.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data92.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 393 patterns found. (out of a total of 500 sites) . 101 sites without polymorphism (20.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17000.8684] [GTR parameters ] . ( 1 sec) [ -16695.4007] [Alpha ][ 0.500960] . ( 1 sec) [ -16428.7670] [ 3380] [depth= 4] . ( 1 sec) [ -15523.8073] [ 3277] [depth= 6] . ( 1 sec) [ -15397.5837] [ 3275] [depth= 4] . ( 1 sec) [ -15252.0973] [ 3267] [depth= 5] . ( 1 sec) [ -15135.4160] [ 3238] [depth= 1] . ( 1 sec) [ -15024.6773] [ 3230] [depth= 7] . ( 1 sec) [ -14892.0204] [ 3217] [depth= 1] . ( 1 sec) [ -14830.9207] [ 3195] [depth= 12] . ( 1 sec) [ -14461.2145] [ 3101] [depth= 16] . ( 1 sec) [ -14317.4012] [ 3072] [depth= 14] . ( 1 sec) [ -14274.5834] [ 3061] [depth= 2] . ( 1 sec) [ -14227.7434] [ 3058] [depth= 1] . ( 1 sec) [ -14088.6675] [ 3009] [depth= 3] . ( 1 sec) [ -13822.7310] [ 3004] [depth= 3] . ( 1 sec) [ -13622.3107] [ 2976] [depth= 3] . ( 1 sec) [ -13610.5236] [ 2980] [depth= 1] . ( 1 sec) [ -13384.6845] [ 2919] [depth= 2] . ( 1 sec) [ -13255.3476] [ 2876] [depth= 12] . ( 1 sec) [ -13092.8096] [ 2817] [depth= 7] . ( 1 sec) [ -13086.1220] [ 2819] [depth= 4] . ( 2 sec) [ -12822.0259] [ 2756] [depth= 10] . ( 2 sec) [ -12749.2253] [ 2755] [depth= 1] . ( 2 sec) [ -12612.8414] [ 2709] [depth= 2] . ( 2 sec) [ -12468.0589] [ 2678] [depth= 3] . ( 2 sec) [ -12399.1660] [ 2637] [depth= 1] . ( 2 sec) [ -12325.0977] [ 2604] [depth= 10] . ( 2 sec) [ -12120.2741] [ 2548] [depth= 4] . ( 2 sec) [ -11899.3925] [ 2520] [depth= 20] . ( 2 sec) [ -11693.8404] [ 2468] [depth= 17] . ( 2 sec) [ -11630.8088] [ 2419] [depth= 1] . ( 2 sec) [ -11430.0011] [ 2370] [depth= 3] . ( 2 sec) [ -10512.4246] [ 2305] [depth= 1] . ( 2 sec) [ -10314.4286] [ 2250] [depth= 16] . ( 2 sec) [ -10148.2122] [ 2205] [depth= 2] . ( 2 sec) [ -10017.7379] [ 2174] [depth= 7] . ( 2 sec) [ -9657.0495] [ 2054] [depth= 14] . ( 2 sec) [ -9598.5045] [ 2031] [depth= 5] . ( 2 sec) [ -9589.0557] [ 2036] [depth= 1] . ( 2 sec) [ -9555.6037] [ 2036] [depth= 1] . ( 2 sec) [ -9530.5402] [ 2031] [depth= 1] . ( 2 sec) [ -9340.0371] [ 1980] [depth= 2] . ( 2 sec) [ -9321.8269] [ 1986] [depth= 1] . ( 3 sec) [ -9317.8712] [ 1995] [depth= 1] . ( 3 sec) [ -9081.0453] [ 1948] [depth= 3] . ( 3 sec) [ -9058.9111] [ 1945] [depth= 2] . ( 3 sec) [ -9042.9111] [ 1939] [depth= 1] . ( 3 sec) [ -9013.0680] [ 1915] [depth= 13] . ( 3 sec) [ -8906.5459] [ 1869] [depth= 12] . ( 3 sec) [ -8895.1419] [ 1864] [depth= 1] . ( 3 sec) [ -8893.7131] [ 1873] [depth= 1] . ( 3 sec) [ -8840.6520] [ 1862] [depth= 1] . ( 3 sec) [ -8804.4022] [ 1861] [depth= 1] . ( 3 sec) [ -8803.3041] [ 1862] [depth= 2] . ( 3 sec) [ -8802.7424] [ 1876] [depth= 1] . ( 3 sec) [ -8771.6219] [ 1859] [depth= 2] . ( 3 sec) [ -8723.0092] [ 1848] [depth= 9] . ( 3 sec) [ -8707.6693] [ 1836] [depth= 1] . ( 3 sec) [ -8691.7704] [ 1806] [depth= 1] . ( 3 sec) [ -8560.4806] [ 1777] [depth= 1] . ( 3 sec) [ -8550.0107] [ 1773] [depth= 1] . ( 3 sec) [ -8468.7290] [ 1726] [depth= 3] . ( 3 sec) [ -8453.4231] [ 1716] [depth= 2] . ( 3 sec) [ -8450.1263] [ 1715] [depth= 1] . ( 4 sec) [ -8440.5679] [ 1713] [depth= 1] . ( 4 sec) [ -8385.9186] [ 1690] [depth= 3] . ( 4 sec) [ -8360.4044] [ 1690] [depth= 3] . ( 4 sec) [ -8342.2501] [ 1678] [depth= 1] . ( 4 sec) [ -8323.3164] [ 1675] [depth= 1] . ( 4 sec) [ -8293.5586] [ 1660] [depth= 5] . ( 4 sec) [ -8266.2140] [ 1645] [depth= 1] . ( 4 sec) [ -8127.7603] [Branch lengths ] . ( 5 sec) [ -8123.8387] [GTR parameters ] . ( 5 sec) [ -8093.2856] [Alpha ][ 0.918608] . ( 5 sec) [ -8081.6372] [ 1630] [depth= 1] . ( 5 sec) [ -8080.9884] [ 1615] [depth= 2] . ( 5 sec) [ -8077.3329] [ 1612] [depth= 2] . ( 5 sec) [ -7998.6843] [ 1593] [depth= 2] . ( 5 sec) [ -7995.7923] [ 1592] [depth= 1] . ( 5 sec) [ -7993.8855] [ 1592] [depth= 1] . ( 5 sec) [ -7986.1831] [ 1581] [depth= 1] . ( 6 sec) [ -7963.3294] [ 1568] [depth= 1] . ( 6 sec) [ -7959.2177] [ 1568] [depth= 1] . ( 6 sec) [ -7945.7438] [ 1554] [depth= 1] . ( 6 sec) [ -7945.6832] [ 1555] [depth= 1] . ( 6 sec) [ -7945.2939] [ 1554] [depth= 1] . ( 6 sec) [ -7943.8512] [ 1555] [depth= 1] . ( 7 sec) [ -7943.6971] [ 1557] [depth= 1] . ( 7 sec) [ -7931.6736] [Branch lengths ] . ( 8 sec) [ -7931.4794] [GTR parameters ] . ( 8 sec) [ -7930.9190] [Alpha ][ 1.002868] . ( 10 sec) [ -7930.6383] [Branch lengths ] . ( 29 sec) [ -7930.6330] [Branch lengths ] . ( 29 sec) [ -7930.6330] [Topology ] . ( 30 sec) [ -7930.6328] [Topology ] . ( 30 sec) [ -7930.6277] [GTR parameters ] . ( 30 sec) [ -7930.6277] [Alpha ][ 1.001865] . ( 30 sec) [ -7930.6277] [Topology ] . ( 31 sec) [ -7930.6275] [Topology ] . ( 31 sec) [ -7930.6275] [GTR parameters ] . ( 31 sec) [ -7930.6275] [Alpha ][ 1.001865] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7930.627496. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19480.5024] [GTR parameters ] . ( 1 sec) [ -19176.1262] [Alpha ][ 0.500960] . ( 1 sec) [ -18931.4294] [ 3433] [depth= 3] . ( 1 sec) [ -18456.2692] [ 3351] [depth= 3] . ( 1 sec) [ -18294.5827] [ 3318] [depth= 3] . ( 1 sec) [ -18198.9340] [ 3312] [depth= 3] . ( 2 sec) [ -18052.7893] [ 3292] [depth= 2] . ( 2 sec) [ -17900.1800] [ 3280] [depth= 4] . ( 2 sec) [ -17881.7935] [ 3276] [depth= 3] . ( 2 sec) [ -17833.4852] [ 3258] [depth= 1] . ( 2 sec) [ -17732.7364] [ 3252] [depth= 3] . ( 2 sec) [ -17567.8782] [ 3187] [depth= 3] . ( 2 sec) [ -17509.2190] [ 3178] [depth= 1] . ( 2 sec) [ -17235.0850] [ 3118] [depth= 8] . ( 2 sec) [ -17191.1979] [ 3114] [depth= 3] . ( 2 sec) [ -17068.9752] [ 3065] [depth= 2] . ( 2 sec) [ -16960.8772] [ 3059] [depth= 19] . ( 2 sec) [ -16856.8898] [ 3023] [depth= 5] . ( 2 sec) [ -16606.1175] [ 3014] [depth= 2] . ( 2 sec) [ -16504.4495] [ 3002] [depth= 1] . ( 2 sec) [ -16380.0447] [ 3005] [depth= 1] . ( 2 sec) [ -16360.6062] [ 2980] [depth= 1] . ( 2 sec) [ -16258.9508] [ 2950] [depth= 6] . ( 2 sec) [ -13164.0243] [ 2860] [depth= 9] . ( 2 sec) [ -13141.6391] [ 2879] [depth= 4] . ( 2 sec) [ -12765.1036] [ 2814] [depth= 7] . ( 2 sec) [ -12731.3873] [ 2808] [depth= 1] . ( 2 sec) [ -12614.2046] [ 2745] [depth= 7] . ( 2 sec) [ -12597.2353] [ 2731] [depth= 10] . ( 2 sec) [ -12553.2465] [ 2731] [depth= 2] . ( 2 sec) [ -12373.2228] [ 2619] [depth= 7] . ( 3 sec) [ -12314.4371] [ 2613] [depth= 6] . ( 3 sec) [ -12169.6958] [ 2606] [depth= 10] . ( 3 sec) [ -12146.2693] [ 2552] [depth= 15] . ( 3 sec) [ -11113.2596] [ 2529] [depth= 15] . ( 3 sec) [ -11015.9161] [ 2492] [depth= 1] . ( 3 sec) [ -10810.1912] [ 2406] [depth= 10] . ( 3 sec) [ -10780.4240] [ 2406] [depth= 1] . ( 3 sec) [ -10757.5738] [ 2403] [depth= 4] . ( 3 sec) [ -10685.2150] [ 2374] [depth= 6] . ( 3 sec) [ -10660.5192] [ 2372] [depth= 1] . ( 3 sec) [ -10537.9420] [ 2323] [depth= 1] . ( 3 sec) [ -10517.1643] [ 2317] [depth= 1] . ( 3 sec) [ -10248.3454] [ 2223] [depth= 8] . ( 3 sec) [ -10220.2831] [ 2226] [depth= 1] . ( 3 sec) [ -10209.3228] [ 2230] [depth= 1] . ( 3 sec) [ -10157.4446] [ 2228] [depth= 2] . ( 3 sec) [ -10070.4693] [ 2222] [depth= 1] . ( 3 sec) [ -10006.1627] [ 2200] [depth= 1] . ( 3 sec) [ -9995.3927] [ 2194] [depth= 1] . ( 3 sec) [ -9992.3003] [ 2190] [depth= 1] . ( 3 sec) [ -9920.9203] [ 2173] [depth= 4] . ( 3 sec) [ -9905.0624] [ 2167] [depth= 1] . ( 4 sec) [ -9904.8710] [ 2164] [depth= 2] . ( 4 sec) [ -9900.6087] [ 2152] [depth= 2] . ( 4 sec) [ -9846.5382] [ 2133] [depth= 1] . ( 4 sec) [ -9822.7044] [ 2123] [depth= 7] . ( 4 sec) [ -9664.9413] [ 2080] [depth= 1] . ( 4 sec) [ -9500.5749] [ 2025] [depth= 1] . ( 4 sec) [ -9431.8167] [ 1993] [depth= 4] . ( 4 sec) [ -9378.6863] [ 1986] [depth= 3] . ( 4 sec) [ -9328.2356] [ 1988] [depth= 2] . ( 4 sec) [ -9286.6824] [ 1961] [depth= 1] . ( 4 sec) [ -9235.8187] [ 1962] [depth= 1] . ( 4 sec) [ -9054.7583] [ 1902] [depth= 9] . ( 4 sec) [ -9035.8222] [ 1888] [depth= 1] . ( 4 sec) [ -9020.9025] [ 1894] [depth= 1] . ( 4 sec) [ -9013.3514] [ 1895] [depth= 1] . ( 4 sec) [ -8848.8363] [ 1854] [depth= 1] . ( 4 sec) [ -8842.7937] [ 1843] [depth= 1] . ( 4 sec) [ -8772.1911] [ 1840] [depth= 1] . ( 5 sec) [ -8764.0002] [ 1837] [depth= 1] . ( 5 sec) [ -8732.0123] [ 1824] [depth= 1] . ( 5 sec) [ -8717.8522] [ 1810] [depth= 1] . ( 5 sec) [ -8692.3335] [ 1792] [depth= 2] . ( 5 sec) [ -8671.4731] [ 1783] [depth= 3] . ( 5 sec) [ -8422.3723] [ 1690] [depth= 3] . ( 5 sec) [ -8374.8238] [ 1676] [depth= 1] . ( 5 sec) [ -8352.5761] [ 1684] [depth= 1] . ( 5 sec) [ -8350.4999] [ 1685] [depth= 1] . ( 5 sec) [ -8263.6069] [Branch lengths ] . ( 6 sec) [ -8259.0671] [GTR parameters ] . ( 6 sec) [ -8234.7685] [Alpha ][ 0.858665] . ( 6 sec) [ -8234.6316] [ 1687] [depth= 1] . ( 6 sec) [ -8228.6579] [ 1675] [depth= 1] . ( 6 sec) [ -8225.3813] [ 1674] [depth= 2] . ( 6 sec) [ -8203.6378] [ 1658] [depth= 1] . ( 6 sec) [ -8123.8554] [ 1627] [depth= 1] . ( 6 sec) [ -8123.7313] [ 1625] [depth= 1] . ( 6 sec) [ -8079.0722] [ 1602] [depth= 1] . ( 7 sec) [ -8063.5727] [ 1600] [depth= 1] . ( 7 sec) [ -8060.5995] [ 1601] [depth= 1] . ( 7 sec) [ -8057.4287] [ 1603] [depth= 1] . ( 7 sec) [ -8028.0975] [ 1587] [depth= 1] . ( 7 sec) [ -8014.9375] [ 1575] [depth= 1] . ( 7 sec) [ -7995.7883] [ 1569] [depth= 1] . ( 7 sec) [ -7985.9415] [ 1557] [depth= 1] . ( 8 sec) [ -7978.3281] [ 1563] [depth= 1] . ( 8 sec) [ -7976.1040] [ 1565] [depth= 1] . ( 8 sec) [ -7958.4347] [ 1559] [depth= 1] . ( 8 sec) [ -7958.4132] [ 1557] [depth= 1] . ( 9 sec) [ -7935.8305] [Branch lengths ] . ( 9 sec) [ -7935.3978] [GTR parameters ] . ( 9 sec) [ -7934.0975] [Alpha ][ 0.982382] . ( 9 sec) [ -7934.0075] [ 1556] [depth= 1] . ( 9 sec) [ -7933.9961] [ 1557] [depth= 1] . ( 9 sec) [ -7933.0532] [ 1556] [depth= 1] . ( 10 sec) [ -7932.9964] [ 1557] [depth= 1] . ( 12 sec) [ -7930.8219] [Branch lengths ] . ( 12 sec) [ -7930.8115] [GTR parameters ] . ( 12 sec) [ -7930.7962] [Alpha ][ 0.997307] . ( 14 sec) [ -7930.6464] [Branch lengths ] . ( 33 sec) [ -7930.6312] [Branch lengths ] . ( 33 sec) [ -7930.6312] [Topology ] . ( 34 sec) [ -7930.6299] [Topology ] . ( 34 sec) [ -7930.6295] [Topology ] . ( 35 sec) [ -7930.6293] [GTR parameters ] . ( 35 sec) [ -7930.6281] [Alpha ][ 1.001521] . ( 35 sec) [ -7930.6281] [Topology ] . ( 35 sec) [ -7930.6278] [Topology ] . ( 36 sec) [ -7930.6278] [GTR parameters ] . ( 36 sec) [ -7930.6278] [Alpha ][ 1.001521] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -7930.6276] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7930.627602. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19315.3216] [GTR parameters ] . ( 1 sec) [ -18983.9198] [Alpha ][ 0.500960] . ( 1 sec) [ -18589.0744] [ 3551] [depth= 8] . ( 1 sec) [ -18018.6899] [ 3468] [depth= 8] . ( 1 sec) [ -18014.9763] [ 3464] [depth= 2] . ( 1 sec) [ -17870.7606] [ 3456] [depth= 6] . ( 1 sec) [ -17697.8627] [ 3418] [depth= 7] . ( 1 sec) [ -17644.7966] [ 3409] [depth= 1] . ( 1 sec) [ -16845.4850] [ 3287] [depth= 17] . ( 1 sec) [ -15032.1148] [ 3264] [depth= 16] . ( 1 sec) [ -14677.2431] [ 3153] [depth= 18] . ( 1 sec) [ -14551.3564] [ 3193] [depth= 1] . ( 1 sec) [ -13556.8133] [ 3114] [depth= 8] . ( 1 sec) [ -13339.8282] [ 3124] [depth= 6] . ( 1 sec) [ -13221.7134] [ 3096] [depth= 1] . ( 1 sec) [ -13081.1756] [ 3094] [depth= 1] . ( 1 sec) [ -12908.0807] [ 3032] [depth= 1] . ( 1 sec) [ -12907.9374] [ 3030] [depth= 8] . ( 2 sec) [ -12738.2608] [ 2967] [depth= 11] . ( 2 sec) [ -12704.9736] [ 2944] [depth= 1] . ( 2 sec) [ -12502.8074] [ 2875] [depth= 6] . ( 2 sec) [ -12335.5073] [ 2837] [depth= 10] . ( 2 sec) [ -11868.9680] [ 2746] [depth= 4] . ( 2 sec) [ -11737.7459] [ 2686] [depth= 10] . ( 2 sec) [ -11597.8712] [ 2647] [depth= 7] . ( 2 sec) [ -11526.9930] [ 2618] [depth= 8] . ( 2 sec) [ -11353.5453] [ 2523] [depth= 7] . ( 2 sec) [ -11313.7280] [ 2514] [depth= 1] . ( 2 sec) [ -11211.6764] [ 2512] [depth= 1] . ( 2 sec) [ -11160.6459] [ 2484] [depth= 1] . ( 2 sec) [ -10983.2652] [ 2475] [depth= 6] . ( 2 sec) [ -10861.9133] [ 2426] [depth= 11] . ( 2 sec) [ -10723.5001] [ 2400] [depth= 10] . ( 2 sec) [ -10628.6254] [ 2385] [depth= 8] . ( 2 sec) [ -10598.2736] [ 2391] [depth= 1] . ( 2 sec) [ -10534.7644] [ 2340] [depth= 9] . ( 2 sec) [ -10480.0292] [ 2312] [depth= 1] . ( 2 sec) [ -10460.9077] [ 2305] [depth= 7] . ( 2 sec) [ -10433.8440] [ 2292] [depth= 1] . ( 2 sec) [ -10144.2635] [ 2212] [depth= 3] . ( 3 sec) [ -9936.1537] [ 2156] [depth= 5] . ( 3 sec) [ -9813.7075] [ 2132] [depth= 1] . ( 3 sec) [ -9764.2449] [ 2140] [depth= 1] . ( 3 sec) [ -9623.2625] [ 2044] [depth= 7] . ( 3 sec) [ -9608.8986] [ 2038] [depth= 1] . ( 3 sec) [ -9601.7121] [ 2029] [depth= 1] . ( 3 sec) [ -9572.7985] [ 2029] [depth= 1] . ( 3 sec) [ -9507.8219] [ 2008] [depth= 3] . ( 3 sec) [ -9494.2890] [ 2011] [depth= 1] . ( 3 sec) [ -9460.7041] [ 2001] [depth= 3] . ( 3 sec) [ -9391.3873] [ 1975] [depth= 2] . ( 3 sec) [ -9331.2266] [ 1922] [depth= 5] . ( 3 sec) [ -9279.5353] [ 1920] [depth= 2] . ( 3 sec) [ -9250.8457] [ 1914] [depth= 1] . ( 3 sec) [ -9193.7160] [ 1892] [depth= 2] . ( 3 sec) [ -9115.9618] [ 1843] [depth= 6] . ( 3 sec) [ -9020.9561] [ 1841] [depth= 4] . ( 3 sec) [ -8869.4564] [ 1770] [depth= 6] . ( 3 sec) [ -8834.7821] [ 1750] [depth= 1] . ( 3 sec) [ -8809.4827] [ 1756] [depth= 1] . ( 3 sec) [ -8658.6105] [ 1725] [depth= 3] . ( 4 sec) [ -8532.9772] [ 1684] [depth= 1] . ( 4 sec) [ -8510.8747] [ 1678] [depth= 1] . ( 4 sec) [ -8493.0075] [ 1679] [depth= 1] . ( 4 sec) [ -8475.9739] [ 1679] [depth= 1] . ( 4 sec) [ -8466.7106] [ 1683] [depth= 1] . ( 4 sec) [ -8440.2840] [ 1677] [depth= 1] . ( 4 sec) [ -8364.1827] [ 1653] [depth= 1] . ( 4 sec) [ -8335.5336] [ 1646] [depth= 2] . ( 4 sec) [ -8331.2976] [ 1645] [depth= 3] . ( 4 sec) [ -8278.8253] [ 1632] [depth= 4] . ( 4 sec) [ -8171.0382] [ 1585] [depth= 4] . ( 4 sec) [ -8166.1264] [ 1594] [depth= 1] . ( 4 sec) [ -8154.6980] [ 1585] [depth= 1] . ( 4 sec) [ -8107.1469] [ 1569] [depth= 1] . ( 4 sec) [ -8106.5896] [ 1568] [depth= 1] . ( 5 sec) [ -8011.1464] [Branch lengths ] . ( 5 sec) [ -8006.2475] [GTR parameters ] . ( 5 sec) [ -7974.1943] [Alpha ][ 0.954784] . ( 5 sec) [ -7973.4185] [ 1567] [depth= 1] . ( 5 sec) [ -7972.3394] [ 1568] [depth= 1] . ( 6 sec) [ -7940.3590] [ 1555] [depth= 2] . ( 6 sec) [ -7940.3187] [ 1556] [depth= 1] . ( 7 sec) [ -7940.1957] [ 1557] [depth= 1] . ( 8 sec) [ -7931.4983] [Branch lengths ] . ( 8 sec) [ -7931.3040] [GTR parameters ] . ( 8 sec) [ -7931.1948] [Alpha ][ 0.992699] . ( 8 sec) [ -7931.1727] [ 1556] [depth= 1] . ( 11 sec) [ -7930.6883] [Branch lengths ] . ( 11 sec) [ -7930.6879] [GTR parameters ] . ( 11 sec) [ -7930.6847] [Alpha ][ 0.999534] . ( 29 sec) [ -7930.6347] [Branch lengths ] . ( 29 sec) [ -7930.6347] [Topology ] . ( 30 sec) [ -7930.6302] [Topology ] . ( 31 sec) [ -7930.6288] [Topology ] . ( 32 sec) [ -7930.6281] [Topology ] . ( 32 sec) [ -7930.6280] [GTR parameters ] . ( 32 sec) [ -7930.6277] [Alpha ][ 1.001530] . ( 32 sec) [ -7930.6277] [Topology ] . ( 33 sec) [ -7930.6273] [Topology ] . ( 33 sec) [ -7930.6273] [GTR parameters ] . ( 33 sec) [ -7930.6273] [Alpha ][ 1.001530] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7930.627279. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19751.4828] [GTR parameters ] . ( 0 sec) [ -19424.4450] [Alpha ][ 0.500960] . ( 0 sec) [ -19061.6080] [ 3553] [depth= 11] . ( 0 sec) [ -18633.7583] [ 3469] [depth= 9] . ( 0 sec) [ -18395.3051] [ 3440] [depth= 2] . ( 0 sec) [ -18290.6460] [ 3383] [depth= 1] . ( 0 sec) [ -18183.6526] [ 3360] [depth= 6] . ( 0 sec) [ -18108.2278] [ 3338] [depth= 2] . ( 0 sec) [ -18034.5335] [ 3334] [depth= 4] . ( 0 sec) [ -17913.2687] [ 3267] [depth= 1] . ( 0 sec) [ -17502.8207] [ 3257] [depth= 3] . ( 0 sec) [ -17417.8465] [ 3215] [depth= 6] . ( 0 sec) [ -17300.3248] [ 3206] [depth= 4] . ( 1 sec) [ -17144.2457] [ 3152] [depth= 1] . ( 1 sec) [ -17143.2451] [ 3148] [depth= 1] . ( 1 sec) [ -17102.9970] [ 3144] [depth= 2] . ( 1 sec) [ -16858.9593] [ 3118] [depth= 4] . ( 1 sec) [ -16821.8279] [ 3106] [depth= 4] . ( 1 sec) [ -16726.0878] [ 3049] [depth= 7] . ( 1 sec) [ -16716.9153] [ 3057] [depth= 1] . ( 1 sec) [ -16603.4872] [ 3016] [depth= 1] . ( 1 sec) [ -16426.1465] [ 2984] [depth= 5] . ( 1 sec) [ -16310.1849] [ 2954] [depth= 1] . ( 1 sec) [ -16168.7907] [ 2932] [depth= 6] . ( 1 sec) [ -16028.5693] [ 2891] [depth= 9] . ( 1 sec) [ -15851.0184] [ 2850] [depth= 1] . ( 1 sec) [ -15680.0536] [ 2812] [depth= 10] . ( 1 sec) [ -15659.9192] [ 2821] [depth= 1] . ( 1 sec) [ -15598.2300] [ 2798] [depth= 1] . ( 1 sec) [ -12360.7939] [ 2786] [depth= 8] . ( 1 sec) [ -12215.6866] [ 2759] [depth= 1] . ( 1 sec) [ -12037.0416] [ 2737] [depth= 5] . ( 1 sec) [ -11772.9684] [ 2712] [depth= 3] . ( 1 sec) [ -11644.0874] [ 2632] [depth= 1] . ( 1 sec) [ -11612.5696] [ 2618] [depth= 1] . ( 1 sec) [ -11437.6570] [ 2566] [depth= 2] . ( 1 sec) [ -11194.2785] [ 2516] [depth= 6] . ( 2 sec) [ -10973.6766] [ 2456] [depth= 13] . ( 2 sec) [ -10823.3622] [ 2451] [depth= 4] . ( 2 sec) [ -10817.3390] [ 2450] [depth= 1] . ( 2 sec) [ -10743.7433] [ 2400] [depth= 10] . ( 2 sec) [ -10716.2601] [ 2394] [depth= 1] . ( 2 sec) [ -10700.7024] [ 2391] [depth= 4] . ( 2 sec) [ -10679.6749] [ 2366] [depth= 1] . ( 2 sec) [ -10576.0699] [ 2347] [depth= 2] . ( 2 sec) [ -10565.3784] [ 2366] [depth= 1] . ( 2 sec) [ -10267.7866] [ 2248] [depth= 9] . ( 2 sec) [ -10267.1114] [ 2245] [depth= 1] . ( 2 sec) [ -10227.6438] [ 2243] [depth= 8] . ( 2 sec) [ -10110.9474] [ 2220] [depth= 1] . ( 2 sec) [ -10094.4410] [ 2207] [depth= 1] . ( 2 sec) [ -10034.7832] [ 2204] [depth= 1] . ( 2 sec) [ -10023.4145] [ 2191] [depth= 1] . ( 2 sec) [ -9869.3824] [ 2122] [depth= 7] . ( 2 sec) [ -9807.9167] [ 2087] [depth= 1] . ( 2 sec) [ -9709.6452] [ 2090] [depth= 4] . ( 2 sec) [ -9703.1461] [ 2092] [depth= 1] . ( 2 sec) [ -9665.8909] [ 2085] [depth= 2] . ( 2 sec) [ -9663.0789] [ 2083] [depth= 1] . ( 3 sec) [ -9662.0216] [ 2088] [depth= 1] . ( 3 sec) [ -9639.5885] [ 2084] [depth= 2] . ( 3 sec) [ -9520.4157] [ 2058] [depth= 2] . ( 3 sec) [ -9433.7142] [ 2046] [depth= 9] . ( 3 sec) [ -9421.4110] [ 2043] [depth= 2] . ( 3 sec) [ -9413.8206] [ 2047] [depth= 1] . ( 3 sec) [ -9335.2476] [ 2020] [depth= 2] . ( 3 sec) [ -9317.1582] [ 2014] [depth= 1] . ( 3 sec) [ -9277.0166] [ 2014] [depth= 1] . ( 3 sec) [ -9248.9521] [ 2021] [depth= 1] . ( 3 sec) [ -9115.1953] [ 1967] [depth= 2] . ( 3 sec) [ -9007.7815] [ 1941] [depth= 1] . ( 3 sec) [ -9004.1602] [ 1942] [depth= 1] . ( 3 sec) [ -8779.6453] [ 1847] [depth= 6] . ( 3 sec) [ -8766.5374] [ 1839] [depth= 1] . ( 3 sec) [ -8719.1160] [ 1826] [depth= 1] . ( 3 sec) [ -8646.5754] [ 1815] [depth= 5] . ( 3 sec) [ -8643.8683] [ 1814] [depth= 2] . ( 3 sec) [ -8568.8744] [ 1773] [depth= 2] . ( 4 sec) [ -8564.0456] [ 1767] [depth= 1] . ( 4 sec) [ -8556.9843] [ 1767] [depth= 1] . ( 4 sec) [ -8543.7249] [ 1761] [depth= 1] . ( 4 sec) [ -8396.9093] [Branch lengths ] . ( 4 sec) [ -8393.2399] [GTR parameters ] . ( 5 sec) [ -8364.5450] [Alpha ][ 0.885624] . ( 5 sec) [ -8364.5091] [ 1760] [depth= 1] . ( 5 sec) [ -8364.3054] [ 1761] [depth= 1] . ( 5 sec) [ -8279.9563] [ 1736] [depth= 5] . ( 5 sec) [ -8157.8475] [ 1684] [depth= 11] . ( 5 sec) [ -8157.7925] [ 1682] [depth= 1] . ( 5 sec) [ -8147.3020] [ 1669] [depth= 1] . ( 5 sec) [ -8138.6726] [ 1659] [depth= 1] . ( 5 sec) [ -8138.5059] [ 1662] [depth= 1] . ( 5 sec) [ -8066.4888] [ 1621] [depth= 1] . ( 5 sec) [ -8066.3178] [ 1622] [depth= 1] . ( 5 sec) [ -8054.3932] [ 1615] [depth= 1] . ( 5 sec) [ -8026.7012] [ 1602] [depth= 1] . ( 6 sec) [ -8025.2835] [ 1605] [depth= 1] . ( 6 sec) [ -8023.8293] [ 1604] [depth= 1] . ( 6 sec) [ -8023.6926] [ 1602] [depth= 2] . ( 6 sec) [ -8023.3497] [ 1605] [depth= 1] . ( 6 sec) [ -8014.3135] [ 1592] [depth= 1] . ( 6 sec) [ -7981.6504] [ 1574] [depth= 4] . ( 6 sec) [ -7947.6580] [ 1560] [depth= 2] . ( 6 sec) [ -7947.6125] [ 1560] [depth= 1] . ( 6 sec) [ -7944.9414] [ 1561] [depth= 1] . ( 7 sec) [ -7944.8174] [ 1561] [depth= 1] . ( 7 sec) [ -7933.0508] [Branch lengths ] . ( 8 sec) [ -7932.5378] [GTR parameters ] . ( 8 sec) [ -7931.6206] [Alpha ][ 0.991450] . ( 10 sec) [ -7931.2644] [Branch lengths ] . ( 11 sec) [ -7930.7853] [ 1557] [depth= 1] . ( 29 sec) [ -7930.6457] [Branch lengths ] . ( 29 sec) [ -7930.6423] [GTR parameters ] . ( 29 sec) [ -7930.6361] [Alpha ][ 1.000993] . ( 29 sec) [ -7930.6361] [Topology ] . ( 30 sec) [ -7930.6305] [Topology ] . ( 31 sec) [ -7930.6288] [Topology ] . ( 32 sec) [ -7930.6281] [Topology ] . ( 32 sec) [ -7930.6281] [GTR parameters ] . ( 32 sec) [ -7930.6281] [Alpha ][ 1.001994] . ( 32 sec) [ -7930.6281] [Topology ] . ( 32 sec) [ -7930.6278] [Topology ] . ( 33 sec) [ -7930.6278] [GTR parameters ] . ( 33 sec) [ -7930.6278] [Alpha ][ 1.001994] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7930.627774. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20291.9138] [GTR parameters ] . ( 1 sec) [ -19966.2123] [Alpha ][ 0.500960] . ( 1 sec) [ -19587.3074] [ 3537] [depth= 7] . ( 1 sec) [ -19172.4683] [ 3451] [depth= 11] . ( 1 sec) [ -19144.1556] [ 3450] [depth= 1] . ( 1 sec) [ -19119.2148] [ 3445] [depth= 3] . ( 1 sec) [ -18897.7715] [ 3433] [depth= 4] . ( 1 sec) [ -18707.4395] [ 3435] [depth= 3] . ( 1 sec) [ -18635.0366] [ 3429] [depth= 1] . ( 1 sec) [ -18521.2201] [ 3416] [depth= 1] . ( 1 sec) [ -18330.2026] [ 3368] [depth= 9] . ( 1 sec) [ -17914.1854] [ 3331] [depth= 16] . ( 1 sec) [ -17702.3414] [ 3240] [depth= 13] . ( 1 sec) [ -17528.2547] [ 3235] [depth= 16] . ( 1 sec) [ -17116.1530] [ 3162] [depth= 15] . ( 1 sec) [ -17067.3475] [ 3146] [depth= 7] . ( 1 sec) [ -17020.8086] [ 3135] [depth= 7] . ( 1 sec) [ -16891.8805] [ 3133] [depth= 2] . ( 1 sec) [ -16596.6467] [ 3105] [depth= 9] . ( 1 sec) [ -16412.6361] [ 3031] [depth= 12] . ( 2 sec) [ -16342.1950] [ 3028] [depth= 2] . ( 2 sec) [ -16309.6603] [ 3034] [depth= 6] . ( 2 sec) [ -16195.7093] [ 3002] [depth= 5] . ( 2 sec) [ -16129.4896] [ 2970] [depth= 12] . ( 2 sec) [ -16048.3615] [ 2938] [depth= 1] . ( 2 sec) [ -15937.9328] [ 2910] [depth= 5] . ( 2 sec) [ -15773.5483] [ 2836] [depth= 10] . ( 2 sec) [ -15392.3446] [ 2790] [depth= 5] . ( 2 sec) [ -15337.8577] [ 2754] [depth= 1] . ( 2 sec) [ -15272.2817] [ 2739] [depth= 1] . ( 2 sec) [ -12329.8269] [ 2690] [depth= 11] . ( 2 sec) [ -12084.2666] [ 2703] [depth= 1] . ( 2 sec) [ -11809.3233] [ 2659] [depth= 5] . ( 2 sec) [ -11384.8020] [ 2618] [depth= 3] . ( 2 sec) [ -11320.2650] [ 2527] [depth= 4] . ( 2 sec) [ -11191.4074] [ 2493] [depth= 8] . ( 2 sec) [ -11104.5259] [ 2492] [depth= 4] . ( 2 sec) [ -11041.2949] [ 2459] [depth= 2] . ( 2 sec) [ -11009.1856] [ 2455] [depth= 1] . ( 2 sec) [ -10959.0098] [ 2442] [depth= 1] . ( 2 sec) [ -10650.5237] [ 2366] [depth= 4] . ( 2 sec) [ -10524.7893] [ 2334] [depth= 4] . ( 2 sec) [ -10325.2680] [ 2332] [depth= 1] . ( 3 sec) [ -10182.0071] [ 2212] [depth= 10] . ( 3 sec) [ -10076.9676] [ 2177] [depth= 1] . ( 3 sec) [ -10039.0733] [ 2169] [depth= 3] . ( 3 sec) [ -9893.8011] [ 2133] [depth= 4] . ( 3 sec) [ -9834.7421] [ 2075] [depth= 6] . ( 3 sec) [ -9666.6241] [ 2016] [depth= 2] . ( 3 sec) [ -9646.1267] [ 2010] [depth= 1] . ( 3 sec) [ -9596.2982] [ 2000] [depth= 3] . ( 3 sec) [ -9559.0119] [ 1996] [depth= 1] . ( 3 sec) [ -9557.8027] [ 1999] [depth= 1] . ( 3 sec) [ -9478.9475] [ 1975] [depth= 1] . ( 3 sec) [ -9430.2430] [ 1972] [depth= 3] . ( 3 sec) [ -9183.8132] [ 1974] [depth= 2] . ( 3 sec) [ -8923.9770] [ 1835] [depth= 8] . ( 3 sec) [ -8890.2987] [ 1838] [depth= 1] . ( 3 sec) [ -8855.3094] [ 1816] [depth= 4] . ( 3 sec) [ -8730.0120] [ 1794] [depth= 5] . ( 3 sec) [ -8720.5650] [ 1795] [depth= 1] . ( 3 sec) [ -8620.3952] [ 1757] [depth= 3] . ( 3 sec) [ -8590.6393] [ 1744] [depth= 1] . ( 3 sec) [ -8580.9027] [ 1743] [depth= 1] . ( 4 sec) [ -8524.8612] [ 1714] [depth= 1] . ( 4 sec) [ -8474.4230] [ 1698] [depth= 1] . ( 4 sec) [ -8347.9134] [ 1653] [depth= 2] . ( 4 sec) [ -8320.7924] [ 1658] [depth= 1] . ( 4 sec) [ -8290.9246] [ 1648] [depth= 1] . ( 4 sec) [ -8279.8001] [ 1643] [depth= 1] . ( 4 sec) [ -8228.7896] [ 1623] [depth= 1] . ( 4 sec) [ -8195.0378] [ 1608] [depth= 1] . ( 4 sec) [ -8117.4094] [ 1588] [depth= 1] . ( 4 sec) [ -8108.1764] [ 1582] [depth= 1] . ( 4 sec) [ -8011.5147] [Branch lengths ] . ( 5 sec) [ -8007.6382] [GTR parameters ] . ( 5 sec) [ -7976.3065] [Alpha ][ 0.939399] . ( 5 sec) [ -7976.2879] [ 1583] [depth= 1] . ( 5 sec) [ -7976.1627] [ 1582] [depth= 1] . ( 5 sec) [ -7962.9096] [ 1573] [depth= 2] . ( 5 sec) [ -7942.4324] [ 1555] [depth= 1] . ( 6 sec) [ -7942.2979] [ 1556] [depth= 1] . ( 7 sec) [ -7942.0969] [ 1556] [depth= 1] . ( 7 sec) [ -7942.0808] [ 1556] [depth= 1] . ( 8 sec) [ -7931.5375] [Branch lengths ] . ( 8 sec) [ -7931.3766] [GTR parameters ] . ( 8 sec) [ -7931.1549] [Alpha ][ 0.993425] . ( 10 sec) [ -7930.6836] [Branch lengths ] . ( 29 sec) [ -7930.6380] [Branch lengths ] . ( 29 sec) [ -7930.6380] [Topology ] . ( 30 sec) [ -7930.6347] [Topology ] . ( 30 sec) [ -7930.6337] [Topology ] . ( 31 sec) [ -7930.6332] [Topology ] . ( 31 sec) [ -7930.6325] [GTR parameters ] . ( 31 sec) [ -7930.6279] [Alpha ][ 1.001602] . ( 31 sec) [ -7930.6279] [Topology ] . ( 32 sec) [ -7930.6274] [Topology ] . ( 32 sec) [ -7930.6274] [GTR parameters ] . ( 32 sec) [ -7930.6274] [Alpha ][ 1.001602] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7930.627372. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7963.047097 . ( 1 sec) [ -7958.8927] [GTR parameters ] . ( 1 sec) [ -7958.7829] [Alpha ][ 0.960038] . ( 1 sec) [ -7958.7829] [Topology ] . ( 2 sec) [ -7935.0414] [Topology ] . ( 2 sec) [ -7932.3359] [Topology ] . ( 3 sec) [ -7931.4845] [Topology ] . ( 4 sec) [ -7931.1483] [Topology ] . ( 5 sec) [ -7931.0049] [Topology ] . ( 5 sec) [ -7930.9412] [Topology ] . ( 6 sec) [ -7930.9121] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7930.912139 . ( 12 sec) [ -7930.7880] [GTR parameters ] . ( 12 sec) [ -7930.6789] [Alpha ][ 0.997965] . ( 12 sec) [ -7930.6789] [Topology ] . ( 13 sec) [ -7930.6511] [Topology ] . ( 14 sec) [ -7930.6388] [Topology ] . ( 15 sec) [ -7930.6332] [Topology ] . ( 15 sec) [ -7930.6306] [Topology ] . ( 16 sec) [ -7930.6294] [Topology ] . ( 17 sec) [ -7930.6289] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -7930.6285] [Topology ] . Before opt ts/t=1.000000 LK=-7930.628483 . ( 23 sec) [ -7930.6284] [GTR parameters ] . ( 23 sec) [ -7930.6275] [Alpha ][ 1.001552] . ( 23 sec) [ -7930.6275] [Topology ] . ( 23 sec) [ -7930.6271] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7930.627050 . ( 29 sec) [ -7930.6270] [GTR parameters ] . ( 29 sec) [ -7930.6270] [Alpha ][ 1.001552] . ( 29 sec) [ -7930.6270] [Topology ] . ( 30 sec) [ -7930.6269] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 41 sec) [ -7958.8927] [GTR parameters ] . ( 41 sec) [ -7958.7829] [Alpha ][ 0.960038] . ( 41 sec) [ -7957.2802] [ 1555] [depth= 1] . ( 42 sec) [ -7956.7962] [ 1557] [depth= 1] . ( 42 sec) [ -7955.8131] [ 1556] [depth= 1] . ( 43 sec) [ -7954.7418] [ 1557] [depth= 1] . ( 44 sec) [ -7932.3481] [Branch lengths ] . ( 44 sec) [ -7932.2535] [GTR parameters ] . ( 44 sec) [ -7932.2091] [Alpha ][ 0.984254] . ( 45 sec) [ -7932.1151] [ 1556] [depth= 1] . ( 47 sec) [ -7930.7932] [Branch lengths ] . ( 47 sec) [ -7930.7919] [GTR parameters ] . ( 47 sec) [ -7930.7792] [Alpha ][ 0.997891] . ( 49 sec) [ -7930.6444] [Branch lengths ] . ( 68 sec) [ -7930.6304] [Branch lengths ] . ( 68 sec) [ -7930.6304] [Topology ] . ( 69 sec) [ -7930.6292] [Topology ] . ( 70 sec) [ -7930.6288] [Topology ] . ( 70 sec) [ -7930.6283] [GTR parameters ] . ( 70 sec) [ -7930.6273] [Alpha ][ 1.001599] . ( 70 sec) [ -7930.6273] [Topology ] . ( 71 sec) [ -7930.6270] [Topology ] . ( 71 sec) [ -7930.6270] [GTR parameters ] . ( 71 sec) [ -7930.6270] [Alpha ][ 1.001599] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7930.626869 . Log likelihood obtained after SPR moves : -7930.627041 . Log likelihood of the current tree: -7930.626869. . Printing the most likely tree in file 'data92.phy_phyml_tree.txt'... . Best log likelihood : -7930.626869 . Time used 0h1m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo