.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data4.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... . 431 patterns found. (out of a total of 500 sites) . 63 sites without polymorphism (12.60%). . [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)... . ( 0 sec) [ -16418.0257] [GTR parameters ] . ( 0 sec) [ -16237.9678] [Alpha ][ 0.500960] . ( 0 sec) [ -15787.2762] [ 3344] [depth= 5] . ( 0 sec) [ -15352.6705] [ 3290] [depth= 8] . ( 0 sec) [ -15008.6486] [ 3276] [depth= 6] . ( 1 sec) [ -14841.3014] [ 3266] [depth= 2] . ( 1 sec) [ -14751.4005] [ 3200] [depth= 2] . ( 1 sec) [ -14646.4465] [ 3188] [depth= 7] . ( 1 sec) [ -14558.0774] [ 3155] [depth= 7] . ( 1 sec) [ -14259.5208] [ 3149] [depth= 10] . ( 1 sec) [ -14090.0191] [ 3092] [depth= 5] . ( 1 sec) [ -13996.0406] [ 3043] [depth= 1] . ( 1 sec) [ -13901.4146] [ 3035] [depth= 8] . ( 1 sec) [ -13755.3749] [ 3042] [depth= 18] . ( 1 sec) [ -13594.0249] [ 3035] [depth= 5] . ( 1 sec) [ -13534.7263] [ 3028] [depth= 3] . ( 1 sec) [ -13462.5594] [ 2992] [depth= 3] . ( 1 sec) [ -13386.9320] [ 2984] [depth= 4] . ( 1 sec) [ -13344.2061] [ 2980] [depth= 3] . ( 1 sec) [ -13312.0065] [ 2968] [depth= 1] . ( 1 sec) [ -13129.9874] [ 2924] [depth= 10] . ( 1 sec) [ -13052.7609] [ 2919] [depth= 1] . ( 1 sec) [ -12886.7475] [ 2877] [depth= 9] . ( 1 sec) [ -12771.2248] [ 2864] [depth= 6] . ( 1 sec) [ -12705.2859] [ 2814] [depth= 5] . ( 1 sec) [ -12546.1882] [ 2769] [depth= 4] . ( 1 sec) [ -12446.2237] [ 2732] [depth= 12] . ( 2 sec) [ -12384.3753] [ 2706] [depth= 4] . ( 2 sec) [ -12159.9192] [ 2659] [depth= 6] . ( 2 sec) [ -12073.4827] [ 2648] [depth= 1] . ( 2 sec) [ -11861.6038] [ 2586] [depth= 4] . ( 2 sec) [ -11842.6466] [ 2598] [depth= 1] . ( 2 sec) [ -11832.3108] [ 2586] [depth= 1] . ( 2 sec) [ -11707.5657] [ 2535] [depth= 4] . ( 2 sec) [ -11612.3202] [ 2520] [depth= 3] . ( 2 sec) [ -11305.4739] [ 2512] [depth= 1] . ( 2 sec) [ -11204.0951] [ 2492] [depth= 12] . ( 2 sec) [ -11187.5391] [ 2524] [depth= 1] . ( 2 sec) [ -11065.4697] [ 2441] [depth= 4] . ( 2 sec) [ -10904.3815] [ 2405] [depth= 9] . ( 2 sec) [ -10878.8136] [ 2401] [depth= 7] . ( 2 sec) [ -10845.9043] [ 2401] [depth= 1] . ( 2 sec) [ -10845.2899] [ 2401] [depth= 2] . ( 2 sec) [ -10843.5451] [ 2399] [depth= 1] . ( 2 sec) [ -10802.3948] [ 2370] [depth= 10] . ( 2 sec) [ -10794.8808] [ 2369] [depth= 3] . ( 3 sec) [ -10785.4074] [ 2365] [depth= 1] . ( 3 sec) [ -10779.7595] [ 2370] [depth= 3] . ( 3 sec) [ -10670.3713] [ 2372] [depth= 6] . ( 3 sec) [ -10617.6618] [ 2326] [depth= 9] . ( 3 sec) [ -10608.7724] [ 2318] [depth= 1] . ( 3 sec) [ -10424.5928] [ 2317] [depth= 1] . ( 3 sec) [ -10418.0635] [ 2329] [depth= 1] . ( 3 sec) [ -10381.6438] [ 2328] [depth= 10] . ( 3 sec) [ -10368.7820] [ 2319] [depth= 1] . ( 3 sec) [ -10321.6546] [ 2304] [depth= 2] . ( 3 sec) [ -10232.2989] [ 2285] [depth= 4] . ( 3 sec) [ -10164.4664] [ 2262] [depth= 8] . ( 3 sec) [ -10130.7908] [ 2260] [depth= 5] . ( 3 sec) [ -10107.3660] [ 2262] [depth= 1] . ( 3 sec) [ -10040.5708] [ 2244] [depth= 2] . ( 3 sec) [ -10036.7119] [ 2244] [depth= 1] . ( 3 sec) [ -10034.4615] [ 2246] [depth= 1] . ( 4 sec) [ -9935.2281] [ 2202] [depth= 10] . ( 4 sec) [ -9884.0832] [ 2162] [depth= 6] . ( 4 sec) [ -9816.7167] [ 2154] [depth= 6] . ( 4 sec) [ -9611.0384] [ 2086] [depth= 4] . ( 4 sec) [ -9536.5041] [ 2076] [depth= 2] . ( 4 sec) [ -9486.7629] [ 2054] [depth= 2] . ( 4 sec) [ -9380.3290] [ 2020] [depth= 1] . ( 4 sec) [ -9372.9297] [ 2017] [depth= 1] . ( 4 sec) [ -9362.9796] [ 2013] [depth= 1] . ( 4 sec) [ -9356.4514] [ 2012] [depth= 3] . ( 4 sec) [ -9299.3159] [ 1984] [depth= 2] . ( 4 sec) [ -9291.3347] [ 1982] [depth= 1] . ( 5 sec) [ -9133.5043] [Branch lengths ] . ( 5 sec) [ -9133.3725] [GTR parameters ] . ( 5 sec) [ -9087.0826] [Alpha ][ 1.000683] . ( 5 sec) [ -9086.2918] [ 1977] [depth= 1] . ( 5 sec) [ -9086.2501] [ 1979] [depth= 1] . ( 6 sec) [ -9076.3855] [ 1970] [depth= 2] . ( 6 sec) [ -9073.2568] [ 1972] [depth= 3] . ( 6 sec) [ -9048.9357] [ 1963] [depth= 1] . ( 6 sec) [ -9047.8391] [ 1964] [depth= 1] . ( 6 sec) [ -9045.4457] [ 1963] [depth= 2] . ( 7 sec) [ -9040.9713] [ 1959] [depth= 2] . ( 7 sec) [ -9040.0167] [ 1959] [depth= 1] . ( 7 sec) [ -9036.7836] [ 1958] [depth= 1] . ( 7 sec) [ -9036.6627] [ 1961] [depth= 1] . ( 7 sec) [ -9036.2268] [ 1960] [depth= 1] . ( 9 sec) [ -9029.4342] [Branch lengths ] . ( 10 sec) [ -9029.1799] [GTR parameters ] . ( 10 sec) [ -9029.0246] [Alpha ][ 1.043207] . ( 11 sec) [ -9028.9504] [ 1959] [depth= 1] . ( 14 sec) [ -9028.4319] [Branch lengths ] . ( 14 sec) [ -9028.4312] [GTR parameters ] . ( 14 sec) [ -9028.4302] [Alpha ][ 1.046660] . ( 40 sec) [ -9028.3777] [Branch lengths ] . ( 40 sec) [ -9028.3777] [Topology ] . ( 41 sec) [ -9028.3731] [Topology ] . ( 42 sec) [ -9028.3714] [Topology ] . ( 43 sec) [ -9028.3707] [Topology ] . ( 43 sec) [ -9028.3706] [GTR parameters ] . ( 43 sec) [ -9028.3706] [Alpha ][ 1.046660] . ( 43 sec) [ -9028.3706] [Topology ] . ( 44 sec) [ -9028.3703] [Topology ] . ( 44 sec) [ -9028.3703] [GTR parameters ] . ( 44 sec) [ -9028.3703] [Alpha ][ 1.046660] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9028.370280. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15683.0768] [GTR parameters ] . ( 1 sec) [ -15508.8606] [Alpha ][ 0.500960] . ( 1 sec) [ -15507.5546] [ 3302] [depth= 2] . ( 2 sec) [ -15288.5687] [ 3244] [depth= 5] . ( 2 sec) [ -15271.5531] [ 3235] [depth= 3] . ( 2 sec) [ -15233.1920] [ 3234] [depth= 1] . ( 2 sec) [ -15131.3158] [ 3184] [depth= 1] . ( 2 sec) [ -14984.3616] [ 3171] [depth= 6] . ( 2 sec) [ -14901.0269] [ 3121] [depth= 2] . ( 2 sec) [ -14794.4397] [ 3121] [depth= 6] . ( 2 sec) [ -14743.0918] [ 3127] [depth= 4] . ( 2 sec) [ -14732.5134] [ 3122] [depth= 2] . ( 2 sec) [ -14637.5037] [ 3109] [depth= 5] . ( 2 sec) [ -14581.8753] [ 3106] [depth= 7] . ( 2 sec) [ -14414.1356] [ 3075] [depth= 3] . ( 2 sec) [ -14332.1277] [ 3072] [depth= 2] . ( 2 sec) [ -14252.9289] [ 3045] [depth= 4] . ( 2 sec) [ -14213.6226] [ 3025] [depth= 11] . ( 2 sec) [ -14144.9519] [ 3018] [depth= 9] . ( 2 sec) [ -14045.0550] [ 3011] [depth= 4] . ( 2 sec) [ -13953.7965] [ 3019] [depth= 1] . ( 2 sec) [ -13926.2813] [ 3013] [depth= 8] . ( 2 sec) [ -13568.6351] [ 2948] [depth= 5] . ( 2 sec) [ -13334.8057] [ 2902] [depth= 8] . ( 2 sec) [ -13269.7015] [ 2894] [depth= 7] . ( 2 sec) [ -13138.3296] [ 2881] [depth= 4] . ( 2 sec) [ -13005.9778] [ 2867] [depth= 9] . ( 3 sec) [ -12982.6481] [ 2871] [depth= 1] . ( 3 sec) [ -12726.2795] [ 2831] [depth= 6] . ( 3 sec) [ -12439.8834] [ 2786] [depth= 4] . ( 3 sec) [ -12263.2057] [ 2714] [depth= 9] . ( 3 sec) [ -12090.1494] [ 2694] [depth= 3] . ( 3 sec) [ -11855.2716] [ 2598] [depth= 1] . ( 3 sec) [ -11714.3868] [ 2565] [depth= 6] . ( 3 sec) [ -11619.8025] [ 2537] [depth= 14] . ( 3 sec) [ -11512.7572] [ 2527] [depth= 8] . ( 3 sec) [ -11182.5549] [ 2469] [depth= 11] . ( 3 sec) [ -10973.5284] [ 2446] [depth= 12] . ( 3 sec) [ -10908.0131] [ 2435] [depth= 9] . ( 3 sec) [ -10679.5387] [ 2420] [depth= 5] . ( 3 sec) [ -10587.1364] [ 2371] [depth= 4] . ( 3 sec) [ -10494.1095] [ 2345] [depth= 2] . ( 3 sec) [ -10492.1171] [ 2348] [depth= 1] . ( 3 sec) [ -10472.9707] [ 2330] [depth= 4] . ( 3 sec) [ -10454.7482] [ 2340] [depth= 1] . ( 3 sec) [ -10378.4616] [ 2321] [depth= 2] . ( 3 sec) [ -10186.0680] [ 2278] [depth= 4] . ( 4 sec) [ -10167.5732] [ 2276] [depth= 3] . ( 4 sec) [ -10158.4330] [ 2276] [depth= 3] . ( 4 sec) [ -10136.1907] [ 2262] [depth= 3] . ( 4 sec) [ -10111.6581] [ 2246] [depth= 2] . ( 4 sec) [ -10108.0705] [ 2240] [depth= 2] . ( 4 sec) [ -10092.6988] [ 2243] [depth= 2] . ( 4 sec) [ -10003.8033] [ 2207] [depth= 5] . ( 4 sec) [ -9984.6490] [ 2183] [depth= 1] . ( 4 sec) [ -9876.4575] [ 2150] [depth= 5] . ( 4 sec) [ -9690.8291] [ 2121] [depth= 1] . ( 4 sec) [ -9657.3183] [ 2121] [depth= 1] . ( 4 sec) [ -9655.9243] [ 2121] [depth= 1] . ( 4 sec) [ -9631.0279] [ 2106] [depth= 2] . ( 4 sec) [ -9613.2433] [ 2109] [depth= 1] . ( 4 sec) [ -9607.6009] [ 2106] [depth= 1] . ( 4 sec) [ -9575.3686] [ 2099] [depth= 1] . ( 4 sec) [ -9574.9344] [ 2113] [depth= 2] . ( 4 sec) [ -9574.7022] [ 2112] [depth= 1] . ( 4 sec) [ -9552.6870] [ 2108] [depth= 4] . ( 4 sec) [ -9545.0553] [ 2105] [depth= 1] . ( 4 sec) [ -9534.3175] [ 2106] [depth= 1] . ( 4 sec) [ -9520.9240] [ 2091] [depth= 3] . ( 5 sec) [ -9457.2967] [ 2066] [depth= 1] . ( 5 sec) [ -9429.8593] [ 2052] [depth= 1] . ( 5 sec) [ -9387.0080] [ 2046] [depth= 1] . ( 5 sec) [ -9378.6948] [ 2048] [depth= 1] . ( 5 sec) [ -9378.2376] [ 2046] [depth= 1] . ( 5 sec) [ -9376.7841] [ 2047] [depth= 1] . ( 5 sec) [ -9361.3159] [ 2044] [depth= 2] . ( 5 sec) [ -9360.8613] [ 2044] [depth= 2] . ( 5 sec) [ -9338.8871] [ 2034] [depth= 1] . ( 5 sec) [ -9338.1943] [ 2042] [depth= 1] . ( 6 sec) [ -9247.4710] [Branch lengths ] . ( 6 sec) [ -9246.3671] [GTR parameters ] . ( 6 sec) [ -9205.3892] [Alpha ][ 0.961616] . ( 6 sec) [ -9202.2327] [ 2041] [depth= 7] . ( 7 sec) [ -9201.3021] [ 2038] [depth= 6] . ( 7 sec) [ -9167.0036] [ 2026] [depth= 1] . ( 7 sec) [ -9166.9299] [ 2023] [depth= 1] . ( 7 sec) [ -9166.8470] [ 2028] [depth= 1] . ( 7 sec) [ -9166.0920] [ 2026] [depth= 1] . ( 7 sec) [ -9125.0663] [ 2006] [depth= 5] . ( 7 sec) [ -9124.0637] [ 2006] [depth= 1] . ( 7 sec) [ -9123.6244] [ 2007] [depth= 1] . ( 7 sec) [ -9121.0333] [ 2003] [depth= 1] . ( 7 sec) [ -9118.1827] [ 1999] [depth= 1] . ( 7 sec) [ -9108.2096] [ 1986] [depth= 1] . ( 7 sec) [ -9104.4184] [ 1984] [depth= 1] . ( 8 sec) [ -9103.1310] [ 1989] [depth= 1] . ( 8 sec) [ -9097.3473] [ 1980] [depth= 2] . ( 8 sec) [ -9088.1002] [ 1979] [depth= 1] . ( 8 sec) [ -9086.2626] [ 1981] [depth= 2] . ( 8 sec) [ -9086.2147] [ 1978] [depth= 1] . ( 8 sec) [ -9081.1809] [ 1976] [depth= 2] . ( 9 sec) [ -9080.9908] [ 1977] [depth= 1] . ( 9 sec) [ -9055.7877] [ 1967] [depth= 1] . ( 9 sec) [ -9055.4655] [ 1966] [depth= 1] . ( 9 sec) [ -9054.9402] [ 1967] [depth= 1] . ( 9 sec) [ -9049.3083] [ 1966] [depth= 1] . ( 10 sec) [ -9047.2565] [ 1966] [depth= 1] . ( 10 sec) [ -9032.3969] [Branch lengths ] . ( 11 sec) [ -9032.0859] [GTR parameters ] . ( 11 sec) [ -9031.5665] [Alpha ][ 1.037867] . ( 11 sec) [ -9031.5210] [ 1963] [depth= 1] . ( 11 sec) [ -9031.4646] [ 1968] [depth= 1] . ( 12 sec) [ -9031.4226] [ 1967] [depth= 1] . ( 14 sec) [ -9031.1015] [ 1971] [depth= 1] . ( 14 sec) [ -9028.6907] [Branch lengths ] . ( 15 sec) [ -9028.6834] [GTR parameters ] . ( 15 sec) [ -9028.6786] [Alpha ][ 1.045585] . ( 19 sec) [ -9028.4216] [Branch lengths ] . ( 45 sec) [ -9028.3829] [Branch lengths ] . ( 45 sec) [ -9028.3829] [Topology ] . ( 46 sec) [ -9028.3790] [Topology ] . ( 47 sec) [ -9028.3776] [Topology ] . ( 47 sec) [ -9028.3769] [Topology ] . ( 47 sec) [ -9028.3764] [GTR parameters ] . ( 48 sec) [ -9028.3764] [Alpha ][ 1.046630] . ( 48 sec) [ -9028.3764] [Topology ] . ( 48 sec) [ -9028.3761] [Topology ] . ( 48 sec) [ -9028.3760] [GTR parameters ] . ( 49 sec) [ -9028.3760] [Alpha ][ 1.046630] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -9028.3704] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9028.370368. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16036.5805] [GTR parameters ] . ( 1 sec) [ -15847.3145] [Alpha ][ 0.500960] . ( 1 sec) [ -15745.8942] [ 3425] [depth= 2] . ( 1 sec) [ -15369.9863] [ 3367] [depth= 9] . ( 1 sec) [ -15367.2276] [ 3365] [depth= 1] . ( 1 sec) [ -15363.5025] [ 3363] [depth= 3] . ( 1 sec) [ -15246.7958] [ 3320] [depth= 5] . ( 1 sec) [ -15063.4277] [ 3319] [depth= 1] . ( 1 sec) [ -14911.2744] [ 3264] [depth= 12] . ( 1 sec) [ -14890.2188] [ 3253] [depth= 12] . ( 1 sec) [ -14580.0121] [ 3227] [depth= 1] . ( 1 sec) [ -14194.0384] [ 3118] [depth= 17] . ( 1 sec) [ -13861.2193] [ 3055] [depth= 14] . ( 1 sec) [ -13656.9112] [ 3031] [depth= 7] . ( 1 sec) [ -13479.4869] [ 3024] [depth= 10] . ( 1 sec) [ -13330.1550] [ 3016] [depth= 1] . ( 1 sec) [ -13285.0517] [ 2996] [depth= 1] . ( 1 sec) [ -13267.4784] [ 2987] [depth= 4] . ( 1 sec) [ -13096.0423] [ 2950] [depth= 2] . ( 1 sec) [ -12940.0034] [ 2948] [depth= 16] . ( 2 sec) [ -12857.0157] [ 2904] [depth= 1] . ( 2 sec) [ -12712.3915] [ 2852] [depth= 1] . ( 2 sec) [ -12698.9522] [ 2848] [depth= 1] . ( 2 sec) [ -12630.5603] [ 2827] [depth= 15] . ( 2 sec) [ -12472.1657] [ 2780] [depth= 13] . ( 2 sec) [ -12450.1870] [ 2773] [depth= 1] . ( 2 sec) [ -12373.9217] [ 2759] [depth= 13] . ( 2 sec) [ -12372.2194] [ 2770] [depth= 9] . ( 2 sec) [ -12081.1703] [ 2712] [depth= 10] . ( 2 sec) [ -11977.6366] [ 2682] [depth= 9] . ( 2 sec) [ -11749.0952] [ 2646] [depth= 9] . ( 2 sec) [ -11703.7091] [ 2604] [depth= 4] . ( 2 sec) [ -11557.0920] [ 2566] [depth= 6] . ( 2 sec) [ -11311.1867] [ 2504] [depth= 9] . ( 2 sec) [ -11236.3169] [ 2487] [depth= 1] . ( 2 sec) [ -11213.7797] [ 2474] [depth= 1] . ( 2 sec) [ -11134.7949] [ 2467] [depth= 8] . ( 2 sec) [ -10968.9471] [ 2428] [depth= 4] . ( 2 sec) [ -10939.4910] [ 2420] [depth= 1] . ( 2 sec) [ -10934.3024] [ 2417] [depth= 1] . ( 3 sec) [ -10853.4978] [ 2382] [depth= 6] . ( 3 sec) [ -10833.3710] [ 2379] [depth= 2] . ( 3 sec) [ -10763.9616] [ 2372] [depth= 5] . ( 3 sec) [ -10698.6666] [ 2370] [depth= 3] . ( 3 sec) [ -10662.1178] [ 2369] [depth= 2] . ( 3 sec) [ -10658.5352] [ 2369] [depth= 1] . ( 3 sec) [ -10632.1590] [ 2369] [depth= 1] . ( 3 sec) [ -10533.3270] [ 2357] [depth= 3] . ( 3 sec) [ -10474.0463] [ 2323] [depth= 1] . ( 3 sec) [ -10387.5418] [ 2322] [depth= 4] . ( 3 sec) [ -10372.5284] [ 2318] [depth= 1] . ( 3 sec) [ -10320.5895] [ 2313] [depth= 5] . ( 3 sec) [ -10319.2920] [ 2311] [depth= 1] . ( 3 sec) [ -10311.1424] [ 2314] [depth= 1] . ( 3 sec) [ -10299.2249] [ 2300] [depth= 5] . ( 3 sec) [ -10241.7144] [ 2257] [depth= 5] . ( 3 sec) [ -10233.3865] [ 2254] [depth= 1] . ( 3 sec) [ -10178.7951] [ 2237] [depth= 3] . ( 4 sec) [ -10120.6601] [ 2229] [depth= 5] . ( 4 sec) [ -10112.8328] [ 2230] [depth= 1] . ( 4 sec) [ -10052.8384] [ 2225] [depth= 1] . ( 4 sec) [ -9842.3274] [ 2138] [depth= 4] . ( 4 sec) [ -9806.3831] [ 2129] [depth= 7] . ( 4 sec) [ -9803.7537] [ 2131] [depth= 1] . ( 4 sec) [ -9658.0464] [ 2083] [depth= 5] . ( 4 sec) [ -9586.4771] [ 2073] [depth= 7] . ( 4 sec) [ -9554.9137] [ 2066] [depth= 2] . ( 4 sec) [ -9505.9599] [ 2059] [depth= 2] . ( 4 sec) [ -9504.8936] [ 2056] [depth= 1] . ( 4 sec) [ -9500.3314] [ 2055] [depth= 2] . ( 5 sec) [ -9490.0309] [ 2052] [depth= 1] . ( 5 sec) [ -9487.4255] [ 2052] [depth= 1] . ( 5 sec) [ -9483.9642] [ 2054] [depth= 1] . ( 5 sec) [ -9437.8920] [ 2055] [depth= 1] . ( 5 sec) [ -9306.8369] [Branch lengths ] . ( 6 sec) [ -9306.3492] [GTR parameters ] . ( 6 sec) [ -9262.0141] [Alpha ][ 0.988231] . ( 6 sec) [ -9261.2669] [ 2051] [depth= 2] . ( 6 sec) [ -9230.3926] [ 2041] [depth= 4] . ( 6 sec) [ -9229.0102] [ 2040] [depth= 1] . ( 6 sec) [ -9223.5004] [ 2037] [depth= 2] . ( 6 sec) [ -9222.3290] [ 2042] [depth= 1] . ( 6 sec) [ -9217.7488] [ 2038] [depth= 1] . ( 6 sec) [ -9217.5564] [ 2038] [depth= 1] . ( 6 sec) [ -9204.0949] [ 2035] [depth= 2] . ( 7 sec) [ -9202.5714] [ 2034] [depth= 1] . ( 7 sec) [ -9197.9499] [ 2028] [depth= 1] . ( 7 sec) [ -9098.2980] [ 1986] [depth= 3] . ( 7 sec) [ -9097.7521] [ 1985] [depth= 1] . ( 7 sec) [ -9094.6656] [ 1980] [depth= 2] . ( 7 sec) [ -9093.7949] [ 1983] [depth= 1] . ( 7 sec) [ -9093.3274] [ 1984] [depth= 1] . ( 7 sec) [ -9090.4662] [ 1983] [depth= 2] . ( 8 sec) [ -9084.2503] [ 1980] [depth= 1] . ( 8 sec) [ -9063.0708] [ 1963] [depth= 3] . ( 8 sec) [ -9061.4300] [ 1963] [depth= 1] . ( 9 sec) [ -9050.9242] [ 1959] [depth= 1] . ( 9 sec) [ -9045.9316] [ 1961] [depth= 2] . ( 9 sec) [ -9042.7968] [ 1958] [depth= 1] . ( 9 sec) [ -9042.3381] [ 1960] [depth= 1] . ( 10 sec) [ -9030.4493] [Branch lengths ] . ( 10 sec) [ -9030.1785] [GTR parameters ] . ( 10 sec) [ -9029.9646] [Alpha ][ 1.038439] . ( 11 sec) [ -9029.7250] [ 1959] [depth= 1] . ( 14 sec) [ -9028.6962] [Branch lengths ] . ( 14 sec) [ -9028.6957] [GTR parameters ] . ( 14 sec) [ -9028.6898] [Alpha ][ 1.047112] . ( 19 sec) [ -9028.4373] [Branch lengths ] . ( 45 sec) [ -9028.3841] [Branch lengths ] . ( 45 sec) [ -9028.3841] [Topology ] . ( 45 sec) [ -9028.3768] [Topology ] . ( 46 sec) [ -9028.3740] [Topology ] . ( 47 sec) [ -9028.3725] [Topology ] . ( 48 sec) [ -9028.3716] [Topology ] . ( 48 sec) [ -9028.3713] [GTR parameters ] . ( 48 sec) [ -9028.3713] [Alpha ][ 1.047112] . ( 48 sec) [ -9028.3713] [Topology ] . ( 49 sec) [ -9028.3708] [Topology ] . ( 49 sec) [ -9028.3708] [GTR parameters ] . ( 49 sec) [ -9028.3708] [Alpha ][ 1.047112] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9028.370778. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15324.2731] [GTR parameters ] . ( 1 sec) [ -15163.1781] [Alpha ][ 0.500960] . ( 1 sec) [ -15153.1015] [ 3283] [depth= 11] . ( 1 sec) [ -14807.9217] [ 3237] [depth= 12] . ( 1 sec) [ -14635.3234] [ 3219] [depth= 7] . ( 1 sec) [ -14564.2271] [ 3161] [depth= 1] . ( 1 sec) [ -14458.6030] [ 3148] [depth= 8] . ( 2 sec) [ -14372.0891] [ 3147] [depth= 1] . ( 2 sec) [ -14226.6533] [ 3143] [depth= 5] . ( 2 sec) [ -13996.9786] [ 3118] [depth= 2] . ( 2 sec) [ -13942.0753] [ 3114] [depth= 3] . ( 2 sec) [ -13896.9269] [ 3112] [depth= 3] . ( 2 sec) [ -13852.2348] [ 3110] [depth= 4] . ( 2 sec) [ -13649.0788] [ 3043] [depth= 3] . ( 2 sec) [ -13576.0280] [ 3010] [depth= 5] . ( 2 sec) [ -13561.1901] [ 3010] [depth= 1] . ( 2 sec) [ -13494.7541] [ 3006] [depth= 1] . ( 2 sec) [ -13446.1153] [ 3006] [depth= 3] . ( 2 sec) [ -13355.2913] [ 2989] [depth= 4] . ( 2 sec) [ -13316.5615] [ 2970] [depth= 12] . ( 2 sec) [ -13182.2074] [ 2940] [depth= 3] . ( 2 sec) [ -13124.9357] [ 2930] [depth= 4] . ( 2 sec) [ -13110.7305] [ 2927] [depth= 1] . ( 2 sec) [ -13105.0222] [ 2930] [depth= 1] . ( 2 sec) [ -12948.8302] [ 2917] [depth= 17] . ( 2 sec) [ -12778.3587] [ 2871] [depth= 1] . ( 2 sec) [ -12691.5303] [ 2850] [depth= 12] . ( 2 sec) [ -12688.4295] [ 2848] [depth= 1] . ( 2 sec) [ -12428.7456] [ 2806] [depth= 13] . ( 3 sec) [ -12290.7236] [ 2771] [depth= 7] . ( 3 sec) [ -12137.9563] [ 2746] [depth= 8] . ( 3 sec) [ -12117.5638] [ 2719] [depth= 7] . ( 3 sec) [ -11666.2597] [ 2659] [depth= 4] . ( 3 sec) [ -11530.0304] [ 2609] [depth= 1] . ( 3 sec) [ -11438.9018] [ 2574] [depth= 7] . ( 3 sec) [ -11382.3876] [ 2548] [depth= 1] . ( 3 sec) [ -11299.7035] [ 2531] [depth= 8] . ( 3 sec) [ -11267.4155] [ 2518] [depth= 3] . ( 3 sec) [ -11154.6180] [ 2449] [depth= 8] . ( 3 sec) [ -11015.3018] [ 2445] [depth= 3] . ( 3 sec) [ -11001.6919] [ 2444] [depth= 1] . ( 3 sec) [ -10882.1761] [ 2425] [depth= 5] . ( 3 sec) [ -10841.9212] [ 2416] [depth= 3] . ( 3 sec) [ -10805.1070] [ 2419] [depth= 4] . ( 3 sec) [ -10652.2436] [ 2382] [depth= 1] . ( 3 sec) [ -10559.4549] [ 2351] [depth= 10] . ( 3 sec) [ -10475.2200] [ 2317] [depth= 1] . ( 3 sec) [ -10365.5004] [ 2313] [depth= 8] . ( 4 sec) [ -10356.7420] [ 2308] [depth= 2] . ( 4 sec) [ -10309.1447] [ 2301] [depth= 6] . ( 4 sec) [ -10268.7110] [ 2292] [depth= 1] . ( 4 sec) [ -10253.7130] [ 2289] [depth= 9] . ( 4 sec) [ -10252.7401] [ 2293] [depth= 1] . ( 4 sec) [ -10244.0471] [ 2290] [depth= 1] . ( 4 sec) [ -9939.4803] [ 2158] [depth= 3] . ( 4 sec) [ -9933.7346] [ 2148] [depth= 1] . ( 4 sec) [ -9927.9878] [ 2144] [depth= 1] . ( 4 sec) [ -9921.9090] [ 2146] [depth= 2] . ( 4 sec) [ -9850.2272] [ 2118] [depth= 8] . ( 4 sec) [ -9749.4230] [ 2080] [depth= 2] . ( 4 sec) [ -9727.7048] [ 2077] [depth= 1] . ( 4 sec) [ -9718.0649] [ 2071] [depth= 2] . ( 4 sec) [ -9696.8599] [ 2067] [depth= 2] . ( 4 sec) [ -9678.8058] [ 2060] [depth= 1] . ( 4 sec) [ -9673.5600] [ 2067] [depth= 1] . ( 4 sec) [ -9662.5999] [ 2067] [depth= 5] . ( 4 sec) [ -9657.3048] [ 2069] [depth= 1] . ( 4 sec) [ -9642.5270] [ 2062] [depth= 1] . ( 5 sec) [ -9640.9255] [ 2060] [depth= 1] . ( 5 sec) [ -9503.8963] [ 2019] [depth= 1] . ( 5 sec) [ -9487.3703] [ 2018] [depth= 1] . ( 5 sec) [ -9455.1196] [ 2016] [depth= 1] . ( 5 sec) [ -9442.0394] [ 2014] [depth= 1] . ( 5 sec) [ -9409.3506] [ 2004] [depth= 2] . ( 5 sec) [ -9393.9077] [ 1990] [depth= 2] . ( 5 sec) [ -9381.5954] [ 1983] [depth= 1] . ( 5 sec) [ -9380.7037] [ 1985] [depth= 1] . ( 5 sec) [ -9380.1646] [ 1986] [depth= 1] . ( 6 sec) [ -9140.4138] [Branch lengths ] . ( 6 sec) [ -9139.9076] [GTR parameters ] . ( 6 sec) [ -9094.0176] [Alpha ][ 0.991900] . ( 6 sec) [ -9093.4892] [ 1989] [depth= 7] . ( 6 sec) [ -9092.5610] [ 1983] [depth= 2] . ( 6 sec) [ -9082.7169] [ 1978] [depth= 1] . ( 7 sec) [ -9082.5888] [ 1983] [depth= 1] . ( 7 sec) [ -9081.5549] [ 1985] [depth= 1] . ( 7 sec) [ -9073.1756] [ 1963] [depth= 3] . ( 8 sec) [ -9071.2822] [ 1962] [depth= 2] . ( 8 sec) [ -9068.4317] [ 1961] [depth= 3] . ( 8 sec) [ -9067.8305] [ 1961] [depth= 1] . ( 8 sec) [ -9066.6973] [ 1961] [depth= 1] . ( 9 sec) [ -9063.9740] [ 1962] [depth= 2] . ( 9 sec) [ -9058.6579] [ 1959] [depth= 1] . ( 9 sec) [ -9058.4588] [ 1959] [depth= 1] . ( 10 sec) [ -9038.6414] [Branch lengths ] . ( 10 sec) [ -9038.4264] [GTR parameters ] . ( 10 sec) [ -9038.1380] [Alpha ][ 1.050018] . ( 10 sec) [ -9036.7224] [ 1968] [depth= 1] . ( 11 sec) [ -9036.5420] [ 1974] [depth= 3] . ( 12 sec) [ -9036.1650] [ 1977] [depth= 3] . ( 12 sec) [ -9034.4003] [ 1975] [depth= 2] . ( 12 sec) [ -9034.3665] [ 1977] [depth= 1] . ( 13 sec) [ -9034.1401] [ 1980] [depth= 1] . ( 13 sec) [ -9032.8558] [ 1977] [depth= 1] . ( 14 sec) [ -9031.4133] [Branch lengths ] . ( 15 sec) [ -9031.4002] [GTR parameters ] . ( 15 sec) [ -9031.3992] [Alpha ][ 1.046371] . ( 15 sec) [ -9029.6322] [ 1971] [depth= 2] . ( 17 sec) [ -9029.4819] [ 1973] [depth= 1] . ( 19 sec) [ -9028.7054] [Branch lengths ] . ( 20 sec) [ -9028.7030] [GTR parameters ] . ( 20 sec) [ -9028.7029] [Alpha ][ 1.045285] . ( 25 sec) [ -9028.4016] [Branch lengths ] . ( 51 sec) [ -9028.3777] [Branch lengths ] . ( 51 sec) [ -9028.3777] [Topology ] . ( 51 sec) [ -9028.3766] [Topology ] . ( 52 sec) [ -9028.3762] [Topology ] . ( 52 sec) [ -9028.3761] [GTR parameters ] . ( 53 sec) [ -9028.3760] [Alpha ][ 1.046331] . ( 53 sec) [ -9028.3760] [Topology ] . ( 53 sec) [ -9028.3758] [Topology ] . ( 53 sec) [ -9028.3758] [GTR parameters ] . ( 53 sec) [ -9028.3758] [Alpha ][ 1.046331] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -9028.3755] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9028.375456. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16339.7501] [GTR parameters ] . ( 1 sec) [ -16133.6743] [Alpha ][ 0.500960] . ( 1 sec) [ -16011.6038] [ 3426] [depth= 5] . ( 1 sec) [ -15599.8443] [ 3375] [depth= 10] . ( 1 sec) [ -15517.4101] [ 3369] [depth= 4] . ( 1 sec) [ -15454.7941] [ 3365] [depth= 5] . ( 1 sec) [ -15431.6289] [ 3355] [depth= 1] . ( 1 sec) [ -15318.9106] [ 3354] [depth= 2] . ( 1 sec) [ -15259.5825] [ 3347] [depth= 5] . ( 1 sec) [ -15015.7976] [ 3278] [depth= 1] . ( 1 sec) [ -14891.4283] [ 3264] [depth= 6] . ( 1 sec) [ -14676.7857] [ 3222] [depth= 1] . ( 1 sec) [ -14665.5827] [ 3208] [depth= 1] . ( 1 sec) [ -14422.9207] [ 3138] [depth= 3] . ( 1 sec) [ -14420.9761] [ 3126] [depth= 1] . ( 1 sec) [ -14395.4035] [ 3124] [depth= 2] . ( 1 sec) [ -14339.9079] [ 3121] [depth= 1] . ( 1 sec) [ -14300.3050] [ 3114] [depth= 8] . ( 1 sec) [ -13977.9875] [ 3054] [depth= 6] . ( 2 sec) [ -13816.3421] [ 3045] [depth= 5] . ( 2 sec) [ -13592.1790] [ 3011] [depth= 12] . ( 2 sec) [ -13550.3076] [ 3004] [depth= 11] . ( 2 sec) [ -13526.4182] [ 2993] [depth= 2] . ( 2 sec) [ -13274.7979] [ 2986] [depth= 4] . ( 2 sec) [ -13225.2538] [ 2981] [depth= 11] . ( 2 sec) [ -13147.4767] [ 2960] [depth= 13] . ( 2 sec) [ -12939.8858] [ 2897] [depth= 9] . ( 2 sec) [ -12920.9839] [ 2896] [depth= 1] . ( 2 sec) [ -12911.5180] [ 2903] [depth= 3] . ( 2 sec) [ -12910.7991] [ 2904] [depth= 6] . ( 2 sec) [ -12761.6827] [ 2858] [depth= 11] . ( 2 sec) [ -12601.3668] [ 2841] [depth= 7] . ( 2 sec) [ -12293.5696] [ 2761] [depth= 4] . ( 2 sec) [ -12244.1672] [ 2745] [depth= 1] . ( 2 sec) [ -12196.6394] [ 2740] [depth= 5] . ( 2 sec) [ -12182.4164] [ 2721] [depth= 1] . ( 2 sec) [ -12181.4384] [ 2723] [depth= 3] . ( 2 sec) [ -12158.2290] [ 2714] [depth= 5] . ( 2 sec) [ -12070.1063] [ 2682] [depth= 9] . ( 3 sec) [ -11662.9023] [ 2554] [depth= 5] . ( 3 sec) [ -11552.5684] [ 2505] [depth= 1] . ( 3 sec) [ -11533.1806] [ 2493] [depth= 3] . ( 3 sec) [ -11396.7892] [ 2426] [depth= 7] . ( 3 sec) [ -11323.9883] [ 2424] [depth= 2] . ( 3 sec) [ -11283.0935] [ 2419] [depth= 1] . ( 3 sec) [ -11258.5745] [ 2411] [depth= 1] . ( 3 sec) [ -11248.8659] [ 2416] [depth= 1] . ( 3 sec) [ -11242.2390] [ 2407] [depth= 3] . ( 3 sec) [ -11110.7730] [ 2391] [depth= 2] . ( 3 sec) [ -11097.2987] [ 2377] [depth= 1] . ( 3 sec) [ -10907.3016] [ 2343] [depth= 1] . ( 3 sec) [ -10857.1749] [ 2332] [depth= 8] . ( 3 sec) [ -10671.6585] [ 2356] [depth= 1] . ( 3 sec) [ -10578.8551] [ 2311] [depth= 7] . ( 3 sec) [ -10577.4435] [ 2309] [depth= 1] . ( 3 sec) [ -10556.5142] [ 2311] [depth= 2] . ( 3 sec) [ -10444.1672] [ 2275] [depth= 7] . ( 3 sec) [ -10429.3486] [ 2268] [depth= 4] . ( 3 sec) [ -10260.7520] [ 2220] [depth= 8] . ( 4 sec) [ -10254.1469] [ 2218] [depth= 2] . ( 4 sec) [ -10232.7483] [ 2219] [depth= 1] . ( 4 sec) [ -10208.0258] [ 2221] [depth= 6] . ( 4 sec) [ -10205.6078] [ 2217] [depth= 2] . ( 4 sec) [ -10195.5958] [ 2218] [depth= 2] . ( 4 sec) [ -10140.6392] [ 2202] [depth= 4] . ( 4 sec) [ -10139.2113] [ 2201] [depth= 2] . ( 4 sec) [ -10132.1213] [ 2200] [depth= 2] . ( 4 sec) [ -10094.5644] [ 2197] [depth= 1] . ( 4 sec) [ -10094.4358] [ 2197] [depth= 1] . ( 4 sec) [ -9941.0640] [ 2162] [depth= 2] . ( 4 sec) [ -9938.8196] [ 2166] [depth= 1] . ( 4 sec) [ -9858.1418] [ 2124] [depth= 4] . ( 4 sec) [ -9703.8649] [ 2065] [depth= 5] . ( 4 sec) [ -9703.0447] [ 2065] [depth= 1] . ( 4 sec) [ -9626.7851] [ 2066] [depth= 1] . ( 4 sec) [ -9584.1531] [ 2060] [depth= 3] . ( 4 sec) [ -9515.9046] [ 2055] [depth= 6] . ( 4 sec) [ -9511.0361] [ 2058] [depth= 1] . ( 5 sec) [ -9454.6452] [ 2056] [depth= 1] . ( 5 sec) [ -9271.3551] [Branch lengths ] . ( 5 sec) [ -9270.9712] [GTR parameters ] . ( 5 sec) [ -9237.1657] [Alpha ][ 0.915532] . ( 6 sec) [ -9235.6748] [ 2063] [depth= 7] . ( 6 sec) [ -9210.6753] [ 2044] [depth= 5] . ( 6 sec) [ -9205.2662] [ 2043] [depth= 1] . ( 6 sec) [ -9201.5982] [ 2008] [depth= 11] . ( 6 sec) [ -9198.9645] [ 2003] [depth= 1] . ( 6 sec) [ -9191.2455] [ 1999] [depth= 1] . ( 6 sec) [ -9185.1428] [ 2003] [depth= 1] . ( 6 sec) [ -9182.9060] [ 2000] [depth= 1] . ( 6 sec) [ -9182.1056] [ 1995] [depth= 1] . ( 6 sec) [ -9131.9002] [ 1980] [depth= 5] . ( 6 sec) [ -9130.1843] [ 1982] [depth= 1] . ( 6 sec) [ -9129.8664] [ 1983] [depth= 1] . ( 7 sec) [ -9129.4701] [ 1981] [depth= 1] . ( 7 sec) [ -9125.0812] [ 1978] [depth= 2] . ( 7 sec) [ -9119.5501] [ 1981] [depth= 1] . ( 7 sec) [ -9111.9809] [ 1978] [depth= 1] . ( 7 sec) [ -9111.0825] [ 1977] [depth= 1] . ( 7 sec) [ -9098.9375] [ 1967] [depth= 5] . ( 7 sec) [ -9087.2055] [ 1961] [depth= 2] . ( 8 sec) [ -9087.0645] [ 1963] [depth= 1] . ( 8 sec) [ -9087.0022] [ 1961] [depth= 1] . ( 8 sec) [ -9077.5418] [ 1959] [depth= 1] . ( 8 sec) [ -9077.2128] [ 1962] [depth= 3] . ( 8 sec) [ -9075.9682] [ 1959] [depth= 2] . ( 8 sec) [ -9069.9638] [ 1959] [depth= 1] . ( 9 sec) [ -9068.4857] [ 1958] [depth= 1] . ( 9 sec) [ -9068.1333] [ 1960] [depth= 1] . ( 9 sec) [ -9068.1127] [ 1962] [depth= 1] . ( 9 sec) [ -9040.0160] [Branch lengths ] . ( 10 sec) [ -9039.3849] [GTR parameters ] . ( 10 sec) [ -9038.1142] [Alpha ][ 1.032627] . ( 10 sec) [ -9034.2259] [ 1961] [depth= 1] . ( 11 sec) [ -9034.1499] [ 1958] [depth= 1] . ( 12 sec) [ -9033.3059] [ 1960] [depth= 1] . ( 13 sec) [ -9032.6899] [ 1959] [depth= 1] . ( 14 sec) [ -9028.9963] [Branch lengths ] . ( 14 sec) [ -9028.9862] [GTR parameters ] . ( 14 sec) [ -9028.9791] [Alpha ][ 1.042124] . ( 18 sec) [ -9028.5246] [Branch lengths ] . ( 44 sec) [ -9028.4559] [Branch lengths ] . ( 44 sec) [ -9028.4559] [Topology ] . ( 45 sec) [ -9028.4494] [Topology ] . ( 45 sec) [ -9028.4472] [Topology ] . ( 46 sec) [ -9028.4462] [Topology ] . ( 46 sec) [ -9028.4457] [GTR parameters ] . ( 46 sec) [ -9028.4448] [Alpha ][ 1.045372] . ( 46 sec) [ -9028.4448] [Topology ] . ( 47 sec) [ -9028.4442] [Topology ] . ( 47 sec) [ -9028.4442] [GTR parameters ] . ( 47 sec) [ -9028.4442] [Alpha ][ 1.045372] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -9028.3721] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9028.372149. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9072.110483 . ( 0 sec) [ -9071.6770] [GTR parameters ] . ( 0 sec) [ -9071.6595] [Alpha ][ 1.015113] . ( 0 sec) [ -9071.6595] [Topology ] . ( 1 sec) [ -9038.0496] [Topology ] . ( 2 sec) [ -9032.4404] [Topology ] . ( 3 sec) [ -9030.4804] [Topology ] . ( 4 sec) [ -9029.5590] [Topology ] . ( 4 sec) [ -9029.0788] [Topology ] . ( 5 sec) [ -9028.8183] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.818253 . ( 11 sec) [ -9028.8056] [GTR parameters ] . ( 11 sec) [ -9028.7296] [Alpha ][ 1.045040] . ( 11 sec) [ -9028.7296] [Topology ] . ( 12 sec) [ -9028.5755] [Topology ] . ( 13 sec) [ -9028.4903] [Topology ] . ( 14 sec) [ -9028.4411] [Topology ] . ( 15 sec) [ -9028.4126] [Topology ] . ( 15 sec) [ -9028.3958] [Topology ] . ( 16 sec) [ -9028.3858] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.385785 . ( 22 sec) [ -9028.3856] [GTR parameters ] . ( 22 sec) [ -9028.3853] [Alpha ][ 1.047166] . ( 22 sec) [ -9028.3853] [Topology ] . ( 23 sec) [ -9028.3792] [Topology ] . ( 24 sec) [ -9028.3756] [Topology ] . ( 24 sec) [ -9028.3735] [Topology ] . ( 25 sec) [ -9028.3721] [Topology ] . ( 26 sec) [ -9028.3713] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9028.371347 . ( 32 sec) [ -9028.3713] [GTR parameters ] . ( 32 sec) [ -9028.3713] [Alpha ][ 1.047166] . ( 32 sec) [ -9028.3713] [Topology ] . ( 33 sec) [ -9028.3708] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -9071.6770] [GTR parameters ] . ( 45 sec) [ -9071.6595] [Alpha ][ 1.015113] . ( 45 sec) [ -9070.9707] [ 1959] [depth= 1] . ( 46 sec) [ -9070.6104] [ 1961] [depth= 1] . ( 47 sec) [ -9066.8071] [ 1969] [depth= 2] . ( 47 sec) [ -9065.9874] [ 1970] [depth= 1] . ( 48 sec) [ -9065.8700] [ 1969] [depth= 1] . ( 48 sec) [ -9065.7317] [ 1972] [depth= 1] . ( 48 sec) [ -9063.6382] [ 1974] [depth= 1] . ( 48 sec) [ -9063.3347] [ 1960] [depth= 2] . ( 48 sec) [ -9061.1474] [ 1962] [depth= 3] . ( 48 sec) [ -9060.8712] [ 1963] [depth= 1] . ( 48 sec) [ -9058.7227] [ 1961] [depth= 1] . ( 49 sec) [ -9034.5647] [Branch lengths ] . ( 49 sec) [ -9034.5580] [GTR parameters ] . ( 49 sec) [ -9034.5164] [Alpha ][ 1.037201] . ( 50 sec) [ -9031.1392] [ 1959] [depth= 1] . ( 53 sec) [ -9028.8280] [Branch lengths ] . ( 54 sec) [ -9028.8252] [GTR parameters ] . ( 54 sec) [ -9028.8204] [Alpha ][ 1.045035] . ( 58 sec) [ -9028.4482] [Branch lengths ] . ( 84 sec) [ -9028.3840] [Branch lengths ] . ( 84 sec) [ -9028.3840] [Topology ] . ( 85 sec) [ -9028.3767] [Topology ] . ( 85 sec) [ -9028.3741] [Topology ] . ( 86 sec) [ -9028.3727] [Topology ] . ( 87 sec) [ -9028.3720] [Topology ] . ( 87 sec) [ -9028.3714] [GTR parameters ] . ( 87 sec) [ -9028.3711] [Alpha ][ 1.046770] . ( 87 sec) [ -9028.3711] [Topology ] . ( 88 sec) [ -9028.3707] [Topology ] . ( 88 sec) [ -9028.3706] [GTR parameters ] . ( 88 sec) [ -9028.3706] [Alpha ][ 1.046770] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9028.370844 . Log likelihood obtained after SPR moves : -9028.370644 . Log likelihood of the current tree: -9028.370644. . Printing the most likely tree in file 'data4.phy_phyml_tree.txt'... . Best log likelihood : -9028.370280 . Time used 0h1m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo