.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2899_25x444_2006.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 365 patterns found. (out of a total of 444 sites) . 112 sites without polymorphism (25.23%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13538.5722] [Alpha ][ 0.500960] . ( 1 sec) [ -13250.1215] [ 2161] [depth= 3] . ( 2 sec) [ -13154.7419] [ 2144] [depth= 2] . ( 2 sec) [ -13062.8494] [ 2121] [depth= 7] . ( 2 sec) [ -13017.3906] [ 2107] [depth= 1] . ( 3 sec) [ -12860.2143] [ 2096] [depth= 5] . ( 3 sec) [ -12771.0020] [ 2063] [depth= 1] . ( 3 sec) [ -12729.6809] [ 2058] [depth= 1] . ( 4 sec) [ -12729.0476] [ 2062] [depth= 3] . ( 4 sec) [ -12433.7392] [ 1998] [depth= 6] . ( 5 sec) [ -12412.1087] [ 2008] [depth= 1] . ( 5 sec) [ -12362.0975] [ 2007] [depth= 1] . ( 5 sec) [ -12290.5487] [ 2007] [depth= 5] . ( 5 sec) [ -12280.7055] [ 2006] [depth= 1] . ( 6 sec) [ -12165.5106] [ 2004] [depth= 1] . ( 6 sec) [ -12042.1939] [ 2004] [depth= 1] . ( 6 sec) [ -11841.5205] [ 1993] [depth= 8] . ( 6 sec) [ -11774.3489] [ 1979] [depth= 2] . ( 7 sec) [ -11708.3158] [ 1976] [depth= 1] . ( 7 sec) [ -11699.6953] [ 1981] [depth= 1] . ( 7 sec) [ -11689.4798] [ 1980] [depth= 1] . ( 7 sec) [ -11666.5850] [ 1976] [depth= 1] . ( 8 sec) [ -11658.4200] [ 1974] [depth= 2] . ( 8 sec) [ -11655.4738] [ 1976] [depth= 1] . ( 8 sec) [ -11653.8726] [ 1975] [depth= 1] . ( 9 sec) [ -11587.4051] [ 1957] [depth= 1] . ( 9 sec) [ -11553.6002] [ 1948] [depth= 1] . ( 10 sec) [ -11552.7769] [ 1947] [depth= 1] . ( 10 sec) [ -11436.0091] [ 1919] [depth= 9] . ( 10 sec) [ -11433.3724] [ 1910] [depth= 3] . ( 11 sec) [ -11268.3931] [ 1915] [depth= 8] . ( 11 sec) [ -11201.3274] [ 1896] [depth= 5] . ( 12 sec) [ -11112.0879] [ 1876] [depth= 7] . ( 12 sec) [ -11068.3106] [ 1872] [depth= 2] . ( 12 sec) [ -11058.3245] [ 1872] [depth= 2] . ( 13 sec) [ -11007.5910] [ 1865] [depth= 1] . ( 13 sec) [ -10994.5068] [ 1860] [depth= 1] . ( 13 sec) [ -10989.1636] [ 1857] [depth= 1] . ( 14 sec) [ -10630.3865] [ 1843] [depth= 5] . ( 14 sec) [ -10444.9793] [ 1817] [depth= 4] . ( 14 sec) [ -10284.9687] [ 1818] [depth= 1] . ( 14 sec) [ -10229.1305] [ 1811] [depth= 2] . ( 15 sec) [ -10178.5626] [ 1804] [depth= 1] . ( 15 sec) [ -10162.4041] [ 1801] [depth= 1] . ( 16 sec) [ -10158.8509] [ 1802] [depth= 1] . ( 16 sec) [ -10136.4089] [ 1794] [depth= 2] . ( 17 sec) [ -10122.3326] [ 1795] [depth= 1] . ( 17 sec) [ -10097.0731] [ 1794] [depth= 1] . ( 18 sec) [ -10059.6939] [ 1794] [depth= 5] . ( 18 sec) [ -10055.4400] [ 1794] [depth= 1] . ( 18 sec) [ -10043.3396] [ 1789] [depth= 1] . ( 19 sec) [ -10027.4397] [ 1785] [depth= 1] . ( 19 sec) [ -10027.4268] [ 1787] [depth= 1] . ( 19 sec) [ -10024.3258] [ 1787] [depth= 1] . ( 20 sec) [ -10023.0749] [ 1791] [depth= 1] . ( 20 sec) [ -10019.0673] [ 1791] [depth= 1] . ( 21 sec) [ -9987.5692] [Branch lengths ] . ( 21 sec) [ -9983.8197] [Alpha ][ 0.605021] . ( 22 sec) [ -9981.7997] [ 1789] [depth= 5] . ( 26 sec) [ -9980.8397] [ 1790] [depth= 1] . ( 29 sec) [ -9978.2000] [ 1784] [depth= 2] . ( 30 sec) [ -9977.9336] [ 1783] [depth= 1] . ( 32 sec) [ -9976.9736] [ 1779] [depth= 1] . ( 35 sec) [ -9975.2205] [ 1782] [depth= 1] . ( 37 sec) [ -9975.0155] [ 1781] [depth= 1] . ( 42 sec) [ -9974.7028] [ 1785] [depth= 1] . ( 54 sec) [ -9966.0705] [Branch lengths ] . ( 55 sec) [ -9965.7906] [Alpha ][ 0.637195] . ( 55 sec) [ -9965.6844] [ 1780] [depth= 3] . ( 62 sec) [ -9965.3906] [ 1782] [depth= 1] . ( 68 sec) [ -9964.6139] [ 1783] [depth= 1] . ( 89 sec) [ -9961.7097] [Branch lengths ] . ( 89 sec) [ -9961.7058] [Alpha ][ 0.641141] . ( 129 sec) [ -9960.9022] [Branch lengths ] . ( 129 sec) [ -9960.9022] [Topology ] . ( 131 sec) [ -9960.7514] [Topology ] . ( 132 sec) [ -9960.6780] [Topology ] . ( 134 sec) [ -9960.6326] [Topology ] . ( 136 sec) [ -9960.6037] [Topology ] . ( 138 sec) [ -9960.5853] [Topology ] . ( 140 sec) [ -9960.5736] [Topology ] . ( 140 sec) [ -9960.5718] [Alpha ][ 0.643805] . ( 140 sec) [ -9960.5718] [Topology ] . ( 142 sec) [ -9960.5642] [Topology ] . ( 144 sec) [ -9960.5593] [Topology ] . ( 146 sec) [ -9960.5562] [Topology ] . ( 148 sec) [ -9960.5542] [Topology ] . ( 150 sec) [ -9960.5529] [Topology ] . ( 152 sec) [ -9960.5521] [Topology ] . ( 152 sec) [ -9960.5521] [Alpha ][ 0.643805] . ( 152 sec) [ -9960.5521] [Topology ] . ( 154 sec) [ -9960.5516] [Topology ] . ( 154 sec) [ -9960.5516] [Alpha ][ 0.643805] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9960.551594. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14136.7945] [Alpha ][ 0.500960] . ( 1 sec) [ -13849.4421] [ 2194] [depth= 8] . ( 2 sec) [ -13764.2556] [ 2182] [depth= 3] . ( 2 sec) [ -13560.2748] [ 2166] [depth= 5] . ( 2 sec) [ -13557.1266] [ 2167] [depth= 1] . ( 3 sec) [ -13539.1783] [ 2143] [depth= 4] . ( 3 sec) [ -13203.2853] [ 2125] [depth= 6] . ( 3 sec) [ -13165.8610] [ 2110] [depth= 1] . ( 3 sec) [ -12897.5170] [ 2087] [depth= 5] . ( 4 sec) [ -12482.7498] [ 2059] [depth= 3] . ( 4 sec) [ -12271.0247] [ 2061] [depth= 3] . ( 4 sec) [ -12058.2694] [ 2040] [depth= 4] . ( 5 sec) [ -11945.7870] [ 2023] [depth= 4] . ( 5 sec) [ -11888.9381] [ 2018] [depth= 1] . ( 5 sec) [ -11771.0962] [ 1989] [depth= 2] . ( 6 sec) [ -11725.8001] [ 1985] [depth= 2] . ( 6 sec) [ -11698.7601] [ 1984] [depth= 1] . ( 6 sec) [ -11654.1420] [ 1977] [depth= 2] . ( 7 sec) [ -11649.7863] [ 1978] [depth= 1] . ( 7 sec) [ -11264.0409] [ 1959] [depth= 2] . ( 7 sec) [ -11238.7582] [ 1948] [depth= 1] . ( 8 sec) [ -11207.8911] [ 1945] [depth= 1] . ( 8 sec) [ -10920.4250] [ 1935] [depth= 2] . ( 8 sec) [ -10803.6723] [ 1934] [depth= 2] . ( 9 sec) [ -10788.4241] [ 1938] [depth= 1] . ( 9 sec) [ -10765.3957] [ 1934] [depth= 1] . ( 9 sec) [ -10762.7395] [ 1923] [depth= 3] . ( 10 sec) [ -10750.0174] [ 1921] [depth= 1] . ( 10 sec) [ -10669.4710] [ 1898] [depth= 3] . ( 11 sec) [ -10648.6328] [ 1903] [depth= 1] . ( 11 sec) [ -10615.8785] [ 1902] [depth= 1] . ( 11 sec) [ -10559.4434] [ 1879] [depth= 5] . ( 12 sec) [ -10547.7562] [ 1875] [depth= 1] . ( 12 sec) [ -10443.0444] [ 1854] [depth= 2] . ( 12 sec) [ -10311.0123] [ 1831] [depth= 3] . ( 13 sec) [ -10296.6918] [ 1831] [depth= 1] . ( 13 sec) [ -10217.0407] [ 1819] [depth= 1] . ( 13 sec) [ -10210.5125] [ 1821] [depth= 1] . ( 14 sec) [ -10175.0907] [ 1811] [depth= 1] . ( 15 sec) [ -10154.4320] [ 1803] [depth= 1] . ( 16 sec) [ -10153.1102] [ 1806] [depth= 1] . ( 16 sec) [ -10141.2112] [ 1801] [depth= 1] . ( 16 sec) [ -10138.1121] [ 1801] [depth= 1] . ( 16 sec) [ -10134.6619] [ 1797] [depth= 2] . ( 17 sec) [ -10121.5468] [ 1790] [depth= 1] . ( 17 sec) [ -10059.5231] [ 1791] [depth= 1] . ( 18 sec) [ -10057.9298] [ 1791] [depth= 2] . ( 18 sec) [ -10054.5424] [ 1792] [depth= 1] . ( 19 sec) [ -10052.4479] [ 1786] [depth= 4] . ( 20 sec) [ -9996.0750] [Branch lengths ] . ( 20 sec) [ -9991.1673] [Alpha ][ 0.621324] . ( 23 sec) [ -9982.1108] [ 1787] [depth= 1] . ( 23 sec) [ -9981.5420] [ 1780] [depth= 1] . ( 23 sec) [ -9981.4409] [ 1779] [depth= 1] . ( 27 sec) [ -9980.9127] [ 1781] [depth= 1] . ( 29 sec) [ -9980.6702] [ 1783] [depth= 1] . ( 29 sec) [ -9977.7049] [ 1778] [depth= 1] . ( 29 sec) [ -9976.3936] [ 1784] [depth= 1] . ( 36 sec) [ -9975.4710] [ 1784] [depth= 1] . ( 37 sec) [ -9974.9470] [ 1784] [depth= 1] . ( 38 sec) [ -9972.7427] [ 1782] [depth= 1] . ( 48 sec) [ -9963.6073] [Branch lengths ] . ( 48 sec) [ -9963.5246] [Alpha ][ 0.638871] . ( 56 sec) [ -9963.1283] [ 1784] [depth= 1] . ( 89 sec) [ -9961.8413] [Branch lengths ] . ( 89 sec) [ -9961.8386] [Alpha ][ 0.642148] . ( 131 sec) [ -9961.4849] [Branch lengths ] . ( 131 sec) [ -9961.4849] [Topology ] . ( 133 sec) [ -9961.2051] [Topology ] . ( 135 sec) [ -9960.6000] [Topology ] . ( 137 sec) [ -9960.5691] [Topology ] . ( 139 sec) [ -9960.5612] [Topology ] . ( 141 sec) [ -9960.5575] [Topology ] . ( 143 sec) [ -9960.5553] [Topology ] . ( 144 sec) [ -9960.5539] [Topology ] . ( 145 sec) [ -9960.5531] [Alpha ][ 0.643900] . ( 145 sec) [ -9960.5531] [Topology ] . ( 147 sec) [ -9960.5522] [Topology ] . ( 147 sec) [ -9960.5522] [Alpha ][ 0.643900] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9960.552218. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13371.2787] [Alpha ][ 0.500960] . ( 1 sec) [ -13259.9617] [ 2166] [depth= 6] . ( 2 sec) [ -13033.5261] [ 2158] [depth= 5] . ( 2 sec) [ -12981.3493] [ 2158] [depth= 2] . ( 2 sec) [ -12936.7289] [ 2148] [depth= 1] . ( 2 sec) [ -12914.6287] [ 2141] [depth= 3] . ( 3 sec) [ -12853.5333] [ 2129] [depth= 3] . ( 3 sec) [ -12726.3257] [ 2125] [depth= 2] . ( 3 sec) [ -12656.6813] [ 2123] [depth= 6] . ( 4 sec) [ -12504.4569] [ 2092] [depth= 12] . ( 4 sec) [ -12446.6013] [ 2094] [depth= 1] . ( 4 sec) [ -12377.4595] [ 2078] [depth= 3] . ( 5 sec) [ -12267.2938] [ 2056] [depth= 2] . ( 5 sec) [ -12244.6543] [ 2052] [depth= 6] . ( 5 sec) [ -12198.2636] [ 2053] [depth= 1] . ( 5 sec) [ -12101.0854] [ 2032] [depth= 2] . ( 6 sec) [ -11760.0734] [ 1968] [depth= 8] . ( 6 sec) [ -11531.1107] [ 1940] [depth= 5] . ( 7 sec) [ -11423.8549] [ 1939] [depth= 1] . ( 7 sec) [ -11296.5364] [ 1928] [depth= 1] . ( 7 sec) [ -11276.6725] [ 1927] [depth= 4] . ( 7 sec) [ -11244.7792] [ 1914] [depth= 1] . ( 8 sec) [ -11222.7946] [ 1918] [depth= 5] . ( 8 sec) [ -11130.5894] [ 1911] [depth= 3] . ( 9 sec) [ -10855.2778] [ 1910] [depth= 1] . ( 9 sec) [ -10762.0072] [ 1890] [depth= 3] . ( 9 sec) [ -10694.1925] [ 1881] [depth= 2] . ( 10 sec) [ -10506.8920] [ 1864] [depth= 2] . ( 10 sec) [ -10367.9035] [ 1857] [depth= 3] . ( 10 sec) [ -10343.6571] [ 1853] [depth= 2] . ( 10 sec) [ -10331.8571] [ 1859] [depth= 1] . ( 11 sec) [ -10329.6912] [ 1856] [depth= 3] . ( 11 sec) [ -10328.8855] [ 1853] [depth= 1] . ( 12 sec) [ -10322.7943] [ 1853] [depth= 3] . ( 12 sec) [ -10313.1497] [ 1851] [depth= 1] . ( 13 sec) [ -10287.0943] [ 1856] [depth= 2] . ( 13 sec) [ -10280.8136] [ 1852] [depth= 2] . ( 14 sec) [ -10262.8298] [ 1845] [depth= 2] . ( 14 sec) [ -10230.8580] [ 1838] [depth= 1] . ( 15 sec) [ -10212.3714] [ 1836] [depth= 2] . ( 15 sec) [ -10212.1501] [ 1838] [depth= 1] . ( 15 sec) [ -10206.8393] [ 1838] [depth= 1] . ( 16 sec) [ -10199.2321] [ 1840] [depth= 1] . ( 16 sec) [ -10193.0482] [ 1837] [depth= 1] . ( 17 sec) [ -10172.8137] [ 1833] [depth= 3] . ( 18 sec) [ -10162.9504] [ 1833] [depth= 1] . ( 19 sec) [ -10162.9155] [ 1834] [depth= 1] . ( 19 sec) [ -10159.8291] [ 1827] [depth= 8] . ( 20 sec) [ -10156.2682] [ 1823] [depth= 1] . ( 21 sec) [ -10116.1313] [Branch lengths ] . ( 21 sec) [ -10111.7391] [Alpha ][ 0.611842] . ( 22 sec) [ -10101.8835] [ 1822] [depth= 4] . ( 22 sec) [ -10097.3870] [ 1819] [depth= 1] . ( 22 sec) [ -10059.1092] [ 1801] [depth= 1] . ( 23 sec) [ -10055.1755] [ 1799] [depth= 1] . ( 25 sec) [ -10052.0305] [ 1801] [depth= 1] . ( 25 sec) [ -10031.9438] [ 1793] [depth= 3] . ( 27 sec) [ -10029.7478] [ 1792] [depth= 1] . ( 27 sec) [ -9990.7896] [ 1784] [depth= 5] . ( 27 sec) [ -9989.5368] [ 1786] [depth= 1] . ( 29 sec) [ -9984.9705] [ 1785] [depth= 1] . ( 31 sec) [ -9981.7344] [ 1787] [depth= 1] . ( 35 sec) [ -9980.7740] [ 1790] [depth= 1] . ( 36 sec) [ -9980.6458] [ 1790] [depth= 1] . ( 40 sec) [ -9979.4208] [ 1783] [depth= 2] . ( 43 sec) [ -9978.9939] [ 1783] [depth= 1] . ( 49 sec) [ -9966.1687] [Branch lengths ] . ( 49 sec) [ -9965.9269] [Alpha ][ 0.641874] . ( 49 sec) [ -9964.3939] [ 1776] [depth= 3] . ( 73 sec) [ -9962.8678] [Branch lengths ] . ( 73 sec) [ -9962.8590] [Alpha ][ 0.647837] . ( 74 sec) [ -9962.5585] [ 1781] [depth= 4] . ( 103 sec) [ -9961.5366] [Branch lengths ] . ( 103 sec) [ -9961.5365] [Alpha ][ 0.647189] . ( 105 sec) [ -9961.2605] [ 1783] [depth= 3] . ( 141 sec) [ -9960.7133] [Branch lengths ] . ( 142 sec) [ -9960.7109] [Alpha ][ 0.643988] . ( 142 sec) [ -9960.7109] [Topology ] . ( 144 sec) [ -9960.6215] [Topology ] . ( 146 sec) [ -9960.5887] [Topology ] . ( 148 sec) [ -9960.5724] [Topology ] . ( 149 sec) [ -9960.5635] [Topology ] . ( 151 sec) [ -9960.5584] [Topology ] . ( 153 sec) [ -9960.5554] [Topology ] . ( 154 sec) [ -9960.5554] [Alpha ][ 0.643988] . ( 154 sec) [ -9960.5554] [Topology ] . ( 156 sec) [ -9960.5536] [Topology ] . ( 157 sec) [ -9960.5525] [Topology ] . ( 159 sec) [ -9960.5518] [Topology ] . ( 160 sec) [ -9960.5518] [Alpha ][ 0.643988] . ( 160 sec) [ -9960.5518] [Topology ] . ( 162 sec) [ -9960.5514] [Topology ] . ( 162 sec) [ -9960.5514] [Alpha ][ 0.643988] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9960.551384. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14214.6888] [Alpha ][ 0.500960] . ( 1 sec) [ -14172.9932] [ 2251] [depth= 7] . ( 2 sec) [ -14065.9670] [ 2245] [depth= 7] . ( 2 sec) [ -13828.2041] [ 2240] [depth= 1] . ( 2 sec) [ -13512.3182] [ 2223] [depth= 10] . ( 2 sec) [ -13390.4716] [ 2203] [depth= 3] . ( 3 sec) [ -13164.2465] [ 2183] [depth= 6] . ( 3 sec) [ -12939.8552] [ 2184] [depth= 1] . ( 3 sec) [ -12721.3678] [ 2177] [depth= 4] . ( 3 sec) [ -12673.4155] [ 2166] [depth= 2] . ( 4 sec) [ -12537.3584] [ 2149] [depth= 1] . ( 4 sec) [ -12493.0511] [ 2143] [depth= 1] . ( 4 sec) [ -12336.1782] [ 2136] [depth= 4] . ( 5 sec) [ -12331.3676] [ 2137] [depth= 1] . ( 5 sec) [ -12311.6116] [ 2124] [depth= 9] . ( 5 sec) [ -11811.0682] [ 2106] [depth= 11] . ( 6 sec) [ -11672.8224] [ 2074] [depth= 14] . ( 6 sec) [ -11540.1246] [ 2069] [depth= 2] . ( 6 sec) [ -11497.3849] [ 2073] [depth= 1] . ( 7 sec) [ -11486.5327] [ 2064] [depth= 1] . ( 7 sec) [ -11253.8907] [ 2041] [depth= 3] . ( 7 sec) [ -11088.4501] [ 1998] [depth= 4] . ( 8 sec) [ -11063.5259] [ 1987] [depth= 1] . ( 8 sec) [ -11019.8904] [ 1985] [depth= 2] . ( 8 sec) [ -10913.6814] [ 1953] [depth= 5] . ( 9 sec) [ -10717.1410] [ 1916] [depth= 9] . ( 9 sec) [ -10706.1103] [ 1920] [depth= 1] . ( 9 sec) [ -10634.2374] [ 1901] [depth= 3] . ( 10 sec) [ -10546.0402] [ 1860] [depth= 10] . ( 10 sec) [ -10463.1558] [ 1849] [depth= 2] . ( 11 sec) [ -10450.8490] [ 1845] [depth= 1] . ( 12 sec) [ -10448.1560] [ 1850] [depth= 2] . ( 12 sec) [ -10443.8428] [ 1846] [depth= 1] . ( 12 sec) [ -10437.3204] [ 1843] [depth= 1] . ( 13 sec) [ -10420.2180] [ 1840] [depth= 5] . ( 13 sec) [ -10350.0340] [ 1830] [depth= 2] . ( 13 sec) [ -10283.2515] [ 1816] [depth= 1] . ( 14 sec) [ -10274.1048] [ 1815] [depth= 1] . ( 14 sec) [ -10271.4579] [ 1817] [depth= 1] . ( 14 sec) [ -10155.1286] [ 1818] [depth= 1] . ( 15 sec) [ -10145.7856] [ 1808] [depth= 2] . ( 15 sec) [ -10114.5049] [ 1801] [depth= 2] . ( 16 sec) [ -10100.1849] [ 1799] [depth= 1] . ( 16 sec) [ -10091.3201] [ 1796] [depth= 1] . ( 16 sec) [ -10050.4784] [ 1792] [depth= 2] . ( 17 sec) [ -10045.1639] [ 1791] [depth= 1] . ( 17 sec) [ -10043.0582] [ 1787] [depth= 2] . ( 19 sec) [ -10040.0246] [ 1790] [depth= 2] . ( 19 sec) [ -10025.1061] [ 1777] [depth= 3] . ( 20 sec) [ -9987.6296] [Branch lengths ] . ( 21 sec) [ -9982.3239] [Alpha ][ 0.626984] . ( 21 sec) [ -9981.4584] [ 1781] [depth= 1] . ( 21 sec) [ -9978.4299] [ 1775] [depth= 3] . ( 22 sec) [ -9978.2232] [ 1777] [depth= 1] . ( 22 sec) [ -9970.8774] [ 1775] [depth= 2] . ( 27 sec) [ -9970.0465] [ 1776] [depth= 1] . ( 42 sec) [ -9964.7730] [Branch lengths ] . ( 42 sec) [ -9964.7176] [Alpha ][ 0.641301] . ( 43 sec) [ -9964.5527] [ 1780] [depth= 1] . ( 66 sec) [ -9964.1591] [ 1782] [depth= 1] . ( 69 sec) [ -9962.0104] [Branch lengths ] . ( 69 sec) [ -9962.0104] [Alpha ][ 0.641301] . ( 71 sec) [ -9961.6851] [ 1783] [depth= 1] . ( 106 sec) [ -9960.9502] [Branch lengths ] . ( 107 sec) [ -9960.9493] [Alpha ][ 0.643176] . ( 146 sec) [ -9960.6599] [Branch lengths ] . ( 146 sec) [ -9960.6599] [Topology ] . ( 148 sec) [ -9960.6102] [Topology ] . ( 150 sec) [ -9960.5881] [Topology ] . ( 152 sec) [ -9960.5745] [Topology ] . ( 154 sec) [ -9960.5660] [Topology ] . ( 155 sec) [ -9960.5605] [Topology ] . ( 157 sec) [ -9960.5570] [Topology ] . ( 158 sec) [ -9960.5569] [Alpha ][ 0.643879] . ( 158 sec) [ -9960.5569] [Topology ] . ( 160 sec) [ -9960.5547] [Topology ] . ( 162 sec) [ -9960.5532] [Topology ] . ( 163 sec) [ -9960.5523] [Topology ] . ( 164 sec) [ -9960.5523] [Alpha ][ 0.643879] . ( 164 sec) [ -9960.5523] [Topology ] . ( 166 sec) [ -9960.5517] [Topology ] . ( 166 sec) [ -9960.5517] [Alpha ][ 0.643879] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9960.551703. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13700.6785] [Alpha ][ 0.500960] . ( 1 sec) [ -13665.5848] [ 2165] [depth= 3] . ( 2 sec) [ -13612.9901] [ 2152] [depth= 2] . ( 2 sec) [ -13591.1700] [ 2152] [depth= 1] . ( 2 sec) [ -13464.7341] [ 2131] [depth= 9] . ( 2 sec) [ -13428.6872] [ 2123] [depth= 1] . ( 3 sec) [ -13420.3624] [ 2128] [depth= 1] . ( 3 sec) [ -12982.9107] [ 2109] [depth= 1] . ( 3 sec) [ -12729.0382] [ 2079] [depth= 2] . ( 3 sec) [ -12723.3561] [ 2068] [depth= 1] . ( 4 sec) [ -12596.9502] [ 2058] [depth= 6] . ( 4 sec) [ -12517.8616] [ 2055] [depth= 3] . ( 4 sec) [ -12506.5145] [ 2072] [depth= 1] . ( 5 sec) [ -12389.3280] [ 2043] [depth= 2] . ( 5 sec) [ -12236.1002] [ 2012] [depth= 4] . ( 5 sec) [ -12160.7946] [ 1986] [depth= 10] . ( 6 sec) [ -11821.2546] [ 1981] [depth= 2] . ( 6 sec) [ -11795.4510] [ 1966] [depth= 3] . ( 6 sec) [ -11743.8535] [ 1956] [depth= 2] . ( 6 sec) [ -11741.6047] [ 1956] [depth= 2] . ( 7 sec) [ -11599.8301] [ 1952] [depth= 1] . ( 7 sec) [ -11406.6469] [ 1927] [depth= 8] . ( 8 sec) [ -11390.8475] [ 1924] [depth= 1] . ( 8 sec) [ -11353.1065] [ 1920] [depth= 4] . ( 8 sec) [ -11251.5558] [ 1918] [depth= 3] . ( 9 sec) [ -11234.3810] [ 1907] [depth= 1] . ( 9 sec) [ -10917.8432] [ 1902] [depth= 1] . ( 9 sec) [ -10917.5005] [ 1888] [depth= 3] . ( 10 sec) [ -10874.6030] [ 1873] [depth= 5] . ( 10 sec) [ -10869.8895] [ 1869] [depth= 1] . ( 10 sec) [ -10818.8658] [ 1854] [depth= 1] . ( 11 sec) [ -10812.5839] [ 1848] [depth= 3] . ( 12 sec) [ -10810.9680] [ 1852] [depth= 1] . ( 13 sec) [ -10787.0261] [ 1846] [depth= 2] . ( 13 sec) [ -10734.4875] [ 1851] [depth= 2] . ( 13 sec) [ -10499.7450] [ 1841] [depth= 2] . ( 14 sec) [ -10454.3152] [ 1830] [depth= 2] . ( 14 sec) [ -10451.9453] [ 1830] [depth= 1] . ( 14 sec) [ -10427.7994] [ 1818] [depth= 1] . ( 14 sec) [ -10427.3547] [ 1823] [depth= 1] . ( 15 sec) [ -10330.4683] [ 1796] [depth= 4] . ( 15 sec) [ -10323.1302] [ 1791] [depth= 1] . ( 16 sec) [ -10309.4877] [ 1809] [depth= 1] . ( 16 sec) [ -10303.1023] [ 1807] [depth= 1] . ( 18 sec) [ -10110.6733] [ 1798] [depth= 2] . ( 19 sec) [ -10051.4024] [ 1778] [depth= 1] . ( 19 sec) [ -10050.0483] [ 1784] [depth= 1] . ( 20 sec) [ -10020.0457] [ 1787] [depth= 1] . ( 20 sec) [ -10017.8600] [ 1789] [depth= 1] . ( 20 sec) [ -10012.9287] [ 1785] [depth= 1] . ( 21 sec) [ -10004.1872] [ 1782] [depth= 1] . ( 21 sec) [ -9975.8283] [Branch lengths ] . ( 22 sec) [ -9970.7755] [Alpha ][ 0.623750] . ( 23 sec) [ -9969.6168] [ 1783] [depth= 2] . ( 50 sec) [ -9968.9693] [ 1782] [depth= 1] . ( 55 sec) [ -9968.9207] [ 1783] [depth= 1] . ( 58 sec) [ -9962.6946] [Branch lengths ] . ( 59 sec) [ -9962.6308] [Alpha ][ 0.639105] . ( 98 sec) [ -9961.2151] [Branch lengths ] . ( 98 sec) [ -9961.2151] [Topology ] . ( 100 sec) [ -9960.9229] [Topology ] . ( 102 sec) [ -9960.7866] [Topology ] . ( 104 sec) [ -9960.7029] [Topology ] . ( 106 sec) [ -9960.6502] [Topology ] . ( 107 sec) [ -9960.6166] [Topology ] . ( 109 sec) [ -9960.5951] [Topology ] . ( 110 sec) [ -9960.5896] [Alpha ][ 0.643760] . ( 110 sec) [ -9960.5896] [Topology ] . ( 112 sec) [ -9960.5755] [Topology ] . ( 113 sec) [ -9960.5666] [Topology ] . ( 115 sec) [ -9960.5609] [Topology ] . ( 117 sec) [ -9960.5572] [Topology ] . ( 119 sec) [ -9960.5549] [Topology ] . ( 121 sec) [ -9960.5534] [Topology ] . ( 121 sec) [ -9960.5534] [Alpha ][ 0.643760] . ( 121 sec) [ -9960.5534] [Topology ] . ( 123 sec) [ -9960.5524] [Topology ] . ( 124 sec) [ -9960.5524] [Alpha ][ 0.643760] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9960.552391. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -10056.3189] [Alpha ][ 0.527413] . ( 1 sec) [ -10056.3189] [Topology ] . ( 3 sec) [ -9992.5648] [Topology ] . ( 5 sec) [ -9980.7430] [Topology ] . ( 7 sec) [ -9970.0285] [Topology ] . ( 8 sec) [ -9967.7955] [Topology ] . ( 10 sec) [ -9966.7252] [Topology ] . ( 12 sec) [ -9966.1293] [Topology ] . ( 14 sec) [ -9965.7364] [Topology ] . ( 16 sec) [ -9965.4689] [Topology ] . ( 18 sec) [ -9965.2838] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -9961.1497] [Alpha ][ 0.639148] . ( 35 sec) [ -9961.1497] [Topology ] . ( 36 sec) [ -9960.8794] [Topology ] . ( 38 sec) [ -9960.7608] [Topology ] . ( 40 sec) [ -9960.6871] [Topology ] . ( 42 sec) [ -9960.6402] [Topology ] . ( 44 sec) [ -9960.6103] [Topology ] . ( 46 sec) [ -9960.5910] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -9960.5856] [Alpha ][ 0.643756] . ( 61 sec) [ -9960.5856] [Topology ] . ( 63 sec) [ -9960.5730] [Topology ] . ( 65 sec) [ -9960.5650] [Topology ] . ( 66 sec) [ -9960.5598] [Topology ] . ( 68 sec) [ -9960.5565] [Topology ] . ( 70 sec) [ -9960.5544] [Topology ] . ( 72 sec) [ -9960.5531] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -9960.5531] [Alpha ][ 0.643756] . ( 87 sec) [ -9960.5531] [Topology ] . ( 89 sec) [ -9960.5522] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 119 sec) [ -10056.3189] [Alpha ][ 0.527413] . ( 121 sec) [ -10055.9442] [ 1783] [depth= 1] . ( 122 sec) [ -10053.8300] [ 1782] [depth= 1] . ( 124 sec) [ -10049.2226] [ 1781] [depth= 1] . ( 125 sec) [ -10048.7893] [ 1785] [depth= 1] . ( 125 sec) [ -10045.8636] [ 1781] [depth= 1] . ( 126 sec) [ -10043.7949] [ 1783] [depth= 1] . ( 127 sec) [ -10037.5562] [ 1779] [depth= 1] . ( 128 sec) [ -10027.9737] [ 1781] [depth= 1] . ( 129 sec) [ -10027.5639] [ 1784] [depth= 1] . ( 129 sec) [ -10026.9130] [ 1782] [depth= 1] . ( 129 sec) [ -10026.2144] [ 1784] [depth= 1] . ( 129 sec) [ -10021.1568] [ 1782] [depth= 1] . ( 130 sec) [ -10013.3564] [ 1782] [depth= 1] . ( 131 sec) [ -10012.6909] [ 1779] [depth= 1] . ( 131 sec) [ -10011.6372] [ 1782] [depth= 1] . ( 132 sec) [ -10006.3388] [ 1782] [depth= 1] . ( 132 sec) [ -10004.2225] [ 1784] [depth= 1] . ( 134 sec) [ -9998.1216] [ 1787] [depth= 1] . ( 135 sec) [ -9998.0778] [ 1782] [depth= 1] . ( 135 sec) [ -9996.5880] [ 1781] [depth= 1] . ( 136 sec) [ -9993.8425] [ 1778] [depth= 1] . ( 136 sec) [ -9992.4525] [ 1780] [depth= 1] . ( 139 sec) [ -9992.0767] [ 1781] [depth= 1] . ( 142 sec) [ -9974.7411] [Branch lengths ] . ( 142 sec) [ -9971.8031] [Alpha ][ 0.623783] . ( 150 sec) [ -9970.9615] [ 1775] [depth= 1] . ( 155 sec) [ -9970.5284] [ 1776] [depth= 1] . ( 159 sec) [ -9968.8445] [ 1780] [depth= 1] . ( 164 sec) [ -9968.6318] [ 1783] [depth= 1] . ( 166 sec) [ -9964.9650] [Branch lengths ] . ( 166 sec) [ -9964.9060] [Alpha ][ 0.638503] . ( 185 sec) [ -9964.5555] [ 1780] [depth= 1] . ( 192 sec) [ -9964.2034] [ 1782] [depth= 1] . ( 193 sec) [ -9962.1992] [Branch lengths ] . ( 193 sec) [ -9962.1964] [Alpha ][ 0.641797] . ( 213 sec) [ -9961.8593] [ 1783] [depth= 1] . ( 226 sec) [ -9960.9768] [Branch lengths ] . ( 226 sec) [ -9960.9763] [Alpha ][ 0.643177] . ( 266 sec) [ -9960.6777] [Branch lengths ] . ( 266 sec) [ -9960.6777] [Topology ] . ( 268 sec) [ -9960.6201] [Topology ] . ( 270 sec) [ -9960.5946] [Topology ] . ( 271 sec) [ -9960.5787] [Topology ] . ( 273 sec) [ -9960.5687] [Topology ] . ( 275 sec) [ -9960.5623] [Topology ] . ( 277 sec) [ -9960.5582] [Topology ] . ( 277 sec) [ -9960.5580] [Alpha ][ 0.643871] . ( 278 sec) [ -9960.5580] [Topology ] . ( 279 sec) [ -9960.5554] [Topology ] . ( 281 sec) [ -9960.5537] [Topology ] . ( 283 sec) [ -9960.5526] [Topology ] . ( 285 sec) [ -9960.5519] [Topology ] . ( 285 sec) [ -9960.5519] [Alpha ][ 0.643871] . ( 285 sec) [ -9960.5519] [Topology ] . ( 287 sec) [ -9960.5514] [Topology ] . ( 288 sec) [ -9960.5514] [Alpha ][ 0.643871] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9960.552215 . Log likelihood obtained after SPR moves : -9960.551445 . Log likelihood of the current tree: -9960.551445. . Printing the most likely tree in file 'proteic_M2899_25x444_2006.phy_phyml_tree.txt'... . Best log likelihood : -9960.551384 . Time used 0h5m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1126.81user 0.00system 18:50.03elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps