.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1993_28x93_2004.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... . 79 patterns found. (out of a total of 93 sites) . 26 sites without polymorphism (27.96%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3155.2085] [Alpha ][ 0.500960] . ( 1 sec) [ -3074.5398] [ 521] [depth= 6] . ( 1 sec) [ -2941.0463] [ 501] [depth= 7] . ( 1 sec) [ -2918.7410] [ 500] [depth= 2] . ( 1 sec) [ -2907.1504] [ 498] [depth= 3] . ( 1 sec) [ -2895.2143] [ 496] [depth= 2] . ( 1 sec) [ -2887.7659] [ 494] [depth= 5] . ( 1 sec) [ -2882.6380] [ 493] [depth= 1] . ( 1 sec) [ -2850.7850] [ 492] [depth= 5] . ( 1 sec) [ -2836.9184] [ 488] [depth= 1] . ( 2 sec) [ -2823.8415] [ 486] [depth= 5] . ( 2 sec) [ -2798.8344] [ 476] [depth= 7] . ( 2 sec) [ -2789.9148] [ 474] [depth= 1] . ( 2 sec) [ -2758.7890] [ 468] [depth= 4] . ( 2 sec) [ -2749.0689] [ 464] [depth= 1] . ( 2 sec) [ -2722.2140] [ 457] [depth= 7] . ( 2 sec) [ -2643.6760] [ 440] [depth= 6] . ( 2 sec) [ -2627.4355] [ 440] [depth= 1] . ( 2 sec) [ -2559.3838] [ 434] [depth= 1] . ( 2 sec) [ -2546.2549] [ 430] [depth= 4] . ( 3 sec) [ -2538.1057] [ 428] [depth= 4] . ( 3 sec) [ -2525.6625] [ 422] [depth= 7] . ( 3 sec) [ -2523.9220] [ 421] [depth= 1] . ( 3 sec) [ -2516.8281] [ 421] [depth= 2] . ( 3 sec) [ -2512.3850] [ 418] [depth= 3] . ( 3 sec) [ -2504.7179] [ 417] [depth= 1] . ( 3 sec) [ -2457.5921] [ 411] [depth= 7] . ( 3 sec) [ -2442.4559] [ 411] [depth= 1] . ( 3 sec) [ -2433.8599] [ 408] [depth= 1] . ( 3 sec) [ -2427.3130] [ 405] [depth= 8] . ( 4 sec) [ -2418.9995] [ 403] [depth= 5] . ( 4 sec) [ -2392.2220] [ 407] [depth= 4] . ( 4 sec) [ -2361.3479] [ 397] [depth= 2] . ( 4 sec) [ -2343.3875] [ 393] [depth= 4] . ( 4 sec) [ -2291.9706] [ 393] [depth= 2] . ( 5 sec) [ -2285.8120] [ 389] [depth= 1] . ( 5 sec) [ -2284.0381] [ 394] [depth= 1] . ( 5 sec) [ -2270.5404] [ 390] [depth= 4] . ( 5 sec) [ -2261.5862] [ 389] [depth= 5] . ( 5 sec) [ -2246.2960] [ 388] [depth= 1] . ( 6 sec) [ -2219.1388] [ 380] [depth= 1] . ( 6 sec) [ -2184.2906] [ 370] [depth= 7] . ( 6 sec) [ -2154.8933] [ 364] [depth= 8] . ( 6 sec) [ -2149.8227] [ 365] [depth= 3] . ( 6 sec) [ -2149.0292] [ 367] [depth= 1] . ( 7 sec) [ -2143.8018] [ 365] [depth= 1] . ( 8 sec) [ -2139.3082] [ 363] [depth= 2] . ( 9 sec) [ -2138.0329] [ 364] [depth= 3] . ( 9 sec) [ -2131.3860] [ 361] [depth= 8] . ( 9 sec) [ -2116.3459] [ 355] [depth= 8] . ( 9 sec) [ -2106.3335] [ 355] [depth= 1] . ( 10 sec) [ -2062.4302] [ 347] [depth= 8] . ( 10 sec) [ -2060.6098] [ 346] [depth= 1] . ( 10 sec) [ -2058.7213] [ 347] [depth= 1] . ( 10 sec) [ -2056.8000] [ 347] [depth= 1] . ( 11 sec) [ -2045.4076] [Branch lengths ] . ( 11 sec) [ -2043.8956] [Alpha ][ 0.657688] . ( 12 sec) [ -2043.1076] [ 347] [depth= 1] . ( 12 sec) [ -2041.0168] [ 346] [depth= 5] . ( 12 sec) [ -2027.7293] [ 342] [depth= 4] . ( 13 sec) [ -2027.3825] [ 343] [depth= 1] . ( 13 sec) [ -2025.5255] [ 342] [depth= 3] . ( 13 sec) [ -2025.4130] [ 340] [depth= 1] . ( 15 sec) [ -2020.7366] [ 339] [depth= 4] . ( 15 sec) [ -2020.4474] [ 339] [depth= 1] . ( 17 sec) [ -2019.9929] [ 339] [depth= 1] . ( 21 sec) [ -2019.9105] [ 340] [depth= 1] . ( 21 sec) [ -2019.3243] [ 340] [depth= 1] . ( 22 sec) [ -2019.0343] [ 340] [depth= 1] . ( 23 sec) [ -2018.9953] [ 340] [depth= 1] . ( 25 sec) [ -2018.5689] [ 342] [depth= 1] . ( 26 sec) [ -2017.4545] [ 342] [depth= 2] . ( 26 sec) [ -2014.8275] [ 341] [depth= 2] . ( 27 sec) [ -2014.6227] [ 341] [depth= 1] . ( 30 sec) [ -2013.6213] [ 341] [depth= 1] . ( 32 sec) [ -2013.0230] [ 342] [depth= 1] . ( 32 sec) [ -2009.5752] [Branch lengths ] . ( 32 sec) [ -2009.5219] [Alpha ][ 0.694667] . ( 41 sec) [ -2008.6083] [ 342] [depth= 5] . ( 43 sec) [ -2008.4423] [ 343] [depth= 1] . ( 55 sec) [ -2008.2123] [ 343] [depth= 1] . ( 60 sec) [ -2007.1655] [ 342] [depth= 1] . ( 60 sec) [ -2006.1747] [Branch lengths ] . ( 60 sec) [ -2006.1417] [Alpha ][ 0.725380] . ( 65 sec) [ -2005.9736] [ 342] [depth= 1] . ( 70 sec) [ -2005.9608] [ 343] [depth= 3] . ( 82 sec) [ -2005.6043] [ 342] [depth= 1] . ( 88 sec) [ -2005.1732] [Branch lengths ] . ( 88 sec) [ -2005.1708] [Alpha ][ 0.734147] . ( 88 sec) [ -2005.1708] [Topology ] . ( 89 sec) [ -2005.1466] [Topology ] . ( 89 sec) [ -2005.1422] [Topology ] . ( 90 sec) [ -2005.1405] [Topology ] . ( 91 sec) [ -2005.1397] [Topology ] . ( 91 sec) [ -2005.1397] [Alpha ][ 0.734147] . ( 91 sec) [ -2005.1397] [Topology ] . ( 91 sec) [ -2005.1393] [Topology ] . ( 92 sec) [ -2005.1393] [Alpha ][ 0.734147] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -2005.0777] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2005.077715. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3263.3627] [Alpha ][ 0.500960] . ( 0 sec) [ -3207.3029] [ 517] [depth= 1] . ( 0 sec) [ -3093.8528] [ 491] [depth= 4] . ( 0 sec) [ -3078.6368] [ 487] [depth= 1] . ( 0 sec) [ -3063.4289] [ 480] [depth= 5] . ( 0 sec) [ -3040.6417] [ 474] [depth= 1] . ( 1 sec) [ -2999.2838] [ 468] [depth= 10] . ( 1 sec) [ -2974.9871] [ 467] [depth= 3] . ( 1 sec) [ -2964.7328] [ 466] [depth= 1] . ( 1 sec) [ -2958.8296] [ 466] [depth= 1] . ( 1 sec) [ -2955.9256] [ 466] [depth= 1] . ( 1 sec) [ -2938.3855] [ 463] [depth= 8] . ( 1 sec) [ -2915.9717] [ 463] [depth= 12] . ( 1 sec) [ -2885.0287] [ 449] [depth= 10] . ( 1 sec) [ -2768.8940] [ 441] [depth= 5] . ( 1 sec) [ -2557.7302] [ 428] [depth= 7] . ( 1 sec) [ -2541.0878] [ 425] [depth= 8] . ( 2 sec) [ -2527.4383] [ 420] [depth= 5] . ( 2 sec) [ -2522.6186] [ 419] [depth= 1] . ( 2 sec) [ -2512.6838] [ 418] [depth= 2] . ( 2 sec) [ -2444.8143] [ 404] [depth= 9] . ( 2 sec) [ -2427.5115] [ 401] [depth= 1] . ( 2 sec) [ -2414.9020] [ 400] [depth= 2] . ( 3 sec) [ -2401.9633] [ 397] [depth= 2] . ( 3 sec) [ -2387.7890] [ 395] [depth= 1] . ( 3 sec) [ -2378.3734] [ 393] [depth= 6] . ( 3 sec) [ -2377.3645] [ 393] [depth= 1] . ( 4 sec) [ -2340.3220] [ 385] [depth= 9] . ( 4 sec) [ -2288.3836] [ 367] [depth= 3] . ( 4 sec) [ -2273.5124] [ 367] [depth= 3] . ( 5 sec) [ -2266.7688] [ 366] [depth= 2] . ( 5 sec) [ -2264.1860] [ 366] [depth= 1] . ( 5 sec) [ -2259.7247] [ 366] [depth= 2] . ( 5 sec) [ -2257.7797] [ 365] [depth= 1] . ( 5 sec) [ -2225.5770] [ 362] [depth= 1] . ( 5 sec) [ -2166.0879] [ 351] [depth= 4] . ( 5 sec) [ -2160.8027] [ 349] [depth= 1] . ( 5 sec) [ -2160.1648] [ 348] [depth= 1] . ( 6 sec) [ -2150.5303] [ 347] [depth= 3] . ( 6 sec) [ -2150.1735] [ 347] [depth= 1] . ( 7 sec) [ -2073.8131] [ 349] [depth= 1] . ( 7 sec) [ -2063.5204] [ 348] [depth= 1] . ( 7 sec) [ -2056.5059] [ 342] [depth= 1] . ( 7 sec) [ -2054.4683] [ 340] [depth= 1] . ( 7 sec) [ -2053.9840] [ 340] [depth= 1] . ( 7 sec) [ -2046.9317] [ 340] [depth= 8] . ( 7 sec) [ -2042.6806] [ 344] [depth= 1] . ( 8 sec) [ -2041.6504] [ 343] [depth= 1] . ( 8 sec) [ -2041.6164] [ 343] [depth= 1] . ( 8 sec) [ -2041.1831] [ 343] [depth= 1] . ( 8 sec) [ -2038.1780] [ 339] [depth= 1] . ( 9 sec) [ -2025.2578] [Branch lengths ] . ( 9 sec) [ -2024.0614] [Alpha ][ 0.644462] . ( 10 sec) [ -2023.0120] [ 340] [depth= 1] . ( 13 sec) [ -2017.9640] [ 339] [depth= 1] . ( 13 sec) [ -2017.4953] [ 339] [depth= 1] . ( 15 sec) [ -2017.4161] [ 339] [depth= 1] . ( 26 sec) [ -2017.4037] [ 339] [depth= 1] . ( 28 sec) [ -2017.2761] [ 340] [depth= 1] . ( 28 sec) [ -2016.9854] [ 341] [depth= 4] . ( 29 sec) [ -2015.2133] [ 341] [depth= 5] . ( 30 sec) [ -2013.6375] [ 341] [depth= 1] . ( 32 sec) [ -2010.9759] [Branch lengths ] . ( 32 sec) [ -2010.8702] [Alpha ][ 0.696169] . ( 33 sec) [ -2010.2775] [ 341] [depth= 1] . ( 36 sec) [ -2009.5500] [ 341] [depth= 1] . ( 37 sec) [ -2009.1171] [ 342] [depth= 1] . ( 41 sec) [ -2008.5605] [ 342] [depth= 1] . ( 43 sec) [ -2008.4398] [ 342] [depth= 1] . ( 44 sec) [ -2008.4237] [ 343] [depth= 1] . ( 44 sec) [ -2008.1149] [ 342] [depth= 1] . ( 56 sec) [ -2006.9925] [ 342] [depth= 2] . ( 60 sec) [ -2005.2942] [Branch lengths ] . ( 61 sec) [ -2005.2521] [Alpha ][ 0.730924] . ( 90 sec) [ -2005.1453] [Branch lengths ] . ( 90 sec) [ -2005.1453] [Topology ] . ( 90 sec) [ -2005.1412] [Topology ] . ( 91 sec) [ -2005.1401] [Topology ] . ( 92 sec) [ -2005.1397] [Topology ] . ( 92 sec) [ -2005.1394] [Alpha ][ 0.733881] . ( 92 sec) [ -2005.1394] [Topology ] . ( 92 sec) [ -2005.1391] [Topology ] . ( 93 sec) [ -2005.1391] [Alpha ][ 0.733881] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -2005.0801] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2005.080118. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3289.0290] [Alpha ][ 0.500960] . ( 1 sec) [ -3227.7785] [ 538] [depth= 11] . ( 1 sec) [ -3073.8376] [ 509] [depth= 4] . ( 1 sec) [ -3039.6979] [ 506] [depth= 1] . ( 1 sec) [ -3011.3866] [ 503] [depth= 8] . ( 1 sec) [ -3010.4391] [ 500] [depth= 1] . ( 1 sec) [ -3005.4849] [ 497] [depth= 2] . ( 1 sec) [ -2958.0511] [ 495] [depth= 7] . ( 1 sec) [ -2875.0405] [ 493] [depth= 3] . ( 1 sec) [ -2850.7024] [ 490] [depth= 10] . ( 2 sec) [ -2823.8305] [ 487] [depth= 1] . ( 2 sec) [ -2789.2348] [ 485] [depth= 3] . ( 2 sec) [ -2779.3014] [ 481] [depth= 1] . ( 2 sec) [ -2744.9481] [ 470] [depth= 10] . ( 2 sec) [ -2739.0648] [ 472] [depth= 11] . ( 2 sec) [ -2725.9019] [ 467] [depth= 3] . ( 2 sec) [ -2695.9623] [ 466] [depth= 10] . ( 2 sec) [ -2688.8937] [ 463] [depth= 1] . ( 2 sec) [ -2663.3685] [ 460] [depth= 2] . ( 2 sec) [ -2610.9778] [ 442] [depth= 6] . ( 2 sec) [ -2592.0264] [ 439] [depth= 4] . ( 3 sec) [ -2591.2230] [ 439] [depth= 1] . ( 3 sec) [ -2580.1218] [ 434] [depth= 2] . ( 3 sec) [ -2536.0744] [ 424] [depth= 7] . ( 3 sec) [ -2532.3487] [ 425] [depth= 1] . ( 3 sec) [ -2511.8360] [ 420] [depth= 1] . ( 3 sec) [ -2468.4328] [ 413] [depth= 2] . ( 3 sec) [ -2421.9205] [ 412] [depth= 4] . ( 3 sec) [ -2415.6244] [ 411] [depth= 1] . ( 4 sec) [ -2388.9800] [ 410] [depth= 2] . ( 4 sec) [ -2356.5307] [ 404] [depth= 7] . ( 4 sec) [ -2340.8089] [ 402] [depth= 1] . ( 5 sec) [ -2307.9268] [ 396] [depth= 9] . ( 6 sec) [ -2294.5184] [ 389] [depth= 1] . ( 6 sec) [ -2293.9331] [ 387] [depth= 2] . ( 6 sec) [ -2272.2958] [ 382] [depth= 2] . ( 6 sec) [ -2259.6361] [ 382] [depth= 1] . ( 6 sec) [ -2226.4076] [ 382] [depth= 2] . ( 6 sec) [ -2218.3629] [ 377] [depth= 1] . ( 6 sec) [ -2201.5381] [ 377] [depth= 2] . ( 6 sec) [ -2171.4055] [ 376] [depth= 1] . ( 6 sec) [ -2138.3485] [ 370] [depth= 2] . ( 6 sec) [ -2128.3638] [ 364] [depth= 3] . ( 6 sec) [ -2123.8194] [ 362] [depth= 1] . ( 7 sec) [ -2114.6547] [ 360] [depth= 2] . ( 7 sec) [ -2111.6263] [ 358] [depth= 1] . ( 7 sec) [ -2105.9050] [ 355] [depth= 2] . ( 7 sec) [ -2103.4104] [ 355] [depth= 1] . ( 8 sec) [ -2096.1811] [ 351] [depth= 2] . ( 8 sec) [ -2094.8761] [ 349] [depth= 2] . ( 8 sec) [ -2094.5584] [ 350] [depth= 1] . ( 8 sec) [ -2089.4899] [ 349] [depth= 1] . ( 8 sec) [ -2086.7834] [ 351] [depth= 3] . ( 9 sec) [ -2086.4902] [ 352] [depth= 1] . ( 9 sec) [ -2073.8004] [ 351] [depth= 4] . ( 9 sec) [ -2071.6089] [ 349] [depth= 1] . ( 10 sec) [ -2071.5126] [ 349] [depth= 1] . ( 10 sec) [ -2053.5024] [Branch lengths ] . ( 10 sec) [ -2051.9278] [Alpha ][ 0.662180] . ( 11 sec) [ -2046.9793] [ 346] [depth= 2] . ( 11 sec) [ -2044.9814] [ 347] [depth= 1] . ( 11 sec) [ -2042.9241] [ 347] [depth= 1] . ( 11 sec) [ -2041.5835] [ 346] [depth= 1] . ( 11 sec) [ -2038.9203] [ 345] [depth= 3] . ( 12 sec) [ -2038.7643] [ 344] [depth= 1] . ( 12 sec) [ -2029.6379] [ 341] [depth= 2] . ( 13 sec) [ -2022.8527] [ 342] [depth= 3] . ( 14 sec) [ -2017.9981] [ 339] [depth= 2] . ( 15 sec) [ -2017.6815] [ 341] [depth= 1] . ( 18 sec) [ -2013.7442] [ 340] [depth= 3] . ( 18 sec) [ -2013.7229] [ 340] [depth= 1] . ( 21 sec) [ -2013.1028] [ 340] [depth= 1] . ( 29 sec) [ -2013.0532] [ 340] [depth= 1] . ( 31 sec) [ -2012.2431] [ 342] [depth= 1] . ( 34 sec) [ -2009.5915] [Branch lengths ] . ( 34 sec) [ -2009.5524] [Alpha ][ 0.693698] . ( 40 sec) [ -2008.6131] [ 343] [depth= 6] . ( 45 sec) [ -2008.0676] [ 342] [depth= 1] . ( 56 sec) [ -2006.9291] [ 341] [depth= 1] . ( 57 sec) [ -2006.7193] [ 342] [depth= 1] . ( 63 sec) [ -2005.7203] [Branch lengths ] . ( 63 sec) [ -2005.6775] [Alpha ][ 0.728651] . ( 68 sec) [ -2005.6268] [ 342] [depth= 1] . ( 92 sec) [ -2005.5937] [Branch lengths ] . ( 92 sec) [ -2005.5935] [Alpha ][ 0.731144] . ( 92 sec) [ -2005.5935] [Topology ] . ( 93 sec) [ -2005.5919] [Topology ] . ( 93 sec) [ -2005.5914] [Topology ] . ( 93 sec) [ -2005.5914] [Alpha ][ 0.731144] . ( 93 sec) [ -2005.5914] [Topology ] . ( 94 sec) [ -2005.5912] [Topology ] . ( 94 sec) [ -2005.5912] [Alpha ][ 0.731875] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -2005.5247] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2005.524733. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3492.5729] [Alpha ][ 0.500960] . ( 0 sec) [ -3438.4239] [ 516] [depth= 4] . ( 0 sec) [ -3246.8100] [ 488] [depth= 2] . ( 0 sec) [ -3151.8045] [ 487] [depth= 2] . ( 0 sec) [ -3099.3709] [ 484] [depth= 3] . ( 0 sec) [ -3076.5321] [ 481] [depth= 2] . ( 1 sec) [ -3044.1526] [ 478] [depth= 5] . ( 1 sec) [ -2991.8017] [ 476] [depth= 1] . ( 1 sec) [ -2940.1795] [ 481] [depth= 1] . ( 1 sec) [ -2939.7828] [ 481] [depth= 1] . ( 1 sec) [ -2831.6368] [ 475] [depth= 2] . ( 1 sec) [ -2801.8816] [ 480] [depth= 7] . ( 1 sec) [ -2790.8904] [ 475] [depth= 1] . ( 1 sec) [ -2785.9376] [ 477] [depth= 3] . ( 1 sec) [ -2772.0366] [ 475] [depth= 3] . ( 1 sec) [ -2754.7166] [ 472] [depth= 3] . ( 2 sec) [ -2726.0869] [ 466] [depth= 8] . ( 2 sec) [ -2708.8268] [ 459] [depth= 2] . ( 2 sec) [ -2702.1502] [ 457] [depth= 1] . ( 2 sec) [ -2699.2049] [ 456] [depth= 2] . ( 2 sec) [ -2646.8242] [ 448] [depth= 3] . ( 2 sec) [ -2615.6049] [ 442] [depth= 1] . ( 2 sec) [ -2592.1191] [ 439] [depth= 4] . ( 2 sec) [ -2575.3896] [ 434] [depth= 5] . ( 3 sec) [ -2573.1000] [ 439] [depth= 1] . ( 3 sec) [ -2480.7202] [ 417] [depth= 4] . ( 3 sec) [ -2475.5307] [ 411] [depth= 3] . ( 3 sec) [ -2457.7176] [ 410] [depth= 3] . ( 3 sec) [ -2423.7888] [ 403] [depth= 2] . ( 4 sec) [ -2412.7281] [ 404] [depth= 2] . ( 4 sec) [ -2368.5576] [ 394] [depth= 4] . ( 4 sec) [ -2347.9645] [ 394] [depth= 2] . ( 4 sec) [ -2342.7026] [ 393] [depth= 3] . ( 4 sec) [ -2341.2582] [ 392] [depth= 5] . ( 4 sec) [ -2323.9317] [ 387] [depth= 1] . ( 4 sec) [ -2304.2345] [ 382] [depth= 9] . ( 4 sec) [ -2202.2387] [ 379] [depth= 3] . ( 4 sec) [ -2196.6796] [ 379] [depth= 2] . ( 4 sec) [ -2176.8901] [ 373] [depth= 2] . ( 5 sec) [ -2175.1815] [ 373] [depth= 1] . ( 5 sec) [ -2155.3830] [ 369] [depth= 2] . ( 5 sec) [ -2151.3232] [ 373] [depth= 1] . ( 7 sec) [ -2148.9531] [ 373] [depth= 1] . ( 7 sec) [ -2145.8060] [ 371] [depth= 1] . ( 9 sec) [ -2131.3710] [ 367] [depth= 4] . ( 10 sec) [ -2121.5869] [ 366] [depth= 2] . ( 10 sec) [ -2106.0327] [ 363] [depth= 1] . ( 10 sec) [ -2090.2880] [ 359] [depth= 1] . ( 11 sec) [ -2080.6713] [ 355] [depth= 1] . ( 11 sec) [ -2076.2378] [ 355] [depth= 2] . ( 11 sec) [ -2075.9213] [ 355] [depth= 1] . ( 16 sec) [ -2060.2403] [Branch lengths ] . ( 16 sec) [ -2058.8237] [Alpha ][ 0.653459] . ( 17 sec) [ -2055.3984] [ 353] [depth= 1] . ( 17 sec) [ -2051.1524] [ 353] [depth= 2] . ( 17 sec) [ -2038.4200] [ 350] [depth= 1] . ( 18 sec) [ -2032.1590] [ 348] [depth= 2] . ( 18 sec) [ -2029.6975] [ 347] [depth= 1] . ( 19 sec) [ -2019.0848] [ 345] [depth= 2] . ( 19 sec) [ -2018.2830] [ 345] [depth= 1] . ( 20 sec) [ -2017.9377] [ 343] [depth= 1] . ( 20 sec) [ -2016.1957] [ 340] [depth= 2] . ( 23 sec) [ -2015.9387] [ 340] [depth= 1] . ( 23 sec) [ -2013.9542] [ 341] [depth= 1] . ( 26 sec) [ -2013.5306] [ 341] [depth= 1] . ( 29 sec) [ -2012.7580] [ 341] [depth= 1] . ( 30 sec) [ -2012.7444] [ 341] [depth= 1] . ( 30 sec) [ -2011.7872] [ 339] [depth= 1] . ( 36 sec) [ -2008.6379] [Branch lengths ] . ( 36 sec) [ -2008.5698] [Alpha ][ 0.694598] . ( 37 sec) [ -2008.2947] [ 342] [depth= 1] . ( 45 sec) [ -2006.6742] [ 342] [depth= 3] . ( 63 sec) [ -2005.3298] [Branch lengths ] . ( 63 sec) [ -2005.2942] [Alpha ][ 0.726477] . ( 92 sec) [ -2005.1559] [Branch lengths ] . ( 92 sec) [ -2005.1559] [Topology ] . ( 93 sec) [ -2005.1481] [Topology ] . ( 93 sec) [ -2005.1451] [Topology ] . ( 94 sec) [ -2005.1435] [Topology ] . ( 95 sec) [ -2005.1425] [Topology ] . ( 95 sec) [ -2005.1410] [Alpha ][ 0.733452] . ( 95 sec) [ -2005.1410] [Topology ] . ( 95 sec) [ -2005.1402] [Topology ] . ( 96 sec) [ -2005.1402] [Alpha ][ 0.733452] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -2005.0837] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2005.083740. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3162.5863] [Alpha ][ 0.500960] . ( 0 sec) [ -3069.0928] [ 509] [depth= 7] . ( 0 sec) [ -2898.9404] [ 482] [depth= 11] . ( 0 sec) [ -2875.0858] [ 480] [depth= 3] . ( 0 sec) [ -2852.0117] [ 479] [depth= 1] . ( 1 sec) [ -2835.3645] [ 477] [depth= 1] . ( 1 sec) [ -2820.6088] [ 477] [depth= 4] . ( 1 sec) [ -2773.7979] [ 465] [depth= 3] . ( 1 sec) [ -2746.2192] [ 457] [depth= 8] . ( 1 sec) [ -2694.1005] [ 449] [depth= 7] . ( 1 sec) [ -2672.2765] [ 445] [depth= 1] . ( 1 sec) [ -2653.3088] [ 444] [depth= 1] . ( 1 sec) [ -2624.2883] [ 441] [depth= 3] . ( 1 sec) [ -2533.4662] [ 424] [depth= 2] . ( 1 sec) [ -2519.8447] [ 420] [depth= 1] . ( 1 sec) [ -2467.8706] [ 418] [depth= 3] . ( 1 sec) [ -2398.0812] [ 404] [depth= 2] . ( 2 sec) [ -2396.9172] [ 405] [depth= 1] . ( 2 sec) [ -2396.8736] [ 404] [depth= 1] . ( 2 sec) [ -2361.8305] [ 397] [depth= 10] . ( 2 sec) [ -2357.6584] [ 396] [depth= 1] . ( 2 sec) [ -2344.1736] [ 390] [depth= 7] . ( 2 sec) [ -2305.9891] [ 383] [depth= 2] . ( 3 sec) [ -2304.6645] [ 385] [depth= 1] . ( 3 sec) [ -2303.7731] [ 383] [depth= 1] . ( 3 sec) [ -2303.6837] [ 385] [depth= 1] . ( 4 sec) [ -2254.1348] [ 374] [depth= 3] . ( 4 sec) [ -2234.5700] [ 373] [depth= 2] . ( 4 sec) [ -2177.0251] [ 372] [depth= 2] . ( 4 sec) [ -2174.7674] [ 371] [depth= 1] . ( 4 sec) [ -2159.1840] [ 370] [depth= 1] . ( 4 sec) [ -2158.7226] [ 371] [depth= 3] . ( 4 sec) [ -2150.8203] [ 369] [depth= 1] . ( 4 sec) [ -2144.8181] [ 367] [depth= 2] . ( 4 sec) [ -2143.8406] [ 370] [depth= 2] . ( 5 sec) [ -2110.6265] [ 357] [depth= 5] . ( 6 sec) [ -2102.6082] [ 355] [depth= 1] . ( 6 sec) [ -2096.6257] [ 350] [depth= 1] . ( 6 sec) [ -2096.2160] [ 353] [depth= 1] . ( 7 sec) [ -2095.9336] [ 354] [depth= 1] . ( 7 sec) [ -2095.5482] [ 356] [depth= 1] . ( 8 sec) [ -2094.2474] [ 356] [depth= 1] . ( 9 sec) [ -2072.1767] [ 354] [depth= 1] . ( 9 sec) [ -2060.6857] [ 351] [depth= 1] . ( 9 sec) [ -2060.5141] [ 351] [depth= 1] . ( 9 sec) [ -2057.8599] [ 348] [depth= 5] . ( 9 sec) [ -2056.8497] [ 346] [depth= 3] . ( 10 sec) [ -2027.5372] [ 338] [depth= 2] . ( 10 sec) [ -2027.3363] [ 339] [depth= 1] . ( 12 sec) [ -2012.1960] [Branch lengths ] . ( 12 sec) [ -2010.2700] [Alpha ][ 0.688158] . ( 15 sec) [ -2010.2460] [ 338] [depth= 1] . ( 22 sec) [ -2010.2052] [ 337] [depth= 1] . ( 29 sec) [ -2009.5601] [ 338] [depth= 1] . ( 32 sec) [ -2009.3219] [ 338] [depth= 6] . ( 35 sec) [ -2007.4699] [Branch lengths ] . ( 36 sec) [ -2007.4535] [Alpha ][ 0.709388] . ( 43 sec) [ -2007.4311] [ 338] [depth= 1] . ( 47 sec) [ -2007.3150] [ 339] [depth= 1] . ( 57 sec) [ -2006.1216] [ 339] [depth= 7] . ( 59 sec) [ -2005.5195] [Branch lengths ] . ( 60 sec) [ -2005.5039] [Alpha ][ 0.730760] . ( 81 sec) [ -2005.4792] [ 341] [depth= 3] . ( 84 sec) [ -2005.3872] [Branch lengths ] . ( 84 sec) [ -2005.3869] [Alpha ][ 0.733770] . ( 84 sec) [ -2005.3869] [Topology ] . ( 85 sec) [ -2005.1350] [Topology ] . ( 85 sec) [ -2005.0760] [Topology ] . ( 86 sec) [ -2005.0581] [Topology ] . ( 87 sec) [ -2005.0494] [Topology ] . ( 87 sec) [ -2005.0451] [Topology ] . ( 88 sec) [ -2005.0429] [Topology ] . ( 89 sec) [ -2005.0418] [Topology ] . ( 89 sec) [ -2005.0417] [Alpha ][ 0.735030] . ( 89 sec) [ -2005.0417] [Topology ] . ( 89 sec) [ -2005.0411] [Topology ] . ( 90 sec) [ -2005.0411] [Alpha ][ 0.735030] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2005.041137. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2041.7950] [Alpha ][ 0.666358] . ( 0 sec) [ -2041.7950] [Topology ] . ( 1 sec) [ -2022.2350] [Topology ] . ( 2 sec) [ -2012.7530] [Topology ] . ( 2 sec) [ -2010.0591] [Topology ] . ( 3 sec) [ -2007.6082] [Topology ] . ( 4 sec) [ -2006.9674] [Topology ] . ( 4 sec) [ -2006.8253] [Topology ] . ( 5 sec) [ -2006.7537] [Topology ] . ( 6 sec) [ -2006.7081] [Topology ] . ( 6 sec) [ -2006.6785] [Topology ] . Checking for NNIs, optimizing five branches... . ( 11 sec) [ -2005.6454] [Topology ] . ( 11 sec) [ -2005.5012] [Alpha ][ 0.729106] . ( 12 sec) [ -2005.5012] [Topology ] . ( 12 sec) [ -2005.4906] [Topology ] . ( 13 sec) [ -2005.4891] [Topology ] . ( 13 sec) [ -2005.4884] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -2005.4882] [Alpha ][ 0.731508] . ( 18 sec) [ -2005.4882] [Topology ] . ( 19 sec) [ -2005.4878] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 27 sec) [ -2041.7950] [Alpha ][ 0.666358] . ( 28 sec) [ -2040.6879] [ 341] [depth= 1] . ( 28 sec) [ -2038.7596] [ 342] [depth= 1] . ( 31 sec) [ -2038.5780] [ 341] [depth= 1] . ( 31 sec) [ -2038.5557] [ 341] [depth= 1] . ( 32 sec) [ -2038.1903] [ 342] [depth= 1] . ( 32 sec) [ -2037.8703] [ 342] [depth= 1] . ( 32 sec) [ -2030.3424] [ 340] [depth= 3] . ( 32 sec) [ -2026.9676] [ 340] [depth= 3] . ( 32 sec) [ -2026.2127] [ 340] [depth= 1] . ( 32 sec) [ -2024.4980] [ 341] [depth= 1] . ( 33 sec) [ -2024.1418] [ 340] [depth= 1] . ( 34 sec) [ -2023.8722] [ 341] [depth= 1] . ( 37 sec) [ -2023.6288] [ 342] [depth= 1] . ( 37 sec) [ -2022.5545] [ 342] [depth= 1] . ( 39 sec) [ -2021.9073] [ 343] [depth= 3] . ( 39 sec) [ -2021.0324] [ 342] [depth= 1] . ( 46 sec) [ -2018.7943] [ 343] [depth= 1] . ( 46 sec) [ -2014.7372] [ 343] [depth= 2] . ( 46 sec) [ -2013.5744] [ 343] [depth= 1] . ( 46 sec) [ -2013.5637] [ 343] [depth= 1] . ( 46 sec) [ -2013.5271] [ 343] [depth= 1] . ( 49 sec) [ -2008.6305] [Branch lengths ] . ( 49 sec) [ -2008.5365] [Alpha ][ 0.716368] . ( 54 sec) [ -2008.5249] [ 344] [depth= 1] . ( 55 sec) [ -2008.4460] [ 344] [depth= 1] . ( 65 sec) [ -2007.7061] [ 343] [depth= 1] . ( 75 sec) [ -2006.9724] [ 342] [depth= 1] . ( 79 sec) [ -2005.6557] [Branch lengths ] . ( 80 sec) [ -2005.6504] [Alpha ][ 0.729164] . ( 95 sec) [ -2005.6342] [ 343] [depth= 2] . ( 97 sec) [ -2005.5462] [ 342] [depth= 1] . ( 107 sec) [ -2005.1672] [Branch lengths ] . ( 107 sec) [ -2005.1667] [Alpha ][ 0.733039] . ( 107 sec) [ -2005.1667] [Topology ] . ( 108 sec) [ -2005.1496] [Topology ] . ( 109 sec) [ -2005.1443] [Topology ] . ( 109 sec) [ -2005.1417] [Topology ] . ( 110 sec) [ -2005.1404] [Topology ] . ( 110 sec) [ -2005.1397] [Topology ] . ( 111 sec) [ -2005.1396] [Alpha ][ 0.733952] . ( 111 sec) [ -2005.1396] [Topology ] . ( 111 sec) [ -2005.1393] [Topology ] . ( 111 sec) [ -2005.1393] [Alpha ][ 0.733952] . Checking for NNIs, optimizing five branches... . ( 116 sec) [ -2005.0786] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2005.487783 . Log likelihood obtained after SPR moves : -2005.078648 . Log likelihood of the current tree: -2005.078648. . Printing the most likely tree in file 'proteic_M1993_28x93_2004.phy_phyml_tree.txt'... . Best log likelihood : -2005.041137 . Time used 0h2m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 613.54user 0.00system 10:22.00elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps