.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data60.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... . 433 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19992.8867] [GTR parameters ] . ( 1 sec) [ -19654.1343] [Alpha ][ 0.500960] . ( 1 sec) [ -19212.5991] [ 4237] [depth= 8] . ( 1 sec) [ -18936.5657] [ 4197] [depth= 6] . ( 1 sec) [ -18866.3126] [ 4181] [depth= 2] . ( 1 sec) [ -18854.1954] [ 4167] [depth= 6] . ( 1 sec) [ -18682.3983] [ 4121] [depth= 3] . ( 1 sec) [ -18599.0644] [ 4119] [depth= 6] . ( 1 sec) [ -18582.2376] [ 4112] [depth= 5] . ( 1 sec) [ -18534.8008] [ 4129] [depth= 1] . ( 1 sec) [ -18483.8606] [ 4112] [depth= 1] . ( 1 sec) [ -18472.7007] [ 4099] [depth= 1] . ( 1 sec) [ -17721.7810] [ 4051] [depth= 9] . ( 1 sec) [ -17630.2918] [ 4016] [depth= 3] . ( 1 sec) [ -17557.9289] [ 4003] [depth= 7] . ( 1 sec) [ -17495.9518] [ 4003] [depth= 1] . ( 1 sec) [ -17348.0832] [ 3978] [depth= 4] . ( 1 sec) [ -17152.9483] [ 3922] [depth= 1] . ( 1 sec) [ -17034.5172] [ 3906] [depth= 4] . ( 1 sec) [ -16977.5776] [ 3902] [depth= 1] . ( 2 sec) [ -16917.2977] [ 3890] [depth= 15] . ( 2 sec) [ -16823.5121] [ 3844] [depth= 16] . ( 2 sec) [ -16548.5517] [ 3797] [depth= 14] . ( 2 sec) [ -16435.4970] [ 3807] [depth= 18] . ( 2 sec) [ -16355.5207] [ 3735] [depth= 1] . ( 2 sec) [ -16171.7693] [ 3722] [depth= 3] . ( 2 sec) [ -15705.4086] [ 3647] [depth= 9] . ( 2 sec) [ -15475.1671] [ 3595] [depth= 2] . ( 2 sec) [ -14757.3697] [ 3535] [depth= 4] . ( 2 sec) [ -14633.2426] [ 3512] [depth= 7] . ( 2 sec) [ -14471.7342] [ 3488] [depth= 7] . ( 2 sec) [ -14434.2820] [ 3480] [depth= 2] . ( 2 sec) [ -14426.8546] [ 3474] [depth= 1] . ( 2 sec) [ -14301.8408] [ 3429] [depth= 4] . ( 2 sec) [ -14292.7212] [ 3414] [depth= 1] . ( 2 sec) [ -14146.3732] [ 3410] [depth= 2] . ( 2 sec) [ -13819.2275] [ 3324] [depth= 2] . ( 2 sec) [ -13595.5717] [ 3261] [depth= 5] . ( 2 sec) [ -13432.8497] [ 3236] [depth= 1] . ( 2 sec) [ -13152.3775] [ 3212] [depth= 11] . ( 2 sec) [ -12796.4247] [ 3130] [depth= 1] . ( 2 sec) [ -12775.3026] [ 3094] [depth= 1] . ( 3 sec) [ -12713.9205] [ 3039] [depth= 8] . ( 3 sec) [ -12617.0298] [ 3052] [depth= 1] . ( 3 sec) [ -12423.6979] [ 3005] [depth= 13] . ( 3 sec) [ -12307.3830] [ 2955] [depth= 1] . ( 3 sec) [ -12180.4914] [ 2925] [depth= 2] . ( 3 sec) [ -12136.4368] [ 2915] [depth= 1] . ( 3 sec) [ -12037.6389] [ 2885] [depth= 3] . ( 3 sec) [ -11826.1522] [ 2834] [depth= 3] . ( 3 sec) [ -11782.9417] [ 2825] [depth= 2] . ( 3 sec) [ -11780.7450] [ 2843] [depth= 1] . ( 3 sec) [ -11662.5853] [ 2809] [depth= 11] . ( 3 sec) [ -11594.2534] [ 2758] [depth= 1] . ( 3 sec) [ -11515.9457] [ 2722] [depth= 7] . ( 3 sec) [ -11484.9036] [ 2704] [depth= 1] . ( 3 sec) [ -11429.6460] [ 2680] [depth= 1] . ( 3 sec) [ -11330.1242] [ 2678] [depth= 3] . ( 3 sec) [ -11325.2335] [ 2678] [depth= 1] . ( 3 sec) [ -11325.1394] [ 2673] [depth= 2] . ( 3 sec) [ -11126.7352] [ 2592] [depth= 1] . ( 3 sec) [ -11113.7056] [ 2582] [depth= 1] . ( 3 sec) [ -11078.6187] [ 2561] [depth= 1] . ( 3 sec) [ -11032.2835] [ 2534] [depth= 1] . ( 4 sec) [ -10933.7187] [ 2516] [depth= 1] . ( 4 sec) [ -10926.3831] [ 2519] [depth= 1] . ( 4 sec) [ -10923.9338] [ 2516] [depth= 1] . ( 4 sec) [ -10923.4304] [ 2518] [depth= 1] . ( 4 sec) [ -10839.5436] [ 2520] [depth= 5] . ( 4 sec) [ -10827.5681] [ 2509] [depth= 2] . ( 4 sec) [ -10795.5897] [ 2506] [depth= 4] . ( 4 sec) [ -10747.5652] [ 2499] [depth= 2] . ( 4 sec) [ -10666.5475] [ 2467] [depth= 3] . ( 4 sec) [ -10655.8369] [ 2464] [depth= 1] . ( 4 sec) [ -10627.6963] [ 2447] [depth= 1] . ( 4 sec) [ -10607.9747] [ 2439] [depth= 1] . ( 4 sec) [ -10606.8388] [ 2440] [depth= 1] . ( 4 sec) [ -10596.0634] [ 2439] [depth= 1] . ( 4 sec) [ -10595.3651] [ 2439] [depth= 1] . ( 5 sec) [ -10593.1537] [ 2439] [depth= 1] . ( 5 sec) [ -10419.9566] [Branch lengths ] . ( 5 sec) [ -10419.3502] [GTR parameters ] . ( 5 sec) [ -10388.4922] [Alpha ][ 0.847502] . ( 5 sec) [ -10387.2161] [ 2437] [depth= 1] . ( 6 sec) [ -10293.7119] [ 2382] [depth= 2] . ( 6 sec) [ -10291.4131] [ 2374] [depth= 1] . ( 6 sec) [ -10289.9966] [ 2367] [depth= 2] . ( 6 sec) [ -10279.9930] [ 2372] [depth= 1] . ( 6 sec) [ -10279.8562] [ 2377] [depth= 1] . ( 6 sec) [ -10279.1644] [ 2381] [depth= 2] . ( 6 sec) [ -10242.7456] [ 2369] [depth= 4] . ( 7 sec) [ -10241.3577] [ 2371] [depth= 1] . ( 7 sec) [ -10241.2060] [ 2372] [depth= 1] . ( 7 sec) [ -10234.5365] [ 2363] [depth= 2] . ( 7 sec) [ -10233.5064] [ 2367] [depth= 1] . ( 7 sec) [ -10233.0556] [ 2368] [depth= 1] . ( 8 sec) [ -10231.5554] [ 2360] [depth= 3] . ( 8 sec) [ -10231.0718] [ 2362] [depth= 1] . ( 8 sec) [ -10230.7865] [ 2360] [depth= 1] . ( 8 sec) [ -10230.6757] [ 2362] [depth= 1] . ( 8 sec) [ -10229.9773] [ 2359] [depth= 1] . ( 8 sec) [ -10223.0713] [ 2350] [depth= 2] . ( 8 sec) [ -10222.8616] [ 2351] [depth= 1] . ( 8 sec) [ -10222.3482] [ 2351] [depth= 1] . ( 9 sec) [ -10222.3197] [ 2353] [depth= 1] . ( 9 sec) [ -10210.0254] [Branch lengths ] . ( 9 sec) [ -10209.6101] [GTR parameters ] . ( 10 sec) [ -10208.9318] [Alpha ][ 0.916904] . ( 11 sec) [ -10208.5462] [ 2350] [depth= 1] . ( 13 sec) [ -10206.9031] [Branch lengths ] . ( 13 sec) [ -10206.9013] [GTR parameters ] . ( 13 sec) [ -10206.8879] [Alpha ][ 0.927265] . ( 17 sec) [ -10206.7700] [Branch lengths ] . ( 24 sec) [ -10206.6712] [ 2347] [depth= 1] . ( 38 sec) [ -10206.5958] [Branch lengths ] . ( 38 sec) [ -10206.5953] [GTR parameters ] . ( 38 sec) [ -10206.5942] [Alpha ][ 0.930220] . ( 38 sec) [ -10206.5942] [Topology ] . ( 39 sec) [ -10206.5881] [Topology ] . ( 40 sec) [ -10206.5859] [Topology ] . ( 41 sec) [ -10206.5846] [Topology ] . ( 42 sec) [ -10206.5837] [Topology ] . ( 42 sec) [ -10206.5836] [GTR parameters ] . ( 42 sec) [ -10206.5835] [Alpha ][ 0.931188] . ( 42 sec) [ -10206.5835] [Topology ] . ( 43 sec) [ -10206.5827] [Topology ] . ( 43 sec) [ -10206.5827] [GTR parameters ] . ( 43 sec) [ -10206.5827] [Alpha ][ 0.931188] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -10206.3234] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10206.323411. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19306.6227] [GTR parameters ] . ( 1 sec) [ -18988.0444] [Alpha ][ 0.500960] . ( 1 sec) [ -18707.9338] [ 4251] [depth= 3] . ( 1 sec) [ -18360.7081] [ 4194] [depth= 3] . ( 1 sec) [ -18273.3060] [ 4184] [depth= 3] . ( 1 sec) [ -17797.1263] [ 4161] [depth= 9] . ( 1 sec) [ -17593.5893] [ 4077] [depth= 2] . ( 1 sec) [ -17390.4443] [ 4067] [depth= 5] . ( 1 sec) [ -17337.9339] [ 4063] [depth= 1] . ( 1 sec) [ -17168.2389] [ 4063] [depth= 5] . ( 1 sec) [ -17141.1399] [ 4032] [depth= 1] . ( 1 sec) [ -16833.2478] [ 4021] [depth= 4] . ( 1 sec) [ -16732.9111] [ 3988] [depth= 5] . ( 1 sec) [ -16629.5176] [ 3980] [depth= 2] . ( 1 sec) [ -16502.7370] [ 3956] [depth= 5] . ( 1 sec) [ -16480.7525] [ 3962] [depth= 10] . ( 1 sec) [ -16038.4812] [ 3838] [depth= 2] . ( 1 sec) [ -15777.5031] [ 3754] [depth= 10] . ( 1 sec) [ -15602.5186] [ 3652] [depth= 6] . ( 2 sec) [ -15600.4550] [ 3634] [depth= 4] . ( 2 sec) [ -15505.7148] [ 3616] [depth= 3] . ( 2 sec) [ -15411.3184] [ 3625] [depth= 1] . ( 2 sec) [ -15374.2861] [ 3603] [depth= 1] . ( 2 sec) [ -15258.4177] [ 3561] [depth= 4] . ( 2 sec) [ -14831.6440] [ 3479] [depth= 6] . ( 2 sec) [ -14760.7680] [ 3473] [depth= 1] . ( 2 sec) [ -14758.4139] [ 3477] [depth= 2] . ( 2 sec) [ -14719.4556] [ 3456] [depth= 3] . ( 2 sec) [ -14667.6880] [ 3440] [depth= 8] . ( 2 sec) [ -14508.0731] [ 3402] [depth= 6] . ( 2 sec) [ -14330.8030] [ 3354] [depth= 5] . ( 2 sec) [ -14204.3591] [ 3369] [depth= 12] . ( 2 sec) [ -14196.1749] [ 3347] [depth= 1] . ( 2 sec) [ -13978.4708] [ 3249] [depth= 11] . ( 2 sec) [ -13932.3274] [ 3218] [depth= 3] . ( 2 sec) [ -13537.7165] [ 3218] [depth= 2] . ( 2 sec) [ -13512.6034] [ 3164] [depth= 12] . ( 2 sec) [ -13439.0929] [ 3127] [depth= 1] . ( 3 sec) [ -13282.0696] [ 3094] [depth= 3] . ( 3 sec) [ -13255.9942] [ 3091] [depth= 3] . ( 3 sec) [ -13104.6803] [ 3090] [depth= 7] . ( 3 sec) [ -13042.0543] [ 3075] [depth= 10] . ( 3 sec) [ -12872.6001] [ 3076] [depth= 1] . ( 3 sec) [ -12831.2317] [ 3060] [depth= 2] . ( 3 sec) [ -12829.5139] [ 3066] [depth= 2] . ( 3 sec) [ -12459.0471] [ 2986] [depth= 1] . ( 3 sec) [ -12437.9693] [ 2984] [depth= 1] . ( 3 sec) [ -12136.4045] [ 2910] [depth= 9] . ( 3 sec) [ -12127.9231] [ 2901] [depth= 3] . ( 3 sec) [ -11866.3312] [ 2800] [depth= 6] . ( 3 sec) [ -11827.5485] [ 2780] [depth= 1] . ( 3 sec) [ -11807.7260] [ 2778] [depth= 3] . ( 3 sec) [ -11423.1145] [ 2690] [depth= 1] . ( 3 sec) [ -11414.7929] [ 2687] [depth= 1] . ( 3 sec) [ -11386.2732] [ 2665] [depth= 5] . ( 3 sec) [ -11379.2058] [ 2664] [depth= 1] . ( 3 sec) [ -11362.6400] [ 2660] [depth= 8] . ( 3 sec) [ -11361.4548] [ 2660] [depth= 1] . ( 4 sec) [ -11342.1419] [ 2648] [depth= 2] . ( 4 sec) [ -11265.7182] [ 2620] [depth= 9] . ( 4 sec) [ -11250.8914] [ 2611] [depth= 1] . ( 4 sec) [ -11203.6915] [ 2601] [depth= 1] . ( 4 sec) [ -11199.9384] [ 2588] [depth= 4] . ( 4 sec) [ -11196.1328] [ 2582] [depth= 1] . ( 4 sec) [ -11176.8081] [ 2574] [depth= 3] . ( 4 sec) [ -11140.3518] [ 2585] [depth= 1] . ( 4 sec) [ -11043.0876] [ 2548] [depth= 2] . ( 4 sec) [ -10997.0352] [ 2534] [depth= 1] . ( 4 sec) [ -10952.8073] [ 2529] [depth= 2] . ( 4 sec) [ -10896.7774] [ 2506] [depth= 1] . ( 4 sec) [ -10895.7255] [ 2504] [depth= 1] . ( 4 sec) [ -10849.8534] [ 2496] [depth= 1] . ( 4 sec) [ -10829.3170] [ 2496] [depth= 1] . ( 4 sec) [ -10826.9571] [ 2494] [depth= 1] . ( 4 sec) [ -10749.1088] [ 2485] [depth= 4] . ( 4 sec) [ -10747.3282] [ 2492] [depth= 1] . ( 5 sec) [ -10722.6145] [ 2493] [depth= 1] . ( 5 sec) [ -10719.9508] [ 2492] [depth= 1] . ( 5 sec) [ -10713.9923] [ 2486] [depth= 1] . ( 5 sec) [ -10564.4807] [Branch lengths ] . ( 6 sec) [ -10563.9284] [GTR parameters ] . ( 6 sec) [ -10532.4657] [Alpha ][ 0.847707] . ( 6 sec) [ -10517.7068] [ 2477] [depth= 7] . ( 6 sec) [ -10471.4562] [ 2417] [depth= 1] . ( 6 sec) [ -10470.8324] [ 2447] [depth= 1] . ( 6 sec) [ -10443.0152] [ 2449] [depth= 2] . ( 6 sec) [ -10398.0563] [ 2437] [depth= 6] . ( 6 sec) [ -10395.2309] [ 2428] [depth= 1] . ( 6 sec) [ -10393.6056] [ 2429] [depth= 1] . ( 6 sec) [ -10381.5612] [ 2427] [depth= 1] . ( 7 sec) [ -10344.2689] [ 2398] [depth= 1] . ( 7 sec) [ -10342.8431] [ 2398] [depth= 3] . ( 7 sec) [ -10324.0998] [ 2393] [depth= 4] . ( 7 sec) [ -10322.2914] [ 2394] [depth= 1] . ( 7 sec) [ -10312.1837] [ 2388] [depth= 3] . ( 7 sec) [ -10279.2034] [ 2365] [depth= 4] . ( 7 sec) [ -10278.2559] [ 2367] [depth= 1] . ( 7 sec) [ -10236.0691] [ 2353] [depth= 3] . ( 7 sec) [ -10235.8276] [ 2353] [depth= 1] . ( 8 sec) [ -10234.0862] [ 2357] [depth= 1] . ( 8 sec) [ -10233.7936] [ 2353] [depth= 1] . ( 8 sec) [ -10231.9894] [ 2354] [depth= 1] . ( 8 sec) [ -10231.2037] [ 2354] [depth= 1] . ( 9 sec) [ -10210.4140] [Branch lengths ] . ( 10 sec) [ -10210.1897] [GTR parameters ] . ( 10 sec) [ -10209.5737] [Alpha ][ 0.913747] . ( 11 sec) [ -10208.6894] [ 2348] [depth= 1] . ( 13 sec) [ -10206.8691] [Branch lengths ] . ( 14 sec) [ -10206.8653] [GTR parameters ] . ( 14 sec) [ -10206.8472] [Alpha ][ 0.925765] . ( 17 sec) [ -10206.6963] [Branch lengths ] . ( 34 sec) [ -10206.5930] [ 2347] [depth= 1] . ( 39 sec) [ -10206.3883] [Branch lengths ] . ( 39 sec) [ -10206.3876] [GTR parameters ] . ( 39 sec) [ -10206.3857] [Alpha ][ 0.929667] . ( 39 sec) [ -10206.3857] [Topology ] . ( 40 sec) [ -10206.3528] [Topology ] . ( 41 sec) [ -10206.3389] [Topology ] . ( 41 sec) [ -10206.3310] [Topology ] . ( 42 sec) [ -10206.3260] [Topology ] . ( 43 sec) [ -10206.3229] [Topology ] . ( 44 sec) [ -10206.3208] [Topology ] . ( 44 sec) [ -10206.3207] [GTR parameters ] . ( 44 sec) [ -10206.3203] [Alpha ][ 0.931386] . ( 44 sec) [ -10206.3203] [Topology ] . ( 45 sec) [ -10206.3188] [Topology ] . ( 46 sec) [ -10206.3177] [Topology ] . ( 47 sec) [ -10206.3168] [Topology ] . ( 47 sec) [ -10206.3168] [GTR parameters ] . ( 47 sec) [ -10206.3168] [Alpha ][ 0.931386] . ( 47 sec) [ -10206.3168] [Topology ] . ( 48 sec) [ -10206.3161] [Topology ] . ( 48 sec) [ -10206.3161] [GTR parameters ] . ( 48 sec) [ -10206.3161] [Alpha ][ 0.931386] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10206.316131. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19842.8527] [GTR parameters ] . ( 1 sec) [ -19517.4601] [Alpha ][ 0.500960] . ( 1 sec) [ -19093.5496] [ 4270] [depth= 8] . ( 1 sec) [ -18588.3967] [ 4226] [depth= 8] . ( 1 sec) [ -18584.1777] [ 4220] [depth= 1] . ( 1 sec) [ -18521.7166] [ 4219] [depth= 2] . ( 1 sec) [ -18470.4265] [ 4187] [depth= 5] . ( 1 sec) [ -18407.9669] [ 4190] [depth= 1] . ( 1 sec) [ -18145.5815] [ 4108] [depth= 7] . ( 1 sec) [ -18059.3199] [ 4097] [depth= 5] . ( 1 sec) [ -17989.3825] [ 4041] [depth= 8] . ( 1 sec) [ -17914.3525] [ 4048] [depth= 13] . ( 2 sec) [ -17367.2903] [ 3967] [depth= 10] . ( 2 sec) [ -17278.3866] [ 3936] [depth= 5] . ( 2 sec) [ -17232.5478] [ 3937] [depth= 1] . ( 2 sec) [ -17147.5697] [ 3918] [depth= 6] . ( 2 sec) [ -17039.8173] [ 3907] [depth= 1] . ( 2 sec) [ -16795.0027] [ 3830] [depth= 11] . ( 2 sec) [ -16665.2394] [ 3821] [depth= 2] . ( 2 sec) [ -16235.6345] [ 3716] [depth= 3] . ( 2 sec) [ -16155.9260] [ 3700] [depth= 1] . ( 2 sec) [ -16095.7533] [ 3695] [depth= 1] . ( 2 sec) [ -15930.2687] [ 3660] [depth= 6] . ( 2 sec) [ -15730.3502] [ 3573] [depth= 10] . ( 2 sec) [ -15582.0246] [ 3454] [depth= 10] . ( 2 sec) [ -14672.3858] [ 3434] [depth= 1] . ( 2 sec) [ -14598.2323] [ 3405] [depth= 4] . ( 2 sec) [ -14590.6856] [ 3384] [depth= 7] . ( 2 sec) [ -14304.0551] [ 3274] [depth= 9] . ( 2 sec) [ -14006.1963] [ 3185] [depth= 6] . ( 2 sec) [ -13851.8066] [ 3135] [depth= 4] . ( 2 sec) [ -13597.7490] [ 3080] [depth= 5] . ( 3 sec) [ -13503.9709] [ 3070] [depth= 4] . ( 3 sec) [ -13490.3238] [ 3069] [depth= 1] . ( 3 sec) [ -13488.2872] [ 3072] [depth= 1] . ( 3 sec) [ -13434.6753] [ 3018] [depth= 9] . ( 3 sec) [ -13432.7468] [ 3015] [depth= 1] . ( 3 sec) [ -13397.0534] [ 2998] [depth= 1] . ( 3 sec) [ -13046.1938] [ 2949] [depth= 4] . ( 3 sec) [ -12692.0320] [ 2909] [depth= 7] . ( 3 sec) [ -12647.6387] [ 2878] [depth= 7] . ( 3 sec) [ -12646.9903] [ 2880] [depth= 1] . ( 3 sec) [ -12596.9143] [ 2876] [depth= 1] . ( 3 sec) [ -12530.4995] [ 2878] [depth= 3] . ( 3 sec) [ -12389.9560] [ 2794] [depth= 4] . ( 3 sec) [ -12361.3185] [ 2795] [depth= 1] . ( 3 sec) [ -12259.3116] [ 2791] [depth= 9] . ( 3 sec) [ -12102.1938] [ 2777] [depth= 1] . ( 3 sec) [ -12061.5715] [ 2767] [depth= 11] . ( 3 sec) [ -12039.5747] [ 2744] [depth= 1] . ( 3 sec) [ -12008.7184] [ 2738] [depth= 1] . ( 3 sec) [ -11971.7607] [ 2722] [depth= 6] . ( 4 sec) [ -11665.3597] [ 2683] [depth= 1] . ( 4 sec) [ -11662.6174] [ 2667] [depth= 4] . ( 4 sec) [ -11406.9374] [ 2659] [depth= 1] . ( 4 sec) [ -11376.7289] [ 2638] [depth= 6] . ( 4 sec) [ -11374.0814] [ 2641] [depth= 1] . ( 4 sec) [ -11241.4626] [ 2606] [depth= 1] . ( 4 sec) [ -11142.0489] [ 2565] [depth= 5] . ( 4 sec) [ -11039.8401] [ 2541] [depth= 1] . ( 4 sec) [ -11004.3788] [ 2538] [depth= 1] . ( 4 sec) [ -10905.5060] [ 2497] [depth= 2] . ( 4 sec) [ -10899.3874] [ 2500] [depth= 1] . ( 4 sec) [ -10833.2313] [ 2466] [depth= 6] . ( 4 sec) [ -10797.3115] [ 2460] [depth= 1] . ( 4 sec) [ -10777.0362] [ 2458] [depth= 2] . ( 4 sec) [ -10774.8076] [ 2459] [depth= 1] . ( 4 sec) [ -10767.1860] [ 2456] [depth= 2] . ( 5 sec) [ -10764.3690] [ 2448] [depth= 3] . ( 5 sec) [ -10761.8005] [ 2451] [depth= 1] . ( 5 sec) [ -10757.8892] [ 2461] [depth= 1] . ( 5 sec) [ -10756.0981] [ 2458] [depth= 1] . ( 5 sec) [ -10653.0906] [ 2425] [depth= 4] . ( 5 sec) [ -10651.3114] [ 2422] [depth= 1] . ( 5 sec) [ -10630.3081] [ 2419] [depth= 1] . ( 5 sec) [ -10628.6672] [ 2423] [depth= 1] . ( 5 sec) [ -10445.0156] [Branch lengths ] . ( 6 sec) [ -10444.9107] [GTR parameters ] . ( 6 sec) [ -10409.2135] [Alpha ][ 0.885739] . ( 6 sec) [ -10297.9114] [ 2363] [depth= 2] . ( 6 sec) [ -10295.7684] [ 2356] [depth= 2] . ( 6 sec) [ -10279.1491] [ 2345] [depth= 1] . ( 6 sec) [ -10278.9063] [ 2346] [depth= 1] . ( 6 sec) [ -10278.4953] [ 2347] [depth= 1] . ( 6 sec) [ -10274.9043] [ 2349] [depth= 1] . ( 6 sec) [ -10247.9140] [ 2351] [depth= 1] . ( 6 sec) [ -10247.0923] [ 2349] [depth= 1] . ( 6 sec) [ -10234.4751] [ 2351] [depth= 1] . ( 6 sec) [ -10234.0568] [ 2352] [depth= 1] . ( 7 sec) [ -10232.1759] [ 2354] [depth= 1] . ( 7 sec) [ -10231.8379] [ 2355] [depth= 1] . ( 8 sec) [ -10231.7959] [ 2353] [depth= 1] . ( 8 sec) [ -10231.2474] [ 2349] [depth= 1] . ( 8 sec) [ -10231.2044] [ 2353] [depth= 1] . ( 8 sec) [ -10230.4095] [ 2351] [depth= 2] . ( 9 sec) [ -10229.8503] [ 2351] [depth= 1] . ( 9 sec) [ -10209.2739] [Branch lengths ] . ( 9 sec) [ -10208.9880] [GTR parameters ] . ( 9 sec) [ -10208.8795] [Alpha ][ 0.914570] . ( 12 sec) [ -10208.7346] [ 2349] [depth= 1] . ( 13 sec) [ -10207.1196] [Branch lengths ] . ( 13 sec) [ -10207.1167] [GTR parameters ] . ( 13 sec) [ -10207.0988] [Alpha ][ 0.926516] . ( 17 sec) [ -10206.9500] [Branch lengths ] . ( 25 sec) [ -10206.8512] [ 2346] [depth= 1] . ( 38 sec) [ -10206.6407] [Branch lengths ] . ( 38 sec) [ -10206.6400] [GTR parameters ] . ( 38 sec) [ -10206.6384] [Alpha ][ 0.930094] . ( 38 sec) [ -10206.6384] [Topology ] . ( 39 sec) [ -10206.6085] [Topology ] . ( 40 sec) [ -10206.5955] [Topology ] . ( 41 sec) [ -10206.5877] [Topology ] . ( 42 sec) [ -10206.5829] [Topology ] . ( 42 sec) [ -10206.5798] [Topology ] . ( 43 sec) [ -10206.5777] [Topology ] . ( 43 sec) [ -10206.5776] [GTR parameters ] . ( 43 sec) [ -10206.5774] [Alpha ][ 0.931364] . ( 43 sec) [ -10206.5774] [Topology ] . ( 44 sec) [ -10206.5759] [Topology ] . ( 45 sec) [ -10206.5749] [Topology ] . ( 46 sec) [ -10206.5741] [Topology ] . ( 46 sec) [ -10206.5740] [GTR parameters ] . ( 46 sec) [ -10206.5740] [Alpha ][ 0.931364] . ( 46 sec) [ -10206.5740] [Topology ] . ( 47 sec) [ -10206.5736] [Topology ] . ( 47 sec) [ -10206.5736] [GTR parameters ] . ( 47 sec) [ -10206.5736] [Alpha ][ 0.931364] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -10206.3141] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10206.314080. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19470.5487] [GTR parameters ] . ( 0 sec) [ -19162.5116] [Alpha ][ 0.500960] . ( 0 sec) [ -18783.5694] [ 4245] [depth= 8] . ( 1 sec) [ -18439.5470] [ 4177] [depth= 9] . ( 1 sec) [ -18313.9544] [ 4139] [depth= 8] . ( 1 sec) [ -18306.9218] [ 4123] [depth= 1] . ( 1 sec) [ -18101.0181] [ 4112] [depth= 9] . ( 1 sec) [ -18077.9195] [ 4105] [depth= 2] . ( 1 sec) [ -18001.0308] [ 4097] [depth= 5] . ( 1 sec) [ -17957.4480] [ 4058] [depth= 3] . ( 1 sec) [ -17692.1382] [ 4043] [depth= 2] . ( 1 sec) [ -17630.3821] [ 4034] [depth= 8] . ( 1 sec) [ -17610.3174] [ 4042] [depth= 3] . ( 1 sec) [ -17433.6522] [ 3973] [depth= 4] . ( 1 sec) [ -17344.9355] [ 3935] [depth= 7] . ( 1 sec) [ -17170.1136] [ 3915] [depth= 4] . ( 1 sec) [ -16722.6239] [ 3882] [depth= 2] . ( 1 sec) [ -16233.6338] [ 3792] [depth= 7] . ( 1 sec) [ -16147.0087] [ 3783] [depth= 2] . ( 1 sec) [ -16050.7196] [ 3731] [depth= 1] . ( 1 sec) [ -15949.4438] [ 3710] [depth= 4] . ( 1 sec) [ -15835.4321] [ 3706] [depth= 2] . ( 1 sec) [ -15649.7471] [ 3605] [depth= 1] . ( 1 sec) [ -15393.2851] [ 3546] [depth= 4] . ( 1 sec) [ -15151.5445] [ 3502] [depth= 8] . ( 1 sec) [ -15120.8374] [ 3487] [depth= 1] . ( 1 sec) [ -15116.5613] [ 3479] [depth= 5] . ( 2 sec) [ -15036.7454] [ 3458] [depth= 5] . ( 2 sec) [ -14928.0774] [ 3421] [depth= 5] . ( 2 sec) [ -14402.0184] [ 3363] [depth= 8] . ( 2 sec) [ -14104.6062] [ 3292] [depth= 2] . ( 2 sec) [ -13775.5549] [ 3208] [depth= 8] . ( 2 sec) [ -13687.8983] [ 3197] [depth= 6] . ( 2 sec) [ -13430.0754] [ 3126] [depth= 8] . ( 2 sec) [ -13386.3182] [ 3121] [depth= 2] . ( 2 sec) [ -13157.2574] [ 3107] [depth= 3] . ( 2 sec) [ -13112.1936] [ 3104] [depth= 2] . ( 2 sec) [ -13049.5283] [ 3104] [depth= 2] . ( 2 sec) [ -12696.1707] [ 3071] [depth= 6] . ( 2 sec) [ -12679.9116] [ 3059] [depth= 7] . ( 2 sec) [ -12651.3836] [ 3037] [depth= 1] . ( 2 sec) [ -12593.7516] [ 3027] [depth= 6] . ( 2 sec) [ -12435.0780] [ 3014] [depth= 8] . ( 2 sec) [ -12413.9447] [ 3003] [depth= 1] . ( 2 sec) [ -12345.7295] [ 2981] [depth= 1] . ( 2 sec) [ -12232.5815] [ 2952] [depth= 6] . ( 2 sec) [ -12201.1460] [ 2943] [depth= 2] . ( 3 sec) [ -12019.0400] [ 2829] [depth= 1] . ( 3 sec) [ -11983.9059] [ 2825] [depth= 3] . ( 3 sec) [ -11945.8581] [ 2798] [depth= 2] . ( 3 sec) [ -11905.0335] [ 2779] [depth= 1] . ( 3 sec) [ -11887.2228] [ 2771] [depth= 2] . ( 3 sec) [ -11641.1294] [ 2716] [depth= 8] . ( 3 sec) [ -11628.9068] [ 2710] [depth= 1] . ( 3 sec) [ -11608.0740] [ 2719] [depth= 1] . ( 3 sec) [ -11603.6250] [ 2721] [depth= 1] . ( 3 sec) [ -11553.2298] [ 2713] [depth= 1] . ( 3 sec) [ -11527.8540] [ 2692] [depth= 2] . ( 3 sec) [ -11455.3690] [ 2655] [depth= 2] . ( 3 sec) [ -11452.4561] [ 2640] [depth= 1] . ( 3 sec) [ -11447.2449] [ 2638] [depth= 1] . ( 3 sec) [ -11362.1305] [ 2648] [depth= 1] . ( 3 sec) [ -11220.2351] [ 2620] [depth= 2] . ( 3 sec) [ -11172.0700] [ 2606] [depth= 1] . ( 3 sec) [ -11011.0696] [ 2526] [depth= 1] . ( 3 sec) [ -11007.2825] [ 2526] [depth= 1] . ( 4 sec) [ -10987.2651] [ 2532] [depth= 1] . ( 4 sec) [ -10909.7987] [ 2519] [depth= 1] . ( 4 sec) [ -10853.0025] [ 2489] [depth= 1] . ( 4 sec) [ -10844.9187] [ 2492] [depth= 1] . ( 4 sec) [ -10805.2811] [ 2491] [depth= 1] . ( 4 sec) [ -10796.2532] [ 2486] [depth= 1] . ( 4 sec) [ -10796.1754] [ 2490] [depth= 1] . ( 4 sec) [ -10795.4839] [ 2486] [depth= 1] . ( 4 sec) [ -10692.8439] [ 2442] [depth= 4] . ( 4 sec) [ -10649.7866] [ 2422] [depth= 1] . ( 4 sec) [ -10631.8942] [ 2413] [depth= 1] . ( 4 sec) [ -10630.3126] [ 2411] [depth= 1] . ( 4 sec) [ -10616.3671] [ 2420] [depth= 1] . ( 4 sec) [ -10603.9797] [ 2419] [depth= 2] . ( 5 sec) [ -10405.4813] [Branch lengths ] . ( 5 sec) [ -10405.1027] [GTR parameters ] . ( 5 sec) [ -10377.9539] [Alpha ][ 0.824500] . ( 5 sec) [ -10350.4386] [ 2394] [depth= 1] . ( 5 sec) [ -10349.7227] [ 2399] [depth= 1] . ( 5 sec) [ -10311.3906] [ 2376] [depth= 1] . ( 6 sec) [ -10310.0098] [ 2376] [depth= 1] . ( 6 sec) [ -10305.4391] [ 2374] [depth= 2] . ( 6 sec) [ -10305.2007] [ 2374] [depth= 1] . ( 6 sec) [ -10293.7185] [ 2369] [depth= 1] . ( 6 sec) [ -10289.7949] [ 2368] [depth= 1] . ( 6 sec) [ -10289.6250] [ 2367] [depth= 1] . ( 6 sec) [ -10286.8397] [ 2369] [depth= 2] . ( 6 sec) [ -10276.5000] [ 2371] [depth= 1] . ( 6 sec) [ -10237.3740] [ 2354] [depth= 3] . ( 7 sec) [ -10236.8115] [ 2353] [depth= 1] . ( 7 sec) [ -10233.7349] [ 2346] [depth= 1] . ( 7 sec) [ -10230.2403] [ 2349] [depth= 1] . ( 8 sec) [ -10229.5423] [ 2349] [depth= 1] . ( 8 sec) [ -10228.9883] [ 2346] [depth= 1] . ( 8 sec) [ -10228.6880] [ 2349] [depth= 1] . ( 8 sec) [ -10226.0886] [ 2349] [depth= 1] . ( 8 sec) [ -10210.7494] [Branch lengths ] . ( 9 sec) [ -10210.4392] [GTR parameters ] . ( 9 sec) [ -10209.4392] [Alpha ][ 0.907662] . ( 9 sec) [ -10208.4433] [ 2348] [depth= 1] . ( 11 sec) [ -10208.4329] [ 2348] [depth= 1] . ( 12 sec) [ -10206.8299] [Branch lengths ] . ( 12 sec) [ -10206.8266] [GTR parameters ] . ( 12 sec) [ -10206.7983] [Alpha ][ 0.922701] . ( 16 sec) [ -10206.5512] [Branch lengths ] . ( 33 sec) [ -10206.4484] [ 2347] [depth= 1] . ( 37 sec) [ -10206.3431] [Branch lengths ] . ( 38 sec) [ -10206.3420] [GTR parameters ] . ( 38 sec) [ -10206.3359] [Alpha ][ 0.929678] . ( 38 sec) [ -10206.3359] [Topology ] . ( 38 sec) [ -10206.3229] [Topology ] . ( 39 sec) [ -10206.3184] [Topology ] . ( 40 sec) [ -10206.3159] [Topology ] . ( 41 sec) [ -10206.3144] [Topology ] . ( 42 sec) [ -10206.3134] [Topology ] . ( 42 sec) [ -10206.3134] [GTR parameters ] . ( 42 sec) [ -10206.3131] [Alpha ][ 0.931185] . ( 42 sec) [ -10206.3131] [Topology ] . ( 43 sec) [ -10206.3125] [Topology ] . ( 43 sec) [ -10206.3125] [GTR parameters ] . ( 43 sec) [ -10206.3125] [Alpha ][ 0.931185] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10206.312451. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19484.9780] [GTR parameters ] . ( 1 sec) [ -19116.9552] [Alpha ][ 0.500960] . ( 1 sec) [ -18732.5927] [ 4288] [depth= 6] . ( 1 sec) [ -18361.5621] [ 4207] [depth= 11] . ( 1 sec) [ -18234.7197] [ 4186] [depth= 3] . ( 1 sec) [ -18200.4226] [ 4182] [depth= 5] . ( 1 sec) [ -18118.2107] [ 4162] [depth= 4] . ( 1 sec) [ -18020.6493] [ 4155] [depth= 2] . ( 1 sec) [ -17970.8688] [ 4144] [depth= 5] . ( 1 sec) [ -17722.4810] [ 4089] [depth= 13] . ( 1 sec) [ -17543.9743] [ 4052] [depth= 15] . ( 2 sec) [ -17176.4710] [ 3972] [depth= 9] . ( 2 sec) [ -17008.7707] [ 3978] [depth= 18] . ( 2 sec) [ -16645.7596] [ 3874] [depth= 17] . ( 2 sec) [ -16601.0347] [ 3866] [depth= 1] . ( 2 sec) [ -16418.7770] [ 3837] [depth= 10] . ( 2 sec) [ -16402.0912] [ 3845] [depth= 1] . ( 2 sec) [ -16322.8035] [ 3829] [depth= 2] . ( 2 sec) [ -16172.3156] [ 3771] [depth= 8] . ( 2 sec) [ -16083.1728] [ 3766] [depth= 2] . ( 2 sec) [ -15969.6938] [ 3746] [depth= 10] . ( 2 sec) [ -15607.2585] [ 3654] [depth= 1] . ( 2 sec) [ -15318.4633] [ 3563] [depth= 2] . ( 2 sec) [ -15196.9495] [ 3521] [depth= 4] . ( 2 sec) [ -15144.6185] [ 3487] [depth= 8] . ( 2 sec) [ -14863.7332] [ 3466] [depth= 2] . ( 2 sec) [ -14815.6717] [ 3467] [depth= 1] . ( 2 sec) [ -14714.8414] [ 3459] [depth= 3] . ( 2 sec) [ -14592.9865] [ 3392] [depth= 3] . ( 2 sec) [ -14531.0057] [ 3389] [depth= 2] . ( 2 sec) [ -14503.0414] [ 3400] [depth= 8] . ( 2 sec) [ -14491.9720] [ 3399] [depth= 1] . ( 2 sec) [ -14417.1617] [ 3404] [depth= 2] . ( 3 sec) [ -14412.0671] [ 3401] [depth= 2] . ( 3 sec) [ -14297.7777] [ 3364] [depth= 6] . ( 3 sec) [ -14019.0603] [ 3302] [depth= 8] . ( 3 sec) [ -13985.9098] [ 3292] [depth= 1] . ( 3 sec) [ -13738.2544] [ 3295] [depth= 9] . ( 3 sec) [ -13595.6671] [ 3234] [depth= 7] . ( 3 sec) [ -13579.4505] [ 3237] [depth= 1] . ( 3 sec) [ -13551.3955] [ 3224] [depth= 1] . ( 3 sec) [ -13384.5865] [ 3197] [depth= 4] . ( 3 sec) [ -13192.2164] [ 3146] [depth= 1] . ( 3 sec) [ -13113.2861] [ 3096] [depth= 6] . ( 3 sec) [ -13101.0069] [ 3126] [depth= 1] . ( 3 sec) [ -12898.0187] [ 3039] [depth= 5] . ( 3 sec) [ -12874.0738] [ 3028] [depth= 7] . ( 3 sec) [ -12863.4324] [ 3025] [depth= 1] . ( 3 sec) [ -12727.6274] [ 2978] [depth= 7] . ( 3 sec) [ -12726.4671] [ 2979] [depth= 1] . ( 3 sec) [ -12493.7346] [ 2908] [depth= 7] . ( 3 sec) [ -12180.6681] [ 2898] [depth= 4] . ( 3 sec) [ -11898.3701] [ 2865] [depth= 2] . ( 3 sec) [ -11714.0444] [ 2794] [depth= 6] . ( 4 sec) [ -11705.7164] [ 2793] [depth= 1] . ( 4 sec) [ -11685.4618] [ 2718] [depth= 1] . ( 4 sec) [ -11678.0606] [ 2709] [depth= 1] . ( 4 sec) [ -11595.0390] [ 2683] [depth= 3] . ( 4 sec) [ -11591.2518] [ 2680] [depth= 1] . ( 4 sec) [ -11437.8721] [ 2634] [depth= 6] . ( 4 sec) [ -11378.5544] [ 2621] [depth= 1] . ( 4 sec) [ -11370.5483] [ 2634] [depth= 1] . ( 4 sec) [ -11353.8312] [ 2657] [depth= 1] . ( 4 sec) [ -11351.0233] [ 2655] [depth= 1] . ( 4 sec) [ -11105.7062] [ 2609] [depth= 6] . ( 4 sec) [ -11042.7995] [ 2608] [depth= 4] . ( 4 sec) [ -11036.8371] [ 2602] [depth= 1] . ( 4 sec) [ -11027.1188] [ 2583] [depth= 8] . ( 4 sec) [ -11022.5377] [ 2589] [depth= 2] . ( 4 sec) [ -10856.7724] [ 2504] [depth= 1] . ( 4 sec) [ -10804.6435] [ 2478] [depth= 4] . ( 4 sec) [ -10759.9189] [ 2496] [depth= 1] . ( 4 sec) [ -10756.7811] [ 2498] [depth= 1] . ( 4 sec) [ -10617.5848] [ 2437] [depth= 4] . ( 5 sec) [ -10564.5516] [ 2433] [depth= 2] . ( 5 sec) [ -10553.6949] [ 2424] [depth= 1] . ( 5 sec) [ -10548.9804] [ 2416] [depth= 1] . ( 5 sec) [ -10533.0825] [ 2414] [depth= 1] . ( 5 sec) [ -10531.1135] [ 2419] [depth= 1] . ( 5 sec) [ -10480.1570] [ 2404] [depth= 1] . ( 5 sec) [ -10465.2312] [ 2381] [depth= 1] . ( 5 sec) [ -10447.3445] [ 2377] [depth= 2] . ( 5 sec) [ -10446.3669] [ 2380] [depth= 1] . ( 5 sec) [ -10424.5041] [ 2368] [depth= 1] . ( 5 sec) [ -10299.3013] [Branch lengths ] . ( 6 sec) [ -10298.4209] [GTR parameters ] . ( 6 sec) [ -10273.7942] [Alpha ][ 0.809749] . ( 6 sec) [ -10273.6641] [ 2365] [depth= 1] . ( 6 sec) [ -10271.5718] [ 2363] [depth= 1] . ( 7 sec) [ -10249.6208] [ 2365] [depth= 3] . ( 7 sec) [ -10249.6102] [ 2366] [depth= 1] . ( 7 sec) [ -10249.4010] [ 2366] [depth= 1] . ( 7 sec) [ -10247.7000] [ 2361] [depth= 1] . ( 7 sec) [ -10245.9751] [ 2358] [depth= 1] . ( 7 sec) [ -10238.2180] [ 2352] [depth= 1] . ( 7 sec) [ -10237.1704] [ 2355] [depth= 1] . ( 7 sec) [ -10236.7261] [ 2357] [depth= 2] . ( 8 sec) [ -10235.7832] [ 2353] [depth= 1] . ( 8 sec) [ -10233.4806] [ 2349] [depth= 1] . ( 8 sec) [ -10232.3739] [ 2349] [depth= 1] . ( 8 sec) [ -10231.8887] [ 2350] [depth= 1] . ( 8 sec) [ -10231.6655] [ 2348] [depth= 1] . ( 9 sec) [ -10231.3050] [ 2350] [depth= 2] . ( 9 sec) [ -10212.7045] [Branch lengths ] . ( 10 sec) [ -10212.6864] [GTR parameters ] . ( 10 sec) [ -10211.7739] [Alpha ][ 0.888308] . ( 11 sec) [ -10211.7348] [ 2347] [depth= 1] . ( 11 sec) [ -10211.6374] [ 2349] [depth= 1] . ( 12 sec) [ -10211.6089] [ 2349] [depth= 1] . ( 12 sec) [ -10210.4857] [ 2347] [depth= 1] . ( 12 sec) [ -10210.4655] [ 2349] [depth= 1] . ( 12 sec) [ -10210.1838] [ 2347] [depth= 1] . ( 13 sec) [ -10207.2181] [Branch lengths ] . ( 13 sec) [ -10207.2148] [GTR parameters ] . ( 14 sec) [ -10207.1098] [Alpha ][ 0.915946] . ( 15 sec) [ -10207.0101] [ 2345] [depth= 1] . ( 17 sec) [ -10206.5014] [Branch lengths ] . ( 17 sec) [ -10206.5007] [GTR parameters ] . ( 17 sec) [ -10206.4900] [Alpha ][ 0.925217] . ( 39 sec) [ -10206.3726] [Branch lengths ] . ( 39 sec) [ -10206.3726] [Topology ] . ( 39 sec) [ -10206.3572] [Topology ] . ( 40 sec) [ -10206.3511] [Topology ] . ( 41 sec) [ -10206.3478] [Topology ] . ( 42 sec) [ -10206.3457] [Topology ] . ( 43 sec) [ -10206.3443] [Topology ] . ( 43 sec) [ -10206.3432] [Topology ] . ( 44 sec) [ -10206.3426] [GTR parameters ] . ( 44 sec) [ -10206.3383] [Alpha ][ 0.931070] . ( 44 sec) [ -10206.3383] [Topology ] . ( 44 sec) [ -10206.3369] [Topology ] . ( 45 sec) [ -10206.3359] [Topology ] . ( 45 sec) [ -10206.3358] [GTR parameters ] . ( 45 sec) [ -10206.3358] [Alpha ][ 0.931070] . ( 45 sec) [ -10206.3358] [Topology ] . ( 46 sec) [ -10206.3350] [Topology ] . ( 46 sec) [ -10206.3350] [GTR parameters ] . ( 46 sec) [ -10206.3350] [Alpha ][ 0.932001] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10206.334990. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10281.311378 . ( 1 sec) [ -10277.3620] [GTR parameters ] . ( 1 sec) [ -10274.9238] [Alpha ][ 0.855959] . ( 1 sec) [ -10274.9238] [Topology ] . ( 2 sec) [ -10222.0737] [Topology ] . ( 2 sec) [ -10212.7676] [Topology ] . ( 3 sec) [ -10210.2910] [Topology ] . ( 4 sec) [ -10209.4383] [Topology ] . ( 5 sec) [ -10207.8763] [Topology ] . ( 6 sec) [ -10207.4713] [Topology ] . ( 7 sec) [ -10207.3341] [Topology ] . ( 7 sec) [ -10207.2782] [Topology ] . ( 8 sec) [ -10207.2521] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10207.238852 . ( 15 sec) [ -10207.0932] [GTR parameters ] . ( 15 sec) [ -10206.4617] [Alpha ][ 0.923249] . ( 15 sec) [ -10206.4617] [Topology ] . ( 16 sec) [ -10206.3940] [Topology ] . ( 17 sec) [ -10206.3682] [Topology ] . ( 18 sec) [ -10206.3549] [Topology ] . ( 19 sec) [ -10206.3476] [Topology ] . ( 19 sec) [ -10206.3434] [Topology ] . ( 20 sec) [ -10206.3409] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10206.340874 . ( 26 sec) [ -10206.3406] [GTR parameters ] . ( 27 sec) [ -10206.3340] [Alpha ][ 0.930562] . ( 27 sec) [ -10206.3340] [Topology ] . ( 27 sec) [ -10206.3313] [Topology ] . ( 28 sec) [ -10206.3297] [Topology ] . ( 29 sec) [ -10206.3286] [Topology ] . ( 30 sec) [ -10206.3277] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10206.327739 . ( 36 sec) [ -10206.3277] [GTR parameters ] . ( 36 sec) [ -10206.3276] [Alpha ][ 0.931492] . ( 36 sec) [ -10206.3276] [Topology ] . ( 37 sec) [ -10206.3268] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -10277.3620] [GTR parameters ] . ( 50 sec) [ -10274.9238] [Alpha ][ 0.855959] . ( 50 sec) [ -10274.0662] [ 2348] [depth= 1] . ( 50 sec) [ -10274.0461] [ 2350] [depth= 1] . ( 50 sec) [ -10272.6954] [ 2348] [depth= 1] . ( 51 sec) [ -10270.5677] [ 2356] [depth= 1] . ( 51 sec) [ -10267.6329] [ 2354] [depth= 1] . ( 51 sec) [ -10264.2339] [ 2356] [depth= 1] . ( 51 sec) [ -10261.1650] [ 2353] [depth= 1] . ( 51 sec) [ -10259.5955] [ 2356] [depth= 1] . ( 51 sec) [ -10258.2228] [ 2356] [depth= 1] . ( 51 sec) [ -10256.3671] [ 2354] [depth= 1] . ( 51 sec) [ -10254.3763] [ 2354] [depth= 1] . ( 51 sec) [ -10254.2504] [ 2354] [depth= 1] . ( 52 sec) [ -10254.0115] [ 2356] [depth= 1] . ( 52 sec) [ -10251.7321] [ 2356] [depth= 1] . ( 52 sec) [ -10247.9251] [ 2359] [depth= 2] . ( 52 sec) [ -10246.0282] [ 2359] [depth= 1] . ( 52 sec) [ -10244.8946] [ 2358] [depth= 1] . ( 52 sec) [ -10244.8108] [ 2354] [depth= 1] . ( 52 sec) [ -10243.9033] [ 2352] [depth= 1] . ( 52 sec) [ -10243.1984] [ 2354] [depth= 1] . ( 53 sec) [ -10215.1069] [Branch lengths ] . ( 53 sec) [ -10214.9407] [GTR parameters ] . ( 53 sec) [ -10214.5210] [Alpha ][ 0.910939] . ( 54 sec) [ -10211.7919] [ 2348] [depth= 1] . ( 55 sec) [ -10210.8529] [ 2348] [depth= 1] . ( 55 sec) [ -10210.8183] [ 2345] [depth= 1] . ( 55 sec) [ -10210.7596] [ 2342] [depth= 1] . ( 55 sec) [ -10210.6871] [ 2345] [depth= 1] . ( 56 sec) [ -10210.4042] [ 2343] [depth= 1] . ( 56 sec) [ -10207.0507] [Branch lengths ] . ( 57 sec) [ -10207.0468] [GTR parameters ] . ( 57 sec) [ -10207.0257] [Alpha ][ 0.923926] . ( 60 sec) [ -10206.7973] [Branch lengths ] . ( 70 sec) [ -10206.6904] [ 2343] [depth= 1] . ( 81 sec) [ -10206.6087] [Branch lengths ] . ( 81 sec) [ -10206.6078] [GTR parameters ] . ( 82 sec) [ -10206.6029] [Alpha ][ 0.930192] . ( 82 sec) [ -10206.6029] [Topology ] . ( 82 sec) [ -10206.5956] [Topology ] . ( 83 sec) [ -10206.5931] [Topology ] . ( 84 sec) [ -10206.5916] [Topology ] . ( 85 sec) [ -10206.5906] [Topology ] . ( 86 sec) [ -10206.5897] [Topology ] . ( 86 sec) [ -10206.5897] [GTR parameters ] . ( 86 sec) [ -10206.5895] [Alpha ][ 0.931308] . ( 86 sec) [ -10206.5895] [Topology ] . ( 87 sec) [ -10206.5887] [Topology ] . ( 87 sec) [ -10206.5887] [GTR parameters ] . ( 87 sec) [ -10206.5887] [Alpha ][ 0.931308] . Checking for NNIs, optimizing five branches... . ( 93 sec) [ -10206.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10206.326827 . Log likelihood obtained after SPR moves : -10206.329453 . Log likelihood of the current tree: -10206.326827. . Printing the most likely tree in file 'data60.phy_phyml_tree.txt'... . Best log likelihood : -10206.312451 . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo