.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data59.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... . 428 patterns found. (out of a total of 500 sites) . 69 sites without polymorphism (13.80%). . [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) [ -19728.6814] [GTR parameters ] . ( 1 sec) [ -19394.1373] [Alpha ][ 0.500960] . ( 1 sec) [ -19287.4500] [ 4466] [depth= 7] . ( 1 sec) [ -18814.4538] [ 4405] [depth= 4] . ( 1 sec) [ -18660.7599] [ 4393] [depth= 4] . ( 1 sec) [ -18636.9076] [ 4376] [depth= 6] . ( 1 sec) [ -18459.5224] [ 4326] [depth= 3] . ( 1 sec) [ -18232.0624] [ 4318] [depth= 6] . ( 1 sec) [ -17938.1072] [ 4286] [depth= 5] . ( 1 sec) [ -17778.2452] [ 4229] [depth= 1] . ( 1 sec) [ -17633.8636] [ 4150] [depth= 8] . ( 1 sec) [ -17350.6176] [ 4082] [depth= 1] . ( 1 sec) [ -16801.8633] [ 3981] [depth= 10] . ( 1 sec) [ -16526.2778] [ 3932] [depth= 4] . ( 1 sec) [ -16428.1844] [ 3917] [depth= 1] . ( 2 sec) [ -16396.4599] [ 3896] [depth= 3] . ( 2 sec) [ -16218.6158] [ 3830] [depth= 1] . ( 2 sec) [ -16159.1064] [ 3819] [depth= 6] . ( 2 sec) [ -16013.4573] [ 3748] [depth= 1] . ( 2 sec) [ -15749.7702] [ 3707] [depth= 14] . ( 2 sec) [ -15688.4623] [ 3704] [depth= 2] . ( 2 sec) [ -15578.0107] [ 3704] [depth= 1] . ( 2 sec) [ -15429.2644] [ 3674] [depth= 5] . ( 2 sec) [ -15083.5982] [ 3548] [depth= 6] . ( 2 sec) [ -15073.0327] [ 3550] [depth= 7] . ( 2 sec) [ -14752.1965] [ 3464] [depth= 6] . ( 2 sec) [ -14717.7286] [ 3420] [depth= 8] . ( 2 sec) [ -14562.6430] [ 3387] [depth= 7] . ( 2 sec) [ -14560.9760] [ 3401] [depth= 7] . ( 2 sec) [ -14462.4532] [ 3363] [depth= 4] . ( 2 sec) [ -14436.3314] [ 3359] [depth= 2] . ( 2 sec) [ -14335.3737] [ 3322] [depth= 1] . ( 2 sec) [ -14189.5540] [ 3307] [depth= 1] . ( 2 sec) [ -14056.5861] [ 3237] [depth= 8] . ( 2 sec) [ -14006.2687] [ 3253] [depth= 1] . ( 2 sec) [ -13995.5319] [ 3284] [depth= 1] . ( 2 sec) [ -13937.4844] [ 3257] [depth= 3] . ( 2 sec) [ -13779.5845] [ 3213] [depth= 5] . ( 3 sec) [ -13778.7691] [ 3214] [depth= 1] . ( 3 sec) [ -13697.6990] [ 3179] [depth= 1] . ( 3 sec) [ -13689.3417] [ 3181] [depth= 1] . ( 3 sec) [ -13557.6992] [ 3138] [depth= 5] . ( 3 sec) [ -12916.2719] [ 3074] [depth= 4] . ( 3 sec) [ -12883.7040] [ 3065] [depth= 2] . ( 3 sec) [ -12872.1957] [ 3065] [depth= 1] . ( 3 sec) [ -12749.3055] [ 3052] [depth= 13] . ( 3 sec) [ -12640.1150] [ 3019] [depth= 2] . ( 3 sec) [ -12638.0666] [ 3044] [depth= 5] . ( 3 sec) [ -12462.5707] [ 2981] [depth= 6] . ( 3 sec) [ -12364.7683] [ 2931] [depth= 13] . ( 3 sec) [ -12181.8425] [ 2913] [depth= 2] . ( 3 sec) [ -12105.2069] [ 2879] [depth= 1] . ( 3 sec) [ -12079.4703] [ 2886] [depth= 9] . ( 3 sec) [ -12034.6178] [ 2885] [depth= 1] . ( 3 sec) [ -11852.3429] [ 2838] [depth= 6] . ( 3 sec) [ -11683.2152] [ 2784] [depth= 1] . ( 3 sec) [ -11674.3030] [ 2784] [depth= 2] . ( 4 sec) [ -11569.8107] [ 2777] [depth= 8] . ( 4 sec) [ -11532.9286] [ 2726] [depth= 6] . ( 4 sec) [ -11515.9150] [ 2724] [depth= 4] . ( 4 sec) [ -11361.0358] [ 2656] [depth= 2] . ( 4 sec) [ -11298.3635] [ 2641] [depth= 1] . ( 4 sec) [ -11245.9252] [ 2618] [depth= 2] . ( 4 sec) [ -11230.5618] [ 2613] [depth= 3] . ( 4 sec) [ -11229.1160] [ 2617] [depth= 1] . ( 4 sec) [ -11171.3138] [ 2571] [depth= 1] . ( 4 sec) [ -11161.0451] [ 2564] [depth= 8] . ( 4 sec) [ -11121.2909] [ 2531] [depth= 1] . ( 4 sec) [ -11005.0276] [ 2490] [depth= 4] . ( 4 sec) [ -10904.8116] [ 2459] [depth= 6] . ( 4 sec) [ -10900.5417] [ 2455] [depth= 1] . ( 4 sec) [ -10898.9925] [ 2456] [depth= 1] . ( 4 sec) [ -10897.3353] [ 2460] [depth= 1] . ( 4 sec) [ -10840.9240] [ 2427] [depth= 1] . ( 4 sec) [ -10646.3586] [ 2377] [depth= 1] . ( 4 sec) [ -10630.9860] [ 2376] [depth= 1] . ( 4 sec) [ -10626.7319] [ 2377] [depth= 2] . ( 5 sec) [ -10616.8878] [ 2384] [depth= 1] . ( 5 sec) [ -10581.0469] [ 2384] [depth= 1] . ( 5 sec) [ -10570.0020] [ 2376] [depth= 1] . ( 5 sec) [ -10566.3835] [ 2388] [depth= 1] . ( 5 sec) [ -10542.0490] [ 2383] [depth= 2] . ( 5 sec) [ -10375.3688] [Branch lengths ] . ( 6 sec) [ -10372.5660] [GTR parameters ] . ( 6 sec) [ -10341.2034] [Alpha ][ 0.858472] . ( 6 sec) [ -10335.5580] [ 2377] [depth= 1] . ( 6 sec) [ -10224.5548] [ 2361] [depth= 5] . ( 6 sec) [ -10214.3638] [ 2356] [depth= 1] . ( 6 sec) [ -10214.2593] [ 2353] [depth= 1] . ( 6 sec) [ -10161.1367] [ 2328] [depth= 1] . ( 6 sec) [ -10158.1572] [ 2327] [depth= 1] . ( 6 sec) [ -10156.0903] [ 2316] [depth= 1] . ( 6 sec) [ -10146.9546] [ 2313] [depth= 1] . ( 6 sec) [ -10137.5109] [ 2307] [depth= 1] . ( 6 sec) [ -10136.7411] [ 2311] [depth= 1] . ( 6 sec) [ -10135.8667] [ 2300] [depth= 3] . ( 7 sec) [ -10134.9739] [ 2304] [depth= 1] . ( 7 sec) [ -10134.3375] [ 2306] [depth= 1] . ( 7 sec) [ -10133.9742] [ 2308] [depth= 1] . ( 7 sec) [ -10132.7177] [ 2308] [depth= 5] . ( 7 sec) [ -10129.9561] [ 2306] [depth= 1] . ( 7 sec) [ -10128.2604] [ 2302] [depth= 1] . ( 7 sec) [ -10128.1836] [ 2303] [depth= 1] . ( 7 sec) [ -10127.5222] [ 2303] [depth= 2] . ( 8 sec) [ -10127.5034] [ 2304] [depth= 1] . ( 8 sec) [ -10124.7537] [ 2309] [depth= 1] . ( 8 sec) [ -10124.5754] [ 2308] [depth= 1] . ( 8 sec) [ -10121.7240] [ 2305] [depth= 1] . ( 8 sec) [ -10121.4203] [ 2307] [depth= 1] . ( 8 sec) [ -10120.1231] [ 2303] [depth= 1] . ( 9 sec) [ -10119.9037] [ 2300] [depth= 1] . ( 9 sec) [ -10119.8341] [ 2304] [depth= 1] . ( 9 sec) [ -10119.3268] [ 2307] [depth= 1] . ( 9 sec) [ -10119.0562] [ 2304] [depth= 1] . ( 9 sec) [ -10119.0121] [ 2308] [depth= 1] . ( 9 sec) [ -10097.8250] [Branch lengths ] . ( 10 sec) [ -10097.6560] [GTR parameters ] . ( 10 sec) [ -10097.4683] [Alpha ][ 0.896210] . ( 10 sec) [ -10096.6425] [ 2305] [depth= 2] . ( 11 sec) [ -10096.5650] [ 2304] [depth= 1] . ( 12 sec) [ -10096.1706] [ 2305] [depth= 1] . ( 13 sec) [ -10096.1556] [ 2308] [depth= 1] . ( 13 sec) [ -10093.4099] [ 2306] [depth= 6] . ( 14 sec) [ -10090.5101] [Branch lengths ] . ( 14 sec) [ -10090.4883] [GTR parameters ] . ( 14 sec) [ -10090.4876] [Alpha ][ 0.893878] . ( 15 sec) [ -10090.4674] [ 2307] [depth= 1] . ( 16 sec) [ -10090.4556] [ 2306] [depth= 1] . ( 18 sec) [ -10090.1548] [Branch lengths ] . ( 18 sec) [ -10090.1545] [GTR parameters ] . ( 18 sec) [ -10090.1545] [Alpha ][ 0.893878] . ( 22 sec) [ -10090.0890] [ 2302] [depth= 1] . ( 24 sec) [ -10090.0051] [ 2299] [depth= 1] . ( 39 sec) [ -10089.9088] [Branch lengths ] . ( 39 sec) [ -10089.9084] [GTR parameters ] . ( 39 sec) [ -10089.9084] [Alpha ][ 0.893878] . ( 39 sec) [ -10089.9084] [Topology ] . ( 40 sec) [ -10089.4804] [Topology ] . ( 41 sec) [ -10089.3491] [Topology ] . ( 42 sec) [ -10089.3199] [Topology ] . ( 43 sec) [ -10089.3094] [Topology ] . ( 43 sec) [ -10089.3054] [Topology ] . ( 44 sec) [ -10089.3038] [Topology ] . ( 45 sec) [ -10089.3032] [Topology ] . ( 45 sec) [ -10089.2988] [GTR parameters ] . ( 45 sec) [ -10089.2988] [Alpha ][ 0.893878] . ( 45 sec) [ -10089.2988] [Topology ] . ( 46 sec) [ -10089.2985] [Topology ] . ( 46 sec) [ -10089.2985] [GTR parameters ] . ( 46 sec) [ -10089.2985] [Alpha ][ 0.893878] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10089.298462. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20025.9659] [GTR parameters ] . ( 0 sec) [ -19703.6585] [Alpha ][ 0.500960] . ( 0 sec) [ -19506.3748] [ 4491] [depth= 6] . ( 1 sec) [ -19365.7146] [ 4465] [depth= 1] . ( 1 sec) [ -19277.7585] [ 4460] [depth= 1] . ( 1 sec) [ -18990.9754] [ 4432] [depth= 7] . ( 1 sec) [ -18738.2003] [ 4306] [depth= 5] . ( 1 sec) [ -18673.4038] [ 4291] [depth= 2] . ( 1 sec) [ -18460.4228] [ 4285] [depth= 1] . ( 1 sec) [ -18386.7951] [ 4260] [depth= 4] . ( 1 sec) [ -18108.1556] [ 4168] [depth= 2] . ( 1 sec) [ -17947.6727] [ 4155] [depth= 13] . ( 1 sec) [ -17887.4196] [ 4126] [depth= 2] . ( 1 sec) [ -17722.7359] [ 4114] [depth= 5] . ( 1 sec) [ -17562.1145] [ 4049] [depth= 7] . ( 1 sec) [ -17363.7491] [ 4064] [depth= 1] . ( 1 sec) [ -16934.2743] [ 3949] [depth= 9] . ( 1 sec) [ -16667.3925] [ 3885] [depth= 12] . ( 1 sec) [ -16231.8441] [ 3802] [depth= 14] . ( 1 sec) [ -16200.0789] [ 3800] [depth= 1] . ( 1 sec) [ -15874.3426] [ 3797] [depth= 1] . ( 1 sec) [ -15745.1962] [ 3734] [depth= 2] . ( 1 sec) [ -15719.1171] [ 3719] [depth= 1] . ( 1 sec) [ -15541.5842] [ 3683] [depth= 7] . ( 1 sec) [ -15524.4173] [ 3677] [depth= 1] . ( 1 sec) [ -15199.9223] [ 3645] [depth= 3] . ( 2 sec) [ -15047.4515] [ 3612] [depth= 1] . ( 2 sec) [ -14927.3263] [ 3550] [depth= 4] . ( 2 sec) [ -14807.7103] [ 3533] [depth= 2] . ( 2 sec) [ -14267.4263] [ 3367] [depth= 7] . ( 2 sec) [ -14197.3547] [ 3343] [depth= 1] . ( 2 sec) [ -14189.0134] [ 3346] [depth= 1] . ( 2 sec) [ -14164.6799] [ 3337] [depth= 1] . ( 2 sec) [ -14137.8440] [ 3302] [depth= 12] . ( 2 sec) [ -13924.1559] [ 3277] [depth= 1] . ( 2 sec) [ -13799.1173] [ 3219] [depth= 2] . ( 2 sec) [ -13403.3222] [ 3195] [depth= 9] . ( 2 sec) [ -13240.8454] [ 3173] [depth= 9] . ( 2 sec) [ -13131.2118] [ 3127] [depth= 12] . ( 2 sec) [ -13123.3867] [ 3127] [depth= 1] . ( 2 sec) [ -13121.2804] [ 3127] [depth= 1] . ( 2 sec) [ -13103.9153] [ 3128] [depth= 1] . ( 2 sec) [ -13102.9396] [ 3127] [depth= 1] . ( 2 sec) [ -12875.7057] [ 3099] [depth= 9] . ( 2 sec) [ -12823.7782] [ 3100] [depth= 1] . ( 2 sec) [ -12798.4181] [ 3098] [depth= 1] . ( 3 sec) [ -12782.3957] [ 3096] [depth= 1] . ( 3 sec) [ -12769.8691] [ 3103] [depth= 2] . ( 3 sec) [ -12566.7464] [ 3068] [depth= 3] . ( 3 sec) [ -12550.3078] [ 3014] [depth= 1] . ( 3 sec) [ -12440.5109] [ 3009] [depth= 7] . ( 3 sec) [ -12413.0548] [ 3010] [depth= 1] . ( 3 sec) [ -12406.0027] [ 3006] [depth= 1] . ( 3 sec) [ -12207.4617] [ 2915] [depth= 5] . ( 3 sec) [ -11980.4341] [ 2870] [depth= 8] . ( 3 sec) [ -11898.1583] [ 2865] [depth= 9] . ( 3 sec) [ -11823.5835] [ 2848] [depth= 5] . ( 3 sec) [ -11657.7790] [ 2738] [depth= 2] . ( 3 sec) [ -11639.7098] [ 2725] [depth= 2] . ( 3 sec) [ -11433.7510] [ 2630] [depth= 11] . ( 3 sec) [ -11187.4299] [ 2556] [depth= 9] . ( 3 sec) [ -11160.7894] [ 2554] [depth= 1] . ( 3 sec) [ -11095.6382] [ 2523] [depth= 1] . ( 3 sec) [ -10995.3483] [ 2511] [depth= 6] . ( 3 sec) [ -10937.1072] [ 2490] [depth= 1] . ( 3 sec) [ -10928.9005] [ 2501] [depth= 1] . ( 4 sec) [ -10911.7210] [ 2510] [depth= 3] . ( 4 sec) [ -10903.9548] [ 2505] [depth= 1] . ( 4 sec) [ -10891.0638] [ 2503] [depth= 2] . ( 4 sec) [ -10884.4895] [ 2502] [depth= 2] . ( 4 sec) [ -10818.5656] [ 2467] [depth= 1] . ( 4 sec) [ -10806.5948] [ 2469] [depth= 1] . ( 4 sec) [ -10637.8123] [ 2385] [depth= 4] . ( 4 sec) [ -10610.2722] [ 2374] [depth= 1] . ( 4 sec) [ -10609.3417] [ 2381] [depth= 1] . ( 4 sec) [ -10600.5080] [ 2377] [depth= 2] . ( 4 sec) [ -10560.8183] [ 2358] [depth= 1] . ( 4 sec) [ -10532.6408] [ 2357] [depth= 1] . ( 4 sec) [ -10528.7128] [ 2362] [depth= 1] . ( 4 sec) [ -10521.6926] [ 2359] [depth= 1] . ( 4 sec) [ -10474.6189] [ 2349] [depth= 8] . ( 4 sec) [ -10470.6927] [ 2347] [depth= 1] . ( 4 sec) [ -10462.4942] [ 2354] [depth= 1] . ( 5 sec) [ -10206.2208] [Branch lengths ] . ( 5 sec) [ -10204.1056] [GTR parameters ] . ( 5 sec) [ -10172.5656] [Alpha ][ 0.857439] . ( 5 sec) [ -10172.5013] [ 2350] [depth= 8] . ( 5 sec) [ -10172.1561] [ 2347] [depth= 1] . ( 6 sec) [ -10164.9269] [ 2341] [depth= 1] . ( 6 sec) [ -10164.7073] [ 2344] [depth= 1] . ( 6 sec) [ -10164.4914] [ 2346] [depth= 1] . ( 6 sec) [ -10164.4665] [ 2345] [depth= 2] . ( 7 sec) [ -10163.8395] [ 2348] [depth= 1] . ( 7 sec) [ -10163.4573] [ 2350] [depth= 2] . ( 7 sec) [ -10163.3164] [ 2337] [depth= 4] . ( 7 sec) [ -10163.1021] [ 2337] [depth= 2] . ( 7 sec) [ -10161.9359] [ 2340] [depth= 1] . ( 8 sec) [ -10154.5035] [ 2334] [depth= 2] . ( 8 sec) [ -10153.1277] [ 2351] [depth= 2] . ( 8 sec) [ -10153.0824] [ 2345] [depth= 3] . ( 9 sec) [ -10145.8533] [ 2331] [depth= 1] . ( 9 sec) [ -10127.3496] [ 2318] [depth= 1] . ( 9 sec) [ -10127.1342] [ 2321] [depth= 1] . ( 9 sec) [ -10124.4362] [ 2310] [depth= 1] . ( 9 sec) [ -10124.4163] [ 2311] [depth= 1] . ( 9 sec) [ -10122.6572] [ 2306] [depth= 1] . ( 9 sec) [ -10122.1558] [ 2310] [depth= 1] . ( 9 sec) [ -10118.5875] [ 2306] [depth= 1] . ( 10 sec) [ -10094.4375] [Branch lengths ] . ( 10 sec) [ -10094.3128] [GTR parameters ] . ( 10 sec) [ -10094.1746] [Alpha ][ 0.889260] . ( 10 sec) [ -10094.1553] [ 2304] [depth= 1] . ( 10 sec) [ -10094.1129] [ 2304] [depth= 1] . ( 11 sec) [ -10092.8713] [ 2303] [depth= 1] . ( 12 sec) [ -10092.8606] [ 2307] [depth= 2] . ( 12 sec) [ -10092.7411] [ 2309] [depth= 1] . ( 13 sec) [ -10092.7047] [ 2308] [depth= 1] . ( 13 sec) [ -10092.6514] [ 2307] [depth= 1] . ( 14 sec) [ -10092.4184] [ 2308] [depth= 1] . ( 14 sec) [ -10092.4018] [ 2308] [depth= 1] . ( 14 sec) [ -10090.5808] [Branch lengths ] . ( 14 sec) [ -10090.5783] [GTR parameters ] . ( 14 sec) [ -10090.5756] [Alpha ][ 0.893821] . ( 19 sec) [ -10090.5623] [ 2308] [depth= 1] . ( 19 sec) [ -10090.3265] [Branch lengths ] . ( 19 sec) [ -10090.3264] [GTR parameters ] . ( 19 sec) [ -10090.3264] [Alpha ][ 0.894715] . ( 20 sec) [ -10090.1286] [ 2303] [depth= 2] . ( 40 sec) [ -10090.0820] [Branch lengths ] . ( 40 sec) [ -10090.0818] [GTR parameters ] . ( 40 sec) [ -10090.0818] [Alpha ][ 0.894715] . ( 40 sec) [ -10090.0818] [Topology ] . ( 41 sec) [ -10089.5879] [Topology ] . ( 42 sec) [ -10089.3648] [Topology ] . ( 43 sec) [ -10089.3233] [Topology ] . ( 44 sec) [ -10089.3102] [Topology ] . ( 44 sec) [ -10089.3055] [Topology ] . ( 45 sec) [ -10089.3037] [Topology ] . ( 46 sec) [ -10089.3030] [Topology ] . ( 46 sec) [ -10089.2990] [GTR parameters ] . ( 46 sec) [ -10089.2990] [Alpha ][ 0.893820] . ( 46 sec) [ -10089.2990] [Topology ] . ( 47 sec) [ -10089.2986] [Topology ] . ( 47 sec) [ -10089.2986] [GTR parameters ] . ( 47 sec) [ -10089.2986] [Alpha ][ 0.893820] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10089.298574. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20316.8899] [GTR parameters ] . ( 1 sec) [ -19984.7369] [Alpha ][ 0.500960] . ( 1 sec) [ -19852.7044] [ 4560] [depth= 8] . ( 1 sec) [ -19654.7502] [ 4528] [depth= 9] . ( 1 sec) [ -19598.6432] [ 4515] [depth= 4] . ( 1 sec) [ -19506.1433] [ 4505] [depth= 1] . ( 1 sec) [ -19421.6106] [ 4400] [depth= 6] . ( 1 sec) [ -19155.4510] [ 4392] [depth= 1] . ( 2 sec) [ -18947.0770] [ 4369] [depth= 1] . ( 2 sec) [ -18590.7740] [ 4366] [depth= 2] . ( 2 sec) [ -18333.4318] [ 4318] [depth= 9] . ( 2 sec) [ -18044.5227] [ 4208] [depth= 9] . ( 2 sec) [ -17623.8721] [ 4110] [depth= 14] . ( 2 sec) [ -17148.8417] [ 4007] [depth= 5] . ( 2 sec) [ -17017.4629] [ 3994] [depth= 8] . ( 2 sec) [ -16917.0224] [ 3988] [depth= 4] . ( 2 sec) [ -16538.3653] [ 3922] [depth= 7] . ( 2 sec) [ -16472.6674] [ 3924] [depth= 1] . ( 2 sec) [ -16400.5819] [ 3900] [depth= 1] . ( 2 sec) [ -16298.8227] [ 3866] [depth= 10] . ( 2 sec) [ -16212.3260] [ 3823] [depth= 1] . ( 2 sec) [ -16008.5416] [ 3778] [depth= 4] . ( 2 sec) [ -15864.3122] [ 3767] [depth= 1] . ( 2 sec) [ -15664.5106] [ 3705] [depth= 7] . ( 2 sec) [ -15474.7865] [ 3703] [depth= 7] . ( 2 sec) [ -15459.6740] [ 3669] [depth= 1] . ( 2 sec) [ -15316.5952] [ 3603] [depth= 1] . ( 2 sec) [ -15255.2453] [ 3588] [depth= 6] . ( 2 sec) [ -15220.3637] [ 3591] [depth= 3] . ( 2 sec) [ -15023.8539] [ 3487] [depth= 7] . ( 3 sec) [ -15005.8437] [ 3484] [depth= 3] . ( 3 sec) [ -14858.6863] [ 3448] [depth= 2] . ( 3 sec) [ -14786.1276] [ 3404] [depth= 11] . ( 3 sec) [ -14521.2866] [ 3393] [depth= 5] . ( 3 sec) [ -14230.0567] [ 3322] [depth= 10] . ( 3 sec) [ -14208.9951] [ 3304] [depth= 4] . ( 3 sec) [ -14191.7324] [ 3307] [depth= 1] . ( 3 sec) [ -14167.7004] [ 3290] [depth= 2] . ( 3 sec) [ -14154.9758] [ 3221] [depth= 1] . ( 3 sec) [ -13808.6617] [ 3211] [depth= 12] . ( 3 sec) [ -13596.4136] [ 3181] [depth= 10] . ( 3 sec) [ -13534.2780] [ 3162] [depth= 7] . ( 3 sec) [ -13459.4055] [ 3166] [depth= 8] . ( 3 sec) [ -13429.4611] [ 3193] [depth= 1] . ( 3 sec) [ -13273.0207] [ 3158] [depth= 4] . ( 3 sec) [ -13250.6699] [ 3153] [depth= 4] . ( 3 sec) [ -13249.1962] [ 3123] [depth= 2] . ( 3 sec) [ -13155.1305] [ 3061] [depth= 4] . ( 3 sec) [ -12839.9111] [ 3010] [depth= 3] . ( 3 sec) [ -12636.6766] [ 2944] [depth= 5] . ( 4 sec) [ -12616.9365] [ 2935] [depth= 3] . ( 4 sec) [ -12476.6117] [ 2934] [depth= 1] . ( 4 sec) [ -12402.7951] [ 2865] [depth= 3] . ( 4 sec) [ -12310.4021] [ 2852] [depth= 6] . ( 4 sec) [ -12281.6084] [ 2854] [depth= 1] . ( 4 sec) [ -12219.8195] [ 2841] [depth= 2] . ( 4 sec) [ -12165.9672] [ 2842] [depth= 1] . ( 4 sec) [ -12119.3335] [ 2784] [depth= 3] . ( 4 sec) [ -11866.0202] [ 2796] [depth= 1] . ( 4 sec) [ -11551.6395] [ 2726] [depth= 2] . ( 4 sec) [ -11376.4512] [ 2672] [depth= 6] . ( 4 sec) [ -11179.8648] [ 2590] [depth= 6] . ( 4 sec) [ -11164.8609] [ 2604] [depth= 1] . ( 4 sec) [ -11120.3901] [ 2608] [depth= 1] . ( 4 sec) [ -11024.2653] [ 2576] [depth= 3] . ( 4 sec) [ -11012.8332] [ 2573] [depth= 1] . ( 4 sec) [ -10960.9166] [ 2573] [depth= 1] . ( 4 sec) [ -10950.5960] [ 2540] [depth= 1] . ( 4 sec) [ -10948.7187] [ 2540] [depth= 1] . ( 4 sec) [ -10945.5619] [ 2541] [depth= 1] . ( 4 sec) [ -10822.8655] [ 2488] [depth= 5] . ( 4 sec) [ -10806.8226] [ 2490] [depth= 1] . ( 4 sec) [ -10469.3074] [ 2408] [depth= 5] . ( 5 sec) [ -10444.4376] [ 2390] [depth= 3] . ( 5 sec) [ -10387.0397] [ 2365] [depth= 3] . ( 5 sec) [ -10379.7060] [ 2371] [depth= 1] . ( 5 sec) [ -10375.7943] [ 2369] [depth= 2] . ( 5 sec) [ -10362.9064] [ 2369] [depth= 3] . ( 5 sec) [ -10358.5172] [ 2389] [depth= 1] . ( 5 sec) [ -10354.3797] [ 2369] [depth= 1] . ( 5 sec) [ -10352.9511] [ 2366] [depth= 3] . ( 5 sec) [ -10352.3113] [ 2365] [depth= 1] . ( 5 sec) [ -10352.1972] [ 2368] [depth= 1] . ( 5 sec) [ -10320.0050] [ 2349] [depth= 1] . ( 5 sec) [ -10204.5411] [Branch lengths ] . ( 6 sec) [ -10201.9909] [GTR parameters ] . ( 6 sec) [ -10169.4795] [Alpha ][ 0.864726] . ( 6 sec) [ -10168.0688] [ 2348] [depth= 1] . ( 7 sec) [ -10167.2992] [ 2352] [depth= 1] . ( 7 sec) [ -10167.2152] [ 2353] [depth= 1] . ( 7 sec) [ -10167.1716] [ 2350] [depth= 1] . ( 7 sec) [ -10166.9715] [ 2351] [depth= 1] . ( 7 sec) [ -10161.9493] [ 2337] [depth= 1] . ( 7 sec) [ -10139.2556] [ 2302] [depth= 4] . ( 8 sec) [ -10138.7333] [ 2304] [depth= 1] . ( 8 sec) [ -10137.1769] [ 2302] [depth= 2] . ( 8 sec) [ -10137.0920] [ 2300] [depth= 1] . ( 8 sec) [ -10137.0026] [ 2300] [depth= 1] . ( 8 sec) [ -10136.6512] [ 2300] [depth= 1] . ( 8 sec) [ -10136.6020] [ 2303] [depth= 1] . ( 9 sec) [ -10136.5768] [ 2306] [depth= 1] . ( 9 sec) [ -10136.5492] [ 2307] [depth= 1] . ( 9 sec) [ -10131.5374] [ 2312] [depth= 1] . ( 9 sec) [ -10127.6043] [ 2307] [depth= 1] . ( 10 sec) [ -10105.3239] [Branch lengths ] . ( 10 sec) [ -10105.2450] [GTR parameters ] . ( 10 sec) [ -10105.0374] [Alpha ][ 0.904669] . ( 10 sec) [ -10101.3640] [ 2314] [depth= 1] . ( 11 sec) [ -10101.2951] [ 2312] [depth= 1] . ( 11 sec) [ -10100.5394] [ 2310] [depth= 2] . ( 11 sec) [ -10099.7734] [ 2315] [depth= 1] . ( 12 sec) [ -10099.3844] [ 2314] [depth= 1] . ( 13 sec) [ -10095.6474] [ 2314] [depth= 4] . ( 13 sec) [ -10095.5807] [ 2312] [depth= 1] . ( 13 sec) [ -10095.5100] [ 2314] [depth= 1] . ( 13 sec) [ -10095.2850] [ 2313] [depth= 1] . ( 14 sec) [ -10091.8459] [Branch lengths ] . ( 14 sec) [ -10091.8130] [GTR parameters ] . ( 14 sec) [ -10091.8035] [Alpha ][ 0.895770] . ( 15 sec) [ -10091.7798] [ 2312] [depth= 1] . ( 19 sec) [ -10091.4864] [Branch lengths ] . ( 19 sec) [ -10091.4861] [GTR parameters ] . ( 19 sec) [ -10091.4859] [Alpha ][ 0.894328] . ( 23 sec) [ -10091.2979] [ 2307] [depth= 2] . ( 39 sec) [ -10091.2572] [Branch lengths ] . ( 40 sec) [ -10091.2570] [GTR parameters ] . ( 40 sec) [ -10091.2570] [Alpha ][ 0.894328] . ( 40 sec) [ -10091.2570] [Topology ] . ( 40 sec) [ -10090.8124] [Topology ] . ( 41 sec) [ -10090.6773] [Topology ] . ( 42 sec) [ -10090.6486] [Topology ] . ( 43 sec) [ -10090.6386] [Topology ] . ( 44 sec) [ -10090.6349] [Topology ] . ( 44 sec) [ -10090.6335] [Topology ] . ( 45 sec) [ -10090.6330] [Topology ] . ( 45 sec) [ -10090.6282] [GTR parameters ] . ( 45 sec) [ -10090.6282] [Alpha ][ 0.894328] . ( 45 sec) [ -10090.6282] [Topology ] . ( 46 sec) [ -10090.6279] [Topology ] . ( 46 sec) [ -10090.6279] [GTR parameters ] . ( 46 sec) [ -10090.6279] [Alpha ][ 0.893434] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -10089.5219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -10089.3118] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10089.311810. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20108.0835] [GTR parameters ] . ( 1 sec) [ -19763.1778] [Alpha ][ 0.500960] . ( 1 sec) [ -19572.6164] [ 4538] [depth= 9] . ( 1 sec) [ -19352.8005] [ 4492] [depth= 8] . ( 1 sec) [ -19300.2151] [ 4508] [depth= 2] . ( 1 sec) [ -19100.2542] [ 4475] [depth= 8] . ( 1 sec) [ -19078.3134] [ 4454] [depth= 1] . ( 1 sec) [ -18625.3131] [ 4439] [depth= 3] . ( 1 sec) [ -18451.0753] [ 4426] [depth= 3] . ( 1 sec) [ -18398.8871] [ 4425] [depth= 6] . ( 1 sec) [ -18256.1894] [ 4302] [depth= 3] . ( 1 sec) [ -18134.0138] [ 4298] [depth= 10] . ( 1 sec) [ -18079.9010] [ 4278] [depth= 3] . ( 1 sec) [ -17996.3219] [ 4250] [depth= 1] . ( 1 sec) [ -17927.6360] [ 4251] [depth= 2] . ( 2 sec) [ -17786.9344] [ 4243] [depth= 7] . ( 2 sec) [ -17605.7144] [ 4164] [depth= 16] . ( 2 sec) [ -17593.8199] [ 4151] [depth= 2] . ( 2 sec) [ -17525.1936] [ 4147] [depth= 6] . ( 2 sec) [ -17100.3839] [ 4057] [depth= 6] . ( 2 sec) [ -17009.6792] [ 4006] [depth= 3] . ( 2 sec) [ -16764.4048] [ 3988] [depth= 3] . ( 2 sec) [ -16694.0078] [ 3940] [depth= 1] . ( 2 sec) [ -16297.2505] [ 3840] [depth= 5] . ( 2 sec) [ -16221.5930] [ 3807] [depth= 8] . ( 2 sec) [ -15944.8903] [ 3812] [depth= 1] . ( 2 sec) [ -15566.0136] [ 3716] [depth= 20] . ( 2 sec) [ -15317.7954] [ 3619] [depth= 19] . ( 2 sec) [ -15127.7039] [ 3590] [depth= 6] . ( 2 sec) [ -15017.4705] [ 3555] [depth= 7] . ( 2 sec) [ -15012.3392] [ 3564] [depth= 1] . ( 2 sec) [ -14780.2058] [ 3502] [depth= 2] . ( 2 sec) [ -14449.0917] [ 3444] [depth= 11] . ( 2 sec) [ -14267.6641] [ 3410] [depth= 12] . ( 2 sec) [ -14185.3682] [ 3374] [depth= 1] . ( 2 sec) [ -14060.9601] [ 3304] [depth= 12] . ( 2 sec) [ -14059.6994] [ 3294] [depth= 5] . ( 3 sec) [ -13950.2904] [ 3279] [depth= 6] . ( 3 sec) [ -13765.1353] [ 3228] [depth= 2] . ( 3 sec) [ -13346.8623] [ 3153] [depth= 5] . ( 3 sec) [ -13332.0825] [ 3145] [depth= 2] . ( 3 sec) [ -13329.8313] [ 3144] [depth= 1] . ( 3 sec) [ -13329.5382] [ 3149] [depth= 1] . ( 3 sec) [ -13215.5709] [ 3118] [depth= 10] . ( 3 sec) [ -13185.5532] [ 3107] [depth= 1] . ( 3 sec) [ -13079.7672] [ 3075] [depth= 5] . ( 3 sec) [ -12989.4299] [ 3062] [depth= 7] . ( 3 sec) [ -12920.7007] [ 3043] [depth= 1] . ( 3 sec) [ -12872.0643] [ 3035] [depth= 1] . ( 3 sec) [ -12635.9209] [ 2947] [depth= 8] . ( 3 sec) [ -12623.4890] [ 2929] [depth= 1] . ( 3 sec) [ -12531.2603] [ 2924] [depth= 4] . ( 3 sec) [ -12508.1267] [ 2911] [depth= 2] . ( 3 sec) [ -12125.7488] [ 2914] [depth= 1] . ( 3 sec) [ -11982.4103] [ 2844] [depth= 7] . ( 3 sec) [ -11896.1953] [ 2805] [depth= 5] . ( 3 sec) [ -11714.8405] [ 2754] [depth= 2] . ( 4 sec) [ -11613.7156] [ 2699] [depth= 2] . ( 4 sec) [ -11501.3446] [ 2702] [depth= 1] . ( 4 sec) [ -11491.9986] [ 2699] [depth= 1] . ( 4 sec) [ -11484.3050] [ 2682] [depth= 1] . ( 4 sec) [ -11416.2676] [ 2690] [depth= 1] . ( 4 sec) [ -11396.6097] [ 2684] [depth= 1] . ( 4 sec) [ -11230.7275] [ 2631] [depth= 2] . ( 4 sec) [ -11192.9980] [ 2617] [depth= 2] . ( 4 sec) [ -10996.1867] [ 2536] [depth= 8] . ( 4 sec) [ -10939.2502] [ 2518] [depth= 1] . ( 4 sec) [ -10930.2968] [ 2516] [depth= 1] . ( 4 sec) [ -10896.5324] [ 2532] [depth= 1] . ( 4 sec) [ -10866.6882] [ 2527] [depth= 2] . ( 4 sec) [ -10814.2435] [ 2526] [depth= 1] . ( 4 sec) [ -10764.7140] [ 2485] [depth= 4] . ( 4 sec) [ -10754.0824] [ 2486] [depth= 1] . ( 4 sec) [ -10711.3880] [ 2509] [depth= 1] . ( 4 sec) [ -10663.4796] [ 2511] [depth= 2] . ( 4 sec) [ -10615.1134] [ 2489] [depth= 2] . ( 4 sec) [ -10593.9088] [ 2480] [depth= 7] . ( 4 sec) [ -10590.9494] [ 2478] [depth= 1] . ( 5 sec) [ -10586.0162] [ 2470] [depth= 1] . ( 5 sec) [ -10547.6805] [ 2427] [depth= 1] . ( 5 sec) [ -10547.3446] [ 2427] [depth= 1] . ( 5 sec) [ -10477.8820] [ 2401] [depth= 8] . ( 5 sec) [ -10477.5261] [ 2403] [depth= 1] . ( 5 sec) [ -10454.3406] [ 2385] [depth= 1] . ( 5 sec) [ -10358.7456] [ 2356] [depth= 3] . ( 5 sec) [ -10354.7278] [ 2354] [depth= 2] . ( 5 sec) [ -10181.0679] [Branch lengths ] . ( 6 sec) [ -10177.3929] [GTR parameters ] . ( 6 sec) [ -10146.1686] [Alpha ][ 0.857722] . ( 6 sec) [ -10123.9118] [ 2324] [depth= 4] . ( 6 sec) [ -10121.8485] [ 2319] [depth= 1] . ( 6 sec) [ -10121.7625] [ 2322] [depth= 1] . ( 6 sec) [ -10121.7151] [ 2321] [depth= 1] . ( 7 sec) [ -10115.3482] [ 2301] [depth= 1] . ( 7 sec) [ -10115.2107] [ 2306] [depth= 1] . ( 8 sec) [ -10114.9612] [ 2316] [depth= 1] . ( 8 sec) [ -10114.6220] [ 2319] [depth= 1] . ( 9 sec) [ -10113.2809] [ 2316] [depth= 1] . ( 9 sec) [ -10113.1938] [ 2311] [depth= 4] . ( 9 sec) [ -10112.8355] [ 2312] [depth= 1] . ( 9 sec) [ -10112.5493] [ 2313] [depth= 3] . ( 9 sec) [ -10112.5303] [ 2311] [depth= 1] . ( 10 sec) [ -10096.7635] [Branch lengths ] . ( 10 sec) [ -10096.6428] [GTR parameters ] . ( 10 sec) [ -10096.4080] [Alpha ][ 0.899847] . ( 10 sec) [ -10096.2291] [ 2310] [depth= 1] . ( 12 sec) [ -10092.8018] [ 2310] [depth= 5] . ( 12 sec) [ -10092.6429] [ 2307] [depth= 1] . ( 12 sec) [ -10092.4888] [ 2307] [depth= 1] . ( 13 sec) [ -10092.4654] [ 2309] [depth= 1] . ( 13 sec) [ -10092.3916] [ 2309] [depth= 2] . ( 14 sec) [ -10090.0117] [Branch lengths ] . ( 14 sec) [ -10089.9645] [GTR parameters ] . ( 14 sec) [ -10089.9639] [Alpha ][ 0.897598] . ( 15 sec) [ -10089.9216] [ 2310] [depth= 1] . ( 18 sec) [ -10089.4347] [Branch lengths ] . ( 18 sec) [ -10089.4345] [GTR parameters ] . ( 19 sec) [ -10089.4342] [Alpha ][ 0.895830] . ( 40 sec) [ -10089.3644] [Branch lengths ] . ( 40 sec) [ -10089.3644] [Topology ] . ( 41 sec) [ -10089.3155] [Topology ] . ( 42 sec) [ -10089.3037] [Topology ] . ( 43 sec) [ -10089.3012] [Topology ] . ( 43 sec) [ -10089.3000] [Topology ] . ( 44 sec) [ -10089.2994] [Topology ] . ( 45 sec) [ -10089.2993] [GTR parameters ] . ( 45 sec) [ -10089.2991] [Alpha ][ 0.894308] . ( 45 sec) [ -10089.2991] [Topology ] . ( 45 sec) [ -10089.2987] [Topology ] . ( 46 sec) [ -10089.2987] [GTR parameters ] . ( 46 sec) [ -10089.2987] [Alpha ][ 0.894308] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10089.298706. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19880.7880] [GTR parameters ] . ( 1 sec) [ -19547.7005] [Alpha ][ 0.500960] . ( 1 sec) [ -19412.6017] [ 4529] [depth= 7] . ( 1 sec) [ -19182.9173] [ 4502] [depth= 4] . ( 1 sec) [ -19172.2784] [ 4471] [depth= 5] . ( 1 sec) [ -19085.7185] [ 4461] [depth= 1] . ( 1 sec) [ -18945.3826] [ 4415] [depth= 10] . ( 1 sec) [ -18875.8054] [ 4412] [depth= 3] . ( 1 sec) [ -18735.4025] [ 4389] [depth= 6] . ( 1 sec) [ -18725.5796] [ 4430] [depth= 1] . ( 1 sec) [ -18290.4673] [ 4310] [depth= 2] . ( 1 sec) [ -17951.9055] [ 4185] [depth= 3] . ( 1 sec) [ -17689.8431] [ 4111] [depth= 8] . ( 1 sec) [ -17506.0036] [ 4081] [depth= 7] . ( 1 sec) [ -17282.3705] [ 4024] [depth= 5] . ( 1 sec) [ -17225.7894] [ 4020] [depth= 1] . ( 1 sec) [ -16969.3912] [ 4012] [depth= 3] . ( 1 sec) [ -16961.9878] [ 4005] [depth= 9] . ( 1 sec) [ -16949.2917] [ 3995] [depth= 1] . ( 2 sec) [ -16888.2469] [ 3939] [depth= 5] . ( 2 sec) [ -16829.2586] [ 3935] [depth= 1] . ( 2 sec) [ -16696.0589] [ 3870] [depth= 9] . ( 2 sec) [ -16493.1768] [ 3866] [depth= 1] . ( 2 sec) [ -16188.6862] [ 3738] [depth= 9] . ( 2 sec) [ -15933.3746] [ 3693] [depth= 1] . ( 2 sec) [ -15678.4258] [ 3678] [depth= 8] . ( 2 sec) [ -15671.2194] [ 3669] [depth= 1] . ( 2 sec) [ -15294.2987] [ 3582] [depth= 11] . ( 2 sec) [ -15118.7153] [ 3531] [depth= 10] . ( 2 sec) [ -15078.4474] [ 3535] [depth= 1] . ( 2 sec) [ -14640.6554] [ 3383] [depth= 9] . ( 2 sec) [ -14596.8568] [ 3372] [depth= 1] . ( 2 sec) [ -14343.7268] [ 3373] [depth= 9] . ( 2 sec) [ -14243.9967] [ 3375] [depth= 1] . ( 2 sec) [ -14202.1607] [ 3358] [depth= 1] . ( 2 sec) [ -14180.9839] [ 3332] [depth= 1] . ( 2 sec) [ -14115.6005] [ 3324] [depth= 1] . ( 2 sec) [ -14085.7718] [ 3317] [depth= 1] . ( 2 sec) [ -14063.0631] [ 3303] [depth= 10] . ( 2 sec) [ -14056.4766] [ 3307] [depth= 1] . ( 2 sec) [ -13859.3687] [ 3298] [depth= 4] . ( 3 sec) [ -13617.0705] [ 3194] [depth= 1] . ( 3 sec) [ -13503.4237] [ 3171] [depth= 10] . ( 3 sec) [ -13039.9193] [ 3016] [depth= 12] . ( 3 sec) [ -13021.3247] [ 3018] [depth= 1] . ( 3 sec) [ -12982.3688] [ 2992] [depth= 1] . ( 3 sec) [ -12971.3494] [ 2986] [depth= 2] . ( 3 sec) [ -12964.5981] [ 2986] [depth= 1] . ( 3 sec) [ -12931.4667] [ 2987] [depth= 2] . ( 3 sec) [ -12922.7617] [ 2975] [depth= 1] . ( 3 sec) [ -12837.9868] [ 2908] [depth= 5] . ( 3 sec) [ -12703.0718] [ 2897] [depth= 2] . ( 3 sec) [ -12488.8584] [ 2823] [depth= 1] . ( 3 sec) [ -12238.7461] [ 2826] [depth= 2] . ( 3 sec) [ -12179.9819] [ 2815] [depth= 2] . ( 3 sec) [ -11781.6596] [ 2678] [depth= 7] . ( 3 sec) [ -11672.0234] [ 2651] [depth= 2] . ( 3 sec) [ -11648.4672] [ 2641] [depth= 1] . ( 3 sec) [ -11505.3561] [ 2625] [depth= 5] . ( 3 sec) [ -11470.9412] [ 2603] [depth= 1] . ( 4 sec) [ -11321.3045] [ 2567] [depth= 4] . ( 4 sec) [ -11287.1718] [ 2548] [depth= 4] . ( 4 sec) [ -11242.9487] [ 2550] [depth= 1] . ( 4 sec) [ -11219.8243] [ 2547] [depth= 1] . ( 4 sec) [ -11206.7884] [ 2547] [depth= 1] . ( 4 sec) [ -11201.5758] [ 2549] [depth= 1] . ( 4 sec) [ -11176.9024] [ 2558] [depth= 5] . ( 4 sec) [ -11174.6413] [ 2571] [depth= 1] . ( 4 sec) [ -11146.1540] [ 2551] [depth= 5] . ( 4 sec) [ -11146.0467] [ 2553] [depth= 1] . ( 4 sec) [ -11145.3085] [ 2547] [depth= 2] . ( 4 sec) [ -11144.4560] [ 2547] [depth= 1] . ( 4 sec) [ -11002.0134] [ 2492] [depth= 6] . ( 4 sec) [ -10986.8820] [ 2497] [depth= 4] . ( 4 sec) [ -10918.4463] [ 2492] [depth= 1] . ( 4 sec) [ -10901.9021] [ 2496] [depth= 2] . ( 4 sec) [ -10896.8762] [ 2497] [depth= 1] . ( 5 sec) [ -10840.0784] [ 2485] [depth= 5] . ( 5 sec) [ -10839.4143] [ 2485] [depth= 1] . ( 5 sec) [ -10765.6333] [ 2489] [depth= 1] . ( 5 sec) [ -10719.2771] [ 2499] [depth= 1] . ( 5 sec) [ -10683.1662] [ 2486] [depth= 2] . ( 5 sec) [ -10683.0021] [ 2485] [depth= 1] . ( 5 sec) [ -10588.9559] [ 2429] [depth= 3] . ( 5 sec) [ -10407.5136] [Branch lengths ] . ( 6 sec) [ -10404.3935] [GTR parameters ] . ( 6 sec) [ -10372.9446] [Alpha ][ 0.851710] . ( 6 sec) [ -10354.4862] [ 2406] [depth= 6] . ( 6 sec) [ -10339.4081] [ 2410] [depth= 1] . ( 6 sec) [ -10337.0417] [ 2405] [depth= 1] . ( 6 sec) [ -10336.9102] [ 2406] [depth= 1] . ( 7 sec) [ -10320.2898] [ 2391] [depth= 1] . ( 7 sec) [ -10318.2916] [ 2347] [depth= 2] . ( 7 sec) [ -10316.0990] [ 2357] [depth= 1] . ( 7 sec) [ -10311.5594] [ 2345] [depth= 5] . ( 7 sec) [ -10309.5866] [ 2343] [depth= 1] . ( 7 sec) [ -10229.8721] [ 2312] [depth= 1] . ( 7 sec) [ -10228.2367] [ 2308] [depth= 3] . ( 7 sec) [ -10225.7683] [ 2313] [depth= 1] . ( 7 sec) [ -10225.7464] [ 2312] [depth= 1] . ( 8 sec) [ -10223.9922] [ 2315] [depth= 1] . ( 8 sec) [ -10216.5795] [ 2314] [depth= 1] . ( 8 sec) [ -10215.6984] [ 2315] [depth= 1] . ( 8 sec) [ -10123.9971] [ 2329] [depth= 1] . ( 8 sec) [ -10123.9461] [ 2322] [depth= 1] . ( 9 sec) [ -10123.8622] [ 2322] [depth= 1] . ( 9 sec) [ -10123.7778] [ 2323] [depth= 1] . ( 9 sec) [ -10123.6444] [ 2321] [depth= 1] . ( 9 sec) [ -10123.3031] [ 2330] [depth= 1] . ( 9 sec) [ -10123.1431] [ 2329] [depth= 1] . ( 9 sec) [ -10108.6312] [ 2315] [depth= 1] . ( 9 sec) [ -10108.4452] [ 2315] [depth= 1] . ( 10 sec) [ -10107.4501] [ 2319] [depth= 1] . ( 10 sec) [ -10095.1270] [Branch lengths ] . ( 10 sec) [ -10094.9681] [GTR parameters ] . ( 10 sec) [ -10094.7468] [Alpha ][ 0.892188] . ( 11 sec) [ -10094.4162] [ 2316] [depth= 2] . ( 11 sec) [ -10093.8205] [ 2318] [depth= 1] . ( 12 sec) [ -10093.6883] [ 2318] [depth= 1] . ( 13 sec) [ -10093.6535] [ 2320] [depth= 1] . ( 14 sec) [ -10093.4586] [ 2316] [depth= 1] . ( 16 sec) [ -10091.1547] [Branch lengths ] . ( 16 sec) [ -10091.1469] [GTR parameters ] . ( 16 sec) [ -10091.1428] [Alpha ][ 0.897848] . ( 21 sec) [ -10090.7616] [Branch lengths ] . ( 42 sec) [ -10090.6413] [Branch lengths ] . ( 42 sec) [ -10090.6413] [Topology ] . ( 43 sec) [ -10090.6158] [Topology ] . ( 44 sec) [ -10090.6026] [Topology ] . ( 44 sec) [ -10090.5950] [Topology ] . ( 45 sec) [ -10090.5637] [Topology ] . ( 46 sec) [ -10090.4517] [Topology ] . ( 47 sec) [ -10090.4284] [Topology ] . ( 48 sec) [ -10090.4217] [Topology ] . ( 48 sec) [ -10090.4193] [Topology ] . ( 49 sec) [ -10090.4183] [Topology ] . ( 49 sec) [ -10090.4163] [GTR parameters ] . ( 49 sec) [ -10090.4149] [Alpha ][ 0.894349] . ( 49 sec) [ -10090.4149] [Topology ] . ( 50 sec) [ -10090.4144] [Topology ] . ( 50 sec) [ -10090.4144] [GTR parameters ] . ( 50 sec) [ -10090.4144] [Alpha ][ 0.894349] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -10089.3106] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10089.310582. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10186.540847 . ( 0 sec) [ -10185.4470] [GTR parameters ] . ( 0 sec) [ -10184.2698] [Alpha ][ 0.894321] . ( 0 sec) [ -10184.2698] [Topology ] . ( 1 sec) [ -10117.0407] [Topology ] . ( 2 sec) [ -10103.8503] [Topology ] . ( 2 sec) [ -10100.4331] [Topology ] . ( 3 sec) [ -10098.0463] [Topology ] . Moving backward . ( 4 sec) [ -10096.1225] [Topology ] . ( 5 sec) [ -10095.2812] [Topology ] . Moving backward . ( 6 sec) [ -10094.3631] [Topology ] . ( 6 sec) [ -10093.8820] [Topology ] . ( 7 sec) [ -10093.6541] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.529204 . ( 15 sec) [ -10093.4996] [GTR parameters ] . ( 15 sec) [ -10093.4945] [Alpha ][ 0.900666] . ( 15 sec) [ -10093.4945] [Topology ] . ( 16 sec) [ -10093.4231] [Topology ] . ( 17 sec) [ -10093.3824] [Topology ] . ( 17 sec) [ -10093.3592] [Topology ] . ( 18 sec) [ -10093.3458] [Topology ] . ( 19 sec) [ -10093.3379] [Topology ] . ( 20 sec) [ -10093.3334] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.333388 . ( 26 sec) [ -10093.3333] [GTR parameters ] . ( 26 sec) [ -10093.3329] [Alpha ][ 0.898930] . ( 26 sec) [ -10093.3329] [Topology ] . ( 27 sec) [ -10093.3301] [Topology ] . ( 28 sec) [ -10093.3285] [Topology ] . ( 29 sec) [ -10093.3276] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10093.327553 . ( 35 sec) [ -10093.3275] [GTR parameters ] . ( 35 sec) [ -10093.3275] [Alpha ][ 0.898930] . ( 35 sec) [ -10093.3275] [Topology ] . ( 36 sec) [ -10093.3269] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -10185.4470] [GTR parameters ] . ( 49 sec) [ -10184.2698] [Alpha ][ 0.894321] . ( 49 sec) [ -10182.9740] [ 2299] [depth= 1] . ( 49 sec) [ -10180.0792] [ 2297] [depth= 1] . ( 49 sec) [ -10179.8263] [ 2299] [depth= 1] . ( 50 sec) [ -10177.7849] [ 2304] [depth= 1] . ( 50 sec) [ -10167.5027] [ 2299] [depth= 1] . ( 50 sec) [ -10167.3872] [ 2304] [depth= 1] . ( 50 sec) [ -10163.7342] [ 2307] [depth= 1] . ( 50 sec) [ -10160.2715] [ 2304] [depth= 1] . ( 50 sec) [ -10160.1251] [ 2307] [depth= 1] . ( 50 sec) [ -10159.3992] [ 2314] [depth= 1] . ( 50 sec) [ -10155.2995] [ 2313] [depth= 1] . ( 51 sec) [ -10152.6096] [ 2310] [depth= 1] . ( 51 sec) [ -10146.4321] [ 2316] [depth= 1] . ( 51 sec) [ -10145.0402] [ 2316] [depth= 2] . ( 51 sec) [ -10144.7030] [ 2316] [depth= 1] . ( 51 sec) [ -10142.8602] [ 2321] [depth= 1] . ( 51 sec) [ -10138.1476] [ 2317] [depth= 2] . ( 51 sec) [ -10134.4438] [ 2314] [depth= 1] . ( 52 sec) [ -10134.1396] [ 2314] [depth= 1] . ( 52 sec) [ -10132.4188] [ 2313] [depth= 4] . ( 52 sec) [ -10132.1312] [ 2317] [depth= 1] . ( 52 sec) [ -10130.4604] [ 2319] [depth= 2] . ( 52 sec) [ -10130.1124] [ 2314] [depth= 2] . ( 53 sec) [ -10105.3413] [Branch lengths ] . ( 53 sec) [ -10105.3144] [GTR parameters ] . ( 53 sec) [ -10105.3039] [Alpha ][ 0.903639] . ( 53 sec) [ -10102.2877] [ 2307] [depth= 1] . ( 53 sec) [ -10102.0767] [ 2307] [depth= 1] . ( 53 sec) [ -10102.0398] [ 2307] [depth= 1] . ( 54 sec) [ -10100.0875] [ 2309] [depth= 1] . ( 55 sec) [ -10098.1574] [ 2308] [depth= 1] . ( 55 sec) [ -10097.9835] [ 2308] [depth= 1] . ( 56 sec) [ -10097.9547] [ 2311] [depth= 1] . ( 57 sec) [ -10094.1137] [Branch lengths ] . ( 57 sec) [ -10094.1131] [GTR parameters ] . ( 57 sec) [ -10094.1123] [Alpha ][ 0.900992] . ( 59 sec) [ -10091.1737] [ 2313] [depth= 5] . ( 59 sec) [ -10091.0091] [ 2313] [depth= 2] . ( 59 sec) [ -10090.9158] [ 2313] [depth= 1] . ( 59 sec) [ -10090.8286] [ 2313] [depth= 1] . ( 60 sec) [ -10090.7076] [ 2311] [depth= 1] . ( 60 sec) [ -10090.6932] [ 2311] [depth= 1] . ( 61 sec) [ -10089.5990] [Branch lengths ] . ( 61 sec) [ -10089.5622] [GTR parameters ] . ( 61 sec) [ -10089.5594] [Alpha ][ 0.896189] . ( 66 sec) [ -10089.3765] [Branch lengths ] . ( 87 sec) [ -10089.3522] [Branch lengths ] . ( 87 sec) [ -10089.3522] [Topology ] . ( 88 sec) [ -10089.3101] [Topology ] . ( 89 sec) [ -10089.3008] [Topology ] . ( 90 sec) [ -10089.2996] [Topology ] . ( 90 sec) [ -10089.2992] [Topology ] . ( 91 sec) [ -10089.2991] [GTR parameters ] . ( 91 sec) [ -10089.2987] [Alpha ][ 0.894264] . ( 91 sec) [ -10089.2987] [Topology ] . ( 91 sec) [ -10089.2985] [Topology ] . ( 92 sec) [ -10089.2985] [GTR parameters ] . ( 92 sec) [ -10089.2985] [Alpha ][ 0.894264] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10093.326949 . Log likelihood obtained after SPR moves : -10089.298461 . Log likelihood of the current tree: -10089.298461. . Printing the most likely tree in file 'data59.phy_phyml_tree.txt'... . Best log likelihood : -10089.298461 . Time used 0h1m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo