.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data85.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... . 460 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . [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) [ -22524.2265] [GTR parameters ] . ( 1 sec) [ -22117.8745] [Alpha ][ 0.500960] . ( 1 sec) [ -22023.2968] [ 5441] [depth= 8] . ( 1 sec) [ -21980.5520] [ 5422] [depth= 7] . ( 1 sec) [ -21723.1733] [ 5395] [depth= 6] . ( 1 sec) [ -21668.0537] [ 5370] [depth= 6] . ( 1 sec) [ -21487.6236] [ 5314] [depth= 3] . ( 1 sec) [ -21389.6624] [ 5304] [depth= 7] . ( 1 sec) [ -21311.7889] [ 5277] [depth= 4] . ( 1 sec) [ -20868.6375] [ 5211] [depth= 9] . ( 1 sec) [ -20725.1205] [ 5115] [depth= 8] . ( 1 sec) [ -20323.1164] [ 5056] [depth= 1] . ( 1 sec) [ -20013.2567] [ 4973] [depth= 12] . ( 1 sec) [ -19886.5007] [ 4917] [depth= 5] . ( 1 sec) [ -19877.8145] [ 4917] [depth= 1] . ( 1 sec) [ -19843.6941] [ 4907] [depth= 2] . ( 1 sec) [ -19585.1011] [ 4822] [depth= 10] . ( 1 sec) [ -19413.3626] [ 4808] [depth= 5] . ( 1 sec) [ -19099.7096] [ 4785] [depth= 3] . ( 1 sec) [ -19033.2105] [ 4781] [depth= 15] . ( 1 sec) [ -18754.7816] [ 4702] [depth= 17] . ( 1 sec) [ -18563.2950] [ 4593] [depth= 1] . ( 2 sec) [ -17793.8639] [ 4561] [depth= 1] . ( 2 sec) [ -17519.5797] [ 4479] [depth= 22] . ( 2 sec) [ -17515.3190] [ 4497] [depth= 1] . ( 2 sec) [ -17373.2656] [ 4489] [depth= 3] . ( 2 sec) [ -17208.2945] [ 4483] [depth= 15] . ( 2 sec) [ -17164.3111] [ 4453] [depth= 1] . ( 2 sec) [ -16849.6825] [ 4285] [depth= 4] . ( 2 sec) [ -16813.3204] [ 4279] [depth= 1] . ( 2 sec) [ -16773.9614] [ 4277] [depth= 1] . ( 2 sec) [ -16648.7459] [ 4246] [depth= 2] . ( 2 sec) [ -16629.0209] [ 4239] [depth= 1] . ( 2 sec) [ -16566.1790] [ 4236] [depth= 1] . ( 2 sec) [ -16445.3742] [ 4205] [depth= 2] . ( 2 sec) [ -16401.1272] [ 4202] [depth= 1] . ( 2 sec) [ -16341.7594] [ 4174] [depth= 2] . ( 2 sec) [ -16137.1583] [ 4069] [depth= 9] . ( 2 sec) [ -16130.1945] [ 4046] [depth= 1] . ( 2 sec) [ -15843.1588] [ 4023] [depth= 2] . ( 2 sec) [ -15813.9517] [ 4016] [depth= 1] . ( 3 sec) [ -15809.9821] [ 3902] [depth= 5] . ( 3 sec) [ -15482.4638] [ 3807] [depth= 3] . ( 3 sec) [ -15373.5994] [ 3803] [depth= 2] . ( 3 sec) [ -15353.8706] [ 3812] [depth= 1] . ( 3 sec) [ -15341.5412] [ 3808] [depth= 20] . ( 3 sec) [ -15329.2916] [ 3804] [depth= 1] . ( 3 sec) [ -14904.7266] [ 3691] [depth= 14] . ( 3 sec) [ -14755.8634] [ 3671] [depth= 3] . ( 3 sec) [ -14745.2509] [ 3662] [depth= 2] . ( 3 sec) [ -14682.6705] [ 3675] [depth= 4] . ( 3 sec) [ -14385.6814] [ 3617] [depth= 11] . ( 3 sec) [ -14381.4590] [ 3611] [depth= 1] . ( 3 sec) [ -14378.1740] [ 3610] [depth= 1] . ( 3 sec) [ -14369.7339] [ 3611] [depth= 2] . ( 3 sec) [ -14368.6344] [ 3606] [depth= 2] . ( 3 sec) [ -14222.2623] [ 3557] [depth= 1] . ( 3 sec) [ -14017.4596] [ 3457] [depth= 11] . ( 3 sec) [ -13992.6383] [ 3423] [depth= 1] . ( 3 sec) [ -13985.1641] [ 3433] [depth= 4] . ( 3 sec) [ -13980.9808] [ 3432] [depth= 1] . ( 4 sec) [ -13857.6650] [ 3399] [depth= 2] . ( 4 sec) [ -13809.7354] [ 3374] [depth= 4] . ( 4 sec) [ -13802.9087] [ 3368] [depth= 4] . ( 4 sec) [ -13786.9744] [ 3362] [depth= 1] . ( 4 sec) [ -13710.2543] [ 3331] [depth= 1] . ( 4 sec) [ -13444.3681] [ 3206] [depth= 6] . ( 4 sec) [ -13088.5060] [ 3120] [depth= 3] . ( 4 sec) [ -13087.1871] [ 3123] [depth= 2] . ( 4 sec) [ -13080.4435] [ 3122] [depth= 1] . ( 4 sec) [ -12980.1993] [ 3090] [depth= 1] . ( 4 sec) [ -12932.0064] [ 3084] [depth= 1] . ( 4 sec) [ -12741.4603] [ 3036] [depth= 3] . ( 4 sec) [ -12718.2917] [ 3037] [depth= 1] . ( 4 sec) [ -12678.8145] [ 3023] [depth= 2] . ( 4 sec) [ -12663.9882] [ 3003] [depth= 1] . ( 4 sec) [ -12495.2679] [ 2930] [depth= 1] . ( 5 sec) [ -12436.0289] [ 2903] [depth= 4] . ( 5 sec) [ -12378.5765] [ 2894] [depth= 2] . ( 5 sec) [ -12366.0274] [ 2893] [depth= 4] . ( 5 sec) [ -12340.4651] [ 2882] [depth= 1] . ( 5 sec) [ -12309.0593] [ 2876] [depth= 1] . ( 5 sec) [ -12303.7631] [ 2868] [depth= 1] . ( 5 sec) [ -12086.1271] [Branch lengths ] . ( 6 sec) [ -12084.9647] [GTR parameters ] . ( 6 sec) [ -12038.2546] [Alpha ][ 0.945056] . ( 6 sec) [ -12029.9872] [ 2855] [depth= 2] . ( 6 sec) [ -12027.0741] [ 2849] [depth= 1] . ( 6 sec) [ -12027.0493] [ 2850] [depth= 1] . ( 6 sec) [ -12026.9264] [ 2850] [depth= 1] . ( 6 sec) [ -12018.8131] [ 2843] [depth= 1] . ( 7 sec) [ -12008.0763] [ 2834] [depth= 1] . ( 7 sec) [ -12002.1292] [ 2824] [depth= 1] . ( 7 sec) [ -12001.7542] [ 2827] [depth= 1] . ( 7 sec) [ -12001.5424] [ 2826] [depth= 1] . ( 7 sec) [ -11999.8102] [ 2822] [depth= 1] . ( 8 sec) [ -11998.5304] [ 2820] [depth= 1] . ( 8 sec) [ -11992.3391] [ 2817] [depth= 1] . ( 8 sec) [ -11991.6216] [ 2821] [depth= 2] . ( 8 sec) [ -11991.4544] [ 2826] [depth= 1] . ( 9 sec) [ -11970.1916] [Branch lengths ] . ( 9 sec) [ -11970.1616] [GTR parameters ] . ( 9 sec) [ -11969.4412] [Alpha ][ 1.023487] . ( 12 sec) [ -11967.3824] [Branch lengths ] . ( 37 sec) [ -11967.0659] [Branch lengths ] . ( 37 sec) [ -11967.0659] [Topology ] . ( 38 sec) [ -11966.9668] [Topology ] . ( 39 sec) [ -11966.8910] [Topology ] . ( 39 sec) [ -11966.8794] [Topology ] . ( 40 sec) [ -11966.8741] [Topology ] . ( 41 sec) [ -11966.8715] [Topology ] . ( 42 sec) [ -11966.8703] [Topology ] . ( 43 sec) [ -11966.8697] [Topology ] . ( 43 sec) [ -11966.8649] [GTR parameters ] . ( 43 sec) [ -11966.8259] [Alpha ][ 1.042895] . ( 43 sec) [ -11966.8259] [Topology ] . ( 44 sec) [ -11966.8234] [Topology ] . ( 45 sec) [ -11966.8227] [Topology ] . ( 45 sec) [ -11966.8226] [GTR parameters ] . ( 45 sec) [ -11966.8226] [Alpha ][ 1.042895] . ( 45 sec) [ -11966.8226] [Topology ] . ( 46 sec) [ -11966.8223] [Topology ] . ( 46 sec) [ -11966.8223] [GTR parameters ] . ( 46 sec) [ -11966.8222] [Alpha ][ 1.043938] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -11966.8219] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.821923. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23086.5066] [GTR parameters ] . ( 1 sec) [ -22666.9491] [Alpha ][ 0.500960] . ( 1 sec) [ -22603.3462] [ 5584] [depth= 3] . ( 1 sec) [ -22388.0067] [ 5525] [depth= 5] . ( 1 sec) [ -22255.8413] [ 5515] [depth= 4] . ( 1 sec) [ -21975.0752] [ 5487] [depth= 7] . ( 2 sec) [ -21814.7593] [ 5421] [depth= 5] . ( 2 sec) [ -21697.4909] [ 5421] [depth= 8] . ( 2 sec) [ -21689.7236] [ 5416] [depth= 1] . ( 2 sec) [ -21650.6186] [ 5399] [depth= 2] . ( 2 sec) [ -21609.4261] [ 5377] [depth= 1] . ( 2 sec) [ -21485.5492] [ 5360] [depth= 4] . ( 2 sec) [ -21242.4558] [ 5295] [depth= 3] . ( 2 sec) [ -20866.7320] [ 5272] [depth= 5] . ( 2 sec) [ -20437.8571] [ 5139] [depth= 5] . ( 2 sec) [ -20187.6744] [ 5116] [depth= 1] . ( 2 sec) [ -19694.2463] [ 4971] [depth= 11] . ( 2 sec) [ -19624.3197] [ 4931] [depth= 9] . ( 2 sec) [ -19500.1470] [ 4886] [depth= 17] . ( 2 sec) [ -19390.0740] [ 4878] [depth= 1] . ( 2 sec) [ -19257.2517] [ 4872] [depth= 1] . ( 2 sec) [ -19116.9435] [ 4811] [depth= 1] . ( 2 sec) [ -18700.1997] [ 4801] [depth= 5] . ( 2 sec) [ -18506.0657] [ 4800] [depth= 1] . ( 2 sec) [ -18309.8884] [ 4713] [depth= 3] . ( 2 sec) [ -18247.6458] [ 4641] [depth= 7] . ( 2 sec) [ -18156.4121] [ 4635] [depth= 7] . ( 2 sec) [ -18092.5940] [ 4636] [depth= 1] . ( 2 sec) [ -18081.6111] [ 4677] [depth= 1] . ( 3 sec) [ -17963.0839] [ 4634] [depth= 3] . ( 3 sec) [ -17704.5577] [ 4504] [depth= 10] . ( 3 sec) [ -17572.4196] [ 4490] [depth= 6] . ( 3 sec) [ -17384.2739] [ 4431] [depth= 1] . ( 3 sec) [ -17269.8961] [ 4371] [depth= 7] . ( 3 sec) [ -17157.0881] [ 4353] [depth= 4] . ( 3 sec) [ -16869.1379] [ 4310] [depth= 4] . ( 3 sec) [ -16424.2730] [ 4177] [depth= 1] . ( 3 sec) [ -16400.6450] [ 4167] [depth= 2] . ( 3 sec) [ -16328.4682] [ 4125] [depth= 5] . ( 3 sec) [ -16323.8235] [ 4126] [depth= 1] . ( 3 sec) [ -16200.4257] [ 4093] [depth= 6] . ( 3 sec) [ -16126.0744] [ 4073] [depth= 1] . ( 3 sec) [ -16118.8861] [ 4074] [depth= 2] . ( 3 sec) [ -16071.8396] [ 4059] [depth= 7] . ( 3 sec) [ -16005.2281] [ 4020] [depth= 1] . ( 3 sec) [ -15871.6802] [ 3958] [depth= 9] . ( 3 sec) [ -15812.6832] [ 3923] [depth= 6] . ( 3 sec) [ -15622.2724] [ 3913] [depth= 2] . ( 3 sec) [ -15457.6746] [ 3939] [depth= 9] . ( 3 sec) [ -15336.1826] [ 3817] [depth= 3] . ( 4 sec) [ -15196.1837] [ 3704] [depth= 3] . ( 4 sec) [ -15161.9961] [ 3701] [depth= 3] . ( 4 sec) [ -15122.0864] [ 3690] [depth= 1] . ( 4 sec) [ -15098.7433] [ 3687] [depth= 7] . ( 4 sec) [ -14976.2101] [ 3671] [depth= 2] . ( 4 sec) [ -14657.4761] [ 3536] [depth= 6] . ( 4 sec) [ -14625.6858] [ 3529] [depth= 1] . ( 4 sec) [ -14264.3010] [ 3518] [depth= 1] . ( 4 sec) [ -14123.9534] [ 3502] [depth= 6] . ( 4 sec) [ -13908.5660] [ 3511] [depth= 2] . ( 4 sec) [ -13840.8441] [ 3459] [depth= 1] . ( 4 sec) [ -13800.0051] [ 3446] [depth= 2] . ( 4 sec) [ -13751.6492] [ 3431] [depth= 1] . ( 4 sec) [ -13602.7204] [ 3347] [depth= 5] . ( 4 sec) [ -13563.3180] [ 3315] [depth= 2] . ( 4 sec) [ -13541.9903] [ 3306] [depth= 3] . ( 4 sec) [ -13420.9868] [ 3277] [depth= 2] . ( 4 sec) [ -13294.2263] [ 3207] [depth= 5] . ( 4 sec) [ -13197.9912] [ 3171] [depth= 2] . ( 5 sec) [ -13193.2535] [ 3177] [depth= 1] . ( 5 sec) [ -13187.7600] [ 3195] [depth= 1] . ( 5 sec) [ -13009.6395] [ 3161] [depth= 3] . ( 5 sec) [ -12893.4232] [ 3150] [depth= 2] . ( 5 sec) [ -12796.7379] [ 3110] [depth= 4] . ( 5 sec) [ -12788.5551] [ 3092] [depth= 1] . ( 5 sec) [ -12745.2007] [ 3094] [depth= 2] . ( 5 sec) [ -12744.9432] [ 3096] [depth= 1] . ( 5 sec) [ -12731.9578] [ 3063] [depth= 5] . ( 5 sec) [ -12728.7832] [ 3055] [depth= 1] . ( 5 sec) [ -12722.7735] [ 3052] [depth= 1] . ( 5 sec) [ -12677.4437] [ 3062] [depth= 2] . ( 5 sec) [ -12673.5803] [ 3038] [depth= 3] . ( 5 sec) [ -12665.5130] [ 3040] [depth= 6] . ( 5 sec) [ -12658.1628] [ 3040] [depth= 1] . ( 6 sec) [ -12556.3597] [ 3028] [depth= 9] . ( 6 sec) [ -12542.5437] [ 3021] [depth= 1] . ( 6 sec) [ -12379.1422] [Branch lengths ] . ( 6 sec) [ -12378.1253] [GTR parameters ] . ( 7 sec) [ -12337.4551] [Alpha ][ 0.885110] . ( 7 sec) [ -12294.0308] [ 2965] [depth= 1] . ( 7 sec) [ -12288.3530] [ 2963] [depth= 3] . ( 7 sec) [ -12272.1493] [ 2963] [depth= 1] . ( 7 sec) [ -12096.1883] [ 2889] [depth= 3] . ( 7 sec) [ -12044.1389] [ 2874] [depth= 7] . ( 7 sec) [ -12042.4401] [ 2873] [depth= 1] . ( 7 sec) [ -12042.3078] [ 2875] [depth= 1] . ( 7 sec) [ -12041.8585] [ 2875] [depth= 1] . ( 8 sec) [ -12032.1107] [ 2865] [depth= 1] . ( 8 sec) [ -12030.0353] [ 2866] [depth= 1] . ( 8 sec) [ -12024.3991] [ 2871] [depth= 1] . ( 8 sec) [ -12024.2075] [ 2871] [depth= 1] . ( 8 sec) [ -12023.3816] [ 2876] [depth= 2] . ( 8 sec) [ -12023.1131] [ 2870] [depth= 2] . ( 9 sec) [ -12001.7409] [ 2846] [depth= 2] . ( 9 sec) [ -12001.4439] [ 2842] [depth= 1] . ( 9 sec) [ -11998.7647] [ 2834] [depth= 2] . ( 10 sec) [ -11997.5622] [ 2829] [depth= 1] . ( 10 sec) [ -11981.5101] [Branch lengths ] . ( 10 sec) [ -11981.2266] [GTR parameters ] . ( 11 sec) [ -11978.9353] [Alpha ][ 1.020039] . ( 12 sec) [ -11978.8027] [ 2827] [depth= 1] . ( 14 sec) [ -11969.7319] [ 2819] [depth= 3] . ( 14 sec) [ -11968.0605] [Branch lengths ] . ( 14 sec) [ -11968.0503] [GTR parameters ] . ( 14 sec) [ -11968.0113] [Alpha ][ 1.039575] . ( 15 sec) [ -11967.4970] [ 2823] [depth= 2] . ( 16 sec) [ -11967.4398] [ 2823] [depth= 1] . ( 16 sec) [ -11967.3087] [ 2823] [depth= 1] . ( 17 sec) [ -11967.1851] [ 2825] [depth= 1] . ( 18 sec) [ -11966.8969] [Branch lengths ] . ( 18 sec) [ -11966.8906] [GTR parameters ] . ( 18 sec) [ -11966.8897] [Alpha ][ 1.042442] . ( 21 sec) [ -11966.8352] [Branch lengths ] . ( 46 sec) [ -11966.8250] [Branch lengths ] . ( 46 sec) [ -11966.8250] [Topology ] . ( 47 sec) [ -11966.8236] [Topology ] . ( 48 sec) [ -11966.8229] [Topology ] . ( 48 sec) [ -11966.8228] [GTR parameters ] . ( 48 sec) [ -11966.8227] [Alpha ][ 1.043536] . ( 48 sec) [ -11966.8227] [Topology ] . ( 49 sec) [ -11966.8223] [Topology ] . ( 49 sec) [ -11966.8223] [GTR parameters ] . ( 49 sec) [ -11966.8223] [Alpha ][ 1.043536] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -11966.8220] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.821965. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23063.4183] [GTR parameters ] . ( 1 sec) [ -22637.0087] [Alpha ][ 0.500960] . ( 1 sec) [ -22427.7483] [ 5552] [depth= 8] . ( 1 sec) [ -22222.5178] [ 5520] [depth= 13] . ( 2 sec) [ -22097.6472] [ 5505] [depth= 3] . ( 2 sec) [ -22058.9639] [ 5486] [depth= 2] . ( 2 sec) [ -21677.3222] [ 5316] [depth= 8] . ( 2 sec) [ -21398.5250] [ 5241] [depth= 11] . ( 2 sec) [ -21160.6337] [ 5216] [depth= 6] . ( 2 sec) [ -20747.0959] [ 5156] [depth= 8] . ( 2 sec) [ -20495.1065] [ 5069] [depth= 8] . ( 2 sec) [ -20297.6466] [ 5012] [depth= 7] . ( 2 sec) [ -20030.3524] [ 4925] [depth= 12] . ( 2 sec) [ -19959.0908] [ 4896] [depth= 11] . ( 2 sec) [ -19463.7640] [ 4889] [depth= 1] . ( 2 sec) [ -19055.4730] [ 4814] [depth= 5] . ( 2 sec) [ -18631.3386] [ 4805] [depth= 3] . ( 2 sec) [ -18410.1881] [ 4716] [depth= 2] . ( 2 sec) [ -17850.9803] [ 4669] [depth= 7] . ( 2 sec) [ -17593.9017] [ 4580] [depth= 3] . ( 2 sec) [ -17268.5203] [ 4617] [depth= 7] . ( 2 sec) [ -17164.8221] [ 4584] [depth= 1] . ( 2 sec) [ -16919.1650] [ 4550] [depth= 6] . ( 2 sec) [ -16685.7341] [ 4437] [depth= 8] . ( 2 sec) [ -16615.4308] [ 4400] [depth= 2] . ( 2 sec) [ -16587.5086] [ 4358] [depth= 6] . ( 3 sec) [ -16345.5635] [ 4277] [depth= 6] . ( 3 sec) [ -15895.1354] [ 4197] [depth= 7] . ( 3 sec) [ -15864.2381] [ 4186] [depth= 4] . ( 3 sec) [ -15833.4867] [ 4182] [depth= 1] . ( 3 sec) [ -15830.7465] [ 4168] [depth= 2] . ( 3 sec) [ -15578.7977] [ 4100] [depth= 9] . ( 3 sec) [ -15577.8655] [ 4105] [depth= 1] . ( 3 sec) [ -15551.3063] [ 4082] [depth= 1] . ( 3 sec) [ -15478.6252] [ 4073] [depth= 1] . ( 3 sec) [ -15416.2927] [ 4072] [depth= 7] . ( 3 sec) [ -15415.7655] [ 4051] [depth= 2] . ( 3 sec) [ -15248.6303] [ 3988] [depth= 4] . ( 3 sec) [ -15198.1260] [ 3902] [depth= 1] . ( 3 sec) [ -15029.9523] [ 3901] [depth= 1] . ( 3 sec) [ -14898.6553] [ 3813] [depth= 4] . ( 3 sec) [ -14886.9803] [ 3808] [depth= 1] . ( 4 sec) [ -14845.4093] [ 3777] [depth= 2] . ( 4 sec) [ -14722.4144] [ 3758] [depth= 2] . ( 4 sec) [ -14685.4656] [ 3714] [depth= 2] . ( 4 sec) [ -14529.8578] [ 3693] [depth= 4] . ( 4 sec) [ -14469.2686] [ 3647] [depth= 2] . ( 4 sec) [ -14253.6461] [ 3591] [depth= 2] . ( 4 sec) [ -14045.8928] [ 3474] [depth= 7] . ( 4 sec) [ -14006.3721] [ 3460] [depth= 2] . ( 4 sec) [ -13964.6109] [ 3459] [depth= 1] . ( 4 sec) [ -13928.4477] [ 3441] [depth= 1] . ( 4 sec) [ -13928.3209] [ 3441] [depth= 1] . ( 4 sec) [ -13808.4650] [ 3349] [depth= 10] . ( 4 sec) [ -13751.5577] [ 3337] [depth= 2] . ( 4 sec) [ -13748.8752] [ 3338] [depth= 1] . ( 4 sec) [ -13732.4618] [ 3337] [depth= 1] . ( 4 sec) [ -13615.3740] [ 3306] [depth= 2] . ( 4 sec) [ -13523.2920] [ 3288] [depth= 4] . ( 4 sec) [ -13463.2737] [ 3274] [depth= 1] . ( 4 sec) [ -13301.3406] [ 3270] [depth= 5] . ( 5 sec) [ -13166.0348] [ 3261] [depth= 2] . ( 5 sec) [ -13145.5797] [ 3262] [depth= 1] . ( 5 sec) [ -13127.4364] [ 3253] [depth= 1] . ( 5 sec) [ -13100.9073] [ 3237] [depth= 3] . ( 5 sec) [ -13082.0774] [ 3212] [depth= 8] . ( 5 sec) [ -12993.5090] [ 3136] [depth= 1] . ( 5 sec) [ -12981.0908] [ 3127] [depth= 2] . ( 5 sec) [ -12952.8864] [ 3121] [depth= 1] . ( 5 sec) [ -12939.5683] [ 3156] [depth= 1] . ( 5 sec) [ -12887.2105] [ 3106] [depth= 4] . ( 5 sec) [ -12885.7415] [ 3108] [depth= 1] . ( 5 sec) [ -12666.5756] [ 2997] [depth= 8] . ( 5 sec) [ -12617.3517] [ 3000] [depth= 1] . ( 5 sec) [ -12558.9117] [ 3003] [depth= 1] . ( 5 sec) [ -12499.1591] [ 2987] [depth= 2] . ( 6 sec) [ -12269.7566] [Branch lengths ] . ( 6 sec) [ -12268.1359] [GTR parameters ] . ( 6 sec) [ -12218.3606] [Alpha ][ 0.947229] . ( 6 sec) [ -12214.4633] [ 2987] [depth= 4] . ( 6 sec) [ -12212.7214] [ 2979] [depth= 1] . ( 7 sec) [ -12212.4145] [ 2983] [depth= 1] . ( 7 sec) [ -12203.0819] [ 2969] [depth= 3] . ( 7 sec) [ -12067.6836] [ 2879] [depth= 7] . ( 7 sec) [ -12055.9951] [ 2883] [depth= 2] . ( 7 sec) [ -12047.8728] [ 2870] [depth= 1] . ( 7 sec) [ -12038.5428] [ 2837] [depth= 1] . ( 7 sec) [ -12035.4938] [ 2836] [depth= 1] . ( 7 sec) [ -12034.2816] [ 2841] [depth= 1] . ( 7 sec) [ -12032.4628] [ 2839] [depth= 1] . ( 8 sec) [ -12029.2116] [ 2844] [depth= 1] . ( 8 sec) [ -12028.2756] [ 2845] [depth= 1] . ( 8 sec) [ -12024.9431] [ 2839] [depth= 1] . ( 8 sec) [ -12024.8159] [ 2841] [depth= 1] . ( 8 sec) [ -12011.9818] [ 2840] [depth= 1] . ( 8 sec) [ -12006.0459] [ 2831] [depth= 2] . ( 8 sec) [ -11999.7680] [ 2824] [depth= 1] . ( 8 sec) [ -11998.3412] [ 2823] [depth= 1] . ( 8 sec) [ -11998.2082] [ 2821] [depth= 1] . ( 9 sec) [ -11998.1952] [ 2821] [depth= 1] . ( 9 sec) [ -11994.8145] [ 2824] [depth= 1] . ( 9 sec) [ -11994.1377] [ 2822] [depth= 1] . ( 10 sec) [ -11974.7430] [Branch lengths ] . ( 10 sec) [ -11974.4817] [GTR parameters ] . ( 10 sec) [ -11973.7907] [Alpha ][ 1.024045] . ( 10 sec) [ -11970.8537] [ 2821] [depth= 1] . ( 11 sec) [ -11970.6553] [ 2821] [depth= 1] . ( 11 sec) [ -11969.7511] [ 2825] [depth= 2] . ( 11 sec) [ -11969.6057] [ 2823] [depth= 1] . ( 12 sec) [ -11969.2506] [ 2824] [depth= 1] . ( 12 sec) [ -11969.1927] [ 2826] [depth= 1] . ( 13 sec) [ -11967.4235] [Branch lengths ] . ( 14 sec) [ -11967.4203] [GTR parameters ] . ( 14 sec) [ -11967.4027] [Alpha ][ 1.037134] . ( 17 sec) [ -11967.0160] [Branch lengths ] . ( 41 sec) [ -11966.9679] [Branch lengths ] . ( 41 sec) [ -11966.9679] [Topology ] . ( 42 sec) [ -11966.8968] [Topology ] . ( 43 sec) [ -11966.8478] [Topology ] . ( 44 sec) [ -11966.8374] [Topology ] . ( 45 sec) [ -11966.8326] [Topology ] . ( 45 sec) [ -11966.8303] [Topology ] . ( 46 sec) [ -11966.8291] [Topology ] . ( 47 sec) [ -11966.8286] [Topology ] . ( 47 sec) [ -11966.8270] [GTR parameters ] . ( 47 sec) [ -11966.8230] [Alpha ][ 1.043383] . ( 47 sec) [ -11966.8230] [Topology ] . ( 48 sec) [ -11966.8224] [Topology ] . ( 48 sec) [ -11966.8223] [GTR parameters ] . ( 48 sec) [ -11966.8223] [Alpha ][ 1.043383] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -11966.8217] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.821651. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22204.9394] [GTR parameters ] . ( 1 sec) [ -21789.7429] [Alpha ][ 0.500960] . ( 1 sec) [ -21764.0853] [ 5537] [depth= 1] . ( 1 sec) [ -21324.8991] [ 5458] [depth= 2] . ( 2 sec) [ -21291.4949] [ 5433] [depth= 1] . ( 2 sec) [ -21045.9551] [ 5331] [depth= 5] . ( 2 sec) [ -21013.3691] [ 5324] [depth= 1] . ( 2 sec) [ -21012.7464] [ 5320] [depth= 2] . ( 2 sec) [ -20976.0699] [ 5302] [depth= 3] . ( 2 sec) [ -20677.8538] [ 5204] [depth= 5] . ( 2 sec) [ -20658.5146] [ 5178] [depth= 2] . ( 2 sec) [ -20638.3308] [ 5162] [depth= 5] . ( 2 sec) [ -20311.4815] [ 5057] [depth= 7] . ( 2 sec) [ -20230.4915] [ 5053] [depth= 2] . ( 2 sec) [ -20053.5810] [ 5034] [depth= 4] . ( 2 sec) [ -19860.4219] [ 4961] [depth= 4] . ( 2 sec) [ -19643.4925] [ 4948] [depth= 12] . ( 2 sec) [ -19639.0055] [ 4942] [depth= 1] . ( 2 sec) [ -19575.9214] [ 4938] [depth= 13] . ( 2 sec) [ -19215.5605] [ 4790] [depth= 1] . ( 2 sec) [ -18972.3484] [ 4749] [depth= 5] . ( 2 sec) [ -18456.5841] [ 4655] [depth= 8] . ( 2 sec) [ -18370.6897] [ 4614] [depth= 1] . ( 2 sec) [ -18080.7801] [ 4563] [depth= 7] . ( 2 sec) [ -18031.7585] [ 4557] [depth= 6] . ( 2 sec) [ -18000.1579] [ 4548] [depth= 1] . ( 3 sec) [ -17565.6783] [ 4531] [depth= 9] . ( 3 sec) [ -17437.9469] [ 4426] [depth= 3] . ( 3 sec) [ -16834.2216] [ 4406] [depth= 13] . ( 3 sec) [ -16504.9022] [ 4284] [depth= 3] . ( 3 sec) [ -16476.7248] [ 4283] [depth= 1] . ( 3 sec) [ -16275.3788] [ 4167] [depth= 7] . ( 3 sec) [ -16260.1931] [ 4167] [depth= 1] . ( 3 sec) [ -16219.4541] [ 4165] [depth= 3] . ( 3 sec) [ -16208.5312] [ 4148] [depth= 1] . ( 3 sec) [ -16180.4240] [ 4135] [depth= 1] . ( 3 sec) [ -16152.8745] [ 4132] [depth= 1] . ( 3 sec) [ -15659.6396] [ 4061] [depth= 8] . ( 3 sec) [ -15640.0947] [ 4034] [depth= 1] . ( 3 sec) [ -15613.1937] [ 3991] [depth= 5] . ( 3 sec) [ -15579.7560] [ 3992] [depth= 1] . ( 3 sec) [ -15461.5676] [ 3991] [depth= 2] . ( 3 sec) [ -15389.5852] [ 3939] [depth= 4] . ( 3 sec) [ -15205.9443] [ 3862] [depth= 9] . ( 3 sec) [ -14749.5404] [ 3778] [depth= 5] . ( 3 sec) [ -14720.9004] [ 3777] [depth= 2] . ( 3 sec) [ -14716.3013] [ 3774] [depth= 2] . ( 4 sec) [ -14710.9603] [ 3766] [depth= 1] . ( 4 sec) [ -14701.1326] [ 3746] [depth= 1] . ( 4 sec) [ -14699.2003] [ 3747] [depth= 1] . ( 4 sec) [ -14681.1621] [ 3759] [depth= 1] . ( 4 sec) [ -14652.1315] [ 3740] [depth= 1] . ( 4 sec) [ -14561.8276] [ 3727] [depth= 3] . ( 4 sec) [ -14500.4579] [ 3702] [depth= 1] . ( 4 sec) [ -14470.1791] [ 3715] [depth= 11] . ( 4 sec) [ -14264.1793] [ 3688] [depth= 4] . ( 4 sec) [ -14175.5516] [ 3641] [depth= 2] . ( 4 sec) [ -14049.0631] [ 3572] [depth= 5] . ( 4 sec) [ -14044.3220] [ 3566] [depth= 1] . ( 4 sec) [ -13946.0577] [ 3493] [depth= 1] . ( 4 sec) [ -13914.1112] [ 3457] [depth= 5] . ( 4 sec) [ -13909.3786] [ 3442] [depth= 1] . ( 4 sec) [ -13675.2911] [ 3361] [depth= 12] . ( 4 sec) [ -13667.3166] [ 3356] [depth= 1] . ( 5 sec) [ -13439.2469] [ 3278] [depth= 5] . ( 5 sec) [ -12862.7508] [ 3098] [depth= 5] . ( 5 sec) [ -12861.3107] [ 3103] [depth= 1] . ( 5 sec) [ -12859.9982] [ 3098] [depth= 1] . ( 5 sec) [ -12845.6236] [ 3097] [depth= 1] . ( 5 sec) [ -12789.0400] [ 3074] [depth= 2] . ( 5 sec) [ -12614.9396] [ 2996] [depth= 1] . ( 5 sec) [ -12592.8375] [ 2988] [depth= 3] . ( 5 sec) [ -12582.9150] [ 2985] [depth= 1] . ( 5 sec) [ -12538.4882] [ 2977] [depth= 3] . ( 5 sec) [ -12479.1688] [ 2913] [depth= 1] . ( 5 sec) [ -12436.0243] [ 2891] [depth= 3] . ( 5 sec) [ -12425.7930] [ 2879] [depth= 2] . ( 5 sec) [ -12418.3773] [ 2880] [depth= 2] . ( 5 sec) [ -12310.0599] [ 2890] [depth= 4] . ( 5 sec) [ -12296.3280] [ 2892] [depth= 3] . ( 6 sec) [ -12286.1939] [ 2892] [depth= 2] . ( 6 sec) [ -12109.5406] [Branch lengths ] . ( 7 sec) [ -12107.7953] [GTR parameters ] . ( 7 sec) [ -12065.5357] [Alpha ][ 0.918995] . ( 7 sec) [ -12055.8741] [ 2881] [depth= 2] . ( 7 sec) [ -12053.5441] [ 2875] [depth= 1] . ( 7 sec) [ -12053.2213] [ 2878] [depth= 1] . ( 7 sec) [ -12046.8534] [ 2875] [depth= 2] . ( 7 sec) [ -12035.0212] [ 2865] [depth= 2] . ( 7 sec) [ -12033.6497] [ 2842] [depth= 3] . ( 7 sec) [ -12033.2933] [ 2839] [depth= 1] . ( 7 sec) [ -12011.6006] [ 2818] [depth= 1] . ( 8 sec) [ -12011.3576] [ 2819] [depth= 1] . ( 8 sec) [ -12011.2842] [ 2819] [depth= 1] . ( 8 sec) [ -12010.5458] [ 2816] [depth= 1] . ( 8 sec) [ -12010.4540] [ 2816] [depth= 1] . ( 9 sec) [ -12010.3111] [ 2820] [depth= 1] . ( 9 sec) [ -12006.1896] [ 2816] [depth= 1] . ( 9 sec) [ -12006.0349] [ 2819] [depth= 1] . ( 10 sec) [ -11972.9676] [Branch lengths ] . ( 10 sec) [ -11972.8501] [GTR parameters ] . ( 10 sec) [ -11971.7245] [Alpha ][ 1.015904] . ( 10 sec) [ -11971.5269] [ 2822] [depth= 1] . ( 10 sec) [ -11971.0955] [ 2823] [depth= 1] . ( 11 sec) [ -11970.9043] [ 2825] [depth= 1] . ( 11 sec) [ -11970.8602] [ 2820] [depth= 1] . ( 12 sec) [ -11970.3708] [ 2824] [depth= 2] . ( 13 sec) [ -11970.1575] [ 2826] [depth= 1] . ( 13 sec) [ -11967.6000] [Branch lengths ] . ( 14 sec) [ -11967.5924] [GTR parameters ] . ( 14 sec) [ -11967.5527] [Alpha ][ 1.035541] . ( 17 sec) [ -11967.0944] [Branch lengths ] . ( 41 sec) [ -11966.9862] [Branch lengths ] . ( 41 sec) [ -11966.9862] [Topology ] . ( 42 sec) [ -11966.8996] [Topology ] . ( 43 sec) [ -11966.8502] [Topology ] . ( 44 sec) [ -11966.8400] [Topology ] . ( 44 sec) [ -11966.8353] [Topology ] . ( 45 sec) [ -11966.8330] [Topology ] . ( 46 sec) [ -11966.8320] [Topology ] . ( 47 sec) [ -11966.8314] [Topology ] . ( 47 sec) [ -11966.8294] [GTR parameters ] . ( 47 sec) [ -11966.8232] [Alpha ][ 1.043301] . ( 47 sec) [ -11966.8232] [Topology ] . ( 48 sec) [ -11966.8224] [Topology ] . ( 48 sec) [ -11966.8224] [GTR parameters ] . ( 48 sec) [ -11966.8224] [Alpha ][ 1.043301] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -11966.8221] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.822091. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22925.4551] [GTR parameters ] . ( 0 sec) [ -22523.1354] [Alpha ][ 0.500960] . ( 0 sec) [ -22425.1259] [ 5544] [depth= 6] . ( 1 sec) [ -22301.5910] [ 5473] [depth= 10] . ( 1 sec) [ -22180.6681] [ 5441] [depth= 3] . ( 1 sec) [ -22147.0208] [ 5439] [depth= 6] . ( 1 sec) [ -21895.0143] [ 5409] [depth= 5] . ( 1 sec) [ -21863.2919] [ 5406] [depth= 4] . ( 1 sec) [ -21640.8184] [ 5383] [depth= 6] . ( 1 sec) [ -21325.8438] [ 5322] [depth= 1] . ( 1 sec) [ -20748.3050] [ 5193] [depth= 6] . ( 1 sec) [ -20619.9067] [ 5152] [depth= 1] . ( 1 sec) [ -20559.7226] [ 5147] [depth= 9] . ( 1 sec) [ -19963.6776] [ 5081] [depth= 2] . ( 1 sec) [ -19951.6424] [ 5072] [depth= 1] . ( 1 sec) [ -19834.3880] [ 5062] [depth= 10] . ( 1 sec) [ -19812.6649] [ 5054] [depth= 8] . ( 1 sec) [ -19746.3782] [ 5031] [depth= 2] . ( 1 sec) [ -19337.2192] [ 4894] [depth= 1] . ( 1 sec) [ -19157.6634] [ 4768] [depth= 10] . ( 1 sec) [ -19040.8003] [ 4725] [depth= 11] . ( 1 sec) [ -18684.3221] [ 4657] [depth= 2] . ( 1 sec) [ -18444.2743] [ 4627] [depth= 8] . ( 1 sec) [ -18349.0019] [ 4612] [depth= 10] . ( 1 sec) [ -18093.4787] [ 4662] [depth= 1] . ( 2 sec) [ -17847.1395] [ 4504] [depth= 5] . ( 2 sec) [ -17846.9861] [ 4515] [depth= 1] . ( 2 sec) [ -17635.7564] [ 4493] [depth= 10] . ( 2 sec) [ -17612.7326] [ 4479] [depth= 1] . ( 2 sec) [ -17451.4243] [ 4379] [depth= 8] . ( 2 sec) [ -17128.9495] [ 4325] [depth= 7] . ( 2 sec) [ -17022.1271] [ 4280] [depth= 6] . ( 2 sec) [ -16815.2039] [ 4200] [depth= 11] . ( 2 sec) [ -16636.3984] [ 4149] [depth= 6] . ( 2 sec) [ -16630.9713] [ 4148] [depth= 1] . ( 2 sec) [ -16523.2562] [ 4112] [depth= 3] . ( 2 sec) [ -16456.6088] [ 4099] [depth= 1] . ( 2 sec) [ -16397.8073] [ 4077] [depth= 2] . ( 2 sec) [ -16378.0928] [ 4070] [depth= 1] . ( 2 sec) [ -16174.5613] [ 4017] [depth= 9] . ( 2 sec) [ -16100.4159] [ 3990] [depth= 1] . ( 2 sec) [ -15411.2578] [ 3889] [depth= 3] . ( 2 sec) [ -15363.1775] [ 3856] [depth= 1] . ( 2 sec) [ -15288.9789] [ 3837] [depth= 8] . ( 2 sec) [ -15273.3445] [ 3836] [depth= 1] . ( 3 sec) [ -15144.0912] [ 3779] [depth= 9] . ( 3 sec) [ -15062.9568] [ 3752] [depth= 5] . ( 3 sec) [ -15034.8900] [ 3711] [depth= 1] . ( 3 sec) [ -14669.9251] [ 3548] [depth= 5] . ( 3 sec) [ -14590.6358] [ 3563] [depth= 6] . ( 3 sec) [ -14429.4562] [ 3503] [depth= 2] . ( 3 sec) [ -14131.0446] [ 3436] [depth= 3] . ( 3 sec) [ -13806.8124] [ 3337] [depth= 3] . ( 3 sec) [ -13757.9076] [ 3342] [depth= 1] . ( 3 sec) [ -13656.1036] [ 3332] [depth= 6] . ( 3 sec) [ -13467.4676] [ 3349] [depth= 1] . ( 3 sec) [ -13453.8006] [ 3345] [depth= 1] . ( 3 sec) [ -13449.7869] [ 3350] [depth= 2] . ( 3 sec) [ -13217.5226] [ 3219] [depth= 7] . ( 3 sec) [ -13158.0154] [ 3202] [depth= 1] . ( 3 sec) [ -12975.7689] [ 3148] [depth= 7] . ( 3 sec) [ -12910.1148] [ 3115] [depth= 3] . ( 3 sec) [ -12908.6005] [ 3116] [depth= 1] . ( 3 sec) [ -12899.4411] [ 3116] [depth= 4] . ( 4 sec) [ -12873.0809] [ 3090] [depth= 1] . ( 4 sec) [ -12819.3354] [ 3074] [depth= 6] . ( 4 sec) [ -12772.4708] [ 3051] [depth= 2] . ( 4 sec) [ -12754.2392] [ 2999] [depth= 1] . ( 4 sec) [ -12733.6047] [ 2976] [depth= 2] . ( 4 sec) [ -12624.1974] [ 2911] [depth= 1] . ( 4 sec) [ -12598.4472] [ 2900] [depth= 1] . ( 4 sec) [ -12578.1525] [ 2888] [depth= 1] . ( 4 sec) [ -12546.6993] [ 2892] [depth= 2] . ( 4 sec) [ -12541.1707] [ 2880] [depth= 3] . ( 4 sec) [ -12501.6758] [ 2874] [depth= 2] . ( 4 sec) [ -12483.5783] [ 2871] [depth= 3] . ( 4 sec) [ -12462.8933] [ 2871] [depth= 1] . ( 4 sec) [ -12460.7294] [ 2874] [depth= 1] . ( 5 sec) [ -12113.7755] [Branch lengths ] . ( 5 sec) [ -12112.2218] [GTR parameters ] . ( 5 sec) [ -12061.2081] [Alpha ][ 0.963669] . ( 5 sec) [ -12053.1515] [ 2869] [depth= 1] . ( 6 sec) [ -12047.8716] [ 2858] [depth= 2] . ( 6 sec) [ -12041.3293] [ 2852] [depth= 2] . ( 6 sec) [ -12038.7499] [ 2851] [depth= 1] . ( 6 sec) [ -12029.5800] [ 2841] [depth= 1] . ( 6 sec) [ -12027.1598] [ 2846] [depth= 1] . ( 6 sec) [ -12027.1273] [ 2845] [depth= 1] . ( 6 sec) [ -12003.6196] [ 2829] [depth= 2] . ( 7 sec) [ -12003.3116] [ 2833] [depth= 1] . ( 7 sec) [ -12002.3985] [ 2835] [depth= 2] . ( 7 sec) [ -12002.2121] [ 2832] [depth= 1] . ( 7 sec) [ -11991.8261] [ 2824] [depth= 3] . ( 7 sec) [ -11988.6523] [ 2824] [depth= 1] . ( 8 sec) [ -11988.4370] [ 2827] [depth= 1] . ( 8 sec) [ -11988.2500] [ 2827] [depth= 1] . ( 8 sec) [ -11987.4146] [ 2825] [depth= 1] . ( 9 sec) [ -11968.7938] [Branch lengths ] . ( 9 sec) [ -11968.6817] [GTR parameters ] . ( 9 sec) [ -11968.1355] [Alpha ][ 1.032758] . ( 12 sec) [ -11968.0411] [ 2823] [depth= 1] . ( 13 sec) [ -11967.0238] [Branch lengths ] . ( 13 sec) [ -11967.0236] [GTR parameters ] . ( 13 sec) [ -11967.0192] [Alpha ][ 1.039251] . ( 16 sec) [ -11966.8679] [Branch lengths ] . ( 40 sec) [ -11966.8338] [Branch lengths ] . ( 40 sec) [ -11966.8338] [Topology ] . ( 41 sec) [ -11966.8286] [Topology ] . ( 42 sec) [ -11966.8266] [Topology ] . ( 43 sec) [ -11966.8256] [Topology ] . ( 44 sec) [ -11966.8251] [Topology ] . ( 44 sec) [ -11966.8247] [GTR parameters ] . ( 44 sec) [ -11966.8229] [Alpha ][ 1.043406] . ( 44 sec) [ -11966.8229] [Topology ] . ( 45 sec) [ -11966.8224] [Topology ] . ( 45 sec) [ -11966.8224] [GTR parameters ] . ( 45 sec) [ -11966.8224] [Alpha ][ 1.043406] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -11966.8214] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.821418. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-12046.112397 . ( 1 sec) [ -12041.9616] [GTR parameters ] . ( 1 sec) [ -12041.7961] [Alpha ][ 0.960910] . ( 1 sec) [ -12041.7961] [Topology ] . ( 2 sec) [ -11980.6757] [Topology ] . ( 3 sec) [ -11972.0740] [Topology ] . ( 4 sec) [ -11969.8220] [Topology ] . ( 5 sec) [ -11968.8175] [Topology ] . ( 5 sec) [ -11968.3196] [Topology ] . ( 6 sec) [ -11968.0585] [Topology ] . ( 7 sec) [ -11967.9172] [Topology ] . ( 8 sec) [ -11967.8397] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -11967.8180] [Topology ] . Before opt ts/t=1.000000 LK=-11967.817956 . ( 15 sec) [ -11967.6718] [GTR parameters ] . ( 15 sec) [ -11967.0266] [Alpha ][ 1.035749] . ( 15 sec) [ -11967.0266] [Topology ] . ( 16 sec) [ -11966.9204] [Topology ] . ( 16 sec) [ -11966.8765] [Topology ] . ( 17 sec) [ -11966.8537] [Topology ] . ( 18 sec) [ -11966.8415] [Topology ] . ( 19 sec) [ -11966.8348] [Topology ] . ( 20 sec) [ -11966.8311] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.831138 . ( 26 sec) [ -11966.8304] [GTR parameters ] . ( 26 sec) [ -11966.8252] [Alpha ][ 1.042902] . ( 26 sec) [ -11966.8252] [Topology ] . ( 27 sec) [ -11966.8224] [Topology ] . ( 28 sec) [ -11966.8210] [Topology ] . ( 29 sec) [ -11966.8203] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.820258 . ( 35 sec) [ -11966.8202] [GTR parameters ] . ( 35 sec) [ -11966.8202] [Alpha ][ 1.043945] . ( 35 sec) [ -11966.8202] [Topology ] . ( 36 sec) [ -11966.8197] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -12041.9616] [GTR parameters ] . ( 49 sec) [ -12041.7961] [Alpha ][ 0.960910] . ( 50 sec) [ -12041.2513] [ 2830] [depth= 2] . ( 50 sec) [ -12039.5922] [ 2832] [depth= 1] . ( 50 sec) [ -12039.3732] [ 2830] [depth= 1] . ( 50 sec) [ -12035.0220] [ 2830] [depth= 2] . ( 51 sec) [ -12032.6794] [ 2825] [depth= 1] . ( 51 sec) [ -12014.8516] [ 2828] [depth= 1] . ( 51 sec) [ -12014.4231] [ 2832] [depth= 2] . ( 52 sec) [ -12010.0128] [ 2833] [depth= 1] . ( 52 sec) [ -12009.4667] [ 2831] [depth= 1] . ( 52 sec) [ -12007.4819] [ 2831] [depth= 2] . ( 52 sec) [ -12003.0060] [ 2828] [depth= 2] . ( 52 sec) [ -12002.7254] [ 2828] [depth= 1] . ( 52 sec) [ -12001.6902] [ 2829] [depth= 1] . ( 53 sec) [ -12001.2296] [ 2834] [depth= 1] . ( 53 sec) [ -11973.7262] [Branch lengths ] . ( 53 sec) [ -11973.5526] [GTR parameters ] . ( 53 sec) [ -11973.1450] [Alpha ][ 1.020335] . ( 55 sec) [ -11971.5100] [ 2833] [depth= 1] . ( 56 sec) [ -11970.2621] [ 2832] [depth= 1] . ( 57 sec) [ -11970.2030] [ 2830] [depth= 1] . ( 57 sec) [ -11970.0801] [ 2832] [depth= 1] . ( 57 sec) [ -11967.5488] [Branch lengths ] . ( 57 sec) [ -11967.5413] [GTR parameters ] . ( 57 sec) [ -11967.5116] [Alpha ][ 1.037303] . ( 61 sec) [ -11967.1131] [Branch lengths ] . ( 85 sec) [ -11967.0211] [Branch lengths ] . ( 85 sec) [ -11967.0211] [Topology ] . ( 86 sec) [ -11966.9430] [Topology ] . ( 87 sec) [ -11966.8850] [Topology ] . ( 88 sec) [ -11966.8756] [Topology ] . ( 89 sec) [ -11966.8713] [Topology ] . ( 90 sec) [ -11966.8693] [Topology ] . ( 90 sec) [ -11966.8683] [Topology ] . ( 91 sec) [ -11966.8668] [GTR parameters ] . ( 91 sec) [ -11966.8630] [Alpha ][ 1.043364] . ( 91 sec) [ -11966.8630] [Topology ] . ( 91 sec) [ -11966.8622] [Topology ] . ( 92 sec) [ -11966.8621] [GTR parameters ] . ( 92 sec) [ -11966.8621] [Alpha ][ 1.043364] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -11966.8618] [Topology ] . Checking for NNIs, optimizing five branches... . ( 105 sec) [ -11966.8615] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11966.819701 . Log likelihood obtained after SPR moves : -11966.861461 . Log likelihood of the current tree: -11966.819701. . Printing the most likely tree in file 'data85.phy_phyml_tree.txt'... . Best log likelihood : -11966.819701 . Time used 0h1m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo