.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1503_23x479_2003.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... . 356 patterns found. (out of a total of 479 sites) . 140 sites without polymorphism (29.23%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13515.0421] [Alpha ][ 0.500960] . ( 1 sec) [ -13233.7351] [ 2174] [depth= 8] . ( 1 sec) [ -13113.6272] [ 2153] [depth= 4] . ( 2 sec) [ -12588.0868] [ 2139] [depth= 5] . ( 2 sec) [ -12496.8376] [ 2110] [depth= 1] . ( 2 sec) [ -12435.1873] [ 2097] [depth= 6] . ( 3 sec) [ -11697.6021] [ 2094] [depth= 2] . ( 3 sec) [ -11676.4673] [ 2089] [depth= 2] . ( 3 sec) [ -11522.9487] [ 2071] [depth= 3] . ( 3 sec) [ -11225.0170] [ 1995] [depth= 4] . ( 4 sec) [ -11198.0383] [ 1986] [depth= 3] . ( 4 sec) [ -11145.2694] [ 1976] [depth= 3] . ( 4 sec) [ -11080.3705] [ 1969] [depth= 2] . ( 5 sec) [ -10879.4647] [ 1965] [depth= 2] . ( 5 sec) [ -10778.5781] [ 1934] [depth= 2] . ( 5 sec) [ -10760.9378] [ 1937] [depth= 1] . ( 6 sec) [ -10669.1469] [ 1926] [depth= 2] . ( 6 sec) [ -10590.7063] [ 1909] [depth= 8] . ( 6 sec) [ -10431.9351] [ 1845] [depth= 5] . ( 7 sec) [ -10355.1982] [ 1837] [depth= 2] . ( 7 sec) [ -10293.4621] [ 1822] [depth= 2] . ( 8 sec) [ -10263.0866] [ 1815] [depth= 5] . ( 8 sec) [ -10257.9269] [ 1825] [depth= 4] . ( 9 sec) [ -10233.0752] [ 1821] [depth= 1] . ( 9 sec) [ -10201.4435] [ 1816] [depth= 2] . ( 9 sec) [ -10192.1698] [ 1810] [depth= 2] . ( 10 sec) [ -10190.5480] [ 1812] [depth= 1] . ( 11 sec) [ -10153.1885] [ 1798] [depth= 2] . ( 12 sec) [ -10114.7691] [ 1791] [depth= 2] . ( 12 sec) [ -10113.3077] [ 1790] [depth= 2] . ( 13 sec) [ -10095.6479] [ 1784] [depth= 1] . ( 13 sec) [ -10084.8589] [ 1781] [depth= 1] . ( 13 sec) [ -10079.4482] [ 1786] [depth= 1] . ( 13 sec) [ -10065.2755] [ 1781] [depth= 1] . ( 15 sec) [ -9980.4849] [ 1750] [depth= 5] . ( 15 sec) [ -9975.5954] [ 1748] [depth= 1] . ( 16 sec) [ -9974.9542] [ 1751] [depth= 1] . ( 16 sec) [ -9892.6603] [Branch lengths ] . ( 17 sec) [ -9891.2613] [Alpha ][ 0.562469] . ( 19 sec) [ -9888.3814] [ 1746] [depth= 1] . ( 21 sec) [ -9887.6175] [ 1748] [depth= 1] . ( 21 sec) [ -9887.1360] [ 1748] [depth= 1] . ( 25 sec) [ -9886.3894] [ 1747] [depth= 1] . ( 30 sec) [ -9886.1654] [ 1749] [depth= 4] . ( 31 sec) [ -9881.3303] [ 1743] [depth= 1] . ( 35 sec) [ -9854.0057] [Branch lengths ] . ( 35 sec) [ -9853.8467] [Alpha ][ 0.585109] . ( 52 sec) [ -9851.2930] [Branch lengths ] . ( 52 sec) [ -9851.2930] [Topology ] . ( 54 sec) [ -9851.2248] [Topology ] . ( 56 sec) [ -9851.2145] [Topology ] . ( 57 sec) [ -9851.2123] [Topology ] . ( 59 sec) [ -9851.2118] [Topology ] . ( 59 sec) [ -9851.2113] [Alpha ][ 0.586394] . ( 59 sec) [ -9851.2113] [Topology ] . ( 61 sec) [ -9851.2112] [Topology ] . ( 61 sec) [ -9851.2112] [Alpha ][ 0.586394] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -9851.2033] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9851.203286. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12063.8065] [Alpha ][ 0.500960] . ( 0 sec) [ -11990.7861] [ 2110] [depth= 3] . ( 1 sec) [ -11791.1600] [ 2094] [depth= 3] . ( 1 sec) [ -11724.9216] [ 2087] [depth= 2] . ( 1 sec) [ -11561.1438] [ 2076] [depth= 2] . ( 1 sec) [ -11424.5877] [ 2061] [depth= 2] . ( 2 sec) [ -11421.8242] [ 2059] [depth= 4] . ( 2 sec) [ -11371.4023] [ 2046] [depth= 3] . ( 2 sec) [ -11354.8988] [ 2038] [depth= 2] . ( 3 sec) [ -11322.0252] [ 2030] [depth= 1] . ( 3 sec) [ -11185.2295] [ 1997] [depth= 1] . ( 3 sec) [ -11003.6158] [ 1964] [depth= 9] . ( 4 sec) [ -10820.8482] [ 1917] [depth= 1] . ( 4 sec) [ -10662.8475] [ 1894] [depth= 3] . ( 5 sec) [ -10622.8783] [ 1892] [depth= 1] . ( 5 sec) [ -10604.5428] [ 1883] [depth= 1] . ( 5 sec) [ -10580.6453] [ 1881] [depth= 4] . ( 5 sec) [ -10563.6798] [ 1885] [depth= 4] . ( 6 sec) [ -10485.6455] [ 1862] [depth= 2] . ( 6 sec) [ -10448.4526] [ 1851] [depth= 2] . ( 6 sec) [ -10446.0068] [ 1853] [depth= 3] . ( 7 sec) [ -10372.2470] [ 1834] [depth= 2] . ( 7 sec) [ -10329.1667] [ 1811] [depth= 9] . ( 7 sec) [ -10300.1893] [ 1804] [depth= 2] . ( 8 sec) [ -10294.2644] [ 1800] [depth= 2] . ( 9 sec) [ -10144.4312] [ 1779] [depth= 11] . ( 9 sec) [ -10084.6093] [ 1774] [depth= 1] . ( 10 sec) [ -10082.9786] [ 1775] [depth= 2] . ( 10 sec) [ -10062.1668] [ 1765] [depth= 2] . ( 11 sec) [ -10055.9048] [ 1763] [depth= 1] . ( 11 sec) [ -10001.1409] [ 1758] [depth= 2] . ( 11 sec) [ -9986.6108] [ 1761] [depth= 4] . ( 12 sec) [ -9963.2930] [ 1758] [depth= 3] . ( 12 sec) [ -9957.6859] [ 1755] [depth= 1] . ( 12 sec) [ -9956.2975] [ 1752] [depth= 1] . ( 13 sec) [ -9953.1682] [ 1754] [depth= 1] . ( 13 sec) [ -9916.8179] [ 1747] [depth= 1] . ( 14 sec) [ -9906.3170] [ 1746] [depth= 1] . ( 14 sec) [ -9868.2405] [Branch lengths ] . ( 15 sec) [ -9867.2310] [Alpha ][ 0.552896] . ( 15 sec) [ -9866.6476] [ 1748] [depth= 1] . ( 19 sec) [ -9865.6828] [ 1748] [depth= 1] . ( 22 sec) [ -9864.1886] [ 1750] [depth= 1] . ( 26 sec) [ -9864.0818] [ 1751] [depth= 1] . ( 32 sec) [ -9862.6022] [ 1750] [depth= 1] . ( 34 sec) [ -9857.2863] [Branch lengths ] . ( 35 sec) [ -9857.1729] [Alpha ][ 0.571458] . ( 57 sec) [ -9856.9002] [Branch lengths ] . ( 57 sec) [ -9856.9002] [Topology ] . ( 59 sec) [ -9856.8732] [Topology ] . ( 61 sec) [ -9856.8657] [Topology ] . ( 62 sec) [ -9856.8626] [Topology ] . ( 64 sec) [ -9856.8613] [Topology ] . ( 65 sec) [ -9856.8607] [Topology ] . ( 66 sec) [ -9856.8363] [Alpha ][ 0.580519] . ( 66 sec) [ -9856.8363] [Topology ] . ( 68 sec) [ -9856.8317] [Topology ] . ( 69 sec) [ -9856.8299] [Topology ] . ( 71 sec) [ -9856.8292] [Topology ] . ( 71 sec) [ -9856.8286] [Alpha ][ 0.581887] . ( 71 sec) [ -9856.8286] [Topology ] . ( 73 sec) [ -9856.8280] [Topology ] . ( 73 sec) [ -9856.8280] [Alpha ][ 0.582469] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9856.827967. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12181.3020] [Alpha ][ 0.500960] . ( 1 sec) [ -12061.4171] [ 2158] [depth= 11] . ( 1 sec) [ -11960.4954] [ 2143] [depth= 3] . ( 1 sec) [ -11850.2303] [ 2123] [depth= 2] . ( 2 sec) [ -11751.0916] [ 2075] [depth= 3] . ( 2 sec) [ -11702.7650] [ 2064] [depth= 7] . ( 2 sec) [ -11613.7240] [ 2037] [depth= 2] . ( 2 sec) [ -11467.0538] [ 2031] [depth= 3] . ( 3 sec) [ -11302.9543] [ 2032] [depth= 1] . ( 3 sec) [ -11105.6713] [ 2029] [depth= 10] . ( 3 sec) [ -11031.0684] [ 2003] [depth= 10] . ( 3 sec) [ -11004.0007] [ 1989] [depth= 2] . ( 4 sec) [ -10969.3816] [ 1980] [depth= 9] . ( 4 sec) [ -10844.0715] [ 1970] [depth= 5] . ( 4 sec) [ -10800.3467] [ 1958] [depth= 4] . ( 5 sec) [ -10771.4375] [ 1939] [depth= 2] . ( 5 sec) [ -10579.8253] [ 1899] [depth= 1] . ( 5 sec) [ -10555.5097] [ 1886] [depth= 3] . ( 6 sec) [ -10545.1012] [ 1886] [depth= 3] . ( 6 sec) [ -10520.2210] [ 1879] [depth= 3] . ( 6 sec) [ -10510.1847] [ 1883] [depth= 1] . ( 7 sec) [ -10499.5350] [ 1886] [depth= 1] . ( 7 sec) [ -10373.0516] [ 1843] [depth= 3] . ( 7 sec) [ -10373.0279] [ 1845] [depth= 1] . ( 8 sec) [ -10353.3143] [ 1839] [depth= 2] . ( 8 sec) [ -10353.0526] [ 1837] [depth= 1] . ( 8 sec) [ -10345.0568] [ 1838] [depth= 1] . ( 8 sec) [ -10339.7654] [ 1836] [depth= 1] . ( 9 sec) [ -10293.5830] [ 1832] [depth= 4] . ( 9 sec) [ -10289.0997] [ 1834] [depth= 2] . ( 10 sec) [ -10265.2506] [ 1830] [depth= 1] . ( 10 sec) [ -10223.3583] [ 1821] [depth= 3] . ( 11 sec) [ -10189.2710] [ 1813] [depth= 2] . ( 11 sec) [ -10117.4786] [ 1798] [depth= 5] . ( 12 sec) [ -10102.9232] [ 1792] [depth= 1] . ( 12 sec) [ -10060.6113] [ 1777] [depth= 1] . ( 12 sec) [ -10050.4921] [ 1772] [depth= 1] . ( 14 sec) [ -10036.4954] [ 1770] [depth= 4] . ( 14 sec) [ -10003.5177] [ 1759] [depth= 4] . ( 14 sec) [ -9941.8464] [ 1744] [depth= 2] . ( 16 sec) [ -9863.9177] [Branch lengths ] . ( 16 sec) [ -9862.3966] [Alpha ][ 0.565156] . ( 16 sec) [ -9859.0742] [ 1744] [depth= 1] . ( 19 sec) [ -9858.3738] [ 1745] [depth= 1] . ( 29 sec) [ -9857.1772] [ 1747] [depth= 1] . ( 36 sec) [ -9851.2441] [Branch lengths ] . ( 37 sec) [ -9851.1883] [Alpha ][ 0.578213] . ( 60 sec) [ -9851.0499] [Branch lengths ] . ( 60 sec) [ -9851.0499] [Topology ] . ( 62 sec) [ -9851.0442] [Topology ] . ( 63 sec) [ -9851.0426] [Topology ] . ( 65 sec) [ -9851.0420] [Topology ] . ( 65 sec) [ -9851.0345] [Alpha ][ 0.583259] . ( 65 sec) [ -9851.0345] [Topology ] . ( 67 sec) [ -9851.0325] [Topology ] . ( 69 sec) [ -9851.0317] [Topology ] . ( 69 sec) [ -9851.0315] [Alpha ][ 0.583988] . ( 69 sec) [ -9851.0315] [Topology ] . ( 71 sec) [ -9851.0310] [Topology ] . ( 71 sec) [ -9851.0310] [Alpha ][ 0.583988] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9851.031002. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11758.8934] [Alpha ][ 0.500960] . ( 1 sec) [ -11612.6693] [ 2086] [depth= 5] . ( 1 sec) [ -11612.6197] [ 2085] [depth= 3] . ( 1 sec) [ -11561.7020] [ 2068] [depth= 6] . ( 2 sec) [ -11506.1044] [ 2047] [depth= 1] . ( 2 sec) [ -11372.3455] [ 2031] [depth= 7] . ( 2 sec) [ -11329.6053] [ 2026] [depth= 1] . ( 2 sec) [ -11301.2997] [ 2023] [depth= 3] . ( 3 sec) [ -11182.8730] [ 2015] [depth= 4] . ( 3 sec) [ -11076.1058] [ 2003] [depth= 1] . ( 3 sec) [ -11067.7806] [ 2014] [depth= 6] . ( 3 sec) [ -10965.6118] [ 1996] [depth= 2] . ( 4 sec) [ -10913.7077] [ 1980] [depth= 7] . ( 4 sec) [ -10763.9140] [ 1948] [depth= 2] . ( 4 sec) [ -10671.0400] [ 1914] [depth= 1] . ( 4 sec) [ -10631.1045] [ 1914] [depth= 2] . ( 5 sec) [ -10531.5429] [ 1896] [depth= 1] . ( 5 sec) [ -10456.3480] [ 1895] [depth= 1] . ( 5 sec) [ -10454.9835] [ 1896] [depth= 1] . ( 6 sec) [ -10369.0726] [ 1852] [depth= 1] . ( 6 sec) [ -10350.7363] [ 1848] [depth= 8] . ( 7 sec) [ -10196.5502] [ 1841] [depth= 6] . ( 7 sec) [ -10166.8882] [ 1836] [depth= 2] . ( 8 sec) [ -10107.7477] [ 1822] [depth= 1] . ( 8 sec) [ -10082.4988] [ 1815] [depth= 1] . ( 8 sec) [ -10057.7399] [ 1808] [depth= 1] . ( 9 sec) [ -10045.5612] [ 1796] [depth= 6] . ( 9 sec) [ -10034.6760] [ 1791] [depth= 1] . ( 10 sec) [ -10029.4769] [ 1791] [depth= 4] . ( 10 sec) [ -10027.0808] [ 1786] [depth= 1] . ( 10 sec) [ -10015.6940] [ 1781] [depth= 1] . ( 11 sec) [ -9983.4349] [ 1771] [depth= 1] . ( 11 sec) [ -9980.4117] [ 1772] [depth= 1] . ( 12 sec) [ -9980.2663] [ 1776] [depth= 1] . ( 13 sec) [ -9976.4239] [ 1772] [depth= 1] . ( 13 sec) [ -9971.8509] [ 1776] [depth= 2] . ( 14 sec) [ -9966.0178] [ 1771] [depth= 2] . ( 15 sec) [ -9959.9514] [ 1771] [depth= 1] . ( 15 sec) [ -9957.5478] [ 1771] [depth= 1] . ( 16 sec) [ -9912.7563] [Branch lengths ] . ( 16 sec) [ -9912.1868] [Alpha ][ 0.539519] . ( 18 sec) [ -9894.2579] [ 1765] [depth= 1] . ( 19 sec) [ -9893.8082] [ 1763] [depth= 1] . ( 19 sec) [ -9892.1042] [ 1763] [depth= 1] . ( 22 sec) [ -9876.6100] [ 1757] [depth= 2] . ( 22 sec) [ -9872.9221] [ 1755] [depth= 1] . ( 23 sec) [ -9872.8851] [ 1750] [depth= 3] . ( 24 sec) [ -9862.9167] [ 1743] [depth= 2] . ( 27 sec) [ -9861.4778] [ 1747] [depth= 1] . ( 34 sec) [ -9854.2212] [Branch lengths ] . ( 34 sec) [ -9853.9849] [Alpha ][ 0.566238] . ( 36 sec) [ -9852.6186] [ 1747] [depth= 1] . ( 56 sec) [ -9851.2603] [Branch lengths ] . ( 57 sec) [ -9851.2317] [Alpha ][ 0.575992] . ( 80 sec) [ -9851.0706] [Branch lengths ] . ( 80 sec) [ -9851.0706] [Topology ] . ( 82 sec) [ -9851.0573] [Topology ] . ( 83 sec) [ -9851.0533] [Topology ] . ( 85 sec) [ -9851.0516] [Topology ] . ( 87 sec) [ -9851.0508] [Topology ] . ( 87 sec) [ -9851.0369] [Alpha ][ 0.582855] . ( 87 sec) [ -9851.0369] [Topology ] . ( 89 sec) [ -9851.0337] [Topology ] . ( 91 sec) [ -9851.0325] [Topology ] . ( 92 sec) [ -9851.0319] [Topology ] . ( 92 sec) [ -9851.0315] [Alpha ][ 0.584016] . ( 93 sec) [ -9851.0315] [Topology ] . ( 94 sec) [ -9851.0310] [Topology ] . ( 95 sec) [ -9851.0310] [Alpha ][ 0.584016] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9851.030974. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11692.1890] [Alpha ][ 0.500960] . ( 1 sec) [ -11581.7464] [ 2136] [depth= 5] . ( 1 sec) [ -11496.3255] [ 2122] [depth= 4] . ( 2 sec) [ -11459.7950] [ 2103] [depth= 3] . ( 2 sec) [ -11409.6719] [ 2056] [depth= 1] . ( 2 sec) [ -11352.5498] [ 2047] [depth= 4] . ( 3 sec) [ -11303.6017] [ 2044] [depth= 1] . ( 3 sec) [ -11296.5100] [ 2036] [depth= 5] . ( 3 sec) [ -11251.8938] [ 2033] [depth= 1] . ( 3 sec) [ -11215.8859] [ 2027] [depth= 11] . ( 4 sec) [ -11155.6532] [ 2007] [depth= 1] . ( 4 sec) [ -11132.0309] [ 2001] [depth= 1] . ( 4 sec) [ -11109.1515] [ 2000] [depth= 2] . ( 5 sec) [ -10918.7991] [ 1943] [depth= 10] . ( 5 sec) [ -10735.8471] [ 1907] [depth= 1] . ( 5 sec) [ -10605.6907] [ 1896] [depth= 9] . ( 6 sec) [ -10540.3357] [ 1876] [depth= 3] . ( 6 sec) [ -10467.5436] [ 1864] [depth= 4] . ( 6 sec) [ -10454.3301] [ 1861] [depth= 3] . ( 6 sec) [ -10438.8409] [ 1857] [depth= 1] . ( 7 sec) [ -10428.8569] [ 1861] [depth= 5] . ( 7 sec) [ -10395.2216] [ 1861] [depth= 5] . ( 7 sec) [ -10392.2726] [ 1859] [depth= 1] . ( 8 sec) [ -10359.8488] [ 1842] [depth= 5] . ( 8 sec) [ -10244.1562] [ 1819] [depth= 2] . ( 8 sec) [ -10196.0988] [ 1806] [depth= 6] . ( 9 sec) [ -10168.9004] [ 1798] [depth= 1] . ( 9 sec) [ -10119.8045] [ 1801] [depth= 1] . ( 9 sec) [ -10099.4624] [ 1797] [depth= 2] . ( 9 sec) [ -10096.4934] [ 1795] [depth= 7] . ( 10 sec) [ -10082.0981] [ 1782] [depth= 3] . ( 10 sec) [ -10074.6489] [ 1777] [depth= 3] . ( 11 sec) [ -10066.6041] [ 1777] [depth= 1] . ( 11 sec) [ -10063.7319] [ 1774] [depth= 2] . ( 12 sec) [ -10060.6480] [ 1775] [depth= 1] . ( 12 sec) [ -10054.5303] [ 1775] [depth= 1] . ( 12 sec) [ -10039.0841] [ 1776] [depth= 1] . ( 12 sec) [ -10021.9820] [ 1767] [depth= 2] . ( 13 sec) [ -10016.1257] [ 1766] [depth= 1] . ( 14 sec) [ -10003.3063] [ 1762] [depth= 1] . ( 14 sec) [ -10001.3160] [ 1765] [depth= 2] . ( 14 sec) [ -9983.5483] [ 1758] [depth= 4] . ( 15 sec) [ -9975.2001] [ 1756] [depth= 2] . ( 15 sec) [ -9900.2169] [Branch lengths ] . ( 16 sec) [ -9896.2548] [Alpha ][ 0.606450] . ( 16 sec) [ -9892.1430] [ 1755] [depth= 1] . ( 17 sec) [ -9869.3908] [ 1746] [depth= 3] . ( 20 sec) [ -9867.5746] [ 1746] [depth= 1] . ( 21 sec) [ -9866.2040] [ 1746] [depth= 2] . ( 24 sec) [ -9860.3884] [ 1747] [depth= 1] . ( 36 sec) [ -9853.7745] [Branch lengths ] . ( 36 sec) [ -9853.6939] [Alpha ][ 0.589768] . ( 38 sec) [ -9852.0352] [ 1747] [depth= 1] . ( 59 sec) [ -9851.0606] [Branch lengths ] . ( 60 sec) [ -9851.0570] [Alpha ][ 0.586149] . ( 83 sec) [ -9851.0317] [Branch lengths ] . ( 83 sec) [ -9851.0317] [Topology ] . ( 85 sec) [ -9851.0309] [Topology ] . ( 85 sec) [ -9851.0307] [Alpha ][ 0.585232] . ( 85 sec) [ -9851.0307] [Topology ] . ( 87 sec) [ -9851.0305] [Topology ] . ( 87 sec) [ -9851.0305] [Alpha ][ 0.585232] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9851.030517. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -9920.9916] [Alpha ][ 0.500960] . ( 0 sec) [ -9920.9916] [Topology ] . ( 2 sec) [ -9858.0273] [Topology ] . ( 4 sec) [ -9854.1883] [Topology ] . ( 5 sec) [ -9853.4558] [Topology ] . ( 7 sec) [ -9853.2048] [Topology ] . ( 9 sec) [ -9853.1061] [Topology ] . ( 10 sec) [ -9853.0648] [Topology ] . ( 12 sec) [ -9853.0467] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -9851.5926] [Alpha ][ 0.563972] . ( 25 sec) [ -9851.5926] [Topology ] . ( 27 sec) [ -9851.3146] [Topology ] . ( 29 sec) [ -9851.2161] [Topology ] . ( 30 sec) [ -9851.1749] [Topology ] . ( 32 sec) [ -9851.1568] [Topology ] . ( 34 sec) [ -9851.1487] [Topology ] . ( 36 sec) [ -9851.1450] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -9851.0669] [Alpha ][ 0.579529] . ( 49 sec) [ -9851.0669] [Topology ] . ( 51 sec) [ -9851.0496] [Topology ] . ( 52 sec) [ -9851.0429] [Topology ] . ( 54 sec) [ -9851.0400] [Topology ] . ( 56 sec) [ -9851.0387] [Topology ] . ( 57 sec) [ -9851.0381] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -9851.0335] [Alpha ][ 0.583469] . ( 71 sec) [ -9851.0335] [Topology ] . ( 72 sec) [ -9851.0320] [Topology ] . ( 74 sec) [ -9851.0314] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -9851.0312] [Alpha ][ 0.584097] . ( 87 sec) [ -9851.0312] [Topology ] . ( 89 sec) [ -9851.0309] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 116 sec) [ -9920.9916] [Alpha ][ 0.500960] . ( 117 sec) [ -9920.4868] [ 1746] [depth= 1] . ( 117 sec) [ -9918.9749] [ 1748] [depth= 1] . ( 118 sec) [ -9916.9721] [ 1749] [depth= 1] . ( 120 sec) [ -9911.0355] [ 1750] [depth= 1] . ( 125 sec) [ -9902.7965] [ 1750] [depth= 2] . ( 126 sec) [ -9896.0069] [ 1744] [depth= 1] . ( 127 sec) [ -9895.2402] [ 1747] [depth= 1] . ( 127 sec) [ -9893.0349] [ 1743] [depth= 1] . ( 128 sec) [ -9892.2817] [ 1747] [depth= 1] . ( 128 sec) [ -9892.2648] [ 1743] [depth= 1] . ( 128 sec) [ -9888.2612] [ 1743] [depth= 1] . ( 129 sec) [ -9887.7172] [ 1751] [depth= 1] . ( 130 sec) [ -9884.1766] [ 1743] [depth= 1] . ( 131 sec) [ -9880.9951] [ 1743] [depth= 1] . ( 133 sec) [ -9879.7464] [ 1743] [depth= 1] . ( 134 sec) [ -9856.8332] [Branch lengths ] . ( 134 sec) [ -9855.8301] [Alpha ][ 0.553326] . ( 146 sec) [ -9853.9110] [ 1743] [depth= 1] . ( 151 sec) [ -9851.7389] [Branch lengths ] . ( 152 sec) [ -9851.6339] [Alpha ][ 0.571283] . ( 169 sec) [ -9851.3159] [Branch lengths ] . ( 169 sec) [ -9851.3159] [Topology ] . ( 171 sec) [ -9851.2852] [Topology ] . ( 172 sec) [ -9851.2763] [Topology ] . ( 174 sec) [ -9851.2725] [Topology ] . ( 176 sec) [ -9851.2708] [Topology ] . ( 178 sec) [ -9851.2701] [Topology ] . ( 178 sec) [ -9851.2269] [Alpha ][ 0.583426] . ( 178 sec) [ -9851.2269] [Topology ] . ( 180 sec) [ -9851.2189] [Topology ] . ( 181 sec) [ -9851.2160] [Topology ] . ( 183 sec) [ -9851.2147] [Topology ] . ( 185 sec) [ -9851.2141] [Topology ] . ( 185 sec) [ -9851.2128] [Alpha ][ 0.585523] . ( 185 sec) [ -9851.2128] [Topology ] . ( 187 sec) [ -9851.2120] [Topology ] . ( 187 sec) [ -9851.2120] [Alpha ][ 0.586109] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -9851.2098] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9851.030860 . Log likelihood obtained after SPR moves : -9851.209848 . Log likelihood of the current tree: -9851.030860. . Printing the most likely tree in file 'proteic_M1503_23x479_2003.phy_phyml_tree.txt'... . Best log likelihood : -9851.030517 . Time used 0h3m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 678.16user 0.00system 11:26.34elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps