.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data52.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... . 402 patterns found. (out of a total of 500 sites) . 89 sites without polymorphism (17.80%). . [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) [ -18235.4467] [GTR parameters ] . ( 0 sec) [ -17893.2439] [Alpha ][ 0.500960] . ( 0 sec) [ -17369.8234] [ 3632] [depth= 4] . ( 1 sec) [ -17032.9606] [ 3524] [depth= 6] . ( 1 sec) [ -16872.5483] [ 3510] [depth= 1] . ( 1 sec) [ -16703.8365] [ 3420] [depth= 6] . ( 1 sec) [ -16694.2659] [ 3422] [depth= 6] . ( 1 sec) [ -16688.7791] [ 3421] [depth= 1] . ( 1 sec) [ -16685.5333] [ 3422] [depth= 1] . ( 1 sec) [ -16524.2823] [ 3386] [depth= 6] . ( 1 sec) [ -16476.0395] [ 3379] [depth= 11] . ( 1 sec) [ -16437.2978] [ 3377] [depth= 7] . ( 1 sec) [ -16168.1265] [ 3352] [depth= 2] . ( 1 sec) [ -15976.0130] [ 3339] [depth= 9] . ( 1 sec) [ -15521.0728] [ 3222] [depth= 14] . ( 1 sec) [ -15455.3523] [ 3218] [depth= 1] . ( 1 sec) [ -15450.1797] [ 3196] [depth= 3] . ( 1 sec) [ -15263.9407] [ 3191] [depth= 3] . ( 1 sec) [ -15126.2956] [ 3126] [depth= 4] . ( 1 sec) [ -15100.1608] [ 3127] [depth= 2] . ( 1 sec) [ -14813.0937] [ 3072] [depth= 3] . ( 1 sec) [ -14764.8920] [ 3068] [depth= 1] . ( 1 sec) [ -14625.1214] [ 3050] [depth= 5] . ( 1 sec) [ -14254.5091] [ 2978] [depth= 4] . ( 1 sec) [ -14254.0205] [ 2978] [depth= 1] . ( 1 sec) [ -14241.5012] [ 2978] [depth= 1] . ( 1 sec) [ -14169.0466] [ 2956] [depth= 1] . ( 1 sec) [ -14123.2799] [ 2933] [depth= 1] . ( 2 sec) [ -14112.9935] [ 2930] [depth= 8] . ( 2 sec) [ -13745.5135] [ 2906] [depth= 15] . ( 2 sec) [ -13518.0875] [ 2804] [depth= 7] . ( 2 sec) [ -13235.3181] [ 2693] [depth= 11] . ( 2 sec) [ -13110.1428] [ 2671] [depth= 8] . ( 2 sec) [ -13044.9351] [ 2653] [depth= 2] . ( 2 sec) [ -12863.6347] [ 2582] [depth= 8] . ( 2 sec) [ -12855.0075] [ 2579] [depth= 1] . ( 2 sec) [ -12681.0405] [ 2592] [depth= 12] . ( 2 sec) [ -12536.9211] [ 2558] [depth= 1] . ( 2 sec) [ -12525.5024] [ 2558] [depth= 1] . ( 2 sec) [ -12390.4961] [ 2520] [depth= 2] . ( 2 sec) [ -12303.9751] [ 2510] [depth= 2] . ( 2 sec) [ -12068.6709] [ 2439] [depth= 2] . ( 2 sec) [ -11822.9745] [ 2402] [depth= 4] . ( 2 sec) [ -11499.6893] [ 2398] [depth= 1] . ( 2 sec) [ -11495.9510] [ 2319] [depth= 7] . ( 2 sec) [ -11480.9684] [ 2313] [depth= 1] . ( 2 sec) [ -11384.6940] [ 2295] [depth= 9] . ( 2 sec) [ -11120.3896] [ 2257] [depth= 8] . ( 2 sec) [ -10992.8896] [ 2234] [depth= 1] . ( 2 sec) [ -10973.9979] [ 2269] [depth= 3] . ( 3 sec) [ -10549.4309] [ 2189] [depth= 5] . ( 3 sec) [ -10482.6141] [ 2163] [depth= 2] . ( 3 sec) [ -10341.1161] [ 2134] [depth= 1] . ( 3 sec) [ -10260.9182] [ 2130] [depth= 7] . ( 3 sec) [ -9982.1545] [ 2080] [depth= 8] . ( 3 sec) [ -9942.4892] [ 2077] [depth= 4] . ( 3 sec) [ -9782.7934] [ 2014] [depth= 2] . ( 3 sec) [ -9647.3219] [ 1960] [depth= 4] . ( 3 sec) [ -9642.5069] [ 1959] [depth= 2] . ( 3 sec) [ -9640.2090] [ 1959] [depth= 1] . ( 3 sec) [ -9612.9674] [ 1928] [depth= 1] . ( 3 sec) [ -9580.2235] [ 1913] [depth= 1] . ( 3 sec) [ -9505.6675] [ 1914] [depth= 3] . ( 3 sec) [ -9499.9775] [ 1913] [depth= 1] . ( 3 sec) [ -9499.3891] [ 1914] [depth= 2] . ( 3 sec) [ -9421.2305] [ 1895] [depth= 1] . ( 3 sec) [ -9366.8714] [ 1888] [depth= 4] . ( 4 sec) [ -9323.8206] [ 1884] [depth= 5] . ( 4 sec) [ -9132.1406] [ 1851] [depth= 3] . ( 4 sec) [ -9113.9646] [ 1841] [depth= 1] . ( 4 sec) [ -9112.2943] [ 1847] [depth= 1] . ( 4 sec) [ -8886.1413] [ 1841] [depth= 2] . ( 4 sec) [ -8820.9118] [ 1832] [depth= 1] . ( 4 sec) [ -8722.7741] [ 1836] [depth= 1] . ( 4 sec) [ -8717.2390] [ 1837] [depth= 1] . ( 4 sec) [ -8704.1003] [ 1837] [depth= 1] . ( 4 sec) [ -8684.5899] [ 1842] [depth= 3] . ( 4 sec) [ -8537.1317] [Branch lengths ] . ( 5 sec) [ -8533.8834] [GTR parameters ] . ( 5 sec) [ -8504.4159] [Alpha ][ 0.886345] . ( 5 sec) [ -8502.9114] [ 1840] [depth= 1] . ( 5 sec) [ -8501.8777] [ 1843] [depth= 2] . ( 5 sec) [ -8455.8134] [ 1799] [depth= 2] . ( 5 sec) [ -8445.0210] [ 1802] [depth= 1] . ( 6 sec) [ -8438.9068] [ 1793] [depth= 2] . ( 6 sec) [ -8429.2115] [ 1781] [depth= 3] . ( 6 sec) [ -8426.1442] [ 1764] [depth= 2] . ( 6 sec) [ -8423.2800] [ 1764] [depth= 2] . ( 6 sec) [ -8399.6292] [ 1726] [depth= 4] . ( 6 sec) [ -8395.7778] [ 1722] [depth= 1] . ( 6 sec) [ -8259.3244] [ 1706] [depth= 2] . ( 6 sec) [ -8240.2892] [ 1729] [depth= 1] . ( 6 sec) [ -8220.7481] [ 1721] [depth= 1] . ( 7 sec) [ -8220.5491] [ 1719] [depth= 1] . ( 7 sec) [ -8215.5279] [ 1696] [depth= 1] . ( 7 sec) [ -8180.5066] [ 1683] [depth= 1] . ( 8 sec) [ -8180.2360] [ 1685] [depth= 1] . ( 8 sec) [ -8178.3942] [ 1686] [depth= 1] . ( 8 sec) [ -8171.9227] [ 1685] [depth= 1] . ( 8 sec) [ -8153.7193] [Branch lengths ] . ( 9 sec) [ -8153.4862] [GTR parameters ] . ( 9 sec) [ -8152.0301] [Alpha ][ 1.016071] . ( 11 sec) [ -8151.8817] [ 1685] [depth= 1] . ( 12 sec) [ -8151.8571] [ 1682] [depth= 1] . ( 12 sec) [ -8148.1124] [Branch lengths ] . ( 12 sec) [ -8148.1074] [GTR parameters ] . ( 13 sec) [ -8148.0805] [Alpha ][ 1.035778] . ( 16 sec) [ -8147.8582] [Branch lengths ] . ( 36 sec) [ -8147.8482] [Branch lengths ] . ( 36 sec) [ -8147.8482] [Topology ] . ( 36 sec) [ -8147.8477] [Topology ] . ( 37 sec) [ -8147.8472] [GTR parameters ] . ( 37 sec) [ -8147.8472] [Alpha ][ 1.036814] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8147.847206. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18079.4859] [GTR parameters ] . ( 1 sec) [ -17720.7450] [Alpha ][ 0.500960] . ( 1 sec) [ -17235.0506] [ 3641] [depth= 4] . ( 1 sec) [ -16037.4389] [ 3544] [depth= 3] . ( 1 sec) [ -15622.9347] [ 3497] [depth= 4] . ( 1 sec) [ -15558.7301] [ 3492] [depth= 3] . ( 1 sec) [ -15342.6163] [ 3451] [depth= 3] . ( 2 sec) [ -15206.6644] [ 3437] [depth= 4] . ( 2 sec) [ -15200.7160] [ 3423] [depth= 1] . ( 2 sec) [ -15021.1811] [ 3403] [depth= 6] . ( 2 sec) [ -14954.0074] [ 3365] [depth= 1] . ( 2 sec) [ -14849.3345] [ 3325] [depth= 1] . ( 2 sec) [ -14733.6522] [ 3285] [depth= 5] . ( 2 sec) [ -14721.5874] [ 3284] [depth= 3] . ( 2 sec) [ -14617.7115] [ 3233] [depth= 6] . ( 2 sec) [ -14524.1525] [ 3219] [depth= 4] . ( 2 sec) [ -13863.9601] [ 3094] [depth= 13] . ( 2 sec) [ -13537.3087] [ 3013] [depth= 9] . ( 2 sec) [ -13458.0554] [ 2996] [depth= 2] . ( 2 sec) [ -13443.9099] [ 2989] [depth= 1] . ( 2 sec) [ -13198.7070] [ 2991] [depth= 1] . ( 2 sec) [ -13034.6853] [ 2942] [depth= 2] . ( 2 sec) [ -12957.4598] [ 2908] [depth= 1] . ( 2 sec) [ -12744.3399] [ 2843] [depth= 7] . ( 2 sec) [ -12551.1788] [ 2823] [depth= 3] . ( 2 sec) [ -12545.5309] [ 2823] [depth= 2] . ( 2 sec) [ -12350.6013] [ 2725] [depth= 7] . ( 2 sec) [ -12105.5364] [ 2664] [depth= 6] . ( 2 sec) [ -12049.7571] [ 2670] [depth= 1] . ( 2 sec) [ -11679.5041] [ 2572] [depth= 11] . ( 2 sec) [ -11613.0638] [ 2573] [depth= 1] . ( 3 sec) [ -11291.9129] [ 2454] [depth= 5] . ( 3 sec) [ -11265.1555] [ 2467] [depth= 2] . ( 3 sec) [ -11258.4615] [ 2469] [depth= 1] . ( 3 sec) [ -11254.5851] [ 2473] [depth= 3] . ( 3 sec) [ -11174.6975] [ 2473] [depth= 1] . ( 3 sec) [ -11101.9256] [ 2433] [depth= 1] . ( 3 sec) [ -10874.5414] [ 2379] [depth= 9] . ( 3 sec) [ -10665.4997] [ 2377] [depth= 1] . ( 3 sec) [ -10646.6595] [ 2366] [depth= 1] . ( 3 sec) [ -10625.8536] [ 2366] [depth= 1] . ( 3 sec) [ -10619.2516] [ 2366] [depth= 1] . ( 3 sec) [ -10342.0279] [ 2366] [depth= 2] . ( 3 sec) [ -10304.3906] [ 2315] [depth= 14] . ( 3 sec) [ -10104.1744] [ 2283] [depth= 10] . ( 3 sec) [ -10095.7407] [ 2283] [depth= 1] . ( 3 sec) [ -10081.5712] [ 2272] [depth= 3] . ( 3 sec) [ -9927.8066] [ 2259] [depth= 2] . ( 3 sec) [ -9902.4594] [ 2256] [depth= 2] . ( 3 sec) [ -9885.1895] [ 2260] [depth= 1] . ( 3 sec) [ -9872.9968] [ 2256] [depth= 1] . ( 3 sec) [ -9861.3039] [ 2253] [depth= 3] . ( 3 sec) [ -9814.4060] [ 2243] [depth= 1] . ( 4 sec) [ -9720.3076] [ 2201] [depth= 1] . ( 4 sec) [ -9599.0197] [ 2193] [depth= 1] . ( 4 sec) [ -9556.4510] [ 2202] [depth= 1] . ( 4 sec) [ -9548.7528] [ 2193] [depth= 1] . ( 4 sec) [ -9367.9535] [ 2086] [depth= 6] . ( 4 sec) [ -9272.3011] [ 2049] [depth= 2] . ( 4 sec) [ -9231.6311] [ 2035] [depth= 5] . ( 4 sec) [ -9226.0399] [ 2034] [depth= 1] . ( 4 sec) [ -9155.4154] [ 1999] [depth= 6] . ( 4 sec) [ -9107.4320] [ 1987] [depth= 1] . ( 4 sec) [ -9100.1009] [ 1996] [depth= 10] . ( 4 sec) [ -9095.8627] [ 2006] [depth= 1] . ( 4 sec) [ -9069.8592] [ 2009] [depth= 1] . ( 4 sec) [ -8949.5926] [ 1967] [depth= 8] . ( 4 sec) [ -8940.7026] [ 1973] [depth= 1] . ( 4 sec) [ -8932.6480] [ 1964] [depth= 2] . ( 4 sec) [ -8920.7360] [ 1954] [depth= 1] . ( 4 sec) [ -8920.1305] [ 1954] [depth= 1] . ( 5 sec) [ -8859.9579] [ 1950] [depth= 1] . ( 5 sec) [ -8848.8927] [ 1960] [depth= 1] . ( 5 sec) [ -8847.6887] [ 1964] [depth= 1] . ( 5 sec) [ -8844.2606] [ 1963] [depth= 1] . ( 5 sec) [ -8832.9384] [ 1953] [depth= 1] . ( 5 sec) [ -8831.8097] [ 1954] [depth= 1] . ( 5 sec) [ -8825.7501] [ 1944] [depth= 1] . ( 5 sec) [ -8817.8535] [ 1941] [depth= 1] . ( 5 sec) [ -8815.1270] [ 1937] [depth= 1] . ( 5 sec) [ -8644.6910] [ 1848] [depth= 6] . ( 5 sec) [ -8642.0717] [ 1846] [depth= 1] . ( 5 sec) [ -8503.1378] [Branch lengths ] . ( 6 sec) [ -8498.8330] [GTR parameters ] . ( 6 sec) [ -8465.3095] [Alpha ][ 0.925596] . ( 6 sec) [ -8457.4041] [ 1836] [depth= 1] . ( 6 sec) [ -8410.6181] [ 1814] [depth= 1] . ( 6 sec) [ -8408.5206] [ 1812] [depth= 2] . ( 6 sec) [ -8408.3514] [ 1811] [depth= 1] . ( 7 sec) [ -8407.0846] [ 1808] [depth= 1] . ( 7 sec) [ -8319.5576] [ 1777] [depth= 5] . ( 7 sec) [ -8282.2201] [ 1758] [depth= 1] . ( 7 sec) [ -8281.2896] [ 1762] [depth= 1] . ( 7 sec) [ -8260.5843] [ 1730] [depth= 3] . ( 7 sec) [ -8260.1876] [ 1728] [depth= 1] . ( 7 sec) [ -8257.0518] [ 1726] [depth= 2] . ( 7 sec) [ -8236.3247] [ 1722] [depth= 1] . ( 8 sec) [ -8233.5565] [ 1721] [depth= 1] . ( 8 sec) [ -8233.2718] [ 1725] [depth= 1] . ( 8 sec) [ -8194.6192] [ 1693] [depth= 2] . ( 8 sec) [ -8194.5091] [ 1697] [depth= 1] . ( 8 sec) [ -8189.5133] [ 1692] [depth= 1] . ( 8 sec) [ -8188.6611] [ 1690] [depth= 1] . ( 8 sec) [ -8186.3529] [ 1683] [depth= 2] . ( 9 sec) [ -8167.6891] [ 1680] [depth= 1] . ( 9 sec) [ -8167.4996] [ 1682] [depth= 1] . ( 9 sec) [ -8163.9847] [ 1685] [depth= 1] . ( 10 sec) [ -8149.4766] [Branch lengths ] . ( 10 sec) [ -8149.3304] [GTR parameters ] . ( 10 sec) [ -8148.5320] [Alpha ][ 1.024932] . ( 11 sec) [ -8148.4795] [ 1685] [depth= 1] . ( 14 sec) [ -8147.9344] [Branch lengths ] . ( 14 sec) [ -8147.9333] [GTR parameters ] . ( 14 sec) [ -8147.9309] [Alpha ][ 1.030831] . ( 34 sec) [ -8147.8707] [Branch lengths ] . ( 34 sec) [ -8147.8707] [Topology ] . ( 35 sec) [ -8147.8643] [Topology ] . ( 35 sec) [ -8147.8622] [Topology ] . ( 36 sec) [ -8147.8612] [Topology ] . ( 36 sec) [ -8147.8611] [GTR parameters ] . ( 36 sec) [ -8147.8599] [Alpha ][ 1.035083] . ( 36 sec) [ -8147.8599] [Topology ] . ( 37 sec) [ -8147.8592] [Topology ] . ( 37 sec) [ -8147.8592] [GTR parameters ] . ( 37 sec) [ -8147.8592] [Alpha ][ 1.035083] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -8147.8590] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8147.859013. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18866.6723] [GTR parameters ] . ( 1 sec) [ -18492.0843] [Alpha ][ 0.500960] . ( 1 sec) [ -18021.1427] [ 3770] [depth= 1] . ( 1 sec) [ -17512.1361] [ 3665] [depth= 4] . ( 1 sec) [ -17447.2396] [ 3663] [depth= 3] . ( 1 sec) [ -17321.8947] [ 3662] [depth= 1] . ( 1 sec) [ -17185.4444] [ 3576] [depth= 6] . ( 1 sec) [ -17058.2720] [ 3574] [depth= 1] . ( 1 sec) [ -16941.8820] [ 3587] [depth= 7] . ( 1 sec) [ -16705.1153] [ 3562] [depth= 6] . ( 1 sec) [ -16536.3559] [ 3480] [depth= 12] . ( 1 sec) [ -16492.9500] [ 3493] [depth= 4] . ( 1 sec) [ -15913.9941] [ 3409] [depth= 9] . ( 1 sec) [ -15845.4179] [ 3396] [depth= 5] . ( 1 sec) [ -15819.3435] [ 3395] [depth= 1] . ( 1 sec) [ -15677.2966] [ 3370] [depth= 6] . ( 1 sec) [ -15504.0035] [ 3365] [depth= 1] . ( 1 sec) [ -15403.4204] [ 3315] [depth= 5] . ( 2 sec) [ -15380.2888] [ 3313] [depth= 1] . ( 2 sec) [ -15168.1888] [ 3270] [depth= 2] . ( 2 sec) [ -15128.4517] [ 3264] [depth= 1] . ( 2 sec) [ -14650.9573] [ 3162] [depth= 3] . ( 2 sec) [ -14619.7879] [ 3162] [depth= 2] . ( 2 sec) [ -14320.1850] [ 3096] [depth= 1] . ( 2 sec) [ -13891.7475] [ 2996] [depth= 8] . ( 2 sec) [ -12875.0151] [ 2865] [depth= 8] . ( 2 sec) [ -12710.3663] [ 2843] [depth= 7] . ( 2 sec) [ -12499.6154] [ 2795] [depth= 3] . ( 2 sec) [ -12188.3064] [ 2722] [depth= 8] . ( 2 sec) [ -12074.0842] [ 2700] [depth= 10] . ( 2 sec) [ -11943.9654] [ 2712] [depth= 1] . ( 2 sec) [ -11714.4313] [ 2644] [depth= 8] . ( 2 sec) [ -11707.7132] [ 2649] [depth= 3] . ( 2 sec) [ -11615.3945] [ 2637] [depth= 3] . ( 2 sec) [ -11438.0748] [ 2586] [depth= 5] . ( 2 sec) [ -11279.2949] [ 2541] [depth= 2] . ( 2 sec) [ -11167.8145] [ 2508] [depth= 1] . ( 2 sec) [ -10887.8480] [ 2432] [depth= 1] . ( 2 sec) [ -10867.8403] [ 2431] [depth= 1] . ( 2 sec) [ -10798.4815] [ 2413] [depth= 5] . ( 3 sec) [ -10742.4541] [ 2391] [depth= 1] . ( 3 sec) [ -10446.5499] [ 2383] [depth= 3] . ( 3 sec) [ -10135.7302] [ 2237] [depth= 5] . ( 3 sec) [ -10036.5993] [ 2271] [depth= 6] . ( 3 sec) [ -9961.0431] [ 2263] [depth= 4] . ( 3 sec) [ -9960.2661] [ 2263] [depth= 1] . ( 3 sec) [ -9906.3975] [ 2260] [depth= 2] . ( 3 sec) [ -9887.6311] [ 2259] [depth= 2] . ( 3 sec) [ -9818.1800] [ 2220] [depth= 4] . ( 3 sec) [ -9794.4944] [ 2219] [depth= 1] . ( 3 sec) [ -9782.8771] [ 2254] [depth= 1] . ( 3 sec) [ -9772.4818] [ 2255] [depth= 1] . ( 3 sec) [ -9720.9611] [ 2220] [depth= 1] . ( 3 sec) [ -9713.5076] [ 2186] [depth= 10] . ( 3 sec) [ -9652.6282] [ 2184] [depth= 3] . ( 3 sec) [ -9434.4900] [ 2129] [depth= 15] . ( 3 sec) [ -9139.9403] [ 1993] [depth= 6] . ( 3 sec) [ -9139.3389] [ 1992] [depth= 1] . ( 4 sec) [ -9135.5298] [ 1984] [depth= 2] . ( 4 sec) [ -9004.8557] [ 1948] [depth= 7] . ( 4 sec) [ -8990.1459] [ 1946] [depth= 2] . ( 4 sec) [ -8959.3614] [ 1950] [depth= 1] . ( 4 sec) [ -8934.8576] [ 1927] [depth= 4] . ( 4 sec) [ -8787.9425] [ 1891] [depth= 11] . ( 4 sec) [ -8735.5655] [ 1863] [depth= 2] . ( 4 sec) [ -8698.3080] [ 1851] [depth= 1] . ( 4 sec) [ -8692.9843] [ 1856] [depth= 2] . ( 4 sec) [ -8679.7212] [ 1856] [depth= 1] . ( 4 sec) [ -8675.0293] [ 1855] [depth= 1] . ( 4 sec) [ -8673.9217] [ 1854] [depth= 1] . ( 4 sec) [ -8672.2963] [ 1852] [depth= 1] . ( 4 sec) [ -8663.1386] [ 1843] [depth= 1] . ( 4 sec) [ -8637.4369] [ 1812] [depth= 7] . ( 4 sec) [ -8594.5383] [ 1789] [depth= 2] . ( 4 sec) [ -8590.5386] [ 1784] [depth= 2] . ( 5 sec) [ -8509.0017] [ 1769] [depth= 2] . ( 5 sec) [ -8508.1402] [ 1770] [depth= 2] . ( 5 sec) [ -8478.0427] [ 1761] [depth= 2] . ( 5 sec) [ -8454.7834] [ 1747] [depth= 1] . ( 5 sec) [ -8436.1346] [ 1733] [depth= 3] . ( 5 sec) [ -8418.5704] [ 1724] [depth= 1] . ( 5 sec) [ -8285.1210] [Branch lengths ] . ( 6 sec) [ -8282.2588] [GTR parameters ] . ( 6 sec) [ -8246.3119] [Alpha ][ 0.968170] . ( 6 sec) [ -8224.3795] [ 1719] [depth= 1] . ( 6 sec) [ -8222.2849] [ 1721] [depth= 1] . ( 6 sec) [ -8217.8065] [ 1723] [depth= 1] . ( 6 sec) [ -8207.7346] [ 1709] [depth= 1] . ( 7 sec) [ -8186.8505] [ 1697] [depth= 1] . ( 7 sec) [ -8169.9719] [ 1689] [depth= 1] . ( 7 sec) [ -8169.7510] [ 1689] [depth= 1] . ( 7 sec) [ -8168.8161] [ 1689] [depth= 1] . ( 8 sec) [ -8160.6881] [ 1682] [depth= 1] . ( 9 sec) [ -8159.6236] [ 1685] [depth= 1] . ( 9 sec) [ -8159.4947] [ 1685] [depth= 1] . ( 9 sec) [ -8159.4704] [ 1682] [depth= 1] . ( 9 sec) [ -8158.8252] [ 1685] [depth= 1] . ( 9 sec) [ -8158.7158] [ 1688] [depth= 1] . ( 10 sec) [ -8149.7234] [Branch lengths ] . ( 10 sec) [ -8149.6529] [GTR parameters ] . ( 10 sec) [ -8149.4218] [Alpha ][ 1.023031] . ( 14 sec) [ -8148.7268] [Branch lengths ] . ( 15 sec) [ -8147.9991] [ 1685] [depth= 1] . ( 33 sec) [ -8147.8878] [Branch lengths ] . ( 33 sec) [ -8147.8837] [GTR parameters ] . ( 34 sec) [ -8147.8759] [Alpha ][ 1.033657] . ( 34 sec) [ -8147.8759] [Topology ] . ( 34 sec) [ -8147.8654] [Topology ] . ( 35 sec) [ -8147.8619] [Topology ] . ( 36 sec) [ -8147.8603] [Topology ] . ( 37 sec) [ -8147.8596] [Topology ] . ( 37 sec) [ -8147.8596] [GTR parameters ] . ( 37 sec) [ -8147.8594] [Alpha ][ 1.035207] . ( 37 sec) [ -8147.8594] [Topology ] . ( 38 sec) [ -8147.8590] [Topology ] . ( 38 sec) [ -8147.8590] [GTR parameters ] . ( 38 sec) [ -8147.8590] [Alpha ][ 1.035207] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -8147.8585] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8147.858455. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18388.2882] [GTR parameters ] . ( 1 sec) [ -18012.5772] [Alpha ][ 0.500960] . ( 1 sec) [ -17172.1286] [ 3735] [depth= 11] . ( 1 sec) [ -16651.4831] [ 3631] [depth= 9] . ( 1 sec) [ -16463.6818] [ 3599] [depth= 2] . ( 1 sec) [ -16403.4649] [ 3554] [depth= 1] . ( 1 sec) [ -16231.3428] [ 3530] [depth= 5] . ( 1 sec) [ -16151.2665] [ 3504] [depth= 3] . ( 1 sec) [ -16028.7600] [ 3493] [depth= 6] . ( 1 sec) [ -15850.2427] [ 3417] [depth= 1] . ( 1 sec) [ -15799.0171] [ 3401] [depth= 1] . ( 1 sec) [ -15478.2682] [ 3314] [depth= 2] . ( 1 sec) [ -15406.4247] [ 3306] [depth= 10] . ( 1 sec) [ -15263.9578] [ 3262] [depth= 3] . ( 1 sec) [ -14992.0809] [ 3249] [depth= 4] . ( 1 sec) [ -14967.0038] [ 3238] [depth= 3] . ( 1 sec) [ -14830.0409] [ 3176] [depth= 9] . ( 1 sec) [ -14716.1904] [ 3171] [depth= 1] . ( 2 sec) [ -14616.8235] [ 3147] [depth= 9] . ( 2 sec) [ -14475.4008] [ 3142] [depth= 1] . ( 2 sec) [ -14200.6641] [ 3061] [depth= 11] . ( 2 sec) [ -14076.9257] [ 3032] [depth= 3] . ( 2 sec) [ -14006.3319] [ 3028] [depth= 1] . ( 2 sec) [ -13931.7508] [ 3015] [depth= 1] . ( 2 sec) [ -13761.5751] [ 2957] [depth= 10] . ( 2 sec) [ -13371.3214] [ 2899] [depth= 16] . ( 2 sec) [ -13018.2937] [ 2882] [depth= 14] . ( 2 sec) [ -12850.5924] [ 2879] [depth= 2] . ( 2 sec) [ -12613.1077] [ 2879] [depth= 18] . ( 2 sec) [ -12350.8230] [ 2823] [depth= 5] . ( 2 sec) [ -12167.0055] [ 2748] [depth= 12] . ( 2 sec) [ -12041.5488] [ 2749] [depth= 1] . ( 2 sec) [ -11902.1840] [ 2687] [depth= 14] . ( 2 sec) [ -11869.5660] [ 2660] [depth= 5] . ( 2 sec) [ -11864.2496] [ 2661] [depth= 1] . ( 2 sec) [ -11700.1223] [ 2606] [depth= 1] . ( 2 sec) [ -11654.1818] [ 2605] [depth= 1] . ( 2 sec) [ -11651.7516] [ 2607] [depth= 1] . ( 2 sec) [ -11651.2863] [ 2605] [depth= 1] . ( 2 sec) [ -11623.4440] [ 2583] [depth= 6] . ( 2 sec) [ -11548.9170] [ 2538] [depth= 1] . ( 3 sec) [ -11544.3153] [ 2537] [depth= 1] . ( 3 sec) [ -11505.7702] [ 2524] [depth= 6] . ( 3 sec) [ -11417.1343] [ 2512] [depth= 9] . ( 3 sec) [ -11285.4848] [ 2498] [depth= 3] . ( 3 sec) [ -11187.7757] [ 2478] [depth= 9] . ( 3 sec) [ -11042.1971] [ 2464] [depth= 9] . ( 3 sec) [ -10998.7025] [ 2433] [depth= 1] . ( 3 sec) [ -10915.9080] [ 2416] [depth= 7] . ( 3 sec) [ -10659.2442] [ 2312] [depth= 4] . ( 3 sec) [ -10605.3870] [ 2300] [depth= 3] . ( 3 sec) [ -10483.3729] [ 2236] [depth= 6] . ( 3 sec) [ -10324.1088] [ 2238] [depth= 2] . ( 3 sec) [ -10317.9182] [ 2231] [depth= 3] . ( 3 sec) [ -10316.7042] [ 2232] [depth= 1] . ( 3 sec) [ -10201.9999] [ 2211] [depth= 2] . ( 3 sec) [ -10198.6449] [ 2208] [depth= 1] . ( 3 sec) [ -10117.4698] [ 2208] [depth= 1] . ( 3 sec) [ -10115.8832] [ 2208] [depth= 1] . ( 3 sec) [ -10059.6665] [ 2213] [depth= 11] . ( 3 sec) [ -10057.1791] [ 2213] [depth= 1] . ( 3 sec) [ -10051.7370] [ 2212] [depth= 1] . ( 3 sec) [ -10029.5868] [ 2192] [depth= 1] . ( 4 sec) [ -9953.4127] [ 2145] [depth= 2] . ( 4 sec) [ -9893.0728] [ 2146] [depth= 1] . ( 4 sec) [ -9874.5828] [ 2146] [depth= 1] . ( 4 sec) [ -9872.0701] [ 2144] [depth= 1] . ( 4 sec) [ -9473.3107] [ 2076] [depth= 4] . ( 4 sec) [ -9369.9042] [ 2027] [depth= 1] . ( 4 sec) [ -9270.3588] [ 2020] [depth= 6] . ( 4 sec) [ -9257.7345] [ 2021] [depth= 1] . ( 4 sec) [ -9248.3975] [ 2020] [depth= 1] . ( 4 sec) [ -9240.1551] [ 2018] [depth= 1] . ( 4 sec) [ -9220.6349] [ 2021] [depth= 1] . ( 4 sec) [ -9108.4066] [ 1959] [depth= 2] . ( 4 sec) [ -8871.9258] [ 1956] [depth= 1] . ( 4 sec) [ -8825.6451] [ 1936] [depth= 5] . ( 4 sec) [ -8760.5934] [ 1894] [depth= 3] . ( 4 sec) [ -8740.8891] [ 1886] [depth= 2] . ( 4 sec) [ -8716.8385] [ 1889] [depth= 1] . ( 4 sec) [ -8693.1737] [ 1890] [depth= 1] . ( 5 sec) [ -8665.8957] [ 1873] [depth= 2] . ( 5 sec) [ -8661.6024] [ 1872] [depth= 1] . ( 5 sec) [ -8626.5249] [ 1836] [depth= 3] . ( 5 sec) [ -8543.5520] [ 1797] [depth= 1] . ( 5 sec) [ -8376.4909] [Branch lengths ] . ( 6 sec) [ -8375.0140] [GTR parameters ] . ( 6 sec) [ -8343.7828] [Alpha ][ 0.918921] . ( 6 sec) [ -8338.8687] [ 1790] [depth= 1] . ( 6 sec) [ -8293.7277] [ 1761] [depth= 1] . ( 6 sec) [ -8279.6479] [ 1733] [depth= 2] . ( 6 sec) [ -8227.9254] [ 1702] [depth= 4] . ( 6 sec) [ -8183.0923] [ 1684] [depth= 2] . ( 7 sec) [ -8182.0640] [ 1680] [depth= 1] . ( 7 sec) [ -8181.9361] [ 1683] [depth= 1] . ( 7 sec) [ -8181.5961] [ 1686] [depth= 1] . ( 8 sec) [ -8181.4940] [ 1689] [depth= 1] . ( 8 sec) [ -8181.2925] [ 1687] [depth= 1] . ( 8 sec) [ -8175.0794] [ 1684] [depth= 1] . ( 9 sec) [ -8165.9542] [ 1686] [depth= 2] . ( 9 sec) [ -8165.8975] [ 1685] [depth= 1] . ( 9 sec) [ -8150.5692] [Branch lengths ] . ( 10 sec) [ -8150.4175] [GTR parameters ] . ( 10 sec) [ -8149.6408] [Alpha ][ 1.016424] . ( 12 sec) [ -8149.6260] [ 1684] [depth= 1] . ( 12 sec) [ -8149.5987] [ 1686] [depth= 1] . ( 13 sec) [ -8148.7823] [Branch lengths ] . ( 13 sec) [ -8148.7808] [GTR parameters ] . ( 13 sec) [ -8148.7685] [Alpha ][ 1.029736] . ( 31 sec) [ -8148.0985] [ 1682] [depth= 1] . ( 33 sec) [ -8147.8981] [Branch lengths ] . ( 33 sec) [ -8147.8953] [GTR parameters ] . ( 33 sec) [ -8147.8938] [Alpha ][ 1.034396] . ( 33 sec) [ -8147.8938] [Topology ] . ( 34 sec) [ -8147.8785] [Topology ] . ( 35 sec) [ -8147.8736] [Topology ] . ( 36 sec) [ -8147.8713] [Topology ] . ( 36 sec) [ -8147.8703] [Topology ] . ( 37 sec) [ -8147.8698] [Topology ] . ( 37 sec) [ -8147.8698] [GTR parameters ] . ( 37 sec) [ -8147.8695] [Alpha ][ 1.036319] . ( 37 sec) [ -8147.8695] [Topology ] . ( 38 sec) [ -8147.8692] [Topology ] . ( 38 sec) [ -8147.8692] [GTR parameters ] . ( 38 sec) [ -8147.8692] [Alpha ][ 1.036319] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -8147.8607] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -8147.8604] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8147.860407. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18615.1105] [GTR parameters ] . ( 1 sec) [ -18250.0700] [Alpha ][ 0.500960] . ( 1 sec) [ -17693.6467] [ 3791] [depth= 7] . ( 1 sec) [ -17331.7457] [ 3689] [depth= 11] . ( 1 sec) [ -17254.8185] [ 3684] [depth= 6] . ( 1 sec) [ -17250.5753] [ 3680] [depth= 1] . ( 1 sec) [ -17186.7100] [ 3649] [depth= 7] . ( 1 sec) [ -17108.0686] [ 3643] [depth= 4] . ( 1 sec) [ -16948.1616] [ 3613] [depth= 5] . ( 2 sec) [ -16937.9702] [ 3621] [depth= 1] . ( 2 sec) [ -16647.7178] [ 3557] [depth= 8] . ( 2 sec) [ -16318.9488] [ 3507] [depth= 12] . ( 2 sec) [ -16034.4672] [ 3399] [depth= 13] . ( 2 sec) [ -15789.9121] [ 3360] [depth= 10] . ( 2 sec) [ -15371.3142] [ 3345] [depth= 9] . ( 2 sec) [ -15308.7307] [ 3337] [depth= 1] . ( 2 sec) [ -15204.7397] [ 3315] [depth= 3] . ( 2 sec) [ -15204.1009] [ 3301] [depth= 5] . ( 2 sec) [ -15068.8285] [ 3279] [depth= 7] . ( 2 sec) [ -14955.0202] [ 3279] [depth= 1] . ( 2 sec) [ -14853.8312] [ 3274] [depth= 3] . ( 2 sec) [ -14658.4864] [ 3189] [depth= 6] . ( 2 sec) [ -14648.6703] [ 3188] [depth= 1] . ( 2 sec) [ -14598.4281] [ 3202] [depth= 11] . ( 2 sec) [ -14585.7215] [ 3180] [depth= 3] . ( 2 sec) [ -13878.6042] [ 3156] [depth= 6] . ( 2 sec) [ -13804.8558] [ 3146] [depth= 10] . ( 2 sec) [ -13579.1344] [ 3142] [depth= 8] . ( 2 sec) [ -13484.5239] [ 3086] [depth= 1] . ( 2 sec) [ -13177.6341] [ 2979] [depth= 10] . ( 2 sec) [ -13155.0537] [ 2972] [depth= 3] . ( 2 sec) [ -13048.9572] [ 2967] [depth= 1] . ( 3 sec) [ -12924.5966] [ 2915] [depth= 3] . ( 3 sec) [ -12728.3261] [ 2865] [depth= 7] . ( 3 sec) [ -12117.1191] [ 2728] [depth= 3] . ( 3 sec) [ -11904.3124] [ 2663] [depth= 2] . ( 3 sec) [ -11898.1609] [ 2663] [depth= 2] . ( 3 sec) [ -11743.8784] [ 2619] [depth= 4] . ( 3 sec) [ -11737.6859] [ 2618] [depth= 1] . ( 3 sec) [ -11528.1191] [ 2579] [depth= 8] . ( 3 sec) [ -11497.5453] [ 2578] [depth= 2] . ( 3 sec) [ -11339.5950] [ 2557] [depth= 5] . ( 3 sec) [ -11336.6211] [ 2558] [depth= 2] . ( 3 sec) [ -11075.8765] [ 2465] [depth= 2] . ( 3 sec) [ -11063.8580] [ 2465] [depth= 1] . ( 3 sec) [ -10810.3786] [ 2388] [depth= 3] . ( 3 sec) [ -10804.6552] [ 2387] [depth= 1] . ( 3 sec) [ -10686.9939] [ 2371] [depth= 1] . ( 3 sec) [ -10600.6702] [ 2354] [depth= 3] . ( 3 sec) [ -10490.1508] [ 2320] [depth= 10] . ( 3 sec) [ -10432.3892] [ 2303] [depth= 8] . ( 3 sec) [ -10372.0193] [ 2305] [depth= 1] . ( 3 sec) [ -10166.7503] [ 2262] [depth= 7] . ( 3 sec) [ -10002.1369] [ 2239] [depth= 5] . ( 3 sec) [ -9982.1003] [ 2242] [depth= 1] . ( 4 sec) [ -9977.4540] [ 2206] [depth= 2] . ( 4 sec) [ -9952.7215] [ 2206] [depth= 1] . ( 4 sec) [ -9741.2163] [ 2161] [depth= 6] . ( 4 sec) [ -9731.7060] [ 2151] [depth= 1] . ( 4 sec) [ -9730.4661] [ 2149] [depth= 2] . ( 4 sec) [ -9637.0079] [ 2124] [depth= 3] . ( 4 sec) [ -9561.8269] [ 2102] [depth= 1] . ( 4 sec) [ -9538.0480] [ 2098] [depth= 3] . ( 4 sec) [ -9343.2540] [ 1991] [depth= 9] . ( 4 sec) [ -9144.8541] [ 1965] [depth= 5] . ( 4 sec) [ -9106.3930] [ 1974] [depth= 1] . ( 4 sec) [ -9099.2216] [ 1965] [depth= 2] . ( 4 sec) [ -9022.7922] [ 1915] [depth= 7] . ( 4 sec) [ -9019.3248] [ 1924] [depth= 1] . ( 4 sec) [ -9009.1178] [ 1936] [depth= 1] . ( 5 sec) [ -8970.0068] [ 1932] [depth= 1] . ( 5 sec) [ -8718.1590] [ 1859] [depth= 2] . ( 5 sec) [ -8653.2814] [ 1847] [depth= 2] . ( 5 sec) [ -8653.1064] [ 1852] [depth= 2] . ( 5 sec) [ -8652.3393] [ 1853] [depth= 1] . ( 5 sec) [ -8527.7374] [ 1783] [depth= 8] . ( 5 sec) [ -8525.1544] [ 1810] [depth= 1] . ( 5 sec) [ -8521.3363] [ 1808] [depth= 1] . ( 5 sec) [ -8499.0119] [ 1781] [depth= 1] . ( 5 sec) [ -8356.6596] [Branch lengths ] . ( 6 sec) [ -8354.1428] [GTR parameters ] . ( 6 sec) [ -8325.0260] [Alpha ][ 0.895316] . ( 6 sec) [ -8322.6070] [ 1779] [depth= 1] . ( 7 sec) [ -8320.5879] [ 1777] [depth= 1] . ( 7 sec) [ -8266.3798] [ 1733] [depth= 2] . ( 7 sec) [ -8230.3073] [ 1704] [depth= 1] . ( 7 sec) [ -8202.2442] [ 1696] [depth= 1] . ( 7 sec) [ -8200.9400] [ 1696] [depth= 1] . ( 7 sec) [ -8200.5623] [ 1693] [depth= 1] . ( 7 sec) [ -8178.9711] [ 1685] [depth= 1] . ( 7 sec) [ -8173.3398] [ 1682] [depth= 1] . ( 8 sec) [ -8167.7465] [ 1683] [depth= 1] . ( 8 sec) [ -8167.2577] [ 1684] [depth= 1] . ( 8 sec) [ -8164.8660] [ 1682] [depth= 1] . ( 9 sec) [ -8163.8986] [ 1685] [depth= 1] . ( 9 sec) [ -8151.5003] [Branch lengths ] . ( 10 sec) [ -8150.9339] [GTR parameters ] . ( 10 sec) [ -8149.8181] [Alpha ][ 1.010350] . ( 11 sec) [ -8149.7898] [ 1684] [depth= 1] . ( 13 sec) [ -8149.6976] [ 1685] [depth= 1] . ( 13 sec) [ -8148.8274] [Branch lengths ] . ( 14 sec) [ -8148.8271] [GTR parameters ] . ( 14 sec) [ -8148.8060] [Alpha ][ 1.027770] . ( 17 sec) [ -8148.6449] [Branch lengths ] . ( 29 sec) [ -8147.9543] [ 1682] [depth= 1] . ( 37 sec) [ -8147.8609] [Branch lengths ] . ( 37 sec) [ -8147.8580] [GTR parameters ] . ( 37 sec) [ -8147.8545] [Alpha ][ 1.034869] . ( 37 sec) [ -8147.8545] [Topology ] . ( 38 sec) [ -8147.8496] [Topology ] . ( 39 sec) [ -8147.8482] [Topology ] . ( 39 sec) [ -8147.8476] [Topology ] . ( 40 sec) [ -8147.8476] [GTR parameters ] . ( 40 sec) [ -8147.8476] [Alpha ][ 1.035903] . ( 40 sec) [ -8147.8476] [Topology ] . ( 40 sec) [ -8147.8473] [Topology ] . ( 40 sec) [ -8147.8473] [GTR parameters ] . ( 41 sec) [ -8147.8473] [Alpha ][ 1.035903] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8147.847277. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8218.396581 . ( 1 sec) [ -8207.7729] [GTR parameters ] . ( 1 sec) [ -8207.7661] [Alpha ][ 0.989870] . ( 1 sec) [ -8207.7661] [Topology ] . ( 2 sec) [ -8163.5971] [Topology ] . ( 3 sec) [ -8152.0230] [Topology ] . ( 3 sec) [ -8148.9805] [Topology ] . ( 4 sec) [ -8148.3847] [Topology ] . ( 5 sec) [ -8148.1924] [Topology ] . ( 6 sec) [ -8148.1169] [Topology ] . ( 6 sec) [ -8148.0838] [Topology ] . ( 7 sec) [ -8148.0686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -8148.0526] [Topology ] . Before opt ts/t=1.000000 LK=-8148.052643 . ( 13 sec) [ -8148.0125] [GTR parameters ] . ( 13 sec) [ -8147.8819] [Alpha ][ 1.031898] . ( 13 sec) [ -8147.8819] [Topology ] . ( 14 sec) [ -8147.8615] [Topology ] . ( 15 sec) [ -8147.8543] [Topology ] . ( 16 sec) [ -8147.8510] [Topology ] . ( 16 sec) [ -8147.8494] [Topology ] . ( 17 sec) [ -8147.8487] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8147.848700 . ( 23 sec) [ -8147.8487] [GTR parameters ] . ( 23 sec) [ -8147.8478] [Alpha ][ 1.035389] . ( 23 sec) [ -8147.8478] [Topology ] . ( 24 sec) [ -8147.8473] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8147.847272 . ( 29 sec) [ -8147.8473] [GTR parameters ] . ( 29 sec) [ -8147.8473] [Alpha ][ 1.035389] . ( 29 sec) [ -8147.8473] [Topology ] . ( 30 sec) [ -8147.8470] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -8207.7729] [GTR parameters ] . ( 42 sec) [ -8207.7661] [Alpha ][ 0.989870] . ( 42 sec) [ -8200.2689] [ 1686] [depth= 1] . ( 43 sec) [ -8189.6151] [ 1684] [depth= 2] . ( 43 sec) [ -8186.8223] [ 1682] [depth= 1] . ( 44 sec) [ -8185.0261] [ 1681] [depth= 1] . ( 44 sec) [ -8183.3290] [ 1682] [depth= 1] . ( 45 sec) [ -8181.6192] [ 1685] [depth= 1] . ( 45 sec) [ -8179.5564] [ 1682] [depth= 1] . ( 45 sec) [ -8178.0386] [ 1685] [depth= 1] . ( 45 sec) [ -8177.7409] [ 1686] [depth= 1] . ( 45 sec) [ -8177.0168] [ 1688] [depth= 1] . ( 45 sec) [ -8176.9467] [ 1686] [depth= 1] . ( 46 sec) [ -8150.1030] [Branch lengths ] . ( 46 sec) [ -8150.0646] [GTR parameters ] . ( 46 sec) [ -8150.0095] [Alpha ][ 1.016763] . ( 50 sec) [ -8148.8127] [Branch lengths ] . ( 64 sec) [ -8148.7884] [ 1686] [depth= 1] . ( 65 sec) [ -8148.0969] [ 1682] [depth= 1] . ( 69 sec) [ -8147.9014] [Branch lengths ] . ( 69 sec) [ -8147.8990] [GTR parameters ] . ( 69 sec) [ -8147.8796] [Alpha ][ 1.033547] . ( 69 sec) [ -8147.8796] [Topology ] . ( 70 sec) [ -8147.8659] [Topology ] . ( 71 sec) [ -8147.8618] [Topology ] . ( 72 sec) [ -8147.8601] [Topology ] . ( 72 sec) [ -8147.8593] [Topology ] . ( 72 sec) [ -8147.8593] [GTR parameters ] . ( 72 sec) [ -8147.8591] [Alpha ][ 1.035226] . ( 72 sec) [ -8147.8591] [Topology ] . ( 73 sec) [ -8147.8587] [Topology ] . ( 73 sec) [ -8147.8587] [GTR parameters ] . ( 73 sec) [ -8147.8587] [Alpha ][ 1.035226] . Checking for NNIs, optimizing five branches... . ( 79 sec) [ -8147.8583] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8147.847031 . Log likelihood obtained after SPR moves : -8147.858315 . Log likelihood of the current tree: -8147.847031. . Printing the most likely tree in file 'data52.phy_phyml_tree.txt'... . Best log likelihood : -8147.847031 . Time used 0h1m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo