.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data88.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... . 401 patterns found. (out of a total of 500 sites) . 94 sites without polymorphism (18.80%). . [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) [ -15476.4858] [GTR parameters ] . ( 0 sec) [ -15233.9058] [Alpha ][ 0.500960] . ( 0 sec) [ -14716.9315] [ 3086] [depth= 8] . ( 0 sec) [ -14638.1033] [ 3088] [depth= 6] . ( 0 sec) [ -14359.5419] [ 3069] [depth= 4] . ( 0 sec) [ -14318.0707] [ 3060] [depth= 5] . ( 0 sec) [ -14184.2958] [ 3000] [depth= 2] . ( 0 sec) [ -14018.3784] [ 2993] [depth= 6] . ( 1 sec) [ -13877.3582] [ 2987] [depth= 5] . ( 1 sec) [ -13810.8132] [ 2978] [depth= 10] . ( 1 sec) [ -13685.1612] [ 2925] [depth= 9] . ( 1 sec) [ -13589.7302] [ 2904] [depth= 1] . ( 1 sec) [ -13460.5273] [ 2877] [depth= 11] . ( 1 sec) [ -13326.2499] [ 2837] [depth= 7] . ( 1 sec) [ -13241.8575] [ 2832] [depth= 2] . ( 1 sec) [ -13170.4575] [ 2826] [depth= 1] . ( 1 sec) [ -13016.7649] [ 2771] [depth= 3] . ( 1 sec) [ -12921.0746] [ 2766] [depth= 2] . ( 1 sec) [ -12877.5838] [ 2763] [depth= 1] . ( 1 sec) [ -12848.2731] [ 2764] [depth= 1] . ( 1 sec) [ -12442.3214] [ 2723] [depth= 4] . ( 1 sec) [ -12430.7377] [ 2726] [depth= 2] . ( 1 sec) [ -12419.2828] [ 2719] [depth= 1] . ( 1 sec) [ -12383.9915] [ 2714] [depth= 5] . ( 1 sec) [ -12349.9638] [ 2713] [depth= 2] . ( 1 sec) [ -12251.3504] [ 2677] [depth= 3] . ( 1 sec) [ -12111.7075] [ 2654] [depth= 7] . ( 1 sec) [ -12026.3991] [ 2622] [depth= 3] . ( 1 sec) [ -11990.8587] [ 2622] [depth= 6] . ( 1 sec) [ -11821.9478] [ 2577] [depth= 18] . ( 1 sec) [ -11672.9910] [ 2542] [depth= 3] . ( 2 sec) [ -11409.0628] [ 2455] [depth= 8] . ( 2 sec) [ -10810.1309] [ 2316] [depth= 6] . ( 2 sec) [ -10680.2550] [ 2304] [depth= 4] . ( 2 sec) [ -10313.9663] [ 2239] [depth= 1] . ( 2 sec) [ -10200.3529] [ 2196] [depth= 15] . ( 2 sec) [ -10105.3311] [ 2151] [depth= 7] . ( 2 sec) [ -10018.3973] [ 2144] [depth= 1] . ( 2 sec) [ -10007.4222] [ 2142] [depth= 1] . ( 2 sec) [ -9941.0502] [ 2105] [depth= 2] . ( 2 sec) [ -9912.6661] [ 2098] [depth= 9] . ( 2 sec) [ -9783.1416] [ 2110] [depth= 1] . ( 2 sec) [ -9694.9858] [ 2071] [depth= 5] . ( 2 sec) [ -9689.2640] [ 2079] [depth= 1] . ( 2 sec) [ -9551.2034] [ 2006] [depth= 10] . ( 2 sec) [ -9517.6615] [ 1988] [depth= 1] . ( 2 sec) [ -9380.3540] [ 1964] [depth= 4] . ( 2 sec) [ -9323.7930] [ 1921] [depth= 1] . ( 2 sec) [ -9301.8270] [ 1916] [depth= 8] . ( 2 sec) [ -9241.7024] [ 1909] [depth= 5] . ( 2 sec) [ -9210.8298] [ 1899] [depth= 1] . ( 2 sec) [ -9087.7922] [ 1855] [depth= 13] . ( 2 sec) [ -9071.4788] [ 1861] [depth= 1] . ( 3 sec) [ -8998.9747] [ 1838] [depth= 4] . ( 3 sec) [ -8893.2016] [ 1830] [depth= 2] . ( 3 sec) [ -8880.3141] [ 1824] [depth= 5] . ( 3 sec) [ -8873.8887] [ 1821] [depth= 1] . ( 3 sec) [ -8867.9667] [ 1810] [depth= 5] . ( 3 sec) [ -8842.8915] [ 1799] [depth= 1] . ( 3 sec) [ -8841.4440] [ 1804] [depth= 1] . ( 3 sec) [ -8824.1077] [ 1799] [depth= 1] . ( 3 sec) [ -8720.8118] [ 1767] [depth= 6] . ( 3 sec) [ -8543.0686] [ 1723] [depth= 1] . ( 3 sec) [ -8462.8418] [ 1712] [depth= 1] . ( 3 sec) [ -8451.0794] [ 1705] [depth= 1] . ( 3 sec) [ -8425.9480] [ 1693] [depth= 3] . ( 3 sec) [ -8374.4782] [ 1652] [depth= 1] . ( 3 sec) [ -8279.3090] [ 1624] [depth= 1] . ( 3 sec) [ -8256.3903] [ 1632] [depth= 1] . ( 3 sec) [ -8236.9707] [ 1623] [depth= 1] . ( 3 sec) [ -8196.0070] [ 1607] [depth= 2] . ( 3 sec) [ -8158.1236] [ 1593] [depth= 2] . ( 4 sec) [ -8157.5966] [ 1594] [depth= 1] . ( 4 sec) [ -8149.4931] [ 1594] [depth= 1] . ( 4 sec) [ -8079.5926] [ 1575] [depth= 2] . ( 4 sec) [ -8078.9157] [ 1581] [depth= 1] . ( 4 sec) [ -8077.9631] [ 1585] [depth= 1] . ( 4 sec) [ -8058.6940] [ 1578] [depth= 2] . ( 4 sec) [ -8057.0099] [ 1573] [depth= 1] . ( 4 sec) [ -8012.8125] [Branch lengths ] . ( 5 sec) [ -8011.6993] [GTR parameters ] . ( 5 sec) [ -7972.5343] [Alpha ][ 1.000226] . ( 5 sec) [ -7945.0484] [ 1562] [depth= 1] . ( 6 sec) [ -7943.7237] [ 1557] [depth= 1] . ( 6 sec) [ -7943.0063] [ 1556] [depth= 1] . ( 7 sec) [ -7937.8937] [Branch lengths ] . ( 8 sec) [ -7937.8377] [GTR parameters ] . ( 8 sec) [ -7937.3053] [Alpha ][ 1.092145] . ( 11 sec) [ -7936.4001] [Branch lengths ] . ( 30 sec) [ -7936.2808] [Branch lengths ] . ( 30 sec) [ -7936.2808] [Topology ] . ( 31 sec) [ -7936.2717] [Topology ] . ( 32 sec) [ -7936.2690] [Topology ] . ( 33 sec) [ -7936.2679] [Topology ] . ( 33 sec) [ -7936.2673] [Topology ] . ( 34 sec) [ -7936.2671] [GTR parameters ] . ( 34 sec) [ -7936.2353] [Alpha ][ 1.115442] . ( 34 sec) [ -7936.2353] [Topology ] . ( 35 sec) [ -7936.2338] [Topology ] . ( 35 sec) [ -7936.2332] [Topology ] . ( 35 sec) [ -7936.2332] [GTR parameters ] . ( 36 sec) [ -7936.2331] [Alpha ][ 1.116649] . ( 36 sec) [ -7936.2331] [Topology ] . ( 36 sec) [ -7936.2328] [Topology ] . ( 36 sec) [ -7936.2328] [GTR parameters ] . ( 37 sec) [ -7936.2328] [Alpha ][ 1.116649] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7936.232829. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15361.0339] [GTR parameters ] . ( 1 sec) [ -15124.4151] [Alpha ][ 0.500960] . ( 1 sec) [ -14534.5400] [ 3053] [depth= 3] . ( 1 sec) [ -14247.9334] [ 2993] [depth= 10] . ( 1 sec) [ -14047.0665] [ 2968] [depth= 4] . ( 1 sec) [ -13982.6147] [ 2966] [depth= 6] . ( 1 sec) [ -13797.7377] [ 2908] [depth= 3] . ( 1 sec) [ -13750.4812] [ 2906] [depth= 6] . ( 1 sec) [ -13720.7560] [ 2893] [depth= 4] . ( 1 sec) [ -13671.0715] [ 2892] [depth= 2] . ( 1 sec) [ -13658.3552] [ 2884] [depth= 2] . ( 1 sec) [ -13602.1999] [ 2880] [depth= 1] . ( 1 sec) [ -13410.4389] [ 2877] [depth= 7] . ( 1 sec) [ -13318.3945] [ 2871] [depth= 1] . ( 1 sec) [ -13203.5672] [ 2807] [depth= 11] . ( 1 sec) [ -13116.1050] [ 2828] [depth= 4] . ( 1 sec) [ -13036.6039] [ 2838] [depth= 8] . ( 1 sec) [ -12697.6738] [ 2736] [depth= 5] . ( 1 sec) [ -12579.9777] [ 2703] [depth= 11] . ( 1 sec) [ -12547.8976] [ 2692] [depth= 2] . ( 1 sec) [ -12459.9537] [ 2678] [depth= 1] . ( 1 sec) [ -12433.3212] [ 2683] [depth= 1] . ( 1 sec) [ -12103.2582] [ 2667] [depth= 12] . ( 1 sec) [ -11934.7281] [ 2668] [depth= 3] . ( 1 sec) [ -11736.2150] [ 2599] [depth= 1] . ( 1 sec) [ -11556.3034] [ 2536] [depth= 11] . ( 2 sec) [ -11506.4366] [ 2519] [depth= 9] . ( 2 sec) [ -11491.5621] [ 2520] [depth= 1] . ( 2 sec) [ -11462.8109] [ 2517] [depth= 2] . ( 2 sec) [ -11409.7393] [ 2498] [depth= 1] . ( 2 sec) [ -11028.3249] [ 2411] [depth= 4] . ( 2 sec) [ -10880.5160] [ 2427] [depth= 1] . ( 2 sec) [ -10825.1063] [ 2381] [depth= 2] . ( 2 sec) [ -10616.5252] [ 2314] [depth= 1] . ( 2 sec) [ -10609.6629] [ 2310] [depth= 1] . ( 2 sec) [ -10561.5803] [ 2290] [depth= 1] . ( 2 sec) [ -10531.9412] [ 2273] [depth= 1] . ( 2 sec) [ -10244.7655] [ 2185] [depth= 10] . ( 2 sec) [ -10113.2316] [ 2152] [depth= 7] . ( 2 sec) [ -10015.3609] [ 2154] [depth= 2] . ( 2 sec) [ -9964.1092] [ 2131] [depth= 2] . ( 2 sec) [ -9954.0707] [ 2129] [depth= 1] . ( 2 sec) [ -9939.9720] [ 2127] [depth= 9] . ( 2 sec) [ -9884.4314] [ 2093] [depth= 7] . ( 2 sec) [ -9881.0383] [ 2100] [depth= 1] . ( 2 sec) [ -9695.4175] [ 2043] [depth= 7] . ( 2 sec) [ -9653.6420] [ 2053] [depth= 1] . ( 3 sec) [ -9480.3773] [ 2006] [depth= 1] . ( 3 sec) [ -9475.6401] [ 1995] [depth= 1] . ( 3 sec) [ -9352.3996] [ 1944] [depth= 5] . ( 3 sec) [ -9155.1588] [ 1921] [depth= 8] . ( 3 sec) [ -9026.6861] [ 1884] [depth= 5] . ( 3 sec) [ -9007.4298] [ 1882] [depth= 2] . ( 3 sec) [ -8963.8906] [ 1877] [depth= 3] . ( 3 sec) [ -8955.4391] [ 1876] [depth= 2] . ( 3 sec) [ -8954.0522] [ 1876] [depth= 2] . ( 3 sec) [ -8953.1038] [ 1882] [depth= 1] . ( 3 sec) [ -8928.6721] [ 1875] [depth= 2] . ( 3 sec) [ -8905.4597] [ 1868] [depth= 1] . ( 3 sec) [ -8876.7622] [ 1862] [depth= 1] . ( 3 sec) [ -8847.5414] [ 1862] [depth= 1] . ( 3 sec) [ -8826.0398] [ 1864] [depth= 2] . ( 3 sec) [ -8805.1912] [ 1854] [depth= 2] . ( 3 sec) [ -8752.8414] [ 1834] [depth= 2] . ( 3 sec) [ -8723.7696] [ 1821] [depth= 1] . ( 3 sec) [ -8717.3587] [ 1821] [depth= 3] . ( 3 sec) [ -8700.0662] [ 1826] [depth= 4] . ( 4 sec) [ -8630.9453] [ 1806] [depth= 1] . ( 4 sec) [ -8602.1220] [ 1800] [depth= 3] . ( 4 sec) [ -8591.4374] [ 1795] [depth= 1] . ( 4 sec) [ -8564.1502] [ 1785] [depth= 3] . ( 4 sec) [ -8554.3838] [ 1777] [depth= 2] . ( 4 sec) [ -8552.4988] [ 1783] [depth= 1] . ( 4 sec) [ -8525.6046] [ 1774] [depth= 1] . ( 4 sec) [ -8504.8643] [ 1768] [depth= 1] . ( 4 sec) [ -8485.0844] [ 1763] [depth= 2] . ( 4 sec) [ -8472.6359] [ 1758] [depth= 1] . ( 4 sec) [ -8335.1240] [ 1696] [depth= 2] . ( 4 sec) [ -8314.8810] [ 1689] [depth= 1] . ( 4 sec) [ -8314.0608] [ 1690] [depth= 1] . ( 5 sec) [ -8107.2560] [ 1618] [depth= 5] . ( 5 sec) [ -8040.2916] [Branch lengths ] . ( 5 sec) [ -8039.1388] [GTR parameters ] . ( 5 sec) [ -8003.8781] [Alpha ][ 0.974190] . ( 5 sec) [ -8001.4933] [ 1612] [depth= 1] . ( 5 sec) [ -7994.0343] [ 1605] [depth= 1] . ( 6 sec) [ -7994.0019] [ 1598] [depth= 1] . ( 7 sec) [ -7993.1963] [ 1593] [depth= 1] . ( 7 sec) [ -7991.7058] [ 1583] [depth= 2] . ( 7 sec) [ -7966.8198] [ 1576] [depth= 1] . ( 8 sec) [ -7951.7743] [ 1557] [depth= 2] . ( 8 sec) [ -7951.2488] [ 1562] [depth= 1] . ( 8 sec) [ -7950.8348] [ 1565] [depth= 1] . ( 8 sec) [ -7950.4827] [ 1565] [depth= 1] . ( 8 sec) [ -7939.2917] [Branch lengths ] . ( 9 sec) [ -7939.1755] [GTR parameters ] . ( 9 sec) [ -7938.3444] [Alpha ][ 1.086353] . ( 9 sec) [ -7937.6617] [ 1559] [depth= 1] . ( 12 sec) [ -7936.6170] [Branch lengths ] . ( 12 sec) [ -7936.6164] [GTR parameters ] . ( 12 sec) [ -7936.5959] [Alpha ][ 1.105789] . ( 15 sec) [ -7936.4916] [Branch lengths ] . ( 35 sec) [ -7936.4831] [Branch lengths ] . ( 35 sec) [ -7936.4831] [Topology ] . ( 35 sec) [ -7936.4480] [Topology ] . ( 36 sec) [ -7936.2749] [Topology ] . ( 37 sec) [ -7936.2526] [Topology ] . ( 38 sec) [ -7936.2460] [Topology ] . ( 38 sec) [ -7936.2436] [Topology ] . ( 39 sec) [ -7936.2427] [Topology ] . ( 40 sec) [ -7936.2403] [GTR parameters ] . ( 40 sec) [ -7936.2335] [Alpha ][ 1.117065] . ( 40 sec) [ -7936.2335] [Topology ] . ( 40 sec) [ -7936.2329] [Topology ] . ( 41 sec) [ -7936.2329] [GTR parameters ] . ( 41 sec) [ -7936.2329] [Alpha ][ 1.117065] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7936.232880. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16225.2876] [GTR parameters ] . ( 1 sec) [ -15954.7580] [Alpha ][ 0.500960] . ( 1 sec) [ -15387.1860] [ 3187] [depth= 8] . ( 1 sec) [ -15110.6447] [ 3127] [depth= 8] . ( 1 sec) [ -15104.5565] [ 3120] [depth= 4] . ( 1 sec) [ -14996.6778] [ 3120] [depth= 1] . ( 1 sec) [ -14891.3582] [ 3105] [depth= 9] . ( 1 sec) [ -14872.1036] [ 3104] [depth= 2] . ( 1 sec) [ -14194.2547] [ 2989] [depth= 7] . ( 1 sec) [ -14164.0897] [ 2984] [depth= 3] . ( 1 sec) [ -13854.2825] [ 2906] [depth= 4] . ( 1 sec) [ -13828.4072] [ 2902] [depth= 1] . ( 1 sec) [ -13759.4933] [ 2854] [depth= 5] . ( 2 sec) [ -13749.9571] [ 2855] [depth= 2] . ( 2 sec) [ -13425.1440] [ 2761] [depth= 7] . ( 2 sec) [ -13409.7868] [ 2749] [depth= 4] . ( 2 sec) [ -13324.7167] [ 2748] [depth= 1] . ( 2 sec) [ -13251.8863] [ 2735] [depth= 7] . ( 2 sec) [ -13246.1597] [ 2737] [depth= 1] . ( 2 sec) [ -13103.8958] [ 2698] [depth= 2] . ( 2 sec) [ -13034.5921] [ 2677] [depth= 4] . ( 2 sec) [ -12941.2427] [ 2655] [depth= 1] . ( 2 sec) [ -12570.9861] [ 2559] [depth= 6] . ( 2 sec) [ -12393.4158] [ 2544] [depth= 8] . ( 2 sec) [ -12287.1989] [ 2506] [depth= 1] . ( 2 sec) [ -12177.0838] [ 2489] [depth= 8] . ( 2 sec) [ -11899.9645] [ 2411] [depth= 9] . ( 2 sec) [ -11886.0583] [ 2412] [depth= 3] . ( 2 sec) [ -11599.5218] [ 2340] [depth= 5] . ( 2 sec) [ -11464.8151] [ 2333] [depth= 7] . ( 2 sec) [ -11260.6563] [ 2309] [depth= 7] . ( 2 sec) [ -11111.5448] [ 2271] [depth= 1] . ( 2 sec) [ -11050.2712] [ 2263] [depth= 2] . ( 2 sec) [ -11041.4888] [ 2256] [depth= 1] . ( 2 sec) [ -11016.0943] [ 2253] [depth= 1] . ( 2 sec) [ -11015.6383] [ 2252] [depth= 1] . ( 3 sec) [ -10999.6501] [ 2247] [depth= 1] . ( 3 sec) [ -10706.0004] [ 2180] [depth= 3] . ( 3 sec) [ -10653.7319] [ 2135] [depth= 8] . ( 3 sec) [ -10651.4478] [ 2135] [depth= 1] . ( 3 sec) [ -10361.1623] [ 2131] [depth= 1] . ( 3 sec) [ -10000.3355] [ 2072] [depth= 1] . ( 3 sec) [ -9945.3633] [ 2086] [depth= 2] . ( 3 sec) [ -9926.8058] [ 2086] [depth= 3] . ( 3 sec) [ -9880.4964] [ 2086] [depth= 2] . ( 3 sec) [ -9817.2775] [ 2083] [depth= 1] . ( 3 sec) [ -9714.6346] [ 2040] [depth= 2] . ( 3 sec) [ -9698.7777] [ 2040] [depth= 1] . ( 3 sec) [ -9662.2347] [ 2025] [depth= 5] . ( 3 sec) [ -9652.0570] [ 2039] [depth= 2] . ( 3 sec) [ -9536.4635] [ 1978] [depth= 3] . ( 3 sec) [ -9465.5431] [ 1984] [depth= 1] . ( 3 sec) [ -9465.4249] [ 1975] [depth= 6] . ( 3 sec) [ -9416.2669] [ 1975] [depth= 1] . ( 3 sec) [ -9404.9886] [ 1978] [depth= 3] . ( 3 sec) [ -9397.2132] [ 1971] [depth= 1] . ( 3 sec) [ -9389.9462] [ 1950] [depth= 1] . ( 3 sec) [ -9366.4748] [ 1949] [depth= 2] . ( 3 sec) [ -9288.0372] [ 1909] [depth= 7] . ( 4 sec) [ -9114.6932] [ 1914] [depth= 1] . ( 4 sec) [ -8827.6629] [ 1840] [depth= 8] . ( 4 sec) [ -8827.0020] [ 1835] [depth= 1] . ( 4 sec) [ -8752.9022] [ 1814] [depth= 5] . ( 4 sec) [ -8752.8031] [ 1814] [depth= 1] . ( 4 sec) [ -8743.9214] [ 1813] [depth= 1] . ( 4 sec) [ -8723.1569] [ 1808] [depth= 4] . ( 4 sec) [ -8616.4278] [ 1778] [depth= 4] . ( 4 sec) [ -8556.5511] [ 1747] [depth= 1] . ( 4 sec) [ -8549.3149] [ 1744] [depth= 1] . ( 4 sec) [ -8548.2700] [ 1747] [depth= 1] . ( 4 sec) [ -8540.5485] [ 1740] [depth= 2] . ( 4 sec) [ -8516.2190] [ 1734] [depth= 1] . ( 4 sec) [ -8512.9702] [ 1723] [depth= 6] . ( 4 sec) [ -8466.0463] [ 1719] [depth= 1] . ( 4 sec) [ -8460.8769] [ 1726] [depth= 1] . ( 4 sec) [ -8400.3960] [ 1686] [depth= 4] . ( 4 sec) [ -8380.0740] [ 1676] [depth= 1] . ( 4 sec) [ -8302.5875] [ 1640] [depth= 6] . ( 4 sec) [ -8300.4973] [ 1644] [depth= 1] . ( 5 sec) [ -8261.3586] [ 1634] [depth= 2] . ( 5 sec) [ -8260.3484] [ 1627] [depth= 1] . ( 5 sec) [ -8247.4179] [ 1623] [depth= 1] . ( 5 sec) [ -8243.0944] [ 1620] [depth= 1] . ( 5 sec) [ -8084.6773] [Branch lengths ] . ( 6 sec) [ -8083.2896] [GTR parameters ] . ( 6 sec) [ -8049.8734] [Alpha ][ 0.957743] . ( 6 sec) [ -8014.1007] [ 1598] [depth= 3] . ( 6 sec) [ -8013.7722] [ 1597] [depth= 1] . ( 6 sec) [ -7997.8237] [ 1593] [depth= 1] . ( 6 sec) [ -7988.1863] [ 1579] [depth= 1] . ( 6 sec) [ -7986.8429] [ 1582] [depth= 1] . ( 6 sec) [ -7973.8145] [ 1574] [depth= 1] . ( 6 sec) [ -7962.4899] [ 1563] [depth= 1] . ( 7 sec) [ -7961.3492] [ 1558] [depth= 1] . ( 7 sec) [ -7959.9722] [ 1560] [depth= 1] . ( 7 sec) [ -7957.8110] [ 1557] [depth= 1] . ( 8 sec) [ -7957.7059] [ 1559] [depth= 1] . ( 8 sec) [ -7957.6125] [ 1559] [depth= 1] . ( 8 sec) [ -7957.2537] [ 1559] [depth= 1] . ( 8 sec) [ -7939.2057] [Branch lengths ] . ( 9 sec) [ -7938.8829] [GTR parameters ] . ( 9 sec) [ -7937.7707] [Alpha ][ 1.086677] . ( 12 sec) [ -7936.6417] [Branch lengths ] . ( 31 sec) [ -7936.5243] [Branch lengths ] . ( 31 sec) [ -7936.5243] [Topology ] . ( 32 sec) [ -7936.4898] [Topology ] . ( 33 sec) [ -7936.3166] [Topology ] . ( 34 sec) [ -7936.2949] [Topology ] . ( 34 sec) [ -7936.2887] [Topology ] . ( 35 sec) [ -7936.2867] [Topology ] . ( 36 sec) [ -7936.2859] [Topology ] . ( 36 sec) [ -7936.2839] [GTR parameters ] . ( 36 sec) [ -7936.2352] [Alpha ][ 1.115712] . ( 36 sec) [ -7936.2352] [Topology ] . ( 37 sec) [ -7936.2334] [Topology ] . ( 38 sec) [ -7936.2330] [Topology ] . ( 38 sec) [ -7936.2329] [GTR parameters ] . ( 38 sec) [ -7936.2329] [Alpha ][ 1.116827] . ( 38 sec) [ -7936.2329] [Topology ] . ( 39 sec) [ -7936.2327] [Topology ] . ( 39 sec) [ -7936.2327] [GTR parameters ] . ( 39 sec) [ -7936.2327] [Alpha ][ 1.116827] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7936.232695. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15958.7655] [GTR parameters ] . ( 0 sec) [ -15689.4174] [Alpha ][ 0.500960] . ( 0 sec) [ -15106.6153] [ 3188] [depth= 8] . ( 0 sec) [ -14833.6348] [ 3126] [depth= 9] . ( 0 sec) [ -14710.3982] [ 3115] [depth= 2] . ( 0 sec) [ -14654.9595] [ 3080] [depth= 1] . ( 1 sec) [ -14577.3699] [ 3066] [depth= 4] . ( 1 sec) [ -14562.6096] [ 3061] [depth= 3] . ( 1 sec) [ -14520.7635] [ 3055] [depth= 4] . ( 1 sec) [ -14439.9755] [ 3011] [depth= 1] . ( 1 sec) [ -14323.0284] [ 2997] [depth= 7] . ( 1 sec) [ -14215.6405] [ 2951] [depth= 2] . ( 1 sec) [ -13903.2252] [ 2946] [depth= 1] . ( 1 sec) [ -13654.8598] [ 2888] [depth= 3] . ( 1 sec) [ -13520.2578] [ 2887] [depth= 2] . ( 1 sec) [ -13457.3861] [ 2885] [depth= 2] . ( 1 sec) [ -13359.1135] [ 2848] [depth= 1] . ( 1 sec) [ -13332.9659] [ 2832] [depth= 1] . ( 1 sec) [ -13309.8565] [ 2825] [depth= 5] . ( 1 sec) [ -13193.8102] [ 2821] [depth= 1] . ( 1 sec) [ -13055.3050] [ 2767] [depth= 8] . ( 1 sec) [ -13040.8328] [ 2762] [depth= 2] . ( 1 sec) [ -12935.6988] [ 2726] [depth= 12] . ( 1 sec) [ -12675.8188] [ 2669] [depth= 5] . ( 1 sec) [ -12611.2466] [ 2667] [depth= 4] . ( 1 sec) [ -12426.8959] [ 2663] [depth= 4] . ( 1 sec) [ -12366.0584] [ 2656] [depth= 1] . ( 1 sec) [ -12230.4278] [ 2621] [depth= 6] . ( 1 sec) [ -12167.5907] [ 2614] [depth= 2] . ( 1 sec) [ -12033.2618] [ 2581] [depth= 7] . ( 2 sec) [ -11790.5020] [ 2532] [depth= 14] . ( 2 sec) [ -11784.8412] [ 2525] [depth= 3] . ( 2 sec) [ -11709.9654] [ 2512] [depth= 1] . ( 2 sec) [ -11591.6192] [ 2509] [depth= 1] . ( 2 sec) [ -11342.0740] [ 2392] [depth= 9] . ( 2 sec) [ -11287.8169] [ 2381] [depth= 5] . ( 2 sec) [ -11287.0294] [ 2376] [depth= 1] . ( 2 sec) [ -11258.6335] [ 2353] [depth= 1] . ( 2 sec) [ -11192.5495] [ 2334] [depth= 3] . ( 2 sec) [ -11170.0394] [ 2326] [depth= 4] . ( 2 sec) [ -10964.8143] [ 2283] [depth= 3] . ( 2 sec) [ -10933.0135] [ 2277] [depth= 2] . ( 2 sec) [ -10857.8386] [ 2264] [depth= 7] . ( 2 sec) [ -10780.7529] [ 2259] [depth= 1] . ( 2 sec) [ -10685.4287] [ 2215] [depth= 1] . ( 2 sec) [ -10589.6895] [ 2200] [depth= 4] . ( 2 sec) [ -10490.2336] [ 2157] [depth= 10] . ( 2 sec) [ -10378.5727] [ 2154] [depth= 2] . ( 2 sec) [ -10145.8816] [ 2130] [depth= 1] . ( 2 sec) [ -10101.2380] [ 2128] [depth= 3] . ( 2 sec) [ -10025.4312] [ 2105] [depth= 1] . ( 3 sec) [ -10021.9456] [ 2104] [depth= 1] . ( 3 sec) [ -9684.8432] [ 2010] [depth= 6] . ( 3 sec) [ -9682.3668] [ 2021] [depth= 1] . ( 3 sec) [ -9635.9813] [ 2008] [depth= 3] . ( 3 sec) [ -9630.0119] [ 1996] [depth= 1] . ( 3 sec) [ -9617.7345] [ 1987] [depth= 1] . ( 3 sec) [ -9614.7066] [ 1992] [depth= 14] . ( 3 sec) [ -9614.5479] [ 1991] [depth= 1] . ( 3 sec) [ -9374.8848] [ 1979] [depth= 13] . ( 3 sec) [ -9063.7356] [ 1903] [depth= 2] . ( 3 sec) [ -9054.4643] [ 1909] [depth= 1] . ( 3 sec) [ -8987.8591] [ 1904] [depth= 1] . ( 3 sec) [ -8983.8930] [ 1909] [depth= 1] . ( 3 sec) [ -8982.2821] [ 1904] [depth= 1] . ( 3 sec) [ -8972.7284] [ 1898] [depth= 1] . ( 3 sec) [ -8936.4133] [ 1877] [depth= 1] . ( 3 sec) [ -8922.4652] [ 1888] [depth= 1] . ( 3 sec) [ -8870.6479] [ 1850] [depth= 2] . ( 3 sec) [ -8804.2148] [ 1842] [depth= 1] . ( 3 sec) [ -8733.6854] [ 1795] [depth= 1] . ( 3 sec) [ -8656.1615] [ 1787] [depth= 1] . ( 4 sec) [ -8656.0552] [ 1797] [depth= 1] . ( 4 sec) [ -8635.6726] [ 1783] [depth= 1] . ( 4 sec) [ -8617.3608] [ 1771] [depth= 2] . ( 4 sec) [ -8592.0305] [ 1769] [depth= 5] . ( 4 sec) [ -8567.6350] [ 1770] [depth= 3] . ( 4 sec) [ -8559.1083] [ 1764] [depth= 1] . ( 4 sec) [ -8344.5244] [ 1691] [depth= 9] . ( 4 sec) [ -8340.6920] [ 1705] [depth= 1] . ( 4 sec) [ -8280.2369] [ 1691] [depth= 1] . ( 4 sec) [ -8273.0966] [ 1684] [depth= 2] . ( 4 sec) [ -8267.1874] [ 1672] [depth= 1] . ( 4 sec) [ -8260.1950] [ 1680] [depth= 1] . ( 4 sec) [ -8235.0800] [ 1674] [depth= 1] . ( 4 sec) [ -8166.9281] [Branch lengths ] . ( 5 sec) [ -8165.6640] [GTR parameters ] . ( 5 sec) [ -8137.0931] [Alpha ][ 0.905658] . ( 5 sec) [ -8137.0150] [ 1675] [depth= 1] . ( 5 sec) [ -8127.0890] [ 1663] [depth= 1] . ( 5 sec) [ -8036.3335] [ 1621] [depth= 3] . ( 5 sec) [ -8026.3312] [ 1616] [depth= 1] . ( 6 sec) [ -8026.0407] [ 1617] [depth= 1] . ( 6 sec) [ -8010.5574] [ 1608] [depth= 1] . ( 6 sec) [ -8010.5467] [ 1611] [depth= 1] . ( 6 sec) [ -8010.1393] [ 1608] [depth= 1] . ( 6 sec) [ -8008.1118] [ 1609] [depth= 1] . ( 6 sec) [ -8007.3436] [ 1612] [depth= 1] . ( 7 sec) [ -8002.2300] [ 1598] [depth= 1] . ( 7 sec) [ -8001.6507] [ 1592] [depth= 1] . ( 7 sec) [ -7956.9365] [ 1563] [depth= 5] . ( 7 sec) [ -7955.5632] [ 1559] [depth= 1] . ( 8 sec) [ -7940.6811] [Branch lengths ] . ( 8 sec) [ -7940.5103] [GTR parameters ] . ( 8 sec) [ -7938.4288] [Alpha ][ 1.076408] . ( 11 sec) [ -7936.8125] [Branch lengths ] . ( 31 sec) [ -7936.5715] [Branch lengths ] . ( 31 sec) [ -7936.5715] [Topology ] . ( 31 sec) [ -7936.5552] [Topology ] . ( 32 sec) [ -7936.5285] [Topology ] . ( 33 sec) [ -7936.3580] [Topology ] . ( 34 sec) [ -7936.3366] [Topology ] . ( 35 sec) [ -7936.3304] [Topology ] . ( 35 sec) [ -7936.3284] [Topology ] . ( 36 sec) [ -7936.3276] [Topology ] . ( 36 sec) [ -7936.3249] [GTR parameters ] . ( 37 sec) [ -7936.2369] [Alpha ][ 1.115593] . ( 37 sec) [ -7936.2369] [Topology ] . ( 37 sec) [ -7936.2340] [Topology ] . ( 38 sec) [ -7936.2332] [Topology ] . ( 38 sec) [ -7936.2332] [GTR parameters ] . ( 38 sec) [ -7936.2331] [Alpha ][ 1.116708] . ( 38 sec) [ -7936.2331] [Topology ] . ( 39 sec) [ -7936.2328] [Topology ] . ( 39 sec) [ -7936.2328] [GTR parameters ] . ( 39 sec) [ -7936.2328] [Alpha ][ 1.116708] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7936.232781. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16082.2175] [GTR parameters ] . ( 1 sec) [ -15818.1727] [Alpha ][ 0.500960] . ( 1 sec) [ -14999.4040] [ 3203] [depth= 6] . ( 1 sec) [ -14823.2240] [ 3134] [depth= 11] . ( 1 sec) [ -14781.1956] [ 3134] [depth= 4] . ( 1 sec) [ -14762.2245] [ 3132] [depth= 7] . ( 1 sec) [ -14592.8321] [ 3096] [depth= 10] . ( 1 sec) [ -14370.2180] [ 3092] [depth= 6] . ( 1 sec) [ -14344.1079] [ 3080] [depth= 4] . ( 1 sec) [ -14320.0728] [ 3075] [depth= 1] . ( 1 sec) [ -14202.1852] [ 3048] [depth= 7] . ( 1 sec) [ -14197.6223] [ 3051] [depth= 1] . ( 1 sec) [ -13859.2763] [ 2996] [depth= 7] . ( 1 sec) [ -13689.7316] [ 2937] [depth= 2] . ( 1 sec) [ -13661.9923] [ 2924] [depth= 1] . ( 1 sec) [ -13477.3292] [ 2894] [depth= 16] . ( 1 sec) [ -13390.3540] [ 2892] [depth= 1] . ( 1 sec) [ -13255.4448] [ 2885] [depth= 3] . ( 1 sec) [ -13172.5203] [ 2882] [depth= 1] . ( 1 sec) [ -13117.3400] [ 2874] [depth= 2] . ( 1 sec) [ -13070.8560] [ 2831] [depth= 1] . ( 1 sec) [ -12955.9612] [ 2822] [depth= 8] . ( 1 sec) [ -12920.5509] [ 2816] [depth= 1] . ( 1 sec) [ -12785.2661] [ 2811] [depth= 7] . ( 1 sec) [ -12569.0250] [ 2745] [depth= 7] . ( 2 sec) [ -12465.7772] [ 2715] [depth= 3] . ( 2 sec) [ -12383.3071] [ 2699] [depth= 2] . ( 2 sec) [ -12309.7050] [ 2680] [depth= 3] . ( 2 sec) [ -12230.8666] [ 2670] [depth= 1] . ( 2 sec) [ -12176.1813] [ 2667] [depth= 1] . ( 2 sec) [ -12097.6515] [ 2628] [depth= 1] . ( 2 sec) [ -11856.0295] [ 2575] [depth= 11] . ( 2 sec) [ -11820.0529] [ 2557] [depth= 1] . ( 2 sec) [ -11766.0000] [ 2567] [depth= 1] . ( 2 sec) [ -11527.8435] [ 2510] [depth= 8] . ( 2 sec) [ -11440.0831] [ 2474] [depth= 8] . ( 2 sec) [ -11249.6572] [ 2459] [depth= 8] . ( 2 sec) [ -10926.8683] [ 2383] [depth= 1] . ( 2 sec) [ -10780.3939] [ 2347] [depth= 8] . ( 2 sec) [ -10697.7243] [ 2321] [depth= 3] . ( 2 sec) [ -10549.1213] [ 2296] [depth= 2] . ( 2 sec) [ -10537.2583] [ 2291] [depth= 1] . ( 2 sec) [ -10478.5516] [ 2286] [depth= 2] . ( 2 sec) [ -10470.1504] [ 2276] [depth= 1] . ( 2 sec) [ -10271.4065] [ 2198] [depth= 2] . ( 2 sec) [ -10261.8898] [ 2177] [depth= 10] . ( 2 sec) [ -10232.1317] [ 2161] [depth= 1] . ( 3 sec) [ -10008.4270] [ 2145] [depth= 8] . ( 3 sec) [ -9893.3846] [ 2122] [depth= 10] . ( 3 sec) [ -9701.6265] [ 2069] [depth= 1] . ( 3 sec) [ -9529.6161] [ 2040] [depth= 4] . ( 3 sec) [ -9505.2650] [ 2039] [depth= 2] . ( 3 sec) [ -9457.1443] [ 2017] [depth= 1] . ( 3 sec) [ -9451.9245] [ 2017] [depth= 1] . ( 3 sec) [ -9423.0046] [ 1995] [depth= 5] . ( 3 sec) [ -9391.6588] [ 2001] [depth= 1] . ( 3 sec) [ -9172.1074] [ 1928] [depth= 1] . ( 3 sec) [ -9083.7407] [ 1890] [depth= 3] . ( 3 sec) [ -9061.0006] [ 1882] [depth= 1] . ( 3 sec) [ -8970.6609] [ 1847] [depth= 6] . ( 3 sec) [ -8871.1050] [ 1851] [depth= 2] . ( 3 sec) [ -8869.0808] [ 1855] [depth= 1] . ( 3 sec) [ -8868.0920] [ 1862] [depth= 1] . ( 3 sec) [ -8856.0609] [ 1863] [depth= 1] . ( 3 sec) [ -8849.8268] [ 1861] [depth= 2] . ( 3 sec) [ -8792.6546] [ 1839] [depth= 1] . ( 3 sec) [ -8763.6111] [ 1837] [depth= 1] . ( 3 sec) [ -8736.0720] [ 1843] [depth= 2] . ( 3 sec) [ -8644.0125] [ 1835] [depth= 6] . ( 4 sec) [ -8592.5824] [ 1780] [depth= 1] . ( 4 sec) [ -8581.4878] [ 1768] [depth= 3] . ( 4 sec) [ -8528.3380] [ 1739] [depth= 3] . ( 4 sec) [ -8435.9805] [ 1691] [depth= 6] . ( 4 sec) [ -8415.5281] [ 1686] [depth= 1] . ( 4 sec) [ -8410.8009] [ 1692] [depth= 1] . ( 4 sec) [ -8398.6901] [ 1686] [depth= 1] . ( 4 sec) [ -8381.1782] [ 1670] [depth= 2] . ( 4 sec) [ -8362.5686] [ 1661] [depth= 1] . ( 4 sec) [ -8343.2203] [ 1665] [depth= 1] . ( 4 sec) [ -8222.2092] [ 1635] [depth= 3] . ( 4 sec) [ -8216.8902] [ 1635] [depth= 1] . ( 4 sec) [ -8185.8199] [ 1609] [depth= 1] . ( 4 sec) [ -8153.2247] [ 1615] [depth= 1] . ( 4 sec) [ -8122.5722] [ 1603] [depth= 2] . ( 4 sec) [ -8106.9323] [ 1597] [depth= 1] . ( 5 sec) [ -8030.9744] [Branch lengths ] . ( 5 sec) [ -8029.9687] [GTR parameters ] . ( 5 sec) [ -7993.1950] [Alpha ][ 0.994344] . ( 5 sec) [ -7983.0663] [ 1590] [depth= 2] . ( 5 sec) [ -7981.4603] [ 1585] [depth= 1] . ( 5 sec) [ -7980.5855] [ 1582] [depth= 1] . ( 5 sec) [ -7974.5571] [ 1577] [depth= 2] . ( 6 sec) [ -7966.0174] [ 1562] [depth= 1] . ( 6 sec) [ -7961.6418] [ 1560] [depth= 1] . ( 6 sec) [ -7959.2509] [ 1564] [depth= 1] . ( 6 sec) [ -7958.9035] [ 1564] [depth= 1] . ( 6 sec) [ -7957.6222] [ 1558] [depth= 1] . ( 6 sec) [ -7952.0211] [ 1559] [depth= 1] . ( 7 sec) [ -7951.8808] [ 1565] [depth= 1] . ( 7 sec) [ -7950.7125] [ 1559] [depth= 1] . ( 8 sec) [ -7938.6391] [Branch lengths ] . ( 8 sec) [ -7938.4285] [GTR parameters ] . ( 8 sec) [ -7937.8704] [Alpha ][ 1.087662] . ( 9 sec) [ -7937.7690] [ 1556] [depth= 1] . ( 11 sec) [ -7936.3659] [Branch lengths ] . ( 11 sec) [ -7936.3625] [GTR parameters ] . ( 11 sec) [ -7936.3293] [Alpha ][ 1.111456] . ( 14 sec) [ -7936.2410] [Branch lengths ] . ( 34 sec) [ -7936.2350] [Branch lengths ] . ( 34 sec) [ -7936.2350] [Topology ] . ( 35 sec) [ -7936.2346] [Topology ] . ( 35 sec) [ -7936.2346] [GTR parameters ] . ( 35 sec) [ -7936.2330] [Alpha ][ 1.116806] . ( 35 sec) [ -7936.2330] [Topology ] . ( 36 sec) [ -7936.2328] [Topology ] . ( 36 sec) [ -7936.2328] [GTR parameters ] . ( 36 sec) [ -7936.2328] [Alpha ][ 1.116806] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7936.232764. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7956.615250 . ( 0 sec) [ -7955.1854] [GTR parameters ] . ( 0 sec) [ -7954.9724] [Alpha ][ 1.057884] . ( 0 sec) [ -7954.9724] [Topology ] . ( 1 sec) [ -7939.3506] [Topology ] . ( 2 sec) [ -7937.3186] [Topology ] . ( 3 sec) [ -7936.8134] [Topology ] . ( 3 sec) [ -7936.6150] [Topology ] . ( 4 sec) [ -7936.5279] [Topology ] . ( 5 sec) [ -7936.4882] [Topology ] . ( 6 sec) [ -7936.4695] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.469519 . ( 11 sec) [ -7936.4470] [GTR parameters ] . ( 11 sec) [ -7936.2709] [Alpha ][ 1.112677] . ( 11 sec) [ -7936.2709] [Topology ] . ( 12 sec) [ -7936.2498] [Topology ] . ( 13 sec) [ -7936.2412] [Topology ] . ( 13 sec) [ -7936.2372] [Topology ] . ( 14 sec) [ -7936.2354] [Topology ] . ( 15 sec) [ -7936.2346] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.234585 . ( 20 sec) [ -7936.2345] [GTR parameters ] . ( 20 sec) [ -7936.2336] [Alpha ][ 1.116587] . ( 20 sec) [ -7936.2336] [Topology ] . ( 21 sec) [ -7936.2331] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7936.233081 . ( 26 sec) [ -7936.2331] [GTR parameters ] . ( 26 sec) [ -7936.2331] [Alpha ][ 1.116587] . ( 26 sec) [ -7936.2331] [Topology ] . ( 27 sec) [ -7936.2328] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 38 sec) [ -7955.1854] [GTR parameters ] . ( 38 sec) [ -7954.9724] [Alpha ][ 1.057884] . ( 40 sec) [ -7954.4398] [ 1559] [depth= 1] . ( 40 sec) [ -7954.2583] [ 1559] [depth= 1] . ( 40 sec) [ -7953.0982] [ 1559] [depth= 1] . ( 40 sec) [ -7951.6454] [ 1563] [depth= 1] . ( 40 sec) [ -7951.0879] [ 1556] [depth= 1] . ( 41 sec) [ -7937.2865] [Branch lengths ] . ( 41 sec) [ -7937.2614] [GTR parameters ] . ( 41 sec) [ -7937.1372] [Alpha ][ 1.104457] . ( 44 sec) [ -7936.3161] [Branch lengths ] . ( 63 sec) [ -7936.2502] [Branch lengths ] . ( 63 sec) [ -7936.2502] [Topology ] . ( 64 sec) [ -7936.2449] [Topology ] . ( 65 sec) [ -7936.2431] [Topology ] . ( 66 sec) [ -7936.2423] [Topology ] . ( 66 sec) [ -7936.2420] [GTR parameters ] . ( 66 sec) [ -7936.2342] [Alpha ][ 1.116562] . ( 66 sec) [ -7936.2342] [Topology ] . ( 67 sec) [ -7936.2333] [Topology ] . ( 67 sec) [ -7936.2333] [GTR parameters ] . ( 67 sec) [ -7936.2333] [Alpha ][ 1.116562] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7936.232830 . Log likelihood obtained after SPR moves : -7936.233301 . Log likelihood of the current tree: -7936.232830. . Printing the most likely tree in file 'data88.phy_phyml_tree.txt'... . Best log likelihood : -7936.232695 . Time used 0h1m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo