.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data95.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... . 415 patterns found. (out of a total of 500 sites) . 84 sites without polymorphism (16.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16417.4401] [GTR parameters ] . ( 1 sec) [ -16186.8532] [Alpha ][ 0.500960] . ( 1 sec) [ -16006.6423] [ 3459] [depth= 4] . ( 1 sec) [ -15818.7458] [ 3420] [depth= 6] . ( 1 sec) [ -15590.5964] [ 3409] [depth= 2] . ( 1 sec) [ -15550.6060] [ 3403] [depth= 2] . ( 1 sec) [ -15364.2843] [ 3324] [depth= 5] . ( 1 sec) [ -15208.2030] [ 3313] [depth= 7] . ( 1 sec) [ -15207.3352] [ 3317] [depth= 1] . ( 1 sec) [ -15140.4044] [ 3319] [depth= 1] . ( 1 sec) [ -15132.4966] [ 3315] [depth= 1] . ( 1 sec) [ -14975.4067] [ 3282] [depth= 8] . ( 1 sec) [ -14894.0230] [ 3283] [depth= 6] . ( 1 sec) [ -14819.0865] [ 3250] [depth= 6] . ( 1 sec) [ -14674.8873] [ 3247] [depth= 2] . ( 1 sec) [ -14502.3432] [ 3222] [depth= 9] . ( 1 sec) [ -14372.6185] [ 3222] [depth= 3] . ( 1 sec) [ -14351.9710] [ 3216] [depth= 3] . ( 1 sec) [ -14328.9581] [ 3203] [depth= 4] . ( 1 sec) [ -14253.2856] [ 3199] [depth= 2] . ( 1 sec) [ -14188.6406] [ 3194] [depth= 3] . ( 1 sec) [ -14118.6494] [ 3160] [depth= 1] . ( 1 sec) [ -14038.8935] [ 3144] [depth= 5] . ( 2 sec) [ -13859.7996] [ 3145] [depth= 2] . ( 2 sec) [ -13633.7717] [ 3094] [depth= 2] . ( 2 sec) [ -13426.0560] [ 3066] [depth= 1] . ( 2 sec) [ -12896.0400] [ 3011] [depth= 7] . ( 2 sec) [ -12813.5197] [ 3006] [depth= 5] . ( 2 sec) [ -12566.7219] [ 2935] [depth= 15] . ( 2 sec) [ -12534.4455] [ 2925] [depth= 5] . ( 2 sec) [ -12511.4569] [ 2926] [depth= 1] . ( 2 sec) [ -12504.3483] [ 2919] [depth= 6] . ( 2 sec) [ -12473.9596] [ 2922] [depth= 1] . ( 2 sec) [ -12360.5558] [ 2907] [depth= 6] . ( 2 sec) [ -12315.6437] [ 2897] [depth= 1] . ( 2 sec) [ -12303.0212] [ 2900] [depth= 1] . ( 2 sec) [ -12269.2654] [ 2893] [depth= 13] . ( 2 sec) [ -12114.7816] [ 2845] [depth= 14] . ( 2 sec) [ -12100.5581] [ 2840] [depth= 11] . ( 2 sec) [ -11769.4844] [ 2766] [depth= 3] . ( 2 sec) [ -11705.5247] [ 2742] [depth= 1] . ( 2 sec) [ -11599.3613] [ 2733] [depth= 13] . ( 2 sec) [ -11525.7151] [ 2702] [depth= 2] . ( 3 sec) [ -11458.6079] [ 2685] [depth= 4] . ( 3 sec) [ -11437.8482] [ 2693] [depth= 1] . ( 3 sec) [ -11394.9077] [ 2662] [depth= 1] . ( 3 sec) [ -11086.7827] [ 2534] [depth= 3] . ( 3 sec) [ -11011.4383] [ 2505] [depth= 1] . ( 3 sec) [ -11010.5797] [ 2507] [depth= 1] . ( 3 sec) [ -10909.5866] [ 2436] [depth= 10] . ( 3 sec) [ -10909.3306] [ 2431] [depth= 7] . ( 3 sec) [ -10801.4831] [ 2436] [depth= 12] . ( 3 sec) [ -10728.2569] [ 2361] [depth= 3] . ( 3 sec) [ -10657.8128] [ 2356] [depth= 1] . ( 3 sec) [ -10632.4861] [ 2348] [depth= 2] . ( 3 sec) [ -10324.8808] [ 2220] [depth= 13] . ( 3 sec) [ -10228.1058] [ 2185] [depth= 6] . ( 3 sec) [ -10209.1055] [ 2186] [depth= 1] . ( 3 sec) [ -10139.7349] [ 2180] [depth= 8] . ( 3 sec) [ -10082.8620] [ 2163] [depth= 2] . ( 3 sec) [ -10076.3848] [ 2163] [depth= 3] . ( 3 sec) [ -10010.3997] [ 2159] [depth= 2] . ( 4 sec) [ -10007.3979] [ 2163] [depth= 1] . ( 4 sec) [ -10000.8765] [ 2160] [depth= 2] . ( 4 sec) [ -9990.0241] [ 2157] [depth= 2] . ( 4 sec) [ -9978.3142] [ 2158] [depth= 1] . ( 4 sec) [ -9970.0466] [ 2156] [depth= 1] . ( 4 sec) [ -9967.5076] [ 2155] [depth= 1] . ( 4 sec) [ -9959.5235] [ 2152] [depth= 1] . ( 4 sec) [ -9937.3107] [ 2146] [depth= 2] . ( 4 sec) [ -9869.2317] [ 2096] [depth= 1] . ( 4 sec) [ -9852.9815] [ 2092] [depth= 1] . ( 4 sec) [ -9844.9766] [ 2093] [depth= 1] . ( 4 sec) [ -9761.8816] [ 2063] [depth= 6] . ( 4 sec) [ -9714.1596] [ 2051] [depth= 3] . ( 4 sec) [ -9708.7815] [ 2048] [depth= 1] . ( 4 sec) [ -9679.1819] [ 2039] [depth= 1] . ( 4 sec) [ -9671.2016] [ 2036] [depth= 1] . ( 5 sec) [ -9660.7314] [ 2036] [depth= 4] . ( 5 sec) [ -9654.0746] [ 2030] [depth= 1] . ( 5 sec) [ -9527.4603] [Branch lengths ] . ( 5 sec) [ -9525.7461] [GTR parameters ] . ( 5 sec) [ -9494.2392] [Alpha ][ 0.898343] . ( 6 sec) [ -9494.2086] [ 2031] [depth= 1] . ( 6 sec) [ -9494.1641] [ 2034] [depth= 1] . ( 6 sec) [ -9489.5818] [ 2029] [depth= 1] . ( 6 sec) [ -9485.6229] [ 2023] [depth= 3] . ( 6 sec) [ -9480.1737] [ 2026] [depth= 2] . ( 6 sec) [ -9468.2535] [ 2021] [depth= 1] . ( 6 sec) [ -9463.4009] [ 2018] [depth= 2] . ( 6 sec) [ -9449.1914] [ 2008] [depth= 4] . ( 7 sec) [ -9442.6217] [ 2002] [depth= 1] . ( 7 sec) [ -9441.6176] [ 2003] [depth= 1] . ( 7 sec) [ -9441.1722] [ 2007] [depth= 3] . ( 7 sec) [ -9415.3821] [ 1994] [depth= 2] . ( 7 sec) [ -9354.0561] [ 1962] [depth= 5] . ( 7 sec) [ -9333.0415] [ 1962] [depth= 1] . ( 7 sec) [ -9331.1563] [ 1956] [depth= 2] . ( 8 sec) [ -9322.2091] [ 1956] [depth= 2] . ( 8 sec) [ -9321.4816] [ 1956] [depth= 2] . ( 8 sec) [ -9321.2190] [ 1957] [depth= 1] . ( 8 sec) [ -9320.6991] [ 1959] [depth= 1] . ( 9 sec) [ -9317.5235] [ 1964] [depth= 1] . ( 9 sec) [ -9315.2165] [ 1961] [depth= 1] . ( 9 sec) [ -9315.0566] [ 1963] [depth= 1] . ( 9 sec) [ -9301.1164] [Branch lengths ] . ( 9 sec) [ -9300.6810] [GTR parameters ] . ( 10 sec) [ -9299.5982] [Alpha ][ 1.007340] . ( 10 sec) [ -9298.7601] [ 1964] [depth= 1] . ( 12 sec) [ -9297.2941] [ 1959] [depth= 2] . ( 13 sec) [ -9296.8589] [ 1956] [depth= 2] . ( 13 sec) [ -9296.7894] [ 1956] [depth= 1] . ( 14 sec) [ -9296.6777] [ 1953] [depth= 1] . ( 14 sec) [ -9292.8837] [Branch lengths ] . ( 15 sec) [ -9292.8768] [GTR parameters ] . ( 15 sec) [ -9292.8185] [Alpha ][ 1.034387] . ( 17 sec) [ -9292.7851] [ 1953] [depth= 1] . ( 20 sec) [ -9292.2281] [Branch lengths ] . ( 20 sec) [ -9292.2262] [GTR parameters ] . ( 20 sec) [ -9292.2192] [Alpha ][ 1.044214] . ( 43 sec) [ -9292.1473] [Branch lengths ] . ( 43 sec) [ -9292.1473] [Topology ] . ( 44 sec) [ -9292.1399] [Topology ] . ( 45 sec) [ -9292.1373] [Topology ] . ( 46 sec) [ -9292.1360] [Topology ] . ( 46 sec) [ -9292.1354] [Topology ] . ( 47 sec) [ -9292.1354] [GTR parameters ] . ( 47 sec) [ -9292.1338] [Alpha ][ 1.048768] . ( 47 sec) [ -9292.1338] [Topology ] . ( 47 sec) [ -9292.1333] [Topology ] . ( 47 sec) [ -9292.1333] [GTR parameters ] . ( 48 sec) [ -9292.1333] [Alpha ][ 1.048768] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9292.133277. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -15944.7631] [GTR parameters ] . ( 0 sec) [ -15723.5841] [Alpha ][ 0.500960] . ( 1 sec) [ -15660.1148] [ 3511] [depth= 4] . ( 1 sec) [ -15475.1176] [ 3473] [depth= 3] . ( 1 sec) [ -15445.9184] [ 3452] [depth= 2] . ( 1 sec) [ -15333.2469] [ 3443] [depth= 7] . ( 1 sec) [ -15217.2793] [ 3405] [depth= 1] . ( 1 sec) [ -15096.4334] [ 3391] [depth= 10] . ( 1 sec) [ -15026.3541] [ 3385] [depth= 1] . ( 1 sec) [ -14982.0721] [ 3379] [depth= 4] . ( 1 sec) [ -14935.1113] [ 3296] [depth= 2] . ( 1 sec) [ -14906.0397] [ 3292] [depth= 5] . ( 1 sec) [ -14757.3071] [ 3279] [depth= 3] . ( 1 sec) [ -14712.8790] [ 3267] [depth= 1] . ( 1 sec) [ -14487.8354] [ 3189] [depth= 9] . ( 1 sec) [ -14457.6298] [ 3181] [depth= 3] . ( 1 sec) [ -14325.0981] [ 3112] [depth= 4] . ( 1 sec) [ -14177.7140] [ 3047] [depth= 10] . ( 1 sec) [ -14171.1865] [ 3021] [depth= 12] . ( 1 sec) [ -13988.9298] [ 2981] [depth= 3] . ( 1 sec) [ -13780.5361] [ 2987] [depth= 1] . ( 1 sec) [ -13761.0445] [ 2961] [depth= 1] . ( 1 sec) [ -13366.3768] [ 2874] [depth= 5] . ( 1 sec) [ -13316.1638] [ 2857] [depth= 8] . ( 1 sec) [ -13276.2915] [ 2859] [depth= 12] . ( 2 sec) [ -13184.0018] [ 2833] [depth= 14] . ( 2 sec) [ -13155.3953] [ 2835] [depth= 1] . ( 2 sec) [ -12431.2048] [ 2706] [depth= 16] . ( 2 sec) [ -12416.0957] [ 2713] [depth= 1] . ( 2 sec) [ -12409.7650] [ 2711] [depth= 2] . ( 2 sec) [ -12140.2553] [ 2680] [depth= 5] . ( 2 sec) [ -11944.9478] [ 2607] [depth= 7] . ( 2 sec) [ -11921.0697] [ 2605] [depth= 1] . ( 2 sec) [ -11693.1240] [ 2513] [depth= 8] . ( 2 sec) [ -11687.5932] [ 2511] [depth= 1] . ( 2 sec) [ -11681.9158] [ 2511] [depth= 2] . ( 2 sec) [ -11648.4943] [ 2508] [depth= 2] . ( 2 sec) [ -11588.6202] [ 2486] [depth= 4] . ( 2 sec) [ -11585.5577] [ 2485] [depth= 1] . ( 2 sec) [ -11565.1781] [ 2478] [depth= 1] . ( 2 sec) [ -11535.3353] [ 2474] [depth= 2] . ( 2 sec) [ -11382.6598] [ 2433] [depth= 7] . ( 2 sec) [ -11265.9633] [ 2414] [depth= 1] . ( 2 sec) [ -11216.4598] [ 2389] [depth= 3] . ( 2 sec) [ -11210.8554] [ 2386] [depth= 1] . ( 2 sec) [ -11162.7181] [ 2352] [depth= 7] . ( 2 sec) [ -11048.2039] [ 2303] [depth= 6] . ( 3 sec) [ -11042.3897] [ 2301] [depth= 2] . ( 3 sec) [ -11024.9646] [ 2297] [depth= 1] . ( 3 sec) [ -10810.8689] [ 2285] [depth= 3] . ( 3 sec) [ -10780.6196] [ 2281] [depth= 1] . ( 3 sec) [ -10760.8410] [ 2281] [depth= 1] . ( 3 sec) [ -10759.2255] [ 2281] [depth= 1] . ( 3 sec) [ -10672.5408] [ 2281] [depth= 1] . ( 3 sec) [ -10585.6748] [ 2293] [depth= 6] . ( 3 sec) [ -10413.1060] [ 2284] [depth= 2] . ( 3 sec) [ -10404.5471] [ 2280] [depth= 1] . ( 3 sec) [ -10341.7650] [ 2242] [depth= 7] . ( 3 sec) [ -10340.2245] [ 2238] [depth= 1] . ( 3 sec) [ -10209.2675] [ 2179] [depth= 5] . ( 3 sec) [ -10146.3357] [ 2182] [depth= 1] . ( 3 sec) [ -10146.2749] [ 2186] [depth= 1] . ( 3 sec) [ -10132.7651] [ 2173] [depth= 4] . ( 3 sec) [ -10061.8857] [ 2146] [depth= 1] . ( 4 sec) [ -9968.1456] [ 2132] [depth= 3] . ( 4 sec) [ -9921.4582] [ 2134] [depth= 2] . ( 4 sec) [ -9915.8704] [ 2137] [depth= 1] . ( 4 sec) [ -9775.8451] [ 2093] [depth= 4] . ( 4 sec) [ -9766.0029] [ 2089] [depth= 1] . ( 4 sec) [ -9753.8569] [ 2085] [depth= 1] . ( 4 sec) [ -9734.5714] [ 2082] [depth= 1] . ( 4 sec) [ -9544.7590] [ 2018] [depth= 3] . ( 4 sec) [ -9533.5151] [ 2017] [depth= 1] . ( 4 sec) [ -9530.6448] [ 2017] [depth= 1] . ( 4 sec) [ -9527.6500] [ 2017] [depth= 1] . ( 4 sec) [ -9525.5294] [ 2009] [depth= 3] . ( 5 sec) [ -9453.6049] [Branch lengths ] . ( 5 sec) [ -9451.9509] [GTR parameters ] . ( 5 sec) [ -9410.4861] [Alpha ][ 0.981498] . ( 5 sec) [ -9325.7173] [ 1978] [depth= 3] . ( 5 sec) [ -9319.5804] [ 1974] [depth= 1] . ( 6 sec) [ -9318.4552] [ 1976] [depth= 2] . ( 6 sec) [ -9318.4210] [ 1977] [depth= 1] . ( 6 sec) [ -9306.2444] [ 1959] [depth= 1] . ( 6 sec) [ -9306.0445] [ 1961] [depth= 2] . ( 7 sec) [ -9305.5885] [ 1957] [depth= 2] . ( 7 sec) [ -9304.7544] [ 1960] [depth= 1] . ( 8 sec) [ -9301.4414] [ 1955] [depth= 1] . ( 9 sec) [ -9300.8767] [ 1954] [depth= 1] . ( 9 sec) [ -9294.2910] [Branch lengths ] . ( 10 sec) [ -9293.9669] [GTR parameters ] . ( 10 sec) [ -9293.7385] [Alpha ][ 1.034708] . ( 11 sec) [ -9293.1676] [ 1953] [depth= 1] . ( 13 sec) [ -9293.1490] [ 1956] [depth= 1] . ( 14 sec) [ -9292.8848] [ 1953] [depth= 1] . ( 15 sec) [ -9292.2289] [Branch lengths ] . ( 15 sec) [ -9292.2255] [GTR parameters ] . ( 15 sec) [ -9292.2179] [Alpha ][ 1.044904] . ( 21 sec) [ -9292.1437] [Branch lengths ] . ( 44 sec) [ -9292.1354] [Branch lengths ] . ( 44 sec) [ -9292.1354] [Topology ] . ( 44 sec) [ -9292.1347] [Topology ] . ( 45 sec) [ -9292.1347] [GTR parameters ] . ( 45 sec) [ -9292.1335] [Alpha ][ 1.048870] . ( 45 sec) [ -9292.1335] [Topology ] . ( 45 sec) [ -9292.1331] [Topology ] . ( 45 sec) [ -9292.1331] [GTR parameters ] . ( 46 sec) [ -9292.1331] [Alpha ][ 1.048870] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9292.133101. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16209.1866] [GTR parameters ] . ( 1 sec) [ -15979.2313] [Alpha ][ 0.500960] . ( 1 sec) [ -15844.0015] [ 3559] [depth= 1] . ( 1 sec) [ -15688.9260] [ 3523] [depth= 8] . ( 1 sec) [ -15633.8146] [ 3515] [depth= 4] . ( 1 sec) [ -15470.5928] [ 3512] [depth= 2] . ( 1 sec) [ -15289.9651] [ 3375] [depth= 7] . ( 1 sec) [ -15221.3271] [ 3378] [depth= 3] . ( 1 sec) [ -15142.0630] [ 3343] [depth= 11] . ( 1 sec) [ -15092.6169] [ 3327] [depth= 10] . ( 1 sec) [ -14628.0107] [ 3236] [depth= 10] . ( 1 sec) [ -14541.1584] [ 3219] [depth= 15] . ( 1 sec) [ -14377.7041] [ 3182] [depth= 6] . ( 1 sec) [ -14190.3716] [ 3149] [depth= 14] . ( 1 sec) [ -14149.1826] [ 3132] [depth= 7] . ( 1 sec) [ -14033.1373] [ 3127] [depth= 1] . ( 2 sec) [ -14016.1020] [ 3119] [depth= 8] . ( 2 sec) [ -13856.1919] [ 3114] [depth= 3] . ( 2 sec) [ -13719.9691] [ 3107] [depth= 1] . ( 2 sec) [ -13598.7380] [ 3109] [depth= 2] . ( 2 sec) [ -13546.9954] [ 3103] [depth= 5] . ( 2 sec) [ -13529.0841] [ 3085] [depth= 2] . ( 2 sec) [ -13343.1207] [ 3015] [depth= 12] . ( 2 sec) [ -13343.0766] [ 3015] [depth= 1] . ( 2 sec) [ -13292.7054] [ 3001] [depth= 1] . ( 2 sec) [ -13148.3403] [ 2922] [depth= 9] . ( 2 sec) [ -13091.7977] [ 2889] [depth= 6] . ( 2 sec) [ -12856.0076] [ 2815] [depth= 7] . ( 2 sec) [ -12753.6465] [ 2806] [depth= 6] . ( 2 sec) [ -12520.1337] [ 2744] [depth= 4] . ( 2 sec) [ -12164.4868] [ 2660] [depth= 6] . ( 2 sec) [ -12067.6929] [ 2649] [depth= 9] . ( 2 sec) [ -12041.9279] [ 2629] [depth= 6] . ( 2 sec) [ -11939.8203] [ 2627] [depth= 1] . ( 2 sec) [ -11937.5222] [ 2626] [depth= 5] . ( 2 sec) [ -11917.7410] [ 2631] [depth= 8] . ( 3 sec) [ -11889.7311] [ 2622] [depth= 1] . ( 3 sec) [ -11885.9800] [ 2608] [depth= 6] . ( 3 sec) [ -11865.0212] [ 2604] [depth= 1] . ( 3 sec) [ -11532.1549] [ 2530] [depth= 6] . ( 3 sec) [ -11460.1905] [ 2508] [depth= 1] . ( 3 sec) [ -11418.6356] [ 2507] [depth= 7] . ( 3 sec) [ -11316.4376] [ 2594] [depth= 7] . ( 3 sec) [ -11254.6063] [ 2553] [depth= 1] . ( 3 sec) [ -11131.1846] [ 2476] [depth= 6] . ( 3 sec) [ -11096.0394] [ 2473] [depth= 1] . ( 3 sec) [ -11076.4093] [ 2470] [depth= 2] . ( 3 sec) [ -10948.0505] [ 2450] [depth= 3] . ( 3 sec) [ -10945.0622] [ 2454] [depth= 1] . ( 3 sec) [ -10879.9990] [ 2451] [depth= 2] . ( 3 sec) [ -10879.2613] [ 2452] [depth= 1] . ( 3 sec) [ -10834.5724] [ 2436] [depth= 3] . ( 3 sec) [ -10625.9541] [ 2382] [depth= 1] . ( 3 sec) [ -10602.8443] [ 2368] [depth= 2] . ( 3 sec) [ -10545.2553] [ 2365] [depth= 3] . ( 3 sec) [ -10502.7360] [ 2355] [depth= 1] . ( 3 sec) [ -10318.0323] [ 2313] [depth= 5] . ( 3 sec) [ -10300.5701] [ 2309] [depth= 1] . ( 3 sec) [ -10186.9616] [ 2311] [depth= 1] . ( 4 sec) [ -10108.6760] [ 2279] [depth= 2] . ( 4 sec) [ -10102.8766] [ 2282] [depth= 1] . ( 4 sec) [ -10102.0287] [ 2277] [depth= 1] . ( 4 sec) [ -10036.2325] [ 2243] [depth= 3] . ( 4 sec) [ -10019.6924] [ 2240] [depth= 1] . ( 4 sec) [ -10009.8403] [ 2228] [depth= 7] . ( 4 sec) [ -9990.3392] [ 2228] [depth= 1] . ( 4 sec) [ -9987.1389] [ 2227] [depth= 6] . ( 4 sec) [ -9961.5479] [ 2193] [depth= 1] . ( 4 sec) [ -9931.8607] [ 2189] [depth= 1] . ( 4 sec) [ -9914.4972] [ 2186] [depth= 2] . ( 4 sec) [ -9902.7899] [ 2186] [depth= 2] . ( 4 sec) [ -9885.0560] [ 2146] [depth= 8] . ( 4 sec) [ -9883.1996] [ 2156] [depth= 2] . ( 4 sec) [ -9858.8274] [ 2150] [depth= 2] . ( 5 sec) [ -9815.9764] [ 2139] [depth= 3] . ( 5 sec) [ -9773.5154] [ 2097] [depth= 10] . ( 5 sec) [ -9605.6176] [Branch lengths ] . ( 5 sec) [ -9604.0330] [GTR parameters ] . ( 5 sec) [ -9574.3732] [Alpha ][ 0.873061] . ( 5 sec) [ -9572.9358] [ 2099] [depth= 5] . ( 6 sec) [ -9564.0306] [ 2097] [depth= 2] . ( 6 sec) [ -9563.1052] [ 2098] [depth= 1] . ( 6 sec) [ -9552.5974] [ 2091] [depth= 2] . ( 6 sec) [ -9428.7088] [ 2029] [depth= 3] . ( 6 sec) [ -9428.6823] [ 2032] [depth= 1] . ( 6 sec) [ -9428.2998] [ 2033] [depth= 1] . ( 6 sec) [ -9427.8998] [ 2032] [depth= 2] . ( 7 sec) [ -9427.8554] [ 2031] [depth= 1] . ( 7 sec) [ -9427.0319] [ 2032] [depth= 3] . ( 7 sec) [ -9426.5954] [ 2034] [depth= 1] . ( 7 sec) [ -9423.4617] [ 2034] [depth= 1] . ( 7 sec) [ -9423.2995] [ 2035] [depth= 2] . ( 7 sec) [ -9423.1813] [ 2032] [depth= 1] . ( 7 sec) [ -9422.2953] [ 2027] [depth= 1] . ( 8 sec) [ -9421.4803] [ 2025] [depth= 2] . ( 8 sec) [ -9418.1485] [ 2024] [depth= 3] . ( 8 sec) [ -9331.7941] [ 1974] [depth= 4] . ( 8 sec) [ -9330.8659] [ 1973] [depth= 1] . ( 8 sec) [ -9330.6426] [ 1971] [depth= 1] . ( 8 sec) [ -9330.4713] [ 1970] [depth= 1] . ( 8 sec) [ -9329.1701] [ 1967] [depth= 1] . ( 8 sec) [ -9328.0482] [ 1970] [depth= 1] . ( 9 sec) [ -9325.7022] [ 1961] [depth= 3] . ( 9 sec) [ -9325.2662] [ 1963] [depth= 1] . ( 9 sec) [ -9324.8787] [ 1963] [depth= 1] . ( 9 sec) [ -9324.8008] [ 1962] [depth= 1] . ( 9 sec) [ -9316.5813] [ 1956] [depth= 1] . ( 10 sec) [ -9297.3994] [Branch lengths ] . ( 10 sec) [ -9297.0368] [GTR parameters ] . ( 10 sec) [ -9295.0628] [Alpha ][ 1.018715] . ( 11 sec) [ -9294.7512] [ 1957] [depth= 2] . ( 11 sec) [ -9294.0399] [ 1956] [depth= 1] . ( 11 sec) [ -9294.0200] [ 1953] [depth= 1] . ( 15 sec) [ -9292.4319] [Branch lengths ] . ( 15 sec) [ -9292.4258] [GTR parameters ] . ( 15 sec) [ -9292.3914] [Alpha ][ 1.040423] . ( 20 sec) [ -9292.1773] [Branch lengths ] . ( 43 sec) [ -9292.1442] [Branch lengths ] . ( 43 sec) [ -9292.1442] [Topology ] . ( 44 sec) [ -9292.1408] [Topology ] . ( 45 sec) [ -9292.1397] [Topology ] . ( 45 sec) [ -9292.1392] [Topology ] . ( 46 sec) [ -9292.1391] [GTR parameters ] . ( 46 sec) [ -9292.1341] [Alpha ][ 1.048724] . ( 46 sec) [ -9292.1341] [Topology ] . ( 46 sec) [ -9292.1334] [Topology ] . ( 47 sec) [ -9292.1334] [GTR parameters ] . ( 47 sec) [ -9292.1334] [Alpha ][ 1.048724] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9292.133383. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16788.4153] [GTR parameters ] . ( 0 sec) [ -16554.7116] [Alpha ][ 0.500960] . ( 0 sec) [ -16305.7714] [ 3539] [depth= 11] . ( 0 sec) [ -16050.0332] [ 3510] [depth= 9] . ( 0 sec) [ -15897.9153] [ 3477] [depth= 8] . ( 0 sec) [ -15750.3512] [ 3435] [depth= 1] . ( 0 sec) [ -15722.2724] [ 3434] [depth= 9] . ( 0 sec) [ -15640.5266] [ 3425] [depth= 2] . ( 1 sec) [ -15437.2722] [ 3422] [depth= 5] . ( 1 sec) [ -15404.4184] [ 3391] [depth= 6] . ( 1 sec) [ -15396.2112] [ 3384] [depth= 3] . ( 1 sec) [ -15349.3272] [ 3379] [depth= 3] . ( 1 sec) [ -15001.7084] [ 3381] [depth= 6] . ( 1 sec) [ -14833.9504] [ 3282] [depth= 11] . ( 1 sec) [ -14689.4320] [ 3274] [depth= 2] . ( 1 sec) [ -14642.1939] [ 3267] [depth= 3] . ( 1 sec) [ -14374.4675] [ 3187] [depth= 4] . ( 1 sec) [ -14324.0658] [ 3142] [depth= 7] . ( 1 sec) [ -14293.1288] [ 3142] [depth= 2] . ( 1 sec) [ -14154.8415] [ 3112] [depth= 2] . ( 1 sec) [ -13872.9620] [ 3077] [depth= 1] . ( 1 sec) [ -13440.1802] [ 2923] [depth= 11] . ( 1 sec) [ -13402.6940] [ 2911] [depth= 1] . ( 1 sec) [ -13360.8461] [ 2899] [depth= 3] . ( 1 sec) [ -13342.3618] [ 2892] [depth= 9] . ( 1 sec) [ -13339.1086] [ 2894] [depth= 1] . ( 1 sec) [ -13079.2823] [ 2865] [depth= 8] . ( 1 sec) [ -13075.7509] [ 2864] [depth= 1] . ( 1 sec) [ -13060.7427] [ 2864] [depth= 2] . ( 2 sec) [ -12755.3168] [ 2776] [depth= 6] . ( 2 sec) [ -12755.1815] [ 2761] [depth= 1] . ( 2 sec) [ -12443.7279] [ 2688] [depth= 12] . ( 2 sec) [ -12422.0451] [ 2688] [depth= 1] . ( 2 sec) [ -12263.7704] [ 2664] [depth= 5] . ( 2 sec) [ -12245.4596] [ 2650] [depth= 4] . ( 2 sec) [ -12239.2099] [ 2651] [depth= 1] . ( 2 sec) [ -12207.4375] [ 2646] [depth= 1] . ( 2 sec) [ -12048.4187] [ 2597] [depth= 1] . ( 2 sec) [ -11915.4881] [ 2574] [depth= 1] . ( 2 sec) [ -11861.2377] [ 2535] [depth= 7] . ( 2 sec) [ -11857.1949] [ 2535] [depth= 3] . ( 2 sec) [ -11855.7137] [ 2541] [depth= 1] . ( 2 sec) [ -11736.1768] [ 2530] [depth= 1] . ( 2 sec) [ -11728.0460] [ 2527] [depth= 2] . ( 2 sec) [ -11720.7924] [ 2522] [depth= 7] . ( 2 sec) [ -11671.4424] [ 2512] [depth= 5] . ( 2 sec) [ -11642.4422] [ 2514] [depth= 1] . ( 2 sec) [ -11555.2075] [ 2463] [depth= 12] . ( 2 sec) [ -11554.3203] [ 2467] [depth= 1] . ( 2 sec) [ -11538.5209] [ 2464] [depth= 1] . ( 2 sec) [ -11537.3911] [ 2462] [depth= 1] . ( 3 sec) [ -11300.2921] [ 2437] [depth= 11] . ( 3 sec) [ -11209.4039] [ 2407] [depth= 2] . ( 3 sec) [ -11209.2626] [ 2408] [depth= 1] . ( 3 sec) [ -11064.0781] [ 2398] [depth= 4] . ( 3 sec) [ -11042.0450] [ 2391] [depth= 3] . ( 3 sec) [ -11025.6163] [ 2389] [depth= 6] . ( 3 sec) [ -10986.9788] [ 2377] [depth= 1] . ( 3 sec) [ -10881.4184] [ 2333] [depth= 5] . ( 3 sec) [ -10879.3170] [ 2335] [depth= 1] . ( 3 sec) [ -10855.7260] [ 2322] [depth= 2] . ( 3 sec) [ -10711.8379] [ 2270] [depth= 9] . ( 3 sec) [ -10700.9650] [ 2266] [depth= 1] . ( 3 sec) [ -10698.7852] [ 2266] [depth= 1] . ( 3 sec) [ -10696.3659] [ 2265] [depth= 1] . ( 3 sec) [ -10689.7475] [ 2266] [depth= 5] . ( 3 sec) [ -10661.2752] [ 2268] [depth= 1] . ( 3 sec) [ -10659.1066] [ 2265] [depth= 5] . ( 3 sec) [ -10650.3931] [ 2262] [depth= 1] . ( 3 sec) [ -10427.9102] [ 2254] [depth= 1] . ( 3 sec) [ -10386.1643] [ 2229] [depth= 2] . ( 4 sec) [ -10319.6045] [ 2214] [depth= 5] . ( 4 sec) [ -10031.9289] [ 2122] [depth= 1] . ( 4 sec) [ -10031.6335] [ 2122] [depth= 1] . ( 4 sec) [ -10030.5128] [ 2127] [depth= 4] . ( 4 sec) [ -9925.2935] [ 2085] [depth= 6] . ( 4 sec) [ -9925.2646] [ 2086] [depth= 1] . ( 4 sec) [ -9915.2743] [ 2095] [depth= 12] . ( 4 sec) [ -9914.0410] [ 2094] [depth= 1] . ( 4 sec) [ -9797.0996] [ 2097] [depth= 2] . ( 4 sec) [ -9784.7168] [ 2099] [depth= 1] . ( 4 sec) [ -9777.1370] [ 2096] [depth= 2] . ( 4 sec) [ -9738.2163] [ 2076] [depth= 2] . ( 4 sec) [ -9725.8607] [ 2070] [depth= 2] . ( 4 sec) [ -9718.0321] [ 2066] [depth= 1] . ( 5 sec) [ -9613.4410] [Branch lengths ] . ( 5 sec) [ -9612.7393] [GTR parameters ] . ( 5 sec) [ -9582.4841] [Alpha ][ 0.882665] . ( 5 sec) [ -9582.3210] [ 2065] [depth= 1] . ( 6 sec) [ -9581.5643] [ 2066] [depth= 1] . ( 6 sec) [ -9581.3445] [ 2063] [depth= 1] . ( 6 sec) [ -9512.3406] [ 2025] [depth= 7] . ( 6 sec) [ -9512.0780] [ 2024] [depth= 2] . ( 7 sec) [ -9511.8659] [ 2023] [depth= 1] . ( 7 sec) [ -9505.8251] [ 2025] [depth= 3] . ( 7 sec) [ -9505.6081] [ 2027] [depth= 1] . ( 7 sec) [ -9501.6608] [ 2024] [depth= 1] . ( 7 sec) [ -9501.3296] [ 2022] [depth= 1] . ( 7 sec) [ -9480.9761] [ 1982] [depth= 4] . ( 7 sec) [ -9456.4620] [ 1973] [depth= 4] . ( 8 sec) [ -9430.6200] [ 1965] [depth= 1] . ( 8 sec) [ -9390.7970] [ 1965] [depth= 1] . ( 8 sec) [ -9384.2338] [ 1958] [depth= 1] . ( 8 sec) [ -9355.4447] [ 1960] [depth= 1] . ( 8 sec) [ -9352.1688] [ 1959] [depth= 4] . ( 9 sec) [ -9344.0487] [ 1958] [depth= 1] . ( 9 sec) [ -9343.7924] [ 1964] [depth= 2] . ( 9 sec) [ -9342.7594] [ 1961] [depth= 1] . ( 9 sec) [ -9341.2823] [ 1962] [depth= 1] . ( 10 sec) [ -9318.6546] [Branch lengths ] . ( 10 sec) [ -9318.3808] [GTR parameters ] . ( 10 sec) [ -9317.0683] [Alpha ][ 1.000338] . ( 11 sec) [ -9317.0191] [ 1962] [depth= 2] . ( 11 sec) [ -9308.9091] [ 1961] [depth= 2] . ( 11 sec) [ -9304.1357] [ 1954] [depth= 1] . ( 12 sec) [ -9303.3917] [ 1953] [depth= 1] . ( 15 sec) [ -9300.6182] [Branch lengths ] . ( 15 sec) [ -9300.6119] [GTR parameters ] . ( 15 sec) [ -9300.5214] [Alpha ][ 1.033950] . ( 20 sec) [ -9299.0114] [Branch lengths ] . ( 43 sec) [ -9293.1577] [Branch lengths ] . ( 43 sec) [ -9293.1577] [Topology ] . ( 44 sec) [ -9292.4092] [Topology ] . ( 45 sec) [ -9292.2413] [Topology ] . ( 46 sec) [ -9292.1875] [Topology ] . ( 46 sec) [ -9292.1689] [Topology ] . ( 47 sec) [ -9292.1619] [Topology ] . ( 48 sec) [ -9292.1593] [Topology ] . ( 48 sec) [ -9292.1517] [GTR parameters ] . ( 48 sec) [ -9292.1356] [Alpha ][ 1.048888] . ( 48 sec) [ -9292.1356] [Topology ] . ( 49 sec) [ -9292.1338] [Topology ] . ( 50 sec) [ -9292.1332] [Topology ] . ( 50 sec) [ -9292.1332] [GTR parameters ] . ( 50 sec) [ -9292.1332] [Alpha ][ 1.048888] . ( 50 sec) [ -9292.1332] [Topology ] . ( 51 sec) [ -9292.1329] [Topology ] . ( 51 sec) [ -9292.1329] [GTR parameters ] . ( 51 sec) [ -9292.1329] [Alpha ][ 1.048888] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9292.132939. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16314.9435] [GTR parameters ] . ( 0 sec) [ -16098.8537] [Alpha ][ 0.500960] . ( 0 sec) [ -15853.6796] [ 3559] [depth= 7] . ( 1 sec) [ -15660.5576] [ 3525] [depth= 11] . ( 1 sec) [ -15621.9181] [ 3520] [depth= 5] . ( 1 sec) [ -15565.2651] [ 3513] [depth= 7] . ( 1 sec) [ -15460.4495] [ 3480] [depth= 10] . ( 1 sec) [ -15360.0858] [ 3484] [depth= 7] . ( 1 sec) [ -15320.6994] [ 3482] [depth= 5] . ( 1 sec) [ -15084.2938] [ 3476] [depth= 9] . ( 1 sec) [ -14968.5292] [ 3411] [depth= 16] . ( 1 sec) [ -14721.8202] [ 3329] [depth= 7] . ( 1 sec) [ -14717.0565] [ 3331] [depth= 3] . ( 1 sec) [ -14352.5833] [ 3271] [depth= 17] . ( 1 sec) [ -14176.9249] [ 3220] [depth= 10] . ( 1 sec) [ -14156.7607] [ 3224] [depth= 1] . ( 1 sec) [ -13815.6066] [ 3207] [depth= 5] . ( 1 sec) [ -13757.7084] [ 3187] [depth= 7] . ( 1 sec) [ -13722.7025] [ 3186] [depth= 1] . ( 1 sec) [ -13649.9663] [ 3183] [depth= 3] . ( 1 sec) [ -13635.9967] [ 3165] [depth= 7] . ( 1 sec) [ -13547.5712] [ 3161] [depth= 1] . ( 1 sec) [ -13510.8488] [ 3139] [depth= 1] . ( 1 sec) [ -13294.6461] [ 3123] [depth= 12] . ( 1 sec) [ -13074.9304] [ 3040] [depth= 10] . ( 1 sec) [ -12925.7824] [ 3011] [depth= 9] . ( 1 sec) [ -12827.8598] [ 2969] [depth= 1] . ( 2 sec) [ -12816.1747] [ 2968] [depth= 2] . ( 2 sec) [ -12709.3982] [ 2935] [depth= 2] . ( 2 sec) [ -12528.9568] [ 2869] [depth= 11] . ( 2 sec) [ -12464.6990] [ 2823] [depth= 4] . ( 2 sec) [ -11884.8618] [ 2744] [depth= 13] . ( 2 sec) [ -11826.3707] [ 2740] [depth= 3] . ( 2 sec) [ -11805.1571] [ 2733] [depth= 1] . ( 2 sec) [ -11651.1532] [ 2710] [depth= 13] . ( 2 sec) [ -11615.8326] [ 2663] [depth= 7] . ( 2 sec) [ -11587.3621] [ 2661] [depth= 1] . ( 2 sec) [ -11549.5853] [ 2646] [depth= 1] . ( 2 sec) [ -11545.9912] [ 2644] [depth= 5] . ( 2 sec) [ -11528.4627] [ 2642] [depth= 1] . ( 2 sec) [ -11483.5127] [ 2615] [depth= 5] . ( 2 sec) [ -11338.2410] [ 2555] [depth= 9] . ( 2 sec) [ -11301.3894] [ 2551] [depth= 1] . ( 2 sec) [ -11268.1329] [ 2561] [depth= 1] . ( 2 sec) [ -11245.1028] [ 2551] [depth= 1] . ( 2 sec) [ -11159.7767] [ 2498] [depth= 3] . ( 2 sec) [ -11153.4889] [ 2498] [depth= 9] . ( 2 sec) [ -11150.9487] [ 2503] [depth= 6] . ( 3 sec) [ -11073.4541] [ 2469] [depth= 4] . ( 3 sec) [ -11065.3790] [ 2468] [depth= 2] . ( 3 sec) [ -10931.1974] [ 2412] [depth= 1] . ( 3 sec) [ -10844.4945] [ 2387] [depth= 8] . ( 3 sec) [ -10794.3456] [ 2381] [depth= 5] . ( 3 sec) [ -10757.1582] [ 2376] [depth= 3] . ( 3 sec) [ -10740.3857] [ 2369] [depth= 1] . ( 3 sec) [ -10713.7550] [ 2359] [depth= 2] . ( 3 sec) [ -10654.2445] [ 2346] [depth= 9] . ( 3 sec) [ -10647.9215] [ 2342] [depth= 1] . ( 3 sec) [ -10624.7726] [ 2340] [depth= 1] . ( 3 sec) [ -10604.2647] [ 2319] [depth= 6] . ( 3 sec) [ -10601.7447] [ 2311] [depth= 1] . ( 3 sec) [ -10589.9356] [ 2308] [depth= 7] . ( 3 sec) [ -10560.1464] [ 2309] [depth= 1] . ( 3 sec) [ -10478.7200] [ 2276] [depth= 7] . ( 3 sec) [ -10414.6963] [ 2252] [depth= 2] . ( 3 sec) [ -10293.4632] [ 2228] [depth= 4] . ( 3 sec) [ -10269.5310] [ 2231] [depth= 1] . ( 3 sec) [ -10204.1357] [ 2228] [depth= 2] . ( 4 sec) [ -10186.4184] [ 2222] [depth= 1] . ( 4 sec) [ -9971.0329] [ 2158] [depth= 5] . ( 4 sec) [ -9948.6283] [ 2154] [depth= 4] . ( 4 sec) [ -9937.6444] [ 2149] [depth= 3] . ( 4 sec) [ -9854.4968] [ 2123] [depth= 1] . ( 4 sec) [ -9845.1441] [ 2118] [depth= 2] . ( 4 sec) [ -9813.4555] [ 2090] [depth= 7] . ( 4 sec) [ -9805.7045] [ 2086] [depth= 1] . ( 4 sec) [ -9764.2096] [ 2087] [depth= 1] . ( 4 sec) [ -9759.3980] [ 2086] [depth= 1] . ( 4 sec) [ -9725.3587] [ 2076] [depth= 3] . ( 5 sec) [ -9629.3495] [Branch lengths ] . ( 5 sec) [ -9627.2128] [GTR parameters ] . ( 5 sec) [ -9594.3819] [Alpha ][ 0.900934] . ( 5 sec) [ -9566.6690] [ 2055] [depth= 1] . ( 5 sec) [ -9483.3450] [ 2023] [depth= 3] . ( 5 sec) [ -9472.7428] [ 2019] [depth= 2] . ( 6 sec) [ -9453.8484] [ 2003] [depth= 1] . ( 6 sec) [ -9387.9745] [ 1968] [depth= 4] . ( 6 sec) [ -9373.1817] [ 1962] [depth= 4] . ( 6 sec) [ -9372.6990] [ 1964] [depth= 3] . ( 6 sec) [ -9371.9296] [ 1966] [depth= 1] . ( 6 sec) [ -9360.9094] [ 1965] [depth= 1] . ( 6 sec) [ -9358.9755] [ 1966] [depth= 2] . ( 6 sec) [ -9353.5706] [ 1964] [depth= 1] . ( 6 sec) [ -9350.1626] [ 1967] [depth= 1] . ( 7 sec) [ -9349.7913] [ 1964] [depth= 1] . ( 7 sec) [ -9342.1291] [ 1964] [depth= 4] . ( 7 sec) [ -9338.4428] [ 1964] [depth= 3] . ( 7 sec) [ -9320.2638] [ 1954] [depth= 3] . ( 7 sec) [ -9319.8663] [ 1955] [depth= 1] . ( 8 sec) [ -9319.8448] [ 1957] [depth= 1] . ( 8 sec) [ -9317.4500] [ 1955] [depth= 1] . ( 10 sec) [ -9297.1807] [Branch lengths ] . ( 10 sec) [ -9296.5278] [GTR parameters ] . ( 10 sec) [ -9295.3325] [Alpha ][ 1.016413] . ( 11 sec) [ -9295.2963] [ 1954] [depth= 1] . ( 11 sec) [ -9294.7189] [ 1953] [depth= 1] . ( 15 sec) [ -9292.5479] [Branch lengths ] . ( 15 sec) [ -9292.5435] [GTR parameters ] . ( 15 sec) [ -9292.5085] [Alpha ][ 1.037241] . ( 20 sec) [ -9292.1987] [Branch lengths ] . ( 43 sec) [ -9292.1513] [Branch lengths ] . ( 43 sec) [ -9292.1513] [Topology ] . ( 44 sec) [ -9292.1467] [Topology ] . ( 45 sec) [ -9292.1451] [Topology ] . ( 46 sec) [ -9292.1443] [Topology ] . ( 46 sec) [ -9292.1442] [GTR parameters ] . ( 46 sec) [ -9292.1350] [Alpha ][ 1.048544] . ( 46 sec) [ -9292.1350] [Topology ] . ( 47 sec) [ -9292.1338] [Topology ] . ( 48 sec) [ -9292.1333] [Topology ] . ( 48 sec) [ -9292.1333] [GTR parameters ] . ( 48 sec) [ -9292.1333] [Alpha ][ 1.048544] . ( 48 sec) [ -9292.1333] [Topology ] . ( 48 sec) [ -9292.1331] [Topology ] . ( 49 sec) [ -9292.1331] [GTR parameters ] . ( 49 sec) [ -9292.1331] [Alpha ][ 1.049593] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9292.133068. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9320.302500 . ( 0 sec) [ -9318.8428] [GTR parameters ] . ( 0 sec) [ -9318.8360] [Alpha ][ 0.990367] . ( 0 sec) [ -9318.8360] [Topology ] . ( 1 sec) [ -9296.9484] [Topology ] . ( 2 sec) [ -9293.9800] [Topology ] . ( 3 sec) [ -9293.0792] [Topology ] . ( 3 sec) [ -9292.6952] [Topology ] . ( 4 sec) [ -9292.5629] [Topology ] . ( 5 sec) [ -9292.5022] [Topology ] . ( 6 sec) [ -9292.4726] [Topology ] . ( 6 sec) [ -9292.4579] [Topology ] . ( 7 sec) [ -9292.4506] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.450570 . ( 13 sec) [ -9292.4042] [GTR parameters ] . ( 13 sec) [ -9292.1729] [Alpha ][ 1.044231] . ( 13 sec) [ -9292.1729] [Topology ] . ( 14 sec) [ -9292.1519] [Topology ] . ( 14 sec) [ -9292.1433] [Topology ] . ( 15 sec) [ -9292.1392] [Topology ] . ( 16 sec) [ -9292.1372] [Topology ] . ( 17 sec) [ -9292.1362] [Topology ] . ( 17 sec) [ -9292.1357] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.135669 . ( 23 sec) [ -9292.1352] [GTR parameters ] . ( 23 sec) [ -9292.1336] [Alpha ][ 1.048822] . ( 23 sec) [ -9292.1336] [Topology ] . ( 24 sec) [ -9292.1332] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.133168 . ( 29 sec) [ -9292.1332] [GTR parameters ] . ( 30 sec) [ -9292.1332] [Alpha ][ 1.048822] . ( 30 sec) [ -9292.1332] [Topology ] . ( 30 sec) [ -9292.1330] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -9318.8428] [GTR parameters ] . ( 42 sec) [ -9318.8360] [Alpha ][ 0.990367] . ( 43 sec) [ -9318.7079] [ 1957] [depth= 1] . ( 43 sec) [ -9318.2107] [ 1955] [depth= 1] . ( 43 sec) [ -9317.4619] [ 1954] [depth= 1] . ( 43 sec) [ -9315.8366] [ 1956] [depth= 1] . ( 43 sec) [ -9313.4815] [ 1955] [depth= 1] . ( 44 sec) [ -9311.7901] [ 1954] [depth= 1] . ( 45 sec) [ -9311.5774] [ 1955] [depth= 1] . ( 45 sec) [ -9311.5122] [ 1954] [depth= 1] . ( 45 sec) [ -9310.4770] [ 1953] [depth= 1] . ( 45 sec) [ -9309.6563] [ 1954] [depth= 1] . ( 45 sec) [ -9309.2220] [ 1953] [depth= 1] . ( 45 sec) [ -9308.8743] [ 1954] [depth= 1] . ( 46 sec) [ -9293.8832] [Branch lengths ] . ( 46 sec) [ -9293.8583] [GTR parameters ] . ( 46 sec) [ -9293.7452] [Alpha ][ 1.027666] . ( 48 sec) [ -9293.6086] [ 1956] [depth= 1] . ( 48 sec) [ -9293.5646] [ 1953] [depth= 1] . ( 51 sec) [ -9292.3182] [Branch lengths ] . ( 51 sec) [ -9292.3157] [GTR parameters ] . ( 51 sec) [ -9292.3014] [Alpha ][ 1.041686] . ( 56 sec) [ -9292.1693] [Branch lengths ] . ( 79 sec) [ -9292.1418] [Branch lengths ] . ( 79 sec) [ -9292.1418] [Topology ] . ( 80 sec) [ -9292.1391] [Topology ] . ( 81 sec) [ -9292.1381] [Topology ] . ( 81 sec) [ -9292.1380] [GTR parameters ] . ( 81 sec) [ -9292.1345] [Alpha ][ 1.048608] . ( 81 sec) [ -9292.1345] [Topology ] . ( 82 sec) [ -9292.1336] [Topology ] . ( 82 sec) [ -9292.1336] [GTR parameters ] . ( 82 sec) [ -9292.1336] [Alpha ][ 1.048608] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9292.132960 . Log likelihood obtained after SPR moves : -9292.133605 . Log likelihood of the current tree: -9292.132960. . Printing the most likely tree in file 'data95.phy_phyml_tree.txt'... . Best log likelihood : -9292.132939 . Time used 0h1m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo