.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2566_73x918_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 541 patterns found. (out of a total of 918 sites) . 442 sites without polymorphism (48.15%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -22882.3730] [GTR parameters ] . ( 4 sec) [ -22285.5019] [Alpha ][ 0.500960] . ( 4 sec) [ -21830.4577] [ 4256] [depth= 12] . ( 4 sec) [ -21629.7509] [ 4226] [depth= 14] . ( 4 sec) [ -21229.0267] [ 4217] [depth= 11] . ( 4 sec) [ -21200.0454] [ 4204] [depth= 1] . ( 4 sec) [ -21172.5504] [ 4203] [depth= 1] . ( 4 sec) [ -21155.2341] [ 4202] [depth= 4] . ( 5 sec) [ -21096.3462] [ 4193] [depth= 2] . ( 5 sec) [ -21058.3503] [ 4180] [depth= 3] . ( 5 sec) [ -21044.6254] [ 4172] [depth= 8] . ( 5 sec) [ -20936.0117] [ 4161] [depth= 15] . ( 5 sec) [ -20865.3198] [ 4157] [depth= 5] . ( 5 sec) [ -20789.5034] [ 4115] [depth= 1] . ( 5 sec) [ -20765.9887] [ 4113] [depth= 2] . ( 5 sec) [ -20684.6266] [ 4111] [depth= 1] . ( 5 sec) [ -20427.2224] [ 4105] [depth= 2] . ( 5 sec) [ -20421.4050] [ 4100] [depth= 1] . ( 5 sec) [ -20306.8769] [ 4100] [depth= 10] . ( 6 sec) [ -19946.0913] [ 4090] [depth= 1] . ( 6 sec) [ -19829.8983] [ 4067] [depth= 5] . ( 6 sec) [ -19644.5706] [ 4013] [depth= 7] . ( 6 sec) [ -19546.4690] [ 4015] [depth= 10] . ( 6 sec) [ -19465.8050] [ 3998] [depth= 17] . ( 6 sec) [ -19445.5682] [ 3997] [depth= 9] . ( 6 sec) [ -19091.5668] [ 3966] [depth= 17] . ( 6 sec) [ -18832.5789] [ 3924] [depth= 11] . ( 6 sec) [ -18653.7397] [ 3872] [depth= 1] . ( 6 sec) [ -18590.8213] [ 3838] [depth= 20] . ( 7 sec) [ -18362.7073] [ 3818] [depth= 10] . ( 7 sec) [ -18301.9967] [ 3794] [depth= 21] . ( 7 sec) [ -18227.3673] [ 3789] [depth= 1] . ( 7 sec) [ -18194.5816] [ 3794] [depth= 2] . ( 7 sec) [ -18181.1635] [ 3784] [depth= 1] . ( 7 sec) [ -18114.1513] [ 3787] [depth= 21] . ( 7 sec) [ -18110.9395] [ 3787] [depth= 1] . ( 7 sec) [ -18083.9912] [ 3775] [depth= 21] . ( 7 sec) [ -17924.1524] [ 3716] [depth= 17] . ( 7 sec) [ -17913.6793] [ 3714] [depth= 4] . ( 8 sec) [ -17805.6060] [ 3700] [depth= 6] . ( 8 sec) [ -17686.2129] [ 3684] [depth= 10] . ( 8 sec) [ -17515.5538] [ 3673] [depth= 4] . ( 8 sec) [ -17286.7806] [ 3633] [depth= 10] . ( 8 sec) [ -17234.7234] [ 3620] [depth= 10] . ( 8 sec) [ -17139.4618] [ 3608] [depth= 2] . ( 8 sec) [ -17129.0619] [ 3605] [depth= 1] . ( 8 sec) [ -16958.1937] [ 3546] [depth= 3] . ( 8 sec) [ -16715.4220] [ 3523] [depth= 8] . ( 9 sec) [ -16543.9346] [ 3506] [depth= 7] . ( 9 sec) [ -16539.6948] [ 3508] [depth= 1] . ( 9 sec) [ -16539.0457] [ 3515] [depth= 1] . ( 9 sec) [ -16437.6390] [ 3494] [depth= 4] . ( 9 sec) [ -16431.6004] [ 3488] [depth= 1] . ( 9 sec) [ -16233.1902] [ 3399] [depth= 12] . ( 9 sec) [ -16013.1206] [ 3359] [depth= 4] . ( 9 sec) [ -15873.0685] [ 3342] [depth= 9] . ( 9 sec) [ -15844.3915] [ 3338] [depth= 1] . ( 10 sec) [ -15841.4906] [ 3335] [depth= 2] . ( 10 sec) [ -15841.3251] [ 3335] [depth= 1] . ( 10 sec) [ -15769.0133] [ 3324] [depth= 13] . ( 10 sec) [ -15707.5028] [ 3332] [depth= 1] . ( 10 sec) [ -15620.4598] [ 3296] [depth= 2] . ( 10 sec) [ -15514.8145] [ 3262] [depth= 11] . ( 10 sec) [ -15490.5856] [ 3263] [depth= 13] . ( 10 sec) [ -15471.1980] [ 3248] [depth= 12] . ( 10 sec) [ -15450.5326] [ 3247] [depth= 15] . ( 10 sec) [ -15397.6986] [ 3237] [depth= 2] . ( 11 sec) [ -15328.2105] [ 3232] [depth= 6] . ( 11 sec) [ -15303.5176] [ 3223] [depth= 5] . ( 11 sec) [ -15267.8834] [ 3209] [depth= 2] . ( 11 sec) [ -15261.7820] [ 3204] [depth= 1] . ( 11 sec) [ -15246.9533] [ 3201] [depth= 1] . ( 11 sec) [ -15216.5906] [ 3195] [depth= 14] . ( 11 sec) [ -15189.3994] [ 3180] [depth= 10] . ( 11 sec) [ -14992.9731] [ 3131] [depth= 7] . ( 11 sec) [ -14937.4642] [ 3122] [depth= 2] . ( 12 sec) [ -14914.3731] [ 3107] [depth= 1] . ( 12 sec) [ -14815.7944] [ 3072] [depth= 1] . ( 12 sec) [ -14807.4599] [ 3075] [depth= 1] . ( 12 sec) [ -14788.3188] [ 3062] [depth= 1] . ( 12 sec) [ -14722.3995] [ 3039] [depth= 15] . ( 12 sec) [ -14677.8640] [ 3035] [depth= 11] . ( 12 sec) [ -14556.8382] [ 2998] [depth= 10] . ( 12 sec) [ -14428.4851] [ 2946] [depth= 9] . ( 12 sec) [ -14420.4997] [ 2943] [depth= 1] . ( 12 sec) [ -14378.2261] [ 2933] [depth= 17] . ( 13 sec) [ -14275.6721] [ 2910] [depth= 14] . ( 13 sec) [ -14266.7823] [ 2912] [depth= 1] . ( 13 sec) [ -14256.1880] [ 2914] [depth= 1] . ( 13 sec) [ -14221.8483] [ 2907] [depth= 2] . ( 13 sec) [ -14186.5309] [ 2904] [depth= 2] . ( 13 sec) [ -14183.9315] [ 2903] [depth= 10] . ( 13 sec) [ -14173.7741] [ 2896] [depth= 1] . ( 13 sec) [ -14131.8572] [ 2888] [depth= 4] . ( 13 sec) [ -14029.6952] [ 2871] [depth= 5] . ( 13 sec) [ -14020.5118] [ 2863] [depth= 2] . ( 13 sec) [ -13960.6365] [ 2849] [depth= 3] . ( 14 sec) [ -13953.3375] [ 2849] [depth= 1] . ( 14 sec) [ -13888.3664] [ 2829] [depth= 1] . ( 14 sec) [ -13879.1855] [ 2825] [depth= 1] . ( 14 sec) [ -13873.0412] [ 2822] [depth= 1] . ( 14 sec) [ -13842.5965] [ 2805] [depth= 4] . ( 14 sec) [ -13765.0722] [ 2784] [depth= 3] . ( 14 sec) [ -13709.1469] [ 2794] [depth= 3] . ( 14 sec) [ -13620.3692] [ 2757] [depth= 12] . ( 14 sec) [ -13608.8527] [ 2756] [depth= 1] . ( 15 sec) [ -13601.3541] [ 2759] [depth= 2] . ( 15 sec) [ -13476.0757] [ 2747] [depth= 3] . ( 15 sec) [ -13427.7668] [ 2728] [depth= 14] . ( 15 sec) [ -13415.5160] [ 2723] [depth= 4] . ( 15 sec) [ -13410.7475] [ 2722] [depth= 6] . ( 15 sec) [ -13380.7222] [ 2719] [depth= 4] . ( 16 sec) [ -13380.4963] [ 2719] [depth= 1] . ( 16 sec) [ -13380.2796] [ 2721] [depth= 1] . ( 16 sec) [ -13348.6097] [ 2718] [depth= 6] . ( 16 sec) [ -13334.1275] [ 2710] [depth= 1] . ( 16 sec) [ -13330.1304] [ 2703] [depth= 3] . ( 16 sec) [ -13327.3715] [ 2702] [depth= 2] . ( 16 sec) [ -13227.0989] [ 2662] [depth= 11] . ( 17 sec) [ -13092.0511] [ 2625] [depth= 4] . ( 17 sec) [ -13081.3444] [ 2623] [depth= 1] . ( 17 sec) [ -13079.3628] [ 2623] [depth= 1] . ( 17 sec) [ -13036.7269] [ 2601] [depth= 1] . ( 17 sec) [ -13021.9602] [ 2594] [depth= 1] . ( 17 sec) [ -12999.1862] [ 2586] [depth= 2] . ( 17 sec) [ -12952.5754] [ 2568] [depth= 2] . ( 17 sec) [ -12935.1082] [ 2564] [depth= 1] . ( 18 sec) [ -12909.7245] [ 2562] [depth= 1] . ( 18 sec) [ -12906.7026] [ 2558] [depth= 1] . ( 18 sec) [ -12904.7467] [ 2555] [depth= 1] . ( 18 sec) [ -12903.5212] [ 2558] [depth= 1] . ( 18 sec) [ -12895.0456] [ 2556] [depth= 2] . ( 18 sec) [ -12841.8939] [ 2541] [depth= 2] . ( 18 sec) [ -12840.1033] [ 2541] [depth= 1] . ( 19 sec) [ -12838.4200] [ 2545] [depth= 1] . ( 19 sec) [ -12838.3233] [ 2545] [depth= 1] . ( 19 sec) [ -12837.1866] [ 2544] [depth= 5] . ( 19 sec) [ -12829.5097] [ 2545] [depth= 1] . ( 19 sec) [ -12812.1197] [ 2536] [depth= 2] . ( 19 sec) [ -12788.7494] [ 2531] [depth= 4] . ( 19 sec) [ -12787.4593] [ 2532] [depth= 1] . ( 19 sec) [ -12786.0452] [ 2527] [depth= 9] . ( 19 sec) [ -12771.8293] [ 2524] [depth= 1] . ( 20 sec) [ -12756.4894] [ 2520] [depth= 3] . ( 20 sec) [ -12720.4532] [ 2512] [depth= 5] . ( 20 sec) [ -12708.8886] [ 2504] [depth= 3] . ( 20 sec) [ -12590.6347] [ 2475] [depth= 8] . ( 20 sec) [ -12589.0460] [ 2476] [depth= 1] . ( 20 sec) [ -12588.3139] [ 2476] [depth= 1] . ( 20 sec) [ -12489.9714] [ 2442] [depth= 3] . ( 20 sec) [ -12461.5481] [ 2434] [depth= 2] . ( 20 sec) [ -12457.5764] [ 2431] [depth= 2] . ( 21 sec) [ -12455.9961] [ 2430] [depth= 2] . ( 21 sec) [ -12453.7439] [ 2429] [depth= 2] . ( 21 sec) [ -12451.7366] [ 2429] [depth= 1] . ( 21 sec) [ -12445.0202] [ 2400] [depth= 15] . ( 22 sec) [ -12305.9278] [Branch lengths ] . ( 23 sec) [ -12286.6712] [GTR parameters ] . ( 23 sec) [ -12254.9455] [Alpha ][ 0.340072] . ( 24 sec) [ -12253.4560] [ 2398] [depth= 1] . ( 24 sec) [ -12252.3424] [ 2400] [depth= 1] . ( 24 sec) [ -12241.5571] [ 2395] [depth= 1] . ( 24 sec) [ -12237.8564] [ 2394] [depth= 1] . ( 24 sec) [ -12227.2260] [ 2383] [depth= 2] . ( 25 sec) [ -12221.8652] [ 2383] [depth= 1] . ( 25 sec) [ -12221.6738] [ 2385] [depth= 1] . ( 25 sec) [ -12221.2954] [ 2385] [depth= 1] . ( 25 sec) [ -12200.7364] [ 2383] [depth= 4] . ( 25 sec) [ -12191.9807] [ 2380] [depth= 2] . ( 26 sec) [ -12186.4590] [ 2379] [depth= 1] . ( 26 sec) [ -12170.3178] [ 2372] [depth= 4] . ( 27 sec) [ -12161.4176] [ 2365] [depth= 1] . ( 27 sec) [ -12161.3717] [ 2363] [depth= 1] . ( 29 sec) [ -12160.3458] [ 2366] [depth= 1] . ( 29 sec) [ -12159.9103] [ 2361] [depth= 2] . ( 30 sec) [ -12159.7624] [ 2366] [depth= 1] . ( 30 sec) [ -12152.4309] [ 2357] [depth= 2] . ( 30 sec) [ -12151.5872] [ 2358] [depth= 1] . ( 30 sec) [ -12148.6521] [ 2356] [depth= 1] . ( 31 sec) [ -12112.9101] [ 2339] [depth= 4] . ( 31 sec) [ -12112.1341] [ 2342] [depth= 1] . ( 31 sec) [ -12111.6285] [ 2342] [depth= 1] . ( 31 sec) [ -12104.5678] [ 2337] [depth= 1] . ( 32 sec) [ -12104.3087] [ 2335] [depth= 1] . ( 32 sec) [ -12102.9693] [ 2336] [depth= 1] . ( 33 sec) [ -12082.4164] [ 2336] [depth= 5] . ( 33 sec) [ -12082.2033] [ 2335] [depth= 1] . ( 34 sec) [ -12080.3885] [ 2336] [depth= 1] . ( 34 sec) [ -12079.2380] [ 2333] [depth= 1] . ( 36 sec) [ -12073.5340] [ 2332] [depth= 1] . ( 36 sec) [ -12073.4211] [ 2331] [depth= 1] . ( 38 sec) [ -12072.6718] [ 2329] [depth= 1] . ( 39 sec) [ -12066.6985] [ 2326] [depth= 1] . ( 39 sec) [ -12065.0611] [ 2326] [depth= 1] . ( 39 sec) [ -12064.0779] [ 2325] [depth= 2] . ( 39 sec) [ -12051.3265] [ 2320] [depth= 1] . ( 40 sec) [ -12050.0754] [ 2318] [depth= 2] . ( 41 sec) [ -12049.9421] [ 2311] [depth= 8] . ( 41 sec) [ -12032.3877] [Branch lengths ] . ( 42 sec) [ -12032.1948] [GTR parameters ] . ( 42 sec) [ -12032.1948] [Alpha ][ 0.340072] . ( 43 sec) [ -12022.0851] [ 2305] [depth= 1] . ( 52 sec) [ -12021.1948] [ 2306] [depth= 2] . ( 53 sec) [ -12021.0032] [ 2307] [depth= 1] . ( 57 sec) [ -12019.6352] [ 2308] [depth= 2] . ( 58 sec) [ -12017.6516] [ 2313] [depth= 8] . ( 58 sec) [ -12007.9473] [Branch lengths ] . ( 59 sec) [ -12007.6189] [GTR parameters ] . ( 60 sec) [ -12007.6167] [Alpha ][ 0.338936] . ( 63 sec) [ -12007.5841] [ 2317] [depth= 1] . ( 69 sec) [ -12007.3696] [ 2316] [depth= 1] . ( 78 sec) [ -12005.5161] [ 2314] [depth= 5] . ( 79 sec) [ -12002.7523] [Branch lengths ] . ( 79 sec) [ -12002.7376] [GTR parameters ] . ( 79 sec) [ -12002.7376] [Alpha ][ 0.338936] . ( 98 sec) [ -12002.4408] [Branch lengths ] . ( 175 sec) [ -12002.3755] [Branch lengths ] . ( 175 sec) [ -12002.3755] [Topology ] . ( 177 sec) [ -12002.1024] [Topology ] . ( 178 sec) [ -12002.0390] [Topology ] . ( 180 sec) [ -12002.0321] [Topology ] . ( 182 sec) [ -12002.0303] [Topology ] . ( 184 sec) [ -12002.0297] [Topology ] . ( 184 sec) [ -12002.0269] [GTR parameters ] . ( 185 sec) [ -12002.0266] [Alpha ][ 0.339342] . ( 185 sec) [ -12002.0266] [Topology ] . ( 186 sec) [ -12002.0262] [Topology ] . ( 187 sec) [ -12002.0262] [GTR parameters ] . ( 187 sec) [ -12002.0262] [Alpha ][ 0.339342] . Checking for NNIs, optimizing five branches... . ( 199 sec) [ -12001.9837] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12001.983682. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -22610.2112] [GTR parameters ] . ( 4 sec) [ -22002.9695] [Alpha ][ 0.500960] . ( 4 sec) [ -21814.2858] [ 4354] [depth= 14] . ( 5 sec) [ -21652.9625] [ 4323] [depth= 11] . ( 5 sec) [ -21573.2191] [ 4306] [depth= 7] . ( 5 sec) [ -21544.6621] [ 4290] [depth= 1] . ( 5 sec) [ -21443.7868] [ 4269] [depth= 8] . ( 5 sec) [ -21419.8948] [ 4265] [depth= 1] . ( 5 sec) [ -21333.1804] [ 4262] [depth= 5] . ( 5 sec) [ -21298.3706] [ 4248] [depth= 3] . ( 5 sec) [ -21264.7881] [ 4249] [depth= 8] . ( 5 sec) [ -21238.4580] [ 4241] [depth= 8] . ( 5 sec) [ -21206.5582] [ 4236] [depth= 5] . ( 5 sec) [ -21088.9789] [ 4212] [depth= 12] . ( 6 sec) [ -21007.3658] [ 4213] [depth= 7] . ( 6 sec) [ -20974.2901] [ 4205] [depth= 2] . ( 6 sec) [ -20931.8104] [ 4201] [depth= 3] . ( 6 sec) [ -20813.9196] [ 4187] [depth= 16] . ( 6 sec) [ -20808.6850] [ 4187] [depth= 2] . ( 6 sec) [ -20756.9081] [ 4173] [depth= 5] . ( 6 sec) [ -20353.3374] [ 4132] [depth= 12] . ( 6 sec) [ -20055.2474] [ 4122] [depth= 20] . ( 6 sec) [ -19914.3109] [ 4092] [depth= 3] . ( 6 sec) [ -19873.9665] [ 4087] [depth= 2] . ( 6 sec) [ -19693.8430] [ 4060] [depth= 20] . ( 7 sec) [ -19618.5699] [ 4045] [depth= 9] . ( 7 sec) [ -19535.2264] [ 4047] [depth= 1] . ( 7 sec) [ -19459.3536] [ 4028] [depth= 5] . ( 7 sec) [ -19341.9878] [ 4014] [depth= 14] . ( 7 sec) [ -19007.5295] [ 3945] [depth= 20] . ( 7 sec) [ -18987.3389] [ 3947] [depth= 1] . ( 7 sec) [ -18853.3301] [ 3891] [depth= 12] . ( 7 sec) [ -18696.7537] [ 3880] [depth= 2] . ( 7 sec) [ -18618.4738] [ 3870] [depth= 8] . ( 7 sec) [ -18498.9998] [ 3858] [depth= 12] . ( 8 sec) [ -18378.7675] [ 3794] [depth= 19] . ( 8 sec) [ -18267.0141] [ 3751] [depth= 17] . ( 8 sec) [ -18176.6318] [ 3724] [depth= 4] . ( 8 sec) [ -18116.0397] [ 3722] [depth= 9] . ( 8 sec) [ -18020.1070] [ 3707] [depth= 8] . ( 8 sec) [ -18016.5175] [ 3708] [depth= 1] . ( 8 sec) [ -17873.3616] [ 3660] [depth= 12] . ( 8 sec) [ -17816.7610] [ 3656] [depth= 8] . ( 8 sec) [ -17805.5272] [ 3654] [depth= 1] . ( 9 sec) [ -17638.6061] [ 3627] [depth= 11] . ( 9 sec) [ -17536.8732] [ 3585] [depth= 1] . ( 9 sec) [ -17465.2231] [ 3562] [depth= 7] . ( 9 sec) [ -17378.1159] [ 3539] [depth= 19] . ( 9 sec) [ -17335.6935] [ 3540] [depth= 1] . ( 9 sec) [ -17274.0308] [ 3530] [depth= 1] . ( 9 sec) [ -17152.3830] [ 3523] [depth= 20] . ( 9 sec) [ -16861.3575] [ 3485] [depth= 20] . ( 9 sec) [ -16776.8940] [ 3464] [depth= 10] . ( 9 sec) [ -16762.1356] [ 3461] [depth= 1] . ( 10 sec) [ -16557.0406] [ 3454] [depth= 8] . ( 10 sec) [ -16527.9733] [ 3439] [depth= 18] . ( 10 sec) [ -16346.2804] [ 3384] [depth= 16] . ( 10 sec) [ -16336.7547] [ 3384] [depth= 3] . ( 10 sec) [ -16157.0681] [ 3357] [depth= 11] . ( 10 sec) [ -16072.7789] [ 3331] [depth= 3] . ( 10 sec) [ -16058.8886] [ 3327] [depth= 3] . ( 10 sec) [ -15925.5082] [ 3286] [depth= 14] . ( 10 sec) [ -15896.1140] [ 3280] [depth= 5] . ( 10 sec) [ -15884.2707] [ 3276] [depth= 1] . ( 11 sec) [ -15715.9169] [ 3253] [depth= 9] . ( 11 sec) [ -15711.2753] [ 3234] [depth= 8] . ( 11 sec) [ -15647.6284] [ 3204] [depth= 2] . ( 11 sec) [ -15532.8220] [ 3177] [depth= 3] . ( 11 sec) [ -15463.0614] [ 3174] [depth= 1] . ( 11 sec) [ -15428.2279] [ 3173] [depth= 1] . ( 11 sec) [ -15421.4977] [ 3173] [depth= 2] . ( 11 sec) [ -15383.6440] [ 3163] [depth= 2] . ( 11 sec) [ -15347.6879] [ 3124] [depth= 4] . ( 11 sec) [ -15222.6428] [ 3126] [depth= 12] . ( 12 sec) [ -15190.5551] [ 3127] [depth= 2] . ( 12 sec) [ -15189.0605] [ 3126] [depth= 1] . ( 12 sec) [ -15178.3184] [ 3127] [depth= 2] . ( 12 sec) [ -15132.2178] [ 3107] [depth= 5] . ( 12 sec) [ -15115.6406] [ 3093] [depth= 2] . ( 12 sec) [ -15018.7975] [ 3066] [depth= 19] . ( 12 sec) [ -15011.2849] [ 3066] [depth= 1] . ( 12 sec) [ -15004.1035] [ 3062] [depth= 2] . ( 12 sec) [ -14913.7039] [ 3032] [depth= 13] . ( 12 sec) [ -14808.0518] [ 3001] [depth= 3] . ( 13 sec) [ -14753.8283] [ 2995] [depth= 12] . ( 13 sec) [ -14705.7704] [ 2982] [depth= 10] . ( 13 sec) [ -14524.5123] [ 2939] [depth= 9] . ( 13 sec) [ -14451.1794] [ 2938] [depth= 1] . ( 13 sec) [ -14388.8086] [ 2912] [depth= 1] . ( 13 sec) [ -14365.5666] [ 2903] [depth= 2] . ( 13 sec) [ -14340.6986] [ 2900] [depth= 2] . ( 13 sec) [ -14337.5993] [ 2900] [depth= 1] . ( 13 sec) [ -14330.4360] [ 2899] [depth= 2] . ( 13 sec) [ -14294.9901] [ 2889] [depth= 10] . ( 14 sec) [ -14237.2195] [ 2869] [depth= 8] . ( 14 sec) [ -14225.6424] [ 2871] [depth= 1] . ( 14 sec) [ -14179.8505] [ 2854] [depth= 7] . ( 14 sec) [ -14146.5955] [ 2836] [depth= 2] . ( 14 sec) [ -14074.8851] [ 2833] [depth= 1] . ( 14 sec) [ -14060.0510] [ 2832] [depth= 6] . ( 14 sec) [ -13994.2159] [ 2799] [depth= 7] . ( 15 sec) [ -13952.7167] [ 2785] [depth= 8] . ( 15 sec) [ -13938.8545] [ 2783] [depth= 4] . ( 15 sec) [ -13882.8941] [ 2773] [depth= 12] . ( 15 sec) [ -13809.5111] [ 2777] [depth= 1] . ( 15 sec) [ -13759.8848] [ 2758] [depth= 7] . ( 15 sec) [ -13635.0891] [ 2719] [depth= 9] . ( 15 sec) [ -13623.3354] [ 2710] [depth= 12] . ( 15 sec) [ -13577.3110] [ 2684] [depth= 7] . ( 15 sec) [ -13551.2986] [ 2676] [depth= 3] . ( 16 sec) [ -13541.5426] [ 2675] [depth= 2] . ( 16 sec) [ -13536.5380] [ 2674] [depth= 1] . ( 16 sec) [ -13358.0815] [ 2680] [depth= 10] . ( 16 sec) [ -13353.3432] [ 2684] [depth= 1] . ( 16 sec) [ -13316.7344] [ 2678] [depth= 1] . ( 16 sec) [ -13297.3118] [ 2671] [depth= 3] . ( 16 sec) [ -13275.3822] [ 2665] [depth= 10] . ( 16 sec) [ -13270.2816] [ 2664] [depth= 2] . ( 16 sec) [ -13242.4869] [ 2651] [depth= 1] . ( 17 sec) [ -13211.7686] [ 2650] [depth= 1] . ( 17 sec) [ -13207.8842] [ 2647] [depth= 4] . ( 17 sec) [ -13207.7380] [ 2647] [depth= 1] . ( 17 sec) [ -13194.9062] [ 2641] [depth= 3] . ( 17 sec) [ -13193.9744] [ 2641] [depth= 2] . ( 17 sec) [ -13168.8209] [ 2630] [depth= 1] . ( 17 sec) [ -13168.8011] [ 2630] [depth= 1] . ( 17 sec) [ -13161.3027] [ 2626] [depth= 2] . ( 18 sec) [ -13116.7134] [ 2608] [depth= 8] . ( 18 sec) [ -13035.3854] [ 2584] [depth= 17] . ( 18 sec) [ -13029.6230] [ 2585] [depth= 1] . ( 18 sec) [ -13008.1156] [ 2582] [depth= 1] . ( 18 sec) [ -12990.5178] [ 2583] [depth= 3] . ( 18 sec) [ -12981.4044] [ 2583] [depth= 2] . ( 18 sec) [ -12960.4964] [ 2567] [depth= 2] . ( 19 sec) [ -12960.3862] [ 2569] [depth= 1] . ( 19 sec) [ -12893.0969] [ 2555] [depth= 9] . ( 19 sec) [ -12878.7693] [ 2548] [depth= 3] . ( 19 sec) [ -12823.5045] [ 2532] [depth= 2] . ( 19 sec) [ -12822.1289] [ 2530] [depth= 1] . ( 19 sec) [ -12809.1409] [ 2522] [depth= 6] . ( 19 sec) [ -12806.3912] [ 2524] [depth= 1] . ( 19 sec) [ -12804.4670] [ 2526] [depth= 1] . ( 20 sec) [ -12801.3455] [ 2521] [depth= 3] . ( 20 sec) [ -12796.1768] [ 2520] [depth= 1] . ( 20 sec) [ -12764.3649] [ 2516] [depth= 3] . ( 20 sec) [ -12753.4123] [ 2510] [depth= 5] . ( 20 sec) [ -12751.8581] [ 2511] [depth= 1] . ( 20 sec) [ -12689.8288] [ 2484] [depth= 3] . ( 20 sec) [ -12680.5765] [ 2482] [depth= 3] . ( 20 sec) [ -12630.6174] [ 2460] [depth= 13] . ( 21 sec) [ -12604.0720] [ 2449] [depth= 3] . ( 21 sec) [ -12586.5225] [ 2446] [depth= 2] . ( 21 sec) [ -12560.3480] [ 2439] [depth= 12] . ( 22 sec) [ -12447.9648] [Branch lengths ] . ( 23 sec) [ -12426.5513] [GTR parameters ] . ( 23 sec) [ -12394.0457] [Alpha ][ 0.340485] . ( 23 sec) [ -12385.0965] [ 2433] [depth= 3] . ( 24 sec) [ -12379.0700] [ 2429] [depth= 1] . ( 24 sec) [ -12350.8573] [ 2420] [depth= 12] . ( 24 sec) [ -12335.4336] [ 2409] [depth= 2] . ( 24 sec) [ -12334.2503] [ 2406] [depth= 1] . ( 25 sec) [ -12323.4201] [ 2403] [depth= 1] . ( 25 sec) [ -12309.7053] [ 2394] [depth= 1] . ( 25 sec) [ -12257.8439] [ 2375] [depth= 1] . ( 25 sec) [ -12252.1671] [ 2378] [depth= 1] . ( 25 sec) [ -12250.8002] [ 2372] [depth= 1] . ( 26 sec) [ -12249.0639] [ 2374] [depth= 2] . ( 26 sec) [ -12239.9857] [ 2375] [depth= 1] . ( 26 sec) [ -12238.8795] [ 2373] [depth= 3] . ( 27 sec) [ -12237.7081] [ 2371] [depth= 1] . ( 27 sec) [ -12233.0579] [ 2368] [depth= 1] . ( 27 sec) [ -12233.0446] [ 2370] [depth= 1] . ( 28 sec) [ -12231.7030] [ 2366] [depth= 1] . ( 29 sec) [ -12229.0707] [ 2365] [depth= 1] . ( 29 sec) [ -12224.1987] [ 2362] [depth= 2] . ( 29 sec) [ -12173.8370] [ 2341] [depth= 6] . ( 30 sec) [ -12172.2273] [ 2339] [depth= 1] . ( 30 sec) [ -12156.8252] [ 2337] [depth= 2] . ( 30 sec) [ -12148.5920] [ 2339] [depth= 3] . ( 30 sec) [ -12146.8873] [ 2338] [depth= 1] . ( 30 sec) [ -12142.9646] [ 2332] [depth= 2] . ( 30 sec) [ -12141.0898] [ 2332] [depth= 1] . ( 31 sec) [ -12140.5738] [ 2336] [depth= 1] . ( 31 sec) [ -12068.3742] [ 2318] [depth= 1] . ( 31 sec) [ -12067.2966] [ 2321] [depth= 2] . ( 33 sec) [ -12061.1154] [ 2319] [depth= 1] . ( 33 sec) [ -12054.5508] [ 2311] [depth= 1] . ( 33 sec) [ -12052.6438] [ 2312] [depth= 1] . ( 33 sec) [ -12052.3869] [ 2310] [depth= 1] . ( 33 sec) [ -12052.3732] [ 2309] [depth= 3] . ( 34 sec) [ -12049.9851] [ 2310] [depth= 1] . ( 35 sec) [ -12049.8411] [ 2311] [depth= 1] . ( 35 sec) [ -12049.8306] [ 2311] [depth= 1] . ( 38 sec) [ -12043.8544] [ 2310] [depth= 1] . ( 38 sec) [ -12043.3111] [ 2310] [depth= 2] . ( 39 sec) [ -12012.7495] [Branch lengths ] . ( 40 sec) [ -12011.5473] [GTR parameters ] . ( 40 sec) [ -12011.5344] [Alpha ][ 0.337764] . ( 42 sec) [ -12005.6031] [ 2314] [depth= 2] . ( 42 sec) [ -12005.5931] [ 2315] [depth= 1] . ( 47 sec) [ -12005.4326] [ 2314] [depth= 1] . ( 49 sec) [ -12004.9316] [ 2313] [depth= 1] . ( 58 sec) [ -12001.2670] [Branch lengths ] . ( 58 sec) [ -12001.2498] [GTR parameters ] . ( 58 sec) [ -12001.2474] [Alpha ][ 0.336582] . ( 76 sec) [ -12001.0284] [Branch lengths ] . ( 148 sec) [ -12001.0045] [Branch lengths ] . ( 148 sec) [ -12001.0045] [Topology ] . ( 150 sec) [ -12000.7980] [Topology ] . ( 152 sec) [ -12000.7598] [Topology ] . ( 153 sec) [ -12000.7560] [Topology ] . ( 155 sec) [ -12000.7551] [Topology ] . ( 156 sec) [ -12000.7506] [GTR parameters ] . ( 156 sec) [ -12000.7486] [Alpha ][ 0.337552] . ( 156 sec) [ -12000.7486] [Topology ] . ( 158 sec) [ -12000.7480] [Topology ] . ( 158 sec) [ -12000.7480] [GTR parameters ] . ( 158 sec) [ -12000.7480] [Alpha ][ 0.337552] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12000.747954. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -22577.5740] [GTR parameters ] . ( 3 sec) [ -21987.6779] [Alpha ][ 0.500960] . ( 3 sec) [ -21746.7299] [ 4259] [depth= 8] . ( 3 sec) [ -21558.1063] [ 4230] [depth= 11] . ( 3 sec) [ -21447.9853] [ 4182] [depth= 1] . ( 3 sec) [ -21439.9811] [ 4181] [depth= 1] . ( 4 sec) [ -21436.8984] [ 4179] [depth= 1] . ( 4 sec) [ -21431.0252] [ 4177] [depth= 1] . ( 4 sec) [ -21136.7704] [ 4162] [depth= 4] . ( 4 sec) [ -21017.0695] [ 4156] [depth= 5] . ( 4 sec) [ -20822.8474] [ 4092] [depth= 5] . ( 4 sec) [ -20766.9408] [ 4083] [depth= 3] . ( 4 sec) [ -20673.3880] [ 4080] [depth= 1] . ( 4 sec) [ -20524.3583] [ 4082] [depth= 6] . ( 4 sec) [ -20347.1670] [ 4018] [depth= 5] . ( 4 sec) [ -20323.4693] [ 4019] [depth= 1] . ( 4 sec) [ -20292.5957] [ 4017] [depth= 3] . ( 4 sec) [ -20194.7933] [ 4006] [depth= 2] . ( 5 sec) [ -20151.5624] [ 3987] [depth= 7] . ( 5 sec) [ -20084.4738] [ 3978] [depth= 6] . ( 5 sec) [ -20062.4446] [ 3975] [depth= 5] . ( 5 sec) [ -20034.9742] [ 3970] [depth= 1] . ( 5 sec) [ -19907.6555] [ 3964] [depth= 2] . ( 5 sec) [ -19710.5877] [ 3956] [depth= 10] . ( 5 sec) [ -19647.2168] [ 3939] [depth= 11] . ( 5 sec) [ -19276.1846] [ 3868] [depth= 17] . ( 5 sec) [ -19163.9336] [ 3845] [depth= 12] . ( 6 sec) [ -19112.3554] [ 3822] [depth= 3] . ( 6 sec) [ -18947.2646] [ 3805] [depth= 7] . ( 6 sec) [ -18943.4031] [ 3807] [depth= 1] . ( 6 sec) [ -18670.0150] [ 3771] [depth= 3] . ( 6 sec) [ -18658.6199] [ 3770] [depth= 2] . ( 6 sec) [ -18549.7320] [ 3737] [depth= 10] . ( 6 sec) [ -18278.6820] [ 3713] [depth= 14] . ( 6 sec) [ -18131.1183] [ 3700] [depth= 7] . ( 6 sec) [ -18031.2969] [ 3664] [depth= 8] . ( 7 sec) [ -17998.4700] [ 3648] [depth= 5] . ( 7 sec) [ -17952.5442] [ 3644] [depth= 4] . ( 7 sec) [ -17850.4381] [ 3612] [depth= 1] . ( 7 sec) [ -17788.2017] [ 3599] [depth= 3] . ( 7 sec) [ -17750.3352] [ 3596] [depth= 8] . ( 7 sec) [ -17673.7535] [ 3571] [depth= 7] . ( 7 sec) [ -17651.7182] [ 3565] [depth= 1] . ( 7 sec) [ -17636.2577] [ 3562] [depth= 5] . ( 7 sec) [ -17604.2540] [ 3557] [depth= 5] . ( 7 sec) [ -17493.8332] [ 3516] [depth= 17] . ( 8 sec) [ -17451.0009] [ 3496] [depth= 7] . ( 8 sec) [ -17410.3460] [ 3494] [depth= 6] . ( 8 sec) [ -17368.6845] [ 3487] [depth= 2] . ( 8 sec) [ -17302.6715] [ 3463] [depth= 5] . ( 8 sec) [ -17270.2032] [ 3469] [depth= 17] . ( 8 sec) [ -17183.5498] [ 3462] [depth= 3] . ( 8 sec) [ -17164.2252] [ 3455] [depth= 2] . ( 8 sec) [ -17059.2496] [ 3416] [depth= 16] . ( 8 sec) [ -17014.0049] [ 3400] [depth= 5] . ( 8 sec) [ -16924.4012] [ 3380] [depth= 8] . ( 8 sec) [ -16907.1191] [ 3377] [depth= 2] . ( 9 sec) [ -16830.8881] [ 3354] [depth= 23] . ( 9 sec) [ -16644.3889] [ 3324] [depth= 9] . ( 9 sec) [ -16505.0003] [ 3316] [depth= 8] . ( 9 sec) [ -16493.2616] [ 3308] [depth= 1] . ( 9 sec) [ -16487.8073] [ 3321] [depth= 1] . ( 9 sec) [ -16423.0744] [ 3309] [depth= 2] . ( 9 sec) [ -16403.9192] [ 3302] [depth= 2] . ( 9 sec) [ -16388.0127] [ 3296] [depth= 2] . ( 9 sec) [ -16147.6961] [ 3312] [depth= 22] . ( 9 sec) [ -16053.8892] [ 3301] [depth= 18] . ( 10 sec) [ -15969.8753] [ 3259] [depth= 11] . ( 10 sec) [ -15964.1929] [ 3260] [depth= 1] . ( 10 sec) [ -15925.1884] [ 3245] [depth= 20] . ( 10 sec) [ -15914.8911] [ 3242] [depth= 1] . ( 10 sec) [ -15868.5319] [ 3216] [depth= 17] . ( 10 sec) [ -15835.2200] [ 3205] [depth= 1] . ( 11 sec) [ -15833.6543] [ 3203] [depth= 1] . ( 11 sec) [ -15828.7114] [ 3188] [depth= 2] . ( 11 sec) [ -15692.9768] [ 3167] [depth= 12] . ( 11 sec) [ -15679.0110] [ 3165] [depth= 7] . ( 11 sec) [ -15433.7101] [ 3109] [depth= 11] . ( 11 sec) [ -15321.1257] [ 3087] [depth= 11] . ( 11 sec) [ -15320.6673] [ 3076] [depth= 8] . ( 11 sec) [ -15261.0507] [ 3076] [depth= 1] . ( 12 sec) [ -15254.5650] [ 3073] [depth= 1] . ( 12 sec) [ -15242.3599] [ 3082] [depth= 1] . ( 12 sec) [ -15060.0269] [ 3037] [depth= 4] . ( 12 sec) [ -14923.8797] [ 2996] [depth= 15] . ( 12 sec) [ -14904.4353] [ 2997] [depth= 1] . ( 12 sec) [ -14900.2349] [ 2989] [depth= 2] . ( 12 sec) [ -14877.8939] [ 2986] [depth= 1] . ( 12 sec) [ -14823.2164] [ 2977] [depth= 8] . ( 12 sec) [ -14772.0207] [ 2966] [depth= 4] . ( 12 sec) [ -14718.2789] [ 2956] [depth= 5] . ( 13 sec) [ -14571.9888] [ 2917] [depth= 10] . ( 13 sec) [ -14563.2462] [ 2914] [depth= 1] . ( 13 sec) [ -14484.0278] [ 2896] [depth= 13] . ( 13 sec) [ -14443.9299] [ 2893] [depth= 1] . ( 13 sec) [ -14349.2850] [ 2853] [depth= 6] . ( 13 sec) [ -14286.7341] [ 2852] [depth= 1] . ( 13 sec) [ -14274.2969] [ 2847] [depth= 1] . ( 13 sec) [ -14128.3537] [ 2808] [depth= 4] . ( 13 sec) [ -13997.4435] [ 2764] [depth= 10] . ( 14 sec) [ -13985.2630] [ 2761] [depth= 2] . ( 14 sec) [ -13973.3470] [ 2757] [depth= 2] . ( 14 sec) [ -13961.6693] [ 2750] [depth= 2] . ( 14 sec) [ -13950.3130] [ 2748] [depth= 2] . ( 14 sec) [ -13932.4942] [ 2736] [depth= 3] . ( 14 sec) [ -13911.8026] [ 2734] [depth= 1] . ( 14 sec) [ -13848.4763] [ 2717] [depth= 11] . ( 14 sec) [ -13841.1497] [ 2714] [depth= 1] . ( 14 sec) [ -13763.4629] [ 2676] [depth= 7] . ( 14 sec) [ -13761.1125] [ 2675] [depth= 1] . ( 14 sec) [ -13733.2590] [ 2665] [depth= 3] . ( 14 sec) [ -13717.8547] [ 2664] [depth= 1] . ( 15 sec) [ -13716.7139] [ 2665] [depth= 1] . ( 15 sec) [ -13698.6275] [ 2650] [depth= 8] . ( 15 sec) [ -13662.7628] [ 2663] [depth= 2] . ( 15 sec) [ -13661.0561] [ 2672] [depth= 1] . ( 15 sec) [ -13660.2089] [ 2671] [depth= 1] . ( 15 sec) [ -13638.7572] [ 2670] [depth= 1] . ( 16 sec) [ -13610.2667] [ 2649] [depth= 13] . ( 16 sec) [ -13595.4472] [ 2642] [depth= 1] . ( 16 sec) [ -13524.7913] [ 2619] [depth= 2] . ( 16 sec) [ -13516.7180] [ 2617] [depth= 1] . ( 16 sec) [ -13516.0138] [ 2616] [depth= 1] . ( 16 sec) [ -13458.7083] [ 2619] [depth= 13] . ( 16 sec) [ -13429.9169] [ 2613] [depth= 2] . ( 17 sec) [ -13410.8490] [ 2602] [depth= 1] . ( 17 sec) [ -13410.1198] [ 2601] [depth= 1] . ( 17 sec) [ -13366.5342] [ 2601] [depth= 9] . ( 17 sec) [ -13362.4924] [ 2603] [depth= 2] . ( 17 sec) [ -13187.6654] [ 2600] [depth= 2] . ( 17 sec) [ -13184.2779] [ 2598] [depth= 5] . ( 18 sec) [ -13162.2774] [ 2583] [depth= 7] . ( 18 sec) [ -13134.7528] [ 2583] [depth= 1] . ( 18 sec) [ -13134.4329] [ 2583] [depth= 1] . ( 18 sec) [ -13134.0605] [ 2583] [depth= 1] . ( 18 sec) [ -12977.1102] [ 2537] [depth= 10] . ( 19 sec) [ -12977.0904] [ 2537] [depth= 1] . ( 19 sec) [ -12968.3599] [ 2538] [depth= 6] . ( 19 sec) [ -12928.9177] [ 2529] [depth= 3] . ( 19 sec) [ -12887.2504] [ 2512] [depth= 1] . ( 19 sec) [ -12885.5884] [ 2511] [depth= 1] . ( 19 sec) [ -12855.5408] [ 2502] [depth= 1] . ( 19 sec) [ -12855.5288] [ 2500] [depth= 1] . ( 19 sec) [ -12850.6913] [ 2497] [depth= 1] . ( 19 sec) [ -12848.6313] [ 2496] [depth= 2] . ( 20 sec) [ -12848.1897] [ 2497] [depth= 1] . ( 20 sec) [ -12804.8568] [ 2498] [depth= 15] . ( 20 sec) [ -12804.5347] [ 2495] [depth= 2] . ( 20 sec) [ -12741.0498] [ 2471] [depth= 3] . ( 20 sec) [ -12721.1992] [ 2472] [depth= 3] . ( 20 sec) [ -12707.0450] [ 2471] [depth= 2] . ( 20 sec) [ -12704.7958] [ 2471] [depth= 1] . ( 20 sec) [ -12702.4093] [ 2468] [depth= 9] . ( 20 sec) [ -12668.6790] [ 2453] [depth= 1] . ( 21 sec) [ -12578.1489] [ 2447] [depth= 3] . ( 21 sec) [ -12572.0823] [ 2444] [depth= 1] . ( 21 sec) [ -12546.2162] [ 2438] [depth= 4] . ( 21 sec) [ -12540.6948] [ 2434] [depth= 1] . ( 21 sec) [ -12447.3096] [ 2382] [depth= 6] . ( 21 sec) [ -12397.9981] [ 2372] [depth= 7] . ( 21 sec) [ -12364.5470] [ 2363] [depth= 2] . ( 22 sec) [ -12359.6620] [ 2362] [depth= 3] . ( 22 sec) [ -12204.3793] [Branch lengths ] . ( 23 sec) [ -12182.8612] [GTR parameters ] . ( 24 sec) [ -12152.0264] [Alpha ][ 0.344472] . ( 24 sec) [ -12136.9016] [ 2355] [depth= 2] . ( 24 sec) [ -12115.1896] [ 2347] [depth= 3] . ( 24 sec) [ -12109.4870] [ 2341] [depth= 5] . ( 25 sec) [ -12106.3386] [ 2339] [depth= 2] . ( 25 sec) [ -12099.6963] [ 2337] [depth= 1] . ( 25 sec) [ -12098.3521] [ 2333] [depth= 1] . ( 25 sec) [ -12097.8171] [ 2334] [depth= 1] . ( 25 sec) [ -12092.7784] [ 2334] [depth= 1] . ( 25 sec) [ -12091.1294] [ 2327] [depth= 1] . ( 26 sec) [ -12086.4412] [ 2325] [depth= 7] . ( 26 sec) [ -12061.2739] [ 2321] [depth= 2] . ( 28 sec) [ -12051.4263] [ 2319] [depth= 4] . ( 28 sec) [ -12049.8190] [ 2319] [depth= 1] . ( 28 sec) [ -12049.7080] [ 2319] [depth= 1] . ( 29 sec) [ -12048.9720] [ 2318] [depth= 1] . ( 29 sec) [ -12048.7753] [ 2318] [depth= 1] . ( 29 sec) [ -12047.6948] [ 2319] [depth= 1] . ( 30 sec) [ -12042.0762] [ 2317] [depth= 4] . ( 31 sec) [ -12038.9188] [ 2318] [depth= 1] . ( 32 sec) [ -12038.6362] [ 2319] [depth= 1] . ( 32 sec) [ -12038.4158] [ 2319] [depth= 1] . ( 32 sec) [ -12028.7299] [ 2314] [depth= 2] . ( 33 sec) [ -12028.6687] [ 2314] [depth= 1] . ( 35 sec) [ -12025.4990] [ 2313] [depth= 1] . ( 35 sec) [ -12023.4406] [ 2316] [depth= 2] . ( 39 sec) [ -12023.2577] [ 2316] [depth= 1] . ( 40 sec) [ -12004.7310] [Branch lengths ] . ( 41 sec) [ -12004.0693] [GTR parameters ] . ( 41 sec) [ -12003.9928] [Alpha ][ 0.338283] . ( 47 sec) [ -12003.7234] [ 2318] [depth= 1] . ( 59 sec) [ -12002.8449] [Branch lengths ] . ( 60 sec) [ -12002.8426] [GTR parameters ] . ( 60 sec) [ -12002.8410] [Alpha ][ 0.337317] . ( 78 sec) [ -12002.8140] [Branch lengths ] . ( 151 sec) [ -12002.8130] [Branch lengths ] . ( 151 sec) [ -12002.8130] [Topology ] . ( 153 sec) [ -12002.8130] [Topology ] . ( 153 sec) [ -12002.8129] [GTR parameters ] . ( 154 sec) [ -12002.8129] [Alpha ][ 0.337317] . Checking for NNIs, optimizing five branches... . ( 167 sec) [ -12002.6780] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12002.677955. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -22725.6629] [GTR parameters ] . ( 7 sec) [ -22135.3906] [Alpha ][ 0.500960] . ( 7 sec) [ -21870.7551] [ 4243] [depth= 13] . ( 7 sec) [ -21731.1180] [ 4201] [depth= 12] . ( 7 sec) [ -21697.2193] [ 4194] [depth= 1] . ( 7 sec) [ -21563.3503] [ 4166] [depth= 11] . ( 7 sec) [ -21386.2168] [ 4147] [depth= 2] . ( 7 sec) [ -21312.3416] [ 4138] [depth= 2] . ( 8 sec) [ -21114.7041] [ 4135] [depth= 1] . ( 8 sec) [ -21054.3120] [ 4125] [depth= 12] . ( 8 sec) [ -20884.3384] [ 4103] [depth= 3] . ( 8 sec) [ -20844.9688] [ 4077] [depth= 9] . ( 8 sec) [ -20601.9731] [ 4070] [depth= 4] . ( 8 sec) [ -20530.2938] [ 4059] [depth= 11] . ( 8 sec) [ -20334.5839] [ 4042] [depth= 6] . ( 8 sec) [ -20192.5903] [ 4041] [depth= 4] . ( 8 sec) [ -19928.5577] [ 3987] [depth= 3] . ( 8 sec) [ -19717.2899] [ 3924] [depth= 18] . ( 8 sec) [ -19709.0958] [ 3925] [depth= 1] . ( 9 sec) [ -19653.8957] [ 3903] [depth= 19] . ( 9 sec) [ -19577.6357] [ 3891] [depth= 1] . ( 9 sec) [ -19514.2936] [ 3887] [depth= 9] . ( 9 sec) [ -19207.5807] [ 3866] [depth= 14] . ( 9 sec) [ -19130.5125] [ 3851] [depth= 12] . ( 9 sec) [ -19091.9207] [ 3836] [depth= 1] . ( 9 sec) [ -19074.7978] [ 3833] [depth= 1] . ( 9 sec) [ -19059.8243] [ 3831] [depth= 1] . ( 9 sec) [ -19053.0442] [ 3836] [depth= 1] . ( 9 sec) [ -18864.1383] [ 3808] [depth= 14] . ( 10 sec) [ -18842.1628] [ 3794] [depth= 1] . ( 10 sec) [ -18729.7490] [ 3774] [depth= 6] . ( 10 sec) [ -18646.6378] [ 3766] [depth= 9] . ( 10 sec) [ -18640.1646] [ 3763] [depth= 1] . ( 10 sec) [ -18622.5277] [ 3756] [depth= 12] . ( 10 sec) [ -18440.1200] [ 3749] [depth= 4] . ( 10 sec) [ -18328.9946] [ 3740] [depth= 2] . ( 10 sec) [ -18296.7106] [ 3717] [depth= 19] . ( 10 sec) [ -18264.5929] [ 3711] [depth= 1] . ( 10 sec) [ -18257.9134] [ 3703] [depth= 13] . ( 10 sec) [ -18148.0028] [ 3682] [depth= 12] . ( 11 sec) [ -17935.2130] [ 3639] [depth= 10] . ( 11 sec) [ -17854.5623] [ 3625] [depth= 13] . ( 11 sec) [ -17764.3360] [ 3593] [depth= 2] . ( 11 sec) [ -17639.5776] [ 3581] [depth= 8] . ( 11 sec) [ -17514.3742] [ 3568] [depth= 12] . ( 11 sec) [ -17388.1529] [ 3530] [depth= 3] . ( 11 sec) [ -17323.5434] [ 3504] [depth= 1] . ( 11 sec) [ -17099.0133] [ 3481] [depth= 8] . ( 11 sec) [ -17059.5795] [ 3485] [depth= 18] . ( 11 sec) [ -17056.3402] [ 3497] [depth= 5] . ( 11 sec) [ -16962.0256] [ 3471] [depth= 2] . ( 12 sec) [ -16867.9649] [ 3439] [depth= 15] . ( 12 sec) [ -16803.3851] [ 3427] [depth= 4] . ( 12 sec) [ -16739.2260] [ 3412] [depth= 9] . ( 12 sec) [ -16616.8004] [ 3386] [depth= 18] . ( 12 sec) [ -16591.1882] [ 3385] [depth= 13] . ( 12 sec) [ -16572.2192] [ 3371] [depth= 17] . ( 12 sec) [ -16571.7214] [ 3372] [depth= 1] . ( 12 sec) [ -16491.5568] [ 3346] [depth= 5] . ( 12 sec) [ -16328.1483] [ 3330] [depth= 4] . ( 13 sec) [ -16127.6206] [ 3287] [depth= 6] . ( 13 sec) [ -16084.9984] [ 3283] [depth= 17] . ( 13 sec) [ -16014.8338] [ 3270] [depth= 12] . ( 13 sec) [ -16010.0562] [ 3265] [depth= 3] . ( 13 sec) [ -15994.9578] [ 3265] [depth= 1] . ( 13 sec) [ -15936.5880] [ 3253] [depth= 3] . ( 13 sec) [ -15909.1777] [ 3249] [depth= 5] . ( 13 sec) [ -15864.9938] [ 3231] [depth= 4] . ( 13 sec) [ -15809.3036] [ 3225] [depth= 12] . ( 13 sec) [ -15803.8715] [ 3231] [depth= 1] . ( 13 sec) [ -15755.4478] [ 3224] [depth= 1] . ( 14 sec) [ -15621.1675] [ 3187] [depth= 9] . ( 14 sec) [ -15452.0535] [ 3142] [depth= 15] . ( 14 sec) [ -15419.9145] [ 3142] [depth= 3] . ( 14 sec) [ -15374.0952] [ 3125] [depth= 1] . ( 14 sec) [ -15373.0249] [ 3137] [depth= 2] . ( 14 sec) [ -15350.1967] [ 3132] [depth= 3] . ( 14 sec) [ -15334.8002] [ 3128] [depth= 6] . ( 14 sec) [ -15214.1458] [ 3122] [depth= 13] . ( 14 sec) [ -15183.7971] [ 3125] [depth= 1] . ( 14 sec) [ -15014.1947] [ 3121] [depth= 14] . ( 15 sec) [ -14985.6315] [ 3110] [depth= 4] . ( 15 sec) [ -14890.0801] [ 3110] [depth= 7] . ( 15 sec) [ -14825.5365] [ 3094] [depth= 1] . ( 15 sec) [ -14795.0807] [ 3073] [depth= 1] . ( 15 sec) [ -14747.9607] [ 3055] [depth= 9] . ( 15 sec) [ -14699.0001] [ 3040] [depth= 1] . ( 15 sec) [ -14648.9957] [ 3019] [depth= 1] . ( 15 sec) [ -14609.0101] [ 3004] [depth= 1] . ( 15 sec) [ -14600.3752] [ 2997] [depth= 1] . ( 15 sec) [ -14486.7969] [ 2970] [depth= 10] . ( 16 sec) [ -14373.2245] [ 2933] [depth= 11] . ( 16 sec) [ -14330.3995] [ 2915] [depth= 5] . ( 16 sec) [ -14226.9769] [ 2892] [depth= 8] . ( 16 sec) [ -14192.6684] [ 2890] [depth= 4] . ( 16 sec) [ -14170.9433] [ 2881] [depth= 1] . ( 16 sec) [ -14133.0284] [ 2865] [depth= 6] . ( 16 sec) [ -14057.7191] [ 2844] [depth= 5] . ( 17 sec) [ -13931.9711] [ 2815] [depth= 14] . ( 17 sec) [ -13924.3666] [ 2816] [depth= 1] . ( 17 sec) [ -13796.0996] [ 2766] [depth= 10] . ( 17 sec) [ -13766.0494] [ 2763] [depth= 3] . ( 17 sec) [ -13743.2125] [ 2748] [depth= 6] . ( 17 sec) [ -13724.8072] [ 2743] [depth= 2] . ( 17 sec) [ -13690.0491] [ 2731] [depth= 2] . ( 17 sec) [ -13680.2007] [ 2730] [depth= 3] . ( 17 sec) [ -13677.6225] [ 2727] [depth= 1] . ( 17 sec) [ -13673.0562] [ 2730] [depth= 1] . ( 18 sec) [ -13616.3212] [ 2712] [depth= 3] . ( 18 sec) [ -13610.2178] [ 2706] [depth= 1] . ( 18 sec) [ -13605.3575] [ 2706] [depth= 1] . ( 18 sec) [ -13600.0683] [ 2704] [depth= 1] . ( 18 sec) [ -13599.1339] [ 2702] [depth= 1] . ( 18 sec) [ -13595.4774] [ 2701] [depth= 1] . ( 18 sec) [ -13578.4528] [ 2699] [depth= 9] . ( 18 sec) [ -13574.4717] [ 2696] [depth= 2] . ( 18 sec) [ -13504.6678] [ 2689] [depth= 1] . ( 18 sec) [ -13479.9420] [ 2690] [depth= 3] . ( 18 sec) [ -13472.5537] [ 2689] [depth= 1] . ( 19 sec) [ -13408.9072] [ 2661] [depth= 1] . ( 19 sec) [ -13390.7047] [ 2652] [depth= 1] . ( 19 sec) [ -13383.4870] [ 2647] [depth= 4] . ( 19 sec) [ -13381.6762] [ 2643] [depth= 1] . ( 19 sec) [ -13381.2888] [ 2645] [depth= 2] . ( 19 sec) [ -13320.0578] [ 2640] [depth= 1] . ( 19 sec) [ -13304.4966] [ 2637] [depth= 1] . ( 20 sec) [ -13304.0482] [ 2642] [depth= 2] . ( 20 sec) [ -13264.9451] [ 2630] [depth= 4] . ( 20 sec) [ -13256.1427] [ 2629] [depth= 2] . ( 20 sec) [ -13228.8164] [ 2623] [depth= 6] . ( 20 sec) [ -13227.7289] [ 2622] [depth= 1] . ( 20 sec) [ -13227.1023] [ 2618] [depth= 10] . ( 21 sec) [ -13196.5038] [ 2599] [depth= 5] . ( 21 sec) [ -13189.8318] [ 2598] [depth= 1] . ( 21 sec) [ -13182.3374] [ 2592] [depth= 1] . ( 21 sec) [ -13172.1229] [ 2592] [depth= 1] . ( 21 sec) [ -13107.8478] [ 2571] [depth= 5] . ( 21 sec) [ -13100.4288] [ 2566] [depth= 2] . ( 21 sec) [ -13090.3339] [ 2562] [depth= 5] . ( 22 sec) [ -13047.5865] [ 2550] [depth= 1] . ( 22 sec) [ -12940.0947] [ 2519] [depth= 4] . ( 22 sec) [ -12931.6665] [ 2519] [depth= 1] . ( 22 sec) [ -12928.8155] [ 2518] [depth= 2] . ( 22 sec) [ -12914.1890] [ 2518] [depth= 2] . ( 22 sec) [ -12903.8814] [ 2516] [depth= 1] . ( 22 sec) [ -12897.9812] [ 2515] [depth= 3] . ( 23 sec) [ -12884.0735] [ 2504] [depth= 6] . ( 23 sec) [ -12878.1597] [ 2506] [depth= 4] . ( 23 sec) [ -12782.0275] [ 2463] [depth= 4] . ( 23 sec) [ -12689.6274] [ 2435] [depth= 1] . ( 23 sec) [ -12621.2905] [ 2433] [depth= 9] . ( 23 sec) [ -12618.4071] [ 2433] [depth= 1] . ( 23 sec) [ -12618.3242] [ 2433] [depth= 1] . ( 24 sec) [ -12596.1772] [ 2437] [depth= 1] . ( 24 sec) [ -12538.9367] [ 2413] [depth= 7] . ( 24 sec) [ -12533.7279] [ 2412] [depth= 2] . ( 24 sec) [ -12524.4139] [ 2416] [depth= 1] . ( 24 sec) [ -12506.3207] [ 2410] [depth= 3] . ( 24 sec) [ -12496.8705] [ 2408] [depth= 1] . ( 25 sec) [ -12297.7545] [Branch lengths ] . ( 28 sec) [ -12275.6080] [GTR parameters ] . ( 28 sec) [ -12241.3144] [Alpha ][ 0.338024] . ( 28 sec) [ -12239.6301] [ 2407] [depth= 1] . ( 29 sec) [ -12239.3105] [ 2407] [depth= 1] . ( 29 sec) [ -12181.2932] [ 2388] [depth= 11] . ( 29 sec) [ -12179.5066] [ 2389] [depth= 1] . ( 30 sec) [ -12167.7337] [ 2386] [depth= 1] . ( 30 sec) [ -12166.8301] [ 2387] [depth= 1] . ( 30 sec) [ -12166.2491] [ 2387] [depth= 1] . ( 30 sec) [ -12163.4263] [ 2385] [depth= 1] . ( 31 sec) [ -12163.3968] [ 2385] [depth= 1] . ( 31 sec) [ -12161.5086] [ 2384] [depth= 1] . ( 31 sec) [ -12141.1398] [ 2371] [depth= 2] . ( 31 sec) [ -12140.8887] [ 2372] [depth= 1] . ( 31 sec) [ -12136.2823] [ 2367] [depth= 1] . ( 31 sec) [ -12136.2086] [ 2364] [depth= 1] . ( 33 sec) [ -12131.2498] [ 2357] [depth= 1] . ( 33 sec) [ -12125.3988] [ 2355] [depth= 1] . ( 33 sec) [ -12124.6153] [ 2350] [depth= 1] . ( 34 sec) [ -12123.5460] [ 2352] [depth= 1] . ( 34 sec) [ -12123.5301] [ 2354] [depth= 1] . ( 34 sec) [ -12123.4717] [ 2353] [depth= 1] . ( 35 sec) [ -12103.2276] [ 2345] [depth= 1] . ( 35 sec) [ -12085.4241] [ 2340] [depth= 8] . ( 35 sec) [ -12085.3886] [ 2341] [depth= 1] . ( 37 sec) [ -12084.9389] [ 2341] [depth= 1] . ( 38 sec) [ -12081.1916] [ 2335] [depth= 2] . ( 38 sec) [ -12073.3817] [ 2335] [depth= 1] . ( 38 sec) [ -12071.8027] [ 2334] [depth= 1] . ( 38 sec) [ -12070.1407] [ 2334] [depth= 1] . ( 38 sec) [ -12068.3624] [ 2333] [depth= 1] . ( 38 sec) [ -12066.0984] [ 2333] [depth= 1] . ( 40 sec) [ -12062.0347] [ 2331] [depth= 1] . ( 40 sec) [ -12060.8930] [ 2329] [depth= 1] . ( 41 sec) [ -12055.7617] [ 2327] [depth= 1] . ( 41 sec) [ -12054.8159] [ 2329] [depth= 1] . ( 42 sec) [ -12047.8507] [ 2324] [depth= 1] . ( 43 sec) [ -12047.3242] [ 2326] [depth= 1] . ( 44 sec) [ -12047.2798] [ 2326] [depth= 1] . ( 45 sec) [ -12046.6601] [ 2325] [depth= 1] . ( 46 sec) [ -12021.4175] [Branch lengths ] . ( 48 sec) [ -12020.1937] [GTR parameters ] . ( 49 sec) [ -12020.1716] [Alpha ][ 0.341454] . ( 50 sec) [ -12019.6186] [ 2324] [depth= 2] . ( 52 sec) [ -12017.9036] [ 2322] [depth= 1] . ( 53 sec) [ -12017.8914] [ 2319] [depth= 1] . ( 53 sec) [ -12016.5845] [ 2317] [depth= 5] . ( 54 sec) [ -12008.3634] [ 2314] [depth= 1] . ( 65 sec) [ -12002.6119] [Branch lengths ] . ( 68 sec) [ -12002.5340] [GTR parameters ] . ( 68 sec) [ -12002.5285] [Alpha ][ 0.339672] . ( 73 sec) [ -12002.4518] [ 2316] [depth= 1] . ( 85 sec) [ -12002.0437] [Branch lengths ] . ( 86 sec) [ -12002.0425] [GTR parameters ] . ( 86 sec) [ -12002.0424] [Alpha ][ 0.339326] . ( 163 sec) [ -12002.0265] [Branch lengths ] . ( 163 sec) [ -12002.0265] [Topology ] . ( 164 sec) [ -12002.0261] [Topology ] . ( 165 sec) [ -12002.0261] [GTR parameters ] . ( 165 sec) [ -12002.0261] [Alpha ][ 0.339326] . Checking for NNIs, optimizing five branches... . ( 177 sec) [ -12001.9823] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12001.982337. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -22866.4698] [GTR parameters ] . ( 3 sec) [ -22270.7230] [Alpha ][ 0.500960] . ( 3 sec) [ -21992.5361] [ 4221] [depth= 13] . ( 4 sec) [ -21877.9682] [ 4190] [depth= 13] . ( 4 sec) [ -21756.6775] [ 4171] [depth= 8] . ( 4 sec) [ -21673.9796] [ 4154] [depth= 1] . ( 4 sec) [ -21537.9802] [ 4146] [depth= 8] . ( 4 sec) [ -21501.6620] [ 4146] [depth= 1] . ( 4 sec) [ -21456.2603] [ 4137] [depth= 12] . ( 4 sec) [ -21312.3486] [ 4109] [depth= 3] . ( 4 sec) [ -21075.3317] [ 4101] [depth= 13] . ( 4 sec) [ -21016.8970] [ 4076] [depth= 10] . ( 4 sec) [ -21004.9797] [ 4074] [depth= 2] . ( 5 sec) [ -20898.4242] [ 4035] [depth= 5] . ( 5 sec) [ -20854.2077] [ 4033] [depth= 1] . ( 5 sec) [ -20550.9932] [ 4016] [depth= 9] . ( 5 sec) [ -20373.3488] [ 4000] [depth= 2] . ( 5 sec) [ -20354.8715] [ 3980] [depth= 13] . ( 5 sec) [ -20151.3671] [ 3903] [depth= 7] . ( 5 sec) [ -20145.3674] [ 3903] [depth= 6] . ( 5 sec) [ -20141.3308] [ 3901] [depth= 1] . ( 5 sec) [ -20082.5555] [ 3896] [depth= 3] . ( 5 sec) [ -20073.4370] [ 3883] [depth= 8] . ( 5 sec) [ -20007.0438] [ 3878] [depth= 1] . ( 6 sec) [ -19721.9184] [ 3852] [depth= 7] . ( 6 sec) [ -19662.4263] [ 3853] [depth= 1] . ( 6 sec) [ -19580.9926] [ 3809] [depth= 10] . ( 6 sec) [ -19532.0342] [ 3805] [depth= 12] . ( 6 sec) [ -19345.4014] [ 3778] [depth= 11] . ( 6 sec) [ -19328.7976] [ 3777] [depth= 14] . ( 6 sec) [ -19105.7693] [ 3777] [depth= 2] . ( 6 sec) [ -19080.7592] [ 3770] [depth= 8] . ( 6 sec) [ -19056.0237] [ 3766] [depth= 4] . ( 6 sec) [ -18753.8641] [ 3763] [depth= 2] . ( 6 sec) [ -18595.9250] [ 3764] [depth= 2] . ( 7 sec) [ -18432.0855] [ 3754] [depth= 3] . ( 7 sec) [ -18379.9860] [ 3743] [depth= 11] . ( 7 sec) [ -18339.7420] [ 3734] [depth= 2] . ( 7 sec) [ -18184.7635] [ 3719] [depth= 9] . ( 7 sec) [ -18174.9576] [ 3711] [depth= 3] . ( 7 sec) [ -18147.1041] [ 3714] [depth= 8] . ( 7 sec) [ -18118.2136] [ 3704] [depth= 10] . ( 7 sec) [ -18031.2595] [ 3683] [depth= 12] . ( 7 sec) [ -17957.3786] [ 3666] [depth= 15] . ( 8 sec) [ -17894.0918] [ 3640] [depth= 9] . ( 8 sec) [ -17754.8174] [ 3596] [depth= 8] . ( 8 sec) [ -17721.6916] [ 3579] [depth= 11] . ( 8 sec) [ -17597.3611] [ 3569] [depth= 5] . ( 8 sec) [ -17432.0796] [ 3575] [depth= 1] . ( 8 sec) [ -17301.5339] [ 3568] [depth= 2] . ( 8 sec) [ -17196.2551] [ 3555] [depth= 15] . ( 8 sec) [ -17158.9275] [ 3529] [depth= 4] . ( 8 sec) [ -17116.6635] [ 3520] [depth= 4] . ( 8 sec) [ -16949.4480] [ 3492] [depth= 14] . ( 8 sec) [ -16902.3071] [ 3475] [depth= 1] . ( 9 sec) [ -16721.3185] [ 3437] [depth= 16] . ( 9 sec) [ -16533.9120] [ 3403] [depth= 13] . ( 9 sec) [ -16482.7881] [ 3394] [depth= 1] . ( 9 sec) [ -16297.2369] [ 3362] [depth= 3] . ( 9 sec) [ -16242.3667] [ 3350] [depth= 1] . ( 9 sec) [ -16147.2816] [ 3331] [depth= 11] . ( 9 sec) [ -15818.1168] [ 3293] [depth= 13] . ( 9 sec) [ -15814.9812] [ 3295] [depth= 1] . ( 9 sec) [ -15718.2960] [ 3270] [depth= 7] . ( 10 sec) [ -15596.2690] [ 3212] [depth= 11] . ( 10 sec) [ -15585.5088] [ 3210] [depth= 6] . ( 10 sec) [ -15564.5900] [ 3199] [depth= 4] . ( 10 sec) [ -15557.8575] [ 3186] [depth= 4] . ( 10 sec) [ -15549.4787] [ 3185] [depth= 3] . ( 10 sec) [ -15409.1903] [ 3166] [depth= 12] . ( 10 sec) [ -15368.1550] [ 3143] [depth= 16] . ( 10 sec) [ -15228.8829] [ 3146] [depth= 1] . ( 11 sec) [ -15164.3956] [ 3127] [depth= 2] . ( 11 sec) [ -15090.4542] [ 3108] [depth= 11] . ( 11 sec) [ -15088.1313] [ 3115] [depth= 15] . ( 11 sec) [ -15063.2047] [ 3108] [depth= 14] . ( 11 sec) [ -15028.2686] [ 3096] [depth= 15] . ( 11 sec) [ -15025.3338] [ 3085] [depth= 9] . ( 12 sec) [ -14986.0575] [ 3084] [depth= 6] . ( 12 sec) [ -14798.8387] [ 3047] [depth= 7] . ( 12 sec) [ -14793.8570] [ 3048] [depth= 1] . ( 12 sec) [ -14741.6341] [ 3036] [depth= 4] . ( 12 sec) [ -14706.9258] [ 3034] [depth= 1] . ( 12 sec) [ -14662.9754] [ 3032] [depth= 2] . ( 12 sec) [ -14654.4417] [ 3027] [depth= 2] . ( 12 sec) [ -14563.8346] [ 3002] [depth= 4] . ( 12 sec) [ -14538.7341] [ 2994] [depth= 4] . ( 12 sec) [ -14459.8009] [ 2990] [depth= 2] . ( 12 sec) [ -14357.0468] [ 2948] [depth= 1] . ( 13 sec) [ -14225.1264] [ 2928] [depth= 6] . ( 13 sec) [ -14173.1704] [ 2902] [depth= 3] . ( 13 sec) [ -14043.2326] [ 2888] [depth= 4] . ( 13 sec) [ -13999.5340] [ 2877] [depth= 2] . ( 13 sec) [ -13873.3123] [ 2838] [depth= 6] . ( 13 sec) [ -13828.8601] [ 2827] [depth= 2] . ( 13 sec) [ -13810.3812] [ 2824] [depth= 1] . ( 13 sec) [ -13806.0043] [ 2825] [depth= 2] . ( 14 sec) [ -13803.7560] [ 2827] [depth= 1] . ( 14 sec) [ -13803.3692] [ 2825] [depth= 2] . ( 14 sec) [ -13790.7789] [ 2821] [depth= 4] . ( 14 sec) [ -13783.8790] [ 2810] [depth= 8] . ( 14 sec) [ -13779.2293] [ 2809] [depth= 4] . ( 14 sec) [ -13776.7070] [ 2809] [depth= 1] . ( 14 sec) [ -13678.1653] [ 2772] [depth= 4] . ( 14 sec) [ -13665.9131] [ 2770] [depth= 1] . ( 14 sec) [ -13637.6130] [ 2767] [depth= 3] . ( 15 sec) [ -13635.6836] [ 2767] [depth= 1] . ( 15 sec) [ -13609.7728] [ 2764] [depth= 8] . ( 15 sec) [ -13596.4500] [ 2757] [depth= 1] . ( 15 sec) [ -13594.0851] [ 2762] [depth= 1] . ( 15 sec) [ -13563.1953] [ 2752] [depth= 1] . ( 15 sec) [ -13435.0428] [ 2712] [depth= 14] . ( 15 sec) [ -13429.3001] [ 2704] [depth= 1] . ( 15 sec) [ -13376.5218] [ 2681] [depth= 3] . ( 15 sec) [ -13310.8973] [ 2660] [depth= 10] . ( 16 sec) [ -13297.5486] [ 2652] [depth= 2] . ( 16 sec) [ -13283.4163] [ 2648] [depth= 1] . ( 16 sec) [ -13282.2444] [ 2648] [depth= 1] . ( 16 sec) [ -13269.9852] [ 2645] [depth= 1] . ( 16 sec) [ -13238.3525] [ 2632] [depth= 5] . ( 16 sec) [ -13229.5883] [ 2629] [depth= 2] . ( 16 sec) [ -13117.0213] [ 2611] [depth= 5] . ( 16 sec) [ -13090.3607] [ 2608] [depth= 8] . ( 16 sec) [ -13079.5047] [ 2609] [depth= 1] . ( 17 sec) [ -13079.4278] [ 2613] [depth= 1] . ( 17 sec) [ -13028.1583] [ 2605] [depth= 3] . ( 17 sec) [ -13001.0205] [ 2593] [depth= 8] . ( 17 sec) [ -12998.5920] [ 2581] [depth= 2] . ( 17 sec) [ -12983.9562] [ 2576] [depth= 2] . ( 17 sec) [ -12980.5617] [ 2578] [depth= 1] . ( 18 sec) [ -12891.7573] [ 2551] [depth= 8] . ( 18 sec) [ -12888.1002] [ 2558] [depth= 1] . ( 18 sec) [ -12863.1491] [ 2547] [depth= 5] . ( 18 sec) [ -12849.8764] [ 2543] [depth= 2] . ( 18 sec) [ -12828.6881] [ 2543] [depth= 3] . ( 18 sec) [ -12824.9583] [ 2541] [depth= 2] . ( 18 sec) [ -12700.1524] [ 2526] [depth= 1] . ( 18 sec) [ -12621.6175] [ 2479] [depth= 4] . ( 18 sec) [ -12621.2351] [ 2479] [depth= 1] . ( 18 sec) [ -12610.9607] [ 2478] [depth= 2] . ( 18 sec) [ -12560.6822] [ 2460] [depth= 2] . ( 19 sec) [ -12559.4441] [ 2460] [depth= 1] . ( 19 sec) [ -12553.9118] [ 2459] [depth= 2] . ( 19 sec) [ -12549.4745] [ 2459] [depth= 1] . ( 19 sec) [ -12529.6279] [ 2452] [depth= 1] . ( 19 sec) [ -12506.2229] [ 2438] [depth= 2] . ( 20 sec) [ -12504.1641] [ 2435] [depth= 6] . ( 20 sec) [ -12504.1518] [ 2436] [depth= 1] . ( 20 sec) [ -12425.5387] [ 2415] [depth= 3] . ( 21 sec) [ -12421.9138] [ 2415] [depth= 1] . ( 21 sec) [ -12421.2158] [ 2418] [depth= 1] . ( 21 sec) [ -12410.9706] [ 2414] [depth= 1] . ( 21 sec) [ -12402.2981] [ 2408] [depth= 1] . ( 22 sec) [ -12388.0041] [ 2406] [depth= 4] . ( 22 sec) [ -12386.0881] [ 2402] [depth= 1] . ( 22 sec) [ -12294.6947] [Branch lengths ] . ( 24 sec) [ -12275.1032] [GTR parameters ] . ( 24 sec) [ -12242.1469] [Alpha ][ 0.338173] . ( 24 sec) [ -12240.7988] [ 2404] [depth= 2] . ( 24 sec) [ -12236.3496] [ 2397] [depth= 2] . ( 24 sec) [ -12236.0540] [ 2391] [depth= 1] . ( 25 sec) [ -12236.0429] [ 2391] [depth= 1] . ( 25 sec) [ -12194.9088] [ 2361] [depth= 6] . ( 25 sec) [ -12167.9673] [ 2351] [depth= 1] . ( 26 sec) [ -12162.7486] [ 2351] [depth= 5] . ( 26 sec) [ -12161.3200] [ 2350] [depth= 1] . ( 26 sec) [ -12161.0038] [ 2351] [depth= 1] . ( 27 sec) [ -12146.6966] [ 2346] [depth= 1] . ( 28 sec) [ -12145.9647] [ 2347] [depth= 1] . ( 28 sec) [ -12141.5990] [ 2348] [depth= 2] . ( 28 sec) [ -12139.1042] [ 2345] [depth= 1] . ( 28 sec) [ -12137.0794] [ 2344] [depth= 1] . ( 29 sec) [ -12121.1672] [ 2340] [depth= 2] . ( 29 sec) [ -12120.5824] [ 2339] [depth= 1] . ( 30 sec) [ -12120.3968] [ 2340] [depth= 2] . ( 31 sec) [ -12120.0604] [ 2340] [depth= 1] . ( 31 sec) [ -12100.5707] [ 2337] [depth= 5] . ( 33 sec) [ -12086.4058] [ 2329] [depth= 2] . ( 33 sec) [ -12072.9835] [ 2324] [depth= 2] . ( 33 sec) [ -12046.4347] [ 2314] [depth= 2] . ( 34 sec) [ -12045.8078] [ 2317] [depth= 1] . ( 34 sec) [ -12045.5199] [ 2314] [depth= 1] . ( 34 sec) [ -12044.7374] [ 2313] [depth= 1] . ( 35 sec) [ -12044.1481] [ 2313] [depth= 1] . ( 36 sec) [ -12043.3410] [ 2315] [depth= 1] . ( 36 sec) [ -12043.0179] [ 2316] [depth= 2] . ( 36 sec) [ -12040.9507] [ 2316] [depth= 1] . ( 37 sec) [ -12039.1113] [ 2315] [depth= 1] . ( 37 sec) [ -12036.6538] [ 2314] [depth= 1] . ( 37 sec) [ -12035.7970] [ 2314] [depth= 1] . ( 40 sec) [ -12033.1376] [ 2315] [depth= 1] . ( 43 sec) [ -12031.6132] [ 2313] [depth= 1] . ( 43 sec) [ -12014.5201] [Branch lengths ] . ( 44 sec) [ -12013.6764] [GTR parameters ] . ( 44 sec) [ -12013.6611] [Alpha ][ 0.341029] . ( 45 sec) [ -12012.7761] [ 2318] [depth= 8] . ( 55 sec) [ -12007.8407] [ 2322] [depth= 1] . ( 55 sec) [ -12007.6703] [ 2321] [depth= 1] . ( 63 sec) [ -12005.8244] [Branch lengths ] . ( 64 sec) [ -12005.5760] [GTR parameters ] . ( 64 sec) [ -12005.5709] [Alpha ][ 0.339293] . ( 65 sec) [ -12004.5959] [ 2319] [depth= 5] . ( 82 sec) [ -12003.6404] [Branch lengths ] . ( 83 sec) [ -12003.6136] [GTR parameters ] . ( 83 sec) [ -12003.6136] [Alpha ][ 0.338954] . ( 103 sec) [ -12003.4585] [Branch lengths ] . ( 181 sec) [ -12003.4250] [Branch lengths ] . ( 181 sec) [ -12003.4250] [Topology ] . ( 183 sec) [ -12002.2839] [Topology ] . ( 184 sec) [ -12002.0629] [Topology ] . ( 186 sec) [ -12002.0424] [Topology ] . ( 188 sec) [ -12002.0384] [Topology ] . ( 190 sec) [ -12002.0375] [Topology ] . ( 190 sec) [ -12002.0267] [GTR parameters ] . ( 190 sec) [ -12002.0263] [Alpha ][ 0.339377] . ( 190 sec) [ -12002.0263] [Topology ] . ( 192 sec) [ -12002.0260] [Topology ] . ( 192 sec) [ -12002.0260] [GTR parameters ] . ( 193 sec) [ -12002.0260] [Alpha ][ 0.339377] . Checking for NNIs, optimizing five branches... . ( 205 sec) [ -12001.9854] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12001.985420. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -12577.0498] [GTR parameters ] . ( 4 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 4 sec) [ -12377.0948] [Topology ] . ( 6 sec) [ -12129.6581] [Topology ] . ( 8 sec) [ -12077.7104] [Topology ] . ( 10 sec) [ -12066.1739] [Topology ] . ( 11 sec) [ -12059.8968] [Topology ] . ( 13 sec) [ -12056.6268] [Topology ] . ( 15 sec) [ -12055.4653] [Topology ] . ( 17 sec) [ -12055.0915] [Topology ] . ( 18 sec) [ -12054.9395] [Topology ] . ( 20 sec) [ -12054.8734] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -12049.4145] [GTR parameters ] . ( 39 sec) [ -12019.0259] [Alpha ][ 0.342808] . ( 39 sec) [ -12019.0259] [Topology ] . ( 41 sec) [ -12018.5158] [Topology ] . ( 42 sec) [ -12018.4764] [Topology ] . ( 44 sec) [ -12018.4681] [Topology ] . ( 46 sec) [ -12018.4656] [Topology ] . ( 48 sec) [ -12018.4647] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -12018.2149] [GTR parameters ] . ( 63 sec) [ -12018.2002] [Alpha ][ 0.339937] . ( 63 sec) [ -12018.2002] [Topology ] . ( 64 sec) [ -12018.1950] [Topology ] . ( 66 sec) [ -12018.1935] [Topology ] . ( 68 sec) [ -12018.1928] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -12018.1923] [GTR parameters ] . ( 82 sec) [ -12018.1923] [Alpha ][ 0.340277] . ( 82 sec) [ -12018.1923] [Topology ] . ( 83 sec) [ -12018.1918] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -12018.1918] [GTR parameters ] . ( 97 sec) [ -12018.1918] [Alpha ][ 0.340277] . ( 97 sec) [ -12018.1918] [Topology ] . ( 99 sec) [ -12018.1916] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 128 sec) [ -12577.0498] [GTR parameters ] . ( 129 sec) [ -12377.0948] [Alpha ][ 0.500960] . ( 129 sec) [ -12365.3304] [ 2346] [depth= 1] . ( 130 sec) [ -12354.0229] [ 2343] [depth= 2] . ( 130 sec) [ -12353.3959] [ 2342] [depth= 1] . ( 131 sec) [ -12351.9309] [ 2349] [depth= 1] . ( 131 sec) [ -12344.2940] [ 2342] [depth= 1] . ( 132 sec) [ -12343.9370] [ 2345] [depth= 1] . ( 132 sec) [ -12341.1247] [ 2342] [depth= 1] . ( 132 sec) [ -12339.7917] [ 2343] [depth= 1] . ( 133 sec) [ -12330.3304] [ 2338] [depth= 1] . ( 133 sec) [ -12326.8104] [ 2337] [depth= 1] . ( 133 sec) [ -12318.9434] [ 2337] [depth= 1] . ( 133 sec) [ -12317.3269] [ 2336] [depth= 2] . ( 134 sec) [ -12315.1793] [ 2341] [depth= 1] . ( 134 sec) [ -12302.5428] [ 2333] [depth= 3] . ( 134 sec) [ -12295.8939] [ 2330] [depth= 1] . ( 134 sec) [ -12285.8561] [ 2329] [depth= 1] . ( 135 sec) [ -12282.8796] [ 2326] [depth= 1] . ( 135 sec) [ -12282.8441] [ 2330] [depth= 1] . ( 135 sec) [ -12278.1742] [ 2333] [depth= 1] . ( 136 sec) [ -12266.9658] [ 2330] [depth= 1] . ( 136 sec) [ -12263.0264] [ 2330] [depth= 1] . ( 136 sec) [ -12249.6816] [ 2322] [depth= 2] . ( 136 sec) [ -12244.2880] [ 2320] [depth= 1] . ( 136 sec) [ -12243.7901] [ 2320] [depth= 1] . ( 136 sec) [ -12242.3925] [ 2321] [depth= 2] . ( 137 sec) [ -12229.5147] [ 2323] [depth= 1] . ( 137 sec) [ -12224.1700] [ 2324] [depth= 1] . ( 137 sec) [ -12220.4438] [ 2323] [depth= 1] . ( 137 sec) [ -12218.3062] [ 2323] [depth= 1] . ( 138 sec) [ -12209.6820] [ 2324] [depth= 1] . ( 138 sec) [ -12207.7561] [ 2320] [depth= 1] . ( 138 sec) [ -12207.2951] [ 2319] [depth= 1] . ( 138 sec) [ -12204.6151] [ 2318] [depth= 1] . ( 138 sec) [ -12199.8629] [ 2319] [depth= 1] . ( 139 sec) [ -12196.1650] [ 2320] [depth= 5] . ( 139 sec) [ -12193.7131] [ 2323] [depth= 1] . ( 139 sec) [ -12185.3317] [ 2319] [depth= 1] . ( 140 sec) [ -12185.1923] [ 2324] [depth= 1] . ( 140 sec) [ -12178.7280] [ 2328] [depth= 1] . ( 140 sec) [ -12178.1013] [ 2329] [depth= 1] . ( 141 sec) [ -12176.5338] [ 2330] [depth= 1] . ( 141 sec) [ -12171.8305] [ 2329] [depth= 1] . ( 142 sec) [ -12170.4235] [ 2324] [depth= 1] . ( 142 sec) [ -12160.5764] [ 2321] [depth= 1] . ( 142 sec) [ -12157.6967] [ 2321] [depth= 1] . ( 143 sec) [ -12157.3158] [ 2320] [depth= 4] . ( 143 sec) [ -12156.8007] [ 2320] [depth= 1] . ( 143 sec) [ -12156.4817] [ 2320] [depth= 1] . ( 143 sec) [ -12156.4257] [ 2320] [depth= 1] . ( 145 sec) [ -12066.3627] [Branch lengths ] . ( 148 sec) [ -12061.7387] [GTR parameters ] . ( 148 sec) [ -12029.8111] [Alpha ][ 0.335117] . ( 149 sec) [ -12029.7924] [ 2321] [depth= 1] . ( 152 sec) [ -12028.6586] [ 2321] [depth= 2] . ( 152 sec) [ -12027.8434] [ 2322] [depth= 2] . ( 153 sec) [ -12027.4406] [ 2311] [depth= 2] . ( 155 sec) [ -12025.2256] [ 2313] [depth= 1] . ( 156 sec) [ -12024.1298] [ 2314] [depth= 1] . ( 157 sec) [ -12023.3466] [ 2317] [depth= 8] . ( 157 sec) [ -12022.5281] [ 2318] [depth= 1] . ( 160 sec) [ -12020.5984] [ 2318] [depth= 5] . ( 163 sec) [ -12004.6389] [Branch lengths ] . ( 166 sec) [ -12004.1797] [GTR parameters ] . ( 166 sec) [ -12004.1775] [Alpha ][ 0.336180] . ( 171 sec) [ -12004.1566] [ 2319] [depth= 1] . ( 185 sec) [ -12002.2446] [Branch lengths ] . ( 187 sec) [ -12002.2318] [GTR parameters ] . ( 187 sec) [ -12002.2282] [Alpha ][ 0.337511] . ( 207 sec) [ -12002.0719] [Branch lengths ] . ( 285 sec) [ -12002.0517] [Branch lengths ] . ( 285 sec) [ -12002.0517] [Topology ] . ( 287 sec) [ -12001.1336] [Topology ] . ( 288 sec) [ -12001.0186] [Topology ] . ( 290 sec) [ -12001.0091] [Topology ] . ( 292 sec) [ -12001.0076] [Topology ] . ( 294 sec) [ -12001.0073] [Topology ] . ( 295 sec) [ -12000.9981] [GTR parameters ] . ( 296 sec) [ -12000.9977] [Alpha ][ 0.337953] . ( 296 sec) [ -12000.9977] [Topology ] . ( 297 sec) [ -12000.9974] [Topology ] . ( 298 sec) [ -12000.9974] [GTR parameters ] . ( 298 sec) [ -12000.9974] [Alpha ][ 0.337953] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12018.191571 . Log likelihood obtained after SPR moves : -12000.997416 . Log likelihood of the current tree: -12000.997416. . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Best log likelihood : -12000.747954 . Time used 0h5m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1280.99user 0.00system 21:27.30elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps