.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data30.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... . 449 patterns found. (out of a total of 500 sites) . 52 sites without polymorphism (10.40%). . [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)... . ( 1 sec) [ -21081.5467] [GTR parameters ] . ( 1 sec) [ -20675.6423] [Alpha ][ 0.500960] . ( 1 sec) [ -20222.8475] [ 5247] [depth= 8] . ( 1 sec) [ -20129.4365] [ 5230] [depth= 9] . ( 1 sec) [ -19873.7046] [ 5194] [depth= 1] . ( 1 sec) [ -19799.1524] [ 5151] [depth= 7] . ( 1 sec) [ -19474.7907] [ 5042] [depth= 5] . ( 1 sec) [ -19372.8262] [ 5044] [depth= 5] . ( 1 sec) [ -18979.6732] [ 4995] [depth= 3] . ( 1 sec) [ -18844.8973] [ 5038] [depth= 1] . ( 1 sec) [ -18543.0085] [ 4905] [depth= 2] . ( 1 sec) [ -18006.1904] [ 4753] [depth= 7] . ( 1 sec) [ -17708.4863] [ 4659] [depth= 7] . ( 1 sec) [ -17494.9643] [ 4580] [depth= 11] . ( 1 sec) [ -17049.0868] [ 4483] [depth= 9] . ( 2 sec) [ -17005.5704] [ 4477] [depth= 1] . ( 2 sec) [ -16907.0428] [ 4465] [depth= 1] . ( 2 sec) [ -16817.1304] [ 4401] [depth= 4] . ( 2 sec) [ -16679.7610] [ 4375] [depth= 2] . ( 2 sec) [ -16678.5566] [ 4367] [depth= 1] . ( 2 sec) [ -16434.4038] [ 4264] [depth= 4] . ( 2 sec) [ -16305.1088] [ 4266] [depth= 2] . ( 2 sec) [ -16282.6438] [ 4270] [depth= 1] . ( 2 sec) [ -16214.9321] [ 4170] [depth= 3] . ( 2 sec) [ -16044.9690] [ 4134] [depth= 2] . ( 2 sec) [ -15555.9399] [ 3925] [depth= 9] . ( 2 sec) [ -15494.1946] [ 3921] [depth= 1] . ( 2 sec) [ -15420.3116] [ 3950] [depth= 15] . ( 2 sec) [ -15142.6486] [ 3841] [depth= 2] . ( 2 sec) [ -14894.2597] [ 3757] [depth= 3] . ( 2 sec) [ -14885.2902] [ 3746] [depth= 5] . ( 2 sec) [ -14707.7805] [ 3675] [depth= 5] . ( 2 sec) [ -14671.3065] [ 3680] [depth= 1] . ( 2 sec) [ -14482.7023] [ 3609] [depth= 10] . ( 2 sec) [ -14480.6045] [ 3602] [depth= 2] . ( 2 sec) [ -14390.7702] [ 3606] [depth= 6] . ( 3 sec) [ -14313.2837] [ 3625] [depth= 1] . ( 3 sec) [ -14004.8928] [ 3505] [depth= 12] . ( 3 sec) [ -13951.4561] [ 3505] [depth= 1] . ( 3 sec) [ -13885.1631] [ 3474] [depth= 1] . ( 3 sec) [ -13556.6523] [ 3362] [depth= 1] . ( 3 sec) [ -13495.7738] [ 3350] [depth= 1] . ( 3 sec) [ -13481.0998] [ 3352] [depth= 9] . ( 3 sec) [ -13471.2097] [ 3373] [depth= 1] . ( 3 sec) [ -13089.9284] [ 3292] [depth= 6] . ( 3 sec) [ -13040.4348] [ 3274] [depth= 2] . ( 3 sec) [ -13016.2426] [ 3233] [depth= 1] . ( 3 sec) [ -12738.2591] [ 3128] [depth= 4] . ( 3 sec) [ -12715.9596] [ 3124] [depth= 1] . ( 3 sec) [ -12690.5426] [ 3118] [depth= 2] . ( 3 sec) [ -12477.3024] [ 3108] [depth= 2] . ( 3 sec) [ -12428.8234] [ 3099] [depth= 1] . ( 3 sec) [ -12425.7632] [ 3110] [depth= 1] . ( 3 sec) [ -12424.9332] [ 3107] [depth= 1] . ( 3 sec) [ -12407.2549] [ 3085] [depth= 1] . ( 3 sec) [ -12381.5217] [ 3028] [depth= 1] . ( 3 sec) [ -12351.3240] [ 3016] [depth= 1] . ( 4 sec) [ -12226.3268] [ 2968] [depth= 2] . ( 4 sec) [ -12213.0183] [ 2973] [depth= 1] . ( 4 sec) [ -12126.9117] [ 2934] [depth= 2] . ( 4 sec) [ -12114.2655] [ 2910] [depth= 1] . ( 4 sec) [ -12106.3143] [ 2909] [depth= 1] . ( 4 sec) [ -12095.3206] [ 2897] [depth= 1] . ( 4 sec) [ -11913.2455] [ 2907] [depth= 1] . ( 4 sec) [ -11891.7620] [ 2908] [depth= 1] . ( 4 sec) [ -11890.1931] [ 2892] [depth= 1] . ( 4 sec) [ -11886.0805] [ 2893] [depth= 1] . ( 4 sec) [ -11836.6783] [ 2844] [depth= 3] . ( 4 sec) [ -11819.5120] [ 2834] [depth= 1] . ( 4 sec) [ -11813.7766] [ 2841] [depth= 2] . ( 4 sec) [ -11796.4607] [ 2817] [depth= 2] . ( 4 sec) [ -11785.3246] [ 2819] [depth= 11] . ( 4 sec) [ -11782.2155] [ 2798] [depth= 1] . ( 5 sec) [ -11719.1296] [ 2767] [depth= 2] . ( 5 sec) [ -11559.1920] [ 2656] [depth= 8] . ( 5 sec) [ -11545.8992] [ 2648] [depth= 1] . ( 5 sec) [ -11393.2517] [ 2578] [depth= 6] . ( 5 sec) [ -11388.0480] [ 2576] [depth= 1] . ( 5 sec) [ -11385.0881] [ 2575] [depth= 1] . ( 5 sec) [ -11384.2779] [ 2576] [depth= 1] . ( 5 sec) [ -11384.1161] [ 2578] [depth= 1] . ( 5 sec) [ -11345.6514] [ 2557] [depth= 1] . ( 5 sec) [ -11345.5630] [ 2556] [depth= 1] . ( 5 sec) [ -11343.8759] [ 2561] [depth= 1] . ( 5 sec) [ -11111.2880] [Branch lengths ] . ( 6 sec) [ -11109.4794] [GTR parameters ] . ( 6 sec) [ -11064.9233] [Alpha ][ 0.943698] . ( 6 sec) [ -11064.2419] [ 2555] [depth= 1] . ( 6 sec) [ -11053.5339] [ 2548] [depth= 1] . ( 6 sec) [ -11052.7000] [ 2553] [depth= 1] . ( 7 sec) [ -11052.4919] [ 2558] [depth= 1] . ( 7 sec) [ -11051.4986] [ 2557] [depth= 2] . ( 7 sec) [ -11051.2767] [ 2559] [depth= 1] . ( 7 sec) [ -11050.7860] [ 2557] [depth= 1] . ( 7 sec) [ -11050.5407] [ 2557] [depth= 1] . ( 7 sec) [ -11049.9289] [ 2546] [depth= 1] . ( 7 sec) [ -11049.8290] [ 2543] [depth= 1] . ( 8 sec) [ -11049.7607] [ 2546] [depth= 1] . ( 9 sec) [ -11039.9273] [Branch lengths ] . ( 10 sec) [ -11039.9116] [GTR parameters ] . ( 10 sec) [ -11039.6141] [Alpha ][ 0.993005] . ( 10 sec) [ -11039.2613] [ 2549] [depth= 1] . ( 10 sec) [ -11037.0546] [ 2552] [depth= 1] . ( 13 sec) [ -11035.1360] [Branch lengths ] . ( 13 sec) [ -11035.1233] [GTR parameters ] . ( 13 sec) [ -11035.1083] [Alpha ][ 1.004723] . ( 17 sec) [ -11034.9972] [Branch lengths ] . ( 37 sec) [ -11034.9809] [Branch lengths ] . ( 37 sec) [ -11034.9809] [Topology ] . ( 38 sec) [ -11034.9786] [Topology ] . ( 39 sec) [ -11034.9776] [Topology ] . ( 39 sec) [ -11034.9775] [GTR parameters ] . ( 39 sec) [ -11034.9775] [Alpha ][ 1.003718] . ( 39 sec) [ -11034.9775] [Topology ] . ( 40 sec) [ -11034.9770] [Topology ] . ( 40 sec) [ -11034.9770] [GTR parameters ] . ( 40 sec) [ -11034.9770] [Alpha ][ 1.003718] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -11034.3677] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11034.367744. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21555.7490] [GTR parameters ] . ( 1 sec) [ -21147.0260] [Alpha ][ 0.500960] . ( 1 sec) [ -20814.1611] [ 5223] [depth= 3] . ( 1 sec) [ -20699.5529] [ 5211] [depth= 3] . ( 1 sec) [ -20567.4424] [ 5162] [depth= 4] . ( 1 sec) [ -20518.2233] [ 5156] [depth= 3] . ( 1 sec) [ -20489.3247] [ 5123] [depth= 1] . ( 1 sec) [ -20398.7217] [ 5118] [depth= 4] . ( 1 sec) [ -20375.6075] [ 5117] [depth= 1] . ( 1 sec) [ -20238.9791] [ 5112] [depth= 3] . ( 1 sec) [ -20099.2750] [ 5081] [depth= 2] . ( 1 sec) [ -20002.0844] [ 5074] [depth= 6] . ( 1 sec) [ -19723.3747] [ 4973] [depth= 3] . ( 1 sec) [ -19354.4214] [ 4935] [depth= 5] . ( 1 sec) [ -18914.2536] [ 4789] [depth= 14] . ( 1 sec) [ -18878.9544] [ 4797] [depth= 1] . ( 1 sec) [ -18509.6498] [ 4682] [depth= 13] . ( 1 sec) [ -17988.9736] [ 4529] [depth= 18] . ( 1 sec) [ -17507.2046] [ 4433] [depth= 12] . ( 2 sec) [ -17346.0054] [ 4415] [depth= 1] . ( 2 sec) [ -17102.1279] [ 4409] [depth= 1] . ( 2 sec) [ -16650.7667] [ 4302] [depth= 8] . ( 2 sec) [ -16458.6835] [ 4281] [depth= 1] . ( 2 sec) [ -16434.1334] [ 4221] [depth= 1] . ( 2 sec) [ -16351.0148] [ 4185] [depth= 13] . ( 2 sec) [ -16225.8786] [ 4192] [depth= 7] . ( 2 sec) [ -15830.4867] [ 4018] [depth= 8] . ( 2 sec) [ -15712.0352] [ 3938] [depth= 1] . ( 2 sec) [ -15585.4441] [ 3888] [depth= 4] . ( 2 sec) [ -15106.9532] [ 3751] [depth= 7] . ( 2 sec) [ -15100.7465] [ 3756] [depth= 1] . ( 2 sec) [ -14910.5179] [ 3753] [depth= 13] . ( 2 sec) [ -14866.7269] [ 3754] [depth= 1] . ( 2 sec) [ -14774.2415] [ 3753] [depth= 1] . ( 2 sec) [ -14730.1483] [ 3748] [depth= 2] . ( 2 sec) [ -14556.4620] [ 3724] [depth= 1] . ( 2 sec) [ -14428.8901] [ 3662] [depth= 11] . ( 2 sec) [ -14387.7516] [ 3665] [depth= 1] . ( 2 sec) [ -14264.0305] [ 3572] [depth= 8] . ( 3 sec) [ -14175.1843] [ 3543] [depth= 8] . ( 3 sec) [ -14086.3439] [ 3500] [depth= 1] . ( 3 sec) [ -14035.6962] [ 3485] [depth= 7] . ( 3 sec) [ -14015.0726] [ 3483] [depth= 1] . ( 3 sec) [ -13850.6641] [ 3447] [depth= 5] . ( 3 sec) [ -13779.7006] [ 3456] [depth= 2] . ( 3 sec) [ -13729.3031] [ 3436] [depth= 2] . ( 3 sec) [ -13549.8774] [ 3403] [depth= 1] . ( 3 sec) [ -13517.5508] [ 3386] [depth= 5] . ( 3 sec) [ -13281.5230] [ 3328] [depth= 1] . ( 3 sec) [ -13272.4591] [ 3314] [depth= 2] . ( 3 sec) [ -13188.7062] [ 3250] [depth= 8] . ( 3 sec) [ -13184.4906] [ 3277] [depth= 1] . ( 3 sec) [ -13117.0763] [ 3250] [depth= 1] . ( 3 sec) [ -12991.3698] [ 3229] [depth= 6] . ( 3 sec) [ -12853.8081] [ 3157] [depth= 2] . ( 3 sec) [ -12803.8897] [ 3136] [depth= 2] . ( 3 sec) [ -12421.4033] [ 3036] [depth= 8] . ( 4 sec) [ -12417.6432] [ 3034] [depth= 1] . ( 4 sec) [ -12214.0156] [ 2941] [depth= 8] . ( 4 sec) [ -12169.1543] [ 2929] [depth= 1] . ( 4 sec) [ -12150.0400] [ 2918] [depth= 1] . ( 4 sec) [ -12149.4145] [ 2920] [depth= 1] . ( 4 sec) [ -12147.6576] [ 2918] [depth= 1] . ( 4 sec) [ -12064.9779] [ 2848] [depth= 10] . ( 4 sec) [ -12064.4876] [ 2849] [depth= 1] . ( 4 sec) [ -12030.7931] [ 2834] [depth= 2] . ( 4 sec) [ -12021.3290] [ 2833] [depth= 1] . ( 4 sec) [ -12019.8260] [ 2829] [depth= 2] . ( 4 sec) [ -12016.9504] [ 2821] [depth= 2] . ( 4 sec) [ -11982.9938] [ 2824] [depth= 1] . ( 4 sec) [ -11941.2901] [ 2814] [depth= 1] . ( 4 sec) [ -11940.9216] [ 2816] [depth= 1] . ( 4 sec) [ -11771.7331] [ 2749] [depth= 1] . ( 4 sec) [ -11769.1507] [ 2746] [depth= 1] . ( 4 sec) [ -11766.8951] [ 2745] [depth= 1] . ( 4 sec) [ -11580.3009] [ 2719] [depth= 6] . ( 5 sec) [ -11547.0960] [ 2731] [depth= 1] . ( 5 sec) [ -11530.0784] [ 2728] [depth= 1] . ( 5 sec) [ -11498.9311] [ 2687] [depth= 2] . ( 5 sec) [ -11473.1534] [ 2679] [depth= 2] . ( 5 sec) [ -11470.3392] [ 2680] [depth= 1] . ( 5 sec) [ -11440.2400] [ 2689] [depth= 1] . ( 5 sec) [ -11314.0659] [Branch lengths ] . ( 6 sec) [ -11311.4725] [GTR parameters ] . ( 6 sec) [ -11280.4966] [Alpha ][ 0.851941] . ( 6 sec) [ -11250.2768] [ 2627] [depth= 2] . ( 6 sec) [ -11246.5666] [ 2624] [depth= 1] . ( 6 sec) [ -11245.8517] [ 2623] [depth= 1] . ( 6 sec) [ -11221.6545] [ 2620] [depth= 1] . ( 6 sec) [ -11176.3605] [ 2610] [depth= 5] . ( 6 sec) [ -11159.6878] [ 2590] [depth= 3] . ( 6 sec) [ -11159.3625] [ 2601] [depth= 1] . ( 7 sec) [ -11146.7388] [ 2594] [depth= 1] . ( 7 sec) [ -11144.7655] [ 2591] [depth= 1] . ( 7 sec) [ -11123.9798] [ 2580] [depth= 1] . ( 7 sec) [ -11123.9513] [ 2579] [depth= 1] . ( 7 sec) [ -11123.1944] [ 2581] [depth= 1] . ( 7 sec) [ -11122.9387] [ 2575] [depth= 1] . ( 7 sec) [ -11121.1169] [ 2574] [depth= 1] . ( 8 sec) [ -11088.8399] [ 2558] [depth= 1] . ( 8 sec) [ -11086.8157] [ 2555] [depth= 1] . ( 8 sec) [ -11077.4696] [ 2541] [depth= 1] . ( 8 sec) [ -11076.9914] [ 2542] [depth= 1] . ( 8 sec) [ -11076.8638] [ 2542] [depth= 1] . ( 8 sec) [ -11076.7194] [ 2539] [depth= 1] . ( 8 sec) [ -11074.7563] [ 2544] [depth= 1] . ( 9 sec) [ -11074.1700] [ 2543] [depth= 1] . ( 9 sec) [ -11073.9259] [ 2544] [depth= 1] . ( 9 sec) [ -11072.2410] [ 2545] [depth= 1] . ( 9 sec) [ -11072.0932] [ 2544] [depth= 1] . ( 9 sec) [ -11043.6603] [Branch lengths ] . ( 10 sec) [ -11043.4554] [GTR parameters ] . ( 10 sec) [ -11041.3485] [Alpha ][ 0.978931] . ( 10 sec) [ -11041.1460] [ 2545] [depth= 1] . ( 11 sec) [ -11040.7324] [ 2543] [depth= 1] . ( 11 sec) [ -11040.6909] [ 2543] [depth= 1] . ( 12 sec) [ -11040.3486] [ 2547] [depth= 1] . ( 12 sec) [ -11040.2842] [ 2549] [depth= 1] . ( 13 sec) [ -11035.4788] [Branch lengths ] . ( 13 sec) [ -11035.4742] [GTR parameters ] . ( 13 sec) [ -11035.4398] [Alpha ][ 0.996647] . ( 16 sec) [ -11035.0393] [Branch lengths ] . ( 37 sec) [ -11034.9923] [Branch lengths ] . ( 37 sec) [ -11034.9923] [Topology ] . ( 38 sec) [ -11034.9868] [Topology ] . ( 39 sec) [ -11034.9846] [Topology ] . ( 40 sec) [ -11034.9836] [Topology ] . ( 40 sec) [ -11034.9830] [Topology ] . ( 41 sec) [ -11034.9827] [GTR parameters ] . ( 41 sec) [ -11034.9777] [Alpha ][ 1.003394] . ( 41 sec) [ -11034.9777] [Topology ] . ( 41 sec) [ -11034.9770] [Topology ] . ( 42 sec) [ -11034.9770] [GTR parameters ] . ( 42 sec) [ -11034.9770] [Alpha ][ 1.003394] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -11034.3669] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -11034.3668] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11034.366813. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21964.6374] [GTR parameters ] . ( 1 sec) [ -21533.5674] [Alpha ][ 0.500960] . ( 1 sec) [ -21133.8334] [ 5380] [depth= 8] . ( 1 sec) [ -20949.3966] [ 5367] [depth= 8] . ( 1 sec) [ -20819.1616] [ 5352] [depth= 5] . ( 1 sec) [ -20803.9701] [ 5332] [depth= 2] . ( 1 sec) [ -20530.0140] [ 5156] [depth= 5] . ( 1 sec) [ -20380.6899] [ 5117] [depth= 11] . ( 1 sec) [ -20321.0801] [ 5111] [depth= 9] . ( 1 sec) [ -20266.9767] [ 5083] [depth= 1] . ( 1 sec) [ -20000.7402] [ 5015] [depth= 16] . ( 1 sec) [ -19652.6587] [ 4931] [depth= 7] . ( 1 sec) [ -19479.1262] [ 4873] [depth= 13] . ( 1 sec) [ -19406.3182] [ 4821] [depth= 7] . ( 1 sec) [ -18950.1232] [ 4800] [depth= 1] . ( 1 sec) [ -18419.4107] [ 4683] [depth= 8] . ( 2 sec) [ -18262.5311] [ 4670] [depth= 1] . ( 2 sec) [ -17939.6660] [ 4592] [depth= 9] . ( 2 sec) [ -17908.2212] [ 4593] [depth= 1] . ( 2 sec) [ -17896.0182] [ 4602] [depth= 1] . ( 2 sec) [ -17564.3383] [ 4565] [depth= 9] . ( 2 sec) [ -17300.3751] [ 4453] [depth= 4] . ( 2 sec) [ -17159.2066] [ 4394] [depth= 1] . ( 2 sec) [ -16960.8751] [ 4295] [depth= 10] . ( 2 sec) [ -16545.6774] [ 4157] [depth= 10] . ( 2 sec) [ -16163.8273] [ 4025] [depth= 9] . ( 2 sec) [ -16021.1400] [ 4020] [depth= 2] . ( 2 sec) [ -16000.5379] [ 4025] [depth= 2] . ( 2 sec) [ -15931.6152] [ 4014] [depth= 4] . ( 2 sec) [ -15865.8063] [ 3944] [depth= 1] . ( 2 sec) [ -15864.6490] [ 3945] [depth= 1] . ( 2 sec) [ -15841.2884] [ 3941] [depth= 4] . ( 2 sec) [ -15726.4843] [ 3879] [depth= 2] . ( 2 sec) [ -15484.5948] [ 3829] [depth= 7] . ( 2 sec) [ -15304.8078] [ 3764] [depth= 8] . ( 2 sec) [ -15248.9897] [ 3763] [depth= 1] . ( 2 sec) [ -14957.2989] [ 3630] [depth= 9] . ( 3 sec) [ -14931.0313] [ 3634] [depth= 1] . ( 3 sec) [ -14925.1074] [ 3637] [depth= 1] . ( 3 sec) [ -14635.3994] [ 3546] [depth= 6] . ( 3 sec) [ -14606.4905] [ 3543] [depth= 1] . ( 3 sec) [ -14603.1269] [ 3539] [depth= 1] . ( 3 sec) [ -14585.1230] [ 3521] [depth= 1] . ( 3 sec) [ -14135.2288] [ 3547] [depth= 7] . ( 3 sec) [ -13768.2834] [ 3380] [depth= 6] . ( 3 sec) [ -13691.0779] [ 3366] [depth= 1] . ( 3 sec) [ -13669.0404] [ 3361] [depth= 1] . ( 3 sec) [ -13606.5480] [ 3333] [depth= 2] . ( 3 sec) [ -13502.4096] [ 3313] [depth= 3] . ( 3 sec) [ -13413.3321] [ 3283] [depth= 2] . ( 3 sec) [ -13283.5202] [ 3280] [depth= 1] . ( 3 sec) [ -13243.5265] [ 3265] [depth= 3] . ( 3 sec) [ -13212.4075] [ 3207] [depth= 2] . ( 3 sec) [ -13061.2717] [ 3186] [depth= 8] . ( 3 sec) [ -12935.9700] [ 3166] [depth= 1] . ( 4 sec) [ -12828.2760] [ 3103] [depth= 2] . ( 4 sec) [ -12817.7584] [ 3100] [depth= 2] . ( 4 sec) [ -12806.6552] [ 3111] [depth= 1] . ( 4 sec) [ -12806.2829] [ 3114] [depth= 1] . ( 4 sec) [ -12806.0799] [ 3115] [depth= 1] . ( 4 sec) [ -12680.0911] [ 3085] [depth= 1] . ( 4 sec) [ -12479.1493] [ 3011] [depth= 6] . ( 4 sec) [ -12348.2138] [ 2981] [depth= 3] . ( 4 sec) [ -12348.1558] [ 2982] [depth= 3] . ( 4 sec) [ -12311.9910] [ 2985] [depth= 1] . ( 4 sec) [ -12017.5655] [ 2901] [depth= 3] . ( 4 sec) [ -11991.5697] [ 2871] [depth= 2] . ( 4 sec) [ -11988.6002] [ 2856] [depth= 2] . ( 4 sec) [ -11987.5309] [ 2856] [depth= 2] . ( 4 sec) [ -11959.3165] [ 2850] [depth= 2] . ( 4 sec) [ -11764.7735] [ 2812] [depth= 2] . ( 5 sec) [ -11706.1417] [ 2784] [depth= 3] . ( 5 sec) [ -11532.9144] [ 2663] [depth= 4] . ( 5 sec) [ -11493.6979] [ 2673] [depth= 2] . ( 5 sec) [ -11489.1682] [ 2671] [depth= 1] . ( 5 sec) [ -11476.2354] [ 2676] [depth= 1] . ( 5 sec) [ -11406.4616] [ 2638] [depth= 1] . ( 5 sec) [ -11390.3957] [ 2635] [depth= 1] . ( 5 sec) [ -11390.3601] [ 2636] [depth= 1] . ( 5 sec) [ -11383.9052] [ 2625] [depth= 2] . ( 5 sec) [ -11368.8239] [ 2631] [depth= 1] . ( 5 sec) [ -11223.5311] [Branch lengths ] . ( 6 sec) [ -11221.2727] [GTR parameters ] . ( 6 sec) [ -11186.9156] [Alpha ][ 0.890215] . ( 6 sec) [ -11186.3736] [ 2631] [depth= 1] . ( 6 sec) [ -11161.6726] [ 2619] [depth= 2] . ( 6 sec) [ -11161.0382] [ 2615] [depth= 1] . ( 6 sec) [ -11153.7790] [ 2604] [depth= 1] . ( 6 sec) [ -11119.4601] [ 2574] [depth= 1] . ( 6 sec) [ -11118.5853] [ 2573] [depth= 1] . ( 7 sec) [ -11118.1660] [ 2578] [depth= 1] . ( 7 sec) [ -11117.0652] [ 2574] [depth= 1] . ( 7 sec) [ -11116.3530] [ 2576] [depth= 1] . ( 7 sec) [ -11112.6712] [ 2573] [depth= 1] . ( 7 sec) [ -11109.4713] [ 2566] [depth= 1] . ( 7 sec) [ -11109.3123] [ 2564] [depth= 1] . ( 8 sec) [ -11108.9505] [ 2566] [depth= 1] . ( 8 sec) [ -11087.3927] [ 2557] [depth= 2] . ( 8 sec) [ -11085.7609] [ 2556] [depth= 1] . ( 8 sec) [ -11084.8958] [ 2556] [depth= 1] . ( 8 sec) [ -11073.4707] [ 2547] [depth= 1] . ( 8 sec) [ -11073.2727] [ 2547] [depth= 1] . ( 8 sec) [ -11073.1053] [ 2539] [depth= 1] . ( 8 sec) [ -11071.6877] [ 2537] [depth= 1] . ( 9 sec) [ -11071.5370] [ 2539] [depth= 1] . ( 9 sec) [ -11070.5969] [ 2545] [depth= 1] . ( 9 sec) [ -11070.5144] [ 2543] [depth= 1] . ( 9 sec) [ -11069.1922] [ 2548] [depth= 1] . ( 10 sec) [ -11040.2888] [Branch lengths ] . ( 10 sec) [ -11039.9096] [GTR parameters ] . ( 10 sec) [ -11038.9357] [Alpha ][ 0.978558] . ( 11 sec) [ -11038.8315] [ 2552] [depth= 1] . ( 11 sec) [ -11038.6894] [ 2550] [depth= 1] . ( 14 sec) [ -11035.4940] [Branch lengths ] . ( 14 sec) [ -11035.4927] [GTR parameters ] . ( 14 sec) [ -11035.4510] [Alpha ][ 0.998131] . ( 17 sec) [ -11035.0519] [Branch lengths ] . ( 38 sec) [ -11034.9921] [Branch lengths ] . ( 38 sec) [ -11034.9921] [Topology ] . ( 39 sec) [ -11034.9855] [Topology ] . ( 40 sec) [ -11034.9831] [Topology ] . ( 40 sec) [ -11034.9820] [Topology ] . ( 41 sec) [ -11034.9814] [Topology ] . ( 41 sec) [ -11034.9807] [GTR parameters ] . ( 41 sec) [ -11034.9776] [Alpha ][ 1.003384] . ( 41 sec) [ -11034.9776] [Topology ] . ( 42 sec) [ -11034.9770] [Topology ] . ( 42 sec) [ -11034.9770] [GTR parameters ] . ( 42 sec) [ -11034.9770] [Alpha ][ 1.003384] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11034.3669] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11034.366879. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21549.2549] [GTR parameters ] . ( 1 sec) [ -21121.6141] [Alpha ][ 0.500960] . ( 1 sec) [ -20671.1341] [ 5336] [depth= 8] . ( 1 sec) [ -20572.1919] [ 5286] [depth= 5] . ( 1 sec) [ -20399.2746] [ 5222] [depth= 7] . ( 1 sec) [ -20176.2051] [ 5111] [depth= 1] . ( 1 sec) [ -20007.3669] [ 5046] [depth= 9] . ( 1 sec) [ -19957.1749] [ 5034] [depth= 2] . ( 1 sec) [ -19632.9347] [ 5021] [depth= 5] . ( 1 sec) [ -19349.7076] [ 4972] [depth= 5] . ( 1 sec) [ -19248.8129] [ 4955] [depth= 6] . ( 1 sec) [ -19115.9558] [ 4936] [depth= 5] . ( 1 sec) [ -18923.2386] [ 4925] [depth= 4] . ( 1 sec) [ -18580.5271] [ 4828] [depth= 15] . ( 1 sec) [ -18291.9960] [ 4735] [depth= 9] . ( 1 sec) [ -18193.1546] [ 4723] [depth= 3] . ( 1 sec) [ -17576.7120] [ 4643] [depth= 14] . ( 1 sec) [ -17488.8896] [ 4615] [depth= 10] . ( 2 sec) [ -17324.3926] [ 4598] [depth= 5] . ( 2 sec) [ -17224.3122] [ 4487] [depth= 1] . ( 2 sec) [ -17037.0158] [ 4432] [depth= 7] . ( 2 sec) [ -17012.1427] [ 4434] [depth= 2] . ( 2 sec) [ -16938.0796] [ 4389] [depth= 1] . ( 2 sec) [ -16751.2007] [ 4288] [depth= 6] . ( 2 sec) [ -16685.3285] [ 4267] [depth= 2] . ( 2 sec) [ -16641.8711] [ 4223] [depth= 1] . ( 2 sec) [ -16569.3439] [ 4169] [depth= 9] . ( 2 sec) [ -16336.3415] [ 4134] [depth= 2] . ( 2 sec) [ -16221.1477] [ 4097] [depth= 6] . ( 2 sec) [ -16211.2654] [ 4100] [depth= 2] . ( 2 sec) [ -16017.1031] [ 4053] [depth= 3] . ( 2 sec) [ -16016.2296] [ 4056] [depth= 1] . ( 2 sec) [ -15518.7217] [ 3946] [depth= 4] . ( 2 sec) [ -15478.8237] [ 3950] [depth= 2] . ( 2 sec) [ -15287.8873] [ 3904] [depth= 15] . ( 2 sec) [ -14891.9624] [ 3810] [depth= 5] . ( 2 sec) [ -14796.7088] [ 3764] [depth= 1] . ( 2 sec) [ -14675.3134] [ 3733] [depth= 2] . ( 2 sec) [ -14659.3684] [ 3732] [depth= 1] . ( 2 sec) [ -14340.2997] [ 3542] [depth= 17] . ( 3 sec) [ -14307.1085] [ 3528] [depth= 2] . ( 3 sec) [ -13900.1106] [ 3362] [depth= 3] . ( 3 sec) [ -13802.3388] [ 3357] [depth= 1] . ( 3 sec) [ -13746.3682] [ 3314] [depth= 1] . ( 3 sec) [ -13597.9473] [ 3312] [depth= 1] . ( 3 sec) [ -13358.8736] [ 3203] [depth= 9] . ( 3 sec) [ -13292.8479] [ 3168] [depth= 1] . ( 3 sec) [ -13239.6602] [ 3129] [depth= 9] . ( 3 sec) [ -13236.1237] [ 3117] [depth= 1] . ( 3 sec) [ -13220.7977] [ 3100] [depth= 4] . ( 3 sec) [ -13176.5993] [ 3109] [depth= 1] . ( 3 sec) [ -13175.2920] [ 3100] [depth= 1] . ( 3 sec) [ -13048.9458] [ 3115] [depth= 1] . ( 3 sec) [ -12904.0072] [ 3055] [depth= 5] . ( 3 sec) [ -12665.0687] [ 3023] [depth= 5] . ( 3 sec) [ -12551.6529] [ 2984] [depth= 3] . ( 3 sec) [ -12521.4677] [ 2999] [depth= 2] . ( 3 sec) [ -12363.7513] [ 2933] [depth= 4] . ( 3 sec) [ -12268.3457] [ 2906] [depth= 1] . ( 3 sec) [ -12253.9912] [ 2906] [depth= 1] . ( 3 sec) [ -12031.4247] [ 2843] [depth= 7] . ( 3 sec) [ -11977.7344] [ 2836] [depth= 1] . ( 4 sec) [ -11925.1310] [ 2815] [depth= 4] . ( 4 sec) [ -11920.4223] [ 2825] [depth= 1] . ( 4 sec) [ -11719.9705] [ 2759] [depth= 3] . ( 4 sec) [ -11627.5465] [ 2715] [depth= 3] . ( 4 sec) [ -11627.2620] [ 2717] [depth= 1] . ( 4 sec) [ -11620.1323] [ 2716] [depth= 1] . ( 4 sec) [ -11619.1252] [ 2717] [depth= 1] . ( 4 sec) [ -11552.3228] [ 2700] [depth= 1] . ( 4 sec) [ -11461.4161] [ 2647] [depth= 2] . ( 4 sec) [ -11455.3786] [ 2646] [depth= 1] . ( 4 sec) [ -11453.2930] [ 2647] [depth= 1] . ( 4 sec) [ -11431.4630] [ 2646] [depth= 1] . ( 4 sec) [ -11420.9323] [ 2651] [depth= 1] . ( 4 sec) [ -11318.3147] [ 2611] [depth= 4] . ( 5 sec) [ -11313.6703] [ 2609] [depth= 2] . ( 5 sec) [ -11258.6152] [ 2590] [depth= 1] . ( 5 sec) [ -11257.8762] [ 2590] [depth= 1] . ( 5 sec) [ -11256.3691] [ 2589] [depth= 1] . ( 5 sec) [ -11224.1392] [ 2573] [depth= 1] . ( 5 sec) [ -11114.4294] [Branch lengths ] . ( 6 sec) [ -11111.8029] [GTR parameters ] . ( 6 sec) [ -11075.3719] [Alpha ][ 0.898022] . ( 6 sec) [ -11075.0407] [ 2575] [depth= 1] . ( 6 sec) [ -11069.2312] [ 2556] [depth= 3] . ( 6 sec) [ -11069.1112] [ 2557] [depth= 1] . ( 6 sec) [ -11068.7638] [ 2559] [depth= 1] . ( 6 sec) [ -11068.6617] [ 2559] [depth= 1] . ( 6 sec) [ -11067.9046] [ 2558] [depth= 1] . ( 7 sec) [ -11063.1908] [ 2556] [depth= 1] . ( 7 sec) [ -11062.9012] [ 2558] [depth= 1] . ( 7 sec) [ -11062.7616] [ 2555] [depth= 1] . ( 7 sec) [ -11061.0099] [ 2550] [depth= 2] . ( 7 sec) [ -11051.2620] [ 2541] [depth= 1] . ( 8 sec) [ -11051.2294] [ 2545] [depth= 1] . ( 8 sec) [ -11051.2018] [ 2545] [depth= 1] . ( 8 sec) [ -11050.0512] [ 2546] [depth= 1] . ( 8 sec) [ -11049.7660] [ 2549] [depth= 1] . ( 9 sec) [ -11049.3411] [ 2544] [depth= 1] . ( 9 sec) [ -11049.2919] [ 2542] [depth= 1] . ( 9 sec) [ -11049.1947] [ 2544] [depth= 1] . ( 9 sec) [ -11040.1203] [Branch lengths ] . ( 10 sec) [ -11040.0338] [GTR parameters ] . ( 10 sec) [ -11039.1797] [Alpha ][ 0.981123] . ( 10 sec) [ -11039.0569] [ 2546] [depth= 1] . ( 11 sec) [ -11039.0060] [ 2546] [depth= 1] . ( 12 sec) [ -11038.6425] [ 2545] [depth= 1] . ( 13 sec) [ -11037.2598] [Branch lengths ] . ( 13 sec) [ -11037.2577] [GTR parameters ] . ( 13 sec) [ -11037.2311] [Alpha ][ 0.996744] . ( 13 sec) [ -11037.1531] [ 2549] [depth= 2] . ( 13 sec) [ -11035.8016] [ 2554] [depth= 1] . ( 16 sec) [ -11035.4307] [Branch lengths ] . ( 17 sec) [ -11035.4266] [GTR parameters ] . ( 17 sec) [ -11035.4242] [Alpha ][ 1.001406] . ( 20 sec) [ -11035.3413] [Branch lengths ] . ( 41 sec) [ -11035.3234] [Branch lengths ] . ( 41 sec) [ -11035.3234] [Topology ] . ( 42 sec) [ -11035.2731] [Topology ] . ( 42 sec) [ -11035.0790] [Topology ] . ( 43 sec) [ -11035.0339] [Topology ] . ( 44 sec) [ -11035.0111] [Topology ] . ( 45 sec) [ -11034.9979] [Topology ] . ( 46 sec) [ -11034.9899] [Topology ] . ( 46 sec) [ -11034.9852] [Topology ] . ( 47 sec) [ -11034.9844] [GTR parameters ] . ( 47 sec) [ -11034.9838] [Alpha ][ 1.003770] . ( 47 sec) [ -11034.9838] [Topology ] . ( 48 sec) [ -11034.9809] [Topology ] . ( 48 sec) [ -11034.9791] [Topology ] . ( 49 sec) [ -11034.9780] [Topology ] . ( 50 sec) [ -11034.9774] [Topology ] . ( 50 sec) [ -11034.9774] [GTR parameters ] . ( 50 sec) [ -11034.9774] [Alpha ][ 1.003770] . ( 50 sec) [ -11034.9774] [Topology ] . ( 51 sec) [ -11034.9770] [Topology ] . ( 51 sec) [ -11034.9770] [GTR parameters ] . ( 51 sec) [ -11034.9770] [Alpha ][ 1.003770] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -11034.3672] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11034.367171. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21763.3504] [GTR parameters ] . ( 0 sec) [ -21306.0115] [Alpha ][ 0.500960] . ( 1 sec) [ -20676.2716] [ 5454] [depth= 6] . ( 1 sec) [ -20530.8562] [ 5411] [depth= 13] . ( 1 sec) [ -20457.5045] [ 5391] [depth= 3] . ( 1 sec) [ -20431.2068] [ 5392] [depth= 1] . ( 1 sec) [ -20149.8862] [ 5303] [depth= 4] . ( 1 sec) [ -19852.4411] [ 5291] [depth= 5] . ( 1 sec) [ -19842.9911] [ 5281] [depth= 1] . ( 1 sec) [ -19600.4779] [ 5193] [depth= 8] . ( 1 sec) [ -19427.5853] [ 5155] [depth= 10] . ( 1 sec) [ -19130.2062] [ 5060] [depth= 1] . ( 1 sec) [ -18898.1471] [ 4974] [depth= 9] . ( 1 sec) [ -18532.5897] [ 4808] [depth= 11] . ( 1 sec) [ -18378.8049] [ 4766] [depth= 10] . ( 1 sec) [ -18336.3073] [ 4755] [depth= 2] . ( 1 sec) [ -18224.1917] [ 4735] [depth= 1] . ( 1 sec) [ -18083.2053] [ 4722] [depth= 2] . ( 1 sec) [ -17966.3026] [ 4683] [depth= 1] . ( 1 sec) [ -17839.9872] [ 4643] [depth= 13] . ( 1 sec) [ -17656.9889] [ 4542] [depth= 3] . ( 1 sec) [ -17558.2639] [ 4549] [depth= 1] . ( 1 sec) [ -17259.5927] [ 4433] [depth= 13] . ( 2 sec) [ -17084.8031] [ 4428] [depth= 2] . ( 2 sec) [ -16943.1957] [ 4396] [depth= 7] . ( 2 sec) [ -16919.7233] [ 4387] [depth= 2] . ( 2 sec) [ -16787.0621] [ 4330] [depth= 11] . ( 2 sec) [ -16176.6798] [ 4231] [depth= 10] . ( 2 sec) [ -16164.6765] [ 4226] [depth= 1] . ( 2 sec) [ -15961.8061] [ 4164] [depth= 7] . ( 2 sec) [ -15666.0932] [ 4068] [depth= 10] . ( 2 sec) [ -15645.6648] [ 4036] [depth= 5] . ( 2 sec) [ -15178.0971] [ 3877] [depth= 2] . ( 2 sec) [ -15019.5140] [ 3864] [depth= 1] . ( 2 sec) [ -14635.8257] [ 3731] [depth= 8] . ( 2 sec) [ -14611.6751] [ 3737] [depth= 14] . ( 2 sec) [ -14520.5845] [ 3700] [depth= 5] . ( 2 sec) [ -14463.5964] [ 3748] [depth= 1] . ( 2 sec) [ -14114.7554] [ 3650] [depth= 11] . ( 2 sec) [ -14048.1214] [ 3658] [depth= 1] . ( 2 sec) [ -14048.0590] [ 3656] [depth= 1] . ( 2 sec) [ -13999.8888] [ 3650] [depth= 2] . ( 3 sec) [ -13851.8810] [ 3518] [depth= 9] . ( 3 sec) [ -13498.3266] [ 3356] [depth= 6] . ( 3 sec) [ -13341.2261] [ 3286] [depth= 1] . ( 3 sec) [ -13219.5351] [ 3277] [depth= 7] . ( 3 sec) [ -13027.1790] [ 3205] [depth= 6] . ( 3 sec) [ -12909.5442] [ 3209] [depth= 1] . ( 3 sec) [ -12778.6113] [ 3178] [depth= 1] . ( 3 sec) [ -12646.0731] [ 3149] [depth= 6] . ( 3 sec) [ -12524.4431] [ 3108] [depth= 6] . ( 3 sec) [ -12519.4228] [ 3099] [depth= 2] . ( 3 sec) [ -12425.2046] [ 3076] [depth= 6] . ( 3 sec) [ -12374.6287] [ 3060] [depth= 1] . ( 3 sec) [ -12362.8013] [ 3063] [depth= 6] . ( 3 sec) [ -12358.1845] [ 3062] [depth= 1] . ( 3 sec) [ -12354.5498] [ 3063] [depth= 1] . ( 3 sec) [ -12313.3366] [ 3003] [depth= 5] . ( 3 sec) [ -12255.3260] [ 3006] [depth= 2] . ( 3 sec) [ -12236.1897] [ 3000] [depth= 2] . ( 3 sec) [ -12233.5472] [ 3001] [depth= 1] . ( 4 sec) [ -12167.8677] [ 2975] [depth= 1] . ( 4 sec) [ -12151.1314] [ 2929] [depth= 3] . ( 4 sec) [ -12053.9423] [ 2918] [depth= 12] . ( 4 sec) [ -11983.2865] [ 2888] [depth= 4] . ( 4 sec) [ -11974.4813] [ 2885] [depth= 1] . ( 4 sec) [ -11834.4059] [ 2818] [depth= 4] . ( 4 sec) [ -11827.9949] [ 2818] [depth= 1] . ( 4 sec) [ -11814.7636] [ 2786] [depth= 2] . ( 4 sec) [ -11733.1273] [ 2737] [depth= 4] . ( 4 sec) [ -11718.3461] [ 2714] [depth= 4] . ( 4 sec) [ -11706.1883] [ 2709] [depth= 1] . ( 4 sec) [ -11634.6026] [ 2708] [depth= 2] . ( 4 sec) [ -11611.4414] [ 2705] [depth= 3] . ( 4 sec) [ -11609.6363] [ 2708] [depth= 1] . ( 4 sec) [ -11588.2202] [ 2704] [depth= 1] . ( 4 sec) [ -11586.0295] [ 2706] [depth= 1] . ( 4 sec) [ -11575.8887] [ 2704] [depth= 2] . ( 4 sec) [ -11542.0757] [ 2677] [depth= 3] . ( 4 sec) [ -11471.9628] [ 2659] [depth= 1] . ( 4 sec) [ -11468.3789] [ 2668] [depth= 1] . ( 5 sec) [ -11466.7546] [ 2660] [depth= 1] . ( 5 sec) [ -11434.3464] [ 2663] [depth= 1] . ( 5 sec) [ -11409.7041] [ 2652] [depth= 1] . ( 5 sec) [ -11404.7770] [ 2671] [depth= 2] . ( 5 sec) [ -11400.9463] [ 2669] [depth= 1] . ( 5 sec) [ -11220.2609] [Branch lengths ] . ( 6 sec) [ -11215.9165] [GTR parameters ] . ( 6 sec) [ -11180.7064] [Alpha ][ 0.879239] . ( 6 sec) [ -11174.0024] [ 2642] [depth= 1] . ( 6 sec) [ -11170.9745] [ 2639] [depth= 1] . ( 6 sec) [ -11170.6204] [ 2630] [depth= 1] . ( 6 sec) [ -11169.2809] [ 2629] [depth= 1] . ( 6 sec) [ -11168.2922] [ 2627] [depth= 1] . ( 7 sec) [ -11127.7507] [ 2600] [depth= 1] . ( 7 sec) [ -11127.4279] [ 2599] [depth= 1] . ( 7 sec) [ -11127.2968] [ 2599] [depth= 1] . ( 7 sec) [ -11077.3790] [ 2563] [depth= 2] . ( 7 sec) [ -11076.1767] [ 2564] [depth= 1] . ( 7 sec) [ -11074.8071] [ 2565] [depth= 2] . ( 7 sec) [ -11073.1425] [ 2565] [depth= 1] . ( 7 sec) [ -11072.9830] [ 2567] [depth= 1] . ( 7 sec) [ -11069.2691] [ 2547] [depth= 1] . ( 7 sec) [ -11069.0448] [ 2547] [depth= 1] . ( 8 sec) [ -11068.6811] [ 2547] [depth= 1] . ( 8 sec) [ -11068.5251] [ 2547] [depth= 1] . ( 9 sec) [ -11068.1431] [ 2552] [depth= 1] . ( 9 sec) [ -11040.9263] [Branch lengths ] . ( 10 sec) [ -11040.7319] [GTR parameters ] . ( 10 sec) [ -11038.9795] [Alpha ][ 0.995491] . ( 12 sec) [ -11038.9458] [ 2552] [depth= 1] . ( 13 sec) [ -11035.3196] [Branch lengths ] . ( 13 sec) [ -11035.3195] [GTR parameters ] . ( 13 sec) [ -11035.3118] [Alpha ][ 1.003839] . ( 17 sec) [ -11035.0283] [Branch lengths ] . ( 37 sec) [ -11034.9879] [Branch lengths ] . ( 37 sec) [ -11034.9879] [Topology ] . ( 38 sec) [ -11034.9821] [Topology ] . ( 39 sec) [ -11034.9797] [Topology ] . ( 40 sec) [ -11034.9784] [Topology ] . ( 41 sec) [ -11034.9777] [Topology ] . ( 41 sec) [ -11034.9775] [GTR parameters ] . ( 41 sec) [ -11034.9775] [Alpha ][ 1.003839] . ( 41 sec) [ -11034.9775] [Topology ] . ( 42 sec) [ -11034.9770] [Topology ] . ( 42 sec) [ -11034.9770] [GTR parameters ] . ( 42 sec) [ -11034.9770] [Alpha ][ 1.003839] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11034.3676] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -11034.3674] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11034.367432. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11119.090036 . ( 0 sec) [ -11116.2486] [GTR parameters ] . ( 0 sec) [ -11116.2215] [Alpha ][ 0.984187] . ( 0 sec) [ -11116.2215] [Topology ] . ( 1 sec) [ -11048.5706] [Topology ] . ( 2 sec) [ -11038.8163] [Topology ] . ( 3 sec) [ -11036.5652] [Topology ] . ( 3 sec) [ -11035.6337] [Topology ] . ( 4 sec) [ -11035.1848] [Topology ] . ( 5 sec) [ -11034.9511] [Topology ] . ( 6 sec) [ -11034.8247] [Topology ] . ( 7 sec) [ -11034.7550] [Topology ] . Checking for NNIs, optimizing five branches... . ( 13 sec) [ -11034.5574] [Topology ] . Before opt ts/t=1.000000 LK=-11034.557431 . ( 14 sec) [ -11034.4919] [GTR parameters ] . ( 14 sec) [ -11034.4580] [Alpha ][ 1.001854] . ( 14 sec) [ -11034.4580] [Topology ] . ( 15 sec) [ -11034.4100] [Topology ] . ( 15 sec) [ -11034.3880] [Topology ] . ( 16 sec) [ -11034.3763] [Topology ] . ( 17 sec) [ -11034.3700] [Topology ] . ( 18 sec) [ -11034.3664] [Topology ] . ( 19 sec) [ -11034.3645] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11034.364482 . ( 25 sec) [ -11034.3644] [GTR parameters ] . ( 26 sec) [ -11034.3636] [Alpha ][ 1.004582] . ( 26 sec) [ -11034.3636] [Topology ] . ( 26 sec) [ -11034.3623] [Topology ] . ( 27 sec) [ -11034.3616] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11034.361630 . ( 34 sec) [ -11034.3616] [GTR parameters ] . ( 35 sec) [ -11034.3616] [Alpha ][ 1.004582] . ( 35 sec) [ -11034.3616] [Topology ] . ( 35 sec) [ -11034.3612] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -11116.2486] [GTR parameters ] . ( 50 sec) [ -11116.2215] [Alpha ][ 0.984187] . ( 50 sec) [ -11113.9572] [ 2548] [depth= 1] . ( 50 sec) [ -11113.9227] [ 2547] [depth= 1] . ( 50 sec) [ -11113.7576] [ 2548] [depth= 1] . ( 50 sec) [ -11112.2497] [ 2552] [depth= 1] . ( 50 sec) [ -11104.0223] [ 2548] [depth= 1] . ( 50 sec) [ -11100.5631] [ 2549] [depth= 1] . ( 50 sec) [ -11099.9397] [ 2548] [depth= 1] . ( 50 sec) [ -11099.2411] [ 2551] [depth= 1] . ( 51 sec) [ -11092.3177] [ 2553] [depth= 1] . ( 51 sec) [ -11091.7772] [ 2554] [depth= 1] . ( 51 sec) [ -11091.4383] [ 2554] [depth= 1] . ( 51 sec) [ -11091.3842] [ 2559] [depth= 1] . ( 51 sec) [ -11091.3067] [ 2554] [depth= 1] . ( 51 sec) [ -11084.4773] [ 2545] [depth= 2] . ( 52 sec) [ -11083.0147] [ 2548] [depth= 1] . ( 52 sec) [ -11076.7092] [ 2551] [depth= 1] . ( 52 sec) [ -11075.7365] [ 2554] [depth= 1] . ( 52 sec) [ -11073.6798] [ 2550] [depth= 2] . ( 53 sec) [ -11041.3002] [Branch lengths ] . ( 53 sec) [ -11041.2088] [GTR parameters ] . ( 53 sec) [ -11041.2088] [Alpha ][ 0.984187] . ( 53 sec) [ -11041.1949] [ 2549] [depth= 1] . ( 53 sec) [ -11040.9243] [ 2548] [depth= 1] . ( 55 sec) [ -11040.7735] [ 2548] [depth= 1] . ( 55 sec) [ -11039.8719] [ 2548] [depth= 1] . ( 57 sec) [ -11035.4082] [Branch lengths ] . ( 57 sec) [ -11035.3975] [GTR parameters ] . ( 57 sec) [ -11035.3761] [Alpha ][ 0.998295] . ( 57 sec) [ -11035.3427] [ 2547] [depth= 1] . ( 60 sec) [ -11034.4633] [Branch lengths ] . ( 61 sec) [ -11034.4621] [GTR parameters ] . ( 61 sec) [ -11034.4598] [Alpha ][ 1.002912] . ( 82 sec) [ -11034.3779] [Branch lengths ] . ( 82 sec) [ -11034.3779] [Topology ] . ( 82 sec) [ -11034.3684] [Topology ] . ( 83 sec) [ -11034.3650] [Topology ] . ( 84 sec) [ -11034.3633] [Topology ] . ( 85 sec) [ -11034.3624] [Topology ] . ( 85 sec) [ -11034.3623] [GTR parameters ] . ( 85 sec) [ -11034.3619] [Alpha ][ 1.004723] . ( 85 sec) [ -11034.3619] [Topology ] . ( 86 sec) [ -11034.3613] [Topology ] . ( 86 sec) [ -11034.3613] [GTR parameters ] . ( 86 sec) [ -11034.3613] [Alpha ][ 1.004723] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11034.361242 . Log likelihood obtained after SPR moves : -11034.361332 . Log likelihood of the current tree: -11034.361242. . Printing the most likely tree in file 'data30.phy_phyml_tree.txt'... . Best log likelihood : -11034.361242 . Time used 0h1m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo