.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2478_30x276_2005.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... . 249 patterns found. (out of a total of 276 sites) . 41 sites without polymorphism (14.86%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12250.1128] [Alpha ][ 0.500960] . ( 1 sec) [ -12041.6390] [ 2337] [depth= 9] . ( 2 sec) [ -11755.4928] [ 2280] [depth= 4] . ( 2 sec) [ -11653.5747] [ 2275] [depth= 1] . ( 2 sec) [ -11575.4260] [ 2264] [depth= 6] . ( 2 sec) [ -11492.7762] [ 2240] [depth= 3] . ( 3 sec) [ -11402.8974] [ 2228] [depth= 3] . ( 4 sec) [ -11215.9593] [ 2204] [depth= 8] . ( 4 sec) [ -11122.8555] [ 2198] [depth= 7] . ( 4 sec) [ -11067.1822] [ 2199] [depth= 1] . ( 4 sec) [ -10930.8021] [ 2164] [depth= 1] . ( 5 sec) [ -10911.9172] [ 2157] [depth= 1] . ( 5 sec) [ -10845.0616] [ 2142] [depth= 1] . ( 5 sec) [ -10783.9780] [ 2130] [depth= 9] . ( 6 sec) [ -10750.6340] [ 2116] [depth= 9] . ( 6 sec) [ -10747.1679] [ 2114] [depth= 1] . ( 6 sec) [ -10678.5680] [ 2092] [depth= 12] . ( 6 sec) [ -10621.3779] [ 2080] [depth= 10] . ( 6 sec) [ -10607.4888] [ 2076] [depth= 1] . ( 7 sec) [ -10597.6401] [ 2078] [depth= 7] . ( 7 sec) [ -10575.1662] [ 2066] [depth= 1] . ( 7 sec) [ -10412.3206] [ 2022] [depth= 3] . ( 8 sec) [ -10392.1045] [ 2011] [depth= 4] . ( 8 sec) [ -10352.8099] [ 2010] [depth= 5] . ( 8 sec) [ -10284.4363] [ 1995] [depth= 3] . ( 8 sec) [ -10277.3375] [ 1996] [depth= 1] . ( 9 sec) [ -10240.1147] [ 1983] [depth= 1] . ( 10 sec) [ -10079.0452] [ 1937] [depth= 5] . ( 10 sec) [ -10025.4726] [ 1937] [depth= 1] . ( 10 sec) [ -9996.9479] [ 1929] [depth= 11] . ( 10 sec) [ -9789.2407] [ 1876] [depth= 5] . ( 11 sec) [ -9646.5103] [ 1849] [depth= 12] . ( 11 sec) [ -9576.6137] [ 1831] [depth= 6] . ( 11 sec) [ -9549.8150] [ 1822] [depth= 2] . ( 12 sec) [ -9372.2394] [ 1806] [depth= 5] . ( 12 sec) [ -9269.5265] [ 1782] [depth= 1] . ( 12 sec) [ -9265.5013] [ 1782] [depth= 2] . ( 13 sec) [ -9177.6938] [ 1756] [depth= 3] . ( 13 sec) [ -8963.5812] [ 1690] [depth= 9] . ( 14 sec) [ -8924.9051] [ 1687] [depth= 6] . ( 14 sec) [ -8913.0781] [ 1685] [depth= 6] . ( 15 sec) [ -8903.6551] [ 1690] [depth= 2] . ( 15 sec) [ -8902.2203] [ 1690] [depth= 1] . ( 15 sec) [ -8888.6436] [ 1683] [depth= 4] . ( 15 sec) [ -8880.8715] [ 1680] [depth= 3] . ( 16 sec) [ -8877.9482] [ 1679] [depth= 1] . ( 16 sec) [ -8875.3658] [ 1680] [depth= 1] . ( 16 sec) [ -8859.8296] [ 1679] [depth= 2] . ( 19 sec) [ -8844.8099] [ 1679] [depth= 1] . ( 20 sec) [ -8784.9518] [Branch lengths ] . ( 20 sec) [ -8768.3483] [Alpha ][ 0.802192] . ( 21 sec) [ -8758.5482] [ 1678] [depth= 1] . ( 22 sec) [ -8748.6422] [ 1671] [depth= 2] . ( 22 sec) [ -8747.4827] [ 1671] [depth= 1] . ( 28 sec) [ -8746.4754] [ 1668] [depth= 2] . ( 30 sec) [ -8741.5899] [ 1666] [depth= 1] . ( 31 sec) [ -8741.4086] [ 1668] [depth= 1] . ( 42 sec) [ -8729.8073] [Branch lengths ] . ( 42 sec) [ -8728.8835] [Alpha ][ 0.901122] . ( 66 sec) [ -8726.5285] [Branch lengths ] . ( 67 sec) [ -8726.5285] [Topology ] . ( 68 sec) [ -8726.1710] [Topology ] . ( 70 sec) [ -8726.0351] [Topology ] . ( 72 sec) [ -8725.9658] [Topology ] . ( 73 sec) [ -8725.9290] [Topology ] . ( 75 sec) [ -8725.9091] [Topology ] . ( 77 sec) [ -8725.8983] [Topology ] . ( 77 sec) [ -8725.5026] [Alpha ][ 0.972528] . ( 77 sec) [ -8725.5026] [Topology ] . ( 79 sec) [ -8725.4451] [Topology ] . ( 80 sec) [ -8725.4193] [Topology ] . ( 82 sec) [ -8725.4059] [Topology ] . ( 84 sec) [ -8725.3988] [Topology ] . ( 86 sec) [ -8725.3950] [Topology ] . ( 87 sec) [ -8725.3929] [Topology ] . ( 88 sec) [ -8725.3824] [Alpha ][ 0.984984] . ( 88 sec) [ -8725.3824] [Topology ] . ( 89 sec) [ -8725.3792] [Topology ] . ( 91 sec) [ -8725.3777] [Topology ] . ( 93 sec) [ -8725.3768] [Topology ] . ( 93 sec) [ -8725.3766] [Alpha ][ 0.986688] . ( 93 sec) [ -8725.3766] [Topology ] . ( 95 sec) [ -8725.3760] [Topology ] . ( 95 sec) [ -8725.3760] [Alpha ][ 0.986688] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8725.375992. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12300.9270] [Alpha ][ 0.500960] . ( 1 sec) [ -12017.4853] [ 2299] [depth= 7] . ( 1 sec) [ -11849.4809] [ 2257] [depth= 4] . ( 2 sec) [ -11802.4510] [ 2245] [depth= 3] . ( 2 sec) [ -11675.7498] [ 2231] [depth= 1] . ( 2 sec) [ -11614.9348] [ 2220] [depth= 2] . ( 2 sec) [ -11554.6019] [ 2215] [depth= 3] . ( 3 sec) [ -11506.2919] [ 2216] [depth= 1] . ( 3 sec) [ -11392.5732] [ 2197] [depth= 6] . ( 3 sec) [ -11349.8858] [ 2188] [depth= 3] . ( 3 sec) [ -11269.8912] [ 2156] [depth= 3] . ( 4 sec) [ -11141.0621] [ 2129] [depth= 1] . ( 4 sec) [ -10924.8391] [ 2082] [depth= 10] . ( 5 sec) [ -10872.6746] [ 2076] [depth= 11] . ( 5 sec) [ -10698.8819] [ 2062] [depth= 7] . ( 5 sec) [ -10631.6333] [ 2036] [depth= 4] . ( 5 sec) [ -10465.5982] [ 2010] [depth= 1] . ( 6 sec) [ -10394.6825] [ 1989] [depth= 2] . ( 6 sec) [ -10254.0287] [ 1959] [depth= 6] . ( 6 sec) [ -10227.3525] [ 1950] [depth= 1] . ( 6 sec) [ -10050.9823] [ 1882] [depth= 7] . ( 7 sec) [ -9940.7355] [ 1850] [depth= 5] . ( 7 sec) [ -9896.1478] [ 1843] [depth= 5] . ( 7 sec) [ -9814.5497] [ 1820] [depth= 3] . ( 8 sec) [ -9788.9152] [ 1815] [depth= 1] . ( 9 sec) [ -9782.6965] [ 1811] [depth= 4] . ( 9 sec) [ -9727.3344] [ 1808] [depth= 1] . ( 9 sec) [ -9669.7059] [ 1786] [depth= 4] . ( 10 sec) [ -9639.6322] [ 1776] [depth= 8] . ( 10 sec) [ -9636.2814] [ 1780] [depth= 1] . ( 10 sec) [ -9480.4774] [ 1765] [depth= 2] . ( 11 sec) [ -9386.3468] [ 1742] [depth= 3] . ( 11 sec) [ -9370.0596] [ 1738] [depth= 4] . ( 11 sec) [ -9216.9370] [ 1731] [depth= 4] . ( 12 sec) [ -9205.2396] [ 1731] [depth= 1] . ( 12 sec) [ -9203.4047] [ 1734] [depth= 2] . ( 12 sec) [ -9199.1128] [ 1729] [depth= 4] . ( 13 sec) [ -9161.0422] [ 1722] [depth= 1] . ( 13 sec) [ -9136.9970] [ 1706] [depth= 5] . ( 14 sec) [ -9078.4397] [ 1691] [depth= 3] . ( 14 sec) [ -9014.1199] [ 1690] [depth= 1] . ( 14 sec) [ -9008.3413] [ 1691] [depth= 1] . ( 15 sec) [ -9008.0349] [ 1693] [depth= 1] . ( 15 sec) [ -8988.5577] [ 1697] [depth= 1] . ( 17 sec) [ -8935.5375] [ 1684] [depth= 5] . ( 17 sec) [ -8929.4320] [ 1693] [depth= 1] . ( 18 sec) [ -8884.4419] [ 1684] [depth= 1] . ( 19 sec) [ -8810.4522] [Branch lengths ] . ( 19 sec) [ -8782.3722] [Alpha ][ 0.922291] . ( 22 sec) [ -8781.4699] [ 1684] [depth= 2] . ( 23 sec) [ -8757.1996] [ 1674] [depth= 5] . ( 24 sec) [ -8753.7865] [ 1672] [depth= 1] . ( 25 sec) [ -8751.5325] [ 1670] [depth= 4] . ( 27 sec) [ -8749.6918] [ 1673] [depth= 1] . ( 28 sec) [ -8748.6638] [ 1672] [depth= 1] . ( 29 sec) [ -8745.0151] [ 1671] [depth= 1] . ( 30 sec) [ -8738.0901] [ 1666] [depth= 2] . ( 37 sec) [ -8737.6778] [ 1668] [depth= 2] . ( 40 sec) [ -8731.1256] [Branch lengths ] . ( 41 sec) [ -8731.0607] [Alpha ][ 0.951101] . ( 51 sec) [ -8729.0543] [ 1668] [depth= 2] . ( 65 sec) [ -8725.7805] [Branch lengths ] . ( 65 sec) [ -8725.7425] [Alpha ][ 0.973573] . ( 90 sec) [ -8725.4151] [Branch lengths ] . ( 90 sec) [ -8725.4151] [Topology ] . ( 92 sec) [ -8725.3972] [Topology ] . ( 93 sec) [ -8725.3928] [Topology ] . ( 95 sec) [ -8725.3907] [Topology ] . ( 97 sec) [ -8725.3897] [Topology ] . ( 99 sec) [ -8725.3891] [Topology ] . ( 99 sec) [ -8725.3788] [Alpha ][ 0.985956] . ( 99 sec) [ -8725.3788] [Topology ] . ( 101 sec) [ -8725.3771] [Topology ] . ( 102 sec) [ -8725.3764] [Topology ] . ( 103 sec) [ -8725.3763] [Alpha ][ 0.986942] . ( 103 sec) [ -8725.3763] [Topology ] . ( 104 sec) [ -8725.3758] [Topology ] . ( 105 sec) [ -8725.3758] [Alpha ][ 0.986942] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8725.375824. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12304.8574] [Alpha ][ 0.500960] . ( 0 sec) [ -11985.4622] [ 2314] [depth= 3] . ( 1 sec) [ -11818.6754] [ 2263] [depth= 10] . ( 1 sec) [ -11785.5692] [ 2251] [depth= 9] . ( 1 sec) [ -11532.7259] [ 2191] [depth= 11] . ( 2 sec) [ -11446.5591] [ 2175] [depth= 3] . ( 2 sec) [ -11413.4247] [ 2165] [depth= 1] . ( 2 sec) [ -11259.4606] [ 2136] [depth= 6] . ( 2 sec) [ -11147.7236] [ 2131] [depth= 5] . ( 3 sec) [ -10957.8153] [ 2131] [depth= 2] . ( 3 sec) [ -10819.3701] [ 2098] [depth= 14] . ( 3 sec) [ -10693.5896] [ 2058] [depth= 5] . ( 3 sec) [ -10681.5021] [ 2056] [depth= 1] . ( 4 sec) [ -10612.4533] [ 2029] [depth= 5] . ( 4 sec) [ -10510.8027] [ 2025] [depth= 1] . ( 4 sec) [ -10353.2968] [ 1997] [depth= 2] . ( 4 sec) [ -10272.6898] [ 1959] [depth= 3] . ( 5 sec) [ -10262.0059] [ 1981] [depth= 1] . ( 5 sec) [ -10237.9242] [ 1959] [depth= 1] . ( 5 sec) [ -10171.7054] [ 1961] [depth= 1] . ( 6 sec) [ -9997.7922] [ 1929] [depth= 2] . ( 6 sec) [ -9938.1229] [ 1922] [depth= 4] . ( 6 sec) [ -9839.0363] [ 1893] [depth= 2] . ( 6 sec) [ -9676.9732] [ 1849] [depth= 3] . ( 7 sec) [ -9651.4835] [ 1848] [depth= 2] . ( 7 sec) [ -9585.9905] [ 1831] [depth= 3] . ( 7 sec) [ -9561.9146] [ 1842] [depth= 1] . ( 8 sec) [ -9375.1932] [ 1795] [depth= 4] . ( 8 sec) [ -9291.4004] [ 1783] [depth= 1] . ( 8 sec) [ -9249.0178] [ 1777] [depth= 1] . ( 8 sec) [ -9211.8069] [ 1763] [depth= 1] . ( 9 sec) [ -9205.3970] [ 1759] [depth= 2] . ( 9 sec) [ -9164.9290] [ 1757] [depth= 2] . ( 9 sec) [ -9104.0744] [ 1740] [depth= 2] . ( 9 sec) [ -9092.1646] [ 1734] [depth= 1] . ( 10 sec) [ -9089.1135] [ 1733] [depth= 1] . ( 10 sec) [ -8976.0866] [ 1710] [depth= 3] . ( 10 sec) [ -8965.1654] [ 1707] [depth= 1] . ( 12 sec) [ -8946.1704] [ 1700] [depth= 3] . ( 12 sec) [ -8913.3931] [ 1693] [depth= 1] . ( 12 sec) [ -8887.0282] [ 1685] [depth= 3] . ( 13 sec) [ -8886.6413] [ 1687] [depth= 1] . ( 14 sec) [ -8884.7650] [ 1685] [depth= 2] . ( 15 sec) [ -8882.7199] [ 1686] [depth= 1] . ( 15 sec) [ -8874.2422] [ 1686] [depth= 2] . ( 15 sec) [ -8852.0225] [ 1677] [depth= 1] . ( 16 sec) [ -8839.5229] [ 1673] [depth= 2] . ( 18 sec) [ -8827.9903] [ 1672] [depth= 2] . ( 18 sec) [ -8819.9129] [ 1671] [depth= 1] . ( 18 sec) [ -8818.5400] [ 1672] [depth= 1] . ( 19 sec) [ -8818.2596] [ 1675] [depth= 2] . ( 19 sec) [ -8773.8435] [Branch lengths ] . ( 20 sec) [ -8751.7920] [Alpha ][ 0.866828] . ( 21 sec) [ -8747.1797] [ 1673] [depth= 2] . ( 27 sec) [ -8746.6427] [ 1671] [depth= 1] . ( 31 sec) [ -8745.8777] [ 1671] [depth= 1] . ( 33 sec) [ -8741.1309] [ 1671] [depth= 1] . ( 38 sec) [ -8740.8652] [ 1670] [depth= 1] . ( 40 sec) [ -8740.4272] [ 1669] [depth= 1] . ( 41 sec) [ -8740.0012] [ 1671] [depth= 1] . ( 43 sec) [ -8729.2072] [Branch lengths ] . ( 43 sec) [ -8728.8185] [Alpha ][ 0.934928] . ( 52 sec) [ -8728.7127] [ 1668] [depth= 1] . ( 69 sec) [ -8727.1808] [Branch lengths ] . ( 69 sec) [ -8727.1217] [Alpha ][ 0.962778] . ( 93 sec) [ -8726.8150] [Branch lengths ] . ( 94 sec) [ -8726.8150] [Topology ] . ( 95 sec) [ -8725.5148] [Topology ] . ( 97 sec) [ -8725.4371] [Topology ] . ( 99 sec) [ -8725.4233] [Topology ] . ( 100 sec) [ -8725.4191] [Topology ] . ( 102 sec) [ -8725.4175] [Topology ] . ( 104 sec) [ -8725.4167] [Topology ] . ( 104 sec) [ -8725.3837] [Alpha ][ 0.983857] . ( 104 sec) [ -8725.3837] [Topology ] . ( 106 sec) [ -8725.3799] [Topology ] . ( 108 sec) [ -8725.3782] [Topology ] . ( 109 sec) [ -8725.3774] [Topology ] . ( 110 sec) [ -8725.3768] [Alpha ][ 0.986570] . ( 110 sec) [ -8725.3768] [Topology ] . ( 111 sec) [ -8725.3761] [Topology ] . ( 112 sec) [ -8725.3761] [Alpha ][ 0.986570] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8725.376130. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12315.9380] [Alpha ][ 0.500960] . ( 0 sec) [ -12172.7383] [ 2233] [depth= 8] . ( 1 sec) [ -11981.0435] [ 2180] [depth= 8] . ( 1 sec) [ -11718.7418] [ 2134] [depth= 3] . ( 1 sec) [ -11650.8480] [ 2130] [depth= 1] . ( 1 sec) [ -11598.6424] [ 2117] [depth= 1] . ( 2 sec) [ -11571.7693] [ 2111] [depth= 4] . ( 2 sec) [ -11559.7260] [ 2104] [depth= 1] . ( 2 sec) [ -11465.4229] [ 2098] [depth= 4] . ( 2 sec) [ -11379.7935] [ 2093] [depth= 2] . ( 3 sec) [ -11333.7976] [ 2086] [depth= 2] . ( 3 sec) [ -11272.4252] [ 2079] [depth= 2] . ( 3 sec) [ -11090.6849] [ 2068] [depth= 2] . ( 3 sec) [ -11056.5559] [ 2057] [depth= 2] . ( 3 sec) [ -10894.9079] [ 2029] [depth= 2] . ( 4 sec) [ -10868.5390] [ 2025] [depth= 2] . ( 4 sec) [ -10864.5735] [ 2027] [depth= 2] . ( 4 sec) [ -10815.8293] [ 2013] [depth= 3] . ( 5 sec) [ -10767.0288] [ 2008] [depth= 5] . ( 5 sec) [ -10596.5222] [ 1997] [depth= 6] . ( 5 sec) [ -10515.9866] [ 1977] [depth= 3] . ( 6 sec) [ -10444.9839] [ 1971] [depth= 3] . ( 6 sec) [ -10439.8607] [ 1971] [depth= 1] . ( 6 sec) [ -10329.9849] [ 1959] [depth= 1] . ( 6 sec) [ -10291.3870] [ 1946] [depth= 7] . ( 7 sec) [ -10279.5920] [ 1939] [depth= 2] . ( 7 sec) [ -10274.0643] [ 1941] [depth= 4] . ( 7 sec) [ -10145.2421] [ 1911] [depth= 2] . ( 7 sec) [ -10084.0074] [ 1900] [depth= 1] . ( 8 sec) [ -10083.4433] [ 1901] [depth= 1] . ( 8 sec) [ -9964.5081] [ 1897] [depth= 2] . ( 8 sec) [ -9899.4853] [ 1884] [depth= 1] . ( 9 sec) [ -9795.2474] [ 1890] [depth= 1] . ( 9 sec) [ -9692.5936] [ 1879] [depth= 2] . ( 10 sec) [ -9481.1251] [ 1842] [depth= 7] . ( 10 sec) [ -9476.6075] [ 1841] [depth= 1] . ( 10 sec) [ -9473.8607] [ 1841] [depth= 1] . ( 11 sec) [ -9343.2857] [ 1796] [depth= 9] . ( 11 sec) [ -9341.6089] [ 1799] [depth= 1] . ( 12 sec) [ -9225.1275] [ 1762] [depth= 10] . ( 12 sec) [ -9203.9814] [ 1756] [depth= 1] . ( 12 sec) [ -9133.8171] [ 1749] [depth= 1] . ( 12 sec) [ -9072.8167] [ 1736] [depth= 3] . ( 12 sec) [ -9062.1426] [ 1733] [depth= 1] . ( 13 sec) [ -9043.9866] [ 1733] [depth= 2] . ( 13 sec) [ -8979.6707] [ 1715] [depth= 4] . ( 13 sec) [ -8977.5416] [ 1712] [depth= 1] . ( 14 sec) [ -8930.6217] [ 1697] [depth= 11] . ( 15 sec) [ -8875.5985] [ 1685] [depth= 1] . ( 16 sec) [ -8873.0984] [ 1682] [depth= 2] . ( 16 sec) [ -8860.1669] [ 1682] [depth= 3] . ( 17 sec) [ -8854.8883] [ 1683] [depth= 1] . ( 19 sec) [ -8800.6698] [Branch lengths ] . ( 19 sec) [ -8781.9253] [Alpha ][ 0.822754] . ( 20 sec) [ -8780.0454] [ 1683] [depth= 1] . ( 22 sec) [ -8778.2614] [ 1685] [depth= 1] . ( 23 sec) [ -8759.7409] [ 1670] [depth= 2] . ( 24 sec) [ -8759.3861] [ 1671] [depth= 1] . ( 25 sec) [ -8756.1159] [ 1672] [depth= 2] . ( 26 sec) [ -8756.0573] [ 1671] [depth= 1] . ( 27 sec) [ -8751.5651] [ 1666] [depth= 2] . ( 37 sec) [ -8750.4379] [ 1667] [depth= 1] . ( 38 sec) [ -8746.8074] [ 1666] [depth= 1] . ( 38 sec) [ -8746.6594] [ 1668] [depth= 1] . ( 39 sec) [ -8745.7440] [ 1670] [depth= 1] . ( 40 sec) [ -8732.8053] [Branch lengths ] . ( 40 sec) [ -8731.9017] [Alpha ][ 0.923502] . ( 43 sec) [ -8730.1097] [ 1670] [depth= 1] . ( 50 sec) [ -8729.2973] [ 1668] [depth= 1] . ( 66 sec) [ -8726.0360] [Branch lengths ] . ( 66 sec) [ -8725.9312] [Alpha ][ 0.960911] . ( 91 sec) [ -8725.5212] [Branch lengths ] . ( 91 sec) [ -8725.5212] [Topology ] . ( 92 sec) [ -8725.4652] [Topology ] . ( 94 sec) [ -8725.4445] [Topology ] . ( 96 sec) [ -8725.4341] [Topology ] . ( 97 sec) [ -8725.4286] [Topology ] . ( 99 sec) [ -8725.4256] [Topology ] . ( 101 sec) [ -8725.4241] [Topology ] . ( 101 sec) [ -8725.3875] [Alpha ][ 0.983147] . ( 101 sec) [ -8725.3875] [Topology ] . ( 103 sec) [ -8725.3821] [Topology ] . ( 105 sec) [ -8725.3796] [Topology ] . ( 106 sec) [ -8725.3783] [Topology ] . ( 108 sec) [ -8725.3776] [Topology ] . ( 108 sec) [ -8725.3767] [Alpha ][ 0.986637] . ( 109 sec) [ -8725.3767] [Topology ] . ( 110 sec) [ -8725.3761] [Topology ] . ( 111 sec) [ -8725.3761] [Alpha ][ 0.986637] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8725.376062. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12241.9948] [Alpha ][ 0.500960] . ( 1 sec) [ -12102.1210] [ 2253] [depth= 6] . ( 1 sec) [ -11881.9000] [ 2215] [depth= 9] . ( 1 sec) [ -11814.1451] [ 2214] [depth= 1] . ( 1 sec) [ -11768.1015] [ 2214] [depth= 4] . ( 2 sec) [ -11697.7830] [ 2201] [depth= 7] . ( 2 sec) [ -11691.6910] [ 2200] [depth= 3] . ( 2 sec) [ -11678.0111] [ 2186] [depth= 4] . ( 2 sec) [ -11480.4345] [ 2187] [depth= 1] . ( 3 sec) [ -11460.6677] [ 2176] [depth= 5] . ( 3 sec) [ -11336.0407] [ 2131] [depth= 7] . ( 3 sec) [ -11216.6039] [ 2101] [depth= 6] . ( 3 sec) [ -11176.5666] [ 2093] [depth= 12] . ( 4 sec) [ -10997.4903] [ 2054] [depth= 6] . ( 4 sec) [ -10983.7673] [ 2053] [depth= 1] . ( 4 sec) [ -10953.3581] [ 2051] [depth= 3] . ( 4 sec) [ -10881.6711] [ 2052] [depth= 1] . ( 5 sec) [ -10861.9154] [ 2049] [depth= 5] . ( 5 sec) [ -10697.0870] [ 2036] [depth= 3] . ( 5 sec) [ -10627.2766] [ 2027] [depth= 1] . ( 5 sec) [ -10563.4471] [ 2019] [depth= 3] . ( 6 sec) [ -10490.9704] [ 1998] [depth= 1] . ( 6 sec) [ -10396.1261] [ 1977] [depth= 8] . ( 6 sec) [ -10386.1471] [ 1972] [depth= 1] . ( 7 sec) [ -10385.8767] [ 1976] [depth= 4] . ( 7 sec) [ -10361.1115] [ 1972] [depth= 6] . ( 7 sec) [ -10323.2423] [ 1967] [depth= 3] . ( 7 sec) [ -10229.3480] [ 1958] [depth= 5] . ( 8 sec) [ -10182.5980] [ 1952] [depth= 3] . ( 8 sec) [ -10087.8822] [ 1925] [depth= 4] . ( 9 sec) [ -9793.3852] [ 1872] [depth= 6] . ( 9 sec) [ -9704.2084] [ 1852] [depth= 2] . ( 9 sec) [ -9688.9582] [ 1848] [depth= 3] . ( 10 sec) [ -9608.9424] [ 1848] [depth= 4] . ( 10 sec) [ -9593.8970] [ 1847] [depth= 1] . ( 10 sec) [ -9434.9114] [ 1809] [depth= 3] . ( 10 sec) [ -9420.6185] [ 1810] [depth= 2] . ( 10 sec) [ -9371.1725] [ 1800] [depth= 4] . ( 11 sec) [ -9364.8245] [ 1801] [depth= 1] . ( 11 sec) [ -9319.5783] [ 1791] [depth= 1] . ( 11 sec) [ -9257.2168] [ 1774] [depth= 1] . ( 12 sec) [ -9210.1600] [ 1764] [depth= 1] . ( 12 sec) [ -9208.6488] [ 1763] [depth= 1] . ( 12 sec) [ -9178.9985] [ 1757] [depth= 4] . ( 13 sec) [ -9178.2911] [ 1755] [depth= 1] . ( 13 sec) [ -9163.1315] [ 1753] [depth= 2] . ( 13 sec) [ -9160.1854] [ 1753] [depth= 2] . ( 13 sec) [ -9156.9754] [ 1756] [depth= 1] . ( 14 sec) [ -9130.2270] [ 1747] [depth= 4] . ( 14 sec) [ -9090.5767] [ 1736] [depth= 1] . ( 14 sec) [ -8967.2649] [ 1705] [depth= 1] . ( 14 sec) [ -8930.1604] [ 1688] [depth= 5] . ( 15 sec) [ -8901.7909] [ 1688] [depth= 4] . ( 16 sec) [ -8900.1911] [ 1687] [depth= 1] . ( 17 sec) [ -8874.3956] [ 1686] [depth= 1] . ( 18 sec) [ -8806.7040] [Branch lengths ] . ( 18 sec) [ -8787.9260] [Alpha ][ 0.824580] . ( 19 sec) [ -8787.4012] [ 1682] [depth= 2] . ( 20 sec) [ -8784.6668] [ 1682] [depth= 1] . ( 20 sec) [ -8760.2422] [ 1672] [depth= 2] . ( 21 sec) [ -8754.4607] [ 1671] [depth= 1] . ( 22 sec) [ -8750.4935] [ 1669] [depth= 1] . ( 27 sec) [ -8743.9085] [ 1665] [depth= 1] . ( 34 sec) [ -8742.2735] [ 1668] [depth= 1] . ( 40 sec) [ -8728.7725] [Branch lengths ] . ( 41 sec) [ -8727.9714] [Alpha ][ 0.918981] . ( 65 sec) [ -8726.1855] [Branch lengths ] . ( 65 sec) [ -8726.1855] [Topology ] . ( 67 sec) [ -8725.9082] [Topology ] . ( 69 sec) [ -8725.8052] [Topology ] . ( 71 sec) [ -8725.7525] [Topology ] . ( 72 sec) [ -8725.7245] [Topology ] . ( 74 sec) [ -8725.7094] [Topology ] . ( 76 sec) [ -8725.7012] [Topology ] . ( 76 sec) [ -8725.4565] [Alpha ][ 0.975852] . ( 76 sec) [ -8725.4565] [Topology ] . ( 78 sec) [ -8725.4199] [Topology ] . ( 80 sec) [ -8725.4033] [Topology ] . ( 81 sec) [ -8725.3946] [Topology ] . ( 83 sec) [ -8725.3900] [Topology ] . ( 85 sec) [ -8725.3875] [Topology ] . ( 86 sec) [ -8725.3862] [Topology ] . ( 87 sec) [ -8725.3798] [Alpha ][ 0.985627] . ( 87 sec) [ -8725.3798] [Topology ] . ( 88 sec) [ -8725.3778] [Topology ] . ( 90 sec) [ -8725.3767] [Topology ] . ( 92 sec) [ -8725.3762] [Topology ] . ( 92 sec) [ -8725.3761] [Alpha ][ 0.986974] . ( 92 sec) [ -8725.3761] [Topology ] . ( 94 sec) [ -8725.3757] [Topology ] . ( 94 sec) [ -8725.3757] [Alpha ][ 0.986974] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8725.375691. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -8811.1519] [Alpha ][ 0.880454] . ( 0 sec) [ -8811.1519] [Topology ] . ( 2 sec) [ -8746.8962] [Topology ] . ( 3 sec) [ -8734.3709] [Topology ] . ( 5 sec) [ -8732.6388] [Topology ] . ( 7 sec) [ -8732.0970] [Topology ] . ( 9 sec) [ -8730.9948] [Topology ] . ( 10 sec) [ -8728.4784] [Topology ] . ( 12 sec) [ -8726.6266] [Topology ] . ( 14 sec) [ -8726.2606] [Topology ] . ( 15 sec) [ -8726.1914] [Topology ] . Checking for NNIs, optimizing five branches... . ( 30 sec) [ -8725.4787] [Alpha ][ 0.974173] . ( 30 sec) [ -8725.4787] [Topology ] . ( 32 sec) [ -8725.4256] [Topology ] . ( 34 sec) [ -8725.4069] [Topology ] . ( 36 sec) [ -8725.3977] [Topology ] . ( 37 sec) [ -8725.3930] [Topology ] . ( 39 sec) [ -8725.3904] [Topology ] . ( 41 sec) [ -8725.3890] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -8725.3805] [Alpha ][ 0.985455] . ( 54 sec) [ -8725.3805] [Topology ] . ( 56 sec) [ -8725.3781] [Topology ] . ( 58 sec) [ -8725.3770] [Topology ] . ( 59 sec) [ -8725.3763] [Topology ] . Checking for NNIs, optimizing five branches... . ( 73 sec) [ -8725.3762] [Alpha ][ 0.986897] . ( 73 sec) [ -8725.3762] [Topology ] . ( 75 sec) [ -8725.3758] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 101 sec) [ -8811.1519] [Alpha ][ 0.880454] . ( 102 sec) [ -8799.7211] [ 1681] [depth= 1] . ( 105 sec) [ -8794.0723] [ 1678] [depth= 1] . ( 108 sec) [ -8792.5920] [ 1678] [depth= 1] . ( 108 sec) [ -8791.5164] [ 1678] [depth= 1] . ( 109 sec) [ -8788.1612] [ 1678] [depth= 1] . ( 110 sec) [ -8787.8672] [ 1678] [depth= 1] . ( 110 sec) [ -8787.5915] [ 1679] [depth= 1] . ( 111 sec) [ -8787.1394] [ 1675] [depth= 2] . ( 111 sec) [ -8782.1493] [ 1675] [depth= 1] . ( 112 sec) [ -8781.7047] [ 1675] [depth= 1] . ( 113 sec) [ -8776.8288] [ 1677] [depth= 1] . ( 113 sec) [ -8770.1167] [ 1671] [depth= 1] . ( 116 sec) [ -8768.2046] [ 1672] [depth= 1] . ( 116 sec) [ -8765.3032] [ 1672] [depth= 1] . ( 117 sec) [ -8762.6609] [ 1672] [depth= 1] . ( 118 sec) [ -8761.2050] [ 1671] [depth= 1] . ( 118 sec) [ -8761.0174] [ 1672] [depth= 1] . ( 119 sec) [ -8760.0796] [ 1671] [depth= 1] . ( 123 sec) [ -8729.5163] [Branch lengths ] . ( 123 sec) [ -8728.7833] [Alpha ][ 0.976436] . ( 130 sec) [ -8728.6757] [ 1668] [depth= 1] . ( 147 sec) [ -8726.7933] [Branch lengths ] . ( 148 sec) [ -8726.7915] [Alpha ][ 0.981506] . ( 173 sec) [ -8726.7047] [Branch lengths ] . ( 173 sec) [ -8726.7047] [Topology ] . ( 174 sec) [ -8725.4580] [Topology ] . ( 176 sec) [ -8725.3897] [Topology ] . ( 178 sec) [ -8725.3804] [Topology ] . ( 179 sec) [ -8725.3785] [Topology ] . ( 181 sec) [ -8725.3781] [Topology ] . ( 181 sec) [ -8725.3757] [Alpha ][ 0.987405] . ( 182 sec) [ -8725.3757] [Topology ] . ( 183 sec) [ -8725.3754] [Topology ] . ( 184 sec) [ -8725.3754] [Alpha ][ 0.987405] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8725.375765 . Log likelihood obtained after SPR moves : -8725.375398 . Log likelihood of the current tree: -8725.375398. . Printing the most likely tree in file 'proteic_M2478_30x276_2005.phy_phyml_tree.txt'... . Best log likelihood : -8725.375398 . Time used 0h3m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 775.35user 0.00system 13:05.47elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps