.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data98.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... . 427 patterns found. (out of a total of 500 sites) . 71 sites without polymorphism (14.20%). . [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) [ -21902.0195] [GTR parameters ] . ( 0 sec) [ -21436.5620] [Alpha ][ 0.500960] . ( 1 sec) [ -20698.6585] [ 4572] [depth= 8] . ( 1 sec) [ -20137.3606] [ 4500] [depth= 6] . ( 1 sec) [ -20113.7370] [ 4494] [depth= 1] . ( 1 sec) [ -20112.3459] [ 4489] [depth= 1] . ( 1 sec) [ -20095.7032] [ 4468] [depth= 2] . ( 1 sec) [ -20013.1166] [ 4464] [depth= 6] . ( 1 sec) [ -19798.2340] [ 4450] [depth= 5] . ( 1 sec) [ -19717.3585] [ 4436] [depth= 1] . ( 1 sec) [ -19692.4559] [ 4438] [depth= 1] . ( 1 sec) [ -19283.5435] [ 4309] [depth= 4] . ( 1 sec) [ -19133.0085] [ 4147] [depth= 4] . ( 1 sec) [ -19080.8902] [ 4122] [depth= 2] . ( 1 sec) [ -18919.6936] [ 4104] [depth= 6] . ( 1 sec) [ -18877.2450] [ 4096] [depth= 3] . ( 2 sec) [ -18758.4442] [ 4083] [depth= 2] . ( 2 sec) [ -17532.6261] [ 3999] [depth= 5] . ( 2 sec) [ -16845.7461] [ 3988] [depth= 2] . ( 2 sec) [ -16754.5786] [ 3821] [depth= 4] . ( 2 sec) [ -16665.0110] [ 3813] [depth= 5] . ( 2 sec) [ -16244.3877] [ 3802] [depth= 7] . ( 2 sec) [ -16220.5290] [ 3801] [depth= 1] . ( 2 sec) [ -16152.1331] [ 3764] [depth= 6] . ( 2 sec) [ -16002.3556] [ 3735] [depth= 2] . ( 2 sec) [ -15863.7949] [ 3673] [depth= 6] . ( 2 sec) [ -15814.5942] [ 3662] [depth= 2] . ( 2 sec) [ -15776.4189] [ 3661] [depth= 1] . ( 2 sec) [ -15733.2595] [ 3632] [depth= 4] . ( 2 sec) [ -15351.0687] [ 3587] [depth= 14] . ( 2 sec) [ -15202.0848] [ 3581] [depth= 8] . ( 3 sec) [ -15037.6113] [ 3568] [depth= 5] . ( 3 sec) [ -15018.2128] [ 3570] [depth= 3] . ( 3 sec) [ -14960.9252] [ 3560] [depth= 2] . ( 3 sec) [ -14926.6604] [ 3551] [depth= 2] . ( 3 sec) [ -14917.5546] [ 3549] [depth= 1] . ( 3 sec) [ -14690.2588] [ 3516] [depth= 9] . ( 3 sec) [ -14261.4070] [ 3406] [depth= 13] . ( 3 sec) [ -14247.8519] [ 3401] [depth= 1] . ( 3 sec) [ -14138.8060] [ 3380] [depth= 3] . ( 3 sec) [ -14036.8674] [ 3381] [depth= 7] . ( 3 sec) [ -13720.7252] [ 3350] [depth= 1] . ( 3 sec) [ -13361.5567] [ 3306] [depth= 9] . ( 3 sec) [ -13161.8147] [ 3315] [depth= 1] . ( 3 sec) [ -12944.3690] [ 3225] [depth= 9] . ( 3 sec) [ -12780.1648] [ 3106] [depth= 1] . ( 3 sec) [ -12616.6530] [ 3055] [depth= 12] . ( 3 sec) [ -12549.2099] [ 3053] [depth= 1] . ( 3 sec) [ -12529.7543] [ 3078] [depth= 1] . ( 3 sec) [ -12452.1482] [ 3061] [depth= 8] . ( 4 sec) [ -12129.8867] [ 2849] [depth= 12] . ( 4 sec) [ -11868.9399] [ 2811] [depth= 6] . ( 4 sec) [ -11814.0391] [ 2773] [depth= 5] . ( 4 sec) [ -11670.7065] [ 2728] [depth= 6] . ( 4 sec) [ -11660.5899] [ 2724] [depth= 1] . ( 4 sec) [ -11344.3349] [ 2605] [depth= 5] . ( 4 sec) [ -11214.9685] [ 2561] [depth= 4] . ( 4 sec) [ -10929.4788] [ 2434] [depth= 9] . ( 4 sec) [ -10807.5866] [ 2393] [depth= 2] . ( 4 sec) [ -10799.4235] [ 2388] [depth= 1] . ( 4 sec) [ -10769.9732] [ 2352] [depth= 1] . ( 4 sec) [ -10715.1021] [ 2354] [depth= 1] . ( 4 sec) [ -10569.7402] [ 2293] [depth= 3] . ( 4 sec) [ -10414.8707] [ 2253] [depth= 7] . ( 4 sec) [ -10404.4405] [ 2272] [depth= 1] . ( 4 sec) [ -10267.8649] [ 2220] [depth= 5] . ( 4 sec) [ -10243.9988] [ 2220] [depth= 2] . ( 5 sec) [ -10235.9459] [ 2218] [depth= 1] . ( 5 sec) [ -10231.3143] [ 2223] [depth= 2] . ( 5 sec) [ -10170.5082] [ 2193] [depth= 7] . ( 5 sec) [ -10027.7153] [ 2185] [depth= 2] . ( 5 sec) [ -9673.8460] [ 2125] [depth= 2] . ( 5 sec) [ -9547.1769] [ 2120] [depth= 3] . ( 5 sec) [ -9526.5712] [ 2117] [depth= 1] . ( 5 sec) [ -9508.6901] [ 2123] [depth= 1] . ( 5 sec) [ -9464.0982] [ 2117] [depth= 1] . ( 5 sec) [ -9462.8966] [ 2118] [depth= 8] . ( 5 sec) [ -9362.8333] [ 1988] [depth= 3] . ( 5 sec) [ -9315.7408] [ 1993] [depth= 1] . ( 5 sec) [ -9298.5015] [ 1985] [depth= 1] . ( 5 sec) [ -9075.9924] [Branch lengths ] . ( 6 sec) [ -9073.2184] [GTR parameters ] . ( 6 sec) [ -9033.4721] [Alpha ][ 0.977945] . ( 6 sec) [ -9020.3060] [ 1990] [depth= 1] . ( 6 sec) [ -9019.7887] [ 1989] [depth= 1] . ( 7 sec) [ -8987.6550] [ 1987] [depth= 8] . ( 7 sec) [ -8962.4072] [ 1960] [depth= 1] . ( 7 sec) [ -8956.9300] [ 1947] [depth= 1] . ( 7 sec) [ -8956.5698] [ 1949] [depth= 1] . ( 7 sec) [ -8936.2334] [ 1947] [depth= 1] . ( 7 sec) [ -8922.4743] [ 1942] [depth= 1] . ( 7 sec) [ -8888.7785] [ 1918] [depth= 8] . ( 8 sec) [ -8875.7888] [ 1908] [depth= 1] . ( 8 sec) [ -8845.8301] [ 1883] [depth= 1] . ( 8 sec) [ -8843.1390] [ 1880] [depth= 2] . ( 8 sec) [ -8791.5736] [ 1851] [depth= 1] . ( 8 sec) [ -8786.8931] [ 1847] [depth= 1] . ( 8 sec) [ -8777.2677] [ 1819] [depth= 2] . ( 8 sec) [ -8773.5806] [ 1818] [depth= 1] . ( 8 sec) [ -8773.2636] [ 1821] [depth= 1] . ( 9 sec) [ -8742.6311] [ 1825] [depth= 1] . ( 9 sec) [ -8742.3461] [ 1830] [depth= 1] . ( 9 sec) [ -8741.9894] [ 1834] [depth= 1] . ( 9 sec) [ -8741.2803] [ 1830] [depth= 1] . ( 9 sec) [ -8735.7205] [ 1836] [depth= 1] . ( 9 sec) [ -8735.3810] [ 1834] [depth= 1] . ( 10 sec) [ -8715.0468] [Branch lengths ] . ( 10 sec) [ -8714.8544] [GTR parameters ] . ( 10 sec) [ -8712.8731] [Alpha ][ 1.148229] . ( 10 sec) [ -8705.7008] [ 1826] [depth= 2] . ( 11 sec) [ -8703.4539] [ 1830] [depth= 1] . ( 11 sec) [ -8702.6197] [ 1832] [depth= 1] . ( 11 sec) [ -8701.0264] [ 1837] [depth= 1] . ( 13 sec) [ -8700.8231] [ 1832] [depth= 1] . ( 14 sec) [ -8694.3055] [Branch lengths ] . ( 14 sec) [ -8694.2704] [GTR parameters ] . ( 15 sec) [ -8694.2624] [Alpha ][ 1.160282] . ( 15 sec) [ -8693.7551] [ 1836] [depth= 2] . ( 16 sec) [ -8692.8384] [ 1835] [depth= 1] . ( 19 sec) [ -8689.5938] [Branch lengths ] . ( 19 sec) [ -8689.5869] [GTR parameters ] . ( 19 sec) [ -8689.5866] [Alpha ][ 1.157845] . ( 24 sec) [ -8688.5228] [Branch lengths ] . ( 50 sec) [ -8688.4332] [Branch lengths ] . ( 50 sec) [ -8688.4332] [Topology ] . ( 51 sec) [ -8688.4151] [Topology ] . ( 52 sec) [ -8688.4045] [Topology ] . ( 53 sec) [ -8688.3968] [Topology ] . ( 54 sec) [ -8688.3910] [Topology ] . ( 55 sec) [ -8688.3864] [Topology ] . ( 57 sec) [ -8688.3828] [Topology ] . ( 57 sec) [ -8688.3821] [GTR parameters ] . ( 57 sec) [ -8688.3819] [Alpha ][ 1.159632] . ( 57 sec) [ -8688.3819] [Topology ] . ( 58 sec) [ -8688.3791] [Topology ] . ( 60 sec) [ -8688.3768] [Topology ] . ( 61 sec) [ -8688.3750] [Topology ] . ( 63 sec) [ -8688.3736] [Topology ] . ( 64 sec) [ -8688.3725] [Topology ] . ( 65 sec) [ -8688.3716] [Topology ] . ( 66 sec) [ -8688.3715] [GTR parameters ] . ( 66 sec) [ -8688.3715] [Alpha ][ 1.159632] . ( 66 sec) [ -8688.3715] [Topology ] . ( 67 sec) [ -8688.3708] [Topology ] . ( 67 sec) [ -8688.3708] [GTR parameters ] . ( 68 sec) [ -8688.3708] [Alpha ][ 1.159632] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8688.370832. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21740.1306] [GTR parameters ] . ( 1 sec) [ -21267.2481] [Alpha ][ 0.500960] . ( 1 sec) [ -19825.2462] [ 4672] [depth= 4] . ( 1 sec) [ -19344.2223] [ 4490] [depth= 3] . ( 1 sec) [ -19175.6427] [ 4462] [depth= 4] . ( 1 sec) [ -19023.8834] [ 4461] [depth= 7] . ( 1 sec) [ -18914.2099] [ 4411] [depth= 1] . ( 2 sec) [ -18867.6083] [ 4396] [depth= 6] . ( 2 sec) [ -18769.1243] [ 4392] [depth= 1] . ( 2 sec) [ -18739.4358] [ 4374] [depth= 4] . ( 2 sec) [ -18670.5932] [ 4239] [depth= 2] . ( 2 sec) [ -18650.7550] [ 4234] [depth= 1] . ( 2 sec) [ -18600.2155] [ 4199] [depth= 15] . ( 2 sec) [ -18383.1301] [ 4191] [depth= 3] . ( 2 sec) [ -17755.2055] [ 4015] [depth= 19] . ( 2 sec) [ -17363.9567] [ 4014] [depth= 6] . ( 2 sec) [ -16917.0611] [ 3918] [depth= 14] . ( 2 sec) [ -16631.0915] [ 3758] [depth= 24] . ( 2 sec) [ -16440.8504] [ 3694] [depth= 7] . ( 2 sec) [ -16008.3323] [ 3654] [depth= 4] . ( 3 sec) [ -15493.3603] [ 3516] [depth= 16] . ( 3 sec) [ -15342.1333] [ 3533] [depth= 3] . ( 3 sec) [ -15279.0278] [ 3508] [depth= 2] . ( 3 sec) [ -15156.1298] [ 3476] [depth= 5] . ( 3 sec) [ -15001.0337] [ 3472] [depth= 20] . ( 3 sec) [ -14791.2296] [ 3409] [depth= 3] . ( 3 sec) [ -14769.5450] [ 3415] [depth= 5] . ( 3 sec) [ -14624.1676] [ 3414] [depth= 1] . ( 3 sec) [ -14445.0419] [ 3289] [depth= 19] . ( 3 sec) [ -14300.7099] [ 3260] [depth= 17] . ( 3 sec) [ -14200.1683] [ 3241] [depth= 1] . ( 3 sec) [ -13820.9147] [ 3101] [depth= 16] . ( 3 sec) [ -13645.2782] [ 2923] [depth= 5] . ( 4 sec) [ -13517.2590] [ 2904] [depth= 2] . ( 4 sec) [ -13342.3390] [ 2884] [depth= 4] . ( 4 sec) [ -13323.4529] [ 2877] [depth= 4] . ( 4 sec) [ -13283.3956] [ 2864] [depth= 2] . ( 4 sec) [ -13072.4596] [ 2837] [depth= 3] . ( 4 sec) [ -12744.8946] [ 2787] [depth= 1] . ( 4 sec) [ -12652.1830] [ 2758] [depth= 9] . ( 4 sec) [ -12615.2634] [ 2748] [depth= 1] . ( 4 sec) [ -12592.3222] [ 2737] [depth= 1] . ( 4 sec) [ -12534.2179] [ 2685] [depth= 5] . ( 4 sec) [ -12108.9858] [ 2683] [depth= 2] . ( 5 sec) [ -12107.4351] [ 2685] [depth= 1] . ( 5 sec) [ -12061.6867] [ 2693] [depth= 1] . ( 5 sec) [ -11914.1605] [ 2545] [depth= 7] . ( 5 sec) [ -11595.7066] [ 2477] [depth= 2] . ( 5 sec) [ -11560.0534] [ 2506] [depth= 1] . ( 5 sec) [ -11548.0807] [ 2477] [depth= 1] . ( 5 sec) [ -11502.0559] [ 2471] [depth= 1] . ( 5 sec) [ -10981.2614] [ 2411] [depth= 4] . ( 5 sec) [ -10934.1553] [ 2417] [depth= 1] . ( 5 sec) [ -10737.1727] [ 2330] [depth= 3] . ( 5 sec) [ -10647.3983] [ 2302] [depth= 2] . ( 5 sec) [ -10567.1564] [ 2303] [depth= 3] . ( 6 sec) [ -10217.8595] [ 2322] [depth= 1] . ( 6 sec) [ -10188.9438] [ 2288] [depth= 4] . ( 6 sec) [ -10017.7282] [ 2269] [depth= 5] . ( 6 sec) [ -9948.8273] [ 2264] [depth= 1] . ( 6 sec) [ -9915.0343] [ 2274] [depth= 1] . ( 6 sec) [ -9883.5059] [ 2262] [depth= 3] . ( 6 sec) [ -9873.2819] [ 2253] [depth= 1] . ( 6 sec) [ -9858.9668] [ 2250] [depth= 1] . ( 6 sec) [ -9772.7982] [ 2184] [depth= 3] . ( 6 sec) [ -9676.4886] [ 2174] [depth= 5] . ( 6 sec) [ -9603.4929] [ 2152] [depth= 5] . ( 6 sec) [ -9602.1413] [ 2150] [depth= 1] . ( 7 sec) [ -9591.0013] [ 2131] [depth= 1] . ( 7 sec) [ -9555.3945] [ 2096] [depth= 2] . ( 7 sec) [ -9551.5492] [ 2089] [depth= 2] . ( 7 sec) [ -9550.9256] [ 2086] [depth= 1] . ( 7 sec) [ -9499.5877] [ 2080] [depth= 1] . ( 7 sec) [ -9489.1290] [ 2077] [depth= 1] . ( 7 sec) [ -9434.8731] [ 2067] [depth= 2] . ( 7 sec) [ -9403.7493] [ 2067] [depth= 1] . ( 7 sec) [ -9389.6946] [ 2065] [depth= 1] . ( 8 sec) [ -9377.7506] [ 2067] [depth= 2] . ( 8 sec) [ -9359.2688] [ 2066] [depth= 1] . ( 8 sec) [ -9330.2011] [ 2062] [depth= 1] . ( 8 sec) [ -9321.4806] [ 2056] [depth= 1] . ( 8 sec) [ -9297.7638] [ 2068] [depth= 1] . ( 8 sec) [ -9293.4450] [ 2045] [depth= 2] . ( 9 sec) [ -9286.8699] [ 2042] [depth= 1] . ( 9 sec) [ -9276.3606] [ 2034] [depth= 1] . ( 9 sec) [ -9078.7145] [Branch lengths ] . ( 10 sec) [ -9075.1553] [GTR parameters ] . ( 10 sec) [ -9031.9906] [Alpha ][ 0.966688] . ( 11 sec) [ -8981.3078] [ 2007] [depth= 2] . ( 11 sec) [ -8914.9542] [ 1950] [depth= 1] . ( 11 sec) [ -8909.7954] [ 1949] [depth= 1] . ( 11 sec) [ -8899.2784] [ 1941] [depth= 1] . ( 11 sec) [ -8865.0981] [ 1905] [depth= 2] . ( 11 sec) [ -8848.9124] [ 1900] [depth= 1] . ( 11 sec) [ -8815.0655] [ 1886] [depth= 2] . ( 12 sec) [ -8754.7702] [ 1854] [depth= 1] . ( 12 sec) [ -8754.6303] [ 1853] [depth= 1] . ( 12 sec) [ -8720.7574] [ 1839] [depth= 2] . ( 13 sec) [ -8719.8456] [ 1836] [depth= 1] . ( 13 sec) [ -8718.5354] [ 1834] [depth= 1] . ( 14 sec) [ -8716.1905] [ 1837] [depth= 1] . ( 14 sec) [ -8713.5213] [ 1838] [depth= 1] . ( 14 sec) [ -8710.7694] [ 1836] [depth= 1] . ( 15 sec) [ -8710.6441] [ 1841] [depth= 2] . ( 15 sec) [ -8696.3603] [Branch lengths ] . ( 16 sec) [ -8696.0664] [GTR parameters ] . ( 16 sec) [ -8693.6493] [Alpha ][ 1.150136] . ( 17 sec) [ -8693.5515] [ 1841] [depth= 1] . ( 18 sec) [ -8692.8662] [ 1841] [depth= 1] . ( 19 sec) [ -8690.7447] [ 1840] [depth= 1] . ( 21 sec) [ -8690.1297] [Branch lengths ] . ( 21 sec) [ -8690.1289] [GTR parameters ] . ( 21 sec) [ -8690.1230] [Alpha ][ 1.160426] . ( 26 sec) [ -8689.4927] [Branch lengths ] . ( 45 sec) [ -8689.2324] [ 1836] [depth= 1] . ( 53 sec) [ -8688.4252] [Branch lengths ] . ( 54 sec) [ -8688.4243] [GTR parameters ] . ( 54 sec) [ -8688.4243] [Alpha ][ 1.160426] . ( 78 sec) [ -8688.4110] [Branch lengths ] . ( 78 sec) [ -8688.4110] [Topology ] . ( 79 sec) [ -8688.4102] [Topology ] . ( 79 sec) [ -8688.4102] [GTR parameters ] . ( 79 sec) [ -8688.4102] [Alpha ][ 1.160426] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -8688.4093] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8688.409253. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22124.8926] [GTR parameters ] . ( 2 sec) [ -21657.1498] [Alpha ][ 0.500960] . ( 2 sec) [ -20925.7359] [ 4737] [depth= 1] . ( 2 sec) [ -20294.9731] [ 4554] [depth= 8] . ( 2 sec) [ -20127.7113] [ 4536] [depth= 4] . ( 2 sec) [ -20083.4230] [ 4525] [depth= 2] . ( 2 sec) [ -19890.6673] [ 4386] [depth= 8] . ( 2 sec) [ -19761.1542] [ 4380] [depth= 6] . ( 3 sec) [ -19476.9104] [ 4297] [depth= 10] . ( 3 sec) [ -19304.4974] [ 4234] [depth= 1] . ( 3 sec) [ -19242.7893] [ 4227] [depth= 1] . ( 3 sec) [ -19137.6928] [ 4278] [depth= 11] . ( 3 sec) [ -18807.8429] [ 4178] [depth= 2] . ( 3 sec) [ -18114.3077] [ 4117] [depth= 10] . ( 3 sec) [ -17868.8890] [ 3992] [depth= 10] . ( 3 sec) [ -17670.0155] [ 3984] [depth= 1] . ( 3 sec) [ -17434.3778] [ 3918] [depth= 11] . ( 3 sec) [ -17349.4442] [ 3914] [depth= 1] . ( 3 sec) [ -17280.0912] [ 3780] [depth= 11] . ( 3 sec) [ -17065.7578] [ 3777] [depth= 1] . ( 4 sec) [ -16838.2829] [ 3723] [depth= 10] . ( 4 sec) [ -16452.8898] [ 3688] [depth= 11] . ( 4 sec) [ -16223.8125] [ 3597] [depth= 6] . ( 4 sec) [ -15850.2788] [ 3609] [depth= 10] . ( 4 sec) [ -15419.9326] [ 3507] [depth= 9] . ( 4 sec) [ -14795.7188] [ 3315] [depth= 12] . ( 4 sec) [ -14569.6357] [ 3266] [depth= 7] . ( 4 sec) [ -13488.5106] [ 3220] [depth= 14] . ( 4 sec) [ -13123.7548] [ 3041] [depth= 10] . ( 4 sec) [ -12986.6695] [ 3042] [depth= 10] . ( 4 sec) [ -12377.0680] [ 2835] [depth= 13] . ( 4 sec) [ -12356.2624] [ 2830] [depth= 1] . ( 4 sec) [ -12306.0387] [ 2818] [depth= 1] . ( 5 sec) [ -12059.0046] [ 2791] [depth= 9] . ( 5 sec) [ -12055.1986] [ 2786] [depth= 1] . ( 5 sec) [ -11928.6767] [ 2732] [depth= 2] . ( 5 sec) [ -11666.3465] [ 2648] [depth= 7] . ( 5 sec) [ -11662.3849] [ 2651] [depth= 1] . ( 5 sec) [ -11474.9130] [ 2525] [depth= 8] . ( 5 sec) [ -11351.3321] [ 2522] [depth= 1] . ( 5 sec) [ -11321.1590] [ 2512] [depth= 1] . ( 5 sec) [ -11256.7011] [ 2489] [depth= 1] . ( 5 sec) [ -11215.2157] [ 2475] [depth= 1] . ( 6 sec) [ -11213.4757] [ 2473] [depth= 1] . ( 6 sec) [ -11171.7671] [ 2464] [depth= 3] . ( 6 sec) [ -11070.8048] [ 2437] [depth= 3] . ( 6 sec) [ -10615.3262] [ 2423] [depth= 1] . ( 6 sec) [ -10480.1503] [ 2323] [depth= 4] . ( 6 sec) [ -10368.9742] [ 2256] [depth= 3] . ( 6 sec) [ -10368.3552] [ 2249] [depth= 1] . ( 6 sec) [ -10324.1509] [ 2251] [depth= 2] . ( 6 sec) [ -9975.3768] [ 2117] [depth= 5] . ( 6 sec) [ -9963.9352] [ 2124] [depth= 2] . ( 6 sec) [ -9925.7792] [ 2123] [depth= 4] . ( 6 sec) [ -9805.6415] [ 2073] [depth= 3] . ( 7 sec) [ -9740.3174] [ 2087] [depth= 1] . ( 7 sec) [ -9560.9996] [ 2075] [depth= 4] . ( 7 sec) [ -9474.4497] [ 2029] [depth= 1] . ( 7 sec) [ -9447.6029] [ 2015] [depth= 2] . ( 7 sec) [ -9376.4003] [ 2007] [depth= 2] . ( 7 sec) [ -9355.3669] [ 2004] [depth= 1] . ( 7 sec) [ -9313.1215] [ 2005] [depth= 3] . ( 7 sec) [ -9303.7602] [ 2005] [depth= 1] . ( 7 sec) [ -9160.2495] [ 1958] [depth= 4] . ( 7 sec) [ -9126.8741] [ 1962] [depth= 2] . ( 7 sec) [ -9123.4854] [ 1960] [depth= 1] . ( 7 sec) [ -9122.5432] [ 1959] [depth= 1] . ( 8 sec) [ -9062.1019] [ 1934] [depth= 2] . ( 8 sec) [ -9038.4788] [ 1934] [depth= 1] . ( 8 sec) [ -9032.3991] [ 1933] [depth= 1] . ( 8 sec) [ -9030.2867] [ 1922] [depth= 2] . ( 8 sec) [ -9028.8539] [ 1922] [depth= 1] . ( 9 sec) [ -8884.8917] [Branch lengths ] . ( 9 sec) [ -8881.4674] [GTR parameters ] . ( 9 sec) [ -8838.7829] [Alpha ][ 1.000057] . ( 10 sec) [ -8798.4625] [ 1895] [depth= 1] . ( 10 sec) [ -8787.0425] [ 1890] [depth= 1] . ( 10 sec) [ -8739.7846] [ 1867] [depth= 3] . ( 10 sec) [ -8738.8242] [ 1868] [depth= 1] . ( 11 sec) [ -8737.0011] [ 1868] [depth= 1] . ( 11 sec) [ -8735.0398] [ 1860] [depth= 1] . ( 12 sec) [ -8731.2390] [ 1862] [depth= 1] . ( 12 sec) [ -8719.3810] [ 1831] [depth= 8] . ( 12 sec) [ -8718.1829] [ 1828] [depth= 1] . ( 12 sec) [ -8716.8728] [ 1827] [depth= 1] . ( 12 sec) [ -8714.1226] [ 1831] [depth= 1] . ( 12 sec) [ -8713.2736] [ 1827] [depth= 1] . ( 13 sec) [ -8712.2518] [ 1828] [depth= 1] . ( 13 sec) [ -8711.7159] [ 1833] [depth= 1] . ( 14 sec) [ -8694.9024] [Branch lengths ] . ( 15 sec) [ -8694.7507] [GTR parameters ] . ( 15 sec) [ -8693.5353] [Alpha ][ 1.134817] . ( 16 sec) [ -8692.7835] [ 1837] [depth= 2] . ( 16 sec) [ -8692.7110] [ 1836] [depth= 1] . ( 17 sec) [ -8692.3555] [ 1839] [depth= 1] . ( 18 sec) [ -8691.5727] [ 1835] [depth= 1] . ( 20 sec) [ -8688.8251] [Branch lengths ] . ( 20 sec) [ -8688.8219] [GTR parameters ] . ( 20 sec) [ -8688.8033] [Alpha ][ 1.153132] . ( 25 sec) [ -8688.4421] [Branch lengths ] . ( 48 sec) [ -8688.3831] [Branch lengths ] . ( 48 sec) [ -8688.3831] [Topology ] . ( 48 sec) [ -8688.3772] [Topology ] . ( 49 sec) [ -8688.3750] [Topology ] . ( 50 sec) [ -8688.3738] [Topology ] . ( 51 sec) [ -8688.3731] [Topology ] . ( 51 sec) [ -8688.3727] [GTR parameters ] . ( 51 sec) [ -8688.3704] [Alpha ][ 1.159380] . ( 51 sec) [ -8688.3704] [Topology ] . ( 52 sec) [ -8688.3698] [Topology ] . ( 52 sec) [ -8688.3697] [GTR parameters ] . ( 52 sec) [ -8688.3697] [Alpha ][ 1.159380] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8688.369744. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21596.1169] [GTR parameters ] . ( 1 sec) [ -21186.3083] [Alpha ][ 0.500960] . ( 1 sec) [ -20776.8751] [ 4759] [depth= 11] . ( 1 sec) [ -20336.2339] [ 4587] [depth= 9] . ( 2 sec) [ -19849.9369] [ 4535] [depth= 8] . ( 2 sec) [ -19785.0259] [ 4380] [depth= 1] . ( 2 sec) [ -19553.2169] [ 4341] [depth= 6] . ( 2 sec) [ -19520.9174] [ 4331] [depth= 1] . ( 2 sec) [ -19514.9490] [ 4322] [depth= 4] . ( 2 sec) [ -19426.8092] [ 4295] [depth= 4] . ( 2 sec) [ -19317.9788] [ 4285] [depth= 5] . ( 2 sec) [ -19049.1466] [ 4269] [depth= 10] . ( 2 sec) [ -18999.5575] [ 4273] [depth= 3] . ( 2 sec) [ -18859.4438] [ 4244] [depth= 4] . ( 2 sec) [ -18849.8625] [ 4221] [depth= 1] . ( 2 sec) [ -18832.7891] [ 4221] [depth= 2] . ( 2 sec) [ -18182.4827] [ 4181] [depth= 14] . ( 3 sec) [ -17766.2494] [ 4127] [depth= 4] . ( 3 sec) [ -17400.2890] [ 4137] [depth= 1] . ( 3 sec) [ -17314.7596] [ 3967] [depth= 13] . ( 3 sec) [ -17252.9888] [ 3968] [depth= 1] . ( 3 sec) [ -16770.0426] [ 3757] [depth= 11] . ( 3 sec) [ -16646.7825] [ 3703] [depth= 11] . ( 3 sec) [ -16343.5122] [ 3617] [depth= 13] . ( 3 sec) [ -16323.2733] [ 3590] [depth= 13] . ( 3 sec) [ -15743.8408] [ 3435] [depth= 8] . ( 3 sec) [ -15429.3744] [ 3339] [depth= 3] . ( 3 sec) [ -14625.1169] [ 3335] [depth= 1] . ( 3 sec) [ -14519.1612] [ 3363] [depth= 10] . ( 3 sec) [ -14505.0897] [ 3328] [depth= 6] . ( 4 sec) [ -14356.8866] [ 3316] [depth= 3] . ( 4 sec) [ -14127.2069] [ 3127] [depth= 6] . ( 4 sec) [ -14043.7728] [ 3126] [depth= 2] . ( 4 sec) [ -13683.6502] [ 3070] [depth= 8] . ( 4 sec) [ -13498.3413] [ 3081] [depth= 1] . ( 4 sec) [ -13305.5070] [ 3049] [depth= 10] . ( 4 sec) [ -13256.6044] [ 3047] [depth= 1] . ( 4 sec) [ -12931.1446] [ 2900] [depth= 3] . ( 4 sec) [ -12515.3209] [ 2876] [depth= 2] . ( 4 sec) [ -12506.5175] [ 2878] [depth= 1] . ( 4 sec) [ -12223.8183] [ 2825] [depth= 7] . ( 4 sec) [ -11932.1946] [ 2726] [depth= 9] . ( 4 sec) [ -11618.3363] [ 2588] [depth= 6] . ( 4 sec) [ -11605.2571] [ 2586] [depth= 3] . ( 5 sec) [ -11472.6937] [ 2506] [depth= 10] . ( 5 sec) [ -11417.1348] [ 2513] [depth= 1] . ( 5 sec) [ -11391.1855] [ 2514] [depth= 1] . ( 5 sec) [ -11380.9409] [ 2494] [depth= 3] . ( 5 sec) [ -11237.7524] [ 2455] [depth= 11] . ( 5 sec) [ -11116.4466] [ 2450] [depth= 1] . ( 5 sec) [ -10909.8625] [ 2427] [depth= 5] . ( 5 sec) [ -10592.2603] [ 2380] [depth= 4] . ( 5 sec) [ -10479.1879] [ 2365] [depth= 1] . ( 5 sec) [ -10376.9696] [ 2387] [depth= 3] . ( 5 sec) [ -10289.4683] [ 2361] [depth= 1] . ( 5 sec) [ -10263.1095] [ 2357] [depth= 1] . ( 5 sec) [ -10234.4385] [ 2341] [depth= 3] . ( 5 sec) [ -10196.5772] [ 2332] [depth= 1] . ( 6 sec) [ -10014.4538] [ 2245] [depth= 11] . ( 6 sec) [ -9965.6760] [ 2232] [depth= 1] . ( 6 sec) [ -9962.3452] [ 2233] [depth= 1] . ( 6 sec) [ -9951.6432] [ 2231] [depth= 1] . ( 6 sec) [ -9822.5494] [ 2214] [depth= 5] . ( 6 sec) [ -9818.0740] [ 2215] [depth= 1] . ( 6 sec) [ -9695.1955] [ 2190] [depth= 3] . ( 6 sec) [ -9564.4804] [ 2130] [depth= 2] . ( 6 sec) [ -9183.7823] [ 2015] [depth= 6] . ( 7 sec) [ -9119.5354] [ 2010] [depth= 1] . ( 7 sec) [ -9104.5274] [ 2004] [depth= 1] . ( 7 sec) [ -9102.8201] [ 2003] [depth= 1] . ( 7 sec) [ -9097.9777] [ 2006] [depth= 1] . ( 7 sec) [ -9086.8752] [ 1996] [depth= 2] . ( 7 sec) [ -8983.9771] [ 1906] [depth= 4] . ( 7 sec) [ -8977.2805] [ 1908] [depth= 2] . ( 7 sec) [ -8970.0508] [ 1909] [depth= 1] . ( 7 sec) [ -8960.5844] [ 1907] [depth= 1] . ( 8 sec) [ -8942.5561] [ 1882] [depth= 2] . ( 8 sec) [ -8941.5472] [ 1887] [depth= 1] . ( 8 sec) [ -8836.5478] [Branch lengths ] . ( 9 sec) [ -8832.9669] [GTR parameters ] . ( 9 sec) [ -8793.6022] [Alpha ][ 0.985425] . ( 9 sec) [ -8792.2425] [ 1891] [depth= 1] . ( 9 sec) [ -8791.7339] [ 1896] [depth= 2] . ( 9 sec) [ -8790.3482] [ 1895] [depth= 1] . ( 9 sec) [ -8762.2352] [ 1879] [depth= 2] . ( 10 sec) [ -8748.1867] [ 1875] [depth= 1] . ( 10 sec) [ -8747.9413] [ 1875] [depth= 1] . ( 10 sec) [ -8738.7074] [ 1840] [depth= 2] . ( 10 sec) [ -8735.9006] [ 1848] [depth= 1] . ( 10 sec) [ -8733.3863] [ 1836] [depth= 3] . ( 10 sec) [ -8725.0550] [ 1837] [depth= 1] . ( 11 sec) [ -8725.0430] [ 1836] [depth= 1] . ( 11 sec) [ -8712.7197] [ 1835] [depth= 1] . ( 11 sec) [ -8710.4535] [ 1834] [depth= 1] . ( 11 sec) [ -8706.2322] [ 1837] [depth= 1] . ( 11 sec) [ -8705.2409] [ 1836] [depth= 1] . ( 12 sec) [ -8703.7551] [ 1837] [depth= 1] . ( 12 sec) [ -8692.9757] [Branch lengths ] . ( 12 sec) [ -8692.9329] [GTR parameters ] . ( 12 sec) [ -8691.3165] [Alpha ][ 1.139243] . ( 13 sec) [ -8691.2848] [ 1838] [depth= 1] . ( 14 sec) [ -8690.1572] [ 1840] [depth= 1] . ( 16 sec) [ -8688.9962] [Branch lengths ] . ( 16 sec) [ -8688.9898] [GTR parameters ] . ( 16 sec) [ -8688.9760] [Alpha ][ 1.155001] . ( 19 sec) [ -8688.7975] [Branch lengths ] . ( 35 sec) [ -8688.5675] [ 1836] [depth= 1] . ( 43 sec) [ -8688.4220] [Branch lengths ] . ( 43 sec) [ -8688.4211] [GTR parameters ] . ( 43 sec) [ -8688.4200] [Alpha ][ 1.159505] . ( 43 sec) [ -8688.4200] [Topology ] . ( 44 sec) [ -8688.4145] [Topology ] . ( 45 sec) [ -8688.4124] [Topology ] . ( 46 sec) [ -8688.4112] [Topology ] . ( 48 sec) [ -8688.4105] [Topology ] . ( 48 sec) [ -8688.4105] [GTR parameters ] . ( 48 sec) [ -8688.4105] [Alpha ][ 1.159505] . ( 48 sec) [ -8688.4105] [Topology ] . ( 49 sec) [ -8688.4100] [Topology ] . ( 49 sec) [ -8688.4100] [GTR parameters ] . ( 50 sec) [ -8688.4100] [Alpha ][ 1.159505] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -8688.4095] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8688.409466. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22671.4390] [GTR parameters ] . ( 2 sec) [ -22169.0961] [Alpha ][ 0.500960] . ( 2 sec) [ -21265.1619] [ 4785] [depth= 7] . ( 2 sec) [ -20665.7955] [ 4615] [depth= 11] . ( 2 sec) [ -20654.9000] [ 4604] [depth= 4] . ( 3 sec) [ -20621.9603] [ 4602] [depth= 3] . ( 3 sec) [ -20261.5378] [ 4550] [depth= 10] . ( 3 sec) [ -20220.7855] [ 4548] [depth= 5] . ( 3 sec) [ -19820.2504] [ 4503] [depth= 6] . ( 3 sec) [ -19553.8727] [ 4525] [depth= 1] . ( 3 sec) [ -18885.4257] [ 4411] [depth= 2] . ( 3 sec) [ -18473.5050] [ 4299] [depth= 10] . ( 4 sec) [ -18213.5730] [ 4179] [depth= 6] . ( 4 sec) [ -17513.4799] [ 4116] [depth= 8] . ( 4 sec) [ -16841.2784] [ 3955] [depth= 5] . ( 4 sec) [ -16738.5329] [ 3949] [depth= 10] . ( 4 sec) [ -16635.3705] [ 3951] [depth= 1] . ( 4 sec) [ -16405.7489] [ 3936] [depth= 12] . ( 4 sec) [ -16360.1365] [ 3901] [depth= 1] . ( 5 sec) [ -16129.0312] [ 3880] [depth= 8] . ( 5 sec) [ -16009.1161] [ 3861] [depth= 16] . ( 5 sec) [ -15534.9401] [ 3824] [depth= 1] . ( 5 sec) [ -15327.1311] [ 3757] [depth= 8] . ( 5 sec) [ -15139.8923] [ 3708] [depth= 6] . ( 5 sec) [ -14813.6274] [ 3664] [depth= 2] . ( 6 sec) [ -14502.5972] [ 3464] [depth= 11] . ( 6 sec) [ -14114.0985] [ 3273] [depth= 3] . ( 6 sec) [ -13446.3926] [ 3180] [depth= 7] . ( 6 sec) [ -13274.5734] [ 3126] [depth= 14] . ( 6 sec) [ -13066.5728] [ 3071] [depth= 5] . ( 6 sec) [ -12649.8811] [ 2925] [depth= 6] . ( 7 sec) [ -12126.0357] [ 2849] [depth= 13] . ( 7 sec) [ -12119.3928] [ 2847] [depth= 6] . ( 7 sec) [ -12114.2074] [ 2836] [depth= 1] . ( 7 sec) [ -12106.1369] [ 2828] [depth= 1] . ( 7 sec) [ -12075.1557] [ 2822] [depth= 6] . ( 7 sec) [ -11942.8106] [ 2819] [depth= 1] . ( 7 sec) [ -11702.8217] [ 2676] [depth= 4] . ( 7 sec) [ -11679.8356] [ 2678] [depth= 1] . ( 7 sec) [ -11588.8391] [ 2666] [depth= 9] . ( 7 sec) [ -11516.1028] [ 2616] [depth= 7] . ( 7 sec) [ -11291.4617] [ 2617] [depth= 1] . ( 7 sec) [ -11255.7379] [ 2589] [depth= 1] . ( 7 sec) [ -11248.8704] [ 2600] [depth= 1] . ( 8 sec) [ -10867.4144] [ 2421] [depth= 4] . ( 8 sec) [ -10848.8699] [ 2425] [depth= 2] . ( 8 sec) [ -10848.3893] [ 2422] [depth= 2] . ( 8 sec) [ -10785.0546] [ 2375] [depth= 1] . ( 8 sec) [ -10746.8866] [ 2372] [depth= 1] . ( 8 sec) [ -10735.5358] [ 2374] [depth= 1] . ( 8 sec) [ -10610.9150] [ 2326] [depth= 7] . ( 8 sec) [ -10481.8141] [ 2266] [depth= 5] . ( 8 sec) [ -10335.7566] [ 2241] [depth= 1] . ( 8 sec) [ -10210.1372] [ 2228] [depth= 5] . ( 9 sec) [ -10174.4451] [ 2221] [depth= 1] . ( 9 sec) [ -10097.2720] [ 2190] [depth= 1] . ( 9 sec) [ -10052.4444] [ 2186] [depth= 1] . ( 9 sec) [ -9910.6589] [ 2138] [depth= 8] . ( 9 sec) [ -9774.6006] [ 2060] [depth= 9] . ( 10 sec) [ -9722.0726] [ 2054] [depth= 2] . ( 10 sec) [ -9698.8105] [ 2025] [depth= 4] . ( 10 sec) [ -9672.1617] [ 1988] [depth= 1] . ( 10 sec) [ -9627.5857] [ 1966] [depth= 5] . ( 10 sec) [ -9525.0739] [ 1926] [depth= 1] . ( 10 sec) [ -9457.6275] [ 1911] [depth= 5] . ( 10 sec) [ -9355.5306] [ 1916] [depth= 1] . ( 10 sec) [ -9290.9385] [ 1905] [depth= 1] . ( 10 sec) [ -9262.9352] [ 1870] [depth= 2] . ( 10 sec) [ -9087.0601] [ 1859] [depth= 1] . ( 11 sec) [ -9073.5747] [ 1852] [depth= 2] . ( 11 sec) [ -9073.2779] [ 1852] [depth= 1] . ( 11 sec) [ -9067.3174] [ 1852] [depth= 1] . ( 11 sec) [ -9055.9579] [ 1848] [depth= 1] . ( 11 sec) [ -8975.9946] [ 1843] [depth= 1] . ( 12 sec) [ -8771.2255] [Branch lengths ] . ( 12 sec) [ -8768.6215] [GTR parameters ] . ( 12 sec) [ -8712.0891] [Alpha ][ 1.000519] . ( 13 sec) [ -8703.8132] [ 1839] [depth= 1] . ( 13 sec) [ -8700.2353] [ 1842] [depth= 1] . ( 13 sec) [ -8699.6525] [ 1842] [depth= 1] . ( 14 sec) [ -8698.8097] [ 1836] [depth= 1] . ( 15 sec) [ -8698.7287] [ 1837] [depth= 1] . ( 15 sec) [ -8698.1801] [ 1840] [depth= 1] . ( 16 sec) [ -8697.1383] [ 1836] [depth= 1] . ( 17 sec) [ -8691.1338] [Branch lengths ] . ( 17 sec) [ -8691.0259] [GTR parameters ] . ( 18 sec) [ -8689.5058] [Alpha ][ 1.148969] . ( 22 sec) [ -8688.9014] [Branch lengths ] . ( 42 sec) [ -8688.6586] [Branch lengths ] . ( 42 sec) [ -8688.6586] [Topology ] . ( 43 sec) [ -8688.5928] [Topology ] . ( 44 sec) [ -8688.5537] [Topology ] . ( 44 sec) [ -8688.5240] [Topology ] . ( 45 sec) [ -8688.5015] [Topology ] . ( 46 sec) [ -8688.4839] [Topology ] . ( 47 sec) [ -8688.4699] [Topology ] . ( 47 sec) [ -8688.4694] [GTR parameters ] . ( 47 sec) [ -8688.4632] [Alpha ][ 1.159447] . ( 47 sec) [ -8688.4632] [Topology ] . ( 48 sec) [ -8688.4516] [Topology ] . ( 49 sec) [ -8688.4426] [Topology ] . ( 49 sec) [ -8688.4355] [Topology ] . ( 50 sec) [ -8688.4299] [Topology ] . ( 51 sec) [ -8688.4255] [Topology ] . ( 52 sec) [ -8688.4220] [Topology ] . ( 52 sec) [ -8688.4220] [GTR parameters ] . ( 52 sec) [ -8688.4220] [Alpha ][ 1.159447] . ( 52 sec) [ -8688.4220] [Topology ] . ( 53 sec) [ -8688.4192] [Topology ] . ( 54 sec) [ -8688.4170] [Topology ] . ( 54 sec) [ -8688.4152] [Topology ] . ( 55 sec) [ -8688.4138] [Topology ] . ( 56 sec) [ -8688.4127] [Topology ] . ( 57 sec) [ -8688.4119] [Topology ] . ( 57 sec) [ -8688.4119] [GTR parameters ] . ( 57 sec) [ -8688.4119] [Alpha ][ 1.160606] . ( 57 sec) [ -8688.4119] [Topology ] . ( 58 sec) [ -8688.4112] [Topology ] . ( 58 sec) [ -8688.4112] [GTR parameters ] . ( 58 sec) [ -8688.4112] [Alpha ][ 1.160606] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -8688.4105] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8688.410545. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8768.396920 . ( 1 sec) [ -8765.3410] [GTR parameters ] . ( 1 sec) [ -8763.4873] [Alpha ][ 1.174574] . ( 1 sec) [ -8763.4873] [Topology ] . ( 2 sec) [ -8706.9612] [Topology ] . ( 3 sec) [ -8694.4275] [Topology ] . ( 4 sec) [ -8691.9231] [Topology ] . ( 4 sec) [ -8691.1687] [Topology ] . ( 5 sec) [ -8690.8831] [Topology ] . ( 6 sec) [ -8690.7542] [Topology ] . ( 7 sec) [ -8690.6895] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -8690.1883] [Topology ] . Before opt ts/t=1.000000 LK=-8690.188347 . ( 14 sec) [ -8690.1757] [GTR parameters ] . ( 14 sec) [ -8690.1739] [Alpha ][ 1.168506] . ( 14 sec) [ -8690.1739] [Topology ] . ( 15 sec) [ -8690.1317] [Topology ] . ( 15 sec) [ -8690.1094] [Topology ] . ( 16 sec) [ -8690.0966] [Topology ] . ( 17 sec) [ -8690.0892] [Topology ] . ( 18 sec) [ -8690.0847] [Topology ] . ( 19 sec) [ -8690.0821] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8690.082072 . ( 25 sec) [ -8690.0819] [GTR parameters ] . ( 26 sec) [ -8690.0818] [Alpha ][ 1.169955] . ( 26 sec) [ -8690.0818] [Topology ] . ( 26 sec) [ -8690.0802] [Topology ] . ( 27 sec) [ -8690.0792] [Topology ] . ( 28 sec) [ -8690.0785] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8690.078535 . ( 35 sec) [ -8690.0785] [GTR parameters ] . ( 35 sec) [ -8690.0785] [Alpha ][ 1.169955] . ( 35 sec) [ -8690.0785] [Topology ] . ( 35 sec) [ -8690.0781] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -8765.3410] [GTR parameters ] . ( 49 sec) [ -8763.4873] [Alpha ][ 1.174574] . ( 49 sec) [ -8736.7899] [ 1825] [depth= 1] . ( 50 sec) [ -8724.8039] [ 1828] [depth= 1] . ( 50 sec) [ -8724.3963] [ 1830] [depth= 1] . ( 50 sec) [ -8723.9811] [ 1828] [depth= 1] . ( 51 sec) [ -8723.2369] [ 1828] [depth= 1] . ( 51 sec) [ -8723.0275] [ 1828] [depth= 1] . ( 51 sec) [ -8720.9832] [ 1833] [depth= 1] . ( 51 sec) [ -8718.5935] [ 1828] [depth= 1] . ( 52 sec) [ -8717.6825] [ 1828] [depth= 1] . ( 52 sec) [ -8691.9707] [Branch lengths ] . ( 53 sec) [ -8691.9562] [GTR parameters ] . ( 53 sec) [ -8691.9438] [Alpha ][ 1.160058] . ( 56 sec) [ -8690.5056] [Branch lengths ] . ( 59 sec) [ -8689.3639] [ 1840] [depth= 2] . ( 68 sec) [ -8689.2582] [ 1836] [depth= 1] . ( 70 sec) [ -8688.9077] [ 1836] [depth= 1] . ( 75 sec) [ -8688.5935] [Branch lengths ] . ( 75 sec) [ -8688.5881] [GTR parameters ] . ( 75 sec) [ -8688.5881] [Alpha ][ 1.160058] . ( 97 sec) [ -8688.4922] [Branch lengths ] . ( 97 sec) [ -8688.4922] [Topology ] . ( 97 sec) [ -8688.4688] [Topology ] . ( 98 sec) [ -8688.4551] [Topology ] . ( 99 sec) [ -8688.4451] [Topology ] . ( 100 sec) [ -8688.4374] [Topology ] . ( 101 sec) [ -8688.4314] [Topology ] . ( 101 sec) [ -8688.4266] [Topology ] . ( 101 sec) [ -8688.4266] [GTR parameters ] . ( 102 sec) [ -8688.4266] [Alpha ][ 1.160058] . ( 102 sec) [ -8688.4266] [Topology ] . ( 102 sec) [ -8688.4229] [Topology ] . ( 103 sec) [ -8688.4199] [Topology ] . ( 104 sec) [ -8688.4176] [Topology ] . ( 105 sec) [ -8688.4157] [Topology ] . ( 105 sec) [ -8688.4142] [Topology ] . ( 106 sec) [ -8688.4131] [Topology ] . ( 106 sec) [ -8688.4131] [GTR parameters ] . ( 106 sec) [ -8688.4131] [Alpha ][ 1.160058] . ( 106 sec) [ -8688.4131] [Topology ] . ( 107 sec) [ -8688.4121] [Topology ] . ( 107 sec) [ -8688.4121] [GTR parameters ] . ( 107 sec) [ -8688.4121] [Alpha ][ 1.160058] . Checking for NNIs, optimizing five branches... . ( 114 sec) [ -8688.4111] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8690.078147 . Log likelihood obtained after SPR moves : -8688.411078 . Log likelihood of the current tree: -8688.411078. . Printing the most likely tree in file 'data98.phy_phyml_tree.txt'... . Best log likelihood : -8688.369744 . Time used 0h2m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo