.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data17.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... . 394 patterns found. (out of a total of 500 sites) . 90 sites without polymorphism (18.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16760.5330] [GTR parameters ] . ( 1 sec) [ -16462.5975] [Alpha ][ 0.500960] . ( 1 sec) [ -16128.7086] [ 3387] [depth= 4] . ( 1 sec) [ -15967.8429] [ 3323] [depth= 6] . ( 1 sec) [ -15827.9223] [ 3322] [depth= 1] . ( 1 sec) [ -15814.4758] [ 3319] [depth= 1] . ( 1 sec) [ -15812.5697] [ 3318] [depth= 1] . ( 1 sec) [ -15795.3345] [ 3310] [depth= 4] . ( 1 sec) [ -15565.1361] [ 3293] [depth= 13] . ( 2 sec) [ -15536.7098] [ 3278] [depth= 7] . ( 2 sec) [ -15133.3316] [ 3189] [depth= 1] . ( 2 sec) [ -14976.7631] [ 3144] [depth= 8] . ( 2 sec) [ -14916.4982] [ 3130] [depth= 2] . ( 2 sec) [ -14846.9847] [ 3120] [depth= 2] . ( 2 sec) [ -14701.1317] [ 3111] [depth= 1] . ( 2 sec) [ -14633.2424] [ 3099] [depth= 4] . ( 2 sec) [ -14613.4288] [ 3088] [depth= 1] . ( 2 sec) [ -14488.5808] [ 3077] [depth= 5] . ( 2 sec) [ -14456.5971] [ 3063] [depth= 2] . ( 2 sec) [ -14423.9654] [ 3059] [depth= 2] . ( 2 sec) [ -14310.2194] [ 3009] [depth= 18] . ( 2 sec) [ -14176.4235] [ 2981] [depth= 12] . ( 2 sec) [ -14032.7406] [ 2917] [depth= 8] . ( 2 sec) [ -13870.2621] [ 2899] [depth= 2] . ( 2 sec) [ -13785.7337] [ 2897] [depth= 13] . ( 2 sec) [ -13753.5873] [ 2887] [depth= 1] . ( 2 sec) [ -13653.8621] [ 2871] [depth= 11] . ( 2 sec) [ -13610.4456] [ 2865] [depth= 2] . ( 2 sec) [ -13480.5615] [ 2864] [depth= 4] . ( 2 sec) [ -13318.6481] [ 2835] [depth= 2] . ( 2 sec) [ -13279.3062] [ 2825] [depth= 1] . ( 2 sec) [ -13269.1061] [ 2823] [depth= 2] . ( 2 sec) [ -13203.1645] [ 2766] [depth= 11] . ( 3 sec) [ -13136.3485] [ 2749] [depth= 2] . ( 3 sec) [ -12999.1195] [ 2734] [depth= 3] . ( 3 sec) [ -12829.2787] [ 2663] [depth= 1] . ( 3 sec) [ -12534.8426] [ 2609] [depth= 14] . ( 3 sec) [ -12416.6615] [ 2563] [depth= 9] . ( 3 sec) [ -12415.4845] [ 2559] [depth= 1] . ( 3 sec) [ -12247.5866] [ 2558] [depth= 5] . ( 3 sec) [ -12141.3432] [ 2496] [depth= 4] . ( 3 sec) [ -11944.2594] [ 2456] [depth= 4] . ( 3 sec) [ -11918.5139] [ 2450] [depth= 4] . ( 3 sec) [ -11916.9053] [ 2453] [depth= 1] . ( 3 sec) [ -11085.6061] [ 2338] [depth= 8] . ( 3 sec) [ -10997.7055] [ 2340] [depth= 1] . ( 3 sec) [ -10987.1267] [ 2341] [depth= 1] . ( 3 sec) [ -10867.7304] [ 2308] [depth= 8] . ( 3 sec) [ -10694.8920] [ 2288] [depth= 1] . ( 3 sec) [ -10495.2293] [ 2284] [depth= 1] . ( 3 sec) [ -10453.2816] [ 2241] [depth= 1] . ( 3 sec) [ -10441.6475] [ 2227] [depth= 8] . ( 3 sec) [ -10253.2129] [ 2198] [depth= 2] . ( 3 sec) [ -10157.3952] [ 2240] [depth= 1] . ( 4 sec) [ -9772.0749] [ 2146] [depth= 2] . ( 4 sec) [ -9668.9968] [ 2107] [depth= 13] . ( 4 sec) [ -9604.9857] [ 2076] [depth= 13] . ( 4 sec) [ -9602.8386] [ 2077] [depth= 1] . ( 4 sec) [ -9592.6432] [ 2078] [depth= 1] . ( 4 sec) [ -9545.8975] [ 2060] [depth= 1] . ( 4 sec) [ -9176.7732] [ 2044] [depth= 2] . ( 4 sec) [ -9057.0402] [ 1996] [depth= 8] . ( 4 sec) [ -9046.5168] [ 1993] [depth= 1] . ( 4 sec) [ -8898.2413] [ 1958] [depth= 1] . ( 4 sec) [ -8879.8543] [ 1954] [depth= 1] . ( 4 sec) [ -8869.1244] [ 1951] [depth= 1] . ( 4 sec) [ -8868.9930] [ 1952] [depth= 1] . ( 4 sec) [ -8867.9586] [ 1952] [depth= 2] . ( 4 sec) [ -8759.9093] [ 1932] [depth= 2] . ( 4 sec) [ -8639.2408] [ 1885] [depth= 4] . ( 4 sec) [ -8621.8464] [ 1851] [depth= 1] . ( 4 sec) [ -8593.7154] [ 1847] [depth= 1] . ( 4 sec) [ -8458.8933] [ 1792] [depth= 4] . ( 4 sec) [ -8271.2929] [ 1715] [depth= 4] . ( 5 sec) [ -8263.7294] [ 1717] [depth= 1] . ( 5 sec) [ -8241.9017] [ 1713] [depth= 2] . ( 5 sec) [ -8239.3911] [ 1711] [depth= 1] . ( 5 sec) [ -8199.3426] [ 1709] [depth= 1] . ( 5 sec) [ -8042.1900] [Branch lengths ] . ( 6 sec) [ -8039.1988] [GTR parameters ] . ( 6 sec) [ -8014.9203] [Alpha ][ 0.860843] . ( 6 sec) [ -7978.4303] [ 1692] [depth= 1] . ( 6 sec) [ -7977.5545] [ 1693] [depth= 1] . ( 6 sec) [ -7976.9219] [ 1689] [depth= 1] . ( 6 sec) [ -7973.3558] [ 1686] [depth= 1] . ( 6 sec) [ -7968.8034] [ 1680] [depth= 2] . ( 6 sec) [ -7968.6554] [ 1680] [depth= 1] . ( 6 sec) [ -7913.6733] [ 1645] [depth= 3] . ( 6 sec) [ -7912.7186] [ 1644] [depth= 1] . ( 6 sec) [ -7912.5579] [ 1644] [depth= 1] . ( 7 sec) [ -7911.7071] [ 1642] [depth= 2] . ( 7 sec) [ -7911.4277] [ 1643] [depth= 1] . ( 7 sec) [ -7907.1307] [ 1642] [depth= 3] . ( 8 sec) [ -7907.1126] [ 1647] [depth= 1] . ( 8 sec) [ -7906.9840] [ 1648] [depth= 1] . ( 8 sec) [ -7905.8702] [ 1646] [depth= 1] . ( 8 sec) [ -7905.7380] [ 1648] [depth= 2] . ( 8 sec) [ -7903.9542] [ 1652] [depth= 1] . ( 8 sec) [ -7903.7688] [ 1651] [depth= 1] . ( 8 sec) [ -7903.7463] [ 1652] [depth= 1] . ( 8 sec) [ -7903.3344] [ 1647] [depth= 2] . ( 9 sec) [ -7903.0486] [ 1649] [depth= 1] . ( 9 sec) [ -7901.7370] [ 1650] [depth= 1] . ( 9 sec) [ -7901.6090] [ 1650] [depth= 1] . ( 9 sec) [ -7901.2115] [ 1648] [depth= 1] . ( 9 sec) [ -7889.7713] [Branch lengths ] . ( 9 sec) [ -7889.6799] [GTR parameters ] . ( 9 sec) [ -7888.9911] [Alpha ][ 0.945644] . ( 10 sec) [ -7888.6990] [ 1646] [depth= 1] . ( 10 sec) [ -7888.5595] [ 1645] [depth= 1] . ( 12 sec) [ -7888.4779] [ 1647] [depth= 1] . ( 13 sec) [ -7887.0484] [Branch lengths ] . ( 13 sec) [ -7887.0441] [GTR parameters ] . ( 13 sec) [ -7887.0179] [Alpha ][ 0.963554] . ( 17 sec) [ -7886.8470] [Branch lengths ] . ( 39 sec) [ -7886.8226] [Branch lengths ] . ( 39 sec) [ -7886.8226] [Topology ] . ( 40 sec) [ -7886.8193] [Topology ] . ( 40 sec) [ -7886.8134] [Topology ] . ( 41 sec) [ -7886.7757] [Topology ] . ( 42 sec) [ -7886.5072] [Topology ] . ( 42 sec) [ -7885.1782] [Topology ] . ( 43 sec) [ -7884.0937] [Topology ] . ( 43 sec) [ -7884.0877] [GTR parameters ] . ( 43 sec) [ -7884.0810] [Alpha ][ 0.972624] . ( 43 sec) [ -7884.0810] [Topology ] . ( 44 sec) [ -7883.7201] [Topology ] . ( 45 sec) [ -7883.5959] [Topology ] . ( 45 sec) [ -7883.5616] [Topology ] . ( 46 sec) [ -7883.5515] [Topology ] . ( 47 sec) [ -7883.5484] [Topology ] . ( 47 sec) [ -7883.5475] [Topology ] . ( 48 sec) [ -7883.5437] [GTR parameters ] . ( 48 sec) [ -7883.5437] [Alpha ][ 0.971550] . ( 48 sec) [ -7883.5437] [Topology ] . ( 48 sec) [ -7883.5433] [Topology ] . ( 49 sec) [ -7883.5433] [GTR parameters ] . ( 49 sec) [ -7883.5433] [Alpha ][ 0.971550] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -7883.5085] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -7883.5084] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -7883.5055] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7883.505523. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16007.9347] [GTR parameters ] . ( 0 sec) [ -15718.2231] [Alpha ][ 0.500960] . ( 0 sec) [ -15386.1952] [ 3326] [depth= 4] . ( 0 sec) [ -15168.5275] [ 3268] [depth= 13] . ( 0 sec) [ -14921.1512] [ 3254] [depth= 4] . ( 0 sec) [ -14878.4255] [ 3248] [depth= 6] . ( 1 sec) [ -14721.0764] [ 3205] [depth= 1] . ( 1 sec) [ -14591.4468] [ 3194] [depth= 9] . ( 1 sec) [ -14501.3922] [ 3196] [depth= 1] . ( 1 sec) [ -14432.7777] [ 3187] [depth= 4] . ( 1 sec) [ -14408.8010] [ 3158] [depth= 2] . ( 1 sec) [ -14306.5107] [ 3143] [depth= 3] . ( 1 sec) [ -14070.2815] [ 3092] [depth= 3] . ( 1 sec) [ -13828.8202] [ 3090] [depth= 1] . ( 1 sec) [ -13677.6951] [ 3044] [depth= 1] . ( 1 sec) [ -13628.8642] [ 3040] [depth= 5] . ( 1 sec) [ -13365.4989] [ 2984] [depth= 6] . ( 1 sec) [ -13232.4848] [ 2934] [depth= 6] . ( 1 sec) [ -13183.3733] [ 2882] [depth= 8] . ( 1 sec) [ -13076.7334] [ 2868] [depth= 5] . ( 1 sec) [ -12658.8555] [ 2845] [depth= 1] . ( 1 sec) [ -12635.5166] [ 2845] [depth= 1] . ( 1 sec) [ -12369.9720] [ 2751] [depth= 4] . ( 1 sec) [ -12258.9599] [ 2733] [depth= 12] . ( 1 sec) [ -12215.3586] [ 2730] [depth= 1] . ( 1 sec) [ -12048.9763] [ 2698] [depth= 3] . ( 1 sec) [ -12046.4085] [ 2701] [depth= 1] . ( 1 sec) [ -11910.7495] [ 2644] [depth= 9] . ( 1 sec) [ -11683.5779] [ 2623] [depth= 17] . ( 1 sec) [ -11483.1260] [ 2612] [depth= 1] . ( 1 sec) [ -11405.3783] [ 2559] [depth= 1] . ( 1 sec) [ -11355.8012] [ 2554] [depth= 17] . ( 2 sec) [ -11242.3722] [ 2525] [depth= 1] . ( 2 sec) [ -10964.5103] [ 2465] [depth= 10] . ( 2 sec) [ -10701.4176] [ 2386] [depth= 4] . ( 2 sec) [ -10701.3028] [ 2386] [depth= 1] . ( 2 sec) [ -10690.7888] [ 2382] [depth= 1] . ( 2 sec) [ -10542.2735] [ 2329] [depth= 2] . ( 2 sec) [ -10477.7541] [ 2340] [depth= 2] . ( 2 sec) [ -10330.3486] [ 2297] [depth= 3] . ( 2 sec) [ -10239.2719] [ 2247] [depth= 6] . ( 2 sec) [ -10200.2205] [ 2243] [depth= 3] . ( 2 sec) [ -10163.4936] [ 2237] [depth= 1] . ( 2 sec) [ -10154.7601] [ 2234] [depth= 1] . ( 2 sec) [ -9995.3712] [ 2200] [depth= 5] . ( 2 sec) [ -9965.4420] [ 2212] [depth= 1] . ( 2 sec) [ -9963.4410] [ 2210] [depth= 1] . ( 2 sec) [ -9910.7058] [ 2195] [depth= 4] . ( 2 sec) [ -9885.7133] [ 2195] [depth= 1] . ( 2 sec) [ -9873.9915] [ 2188] [depth= 2] . ( 2 sec) [ -9793.7454] [ 2161] [depth= 1] . ( 2 sec) [ -9768.1087] [ 2145] [depth= 6] . ( 2 sec) [ -9761.3830] [ 2143] [depth= 1] . ( 3 sec) [ -9719.5203] [ 2125] [depth= 8] . ( 3 sec) [ -9560.7283] [ 2116] [depth= 10] . ( 3 sec) [ -9540.5451] [ 2132] [depth= 9] . ( 3 sec) [ -9468.7532] [ 2100] [depth= 9] . ( 3 sec) [ -9313.0406] [ 2055] [depth= 5] . ( 3 sec) [ -9230.9574] [ 2034] [depth= 2] . ( 3 sec) [ -9198.1686] [ 1999] [depth= 1] . ( 3 sec) [ -9115.1439] [ 1952] [depth= 2] . ( 3 sec) [ -9051.1325] [ 1943] [depth= 6] . ( 3 sec) [ -8870.0793] [ 1873] [depth= 7] . ( 3 sec) [ -8810.0133] [ 1857] [depth= 1] . ( 3 sec) [ -8606.6408] [ 1813] [depth= 9] . ( 3 sec) [ -8585.3641] [ 1798] [depth= 1] . ( 3 sec) [ -8531.7962] [ 1771] [depth= 6] . ( 3 sec) [ -8524.9916] [ 1769] [depth= 1] . ( 3 sec) [ -8473.9883] [ 1753] [depth= 2] . ( 3 sec) [ -8458.6369] [ 1748] [depth= 3] . ( 3 sec) [ -8420.5228] [ 1729] [depth= 1] . ( 4 sec) [ -8400.5001] [ 1733] [depth= 8] . ( 4 sec) [ -8355.0491] [ 1708] [depth= 5] . ( 4 sec) [ -8354.3178] [ 1708] [depth= 1] . ( 4 sec) [ -8311.7382] [ 1704] [depth= 1] . ( 4 sec) [ -8311.5712] [ 1704] [depth= 1] . ( 4 sec) [ -8307.3633] [ 1700] [depth= 1] . ( 4 sec) [ -8075.8227] [Branch lengths ] . ( 5 sec) [ -8071.7089] [GTR parameters ] . ( 5 sec) [ -8047.0427] [Alpha ][ 0.858424] . ( 5 sec) [ -8046.3419] [ 1700] [depth= 1] . ( 5 sec) [ -7992.7868] [ 1668] [depth= 3] . ( 5 sec) [ -7990.8972] [ 1666] [depth= 2] . ( 6 sec) [ -7984.7511] [ 1667] [depth= 1] . ( 6 sec) [ -7982.0404] [ 1671] [depth= 1] . ( 6 sec) [ -7981.9353] [ 1675] [depth= 1] . ( 6 sec) [ -7979.9676] [ 1677] [depth= 1] . ( 6 sec) [ -7975.4656] [ 1675] [depth= 1] . ( 6 sec) [ -7972.9619] [ 1670] [depth= 1] . ( 7 sec) [ -7970.9993] [ 1666] [depth= 1] . ( 7 sec) [ -7970.8443] [ 1665] [depth= 2] . ( 7 sec) [ -7968.5208] [ 1670] [depth= 1] . ( 7 sec) [ -7941.8783] [ 1654] [depth= 2] . ( 7 sec) [ -7940.9192] [ 1657] [depth= 1] . ( 7 sec) [ -7939.5448] [ 1658] [depth= 1] . ( 7 sec) [ -7928.7617] [ 1656] [depth= 1] . ( 7 sec) [ -7927.4351] [ 1657] [depth= 1] . ( 7 sec) [ -7927.2998] [ 1660] [depth= 1] . ( 8 sec) [ -7920.7058] [ 1651] [depth= 2] . ( 8 sec) [ -7920.5520] [ 1652] [depth= 1] . ( 8 sec) [ -7898.7911] [Branch lengths ] . ( 8 sec) [ -7898.6439] [GTR parameters ] . ( 9 sec) [ -7897.8977] [Alpha ][ 0.946336] . ( 9 sec) [ -7897.8790] [ 1645] [depth= 2] . ( 10 sec) [ -7897.8401] [ 1648] [depth= 1] . ( 10 sec) [ -7897.8289] [ 1650] [depth= 1] . ( 11 sec) [ -7896.7912] [ 1647] [depth= 2] . ( 12 sec) [ -7896.5416] [ 1646] [depth= 1] . ( 12 sec) [ -7895.4919] [Branch lengths ] . ( 13 sec) [ -7895.4860] [GTR parameters ] . ( 13 sec) [ -7895.4592] [Alpha ][ 0.964467] . ( 13 sec) [ -7895.3710] [ 1647] [depth= 2] . ( 17 sec) [ -7895.1987] [Branch lengths ] . ( 17 sec) [ -7895.1984] [GTR parameters ] . ( 17 sec) [ -7895.1971] [Alpha ][ 0.968386] . ( 39 sec) [ -7895.1737] [Branch lengths ] . ( 39 sec) [ -7895.1737] [Topology ] . ( 39 sec) [ -7895.1681] [Topology ] . ( 40 sec) [ -7895.1522] [Topology ] . ( 41 sec) [ -7895.0388] [Topology ] . ( 41 sec) [ -7894.2440] [Topology ] . ( 42 sec) [ -7890.5423] [Topology ] . ( 43 sec) [ -7886.6211] [Topology ] . ( 43 sec) [ -7886.6149] [GTR parameters ] . ( 43 sec) [ -7886.6138] [Alpha ][ 0.972018] . ( 43 sec) [ -7886.6138] [Topology ] . ( 44 sec) [ -7884.9315] [Topology ] . ( 45 sec) [ -7884.1996] [Topology ] . ( 45 sec) [ -7883.8582] [Topology ] . ( 46 sec) [ -7883.6977] [Topology ] . ( 47 sec) [ -7883.6196] [Topology ] . ( 47 sec) [ -7883.5809] [Topology ] . ( 48 sec) [ -7883.5618] [Topology ] . ( 49 sec) [ -7883.5522] [Topology ] . ( 49 sec) [ -7883.5492] [GTR parameters ] . ( 49 sec) [ -7883.5492] [Alpha ][ 0.972018] . ( 49 sec) [ -7883.5492] [Topology ] . ( 50 sec) [ -7883.5441] [Topology ] . ( 51 sec) [ -7883.5415] [Topology ] . ( 51 sec) [ -7883.5402] [Topology ] . ( 52 sec) [ -7883.5396] [Topology ] . ( 52 sec) [ -7883.5396] [GTR parameters ] . ( 52 sec) [ -7883.5396] [Alpha ][ 0.972018] . ( 52 sec) [ -7883.5396] [Topology ] . ( 53 sec) [ -7883.5393] [Topology ] . ( 53 sec) [ -7883.5393] [GTR parameters ] . ( 53 sec) [ -7883.5393] [Alpha ][ 0.972018] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -7883.5047] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7883.504718. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17277.5706] [GTR parameters ] . ( 0 sec) [ -16942.3005] [Alpha ][ 0.500960] . ( 0 sec) [ -16675.7612] [ 3482] [depth= 1] . ( 0 sec) [ -16428.1221] [ 3426] [depth= 4] . ( 0 sec) [ -15887.7495] [ 3413] [depth= 4] . ( 0 sec) [ -15782.1329] [ 3408] [depth= 1] . ( 0 sec) [ -15692.6618] [ 3379] [depth= 6] . ( 1 sec) [ -15622.9568] [ 3367] [depth= 2] . ( 1 sec) [ -15466.9694] [ 3362] [depth= 7] . ( 1 sec) [ -15170.4301] [ 3330] [depth= 6] . ( 1 sec) [ -14560.6733] [ 3207] [depth= 8] . ( 1 sec) [ -14233.7440] [ 3109] [depth= 5] . ( 1 sec) [ -14223.4896] [ 3111] [depth= 1] . ( 1 sec) [ -13857.7384] [ 3093] [depth= 15] . ( 1 sec) [ -13837.0701] [ 3087] [depth= 2] . ( 1 sec) [ -13759.8451] [ 3081] [depth= 1] . ( 1 sec) [ -13478.2498] [ 2999] [depth= 9] . ( 1 sec) [ -13443.7643] [ 3008] [depth= 3] . ( 1 sec) [ -13292.2968] [ 2975] [depth= 3] . ( 1 sec) [ -13191.6925] [ 2960] [depth= 4] . ( 1 sec) [ -12808.8372] [ 2849] [depth= 6] . ( 1 sec) [ -12561.6665] [ 2812] [depth= 9] . ( 1 sec) [ -12554.0614] [ 2772] [depth= 1] . ( 1 sec) [ -12496.5129] [ 2742] [depth= 6] . ( 1 sec) [ -12421.2009] [ 2714] [depth= 1] . ( 1 sec) [ -12298.0347] [ 2678] [depth= 11] . ( 1 sec) [ -12106.2916] [ 2587] [depth= 4] . ( 1 sec) [ -12059.0715] [ 2533] [depth= 1] . ( 1 sec) [ -11915.0713] [ 2522] [depth= 10] . ( 1 sec) [ -11808.0431] [ 2520] [depth= 2] . ( 1 sec) [ -11796.1399] [ 2563] [depth= 1] . ( 2 sec) [ -11693.3143] [ 2531] [depth= 8] . ( 2 sec) [ -11683.9003] [ 2533] [depth= 1] . ( 2 sec) [ -11683.5852] [ 2530] [depth= 1] . ( 2 sec) [ -11603.5737] [ 2513] [depth= 1] . ( 2 sec) [ -11597.8384] [ 2495] [depth= 7] . ( 2 sec) [ -11526.9078] [ 2500] [depth= 1] . ( 2 sec) [ -11314.6519] [ 2468] [depth= 1] . ( 2 sec) [ -11117.4319] [ 2436] [depth= 8] . ( 2 sec) [ -11083.4943] [ 2431] [depth= 1] . ( 2 sec) [ -11075.8669] [ 2433] [depth= 1] . ( 2 sec) [ -10932.2769] [ 2391] [depth= 6] . ( 2 sec) [ -10851.8121] [ 2383] [depth= 1] . ( 2 sec) [ -10791.5938] [ 2382] [depth= 3] . ( 2 sec) [ -10667.8858] [ 2332] [depth= 2] . ( 2 sec) [ -10590.4609] [ 2323] [depth= 1] . ( 2 sec) [ -10567.8378] [ 2310] [depth= 6] . ( 2 sec) [ -10316.9571] [ 2279] [depth= 2] . ( 2 sec) [ -10163.8989] [ 2275] [depth= 1] . ( 3 sec) [ -10116.7002] [ 2274] [depth= 1] . ( 3 sec) [ -10108.2577] [ 2274] [depth= 1] . ( 3 sec) [ -10058.6214] [ 2256] [depth= 2] . ( 3 sec) [ -10056.1079] [ 2254] [depth= 1] . ( 3 sec) [ -10002.4169] [ 2254] [depth= 3] . ( 3 sec) [ -9999.3591] [ 2254] [depth= 1] . ( 3 sec) [ -9997.9024] [ 2256] [depth= 1] . ( 3 sec) [ -9851.2321] [ 2181] [depth= 10] . ( 3 sec) [ -9849.9663] [ 2181] [depth= 1] . ( 3 sec) [ -9848.1778] [ 2184] [depth= 1] . ( 3 sec) [ -9847.9529] [ 2186] [depth= 3] . ( 3 sec) [ -9837.8408] [ 2190] [depth= 4] . ( 3 sec) [ -9760.4064] [ 2133] [depth= 5] . ( 3 sec) [ -9759.7904] [ 2138] [depth= 4] . ( 3 sec) [ -9603.0300] [ 2159] [depth= 9] . ( 3 sec) [ -9579.2844] [ 2153] [depth= 4] . ( 3 sec) [ -9571.0421] [ 2147] [depth= 1] . ( 3 sec) [ -9544.2694] [ 2139] [depth= 3] . ( 4 sec) [ -9543.0459] [ 2140] [depth= 1] . ( 4 sec) [ -9542.3493] [ 2136] [depth= 2] . ( 4 sec) [ -9536.8782] [ 2136] [depth= 1] . ( 4 sec) [ -9530.6365] [ 2132] [depth= 1] . ( 4 sec) [ -9432.2521] [ 2088] [depth= 1] . ( 4 sec) [ -9339.7569] [ 2062] [depth= 5] . ( 4 sec) [ -9198.1211] [ 2006] [depth= 7] . ( 4 sec) [ -9128.9617] [ 1971] [depth= 4] . ( 4 sec) [ -9009.6393] [ 1906] [depth= 4] . ( 4 sec) [ -9002.4038] [ 1908] [depth= 1] . ( 4 sec) [ -8906.0017] [ 1884] [depth= 2] . ( 4 sec) [ -8773.4296] [ 1836] [depth= 2] . ( 4 sec) [ -8755.3852] [ 1836] [depth= 1] . ( 4 sec) [ -8705.9406] [ 1818] [depth= 1] . ( 4 sec) [ -8705.7288] [ 1819] [depth= 1] . ( 4 sec) [ -8558.2151] [ 1768] [depth= 3] . ( 4 sec) [ -8548.2222] [ 1766] [depth= 2] . ( 5 sec) [ -8293.2591] [Branch lengths ] . ( 5 sec) [ -8289.5797] [GTR parameters ] . ( 5 sec) [ -8259.3212] [Alpha ][ 0.890765] . ( 5 sec) [ -8236.8364] [ 1761] [depth= 1] . ( 5 sec) [ -8235.8514] [ 1760] [depth= 1] . ( 5 sec) [ -8232.8419] [ 1761] [depth= 1] . ( 5 sec) [ -8098.8100] [ 1714] [depth= 1] . ( 6 sec) [ -8086.2682] [ 1707] [depth= 1] . ( 6 sec) [ -8045.5777] [ 1700] [depth= 3] . ( 6 sec) [ -8041.5797] [ 1697] [depth= 1] . ( 6 sec) [ -8033.1919] [ 1697] [depth= 4] . ( 6 sec) [ -8032.7594] [ 1699] [depth= 1] . ( 6 sec) [ -8030.2671] [ 1698] [depth= 1] . ( 6 sec) [ -8007.7958] [ 1693] [depth= 2] . ( 6 sec) [ -7995.8648] [ 1675] [depth= 1] . ( 6 sec) [ -7995.8470] [ 1675] [depth= 1] . ( 6 sec) [ -7990.5025] [ 1672] [depth= 1] . ( 6 sec) [ -7988.3141] [ 1676] [depth= 1] . ( 6 sec) [ -7986.5702] [ 1646] [depth= 1] . ( 6 sec) [ -7985.0670] [ 1643] [depth= 1] . ( 7 sec) [ -7977.2526] [ 1646] [depth= 1] . ( 7 sec) [ -7975.3884] [ 1653] [depth= 3] . ( 7 sec) [ -7931.6451] [ 1650] [depth= 3] . ( 7 sec) [ -7931.3024] [ 1648] [depth= 1] . ( 7 sec) [ -7928.6534] [ 1648] [depth= 1] . ( 7 sec) [ -7925.3654] [ 1654] [depth= 1] . ( 7 sec) [ -7923.6923] [ 1655] [depth= 1] . ( 7 sec) [ -7922.6127] [ 1654] [depth= 1] . ( 7 sec) [ -7922.2713] [ 1656] [depth= 1] . ( 8 sec) [ -7922.1006] [ 1661] [depth= 1] . ( 8 sec) [ -7919.4211] [ 1666] [depth= 1] . ( 8 sec) [ -7919.1009] [ 1665] [depth= 1] . ( 9 sec) [ -7915.6854] [ 1652] [depth= 2] . ( 9 sec) [ -7911.9498] [ 1651] [depth= 2] . ( 9 sec) [ -7886.3080] [Branch lengths ] . ( 9 sec) [ -7886.1487] [GTR parameters ] . ( 10 sec) [ -7885.6374] [Alpha ][ 0.965117] . ( 12 sec) [ -7885.6257] [ 1647] [depth= 1] . ( 12 sec) [ -7885.4670] [ 1648] [depth= 1] . ( 13 sec) [ -7885.4107] [ 1649] [depth= 1] . ( 13 sec) [ -7884.1795] [Branch lengths ] . ( 14 sec) [ -7884.1774] [GTR parameters ] . ( 14 sec) [ -7884.1769] [Alpha ][ 0.967370] . ( 14 sec) [ -7883.9651] [ 1648] [depth= 1] . ( 16 sec) [ -7883.9284] [ 1647] [depth= 1] . ( 18 sec) [ -7883.5790] [Branch lengths ] . ( 18 sec) [ -7883.5777] [GTR parameters ] . ( 18 sec) [ -7883.5772] [Alpha ][ 0.969702] . ( 40 sec) [ -7883.5720] [Branch lengths ] . ( 40 sec) [ -7883.5720] [Topology ] . ( 40 sec) [ -7883.5717] [Topology ] . ( 40 sec) [ -7883.5717] [GTR parameters ] . ( 40 sec) [ -7883.5716] [Alpha ][ 0.970671] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -7883.5419] [Topology ] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -7883.5090] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -7883.5073] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -7883.5071] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7883.507076. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17388.7055] [GTR parameters ] . ( 1 sec) [ -17062.4605] [Alpha ][ 0.500960] . ( 1 sec) [ -16729.6337] [ 3455] [depth= 11] . ( 1 sec) [ -16304.1501] [ 3395] [depth= 3] . ( 1 sec) [ -16001.2592] [ 3317] [depth= 7] . ( 1 sec) [ -15875.5493] [ 3278] [depth= 1] . ( 1 sec) [ -15573.1421] [ 3205] [depth= 9] . ( 1 sec) [ -15281.1315] [ 3195] [depth= 2] . ( 1 sec) [ -14854.9298] [ 3191] [depth= 3] . ( 1 sec) [ -14763.1946] [ 3175] [depth= 6] . ( 1 sec) [ -14634.6087] [ 3165] [depth= 7] . ( 1 sec) [ -14116.8814] [ 3150] [depth= 4] . ( 2 sec) [ -14013.7436] [ 3146] [depth= 7] . ( 2 sec) [ -13848.8387] [ 3090] [depth= 3] . ( 2 sec) [ -13807.1625] [ 3011] [depth= 5] . ( 2 sec) [ -13447.8897] [ 3013] [depth= 1] . ( 2 sec) [ -13101.7519] [ 2933] [depth= 17] . ( 2 sec) [ -13021.6820] [ 2930] [depth= 1] . ( 2 sec) [ -12926.8931] [ 2924] [depth= 8] . ( 2 sec) [ -12714.2341] [ 2832] [depth= 13] . ( 2 sec) [ -12642.8971] [ 2812] [depth= 1] . ( 2 sec) [ -12571.4152] [ 2798] [depth= 8] . ( 2 sec) [ -12294.6363] [ 2719] [depth= 5] . ( 2 sec) [ -12169.4740] [ 2681] [depth= 3] . ( 2 sec) [ -12054.2176] [ 2620] [depth= 1] . ( 2 sec) [ -12021.2463] [ 2598] [depth= 1] . ( 2 sec) [ -11930.7500] [ 2527] [depth= 6] . ( 2 sec) [ -11710.1909] [ 2487] [depth= 2] . ( 2 sec) [ -11590.3130] [ 2452] [depth= 4] . ( 2 sec) [ -11517.5791] [ 2452] [depth= 1] . ( 2 sec) [ -11448.3578] [ 2427] [depth= 5] . ( 2 sec) [ -11265.5609] [ 2398] [depth= 7] . ( 2 sec) [ -11262.4484] [ 2365] [depth= 3] . ( 2 sec) [ -11165.7467] [ 2334] [depth= 10] . ( 2 sec) [ -10814.7593] [ 2187] [depth= 9] . ( 3 sec) [ -10791.9565] [ 2179] [depth= 2] . ( 3 sec) [ -10791.5266] [ 2192] [depth= 3] . ( 3 sec) [ -10745.8098] [ 2169] [depth= 7] . ( 3 sec) [ -10743.7544] [ 2168] [depth= 2] . ( 3 sec) [ -10740.9037] [ 2167] [depth= 1] . ( 3 sec) [ -10361.8134] [ 2165] [depth= 1] . ( 3 sec) [ -9851.0111] [ 2098] [depth= 4] . ( 3 sec) [ -9705.1760] [ 2067] [depth= 2] . ( 3 sec) [ -9609.5180] [ 2036] [depth= 8] . ( 3 sec) [ -9205.5193] [ 1963] [depth= 9] . ( 3 sec) [ -9088.3080] [ 1894] [depth= 6] . ( 3 sec) [ -9074.9591] [ 1897] [depth= 1] . ( 3 sec) [ -9013.8738] [ 1880] [depth= 1] . ( 3 sec) [ -8989.8584] [ 1874] [depth= 2] . ( 3 sec) [ -8975.6402] [ 1887] [depth= 1] . ( 3 sec) [ -8962.5580] [ 1892] [depth= 2] . ( 3 sec) [ -8909.8332] [ 1881] [depth= 3] . ( 3 sec) [ -8908.9215] [ 1883] [depth= 1] . ( 3 sec) [ -8774.5274] [ 1863] [depth= 3] . ( 3 sec) [ -8734.2884] [ 1841] [depth= 7] . ( 3 sec) [ -8731.5335] [ 1851] [depth= 2] . ( 3 sec) [ -8669.0703] [ 1827] [depth= 2] . ( 4 sec) [ -8570.6600] [ 1790] [depth= 2] . ( 4 sec) [ -8527.5192] [ 1771] [depth= 2] . ( 4 sec) [ -8475.3835] [ 1754] [depth= 4] . ( 4 sec) [ -8438.8211] [ 1752] [depth= 1] . ( 4 sec) [ -8380.1966] [ 1739] [depth= 4] . ( 4 sec) [ -8307.0993] [ 1721] [depth= 1] . ( 4 sec) [ -8255.9107] [ 1704] [depth= 1] . ( 4 sec) [ -8218.3125] [ 1694] [depth= 6] . ( 4 sec) [ -8212.6265] [ 1693] [depth= 2] . ( 4 sec) [ -8210.4363] [ 1692] [depth= 1] . ( 4 sec) [ -8155.6758] [ 1673] [depth= 1] . ( 4 sec) [ -8153.7132] [ 1677] [depth= 1] . ( 4 sec) [ -8148.0867] [ 1678] [depth= 1] . ( 4 sec) [ -8118.7693] [ 1681] [depth= 1] . ( 4 sec) [ -8108.8283] [ 1675] [depth= 2] . ( 4 sec) [ -8107.4598] [ 1673] [depth= 1] . ( 4 sec) [ -8105.0258] [ 1676] [depth= 1] . ( 5 sec) [ -8098.4451] [ 1673] [depth= 1] . ( 5 sec) [ -7985.8565] [Branch lengths ] . ( 6 sec) [ -7983.3591] [GTR parameters ] . ( 6 sec) [ -7954.3091] [Alpha ][ 0.901003] . ( 6 sec) [ -7941.3460] [ 1667] [depth= 1] . ( 6 sec) [ -7940.9921] [ 1666] [depth= 1] . ( 6 sec) [ -7937.3389] [ 1664] [depth= 1] . ( 6 sec) [ -7937.2963] [ 1662] [depth= 1] . ( 6 sec) [ -7914.2401] [ 1649] [depth= 1] . ( 6 sec) [ -7910.8180] [ 1647] [depth= 1] . ( 6 sec) [ -7910.4530] [ 1645] [depth= 1] . ( 6 sec) [ -7907.5674] [ 1640] [depth= 1] . ( 6 sec) [ -7907.4468] [ 1642] [depth= 1] . ( 7 sec) [ -7907.4042] [ 1641] [depth= 1] . ( 7 sec) [ -7904.7420] [ 1646] [depth= 1] . ( 8 sec) [ -7904.6745] [ 1647] [depth= 1] . ( 8 sec) [ -7901.2282] [ 1649] [depth= 1] . ( 8 sec) [ -7901.2001] [ 1647] [depth= 2] . ( 8 sec) [ -7894.7507] [ 1644] [depth= 1] . ( 8 sec) [ -7893.7664] [ 1643] [depth= 1] . ( 8 sec) [ -7893.7400] [ 1642] [depth= 1] . ( 9 sec) [ -7893.4857] [ 1643] [depth= 1] . ( 9 sec) [ -7893.3814] [ 1644] [depth= 1] . ( 9 sec) [ -7884.9888] [Branch lengths ] . ( 10 sec) [ -7884.8054] [GTR parameters ] . ( 10 sec) [ -7884.4955] [Alpha ][ 0.959514] . ( 14 sec) [ -7883.8511] [Branch lengths ] . ( 15 sec) [ -7883.7734] [ 1646] [depth= 2] . ( 35 sec) [ -7883.6559] [Branch lengths ] . ( 35 sec) [ -7883.6556] [GTR parameters ] . ( 35 sec) [ -7883.6465] [Alpha ][ 0.970144] . ( 35 sec) [ -7883.6465] [Topology ] . ( 36 sec) [ -7883.6024] [Topology ] . ( 37 sec) [ -7883.5801] [Topology ] . ( 38 sec) [ -7883.5766] [Topology ] . ( 38 sec) [ -7883.5754] [Topology ] . ( 39 sec) [ -7883.5748] [Topology ] . ( 39 sec) [ -7883.5725] [GTR parameters ] . ( 39 sec) [ -7883.5725] [Alpha ][ 0.970144] . ( 40 sec) [ -7883.5725] [Topology ] . ( 40 sec) [ -7883.5722] [Topology ] . ( 40 sec) [ -7883.5721] [GTR parameters ] . ( 40 sec) [ -7883.5721] [Alpha ][ 0.970144] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -7883.5422] [Topology ] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -7883.5412] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7883.541199. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17491.4997] [GTR parameters ] . ( 0 sec) [ -17165.0296] [Alpha ][ 0.500960] . ( 0 sec) [ -16651.4593] [ 3449] [depth= 7] . ( 0 sec) [ -16240.4178] [ 3422] [depth= 11] . ( 0 sec) [ -16155.7744] [ 3402] [depth= 3] . ( 1 sec) [ -16136.8635] [ 3402] [depth= 1] . ( 1 sec) [ -16125.0717] [ 3388] [depth= 3] . ( 1 sec) [ -16116.5733] [ 3386] [depth= 1] . ( 1 sec) [ -15936.5304] [ 3366] [depth= 10] . ( 1 sec) [ -15724.5904] [ 3277] [depth= 8] . ( 1 sec) [ -15619.3426] [ 3260] [depth= 2] . ( 1 sec) [ -15588.7147] [ 3246] [depth= 1] . ( 1 sec) [ -15573.3658] [ 3242] [depth= 1] . ( 1 sec) [ -15357.8594] [ 3240] [depth= 9] . ( 1 sec) [ -15353.8331] [ 3239] [depth= 1] . ( 1 sec) [ -14839.5141] [ 3232] [depth= 9] . ( 1 sec) [ -14774.4004] [ 3229] [depth= 3] . ( 1 sec) [ -14686.7134] [ 3221] [depth= 2] . ( 1 sec) [ -14468.5503] [ 3132] [depth= 11] . ( 1 sec) [ -14329.9165] [ 3120] [depth= 15] . ( 1 sec) [ -14260.6997] [ 3145] [depth= 2] . ( 1 sec) [ -13900.4128] [ 3030] [depth= 3] . ( 1 sec) [ -13859.8951] [ 3011] [depth= 1] . ( 1 sec) [ -13812.5041] [ 2991] [depth= 7] . ( 1 sec) [ -13736.2830] [ 2972] [depth= 12] . ( 1 sec) [ -13312.4888] [ 2876] [depth= 2] . ( 1 sec) [ -12906.9777] [ 2831] [depth= 7] . ( 1 sec) [ -12557.0381] [ 2797] [depth= 6] . ( 2 sec) [ -12179.4326] [ 2694] [depth= 8] . ( 2 sec) [ -12030.4116] [ 2666] [depth= 18] . ( 2 sec) [ -11908.9736] [ 2642] [depth= 9] . ( 2 sec) [ -11388.6980] [ 2550] [depth= 7] . ( 2 sec) [ -11279.6142] [ 2512] [depth= 14] . ( 2 sec) [ -11256.6800] [ 2497] [depth= 1] . ( 2 sec) [ -11160.3535] [ 2467] [depth= 1] . ( 2 sec) [ -11150.0077] [ 2456] [depth= 1] . ( 2 sec) [ -11027.9333] [ 2460] [depth= 1] . ( 2 sec) [ -10907.1907] [ 2401] [depth= 11] . ( 2 sec) [ -10889.9006] [ 2400] [depth= 6] . ( 2 sec) [ -10883.6762] [ 2394] [depth= 15] . ( 2 sec) [ -10881.2783] [ 2391] [depth= 1] . ( 2 sec) [ -10777.7189] [ 2381] [depth= 3] . ( 2 sec) [ -10459.4582] [ 2302] [depth= 1] . ( 2 sec) [ -10306.6446] [ 2256] [depth= 5] . ( 2 sec) [ -10050.2470] [ 2201] [depth= 5] . ( 2 sec) [ -9947.8517] [ 2136] [depth= 11] . ( 2 sec) [ -9746.9481] [ 2086] [depth= 7] . ( 2 sec) [ -9687.8747] [ 2040] [depth= 5] . ( 2 sec) [ -9669.8361] [ 2042] [depth= 3] . ( 3 sec) [ -9610.4359] [ 2039] [depth= 1] . ( 3 sec) [ -9432.0851] [ 2024] [depth= 5] . ( 3 sec) [ -9361.2631] [ 1966] [depth= 1] . ( 3 sec) [ -9242.5876] [ 1908] [depth= 4] . ( 3 sec) [ -9242.5301] [ 1907] [depth= 1] . ( 3 sec) [ -8996.8573] [ 1850] [depth= 4] . ( 3 sec) [ -8958.7932] [ 1852] [depth= 1] . ( 3 sec) [ -8922.2799] [ 1869] [depth= 1] . ( 3 sec) [ -8889.1277] [ 1863] [depth= 3] . ( 3 sec) [ -8861.8190] [ 1862] [depth= 2] . ( 3 sec) [ -8847.6020] [ 1855] [depth= 1] . ( 3 sec) [ -8803.7214] [ 1841] [depth= 3] . ( 3 sec) [ -8796.7551] [ 1843] [depth= 1] . ( 3 sec) [ -8795.4890] [ 1841] [depth= 1] . ( 3 sec) [ -8717.1410] [ 1838] [depth= 11] . ( 3 sec) [ -8715.3836] [ 1838] [depth= 1] . ( 3 sec) [ -8714.4677] [ 1843] [depth= 1] . ( 3 sec) [ -8671.5525] [ 1829] [depth= 2] . ( 3 sec) [ -8669.7302] [ 1830] [depth= 1] . ( 4 sec) [ -8386.2642] [ 1824] [depth= 2] . ( 4 sec) [ -8385.2760] [ 1820] [depth= 2] . ( 4 sec) [ -8350.6220] [ 1779] [depth= 2] . ( 4 sec) [ -8350.0076] [ 1781] [depth= 1] . ( 4 sec) [ -8306.2167] [ 1769] [depth= 1] . ( 4 sec) [ -8236.0885] [ 1746] [depth= 12] . ( 4 sec) [ -8223.9769] [ 1738] [depth= 2] . ( 4 sec) [ -8218.1534] [ 1730] [depth= 1] . ( 4 sec) [ -8216.9063] [ 1728] [depth= 1] . ( 4 sec) [ -8163.5692] [Branch lengths ] . ( 5 sec) [ -8158.6401] [GTR parameters ] . ( 5 sec) [ -8133.5896] [Alpha ][ 0.853151] . ( 5 sec) [ -8130.9553] [ 1743] [depth= 3] . ( 5 sec) [ -8087.0524] [ 1731] [depth= 1] . ( 5 sec) [ -8066.7544] [ 1733] [depth= 1] . ( 5 sec) [ -8064.1376] [ 1733] [depth= 1] . ( 6 sec) [ -8063.7594] [ 1732] [depth= 1] . ( 6 sec) [ -8063.3044] [ 1732] [depth= 1] . ( 6 sec) [ -8062.9412] [ 1729] [depth= 1] . ( 6 sec) [ -8059.8219] [ 1717] [depth= 5] . ( 6 sec) [ -8059.5040] [ 1720] [depth= 1] . ( 6 sec) [ -8057.8924] [ 1725] [depth= 2] . ( 6 sec) [ -8051.8372] [ 1726] [depth= 1] . ( 6 sec) [ -8051.3565] [ 1727] [depth= 1] . ( 7 sec) [ -8032.1558] [ 1704] [depth= 5] . ( 7 sec) [ -7984.2885] [ 1678] [depth= 2] . ( 7 sec) [ -7981.0689] [ 1677] [depth= 1] . ( 7 sec) [ -7921.3382] [ 1657] [depth= 1] . ( 7 sec) [ -7921.2118] [ 1655] [depth= 1] . ( 7 sec) [ -7918.2770] [ 1652] [depth= 3] . ( 7 sec) [ -7911.6177] [ 1645] [depth= 2] . ( 7 sec) [ -7911.4652] [ 1644] [depth= 1] . ( 7 sec) [ -7909.1901] [ 1645] [depth= 1] . ( 7 sec) [ -7906.7653] [ 1646] [depth= 1] . ( 8 sec) [ -7904.9154] [ 1643] [depth= 1] . ( 8 sec) [ -7904.0481] [ 1646] [depth= 1] . ( 8 sec) [ -7903.9963] [ 1643] [depth= 1] . ( 8 sec) [ -7898.6081] [ 1645] [depth= 1] . ( 8 sec) [ -7887.7489] [Branch lengths ] . ( 9 sec) [ -7887.3949] [GTR parameters ] . ( 9 sec) [ -7886.4639] [Alpha ][ 0.951294] . ( 9 sec) [ -7886.2357] [ 1645] [depth= 1] . ( 9 sec) [ -7885.6943] [ 1645] [depth= 2] . ( 9 sec) [ -7885.6294] [ 1644] [depth= 1] . ( 10 sec) [ -7885.2336] [ 1645] [depth= 1] . ( 10 sec) [ -7885.1734] [ 1644] [depth= 1] . ( 10 sec) [ -7884.9938] [ 1646] [depth= 1] . ( 11 sec) [ -7884.7967] [ 1645] [depth= 1] . ( 12 sec) [ -7884.7862] [ 1643] [depth= 1] . ( 12 sec) [ -7883.7567] [Branch lengths ] . ( 13 sec) [ -7883.7491] [GTR parameters ] . ( 13 sec) [ -7883.7353] [Alpha ][ 0.964304] . ( 14 sec) [ -7883.6844] [ 1646] [depth= 2] . ( 16 sec) [ -7883.5275] [Branch lengths ] . ( 16 sec) [ -7883.5272] [GTR parameters ] . ( 16 sec) [ -7883.5258] [Alpha ][ 0.968378] . ( 38 sec) [ -7883.5088] [Branch lengths ] . ( 38 sec) [ -7883.5088] [Topology ] . ( 39 sec) [ -7883.5069] [Topology ] . ( 39 sec) [ -7883.5062] [Topology ] . ( 39 sec) [ -7883.5062] [GTR parameters ] . ( 40 sec) [ -7883.5060] [Alpha ][ 0.969635] . ( 40 sec) [ -7883.5060] [Topology ] . ( 40 sec) [ -7883.5055] [Topology ] . ( 40 sec) [ -7883.5055] [GTR parameters ] . ( 40 sec) [ -7883.5055] [Alpha ][ 0.969635] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -7883.5029] [Topology ] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -7883.5027] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7883.502725. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7947.170164 . ( 1 sec) [ -7944.4534] [GTR parameters ] . ( 1 sec) [ -7943.8676] [Alpha ][ 0.913664] . ( 1 sec) [ -7943.8676] [Topology ] . ( 1 sec) [ -7907.6242] [Topology ] . ( 2 sec) [ -7899.5631] [Topology ] . ( 3 sec) [ -7895.5710] [Topology ] . ( 4 sec) [ -7894.5882] [Topology ] . ( 4 sec) [ -7894.2081] [Topology ] . ( 5 sec) [ -7894.0524] [Topology ] . ( 6 sec) [ -7893.9831] [Topology ] . ( 6 sec) [ -7893.9520] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -7893.8894] [Topology ] . Before opt ts/t=1.000000 LK=-7893.889429 . ( 12 sec) [ -7893.8379] [GTR parameters ] . ( 12 sec) [ -7893.5614] [Alpha ][ 0.969457] . ( 12 sec) [ -7893.5614] [Topology ] . ( 13 sec) [ -7893.5239] [Topology ] . ( 14 sec) [ -7893.5111] [Topology ] . ( 14 sec) [ -7893.5055] [Topology ] . ( 15 sec) [ -7893.5029] [Topology ] . ( 16 sec) [ -7893.5016] [Topology ] . ( 17 sec) [ -7893.5010] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7893.501048 . ( 22 sec) [ -7893.5008] [GTR parameters ] . ( 22 sec) [ -7893.4986] [Alpha ][ 0.974705] . ( 22 sec) [ -7893.4986] [Topology ] . ( 23 sec) [ -7893.4980] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7893.498049 . ( 28 sec) [ -7893.4980] [GTR parameters ] . ( 28 sec) [ -7893.4980] [Alpha ][ 0.974705] . ( 28 sec) [ -7893.4980] [Topology ] . ( 29 sec) [ -7893.4978] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 40 sec) [ -7944.4534] [GTR parameters ] . ( 40 sec) [ -7943.8676] [Alpha ][ 0.913664] . ( 41 sec) [ -7943.5295] [ 1648] [depth= 1] . ( 41 sec) [ -7942.5763] [ 1648] [depth= 1] . ( 41 sec) [ -7941.5718] [ 1650] [depth= 1] . ( 41 sec) [ -7941.5588] [ 1653] [depth= 1] . ( 41 sec) [ -7940.4075] [ 1652] [depth= 1] . ( 41 sec) [ -7932.3731] [ 1649] [depth= 1] . ( 42 sec) [ -7930.6840] [ 1649] [depth= 1] . ( 42 sec) [ -7928.2296] [ 1649] [depth= 1] . ( 42 sec) [ -7927.6559] [ 1645] [depth= 2] . ( 42 sec) [ -7926.9617] [ 1650] [depth= 1] . ( 42 sec) [ -7926.1280] [ 1645] [depth= 1] . ( 42 sec) [ -7925.4974] [ 1647] [depth= 1] . ( 42 sec) [ -7921.7899] [ 1647] [depth= 2] . ( 42 sec) [ -7921.7274] [ 1649] [depth= 1] . ( 42 sec) [ -7920.2920] [ 1647] [depth= 1] . ( 42 sec) [ -7920.1528] [ 1646] [depth= 1] . ( 42 sec) [ -7920.1230] [ 1647] [depth= 1] . ( 42 sec) [ -7919.1391] [ 1646] [depth= 1] . ( 43 sec) [ -7918.6228] [ 1647] [depth= 1] . ( 43 sec) [ -7910.8072] [ 1646] [depth= 3] . ( 43 sec) [ -7908.4620] [ 1647] [depth= 2] . ( 43 sec) [ -7907.8269] [ 1649] [depth= 1] . ( 43 sec) [ -7906.7101] [ 1648] [depth= 1] . ( 43 sec) [ -7906.3968] [ 1647] [depth= 1] . ( 43 sec) [ -7906.2626] [ 1648] [depth= 1] . ( 44 sec) [ -7905.3765] [ 1647] [depth= 1] . ( 44 sec) [ -7904.6535] [ 1651] [depth= 1] . ( 44 sec) [ -7903.6269] [ 1647] [depth= 1] . ( 44 sec) [ -7903.2113] [ 1648] [depth= 1] . ( 44 sec) [ -7885.3570] [Branch lengths ] . ( 44 sec) [ -7885.3084] [GTR parameters ] . ( 44 sec) [ -7885.1269] [Alpha ][ 0.959010] . ( 46 sec) [ -7884.8654] [ 1646] [depth= 1] . ( 48 sec) [ -7883.8589] [Branch lengths ] . ( 49 sec) [ -7883.8576] [GTR parameters ] . ( 49 sec) [ -7883.8534] [Alpha ][ 0.966145] . ( 52 sec) [ -7883.7885] [Branch lengths ] . ( 58 sec) [ -7883.7131] [ 1643] [depth= 1] . ( 72 sec) [ -7883.6394] [ 1642] [depth= 1] . ( 73 sec) [ -7883.5837] [Branch lengths ] . ( 74 sec) [ -7883.5830] [GTR parameters ] . ( 74 sec) [ -7883.5819] [Alpha ][ 0.969631] . ( 74 sec) [ -7883.5819] [Topology ] . ( 75 sec) [ -7883.5747] [Topology ] . ( 75 sec) [ -7883.5729] [Topology ] . ( 76 sec) [ -7883.5723] [Topology ] . ( 76 sec) [ -7883.5722] [GTR parameters ] . ( 76 sec) [ -7883.5722] [Alpha ][ 0.970600] . ( 76 sec) [ -7883.5722] [Topology ] . ( 77 sec) [ -7883.5719] [Topology ] . ( 77 sec) [ -7883.5719] [GTR parameters ] . ( 77 sec) [ -7883.5719] [Alpha ][ 0.970600] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -7883.5420] [Topology ] . Checking for NNIs, optimizing five branches... . ( 88 sec) [ -7883.5063] [Topology ] . Checking for NNIs, optimizing five branches... . ( 94 sec) [ -7883.5060] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7893.497825 . Log likelihood obtained after SPR moves : -7883.506001 . Log likelihood of the current tree: -7883.506001. . Printing the most likely tree in file 'data17.phy_phyml_tree.txt'... . Best log likelihood : -7883.502725 . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo