.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data90.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... . 399 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)... . ( 0 sec) [ -17745.5950] [GTR parameters ] . ( 0 sec) [ -17381.2513] [Alpha ][ 0.500960] . ( 1 sec) [ -16694.2646] [ 3509] [depth= 8] . ( 1 sec) [ -16464.9933] [ 3508] [depth= 6] . ( 1 sec) [ -16054.2306] [ 3503] [depth= 4] . ( 1 sec) [ -15980.7035] [ 3491] [depth= 6] . ( 1 sec) [ -15911.2898] [ 3445] [depth= 4] . ( 1 sec) [ -15466.2324] [ 3434] [depth= 7] . ( 1 sec) [ -15273.0898] [ 3415] [depth= 3] . ( 1 sec) [ -15224.1934] [ 3416] [depth= 1] . ( 1 sec) [ -15005.3697] [ 3378] [depth= 8] . ( 1 sec) [ -14691.4450] [ 3263] [depth= 7] . ( 1 sec) [ -14426.1325] [ 3163] [depth= 8] . ( 1 sec) [ -14292.0425] [ 3118] [depth= 2] . ( 1 sec) [ -13936.5212] [ 3022] [depth= 5] . ( 1 sec) [ -13930.0381] [ 3011] [depth= 1] . ( 1 sec) [ -13841.7351] [ 2999] [depth= 3] . ( 1 sec) [ -13494.3997] [ 2934] [depth= 8] . ( 1 sec) [ -13394.3902] [ 2927] [depth= 2] . ( 1 sec) [ -13349.3432] [ 2927] [depth= 2] . ( 1 sec) [ -13107.3847] [ 2919] [depth= 2] . ( 1 sec) [ -12980.2204] [ 2887] [depth= 22] . ( 1 sec) [ -12878.3403] [ 2792] [depth= 3] . ( 1 sec) [ -12730.2746] [ 2788] [depth= 1] . ( 1 sec) [ -12592.1762] [ 2679] [depth= 3] . ( 1 sec) [ -12477.0272] [ 2632] [depth= 4] . ( 1 sec) [ -12281.7548] [ 2626] [depth= 2] . ( 2 sec) [ -12154.8917] [ 2625] [depth= 3] . ( 2 sec) [ -11884.3736] [ 2625] [depth= 11] . ( 2 sec) [ -11852.1159] [ 2620] [depth= 5] . ( 2 sec) [ -11529.8934] [ 2540] [depth= 10] . ( 2 sec) [ -11421.6352] [ 2506] [depth= 1] . ( 2 sec) [ -11336.4903] [ 2497] [depth= 14] . ( 2 sec) [ -11329.2696] [ 2496] [depth= 1] . ( 2 sec) [ -11328.4620] [ 2496] [depth= 1] . ( 2 sec) [ -11145.9499] [ 2447] [depth= 2] . ( 2 sec) [ -10870.2307] [ 2398] [depth= 1] . ( 2 sec) [ -10745.7540] [ 2316] [depth= 8] . ( 2 sec) [ -10656.4321] [ 2283] [depth= 3] . ( 2 sec) [ -10553.4734] [ 2241] [depth= 10] . ( 2 sec) [ -10467.8615] [ 2244] [depth= 1] . ( 2 sec) [ -10441.8248] [ 2243] [depth= 1] . ( 2 sec) [ -10257.0241] [ 2220] [depth= 5] . ( 2 sec) [ -10205.8389] [ 2250] [depth= 4] . ( 2 sec) [ -10080.6134] [ 2199] [depth= 8] . ( 2 sec) [ -10069.4302] [ 2193] [depth= 1] . ( 2 sec) [ -10054.6341] [ 2193] [depth= 1] . ( 2 sec) [ -9747.7073] [ 2143] [depth= 2] . ( 2 sec) [ -9656.6627] [ 2137] [depth= 1] . ( 3 sec) [ -9639.6644] [ 2138] [depth= 2] . ( 3 sec) [ -9445.5454] [ 2133] [depth= 2] . ( 3 sec) [ -9396.3793] [ 2115] [depth= 9] . ( 3 sec) [ -9367.7996] [ 2110] [depth= 1] . ( 3 sec) [ -9315.3764] [ 2089] [depth= 7] . ( 3 sec) [ -9180.9633] [ 2038] [depth= 1] . ( 3 sec) [ -9127.2977] [ 2025] [depth= 1] . ( 3 sec) [ -9120.0828] [ 2023] [depth= 1] . ( 3 sec) [ -9070.2002] [ 2024] [depth= 1] . ( 3 sec) [ -9051.2934] [ 2015] [depth= 2] . ( 3 sec) [ -9049.6961] [ 2015] [depth= 1] . ( 3 sec) [ -9046.9489] [ 2013] [depth= 2] . ( 3 sec) [ -9044.9416] [ 2012] [depth= 1] . ( 3 sec) [ -8954.1499] [ 1975] [depth= 2] . ( 3 sec) [ -8900.4110] [ 1911] [depth= 7] . ( 3 sec) [ -8737.2990] [ 1887] [depth= 4] . ( 3 sec) [ -8723.4072] [ 1881] [depth= 1] . ( 3 sec) [ -8717.9085] [ 1881] [depth= 1] . ( 3 sec) [ -8672.8861] [ 1863] [depth= 1] . ( 3 sec) [ -8670.8471] [ 1863] [depth= 1] . ( 3 sec) [ -8607.0832] [ 1836] [depth= 4] . ( 4 sec) [ -8600.9167] [ 1835] [depth= 1] . ( 4 sec) [ -8559.1354] [ 1824] [depth= 5] . ( 4 sec) [ -8555.9799] [ 1822] [depth= 1] . ( 4 sec) [ -8555.2493] [ 1822] [depth= 1] . ( 4 sec) [ -8428.7824] [ 1798] [depth= 8] . ( 4 sec) [ -8428.7312] [ 1797] [depth= 1] . ( 4 sec) [ -8414.2389] [ 1799] [depth= 1] . ( 4 sec) [ -8245.5678] [ 1750] [depth= 4] . ( 4 sec) [ -8237.0163] [ 1755] [depth= 1] . ( 4 sec) [ -8148.6125] [ 1695] [depth= 4] . ( 4 sec) [ -8137.5759] [ 1677] [depth= 2] . ( 4 sec) [ -8093.4101] [ 1670] [depth= 2] . ( 4 sec) [ -8093.2647] [ 1671] [depth= 2] . ( 4 sec) [ -8068.6348] [ 1663] [depth= 1] . ( 4 sec) [ -8040.7120] [ 1657] [depth= 1] . ( 4 sec) [ -8002.2226] [ 1640] [depth= 5] . ( 4 sec) [ -7998.3998] [ 1638] [depth= 1] . ( 4 sec) [ -7998.1367] [ 1638] [depth= 1] . ( 4 sec) [ -7940.9645] [ 1601] [depth= 1] . ( 5 sec) [ -7833.4556] [Branch lengths ] . ( 5 sec) [ -7825.7068] [GTR parameters ] . ( 5 sec) [ -7797.3151] [Alpha ][ 0.907865] . ( 6 sec) [ -7797.2994] [ 1601] [depth= 1] . ( 6 sec) [ -7797.2371] [ 1600] [depth= 1] . ( 6 sec) [ -7795.9577] [ 1600] [depth= 1] . ( 6 sec) [ -7791.0237] [ 1599] [depth= 2] . ( 6 sec) [ -7787.7325] [ 1598] [depth= 1] . ( 6 sec) [ -7782.0762] [ 1592] [depth= 1] . ( 6 sec) [ -7781.9270] [ 1592] [depth= 1] . ( 6 sec) [ -7781.0248] [ 1590] [depth= 2] . ( 7 sec) [ -7780.5885] [ 1589] [depth= 1] . ( 7 sec) [ -7767.2103] [ 1575] [depth= 2] . ( 7 sec) [ -7767.0560] [ 1578] [depth= 1] . ( 7 sec) [ -7764.5902] [ 1576] [depth= 2] . ( 7 sec) [ -7763.6352] [ 1576] [depth= 1] . ( 8 sec) [ -7761.9814] [ 1576] [depth= 1] . ( 8 sec) [ -7760.5886] [ 1573] [depth= 1] . ( 8 sec) [ -7757.4193] [ 1572] [depth= 1] . ( 8 sec) [ -7757.0726] [ 1572] [depth= 2] . ( 8 sec) [ -7756.9276] [ 1574] [depth= 1] . ( 8 sec) [ -7756.8024] [ 1575] [depth= 1] . ( 8 sec) [ -7756.5442] [ 1575] [depth= 1] . ( 9 sec) [ -7754.2985] [ 1577] [depth= 4] . ( 9 sec) [ -7744.7381] [Branch lengths ] . ( 10 sec) [ -7744.6728] [GTR parameters ] . ( 10 sec) [ -7744.1434] [Alpha ][ 0.988976] . ( 14 sec) [ -7743.6838] [ 1582] [depth= 1] . ( 15 sec) [ -7742.6902] [Branch lengths ] . ( 15 sec) [ -7742.6866] [GTR parameters ] . ( 15 sec) [ -7742.6830] [Alpha ][ 0.996047] . ( 15 sec) [ -7742.6551] [ 1577] [depth= 1] . ( 20 sec) [ -7742.4234] [Branch lengths ] . ( 20 sec) [ -7742.4232] [GTR parameters ] . ( 20 sec) [ -7742.4200] [Alpha ][ 1.002748] . ( 35 sec) [ -7742.3453] [ 1575] [depth= 1] . ( 42 sec) [ -7742.3076] [Branch lengths ] . ( 42 sec) [ -7742.3073] [GTR parameters ] . ( 42 sec) [ -7742.3070] [Alpha ][ 1.004776] . ( 42 sec) [ -7742.3070] [Topology ] . ( 43 sec) [ -7742.3048] [Topology ] . ( 44 sec) [ -7742.3041] [Topology ] . ( 44 sec) [ -7742.3041] [GTR parameters ] . ( 44 sec) [ -7742.3041] [Alpha ][ 1.004776] . ( 44 sec) [ -7742.3041] [Topology ] . ( 44 sec) [ -7742.3038] [Topology ] . ( 45 sec) [ -7742.3038] [GTR parameters ] . ( 45 sec) [ -7742.3038] [Alpha ][ 1.005781] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.303786. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18203.4110] [GTR parameters ] . ( 1 sec) [ -17819.4328] [Alpha ][ 0.500960] . ( 1 sec) [ -17750.6480] [ 3673] [depth= 1] . ( 1 sec) [ -17616.0434] [ 3641] [depth= 3] . ( 1 sec) [ -17593.6829] [ 3616] [depth= 2] . ( 1 sec) [ -17086.9027] [ 3594] [depth= 7] . ( 1 sec) [ -16961.6445] [ 3529] [depth= 1] . ( 1 sec) [ -16772.6063] [ 3504] [depth= 8] . ( 1 sec) [ -16736.6046] [ 3492] [depth= 1] . ( 1 sec) [ -16483.5790] [ 3489] [depth= 5] . ( 1 sec) [ -16209.5905] [ 3418] [depth= 1] . ( 1 sec) [ -15743.3953] [ 3407] [depth= 3] . ( 1 sec) [ -15700.8311] [ 3390] [depth= 3] . ( 1 sec) [ -15550.0375] [ 3384] [depth= 7] . ( 1 sec) [ -15539.8315] [ 3381] [depth= 1] . ( 1 sec) [ -15415.9992] [ 3378] [depth= 8] . ( 1 sec) [ -14416.0327] [ 3246] [depth= 11] . ( 1 sec) [ -14315.9700] [ 3218] [depth= 5] . ( 2 sec) [ -13856.0669] [ 3128] [depth= 20] . ( 2 sec) [ -13688.3007] [ 3124] [depth= 1] . ( 2 sec) [ -13447.6962] [ 3118] [depth= 1] . ( 2 sec) [ -13288.4455] [ 3088] [depth= 6] . ( 2 sec) [ -13286.5264] [ 3091] [depth= 1] . ( 2 sec) [ -13221.2458] [ 3075] [depth= 8] . ( 2 sec) [ -12989.9066] [ 2974] [depth= 8] . ( 2 sec) [ -12968.8390] [ 2976] [depth= 4] . ( 2 sec) [ -12814.6450] [ 2979] [depth= 8] . ( 2 sec) [ -12789.9354] [ 2985] [depth= 1] . ( 2 sec) [ -12513.2512] [ 2896] [depth= 11] . ( 2 sec) [ -12229.8193] [ 2815] [depth= 16] . ( 2 sec) [ -11779.0254] [ 2793] [depth= 17] . ( 2 sec) [ -11137.8009] [ 2708] [depth= 1] . ( 2 sec) [ -11043.2963] [ 2683] [depth= 12] . ( 2 sec) [ -11004.2148] [ 2669] [depth= 3] . ( 2 sec) [ -10773.7028] [ 2553] [depth= 9] . ( 2 sec) [ -10769.0121] [ 2551] [depth= 1] . ( 2 sec) [ -10500.9766] [ 2435] [depth= 7] . ( 2 sec) [ -10455.1502] [ 2432] [depth= 1] . ( 3 sec) [ -10356.0277] [ 2415] [depth= 11] . ( 3 sec) [ -10287.4741] [ 2320] [depth= 10] . ( 3 sec) [ -10186.6538] [ 2293] [depth= 3] . ( 3 sec) [ -10065.7325] [ 2295] [depth= 1] . ( 3 sec) [ -10059.1986] [ 2295] [depth= 2] . ( 3 sec) [ -9894.4883] [ 2251] [depth= 1] . ( 3 sec) [ -9876.6453] [ 2243] [depth= 1] . ( 3 sec) [ -9768.6648] [ 2228] [depth= 8] . ( 3 sec) [ -9715.8125] [ 2227] [depth= 1] . ( 3 sec) [ -9698.3379] [ 2226] [depth= 1] . ( 3 sec) [ -9697.2046] [ 2227] [depth= 1] . ( 3 sec) [ -9679.7177] [ 2227] [depth= 1] . ( 3 sec) [ -9403.8566] [ 2134] [depth= 6] . ( 3 sec) [ -9402.5521] [ 2135] [depth= 1] . ( 3 sec) [ -9399.6087] [ 2126] [depth= 1] . ( 3 sec) [ -9395.0486] [ 2128] [depth= 3] . ( 3 sec) [ -9315.5928] [ 2097] [depth= 2] . ( 3 sec) [ -8958.6363] [ 1987] [depth= 2] . ( 3 sec) [ -8948.3492] [ 1988] [depth= 1] . ( 3 sec) [ -8945.4833] [ 1987] [depth= 1] . ( 3 sec) [ -8906.2687] [ 1972] [depth= 4] . ( 4 sec) [ -8892.4814] [ 1967] [depth= 1] . ( 4 sec) [ -8880.0848] [ 1969] [depth= 3] . ( 4 sec) [ -8876.9990] [ 1971] [depth= 2] . ( 4 sec) [ -8873.1582] [ 1971] [depth= 1] . ( 4 sec) [ -8867.4844] [ 1966] [depth= 1] . ( 4 sec) [ -8855.2882] [ 1960] [depth= 1] . ( 4 sec) [ -8854.6497] [ 1958] [depth= 2] . ( 4 sec) [ -8849.3821] [ 1953] [depth= 1] . ( 4 sec) [ -8716.1620] [ 1878] [depth= 4] . ( 4 sec) [ -8693.5915] [ 1872] [depth= 3] . ( 4 sec) [ -8531.0995] [ 1829] [depth= 1] . ( 4 sec) [ -8462.5523] [ 1785] [depth= 1] . ( 4 sec) [ -8278.9565] [ 1715] [depth= 3] . ( 4 sec) [ -8267.3810] [ 1702] [depth= 4] . ( 5 sec) [ -8189.3346] [ 1659] [depth= 2] . ( 5 sec) [ -8135.6659] [ 1649] [depth= 4] . ( 5 sec) [ -8110.7344] [ 1635] [depth= 2] . ( 5 sec) [ -8101.5487] [ 1635] [depth= 1] . ( 5 sec) [ -7976.4315] [ 1611] [depth= 7] . ( 5 sec) [ -7974.5895] [ 1611] [depth= 1] . ( 5 sec) [ -7974.3868] [ 1611] [depth= 1] . ( 5 sec) [ -7969.6190] [ 1611] [depth= 2] . ( 5 sec) [ -7966.9236] [ 1601] [depth= 1] . ( 5 sec) [ -7961.3125] [ 1604] [depth= 2] . ( 5 sec) [ -7879.8429] [Branch lengths ] . ( 6 sec) [ -7874.0306] [GTR parameters ] . ( 6 sec) [ -7842.4506] [Alpha ][ 0.937235] . ( 6 sec) [ -7838.4332] [ 1605] [depth= 3] . ( 6 sec) [ -7783.7619] [ 1573] [depth= 1] . ( 6 sec) [ -7782.9529] [ 1571] [depth= 2] . ( 7 sec) [ -7779.0637] [ 1569] [depth= 3] . ( 7 sec) [ -7771.6353] [ 1568] [depth= 1] . ( 7 sec) [ -7771.3281] [ 1569] [depth= 3] . ( 7 sec) [ -7770.6560] [ 1566] [depth= 1] . ( 7 sec) [ -7770.2482] [ 1567] [depth= 1] . ( 7 sec) [ -7769.8478] [ 1567] [depth= 1] . ( 8 sec) [ -7768.5406] [ 1566] [depth= 1] . ( 8 sec) [ -7768.4216] [ 1567] [depth= 1] . ( 8 sec) [ -7768.3514] [ 1566] [depth= 1] . ( 8 sec) [ -7768.1954] [ 1567] [depth= 1] . ( 8 sec) [ -7767.6261] [ 1569] [depth= 1] . ( 8 sec) [ -7767.2924] [ 1574] [depth= 1] . ( 8 sec) [ -7767.2694] [ 1577] [depth= 2] . ( 9 sec) [ -7766.9632] [ 1578] [depth= 1] . ( 9 sec) [ -7764.9475] [ 1580] [depth= 1] . ( 9 sec) [ -7762.2825] [ 1576] [depth= 2] . ( 9 sec) [ -7762.1950] [ 1576] [depth= 1] . ( 10 sec) [ -7743.7173] [Branch lengths ] . ( 10 sec) [ -7743.6415] [GTR parameters ] . ( 11 sec) [ -7743.3623] [Alpha ][ 0.997279] . ( 12 sec) [ -7743.1840] [ 1581] [depth= 1] . ( 12 sec) [ -7743.1731] [ 1581] [depth= 1] . ( 13 sec) [ -7743.1332] [ 1580] [depth= 1] . ( 13 sec) [ -7743.0562] [ 1578] [depth= 1] . ( 15 sec) [ -7742.3959] [Branch lengths ] . ( 16 sec) [ -7742.3947] [GTR parameters ] . ( 16 sec) [ -7742.3941] [Alpha ][ 1.000010] . ( 23 sec) [ -7742.3588] [ 1576] [depth= 1] . ( 37 sec) [ -7742.2346] [Branch lengths ] . ( 38 sec) [ -7742.2343] [GTR parameters ] . ( 38 sec) [ -7742.2334] [Alpha ][ 1.003375] . ( 38 sec) [ -7742.2334] [Topology ] . ( 38 sec) [ -7742.2242] [Topology ] . ( 39 sec) [ -7742.2207] [Topology ] . ( 40 sec) [ -7742.2189] [Topology ] . ( 41 sec) [ -7742.2181] [Topology ] . ( 41 sec) [ -7742.2180] [GTR parameters ] . ( 41 sec) [ -7742.2180] [Alpha ][ 1.004379] . ( 41 sec) [ -7742.2180] [Topology ] . ( 41 sec) [ -7742.2175] [Topology ] . ( 42 sec) [ -7742.2175] [GTR parameters ] . ( 42 sec) [ -7742.2175] [Alpha ][ 1.004379] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -7742.2166] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.216564. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17778.2070] [GTR parameters ] . ( 0 sec) [ -17386.3452] [Alpha ][ 0.500960] . ( 0 sec) [ -17152.0045] [ 3723] [depth= 8] . ( 0 sec) [ -17039.2738] [ 3693] [depth= 12] . ( 1 sec) [ -16953.8797] [ 3664] [depth= 4] . ( 1 sec) [ -16722.7851] [ 3656] [depth= 2] . ( 1 sec) [ -16417.2566] [ 3559] [depth= 5] . ( 1 sec) [ -16406.0783] [ 3566] [depth= 5] . ( 1 sec) [ -15684.9887] [ 3452] [depth= 13] . ( 1 sec) [ -15445.8954] [ 3425] [depth= 15] . ( 1 sec) [ -15003.5696] [ 3279] [depth= 15] . ( 1 sec) [ -14630.9419] [ 3279] [depth= 20] . ( 1 sec) [ -14304.6194] [ 3173] [depth= 6] . ( 1 sec) [ -13865.3327] [ 3090] [depth= 19] . ( 1 sec) [ -13678.5350] [ 3081] [depth= 11] . ( 1 sec) [ -13591.8116] [ 3078] [depth= 3] . ( 1 sec) [ -13358.0254] [ 3045] [depth= 8] . ( 1 sec) [ -13039.5094] [ 3012] [depth= 1] . ( 1 sec) [ -12985.4996] [ 2998] [depth= 11] . ( 1 sec) [ -12710.1784] [ 2928] [depth= 10] . ( 1 sec) [ -12572.0303] [ 2895] [depth= 6] . ( 1 sec) [ -12483.5073] [ 2896] [depth= 7] . ( 1 sec) [ -12285.2729] [ 2799] [depth= 2] . ( 1 sec) [ -12275.5667] [ 2795] [depth= 9] . ( 1 sec) [ -12072.1091] [ 2739] [depth= 1] . ( 1 sec) [ -12065.6011] [ 2739] [depth= 1] . ( 1 sec) [ -11878.9806] [ 2725] [depth= 10] . ( 1 sec) [ -11760.9287] [ 2665] [depth= 11] . ( 2 sec) [ -11741.7525] [ 2649] [depth= 1] . ( 2 sec) [ -11654.2124] [ 2657] [depth= 1] . ( 2 sec) [ -11368.6952] [ 2553] [depth= 7] . ( 2 sec) [ -11219.5287] [ 2550] [depth= 5] . ( 2 sec) [ -11184.0397] [ 2536] [depth= 2] . ( 2 sec) [ -10843.9366] [ 2485] [depth= 3] . ( 2 sec) [ -10830.8854] [ 2486] [depth= 1] . ( 2 sec) [ -10780.2135] [ 2459] [depth= 3] . ( 2 sec) [ -10725.2317] [ 2462] [depth= 1] . ( 2 sec) [ -10669.5950] [ 2439] [depth= 3] . ( 2 sec) [ -10648.1777] [ 2432] [depth= 8] . ( 2 sec) [ -10447.0503] [ 2357] [depth= 8] . ( 2 sec) [ -10277.8993] [ 2352] [depth= 2] . ( 2 sec) [ -10249.0106] [ 2342] [depth= 12] . ( 2 sec) [ -9956.2090] [ 2223] [depth= 3] . ( 2 sec) [ -9931.9028] [ 2219] [depth= 3] . ( 2 sec) [ -9880.5590] [ 2198] [depth= 4] . ( 2 sec) [ -9865.4206] [ 2188] [depth= 2] . ( 2 sec) [ -9855.9694] [ 2186] [depth= 1] . ( 2 sec) [ -9734.2927] [ 2140] [depth= 5] . ( 2 sec) [ -9724.7853] [ 2135] [depth= 2] . ( 2 sec) [ -9639.6607] [ 2094] [depth= 1] . ( 2 sec) [ -9433.6874] [ 2062] [depth= 4] . ( 3 sec) [ -9421.9934] [ 2050] [depth= 1] . ( 3 sec) [ -9403.0775] [ 2046] [depth= 4] . ( 3 sec) [ -9342.0662] [ 2029] [depth= 3] . ( 3 sec) [ -9308.5806] [ 2014] [depth= 3] . ( 3 sec) [ -9269.0510] [ 2006] [depth= 6] . ( 3 sec) [ -9251.8505] [ 2005] [depth= 2] . ( 3 sec) [ -9201.1269] [ 2005] [depth= 2] . ( 3 sec) [ -8892.7024] [ 1917] [depth= 5] . ( 3 sec) [ -8847.6308] [ 1918] [depth= 1] . ( 3 sec) [ -8777.6032] [ 1862] [depth= 1] . ( 3 sec) [ -8772.2355] [ 1863] [depth= 1] . ( 3 sec) [ -8769.9257] [ 1867] [depth= 1] . ( 3 sec) [ -8754.5831] [ 1876] [depth= 1] . ( 3 sec) [ -8574.4162] [ 1832] [depth= 3] . ( 3 sec) [ -8561.6581] [ 1829] [depth= 1] . ( 3 sec) [ -8533.7764] [ 1831] [depth= 1] . ( 3 sec) [ -8531.1169] [ 1831] [depth= 1] . ( 3 sec) [ -8529.8891] [ 1828] [depth= 1] . ( 3 sec) [ -8506.8933] [ 1826] [depth= 2] . ( 4 sec) [ -8500.2440] [ 1824] [depth= 1] . ( 4 sec) [ -8488.9415] [ 1822] [depth= 1] . ( 4 sec) [ -8439.1622] [ 1780] [depth= 1] . ( 4 sec) [ -8426.8115] [ 1773] [depth= 1] . ( 4 sec) [ -8412.4328] [ 1771] [depth= 1] . ( 4 sec) [ -8393.8875] [ 1761] [depth= 1] . ( 4 sec) [ -8275.3190] [ 1721] [depth= 2] . ( 4 sec) [ -8270.0256] [ 1708] [depth= 1] . ( 4 sec) [ -8265.9280] [ 1709] [depth= 1] . ( 4 sec) [ -8262.0198] [ 1708] [depth= 1] . ( 4 sec) [ -8209.6051] [ 1694] [depth= 4] . ( 4 sec) [ -8171.0867] [ 1679] [depth= 1] . ( 4 sec) [ -8170.4743] [ 1679] [depth= 1] . ( 4 sec) [ -8024.5909] [Branch lengths ] . ( 5 sec) [ -8019.6023] [GTR parameters ] . ( 5 sec) [ -7988.2846] [Alpha ][ 0.912456] . ( 5 sec) [ -7986.6189] [ 1675] [depth= 2] . ( 5 sec) [ -7982.5025] [ 1669] [depth= 1] . ( 5 sec) [ -7978.4068] [ 1665] [depth= 2] . ( 5 sec) [ -7977.4739] [ 1664] [depth= 1] . ( 5 sec) [ -7928.5739] [ 1639] [depth= 4] . ( 6 sec) [ -7910.8624] [ 1639] [depth= 1] . ( 6 sec) [ -7908.9635] [ 1640] [depth= 1] . ( 6 sec) [ -7905.4714] [ 1638] [depth= 1] . ( 6 sec) [ -7900.6665] [ 1635] [depth= 1] . ( 6 sec) [ -7899.9401] [ 1636] [depth= 1] . ( 6 sec) [ -7892.9117] [ 1635] [depth= 1] . ( 6 sec) [ -7884.0668] [ 1631] [depth= 1] . ( 6 sec) [ -7883.7547] [ 1632] [depth= 1] . ( 6 sec) [ -7882.3749] [ 1632] [depth= 1] . ( 6 sec) [ -7880.0270] [ 1623] [depth= 3] . ( 6 sec) [ -7879.9690] [ 1622] [depth= 1] . ( 6 sec) [ -7873.7547] [ 1607] [depth= 2] . ( 6 sec) [ -7873.7177] [ 1607] [depth= 1] . ( 6 sec) [ -7871.5127] [ 1612] [depth= 1] . ( 7 sec) [ -7852.1634] [ 1617] [depth= 3] . ( 7 sec) [ -7822.1366] [ 1599] [depth= 3] . ( 7 sec) [ -7818.7236] [ 1595] [depth= 1] . ( 7 sec) [ -7797.5626] [ 1581] [depth= 2] . ( 7 sec) [ -7797.4659] [ 1581] [depth= 1] . ( 7 sec) [ -7796.7500] [ 1578] [depth= 1] . ( 7 sec) [ -7793.5510] [ 1578] [depth= 1] . ( 7 sec) [ -7793.0832] [ 1581] [depth= 1] . ( 7 sec) [ -7790.0423] [ 1578] [depth= 2] . ( 8 sec) [ -7781.5567] [ 1577] [depth= 2] . ( 8 sec) [ -7781.3938] [ 1578] [depth= 1] . ( 8 sec) [ -7781.1273] [ 1579] [depth= 1] . ( 8 sec) [ -7775.8114] [ 1579] [depth= 1] . ( 8 sec) [ -7774.1507] [ 1578] [depth= 3] . ( 8 sec) [ -7771.1014] [ 1578] [depth= 2] . ( 9 sec) [ -7761.1738] [Branch lengths ] . ( 9 sec) [ -7760.6870] [GTR parameters ] . ( 9 sec) [ -7760.1666] [Alpha ][ 0.992594] . ( 9 sec) [ -7759.7839] [ 1575] [depth= 1] . ( 10 sec) [ -7751.2145] [ 1573] [depth= 2] . ( 10 sec) [ -7751.0872] [ 1573] [depth= 1] . ( 10 sec) [ -7750.4520] [ 1578] [depth= 2] . ( 10 sec) [ -7748.7387] [ 1578] [depth= 1] . ( 12 sec) [ -7748.5246] [ 1579] [depth= 1] . ( 12 sec) [ -7748.5143] [ 1579] [depth= 1] . ( 13 sec) [ -7748.0122] [ 1580] [depth= 1] . ( 13 sec) [ -7746.4691] [ 1581] [depth= 2] . ( 13 sec) [ -7744.0556] [Branch lengths ] . ( 14 sec) [ -7744.0251] [GTR parameters ] . ( 14 sec) [ -7744.0232] [Alpha ][ 0.997699] . ( 18 sec) [ -7743.9928] [ 1576] [depth= 1] . ( 19 sec) [ -7742.9060] [Branch lengths ] . ( 19 sec) [ -7742.9054] [GTR parameters ] . ( 19 sec) [ -7742.9029] [Alpha ][ 1.003672] . ( 24 sec) [ -7742.2716] [Branch lengths ] . ( 46 sec) [ -7742.2687] [Branch lengths ] . ( 46 sec) [ -7742.2687] [Topology ] . ( 47 sec) [ -7742.2686] [Topology ] . ( 47 sec) [ -7742.2685] [GTR parameters ] . ( 47 sec) [ -7742.2682] [Alpha ][ 1.005708] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -7742.2275] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -7742.2265] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.226502. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17704.1174] [GTR parameters ] . ( 0 sec) [ -17317.3483] [Alpha ][ 0.500960] . ( 0 sec) [ -17186.8728] [ 3732] [depth= 8] . ( 0 sec) [ -17057.2809] [ 3650] [depth= 7] . ( 0 sec) [ -16869.2476] [ 3602] [depth= 8] . ( 0 sec) [ -16841.6057] [ 3595] [depth= 1] . ( 0 sec) [ -16714.4507] [ 3591] [depth= 9] . ( 1 sec) [ -16585.7912] [ 3566] [depth= 3] . ( 1 sec) [ -16474.7649] [ 3561] [depth= 4] . ( 1 sec) [ -16246.9837] [ 3465] [depth= 7] . ( 1 sec) [ -16200.6419] [ 3452] [depth= 8] . ( 1 sec) [ -16058.8846] [ 3447] [depth= 3] . ( 1 sec) [ -15919.3093] [ 3441] [depth= 3] . ( 1 sec) [ -15681.8455] [ 3421] [depth= 10] . ( 1 sec) [ -15595.6059] [ 3372] [depth= 1] . ( 1 sec) [ -15388.8864] [ 3367] [depth= 2] . ( 1 sec) [ -14836.9887] [ 3289] [depth= 4] . ( 1 sec) [ -14562.3363] [ 3277] [depth= 10] . ( 1 sec) [ -14483.5547] [ 3268] [depth= 1] . ( 1 sec) [ -14387.6092] [ 3191] [depth= 7] . ( 1 sec) [ -14324.5429] [ 3124] [depth= 3] . ( 1 sec) [ -14233.1347] [ 3101] [depth= 1] . ( 1 sec) [ -13896.4610] [ 3103] [depth= 9] . ( 1 sec) [ -13471.7357] [ 3024] [depth= 20] . ( 1 sec) [ -13422.0188] [ 3021] [depth= 2] . ( 1 sec) [ -13233.9200] [ 2961] [depth= 11] . ( 1 sec) [ -12916.7385] [ 2908] [depth= 14] . ( 1 sec) [ -12781.5624] [ 2926] [depth= 7] . ( 1 sec) [ -12472.5353] [ 2822] [depth= 8] . ( 1 sec) [ -12280.8476] [ 2774] [depth= 8] . ( 1 sec) [ -12277.8479] [ 2787] [depth= 1] . ( 1 sec) [ -12229.3244] [ 2785] [depth= 8] . ( 2 sec) [ -12190.0670] [ 2775] [depth= 1] . ( 2 sec) [ -11648.6944] [ 2702] [depth= 9] . ( 2 sec) [ -11450.7141] [ 2693] [depth= 8] . ( 2 sec) [ -11172.8440] [ 2562] [depth= 10] . ( 2 sec) [ -11134.7796] [ 2561] [depth= 4] . ( 2 sec) [ -11113.0135] [ 2563] [depth= 6] . ( 2 sec) [ -10962.6689] [ 2482] [depth= 9] . ( 2 sec) [ -10950.7042] [ 2486] [depth= 5] . ( 2 sec) [ -10895.4799] [ 2482] [depth= 1] . ( 2 sec) [ -10795.4018] [ 2485] [depth= 14] . ( 2 sec) [ -10774.3518] [ 2471] [depth= 2] . ( 2 sec) [ -10722.0215] [ 2449] [depth= 4] . ( 2 sec) [ -10650.3382] [ 2439] [depth= 2] . ( 2 sec) [ -10647.9569] [ 2441] [depth= 1] . ( 2 sec) [ -10466.0553] [ 2435] [depth= 3] . ( 2 sec) [ -10459.5888] [ 2436] [depth= 1] . ( 2 sec) [ -10406.9536] [ 2437] [depth= 6] . ( 2 sec) [ -10343.4020] [ 2389] [depth= 1] . ( 2 sec) [ -10341.1953] [ 2385] [depth= 1] . ( 2 sec) [ -10334.1382] [ 2370] [depth= 3] . ( 2 sec) [ -10333.0240] [ 2366] [depth= 1] . ( 2 sec) [ -10332.7394] [ 2365] [depth= 1] . ( 2 sec) [ -10327.8600] [ 2366] [depth= 1] . ( 3 sec) [ -10292.7305] [ 2376] [depth= 1] . ( 3 sec) [ -10272.5658] [ 2368] [depth= 1] . ( 3 sec) [ -10266.7037] [ 2367] [depth= 7] . ( 3 sec) [ -10246.6412] [ 2348] [depth= 2] . ( 3 sec) [ -10243.2116] [ 2330] [depth= 1] . ( 3 sec) [ -9948.8494] [ 2246] [depth= 6] . ( 3 sec) [ -9938.4368] [ 2236] [depth= 1] . ( 3 sec) [ -9899.0466] [ 2168] [depth= 4] . ( 3 sec) [ -9543.7114] [ 2034] [depth= 5] . ( 3 sec) [ -9531.0008] [ 2031] [depth= 1] . ( 3 sec) [ -9435.2308] [ 2023] [depth= 1] . ( 3 sec) [ -9218.1189] [ 1914] [depth= 3] . ( 3 sec) [ -9203.4261] [ 1914] [depth= 1] . ( 3 sec) [ -9188.9067] [ 1907] [depth= 1] . ( 3 sec) [ -9123.4458] [ 1890] [depth= 3] . ( 3 sec) [ -9122.5878] [ 1891] [depth= 1] . ( 3 sec) [ -9017.2801] [ 1879] [depth= 3] . ( 3 sec) [ -9013.1224] [ 1920] [depth= 10] . ( 3 sec) [ -8965.3779] [ 1920] [depth= 1] . ( 3 sec) [ -8917.7350] [ 1915] [depth= 7] . ( 3 sec) [ -8855.0825] [ 1901] [depth= 1] . ( 4 sec) [ -8849.5767] [ 1904] [depth= 1] . ( 4 sec) [ -8847.4586] [ 1905] [depth= 1] . ( 4 sec) [ -8832.7372] [ 1905] [depth= 1] . ( 4 sec) [ -8832.0388] [ 1906] [depth= 1] . ( 4 sec) [ -8830.0706] [ 1906] [depth= 1] . ( 4 sec) [ -8812.0757] [ 1901] [depth= 3] . ( 4 sec) [ -8806.7807] [ 1899] [depth= 1] . ( 4 sec) [ -8789.3392] [ 1901] [depth= 1] . ( 4 sec) [ -8786.5761] [ 1902] [depth= 2] . ( 4 sec) [ -8785.3014] [ 1903] [depth= 1] . ( 4 sec) [ -8617.4038] [Branch lengths ] . ( 5 sec) [ -8613.5529] [GTR parameters ] . ( 5 sec) [ -8594.6337] [Alpha ][ 0.781166] . ( 5 sec) [ -8594.2298] [ 1906] [depth= 1] . ( 6 sec) [ -8594.0758] [ 1905] [depth= 1] . ( 6 sec) [ -8586.7242] [ 1899] [depth= 7] . ( 6 sec) [ -8518.8396] [ 1884] [depth= 8] . ( 6 sec) [ -8471.7952] [ 1900] [depth= 16] . ( 6 sec) [ -8421.4316] [ 1895] [depth= 2] . ( 6 sec) [ -8420.9599] [ 1895] [depth= 1] . ( 6 sec) [ -8405.7620] [ 1863] [depth= 17] . ( 6 sec) [ -8254.0480] [ 1773] [depth= 17] . ( 6 sec) [ -8252.4339] [ 1778] [depth= 1] . ( 6 sec) [ -8105.6603] [ 1703] [depth= 17] . ( 6 sec) [ -8026.8099] [ 1717] [depth= 1] . ( 6 sec) [ -8025.7621] [ 1711] [depth= 1] . ( 6 sec) [ -8024.8845] [ 1710] [depth= 2] . ( 6 sec) [ -8019.1866] [ 1703] [depth= 5] . ( 6 sec) [ -8009.9221] [ 1689] [depth= 1] . ( 7 sec) [ -8007.3110] [ 1689] [depth= 1] . ( 7 sec) [ -8000.5171] [ 1686] [depth= 1] . ( 7 sec) [ -7937.2258] [ 1685] [depth= 2] . ( 7 sec) [ -7934.0668] [ 1688] [depth= 1] . ( 7 sec) [ -7927.2711] [ 1681] [depth= 1] . ( 7 sec) [ -7926.6734] [ 1682] [depth= 1] . ( 7 sec) [ -7926.6014] [ 1681] [depth= 1] . ( 7 sec) [ -7926.3971] [ 1681] [depth= 1] . ( 7 sec) [ -7925.3636] [ 1680] [depth= 1] . ( 7 sec) [ -7903.0417] [ 1653] [depth= 1] . ( 7 sec) [ -7890.6355] [ 1646] [depth= 2] . ( 8 sec) [ -7890.3425] [ 1646] [depth= 1] . ( 8 sec) [ -7890.3283] [ 1642] [depth= 1] . ( 8 sec) [ -7890.3133] [ 1646] [depth= 1] . ( 8 sec) [ -7887.2904] [ 1639] [depth= 1] . ( 8 sec) [ -7886.8450] [ 1643] [depth= 3] . ( 8 sec) [ -7886.7700] [ 1643] [depth= 1] . ( 8 sec) [ -7885.6265] [ 1645] [depth= 1] . ( 8 sec) [ -7883.6397] [ 1648] [depth= 1] . ( 8 sec) [ -7883.5777] [ 1650] [depth= 1] . ( 8 sec) [ -7879.8657] [ 1649] [depth= 1] . ( 9 sec) [ -7873.7713] [ 1642] [depth= 3] . ( 9 sec) [ -7873.3632] [ 1642] [depth= 1] . ( 9 sec) [ -7868.0033] [ 1642] [depth= 2] . ( 9 sec) [ -7865.2954] [ 1639] [depth= 1] . ( 9 sec) [ -7860.6419] [ 1643] [depth= 1] . ( 9 sec) [ -7845.1884] [Branch lengths ] . ( 10 sec) [ -7844.9061] [GTR parameters ] . ( 10 sec) [ -7841.8961] [Alpha ][ 0.950437] . ( 10 sec) [ -7841.7198] [ 1645] [depth= 2] . ( 10 sec) [ -7811.7694] [ 1617] [depth= 3] . ( 11 sec) [ -7809.5425] [ 1613] [depth= 1] . ( 11 sec) [ -7784.5442] [ 1598] [depth= 1] . ( 11 sec) [ -7771.9038] [ 1581] [depth= 2] . ( 11 sec) [ -7764.9521] [ 1575] [depth= 3] . ( 11 sec) [ -7764.9332] [ 1574] [depth= 2] . ( 11 sec) [ -7762.0551] [ 1573] [depth= 1] . ( 11 sec) [ -7761.7153] [ 1578] [depth= 1] . ( 12 sec) [ -7760.9044] [ 1583] [depth= 1] . ( 12 sec) [ -7755.3410] [ 1578] [depth= 1] . ( 12 sec) [ -7755.0296] [ 1578] [depth= 1] . ( 12 sec) [ -7754.9281] [ 1577] [depth= 1] . ( 13 sec) [ -7752.3633] [ 1574] [depth= 2] . ( 14 sec) [ -7752.2818] [ 1575] [depth= 1] . ( 14 sec) [ -7752.2615] [ 1575] [depth= 1] . ( 14 sec) [ -7752.1026] [ 1572] [depth= 1] . ( 14 sec) [ -7744.1356] [Branch lengths ] . ( 15 sec) [ -7744.0168] [GTR parameters ] . ( 15 sec) [ -7743.7387] [Alpha ][ 1.010792] . ( 15 sec) [ -7743.0881] [ 1574] [depth= 1] . ( 16 sec) [ -7742.9096] [ 1572] [depth= 1] . ( 19 sec) [ -7742.2078] [Branch lengths ] . ( 19 sec) [ -7742.1995] [GTR parameters ] . ( 19 sec) [ -7742.1979] [Alpha ][ 1.005770] . ( 24 sec) [ -7742.1794] [Branch lengths ] . ( 45 sec) [ -7742.1788] [Branch lengths ] . ( 45 sec) [ -7742.1788] [Topology ] . ( 46 sec) [ -7742.1787] [Topology ] . ( 46 sec) [ -7742.1787] [GTR parameters ] . ( 46 sec) [ -7742.1787] [Alpha ][ 1.006776] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -7742.1782] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.178173. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18480.5598] [GTR parameters ] . ( 1 sec) [ -18083.5401] [Alpha ][ 0.500960] . ( 1 sec) [ -17483.5312] [ 3720] [depth= 6] . ( 1 sec) [ -17230.8163] [ 3675] [depth= 11] . ( 1 sec) [ -17160.7097] [ 3642] [depth= 3] . ( 1 sec) [ -17074.4765] [ 3637] [depth= 3] . ( 1 sec) [ -16738.2333] [ 3583] [depth= 7] . ( 1 sec) [ -16691.3437] [ 3576] [depth= 4] . ( 1 sec) [ -16369.3178] [ 3563] [depth= 5] . ( 1 sec) [ -16156.9394] [ 3560] [depth= 1] . ( 1 sec) [ -15928.9294] [ 3440] [depth= 8] . ( 1 sec) [ -15547.2304] [ 3348] [depth= 10] . ( 1 sec) [ -15471.7130] [ 3331] [depth= 1] . ( 1 sec) [ -15206.7964] [ 3328] [depth= 6] . ( 2 sec) [ -14835.3490] [ 3283] [depth= 7] . ( 2 sec) [ -14820.6670] [ 3277] [depth= 1] . ( 2 sec) [ -14779.6732] [ 3263] [depth= 2] . ( 2 sec) [ -14615.2311] [ 3270] [depth= 1] . ( 2 sec) [ -14526.4248] [ 3259] [depth= 10] . ( 2 sec) [ -14481.4183] [ 3206] [depth= 2] . ( 2 sec) [ -14177.5136] [ 3144] [depth= 8] . ( 2 sec) [ -13873.8003] [ 3124] [depth= 11] . ( 2 sec) [ -13568.0599] [ 2968] [depth= 3] . ( 2 sec) [ -13413.9973] [ 2986] [depth= 16] . ( 2 sec) [ -13285.8584] [ 2954] [depth= 15] . ( 2 sec) [ -13242.9543] [ 2957] [depth= 1] . ( 2 sec) [ -13039.0841] [ 2881] [depth= 9] . ( 2 sec) [ -13012.3474] [ 2859] [depth= 13] . ( 2 sec) [ -13000.3588] [ 2856] [depth= 1] . ( 2 sec) [ -12895.7503] [ 2844] [depth= 3] . ( 2 sec) [ -12536.4896] [ 2712] [depth= 6] . ( 2 sec) [ -12185.2455] [ 2647] [depth= 12] . ( 2 sec) [ -11894.3213] [ 2572] [depth= 2] . ( 2 sec) [ -11437.5465] [ 2463] [depth= 1] . ( 2 sec) [ -11427.6371] [ 2462] [depth= 3] . ( 2 sec) [ -11385.2053] [ 2426] [depth= 1] . ( 2 sec) [ -11376.4676] [ 2426] [depth= 1] . ( 3 sec) [ -11334.4027] [ 2411] [depth= 1] . ( 3 sec) [ -11208.9076] [ 2320] [depth= 3] . ( 3 sec) [ -11167.5804] [ 2306] [depth= 3] . ( 3 sec) [ -11130.7549] [ 2295] [depth= 3] . ( 3 sec) [ -11002.1593] [ 2282] [depth= 8] . ( 3 sec) [ -10991.4045] [ 2278] [depth= 2] . ( 3 sec) [ -10549.3734] [ 2222] [depth= 10] . ( 3 sec) [ -10390.5835] [ 2251] [depth= 4] . ( 3 sec) [ -10386.1409] [ 2251] [depth= 7] . ( 3 sec) [ -10362.4195] [ 2236] [depth= 8] . ( 3 sec) [ -10283.5559] [ 2236] [depth= 3] . ( 3 sec) [ -10273.9862] [ 2234] [depth= 1] . ( 3 sec) [ -10272.3999] [ 2235] [depth= 1] . ( 3 sec) [ -10254.6352] [ 2227] [depth= 4] . ( 3 sec) [ -10252.9935] [ 2226] [depth= 1] . ( 3 sec) [ -10145.4518] [ 2151] [depth= 13] . ( 3 sec) [ -10048.6439] [ 2147] [depth= 3] . ( 3 sec) [ -10036.2960] [ 2136] [depth= 1] . ( 3 sec) [ -9858.0425] [ 2045] [depth= 5] . ( 3 sec) [ -9857.2239] [ 2047] [depth= 1] . ( 3 sec) [ -9853.7666] [ 2045] [depth= 1] . ( 3 sec) [ -9697.5022] [ 2020] [depth= 5] . ( 4 sec) [ -9696.4308] [ 2022] [depth= 1] . ( 4 sec) [ -9650.4901] [ 2035] [depth= 1] . ( 4 sec) [ -9648.6323] [ 2066] [depth= 1] . ( 4 sec) [ -9543.0974] [ 2039] [depth= 4] . ( 4 sec) [ -9322.1542] [ 1928] [depth= 7] . ( 4 sec) [ -9258.7330] [ 1887] [depth= 1] . ( 4 sec) [ -9216.3362] [ 1871] [depth= 2] . ( 4 sec) [ -9004.8033] [ 1871] [depth= 1] . ( 4 sec) [ -8883.1888] [ 1828] [depth= 4] . ( 4 sec) [ -8826.7982] [ 1806] [depth= 3] . ( 4 sec) [ -8759.0258] [ 1810] [depth= 1] . ( 4 sec) [ -8703.6794] [ 1821] [depth= 2] . ( 4 sec) [ -8552.2057] [ 1755] [depth= 1] . ( 4 sec) [ -8535.0698] [ 1768] [depth= 4] . ( 4 sec) [ -8441.2085] [ 1740] [depth= 5] . ( 4 sec) [ -8304.3290] [ 1694] [depth= 2] . ( 4 sec) [ -8212.4621] [ 1679] [depth= 3] . ( 4 sec) [ -8211.4658] [ 1680] [depth= 1] . ( 4 sec) [ -8197.2612] [ 1689] [depth= 3] . ( 4 sec) [ -8162.7635] [ 1650] [depth= 1] . ( 5 sec) [ -8160.5710] [ 1650] [depth= 2] . ( 5 sec) [ -8122.0586] [ 1627] [depth= 1] . ( 5 sec) [ -8121.5048] [ 1628] [depth= 2] . ( 5 sec) [ -8120.7817] [ 1628] [depth= 1] . ( 5 sec) [ -8120.5405] [ 1630] [depth= 1] . ( 5 sec) [ -8017.8291] [Branch lengths ] . ( 6 sec) [ -8013.6280] [GTR parameters ] . ( 6 sec) [ -7985.3618] [Alpha ][ 0.890521] . ( 6 sec) [ -7974.6496] [ 1633] [depth= 1] . ( 6 sec) [ -7885.1660] [ 1634] [depth= 1] . ( 6 sec) [ -7864.8069] [ 1618] [depth= 3] . ( 6 sec) [ -7863.3651] [ 1616] [depth= 1] . ( 6 sec) [ -7859.6077] [ 1614] [depth= 1] . ( 6 sec) [ -7859.3329] [ 1612] [depth= 1] . ( 6 sec) [ -7854.3231] [ 1614] [depth= 1] . ( 7 sec) [ -7832.8091] [ 1613] [depth= 2] . ( 7 sec) [ -7832.2013] [ 1616] [depth= 1] . ( 7 sec) [ -7831.0854] [ 1614] [depth= 1] . ( 7 sec) [ -7808.4417] [ 1606] [depth= 1] . ( 7 sec) [ -7800.2232] [ 1607] [depth= 1] . ( 7 sec) [ -7800.1904] [ 1608] [depth= 1] . ( 8 sec) [ -7782.9143] [ 1589] [depth= 4] . ( 8 sec) [ -7782.1189] [ 1589] [depth= 1] . ( 8 sec) [ -7781.9545] [ 1589] [depth= 1] . ( 8 sec) [ -7780.9642] [ 1586] [depth= 1] . ( 8 sec) [ -7780.6929] [ 1587] [depth= 1] . ( 9 sec) [ -7777.5597] [ 1583] [depth= 2] . ( 9 sec) [ -7772.1286] [ 1582] [depth= 3] . ( 9 sec) [ -7771.1473] [ 1584] [depth= 1] . ( 9 sec) [ -7771.0791] [ 1584] [depth= 1] . ( 9 sec) [ -7770.5733] [ 1586] [depth= 1] . ( 10 sec) [ -7770.1487] [ 1587] [depth= 1] . ( 10 sec) [ -7759.5920] [Branch lengths ] . ( 10 sec) [ -7759.3070] [GTR parameters ] . ( 10 sec) [ -7758.6118] [Alpha ][ 0.981164] . ( 11 sec) [ -7758.5626] [ 1588] [depth= 1] . ( 11 sec) [ -7758.4759] [ 1587] [depth= 1] . ( 11 sec) [ -7747.6029] [ 1579] [depth= 2] . ( 11 sec) [ -7746.3211] [ 1581] [depth= 1] . ( 11 sec) [ -7745.8837] [ 1576] [depth= 1] . ( 11 sec) [ -7744.7633] [ 1575] [depth= 1] . ( 12 sec) [ -7743.8552] [ 1576] [depth= 1] . ( 12 sec) [ -7743.7741] [ 1581] [depth= 1] . ( 12 sec) [ -7743.7231] [ 1581] [depth= 1] . ( 13 sec) [ -7743.4995] [ 1576] [depth= 1] . ( 15 sec) [ -7742.4230] [Branch lengths ] . ( 15 sec) [ -7742.4077] [GTR parameters ] . ( 15 sec) [ -7742.3766] [Alpha ][ 1.001246] . ( 20 sec) [ -7742.2825] [Branch lengths ] . ( 37 sec) [ -7742.2539] [ 1574] [depth= 1] . ( 41 sec) [ -7742.1836] [Branch lengths ] . ( 41 sec) [ -7742.1835] [GTR parameters ] . ( 42 sec) [ -7742.1819] [Alpha ][ 1.005987] . ( 42 sec) [ -7742.1819] [Topology ] . ( 42 sec) [ -7742.1797] [Topology ] . ( 43 sec) [ -7742.1792] [Topology ] . ( 43 sec) [ -7742.1791] [GTR parameters ] . ( 43 sec) [ -7742.1791] [Alpha ][ 1.005987] . ( 43 sec) [ -7742.1791] [Topology ] . ( 44 sec) [ -7742.1789] [Topology ] . ( 44 sec) [ -7742.1789] [GTR parameters ] . ( 44 sec) [ -7742.1789] [Alpha ][ 1.005987] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -7742.1379] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.137902. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7804.366693 . ( 0 sec) [ -7802.1644] [GTR parameters ] . ( 0 sec) [ -7801.9691] [Alpha ][ 0.948006] . ( 0 sec) [ -7801.9691] [Topology ] . ( 1 sec) [ -7762.6758] [Topology ] . ( 2 sec) [ -7752.3946] [Topology ] . ( 2 sec) [ -7747.7755] [Topology ] . ( 3 sec) [ -7744.2828] [Topology ] . ( 4 sec) [ -7742.8247] [Topology ] . ( 5 sec) [ -7742.5889] [Topology ] . ( 5 sec) [ -7742.5291] [Topology ] . ( 6 sec) [ -7742.5065] [Topology ] . ( 7 sec) [ -7742.4959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -7742.4158] [Topology ] . Before opt ts/t=1.000000 LK=-7742.415787 . ( 14 sec) [ -7742.4033] [GTR parameters ] . ( 14 sec) [ -7742.1531] [Alpha ][ 1.005038] . ( 14 sec) [ -7742.1531] [Topology ] . ( 14 sec) [ -7742.1429] [Topology ] . ( 15 sec) [ -7742.1399] [Topology ] . ( 16 sec) [ -7742.1387] [Topology ] . ( 17 sec) [ -7742.1382] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7742.138223 . ( 22 sec) [ -7742.1382] [GTR parameters ] . ( 22 sec) [ -7742.1378] [Alpha ][ 1.007282] . ( 22 sec) [ -7742.1378] [Topology ] . ( 23 sec) [ -7742.1375] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 34 sec) [ -7802.1644] [GTR parameters ] . ( 34 sec) [ -7801.9691] [Alpha ][ 0.948006] . ( 34 sec) [ -7801.9550] [ 1577] [depth= 1] . ( 34 sec) [ -7801.9414] [ 1577] [depth= 1] . ( 34 sec) [ -7801.6532] [ 1577] [depth= 1] . ( 35 sec) [ -7797.9590] [ 1575] [depth= 1] . ( 35 sec) [ -7791.7923] [ 1574] [depth= 1] . ( 35 sec) [ -7789.4085] [ 1576] [depth= 2] . ( 35 sec) [ -7788.2794] [ 1573] [depth= 1] . ( 35 sec) [ -7786.3456] [ 1574] [depth= 1] . ( 35 sec) [ -7785.3166] [ 1573] [depth= 1] . ( 35 sec) [ -7784.6914] [ 1575] [depth= 1] . ( 35 sec) [ -7784.6573] [ 1576] [depth= 1] . ( 35 sec) [ -7782.7528] [ 1575] [depth= 1] . ( 36 sec) [ -7782.4295] [ 1576] [depth= 1] . ( 36 sec) [ -7782.4002] [ 1576] [depth= 1] . ( 36 sec) [ -7780.0786] [ 1574] [depth= 2] . ( 36 sec) [ -7768.9048] [ 1575] [depth= 4] . ( 36 sec) [ -7766.0780] [ 1577] [depth= 2] . ( 37 sec) [ -7765.5159] [ 1579] [depth= 1] . ( 37 sec) [ -7765.0402] [ 1580] [depth= 2] . ( 37 sec) [ -7764.4642] [ 1578] [depth= 1] . ( 37 sec) [ -7763.9865] [ 1580] [depth= 1] . ( 37 sec) [ -7763.7058] [ 1573] [depth= 1] . ( 38 sec) [ -7743.6835] [Branch lengths ] . ( 38 sec) [ -7743.6712] [GTR parameters ] . ( 38 sec) [ -7743.5090] [Alpha ][ 0.993719] . ( 38 sec) [ -7743.3733] [ 1573] [depth= 1] . ( 40 sec) [ -7743.3536] [ 1572] [depth= 1] . ( 41 sec) [ -7743.2672] [ 1573] [depth= 1] . ( 41 sec) [ -7743.2511] [ 1578] [depth= 1] . ( 42 sec) [ -7743.0770] [ 1580] [depth= 1] . ( 43 sec) [ -7742.3507] [Branch lengths ] . ( 43 sec) [ -7742.3495] [GTR parameters ] . ( 43 sec) [ -7742.3463] [Alpha ][ 1.000447] . ( 48 sec) [ -7742.2706] [Branch lengths ] . ( 69 sec) [ -7742.2601] [Branch lengths ] . ( 69 sec) [ -7742.2601] [Topology ] . ( 70 sec) [ -7742.2591] [Topology ] . ( 70 sec) [ -7742.2590] [GTR parameters ] . ( 70 sec) [ -7742.2585] [Alpha ][ 1.003264] . ( 70 sec) [ -7742.2585] [Topology ] . ( 71 sec) [ -7742.2580] [Topology ] . ( 71 sec) [ -7742.2580] [GTR parameters ] . ( 71 sec) [ -7742.2580] [Alpha ][ 1.003264] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -7742.2576] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -7742.2572] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7742.137484 . Log likelihood obtained after SPR moves : -7742.257181 . Log likelihood of the current tree: -7742.137484. . Printing the most likely tree in file 'data90.phy_phyml_tree.txt'... . Best log likelihood : -7742.137484 . Time used 0h1m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo