.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data40.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... . 426 patterns found. (out of a total of 500 sites) . 70 sites without polymorphism (14.00%). . [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)... . ( 1 sec) [ -17403.7369] [GTR parameters ] . ( 1 sec) [ -17182.9980] [Alpha ][ 0.500960] . ( 1 sec) [ -16987.9478] [ 3695] [depth= 8] . ( 1 sec) [ -16686.4335] [ 3651] [depth= 6] . ( 1 sec) [ -16645.9195] [ 3633] [depth= 1] . ( 1 sec) [ -16608.8224] [ 3619] [depth= 6] . ( 1 sec) [ -16570.0507] [ 3591] [depth= 1] . ( 1 sec) [ -16544.4920] [ 3579] [depth= 7] . ( 1 sec) [ -16504.3624] [ 3558] [depth= 11] . ( 1 sec) [ -16497.0758] [ 3557] [depth= 1] . ( 2 sec) [ -16428.1986] [ 3535] [depth= 1] . ( 2 sec) [ -16320.2043] [ 3515] [depth= 13] . ( 2 sec) [ -16233.1809] [ 3452] [depth= 1] . ( 2 sec) [ -16050.8281] [ 3419] [depth= 2] . ( 2 sec) [ -15749.7214] [ 3408] [depth= 5] . ( 2 sec) [ -15690.3768] [ 3414] [depth= 1] . ( 2 sec) [ -15618.3068] [ 3403] [depth= 4] . ( 2 sec) [ -15517.1998] [ 3355] [depth= 2] . ( 2 sec) [ -15462.1557] [ 3350] [depth= 1] . ( 2 sec) [ -15300.4634] [ 3328] [depth= 8] . ( 2 sec) [ -15296.0972] [ 3320] [depth= 2] . ( 2 sec) [ -15212.0467] [ 3283] [depth= 6] . ( 2 sec) [ -15014.1507] [ 3197] [depth= 15] . ( 2 sec) [ -15006.6290] [ 3198] [depth= 1] . ( 2 sec) [ -14805.5119] [ 3178] [depth= 11] . ( 2 sec) [ -14802.5622] [ 3184] [depth= 1] . ( 2 sec) [ -14708.7477] [ 3163] [depth= 10] . ( 2 sec) [ -14644.4143] [ 3154] [depth= 2] . ( 2 sec) [ -14510.4092] [ 3075] [depth= 7] . ( 2 sec) [ -14422.8533] [ 3096] [depth= 11] . ( 3 sec) [ -14155.4970] [ 3042] [depth= 5] . ( 3 sec) [ -13991.9734] [ 3022] [depth= 3] . ( 3 sec) [ -13934.3777] [ 3019] [depth= 1] . ( 3 sec) [ -13838.3842] [ 2989] [depth= 1] . ( 3 sec) [ -13799.4996] [ 2986] [depth= 2] . ( 3 sec) [ -13795.0035] [ 2984] [depth= 2] . ( 3 sec) [ -13662.6714] [ 2962] [depth= 1] . ( 3 sec) [ -13036.7571] [ 2912] [depth= 17] . ( 3 sec) [ -12939.8491] [ 2915] [depth= 3] . ( 3 sec) [ -12756.4737] [ 2817] [depth= 23] . ( 3 sec) [ -12752.6591] [ 2812] [depth= 1] . ( 3 sec) [ -12681.2685] [ 2788] [depth= 2] . ( 3 sec) [ -12564.1149] [ 2770] [depth= 1] . ( 3 sec) [ -12376.2546] [ 2709] [depth= 1] . ( 3 sec) [ -12215.1654] [ 2663] [depth= 7] . ( 3 sec) [ -12187.3583] [ 2654] [depth= 1] . ( 3 sec) [ -12184.8043] [ 2651] [depth= 1] . ( 3 sec) [ -12076.4117] [ 2618] [depth= 5] . ( 3 sec) [ -12036.8844] [ 2605] [depth= 2] . ( 3 sec) [ -11597.7302] [ 2566] [depth= 7] . ( 4 sec) [ -11176.8535] [ 2476] [depth= 1] . ( 4 sec) [ -11019.8825] [ 2427] [depth= 2] . ( 4 sec) [ -10866.1389] [ 2394] [depth= 6] . ( 4 sec) [ -10855.4618] [ 2390] [depth= 5] . ( 4 sec) [ -10720.2586] [ 2388] [depth= 2] . ( 4 sec) [ -10645.0866] [ 2350] [depth= 1] . ( 4 sec) [ -10588.7811] [ 2321] [depth= 7] . ( 4 sec) [ -10540.9731] [ 2296] [depth= 1] . ( 4 sec) [ -10442.7029] [ 2243] [depth= 7] . ( 4 sec) [ -10425.0774] [ 2231] [depth= 1] . ( 4 sec) [ -10398.2815] [ 2230] [depth= 1] . ( 4 sec) [ -10393.9502] [ 2244] [depth= 1] . ( 4 sec) [ -10390.5729] [ 2262] [depth= 1] . ( 4 sec) [ -10270.2178] [ 2217] [depth= 2] . ( 4 sec) [ -10226.8277] [ 2183] [depth= 2] . ( 4 sec) [ -10206.0008] [ 2174] [depth= 2] . ( 5 sec) [ -10200.8027] [ 2172] [depth= 1] . ( 5 sec) [ -10170.8233] [ 2180] [depth= 1] . ( 5 sec) [ -10137.4603] [ 2171] [depth= 1] . ( 5 sec) [ -10131.7582] [ 2166] [depth= 1] . ( 5 sec) [ -10131.5670] [ 2166] [depth= 1] . ( 5 sec) [ -10106.7737] [ 2155] [depth= 1] . ( 5 sec) [ -10103.6812] [ 2148] [depth= 2] . ( 5 sec) [ -10085.3134] [ 2139] [depth= 1] . ( 5 sec) [ -10080.7577] [ 2142] [depth= 1] . ( 5 sec) [ -10079.4648] [ 2143] [depth= 1] . ( 5 sec) [ -10065.2829] [ 2155] [depth= 1] . ( 5 sec) [ -10063.5176] [ 2154] [depth= 1] . ( 5 sec) [ -9925.9412] [Branch lengths ] . ( 6 sec) [ -9924.1602] [GTR parameters ] . ( 6 sec) [ -9884.0873] [Alpha ][ 0.948174] . ( 6 sec) [ -9878.1960] [ 2147] [depth= 2] . ( 7 sec) [ -9877.9770] [ 2148] [depth= 2] . ( 7 sec) [ -9877.6592] [ 2150] [depth= 1] . ( 7 sec) [ -9865.1436] [ 2138] [depth= 1] . ( 7 sec) [ -9864.2302] [ 2140] [depth= 1] . ( 8 sec) [ -9833.1511] [ 2124] [depth= 1] . ( 8 sec) [ -9833.0088] [ 2123] [depth= 1] . ( 8 sec) [ -9826.7803] [ 2118] [depth= 1] . ( 8 sec) [ -9825.5888] [ 2120] [depth= 1] . ( 8 sec) [ -9798.0712] [ 2111] [depth= 1] . ( 8 sec) [ -9795.1517] [ 2109] [depth= 1] . ( 9 sec) [ -9795.0100] [ 2113] [depth= 1] . ( 9 sec) [ -9783.4613] [ 2102] [depth= 1] . ( 10 sec) [ -9782.9744] [ 2103] [depth= 1] . ( 10 sec) [ -9782.8514] [ 2102] [depth= 2] . ( 10 sec) [ -9782.0178] [ 2101] [depth= 1] . ( 10 sec) [ -9781.8594] [ 2100] [depth= 1] . ( 10 sec) [ -9768.8999] [Branch lengths ] . ( 11 sec) [ -9768.7879] [GTR parameters ] . ( 11 sec) [ -9768.5368] [Alpha ][ 0.999205] . ( 11 sec) [ -9768.5245] [ 2101] [depth= 1] . ( 12 sec) [ -9768.5066] [ 2102] [depth= 1] . ( 15 sec) [ -9768.4761] [ 2101] [depth= 1] . ( 16 sec) [ -9767.4473] [Branch lengths ] . ( 16 sec) [ -9767.4466] [GTR parameters ] . ( 16 sec) [ -9767.4388] [Alpha ][ 1.008606] . ( 20 sec) [ -9767.3249] [Branch lengths ] . ( 24 sec) [ -9767.1644] [ 2095] [depth= 1] . ( 31 sec) [ -9767.1373] [ 2095] [depth= 1] . ( 44 sec) [ -9767.0118] [Branch lengths ] . ( 45 sec) [ -9767.0114] [GTR parameters ] . ( 45 sec) [ -9767.0107] [Alpha ][ 1.011305] . ( 45 sec) [ -9767.0107] [Topology ] . ( 46 sec) [ -9766.9614] [Topology ] . ( 47 sec) [ -9766.9323] [Topology ] . ( 48 sec) [ -9766.9292] [Topology ] . ( 49 sec) [ -9766.9282] [Topology ] . ( 49 sec) [ -9766.9279] [GTR parameters ] . ( 49 sec) [ -9766.9279] [Alpha ][ 1.011305] . ( 49 sec) [ -9766.9279] [Topology ] . ( 50 sec) [ -9766.9274] [Topology ] . ( 50 sec) [ -9766.9274] [GTR parameters ] . ( 50 sec) [ -9766.9274] [Alpha ][ 1.011305] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.927420. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17758.3318] [GTR parameters ] . ( 1 sec) [ -17512.5350] [Alpha ][ 0.500960] . ( 1 sec) [ -17320.9977] [ 3733] [depth= 4] . ( 2 sec) [ -16936.3139] [ 3658] [depth= 3] . ( 2 sec) [ -16844.1892] [ 3632] [depth= 4] . ( 2 sec) [ -16465.0227] [ 3625] [depth= 4] . ( 2 sec) [ -16358.9140] [ 3602] [depth= 1] . ( 2 sec) [ -16269.9608] [ 3600] [depth= 8] . ( 2 sec) [ -16237.4822] [ 3594] [depth= 1] . ( 2 sec) [ -16207.5351] [ 3587] [depth= 5] . ( 2 sec) [ -16089.1166] [ 3528] [depth= 1] . ( 2 sec) [ -15843.0717] [ 3515] [depth= 3] . ( 2 sec) [ -15671.4303] [ 3487] [depth= 4] . ( 2 sec) [ -15337.5256] [ 3468] [depth= 3] . ( 2 sec) [ -15150.9085] [ 3411] [depth= 7] . ( 2 sec) [ -14937.3478] [ 3393] [depth= 10] . ( 2 sec) [ -14713.7348] [ 3354] [depth= 15] . ( 3 sec) [ -14527.3761] [ 3293] [depth= 11] . ( 3 sec) [ -14421.5432] [ 3249] [depth= 9] . ( 3 sec) [ -14077.9931] [ 3237] [depth= 1] . ( 3 sec) [ -13910.1562] [ 3192] [depth= 7] . ( 3 sec) [ -13838.9232] [ 3187] [depth= 3] . ( 3 sec) [ -13441.9784] [ 3035] [depth= 3] . ( 3 sec) [ -13393.9739] [ 3051] [depth= 11] . ( 3 sec) [ -13266.2777] [ 3037] [depth= 8] . ( 3 sec) [ -13215.3856] [ 3031] [depth= 2] . ( 3 sec) [ -13092.4017] [ 2992] [depth= 7] . ( 3 sec) [ -13076.4143] [ 2980] [depth= 1] . ( 3 sec) [ -12917.6953] [ 2953] [depth= 7] . ( 4 sec) [ -12881.6634] [ 2946] [depth= 1] . ( 4 sec) [ -12875.2913] [ 2946] [depth= 3] . ( 4 sec) [ -12684.4723] [ 2882] [depth= 10] . ( 4 sec) [ -12625.8589] [ 2870] [depth= 7] . ( 4 sec) [ -12614.3751] [ 2862] [depth= 2] . ( 4 sec) [ -12511.8105] [ 2841] [depth= 2] . ( 4 sec) [ -12497.8475] [ 2837] [depth= 1] . ( 4 sec) [ -12483.4120] [ 2830] [depth= 1] . ( 4 sec) [ -12369.6831] [ 2782] [depth= 9] . ( 4 sec) [ -12278.3082] [ 2752] [depth= 1] . ( 4 sec) [ -12169.6203] [ 2750] [depth= 1] . ( 4 sec) [ -11985.3517] [ 2707] [depth= 9] . ( 4 sec) [ -11936.6941] [ 2674] [depth= 2] . ( 4 sec) [ -11922.2445] [ 2664] [depth= 1] . ( 4 sec) [ -11894.0701] [ 2661] [depth= 1] . ( 4 sec) [ -11893.6172] [ 2672] [depth= 2] . ( 4 sec) [ -11745.7838] [ 2662] [depth= 7] . ( 4 sec) [ -11641.1055] [ 2606] [depth= 1] . ( 5 sec) [ -11607.2700] [ 2602] [depth= 2] . ( 5 sec) [ -11592.2248] [ 2612] [depth= 1] . ( 5 sec) [ -11364.1572] [ 2550] [depth= 5] . ( 5 sec) [ -11205.6759] [ 2506] [depth= 3] . ( 5 sec) [ -11161.2667] [ 2485] [depth= 1] . ( 5 sec) [ -11053.7883] [ 2470] [depth= 3] . ( 5 sec) [ -10870.8697] [ 2434] [depth= 4] . ( 5 sec) [ -10846.7849] [ 2422] [depth= 1] . ( 5 sec) [ -10807.5896] [ 2397] [depth= 6] . ( 5 sec) [ -10791.1568] [ 2392] [depth= 1] . ( 5 sec) [ -10755.6153] [ 2360] [depth= 2] . ( 5 sec) [ -10754.0511] [ 2363] [depth= 8] . ( 5 sec) [ -10724.0995] [ 2343] [depth= 2] . ( 5 sec) [ -10697.1179] [ 2331] [depth= 9] . ( 5 sec) [ -10608.8668] [ 2298] [depth= 10] . ( 5 sec) [ -10529.8639] [ 2285] [depth= 3] . ( 5 sec) [ -10502.8387] [ 2284] [depth= 2] . ( 5 sec) [ -10441.4516] [ 2284] [depth= 1] . ( 6 sec) [ -10430.0412] [ 2286] [depth= 1] . ( 6 sec) [ -10373.0135] [ 2266] [depth= 1] . ( 6 sec) [ -10327.6470] [ 2243] [depth= 3] . ( 6 sec) [ -10314.0541] [ 2243] [depth= 1] . ( 6 sec) [ -10261.9440] [ 2206] [depth= 2] . ( 6 sec) [ -10252.5444] [ 2203] [depth= 1] . ( 6 sec) [ -10226.7895] [ 2196] [depth= 1] . ( 6 sec) [ -10221.6065] [ 2192] [depth= 3] . ( 6 sec) [ -10213.3521] [ 2196] [depth= 1] . ( 6 sec) [ -10202.9360] [ 2183] [depth= 3] . ( 6 sec) [ -10180.7845] [ 2175] [depth= 1] . ( 6 sec) [ -10028.5756] [Branch lengths ] . ( 7 sec) [ -10025.3039] [GTR parameters ] . ( 7 sec) [ -9981.8270] [Alpha ][ 0.962937] . ( 7 sec) [ -9967.3152] [ 2179] [depth= 3] . ( 7 sec) [ -9956.3668] [ 2178] [depth= 1] . ( 7 sec) [ -9930.9401] [ 2162] [depth= 1] . ( 7 sec) [ -9898.3394] [ 2150] [depth= 4] . ( 7 sec) [ -9897.5395] [ 2153] [depth= 1] . ( 8 sec) [ -9866.6695] [ 2140] [depth= 2] . ( 8 sec) [ -9841.9376] [ 2126] [depth= 2] . ( 8 sec) [ -9828.0858] [ 2122] [depth= 1] . ( 8 sec) [ -9826.0222] [ 2121] [depth= 1] . ( 8 sec) [ -9822.9156] [ 2116] [depth= 1] . ( 8 sec) [ -9820.5942] [ 2117] [depth= 1] . ( 8 sec) [ -9820.2827] [ 2121] [depth= 1] . ( 9 sec) [ -9820.0317] [ 2117] [depth= 1] . ( 9 sec) [ -9819.4161] [ 2118] [depth= 1] . ( 9 sec) [ -9788.9773] [ 2105] [depth= 1] . ( 10 sec) [ -9788.1652] [ 2100] [depth= 1] . ( 10 sec) [ -9786.0311] [ 2105] [depth= 1] . ( 10 sec) [ -9785.7716] [ 2098] [depth= 1] . ( 10 sec) [ -9771.3051] [Branch lengths ] . ( 11 sec) [ -9771.1081] [GTR parameters ] . ( 11 sec) [ -9770.9404] [Alpha ][ 1.004537] . ( 11 sec) [ -9770.6371] [ 2094] [depth= 1] . ( 15 sec) [ -9769.3608] [Branch lengths ] . ( 15 sec) [ -9769.3570] [GTR parameters ] . ( 15 sec) [ -9769.3536] [Alpha ][ 1.010701] . ( 20 sec) [ -9769.2587] [Branch lengths ] . ( 30 sec) [ -9767.9218] [ 2093] [depth= 2] . ( 44 sec) [ -9767.1774] [ 2092] [depth= 1] . ( 48 sec) [ -9766.9994] [Branch lengths ] . ( 48 sec) [ -9766.9954] [GTR parameters ] . ( 48 sec) [ -9766.9953] [Alpha ][ 1.011831] . ( 75 sec) [ -9766.9910] [Branch lengths ] . ( 75 sec) [ -9766.9910] [Topology ] . ( 76 sec) [ -9766.9904] [Topology ] . ( 76 sec) [ -9766.9903] [GTR parameters ] . ( 76 sec) [ -9766.9903] [Alpha ][ 1.011831] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.990350. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17997.0759] [GTR parameters ] . ( 1 sec) [ -17758.8871] [Alpha ][ 0.500960] . ( 1 sec) [ -17581.6799] [ 3796] [depth= 1] . ( 1 sec) [ -17356.4054] [ 3717] [depth= 8] . ( 1 sec) [ -17271.7734] [ 3705] [depth= 5] . ( 2 sec) [ -17094.2675] [ 3700] [depth= 6] . ( 2 sec) [ -16942.5575] [ 3667] [depth= 7] . ( 2 sec) [ -16473.6234] [ 3578] [depth= 10] . ( 2 sec) [ -16352.3515] [ 3565] [depth= 2] . ( 2 sec) [ -16221.1055] [ 3505] [depth= 1] . ( 2 sec) [ -15918.8689] [ 3436] [depth= 7] . ( 2 sec) [ -15545.2418] [ 3367] [depth= 6] . ( 2 sec) [ -15143.1197] [ 3293] [depth= 10] . ( 2 sec) [ -15065.8665] [ 3281] [depth= 1] . ( 2 sec) [ -14879.2264] [ 3271] [depth= 1] . ( 2 sec) [ -14556.6473] [ 3173] [depth= 6] . ( 2 sec) [ -14401.9564] [ 3163] [depth= 10] . ( 2 sec) [ -14342.0526] [ 3154] [depth= 1] . ( 2 sec) [ -14146.3134] [ 3067] [depth= 10] . ( 2 sec) [ -14125.8087] [ 3077] [depth= 4] . ( 3 sec) [ -14105.6452] [ 3066] [depth= 1] . ( 3 sec) [ -13970.7004] [ 3001] [depth= 10] . ( 3 sec) [ -13954.1760] [ 2988] [depth= 1] . ( 3 sec) [ -13931.0803] [ 2977] [depth= 1] . ( 3 sec) [ -13740.9386] [ 2934] [depth= 7] . ( 3 sec) [ -13693.7948] [ 2911] [depth= 1] . ( 3 sec) [ -13590.4094] [ 2863] [depth= 7] . ( 3 sec) [ -13148.5122] [ 2841] [depth= 11] . ( 3 sec) [ -12965.4950] [ 2788] [depth= 6] . ( 4 sec) [ -12951.0928] [ 2777] [depth= 1] . ( 4 sec) [ -12850.4183] [ 2772] [depth= 5] . ( 4 sec) [ -12665.9200] [ 2729] [depth= 10] . ( 4 sec) [ -12581.7491] [ 2705] [depth= 1] . ( 4 sec) [ -12563.3512] [ 2697] [depth= 1] . ( 4 sec) [ -12470.3234] [ 2665] [depth= 8] . ( 4 sec) [ -12458.8284] [ 2743] [depth= 1] . ( 4 sec) [ -12022.5338] [ 2727] [depth= 6] . ( 4 sec) [ -11997.8035] [ 2709] [depth= 1] . ( 4 sec) [ -11989.1909] [ 2603] [depth= 1] . ( 4 sec) [ -11864.9320] [ 2588] [depth= 4] . ( 5 sec) [ -11804.3956] [ 2584] [depth= 1] . ( 5 sec) [ -11770.3905] [ 2581] [depth= 1] . ( 5 sec) [ -11590.1785] [ 2520] [depth= 2] . ( 5 sec) [ -11520.9486] [ 2516] [depth= 1] . ( 5 sec) [ -11511.4440] [ 2507] [depth= 3] . ( 5 sec) [ -11501.7576] [ 2504] [depth= 2] . ( 5 sec) [ -11414.9449] [ 2462] [depth= 7] . ( 5 sec) [ -11187.1634] [ 2413] [depth= 8] . ( 5 sec) [ -10833.1701] [ 2376] [depth= 1] . ( 5 sec) [ -10808.1226] [ 2327] [depth= 1] . ( 5 sec) [ -10707.8955] [ 2320] [depth= 4] . ( 6 sec) [ -10655.8870] [ 2308] [depth= 7] . ( 6 sec) [ -10655.7757] [ 2310] [depth= 1] . ( 6 sec) [ -10579.0304] [ 2283] [depth= 2] . ( 6 sec) [ -10559.5500] [ 2274] [depth= 1] . ( 6 sec) [ -10490.3376] [ 2252] [depth= 1] . ( 6 sec) [ -10447.3169] [ 2256] [depth= 1] . ( 6 sec) [ -10348.1556] [ 2212] [depth= 3] . ( 6 sec) [ -10345.6425] [ 2212] [depth= 1] . ( 6 sec) [ -10280.2400] [ 2190] [depth= 4] . ( 7 sec) [ -10227.1859] [ 2163] [depth= 10] . ( 7 sec) [ -10083.1802] [ 2182] [depth= 1] . ( 7 sec) [ -10066.2616] [ 2163] [depth= 1] . ( 7 sec) [ -10044.9765] [ 2155] [depth= 2] . ( 7 sec) [ -10030.5766] [ 2153] [depth= 2] . ( 7 sec) [ -10028.5532] [ 2153] [depth= 1] . ( 7 sec) [ -10025.9906] [ 2152] [depth= 1] . ( 7 sec) [ -10018.1906] [ 2150] [depth= 1] . ( 8 sec) [ -10014.9923] [ 2154] [depth= 1] . ( 8 sec) [ -10001.1557] [ 2151] [depth= 1] . ( 8 sec) [ -9993.0654] [ 2144] [depth= 1] . ( 8 sec) [ -9956.8697] [ 2130] [depth= 1] . ( 8 sec) [ -9954.6595] [ 2131] [depth= 1] . ( 8 sec) [ -9952.1997] [ 2125] [depth= 1] . ( 9 sec) [ -9872.4293] [Branch lengths ] . ( 9 sec) [ -9868.8620] [GTR parameters ] . ( 10 sec) [ -9829.6460] [Alpha ][ 0.948255] . ( 10 sec) [ -9809.1880] [ 2104] [depth= 1] . ( 10 sec) [ -9806.9830] [ 2100] [depth= 1] . ( 10 sec) [ -9806.1582] [ 2098] [depth= 1] . ( 10 sec) [ -9801.4713] [ 2095] [depth= 1] . ( 11 sec) [ -9801.3292] [ 2097] [depth= 1] . ( 11 sec) [ -9800.8707] [ 2095] [depth= 1] . ( 11 sec) [ -9797.9320] [ 2096] [depth= 1] . ( 12 sec) [ -9790.2499] [ 2102] [depth= 2] . ( 13 sec) [ -9790.0556] [ 2101] [depth= 1] . ( 13 sec) [ -9789.6715] [ 2101] [depth= 1] . ( 13 sec) [ -9788.7336] [ 2097] [depth= 1] . ( 13 sec) [ -9787.6090] [ 2102] [depth= 2] . ( 14 sec) [ -9787.0109] [ 2098] [depth= 2] . ( 14 sec) [ -9786.7043] [ 2098] [depth= 2] . ( 14 sec) [ -9784.2091] [ 2095] [depth= 1] . ( 15 sec) [ -9783.6309] [ 2092] [depth= 1] . ( 15 sec) [ -9771.4641] [Branch lengths ] . ( 16 sec) [ -9771.4063] [GTR parameters ] . ( 16 sec) [ -9771.1106] [Alpha ][ 1.003872] . ( 19 sec) [ -9769.8795] [Branch lengths ] . ( 30 sec) [ -9768.5892] [ 2091] [depth= 2] . ( 36 sec) [ -9767.8525] [ 2090] [depth= 1] . ( 39 sec) [ -9767.7810] [ 2090] [depth= 1] . ( 40 sec) [ -9767.4467] [Branch lengths ] . ( 40 sec) [ -9767.4396] [GTR parameters ] . ( 40 sec) [ -9767.4313] [Alpha ][ 1.013599] . ( 62 sec) [ -9767.3921] [Branch lengths ] . ( 62 sec) [ -9767.3921] [Topology ] . ( 63 sec) [ -9767.0410] [Topology ] . ( 63 sec) [ -9767.0053] [Topology ] . ( 64 sec) [ -9766.9986] [Topology ] . ( 65 sec) [ -9766.9959] [Topology ] . ( 66 sec) [ -9766.9943] [Topology ] . ( 67 sec) [ -9766.9933] [Topology ] . ( 67 sec) [ -9766.9926] [Topology ] . ( 68 sec) [ -9766.9911] [GTR parameters ] . ( 68 sec) [ -9766.9910] [Alpha ][ 1.012015] . ( 68 sec) [ -9766.9910] [Topology ] . ( 68 sec) [ -9766.9905] [Topology ] . ( 69 sec) [ -9766.9904] [GTR parameters ] . ( 69 sec) [ -9766.9904] [Alpha ][ 1.012015] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.990450. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17267.7748] [GTR parameters ] . ( 1 sec) [ -17023.3592] [Alpha ][ 0.500960] . ( 1 sec) [ -16812.7855] [ 3736] [depth= 8] . ( 1 sec) [ -16539.5052] [ 3657] [depth= 9] . ( 1 sec) [ -16108.5553] [ 3620] [depth= 8] . ( 1 sec) [ -15804.9231] [ 3525] [depth= 1] . ( 1 sec) [ -15508.9242] [ 3515] [depth= 1] . ( 1 sec) [ -15380.8615] [ 3497] [depth= 3] . ( 1 sec) [ -15355.4536] [ 3488] [depth= 5] . ( 1 sec) [ -15202.4332] [ 3399] [depth= 5] . ( 1 sec) [ -15073.9007] [ 3386] [depth= 2] . ( 1 sec) [ -15051.0143] [ 3380] [depth= 3] . ( 1 sec) [ -15038.6865] [ 3379] [depth= 1] . ( 1 sec) [ -15021.4499] [ 3356] [depth= 4] . ( 1 sec) [ -14882.7800] [ 3359] [depth= 1] . ( 1 sec) [ -14662.7072] [ 3337] [depth= 4] . ( 2 sec) [ -14622.1772] [ 3321] [depth= 9] . ( 2 sec) [ -14614.4355] [ 3318] [depth= 1] . ( 2 sec) [ -14602.0606] [ 3305] [depth= 2] . ( 2 sec) [ -14570.5841] [ 3304] [depth= 1] . ( 2 sec) [ -14384.1936] [ 3247] [depth= 4] . ( 2 sec) [ -14286.7064] [ 3204] [depth= 11] . ( 2 sec) [ -14070.6704] [ 3152] [depth= 1] . ( 2 sec) [ -13982.4171] [ 3161] [depth= 6] . ( 2 sec) [ -13932.8145] [ 3145] [depth= 12] . ( 2 sec) [ -13672.3045] [ 3081] [depth= 5] . ( 2 sec) [ -13625.7135] [ 3069] [depth= 4] . ( 2 sec) [ -13602.4932] [ 3062] [depth= 9] . ( 2 sec) [ -13590.5367] [ 3051] [depth= 7] . ( 2 sec) [ -13557.0809] [ 3048] [depth= 1] . ( 2 sec) [ -13530.5647] [ 3044] [depth= 9] . ( 2 sec) [ -13518.6858] [ 3043] [depth= 3] . ( 2 sec) [ -13464.9913] [ 3027] [depth= 1] . ( 2 sec) [ -13240.3372] [ 2989] [depth= 8] . ( 3 sec) [ -13099.8686] [ 2948] [depth= 1] . ( 3 sec) [ -13048.2970] [ 2930] [depth= 1] . ( 3 sec) [ -12897.5260] [ 2888] [depth= 6] . ( 3 sec) [ -12653.3225] [ 2859] [depth= 13] . ( 3 sec) [ -12512.3738] [ 2806] [depth= 1] . ( 3 sec) [ -12490.3971] [ 2812] [depth= 12] . ( 3 sec) [ -12393.0950] [ 2799] [depth= 3] . ( 3 sec) [ -12344.8092] [ 2790] [depth= 5] . ( 3 sec) [ -12266.0928] [ 2789] [depth= 1] . ( 3 sec) [ -12186.6978] [ 2766] [depth= 7] . ( 3 sec) [ -12072.4219] [ 2718] [depth= 1] . ( 3 sec) [ -11951.5714] [ 2695] [depth= 7] . ( 3 sec) [ -11916.6700] [ 2692] [depth= 1] . ( 3 sec) [ -11770.0000] [ 2648] [depth= 2] . ( 3 sec) [ -11767.2414] [ 2646] [depth= 1] . ( 3 sec) [ -11752.2369] [ 2638] [depth= 1] . ( 3 sec) [ -11581.4774] [ 2624] [depth= 3] . ( 3 sec) [ -11561.6644] [ 2624] [depth= 1] . ( 3 sec) [ -11488.9770] [ 2588] [depth= 1] . ( 4 sec) [ -11457.9375] [ 2580] [depth= 5] . ( 4 sec) [ -11417.4336] [ 2571] [depth= 2] . ( 4 sec) [ -11416.8996] [ 2569] [depth= 1] . ( 4 sec) [ -11211.1710] [ 2567] [depth= 4] . ( 4 sec) [ -11180.3018] [ 2555] [depth= 2] . ( 4 sec) [ -11168.5932] [ 2545] [depth= 2] . ( 4 sec) [ -11053.5564] [ 2512] [depth= 3] . ( 4 sec) [ -10979.6358] [ 2487] [depth= 3] . ( 4 sec) [ -10887.5689] [ 2477] [depth= 4] . ( 4 sec) [ -10837.0110] [ 2457] [depth= 1] . ( 4 sec) [ -10816.7662] [ 2454] [depth= 1] . ( 4 sec) [ -10794.7352] [ 2466] [depth= 1] . ( 4 sec) [ -10791.6608] [ 2466] [depth= 4] . ( 4 sec) [ -10774.1354] [ 2452] [depth= 1] . ( 4 sec) [ -10736.6212] [ 2436] [depth= 1] . ( 4 sec) [ -10707.0612] [ 2418] [depth= 2] . ( 5 sec) [ -10706.9442] [ 2419] [depth= 1] . ( 5 sec) [ -10704.6333] [ 2420] [depth= 2] . ( 5 sec) [ -10626.0649] [ 2389] [depth= 1] . ( 5 sec) [ -10590.0343] [ 2372] [depth= 2] . ( 5 sec) [ -10564.2490] [ 2365] [depth= 2] . ( 5 sec) [ -10552.2685] [ 2367] [depth= 3] . ( 5 sec) [ -10525.5192] [ 2356] [depth= 1] . ( 5 sec) [ -10509.4420] [ 2351] [depth= 2] . ( 5 sec) [ -10485.9186] [ 2332] [depth= 1] . ( 6 sec) [ -10272.4943] [Branch lengths ] . ( 6 sec) [ -10269.9434] [GTR parameters ] . ( 6 sec) [ -10238.8858] [Alpha ][ 0.858616] . ( 6 sec) [ -10118.1511] [ 2262] [depth= 5] . ( 6 sec) [ -10114.8005] [ 2256] [depth= 2] . ( 6 sec) [ -10028.1357] [ 2221] [depth= 2] . ( 6 sec) [ -10014.3428] [ 2211] [depth= 3] . ( 7 sec) [ -9967.7916] [ 2188] [depth= 6] . ( 7 sec) [ -9964.5864] [ 2187] [depth= 1] . ( 7 sec) [ -9957.4403] [ 2181] [depth= 1] . ( 7 sec) [ -9957.3676] [ 2182] [depth= 1] . ( 7 sec) [ -9891.4729] [ 2141] [depth= 7] . ( 7 sec) [ -9882.9373] [ 2140] [depth= 4] . ( 7 sec) [ -9881.6678] [ 2138] [depth= 2] . ( 7 sec) [ -9865.7642] [ 2125] [depth= 1] . ( 7 sec) [ -9863.4236] [ 2125] [depth= 1] . ( 7 sec) [ -9856.9997] [ 2119] [depth= 1] . ( 7 sec) [ -9834.2900] [ 2115] [depth= 1] . ( 8 sec) [ -9834.0628] [ 2113] [depth= 1] . ( 8 sec) [ -9833.1654] [ 2114] [depth= 2] . ( 8 sec) [ -9828.1119] [ 2115] [depth= 1] . ( 8 sec) [ -9828.0140] [ 2116] [depth= 1] . ( 8 sec) [ -9824.5685] [ 2109] [depth= 1] . ( 9 sec) [ -9823.7713] [ 2112] [depth= 1] . ( 9 sec) [ -9821.9162] [ 2112] [depth= 1] . ( 9 sec) [ -9809.7152] [ 2102] [depth= 2] . ( 9 sec) [ -9802.1951] [ 2101] [depth= 1] . ( 9 sec) [ -9802.0710] [ 2100] [depth= 1] . ( 9 sec) [ -9801.9619] [ 2101] [depth= 1] . ( 10 sec) [ -9775.7179] [Branch lengths ] . ( 10 sec) [ -9775.4803] [GTR parameters ] . ( 10 sec) [ -9773.4551] [Alpha ][ 0.996282] . ( 10 sec) [ -9773.2762] [ 2104] [depth= 1] . ( 10 sec) [ -9773.1857] [ 2101] [depth= 2] . ( 11 sec) [ -9773.1380] [ 2105] [depth= 1] . ( 11 sec) [ -9773.0378] [ 2103] [depth= 1] . ( 12 sec) [ -9773.0201] [ 2101] [depth= 2] . ( 12 sec) [ -9770.6785] [ 2093] [depth= 1] . ( 13 sec) [ -9768.4821] [Branch lengths ] . ( 13 sec) [ -9768.4683] [GTR parameters ] . ( 13 sec) [ -9768.4507] [Alpha ][ 1.010530] . ( 16 sec) [ -9768.0747] [Branch lengths ] . ( 38 sec) [ -9767.4724] [Branch lengths ] . ( 38 sec) [ -9767.4724] [Topology ] . ( 39 sec) [ -9767.0800] [Topology ] . ( 40 sec) [ -9767.0083] [Topology ] . ( 40 sec) [ -9766.9808] [Topology ] . ( 41 sec) [ -9766.9650] [Topology ] . ( 42 sec) [ -9766.9549] [Topology ] . ( 43 sec) [ -9766.9482] [Topology ] . ( 43 sec) [ -9766.9438] [Topology ] . ( 44 sec) [ -9766.9377] [GTR parameters ] . ( 44 sec) [ -9766.9375] [Alpha ][ 1.011777] . ( 44 sec) [ -9766.9375] [Topology ] . ( 44 sec) [ -9766.9343] [Topology ] . ( 45 sec) [ -9766.9321] [Topology ] . ( 46 sec) [ -9766.9306] [Topology ] . ( 47 sec) [ -9766.9295] [Topology ] . ( 47 sec) [ -9766.9288] [Topology ] . ( 48 sec) [ -9766.9288] [GTR parameters ] . ( 48 sec) [ -9766.9288] [Alpha ][ 1.011777] . ( 48 sec) [ -9766.9288] [Topology ] . ( 48 sec) [ -9766.9282] [Topology ] . ( 49 sec) [ -9766.9282] [GTR parameters ] . ( 49 sec) [ -9766.9282] [Alpha ][ 1.011777] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.928226. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17752.9485] [GTR parameters ] . ( 1 sec) [ -17512.3784] [Alpha ][ 0.500960] . ( 1 sec) [ -17348.8529] [ 3802] [depth= 7] . ( 1 sec) [ -16844.1119] [ 3740] [depth= 11] . ( 1 sec) [ -16555.8803] [ 3716] [depth= 6] . ( 1 sec) [ -16501.2780] [ 3705] [depth= 3] . ( 1 sec) [ -16374.6742] [ 3634] [depth= 4] . ( 1 sec) [ -16293.2004] [ 3636] [depth= 2] . ( 1 sec) [ -16124.5847] [ 3632] [depth= 6] . ( 1 sec) [ -16063.9378] [ 3592] [depth= 15] . ( 1 sec) [ -15858.0473] [ 3571] [depth= 6] . ( 1 sec) [ -15688.0371] [ 3521] [depth= 1] . ( 1 sec) [ -15490.4273] [ 3466] [depth= 14] . ( 1 sec) [ -15319.6027] [ 3432] [depth= 7] . ( 1 sec) [ -15268.4285] [ 3432] [depth= 1] . ( 1 sec) [ -15135.0581] [ 3425] [depth= 5] . ( 1 sec) [ -15093.2094] [ 3414] [depth= 4] . ( 1 sec) [ -15071.0145] [ 3414] [depth= 1] . ( 1 sec) [ -15022.8559] [ 3393] [depth= 2] . ( 2 sec) [ -14999.2104] [ 3383] [depth= 2] . ( 2 sec) [ -14786.4663] [ 3383] [depth= 2] . ( 2 sec) [ -14649.3227] [ 3361] [depth= 11] . ( 2 sec) [ -14305.9280] [ 3225] [depth= 9] . ( 2 sec) [ -14229.9569] [ 3229] [depth= 1] . ( 2 sec) [ -13834.8338] [ 3088] [depth= 9] . ( 2 sec) [ -13768.7715] [ 3057] [depth= 2] . ( 2 sec) [ -13757.2847] [ 3056] [depth= 1] . ( 2 sec) [ -13644.9969] [ 3024] [depth= 5] . ( 2 sec) [ -13523.1163] [ 2983] [depth= 4] . ( 2 sec) [ -13521.5507] [ 2987] [depth= 1] . ( 2 sec) [ -13283.9880] [ 2966] [depth= 5] . ( 2 sec) [ -13189.2256] [ 2931] [depth= 4] . ( 2 sec) [ -13115.0393] [ 2905] [depth= 1] . ( 2 sec) [ -12801.1961] [ 2829] [depth= 12] . ( 2 sec) [ -12738.5105] [ 2815] [depth= 6] . ( 2 sec) [ -12711.3596] [ 2813] [depth= 10] . ( 2 sec) [ -12512.2015] [ 2769] [depth= 1] . ( 2 sec) [ -12361.8421] [ 2741] [depth= 4] . ( 3 sec) [ -12310.0041] [ 2699] [depth= 1] . ( 3 sec) [ -12186.8792] [ 2656] [depth= 1] . ( 3 sec) [ -12167.2055] [ 2648] [depth= 1] . ( 3 sec) [ -12069.4239] [ 2608] [depth= 6] . ( 3 sec) [ -11883.8680] [ 2583] [depth= 2] . ( 3 sec) [ -11711.1187] [ 2529] [depth= 6] . ( 3 sec) [ -11658.4581] [ 2499] [depth= 9] . ( 3 sec) [ -11599.8891] [ 2480] [depth= 4] . ( 3 sec) [ -11526.2155] [ 2464] [depth= 2] . ( 3 sec) [ -11315.1885] [ 2425] [depth= 1] . ( 3 sec) [ -11220.7204] [ 2414] [depth= 4] . ( 3 sec) [ -11168.7958] [ 2388] [depth= 1] . ( 3 sec) [ -11143.8749] [ 2377] [depth= 1] . ( 3 sec) [ -11067.8954] [ 2362] [depth= 6] . ( 3 sec) [ -11042.8449] [ 2366] [depth= 1] . ( 3 sec) [ -10984.8914] [ 2345] [depth= 2] . ( 4 sec) [ -10936.7971] [ 2332] [depth= 6] . ( 4 sec) [ -10913.3533] [ 2316] [depth= 1] . ( 4 sec) [ -10845.5386] [ 2288] [depth= 7] . ( 4 sec) [ -10805.4579] [ 2266] [depth= 5] . ( 4 sec) [ -10802.5256] [ 2266] [depth= 1] . ( 4 sec) [ -10528.8898] [ 2261] [depth= 3] . ( 4 sec) [ -10457.5579] [ 2236] [depth= 2] . ( 4 sec) [ -10326.3397] [ 2208] [depth= 1] . ( 4 sec) [ -10322.5273] [ 2209] [depth= 1] . ( 4 sec) [ -10176.3921] [ 2198] [depth= 4] . ( 4 sec) [ -10169.5973] [ 2191] [depth= 3] . ( 4 sec) [ -10166.4966] [ 2191] [depth= 1] . ( 4 sec) [ -10097.6791] [ 2162] [depth= 1] . ( 4 sec) [ -10079.9655] [ 2148] [depth= 1] . ( 4 sec) [ -10075.8912] [ 2147] [depth= 1] . ( 4 sec) [ -10068.8302] [ 2147] [depth= 3] . ( 4 sec) [ -10067.1908] [ 2150] [depth= 1] . ( 5 sec) [ -9922.8384] [Branch lengths ] . ( 5 sec) [ -9918.9645] [GTR parameters ] . ( 5 sec) [ -9876.3891] [Alpha ][ 0.964028] . ( 6 sec) [ -9875.6775] [ 2154] [depth= 1] . ( 6 sec) [ -9870.1331] [ 2148] [depth= 1] . ( 6 sec) [ -9867.7828] [ 2146] [depth= 2] . ( 6 sec) [ -9861.9820] [ 2143] [depth= 1] . ( 6 sec) [ -9861.3989] [ 2144] [depth= 1] . ( 6 sec) [ -9836.8869] [ 2134] [depth= 1] . ( 6 sec) [ -9799.3644] [ 2113] [depth= 4] . ( 6 sec) [ -9793.9333] [ 2110] [depth= 1] . ( 6 sec) [ -9793.5836] [ 2107] [depth= 1] . ( 7 sec) [ -9786.9324] [ 2099] [depth= 1] . ( 7 sec) [ -9785.3158] [ 2102] [depth= 1] . ( 7 sec) [ -9784.6833] [ 2104] [depth= 1] . ( 7 sec) [ -9784.0663] [ 2104] [depth= 1] . ( 7 sec) [ -9782.5058] [ 2101] [depth= 1] . ( 8 sec) [ -9781.8774] [ 2104] [depth= 1] . ( 8 sec) [ -9781.8603] [ 2104] [depth= 1] . ( 8 sec) [ -9781.8001] [ 2104] [depth= 1] . ( 8 sec) [ -9780.7213] [ 2102] [depth= 1] . ( 8 sec) [ -9779.5074] [ 2105] [depth= 2] . ( 9 sec) [ -9770.1334] [Branch lengths ] . ( 9 sec) [ -9770.0635] [GTR parameters ] . ( 9 sec) [ -9769.9184] [Alpha ][ 1.003242] . ( 9 sec) [ -9769.7227] [ 2102] [depth= 1] . ( 9 sec) [ -9769.3692] [ 2095] [depth= 1] . ( 9 sec) [ -9769.0954] [ 2092] [depth= 1] . ( 12 sec) [ -9767.9994] [Branch lengths ] . ( 12 sec) [ -9767.9979] [GTR parameters ] . ( 12 sec) [ -9767.9931] [Alpha ][ 1.010591] . ( 15 sec) [ -9767.7310] [Branch lengths ] . ( 36 sec) [ -9767.1568] [Branch lengths ] . ( 36 sec) [ -9767.1568] [Topology ] . ( 37 sec) [ -9767.0842] [Topology ] . ( 38 sec) [ -9767.0497] [Topology ] . ( 39 sec) [ -9767.0298] [Topology ] . ( 39 sec) [ -9767.0173] [Topology ] . ( 40 sec) [ -9767.0091] [Topology ] . ( 41 sec) [ -9767.0037] [Topology ] . ( 41 sec) [ -9767.0018] [GTR parameters ] . ( 41 sec) [ -9767.0015] [Alpha ][ 1.012239] . ( 41 sec) [ -9767.0015] [Topology ] . ( 42 sec) [ -9766.9977] [Topology ] . ( 43 sec) [ -9766.9952] [Topology ] . ( 43 sec) [ -9766.9934] [Topology ] . ( 44 sec) [ -9766.9922] [Topology ] . ( 45 sec) [ -9766.9913] [Topology ] . ( 45 sec) [ -9766.9913] [GTR parameters ] . ( 45 sec) [ -9766.9913] [Alpha ][ 1.012239] . ( 45 sec) [ -9766.9913] [Topology ] . ( 46 sec) [ -9766.9907] [Topology ] . ( 46 sec) [ -9766.9907] [GTR parameters ] . ( 46 sec) [ -9766.9907] [Alpha ][ 1.012239] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9766.990703. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9827.155972 . ( 1 sec) [ -9824.3441] [GTR parameters ] . ( 1 sec) [ -9824.0535] [Alpha ][ 0.943410] . ( 1 sec) [ -9824.0535] [Topology ] . ( 2 sec) [ -9781.0533] [Topology ] . ( 3 sec) [ -9771.4895] [Topology ] . ( 4 sec) [ -9769.0992] [Topology ] . ( 4 sec) [ -9768.2834] [Topology ] . ( 5 sec) [ -9767.8984] [Topology ] . ( 6 sec) [ -9767.7052] [Topology ] . ( 7 sec) [ -9767.6057] [Topology ] . ( 7 sec) [ -9767.5536] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9767.553606 . ( 14 sec) [ -9767.4435] [GTR parameters ] . ( 14 sec) [ -9767.0408] [Alpha ][ 1.007628] . ( 14 sec) [ -9767.0408] [Topology ] . ( 14 sec) [ -9766.9849] [Topology ] . ( 15 sec) [ -9766.9584] [Topology ] . ( 16 sec) [ -9766.9447] [Topology ] . ( 17 sec) [ -9766.9375] [Topology ] . ( 17 sec) [ -9766.9336] [Topology ] . ( 18 sec) [ -9766.9315] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.931452 . ( 24 sec) [ -9766.9314] [GTR parameters ] . ( 24 sec) [ -9766.9301] [Alpha ][ 1.011385] . ( 24 sec) [ -9766.9301] [Topology ] . ( 25 sec) [ -9766.9288] [Topology ] . ( 25 sec) [ -9766.9280] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.928011 . ( 31 sec) [ -9766.9280] [GTR parameters ] . ( 31 sec) [ -9766.9280] [Alpha ][ 1.011385] . ( 31 sec) [ -9766.9280] [Topology ] . ( 32 sec) [ -9766.9276] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -9824.3441] [GTR parameters ] . ( 44 sec) [ -9824.0535] [Alpha ][ 0.943410] . ( 45 sec) [ -9822.6627] [ 2112] [depth= 1] . ( 45 sec) [ -9821.9513] [ 2111] [depth= 1] . ( 45 sec) [ -9821.4004] [ 2112] [depth= 1] . ( 45 sec) [ -9821.0707] [ 2112] [depth= 1] . ( 45 sec) [ -9819.9794] [ 2112] [depth= 1] . ( 46 sec) [ -9818.3978] [ 2115] [depth= 1] . ( 46 sec) [ -9815.7389] [ 2112] [depth= 1] . ( 46 sec) [ -9815.7194] [ 2117] [depth= 2] . ( 46 sec) [ -9810.5380] [ 2110] [depth= 3] . ( 46 sec) [ -9803.8708] [ 2108] [depth= 1] . ( 46 sec) [ -9803.6585] [ 2107] [depth= 1] . ( 46 sec) [ -9803.3043] [ 2109] [depth= 1] . ( 46 sec) [ -9800.2978] [ 2114] [depth= 1] . ( 46 sec) [ -9797.4250] [ 2114] [depth= 2] . ( 46 sec) [ -9795.1512] [ 2107] [depth= 1] . ( 47 sec) [ -9795.0851] [ 2109] [depth= 2] . ( 47 sec) [ -9794.8636] [ 2112] [depth= 1] . ( 47 sec) [ -9794.3837] [ 2109] [depth= 1] . ( 47 sec) [ -9773.0167] [Branch lengths ] . ( 47 sec) [ -9772.9113] [GTR parameters ] . ( 48 sec) [ -9772.6790] [Alpha ][ 0.992215] . ( 48 sec) [ -9772.3306] [ 2103] [depth= 1] . ( 51 sec) [ -9769.6066] [Branch lengths ] . ( 51 sec) [ -9769.5999] [GTR parameters ] . ( 51 sec) [ -9769.5822] [Alpha ][ 1.006393] . ( 54 sec) [ -9769.2523] [Branch lengths ] . ( 73 sec) [ -9767.6878] [ 2101] [depth= 2] . ( 73 sec) [ -9767.2244] [ 2101] [depth= 1] . ( 74 sec) [ -9767.1671] [ 2102] [depth= 1] . ( 75 sec) [ -9766.9640] [Branch lengths ] . ( 75 sec) [ -9766.9591] [GTR parameters ] . ( 75 sec) [ -9766.9576] [Alpha ][ 1.010436] . ( 97 sec) [ -9766.9362] [Branch lengths ] . ( 97 sec) [ -9766.9362] [Topology ] . ( 98 sec) [ -9766.9332] [Topology ] . ( 98 sec) [ -9766.9321] [Topology ] . ( 99 sec) [ -9766.9314] [Topology ] . ( 99 sec) [ -9766.9313] [GTR parameters ] . ( 99 sec) [ -9766.9312] [Alpha ][ 1.011457] . ( 99 sec) [ -9766.9312] [Topology ] . ( 100 sec) [ -9766.9308] [Topology ] . ( 100 sec) [ -9766.9308] [GTR parameters ] . ( 100 sec) [ -9766.9308] [Alpha ][ 1.011457] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -9766.9307] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9766.927571 . Log likelihood obtained after SPR moves : -9766.930704 . Log likelihood of the current tree: -9766.927571. . Printing the most likely tree in file 'data40.phy_phyml_tree.txt'... . Best log likelihood : -9766.927420 . Time used 0h1m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo