [depth= 2] . ( 3 sec) [ -6662.5117] [ 1341] [depth= 3] . ( 3 sec) [ -6593.2440] [ 1332] [depth= 4] . ( 3 sec) [ -6589.7173] [ 1330] [depth= 1] . ( 3 sec) [ -6581.8194] [ 1325] [depth= 2] . ( 3 sec) [ -6506.6546] [ 1308] [depth= 4] . ( 3 sec) [ -6454.2959] [ 1295] [depth= 1] . ( 3 sec) [ -6426.3674] [ 1294] [depth= 1] . ( 3 sec) [ -6263.7807] [ 1195] [depth= 7] . ( 3 sec) [ -6051.4567] [ 1199] [depth= 1] . ( 4 sec) [ -6042.5213] [ 1198] [depth= 1] . ( 4 sec) [ -6031.4512] [ 1214] [depth= 1] . ( 4 sec) [ -6026.7454] [ 1214] [depth= 2] . ( 4 sec) [ -6026.6018] [ 1214] [depth= 1] . ( 4 sec) [ -6021.6710] [ 1216] [depth= 2] . ( 4 sec) [ -6009.3468] [ 1212] [depth= 1] . ( 4 sec) [ -5976.0155] [ 1211] [depth= 2] . ( 4 sec) [ -5863.7332] [ 1137] [depth= 6] . ( 4 sec) [ -5862.8463] [ 1136] [depth= 1] . ( 4 sec) [ -5859.7014] [ 1137] [depth= 2] . ( 4 sec) [ -5852.3699] [ 1122] [depth= 1] . ( 4 sec) [ -5849.3746] [ 1121] [depth= 2] . ( 4 sec) [ -5832.9268] [ 1121] [depth= 1] . ( 4 sec) [ -5821.0887] [ 1102] [depth= 1] . ( 4 sec) [ -5769.8236] [Branch lengths ] . ( 5 sec) [ -5769.3893] [GTR parameters ] . ( 5 sec) [ -5750.8806] [Alpha ][ 0.846216] . ( 5 sec) [ -5750.8420] [ 1102] [depth= 1] . ( 5 sec) [ -5746.5798] [ 1068] [depth= 5] . ( 5 sec) [ -5746.2694] [ 1067] [depth= 1] . ( 5 sec) [ -5695.1486] [ 1016] [depth= 5] . ( 5 sec) [ -5658.8596] [ 1025] [depth= 1] . ( 5 sec) [ -5653.9346] [ 1023] [depth= 1] . ( 6 sec) [ -5629.3911] [ 1027] [depth= 2] . ( 6 sec) [ -5629.2600] [ 1027] [depth= 1] . ( 6 sec) [ -5581.5341] [ 990] [depth= 2] . ( 6 sec) [ -5581.0610] [ 989] [depth= 1] . ( 7 sec) [ -5581.0408] [ 989] [depth= 1] . ( 8 sec) [ -5579.9267] [ 989] [depth= 1] . ( 9 sec) [ -5575.1943] [Branch lengths ] . ( 9 sec) [ -5574.6417] [GTR parameters ] . ( 9 sec) [ -5570.9972] [Alpha ][ 1.118667] . ( 11 sec) [ -5570.8169] [ 988] [depth= 1] . ( 13 sec) [ -5568.2009] [Branch lengths ] . ( 14 sec) [ -5568.1960] [GTR parameters ] . ( 14 sec) [ -5568.1868] [Alpha ][ 1.135716] . ( 18 sec) [ -5567.6203] [Branch lengths ] . ( 36 sec) [ -5567.6141] [Branch lengths ] . ( 37 sec) [ -5567.6141] [Topology ] . ( 37 sec) [ -5567.6139] [Topology ] . ( 37 sec) [ -5567.6137] [GTR parameters ] . ( 38 sec) [ -5567.6137] [Alpha ][ 1.136851] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.613685. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16989.1868] [GTR parameters ] . ( 1 sec) [ -16593.9742] [Alpha ][ 0.500960] . ( 1 sec) [ -16257.1394] [ 3128] [depth= 1] . ( 1 sec) [ -15660.7179] [ 2997] [depth= 8] . ( 1 sec) [ -15618.7992] [ 2995] [depth= 4] . ( 1 sec) [ -15578.2112] [ 2993] [depth= 1] . ( 1 sec) [ -15387.9630] [ 2983] [depth= 8] . ( 1 sec) [ -15375.3078] [ 2978] [depth= 5] . ( 1 sec) [ -15301.5546] [ 2960] [depth= 7] . ( 1 sec) [ -15016.3244] [ 2949] [depth= 2] . ( 1 sec) [ -14539.4281] [ 2798] [depth= 2] . ( 1 sec) [ -14278.4606] [ 2800] [depth= 1] . ( 1 sec) [ -13877.9416] [ 2699] [depth= 1] . ( 2 sec) [ -13867.4065] [ 2695] [depth= 1] . ( 2 sec) [ -13865.5142] [ 2699] [depth= 2] . ( 2 sec) [ -13498.1299] [ 2691] [depth= 10] . ( 2 sec) [ -13306.0401] [ 2690] [depth= 2] . ( 2 sec) [ -13053.2853] [ 2652] [depth= 1] . ( 2 sec) [ -12992.7508] [ 2646] [depth= 1] . ( 2 sec) [ -12905.5176] [ 2580] [depth= 10] . ( 2 sec) [ -12529.4306] [ 2576] [depth= 2] . ( 2 sec) [ -12455.5836] [ 2575] [depth= 1] . ( 2 sec) [ -12388.5364] [ 2557] [depth= 6] . ( 2 sec) [ -12363.6100] [ 2548] [depth= 6] . ( 2 sec) [ -11574.2328] [ 2469] [depth= 11] . ( 2 sec) [ -11456.8735] [ 2485] [depth= 2] . ( 2 sec) [ -11247.5801] [ 2458] [depth= 3] . ( 2 sec) [ -11238.0719] [ 2456] [depth= 2] . ( 2 sec) [ -11149.4602] [ 2385] [depth= 3] . ( 2 sec) [ -10737.2954] [ 2300] [depth= 3] . ( 2 sec) [ -10247.0739] [ 2150] [depth= 12] . ( 2 sec) [ -10063.9852] [ 2150] [depth= 2] . ( 2 sec) [ -9809.9888] [ 2113] [depth= 9] . ( 2 sec) [ -9672.3512] [ 2087] [depth= 5] . ( 2 sec) [ -9672.0217] [ 2083] [depth= 1] . ( 2 sec) [ -9645.4795] [ 1954] [depth= 1] . ( 2 sec) [ -9319.8534] [ 1947] [depth= 2] . ( 2 sec) [ -9314.6294] [ 1938] [depth= 2] . ( 2 sec) [ -9311.8325] [ 1924] [depth= 6] . ( 3 sec) [ -9310.4561] [ 1924] [depth= 1] . ( 3 sec) [ -9109.5665] [ 1793] [depth= 9] . ( 3 sec) [ -8932.8424] [ 1761] [depth= 9] . ( 3 sec) [ -8785.4936] [ 1756] [depth= 1] . ( 3 sec) [ -8576.2365] [ 1740] [depth= 1] . ( 3 sec) [ -8305.5434] [ 1717] [depth= 7] . ( 3 sec) [ -8294.2609] [ 1717] [depth= 1] . ( 3 sec) [ -8273.4197] [ 1714] [depth= 2] . ( 3 sec) [ -8169.1125] [ 1703] [depth= 4] . ( 3 sec) [ -7966.3222] [ 1704] [depth= 2] . ( 3 sec) [ -7827.2164] [ 1697] [depth= 2] . ( 3 sec) [ -7284.6341] [ 1588] [depth= 1] . ( 3 sec) [ -7157.8716] [ 1573] [depth= 3] . ( 3 sec) [ -7148.5051] [ 1567] [depth= 1] . ( 3 sec) [ -7121.9917] [ 1563] [depth= 2] . ( 3 sec) [ -6942.1531] [ 1503] [depth= 1] . ( 3 sec) [ -6940.9790] [ 1494] [depth= 1] . ( 3 sec) [ -6909.7720] [ 1485] [depth= 6] . ( 3 sec) [ -6902.4137] [ 1489] [depth= 1] . ( 3 sec) [ -6759.3763] [ 1407] [depth= 4] . ( 3 sec) [ -6752.8646] [ 1402] [depth= 6] . ( 3 sec) [ -6738.0646] [ 1393] [depth= 1] . ( 4 sec) [ -6706.7441] [ 1382] [depth= 6] . ( 4 sec) [ -6606.3044] [ 1364] [depth= 5] . ( 4 sec) [ -6569.7162] [ 1359] [depth= 3] . ( 4 sec) [ -6480.8542] [ 1360] [depth= 1] . ( 4 sec) [ -6464.7855] [ 1359] [depth= 2] . ( 4 sec) [ -6463.8390] [ 1361] [depth= 1] . ( 4 sec) [ -6432.2823] [ 1254] [depth= 6] . ( 4 sec) [ -6364.7865] [ 1233] [depth= 6] . ( 4 sec) [ -6364.3682] [ 1232] [depth= 1] . ( 4 sec) [ -6358.8261] [ 1229] [depth= 2] . ( 4 sec) [ -6357.4530] [ 1228] [depth= 1] . ( 4 sec) [ -6354.8231] [ 1226] [depth= 1] . ( 4 sec) [ -6164.0508] [ 1201] [depth= 2] . ( 4 sec) [ -6162.5799] [ 1201] [depth= 1] . ( 4 sec) [ -6118.4587] [ 1205] [depth= 3] . ( 4 sec) [ -6097.5366] [ 1206] [depth= 1] . ( 5 sec) [ -5963.9368] [Branch lengths ] . ( 5 sec) [ -5962.3211] [GTR parameters ] . ( 5 sec) [ -5948.3476] [Alpha ][ 0.777993] . ( 5 sec) [ -5947.6553] [ 1205] [depth= 2] . ( 6 sec) [ -5829.1282] [ 1112] [depth= 6] . ( 6 sec) [ -5822.3124] [ 1045] [depth= 2] . ( 6 sec) [ -5821.2331] [ 1042] [depth= 1] . ( 6 sec) [ -5819.5879] [ 1039] [depth= 1] . ( 6 sec) [ -5790.0494] [ 1029] [depth= 1] . ( 6 sec) [ -5747.2793] [ 1036] [depth= 1] . ( 6 sec) [ -5699.4679] [ 998] [depth= 4] . ( 6 sec) [ -5682.3322] [ 1013] [depth= 1] . ( 6 sec) [ -5648.7141] [ 998] [depth= 1] . ( 6 sec) [ -5628.6096] [ 994] [depth= 1] . ( 6 sec) [ -5627.5420] [ 995] [depth= 1] . ( 6 sec) [ -5627.3215] [ 995] [depth= 1] . ( 6 sec) [ -5626.9158] [ 994] [depth= 1] . ( 7 sec) [ -5619.1847] [ 991] [depth= 1] . ( 7 sec) [ -5616.8384] [ 998] [depth= 1] . ( 8 sec) [ -5611.4178] [ 991] [depth= 1] . ( 8 sec) [ -5608.6948] [ 989] [depth= 1] . ( 8 sec) [ -5608.5244] [ 990] [depth= 1] . ( 8 sec) [ -5608.0296] [ 989] [depth= 1] . ( 8 sec) [ -5607.4322] [ 988] [depth= 1] . ( 9 sec) [ -5576.6284] [Branch lengths ] . ( 9 sec) [ -5576.1473] [GTR parameters ] . ( 9 sec) [ -5570.1081] [Alpha ][ 1.106021] . ( 10 sec) [ -5570.0959] [ 988] [depth= 1] . ( 11 sec) [ -5570.0619] [ 989] [depth= 1] . ( 14 sec) [ -5567.7480] [Branch lengths ] . ( 14 sec) [ -5567.7410] [GTR parameters ] . ( 14 sec) [ -5567.7136] [Alpha ][ 1.134059] . ( 19 sec) [ -5567.6194] [Branch lengths ] . ( 37 sec) [ -5567.6144] [Branch lengths ] . ( 37 sec) [ -5567.6144] [Topology ] . ( 38 sec) [ -5567.6143] [Topology ] . ( 38 sec) [ -5567.6138] [GTR parameters ] . ( 38 sec) [ -5567.6136] [Alpha ][ 1.136268] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.613603. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16112.2687] [GTR parameters ] . ( 0 sec) [ -15751.0204] [Alpha ][ 0.500960] . ( 0 sec) [ -15113.6030] [ 3011] [depth= 11] . ( 0 sec) [ -14604.8642] [ 2890] [depth= 9] . ( 0 sec) [ -14351.5102] [ 2804] [depth= 2] . ( 0 sec) [ -14272.3130] [ 2737] [depth= 1] . ( 1 sec) [ -13886.0317] [ 2648] [depth= 5] . ( 1 sec) [ -13859.0886] [ 2646] [depth= 1] . ( 1 sec) [ -13846.6901] [ 2644] [depth= 2] . ( 1 sec) [ -13549.6022] [ 2559] [depth= 1] . ( 1 sec) [ -13114.3618] [ 2482] [depth= 8] . ( 1 sec) [ -13080.1311] [ 2478] [depth= 4] . ( 1 sec) [ -13008.0669] [ 2478] [depth= 4] . ( 1 sec) [ -12847.1792] [ 2459] [depth= 10] . ( 1 sec) [ -12771.0207] [ 2458] [depth= 1] . ( 1 sec) [ -12728.5255] [ 2455] [depth= 6] . ( 1 sec) [ -12713.8629] [ 2455] [depth= 4] . ( 1 sec) [ -12698.7902] [ 2452] [depth= 3] . ( 1 sec) [ -12423.5041] [ 2437] [depth= 7] . ( 1 sec) [ -12115.7420] [ 2346] [depth= 1] . ( 1 sec) [ -11931.7573] [ 2321] [depth= 6] . ( 1 sec) [ -11799.7797] [ 2303] [depth= 11] . ( 1 sec) [ -11212.0491] [ 2216] [depth= 14] . ( 1 sec) [ -11119.2208] [ 2216] [depth= 3] . ( 1 sec) [ -10746.4203] [ 2153] [depth= 4] . ( 1 sec) [ -10374.5141] [ 2059] [depth= 18] . ( 1 sec) [ -10181.8057] [ 2006] [depth= 1] . ( 1 sec) [ -10159.4684] [ 2018] [depth= 1] . ( 1 sec) [ -9783.4990] [ 1918] [depth= 7] . ( 1 sec) [ -9609.1272] [ 1838] [depth= 2] . ( 1 sec) [ -9249.2685] [ 1828] [depth= 4] . ( 1 sec) [ -9169.1261] [ 1828] [depth= 1] . ( 1 sec) [ -8947.7591] [ 1850] [depth= 1] . ( 1 sec) [ -8622.7810] [ 1762] [depth= 9] . ( 1 sec) [ -8459.7693] [ 1722] [depth= 7] . ( 2 sec) [ -8444.6436] [ 1702] [depth= 4] . ( 2 sec) [ -8405.3365] [ 1685] [depth= 13] . ( 2 sec) [ -8296.2800] [ 1672] [depth= 9] . ( 2 sec) [ -8291.6398] [ 1673] [depth= 1] . ( 2 sec) [ -8288.8144] [ 1672] [depth= 1] . ( 2 sec) [ -8069.3985] [ 1671] [depth= 3] . ( 2 sec) [ -8064.0061] [ 1672] [depth= 1] . ( 2 sec) [ -7980.4233] [ 1656] [depth= 2] . ( 2 sec) [ -7957.9450] [ 1652] [depth= 3] . ( 2 sec) [ -7933.2850] [ 1651] [depth= 3] . ( 2 sec) [ -7923.9896] [ 1656] [depth= 1] . ( 2 sec) [ -7913.5152] [ 1653] [depth= 2] . ( 2 sec) [ -7905.5554] [ 1651] [depth= 5] . ( 2 sec) [ -7807.0337] [ 1638] [depth= 1] . ( 2 sec) [ -7678.9792] [ 1606] [depth= 6] . ( 2 sec) [ -7575.8356] [ 1596] [depth= 4] . ( 2 sec) [ -7423.6703] [ 1571] [depth= 3] . ( 2 sec) [ -7380.0760] [ 1560] [depth= 1] . ( 2 sec) [ -7375.5184] [ 1562] [depth= 4] . ( 3 sec) [ -7364.6767] [ 1561] [depth= 1] . ( 3 sec) [ -7333.4527] [ 1549] [depth= 3] . ( 3 sec) [ -7320.5923] [ 1549] [depth= 1] . ( 3 sec) [ -7236.3107] [ 1536] [depth= 6] . ( 3 sec) [ -7234.7969] [ 1536] [depth= 1] . ( 3 sec) [ -7184.5692] [ 1472] [depth= 4] . ( 3 sec) [ -7139.6855] [ 1402] [depth= 7] . ( 3 sec) [ -7117.7072] [ 1397] [depth= 7] . ( 3 sec) [ -7066.3717] [ 1385] [depth= 3] . ( 3 sec) [ -6738.8499] [ 1378] [depth= 2] . ( 3 sec) [ -6738.2832] [ 1380] [depth= 2] . ( 3 sec) [ -6380.9064] [ 1268] [depth= 1] . ( 3 sec) [ -6352.1297] [ 1271] [depth= 1] . ( 3 sec) [ -6343.3403] [ 1264] [depth= 2] . ( 3 sec) [ -6296.8904] [ 1259] [depth= 1] . ( 3 sec) [ -6288.9734] [ 1256] [depth= 1] . ( 3 sec) [ -6288.1852] [ 1259] [depth= 1] . ( 3 sec) [ -6226.8700] [ 1244] [depth= 1] . ( 3 sec) [ -6210.5246] [ 1243] [depth= 1] . ( 3 sec) [ -6151.2796] [ 1228] [depth= 1] . ( 3 sec) [ -6146.7230] [ 1228] [depth= 6] . ( 4 sec) [ -6142.5796] [ 1227] [depth= 1] . ( 4 sec) [ -6136.7636] [ 1225] [depth= 2] . ( 4 sec) [ -6120.7605] [ 1230] [depth= 1] . ( 4 sec) [ -6114.0977] [ 1228] [depth= 3] . ( 4 sec) [ -6111.8380] [ 1231] [depth= 1] . ( 4 sec) [ -6024.2043] [ 1187] [depth= 1] . ( 4 sec) [ -6016.9093] [ 1184] [depth= 1] . ( 4 sec) [ -5965.2823] [Branch lengths ] . ( 5 sec) [ -5964.4661] [GTR parameters ] . ( 5 sec) [ -5951.3232] [Alpha ][ 0.782278] . ( 5 sec) [ -5948.5285] [ 1182] [depth= 1] . ( 5 sec) [ -5947.0566] [ 1180] [depth= 1] . ( 5 sec) [ -5946.9907] [ 1180] [depth= 1] . ( 5 sec) [ -5946.7793] [ 1177] [depth= 3] . ( 5 sec) [ -5940.9137] [ 1146] [depth= 1] . ( 5 sec) [ -5937.7741] [ 1144] [depth= 2] . ( 5 sec) [ -5937.5254] [ 1145] [depth= 1] . ( 6 sec) [ -5937.3830] [ 1145] [depth= 1] . ( 6 sec) [ -5808.7811] [ 1105] [depth= 9] . ( 6 sec) [ -5806.3355] [ 1106] [depth= 4] . ( 6 sec) [ -5692.3990] [ 1053] [depth= 8] . ( 6 sec) [ -5691.8940] [ 1054] [depth= 1] . ( 6 sec) [ -5691.3470] [ 1054] [depth= 1] . ( 6 sec) [ -5691.0092] [ 1052] [depth= 1] . ( 6 sec) [ -5688.0380] [ 1049] [depth= 1] . ( 6 sec) [ -5686.7901] [ 1049] [depth= 1] . ( 6 sec) [ -5679.4117] [ 1044] [depth= 5] . ( 6 sec) [ -5677.9932] [ 1048] [depth= 1] . ( 7 sec) [ -5677.2790] [ 1049] [depth= 2] . ( 7 sec) [ -5668.6403] [ 1043] [depth= 1] . ( 7 sec) [ -5666.8629] [ 1043] [depth= 1] . ( 7 sec) [ -5664.6226] [ 1037] [depth= 2] . ( 7 sec) [ -5663.8249] [ 1049] [depth= 1] . ( 7 sec) [ -5655.3338] [ 1042] [depth= 1] . ( 7 sec) [ -5648.6252] [ 1040] [depth= 1] . ( 7 sec) [ -5648.1543] [ 1039] [depth= 1] . ( 7 sec) [ -5646.3239] [ 1038] [depth= 1] . ( 7 sec) [ -5643.8621] [ 1051] [depth= 1] . ( 8 sec) [ -5641.0518] [ 1038] [depth= 1] . ( 8 sec) [ -5640.0371] [ 1037] [depth= 2] . ( 8 sec) [ -5638.3886] [ 1032] [depth= 1] . ( 8 sec) [ -5621.1043] [ 1002] [depth= 3] . ( 8 sec) [ -5604.9374] [ 988] [depth= 1] . ( 8 sec) [ -5577.8160] [Branch lengths ] . ( 9 sec) [ -5577.1271] [GTR parameters ] . ( 9 sec) [ -5571.3036] [Alpha ][ 1.111546] . ( 9 sec) [ -5570.8084] [ 988] [depth= 1] . ( 10 sec) [ -5570.7920] [ 989] [depth= 1] . ( 10 sec) [ -5570.7223] [ 988] [depth= 1] . ( 10 sec) [ -5570.7065] [ 988] [depth= 1] . ( 13 sec) [ -5567.8467] [Branch lengths ] . ( 13 sec) [ -5567.8253] [GTR parameters ] . ( 13 sec) [ -5567.8073] [Alpha ][ 1.134240] . ( 17 sec) [ -5567.6216] [Branch lengths ] . ( 36 sec) [ -5567.6144] [Branch lengths ] . ( 36 sec) [ -5567.6144] [Topology ] . ( 37 sec) [ -5567.6143] [Topology ] . ( 37 sec) [ -5567.6138] [GTR parameters ] . ( 37 sec) [ -5567.6137] [Alpha ][ 1.136239] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.613679. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16516.6226] [GTR parameters ] . ( 0 sec) [ -16117.2926] [Alpha ][ 0.500960] . ( 0 sec) [ -15326.0916] [ 3123] [depth= 6] . ( 0 sec) [ -14611.6623] [ 2998] [depth= 11] . ( 1 sec) [ -14532.6613] [ 2985] [depth= 4] . ( 1 sec) [ -14509.2504] [ 2985] [depth= 2] . ( 1 sec) [ -14477.7287] [ 2978] [depth= 6] . ( 1 sec) [ -14115.4222] [ 2976] [depth= 5] . ( 1 sec) [ -13959.7202] [ 2974] [depth= 1] . ( 1 sec) [ -13584.7134] [ 2978] [depth= 1] . ( 1 sec) [ -13238.1706] [ 2913] [depth= 16] . ( 1 sec) [ -13151.9287] [ 2893] [depth= 13] . ( 1 sec) [ -12848.7313] [ 2815] [depth= 7] . ( 1 sec) [ -12585.1575] [ 2706] [depth= 4] . ( 1 sec) [ -12448.8199] [ 2570] [depth= 2] . ( 1 sec) [ -12425.2067] [ 2568] [depth= 3] . ( 1 sec) [ -11588.2128] [ 2448] [depth= 9] . ( 1 sec) [ -11480.5327] [ 2443] [depth= 2] . ( 1 sec) [ -11408.6567] [ 2438] [depth= 11] . ( 1 sec) [ -11309.4234] [ 2410] [depth= 2] . ( 1 sec) [ -11216.9665] [ 2410] [depth= 2] . ( 1 sec) [ -11184.0352] [ 2402] [depth= 1] . ( 1 sec) [ -10953.3455] [ 2402] [depth= 8] . ( 1 sec) [ -10915.3634] [ 2380] [depth= 1] . ( 1 sec) [ -10703.7846] [ 2346] [depth= 6] . ( 1 sec) [ -10678.4451] [ 2304] [depth= 1] . ( 1 sec) [ -10445.9787] [ 2301] [depth= 2] . ( 1 sec) [ -10124.8584] [ 2183] [depth= 10] . ( 1 sec) [ -9958.7836] [ 2185] [depth= 1] . ( 1 sec) [ -9474.2809] [ 2051] [depth= 12] . ( 1 sec) [ -9210.5058] [ 2013] [depth= 4] . ( 1 sec) [ -9164.9711] [ 2003] [depth= 5] . ( 2 sec) [ -8863.8737] [ 2005] [depth= 9] . ( 2 sec) [ -8818.0875] [ 1967] [depth= 9] . ( 2 sec) [ -8453.2665] [ 1844] [depth= 6] . ( 2 sec) [ -8310.3045] [ 1757] [depth= 14] . ( 2 sec) [ -8310.2448] [ 1765] [depth= 10] . ( 2 sec) [ -8230.8311] [ 1777] [depth= 1] . ( 2 sec) [ -8158.1065] [ 1763] [depth= 8] . ( 2 sec) [ -7877.5808] [ 1691] [depth= 10] . ( 2 sec) [ -7848.1030] [ 1690] [depth= 1] . ( 2 sec) [ -7825.6817] [ 1685] [depth= 2] . ( 2 sec) [ -7819.7811] [ 1684] [depth= 1] . ( 2 sec) [ -7650.1721] [ 1624] [depth= 6] . ( 2 sec) [ -7638.8151] [ 1625] [depth= 3] . ( 2 sec) [ -7635.4328] [ 1623] [depth= 2] . ( 2 sec) [ -7610.8745] [ 1546] [depth= 5] . ( 2 sec) [ -7532.0285] [ 1523] [depth= 4] . ( 2 sec) [ -7470.5561] [ 1510] [depth= 4] . ( 2 sec) [ -7203.2305] [ 1481] [depth= 6] . ( 2 sec) [ -7201.6759] [ 1480] [depth= 1] . ( 2 sec) [ -7199.0345] [ 1478] [depth= 2] . ( 2 sec) [ -7145.2420] [ 1425] [depth= 6] . ( 2 sec) [ -7093.0862] [ 1407] [depth= 2] . ( 2 sec) [ -7036.8363] [ 1362] [depth= 1] . ( 2 sec) [ -6796.4212] [ 1359] [depth= 2] . ( 3 sec) [ -6702.3921] [ 1356] [depth= 1] . ( 3 sec) [ -6368.4759] [ 1242] [depth= 8] . ( 3 sec) [ -6283.8850] [ 1230] [depth= 1] . ( 3 sec) [ -6273.6094] [ 1226] [depth= 2] . ( 3 sec) [ -6271.7782] [ 1225] [depth= 1] . ( 3 sec) [ -6213.0380] [ 1202] [depth= 1] . ( 3 sec) [ -5947.4066] [ 1131] [depth= 5] . ( 3 sec) [ -5915.4912] [ 1119] [depth= 1] . ( 3 sec) [ -5895.5077] [ 1119] [depth= 1] . ( 3 sec) [ -5894.0823] [ 1115] [depth= 1] . ( 3 sec) [ -5729.7279] [ 1043] [depth= 1] . ( 3 sec) [ -5726.2227] [ 1036] [depth= 1] . ( 3 sec) [ -5722.9980] [ 1040] [depth= 2] . ( 3 sec) [ -5721.2888] [ 1038] [depth= 2] . ( 3 sec) [ -5715.6788] [ 1036] [depth= 1] . ( 3 sec) [ -5709.9524] [ 1033] [depth= 1] . ( 4 sec) [ -5707.3232] [ 1032] [depth= 2] . ( 4 sec) [ -5696.6414] [ 1020] [depth= 1] . ( 4 sec) [ -5690.4901] [ 1018] [depth= 1] . ( 4 sec) [ -5641.2035] [Branch lengths ] . ( 4 sec) [ -5639.9080] [GTR parameters ] . ( 5 sec) [ -5610.5877] [Alpha ][ 1.000126] . ( 5 sec) [ -5579.7628] [ 990] [depth= 1] . ( 5 sec) [ -5578.2128] [ 987] [depth= 1] . ( 5 sec) [ -5577.4893] [ 988] [depth= 1] . ( 6 sec) [ -5575.5674] [ 988] [depth= 1] . ( 6 sec) [ -5574.8364] [ 988] [depth= 1] . ( 7 sec) [ -5574.7346] [ 988] [depth= 1] . ( 8 sec) [ -5574.6462] [ 988] [depth= 1] . ( 8 sec) [ -5568.6211] [Branch lengths ] . ( 9 sec) [ -5568.5323] [GTR parameters ] . ( 9 sec) [ -5567.8485] [Alpha ][ 1.132603] . ( 13 sec) [ -5567.6214] [Branch lengths ] . ( 32 sec) [ -5567.6151] [Branch lengths ] . ( 32 sec) [ -5567.6151] [Topology ] . ( 32 sec) [ -5567.6147] [Topology ] . ( 33 sec) [ -5567.6142] [GTR parameters ] . ( 33 sec) [ -5567.6138] [Alpha ][ 1.136309] . ( 33 sec) [ -5567.6138] [Topology ] . ( 34 sec) [ -5567.6136] [Topology ] . ( 34 sec) [ -5567.6136] [GTR parameters ] . ( 34 sec) [ -5567.6136] [Alpha ][ 1.136309] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.613622. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5599.082085 . ( 0 sec) [ -5595.4304] [GTR parameters ] . ( 0 sec) [ -5594.7581] [Alpha ][ 1.136695] . ( 0 sec) [ -5594.7581] [Topology ] . ( 1 sec) [ -5573.7572] [Topology ] . ( 2 sec) [ -5569.6965] [Topology ] . ( 2 sec) [ -5568.0928] [Topology ] . ( 3 sec) [ -5567.7576] [Topology ] . ( 4 sec) [ -5567.6754] [Topology ] . ( 4 sec) [ -5567.6516] [Topology ] . ( 5 sec) [ -5567.6443] [Topology ] . ( 6 sec) [ -5567.6419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5567.641893 . ( 11 sec) [ -5567.6153] [GTR parameters ] . ( 11 sec) [ -5567.6153] [Alpha ][ 1.136695] . ( 11 sec) [ -5567.6153] [Topology ] . ( 12 sec) [ -5567.6141] [Topology ] . ( 12 sec) [ -5567.6137] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5567.613694 . ( 17 sec) [ -5567.6137] [GTR parameters ] . ( 17 sec) [ -5567.6137] [Alpha ][ 1.136695] . ( 17 sec) [ -5567.6137] [Topology ] . ( 18 sec) [ -5567.6136] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 29 sec) [ -5595.4304] [GTR parameters ] . ( 29 sec) [ -5594.7581] [Alpha ][ 1.136695] . ( 29 sec) [ -5594.0482] [ 989] [depth= 1] . ( 29 sec) [ -5592.4546] [ 989] [depth= 1] . ( 30 sec) [ -5592.3055] [ 990] [depth= 1] . ( 30 sec) [ -5592.2777] [ 989] [depth= 1] . ( 30 sec) [ -5591.1113] [ 988] [depth= 1] . ( 30 sec) [ -5591.0384] [ 989] [depth= 1] . ( 31 sec) [ -5590.9881] [ 988] [depth= 1] . ( 31 sec) [ -5587.3950] [ 987] [depth= 1] . ( 32 sec) [ -5587.0676] [ 987] [depth= 1] . ( 32 sec) [ -5586.6693] [ 987] [depth= 1] . ( 32 sec) [ -5586.3154] [ 987] [depth= 1] . ( 32 sec) [ -5568.6704] [Branch lengths ] . ( 33 sec) [ -5568.6436] [GTR parameters ] . ( 33 sec) [ -5568.6430] [Alpha ][ 1.141000] . ( 34 sec) [ -5568.3735] [ 988] [depth= 1] . ( 37 sec) [ -5567.6563] [Branch lengths ] . ( 37 sec) [ -5567.6509] [GTR parameters ] . ( 37 sec) [ -5567.6503] [Alpha ][ 1.136477] . ( 56 sec) [ -5567.6146] [Branch lengths ] . ( 56 sec) [ -5567.6146] [Topology ] . ( 56 sec) [ -5567.6138] [Topology ] . ( 56 sec) [ -5567.6137] [GTR parameters ] . ( 56 sec) [ -5567.6137] [Alpha ][ 1.136477] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5567.613565 . Log likelihood obtained after SPR moves : -5567.613659 . Log likelihood of the current tree: -5567.613565. . Printing the most likely tree in file 'data41.phy_phyml_tree.txt'... . Best log likelihood : -5567.613562 . Time used 0h1m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo