.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2764_57x803_2006.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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 628 patterns found. (out of a total of 803 sites) . 286 sites without polymorphism (35.62%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -17033.8918] [GTR parameters ] . ( 2 sec) [ -16736.6359] [Alpha ][ 0.500960] . ( 2 sec) [ -16540.3368] [ 3038] [depth= 12] . ( 3 sec) [ -16072.9022] [ 3015] [depth= 3] . ( 3 sec) [ -15957.4028] [ 3008] [depth= 11] . ( 3 sec) [ -15902.2066] [ 2987] [depth= 1] . ( 3 sec) [ -15800.2771] [ 2982] [depth= 4] . ( 3 sec) [ -15770.5187] [ 2980] [depth= 3] . ( 3 sec) [ -15739.7657] [ 2976] [depth= 6] . ( 3 sec) [ -15692.2165] [ 2964] [depth= 4] . ( 3 sec) [ -15647.6601] [ 2948] [depth= 3] . ( 3 sec) [ -15607.0166] [ 2939] [depth= 2] . ( 3 sec) [ -15598.5525] [ 2935] [depth= 6] . ( 3 sec) [ -15570.3537] [ 2925] [depth= 1] . ( 3 sec) [ -15459.3566] [ 2925] [depth= 2] . ( 4 sec) [ -15443.9980] [ 2914] [depth= 4] . ( 4 sec) [ -15306.6439] [ 2910] [depth= 2] . ( 4 sec) [ -15183.7649] [ 2890] [depth= 4] . ( 4 sec) [ -15103.9880] [ 2882] [depth= 6] . ( 4 sec) [ -15041.3474] [ 2872] [depth= 6] . ( 4 sec) [ -14982.3437] [ 2873] [depth= 12] . ( 4 sec) [ -14878.3385] [ 2864] [depth= 14] . ( 4 sec) [ -14736.5006] [ 2828] [depth= 4] . ( 4 sec) [ -14578.4027] [ 2797] [depth= 12] . ( 4 sec) [ -14573.9992] [ 2788] [depth= 5] . ( 5 sec) [ -14549.7912] [ 2784] [depth= 13] . ( 5 sec) [ -14453.1634] [ 2771] [depth= 9] . ( 5 sec) [ -14384.8783] [ 2769] [depth= 1] . ( 5 sec) [ -14306.8807] [ 2750] [depth= 6] . ( 5 sec) [ -14155.1443] [ 2726] [depth= 11] . ( 5 sec) [ -14061.1342] [ 2693] [depth= 8] . ( 5 sec) [ -13730.9681] [ 2644] [depth= 15] . ( 5 sec) [ -13702.2104] [ 2645] [depth= 1] . ( 5 sec) [ -13585.2178] [ 2602] [depth= 6] . ( 5 sec) [ -13486.7937] [ 2601] [depth= 2] . ( 5 sec) [ -13486.7376] [ 2602] [depth= 1] . ( 6 sec) [ -13426.5963] [ 2595] [depth= 3] . ( 6 sec) [ -13381.1680] [ 2575] [depth= 1] . ( 6 sec) [ -13289.0649] [ 2561] [depth= 5] . ( 6 sec) [ -13213.9932] [ 2539] [depth= 3] . ( 6 sec) [ -13181.4794] [ 2526] [depth= 8] . ( 6 sec) [ -13067.8202] [ 2520] [depth= 19] . ( 6 sec) [ -12990.7470] [ 2492] [depth= 5] . ( 6 sec) [ -12936.9286] [ 2477] [depth= 1] . ( 6 sec) [ -12884.2560] [ 2471] [depth= 2] . ( 6 sec) [ -12860.0241] [ 2469] [depth= 10] . ( 7 sec) [ -12854.7803] [ 2466] [depth= 4] . ( 7 sec) [ -12843.5441] [ 2467] [depth= 1] . ( 7 sec) [ -12831.0020] [ 2462] [depth= 5] . ( 7 sec) [ -12757.0561] [ 2440] [depth= 11] . ( 7 sec) [ -12717.9031] [ 2435] [depth= 4] . ( 7 sec) [ -12686.0665] [ 2425] [depth= 7] . ( 7 sec) [ -12579.4839] [ 2393] [depth= 15] . ( 7 sec) [ -12489.2660] [ 2372] [depth= 2] . ( 7 sec) [ -12465.0523] [ 2369] [depth= 1] . ( 7 sec) [ -12446.8854] [ 2370] [depth= 2] . ( 7 sec) [ -12398.9917] [ 2346] [depth= 5] . ( 7 sec) [ -12308.4116] [ 2351] [depth= 1] . ( 8 sec) [ -12268.6852] [ 2327] [depth= 21] . ( 8 sec) [ -12268.0442] [ 2326] [depth= 1] . ( 8 sec) [ -12251.2070] [ 2317] [depth= 8] . ( 8 sec) [ -12205.8807] [ 2304] [depth= 2] . ( 8 sec) [ -12198.4488] [ 2309] [depth= 1] . ( 8 sec) [ -12197.9868] [ 2309] [depth= 1] . ( 8 sec) [ -12011.0940] [ 2256] [depth= 6] . ( 8 sec) [ -11976.5956] [ 2251] [depth= 3] . ( 8 sec) [ -11971.4575] [ 2251] [depth= 1] . ( 9 sec) [ -11971.2896] [ 2251] [depth= 2] . ( 9 sec) [ -11903.1687] [ 2235] [depth= 8] . ( 9 sec) [ -11864.0752] [ 2226] [depth= 1] . ( 9 sec) [ -11727.5735] [ 2224] [depth= 13] . ( 9 sec) [ -11720.5390] [ 2220] [depth= 1] . ( 9 sec) [ -11711.5756] [ 2222] [depth= 2] . ( 9 sec) [ -11628.6941] [ 2199] [depth= 1] . ( 9 sec) [ -11508.8945] [ 2169] [depth= 11] . ( 9 sec) [ -11504.3670] [ 2168] [depth= 1] . ( 10 sec) [ -11502.9363] [ 2167] [depth= 1] . ( 10 sec) [ -11481.7520] [ 2161] [depth= 1] . ( 10 sec) [ -11481.3436] [ 2163] [depth= 1] . ( 10 sec) [ -11461.1065] [ 2157] [depth= 3] . ( 10 sec) [ -11397.0622] [ 2145] [depth= 12] . ( 10 sec) [ -11395.0376] [ 2145] [depth= 1] . ( 10 sec) [ -11392.6715] [ 2144] [depth= 1] . ( 10 sec) [ -11392.4027] [ 2144] [depth= 1] . ( 10 sec) [ -11383.7996] [ 2142] [depth= 3] . ( 10 sec) [ -11373.6436] [ 2141] [depth= 1] . ( 10 sec) [ -11370.4739] [ 2139] [depth= 1] . ( 11 sec) [ -11364.9927] [ 2141] [depth= 1] . ( 11 sec) [ -11330.0204] [ 2132] [depth= 1] . ( 11 sec) [ -11194.4209] [ 2118] [depth= 2] . ( 11 sec) [ -11191.7045] [ 2117] [depth= 1] . ( 11 sec) [ -11186.7595] [ 2118] [depth= 1] . ( 11 sec) [ -11186.6166] [ 2117] [depth= 1] . ( 11 sec) [ -11185.3874] [ 2118] [depth= 1] . ( 11 sec) [ -11177.8304] [ 2116] [depth= 2] . ( 11 sec) [ -11140.8807] [ 2105] [depth= 6] . ( 12 sec) [ -11140.2862] [ 2107] [depth= 2] . ( 12 sec) [ -11139.9111] [ 2108] [depth= 1] . ( 12 sec) [ -10995.2938] [ 2102] [depth= 3] . ( 12 sec) [ -10994.4023] [ 2102] [depth= 1] . ( 12 sec) [ -10960.0663] [ 2087] [depth= 8] . ( 12 sec) [ -10956.9367] [ 2089] [depth= 1] . ( 12 sec) [ -10951.3543] [ 2081] [depth= 2] . ( 12 sec) [ -10950.6393] [ 2083] [depth= 1] . ( 12 sec) [ -10949.6251] [ 2088] [depth= 3] . ( 13 sec) [ -10948.5539] [ 2100] [depth= 1] . ( 13 sec) [ -10944.0352] [ 2099] [depth= 4] . ( 13 sec) [ -10940.3752] [ 2098] [depth= 1] . ( 13 sec) [ -10935.1781] [ 2099] [depth= 1] . ( 13 sec) [ -10925.6667] [ 2092] [depth= 5] . ( 13 sec) [ -10904.9929] [ 2084] [depth= 2] . ( 13 sec) [ -10774.0809] [ 2032] [depth= 8] . ( 13 sec) [ -10714.6924] [ 2029] [depth= 1] . ( 13 sec) [ -10712.3781] [ 2029] [depth= 1] . ( 13 sec) [ -10705.9574] [ 2027] [depth= 1] . ( 13 sec) [ -10693.8249] [ 2026] [depth= 3] . ( 14 sec) [ -10578.8486] [ 2015] [depth= 1] . ( 14 sec) [ -10553.6913] [ 2018] [depth= 1] . ( 14 sec) [ -10552.2886] [ 2018] [depth= 1] . ( 14 sec) [ -10551.0802] [ 2019] [depth= 1] . ( 14 sec) [ -10530.5767] [ 2023] [depth= 5] . ( 14 sec) [ -10528.0855] [ 2021] [depth= 1] . ( 14 sec) [ -10487.2444] [ 2009] [depth= 7] . ( 14 sec) [ -10484.8383] [ 2014] [depth= 1] . ( 14 sec) [ -10483.4122] [ 2019] [depth= 1] . ( 14 sec) [ -10466.3836] [ 2021] [depth= 2] . ( 15 sec) [ -10452.7265] [ 2016] [depth= 1] . ( 15 sec) [ -10451.1939] [ 2015] [depth= 1] . ( 15 sec) [ -10439.5428] [ 2011] [depth= 2] . ( 15 sec) [ -10435.5903] [ 2017] [depth= 1] . ( 16 sec) [ -10303.6266] [Branch lengths ] . ( 17 sec) [ -10299.2616] [GTR parameters ] . ( 17 sec) [ -10298.8093] [Alpha ][ 0.530443] . ( 17 sec) [ -10298.4089] [ 2015] [depth= 2] . ( 18 sec) [ -10298.1849] [ 2014] [depth= 2] . ( 18 sec) [ -10296.5785] [ 2009] [depth= 3] . ( 18 sec) [ -10296.2542] [ 2009] [depth= 2] . ( 18 sec) [ -10294.9948] [ 2008] [depth= 1] . ( 19 sec) [ -10292.1055] [ 2006] [depth= 1] . ( 19 sec) [ -10291.7415] [ 2007] [depth= 1] . ( 19 sec) [ -10291.7288] [ 2007] [depth= 1] . ( 19 sec) [ -10280.9635] [ 2005] [depth= 1] . ( 19 sec) [ -10280.2812] [ 2005] [depth= 1] . ( 20 sec) [ -10280.0519] [ 2005] [depth= 1] . ( 20 sec) [ -10274.9894] [ 1999] [depth= 2] . ( 21 sec) [ -10274.9300] [ 1998] [depth= 1] . ( 21 sec) [ -10274.3035] [ 1997] [depth= 1] . ( 21 sec) [ -10273.9237] [ 1999] [depth= 4] . ( 21 sec) [ -10266.6492] [ 1993] [depth= 3] . ( 21 sec) [ -10264.5606] [ 1994] [depth= 1] . ( 22 sec) [ -10264.3783] [ 1995] [depth= 1] . ( 22 sec) [ -10262.7107] [ 1993] [depth= 3] . ( 22 sec) [ -10250.4556] [ 1986] [depth= 3] . ( 22 sec) [ -10250.1491] [ 1986] [depth= 2] . ( 22 sec) [ -10246.5612] [ 1980] [depth= 2] . ( 22 sec) [ -10245.5813] [ 1979] [depth= 1] . ( 23 sec) [ -10244.2206] [ 1976] [depth= 1] . ( 23 sec) [ -10244.2002] [ 1977] [depth= 1] . ( 23 sec) [ -10241.5293] [ 1975] [depth= 1] . ( 23 sec) [ -10240.3615] [ 1969] [depth= 1] . ( 24 sec) [ -10239.7216] [ 1974] [depth= 1] . ( 24 sec) [ -10239.7030] [ 1974] [depth= 1] . ( 24 sec) [ -10239.5057] [ 1974] [depth= 1] . ( 25 sec) [ -10220.7045] [ 1967] [depth= 1] . ( 25 sec) [ -10220.3081] [ 1970] [depth= 1] . ( 25 sec) [ -10216.1562] [ 1965] [depth= 5] . ( 25 sec) [ -10215.4058] [ 1964] [depth= 1] . ( 26 sec) [ -10214.3273] [ 1966] [depth= 1] . ( 26 sec) [ -10213.1912] [ 1966] [depth= 1] . ( 26 sec) [ -10212.5385] [ 1969] [depth= 1] . ( 27 sec) [ -10211.4404] [ 1969] [depth= 1] . ( 27 sec) [ -10208.5301] [ 1968] [depth= 2] . ( 28 sec) [ -10207.8899] [ 1969] [depth= 1] . ( 28 sec) [ -10207.4005] [ 1967] [depth= 2] . ( 28 sec) [ -10206.5407] [ 1959] [depth= 2] . ( 29 sec) [ -10203.5280] [ 1953] [depth= 7] . ( 29 sec) [ -10200.3814] [ 1950] [depth= 2] . ( 30 sec) [ -10199.7474] [ 1948] [depth= 1] . ( 31 sec) [ -10177.8202] [Branch lengths ] . ( 32 sec) [ -10177.7004] [GTR parameters ] . ( 32 sec) [ -10177.5292] [Alpha ][ 0.549602] . ( 35 sec) [ -10176.6968] [ 1949] [depth= 1] . ( 35 sec) [ -10176.6176] [ 1950] [depth= 1] . ( 36 sec) [ -10174.3789] [ 1951] [depth= 1] . ( 36 sec) [ -10167.1382] [ 1949] [depth= 2] . ( 37 sec) [ -10166.5791] [ 1949] [depth= 1] . ( 43 sec) [ -10166.0056] [ 1949] [depth= 1] . ( 44 sec) [ -10165.9381] [ 1948] [depth= 1] . ( 45 sec) [ -10164.6617] [ 1953] [depth= 5] . ( 46 sec) [ -10163.8735] [ 1950] [depth= 1] . ( 47 sec) [ -10160.0578] [Branch lengths ] . ( 48 sec) [ -10159.9399] [GTR parameters ] . ( 48 sec) [ -10159.9340] [Alpha ][ 0.553299] . ( 61 sec) [ -10159.7168] [ 1950] [depth= 1] . ( 66 sec) [ -10159.3826] [Branch lengths ] . ( 66 sec) [ -10159.3820] [GTR parameters ] . ( 66 sec) [ -10159.3816] [Alpha ][ 0.554192] . ( 67 sec) [ -10159.3110] [ 1946] [depth= 1] . ( 69 sec) [ -10159.1718] [ 1943] [depth= 1] . ( 73 sec) [ -10159.0455] [ 1940] [depth= 1] . ( 132 sec) [ -10157.7421] [Branch lengths ] . ( 133 sec) [ -10157.7398] [GTR parameters ] . ( 133 sec) [ -10157.7345] [Alpha ][ 0.557728] . ( 172 sec) [ -10157.7150] [ 1939] [depth= 1] . ( 197 sec) [ -10157.6470] [Branch lengths ] . ( 197 sec) [ -10157.6467] [GTR parameters ] . ( 197 sec) [ -10157.6464] [Alpha ][ 0.558562] . ( 197 sec) [ -10157.6464] [Topology ] . ( 199 sec) [ -10157.6447] [Topology ] . ( 200 sec) [ -10157.6444] [Topology ] . ( 201 sec) [ -10157.6444] [GTR parameters ] . ( 201 sec) [ -10157.6444] [Alpha ][ 0.558562] . ( 201 sec) [ -10157.6444] [Topology ] . ( 202 sec) [ -10157.6443] [Topology ] . ( 203 sec) [ -10157.6443] [GTR parameters ] . ( 203 sec) [ -10157.6443] [Alpha ][ 0.558562] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.644335. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -16807.6045] [GTR parameters ] . ( 2 sec) [ -16488.4188] [Alpha ][ 0.500960] . ( 2 sec) [ -16110.0548] [ 3132] [depth= 8] . ( 2 sec) [ -15836.5404] [ 3102] [depth= 4] . ( 2 sec) [ -15795.5014] [ 3091] [depth= 3] . ( 2 sec) [ -15720.1134] [ 3077] [depth= 7] . ( 2 sec) [ -15656.3946] [ 3059] [depth= 2] . ( 3 sec) [ -15612.0829] [ 3057] [depth= 17] . ( 3 sec) [ -15541.6991] [ 3044] [depth= 5] . ( 3 sec) [ -15487.1534] [ 3034] [depth= 9] . ( 3 sec) [ -15448.6049] [ 3015] [depth= 1] . ( 3 sec) [ -15423.4423] [ 3008] [depth= 10] . ( 3 sec) [ -15401.1181] [ 2997] [depth= 8] . ( 3 sec) [ -15395.9077] [ 2995] [depth= 3] . ( 3 sec) [ -15344.4887] [ 2978] [depth= 5] . ( 3 sec) [ -15217.0461] [ 2974] [depth= 4] . ( 3 sec) [ -15129.3926] [ 2961] [depth= 12] . ( 3 sec) [ -15106.1773] [ 2967] [depth= 1] . ( 4 sec) [ -15074.9795] [ 2962] [depth= 1] . ( 4 sec) [ -14956.9007] [ 2933] [depth= 16] . ( 4 sec) [ -14771.4704] [ 2878] [depth= 2] . ( 4 sec) [ -14714.4960] [ 2869] [depth= 1] . ( 4 sec) [ -14613.0746] [ 2850] [depth= 15] . ( 4 sec) [ -14503.4225] [ 2831] [depth= 7] . ( 4 sec) [ -14341.7703] [ 2808] [depth= 10] . ( 4 sec) [ -14149.8833] [ 2782] [depth= 2] . ( 4 sec) [ -14103.5312] [ 2777] [depth= 4] . ( 4 sec) [ -14077.4959] [ 2777] [depth= 1] . ( 5 sec) [ -14055.0200] [ 2765] [depth= 1] . ( 5 sec) [ -14050.7814] [ 2765] [depth= 8] . ( 5 sec) [ -13992.1232] [ 2743] [depth= 11] . ( 5 sec) [ -13804.1260] [ 2696] [depth= 7] . ( 5 sec) [ -13707.1158] [ 2679] [depth= 14] . ( 5 sec) [ -13687.5752] [ 2673] [depth= 1] . ( 5 sec) [ -13617.0813] [ 2658] [depth= 5] . ( 5 sec) [ -13615.7223] [ 2656] [depth= 5] . ( 5 sec) [ -13589.1275] [ 2655] [depth= 4] . ( 5 sec) [ -13556.9840] [ 2629] [depth= 1] . ( 6 sec) [ -13514.0079] [ 2614] [depth= 5] . ( 6 sec) [ -13501.0022] [ 2609] [depth= 1] . ( 6 sec) [ -13454.3474] [ 2605] [depth= 4] . ( 6 sec) [ -13409.1889] [ 2595] [depth= 5] . ( 6 sec) [ -13321.9018] [ 2592] [depth= 2] . ( 6 sec) [ -13226.4653] [ 2564] [depth= 4] . ( 6 sec) [ -13222.0830] [ 2558] [depth= 1] . ( 6 sec) [ -13221.4527] [ 2564] [depth= 1] . ( 6 sec) [ -13148.5385] [ 2542] [depth= 6] . ( 6 sec) [ -13117.6484] [ 2539] [depth= 1] . ( 7 sec) [ -13027.5549] [ 2535] [depth= 2] . ( 7 sec) [ -13002.9856] [ 2536] [depth= 1] . ( 7 sec) [ -12995.5285] [ 2535] [depth= 1] . ( 7 sec) [ -12951.5245] [ 2537] [depth= 7] . ( 7 sec) [ -12837.3249] [ 2516] [depth= 8] . ( 7 sec) [ -12708.0389] [ 2533] [depth= 1] . ( 7 sec) [ -12531.5610] [ 2481] [depth= 12] . ( 7 sec) [ -12510.3165] [ 2478] [depth= 4] . ( 7 sec) [ -12494.0260] [ 2470] [depth= 1] . ( 7 sec) [ -12472.5642] [ 2461] [depth= 5] . ( 8 sec) [ -12424.4304] [ 2456] [depth= 6] . ( 8 sec) [ -12372.5009] [ 2455] [depth= 1] . ( 8 sec) [ -12276.8459] [ 2423] [depth= 2] . ( 8 sec) [ -12237.2817] [ 2415] [depth= 7] . ( 8 sec) [ -12234.5682] [ 2417] [depth= 1] . ( 8 sec) [ -12232.0621] [ 2423] [depth= 1] . ( 8 sec) [ -12172.2994] [ 2403] [depth= 14] . ( 8 sec) [ -12137.5624] [ 2382] [depth= 13] . ( 8 sec) [ -12046.1973] [ 2370] [depth= 6] . ( 9 sec) [ -12034.2959] [ 2368] [depth= 1] . ( 9 sec) [ -12022.3717] [ 2364] [depth= 1] . ( 9 sec) [ -11968.2800] [ 2349] [depth= 4] . ( 9 sec) [ -11945.2661] [ 2336] [depth= 1] . ( 9 sec) [ -11944.0378] [ 2341] [depth= 1] . ( 9 sec) [ -11820.4838] [ 2329] [depth= 3] . ( 10 sec) [ -11820.3595] [ 2332] [depth= 4] . ( 10 sec) [ -11757.4693] [ 2330] [depth= 1] . ( 10 sec) [ -11728.4545] [ 2319] [depth= 7] . ( 10 sec) [ -11719.2409] [ 2308] [depth= 8] . ( 10 sec) [ -11717.8330] [ 2303] [depth= 2] . ( 10 sec) [ -11665.8013] [ 2292] [depth= 1] . ( 10 sec) [ -11655.5129] [ 2292] [depth= 1] . ( 10 sec) [ -11613.7793] [ 2281] [depth= 1] . ( 10 sec) [ -11581.5511] [ 2274] [depth= 1] . ( 10 sec) [ -11567.5070] [ 2260] [depth= 2] . ( 10 sec) [ -11543.2295] [ 2260] [depth= 3] . ( 11 sec) [ -11461.9673] [ 2226] [depth= 8] . ( 11 sec) [ -11447.4143] [ 2224] [depth= 1] . ( 11 sec) [ -11435.0163] [ 2220] [depth= 1] . ( 11 sec) [ -11428.2814] [ 2218] [depth= 1] . ( 11 sec) [ -11386.6046] [ 2198] [depth= 1] . ( 11 sec) [ -11360.4759] [ 2189] [depth= 8] . ( 12 sec) [ -11356.2452] [ 2184] [depth= 1] . ( 12 sec) [ -11356.0297] [ 2184] [depth= 1] . ( 12 sec) [ -11323.4439] [ 2177] [depth= 12] . ( 12 sec) [ -11322.8146] [ 2177] [depth= 2] . ( 12 sec) [ -11322.0147] [ 2177] [depth= 1] . ( 12 sec) [ -11318.9592] [ 2178] [depth= 1] . ( 12 sec) [ -11294.4574] [ 2168] [depth= 6] . ( 12 sec) [ -11282.6671] [ 2162] [depth= 2] . ( 12 sec) [ -11263.1314] [ 2158] [depth= 1] . ( 12 sec) [ -11157.2726] [ 2159] [depth= 1] . ( 13 sec) [ -11154.8806] [ 2162] [depth= 2] . ( 13 sec) [ -11118.6179] [ 2141] [depth= 2] . ( 13 sec) [ -11061.0694] [ 2122] [depth= 3] . ( 13 sec) [ -11046.7993] [ 2119] [depth= 1] . ( 13 sec) [ -11045.2814] [ 2121] [depth= 1] . ( 13 sec) [ -11044.9412] [ 2123] [depth= 1] . ( 13 sec) [ -11036.4104] [ 2118] [depth= 1] . ( 13 sec) [ -11023.2822] [ 2114] [depth= 1] . ( 13 sec) [ -10774.4827] [ 2108] [depth= 5] . ( 14 sec) [ -10699.4156] [ 2079] [depth= 8] . ( 14 sec) [ -10679.7823] [ 2077] [depth= 1] . ( 14 sec) [ -10676.6700] [ 2074] [depth= 2] . ( 14 sec) [ -10637.3721] [ 2060] [depth= 3] . ( 14 sec) [ -10635.5419] [ 2061] [depth= 1] . ( 14 sec) [ -10634.8100] [ 2065] [depth= 3] . ( 14 sec) [ -10612.0981] [ 2059] [depth= 3] . ( 14 sec) [ -10609.0839] [ 2055] [depth= 1] . ( 15 sec) [ -10590.7454] [ 2053] [depth= 7] . ( 15 sec) [ -10578.9384] [ 2052] [depth= 5] . ( 15 sec) [ -10577.9428] [ 2051] [depth= 1] . ( 15 sec) [ -10577.6360] [ 2052] [depth= 1] . ( 15 sec) [ -10577.1037] [ 2050] [depth= 4] . ( 15 sec) [ -10569.9912] [ 2047] [depth= 1] . ( 15 sec) [ -10564.7952] [ 2042] [depth= 1] . ( 15 sec) [ -10546.7120] [ 2029] [depth= 4] . ( 16 sec) [ -10530.3838] [ 2023] [depth= 2] . ( 16 sec) [ -10517.6822] [ 2021] [depth= 6] . ( 16 sec) [ -10508.4927] [ 2018] [depth= 1] . ( 16 sec) [ -10493.8863] [ 2004] [depth= 1] . ( 17 sec) [ -10339.2644] [Branch lengths ] . ( 18 sec) [ -10337.5027] [GTR parameters ] . ( 18 sec) [ -10336.4211] [Alpha ][ 0.547123] . ( 18 sec) [ -10330.9334] [ 1999] [depth= 5] . ( 18 sec) [ -10325.9170] [ 1996] [depth= 1] . ( 18 sec) [ -10325.5100] [ 1994] [depth= 1] . ( 19 sec) [ -10293.1882] [ 1983] [depth= 2] . ( 19 sec) [ -10262.1899] [ 1975] [depth= 1] . ( 20 sec) [ -10253.8986] [ 1973] [depth= 4] . ( 20 sec) [ -10250.5618] [ 1974] [depth= 1] . ( 20 sec) [ -10234.6698] [ 1965] [depth= 3] . ( 20 sec) [ -10233.5633] [ 1964] [depth= 1] . ( 21 sec) [ -10219.0400] [ 1962] [depth= 1] . ( 21 sec) [ -10216.3083] [ 1961] [depth= 1] . ( 21 sec) [ -10214.7640] [ 1962] [depth= 1] . ( 22 sec) [ -10214.3795] [ 1959] [depth= 2] . ( 22 sec) [ -10204.0930] [ 1957] [depth= 1] . ( 22 sec) [ -10202.5191] [ 1955] [depth= 1] . ( 23 sec) [ -10201.1859] [ 1954] [depth= 1] . ( 23 sec) [ -10200.7829] [ 1955] [depth= 1] . ( 23 sec) [ -10200.2074] [ 1956] [depth= 1] . ( 24 sec) [ -10183.6247] [ 1950] [depth= 4] . ( 24 sec) [ -10183.1766] [ 1950] [depth= 1] . ( 25 sec) [ -10183.0389] [ 1952] [depth= 1] . ( 25 sec) [ -10183.0184] [ 1946] [depth= 2] . ( 26 sec) [ -10179.9496] [ 1945] [depth= 2] . ( 26 sec) [ -10179.1906] [ 1949] [depth= 2] . ( 27 sec) [ -10178.9998] [ 1949] [depth= 1] . ( 31 sec) [ -10173.7199] [ 1944] [depth= 2] . ( 34 sec) [ -10165.4910] [Branch lengths ] . ( 35 sec) [ -10165.0412] [GTR parameters ] . ( 35 sec) [ -10165.0120] [Alpha ][ 0.555437] . ( 36 sec) [ -10164.6869] [ 1945] [depth= 1] . ( 37 sec) [ -10163.9603] [ 1945] [depth= 3] . ( 38 sec) [ -10163.2387] [ 1945] [depth= 1] . ( 45 sec) [ -10163.0611] [ 1945] [depth= 1] . ( 51 sec) [ -10160.3416] [Branch lengths ] . ( 53 sec) [ -10160.3254] [GTR parameters ] . ( 53 sec) [ -10160.3253] [Alpha ][ 0.555993] . ( 69 sec) [ -10160.1726] [Branch lengths ] . ( 75 sec) [ -10160.1391] [ 1944] [depth= 1] . ( 103 sec) [ -10160.0703] [ 1941] [depth= 1] . ( 103 sec) [ -10159.9835] [ 1940] [depth= 1] . ( 132 sec) [ -10159.2671] [Branch lengths ] . ( 133 sec) [ -10159.2618] [GTR parameters ] . ( 133 sec) [ -10159.2585] [Alpha ][ 0.558768] . ( 133 sec) [ -10159.2585] [Topology ] . ( 135 sec) [ -10158.6478] [Topology ] . ( 136 sec) [ -10158.3934] [Topology ] . ( 138 sec) [ -10157.8284] [Topology ] . ( 140 sec) [ -10157.6696] [Topology ] . ( 141 sec) [ -10157.6517] [Topology ] . ( 143 sec) [ -10157.6488] [Topology ] . ( 144 sec) [ -10157.6483] [Topology ] . ( 145 sec) [ -10157.6445] [GTR parameters ] . ( 146 sec) [ -10157.6445] [Alpha ][ 0.558768] . ( 146 sec) [ -10157.6445] [Topology ] . ( 147 sec) [ -10157.6444] [Topology ] . ( 147 sec) [ -10157.6444] [GTR parameters ] . ( 148 sec) [ -10157.6444] [Alpha ][ 0.558768] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.644395. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16562.7289] [GTR parameters ] . ( 2 sec) [ -16260.0464] [Alpha ][ 0.500960] . ( 2 sec) [ -16148.6883] [ 3076] [depth= 10] . ( 2 sec) [ -15941.0116] [ 3053] [depth= 3] . ( 2 sec) [ -15927.9603] [ 3056] [depth= 1] . ( 2 sec) [ -15883.4195] [ 3048] [depth= 4] . ( 2 sec) [ -15850.8032] [ 3021] [depth= 2] . ( 2 sec) [ -15748.4721] [ 3015] [depth= 5] . ( 2 sec) [ -15706.5753] [ 3011] [depth= 3] . ( 2 sec) [ -15680.5361] [ 3009] [depth= 5] . ( 2 sec) [ -15572.8260] [ 2980] [depth= 6] . ( 2 sec) [ -15453.7159] [ 2960] [depth= 6] . ( 3 sec) [ -15409.3537] [ 2954] [depth= 5] . ( 3 sec) [ -15398.4409] [ 2935] [depth= 7] . ( 3 sec) [ -15368.2218] [ 2934] [depth= 2] . ( 3 sec) [ -15330.1569] [ 2932] [depth= 1] . ( 3 sec) [ -15094.7863] [ 2932] [depth= 1] . ( 3 sec) [ -15074.4823] [ 2930] [depth= 2] . ( 3 sec) [ -14925.6368] [ 2918] [depth= 5] . ( 3 sec) [ -14895.4250] [ 2921] [depth= 1] . ( 3 sec) [ -14805.2086] [ 2894] [depth= 2] . ( 3 sec) [ -14747.9464] [ 2885] [depth= 11] . ( 3 sec) [ -14722.5179] [ 2879] [depth= 1] . ( 4 sec) [ -14590.8901] [ 2860] [depth= 12] . ( 4 sec) [ -14485.2803] [ 2833] [depth= 1] . ( 4 sec) [ -14377.2050] [ 2811] [depth= 8] . ( 4 sec) [ -14276.9021] [ 2812] [depth= 5] . ( 4 sec) [ -14148.2813] [ 2810] [depth= 3] . ( 4 sec) [ -14034.0857] [ 2770] [depth= 10] . ( 4 sec) [ -14006.4515] [ 2761] [depth= 6] . ( 4 sec) [ -13875.4084] [ 2773] [depth= 1] . ( 4 sec) [ -13864.2784] [ 2761] [depth= 1] . ( 4 sec) [ -13805.2223] [ 2739] [depth= 7] . ( 4 sec) [ -13730.7322] [ 2716] [depth= 14] . ( 5 sec) [ -13645.8735] [ 2701] [depth= 6] . ( 5 sec) [ -13590.7408] [ 2693] [depth= 1] . ( 5 sec) [ -13584.9332] [ 2697] [depth= 6] . ( 5 sec) [ -13537.7589] [ 2685] [depth= 4] . ( 5 sec) [ -13433.8212] [ 2654] [depth= 4] . ( 5 sec) [ -13381.0174] [ 2638] [depth= 10] . ( 5 sec) [ -13377.0756] [ 2640] [depth= 1] . ( 5 sec) [ -13310.1979] [ 2633] [depth= 1] . ( 5 sec) [ -13303.5129] [ 2629] [depth= 9] . ( 5 sec) [ -13210.2422] [ 2631] [depth= 1] . ( 6 sec) [ -13165.4245] [ 2621] [depth= 9] . ( 6 sec) [ -13156.9515] [ 2619] [depth= 1] . ( 6 sec) [ -13109.8678] [ 2600] [depth= 8] . ( 6 sec) [ -13058.2036] [ 2589] [depth= 12] . ( 6 sec) [ -13052.9853] [ 2583] [depth= 9] . ( 6 sec) [ -13022.5032] [ 2593] [depth= 1] . ( 6 sec) [ -12988.5257] [ 2589] [depth= 3] . ( 6 sec) [ -12926.7859] [ 2588] [depth= 9] . ( 6 sec) [ -12865.2799] [ 2561] [depth= 9] . ( 6 sec) [ -12859.1259] [ 2557] [depth= 3] . ( 6 sec) [ -12778.1306] [ 2553] [depth= 4] . ( 7 sec) [ -12625.8639] [ 2504] [depth= 3] . ( 7 sec) [ -12530.5109] [ 2469] [depth= 8] . ( 7 sec) [ -12519.8071] [ 2467] [depth= 2] . ( 7 sec) [ -12477.4005] [ 2443] [depth= 4] . ( 7 sec) [ -12366.2140] [ 2407] [depth= 5] . ( 7 sec) [ -12204.1832] [ 2364] [depth= 5] . ( 7 sec) [ -12195.9782] [ 2365] [depth= 3] . ( 7 sec) [ -12149.5150] [ 2357] [depth= 2] . ( 7 sec) [ -12112.4321] [ 2354] [depth= 8] . ( 7 sec) [ -12099.9450] [ 2344] [depth= 1] . ( 8 sec) [ -12073.3949] [ 2340] [depth= 2] . ( 8 sec) [ -12072.2031] [ 2347] [depth= 11] . ( 8 sec) [ -12006.5079] [ 2345] [depth= 2] . ( 8 sec) [ -11995.0685] [ 2344] [depth= 2] . ( 8 sec) [ -11976.2599] [ 2344] [depth= 1] . ( 8 sec) [ -11821.5488] [ 2343] [depth= 2] . ( 8 sec) [ -11801.9376] [ 2338] [depth= 4] . ( 8 sec) [ -11747.1463] [ 2324] [depth= 4] . ( 8 sec) [ -11663.9954] [ 2302] [depth= 1] . ( 8 sec) [ -11655.0665] [ 2286] [depth= 6] . ( 9 sec) [ -11577.5468] [ 2260] [depth= 8] . ( 9 sec) [ -11544.3119] [ 2239] [depth= 12] . ( 9 sec) [ -11493.6612] [ 2231] [depth= 6] . ( 9 sec) [ -11422.2365] [ 2211] [depth= 1] . ( 9 sec) [ -11353.5570] [ 2195] [depth= 3] . ( 9 sec) [ -11262.0971] [ 2176] [depth= 8] . ( 9 sec) [ -11250.8074] [ 2172] [depth= 13] . ( 9 sec) [ -11241.4319] [ 2165] [depth= 5] . ( 9 sec) [ -11230.4441] [ 2162] [depth= 1] . ( 9 sec) [ -11211.9458] [ 2156] [depth= 3] . ( 10 sec) [ -11194.1841] [ 2151] [depth= 5] . ( 10 sec) [ -11092.9765] [ 2145] [depth= 5] . ( 10 sec) [ -11054.7800] [ 2126] [depth= 10] . ( 10 sec) [ -11013.0704] [ 2118] [depth= 2] . ( 10 sec) [ -10938.5884] [ 2098] [depth= 1] . ( 10 sec) [ -10936.6825] [ 2099] [depth= 1] . ( 10 sec) [ -10912.4011] [ 2092] [depth= 2] . ( 10 sec) [ -10911.5677] [ 2099] [depth= 1] . ( 11 sec) [ -10881.9398] [ 2095] [depth= 2] . ( 11 sec) [ -10828.2998] [ 2081] [depth= 1] . ( 11 sec) [ -10789.8873] [ 2076] [depth= 10] . ( 11 sec) [ -10787.1996] [ 2078] [depth= 1] . ( 11 sec) [ -10785.7609] [ 2076] [depth= 1] . ( 11 sec) [ -10726.1334] [ 2052] [depth= 8] . ( 11 sec) [ -10724.3365] [ 2054] [depth= 1] . ( 12 sec) [ -10724.1409] [ 2054] [depth= 1] . ( 12 sec) [ -10722.5246] [ 2054] [depth= 1] . ( 12 sec) [ -10716.1599] [ 2057] [depth= 1] . ( 12 sec) [ -10677.7270] [ 2040] [depth= 1] . ( 12 sec) [ -10676.0051] [ 2043] [depth= 1] . ( 12 sec) [ -10668.6753] [ 2040] [depth= 1] . ( 12 sec) [ -10663.3624] [ 2038] [depth= 2] . ( 12 sec) [ -10644.8742] [ 2034] [depth= 1] . ( 13 sec) [ -10631.9102] [ 2030] [depth= 1] . ( 13 sec) [ -10626.5403] [ 2031] [depth= 2] . ( 13 sec) [ -10622.7314] [ 2030] [depth= 1] . ( 13 sec) [ -10622.0813] [ 2030] [depth= 1] . ( 14 sec) [ -10558.3430] [ 2028] [depth= 1] . ( 14 sec) [ -10546.5797] [ 2023] [depth= 2] . ( 14 sec) [ -10470.6686] [ 1986] [depth= 4] . ( 14 sec) [ -10465.0694] [ 1987] [depth= 1] . ( 14 sec) [ -10458.9636] [ 1986] [depth= 6] . ( 15 sec) [ -10333.5906] [Branch lengths ] . ( 16 sec) [ -10329.8736] [GTR parameters ] . ( 17 sec) [ -10328.3193] [Alpha ][ 0.557082] . ( 17 sec) [ -10327.4947] [ 1985] [depth= 1] . ( 17 sec) [ -10325.3761] [ 1984] [depth= 1] . ( 18 sec) [ -10323.4914] [ 1984] [depth= 1] . ( 18 sec) [ -10323.3295] [ 1986] [depth= 1] . ( 18 sec) [ -10323.2860] [ 1984] [depth= 1] . ( 19 sec) [ -10323.2558] [ 1987] [depth= 9] . ( 20 sec) [ -10299.2000] [ 1976] [depth= 9] . ( 20 sec) [ -10298.4983] [ 1976] [depth= 1] . ( 21 sec) [ -10298.0862] [ 1976] [depth= 1] . ( 21 sec) [ -10278.6306] [ 1977] [depth= 2] . ( 21 sec) [ -10238.6292] [ 1965] [depth= 1] . ( 22 sec) [ -10231.2858] [ 1959] [depth= 3] . ( 22 sec) [ -10230.7482] [ 1958] [depth= 1] . ( 22 sec) [ -10227.6926] [ 1955] [depth= 1] . ( 22 sec) [ -10217.9305] [ 1953] [depth= 1] . ( 22 sec) [ -10217.8152] [ 1956] [depth= 1] . ( 22 sec) [ -10206.3023] [ 1953] [depth= 1] . ( 24 sec) [ -10204.1832] [ 1950] [depth= 3] . ( 24 sec) [ -10202.1061] [ 1947] [depth= 1] . ( 26 sec) [ -10200.0907] [ 1947] [depth= 1] . ( 26 sec) [ -10199.3474] [ 1947] [depth= 1] . ( 26 sec) [ -10198.0367] [ 1948] [depth= 1] . ( 29 sec) [ -10185.7354] [ 1946] [depth= 1] . ( 29 sec) [ -10185.4877] [ 1945] [depth= 1] . ( 30 sec) [ -10185.1669] [ 1944] [depth= 1] . ( 30 sec) [ -10183.5261] [ 1947] [depth= 5] . ( 31 sec) [ -10170.3952] [Branch lengths ] . ( 32 sec) [ -10170.1582] [GTR parameters ] . ( 32 sec) [ -10170.1576] [Alpha ][ 0.555821] . ( 32 sec) [ -10168.3936] [ 1948] [depth= 2] . ( 33 sec) [ -10168.3619] [ 1944] [depth= 1] . ( 36 sec) [ -10167.8011] [ 1945] [depth= 1] . ( 36 sec) [ -10166.1463] [ 1944] [depth= 1] . ( 36 sec) [ -10165.1324] [ 1945] [depth= 1] . ( 36 sec) [ -10163.9672] [ 1942] [depth= 1] . ( 41 sec) [ -10163.7620] [ 1945] [depth= 1] . ( 42 sec) [ -10162.6682] [ 1942] [depth= 1] . ( 46 sec) [ -10162.5112] [ 1943] [depth= 1] . ( 47 sec) [ -10158.2688] [Branch lengths ] . ( 48 sec) [ -10158.2249] [GTR parameters ] . ( 48 sec) [ -10158.2249] [Alpha ][ 0.555821] . ( 64 sec) [ -10158.0834] [Branch lengths ] . ( 97 sec) [ -10158.0104] [ 1941] [depth= 1] . ( 118 sec) [ -10157.9925] [ 1940] [depth= 1] . ( 126 sec) [ -10157.7013] [Branch lengths ] . ( 127 sec) [ -10157.6983] [GTR parameters ] . ( 127 sec) [ -10157.6962] [Alpha ][ 0.558046] . ( 127 sec) [ -10157.6962] [Topology ] . ( 129 sec) [ -10157.6557] [Topology ] . ( 130 sec) [ -10157.6465] [Topology ] . ( 132 sec) [ -10157.6452] [Topology ] . ( 134 sec) [ -10157.6449] [Topology ] . ( 135 sec) [ -10157.6445] [GTR parameters ] . ( 135 sec) [ -10157.6444] [Alpha ][ 0.558604] . ( 135 sec) [ -10157.6444] [Topology ] . ( 136 sec) [ -10157.6443] [Topology ] . ( 137 sec) [ -10157.6443] [GTR parameters ] . ( 137 sec) [ -10157.6443] [Alpha ][ 0.558604] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.644335. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -16593.2406] [GTR parameters ] . ( 2 sec) [ -16299.7079] [Alpha ][ 0.500960] . ( 3 sec) [ -16138.7284] [ 3059] [depth= 6] . ( 3 sec) [ -15921.6052] [ 3037] [depth= 4] . ( 3 sec) [ -15856.3839] [ 3030] [depth= 11] . ( 3 sec) [ -15793.0767] [ 3013] [depth= 1] . ( 3 sec) [ -15753.9209] [ 3011] [depth= 11] . ( 3 sec) [ -15697.1958] [ 3008] [depth= 2] . ( 3 sec) [ -15651.7987] [ 3003] [depth= 8] . ( 3 sec) [ -15607.7659] [ 2990] [depth= 5] . ( 3 sec) [ -15538.2321] [ 2985] [depth= 3] . ( 3 sec) [ -15465.7792] [ 2975] [depth= 3] . ( 3 sec) [ -15460.4008] [ 2970] [depth= 4] . ( 3 sec) [ -15350.2143] [ 2939] [depth= 1] . ( 3 sec) [ -15259.5600] [ 2934] [depth= 3] . ( 4 sec) [ -15236.4836] [ 2931] [depth= 4] . ( 4 sec) [ -15136.3448] [ 2931] [depth= 1] . ( 4 sec) [ -15131.8419] [ 2924] [depth= 5] . ( 4 sec) [ -15129.7722] [ 2928] [depth= 1] . ( 4 sec) [ -15077.7665] [ 2919] [depth= 5] . ( 4 sec) [ -15046.3524] [ 2918] [depth= 2] . ( 4 sec) [ -14971.9631] [ 2907] [depth= 8] . ( 4 sec) [ -14924.3878] [ 2890] [depth= 1] . ( 4 sec) [ -14850.9254] [ 2869] [depth= 7] . ( 4 sec) [ -14821.8272] [ 2859] [depth= 9] . ( 4 sec) [ -14754.3708] [ 2855] [depth= 1] . ( 5 sec) [ -14667.7475] [ 2854] [depth= 3] . ( 5 sec) [ -14596.6692] [ 2831] [depth= 1] . ( 5 sec) [ -14543.5243] [ 2829] [depth= 1] . ( 5 sec) [ -14519.1693] [ 2825] [depth= 1] . ( 5 sec) [ -14433.8223] [ 2809] [depth= 9] . ( 5 sec) [ -14383.0030] [ 2798] [depth= 13] . ( 5 sec) [ -14342.8210] [ 2790] [depth= 9] . ( 5 sec) [ -14296.1367] [ 2779] [depth= 6] . ( 5 sec) [ -14237.2431] [ 2780] [depth= 1] . ( 5 sec) [ -14185.6031] [ 2774] [depth= 6] . ( 5 sec) [ -13931.3939] [ 2733] [depth= 12] . ( 6 sec) [ -13893.5576] [ 2730] [depth= 2] . ( 6 sec) [ -13840.4666] [ 2721] [depth= 11] . ( 6 sec) [ -13780.7166] [ 2706] [depth= 5] . ( 6 sec) [ -13632.3609] [ 2671] [depth= 11] . ( 6 sec) [ -13565.6091] [ 2650] [depth= 9] . ( 6 sec) [ -13495.7580] [ 2640] [depth= 2] . ( 6 sec) [ -13352.3627] [ 2621] [depth= 16] . ( 6 sec) [ -13254.7395] [ 2587] [depth= 15] . ( 6 sec) [ -13070.6629] [ 2565] [depth= 7] . ( 6 sec) [ -13061.3255] [ 2564] [depth= 1] . ( 7 sec) [ -13049.8292] [ 2561] [depth= 5] . ( 7 sec) [ -12933.1798] [ 2543] [depth= 7] . ( 7 sec) [ -12899.2030] [ 2528] [depth= 6] . ( 7 sec) [ -12859.7704] [ 2515] [depth= 8] . ( 7 sec) [ -12846.9622] [ 2507] [depth= 7] . ( 7 sec) [ -12815.8039] [ 2505] [depth= 5] . ( 7 sec) [ -12812.7108] [ 2505] [depth= 7] . ( 7 sec) [ -12791.1778] [ 2501] [depth= 3] . ( 8 sec) [ -12755.8228] [ 2493] [depth= 1] . ( 8 sec) [ -12739.6637] [ 2488] [depth= 1] . ( 8 sec) [ -12699.5322] [ 2474] [depth= 8] . ( 8 sec) [ -12699.0498] [ 2473] [depth= 8] . ( 8 sec) [ -12689.4105] [ 2471] [depth= 13] . ( 8 sec) [ -12591.0508] [ 2447] [depth= 7] . ( 8 sec) [ -12570.4407] [ 2444] [depth= 1] . ( 8 sec) [ -12540.5584] [ 2443] [depth= 4] . ( 8 sec) [ -12465.8981] [ 2420] [depth= 2] . ( 8 sec) [ -12442.3798] [ 2416] [depth= 1] . ( 9 sec) [ -12436.8294] [ 2412] [depth= 2] . ( 9 sec) [ -12410.8467] [ 2405] [depth= 1] . ( 9 sec) [ -12405.4688] [ 2404] [depth= 1] . ( 9 sec) [ -12381.9418] [ 2395] [depth= 1] . ( 9 sec) [ -12374.6670] [ 2388] [depth= 4] . ( 9 sec) [ -12373.8098] [ 2388] [depth= 1] . ( 9 sec) [ -12364.5762] [ 2387] [depth= 1] . ( 9 sec) [ -12323.8594] [ 2374] [depth= 1] . ( 9 sec) [ -12281.6001] [ 2354] [depth= 6] . ( 9 sec) [ -12280.7884] [ 2354] [depth= 1] . ( 10 sec) [ -12213.5557] [ 2340] [depth= 4] . ( 10 sec) [ -12106.4002] [ 2340] [depth= 1] . ( 10 sec) [ -12090.6155] [ 2333] [depth= 9] . ( 10 sec) [ -11938.9368] [ 2334] [depth= 5] . ( 10 sec) [ -11935.5327] [ 2340] [depth= 1] . ( 10 sec) [ -11883.1714] [ 2325] [depth= 1] . ( 10 sec) [ -11840.8371] [ 2320] [depth= 11] . ( 10 sec) [ -11831.9909] [ 2322] [depth= 6] . ( 10 sec) [ -11821.3141] [ 2323] [depth= 1] . ( 10 sec) [ -11819.4536] [ 2321] [depth= 2] . ( 11 sec) [ -11808.0217] [ 2308] [depth= 3] . ( 11 sec) [ -11767.5017] [ 2294] [depth= 5] . ( 11 sec) [ -11748.9140] [ 2285] [depth= 2] . ( 11 sec) [ -11748.3580] [ 2285] [depth= 1] . ( 11 sec) [ -11746.8655] [ 2290] [depth= 3] . ( 11 sec) [ -11729.2515] [ 2274] [depth= 3] . ( 11 sec) [ -11620.7924] [ 2276] [depth= 2] . ( 12 sec) [ -11588.6817] [ 2276] [depth= 1] . ( 12 sec) [ -11506.8156] [ 2256] [depth= 10] . ( 12 sec) [ -11505.6806] [ 2255] [depth= 1] . ( 12 sec) [ -11504.7619] [ 2258] [depth= 3] . ( 12 sec) [ -11478.7630] [ 2257] [depth= 2] . ( 12 sec) [ -11464.4851] [ 2254] [depth= 1] . ( 12 sec) [ -11455.0513] [ 2253] [depth= 1] . ( 12 sec) [ -11443.3364] [ 2250] [depth= 3] . ( 12 sec) [ -11437.0611] [ 2249] [depth= 3] . ( 12 sec) [ -11435.7062] [ 2249] [depth= 3] . ( 13 sec) [ -11393.3884] [ 2228] [depth= 2] . ( 13 sec) [ -11393.1301] [ 2227] [depth= 1] . ( 13 sec) [ -11393.0175] [ 2227] [depth= 1] . ( 13 sec) [ -11372.0474] [ 2223] [depth= 4] . ( 13 sec) [ -11236.7319] [ 2210] [depth= 1] . ( 13 sec) [ -11219.7984] [ 2212] [depth= 3] . ( 13 sec) [ -11139.0727] [ 2185] [depth= 2] . ( 13 sec) [ -11088.1560] [ 2183] [depth= 1] . ( 13 sec) [ -11062.4283] [ 2171] [depth= 1] . ( 13 sec) [ -11060.9425] [ 2171] [depth= 1] . ( 14 sec) [ -11058.6889] [ 2175] [depth= 1] . ( 14 sec) [ -11055.3317] [ 2172] [depth= 1] . ( 14 sec) [ -11053.9108] [ 2169] [depth= 2] . ( 14 sec) [ -11018.6357] [ 2160] [depth= 3] . ( 14 sec) [ -11002.3374] [ 2146] [depth= 1] . ( 14 sec) [ -10972.0812] [ 2144] [depth= 14] . ( 14 sec) [ -10891.8067] [ 2127] [depth= 6] . ( 15 sec) [ -10820.5180] [ 2107] [depth= 14] . ( 15 sec) [ -10801.5488] [ 2106] [depth= 6] . ( 15 sec) [ -10629.9401] [Branch lengths ] . ( 17 sec) [ -10627.4102] [GTR parameters ] . ( 17 sec) [ -10627.2677] [Alpha ][ 0.516761] . ( 17 sec) [ -10620.3718] [ 2098] [depth= 1] . ( 17 sec) [ -10512.1428] [ 2061] [depth= 5] . ( 17 sec) [ -10484.1674] [ 2053] [depth= 12] . ( 17 sec) [ -10437.5683] [ 2036] [depth= 10] . ( 17 sec) [ -10437.5048] [ 2037] [depth= 1] . ( 18 sec) [ -10430.9862] [ 2039] [depth= 3] . ( 18 sec) [ -10415.4180] [ 2031] [depth= 1] . ( 18 sec) [ -10384.2570] [ 2024] [depth= 8] . ( 18 sec) [ -10371.1674] [ 2021] [depth= 2] . ( 18 sec) [ -10369.8248] [ 2016] [depth= 1] . ( 18 sec) [ -10353.9414] [ 2001] [depth= 5] . ( 19 sec) [ -10348.3719] [ 2004] [depth= 1] . ( 19 sec) [ -10342.6933] [ 2002] [depth= 1] . ( 19 sec) [ -10337.8440] [ 2008] [depth= 1] . ( 19 sec) [ -10334.6757] [ 2012] [depth= 1] . ( 19 sec) [ -10330.1320] [ 2013] [depth= 1] . ( 20 sec) [ -10312.2436] [ 2003] [depth= 2] . ( 20 sec) [ -10310.1878] [ 2002] [depth= 2] . ( 20 sec) [ -10309.9918] [ 1997] [depth= 1] . ( 21 sec) [ -10307.6922] [ 1996] [depth= 3] . ( 21 sec) [ -10301.6805] [ 1992] [depth= 1] . ( 21 sec) [ -10298.0985] [ 1992] [depth= 1] . ( 21 sec) [ -10295.9555] [ 1992] [depth= 1] . ( 21 sec) [ -10295.7691] [ 1992] [depth= 1] . ( 21 sec) [ -10287.8492] [ 1986] [depth= 2] . ( 22 sec) [ -10285.1158] [ 1986] [depth= 2] . ( 22 sec) [ -10283.2534] [ 1986] [depth= 2] . ( 22 sec) [ -10282.1346] [ 1985] [depth= 3] . ( 22 sec) [ -10281.1043] [ 1986] [depth= 1] . ( 22 sec) [ -10278.5140] [ 1980] [depth= 1] . ( 23 sec) [ -10274.6559] [ 1982] [depth= 4] . ( 23 sec) [ -10268.5957] [ 1981] [depth= 1] . ( 23 sec) [ -10260.5670] [ 1977] [depth= 2] . ( 23 sec) [ -10258.3831] [ 1974] [depth= 1] . ( 23 sec) [ -10232.0071] [ 1964] [depth= 3] . ( 24 sec) [ -10221.9305] [ 1961] [depth= 2] . ( 24 sec) [ -10214.4185] [ 1955] [depth= 4] . ( 25 sec) [ -10213.1422] [ 1958] [depth= 1] . ( 25 sec) [ -10213.1314] [ 1957] [depth= 1] . ( 25 sec) [ -10206.2453] [ 1954] [depth= 1] . ( 26 sec) [ -10205.0103] [ 1954] [depth= 3] . ( 26 sec) [ -10204.2784] [ 1955] [depth= 1] . ( 26 sec) [ -10203.3232] [ 1956] [depth= 1] . ( 27 sec) [ -10202.9865] [ 1953] [depth= 1] . ( 27 sec) [ -10202.7407] [ 1954] [depth= 1] . ( 27 sec) [ -10199.1900] [ 1950] [depth= 1] . ( 28 sec) [ -10191.0241] [ 1944] [depth= 3] . ( 28 sec) [ -10190.1751] [ 1945] [depth= 1] . ( 28 sec) [ -10189.3973] [ 1944] [depth= 1] . ( 29 sec) [ -10188.4632] [ 1944] [depth= 1] . ( 30 sec) [ -10187.2514] [ 1945] [depth= 2] . ( 30 sec) [ -10165.4701] [Branch lengths ] . ( 31 sec) [ -10164.3516] [GTR parameters ] . ( 32 sec) [ -10163.7700] [Alpha ][ 0.551943] . ( 34 sec) [ -10163.4366] [ 1946] [depth= 1] . ( 34 sec) [ -10162.4188] [ 1942] [depth= 2] . ( 35 sec) [ -10162.0066] [ 1946] [depth= 4] . ( 41 sec) [ -10161.8438] [ 1946] [depth= 1] . ( 44 sec) [ -10161.7078] [ 1946] [depth= 1] . ( 48 sec) [ -10160.0425] [Branch lengths ] . ( 49 sec) [ -10160.0331] [GTR parameters ] . ( 49 sec) [ -10160.0325] [Alpha ][ 0.553128] . ( 60 sec) [ -10159.9414] [ 1945] [depth= 1] . ( 68 sec) [ -10159.6583] [Branch lengths ] . ( 69 sec) [ -10159.6582] [GTR parameters ] . ( 69 sec) [ -10159.6576] [Alpha ][ 0.554263] . ( 135 sec) [ -10159.5121] [Branch lengths ] . ( 135 sec) [ -10159.5121] [Topology ] . ( 136 sec) [ -10158.8735] [Topology ] . ( 138 sec) [ -10158.3299] [Topology ] . ( 140 sec) [ -10157.6851] [Topology ] . ( 141 sec) [ -10157.5333] [Topology ] . ( 143 sec) [ -10157.5146] [Topology ] . ( 144 sec) [ -10157.5116] [Topology ] . ( 146 sec) [ -10157.5110] [Topology ] . ( 147 sec) [ -10157.5079] [GTR parameters ] . ( 147 sec) [ -10157.5066] [Alpha ][ 0.555991] . ( 147 sec) [ -10157.5066] [Topology ] . ( 148 sec) [ -10157.5064] [Topology ] . ( 149 sec) [ -10157.5064] [GTR parameters ] . ( 149 sec) [ -10157.5064] [Alpha ][ 0.555991] . Checking for NNIs, optimizing five branches... . ( 161 sec) [ -10157.4521] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.452105. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16648.6220] [GTR parameters ] . ( 1 sec) [ -16350.5274] [Alpha ][ 0.500960] . ( 2 sec) [ -16229.8056] [ 3102] [depth= 11] . ( 2 sec) [ -15926.3341] [ 3080] [depth= 2] . ( 2 sec) [ -15830.2223] [ 3048] [depth= 9] . ( 2 sec) [ -15825.7312] [ 3046] [depth= 1] . ( 2 sec) [ -15731.1916] [ 3034] [depth= 7] . ( 2 sec) [ -15662.8333] [ 3020] [depth= 3] . ( 2 sec) [ -15652.6989] [ 3011] [depth= 1] . ( 2 sec) [ -15518.2026] [ 2990] [depth= 5] . ( 2 sec) [ -15506.3838] [ 2985] [depth= 2] . ( 2 sec) [ -15501.2641] [ 2980] [depth= 3] . ( 3 sec) [ -15465.9385] [ 2974] [depth= 5] . ( 3 sec) [ -15435.9905] [ 2974] [depth= 4] . ( 3 sec) [ -15336.5331] [ 2965] [depth= 3] . ( 3 sec) [ -15299.9033] [ 2960] [depth= 10] . ( 3 sec) [ -15279.1293] [ 2957] [depth= 1] . ( 3 sec) [ -15249.8272] [ 2953] [depth= 3] . ( 3 sec) [ -15184.2217] [ 2950] [depth= 6] . ( 3 sec) [ -15093.9921] [ 2947] [depth= 1] . ( 3 sec) [ -14975.1455] [ 2922] [depth= 2] . ( 4 sec) [ -14840.4021] [ 2909] [depth= 11] . ( 4 sec) [ -14774.9929] [ 2892] [depth= 9] . ( 4 sec) [ -14693.6591] [ 2864] [depth= 12] . ( 4 sec) [ -14594.8100] [ 2846] [depth= 10] . ( 4 sec) [ -14560.1136] [ 2838] [depth= 3] . ( 4 sec) [ -14545.4944] [ 2835] [depth= 4] . ( 4 sec) [ -14476.8980] [ 2821] [depth= 10] . ( 4 sec) [ -14399.8755] [ 2807] [depth= 9] . ( 4 sec) [ -14307.7606] [ 2803] [depth= 8] . ( 4 sec) [ -13948.3510] [ 2787] [depth= 21] . ( 5 sec) [ -13907.2998] [ 2775] [depth= 8] . ( 5 sec) [ -13893.8515] [ 2774] [depth= 13] . ( 5 sec) [ -13817.0919] [ 2762] [depth= 13] . ( 5 sec) [ -13711.5993] [ 2732] [depth= 6] . ( 5 sec) [ -13618.7636] [ 2714] [depth= 13] . ( 5 sec) [ -13518.7863] [ 2709] [depth= 4] . ( 5 sec) [ -13483.3017] [ 2699] [depth= 10] . ( 5 sec) [ -13463.2462] [ 2692] [depth= 1] . ( 5 sec) [ -13426.6981] [ 2682] [depth= 2] . ( 5 sec) [ -13371.3916] [ 2674] [depth= 14] . ( 6 sec) [ -13326.7687] [ 2673] [depth= 1] . ( 6 sec) [ -13264.4489] [ 2658] [depth= 15] . ( 6 sec) [ -13211.4796] [ 2649] [depth= 4] . ( 6 sec) [ -13065.7507] [ 2612] [depth= 10] . ( 6 sec) [ -13000.7504] [ 2593] [depth= 15] . ( 6 sec) [ -12907.8257] [ 2573] [depth= 8] . ( 6 sec) [ -12856.1316] [ 2566] [depth= 7] . ( 6 sec) [ -12765.5862] [ 2562] [depth= 1] . ( 6 sec) [ -12712.7890] [ 2552] [depth= 11] . ( 6 sec) [ -12711.0199] [ 2552] [depth= 1] . ( 7 sec) [ -12545.9990] [ 2514] [depth= 16] . ( 7 sec) [ -12486.3082] [ 2494] [depth= 6] . ( 7 sec) [ -12475.4684] [ 2482] [depth= 15] . ( 7 sec) [ -12377.7800] [ 2453] [depth= 2] . ( 7 sec) [ -12310.6222] [ 2444] [depth= 1] . ( 7 sec) [ -12288.1115] [ 2437] [depth= 1] . ( 7 sec) [ -12254.8881] [ 2430] [depth= 6] . ( 7 sec) [ -12226.3171] [ 2423] [depth= 3] . ( 7 sec) [ -12170.0114] [ 2418] [depth= 2] . ( 7 sec) [ -12122.3163] [ 2417] [depth= 5] . ( 8 sec) [ -12114.8040] [ 2413] [depth= 3] . ( 8 sec) [ -12111.6180] [ 2412] [depth= 1] . ( 8 sec) [ -12104.2147] [ 2414] [depth= 4] . ( 8 sec) [ -12098.4908] [ 2412] [depth= 1] . ( 8 sec) [ -12088.8746] [ 2413] [depth= 5] . ( 8 sec) [ -11969.4172] [ 2387] [depth= 3] . ( 8 sec) [ -11968.1942] [ 2385] [depth= 1] . ( 8 sec) [ -11938.1272] [ 2375] [depth= 2] . ( 8 sec) [ -11881.8854] [ 2357] [depth= 2] . ( 8 sec) [ -11766.0097] [ 2321] [depth= 11] . ( 9 sec) [ -11735.4130] [ 2314] [depth= 5] . ( 9 sec) [ -11731.3764] [ 2315] [depth= 1] . ( 9 sec) [ -11684.9626] [ 2307] [depth= 1] . ( 9 sec) [ -11664.8263] [ 2299] [depth= 2] . ( 9 sec) [ -11663.4324] [ 2293] [depth= 1] . ( 9 sec) [ -11529.9523] [ 2262] [depth= 5] . ( 9 sec) [ -11529.1153] [ 2263] [depth= 1] . ( 9 sec) [ -11446.7765] [ 2264] [depth= 7] . ( 10 sec) [ -11363.5060] [ 2245] [depth= 5] . ( 10 sec) [ -11353.4313] [ 2241] [depth= 2] . ( 10 sec) [ -11336.9481] [ 2236] [depth= 2] . ( 10 sec) [ -11266.1326] [ 2209] [depth= 4] . ( 10 sec) [ -11265.3587] [ 2207] [depth= 3] . ( 10 sec) [ -11237.2720] [ 2203] [depth= 1] . ( 10 sec) [ -11235.5175] [ 2206] [depth= 1] . ( 10 sec) [ -11226.8416] [ 2207] [depth= 1] . ( 10 sec) [ -11221.7553] [ 2207] [depth= 1] . ( 11 sec) [ -11219.8540] [ 2204] [depth= 1] . ( 11 sec) [ -11116.4688] [ 2197] [depth= 6] . ( 11 sec) [ -11017.4045] [ 2162] [depth= 2] . ( 11 sec) [ -11016.4381] [ 2160] [depth= 2] . ( 11 sec) [ -10915.4066] [ 2129] [depth= 4] . ( 12 sec) [ -10914.7329] [ 2135] [depth= 1] . ( 12 sec) [ -10913.2843] [ 2134] [depth= 1] . ( 12 sec) [ -10904.8129] [ 2132] [depth= 1] . ( 12 sec) [ -10842.1050] [ 2108] [depth= 3] . ( 12 sec) [ -10820.8334] [ 2109] [depth= 1] . ( 12 sec) [ -10799.0569] [ 2103] [depth= 2] . ( 12 sec) [ -10796.3825] [ 2097] [depth= 1] . ( 12 sec) [ -10795.9225] [ 2099] [depth= 1] . ( 12 sec) [ -10786.3231] [ 2103] [depth= 5] . ( 12 sec) [ -10784.4597] [ 2103] [depth= 1] . ( 13 sec) [ -10782.3297] [ 2102] [depth= 1] . ( 13 sec) [ -10773.2566] [ 2103] [depth= 1] . ( 13 sec) [ -10725.5460] [ 2085] [depth= 4] . ( 13 sec) [ -10691.0524] [ 2079] [depth= 9] . ( 13 sec) [ -10688.9917] [ 2080] [depth= 1] . ( 13 sec) [ -10625.2776] [ 2056] [depth= 3] . ( 13 sec) [ -10600.4357] [ 2055] [depth= 1] . ( 13 sec) [ -10590.6796] [ 2051] [depth= 2] . ( 13 sec) [ -10587.2064] [ 2049] [depth= 1] . ( 14 sec) [ -10581.7252] [ 2047] [depth= 5] . ( 14 sec) [ -10507.4964] [ 2014] [depth= 8] . ( 14 sec) [ -10507.2725] [ 2017] [depth= 1] . ( 14 sec) [ -10486.0192] [ 2010] [depth= 2] . ( 14 sec) [ -10484.8114] [ 2011] [depth= 1] . ( 14 sec) [ -10465.1639] [ 2010] [depth= 1] . ( 14 sec) [ -10460.6646] [ 2010] [depth= 1] . ( 14 sec) [ -10409.2138] [ 2003] [depth= 1] . ( 14 sec) [ -10402.5687] [ 2006] [depth= 1] . ( 14 sec) [ -10402.3203] [ 2006] [depth= 1] . ( 15 sec) [ -10400.7341] [ 2003] [depth= 1] . ( 15 sec) [ -10396.0465] [ 1996] [depth= 3] . ( 15 sec) [ -10394.6240] [ 1994] [depth= 1] . ( 15 sec) [ -10394.0981] [ 1995] [depth= 1] . ( 15 sec) [ -10392.5965] [ 1999] [depth= 1] . ( 15 sec) [ -10388.2899] [ 1998] [depth= 1] . ( 15 sec) [ -10385.3742] [ 1994] [depth= 1] . ( 16 sec) [ -10290.4507] [Branch lengths ] . ( 18 sec) [ -10285.4266] [GTR parameters ] . ( 18 sec) [ -10284.9259] [Alpha ][ 0.532574] . ( 18 sec) [ -10249.3993] [ 1981] [depth= 6] . ( 19 sec) [ -10244.5784] [ 1978] [depth= 2] . ( 19 sec) [ -10243.3411] [ 1978] [depth= 1] . ( 21 sec) [ -10213.4988] [ 1968] [depth= 2] . ( 21 sec) [ -10196.8252] [ 1955] [depth= 7] . ( 21 sec) [ -10182.9921] [ 1948] [depth= 5] . ( 22 sec) [ -10180.3638] [ 1948] [depth= 1] . ( 22 sec) [ -10180.1114] [ 1946] [depth= 1] . ( 23 sec) [ -10179.7592] [ 1945] [depth= 1] . ( 23 sec) [ -10178.6214] [ 1946] [depth= 1] . ( 23 sec) [ -10177.6253] [ 1944] [depth= 1] . ( 23 sec) [ -10177.3069] [ 1944] [depth= 1] . ( 23 sec) [ -10176.8868] [ 1944] [depth= 1] . ( 23 sec) [ -10175.2498] [ 1945] [depth= 2] . ( 24 sec) [ -10174.9632] [ 1945] [depth= 1] . ( 25 sec) [ -10174.9511] [ 1946] [depth= 1] . ( 27 sec) [ -10174.8718] [ 1947] [depth= 1] . ( 27 sec) [ -10174.8157] [ 1947] [depth= 1] . ( 27 sec) [ -10173.5539] [ 1946] [depth= 1] . ( 27 sec) [ -10173.4196] [ 1948] [depth= 1] . ( 28 sec) [ -10173.1078] [ 1947] [depth= 2] . ( 28 sec) [ -10172.9078] [ 1950] [depth= 1] . ( 28 sec) [ -10172.6644] [ 1950] [depth= 1] . ( 28 sec) [ -10172.0408] [ 1950] [depth= 1] . ( 30 sec) [ -10171.7081] [ 1950] [depth= 1] . ( 30 sec) [ -10171.2938] [ 1951] [depth= 1] . ( 34 sec) [ -10160.5484] [Branch lengths ] . ( 36 sec) [ -10160.1638] [GTR parameters ] . ( 36 sec) [ -10160.0500] [Alpha ][ 0.548298] . ( 36 sec) [ -10159.9312] [ 1950] [depth= 1] . ( 37 sec) [ -10159.8361] [ 1948] [depth= 1] . ( 49 sec) [ -10159.3821] [ 1948] [depth= 1] . ( 56 sec) [ -10158.0590] [Branch lengths ] . ( 56 sec) [ -10158.0526] [GTR parameters ] . ( 56 sec) [ -10158.0453] [Alpha ][ 0.552446] . ( 74 sec) [ -10157.8604] [Branch lengths ] . ( 139 sec) [ -10157.8197] [Branch lengths ] . ( 139 sec) [ -10157.8197] [Topology ] . ( 141 sec) [ -10157.8142] [Topology ] . ( 142 sec) [ -10157.8120] [Topology ] . ( 144 sec) [ -10157.8108] [Topology ] . ( 145 sec) [ -10157.8101] [Topology ] . ( 146 sec) [ -10157.8042] [GTR parameters ] . ( 146 sec) [ -10157.8016] [Alpha ][ 0.554895] . ( 146 sec) [ -10157.8016] [Topology ] . ( 148 sec) [ -10157.8003] [Topology ] . ( 149 sec) [ -10157.7996] [Topology ] . ( 150 sec) [ -10157.7996] [GTR parameters ] . ( 150 sec) [ -10157.7996] [Alpha ][ 0.554895] . ( 150 sec) [ -10157.7996] [Topology ] . ( 152 sec) [ -10157.7992] [Topology ] . ( 152 sec) [ -10157.7992] [GTR parameters ] . ( 152 sec) [ -10157.7992] [Alpha ][ 0.554895] . Checking for NNIs, optimizing five branches... . ( 163 sec) [ -10157.7488] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.748800. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -10411.1053] [GTR parameters ] . ( 4 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 4 sec) [ -10335.0128] [Topology ] . ( 6 sec) [ -10195.6434] [Topology ] . ( 7 sec) [ -10172.9119] [Topology ] . ( 9 sec) [ -10166.8129] [Topology ] . ( 10 sec) [ -10164.3617] [Topology ] . ( 12 sec) [ -10162.8738] [Topology ] . ( 13 sec) [ -10161.8960] [Topology ] . ( 15 sec) [ -10161.4684] [Topology ] . ( 17 sec) [ -10161.2425] [Topology ] . ( 18 sec) [ -10161.1170] [Topology ] . ( 21 sec) [ -10159.7359] [GTR parameters ] . ( 21 sec) [ -10158.5137] [Alpha ][ 0.551183] . ( 21 sec) [ -10158.5137] [Topology ] . ( 23 sec) [ -10158.2651] [Topology ] . ( 24 sec) [ -10158.0260] [Topology ] . ( 26 sec) [ -10157.8174] [Topology ] . ( 27 sec) [ -10157.7549] [Topology ] . ( 29 sec) [ -10157.7235] [Topology ] . ( 31 sec) [ -10157.7057] [Topology ] . ( 32 sec) [ -10157.6954] [Topology ] . ( 34 sec) [ -10157.6894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -10157.6802] [GTR parameters ] . ( 46 sec) [ -10157.6621] [Alpha ][ 0.557749] . ( 46 sec) [ -10157.6621] [Topology ] . ( 47 sec) [ -10157.6548] [Topology ] . ( 49 sec) [ -10157.6507] [Topology ] . ( 50 sec) [ -10157.6484] [Topology ] . ( 52 sec) [ -10157.6470] [Topology ] . ( 53 sec) [ -10157.6462] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -10157.6460] [GTR parameters ] . ( 65 sec) [ -10157.6459] [Alpha ][ 0.558307] . ( 65 sec) [ -10157.6459] [Topology ] . ( 67 sec) [ -10157.6452] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 92 sec) [ -10411.1053] [GTR parameters ] . ( 92 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 92 sec) [ -10332.5377] [ 1957] [depth= 1] . ( 92 sec) [ -10328.1906] [ 1951] [depth= 1] . ( 93 sec) [ -10328.1000] [ 1957] [depth= 1] . ( 94 sec) [ -10322.0485] [ 1953] [depth= 2] . ( 94 sec) [ -10321.5223] [ 1957] [depth= 1] . ( 94 sec) [ -10318.8466] [ 1953] [depth= 1] . ( 94 sec) [ -10318.7421] [ 1953] [depth= 1] . ( 94 sec) [ -10318.5053] [ 1953] [depth= 1] . ( 95 sec) [ -10317.9252] [ 1954] [depth= 1] . ( 95 sec) [ -10317.3941] [ 1954] [depth= 1] . ( 95 sec) [ -10317.1936] [ 1953] [depth= 1] . ( 95 sec) [ -10317.1467] [ 1952] [depth= 1] . ( 95 sec) [ -10316.1576] [ 1952] [depth= 1] . ( 95 sec) [ -10315.7973] [ 1952] [depth= 1] . ( 95 sec) [ -10315.6060] [ 1952] [depth= 1] . ( 95 sec) [ -10315.5532] [ 1952] [depth= 1] . ( 95 sec) [ -10314.4237] [ 1954] [depth= 1] . ( 96 sec) [ -10311.8066] [ 1956] [depth= 2] . ( 96 sec) [ -10298.4200] [ 1960] [depth= 1] . ( 96 sec) [ -10296.7188] [ 1964] [depth= 3] . ( 96 sec) [ -10290.8688] [ 1958] [depth= 3] . ( 97 sec) [ -10287.8786] [ 1957] [depth= 1] . ( 97 sec) [ -10287.2467] [ 1958] [depth= 1] . ( 97 sec) [ -10286.6646] [ 1960] [depth= 2] . ( 98 sec) [ -10285.3626] [ 1958] [depth= 1] . ( 98 sec) [ -10284.7476] [ 1960] [depth= 1] . ( 98 sec) [ -10284.4485] [ 1962] [depth= 1] . ( 98 sec) [ -10283.5669] [ 1962] [depth= 1] . ( 98 sec) [ -10282.5503] [ 1961] [depth= 1] . ( 99 sec) [ -10280.7221] [ 1959] [depth= 1] . ( 99 sec) [ -10275.0930] [ 1961] [depth= 1] . ( 99 sec) [ -10271.5810] [ 1959] [depth= 1] . ( 99 sec) [ -10269.1582] [ 1960] [depth= 1] . ( 99 sec) [ -10265.8986] [ 1959] [depth= 1] . ( 99 sec) [ -10255.9269] [ 1954] [depth= 1] . ( 99 sec) [ -10255.6999] [ 1954] [depth= 1] . ( 100 sec) [ -10255.0256] [ 1955] [depth= 1] . ( 100 sec) [ -10254.3015] [ 1957] [depth= 1] . ( 100 sec) [ -10254.0739] [ 1955] [depth= 1] . ( 101 sec) [ -10252.2304] [ 1955] [depth= 1] . ( 101 sec) [ -10249.1318] [ 1956] [depth= 1] . ( 101 sec) [ -10248.1783] [ 1956] [depth= 1] . ( 101 sec) [ -10245.7845] [ 1956] [depth= 1] . ( 101 sec) [ -10241.9436] [ 1952] [depth= 1] . ( 101 sec) [ -10241.4605] [ 1955] [depth= 1] . ( 101 sec) [ -10241.4040] [ 1956] [depth= 1] . ( 101 sec) [ -10239.7131] [ 1952] [depth= 1] . ( 102 sec) [ -10239.0104] [ 1952] [depth= 1] . ( 102 sec) [ -10238.1532] [ 1957] [depth= 2] . ( 102 sec) [ -10237.2127] [ 1957] [depth= 1] . ( 103 sec) [ -10236.9476] [ 1957] [depth= 1] . ( 103 sec) [ -10236.7877] [ 1958] [depth= 1] . ( 104 sec) [ -10235.0013] [ 1960] [depth= 1] . ( 104 sec) [ -10234.7534] [ 1958] [depth= 1] . ( 105 sec) [ -10233.4427] [ 1959] [depth= 1] . ( 105 sec) [ -10232.8847] [ 1959] [depth= 1] . ( 105 sec) [ -10174.7437] [Branch lengths ] . ( 107 sec) [ -10173.5724] [GTR parameters ] . ( 107 sec) [ -10173.1806] [Alpha ][ 0.529333] . ( 108 sec) [ -10172.0753] [ 1954] [depth= 1] . ( 109 sec) [ -10170.8253] [ 1952] [depth= 1] . ( 110 sec) [ -10170.3291] [ 1952] [depth= 1] . ( 110 sec) [ -10170.0245] [ 1952] [depth= 2] . ( 111 sec) [ -10168.8694] [ 1950] [depth= 2] . ( 119 sec) [ -10168.2110] [ 1950] [depth= 1] . ( 125 sec) [ -10167.9359] [ 1950] [depth= 1] . ( 125 sec) [ -10160.5292] [Branch lengths ] . ( 126 sec) [ -10160.4897] [GTR parameters ] . ( 126 sec) [ -10160.3695] [Alpha ][ 0.545447] . ( 145 sec) [ -10159.0871] [Branch lengths ] . ( 177 sec) [ -10159.0322] [ 1949] [depth= 1] . ( 211 sec) [ -10158.8062] [Branch lengths ] . ( 212 sec) [ -10158.7858] [GTR parameters ] . ( 212 sec) [ -10158.7576] [Alpha ][ 0.553586] . ( 212 sec) [ -10158.7576] [Topology ] . ( 213 sec) [ -10158.6050] [Topology ] . ( 215 sec) [ -10158.3544] [Topology ] . ( 217 sec) [ -10158.3113] [Topology ] . ( 218 sec) [ -10158.2964] [Topology ] . ( 220 sec) [ -10158.2902] [Topology ] . ( 221 sec) [ -10158.2873] [Topology ] . ( 223 sec) [ -10158.2857] [Topology ] . ( 224 sec) [ -10158.2808] [GTR parameters ] . ( 224 sec) [ -10158.2786] [Alpha ][ 0.555807] . ( 224 sec) [ -10158.2786] [Topology ] . ( 225 sec) [ -10158.2773] [Topology ] . ( 227 sec) [ -10158.2765] [Topology ] . ( 227 sec) [ -10158.2765] [GTR parameters ] . ( 227 sec) [ -10158.2765] [Alpha ][ 0.555807] . ( 227 sec) [ -10158.2765] [Topology ] . ( 229 sec) [ -10158.2760] [Topology ] . ( 229 sec) [ -10158.2760] [GTR parameters ] . ( 229 sec) [ -10158.2760] [Alpha ][ 0.555807] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10157.645233 . Log likelihood obtained after SPR moves : -10158.276012 . Log likelihood of the current tree: -10157.645233. . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Best log likelihood : -10157.452105 . Time used 0h4m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1108.68user 0.00system 18:34.28elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps