.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data57.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... . 398 patterns found. (out of a total of 500 sites) . 97 sites without polymorphism (19.40%). . [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)... . ( 1 sec) [ -21043.8431] [GTR parameters ] . ( 1 sec) [ -20664.8082] [Alpha ][ 0.500960] . ( 1 sec) [ -20326.2602] [ 3642] [depth= 9] . ( 1 sec) [ -19780.5849] [ 3589] [depth= 5] . ( 1 sec) [ -19633.0716] [ 3567] [depth= 4] . ( 1 sec) [ -19573.7008] [ 3554] [depth= 7] . ( 1 sec) [ -19466.6255] [ 3497] [depth= 1] . ( 1 sec) [ -19364.1452] [ 3496] [depth= 7] . ( 1 sec) [ -19121.6319] [ 3453] [depth= 4] . ( 1 sec) [ -19081.4179] [ 3454] [depth= 2] . ( 1 sec) [ -18843.7826] [ 3345] [depth= 4] . ( 1 sec) [ -18800.1481] [ 3328] [depth= 10] . ( 1 sec) [ -18584.6094] [ 3334] [depth= 1] . ( 1 sec) [ -14989.0924] [ 3278] [depth= 10] . ( 1 sec) [ -14857.7365] [ 3166] [depth= 16] . ( 1 sec) [ -14810.1866] [ 3164] [depth= 4] . ( 1 sec) [ -14761.4887] [ 3159] [depth= 7] . ( 2 sec) [ -14756.7685] [ 3145] [depth= 2] . ( 2 sec) [ -14707.1794] [ 3139] [depth= 3] . ( 2 sec) [ -14580.5644] [ 3113] [depth= 4] . ( 2 sec) [ -14560.6839] [ 3110] [depth= 3] . ( 2 sec) [ -14422.9861] [ 3075] [depth= 6] . ( 2 sec) [ -14332.3601] [ 3077] [depth= 2] . ( 2 sec) [ -14169.4996] [ 3036] [depth= 3] . ( 2 sec) [ -14060.3651] [ 3008] [depth= 7] . ( 2 sec) [ -13977.9792] [ 2980] [depth= 3] . ( 2 sec) [ -13915.0349] [ 2968] [depth= 5] . ( 2 sec) [ -13876.7971] [ 2968] [depth= 1] . ( 2 sec) [ -13647.6382] [ 2906] [depth= 7] . ( 2 sec) [ -13445.6088] [ 2831] [depth= 8] . ( 2 sec) [ -13292.3243] [ 2731] [depth= 5] . ( 2 sec) [ -13286.4210] [ 2734] [depth= 1] . ( 2 sec) [ -13120.7409] [ 2675] [depth= 5] . ( 2 sec) [ -13039.1265] [ 2661] [depth= 4] . ( 2 sec) [ -12802.1658] [ 2604] [depth= 4] . ( 2 sec) [ -12605.6676] [ 2564] [depth= 6] . ( 2 sec) [ -12164.3062] [ 2443] [depth= 7] . ( 2 sec) [ -12146.9561] [ 2445] [depth= 2] . ( 2 sec) [ -12146.0396] [ 2453] [depth= 1] . ( 2 sec) [ -12136.7982] [ 2449] [depth= 1] . ( 3 sec) [ -12074.6312] [ 2435] [depth= 2] . ( 3 sec) [ -12020.6924] [ 2419] [depth= 2] . ( 3 sec) [ -11937.8239] [ 2417] [depth= 4] . ( 3 sec) [ -11580.6333] [ 2306] [depth= 5] . ( 3 sec) [ -11532.2105] [ 2277] [depth= 3] . ( 3 sec) [ -11463.2320] [ 2286] [depth= 1] . ( 3 sec) [ -11046.6085] [ 2227] [depth= 5] . ( 3 sec) [ -10583.9052] [ 2196] [depth= 11] . ( 3 sec) [ -10076.1448] [ 2138] [depth= 1] . ( 3 sec) [ -9750.4073] [ 2009] [depth= 11] . ( 3 sec) [ -9425.0816] [ 1892] [depth= 3] . ( 3 sec) [ -9400.5480] [ 1889] [depth= 2] . ( 3 sec) [ -9334.9400] [ 1885] [depth= 1] . ( 3 sec) [ -9281.6454] [ 1873] [depth= 1] . ( 3 sec) [ -9168.3409] [ 1873] [depth= 1] . ( 3 sec) [ -9067.3015] [ 1781] [depth= 12] . ( 3 sec) [ -9059.8633] [ 1779] [depth= 1] . ( 3 sec) [ -8979.3333] [ 1798] [depth= 3] . ( 3 sec) [ -8847.2028] [ 1736] [depth= 3] . ( 3 sec) [ -8783.1402] [ 1694] [depth= 1] . ( 3 sec) [ -8270.5175] [ 1613] [depth= 2] . ( 3 sec) [ -8173.5529] [ 1602] [depth= 2] . ( 3 sec) [ -8172.9169] [ 1604] [depth= 1] . ( 3 sec) [ -8098.4772] [ 1595] [depth= 2] . ( 4 sec) [ -8091.6401] [ 1593] [depth= 1] . ( 4 sec) [ -8005.1776] [ 1594] [depth= 3] . ( 4 sec) [ -7997.7356] [ 1595] [depth= 2] . ( 4 sec) [ -7948.9374] [ 1589] [depth= 2] . ( 4 sec) [ -7948.4703] [ 1591] [depth= 1] . ( 4 sec) [ -7944.2725] [ 1589] [depth= 1] . ( 4 sec) [ -7943.4535] [ 1594] [depth= 1] . ( 4 sec) [ -7876.1097] [ 1570] [depth= 3] . ( 4 sec) [ -7846.7817] [ 1563] [depth= 1] . ( 4 sec) [ -7810.3961] [ 1550] [depth= 2] . ( 4 sec) [ -7805.1005] [ 1548] [depth= 2] . ( 5 sec) [ -7573.8358] [ 1504] [depth= 1] . ( 5 sec) [ -7536.5568] [ 1497] [depth= 3] . ( 5 sec) [ -7532.0909] [ 1500] [depth= 1] . ( 5 sec) [ -7524.7032] [ 1498] [depth= 1] . ( 5 sec) [ -7524.6069] [ 1497] [depth= 1] . ( 5 sec) [ -7500.0428] [ 1496] [depth= 2] . ( 5 sec) [ -7497.6667] [ 1498] [depth= 1] . ( 5 sec) [ -7486.0245] [ 1496] [depth= 1] . ( 5 sec) [ -7485.7775] [ 1497] [depth= 1] . ( 5 sec) [ -7484.7838] [ 1507] [depth= 1] . ( 5 sec) [ -7476.4942] [ 1502] [depth= 1] . ( 5 sec) [ -7359.0803] [Branch lengths ] . ( 6 sec) [ -7352.2375] [GTR parameters ] . ( 6 sec) [ -7316.9267] [Alpha ][ 1.000683] . ( 6 sec) [ -7297.5617] [ 1492] [depth= 1] . ( 6 sec) [ -7273.8427] [ 1484] [depth= 1] . ( 6 sec) [ -7272.5623] [ 1482] [depth= 1] . ( 6 sec) [ -7266.3514] [ 1467] [depth= 3] . ( 7 sec) [ -7265.9471] [ 1466] [depth= 1] . ( 7 sec) [ -7261.8299] [ 1469] [depth= 1] . ( 7 sec) [ -7258.0144] [ 1466] [depth= 1] . ( 7 sec) [ -7228.1418] [ 1442] [depth= 3] . ( 7 sec) [ -7225.9139] [ 1439] [depth= 1] . ( 7 sec) [ -7210.0093] [ 1435] [depth= 1] . ( 7 sec) [ -7209.9054] [ 1438] [depth= 1] . ( 7 sec) [ -7209.8623] [ 1436] [depth= 1] . ( 8 sec) [ -7209.0633] [ 1433] [depth= 1] . ( 8 sec) [ -7209.0232] [ 1434] [depth= 1] . ( 9 sec) [ -7207.3631] [ 1437] [depth= 1] . ( 9 sec) [ -7199.5413] [Branch lengths ] . ( 10 sec) [ -7199.4073] [GTR parameters ] . ( 10 sec) [ -7198.7432] [Alpha ][ 1.109716] . ( 11 sec) [ -7198.3407] [ 1436] [depth= 1] . ( 14 sec) [ -7197.2852] [Branch lengths ] . ( 14 sec) [ -7197.2846] [GTR parameters ] . ( 14 sec) [ -7197.2695] [Alpha ][ 1.127724] . ( 18 sec) [ -7197.1245] [Branch lengths ] . ( 39 sec) [ -7197.1067] [Branch lengths ] . ( 39 sec) [ -7197.1067] [Topology ] . ( 40 sec) [ -7197.1052] [Topology ] . ( 40 sec) [ -7197.1047] [Topology ] . ( 41 sec) [ -7197.1045] [GTR parameters ] . ( 41 sec) [ -7197.1036] [Alpha ][ 1.132089] . ( 41 sec) [ -7197.1036] [Topology ] . ( 42 sec) [ -7197.1033] [Topology ] . ( 42 sec) [ -7197.1033] [GTR parameters ] . ( 42 sec) [ -7197.1033] [Alpha ][ 1.132089] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7197.103337. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19094.7081] [GTR parameters ] . ( 1 sec) [ -18656.8103] [Alpha ][ 0.500960] . ( 1 sec) [ -18497.5635] [ 3637] [depth= 7] . ( 1 sec) [ -18134.9212] [ 3573] [depth= 5] . ( 1 sec) [ -17977.7866] [ 3530] [depth= 4] . ( 1 sec) [ -17956.9971] [ 3526] [depth= 3] . ( 1 sec) [ -17910.6233] [ 3507] [depth= 1] . ( 1 sec) [ -17842.6136] [ 3499] [depth= 2] . ( 1 sec) [ -17839.2289] [ 3511] [depth= 1] . ( 1 sec) [ -17782.2656] [ 3499] [depth= 4] . ( 1 sec) [ -17676.5621] [ 3458] [depth= 2] . ( 1 sec) [ -17617.0420] [ 3455] [depth= 4] . ( 1 sec) [ -17442.4996] [ 3427] [depth= 6] . ( 1 sec) [ -17435.6863] [ 3428] [depth= 3] . ( 1 sec) [ -16322.0694] [ 3369] [depth= 1] . ( 1 sec) [ -16066.9152] [ 3280] [depth= 13] . ( 2 sec) [ -15692.8744] [ 3140] [depth= 9] . ( 2 sec) [ -15532.8806] [ 3146] [depth= 1] . ( 2 sec) [ -15273.2132] [ 3072] [depth= 1] . ( 2 sec) [ -14176.6928] [ 3068] [depth= 3] . ( 2 sec) [ -13875.8445] [ 3071] [depth= 1] . ( 2 sec) [ -13617.9255] [ 3064] [depth= 2] . ( 2 sec) [ -13617.8168] [ 2882] [depth= 2] . ( 2 sec) [ -13593.3354] [ 2880] [depth= 1] . ( 2 sec) [ -13581.3270] [ 2875] [depth= 1] . ( 2 sec) [ -13099.2211] [ 2869] [depth= 9] . ( 2 sec) [ -13097.5897] [ 2871] [depth= 1] . ( 2 sec) [ -13002.9536] [ 2843] [depth= 3] . ( 2 sec) [ -12928.5697] [ 2816] [depth= 5] . ( 2 sec) [ -12813.4235] [ 2814] [depth= 5] . ( 2 sec) [ -12798.1887] [ 2709] [depth= 8] . ( 2 sec) [ -12761.1646] [ 2687] [depth= 6] . ( 2 sec) [ -12544.5389] [ 2672] [depth= 1] . ( 2 sec) [ -11945.9449] [ 2592] [depth= 12] . ( 2 sec) [ -11629.7810] [ 2507] [depth= 1] . ( 2 sec) [ -11625.8142] [ 2508] [depth= 2] . ( 2 sec) [ -11205.8065] [ 2417] [depth= 4] . ( 2 sec) [ -11127.8564] [ 2417] [depth= 7] . ( 2 sec) [ -11082.8568] [ 2426] [depth= 8] . ( 2 sec) [ -11071.5423] [ 2426] [depth= 2] . ( 3 sec) [ -11033.4760] [ 2433] [depth= 1] . ( 3 sec) [ -10999.7921] [ 2423] [depth= 2] . ( 3 sec) [ -10976.9614] [ 2415] [depth= 2] . ( 3 sec) [ -10972.0416] [ 2414] [depth= 1] . ( 3 sec) [ -10970.5659] [ 2403] [depth= 1] . ( 3 sec) [ -10969.0356] [ 2401] [depth= 2] . ( 3 sec) [ -10594.4793] [ 2394] [depth= 3] . ( 3 sec) [ -10438.1380] [ 2311] [depth= 10] . ( 3 sec) [ -10437.0028] [ 2322] [depth= 1] . ( 3 sec) [ -10425.1945] [ 2321] [depth= 1] . ( 3 sec) [ -10326.1866] [ 2340] [depth= 1] . ( 3 sec) [ -10053.0858] [ 2309] [depth= 5] . ( 3 sec) [ -10014.3688] [ 2300] [depth= 1] . ( 3 sec) [ -10014.1408] [ 2279] [depth= 7] . ( 3 sec) [ -9852.0219] [ 2221] [depth= 2] . ( 3 sec) [ -9818.0695] [ 2207] [depth= 4] . ( 3 sec) [ -9738.3799] [ 2208] [depth= 1] . ( 3 sec) [ -9531.3218] [ 2192] [depth= 3] . ( 3 sec) [ -9436.0502] [ 2175] [depth= 3] . ( 3 sec) [ -9379.4972] [ 2169] [depth= 2] . ( 3 sec) [ -9367.3035] [ 2166] [depth= 1] . ( 3 sec) [ -9362.2475] [ 2162] [depth= 2] . ( 3 sec) [ -9291.6839] [ 2157] [depth= 4] . ( 4 sec) [ -9222.9422] [ 2136] [depth= 3] . ( 4 sec) [ -9168.4217] [ 2129] [depth= 1] . ( 4 sec) [ -9151.1037] [ 2132] [depth= 1] . ( 4 sec) [ -9145.5961] [ 2132] [depth= 1] . ( 4 sec) [ -9127.5374] [ 2130] [depth= 2] . ( 4 sec) [ -9126.3687] [ 2134] [depth= 2] . ( 4 sec) [ -9123.3275] [ 2131] [depth= 1] . ( 4 sec) [ -9009.6609] [ 2136] [depth= 6] . ( 4 sec) [ -9004.9522] [ 2111] [depth= 9] . ( 4 sec) [ -8997.5773] [ 2071] [depth= 8] . ( 4 sec) [ -8911.2403] [ 2046] [depth= 3] . ( 4 sec) [ -8871.5496] [ 2026] [depth= 4] . ( 4 sec) [ -8863.9126] [ 2022] [depth= 1] . ( 4 sec) [ -8836.3606] [ 2000] [depth= 1] . ( 5 sec) [ -8783.7786] [ 1914] [depth= 5] . ( 5 sec) [ -8668.0283] [ 1891] [depth= 6] . ( 5 sec) [ -8636.2690] [ 1874] [depth= 10] . ( 5 sec) [ -8625.6240] [ 1868] [depth= 1] . ( 5 sec) [ -8402.8807] [ 1830] [depth= 1] . ( 5 sec) [ -8381.1210] [ 1826] [depth= 2] . ( 5 sec) [ -8367.6805] [ 1830] [depth= 9] . ( 5 sec) [ -8170.2439] [ 1776] [depth= 7] . ( 5 sec) [ -7984.8175] [ 1737] [depth= 9] . ( 5 sec) [ -7864.5643] [Branch lengths ] . ( 6 sec) [ -7861.3057] [GTR parameters ] . ( 6 sec) [ -7840.8254] [Alpha ][ 0.818465] . ( 6 sec) [ -7788.4620] [ 1693] [depth= 3] . ( 6 sec) [ -7731.3068] [ 1627] [depth= 3] . ( 6 sec) [ -7702.2142] [ 1615] [depth= 2] . ( 6 sec) [ -7698.0278] [ 1610] [depth= 1] . ( 6 sec) [ -7660.5342] [ 1620] [depth= 4] . ( 6 sec) [ -7636.9644] [ 1577] [depth= 1] . ( 6 sec) [ -7627.7109] [ 1570] [depth= 1] . ( 6 sec) [ -7627.5505] [ 1570] [depth= 1] . ( 6 sec) [ -7627.3819] [ 1571] [depth= 1] . ( 6 sec) [ -7590.6391] [ 1591] [depth= 1] . ( 6 sec) [ -7566.8864] [ 1566] [depth= 2] . ( 6 sec) [ -7566.4246] [ 1562] [depth= 1] . ( 7 sec) [ -7565.2082] [ 1563] [depth= 1] . ( 7 sec) [ -7565.0146] [ 1563] [depth= 1] . ( 7 sec) [ -7556.0005] [ 1546] [depth= 1] . ( 7 sec) [ -7555.7432] [ 1546] [depth= 1] . ( 7 sec) [ -7554.7448] [ 1545] [depth= 1] . ( 7 sec) [ -7534.3808] [ 1536] [depth= 2] . ( 7 sec) [ -7533.8899] [ 1536] [depth= 1] . ( 7 sec) [ -7532.2438] [ 1535] [depth= 1] . ( 7 sec) [ -7515.8770] [ 1531] [depth= 2] . ( 7 sec) [ -7515.8174] [ 1530] [depth= 1] . ( 8 sec) [ -7498.5162] [ 1544] [depth= 2] . ( 8 sec) [ -7491.2174] [ 1541] [depth= 1] . ( 8 sec) [ -7347.7060] [ 1518] [depth= 2] . ( 8 sec) [ -7333.9584] [ 1521] [depth= 1] . ( 8 sec) [ -7332.3753] [ 1524] [depth= 2] . ( 8 sec) [ -7322.4615] [ 1519] [depth= 1] . ( 9 sec) [ -7300.2448] [ 1501] [depth= 1] . ( 9 sec) [ -7297.8261] [ 1502] [depth= 1] . ( 9 sec) [ -7270.8295] [ 1480] [depth= 1] . ( 9 sec) [ -7237.7576] [ 1453] [depth= 2] . ( 9 sec) [ -7236.1251] [ 1452] [depth= 1] . ( 9 sec) [ -7234.2494] [ 1450] [depth= 1] . ( 9 sec) [ -7232.5796] [ 1448] [depth= 1] . ( 10 sec) [ -7210.7723] [Branch lengths ] . ( 10 sec) [ -7209.7300] [GTR parameters ] . ( 10 sec) [ -7204.4894] [Alpha ][ 1.085150] . ( 11 sec) [ -7203.2329] [ 1435] [depth= 2] . ( 11 sec) [ -7200.8787] [ 1434] [depth= 1] . ( 14 sec) [ -7198.7009] [Branch lengths ] . ( 14 sec) [ -7198.6867] [GTR parameters ] . ( 14 sec) [ -7198.5891] [Alpha ][ 1.128930] . ( 18 sec) [ -7198.4412] [Branch lengths ] . ( 39 sec) [ -7198.1756] [Branch lengths ] . ( 39 sec) [ -7198.1756] [Topology ] . ( 40 sec) [ -7198.0875] [Topology ] . ( 41 sec) [ -7198.0564] [Topology ] . ( 42 sec) [ -7198.0435] [Topology ] . ( 42 sec) [ -7198.0379] [Topology ] . ( 43 sec) [ -7198.0354] [Topology ] . ( 44 sec) [ -7198.0343] [Topology ] . ( 44 sec) [ -7198.0331] [GTR parameters ] . ( 44 sec) [ -7198.0278] [Alpha ][ 1.139636] . ( 44 sec) [ -7198.0278] [Topology ] . ( 45 sec) [ -7198.0271] [Topology ] . ( 45 sec) [ -7198.0270] [GTR parameters ] . ( 45 sec) [ -7198.0270] [Alpha ][ 1.139636] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7198.027037. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21583.8808] [GTR parameters ] . ( 1 sec) [ -21187.4232] [Alpha ][ 0.500960] . ( 1 sec) [ -20990.4630] [ 3818] [depth= 8] . ( 1 sec) [ -20511.7528] [ 3749] [depth= 8] . ( 1 sec) [ -20427.3432] [ 3745] [depth= 2] . ( 1 sec) [ -20256.6250] [ 3743] [depth= 2] . ( 1 sec) [ -20166.6114] [ 3710] [depth= 5] . ( 1 sec) [ -19981.7482] [ 3707] [depth= 2] . ( 1 sec) [ -19240.8511] [ 3581] [depth= 6] . ( 1 sec) [ -18918.3179] [ 3524] [depth= 11] . ( 1 sec) [ -18563.9452] [ 3470] [depth= 9] . ( 1 sec) [ -18542.4294] [ 3475] [depth= 10] . ( 1 sec) [ -18086.5657] [ 3350] [depth= 8] . ( 1 sec) [ -17744.7594] [ 3248] [depth= 1] . ( 1 sec) [ -17683.5453] [ 3225] [depth= 9] . ( 1 sec) [ -17408.4815] [ 3186] [depth= 7] . ( 1 sec) [ -16996.3557] [ 3185] [depth= 1] . ( 2 sec) [ -16943.8559] [ 3176] [depth= 4] . ( 2 sec) [ -13599.7325] [ 3178] [depth= 1] . ( 2 sec) [ -13485.3309] [ 3171] [depth= 1] . ( 2 sec) [ -13420.1446] [ 3165] [depth= 2] . ( 2 sec) [ -13389.6520] [ 3148] [depth= 8] . ( 2 sec) [ -13218.8677] [ 3047] [depth= 6] . ( 2 sec) [ -12900.6170] [ 3005] [depth= 10] . ( 2 sec) [ -12607.5373] [ 2973] [depth= 6] . ( 2 sec) [ -12309.1821] [ 2929] [depth= 2] . ( 2 sec) [ -12097.6796] [ 2799] [depth= 5] . ( 2 sec) [ -12029.2143] [ 2799] [depth= 6] . ( 2 sec) [ -11969.3022] [ 2805] [depth= 1] . ( 2 sec) [ -11465.4368] [ 2801] [depth= 8] . ( 2 sec) [ -11079.8799] [ 2731] [depth= 6] . ( 2 sec) [ -10640.6897] [ 2614] [depth= 10] . ( 2 sec) [ -10631.2584] [ 2610] [depth= 2] . ( 2 sec) [ -10603.0065] [ 2604] [depth= 1] . ( 2 sec) [ -10468.5987] [ 2583] [depth= 7] . ( 2 sec) [ -10454.7572] [ 2567] [depth= 1] . ( 2 sec) [ -10400.3818] [ 2549] [depth= 2] . ( 2 sec) [ -10394.2829] [ 2548] [depth= 1] . ( 2 sec) [ -10303.4838] [ 2499] [depth= 1] . ( 2 sec) [ -10147.9109] [ 2422] [depth= 3] . ( 3 sec) [ -10085.4964] [ 2420] [depth= 1] . ( 3 sec) [ -9956.8805] [ 2348] [depth= 9] . ( 3 sec) [ -9956.5057] [ 2352] [depth= 1] . ( 3 sec) [ -9939.6777] [ 2348] [depth= 2] . ( 3 sec) [ -9874.2426] [ 2326] [depth= 1] . ( 3 sec) [ -9843.9133] [ 2224] [depth= 1] . ( 3 sec) [ -9813.5320] [ 2221] [depth= 4] . ( 3 sec) [ -9799.4645] [ 2221] [depth= 1] . ( 3 sec) [ -9771.4610] [ 2221] [depth= 1] . ( 3 sec) [ -9755.5731] [ 2212] [depth= 2] . ( 3 sec) [ -9751.0410] [ 2214] [depth= 1] . ( 3 sec) [ -9714.1916] [ 2211] [depth= 3] . ( 3 sec) [ -9674.5313] [ 2185] [depth= 3] . ( 3 sec) [ -9532.6599] [ 2152] [depth= 5] . ( 3 sec) [ -9531.0651] [ 2153] [depth= 1] . ( 3 sec) [ -9498.8364] [ 2154] [depth= 1] . ( 3 sec) [ -9118.9529] [ 2023] [depth= 3] . ( 3 sec) [ -9115.5114] [ 2027] [depth= 1] . ( 3 sec) [ -8958.4984] [ 2008] [depth= 6] . ( 3 sec) [ -8823.1011] [ 2007] [depth= 10] . ( 3 sec) [ -8806.4434] [ 2011] [depth= 2] . ( 4 sec) [ -8745.8159] [ 1994] [depth= 4] . ( 4 sec) [ -8723.1829] [ 1980] [depth= 4] . ( 4 sec) [ -8719.0393] [ 1963] [depth= 1] . ( 4 sec) [ -8375.0539] [ 1850] [depth= 8] . ( 4 sec) [ -8373.1650] [ 1842] [depth= 1] . ( 4 sec) [ -8372.2600] [ 1842] [depth= 1] . ( 4 sec) [ -8348.8485] [ 1826] [depth= 1] . ( 4 sec) [ -8340.0311] [ 1822] [depth= 1] . ( 4 sec) [ -8334.2798] [ 1825] [depth= 5] . ( 4 sec) [ -8293.2829] [ 1825] [depth= 1] . ( 4 sec) [ -8110.5107] [ 1780] [depth= 3] . ( 4 sec) [ -8110.4805] [ 1781] [depth= 1] . ( 4 sec) [ -7875.5536] [ 1668] [depth= 3] . ( 4 sec) [ -7792.5729] [ 1656] [depth= 1] . ( 4 sec) [ -7782.0422] [ 1655] [depth= 2] . ( 4 sec) [ -7759.6412] [ 1655] [depth= 1] . ( 4 sec) [ -7741.6170] [ 1657] [depth= 2] . ( 4 sec) [ -7740.9198] [ 1654] [depth= 1] . ( 4 sec) [ -7740.1736] [ 1637] [depth= 4] . ( 4 sec) [ -7639.9811] [ 1632] [depth= 1] . ( 5 sec) [ -7628.8078] [ 1636] [depth= 2] . ( 5 sec) [ -7626.7942] [ 1635] [depth= 1] . ( 5 sec) [ -7513.6786] [ 1565] [depth= 5] . ( 5 sec) [ -7472.2617] [ 1541] [depth= 2] . ( 5 sec) [ -7401.4334] [Branch lengths ] . ( 6 sec) [ -7395.4071] [GTR parameters ] . ( 6 sec) [ -7361.4297] [Alpha ][ 0.980178] . ( 6 sec) [ -7307.5481] [ 1493] [depth= 1] . ( 6 sec) [ -7306.6677] [ 1493] [depth= 1] . ( 6 sec) [ -7295.3607] [ 1489] [depth= 1] . ( 6 sec) [ -7295.0400] [ 1488] [depth= 1] . ( 6 sec) [ -7294.0453] [ 1488] [depth= 1] . ( 6 sec) [ -7293.8179] [ 1489] [depth= 1] . ( 7 sec) [ -7289.7548] [ 1500] [depth= 3] . ( 7 sec) [ -7289.5993] [ 1503] [depth= 1] . ( 7 sec) [ -7278.5202] [ 1499] [depth= 1] . ( 7 sec) [ -7268.4226] [ 1495] [depth= 1] . ( 7 sec) [ -7266.7738] [ 1487] [depth= 1] . ( 7 sec) [ -7264.2630] [ 1481] [depth= 2] . ( 7 sec) [ -7263.7895] [ 1484] [depth= 1] . ( 8 sec) [ -7263.3378] [ 1489] [depth= 2] . ( 8 sec) [ -7244.7865] [ 1459] [depth= 4] . ( 8 sec) [ -7233.6578] [ 1446] [depth= 3] . ( 8 sec) [ -7233.1662] [ 1447] [depth= 1] . ( 8 sec) [ -7228.2868] [ 1444] [depth= 1] . ( 8 sec) [ -7227.3480] [ 1443] [depth= 1] . ( 9 sec) [ -7224.0571] [ 1440] [depth= 1] . ( 9 sec) [ -7222.4176] [ 1443] [depth= 1] . ( 9 sec) [ -7208.8420] [ 1436] [depth= 1] . ( 10 sec) [ -7199.2302] [Branch lengths ] . ( 10 sec) [ -7198.8789] [GTR parameters ] . ( 10 sec) [ -7197.7998] [Alpha ][ 1.117507] . ( 14 sec) [ -7197.1633] [Branch lengths ] . ( 35 sec) [ -7197.1188] [Branch lengths ] . ( 35 sec) [ -7197.1188] [Topology ] . ( 36 sec) [ -7197.1159] [Topology ] . ( 37 sec) [ -7197.1151] [Topology ] . ( 37 sec) [ -7197.1141] [GTR parameters ] . ( 37 sec) [ -7197.1043] [Alpha ][ 1.131971] . ( 37 sec) [ -7197.1043] [Topology ] . ( 38 sec) [ -7197.1036] [Topology ] . ( 38 sec) [ -7197.1035] [GTR parameters ] . ( 38 sec) [ -7197.1035] [Alpha ][ 1.131971] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7197.103541. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19082.3137] [GTR parameters ] . ( 1 sec) [ -18641.0340] [Alpha ][ 0.500960] . ( 1 sec) [ -18398.3847] [ 3821] [depth= 5] . ( 1 sec) [ -17968.2416] [ 3745] [depth= 5] . ( 1 sec) [ -17519.4113] [ 3721] [depth= 7] . ( 1 sec) [ -17300.3068] [ 3605] [depth= 1] . ( 1 sec) [ -16973.7626] [ 3588] [depth= 9] . ( 1 sec) [ -16646.7360] [ 3573] [depth= 2] . ( 1 sec) [ -16610.4538] [ 3565] [depth= 5] . ( 1 sec) [ -16477.6205] [ 3541] [depth= 1] . ( 1 sec) [ -16231.8423] [ 3539] [depth= 3] . ( 1 sec) [ -16165.1743] [ 3523] [depth= 5] . ( 2 sec) [ -16085.1172] [ 3524] [depth= 5] . ( 2 sec) [ -15961.6118] [ 3495] [depth= 7] . ( 2 sec) [ -15321.4770] [ 3424] [depth= 8] . ( 2 sec) [ -15068.2970] [ 3423] [depth= 1] . ( 2 sec) [ -14989.8255] [ 3401] [depth= 12] . ( 2 sec) [ -14715.6572] [ 3396] [depth= 1] . ( 2 sec) [ -14392.8364] [ 3244] [depth= 13] . ( 2 sec) [ -14344.6407] [ 3236] [depth= 1] . ( 2 sec) [ -14312.0542] [ 3228] [depth= 1] . ( 2 sec) [ -14308.7100] [ 3236] [depth= 1] . ( 2 sec) [ -14080.7927] [ 3196] [depth= 9] . ( 2 sec) [ -13980.1008] [ 3163] [depth= 1] . ( 2 sec) [ -13923.2939] [ 3146] [depth= 4] . ( 2 sec) [ -13400.3570] [ 3002] [depth= 12] . ( 2 sec) [ -13102.5951] [ 3004] [depth= 10] . ( 2 sec) [ -13068.7859] [ 2996] [depth= 1] . ( 2 sec) [ -12657.0444] [ 2965] [depth= 7] . ( 2 sec) [ -12314.3642] [ 2820] [depth= 9] . ( 2 sec) [ -12303.3255] [ 2803] [depth= 2] . ( 2 sec) [ -12146.2646] [ 2802] [depth= 2] . ( 2 sec) [ -12108.5842] [ 2615] [depth= 12] . ( 2 sec) [ -11788.1479] [ 2611] [depth= 1] . ( 2 sec) [ -11752.6792] [ 2609] [depth= 8] . ( 3 sec) [ -11697.8500] [ 2604] [depth= 1] . ( 3 sec) [ -11287.0678] [ 2527] [depth= 6] . ( 3 sec) [ -11125.5971] [ 2516] [depth= 1] . ( 3 sec) [ -11073.7653] [ 2500] [depth= 1] . ( 3 sec) [ -11043.0701] [ 2498] [depth= 1] . ( 3 sec) [ -10835.5174] [ 2424] [depth= 11] . ( 3 sec) [ -10768.9831] [ 2405] [depth= 6] . ( 3 sec) [ -10687.0044] [ 2440] [depth= 2] . ( 3 sec) [ -10612.0808] [ 2389] [depth= 6] . ( 3 sec) [ -10393.3296] [ 2353] [depth= 2] . ( 3 sec) [ -10371.6956] [ 2352] [depth= 1] . ( 3 sec) [ -9978.6144] [ 2218] [depth= 12] . ( 3 sec) [ -9898.9743] [ 2223] [depth= 1] . ( 3 sec) [ -9861.9432] [ 2211] [depth= 2] . ( 3 sec) [ -9488.3935] [ 2122] [depth= 3] . ( 3 sec) [ -9365.3183] [ 2079] [depth= 7] . ( 3 sec) [ -9356.4335] [ 2080] [depth= 1] . ( 3 sec) [ -9269.5559] [ 2082] [depth= 7] . ( 3 sec) [ -9269.4817] [ 2087] [depth= 1] . ( 3 sec) [ -9057.6955] [ 2046] [depth= 5] . ( 3 sec) [ -8845.2109] [ 1945] [depth= 2] . ( 4 sec) [ -8711.9939] [ 1890] [depth= 4] . ( 4 sec) [ -8681.2886] [ 1877] [depth= 1] . ( 4 sec) [ -8454.0302] [ 1797] [depth= 3] . ( 4 sec) [ -8443.0430] [ 1798] [depth= 1] . ( 4 sec) [ -8295.3349] [ 1696] [depth= 7] . ( 4 sec) [ -8270.3120] [ 1698] [depth= 1] . ( 4 sec) [ -7846.2412] [ 1572] [depth= 7] . ( 4 sec) [ -7826.9584] [ 1568] [depth= 1] . ( 4 sec) [ -7772.9452] [ 1560] [depth= 3] . ( 4 sec) [ -7769.8983] [ 1561] [depth= 1] . ( 4 sec) [ -7732.2238] [ 1567] [depth= 1] . ( 4 sec) [ -7727.2752] [ 1569] [depth= 2] . ( 4 sec) [ -7660.2406] [ 1569] [depth= 1] . ( 4 sec) [ -7654.5752] [ 1574] [depth= 1] . ( 4 sec) [ -7528.2537] [ 1517] [depth= 2] . ( 4 sec) [ -7485.4982] [ 1521] [depth= 1] . ( 4 sec) [ -7475.8244] [ 1516] [depth= 1] . ( 5 sec) [ -7466.4112] [ 1512] [depth= 1] . ( 5 sec) [ -7429.0191] [ 1511] [depth= 3] . ( 5 sec) [ -7412.9928] [ 1496] [depth= 1] . ( 5 sec) [ -7405.4052] [ 1493] [depth= 1] . ( 5 sec) [ -7405.1921] [ 1497] [depth= 1] . ( 5 sec) [ -7397.3439] [ 1490] [depth= 1] . ( 5 sec) [ -7396.9947] [ 1487] [depth= 1] . ( 5 sec) [ -7384.9804] [ 1483] [depth= 1] . ( 5 sec) [ -7376.0042] [ 1478] [depth= 2] . ( 5 sec) [ -7363.0523] [ 1473] [depth= 1] . ( 5 sec) [ -7314.5724] [Branch lengths ] . ( 6 sec) [ -7311.7150] [GTR parameters ] . ( 6 sec) [ -7268.4149] [Alpha ][ 1.000277] . ( 6 sec) [ -7266.6305] [ 1465] [depth= 1] . ( 6 sec) [ -7265.9657] [ 1464] [depth= 1] . ( 6 sec) [ -7263.3520] [ 1463] [depth= 1] . ( 6 sec) [ -7235.4259] [ 1454] [depth= 1] . ( 7 sec) [ -7234.6464] [ 1452] [depth= 1] . ( 7 sec) [ -7230.4526] [ 1451] [depth= 1] . ( 7 sec) [ -7225.3761] [ 1440] [depth= 1] . ( 8 sec) [ -7225.2055] [ 1439] [depth= 1] . ( 8 sec) [ -7224.6947] [ 1440] [depth= 1] . ( 8 sec) [ -7224.5177] [ 1440] [depth= 1] . ( 8 sec) [ -7209.9323] [ 1434] [depth= 1] . ( 9 sec) [ -7209.5384] [ 1438] [depth= 1] . ( 10 sec) [ -7200.1168] [Branch lengths ] . ( 10 sec) [ -7199.8224] [GTR parameters ] . ( 10 sec) [ -7198.8664] [Alpha ][ 1.130650] . ( 12 sec) [ -7198.7062] [ 1434] [depth= 1] . ( 13 sec) [ -7198.0618] [Branch lengths ] . ( 14 sec) [ -7198.0588] [GTR parameters ] . ( 14 sec) [ -7198.0557] [Alpha ][ 1.138805] . ( 15 sec) [ -7197.3124] [ 1436] [depth= 2] . ( 35 sec) [ -7197.1222] [Branch lengths ] . ( 35 sec) [ -7197.1164] [GTR parameters ] . ( 35 sec) [ -7197.1142] [Alpha ][ 1.131558] . ( 35 sec) [ -7197.1142] [Topology ] . ( 36 sec) [ -7197.1053] [Topology ] . ( 37 sec) [ -7197.1039] [Topology ] . ( 38 sec) [ -7197.1035] [Topology ] . ( 38 sec) [ -7197.1035] [GTR parameters ] . ( 38 sec) [ -7197.1035] [Alpha ][ 1.132690] . ( 38 sec) [ -7197.1035] [Topology ] . ( 39 sec) [ -7197.1033] [Topology ] . ( 39 sec) [ -7197.1033] [GTR parameters ] . ( 39 sec) [ -7197.1033] [Alpha ][ 1.132690] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7197.103289. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19098.3691] [GTR parameters ] . ( 1 sec) [ -18673.6386] [Alpha ][ 0.500960] . ( 1 sec) [ -18213.9623] [ 3914] [depth= 7] . ( 1 sec) [ -17869.5909] [ 3847] [depth= 11] . ( 1 sec) [ -17785.3387] [ 3827] [depth= 6] . ( 1 sec) [ -17551.1808] [ 3826] [depth= 1] . ( 1 sec) [ -17534.7799] [ 3804] [depth= 11] . ( 1 sec) [ -17501.8509] [ 3804] [depth= 6] . ( 1 sec) [ -17118.0833] [ 3778] [depth= 5] . ( 1 sec) [ -16741.1417] [ 3768] [depth= 1] . ( 1 sec) [ -16399.2459] [ 3699] [depth= 8] . ( 1 sec) [ -16235.7947] [ 3656] [depth= 3] . ( 1 sec) [ -15947.9858] [ 3575] [depth= 1] . ( 2 sec) [ -15925.6398] [ 3566] [depth= 5] . ( 2 sec) [ -15345.4579] [ 3446] [depth= 17] . ( 2 sec) [ -15283.2009] [ 3436] [depth= 1] . ( 2 sec) [ -15260.5104] [ 3427] [depth= 2] . ( 2 sec) [ -15191.4707] [ 3415] [depth= 3] . ( 2 sec) [ -15158.0463] [ 3397] [depth= 1] . ( 2 sec) [ -15011.9768] [ 3376] [depth= 7] . ( 2 sec) [ -14976.0629] [ 3376] [depth= 4] . ( 2 sec) [ -14894.3164] [ 3367] [depth= 6] . ( 2 sec) [ -14812.9767] [ 3347] [depth= 7] . ( 2 sec) [ -14757.1908] [ 3325] [depth= 7] . ( 2 sec) [ -14741.3751] [ 3323] [depth= 1] . ( 2 sec) [ -14738.4736] [ 3326] [depth= 1] . ( 2 sec) [ -14571.9213] [ 3285] [depth= 13] . ( 2 sec) [ -14118.5492] [ 3207] [depth= 4] . ( 2 sec) [ -14076.9596] [ 3188] [depth= 4] . ( 2 sec) [ -13436.6892] [ 3126] [depth= 12] . ( 2 sec) [ -13394.7367] [ 3121] [depth= 2] . ( 2 sec) [ -13269.5626] [ 3134] [depth= 12] . ( 2 sec) [ -13163.0084] [ 3101] [depth= 10] . ( 2 sec) [ -13152.0226] [ 3103] [depth= 3] . ( 3 sec) [ -13151.4042] [ 3105] [depth= 1] . ( 3 sec) [ -13097.6521] [ 3052] [depth= 1] . ( 3 sec) [ -12648.6302] [ 2920] [depth= 5] . ( 3 sec) [ -12644.6702] [ 2922] [depth= 1] . ( 3 sec) [ -12164.5793] [ 2794] [depth= 3] . ( 3 sec) [ -11796.4693] [ 2739] [depth= 4] . ( 3 sec) [ -11771.9495] [ 2734] [depth= 3] . ( 3 sec) [ -11762.0694] [ 2713] [depth= 1] . ( 3 sec) [ -11760.0173] [ 2722] [depth= 2] . ( 3 sec) [ -11379.8005] [ 2680] [depth= 10] . ( 3 sec) [ -11286.9496] [ 2671] [depth= 1] . ( 3 sec) [ -10802.1725] [ 2532] [depth= 3] . ( 3 sec) [ -10796.9457] [ 2531] [depth= 2] . ( 3 sec) [ -10771.6507] [ 2528] [depth= 2] . ( 3 sec) [ -10742.3239] [ 2487] [depth= 1] . ( 3 sec) [ -10695.4192] [ 2492] [depth= 1] . ( 3 sec) [ -10361.5991] [ 2376] [depth= 5] . ( 3 sec) [ -10347.4177] [ 2378] [depth= 8] . ( 3 sec) [ -9881.4423] [ 2239] [depth= 9] . ( 3 sec) [ -9404.5696] [ 2133] [depth= 7] . ( 3 sec) [ -9281.8981] [ 2115] [depth= 2] . ( 3 sec) [ -9257.3727] [ 2107] [depth= 3] . ( 3 sec) [ -9213.0368] [ 2093] [depth= 3] . ( 4 sec) [ -9203.2473] [ 2090] [depth= 2] . ( 4 sec) [ -9202.3454] [ 2089] [depth= 3] . ( 4 sec) [ -9192.2931] [ 2081] [depth= 6] . ( 4 sec) [ -9187.5405] [ 2079] [depth= 1] . ( 4 sec) [ -9184.4743] [ 2072] [depth= 4] . ( 4 sec) [ -9164.0930] [ 2053] [depth= 6] . ( 4 sec) [ -9090.6826] [ 2029] [depth= 3] . ( 4 sec) [ -9090.3940] [ 2027] [depth= 7] . ( 4 sec) [ -8839.8195] [ 1890] [depth= 6] . ( 4 sec) [ -8784.4962] [ 1887] [depth= 1] . ( 4 sec) [ -8767.4194] [ 1900] [depth= 1] . ( 4 sec) [ -8760.6042] [ 1906] [depth= 1] . ( 4 sec) [ -8750.9095] [ 1906] [depth= 7] . ( 4 sec) [ -8749.2503] [ 1909] [depth= 1] . ( 4 sec) [ -8740.0765] [ 1877] [depth= 6] . ( 4 sec) [ -8537.8392] [ 1837] [depth= 3] . ( 4 sec) [ -8530.8782] [ 1840] [depth= 1] . ( 4 sec) [ -8492.7553] [ 1824] [depth= 1] . ( 4 sec) [ -8485.8104] [ 1819] [depth= 1] . ( 4 sec) [ -8256.9306] [ 1723] [depth= 10] . ( 4 sec) [ -8191.8642] [ 1714] [depth= 2] . ( 5 sec) [ -8122.8932] [ 1689] [depth= 1] . ( 5 sec) [ -8051.5954] [ 1709] [depth= 2] . ( 5 sec) [ -7889.5432] [ 1666] [depth= 1] . ( 5 sec) [ -7837.0480] [ 1655] [depth= 1] . ( 5 sec) [ -7834.8705] [ 1660] [depth= 1] . ( 5 sec) [ -7786.3511] [ 1646] [depth= 1] . ( 5 sec) [ -7765.2894] [ 1645] [depth= 2] . ( 5 sec) [ -7758.9249] [ 1643] [depth= 1] . ( 5 sec) [ -7731.6273] [ 1641] [depth= 2] . ( 5 sec) [ -7711.5401] [ 1634] [depth= 1] . ( 5 sec) [ -7709.8907] [ 1634] [depth= 1] . ( 5 sec) [ -7674.0058] [ 1628] [depth= 2] . ( 5 sec) [ -7588.3748] [Branch lengths ] . ( 6 sec) [ -7586.6555] [GTR parameters ] . ( 6 sec) [ -7561.3777] [Alpha ][ 0.871914] . ( 6 sec) [ -7532.5748] [ 1587] [depth= 2] . ( 6 sec) [ -7523.0162] [ 1584] [depth= 1] . ( 6 sec) [ -7520.3136] [ 1583] [depth= 1] . ( 6 sec) [ -7513.0717] [ 1571] [depth= 2] . ( 6 sec) [ -7472.5144] [ 1544] [depth= 2] . ( 6 sec) [ -7472.2875] [ 1543] [depth= 1] . ( 7 sec) [ -7450.9251] [ 1542] [depth= 1] . ( 7 sec) [ -7431.7601] [ 1537] [depth= 1] . ( 7 sec) [ -7428.6736] [ 1537] [depth= 1] . ( 7 sec) [ -7410.2491] [ 1539] [depth= 7] . ( 7 sec) [ -7410.0819] [ 1540] [depth= 1] . ( 7 sec) [ -7356.8919] [ 1528] [depth= 1] . ( 8 sec) [ -7351.2520] [ 1520] [depth= 1] . ( 8 sec) [ -7343.8975] [ 1515] [depth= 1] . ( 8 sec) [ -7339.8235] [ 1503] [depth= 1] . ( 8 sec) [ -7338.8708] [ 1506] [depth= 1] . ( 8 sec) [ -7338.4346] [ 1505] [depth= 1] . ( 8 sec) [ -7338.2025] [ 1505] [depth= 1] . ( 8 sec) [ -7329.9961] [ 1498] [depth= 1] . ( 8 sec) [ -7329.5537] [ 1498] [depth= 1] . ( 9 sec) [ -7329.4670] [ 1495] [depth= 1] . ( 9 sec) [ -7329.4447] [ 1498] [depth= 1] . ( 9 sec) [ -7311.8689] [ 1462] [depth= 1] . ( 9 sec) [ -7282.9088] [ 1466] [depth= 8] . ( 10 sec) [ -7254.0661] [ 1436] [depth= 8] . ( 10 sec) [ -7207.9977] [Branch lengths ] . ( 10 sec) [ -7207.5866] [GTR parameters ] . ( 10 sec) [ -7203.5460] [Alpha ][ 1.119929] . ( 11 sec) [ -7200.1624] [ 1433] [depth= 1] . ( 11 sec) [ -7199.9091] [ 1434] [depth= 1] . ( 11 sec) [ -7199.5101] [ 1438] [depth= 1] . ( 13 sec) [ -7199.4032] [ 1434] [depth= 1] . ( 14 sec) [ -7198.0778] [Branch lengths ] . ( 14 sec) [ -7198.0706] [GTR parameters ] . ( 14 sec) [ -7198.0551] [Alpha ][ 1.138303] . ( 18 sec) [ -7198.0295] [Branch lengths ] . ( 38 sec) [ -7197.3382] [ 1436] [depth= 2] . ( 39 sec) [ -7197.1227] [Branch lengths ] . ( 40 sec) [ -7197.1164] [GTR parameters ] . ( 40 sec) [ -7197.1146] [Alpha ][ 1.131761] . ( 40 sec) [ -7197.1146] [Topology ] . ( 40 sec) [ -7197.1056] [Topology ] . ( 41 sec) [ -7197.1040] [Topology ] . ( 42 sec) [ -7197.1035] [Topology ] . ( 42 sec) [ -7197.1035] [GTR parameters ] . ( 42 sec) [ -7197.1035] [Alpha ][ 1.131761] . ( 42 sec) [ -7197.1035] [Topology ] . ( 43 sec) [ -7197.1033] [Topology ] . ( 43 sec) [ -7197.1033] [GTR parameters ] . ( 43 sec) [ -7197.1033] [Alpha ][ 1.131761] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7197.103281. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7252.857742 . ( 1 sec) [ -7242.8403] [GTR parameters ] . ( 1 sec) [ -7242.1885] [Alpha ][ 1.109718] . ( 1 sec) [ -7242.1885] [Topology ] . ( 2 sec) [ -7202.1609] [Topology ] . ( 3 sec) [ -7198.2279] [Topology ] . ( 4 sec) [ -7197.5078] [Topology ] . ( 4 sec) [ -7197.2985] [Topology ] . ( 5 sec) [ -7197.2249] [Topology ] . ( 6 sec) [ -7197.1964] [Topology ] . ( 7 sec) [ -7197.1847] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.184696 . ( 12 sec) [ -7197.1380] [GTR parameters ] . ( 12 sec) [ -7197.1167] [Alpha ][ 1.131102] . ( 12 sec) [ -7197.1167] [Topology ] . ( 13 sec) [ -7197.1086] [Topology ] . ( 14 sec) [ -7197.1054] [Topology ] . ( 15 sec) [ -7197.1040] [Topology ] . ( 15 sec) [ -7197.1034] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7197.103429 . ( 20 sec) [ -7197.1034] [GTR parameters ] . ( 21 sec) [ -7197.1034] [Alpha ][ 1.132233] . ( 21 sec) [ -7197.1034] [Topology ] . ( 21 sec) [ -7197.1031] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -7242.8403] [GTR parameters ] . ( 32 sec) [ -7242.1885] [Alpha ][ 1.109718] . ( 32 sec) [ -7239.0080] [ 1435] [depth= 1] . ( 33 sec) [ -7238.7123] [ 1436] [depth= 1] . ( 33 sec) [ -7227.8420] [ 1434] [depth= 1] . ( 33 sec) [ -7227.7182] [ 1435] [depth= 1] . ( 33 sec) [ -7227.0615] [ 1433] [depth= 1] . ( 34 sec) [ -7226.0591] [ 1438] [depth= 1] . ( 34 sec) [ -7225.3600] [ 1433] [depth= 1] . ( 35 sec) [ -7202.3762] [Branch lengths ] . ( 36 sec) [ -7202.3382] [GTR parameters ] . ( 36 sec) [ -7202.3331] [Alpha ][ 1.120024] . ( 36 sec) [ -7201.6025] [ 1432] [depth= 1] . ( 36 sec) [ -7201.5705] [ 1433] [depth= 1] . ( 36 sec) [ -7201.4926] [ 1432] [depth= 1] . ( 37 sec) [ -7200.9370] [ 1431] [depth= 1] . ( 37 sec) [ -7200.3871] [ 1433] [depth= 1] . ( 38 sec) [ -7200.2393] [ 1438] [depth= 1] . ( 38 sec) [ -7199.1105] [ 1436] [depth= 1] . ( 40 sec) [ -7197.2316] [Branch lengths ] . ( 40 sec) [ -7197.2201] [GTR parameters ] . ( 40 sec) [ -7197.2149] [Alpha ][ 1.130556] . ( 44 sec) [ -7197.1087] [Branch lengths ] . ( 65 sec) [ -7197.1037] [Branch lengths ] . ( 65 sec) [ -7197.1037] [Topology ] . ( 66 sec) [ -7197.1032] [Topology ] . ( 66 sec) [ -7197.1032] [GTR parameters ] . ( 66 sec) [ -7197.1031] [Alpha ][ 1.132044] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7197.103097 . Log likelihood obtained after SPR moves : -7197.103094 . Log likelihood of the current tree: -7197.103094. . Printing the most likely tree in file 'data57.phy_phyml_tree.txt'... . Best log likelihood : -7197.103094 . Time used 0h1m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo