.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data56.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... . 403 patterns found. (out of a total of 500 sites) . 86 sites without polymorphism (17.20%). . [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) [ -17543.8591] [GTR parameters ] . ( 0 sec) [ -17208.8427] [Alpha ][ 0.500960] . ( 0 sec) [ -16837.5768] [ 3716] [depth= 8] . ( 0 sec) [ -16626.6993] [ 3706] [depth= 4] . ( 0 sec) [ -16468.8198] [ 3685] [depth= 6] . ( 0 sec) [ -16461.6718] [ 3677] [depth= 2] . ( 0 sec) [ -16429.6927] [ 3652] [depth= 1] . ( 1 sec) [ -16313.4838] [ 3649] [depth= 1] . ( 1 sec) [ -16291.9852] [ 3641] [depth= 1] . ( 1 sec) [ -16267.7419] [ 3636] [depth= 6] . ( 1 sec) [ -16093.2248] [ 3574] [depth= 11] . ( 1 sec) [ -16024.4963] [ 3553] [depth= 3] . ( 1 sec) [ -15867.2566] [ 3545] [depth= 1] . ( 1 sec) [ -15763.8034] [ 3513] [depth= 8] . ( 1 sec) [ -15666.3774] [ 3492] [depth= 5] . ( 1 sec) [ -15637.4997] [ 3491] [depth= 1] . ( 1 sec) [ -15577.5366] [ 3488] [depth= 1] . ( 1 sec) [ -15518.7780] [ 3486] [depth= 1] . ( 1 sec) [ -15367.8168] [ 3426] [depth= 6] . ( 1 sec) [ -15262.5888] [ 3416] [depth= 4] . ( 1 sec) [ -15021.2290] [ 3393] [depth= 3] . ( 1 sec) [ -14810.2887] [ 3266] [depth= 5] . ( 1 sec) [ -14433.9658] [ 3158] [depth= 7] . ( 1 sec) [ -14395.2444] [ 3158] [depth= 2] . ( 1 sec) [ -14340.6568] [ 3153] [depth= 12] . ( 1 sec) [ -14200.6169] [ 3111] [depth= 4] . ( 1 sec) [ -14148.5182] [ 3097] [depth= 9] . ( 1 sec) [ -14033.3138] [ 3068] [depth= 1] . ( 1 sec) [ -13999.5967] [ 3052] [depth= 1] . ( 1 sec) [ -13827.8056] [ 3004] [depth= 1] . ( 1 sec) [ -13388.1192] [ 2871] [depth= 3] . ( 1 sec) [ -13325.3844] [ 2860] [depth= 1] . ( 2 sec) [ -13218.4466] [ 2829] [depth= 8] . ( 2 sec) [ -13192.1260] [ 2830] [depth= 1] . ( 2 sec) [ -12813.6558] [ 2700] [depth= 3] . ( 2 sec) [ -12557.5242] [ 2709] [depth= 4] . ( 2 sec) [ -12483.6363] [ 2674] [depth= 2] . ( 2 sec) [ -12434.4878] [ 2644] [depth= 5] . ( 2 sec) [ -12323.8061] [ 2625] [depth= 6] . ( 2 sec) [ -12302.2999] [ 2618] [depth= 1] . ( 2 sec) [ -11902.1053] [ 2605] [depth= 6] . ( 2 sec) [ -11880.7597] [ 2602] [depth= 1] . ( 2 sec) [ -11833.5143] [ 2593] [depth= 3] . ( 2 sec) [ -11699.8590] [ 2596] [depth= 3] . ( 2 sec) [ -11677.3207] [ 2599] [depth= 5] . ( 2 sec) [ -11599.8276] [ 2573] [depth= 6] . ( 2 sec) [ -11098.6025] [ 2515] [depth= 10] . ( 2 sec) [ -11047.4951] [ 2549] [depth= 1] . ( 2 sec) [ -11046.7852] [ 2545] [depth= 2] . ( 2 sec) [ -11040.9316] [ 2542] [depth= 2] . ( 2 sec) [ -10944.9403] [ 2521] [depth= 6] . ( 3 sec) [ -10751.4911] [ 2408] [depth= 13] . ( 3 sec) [ -10751.3531] [ 2408] [depth= 1] . ( 3 sec) [ -10747.5591] [ 2409] [depth= 1] . ( 3 sec) [ -10718.7648] [ 2411] [depth= 1] . ( 3 sec) [ -10671.5559] [ 2375] [depth= 2] . ( 3 sec) [ -10662.6776] [ 2379] [depth= 2] . ( 3 sec) [ -10250.1339] [ 2306] [depth= 3] . ( 3 sec) [ -9785.4070] [ 2206] [depth= 1] . ( 3 sec) [ -9478.6983] [ 2127] [depth= 9] . ( 3 sec) [ -9472.0947] [ 2132] [depth= 1] . ( 3 sec) [ -9462.4955] [ 2114] [depth= 3] . ( 3 sec) [ -9371.3427] [ 2087] [depth= 7] . ( 3 sec) [ -9331.7241] [ 2081] [depth= 1] . ( 3 sec) [ -9030.4315] [ 1943] [depth= 5] . ( 3 sec) [ -9024.7509] [ 1945] [depth= 1] . ( 4 sec) [ -9014.2791] [ 1951] [depth= 1] . ( 4 sec) [ -8976.5918] [ 1939] [depth= 1] . ( 4 sec) [ -8939.3163] [ 1925] [depth= 2] . ( 4 sec) [ -8906.6622] [ 1909] [depth= 1] . ( 4 sec) [ -8862.9518] [ 1896] [depth= 4] . ( 4 sec) [ -8752.9310] [ 1907] [depth= 7] . ( 4 sec) [ -8734.1231] [ 1899] [depth= 2] . ( 4 sec) [ -8732.0462] [ 1896] [depth= 1] . ( 4 sec) [ -8718.0380] [ 1901] [depth= 4] . ( 4 sec) [ -8708.8810] [ 1898] [depth= 3] . ( 4 sec) [ -8706.3055] [ 1900] [depth= 1] . ( 4 sec) [ -8590.2889] [ 1809] [depth= 9] . ( 5 sec) [ -8465.9580] [Branch lengths ] . ( 5 sec) [ -8465.0544] [GTR parameters ] . ( 5 sec) [ -8438.6131] [Alpha ][ 0.862200] . ( 5 sec) [ -8435.1982] [ 1802] [depth= 1] . ( 5 sec) [ -8423.7065] [ 1782] [depth= 3] . ( 6 sec) [ -8407.3937] [ 1771] [depth= 1] . ( 6 sec) [ -8407.3256] [ 1772] [depth= 1] . ( 6 sec) [ -8400.3368] [ 1757] [depth= 2] . ( 6 sec) [ -8343.1557] [ 1745] [depth= 4] . ( 6 sec) [ -8340.8252] [ 1742] [depth= 1] . ( 6 sec) [ -8340.8034] [ 1741] [depth= 1] . ( 7 sec) [ -8329.2980] [ 1731] [depth= 2] . ( 7 sec) [ -8329.2316] [ 1735] [depth= 2] . ( 7 sec) [ -8329.1032] [ 1735] [depth= 1] . ( 7 sec) [ -8328.8722] [ 1745] [depth= 1] . ( 7 sec) [ -8328.8422] [ 1746] [depth= 1] . ( 7 sec) [ -8328.4218] [ 1744] [depth= 1] . ( 7 sec) [ -8272.7489] [ 1725] [depth= 2] . ( 7 sec) [ -8270.4481] [ 1723] [depth= 1] . ( 8 sec) [ -8268.7105] [ 1723] [depth= 1] . ( 8 sec) [ -8268.0931] [ 1724] [depth= 1] . ( 8 sec) [ -8267.5506] [ 1722] [depth= 2] . ( 9 sec) [ -8254.6023] [Branch lengths ] . ( 9 sec) [ -8254.4224] [GTR parameters ] . ( 9 sec) [ -8253.1779] [Alpha ][ 0.975881] . ( 10 sec) [ -8234.1304] [ 1713] [depth= 5] . ( 10 sec) [ -8234.0155] [ 1713] [depth= 1] . ( 10 sec) [ -8233.7967] [ 1711] [depth= 1] . ( 11 sec) [ -8233.6112] [ 1712] [depth= 1] . ( 12 sec) [ -8232.5131] [ 1715] [depth= 1] . ( 13 sec) [ -8232.2096] [ 1718] [depth= 1] . ( 13 sec) [ -8231.1895] [Branch lengths ] . ( 13 sec) [ -8231.1466] [GTR parameters ] . ( 13 sec) [ -8231.1192] [Alpha ][ 0.994538] . ( 17 sec) [ -8230.9945] [Branch lengths ] . ( 38 sec) [ -8230.9694] [Branch lengths ] . ( 38 sec) [ -8230.9694] [Topology ] . ( 39 sec) [ -8230.7117] [Topology ] . ( 40 sec) [ -8230.4997] [Topology ] . ( 41 sec) [ -8230.4676] [Topology ] . ( 41 sec) [ -8230.4556] [Topology ] . ( 42 sec) [ -8230.4500] [Topology ] . ( 43 sec) [ -8230.4473] [Topology ] . ( 44 sec) [ -8230.4459] [Topology ] . ( 44 sec) [ -8230.4363] [GTR parameters ] . ( 44 sec) [ -8230.4333] [Alpha ][ 1.000788] . ( 44 sec) [ -8230.4333] [Topology ] . ( 45 sec) [ -8230.4325] [Topology ] . ( 45 sec) [ -8230.4325] [GTR parameters ] . ( 45 sec) [ -8230.4325] [Alpha ][ 1.000788] . Checking for NNIs, optimizing five branches... . ( 51 sec) [ -8230.4241] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8230.424103. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17362.9663] [GTR parameters ] . ( 1 sec) [ -17041.4985] [Alpha ][ 0.500960] . ( 1 sec) [ -16667.4672] [ 3647] [depth= 3] . ( 1 sec) [ -16432.5525] [ 3571] [depth= 10] . ( 1 sec) [ -16285.1842] [ 3541] [depth= 4] . ( 1 sec) [ -16282.1249] [ 3538] [depth= 3] . ( 1 sec) [ -16219.5223] [ 3514] [depth= 1] . ( 1 sec) [ -16157.5199] [ 3512] [depth= 3] . ( 1 sec) [ -16108.1265] [ 3506] [depth= 4] . ( 1 sec) [ -16094.4028] [ 3505] [depth= 1] . ( 1 sec) [ -16081.5311] [ 3500] [depth= 2] . ( 1 sec) [ -16014.7588] [ 3500] [depth= 1] . ( 1 sec) [ -15997.0748] [ 3499] [depth= 1] . ( 1 sec) [ -15944.3036] [ 3493] [depth= 1] . ( 2 sec) [ -15745.0490] [ 3456] [depth= 9] . ( 2 sec) [ -15636.0643] [ 3476] [depth= 3] . ( 2 sec) [ -15606.2800] [ 3465] [depth= 2] . ( 2 sec) [ -15187.5644] [ 3297] [depth= 4] . ( 2 sec) [ -14880.8017] [ 3246] [depth= 5] . ( 2 sec) [ -14816.4322] [ 3239] [depth= 2] . ( 2 sec) [ -14654.8180] [ 3212] [depth= 3] . ( 2 sec) [ -14614.6204] [ 3221] [depth= 1] . ( 2 sec) [ -14521.6670] [ 3190] [depth= 1] . ( 2 sec) [ -14439.7251] [ 3171] [depth= 7] . ( 2 sec) [ -14312.0227] [ 3124] [depth= 13] . ( 2 sec) [ -14127.5320] [ 3087] [depth= 1] . ( 2 sec) [ -13448.4245] [ 2895] [depth= 4] . ( 2 sec) [ -13323.6383] [ 2866] [depth= 2] . ( 2 sec) [ -12953.5572] [ 2797] [depth= 12] . ( 2 sec) [ -12909.5470] [ 2777] [depth= 1] . ( 2 sec) [ -12886.8937] [ 2771] [depth= 1] . ( 2 sec) [ -12799.7389] [ 2771] [depth= 1] . ( 2 sec) [ -12608.1995] [ 2704] [depth= 8] . ( 2 sec) [ -12544.3158] [ 2689] [depth= 3] . ( 2 sec) [ -12484.6887] [ 2699] [depth= 11] . ( 2 sec) [ -12414.5707] [ 2696] [depth= 2] . ( 2 sec) [ -12273.1444] [ 2678] [depth= 6] . ( 2 sec) [ -12145.2760] [ 2686] [depth= 3] . ( 3 sec) [ -11930.5375] [ 2633] [depth= 4] . ( 3 sec) [ -11845.6077] [ 2588] [depth= 10] . ( 3 sec) [ -11820.4718] [ 2587] [depth= 1] . ( 3 sec) [ -11806.8370] [ 2573] [depth= 6] . ( 3 sec) [ -11800.0091] [ 2577] [depth= 1] . ( 3 sec) [ -11376.0321] [ 2567] [depth= 2] . ( 3 sec) [ -11129.7422] [ 2503] [depth= 5] . ( 3 sec) [ -11027.1224] [ 2401] [depth= 9] . ( 3 sec) [ -10656.2131] [ 2369] [depth= 8] . ( 3 sec) [ -10634.8513] [ 2419] [depth= 1] . ( 3 sec) [ -10545.0148] [ 2411] [depth= 1] . ( 3 sec) [ -10474.4670] [ 2373] [depth= 8] . ( 3 sec) [ -10465.4161] [ 2376] [depth= 1] . ( 3 sec) [ -10405.7487] [ 2348] [depth= 2] . ( 3 sec) [ -10365.4610] [ 2341] [depth= 2] . ( 3 sec) [ -10337.3940] [ 2314] [depth= 4] . ( 3 sec) [ -10153.4272] [ 2388] [depth= 1] . ( 3 sec) [ -10125.2244] [ 2314] [depth= 1] . ( 3 sec) [ -9879.9889] [ 2238] [depth= 4] . ( 3 sec) [ -9879.0016] [ 2239] [depth= 2] . ( 3 sec) [ -9849.8798] [ 2239] [depth= 2] . ( 4 sec) [ -9820.5483] [ 2193] [depth= 1] . ( 4 sec) [ -9731.0198] [ 2193] [depth= 3] . ( 4 sec) [ -9712.5152] [ 2192] [depth= 10] . ( 4 sec) [ -9560.3115] [ 2166] [depth= 1] . ( 4 sec) [ -9533.2267] [ 2166] [depth= 1] . ( 4 sec) [ -9511.6075] [ 2142] [depth= 5] . ( 4 sec) [ -9504.7095] [ 2141] [depth= 1] . ( 4 sec) [ -9504.2139] [ 2141] [depth= 2] . ( 4 sec) [ -9340.0117] [ 2145] [depth= 3] . ( 4 sec) [ -9334.5606] [ 2001] [depth= 2] . ( 4 sec) [ -9333.7040] [ 1998] [depth= 1] . ( 4 sec) [ -9323.0574] [ 1982] [depth= 3] . ( 4 sec) [ -9267.0336] [ 1975] [depth= 1] . ( 4 sec) [ -9122.8463] [ 1923] [depth= 1] . ( 4 sec) [ -9069.7657] [ 1919] [depth= 1] . ( 4 sec) [ -9064.5086] [ 1917] [depth= 1] . ( 4 sec) [ -9048.3575] [ 1909] [depth= 1] . ( 4 sec) [ -9044.1676] [ 1917] [depth= 1] . ( 4 sec) [ -9035.8582] [ 1912] [depth= 1] . ( 4 sec) [ -9016.6339] [ 1908] [depth= 1] . ( 5 sec) [ -9014.4424] [ 1911] [depth= 1] . ( 5 sec) [ -8844.3214] [ 1862] [depth= 5] . ( 5 sec) [ -8799.0255] [ 1854] [depth= 1] . ( 5 sec) [ -8774.0776] [ 1849] [depth= 1] . ( 5 sec) [ -8697.5266] [Branch lengths ] . ( 5 sec) [ -8696.6824] [GTR parameters ] . ( 6 sec) [ -8673.6333] [Alpha ][ 0.810570] . ( 6 sec) [ -8673.4917] [ 1850] [depth= 1] . ( 6 sec) [ -8673.1349] [ 1847] [depth= 1] . ( 6 sec) [ -8673.0164] [ 1848] [depth= 1] . ( 6 sec) [ -8628.5451] [ 1909] [depth= 7] . ( 6 sec) [ -8626.3081] [ 1906] [depth= 1] . ( 6 sec) [ -8626.0689] [ 1906] [depth= 1] . ( 7 sec) [ -8625.9945] [ 1906] [depth= 1] . ( 7 sec) [ -8625.7845] [ 1905] [depth= 1] . ( 7 sec) [ -8622.0323] [ 1906] [depth= 1] . ( 7 sec) [ -8614.5631] [ 1905] [depth= 1] . ( 7 sec) [ -8384.1781] [ 1844] [depth= 7] . ( 7 sec) [ -8379.6548] [ 1843] [depth= 1] . ( 7 sec) [ -8377.4857] [ 1846] [depth= 1] . ( 7 sec) [ -8375.8865] [ 1824] [depth= 1] . ( 7 sec) [ -8307.0529] [ 1725] [depth= 5] . ( 8 sec) [ -8306.8200] [ 1725] [depth= 2] . ( 8 sec) [ -8279.4089] [ 1731] [depth= 1] . ( 8 sec) [ -8279.0681] [ 1730] [depth= 2] . ( 8 sec) [ -8276.1950] [ 1724] [depth= 1] . ( 8 sec) [ -8259.4266] [ 1712] [depth= 4] . ( 8 sec) [ -8255.5110] [ 1710] [depth= 1] . ( 8 sec) [ -8254.8962] [ 1710] [depth= 1] . ( 9 sec) [ -8237.3588] [Branch lengths ] . ( 10 sec) [ -8236.9018] [GTR parameters ] . ( 10 sec) [ -8233.8121] [Alpha ][ 0.985546] . ( 10 sec) [ -8233.7995] [ 1710] [depth= 1] . ( 11 sec) [ -8233.5039] [ 1713] [depth= 1] . ( 13 sec) [ -8233.2674] [ 1716] [depth= 1] . ( 14 sec) [ -8230.8809] [Branch lengths ] . ( 14 sec) [ -8230.8799] [GTR parameters ] . ( 14 sec) [ -8230.8699] [Alpha ][ 0.996902] . ( 18 sec) [ -8230.6838] [Branch lengths ] . ( 39 sec) [ -8230.6597] [Branch lengths ] . ( 39 sec) [ -8230.6597] [Topology ] . ( 40 sec) [ -8230.5542] [Topology ] . ( 40 sec) [ -8230.4708] [Topology ] . ( 41 sec) [ -8230.4470] [Topology ] . ( 42 sec) [ -8230.4360] [Topology ] . ( 43 sec) [ -8230.4305] [Topology ] . ( 43 sec) [ -8230.4278] [Topology ] . ( 44 sec) [ -8230.4264] [Topology ] . ( 44 sec) [ -8230.4261] [GTR parameters ] . ( 44 sec) [ -8230.4249] [Alpha ][ 1.000694] . ( 44 sec) [ -8230.4249] [Topology ] . ( 45 sec) [ -8230.4242] [Topology ] . ( 45 sec) [ -8230.4242] [GTR parameters ] . ( 45 sec) [ -8230.4242] [Alpha ][ 1.000694] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8230.424163. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17717.0653] [GTR parameters ] . ( 1 sec) [ -17371.0612] [Alpha ][ 0.500960] . ( 1 sec) [ -16953.7903] [ 3845] [depth= 8] . ( 1 sec) [ -16287.0847] [ 3759] [depth= 12] . ( 1 sec) [ -16172.0788] [ 3754] [depth= 5] . ( 1 sec) [ -16115.0160] [ 3751] [depth= 6] . ( 1 sec) [ -15720.9290] [ 3713] [depth= 7] . ( 1 sec) [ -15639.3751] [ 3702] [depth= 5] . ( 1 sec) [ -15368.3724] [ 3640] [depth= 6] . ( 1 sec) [ -15348.5459] [ 3624] [depth= 11] . ( 1 sec) [ -15067.3387] [ 3613] [depth= 3] . ( 1 sec) [ -14591.6929] [ 3449] [depth= 15] . ( 1 sec) [ -14484.7086] [ 3436] [depth= 8] . ( 1 sec) [ -14066.8758] [ 3364] [depth= 14] . ( 1 sec) [ -13940.2059] [ 3344] [depth= 8] . ( 1 sec) [ -13900.7909] [ 3330] [depth= 2] . ( 1 sec) [ -13862.9963] [ 3313] [depth= 8] . ( 1 sec) [ -13617.7611] [ 3287] [depth= 2] . ( 1 sec) [ -13539.9939] [ 3260] [depth= 1] . ( 1 sec) [ -13254.4766] [ 3229] [depth= 1] . ( 1 sec) [ -13169.3673] [ 3225] [depth= 6] . ( 1 sec) [ -13084.2677] [ 3199] [depth= 3] . ( 2 sec) [ -12841.4982] [ 3130] [depth= 8] . ( 2 sec) [ -12649.0613] [ 3002] [depth= 5] . ( 2 sec) [ -12575.7079] [ 2995] [depth= 1] . ( 2 sec) [ -12448.7328] [ 2981] [depth= 8] . ( 2 sec) [ -12441.2064] [ 3024] [depth= 1] . ( 2 sec) [ -12247.4810] [ 2928] [depth= 2] . ( 2 sec) [ -12185.7618] [ 2855] [depth= 1] . ( 2 sec) [ -12093.2846] [ 2773] [depth= 10] . ( 2 sec) [ -12014.3900] [ 2706] [depth= 8] . ( 2 sec) [ -11794.1317] [ 2635] [depth= 5] . ( 2 sec) [ -11719.8643] [ 2607] [depth= 5] . ( 2 sec) [ -11385.7120] [ 2583] [depth= 8] . ( 2 sec) [ -11074.1352] [ 2577] [depth= 7] . ( 2 sec) [ -10952.0297] [ 2543] [depth= 1] . ( 2 sec) [ -10879.7743] [ 2516] [depth= 8] . ( 2 sec) [ -10768.5267] [ 2505] [depth= 3] . ( 2 sec) [ -10624.4758] [ 2456] [depth= 1] . ( 2 sec) [ -10597.5190] [ 2435] [depth= 7] . ( 2 sec) [ -10468.0336] [ 2438] [depth= 1] . ( 2 sec) [ -10450.5907] [ 2431] [depth= 1] . ( 2 sec) [ -10383.9482] [ 2401] [depth= 1] . ( 2 sec) [ -10318.5196] [ 2348] [depth= 9] . ( 3 sec) [ -10270.4621] [ 2333] [depth= 7] . ( 3 sec) [ -10251.5531] [ 2331] [depth= 1] . ( 3 sec) [ -10227.9330] [ 2331] [depth= 1] . ( 3 sec) [ -10179.8051] [ 2296] [depth= 5] . ( 3 sec) [ -10166.4564] [ 2326] [depth= 2] . ( 3 sec) [ -10149.1344] [ 2320] [depth= 1] . ( 3 sec) [ -10145.5920] [ 2324] [depth= 2] . ( 3 sec) [ -10002.8093] [ 2281] [depth= 4] . ( 3 sec) [ -9934.0939] [ 2277] [depth= 8] . ( 3 sec) [ -9832.3486] [ 2237] [depth= 2] . ( 3 sec) [ -9787.0730] [ 2237] [depth= 9] . ( 3 sec) [ -9777.4313] [ 2233] [depth= 2] . ( 3 sec) [ -9741.4814] [ 2229] [depth= 1] . ( 3 sec) [ -9675.2783] [ 2222] [depth= 5] . ( 3 sec) [ -9657.8303] [ 2191] [depth= 1] . ( 3 sec) [ -9638.3711] [ 2186] [depth= 4] . ( 3 sec) [ -9634.4376] [ 2183] [depth= 1] . ( 3 sec) [ -9536.2076] [ 2153] [depth= 1] . ( 3 sec) [ -9410.3242] [ 2106] [depth= 4] . ( 3 sec) [ -9407.4585] [ 2102] [depth= 1] . ( 3 sec) [ -9400.0103] [ 2104] [depth= 1] . ( 3 sec) [ -9275.8135] [ 2076] [depth= 4] . ( 4 sec) [ -9235.1358] [ 2077] [depth= 1] . ( 4 sec) [ -9232.5077] [ 2089] [depth= 1] . ( 4 sec) [ -9152.0921] [ 2030] [depth= 8] . ( 4 sec) [ -9151.9447] [ 2032] [depth= 1] . ( 4 sec) [ -9123.5253] [ 2027] [depth= 1] . ( 4 sec) [ -9123.4175] [ 2026] [depth= 1] . ( 4 sec) [ -9071.2138] [ 2007] [depth= 1] . ( 4 sec) [ -9069.2716] [ 2009] [depth= 1] . ( 4 sec) [ -8987.8506] [ 2002] [depth= 2] . ( 4 sec) [ -8984.8241] [ 2002] [depth= 1] . ( 4 sec) [ -8983.7304] [ 2005] [depth= 2] . ( 5 sec) [ -8974.2231] [ 2001] [depth= 1] . ( 5 sec) [ -8849.4261] [Branch lengths ] . ( 5 sec) [ -8849.1117] [GTR parameters ] . ( 5 sec) [ -8828.9896] [Alpha ][ 0.778866] . ( 6 sec) [ -8828.8460] [ 2003] [depth= 2] . ( 6 sec) [ -8828.8180] [ 2004] [depth= 1] . ( 6 sec) [ -8758.9000] [ 1927] [depth= 7] . ( 6 sec) [ -8738.4524] [ 1911] [depth= 1] . ( 6 sec) [ -8717.3538] [ 1898] [depth= 1] . ( 6 sec) [ -8714.6111] [ 1918] [depth= 1] . ( 7 sec) [ -8479.4991] [ 1856] [depth= 4] . ( 7 sec) [ -8375.9209] [ 1744] [depth= 6] . ( 7 sec) [ -8300.1425] [ 1743] [depth= 1] . ( 7 sec) [ -8299.9650] [ 1744] [depth= 2] . ( 7 sec) [ -8299.6331] [ 1745] [depth= 1] . ( 7 sec) [ -8299.3063] [ 1744] [depth= 1] . ( 7 sec) [ -8299.2760] [ 1744] [depth= 1] . ( 7 sec) [ -8298.8938] [ 1741] [depth= 1] . ( 7 sec) [ -8298.6963] [ 1741] [depth= 2] . ( 8 sec) [ -8297.5195] [ 1743] [depth= 1] . ( 8 sec) [ -8292.3998] [ 1739] [depth= 1] . ( 8 sec) [ -8291.8686] [ 1724] [depth= 1] . ( 8 sec) [ -8287.2343] [ 1721] [depth= 1] . ( 8 sec) [ -8287.0653] [ 1721] [depth= 1] . ( 8 sec) [ -8286.7578] [ 1727] [depth= 2] . ( 9 sec) [ -8286.0593] [ 1725] [depth= 1] . ( 9 sec) [ -8285.0100] [ 1724] [depth= 1] . ( 9 sec) [ -8270.1977] [Branch lengths ] . ( 10 sec) [ -8269.8504] [GTR parameters ] . ( 10 sec) [ -8266.0882] [Alpha ][ 0.963285] . ( 10 sec) [ -8238.2821] [ 1699] [depth= 6] . ( 10 sec) [ -8238.2656] [ 1700] [depth= 1] . ( 11 sec) [ -8237.0571] [ 1702] [depth= 1] . ( 12 sec) [ -8236.7117] [ 1704] [depth= 1] . ( 13 sec) [ -8235.3092] [Branch lengths ] . ( 14 sec) [ -8235.2173] [GTR parameters ] . ( 14 sec) [ -8235.1605] [Alpha ][ 0.988939] . ( 18 sec) [ -8234.5921] [Branch lengths ] . ( 39 sec) [ -8231.7433] [Branch lengths ] . ( 39 sec) [ -8231.7433] [Topology ] . ( 39 sec) [ -8230.6248] [Topology ] . ( 40 sec) [ -8230.4985] [Topology ] . ( 41 sec) [ -8230.4725] [Topology ] . ( 42 sec) [ -8230.4610] [Topology ] . ( 43 sec) [ -8230.4554] [Topology ] . ( 43 sec) [ -8230.4525] [Topology ] . ( 44 sec) [ -8230.4511] [Topology ] . ( 44 sec) [ -8230.4444] [GTR parameters ] . ( 45 sec) [ -8230.4338] [Alpha ][ 1.000598] . ( 45 sec) [ -8230.4338] [Topology ] . ( 45 sec) [ -8230.4326] [Topology ] . ( 46 sec) [ -8230.4322] [Topology ] . ( 46 sec) [ -8230.4322] [GTR parameters ] . ( 46 sec) [ -8230.4322] [Alpha ][ 1.000598] . ( 46 sec) [ -8230.4322] [Topology ] . ( 47 sec) [ -8230.4320] [Topology ] . ( 47 sec) [ -8230.4320] [GTR parameters ] . ( 47 sec) [ -8230.4320] [Alpha ][ 1.000598] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -8230.4237] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8230.423659. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17854.3932] [GTR parameters ] . ( 1 sec) [ -17513.3089] [Alpha ][ 0.500960] . ( 1 sec) [ -17097.7375] [ 3787] [depth= 8] . ( 1 sec) [ -16752.3452] [ 3713] [depth= 5] . ( 1 sec) [ -16368.8891] [ 3663] [depth= 2] . ( 1 sec) [ -16161.7217] [ 3586] [depth= 1] . ( 1 sec) [ -15884.0467] [ 3516] [depth= 6] . ( 1 sec) [ -15871.7204] [ 3516] [depth= 2] . ( 1 sec) [ -15763.0004] [ 3506] [depth= 4] . ( 1 sec) [ -15570.8483] [ 3411] [depth= 1] . ( 2 sec) [ -15326.0236] [ 3360] [depth= 14] . ( 2 sec) [ -15203.3977] [ 3342] [depth= 2] . ( 2 sec) [ -15135.8805] [ 3346] [depth= 2] . ( 2 sec) [ -15034.5547] [ 3331] [depth= 4] . ( 2 sec) [ -14970.7719] [ 3321] [depth= 3] . ( 2 sec) [ -14955.5920] [ 3316] [depth= 2] . ( 2 sec) [ -14842.2254] [ 3253] [depth= 5] . ( 2 sec) [ -14828.2737] [ 3247] [depth= 1] . ( 2 sec) [ -14569.4528] [ 3229] [depth= 2] . ( 2 sec) [ -14318.4403] [ 3183] [depth= 1] . ( 2 sec) [ -14153.9578] [ 3123] [depth= 11] . ( 2 sec) [ -14008.1541] [ 3109] [depth= 1] . ( 2 sec) [ -13888.1995] [ 3073] [depth= 5] . ( 2 sec) [ -13404.2532] [ 3031] [depth= 16] . ( 2 sec) [ -13218.4138] [ 3054] [depth= 1] . ( 2 sec) [ -12887.2296] [ 2919] [depth= 2] . ( 2 sec) [ -12797.1300] [ 2900] [depth= 15] . ( 2 sec) [ -12483.7816] [ 2875] [depth= 16] . ( 2 sec) [ -12218.0074] [ 2797] [depth= 12] . ( 2 sec) [ -12119.2472] [ 2719] [depth= 13] . ( 2 sec) [ -11923.3556] [ 2634] [depth= 6] . ( 2 sec) [ -11819.4699] [ 2631] [depth= 1] . ( 2 sec) [ -11551.4943] [ 2560] [depth= 12] . ( 3 sec) [ -11535.5985] [ 2558] [depth= 1] . ( 3 sec) [ -11336.1700] [ 2470] [depth= 11] . ( 3 sec) [ -11080.3186] [ 2384] [depth= 1] . ( 3 sec) [ -10929.5027] [ 2316] [depth= 12] . ( 3 sec) [ -10730.2181] [ 2310] [depth= 1] . ( 3 sec) [ -10681.6228] [ 2310] [depth= 1] . ( 3 sec) [ -10642.7017] [ 2313] [depth= 8] . ( 3 sec) [ -10607.7730] [ 2296] [depth= 5] . ( 3 sec) [ -10589.6720] [ 2286] [depth= 10] . ( 3 sec) [ -10209.8810] [ 2254] [depth= 6] . ( 3 sec) [ -9944.0858] [ 2210] [depth= 3] . ( 3 sec) [ -9689.0099] [ 2124] [depth= 9] . ( 3 sec) [ -9624.3274] [ 2089] [depth= 1] . ( 3 sec) [ -9586.8205] [ 2086] [depth= 2] . ( 3 sec) [ -9562.8481] [ 2082] [depth= 1] . ( 3 sec) [ -9552.7200] [ 2082] [depth= 2] . ( 3 sec) [ -9505.7139] [ 2072] [depth= 1] . ( 3 sec) [ -9375.2195] [ 2046] [depth= 3] . ( 3 sec) [ -9282.4940] [ 1994] [depth= 1] . ( 3 sec) [ -9196.1353] [ 1981] [depth= 3] . ( 3 sec) [ -9173.9256] [ 1977] [depth= 1] . ( 4 sec) [ -9167.2118] [ 1975] [depth= 1] . ( 4 sec) [ -9158.3597] [ 1974] [depth= 1] . ( 4 sec) [ -9149.5645] [ 1960] [depth= 3] . ( 4 sec) [ -9077.4788] [ 1939] [depth= 4] . ( 4 sec) [ -9064.0902] [ 1934] [depth= 1] . ( 4 sec) [ -8967.5211] [ 1903] [depth= 3] . ( 4 sec) [ -8956.6564] [ 1906] [depth= 3] . ( 4 sec) [ -8903.6778] [ 1874] [depth= 3] . ( 4 sec) [ -8901.9566] [ 1878] [depth= 1] . ( 4 sec) [ -8898.3862] [ 1874] [depth= 1] . ( 4 sec) [ -8843.3560] [ 1856] [depth= 1] . ( 4 sec) [ -8841.3684] [ 1855] [depth= 1] . ( 4 sec) [ -8792.1252] [ 1839] [depth= 2] . ( 4 sec) [ -8778.3111] [ 1831] [depth= 2] . ( 4 sec) [ -8768.7380] [ 1825] [depth= 1] . ( 4 sec) [ -8766.5141] [ 1827] [depth= 1] . ( 5 sec) [ -8766.1654] [ 1827] [depth= 1] . ( 5 sec) [ -8749.2792] [ 1823] [depth= 1] . ( 5 sec) [ -8687.2887] [ 1827] [depth= 1] . ( 5 sec) [ -8681.4354] [ 1829] [depth= 1] . ( 5 sec) [ -8549.3930] [ 1757] [depth= 6] . ( 5 sec) [ -8441.2856] [Branch lengths ] . ( 6 sec) [ -8440.3609] [GTR parameters ] . ( 6 sec) [ -8406.1998] [Alpha ][ 0.924227] . ( 6 sec) [ -8382.5967] [ 1748] [depth= 2] . ( 6 sec) [ -8298.7704] [ 1724] [depth= 1] . ( 6 sec) [ -8295.6267] [ 1721] [depth= 2] . ( 6 sec) [ -8295.0872] [ 1723] [depth= 1] . ( 6 sec) [ -8287.3795] [ 1722] [depth= 1] . ( 6 sec) [ -8266.6354] [ 1712] [depth= 1] . ( 7 sec) [ -8264.6889] [ 1710] [depth= 4] . ( 7 sec) [ -8262.4014] [ 1714] [depth= 1] . ( 7 sec) [ -8256.8636] [ 1709] [depth= 1] . ( 7 sec) [ -8255.0729] [ 1709] [depth= 1] . ( 7 sec) [ -8253.2454] [ 1709] [depth= 1] . ( 8 sec) [ -8253.2043] [ 1709] [depth= 1] . ( 8 sec) [ -8251.7576] [ 1707] [depth= 2] . ( 8 sec) [ -8249.0151] [ 1705] [depth= 1] . ( 8 sec) [ -8245.8059] [ 1701] [depth= 1] . ( 8 sec) [ -8244.9287] [ 1700] [depth= 1] . ( 8 sec) [ -8244.6305] [ 1700] [depth= 1] . ( 8 sec) [ -8244.4264] [ 1699] [depth= 1] . ( 9 sec) [ -8231.8605] [Branch lengths ] . ( 9 sec) [ -8231.8006] [GTR parameters ] . ( 9 sec) [ -8231.3426] [Alpha ][ 0.996398] . ( 10 sec) [ -8231.3278] [ 1703] [depth= 1] . ( 13 sec) [ -8230.7214] [Branch lengths ] . ( 14 sec) [ -8230.7211] [GTR parameters ] . ( 14 sec) [ -8230.7210] [Alpha ][ 0.997394] . ( 34 sec) [ -8230.6665] [Branch lengths ] . ( 34 sec) [ -8230.6665] [Topology ] . ( 35 sec) [ -8230.5561] [Topology ] . ( 36 sec) [ -8230.4800] [Topology ] . ( 36 sec) [ -8230.4563] [Topology ] . ( 37 sec) [ -8230.4450] [Topology ] . ( 38 sec) [ -8230.4393] [Topology ] . ( 39 sec) [ -8230.4364] [Topology ] . ( 39 sec) [ -8230.4349] [Topology ] . ( 39 sec) [ -8230.4344] [GTR parameters ] . ( 39 sec) [ -8230.4334] [Alpha ][ 1.000869] . ( 39 sec) [ -8230.4334] [Topology ] . ( 40 sec) [ -8230.4326] [Topology ] . ( 40 sec) [ -8230.4326] [GTR parameters ] . ( 40 sec) [ -8230.4326] [Alpha ][ 1.000869] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -8230.4242] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8230.424214. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17832.4475] [GTR parameters ] . ( 1 sec) [ -17458.4078] [Alpha ][ 0.500960] . ( 1 sec) [ -16880.9767] [ 3863] [depth= 6] . ( 1 sec) [ -16577.6347] [ 3781] [depth= 12] . ( 1 sec) [ -16509.2445] [ 3773] [depth= 5] . ( 1 sec) [ -16498.5672] [ 3764] [depth= 6] . ( 1 sec) [ -16436.5203] [ 3742] [depth= 2] . ( 1 sec) [ -16323.8242] [ 3734] [depth= 2] . ( 1 sec) [ -16261.8471] [ 3719] [depth= 4] . ( 1 sec) [ -16084.7876] [ 3717] [depth= 1] . ( 1 sec) [ -15692.0819] [ 3654] [depth= 9] . ( 1 sec) [ -15687.6789] [ 3650] [depth= 2] . ( 1 sec) [ -15463.6543] [ 3479] [depth= 8] . ( 1 sec) [ -14841.9401] [ 3464] [depth= 21] . ( 1 sec) [ -14312.4403] [ 3323] [depth= 10] . ( 1 sec) [ -14252.7163] [ 3310] [depth= 1] . ( 1 sec) [ -14113.6144] [ 3280] [depth= 12] . ( 1 sec) [ -14094.1497] [ 3282] [depth= 1] . ( 2 sec) [ -14060.7188] [ 3276] [depth= 2] . ( 2 sec) [ -14039.4251] [ 3243] [depth= 2] . ( 2 sec) [ -14015.8079] [ 3239] [depth= 11] . ( 2 sec) [ -14007.9734] [ 3239] [depth= 1] . ( 2 sec) [ -13983.2620] [ 3232] [depth= 1] . ( 2 sec) [ -13838.6494] [ 3204] [depth= 8] . ( 2 sec) [ -13788.8996] [ 3196] [depth= 9] . ( 2 sec) [ -13784.1604] [ 3191] [depth= 1] . ( 2 sec) [ -13728.2059] [ 3145] [depth= 4] . ( 2 sec) [ -13662.6444] [ 3136] [depth= 1] . ( 2 sec) [ -13397.3914] [ 3086] [depth= 1] . ( 2 sec) [ -12989.1971] [ 3091] [depth= 2] . ( 2 sec) [ -12979.3349] [ 3089] [depth= 1] . ( 2 sec) [ -12635.6336] [ 2913] [depth= 9] . ( 2 sec) [ -12545.7613] [ 2885] [depth= 1] . ( 2 sec) [ -12503.0696] [ 2872] [depth= 9] . ( 2 sec) [ -12462.9622] [ 2872] [depth= 1] . ( 2 sec) [ -12390.9973] [ 2860] [depth= 2] . ( 2 sec) [ -12289.3268] [ 2811] [depth= 10] . ( 2 sec) [ -12276.0586] [ 2805] [depth= 2] . ( 2 sec) [ -12097.5571] [ 2744] [depth= 1] . ( 2 sec) [ -12058.0657] [ 2728] [depth= 3] . ( 2 sec) [ -12028.2207] [ 2684] [depth= 1] . ( 3 sec) [ -11653.4758] [ 2524] [depth= 11] . ( 3 sec) [ -11168.2785] [ 2525] [depth= 8] . ( 3 sec) [ -10814.5133] [ 2386] [depth= 7] . ( 3 sec) [ -10714.2188] [ 2326] [depth= 8] . ( 3 sec) [ -10210.3373] [ 2340] [depth= 1] . ( 3 sec) [ -10100.9352] [ 2323] [depth= 7] . ( 3 sec) [ -9895.4473] [ 2234] [depth= 6] . ( 3 sec) [ -9786.8294] [ 2230] [depth= 1] . ( 3 sec) [ -9731.4814] [ 2217] [depth= 1] . ( 3 sec) [ -9717.3464] [ 2213] [depth= 1] . ( 3 sec) [ -9646.5363] [ 2109] [depth= 7] . ( 3 sec) [ -9613.8072] [ 2127] [depth= 1] . ( 3 sec) [ -9474.4418] [ 2034] [depth= 5] . ( 3 sec) [ -9457.2942] [ 2018] [depth= 4] . ( 3 sec) [ -9262.6593] [ 2011] [depth= 2] . ( 3 sec) [ -9189.3615] [ 1985] [depth= 8] . ( 3 sec) [ -9127.4218] [ 1973] [depth= 7] . ( 3 sec) [ -8871.5895] [ 1884] [depth= 5] . ( 3 sec) [ -8863.5237] [ 1888] [depth= 1] . ( 3 sec) [ -8856.0101] [ 1884] [depth= 1] . ( 3 sec) [ -8746.4079] [ 1864] [depth= 6] . ( 4 sec) [ -8729.8784] [ 1861] [depth= 1] . ( 4 sec) [ -8722.7808] [ 1844] [depth= 1] . ( 4 sec) [ -8711.2661] [ 1836] [depth= 1] . ( 4 sec) [ -8618.3511] [ 1809] [depth= 4] . ( 4 sec) [ -8603.6340] [ 1811] [depth= 1] . ( 4 sec) [ -8577.2136] [ 1807] [depth= 3] . ( 4 sec) [ -8569.6408] [ 1805] [depth= 1] . ( 4 sec) [ -8567.7746] [ 1804] [depth= 1] . ( 4 sec) [ -8549.0641] [ 1786] [depth= 1] . ( 4 sec) [ -8504.1054] [ 1763] [depth= 4] . ( 4 sec) [ -8499.2036] [ 1764] [depth= 1] . ( 4 sec) [ -8490.9027] [ 1750] [depth= 5] . ( 4 sec) [ -8469.0420] [ 1755] [depth= 1] . ( 4 sec) [ -8443.0344] [ 1751] [depth= 1] . ( 4 sec) [ -8438.7506] [ 1747] [depth= 1] . ( 4 sec) [ -8431.1310] [ 1742] [depth= 1] . ( 5 sec) [ -8334.2843] [Branch lengths ] . ( 5 sec) [ -8334.1846] [GTR parameters ] . ( 5 sec) [ -8303.9774] [Alpha ][ 0.901333] . ( 5 sec) [ -8297.1124] [ 1743] [depth= 2] . ( 6 sec) [ -8296.4073] [ 1742] [depth= 2] . ( 6 sec) [ -8284.8817] [ 1728] [depth= 2] . ( 6 sec) [ -8267.9825] [ 1718] [depth= 1] . ( 6 sec) [ -8261.5206] [ 1709] [depth= 1] . ( 6 sec) [ -8261.3512] [ 1709] [depth= 1] . ( 6 sec) [ -8255.6085] [ 1704] [depth= 1] . ( 6 sec) [ -8255.5771] [ 1704] [depth= 1] . ( 7 sec) [ -8255.2155] [ 1706] [depth= 1] . ( 7 sec) [ -8242.2937] [ 1702] [depth= 3] . ( 8 sec) [ -8242.2342] [ 1703] [depth= 1] . ( 9 sec) [ -8233.3161] [Branch lengths ] . ( 9 sec) [ -8233.0632] [GTR parameters ] . ( 9 sec) [ -8232.3488] [Alpha ][ 0.989906] . ( 10 sec) [ -8232.2068] [ 1705] [depth= 1] . ( 11 sec) [ -8231.9817] [ 1703] [depth= 1] . ( 11 sec) [ -8231.7563] [ 1705] [depth= 1] . ( 12 sec) [ -8231.5775] [ 1706] [depth= 1] . ( 13 sec) [ -8231.0520] [Branch lengths ] . ( 13 sec) [ -8231.0495] [GTR parameters ] . ( 13 sec) [ -8231.0463] [Alpha ][ 0.996282] . ( 17 sec) [ -8230.9712] [Branch lengths ] . ( 37 sec) [ -8230.9642] [Branch lengths ] . ( 37 sec) [ -8230.9642] [Topology ] . ( 38 sec) [ -8230.7107] [Topology ] . ( 39 sec) [ -8230.4988] [Topology ] . ( 40 sec) [ -8230.4665] [Topology ] . ( 40 sec) [ -8230.4543] [Topology ] . ( 41 sec) [ -8230.4486] [Topology ] . ( 42 sec) [ -8230.4458] [Topology ] . ( 42 sec) [ -8230.4444] [Topology ] . ( 43 sec) [ -8230.4350] [GTR parameters ] . ( 43 sec) [ -8230.4333] [Alpha ][ 1.000886] . ( 43 sec) [ -8230.4333] [Topology ] . ( 43 sec) [ -8230.4325] [Topology ] . ( 44 sec) [ -8230.4325] [GTR parameters ] . ( 44 sec) [ -8230.4325] [Alpha ][ 1.000886] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -8230.4241] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8230.424119. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8289.945444 . ( 0 sec) [ -8288.3499] [GTR parameters ] . ( 0 sec) [ -8288.3411] [Alpha ][ 0.988651] . ( 0 sec) [ -8288.3411] [Topology ] . ( 1 sec) [ -8244.1423] [Topology ] . ( 2 sec) [ -8236.4087] [Topology ] . ( 3 sec) [ -8234.2678] [Topology ] . ( 3 sec) [ -8233.3628] [Topology ] . ( 4 sec) [ -8232.9429] [Topology ] . ( 5 sec) [ -8232.6466] [Topology ] . ( 6 sec) [ -8232.4177] [Topology ] . ( 6 sec) [ -8232.3566] [Topology ] . ( 7 sec) [ -8232.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8232.316719 . ( 14 sec) [ -8232.2915] [GTR parameters ] . ( 14 sec) [ -8232.2787] [Alpha ][ 1.001505] . ( 14 sec) [ -8232.2787] [Topology ] . ( 14 sec) [ -8232.2703] [Topology ] . ( 15 sec) [ -8232.2664] [Topology ] . ( 16 sec) [ -8232.2645] [Topology ] . ( 17 sec) [ -8232.2636] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8232.263567 . ( 22 sec) [ -8232.2635] [GTR parameters ] . ( 22 sec) [ -8232.2634] [Alpha ][ 1.002599] . ( 22 sec) [ -8232.2634] [Topology ] . ( 23 sec) [ -8232.2629] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 35 sec) [ -8288.3499] [GTR parameters ] . ( 35 sec) [ -8288.3411] [Alpha ][ 0.988651] . ( 35 sec) [ -8277.2816] [ 1708] [depth= 1] . ( 35 sec) [ -8276.1095] [ 1703] [depth= 1] . ( 35 sec) [ -8269.1435] [ 1701] [depth= 2] . ( 36 sec) [ -8262.5412] [ 1711] [depth= 1] . ( 36 sec) [ -8262.0841] [ 1714] [depth= 1] . ( 36 sec) [ -8261.5964] [ 1717] [depth= 1] . ( 37 sec) [ -8258.4061] [ 1718] [depth= 1] . ( 37 sec) [ -8256.9569] [ 1718] [depth= 3] . ( 38 sec) [ -8256.3808] [ 1717] [depth= 2] . ( 38 sec) [ -8255.6193] [ 1717] [depth= 1] . ( 38 sec) [ -8255.4415] [ 1718] [depth= 1] . ( 39 sec) [ -8232.0786] [Branch lengths ] . ( 39 sec) [ -8232.0481] [GTR parameters ] . ( 39 sec) [ -8232.0472] [Alpha ][ 0.992001] . ( 40 sec) [ -8231.9472] [ 1718] [depth= 1] . ( 43 sec) [ -8231.0530] [Branch lengths ] . ( 43 sec) [ -8231.0526] [GTR parameters ] . ( 43 sec) [ -8231.0512] [Alpha ][ 0.996082] . ( 64 sec) [ -8230.9774] [Branch lengths ] . ( 64 sec) [ -8230.9774] [Topology ] . ( 65 sec) [ -8230.7117] [Topology ] . ( 65 sec) [ -8230.4978] [Topology ] . ( 66 sec) [ -8230.4656] [Topology ] . ( 67 sec) [ -8230.4537] [Topology ] . ( 68 sec) [ -8230.4482] [Topology ] . ( 68 sec) [ -8230.4455] [Topology ] . ( 69 sec) [ -8230.4441] [Topology ] . ( 69 sec) [ -8230.4350] [GTR parameters ] . ( 69 sec) [ -8230.4332] [Alpha ][ 1.000787] . ( 69 sec) [ -8230.4332] [Topology ] . ( 70 sec) [ -8230.4325] [Topology ] . ( 70 sec) [ -8230.4325] [GTR parameters ] . ( 70 sec) [ -8230.4325] [Alpha ][ 1.000787] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -8230.4242] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8232.262930 . Log likelihood obtained after SPR moves : -8230.424162 . Log likelihood of the current tree: -8230.424162. . Printing the most likely tree in file 'data56.phy_phyml_tree.txt'... . Best log likelihood : -8230.423659 . Time used 0h1m21s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo