.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_2006.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... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10550.2803] [GTR parameters ] . ( 1 sec) [ -10363.0674] [Alpha ][ 0.500960] . ( 1 sec) [ -10169.3783] [ 944] [depth= 7] . ( 1 sec) [ -10118.9057] [ 943] [depth= 4] . ( 1 sec) [ -9819.3591] [ 944] [depth= 1] . ( 1 sec) [ -9807.5135] [ 942] [depth= 3] . ( 1 sec) [ -9785.7427] [ 942] [depth= 2] . ( 1 sec) [ -9777.5291] [ 941] [depth= 4] . ( 1 sec) [ -9732.6977] [ 939] [depth= 9] . ( 1 sec) [ -9657.2369] [ 939] [depth= 6] . ( 1 sec) [ -9563.2959] [ 934] [depth= 5] . ( 1 sec) [ -9558.8332] [ 934] [depth= 4] . ( 1 sec) [ -9491.8828] [ 934] [depth= 2] . ( 1 sec) [ -9410.5694] [ 934] [depth= 9] . ( 2 sec) [ -9364.7010] [ 932] [depth= 3] . ( 2 sec) [ -9262.5891] [ 932] [depth= 1] . ( 2 sec) [ -8927.6361] [ 904] [depth= 13] . ( 2 sec) [ -8926.5370] [ 904] [depth= 1] . ( 2 sec) [ -8913.5519] [ 904] [depth= 2] . ( 2 sec) [ -8911.8753] [ 903] [depth= 14] . ( 2 sec) [ -8867.3752] [ 903] [depth= 1] . ( 2 sec) [ -8684.7821] [ 899] [depth= 12] . ( 2 sec) [ -8678.8557] [ 899] [depth= 11] . ( 2 sec) [ -8641.4798] [ 890] [depth= 27] . ( 2 sec) [ -8612.9202] [ 883] [depth= 20] . ( 2 sec) [ -8591.2627] [ 882] [depth= 16] . ( 2 sec) [ -8275.5456] [ 852] [depth= 12] . ( 2 sec) [ -8249.1146] [ 846] [depth= 11] . ( 2 sec) [ -8086.8490] [ 837] [depth= 11] . ( 2 sec) [ -8049.7195] [ 833] [depth= 21] . ( 2 sec) [ -8033.4833] [ 832] [depth= 1] . ( 2 sec) [ -8029.3298] [ 832] [depth= 3] . ( 2 sec) [ -7895.6356] [ 832] [depth= 1] . ( 2 sec) [ -7840.1224] [ 824] [depth= 14] . ( 2 sec) [ -7780.6367] [ 816] [depth= 4] . ( 2 sec) [ -7761.7279] [ 815] [depth= 14] . ( 2 sec) [ -7734.7682] [ 810] [depth= 3] . ( 2 sec) [ -7570.7520] [ 808] [depth= 15] . ( 2 sec) [ -7554.5269] [ 808] [depth= 9] . ( 2 sec) [ -7510.8138] [ 805] [depth= 23] . ( 2 sec) [ -7457.8963] [ 795] [depth= 7] . ( 2 sec) [ -7334.9546] [ 792] [depth= 17] . ( 2 sec) [ -7276.4164] [ 786] [depth= 24] . ( 3 sec) [ -7275.2898] [ 786] [depth= 7] . ( 3 sec) [ -7273.1187] [ 786] [depth= 7] . ( 3 sec) [ -7265.0952] [ 785] [depth= 7] . ( 3 sec) [ -7264.6244] [ 785] [depth= 1] . ( 3 sec) [ -7204.5335] [ 780] [depth= 6] . ( 3 sec) [ -7200.9756] [ 763] [depth= 1] . ( 3 sec) [ -6892.6526] [ 761] [depth= 12] . ( 3 sec) [ -6796.2076] [ 751] [depth= 7] . ( 3 sec) [ -6786.0484] [ 735] [depth= 1] . ( 3 sec) [ -6784.6540] [ 735] [depth= 19] . ( 3 sec) [ -6782.3347] [ 735] [depth= 14] . ( 3 sec) [ -6746.4330] [ 730] [depth= 12] . ( 3 sec) [ -6718.8629] [ 730] [depth= 1] . ( 3 sec) [ -6666.2232] [ 720] [depth= 12] . ( 3 sec) [ -6655.7591] [ 718] [depth= 4] . ( 3 sec) [ -6653.1464] [ 718] [depth= 1] . ( 3 sec) [ -6651.0089] [ 718] [depth= 12] . ( 3 sec) [ -6641.5645] [ 716] [depth= 13] . ( 3 sec) [ -6442.7230] [ 683] [depth= 23] . ( 3 sec) [ -6423.5283] [ 680] [depth= 4] . ( 3 sec) [ -6400.0148] [ 671] [depth= 10] . ( 3 sec) [ -6367.7338] [ 664] [depth= 9] . ( 3 sec) [ -6356.5147] [ 665] [depth= 1] . ( 3 sec) [ -6347.8700] [ 663] [depth= 21] . ( 3 sec) [ -6312.1309] [ 655] [depth= 12] . ( 3 sec) [ -6303.5726] [ 657] [depth= 8] . ( 3 sec) [ -6290.7151] [ 655] [depth= 13] . ( 3 sec) [ -6289.5119] [ 655] [depth= 1] . ( 4 sec) [ -6240.7555] [ 647] [depth= 16] . ( 4 sec) [ -6236.9042] [ 647] [depth= 12] . ( 4 sec) [ -6228.9653] [ 646] [depth= 12] . ( 4 sec) [ -6221.1322] [ 645] [depth= 7] . ( 4 sec) [ -6209.8495] [ 645] [depth= 1] . ( 4 sec) [ -6154.1921] [ 637] [depth= 10] . ( 4 sec) [ -6150.8267] [ 637] [depth= 6] . ( 4 sec) [ -6123.6208] [ 637] [depth= 1] . ( 4 sec) [ -6118.4289] [ 636] [depth= 2] . ( 4 sec) [ -6112.5320] [ 636] [depth= 1] . ( 4 sec) [ -6094.6402] [ 636] [depth= 1] . ( 4 sec) [ -6093.9926] [ 636] [depth= 1] . ( 4 sec) [ -6078.4744] [ 635] [depth= 12] . ( 4 sec) [ -6076.9869] [ 635] [depth= 19] . ( 4 sec) [ -6076.9115] [ 635] [depth= 1] . ( 4 sec) [ -6076.7116] [ 635] [depth= 1] . ( 4 sec) [ -6054.6956] [ 631] [depth= 1] . ( 4 sec) [ -6052.2839] [ 631] [depth= 1] . ( 4 sec) [ -6047.3266] [ 635] [depth= 1] . ( 4 sec) [ -6047.3126] [ 631] [depth= 3] . ( 4 sec) [ -6046.8203] [ 631] [depth= 8] . ( 4 sec) [ -5971.5435] [ 632] [depth= 5] . ( 4 sec) [ -5963.9600] [ 632] [depth= 2] . ( 4 sec) [ -5926.0949] [ 623] [depth= 11] . ( 4 sec) [ -5873.4455] [ 623] [depth= 3] . ( 4 sec) [ -5579.2257] [ 624] [depth= 1] . ( 4 sec) [ -5531.7982] [ 619] [depth= 6] . ( 4 sec) [ -5530.4302] [ 620] [depth= 2] . ( 4 sec) [ -5423.2104] [ 614] [depth= 8] . ( 4 sec) [ -5388.4059] [ 608] [depth= 17] . ( 5 sec) [ -5273.2689] [ 604] [depth= 7] . ( 5 sec) [ -4914.8334] [ 568] [depth= 9] . ( 5 sec) [ -4908.0168] [ 567] [depth= 3] . ( 5 sec) [ -4907.9468] [ 567] [depth= 1] . ( 5 sec) [ -4899.6698] [ 561] [depth= 3] . ( 5 sec) [ -4894.7812] [ 561] [depth= 1] . ( 5 sec) [ -4882.0156] [ 562] [depth= 1] . ( 5 sec) [ -4865.8532] [ 561] [depth= 9] . ( 5 sec) [ -4840.9102] [ 556] [depth= 10] . ( 5 sec) [ -4839.1869] [ 556] [depth= 14] . ( 5 sec) [ -4839.1633] [ 556] [depth= 2] . ( 5 sec) [ -4833.9327] [ 555] [depth= 5] . ( 5 sec) [ -4817.2636] [ 553] [depth= 10] . ( 5 sec) [ -4804.9048] [ 552] [depth= 11] . ( 5 sec) [ -4802.3850] [ 553] [depth= 4] . ( 5 sec) [ -4794.0754] [ 552] [depth= 18] . ( 5 sec) [ -4782.0274] [ 551] [depth= 5] . ( 5 sec) [ -4774.1271] [ 551] [depth= 1] . ( 5 sec) [ -4472.6072] [ 550] [depth= 1] . ( 5 sec) [ -4448.1033] [ 550] [depth= 1] . ( 5 sec) [ -4432.0742] [ 548] [depth= 12] . ( 5 sec) [ -4431.9768] [ 548] [depth= 1] . ( 5 sec) [ -4431.9491] [ 548] [depth= 4] . ( 5 sec) [ -4374.8104] [ 547] [depth= 9] . ( 5 sec) [ -4325.5778] [ 598] [depth= 1] . ( 5 sec) [ -4318.8657] [ 597] [depth= 6] . ( 5 sec) [ -4062.3776] [ 525] [depth= 23] . ( 5 sec) [ -3985.0832] [ 524] [depth= 11] . ( 5 sec) [ -3877.1358] [ 489] [depth= 5] . ( 6 sec) [ -3849.7952] [ 489] [depth= 14] . ( 6 sec) [ -3821.6644] [ 483] [depth= 6] . ( 6 sec) [ -3820.8070] [ 483] [depth= 5] . ( 6 sec) [ -3816.1867] [ 483] [depth= 6] . ( 6 sec) [ -3814.6254] [ 483] [depth= 2] . ( 6 sec) [ -3814.2446] [ 483] [depth= 3] . ( 6 sec) [ -3800.8063] [ 481] [depth= 12] . ( 7 sec) [ -3779.0229] [ 474] [depth= 11] . ( 7 sec) [ -3778.9218] [ 474] [depth= 1] . ( 7 sec) [ -3778.8440] [ 474] [depth= 3] . ( 7 sec) [ -3768.1837] [ 473] [depth= 8] . ( 7 sec) [ -3751.7502] [ 472] [depth= 8] . ( 7 sec) [ -3751.2584] [ 472] [depth= 1] . ( 7 sec) [ -3743.3310] [ 473] [depth= 1] . ( 7 sec) [ -3732.0165] [ 471] [depth= 8] . ( 7 sec) [ -3727.4693] [ 471] [depth= 4] . ( 7 sec) [ -3716.5691] [ 471] [depth= 1] . ( 7 sec) [ -3613.2314] [ 439] [depth= 5] . ( 7 sec) [ -3607.6704] [ 439] [depth= 1] . ( 8 sec) [ -3607.4803] [ 439] [depth= 1] . ( 8 sec) [ -3596.2695] [ 436] [depth= 9] . ( 8 sec) [ -3592.2158] [ 434] [depth= 2] . ( 8 sec) [ -3513.1297] [ 405] [depth= 22] . ( 8 sec) [ -3513.1067] [ 409] [depth= 2] . ( 8 sec) [ -3513.0091] [ 409] [depth= 8] . ( 8 sec) [ -3512.9914] [ 409] [depth= 2] . ( 8 sec) [ -3486.4472] [ 404] [depth= 5] . ( 8 sec) [ -3485.7441] [ 404] [depth= 1] . ( 8 sec) [ -3485.6937] [ 404] [depth= 2] . ( 9 sec) [ -3484.5993] [ 404] [depth= 9] . ( 9 sec) [ -3484.5195] [ 404] [depth= 2] . ( 9 sec) [ -3484.4515] [ 404] [depth= 1] . ( 9 sec) [ -3484.3727] [ 404] [depth= 2] . ( 9 sec) [ -3484.3218] [ 404] [depth= 2] . ( 9 sec) [ -3484.3111] [ 404] [depth= 1] . ( 9 sec) [ -3484.2986] [ 404] [depth= 2] . ( 9 sec) [ -3479.5552] [ 403] [depth= 7] . ( 9 sec) [ -3462.7410] [ 395] [depth= 6] . ( 9 sec) [ -3462.3384] [ 395] [depth= 2] . ( 9 sec) [ -3462.3114] [ 395] [depth= 3] . ( 9 sec) [ -3462.1211] [ 395] [depth= 1] . ( 9 sec) [ -3449.1172] [ 395] [depth= 4] . ( 9 sec) [ -3438.1458] [ 395] [depth= 2] . ( 9 sec) [ -3425.3503] [ 381] [depth= 22] . ( 9 sec) [ -3424.5888] [ 382] [depth= 3] . ( 9 sec) [ -3422.9484] [ 382] [depth= 1] . ( 9 sec) [ -3422.7305] [ 382] [depth= 2] . ( 9 sec) [ -3416.9687] [ 382] [depth= 1] . ( 9 sec) [ -3412.0609] [ 381] [depth= 2] . ( 9 sec) [ -3405.0587] [ 382] [depth= 5] . ( 10 sec) [ -3405.0158] [ 382] [depth= 3] . ( 10 sec) [ -3398.8209] [ 381] [depth= 10] . ( 10 sec) [ -3398.7951] [ 381] [depth= 1] . ( 10 sec) [ -3397.6809] [ 381] [depth= 5] . ( 10 sec) [ -3397.3404] [ 381] [depth= 1] . ( 10 sec) [ -3397.2635] [ 381] [depth= 2] . ( 10 sec) [ -3397.2371] [ 381] [depth= 3] . ( 10 sec) [ -3363.5128] [ 351] [depth= 7] . ( 10 sec) [ -3346.5565] [Branch lengths ] . ( 12 sec) [ -3306.2970] [GTR parameters ] . ( 12 sec) [ -3274.1680] [Alpha ][ 0.250961] . ( 12 sec) [ -3274.0526] [ 344] [depth= 1] . ( 12 sec) [ -3268.5609] [ 343] [depth= 3] . ( 13 sec) [ -3250.6830] [ 343] [depth= 1] . ( 13 sec) [ -3250.6333] [ 343] [depth= 1] . ( 13 sec) [ -3247.7618] [ 343] [depth= 4] . ( 14 sec) [ -3246.8894] [ 344] [depth= 5] . ( 15 sec) [ -3246.8619] [ 343] [depth= 1] . ( 16 sec) [ -3245.4979] [ 343] [depth= 3] . ( 16 sec) [ -3239.1147] [ 342] [depth= 8] . ( 16 sec) [ -3239.0741] [ 342] [depth= 1] . ( 16 sec) [ -3237.9498] [ 342] [depth= 1] . ( 16 sec) [ -3236.8687] [ 342] [depth= 1] . ( 17 sec) [ -3236.8499] [ 342] [depth= 1] . ( 18 sec) [ -3236.8371] [ 342] [depth= 1] . ( 18 sec) [ -3187.0692] [ 324] [depth= 2] . ( 18 sec) [ -3187.0570] [ 324] [depth= 2] . ( 18 sec) [ -3186.1928] [ 325] [depth= 4] . ( 18 sec) [ -3162.9539] [ 321] [depth= 4] . ( 19 sec) [ -3152.2865] [ 307] [depth= 1] . ( 19 sec) [ -3151.9923] [ 307] [depth= 1] . ( 19 sec) [ -3147.4209] [ 306] [depth= 5] . ( 20 sec) [ -3147.4092] [ 306] [depth= 2] . ( 20 sec) [ -3130.3579] [ 302] [depth= 15] . ( 21 sec) [ -3103.0519] [ 295] [depth= 4] . ( 22 sec) [ -3098.8667] [ 294] [depth= 1] . ( 22 sec) [ -3098.8486] [ 294] [depth= 1] . ( 22 sec) [ -3098.8259] [ 294] [depth= 2] . ( 22 sec) [ -3098.7821] [ 294] [depth= 3] . ( 22 sec) [ -3094.7720] [ 293] [depth= 3] . ( 24 sec) [ -3093.9168] [ 289] [depth= 3] . ( 24 sec) [ -3093.9013] [ 289] [depth= 1] . ( 24 sec) [ -3091.3471] [ 289] [depth= 2] . ( 24 sec) [ -3088.3008] [ 291] [depth= 1] . ( 31 sec) [ -3076.7205] [ 288] [depth= 12] . ( 31 sec) [ -3075.6629] [ 287] [depth= 1] . ( 37 sec) [ -3071.9534] [ 284] [depth= 1] . ( 38 sec) [ -3069.0828] [ 283] [depth= 3] . ( 39 sec) [ -3068.8669] [ 283] [depth= 2] . ( 40 sec) [ -3063.4609] [ 282] [depth= 2] . ( 40 sec) [ -3063.4125] [ 282] [depth= 1] . ( 40 sec) [ -3063.1577] [ 282] [depth= 1] . ( 40 sec) [ -3063.0471] [ 282] [depth= 2] . ( 40 sec) [ -3062.0785] [ 282] [depth= 1] . ( 41 sec) [ -3061.8784] [ 285] [depth= 1] . ( 42 sec) [ -3060.1450] [ 285] [depth= 5] . ( 46 sec) [ -3059.9418] [ 286] [depth= 4] . ( 47 sec) [ -3059.9066] [ 286] [depth= 2] . ( 50 sec) [ -3055.7362] [Branch lengths ] . ( 51 sec) [ -3055.0019] [GTR parameters ] . ( 51 sec) [ -3050.2843] [Alpha ][ 0.136594] . ( 52 sec) [ -3045.9142] [ 286] [depth= 11] . ( 54 sec) [ -3045.8700] [ 286] [depth= 1] . ( 67 sec) [ -3045.8550] [ 286] [depth= 1] . ( 87 sec) [ -3045.8387] [ 283] [depth= 1] . ( 93 sec) [ -3045.8274] [ 281] [depth= 10] . ( 95 sec) [ -3045.8149] [ 281] [depth= 2] . ( 98 sec) [ -3044.5753] [Branch lengths ] . ( 99 sec) [ -3044.5022] [GTR parameters ] . ( 99 sec) [ -3044.5015] [Alpha ][ 0.135450] . ( 141 sec) [ -3037.2703] [ 284] [depth= 10] . ( 146 sec) [ -3034.0538] [Branch lengths ] . ( 147 sec) [ -3033.9860] [GTR parameters ] . ( 147 sec) [ -3033.9720] [Alpha ][ 0.130453] . ( 150 sec) [ -3033.8582] [ 288] [depth= 1] . ( 183 sec) [ -3033.8344] [ 286] [depth= 1] . ( 189 sec) [ -3033.7038] [ 288] [depth= 1] . ( 193 sec) [ -3033.5795] [Branch lengths ] . ( 194 sec) [ -3033.5780] [GTR parameters ] . ( 194 sec) [ -3033.5767] [Alpha ][ 0.131942] . ( 220 sec) [ -3033.5748] [Branch lengths ] . ( 220 sec) [ -3033.5748] [Topology ] . ( 220 sec) [ -3033.5748] [Topology ] . ( 221 sec) [ -3033.5748] [GTR parameters ] . ( 221 sec) [ -3033.5748] [Alpha ][ 0.131942] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3033.574780. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9752.1064] [GTR parameters ] . ( 1 sec) [ -9594.8395] [Alpha ][ 0.500960] . ( 1 sec) [ -9291.6154] [ 883] [depth= 4] . ( 1 sec) [ -9256.8897] [ 877] [depth= 5] . ( 1 sec) [ -9245.5186] [ 876] [depth= 1] . ( 1 sec) [ -9243.2550] [ 876] [depth= 1] . ( 1 sec) [ -9178.1381] [ 875] [depth= 5] . ( 1 sec) [ -9165.6718] [ 873] [depth= 1] . ( 1 sec) [ -9071.8127] [ 872] [depth= 1] . ( 1 sec) [ -9071.4455] [ 872] [depth= 1] . ( 1 sec) [ -9020.6855] [ 866] [depth= 2] . ( 1 sec) [ -8999.4243] [ 866] [depth= 4] . ( 1 sec) [ -8843.6250] [ 866] [depth= 5] . ( 1 sec) [ -8695.6807] [ 854] [depth= 11] . ( 1 sec) [ -8693.9447] [ 854] [depth= 2] . ( 1 sec) [ -8092.2252] [ 852] [depth= 15] . ( 1 sec) [ -7836.4531] [ 852] [depth= 2] . ( 1 sec) [ -7740.5363] [ 835] [depth= 5] . ( 2 sec) [ -7720.6687] [ 834] [depth= 7] . ( 2 sec) [ -7555.8415] [ 830] [depth= 1] . ( 2 sec) [ -7437.8251] [ 828] [depth= 4] . ( 2 sec) [ -7382.4011] [ 813] [depth= 4] . ( 2 sec) [ -7378.3733] [ 813] [depth= 4] . ( 2 sec) [ -7339.9785] [ 812] [depth= 2] . ( 2 sec) [ -7327.8002] [ 812] [depth= 1] . ( 2 sec) [ -7317.6616] [ 811] [depth= 7] . ( 2 sec) [ -7293.9000] [ 811] [depth= 1] . ( 2 sec) [ -7291.2805] [ 809] [depth= 10] . ( 2 sec) [ -6989.4655] [ 809] [depth= 3] . ( 2 sec) [ -6981.5728] [ 809] [depth= 7] . ( 2 sec) [ -6977.8321] [ 809] [depth= 2] . ( 2 sec) [ -6973.6790] [ 808] [depth= 11] . ( 2 sec) [ -6935.1087] [ 801] [depth= 11] . ( 2 sec) [ -6902.2130] [ 795] [depth= 16] . ( 2 sec) [ -6899.6867] [ 795] [depth= 4] . ( 2 sec) [ -6805.5934] [ 794] [depth= 11] . ( 2 sec) [ -6799.1934] [ 793] [depth= 8] . ( 2 sec) [ -6631.0551] [ 791] [depth= 12] . ( 2 sec) [ -6571.5587] [ 784] [depth= 9] . ( 2 sec) [ -6555.2397] [ 782] [depth= 10] . ( 2 sec) [ -6547.2229] [ 763] [depth= 1] . ( 2 sec) [ -6494.6075] [ 762] [depth= 3] . ( 2 sec) [ -6396.8770] [ 741] [depth= 10] . ( 2 sec) [ -6350.3679] [ 729] [depth= 6] . ( 2 sec) [ -5912.5767] [ 661] [depth= 3] . ( 2 sec) [ -5907.6697] [ 661] [depth= 11] . ( 2 sec) [ -5871.1514] [ 655] [depth= 4] . ( 2 sec) [ -5835.0343] [ 648] [depth= 19] . ( 2 sec) [ -5774.2355] [ 641] [depth= 14] . ( 2 sec) [ -5750.0920] [ 640] [depth= 20] . ( 3 sec) [ -5739.1570] [ 639] [depth= 7] . ( 3 sec) [ -5723.3055] [ 638] [depth= 3] . ( 3 sec) [ -5651.9265] [ 638] [depth= 1] . ( 3 sec) [ -5580.4338] [ 637] [depth= 11] . ( 3 sec) [ -5548.0993] [ 633] [depth= 25] . ( 3 sec) [ -5503.9158] [ 597] [depth= 14] . ( 3 sec) [ -5488.8982] [ 594] [depth= 1] . ( 3 sec) [ -5460.6507] [ 593] [depth= 8] . ( 3 sec) [ -5438.6295] [ 589] [depth= 13] . ( 3 sec) [ -5338.5139] [ 588] [depth= 12] . ( 3 sec) [ -5315.0281] [ 585] [depth= 9] . ( 3 sec) [ -5275.4594] [ 578] [depth= 3] . ( 3 sec) [ -4985.1929] [ 560] [depth= 15] . ( 3 sec) [ -4970.6875] [ 558] [depth= 6] . ( 3 sec) [ -4962.5442] [ 557] [depth= 8] . ( 3 sec) [ -4953.1346] [ 555] [depth= 1] . ( 3 sec) [ -4952.6824] [ 555] [depth= 2] . ( 3 sec) [ -4924.4833] [ 550] [depth= 3] . ( 3 sec) [ -4910.8415] [ 548] [depth= 7] . ( 3 sec) [ -4878.4140] [ 548] [depth= 17] . ( 3 sec) [ -4854.1920] [ 546] [depth= 1] . ( 3 sec) [ -4844.4193] [ 545] [depth= 9] . ( 3 sec) [ -4842.0728] [ 545] [depth= 9] . ( 3 sec) [ -4827.7967] [ 545] [depth= 19] . ( 3 sec) [ -4823.7238] [ 544] [depth= 1] . ( 3 sec) [ -4781.6209] [ 544] [depth= 1] . ( 3 sec) [ -4772.3582] [ 543] [depth= 7] . ( 3 sec) [ -4735.0830] [ 545] [depth= 1] . ( 3 sec) [ -4734.4377] [ 543] [depth= 1] . ( 3 sec) [ -4700.0805] [ 532] [depth= 3] . ( 4 sec) [ -4687.6133] [ 547] [depth= 1] . ( 4 sec) [ -4545.6115] [ 526] [depth= 11] . ( 4 sec) [ -4419.2978] [ 496] [depth= 9] . ( 4 sec) [ -4419.1685] [ 496] [depth= 1] . ( 4 sec) [ -4417.3723] [ 496] [depth= 9] . ( 4 sec) [ -4411.0168] [ 496] [depth= 19] . ( 4 sec) [ -4336.3595] [ 486] [depth= 1] . ( 4 sec) [ -4331.1524] [ 489] [depth= 20] . ( 4 sec) [ -4329.0909] [ 489] [depth= 3] . ( 4 sec) [ -4289.1316] [ 478] [depth= 2] . ( 4 sec) [ -4231.5458] [ 472] [depth= 12] . ( 4 sec) [ -4221.7058] [ 468] [depth= 17] . ( 4 sec) [ -4202.2880] [ 467] [depth= 1] . ( 4 sec) [ -4198.7276] [ 459] [depth= 1] . ( 4 sec) [ -4188.5785] [ 458] [depth= 3] . ( 4 sec) [ -4172.0183] [ 451] [depth= 2] . ( 4 sec) [ -4165.9187] [ 451] [depth= 2] . ( 4 sec) [ -4123.4604] [ 450] [depth= 13] . ( 4 sec) [ -4123.3090] [ 450] [depth= 1] . ( 4 sec) [ -4031.3221] [ 443] [depth= 10] . ( 4 sec) [ -3970.1040] [ 433] [depth= 12] . ( 4 sec) [ -3933.5165] [ 431] [depth= 13] . ( 4 sec) [ -3932.1597] [ 431] [depth= 1] . ( 4 sec) [ -3911.3088] [ 425] [depth= 2] . ( 5 sec) [ -3909.7049] [ 428] [depth= 11] . ( 5 sec) [ -3881.3835] [ 426] [depth= 11] . ( 5 sec) [ -3878.3331] [ 425] [depth= 2] . ( 5 sec) [ -3871.4123] [ 424] [depth= 6] . ( 5 sec) [ -3868.3778] [ 424] [depth= 18] . ( 5 sec) [ -3866.5955] [ 424] [depth= 17] . ( 5 sec) [ -3851.2160] [ 422] [depth= 19] . ( 5 sec) [ -3826.8610] [ 414] [depth= 16] . ( 5 sec) [ -3803.2644] [ 410] [depth= 6] . ( 5 sec) [ -3780.8444] [ 410] [depth= 2] . ( 5 sec) [ -3774.1523] [ 409] [depth= 12] . ( 5 sec) [ -3748.9787] [ 405] [depth= 19] . ( 5 sec) [ -3741.2103] [ 406] [depth= 4] . ( 5 sec) [ -3740.8623] [ 406] [depth= 14] . ( 5 sec) [ -3739.7810] [ 406] [depth= 1] . ( 5 sec) [ -3665.8596] [ 398] [depth= 14] . ( 5 sec) [ -3665.0377] [ 398] [depth= 3] . ( 5 sec) [ -3664.9693] [ 398] [depth= 2] . ( 5 sec) [ -3664.6778] [ 398] [depth= 2] . ( 5 sec) [ -3664.6498] [ 398] [depth= 6] . ( 5 sec) [ -3664.0806] [ 398] [depth= 10] . ( 5 sec) [ -3664.0529] [ 398] [depth= 1] . ( 5 sec) [ -3663.7014] [ 397] [depth= 4] . ( 5 sec) [ -3662.1020] [ 397] [depth= 2] . ( 5 sec) [ -3656.6329] [ 397] [depth= 1] . ( 5 sec) [ -3650.1506] [ 397] [depth= 2] . ( 6 sec) [ -3637.2717] [ 392] [depth= 1] . ( 6 sec) [ -3621.0707] [ 391] [depth= 10] . ( 6 sec) [ -3614.7175] [ 391] [depth= 1] . ( 6 sec) [ -3614.2962] [ 391] [depth= 5] . ( 6 sec) [ -3612.7792] [ 391] [depth= 10] . ( 6 sec) [ -3577.6255] [ 385] [depth= 8] . ( 6 sec) [ -3572.6202] [ 384] [depth= 1] . ( 6 sec) [ -3553.1756] [ 380] [depth= 3] . ( 6 sec) [ -3547.7676] [ 380] [depth= 1] . ( 6 sec) [ -3547.7201] [ 380] [depth= 2] . ( 6 sec) [ -3517.9571] [ 375] [depth= 4] . ( 6 sec) [ -3511.4244] [ 375] [depth= 1] . ( 6 sec) [ -3511.4012] [ 375] [depth= 4] . ( 6 sec) [ -3511.2413] [ 375] [depth= 1] . ( 7 sec) [ -3510.9507] [ 375] [depth= 4] . ( 7 sec) [ -3510.9186] [ 375] [depth= 5] . ( 7 sec) [ -3509.6310] [ 375] [depth= 4] . ( 7 sec) [ -3479.4336] [ 351] [depth= 11] . ( 7 sec) [ -3456.4549] [ 339] [depth= 1] . ( 7 sec) [ -3447.3598] [ 341] [depth= 4] . ( 7 sec) [ -3439.1217] [ 339] [depth= 3] . ( 7 sec) [ -3438.7988] [ 339] [depth= 3] . ( 7 sec) [ -3438.4555] [ 339] [depth= 4] . ( 7 sec) [ -3437.9273] [ 339] [depth= 4] . ( 7 sec) [ -3428.9506] [ 339] [depth= 1] . ( 7 sec) [ -3427.0594] [ 339] [depth= 1] . ( 7 sec) [ -3426.8012] [ 339] [depth= 1] . ( 7 sec) [ -3426.7286] [ 339] [depth= 2] . ( 7 sec) [ -3426.6246] [ 339] [depth= 1] . ( 7 sec) [ -3426.6000] [ 339] [depth= 3] . ( 7 sec) [ -3425.9092] [ 339] [depth= 12] . ( 7 sec) [ -3422.9692] [ 339] [depth= 1] . ( 7 sec) [ -3421.1609] [ 339] [depth= 1] . ( 7 sec) [ -3419.0804] [ 351] [depth= 1] . ( 7 sec) [ -3398.5731] [ 348] [depth= 6] . ( 7 sec) [ -3398.5459] [ 348] [depth= 9] . ( 7 sec) [ -3398.5257] [ 348] [depth= 1] . ( 7 sec) [ -3397.8030] [ 347] [depth= 1] . ( 7 sec) [ -3385.9252] [ 346] [depth= 8] . ( 7 sec) [ -3380.1854] [ 345] [depth= 9] . ( 7 sec) [ -3359.9401] [ 340] [depth= 1] . ( 7 sec) [ -3359.9296] [ 340] [depth= 2] . ( 8 sec) [ -3358.2682] [ 340] [depth= 2] . ( 8 sec) [ -3357.8465] [ 340] [depth= 1] . ( 8 sec) [ -3357.3408] [ 340] [depth= 1] . ( 9 sec) [ -3357.3274] [ 340] [depth= 2] . ( 9 sec) [ -3357.3077] [ 340] [depth= 1] . ( 9 sec) [ -3354.0120] [ 339] [depth= 8] . ( 9 sec) [ -3353.9866] [ 339] [depth= 1] . ( 9 sec) [ -3348.4471] [ 338] [depth= 3] . ( 9 sec) [ -3345.8998] [ 338] [depth= 1] . ( 10 sec) [ -3345.8660] [ 338] [depth= 1] . ( 10 sec) [ -3344.9867] [ 338] [depth= 1] . ( 10 sec) [ -3344.8561] [ 338] [depth= 1] . ( 10 sec) [ -3344.8440] [ 338] [depth= 1] . ( 10 sec) [ -3339.2527] [ 337] [depth= 8] . ( 10 sec) [ -3328.3942] [Branch lengths ] . ( 12 sec) [ -3262.2482] [GTR parameters ] . ( 12 sec) [ -3234.3253] [Alpha ][ 0.250961] . ( 13 sec) [ -3224.2608] [ 335] [depth= 5] . ( 13 sec) [ -3223.6350] [ 334] [depth= 12] . ( 13 sec) [ -3216.7665] [ 333] [depth= 6] . ( 13 sec) [ -3211.3084] [ 332] [depth= 7] . ( 14 sec) [ -3206.2860] [ 331] [depth= 2] . ( 14 sec) [ -3206.2423] [ 331] [depth= 2] . ( 16 sec) [ -3185.8443] [ 327] [depth= 12] . ( 16 sec) [ -3180.3315] [ 326] [depth= 4] . ( 17 sec) [ -3168.9353] [ 324] [depth= 6] . ( 17 sec) [ -3168.9034] [ 324] [depth= 3] . ( 17 sec) [ -3165.0962] [ 323] [depth= 9] . ( 19 sec) [ -3150.2159] [ 315] [depth= 18] . ( 19 sec) [ -3144.2127] [ 317] [depth= 16] . ( 19 sec) [ -3139.3369] [ 306] [depth= 1] . ( 19 sec) [ -3139.3100] [ 306] [depth= 1] . ( 22 sec) [ -3124.3602] [ 304] [depth= 3] . ( 22 sec) [ -3094.4681] [ 297] [depth= 18] . ( 22 sec) [ -3082.9238] [ 296] [depth= 1] . ( 24 sec) [ -3082.6648] [ 296] [depth= 5] . ( 24 sec) [ -3082.6158] [ 296] [depth= 1] . ( 25 sec) [ -3082.5986] [ 294] [depth= 1] . ( 25 sec) [ -3082.5878] [ 294] [depth= 3] . ( 26 sec) [ -3082.5458] [ 294] [depth= 2] . ( 26 sec) [ -3082.3221] [ 294] [depth= 2] . ( 27 sec) [ -3077.8957] [ 292] [depth= 1] . ( 28 sec) [ -3076.3379] [ 284] [depth= 1] . ( 28 sec) [ -3074.7081] [ 283] [depth= 5] . ( 28 sec) [ -3070.8462] [ 282] [depth= 1] . ( 28 sec) [ -3070.8319] [ 282] [depth= 2] . ( 28 sec) [ -3070.7760] [ 285] [depth= 1] . ( 28 sec) [ -3070.7645] [ 285] [depth= 2] . ( 28 sec) [ -3063.0038] [ 284] [depth= 3] . ( 28 sec) [ -3057.8105] [ 283] [depth= 4] . ( 31 sec) [ -3057.7447] [ 283] [depth= 3] . ( 31 sec) [ -3057.7188] [ 283] [depth= 2] . ( 32 sec) [ -3057.6567] [ 283] [depth= 1] . ( 34 sec) [ -3057.6425] [ 283] [depth= 3] . ( 34 sec) [ -3057.6214] [ 283] [depth= 2] . ( 34 sec) [ -3057.5803] [ 283] [depth= 2] . ( 35 sec) [ -3057.5485] [ 283] [depth= 1] . ( 35 sec) [ -3057.5092] [ 283] [depth= 1] . ( 37 sec) [ -3055.8463] [ 283] [depth= 6] . ( 39 sec) [ -3054.5622] [ 280] [depth= 1] . ( 42 sec) [ -3054.5184] [ 280] [depth= 1] . ( 45 sec) [ -3054.4243] [ 280] [depth= 1] . ( 48 sec) [ -3054.4062] [ 280] [depth= 1] . ( 51 sec) [ -3046.5016] [Branch lengths ] . ( 52 sec) [ -3045.7536] [GTR parameters ] . ( 52 sec) [ -3041.2795] [Alpha ][ 0.141409] . ( 73 sec) [ -3041.2663] [ 280] [depth= 1] . ( 101 sec) [ -3040.0710] [Branch lengths ] . ( 102 sec) [ -3040.0135] [GTR parameters ] . ( 102 sec) [ -3040.0070] [Alpha ][ 0.137957] . ( 124 sec) [ -3032.4121] [ 283] [depth= 13] . ( 141 sec) [ -3031.8345] [ 286] [depth= 1] . ( 144 sec) [ -3030.8809] [ 283] [depth= 1] . ( 144 sec) [ -3030.8516] [ 283] [depth= 1] . ( 152 sec) [ -3030.8333] [ 283] [depth= 1] . ( 153 sec) [ -3029.2616] [Branch lengths ] . ( 154 sec) [ -3029.2094] [GTR parameters ] . ( 154 sec) [ -3029.1908] [Alpha ][ 0.132135] . ( 206 sec) [ -3029.1668] [Branch lengths ] . ( 233 sec) [ -3029.1661] [Branch lengths ] . ( 233 sec) [ -3029.1661] [Topology ] . ( 234 sec) [ -3029.1661] [Topology ] . ( 234 sec) [ -3029.1653] [GTR parameters ] . ( 234 sec) [ -3029.1651] [Alpha ][ 0.132684] . ( 234 sec) [ -3029.1651] [Topology ] . ( 235 sec) [ -3029.1650] [Topology ] . ( 235 sec) [ -3029.1650] [GTR parameters ] . ( 235 sec) [ -3029.1650] [Alpha ][ 0.132684] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3029.165025. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11708.9632] [GTR parameters ] . ( 1 sec) [ -11505.0561] [Alpha ][ 0.500960] . ( 1 sec) [ -11418.8839] [ 899] [depth= 5] . ( 1 sec) [ -11325.4344] [ 893] [depth= 4] . ( 1 sec) [ -11317.7829] [ 894] [depth= 2] . ( 1 sec) [ -11247.0338] [ 893] [depth= 5] . ( 1 sec) [ -11214.5602] [ 889] [depth= 3] . ( 1 sec) [ -10932.6024] [ 889] [depth= 1] . ( 1 sec) [ -10900.5818] [ 890] [depth= 1] . ( 1 sec) [ -10883.1350] [ 888] [depth= 6] . ( 1 sec) [ -10879.8278] [ 888] [depth= 1] . ( 1 sec) [ -10873.0822] [ 888] [depth= 3] . ( 1 sec) [ -10793.1978] [ 887] [depth= 6] . ( 1 sec) [ -10792.8554] [ 887] [depth= 5] . ( 1 sec) [ -10774.7657] [ 887] [depth= 5] . ( 2 sec) [ -10773.2074] [ 887] [depth= 1] . ( 2 sec) [ -10749.7255] [ 887] [depth= 2] . ( 2 sec) [ -10695.6387] [ 887] [depth= 3] . ( 2 sec) [ -10587.3697] [ 884] [depth= 14] . ( 2 sec) [ -10555.6739] [ 884] [depth= 1] . ( 2 sec) [ -10538.6825] [ 884] [depth= 1] . ( 2 sec) [ -10266.3640] [ 884] [depth= 2] . ( 2 sec) [ -10150.2362] [ 881] [depth= 20] . ( 2 sec) [ -9724.6870] [ 881] [depth= 1] . ( 2 sec) [ -9611.2327] [ 874] [depth= 18] . ( 2 sec) [ -9609.4516] [ 874] [depth= 14] . ( 2 sec) [ -9609.3927] [ 874] [depth= 14] . ( 2 sec) [ -9392.8387] [ 873] [depth= 1] . ( 2 sec) [ -9305.6862] [ 825] [depth= 13] . ( 2 sec) [ -9255.4082] [ 821] [depth= 13] . ( 2 sec) [ -9233.5265] [ 818] [depth= 18] . ( 2 sec) [ -9174.4702] [ 818] [depth= 2] . ( 2 sec) [ -9168.0864] [ 818] [depth= 1] . ( 2 sec) [ -9107.8268] [ 817] [depth= 2] . ( 2 sec) [ -9081.8628] [ 816] [depth= 2] . ( 2 sec) [ -9077.3661] [ 816] [depth= 21] . ( 2 sec) [ -9052.4652] [ 809] [depth= 7] . ( 2 sec) [ -9025.0653] [ 808] [depth= 6] . ( 2 sec) [ -8992.6032] [ 803] [depth= 5] . ( 2 sec) [ -8962.1653] [ 800] [depth= 15] . ( 2 sec) [ -8877.9468] [ 797] [depth= 8] . ( 2 sec) [ -8843.1040] [ 797] [depth= 2] . ( 2 sec) [ -8802.2761] [ 789] [depth= 14] . ( 2 sec) [ -8795.9755] [ 789] [depth= 11] . ( 2 sec) [ -8791.9957] [ 791] [depth= 1] . ( 2 sec) [ -8783.9492] [ 790] [depth= 5] . ( 3 sec) [ -8759.4698] [ 786] [depth= 16] . ( 3 sec) [ -8728.5668] [ 782] [depth= 10] . ( 3 sec) [ -8717.0162] [ 780] [depth= 15] . ( 3 sec) [ -8694.9323] [ 778] [depth= 15] . ( 3 sec) [ -8694.3002] [ 778] [depth= 14] . ( 3 sec) [ -8685.6430] [ 774] [depth= 14] . ( 3 sec) [ -8652.3044] [ 774] [depth= 3] . ( 3 sec) [ -7984.0038] [ 747] [depth= 20] . ( 3 sec) [ -7658.1466] [ 748] [depth= 9] . ( 3 sec) [ -7658.1042] [ 748] [depth= 21] . ( 3 sec) [ -7635.7445] [ 745] [depth= 3] . ( 3 sec) [ -7635.5308] [ 745] [depth= 7] . ( 3 sec) [ -7635.5117] [ 745] [depth= 1] . ( 3 sec) [ -7633.7760] [ 745] [depth= 4] . ( 3 sec) [ -7467.4192] [ 731] [depth= 6] . ( 3 sec) [ -7433.5726] [ 731] [depth= 12] . ( 3 sec) [ -7417.3317] [ 731] [depth= 15] . ( 3 sec) [ -7408.7408] [ 729] [depth= 6] . ( 3 sec) [ -7358.3525] [ 724] [depth= 11] . ( 3 sec) [ -7057.9119] [ 678] [depth= 17] . ( 3 sec) [ -7047.0548] [ 678] [depth= 1] . ( 3 sec) [ -7035.8557] [ 678] [depth= 1] . ( 3 sec) [ -6899.4234] [ 666] [depth= 16] . ( 3 sec) [ -6894.8461] [ 666] [depth= 14] . ( 3 sec) [ -6841.7709] [ 659] [depth= 3] . ( 3 sec) [ -6822.1676] [ 659] [depth= 3] . ( 3 sec) [ -6782.7157] [ 654] [depth= 12] . ( 4 sec) [ -6760.2497] [ 654] [depth= 1] . ( 4 sec) [ -6735.2865] [ 651] [depth= 10] . ( 4 sec) [ -6734.1616] [ 651] [depth= 1] . ( 4 sec) [ -6698.0726] [ 643] [depth= 10] . ( 4 sec) [ -6693.0652] [ 642] [depth= 12] . ( 4 sec) [ -6617.6307] [ 635] [depth= 9] . ( 4 sec) [ -6555.8947] [ 636] [depth= 13] . ( 4 sec) [ -6534.5737] [ 636] [depth= 8] . ( 4 sec) [ -6527.1184] [ 631] [depth= 5] . ( 4 sec) [ -6526.6036] [ 631] [depth= 3] . ( 4 sec) [ -6471.0703] [ 629] [depth= 6] . ( 4 sec) [ -6413.8487] [ 629] [depth= 3] . ( 4 sec) [ -6302.2005] [ 629] [depth= 10] . ( 4 sec) [ -6291.8776] [ 629] [depth= 1] . ( 4 sec) [ -6277.4601] [ 629] [depth= 1] . ( 4 sec) [ -6276.7948] [ 629] [depth= 4] . ( 4 sec) [ -6020.2875] [ 623] [depth= 5] . ( 4 sec) [ -6010.6634] [ 622] [depth= 12] . ( 4 sec) [ -5983.5429] [ 621] [depth= 12] . ( 4 sec) [ -5790.8340] [ 616] [depth= 11] . ( 4 sec) [ -5788.4665] [ 616] [depth= 1] . ( 4 sec) [ -5788.4264] [ 616] [depth= 1] . ( 4 sec) [ -5788.4075] [ 616] [depth= 1] . ( 4 sec) [ -5740.0601] [ 605] [depth= 10] . ( 4 sec) [ -5740.0131] [ 605] [depth= 4] . ( 4 sec) [ -5668.2121] [ 610] [depth= 14] . ( 5 sec) [ -5660.3228] [ 609] [depth= 11] . ( 5 sec) [ -5653.7617] [ 610] [depth= 1] . ( 5 sec) [ -5651.2567] [ 608] [depth= 9] . ( 5 sec) [ -5608.9118] [ 579] [depth= 2] . ( 5 sec) [ -5594.9191] [ 578] [depth= 7] . ( 5 sec) [ -5293.9701] [ 573] [depth= 9] . ( 5 sec) [ -5104.5862] [ 503] [depth= 10] . ( 5 sec) [ -5089.6781] [ 502] [depth= 1] . ( 5 sec) [ -5053.6631] [ 500] [depth= 6] . ( 5 sec) [ -4958.3729] [ 497] [depth= 12] . ( 5 sec) [ -4932.0974] [ 495] [depth= 9] . ( 5 sec) [ -4929.6161] [ 493] [depth= 4] . ( 5 sec) [ -4907.1110] [ 493] [depth= 1] . ( 5 sec) [ -4791.4697] [ 459] [depth= 18] . ( 5 sec) [ -4484.4542] [ 463] [depth= 6] . ( 5 sec) [ -4484.4143] [ 463] [depth= 1] . ( 5 sec) [ -4452.7183] [ 461] [depth= 5] . ( 6 sec) [ -4452.3700] [ 461] [depth= 2] . ( 6 sec) [ -4449.2534] [ 457] [depth= 10] . ( 6 sec) [ -4226.6384] [ 457] [depth= 3] . ( 6 sec) [ -3982.1359] [ 425] [depth= 13] . ( 6 sec) [ -3975.1765] [ 425] [depth= 2] . ( 6 sec) [ -3972.8856] [ 425] [depth= 13] . ( 6 sec) [ -3933.6897] [ 417] [depth= 7] . ( 6 sec) [ -3933.2903] [ 417] [depth= 2] . ( 6 sec) [ -3932.2891] [ 417] [depth= 3] . ( 6 sec) [ -3931.4475] [ 418] [depth= 1] . ( 6 sec) [ -3917.9037] [ 417] [depth= 18] . ( 6 sec) [ -3899.4040] [ 413] [depth= 14] . ( 6 sec) [ -3895.2505] [ 412] [depth= 2] . ( 6 sec) [ -3895.1819] [ 412] [depth= 15] . ( 6 sec) [ -3895.1129] [ 412] [depth= 15] . ( 6 sec) [ -3892.5318] [ 411] [depth= 8] . ( 7 sec) [ -3891.8890] [ 411] [depth= 7] . ( 7 sec) [ -3886.2646] [ 410] [depth= 13] . ( 7 sec) [ -3868.2948] [ 407] [depth= 19] . ( 7 sec) [ -3838.6514] [ 399] [depth= 6] . ( 7 sec) [ -3794.7928] [ 392] [depth= 10] . ( 7 sec) [ -3788.2499] [ 392] [depth= 5] . ( 7 sec) [ -3783.0479] [ 392] [depth= 1] . ( 7 sec) [ -3774.6235] [ 391] [depth= 4] . ( 7 sec) [ -3731.5013] [ 383] [depth= 12] . ( 7 sec) [ -3731.4211] [ 383] [depth= 3] . ( 7 sec) [ -3731.1204] [ 383] [depth= 2] . ( 7 sec) [ -3720.4891] [ 381] [depth= 5] . ( 7 sec) [ -3676.4549] [ 364] [depth= 4] . ( 7 sec) [ -3581.8079] [ 350] [depth= 1] . ( 7 sec) [ -3578.8220] [ 350] [depth= 3] . ( 7 sec) [ -3543.2029] [ 346] [depth= 6] . ( 7 sec) [ -3542.4643] [ 346] [depth= 7] . ( 7 sec) [ -3542.0352] [ 346] [depth= 1] . ( 7 sec) [ -3539.4380] [ 343] [depth= 9] . ( 8 sec) [ -3539.1227] [ 343] [depth= 21] . ( 8 sec) [ -3537.7081] [ 343] [depth= 12] . ( 8 sec) [ -3537.2540] [ 343] [depth= 3] . ( 8 sec) [ -3511.3575] [ 338] [depth= 9] . ( 8 sec) [ -3498.1356] [ 336] [depth= 11] . ( 8 sec) [ -3496.5900] [ 336] [depth= 2] . ( 8 sec) [ -3489.6782] [ 335] [depth= 3] . ( 8 sec) [ -3463.8863] [ 335] [depth= 4] . ( 8 sec) [ -3463.8675] [ 335] [depth= 2] . ( 8 sec) [ -3458.2419] [ 333] [depth= 10] . ( 9 sec) [ -3450.3004] [ 332] [depth= 8] . ( 9 sec) [ -3446.3104] [ 332] [depth= 1] . ( 9 sec) [ -3444.4576] [ 332] [depth= 3] . ( 9 sec) [ -3443.2657] [ 332] [depth= 8] . ( 9 sec) [ -3400.6186] [ 331] [depth= 1] . ( 9 sec) [ -3398.2749] [ 332] [depth= 1] . ( 9 sec) [ -3398.2396] [ 332] [depth= 5] . ( 10 sec) [ -3396.6777] [ 332] [depth= 3] . ( 10 sec) [ -3389.7792] [ 331] [depth= 8] . ( 10 sec) [ -3389.3045] [ 329] [depth= 8] . ( 10 sec) [ -3387.5495] [ 328] [depth= 1] . ( 10 sec) [ -3387.0169] [ 327] [depth= 2] . ( 10 sec) [ -3385.2705] [ 327] [depth= 2] . ( 10 sec) [ -3385.0126] [ 327] [depth= 3] . ( 10 sec) [ -3384.9355] [ 326] [depth= 4] . ( 10 sec) [ -3384.2632] [ 326] [depth= 2] . ( 11 sec) [ -3384.0397] [ 326] [depth= 7] . ( 11 sec) [ -3372.8002] [ 324] [depth= 3] . ( 11 sec) [ -3372.7844] [ 324] [depth= 1] . ( 11 sec) [ -3359.4017] [ 324] [depth= 1] . ( 11 sec) [ -3357.7565] [ 324] [depth= 2] . ( 11 sec) [ -3351.6957] [ 323] [depth= 9] . ( 11 sec) [ -3351.6741] [ 323] [depth= 15] . ( 12 sec) [ -3284.8639] [Branch lengths ] . ( 12 sec) [ -3244.9342] [GTR parameters ] . ( 13 sec) [ -3218.0050] [Alpha ][ 0.250961] . ( 13 sec) [ -3217.2476] [ 323] [depth= 1] . ( 13 sec) [ -3216.7896] [ 323] [depth= 2] . ( 13 sec) [ -3163.5990] [ 313] [depth= 12] . ( 13 sec) [ -3162.9460] [ 313] [depth= 4] . ( 13 sec) [ -3142.2246] [ 307] [depth= 3] . ( 13 sec) [ -3133.5170] [ 306] [depth= 4] . ( 13 sec) [ -3132.5026] [ 305] [depth= 3] . ( 13 sec) [ -3131.6620] [ 304] [depth= 3] . ( 13 sec) [ -3120.7044] [ 303] [depth= 1] . ( 13 sec) [ -3120.6514] [ 303] [depth= 1] . ( 13 sec) [ -3119.7138] [ 303] [depth= 1] . ( 15 sec) [ -3119.3596] [ 295] [depth= 1] . ( 15 sec) [ -3111.4560] [ 294] [depth= 5] . ( 15 sec) [ -3109.0392] [ 294] [depth= 1] . ( 15 sec) [ -3093.7688] [ 294] [depth= 8] . ( 15 sec) [ -3093.4540] [ 294] [depth= 2] . ( 16 sec) [ -3093.0396] [ 293] [depth= 1] . ( 16 sec) [ -3090.5443] [ 293] [depth= 1] . ( 17 sec) [ -3089.5713] [ 293] [depth= 1] . ( 17 sec) [ -3089.5576] [ 293] [depth= 1] . ( 17 sec) [ -3086.1588] [ 293] [depth= 3] . ( 18 sec) [ -3086.1339] [ 293] [depth= 2] . ( 19 sec) [ -3086.1006] [ 293] [depth= 1] . ( 19 sec) [ -3085.7116] [ 292] [depth= 2] . ( 19 sec) [ -3085.2841] [ 288] [depth= 3] . ( 20 sec) [ -3080.7449] [ 288] [depth= 1] . ( 20 sec) [ -3080.2512] [ 288] [depth= 1] . ( 20 sec) [ -3068.1952] [ 285] [depth= 8] . ( 20 sec) [ -3068.1829] [ 285] [depth= 4] . ( 20 sec) [ -3068.1705] [ 285] [depth= 2] . ( 21 sec) [ -3068.0102] [ 285] [depth= 1] . ( 22 sec) [ -3066.9945] [ 285] [depth= 3] . ( 22 sec) [ -3058.9248] [ 284] [depth= 5] . ( 23 sec) [ -3058.5739] [ 284] [depth= 1] . ( 23 sec) [ -3058.5629] [ 284] [depth= 1] . ( 23 sec) [ -3057.5652] [ 284] [depth= 2] . ( 24 sec) [ -3056.7989] [ 284] [depth= 1] . ( 24 sec) [ -3056.7218] [ 284] [depth= 2] . ( 25 sec) [ -3056.6792] [ 284] [depth= 1] . ( 27 sec) [ -3056.5899] [ 284] [depth= 2] . ( 27 sec) [ -3049.9944] [ 286] [depth= 1] . ( 29 sec) [ -3049.9769] [ 286] [depth= 1] . ( 30 sec) [ -3049.9617] [ 286] [depth= 2] . ( 32 sec) [ -3048.5440] [ 286] [depth= 4] . ( 35 sec) [ -3043.5555] [ 284] [depth= 1] . ( 35 sec) [ -3042.6486] [ 287] [depth= 1] . ( 36 sec) [ -3042.5567] [ 287] [depth= 1] . ( 37 sec) [ -3040.7268] [ 286] [depth= 2] . ( 38 sec) [ -3040.7150] [ 285] [depth= 1] . ( 41 sec) [ -3040.6954] [ 285] [depth= 3] . ( 48 sec) [ -3035.7700] [Branch lengths ] . ( 48 sec) [ -3035.6894] [GTR parameters ] . ( 48 sec) [ -3030.5384] [Alpha ][ 0.133314] . ( 61 sec) [ -3030.3122] [ 289] [depth= 2] . ( 61 sec) [ -3030.2956] [ 289] [depth= 1] . ( 64 sec) [ -3029.9567] [ 283] [depth= 2] . ( 96 sec) [ -3029.6041] [Branch lengths ] . ( 96 sec) [ -3029.5457] [GTR parameters ] . ( 97 sec) [ -3029.5455] [Alpha ][ 0.132803] . ( 123 sec) [ -3029.5273] [Branch lengths ] . ( 123 sec) [ -3029.5273] [Topology ] . ( 123 sec) [ -3029.5272] [Topology ] . ( 123 sec) [ -3029.5271] [GTR parameters ] . ( 123 sec) [ -3029.5271] [Alpha ][ 0.132553] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3029.527085. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10339.5466] [GTR parameters ] . ( 1 sec) [ -10172.4902] [Alpha ][ 0.500960] . ( 1 sec) [ -9965.5416] [ 915] [depth= 3] . ( 1 sec) [ -9945.0280] [ 916] [depth= 1] . ( 1 sec) [ -9824.1236] [ 910] [depth= 6] . ( 1 sec) [ -9820.1983] [ 909] [depth= 2] . ( 1 sec) [ -9815.6503] [ 908] [depth= 1] . ( 1 sec) [ -9795.6688] [ 907] [depth= 6] . ( 1 sec) [ -9731.7350] [ 904] [depth= 5] . ( 1 sec) [ -9729.2176] [ 902] [depth= 1] . ( 1 sec) [ -9665.7980] [ 896] [depth= 6] . ( 1 sec) [ -9658.1659] [ 893] [depth= 5] . ( 1 sec) [ -9650.4843] [ 893] [depth= 2] . ( 1 sec) [ -9641.5951] [ 892] [depth= 1] . ( 1 sec) [ -9609.0164] [ 892] [depth= 1] . ( 2 sec) [ -9549.2164] [ 892] [depth= 9] . ( 2 sec) [ -9538.9899] [ 892] [depth= 1] . ( 2 sec) [ -9513.6192] [ 888] [depth= 7] . ( 2 sec) [ -9475.7949] [ 888] [depth= 1] . ( 2 sec) [ -9462.4268] [ 888] [depth= 10] . ( 2 sec) [ -9445.0854] [ 888] [depth= 1] . ( 2 sec) [ -9401.4420] [ 888] [depth= 12] . ( 2 sec) [ -9388.8348] [ 888] [depth= 2] . ( 2 sec) [ -9333.1388] [ 888] [depth= 5] . ( 2 sec) [ -9259.3636] [ 888] [depth= 1] . ( 2 sec) [ -9183.6372] [ 882] [depth= 8] . ( 2 sec) [ -9174.5668] [ 882] [depth= 2] . ( 2 sec) [ -9165.0133] [ 882] [depth= 5] . ( 2 sec) [ -9154.8754] [ 882] [depth= 1] . ( 2 sec) [ -8715.8521] [ 880] [depth= 14] . ( 2 sec) [ -8471.0373] [ 885] [depth= 1] . ( 2 sec) [ -8433.2470] [ 877] [depth= 16] . ( 2 sec) [ -8375.4954] [ 828] [depth= 16] . ( 2 sec) [ -8340.7702] [ 827] [depth= 17] . ( 2 sec) [ -8068.3479] [ 805] [depth= 7] . ( 2 sec) [ -8066.8693] [ 805] [depth= 5] . ( 2 sec) [ -8030.8176] [ 804] [depth= 4] . ( 2 sec) [ -7997.0905] [ 800] [depth= 21] . ( 2 sec) [ -7975.2578] [ 800] [depth= 1] . ( 2 sec) [ -7975.1845] [ 800] [depth= 1] . ( 2 sec) [ -7962.6014] [ 798] [depth= 7] . ( 2 sec) [ -7956.4374] [ 798] [depth= 9] . ( 2 sec) [ -7942.3949] [ 795] [depth= 6] . ( 2 sec) [ -7833.6841] [ 787] [depth= 16] . ( 2 sec) [ -7811.1217] [ 787] [depth= 3] . ( 2 sec) [ -7655.7501] [ 787] [depth= 4] . ( 2 sec) [ -7603.2514] [ 788] [depth= 1] . ( 3 sec) [ -7561.9932] [ 781] [depth= 20] . ( 3 sec) [ -7557.6059] [ 780] [depth= 2] . ( 3 sec) [ -7534.5775] [ 780] [depth= 12] . ( 3 sec) [ -7192.6154] [ 777] [depth= 26] . ( 3 sec) [ -7057.6131] [ 742] [depth= 15] . ( 3 sec) [ -7024.7360] [ 742] [depth= 1] . ( 3 sec) [ -6924.6604] [ 714] [depth= 6] . ( 3 sec) [ -6895.8657] [ 712] [depth= 14] . ( 3 sec) [ -6721.0643] [ 711] [depth= 11] . ( 3 sec) [ -6631.3125] [ 709] [depth= 10] . ( 3 sec) [ -6571.8716] [ 696] [depth= 20] . ( 3 sec) [ -6558.3576] [ 695] [depth= 1] . ( 3 sec) [ -6518.0872] [ 693] [depth= 20] . ( 3 sec) [ -6503.7487] [ 693] [depth= 1] . ( 3 sec) [ -6502.5653] [ 693] [depth= 12] . ( 3 sec) [ -6468.4131] [ 687] [depth= 2] . ( 3 sec) [ -6396.2163] [ 684] [depth= 17] . ( 3 sec) [ -6392.6661] [ 685] [depth= 16] . ( 3 sec) [ -6360.4386] [ 678] [depth= 4] . ( 3 sec) [ -6302.7236] [ 678] [depth= 3] . ( 3 sec) [ -6302.6004] [ 678] [depth= 1] . ( 3 sec) [ -6301.9323] [ 678] [depth= 2] . ( 3 sec) [ -6294.7464] [ 676] [depth= 2] . ( 3 sec) [ -6022.8405] [ 676] [depth= 11] . ( 3 sec) [ -6022.7430] [ 676] [depth= 1] . ( 3 sec) [ -5976.7948] [ 667] [depth= 7] . ( 3 sec) [ -5953.6110] [ 663] [depth= 14] . ( 3 sec) [ -5923.2411] [ 658] [depth= 9] . ( 4 sec) [ -5922.9027] [ 658] [depth= 5] . ( 4 sec) [ -5922.2516] [ 658] [depth= 2] . ( 4 sec) [ -5782.7963] [ 618] [depth= 3] . ( 4 sec) [ -5749.2719] [ 617] [depth= 13] . ( 4 sec) [ -5747.7083] [ 617] [depth= 1] . ( 4 sec) [ -5708.8649] [ 616] [depth= 8] . ( 4 sec) [ -5708.8000] [ 616] [depth= 1] . ( 4 sec) [ -5670.3739] [ 608] [depth= 14] . ( 4 sec) [ -5664.6872] [ 609] [depth= 2] . ( 4 sec) [ -5651.4173] [ 608] [depth= 4] . ( 4 sec) [ -5395.6704] [ 601] [depth= 12] . ( 4 sec) [ -5324.4334] [ 601] [depth= 1] . ( 4 sec) [ -5273.5914] [ 597] [depth= 10] . ( 4 sec) [ -5246.0389] [ 592] [depth= 22] . ( 4 sec) [ -5239.1398] [ 592] [depth= 13] . ( 4 sec) [ -5083.6816] [ 562] [depth= 1] . ( 4 sec) [ -5025.5909] [ 552] [depth= 15] . ( 4 sec) [ -5023.7683] [ 552] [depth= 1] . ( 4 sec) [ -5014.3134] [ 552] [depth= 1] . ( 4 sec) [ -4987.5356] [ 551] [depth= 7] . ( 4 sec) [ -4985.1946] [ 551] [depth= 11] . ( 4 sec) [ -4962.7018] [ 546] [depth= 2] . ( 4 sec) [ -4961.7911] [ 546] [depth= 1] . ( 4 sec) [ -4960.6000] [ 542] [depth= 5] . ( 4 sec) [ -4957.2142] [ 542] [depth= 2] . ( 5 sec) [ -4955.3466] [ 542] [depth= 1] . ( 5 sec) [ -4930.2878] [ 542] [depth= 2] . ( 5 sec) [ -4929.7217] [ 542] [depth= 18] . ( 5 sec) [ -4871.5585] [ 531] [depth= 14] . ( 5 sec) [ -4871.4904] [ 531] [depth= 1] . ( 5 sec) [ -4864.2385] [ 530] [depth= 10] . ( 5 sec) [ -4864.1922] [ 530] [depth= 1] . ( 5 sec) [ -4862.6379] [ 530] [depth= 2] . ( 5 sec) [ -4859.0898] [ 530] [depth= 12] . ( 5 sec) [ -4847.6259] [ 529] [depth= 10] . ( 5 sec) [ -4839.7611] [ 529] [depth= 1] . ( 5 sec) [ -4820.6550] [ 525] [depth= 15] . ( 5 sec) [ -4820.5422] [ 525] [depth= 8] . ( 5 sec) [ -4820.3551] [ 525] [depth= 2] . ( 5 sec) [ -4820.2981] [ 525] [depth= 1] . ( 5 sec) [ -4771.2091] [ 519] [depth= 13] . ( 5 sec) [ -4769.4219] [ 519] [depth= 1] . ( 5 sec) [ -4764.8962] [ 518] [depth= 7] . ( 5 sec) [ -4698.5228] [ 518] [depth= 1] . ( 5 sec) [ -4697.8005] [ 518] [depth= 19] . ( 5 sec) [ -4674.6226] [ 514] [depth= 6] . ( 5 sec) [ -4673.6041] [ 514] [depth= 11] . ( 5 sec) [ -4665.8088] [ 513] [depth= 18] . ( 5 sec) [ -4622.8748] [ 505] [depth= 12] . ( 5 sec) [ -4600.9601] [ 502] [depth= 13] . ( 5 sec) [ -4595.7981] [ 503] [depth= 1] . ( 5 sec) [ -4593.6512] [ 502] [depth= 2] . ( 5 sec) [ -4592.8450] [ 502] [depth= 1] . ( 5 sec) [ -4592.8221] [ 502] [depth= 1] . ( 6 sec) [ -4459.7949] [ 471] [depth= 8] . ( 6 sec) [ -4054.9497] [ 476] [depth= 19] . ( 6 sec) [ -4032.2408] [ 478] [depth= 16] . ( 6 sec) [ -4032.1834] [ 478] [depth= 1] . ( 6 sec) [ -4032.0993] [ 478] [depth= 3] . ( 6 sec) [ -4025.7741] [ 477] [depth= 3] . ( 6 sec) [ -4021.7100] [ 477] [depth= 9] . ( 6 sec) [ -4017.0646] [ 477] [depth= 2] . ( 6 sec) [ -4015.4008] [ 477] [depth= 1] . ( 7 sec) [ -4009.2275] [ 476] [depth= 9] . ( 7 sec) [ -4005.3563] [ 476] [depth= 3] . ( 7 sec) [ -3981.4704] [ 472] [depth= 14] . ( 7 sec) [ -3975.8649] [ 472] [depth= 2] . ( 7 sec) [ -3975.8372] [ 472] [depth= 3] . ( 7 sec) [ -3916.3992] [ 467] [depth= 9] . ( 7 sec) [ -3896.7406] [ 467] [depth= 1] . ( 7 sec) [ -3894.0308] [ 467] [depth= 15] . ( 7 sec) [ -3891.1917] [ 469] [depth= 1] . ( 7 sec) [ -3796.4859] [ 421] [depth= 9] . ( 7 sec) [ -3795.0444] [ 421] [depth= 3] . ( 7 sec) [ -3788.4325] [ 421] [depth= 17] . ( 7 sec) [ -3783.9205] [ 420] [depth= 7] . ( 7 sec) [ -3773.0621] [ 414] [depth= 3] . ( 7 sec) [ -3761.6287] [ 414] [depth= 6] . ( 7 sec) [ -3761.3114] [ 414] [depth= 1] . ( 7 sec) [ -3744.7368] [ 411] [depth= 12] . ( 8 sec) [ -3741.5602] [ 411] [depth= 7] . ( 8 sec) [ -3741.5250] [ 411] [depth= 2] . ( 8 sec) [ -3721.3783] [ 406] [depth= 11] . ( 8 sec) [ -3720.3617] [ 406] [depth= 9] . ( 8 sec) [ -3716.2327] [ 404] [depth= 1] . ( 8 sec) [ -3715.3953] [ 404] [depth= 8] . ( 8 sec) [ -3715.3469] [ 404] [depth= 10] . ( 8 sec) [ -3709.7204] [ 404] [depth= 1] . ( 8 sec) [ -3709.4329] [ 404] [depth= 2] . ( 9 sec) [ -3708.0561] [ 404] [depth= 15] . ( 9 sec) [ -3707.1539] [ 404] [depth= 7] . ( 9 sec) [ -3707.1329] [ 404] [depth= 9] . ( 10 sec) [ -3694.2484] [ 402] [depth= 5] . ( 10 sec) [ -3690.8685] [ 402] [depth= 8] . ( 10 sec) [ -3690.8176] [ 402] [depth= 6] . ( 10 sec) [ -3690.5751] [ 399] [depth= 3] . ( 10 sec) [ -3653.1317] [ 372] [depth= 13] . ( 11 sec) [ -3653.1004] [ 372] [depth= 9] . ( 11 sec) [ -3653.0713] [ 372] [depth= 3] . ( 11 sec) [ -3652.3285] [ 372] [depth= 3] . ( 11 sec) [ -3648.6643] [ 372] [depth= 4] . ( 11 sec) [ -3647.0517] [ 372] [depth= 4] . ( 11 sec) [ -3646.8854] [ 367] [depth= 10] . ( 11 sec) [ -3646.6766] [ 367] [depth= 3] . ( 11 sec) [ -3646.3857] [ 367] [depth= 4] . ( 11 sec) [ -3646.3604] [ 367] [depth= 1] . ( 11 sec) [ -3643.1271] [ 366] [depth= 1] . ( 11 sec) [ -3534.3238] [ 336] [depth= 15] . ( 11 sec) [ -3528.6151] [ 335] [depth= 2] . ( 11 sec) [ -3528.4026] [ 337] [depth= 3] . ( 11 sec) [ -3527.1371] [ 342] [depth= 3] . ( 12 sec) [ -3523.7582] [ 344] [depth= 4] . ( 12 sec) [ -3487.8178] [Branch lengths ] . ( 12 sec) [ -3374.4487] [GTR parameters ] . ( 13 sec) [ -3344.0308] [Alpha ][ 0.250961] . ( 13 sec) [ -3314.2821] [ 338] [depth= 10] . ( 13 sec) [ -3294.6561] [ 324] [depth= 18] . ( 13 sec) [ -3265.0355] [ 317] [depth= 15] . ( 13 sec) [ -3262.0209] [ 316] [depth= 1] . ( 13 sec) [ -3254.8745] [ 314] [depth= 4] . ( 13 sec) [ -3245.0644] [ 312] [depth= 2] . ( 14 sec) [ -3245.0474] [ 312] [depth= 6] . ( 14 sec) [ -3243.5030] [ 308] [depth= 16] . ( 14 sec) [ -3243.3630] [ 308] [depth= 4] . ( 15 sec) [ -3241.9750] [ 308] [depth= 10] . ( 16 sec) [ -3234.8650] [ 307] [depth= 10] . ( 16 sec) [ -3234.8528] [ 307] [depth= 3] . ( 16 sec) [ -3234.8360] [ 307] [depth= 2] . ( 17 sec) [ -3206.5349] [ 302] [depth= 4] . ( 17 sec) [ -3206.3460] [ 302] [depth= 2] . ( 18 sec) [ -3195.9036] [ 300] [depth= 4] . ( 18 sec) [ -3195.8806] [ 300] [depth= 2] . ( 18 sec) [ -3194.5369] [ 300] [depth= 8] . ( 20 sec) [ -3164.4576] [ 297] [depth= 20] . ( 20 sec) [ -3164.4410] [ 297] [depth= 2] . ( 20 sec) [ -3164.4145] [ 297] [depth= 1] . ( 22 sec) [ -3164.3926] [ 297] [depth= 4] . ( 23 sec) [ -3164.3817] [ 297] [depth= 1] . ( 24 sec) [ -3159.1298] [ 296] [depth= 3] . ( 25 sec) [ -3154.1004] [ 295] [depth= 2] . ( 26 sec) [ -3148.8511] [ 294] [depth= 4] . ( 27 sec) [ -3148.8312] [ 294] [depth= 1] . ( 27 sec) [ -3148.8046] [ 294] [depth= 2] . ( 29 sec) [ -3148.7838] [ 294] [depth= 1] . ( 30 sec) [ -3148.7728] [ 294] [depth= 4] . ( 32 sec) [ -3147.2575] [ 293] [depth= 5] . ( 33 sec) [ -3131.6327] [ 290] [depth= 1] . ( 34 sec) [ -3126.1351] [ 289] [depth= 8] . ( 35 sec) [ -3121.0448] [ 288] [depth= 5] . ( 35 sec) [ -3120.9960] [ 288] [depth= 1] . ( 39 sec) [ -3119.1524] [ 287] [depth= 3] . ( 39 sec) [ -3119.1364] [ 287] [depth= 1] . ( 40 sec) [ -3119.1249] [ 287] [depth= 1] . ( 42 sec) [ -3118.7610] [ 287] [depth= 1] . ( 42 sec) [ -3113.3610] [ 286] [depth= 3] . ( 42 sec) [ -3113.3239] [ 286] [depth= 2] . ( 45 sec) [ -3113.0809] [ 286] [depth= 2] . ( 47 sec) [ -3113.0683] [ 286] [depth= 1] . ( 47 sec) [ -3113.0514] [ 286] [depth= 2] . ( 48 sec) [ -3112.1147] [ 286] [depth= 2] . ( 49 sec) [ -3109.1770] [Branch lengths ] . ( 50 sec) [ -3077.7600] [GTR parameters ] . ( 50 sec) [ -3073.5183] [Alpha ][ 0.142324] . ( 51 sec) [ -3069.2950] [ 283] [depth= 2] . ( 51 sec) [ -3069.2848] [ 283] [depth= 2] . ( 53 sec) [ -3068.9838] [ 285] [depth= 1] . ( 53 sec) [ -3064.6162] [ 284] [depth= 10] . ( 53 sec) [ -3064.6059] [ 284] [depth= 2] . ( 54 sec) [ -3064.5781] [ 284] [depth= 2] . ( 60 sec) [ -3063.4979] [ 281] [depth= 1] . ( 76 sec) [ -3060.4361] [ 280] [depth= 1] . ( 76 sec) [ -3060.4195] [ 280] [depth= 1] . ( 83 sec) [ -3060.3024] [ 280] [depth= 1] . ( 95 sec) [ -3059.2903] [Branch lengths ] . ( 96 sec) [ -3057.0411] [GTR parameters ] . ( 96 sec) [ -3057.0400] [Alpha ][ 0.143876] . ( 99 sec) [ -3050.7035] [ 283] [depth= 12] . ( 117 sec) [ -3048.9206] [ 285] [depth= 1] . ( 140 sec) [ -3048.7412] [ 287] [depth= 1] . ( 141 sec) [ -3047.6205] [ 285] [depth= 1] . ( 142 sec) [ -3047.4296] [ 283] [depth= 1] . ( 143 sec) [ -3044.9534] [Branch lengths ] . ( 143 sec) [ -3044.1476] [GTR parameters ] . ( 143 sec) [ -3044.1319] [Alpha ][ 0.138258] . ( 166 sec) [ -3044.0964] [ 283] [depth= 1] . ( 191 sec) [ -3041.2680] [Branch lengths ] . ( 192 sec) [ -3034.0159] [GTR parameters ] . ( 192 sec) [ -3034.0043] [Alpha ][ 0.133431] . ( 240 sec) [ -3031.5787] [Branch lengths ] . ( 267 sec) [ -3029.9631] [Branch lengths ] . ( 267 sec) [ -3029.9631] [Topology ] . ( 267 sec) [ -3029.9353] [Topology ] . ( 268 sec) [ -3029.9335] [Topology ] . ( 268 sec) [ -3029.9333] [Topology ] . ( 270 sec) [ -3029.5184] [GTR parameters ] . ( 270 sec) [ -3029.5182] [Alpha ][ 0.132785] . ( 270 sec) [ -3029.5182] [Topology ] . ( 270 sec) [ -3029.5136] [Topology ] . ( 271 sec) [ -3029.5129] [Topology ] . ( 271 sec) [ -3029.5129] [GTR parameters ] . ( 271 sec) [ -3029.5129] [Alpha ][ 0.132785] . ( 271 sec) [ -3029.5129] [Topology ] . ( 272 sec) [ -3029.5128] [Topology ] . ( 272 sec) [ -3029.5126] [GTR parameters ] . ( 272 sec) [ -3029.5126] [Alpha ][ 0.132652] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3029.512597. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11071.0691] [GTR parameters ] . ( 1 sec) [ -10873.7509] [Alpha ][ 0.500960] . ( 1 sec) [ -10818.5208] [ 912] [depth= 3] . ( 1 sec) [ -10694.8980] [ 912] [depth= 4] . ( 1 sec) [ -10636.7829] [ 908] [depth= 4] . ( 1 sec) [ -10603.7262] [ 908] [depth= 8] . ( 1 sec) [ -10318.1818] [ 904] [depth= 5] . ( 1 sec) [ -10297.5829] [ 904] [depth= 1] . ( 1 sec) [ -10240.9053] [ 904] [depth= 2] . ( 1 sec) [ -10235.2601] [ 904] [depth= 1] . ( 1 sec) [ -10184.3775] [ 897] [depth= 7] . ( 1 sec) [ -10129.3895] [ 895] [depth= 4] . ( 1 sec) [ -10123.3584] [ 895] [depth= 4] . ( 1 sec) [ -10118.7688] [ 893] [depth= 5] . ( 1 sec) [ -10062.0389] [ 882] [depth= 3] . ( 1 sec) [ -10057.1282] [ 882] [depth= 10] . ( 1 sec) [ -9971.2187] [ 879] [depth= 11] . ( 1 sec) [ -9971.0646] [ 879] [depth= 2] . ( 1 sec) [ -9943.4432] [ 878] [depth= 9] . ( 1 sec) [ -9926.7030] [ 878] [depth= 6] . ( 1 sec) [ -9925.8800] [ 878] [depth= 1] . ( 1 sec) [ -9922.4352] [ 877] [depth= 6] . ( 1 sec) [ -9287.8409] [ 878] [depth= 1] . ( 1 sec) [ -9277.3115] [ 877] [depth= 3] . ( 1 sec) [ -9228.1073] [ 869] [depth= 14] . ( 1 sec) [ -9177.5137] [ 863] [depth= 17] . ( 1 sec) [ -9173.3610] [ 862] [depth= 11] . ( 2 sec) [ -9172.8699] [ 862] [depth= 1] . ( 2 sec) [ -9153.5289] [ 860] [depth= 2] . ( 2 sec) [ -9112.5655] [ 854] [depth= 9] . ( 2 sec) [ -8856.9920] [ 820] [depth= 12] . ( 2 sec) [ -8765.1538] [ 818] [depth= 12] . ( 2 sec) [ -8684.2679] [ 811] [depth= 18] . ( 2 sec) [ -8684.1833] [ 811] [depth= 1] . ( 2 sec) [ -8681.2339] [ 811] [depth= 8] . ( 2 sec) [ -8676.1734] [ 811] [depth= 1] . ( 2 sec) [ -8558.6302] [ 808] [depth= 7] . ( 2 sec) [ -8516.4781] [ 803] [depth= 10] . ( 2 sec) [ -8500.0753] [ 802] [depth= 11] . ( 2 sec) [ -8474.9970] [ 799] [depth= 8] . ( 2 sec) [ -8472.6212] [ 802] [depth= 5] . ( 2 sec) [ -8463.5637] [ 799] [depth= 6] . ( 2 sec) [ -8461.0557] [ 799] [depth= 4] . ( 2 sec) [ -8460.0800] [ 800] [depth= 21] . ( 2 sec) [ -8308.8673] [ 791] [depth= 4] . ( 2 sec) [ -8307.4297] [ 791] [depth= 1] . ( 2 sec) [ -8305.9619] [ 781] [depth= 4] . ( 2 sec) [ -8283.6800] [ 781] [depth= 2] . ( 2 sec) [ -8240.4788] [ 781] [depth= 1] . ( 2 sec) [ -8030.2491] [ 776] [depth= 2] . ( 2 sec) [ -7999.3469] [ 776] [depth= 1] . ( 2 sec) [ -7944.9068] [ 770] [depth= 10] . ( 2 sec) [ -7926.8600] [ 768] [depth= 4] . ( 2 sec) [ -7553.8049] [ 723] [depth= 2] . ( 2 sec) [ -7544.4882] [ 722] [depth= 20] . ( 2 sec) [ -7537.3413] [ 721] [depth= 15] . ( 3 sec) [ -7462.7812] [ 713] [depth= 3] . ( 3 sec) [ -7440.2533] [ 713] [depth= 1] . ( 3 sec) [ -7439.2392] [ 712] [depth= 2] . ( 3 sec) [ -7436.4917] [ 711] [depth= 18] . ( 3 sec) [ -7427.7813] [ 707] [depth= 9] . ( 3 sec) [ -7374.2766] [ 707] [depth= 7] . ( 3 sec) [ -7355.6108] [ 705] [depth= 9] . ( 3 sec) [ -7355.0750] [ 704] [depth= 4] . ( 3 sec) [ -7343.3842] [ 704] [depth= 1] . ( 3 sec) [ -7292.1991] [ 698] [depth= 2] . ( 3 sec) [ -7292.1293] [ 698] [depth= 1] . ( 3 sec) [ -7245.5418] [ 692] [depth= 4] . ( 3 sec) [ -7240.2866] [ 692] [depth= 1] . ( 3 sec) [ -7232.2525] [ 692] [depth= 1] . ( 3 sec) [ -7232.2322] [ 692] [depth= 1] . ( 3 sec) [ -7200.6258] [ 692] [depth= 1] . ( 3 sec) [ -7196.7396] [ 692] [depth= 8] . ( 3 sec) [ -6889.1208] [ 694] [depth= 3] . ( 3 sec) [ -6886.4621] [ 693] [depth= 3] . ( 3 sec) [ -6885.4339] [ 693] [depth= 2] . ( 3 sec) [ -6812.7062] [ 693] [depth= 5] . ( 3 sec) [ -6684.5237] [ 660] [depth= 19] . ( 3 sec) [ -6681.4930] [ 657] [depth= 1] . ( 3 sec) [ -6668.4486] [ 655] [depth= 7] . ( 3 sec) [ -6668.2411] [ 655] [depth= 4] . ( 3 sec) [ -6658.5655] [ 654] [depth= 6] . ( 4 sec) [ -6625.4985] [ 652] [depth= 5] . ( 4 sec) [ -6520.5559] [ 618] [depth= 8] . ( 4 sec) [ -6510.7903] [ 617] [depth= 4] . ( 4 sec) [ -6493.0912] [ 615] [depth= 7] . ( 4 sec) [ -6481.0095] [ 614] [depth= 10] . ( 4 sec) [ -6466.4715] [ 612] [depth= 12] . ( 4 sec) [ -6449.5175] [ 604] [depth= 9] . ( 4 sec) [ -6432.3377] [ 603] [depth= 8] . ( 4 sec) [ -5878.7891] [ 603] [depth= 3] . ( 4 sec) [ -5846.0582] [ 603] [depth= 4] . ( 4 sec) [ -5590.2243] [ 603] [depth= 1] . ( 4 sec) [ -5587.9343] [ 602] [depth= 15] . ( 4 sec) [ -5585.9752] [ 602] [depth= 1] . ( 4 sec) [ -5564.2307] [ 602] [depth= 4] . ( 4 sec) [ -5551.5221] [ 602] [depth= 8] . ( 4 sec) [ -5524.7072] [ 593] [depth= 8] . ( 4 sec) [ -5524.6555] [ 593] [depth= 1] . ( 4 sec) [ -5517.3259] [ 592] [depth= 2] . ( 4 sec) [ -5515.8945] [ 591] [depth= 18] . ( 4 sec) [ -5472.5482] [ 582] [depth= 24] . ( 4 sec) [ -5471.1417] [ 582] [depth= 2] . ( 4 sec) [ -5469.6760] [ 582] [depth= 19] . ( 4 sec) [ -5469.1828] [ 582] [depth= 1] . ( 4 sec) [ -5457.0658] [ 581] [depth= 12] . ( 4 sec) [ -5447.5009] [ 581] [depth= 25] . ( 4 sec) [ -5410.2171] [ 574] [depth= 7] . ( 4 sec) [ -5410.1524] [ 574] [depth= 2] . ( 5 sec) [ -5399.0769] [ 572] [depth= 3] . ( 5 sec) [ -5398.1104] [ 570] [depth= 1] . ( 5 sec) [ -5398.0535] [ 570] [depth= 1] . ( 5 sec) [ -5257.2042] [ 539] [depth= 18] . ( 5 sec) [ -5238.8245] [ 539] [depth= 1] . ( 5 sec) [ -5213.4445] [ 535] [depth= 4] . ( 5 sec) [ -5212.9544] [ 532] [depth= 1] . ( 5 sec) [ -5182.8411] [ 523] [depth= 14] . ( 5 sec) [ -5175.3190] [ 522] [depth= 2] . ( 5 sec) [ -5172.3827] [ 522] [depth= 1] . ( 5 sec) [ -5171.4763] [ 522] [depth= 1] . ( 5 sec) [ -5171.4634] [ 522] [depth= 1] . ( 5 sec) [ -5170.5457] [ 525] [depth= 12] . ( 5 sec) [ -5170.3690] [ 525] [depth= 1] . ( 5 sec) [ -4954.8051] [ 524] [depth= 7] . ( 5 sec) [ -4950.9995] [ 524] [depth= 3] . ( 5 sec) [ -4942.0930] [ 523] [depth= 13] . ( 6 sec) [ -4941.8290] [ 528] [depth= 13] . ( 6 sec) [ -4940.6691] [ 528] [depth= 8] . ( 6 sec) [ -4937.8113] [ 528] [depth= 2] . ( 6 sec) [ -4465.5320] [ 460] [depth= 12] . ( 6 sec) [ -4463.1897] [ 460] [depth= 12] . ( 6 sec) [ -4460.9751] [ 460] [depth= 15] . ( 6 sec) [ -4438.7617] [ 456] [depth= 4] . ( 6 sec) [ -4429.5990] [ 456] [depth= 4] . ( 6 sec) [ -4417.8680] [ 455] [depth= 3] . ( 6 sec) [ -4408.5075] [ 455] [depth= 12] . ( 6 sec) [ -4404.5465] [ 455] [depth= 2] . ( 6 sec) [ -4401.6148] [ 454] [depth= 9] . ( 6 sec) [ -4381.6382] [ 454] [depth= 5] . ( 6 sec) [ -4378.7635] [ 454] [depth= 8] . ( 6 sec) [ -4374.8590] [ 454] [depth= 6] . ( 6 sec) [ -3912.8852] [ 412] [depth= 14] . ( 6 sec) [ -3912.6756] [ 412] [depth= 17] . ( 6 sec) [ -3912.6111] [ 412] [depth= 4] . ( 6 sec) [ -3912.3713] [ 412] [depth= 1] . ( 6 sec) [ -3912.0256] [ 412] [depth= 1] . ( 6 sec) [ -3909.7811] [ 412] [depth= 10] . ( 6 sec) [ -3909.7241] [ 412] [depth= 2] . ( 6 sec) [ -3904.5576] [ 411] [depth= 8] . ( 6 sec) [ -3860.4401] [ 401] [depth= 7] . ( 6 sec) [ -3835.4127] [ 397] [depth= 14] . ( 7 sec) [ -3834.0974] [ 396] [depth= 1] . ( 7 sec) [ -3825.6475] [ 395] [depth= 5] . ( 7 sec) [ -3819.2579] [ 395] [depth= 2] . ( 7 sec) [ -3807.9775] [ 397] [depth= 8] . ( 7 sec) [ -3789.3551] [ 394] [depth= 11] . ( 7 sec) [ -3784.6676] [ 393] [depth= 2] . ( 7 sec) [ -3784.6352] [ 393] [depth= 6] . ( 7 sec) [ -3784.6219] [ 393] [depth= 3] . ( 7 sec) [ -3778.3618] [ 393] [depth= 6] . ( 7 sec) [ -3772.6187] [ 393] [depth= 3] . ( 8 sec) [ -3766.5517] [ 392] [depth= 12] . ( 8 sec) [ -3766.5059] [ 392] [depth= 16] . ( 8 sec) [ -3764.8304] [ 392] [depth= 7] . ( 8 sec) [ -3764.7967] [ 391] [depth= 2] . ( 8 sec) [ -3743.3832] [ 391] [depth= 11] . ( 8 sec) [ -3742.5246] [ 391] [depth= 6] . ( 8 sec) [ -3741.9265] [ 392] [depth= 1] . ( 8 sec) [ -3737.7178] [ 391] [depth= 12] . ( 8 sec) [ -3723.6700] [ 387] [depth= 2] . ( 8 sec) [ -3723.5964] [ 387] [depth= 1] . ( 8 sec) [ -3695.2721] [ 382] [depth= 5] . ( 8 sec) [ -3694.5872] [ 382] [depth= 2] . ( 8 sec) [ -3693.6895] [ 382] [depth= 3] . ( 8 sec) [ -3688.8821] [ 382] [depth= 5] . ( 8 sec) [ -3685.7908] [ 382] [depth= 9] . ( 8 sec) [ -3662.7094] [ 393] [depth= 1] . ( 9 sec) [ -3653.3191] [ 392] [depth= 2] . ( 9 sec) [ -3653.3031] [ 392] [depth= 2] . ( 9 sec) [ -3645.5364] [ 392] [depth= 3] . ( 9 sec) [ -3640.8747] [ 392] [depth= 19] . ( 9 sec) [ -3596.0334] [ 383] [depth= 16] . ( 9 sec) [ -3595.8716] [ 383] [depth= 2] . ( 9 sec) [ -3592.6862] [ 383] [depth= 13] . ( 9 sec) [ -3592.4127] [ 383] [depth= 3] . ( 9 sec) [ -3592.3386] [ 383] [depth= 1] . ( 9 sec) [ -3591.6094] [ 383] [depth= 1] . ( 9 sec) [ -3571.6226] [ 381] [depth= 17] . ( 9 sec) [ -3529.1464] [ 373] [depth= 14] . ( 9 sec) [ -3529.1028] [ 373] [depth= 1] . ( 9 sec) [ -3528.9104] [ 374] [depth= 1] . ( 9 sec) [ -3528.8849] [ 374] [depth= 8] . ( 9 sec) [ -3461.0901] [Branch lengths ] . ( 14 sec) [ -3415.5826] [GTR parameters ] . ( 14 sec) [ -3370.0254] [Alpha ][ 0.250961] . ( 14 sec) [ -3370.0108] [ 374] [depth= 2] . ( 14 sec) [ -3364.8067] [ 374] [depth= 3] . ( 15 sec) [ -3363.9299] [ 374] [depth= 4] . ( 16 sec) [ -3360.4467] [ 373] [depth= 2] . ( 16 sec) [ -3356.6854] [ 372] [depth= 1] . ( 16 sec) [ -3356.6707] [ 372] [depth= 2] . ( 16 sec) [ -3350.3152] [ 373] [depth= 10] . ( 16 sec) [ -3349.1374] [ 372] [depth= 1] . ( 16 sec) [ -3326.5420] [ 370] [depth= 2] . ( 16 sec) [ -3316.5678] [ 368] [depth= 1] . ( 16 sec) [ -3314.6640] [ 368] [depth= 7] . ( 16 sec) [ -3309.0539] [ 367] [depth= 9] . ( 16 sec) [ -3308.9967] [ 367] [depth= 3] . ( 16 sec) [ -3289.0342] [ 362] [depth= 7] . ( 16 sec) [ -3279.7914] [ 351] [depth= 1] . ( 17 sec) [ -3261.5934] [ 347] [depth= 13] . ( 17 sec) [ -3255.7715] [ 344] [depth= 5] . ( 17 sec) [ -3255.7053] [ 344] [depth= 4] . ( 17 sec) [ -3254.7196] [ 344] [depth= 1] . ( 17 sec) [ -3244.9835] [ 342] [depth= 5] . ( 18 sec) [ -3225.6490] [ 336] [depth= 15] . ( 18 sec) [ -3225.6291] [ 336] [depth= 2] . ( 19 sec) [ -3223.4855] [ 336] [depth= 9] . ( 21 sec) [ -3223.4034] [ 336] [depth= 1] . ( 21 sec) [ -3223.2686] [ 336] [depth= 4] . ( 21 sec) [ -3223.2016] [ 336] [depth= 1] . ( 22 sec) [ -3215.7815] [ 319] [depth= 9] . ( 22 sec) [ -3213.8258] [ 318] [depth= 1] . ( 22 sec) [ -3153.9765] [ 298] [depth= 16] . ( 22 sec) [ -3149.6851] [ 297] [depth= 5] . ( 23 sec) [ -3149.3378] [ 297] [depth= 3] . ( 23 sec) [ -3146.4146] [ 298] [depth= 1] . ( 23 sec) [ -3146.4042] [ 298] [depth= 1] . ( 24 sec) [ -3123.0906] [ 292] [depth= 4] . ( 24 sec) [ -3123.0045] [ 292] [depth= 6] . ( 25 sec) [ -3122.8608] [ 293] [depth= 1] . ( 25 sec) [ -3122.8360] [ 293] [depth= 4] . ( 25 sec) [ -3118.8685] [ 292] [depth= 2] . ( 25 sec) [ -3118.8085] [ 292] [depth= 4] . ( 26 sec) [ -3118.3141] [ 292] [depth= 2] . ( 26 sec) [ -3118.0267] [ 292] [depth= 1] . ( 26 sec) [ -3111.9022] [ 291] [depth= 4] . ( 28 sec) [ -3108.8862] [ 290] [depth= 6] . ( 28 sec) [ -3108.8676] [ 290] [depth= 1] . ( 29 sec) [ -3108.5667] [ 292] [depth= 1] . ( 31 sec) [ -3106.0650] [ 291] [depth= 3] . ( 32 sec) [ -3104.4511] [ 289] [depth= 1] . ( 32 sec) [ -3100.3535] [ 298] [depth= 3] . ( 32 sec) [ -3086.1299] [ 295] [depth= 5] . ( 32 sec) [ -3084.6604] [ 294] [depth= 1] . ( 32 sec) [ -3084.3954] [ 295] [depth= 1] . ( 34 sec) [ -3083.5074] [ 295] [depth= 2] . ( 34 sec) [ -3083.2086] [ 295] [depth= 2] . ( 34 sec) [ -3083.1815] [ 295] [depth= 1] . ( 34 sec) [ -3077.1393] [ 294] [depth= 8] . ( 34 sec) [ -3075.8765] [ 294] [depth= 1] . ( 34 sec) [ -3075.3325] [ 295] [depth= 1] . ( 34 sec) [ -3075.2495] [ 295] [depth= 1] . ( 35 sec) [ -3075.2370] [ 295] [depth= 1] . ( 35 sec) [ -3074.8844] [ 295] [depth= 2] . ( 35 sec) [ -3074.8547] [ 295] [depth= 3] . ( 35 sec) [ -3067.9209] [ 294] [depth= 5] . ( 35 sec) [ -3067.8956] [ 294] [depth= 1] . ( 36 sec) [ -3067.8507] [ 294] [depth= 1] . ( 36 sec) [ -3067.8248] [ 294] [depth= 2] . ( 36 sec) [ -3065.0208] [ 293] [depth= 1] . ( 40 sec) [ -3064.9421] [ 293] [depth= 2] . ( 41 sec) [ -3064.8367] [ 293] [depth= 1] . ( 41 sec) [ -3064.3185] [ 293] [depth= 4] . ( 41 sec) [ -3063.7708] [ 294] [depth= 1] . ( 42 sec) [ -3063.7397] [ 294] [depth= 2] . ( 42 sec) [ -3063.7221] [ 294] [depth= 1] . ( 42 sec) [ -3056.8698] [ 292] [depth= 4] . ( 45 sec) [ -3056.7779] [ 292] [depth= 1] . ( 45 sec) [ -3055.5297] [ 292] [depth= 1] . ( 46 sec) [ -3044.2109] [ 289] [depth= 13] . ( 46 sec) [ -3044.1920] [ 289] [depth= 1] . ( 47 sec) [ -3035.7580] [Branch lengths ] . ( 48 sec) [ -3035.4859] [GTR parameters ] . ( 48 sec) [ -3030.5117] [Alpha ][ 0.138823] . ( 51 sec) [ -3030.4968] [ 289] [depth= 3] . ( 52 sec) [ -3030.2895] [ 289] [depth= 1] . ( 53 sec) [ -3030.2778] [ 289] [depth= 2] . ( 61 sec) [ -3030.2151] [ 289] [depth= 1] . ( 61 sec) [ -3030.2044] [ 289] [depth= 2] . ( 62 sec) [ -3030.1904] [ 289] [depth= 2] . ( 69 sec) [ -3030.1800] [ 289] [depth= 3] . ( 72 sec) [ -3030.1557] [ 287] [depth= 2] . ( 73 sec) [ -3030.0005] [ 285] [depth= 1] . ( 74 sec) [ -3029.9883] [ 285] [depth= 3] . ( 92 sec) [ -3029.9160] [ 287] [depth= 1] . ( 93 sec) [ -3029.6277] [Branch lengths ] . ( 93 sec) [ -3029.5752] [GTR parameters ] . ( 93 sec) [ -3029.5613] [Alpha ][ 0.133914] . ( 108 sec) [ -3029.4317] [ 285] [depth= 1] . ( 108 sec) [ -3029.4034] [ 287] [depth= 1] . ( 119 sec) [ -3029.2490] [Branch lengths ] . ( 121 sec) [ -3029.1742] [GTR parameters ] . ( 121 sec) [ -3029.1739] [Alpha ][ 0.133229] . ( 121 sec) [ -3029.1739] [Topology ] . ( 121 sec) [ -3029.1664] [Topology ] . ( 122 sec) [ -3029.1651] [Topology ] . ( 122 sec) [ -3029.1648] [Topology ] . ( 122 sec) [ -3029.1648] [GTR parameters ] . ( 122 sec) [ -3029.1647] [Alpha ][ 0.132864] . ( 122 sec) [ -3029.1647] [Topology ] . ( 123 sec) [ -3029.1645] [Topology ] . ( 123 sec) [ -3029.1645] [GTR parameters ] . ( 123 sec) [ -3029.1645] [Alpha ][ 0.132864] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3029.164548. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -3268.3123] [GTR parameters ] . ( 0 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 0 sec) [ -3255.0160] [Topology ] . ( 1 sec) [ -3235.7288] [Topology ] . ( 2 sec) [ -3225.5065] [Topology ] . ( 2 sec) [ -3221.9728] [Topology ] . ( 3 sec) [ -3221.2756] [Topology ] . ( 3 sec) [ -3221.1176] [Topology ] . ( 4 sec) [ -3221.0803] [Topology ] . ( 4 sec) [ -3221.0709] [Topology ] . ( 5 sec) [ -3221.0686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8 sec) [ -3111.9592] [GTR parameters ] . ( 9 sec) [ -3101.6790] [Alpha ][ 0.250961] . ( 9 sec) [ -3101.6790] [Topology ] . ( 9 sec) [ -3101.2469] [Topology ] . ( 9 sec) [ -3101.1951] [Topology ] . ( 10 sec) [ -3101.1835] [Topology ] . ( 10 sec) [ -3101.1807] [Topology ] . ( 11 sec) [ -3101.1800] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -3096.7030] [GTR parameters ] . ( 15 sec) [ -3094.6692] [Alpha ][ 0.159093] . ( 15 sec) [ -3094.6692] [Topology ] . ( 15 sec) [ -3094.6282] [Topology ] . ( 16 sec) [ -3094.6257] [Topology ] . ( 16 sec) [ -3094.6253] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -3089.9543] [GTR parameters ] . ( 20 sec) [ -3089.9515] [Alpha ][ 0.156168] . ( 20 sec) [ -3089.9515] [Topology ] . ( 20 sec) [ -3089.9489] [Topology ] . ( 21 sec) [ -3089.9485] [Topology ] . Checking for NNIs, optimizing five branches... . ( 24 sec) [ -3085.2057] [GTR parameters ] . ( 25 sec) [ -3085.2053] [Alpha ][ 0.154998] . ( 25 sec) [ -3085.2053] [Topology ] . ( 25 sec) [ -3085.2010] [Topology ] . ( 25 sec) [ -3085.2002] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -3080.3925] [GTR parameters ] . ( 29 sec) [ -3080.3922] [Alpha ][ 0.153972] . ( 29 sec) [ -3080.3922] [Topology ] . ( 30 sec) [ -3080.3863] [Topology ] . ( 30 sec) [ -3080.3852] [Topology ] . ( 31 sec) [ -3080.3848] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -3075.5240] [GTR parameters ] . ( 34 sec) [ -3075.5237] [Alpha ][ 0.152988] . ( 34 sec) [ -3075.5237] [Topology ] . ( 35 sec) [ -3075.5172] [Topology ] . ( 35 sec) [ -3075.5160] [Topology ] . ( 36 sec) [ -3075.5157] [Topology ] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -3039.0349] [GTR parameters ] . ( 40 sec) [ -3038.7796] [Alpha ][ 0.128324] . ( 40 sec) [ -3038.7796] [Topology ] . ( 41 sec) [ -3037.3507] [Topology ] . ( 41 sec) [ -3037.1439] [Topology ] . ( 42 sec) [ -3037.0788] [Topology ] . ( 42 sec) [ -3037.0592] [Topology ] . ( 42 sec) [ -3037.0539] [Topology ] . ( 43 sec) [ -3037.0525] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3036.9165] [GTR parameters ] . ( 47 sec) [ -3036.9104] [Alpha ][ 0.131591] . ( 47 sec) [ -3036.9104] [Topology ] . ( 48 sec) [ -3036.8963] [Topology ] . ( 48 sec) [ -3036.8936] [Topology ] . ( 49 sec) [ -3036.8929] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -3036.8920] [GTR parameters ] . ( 53 sec) [ -3036.8918] [Alpha ][ 0.132183] . ( 53 sec) [ -3036.8918] [Topology ] . ( 53 sec) [ -3036.8913] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -3036.8913] [GTR parameters ] . ( 57 sec) [ -3036.8913] [Alpha ][ 0.132315] . ( 57 sec) [ -3036.8913] [Topology ] . ( 57 sec) [ -3036.8912] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 64 sec) [ -3268.3123] [GTR parameters ] . ( 65 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 65 sec) [ -3254.2192] [ 285] [depth= 1] . ( 65 sec) [ -3254.0206] [ 285] [depth= 1] . ( 65 sec) [ -3249.8435] [ 287] [depth= 1] . ( 68 sec) [ -3249.7182] [ 287] [depth= 1] . ( 68 sec) [ -3249.6907] [ 287] [depth= 1] . ( 68 sec) [ -3249.6645] [ 287] [depth= 1] . ( 68 sec) [ -3249.5797] [ 287] [depth= 2] . ( 72 sec) [ -3249.5506] [ 287] [depth= 1] . ( 72 sec) [ -3249.4221] [ 287] [depth= 2] . ( 72 sec) [ -3249.0013] [ 287] [depth= 2] . ( 72 sec) [ -3244.7325] [ 287] [depth= 4] . ( 72 sec) [ -3244.2633] [ 287] [depth= 2] . ( 72 sec) [ -3243.7508] [ 287] [depth= 1] . ( 72 sec) [ -3243.7402] [ 287] [depth= 3] . ( 72 sec) [ -3237.5172] [ 286] [depth= 3] . ( 73 sec) [ -3236.8494] [ 286] [depth= 2] . ( 73 sec) [ -3236.8378] [ 286] [depth= 1] . ( 74 sec) [ -3236.7549] [ 286] [depth= 1] . ( 74 sec) [ -3236.2186] [ 286] [depth= 1] . ( 74 sec) [ -3236.1944] [ 286] [depth= 1] . ( 76 sec) [ -3235.2068] [ 286] [depth= 2] . ( 76 sec) [ -3232.8330] [ 286] [depth= 2] . ( 76 sec) [ -3232.8083] [ 286] [depth= 1] . ( 78 sec) [ -3232.7844] [ 286] [depth= 4] . ( 78 sec) [ -3232.7563] [ 286] [depth= 1] . ( 78 sec) [ -3232.7366] [ 286] [depth= 1] . ( 78 sec) [ -3232.5855] [ 286] [depth= 2] . ( 79 sec) [ -3232.4975] [ 286] [depth= 1] . ( 80 sec) [ -3232.4602] [ 286] [depth= 1] . ( 81 sec) [ -3232.4367] [ 286] [depth= 2] . ( 85 sec) [ -3232.4157] [ 286] [depth= 3] . ( 85 sec) [ -3232.2600] [ 286] [depth= 1] . ( 88 sec) [ -3232.1425] [ 286] [depth= 1] . ( 90 sec) [ -3231.3343] [ 286] [depth= 4] . ( 90 sec) [ -3230.5993] [ 286] [depth= 2] . ( 90 sec) [ -3230.5753] [ 286] [depth= 1] . ( 90 sec) [ -3230.4740] [ 286] [depth= 2] . ( 90 sec) [ -3230.4378] [ 286] [depth= 2] . ( 90 sec) [ -3229.9582] [ 286] [depth= 1] . ( 90 sec) [ -3229.7321] [ 286] [depth= 1] . ( 90 sec) [ -3229.6998] [ 286] [depth= 1] . ( 91 sec) [ -3229.6813] [ 286] [depth= 1] . ( 91 sec) [ -3229.5369] [ 286] [depth= 2] . ( 92 sec) [ -3229.5083] [ 286] [depth= 1] . ( 97 sec) [ -3218.7872] [Branch lengths ] . ( 98 sec) [ -3057.8348] [GTR parameters ] . ( 99 sec) [ -3044.6318] [Alpha ][ 0.250961] . ( 99 sec) [ -3044.0260] [ 284] [depth= 1] . ( 99 sec) [ -3043.7893] [ 286] [depth= 1] . ( 132 sec) [ -3042.3307] [ 286] [depth= 4] . ( 143 sec) [ -3039.5370] [Branch lengths ] . ( 144 sec) [ -3039.1025] [GTR parameters ] . ( 144 sec) [ -3034.3465] [Alpha ][ 0.133727] . ( 145 sec) [ -3034.3146] [ 288] [depth= 1] . ( 189 sec) [ -3033.9829] [Branch lengths ] . ( 190 sec) [ -3033.8365] [GTR parameters ] . ( 190 sec) [ -3033.8338] [Alpha ][ 0.131597] . ( 216 sec) [ -3033.8075] [Branch lengths ] . ( 216 sec) [ -3033.8075] [Topology ] . ( 217 sec) [ -3033.8064] [Topology ] . ( 217 sec) [ -3033.8062] [Topology ] . ( 218 sec) [ -3033.8053] [GTR parameters ] . ( 218 sec) [ -3033.8051] [Alpha ][ 0.132170] . ( 218 sec) [ -3033.8051] [Topology ] . ( 218 sec) [ -3033.8049] [Topology ] . ( 218 sec) [ -3033.8049] [GTR parameters ] . ( 218 sec) [ -3033.8049] [Alpha ][ 0.132170] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3036.891188 . Log likelihood obtained after SPR moves : -3033.804930 . Log likelihood of the current tree: -3033.804930. . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Best log likelihood : -3029.164548 . Time used 0h3m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1194.44user 0.00system 20:21.37elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps