.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data38.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... . 417 patterns found. (out of a total of 500 sites) . 82 sites without polymorphism (16.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18397.7253] [GTR parameters ] . ( 0 sec) [ -18105.4553] [Alpha ][ 0.500960] . ( 0 sec) [ -17765.1371] [ 4056] [depth= 8] . ( 0 sec) [ -17449.0668] [ 4043] [depth= 13] . ( 0 sec) [ -17308.7481] [ 4015] [depth= 1] . ( 0 sec) [ -17212.9079] [ 4005] [depth= 7] . ( 1 sec) [ -17004.0573] [ 3975] [depth= 5] . ( 1 sec) [ -16831.0022] [ 3958] [depth= 8] . ( 1 sec) [ -16788.7726] [ 3929] [depth= 4] . ( 1 sec) [ -16711.7145] [ 3938] [depth= 1] . ( 1 sec) [ -16399.4625] [ 3790] [depth= 2] . ( 1 sec) [ -15708.7241] [ 3657] [depth= 4] . ( 1 sec) [ -15476.0323] [ 3607] [depth= 10] . ( 1 sec) [ -15223.7256] [ 3537] [depth= 4] . ( 1 sec) [ -15045.7682] [ 3553] [depth= 1] . ( 1 sec) [ -14668.4636] [ 3426] [depth= 6] . ( 1 sec) [ -14492.7520] [ 3409] [depth= 4] . ( 1 sec) [ -14473.2771] [ 3401] [depth= 3] . ( 1 sec) [ -14263.7203] [ 3323] [depth= 6] . ( 1 sec) [ -14251.0477] [ 3337] [depth= 6] . ( 1 sec) [ -14123.2932] [ 3302] [depth= 11] . ( 1 sec) [ -14109.1115] [ 3301] [depth= 1] . ( 1 sec) [ -13930.8302] [ 3252] [depth= 2] . ( 1 sec) [ -13860.9210] [ 3209] [depth= 8] . ( 1 sec) [ -13702.8893] [ 3216] [depth= 1] . ( 1 sec) [ -13697.3487] [ 3209] [depth= 1] . ( 1 sec) [ -13547.4430] [ 3133] [depth= 12] . ( 1 sec) [ -13399.6435] [ 3133] [depth= 13] . ( 1 sec) [ -13249.8154] [ 3079] [depth= 6] . ( 1 sec) [ -13157.9645] [ 3083] [depth= 13] . ( 2 sec) [ -13148.9892] [ 3094] [depth= 1] . ( 2 sec) [ -13056.5396] [ 3036] [depth= 12] . ( 2 sec) [ -13033.7345] [ 3023] [depth= 3] . ( 2 sec) [ -12970.6144] [ 3012] [depth= 4] . ( 2 sec) [ -12729.7573] [ 3004] [depth= 4] . ( 2 sec) [ -12645.2250] [ 2989] [depth= 10] . ( 2 sec) [ -12625.2014] [ 2978] [depth= 1] . ( 2 sec) [ -12482.9392] [ 2949] [depth= 6] . ( 2 sec) [ -12372.5014] [ 2923] [depth= 4] . ( 2 sec) [ -12207.4688] [ 2881] [depth= 3] . ( 2 sec) [ -12023.7530] [ 2804] [depth= 6] . ( 2 sec) [ -12007.9558] [ 2793] [depth= 4] . ( 2 sec) [ -11921.4215] [ 2781] [depth= 1] . ( 2 sec) [ -11833.5188] [ 2755] [depth= 1] . ( 2 sec) [ -11811.5136] [ 2750] [depth= 5] . ( 2 sec) [ -11738.8094] [ 2721] [depth= 3] . ( 2 sec) [ -11482.6863] [ 2624] [depth= 11] . ( 2 sec) [ -11429.2759] [ 2628] [depth= 1] . ( 2 sec) [ -11249.1429] [ 2564] [depth= 7] . ( 2 sec) [ -11248.8401] [ 2538] [depth= 7] . ( 2 sec) [ -11209.9501] [ 2526] [depth= 1] . ( 2 sec) [ -11058.8888] [ 2496] [depth= 3] . ( 2 sec) [ -11049.5785] [ 2497] [depth= 2] . ( 3 sec) [ -11049.1546] [ 2499] [depth= 1] . ( 3 sec) [ -11025.6328] [ 2483] [depth= 1] . ( 3 sec) [ -10715.4332] [ 2390] [depth= 2] . ( 3 sec) [ -10659.9548] [ 2373] [depth= 1] . ( 3 sec) [ -10631.5409] [ 2383] [depth= 1] . ( 3 sec) [ -10630.8948] [ 2386] [depth= 3] . ( 3 sec) [ -10523.7157] [ 2328] [depth= 5] . ( 3 sec) [ -10520.3500] [ 2329] [depth= 1] . ( 3 sec) [ -10513.0928] [ 2327] [depth= 2] . ( 3 sec) [ -10502.1846] [ 2325] [depth= 1] . ( 3 sec) [ -10487.7382] [ 2318] [depth= 3] . ( 3 sec) [ -10460.6870] [ 2301] [depth= 4] . ( 3 sec) [ -10370.1129] [ 2257] [depth= 7] . ( 3 sec) [ -10367.7531] [ 2254] [depth= 2] . ( 3 sec) [ -10355.8966] [ 2254] [depth= 3] . ( 3 sec) [ -10302.5173] [ 2253] [depth= 3] . ( 3 sec) [ -10240.5034] [ 2231] [depth= 3] . ( 3 sec) [ -10236.1070] [ 2230] [depth= 1] . ( 3 sec) [ -10201.8137] [ 2219] [depth= 1] . ( 4 sec) [ -10169.4155] [ 2199] [depth= 2] . ( 4 sec) [ -10166.6010] [ 2198] [depth= 1] . ( 4 sec) [ -10161.2651] [ 2211] [depth= 1] . ( 4 sec) [ -10147.6616] [ 2210] [depth= 1] . ( 4 sec) [ -10122.8880] [ 2208] [depth= 1] . ( 4 sec) [ -10017.5707] [ 2172] [depth= 2] . ( 4 sec) [ -10014.7816] [ 2174] [depth= 1] . ( 4 sec) [ -10010.7041] [ 2172] [depth= 1] . ( 4 sec) [ -9982.0026] [ 2168] [depth= 1] . ( 4 sec) [ -9967.8742] [ 2170] [depth= 1] . ( 4 sec) [ -9967.5991] [ 2171] [depth= 1] . ( 4 sec) [ -9966.9167] [ 2172] [depth= 2] . ( 4 sec) [ -9836.5123] [Branch lengths ] . ( 5 sec) [ -9834.8892] [GTR parameters ] . ( 5 sec) [ -9810.9258] [Alpha ][ 0.819068] . ( 5 sec) [ -9810.6737] [ 2177] [depth= 2] . ( 5 sec) [ -9809.1837] [ 2169] [depth= 2] . ( 5 sec) [ -9808.5343] [ 2168] [depth= 1] . ( 6 sec) [ -9799.4322] [ 2160] [depth= 1] . ( 6 sec) [ -9783.0760] [ 2137] [depth= 3] . ( 6 sec) [ -9781.9256] [ 2137] [depth= 1] . ( 6 sec) [ -9768.1170] [ 2130] [depth= 3] . ( 6 sec) [ -9766.9273] [ 2129] [depth= 2] . ( 6 sec) [ -9755.8406] [ 2130] [depth= 1] . ( 6 sec) [ -9754.6656] [ 2128] [depth= 1] . ( 7 sec) [ -9753.2226] [ 2128] [depth= 1] . ( 7 sec) [ -9752.8967] [ 2130] [depth= 3] . ( 7 sec) [ -9752.8030] [ 2125] [depth= 4] . ( 7 sec) [ -9745.0592] [ 2122] [depth= 1] . ( 7 sec) [ -9744.1844] [ 2121] [depth= 1] . ( 7 sec) [ -9743.9549] [ 2123] [depth= 1] . ( 7 sec) [ -9743.6181] [ 2121] [depth= 1] . ( 7 sec) [ -9741.0240] [ 2118] [depth= 2] . ( 8 sec) [ -9736.9673] [ 2119] [depth= 1] . ( 8 sec) [ -9728.3801] [ 2115] [depth= 1] . ( 8 sec) [ -9726.9889] [ 2116] [depth= 2] . ( 9 sec) [ -9712.2411] [Branch lengths ] . ( 9 sec) [ -9711.9008] [GTR parameters ] . ( 9 sec) [ -9711.1305] [Alpha ][ 0.897026] . ( 12 sec) [ -9711.0916] [ 2117] [depth= 1] . ( 13 sec) [ -9710.8534] [ 2116] [depth= 1] . ( 14 sec) [ -9709.5930] [Branch lengths ] . ( 14 sec) [ -9709.5921] [GTR parameters ] . ( 14 sec) [ -9709.5676] [Alpha ][ 0.912044] . ( 19 sec) [ -9709.3419] [Branch lengths ] . ( 40 sec) [ -9709.3036] [Branch lengths ] . ( 40 sec) [ -9709.3036] [Topology ] . ( 41 sec) [ -9709.2731] [Topology ] . ( 42 sec) [ -9709.1723] [Topology ] . ( 43 sec) [ -9709.1538] [Topology ] . ( 44 sec) [ -9709.1481] [Topology ] . ( 44 sec) [ -9709.1460] [Topology ] . ( 45 sec) [ -9709.1452] [Topology ] . ( 45 sec) [ -9709.1424] [GTR parameters ] . ( 45 sec) [ -9709.1361] [Alpha ][ 0.919665] . ( 45 sec) [ -9709.1361] [Topology ] . ( 46 sec) [ -9709.1353] [Topology ] . ( 46 sec) [ -9709.1353] [GTR parameters ] . ( 46 sec) [ -9709.1353] [Alpha ][ 0.919665] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.135295. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18095.2630] [GTR parameters ] . ( 1 sec) [ -17801.6038] [Alpha ][ 0.500960] . ( 1 sec) [ -17495.6412] [ 4000] [depth= 3] . ( 1 sec) [ -16859.8105] [ 3907] [depth= 10] . ( 1 sec) [ -16749.7770] [ 3878] [depth= 4] . ( 1 sec) [ -16712.8440] [ 3860] [depth= 6] . ( 1 sec) [ -16655.9499] [ 3833] [depth= 1] . ( 2 sec) [ -16626.3809] [ 3830] [depth= 1] . ( 2 sec) [ -16541.9435] [ 3835] [depth= 1] . ( 2 sec) [ -16467.4942] [ 3824] [depth= 5] . ( 2 sec) [ -16344.1227] [ 3761] [depth= 2] . ( 2 sec) [ -16268.3670] [ 3747] [depth= 4] . ( 2 sec) [ -16083.0052] [ 3692] [depth= 9] . ( 2 sec) [ -15891.7569] [ 3685] [depth= 3] . ( 2 sec) [ -15547.4752] [ 3596] [depth= 1] . ( 2 sec) [ -15105.6012] [ 3504] [depth= 12] . ( 2 sec) [ -14738.5744] [ 3337] [depth= 16] . ( 2 sec) [ -14517.3759] [ 3308] [depth= 7] . ( 2 sec) [ -14345.9634] [ 3292] [depth= 1] . ( 2 sec) [ -14203.1031] [ 3294] [depth= 1] . ( 2 sec) [ -14075.6176] [ 3250] [depth= 2] . ( 2 sec) [ -14074.4436] [ 3249] [depth= 1] . ( 2 sec) [ -13932.8214] [ 3171] [depth= 1] . ( 2 sec) [ -13931.2634] [ 3170] [depth= 1] . ( 2 sec) [ -13710.7422] [ 3095] [depth= 14] . ( 2 sec) [ -13693.6413] [ 3079] [depth= 1] . ( 2 sec) [ -13533.4762] [ 3055] [depth= 10] . ( 2 sec) [ -13310.5539] [ 3080] [depth= 1] . ( 2 sec) [ -13064.1588] [ 2990] [depth= 2] . ( 3 sec) [ -13049.1515] [ 2973] [depth= 5] . ( 3 sec) [ -12715.4333] [ 2892] [depth= 5] . ( 3 sec) [ -12520.7633] [ 2848] [depth= 8] . ( 3 sec) [ -12519.5268] [ 2847] [depth= 1] . ( 3 sec) [ -12364.6206] [ 2837] [depth= 4] . ( 3 sec) [ -12227.2147] [ 2803] [depth= 5] . ( 3 sec) [ -11920.6118] [ 2796] [depth= 6] . ( 3 sec) [ -11812.2565] [ 2782] [depth= 1] . ( 3 sec) [ -11626.2932] [ 2716] [depth= 9] . ( 3 sec) [ -11599.0609] [ 2707] [depth= 4] . ( 3 sec) [ -11558.8220] [ 2673] [depth= 8] . ( 3 sec) [ -11538.2340] [ 2657] [depth= 3] . ( 3 sec) [ -11501.4775] [ 2642] [depth= 4] . ( 3 sec) [ -11478.7741] [ 2646] [depth= 1] . ( 3 sec) [ -11345.1961] [ 2594] [depth= 3] . ( 3 sec) [ -11297.3140] [ 2587] [depth= 2] . ( 3 sec) [ -11259.5525] [ 2554] [depth= 12] . ( 3 sec) [ -11199.2762] [ 2507] [depth= 2] . ( 3 sec) [ -11048.0387] [ 2461] [depth= 7] . ( 3 sec) [ -11041.4578] [ 2457] [depth= 1] . ( 3 sec) [ -10992.1200] [ 2460] [depth= 1] . ( 4 sec) [ -10990.2600] [ 2458] [depth= 3] . ( 4 sec) [ -10983.8133] [ 2459] [depth= 2] . ( 4 sec) [ -10983.7482] [ 2458] [depth= 3] . ( 4 sec) [ -10977.8833] [ 2457] [depth= 2] . ( 4 sec) [ -10857.1263] [ 2436] [depth= 3] . ( 4 sec) [ -10850.3111] [ 2400] [depth= 1] . ( 4 sec) [ -10832.2478] [ 2393] [depth= 1] . ( 4 sec) [ -10585.5777] [ 2322] [depth= 1] . ( 4 sec) [ -10568.4026] [ 2320] [depth= 1] . ( 4 sec) [ -10565.5333] [ 2320] [depth= 1] . ( 4 sec) [ -10473.9492] [ 2283] [depth= 1] . ( 4 sec) [ -10436.1767] [ 2286] [depth= 1] . ( 4 sec) [ -10418.9488] [ 2292] [depth= 3] . ( 4 sec) [ -10404.9102] [ 2289] [depth= 1] . ( 4 sec) [ -10320.7561] [ 2258] [depth= 5] . ( 4 sec) [ -10295.2991] [ 2255] [depth= 1] . ( 4 sec) [ -10227.7707] [ 2232] [depth= 1] . ( 4 sec) [ -10206.9128] [ 2226] [depth= 7] . ( 4 sec) [ -10168.0688] [ 2226] [depth= 1] . ( 5 sec) [ -10144.8118] [ 2222] [depth= 1] . ( 5 sec) [ -10133.0745] [ 2223] [depth= 1] . ( 5 sec) [ -10098.9895] [ 2203] [depth= 1] . ( 5 sec) [ -10083.9036] [ 2194] [depth= 1] . ( 5 sec) [ -10083.4234] [ 2195] [depth= 1] . ( 5 sec) [ -10068.2678] [ 2184] [depth= 1] . ( 5 sec) [ -9956.7030] [ 2137] [depth= 8] . ( 5 sec) [ -9954.9688] [ 2138] [depth= 1] . ( 5 sec) [ -9953.5261] [ 2138] [depth= 1] . ( 5 sec) [ -9797.2292] [Branch lengths ] . ( 6 sec) [ -9795.1127] [GTR parameters ] . ( 6 sec) [ -9762.0744] [Alpha ][ 0.888840] . ( 6 sec) [ -9760.6292] [ 2141] [depth= 2] . ( 6 sec) [ -9759.9938] [ 2140] [depth= 1] . ( 6 sec) [ -9758.6529] [ 2137] [depth= 2] . ( 6 sec) [ -9758.4537] [ 2138] [depth= 1] . ( 6 sec) [ -9726.7591] [ 2121] [depth= 4] . ( 7 sec) [ -9726.2642] [ 2120] [depth= 1] . ( 7 sec) [ -9725.9663] [ 2125] [depth= 1] . ( 8 sec) [ -9725.7137] [ 2128] [depth= 3] . ( 8 sec) [ -9723.9620] [ 2125] [depth= 1] . ( 8 sec) [ -9723.8776] [ 2121] [depth= 1] . ( 9 sec) [ -9723.4134] [ 2118] [depth= 1] . ( 9 sec) [ -9711.6879] [Branch lengths ] . ( 10 sec) [ -9711.4611] [GTR parameters ] . ( 10 sec) [ -9711.3985] [Alpha ][ 0.911722] . ( 12 sec) [ -9711.3203] [ 2123] [depth= 2] . ( 13 sec) [ -9711.1089] [ 2124] [depth= 2] . ( 14 sec) [ -9710.7024] [Branch lengths ] . ( 14 sec) [ -9710.7017] [GTR parameters ] . ( 14 sec) [ -9710.7005] [Alpha ][ 0.914974] . ( 15 sec) [ -9710.6516] [ 2116] [depth= 1] . ( 16 sec) [ -9709.8824] [ 2115] [depth= 1] . ( 27 sec) [ -9709.8298] [ 2115] [depth= 1] . ( 36 sec) [ -9709.2774] [Branch lengths ] . ( 36 sec) [ -9709.2716] [GTR parameters ] . ( 36 sec) [ -9709.2689] [Alpha ][ 0.919907] . ( 58 sec) [ -9709.1451] [Branch lengths ] . ( 58 sec) [ -9709.1451] [Topology ] . ( 59 sec) [ -9709.1380] [Topology ] . ( 60 sec) [ -9709.1361] [Topology ] . ( 60 sec) [ -9709.1354] [Topology ] . ( 61 sec) [ -9709.1353] [GTR parameters ] . ( 61 sec) [ -9709.1353] [Alpha ][ 0.919907] . ( 61 sec) [ -9709.1353] [Topology ] . ( 61 sec) [ -9709.1350] [Topology ] . ( 62 sec) [ -9709.1350] [GTR parameters ] . ( 62 sec) [ -9709.1350] [Alpha ][ 0.919907] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.135010. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19146.7387] [GTR parameters ] . ( 1 sec) [ -18817.1995] [Alpha ][ 0.500960] . ( 1 sec) [ -18379.5690] [ 4161] [depth= 8] . ( 1 sec) [ -17967.5919] [ 4091] [depth= 12] . ( 1 sec) [ -17957.5977] [ 4085] [depth= 5] . ( 1 sec) [ -17834.9499] [ 4075] [depth= 6] . ( 1 sec) [ -17770.4164] [ 4027] [depth= 8] . ( 1 sec) [ -17717.1194] [ 4025] [depth= 2] . ( 1 sec) [ -17249.2722] [ 3937] [depth= 14] . ( 1 sec) [ -17026.1437] [ 3900] [depth= 13] . ( 1 sec) [ -16671.5281] [ 3847] [depth= 1] . ( 1 sec) [ -16593.7548] [ 3833] [depth= 11] . ( 1 sec) [ -16210.7501] [ 3780] [depth= 8] . ( 1 sec) [ -16070.3062] [ 3745] [depth= 6] . ( 1 sec) [ -15979.2247] [ 3742] [depth= 1] . ( 1 sec) [ -15787.2119] [ 3719] [depth= 1] . ( 1 sec) [ -15540.6017] [ 3602] [depth= 3] . ( 1 sec) [ -15395.9421] [ 3583] [depth= 7] . ( 1 sec) [ -15247.2073] [ 3557] [depth= 8] . ( 1 sec) [ -15183.2288] [ 3497] [depth= 1] . ( 1 sec) [ -15060.7208] [ 3453] [depth= 4] . ( 1 sec) [ -14811.6575] [ 3389] [depth= 2] . ( 1 sec) [ -14799.9123] [ 3399] [depth= 11] . ( 2 sec) [ -14610.0531] [ 3397] [depth= 2] . ( 2 sec) [ -14594.6492] [ 3400] [depth= 1] . ( 2 sec) [ -14379.8721] [ 3362] [depth= 1] . ( 2 sec) [ -14228.9097] [ 3306] [depth= 13] . ( 2 sec) [ -14196.6329] [ 3260] [depth= 10] . ( 2 sec) [ -14154.6067] [ 3244] [depth= 10] . ( 2 sec) [ -14041.9388] [ 3161] [depth= 2] . ( 2 sec) [ -13858.3505] [ 3161] [depth= 13] . ( 2 sec) [ -13769.2136] [ 3132] [depth= 1] . ( 2 sec) [ -13460.8490] [ 3072] [depth= 12] . ( 2 sec) [ -13332.6688] [ 3041] [depth= 1] . ( 2 sec) [ -13232.1870] [ 3040] [depth= 1] . ( 2 sec) [ -13207.0265] [ 3022] [depth= 1] . ( 2 sec) [ -12954.5110] [ 2927] [depth= 5] . ( 2 sec) [ -12799.6014] [ 2860] [depth= 6] . ( 2 sec) [ -12796.9829] [ 2873] [depth= 1] . ( 2 sec) [ -12587.1543] [ 2832] [depth= 9] . ( 2 sec) [ -12541.0372] [ 2796] [depth= 1] . ( 2 sec) [ -12527.3355] [ 2797] [depth= 1] . ( 2 sec) [ -12465.6117] [ 2783] [depth= 9] . ( 2 sec) [ -12322.4633] [ 2766] [depth= 2] . ( 3 sec) [ -12255.3319] [ 2758] [depth= 3] . ( 3 sec) [ -12160.0951] [ 2713] [depth= 4] . ( 3 sec) [ -12130.6851] [ 2713] [depth= 1] . ( 3 sec) [ -11946.2227] [ 2696] [depth= 6] . ( 3 sec) [ -11878.1352] [ 2656] [depth= 2] . ( 3 sec) [ -11809.5999] [ 2639] [depth= 6] . ( 3 sec) [ -11793.9650] [ 2642] [depth= 1] . ( 3 sec) [ -11782.5358] [ 2664] [depth= 1] . ( 3 sec) [ -11660.6989] [ 2598] [depth= 4] . ( 3 sec) [ -11650.5943] [ 2600] [depth= 1] . ( 3 sec) [ -11649.6080] [ 2598] [depth= 1] . ( 3 sec) [ -11648.3700] [ 2600] [depth= 2] . ( 3 sec) [ -11558.0323] [ 2586] [depth= 1] . ( 3 sec) [ -11553.0728] [ 2583] [depth= 1] . ( 3 sec) [ -11550.1066] [ 2582] [depth= 1] . ( 3 sec) [ -11505.8538] [ 2557] [depth= 8] . ( 3 sec) [ -11295.3458] [ 2541] [depth= 8] . ( 3 sec) [ -11286.0222] [ 2540] [depth= 1] . ( 3 sec) [ -10911.0357] [ 2508] [depth= 6] . ( 4 sec) [ -10910.3445] [ 2508] [depth= 1] . ( 4 sec) [ -10583.7813] [ 2376] [depth= 7] . ( 4 sec) [ -10530.6168] [ 2345] [depth= 6] . ( 4 sec) [ -10523.0263] [ 2345] [depth= 1] . ( 4 sec) [ -10373.0347] [ 2310] [depth= 4] . ( 4 sec) [ -10267.0289] [ 2271] [depth= 2] . ( 4 sec) [ -10263.3643] [ 2265] [depth= 2] . ( 4 sec) [ -10193.5518] [ 2263] [depth= 1] . ( 4 sec) [ -10144.2626] [ 2235] [depth= 1] . ( 4 sec) [ -10121.1042] [ 2217] [depth= 1] . ( 4 sec) [ -10109.8506] [ 2224] [depth= 1] . ( 4 sec) [ -10068.1022] [ 2206] [depth= 3] . ( 4 sec) [ -10057.6408] [ 2197] [depth= 1] . ( 5 sec) [ -9894.1777] [Branch lengths ] . ( 5 sec) [ -9892.0982] [GTR parameters ] . ( 5 sec) [ -9864.0294] [Alpha ][ 0.846822] . ( 5 sec) [ -9815.7254] [ 2153] [depth= 8] . ( 5 sec) [ -9799.1820] [ 2125] [depth= 2] . ( 5 sec) [ -9774.5051] [ 2113] [depth= 1] . ( 6 sec) [ -9732.5726] [ 2111] [depth= 1] . ( 6 sec) [ -9731.2177] [ 2112] [depth= 1] . ( 6 sec) [ -9730.4847] [ 2112] [depth= 2] . ( 6 sec) [ -9730.1820] [ 2112] [depth= 1] . ( 6 sec) [ -9729.1383] [ 2111] [depth= 1] . ( 7 sec) [ -9726.2317] [ 2114] [depth= 1] . ( 7 sec) [ -9725.2629] [ 2115] [depth= 1] . ( 7 sec) [ -9724.7839] [ 2114] [depth= 2] . ( 7 sec) [ -9724.3740] [ 2113] [depth= 1] . ( 9 sec) [ -9711.1305] [Branch lengths ] . ( 9 sec) [ -9710.9597] [GTR parameters ] . ( 9 sec) [ -9710.6352] [Alpha ][ 0.898412] . ( 10 sec) [ -9710.5637] [ 2115] [depth= 1] . ( 14 sec) [ -9709.4171] [Branch lengths ] . ( 14 sec) [ -9709.4167] [GTR parameters ] . ( 14 sec) [ -9709.3934] [Alpha ][ 0.913070] . ( 19 sec) [ -9709.1765] [Branch lengths ] . ( 41 sec) [ -9709.1454] [Branch lengths ] . ( 41 sec) [ -9709.1454] [Topology ] . ( 41 sec) [ -9709.1424] [Topology ] . ( 42 sec) [ -9709.1415] [Topology ] . ( 42 sec) [ -9709.1410] [GTR parameters ] . ( 42 sec) [ -9709.1367] [Alpha ][ 0.919414] . ( 42 sec) [ -9709.1367] [Topology ] . ( 43 sec) [ -9709.1357] [Topology ] . ( 43 sec) [ -9709.1357] [GTR parameters ] . ( 43 sec) [ -9709.1357] [Alpha ][ 0.919414] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.135675. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18204.5574] [GTR parameters ] . ( 1 sec) [ -17896.9645] [Alpha ][ 0.500960] . ( 1 sec) [ -17677.5002] [ 4183] [depth= 8] . ( 1 sec) [ -17431.7521] [ 4089] [depth= 5] . ( 1 sec) [ -17248.8658] [ 4040] [depth= 8] . ( 1 sec) [ -17226.4568] [ 3946] [depth= 1] . ( 1 sec) [ -17028.5347] [ 3891] [depth= 6] . ( 1 sec) [ -16948.5357] [ 3876] [depth= 3] . ( 1 sec) [ -16927.7258] [ 3873] [depth= 3] . ( 1 sec) [ -16892.2755] [ 3859] [depth= 1] . ( 1 sec) [ -16771.8368] [ 3857] [depth= 1] . ( 1 sec) [ -16715.5289] [ 3832] [depth= 4] . ( 1 sec) [ -16583.8671] [ 3830] [depth= 1] . ( 1 sec) [ -16483.1609] [ 3795] [depth= 7] . ( 1 sec) [ -16349.5584] [ 3762] [depth= 6] . ( 2 sec) [ -16322.8399] [ 3748] [depth= 3] . ( 2 sec) [ -16306.0206] [ 3742] [depth= 1] . ( 2 sec) [ -16132.4260] [ 3733] [depth= 12] . ( 2 sec) [ -16022.3858] [ 3753] [depth= 1] . ( 2 sec) [ -15812.2529] [ 3694] [depth= 6] . ( 2 sec) [ -15548.7654] [ 3630] [depth= 4] . ( 2 sec) [ -15513.2933] [ 3619] [depth= 2] . ( 2 sec) [ -15106.3861] [ 3537] [depth= 2] . ( 2 sec) [ -15069.5203] [ 3526] [depth= 5] . ( 2 sec) [ -14934.7801] [ 3524] [depth= 11] . ( 2 sec) [ -14908.9609] [ 3485] [depth= 17] . ( 2 sec) [ -14898.0303] [ 3443] [depth= 1] . ( 2 sec) [ -14707.5616] [ 3414] [depth= 2] . ( 2 sec) [ -14310.0876] [ 3414] [depth= 4] . ( 2 sec) [ -14197.4891] [ 3411] [depth= 9] . ( 2 sec) [ -14096.8450] [ 3390] [depth= 7] . ( 2 sec) [ -14085.3002] [ 3372] [depth= 1] . ( 2 sec) [ -14059.4297] [ 3370] [depth= 4] . ( 2 sec) [ -13984.9893] [ 3362] [depth= 1] . ( 2 sec) [ -13849.4782] [ 3342] [depth= 1] . ( 2 sec) [ -13572.0145] [ 3271] [depth= 3] . ( 2 sec) [ -13435.6369] [ 3225] [depth= 1] . ( 2 sec) [ -13343.3394] [ 3137] [depth= 7] . ( 2 sec) [ -13278.7409] [ 3131] [depth= 7] . ( 3 sec) [ -13191.3542] [ 3070] [depth= 1] . ( 3 sec) [ -12973.2101] [ 2992] [depth= 6] . ( 3 sec) [ -12847.5870] [ 2947] [depth= 16] . ( 3 sec) [ -12804.9217] [ 2937] [depth= 3] . ( 3 sec) [ -12325.3675] [ 2921] [depth= 12] . ( 3 sec) [ -12251.4412] [ 2903] [depth= 1] . ( 3 sec) [ -12201.8595] [ 2891] [depth= 4] . ( 3 sec) [ -12104.0173] [ 2853] [depth= 10] . ( 3 sec) [ -12027.4108] [ 2792] [depth= 2] . ( 3 sec) [ -11948.2791] [ 2748] [depth= 1] . ( 3 sec) [ -11817.4771] [ 2734] [depth= 3] . ( 3 sec) [ -11706.8256] [ 2734] [depth= 2] . ( 3 sec) [ -11574.2123] [ 2693] [depth= 1] . ( 3 sec) [ -11460.0715] [ 2685] [depth= 2] . ( 3 sec) [ -11346.3222] [ 2681] [depth= 1] . ( 3 sec) [ -11177.8707] [ 2634] [depth= 1] . ( 3 sec) [ -11116.3806] [ 2594] [depth= 12] . ( 3 sec) [ -11091.4740] [ 2571] [depth= 1] . ( 3 sec) [ -11078.4982] [ 2570] [depth= 11] . ( 3 sec) [ -10924.4820] [ 2493] [depth= 5] . ( 3 sec) [ -10910.3838] [ 2485] [depth= 2] . ( 3 sec) [ -10883.9419] [ 2486] [depth= 2] . ( 3 sec) [ -10870.3071] [ 2479] [depth= 2] . ( 4 sec) [ -10857.0321] [ 2473] [depth= 1] . ( 4 sec) [ -10761.1419] [ 2445] [depth= 8] . ( 4 sec) [ -10751.6132] [ 2448] [depth= 1] . ( 4 sec) [ -10665.8654] [ 2412] [depth= 6] . ( 4 sec) [ -10662.6279] [ 2405] [depth= 1] . ( 4 sec) [ -10602.8305] [ 2393] [depth= 3] . ( 4 sec) [ -10439.4647] [ 2353] [depth= 1] . ( 4 sec) [ -10401.3250] [ 2327] [depth= 3] . ( 4 sec) [ -10332.0318] [ 2315] [depth= 1] . ( 4 sec) [ -10326.9796] [ 2318] [depth= 1] . ( 4 sec) [ -10229.1371] [ 2281] [depth= 7] . ( 4 sec) [ -10171.4811] [ 2259] [depth= 1] . ( 4 sec) [ -10121.3213] [ 2235] [depth= 3] . ( 4 sec) [ -10116.6428] [ 2236] [depth= 1] . ( 4 sec) [ -10113.3383] [ 2235] [depth= 1] . ( 5 sec) [ -10109.2907] [ 2234] [depth= 2] . ( 5 sec) [ -10092.2974] [ 2237] [depth= 2] . ( 5 sec) [ -10086.1496] [ 2239] [depth= 1] . ( 5 sec) [ -10073.1376] [ 2251] [depth= 1] . ( 5 sec) [ -10064.2669] [ 2252] [depth= 2] . ( 5 sec) [ -9985.9399] [Branch lengths ] . ( 6 sec) [ -9984.2700] [GTR parameters ] . ( 6 sec) [ -9958.6722] [Alpha ][ 0.822954] . ( 6 sec) [ -9956.0877] [ 2233] [depth= 2] . ( 6 sec) [ -9886.1652] [ 2202] [depth= 2] . ( 6 sec) [ -9885.9026] [ 2202] [depth= 1] . ( 6 sec) [ -9885.8249] [ 2200] [depth= 1] . ( 6 sec) [ -9872.8206] [ 2192] [depth= 1] . ( 6 sec) [ -9863.4416] [ 2193] [depth= 2] . ( 6 sec) [ -9763.7545] [ 2128] [depth= 2] . ( 6 sec) [ -9763.3827] [ 2133] [depth= 1] . ( 7 sec) [ -9761.0371] [ 2134] [depth= 1] . ( 7 sec) [ -9760.7799] [ 2135] [depth= 1] . ( 7 sec) [ -9760.2199] [ 2137] [depth= 1] . ( 7 sec) [ -9745.6638] [ 2123] [depth= 1] . ( 7 sec) [ -9744.4527] [ 2124] [depth= 1] . ( 7 sec) [ -9743.8361] [ 2117] [depth= 3] . ( 7 sec) [ -9743.5212] [ 2117] [depth= 1] . ( 8 sec) [ -9741.5317] [ 2116] [depth= 1] . ( 8 sec) [ -9741.4680] [ 2114] [depth= 1] . ( 8 sec) [ -9731.7155] [ 2111] [depth= 1] . ( 8 sec) [ -9731.7037] [ 2114] [depth= 3] . ( 8 sec) [ -9730.1036] [ 2119] [depth= 1] . ( 9 sec) [ -9730.0774] [ 2121] [depth= 1] . ( 9 sec) [ -9728.4766] [ 2120] [depth= 1] . ( 9 sec) [ -9727.5650] [ 2119] [depth= 1] . ( 9 sec) [ -9718.0953] [Branch lengths ] . ( 10 sec) [ -9717.8007] [GTR parameters ] . ( 10 sec) [ -9717.0714] [Alpha ][ 0.898680] . ( 11 sec) [ -9710.8809] [ 2113] [depth= 1] . ( 11 sec) [ -9710.8701] [ 2116] [depth= 1] . ( 14 sec) [ -9709.4192] [Branch lengths ] . ( 14 sec) [ -9709.3989] [GTR parameters ] . ( 15 sec) [ -9709.3742] [Alpha ][ 0.913726] . ( 19 sec) [ -9709.1980] [Branch lengths ] . ( 41 sec) [ -9709.1724] [Branch lengths ] . ( 41 sec) [ -9709.1724] [Topology ] . ( 42 sec) [ -9709.1699] [Topology ] . ( 42 sec) [ -9709.1690] [Topology ] . ( 42 sec) [ -9709.1688] [GTR parameters ] . ( 43 sec) [ -9709.1658] [Alpha ][ 0.918950] . ( 43 sec) [ -9709.1658] [Topology ] . ( 43 sec) [ -9709.1651] [Topology ] . ( 43 sec) [ -9709.1651] [GTR parameters ] . ( 43 sec) [ -9709.1651] [Alpha ][ 0.918950] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -9709.1647] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.164666. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19115.1904] [GTR parameters ] . ( 1 sec) [ -18777.5855] [Alpha ][ 0.500960] . ( 1 sec) [ -18365.0553] [ 4219] [depth= 6] . ( 1 sec) [ -18110.6608] [ 4116] [depth= 12] . ( 1 sec) [ -17952.9588] [ 4100] [depth= 2] . ( 1 sec) [ -17924.0068] [ 4095] [depth= 4] . ( 1 sec) [ -17910.1338] [ 4091] [depth= 1] . ( 1 sec) [ -17741.9057] [ 4088] [depth= 3] . ( 1 sec) [ -17597.8699] [ 4071] [depth= 5] . ( 1 sec) [ -17385.1631] [ 3999] [depth= 1] . ( 2 sec) [ -17200.5047] [ 3955] [depth= 6] . ( 2 sec) [ -16923.8291] [ 3842] [depth= 1] . ( 2 sec) [ -16572.8934] [ 3822] [depth= 12] . ( 2 sec) [ -16217.6020] [ 3799] [depth= 14] . ( 2 sec) [ -16083.2748] [ 3793] [depth= 7] . ( 2 sec) [ -16070.3129] [ 3779] [depth= 2] . ( 2 sec) [ -16028.2004] [ 3759] [depth= 6] . ( 2 sec) [ -15940.2672] [ 3754] [depth= 1] . ( 2 sec) [ -15860.1427] [ 3750] [depth= 10] . ( 2 sec) [ -15853.9408] [ 3753] [depth= 1] . ( 2 sec) [ -15822.5819] [ 3733] [depth= 13] . ( 2 sec) [ -15261.4086] [ 3674] [depth= 15] . ( 2 sec) [ -15115.8414] [ 3645] [depth= 9] . ( 2 sec) [ -14914.4095] [ 3622] [depth= 12] . ( 2 sec) [ -14581.7686] [ 3481] [depth= 9] . ( 2 sec) [ -14521.2241] [ 3472] [depth= 9] . ( 2 sec) [ -14474.9245] [ 3474] [depth= 2] . ( 2 sec) [ -14346.8359] [ 3406] [depth= 12] . ( 2 sec) [ -14283.3717] [ 3396] [depth= 4] . ( 2 sec) [ -14206.4926] [ 3342] [depth= 1] . ( 2 sec) [ -14134.1854] [ 3306] [depth= 7] . ( 2 sec) [ -13983.0056] [ 3296] [depth= 1] . ( 3 sec) [ -13829.2713] [ 3203] [depth= 9] . ( 3 sec) [ -13677.2967] [ 3173] [depth= 1] . ( 3 sec) [ -13510.2493] [ 3128] [depth= 7] . ( 3 sec) [ -13288.9968] [ 3091] [depth= 1] . ( 3 sec) [ -13247.8940] [ 3038] [depth= 1] . ( 3 sec) [ -13077.0118] [ 2990] [depth= 6] . ( 3 sec) [ -13045.9222] [ 2977] [depth= 5] . ( 3 sec) [ -12755.3361] [ 2939] [depth= 8] . ( 3 sec) [ -12754.0406] [ 2940] [depth= 1] . ( 3 sec) [ -12738.7608] [ 2937] [depth= 4] . ( 3 sec) [ -12623.8577] [ 2895] [depth= 1] . ( 3 sec) [ -12578.7327] [ 2827] [depth= 5] . ( 3 sec) [ -12375.5600] [ 2729] [depth= 7] . ( 3 sec) [ -12299.4828] [ 2711] [depth= 1] . ( 3 sec) [ -12297.1596] [ 2712] [depth= 2] . ( 3 sec) [ -12186.2308] [ 2682] [depth= 4] . ( 3 sec) [ -12057.9153] [ 2663] [depth= 3] . ( 3 sec) [ -12009.9712] [ 2646] [depth= 5] . ( 3 sec) [ -11902.6053] [ 2625] [depth= 9] . ( 3 sec) [ -11839.2495] [ 2621] [depth= 2] . ( 3 sec) [ -11760.0530] [ 2587] [depth= 12] . ( 4 sec) [ -11694.8526] [ 2591] [depth= 1] . ( 4 sec) [ -11504.0235] [ 2543] [depth= 12] . ( 4 sec) [ -11502.7321] [ 2543] [depth= 1] . ( 4 sec) [ -11352.8926] [ 2468] [depth= 4] . ( 4 sec) [ -11340.5524] [ 2492] [depth= 5] . ( 4 sec) [ -10930.3834] [ 2441] [depth= 2] . ( 4 sec) [ -10801.3562] [ 2415] [depth= 3] . ( 4 sec) [ -10722.4603] [ 2392] [depth= 1] . ( 4 sec) [ -10581.1597] [ 2368] [depth= 3] . ( 4 sec) [ -10577.9176] [ 2365] [depth= 3] . ( 4 sec) [ -10557.3562] [ 2339] [depth= 6] . ( 4 sec) [ -10490.9771] [ 2329] [depth= 3] . ( 4 sec) [ -10488.9161] [ 2326] [depth= 1] . ( 4 sec) [ -10460.1228] [ 2315] [depth= 1] . ( 4 sec) [ -10378.7127] [ 2295] [depth= 1] . ( 4 sec) [ -10341.8376] [ 2282] [depth= 1] . ( 4 sec) [ -10318.0149] [ 2256] [depth= 3] . ( 4 sec) [ -10302.3576] [ 2254] [depth= 1] . ( 4 sec) [ -10302.0135] [ 2256] [depth= 1] . ( 4 sec) [ -10255.7492] [ 2232] [depth= 2] . ( 4 sec) [ -10159.5479] [ 2199] [depth= 1] . ( 4 sec) [ -10143.6991] [ 2188] [depth= 1] . ( 5 sec) [ -10122.4439] [ 2184] [depth= 1] . ( 5 sec) [ -10071.5969] [ 2172] [depth= 1] . ( 5 sec) [ -10058.7414] [ 2169] [depth= 3] . ( 5 sec) [ -9972.5201] [ 2136] [depth= 1] . ( 5 sec) [ -9971.3972] [ 2139] [depth= 1] . ( 5 sec) [ -9932.7305] [ 2140] [depth= 1] . ( 5 sec) [ -9790.4235] [Branch lengths ] . ( 6 sec) [ -9789.4191] [GTR parameters ] . ( 6 sec) [ -9764.1535] [Alpha ][ 0.834198] . ( 6 sec) [ -9763.9532] [ 2133] [depth= 4] . ( 6 sec) [ -9760.1322] [ 2133] [depth= 1] . ( 6 sec) [ -9748.3888] [ 2124] [depth= 2] . ( 6 sec) [ -9747.5254] [ 2123] [depth= 1] . ( 6 sec) [ -9745.0421] [ 2124] [depth= 1] . ( 6 sec) [ -9744.3771] [ 2123] [depth= 1] . ( 6 sec) [ -9744.3281] [ 2123] [depth= 2] . ( 6 sec) [ -9743.7490] [ 2122] [depth= 1] . ( 6 sec) [ -9743.5979] [ 2127] [depth= 3] . ( 6 sec) [ -9742.6303] [ 2132] [depth= 1] . ( 7 sec) [ -9741.4754] [ 2131] [depth= 1] . ( 7 sec) [ -9741.2606] [ 2130] [depth= 2] . ( 7 sec) [ -9740.7326] [ 2130] [depth= 2] . ( 7 sec) [ -9740.7216] [ 2130] [depth= 1] . ( 7 sec) [ -9740.6827] [ 2130] [depth= 1] . ( 7 sec) [ -9740.4531] [ 2130] [depth= 1] . ( 8 sec) [ -9733.8317] [ 2121] [depth= 2] . ( 8 sec) [ -9733.6174] [ 2123] [depth= 1] . ( 8 sec) [ -9727.0212] [ 2122] [depth= 1] . ( 8 sec) [ -9726.6709] [ 2124] [depth= 1] . ( 9 sec) [ -9724.9296] [ 2128] [depth= 2] . ( 9 sec) [ -9713.1122] [Branch lengths ] . ( 9 sec) [ -9713.0579] [GTR parameters ] . ( 9 sec) [ -9712.5992] [Alpha ][ 0.894594] . ( 9 sec) [ -9712.1661] [ 2119] [depth= 1] . ( 11 sec) [ -9711.9525] [ 2117] [depth= 1] . ( 11 sec) [ -9711.8875] [ 2116] [depth= 1] . ( 11 sec) [ -9711.6987] [ 2116] [depth= 1] . ( 12 sec) [ -9711.3124] [ 2119] [depth= 1] . ( 12 sec) [ -9711.1548] [ 2116] [depth= 1] . ( 12 sec) [ -9711.1099] [ 2116] [depth= 1] . ( 13 sec) [ -9709.5205] [Branch lengths ] . ( 13 sec) [ -9709.5186] [GTR parameters ] . ( 13 sec) [ -9709.4759] [Alpha ][ 0.914358] . ( 18 sec) [ -9709.3141] [Branch lengths ] . ( 40 sec) [ -9709.2966] [Branch lengths ] . ( 40 sec) [ -9709.2966] [Topology ] . ( 41 sec) [ -9709.2664] [Topology ] . ( 41 sec) [ -9709.1680] [Topology ] . ( 42 sec) [ -9709.1498] [Topology ] . ( 43 sec) [ -9709.1443] [Topology ] . ( 44 sec) [ -9709.1423] [Topology ] . ( 45 sec) [ -9709.1416] [Topology ] . ( 45 sec) [ -9709.1389] [GTR parameters ] . ( 45 sec) [ -9709.1357] [Alpha ][ 0.919783] . ( 45 sec) [ -9709.1357] [Topology ] . ( 46 sec) [ -9709.1352] [Topology ] . ( 46 sec) [ -9709.1351] [GTR parameters ] . ( 46 sec) [ -9709.1351] [Alpha ][ 0.919783] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9709.135137. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9766.742204 . ( 0 sec) [ -9764.5406] [GTR parameters ] . ( 0 sec) [ -9762.3882] [Alpha ][ 0.854371] . ( 0 sec) [ -9762.3882] [Topology ] . ( 1 sec) [ -9719.6165] [Topology ] . ( 2 sec) [ -9712.6303] [Topology ] . ( 3 sec) [ -9710.9518] [Topology ] . ( 3 sec) [ -9710.2725] [Topology ] . ( 4 sec) [ -9709.9654] [Topology ] . ( 5 sec) [ -9709.8205] [Topology ] . ( 6 sec) [ -9709.7502] [Topology ] . ( 6 sec) [ -9709.7153] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.715254 . ( 12 sec) [ -9709.6642] [GTR parameters ] . ( 12 sec) [ -9709.2487] [Alpha ][ 0.913010] . ( 12 sec) [ -9709.2487] [Topology ] . ( 13 sec) [ -9709.1890] [Topology ] . ( 14 sec) [ -9709.1643] [Topology ] . ( 15 sec) [ -9709.1525] [Topology ] . ( 15 sec) [ -9709.1467] [Topology ] . ( 16 sec) [ -9709.1438] [Topology ] . ( 17 sec) [ -9709.1423] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.142282 . ( 23 sec) [ -9709.1416] [GTR parameters ] . ( 23 sec) [ -9709.1373] [Alpha ][ 0.919319] . ( 23 sec) [ -9709.1373] [Topology ] . ( 23 sec) [ -9709.1361] [Topology ] . ( 24 sec) [ -9709.1355] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.135472 . ( 30 sec) [ -9709.1354] [GTR parameters ] . ( 30 sec) [ -9709.1354] [Alpha ][ 0.919319] . ( 30 sec) [ -9709.1354] [Topology ] . ( 31 sec) [ -9709.1352] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -9764.5406] [GTR parameters ] . ( 42 sec) [ -9762.3882] [Alpha ][ 0.854371] . ( 42 sec) [ -9760.8577] [ 2112] [depth= 1] . ( 44 sec) [ -9757.4661] [ 2113] [depth= 1] . ( 44 sec) [ -9757.2701] [ 2112] [depth= 1] . ( 44 sec) [ -9757.0556] [ 2115] [depth= 1] . ( 44 sec) [ -9749.7870] [ 2112] [depth= 1] . ( 45 sec) [ -9749.0051] [ 2113] [depth= 1] . ( 45 sec) [ -9747.9970] [ 2115] [depth= 1] . ( 45 sec) [ -9746.6938] [ 2115] [depth= 1] . ( 45 sec) [ -9744.3172] [ 2115] [depth= 2] . ( 45 sec) [ -9744.2986] [ 2115] [depth= 2] . ( 45 sec) [ -9742.9163] [ 2116] [depth= 1] . ( 46 sec) [ -9742.5842] [ 2118] [depth= 1] . ( 46 sec) [ -9717.7760] [Branch lengths ] . ( 46 sec) [ -9717.7457] [GTR parameters ] . ( 46 sec) [ -9717.4369] [Alpha ][ 0.905039] . ( 48 sec) [ -9712.8435] [ 2116] [depth= 1] . ( 49 sec) [ -9712.6392] [ 2115] [depth= 1] . ( 50 sec) [ -9712.3262] [ 2114] [depth= 1] . ( 50 sec) [ -9712.2889] [ 2113] [depth= 1] . ( 50 sec) [ -9711.9323] [ 2114] [depth= 1] . ( 51 sec) [ -9709.5417] [Branch lengths ] . ( 51 sec) [ -9709.5293] [GTR parameters ] . ( 51 sec) [ -9709.5173] [Alpha ][ 0.915573] . ( 55 sec) [ -9709.4609] [ 2115] [depth= 1] . ( 55 sec) [ -9709.1755] [Branch lengths ] . ( 55 sec) [ -9709.1753] [GTR parameters ] . ( 55 sec) [ -9709.1743] [Alpha ][ 0.918535] . ( 77 sec) [ -9709.1400] [Branch lengths ] . ( 77 sec) [ -9709.1400] [Topology ] . ( 78 sec) [ -9709.1369] [Topology ] . ( 79 sec) [ -9709.1360] [Topology ] . ( 79 sec) [ -9709.1359] [GTR parameters ] . ( 79 sec) [ -9709.1357] [Alpha ][ 0.919786] . ( 79 sec) [ -9709.1357] [Topology ] . ( 80 sec) [ -9709.1352] [Topology ] . ( 80 sec) [ -9709.1352] [GTR parameters ] . ( 80 sec) [ -9709.1352] [Alpha ][ 0.919786] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9709.135166 . Log likelihood obtained after SPR moves : -9709.135246 . Log likelihood of the current tree: -9709.135166. . Printing the most likely tree in file 'data38.phy_phyml_tree.txt'... . Best log likelihood : -9709.135010 . Time used 0h1m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo