.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data83.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... . 390 patterns found. (out of a total of 500 sites) . 100 sites without polymorphism (20.00%). . [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) [ -14875.2958] [GTR parameters ] . ( 1 sec) [ -14648.6793] [Alpha ][ 0.500960] . ( 1 sec) [ -14491.6542] [ 3003] [depth= 6] . ( 1 sec) [ -14029.3461] [ 2946] [depth= 13] . ( 1 sec) [ -13868.9332] [ 2938] [depth= 1] . ( 1 sec) [ -13717.0901] [ 2933] [depth= 3] . ( 1 sec) [ -13237.1264] [ 2912] [depth= 5] . ( 1 sec) [ -13137.0714] [ 2905] [depth= 6] . ( 1 sec) [ -12993.1002] [ 2894] [depth= 5] . ( 1 sec) [ -12915.4229] [ 2865] [depth= 1] . ( 2 sec) [ -12902.9425] [ 2856] [depth= 4] . ( 2 sec) [ -12843.9231] [ 2852] [depth= 8] . ( 2 sec) [ -12541.0697] [ 2762] [depth= 10] . ( 2 sec) [ -12484.0369] [ 2751] [depth= 1] . ( 2 sec) [ -12235.2133] [ 2748] [depth= 4] . ( 2 sec) [ -12182.7654] [ 2743] [depth= 4] . ( 2 sec) [ -12094.5049] [ 2739] [depth= 4] . ( 2 sec) [ -12002.6907] [ 2710] [depth= 6] . ( 2 sec) [ -11962.4168] [ 2698] [depth= 3] . ( 2 sec) [ -11800.6488] [ 2690] [depth= 5] . ( 2 sec) [ -11738.1132] [ 2684] [depth= 4] . ( 2 sec) [ -11701.5108] [ 2669] [depth= 1] . ( 2 sec) [ -11686.9330] [ 2666] [depth= 2] . ( 2 sec) [ -11670.5672] [ 2616] [depth= 6] . ( 2 sec) [ -11586.2497] [ 2588] [depth= 4] . ( 2 sec) [ -11499.2269] [ 2581] [depth= 4] . ( 2 sec) [ -11206.9520] [ 2526] [depth= 13] . ( 2 sec) [ -11142.2214] [ 2491] [depth= 11] . ( 2 sec) [ -11048.2735] [ 2481] [depth= 4] . ( 2 sec) [ -11012.4611] [ 2480] [depth= 1] . ( 2 sec) [ -10843.2015] [ 2420] [depth= 11] . ( 2 sec) [ -10742.3145] [ 2416] [depth= 2] . ( 2 sec) [ -10733.5737] [ 2407] [depth= 1] . ( 2 sec) [ -10719.6224] [ 2415] [depth= 1] . ( 3 sec) [ -10492.2091] [ 2323] [depth= 9] . ( 3 sec) [ -10380.4144] [ 2288] [depth= 13] . ( 3 sec) [ -10263.8735] [ 2266] [depth= 5] . ( 3 sec) [ -10254.5595] [ 2266] [depth= 1] . ( 3 sec) [ -9982.8048] [ 2193] [depth= 9] . ( 3 sec) [ -9973.2963] [ 2190] [depth= 1] . ( 3 sec) [ -9968.6836] [ 2184] [depth= 1] . ( 3 sec) [ -9771.5228] [ 2090] [depth= 10] . ( 3 sec) [ -9581.1263] [ 2038] [depth= 3] . ( 3 sec) [ -9566.7322] [ 2043] [depth= 2] . ( 3 sec) [ -9357.3638] [ 2043] [depth= 1] . ( 3 sec) [ -9341.5141] [ 2028] [depth= 1] . ( 3 sec) [ -9339.7747] [ 2026] [depth= 3] . ( 3 sec) [ -9310.8736] [ 2025] [depth= 6] . ( 3 sec) [ -9260.3224] [ 2066] [depth= 1] . ( 3 sec) [ -9200.8907] [ 2034] [depth= 6] . ( 3 sec) [ -9129.9192] [ 2003] [depth= 6] . ( 3 sec) [ -8852.5657] [ 1917] [depth= 3] . ( 3 sec) [ -8773.0607] [ 1874] [depth= 2] . ( 3 sec) [ -8736.6970] [ 1860] [depth= 3] . ( 3 sec) [ -8615.0673] [ 1820] [depth= 2] . ( 4 sec) [ -8528.8589] [ 1779] [depth= 10] . ( 4 sec) [ -8456.6415] [ 1776] [depth= 1] . ( 4 sec) [ -8447.9345] [ 1778] [depth= 1] . ( 4 sec) [ -8415.1458] [ 1757] [depth= 1] . ( 4 sec) [ -8413.6345] [ 1752] [depth= 1] . ( 4 sec) [ -8409.8454] [ 1747] [depth= 1] . ( 4 sec) [ -8300.7346] [ 1722] [depth= 1] . ( 4 sec) [ -8297.0261] [ 1712] [depth= 4] . ( 4 sec) [ -8273.0931] [ 1715] [depth= 2] . ( 4 sec) [ -8249.3764] [ 1713] [depth= 1] . ( 4 sec) [ -8239.4910] [ 1711] [depth= 2] . ( 4 sec) [ -8236.3056] [ 1710] [depth= 1] . ( 4 sec) [ -8213.4678] [ 1708] [depth= 1] . ( 4 sec) [ -8202.1474] [ 1685] [depth= 5] . ( 4 sec) [ -8192.8592] [ 1680] [depth= 4] . ( 4 sec) [ -8189.8693] [ 1679] [depth= 1] . ( 5 sec) [ -8131.0113] [ 1656] [depth= 12] . ( 5 sec) [ -8094.8823] [ 1670] [depth= 1] . ( 5 sec) [ -8083.3210] [ 1655] [depth= 2] . ( 5 sec) [ -8065.8949] [ 1649] [depth= 1] . ( 5 sec) [ -8063.6389] [ 1648] [depth= 1] . ( 5 sec) [ -8030.3217] [ 1645] [depth= 5] . ( 5 sec) [ -7970.7900] [ 1623] [depth= 1] . ( 5 sec) [ -7875.6153] [ 1575] [depth= 9] . ( 5 sec) [ -7794.2622] [ 1551] [depth= 3] . ( 5 sec) [ -7696.6439] [Branch lengths ] . ( 6 sec) [ -7695.6297] [GTR parameters ] . ( 6 sec) [ -7666.0146] [Alpha ][ 0.933675] . ( 6 sec) [ -7662.3481] [ 1550] [depth= 1] . ( 6 sec) [ -7660.7267] [ 1547] [depth= 1] . ( 6 sec) [ -7596.0567] [ 1528] [depth= 2] . ( 6 sec) [ -7594.6362] [ 1528] [depth= 1] . ( 6 sec) [ -7594.2149] [ 1532] [depth= 1] . ( 6 sec) [ -7580.8327] [ 1525] [depth= 2] . ( 7 sec) [ -7580.7803] [ 1528] [depth= 1] . ( 7 sec) [ -7580.4957] [ 1527] [depth= 1] . ( 7 sec) [ -7580.4578] [ 1523] [depth= 2] . ( 8 sec) [ -7564.6789] [ 1514] [depth= 1] . ( 8 sec) [ -7554.6831] [ 1509] [depth= 1] . ( 8 sec) [ -7548.2524] [ 1509] [depth= 2] . ( 8 sec) [ -7546.1845] [ 1509] [depth= 2] . ( 8 sec) [ -7527.8832] [ 1494] [depth= 5] . ( 8 sec) [ -7527.4399] [ 1496] [depth= 1] . ( 8 sec) [ -7527.2957] [ 1496] [depth= 1] . ( 9 sec) [ -7526.6027] [ 1496] [depth= 1] . ( 9 sec) [ -7526.5620] [ 1496] [depth= 1] . ( 10 sec) [ -7517.3096] [Branch lengths ] . ( 10 sec) [ -7517.2662] [GTR parameters ] . ( 10 sec) [ -7516.6717] [Alpha ][ 1.026174] . ( 10 sec) [ -7516.4083] [ 1496] [depth= 1] . ( 12 sec) [ -7516.2641] [ 1496] [depth= 1] . ( 14 sec) [ -7515.2843] [Branch lengths ] . ( 14 sec) [ -7515.2724] [GTR parameters ] . ( 14 sec) [ -7515.2663] [Alpha ][ 1.036268] . ( 18 sec) [ -7515.0910] [Branch lengths ] . ( 39 sec) [ -7515.0667] [Branch lengths ] . ( 39 sec) [ -7515.0667] [Topology ] . ( 40 sec) [ -7514.9609] [Topology ] . ( 41 sec) [ -7514.9099] [Topology ] . ( 42 sec) [ -7514.9013] [Topology ] . ( 42 sec) [ -7514.8992] [Topology ] . ( 43 sec) [ -7514.8986] [Topology ] . ( 43 sec) [ -7514.8908] [GTR parameters ] . ( 43 sec) [ -7514.8906] [Alpha ][ 1.038212] . ( 43 sec) [ -7514.8906] [Topology ] . ( 44 sec) [ -7514.8903] [Topology ] . ( 44 sec) [ -7514.8903] [GTR parameters ] . ( 44 sec) [ -7514.8903] [Alpha ][ 1.038212] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -7514.6553] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7514.5448] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7514.544820. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16025.4175] [GTR parameters ] . ( 1 sec) [ -15816.4371] [Alpha ][ 0.500960] . ( 1 sec) [ -15605.9268] [ 2922] [depth= 9] . ( 1 sec) [ -15425.0258] [ 2870] [depth= 9] . ( 1 sec) [ -15332.7883] [ 2844] [depth= 4] . ( 1 sec) [ -15320.6909] [ 2839] [depth= 3] . ( 1 sec) [ -15130.9269] [ 2832] [depth= 3] . ( 1 sec) [ -15112.2209] [ 2829] [depth= 7] . ( 1 sec) [ -15107.7682] [ 2829] [depth= 1] . ( 1 sec) [ -15087.0506] [ 2827] [depth= 2] . ( 1 sec) [ -15075.6542] [ 2826] [depth= 2] . ( 1 sec) [ -14977.7248] [ 2821] [depth= 2] . ( 1 sec) [ -14823.7329] [ 2779] [depth= 3] . ( 1 sec) [ -14810.1694] [ 2774] [depth= 1] . ( 1 sec) [ -14600.8918] [ 2689] [depth= 6] . ( 1 sec) [ -14518.5010] [ 2683] [depth= 9] . ( 1 sec) [ -14316.4690] [ 2625] [depth= 5] . ( 1 sec) [ -14244.5712] [ 2698] [depth= 14] . ( 1 sec) [ -14207.3535] [ 2685] [depth= 1] . ( 2 sec) [ -14169.7903] [ 2677] [depth= 4] . ( 2 sec) [ -14110.8169] [ 2673] [depth= 1] . ( 2 sec) [ -14002.0456] [ 2612] [depth= 1] . ( 2 sec) [ -13997.4484] [ 2605] [depth= 8] . ( 2 sec) [ -13885.7538] [ 2589] [depth= 1] . ( 2 sec) [ -13699.3692] [ 2545] [depth= 2] . ( 2 sec) [ -13646.3006] [ 2539] [depth= 7] . ( 2 sec) [ -12010.4216] [ 2536] [depth= 7] . ( 2 sec) [ -11913.0349] [ 2510] [depth= 8] . ( 2 sec) [ -11826.8925] [ 2489] [depth= 4] . ( 2 sec) [ -11677.4844] [ 2442] [depth= 6] . ( 2 sec) [ -11655.9489] [ 2488] [depth= 1] . ( 2 sec) [ -11427.2956] [ 2389] [depth= 2] . ( 2 sec) [ -11423.8834] [ 2395] [depth= 7] . ( 2 sec) [ -11180.4940] [ 2363] [depth= 1] . ( 2 sec) [ -10976.7548] [ 2344] [depth= 4] . ( 2 sec) [ -10892.3917] [ 2320] [depth= 1] . ( 2 sec) [ -10862.7564] [ 2320] [depth= 5] . ( 2 sec) [ -10800.6523] [ 2322] [depth= 1] . ( 2 sec) [ -10694.1701] [ 2287] [depth= 7] . ( 2 sec) [ -10645.3877] [ 2268] [depth= 5] . ( 2 sec) [ -10574.3143] [ 2264] [depth= 2] . ( 2 sec) [ -10376.7443] [ 2237] [depth= 9] . ( 3 sec) [ -10369.8610] [ 2242] [depth= 1] . ( 3 sec) [ -10158.1700] [ 2223] [depth= 12] . ( 3 sec) [ -10136.1992] [ 2223] [depth= 2] . ( 3 sec) [ -9791.3836] [ 2110] [depth= 13] . ( 3 sec) [ -9567.5714] [ 2037] [depth= 11] . ( 3 sec) [ -9560.5750] [ 2034] [depth= 1] . ( 3 sec) [ -9542.7080] [ 2043] [depth= 1] . ( 3 sec) [ -9393.4433] [ 2002] [depth= 9] . ( 3 sec) [ -9388.6936] [ 2001] [depth= 1] . ( 3 sec) [ -9309.5079] [ 1952] [depth= 1] . ( 3 sec) [ -9160.2543] [ 1896] [depth= 6] . ( 3 sec) [ -9159.9662] [ 1896] [depth= 1] . ( 3 sec) [ -9140.0833] [ 1892] [depth= 1] . ( 3 sec) [ -9019.1785] [ 1849] [depth= 6] . ( 3 sec) [ -8954.1047] [ 1833] [depth= 5] . ( 3 sec) [ -8905.8200] [ 1820] [depth= 1] . ( 3 sec) [ -8850.6841] [ 1803] [depth= 1] . ( 3 sec) [ -8790.8849] [ 1799] [depth= 1] . ( 3 sec) [ -8779.0937] [ 1796] [depth= 1] . ( 3 sec) [ -8776.4149] [ 1795] [depth= 1] . ( 4 sec) [ -8765.6607] [ 1796] [depth= 3] . ( 4 sec) [ -8756.5659] [ 1807] [depth= 1] . ( 4 sec) [ -8738.1335] [ 1803] [depth= 1] . ( 4 sec) [ -8736.9517] [ 1802] [depth= 2] . ( 4 sec) [ -8676.3956] [ 1791] [depth= 1] . ( 4 sec) [ -8675.3261] [ 1793] [depth= 1] . ( 4 sec) [ -8472.6944] [ 1759] [depth= 6] . ( 4 sec) [ -8457.1167] [ 1758] [depth= 4] . ( 4 sec) [ -8447.9351] [ 1751] [depth= 1] . ( 4 sec) [ -8442.7117] [ 1749] [depth= 1] . ( 4 sec) [ -8441.3594] [ 1750] [depth= 1] . ( 4 sec) [ -8364.1571] [ 1746] [depth= 1] . ( 4 sec) [ -8286.7813] [ 1739] [depth= 1] . ( 4 sec) [ -8252.7836] [ 1709] [depth= 1] . ( 4 sec) [ -8224.0185] [ 1709] [depth= 1] . ( 5 sec) [ -8172.9954] [ 1699] [depth= 1] . ( 5 sec) [ -8113.1823] [ 1669] [depth= 1] . ( 5 sec) [ -7904.1603] [Branch lengths ] . ( 6 sec) [ -7900.5010] [GTR parameters ] . ( 6 sec) [ -7871.0755] [Alpha ][ 0.895430] . ( 6 sec) [ -7862.3579] [ 1668] [depth= 1] . ( 6 sec) [ -7840.1421] [ 1646] [depth= 2] . ( 6 sec) [ -7836.3028] [ 1644] [depth= 1] . ( 6 sec) [ -7767.7749] [ 1623] [depth= 1] . ( 6 sec) [ -7765.7909] [ 1622] [depth= 1] . ( 6 sec) [ -7762.1491] [ 1619] [depth= 2] . ( 6 sec) [ -7747.4950] [ 1614] [depth= 2] . ( 6 sec) [ -7731.1738] [ 1604] [depth= 1] . ( 7 sec) [ -7731.1389] [ 1604] [depth= 1] . ( 7 sec) [ -7581.6897] [ 1504] [depth= 8] . ( 8 sec) [ -7581.1545] [ 1502] [depth= 1] . ( 8 sec) [ -7552.7154] [ 1493] [depth= 2] . ( 8 sec) [ -7552.4747] [ 1494] [depth= 1] . ( 8 sec) [ -7551.7656] [ 1495] [depth= 1] . ( 8 sec) [ -7551.4386] [ 1495] [depth= 1] . ( 8 sec) [ -7549.5892] [ 1495] [depth= 1] . ( 9 sec) [ -7548.6016] [ 1497] [depth= 2] . ( 9 sec) [ -7547.7817] [ 1495] [depth= 1] . ( 9 sec) [ -7521.0531] [Branch lengths ] . ( 10 sec) [ -7520.9664] [GTR parameters ] . ( 10 sec) [ -7519.5161] [Alpha ][ 1.034924] . ( 10 sec) [ -7519.1224] [ 1494] [depth= 1] . ( 10 sec) [ -7519.1065] [ 1494] [depth= 1] . ( 12 sec) [ -7518.9004] [ 1494] [depth= 1] . ( 13 sec) [ -7514.8763] [Branch lengths ] . ( 14 sec) [ -7514.8752] [GTR parameters ] . ( 14 sec) [ -7514.8726] [Alpha ][ 1.041412] . ( 18 sec) [ -7514.7831] [Branch lengths ] . ( 39 sec) [ -7514.7793] [Branch lengths ] . ( 39 sec) [ -7514.7793] [Topology ] . ( 39 sec) [ -7514.7791] [Topology ] . ( 40 sec) [ -7514.7790] [GTR parameters ] . ( 40 sec) [ -7514.7789] [Alpha ][ 1.039989] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -7514.5422] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7514.542160. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14460.7450] [GTR parameters ] . ( 1 sec) [ -14245.1908] [Alpha ][ 0.500960] . ( 1 sec) [ -14161.1924] [ 3044] [depth= 8] . ( 1 sec) [ -13699.6703] [ 2994] [depth= 8] . ( 1 sec) [ -13612.9037] [ 2992] [depth= 3] . ( 1 sec) [ -13604.2664] [ 2991] [depth= 3] . ( 1 sec) [ -13577.7230] [ 2974] [depth= 8] . ( 1 sec) [ -13559.3150] [ 2972] [depth= 2] . ( 1 sec) [ -13116.2897] [ 2871] [depth= 13] . ( 1 sec) [ -12998.9471] [ 2864] [depth= 2] . ( 1 sec) [ -12856.8221] [ 2829] [depth= 1] . ( 1 sec) [ -12730.2405] [ 2799] [depth= 6] . ( 1 sec) [ -12378.1284] [ 2731] [depth= 6] . ( 1 sec) [ -12146.1473] [ 2720] [depth= 7] . ( 1 sec) [ -12079.9297] [ 2710] [depth= 2] . ( 1 sec) [ -12079.0934] [ 2711] [depth= 2] . ( 1 sec) [ -12005.4249] [ 2709] [depth= 1] . ( 1 sec) [ -11749.4425] [ 2702] [depth= 11] . ( 1 sec) [ -11736.6601] [ 2694] [depth= 2] . ( 1 sec) [ -11676.2970] [ 2695] [depth= 1] . ( 1 sec) [ -11569.1149] [ 2691] [depth= 5] . ( 2 sec) [ -11374.2445] [ 2653] [depth= 3] . ( 2 sec) [ -11099.9557] [ 2538] [depth= 10] . ( 2 sec) [ -11086.8552] [ 2500] [depth= 1] . ( 2 sec) [ -11062.7721] [ 2499] [depth= 3] . ( 2 sec) [ -11052.7954] [ 2458] [depth= 7] . ( 2 sec) [ -10991.4342] [ 2457] [depth= 1] . ( 2 sec) [ -10950.9501] [ 2436] [depth= 8] . ( 2 sec) [ -10708.7968] [ 2363] [depth= 7] . ( 2 sec) [ -10477.1915] [ 2346] [depth= 10] . ( 2 sec) [ -10251.6780] [ 2278] [depth= 1] . ( 2 sec) [ -10176.3072] [ 2251] [depth= 1] . ( 2 sec) [ -10051.5325] [ 2215] [depth= 5] . ( 2 sec) [ -10026.9338] [ 2213] [depth= 1] . ( 2 sec) [ -10026.8804] [ 2213] [depth= 1] . ( 2 sec) [ -10013.1097] [ 2206] [depth= 1] . ( 2 sec) [ -9901.4422] [ 2189] [depth= 7] . ( 2 sec) [ -9896.7281] [ 2188] [depth= 2] . ( 2 sec) [ -9844.7548] [ 2136] [depth= 6] . ( 2 sec) [ -9805.6836] [ 2119] [depth= 1] . ( 2 sec) [ -9554.5689] [ 2025] [depth= 10] . ( 2 sec) [ -9553.2669] [ 2024] [depth= 1] . ( 3 sec) [ -9473.0580] [ 2012] [depth= 10] . ( 3 sec) [ -9402.1775] [ 1989] [depth= 8] . ( 3 sec) [ -9372.9037] [ 1987] [depth= 1] . ( 3 sec) [ -9208.7013] [ 1936] [depth= 6] . ( 3 sec) [ -9198.7145] [ 1936] [depth= 1] . ( 3 sec) [ -9197.4384] [ 1939] [depth= 2] . ( 3 sec) [ -9196.1566] [ 1937] [depth= 3] . ( 3 sec) [ -9183.3790] [ 1935] [depth= 1] . ( 3 sec) [ -9130.4207] [ 1912] [depth= 4] . ( 3 sec) [ -9083.0421] [ 1909] [depth= 3] . ( 3 sec) [ -8960.9941] [ 1888] [depth= 3] . ( 3 sec) [ -8890.8211] [ 1870] [depth= 1] . ( 3 sec) [ -8827.1789] [ 1857] [depth= 2] . ( 3 sec) [ -8823.8307] [ 1858] [depth= 1] . ( 3 sec) [ -8695.1423] [ 1826] [depth= 2] . ( 3 sec) [ -8660.1348] [ 1822] [depth= 7] . ( 3 sec) [ -8636.0167] [ 1822] [depth= 4] . ( 3 sec) [ -8484.6472] [ 1794] [depth= 4] . ( 3 sec) [ -8389.0862] [ 1747] [depth= 7] . ( 3 sec) [ -8351.1596] [ 1742] [depth= 2] . ( 4 sec) [ -8329.1153] [ 1734] [depth= 1] . ( 4 sec) [ -8326.6152] [ 1734] [depth= 1] . ( 4 sec) [ -8240.5124] [ 1707] [depth= 1] . ( 4 sec) [ -8216.7944] [ 1707] [depth= 1] . ( 4 sec) [ -8137.7294] [ 1667] [depth= 1] . ( 4 sec) [ -8055.8183] [ 1647] [depth= 2] . ( 4 sec) [ -8046.5520] [ 1649] [depth= 1] . ( 4 sec) [ -8040.7949] [ 1647] [depth= 1] . ( 4 sec) [ -8028.1346] [ 1639] [depth= 1] . ( 4 sec) [ -7990.0635] [ 1631] [depth= 1] . ( 4 sec) [ -7710.6099] [ 1514] [depth= 7] . ( 4 sec) [ -7709.6437] [ 1510] [depth= 2] . ( 4 sec) [ -7692.0486] [ 1498] [depth= 5] . ( 4 sec) [ -7689.7287] [ 1496] [depth= 3] . ( 4 sec) [ -7684.5447] [ 1495] [depth= 1] . ( 4 sec) [ -7684.0815] [ 1496] [depth= 1] . ( 4 sec) [ -7681.9542] [ 1495] [depth= 2] . ( 4 sec) [ -7681.0249] [ 1500] [depth= 1] . ( 4 sec) [ -7675.7346] [ 1500] [depth= 1] . ( 4 sec) [ -7650.7824] [ 1499] [depth= 1] . ( 5 sec) [ -7566.3937] [Branch lengths ] . ( 5 sec) [ -7564.4417] [GTR parameters ] . ( 5 sec) [ -7528.8215] [Alpha ][ 1.000835] . ( 6 sec) [ -7524.4345] [ 1493] [depth= 1] . ( 6 sec) [ -7524.2033] [ 1494] [depth= 1] . ( 6 sec) [ -7524.1885] [ 1496] [depth= 1] . ( 6 sec) [ -7523.6595] [ 1494] [depth= 1] . ( 6 sec) [ -7523.5685] [ 1495] [depth= 1] . ( 6 sec) [ -7523.4463] [ 1495] [depth= 1] . ( 6 sec) [ -7520.5916] [ 1494] [depth= 1] . ( 6 sec) [ -7519.8339] [ 1494] [depth= 1] . ( 7 sec) [ -7519.5799] [ 1494] [depth= 1] . ( 8 sec) [ -7518.8989] [ 1496] [depth= 1] . ( 9 sec) [ -7515.1138] [Branch lengths ] . ( 10 sec) [ -7515.0343] [GTR parameters ] . ( 10 sec) [ -7514.9698] [Alpha ][ 1.032441] . ( 14 sec) [ -7514.6944] [Branch lengths ] . ( 34 sec) [ -7514.5949] [ 1494] [depth= 1] . ( 35 sec) [ -7514.5425] [Branch lengths ] . ( 35 sec) [ -7514.5417] [GTR parameters ] . ( 35 sec) [ -7514.5377] [Alpha ][ 1.040530] . ( 35 sec) [ -7514.5377] [Topology ] . ( 36 sec) [ -7514.5343] [Topology ] . ( 37 sec) [ -7514.5331] [Topology ] . ( 37 sec) [ -7514.5326] [Topology ] . ( 37 sec) [ -7514.5326] [GTR parameters ] . ( 37 sec) [ -7514.5326] [Alpha ][ 1.040530] . ( 37 sec) [ -7514.5326] [Topology ] . ( 38 sec) [ -7514.5323] [Topology ] . ( 38 sec) [ -7514.5323] [GTR parameters ] . ( 38 sec) [ -7514.5323] [Alpha ][ 1.040530] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7514.532321. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -14399.1109] [GTR parameters ] . ( 1 sec) [ -14191.7936] [Alpha ][ 0.500960] . ( 1 sec) [ -13972.6677] [ 3030] [depth= 10] . ( 1 sec) [ -13787.1903] [ 2973] [depth= 9] . ( 1 sec) [ -13675.2379] [ 2963] [depth= 7] . ( 1 sec) [ -13663.7037] [ 2918] [depth= 1] . ( 1 sec) [ -13624.6655] [ 2908] [depth= 9] . ( 1 sec) [ -13592.4848] [ 2896] [depth= 2] . ( 1 sec) [ -13319.7657] [ 2893] [depth= 5] . ( 1 sec) [ -13269.1075] [ 2865] [depth= 6] . ( 1 sec) [ -13223.3452] [ 2863] [depth= 1] . ( 1 sec) [ -13207.3133] [ 2859] [depth= 3] . ( 1 sec) [ -13028.4772] [ 2858] [depth= 2] . ( 1 sec) [ -12896.9400] [ 2838] [depth= 5] . ( 1 sec) [ -12853.7911] [ 2826] [depth= 6] . ( 1 sec) [ -12793.0021] [ 2819] [depth= 4] . ( 1 sec) [ -12647.8221] [ 2799] [depth= 3] . ( 1 sec) [ -12513.9674] [ 2784] [depth= 13] . ( 2 sec) [ -12475.8761] [ 2784] [depth= 1] . ( 2 sec) [ -12305.8350] [ 2706] [depth= 6] . ( 2 sec) [ -11946.8271] [ 2638] [depth= 3] . ( 2 sec) [ -11940.1671] [ 2633] [depth= 3] . ( 2 sec) [ -11651.5815] [ 2620] [depth= 8] . ( 2 sec) [ -11595.5450] [ 2601] [depth= 1] . ( 2 sec) [ -11547.7419] [ 2600] [depth= 2] . ( 2 sec) [ -11507.4882] [ 2573] [depth= 1] . ( 2 sec) [ -11373.6453] [ 2547] [depth= 15] . ( 2 sec) [ -11164.9672] [ 2470] [depth= 8] . ( 2 sec) [ -11031.3537] [ 2442] [depth= 2] . ( 2 sec) [ -11024.3757] [ 2438] [depth= 1] . ( 2 sec) [ -10772.9078] [ 2424] [depth= 8] . ( 2 sec) [ -10399.7051] [ 2282] [depth= 8] . ( 2 sec) [ -10347.1954] [ 2261] [depth= 5] . ( 2 sec) [ -10272.8331] [ 2262] [depth= 1] . ( 2 sec) [ -10102.3887] [ 2257] [depth= 13] . ( 2 sec) [ -9940.6781] [ 2180] [depth= 8] . ( 2 sec) [ -9873.0941] [ 2160] [depth= 1] . ( 2 sec) [ -9589.8479] [ 2050] [depth= 15] . ( 2 sec) [ -9398.2229] [ 1984] [depth= 4] . ( 2 sec) [ -9380.7289] [ 1988] [depth= 1] . ( 3 sec) [ -9361.6688] [ 1986] [depth= 4] . ( 3 sec) [ -9317.4844] [ 1979] [depth= 3] . ( 3 sec) [ -9271.2740] [ 1965] [depth= 5] . ( 3 sec) [ -9017.7722] [ 1879] [depth= 2] . ( 3 sec) [ -8975.3224] [ 1861] [depth= 1] . ( 3 sec) [ -8876.7533] [ 1848] [depth= 2] . ( 3 sec) [ -8689.3951] [ 1842] [depth= 3] . ( 3 sec) [ -8680.2507] [ 1841] [depth= 4] . ( 3 sec) [ -8598.4543] [ 1816] [depth= 1] . ( 3 sec) [ -8590.8443] [ 1820] [depth= 3] . ( 3 sec) [ -8579.7633] [ 1814] [depth= 1] . ( 3 sec) [ -8551.9888] [ 1809] [depth= 1] . ( 3 sec) [ -8509.6882] [ 1792] [depth= 1] . ( 3 sec) [ -8416.6078] [ 1767] [depth= 1] . ( 3 sec) [ -8306.4081] [ 1733] [depth= 1] . ( 3 sec) [ -8294.2530] [ 1733] [depth= 1] . ( 3 sec) [ -8205.7761] [ 1705] [depth= 5] . ( 3 sec) [ -8171.7940] [ 1697] [depth= 4] . ( 4 sec) [ -8171.7231] [ 1699] [depth= 1] . ( 4 sec) [ -8161.1456] [ 1688] [depth= 3] . ( 4 sec) [ -8118.9538] [ 1665] [depth= 1] . ( 4 sec) [ -8019.7880] [ 1621] [depth= 1] . ( 4 sec) [ -7909.4756] [ 1572] [depth= 6] . ( 4 sec) [ -7907.7470] [ 1572] [depth= 1] . ( 4 sec) [ -7884.0713] [ 1568] [depth= 1] . ( 4 sec) [ -7856.1093] [ 1554] [depth= 1] . ( 4 sec) [ -7798.0986] [ 1514] [depth= 1] . ( 4 sec) [ -7796.8064] [ 1512] [depth= 2] . ( 4 sec) [ -7768.3506] [ 1524] [depth= 1] . ( 4 sec) [ -7735.2017] [ 1513] [depth= 4] . ( 4 sec) [ -7600.6780] [Branch lengths ] . ( 5 sec) [ -7598.2118] [GTR parameters ] . ( 5 sec) [ -7559.7305] [Alpha ][ 1.000113] . ( 5 sec) [ -7557.6008] [ 1514] [depth= 2] . ( 5 sec) [ -7557.0584] [ 1514] [depth= 1] . ( 5 sec) [ -7541.1613] [ 1502] [depth= 1] . ( 6 sec) [ -7541.1120] [ 1503] [depth= 2] . ( 6 sec) [ -7538.6965] [ 1502] [depth= 1] . ( 6 sec) [ -7538.6651] [ 1503] [depth= 1] . ( 6 sec) [ -7538.4751] [ 1504] [depth= 1] . ( 6 sec) [ -7538.4430] [ 1504] [depth= 1] . ( 6 sec) [ -7533.7004] [ 1498] [depth= 2] . ( 6 sec) [ -7533.0724] [ 1497] [depth= 2] . ( 6 sec) [ -7533.0214] [ 1494] [depth= 1] . ( 6 sec) [ -7531.9266] [ 1493] [depth= 1] . ( 7 sec) [ -7531.8943] [ 1496] [depth= 1] . ( 7 sec) [ -7531.1081] [ 1495] [depth= 1] . ( 7 sec) [ -7531.0854] [ 1496] [depth= 1] . ( 7 sec) [ -7528.1092] [ 1498] [depth= 1] . ( 7 sec) [ -7525.0194] [ 1495] [depth= 1] . ( 8 sec) [ -7523.5704] [ 1494] [depth= 1] . ( 8 sec) [ -7522.7092] [ 1496] [depth= 2] . ( 9 sec) [ -7515.1026] [Branch lengths ] . ( 9 sec) [ -7514.9087] [GTR parameters ] . ( 9 sec) [ -7514.8219] [Alpha ][ 1.036693] . ( 13 sec) [ -7514.6521] [Branch lengths ] . ( 35 sec) [ -7514.6462] [Branch lengths ] . ( 35 sec) [ -7514.6462] [Topology ] . ( 35 sec) [ -7514.6460] [Topology ] . ( 35 sec) [ -7514.6455] [GTR parameters ] . ( 36 sec) [ -7514.6451] [Alpha ][ 1.039352] . ( 36 sec) [ -7514.6451] [Topology ] . ( 36 sec) [ -7514.6450] [Topology ] . ( 36 sec) [ -7514.6450] [GTR parameters ] . ( 36 sec) [ -7514.6450] [Alpha ][ 1.039352] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -7514.5336] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7514.533616. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15099.7226] [GTR parameters ] . ( 1 sec) [ -14840.4156] [Alpha ][ 0.500960] . ( 1 sec) [ -14477.7582] [ 3074] [depth= 9] . ( 1 sec) [ -14200.5926] [ 3023] [depth= 11] . ( 1 sec) [ -14097.7109] [ 3007] [depth= 6] . ( 1 sec) [ -14087.3788] [ 3006] [depth= 3] . ( 1 sec) [ -13987.2643] [ 2961] [depth= 7] . ( 1 sec) [ -13953.2649] [ 2965] [depth= 1] . ( 1 sec) [ -13944.2003] [ 2954] [depth= 7] . ( 1 sec) [ -13909.7200] [ 2938] [depth= 5] . ( 1 sec) [ -13906.3052] [ 2928] [depth= 6] . ( 2 sec) [ -13742.3778] [ 2876] [depth= 1] . ( 2 sec) [ -13639.4443] [ 2860] [depth= 13] . ( 2 sec) [ -13486.6447] [ 2822] [depth= 10] . ( 2 sec) [ -13373.6436] [ 2807] [depth= 7] . ( 2 sec) [ -13288.6911] [ 2805] [depth= 3] . ( 2 sec) [ -13243.1961] [ 2801] [depth= 1] . ( 2 sec) [ -13232.4375] [ 2801] [depth= 3] . ( 2 sec) [ -13202.8369] [ 2795] [depth= 1] . ( 2 sec) [ -13186.2675] [ 2792] [depth= 6] . ( 2 sec) [ -13176.5943] [ 2790] [depth= 1] . ( 2 sec) [ -13102.0597] [ 2778] [depth= 9] . ( 2 sec) [ -13035.6956] [ 2766] [depth= 3] . ( 2 sec) [ -12872.7674] [ 2732] [depth= 2] . ( 2 sec) [ -12745.5462] [ 2692] [depth= 5] . ( 2 sec) [ -12712.6881] [ 2665] [depth= 1] . ( 2 sec) [ -12662.2513] [ 2662] [depth= 5] . ( 2 sec) [ -12560.3538] [ 2635] [depth= 1] . ( 2 sec) [ -12483.1638] [ 2616] [depth= 8] . ( 2 sec) [ -12423.9798] [ 2600] [depth= 3] . ( 2 sec) [ -12228.9616] [ 2577] [depth= 4] . ( 2 sec) [ -12096.4728] [ 2448] [depth= 2] . ( 2 sec) [ -11887.4054] [ 2393] [depth= 5] . ( 3 sec) [ -11752.9530] [ 2385] [depth= 8] . ( 3 sec) [ -11683.5723] [ 2380] [depth= 3] . ( 3 sec) [ -11626.3280] [ 2354] [depth= 1] . ( 3 sec) [ -11581.2999] [ 2351] [depth= 10] . ( 3 sec) [ -11277.2633] [ 2347] [depth= 1] . ( 3 sec) [ -11272.2555] [ 2347] [depth= 1] . ( 3 sec) [ -10914.0488] [ 2230] [depth= 13] . ( 3 sec) [ -10913.7208] [ 2212] [depth= 2] . ( 3 sec) [ -10870.3882] [ 2209] [depth= 6] . ( 3 sec) [ -10843.4258] [ 2220] [depth= 1] . ( 3 sec) [ -10709.2365] [ 2135] [depth= 3] . ( 3 sec) [ -10315.7700] [ 2122] [depth= 9] . ( 3 sec) [ -9835.2626] [ 1976] [depth= 9] . ( 3 sec) [ -9780.2138] [ 1958] [depth= 2] . ( 3 sec) [ -9750.6387] [ 1952] [depth= 4] . ( 3 sec) [ -9711.7517] [ 1945] [depth= 4] . ( 3 sec) [ -9706.1035] [ 1946] [depth= 1] . ( 3 sec) [ -9689.9349] [ 1956] [depth= 1] . ( 3 sec) [ -9524.4261] [ 1947] [depth= 7] . ( 3 sec) [ -9494.9123] [ 1924] [depth= 3] . ( 3 sec) [ -9407.7122] [ 1916] [depth= 2] . ( 4 sec) [ -9323.3887] [ 1905] [depth= 3] . ( 4 sec) [ -9085.4033] [ 1858] [depth= 11] . ( 4 sec) [ -9077.3300] [ 1857] [depth= 1] . ( 4 sec) [ -9049.4177] [ 1855] [depth= 1] . ( 4 sec) [ -9023.1599] [ 1837] [depth= 1] . ( 4 sec) [ -8783.7606] [ 1823] [depth= 4] . ( 4 sec) [ -8632.8781] [ 1811] [depth= 1] . ( 4 sec) [ -8598.7898] [ 1810] [depth= 1] . ( 4 sec) [ -8584.9622] [ 1809] [depth= 1] . ( 4 sec) [ -8519.5864] [ 1781] [depth= 1] . ( 4 sec) [ -8448.4821] [ 1759] [depth= 1] . ( 4 sec) [ -8331.9106] [ 1664] [depth= 5] . ( 4 sec) [ -8316.1252] [ 1656] [depth= 1] . ( 4 sec) [ -8259.7243] [ 1658] [depth= 1] . ( 4 sec) [ -8220.1703] [ 1645] [depth= 4] . ( 4 sec) [ -8218.8444] [ 1646] [depth= 1] . ( 4 sec) [ -8199.4252] [ 1645] [depth= 9] . ( 4 sec) [ -8159.4219] [ 1645] [depth= 2] . ( 4 sec) [ -8145.5412] [ 1634] [depth= 1] . ( 5 sec) [ -8143.3966] [ 1632] [depth= 1] . ( 5 sec) [ -8128.1337] [ 1626] [depth= 1] . ( 5 sec) [ -7976.1561] [ 1568] [depth= 2] . ( 5 sec) [ -7780.3125] [Branch lengths ] . ( 6 sec) [ -7778.8521] [GTR parameters ] . ( 6 sec) [ -7745.8370] [Alpha ][ 0.955909] . ( 6 sec) [ -7727.8351] [ 1577] [depth= 7] . ( 6 sec) [ -7684.8680] [ 1551] [depth= 2] . ( 6 sec) [ -7684.7904] [ 1550] [depth= 1] . ( 6 sec) [ -7667.8538] [ 1549] [depth= 4] . ( 6 sec) [ -7667.3236] [ 1553] [depth= 1] . ( 7 sec) [ -7658.8894] [ 1549] [depth= 1] . ( 7 sec) [ -7643.7163] [ 1541] [depth= 1] . ( 7 sec) [ -7637.0850] [ 1535] [depth= 4] . ( 8 sec) [ -7636.4071] [ 1535] [depth= 1] . ( 8 sec) [ -7633.7706] [ 1536] [depth= 2] . ( 8 sec) [ -7633.7088] [ 1536] [depth= 1] . ( 8 sec) [ -7544.5293] [ 1504] [depth= 3] . ( 8 sec) [ -7535.1051] [ 1494] [depth= 1] . ( 8 sec) [ -7533.8896] [ 1493] [depth= 1] . ( 9 sec) [ -7531.4603] [ 1492] [depth= 1] . ( 9 sec) [ -7530.3379] [ 1494] [depth= 1] . ( 9 sec) [ -7515.7689] [Branch lengths ] . ( 10 sec) [ -7515.5685] [GTR parameters ] . ( 10 sec) [ -7515.1265] [Alpha ][ 1.036611] . ( 14 sec) [ -7514.5906] [Branch lengths ] . ( 35 sec) [ -7514.5408] [Branch lengths ] . ( 35 sec) [ -7514.5408] [Topology ] . ( 36 sec) [ -7514.5367] [Topology ] . ( 37 sec) [ -7514.5353] [Topology ] . ( 37 sec) [ -7514.5347] [Topology ] . ( 38 sec) [ -7514.5341] [GTR parameters ] . ( 38 sec) [ -7514.5329] [Alpha ][ 1.040933] . ( 38 sec) [ -7514.5329] [Topology ] . ( 38 sec) [ -7514.5326] [Topology ] . ( 39 sec) [ -7514.5326] [GTR parameters ] . ( 39 sec) [ -7514.5326] [Alpha ][ 1.040933] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7514.532568. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7561.691620 . ( 1 sec) [ -7552.1318] [GTR parameters ] . ( 1 sec) [ -7552.1260] [Alpha ][ 0.990008] . ( 1 sec) [ -7552.1260] [Topology ] . ( 2 sec) [ -7524.8516] [Topology ] . ( 2 sec) [ -7518.9915] [Topology ] . ( 3 sec) [ -7516.0097] [Topology ] . ( 4 sec) [ -7515.2027] [Topology ] . ( 5 sec) [ -7514.9296] [Topology ] . ( 5 sec) [ -7514.8573] [Topology ] . ( 6 sec) [ -7514.8285] [Topology ] . ( 7 sec) [ -7514.8156] [Topology ] . ( 8 sec) [ -7514.8095] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7514.806675 . ( 14 sec) [ -7514.7032] [GTR parameters ] . ( 14 sec) [ -7514.5454] [Alpha ][ 1.039178] . ( 14 sec) [ -7514.5454] [Topology ] . ( 15 sec) [ -7514.5374] [Topology ] . ( 16 sec) [ -7514.5347] [Topology ] . ( 17 sec) [ -7514.5335] [Topology ] . ( 17 sec) [ -7514.5329] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7514.532913 . ( 23 sec) [ -7514.5327] [GTR parameters ] . ( 23 sec) [ -7514.5325] [Alpha ][ 1.040837] . ( 23 sec) [ -7514.5325] [Topology ] . ( 24 sec) [ -7514.5323] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 35 sec) [ -7552.1318] [GTR parameters ] . ( 35 sec) [ -7552.1260] [Alpha ][ 0.990008] . ( 36 sec) [ -7549.9773] [ 1498] [depth= 1] . ( 36 sec) [ -7548.8446] [ 1498] [depth= 1] . ( 36 sec) [ -7547.7971] [ 1496] [depth= 1] . ( 36 sec) [ -7547.5127] [ 1498] [depth= 1] . ( 36 sec) [ -7545.4285] [ 1496] [depth= 1] . ( 37 sec) [ -7543.5265] [ 1495] [depth= 1] . ( 37 sec) [ -7542.9340] [ 1496] [depth= 1] . ( 37 sec) [ -7541.6378] [ 1498] [depth= 2] . ( 37 sec) [ -7541.3508] [ 1498] [depth= 1] . ( 37 sec) [ -7541.1682] [ 1497] [depth= 1] . ( 38 sec) [ -7540.5468] [ 1497] [depth= 3] . ( 38 sec) [ -7539.6281] [ 1496] [depth= 2] . ( 38 sec) [ -7538.9150] [ 1496] [depth= 1] . ( 38 sec) [ -7533.4348] [ 1494] [depth= 3] . ( 39 sec) [ -7516.1541] [Branch lengths ] . ( 39 sec) [ -7516.0673] [GTR parameters ] . ( 39 sec) [ -7515.9652] [Alpha ][ 1.029534] . ( 43 sec) [ -7514.6971] [Branch lengths ] . ( 64 sec) [ -7514.5614] [Branch lengths ] . ( 64 sec) [ -7514.5614] [Topology ] . ( 65 sec) [ -7514.5491] [Topology ] . ( 66 sec) [ -7514.5450] [Topology ] . ( 67 sec) [ -7514.5431] [Topology ] . ( 67 sec) [ -7514.5422] [Topology ] . ( 67 sec) [ -7514.5411] [GTR parameters ] . ( 68 sec) [ -7514.5334] [Alpha ][ 1.040890] . ( 68 sec) [ -7514.5334] [Topology ] . ( 68 sec) [ -7514.5326] [Topology ] . ( 68 sec) [ -7514.5326] [GTR parameters ] . ( 68 sec) [ -7514.5326] [Alpha ][ 1.040890] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7514.532262 . Log likelihood obtained after SPR moves : -7514.532624 . Log likelihood of the current tree: -7514.532262. . Printing the most likely tree in file 'data83.phy_phyml_tree.txt'... . Best log likelihood : -7514.532262 . Time used 0h1m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo