.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data89.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 394 patterns found. (out of a total of 500 sites) . 98 sites without polymorphism (19.60%). . [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) [ -21615.6233] [GTR parameters ] . ( 0 sec) [ -21231.2167] [Alpha ][ 0.500960] . ( 0 sec) [ -21115.5640] [ 3847] [depth= 8] . ( 0 sec) [ -20607.1862] [ 3822] [depth= 13] . ( 0 sec) [ -20508.8640] [ 3815] [depth= 1] . ( 0 sec) [ -20500.5561] [ 3810] [depth= 7] . ( 0 sec) [ -20346.4110] [ 3765] [depth= 7] . ( 0 sec) [ -17507.2940] [ 3750] [depth= 8] . ( 0 sec) [ -17214.8990] [ 3719] [depth= 5] . ( 0 sec) [ -16764.6419] [ 3734] [depth= 3] . ( 0 sec) [ -16307.8335] [ 3595] [depth= 4] . ( 0 sec) [ -16030.7096] [ 3504] [depth= 10] . ( 0 sec) [ -15954.1426] [ 3501] [depth= 6] . ( 0 sec) [ -14915.8211] [ 3333] [depth= 5] . ( 1 sec) [ -14741.9278] [ 3330] [depth= 6] . ( 1 sec) [ -14214.8953] [ 3332] [depth= 4] . ( 1 sec) [ -14142.7044] [ 3322] [depth= 2] . ( 1 sec) [ -14118.2558] [ 3321] [depth= 2] . ( 1 sec) [ -14055.1671] [ 3307] [depth= 2] . ( 1 sec) [ -13944.1428] [ 3296] [depth= 1] . ( 1 sec) [ -13678.4340] [ 3277] [depth= 1] . ( 1 sec) [ -13463.6372] [ 3183] [depth= 1] . ( 1 sec) [ -13266.4433] [ 3170] [depth= 6] . ( 1 sec) [ -13195.4817] [ 3164] [depth= 1] . ( 1 sec) [ -13006.7342] [ 3137] [depth= 7] . ( 1 sec) [ -12841.5051] [ 3011] [depth= 18] . ( 1 sec) [ -12630.3449] [ 2976] [depth= 5] . ( 1 sec) [ -12588.9111] [ 2975] [depth= 3] . ( 1 sec) [ -12251.9401] [ 2890] [depth= 7] . ( 1 sec) [ -12097.6628] [ 2839] [depth= 9] . ( 1 sec) [ -11947.8915] [ 2796] [depth= 7] . ( 1 sec) [ -11927.9739] [ 2784] [depth= 7] . ( 1 sec) [ -11724.3985] [ 2762] [depth= 5] . ( 1 sec) [ -11647.4966] [ 2750] [depth= 2] . ( 1 sec) [ -11628.9105] [ 2739] [depth= 1] . ( 1 sec) [ -11514.1131] [ 2727] [depth= 3] . ( 1 sec) [ -11379.0146] [ 2691] [depth= 3] . ( 2 sec) [ -10969.9971] [ 2575] [depth= 5] . ( 2 sec) [ -10784.2200] [ 2492] [depth= 1] . ( 2 sec) [ -10715.2603] [ 2479] [depth= 1] . ( 2 sec) [ -10709.5152] [ 2482] [depth= 2] . ( 2 sec) [ -10536.8145] [ 2379] [depth= 12] . ( 2 sec) [ -10365.8147] [ 2280] [depth= 4] . ( 2 sec) [ -10329.3205] [ 2259] [depth= 3] . ( 2 sec) [ -10327.5298] [ 2259] [depth= 1] . ( 2 sec) [ -10063.1734] [ 2146] [depth= 5] . ( 2 sec) [ -9955.1696] [ 2131] [depth= 1] . ( 2 sec) [ -9943.8759] [ 2140] [depth= 1] . ( 2 sec) [ -9938.1052] [ 2139] [depth= 1] . ( 2 sec) [ -9875.9462] [ 2134] [depth= 4] . ( 2 sec) [ -9789.4172] [ 2135] [depth= 1] . ( 2 sec) [ -9730.2846] [ 2117] [depth= 1] . ( 2 sec) [ -9620.3498] [ 2113] [depth= 3] . ( 2 sec) [ -9589.3611] [ 2096] [depth= 2] . ( 2 sec) [ -9463.9648] [ 2086] [depth= 4] . ( 2 sec) [ -9235.5950] [ 1984] [depth= 3] . ( 2 sec) [ -9229.5396] [ 1981] [depth= 1] . ( 2 sec) [ -9171.3601] [ 1946] [depth= 2] . ( 3 sec) [ -9110.4615] [ 1934] [depth= 1] . ( 3 sec) [ -9053.7150] [ 1906] [depth= 1] . ( 3 sec) [ -9003.6845] [ 1893] [depth= 2] . ( 3 sec) [ -8778.7798] [ 1877] [depth= 2] . ( 3 sec) [ -8762.3090] [ 1870] [depth= 1] . ( 3 sec) [ -8746.2788] [ 1862] [depth= 1] . ( 3 sec) [ -8590.6678] [ 1832] [depth= 4] . ( 3 sec) [ -8585.5162] [ 1831] [depth= 1] . ( 3 sec) [ -8544.0554] [ 1743] [depth= 4] . ( 3 sec) [ -8531.7751] [ 1745] [depth= 1] . ( 4 sec) [ -8246.8069] [ 1717] [depth= 2] . ( 4 sec) [ -8243.9348] [ 1717] [depth= 1] . ( 4 sec) [ -8213.3822] [ 1706] [depth= 1] . ( 4 sec) [ -8209.2737] [ 1708] [depth= 5] . ( 4 sec) [ -8206.5448] [ 1708] [depth= 5] . ( 4 sec) [ -8187.9805] [ 1700] [depth= 4] . ( 4 sec) [ -8177.5832] [ 1703] [depth= 1] . ( 4 sec) [ -8083.2381] [ 1691] [depth= 1] . ( 4 sec) [ -8077.2664] [ 1673] [depth= 1] . ( 4 sec) [ -8076.3820] [ 1674] [depth= 1] . ( 5 sec) [ -7874.4957] [Branch lengths ] . ( 5 sec) [ -7869.8057] [GTR parameters ] . ( 5 sec) [ -7846.6824] [Alpha ][ 0.836341] . ( 5 sec) [ -7846.4011] [ 1675] [depth= 1] . ( 5 sec) [ -7838.9331] [ 1665] [depth= 3] . ( 5 sec) [ -7829.3500] [ 1651] [depth= 3] . ( 5 sec) [ -7826.8012] [ 1642] [depth= 2] . ( 6 sec) [ -7825.7930] [ 1640] [depth= 1] . ( 6 sec) [ -7809.5050] [ 1640] [depth= 2] . ( 6 sec) [ -7665.9426] [ 1548] [depth= 2] . ( 6 sec) [ -7662.4376] [ 1541] [depth= 1] . ( 6 sec) [ -7656.7775] [ 1544] [depth= 1] . ( 6 sec) [ -7654.1507] [ 1544] [depth= 3] . ( 6 sec) [ -7621.2930] [ 1541] [depth= 1] . ( 7 sec) [ -7620.5484] [ 1544] [depth= 1] . ( 7 sec) [ -7620.4095] [ 1544] [depth= 1] . ( 7 sec) [ -7620.1770] [ 1544] [depth= 1] . ( 7 sec) [ -7619.3793] [ 1551] [depth= 1] . ( 7 sec) [ -7605.9564] [ 1543] [depth= 2] . ( 8 sec) [ -7605.8843] [ 1543] [depth= 2] . ( 8 sec) [ -7605.4598] [ 1541] [depth= 1] . ( 8 sec) [ -7604.5334] [ 1542] [depth= 1] . ( 8 sec) [ -7600.1715] [ 1541] [depth= 2] . ( 8 sec) [ -7599.7394] [ 1541] [depth= 1] . ( 8 sec) [ -7599.3691] [ 1541] [depth= 1] . ( 8 sec) [ -7599.3356] [ 1541] [depth= 1] . ( 9 sec) [ -7585.5152] [Branch lengths ] . ( 9 sec) [ -7585.0073] [GTR parameters ] . ( 9 sec) [ -7582.1593] [Alpha ][ 1.020509] . ( 9 sec) [ -7581.9934] [ 1543] [depth= 1] . ( 10 sec) [ -7581.8824] [ 1543] [depth= 1] . ( 12 sec) [ -7581.2926] [Branch lengths ] . ( 13 sec) [ -7581.2844] [GTR parameters ] . ( 13 sec) [ -7581.2748] [Alpha ][ 1.032851] . ( 14 sec) [ -7580.9538] [ 1540] [depth= 1] . ( 22 sec) [ -7580.9423] [ 1540] [depth= 1] . ( 33 sec) [ -7580.7755] [Branch lengths ] . ( 34 sec) [ -7580.7752] [GTR parameters ] . ( 34 sec) [ -7580.7751] [Alpha ][ 1.034117] . ( 34 sec) [ -7580.7751] [Topology ] . ( 34 sec) [ -7580.6382] [Topology ] . ( 35 sec) [ -7580.3570] [Topology ] . ( 36 sec) [ -7579.6674] [Topology ] . ( 37 sec) [ -7579.5762] [Topology ] . ( 37 sec) [ -7579.5648] [Topology ] . ( 38 sec) [ -7579.5633] [Topology ] . ( 39 sec) [ -7579.5630] [Topology ] . ( 39 sec) [ -7579.5591] [GTR parameters ] . ( 39 sec) [ -7579.5570] [Alpha ][ 1.039920] . ( 39 sec) [ -7579.5570] [Topology ] . ( 40 sec) [ -7579.5568] [Topology ] . ( 40 sec) [ -7579.5568] [GTR parameters ] . ( 40 sec) [ -7579.5568] [Alpha ][ 1.039920] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.556793. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18436.1567] [GTR parameters ] . ( 1 sec) [ -18029.9098] [Alpha ][ 0.500960] . ( 1 sec) [ -18020.9309] [ 3849] [depth= 1] . ( 1 sec) [ -17734.5536] [ 3802] [depth= 4] . ( 1 sec) [ -17490.8092] [ 3770] [depth= 4] . ( 1 sec) [ -17115.0286] [ 3774] [depth= 7] . ( 1 sec) [ -16870.1532] [ 3681] [depth= 1] . ( 1 sec) [ -16825.8604] [ 3668] [depth= 6] . ( 1 sec) [ -16812.8146] [ 3657] [depth= 1] . ( 1 sec) [ -16737.2398] [ 3654] [depth= 4] . ( 1 sec) [ -16587.2903] [ 3614] [depth= 4] . ( 1 sec) [ -16347.2351] [ 3608] [depth= 4] . ( 1 sec) [ -16037.2594] [ 3517] [depth= 12] . ( 1 sec) [ -15961.5310] [ 3512] [depth= 3] . ( 1 sec) [ -15945.4339] [ 3440] [depth= 1] . ( 1 sec) [ -15898.9815] [ 3430] [depth= 4] . ( 1 sec) [ -15501.3643] [ 3346] [depth= 22] . ( 1 sec) [ -15298.2183] [ 3304] [depth= 4] . ( 2 sec) [ -15106.8146] [ 3278] [depth= 5] . ( 2 sec) [ -15076.2921] [ 3282] [depth= 1] . ( 2 sec) [ -14922.9847] [ 3282] [depth= 1] . ( 2 sec) [ -14118.4792] [ 3208] [depth= 2] . ( 2 sec) [ -13865.8432] [ 3182] [depth= 2] . ( 2 sec) [ -13664.5892] [ 3136] [depth= 13] . ( 2 sec) [ -13284.8532] [ 3081] [depth= 18] . ( 2 sec) [ -12940.3600] [ 2946] [depth= 10] . ( 2 sec) [ -12415.4278] [ 2869] [depth= 9] . ( 2 sec) [ -12167.3990] [ 2794] [depth= 2] . ( 2 sec) [ -11944.3287] [ 2728] [depth= 12] . ( 2 sec) [ -11930.1542] [ 2727] [depth= 1] . ( 2 sec) [ -11630.9545] [ 2634] [depth= 5] . ( 2 sec) [ -11615.5427] [ 2635] [depth= 1] . ( 2 sec) [ -11596.5027] [ 2614] [depth= 1] . ( 2 sec) [ -11589.0985] [ 2635] [depth= 1] . ( 2 sec) [ -11401.3655] [ 2512] [depth= 12] . ( 2 sec) [ -11246.0322] [ 2489] [depth= 2] . ( 2 sec) [ -10936.0348] [ 2468] [depth= 6] . ( 2 sec) [ -10808.3420] [ 2427] [depth= 5] . ( 2 sec) [ -10783.2486] [ 2430] [depth= 1] . ( 2 sec) [ -10759.8735] [ 2400] [depth= 10] . ( 3 sec) [ -10520.1842] [ 2272] [depth= 7] . ( 3 sec) [ -10316.3894] [ 2274] [depth= 2] . ( 3 sec) [ -10041.4401] [ 2229] [depth= 5] . ( 3 sec) [ -10020.9619] [ 2207] [depth= 1] . ( 3 sec) [ -10016.5440] [ 2206] [depth= 1] . ( 3 sec) [ -9983.8681] [ 2203] [depth= 1] . ( 3 sec) [ -9610.0472] [ 2078] [depth= 4] . ( 3 sec) [ -9538.6083] [ 2045] [depth= 1] . ( 3 sec) [ -9416.8729] [ 2020] [depth= 7] . ( 3 sec) [ -9315.0512] [ 1978] [depth= 5] . ( 3 sec) [ -9207.9300] [ 1959] [depth= 2] . ( 3 sec) [ -9080.2252] [ 1934] [depth= 2] . ( 3 sec) [ -9069.1601] [ 1934] [depth= 1] . ( 3 sec) [ -8848.1412] [ 1852] [depth= 4] . ( 3 sec) [ -8831.6115] [ 1857] [depth= 5] . ( 3 sec) [ -8818.8628] [ 1857] [depth= 1] . ( 3 sec) [ -8771.4710] [ 1858] [depth= 1] . ( 3 sec) [ -8680.8089] [ 1817] [depth= 7] . ( 3 sec) [ -8634.2851] [ 1819] [depth= 1] . ( 4 sec) [ -8634.0534] [ 1820] [depth= 1] . ( 4 sec) [ -8626.8879] [ 1818] [depth= 1] . ( 4 sec) [ -8601.3590] [ 1819] [depth= 2] . ( 4 sec) [ -8598.0036] [ 1820] [depth= 4] . ( 4 sec) [ -8446.7612] [ 1791] [depth= 6] . ( 4 sec) [ -8446.2373] [ 1793] [depth= 1] . ( 4 sec) [ -8426.0951] [ 1786] [depth= 4] . ( 4 sec) [ -8421.3784] [ 1782] [depth= 1] . ( 4 sec) [ -8245.5303] [ 1734] [depth= 1] . ( 4 sec) [ -8198.7772] [ 1723] [depth= 2] . ( 4 sec) [ -8117.8200] [ 1685] [depth= 3] . ( 4 sec) [ -8078.5489] [ 1667] [depth= 2] . ( 4 sec) [ -8077.6171] [ 1670] [depth= 2] . ( 4 sec) [ -8076.6567] [ 1668] [depth= 1] . ( 4 sec) [ -8051.2706] [ 1663] [depth= 2] . ( 4 sec) [ -8030.6674] [ 1649] [depth= 3] . ( 4 sec) [ -8022.7877] [ 1644] [depth= 1] . ( 4 sec) [ -7926.0937] [ 1609] [depth= 3] . ( 4 sec) [ -7848.4837] [ 1588] [depth= 1] . ( 5 sec) [ -7823.9600] [ 1579] [depth= 1] . ( 5 sec) [ -7673.6416] [Branch lengths ] . ( 5 sec) [ -7669.7711] [GTR parameters ] . ( 5 sec) [ -7635.6636] [Alpha ][ 0.967085] . ( 6 sec) [ -7634.8168] [ 1582] [depth= 1] . ( 6 sec) [ -7634.3552] [ 1585] [depth= 1] . ( 6 sec) [ -7622.6431] [ 1569] [depth= 1] . ( 6 sec) [ -7615.8233] [ 1568] [depth= 2] . ( 6 sec) [ -7605.9016] [ 1560] [depth= 1] . ( 6 sec) [ -7605.8322] [ 1559] [depth= 1] . ( 6 sec) [ -7605.8209] [ 1559] [depth= 1] . ( 6 sec) [ -7604.2541] [ 1559] [depth= 1] . ( 6 sec) [ -7602.5902] [ 1555] [depth= 1] . ( 7 sec) [ -7602.4525] [ 1555] [depth= 1] . ( 7 sec) [ -7592.2090] [ 1546] [depth= 1] . ( 7 sec) [ -7591.6498] [ 1547] [depth= 1] . ( 7 sec) [ -7591.6334] [ 1547] [depth= 1] . ( 7 sec) [ -7591.6224] [ 1547] [depth= 1] . ( 8 sec) [ -7590.5086] [ 1543] [depth= 1] . ( 8 sec) [ -7588.9426] [ 1539] [depth= 1] . ( 9 sec) [ -7580.9594] [Branch lengths ] . ( 9 sec) [ -7580.8477] [GTR parameters ] . ( 9 sec) [ -7580.5917] [Alpha ][ 1.027526] . ( 12 sec) [ -7580.0555] [Branch lengths ] . ( 25 sec) [ -7579.7387] [ 1537] [depth= 1] . ( 31 sec) [ -7579.5793] [Branch lengths ] . ( 31 sec) [ -7579.5791] [GTR parameters ] . ( 31 sec) [ -7579.5716] [Alpha ][ 1.038478] . ( 32 sec) [ -7579.5716] [Topology ] . ( 32 sec) [ -7579.5621] [Topology ] . ( 33 sec) [ -7579.5593] [Topology ] . ( 34 sec) [ -7579.5581] [Topology ] . ( 35 sec) [ -7579.5575] [Topology ] . ( 35 sec) [ -7579.5575] [GTR parameters ] . ( 35 sec) [ -7579.5574] [Alpha ][ 1.039573] . ( 35 sec) [ -7579.5574] [Topology ] . ( 35 sec) [ -7579.5571] [Topology ] . ( 36 sec) [ -7579.5571] [GTR parameters ] . ( 36 sec) [ -7579.5571] [Alpha ][ 1.039573] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.557108. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20171.5930] [GTR parameters ] . ( 1 sec) [ -19701.1250] [Alpha ][ 0.500960] . ( 1 sec) [ -19524.7544] [ 4035] [depth= 4] . ( 1 sec) [ -19235.9028] [ 3977] [depth= 4] . ( 1 sec) [ -18899.1089] [ 3939] [depth= 4] . ( 1 sec) [ -18429.2101] [ 3938] [depth= 2] . ( 1 sec) [ -18366.6912] [ 3878] [depth= 1] . ( 1 sec) [ -18285.8435] [ 3877] [depth= 1] . ( 1 sec) [ -17778.1309] [ 3808] [depth= 7] . ( 1 sec) [ -17747.0230] [ 3811] [depth= 8] . ( 1 sec) [ -17746.4083] [ 3812] [depth= 1] . ( 1 sec) [ -17740.9460] [ 3811] [depth= 1] . ( 1 sec) [ -17236.5116] [ 3707] [depth= 16] . ( 1 sec) [ -17234.1130] [ 3708] [depth= 2] . ( 1 sec) [ -17211.2646] [ 3705] [depth= 7] . ( 1 sec) [ -17201.8606] [ 3682] [depth= 2] . ( 2 sec) [ -17092.5020] [ 3657] [depth= 4] . ( 2 sec) [ -16985.5397] [ 3656] [depth= 1] . ( 2 sec) [ -16786.1772] [ 3599] [depth= 10] . ( 2 sec) [ -16675.7620] [ 3556] [depth= 6] . ( 2 sec) [ -16562.7718] [ 3549] [depth= 1] . ( 2 sec) [ -16490.3801] [ 3548] [depth= 1] . ( 2 sec) [ -16255.9954] [ 3522] [depth= 4] . ( 2 sec) [ -16094.2725] [ 3397] [depth= 9] . ( 2 sec) [ -15979.1366] [ 3285] [depth= 2] . ( 2 sec) [ -15874.2154] [ 3278] [depth= 1] . ( 2 sec) [ -15810.4339] [ 3252] [depth= 1] . ( 2 sec) [ -15568.7669] [ 3176] [depth= 6] . ( 2 sec) [ -15565.9448] [ 3183] [depth= 1] . ( 2 sec) [ -15322.2859] [ 3119] [depth= 9] . ( 2 sec) [ -15226.7988] [ 3087] [depth= 1] . ( 2 sec) [ -14987.9280] [ 3061] [depth= 12] . ( 2 sec) [ -14984.4452] [ 3061] [depth= 1] . ( 2 sec) [ -14832.0753] [ 3063] [depth= 2] . ( 2 sec) [ -14645.7733] [ 2954] [depth= 10] . ( 2 sec) [ -14523.9605] [ 2925] [depth= 1] . ( 2 sec) [ -14399.1902] [ 2881] [depth= 1] . ( 2 sec) [ -14296.0276] [ 2854] [depth= 8] . ( 2 sec) [ -14271.2360] [ 2860] [depth= 1] . ( 3 sec) [ -14020.1267] [ 2754] [depth= 11] . ( 3 sec) [ -14014.7952] [ 2755] [depth= 1] . ( 3 sec) [ -13969.5046] [ 2750] [depth= 1] . ( 3 sec) [ -13969.4207] [ 2750] [depth= 2] . ( 3 sec) [ -13811.8326] [ 2729] [depth= 6] . ( 3 sec) [ -13105.6499] [ 2706] [depth= 1] . ( 3 sec) [ -12904.7674] [ 2703] [depth= 1] . ( 3 sec) [ -12837.0221] [ 2672] [depth= 3] . ( 3 sec) [ -12819.2600] [ 2673] [depth= 2] . ( 3 sec) [ -12627.8172] [ 2582] [depth= 1] . ( 3 sec) [ -12625.1875] [ 2582] [depth= 2] . ( 3 sec) [ -12414.6283] [ 2425] [depth= 5] . ( 3 sec) [ -12169.0581] [ 2422] [depth= 1] . ( 3 sec) [ -12141.4425] [ 2368] [depth= 2] . ( 3 sec) [ -12137.4001] [ 2369] [depth= 2] . ( 3 sec) [ -12103.3372] [ 2340] [depth= 1] . ( 3 sec) [ -11765.8221] [ 2319] [depth= 4] . ( 3 sec) [ -11755.8158] [ 2318] [depth= 1] . ( 3 sec) [ -11699.4600] [ 2311] [depth= 1] . ( 3 sec) [ -11548.9192] [ 2234] [depth= 6] . ( 4 sec) [ -10899.7592] [ 2263] [depth= 6] . ( 4 sec) [ -10872.9377] [ 2248] [depth= 3] . ( 4 sec) [ -10669.5173] [ 2251] [depth= 1] . ( 4 sec) [ -10623.0218] [ 2255] [depth= 11] . ( 4 sec) [ -10482.1297] [ 2261] [depth= 11] . ( 4 sec) [ -10438.3086] [ 2259] [depth= 8] . ( 4 sec) [ -10174.3180] [ 2249] [depth= 1] . ( 4 sec) [ -10034.8863] [ 2143] [depth= 1] . ( 4 sec) [ -9629.0055] [ 1990] [depth= 5] . ( 4 sec) [ -9440.8197] [ 1985] [depth= 1] . ( 4 sec) [ -9440.7355] [ 2025] [depth= 1] . ( 4 sec) [ -9419.0434] [ 2012] [depth= 1] . ( 4 sec) [ -9279.9943] [ 1986] [depth= 1] . ( 4 sec) [ -9189.5321] [ 1987] [depth= 1] . ( 4 sec) [ -9177.5839] [ 1983] [depth= 1] . ( 4 sec) [ -9169.3621] [ 1982] [depth= 4] . ( 4 sec) [ -9085.4032] [ 1982] [depth= 4] . ( 4 sec) [ -8939.5275] [ 1970] [depth= 5] . ( 4 sec) [ -8908.6625] [ 1956] [depth= 1] . ( 4 sec) [ -8677.4875] [ 1878] [depth= 3] . ( 4 sec) [ -8665.7391] [ 1878] [depth= 1] . ( 4 sec) [ -8663.0792] [ 1878] [depth= 1] . ( 4 sec) [ -8600.5479] [ 1856] [depth= 7] . ( 5 sec) [ -8420.7469] [ 1859] [depth= 1] . ( 5 sec) [ -8416.7608] [ 1856] [depth= 1] . ( 5 sec) [ -8224.7112] [ 1812] [depth= 9] . ( 5 sec) [ -8054.5096] [Branch lengths ] . ( 5 sec) [ -8049.3869] [GTR parameters ] . ( 5 sec) [ -8030.0218] [Alpha ][ 0.802183] . ( 6 sec) [ -7977.5121] [ 1784] [depth= 1] . ( 6 sec) [ -7977.2484] [ 1788] [depth= 2] . ( 6 sec) [ -7977.0393] [ 1796] [depth= 2] . ( 6 sec) [ -7967.2737] [ 1772] [depth= 1] . ( 6 sec) [ -7966.9877] [ 1766] [depth= 2] . ( 6 sec) [ -7966.6394] [ 1766] [depth= 2] . ( 6 sec) [ -7962.3390] [ 1765] [depth= 1] . ( 6 sec) [ -7927.0656] [ 1743] [depth= 1] . ( 6 sec) [ -7922.5363] [ 1748] [depth= 1] . ( 6 sec) [ -7872.1123] [ 1716] [depth= 1] . ( 6 sec) [ -7825.5342] [ 1667] [depth= 1] . ( 6 sec) [ -7749.1147] [ 1596] [depth= 4] . ( 6 sec) [ -7735.9535] [ 1581] [depth= 1] . ( 6 sec) [ -7732.0604] [ 1583] [depth= 1] . ( 6 sec) [ -7730.0114] [ 1577] [depth= 2] . ( 7 sec) [ -7729.8744] [ 1577] [depth= 1] . ( 7 sec) [ -7729.8566] [ 1577] [depth= 1] . ( 7 sec) [ -7718.9603] [ 1578] [depth= 2] . ( 7 sec) [ -7718.9383] [ 1578] [depth= 1] . ( 7 sec) [ -7672.4000] [ 1575] [depth= 1] . ( 7 sec) [ -7670.0445] [ 1573] [depth= 1] . ( 7 sec) [ -7656.3875] [ 1569] [depth= 1] . ( 7 sec) [ -7656.1049] [ 1570] [depth= 1] . ( 7 sec) [ -7654.5613] [ 1569] [depth= 1] . ( 7 sec) [ -7654.1968] [ 1569] [depth= 1] . ( 7 sec) [ -7652.2625] [ 1564] [depth= 1] . ( 7 sec) [ -7635.3022] [ 1555] [depth= 2] . ( 8 sec) [ -7633.7701] [ 1560] [depth= 2] . ( 8 sec) [ -7617.1363] [ 1540] [depth= 2] . ( 8 sec) [ -7604.7017] [ 1541] [depth= 1] . ( 8 sec) [ -7604.6140] [ 1541] [depth= 1] . ( 8 sec) [ -7601.9622] [ 1539] [depth= 1] . ( 8 sec) [ -7601.9487] [ 1539] [depth= 1] . ( 8 sec) [ -7601.0372] [ 1538] [depth= 1] . ( 8 sec) [ -7601.0209] [ 1539] [depth= 1] . ( 9 sec) [ -7585.7764] [Branch lengths ] . ( 9 sec) [ -7585.6172] [GTR parameters ] . ( 9 sec) [ -7581.5269] [Alpha ][ 1.018724] . ( 11 sec) [ -7581.4741] [ 1541] [depth= 1] . ( 11 sec) [ -7581.2572] [ 1537] [depth= 1] . ( 11 sec) [ -7581.1851] [ 1536] [depth= 1] . ( 12 sec) [ -7579.7568] [Branch lengths ] . ( 13 sec) [ -7579.7171] [GTR parameters ] . ( 13 sec) [ -7579.6989] [Alpha ][ 1.035749] . ( 16 sec) [ -7579.5857] [Branch lengths ] . ( 36 sec) [ -7579.5739] [Branch lengths ] . ( 36 sec) [ -7579.5739] [Topology ] . ( 37 sec) [ -7579.5732] [Topology ] . ( 37 sec) [ -7579.5730] [GTR parameters ] . ( 37 sec) [ -7579.5721] [Alpha ][ 1.039413] . ( 37 sec) [ -7579.5721] [Topology ] . ( 38 sec) [ -7579.5718] [Topology ] . ( 39 sec) [ -7579.5718] [GTR parameters ] . ( 39 sec) [ -7579.5718] [Alpha ][ 1.039413] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -7579.5575] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.557471. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19603.3004] [GTR parameters ] . ( 1 sec) [ -19148.6527] [Alpha ][ 0.500960] . ( 1 sec) [ -18974.3983] [ 4041] [depth= 9] . ( 1 sec) [ -18809.4600] [ 3992] [depth= 8] . ( 2 sec) [ -18802.1878] [ 3993] [depth= 2] . ( 2 sec) [ -18653.2776] [ 3955] [depth= 6] . ( 2 sec) [ -18607.1493] [ 3928] [depth= 1] . ( 2 sec) [ -18379.9982] [ 3876] [depth= 8] . ( 2 sec) [ -18189.0524] [ 3856] [depth= 2] . ( 2 sec) [ -17032.9397] [ 3843] [depth= 5] . ( 2 sec) [ -16117.5481] [ 3794] [depth= 2] . ( 2 sec) [ -15705.8419] [ 3795] [depth= 4] . ( 2 sec) [ -15591.2842] [ 3766] [depth= 7] . ( 2 sec) [ -15526.6806] [ 3769] [depth= 1] . ( 2 sec) [ -15203.4299] [ 3663] [depth= 2] . ( 2 sec) [ -14829.9800] [ 3542] [depth= 4] . ( 2 sec) [ -14667.3808] [ 3509] [depth= 10] . ( 2 sec) [ -14654.4423] [ 3510] [depth= 1] . ( 2 sec) [ -14518.1222] [ 3501] [depth= 1] . ( 2 sec) [ -14234.5508] [ 3434] [depth= 8] . ( 2 sec) [ -13814.4074] [ 3277] [depth= 14] . ( 2 sec) [ -13541.2748] [ 3216] [depth= 1] . ( 2 sec) [ -13540.7153] [ 3208] [depth= 4] . ( 2 sec) [ -13193.1183] [ 3175] [depth= 3] . ( 2 sec) [ -13085.7564] [ 3178] [depth= 19] . ( 2 sec) [ -13063.4723] [ 3178] [depth= 18] . ( 2 sec) [ -13008.3464] [ 3215] [depth= 5] . ( 2 sec) [ -12876.2895] [ 3169] [depth= 4] . ( 2 sec) [ -12672.4055] [ 3058] [depth= 5] . ( 3 sec) [ -12506.2125] [ 3031] [depth= 19] . ( 3 sec) [ -12428.9068] [ 3000] [depth= 12] . ( 3 sec) [ -12332.8693] [ 2990] [depth= 1] . ( 3 sec) [ -12023.4013] [ 2965] [depth= 5] . ( 3 sec) [ -11876.3819] [ 2930] [depth= 1] . ( 3 sec) [ -11807.2629] [ 2850] [depth= 5] . ( 3 sec) [ -11056.4639] [ 2700] [depth= 5] . ( 3 sec) [ -10959.7482] [ 2655] [depth= 3] . ( 3 sec) [ -10845.0351] [ 2609] [depth= 6] . ( 3 sec) [ -10701.2850] [ 2550] [depth= 3] . ( 3 sec) [ -10502.0777] [ 2455] [depth= 5] . ( 3 sec) [ -10472.7541] [ 2431] [depth= 1] . ( 3 sec) [ -10353.2250] [ 2411] [depth= 11] . ( 3 sec) [ -10321.3765] [ 2411] [depth= 4] . ( 3 sec) [ -10115.6280] [ 2321] [depth= 15] . ( 3 sec) [ -10107.4051] [ 2318] [depth= 1] . ( 3 sec) [ -10099.8204] [ 2317] [depth= 4] . ( 3 sec) [ -10054.6331] [ 2264] [depth= 3] . ( 3 sec) [ -10024.6296] [ 2262] [depth= 2] . ( 3 sec) [ -10023.7392] [ 2260] [depth= 1] . ( 3 sec) [ -10011.1218] [ 2258] [depth= 3] . ( 3 sec) [ -10011.0951] [ 2258] [depth= 1] . ( 3 sec) [ -9853.2714] [ 2243] [depth= 1] . ( 4 sec) [ -9847.6517] [ 2242] [depth= 2] . ( 4 sec) [ -9813.4640] [ 2226] [depth= 1] . ( 4 sec) [ -9689.1934] [ 2207] [depth= 10] . ( 4 sec) [ -9675.1896] [ 2180] [depth= 10] . ( 4 sec) [ -9596.6755] [ 2149] [depth= 2] . ( 4 sec) [ -9527.4259] [ 2141] [depth= 6] . ( 4 sec) [ -9381.2384] [ 2118] [depth= 4] . ( 4 sec) [ -9338.9658] [ 2089] [depth= 1] . ( 4 sec) [ -9335.0546] [ 2088] [depth= 1] . ( 4 sec) [ -9123.4316] [ 2057] [depth= 6] . ( 4 sec) [ -9099.6997] [ 2068] [depth= 1] . ( 4 sec) [ -8983.3400] [ 2068] [depth= 2] . ( 4 sec) [ -8960.0677] [ 2060] [depth= 1] . ( 5 sec) [ -8951.8499] [ 2060] [depth= 1] . ( 5 sec) [ -8943.0578] [ 2059] [depth= 3] . ( 5 sec) [ -8938.6896] [ 2057] [depth= 1] . ( 5 sec) [ -8914.8041] [ 2059] [depth= 2] . ( 5 sec) [ -8905.6168] [ 2069] [depth= 1] . ( 5 sec) [ -8898.5459] [ 2070] [depth= 2] . ( 5 sec) [ -8896.5727] [ 2073] [depth= 1] . ( 5 sec) [ -8802.0300] [ 2022] [depth= 4] . ( 5 sec) [ -8605.7716] [ 1887] [depth= 4] . ( 5 sec) [ -8597.6802] [ 1888] [depth= 1] . ( 5 sec) [ -8591.7399] [ 1889] [depth= 1] . ( 5 sec) [ -8577.1087] [ 1885] [depth= 4] . ( 5 sec) [ -8526.6105] [ 1878] [depth= 3] . ( 5 sec) [ -8496.6523] [ 1867] [depth= 1] . ( 5 sec) [ -8496.3376] [ 1866] [depth= 2] . ( 6 sec) [ -8310.1816] [Branch lengths ] . ( 6 sec) [ -8304.5673] [GTR parameters ] . ( 6 sec) [ -8282.1062] [Alpha ][ 0.812746] . ( 6 sec) [ -8257.1833] [ 1802] [depth= 5] . ( 6 sec) [ -8256.6123] [ 1803] [depth= 1] . ( 6 sec) [ -8088.0252] [ 1680] [depth= 8] . ( 6 sec) [ -7965.8767] [ 1652] [depth= 1] . ( 6 sec) [ -7957.0307] [ 1656] [depth= 1] . ( 6 sec) [ -7915.2590] [ 1637] [depth= 3] . ( 7 sec) [ -7896.6505] [ 1631] [depth= 1] . ( 7 sec) [ -7896.6378] [ 1631] [depth= 1] . ( 7 sec) [ -7891.0965] [ 1629] [depth= 1] . ( 7 sec) [ -7868.2996] [ 1622] [depth= 3] . ( 7 sec) [ -7857.0367] [ 1619] [depth= 1] . ( 7 sec) [ -7621.5874] [ 1545] [depth= 2] . ( 7 sec) [ -7618.1653] [ 1544] [depth= 2] . ( 7 sec) [ -7611.8688] [ 1547] [depth= 1] . ( 8 sec) [ -7611.8523] [ 1547] [depth= 2] . ( 8 sec) [ -7601.6064] [ 1542] [depth= 2] . ( 8 sec) [ -7600.6042] [ 1545] [depth= 1] . ( 8 sec) [ -7596.1160] [ 1544] [depth= 2] . ( 8 sec) [ -7596.0283] [ 1543] [depth= 1] . ( 8 sec) [ -7595.6912] [ 1544] [depth= 1] . ( 8 sec) [ -7595.4790] [ 1542] [depth= 1] . ( 8 sec) [ -7595.1520] [ 1542] [depth= 1] . ( 9 sec) [ -7595.0898] [ 1542] [depth= 1] . ( 9 sec) [ -7594.7129] [ 1542] [depth= 1] . ( 9 sec) [ -7587.1320] [Branch lengths ] . ( 10 sec) [ -7586.8761] [GTR parameters ] . ( 10 sec) [ -7583.2030] [Alpha ][ 1.018626] . ( 11 sec) [ -7583.1532] [ 1543] [depth= 1] . ( 11 sec) [ -7582.7657] [ 1543] [depth= 1] . ( 13 sec) [ -7581.8214] [Branch lengths ] . ( 13 sec) [ -7581.7925] [GTR parameters ] . ( 13 sec) [ -7581.7748] [Alpha ][ 1.035379] . ( 16 sec) [ -7580.5809] [Branch lengths ] . ( 26 sec) [ -7580.1904] [ 1540] [depth= 1] . ( 27 sec) [ -7580.1742] [ 1540] [depth= 1] . ( 35 sec) [ -7579.6546] [Branch lengths ] . ( 36 sec) [ -7579.6541] [GTR parameters ] . ( 36 sec) [ -7579.6534] [Alpha ][ 1.038499] . ( 36 sec) [ -7579.6534] [Topology ] . ( 36 sec) [ -7579.5664] [Topology ] . ( 37 sec) [ -7579.5587] [Topology ] . ( 38 sec) [ -7579.5575] [Topology ] . ( 39 sec) [ -7579.5572] [Topology ] . ( 39 sec) [ -7579.5571] [GTR parameters ] . ( 39 sec) [ -7579.5569] [Alpha ][ 1.039877] . ( 39 sec) [ -7579.5569] [Topology ] . ( 40 sec) [ -7579.5569] [Topology ] . ( 40 sec) [ -7579.5568] [GTR parameters ] . ( 40 sec) [ -7579.5568] [Alpha ][ 1.039877] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.556841. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19535.1063] [GTR parameters ] . ( 1 sec) [ -19096.3212] [Alpha ][ 0.500960] . ( 1 sec) [ -19000.7116] [ 4034] [depth= 9] . ( 1 sec) [ -18643.6118] [ 3976] [depth= 11] . ( 1 sec) [ -18275.4206] [ 3957] [depth= 6] . ( 1 sec) [ -18228.8941] [ 3956] [depth= 5] . ( 1 sec) [ -18132.0580] [ 3919] [depth= 4] . ( 1 sec) [ -17949.6905] [ 3915] [depth= 4] . ( 1 sec) [ -17797.2461] [ 3887] [depth= 7] . ( 1 sec) [ -17703.1864] [ 3852] [depth= 2] . ( 1 sec) [ -17524.2317] [ 3799] [depth= 10] . ( 1 sec) [ -17073.3110] [ 3697] [depth= 1] . ( 1 sec) [ -16966.9890] [ 3662] [depth= 1] . ( 2 sec) [ -16682.1832] [ 3598] [depth= 10] . ( 2 sec) [ -16620.5877] [ 3573] [depth= 3] . ( 2 sec) [ -16572.9064] [ 3569] [depth= 2] . ( 2 sec) [ -16483.9733] [ 3574] [depth= 1] . ( 2 sec) [ -16399.8473] [ 3546] [depth= 5] . ( 2 sec) [ -16162.8697] [ 3446] [depth= 5] . ( 2 sec) [ -15763.6316] [ 3435] [depth= 1] . ( 2 sec) [ -15722.6349] [ 3425] [depth= 1] . ( 2 sec) [ -15383.7510] [ 3410] [depth= 8] . ( 2 sec) [ -14989.2243] [ 3305] [depth= 14] . ( 2 sec) [ -14778.3985] [ 3258] [depth= 1] . ( 2 sec) [ -14491.7762] [ 3257] [depth= 2] . ( 2 sec) [ -14339.9087] [ 3257] [depth= 1] . ( 2 sec) [ -14134.5887] [ 3215] [depth= 1] . ( 2 sec) [ -13748.7299] [ 3166] [depth= 5] . ( 2 sec) [ -13723.5895] [ 3180] [depth= 1] . ( 2 sec) [ -13599.2742] [ 3179] [depth= 2] . ( 2 sec) [ -13595.6396] [ 3170] [depth= 1] . ( 2 sec) [ -13134.6485] [ 3008] [depth= 10] . ( 2 sec) [ -13130.9981] [ 3011] [depth= 13] . ( 2 sec) [ -13124.0759] [ 2979] [depth= 1] . ( 2 sec) [ -12942.1948] [ 2964] [depth= 5] . ( 2 sec) [ -12583.2903] [ 2863] [depth= 7] . ( 3 sec) [ -12496.0556] [ 2856] [depth= 9] . ( 3 sec) [ -12112.3875] [ 2831] [depth= 4] . ( 3 sec) [ -12021.6284] [ 2751] [depth= 3] . ( 3 sec) [ -11991.2354] [ 2714] [depth= 1] . ( 3 sec) [ -11776.2010] [ 2685] [depth= 5] . ( 3 sec) [ -11674.1776] [ 2657] [depth= 1] . ( 3 sec) [ -11474.0000] [ 2579] [depth= 7] . ( 3 sec) [ -11455.1440] [ 2542] [depth= 11] . ( 3 sec) [ -11364.3942] [ 2550] [depth= 1] . ( 3 sec) [ -11356.9623] [ 2549] [depth= 1] . ( 3 sec) [ -10899.7835] [ 2459] [depth= 6] . ( 3 sec) [ -10720.7714] [ 2456] [depth= 4] . ( 3 sec) [ -10713.7673] [ 2442] [depth= 9] . ( 3 sec) [ -10709.0915] [ 2442] [depth= 1] . ( 3 sec) [ -10466.8917] [ 2390] [depth= 5] . ( 3 sec) [ -10456.5702] [ 2390] [depth= 1] . ( 3 sec) [ -10121.3299] [ 2308] [depth= 11] . ( 3 sec) [ -10095.0083] [ 2247] [depth= 3] . ( 3 sec) [ -9999.3187] [ 2240] [depth= 2] . ( 3 sec) [ -9975.7821] [ 2263] [depth= 1] . ( 3 sec) [ -9654.0812] [ 2165] [depth= 3] . ( 3 sec) [ -9610.4423] [ 2136] [depth= 1] . ( 3 sec) [ -9536.2731] [ 2120] [depth= 4] . ( 4 sec) [ -9195.4187] [ 1971] [depth= 4] . ( 4 sec) [ -9174.1604] [ 1955] [depth= 2] . ( 4 sec) [ -9129.7768] [ 1945] [depth= 4] . ( 4 sec) [ -9099.2326] [ 1947] [depth= 1] . ( 4 sec) [ -9069.3815] [ 1946] [depth= 2] . ( 4 sec) [ -9004.0302] [ 1904] [depth= 6] . ( 4 sec) [ -8957.0434] [ 1897] [depth= 1] . ( 4 sec) [ -8951.8977] [ 1896] [depth= 1] . ( 4 sec) [ -8929.9642] [ 1889] [depth= 1] . ( 4 sec) [ -8897.0840] [ 1887] [depth= 2] . ( 4 sec) [ -8822.2637] [ 1872] [depth= 2] . ( 4 sec) [ -8755.6697] [ 1868] [depth= 1] . ( 4 sec) [ -8637.7280] [ 1859] [depth= 4] . ( 4 sec) [ -8613.8764] [ 1863] [depth= 1] . ( 4 sec) [ -8505.0143] [ 1831] [depth= 3] . ( 4 sec) [ -8471.2510] [ 1798] [depth= 3] . ( 4 sec) [ -8465.9433] [ 1801] [depth= 1] . ( 5 sec) [ -8445.7864] [ 1802] [depth= 1] . ( 5 sec) [ -8430.6673] [ 1785] [depth= 2] . ( 5 sec) [ -8407.4283] [ 1784] [depth= 1] . ( 5 sec) [ -8406.7752] [ 1784] [depth= 1] . ( 5 sec) [ -8380.4567] [ 1678] [depth= 3] . ( 5 sec) [ -8341.6560] [ 1666] [depth= 1] . ( 5 sec) [ -8246.7646] [Branch lengths ] . ( 6 sec) [ -8243.0671] [GTR parameters ] . ( 6 sec) [ -8221.8171] [Alpha ][ 0.805265] . ( 6 sec) [ -8131.1655] [ 1586] [depth= 13] . ( 6 sec) [ -8066.2522] [ 1600] [depth= 1] . ( 6 sec) [ -7849.3739] [ 1586] [depth= 3] . ( 6 sec) [ -7838.1606] [ 1573] [depth= 3] . ( 6 sec) [ -7834.4654] [ 1550] [depth= 2] . ( 6 sec) [ -7833.6610] [ 1548] [depth= 1] . ( 6 sec) [ -7833.2828] [ 1548] [depth= 1] . ( 6 sec) [ -7831.4015] [ 1548] [depth= 1] . ( 7 sec) [ -7800.4507] [ 1569] [depth= 1] . ( 7 sec) [ -7777.5239] [ 1573] [depth= 2] . ( 7 sec) [ -7777.4517] [ 1573] [depth= 1] . ( 7 sec) [ -7775.6446] [ 1572] [depth= 1] . ( 7 sec) [ -7759.7614] [ 1569] [depth= 1] . ( 7 sec) [ -7759.6570] [ 1570] [depth= 1] . ( 7 sec) [ -7759.6433] [ 1570] [depth= 1] . ( 7 sec) [ -7736.5657] [ 1561] [depth= 1] . ( 7 sec) [ -7725.5879] [ 1539] [depth= 1] . ( 8 sec) [ -7717.4279] [ 1540] [depth= 1] . ( 8 sec) [ -7712.2925] [ 1543] [depth= 2] . ( 8 sec) [ -7659.9477] [ 1552] [depth= 1] . ( 8 sec) [ -7659.9227] [ 1552] [depth= 1] . ( 8 sec) [ -7656.3917] [ 1549] [depth= 1] . ( 8 sec) [ -7652.6575] [ 1552] [depth= 1] . ( 8 sec) [ -7652.5594] [ 1552] [depth= 1] . ( 8 sec) [ -7651.6655] [ 1548] [depth= 1] . ( 9 sec) [ -7651.6134] [ 1548] [depth= 1] . ( 9 sec) [ -7649.3348] [ 1548] [depth= 1] . ( 9 sec) [ -7637.2069] [Branch lengths ] . ( 10 sec) [ -7636.5129] [GTR parameters ] . ( 10 sec) [ -7633.2051] [Alpha ][ 0.992047] . ( 10 sec) [ -7633.1400] [ 1551] [depth= 1] . ( 10 sec) [ -7633.0193] [ 1548] [depth= 1] . ( 10 sec) [ -7628.2187] [ 1539] [depth= 1] . ( 11 sec) [ -7627.9910] [ 1541] [depth= 1] . ( 13 sec) [ -7627.3225] [Branch lengths ] . ( 14 sec) [ -7627.2432] [GTR parameters ] . ( 14 sec) [ -7627.2397] [Alpha ][ 0.998969] . ( 17 sec) [ -7626.4874] [Branch lengths ] . ( 36 sec) [ -7620.1535] [Branch lengths ] . ( 36 sec) [ -7620.1535] [Topology ] . ( 37 sec) [ -7598.2539] [Topology ] . ( 37 sec) [ -7583.8653] [Topology ] . ( 38 sec) [ -7580.5231] [Topology ] . ( 39 sec) [ -7580.0220] [Topology ] . ( 40 sec) [ -7579.9391] [Topology ] . ( 40 sec) [ -7579.9168] [Topology ] . ( 41 sec) [ -7579.9082] [Topology ] . ( 41 sec) [ -7579.8871] [GTR parameters ] . ( 41 sec) [ -7579.7812] [Alpha ][ 1.038063] . ( 41 sec) [ -7579.7812] [Topology ] . ( 42 sec) [ -7579.7779] [Topology ] . ( 43 sec) [ -7579.7774] [Topology ] . ( 43 sec) [ -7579.7767] [GTR parameters ] . ( 43 sec) [ -7579.7766] [Alpha ][ 1.039159] . ( 43 sec) [ -7579.7766] [Topology ] . ( 44 sec) [ -7579.7764] [Topology ] . ( 44 sec) [ -7579.7764] [GTR parameters ] . ( 44 sec) [ -7579.7764] [Alpha ][ 1.039159] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -7579.5730] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -7579.5592] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7579.559196. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7626.759928 . ( 1 sec) [ -7623.0405] [GTR parameters ] . ( 1 sec) [ -7623.0403] [Alpha ][ 0.998309] . ( 1 sec) [ -7623.0403] [Topology ] . ( 2 sec) [ -7584.2163] [Topology ] . ( 2 sec) [ -7580.8218] [Topology ] . ( 3 sec) [ -7580.1370] [Topology ] . ( 4 sec) [ -7579.9092] [Topology ] . ( 5 sec) [ -7579.8162] [Topology ] . ( 5 sec) [ -7579.7754] [Topology ] . ( 6 sec) [ -7579.7569] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.756885 . ( 12 sec) [ -7579.6895] [GTR parameters ] . ( 12 sec) [ -7579.5945] [Alpha ][ 1.035635] . ( 12 sec) [ -7579.5945] [Topology ] . ( 12 sec) [ -7579.5739] [Topology ] . ( 13 sec) [ -7579.5652] [Topology ] . ( 14 sec) [ -7579.5613] [Topology ] . ( 15 sec) [ -7579.5595] [Topology ] . ( 16 sec) [ -7579.5587] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.558706 . ( 21 sec) [ -7579.5585] [GTR parameters ] . ( 21 sec) [ -7579.5576] [Alpha ][ 1.039455] . ( 21 sec) [ -7579.5576] [Topology ] . ( 22 sec) [ -7579.5571] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.557055 . ( 27 sec) [ -7579.5570] [GTR parameters ] . ( 27 sec) [ -7579.5570] [Alpha ][ 1.039455] . ( 27 sec) [ -7579.5570] [Topology ] . ( 28 sec) [ -7579.5568] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -7623.0405] [GTR parameters ] . ( 39 sec) [ -7623.0403] [Alpha ][ 0.998309] . ( 39 sec) [ -7616.5408] [ 1537] [depth= 1] . ( 39 sec) [ -7616.4135] [ 1539] [depth= 1] . ( 39 sec) [ -7609.9858] [ 1538] [depth= 1] . ( 39 sec) [ -7608.1413] [ 1535] [depth= 1] . ( 39 sec) [ -7607.8058] [ 1537] [depth= 2] . ( 40 sec) [ -7607.5327] [ 1538] [depth= 1] . ( 40 sec) [ -7606.0527] [ 1537] [depth= 1] . ( 40 sec) [ -7605.7705] [ 1538] [depth= 1] . ( 40 sec) [ -7605.1930] [ 1541] [depth= 1] . ( 40 sec) [ -7603.6643] [ 1540] [depth= 1] . ( 40 sec) [ -7602.8445] [ 1539] [depth= 1] . ( 40 sec) [ -7602.8066] [ 1540] [depth= 1] . ( 41 sec) [ -7601.6894] [ 1543] [depth= 1] . ( 41 sec) [ -7601.3458] [ 1544] [depth= 1] . ( 41 sec) [ -7601.2756] [ 1544] [depth= 1] . ( 41 sec) [ -7601.2532] [ 1544] [depth= 1] . ( 41 sec) [ -7601.2270] [ 1544] [depth= 1] . ( 41 sec) [ -7601.1958] [ 1544] [depth= 1] . ( 42 sec) [ -7581.4935] [Branch lengths ] . ( 42 sec) [ -7581.3826] [GTR parameters ] . ( 42 sec) [ -7581.3201] [Alpha ][ 1.028495] . ( 43 sec) [ -7581.0498] [ 1544] [depth= 1] . ( 44 sec) [ -7581.0022] [ 1543] [depth= 1] . ( 45 sec) [ -7580.1785] [Branch lengths ] . ( 45 sec) [ -7580.1738] [GTR parameters ] . ( 46 sec) [ -7580.1688] [Alpha ][ 1.037407] . ( 49 sec) [ -7580.0718] [Branch lengths ] . ( 65 sec) [ -7579.7724] [ 1540] [depth= 1] . ( 66 sec) [ -7579.7605] [ 1540] [depth= 1] . ( 68 sec) [ -7579.6569] [Branch lengths ] . ( 68 sec) [ -7579.6561] [GTR parameters ] . ( 68 sec) [ -7579.6561] [Alpha ][ 1.038444] . ( 68 sec) [ -7579.6561] [Topology ] . ( 69 sec) [ -7579.5662] [Topology ] . ( 69 sec) [ -7579.5582] [Topology ] . ( 70 sec) [ -7579.5572] [Topology ] . ( 71 sec) [ -7579.5570] [Topology ] . ( 71 sec) [ -7579.5568] [GTR parameters ] . ( 71 sec) [ -7579.5566] [Alpha ][ 1.039872] . ( 71 sec) [ -7579.5566] [Topology ] . ( 72 sec) [ -7579.5566] [Topology ] . ( 72 sec) [ -7579.5566] [GTR parameters ] . ( 72 sec) [ -7579.5566] [Alpha ][ 1.039872] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7579.556808 . Log likelihood obtained after SPR moves : -7579.556552 . Log likelihood of the current tree: -7579.556552. . Printing the most likely tree in file 'data89.phy_phyml_tree.txt'... . Best log likelihood : -7579.556552 . Time used 0h1m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo