.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2599_66x1137_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... . 131 patterns found. (out of a total of 1137 sites) . 1062 sites without polymorphism (93.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6600.0528] [GTR parameters ] . ( 0 sec) [ -6511.2300] [Alpha ][ 0.500960] . ( 1 sec) [ -6502.2704] [ 490] [depth= 3] . ( 1 sec) [ -6474.0429] [ 488] [depth= 2] . ( 1 sec) [ -6413.0670] [ 488] [depth= 1] . ( 1 sec) [ -6368.0485] [ 488] [depth= 3] . ( 1 sec) [ -6332.4066] [ 472] [depth= 4] . ( 1 sec) [ -6319.0546] [ 472] [depth= 1] . ( 1 sec) [ -6209.4574] [ 472] [depth= 6] . ( 1 sec) [ -6132.0068] [ 472] [depth= 3] . ( 1 sec) [ -6107.8181] [ 472] [depth= 4] . ( 1 sec) [ -6088.7917] [ 472] [depth= 9] . ( 1 sec) [ -6045.1366] [ 470] [depth= 7] . ( 1 sec) [ -5939.3863] [ 470] [depth= 6] . ( 1 sec) [ -5825.8782] [ 469] [depth= 17] . ( 1 sec) [ -5784.0121] [ 467] [depth= 10] . ( 1 sec) [ -5725.3227] [ 464] [depth= 19] . ( 1 sec) [ -5722.5255] [ 464] [depth= 2] . ( 1 sec) [ -5644.6276] [ 462] [depth= 11] . ( 1 sec) [ -5555.0330] [ 447] [depth= 13] . ( 1 sec) [ -5491.5809] [ 430] [depth= 1] . ( 1 sec) [ -5484.2694] [ 427] [depth= 10] . ( 1 sec) [ -5472.3188] [ 425] [depth= 8] . ( 1 sec) [ -5456.0623] [ 425] [depth= 16] . ( 1 sec) [ -5454.5171] [ 425] [depth= 16] . ( 1 sec) [ -5413.6387] [ 415] [depth= 7] . ( 1 sec) [ -5360.5418] [ 415] [depth= 1] . ( 1 sec) [ -5214.8720] [ 415] [depth= 2] . ( 1 sec) [ -5128.0844] [ 397] [depth= 9] . ( 1 sec) [ -5033.9475] [ 397] [depth= 6] . ( 1 sec) [ -5019.6748] [ 397] [depth= 1] . ( 1 sec) [ -5016.2098] [ 396] [depth= 5] . ( 1 sec) [ -5009.3961] [ 396] [depth= 1] . ( 1 sec) [ -5004.0976] [ 396] [depth= 7] . ( 1 sec) [ -5001.3131] [ 396] [depth= 1] . ( 1 sec) [ -4971.5300] [ 391] [depth= 3] . ( 1 sec) [ -4948.8501] [ 391] [depth= 1] . ( 1 sec) [ -4942.4483] [ 390] [depth= 6] . ( 1 sec) [ -4917.6990] [ 390] [depth= 19] . ( 1 sec) [ -4897.1794] [ 389] [depth= 1] . ( 1 sec) [ -4887.1011] [ 388] [depth= 5] . ( 1 sec) [ -4845.3833] [ 387] [depth= 20] . ( 1 sec) [ -4832.0960] [ 387] [depth= 6] . ( 1 sec) [ -4831.9972] [ 387] [depth= 4] . ( 1 sec) [ -4812.1858] [ 385] [depth= 5] . ( 1 sec) [ -4738.5090] [ 368] [depth= 12] . ( 2 sec) [ -4730.8310] [ 368] [depth= 6] . ( 2 sec) [ -4722.5056] [ 368] [depth= 12] . ( 2 sec) [ -4680.7902] [ 368] [depth= 6] . ( 2 sec) [ -4657.9710] [ 366] [depth= 10] . ( 2 sec) [ -4626.8296] [ 366] [depth= 2] . ( 2 sec) [ -4551.8807] [ 349] [depth= 8] . ( 2 sec) [ -4537.7154] [ 349] [depth= 1] . ( 2 sec) [ -4537.6657] [ 349] [depth= 1] . ( 2 sec) [ -4536.4706] [ 349] [depth= 8] . ( 2 sec) [ -4532.4704] [ 348] [depth= 7] . ( 2 sec) [ -4517.9996] [ 346] [depth= 8] . ( 2 sec) [ -4508.8280] [ 344] [depth= 1] . ( 2 sec) [ -4486.6584] [ 344] [depth= 6] . ( 2 sec) [ -4469.1949] [ 344] [depth= 12] . ( 2 sec) [ -4336.3541] [ 344] [depth= 4] . ( 2 sec) [ -4242.8000] [ 342] [depth= 3] . ( 2 sec) [ -4240.9831] [ 342] [depth= 2] . ( 2 sec) [ -4240.9556] [ 342] [depth= 1] . ( 2 sec) [ -4232.1624] [ 340] [depth= 15] . ( 2 sec) [ -4142.1199] [ 321] [depth= 10] . ( 2 sec) [ -4135.7923] [ 320] [depth= 10] . ( 2 sec) [ -4101.3576] [ 319] [depth= 11] . ( 2 sec) [ -4099.9079] [ 319] [depth= 1] . ( 2 sec) [ -4099.8722] [ 319] [depth= 2] . ( 2 sec) [ -4093.0745] [ 318] [depth= 13] . ( 2 sec) [ -4090.2827] [ 318] [depth= 1] . ( 2 sec) [ -4085.4795] [ 318] [depth= 15] . ( 2 sec) [ -4081.9316] [ 318] [depth= 7] . ( 2 sec) [ -4081.0080] [ 318] [depth= 15] . ( 2 sec) [ -4078.7877] [ 318] [depth= 14] . ( 2 sec) [ -4071.3603] [ 317] [depth= 6] . ( 2 sec) [ -3989.0506] [ 300] [depth= 8] . ( 2 sec) [ -3910.7467] [ 284] [depth= 7] . ( 2 sec) [ -3901.7432] [ 276] [depth= 10] . ( 2 sec) [ -3901.3314] [ 276] [depth= 15] . ( 2 sec) [ -3809.2951] [ 276] [depth= 4] . ( 2 sec) [ -3674.4107] [ 276] [depth= 3] . ( 2 sec) [ -3477.0257] [ 263] [depth= 14] . ( 2 sec) [ -3467.2266] [ 263] [depth= 15] . ( 2 sec) [ -3465.9302] [ 263] [depth= 15] . ( 2 sec) [ -3407.9509] [ 251] [depth= 1] . ( 2 sec) [ -3396.2178] [ 247] [depth= 2] . ( 2 sec) [ -3351.8140] [ 243] [depth= 1] . ( 3 sec) [ -3349.1652] [ 243] [depth= 16] . ( 3 sec) [ -3265.7310] [ 248] [depth= 7] . ( 3 sec) [ -3230.8181] [ 241] [depth= 2] . ( 3 sec) [ -3229.3123] [ 241] [depth= 17] . ( 3 sec) [ -3223.2141] [ 241] [depth= 5] . ( 3 sec) [ -3222.8899] [ 241] [depth= 3] . ( 3 sec) [ -3222.8101] [ 241] [depth= 1] . ( 3 sec) [ -3220.7335] [ 241] [depth= 13] . ( 3 sec) [ -3139.3339] [ 225] [depth= 7] . ( 3 sec) [ -3138.1307] [ 225] [depth= 1] . ( 3 sec) [ -3128.3660] [ 225] [depth= 1] . ( 3 sec) [ -3113.5867] [ 225] [depth= 1] . ( 3 sec) [ -3080.8424] [ 225] [depth= 4] . ( 3 sec) [ -3076.3833] [ 225] [depth= 2] . ( 3 sec) [ -3047.8418] [ 217] [depth= 17] . ( 3 sec) [ -3044.8656] [ 217] [depth= 17] . ( 3 sec) [ -2962.7239] [ 199] [depth= 16] . ( 3 sec) [ -2959.9711] [ 199] [depth= 2] . ( 3 sec) [ -2954.9277] [ 198] [depth= 5] . ( 3 sec) [ -2836.8026] [ 198] [depth= 10] . ( 3 sec) [ -2822.1192] [ 198] [depth= 9] . ( 3 sec) [ -2820.2386] [ 198] [depth= 1] . ( 3 sec) [ -2818.3140] [ 198] [depth= 10] . ( 3 sec) [ -2801.3499] [ 196] [depth= 16] . ( 3 sec) [ -2783.4069] [ 195] [depth= 17] . ( 3 sec) [ -2783.2400] [ 195] [depth= 4] . ( 3 sec) [ -2777.6356] [ 194] [depth= 4] . ( 3 sec) [ -2769.2374] [ 193] [depth= 12] . ( 3 sec) [ -2768.6551] [ 191] [depth= 3] . ( 3 sec) [ -2767.8720] [ 191] [depth= 1] . ( 3 sec) [ -2767.7722] [ 191] [depth= 4] . ( 3 sec) [ -2765.0121] [ 191] [depth= 1] . ( 3 sec) [ -2764.8034] [ 191] [depth= 4] . ( 3 sec) [ -2762.6168] [ 190] [depth= 7] . ( 3 sec) [ -2761.7653] [ 190] [depth= 1] . ( 3 sec) [ -2761.5983] [ 190] [depth= 17] . ( 3 sec) [ -2761.5663] [ 190] [depth= 1] . ( 3 sec) [ -2761.3429] [ 190] [depth= 8] . ( 4 sec) [ -2756.4253] [ 190] [depth= 2] . ( 4 sec) [ -2753.5827] [ 190] [depth= 5] . ( 4 sec) [ -2752.8542] [ 190] [depth= 3] . ( 4 sec) [ -2752.5699] [ 190] [depth= 1] . ( 4 sec) [ -2751.8217] [ 190] [depth= 4] . ( 4 sec) [ -2664.6290] [ 172] [depth= 12] . ( 4 sec) [ -2656.6610] [ 172] [depth= 5] . ( 4 sec) [ -2649.6984] [ 171] [depth= 17] . ( 4 sec) [ -2649.5804] [ 171] [depth= 1] . ( 4 sec) [ -2649.1378] [ 171] [depth= 17] . ( 4 sec) [ -2641.9602] [ 171] [depth= 16] . ( 4 sec) [ -2629.0868] [ 171] [depth= 4] . ( 4 sec) [ -2628.9439] [ 171] [depth= 1] . ( 4 sec) [ -2628.8677] [ 171] [depth= 5] . ( 4 sec) [ -2623.0598] [ 152] [depth= 8] . ( 4 sec) [ -2622.3139] [ 152] [depth= 1] . ( 4 sec) [ -2622.1891] [ 152] [depth= 7] . ( 4 sec) [ -2618.1276] [ 151] [depth= 6] . ( 4 sec) [ -2613.3645] [ 151] [depth= 2] . ( 4 sec) [ -2611.3837] [ 151] [depth= 5] . ( 4 sec) [ -2609.7111] [ 151] [depth= 1] . ( 4 sec) [ -2609.6957] [ 151] [depth= 4] . ( 4 sec) [ -2603.8001] [ 150] [depth= 10] . ( 4 sec) [ -2603.7066] [ 150] [depth= 4] . ( 4 sec) [ -2539.3939] [ 134] [depth= 4] . ( 4 sec) [ -2538.9194] [ 134] [depth= 2] . ( 4 sec) [ -2527.1895] [ 132] [depth= 5] . ( 4 sec) [ -2525.6475] [ 132] [depth= 1] . ( 4 sec) [ -2525.6198] [ 132] [depth= 2] . ( 4 sec) [ -2453.1120] [ 132] [depth= 10] . ( 5 sec) [ -2453.0475] [ 132] [depth= 1] . ( 5 sec) [ -2453.0284] [ 132] [depth= 2] . ( 5 sec) [ -2452.7290] [ 132] [depth= 3] . ( 5 sec) [ -2452.6581] [ 132] [depth= 2] . ( 5 sec) [ -2452.5296] [ 132] [depth= 5] . ( 5 sec) [ -2452.5114] [ 132] [depth= 1] . ( 5 sec) [ -2452.2577] [ 132] [depth= 5] . ( 5 sec) [ -2431.3615] [Branch lengths ] . ( 5 sec) [ -2400.7962] [GTR parameters ] . ( 5 sec) [ -2387.5539] [Alpha ][ 0.250961] . ( 11 sec) [ -2352.0054] [ 120] [depth= 8] . ( 12 sec) [ -2321.6262] [ 112] [depth= 10] . ( 14 sec) [ -2313.4051] [ 111] [depth= 10] . ( 14 sec) [ -2313.3505] [ 111] [depth= 2] . ( 15 sec) [ -2237.5178] [ 93] [depth= 4] . ( 15 sec) [ -2237.4033] [ 93] [depth= 1] . ( 16 sec) [ -2236.1130] [ 95] [depth= 7] . ( 16 sec) [ -2236.1002] [ 95] [depth= 1] . ( 17 sec) [ -2233.8826] [ 95] [depth= 1] . ( 19 sec) [ -2233.8627] [ 95] [depth= 6] . ( 20 sec) [ -2227.2814] [ 94] [depth= 8] . ( 20 sec) [ -2222.5186] [ 93] [depth= 3] . ( 20 sec) [ -2215.3149] [ 92] [depth= 5] . ( 20 sec) [ -2215.2097] [ 92] [depth= 9] . ( 23 sec) [ -2215.1370] [ 92] [depth= 3] . ( 24 sec) [ -2215.0598] [ 92] [depth= 2] . ( 25 sec) [ -2209.6745] [ 91] [depth= 3] . ( 25 sec) [ -2202.9787] [ 90] [depth= 3] . ( 25 sec) [ -2202.9637] [ 90] [depth= 1] . ( 25 sec) [ -2202.9487] [ 90] [depth= 1] . ( 27 sec) [ -2202.5279] [ 90] [depth= 4] . ( 27 sec) [ -2202.4758] [ 90] [depth= 4] . ( 29 sec) [ -2177.7609] [ 83] [depth= 10] . ( 29 sec) [ -2177.5859] [ 83] [depth= 2] . ( 30 sec) [ -2177.5546] [ 83] [depth= 2] . ( 31 sec) [ -2177.3981] [ 82] [depth= 8] . ( 31 sec) [ -2177.1383] [ 82] [depth= 1] . ( 32 sec) [ -2176.9307] [ 82] [depth= 2] . ( 33 sec) [ -2176.8841] [ 82] [depth= 4] . ( 34 sec) [ -2176.8138] [ 82] [depth= 3] . ( 35 sec) [ -2176.7191] [ 82] [depth= 1] . ( 37 sec) [ -2176.6681] [ 82] [depth= 1] . ( 37 sec) [ -2176.5948] [ 82] [depth= 1] . ( 39 sec) [ -2176.5790] [ 82] [depth= 2] . ( 39 sec) [ -2165.8210] [ 80] [depth= 10] . ( 39 sec) [ -2165.8092] [ 80] [depth= 1] . ( 40 sec) [ -2165.5406] [Branch lengths ] . ( 40 sec) [ -2164.1896] [GTR parameters ] . ( 40 sec) [ -2163.5814] [Alpha ][ 0.501328] . ( 85 sec) [ -2163.5785] [Branch lengths ] . ( 103 sec) [ -2163.5785] [Branch lengths ] . ( 103 sec) [ -2163.5785] [Topology ] . ( 104 sec) [ -2163.5785] [Topology ] . ( 104 sec) [ -2163.5759] [GTR parameters ] . ( 104 sec) [ -2163.4889] [Alpha ][ 0.756764] . ( 104 sec) [ -2163.4889] [Topology ] . ( 104 sec) [ -2163.4888] [Topology ] . ( 104 sec) [ -2163.4883] [GTR parameters ] . ( 104 sec) [ -2163.4883] [Alpha ][ 0.758968] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.488324. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6863.0441] [GTR parameters ] . ( 0 sec) [ -6781.8250] [Alpha ][ 0.500960] . ( 0 sec) [ -6775.2629] [ 414] [depth= 8] . ( 1 sec) [ -6732.6911] [ 413] [depth= 8] . ( 1 sec) [ -6631.0194] [ 418] [depth= 1] . ( 1 sec) [ -6477.6335] [ 413] [depth= 3] . ( 1 sec) [ -6467.7681] [ 412] [depth= 2] . ( 1 sec) [ -6293.5804] [ 412] [depth= 3] . ( 1 sec) [ -6216.0572] [ 401] [depth= 1] . ( 1 sec) [ -5989.9315] [ 401] [depth= 3] . ( 1 sec) [ -5967.4451] [ 396] [depth= 1] . ( 1 sec) [ -5729.6307] [ 395] [depth= 8] . ( 1 sec) [ -5664.2996] [ 394] [depth= 2] . ( 1 sec) [ -5539.9838] [ 394] [depth= 5] . ( 1 sec) [ -5525.2610] [ 381] [depth= 4] . ( 1 sec) [ -5519.8122] [ 381] [depth= 1] . ( 1 sec) [ -5508.5790] [ 381] [depth= 6] . ( 1 sec) [ -5508.0822] [ 381] [depth= 2] . ( 1 sec) [ -5480.9565] [ 380] [depth= 1] . ( 1 sec) [ -5358.0982] [ 377] [depth= 8] . ( 1 sec) [ -5357.8928] [ 377] [depth= 4] . ( 1 sec) [ -5355.8929] [ 377] [depth= 3] . ( 1 sec) [ -5315.2562] [ 375] [depth= 2] . ( 1 sec) [ -5187.9753] [ 375] [depth= 1] . ( 1 sec) [ -5157.0050] [ 375] [depth= 4] . ( 1 sec) [ -5093.6206] [ 375] [depth= 1] . ( 1 sec) [ -5056.6179] [ 375] [depth= 2] . ( 1 sec) [ -5055.5621] [ 375] [depth= 1] . ( 1 sec) [ -5047.1949] [ 373] [depth= 9] . ( 1 sec) [ -4957.6658] [ 353] [depth= 14] . ( 1 sec) [ -4823.9986] [ 337] [depth= 11] . ( 1 sec) [ -4823.3309] [ 337] [depth= 1] . ( 1 sec) [ -4818.7631] [ 337] [depth= 1] . ( 1 sec) [ -4777.7453] [ 334] [depth= 3] . ( 1 sec) [ -4764.5326] [ 334] [depth= 1] . ( 1 sec) [ -4760.6423] [ 334] [depth= 1] . ( 1 sec) [ -4755.3983] [ 334] [depth= 1] . ( 1 sec) [ -4754.0820] [ 333] [depth= 9] . ( 1 sec) [ -4426.3138] [ 333] [depth= 2] . ( 1 sec) [ -4419.4034] [ 333] [depth= 3] . ( 1 sec) [ -4398.2564] [ 333] [depth= 4] . ( 1 sec) [ -4379.3646] [ 330] [depth= 4] . ( 1 sec) [ -4347.7211] [ 329] [depth= 2] . ( 1 sec) [ -4347.0796] [ 329] [depth= 2] . ( 1 sec) [ -4305.9259] [ 328] [depth= 3] . ( 1 sec) [ -4225.7522] [ 311] [depth= 5] . ( 1 sec) [ -4218.6267] [ 310] [depth= 7] . ( 2 sec) [ -4196.8423] [ 308] [depth= 3] . ( 2 sec) [ -4182.4954] [ 306] [depth= 2] . ( 2 sec) [ -4182.1694] [ 306] [depth= 19] . ( 2 sec) [ -4182.0511] [ 306] [depth= 6] . ( 2 sec) [ -4181.7598] [ 306] [depth= 1] . ( 2 sec) [ -4156.4263] [ 302] [depth= 18] . ( 2 sec) [ -4156.2930] [ 302] [depth= 2] . ( 2 sec) [ -4149.1145] [ 302] [depth= 1] . ( 2 sec) [ -4141.2253] [ 301] [depth= 4] . ( 2 sec) [ -4141.1383] [ 301] [depth= 3] . ( 2 sec) [ -4140.6536] [ 301] [depth= 1] . ( 2 sec) [ -4127.4433] [ 299] [depth= 17] . ( 2 sec) [ -4044.0051] [ 281] [depth= 6] . ( 2 sec) [ -4042.8047] [ 281] [depth= 2] . ( 2 sec) [ -4042.5854] [ 281] [depth= 20] . ( 2 sec) [ -4040.3397] [ 281] [depth= 1] . ( 2 sec) [ -4029.0962] [ 281] [depth= 1] . ( 2 sec) [ -3869.4999] [ 266] [depth= 4] . ( 2 sec) [ -3739.0956] [ 266] [depth= 1] . ( 2 sec) [ -3720.1075] [ 265] [depth= 20] . ( 2 sec) [ -3670.9052] [ 265] [depth= 19] . ( 2 sec) [ -3646.0420] [ 263] [depth= 4] . ( 2 sec) [ -3644.1459] [ 263] [depth= 8] . ( 2 sec) [ -3640.7691] [ 263] [depth= 2] . ( 2 sec) [ -3640.6763] [ 263] [depth= 2] . ( 2 sec) [ -3640.6449] [ 263] [depth= 2] . ( 2 sec) [ -3640.3835] [ 263] [depth= 19] . ( 2 sec) [ -3638.4906] [ 263] [depth= 10] . ( 2 sec) [ -3638.4161] [ 263] [depth= 1] . ( 2 sec) [ -3638.3430] [ 263] [depth= 9] . ( 2 sec) [ -3557.9705] [ 246] [depth= 4] . ( 2 sec) [ -3554.8633] [ 246] [depth= 3] . ( 2 sec) [ -3553.1408] [ 246] [depth= 3] . ( 2 sec) [ -3552.3207] [ 246] [depth= 17] . ( 2 sec) [ -3550.5006] [ 246] [depth= 1] . ( 2 sec) [ -3549.8114] [ 245] [depth= 8] . ( 3 sec) [ -3392.7885] [ 245] [depth= 12] . ( 3 sec) [ -3310.1301] [ 243] [depth= 18] . ( 3 sec) [ -3301.9745] [ 242] [depth= 13] . ( 3 sec) [ -3295.9953] [ 242] [depth= 2] . ( 3 sec) [ -3263.4440] [ 238] [depth= 18] . ( 3 sec) [ -3192.4790] [ 221] [depth= 3] . ( 3 sec) [ -3192.4237] [ 221] [depth= 17] . ( 3 sec) [ -3192.3080] [ 221] [depth= 10] . ( 3 sec) [ -3189.7648] [ 221] [depth= 22] . ( 3 sec) [ -3189.1874] [ 220] [depth= 8] . ( 3 sec) [ -3188.2769] [ 220] [depth= 2] . ( 3 sec) [ -3183.0536] [ 220] [depth= 2] . ( 3 sec) [ -3179.5512] [ 219] [depth= 2] . ( 3 sec) [ -3179.3698] [ 219] [depth= 2] . ( 3 sec) [ -3134.6728] [ 219] [depth= 9] . ( 3 sec) [ -3134.6588] [ 219] [depth= 15] . ( 3 sec) [ -3127.9350] [ 218] [depth= 9] . ( 3 sec) [ -3120.2841] [ 217] [depth= 9] . ( 3 sec) [ -3120.1738] [ 217] [depth= 2] . ( 3 sec) [ -3119.8552] [ 217] [depth= 16] . ( 3 sec) [ -3119.8413] [ 217] [depth= 14] . ( 3 sec) [ -3119.7341] [ 217] [depth= 2] . ( 3 sec) [ -3119.6603] [ 217] [depth= 1] . ( 3 sec) [ -3108.3909] [ 214] [depth= 19] . ( 3 sec) [ -3108.3568] [ 214] [depth= 3] . ( 3 sec) [ -3107.4933] [ 214] [depth= 13] . ( 3 sec) [ -3104.1711] [ 214] [depth= 3] . ( 3 sec) [ -3104.0276] [ 214] [depth= 2] . ( 3 sec) [ -3085.9108] [ 214] [depth= 5] . ( 3 sec) [ -3085.7071] [ 214] [depth= 9] . ( 4 sec) [ -3022.9280] [ 214] [depth= 5] . ( 4 sec) [ -3022.7459] [ 214] [depth= 1] . ( 4 sec) [ -3010.0429] [ 211] [depth= 12] . ( 4 sec) [ -3009.3351] [ 211] [depth= 16] . ( 4 sec) [ -2910.3116] [ 201] [depth= 7] . ( 4 sec) [ -2884.8440] [ 201] [depth= 5] . ( 4 sec) [ -2881.2814] [ 201] [depth= 16] . ( 4 sec) [ -2881.2588] [ 201] [depth= 3] . ( 4 sec) [ -2881.1873] [ 201] [depth= 1] . ( 4 sec) [ -2881.0202] [ 201] [depth= 2] . ( 4 sec) [ -2880.9426] [ 201] [depth= 2] . ( 4 sec) [ -2880.7538] [ 201] [depth= 4] . ( 4 sec) [ -2871.3104] [ 198] [depth= 2] . ( 4 sec) [ -2790.0072] [ 182] [depth= 8] . ( 4 sec) [ -2789.5051] [ 180] [depth= 4] . ( 4 sec) [ -2779.3563] [ 163] [depth= 3] . ( 4 sec) [ -2772.1714] [ 162] [depth= 8] . ( 4 sec) [ -2772.1174] [ 162] [depth= 2] . ( 4 sec) [ -2738.2379] [ 156] [depth= 2] . ( 4 sec) [ -2732.0532] [ 155] [depth= 20] . ( 4 sec) [ -2659.2010] [ 140] [depth= 2] . ( 4 sec) [ -2658.5323] [ 140] [depth= 8] . ( 4 sec) [ -2647.1002] [ 135] [depth= 1] . ( 4 sec) [ -2600.4187] [ 135] [depth= 3] . ( 4 sec) [ -2585.8159] [ 135] [depth= 7] . ( 4 sec) [ -2559.7509] [ 133] [depth= 11] . ( 4 sec) [ -2552.1525] [ 133] [depth= 7] . ( 4 sec) [ -2544.2879] [ 133] [depth= 5] . ( 4 sec) [ -2544.2529] [ 133] [depth= 5] . ( 4 sec) [ -2529.6572] [ 131] [depth= 9] . ( 4 sec) [ -2527.5225] [ 131] [depth= 3] . ( 4 sec) [ -2527.3845] [ 131] [depth= 3] . ( 4 sec) [ -2525.2848] [ 131] [depth= 3] . ( 4 sec) [ -2525.2418] [ 131] [depth= 5] . ( 4 sec) [ -2519.2929] [ 131] [depth= 1] . ( 4 sec) [ -2514.1713] [ 131] [depth= 5] . ( 5 sec) [ -2512.7744] [ 131] [depth= 9] . ( 5 sec) [ -2511.9667] [ 131] [depth= 2] . ( 5 sec) [ -2511.9183] [ 131] [depth= 3] . ( 5 sec) [ -2504.4713] [ 130] [depth= 17] . ( 5 sec) [ -2472.6665] [ 123] [depth= 4] . ( 5 sec) [ -2466.7048] [ 123] [depth= 2] . ( 5 sec) [ -2466.6042] [ 123] [depth= 6] . ( 5 sec) [ -2438.0526] [ 121] [depth= 6] . ( 5 sec) [ -2411.6111] [ 116] [depth= 10] . ( 5 sec) [ -2411.0990] [ 116] [depth= 7] . ( 5 sec) [ -2411.0442] [ 116] [depth= 7] . ( 5 sec) [ -2410.4427] [ 116] [depth= 2] . ( 5 sec) [ -2404.6790] [ 115] [depth= 2] . ( 5 sec) [ -2388.7067] [ 115] [depth= 5] . ( 5 sec) [ -2383.9341] [ 114] [depth= 3] . ( 5 sec) [ -2383.7050] [ 114] [depth= 3] . ( 5 sec) [ -2377.1627] [ 113] [depth= 3] . ( 5 sec) [ -2377.0167] [ 113] [depth= 4] . ( 5 sec) [ -2376.9581] [ 113] [depth= 1] . ( 5 sec) [ -2376.9327] [ 113] [depth= 2] . ( 5 sec) [ -2376.1738] [ 113] [depth= 6] . ( 5 sec) [ -2375.1520] [ 113] [depth= 1] . ( 6 sec) [ -2375.0322] [ 113] [depth= 6] . ( 6 sec) [ -2353.6546] [Branch lengths ] . ( 6 sec) [ -2336.0995] [GTR parameters ] . ( 6 sec) [ -2327.6701] [Alpha ][ 0.250961] . ( 7 sec) [ -2299.4625] [ 104] [depth= 9] . ( 7 sec) [ -2264.7373] [ 97] [depth= 8] . ( 7 sec) [ -2251.0656] [ 97] [depth= 1] . ( 9 sec) [ -2239.7951] [ 95] [depth= 4] . ( 9 sec) [ -2232.8275] [ 94] [depth= 12] . ( 9 sec) [ -2225.1246] [ 93] [depth= 9] . ( 9 sec) [ -2225.0776] [ 93] [depth= 2] . ( 10 sec) [ -2224.9720] [ 93] [depth= 3] . ( 11 sec) [ -2224.3412] [ 92] [depth= 6] . ( 11 sec) [ -2217.5330] [ 92] [depth= 2] . ( 11 sec) [ -2217.4436] [ 92] [depth= 3] . ( 12 sec) [ -2217.2505] [ 92] [depth= 5] . ( 12 sec) [ -2217.1456] [ 92] [depth= 2] . ( 12 sec) [ -2217.0883] [ 92] [depth= 3] . ( 13 sec) [ -2217.0416] [ 92] [depth= 1] . ( 13 sec) [ -2217.0304] [ 92] [depth= 7] . ( 14 sec) [ -2217.0092] [ 92] [depth= 1] . ( 16 sec) [ -2203.5620] [ 90] [depth= 3] . ( 20 sec) [ -2203.4592] [ 90] [depth= 5] . ( 21 sec) [ -2203.2834] [ 90] [depth= 2] . ( 21 sec) [ -2196.8220] [ 89] [depth= 10] . ( 24 sec) [ -2196.7077] [ 89] [depth= 3] . ( 24 sec) [ -2196.6714] [ 89] [depth= 1] . ( 27 sec) [ -2196.6577] [ 89] [depth= 3] . ( 29 sec) [ -2196.6465] [ 89] [depth= 5] . ( 31 sec) [ -2166.6836] [ 80] [depth= 1] . ( 35 sec) [ -2166.5141] [ 80] [depth= 1] . ( 39 sec) [ -2166.4840] [ 80] [depth= 1] . ( 43 sec) [ -2166.4079] [Branch lengths ] . ( 43 sec) [ -2164.1883] [GTR parameters ] . ( 44 sec) [ -2163.5795] [Alpha ][ 0.501341] . ( 88 sec) [ -2163.5781] [Branch lengths ] . ( 107 sec) [ -2163.5781] [Branch lengths ] . ( 107 sec) [ -2163.5781] [Topology ] . ( 107 sec) [ -2163.5781] [Topology ] . ( 107 sec) [ -2163.5758] [GTR parameters ] . ( 107 sec) [ -2163.4889] [Alpha ][ 0.756732] . ( 107 sec) [ -2163.4889] [Topology ] . ( 107 sec) [ -2163.4888] [Topology ] . ( 107 sec) [ -2163.4883] [GTR parameters ] . ( 108 sec) [ -2163.4883] [Alpha ][ 0.758946] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.488323. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8048.9510] [GTR parameters ] . ( 1 sec) [ -7948.4806] [Alpha ][ 0.500960] . ( 1 sec) [ -7835.0819] [ 514] [depth= 5] . ( 1 sec) [ -7632.9259] [ 513] [depth= 4] . ( 1 sec) [ -7627.5243] [ 513] [depth= 2] . ( 1 sec) [ -7544.6476] [ 512] [depth= 6] . ( 1 sec) [ -7544.4862] [ 512] [depth= 3] . ( 1 sec) [ -7450.6981] [ 512] [depth= 5] . ( 1 sec) [ -7331.8950] [ 512] [depth= 3] . ( 1 sec) [ -7275.0835] [ 502] [depth= 1] . ( 1 sec) [ -7240.1398] [ 501] [depth= 13] . ( 1 sec) [ -7034.5148] [ 501] [depth= 2] . ( 1 sec) [ -6995.2962] [ 501] [depth= 4] . ( 1 sec) [ -6974.3397] [ 490] [depth= 7] . ( 1 sec) [ -6971.4114] [ 490] [depth= 4] . ( 1 sec) [ -6896.7333] [ 474] [depth= 12] . ( 1 sec) [ -6879.3188] [ 474] [depth= 1] . ( 1 sec) [ -6747.2286] [ 473] [depth= 2] . ( 1 sec) [ -6641.6517] [ 473] [depth= 6] . ( 1 sec) [ -6562.7022] [ 472] [depth= 12] . ( 1 sec) [ -6558.7117] [ 472] [depth= 1] . ( 1 sec) [ -6396.3157] [ 472] [depth= 1] . ( 1 sec) [ -6333.5139] [ 472] [depth= 3] . ( 1 sec) [ -6202.4715] [ 465] [depth= 15] . ( 1 sec) [ -6200.9222] [ 465] [depth= 3] . ( 1 sec) [ -6164.5581] [ 465] [depth= 3] . ( 1 sec) [ -6156.9239] [ 465] [depth= 5] . ( 1 sec) [ -6155.8794] [ 465] [depth= 1] . ( 1 sec) [ -6070.5274] [ 446] [depth= 4] . ( 1 sec) [ -6066.1319] [ 446] [depth= 8] . ( 1 sec) [ -6066.1087] [ 446] [depth= 4] . ( 1 sec) [ -5899.5976] [ 445] [depth= 27] . ( 1 sec) [ -5871.2079] [ 435] [depth= 13] . ( 2 sec) [ -5858.0064] [ 434] [depth= 2] . ( 2 sec) [ -5808.8317] [ 418] [depth= 4] . ( 2 sec) [ -5797.2130] [ 418] [depth= 2] . ( 2 sec) [ -5769.0987] [ 418] [depth= 7] . ( 2 sec) [ -5749.7981] [ 417] [depth= 1] . ( 2 sec) [ -5742.6506] [ 416] [depth= 6] . ( 2 sec) [ -5658.5910] [ 412] [depth= 26] . ( 2 sec) [ -5546.2284] [ 412] [depth= 8] . ( 2 sec) [ -5541.2969] [ 412] [depth= 6] . ( 2 sec) [ -5527.2752] [ 410] [depth= 1] . ( 2 sec) [ -5512.8896] [ 410] [depth= 2] . ( 2 sec) [ -5499.4349] [ 410] [depth= 5] . ( 2 sec) [ -5467.3002] [ 411] [depth= 1] . ( 2 sec) [ -5374.8646] [ 391] [depth= 7] . ( 2 sec) [ -5356.3438] [ 384] [depth= 5] . ( 2 sec) [ -5328.2967] [ 384] [depth= 10] . ( 2 sec) [ -5318.0969] [ 383] [depth= 10] . ( 2 sec) [ -5234.9126] [ 383] [depth= 10] . ( 2 sec) [ -4952.2673] [ 366] [depth= 1] . ( 2 sec) [ -4897.3359] [ 366] [depth= 4] . ( 2 sec) [ -4870.2116] [ 383] [depth= 1] . ( 2 sec) [ -4791.4111] [ 366] [depth= 1] . ( 2 sec) [ -4773.5551] [ 365] [depth= 10] . ( 2 sec) [ -4733.0235] [ 364] [depth= 9] . ( 2 sec) [ -4668.8199] [ 363] [depth= 8] . ( 2 sec) [ -4664.9433] [ 363] [depth= 1] . ( 2 sec) [ -4620.3383] [ 366] [depth= 2] . ( 2 sec) [ -4596.9665] [ 363] [depth= 5] . ( 2 sec) [ -4470.6288] [ 363] [depth= 4] . ( 2 sec) [ -4463.6660] [ 360] [depth= 1] . ( 2 sec) [ -4373.1127] [ 343] [depth= 14] . ( 2 sec) [ -4363.1498] [ 342] [depth= 9] . ( 2 sec) [ -4346.2611] [ 341] [depth= 25] . ( 2 sec) [ -4259.0167] [ 330] [depth= 13] . ( 2 sec) [ -4258.4609] [ 330] [depth= 1] . ( 3 sec) [ -4258.1833] [ 330] [depth= 1] . ( 3 sec) [ -4257.5940] [ 330] [depth= 1] . ( 3 sec) [ -4257.3405] [ 330] [depth= 2] . ( 3 sec) [ -4256.7599] [ 330] [depth= 17] . ( 3 sec) [ -4255.7945] [ 330] [depth= 2] . ( 3 sec) [ -4168.4007] [ 310] [depth= 7] . ( 3 sec) [ -4155.7160] [ 308] [depth= 18] . ( 3 sec) [ -4147.7688] [ 307] [depth= 22] . ( 3 sec) [ -3904.7694] [ 305] [depth= 6] . ( 3 sec) [ -3878.2831] [ 296] [depth= 13] . ( 3 sec) [ -3859.5776] [ 293] [depth= 18] . ( 3 sec) [ -3702.8109] [ 293] [depth= 1] . ( 3 sec) [ -3702.0097] [ 293] [depth= 15] . ( 3 sec) [ -3692.0383] [ 293] [depth= 13] . ( 3 sec) [ -3683.6852] [ 296] [depth= 3] . ( 3 sec) [ -3648.1284] [ 293] [depth= 12] . ( 3 sec) [ -3647.4064] [ 293] [depth= 2] . ( 3 sec) [ -3587.2461] [ 278] [depth= 2] . ( 3 sec) [ -3576.7535] [ 279] [depth= 3] . ( 3 sec) [ -3572.9798] [ 277] [depth= 14] . ( 3 sec) [ -3568.6054] [ 277] [depth= 5] . ( 3 sec) [ -3544.8839] [ 277] [depth= 3] . ( 3 sec) [ -3533.0404] [ 277] [depth= 10] . ( 3 sec) [ -3529.6010] [ 276] [depth= 2] . ( 3 sec) [ -3446.8397] [ 258] [depth= 9] . ( 3 sec) [ -3434.1116] [ 255] [depth= 7] . ( 3 sec) [ -3426.6125] [ 254] [depth= 18] . ( 3 sec) [ -3419.6363] [ 253] [depth= 5] . ( 3 sec) [ -3415.8988] [ 253] [depth= 5] . ( 3 sec) [ -3393.8935] [ 253] [depth= 5] . ( 3 sec) [ -3365.1634] [ 271] [depth= 1] . ( 3 sec) [ -3284.2746] [ 253] [depth= 1] . ( 3 sec) [ -3274.8423] [ 253] [depth= 2] . ( 3 sec) [ -3271.6174] [ 253] [depth= 6] . ( 4 sec) [ -3198.4541] [ 252] [depth= 7] . ( 4 sec) [ -3189.5638] [ 253] [depth= 19] . ( 4 sec) [ -3189.2275] [ 253] [depth= 16] . ( 4 sec) [ -3189.0625] [ 253] [depth= 17] . ( 4 sec) [ -3120.8297] [ 239] [depth= 2] . ( 4 sec) [ -3095.8274] [ 222] [depth= 3] . ( 4 sec) [ -3087.4572] [ 222] [depth= 3] . ( 4 sec) [ -3086.7312] [ 222] [depth= 9] . ( 4 sec) [ -3056.7915] [ 221] [depth= 10] . ( 4 sec) [ -2951.5336] [ 204] [depth= 7] . ( 4 sec) [ -2950.0377] [ 203] [depth= 10] . ( 4 sec) [ -2936.2574] [ 203] [depth= 1] . ( 4 sec) [ -2936.2468] [ 203] [depth= 30] . ( 4 sec) [ -2934.1451] [ 203] [depth= 14] . ( 4 sec) [ -2933.1426] [ 203] [depth= 23] . ( 4 sec) [ -2930.1483] [ 203] [depth= 27] . ( 4 sec) [ -2928.7345] [ 203] [depth= 8] . ( 4 sec) [ -2928.2983] [ 203] [depth= 3] . ( 4 sec) [ -2918.7140] [ 202] [depth= 22] . ( 4 sec) [ -2911.1011] [ 201] [depth= 24] . ( 4 sec) [ -2894.5296] [ 198] [depth= 16] . ( 4 sec) [ -2889.9659] [ 198] [depth= 1] . ( 4 sec) [ -2889.0861] [ 198] [depth= 2] . ( 4 sec) [ -2888.0654] [ 198] [depth= 4] . ( 4 sec) [ -2887.9421] [ 198] [depth= 30] . ( 4 sec) [ -2874.5923] [ 196] [depth= 12] . ( 4 sec) [ -2874.2823] [ 196] [depth= 1] . ( 4 sec) [ -2871.8542] [ 196] [depth= 11] . ( 5 sec) [ -2871.8105] [ 196] [depth= 3] . ( 5 sec) [ -2871.0706] [ 196] [depth= 1] . ( 5 sec) [ -2870.7815] [ 196] [depth= 1] . ( 5 sec) [ -2870.7672] [ 196] [depth= 3] . ( 5 sec) [ -2869.4694] [ 196] [depth= 3] . ( 5 sec) [ -2869.4515] [ 196] [depth= 6] . ( 5 sec) [ -2867.8798] [ 196] [depth= 10] . ( 5 sec) [ -2867.8685] [ 196] [depth= 1] . ( 5 sec) [ -2867.7643] [ 196] [depth= 1] . ( 5 sec) [ -2867.4168] [ 196] [depth= 13] . ( 5 sec) [ -2867.0023] [ 196] [depth= 3] . ( 5 sec) [ -2866.2670] [ 196] [depth= 4] . ( 5 sec) [ -2865.1372] [ 196] [depth= 3] . ( 5 sec) [ -2864.5149] [ 196] [depth= 16] . ( 5 sec) [ -2848.5027] [ 183] [depth= 16] . ( 5 sec) [ -2848.3012] [ 183] [depth= 1] . ( 5 sec) [ -2848.2417] [ 183] [depth= 1] . ( 5 sec) [ -2846.3407] [ 183] [depth= 14] . ( 5 sec) [ -2846.0227] [ 183] [depth= 5] . ( 5 sec) [ -2845.9711] [ 183] [depth= 2] . ( 5 sec) [ -2841.5277] [ 183] [depth= 2] . ( 5 sec) [ -2841.4424] [ 183] [depth= 5] . ( 5 sec) [ -2841.3968] [ 183] [depth= 1] . ( 5 sec) [ -2767.7188] [ 183] [depth= 3] . ( 5 sec) [ -2749.8474] [ 183] [depth= 9] . ( 5 sec) [ -2749.8268] [ 183] [depth= 4] . ( 5 sec) [ -2664.7916] [ 165] [depth= 14] . ( 5 sec) [ -2663.9596] [ 165] [depth= 2] . ( 5 sec) [ -2663.9408] [ 165] [depth= 5] . ( 5 sec) [ -2623.3078] [ 155] [depth= 2] . ( 5 sec) [ -2616.9960] [ 154] [depth= 9] . ( 5 sec) [ -2616.9829] [ 154] [depth= 1] . ( 5 sec) [ -2615.9406] [ 154] [depth= 12] . ( 5 sec) [ -2615.8755] [ 154] [depth= 3] . ( 6 sec) [ -2602.7887] [ 152] [depth= 16] . ( 6 sec) [ -2569.2045] [Branch lengths ] . ( 6 sec) [ -2542.9698] [GTR parameters ] . ( 6 sec) [ -2523.6861] [Alpha ][ 0.250961] . ( 9 sec) [ -2509.0012] [ 152] [depth= 11] . ( 10 sec) [ -2508.5876] [ 152] [depth= 10] . ( 10 sec) [ -2507.6058] [ 152] [depth= 1] . ( 10 sec) [ -2495.3336] [ 151] [depth= 12] . ( 10 sec) [ -2495.3145] [ 151] [depth= 2] . ( 10 sec) [ -2495.1786] [ 151] [depth= 8] . ( 12 sec) [ -2418.0660] [ 133] [depth= 6] . ( 12 sec) [ -2416.3433] [ 133] [depth= 6] . ( 12 sec) [ -2416.3049] [ 133] [depth= 2] . ( 12 sec) [ -2416.1065] [ 133] [depth= 6] . ( 12 sec) [ -2408.0439] [ 132] [depth= 20] . ( 12 sec) [ -2379.1581] [ 125] [depth= 9] . ( 12 sec) [ -2370.8594] [ 125] [depth= 2] . ( 12 sec) [ -2370.8455] [ 125] [depth= 4] . ( 12 sec) [ -2370.8314] [ 125] [depth= 5] . ( 13 sec) [ -2370.7872] [ 126] [depth= 1] . ( 13 sec) [ -2370.6798] [ 126] [depth= 3] . ( 13 sec) [ -2370.0228] [ 126] [depth= 2] . ( 14 sec) [ -2365.1767] [ 125] [depth= 10] . ( 14 sec) [ -2365.0755] [ 125] [depth= 6] . ( 14 sec) [ -2287.8898] [ 108] [depth= 9] . ( 14 sec) [ -2285.8692] [ 108] [depth= 1] . ( 14 sec) [ -2285.8549] [ 108] [depth= 6] . ( 14 sec) [ -2285.8021] [ 108] [depth= 2] . ( 14 sec) [ -2285.6934] [ 108] [depth= 1] . ( 15 sec) [ -2285.6813] [ 108] [depth= 3] . ( 15 sec) [ -2285.5604] [ 108] [depth= 3] . ( 15 sec) [ -2285.5499] [ 108] [depth= 1] . ( 16 sec) [ -2285.5376] [ 108] [depth= 6] . ( 16 sec) [ -2285.5221] [ 107] [depth= 3] . ( 16 sec) [ -2284.2009] [ 107] [depth= 9] . ( 16 sec) [ -2283.3563] [ 107] [depth= 4] . ( 18 sec) [ -2283.3425] [ 107] [depth= 1] . ( 18 sec) [ -2283.2251] [ 107] [depth= 2] . ( 18 sec) [ -2283.2139] [ 107] [depth= 2] . ( 19 sec) [ -2283.2031] [ 107] [depth= 2] . ( 19 sec) [ -2282.5963] [ 107] [depth= 1] . ( 19 sec) [ -2282.4785] [ 107] [depth= 1] . ( 19 sec) [ -2212.9533] [ 91] [depth= 9] . ( 19 sec) [ -2212.0823] [ 91] [depth= 1] . ( 19 sec) [ -2212.0191] [ 91] [depth= 2] . ( 19 sec) [ -2212.0026] [ 91] [depth= 5] . ( 20 sec) [ -2211.0948] [ 91] [depth= 3] . ( 20 sec) [ -2208.2228] [ 91] [depth= 4] . ( 21 sec) [ -2208.2023] [ 91] [depth= 2] . ( 21 sec) [ -2208.1340] [ 91] [depth= 1] . ( 22 sec) [ -2207.9808] [ 91] [depth= 5] . ( 23 sec) [ -2207.9635] [ 91] [depth= 6] . ( 24 sec) [ -2207.9436] [ 91] [depth= 2] . ( 24 sec) [ -2207.9153] [ 91] [depth= 2] . ( 25 sec) [ -2207.1649] [ 91] [depth= 1] . ( 26 sec) [ -2206.9477] [ 91] [depth= 1] . ( 27 sec) [ -2200.9530] [ 90] [depth= 9] . ( 28 sec) [ -2200.9414] [ 90] [depth= 3] . ( 28 sec) [ -2200.8875] [ 90] [depth= 4] . ( 28 sec) [ -2200.8690] [ 90] [depth= 1] . ( 29 sec) [ -2200.8180] [ 90] [depth= 4] . ( 29 sec) [ -2167.0477] [ 80] [depth= 5] . ( 29 sec) [ -2166.8252] [ 80] [depth= 2] . ( 35 sec) [ -2166.7917] [ 80] [depth= 1] . ( 39 sec) [ -2165.4562] [Branch lengths ] . ( 39 sec) [ -2164.1899] [GTR parameters ] . ( 39 sec) [ -2163.5814] [Alpha ][ 0.501332] . ( 83 sec) [ -2163.5783] [Branch lengths ] . ( 101 sec) [ -2163.5783] [Branch lengths ] . ( 101 sec) [ -2163.5783] [Topology ] . ( 101 sec) [ -2163.5783] [Topology ] . ( 102 sec) [ -2163.5758] [GTR parameters ] . ( 102 sec) [ -2163.4889] [Alpha ][ 0.756755] . ( 102 sec) [ -2163.4889] [Topology ] . ( 102 sec) [ -2163.4888] [Topology ] . ( 102 sec) [ -2163.4884] [GTR parameters ] . ( 102 sec) [ -2163.4884] [Alpha ][ 0.758978] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.488358. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7824.7517] [GTR parameters ] . ( 1 sec) [ -7721.5880] [Alpha ][ 0.500960] . ( 1 sec) [ -7701.1013] [ 484] [depth= 2] . ( 1 sec) [ -7678.0030] [ 483] [depth= 7] . ( 1 sec) [ -7508.0101] [ 481] [depth= 1] . ( 1 sec) [ -7463.2589] [ 481] [depth= 1] . ( 1 sec) [ -7456.5476] [ 480] [depth= 1] . ( 1 sec) [ -7395.0105] [ 477] [depth= 11] . ( 1 sec) [ -7333.9801] [ 474] [depth= 1] . ( 1 sec) [ -7301.1968] [ 474] [depth= 5] . ( 1 sec) [ -7230.3333] [ 459] [depth= 4] . ( 1 sec) [ -7205.4357] [ 459] [depth= 7] . ( 1 sec) [ -7171.0733] [ 458] [depth= 6] . ( 1 sec) [ -7123.1582] [ 458] [depth= 1] . ( 1 sec) [ -7121.4721] [ 458] [depth= 1] . ( 1 sec) [ -6843.9604] [ 458] [depth= 2] . ( 1 sec) [ -6691.6227] [ 458] [depth= 2] . ( 1 sec) [ -6689.4250] [ 458] [depth= 2] . ( 1 sec) [ -6622.9815] [ 448] [depth= 2] . ( 1 sec) [ -6514.6762] [ 448] [depth= 3] . ( 1 sec) [ -6428.1527] [ 445] [depth= 3] . ( 1 sec) [ -6427.1915] [ 445] [depth= 1] . ( 1 sec) [ -6408.8108] [ 447] [depth= 1] . ( 1 sec) [ -6140.4894] [ 445] [depth= 3] . ( 1 sec) [ -6140.4523] [ 445] [depth= 21] . ( 1 sec) [ -6140.3542] [ 445] [depth= 20] . ( 1 sec) [ -6040.9590] [ 429] [depth= 2] . ( 1 sec) [ -5911.6105] [ 429] [depth= 3] . ( 1 sec) [ -5902.5004] [ 429] [depth= 1] . ( 1 sec) [ -5726.4963] [ 411] [depth= 3] . ( 1 sec) [ -5705.9285] [ 408] [depth= 12] . ( 1 sec) [ -5699.4641] [ 408] [depth= 22] . ( 1 sec) [ -5693.0386] [ 408] [depth= 26] . ( 1 sec) [ -5556.0430] [ 406] [depth= 19] . ( 1 sec) [ -5543.3115] [ 405] [depth= 3] . ( 1 sec) [ -5528.7415] [ 404] [depth= 10] . ( 1 sec) [ -5519.7765] [ 404] [depth= 1] . ( 2 sec) [ -5518.6948] [ 406] [depth= 1] . ( 2 sec) [ -5503.3191] [ 404] [depth= 29] . ( 2 sec) [ -5421.1926] [ 386] [depth= 10] . ( 2 sec) [ -5401.8814] [ 385] [depth= 2] . ( 2 sec) [ -5401.5984] [ 385] [depth= 2] . ( 2 sec) [ -5401.3534] [ 385] [depth= 2] . ( 2 sec) [ -5401.2732] [ 385] [depth= 4] . ( 2 sec) [ -5401.1886] [ 385] [depth= 5] . ( 2 sec) [ -5183.2009] [ 384] [depth= 14] . ( 2 sec) [ -5152.8927] [ 379] [depth= 22] . ( 2 sec) [ -5131.5674] [ 378] [depth= 2] . ( 2 sec) [ -5130.9043] [ 378] [depth= 2] . ( 2 sec) [ -5123.3605] [ 378] [depth= 4] . ( 2 sec) [ -4999.0676] [ 362] [depth= 5] . ( 2 sec) [ -4975.0306] [ 362] [depth= 1] . ( 2 sec) [ -4902.1185] [ 358] [depth= 9] . ( 2 sec) [ -4694.8597] [ 358] [depth= 10] . ( 2 sec) [ -4694.4723] [ 358] [depth= 1] . ( 2 sec) [ -4676.2565] [ 355] [depth= 10] . ( 2 sec) [ -4591.7048] [ 338] [depth= 19] . ( 2 sec) [ -4574.5406] [ 336] [depth= 26] . ( 2 sec) [ -4562.4597] [ 333] [depth= 12] . ( 2 sec) [ -4532.8365] [ 333] [depth= 1] . ( 2 sec) [ -4529.8216] [ 333] [depth= 3] . ( 2 sec) [ -4526.9077] [ 333] [depth= 4] . ( 2 sec) [ -4517.7957] [ 330] [depth= 1] . ( 2 sec) [ -4514.4021] [ 330] [depth= 5] . ( 2 sec) [ -4514.3873] [ 330] [depth= 1] . ( 2 sec) [ -4485.2050] [ 330] [depth= 4] . ( 2 sec) [ -4418.1085] [ 330] [depth= 5] . ( 2 sec) [ -4342.3021] [ 312] [depth= 5] . ( 2 sec) [ -4169.3939] [ 312] [depth= 16] . ( 2 sec) [ -4074.7797] [ 313] [depth= 19] . ( 2 sec) [ -4074.7607] [ 313] [depth= 1] . ( 2 sec) [ -4074.7427] [ 313] [depth= 1] . ( 3 sec) [ -4074.3611] [ 313] [depth= 10] . ( 3 sec) [ -4061.0466] [ 311] [depth= 7] . ( 3 sec) [ -4048.8519] [ 312] [depth= 2] . ( 3 sec) [ -3971.3717] [ 296] [depth= 19] . ( 3 sec) [ -3960.7712] [ 294] [depth= 9] . ( 3 sec) [ -3622.8977] [ 294] [depth= 20] . ( 3 sec) [ -3621.3243] [ 294] [depth= 2] . ( 3 sec) [ -3620.8485] [ 294] [depth= 1] . ( 3 sec) [ -3619.0601] [ 294] [depth= 4] . ( 3 sec) [ -3605.1572] [ 292] [depth= 22] . ( 3 sec) [ -3600.1022] [ 292] [depth= 21] . ( 3 sec) [ -3595.3739] [ 292] [depth= 3] . ( 3 sec) [ -3590.2557] [ 292] [depth= 18] . ( 3 sec) [ -3535.3812] [ 282] [depth= 20] . ( 3 sec) [ -3499.9884] [ 284] [depth= 5] . ( 3 sec) [ -3491.9434] [ 282] [depth= 5] . ( 3 sec) [ -3406.4132] [ 264] [depth= 9] . ( 3 sec) [ -3392.2660] [ 263] [depth= 2] . ( 3 sec) [ -3389.1892] [ 263] [depth= 1] . ( 3 sec) [ -3389.1324] [ 263] [depth= 10] . ( 3 sec) [ -3384.3739] [ 263] [depth= 2] . ( 3 sec) [ -3375.7701] [ 262] [depth= 16] . ( 3 sec) [ -3359.0611] [ 260] [depth= 17] . ( 3 sec) [ -3356.4317] [ 260] [depth= 1] . ( 3 sec) [ -3344.4105] [ 260] [depth= 2] . ( 3 sec) [ -3343.9454] [ 260] [depth= 1] . ( 3 sec) [ -3321.1561] [ 259] [depth= 2] . ( 3 sec) [ -3321.1256] [ 259] [depth= 1] . ( 3 sec) [ -3285.2260] [ 255] [depth= 6] . ( 3 sec) [ -3285.1079] [ 255] [depth= 2] . ( 3 sec) [ -3283.6990] [ 256] [depth= 2] . ( 3 sec) [ -3283.6288] [ 256] [depth= 1] . ( 3 sec) [ -3171.7044] [ 256] [depth= 6] . ( 3 sec) [ -3152.7911] [ 254] [depth= 16] . ( 3 sec) [ -3152.3731] [ 254] [depth= 1] . ( 3 sec) [ -3096.1603] [ 243] [depth= 7] . ( 4 sec) [ -3092.9695] [ 243] [depth= 8] . ( 4 sec) [ -3089.3325] [ 242] [depth= 1] . ( 4 sec) [ -3089.2665] [ 242] [depth= 5] . ( 4 sec) [ -3059.1772] [ 237] [depth= 16] . ( 4 sec) [ -3059.1347] [ 237] [depth= 5] . ( 4 sec) [ -3058.1834] [ 237] [depth= 1] . ( 4 sec) [ -3056.4268] [ 237] [depth= 2] . ( 4 sec) [ -3049.5050] [ 236] [depth= 1] . ( 4 sec) [ -3049.4358] [ 236] [depth= 1] . ( 4 sec) [ -3049.3785] [ 236] [depth= 1] . ( 4 sec) [ -3047.7968] [ 236] [depth= 2] . ( 4 sec) [ -3047.5366] [ 236] [depth= 7] . ( 4 sec) [ -3041.1839] [ 235] [depth= 6] . ( 4 sec) [ -3040.6816] [ 235] [depth= 2] . ( 4 sec) [ -2980.3594] [ 235] [depth= 14] . ( 4 sec) [ -2975.1572] [ 235] [depth= 3] . ( 4 sec) [ -2970.4070] [ 234] [depth= 5] . ( 4 sec) [ -2970.2332] [ 234] [depth= 6] . ( 4 sec) [ -2970.1920] [ 234] [depth= 6] . ( 4 sec) [ -2970.0997] [ 234] [depth= 4] . ( 4 sec) [ -2969.3033] [ 234] [depth= 4] . ( 4 sec) [ -2882.6168] [ 215] [depth= 7] . ( 4 sec) [ -2869.2469] [ 213] [depth= 7] . ( 4 sec) [ -2868.9103] [ 213] [depth= 1] . ( 4 sec) [ -2868.6517] [ 213] [depth= 3] . ( 4 sec) [ -2868.6404] [ 213] [depth= 1] . ( 4 sec) [ -2868.6039] [ 213] [depth= 1] . ( 4 sec) [ -2868.5577] [ 213] [depth= 6] . ( 4 sec) [ -2866.4908] [ 212] [depth= 7] . ( 4 sec) [ -2864.8081] [ 212] [depth= 1] . ( 4 sec) [ -2864.7707] [ 212] [depth= 1] . ( 4 sec) [ -2864.5895] [ 212] [depth= 10] . ( 5 sec) [ -2864.5157] [ 212] [depth= 11] . ( 5 sec) [ -2864.4508] [ 212] [depth= 10] . ( 5 sec) [ -2864.2800] [ 212] [depth= 9] . ( 5 sec) [ -2861.5068] [ 212] [depth= 2] . ( 5 sec) [ -2857.4598] [ 212] [depth= 7] . ( 5 sec) [ -2857.4458] [ 212] [depth= 8] . ( 5 sec) [ -2774.9179] [ 193] [depth= 7] . ( 5 sec) [ -2774.7426] [ 193] [depth= 1] . ( 5 sec) [ -2759.7857] [ 193] [depth= 1] . ( 5 sec) [ -2749.2383] [ 193] [depth= 4] . ( 5 sec) [ -2748.7723] [ 193] [depth= 3] . ( 5 sec) [ -2726.1251] [ 191] [depth= 3] . ( 5 sec) [ -2649.1312] [ 174] [depth= 23] . ( 5 sec) [ -2648.5898] [ 174] [depth= 1] . ( 5 sec) [ -2645.8292] [ 174] [depth= 15] . ( 5 sec) [ -2645.6734] [ 174] [depth= 12] . ( 5 sec) [ -2645.0387] [ 174] [depth= 2] . ( 5 sec) [ -2644.8158] [ 174] [depth= 4] . ( 5 sec) [ -2643.1341] [ 174] [depth= 9] . ( 5 sec) [ -2640.2407] [ 174] [depth= 2] . ( 5 sec) [ -2640.2117] [ 174] [depth= 2] . ( 5 sec) [ -2562.3139] [ 157] [depth= 16] . ( 5 sec) [ -2561.5433] [ 157] [depth= 1] . ( 5 sec) [ -2561.3757] [ 157] [depth= 2] . ( 5 sec) [ -2560.7209] [ 157] [depth= 7] . ( 5 sec) [ -2560.7036] [ 157] [depth= 5] . ( 5 sec) [ -2559.9154] [ 157] [depth= 1] . ( 5 sec) [ -2559.7148] [ 157] [depth= 1] . ( 6 sec) [ -2555.5801] [ 156] [depth= 4] . ( 6 sec) [ -2555.5632] [ 156] [depth= 4] . ( 6 sec) [ -2555.5084] [ 156] [depth= 5] . ( 7 sec) [ -2554.7872] [ 156] [depth= 13] . ( 7 sec) [ -2547.9530] [Branch lengths ] . ( 7 sec) [ -2520.5525] [GTR parameters ] . ( 7 sec) [ -2500.6206] [Alpha ][ 0.250961] . ( 8 sec) [ -2500.5857] [ 156] [depth= 5] . ( 11 sec) [ -2494.2928] [ 155] [depth= 8] . ( 12 sec) [ -2417.7326] [ 136] [depth= 9] . ( 12 sec) [ -2415.7706] [ 136] [depth= 5] . ( 13 sec) [ -2415.7279] [ 136] [depth= 6] . ( 13 sec) [ -2414.9649] [ 136] [depth= 2] . ( 13 sec) [ -2413.5667] [ 136] [depth= 9] . ( 13 sec) [ -2341.6036] [ 119] [depth= 7] . ( 14 sec) [ -2332.3182] [ 118] [depth= 11] . ( 14 sec) [ -2323.8129] [ 117] [depth= 8] . ( 15 sec) [ -2323.7203] [ 117] [depth= 2] . ( 17 sec) [ -2323.4628] [ 117] [depth= 2] . ( 18 sec) [ -2323.4273] [ 117] [depth= 1] . ( 18 sec) [ -2323.3224] [ 117] [depth= 2] . ( 21 sec) [ -2323.3073] [ 117] [depth= 1] . ( 22 sec) [ -2289.7606] [ 108] [depth= 9] . ( 22 sec) [ -2289.7471] [ 108] [depth= 2] . ( 25 sec) [ -2289.6963] [ 108] [depth= 3] . ( 25 sec) [ -2289.6620] [ 108] [depth= 2] . ( 26 sec) [ -2287.9053] [ 109] [depth= 1] . ( 26 sec) [ -2282.3752] [ 108] [depth= 1] . ( 27 sec) [ -2282.3315] [ 108] [depth= 1] . ( 27 sec) [ -2280.6560] [ 108] [depth= 14] . ( 27 sec) [ -2280.6456] [ 108] [depth= 3] . ( 29 sec) [ -2280.6351] [ 108] [depth= 6] . ( 29 sec) [ -2200.6752] [ 90] [depth= 9] . ( 33 sec) [ -2199.0826] [ 90] [depth= 4] . ( 34 sec) [ -2199.0012] [ 90] [depth= 4] . ( 35 sec) [ -2198.9320] [ 90] [depth= 1] . ( 36 sec) [ -2198.9088] [ 90] [depth= 1] . ( 38 sec) [ -2198.8944] [ 90] [depth= 5] . ( 38 sec) [ -2198.8842] [ 90] [depth= 3] . ( 40 sec) [ -2195.0182] [ 89] [depth= 5] . ( 40 sec) [ -2195.0020] [ 89] [depth= 2] . ( 43 sec) [ -2194.9916] [ 89] [depth= 2] . ( 47 sec) [ -2194.7572] [Branch lengths ] . ( 47 sec) [ -2193.9862] [GTR parameters ] . ( 47 sec) [ -2192.8284] [Alpha ][ 0.125721] . ( 65 sec) [ -2165.3909] [ 80] [depth= 3] . ( 65 sec) [ -2165.3760] [ 80] [depth= 4] . ( 92 sec) [ -2165.1002] [Branch lengths ] . ( 93 sec) [ -2164.7210] [GTR parameters ] . ( 93 sec) [ -2163.7614] [Alpha ][ 0.251061] . ( 138 sec) [ -2163.7606] [Branch lengths ] . ( 157 sec) [ -2163.7606] [Branch lengths ] . ( 157 sec) [ -2163.7606] [Topology ] . ( 157 sec) [ -2163.7606] [Topology ] . ( 157 sec) [ -2163.7579] [GTR parameters ] . ( 157 sec) [ -2163.1489] [Alpha ][ 0.501548] . ( 157 sec) [ -2163.1489] [Topology ] . ( 158 sec) [ -2163.1487] [Topology ] . ( 158 sec) [ -2163.1464] [GTR parameters ] . ( 158 sec) [ -2163.0595] [Alpha ][ 0.757113] . ( 158 sec) [ -2163.0595] [Topology ] . ( 158 sec) [ -2163.0593] [Topology ] . ( 158 sec) [ -2163.0589] [GTR parameters ] . ( 158 sec) [ -2163.0589] [Alpha ][ 0.759274] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.058909. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8640.0177] [GTR parameters ] . ( 2 sec) [ -8527.7043] [Alpha ][ 0.500960] . ( 2 sec) [ -8519.4922] [ 536] [depth= 8] . ( 2 sec) [ -8445.7224] [ 519] [depth= 8] . ( 2 sec) [ -8445.6742] [ 519] [depth= 1] . ( 2 sec) [ -8445.6383] [ 519] [depth= 1] . ( 2 sec) [ -8433.4501] [ 519] [depth= 2] . ( 2 sec) [ -8427.4367] [ 519] [depth= 5] . ( 2 sec) [ -8293.2710] [ 519] [depth= 2] . ( 2 sec) [ -8282.3446] [ 516] [depth= 5] . ( 2 sec) [ -8276.0656] [ 516] [depth= 1] . ( 2 sec) [ -8067.9004] [ 515] [depth= 1] . ( 2 sec) [ -7925.0804] [ 515] [depth= 1] . ( 2 sec) [ -7624.4984] [ 515] [depth= 2] . ( 2 sec) [ -7591.5145] [ 515] [depth= 9] . ( 2 sec) [ -7343.3020] [ 496] [depth= 17] . ( 2 sec) [ -7283.1599] [ 496] [depth= 8] . ( 2 sec) [ -7177.4446] [ 478] [depth= 2] . ( 2 sec) [ -7176.7895] [ 478] [depth= 7] . ( 2 sec) [ -6920.2148] [ 478] [depth= 1] . ( 2 sec) [ -6905.1571] [ 478] [depth= 1] . ( 2 sec) [ -6836.1405] [ 462] [depth= 14] . ( 2 sec) [ -6830.1441] [ 461] [depth= 4] . ( 2 sec) [ -6660.4248] [ 461] [depth= 3] . ( 2 sec) [ -6344.0445] [ 444] [depth= 1] . ( 2 sec) [ -6342.4719] [ 444] [depth= 1] . ( 2 sec) [ -6340.1560] [ 444] [depth= 2] . ( 2 sec) [ -6272.2453] [ 444] [depth= 3] . ( 2 sec) [ -6268.0007] [ 443] [depth= 6] . ( 2 sec) [ -6254.7662] [ 443] [depth= 6] . ( 2 sec) [ -6248.0662] [ 443] [depth= 4] . ( 2 sec) [ -6136.7693] [ 425] [depth= 4] . ( 2 sec) [ -5645.0633] [ 425] [depth= 6] . ( 2 sec) [ -5619.2245] [ 423] [depth= 18] . ( 2 sec) [ -5481.8781] [ 422] [depth= 15] . ( 2 sec) [ -5472.7717] [ 422] [depth= 3] . ( 2 sec) [ -5455.9777] [ 422] [depth= 24] . ( 2 sec) [ -5416.5499] [ 422] [depth= 3] . ( 3 sec) [ -5414.2478] [ 422] [depth= 3] . ( 3 sec) [ -5408.5276] [ 421] [depth= 2] . ( 3 sec) [ -5390.1168] [ 420] [depth= 21] . ( 3 sec) [ -5389.2495] [ 420] [depth= 22] . ( 3 sec) [ -5320.8587] [ 404] [depth= 22] . ( 3 sec) [ -5308.6360] [ 404] [depth= 1] . ( 3 sec) [ -5261.6304] [ 403] [depth= 10] . ( 3 sec) [ -5159.1193] [ 402] [depth= 4] . ( 3 sec) [ -5011.3681] [ 402] [depth= 1] . ( 3 sec) [ -4848.5061] [ 386] [depth= 3] . ( 3 sec) [ -4848.4340] [ 386] [depth= 21] . ( 3 sec) [ -4848.3111] [ 386] [depth= 7] . ( 3 sec) [ -4836.1559] [ 386] [depth= 1] . ( 3 sec) [ -4824.6906] [ 390] [depth= 1] . ( 3 sec) [ -4796.3653] [ 386] [depth= 28] . ( 3 sec) [ -4783.5021] [ 385] [depth= 23] . ( 3 sec) [ -4769.6460] [ 384] [depth= 10] . ( 3 sec) [ -4665.3860] [ 364] [depth= 8] . ( 3 sec) [ -4635.0502] [ 364] [depth= 8] . ( 3 sec) [ -4604.1934] [ 361] [depth= 11] . ( 3 sec) [ -4593.5956] [ 359] [depth= 20] . ( 3 sec) [ -4591.9782] [ 359] [depth= 4] . ( 3 sec) [ -4463.1172] [ 359] [depth= 2] . ( 3 sec) [ -4461.7465] [ 359] [depth= 4] . ( 3 sec) [ -4460.9708] [ 359] [depth= 10] . ( 3 sec) [ -4459.7066] [ 359] [depth= 4] . ( 3 sec) [ -4436.9886] [ 357] [depth= 15] . ( 3 sec) [ -4436.8670] [ 357] [depth= 1] . ( 3 sec) [ -4436.5822] [ 357] [depth= 4] . ( 3 sec) [ -4436.5614] [ 357] [depth= 5] . ( 3 sec) [ -4400.7888] [ 357] [depth= 12] . ( 3 sec) [ -4385.4979] [ 356] [depth= 14] . ( 3 sec) [ -4384.5285] [ 347] [depth= 4] . ( 3 sec) [ -4383.9145] [ 347] [depth= 4] . ( 3 sec) [ -4375.8901] [ 345] [depth= 2] . ( 3 sec) [ -4299.7138] [ 335] [depth= 3] . ( 3 sec) [ -4253.3874] [ 335] [depth= 23] . ( 4 sec) [ -4241.9351] [ 324] [depth= 11] . ( 4 sec) [ -4184.7493] [ 321] [depth= 20] . ( 4 sec) [ -4050.2175] [ 306] [depth= 6] . ( 4 sec) [ -4037.7430] [ 306] [depth= 1] . ( 4 sec) [ -4017.5818] [ 289] [depth= 15] . ( 4 sec) [ -4012.2084] [ 289] [depth= 17] . ( 4 sec) [ -4011.7870] [ 289] [depth= 10] . ( 4 sec) [ -4000.1361] [ 287] [depth= 9] . ( 4 sec) [ -3944.7389] [ 288] [depth= 1] . ( 4 sec) [ -3866.3454] [ 272] [depth= 14] . ( 4 sec) [ -3856.9257] [ 270] [depth= 12] . ( 4 sec) [ -3836.9857] [ 269] [depth= 2] . ( 4 sec) [ -3788.9119] [ 269] [depth= 1] . ( 4 sec) [ -3772.2606] [ 267] [depth= 9] . ( 4 sec) [ -3768.9614] [ 267] [depth= 11] . ( 4 sec) [ -3767.5751] [ 267] [depth= 11] . ( 4 sec) [ -3764.5094] [ 267] [depth= 14] . ( 4 sec) [ -3763.5495] [ 267] [depth= 2] . ( 4 sec) [ -3763.5077] [ 267] [depth= 1] . ( 4 sec) [ -3755.7628] [ 267] [depth= 8] . ( 4 sec) [ -3755.3116] [ 267] [depth= 1] . ( 4 sec) [ -3706.3915] [ 266] [depth= 3] . ( 4 sec) [ -3698.7982] [ 266] [depth= 3] . ( 4 sec) [ -3475.2017] [ 271] [depth= 16] . ( 4 sec) [ -3474.5306] [ 271] [depth= 3] . ( 4 sec) [ -3465.1268] [ 269] [depth= 8] . ( 4 sec) [ -3465.0454] [ 269] [depth= 1] . ( 4 sec) [ -3465.0281] [ 269] [depth= 3] . ( 4 sec) [ -3463.3573] [ 269] [depth= 3] . ( 4 sec) [ -3462.7187] [ 269] [depth= 6] . ( 4 sec) [ -3462.6616] [ 269] [depth= 12] . ( 4 sec) [ -3400.9116] [ 252] [depth= 17] . ( 4 sec) [ -3396.9082] [ 251] [depth= 15] . ( 4 sec) [ -3395.6665] [ 251] [depth= 12] . ( 4 sec) [ -3385.4242] [ 251] [depth= 2] . ( 4 sec) [ -3382.1268] [ 250] [depth= 22] . ( 4 sec) [ -3366.9046] [ 249] [depth= 15] . ( 4 sec) [ -3350.6889] [ 249] [depth= 1] . ( 4 sec) [ -3259.2082] [ 247] [depth= 9] . ( 4 sec) [ -3201.7620] [ 231] [depth= 8] . ( 4 sec) [ -3196.4128] [ 231] [depth= 7] . ( 5 sec) [ -3196.4012] [ 231] [depth= 15] . ( 5 sec) [ -3194.5549] [ 230] [depth= 7] . ( 5 sec) [ -3192.3812] [ 230] [depth= 10] . ( 5 sec) [ -3191.7927] [ 230] [depth= 2] . ( 5 sec) [ -3187.8518] [ 230] [depth= 8] . ( 5 sec) [ -3187.7666] [ 230] [depth= 4] . ( 5 sec) [ -3016.1813] [ 229] [depth= 15] . ( 5 sec) [ -2934.1489] [ 211] [depth= 3] . ( 5 sec) [ -2930.8462] [ 211] [depth= 22] . ( 5 sec) [ -2930.7409] [ 211] [depth= 22] . ( 5 sec) [ -2924.1611] [ 210] [depth= 12] . ( 5 sec) [ -2924.1471] [ 210] [depth= 4] . ( 5 sec) [ -2923.7937] [ 210] [depth= 1] . ( 5 sec) [ -2915.8527] [ 209] [depth= 12] . ( 5 sec) [ -2915.8369] [ 209] [depth= 2] . ( 5 sec) [ -2915.2568] [ 209] [depth= 13] . ( 5 sec) [ -2915.2420] [ 209] [depth= 13] . ( 5 sec) [ -2915.1071] [ 209] [depth= 2] . ( 5 sec) [ -2900.1392] [ 208] [depth= 6] . ( 5 sec) [ -2900.1258] [ 208] [depth= 2] . ( 5 sec) [ -2900.0928] [ 208] [depth= 1] . ( 5 sec) [ -2900.0053] [ 208] [depth= 12] . ( 5 sec) [ -2883.5808] [ 197] [depth= 12] . ( 5 sec) [ -2883.4423] [ 197] [depth= 3] . ( 5 sec) [ -2883.4282] [ 197] [depth= 3] . ( 5 sec) [ -2877.6194] [ 196] [depth= 19] . ( 5 sec) [ -2875.5005] [ 196] [depth= 16] . ( 5 sec) [ -2873.9004] [ 196] [depth= 14] . ( 5 sec) [ -2872.3172] [ 196] [depth= 4] . ( 5 sec) [ -2869.3535] [ 195] [depth= 9] . ( 5 sec) [ -2856.2748] [ 193] [depth= 4] . ( 5 sec) [ -2752.7730] [ 185] [depth= 3] . ( 6 sec) [ -2732.1276] [ 186] [depth= 1] . ( 6 sec) [ -2732.1126] [ 186] [depth= 1] . ( 6 sec) [ -2730.6949] [ 186] [depth= 18] . ( 6 sec) [ -2730.6552] [ 186] [depth= 8] . ( 6 sec) [ -2730.5497] [ 186] [depth= 2] . ( 6 sec) [ -2730.4658] [ 186] [depth= 3] . ( 6 sec) [ -2729.4540] [ 186] [depth= 2] . ( 6 sec) [ -2729.3486] [ 186] [depth= 1] . ( 6 sec) [ -2728.9883] [ 186] [depth= 8] . ( 6 sec) [ -2728.9348] [ 186] [depth= 3] . ( 6 sec) [ -2728.7947] [ 186] [depth= 3] . ( 6 sec) [ -2728.5855] [ 186] [depth= 1] . ( 6 sec) [ -2650.9514] [ 170] [depth= 10] . ( 6 sec) [ -2647.4232] [ 169] [depth= 6] . ( 6 sec) [ -2642.3126] [ 168] [depth= 3] . ( 7 sec) [ -2640.0498] [ 168] [depth= 4] . ( 7 sec) [ -2639.8348] [ 168] [depth= 1] . ( 7 sec) [ -2614.3321] [Branch lengths ] . ( 7 sec) [ -2593.4309] [GTR parameters ] . ( 7 sec) [ -2570.0466] [Alpha ][ 0.250961] . ( 8 sec) [ -2563.1054] [ 167] [depth= 11] . ( 8 sec) [ -2500.7187] [ 151] [depth= 11] . ( 8 sec) [ -2494.4661] [ 150] [depth= 10] . ( 8 sec) [ -2494.3876] [ 150] [depth= 2] . ( 9 sec) [ -2488.6121] [ 148] [depth= 11] . ( 9 sec) [ -2488.5825] [ 148] [depth= 1] . ( 9 sec) [ -2485.8496] [ 148] [depth= 19] . ( 9 sec) [ -2485.8157] [ 148] [depth= 2] . ( 9 sec) [ -2485.3393] [ 148] [depth= 10] . ( 9 sec) [ -2483.9835] [ 148] [depth= 1] . ( 10 sec) [ -2483.9270] [ 148] [depth= 5] . ( 10 sec) [ -2483.3097] [ 148] [depth= 1] . ( 10 sec) [ -2483.2681] [ 148] [depth= 3] . ( 10 sec) [ -2483.0100] [ 148] [depth= 7] . ( 10 sec) [ -2482.9526] [ 148] [depth= 7] . ( 10 sec) [ -2477.6862] [ 147] [depth= 9] . ( 10 sec) [ -2472.1314] [ 146] [depth= 6] . ( 10 sec) [ -2401.7093] [ 129] [depth= 8] . ( 10 sec) [ -2397.9860] [ 129] [depth= 11] . ( 11 sec) [ -2397.9719] [ 129] [depth= 3] . ( 11 sec) [ -2397.9575] [ 129] [depth= 4] . ( 12 sec) [ -2396.7112] [ 128] [depth= 1] . ( 12 sec) [ -2396.6342] [ 128] [depth= 2] . ( 12 sec) [ -2393.6384] [ 127] [depth= 5] . ( 12 sec) [ -2393.5375] [ 127] [depth= 4] . ( 13 sec) [ -2393.4721] [ 127] [depth= 2] . ( 14 sec) [ -2393.4559] [ 127] [depth= 2] . ( 15 sec) [ -2386.6681] [ 127] [depth= 11] . ( 16 sec) [ -2385.9924] [ 127] [depth= 10] . ( 16 sec) [ -2379.0293] [ 127] [depth= 6] . ( 16 sec) [ -2378.8950] [ 127] [depth= 1] . ( 16 sec) [ -2378.8437] [ 127] [depth= 1] . ( 16 sec) [ -2378.7867] [ 127] [depth= 1] . ( 16 sec) [ -2372.5009] [ 125] [depth= 5] . ( 16 sec) [ -2372.4640] [ 125] [depth= 1] . ( 16 sec) [ -2372.4514] [ 125] [depth= 2] . ( 16 sec) [ -2372.4413] [ 125] [depth= 4] . ( 17 sec) [ -2372.2987] [ 125] [depth= 1] . ( 17 sec) [ -2351.8736] [ 122] [depth= 1] . ( 18 sec) [ -2351.8621] [ 122] [depth= 1] . ( 20 sec) [ -2351.0246] [ 122] [depth= 1] . ( 21 sec) [ -2350.9573] [ 122] [depth= 1] . ( 22 sec) [ -2342.7999] [ 121] [depth= 5] . ( 22 sec) [ -2342.6976] [ 121] [depth= 2] . ( 22 sec) [ -2342.0247] [ 121] [depth= 2] . ( 22 sec) [ -2342.0059] [ 121] [depth= 6] . ( 22 sec) [ -2341.9160] [ 121] [depth= 1] . ( 22 sec) [ -2341.9022] [ 121] [depth= 5] . ( 23 sec) [ -2338.3155] [ 120] [depth= 6] . ( 23 sec) [ -2338.2308] [ 120] [depth= 1] . ( 25 sec) [ -2338.2196] [ 120] [depth= 8] . ( 25 sec) [ -2338.1966] [ 120] [depth= 2] . ( 26 sec) [ -2333.3509] [ 120] [depth= 7] . ( 27 sec) [ -2331.2010] [ 120] [depth= 2] . ( 32 sec) [ -2329.5374] [ 119] [depth= 1] . ( 32 sec) [ -2260.3705] [ 103] [depth= 6] . ( 33 sec) [ -2260.3593] [ 103] [depth= 6] . ( 33 sec) [ -2260.3476] [ 103] [depth= 5] . ( 33 sec) [ -2260.3331] [ 103] [depth= 2] . ( 33 sec) [ -2260.3218] [ 103] [depth= 1] . ( 33 sec) [ -2260.2989] [ 103] [depth= 1] . ( 33 sec) [ -2260.2865] [ 103] [depth= 5] . ( 34 sec) [ -2260.2670] [ 103] [depth= 3] . ( 34 sec) [ -2260.2543] [ 103] [depth= 5] . ( 35 sec) [ -2257.9450] [Branch lengths ] . ( 36 sec) [ -2256.5990] [GTR parameters ] . ( 36 sec) [ -2252.6983] [Alpha ][ 0.125721] . ( 37 sec) [ -2240.1785] [ 98] [depth= 4] . ( 37 sec) [ -2240.1682] [ 98] [depth= 1] . ( 38 sec) [ -2240.1547] [ 98] [depth= 3] . ( 40 sec) [ -2206.3861] [ 92] [depth= 8] . ( 40 sec) [ -2203.6354] [ 92] [depth= 6] . ( 40 sec) [ -2203.5369] [ 92] [depth= 5] . ( 43 sec) [ -2203.1975] [ 92] [depth= 2] . ( 45 sec) [ -2203.0699] [ 92] [depth= 5] . ( 46 sec) [ -2200.6423] [ 91] [depth= 2] . ( 47 sec) [ -2200.4993] [ 91] [depth= 5] . ( 48 sec) [ -2200.2576] [ 91] [depth= 3] . ( 49 sec) [ -2200.1177] [ 91] [depth= 3] . ( 49 sec) [ -2200.0871] [ 91] [depth= 5] . ( 49 sec) [ -2193.9869] [ 89] [depth= 5] . ( 50 sec) [ -2193.8178] [ 89] [depth= 2] . ( 50 sec) [ -2193.7289] [ 89] [depth= 3] . ( 52 sec) [ -2193.7166] [ 89] [depth= 1] . ( 57 sec) [ -2193.6841] [ 89] [depth= 2] . ( 59 sec) [ -2193.6462] [ 89] [depth= 2] . ( 61 sec) [ -2193.6301] [ 89] [depth= 6] . ( 64 sec) [ -2193.5815] [ 89] [depth= 1] . ( 71 sec) [ -2193.5713] [ 89] [depth= 3] . ( 74 sec) [ -2193.5320] [ 89] [depth= 2] . ( 77 sec) [ -2193.4908] [Branch lengths ] . ( 77 sec) [ -2192.8202] [GTR parameters ] . ( 77 sec) [ -2192.4823] [Alpha ][ 0.062981] . ( 78 sec) [ -2165.9967] [ 80] [depth= 2] . ( 78 sec) [ -2165.9806] [ 80] [depth= 2] . ( 122 sec) [ -2165.6935] [Branch lengths ] . ( 122 sec) [ -2165.2547] [GTR parameters ] . ( 122 sec) [ -2164.7203] [Alpha ][ 0.125772] . ( 166 sec) [ -2164.7191] [Branch lengths ] . ( 184 sec) [ -2164.7191] [Branch lengths ] . ( 184 sec) [ -2164.7191] [Topology ] . ( 184 sec) [ -2164.7191] [Topology ] . ( 184 sec) [ -2164.7184] [GTR parameters ] . ( 184 sec) [ -2163.7602] [Alpha ][ 0.251162] . ( 184 sec) [ -2163.7602] [Topology ] . ( 185 sec) [ -2163.7595] [Topology ] . ( 185 sec) [ -2163.7570] [GTR parameters ] . ( 185 sec) [ -2163.1485] [Alpha ][ 0.501749] . ( 185 sec) [ -2163.1485] [Topology ] . ( 185 sec) [ -2163.1481] [Topology ] . ( 185 sec) [ -2163.1458] [GTR parameters ] . ( 185 sec) [ -2163.0591] [Alpha ][ 0.757246] . ( 185 sec) [ -2163.0591] [Topology ] . ( 185 sec) [ -2163.0589] [Topology ] . ( 186 sec) [ -2163.0585] [GTR parameters ] . ( 186 sec) [ -2163.0585] [Alpha ][ 0.759364] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.058468. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -2167.7777] [GTR parameters ] . ( 1 sec) [ -2167.7484] [Alpha ][ 0.762192] . ( 1 sec) [ -2167.7484] [Topology ] . ( 1 sec) [ -2164.8151] [Topology ] . ( 2 sec) [ -2164.1354] [Topology ] . ( 2 sec) [ -2163.7186] [Topology ] . ( 2 sec) [ -2163.5431] [Topology ] . ( 2 sec) [ -2163.5011] [Topology ] . ( 3 sec) [ -2163.4908] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4 sec) [ -2163.4906] [GTR parameters ] . ( 4 sec) [ -2163.4906] [Alpha ][ 0.759129] . ( 4 sec) [ -2163.4906] [Topology ] . ( 5 sec) [ -2163.4878] [Topology ] . ( 5 sec) [ -2163.4872] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6 sec) [ -2163.4872] [GTR parameters ] . ( 7 sec) [ -2163.4872] [Alpha ][ 0.759129] . ( 7 sec) [ -2163.4872] [Topology ] . ( 7 sec) [ -2163.4870] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 10 sec) [ -2167.7777] [GTR parameters ] . ( 10 sec) [ -2167.7484] [Alpha ][ 0.762192] . ( 10 sec) [ -2167.5690] [ 80] [depth= 5] . ( 11 sec) [ -2167.5255] [ 80] [depth= 1] . ( 11 sec) [ -2167.4612] [ 80] [depth= 1] . ( 11 sec) [ -2167.4301] [ 80] [depth= 2] . ( 11 sec) [ -2167.3835] [ 80] [depth= 2] . ( 11 sec) [ -2167.2964] [ 80] [depth= 1] . ( 11 sec) [ -2167.2521] [ 80] [depth= 1] . ( 12 sec) [ -2167.2139] [ 80] [depth= 3] . ( 12 sec) [ -2167.1975] [ 80] [depth= 3] . ( 12 sec) [ -2167.1458] [ 80] [depth= 1] . ( 13 sec) [ -2166.6462] [ 80] [depth= 5] . ( 13 sec) [ -2166.6336] [ 80] [depth= 5] . ( 13 sec) [ -2166.5335] [ 80] [depth= 3] . ( 13 sec) [ -2166.5235] [ 80] [depth= 3] . ( 13 sec) [ -2166.5082] [ 80] [depth= 1] . ( 13 sec) [ -2166.4108] [ 80] [depth= 2] . ( 14 sec) [ -2165.9948] [ 80] [depth= 2] . ( 14 sec) [ -2165.9793] [ 80] [depth= 1] . ( 14 sec) [ -2165.8827] [ 80] [depth= 3] . ( 14 sec) [ -2165.7892] [ 80] [depth= 4] . ( 14 sec) [ -2165.6397] [ 80] [depth= 4] . ( 14 sec) [ -2165.6014] [ 80] [depth= 4] . ( 14 sec) [ -2165.5608] [ 80] [depth= 3] . ( 15 sec) [ -2165.5485] [ 80] [depth= 5] . ( 18 sec) [ -2165.5263] [ 80] [depth= 1] . ( 20 sec) [ -2165.4871] [ 80] [depth= 2] . ( 20 sec) [ -2165.4203] [ 80] [depth= 2] . ( 20 sec) [ -2165.3554] [ 80] [depth= 1] . ( 21 sec) [ -2165.3401] [ 80] [depth= 1] . ( 21 sec) [ -2164.9097] [ 80] [depth= 1] . ( 21 sec) [ -2164.8711] [ 80] [depth= 3] . ( 21 sec) [ -2164.8555] [ 80] [depth= 2] . ( 22 sec) [ -2164.8322] [ 80] [depth= 3] . ( 22 sec) [ -2164.7953] [ 80] [depth= 1] . ( 22 sec) [ -2164.7507] [ 80] [depth= 2] . ( 22 sec) [ -2164.7201] [ 80] [depth= 1] . ( 24 sec) [ -2164.6756] [ 80] [depth= 4] . ( 24 sec) [ -2164.5015] [ 80] [depth= 5] . ( 24 sec) [ -2164.4504] [ 80] [depth= 6] . ( 24 sec) [ -2164.3594] [ 80] [depth= 2] . ( 24 sec) [ -2164.1632] [ 80] [depth= 1] . ( 25 sec) [ -2164.0895] [ 80] [depth= 1] . ( 30 sec) [ -2163.8452] [ 80] [depth= 1] . ( 35 sec) [ -2163.7936] [ 80] [depth= 6] . ( 35 sec) [ -2163.7456] [ 80] [depth= 5] . ( 43 sec) [ -2163.4890] [Branch lengths ] . ( 43 sec) [ -2163.4889] [GTR parameters ] . ( 43 sec) [ -2163.4888] [Alpha ][ 0.759420] . ( 87 sec) [ -2163.4873] [Branch lengths ] . ( 105 sec) [ -2163.4873] [Branch lengths ] . ( 105 sec) [ -2163.4873] [Topology ] . ( 105 sec) [ -2163.4873] [Topology ] . ( 105 sec) [ -2163.4873] [GTR parameters ] . ( 105 sec) [ -2163.4873] [Alpha ][ 0.759420] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2163.487012 . Log likelihood obtained after SPR moves : -2163.487251 . Log likelihood of the current tree: -2163.487012. . Printing the most likely tree in file 'nucleic_M2599_66x1137_2006.phy_phyml_tree.txt'... . Best log likelihood : -2163.058468 . Time used 0h1m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 760.52user 0.00system 12:58.79elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps