.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data94.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... . 404 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . [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)... . ( 0 sec) [ -27179.8187] [GTR parameters ] . ( 1 sec) [ -26675.3154] [Alpha ][ 0.500960] . ( 1 sec) [ -24988.1168] [ 4267] [depth= 8] . ( 1 sec) [ -21229.7044] [ 4263] [depth= 4] . ( 1 sec) [ -20785.8405] [ 4247] [depth= 4] . ( 1 sec) [ -20728.8186] [ 4241] [depth= 6] . ( 1 sec) [ -20712.5646] [ 4235] [depth= 1] . ( 1 sec) [ -20679.3864] [ 4233] [depth= 1] . ( 1 sec) [ -20246.0670] [ 4213] [depth= 4] . ( 1 sec) [ -20175.1144] [ 4125] [depth= 6] . ( 1 sec) [ -19625.3574] [ 4094] [depth= 16] . ( 1 sec) [ -19107.2452] [ 3925] [depth= 6] . ( 1 sec) [ -18989.9361] [ 3954] [depth= 16] . ( 1 sec) [ -18644.7616] [ 3845] [depth= 15] . ( 1 sec) [ -18578.0637] [ 3844] [depth= 3] . ( 1 sec) [ -18429.4933] [ 3843] [depth= 2] . ( 1 sec) [ -18209.8529] [ 3753] [depth= 1] . ( 1 sec) [ -18080.8711] [ 3742] [depth= 11] . ( 1 sec) [ -17963.7409] [ 3639] [depth= 16] . ( 1 sec) [ -17926.8138] [ 3642] [depth= 1] . ( 1 sec) [ -17863.3059] [ 3621] [depth= 2] . ( 1 sec) [ -17732.8500] [ 3577] [depth= 5] . ( 1 sec) [ -17354.4809] [ 3431] [depth= 5] . ( 1 sec) [ -17301.8751] [ 3431] [depth= 2] . ( 2 sec) [ -17049.9139] [ 3338] [depth= 6] . ( 2 sec) [ -17015.3492] [ 3317] [depth= 1] . ( 2 sec) [ -16873.6601] [ 3280] [depth= 11] . ( 2 sec) [ -16268.7227] [ 3137] [depth= 7] . ( 2 sec) [ -16081.8802] [ 3109] [depth= 2] . ( 2 sec) [ -16070.8893] [ 3109] [depth= 9] . ( 2 sec) [ -13761.9250] [ 3100] [depth= 15] . ( 2 sec) [ -13722.4916] [ 3111] [depth= 1] . ( 2 sec) [ -13624.8108] [ 3088] [depth= 14] . ( 2 sec) [ -13516.0893] [ 3052] [depth= 1] . ( 2 sec) [ -12897.5808] [ 2869] [depth= 12] . ( 2 sec) [ -12739.0526] [ 2730] [depth= 9] . ( 2 sec) [ -12546.5102] [ 2687] [depth= 1] . ( 2 sec) [ -12380.1466] [ 2621] [depth= 7] . ( 2 sec) [ -12120.2761] [ 2618] [depth= 4] . ( 2 sec) [ -11978.4084] [ 2588] [depth= 11] . ( 2 sec) [ -11833.7335] [ 2593] [depth= 1] . ( 2 sec) [ -11817.8507] [ 2588] [depth= 1] . ( 2 sec) [ -11714.8126] [ 2570] [depth= 12] . ( 2 sec) [ -11647.2255] [ 2561] [depth= 1] . ( 2 sec) [ -11591.3407] [ 2551] [depth= 3] . ( 3 sec) [ -11401.0809] [ 2519] [depth= 5] . ( 3 sec) [ -11244.6559] [ 2513] [depth= 1] . ( 3 sec) [ -11183.3330] [ 2505] [depth= 3] . ( 3 sec) [ -10388.9950] [ 2506] [depth= 1] . ( 3 sec) [ -10387.4110] [ 2439] [depth= 1] . ( 3 sec) [ -10381.8386] [ 2386] [depth= 1] . ( 3 sec) [ -10336.3194] [ 2382] [depth= 1] . ( 3 sec) [ -10313.8395] [ 2312] [depth= 4] . ( 3 sec) [ -10187.5076] [ 2276] [depth= 2] . ( 3 sec) [ -9972.4269] [ 2213] [depth= 1] . ( 3 sec) [ -9929.9587] [ 2209] [depth= 1] . ( 3 sec) [ -9917.1183] [ 2212] [depth= 1] . ( 3 sec) [ -9621.6506] [ 2119] [depth= 2] . ( 3 sec) [ -9521.3551] [ 2117] [depth= 2] . ( 3 sec) [ -9494.4892] [ 2118] [depth= 1] . ( 3 sec) [ -9489.0217] [ 2109] [depth= 2] . ( 3 sec) [ -9431.0536] [ 2090] [depth= 2] . ( 3 sec) [ -9419.5201] [ 2112] [depth= 1] . ( 3 sec) [ -9417.0181] [ 2123] [depth= 1] . ( 3 sec) [ -9192.6812] [ 2038] [depth= 7] . ( 3 sec) [ -9179.8778] [ 2035] [depth= 2] . ( 4 sec) [ -8924.6179] [ 1898] [depth= 9] . ( 4 sec) [ -8837.6370] [ 1878] [depth= 3] . ( 4 sec) [ -8833.8923] [ 1878] [depth= 1] . ( 4 sec) [ -8694.6061] [ 1829] [depth= 2] . ( 4 sec) [ -8682.0518] [ 1863] [depth= 2] . ( 4 sec) [ -8565.8084] [ 1835] [depth= 1] . ( 4 sec) [ -8562.0533] [ 1839] [depth= 1] . ( 4 sec) [ -8560.4530] [ 1851] [depth= 1] . ( 4 sec) [ -8515.6035] [ 1854] [depth= 3] . ( 4 sec) [ -8515.2508] [ 1823] [depth= 2] . ( 4 sec) [ -8493.0649] [ 1833] [depth= 1] . ( 4 sec) [ -8489.2032] [ 1836] [depth= 1] . ( 4 sec) [ -8487.9613] [ 1857] [depth= 1] . ( 4 sec) [ -8482.4634] [ 1851] [depth= 2] . ( 4 sec) [ -8382.6494] [Branch lengths ] . ( 5 sec) [ -8378.5672] [GTR parameters ] . ( 5 sec) [ -8352.3129] [Alpha ][ 0.857244] . ( 5 sec) [ -8351.9095] [ 1850] [depth= 1] . ( 6 sec) [ -8350.9801] [ 1849] [depth= 1] . ( 6 sec) [ -8350.8800] [ 1846] [depth= 1] . ( 6 sec) [ -8337.9550] [ 1843] [depth= 6] . ( 6 sec) [ -8308.9040] [ 1819] [depth= 1] . ( 6 sec) [ -8308.8749] [ 1820] [depth= 1] . ( 6 sec) [ -8308.5101] [ 1823] [depth= 1] . ( 6 sec) [ -8308.2654] [ 1826] [depth= 1] . ( 6 sec) [ -8303.8934] [ 1798] [depth= 3] . ( 6 sec) [ -8264.2161] [ 1758] [depth= 1] . ( 6 sec) [ -8264.1174] [ 1758] [depth= 1] . ( 6 sec) [ -8257.2554] [ 1740] [depth= 1] . ( 6 sec) [ -8252.7117] [ 1741] [depth= 2] . ( 7 sec) [ -8251.7408] [ 1736] [depth= 2] . ( 7 sec) [ -8229.5632] [ 1736] [depth= 2] . ( 7 sec) [ -8220.1601] [ 1729] [depth= 2] . ( 7 sec) [ -8212.0925] [ 1725] [depth= 2] . ( 7 sec) [ -8167.2723] [ 1699] [depth= 1] . ( 7 sec) [ -8159.2656] [ 1692] [depth= 1] . ( 7 sec) [ -8154.1578] [ 1689] [depth= 2] . ( 7 sec) [ -8153.9091] [ 1695] [depth= 1] . ( 8 sec) [ -8153.3172] [ 1695] [depth= 1] . ( 8 sec) [ -8149.7095] [ 1689] [depth= 1] . ( 8 sec) [ -8148.9929] [ 1687] [depth= 1] . ( 8 sec) [ -8148.8039] [ 1692] [depth= 1] . ( 8 sec) [ -8148.3108] [ 1692] [depth= 1] . ( 8 sec) [ -8147.9986] [ 1694] [depth= 2] . ( 8 sec) [ -8144.1880] [ 1698] [depth= 1] . ( 9 sec) [ -8144.1063] [ 1694] [depth= 2] . ( 9 sec) [ -8142.4359] [ 1698] [depth= 3] . ( 9 sec) [ -8131.9744] [Branch lengths ] . ( 10 sec) [ -8131.7459] [GTR parameters ] . ( 10 sec) [ -8130.3256] [Alpha ][ 0.979492] . ( 13 sec) [ -8129.6991] [ 1700] [depth= 2] . ( 13 sec) [ -8128.7967] [Branch lengths ] . ( 14 sec) [ -8128.7956] [GTR parameters ] . ( 14 sec) [ -8128.7830] [Alpha ][ 0.992262] . ( 18 sec) [ -8128.7042] [Branch lengths ] . ( 24 sec) [ -8128.5647] [ 1693] [depth= 1] . ( 39 sec) [ -8128.4424] [Branch lengths ] . ( 40 sec) [ -8128.4418] [GTR parameters ] . ( 40 sec) [ -8128.4404] [Alpha ][ 0.996379] . ( 40 sec) [ -8128.4404] [Topology ] . ( 40 sec) [ -8128.4346] [Topology ] . ( 41 sec) [ -8128.4329] [Topology ] . ( 42 sec) [ -8128.4323] [Topology ] . ( 42 sec) [ -8128.4323] [GTR parameters ] . ( 42 sec) [ -8128.4323] [Alpha ][ 0.996379] . ( 42 sec) [ -8128.4323] [Topology ] . ( 43 sec) [ -8128.4320] [Topology ] . ( 43 sec) [ -8128.4320] [GTR parameters ] . ( 43 sec) [ -8128.4320] [Alpha ][ 0.996379] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8128.431986. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20435.6867] [GTR parameters ] . ( 1 sec) [ -19937.0237] [Alpha ][ 0.500960] . ( 1 sec) [ -19121.1507] [ 4375] [depth= 3] . ( 1 sec) [ -18738.3559] [ 4291] [depth= 3] . ( 1 sec) [ -18359.0619] [ 4274] [depth= 4] . ( 1 sec) [ -18135.5175] [ 4278] [depth= 5] . ( 1 sec) [ -18056.3131] [ 4144] [depth= 6] . ( 1 sec) [ -17711.4647] [ 4137] [depth= 8] . ( 1 sec) [ -17703.1932] [ 4087] [depth= 1] . ( 1 sec) [ -17585.3296] [ 4076] [depth= 4] . ( 1 sec) [ -17565.3835] [ 4054] [depth= 1] . ( 1 sec) [ -17088.5006] [ 4040] [depth= 2] . ( 1 sec) [ -17073.4996] [ 4038] [depth= 3] . ( 1 sec) [ -16658.1494] [ 3993] [depth= 5] . ( 1 sec) [ -16345.5647] [ 3860] [depth= 7] . ( 1 sec) [ -16132.4615] [ 3847] [depth= 8] . ( 1 sec) [ -15445.2691] [ 3711] [depth= 11] . ( 1 sec) [ -15362.6545] [ 3667] [depth= 2] . ( 1 sec) [ -15161.8332] [ 3572] [depth= 4] . ( 1 sec) [ -15017.0818] [ 3564] [depth= 2] . ( 1 sec) [ -14957.5067] [ 3574] [depth= 11] . ( 1 sec) [ -14935.7002] [ 3565] [depth= 1] . ( 1 sec) [ -14387.4259] [ 3487] [depth= 8] . ( 2 sec) [ -14338.0972] [ 3422] [depth= 1] . ( 2 sec) [ -13962.3686] [ 3285] [depth= 10] . ( 2 sec) [ -13572.7744] [ 3158] [depth= 6] . ( 2 sec) [ -13521.7008] [ 3152] [depth= 2] . ( 2 sec) [ -13489.3421] [ 3117] [depth= 11] . ( 2 sec) [ -13434.5622] [ 3121] [depth= 1] . ( 2 sec) [ -13098.7867] [ 2975] [depth= 4] . ( 2 sec) [ -12949.3010] [ 2976] [depth= 9] . ( 2 sec) [ -12936.3299] [ 2973] [depth= 1] . ( 2 sec) [ -12873.2061] [ 2885] [depth= 1] . ( 2 sec) [ -12738.1943] [ 2804] [depth= 9] . ( 2 sec) [ -12619.3144] [ 2809] [depth= 10] . ( 2 sec) [ -12522.0548] [ 2811] [depth= 9] . ( 2 sec) [ -12420.3359] [ 2779] [depth= 8] . ( 2 sec) [ -12155.2170] [ 2764] [depth= 3] . ( 2 sec) [ -11934.8871] [ 2754] [depth= 11] . ( 2 sec) [ -11706.0032] [ 2693] [depth= 5] . ( 2 sec) [ -11440.7367] [ 2624] [depth= 6] . ( 2 sec) [ -11227.3951] [ 2559] [depth= 6] . ( 2 sec) [ -11154.4417] [ 2550] [depth= 1] . ( 2 sec) [ -11127.0960] [ 2529] [depth= 2] . ( 3 sec) [ -11062.8944] [ 2530] [depth= 14] . ( 3 sec) [ -11013.5984] [ 2531] [depth= 2] . ( 3 sec) [ -10668.4124] [ 2390] [depth= 6] . ( 3 sec) [ -10590.6813] [ 2376] [depth= 4] . ( 3 sec) [ -10556.8374] [ 2371] [depth= 1] . ( 3 sec) [ -10533.6838] [ 2294] [depth= 1] . ( 3 sec) [ -10501.0072] [ 2256] [depth= 3] . ( 3 sec) [ -10366.8229] [ 2173] [depth= 1] . ( 3 sec) [ -10245.8393] [ 2149] [depth= 3] . ( 3 sec) [ -9680.6541] [ 2177] [depth= 1] . ( 3 sec) [ -9633.1061] [ 2149] [depth= 1] . ( 3 sec) [ -9274.1566] [ 2026] [depth= 2] . ( 3 sec) [ -9243.6651] [ 2028] [depth= 1] . ( 3 sec) [ -9063.5236] [ 1934] [depth= 4] . ( 3 sec) [ -9045.5239] [ 1925] [depth= 2] . ( 3 sec) [ -8911.5582] [ 1864] [depth= 1] . ( 3 sec) [ -8873.4530] [ 1869] [depth= 1] . ( 3 sec) [ -8859.5172] [ 1870] [depth= 1] . ( 4 sec) [ -8849.3514] [ 1858] [depth= 4] . ( 4 sec) [ -8748.8780] [ 1808] [depth= 8] . ( 4 sec) [ -8671.2702] [ 1804] [depth= 2] . ( 4 sec) [ -8669.6468] [ 1804] [depth= 1] . ( 4 sec) [ -8647.5387] [ 1786] [depth= 2] . ( 4 sec) [ -8622.4970] [ 1788] [depth= 3] . ( 4 sec) [ -8554.2296] [ 1761] [depth= 1] . ( 4 sec) [ -8550.6379] [ 1755] [depth= 1] . ( 4 sec) [ -8543.3745] [ 1753] [depth= 3] . ( 4 sec) [ -8501.0329] [ 1714] [depth= 3] . ( 4 sec) [ -8488.5502] [ 1710] [depth= 1] . ( 4 sec) [ -8466.4933] [ 1708] [depth= 1] . ( 5 sec) [ -8373.0926] [Branch lengths ] . ( 5 sec) [ -8370.9580] [GTR parameters ] . ( 5 sec) [ -8340.4108] [Alpha ][ 0.896251] . ( 6 sec) [ -8340.3502] [ 1708] [depth= 1] . ( 6 sec) [ -8332.8274] [ 1704] [depth= 2] . ( 6 sec) [ -8332.7172] [ 1704] [depth= 1] . ( 7 sec) [ -8332.2944] [ 1704] [depth= 1] . ( 7 sec) [ -8293.4100] [ 1681] [depth= 3] . ( 7 sec) [ -8292.1968] [ 1686] [depth= 1] . ( 7 sec) [ -8175.1417] [ 1686] [depth= 2] . ( 7 sec) [ -8174.8110] [ 1689] [depth= 1] . ( 8 sec) [ -8174.7235] [ 1690] [depth= 1] . ( 8 sec) [ -8174.3311] [ 1690] [depth= 1] . ( 8 sec) [ -8174.3211] [ 1690] [depth= 1] . ( 8 sec) [ -8174.2434] [ 1694] [depth= 1] . ( 9 sec) [ -8174.1741] [ 1689] [depth= 1] . ( 9 sec) [ -8168.1355] [Branch lengths ] . ( 9 sec) [ -8167.9880] [GTR parameters ] . ( 9 sec) [ -8167.4291] [Alpha ][ 0.973777] . ( 10 sec) [ -8167.3966] [ 1693] [depth= 2] . ( 11 sec) [ -8167.2772] [ 1691] [depth= 1] . ( 11 sec) [ -8167.2589] [ 1693] [depth= 2] . ( 12 sec) [ -8167.0083] [ 1690] [depth= 1] . ( 12 sec) [ -8166.2544] [ 1690] [depth= 2] . ( 13 sec) [ -8165.4973] [Branch lengths ] . ( 13 sec) [ -8165.4954] [GTR parameters ] . ( 13 sec) [ -8165.4912] [Alpha ][ 0.980882] . ( 15 sec) [ -8165.4628] [ 1690] [depth= 1] . ( 16 sec) [ -8165.4273] [ 1691] [depth= 1] . ( 16 sec) [ -8164.9178] [ 1694] [depth= 1] . ( 17 sec) [ -8162.0338] [Branch lengths ] . ( 17 sec) [ -8162.0322] [GTR parameters ] . ( 17 sec) [ -8162.0320] [Alpha ][ 0.982658] . ( 18 sec) [ -8161.1063] [ 1697] [depth= 4] . ( 19 sec) [ -8161.0695] [ 1695] [depth= 1] . ( 20 sec) [ -8161.0253] [ 1697] [depth= 1] . ( 21 sec) [ -8145.4392] [Branch lengths ] . ( 21 sec) [ -8145.4025] [GTR parameters ] . ( 21 sec) [ -8145.3943] [Alpha ][ 0.992876] . ( 23 sec) [ -8144.7280] [ 1696] [depth= 1] . ( 25 sec) [ -8144.5817] [ 1695] [depth= 1] . ( 25 sec) [ -8129.8088] [Branch lengths ] . ( 26 sec) [ -8129.8046] [GTR parameters ] . ( 26 sec) [ -8129.7995] [Alpha ][ 1.000980] . ( 27 sec) [ -8129.5266] [ 1697] [depth= 1] . ( 30 sec) [ -8128.7135] [Branch lengths ] . ( 30 sec) [ -8128.7132] [GTR parameters ] . ( 30 sec) [ -8128.7124] [Alpha ][ 0.997537] . ( 34 sec) [ -8128.6952] [Branch lengths ] . ( 56 sec) [ -8128.6928] [Branch lengths ] . ( 56 sec) [ -8128.6928] [Topology ] . ( 57 sec) [ -8128.6926] [Topology ] . ( 57 sec) [ -8128.6926] [GTR parameters ] . ( 57 sec) [ -8128.6924] [Alpha ][ 0.995757] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -8128.4332] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8128.433171. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -26363.8001] [GTR parameters ] . ( 0 sec) [ -25887.7013] [Alpha ][ 0.500960] . ( 0 sec) [ -25444.3737] [ 4394] [depth= 8] . ( 1 sec) [ -24960.3073] [ 4304] [depth= 8] . ( 1 sec) [ -24480.1880] [ 4261] [depth= 2] . ( 1 sec) [ -24036.1921] [ 4261] [depth= 2] . ( 1 sec) [ -24014.1827] [ 4183] [depth= 3] . ( 1 sec) [ -23950.5690] [ 4181] [depth= 2] . ( 1 sec) [ -23900.4549] [ 4169] [depth= 2] . ( 1 sec) [ -23754.2688] [ 4148] [depth= 2] . ( 1 sec) [ -23727.0500] [ 4136] [depth= 1] . ( 1 sec) [ -23370.3320] [ 3962] [depth= 9] . ( 1 sec) [ -23229.1086] [ 3946] [depth= 9] . ( 1 sec) [ -23199.1428] [ 3881] [depth= 2] . ( 1 sec) [ -23116.0913] [ 3879] [depth= 1] . ( 1 sec) [ -23113.9037] [ 3854] [depth= 9] . ( 1 sec) [ -20738.1699] [ 3850] [depth= 7] . ( 1 sec) [ -20649.4563] [ 3845] [depth= 2] . ( 1 sec) [ -20261.4165] [ 3811] [depth= 9] . ( 1 sec) [ -20195.1726] [ 3804] [depth= 1] . ( 1 sec) [ -16298.6439] [ 3710] [depth= 9] . ( 1 sec) [ -15879.6217] [ 3556] [depth= 7] . ( 1 sec) [ -15633.3579] [ 3590] [depth= 1] . ( 1 sec) [ -15543.2611] [ 3587] [depth= 3] . ( 1 sec) [ -15372.4417] [ 3572] [depth= 1] . ( 1 sec) [ -14530.1103] [ 3497] [depth= 8] . ( 2 sec) [ -14356.5679] [ 3396] [depth= 8] . ( 2 sec) [ -14238.5286] [ 3399] [depth= 7] . ( 2 sec) [ -13861.9471] [ 3231] [depth= 9] . ( 2 sec) [ -13761.5092] [ 3226] [depth= 9] . ( 2 sec) [ -13553.2894] [ 3096] [depth= 10] . ( 2 sec) [ -13475.7139] [ 3078] [depth= 1] . ( 2 sec) [ -13048.2815] [ 2941] [depth= 7] . ( 2 sec) [ -13046.0828] [ 2947] [depth= 2] . ( 2 sec) [ -12767.6131] [ 2829] [depth= 6] . ( 2 sec) [ -12763.4189] [ 2786] [depth= 10] . ( 2 sec) [ -12200.0122] [ 2632] [depth= 11] . ( 2 sec) [ -12152.4545] [ 2637] [depth= 1] . ( 2 sec) [ -11856.0540] [ 2549] [depth= 5] . ( 2 sec) [ -11850.3886] [ 2539] [depth= 1] . ( 2 sec) [ -11816.0712] [ 2584] [depth= 1] . ( 2 sec) [ -11805.6179] [ 2595] [depth= 1] . ( 2 sec) [ -11437.1051] [ 2433] [depth= 8] . ( 2 sec) [ -11432.2981] [ 2432] [depth= 2] . ( 2 sec) [ -11397.2219] [ 2422] [depth= 1] . ( 2 sec) [ -11001.0156] [ 2315] [depth= 3] . ( 2 sec) [ -10468.3695] [ 2305] [depth= 2] . ( 2 sec) [ -10456.1508] [ 2287] [depth= 2] . ( 3 sec) [ -10218.0830] [ 2207] [depth= 1] . ( 3 sec) [ -10212.9271] [ 2212] [depth= 1] . ( 3 sec) [ -10158.1842] [ 2190] [depth= 1] . ( 3 sec) [ -10099.8485] [ 2222] [depth= 5] . ( 3 sec) [ -9947.0575] [ 2122] [depth= 15] . ( 3 sec) [ -9907.6629] [ 2117] [depth= 4] . ( 3 sec) [ -9891.7017] [ 2138] [depth= 3] . ( 3 sec) [ -9866.6028] [ 2103] [depth= 3] . ( 3 sec) [ -9785.9079] [ 2004] [depth= 4] . ( 3 sec) [ -9780.6232] [ 2000] [depth= 2] . ( 3 sec) [ -9710.1961] [ 1995] [depth= 2] . ( 3 sec) [ -9606.0661] [ 1972] [depth= 4] . ( 3 sec) [ -9564.2515] [ 1958] [depth= 3] . ( 3 sec) [ -9426.5244] [ 1953] [depth= 1] . ( 3 sec) [ -9414.2651] [ 1913] [depth= 6] . ( 3 sec) [ -9412.0986] [ 1910] [depth= 1] . ( 3 sec) [ -9256.7164] [ 1914] [depth= 1] . ( 3 sec) [ -9143.0929] [ 1815] [depth= 5] . ( 3 sec) [ -8876.5636] [ 1772] [depth= 2] . ( 3 sec) [ -8841.1015] [ 1791] [depth= 3] . ( 3 sec) [ -8799.8497] [ 1836] [depth= 4] . ( 3 sec) [ -8793.8845] [ 1828] [depth= 1] . ( 3 sec) [ -8779.0566] [ 1823] [depth= 1] . ( 4 sec) [ -8739.1048] [ 1805] [depth= 3] . ( 4 sec) [ -8695.5006] [ 1795] [depth= 3] . ( 4 sec) [ -8637.3724] [ 1790] [depth= 3] . ( 4 sec) [ -8635.7308] [ 1791] [depth= 1] . ( 4 sec) [ -8627.7404] [ 1777] [depth= 3] . ( 4 sec) [ -8624.6483] [ 1777] [depth= 1] . ( 4 sec) [ -8575.8363] [ 1761] [depth= 1] . ( 4 sec) [ -8568.4923] [ 1760] [depth= 1] . ( 4 sec) [ -8562.6577] [ 1757] [depth= 2] . ( 4 sec) [ -8555.7898] [ 1756] [depth= 1] . ( 4 sec) [ -8554.3893] [ 1757] [depth= 1] . ( 4 sec) [ -8550.0902] [ 1760] [depth= 1] . ( 4 sec) [ -8548.3597] [ 1762] [depth= 1] . ( 4 sec) [ -8529.2328] [ 1758] [depth= 1] . ( 5 sec) [ -8352.4109] [Branch lengths ] . ( 5 sec) [ -8350.0755] [GTR parameters ] . ( 5 sec) [ -8314.2744] [Alpha ][ 0.940198] . ( 6 sec) [ -8314.1668] [ 1759] [depth= 1] . ( 6 sec) [ -8314.1547] [ 1759] [depth= 1] . ( 6 sec) [ -8177.4776] [ 1698] [depth= 2] . ( 6 sec) [ -8173.9622] [ 1699] [depth= 1] . ( 7 sec) [ -8170.6229] [ 1700] [depth= 1] . ( 7 sec) [ -8159.2023] [ 1699] [depth= 1] . ( 7 sec) [ -8158.6297] [ 1704] [depth= 1] . ( 7 sec) [ -8158.1257] [ 1706] [depth= 1] . ( 7 sec) [ -8151.3566] [ 1700] [depth= 2] . ( 8 sec) [ -8150.9626] [ 1699] [depth= 2] . ( 8 sec) [ -8150.4327] [ 1694] [depth= 2] . ( 8 sec) [ -8150.3459] [ 1694] [depth= 1] . ( 9 sec) [ -8150.2366] [ 1696] [depth= 1] . ( 9 sec) [ -8150.2152] [ 1695] [depth= 1] . ( 9 sec) [ -8139.0631] [Branch lengths ] . ( 9 sec) [ -8138.9777] [GTR parameters ] . ( 9 sec) [ -8138.7542] [Alpha ][ 0.991231] . ( 12 sec) [ -8137.9544] [ 1697] [depth= 2] . ( 12 sec) [ -8137.4524] [ 1699] [depth= 1] . ( 13 sec) [ -8137.4152] [ 1697] [depth= 1] . ( 13 sec) [ -8131.9264] [Branch lengths ] . ( 13 sec) [ -8131.9184] [GTR parameters ] . ( 14 sec) [ -8131.9172] [Alpha ][ 0.995096] . ( 16 sec) [ -8131.8184] [ 1695] [depth= 1] . ( 17 sec) [ -8131.2087] [Branch lengths ] . ( 18 sec) [ -8131.2078] [GTR parameters ] . ( 18 sec) [ -8131.2077] [Alpha ][ 0.996305] . ( 29 sec) [ -8129.8893] [ 1701] [depth= 4] . ( 39 sec) [ -8128.8666] [Branch lengths ] . ( 39 sec) [ -8128.8491] [GTR parameters ] . ( 39 sec) [ -8128.8491] [Alpha ][ 0.996305] . ( 60 sec) [ -8128.7010] [Branch lengths ] . ( 60 sec) [ -8128.7010] [Topology ] . ( 61 sec) [ -8128.6948] [Topology ] . ( 62 sec) [ -8128.6933] [Topology ] . ( 63 sec) [ -8128.6928] [Topology ] . ( 63 sec) [ -8128.6925] [GTR parameters ] . ( 63 sec) [ -8128.6925] [Alpha ][ 0.995309] . ( 63 sec) [ -8128.6925] [Topology ] . ( 64 sec) [ -8128.6923] [Topology ] . ( 64 sec) [ -8128.6922] [GTR parameters ] . ( 64 sec) [ -8128.6922] [Alpha ][ 0.995309] . Checking for NNIs, optimizing five branches... . ( 69 sec) [ -8128.6912] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8128.691172. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24776.8424] [GTR parameters ] . ( 1 sec) [ -24237.1419] [Alpha ][ 0.500960] . ( 1 sec) [ -23749.3189] [ 4513] [depth= 8] . ( 1 sec) [ -23266.9840] [ 4345] [depth= 9] . ( 1 sec) [ -23179.9160] [ 4302] [depth= 8] . ( 1 sec) [ -23006.4198] [ 4207] [depth= 3] . ( 1 sec) [ -22442.5576] [ 4176] [depth= 3] . ( 1 sec) [ -21958.2566] [ 4165] [depth= 7] . ( 1 sec) [ -21736.5805] [ 4021] [depth= 6] . ( 1 sec) [ -21534.2877] [ 4010] [depth= 7] . ( 2 sec) [ -21059.0652] [ 3969] [depth= 11] . ( 2 sec) [ -20960.3325] [ 3975] [depth= 5] . ( 2 sec) [ -20775.4407] [ 3901] [depth= 6] . ( 2 sec) [ -20437.1746] [ 3816] [depth= 15] . ( 2 sec) [ -20404.7501] [ 3814] [depth= 1] . ( 2 sec) [ -20400.8635] [ 3813] [depth= 1] . ( 2 sec) [ -20136.7041] [ 3762] [depth= 11] . ( 2 sec) [ -19986.7623] [ 3761] [depth= 1] . ( 2 sec) [ -19550.3352] [ 3728] [depth= 16] . ( 2 sec) [ -19549.5560] [ 3663] [depth= 1] . ( 2 sec) [ -19478.5789] [ 3548] [depth= 15] . ( 2 sec) [ -19413.6711] [ 3530] [depth= 1] . ( 2 sec) [ -19372.1925] [ 3529] [depth= 14] . ( 2 sec) [ -19067.6632] [ 3465] [depth= 14] . ( 2 sec) [ -19031.4127] [ 3432] [depth= 1] . ( 2 sec) [ -18998.4659] [ 3371] [depth= 1] . ( 2 sec) [ -18724.2793] [ 3302] [depth= 3] . ( 2 sec) [ -18609.0332] [ 3310] [depth= 1] . ( 2 sec) [ -18403.8119] [ 3299] [depth= 6] . ( 2 sec) [ -18111.3295] [ 3248] [depth= 6] . ( 2 sec) [ -17678.0391] [ 3110] [depth= 12] . ( 2 sec) [ -17609.2137] [ 3083] [depth= 1] . ( 2 sec) [ -17550.4053] [ 3080] [depth= 2] . ( 2 sec) [ -17002.2360] [ 2884] [depth= 13] . ( 2 sec) [ -16971.9175] [ 2881] [depth= 1] . ( 3 sec) [ -16876.3204] [ 2883] [depth= 1] . ( 3 sec) [ -16868.0119] [ 2885] [depth= 1] . ( 3 sec) [ -16860.7473] [ 2878] [depth= 1] . ( 3 sec) [ -16610.5649] [ 2778] [depth= 12] . ( 3 sec) [ -16472.8868] [ 2766] [depth= 8] . ( 3 sec) [ -16244.5778] [ 2714] [depth= 1] . ( 3 sec) [ -11909.1699] [ 2727] [depth= 12] . ( 3 sec) [ -11908.4088] [ 2728] [depth= 8] . ( 3 sec) [ -11751.6172] [ 2726] [depth= 3] . ( 3 sec) [ -11618.6148] [ 2659] [depth= 12] . ( 3 sec) [ -11353.3887] [ 2564] [depth= 1] . ( 3 sec) [ -11145.7012] [ 2564] [depth= 8] . ( 3 sec) [ -11074.6542] [ 2460] [depth= 9] . ( 3 sec) [ -11066.7600] [ 2448] [depth= 1] . ( 3 sec) [ -10944.9710] [ 2441] [depth= 1] . ( 3 sec) [ -10928.9994] [ 2570] [depth= 1] . ( 3 sec) [ -10647.0627] [ 2412] [depth= 2] . ( 3 sec) [ -10455.1878] [ 2405] [depth= 1] . ( 3 sec) [ -10363.9054] [ 2427] [depth= 3] . ( 4 sec) [ -10158.2082] [ 2366] [depth= 1] . ( 4 sec) [ -9988.3434] [ 2316] [depth= 4] . ( 4 sec) [ -9973.8964] [ 2333] [depth= 1] . ( 4 sec) [ -9962.5890] [ 2334] [depth= 8] . ( 4 sec) [ -9876.3942] [ 2315] [depth= 5] . ( 4 sec) [ -9870.3225] [ 2312] [depth= 2] . ( 4 sec) [ -9581.0910] [ 2184] [depth= 9] . ( 4 sec) [ -9555.3801] [ 2176] [depth= 3] . ( 4 sec) [ -9540.6024] [ 2176] [depth= 1] . ( 4 sec) [ -9540.2582] [ 2171] [depth= 1] . ( 4 sec) [ -9534.1568] [ 2170] [depth= 1] . ( 4 sec) [ -9467.7603] [ 2131] [depth= 5] . ( 4 sec) [ -9462.8964] [ 2136] [depth= 1] . ( 4 sec) [ -9310.5830] [ 2065] [depth= 4] . ( 4 sec) [ -9310.3910] [ 2069] [depth= 1] . ( 5 sec) [ -9257.2288] [ 2063] [depth= 2] . ( 5 sec) [ -9146.6112] [ 2068] [depth= 1] . ( 5 sec) [ -9136.6681] [ 2063] [depth= 1] . ( 5 sec) [ -9122.8355] [ 2065] [depth= 2] . ( 5 sec) [ -9081.5790] [ 2039] [depth= 1] . ( 5 sec) [ -9047.4129] [ 2003] [depth= 1] . ( 5 sec) [ -8972.2011] [ 2011] [depth= 2] . ( 5 sec) [ -8840.0435] [ 2007] [depth= 1] . ( 5 sec) [ -8690.8491] [Branch lengths ] . ( 6 sec) [ -8684.6350] [GTR parameters ] . ( 6 sec) [ -8663.0358] [Alpha ][ 0.782395] . ( 6 sec) [ -8657.2435] [ 2004] [depth= 1] . ( 6 sec) [ -8650.3642] [ 1994] [depth= 1] . ( 6 sec) [ -8536.1052] [ 1868] [depth= 6] . ( 6 sec) [ -8475.2668] [ 1870] [depth= 2] . ( 6 sec) [ -8474.6648] [ 1870] [depth= 1] . ( 6 sec) [ -8364.4778] [ 1833] [depth= 4] . ( 6 sec) [ -8300.4035] [ 1747] [depth= 4] . ( 7 sec) [ -8299.8212] [ 1747] [depth= 1] . ( 7 sec) [ -8289.9394] [ 1743] [depth= 2] . ( 7 sec) [ -8285.7784] [ 1743] [depth= 2] . ( 7 sec) [ -8283.9513] [ 1737] [depth= 1] . ( 7 sec) [ -8283.7484] [ 1736] [depth= 1] . ( 7 sec) [ -8254.8622] [ 1738] [depth= 1] . ( 7 sec) [ -8234.8327] [ 1737] [depth= 1] . ( 7 sec) [ -8234.6658] [ 1737] [depth= 1] . ( 8 sec) [ -8215.1019] [ 1716] [depth= 1] . ( 8 sec) [ -8214.7004] [ 1718] [depth= 1] . ( 8 sec) [ -8214.4976] [ 1718] [depth= 1] . ( 8 sec) [ -8196.9410] [ 1715] [depth= 2] . ( 8 sec) [ -8196.7831] [ 1715] [depth= 1] . ( 8 sec) [ -8158.2101] [ 1693] [depth= 1] . ( 9 sec) [ -8156.2985] [ 1694] [depth= 1] . ( 10 sec) [ -8134.9657] [Branch lengths ] . ( 10 sec) [ -8134.6164] [GTR parameters ] . ( 10 sec) [ -8130.0933] [Alpha ][ 0.989189] . ( 14 sec) [ -8129.4370] [Branch lengths ] . ( 20 sec) [ -8128.8323] [ 1704] [depth= 2] . ( 25 sec) [ -8128.6753] [ 1696] [depth= 1] . ( 35 sec) [ -8128.4947] [Branch lengths ] . ( 35 sec) [ -8128.4902] [GTR parameters ] . ( 35 sec) [ -8128.4862] [Alpha ][ 0.996331] . ( 35 sec) [ -8128.4862] [Topology ] . ( 36 sec) [ -8128.4468] [Topology ] . ( 37 sec) [ -8128.4348] [Topology ] . ( 38 sec) [ -8128.4329] [Topology ] . ( 38 sec) [ -8128.4324] [Topology ] . ( 39 sec) [ -8128.4319] [GTR parameters ] . ( 39 sec) [ -8128.4319] [Alpha ][ 0.997327] . ( 39 sec) [ -8128.4319] [Topology ] . ( 40 sec) [ -8128.4317] [Topology ] . ( 40 sec) [ -8128.4317] [GTR parameters ] . ( 40 sec) [ -8128.4317] [Alpha ][ 0.997327] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8128.431720. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -27791.2473] [GTR parameters ] . ( 2 sec) [ -27250.9428] [Alpha ][ 0.500960] . ( 2 sec) [ -26471.3566] [ 4538] [depth= 6] . ( 2 sec) [ -26147.8785] [ 4428] [depth= 11] . ( 2 sec) [ -26092.0399] [ 4409] [depth= 3] . ( 2 sec) [ -26089.5868] [ 4411] [depth= 2] . ( 2 sec) [ -25962.2454] [ 4392] [depth= 2] . ( 2 sec) [ -25755.9133] [ 4390] [depth= 2] . ( 2 sec) [ -25583.3777] [ 4384] [depth= 1] . ( 2 sec) [ -25452.3677] [ 4368] [depth= 6] . ( 2 sec) [ -25090.2686] [ 4239] [depth= 8] . ( 2 sec) [ -25063.1486] [ 4224] [depth= 5] . ( 2 sec) [ -24549.2075] [ 4151] [depth= 7] . ( 2 sec) [ -24360.7667] [ 4091] [depth= 10] . ( 2 sec) [ -24218.1392] [ 4023] [depth= 3] . ( 2 sec) [ -24101.5744] [ 3988] [depth= 1] . ( 2 sec) [ -23838.8995] [ 3911] [depth= 2] . ( 2 sec) [ -23617.0845] [ 3893] [depth= 3] . ( 2 sec) [ -23581.5624] [ 3892] [depth= 2] . ( 2 sec) [ -23500.4653] [ 3884] [depth= 8] . ( 2 sec) [ -23384.0117] [ 3881] [depth= 3] . ( 2 sec) [ -23215.4976] [ 3857] [depth= 11] . ( 2 sec) [ -23067.2047] [ 3806] [depth= 1] . ( 2 sec) [ -22872.8923] [ 3689] [depth= 4] . ( 3 sec) [ -22723.4308] [ 3588] [depth= 8] . ( 3 sec) [ -22696.0366] [ 3593] [depth= 1] . ( 3 sec) [ -22518.6372] [ 3489] [depth= 6] . ( 3 sec) [ -18876.8688] [ 3390] [depth= 10] . ( 3 sec) [ -18764.3351] [ 3422] [depth= 14] . ( 3 sec) [ -18488.5221] [ 3415] [depth= 6] . ( 3 sec) [ -18224.3005] [ 3252] [depth= 2] . ( 3 sec) [ -17989.8907] [ 3241] [depth= 6] . ( 3 sec) [ -17848.7997] [ 3214] [depth= 13] . ( 3 sec) [ -17740.5676] [ 3183] [depth= 4] . ( 3 sec) [ -17509.1360] [ 3115] [depth= 5] . ( 3 sec) [ -17351.6791] [ 3094] [depth= 1] . ( 3 sec) [ -17318.9791] [ 3086] [depth= 1] . ( 3 sec) [ -13226.6542] [ 3074] [depth= 7] . ( 3 sec) [ -13189.9918] [ 3073] [depth= 1] . ( 3 sec) [ -13095.9487] [ 3035] [depth= 1] . ( 3 sec) [ -12996.7546] [ 2917] [depth= 10] . ( 3 sec) [ -12843.6803] [ 2860] [depth= 8] . ( 3 sec) [ -12643.2357] [ 2800] [depth= 1] . ( 3 sec) [ -12566.6226] [ 2801] [depth= 5] . ( 3 sec) [ -12328.7990] [ 2751] [depth= 6] . ( 4 sec) [ -11963.5815] [ 2597] [depth= 5] . ( 4 sec) [ -11941.4108] [ 2592] [depth= 1] . ( 4 sec) [ -11833.5791] [ 2588] [depth= 7] . ( 4 sec) [ -11765.0784] [ 2582] [depth= 3] . ( 4 sec) [ -11692.9487] [ 2582] [depth= 2] . ( 4 sec) [ -11637.7676] [ 2576] [depth= 1] . ( 4 sec) [ -11469.2006] [ 2447] [depth= 5] . ( 4 sec) [ -11458.7376] [ 2445] [depth= 1] . ( 4 sec) [ -11395.2388] [ 2432] [depth= 2] . ( 4 sec) [ -11385.6711] [ 2426] [depth= 2] . ( 4 sec) [ -11141.8587] [ 2272] [depth= 8] . ( 4 sec) [ -11141.2614] [ 2277] [depth= 3] . ( 4 sec) [ -11101.5423] [ 2171] [depth= 4] . ( 4 sec) [ -10976.3765] [ 2023] [depth= 4] . ( 4 sec) [ -10951.7365] [ 2020] [depth= 2] . ( 4 sec) [ -10875.4291] [ 2020] [depth= 1] . ( 4 sec) [ -10493.2394] [ 2050] [depth= 2] . ( 4 sec) [ -10234.1912] [ 2023] [depth= 1] . ( 4 sec) [ -10006.8283] [ 2031] [depth= 1] . ( 4 sec) [ -9782.2894] [ 1970] [depth= 1] . ( 5 sec) [ -9758.8013] [ 1962] [depth= 1] . ( 5 sec) [ -9734.6195] [ 1962] [depth= 1] . ( 5 sec) [ -9704.9032] [ 1981] [depth= 1] . ( 5 sec) [ -9660.3088] [ 1967] [depth= 1] . ( 5 sec) [ -9397.7509] [ 1974] [depth= 1] . ( 5 sec) [ -9168.1266] [ 1831] [depth= 9] . ( 5 sec) [ -9157.9356] [ 1836] [depth= 1] . ( 5 sec) [ -9143.1620] [ 1837] [depth= 1] . ( 5 sec) [ -9142.1624] [ 1837] [depth= 1] . ( 5 sec) [ -9105.8051] [ 1828] [depth= 1] . ( 5 sec) [ -9067.5959] [ 1824] [depth= 1] . ( 5 sec) [ -9065.9465] [ 1823] [depth= 1] . ( 5 sec) [ -9055.7738] [ 1823] [depth= 2] . ( 5 sec) [ -8925.5560] [ 1811] [depth= 3] . ( 5 sec) [ -8767.8054] [ 1820] [depth= 1] . ( 5 sec) [ -8724.3724] [ 1823] [depth= 1] . ( 6 sec) [ -8418.2072] [Branch lengths ] . ( 6 sec) [ -8413.7545] [GTR parameters ] . ( 6 sec) [ -8384.4449] [Alpha ][ 0.875917] . ( 6 sec) [ -8381.2014] [ 1818] [depth= 1] . ( 6 sec) [ -8378.0427] [ 1818] [depth= 3] . ( 7 sec) [ -8364.6502] [ 1808] [depth= 3] . ( 7 sec) [ -8364.4357] [ 1808] [depth= 1] . ( 7 sec) [ -8364.3520] [ 1810] [depth= 1] . ( 7 sec) [ -8355.9867] [ 1809] [depth= 2] . ( 7 sec) [ -8355.2792] [ 1814] [depth= 1] . ( 7 sec) [ -8350.0303] [ 1805] [depth= 1] . ( 7 sec) [ -8345.9572] [ 1781] [depth= 4] . ( 7 sec) [ -8343.4080] [ 1781] [depth= 4] . ( 8 sec) [ -8262.6782] [ 1725] [depth= 2] . ( 8 sec) [ -8247.5706] [ 1752] [depth= 3] . ( 8 sec) [ -8247.5236] [ 1752] [depth= 1] . ( 8 sec) [ -8247.2221] [ 1758] [depth= 1] . ( 8 sec) [ -8247.1207] [ 1739] [depth= 1] . ( 8 sec) [ -8216.4882] [ 1738] [depth= 1] . ( 8 sec) [ -8213.4070] [ 1732] [depth= 1] . ( 8 sec) [ -8213.3782] [ 1736] [depth= 1] . ( 9 sec) [ -8205.2867] [ 1727] [depth= 1] . ( 9 sec) [ -8187.7100] [ 1701] [depth= 1] . ( 9 sec) [ -8187.4404] [ 1701] [depth= 1] . ( 9 sec) [ -8180.8962] [ 1692] [depth= 2] . ( 9 sec) [ -8179.8160] [ 1687] [depth= 1] . ( 9 sec) [ -8179.7599] [ 1687] [depth= 1] . ( 10 sec) [ -8143.8880] [Branch lengths ] . ( 10 sec) [ -8143.4335] [GTR parameters ] . ( 10 sec) [ -8142.3741] [Alpha ][ 0.980403] . ( 10 sec) [ -8141.2178] [ 1692] [depth= 1] . ( 10 sec) [ -8136.9644] [ 1687] [depth= 1] . ( 11 sec) [ -8136.7463] [ 1683] [depth= 1] . ( 14 sec) [ -8133.3476] [Branch lengths ] . ( 14 sec) [ -8133.3101] [GTR parameters ] . ( 14 sec) [ -8133.2950] [Alpha ][ 0.994283] . ( 17 sec) [ -8129.8503] [Branch lengths ] . ( 19 sec) [ -8129.8303] [ 1681] [depth= 1] . ( 23 sec) [ -8129.6267] [ 1695] [depth= 2] . ( 29 sec) [ -8129.4557] [ 1693] [depth= 1] . ( 38 sec) [ -8128.4681] [Branch lengths ] . ( 38 sec) [ -8128.4670] [GTR parameters ] . ( 38 sec) [ -8128.4663] [Alpha ][ 0.997316] . ( 60 sec) [ -8128.4358] [Branch lengths ] . ( 60 sec) [ -8128.4358] [Topology ] . ( 61 sec) [ -8128.4334] [Topology ] . ( 61 sec) [ -8128.4326] [Topology ] . ( 61 sec) [ -8128.4325] [GTR parameters ] . ( 61 sec) [ -8128.4325] [Alpha ][ 0.997316] . ( 61 sec) [ -8128.4325] [Topology ] . ( 62 sec) [ -8128.4322] [Topology ] . ( 62 sec) [ -8128.4322] [GTR parameters ] . ( 62 sec) [ -8128.4322] [Alpha ][ 0.997316] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8128.432202. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8212.880884 . ( 0 sec) [ -8210.1139] [GTR parameters ] . ( 0 sec) [ -8210.0646] [Alpha ][ 0.974422] . ( 0 sec) [ -8210.0646] [Topology ] . ( 1 sec) [ -8156.1994] [Topology ] . ( 2 sec) [ -8148.1552] [Topology ] . ( 3 sec) [ -8142.4795] [Topology ] . ( 3 sec) [ -8134.5723] [Topology ] . ( 4 sec) [ -8132.9551] [Topology ] . ( 5 sec) [ -8132.6711] [Topology ] . ( 6 sec) [ -8132.6161] [Topology ] . ( 6 sec) [ -8132.6018] [Topology ] . ( 7 sec) [ -8132.5970] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8132.597018 . ( 13 sec) [ -8132.5816] [GTR parameters ] . ( 13 sec) [ -8132.5425] [Alpha ][ 0.996004] . ( 13 sec) [ -8132.5425] [Topology ] . ( 14 sec) [ -8132.5376] [Topology ] . ( 14 sec) [ -8132.5358] [Topology ] . ( 15 sec) [ -8132.5350] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8132.534999 . ( 21 sec) [ -8132.5349] [GTR parameters ] . ( 21 sec) [ -8132.5347] [Alpha ][ 0.997812] . ( 21 sec) [ -8132.5347] [Topology ] . ( 22 sec) [ -8132.5342] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 34 sec) [ -8210.1139] [GTR parameters ] . ( 34 sec) [ -8210.0646] [Alpha ][ 0.974422] . ( 34 sec) [ -8201.8939] [ 1692] [depth= 1] . ( 35 sec) [ -8200.2394] [ 1691] [depth= 1] . ( 35 sec) [ -8198.3227] [ 1692] [depth= 1] . ( 35 sec) [ -8198.1399] [ 1691] [depth= 1] . ( 35 sec) [ -8192.0534] [ 1689] [depth= 1] . ( 35 sec) [ -8191.6431] [ 1688] [depth= 1] . ( 35 sec) [ -8190.1250] [ 1687] [depth= 1] . ( 35 sec) [ -8173.0889] [ 1679] [depth= 1] . ( 35 sec) [ -8172.9441] [ 1682] [depth= 1] . ( 35 sec) [ -8172.8690] [ 1682] [depth= 1] . ( 35 sec) [ -8172.2274] [ 1684] [depth= 1] . ( 35 sec) [ -8166.8175] [ 1682] [depth= 1] . ( 35 sec) [ -8161.9383] [ 1684] [depth= 1] . ( 36 sec) [ -8151.0564] [ 1689] [depth= 1] . ( 36 sec) [ -8150.9687] [ 1693] [depth= 3] . ( 36 sec) [ -8150.6793] [ 1687] [depth= 1] . ( 36 sec) [ -8150.3505] [ 1690] [depth= 1] . ( 36 sec) [ -8150.0049] [ 1687] [depth= 1] . ( 36 sec) [ -8149.7859] [ 1690] [depth= 1] . ( 37 sec) [ -8149.5794] [ 1690] [depth= 1] . ( 37 sec) [ -8149.4249] [ 1690] [depth= 1] . ( 37 sec) [ -8149.0719] [ 1690] [depth= 1] . ( 37 sec) [ -8134.2043] [Branch lengths ] . ( 37 sec) [ -8134.1858] [GTR parameters ] . ( 37 sec) [ -8134.1778] [Alpha ][ 0.984489] . ( 38 sec) [ -8133.6434] [ 1695] [depth= 3] . ( 39 sec) [ -8133.6144] [ 1696] [depth= 1] . ( 39 sec) [ -8133.5610] [ 1692] [depth= 1] . ( 39 sec) [ -8132.8402] [ 1692] [depth= 2] . ( 39 sec) [ -8132.7004] [ 1692] [depth= 2] . ( 39 sec) [ -8132.0979] [ 1691] [depth= 1] . ( 41 sec) [ -8131.3403] [Branch lengths ] . ( 41 sec) [ -8131.3359] [GTR parameters ] . ( 41 sec) [ -8131.3292] [Alpha ][ 0.993850] . ( 45 sec) [ -8131.2978] [Branch lengths ] . ( 56 sec) [ -8129.8985] [ 1699] [depth= 3] . ( 66 sec) [ -8128.9234] [Branch lengths ] . ( 67 sec) [ -8128.9063] [GTR parameters ] . ( 67 sec) [ -8128.9061] [Alpha ][ 0.995243] . ( 88 sec) [ -8128.7614] [Branch lengths ] . ( 88 sec) [ -8128.7614] [Topology ] . ( 89 sec) [ -8128.7073] [Topology ] . ( 90 sec) [ -8128.6958] [Topology ] . ( 91 sec) [ -8128.6939] [Topology ] . ( 91 sec) [ -8128.6934] [Topology ] . ( 92 sec) [ -8128.6923] [GTR parameters ] . ( 92 sec) [ -8128.6923] [Alpha ][ 0.995243] . ( 92 sec) [ -8128.6923] [Topology ] . ( 92 sec) [ -8128.6921] [Topology ] . ( 93 sec) [ -8128.6921] [GTR parameters ] . ( 93 sec) [ -8128.6921] [Alpha ][ 0.995243] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -8128.4334] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8132.534195 . Log likelihood obtained after SPR moves : -8128.433371 . Log likelihood of the current tree: -8128.433371. . Printing the most likely tree in file 'data94.phy_phyml_tree.txt'... . Best log likelihood : -8128.431720 . Time used 0h1m45s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo