.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data50.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... . 440 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) [ -19568.8507] [GTR parameters ] . ( 1 sec) [ -19274.2068] [Alpha ][ 0.500960] . ( 1 sec) [ -18849.1208] [ 4224] [depth= 6] . ( 1 sec) [ -18433.7657] [ 4173] [depth= 14] . ( 1 sec) [ -18244.4620] [ 4156] [depth= 1] . ( 1 sec) [ -18121.5029] [ 4143] [depth= 7] . ( 1 sec) [ -17987.7805] [ 4070] [depth= 1] . ( 1 sec) [ -17837.0245] [ 4058] [depth= 7] . ( 1 sec) [ -17447.9446] [ 4029] [depth= 3] . ( 1 sec) [ -17220.0648] [ 3946] [depth= 6] . ( 1 sec) [ -17009.8887] [ 3909] [depth= 10] . ( 1 sec) [ -16693.0995] [ 3874] [depth= 5] . ( 1 sec) [ -16557.7625] [ 3840] [depth= 4] . ( 1 sec) [ -16477.4256] [ 3829] [depth= 3] . ( 1 sec) [ -16444.4891] [ 3823] [depth= 2] . ( 1 sec) [ -16386.5308] [ 3760] [depth= 5] . ( 1 sec) [ -16266.5864] [ 3745] [depth= 1] . ( 1 sec) [ -16256.3178] [ 3742] [depth= 1] . ( 1 sec) [ -16190.9870] [ 3739] [depth= 1] . ( 2 sec) [ -16057.5077] [ 3661] [depth= 3] . ( 2 sec) [ -15985.5854] [ 3622] [depth= 9] . ( 2 sec) [ -15869.8765] [ 3584] [depth= 10] . ( 2 sec) [ -15608.7081] [ 3561] [depth= 1] . ( 2 sec) [ -15162.5323] [ 3512] [depth= 8] . ( 2 sec) [ -15156.6807] [ 3504] [depth= 9] . ( 2 sec) [ -15006.3372] [ 3497] [depth= 1] . ( 2 sec) [ -14787.6491] [ 3360] [depth= 15] . ( 2 sec) [ -14655.8617] [ 3329] [depth= 1] . ( 2 sec) [ -14600.0527] [ 3284] [depth= 1] . ( 2 sec) [ -14443.9691] [ 3241] [depth= 15] . ( 2 sec) [ -13747.5480] [ 3186] [depth= 4] . ( 2 sec) [ -13634.6694] [ 3151] [depth= 1] . ( 2 sec) [ -13566.1868] [ 3146] [depth= 2] . ( 2 sec) [ -13269.3553] [ 3075] [depth= 2] . ( 2 sec) [ -12904.4766] [ 3043] [depth= 8] . ( 2 sec) [ -12819.5027] [ 3011] [depth= 1] . ( 2 sec) [ -12574.0765] [ 2893] [depth= 11] . ( 2 sec) [ -12229.2405] [ 2819] [depth= 7] . ( 2 sec) [ -12148.5930] [ 2791] [depth= 1] . ( 2 sec) [ -12079.3706] [ 2775] [depth= 4] . ( 3 sec) [ -12064.4837] [ 2769] [depth= 5] . ( 3 sec) [ -12001.6296] [ 2753] [depth= 4] . ( 3 sec) [ -11996.7809] [ 2742] [depth= 1] . ( 3 sec) [ -11987.7508] [ 2737] [depth= 1] . ( 3 sec) [ -11951.4793] [ 2730] [depth= 2] . ( 3 sec) [ -11943.8726] [ 2753] [depth= 1] . ( 3 sec) [ -11919.2324] [ 2754] [depth= 1] . ( 3 sec) [ -11842.1217] [ 2734] [depth= 1] . ( 3 sec) [ -11794.0027] [ 2713] [depth= 1] . ( 3 sec) [ -11712.1428] [ 2699] [depth= 1] . ( 3 sec) [ -11711.8197] [ 2673] [depth= 3] . ( 3 sec) [ -11444.0889] [ 2667] [depth= 1] . ( 3 sec) [ -11391.4106] [ 2637] [depth= 1] . ( 3 sec) [ -11383.5136] [ 2640] [depth= 2] . ( 3 sec) [ -11299.5100] [ 2586] [depth= 2] . ( 3 sec) [ -11285.4267] [ 2586] [depth= 1] . ( 3 sec) [ -11150.8870] [ 2597] [depth= 1] . ( 3 sec) [ -10994.9763] [ 2535] [depth= 4] . ( 4 sec) [ -10953.8086] [ 2509] [depth= 1] . ( 4 sec) [ -10942.6417] [ 2495] [depth= 3] . ( 4 sec) [ -10845.7855] [ 2486] [depth= 2] . ( 4 sec) [ -10842.0913] [ 2483] [depth= 2] . ( 4 sec) [ -10836.9046] [ 2487] [depth= 2] . ( 4 sec) [ -10805.6758] [ 2462] [depth= 1] . ( 4 sec) [ -10793.6727] [ 2464] [depth= 2] . ( 4 sec) [ -10782.3008] [ 2445] [depth= 2] . ( 4 sec) [ -10770.2822] [ 2445] [depth= 1] . ( 4 sec) [ -10765.8675] [ 2445] [depth= 1] . ( 4 sec) [ -10688.6258] [ 2418] [depth= 4] . ( 4 sec) [ -10660.7034] [ 2406] [depth= 1] . ( 4 sec) [ -10658.0445] [ 2405] [depth= 1] . ( 4 sec) [ -10578.2451] [ 2377] [depth= 1] . ( 4 sec) [ -10565.5492] [ 2371] [depth= 2] . ( 4 sec) [ -10543.3743] [ 2363] [depth= 1] . ( 5 sec) [ -10536.8006] [ 2362] [depth= 1] . ( 5 sec) [ -10532.4841] [ 2362] [depth= 1] . ( 5 sec) [ -10532.4559] [ 2362] [depth= 1] . ( 5 sec) [ -10523.3014] [ 2361] [depth= 1] . ( 5 sec) [ -10380.4775] [Branch lengths ] . ( 6 sec) [ -10375.3710] [GTR parameters ] . ( 6 sec) [ -10326.6240] [Alpha ][ 0.993589] . ( 6 sec) [ -10299.7717] [ 2337] [depth= 4] . ( 6 sec) [ -10299.1984] [ 2336] [depth= 2] . ( 6 sec) [ -10283.7842] [ 2332] [depth= 2] . ( 6 sec) [ -10283.4314] [ 2330] [depth= 1] . ( 6 sec) [ -10281.5040] [ 2327] [depth= 1] . ( 6 sec) [ -10280.9620] [ 2323] [depth= 2] . ( 6 sec) [ -10280.7458] [ 2325] [depth= 1] . ( 6 sec) [ -10280.6697] [ 2325] [depth= 1] . ( 7 sec) [ -10280.3984] [ 2322] [depth= 1] . ( 7 sec) [ -10238.7383] [ 2293] [depth= 1] . ( 7 sec) [ -10238.6285] [ 2296] [depth= 1] . ( 7 sec) [ -10235.7374] [ 2297] [depth= 1] . ( 7 sec) [ -10235.5547] [ 2297] [depth= 1] . ( 8 sec) [ -10234.1953] [ 2297] [depth= 2] . ( 8 sec) [ -10233.1438] [ 2301] [depth= 1] . ( 8 sec) [ -10233.1183] [ 2302] [depth= 1] . ( 9 sec) [ -10233.0148] [ 2302] [depth= 1] . ( 9 sec) [ -10232.6000] [ 2299] [depth= 1] . ( 9 sec) [ -10231.8805] [ 2296] [depth= 1] . ( 9 sec) [ -10230.9709] [ 2296] [depth= 1] . ( 10 sec) [ -10228.2573] [ 2300] [depth= 1] . ( 10 sec) [ -10219.7762] [Branch lengths ] . ( 10 sec) [ -10219.6516] [GTR parameters ] . ( 10 sec) [ -10219.5786] [Alpha ][ 1.020740] . ( 11 sec) [ -10219.5385] [ 2301] [depth= 1] . ( 12 sec) [ -10219.0698] [ 2298] [depth= 1] . ( 15 sec) [ -10218.2632] [Branch lengths ] . ( 15 sec) [ -10218.2584] [GTR parameters ] . ( 15 sec) [ -10218.2573] [Alpha ][ 1.024064] . ( 20 sec) [ -10218.1897] [Branch lengths ] . ( 44 sec) [ -10218.1787] [Branch lengths ] . ( 44 sec) [ -10218.1787] [Topology ] . ( 45 sec) [ -10218.1775] [Topology ] . ( 46 sec) [ -10218.1771] [Topology ] . ( 46 sec) [ -10218.1771] [GTR parameters ] . ( 46 sec) [ -10218.1768] [Alpha ][ 1.025896] . ( 46 sec) [ -10218.1768] [Topology ] . ( 47 sec) [ -10218.1765] [Topology ] . ( 47 sec) [ -10218.1765] [GTR parameters ] . ( 47 sec) [ -10218.1765] [Alpha ][ 1.025896] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -10218.1763] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.176336. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19075.1666] [GTR parameters ] . ( 1 sec) [ -18785.6219] [Alpha ][ 0.500960] . ( 1 sec) [ -18768.5535] [ 4196] [depth= 8] . ( 1 sec) [ -18284.3115] [ 4116] [depth= 9] . ( 1 sec) [ -18135.6258] [ 4073] [depth= 4] . ( 1 sec) [ -18101.7333] [ 4056] [depth= 4] . ( 1 sec) [ -18067.2396] [ 4037] [depth= 1] . ( 1 sec) [ -17844.3047] [ 4024] [depth= 4] . ( 1 sec) [ -17794.4923] [ 4016] [depth= 4] . ( 1 sec) [ -17733.0303] [ 4004] [depth= 2] . ( 1 sec) [ -17655.4876] [ 3995] [depth= 2] . ( 1 sec) [ -17445.4142] [ 3897] [depth= 8] . ( 2 sec) [ -17316.0422] [ 3890] [depth= 3] . ( 2 sec) [ -17174.0865] [ 3849] [depth= 1] . ( 2 sec) [ -16889.7098] [ 3837] [depth= 4] . ( 2 sec) [ -16612.4889] [ 3758] [depth= 9] . ( 2 sec) [ -16331.5626] [ 3714] [depth= 8] . ( 2 sec) [ -16169.3141] [ 3708] [depth= 3] . ( 2 sec) [ -16066.3237] [ 3666] [depth= 1] . ( 2 sec) [ -15948.9041] [ 3656] [depth= 3] . ( 2 sec) [ -15745.5985] [ 3582] [depth= 1] . ( 2 sec) [ -15236.1529] [ 3574] [depth= 2] . ( 2 sec) [ -15224.8035] [ 3575] [depth= 1] . ( 2 sec) [ -14652.5143] [ 3421] [depth= 12] . ( 2 sec) [ -14574.2297] [ 3379] [depth= 7] . ( 2 sec) [ -14256.5789] [ 3318] [depth= 4] . ( 2 sec) [ -14143.3939] [ 3286] [depth= 5] . ( 2 sec) [ -14114.4938] [ 3284] [depth= 1] . ( 2 sec) [ -14024.3716] [ 3269] [depth= 11] . ( 2 sec) [ -13829.8665] [ 3253] [depth= 1] . ( 2 sec) [ -13525.7122] [ 3241] [depth= 8] . ( 2 sec) [ -13480.5780] [ 3190] [depth= 1] . ( 2 sec) [ -13105.4175] [ 3108] [depth= 10] . ( 2 sec) [ -13068.9965] [ 3114] [depth= 1] . ( 3 sec) [ -12864.4460] [ 3075] [depth= 11] . ( 3 sec) [ -12819.4901] [ 3063] [depth= 1] . ( 3 sec) [ -12794.9831] [ 3060] [depth= 8] . ( 3 sec) [ -12683.1916] [ 3020] [depth= 3] . ( 3 sec) [ -12680.6255] [ 3028] [depth= 1] . ( 3 sec) [ -12472.4853] [ 2919] [depth= 7] . ( 3 sec) [ -12468.2620] [ 2927] [depth= 2] . ( 3 sec) [ -12209.3502] [ 2863] [depth= 3] . ( 3 sec) [ -12207.9747] [ 2863] [depth= 1] . ( 3 sec) [ -12193.1056] [ 2861] [depth= 2] . ( 3 sec) [ -12191.7473] [ 2865] [depth= 3] . ( 3 sec) [ -12059.9396] [ 2831] [depth= 1] . ( 3 sec) [ -12034.1182] [ 2811] [depth= 2] . ( 3 sec) [ -11990.4854] [ 2797] [depth= 1] . ( 3 sec) [ -11988.3306] [ 2798] [depth= 1] . ( 3 sec) [ -11986.3242] [ 2799] [depth= 1] . ( 3 sec) [ -11937.2572] [ 2771] [depth= 1] . ( 3 sec) [ -11937.2069] [ 2769] [depth= 2] . ( 3 sec) [ -11894.3332] [ 2745] [depth= 3] . ( 4 sec) [ -11811.2693] [ 2717] [depth= 1] . ( 4 sec) [ -11528.7267] [ 2688] [depth= 1] . ( 4 sec) [ -11409.9086] [ 2674] [depth= 1] . ( 4 sec) [ -11400.4308] [ 2679] [depth= 3] . ( 4 sec) [ -11360.3066] [ 2660] [depth= 1] . ( 4 sec) [ -11357.9042] [ 2660] [depth= 1] . ( 4 sec) [ -11292.7690] [ 2633] [depth= 3] . ( 4 sec) [ -11284.8079] [ 2634] [depth= 1] . ( 4 sec) [ -11260.3597] [ 2623] [depth= 3] . ( 4 sec) [ -11224.3779] [ 2616] [depth= 2] . ( 4 sec) [ -11194.0735] [ 2605] [depth= 3] . ( 4 sec) [ -11188.9691] [ 2607] [depth= 1] . ( 4 sec) [ -11123.9738] [ 2588] [depth= 2] . ( 4 sec) [ -10979.6379] [ 2543] [depth= 5] . ( 4 sec) [ -10968.8650] [ 2543] [depth= 1] . ( 4 sec) [ -10802.7099] [ 2458] [depth= 7] . ( 4 sec) [ -10788.9509] [ 2461] [depth= 1] . ( 4 sec) [ -10715.2236] [ 2419] [depth= 2] . ( 5 sec) [ -10689.6173] [ 2412] [depth= 5] . ( 5 sec) [ -10681.8735] [ 2403] [depth= 1] . ( 5 sec) [ -10680.6972] [ 2402] [depth= 1] . ( 5 sec) [ -10658.8834] [ 2396] [depth= 2] . ( 5 sec) [ -10620.9005] [ 2369] [depth= 2] . ( 5 sec) [ -10462.6226] [ 2329] [depth= 3] . ( 5 sec) [ -10454.8860] [ 2327] [depth= 1] . ( 5 sec) [ -10454.6998] [ 2328] [depth= 1] . ( 5 sec) [ -10453.3551] [ 2330] [depth= 2] . ( 5 sec) [ -10330.3753] [Branch lengths ] . ( 6 sec) [ -10326.8194] [GTR parameters ] . ( 6 sec) [ -10296.2573] [Alpha ][ 0.861575] . ( 6 sec) [ -10296.1193] [ 2331] [depth= 1] . ( 6 sec) [ -10294.1408] [ 2329] [depth= 1] . ( 7 sec) [ -10270.7744] [ 2303] [depth= 1] . ( 7 sec) [ -10269.4898] [ 2304] [depth= 2] . ( 7 sec) [ -10267.2548] [ 2302] [depth= 1] . ( 7 sec) [ -10266.4023] [ 2300] [depth= 1] . ( 7 sec) [ -10265.3486] [ 2296] [depth= 1] . ( 7 sec) [ -10265.2385] [ 2294] [depth= 1] . ( 7 sec) [ -10264.0139] [ 2296] [depth= 1] . ( 7 sec) [ -10262.4966] [ 2297] [depth= 1] . ( 8 sec) [ -10262.3000] [ 2296] [depth= 1] . ( 8 sec) [ -10260.2194] [ 2299] [depth= 3] . ( 8 sec) [ -10259.0727] [ 2297] [depth= 1] . ( 8 sec) [ -10255.2378] [ 2296] [depth= 1] . ( 9 sec) [ -10254.3057] [ 2297] [depth= 1] . ( 9 sec) [ -10254.2401] [ 2295] [depth= 1] . ( 9 sec) [ -10253.8933] [ 2295] [depth= 1] . ( 9 sec) [ -10253.0856] [ 2297] [depth= 1] . ( 9 sec) [ -10252.6007] [ 2299] [depth= 1] . ( 10 sec) [ -10252.0147] [ 2297] [depth= 1] . ( 10 sec) [ -10251.9055] [ 2299] [depth= 1] . ( 11 sec) [ -10226.5765] [Branch lengths ] . ( 11 sec) [ -10226.4947] [GTR parameters ] . ( 11 sec) [ -10224.3763] [Alpha ][ 0.999571] . ( 12 sec) [ -10224.3630] [ 2299] [depth= 1] . ( 16 sec) [ -10223.9315] [ 2300] [depth= 2] . ( 16 sec) [ -10220.3185] [Branch lengths ] . ( 17 sec) [ -10220.3072] [GTR parameters ] . ( 17 sec) [ -10220.2878] [Alpha ][ 1.014134] . ( 18 sec) [ -10219.6254] [ 2298] [depth= 1] . ( 22 sec) [ -10218.3964] [Branch lengths ] . ( 22 sec) [ -10218.3948] [GTR parameters ] . ( 22 sec) [ -10218.3885] [Alpha ][ 1.022464] . ( 28 sec) [ -10218.2032] [Branch lengths ] . ( 52 sec) [ -10218.1736] [Branch lengths ] . ( 52 sec) [ -10218.1736] [Topology ] . ( 53 sec) [ -10218.1703] [Topology ] . ( 53 sec) [ -10218.1692] [Topology ] . ( 54 sec) [ -10218.1686] [Topology ] . ( 55 sec) [ -10218.1683] [GTR parameters ] . ( 55 sec) [ -10218.1669] [Alpha ][ 1.026347] . ( 55 sec) [ -10218.1669] [Topology ] . ( 55 sec) [ -10218.1664] [Topology ] . ( 56 sec) [ -10218.1664] [GTR parameters ] . ( 56 sec) [ -10218.1664] [Alpha ][ 1.026347] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -10218.1511] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.151125. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19749.1168] [GTR parameters ] . ( 0 sec) [ -19439.8276] [Alpha ][ 0.500960] . ( 0 sec) [ -19083.5961] [ 4398] [depth= 4] . ( 0 sec) [ -18626.5186] [ 4335] [depth= 4] . ( 0 sec) [ -18598.6829] [ 4329] [depth= 3] . ( 1 sec) [ -18500.0044] [ 4327] [depth= 1] . ( 1 sec) [ -18089.3850] [ 4286] [depth= 6] . ( 1 sec) [ -17954.4339] [ 4276] [depth= 2] . ( 1 sec) [ -17664.1140] [ 4219] [depth= 7] . ( 1 sec) [ -17423.9298] [ 4179] [depth= 12] . ( 1 sec) [ -17196.6610] [ 4070] [depth= 15] . ( 1 sec) [ -17077.5782] [ 4091] [depth= 18] . ( 1 sec) [ -16952.2926] [ 3995] [depth= 2] . ( 1 sec) [ -16950.1924] [ 3993] [depth= 1] . ( 1 sec) [ -16611.4085] [ 3878] [depth= 16] . ( 1 sec) [ -16547.0397] [ 3845] [depth= 3] . ( 1 sec) [ -16146.1050] [ 3836] [depth= 1] . ( 1 sec) [ -15997.2186] [ 3777] [depth= 9] . ( 1 sec) [ -15983.0836] [ 3771] [depth= 2] . ( 1 sec) [ -15749.3613] [ 3735] [depth= 1] . ( 1 sec) [ -15561.0298] [ 3658] [depth= 10] . ( 1 sec) [ -15198.8683] [ 3537] [depth= 6] . ( 1 sec) [ -15146.8610] [ 3509] [depth= 1] . ( 1 sec) [ -14936.1180] [ 3483] [depth= 3] . ( 1 sec) [ -14835.7541] [ 3422] [depth= 7] . ( 1 sec) [ -14809.9617] [ 3406] [depth= 1] . ( 1 sec) [ -14688.7005] [ 3372] [depth= 11] . ( 2 sec) [ -14661.1574] [ 3346] [depth= 2] . ( 2 sec) [ -14504.8396] [ 3272] [depth= 7] . ( 2 sec) [ -14241.8955] [ 3229] [depth= 4] . ( 2 sec) [ -14235.6721] [ 3208] [depth= 9] . ( 2 sec) [ -14185.9539] [ 3211] [depth= 1] . ( 2 sec) [ -14181.6682] [ 3208] [depth= 1] . ( 2 sec) [ -14121.0408] [ 3176] [depth= 1] . ( 2 sec) [ -14087.1113] [ 3154] [depth= 1] . ( 2 sec) [ -14048.3003] [ 3153] [depth= 4] . ( 2 sec) [ -13728.7122] [ 3073] [depth= 15] . ( 2 sec) [ -13342.6196] [ 2954] [depth= 8] . ( 2 sec) [ -13171.8103] [ 2962] [depth= 8] . ( 2 sec) [ -13160.0127] [ 2963] [depth= 1] . ( 2 sec) [ -13076.1244] [ 2961] [depth= 1] . ( 2 sec) [ -12480.9730] [ 2874] [depth= 7] . ( 2 sec) [ -12456.7932] [ 2868] [depth= 1] . ( 2 sec) [ -12442.0371] [ 2866] [depth= 1] . ( 2 sec) [ -12437.0430] [ 2848] [depth= 3] . ( 3 sec) [ -12380.6022] [ 2839] [depth= 2] . ( 3 sec) [ -12308.0393] [ 2819] [depth= 2] . ( 3 sec) [ -12292.0231] [ 2814] [depth= 1] . ( 3 sec) [ -12264.8983] [ 2801] [depth= 1] . ( 3 sec) [ -12236.7894] [ 2785] [depth= 2] . ( 3 sec) [ -12199.4725] [ 2734] [depth= 8] . ( 3 sec) [ -11998.3920] [ 2706] [depth= 2] . ( 3 sec) [ -11981.5564] [ 2691] [depth= 4] . ( 3 sec) [ -11910.5313] [ 2685] [depth= 3] . ( 3 sec) [ -11865.1427] [ 2621] [depth= 8] . ( 3 sec) [ -11440.2731] [ 2504] [depth= 11] . ( 3 sec) [ -11339.9507] [ 2485] [depth= 1] . ( 3 sec) [ -11283.3056] [ 2469] [depth= 2] . ( 3 sec) [ -11240.3811] [ 2455] [depth= 3] . ( 3 sec) [ -11211.8139] [ 2457] [depth= 1] . ( 3 sec) [ -11211.2273] [ 2455] [depth= 1] . ( 3 sec) [ -11171.6033] [ 2484] [depth= 1] . ( 3 sec) [ -11090.4859] [ 2457] [depth= 2] . ( 3 sec) [ -11027.7244] [ 2456] [depth= 1] . ( 4 sec) [ -11007.4182] [ 2457] [depth= 2] . ( 4 sec) [ -11000.1125] [ 2457] [depth= 1] . ( 4 sec) [ -10903.0020] [ 2449] [depth= 1] . ( 4 sec) [ -10876.0459] [ 2442] [depth= 1] . ( 4 sec) [ -10873.2477] [ 2440] [depth= 1] . ( 4 sec) [ -10830.3583] [ 2412] [depth= 1] . ( 4 sec) [ -10825.1963] [ 2409] [depth= 3] . ( 4 sec) [ -10815.8783] [ 2412] [depth= 2] . ( 4 sec) [ -10776.5289] [ 2411] [depth= 3] . ( 4 sec) [ -10771.4488] [ 2401] [depth= 3] . ( 4 sec) [ -10706.2706] [ 2350] [depth= 6] . ( 4 sec) [ -10661.1038] [ 2348] [depth= 1] . ( 4 sec) [ -10627.0475] [ 2350] [depth= 3] . ( 4 sec) [ -10626.3851] [ 2350] [depth= 1] . ( 4 sec) [ -10623.5600] [ 2349] [depth= 2] . ( 5 sec) [ -10397.7354] [Branch lengths ] . ( 5 sec) [ -10392.7345] [GTR parameters ] . ( 5 sec) [ -10344.3101] [Alpha ][ 0.988423] . ( 5 sec) [ -10293.0608] [ 2322] [depth= 2] . ( 6 sec) [ -10250.6133] [ 2297] [depth= 4] . ( 6 sec) [ -10250.2722] [ 2299] [depth= 1] . ( 6 sec) [ -10248.8904] [ 2299] [depth= 1] . ( 6 sec) [ -10248.3181] [ 2299] [depth= 2] . ( 6 sec) [ -10240.5060] [ 2302] [depth= 1] . ( 7 sec) [ -10239.8244] [ 2299] [depth= 1] . ( 7 sec) [ -10239.1655] [ 2300] [depth= 1] . ( 7 sec) [ -10237.3439] [ 2300] [depth= 1] . ( 7 sec) [ -10237.2548] [ 2301] [depth= 1] . ( 7 sec) [ -10235.3576] [ 2296] [depth= 1] . ( 7 sec) [ -10235.3259] [ 2296] [depth= 1] . ( 8 sec) [ -10234.6358] [ 2295] [depth= 1] . ( 8 sec) [ -10234.4163] [ 2296] [depth= 1] . ( 8 sec) [ -10234.1431] [ 2297] [depth= 1] . ( 9 sec) [ -10234.1316] [ 2296] [depth= 1] . ( 9 sec) [ -10234.1203] [ 2296] [depth= 1] . ( 10 sec) [ -10220.0662] [Branch lengths ] . ( 10 sec) [ -10220.0053] [GTR parameters ] . ( 10 sec) [ -10219.9107] [Alpha ][ 1.019456] . ( 11 sec) [ -10219.4354] [ 2299] [depth= 1] . ( 12 sec) [ -10219.1785] [ 2298] [depth= 1] . ( 15 sec) [ -10218.2801] [Branch lengths ] . ( 15 sec) [ -10218.2758] [GTR parameters ] . ( 15 sec) [ -10218.2742] [Alpha ][ 1.023648] . ( 20 sec) [ -10218.1936] [Branch lengths ] . ( 44 sec) [ -10218.1795] [Branch lengths ] . ( 44 sec) [ -10218.1795] [Topology ] . ( 45 sec) [ -10218.1781] [Topology ] . ( 46 sec) [ -10218.1775] [Topology ] . ( 46 sec) [ -10218.1774] [GTR parameters ] . ( 46 sec) [ -10218.1770] [Alpha ][ 1.025873] . ( 46 sec) [ -10218.1770] [Topology ] . ( 47 sec) [ -10218.1766] [Topology ] . ( 47 sec) [ -10218.1766] [GTR parameters ] . ( 47 sec) [ -10218.1766] [Alpha ][ 1.025873] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -10218.1765] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.176460. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19290.5804] [GTR parameters ] . ( 0 sec) [ -18968.1203] [Alpha ][ 0.500960] . ( 0 sec) [ -18545.9886] [ 4272] [depth= 10] . ( 0 sec) [ -18239.8570] [ 4224] [depth= 9] . ( 0 sec) [ -18099.3721] [ 4182] [depth= 7] . ( 0 sec) [ -17941.4447] [ 4108] [depth= 1] . ( 0 sec) [ -17724.3906] [ 4064] [depth= 10] . ( 0 sec) [ -17579.8544] [ 4030] [depth= 2] . ( 0 sec) [ -17216.9727] [ 4027] [depth= 2] . ( 0 sec) [ -17142.1861] [ 4002] [depth= 1] . ( 0 sec) [ -17070.0971] [ 3998] [depth= 2] . ( 1 sec) [ -17061.8355] [ 3995] [depth= 3] . ( 1 sec) [ -17060.7892] [ 3998] [depth= 2] . ( 1 sec) [ -16891.9758] [ 3950] [depth= 6] . ( 1 sec) [ -16886.8616] [ 3948] [depth= 2] . ( 1 sec) [ -16780.0322] [ 3937] [depth= 2] . ( 1 sec) [ -16574.6481] [ 3845] [depth= 7] . ( 1 sec) [ -16468.0158] [ 3842] [depth= 1] . ( 1 sec) [ -16461.3030] [ 3838] [depth= 1] . ( 1 sec) [ -16457.7426] [ 3835] [depth= 1] . ( 1 sec) [ -16170.2371] [ 3805] [depth= 1] . ( 1 sec) [ -16108.4885] [ 3789] [depth= 7] . ( 1 sec) [ -16052.6444] [ 3784] [depth= 1] . ( 1 sec) [ -15918.6877] [ 3755] [depth= 10] . ( 1 sec) [ -15856.9294] [ 3731] [depth= 9] . ( 1 sec) [ -15625.9905] [ 3714] [depth= 5] . ( 1 sec) [ -15530.5922] [ 3648] [depth= 1] . ( 1 sec) [ -15503.1669] [ 3617] [depth= 1] . ( 1 sec) [ -15373.6529] [ 3557] [depth= 4] . ( 1 sec) [ -15039.5916] [ 3499] [depth= 11] . ( 1 sec) [ -14753.0209] [ 3421] [depth= 9] . ( 1 sec) [ -14444.2599] [ 3351] [depth= 4] . ( 1 sec) [ -14414.2627] [ 3342] [depth= 1] . ( 2 sec) [ -14269.2883] [ 3307] [depth= 2] . ( 2 sec) [ -14209.8113] [ 3303] [depth= 1] . ( 2 sec) [ -14121.6372] [ 3269] [depth= 8] . ( 2 sec) [ -13865.9677] [ 3208] [depth= 3] . ( 2 sec) [ -13826.8462] [ 3206] [depth= 3] . ( 2 sec) [ -13821.3181] [ 3212] [depth= 1] . ( 2 sec) [ -13658.1374] [ 3179] [depth= 4] . ( 2 sec) [ -13483.4275] [ 3117] [depth= 8] . ( 2 sec) [ -13363.3639] [ 3083] [depth= 5] . ( 2 sec) [ -13277.8477] [ 3074] [depth= 1] . ( 2 sec) [ -13244.1470] [ 3059] [depth= 4] . ( 2 sec) [ -13019.8727] [ 2994] [depth= 2] . ( 2 sec) [ -12923.2519] [ 2986] [depth= 2] . ( 2 sec) [ -12757.9761] [ 2981] [depth= 2] . ( 2 sec) [ -12753.1561] [ 2978] [depth= 1] . ( 2 sec) [ -12510.0668] [ 2953] [depth= 5] . ( 2 sec) [ -12401.5791] [ 2945] [depth= 3] . ( 2 sec) [ -12362.2452] [ 2919] [depth= 1] . ( 2 sec) [ -12335.3389] [ 2920] [depth= 1] . ( 3 sec) [ -12268.2613] [ 2924] [depth= 3] . ( 3 sec) [ -12135.7439] [ 2909] [depth= 2] . ( 3 sec) [ -11984.5187] [ 2864] [depth= 5] . ( 3 sec) [ -11980.3177] [ 2869] [depth= 2] . ( 3 sec) [ -11946.2441] [ 2865] [depth= 2] . ( 3 sec) [ -11921.1790] [ 2870] [depth= 4] . ( 3 sec) [ -11899.3346] [ 2875] [depth= 4] . ( 3 sec) [ -11791.5282] [ 2815] [depth= 3] . ( 3 sec) [ -11786.8408] [ 2814] [depth= 1] . ( 3 sec) [ -11756.2715] [ 2799] [depth= 6] . ( 3 sec) [ -11712.2908] [ 2803] [depth= 4] . ( 3 sec) [ -11623.5983] [ 2784] [depth= 1] . ( 3 sec) [ -11588.1063] [ 2762] [depth= 3] . ( 3 sec) [ -11528.8319] [ 2728] [depth= 12] . ( 3 sec) [ -11463.8420] [ 2710] [depth= 2] . ( 3 sec) [ -11351.4844] [ 2660] [depth= 5] . ( 3 sec) [ -11286.9538] [ 2597] [depth= 13] . ( 3 sec) [ -11223.5413] [ 2570] [depth= 5] . ( 3 sec) [ -11218.3288] [ 2565] [depth= 1] . ( 4 sec) [ -11175.9593] [ 2529] [depth= 1] . ( 4 sec) [ -11151.5742] [ 2511] [depth= 1] . ( 4 sec) [ -10947.8506] [ 2468] [depth= 2] . ( 4 sec) [ -10934.9002] [ 2455] [depth= 1] . ( 4 sec) [ -10913.8659] [ 2442] [depth= 3] . ( 4 sec) [ -10886.5783] [ 2432] [depth= 2] . ( 4 sec) [ -10885.7744] [ 2434] [depth= 1] . ( 4 sec) [ -10883.8803] [ 2432] [depth= 1] . ( 4 sec) [ -10867.9330] [ 2434] [depth= 1] . ( 4 sec) [ -10867.8495] [ 2435] [depth= 1] . ( 4 sec) [ -10850.7556] [ 2433] [depth= 2] . ( 4 sec) [ -10712.6929] [ 2361] [depth= 5] . ( 4 sec) [ -10706.5472] [ 2376] [depth= 1] . ( 4 sec) [ -10669.3886] [ 2368] [depth= 3] . ( 4 sec) [ -10569.2135] [ 2346] [depth= 1] . ( 5 sec) [ -10377.0605] [Branch lengths ] . ( 5 sec) [ -10373.1622] [GTR parameters ] . ( 6 sec) [ -10331.4383] [Alpha ][ 0.944079] . ( 6 sec) [ -10326.5178] [ 2341] [depth= 2] . ( 6 sec) [ -10292.0220] [ 2317] [depth= 2] . ( 6 sec) [ -10291.6494] [ 2317] [depth= 1] . ( 6 sec) [ -10289.6558] [ 2318] [depth= 2] . ( 6 sec) [ -10287.5200] [ 2316] [depth= 2] . ( 6 sec) [ -10271.6294] [ 2310] [depth= 4] . ( 6 sec) [ -10259.3882] [ 2297] [depth= 1] . ( 7 sec) [ -10256.5286] [ 2295] [depth= 1] . ( 7 sec) [ -10254.2508] [ 2294] [depth= 1] . ( 7 sec) [ -10253.9754] [ 2297] [depth= 1] . ( 7 sec) [ -10252.8051] [ 2297] [depth= 1] . ( 7 sec) [ -10252.1433] [ 2295] [depth= 1] . ( 7 sec) [ -10248.7810] [ 2295] [depth= 1] . ( 7 sec) [ -10248.1465] [ 2298] [depth= 1] . ( 8 sec) [ -10247.6113] [ 2299] [depth= 1] . ( 8 sec) [ -10247.4883] [ 2299] [depth= 1] . ( 8 sec) [ -10247.3685] [ 2301] [depth= 2] . ( 8 sec) [ -10247.2995] [ 2303] [depth= 1] . ( 9 sec) [ -10245.1605] [ 2300] [depth= 2] . ( 9 sec) [ -10244.5014] [ 2297] [depth= 1] . ( 9 sec) [ -10244.1868] [ 2301] [depth= 1] . ( 9 sec) [ -10242.3935] [ 2300] [depth= 1] . ( 10 sec) [ -10226.9044] [Branch lengths ] . ( 10 sec) [ -10226.5148] [GTR parameters ] . ( 10 sec) [ -10226.0021] [Alpha ][ 1.014952] . ( 11 sec) [ -10224.8466] [ 2298] [depth= 1] . ( 11 sec) [ -10224.7290] [ 2301] [depth= 4] . ( 13 sec) [ -10224.5885] [ 2301] [depth= 2] . ( 14 sec) [ -10223.2037] [ 2302] [depth= 1] . ( 14 sec) [ -10222.7819] [ 2301] [depth= 1] . ( 14 sec) [ -10222.3986] [ 2297] [depth= 1] . ( 15 sec) [ -10221.9080] [ 2297] [depth= 1] . ( 15 sec) [ -10218.8986] [Branch lengths ] . ( 15 sec) [ -10218.8657] [GTR parameters ] . ( 16 sec) [ -10218.8594] [Alpha ][ 1.023227] . ( 19 sec) [ -10218.8049] [ 2298] [depth= 1] . ( 20 sec) [ -10218.2445] [Branch lengths ] . ( 20 sec) [ -10218.2431] [GTR parameters ] . ( 20 sec) [ -10218.2428] [Alpha ][ 1.024705] . ( 44 sec) [ -10218.1834] [Branch lengths ] . ( 44 sec) [ -10218.1834] [Topology ] . ( 45 sec) [ -10218.1792] [Topology ] . ( 46 sec) [ -10218.1779] [Topology ] . ( 47 sec) [ -10218.1772] [Topology ] . ( 47 sec) [ -10218.1772] [GTR parameters ] . ( 47 sec) [ -10218.1770] [Alpha ][ 1.025844] . ( 47 sec) [ -10218.1770] [Topology ] . ( 48 sec) [ -10218.1767] [Topology ] . ( 48 sec) [ -10218.1767] [GTR parameters ] . ( 48 sec) [ -10218.1767] [Alpha ][ 1.025844] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -10218.1765] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.176485. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19699.5473] [GTR parameters ] . ( 1 sec) [ -19366.0569] [Alpha ][ 0.500960] . ( 1 sec) [ -19240.5766] [ 4361] [depth= 9] . ( 1 sec) [ -18983.7298] [ 4308] [depth= 8] . ( 1 sec) [ -18898.3141] [ 4284] [depth= 4] . ( 1 sec) [ -18819.7825] [ 4281] [depth= 4] . ( 1 sec) [ -18799.6824] [ 4259] [depth= 9] . ( 1 sec) [ -18727.1199] [ 4249] [depth= 2] . ( 1 sec) [ -18678.2316] [ 4232] [depth= 4] . ( 1 sec) [ -18617.5202] [ 4224] [depth= 1] . ( 1 sec) [ -18347.6035] [ 4105] [depth= 10] . ( 1 sec) [ -18194.1779] [ 4038] [depth= 10] . ( 1 sec) [ -18060.0419] [ 4007] [depth= 1] . ( 1 sec) [ -17494.8367] [ 3967] [depth= 8] . ( 1 sec) [ -17164.9704] [ 3886] [depth= 3] . ( 1 sec) [ -17119.1561] [ 3878] [depth= 1] . ( 1 sec) [ -17054.5383] [ 3867] [depth= 2] . ( 1 sec) [ -16736.2792] [ 3782] [depth= 7] . ( 1 sec) [ -16698.1226] [ 3775] [depth= 3] . ( 1 sec) [ -16670.9862] [ 3780] [depth= 13] . ( 1 sec) [ -16554.8121] [ 3775] [depth= 1] . ( 1 sec) [ -16456.1375] [ 3771] [depth= 1] . ( 1 sec) [ -16371.9099] [ 3754] [depth= 17] . ( 1 sec) [ -16295.7586] [ 3699] [depth= 16] . ( 2 sec) [ -16187.7934] [ 3646] [depth= 1] . ( 2 sec) [ -16063.6516] [ 3612] [depth= 2] . ( 2 sec) [ -16007.9899] [ 3569] [depth= 1] . ( 2 sec) [ -15797.3665] [ 3508] [depth= 13] . ( 2 sec) [ -15661.7228] [ 3497] [depth= 1] . ( 2 sec) [ -15628.1315] [ 3501] [depth= 1] . ( 2 sec) [ -15322.2682] [ 3414] [depth= 13] . ( 2 sec) [ -15298.4638] [ 3427] [depth= 1] . ( 2 sec) [ -15287.1562] [ 3432] [depth= 1] . ( 2 sec) [ -15259.3744] [ 3420] [depth= 1] . ( 2 sec) [ -15199.6406] [ 3418] [depth= 1] . ( 2 sec) [ -14846.3431] [ 3291] [depth= 10] . ( 2 sec) [ -14739.8186] [ 3268] [depth= 1] . ( 2 sec) [ -14662.7613] [ 3267] [depth= 1] . ( 2 sec) [ -14577.1191] [ 3220] [depth= 2] . ( 2 sec) [ -14418.0721] [ 3167] [depth= 1] . ( 2 sec) [ -14355.5602] [ 3143] [depth= 8] . ( 2 sec) [ -14170.0508] [ 3080] [depth= 2] . ( 2 sec) [ -13950.2061] [ 2998] [depth= 8] . ( 2 sec) [ -13754.5978] [ 2925] [depth= 7] . ( 3 sec) [ -13645.9224] [ 2899] [depth= 7] . ( 3 sec) [ -13483.0079] [ 2841] [depth= 2] . ( 3 sec) [ -13477.5597] [ 2851] [depth= 1] . ( 3 sec) [ -13475.8776] [ 2850] [depth= 1] . ( 3 sec) [ -13225.7568] [ 2827] [depth= 2] . ( 3 sec) [ -13081.9199] [ 2796] [depth= 1] . ( 3 sec) [ -12961.6086] [ 2763] [depth= 1] . ( 3 sec) [ -12766.5565] [ 2722] [depth= 4] . ( 3 sec) [ -12734.9080] [ 2718] [depth= 3] . ( 3 sec) [ -12654.8183] [ 2718] [depth= 1] . ( 3 sec) [ -12640.9993] [ 2707] [depth= 1] . ( 3 sec) [ -12543.5176] [ 2657] [depth= 3] . ( 3 sec) [ -12409.8016] [ 2649] [depth= 4] . ( 3 sec) [ -12306.5171] [ 2671] [depth= 1] . ( 3 sec) [ -12207.7512] [ 2612] [depth= 6] . ( 3 sec) [ -12164.3213] [ 2621] [depth= 1] . ( 3 sec) [ -12158.5193] [ 2639] [depth= 1] . ( 3 sec) [ -12150.2256] [ 2621] [depth= 1] . ( 3 sec) [ -12147.6449] [ 2621] [depth= 1] . ( 4 sec) [ -11935.6888] [ 2624] [depth= 1] . ( 4 sec) [ -11827.9546] [ 2619] [depth= 1] . ( 4 sec) [ -11821.0793] [ 2621] [depth= 1] . ( 4 sec) [ -11797.2478] [ 2621] [depth= 3] . ( 4 sec) [ -11751.2052] [ 2620] [depth= 3] . ( 4 sec) [ -11713.7508] [ 2604] [depth= 2] . ( 4 sec) [ -11341.0648] [ 2542] [depth= 6] . ( 4 sec) [ -11299.4835] [ 2524] [depth= 1] . ( 4 sec) [ -11116.7198] [ 2426] [depth= 5] . ( 4 sec) [ -11082.6111] [ 2426] [depth= 1] . ( 4 sec) [ -10890.3347] [ 2379] [depth= 9] . ( 4 sec) [ -10841.5881] [ 2384] [depth= 1] . ( 4 sec) [ -10818.8045] [ 2387] [depth= 1] . ( 4 sec) [ -10813.4678] [ 2376] [depth= 4] . ( 4 sec) [ -10669.5415] [ 2370] [depth= 5] . ( 4 sec) [ -10658.1666] [ 2369] [depth= 1] . ( 4 sec) [ -10649.3471] [ 2359] [depth= 1] . ( 4 sec) [ -10639.5983] [ 2356] [depth= 1] . ( 4 sec) [ -10628.8692] [ 2349] [depth= 1] . ( 5 sec) [ -10628.8023] [ 2349] [depth= 1] . ( 5 sec) [ -10626.8623] [ 2353] [depth= 3] . ( 5 sec) [ -10564.4118] [ 2347] [depth= 3] . ( 5 sec) [ -10527.2389] [ 2332] [depth= 2] . ( 5 sec) [ -10520.9730] [ 2324] [depth= 3] . ( 5 sec) [ -10510.5497] [ 2328] [depth= 1] . ( 5 sec) [ -10337.2396] [Branch lengths ] . ( 6 sec) [ -10334.5800] [GTR parameters ] . ( 6 sec) [ -10301.1262] [Alpha ][ 0.886257] . ( 6 sec) [ -10265.3083] [ 2296] [depth= 1] . ( 6 sec) [ -10264.6397] [ 2293] [depth= 1] . ( 6 sec) [ -10260.0433] [ 2289] [depth= 1] . ( 6 sec) [ -10259.8870] [ 2291] [depth= 1] . ( 6 sec) [ -10258.1496] [ 2289] [depth= 1] . ( 6 sec) [ -10257.8444] [ 2292] [depth= 1] . ( 6 sec) [ -10252.6243] [ 2296] [depth= 2] . ( 7 sec) [ -10252.2971] [ 2297] [depth= 1] . ( 7 sec) [ -10251.6782] [ 2300] [depth= 1] . ( 8 sec) [ -10248.8189] [ 2301] [depth= 2] . ( 8 sec) [ -10247.9536] [ 2299] [depth= 1] . ( 8 sec) [ -10247.7186] [ 2298] [depth= 1] . ( 8 sec) [ -10247.2129] [ 2300] [depth= 1] . ( 9 sec) [ -10247.0080] [ 2300] [depth= 1] . ( 9 sec) [ -10245.8185] [ 2300] [depth= 1] . ( 9 sec) [ -10243.9863] [ 2299] [depth= 1] . ( 9 sec) [ -10243.2850] [ 2297] [depth= 1] . ( 10 sec) [ -10242.9790] [ 2295] [depth= 1] . ( 10 sec) [ -10224.0660] [Branch lengths ] . ( 11 sec) [ -10224.0361] [GTR parameters ] . ( 11 sec) [ -10222.8196] [Alpha ][ 0.992206] . ( 11 sec) [ -10222.6853] [ 2297] [depth= 1] . ( 14 sec) [ -10222.3940] [ 2298] [depth= 1] . ( 15 sec) [ -10222.2790] [ 2298] [depth= 1] . ( 15 sec) [ -10219.1404] [Branch lengths ] . ( 16 sec) [ -10219.1392] [GTR parameters ] . ( 16 sec) [ -10219.0815] [Alpha ][ 1.016307] . ( 21 sec) [ -10218.3873] [Branch lengths ] . ( 45 sec) [ -10218.2165] [Branch lengths ] . ( 45 sec) [ -10218.2165] [Topology ] . ( 45 sec) [ -10218.1983] [Topology ] . ( 46 sec) [ -10218.1922] [Topology ] . ( 47 sec) [ -10218.1892] [Topology ] . ( 48 sec) [ -10218.1877] [Topology ] . ( 49 sec) [ -10218.1869] [Topology ] . ( 49 sec) [ -10218.1863] [GTR parameters ] . ( 49 sec) [ -10218.1781] [Alpha ][ 1.025810] . ( 49 sec) [ -10218.1781] [Topology ] . ( 50 sec) [ -10218.1772] [Topology ] . ( 50 sec) [ -10218.1772] [GTR parameters ] . ( 50 sec) [ -10218.1772] [Alpha ][ 1.025810] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -10218.1613] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -10218.1612] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10218.161151. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10296.740802 . ( 1 sec) [ -10294.9392] [GTR parameters ] . ( 1 sec) [ -10294.7927] [Alpha ][ 0.960616] . ( 1 sec) [ -10294.7927] [Topology ] . ( 2 sec) [ -10235.5620] [Topology ] . ( 2 sec) [ -10223.5704] [Topology ] . ( 3 sec) [ -10220.9334] [Topology ] . ( 4 sec) [ -10219.8027] [Topology ] . ( 5 sec) [ -10219.2500] [Topology ] . ( 6 sec) [ -10218.9647] [Topology ] . ( 6 sec) [ -10218.8140] [Topology ] . ( 7 sec) [ -10218.7333] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.733311 . ( 14 sec) [ -10218.6801] [GTR parameters ] . ( 14 sec) [ -10218.3007] [Alpha ][ 1.022180] . ( 14 sec) [ -10218.3007] [Topology ] . ( 15 sec) [ -10218.2286] [Topology ] . ( 15 sec) [ -10218.1933] [Topology ] . ( 16 sec) [ -10218.1745] [Topology ] . ( 17 sec) [ -10218.1645] [Topology ] . ( 18 sec) [ -10218.1591] [Topology ] . ( 19 sec) [ -10218.1562] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.156228 . ( 25 sec) [ -10218.1561] [GTR parameters ] . ( 25 sec) [ -10218.1545] [Alpha ][ 1.026389] . ( 25 sec) [ -10218.1545] [Topology ] . ( 26 sec) [ -10218.1527] [Topology ] . ( 27 sec) [ -10218.1518] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10218.151758 . ( 33 sec) [ -10218.1517] [GTR parameters ] . ( 33 sec) [ -10218.1517] [Alpha ][ 1.026389] . ( 33 sec) [ -10218.1517] [Topology ] . ( 34 sec) [ -10218.1512] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 47 sec) [ -10294.9392] [GTR parameters ] . ( 47 sec) [ -10294.7927] [Alpha ][ 0.960616] . ( 48 sec) [ -10292.1127] [ 2297] [depth= 1] . ( 48 sec) [ -10290.6536] [ 2295] [depth= 1] . ( 48 sec) [ -10290.1125] [ 2294] [depth= 1] . ( 48 sec) [ -10289.4637] [ 2297] [depth= 1] . ( 48 sec) [ -10288.9441] [ 2297] [depth= 1] . ( 48 sec) [ -10286.3863] [ 2302] [depth= 2] . ( 48 sec) [ -10286.0752] [ 2303] [depth= 1] . ( 48 sec) [ -10286.0115] [ 2299] [depth= 1] . ( 48 sec) [ -10284.9665] [ 2298] [depth= 2] . ( 49 sec) [ -10282.3121] [ 2299] [depth= 1] . ( 49 sec) [ -10281.6755] [ 2298] [depth= 1] . ( 49 sec) [ -10281.5537] [ 2299] [depth= 1] . ( 50 sec) [ -10281.4090] [ 2304] [depth= 2] . ( 50 sec) [ -10281.0173] [ 2296] [depth= 2] . ( 50 sec) [ -10279.5703] [ 2296] [depth= 1] . ( 50 sec) [ -10274.9183] [ 2296] [depth= 1] . ( 50 sec) [ -10274.7389] [ 2299] [depth= 1] . ( 50 sec) [ -10270.0398] [ 2296] [depth= 1] . ( 50 sec) [ -10269.7605] [ 2299] [depth= 1] . ( 50 sec) [ -10268.8129] [ 2296] [depth= 1] . ( 50 sec) [ -10268.6292] [ 2299] [depth= 1] . ( 51 sec) [ -10256.3184] [ 2301] [depth= 2] . ( 51 sec) [ -10223.9581] [Branch lengths ] . ( 51 sec) [ -10223.9128] [GTR parameters ] . ( 51 sec) [ -10223.8016] [Alpha ][ 0.994571] . ( 52 sec) [ -10223.3026] [ 2298] [depth= 1] . ( 53 sec) [ -10223.2835] [ 2297] [depth= 1] . ( 54 sec) [ -10223.2693] [ 2298] [depth= 1] . ( 57 sec) [ -10219.0848] [Branch lengths ] . ( 57 sec) [ -10219.0826] [GTR parameters ] . ( 57 sec) [ -10219.0351] [Alpha ][ 1.017365] . ( 62 sec) [ -10218.3452] [Branch lengths ] . ( 86 sec) [ -10218.2023] [Branch lengths ] . ( 86 sec) [ -10218.2023] [Topology ] . ( 87 sec) [ -10218.1864] [Topology ] . ( 88 sec) [ -10218.1807] [Topology ] . ( 89 sec) [ -10218.1778] [Topology ] . ( 90 sec) [ -10218.1762] [Topology ] . ( 90 sec) [ -10218.1754] [Topology ] . ( 91 sec) [ -10218.1750] [GTR parameters ] . ( 91 sec) [ -10218.1677] [Alpha ][ 1.026316] . ( 91 sec) [ -10218.1677] [Topology ] . ( 91 sec) [ -10218.1668] [Topology ] . ( 92 sec) [ -10218.1668] [GTR parameters ] . ( 92 sec) [ -10218.1668] [Alpha ][ 1.026316] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -10218.1667] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10218.151240 . Log likelihood obtained after SPR moves : -10218.166656 . Log likelihood of the current tree: -10218.151240. . Printing the most likely tree in file 'data50.phy_phyml_tree.txt'... . Best log likelihood : -10218.151125 . Time used 0h1m44s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo