.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data8.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... . 419 patterns found. (out of a total of 500 sites) . 76 sites without polymorphism (15.20%). . [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) [ -21243.6182] [GTR parameters ] . ( 2 sec) [ -20761.0462] [Alpha ][ 0.500960] . ( 2 sec) [ -20443.0995] [ 4902] [depth= 8] . ( 2 sec) [ -20310.3338] [ 4891] [depth= 9] . ( 2 sec) [ -19669.0688] [ 4876] [depth= 6] . ( 2 sec) [ -19508.6633] [ 4863] [depth= 5] . ( 2 sec) [ -19476.6141] [ 4714] [depth= 4] . ( 2 sec) [ -19272.7885] [ 4697] [depth= 1] . ( 2 sec) [ -19222.7613] [ 4669] [depth= 4] . ( 2 sec) [ -19163.9436] [ 4669] [depth= 1] . ( 2 sec) [ -18656.6485] [ 4636] [depth= 2] . ( 2 sec) [ -18384.6553] [ 4604] [depth= 4] . ( 2 sec) [ -18119.6658] [ 4547] [depth= 12] . ( 2 sec) [ -18071.6203] [ 4420] [depth= 11] . ( 3 sec) [ -17860.8122] [ 4433] [depth= 1] . ( 3 sec) [ -17314.9705] [ 4374] [depth= 5] . ( 3 sec) [ -17078.4281] [ 4286] [depth= 3] . ( 3 sec) [ -16919.3090] [ 4264] [depth= 6] . ( 3 sec) [ -16892.8288] [ 4224] [depth= 3] . ( 3 sec) [ -16710.5751] [ 4203] [depth= 3] . ( 3 sec) [ -16552.0443] [ 4172] [depth= 4] . ( 3 sec) [ -16509.3398] [ 4155] [depth= 1] . ( 3 sec) [ -16305.7378] [ 4125] [depth= 13] . ( 3 sec) [ -16136.6273] [ 4118] [depth= 1] . ( 3 sec) [ -15949.6274] [ 4075] [depth= 7] . ( 3 sec) [ -15803.7970] [ 3886] [depth= 5] . ( 3 sec) [ -15406.2106] [ 3876] [depth= 10] . ( 3 sec) [ -15304.5934] [ 3836] [depth= 1] . ( 3 sec) [ -15254.0065] [ 3834] [depth= 1] . ( 3 sec) [ -14880.6428] [ 3730] [depth= 4] . ( 3 sec) [ -14846.7277] [ 3690] [depth= 2] . ( 3 sec) [ -14641.3562] [ 3653] [depth= 8] . ( 3 sec) [ -13966.3087] [ 3495] [depth= 10] . ( 3 sec) [ -13909.0854] [ 3485] [depth= 1] . ( 3 sec) [ -13882.6884] [ 3470] [depth= 1] . ( 4 sec) [ -13853.9964] [ 3437] [depth= 1] . ( 4 sec) [ -13602.2191] [ 3406] [depth= 11] . ( 4 sec) [ -13206.3895] [ 3286] [depth= 13] . ( 4 sec) [ -13040.2636] [ 3229] [depth= 8] . ( 4 sec) [ -12724.8070] [ 3067] [depth= 7] . ( 4 sec) [ -12695.9630] [ 2922] [depth= 1] . ( 4 sec) [ -12304.4074] [ 2925] [depth= 5] . ( 4 sec) [ -12120.3004] [ 2908] [depth= 6] . ( 4 sec) [ -11826.4085] [ 2857] [depth= 5] . ( 4 sec) [ -11815.6328] [ 2867] [depth= 3] . ( 4 sec) [ -11784.9265] [ 2849] [depth= 1] . ( 4 sec) [ -11526.3701] [ 2762] [depth= 8] . ( 4 sec) [ -11418.3221] [ 2741] [depth= 2] . ( 4 sec) [ -11374.4291] [ 2740] [depth= 1] . ( 4 sec) [ -11286.9295] [ 2743] [depth= 1] . ( 4 sec) [ -11136.8377] [ 2717] [depth= 3] . ( 5 sec) [ -11114.3233] [ 2707] [depth= 1] . ( 5 sec) [ -11081.8257] [ 2696] [depth= 3] . ( 5 sec) [ -11075.1379] [ 2698] [depth= 1] . ( 5 sec) [ -11059.4438] [ 2680] [depth= 1] . ( 5 sec) [ -10932.7218] [ 2673] [depth= 1] . ( 5 sec) [ -10927.2476] [ 2671] [depth= 1] . ( 5 sec) [ -10906.3305] [ 2675] [depth= 1] . ( 5 sec) [ -10857.2103] [ 2646] [depth= 2] . ( 5 sec) [ -10832.9567] [ 2643] [depth= 1] . ( 5 sec) [ -10650.7568] [ 2483] [depth= 5] . ( 5 sec) [ -10649.4069] [ 2483] [depth= 1] . ( 5 sec) [ -10460.5847] [ 2410] [depth= 2] . ( 5 sec) [ -10275.4000] [ 2431] [depth= 1] . ( 5 sec) [ -9777.1543] [ 2224] [depth= 4] . ( 5 sec) [ -9747.1444] [ 2222] [depth= 1] . ( 5 sec) [ -9746.0943] [ 2212] [depth= 2] . ( 6 sec) [ -9744.7761] [ 2214] [depth= 1] . ( 6 sec) [ -9685.4451] [ 2146] [depth= 4] . ( 6 sec) [ -9684.0633] [ 2148] [depth= 1] . ( 6 sec) [ -9638.0673] [ 2127] [depth= 1] . ( 6 sec) [ -9637.9207] [ 2128] [depth= 1] . ( 6 sec) [ -9628.1380] [ 2125] [depth= 1] . ( 6 sec) [ -9622.6055] [ 2118] [depth= 2] . ( 6 sec) [ -9601.5821] [ 2118] [depth= 1] . ( 6 sec) [ -9589.2360] [ 2104] [depth= 1] . ( 7 sec) [ -9583.1609] [ 2139] [depth= 1] . ( 7 sec) [ -9581.1687] [ 2139] [depth= 1] . ( 7 sec) [ -9580.9982] [ 2139] [depth= 1] . ( 7 sec) [ -9575.9338] [ 2104] [depth= 1] . ( 7 sec) [ -9323.8435] [Branch lengths ] . ( 8 sec) [ -9317.4439] [GTR parameters ] . ( 8 sec) [ -9303.7798] [Alpha ][ 0.713277] . ( 8 sec) [ -9293.5649] [ 2099] [depth= 2] . ( 8 sec) [ -9290.5198] [ 2104] [depth= 2] . ( 8 sec) [ -9290.3439] [ 2104] [depth= 1] . ( 9 sec) [ -9077.5278] [ 2035] [depth= 2] . ( 9 sec) [ -9040.8543] [ 2042] [depth= 1] . ( 9 sec) [ -9033.8998] [ 2041] [depth= 1] . ( 9 sec) [ -9032.8408] [ 2036] [depth= 1] . ( 9 sec) [ -9008.6574] [ 2031] [depth= 1] . ( 9 sec) [ -8999.0038] [ 2028] [depth= 2] . ( 9 sec) [ -8996.5674] [ 2028] [depth= 1] . ( 9 sec) [ -8996.5180] [ 2028] [depth= 1] . ( 9 sec) [ -8985.3358] [ 1954] [depth= 1] . ( 9 sec) [ -8981.2064] [ 1951] [depth= 1] . ( 9 sec) [ -8981.0568] [ 1951] [depth= 1] . ( 10 sec) [ -8980.6562] [ 1956] [depth= 1] . ( 10 sec) [ -8908.5226] [ 1971] [depth= 2] . ( 10 sec) [ -8900.2731] [ 1975] [depth= 1] . ( 11 sec) [ -8900.0234] [ 1975] [depth= 1] . ( 11 sec) [ -8899.3765] [ 1978] [depth= 1] . ( 12 sec) [ -8899.1055] [ 1983] [depth= 1] . ( 12 sec) [ -8896.4246] [ 1962] [depth= 1] . ( 12 sec) [ -8896.3860] [ 1962] [depth= 1] . ( 12 sec) [ -8896.1894] [ 1964] [depth= 1] . ( 14 sec) [ -8883.6502] [Branch lengths ] . ( 14 sec) [ -8883.5498] [GTR parameters ] . ( 14 sec) [ -8879.7988] [Alpha ][ 0.869051] . ( 15 sec) [ -8879.7149] [ 1962] [depth= 1] . ( 16 sec) [ -8878.7466] [ 1967] [depth= 1] . ( 16 sec) [ -8878.7198] [ 1962] [depth= 1] . ( 16 sec) [ -8878.6334] [ 1962] [depth= 1] . ( 18 sec) [ -8878.4652] [ 1959] [depth= 1] . ( 19 sec) [ -8878.2717] [ 1959] [depth= 1] . ( 20 sec) [ -8876.5237] [Branch lengths ] . ( 20 sec) [ -8876.5094] [GTR parameters ] . ( 20 sec) [ -8876.4793] [Alpha ][ 0.885025] . ( 26 sec) [ -8876.2329] [Branch lengths ] . ( 54 sec) [ -8875.8989] [ 1968] [depth= 2] . ( 59 sec) [ -8875.8341] [Branch lengths ] . ( 59 sec) [ -8875.8336] [GTR parameters ] . ( 59 sec) [ -8875.8329] [Alpha ][ 0.887409] . ( 59 sec) [ -8875.8329] [Topology ] . ( 60 sec) [ -8875.7107] [Topology ] . ( 61 sec) [ -8875.0775] [Topology ] . ( 62 sec) [ -8874.8750] [Topology ] . ( 64 sec) [ -8874.7453] [Topology ] . ( 65 sec) [ -8874.6563] [Topology ] . ( 66 sec) [ -8874.5931] [Topology ] . ( 67 sec) [ -8874.5467] [Topology ] . ( 67 sec) [ -8874.5445] [GTR parameters ] . ( 67 sec) [ -8874.5445] [Alpha ][ 0.888297] . ( 67 sec) [ -8874.5445] [Topology ] . ( 68 sec) [ -8874.5099] [Topology ] . ( 69 sec) [ -8874.4843] [Topology ] . ( 70 sec) [ -8874.4653] [Topology ] . ( 71 sec) [ -8874.4509] [Topology ] . ( 72 sec) [ -8874.4401] [Topology ] . ( 73 sec) [ -8874.4319] [Topology ] . ( 73 sec) [ -8874.4318] [GTR parameters ] . ( 73 sec) [ -8874.4318] [Alpha ][ 0.888297] . ( 73 sec) [ -8874.4318] [Topology ] . ( 74 sec) [ -8874.4255] [Topology ] . ( 75 sec) [ -8874.4206] [Topology ] . ( 76 sec) [ -8874.4168] [Topology ] . ( 77 sec) [ -8874.4139] [Topology ] . ( 78 sec) [ -8874.4116] [Topology ] . ( 80 sec) [ -8874.4099] [Topology ] . ( 80 sec) [ -8874.4099] [GTR parameters ] . ( 80 sec) [ -8874.4099] [Alpha ][ 0.888297] . ( 80 sec) [ -8874.4099] [Topology ] . ( 81 sec) [ -8874.4085] [Topology ] . ( 82 sec) [ -8874.4075] [Topology ] . ( 83 sec) [ -8874.4066] [Topology ] . ( 83 sec) [ -8874.4066] [GTR parameters ] . ( 84 sec) [ -8874.4066] [Alpha ][ 0.888297] . ( 84 sec) [ -8874.4066] [Topology ] . ( 85 sec) [ -8874.4060] [Topology ] . ( 85 sec) [ -8874.4060] [GTR parameters ] . ( 85 sec) [ -8874.4060] [Alpha ][ 0.888297] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.406010. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22415.1871] [GTR parameters ] . ( 1 sec) [ -21881.5656] [Alpha ][ 0.500960] . ( 1 sec) [ -21697.3874] [ 5135] [depth= 3] . ( 1 sec) [ -21381.0853] [ 5133] [depth= 3] . ( 1 sec) [ -21330.7679] [ 5107] [depth= 3] . ( 1 sec) [ -21205.1440] [ 5085] [depth= 2] . ( 1 sec) [ -20959.6446] [ 5050] [depth= 5] . ( 1 sec) [ -20167.0763] [ 5021] [depth= 7] . ( 1 sec) [ -19973.8318] [ 5008] [depth= 4] . ( 1 sec) [ -19936.3234] [ 4938] [depth= 1] . ( 1 sec) [ -19839.5054] [ 4914] [depth= 4] . ( 1 sec) [ -19707.8608] [ 4904] [depth= 3] . ( 1 sec) [ -19498.6036] [ 4886] [depth= 1] . ( 2 sec) [ -19193.9099] [ 4823] [depth= 9] . ( 2 sec) [ -19142.1570] [ 4816] [depth= 4] . ( 2 sec) [ -19140.8842] [ 4668] [depth= 4] . ( 2 sec) [ -19081.9148] [ 4674] [depth= 19] . ( 2 sec) [ -18805.2937] [ 4542] [depth= 9] . ( 2 sec) [ -18656.9102] [ 4529] [depth= 9] . ( 2 sec) [ -18241.1847] [ 4524] [depth= 1] . ( 2 sec) [ -18166.7497] [ 4521] [depth= 1] . ( 2 sec) [ -17813.2080] [ 4335] [depth= 1] . ( 2 sec) [ -17577.0092] [ 4319] [depth= 2] . ( 2 sec) [ -17548.5524] [ 4286] [depth= 2] . ( 2 sec) [ -17401.6326] [ 4301] [depth= 1] . ( 2 sec) [ -17092.7605] [ 4265] [depth= 3] . ( 3 sec) [ -16964.2812] [ 4263] [depth= 7] . ( 3 sec) [ -16780.7023] [ 4268] [depth= 1] . ( 3 sec) [ -16511.2242] [ 4233] [depth= 2] . ( 3 sec) [ -16505.7903] [ 4228] [depth= 1] . ( 3 sec) [ -16489.4803] [ 4227] [depth= 8] . ( 3 sec) [ -16281.6110] [ 4177] [depth= 6] . ( 3 sec) [ -15989.2304] [ 4110] [depth= 6] . ( 3 sec) [ -15962.7375] [ 4103] [depth= 2] . ( 3 sec) [ -15252.0542] [ 3934] [depth= 2] . ( 3 sec) [ -15219.4625] [ 3923] [depth= 2] . ( 3 sec) [ -14945.3904] [ 3776] [depth= 11] . ( 3 sec) [ -14862.3065] [ 3629] [depth= 3] . ( 4 sec) [ -14398.2532] [ 3478] [depth= 6] . ( 4 sec) [ -14344.4544] [ 3469] [depth= 8] . ( 4 sec) [ -14133.4605] [ 3442] [depth= 7] . ( 4 sec) [ -14080.4434] [ 3397] [depth= 5] . ( 4 sec) [ -13650.1856] [ 3236] [depth= 2] . ( 4 sec) [ -13617.6301] [ 3223] [depth= 2] . ( 4 sec) [ -13553.4991] [ 3226] [depth= 7] . ( 4 sec) [ -12516.0750] [ 3181] [depth= 8] . ( 4 sec) [ -12400.8515] [ 3069] [depth= 4] . ( 4 sec) [ -12356.2535] [ 3036] [depth= 1] . ( 5 sec) [ -12345.0729] [ 3034] [depth= 2] . ( 5 sec) [ -12271.4197] [ 3007] [depth= 2] . ( 5 sec) [ -12129.4380] [ 3009] [depth= 1] . ( 5 sec) [ -12055.0586] [ 2963] [depth= 4] . ( 5 sec) [ -12052.5826] [ 2963] [depth= 1] . ( 5 sec) [ -11512.2652] [ 2822] [depth= 6] . ( 5 sec) [ -11492.2298] [ 2812] [depth= 3] . ( 5 sec) [ -11490.1512] [ 2811] [depth= 1] . ( 5 sec) [ -11413.5874] [ 2781] [depth= 2] . ( 5 sec) [ -11403.6731] [ 2783] [depth= 2] . ( 5 sec) [ -11098.9623] [ 2642] [depth= 8] . ( 5 sec) [ -11029.1170] [ 2645] [depth= 1] . ( 5 sec) [ -11021.0032] [ 2642] [depth= 1] . ( 6 sec) [ -11008.0976] [ 2650] [depth= 2] . ( 6 sec) [ -10975.1648] [ 2628] [depth= 1] . ( 6 sec) [ -10962.4141] [ 2617] [depth= 3] . ( 6 sec) [ -10960.4411] [ 2616] [depth= 2] . ( 6 sec) [ -10879.1687] [ 2592] [depth= 1] . ( 6 sec) [ -10728.2713] [ 2571] [depth= 2] . ( 6 sec) [ -10724.8448] [ 2577] [depth= 1] . ( 6 sec) [ -10721.8231] [ 2560] [depth= 3] . ( 6 sec) [ -10455.5288] [ 2498] [depth= 6] . ( 6 sec) [ -10381.8526] [ 2495] [depth= 6] . ( 6 sec) [ -10286.2720] [ 2497] [depth= 1] . ( 6 sec) [ -10284.7564] [ 2514] [depth= 1] . ( 6 sec) [ -10248.0865] [ 2512] [depth= 1] . ( 7 sec) [ -10094.8494] [ 2488] [depth= 4] . ( 7 sec) [ -9810.7220] [ 2325] [depth= 6] . ( 7 sec) [ -9783.3613] [ 2325] [depth= 1] . ( 7 sec) [ -9712.9606] [ 2310] [depth= 4] . ( 7 sec) [ -9644.3227] [ 2303] [depth= 2] . ( 7 sec) [ -9581.2028] [ 2267] [depth= 3] . ( 7 sec) [ -9458.3910] [ 2237] [depth= 2] . ( 7 sec) [ -9438.0412] [ 2250] [depth= 2] . ( 7 sec) [ -9431.5497] [ 2248] [depth= 1] . ( 7 sec) [ -9418.7368] [ 2232] [depth= 1] . ( 8 sec) [ -9395.6059] [ 2234] [depth= 5] . ( 8 sec) [ -9390.2860] [ 2232] [depth= 1] . ( 8 sec) [ -9237.3867] [Branch lengths ] . ( 10 sec) [ -9228.6515] [GTR parameters ] . ( 10 sec) [ -9212.6275] [Alpha ][ 0.722196] . ( 11 sec) [ -9212.3277] [ 2223] [depth= 2] . ( 11 sec) [ -9211.5344] [ 2224] [depth= 1] . ( 11 sec) [ -9211.3844] [ 2223] [depth= 1] . ( 11 sec) [ -9198.3840] [ 2216] [depth= 1] . ( 11 sec) [ -9194.7298] [ 2216] [depth= 1] . ( 11 sec) [ -9194.5050] [ 2221] [depth= 1] . ( 12 sec) [ -9193.3144] [ 2220] [depth= 1] . ( 13 sec) [ -9193.3027] [ 2220] [depth= 1] . ( 13 sec) [ -9015.1471] [ 2089] [depth= 7] . ( 13 sec) [ -9014.6836] [ 2061] [depth= 1] . ( 13 sec) [ -9012.7402] [ 2058] [depth= 1] . ( 13 sec) [ -9012.7086] [ 2058] [depth= 1] . ( 14 sec) [ -9011.7691] [ 2059] [depth= 1] . ( 14 sec) [ -8966.5888] [ 1946] [depth= 5] . ( 14 sec) [ -8966.4900] [ 1951] [depth= 1] . ( 14 sec) [ -8966.0482] [ 1951] [depth= 1] . ( 15 sec) [ -8966.0379] [ 1951] [depth= 1] . ( 15 sec) [ -8952.2973] [ 1958] [depth= 2] . ( 15 sec) [ -8945.2439] [ 1984] [depth= 1] . ( 15 sec) [ -8936.1049] [ 1988] [depth= 2] . ( 16 sec) [ -8935.5452] [ 1989] [depth= 1] . ( 16 sec) [ -8929.7069] [ 1983] [depth= 2] . ( 16 sec) [ -8908.6827] [ 1977] [depth= 1] . ( 17 sec) [ -8885.4610] [Branch lengths ] . ( 17 sec) [ -8885.4168] [GTR parameters ] . ( 17 sec) [ -8882.3465] [Alpha ][ 0.862715] . ( 18 sec) [ -8882.3087] [ 1977] [depth= 1] . ( 19 sec) [ -8881.8681] [ 1984] [depth= 2] . ( 19 sec) [ -8881.6699] [ 1987] [depth= 1] . ( 22 sec) [ -8879.6580] [ 1963] [depth= 1] . ( 22 sec) [ -8879.4934] [ 1967] [depth= 1] . ( 22 sec) [ -8879.3306] [ 1963] [depth= 1] . ( 23 sec) [ -8879.2447] [ 1959] [depth= 1] . ( 23 sec) [ -8876.5812] [Branch lengths ] . ( 24 sec) [ -8876.5621] [GTR parameters ] . ( 24 sec) [ -8876.5063] [Alpha ][ 0.883492] . ( 29 sec) [ -8876.2275] [Branch lengths ] . ( 38 sec) [ -8875.8951] [ 1971] [depth= 2] . ( 44 sec) [ -8874.8637] [ 1970] [depth= 1] . ( 62 sec) [ -8874.4643] [Branch lengths ] . ( 62 sec) [ -8874.4618] [GTR parameters ] . ( 62 sec) [ -8874.4597] [Alpha ][ 0.887613] . ( 92 sec) [ -8874.4250] [Branch lengths ] . ( 92 sec) [ -8874.4250] [Topology ] . ( 93 sec) [ -8874.4180] [Topology ] . ( 95 sec) [ -8874.4140] [Topology ] . ( 96 sec) [ -8874.4113] [Topology ] . ( 97 sec) [ -8874.4094] [Topology ] . ( 99 sec) [ -8874.4080] [Topology ] . ( 100 sec) [ -8874.4070] [Topology ] . ( 101 sec) [ -8874.4069] [GTR parameters ] . ( 101 sec) [ -8874.4069] [Alpha ][ 0.887613] . ( 101 sec) [ -8874.4069] [Topology ] . ( 102 sec) [ -8874.4062] [Topology ] . ( 102 sec) [ -8874.4062] [GTR parameters ] . ( 102 sec) [ -8874.4062] [Alpha ][ 0.887613] . Checking for NNIs, optimizing five branches... . ( 112 sec) [ -8874.4060] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.405971. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21635.3515] [GTR parameters ] . ( 1 sec) [ -21145.7264] [Alpha ][ 0.500960] . ( 1 sec) [ -20873.9489] [ 4997] [depth= 8] . ( 1 sec) [ -20514.6180] [ 4996] [depth= 9] . ( 1 sec) [ -20447.1646] [ 4957] [depth= 4] . ( 1 sec) [ -20422.2558] [ 4950] [depth= 2] . ( 1 sec) [ -20133.2596] [ 4783] [depth= 5] . ( 1 sec) [ -20067.2282] [ 4793] [depth= 1] . ( 1 sec) [ -19262.0619] [ 4639] [depth= 7] . ( 2 sec) [ -19108.2674] [ 4618] [depth= 6] . ( 2 sec) [ -18552.1991] [ 4490] [depth= 1] . ( 2 sec) [ -18424.0000] [ 4448] [depth= 13] . ( 2 sec) [ -17294.9782] [ 4270] [depth= 12] . ( 2 sec) [ -17129.9866] [ 4209] [depth= 10] . ( 2 sec) [ -17072.3772] [ 4201] [depth= 2] . ( 2 sec) [ -16938.5497] [ 4207] [depth= 2] . ( 2 sec) [ -16200.5735] [ 4199] [depth= 1] . ( 2 sec) [ -16191.7396] [ 4122] [depth= 1] . ( 2 sec) [ -15634.7034] [ 4101] [depth= 3] . ( 2 sec) [ -15537.3523] [ 4057] [depth= 10] . ( 2 sec) [ -15364.2209] [ 4041] [depth= 1] . ( 2 sec) [ -15067.2608] [ 3920] [depth= 6] . ( 2 sec) [ -14932.9255] [ 3886] [depth= 1] . ( 3 sec) [ -14763.5205] [ 3859] [depth= 8] . ( 3 sec) [ -14651.4156] [ 3858] [depth= 1] . ( 3 sec) [ -14506.6613] [ 3707] [depth= 3] . ( 3 sec) [ -14340.4494] [ 3669] [depth= 4] . ( 3 sec) [ -14333.6442] [ 3664] [depth= 1] . ( 3 sec) [ -14286.5634] [ 3632] [depth= 3] . ( 3 sec) [ -14286.1356] [ 3631] [depth= 2] . ( 3 sec) [ -14227.3080] [ 3610] [depth= 4] . ( 3 sec) [ -14196.5315] [ 3593] [depth= 1] . ( 3 sec) [ -13894.3251] [ 3485] [depth= 7] . ( 3 sec) [ -13887.9375] [ 3485] [depth= 8] . ( 4 sec) [ -13515.5166] [ 3263] [depth= 10] . ( 4 sec) [ -13474.5172] [ 3245] [depth= 5] . ( 4 sec) [ -13124.7399] [ 3197] [depth= 8] . ( 4 sec) [ -13014.8550] [ 3171] [depth= 9] . ( 4 sec) [ -12836.9739] [ 3048] [depth= 10] . ( 4 sec) [ -12715.5189] [ 3010] [depth= 3] . ( 4 sec) [ -12707.8108] [ 3011] [depth= 2] . ( 4 sec) [ -12694.7440] [ 3026] [depth= 2] . ( 4 sec) [ -12570.9301] [ 2871] [depth= 7] . ( 5 sec) [ -12399.1300] [ 2850] [depth= 3] . ( 5 sec) [ -12379.7214] [ 2853] [depth= 1] . ( 5 sec) [ -12375.4271] [ 2849] [depth= 2] . ( 5 sec) [ -12360.0126] [ 2854] [depth= 1] . ( 5 sec) [ -12239.9517] [ 2840] [depth= 3] . ( 5 sec) [ -11935.8674] [ 2688] [depth= 4] . ( 5 sec) [ -11921.3999] [ 2683] [depth= 1] . ( 5 sec) [ -11901.0344] [ 2672] [depth= 2] . ( 5 sec) [ -11809.4034] [ 2657] [depth= 4] . ( 5 sec) [ -11802.3142] [ 2655] [depth= 1] . ( 5 sec) [ -11715.6980] [ 2562] [depth= 1] . ( 6 sec) [ -11593.8216] [ 2552] [depth= 1] . ( 6 sec) [ -11532.3627] [ 2578] [depth= 5] . ( 6 sec) [ -11364.5412] [ 2546] [depth= 1] . ( 6 sec) [ -11109.7831] [ 2511] [depth= 4] . ( 6 sec) [ -10917.3582] [ 2406] [depth= 5] . ( 6 sec) [ -10741.0527] [ 2408] [depth= 1] . ( 6 sec) [ -10737.1189] [ 2412] [depth= 1] . ( 6 sec) [ -10693.0430] [ 2405] [depth= 4] . ( 6 sec) [ -10456.4006] [ 2351] [depth= 6] . ( 6 sec) [ -10452.8203] [ 2353] [depth= 1] . ( 6 sec) [ -10190.6289] [ 2282] [depth= 8] . ( 6 sec) [ -10183.6213] [ 2278] [depth= 1] . ( 7 sec) [ -10082.1078] [ 2232] [depth= 5] . ( 7 sec) [ -10078.1943] [ 2230] [depth= 1] . ( 7 sec) [ -10077.9608] [ 2230] [depth= 1] . ( 7 sec) [ -10030.5602] [ 2215] [depth= 1] . ( 7 sec) [ -9894.9428] [ 2184] [depth= 2] . ( 7 sec) [ -9878.7159] [ 2180] [depth= 1] . ( 7 sec) [ -9726.3462] [ 2132] [depth= 6] . ( 7 sec) [ -9558.7078] [ 2110] [depth= 3] . ( 7 sec) [ -9549.5624] [ 2118] [depth= 2] . ( 7 sec) [ -9549.4692] [ 2118] [depth= 1] . ( 8 sec) [ -9532.9936] [ 2145] [depth= 1] . ( 8 sec) [ -9307.3371] [ 2086] [depth= 2] . ( 8 sec) [ -9296.5258] [ 2060] [depth= 2] . ( 8 sec) [ -9292.8804] [ 2056] [depth= 2] . ( 8 sec) [ -9292.5947] [ 2040] [depth= 1] . ( 8 sec) [ -9290.1051] [ 2036] [depth= 1] . ( 8 sec) [ -9286.0494] [ 2031] [depth= 1] . ( 8 sec) [ -9243.8762] [ 2010] [depth= 1] . ( 8 sec) [ -9243.4506] [ 2010] [depth= 1] . ( 8 sec) [ -9236.5438] [ 2007] [depth= 1] . ( 9 sec) [ -9063.7263] [Branch lengths ] . ( 10 sec) [ -9054.0165] [GTR parameters ] . ( 10 sec) [ -9030.0715] [Alpha ][ 0.815956] . ( 10 sec) [ -9025.4558] [ 2005] [depth= 1] . ( 10 sec) [ -9009.3164] [ 1997] [depth= 2] . ( 10 sec) [ -9008.1725] [ 2006] [depth= 2] . ( 11 sec) [ -8999.2346] [ 1994] [depth= 2] . ( 11 sec) [ -8994.2986] [ 1989] [depth= 2] . ( 11 sec) [ -8979.0153] [ 1976] [depth= 1] . ( 11 sec) [ -8953.5669] [ 1944] [depth= 3] . ( 12 sec) [ -8952.9223] [ 1944] [depth= 1] . ( 12 sec) [ -8948.8479] [ 1949] [depth= 1] . ( 12 sec) [ -8948.7999] [ 1949] [depth= 1] . ( 12 sec) [ -8945.6017] [ 1959] [depth= 1] . ( 12 sec) [ -8944.1716] [ 1963] [depth= 1] . ( 12 sec) [ -8933.6954] [ 1958] [depth= 1] . ( 13 sec) [ -8933.6317] [ 1958] [depth= 1] . ( 13 sec) [ -8933.0692] [ 1958] [depth= 1] . ( 13 sec) [ -8928.7377] [ 1962] [depth= 1] . ( 13 sec) [ -8925.2568] [ 1965] [depth= 2] . ( 14 sec) [ -8921.4542] [ 1967] [depth= 2] . ( 15 sec) [ -8921.4410] [ 1965] [depth= 1] . ( 15 sec) [ -8906.3380] [ 1959] [depth= 2] . ( 16 sec) [ -8879.4187] [Branch lengths ] . ( 16 sec) [ -8879.2343] [GTR parameters ] . ( 16 sec) [ -8878.5245] [Alpha ][ 0.889028] . ( 21 sec) [ -8878.4885] [ 1959] [depth= 1] . ( 21 sec) [ -8877.2395] [ 1963] [depth= 1] . ( 22 sec) [ -8876.2536] [Branch lengths ] . ( 22 sec) [ -8876.2455] [GTR parameters ] . ( 22 sec) [ -8876.2454] [Alpha ][ 0.888027] . ( 27 sec) [ -8876.1805] [Branch lengths ] . ( 43 sec) [ -8875.8242] [ 1971] [depth= 2] . ( 51 sec) [ -8875.7982] [ 1970] [depth= 1] . ( 52 sec) [ -8875.1118] [Branch lengths ] . ( 52 sec) [ -8875.1106] [GTR parameters ] . ( 52 sec) [ -8875.1104] [Alpha ][ 0.886556] . ( 69 sec) [ -8874.8395] [ 1969] [depth= 1] . ( 78 sec) [ -8874.8262] [Branch lengths ] . ( 78 sec) [ -8874.8247] [GTR parameters ] . ( 78 sec) [ -8874.8247] [Alpha ][ 0.886556] . ( 78 sec) [ -8874.8247] [Topology ] . ( 79 sec) [ -8874.8212] [Topology ] . ( 80 sec) [ -8874.8190] [Topology ] . ( 81 sec) [ -8874.8174] [Topology ] . ( 82 sec) [ -8874.8162] [Topology ] . ( 82 sec) [ -8874.8153] [Topology ] . ( 83 sec) [ -8874.8152] [GTR parameters ] . ( 83 sec) [ -8874.8152] [Alpha ][ 0.886556] . ( 83 sec) [ -8874.8152] [Topology ] . ( 84 sec) [ -8874.8145] [Topology ] . ( 84 sec) [ -8874.8144] [GTR parameters ] . ( 84 sec) [ -8874.8144] [Alpha ][ 0.886556] . Checking for NNIs, optimizing five branches... . ( 91 sec) [ -8874.4158] [Topology ] . Checking for NNIs, optimizing five branches... . ( 100 sec) [ -8874.4144] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.414366. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22816.8661] [GTR parameters ] . ( 1 sec) [ -22285.6771] [Alpha ][ 0.500960] . ( 2 sec) [ -22059.6877] [ 5152] [depth= 8] . ( 2 sec) [ -21760.5380] [ 5079] [depth= 9] . ( 2 sec) [ -21493.7157] [ 5027] [depth= 7] . ( 2 sec) [ -21399.6043] [ 5000] [depth= 1] . ( 2 sec) [ -21228.2746] [ 4905] [depth= 5] . ( 2 sec) [ -20853.7081] [ 4836] [depth= 3] . ( 2 sec) [ -20517.7109] [ 4816] [depth= 5] . ( 2 sec) [ -19780.4745] [ 4679] [depth= 2] . ( 3 sec) [ -19313.2776] [ 4661] [depth= 4] . ( 3 sec) [ -19060.8316] [ 4653] [depth= 10] . ( 3 sec) [ -18952.9285] [ 4651] [depth= 2] . ( 3 sec) [ -18846.8258] [ 4584] [depth= 11] . ( 3 sec) [ -18798.4665] [ 4578] [depth= 1] . ( 3 sec) [ -18174.4444] [ 4525] [depth= 14] . ( 4 sec) [ -18162.6201] [ 4520] [depth= 1] . ( 4 sec) [ -17775.9324] [ 4500] [depth= 2] . ( 4 sec) [ -17762.0569] [ 4483] [depth= 3] . ( 4 sec) [ -17379.7531] [ 4355] [depth= 5] . ( 4 sec) [ -17072.7393] [ 4286] [depth= 6] . ( 4 sec) [ -16662.0261] [ 4236] [depth= 9] . ( 4 sec) [ -16580.9457] [ 4238] [depth= 2] . ( 5 sec) [ -16457.8004] [ 4230] [depth= 19] . ( 5 sec) [ -16317.9839] [ 4222] [depth= 1] . ( 5 sec) [ -16187.6929] [ 4213] [depth= 12] . ( 5 sec) [ -15922.9191] [ 4152] [depth= 15] . ( 5 sec) [ -15765.6906] [ 4073] [depth= 5] . ( 5 sec) [ -15416.3650] [ 4082] [depth= 14] . ( 5 sec) [ -15398.0682] [ 3980] [depth= 2] . ( 5 sec) [ -14901.6094] [ 3959] [depth= 16] . ( 5 sec) [ -14515.5227] [ 3790] [depth= 7] . ( 5 sec) [ -14428.3726] [ 3784] [depth= 2] . ( 5 sec) [ -14406.6484] [ 3758] [depth= 3] . ( 6 sec) [ -14404.8715] [ 3757] [depth= 2] . ( 6 sec) [ -14355.9088] [ 3769] [depth= 1] . ( 6 sec) [ -14314.3485] [ 3742] [depth= 15] . ( 6 sec) [ -14074.5268] [ 3673] [depth= 8] . ( 6 sec) [ -13931.3149] [ 3635] [depth= 3] . ( 6 sec) [ -13867.6484] [ 3560] [depth= 1] . ( 6 sec) [ -13767.6361] [ 3535] [depth= 2] . ( 6 sec) [ -13714.7815] [ 3529] [depth= 3] . ( 6 sec) [ -13305.7800] [ 3399] [depth= 5] . ( 6 sec) [ -13207.7108] [ 3400] [depth= 1] . ( 6 sec) [ -12859.6747] [ 3209] [depth= 9] . ( 6 sec) [ -12840.7759] [ 3175] [depth= 4] . ( 7 sec) [ -12753.5430] [ 3166] [depth= 10] . ( 7 sec) [ -12550.5657] [ 3131] [depth= 5] . ( 7 sec) [ -12538.4502] [ 3134] [depth= 1] . ( 7 sec) [ -12505.6429] [ 3107] [depth= 1] . ( 7 sec) [ -12291.8838] [ 2982] [depth= 11] . ( 7 sec) [ -11912.6652] [ 2832] [depth= 1] . ( 7 sec) [ -11711.2624] [ 2760] [depth= 1] . ( 7 sec) [ -11547.9753] [ 2737] [depth= 4] . ( 7 sec) [ -11530.3509] [ 2737] [depth= 1] . ( 8 sec) [ -11298.7025] [ 2726] [depth= 1] . ( 8 sec) [ -11287.4683] [ 2729] [depth= 1] . ( 8 sec) [ -11029.7506] [ 2577] [depth= 5] . ( 8 sec) [ -10993.8916] [ 2553] [depth= 3] . ( 8 sec) [ -10568.0790] [ 2416] [depth= 11] . ( 8 sec) [ -10538.6021] [ 2421] [depth= 6] . ( 8 sec) [ -10520.9435] [ 2411] [depth= 1] . ( 8 sec) [ -10520.3002] [ 2397] [depth= 6] . ( 8 sec) [ -10261.3847] [ 2255] [depth= 11] . ( 8 sec) [ -10225.1192] [ 2255] [depth= 1] . ( 8 sec) [ -10128.8931] [ 2243] [depth= 2] . ( 8 sec) [ -10094.9934] [ 2245] [depth= 1] . ( 9 sec) [ -10064.4859] [ 2246] [depth= 2] . ( 9 sec) [ -10055.6468] [ 2261] [depth= 1] . ( 9 sec) [ -10013.4414] [ 2241] [depth= 6] . ( 9 sec) [ -9954.3028] [ 2237] [depth= 1] . ( 9 sec) [ -9937.5358] [ 2232] [depth= 4] . ( 9 sec) [ -9882.7046] [ 2233] [depth= 1] . ( 9 sec) [ -9879.7780] [ 2238] [depth= 2] . ( 9 sec) [ -9852.8272] [ 2210] [depth= 1] . ( 9 sec) [ -9846.1338] [ 2211] [depth= 1] . ( 9 sec) [ -9676.3796] [ 2229] [depth= 1] . ( 9 sec) [ -9674.2020] [ 2226] [depth= 3] . ( 9 sec) [ -9658.1038] [ 2225] [depth= 1] . ( 10 sec) [ -9655.4315] [ 2246] [depth= 2] . ( 10 sec) [ -9586.5664] [ 2233] [depth= 3] . ( 10 sec) [ -9582.0275] [ 2232] [depth= 1] . ( 10 sec) [ -9569.5348] [ 2216] [depth= 1] . ( 10 sec) [ -9568.0356] [ 2220] [depth= 1] . ( 10 sec) [ -9536.9632] [ 2219] [depth= 1] . ( 10 sec) [ -9529.8396] [ 2218] [depth= 1] . ( 10 sec) [ -9350.6932] [ 2135] [depth= 7] . ( 10 sec) [ -9343.0086] [ 2135] [depth= 1] . ( 10 sec) [ -9326.8738] [ 2129] [depth= 1] . ( 11 sec) [ -9286.3191] [ 2116] [depth= 1] . ( 11 sec) [ -9126.5091] [Branch lengths ] . ( 13 sec) [ -9116.7528] [GTR parameters ] . ( 13 sec) [ -9100.3039] [Alpha ][ 0.734452] . ( 14 sec) [ -9076.9605] [ 2105] [depth= 2] . ( 14 sec) [ -9076.2024] [ 2106] [depth= 1] . ( 15 sec) [ -9061.4313] [ 2103] [depth= 2] . ( 15 sec) [ -9055.6336] [ 2094] [depth= 2] . ( 15 sec) [ -9012.9396] [ 2062] [depth= 1] . ( 15 sec) [ -9005.7964] [ 2053] [depth= 1] . ( 16 sec) [ -8937.6112] [ 1957] [depth= 5] . ( 16 sec) [ -8936.8656] [ 1960] [depth= 1] . ( 16 sec) [ -8921.7181] [ 1957] [depth= 1] . ( 16 sec) [ -8920.0261] [ 1955] [depth= 2] . ( 16 sec) [ -8914.2880] [ 1956] [depth= 1] . ( 17 sec) [ -8913.8102] [ 1959] [depth= 1] . ( 17 sec) [ -8905.9800] [ 1960] [depth= 1] . ( 17 sec) [ -8905.7659] [ 1982] [depth= 1] . ( 17 sec) [ -8905.3431] [ 1960] [depth= 1] . ( 17 sec) [ -8905.3329] [ 1960] [depth= 1] . ( 18 sec) [ -8904.4862] [ 1946] [depth= 3] . ( 18 sec) [ -8899.5518] [ 1946] [depth= 1] . ( 18 sec) [ -8895.8254] [ 1944] [depth= 1] . ( 18 sec) [ -8882.5806] [Branch lengths ] . ( 19 sec) [ -8882.2283] [GTR parameters ] . ( 19 sec) [ -8879.9941] [Alpha ][ 0.854170] . ( 19 sec) [ -8879.5723] [ 1949] [depth= 1] . ( 19 sec) [ -8879.5522] [ 1950] [depth= 1] . ( 20 sec) [ -8878.6361] [ 1955] [depth= 1] . ( 23 sec) [ -8876.9138] [Branch lengths ] . ( 23 sec) [ -8876.8790] [GTR parameters ] . ( 24 sec) [ -8876.7579] [Alpha ][ 0.885487] . ( 28 sec) [ -8876.5647] [Branch lengths ] . ( 57 sec) [ -8876.1941] [ 1965] [depth= 1] . ( 59 sec) [ -8876.1713] [Branch lengths ] . ( 60 sec) [ -8876.1709] [GTR parameters ] . ( 60 sec) [ -8876.1708] [Alpha ][ 0.886372] . ( 60 sec) [ -8876.1708] [Topology ] . ( 61 sec) [ -8876.0268] [Topology ] . ( 62 sec) [ -8875.4134] [Topology ] . ( 63 sec) [ -8875.2121] [Topology ] . ( 64 sec) [ -8875.0853] [Topology ] . ( 65 sec) [ -8874.9987] [Topology ] . ( 66 sec) [ -8874.9372] [Topology ] . ( 67 sec) [ -8874.8920] [Topology ] . ( 67 sec) [ -8874.8899] [GTR parameters ] . ( 67 sec) [ -8874.8899] [Alpha ][ 0.886372] . ( 67 sec) [ -8874.8899] [Topology ] . ( 68 sec) [ -8874.8564] [Topology ] . ( 69 sec) [ -8874.8316] [Topology ] . ( 71 sec) [ -8874.8131] [Topology ] . ( 72 sec) [ -8874.7993] [Topology ] . ( 73 sec) [ -8874.7888] [Topology ] . ( 75 sec) [ -8874.7809] [Topology ] . ( 75 sec) [ -8874.7809] [GTR parameters ] . ( 75 sec) [ -8874.7809] [Alpha ][ 0.886372] . ( 75 sec) [ -8874.7809] [Topology ] . ( 76 sec) [ -8874.7748] [Topology ] . ( 77 sec) [ -8874.7701] [Topology ] . ( 78 sec) [ -8874.7664] [Topology ] . ( 79 sec) [ -8874.7637] [Topology ] . ( 81 sec) [ -8874.7615] [Topology ] . ( 82 sec) [ -8874.7599] [Topology ] . ( 82 sec) [ -8874.7599] [GTR parameters ] . ( 82 sec) [ -8874.7599] [Alpha ][ 0.886372] . ( 82 sec) [ -8874.7599] [Topology ] . ( 84 sec) [ -8874.7586] [Topology ] . ( 85 sec) [ -8874.7576] [Topology ] . ( 85 sec) [ -8874.7576] [GTR parameters ] . ( 85 sec) [ -8874.7576] [Alpha ][ 0.886372] . ( 85 sec) [ -8874.7576] [Topology ] . ( 86 sec) [ -8874.7568] [Topology ] . ( 86 sec) [ -8874.7568] [GTR parameters ] . ( 87 sec) [ -8874.7568] [Alpha ][ 0.886372] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -8874.7558] [Topology ] . Checking for NNIs, optimizing five branches... . ( 107 sec) [ -8874.7549] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.754903. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22550.9494] [GTR parameters ] . ( 1 sec) [ -22007.5885] [Alpha ][ 0.500960] . ( 1 sec) [ -21468.5613] [ 5212] [depth= 6] . ( 1 sec) [ -21429.7387] [ 5198] [depth= 11] . ( 1 sec) [ -21292.4449] [ 5183] [depth= 5] . ( 1 sec) [ -21253.6770] [ 5177] [depth= 5] . ( 1 sec) [ -21012.9640] [ 5120] [depth= 9] . ( 1 sec) [ -20443.8490] [ 5111] [depth= 1] . ( 1 sec) [ -20434.4913] [ 5097] [depth= 6] . ( 1 sec) [ -20347.6588] [ 5113] [depth= 1] . ( 1 sec) [ -19818.9047] [ 4931] [depth= 18] . ( 1 sec) [ -18899.4391] [ 4864] [depth= 16] . ( 2 sec) [ -18727.4861] [ 4802] [depth= 8] . ( 2 sec) [ -18529.8579] [ 4727] [depth= 7] . ( 2 sec) [ -17806.5207] [ 4649] [depth= 11] . ( 2 sec) [ -17561.1140] [ 4642] [depth= 1] . ( 2 sec) [ -17370.5150] [ 4622] [depth= 11] . ( 2 sec) [ -17156.9255] [ 4591] [depth= 9] . ( 2 sec) [ -16888.2057] [ 4464] [depth= 1] . ( 2 sec) [ -16774.4850] [ 4460] [depth= 7] . ( 2 sec) [ -16644.3056] [ 4422] [depth= 13] . ( 2 sec) [ -16163.6498] [ 4241] [depth= 8] . ( 3 sec) [ -15937.8475] [ 4178] [depth= 2] . ( 3 sec) [ -15870.4970] [ 4166] [depth= 11] . ( 3 sec) [ -15134.4701] [ 4143] [depth= 11] . ( 3 sec) [ -15046.3839] [ 4028] [depth= 12] . ( 3 sec) [ -15037.2030] [ 4053] [depth= 2] . ( 3 sec) [ -14639.0354] [ 3885] [depth= 7] . ( 3 sec) [ -14425.8595] [ 3828] [depth= 5] . ( 3 sec) [ -14337.9709] [ 3828] [depth= 2] . ( 3 sec) [ -14211.7505] [ 3784] [depth= 2] . ( 3 sec) [ -14150.4715] [ 3776] [depth= 4] . ( 3 sec) [ -13997.2725] [ 3760] [depth= 3] . ( 3 sec) [ -13905.0761] [ 3632] [depth= 5] . ( 4 sec) [ -13443.6751] [ 3584] [depth= 1] . ( 4 sec) [ -13286.6120] [ 3400] [depth= 5] . ( 4 sec) [ -13261.9836] [ 3391] [depth= 1] . ( 4 sec) [ -13185.6100] [ 3383] [depth= 1] . ( 4 sec) [ -13039.9069] [ 3222] [depth= 6] . ( 4 sec) [ -12796.0369] [ 3189] [depth= 7] . ( 4 sec) [ -12770.5814] [ 3200] [depth= 1] . ( 4 sec) [ -12378.4946] [ 3086] [depth= 8] . ( 4 sec) [ -11906.7824] [ 3072] [depth= 1] . ( 4 sec) [ -11900.9991] [ 3072] [depth= 1] . ( 4 sec) [ -11860.1516] [ 3045] [depth= 7] . ( 5 sec) [ -11710.7129] [ 2890] [depth= 4] . ( 5 sec) [ -11559.1234] [ 2826] [depth= 7] . ( 5 sec) [ -11543.8075] [ 2825] [depth= 1] . ( 5 sec) [ -11518.7148] [ 2818] [depth= 1] . ( 5 sec) [ -11292.2613] [ 2704] [depth= 5] . ( 5 sec) [ -11234.1612] [ 2601] [depth= 5] . ( 5 sec) [ -11060.9678] [ 2604] [depth= 4] . ( 5 sec) [ -10993.9521] [ 2593] [depth= 1] . ( 5 sec) [ -10930.4249] [ 2586] [depth= 6] . ( 5 sec) [ -10794.9604] [ 2612] [depth= 1] . ( 5 sec) [ -10492.3284] [ 2408] [depth= 7] . ( 6 sec) [ -10481.7819] [ 2408] [depth= 1] . ( 6 sec) [ -10453.1437] [ 2405] [depth= 1] . ( 6 sec) [ -10424.7661] [ 2393] [depth= 2] . ( 6 sec) [ -10399.2673] [ 2396] [depth= 1] . ( 6 sec) [ -10393.2401] [ 2396] [depth= 1] . ( 6 sec) [ -10224.4415] [ 2385] [depth= 2] . ( 6 sec) [ -9629.0067] [ 2202] [depth= 5] . ( 6 sec) [ -9601.8299] [ 2199] [depth= 2] . ( 7 sec) [ -9592.6814] [ 2197] [depth= 1] . ( 7 sec) [ -9590.7502] [ 2199] [depth= 1] . ( 7 sec) [ -9590.5025] [ 2197] [depth= 1] . ( 7 sec) [ -9586.0658] [ 2201] [depth= 1] . ( 7 sec) [ -9510.0199] [ 2172] [depth= 3] . ( 7 sec) [ -9509.5325] [ 2167] [depth= 3] . ( 7 sec) [ -9479.9661] [ 2167] [depth= 6] . ( 7 sec) [ -9463.0737] [ 2160] [depth= 3] . ( 7 sec) [ -9442.8791] [ 2155] [depth= 1] . ( 7 sec) [ -9437.3210] [ 2150] [depth= 1] . ( 7 sec) [ -9426.6629] [ 2148] [depth= 2] . ( 7 sec) [ -9413.6547] [ 2136] [depth= 1] . ( 7 sec) [ -9411.3276] [ 2137] [depth= 1] . ( 8 sec) [ -9411.1384] [ 2137] [depth= 1] . ( 8 sec) [ -9407.3142] [ 2137] [depth= 1] . ( 8 sec) [ -9381.0183] [ 2133] [depth= 4] . ( 8 sec) [ -9376.8109] [ 2132] [depth= 1] . ( 9 sec) [ -9263.7138] [Branch lengths ] . ( 10 sec) [ -9256.2807] [GTR parameters ] . ( 10 sec) [ -9240.5638] [Alpha ][ 0.737395] . ( 10 sec) [ -9240.4630] [ 2134] [depth= 2] . ( 10 sec) [ -9115.0098] [ 1999] [depth= 8] . ( 10 sec) [ -9114.6613] [ 2000] [depth= 1] . ( 10 sec) [ -9114.6306] [ 1999] [depth= 1] . ( 11 sec) [ -9102.1205] [ 1987] [depth= 2] . ( 11 sec) [ -8958.3854] [ 1989] [depth= 1] . ( 11 sec) [ -8957.8853] [ 2003] [depth= 1] . ( 11 sec) [ -8957.6743] [ 2003] [depth= 1] . ( 11 sec) [ -8957.6375] [ 2003] [depth= 1] . ( 11 sec) [ -8954.6043] [ 2004] [depth= 1] . ( 12 sec) [ -8921.6666] [ 1974] [depth= 4] . ( 12 sec) [ -8918.7857] [ 1973] [depth= 3] . ( 12 sec) [ -8918.6771] [ 1977] [depth= 2] . ( 12 sec) [ -8918.5946] [ 1969] [depth= 3] . ( 13 sec) [ -8917.0962] [ 1974] [depth= 1] . ( 13 sec) [ -8916.9145] [ 1974] [depth= 1] . ( 13 sec) [ -8911.8973] [ 1969] [depth= 1] . ( 13 sec) [ -8911.6816] [ 1972] [depth= 1] . ( 14 sec) [ -8911.5277] [ 1976] [depth= 1] . ( 14 sec) [ -8910.3160] [ 1975] [depth= 1] . ( 14 sec) [ -8908.5179] [ 1984] [depth= 2] . ( 14 sec) [ -8908.2526] [ 1988] [depth= 1] . ( 14 sec) [ -8907.9821] [ 1986] [depth= 2] . ( 15 sec) [ -8907.9266] [ 1986] [depth= 1] . ( 16 sec) [ -8889.7346] [Branch lengths ] . ( 16 sec) [ -8889.5726] [GTR parameters ] . ( 16 sec) [ -8887.2171] [Alpha ][ 0.863717] . ( 16 sec) [ -8886.0301] [ 1984] [depth= 1] . ( 17 sec) [ -8883.6330] [ 1981] [depth= 1] . ( 17 sec) [ -8883.5753] [ 1982] [depth= 1] . ( 18 sec) [ -8878.5945] [ 1974] [depth= 1] . ( 19 sec) [ -8878.1522] [ 1971] [depth= 1] . ( 22 sec) [ -8875.0742] [Branch lengths ] . ( 22 sec) [ -8875.0544] [GTR parameters ] . ( 23 sec) [ -8875.0081] [Alpha ][ 0.883555] . ( 24 sec) [ -8874.9964] [ 1972] [depth= 1] . ( 28 sec) [ -8874.7681] [Branch lengths ] . ( 28 sec) [ -8874.7681] [GTR parameters ] . ( 29 sec) [ -8874.7675] [Alpha ][ 0.885786] . ( 57 sec) [ -8874.7274] [Branch lengths ] . ( 57 sec) [ -8874.7274] [Topology ] . ( 58 sec) [ -8874.7224] [Topology ] . ( 59 sec) [ -8874.7206] [Topology ] . ( 59 sec) [ -8874.7196] [Topology ] . ( 60 sec) [ -8874.7195] [GTR parameters ] . ( 60 sec) [ -8874.7195] [Alpha ][ 0.886672] . ( 60 sec) [ -8874.7195] [Topology ] . ( 61 sec) [ -8874.7189] [Topology ] . ( 61 sec) [ -8874.7189] [GTR parameters ] . ( 61 sec) [ -8874.7189] [Alpha ][ 0.886672] . Checking for NNIs, optimizing five branches... . ( 68 sec) [ -8874.7180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 78 sec) [ -8874.7178] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8874.717813. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8988.698459 . ( 1 sec) [ -8984.7515] [GTR parameters ] . ( 1 sec) [ -8984.0081] [Alpha ][ 0.908527] . ( 1 sec) [ -8984.0081] [Topology ] . ( 2 sec) [ -8898.6998] [Topology ] . ( 3 sec) [ -8882.6992] [Topology ] . ( 4 sec) [ -8878.8739] [Topology ] . ( 5 sec) [ -8877.7173] [Topology ] . ( 6 sec) [ -8877.2412] [Topology ] . ( 7 sec) [ -8876.9976] [Topology ] . ( 8 sec) [ -8876.8604] [Topology ] . ( 9 sec) [ -8876.7778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -8876.3657] [Topology ] . Before opt ts/t=1.000000 LK=-8876.365684 . ( 20 sec) [ -8875.9438] [GTR parameters ] . ( 20 sec) [ -8875.8939] [Alpha ][ 0.888108] . ( 20 sec) [ -8875.8939] [Topology ] . ( 21 sec) [ -8875.7268] [Topology ] . ( 23 sec) [ -8875.0780] [Topology ] . ( 24 sec) [ -8874.8683] [Topology ] . ( 24 sec) [ -8874.7383] [Topology ] . ( 25 sec) [ -8874.6503] [Topology ] . ( 27 sec) [ -8874.5883] [Topology ] . ( 28 sec) [ -8874.5429] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.542850 . ( 36 sec) [ -8874.5400] [GTR parameters ] . ( 36 sec) [ -8874.5400] [Alpha ][ 0.888108] . ( 36 sec) [ -8874.5400] [Topology ] . ( 37 sec) [ -8874.5064] [Topology ] . ( 38 sec) [ -8874.4814] [Topology ] . ( 39 sec) [ -8874.4629] [Topology ] . ( 40 sec) [ -8874.4489] [Topology ] . ( 41 sec) [ -8874.4384] [Topology ] . ( 42 sec) [ -8874.4303] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.430347 . ( 53 sec) [ -8874.4303] [GTR parameters ] . ( 53 sec) [ -8874.4303] [Alpha ][ 0.888108] . ( 53 sec) [ -8874.4303] [Topology ] . ( 54 sec) [ -8874.4241] [Topology ] . ( 55 sec) [ -8874.4193] [Topology ] . ( 56 sec) [ -8874.4156] [Topology ] . ( 57 sec) [ -8874.4128] [Topology ] . ( 58 sec) [ -8874.4105] [Topology ] . ( 59 sec) [ -8874.4088] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.408835 . ( 67 sec) [ -8874.4088] [GTR parameters ] . ( 67 sec) [ -8874.4088] [Alpha ][ 0.888108] . ( 67 sec) [ -8874.4088] [Topology ] . ( 68 sec) [ -8874.4075] [Topology ] . ( 69 sec) [ -8874.4065] [Topology ] . ( 70 sec) [ -8874.4057] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8874.405690 . ( 76 sec) [ -8874.4057] [GTR parameters ] . ( 76 sec) [ -8874.4057] [Alpha ][ 0.888108] . ( 76 sec) [ -8874.4057] [Topology ] . ( 77 sec) [ -8874.4051] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 96 sec) [ -8984.7515] [GTR parameters ] . ( 96 sec) [ -8984.0081] [Alpha ][ 0.908527] . ( 96 sec) [ -8981.9228] [ 1952] [depth= 1] . ( 96 sec) [ -8980.7063] [ 1952] [depth= 1] . ( 96 sec) [ -8980.6844] [ 1952] [depth= 1] . ( 96 sec) [ -8980.6147] [ 1952] [depth= 1] . ( 97 sec) [ -8970.6809] [ 1950] [depth= 1] . ( 97 sec) [ -8968.5819] [ 1950] [depth= 3] . ( 97 sec) [ -8960.8257] [ 1952] [depth= 1] . ( 97 sec) [ -8952.0226] [ 1960] [depth= 1] . ( 97 sec) [ -8948.0852] [ 1973] [depth= 1] . ( 98 sec) [ -8947.8460] [ 1975] [depth= 1] . ( 98 sec) [ -8945.7109] [ 1977] [depth= 1] . ( 98 sec) [ -8944.2047] [ 1975] [depth= 1] . ( 98 sec) [ -8939.4866] [ 1964] [depth= 1] . ( 99 sec) [ -8938.3876] [ 1965] [depth= 1] . ( 99 sec) [ -8937.4598] [ 1964] [depth= 1] . ( 99 sec) [ -8935.9631] [ 1965] [depth= 1] . ( 99 sec) [ -8934.9123] [ 1965] [depth= 1] . ( 99 sec) [ -8934.6651] [ 1965] [depth= 1] . ( 99 sec) [ -8933.9542] [ 1965] [depth= 1] . ( 100 sec) [ -8927.3424] [ 1978] [depth= 2] . ( 100 sec) [ -8925.6618] [ 1977] [depth= 1] . ( 100 sec) [ -8925.3041] [ 1982] [depth= 1] . ( 100 sec) [ -8924.9177] [ 1981] [depth= 1] . ( 100 sec) [ -8921.8065] [ 1989] [depth= 1] . ( 100 sec) [ -8921.6984] [ 1992] [depth= 1] . ( 101 sec) [ -8919.9112] [ 1989] [depth= 1] . ( 101 sec) [ -8919.8347] [ 1978] [depth= 2] . ( 101 sec) [ -8919.5004] [ 1981] [depth= 1] . ( 101 sec) [ -8919.3624] [ 1981] [depth= 1] . ( 102 sec) [ -8892.7533] [Branch lengths ] . ( 102 sec) [ -8892.5878] [GTR parameters ] . ( 102 sec) [ -8892.4633] [Alpha ][ 0.875672] . ( 104 sec) [ -8892.4182] [ 1986] [depth= 1] . ( 104 sec) [ -8884.0682] [ 1979] [depth= 3] . ( 105 sec) [ -8883.9909] [ 1982] [depth= 1] . ( 105 sec) [ -8882.9711] [ 1985] [depth= 1] . ( 105 sec) [ -8880.9338] [ 1964] [depth= 1] . ( 107 sec) [ -8880.8322] [ 1962] [depth= 1] . ( 108 sec) [ -8876.9242] [Branch lengths ] . ( 108 sec) [ -8876.8415] [GTR parameters ] . ( 109 sec) [ -8876.8275] [Alpha ][ 0.886633] . ( 109 sec) [ -8876.7900] [ 1959] [depth= 1] . ( 114 sec) [ -8876.2734] [Branch lengths ] . ( 114 sec) [ -8876.2732] [GTR parameters ] . ( 114 sec) [ -8876.2732] [Alpha ][ 0.886633] . ( 124 sec) [ -8875.9278] [ 1968] [depth= 2] . ( 135 sec) [ -8875.8592] [ 1969] [depth= 1] . ( 136 sec) [ -8875.7478] [ 1970] [depth= 1] . ( 138 sec) [ -8875.7160] [ 1968] [depth= 1] . ( 140 sec) [ -8875.1211] [Branch lengths ] . ( 140 sec) [ -8875.1195] [GTR parameters ] . ( 140 sec) [ -8875.1195] [Alpha ][ 0.886633] . ( 149 sec) [ -8874.8589] [ 1970] [depth= 1] . ( 162 sec) [ -8874.8301] [Branch lengths ] . ( 162 sec) [ -8874.8289] [GTR parameters ] . ( 162 sec) [ -8874.8289] [Alpha ][ 0.885746] . ( 162 sec) [ -8874.8289] [Topology ] . ( 163 sec) [ -8874.8233] [Topology ] . ( 163 sec) [ -8874.8202] [Topology ] . ( 164 sec) [ -8874.8180] [Topology ] . ( 165 sec) [ -8874.8164] [Topology ] . ( 166 sec) [ -8874.8153] [Topology ] . ( 166 sec) [ -8874.8144] [Topology ] . ( 166 sec) [ -8874.8143] [GTR parameters ] . ( 167 sec) [ -8874.8143] [Alpha ][ 0.886632] . ( 167 sec) [ -8874.8143] [Topology ] . ( 167 sec) [ -8874.8135] [Topology ] . ( 167 sec) [ -8874.8135] [GTR parameters ] . ( 168 sec) [ -8874.8135] [Alpha ][ 0.886632] . Checking for NNIs, optimizing five branches... . ( 174 sec) [ -8874.4160] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8874.405073 . Log likelihood obtained after SPR moves : -8874.416035 . Log likelihood of the current tree: -8874.405073. . Printing the most likely tree in file 'data8.phy_phyml_tree.txt'... . Best log likelihood : -8874.405073 . Time used 0h3m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo