.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data68.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... . 417 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22125.5740] [GTR parameters ] . ( 1 sec) [ -21715.7268] [Alpha ][ 0.500960] . ( 1 sec) [ -20803.5744] [ 4093] [depth= 8] . ( 1 sec) [ -20755.8510] [ 4093] [depth= 7] . ( 1 sec) [ -20544.3222] [ 4089] [depth= 1] . ( 1 sec) [ -20417.4029] [ 4084] [depth= 7] . ( 1 sec) [ -20412.5845] [ 4024] [depth= 5] . ( 1 sec) [ -19619.9093] [ 4007] [depth= 6] . ( 1 sec) [ -19462.0331] [ 3971] [depth= 4] . ( 1 sec) [ -19329.4722] [ 3918] [depth= 1] . ( 1 sec) [ -18936.7179] [ 3893] [depth= 16] . ( 1 sec) [ -18725.7666] [ 3776] [depth= 17] . ( 1 sec) [ -18471.4007] [ 3783] [depth= 6] . ( 1 sec) [ -18233.6409] [ 3715] [depth= 5] . ( 1 sec) [ -18126.3811] [ 3708] [depth= 3] . ( 1 sec) [ -18049.0415] [ 3701] [depth= 4] . ( 1 sec) [ -17821.5582] [ 3621] [depth= 4] . ( 2 sec) [ -17795.6695] [ 3619] [depth= 2] . ( 2 sec) [ -17509.0133] [ 3584] [depth= 2] . ( 2 sec) [ -17267.5270] [ 3572] [depth= 9] . ( 2 sec) [ -17184.7186] [ 3535] [depth= 10] . ( 2 sec) [ -14512.2988] [ 3454] [depth= 7] . ( 2 sec) [ -14477.4509] [ 3435] [depth= 8] . ( 2 sec) [ -14236.8043] [ 3411] [depth= 6] . ( 2 sec) [ -14064.8780] [ 3364] [depth= 1] . ( 2 sec) [ -13949.6038] [ 3354] [depth= 11] . ( 2 sec) [ -13880.2232] [ 3319] [depth= 12] . ( 2 sec) [ -13733.4172] [ 3237] [depth= 9] . ( 2 sec) [ -13690.0995] [ 3228] [depth= 12] . ( 2 sec) [ -13657.6377] [ 3208] [depth= 1] . ( 2 sec) [ -13633.5021] [ 3198] [depth= 5] . ( 2 sec) [ -13581.1091] [ 3179] [depth= 15] . ( 2 sec) [ -13151.3924] [ 3099] [depth= 4] . ( 2 sec) [ -12912.4131] [ 3032] [depth= 5] . ( 2 sec) [ -12753.6624] [ 2985] [depth= 10] . ( 2 sec) [ -12458.7249] [ 2936] [depth= 16] . ( 2 sec) [ -12405.0186] [ 2902] [depth= 1] . ( 2 sec) [ -12206.0595] [ 2869] [depth= 1] . ( 2 sec) [ -12089.9727] [ 2843] [depth= 2] . ( 3 sec) [ -12078.6637] [ 2866] [depth= 1] . ( 3 sec) [ -11814.0493] [ 2740] [depth= 14] . ( 3 sec) [ -11771.0597] [ 2741] [depth= 10] . ( 3 sec) [ -11655.5177] [ 2709] [depth= 6] . ( 3 sec) [ -11504.6244] [ 2655] [depth= 4] . ( 3 sec) [ -11309.6455] [ 2620] [depth= 3] . ( 3 sec) [ -11303.5679] [ 2623] [depth= 1] . ( 3 sec) [ -11084.8441] [ 2541] [depth= 6] . ( 3 sec) [ -11072.9847] [ 2546] [depth= 1] . ( 3 sec) [ -11044.6210] [ 2535] [depth= 2] . ( 3 sec) [ -10834.2184] [ 2481] [depth= 9] . ( 3 sec) [ -10822.2581] [ 2484] [depth= 7] . ( 3 sec) [ -10812.3954] [ 2481] [depth= 6] . ( 3 sec) [ -10709.3693] [ 2439] [depth= 1] . ( 3 sec) [ -10700.7639] [ 2422] [depth= 4] . ( 3 sec) [ -10521.2466] [ 2389] [depth= 5] . ( 3 sec) [ -10375.7105] [ 2324] [depth= 4] . ( 3 sec) [ -10283.7402] [ 2304] [depth= 1] . ( 3 sec) [ -10242.0682] [ 2304] [depth= 2] . ( 3 sec) [ -10112.1331] [ 2277] [depth= 5] . ( 4 sec) [ -10110.6046] [ 2277] [depth= 1] . ( 4 sec) [ -10071.3277] [ 2258] [depth= 1] . ( 4 sec) [ -10068.2534] [ 2259] [depth= 1] . ( 4 sec) [ -10067.6028] [ 2260] [depth= 1] . ( 4 sec) [ -10067.2624] [ 2277] [depth= 1] . ( 4 sec) [ -10053.5153] [ 2260] [depth= 2] . ( 4 sec) [ -10017.7495] [ 2256] [depth= 1] . ( 4 sec) [ -10012.9841] [ 2262] [depth= 1] . ( 4 sec) [ -9774.4837] [ 2172] [depth= 5] . ( 4 sec) [ -9765.0085] [ 2172] [depth= 1] . ( 4 sec) [ -9660.8872] [ 2140] [depth= 1] . ( 4 sec) [ -9634.9192] [ 2123] [depth= 2] . ( 4 sec) [ -9592.0196] [ 2096] [depth= 1] . ( 4 sec) [ -9549.5977] [ 2088] [depth= 1] . ( 4 sec) [ -9548.1790] [ 2088] [depth= 1] . ( 4 sec) [ -9516.9382] [ 2082] [depth= 1] . ( 4 sec) [ -9471.2519] [ 2076] [depth= 2] . ( 4 sec) [ -9470.5379] [ 2077] [depth= 1] . ( 4 sec) [ -9467.1807] [ 2076] [depth= 1] . ( 5 sec) [ -9461.6991] [ 2079] [depth= 1] . ( 5 sec) [ -9405.4492] [ 2047] [depth= 2] . ( 5 sec) [ -9396.3246] [ 2051] [depth= 1] . ( 5 sec) [ -9371.5902] [ 2045] [depth= 1] . ( 5 sec) [ -9280.4663] [Branch lengths ] . ( 6 sec) [ -9275.6913] [GTR parameters ] . ( 6 sec) [ -9240.4358] [Alpha ][ 0.918709] . ( 6 sec) [ -9240.2643] [ 2047] [depth= 1] . ( 6 sec) [ -9239.3031] [ 2051] [depth= 1] . ( 6 sec) [ -9200.5453] [ 2028] [depth= 1] . ( 6 sec) [ -9125.8314] [ 1992] [depth= 2] . ( 6 sec) [ -9123.6154] [ 1988] [depth= 1] . ( 6 sec) [ -9122.8584] [ 1983] [depth= 1] . ( 6 sec) [ -9089.6800] [ 1979] [depth= 6] . ( 7 sec) [ -9087.4775] [ 1983] [depth= 1] . ( 7 sec) [ -9086.0363] [ 1965] [depth= 1] . ( 7 sec) [ -9079.4432] [ 1968] [depth= 2] . ( 7 sec) [ -9077.1823] [ 1968] [depth= 1] . ( 7 sec) [ -9074.4679] [ 1963] [depth= 1] . ( 7 sec) [ -9073.7318] [ 1964] [depth= 1] . ( 7 sec) [ -9063.1539] [ 1960] [depth= 1] . ( 7 sec) [ -9063.0459] [ 1957] [depth= 1] . ( 8 sec) [ -9060.5127] [ 1954] [depth= 1] . ( 8 sec) [ -9057.9377] [ 1950] [depth= 1] . ( 8 sec) [ -9057.2524] [ 1945] [depth= 1] . ( 8 sec) [ -9041.5278] [ 1937] [depth= 1] . ( 8 sec) [ -9012.0708] [ 1921] [depth= 2] . ( 8 sec) [ -9010.4055] [ 1926] [depth= 1] . ( 9 sec) [ -9008.1861] [ 1925] [depth= 1] . ( 9 sec) [ -9002.9159] [ 1919] [depth= 2] . ( 9 sec) [ -8983.6382] [Branch lengths ] . ( 10 sec) [ -8983.5507] [GTR parameters ] . ( 10 sec) [ -8982.5080] [Alpha ][ 1.026443] . ( 10 sec) [ -8967.4814] [ 1908] [depth= 3] . ( 10 sec) [ -8967.1913] [ 1912] [depth= 1] . ( 11 sec) [ -8967.1598] [ 1912] [depth= 1] . ( 11 sec) [ -8967.1046] [ 1912] [depth= 1] . ( 11 sec) [ -8966.1228] [ 1915] [depth= 1] . ( 13 sec) [ -8964.3951] [Branch lengths ] . ( 14 sec) [ -8964.3871] [GTR parameters ] . ( 14 sec) [ -8964.3870] [Alpha ][ 1.027584] . ( 17 sec) [ -8964.2747] [Branch lengths ] . ( 39 sec) [ -8964.2581] [Branch lengths ] . ( 39 sec) [ -8964.2581] [Topology ] . ( 40 sec) [ -8964.0140] [Topology ] . ( 41 sec) [ -8963.9745] [Topology ] . ( 42 sec) [ -8963.9661] [Topology ] . ( 43 sec) [ -8963.9637] [Topology ] . ( 43 sec) [ -8963.9629] [Topology ] . ( 44 sec) [ -8963.9620] [GTR parameters ] . ( 44 sec) [ -8963.9620] [Alpha ][ 1.027584] . ( 44 sec) [ -8963.9620] [Topology ] . ( 44 sec) [ -8963.9618] [Topology ] . ( 45 sec) [ -8963.9618] [GTR parameters ] . ( 45 sec) [ -8963.9618] [Alpha ][ 1.027584] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -8963.7217] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.721709. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23608.8199] [GTR parameters ] . ( 1 sec) [ -23181.8640] [Alpha ][ 0.500960] . ( 1 sec) [ -22281.3917] [ 4027] [depth= 3] . ( 1 sec) [ -22153.0447] [ 3986] [depth= 3] . ( 1 sec) [ -22035.6968] [ 3957] [depth= 3] . ( 1 sec) [ -18403.2388] [ 3918] [depth= 9] . ( 1 sec) [ -18137.0847] [ 3839] [depth= 2] . ( 1 sec) [ -17855.5921] [ 3817] [depth= 2] . ( 1 sec) [ -17784.0478] [ 3775] [depth= 1] . ( 1 sec) [ -17729.7028] [ 3765] [depth= 4] . ( 1 sec) [ -17528.4574] [ 3685] [depth= 1] . ( 1 sec) [ -17377.1533] [ 3676] [depth= 2] . ( 1 sec) [ -17117.7859] [ 3623] [depth= 3] . ( 2 sec) [ -16877.1341] [ 3617] [depth= 3] . ( 2 sec) [ -16806.3951] [ 3554] [depth= 1] . ( 2 sec) [ -16160.5737] [ 3548] [depth= 4] . ( 2 sec) [ -15402.8774] [ 3398] [depth= 11] . ( 2 sec) [ -15070.9414] [ 3344] [depth= 10] . ( 2 sec) [ -14221.7651] [ 3278] [depth= 19] . ( 2 sec) [ -14195.2582] [ 3277] [depth= 1] . ( 2 sec) [ -13932.9807] [ 3208] [depth= 8] . ( 2 sec) [ -13902.8757] [ 3200] [depth= 1] . ( 2 sec) [ -13796.2704] [ 3156] [depth= 3] . ( 2 sec) [ -13750.5768] [ 3157] [depth= 2] . ( 2 sec) [ -13547.1360] [ 3066] [depth= 7] . ( 2 sec) [ -13461.8989] [ 3060] [depth= 10] . ( 2 sec) [ -13339.8053] [ 3042] [depth= 1] . ( 2 sec) [ -13234.6728] [ 2990] [depth= 1] . ( 2 sec) [ -13156.5246] [ 2968] [depth= 7] . ( 2 sec) [ -12863.9300] [ 2854] [depth= 14] . ( 2 sec) [ -12832.6339] [ 2859] [depth= 1] . ( 2 sec) [ -12831.8787] [ 2863] [depth= 2] . ( 2 sec) [ -12779.2570] [ 2852] [depth= 2] . ( 2 sec) [ -12731.8234] [ 2840] [depth= 3] . ( 3 sec) [ -12723.2615] [ 2838] [depth= 1] . ( 3 sec) [ -12671.5360] [ 2820] [depth= 2] . ( 3 sec) [ -12152.2548] [ 2806] [depth= 3] . ( 3 sec) [ -11953.6556] [ 2706] [depth= 2] . ( 3 sec) [ -11712.4858] [ 2701] [depth= 5] . ( 3 sec) [ -11643.8116] [ 2691] [depth= 2] . ( 3 sec) [ -11631.0944] [ 2683] [depth= 2] . ( 3 sec) [ -11568.7083] [ 2673] [depth= 2] . ( 3 sec) [ -11396.7261] [ 2658] [depth= 1] . ( 3 sec) [ -11323.2119] [ 2645] [depth= 1] . ( 3 sec) [ -11318.3959] [ 2645] [depth= 1] . ( 3 sec) [ -11069.8854] [ 2653] [depth= 1] . ( 3 sec) [ -11064.9958] [ 2645] [depth= 1] . ( 3 sec) [ -11049.1963] [ 2636] [depth= 2] . ( 3 sec) [ -10753.4875] [ 2512] [depth= 3] . ( 3 sec) [ -10701.9600] [ 2512] [depth= 1] . ( 3 sec) [ -10698.3873] [ 2512] [depth= 1] . ( 3 sec) [ -10557.4782] [ 2478] [depth= 4] . ( 3 sec) [ -10510.8511] [ 2412] [depth= 3] . ( 3 sec) [ -10448.6707] [ 2373] [depth= 3] . ( 3 sec) [ -10425.4698] [ 2376] [depth= 1] . ( 3 sec) [ -10338.6653] [ 2374] [depth= 1] . ( 4 sec) [ -10163.6936] [ 2258] [depth= 2] . ( 4 sec) [ -10145.9820] [ 2246] [depth= 4] . ( 4 sec) [ -10052.5378] [ 2215] [depth= 1] . ( 4 sec) [ -9891.0635] [ 2220] [depth= 1] . ( 4 sec) [ -9755.9771] [ 2151] [depth= 2] . ( 4 sec) [ -9696.8953] [ 2121] [depth= 6] . ( 4 sec) [ -9684.0369] [ 2119] [depth= 1] . ( 4 sec) [ -9675.5526] [ 2119] [depth= 1] . ( 4 sec) [ -9599.5595] [ 2101] [depth= 2] . ( 4 sec) [ -9590.1815] [ 2093] [depth= 2] . ( 4 sec) [ -9490.7426] [ 2050] [depth= 3] . ( 4 sec) [ -9343.8861] [ 1993] [depth= 7] . ( 4 sec) [ -9341.1710] [ 1997] [depth= 1] . ( 4 sec) [ -9336.1873] [ 1993] [depth= 1] . ( 4 sec) [ -9333.2257] [ 1990] [depth= 1] . ( 4 sec) [ -9257.2034] [ 1961] [depth= 3] . ( 5 sec) [ -9253.1193] [ 1964] [depth= 1] . ( 5 sec) [ -9231.1563] [ 1943] [depth= 4] . ( 5 sec) [ -9226.3928] [ 1945] [depth= 1] . ( 5 sec) [ -9156.2634] [ 1948] [depth= 1] . ( 5 sec) [ -9119.8539] [ 1940] [depth= 1] . ( 5 sec) [ -9116.4613] [ 1936] [depth= 2] . ( 5 sec) [ -9092.3593] [ 1918] [depth= 2] . ( 5 sec) [ -9089.3146] [ 1920] [depth= 1] . ( 5 sec) [ -9026.7881] [Branch lengths ] . ( 6 sec) [ -9021.3737] [GTR parameters ] . ( 6 sec) [ -8979.6349] [Alpha ][ 0.990941] . ( 6 sec) [ -8979.5568] [ 1919] [depth= 1] . ( 6 sec) [ -8971.8079] [ 1916] [depth= 1] . ( 6 sec) [ -8971.7475] [ 1915] [depth= 2] . ( 7 sec) [ -8971.6011] [ 1916] [depth= 1] . ( 8 sec) [ -8970.7150] [ 1911] [depth= 1] . ( 9 sec) [ -8964.8921] [Branch lengths ] . ( 10 sec) [ -8964.7650] [GTR parameters ] . ( 10 sec) [ -8964.6787] [Alpha ][ 1.023205] . ( 12 sec) [ -8964.6503] [ 1912] [depth= 1] . ( 13 sec) [ -8964.1706] [Branch lengths ] . ( 13 sec) [ -8964.1697] [GTR parameters ] . ( 13 sec) [ -8964.1680] [Alpha ][ 1.027801] . ( 35 sec) [ -8964.0882] [Branch lengths ] . ( 35 sec) [ -8964.0882] [Topology ] . ( 35 sec) [ -8963.7701] [Topology ] . ( 36 sec) [ -8963.7147] [Topology ] . ( 37 sec) [ -8963.7019] [Topology ] . ( 38 sec) [ -8963.6978] [Topology ] . ( 39 sec) [ -8963.6964] [Topology ] . ( 39 sec) [ -8963.6958] [Topology ] . ( 40 sec) [ -8963.6951] [GTR parameters ] . ( 40 sec) [ -8963.6951] [Alpha ][ 1.028829] . ( 40 sec) [ -8963.6951] [Topology ] . ( 40 sec) [ -8963.6948] [Topology ] . ( 41 sec) [ -8963.6948] [GTR parameters ] . ( 41 sec) [ -8963.6948] [Alpha ][ 1.028829] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.694830. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23201.8309] [GTR parameters ] . ( 1 sec) [ -22738.1847] [Alpha ][ 0.500960] . ( 1 sec) [ -21967.1700] [ 4248] [depth= 8] . ( 1 sec) [ -21669.4483] [ 4220] [depth= 6] . ( 1 sec) [ -21608.9184] [ 4213] [depth= 5] . ( 1 sec) [ -21475.6560] [ 4199] [depth= 6] . ( 1 sec) [ -21230.2889] [ 4141] [depth= 4] . ( 1 sec) [ -21095.0396] [ 4132] [depth= 2] . ( 1 sec) [ -20886.3905] [ 4048] [depth= 17] . ( 1 sec) [ -20667.6497] [ 4018] [depth= 15] . ( 1 sec) [ -20428.1591] [ 3990] [depth= 1] . ( 1 sec) [ -20024.6711] [ 3847] [depth= 8] . ( 1 sec) [ -19670.0224] [ 3765] [depth= 11] . ( 2 sec) [ -19402.8144] [ 3719] [depth= 15] . ( 2 sec) [ -19347.6654] [ 3681] [depth= 2] . ( 2 sec) [ -19259.5783] [ 3669] [depth= 9] . ( 2 sec) [ -19035.1288] [ 3542] [depth= 4] . ( 2 sec) [ -18942.9411] [ 3531] [depth= 7] . ( 2 sec) [ -15088.9605] [ 3507] [depth= 1] . ( 2 sec) [ -14918.9150] [ 3473] [depth= 15] . ( 2 sec) [ -14853.9662] [ 3440] [depth= 2] . ( 2 sec) [ -14679.8893] [ 3394] [depth= 5] . ( 2 sec) [ -14492.6481] [ 3365] [depth= 4] . ( 2 sec) [ -14472.4399] [ 3359] [depth= 6] . ( 2 sec) [ -14402.2071] [ 3350] [depth= 7] . ( 2 sec) [ -14074.4968] [ 3249] [depth= 6] . ( 2 sec) [ -13799.2510] [ 3146] [depth= 13] . ( 2 sec) [ -13762.9090] [ 3148] [depth= 4] . ( 2 sec) [ -13498.0081] [ 3140] [depth= 12] . ( 2 sec) [ -13395.1390] [ 3139] [depth= 1] . ( 2 sec) [ -13391.0799] [ 3140] [depth= 2] . ( 2 sec) [ -13310.6257] [ 3090] [depth= 6] . ( 2 sec) [ -13247.5727] [ 3084] [depth= 7] . ( 2 sec) [ -13220.3676] [ 3085] [depth= 1] . ( 2 sec) [ -13060.5904] [ 3032] [depth= 8] . ( 2 sec) [ -12794.6622] [ 3028] [depth= 1] . ( 3 sec) [ -12613.5845] [ 2976] [depth= 4] . ( 3 sec) [ -12594.5326] [ 2938] [depth= 7] . ( 3 sec) [ -12367.4878] [ 2854] [depth= 10] . ( 3 sec) [ -12285.6280] [ 2838] [depth= 10] . ( 3 sec) [ -12208.1309] [ 2809] [depth= 8] . ( 3 sec) [ -12197.6870] [ 2811] [depth= 1] . ( 3 sec) [ -12195.5343] [ 2811] [depth= 1] . ( 3 sec) [ -12192.3952] [ 2809] [depth= 1] . ( 3 sec) [ -12009.9097] [ 2761] [depth= 9] . ( 3 sec) [ -11953.3324] [ 2752] [depth= 1] . ( 3 sec) [ -11937.4834] [ 2752] [depth= 1] . ( 3 sec) [ -11924.0625] [ 2747] [depth= 1] . ( 3 sec) [ -11905.6136] [ 2742] [depth= 2] . ( 3 sec) [ -11903.2269] [ 2743] [depth= 1] . ( 3 sec) [ -11811.5458] [ 2729] [depth= 5] . ( 3 sec) [ -11773.6361] [ 2673] [depth= 3] . ( 3 sec) [ -11696.9687] [ 2665] [depth= 1] . ( 3 sec) [ -11639.2181] [ 2648] [depth= 9] . ( 3 sec) [ -11587.4769] [ 2629] [depth= 6] . ( 3 sec) [ -11469.8724] [ 2593] [depth= 2] . ( 3 sec) [ -11396.8216] [ 2549] [depth= 2] . ( 4 sec) [ -11019.4470] [ 2519] [depth= 5] . ( 4 sec) [ -10963.0492] [ 2411] [depth= 8] . ( 4 sec) [ -10907.1290] [ 2412] [depth= 1] . ( 4 sec) [ -10904.9854] [ 2410] [depth= 1] . ( 4 sec) [ -10789.1673] [ 2367] [depth= 10] . ( 4 sec) [ -10721.4105] [ 2363] [depth= 2] . ( 4 sec) [ -10666.2936] [ 2360] [depth= 5] . ( 4 sec) [ -10663.8747] [ 2356] [depth= 1] . ( 4 sec) [ -10652.6214] [ 2356] [depth= 1] . ( 4 sec) [ -10504.0307] [ 2315] [depth= 10] . ( 4 sec) [ -10487.6640] [ 2315] [depth= 1] . ( 4 sec) [ -10257.4484] [ 2243] [depth= 4] . ( 4 sec) [ -10216.4213] [ 2237] [depth= 1] . ( 4 sec) [ -10198.9653] [ 2255] [depth= 1] . ( 4 sec) [ -10067.5582] [ 2193] [depth= 2] . ( 4 sec) [ -9881.3705] [ 2166] [depth= 2] . ( 4 sec) [ -9875.7580] [ 2172] [depth= 1] . ( 4 sec) [ -9868.0141] [ 2171] [depth= 1] . ( 4 sec) [ -9864.0745] [ 2168] [depth= 1] . ( 4 sec) [ -9831.8507] [ 2157] [depth= 1] . ( 4 sec) [ -9818.8183] [ 2150] [depth= 2] . ( 5 sec) [ -9784.5326] [ 2157] [depth= 2] . ( 5 sec) [ -9781.3955] [ 2158] [depth= 1] . ( 5 sec) [ -9602.9338] [ 2070] [depth= 4] . ( 5 sec) [ -9465.2492] [ 2016] [depth= 1] . ( 5 sec) [ -9464.6773] [ 2016] [depth= 1] . ( 5 sec) [ -9456.0222] [ 2018] [depth= 1] . ( 5 sec) [ -9341.3294] [Branch lengths ] . ( 6 sec) [ -9335.6454] [GTR parameters ] . ( 6 sec) [ -9305.2490] [Alpha ][ 0.877455] . ( 6 sec) [ -9305.2085] [ 2019] [depth= 2] . ( 6 sec) [ -9249.9448] [ 2005] [depth= 3] . ( 6 sec) [ -9243.4753] [ 1989] [depth= 1] . ( 6 sec) [ -9242.8949] [ 1989] [depth= 1] . ( 7 sec) [ -9241.6185] [ 1987] [depth= 1] . ( 7 sec) [ -9177.3780] [ 1978] [depth= 2] . ( 7 sec) [ -9176.2140] [ 1979] [depth= 1] . ( 7 sec) [ -9176.0544] [ 1982] [depth= 1] . ( 7 sec) [ -9176.0381] [ 1985] [depth= 1] . ( 7 sec) [ -9173.1223] [ 1990] [depth= 1] . ( 7 sec) [ -9162.7065] [ 1979] [depth= 1] . ( 7 sec) [ -9045.7746] [ 1993] [depth= 1] . ( 8 sec) [ -9030.7924] [ 1968] [depth= 2] . ( 8 sec) [ -9030.6609] [ 1968] [depth= 1] . ( 8 sec) [ -9027.8996] [ 1964] [depth= 2] . ( 8 sec) [ -9026.8427] [ 1953] [depth= 3] . ( 8 sec) [ -9017.0224] [ 1930] [depth= 4] . ( 8 sec) [ -8991.3292] [ 1916] [depth= 1] . ( 9 sec) [ -8989.7703] [ 1919] [depth= 1] . ( 9 sec) [ -8988.2430] [ 1921] [depth= 1] . ( 9 sec) [ -8987.2855] [ 1922] [depth= 1] . ( 9 sec) [ -8987.0184] [ 1921] [depth= 1] . ( 10 sec) [ -8968.8480] [Branch lengths ] . ( 10 sec) [ -8968.7349] [GTR parameters ] . ( 10 sec) [ -8967.0505] [Alpha ][ 1.010618] . ( 11 sec) [ -8966.9645] [ 1921] [depth= 1] . ( 11 sec) [ -8966.3415] [ 1916] [depth= 1] . ( 14 sec) [ -8964.8253] [Branch lengths ] . ( 14 sec) [ -8964.8210] [GTR parameters ] . ( 14 sec) [ -8964.8076] [Alpha ][ 1.023810] . ( 15 sec) [ -8964.7879] [ 1916] [depth= 1] . ( 17 sec) [ -8964.4350] [Branch lengths ] . ( 17 sec) [ -8964.4347] [GTR parameters ] . ( 17 sec) [ -8964.4344] [Alpha ][ 1.025715] . ( 23 sec) [ -8964.3303] [ 1913] [depth= 2] . ( 26 sec) [ -8964.2154] [ 1914] [depth= 1] . ( 29 sec) [ -8964.2002] [ 1915] [depth= 1] . ( 39 sec) [ -8964.0272] [Branch lengths ] . ( 39 sec) [ -8964.0261] [GTR parameters ] . ( 39 sec) [ -8964.0261] [Alpha ][ 1.025715] . ( 39 sec) [ -8964.0261] [Topology ] . ( 40 sec) [ -8964.0115] [Topology ] . ( 41 sec) [ -8964.0061] [Topology ] . ( 42 sec) [ -8964.0034] [Topology ] . ( 42 sec) [ -8964.0020] [Topology ] . ( 43 sec) [ -8964.0013] [Topology ] . ( 43 sec) [ -8964.0013] [GTR parameters ] . ( 43 sec) [ -8964.0012] [Alpha ][ 1.026741] . ( 43 sec) [ -8964.0012] [Topology ] . ( 44 sec) [ -8964.0008] [Topology ] . ( 44 sec) [ -8964.0008] [GTR parameters ] . ( 44 sec) [ -8964.0008] [Alpha ][ 1.026741] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -8963.7612] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -8963.7590] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.759006. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26473.6144] [GTR parameters ] . ( 1 sec) [ -26082.9832] [Alpha ][ 0.500960] . ( 1 sec) [ -25192.6137] [ 4063] [depth= 8] . ( 1 sec) [ -25034.8984] [ 4017] [depth= 5] . ( 1 sec) [ -24744.1448] [ 3935] [depth= 8] . ( 1 sec) [ -24603.1764] [ 3921] [depth= 1] . ( 1 sec) [ -24411.9721] [ 3875] [depth= 10] . ( 1 sec) [ -20704.5817] [ 3852] [depth= 3] . ( 1 sec) [ -20271.4807] [ 3846] [depth= 5] . ( 1 sec) [ -20128.1725] [ 3722] [depth= 3] . ( 1 sec) [ -19896.9240] [ 3716] [depth= 6] . ( 1 sec) [ -19685.3262] [ 3698] [depth= 11] . ( 1 sec) [ -19519.7705] [ 3665] [depth= 1] . ( 1 sec) [ -19408.8191] [ 3638] [depth= 2] . ( 1 sec) [ -19399.0976] [ 3636] [depth= 2] . ( 1 sec) [ -19322.0679] [ 3605] [depth= 11] . ( 1 sec) [ -19290.5355] [ 3603] [depth= 3] . ( 1 sec) [ -19169.7699] [ 3598] [depth= 2] . ( 1 sec) [ -19048.3798] [ 3582] [depth= 10] . ( 1 sec) [ -18858.7273] [ 3495] [depth= 12] . ( 1 sec) [ -18704.2372] [ 3461] [depth= 6] . ( 2 sec) [ -18687.1347] [ 3447] [depth= 1] . ( 2 sec) [ -18588.9351] [ 3429] [depth= 6] . ( 2 sec) [ -18306.4335] [ 3335] [depth= 11] . ( 2 sec) [ -18226.7346] [ 3340] [depth= 1] . ( 2 sec) [ -18131.7088] [ 3314] [depth= 2] . ( 2 sec) [ -18109.8944] [ 3278] [depth= 1] . ( 2 sec) [ -17935.9534] [ 3227] [depth= 14] . ( 2 sec) [ -17721.4096] [ 3185] [depth= 10] . ( 2 sec) [ -17618.9728] [ 3165] [depth= 9] . ( 2 sec) [ -17548.2344] [ 3162] [depth= 1] . ( 2 sec) [ -17002.5697] [ 3012] [depth= 10] . ( 2 sec) [ -16796.3515] [ 3019] [depth= 1] . ( 2 sec) [ -16777.0591] [ 3024] [depth= 1] . ( 2 sec) [ -16715.5155] [ 3012] [depth= 3] . ( 2 sec) [ -16669.3078] [ 3004] [depth= 8] . ( 2 sec) [ -16435.2681] [ 2942] [depth= 13] . ( 2 sec) [ -16424.9519] [ 2944] [depth= 2] . ( 2 sec) [ -16398.7621] [ 2917] [depth= 1] . ( 2 sec) [ -16109.2857] [ 2920] [depth= 4] . ( 2 sec) [ -16059.5356] [ 2912] [depth= 1] . ( 2 sec) [ -15983.2185] [ 2879] [depth= 1] . ( 2 sec) [ -15847.4940] [ 2811] [depth= 6] . ( 2 sec) [ -15655.5879] [ 2793] [depth= 10] . ( 3 sec) [ -15572.5333] [ 2778] [depth= 2] . ( 3 sec) [ -15455.5596] [ 2773] [depth= 4] . ( 3 sec) [ -11226.8189] [ 2722] [depth= 3] . ( 3 sec) [ -11210.4962] [ 2713] [depth= 1] . ( 3 sec) [ -10945.4174] [ 2635] [depth= 15] . ( 3 sec) [ -10923.2432] [ 2629] [depth= 1] . ( 3 sec) [ -10921.6832] [ 2571] [depth= 2] . ( 3 sec) [ -10785.9941] [ 2500] [depth= 4] . ( 3 sec) [ -10755.3152] [ 2490] [depth= 3] . ( 3 sec) [ -10621.6807] [ 2483] [depth= 2] . ( 3 sec) [ -10543.9266] [ 2446] [depth= 2] . ( 3 sec) [ -10380.8717] [ 2382] [depth= 9] . ( 3 sec) [ -10371.5945] [ 2375] [depth= 1] . ( 3 sec) [ -10334.7700] [ 2344] [depth= 1] . ( 3 sec) [ -10330.7851] [ 2348] [depth= 1] . ( 3 sec) [ -10180.3928] [ 2333] [depth= 9] . ( 3 sec) [ -10177.2097] [ 2330] [depth= 1] . ( 3 sec) [ -10126.4229] [ 2299] [depth= 1] . ( 3 sec) [ -10114.5684] [ 2302] [depth= 1] . ( 3 sec) [ -9976.4623] [ 2257] [depth= 8] . ( 3 sec) [ -9932.1826] [ 2236] [depth= 4] . ( 4 sec) [ -9931.8071] [ 2254] [depth= 4] . ( 4 sec) [ -9839.0165] [ 2227] [depth= 6] . ( 4 sec) [ -9838.4847] [ 2226] [depth= 1] . ( 4 sec) [ -9780.5101] [ 2199] [depth= 2] . ( 4 sec) [ -9767.1335] [ 2193] [depth= 1] . ( 4 sec) [ -9757.7716] [ 2184] [depth= 4] . ( 4 sec) [ -9720.2609] [ 2151] [depth= 4] . ( 4 sec) [ -9676.3759] [ 2133] [depth= 1] . ( 4 sec) [ -9676.1538] [ 2136] [depth= 1] . ( 4 sec) [ -9631.0278] [ 2109] [depth= 4] . ( 4 sec) [ -9603.9844] [ 2109] [depth= 3] . ( 4 sec) [ -9590.7418] [ 2118] [depth= 1] . ( 4 sec) [ -9586.7916] [ 2117] [depth= 1] . ( 4 sec) [ -9585.1786] [ 2121] [depth= 1] . ( 4 sec) [ -9366.9208] [ 2049] [depth= 3] . ( 4 sec) [ -9356.8285] [ 2041] [depth= 1] . ( 5 sec) [ -9356.7400] [ 2041] [depth= 1] . ( 5 sec) [ -9343.0613] [ 2028] [depth= 2] . ( 5 sec) [ -9341.2677] [ 2024] [depth= 1] . ( 5 sec) [ -9289.8104] [ 2006] [depth= 2] . ( 5 sec) [ -9187.6036] [Branch lengths ] . ( 6 sec) [ -9185.5481] [GTR parameters ] . ( 6 sec) [ -9150.4787] [Alpha ][ 0.930986] . ( 6 sec) [ -9149.7565] [ 2005] [depth= 1] . ( 6 sec) [ -9149.1837] [ 2006] [depth= 1] . ( 6 sec) [ -9128.7795] [ 1995] [depth= 1] . ( 6 sec) [ -9126.1759] [ 1993] [depth= 1] . ( 6 sec) [ -9038.5596] [ 1934] [depth= 3] . ( 6 sec) [ -9016.4174] [ 1919] [depth= 2] . ( 6 sec) [ -9006.3750] [ 1919] [depth= 3] . ( 6 sec) [ -8989.6857] [ 1920] [depth= 1] . ( 7 sec) [ -8989.5831] [ 1919] [depth= 1] . ( 7 sec) [ -8982.4037] [ 1917] [depth= 1] . ( 7 sec) [ -8979.6718] [ 1917] [depth= 1] . ( 7 sec) [ -8979.2052] [ 1913] [depth= 1] . ( 7 sec) [ -8978.5289] [ 1917] [depth= 1] . ( 8 sec) [ -8977.9485] [ 1917] [depth= 1] . ( 8 sec) [ -8975.9490] [ 1915] [depth= 1] . ( 9 sec) [ -8975.2733] [ 1917] [depth= 2] . ( 9 sec) [ -8967.1171] [Branch lengths ] . ( 9 sec) [ -8967.0395] [GTR parameters ] . ( 9 sec) [ -8966.4244] [Alpha ][ 1.014406] . ( 10 sec) [ -8966.2371] [ 1916] [depth= 1] . ( 10 sec) [ -8966.0292] [ 1916] [depth= 1] . ( 13 sec) [ -8964.7077] [Branch lengths ] . ( 13 sec) [ -8964.7066] [GTR parameters ] . ( 13 sec) [ -8964.7014] [Alpha ][ 1.022540] . ( 16 sec) [ -8964.4245] [Branch lengths ] . ( 17 sec) [ -8964.3531] [ 1913] [depth= 2] . ( 17 sec) [ -8964.1918] [ 1915] [depth= 1] . ( 23 sec) [ -8964.1577] [ 1914] [depth= 1] . ( 38 sec) [ -8963.9908] [Branch lengths ] . ( 38 sec) [ -8963.9896] [GTR parameters ] . ( 38 sec) [ -8963.9883] [Alpha ][ 1.026579] . ( 38 sec) [ -8963.9883] [Topology ] . ( 39 sec) [ -8963.9729] [Topology ] . ( 40 sec) [ -8963.9674] [Topology ] . ( 41 sec) [ -8963.9647] [Topology ] . ( 41 sec) [ -8963.9633] [Topology ] . ( 42 sec) [ -8963.9625] [Topology ] . ( 42 sec) [ -8963.9625] [GTR parameters ] . ( 42 sec) [ -8963.9625] [Alpha ][ 1.027605] . ( 42 sec) [ -8963.9625] [Topology ] . ( 43 sec) [ -8963.9621] [Topology ] . ( 43 sec) [ -8963.9621] [GTR parameters ] . ( 43 sec) [ -8963.9621] [Alpha ][ 1.027605] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -8963.7204] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.720377. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20654.6064] [GTR parameters ] . ( 1 sec) [ -20209.9333] [Alpha ][ 0.500960] . ( 1 sec) [ -19354.1760] [ 4170] [depth= 6] . ( 1 sec) [ -19201.3103] [ 4130] [depth= 12] . ( 1 sec) [ -19117.5529] [ 4117] [depth= 3] . ( 2 sec) [ -19009.2185] [ 4109] [depth= 6] . ( 2 sec) [ -18844.5471] [ 4070] [depth= 1] . ( 2 sec) [ -18807.8946] [ 4060] [depth= 1] . ( 2 sec) [ -18750.3375] [ 4041] [depth= 6] . ( 2 sec) [ -18547.9971] [ 3968] [depth= 1] . ( 2 sec) [ -18218.9656] [ 3917] [depth= 17] . ( 2 sec) [ -17890.8035] [ 3824] [depth= 18] . ( 2 sec) [ -17423.8061] [ 3745] [depth= 15] . ( 2 sec) [ -17246.3054] [ 3741] [depth= 1] . ( 2 sec) [ -17191.9780] [ 3720] [depth= 2] . ( 2 sec) [ -17083.5759] [ 3724] [depth= 1] . ( 2 sec) [ -16249.5010] [ 3717] [depth= 10] . ( 2 sec) [ -15241.9818] [ 3622] [depth= 3] . ( 2 sec) [ -15169.7134] [ 3617] [depth= 11] . ( 2 sec) [ -14873.7447] [ 3545] [depth= 10] . ( 2 sec) [ -14765.9883] [ 3546] [depth= 1] . ( 2 sec) [ -14460.5698] [ 3525] [depth= 8] . ( 2 sec) [ -14334.1697] [ 3472] [depth= 3] . ( 2 sec) [ -14266.1436] [ 3454] [depth= 1] . ( 2 sec) [ -13977.9180] [ 3444] [depth= 5] . ( 2 sec) [ -13933.8690] [ 3446] [depth= 1] . ( 2 sec) [ -13781.9267] [ 3367] [depth= 9] . ( 2 sec) [ -13661.6796] [ 3314] [depth= 5] . ( 2 sec) [ -13650.7028] [ 3311] [depth= 1] . ( 3 sec) [ -13439.5204] [ 3233] [depth= 6] . ( 3 sec) [ -13141.1957] [ 3163] [depth= 11] . ( 3 sec) [ -13020.8502] [ 3083] [depth= 8] . ( 3 sec) [ -12823.1232] [ 3031] [depth= 2] . ( 3 sec) [ -12343.5932] [ 2952] [depth= 10] . ( 3 sec) [ -12314.6229] [ 2984] [depth= 1] . ( 3 sec) [ -12037.6472] [ 2904] [depth= 8] . ( 3 sec) [ -11992.5399] [ 2878] [depth= 1] . ( 3 sec) [ -11968.8983] [ 2871] [depth= 2] . ( 3 sec) [ -11887.6412] [ 2833] [depth= 4] . ( 3 sec) [ -11733.0664] [ 2771] [depth= 11] . ( 3 sec) [ -11685.5950] [ 2771] [depth= 1] . ( 3 sec) [ -11660.9448] [ 2766] [depth= 1] . ( 3 sec) [ -11567.1499] [ 2722] [depth= 8] . ( 3 sec) [ -11535.1538] [ 2720] [depth= 2] . ( 3 sec) [ -11319.6967] [ 2627] [depth= 11] . ( 3 sec) [ -11318.4873] [ 2603] [depth= 1] . ( 3 sec) [ -11198.9831] [ 2573] [depth= 10] . ( 3 sec) [ -11140.6388] [ 2561] [depth= 6] . ( 3 sec) [ -11093.6934] [ 2550] [depth= 2] . ( 3 sec) [ -11029.3709] [ 2529] [depth= 1] . ( 3 sec) [ -11015.8975] [ 2523] [depth= 7] . ( 4 sec) [ -10745.1846] [ 2470] [depth= 5] . ( 4 sec) [ -10744.0818] [ 2437] [depth= 3] . ( 4 sec) [ -10685.7844] [ 2428] [depth= 2] . ( 4 sec) [ -10679.1268] [ 2465] [depth= 1] . ( 4 sec) [ -10586.8867] [ 2433] [depth= 6] . ( 4 sec) [ -10529.7448] [ 2429] [depth= 5] . ( 4 sec) [ -10372.6709] [ 2373] [depth= 6] . ( 4 sec) [ -10364.2591] [ 2378] [depth= 1] . ( 4 sec) [ -10218.9668] [ 2347] [depth= 10] . ( 4 sec) [ -10208.2981] [ 2351] [depth= 1] . ( 4 sec) [ -10203.6184] [ 2345] [depth= 1] . ( 4 sec) [ -10075.1903] [ 2289] [depth= 8] . ( 4 sec) [ -9855.0424] [ 2190] [depth= 5] . ( 4 sec) [ -9848.9287] [ 2196] [depth= 1] . ( 4 sec) [ -9785.3420] [ 2179] [depth= 1] . ( 4 sec) [ -9741.3151] [ 2165] [depth= 1] . ( 4 sec) [ -9736.9770] [ 2164] [depth= 1] . ( 4 sec) [ -9715.1823] [ 2156] [depth= 1] . ( 4 sec) [ -9689.2022] [ 2144] [depth= 2] . ( 5 sec) [ -9606.2571] [ 2140] [depth= 1] . ( 5 sec) [ -9545.7089] [ 2140] [depth= 1] . ( 5 sec) [ -9489.7787] [ 2119] [depth= 2] . ( 5 sec) [ -9470.3900] [ 2120] [depth= 2] . ( 5 sec) [ -9469.7430] [ 2118] [depth= 1] . ( 5 sec) [ -9455.1105] [ 2112] [depth= 1] . ( 5 sec) [ -9452.1824] [ 2112] [depth= 1] . ( 5 sec) [ -9447.8539] [ 2110] [depth= 1] . ( 5 sec) [ -9383.6943] [Branch lengths ] . ( 6 sec) [ -9383.0882] [GTR parameters ] . ( 6 sec) [ -9351.6530] [Alpha ][ 0.887148] . ( 6 sec) [ -9348.2759] [ 2106] [depth= 1] . ( 6 sec) [ -9348.1875] [ 2108] [depth= 1] . ( 6 sec) [ -9223.7509] [ 2018] [depth= 5] . ( 6 sec) [ -9201.2455] [ 2019] [depth= 1] . ( 6 sec) [ -9163.5227] [ 1988] [depth= 3] . ( 7 sec) [ -9161.2038] [ 1988] [depth= 1] . ( 7 sec) [ -9160.8558] [ 1988] [depth= 1] . ( 7 sec) [ -9158.8156] [ 1985] [depth= 1] . ( 7 sec) [ -9149.0723] [ 1979] [depth= 1] . ( 8 sec) [ -9105.0235] [ 1934] [depth= 2] . ( 8 sec) [ -9068.4976] [ 1929] [depth= 2] . ( 8 sec) [ -9010.1631] [ 1918] [depth= 2] . ( 8 sec) [ -9009.9552] [ 1918] [depth= 1] . ( 8 sec) [ -9009.5216] [ 1922] [depth= 1] . ( 8 sec) [ -9009.2963] [ 1920] [depth= 1] . ( 8 sec) [ -9001.5220] [ 1918] [depth= 1] . ( 8 sec) [ -9000.9454] [ 1918] [depth= 1] . ( 9 sec) [ -8997.3422] [ 1920] [depth= 1] . ( 9 sec) [ -8996.0673] [ 1915] [depth= 2] . ( 9 sec) [ -8987.9825] [ 1912] [depth= 1] . ( 9 sec) [ -8987.9349] [ 1912] [depth= 2] . ( 9 sec) [ -8986.4052] [ 1914] [depth= 1] . ( 9 sec) [ -8986.0731] [ 1915] [depth= 1] . ( 9 sec) [ -8982.3724] [ 1914] [depth= 1] . ( 10 sec) [ -8968.6519] [Branch lengths ] . ( 10 sec) [ -8968.1875] [GTR parameters ] . ( 10 sec) [ -8966.7535] [Alpha ][ 1.011301] . ( 10 sec) [ -8966.6902] [ 1913] [depth= 2] . ( 10 sec) [ -8966.1260] [ 1910] [depth= 1] . ( 13 sec) [ -8965.8409] [ 1912] [depth= 1] . ( 13 sec) [ -8964.0592] [Branch lengths ] . ( 14 sec) [ -8964.0570] [GTR parameters ] . ( 14 sec) [ -8964.0448] [Alpha ][ 1.023882] . ( 17 sec) [ -8964.0298] [ 1910] [depth= 1] . ( 17 sec) [ -8963.7613] [Branch lengths ] . ( 17 sec) [ -8963.7608] [GTR parameters ] . ( 17 sec) [ -8963.7600] [Alpha ][ 1.026971] . ( 39 sec) [ -8963.7097] [Branch lengths ] . ( 39 sec) [ -8963.7097] [Topology ] . ( 40 sec) [ -8963.7015] [Topology ] . ( 41 sec) [ -8963.6983] [Topology ] . ( 42 sec) [ -8963.6967] [Topology ] . ( 42 sec) [ -8963.6958] [Topology ] . ( 43 sec) [ -8963.6958] [GTR parameters ] . ( 43 sec) [ -8963.6956] [Alpha ][ 1.028310] . ( 43 sec) [ -8963.6956] [Topology ] . ( 43 sec) [ -8963.6952] [Topology ] . ( 44 sec) [ -8963.6952] [GTR parameters ] . ( 44 sec) [ -8963.6952] [Alpha ][ 1.028310] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8963.695173. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9047.095058 . ( 0 sec) [ -9041.3256] [GTR parameters ] . ( 0 sec) [ -9041.2523] [Alpha ][ 0.970005] . ( 0 sec) [ -9041.2523] [Topology ] . ( 1 sec) [ -8996.4322] [Topology ] . ( 2 sec) [ -8988.7327] [Topology ] . ( 3 sec) [ -8970.9581] [Topology ] . ( 3 sec) [ -8965.6059] [Topology ] . ( 4 sec) [ -8964.7395] [Topology ] . ( 5 sec) [ -8964.4999] [Topology ] . ( 6 sec) [ -8964.4081] [Topology ] . ( 6 sec) [ -8964.3656] [Topology ] . ( 7 sec) [ -8964.3441] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -8964.0843] [Topology ] . Before opt ts/t=1.000000 LK=-8964.084298 . ( 14 sec) [ -8964.0076] [GTR parameters ] . ( 14 sec) [ -8963.7412] [Alpha ][ 1.026015] . ( 14 sec) [ -8963.7412] [Topology ] . ( 15 sec) [ -8963.7104] [Topology ] . ( 15 sec) [ -8963.7021] [Topology ] . ( 16 sec) [ -8963.6987] [Topology ] . ( 17 sec) [ -8963.6971] [Topology ] . ( 18 sec) [ -8963.6963] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.696322 . ( 23 sec) [ -8963.6956] [GTR parameters ] . ( 23 sec) [ -8963.6952] [Alpha ][ 1.028310] . ( 23 sec) [ -8963.6952] [Topology ] . ( 24 sec) [ -8963.6948] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.694758 . ( 30 sec) [ -8963.6948] [GTR parameters ] . ( 30 sec) [ -8963.6948] [Alpha ][ 1.028310] . ( 30 sec) [ -8963.6948] [Topology ] . ( 31 sec) [ -8963.6945] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -9041.3256] [GTR parameters ] . ( 42 sec) [ -9041.2523] [Alpha ][ 0.970005] . ( 42 sec) [ -9041.1947] [ 1929] [depth= 1] . ( 42 sec) [ -9040.9304] [ 1932] [depth= 1] . ( 43 sec) [ -9016.4106] [ 1924] [depth= 3] . ( 43 sec) [ -9015.0278] [ 1922] [depth= 2] . ( 43 sec) [ -9014.4302] [ 1926] [depth= 1] . ( 43 sec) [ -9013.9366] [ 1922] [depth= 1] . ( 43 sec) [ -9013.8608] [ 1924] [depth= 2] . ( 43 sec) [ -9012.5102] [ 1922] [depth= 1] . ( 43 sec) [ -9012.1884] [ 1924] [depth= 1] . ( 43 sec) [ -9009.4524] [ 1924] [depth= 1] . ( 43 sec) [ -9009.2256] [ 1923] [depth= 1] . ( 43 sec) [ -9007.0731] [ 1924] [depth= 1] . ( 43 sec) [ -9005.5487] [ 1924] [depth= 1] . ( 44 sec) [ -9002.1786] [ 1922] [depth= 1] . ( 44 sec) [ -8999.7411] [ 1922] [depth= 1] . ( 44 sec) [ -8999.7100] [ 1927] [depth= 1] . ( 44 sec) [ -8998.1731] [ 1928] [depth= 1] . ( 44 sec) [ -8997.9680] [ 1922] [depth= 2] . ( 44 sec) [ -8993.5245] [ 1918] [depth= 1] . ( 44 sec) [ -8992.0611] [ 1923] [depth= 1] . ( 44 sec) [ -8991.6815] [ 1918] [depth= 1] . ( 45 sec) [ -8969.9836] [Branch lengths ] . ( 46 sec) [ -8969.8936] [GTR parameters ] . ( 46 sec) [ -8969.7414] [Alpha ][ 1.012304] . ( 46 sec) [ -8968.6087] [ 1914] [depth= 1] . ( 46 sec) [ -8967.5179] [ 1912] [depth= 1] . ( 46 sec) [ -8967.3678] [ 1912] [depth= 1] . ( 49 sec) [ -8964.6489] [Branch lengths ] . ( 49 sec) [ -8964.6273] [GTR parameters ] . ( 49 sec) [ -8964.6064] [Alpha ][ 1.028833] . ( 50 sec) [ -8964.5824] [ 1913] [depth= 1] . ( 53 sec) [ -8964.3557] [Branch lengths ] . ( 53 sec) [ -8964.3554] [GTR parameters ] . ( 53 sec) [ -8964.3554] [Alpha ][ 1.028833] . ( 75 sec) [ -8964.3272] [Branch lengths ] . ( 75 sec) [ -8964.3272] [Topology ] . ( 75 sec) [ -8964.1244] [Topology ] . ( 76 sec) [ -8964.0823] [Topology ] . ( 77 sec) [ -8964.0739] [Topology ] . ( 78 sec) [ -8964.0716] [Topology ] . ( 79 sec) [ -8964.0708] [Topology ] . ( 79 sec) [ -8964.0693] [GTR parameters ] . ( 79 sec) [ -8964.0693] [Alpha ][ 1.027777] . ( 79 sec) [ -8964.0693] [Topology ] . ( 80 sec) [ -8964.0690] [Topology ] . ( 80 sec) [ -8964.0690] [GTR parameters ] . ( 80 sec) [ -8964.0690] [Alpha ][ 1.027777] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8963.694528 . Log likelihood obtained after SPR moves : -8964.068967 . Log likelihood of the current tree: -8963.694528. . Printing the most likely tree in file 'data68.phy_phyml_tree.txt'... . Best log likelihood : -8963.694528 . Time used 0h1m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo