.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2928_81x1651_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 . Compressing sequences... . 507 patterns found. (out of a total of 1651 sites) . 1189 sites without polymorphism (72.02%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -43023.0377] [GTR parameters ] . ( 2 sec) [ -42138.7917] [Alpha ][ 0.500960] . ( 2 sec) [ -41705.9501] [ 3875] [depth= 8] . ( 2 sec) [ -41027.3662] [ 3858] [depth= 5] . ( 2 sec) [ -40703.3556] [ 3850] [depth= 14] . ( 2 sec) [ -40523.3881] [ 3801] [depth= 1] . ( 2 sec) [ -40326.9484] [ 3770] [depth= 14] . ( 2 sec) [ -40220.4971] [ 3774] [depth= 1] . ( 2 sec) [ -40054.9611] [ 3768] [depth= 9] . ( 2 sec) [ -39700.5442] [ 3717] [depth= 1] . ( 3 sec) [ -39403.3354] [ 3712] [depth= 8] . ( 3 sec) [ -39260.8292] [ 3705] [depth= 6] . ( 3 sec) [ -39167.5390] [ 3695] [depth= 9] . ( 3 sec) [ -39166.3267] [ 3695] [depth= 1] . ( 3 sec) [ -38043.3304] [ 3694] [depth= 5] . ( 3 sec) [ -37458.2660] [ 3694] [depth= 2] . ( 3 sec) [ -36294.5536] [ 3673] [depth= 10] . ( 3 sec) [ -34968.7690] [ 3673] [depth= 2] . ( 3 sec) [ -34513.9213] [ 3667] [depth= 8] . ( 3 sec) [ -34139.9268] [ 3667] [depth= 4] . ( 3 sec) [ -33645.0179] [ 3621] [depth= 4] . ( 4 sec) [ -33368.5735] [ 3591] [depth= 14] . ( 4 sec) [ -33163.9593] [ 3596] [depth= 4] . ( 4 sec) [ -33051.8749] [ 3595] [depth= 8] . ( 4 sec) [ -32402.0661] [ 3577] [depth= 25] . ( 4 sec) [ -32140.1023] [ 3527] [depth= 2] . ( 4 sec) [ -31729.0076] [ 3520] [depth= 5] . ( 4 sec) [ -29948.6921] [ 3486] [depth= 23] . ( 4 sec) [ -29354.3444] [ 3444] [depth= 21] . ( 4 sec) [ -28420.0795] [ 3338] [depth= 13] . ( 4 sec) [ -28265.3663] [ 3314] [depth= 11] . ( 5 sec) [ -27603.4359] [ 3222] [depth= 4] . ( 5 sec) [ -27415.5113] [ 3167] [depth= 9] . ( 5 sec) [ -26055.8974] [ 3141] [depth= 23] . ( 5 sec) [ -24931.7558] [ 3052] [depth= 12] . ( 5 sec) [ -24928.5241] [ 3052] [depth= 1] . ( 5 sec) [ -24927.7467] [ 3052] [depth= 1] . ( 5 sec) [ -24896.7678] [ 3061] [depth= 1] . ( 5 sec) [ -24896.6946] [ 3061] [depth= 1] . ( 5 sec) [ -24730.8704] [ 3043] [depth= 7] . ( 5 sec) [ -23597.9332] [ 3033] [depth= 12] . ( 6 sec) [ -23355.2610] [ 3033] [depth= 2] . ( 6 sec) [ -23244.3932] [ 3030] [depth= 2] . ( 6 sec) [ -23143.0610] [ 3030] [depth= 4] . ( 6 sec) [ -21688.4615] [ 3011] [depth= 3] . ( 6 sec) [ -21048.5077] [ 2986] [depth= 10] . ( 6 sec) [ -19952.4898] [ 2942] [depth= 5] . ( 6 sec) [ -19878.3819] [ 2934] [depth= 4] . ( 6 sec) [ -19739.5956] [ 2933] [depth= 2] . ( 6 sec) [ -19441.1530] [ 2878] [depth= 11] . ( 6 sec) [ -19282.2927] [ 2847] [depth= 1] . ( 6 sec) [ -18822.8812] [ 2821] [depth= 18] . ( 7 sec) [ -18804.3014] [ 2821] [depth= 10] . ( 7 sec) [ -18737.8342] [ 2822] [depth= 1] . ( 7 sec) [ -18731.2378] [ 2820] [depth= 7] . ( 7 sec) [ -18392.9168] [ 2701] [depth= 17] . ( 7 sec) [ -18341.2744] [ 2703] [depth= 18] . ( 7 sec) [ -18341.1183] [ 2703] [depth= 7] . ( 7 sec) [ -18190.3804] [ 2681] [depth= 6] . ( 7 sec) [ -18184.6778] [ 2681] [depth= 1] . ( 7 sec) [ -18050.3100] [ 2681] [depth= 8] . ( 7 sec) [ -17996.2761] [ 2674] [depth= 11] . ( 8 sec) [ -17390.7699] [ 2542] [depth= 19] . ( 8 sec) [ -17360.6843] [ 2516] [depth= 3] . ( 8 sec) [ -17161.3648] [ 2502] [depth= 18] . ( 8 sec) [ -17143.3574] [ 2502] [depth= 4] . ( 8 sec) [ -16489.7367] [ 2407] [depth= 15] . ( 8 sec) [ -16469.7376] [ 2407] [depth= 12] . ( 8 sec) [ -16396.1615] [ 2427] [depth= 1] . ( 8 sec) [ -16279.9292] [ 2411] [depth= 14] . ( 8 sec) [ -16101.1498] [ 2392] [depth= 7] . ( 8 sec) [ -15713.3726] [ 2305] [depth= 11] . ( 9 sec) [ -15628.4996] [ 2305] [depth= 8] . ( 9 sec) [ -15552.6689] [ 2304] [depth= 1] . ( 9 sec) [ -15219.4486] [ 2209] [depth= 23] . ( 9 sec) [ -15075.2781] [ 2183] [depth= 15] . ( 9 sec) [ -15036.9343] [ 2183] [depth= 5] . ( 9 sec) [ -15036.9101] [ 2183] [depth= 3] . ( 9 sec) [ -14840.2965] [ 2165] [depth= 11] . ( 9 sec) [ -14779.7338] [ 2155] [depth= 3] . ( 9 sec) [ -14518.8052] [ 2060] [depth= 12] . ( 9 sec) [ -14386.9496] [ 2045] [depth= 2] . ( 10 sec) [ -14302.8181] [ 2044] [depth= 1] . ( 10 sec) [ -14302.2028] [ 2056] [depth= 1] . ( 10 sec) [ -13997.5733] [ 1964] [depth= 13] . ( 10 sec) [ -13644.3380] [ 1886] [depth= 23] . ( 10 sec) [ -13620.3794] [ 1887] [depth= 10] . ( 10 sec) [ -13597.5429] [ 1886] [depth= 11] . ( 10 sec) [ -13595.1619] [ 1886] [depth= 3] . ( 10 sec) [ -13486.6495] [ 1858] [depth= 2] . ( 10 sec) [ -13485.9342] [ 1859] [depth= 3] . ( 10 sec) [ -13484.9464] [ 1859] [depth= 1] . ( 11 sec) [ -13363.2448] [ 1839] [depth= 8] . ( 11 sec) [ -13346.8114] [ 1837] [depth= 5] . ( 11 sec) [ -13262.9439] [ 1837] [depth= 2] . ( 11 sec) [ -13262.0008] [ 1837] [depth= 2] . ( 11 sec) [ -13137.4969] [ 1795] [depth= 4] . ( 11 sec) [ -13130.0861] [ 1768] [depth= 1] . ( 11 sec) [ -13128.2984] [ 1768] [depth= 4] . ( 11 sec) [ -13127.4244] [ 1767] [depth= 1] . ( 12 sec) [ -13127.1293] [ 1767] [depth= 1] . ( 12 sec) [ -12762.4680] [ 1746] [depth= 7] . ( 12 sec) [ -12762.3481] [ 1746] [depth= 1] . ( 12 sec) [ -12759.9890] [ 1745] [depth= 1] . ( 12 sec) [ -12757.9622] [ 1745] [depth= 2] . ( 12 sec) [ -12754.1019] [ 1745] [depth= 5] . ( 12 sec) [ -12735.1270] [ 1737] [depth= 1] . ( 12 sec) [ -12725.4075] [ 1729] [depth= 1] . ( 12 sec) [ -12577.3796] [ 1701] [depth= 11] . ( 12 sec) [ -12491.6572] [ 1687] [depth= 1] . ( 13 sec) [ -12307.2809] [ 1687] [depth= 1] . ( 13 sec) [ -12267.6782] [ 1699] [depth= 1] . ( 13 sec) [ -11981.6814] [ 1680] [depth= 10] . ( 13 sec) [ -11898.4276] [ 1661] [depth= 4] . ( 13 sec) [ -11882.5883] [ 1659] [depth= 3] . ( 13 sec) [ -11569.8258] [ 1631] [depth= 5] . ( 13 sec) [ -11389.3810] [ 1631] [depth= 1] . ( 13 sec) [ -11330.8521] [ 1617] [depth= 6] . ( 13 sec) [ -11321.4078] [ 1617] [depth= 6] . ( 13 sec) [ -11081.3293] [ 1602] [depth= 2] . ( 13 sec) [ -11037.7704] [ 1602] [depth= 1] . ( 13 sec) [ -10994.6861] [ 1604] [depth= 2] . ( 14 sec) [ -10865.0410] [ 1587] [depth= 14] . ( 14 sec) [ -10864.8942] [ 1587] [depth= 4] . ( 14 sec) [ -10849.3373] [ 1560] [depth= 5] . ( 14 sec) [ -10801.3501] [ 1560] [depth= 1] . ( 14 sec) [ -10792.0530] [ 1562] [depth= 10] . ( 14 sec) [ -10744.2127] [ 1550] [depth= 4] . ( 14 sec) [ -10744.1602] [ 1550] [depth= 2] . ( 14 sec) [ -10624.0457] [ 1522] [depth= 9] . ( 15 sec) [ -10624.0232] [ 1522] [depth= 3] . ( 15 sec) [ -10538.2039] [ 1512] [depth= 6] . ( 15 sec) [ -10538.1501] [ 1512] [depth= 10] . ( 15 sec) [ -10365.1383] [ 1496] [depth= 11] . ( 15 sec) [ -10364.9971] [ 1496] [depth= 17] . ( 15 sec) [ -10335.0311] [ 1496] [depth= 18] . ( 15 sec) [ -10329.4278] [ 1496] [depth= 1] . ( 15 sec) [ -10329.4004] [ 1496] [depth= 19] . ( 16 sec) [ -10302.2147] [ 1496] [depth= 15] . ( 16 sec) [ -10271.4890] [ 1457] [depth= 5] . ( 16 sec) [ -10226.1666] [ 1437] [depth= 6] . ( 16 sec) [ -10226.1378] [ 1437] [depth= 1] . ( 16 sec) [ -10197.7675] [ 1437] [depth= 1] . ( 16 sec) [ -10196.7272] [ 1437] [depth= 4] . ( 16 sec) [ -9910.8629] [ 1355] [depth= 10] . ( 16 sec) [ -9910.8202] [ 1355] [depth= 1] . ( 16 sec) [ -9908.3473] [ 1355] [depth= 2] . ( 16 sec) [ -9908.3192] [ 1355] [depth= 1] . ( 16 sec) [ -9856.6916] [ 1324] [depth= 3] . ( 17 sec) [ -9613.5674] [ 1318] [depth= 5] . ( 17 sec) [ -9165.9506] [ 1280] [depth= 4] . ( 17 sec) [ -9070.1448] [ 1281] [depth= 3] . ( 17 sec) [ -9055.6914] [ 1279] [depth= 11] . ( 17 sec) [ -9055.0622] [ 1279] [depth= 9] . ( 17 sec) [ -9000.2535] [ 1260] [depth= 6] . ( 17 sec) [ -8945.5222] [ 1255] [depth= 7] . ( 17 sec) [ -8945.3989] [ 1255] [depth= 1] . ( 17 sec) [ -8745.1594] [ 1244] [depth= 3] . ( 17 sec) [ -8720.5608] [ 1243] [depth= 1] . ( 17 sec) [ -8477.6510] [ 1207] [depth= 1] . ( 18 sec) [ -8409.0235] [ 1195] [depth= 2] . ( 18 sec) [ -8400.1822] [ 1170] [depth= 7] . ( 18 sec) [ -8382.8600] [ 1160] [depth= 1] . ( 18 sec) [ -8358.8015] [ 1161] [depth= 3] . ( 18 sec) [ -8358.4745] [ 1161] [depth= 3] . ( 18 sec) [ -8358.4625] [ 1161] [depth= 9] . ( 18 sec) [ -8355.9769] [ 1158] [depth= 2] . ( 18 sec) [ -8234.5898] [ 1109] [depth= 2] . ( 18 sec) [ -7972.6684] [ 1111] [depth= 2] . ( 19 sec) [ -7964.9234] [ 1075] [depth= 3] . ( 19 sec) [ -7964.7031] [ 1075] [depth= 1] . ( 19 sec) [ -7943.0893] [ 1075] [depth= 7] . ( 19 sec) [ -7942.0050] [ 1075] [depth= 1] . ( 19 sec) [ -7872.6573] [ 1051] [depth= 1] . ( 19 sec) [ -7872.6374] [ 1051] [depth= 3] . ( 19 sec) [ -7872.6209] [ 1051] [depth= 11] . ( 19 sec) [ -7844.4000] [ 1035] [depth= 3] . ( 20 sec) [ -7843.1840] [ 1035] [depth= 2] . ( 20 sec) [ -7839.9831] [ 1035] [depth= 1] . ( 20 sec) [ -7838.1383] [ 1035] [depth= 5] . ( 20 sec) [ -7817.6469] [ 1030] [depth= 1] . ( 20 sec) [ -7770.5974] [ 1030] [depth= 2] . ( 20 sec) [ -7768.8550] [ 1021] [depth= 5] . ( 20 sec) [ -7761.5656] [ 1021] [depth= 5] . ( 20 sec) [ -7760.2004] [ 1021] [depth= 6] . ( 20 sec) [ -7714.0101] [ 1014] [depth= 3] . ( 21 sec) [ -7713.8494] [ 1014] [depth= 4] . ( 21 sec) [ -7713.8143] [ 1014] [depth= 4] . ( 21 sec) [ -7713.5511] [ 1015] [depth= 6] . ( 21 sec) [ -7712.6260] [ 1015] [depth= 7] . ( 21 sec) [ -7712.5786] [ 1015] [depth= 6] . ( 21 sec) [ -7704.6620] [ 1014] [depth= 2] . ( 21 sec) [ -7704.6285] [ 1014] [depth= 1] . ( 22 sec) [ -7704.6080] [ 1014] [depth= 2] . ( 22 sec) [ -7611.2125] [ 991] [depth= 12] . ( 22 sec) [ -7606.9307] [ 992] [depth= 2] . ( 22 sec) [ -7537.0450] [ 976] [depth= 3] . ( 22 sec) [ -7536.9943] [ 976] [depth= 2] . ( 22 sec) [ -7536.9326] [ 976] [depth= 1] . ( 23 sec) [ -7536.8758] [ 976] [depth= 8] . ( 23 sec) [ -7397.8309] [Branch lengths ] . ( 25 sec) [ -7126.0996] [GTR parameters ] . ( 26 sec) [ -7062.9511] [Alpha ][ 0.250961] . ( 26 sec) [ -7062.9293] [ 976] [depth= 5] . ( 26 sec) [ -7062.9151] [ 976] [depth= 1] . ( 26 sec) [ -7062.7739] [ 976] [depth= 5] . ( 27 sec) [ -7060.2573] [ 968] [depth= 2] . ( 27 sec) [ -7060.2426] [ 968] [depth= 1] . ( 28 sec) [ -7060.2219] [ 969] [depth= 5] . ( 28 sec) [ -7057.8804] [ 971] [depth= 6] . ( 29 sec) [ -7045.0542] [ 970] [depth= 7] . ( 29 sec) [ -7045.0414] [ 970] [depth= 3] . ( 30 sec) [ -7036.0220] [ 967] [depth= 13] . ( 30 sec) [ -7035.9735] [ 967] [depth= 5] . ( 30 sec) [ -7035.8840] [ 967] [depth= 3] . ( 31 sec) [ -7035.8105] [ 967] [depth= 1] . ( 31 sec) [ -7035.7436] [ 967] [depth= 1] . ( 31 sec) [ -7030.7481] [ 965] [depth= 3] . ( 32 sec) [ -6919.4096] [ 947] [depth= 2] . ( 33 sec) [ -6919.2847] [ 947] [depth= 4] . ( 34 sec) [ -6850.7649] [ 933] [depth= 7] . ( 34 sec) [ -6850.1490] [ 930] [depth= 1] . ( 35 sec) [ -6849.5359] [ 930] [depth= 3] . ( 35 sec) [ -6849.5239] [ 930] [depth= 5] . ( 35 sec) [ -6849.5063] [ 930] [depth= 4] . ( 36 sec) [ -6837.9489] [ 928] [depth= 7] . ( 36 sec) [ -6837.2235] [ 929] [depth= 2] . ( 37 sec) [ -6837.1578] [ 929] [depth= 6] . ( 37 sec) [ -6826.1200] [ 918] [depth= 3] . ( 37 sec) [ -6824.1434] [ 918] [depth= 1] . ( 38 sec) [ -6823.8802] [ 918] [depth= 4] . ( 38 sec) [ -6823.6959] [ 918] [depth= 1] . ( 39 sec) [ -6823.6430] [ 918] [depth= 4] . ( 41 sec) [ -6823.6017] [ 918] [depth= 1] . ( 41 sec) [ -6821.9513] [ 917] [depth= 5] . ( 42 sec) [ -6821.9280] [ 917] [depth= 2] . ( 44 sec) [ -6821.9159] [ 917] [depth= 7] . ( 45 sec) [ -6793.3980] [ 914] [depth= 2] . ( 45 sec) [ -6780.0587] [ 914] [depth= 1] . ( 45 sec) [ -6777.3361] [ 913] [depth= 2] . ( 46 sec) [ -6777.3230] [ 913] [depth= 2] . ( 46 sec) [ -6776.5943] [ 913] [depth= 6] . ( 46 sec) [ -6770.9772] [ 913] [depth= 2] . ( 46 sec) [ -6770.3307] [ 913] [depth= 7] . ( 46 sec) [ -6756.2271] [ 907] [depth= 1] . ( 46 sec) [ -6756.2071] [ 907] [depth= 6] . ( 47 sec) [ -6756.1757] [ 907] [depth= 3] . ( 49 sec) [ -6755.6438] [ 907] [depth= 1] . ( 49 sec) [ -6755.6241] [ 907] [depth= 3] . ( 53 sec) [ -6717.5092] [ 894] [depth= 2] . ( 55 sec) [ -6717.4913] [ 894] [depth= 2] . ( 56 sec) [ -6717.4476] [ 894] [depth= 3] . ( 57 sec) [ -6717.3602] [ 894] [depth= 1] . ( 58 sec) [ -6717.1949] [ 891] [depth= 1] . ( 60 sec) [ -6717.1756] [ 891] [depth= 2] . ( 60 sec) [ -6710.1037] [ 890] [depth= 9] . ( 61 sec) [ -6710.0811] [ 890] [depth= 4] . ( 62 sec) [ -6710.0620] [ 890] [depth= 2] . ( 64 sec) [ -6699.2997] [Branch lengths ] . ( 65 sec) [ -6698.2439] [GTR parameters ] . ( 65 sec) [ -6696.0905] [Alpha ][ 0.210785] . ( 78 sec) [ -6690.5088] [ 889] [depth= 7] . ( 78 sec) [ -6690.4921] [ 889] [depth= 3] . ( 85 sec) [ -6690.4050] [ 889] [depth= 2] . ( 87 sec) [ -6690.3910] [ 889] [depth= 2] . ( 98 sec) [ -6690.3693] [ 889] [depth= 1] . ( 110 sec) [ -6689.8303] [Branch lengths ] . ( 111 sec) [ -6689.7754] [GTR parameters ] . ( 111 sec) [ -6689.7500] [Alpha ][ 0.206666] . ( 120 sec) [ -6689.7348] [ 889] [depth= 8] . ( 121 sec) [ -6689.7215] [ 889] [depth= 6] . ( 158 sec) [ -6689.6701] [Branch lengths ] . ( 159 sec) [ -6689.6638] [GTR parameters ] . ( 159 sec) [ -6689.6632] [Alpha ][ 0.205991] . ( 228 sec) [ -6689.6601] [Branch lengths ] . ( 228 sec) [ -6689.6601] [Topology ] . ( 230 sec) [ -6689.6599] [Topology ] . ( 230 sec) [ -6689.6599] [GTR parameters ] . ( 230 sec) [ -6689.6599] [Alpha ][ 0.205991] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.659907. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -37754.5886] [GTR parameters ] . ( 1 sec) [ -37029.2904] [Alpha ][ 0.500960] . ( 2 sec) [ -36218.5618] [ 3650] [depth= 3] . ( 2 sec) [ -35446.8250] [ 3629] [depth= 9] . ( 2 sec) [ -35043.0511] [ 3603] [depth= 12] . ( 2 sec) [ -34844.6442] [ 3603] [depth= 1] . ( 2 sec) [ -34188.0340] [ 3575] [depth= 4] . ( 2 sec) [ -34147.5723] [ 3575] [depth= 1] . ( 2 sec) [ -33746.8866] [ 3469] [depth= 16] . ( 2 sec) [ -33562.2668] [ 3462] [depth= 2] . ( 2 sec) [ -33360.7565] [ 3461] [depth= 4] . ( 3 sec) [ -32839.5104] [ 3448] [depth= 7] . ( 3 sec) [ -32651.1081] [ 3448] [depth= 6] . ( 3 sec) [ -32380.8771] [ 3439] [depth= 15] . ( 3 sec) [ -32280.5448] [ 3439] [depth= 1] . ( 3 sec) [ -32052.1204] [ 3426] [depth= 19] . ( 3 sec) [ -32020.9364] [ 3426] [depth= 1] . ( 3 sec) [ -31971.3915] [ 3423] [depth= 1] . ( 3 sec) [ -31922.9810] [ 3422] [depth= 1] . ( 3 sec) [ -31560.9029] [ 3380] [depth= 8] . ( 3 sec) [ -31496.1432] [ 3398] [depth= 1] . ( 3 sec) [ -30499.4286] [ 3356] [depth= 11] . ( 4 sec) [ -30136.2312] [ 3252] [depth= 9] . ( 4 sec) [ -29883.9838] [ 3193] [depth= 8] . ( 4 sec) [ -28971.5447] [ 3165] [depth= 18] . ( 4 sec) [ -28849.8014] [ 3164] [depth= 12] . ( 4 sec) [ -28668.7874] [ 3132] [depth= 12] . ( 4 sec) [ -28525.7842] [ 3115] [depth= 4] . ( 4 sec) [ -28414.4252] [ 3114] [depth= 6] . ( 4 sec) [ -27991.2531] [ 3011] [depth= 12] . ( 5 sec) [ -27990.7787] [ 3011] [depth= 17] . ( 5 sec) [ -27699.4010] [ 2999] [depth= 3] . ( 5 sec) [ -27592.8903] [ 3000] [depth= 1] . ( 5 sec) [ -27401.9030] [ 2969] [depth= 16] . ( 5 sec) [ -27114.1523] [ 2960] [depth= 13] . ( 5 sec) [ -26299.7178] [ 2960] [depth= 1] . ( 5 sec) [ -25973.4613] [ 2955] [depth= 8] . ( 5 sec) [ -25859.5275] [ 2955] [depth= 1] . ( 5 sec) [ -24906.6797] [ 2912] [depth= 7] . ( 5 sec) [ -24061.1405] [ 2843] [depth= 5] . ( 6 sec) [ -23503.6041] [ 2752] [depth= 9] . ( 6 sec) [ -23502.7361] [ 2752] [depth= 16] . ( 6 sec) [ -21806.2572] [ 2661] [depth= 10] . ( 6 sec) [ -21727.3210] [ 2653] [depth= 2] . ( 6 sec) [ -21412.7168] [ 2624] [depth= 8] . ( 6 sec) [ -21412.4477] [ 2624] [depth= 1] . ( 6 sec) [ -21410.4955] [ 2624] [depth= 1] . ( 6 sec) [ -21410.4647] [ 2624] [depth= 25] . ( 6 sec) [ -21409.8835] [ 2624] [depth= 23] . ( 6 sec) [ -21268.2297] [ 2610] [depth= 6] . ( 7 sec) [ -21264.1437] [ 2610] [depth= 26] . ( 7 sec) [ -21243.7106] [ 2607] [depth= 26] . ( 7 sec) [ -21243.6953] [ 2607] [depth= 1] . ( 7 sec) [ -21229.6503] [ 2607] [depth= 21] . ( 7 sec) [ -20811.2600] [ 2572] [depth= 14] . ( 7 sec) [ -20182.5264] [ 2577] [depth= 1] . ( 7 sec) [ -20038.0122] [ 2558] [depth= 2] . ( 7 sec) [ -19879.1123] [ 2521] [depth= 7] . ( 7 sec) [ -19719.9468] [ 2471] [depth= 12] . ( 8 sec) [ -19681.6122] [ 2480] [depth= 1] . ( 8 sec) [ -19659.6029] [ 2471] [depth= 1] . ( 8 sec) [ -19529.4952] [ 2456] [depth= 7] . ( 8 sec) [ -19494.3770] [ 2453] [depth= 12] . ( 8 sec) [ -19494.3532] [ 2453] [depth= 3] . ( 8 sec) [ -19489.4918] [ 2453] [depth= 6] . ( 8 sec) [ -18909.8085] [ 2451] [depth= 6] . ( 8 sec) [ -18877.4270] [ 2451] [depth= 1] . ( 8 sec) [ -18266.6496] [ 2440] [depth= 2] . ( 9 sec) [ -18212.6404] [ 2440] [depth= 2] . ( 9 sec) [ -17976.3164] [ 2406] [depth= 6] . ( 9 sec) [ -17954.3990] [ 2406] [depth= 1] . ( 9 sec) [ -17923.1991] [ 2397] [depth= 10] . ( 9 sec) [ -17918.2911] [ 2404] [depth= 1] . ( 9 sec) [ -17900.3893] [ 2403] [depth= 1] . ( 9 sec) [ -17468.5741] [ 2325] [depth= 19] . ( 9 sec) [ -17458.4793] [ 2325] [depth= 2] . ( 9 sec) [ -17128.8632] [ 2301] [depth= 11] . ( 10 sec) [ -16866.3956] [ 2257] [depth= 5] . ( 10 sec) [ -16135.4448] [ 2134] [depth= 16] . ( 10 sec) [ -16006.0568] [ 2112] [depth= 10] . ( 10 sec) [ -16005.5512] [ 2112] [depth= 1] . ( 10 sec) [ -15985.0788] [ 2112] [depth= 8] . ( 10 sec) [ -15972.1866] [ 2111] [depth= 2] . ( 10 sec) [ -15972.0841] [ 2111] [depth= 1] . ( 10 sec) [ -15843.7350] [ 2085] [depth= 10] . ( 10 sec) [ -15836.6696] [ 2085] [depth= 16] . ( 10 sec) [ -15675.2936] [ 2068] [depth= 11] . ( 11 sec) [ -15624.8251] [ 2069] [depth= 14] . ( 11 sec) [ -15624.7639] [ 2069] [depth= 25] . ( 11 sec) [ -15599.3948] [ 2078] [depth= 1] . ( 11 sec) [ -15582.2756] [ 2067] [depth= 10] . ( 11 sec) [ -15581.8081] [ 2067] [depth= 1] . ( 11 sec) [ -15575.9215] [ 2067] [depth= 1] . ( 11 sec) [ -15569.3236] [ 2067] [depth= 9] . ( 11 sec) [ -15429.0977] [ 2057] [depth= 13] . ( 11 sec) [ -15425.7733] [ 2057] [depth= 2] . ( 12 sec) [ -15390.6766] [ 2059] [depth= 2] . ( 12 sec) [ -14866.6215] [ 2039] [depth= 2] . ( 12 sec) [ -14835.1335] [ 2029] [depth= 2] . ( 12 sec) [ -14833.1098] [ 2029] [depth= 1] . ( 12 sec) [ -14556.5485] [ 2006] [depth= 4] . ( 12 sec) [ -14418.2134] [ 2004] [depth= 14] . ( 12 sec) [ -13895.1485] [ 1903] [depth= 14] . ( 12 sec) [ -13880.4040] [ 1903] [depth= 4] . ( 12 sec) [ -13794.8288] [ 1888] [depth= 20] . ( 12 sec) [ -13651.1572] [ 1888] [depth= 1] . ( 13 sec) [ -13650.7291] [ 1888] [depth= 2] . ( 13 sec) [ -13401.1821] [ 1844] [depth= 2] . ( 13 sec) [ -13401.1683] [ 1844] [depth= 1] . ( 13 sec) [ -13353.1471] [ 1836] [depth= 16] . ( 13 sec) [ -13350.4666] [ 1836] [depth= 2] . ( 13 sec) [ -13350.1430] [ 1836] [depth= 9] . ( 13 sec) [ -13348.6309] [ 1836] [depth= 1] . ( 13 sec) [ -13348.3708] [ 1836] [depth= 3] . ( 13 sec) [ -13269.4241] [ 1836] [depth= 1] . ( 14 sec) [ -13268.9032] [ 1829] [depth= 19] . ( 14 sec) [ -13002.1212] [ 1829] [depth= 1] . ( 14 sec) [ -12997.6821] [ 1829] [depth= 1] . ( 14 sec) [ -12651.4346] [ 1721] [depth= 15] . ( 14 sec) [ -12645.6354] [ 1721] [depth= 1] . ( 14 sec) [ -12417.0454] [ 1712] [depth= 5] . ( 14 sec) [ -12291.9343] [ 1739] [depth= 1] . ( 14 sec) [ -11563.0115] [ 1682] [depth= 2] . ( 14 sec) [ -11253.8774] [ 1627] [depth= 3] . ( 14 sec) [ -10905.8992] [ 1575] [depth= 7] . ( 15 sec) [ -10666.3914] [ 1519] [depth= 8] . ( 15 sec) [ -10625.9889] [ 1509] [depth= 2] . ( 15 sec) [ -10503.1407] [ 1487] [depth= 6] . ( 15 sec) [ -10495.1108] [ 1487] [depth= 3] . ( 15 sec) [ -10464.9130] [ 1483] [depth= 2] . ( 15 sec) [ -10245.6725] [ 1475] [depth= 7] . ( 15 sec) [ -10093.8570] [ 1448] [depth= 1] . ( 15 sec) [ -10039.9893] [ 1444] [depth= 5] . ( 15 sec) [ -9878.5728] [ 1431] [depth= 5] . ( 16 sec) [ -9769.9066] [ 1486] [depth= 15] . ( 16 sec) [ -9687.3874] [ 1484] [depth= 4] . ( 16 sec) [ -9685.5553] [ 1475] [depth= 3] . ( 16 sec) [ -9549.9010] [ 1454] [depth= 1] . ( 16 sec) [ -9547.4730] [ 1455] [depth= 3] . ( 16 sec) [ -9541.8644] [ 1456] [depth= 1] . ( 16 sec) [ -9526.1071] [ 1454] [depth= 2] . ( 16 sec) [ -9508.4392] [ 1454] [depth= 2] . ( 16 sec) [ -9470.9566] [ 1453] [depth= 4] . ( 17 sec) [ -9470.9364] [ 1453] [depth= 1] . ( 17 sec) [ -9459.5707] [ 1452] [depth= 7] . ( 17 sec) [ -9451.4556] [ 1451] [depth= 7] . ( 17 sec) [ -9426.4082] [ 1451] [depth= 2] . ( 17 sec) [ -9096.1706] [ 1360] [depth= 7] . ( 17 sec) [ -9096.1399] [ 1360] [depth= 2] . ( 17 sec) [ -9093.1086] [ 1360] [depth= 1] . ( 17 sec) [ -9079.6036] [ 1359] [depth= 1] . ( 17 sec) [ -9025.6313] [ 1325] [depth= 10] . ( 17 sec) [ -9023.7801] [ 1325] [depth= 2] . ( 18 sec) [ -8996.8180] [ 1303] [depth= 17] . ( 18 sec) [ -8968.7690] [ 1303] [depth= 3] . ( 18 sec) [ -8869.2258] [ 1283] [depth= 1] . ( 18 sec) [ -8864.8242] [ 1283] [depth= 3] . ( 19 sec) [ -8855.1082] [ 1286] [depth= 2] . ( 19 sec) [ -8854.7418] [ 1286] [depth= 1] . ( 19 sec) [ -8853.2463] [ 1285] [depth= 1] . ( 19 sec) [ -8847.9609] [ 1285] [depth= 2] . ( 19 sec) [ -8847.4602] [ 1285] [depth= 4] . ( 19 sec) [ -8825.8186] [ 1283] [depth= 8] . ( 19 sec) [ -8800.6202] [ 1284] [depth= 2] . ( 19 sec) [ -8708.6872] [ 1280] [depth= 2] . ( 20 sec) [ -8704.5843] [ 1266] [depth= 1] . ( 20 sec) [ -8556.1130] [ 1236] [depth= 2] . ( 20 sec) [ -8483.1118] [ 1229] [depth= 5] . ( 20 sec) [ -8411.4729] [ 1204] [depth= 6] . ( 20 sec) [ -8292.1219] [ 1198] [depth= 19] . ( 21 sec) [ -8277.5809] [ 1187] [depth= 3] . ( 21 sec) [ -8259.1061] [ 1177] [depth= 1] . ( 21 sec) [ -8257.0469] [ 1177] [depth= 2] . ( 21 sec) [ -8256.3665] [ 1177] [depth= 2] . ( 21 sec) [ -8255.5023] [ 1177] [depth= 8] . ( 21 sec) [ -8255.3662] [ 1177] [depth= 3] . ( 22 sec) [ -8222.8351] [ 1177] [depth= 4] . ( 22 sec) [ -8222.8225] [ 1177] [depth= 2] . ( 22 sec) [ -8216.0675] [ 1177] [depth= 2] . ( 22 sec) [ -8212.9132] [ 1177] [depth= 2] . ( 22 sec) [ -8154.6548] [ 1153] [depth= 9] . ( 22 sec) [ -8146.5480] [ 1155] [depth= 1] . ( 22 sec) [ -7975.6960] [ 1088] [depth= 6] . ( 22 sec) [ -7966.1782] [ 1088] [depth= 8] . ( 23 sec) [ -7963.5788] [ 1088] [depth= 6] . ( 23 sec) [ -7963.5155] [ 1088] [depth= 2] . ( 23 sec) [ -7960.1207] [ 1089] [depth= 3] . ( 23 sec) [ -7956.8875] [ 1089] [depth= 2] . ( 23 sec) [ -7955.1161] [ 1089] [depth= 4] . ( 23 sec) [ -7954.2870] [ 1089] [depth= 4] . ( 23 sec) [ -7954.2634] [ 1089] [depth= 3] . ( 23 sec) [ -7954.0370] [ 1089] [depth= 1] . ( 24 sec) [ -7953.9033] [ 1089] [depth= 9] . ( 24 sec) [ -7953.6246] [ 1089] [depth= 7] . ( 24 sec) [ -7953.5240] [ 1089] [depth= 3] . ( 24 sec) [ -7953.0353] [ 1089] [depth= 4] . ( 24 sec) [ -7952.4355] [ 1089] [depth= 1] . ( 25 sec) [ -7877.6198] [Branch lengths ] . ( 27 sec) [ -7299.5737] [GTR parameters ] . ( 27 sec) [ -7210.2958] [Alpha ][ 0.250961] . ( 28 sec) [ -7210.2668] [ 1089] [depth= 2] . ( 28 sec) [ -7210.2077] [ 1089] [depth= 1] . ( 29 sec) [ -7210.1095] [ 1089] [depth= 7] . ( 29 sec) [ -7210.0969] [ 1089] [depth= 2] . ( 29 sec) [ -7207.8627] [ 1086] [depth= 1] . ( 29 sec) [ -7206.8946] [ 1085] [depth= 4] . ( 30 sec) [ -7158.7369] [ 1076] [depth= 1] . ( 31 sec) [ -7158.6663] [ 1077] [depth= 6] . ( 31 sec) [ -7158.6212] [ 1077] [depth= 1] . ( 32 sec) [ -7158.5346] [ 1077] [depth= 1] . ( 32 sec) [ -7158.5234] [ 1077] [depth= 3] . ( 32 sec) [ -7158.4818] [ 1077] [depth= 2] . ( 32 sec) [ -7158.4713] [ 1077] [depth= 4] . ( 33 sec) [ -7151.5874] [ 1076] [depth= 4] . ( 33 sec) [ -7151.5432] [ 1076] [depth= 3] . ( 33 sec) [ -7151.4347] [ 1076] [depth= 6] . ( 33 sec) [ -7151.3950] [ 1076] [depth= 4] . ( 34 sec) [ -6998.0253] [ 989] [depth= 17] . ( 37 sec) [ -6997.6938] [ 988] [depth= 6] . ( 37 sec) [ -6997.3605] [ 987] [depth= 9] . ( 37 sec) [ -6997.1384] [ 987] [depth= 5] . ( 38 sec) [ -6965.5069] [ 970] [depth= 7] . ( 38 sec) [ -6955.9438] [ 967] [depth= 1] . ( 41 sec) [ -6906.5798] [ 953] [depth= 1] . ( 41 sec) [ -6894.8628] [ 952] [depth= 1] . ( 42 sec) [ -6891.3197] [ 951] [depth= 4] . ( 42 sec) [ -6891.2861] [ 951] [depth= 3] . ( 43 sec) [ -6891.2609] [ 951] [depth= 1] . ( 44 sec) [ -6890.9867] [ 950] [depth= 5] . ( 45 sec) [ -6883.8353] [ 949] [depth= 4] . ( 45 sec) [ -6883.8125] [ 949] [depth= 4] . ( 46 sec) [ -6883.1170] [ 949] [depth= 3] . ( 46 sec) [ -6883.1060] [ 949] [depth= 2] . ( 47 sec) [ -6882.4751] [ 949] [depth= 1] . ( 48 sec) [ -6857.9663] [ 937] [depth= 1] . ( 49 sec) [ -6830.3172] [ 930] [depth= 2] . ( 49 sec) [ -6830.2920] [ 930] [depth= 1] . ( 49 sec) [ -6824.2769] [ 927] [depth= 1] . ( 50 sec) [ -6786.0715] [ 912] [depth= 1] . ( 50 sec) [ -6785.9903] [ 912] [depth= 5] . ( 51 sec) [ -6785.9663] [ 912] [depth= 3] . ( 51 sec) [ -6785.9511] [ 912] [depth= 3] . ( 51 sec) [ -6785.8937] [ 912] [depth= 2] . ( 52 sec) [ -6782.7425] [ 909] [depth= 1] . ( 52 sec) [ -6782.7272] [ 909] [depth= 4] . ( 53 sec) [ -6782.3545] [ 910] [depth= 6] . ( 53 sec) [ -6781.4803] [ 910] [depth= 2] . ( 54 sec) [ -6781.3893] [ 910] [depth= 6] . ( 54 sec) [ -6781.1728] [ 910] [depth= 6] . ( 55 sec) [ -6781.1614] [ 910] [depth= 3] . ( 55 sec) [ -6781.1402] [ 910] [depth= 2] . ( 56 sec) [ -6769.6202] [ 908] [depth= 7] . ( 56 sec) [ -6769.6091] [ 908] [depth= 2] . ( 60 sec) [ -6768.7225] [ 906] [depth= 1] . ( 61 sec) [ -6747.0362] [ 893] [depth= 2] . ( 61 sec) [ -6743.1183] [ 889] [depth= 1] . ( 61 sec) [ -6742.7146] [ 891] [depth= 1] . ( 61 sec) [ -6741.1206] [ 889] [depth= 1] . ( 62 sec) [ -6737.3868] [ 888] [depth= 1] . ( 64 sec) [ -6736.4482] [ 890] [depth= 1] . ( 65 sec) [ -6736.4317] [ 890] [depth= 1] . ( 65 sec) [ -6736.4140] [ 890] [depth= 2] . ( 66 sec) [ -6736.2781] [ 890] [depth= 1] . ( 69 sec) [ -6703.4751] [Branch lengths ] . ( 70 sec) [ -6698.2441] [GTR parameters ] . ( 71 sec) [ -6696.1745] [Alpha ][ 0.212037] . ( 82 sec) [ -6695.5017] [ 889] [depth= 5] . ( 82 sec) [ -6695.2777] [ 888] [depth= 5] . ( 82 sec) [ -6695.2430] [ 888] [depth= 7] . ( 83 sec) [ -6695.2099] [ 889] [depth= 1] . ( 107 sec) [ -6694.5687] [ 889] [depth= 1] . ( 117 sec) [ -6694.5381] [ 889] [depth= 3] . ( 118 sec) [ -6693.1302] [Branch lengths ] . ( 119 sec) [ -6693.0345] [GTR parameters ] . ( 120 sec) [ -6693.0009] [Alpha ][ 0.207522] . ( 132 sec) [ -6692.9888] [ 888] [depth= 1] . ( 134 sec) [ -6692.9767] [ 889] [depth= 4] . ( 165 sec) [ -6692.9591] [ 889] [depth= 5] . ( 166 sec) [ -6692.8210] [Branch lengths ] . ( 167 sec) [ -6692.8141] [GTR parameters ] . ( 167 sec) [ -6692.8116] [Alpha ][ 0.206236] . ( 234 sec) [ -6692.7558] [Branch lengths ] . ( 234 sec) [ -6692.7558] [Topology ] . ( 236 sec) [ -6692.4804] [Topology ] . ( 237 sec) [ -6691.3160] [Topology ] . ( 239 sec) [ -6689.8642] [Topology ] . ( 240 sec) [ -6689.7057] [Topology ] . ( 242 sec) [ -6689.6717] [Topology ] . ( 243 sec) [ -6689.6636] [Topology ] . ( 244 sec) [ -6689.6621] [GTR parameters ] . ( 245 sec) [ -6689.6620] [Alpha ][ 0.205993] . ( 245 sec) [ -6689.6620] [Topology ] . ( 246 sec) [ -6689.6601] [Topology ] . ( 248 sec) [ -6689.6595] [Topology ] . ( 248 sec) [ -6689.6595] [GTR parameters ] . ( 248 sec) [ -6689.6595] [Alpha ][ 0.205993] . ( 248 sec) [ -6689.6595] [Topology ] . ( 250 sec) [ -6689.6594] [Topology ] . ( 250 sec) [ -6689.6594] [GTR parameters ] . ( 250 sec) [ -6689.6594] [Alpha ][ 0.205993] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.659397. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -40180.8195] [GTR parameters ] . ( 3 sec) [ -39337.2192] [Alpha ][ 0.500960] . ( 3 sec) [ -39100.7747] [ 3873] [depth= 6] . ( 3 sec) [ -38147.8328] [ 3853] [depth= 8] . ( 3 sec) [ -38112.8163] [ 3851] [depth= 1] . ( 3 sec) [ -37991.8876] [ 3851] [depth= 4] . ( 3 sec) [ -37913.3941] [ 3783] [depth= 3] . ( 3 sec) [ -37904.9501] [ 3783] [depth= 1] . ( 3 sec) [ -37190.9366] [ 3781] [depth= 4] . ( 4 sec) [ -36864.5000] [ 3781] [depth= 5] . ( 4 sec) [ -36635.7906] [ 3778] [depth= 5] . ( 4 sec) [ -36155.2752] [ 3777] [depth= 5] . ( 4 sec) [ -36076.5198] [ 3766] [depth= 7] . ( 4 sec) [ -36022.0977] [ 3766] [depth= 1] . ( 4 sec) [ -33828.4510] [ 3724] [depth= 13] . ( 4 sec) [ -33117.2867] [ 3728] [depth= 1] . ( 4 sec) [ -33058.2510] [ 3724] [depth= 8] . ( 4 sec) [ -33023.5700] [ 3724] [depth= 10] . ( 4 sec) [ -31849.5709] [ 3636] [depth= 16] . ( 4 sec) [ -31564.2894] [ 3535] [depth= 7] . ( 5 sec) [ -30947.9967] [ 3513] [depth= 15] . ( 5 sec) [ -30630.2258] [ 3494] [depth= 11] . ( 5 sec) [ -30236.2502] [ 3492] [depth= 10] . ( 5 sec) [ -29517.8243] [ 3413] [depth= 6] . ( 5 sec) [ -29285.5724] [ 3414] [depth= 10] . ( 5 sec) [ -29277.5007] [ 3413] [depth= 8] . ( 5 sec) [ -29254.5878] [ 3413] [depth= 1] . ( 5 sec) [ -28890.8690] [ 3382] [depth= 6] . ( 5 sec) [ -28727.0741] [ 3355] [depth= 14] . ( 5 sec) [ -28534.9221] [ 3326] [depth= 9] . ( 6 sec) [ -27773.3254] [ 3326] [depth= 11] . ( 6 sec) [ -27201.5756] [ 3268] [depth= 8] . ( 6 sec) [ -27043.0248] [ 3260] [depth= 13] . ( 6 sec) [ -26908.0836] [ 3234] [depth= 14] . ( 6 sec) [ -26886.6446] [ 3233] [depth= 15] . ( 6 sec) [ -25831.9908] [ 3210] [depth= 9] . ( 6 sec) [ -24928.7649] [ 3121] [depth= 9] . ( 6 sec) [ -24414.4254] [ 3129] [depth= 18] . ( 6 sec) [ -24374.8529] [ 3129] [depth= 4] . ( 7 sec) [ -24343.0691] [ 3128] [depth= 6] . ( 7 sec) [ -23171.2194] [ 3087] [depth= 17] . ( 7 sec) [ -23170.9334] [ 3087] [depth= 3] . ( 7 sec) [ -22848.7455] [ 3009] [depth= 4] . ( 7 sec) [ -22409.4097] [ 2995] [depth= 6] . ( 7 sec) [ -22133.3074] [ 2907] [depth= 16] . ( 7 sec) [ -21916.5994] [ 2906] [depth= 7] . ( 7 sec) [ -21882.5306] [ 2906] [depth= 2] . ( 7 sec) [ -21618.2848] [ 2888] [depth= 7] . ( 7 sec) [ -21583.3810] [ 2888] [depth= 1] . ( 7 sec) [ -21491.5291] [ 2875] [depth= 11] . ( 8 sec) [ -21376.6835] [ 2875] [depth= 5] . ( 8 sec) [ -21242.5779] [ 2846] [depth= 10] . ( 8 sec) [ -21218.9616] [ 2846] [depth= 4] . ( 8 sec) [ -21120.6171] [ 2815] [depth= 17] . ( 8 sec) [ -21113.3291] [ 2816] [depth= 1] . ( 8 sec) [ -20851.9141] [ 2798] [depth= 13] . ( 8 sec) [ -20765.9968] [ 2890] [depth= 13] . ( 8 sec) [ -20564.9435] [ 2844] [depth= 18] . ( 8 sec) [ -20563.7863] [ 2844] [depth= 1] . ( 8 sec) [ -20443.9013] [ 2844] [depth= 8] . ( 9 sec) [ -19998.4234] [ 2733] [depth= 9] . ( 9 sec) [ -19591.5830] [ 2733] [depth= 1] . ( 9 sec) [ -19337.4594] [ 2730] [depth= 22] . ( 9 sec) [ -18807.2942] [ 2662] [depth= 7] . ( 9 sec) [ -18566.7680] [ 2641] [depth= 1] . ( 9 sec) [ -18384.6451] [ 2642] [depth= 8] . ( 9 sec) [ -18300.5284] [ 2627] [depth= 14] . ( 9 sec) [ -18208.3226] [ 2626] [depth= 3] . ( 9 sec) [ -18191.6483] [ 2626] [depth= 1] . ( 9 sec) [ -17565.6579] [ 2577] [depth= 11] . ( 9 sec) [ -17177.7671] [ 2577] [depth= 1] . ( 10 sec) [ -17174.6643] [ 2577] [depth= 6] . ( 10 sec) [ -17077.2413] [ 2578] [depth= 1] . ( 10 sec) [ -17059.0154] [ 2562] [depth= 7] . ( 10 sec) [ -17058.6697] [ 2561] [depth= 5] . ( 10 sec) [ -16814.8117] [ 2511] [depth= 18] . ( 10 sec) [ -16451.5562] [ 2379] [depth= 13] . ( 10 sec) [ -16451.2372] [ 2379] [depth= 4] . ( 10 sec) [ -16426.8846] [ 2366] [depth= 12] . ( 10 sec) [ -16194.9712] [ 2290] [depth= 5] . ( 10 sec) [ -16177.1026] [ 2285] [depth= 1] . ( 11 sec) [ -15533.3951] [ 2259] [depth= 6] . ( 11 sec) [ -15426.0321] [ 2247] [depth= 11] . ( 11 sec) [ -15409.1288] [ 2225] [depth= 1] . ( 11 sec) [ -15383.3366] [ 2223] [depth= 14] . ( 11 sec) [ -14418.8973] [ 2211] [depth= 11] . ( 11 sec) [ -14395.9134] [ 2211] [depth= 4] . ( 11 sec) [ -14386.6190] [ 2201] [depth= 7] . ( 11 sec) [ -14372.7376] [ 2201] [depth= 1] . ( 11 sec) [ -14359.8577] [ 2161] [depth= 5] . ( 11 sec) [ -14104.2974] [ 2161] [depth= 10] . ( 11 sec) [ -14083.5849] [ 2161] [depth= 3] . ( 12 sec) [ -14083.2376] [ 2161] [depth= 2] . ( 12 sec) [ -13924.8303] [ 2120] [depth= 10] . ( 12 sec) [ -13894.8055] [ 2119] [depth= 2] . ( 12 sec) [ -13181.0421] [ 2095] [depth= 9] . ( 12 sec) [ -13155.4515] [ 2095] [depth= 6] . ( 12 sec) [ -12965.0118] [ 2095] [depth= 2] . ( 12 sec) [ -12786.7925] [ 2052] [depth= 25] . ( 12 sec) [ -12771.3421] [ 2052] [depth= 11] . ( 12 sec) [ -12538.6699] [ 1973] [depth= 10] . ( 12 sec) [ -12538.5532] [ 1973] [depth= 1] . ( 13 sec) [ -12538.5322] [ 1973] [depth= 8] . ( 13 sec) [ -12528.8103] [ 1973] [depth= 13] . ( 13 sec) [ -12481.9074] [ 1933] [depth= 2] . ( 13 sec) [ -12434.5480] [ 1919] [depth= 6] . ( 13 sec) [ -12188.2014] [ 1891] [depth= 2] . ( 13 sec) [ -12186.4763] [ 1891] [depth= 3] . ( 13 sec) [ -11860.2967] [ 1797] [depth= 9] . ( 13 sec) [ -11680.3960] [ 1776] [depth= 8] . ( 13 sec) [ -11650.2822] [ 1776] [depth= 10] . ( 13 sec) [ -11466.6619] [ 1773] [depth= 2] . ( 13 sec) [ -11348.5514] [ 1773] [depth= 1] . ( 14 sec) [ -11272.8620] [ 1760] [depth= 7] . ( 14 sec) [ -11248.2743] [ 1760] [depth= 6] . ( 14 sec) [ -11186.5132] [ 1757] [depth= 7] . ( 14 sec) [ -11179.9076] [ 1758] [depth= 5] . ( 14 sec) [ -11178.7847] [ 1757] [depth= 1] . ( 14 sec) [ -11144.6100] [ 1724] [depth= 7] . ( 14 sec) [ -11143.8743] [ 1725] [depth= 1] . ( 14 sec) [ -11025.7333] [ 1726] [depth= 3] . ( 14 sec) [ -11015.6657] [ 1725] [depth= 4] . ( 15 sec) [ -11015.5039] [ 1725] [depth= 2] . ( 15 sec) [ -11013.4883] [ 1725] [depth= 11] . ( 15 sec) [ -10786.4990] [ 1637] [depth= 8] . ( 15 sec) [ -10739.3875] [ 1637] [depth= 1] . ( 15 sec) [ -10720.4130] [ 1637] [depth= 1] . ( 15 sec) [ -10666.4384] [ 1633] [depth= 5] . ( 15 sec) [ -10620.1679] [ 1628] [depth= 5] . ( 15 sec) [ -10618.2526] [ 1615] [depth= 1] . ( 15 sec) [ -10616.4072] [ 1613] [depth= 4] . ( 15 sec) [ -10615.5597] [ 1613] [depth= 1] . ( 16 sec) [ -10337.6557] [ 1610] [depth= 2] . ( 16 sec) [ -10255.0427] [ 1604] [depth= 3] . ( 16 sec) [ -10230.9543] [ 1595] [depth= 1] . ( 16 sec) [ -10215.9903] [ 1595] [depth= 8] . ( 16 sec) [ -10213.6757] [ 1595] [depth= 8] . ( 16 sec) [ -10049.9349] [ 1551] [depth= 11] . ( 16 sec) [ -9996.1446] [ 1532] [depth= 4] . ( 16 sec) [ -9992.3736] [ 1532] [depth= 5] . ( 16 sec) [ -9989.0904] [ 1532] [depth= 3] . ( 16 sec) [ -9988.6007] [ 1532] [depth= 3] . ( 16 sec) [ -9936.0940] [ 1524] [depth= 7] . ( 17 sec) [ -9936.0206] [ 1524] [depth= 3] . ( 17 sec) [ -9923.8895] [ 1525] [depth= 4] . ( 17 sec) [ -9919.4038] [ 1526] [depth= 3] . ( 17 sec) [ -9818.9210] [ 1524] [depth= 12] . ( 17 sec) [ -9799.6563] [ 1521] [depth= 11] . ( 18 sec) [ -9667.8752] [ 1499] [depth= 4] . ( 18 sec) [ -9662.9489] [ 1499] [depth= 1] . ( 18 sec) [ -9409.5490] [ 1474] [depth= 7] . ( 18 sec) [ -9311.7083] [ 1476] [depth= 1] . ( 18 sec) [ -9277.6468] [ 1439] [depth= 3] . ( 18 sec) [ -9140.9605] [ 1441] [depth= 3] . ( 18 sec) [ -9013.0078] [ 1415] [depth= 2] . ( 18 sec) [ -9012.9074] [ 1415] [depth= 1] . ( 18 sec) [ -9002.1536] [ 1415] [depth= 2] . ( 18 sec) [ -9001.8360] [ 1415] [depth= 1] . ( 18 sec) [ -8921.3506] [ 1402] [depth= 12] . ( 19 sec) [ -8854.8867] [ 1390] [depth= 6] . ( 19 sec) [ -8853.4581] [ 1390] [depth= 1] . ( 19 sec) [ -8736.8600] [ 1385] [depth= 8] . ( 19 sec) [ -8726.0198] [ 1385] [depth= 3] . ( 19 sec) [ -8725.9716] [ 1385] [depth= 9] . ( 19 sec) [ -8723.5996] [ 1385] [depth= 2] . ( 19 sec) [ -8682.5755] [ 1387] [depth= 6] . ( 19 sec) [ -8675.6609] [ 1387] [depth= 11] . ( 20 sec) [ -8675.6260] [ 1387] [depth= 1] . ( 20 sec) [ -8641.5687] [ 1381] [depth= 5] . ( 20 sec) [ -8522.6452] [ 1344] [depth= 5] . ( 20 sec) [ -8522.5006] [ 1344] [depth= 1] . ( 20 sec) [ -8522.2081] [ 1344] [depth= 11] . ( 20 sec) [ -8341.0174] [ 1256] [depth= 11] . ( 20 sec) [ -8338.6683] [ 1256] [depth= 3] . ( 21 sec) [ -8337.7769] [ 1256] [depth= 3] . ( 21 sec) [ -8296.8414] [ 1232] [depth= 3] . ( 21 sec) [ -8202.4092] [ 1188] [depth= 2] . ( 21 sec) [ -8202.3968] [ 1188] [depth= 1] . ( 21 sec) [ -8195.5893] [ 1177] [depth= 4] . ( 21 sec) [ -8027.5539] [ 1131] [depth= 5] . ( 21 sec) [ -7931.4803] [ 1101] [depth= 3] . ( 21 sec) [ -7931.1728] [ 1101] [depth= 8] . ( 21 sec) [ -7931.1494] [ 1101] [depth= 2] . ( 21 sec) [ -7880.2914] [ 1085] [depth= 1] . ( 22 sec) [ -7873.6475] [ 1083] [depth= 2] . ( 22 sec) [ -7857.5155] [ 1083] [depth= 6] . ( 22 sec) [ -7857.4818] [ 1083] [depth= 6] . ( 22 sec) [ -7855.9692] [ 1083] [depth= 3] . ( 22 sec) [ -7846.7432] [ 1082] [depth= 4] . ( 22 sec) [ -7846.6922] [ 1082] [depth= 1] . ( 23 sec) [ -7829.3535] [ 1082] [depth= 2] . ( 23 sec) [ -7829.3008] [ 1082] [depth= 4] . ( 24 sec) [ -7797.5938] [ 1065] [depth= 2] . ( 24 sec) [ -7752.6869] [ 1058] [depth= 1] . ( 24 sec) [ -7744.6989] [ 1058] [depth= 1] . ( 24 sec) [ -7675.8813] [ 1057] [depth= 7] . ( 25 sec) [ -7509.9476] [Branch lengths ] . ( 27 sec) [ -7205.3044] [GTR parameters ] . ( 27 sec) [ -7115.7299] [Alpha ][ 0.250961] . ( 28 sec) [ -7066.3353] [ 1037] [depth= 3] . ( 28 sec) [ -7066.1882] [ 1037] [depth= 1] . ( 28 sec) [ -7011.2791] [ 1020] [depth= 15] . ( 29 sec) [ -7011.1178] [ 1020] [depth= 3] . ( 29 sec) [ -7006.0563] [ 1017] [depth= 3] . ( 29 sec) [ -7006.0437] [ 1017] [depth= 5] . ( 29 sec) [ -7006.0069] [ 1017] [depth= 1] . ( 29 sec) [ -7005.9800] [ 1017] [depth= 3] . ( 29 sec) [ -7005.9446] [ 1017] [depth= 5] . ( 30 sec) [ -7005.8871] [ 1017] [depth= 3] . ( 30 sec) [ -7005.8742] [ 1017] [depth= 1] . ( 31 sec) [ -6990.0669] [ 1006] [depth= 2] . ( 31 sec) [ -6988.8694] [ 1005] [depth= 1] . ( 31 sec) [ -6985.6186] [ 1004] [depth= 11] . ( 31 sec) [ -6985.6033] [ 1004] [depth= 8] . ( 32 sec) [ -6985.5792] [ 1004] [depth= 5] . ( 33 sec) [ -6818.5043] [ 966] [depth= 4] . ( 33 sec) [ -6818.4913] [ 966] [depth= 1] . ( 34 sec) [ -6818.4725] [ 966] [depth= 4] . ( 36 sec) [ -6818.4465] [ 966] [depth= 1] . ( 38 sec) [ -6817.8098] [ 964] [depth= 1] . ( 38 sec) [ -6808.3589] [ 955] [depth= 7] . ( 39 sec) [ -6802.8482] [ 951] [depth= 1] . ( 39 sec) [ -6801.4110] [ 950] [depth= 6] . ( 41 sec) [ -6761.6946] [ 907] [depth= 3] . ( 41 sec) [ -6761.6495] [ 907] [depth= 1] . ( 43 sec) [ -6761.5632] [ 910] [depth= 1] . ( 43 sec) [ -6761.5215] [ 910] [depth= 1] . ( 47 sec) [ -6756.9499] [ 909] [depth= 3] . ( 49 sec) [ -6750.0171] [ 908] [depth= 4] . ( 51 sec) [ -6725.2798] [ 893] [depth= 2] . ( 53 sec) [ -6725.2267] [ 893] [depth= 5] . ( 54 sec) [ -6725.1911] [ 893] [depth= 2] . ( 55 sec) [ -6723.6833] [ 898] [depth= 1] . ( 55 sec) [ -6721.3923] [ 893] [depth= 1] . ( 56 sec) [ -6714.4669] [ 892] [depth= 1] . ( 57 sec) [ -6712.1629] [ 891] [depth= 1] . ( 64 sec) [ -6712.1522] [ 891] [depth= 4] . ( 71 sec) [ -6699.4541] [Branch lengths ] . ( 73 sec) [ -6697.0798] [GTR parameters ] . ( 73 sec) [ -6694.5840] [Alpha ][ 0.208818] . ( 74 sec) [ -6694.5525] [ 891] [depth= 2] . ( 77 sec) [ -6694.5390] [ 891] [depth= 2] . ( 81 sec) [ -6694.5122] [ 891] [depth= 1] . ( 85 sec) [ -6694.4930] [ 891] [depth= 1] . ( 85 sec) [ -6694.4658] [ 891] [depth= 1] . ( 119 sec) [ -6693.3001] [Branch lengths ] . ( 121 sec) [ -6693.2513] [GTR parameters ] . ( 121 sec) [ -6693.2024] [Alpha ][ 0.203482] . ( 147 sec) [ -6693.1840] [ 891] [depth= 4] . ( 152 sec) [ -6693.1664] [ 891] [depth= 3] . ( 165 sec) [ -6691.7893] [Branch lengths ] . ( 167 sec) [ -6691.7807] [GTR parameters ] . ( 167 sec) [ -6691.7807] [Alpha ][ 0.203482] . ( 212 sec) [ -6690.8794] [Branch lengths ] . ( 268 sec) [ -6690.7878] [ 892] [depth= 1] . ( 280 sec) [ -6690.4218] [Branch lengths ] . ( 281 sec) [ -6690.4085] [GTR parameters ] . ( 282 sec) [ -6690.4028] [Alpha ][ 0.205362] . ( 282 sec) [ -6690.4028] [Topology ] . ( 283 sec) [ -6690.3639] [Topology ] . ( 284 sec) [ -6690.3574] [Topology ] . ( 286 sec) [ -6690.3557] [Topology ] . ( 287 sec) [ -6690.3552] [Topology ] . ( 288 sec) [ -6690.3549] [GTR parameters ] . ( 288 sec) [ -6690.3548] [Alpha ][ 0.205567] . ( 288 sec) [ -6690.3548] [Topology ] . ( 290 sec) [ -6690.3546] [Topology ] . ( 290 sec) [ -6690.3546] [GTR parameters ] . ( 290 sec) [ -6690.3546] [Alpha ][ 0.205567] . Checking for NNIs, optimizing five branches... . ( 302 sec) [ -6689.6748] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.674763. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -40343.4160] [GTR parameters ] . ( 2 sec) [ -39502.0123] [Alpha ][ 0.500960] . ( 3 sec) [ -37620.1486] [ 3870] [depth= 2] . ( 3 sec) [ -37514.6563] [ 3857] [depth= 3] . ( 3 sec) [ -36821.8986] [ 3820] [depth= 1] . ( 3 sec) [ -36791.4317] [ 3819] [depth= 1] . ( 3 sec) [ -36790.4774] [ 3819] [depth= 1] . ( 3 sec) [ -36672.9773] [ 3819] [depth= 1] . ( 3 sec) [ -36672.9384] [ 3819] [depth= 2] . ( 3 sec) [ -36666.8552] [ 3819] [depth= 1] . ( 3 sec) [ -36659.7000] [ 3807] [depth= 4] . ( 3 sec) [ -36533.2077] [ 3806] [depth= 1] . ( 3 sec) [ -36505.1850] [ 3788] [depth= 2] . ( 4 sec) [ -36497.2281] [ 3785] [depth= 3] . ( 4 sec) [ -36370.6185] [ 3786] [depth= 3] . ( 4 sec) [ -35927.2275] [ 3784] [depth= 1] . ( 4 sec) [ -35421.4788] [ 3740] [depth= 4] . ( 4 sec) [ -34541.1112] [ 3739] [depth= 8] . ( 4 sec) [ -33481.0929] [ 3707] [depth= 3] . ( 4 sec) [ -32989.6163] [ 3701] [depth= 7] . ( 4 sec) [ -32724.2003] [ 3699] [depth= 2] . ( 4 sec) [ -31685.8963] [ 3699] [depth= 1] . ( 4 sec) [ -31298.5842] [ 3618] [depth= 4] . ( 4 sec) [ -30356.3426] [ 3537] [depth= 14] . ( 5 sec) [ -30023.9630] [ 3525] [depth= 3] . ( 5 sec) [ -29952.2460] [ 3525] [depth= 1] . ( 5 sec) [ -29699.4437] [ 3525] [depth= 2] . ( 5 sec) [ -29599.1232] [ 3525] [depth= 1] . ( 5 sec) [ -28935.4618] [ 3504] [depth= 7] . ( 5 sec) [ -28079.9964] [ 3504] [depth= 3] . ( 5 sec) [ -27967.8799] [ 3504] [depth= 2] . ( 5 sec) [ -26602.0496] [ 3504] [depth= 3] . ( 5 sec) [ -25878.7603] [ 3398] [depth= 17] . ( 5 sec) [ -25876.4900] [ 3398] [depth= 3] . ( 5 sec) [ -25839.5837] [ 3398] [depth= 1] . ( 6 sec) [ -25697.7442] [ 3396] [depth= 2] . ( 6 sec) [ -25520.4755] [ 3388] [depth= 2] . ( 6 sec) [ -25349.2243] [ 3354] [depth= 12] . ( 6 sec) [ -25319.3578] [ 3353] [depth= 6] . ( 6 sec) [ -25214.0961] [ 3351] [depth= 11] . ( 6 sec) [ -25013.5450] [ 3344] [depth= 4] . ( 6 sec) [ -24810.6220] [ 3318] [depth= 10] . ( 6 sec) [ -24801.4328] [ 3318] [depth= 1] . ( 6 sec) [ -24507.2926] [ 3269] [depth= 18] . ( 6 sec) [ -24452.3903] [ 3268] [depth= 1] . ( 6 sec) [ -24206.1274] [ 3268] [depth= 1] . ( 7 sec) [ -24206.0354] [ 3268] [depth= 1] . ( 7 sec) [ -24205.1049] [ 3246] [depth= 5] . ( 7 sec) [ -23565.6273] [ 3218] [depth= 4] . ( 7 sec) [ -23565.4508] [ 3218] [depth= 3] . ( 7 sec) [ -23532.9904] [ 3218] [depth= 18] . ( 7 sec) [ -23532.9619] [ 3218] [depth= 18] . ( 7 sec) [ -23325.6386] [ 3192] [depth= 3] . ( 7 sec) [ -22966.1716] [ 3127] [depth= 11] . ( 7 sec) [ -22912.5319] [ 3127] [depth= 2] . ( 7 sec) [ -22523.4141] [ 3100] [depth= 14] . ( 8 sec) [ -22321.3831] [ 3079] [depth= 6] . ( 8 sec) [ -22053.3908] [ 3012] [depth= 8] . ( 8 sec) [ -21770.2692] [ 3012] [depth= 2] . ( 8 sec) [ -21750.7367] [ 3012] [depth= 1] . ( 8 sec) [ -21555.1046] [ 3011] [depth= 12] . ( 8 sec) [ -21030.7172] [ 2994] [depth= 2] . ( 8 sec) [ -20901.2654] [ 2985] [depth= 4] . ( 8 sec) [ -20713.5867] [ 2969] [depth= 6] . ( 8 sec) [ -20459.2490] [ 2969] [depth= 1] . ( 8 sec) [ -20415.7824] [ 2903] [depth= 10] . ( 8 sec) [ -20381.6512] [ 2903] [depth= 1] . ( 9 sec) [ -20102.9666] [ 2807] [depth= 8] . ( 9 sec) [ -20035.5987] [ 2809] [depth= 1] . ( 9 sec) [ -19746.0965] [ 2804] [depth= 9] . ( 9 sec) [ -19652.8030] [ 2784] [depth= 6] . ( 9 sec) [ -19516.5819] [ 2784] [depth= 7] . ( 9 sec) [ -19421.3018] [ 2764] [depth= 2] . ( 9 sec) [ -19378.2733] [ 2756] [depth= 5] . ( 9 sec) [ -19040.0429] [ 2678] [depth= 22] . ( 9 sec) [ -18930.7185] [ 2671] [depth= 2] . ( 9 sec) [ -18788.0529] [ 2670] [depth= 4] . ( 10 sec) [ -18306.0585] [ 2654] [depth= 15] . ( 10 sec) [ -18293.7945] [ 2654] [depth= 7] . ( 10 sec) [ -18007.8257] [ 2645] [depth= 21] . ( 10 sec) [ -17633.3084] [ 2693] [depth= 1] . ( 10 sec) [ -17329.1464] [ 2637] [depth= 5] . ( 10 sec) [ -17329.0677] [ 2637] [depth= 19] . ( 10 sec) [ -16941.2418] [ 2593] [depth= 9] . ( 10 sec) [ -16649.6066] [ 2492] [depth= 19] . ( 10 sec) [ -16621.6251] [ 2489] [depth= 2] . ( 10 sec) [ -16402.3047] [ 2489] [depth= 2] . ( 10 sec) [ -16188.0303] [ 2460] [depth= 2] . ( 11 sec) [ -16176.7049] [ 2460] [depth= 1] . ( 11 sec) [ -16176.6833] [ 2460] [depth= 20] . ( 11 sec) [ -16167.8272] [ 2460] [depth= 1] . ( 11 sec) [ -16167.5078] [ 2460] [depth= 20] . ( 11 sec) [ -16167.3670] [ 2460] [depth= 19] . ( 11 sec) [ -16109.8077] [ 2446] [depth= 11] . ( 11 sec) [ -15953.0594] [ 2403] [depth= 16] . ( 11 sec) [ -15945.7357] [ 2403] [depth= 11] . ( 11 sec) [ -15920.3520] [ 2396] [depth= 1] . ( 11 sec) [ -15860.8710] [ 2377] [depth= 25] . ( 12 sec) [ -15560.7339] [ 2282] [depth= 23] . ( 12 sec) [ -15458.5305] [ 2258] [depth= 23] . ( 12 sec) [ -15430.2427] [ 2258] [depth= 1] . ( 12 sec) [ -15401.0666] [ 2257] [depth= 13] . ( 12 sec) [ -15401.0144] [ 2257] [depth= 1] . ( 12 sec) [ -15399.9848] [ 2257] [depth= 2] . ( 12 sec) [ -15394.7350] [ 2257] [depth= 2] . ( 12 sec) [ -15145.2670] [ 2187] [depth= 7] . ( 12 sec) [ -14910.9110] [ 2148] [depth= 13] . ( 13 sec) [ -14883.2001] [ 2150] [depth= 17] . ( 13 sec) [ -14842.7402] [ 2151] [depth= 12] . ( 13 sec) [ -14838.8246] [ 2151] [depth= 13] . ( 13 sec) [ -14836.2342] [ 2151] [depth= 8] . ( 13 sec) [ -14370.6895] [ 2151] [depth= 2] . ( 13 sec) [ -13484.4821] [ 2008] [depth= 19] . ( 13 sec) [ -13484.2350] [ 2008] [depth= 10] . ( 13 sec) [ -13469.8015] [ 2008] [depth= 27] . ( 14 sec) [ -13462.7868] [ 2008] [depth= 2] . ( 14 sec) [ -13444.3049] [ 2007] [depth= 3] . ( 14 sec) [ -13177.7022] [ 2004] [depth= 2] . ( 14 sec) [ -13162.9208] [ 1968] [depth= 4] . ( 14 sec) [ -13144.2835] [ 1967] [depth= 10] . ( 14 sec) [ -12932.5149] [ 1954] [depth= 4] . ( 14 sec) [ -12928.7764] [ 1947] [depth= 16] . ( 14 sec) [ -12812.0848] [ 1925] [depth= 16] . ( 14 sec) [ -12796.7936] [ 1925] [depth= 5] . ( 14 sec) [ -12796.6565] [ 1925] [depth= 1] . ( 14 sec) [ -12795.7386] [ 1925] [depth= 2] . ( 15 sec) [ -12033.0940] [ 1897] [depth= 9] . ( 15 sec) [ -12015.2473] [ 1923] [depth= 2] . ( 15 sec) [ -12011.6883] [ 1923] [depth= 2] . ( 15 sec) [ -12007.3111] [ 1923] [depth= 1] . ( 15 sec) [ -11835.2521] [ 1880] [depth= 16] . ( 15 sec) [ -11786.5790] [ 1878] [depth= 1] . ( 15 sec) [ -11521.5461] [ 1858] [depth= 13] . ( 15 sec) [ -11479.1859] [ 1845] [depth= 2] . ( 15 sec) [ -11461.0480] [ 1835] [depth= 4] . ( 15 sec) [ -11298.8492] [ 1818] [depth= 16] . ( 15 sec) [ -11279.0271] [ 1817] [depth= 1] . ( 16 sec) [ -11243.0963] [ 1807] [depth= 1] . ( 16 sec) [ -11076.9812] [ 1764] [depth= 27] . ( 16 sec) [ -10743.6999] [ 1734] [depth= 15] . ( 16 sec) [ -10583.1824] [ 1699] [depth= 1] . ( 16 sec) [ -10574.8892] [ 1699] [depth= 1] . ( 16 sec) [ -10451.5343] [ 1667] [depth= 13] . ( 16 sec) [ -10382.2630] [ 1595] [depth= 9] . ( 16 sec) [ -10229.8892] [ 1595] [depth= 1] . ( 16 sec) [ -10221.9010] [ 1595] [depth= 7] . ( 16 sec) [ -10212.0082] [ 1595] [depth= 2] . ( 17 sec) [ -10211.8869] [ 1595] [depth= 8] . ( 17 sec) [ -10211.0951] [ 1595] [depth= 5] . ( 17 sec) [ -10211.0816] [ 1595] [depth= 6] . ( 17 sec) [ -9967.0260] [ 1586] [depth= 2] . ( 17 sec) [ -9860.5832] [ 1565] [depth= 1] . ( 17 sec) [ -9670.8995] [ 1539] [depth= 4] . ( 17 sec) [ -9662.8880] [ 1539] [depth= 9] . ( 17 sec) [ -9614.7609] [ 1512] [depth= 19] . ( 18 sec) [ -9613.8231] [ 1512] [depth= 1] . ( 18 sec) [ -9561.8693] [ 1490] [depth= 5] . ( 18 sec) [ -9549.5367] [ 1488] [depth= 4] . ( 18 sec) [ -9408.1927] [ 1486] [depth= 7] . ( 18 sec) [ -9284.7223] [ 1461] [depth= 8] . ( 18 sec) [ -9231.9929] [ 1398] [depth= 9] . ( 18 sec) [ -8940.3759] [ 1392] [depth= 7] . ( 18 sec) [ -8624.1992] [ 1388] [depth= 2] . ( 19 sec) [ -8621.6962] [ 1388] [depth= 1] . ( 19 sec) [ -8615.9129] [ 1389] [depth= 1] . ( 19 sec) [ -8615.2349] [ 1389] [depth= 1] . ( 19 sec) [ -8613.4456] [ 1389] [depth= 2] . ( 19 sec) [ -8612.6269] [ 1389] [depth= 1] . ( 19 sec) [ -8498.0647] [ 1361] [depth= 2] . ( 19 sec) [ -8456.4739] [ 1349] [depth= 9] . ( 20 sec) [ -8454.2431] [ 1347] [depth= 1] . ( 20 sec) [ -8452.7236] [ 1347] [depth= 2] . ( 20 sec) [ -8452.6489] [ 1347] [depth= 1] . ( 20 sec) [ -8447.6622] [ 1346] [depth= 5] . ( 20 sec) [ -8445.0257] [ 1346] [depth= 2] . ( 20 sec) [ -8444.8355] [ 1346] [depth= 10] . ( 21 sec) [ -8357.3546] [ 1321] [depth= 2] . ( 21 sec) [ -8281.6847] [ 1313] [depth= 10] . ( 21 sec) [ -8273.7944] [ 1313] [depth= 1] . ( 21 sec) [ -8246.3293] [ 1312] [depth= 3] . ( 21 sec) [ -8235.8332] [ 1312] [depth= 1] . ( 21 sec) [ -8235.7730] [ 1312] [depth= 1] . ( 21 sec) [ -8235.6526] [ 1312] [depth= 12] . ( 21 sec) [ -8199.5713] [ 1312] [depth= 3] . ( 21 sec) [ -7949.7846] [ 1201] [depth= 5] . ( 21 sec) [ -7949.3960] [ 1201] [depth= 3] . ( 22 sec) [ -7939.1888] [ 1201] [depth= 1] . ( 22 sec) [ -7939.1082] [ 1201] [depth= 2] . ( 22 sec) [ -7925.1698] [ 1201] [depth= 1] . ( 22 sec) [ -7925.0815] [ 1201] [depth= 1] . ( 22 sec) [ -7906.4501] [ 1201] [depth= 1] . ( 22 sec) [ -7905.8931] [ 1201] [depth= 3] . ( 22 sec) [ -7904.9483] [ 1201] [depth= 2] . ( 22 sec) [ -7819.8002] [ 1201] [depth= 4] . ( 23 sec) [ -7819.7734] [ 1201] [depth= 3] . ( 23 sec) [ -7500.1021] [ 1093] [depth= 5] . ( 23 sec) [ -7500.0745] [ 1093] [depth= 5] . ( 24 sec) [ -7369.2345] [Branch lengths ] . ( 28 sec) [ -7182.7994] [GTR parameters ] . ( 28 sec) [ -7095.2538] [Alpha ][ 0.250961] . ( 28 sec) [ -7095.2437] [ 1093] [depth= 3] . ( 29 sec) [ -7088.2018] [ 1092] [depth= 7] . ( 29 sec) [ -7088.1886] [ 1092] [depth= 4] . ( 30 sec) [ -7088.1773] [ 1092] [depth= 1] . ( 30 sec) [ -7088.1444] [ 1084] [depth= 3] . ( 30 sec) [ -7088.0969] [ 1085] [depth= 4] . ( 30 sec) [ -7087.2233] [ 1085] [depth= 4] . ( 30 sec) [ -7087.2087] [ 1085] [depth= 4] . ( 31 sec) [ -7079.4448] [ 1084] [depth= 1] . ( 31 sec) [ -7079.4307] [ 1084] [depth= 2] . ( 31 sec) [ -7079.4036] [ 1084] [depth= 10] . ( 32 sec) [ -7052.3494] [ 1051] [depth= 1] . ( 32 sec) [ -7047.6242] [ 1051] [depth= 1] . ( 33 sec) [ -7033.1033] [ 1030] [depth= 6] . ( 33 sec) [ -7022.5667] [ 1021] [depth= 8] . ( 35 sec) [ -6994.9986] [ 983] [depth= 12] . ( 35 sec) [ -6987.0732] [ 981] [depth= 3] . ( 35 sec) [ -6985.5967] [ 982] [depth= 5] . ( 36 sec) [ -6985.5857] [ 982] [depth= 2] . ( 39 sec) [ -6980.1986] [ 982] [depth= 5] . ( 39 sec) [ -6968.6469] [ 980] [depth= 5] . ( 39 sec) [ -6966.5129] [ 980] [depth= 5] . ( 39 sec) [ -6959.4094] [ 979] [depth= 2] . ( 39 sec) [ -6958.6290] [ 979] [depth= 4] . ( 40 sec) [ -6957.9032] [ 979] [depth= 1] . ( 40 sec) [ -6933.3280] [ 968] [depth= 1] . ( 40 sec) [ -6932.8064] [ 968] [depth= 1] . ( 40 sec) [ -6931.1333] [ 966] [depth= 5] . ( 41 sec) [ -6930.8572] [ 966] [depth= 2] . ( 42 sec) [ -6774.8529] [ 899] [depth= 6] . ( 42 sec) [ -6751.3910] [ 890] [depth= 2] . ( 42 sec) [ -6751.2682] [ 890] [depth= 2] . ( 42 sec) [ -6751.1748] [ 890] [depth= 2] . ( 43 sec) [ -6750.2694] [ 890] [depth= 1] . ( 44 sec) [ -6750.2590] [ 890] [depth= 3] . ( 46 sec) [ -6750.2317] [ 890] [depth= 9] . ( 49 sec) [ -6743.2467] [ 889] [depth= 8] . ( 50 sec) [ -6743.2364] [ 888] [depth= 2] . ( 52 sec) [ -6742.0546] [ 887] [depth= 1] . ( 53 sec) [ -6741.2525] [ 887] [depth= 1] . ( 54 sec) [ -6738.7108] [ 885] [depth= 2] . ( 55 sec) [ -6725.1871] [ 888] [depth= 1] . ( 55 sec) [ -6724.2138] [ 888] [depth= 3] . ( 55 sec) [ -6723.0848] [ 888] [depth= 1] . ( 55 sec) [ -6722.0320] [ 889] [depth= 1] . ( 56 sec) [ -6721.9966] [ 889] [depth= 6] . ( 59 sec) [ -6721.9767] [ 889] [depth= 1] . ( 59 sec) [ -6716.4952] [ 887] [depth= 1] . ( 59 sec) [ -6716.4838] [ 887] [depth= 7] . ( 61 sec) [ -6716.3648] [ 887] [depth= 6] . ( 61 sec) [ -6715.8983] [ 887] [depth= 4] . ( 61 sec) [ -6715.7584] [ 887] [depth= 1] . ( 61 sec) [ -6715.7086] [ 887] [depth= 10] . ( 61 sec) [ -6715.4076] [ 887] [depth= 9] . ( 62 sec) [ -6715.3961] [ 887] [depth= 4] . ( 62 sec) [ -6715.3771] [ 887] [depth= 9] . ( 66 sec) [ -6715.2184] [ 889] [depth= 1] . ( 67 sec) [ -6704.7791] [Branch lengths ] . ( 71 sec) [ -6702.7806] [GTR parameters ] . ( 71 sec) [ -6700.5640] [Alpha ][ 0.210359] . ( 74 sec) [ -6699.5010] [ 887] [depth= 1] . ( 74 sec) [ -6699.4465] [ 887] [depth= 4] . ( 86 sec) [ -6699.1936] [ 889] [depth= 1] . ( 101 sec) [ -6699.1075] [ 889] [depth= 5] . ( 102 sec) [ -6698.3361] [ 889] [depth= 1] . ( 115 sec) [ -6694.9707] [Branch lengths ] . ( 119 sec) [ -6694.7542] [GTR parameters ] . ( 119 sec) [ -6694.7202] [Alpha ][ 0.205824] . ( 163 sec) [ -6693.2574] [Branch lengths ] . ( 231 sec) [ -6689.8349] [Branch lengths ] . ( 231 sec) [ -6689.8349] [Topology ] . ( 232 sec) [ -6689.7454] [Topology ] . ( 234 sec) [ -6689.7322] [Topology ] . ( 235 sec) [ -6689.7289] [Topology ] . ( 236 sec) [ -6689.7280] [Topology ] . ( 240 sec) [ -6689.7098] [GTR parameters ] . ( 240 sec) [ -6689.7097] [Alpha ][ 0.206106] . ( 240 sec) [ -6689.7097] [Topology ] . ( 242 sec) [ -6689.7094] [Topology ] . ( 245 sec) [ -6689.7092] [GTR parameters ] . ( 245 sec) [ -6689.7092] [Alpha ][ 0.206106] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.709181. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -35727.6533] [GTR parameters ] . ( 2 sec) [ -34912.4025] [Alpha ][ 0.500960] . ( 2 sec) [ -34679.5226] [ 3897] [depth= 1] . ( 2 sec) [ -34545.6153] [ 3880] [depth= 4] . ( 2 sec) [ -34545.3122] [ 3880] [depth= 1] . ( 2 sec) [ -34147.0829] [ 3863] [depth= 9] . ( 2 sec) [ -33839.3874] [ 3862] [depth= 3] . ( 2 sec) [ -33530.4476] [ 3858] [depth= 4] . ( 2 sec) [ -33461.5584] [ 3807] [depth= 2] . ( 3 sec) [ -33450.5084] [ 3807] [depth= 1] . ( 3 sec) [ -33201.3801] [ 3805] [depth= 2] . ( 3 sec) [ -32816.4935] [ 3802] [depth= 7] . ( 3 sec) [ -32525.1850] [ 3802] [depth= 1] . ( 3 sec) [ -32134.3081] [ 3802] [depth= 2] . ( 3 sec) [ -32104.3731] [ 3796] [depth= 4] . ( 3 sec) [ -31300.0745] [ 3796] [depth= 10] . ( 3 sec) [ -30250.0008] [ 3689] [depth= 20] . ( 3 sec) [ -30189.2631] [ 3659] [depth= 11] . ( 3 sec) [ -30102.0092] [ 3659] [depth= 1] . ( 3 sec) [ -29779.3766] [ 3659] [depth= 14] . ( 4 sec) [ -29643.0137] [ 3659] [depth= 14] . ( 4 sec) [ -29205.1381] [ 3582] [depth= 5] . ( 4 sec) [ -29031.4985] [ 3581] [depth= 9] . ( 4 sec) [ -28011.2915] [ 3487] [depth= 11] . ( 4 sec) [ -27900.2423] [ 3486] [depth= 15] . ( 4 sec) [ -27703.9638] [ 3469] [depth= 8] . ( 4 sec) [ -27703.9373] [ 3469] [depth= 6] . ( 4 sec) [ -27669.8431] [ 3465] [depth= 3] . ( 4 sec) [ -27440.8619] [ 3465] [depth= 1] . ( 4 sec) [ -27288.5590] [ 3429] [depth= 8] . ( 5 sec) [ -27235.0225] [ 3429] [depth= 1] . ( 5 sec) [ -27205.5062] [ 3421] [depth= 6] . ( 5 sec) [ -25883.4176] [ 3307] [depth= 9] . ( 5 sec) [ -25841.3508] [ 3307] [depth= 3] . ( 5 sec) [ -25598.9237] [ 3256] [depth= 8] . ( 5 sec) [ -25265.9828] [ 3151] [depth= 15] . ( 5 sec) [ -25210.3789] [ 3150] [depth= 1] . ( 5 sec) [ -25067.7865] [ 3148] [depth= 17] . ( 5 sec) [ -24459.8711] [ 3148] [depth= 16] . ( 5 sec) [ -24384.0327] [ 3146] [depth= 4] . ( 6 sec) [ -24349.1425] [ 3143] [depth= 17] . ( 6 sec) [ -23363.1440] [ 3067] [depth= 14] . ( 6 sec) [ -22930.2882] [ 2984] [depth= 14] . ( 6 sec) [ -22467.0519] [ 2934] [depth= 20] . ( 6 sec) [ -22315.3393] [ 2934] [depth= 1] . ( 6 sec) [ -22025.7370] [ 2890] [depth= 3] . ( 6 sec) [ -21597.6375] [ 2890] [depth= 14] . ( 6 sec) [ -21354.3973] [ 2876] [depth= 1] . ( 6 sec) [ -21298.2349] [ 2877] [depth= 1] . ( 7 sec) [ -21297.5905] [ 2876] [depth= 1] . ( 7 sec) [ -21297.2982] [ 2876] [depth= 1] . ( 7 sec) [ -21037.8896] [ 2831] [depth= 18] . ( 7 sec) [ -20941.1708] [ 2786] [depth= 1] . ( 7 sec) [ -20582.8036] [ 2772] [depth= 11] . ( 7 sec) [ -20452.6067] [ 2759] [depth= 17] . ( 7 sec) [ -20297.2158] [ 2725] [depth= 10] . ( 7 sec) [ -20296.2633] [ 2725] [depth= 2] . ( 7 sec) [ -20275.7339] [ 2725] [depth= 1] . ( 7 sec) [ -20275.5002] [ 2725] [depth= 17] . ( 7 sec) [ -20173.5627] [ 2711] [depth= 6] . ( 8 sec) [ -20172.6500] [ 2711] [depth= 1] . ( 8 sec) [ -20097.3331] [ 2702] [depth= 11] . ( 8 sec) [ -20020.8762] [ 2701] [depth= 12] . ( 8 sec) [ -19988.8679] [ 2701] [depth= 16] . ( 8 sec) [ -19686.9242] [ 2668] [depth= 9] . ( 8 sec) [ -19667.4757] [ 2666] [depth= 7] . ( 8 sec) [ -19605.0053] [ 2665] [depth= 16] . ( 8 sec) [ -19604.5607] [ 2665] [depth= 3] . ( 8 sec) [ -19437.5756] [ 2623] [depth= 18] . ( 8 sec) [ -19420.7793] [ 2623] [depth= 23] . ( 9 sec) [ -18695.6594] [ 2604] [depth= 12] . ( 9 sec) [ -18695.2373] [ 2604] [depth= 1] . ( 9 sec) [ -18672.6883] [ 2600] [depth= 3] . ( 9 sec) [ -18671.1417] [ 2596] [depth= 2] . ( 9 sec) [ -18350.4214] [ 2582] [depth= 6] . ( 9 sec) [ -18336.3553] [ 2580] [depth= 1] . ( 9 sec) [ -18264.9594] [ 2491] [depth= 2] . ( 9 sec) [ -18258.6251] [ 2494] [depth= 1] . ( 9 sec) [ -18175.3517] [ 2527] [depth= 12] . ( 9 sec) [ -18163.8429] [ 2524] [depth= 1] . ( 9 sec) [ -18064.0117] [ 2498] [depth= 11] . ( 10 sec) [ -16813.2231] [ 2492] [depth= 6] . ( 10 sec) [ -16773.6104] [ 2488] [depth= 1] . ( 10 sec) [ -16493.4035] [ 2420] [depth= 7] . ( 10 sec) [ -16346.6595] [ 2352] [depth= 15] . ( 10 sec) [ -15542.6707] [ 2335] [depth= 2] . ( 10 sec) [ -15035.6170] [ 2206] [depth= 16] . ( 10 sec) [ -15005.9137] [ 2206] [depth= 1] . ( 10 sec) [ -14677.1928] [ 2161] [depth= 3] . ( 10 sec) [ -14438.6884] [ 2106] [depth= 10] . ( 10 sec) [ -14264.0163] [ 2105] [depth= 3] . ( 11 sec) [ -14240.3568] [ 2105] [depth= 1] . ( 11 sec) [ -13907.6580] [ 2079] [depth= 10] . ( 11 sec) [ -13549.0529] [ 2046] [depth= 15] . ( 11 sec) [ -13477.2321] [ 2047] [depth= 1] . ( 11 sec) [ -13241.5912] [ 2005] [depth= 21] . ( 11 sec) [ -13233.6299] [ 2005] [depth= 3] . ( 11 sec) [ -13226.8736] [ 2005] [depth= 1] . ( 11 sec) [ -13178.7637] [ 2005] [depth= 4] . ( 11 sec) [ -12799.8593] [ 1922] [depth= 13] . ( 11 sec) [ -12562.4132] [ 1897] [depth= 23] . ( 12 sec) [ -12561.8051] [ 1899] [depth= 20] . ( 12 sec) [ -12519.5220] [ 1871] [depth= 11] . ( 12 sec) [ -12514.9520] [ 1871] [depth= 2] . ( 12 sec) [ -12512.8058] [ 1870] [depth= 3] . ( 12 sec) [ -12512.7768] [ 1855] [depth= 1] . ( 12 sec) [ -12509.8340] [ 1854] [depth= 3] . ( 12 sec) [ -12508.2019] [ 1850] [depth= 7] . ( 12 sec) [ -12104.4033] [ 1827] [depth= 19] . ( 12 sec) [ -11961.0370] [ 1830] [depth= 1] . ( 12 sec) [ -11741.8533] [ 1787] [depth= 2] . ( 13 sec) [ -11624.0974] [ 1755] [depth= 15] . ( 13 sec) [ -11619.4347] [ 1755] [depth= 1] . ( 13 sec) [ -11386.7737] [ 1750] [depth= 5] . ( 13 sec) [ -11385.5760] [ 1750] [depth= 13] . ( 13 sec) [ -11385.5513] [ 1750] [depth= 2] . ( 13 sec) [ -11378.3711] [ 1733] [depth= 12] . ( 13 sec) [ -11370.3066] [ 1733] [depth= 8] . ( 13 sec) [ -11074.2925] [ 1642] [depth= 12] . ( 14 sec) [ -11072.0855] [ 1642] [depth= 1] . ( 14 sec) [ -10911.6652] [ 1618] [depth= 7] . ( 14 sec) [ -10897.7597] [ 1616] [depth= 7] . ( 14 sec) [ -10897.2308] [ 1616] [depth= 4] . ( 14 sec) [ -10896.0759] [ 1616] [depth= 2] . ( 14 sec) [ -10896.0432] [ 1616] [depth= 2] . ( 14 sec) [ -10535.7276] [ 1587] [depth= 7] . ( 14 sec) [ -10467.4422] [ 1584] [depth= 3] . ( 14 sec) [ -10425.4083] [ 1581] [depth= 1] . ( 14 sec) [ -10424.2912] [ 1580] [depth= 2] . ( 14 sec) [ -10413.5459] [ 1577] [depth= 1] . ( 15 sec) [ -10256.5279] [ 1541] [depth= 11] . ( 15 sec) [ -10244.6980] [ 1541] [depth= 3] . ( 15 sec) [ -10244.5339] [ 1541] [depth= 1] . ( 15 sec) [ -10244.5093] [ 1541] [depth= 4] . ( 15 sec) [ -10244.3110] [ 1541] [depth= 2] . ( 15 sec) [ -10244.1921] [ 1541] [depth= 6] . ( 15 sec) [ -10244.1717] [ 1541] [depth= 4] . ( 16 sec) [ -10174.6040] [ 1492] [depth= 7] . ( 16 sec) [ -10174.5250] [ 1492] [depth= 3] . ( 16 sec) [ -10120.1681] [ 1475] [depth= 17] . ( 16 sec) [ -10006.7203] [ 1463] [depth= 10] . ( 16 sec) [ -10006.6683] [ 1463] [depth= 1] . ( 17 sec) [ -10006.0414] [ 1466] [depth= 4] . ( 17 sec) [ -9336.9474] [ 1390] [depth= 3] . ( 17 sec) [ -9334.8239] [ 1390] [depth= 3] . ( 17 sec) [ -9280.1582] [ 1370] [depth= 9] . ( 17 sec) [ -9280.1346] [ 1370] [depth= 1] . ( 17 sec) [ -9277.9136] [ 1370] [depth= 3] . ( 17 sec) [ -9277.7010] [ 1370] [depth= 16] . ( 17 sec) [ -9125.1999] [ 1350] [depth= 6] . ( 17 sec) [ -8917.6347] [ 1318] [depth= 3] . ( 17 sec) [ -8836.2180] [ 1318] [depth= 1] . ( 18 sec) [ -8836.0612] [ 1318] [depth= 2] . ( 18 sec) [ -8830.9264] [ 1318] [depth= 2] . ( 18 sec) [ -8818.1411] [ 1318] [depth= 2] . ( 18 sec) [ -8813.9255] [ 1301] [depth= 6] . ( 19 sec) [ -8720.4679] [ 1275] [depth= 7] . ( 19 sec) [ -8697.2280] [ 1256] [depth= 6] . ( 19 sec) [ -8464.7776] [ 1193] [depth= 9] . ( 20 sec) [ -8464.7422] [ 1193] [depth= 2] . ( 20 sec) [ -8464.0850] [ 1193] [depth= 2] . ( 20 sec) [ -8445.9715] [ 1181] [depth= 3] . ( 20 sec) [ -8348.8190] [ 1167] [depth= 1] . ( 20 sec) [ -8220.9123] [ 1126] [depth= 1] . ( 20 sec) [ -8209.0222] [ 1118] [depth= 1] . ( 20 sec) [ -8201.7440] [ 1118] [depth= 1] . ( 20 sec) [ -8175.9527] [ 1118] [depth= 4] . ( 20 sec) [ -8175.8693] [ 1118] [depth= 1] . ( 20 sec) [ -8175.5560] [ 1118] [depth= 4] . ( 20 sec) [ -8175.4992] [ 1118] [depth= 3] . ( 21 sec) [ -8175.4827] [ 1118] [depth= 4] . ( 21 sec) [ -8174.3841] [ 1118] [depth= 5] . ( 21 sec) [ -8166.7979] [ 1117] [depth= 4] . ( 21 sec) [ -8149.4143] [ 1116] [depth= 1] . ( 21 sec) [ -8127.4754] [ 1120] [depth= 2] . ( 22 sec) [ -8127.4509] [ 1120] [depth= 4] . ( 22 sec) [ -7924.1249] [ 1093] [depth= 8] . ( 22 sec) [ -7924.0534] [ 1093] [depth= 4] . ( 22 sec) [ -7924.0202] [ 1093] [depth= 2] . ( 23 sec) [ -7923.2480] [ 1093] [depth= 5] . ( 23 sec) [ -7852.3964] [ 1073] [depth= 1] . ( 23 sec) [ -7848.8477] [ 1072] [depth= 6] . ( 23 sec) [ -7798.5537] [ 1053] [depth= 6] . ( 23 sec) [ -7794.2409] [ 1049] [depth= 1] . ( 23 sec) [ -7678.3327] [ 1017] [depth= 1] . ( 23 sec) [ -7662.5137] [ 1010] [depth= 1] . ( 23 sec) [ -7654.6354] [ 1012] [depth= 1] . ( 24 sec) [ -7654.2166] [ 1012] [depth= 1] . ( 24 sec) [ -7564.5031] [ 1012] [depth= 2] . ( 24 sec) [ -7563.6812] [ 1012] [depth= 7] . ( 25 sec) [ -7461.2464] [Branch lengths ] . ( 26 sec) [ -7236.9651] [GTR parameters ] . ( 26 sec) [ -7177.0533] [Alpha ][ 0.250961] . ( 28 sec) [ -7175.5639] [ 1009] [depth= 1] . ( 29 sec) [ -7175.5088] [ 1009] [depth= 1] . ( 29 sec) [ -7131.9998] [ 992] [depth= 4] . ( 29 sec) [ -7128.6034] [ 991] [depth= 5] . ( 29 sec) [ -7128.5540] [ 953] [depth= 2] . ( 30 sec) [ -7128.5435] [ 953] [depth= 1] . ( 31 sec) [ -7059.5730] [ 912] [depth= 3] . ( 32 sec) [ -7059.5600] [ 912] [depth= 3] . ( 35 sec) [ -7045.7346] [ 918] [depth= 1] . ( 35 sec) [ -6984.1326] [ 904] [depth= 3] . ( 38 sec) [ -6978.3606] [ 903] [depth= 10] . ( 41 sec) [ -6978.2046] [ 904] [depth= 1] . ( 41 sec) [ -6978.1848] [ 904] [depth= 2] . ( 42 sec) [ -6963.9708] [ 902] [depth= 3] . ( 43 sec) [ -6958.7091] [ 897] [depth= 1] . ( 44 sec) [ -6957.7786] [ 898] [depth= 1] . ( 45 sec) [ -6957.6955] [ 898] [depth= 1] . ( 47 sec) [ -6951.4860] [ 908] [depth= 1] . ( 54 sec) [ -6949.4679] [ 907] [depth= 1] . ( 57 sec) [ -6948.0665] [ 906] [depth= 3] . ( 57 sec) [ -6937.1461] [ 895] [depth= 1] . ( 58 sec) [ -6937.1191] [ 895] [depth= 3] . ( 59 sec) [ -6937.0977] [ 895] [depth= 2] . ( 61 sec) [ -6937.0867] [ 895] [depth= 7] . ( 68 sec) [ -6935.4669] [ 896] [depth= 1] . ( 68 sec) [ -6910.7109] [ 887] [depth= 1] . ( 68 sec) [ -6909.5725] [ 883] [depth= 1] . ( 69 sec) [ -6909.5509] [ 883] [depth= 1] . ( 70 sec) [ -6900.2134] [Branch lengths ] . ( 75 sec) [ -6714.1879] [GTR parameters ] . ( 75 sec) [ -6711.5557] [Alpha ][ 0.204622] . ( 76 sec) [ -6711.3859] [ 886] [depth= 2] . ( 77 sec) [ -6710.9166] [ 886] [depth= 1] . ( 82 sec) [ -6710.9062] [ 886] [depth= 5] . ( 85 sec) [ -6710.8221] [ 886] [depth= 3] . ( 95 sec) [ -6710.3765] [ 887] [depth= 2] . ( 96 sec) [ -6710.3463] [ 887] [depth= 2] . ( 106 sec) [ -6709.4178] [ 889] [depth= 2] . ( 110 sec) [ -6709.3904] [ 889] [depth= 2] . ( 118 sec) [ -6708.8752] [ 892] [depth= 1] . ( 120 sec) [ -6704.3688] [Branch lengths ] . ( 123 sec) [ -6703.7481] [GTR parameters ] . ( 123 sec) [ -6703.7325] [Alpha ][ 0.201460] . ( 133 sec) [ -6703.7212] [ 892] [depth= 5] . ( 138 sec) [ -6703.7080] [ 891] [depth= 1] . ( 139 sec) [ -6703.3614] [ 888] [depth= 1] . ( 144 sec) [ -6703.3496] [ 889] [depth= 10] . ( 166 sec) [ -6701.1871] [Branch lengths ] . ( 169 sec) [ -6701.1703] [GTR parameters ] . ( 169 sec) [ -6701.1608] [Alpha ][ 0.203894] . ( 212 sec) [ -6701.0575] [Branch lengths ] . ( 275 sec) [ -6698.7854] [ 898] [depth= 1] . ( 276 sec) [ -6697.5325] [ 897] [depth= 1] . ( 279 sec) [ -6696.8979] [Branch lengths ] . ( 285 sec) [ -6696.8811] [GTR parameters ] . ( 285 sec) [ -6696.8763] [Alpha ][ 0.202130] . ( 292 sec) [ -6690.6740] [ 889] [depth= 1] . ( 352 sec) [ -6689.8227] [Branch lengths ] . ( 355 sec) [ -6689.8098] [GTR parameters ] . ( 356 sec) [ -6689.7898] [Alpha ][ 0.205692] . ( 422 sec) [ -6689.6728] [Branch lengths ] . ( 422 sec) [ -6689.6728] [Topology ] . ( 424 sec) [ -6689.6679] [Topology ] . ( 425 sec) [ -6689.6668] [Topology ] . ( 427 sec) [ -6689.6664] [Topology ] . ( 428 sec) [ -6689.6660] [GTR parameters ] . ( 428 sec) [ -6689.6660] [Alpha ][ 0.205898] . ( 428 sec) [ -6689.6660] [Topology ] . ( 429 sec) [ -6689.6657] [Topology ] . ( 431 sec) [ -6689.6651] [GTR parameters ] . ( 431 sec) [ -6689.6651] [Alpha ][ 0.206104] . Checking for NNIs, optimizing five branches... . ( 442 sec) [ -6689.6650] [Topology ] . Checking for NNIs, optimizing five branches... . ( 452 sec) [ -6689.6596] [Topology ] . Checking for NNIs, optimizing five branches... . ( 462 sec) [ -6689.6595] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6689.659497. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -7271.1166] [GTR parameters ] . ( 1 sec) [ -7211.7409] [Alpha ][ 0.500960] . ( 1 sec) [ -7211.7409] [Topology ] . ( 3 sec) [ -7160.8695] [Topology ] . ( 4 sec) [ -7154.3487] [Topology ] . ( 6 sec) [ -7153.3527] [Topology ] . ( 8 sec) [ -7153.1361] [Topology ] . ( 9 sec) [ -7153.0829] [Topology ] . ( 11 sec) [ -7153.0680] [Topology ] . ( 12 sec) [ -7153.0627] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -7153.0624] [Topology ] . ( 23 sec) [ -6779.6365] [GTR parameters ] . ( 23 sec) [ -6743.8588] [Alpha ][ 0.250961] . ( 23 sec) [ -6743.8588] [Topology ] . ( 24 sec) [ -6741.1234] [Topology ] . ( 26 sec) [ -6739.6027] [Topology ] . ( 27 sec) [ -6739.2739] [Topology ] . ( 29 sec) [ -6738.9728] [Topology ] . ( 30 sec) [ -6738.7325] [Topology ] . ( 31 sec) [ -6738.6617] [Topology ] . ( 33 sec) [ -6738.6343] [Topology ] . ( 34 sec) [ -6738.6228] [Topology ] . ( 35 sec) [ -6738.6179] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -6738.6022] [Topology ] . ( 51 sec) [ -6693.1323] [GTR parameters ] . ( 51 sec) [ -6690.7125] [Alpha ][ 0.206643] . ( 51 sec) [ -6690.7125] [Topology ] . ( 53 sec) [ -6690.0654] [Topology ] . ( 54 sec) [ -6689.9338] [Topology ] . ( 55 sec) [ -6689.8854] [Topology ] . ( 57 sec) [ -6689.8660] [Topology ] . ( 58 sec) [ -6689.8580] [Topology ] . ( 60 sec) [ -6689.8546] [Topology ] . Checking for NNIs, optimizing five branches... . ( 69 sec) [ -6689.8543] [Topology ] . ( 73 sec) [ -6689.7198] [GTR parameters ] . ( 73 sec) [ -6689.7187] [Alpha ][ 0.205782] . ( 73 sec) [ -6689.7187] [Topology ] . ( 75 sec) [ -6689.7127] [Topology ] . ( 76 sec) [ -6689.7105] [Topology ] . ( 77 sec) [ -6689.7096] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -6689.7095] [Topology ] . ( 88 sec) [ -6689.7092] [GTR parameters ] . ( 88 sec) [ -6689.7091] [Alpha ][ 0.206039] . ( 88 sec) [ -6689.7091] [Topology ] . ( 90 sec) [ -6689.7086] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 110 sec) [ -7271.1166] [GTR parameters ] . ( 110 sec) [ -7211.7409] [Alpha ][ 0.500960] . ( 110 sec) [ -7211.1362] [ 888] [depth= 1] . ( 110 sec) [ -7210.8001] [ 888] [depth= 1] . ( 111 sec) [ -7210.5133] [ 888] [depth= 3] . ( 111 sec) [ -7210.3174] [ 888] [depth= 2] . ( 111 sec) [ -7209.9139] [ 888] [depth= 2] . ( 112 sec) [ -7209.8287] [ 888] [depth= 3] . ( 112 sec) [ -7209.7725] [ 888] [depth= 1] . ( 112 sec) [ -7209.7412] [ 888] [depth= 3] . ( 112 sec) [ -7209.7265] [ 888] [depth= 1] . ( 113 sec) [ -7209.7034] [ 888] [depth= 2] . ( 114 sec) [ -7208.7158] [ 888] [depth= 1] . ( 114 sec) [ -7208.6945] [ 888] [depth= 1] . ( 114 sec) [ -7208.5133] [ 888] [depth= 1] . ( 114 sec) [ -7208.4151] [ 888] [depth= 1] . ( 114 sec) [ -7208.3997] [ 888] [depth= 1] . ( 114 sec) [ -7208.2465] [ 888] [depth= 2] . ( 115 sec) [ -7207.4561] [ 889] [depth= 1] . ( 116 sec) [ -7206.4516] [ 887] [depth= 1] . ( 116 sec) [ -7205.6860] [ 889] [depth= 1] . ( 116 sec) [ -7203.5849] [ 887] [depth= 1] . ( 116 sec) [ -7190.0457] [ 884] [depth= 1] . ( 117 sec) [ -7190.0119] [ 884] [depth= 1] . ( 117 sec) [ -7189.9991] [ 884] [depth= 1] . ( 117 sec) [ -7189.8583] [ 884] [depth= 1] . ( 117 sec) [ -7188.2574] [ 884] [depth= 2] . ( 117 sec) [ -7188.0455] [ 885] [depth= 3] . ( 118 sec) [ -7185.7992] [ 885] [depth= 3] . ( 118 sec) [ -7183.8886] [ 885] [depth= 3] . ( 118 sec) [ -7181.8647] [ 884] [depth= 3] . ( 118 sec) [ -7177.9590] [ 884] [depth= 1] . ( 118 sec) [ -7176.6290] [ 885] [depth= 2] . ( 118 sec) [ -7176.5645] [ 885] [depth= 3] . ( 118 sec) [ -7176.5506] [ 885] [depth= 2] . ( 119 sec) [ -7176.4118] [ 885] [depth= 1] . ( 119 sec) [ -7176.1060] [ 885] [depth= 1] . ( 119 sec) [ -7176.0425] [ 885] [depth= 7] . ( 119 sec) [ -7175.8736] [ 885] [depth= 6] . ( 119 sec) [ -7175.6326] [ 885] [depth= 2] . ( 119 sec) [ -7175.3919] [ 885] [depth= 6] . ( 119 sec) [ -7175.2108] [ 885] [depth= 5] . ( 120 sec) [ -7175.1302] [ 885] [depth= 4] . ( 120 sec) [ -7175.0121] [ 885] [depth= 4] . ( 121 sec) [ -7174.9287] [ 885] [depth= 1] . ( 123 sec) [ -7174.6081] [ 885] [depth= 1] . ( 123 sec) [ -7174.3594] [ 885] [depth= 1] . ( 125 sec) [ -7174.1200] [ 885] [depth= 2] . ( 125 sec) [ -7174.1077] [ 885] [depth= 4] . ( 126 sec) [ -7173.9541] [ 885] [depth= 2] . ( 130 sec) [ -7172.2775] [ 884] [depth= 4] . ( 132 sec) [ -7172.2667] [ 884] [depth= 2] . ( 134 sec) [ -7171.5736] [ 884] [depth= 1] . ( 134 sec) [ -7170.9054] [ 883] [depth= 3] . ( 135 sec) [ -7170.8902] [ 883] [depth= 1] . ( 135 sec) [ -7170.8767] [ 883] [depth= 1] . ( 135 sec) [ -7170.8318] [ 883] [depth= 2] . ( 135 sec) [ -7170.8179] [ 883] [depth= 1] . ( 136 sec) [ -7170.7352] [ 884] [depth= 1] . ( 136 sec) [ -7170.6708] [ 884] [depth= 1] . ( 137 sec) [ -7170.6602] [ 884] [depth= 1] . ( 146 sec) [ -7155.7635] [Branch lengths ] . ( 147 sec) [ -6772.7925] [GTR parameters ] . ( 147 sec) [ -6736.3579] [Alpha ][ 0.250961] . ( 151 sec) [ -6736.2701] [ 884] [depth= 2] . ( 152 sec) [ -6736.2579] [ 883] [depth= 1] . ( 152 sec) [ -6736.2305] [ 884] [depth= 1] . ( 153 sec) [ -6736.1014] [ 886] [depth= 1] . ( 153 sec) [ -6736.0379] [ 886] [depth= 1] . ( 153 sec) [ -6733.4532] [ 890] [depth= 1] . ( 192 sec) [ -6729.9131] [Branch lengths ] . ( 197 sec) [ -6694.7153] [GTR parameters ] . ( 197 sec) [ -6692.2429] [Alpha ][ 0.206118] . ( 202 sec) [ -6691.2192] [ 889] [depth= 1] . ( 241 sec) [ -6690.0092] [Branch lengths ] . ( 244 sec) [ -6689.8642] [GTR parameters ] . ( 244 sec) [ -6689.8635] [Alpha ][ 0.205413] . ( 275 sec) [ -6689.8496] [ 888] [depth= 1] . ( 277 sec) [ -6689.8367] [ 889] [depth= 2] . ( 287 sec) [ -6689.6848] [Branch lengths ] . ( 291 sec) [ -6689.6763] [GTR parameters ] . ( 291 sec) [ -6689.6762] [Alpha ][ 0.205699] . ( 358 sec) [ -6689.6603] [Branch lengths ] . ( 359 sec) [ -6689.6603] [Topology ] . ( 360 sec) [ -6689.6592] [Topology ] . ( 361 sec) [ -6689.6589] [Topology ] . ( 364 sec) [ -6689.6587] [GTR parameters ] . ( 364 sec) [ -6689.6586] [Alpha ][ 0.205936] . ( 364 sec) [ -6689.6586] [Topology ] . ( 365 sec) [ -6689.6584] [Topology ] . ( 366 sec) [ -6689.6584] [GTR parameters ] . ( 366 sec) [ -6689.6584] [Alpha ][ 0.205936] . Checking for NNIs, optimizing five branches... . ( 376 sec) [ -6689.6583] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6689.708590 . Log likelihood obtained after SPR moves : -6689.658291 . Log likelihood of the current tree: -6689.658291. . Printing the most likely tree in file 'nucleic_M2928_81x1651_2006.phy_phyml_tree.txt'... . Best log likelihood : -6689.658291 . Time used 0h6m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1900.76user 0.00system 32:14.52elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps