.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data46.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... . 436 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) [ -21815.1095] [GTR parameters ] . ( 1 sec) [ -21368.3711] [Alpha ][ 0.500960] . ( 1 sec) [ -21087.1257] [ 5171] [depth= 8] . ( 1 sec) [ -20617.2231] [ 5114] [depth= 6] . ( 1 sec) [ -20521.8548] [ 5085] [depth= 2] . ( 1 sec) [ -20465.0112] [ 5075] [depth= 3] . ( 1 sec) [ -20331.3799] [ 5065] [depth= 3] . ( 1 sec) [ -20229.2939] [ 5040] [depth= 5] . ( 1 sec) [ -20171.2615] [ 5032] [depth= 5] . ( 1 sec) [ -20149.3642] [ 5017] [depth= 1] . ( 1 sec) [ -19929.1118] [ 4926] [depth= 7] . ( 1 sec) [ -19854.3593] [ 4901] [depth= 1] . ( 1 sec) [ -19519.7218] [ 4813] [depth= 2] . ( 2 sec) [ -19338.6121] [ 4785] [depth= 2] . ( 2 sec) [ -19224.9397] [ 4784] [depth= 3] . ( 2 sec) [ -18972.6498] [ 4784] [depth= 7] . ( 2 sec) [ -18469.1259] [ 4709] [depth= 4] . ( 2 sec) [ -17860.7075] [ 4670] [depth= 12] . ( 2 sec) [ -17434.7316] [ 4540] [depth= 15] . ( 2 sec) [ -16948.1792] [ 4533] [depth= 11] . ( 2 sec) [ -16939.4219] [ 4531] [depth= 1] . ( 2 sec) [ -16834.5256] [ 4423] [depth= 5] . ( 2 sec) [ -16744.7916] [ 4394] [depth= 11] . ( 2 sec) [ -16421.7557] [ 4357] [depth= 13] . ( 2 sec) [ -16358.4194] [ 4352] [depth= 1] . ( 2 sec) [ -16115.9025] [ 4268] [depth= 1] . ( 2 sec) [ -15846.3531] [ 4179] [depth= 18] . ( 2 sec) [ -15843.7380] [ 4108] [depth= 4] . ( 2 sec) [ -15716.7489] [ 4081] [depth= 9] . ( 2 sec) [ -15497.6157] [ 4014] [depth= 10] . ( 2 sec) [ -15365.5736] [ 3910] [depth= 8] . ( 2 sec) [ -15128.8846] [ 3912] [depth= 1] . ( 2 sec) [ -14996.0484] [ 3741] [depth= 14] . ( 2 sec) [ -14973.8263] [ 3747] [depth= 1] . ( 3 sec) [ -14635.3383] [ 3601] [depth= 9] . ( 3 sec) [ -14505.6958] [ 3596] [depth= 1] . ( 3 sec) [ -14288.6103] [ 3471] [depth= 4] . ( 3 sec) [ -14061.8683] [ 3466] [depth= 7] . ( 3 sec) [ -13859.6477] [ 3412] [depth= 2] . ( 3 sec) [ -13641.4476] [ 3361] [depth= 3] . ( 3 sec) [ -13282.8487] [ 3308] [depth= 11] . ( 3 sec) [ -13223.5488] [ 3237] [depth= 1] . ( 3 sec) [ -12964.0996] [ 3138] [depth= 11] . ( 3 sec) [ -12936.5471] [ 3169] [depth= 1] . ( 3 sec) [ -12919.5166] [ 3166] [depth= 9] . ( 3 sec) [ -12888.4274] [ 3110] [depth= 1] . ( 3 sec) [ -12591.2474] [ 3061] [depth= 1] . ( 3 sec) [ -12528.2316] [ 3012] [depth= 8] . ( 3 sec) [ -12486.1524] [ 3002] [depth= 1] . ( 3 sec) [ -12435.1430] [ 3016] [depth= 2] . ( 3 sec) [ -12327.4993] [ 2965] [depth= 3] . ( 3 sec) [ -12291.0829] [ 2954] [depth= 6] . ( 3 sec) [ -12050.9859] [ 2834] [depth= 6] . ( 3 sec) [ -11997.2738] [ 2770] [depth= 1] . ( 4 sec) [ -11971.9140] [ 2761] [depth= 2] . ( 4 sec) [ -11958.9088] [ 2760] [depth= 1] . ( 4 sec) [ -11869.4028] [ 2721] [depth= 1] . ( 4 sec) [ -11784.4945] [ 2666] [depth= 6] . ( 4 sec) [ -11740.3063] [ 2656] [depth= 2] . ( 4 sec) [ -11730.8292] [ 2653] [depth= 1] . ( 4 sec) [ -11396.7928] [ 2641] [depth= 9] . ( 4 sec) [ -11268.4956] [ 2642] [depth= 1] . ( 4 sec) [ -11241.3247] [ 2625] [depth= 1] . ( 4 sec) [ -11112.9098] [ 2542] [depth= 9] . ( 4 sec) [ -11084.5429] [ 2558] [depth= 1] . ( 4 sec) [ -11074.9050] [ 2557] [depth= 1] . ( 4 sec) [ -11065.6852] [ 2562] [depth= 1] . ( 4 sec) [ -10976.3472] [ 2517] [depth= 3] . ( 4 sec) [ -10972.3737] [ 2511] [depth= 1] . ( 4 sec) [ -10951.3274] [ 2499] [depth= 1] . ( 5 sec) [ -10913.5655] [ 2501] [depth= 3] . ( 5 sec) [ -10908.6778] [ 2500] [depth= 1] . ( 5 sec) [ -10620.5692] [Branch lengths ] . ( 6 sec) [ -10618.1488] [GTR parameters ] . ( 6 sec) [ -10582.9522] [Alpha ][ 0.878970] . ( 6 sec) [ -10564.3426] [ 2497] [depth= 2] . ( 6 sec) [ -10564.2998] [ 2494] [depth= 1] . ( 6 sec) [ -10501.3514] [ 2431] [depth= 4] . ( 6 sec) [ -10464.0286] [ 2412] [depth= 2] . ( 6 sec) [ -10462.5270] [ 2410] [depth= 2] . ( 6 sec) [ -10461.4153] [ 2412] [depth= 1] . ( 6 sec) [ -10448.3375] [ 2389] [depth= 1] . ( 6 sec) [ -10447.2528] [ 2386] [depth= 1] . ( 6 sec) [ -10443.7775] [ 2377] [depth= 1] . ( 6 sec) [ -10435.8411] [ 2371] [depth= 1] . ( 7 sec) [ -10434.9072] [ 2369] [depth= 1] . ( 7 sec) [ -10434.0869] [ 2371] [depth= 1] . ( 7 sec) [ -10424.8925] [ 2372] [depth= 1] . ( 7 sec) [ -10407.9280] [ 2359] [depth= 1] . ( 7 sec) [ -10407.8560] [ 2360] [depth= 1] . ( 8 sec) [ -10405.1588] [ 2359] [depth= 1] . ( 8 sec) [ -10399.1555] [ 2365] [depth= 1] . ( 8 sec) [ -10396.4776] [ 2369] [depth= 1] . ( 8 sec) [ -10392.8398] [ 2370] [depth= 1] . ( 9 sec) [ -10374.0449] [Branch lengths ] . ( 9 sec) [ -10373.7791] [GTR parameters ] . ( 9 sec) [ -10372.9645] [Alpha ][ 0.961326] . ( 10 sec) [ -10365.0257] [ 2366] [depth= 1] . ( 10 sec) [ -10361.7177] [ 2365] [depth= 1] . ( 10 sec) [ -10361.1077] [ 2367] [depth= 1] . ( 11 sec) [ -10358.1444] [ 2363] [depth= 2] . ( 11 sec) [ -10357.5084] [ 2367] [depth= 1] . ( 12 sec) [ -10353.7438] [Branch lengths ] . ( 13 sec) [ -10353.7125] [GTR parameters ] . ( 13 sec) [ -10353.7118] [Alpha ][ 0.963786] . ( 14 sec) [ -10353.0324] [ 2363] [depth= 1] . ( 16 sec) [ -10352.5460] [Branch lengths ] . ( 16 sec) [ -10352.5434] [GTR parameters ] . ( 16 sec) [ -10352.5434] [Alpha ][ 0.963786] . ( 19 sec) [ -10352.5240] [Branch lengths ] . ( 40 sec) [ -10352.5234] [Branch lengths ] . ( 40 sec) [ -10352.5234] [Topology ] . ( 41 sec) [ -10352.5233] [Topology ] . ( 41 sec) [ -10352.5233] [GTR parameters ] . ( 41 sec) [ -10352.5233] [Alpha ][ 0.962822] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10352.523270. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22002.6147] [GTR parameters ] . ( 0 sec) [ -21540.8185] [Alpha ][ 0.500960] . ( 0 sec) [ -21327.9816] [ 5276] [depth= 3] . ( 0 sec) [ -20827.1592] [ 5176] [depth= 3] . ( 1 sec) [ -20570.7419] [ 5073] [depth= 4] . ( 1 sec) [ -20425.7119] [ 5065] [depth= 7] . ( 1 sec) [ -20134.2974] [ 4977] [depth= 5] . ( 1 sec) [ -19650.5303] [ 4969] [depth= 1] . ( 1 sec) [ -19581.9335] [ 4947] [depth= 9] . ( 1 sec) [ -19573.5157] [ 4812] [depth= 1] . ( 1 sec) [ -19354.9925] [ 4790] [depth= 12] . ( 1 sec) [ -19218.0249] [ 4752] [depth= 3] . ( 1 sec) [ -19095.6704] [ 4745] [depth= 1] . ( 1 sec) [ -18856.9682] [ 4657] [depth= 9] . ( 1 sec) [ -18792.9540] [ 4671] [depth= 3] . ( 1 sec) [ -18432.3012] [ 4527] [depth= 4] . ( 1 sec) [ -18187.2772] [ 4540] [depth= 13] . ( 1 sec) [ -18105.8759] [ 4444] [depth= 9] . ( 1 sec) [ -18003.0026] [ 4423] [depth= 3] . ( 1 sec) [ -17964.4017] [ 4411] [depth= 3] . ( 1 sec) [ -17740.1990] [ 4408] [depth= 1] . ( 1 sec) [ -17435.0562] [ 4357] [depth= 2] . ( 1 sec) [ -17080.1674] [ 4226] [depth= 4] . ( 1 sec) [ -16995.4447] [ 4161] [depth= 1] . ( 1 sec) [ -16960.2125] [ 4152] [depth= 1] . ( 1 sec) [ -16381.2786] [ 4026] [depth= 10] . ( 2 sec) [ -16318.1998] [ 4011] [depth= 8] . ( 2 sec) [ -15735.8482] [ 3814] [depth= 6] . ( 2 sec) [ -15651.3025] [ 3802] [depth= 1] . ( 2 sec) [ -15218.2712] [ 3702] [depth= 10] . ( 2 sec) [ -15182.0828] [ 3685] [depth= 1] . ( 2 sec) [ -15129.9905] [ 3690] [depth= 1] . ( 2 sec) [ -15066.2669] [ 3644] [depth= 2] . ( 2 sec) [ -14877.5680] [ 3620] [depth= 7] . ( 2 sec) [ -14592.7829] [ 3595] [depth= 13] . ( 2 sec) [ -14392.4834] [ 3552] [depth= 8] . ( 2 sec) [ -14156.1283] [ 3553] [depth= 5] . ( 2 sec) [ -13974.3770] [ 3426] [depth= 6] . ( 2 sec) [ -13898.1098] [ 3424] [depth= 1] . ( 2 sec) [ -13723.2320] [ 3397] [depth= 9] . ( 2 sec) [ -13538.8636] [ 3298] [depth= 6] . ( 2 sec) [ -13361.9821] [ 3260] [depth= 2] . ( 2 sec) [ -13284.6338] [ 3246] [depth= 1] . ( 2 sec) [ -13235.4423] [ 3199] [depth= 1] . ( 3 sec) [ -13095.2322] [ 3176] [depth= 3] . ( 3 sec) [ -13055.2777] [ 3192] [depth= 1] . ( 3 sec) [ -13031.6935] [ 3176] [depth= 1] . ( 3 sec) [ -12857.6723] [ 3151] [depth= 5] . ( 3 sec) [ -12735.2108] [ 3069] [depth= 11] . ( 3 sec) [ -12460.5641] [ 3023] [depth= 1] . ( 3 sec) [ -12448.8627] [ 3023] [depth= 1] . ( 3 sec) [ -12390.7165] [ 2915] [depth= 2] . ( 3 sec) [ -12299.1269] [ 2881] [depth= 4] . ( 3 sec) [ -12264.9924] [ 2867] [depth= 1] . ( 3 sec) [ -12223.5933] [ 2841] [depth= 1] . ( 3 sec) [ -12054.7841] [ 2651] [depth= 2] . ( 3 sec) [ -12047.4045] [ 2650] [depth= 1] . ( 3 sec) [ -11996.8018] [ 2635] [depth= 1] . ( 3 sec) [ -11995.8922] [ 2639] [depth= 3] . ( 3 sec) [ -11969.0552] [ 2638] [depth= 2] . ( 4 sec) [ -11682.8025] [ 2641] [depth= 1] . ( 4 sec) [ -11649.1551] [ 2633] [depth= 9] . ( 4 sec) [ -11631.6869] [ 2630] [depth= 1] . ( 4 sec) [ -11623.7171] [ 2632] [depth= 1] . ( 4 sec) [ -11503.5873] [ 2604] [depth= 1] . ( 4 sec) [ -11380.1627] [ 2605] [depth= 6] . ( 4 sec) [ -11336.4967] [ 2588] [depth= 1] . ( 4 sec) [ -11067.9437] [ 2584] [depth= 1] . ( 4 sec) [ -11012.5618] [ 2555] [depth= 1] . ( 4 sec) [ -10938.2417] [ 2547] [depth= 4] . ( 4 sec) [ -10903.1121] [ 2528] [depth= 1] . ( 4 sec) [ -10896.7608] [ 2524] [depth= 2] . ( 4 sec) [ -10878.0284] [ 2501] [depth= 1] . ( 4 sec) [ -10792.8503] [ 2476] [depth= 1] . ( 4 sec) [ -10791.2957] [ 2473] [depth= 1] . ( 5 sec) [ -10620.6936] [Branch lengths ] . ( 5 sec) [ -10618.3541] [GTR parameters ] . ( 5 sec) [ -10586.1065] [Alpha ][ 0.862309] . ( 5 sec) [ -10584.9887] [ 2474] [depth= 1] . ( 6 sec) [ -10566.4192] [ 2464] [depth= 1] . ( 6 sec) [ -10564.1067] [ 2467] [depth= 1] . ( 6 sec) [ -10555.0804] [ 2463] [depth= 2] . ( 6 sec) [ -10554.4046] [ 2459] [depth= 1] . ( 6 sec) [ -10551.8554] [ 2462] [depth= 1] . ( 6 sec) [ -10522.7532] [ 2458] [depth= 4] . ( 6 sec) [ -10472.6281] [ 2427] [depth= 3] . ( 7 sec) [ -10471.5709] [ 2428] [depth= 1] . ( 7 sec) [ -10464.8372] [ 2413] [depth= 1] . ( 7 sec) [ -10463.2707] [ 2400] [depth= 1] . ( 7 sec) [ -10460.5906] [ 2408] [depth= 1] . ( 7 sec) [ -10446.5337] [ 2409] [depth= 1] . ( 7 sec) [ -10442.9123] [ 2413] [depth= 1] . ( 8 sec) [ -10435.5959] [ 2413] [depth= 1] . ( 8 sec) [ -10435.3123] [ 2409] [depth= 1] . ( 8 sec) [ -10425.0334] [ 2406] [depth= 1] . ( 8 sec) [ -10385.7902] [ 2363] [depth= 2] . ( 8 sec) [ -10383.0396] [ 2364] [depth= 1] . ( 8 sec) [ -10358.2055] [Branch lengths ] . ( 9 sec) [ -10357.9507] [GTR parameters ] . ( 9 sec) [ -10357.0440] [Alpha ][ 0.948273] . ( 10 sec) [ -10356.3531] [ 2357] [depth= 1] . ( 11 sec) [ -10355.4218] [ 2355] [depth= 1] . ( 12 sec) [ -10352.7780] [Branch lengths ] . ( 12 sec) [ -10352.7734] [GTR parameters ] . ( 12 sec) [ -10352.7537] [Alpha ][ 0.961949] . ( 15 sec) [ -10352.5604] [Branch lengths ] . ( 35 sec) [ -10352.5295] [Branch lengths ] . ( 35 sec) [ -10352.5295] [Topology ] . ( 36 sec) [ -10352.5260] [Topology ] . ( 37 sec) [ -10352.5247] [Topology ] . ( 38 sec) [ -10352.5241] [Topology ] . ( 38 sec) [ -10352.5241] [GTR parameters ] . ( 38 sec) [ -10352.5240] [Alpha ][ 0.962911] . ( 38 sec) [ -10352.5240] [Topology ] . ( 39 sec) [ -10352.5236] [Topology ] . ( 39 sec) [ -10352.5236] [GTR parameters ] . ( 39 sec) [ -10352.5236] [Alpha ][ 0.962911] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10352.523648. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22756.2714] [GTR parameters ] . ( 1 sec) [ -22271.2529] [Alpha ][ 0.500960] . ( 1 sec) [ -21992.4684] [ 5382] [depth= 1] . ( 1 sec) [ -21627.6489] [ 5248] [depth= 8] . ( 1 sec) [ -21371.4144] [ 5221] [depth= 3] . ( 1 sec) [ -21246.2751] [ 5218] [depth= 1] . ( 1 sec) [ -21203.7549] [ 5137] [depth= 6] . ( 1 sec) [ -21154.1364] [ 5120] [depth= 2] . ( 1 sec) [ -20445.8311] [ 5064] [depth= 1] . ( 1 sec) [ -20276.3494] [ 5027] [depth= 2] . ( 1 sec) [ -19567.6662] [ 4942] [depth= 1] . ( 1 sec) [ -19444.3814] [ 4915] [depth= 7] . ( 1 sec) [ -19291.9000] [ 4813] [depth= 1] . ( 1 sec) [ -18740.9568] [ 4751] [depth= 11] . ( 1 sec) [ -18573.9238] [ 4715] [depth= 9] . ( 1 sec) [ -18482.4984] [ 4707] [depth= 1] . ( 1 sec) [ -18305.7233] [ 4628] [depth= 2] . ( 1 sec) [ -18189.2139] [ 4616] [depth= 2] . ( 1 sec) [ -17922.1102] [ 4557] [depth= 7] . ( 1 sec) [ -17826.5779] [ 4557] [depth= 2] . ( 1 sec) [ -17748.1509] [ 4490] [depth= 9] . ( 1 sec) [ -17696.8578] [ 4494] [depth= 2] . ( 2 sec) [ -17428.1049] [ 4446] [depth= 4] . ( 2 sec) [ -17126.5596] [ 4333] [depth= 10] . ( 2 sec) [ -16656.6336] [ 4207] [depth= 10] . ( 2 sec) [ -16010.6038] [ 4003] [depth= 8] . ( 2 sec) [ -15931.2825] [ 3963] [depth= 1] . ( 2 sec) [ -15491.2064] [ 3877] [depth= 6] . ( 2 sec) [ -15489.9349] [ 3880] [depth= 1] . ( 2 sec) [ -15404.7807] [ 3840] [depth= 7] . ( 2 sec) [ -15323.5542] [ 3836] [depth= 1] . ( 2 sec) [ -15285.0127] [ 3846] [depth= 1] . ( 2 sec) [ -15280.8858] [ 3847] [depth= 1] . ( 2 sec) [ -15159.9894] [ 3781] [depth= 10] . ( 2 sec) [ -14116.1893] [ 3640] [depth= 10] . ( 2 sec) [ -13992.0752] [ 3638] [depth= 1] . ( 2 sec) [ -13928.4096] [ 3572] [depth= 1] . ( 2 sec) [ -13918.6315] [ 3575] [depth= 1] . ( 2 sec) [ -13877.0478] [ 3559] [depth= 1] . ( 2 sec) [ -13852.2333] [ 3595] [depth= 2] . ( 2 sec) [ -13821.8223] [ 3579] [depth= 1] . ( 2 sec) [ -13796.2395] [ 3541] [depth= 1] . ( 2 sec) [ -13793.3277] [ 3538] [depth= 1] . ( 3 sec) [ -13444.6960] [ 3372] [depth= 8] . ( 3 sec) [ -13227.6093] [ 3344] [depth= 1] . ( 3 sec) [ -13041.0791] [ 3320] [depth= 3] . ( 3 sec) [ -13034.5980] [ 3336] [depth= 1] . ( 3 sec) [ -13016.0470] [ 3320] [depth= 3] . ( 3 sec) [ -12941.0048] [ 3314] [depth= 2] . ( 3 sec) [ -12929.9457] [ 3266] [depth= 4] . ( 3 sec) [ -12737.3889] [ 3246] [depth= 2] . ( 3 sec) [ -12487.0227] [ 3157] [depth= 9] . ( 3 sec) [ -12403.2417] [ 3087] [depth= 10] . ( 3 sec) [ -12369.3811] [ 3080] [depth= 2] . ( 3 sec) [ -12324.6813] [ 3080] [depth= 2] . ( 3 sec) [ -12187.3243] [ 3061] [depth= 2] . ( 3 sec) [ -12069.2342] [ 3072] [depth= 1] . ( 3 sec) [ -11921.5828] [ 2969] [depth= 4] . ( 3 sec) [ -11899.1056] [ 2958] [depth= 1] . ( 3 sec) [ -11836.5958] [ 2941] [depth= 1] . ( 3 sec) [ -11812.5059] [ 2938] [depth= 1] . ( 4 sec) [ -11685.8894] [ 2917] [depth= 1] . ( 4 sec) [ -11651.5026] [ 2912] [depth= 1] . ( 4 sec) [ -11651.4410] [ 2892] [depth= 1] . ( 4 sec) [ -11627.0878] [ 2882] [depth= 1] . ( 4 sec) [ -11590.2768] [ 2869] [depth= 3] . ( 4 sec) [ -11584.4832] [ 2866] [depth= 1] . ( 4 sec) [ -11563.8165] [ 2855] [depth= 1] . ( 4 sec) [ -11245.6414] [ 2716] [depth= 5] . ( 4 sec) [ -11240.0399] [ 2687] [depth= 1] . ( 4 sec) [ -11240.0195] [ 2691] [depth= 1] . ( 4 sec) [ -11226.5246] [ 2684] [depth= 2] . ( 4 sec) [ -11175.7151] [ 2613] [depth= 1] . ( 4 sec) [ -11158.3874] [ 2632] [depth= 1] . ( 4 sec) [ -11157.4137] [ 2632] [depth= 1] . ( 4 sec) [ -11056.6190] [ 2611] [depth= 2] . ( 4 sec) [ -11054.6840] [ 2611] [depth= 1] . ( 4 sec) [ -11019.2882] [ 2591] [depth= 1] . ( 4 sec) [ -11016.6393] [ 2592] [depth= 1] . ( 5 sec) [ -10800.7638] [Branch lengths ] . ( 5 sec) [ -10798.6111] [GTR parameters ] . ( 5 sec) [ -10766.0930] [Alpha ][ 0.859097] . ( 5 sec) [ -10607.7188] [ 2489] [depth= 10] . ( 5 sec) [ -10607.0260] [ 2492] [depth= 1] . ( 6 sec) [ -10573.0158] [ 2453] [depth= 2] . ( 6 sec) [ -10570.1894] [ 2458] [depth= 1] . ( 6 sec) [ -10523.5033] [ 2428] [depth= 1] . ( 6 sec) [ -10518.4757] [ 2425] [depth= 1] . ( 6 sec) [ -10516.3624] [ 2428] [depth= 1] . ( 6 sec) [ -10516.1935] [ 2428] [depth= 1] . ( 6 sec) [ -10509.5821] [ 2427] [depth= 1] . ( 6 sec) [ -10472.7379] [ 2410] [depth= 1] . ( 6 sec) [ -10467.9969] [ 2400] [depth= 1] . ( 6 sec) [ -10428.1542] [ 2391] [depth= 1] . ( 7 sec) [ -10421.2450] [ 2386] [depth= 2] . ( 7 sec) [ -10418.5877] [ 2386] [depth= 2] . ( 7 sec) [ -10407.0322] [ 2371] [depth= 1] . ( 7 sec) [ -10406.9005] [ 2365] [depth= 1] . ( 7 sec) [ -10404.3262] [ 2363] [depth= 1] . ( 7 sec) [ -10403.3888] [ 2368] [depth= 1] . ( 7 sec) [ -10402.4791] [ 2369] [depth= 1] . ( 8 sec) [ -10401.6834] [ 2371] [depth= 1] . ( 8 sec) [ -10398.2978] [ 2377] [depth= 1] . ( 8 sec) [ -10398.2021] [ 2379] [depth= 1] . ( 8 sec) [ -10396.8731] [ 2376] [depth= 1] . ( 9 sec) [ -10364.8730] [Branch lengths ] . ( 9 sec) [ -10364.6888] [GTR parameters ] . ( 9 sec) [ -10363.6733] [Alpha ][ 0.950184] . ( 9 sec) [ -10363.6334] [ 2379] [depth= 1] . ( 9 sec) [ -10361.3720] [ 2372] [depth= 1] . ( 10 sec) [ -10361.3601] [ 2366] [depth= 1] . ( 10 sec) [ -10358.6312] [ 2362] [depth= 1] . ( 11 sec) [ -10358.1652] [ 2362] [depth= 1] . ( 11 sec) [ -10357.3345] [ 2358] [depth= 1] . ( 12 sec) [ -10353.0716] [Branch lengths ] . ( 12 sec) [ -10353.0547] [GTR parameters ] . ( 12 sec) [ -10353.0416] [Alpha ][ 0.961323] . ( 15 sec) [ -10352.5991] [Branch lengths ] . ( 35 sec) [ -10352.5320] [Branch lengths ] . ( 35 sec) [ -10352.5320] [Topology ] . ( 36 sec) [ -10352.5269] [Topology ] . ( 37 sec) [ -10352.5253] [Topology ] . ( 38 sec) [ -10352.5246] [Topology ] . ( 38 sec) [ -10352.5243] [GTR parameters ] . ( 38 sec) [ -10352.5241] [Alpha ][ 0.962700] . ( 38 sec) [ -10352.5241] [Topology ] . ( 39 sec) [ -10352.5237] [Topology ] . ( 39 sec) [ -10352.5237] [GTR parameters ] . ( 39 sec) [ -10352.5237] [Alpha ][ 0.962700] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10352.523685. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20904.4935] [GTR parameters ] . ( 1 sec) [ -20458.3568] [Alpha ][ 0.500960] . ( 1 sec) [ -20236.8589] [ 5102] [depth= 8] . ( 1 sec) [ -19725.3064] [ 4980] [depth= 9] . ( 1 sec) [ -19185.9336] [ 4912] [depth= 2] . ( 1 sec) [ -19080.6696] [ 4820] [depth= 1] . ( 1 sec) [ -18768.9393] [ 4736] [depth= 4] . ( 1 sec) [ -18657.8932] [ 4699] [depth= 2] . ( 2 sec) [ -18655.0809] [ 4697] [depth= 1] . ( 2 sec) [ -18313.5250] [ 4605] [depth= 1] . ( 2 sec) [ -17742.3178] [ 4492] [depth= 1] . ( 2 sec) [ -17431.6652] [ 4409] [depth= 2] . ( 2 sec) [ -17388.5190] [ 4412] [depth= 1] . ( 2 sec) [ -17319.0014] [ 4384] [depth= 2] . ( 2 sec) [ -17128.7678] [ 4376] [depth= 4] . ( 2 sec) [ -16927.3945] [ 4364] [depth= 3] . ( 2 sec) [ -16792.0283] [ 4302] [depth= 5] . ( 2 sec) [ -16681.2756] [ 4293] [depth= 4] . ( 2 sec) [ -16545.3792] [ 4259] [depth= 2] . ( 2 sec) [ -16485.4214] [ 4264] [depth= 7] . ( 2 sec) [ -16280.6750] [ 4159] [depth= 8] . ( 2 sec) [ -15935.0426] [ 4064] [depth= 8] . ( 2 sec) [ -15831.8937] [ 4045] [depth= 1] . ( 2 sec) [ -15714.3553] [ 4046] [depth= 2] . ( 2 sec) [ -15644.6759] [ 4023] [depth= 15] . ( 2 sec) [ -15596.0731] [ 4029] [depth= 13] . ( 2 sec) [ -15484.0612] [ 3989] [depth= 2] . ( 2 sec) [ -15325.2123] [ 3942] [depth= 1] . ( 2 sec) [ -15269.6946] [ 3889] [depth= 13] . ( 2 sec) [ -14908.3944] [ 3782] [depth= 10] . ( 2 sec) [ -14853.6838] [ 3747] [depth= 8] . ( 3 sec) [ -14569.9941] [ 3606] [depth= 5] . ( 3 sec) [ -14540.0347] [ 3614] [depth= 1] . ( 3 sec) [ -14220.9312] [ 3577] [depth= 8] . ( 3 sec) [ -13972.9701] [ 3545] [depth= 1] . ( 3 sec) [ -13947.1625] [ 3530] [depth= 1] . ( 3 sec) [ -13884.3410] [ 3482] [depth= 9] . ( 3 sec) [ -13860.3527] [ 3452] [depth= 1] . ( 3 sec) [ -13433.4958] [ 3314] [depth= 10] . ( 3 sec) [ -13316.1388] [ 3281] [depth= 4] . ( 3 sec) [ -13300.7308] [ 3245] [depth= 1] . ( 3 sec) [ -13076.7263] [ 3210] [depth= 4] . ( 3 sec) [ -12928.3297] [ 3097] [depth= 6] . ( 3 sec) [ -12837.0143] [ 3097] [depth= 1] . ( 3 sec) [ -12820.8646] [ 3099] [depth= 1] . ( 3 sec) [ -12815.2262] [ 3088] [depth= 12] . ( 3 sec) [ -12682.4390] [ 3064] [depth= 1] . ( 3 sec) [ -12662.7638] [ 3046] [depth= 1] . ( 3 sec) [ -12639.0907] [ 3033] [depth= 1] . ( 3 sec) [ -12413.5586] [ 3002] [depth= 2] . ( 3 sec) [ -12397.5959] [ 2998] [depth= 1] . ( 4 sec) [ -12394.5567] [ 2998] [depth= 1] . ( 4 sec) [ -12393.4714] [ 3000] [depth= 2] . ( 4 sec) [ -12187.7286] [ 2886] [depth= 8] . ( 4 sec) [ -12186.5426] [ 2886] [depth= 1] . ( 4 sec) [ -12174.6507] [ 2885] [depth= 2] . ( 4 sec) [ -12054.6710] [ 2794] [depth= 12] . ( 4 sec) [ -12047.2736] [ 2809] [depth= 2] . ( 4 sec) [ -12028.5370] [ 2799] [depth= 1] . ( 4 sec) [ -11772.9775] [ 2683] [depth= 2] . ( 4 sec) [ -11421.1122] [ 2668] [depth= 1] . ( 4 sec) [ -11419.2012] [ 2665] [depth= 1] . ( 4 sec) [ -11156.8752] [ 2521] [depth= 3] . ( 4 sec) [ -10994.1513] [ 2508] [depth= 1] . ( 4 sec) [ -10899.1847] [ 2487] [depth= 1] . ( 4 sec) [ -10799.4055] [ 2462] [depth= 5] . ( 4 sec) [ -10728.8366] [ 2441] [depth= 1] . ( 4 sec) [ -10674.6505] [ 2402] [depth= 1] . ( 4 sec) [ -10658.2168] [ 2393] [depth= 1] . ( 4 sec) [ -10655.2521] [ 2397] [depth= 1] . ( 4 sec) [ -10651.3136] [ 2408] [depth= 1] . ( 5 sec) [ -10629.1557] [ 2402] [depth= 1] . ( 5 sec) [ -10617.0322] [ 2398] [depth= 1] . ( 5 sec) [ -10478.8317] [Branch lengths ] . ( 6 sec) [ -10476.9670] [GTR parameters ] . ( 6 sec) [ -10447.6673] [Alpha ][ 0.847906] . ( 6 sec) [ -10446.1766] [ 2400] [depth= 1] . ( 6 sec) [ -10442.7204] [ 2398] [depth= 1] . ( 6 sec) [ -10440.0267] [ 2386] [depth= 1] . ( 7 sec) [ -10431.0824] [ 2390] [depth= 2] . ( 7 sec) [ -10418.5577] [ 2375] [depth= 2] . ( 7 sec) [ -10416.6297] [ 2376] [depth= 1] . ( 7 sec) [ -10416.2851] [ 2379] [depth= 1] . ( 7 sec) [ -10397.1871] [ 2367] [depth= 3] . ( 7 sec) [ -10396.8441] [ 2367] [depth= 2] . ( 8 sec) [ -10396.4614] [ 2369] [depth= 1] . ( 8 sec) [ -10395.3036] [ 2364] [depth= 1] . ( 8 sec) [ -10393.7976] [ 2361] [depth= 1] . ( 9 sec) [ -10360.5068] [Branch lengths ] . ( 10 sec) [ -10360.3771] [GTR parameters ] . ( 10 sec) [ -10359.0952] [Alpha ][ 0.949706] . ( 10 sec) [ -10356.4726] [ 2361] [depth= 1] . ( 13 sec) [ -10353.1358] [Branch lengths ] . ( 13 sec) [ -10353.1167] [GTR parameters ] . ( 13 sec) [ -10353.1075] [Alpha ][ 0.958993] . ( 17 sec) [ -10352.7606] [Branch lengths ] . ( 25 sec) [ -10352.7503] [ 2355] [depth= 1] . ( 37 sec) [ -10352.5337] [Branch lengths ] . ( 37 sec) [ -10352.5330] [GTR parameters ] . ( 37 sec) [ -10352.5316] [Alpha ][ 0.962547] . ( 37 sec) [ -10352.5316] [Topology ] . ( 38 sec) [ -10352.5263] [Topology ] . ( 39 sec) [ -10352.5248] [Topology ] . ( 40 sec) [ -10352.5241] [Topology ] . ( 40 sec) [ -10352.5240] [GTR parameters ] . ( 40 sec) [ -10352.5240] [Alpha ][ 0.962547] . ( 40 sec) [ -10352.5240] [Topology ] . ( 41 sec) [ -10352.5237] [Topology ] . ( 41 sec) [ -10352.5237] [GTR parameters ] . ( 41 sec) [ -10352.5237] [Alpha ][ 0.962547] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10352.523662. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -23051.5833] [GTR parameters ] . ( 0 sec) [ -22583.7620] [Alpha ][ 0.500960] . ( 1 sec) [ -22299.6818] [ 5336] [depth= 7] . ( 1 sec) [ -21801.6792] [ 5251] [depth= 11] . ( 1 sec) [ -21796.8628] [ 5234] [depth= 3] . ( 1 sec) [ -21639.5039] [ 5229] [depth= 3] . ( 1 sec) [ -21523.4024] [ 5170] [depth= 3] . ( 1 sec) [ -20773.9454] [ 5178] [depth= 6] . ( 1 sec) [ -20590.0713] [ 5136] [depth= 6] . ( 1 sec) [ -20577.2730] [ 5082] [depth= 1] . ( 1 sec) [ -20427.4927] [ 5020] [depth= 12] . ( 1 sec) [ -20049.3558] [ 4967] [depth= 7] . ( 1 sec) [ -20011.4810] [ 4961] [depth= 15] . ( 1 sec) [ -19754.3197] [ 4900] [depth= 3] . ( 1 sec) [ -19713.5359] [ 4894] [depth= 1] . ( 1 sec) [ -19474.4738] [ 4862] [depth= 10] . ( 1 sec) [ -19259.0532] [ 4852] [depth= 1] . ( 1 sec) [ -19100.1762] [ 4811] [depth= 12] . ( 1 sec) [ -18849.2011] [ 4784] [depth= 1] . ( 1 sec) [ -18695.4993] [ 4765] [depth= 13] . ( 1 sec) [ -18568.8798] [ 4661] [depth= 10] . ( 1 sec) [ -18546.7612] [ 4654] [depth= 1] . ( 1 sec) [ -18500.3742] [ 4629] [depth= 1] . ( 1 sec) [ -18429.7272] [ 4623] [depth= 2] . ( 2 sec) [ -18194.9427] [ 4586] [depth= 2] . ( 2 sec) [ -17784.3728] [ 4543] [depth= 9] . ( 2 sec) [ -17552.4011] [ 4441] [depth= 3] . ( 2 sec) [ -17005.7683] [ 4328] [depth= 8] . ( 2 sec) [ -16995.1878] [ 4339] [depth= 4] . ( 2 sec) [ -16912.1853] [ 4325] [depth= 1] . ( 2 sec) [ -16838.4851] [ 4324] [depth= 6] . ( 2 sec) [ -16393.0797] [ 4199] [depth= 8] . ( 2 sec) [ -16330.2012] [ 4133] [depth= 9] . ( 2 sec) [ -16322.9175] [ 4136] [depth= 1] . ( 2 sec) [ -16233.3708] [ 4104] [depth= 8] . ( 2 sec) [ -15807.1034] [ 4106] [depth= 4] . ( 2 sec) [ -15738.9841] [ 4110] [depth= 2] . ( 2 sec) [ -15473.8782] [ 4101] [depth= 1] . ( 2 sec) [ -15454.7129] [ 4016] [depth= 3] . ( 2 sec) [ -15362.7021] [ 3993] [depth= 1] . ( 2 sec) [ -15340.2151] [ 3979] [depth= 1] . ( 2 sec) [ -14974.3276] [ 3879] [depth= 8] . ( 2 sec) [ -14613.9973] [ 3761] [depth= 2] . ( 2 sec) [ -14192.9951] [ 3632] [depth= 10] . ( 3 sec) [ -14153.6821] [ 3650] [depth= 1] . ( 3 sec) [ -13880.8865] [ 3569] [depth= 3] . ( 3 sec) [ -13588.0075] [ 3423] [depth= 8] . ( 3 sec) [ -13231.2821] [ 3343] [depth= 3] . ( 3 sec) [ -13200.4503] [ 3336] [depth= 1] . ( 3 sec) [ -13012.4934] [ 3272] [depth= 10] . ( 3 sec) [ -12921.5731] [ 3212] [depth= 3] . ( 3 sec) [ -12884.1095] [ 3192] [depth= 5] . ( 3 sec) [ -12829.9002] [ 3170] [depth= 2] . ( 3 sec) [ -12710.4296] [ 3141] [depth= 2] . ( 3 sec) [ -12538.6135] [ 3062] [depth= 3] . ( 3 sec) [ -12431.9699] [ 3013] [depth= 4] . ( 3 sec) [ -12324.1100] [ 2997] [depth= 2] . ( 3 sec) [ -12286.9119] [ 2938] [depth= 1] . ( 3 sec) [ -12195.4536] [ 2944] [depth= 1] . ( 3 sec) [ -12138.9432] [ 2897] [depth= 10] . ( 3 sec) [ -12134.5476] [ 2897] [depth= 1] . ( 3 sec) [ -12133.7760] [ 2957] [depth= 1] . ( 3 sec) [ -12055.1330] [ 2905] [depth= 3] . ( 3 sec) [ -12002.6535] [ 2922] [depth= 1] . ( 3 sec) [ -12002.4148] [ 2911] [depth= 1] . ( 4 sec) [ -11960.7915] [ 2914] [depth= 1] . ( 4 sec) [ -11957.8834] [ 2874] [depth= 1] . ( 4 sec) [ -11914.8687] [ 2870] [depth= 1] . ( 4 sec) [ -11912.6419] [ 2864] [depth= 1] . ( 4 sec) [ -11887.2776] [ 2826] [depth= 3] . ( 4 sec) [ -11830.0672] [ 2863] [depth= 1] . ( 4 sec) [ -11680.4433] [ 2824] [depth= 5] . ( 4 sec) [ -11619.2868] [ 2780] [depth= 1] . ( 4 sec) [ -11508.3664] [ 2763] [depth= 1] . ( 4 sec) [ -11289.9215] [ 2683] [depth= 9] . ( 4 sec) [ -11268.9320] [ 2684] [depth= 2] . ( 4 sec) [ -11125.3208] [ 2632] [depth= 2] . ( 4 sec) [ -11120.9901] [ 2631] [depth= 1] . ( 4 sec) [ -11115.9196] [ 2630] [depth= 1] . ( 4 sec) [ -11090.5767] [ 2628] [depth= 1] . ( 5 sec) [ -11082.9091] [ 2637] [depth= 2] . ( 5 sec) [ -10838.0292] [Branch lengths ] . ( 5 sec) [ -10836.1718] [GTR parameters ] . ( 5 sec) [ -10809.6175] [Alpha ][ 0.815589] . ( 6 sec) [ -10788.4210] [ 2625] [depth= 2] . ( 6 sec) [ -10784.4797] [ 2620] [depth= 2] . ( 6 sec) [ -10619.0184] [ 2527] [depth= 9] . ( 6 sec) [ -10603.1330] [ 2530] [depth= 1] . ( 6 sec) [ -10602.5864] [ 2534] [depth= 1] . ( 6 sec) [ -10593.5301] [ 2531] [depth= 1] . ( 6 sec) [ -10592.5979] [ 2511] [depth= 1] . ( 6 sec) [ -10581.0494] [ 2519] [depth= 1] . ( 6 sec) [ -10450.0250] [ 2419] [depth= 8] . ( 6 sec) [ -10446.7583] [ 2418] [depth= 1] . ( 7 sec) [ -10436.1324] [ 2431] [depth= 1] . ( 7 sec) [ -10435.9743] [ 2435] [depth= 1] . ( 7 sec) [ -10435.6651] [ 2435] [depth= 1] . ( 7 sec) [ -10420.0732] [ 2404] [depth= 1] . ( 7 sec) [ -10386.7345] [ 2378] [depth= 2] . ( 8 sec) [ -10386.2733] [ 2380] [depth= 1] . ( 8 sec) [ -10383.6047] [ 2368] [depth= 1] . ( 9 sec) [ -10360.1477] [Branch lengths ] . ( 9 sec) [ -10359.8833] [GTR parameters ] . ( 9 sec) [ -10357.4842] [Alpha ][ 0.951179] . ( 10 sec) [ -10356.5119] [ 2364] [depth= 1] . ( 10 sec) [ -10355.0028] [ 2361] [depth= 1] . ( 11 sec) [ -10354.9866] [ 2361] [depth= 1] . ( 12 sec) [ -10354.9592] [ 2355] [depth= 1] . ( 13 sec) [ -10353.0939] [Branch lengths ] . ( 13 sec) [ -10353.0900] [GTR parameters ] . ( 13 sec) [ -10353.0791] [Alpha ][ 0.961283] . ( 16 sec) [ -10352.5378] [Branch lengths ] . ( 36 sec) [ -10352.5248] [Branch lengths ] . ( 36 sec) [ -10352.5248] [Topology ] . ( 37 sec) [ -10352.5244] [Topology ] . ( 37 sec) [ -10352.5237] [GTR parameters ] . ( 37 sec) [ -10352.5234] [Alpha ][ 0.962868] . ( 37 sec) [ -10352.5234] [Topology ] . ( 38 sec) [ -10352.5233] [Topology ] . ( 38 sec) [ -10352.5233] [GTR parameters ] . ( 38 sec) [ -10352.5233] [Alpha ][ 0.962868] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10352.523288. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10431.263771 . ( 1 sec) [ -10427.9988] [GTR parameters ] . ( 1 sec) [ -10427.3751] [Alpha ][ 0.921352] . ( 1 sec) [ -10427.3751] [Topology ] . ( 2 sec) [ -10366.0401] [Topology ] . ( 3 sec) [ -10358.1689] [Topology ] . ( 4 sec) [ -10355.5306] [Topology ] . ( 5 sec) [ -10353.9275] [Topology ] . ( 5 sec) [ -10353.3427] [Topology ] . ( 6 sec) [ -10353.0657] [Topology ] . ( 7 sec) [ -10352.9283] [Topology ] . ( 8 sec) [ -10352.8601] [Topology ] . ( 9 sec) [ -10352.8259] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.825858 . ( 16 sec) [ -10352.7481] [GTR parameters ] . ( 16 sec) [ -10352.5836] [Alpha ][ 0.959089] . ( 16 sec) [ -10352.5836] [Topology ] . ( 17 sec) [ -10352.5521] [Topology ] . ( 18 sec) [ -10352.5389] [Topology ] . ( 19 sec) [ -10352.5323] [Topology ] . ( 20 sec) [ -10352.5289] [Topology ] . ( 21 sec) [ -10352.5271] [Topology ] . ( 21 sec) [ -10352.5261] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.526138 . ( 29 sec) [ -10352.5259] [GTR parameters ] . ( 29 sec) [ -10352.5246] [Alpha ][ 0.962592] . ( 29 sec) [ -10352.5246] [Topology ] . ( 29 sec) [ -10352.5240] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10352.523974 . ( 37 sec) [ -10352.5239] [GTR parameters ] . ( 37 sec) [ -10352.5239] [Alpha ][ 0.962592] . ( 37 sec) [ -10352.5239] [Topology ] . ( 37 sec) [ -10352.5236] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -10427.9988] [GTR parameters ] . ( 53 sec) [ -10427.3751] [Alpha ][ 0.921352] . ( 53 sec) [ -10427.3254] [ 2361] [depth= 1] . ( 53 sec) [ -10427.1830] [ 2359] [depth= 1] . ( 54 sec) [ -10427.0571] [ 2374] [depth= 1] . ( 54 sec) [ -10424.6917] [ 2359] [depth= 1] . ( 54 sec) [ -10422.3320] [ 2362] [depth= 1] . ( 54 sec) [ -10420.1469] [ 2367] [depth= 1] . ( 54 sec) [ -10410.4417] [ 2370] [depth= 1] . ( 54 sec) [ -10408.2363] [ 2366] [depth= 1] . ( 54 sec) [ -10408.0992] [ 2368] [depth= 1] . ( 54 sec) [ -10404.7814] [ 2366] [depth= 1] . ( 55 sec) [ -10404.7115] [ 2366] [depth= 1] . ( 55 sec) [ -10400.7572] [ 2372] [depth= 1] . ( 55 sec) [ -10398.0205] [ 2367] [depth= 1] . ( 56 sec) [ -10397.9246] [ 2372] [depth= 1] . ( 56 sec) [ -10361.0283] [Branch lengths ] . ( 56 sec) [ -10360.9881] [GTR parameters ] . ( 56 sec) [ -10360.9449] [Alpha ][ 0.941265] . ( 56 sec) [ -10360.3662] [ 2374] [depth= 1] . ( 57 sec) [ -10359.7577] [ 2368] [depth= 1] . ( 58 sec) [ -10358.4052] [ 2363] [depth= 1] . ( 59 sec) [ -10353.1655] [Branch lengths ] . ( 59 sec) [ -10353.1529] [GTR parameters ] . ( 59 sec) [ -10353.1049] [Alpha ][ 0.962539] . ( 63 sec) [ -10352.7296] [Branch lengths ] . ( 83 sec) [ -10352.6924] [Branch lengths ] . ( 83 sec) [ -10352.6924] [Topology ] . ( 84 sec) [ -10352.6896] [Topology ] . ( 85 sec) [ -10352.6887] [Topology ] . ( 85 sec) [ -10352.6886] [GTR parameters ] . ( 85 sec) [ -10352.6886] [Alpha ][ 0.962539] . ( 85 sec) [ -10352.6886] [Topology ] . ( 86 sec) [ -10352.6882] [Topology ] . ( 86 sec) [ -10352.6882] [GTR parameters ] . ( 86 sec) [ -10352.6882] [Alpha ][ 0.962539] . Checking for NNIs, optimizing five branches... . ( 93 sec) [ -10352.5259] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10352.523643 . Log likelihood obtained after SPR moves : -10352.525919 . Log likelihood of the current tree: -10352.523643. . Printing the most likely tree in file 'data46.phy_phyml_tree.txt'... . Best log likelihood : -10352.523270 . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo