.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data28.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... . 421 patterns found. (out of a total of 500 sites) . 74 sites without polymorphism (14.80%). . [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) [ -18367.9515] [GTR parameters ] . ( 0 sec) [ -18040.9612] [Alpha ][ 0.500960] . ( 0 sec) [ -17766.7341] [ 4014] [depth= 8] . ( 0 sec) [ -17700.0767] [ 4012] [depth= 6] . ( 0 sec) [ -17548.4192] [ 3986] [depth= 4] . ( 0 sec) [ -17525.9050] [ 3956] [depth= 6] . ( 0 sec) [ -17370.6582] [ 3876] [depth= 3] . ( 1 sec) [ -17197.8182] [ 3859] [depth= 9] . ( 1 sec) [ -17070.9739] [ 3827] [depth= 4] . ( 1 sec) [ -16983.7843] [ 3828] [depth= 1] . ( 1 sec) [ -16941.9973] [ 3824] [depth= 2] . ( 1 sec) [ -16904.1672] [ 3778] [depth= 1] . ( 1 sec) [ -16784.9631] [ 3786] [depth= 6] . ( 1 sec) [ -16625.3756] [ 3730] [depth= 6] . ( 1 sec) [ -16520.9816] [ 3718] [depth= 2] . ( 1 sec) [ -16498.6317] [ 3703] [depth= 9] . ( 1 sec) [ -16481.4790] [ 3694] [depth= 3] . ( 1 sec) [ -16325.2837] [ 3687] [depth= 4] . ( 1 sec) [ -16150.8401] [ 3600] [depth= 4] . ( 1 sec) [ -16061.2364] [ 3589] [depth= 6] . ( 1 sec) [ -15896.9005] [ 3544] [depth= 3] . ( 1 sec) [ -15548.1178] [ 3483] [depth= 7] . ( 1 sec) [ -15438.5326] [ 3472] [depth= 10] . ( 1 sec) [ -15270.4873] [ 3457] [depth= 1] . ( 1 sec) [ -14998.6862] [ 3420] [depth= 5] . ( 1 sec) [ -14963.3920] [ 3412] [depth= 2] . ( 1 sec) [ -14604.7410] [ 3382] [depth= 4] . ( 1 sec) [ -14490.1552] [ 3407] [depth= 4] . ( 1 sec) [ -14249.2021] [ 3369] [depth= 3] . ( 1 sec) [ -13970.8747] [ 3219] [depth= 8] . ( 2 sec) [ -13818.0268] [ 3162] [depth= 14] . ( 2 sec) [ -13562.0685] [ 3071] [depth= 7] . ( 2 sec) [ -13484.3063] [ 3068] [depth= 1] . ( 2 sec) [ -13482.6107] [ 3061] [depth= 1] . ( 2 sec) [ -13472.4098] [ 3068] [depth= 10] . ( 2 sec) [ -13455.2329] [ 3036] [depth= 1] . ( 2 sec) [ -13366.0802] [ 2996] [depth= 3] . ( 2 sec) [ -13220.9017] [ 2958] [depth= 7] . ( 2 sec) [ -13198.4223] [ 2961] [depth= 2] . ( 2 sec) [ -12611.3596] [ 2865] [depth= 9] . ( 2 sec) [ -12499.4517] [ 2844] [depth= 1] . ( 2 sec) [ -12429.9310] [ 2823] [depth= 1] . ( 2 sec) [ -12392.8383] [ 2817] [depth= 1] . ( 2 sec) [ -12049.2241] [ 2812] [depth= 1] . ( 2 sec) [ -11774.4586] [ 2693] [depth= 10] . ( 2 sec) [ -11715.3226] [ 2660] [depth= 6] . ( 2 sec) [ -11709.6282] [ 2663] [depth= 1] . ( 2 sec) [ -11706.6823] [ 2660] [depth= 1] . ( 2 sec) [ -11582.3811] [ 2584] [depth= 1] . ( 2 sec) [ -11575.9291] [ 2586] [depth= 4] . ( 2 sec) [ -11562.1101] [ 2603] [depth= 1] . ( 3 sec) [ -11350.4098] [ 2506] [depth= 4] . ( 3 sec) [ -11330.7113] [ 2494] [depth= 2] . ( 3 sec) [ -10841.6764] [ 2415] [depth= 8] . ( 3 sec) [ -10801.3756] [ 2408] [depth= 2] . ( 3 sec) [ -10761.4631] [ 2384] [depth= 2] . ( 3 sec) [ -10738.1012] [ 2382] [depth= 2] . ( 3 sec) [ -10705.3346] [ 2383] [depth= 1] . ( 3 sec) [ -10697.9537] [ 2386] [depth= 2] . ( 3 sec) [ -10535.7624] [ 2310] [depth= 3] . ( 3 sec) [ -10472.1371] [ 2281] [depth= 2] . ( 3 sec) [ -10405.5065] [ 2249] [depth= 1] . ( 3 sec) [ -10244.4358] [ 2203] [depth= 2] . ( 3 sec) [ -10232.1567] [ 2203] [depth= 1] . ( 3 sec) [ -10056.9406] [ 2171] [depth= 2] . ( 3 sec) [ -10042.4793] [ 2154] [depth= 2] . ( 4 sec) [ -10031.0232] [ 2151] [depth= 1] . ( 4 sec) [ -10020.1152] [ 2151] [depth= 2] . ( 4 sec) [ -10014.2571] [ 2145] [depth= 1] . ( 4 sec) [ -9979.0381] [ 2138] [depth= 1] . ( 4 sec) [ -9942.2374] [ 2120] [depth= 3] . ( 4 sec) [ -9892.3364] [ 2095] [depth= 1] . ( 4 sec) [ -9868.5921] [ 2083] [depth= 4] . ( 4 sec) [ -9857.4516] [ 2084] [depth= 1] . ( 4 sec) [ -9800.5841] [ 2112] [depth= 1] . ( 4 sec) [ -9748.4082] [ 2084] [depth= 2] . ( 4 sec) [ -9604.7088] [Branch lengths ] . ( 5 sec) [ -9600.2951] [GTR parameters ] . ( 5 sec) [ -9566.4224] [Alpha ][ 0.908602] . ( 5 sec) [ -9566.3866] [ 2083] [depth= 1] . ( 5 sec) [ -9565.4985] [ 2080] [depth= 1] . ( 5 sec) [ -9499.3979] [ 2048] [depth= 1] . ( 6 sec) [ -9495.8623] [ 2044] [depth= 1] . ( 6 sec) [ -9495.4926] [ 2045] [depth= 1] . ( 6 sec) [ -9495.4743] [ 2046] [depth= 1] . ( 6 sec) [ -9495.1688] [ 2047] [depth= 1] . ( 6 sec) [ -9495.0637] [ 2046] [depth= 1] . ( 7 sec) [ -9495.0513] [ 2047] [depth= 1] . ( 7 sec) [ -9494.5675] [ 2047] [depth= 1] . ( 7 sec) [ -9493.8328] [ 2050] [depth= 1] . ( 7 sec) [ -9493.3640] [ 2050] [depth= 1] . ( 8 sec) [ -9492.7712] [ 2055] [depth= 1] . ( 8 sec) [ -9479.5886] [Branch lengths ] . ( 9 sec) [ -9479.4125] [GTR parameters ] . ( 9 sec) [ -9478.7922] [Alpha ][ 0.987210] . ( 10 sec) [ -9478.0085] [ 2050] [depth= 1] . ( 10 sec) [ -9477.9394] [ 2050] [depth= 1] . ( 12 sec) [ -9476.5034] [Branch lengths ] . ( 12 sec) [ -9476.5007] [GTR parameters ] . ( 12 sec) [ -9476.4707] [Alpha ][ 1.005808] . ( 15 sec) [ -9476.2168] [Branch lengths ] . ( 28 sec) [ -9475.2913] [ 2048] [depth= 1] . ( 36 sec) [ -9475.0665] [Branch lengths ] . ( 36 sec) [ -9475.0653] [GTR parameters ] . ( 36 sec) [ -9475.0620] [Alpha ][ 1.012032] . ( 57 sec) [ -9475.0532] [Branch lengths ] . ( 57 sec) [ -9475.0532] [Topology ] . ( 58 sec) [ -9475.0523] [Topology ] . ( 58 sec) [ -9475.0523] [GTR parameters ] . ( 58 sec) [ -9475.0523] [Alpha ][ 1.013044] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -9473.7606] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9473.760645. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19565.9568] [GTR parameters ] . ( 1 sec) [ -19225.6409] [Alpha ][ 0.500960] . ( 1 sec) [ -18901.9160] [ 4194] [depth= 3] . ( 1 sec) [ -18592.9682] [ 4131] [depth= 10] . ( 1 sec) [ -18424.4101] [ 4107] [depth= 4] . ( 1 sec) [ -18319.3696] [ 4085] [depth= 7] . ( 1 sec) [ -18196.7590] [ 4020] [depth= 5] . ( 1 sec) [ -17642.2262] [ 4026] [depth= 10] . ( 1 sec) [ -17548.7929] [ 4003] [depth= 1] . ( 1 sec) [ -17486.1887] [ 3977] [depth= 12] . ( 1 sec) [ -17320.2260] [ 3923] [depth= 1] . ( 1 sec) [ -17110.1095] [ 3878] [depth= 3] . ( 1 sec) [ -16875.1930] [ 3862] [depth= 3] . ( 1 sec) [ -16821.8054] [ 3847] [depth= 1] . ( 1 sec) [ -16587.2499] [ 3778] [depth= 9] . ( 1 sec) [ -16517.5629] [ 3775] [depth= 3] . ( 1 sec) [ -16210.2858] [ 3654] [depth= 2] . ( 2 sec) [ -15931.1794] [ 3539] [depth= 10] . ( 2 sec) [ -15816.8767] [ 3529] [depth= 4] . ( 2 sec) [ -15629.5153] [ 3522] [depth= 3] . ( 2 sec) [ -15619.0819] [ 3538] [depth= 1] . ( 2 sec) [ -15548.3143] [ 3512] [depth= 1] . ( 2 sec) [ -15366.0555] [ 3473] [depth= 1] . ( 2 sec) [ -15091.0819] [ 3347] [depth= 3] . ( 2 sec) [ -14986.0774] [ 3315] [depth= 4] . ( 2 sec) [ -14665.3156] [ 3221] [depth= 4] . ( 2 sec) [ -14562.7658] [ 3209] [depth= 9] . ( 2 sec) [ -14551.9237] [ 3211] [depth= 1] . ( 2 sec) [ -14221.4083] [ 3171] [depth= 6] . ( 2 sec) [ -14081.4580] [ 3149] [depth= 9] . ( 2 sec) [ -14028.0384] [ 3132] [depth= 1] . ( 2 sec) [ -13990.5133] [ 3122] [depth= 1] . ( 2 sec) [ -13895.9517] [ 3100] [depth= 1] . ( 2 sec) [ -13772.4653] [ 3093] [depth= 1] . ( 2 sec) [ -13715.0125] [ 3078] [depth= 8] . ( 2 sec) [ -13542.0028] [ 3058] [depth= 3] . ( 2 sec) [ -13540.6543] [ 3066] [depth= 1] . ( 2 sec) [ -13271.1209] [ 3019] [depth= 2] . ( 3 sec) [ -13187.5497] [ 2991] [depth= 2] . ( 3 sec) [ -13150.8075] [ 2975] [depth= 2] . ( 3 sec) [ -12944.7571] [ 2965] [depth= 5] . ( 3 sec) [ -12628.6254] [ 2933] [depth= 12] . ( 3 sec) [ -12531.8947] [ 2866] [depth= 1] . ( 3 sec) [ -12354.8161] [ 2822] [depth= 3] . ( 3 sec) [ -12188.7874] [ 2754] [depth= 5] . ( 3 sec) [ -12098.2999] [ 2746] [depth= 2] . ( 3 sec) [ -11676.8074] [ 2606] [depth= 6] . ( 3 sec) [ -11607.5861] [ 2567] [depth= 3] . ( 3 sec) [ -11406.9423] [ 2514] [depth= 2] . ( 3 sec) [ -11215.2479] [ 2456] [depth= 8] . ( 3 sec) [ -11207.0765] [ 2459] [depth= 1] . ( 3 sec) [ -11099.9786] [ 2422] [depth= 3] . ( 3 sec) [ -10843.2115] [ 2426] [depth= 1] . ( 3 sec) [ -10814.4098] [ 2422] [depth= 1] . ( 3 sec) [ -10807.2595] [ 2424] [depth= 1] . ( 3 sec) [ -10778.7183] [ 2410] [depth= 1] . ( 4 sec) [ -10753.7076] [ 2393] [depth= 1] . ( 4 sec) [ -10696.0161] [ 2363] [depth= 1] . ( 4 sec) [ -10529.1020] [ 2318] [depth= 3] . ( 4 sec) [ -10450.5039] [ 2338] [depth= 7] . ( 4 sec) [ -10416.2184] [ 2305] [depth= 1] . ( 4 sec) [ -10411.0646] [ 2297] [depth= 1] . ( 4 sec) [ -10404.3841] [ 2289] [depth= 1] . ( 4 sec) [ -10355.7098] [ 2294] [depth= 1] . ( 4 sec) [ -10348.9118] [ 2297] [depth= 1] . ( 4 sec) [ -10282.7557] [ 2268] [depth= 1] . ( 4 sec) [ -10281.1309] [ 2266] [depth= 1] . ( 4 sec) [ -10233.4776] [ 2261] [depth= 5] . ( 4 sec) [ -10143.3781] [ 2242] [depth= 2] . ( 4 sec) [ -10124.5644] [ 2238] [depth= 1] . ( 4 sec) [ -9992.2432] [ 2195] [depth= 4] . ( 4 sec) [ -9982.7074] [ 2195] [depth= 1] . ( 4 sec) [ -9982.0646] [ 2194] [depth= 2] . ( 5 sec) [ -9849.8125] [ 2137] [depth= 2] . ( 5 sec) [ -9834.5019] [ 2126] [depth= 1] . ( 5 sec) [ -9814.7967] [ 2122] [depth= 1] . ( 5 sec) [ -9652.0793] [Branch lengths ] . ( 5 sec) [ -9646.8746] [GTR parameters ] . ( 5 sec) [ -9613.0386] [Alpha ][ 0.904501] . ( 6 sec) [ -9594.1468] [ 2101] [depth= 1] . ( 6 sec) [ -9593.4615] [ 2098] [depth= 3] . ( 6 sec) [ -9582.0254] [ 2093] [depth= 1] . ( 7 sec) [ -9573.4905] [ 2073] [depth= 4] . ( 7 sec) [ -9514.3246] [ 2046] [depth= 1] . ( 7 sec) [ -9509.9231] [ 2046] [depth= 1] . ( 7 sec) [ -9508.5055] [ 2045] [depth= 1] . ( 8 sec) [ -9505.5692] [ 2044] [depth= 2] . ( 8 sec) [ -9501.4256] [ 2040] [depth= 1] . ( 8 sec) [ -9501.2425] [ 2038] [depth= 1] . ( 8 sec) [ -9500.1474] [ 2040] [depth= 1] . ( 8 sec) [ -9490.2373] [ 2038] [depth= 1] . ( 8 sec) [ -9478.1729] [Branch lengths ] . ( 9 sec) [ -9477.7358] [GTR parameters ] . ( 9 sec) [ -9476.8888] [Alpha ][ 0.996588] . ( 10 sec) [ -9476.4503] [ 2038] [depth= 1] . ( 12 sec) [ -9474.7622] [Branch lengths ] . ( 13 sec) [ -9474.7593] [GTR parameters ] . ( 13 sec) [ -9474.7423] [Alpha ][ 1.010658] . ( 16 sec) [ -9474.4881] [Branch lengths ] . ( 36 sec) [ -9474.4455] [Branch lengths ] . ( 36 sec) [ -9474.4455] [Topology ] . ( 37 sec) [ -9474.4411] [Topology ] . ( 38 sec) [ -9474.4394] [Topology ] . ( 38 sec) [ -9474.4387] [Topology ] . ( 39 sec) [ -9474.4382] [GTR parameters ] . ( 39 sec) [ -9474.4364] [Alpha ][ 1.015164] . ( 39 sec) [ -9474.4364] [Topology ] . ( 39 sec) [ -9474.4358] [Topology ] . ( 40 sec) [ -9474.4358] [GTR parameters ] . ( 40 sec) [ -9474.4358] [Alpha ][ 1.015164] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9474.435793. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19198.3955] [GTR parameters ] . ( 1 sec) [ -18857.3612] [Alpha ][ 0.500960] . ( 1 sec) [ -18558.8706] [ 4197] [depth= 8] . ( 1 sec) [ -18161.6166] [ 4128] [depth= 8] . ( 1 sec) [ -17829.2780] [ 4124] [depth= 4] . ( 1 sec) [ -17618.8655] [ 4111] [depth= 6] . ( 1 sec) [ -17536.7649] [ 3995] [depth= 6] . ( 1 sec) [ -17459.9198] [ 3996] [depth= 2] . ( 1 sec) [ -17239.2610] [ 3878] [depth= 13] . ( 1 sec) [ -17115.4274] [ 3857] [depth= 2] . ( 1 sec) [ -16923.4933] [ 3819] [depth= 11] . ( 1 sec) [ -16742.5786] [ 3792] [depth= 7] . ( 2 sec) [ -16418.6782] [ 3796] [depth= 8] . ( 2 sec) [ -16278.7617] [ 3753] [depth= 6] . ( 2 sec) [ -16097.1769] [ 3744] [depth= 1] . ( 2 sec) [ -16073.1401] [ 3740] [depth= 3] . ( 2 sec) [ -15991.2277] [ 3708] [depth= 1] . ( 2 sec) [ -15701.4630] [ 3693] [depth= 3] . ( 2 sec) [ -15350.5219] [ 3651] [depth= 1] . ( 2 sec) [ -15303.7405] [ 3642] [depth= 9] . ( 2 sec) [ -15070.5099] [ 3559] [depth= 9] . ( 2 sec) [ -15020.7991] [ 3563] [depth= 9] . ( 2 sec) [ -14938.0159] [ 3497] [depth= 6] . ( 2 sec) [ -14711.0574] [ 3503] [depth= 1] . ( 2 sec) [ -14171.6519] [ 3461] [depth= 15] . ( 2 sec) [ -14154.4942] [ 3420] [depth= 1] . ( 2 sec) [ -14014.9915] [ 3361] [depth= 11] . ( 2 sec) [ -13954.9929] [ 3363] [depth= 1] . ( 2 sec) [ -13871.5268] [ 3343] [depth= 1] . ( 2 sec) [ -13536.2187] [ 3210] [depth= 6] . ( 2 sec) [ -13416.3238] [ 3196] [depth= 1] . ( 2 sec) [ -13398.9911] [ 3199] [depth= 1] . ( 2 sec) [ -13396.6233] [ 3196] [depth= 1] . ( 3 sec) [ -13385.6019] [ 3167] [depth= 2] . ( 3 sec) [ -13090.8182] [ 3159] [depth= 10] . ( 3 sec) [ -13031.7626] [ 3130] [depth= 6] . ( 3 sec) [ -12798.0461] [ 3072] [depth= 4] . ( 3 sec) [ -12796.4221] [ 3077] [depth= 1] . ( 3 sec) [ -12601.2266] [ 3010] [depth= 3] . ( 3 sec) [ -12289.4387] [ 2875] [depth= 9] . ( 3 sec) [ -12271.7632] [ 2869] [depth= 1] . ( 3 sec) [ -12078.1163] [ 2847] [depth= 8] . ( 3 sec) [ -11999.6274] [ 2782] [depth= 9] . ( 3 sec) [ -11957.4580] [ 2781] [depth= 1] . ( 3 sec) [ -11930.0677] [ 2779] [depth= 1] . ( 3 sec) [ -11916.7105] [ 2769] [depth= 3] . ( 3 sec) [ -11914.8156] [ 2773] [depth= 3] . ( 3 sec) [ -11832.5771] [ 2764] [depth= 10] . ( 3 sec) [ -11788.3240] [ 2754] [depth= 1] . ( 3 sec) [ -11653.5891] [ 2718] [depth= 14] . ( 3 sec) [ -11575.7374] [ 2684] [depth= 1] . ( 3 sec) [ -11567.6299] [ 2670] [depth= 1] . ( 3 sec) [ -11458.7377] [ 2612] [depth= 9] . ( 3 sec) [ -11442.6553] [ 2611] [depth= 2] . ( 4 sec) [ -11287.4320] [ 2607] [depth= 2] . ( 4 sec) [ -11251.5101] [ 2588] [depth= 2] . ( 4 sec) [ -10922.7367] [ 2478] [depth= 6] . ( 4 sec) [ -10882.5053] [ 2462] [depth= 1] . ( 4 sec) [ -10785.3428] [ 2444] [depth= 2] . ( 4 sec) [ -10700.5505] [ 2423] [depth= 6] . ( 4 sec) [ -10602.1349] [ 2384] [depth= 9] . ( 4 sec) [ -10584.2148] [ 2384] [depth= 1] . ( 4 sec) [ -10547.8130] [ 2379] [depth= 1] . ( 4 sec) [ -10539.1567] [ 2359] [depth= 3] . ( 4 sec) [ -10516.7644] [ 2348] [depth= 1] . ( 4 sec) [ -10502.4870] [ 2337] [depth= 2] . ( 4 sec) [ -10486.2665] [ 2316] [depth= 1] . ( 4 sec) [ -10320.8651] [ 2291] [depth= 1] . ( 4 sec) [ -10265.4002] [ 2276] [depth= 1] . ( 4 sec) [ -10150.9015] [ 2261] [depth= 1] . ( 4 sec) [ -10142.1381] [ 2262] [depth= 1] . ( 5 sec) [ -10142.0929] [ 2264] [depth= 2] . ( 5 sec) [ -10014.8532] [ 2190] [depth= 3] . ( 5 sec) [ -9977.1862] [ 2182] [depth= 6] . ( 5 sec) [ -9941.6949] [ 2165] [depth= 1] . ( 5 sec) [ -9940.2020] [ 2166] [depth= 1] . ( 5 sec) [ -9926.8500] [ 2164] [depth= 1] . ( 5 sec) [ -9910.3462] [ 2157] [depth= 1] . ( 5 sec) [ -9884.7407] [ 2147] [depth= 4] . ( 5 sec) [ -9854.4514] [ 2139] [depth= 1] . ( 5 sec) [ -9716.1938] [Branch lengths ] . ( 6 sec) [ -9710.1845] [GTR parameters ] . ( 6 sec) [ -9679.3559] [Alpha ][ 0.876327] . ( 6 sec) [ -9670.1565] [ 2126] [depth= 1] . ( 6 sec) [ -9620.8004] [ 2101] [depth= 4] . ( 6 sec) [ -9561.8098] [ 2069] [depth= 3] . ( 6 sec) [ -9551.8744] [ 2065] [depth= 1] . ( 7 sec) [ -9529.7033] [ 2043] [depth= 2] . ( 7 sec) [ -9529.4193] [ 2045] [depth= 1] . ( 7 sec) [ -9512.4204] [ 2036] [depth= 1] . ( 7 sec) [ -9508.9232] [ 2038] [depth= 1] . ( 7 sec) [ -9508.8192] [ 2036] [depth= 1] . ( 8 sec) [ -9507.9235] [ 2039] [depth= 1] . ( 8 sec) [ -9505.1492] [ 2038] [depth= 1] . ( 8 sec) [ -9504.5856] [ 2038] [depth= 1] . ( 8 sec) [ -9504.5535] [ 2040] [depth= 1] . ( 8 sec) [ -9499.8031] [ 2041] [depth= 1] . ( 8 sec) [ -9499.3118] [ 2040] [depth= 1] . ( 8 sec) [ -9497.9036] [ 2045] [depth= 1] . ( 9 sec) [ -9497.7826] [ 2043] [depth= 1] . ( 9 sec) [ -9497.5356] [ 2047] [depth= 1] . ( 9 sec) [ -9497.1433] [ 2050] [depth= 1] . ( 9 sec) [ -9484.3147] [Branch lengths ] . ( 10 sec) [ -9483.9700] [GTR parameters ] . ( 10 sec) [ -9482.7168] [Alpha ][ 0.985757] . ( 10 sec) [ -9482.4754] [ 2041] [depth= 2] . ( 11 sec) [ -9482.4311] [ 2042] [depth= 1] . ( 11 sec) [ -9481.3060] [ 2041] [depth= 1] . ( 12 sec) [ -9481.1973] [ 2046] [depth= 1] . ( 12 sec) [ -9479.6523] [ 2050] [depth= 1] . ( 12 sec) [ -9478.9023] [ 2046] [depth= 1] . ( 12 sec) [ -9478.5243] [ 2041] [depth= 1] . ( 12 sec) [ -9478.5099] [ 2040] [depth= 1] . ( 13 sec) [ -9476.5259] [Branch lengths ] . ( 13 sec) [ -9476.5051] [GTR parameters ] . ( 13 sec) [ -9476.4597] [Alpha ][ 1.007662] . ( 16 sec) [ -9476.1811] [Branch lengths ] . ( 37 sec) [ -9476.1280] [Branch lengths ] . ( 37 sec) [ -9476.1280] [Topology ] . ( 37 sec) [ -9474.5602] [Topology ] . ( 38 sec) [ -9474.4602] [Topology ] . ( 39 sec) [ -9474.4461] [Topology ] . ( 40 sec) [ -9474.4428] [Topology ] . ( 41 sec) [ -9474.4420] [Topology ] . ( 41 sec) [ -9474.4410] [GTR parameters ] . ( 41 sec) [ -9474.4358] [Alpha ][ 1.015406] . ( 41 sec) [ -9474.4358] [Topology ] . ( 42 sec) [ -9474.4354] [Topology ] . ( 42 sec) [ -9474.4354] [GTR parameters ] . ( 42 sec) [ -9474.4354] [Alpha ][ 1.015406] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9474.435396. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18580.6988] [GTR parameters ] . ( 1 sec) [ -18249.0619] [Alpha ][ 0.500960] . ( 1 sec) [ -17916.7689] [ 4090] [depth= 8] . ( 1 sec) [ -17566.6938] [ 3977] [depth= 9] . ( 1 sec) [ -17339.2625] [ 3944] [depth= 2] . ( 1 sec) [ -17230.5565] [ 3886] [depth= 1] . ( 1 sec) [ -17034.8769] [ 3850] [depth= 6] . ( 1 sec) [ -16954.1562] [ 3821] [depth= 2] . ( 1 sec) [ -16949.4155] [ 3818] [depth= 1] . ( 1 sec) [ -16768.0785] [ 3750] [depth= 1] . ( 1 sec) [ -16680.6493] [ 3735] [depth= 6] . ( 1 sec) [ -16592.8856] [ 3706] [depth= 2] . ( 1 sec) [ -16588.8137] [ 3711] [depth= 3] . ( 1 sec) [ -16378.0428] [ 3634] [depth= 4] . ( 1 sec) [ -16301.9611] [ 3628] [depth= 1] . ( 1 sec) [ -16139.0759] [ 3628] [depth= 1] . ( 2 sec) [ -15997.6784] [ 3615] [depth= 5] . ( 2 sec) [ -15825.2186] [ 3610] [depth= 2] . ( 2 sec) [ -15729.9895] [ 3591] [depth= 3] . ( 2 sec) [ -15546.8970] [ 3550] [depth= 1] . ( 2 sec) [ -15450.4925] [ 3481] [depth= 17] . ( 2 sec) [ -15127.7764] [ 3426] [depth= 1] . ( 2 sec) [ -15078.5046] [ 3401] [depth= 6] . ( 2 sec) [ -14962.8803] [ 3387] [depth= 2] . ( 2 sec) [ -14913.2982] [ 3384] [depth= 1] . ( 2 sec) [ -14779.3008] [ 3354] [depth= 3] . ( 2 sec) [ -14741.4299] [ 3317] [depth= 1] . ( 2 sec) [ -14711.8847] [ 3301] [depth= 1] . ( 2 sec) [ -14313.2971] [ 3272] [depth= 17] . ( 2 sec) [ -14115.6654] [ 3204] [depth= 1] . ( 2 sec) [ -14054.5098] [ 3181] [depth= 2] . ( 2 sec) [ -14030.3980] [ 3170] [depth= 2] . ( 2 sec) [ -13979.1460] [ 3160] [depth= 1] . ( 2 sec) [ -13956.8638] [ 3152] [depth= 3] . ( 2 sec) [ -13881.2520] [ 3121] [depth= 13] . ( 2 sec) [ -13716.4153] [ 3067] [depth= 11] . ( 3 sec) [ -13666.7420] [ 3072] [depth= 1] . ( 3 sec) [ -13345.7969] [ 2977] [depth= 5] . ( 3 sec) [ -13100.5799] [ 2880] [depth= 4] . ( 3 sec) [ -12903.5876] [ 2871] [depth= 1] . ( 3 sec) [ -12753.8123] [ 2858] [depth= 1] . ( 3 sec) [ -12662.0354] [ 2803] [depth= 5] . ( 3 sec) [ -12510.6782] [ 2804] [depth= 1] . ( 3 sec) [ -12489.8588] [ 2786] [depth= 1] . ( 3 sec) [ -12305.4455] [ 2761] [depth= 7] . ( 3 sec) [ -12223.6259] [ 2720] [depth= 5] . ( 3 sec) [ -12062.1733] [ 2672] [depth= 2] . ( 3 sec) [ -11935.7851] [ 2669] [depth= 1] . ( 3 sec) [ -11852.7500] [ 2671] [depth= 1] . ( 3 sec) [ -11842.3282] [ 2664] [depth= 1] . ( 3 sec) [ -11841.7787] [ 2664] [depth= 1] . ( 3 sec) [ -11811.9214] [ 2610] [depth= 1] . ( 3 sec) [ -11794.3542] [ 2605] [depth= 1] . ( 3 sec) [ -11733.1442] [ 2604] [depth= 2] . ( 3 sec) [ -11651.8240] [ 2620] [depth= 1] . ( 3 sec) [ -11646.3673] [ 2604] [depth= 1] . ( 3 sec) [ -11439.5021] [ 2502] [depth= 9] . ( 3 sec) [ -10892.4722] [ 2478] [depth= 1] . ( 4 sec) [ -10881.7913] [ 2473] [depth= 2] . ( 4 sec) [ -10857.1920] [ 2436] [depth= 1] . ( 4 sec) [ -10645.7649] [ 2377] [depth= 4] . ( 4 sec) [ -10605.1980] [ 2373] [depth= 1] . ( 4 sec) [ -10567.1642] [ 2356] [depth= 1] . ( 4 sec) [ -10563.2677] [ 2367] [depth= 1] . ( 4 sec) [ -10526.3196] [ 2359] [depth= 1] . ( 4 sec) [ -10449.6771] [ 2351] [depth= 1] . ( 4 sec) [ -10419.8753] [ 2353] [depth= 1] . ( 4 sec) [ -10252.8447] [ 2234] [depth= 5] . ( 4 sec) [ -10062.6727] [ 2208] [depth= 1] . ( 4 sec) [ -10029.7660] [ 2181] [depth= 2] . ( 4 sec) [ -10025.6419] [ 2184] [depth= 1] . ( 4 sec) [ -9947.1673] [ 2187] [depth= 2] . ( 4 sec) [ -9945.9762] [ 2191] [depth= 1] . ( 4 sec) [ -9899.7459] [ 2158] [depth= 2] . ( 5 sec) [ -9843.3789] [ 2137] [depth= 1] . ( 5 sec) [ -9816.7974] [ 2132] [depth= 1] . ( 5 sec) [ -9811.7808] [ 2129] [depth= 1] . ( 5 sec) [ -9701.0769] [Branch lengths ] . ( 6 sec) [ -9696.2206] [GTR parameters ] . ( 6 sec) [ -9661.1170] [Alpha ][ 0.917325] . ( 6 sec) [ -9660.3835] [ 2124] [depth= 1] . ( 6 sec) [ -9591.3661] [ 2092] [depth= 3] . ( 6 sec) [ -9577.1049] [ 2077] [depth= 1] . ( 6 sec) [ -9534.0934] [ 2059] [depth= 1] . ( 7 sec) [ -9532.0653] [ 2059] [depth= 1] . ( 7 sec) [ -9514.9738] [ 2042] [depth= 1] . ( 7 sec) [ -9509.6300] [ 2040] [depth= 1] . ( 7 sec) [ -9508.6794] [ 2046] [depth= 1] . ( 7 sec) [ -9508.1512] [ 2047] [depth= 1] . ( 8 sec) [ -9503.4142] [ 2045] [depth= 1] . ( 8 sec) [ -9502.7237] [ 2049] [depth= 1] . ( 8 sec) [ -9502.5882] [ 2045] [depth= 1] . ( 8 sec) [ -9499.8920] [ 2048] [depth= 1] . ( 9 sec) [ -9478.6116] [Branch lengths ] . ( 9 sec) [ -9478.3213] [GTR parameters ] . ( 9 sec) [ -9477.7594] [Alpha ][ 0.992793] . ( 10 sec) [ -9477.6302] [ 2041] [depth= 1] . ( 12 sec) [ -9475.8953] [Branch lengths ] . ( 13 sec) [ -9475.8947] [GTR parameters ] . ( 13 sec) [ -9475.8700] [Alpha ][ 1.009726] . ( 16 sec) [ -9475.5878] [Branch lengths ] . ( 29 sec) [ -9474.6849] [ 2038] [depth= 1] . ( 36 sec) [ -9474.4499] [Branch lengths ] . ( 36 sec) [ -9474.4495] [GTR parameters ] . ( 36 sec) [ -9474.4472] [Alpha ][ 1.014845] . ( 56 sec) [ -9474.4369] [Branch lengths ] . ( 56 sec) [ -9474.4369] [Topology ] . ( 57 sec) [ -9474.4360] [Topology ] . ( 57 sec) [ -9474.4359] [GTR parameters ] . ( 57 sec) [ -9474.4359] [Alpha ][ 1.015860] . ( 57 sec) [ -9474.4359] [Topology ] . ( 58 sec) [ -9474.4356] [Topology ] . ( 58 sec) [ -9474.4356] [GTR parameters ] . ( 58 sec) [ -9474.4356] [Alpha ][ 1.015860] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9474.435567. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19269.0507] [GTR parameters ] . ( 1 sec) [ -18905.9242] [Alpha ][ 0.500960] . ( 1 sec) [ -18456.5476] [ 4258] [depth= 6] . ( 1 sec) [ -18179.0001] [ 4186] [depth= 11] . ( 1 sec) [ -17858.0400] [ 4167] [depth= 6] . ( 1 sec) [ -17800.6177] [ 4164] [depth= 1] . ( 1 sec) [ -17677.0359] [ 4085] [depth= 10] . ( 2 sec) [ -17604.1228] [ 4064] [depth= 6] . ( 2 sec) [ -17545.5651] [ 4073] [depth= 1] . ( 2 sec) [ -17253.0857] [ 4003] [depth= 2] . ( 2 sec) [ -16999.8354] [ 3963] [depth= 10] . ( 2 sec) [ -16737.1595] [ 3868] [depth= 8] . ( 2 sec) [ -16550.1602] [ 3818] [depth= 6] . ( 2 sec) [ -16549.6720] [ 3827] [depth= 1] . ( 2 sec) [ -16454.5680] [ 3799] [depth= 8] . ( 2 sec) [ -16376.4049] [ 3796] [depth= 1] . ( 2 sec) [ -16356.1721] [ 3797] [depth= 1] . ( 2 sec) [ -16187.5774] [ 3793] [depth= 2] . ( 2 sec) [ -15999.1206] [ 3714] [depth= 9] . ( 2 sec) [ -15973.6546] [ 3720] [depth= 3] . ( 2 sec) [ -15844.3416] [ 3653] [depth= 5] . ( 2 sec) [ -15642.2751] [ 3620] [depth= 1] . ( 2 sec) [ -15439.6870] [ 3562] [depth= 12] . ( 2 sec) [ -15178.4669] [ 3492] [depth= 8] . ( 2 sec) [ -15030.8770] [ 3433] [depth= 10] . ( 2 sec) [ -14855.8633] [ 3431] [depth= 2] . ( 2 sec) [ -14449.9837] [ 3342] [depth= 11] . ( 2 sec) [ -14242.6803] [ 3300] [depth= 7] . ( 2 sec) [ -13985.0825] [ 3263] [depth= 4] . ( 3 sec) [ -13813.1934] [ 3223] [depth= 1] . ( 3 sec) [ -13600.4628] [ 3166] [depth= 6] . ( 3 sec) [ -13435.9410] [ 3094] [depth= 2] . ( 3 sec) [ -13321.5088] [ 3068] [depth= 8] . ( 3 sec) [ -13169.6454] [ 3040] [depth= 9] . ( 3 sec) [ -13035.1672] [ 2982] [depth= 8] . ( 3 sec) [ -13025.1367] [ 2974] [depth= 1] . ( 3 sec) [ -13017.6871] [ 2969] [depth= 1] . ( 3 sec) [ -12629.3647] [ 2857] [depth= 5] . ( 3 sec) [ -12553.3480] [ 2846] [depth= 5] . ( 3 sec) [ -12253.1074] [ 2761] [depth= 6] . ( 3 sec) [ -11997.1777] [ 2659] [depth= 8] . ( 3 sec) [ -11964.5181] [ 2611] [depth= 3] . ( 3 sec) [ -11791.1116] [ 2654] [depth= 9] . ( 3 sec) [ -11737.4956] [ 2640] [depth= 8] . ( 3 sec) [ -11518.0006] [ 2616] [depth= 7] . ( 3 sec) [ -11429.6834] [ 2581] [depth= 1] . ( 3 sec) [ -11281.3146] [ 2511] [depth= 4] . ( 3 sec) [ -11184.7661] [ 2469] [depth= 4] . ( 4 sec) [ -11091.4499] [ 2419] [depth= 4] . ( 4 sec) [ -11087.5131] [ 2415] [depth= 4] . ( 4 sec) [ -11083.4507] [ 2414] [depth= 1] . ( 4 sec) [ -11075.0811] [ 2419] [depth= 1] . ( 4 sec) [ -11062.2844] [ 2417] [depth= 1] . ( 4 sec) [ -11053.0641] [ 2418] [depth= 1] . ( 4 sec) [ -10936.2929] [ 2382] [depth= 3] . ( 4 sec) [ -10919.5861] [ 2378] [depth= 1] . ( 4 sec) [ -10836.3262] [ 2350] [depth= 1] . ( 4 sec) [ -10823.3751] [ 2354] [depth= 1] . ( 4 sec) [ -10784.4103] [ 2343] [depth= 1] . ( 4 sec) [ -10731.4440] [ 2338] [depth= 3] . ( 4 sec) [ -10717.3910] [ 2338] [depth= 4] . ( 4 sec) [ -10691.6325] [ 2339] [depth= 1] . ( 4 sec) [ -10685.9217] [ 2336] [depth= 1] . ( 4 sec) [ -10571.2615] [ 2330] [depth= 2] . ( 4 sec) [ -10547.0536] [ 2312] [depth= 4] . ( 4 sec) [ -10348.6606] [ 2269] [depth= 5] . ( 4 sec) [ -10103.0831] [ 2177] [depth= 3] . ( 5 sec) [ -10021.5841] [ 2149] [depth= 3] . ( 5 sec) [ -10006.3880] [ 2142] [depth= 1] . ( 5 sec) [ -9996.3537] [ 2145] [depth= 1] . ( 5 sec) [ -9991.0120] [ 2145] [depth= 1] . ( 5 sec) [ -9943.8875] [ 2145] [depth= 1] . ( 5 sec) [ -9937.7683] [ 2145] [depth= 1] . ( 5 sec) [ -9909.1104] [ 2140] [depth= 1] . ( 5 sec) [ -9892.8663] [ 2145] [depth= 1] . ( 5 sec) [ -9781.9789] [ 2110] [depth= 3] . ( 5 sec) [ -9755.8711] [ 2101] [depth= 1] . ( 5 sec) [ -9742.4854] [ 2096] [depth= 1] . ( 5 sec) [ -9591.8184] [Branch lengths ] . ( 6 sec) [ -9584.9129] [GTR parameters ] . ( 6 sec) [ -9546.8720] [Alpha ][ 0.932685] . ( 6 sec) [ -9518.9277] [ 2080] [depth= 1] . ( 6 sec) [ -9518.0039] [ 2080] [depth= 1] . ( 7 sec) [ -9514.1167] [ 2074] [depth= 1] . ( 7 sec) [ -9513.1955] [ 2069] [depth= 1] . ( 7 sec) [ -9510.9360] [ 2064] [depth= 3] . ( 7 sec) [ -9502.3428] [ 2047] [depth= 1] . ( 7 sec) [ -9502.1218] [ 2045] [depth= 1] . ( 7 sec) [ -9500.4630] [ 2046] [depth= 1] . ( 8 sec) [ -9496.1271] [ 2050] [depth= 1] . ( 8 sec) [ -9494.1245] [ 2051] [depth= 1] . ( 8 sec) [ -9493.6835] [ 2050] [depth= 1] . ( 8 sec) [ -9493.5244] [ 2051] [depth= 1] . ( 8 sec) [ -9492.7921] [ 2047] [depth= 1] . ( 9 sec) [ -9492.7490] [ 2039] [depth= 1] . ( 9 sec) [ -9478.5094] [Branch lengths ] . ( 10 sec) [ -9478.0253] [GTR parameters ] . ( 10 sec) [ -9477.4501] [Alpha ][ 1.010045] . ( 11 sec) [ -9476.5942] [ 2041] [depth= 1] . ( 13 sec) [ -9475.6271] [Branch lengths ] . ( 13 sec) [ -9475.6264] [GTR parameters ] . ( 13 sec) [ -9475.6255] [Alpha ][ 1.013250] . ( 16 sec) [ -9475.5451] [Branch lengths ] . ( 33 sec) [ -9474.6472] [ 2038] [depth= 1] . ( 36 sec) [ -9474.4408] [Branch lengths ] . ( 36 sec) [ -9474.4399] [GTR parameters ] . ( 36 sec) [ -9474.4395] [Alpha ][ 1.015152] . ( 57 sec) [ -9474.4357] [Branch lengths ] . ( 57 sec) [ -9474.4357] [Topology ] . ( 57 sec) [ -9474.4354] [Topology ] . ( 58 sec) [ -9474.4354] [GTR parameters ] . ( 58 sec) [ -9474.4354] [Alpha ][ 1.015152] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9474.435438. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9517.729777 . ( 0 sec) [ -9512.4274] [GTR parameters ] . ( 0 sec) [ -9512.2160] [Alpha ][ 0.951124] . ( 0 sec) [ -9512.2160] [Topology ] . ( 1 sec) [ -9481.7224] [Topology ] . ( 2 sec) [ -9477.1726] [Topology ] . ( 3 sec) [ -9475.9502] [Topology ] . ( 3 sec) [ -9475.4351] [Topology ] . ( 4 sec) [ -9475.1891] [Topology ] . ( 5 sec) [ -9475.0652] [Topology ] . ( 6 sec) [ -9475.0016] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9475.001637 . ( 12 sec) [ -9474.8908] [GTR parameters ] . ( 12 sec) [ -9474.5736] [Alpha ][ 1.008942] . ( 12 sec) [ -9474.5736] [Topology ] . ( 13 sec) [ -9474.5046] [Topology ] . ( 14 sec) [ -9474.4727] [Topology ] . ( 15 sec) [ -9474.4565] [Topology ] . ( 16 sec) [ -9474.4482] [Topology ] . ( 16 sec) [ -9474.4439] [Topology ] . ( 17 sec) [ -9474.4417] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9474.441742 . ( 23 sec) [ -9474.4413] [GTR parameters ] . ( 23 sec) [ -9474.4384] [Alpha ][ 1.014807] . ( 23 sec) [ -9474.4384] [Topology ] . ( 24 sec) [ -9474.4368] [Topology ] . ( 25 sec) [ -9474.4361] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9474.436096 . ( 31 sec) [ -9474.4361] [GTR parameters ] . ( 31 sec) [ -9474.4361] [Alpha ][ 1.014807] . ( 31 sec) [ -9474.4361] [Topology ] . ( 32 sec) [ -9474.4357] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -9512.4274] [GTR parameters ] . ( 44 sec) [ -9512.2160] [Alpha ][ 0.951124] . ( 45 sec) [ -9511.2588] [ 2039] [depth= 1] . ( 45 sec) [ -9510.0321] [ 2039] [depth= 1] . ( 46 sec) [ -9509.4415] [ 2044] [depth= 1] . ( 46 sec) [ -9509.2955] [ 2043] [depth= 1] . ( 46 sec) [ -9509.0728] [ 2044] [depth= 1] . ( 46 sec) [ -9507.7938] [ 2049] [depth= 1] . ( 46 sec) [ -9507.0333] [ 2042] [depth= 1] . ( 46 sec) [ -9505.5483] [ 2040] [depth= 1] . ( 46 sec) [ -9504.0519] [ 2042] [depth= 1] . ( 46 sec) [ -9503.6797] [ 2044] [depth= 1] . ( 46 sec) [ -9501.7307] [ 2042] [depth= 1] . ( 47 sec) [ -9500.4782] [ 2045] [depth= 2] . ( 47 sec) [ -9500.0698] [ 2046] [depth= 1] . ( 47 sec) [ -9499.3692] [ 2044] [depth= 2] . ( 47 sec) [ -9498.5631] [ 2048] [depth= 1] . ( 47 sec) [ -9497.9218] [ 2049] [depth= 1] . ( 47 sec) [ -9482.2410] [Branch lengths ] . ( 48 sec) [ -9482.1601] [GTR parameters ] . ( 48 sec) [ -9481.9413] [Alpha ][ 0.999289] . ( 50 sec) [ -9480.1115] [ 2051] [depth= 1] . ( 50 sec) [ -9480.0723] [ 2046] [depth= 1] . ( 51 sec) [ -9477.8086] [Branch lengths ] . ( 51 sec) [ -9477.7994] [GTR parameters ] . ( 51 sec) [ -9477.7926] [Alpha ][ 1.008104] . ( 54 sec) [ -9477.6160] [ 2048] [depth= 2] . ( 54 sec) [ -9477.1848] [ 2048] [depth= 1] . ( 54 sec) [ -9476.8434] [Branch lengths ] . ( 55 sec) [ -9476.8412] [GTR parameters ] . ( 55 sec) [ -9476.8401] [Alpha ][ 1.011670] . ( 58 sec) [ -9475.9728] [ 2045] [depth= 1] . ( 75 sec) [ -9475.7123] [Branch lengths ] . ( 75 sec) [ -9475.7112] [GTR parameters ] . ( 75 sec) [ -9475.7112] [Alpha ][ 1.011670] . ( 96 sec) [ -9475.7024] [Branch lengths ] . ( 96 sec) [ -9475.7024] [Topology ] . ( 96 sec) [ -9475.0963] [Topology ] . ( 97 sec) [ -9475.0575] [Topology ] . ( 98 sec) [ -9475.0541] [Topology ] . ( 99 sec) [ -9475.0535] [Topology ] . ( 99 sec) [ -9475.0521] [GTR parameters ] . ( 99 sec) [ -9475.0519] [Alpha ][ 1.013113] . ( 99 sec) [ -9475.0519] [Topology ] . ( 100 sec) [ -9475.0518] [Topology ] . ( 100 sec) [ -9475.0518] [GTR parameters ] . ( 100 sec) [ -9475.0518] [Alpha ][ 1.013113] . Checking for NNIs, optimizing five branches... . ( 106 sec) [ -9473.7597] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9474.435707 . Log likelihood obtained after SPR moves : -9473.759734 . Log likelihood of the current tree: -9473.759734. . Printing the most likely tree in file 'data28.phy_phyml_tree.txt'... . Best log likelihood : -9473.759734 . Time used 0h1m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo