.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data96.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... . 437 patterns found. (out of a total of 500 sites) . 57 sites without polymorphism (11.40%). . [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) [ -21087.7040] [GTR parameters ] . ( 1 sec) [ -20659.0962] [Alpha ][ 0.500960] . ( 2 sec) [ -20253.2509] [ 4680] [depth= 8] . ( 2 sec) [ -19896.6546] [ 4665] [depth= 6] . ( 2 sec) [ -19578.0252] [ 4634] [depth= 1] . ( 2 sec) [ -19547.3007] [ 4621] [depth= 3] . ( 2 sec) [ -19373.0949] [ 4528] [depth= 6] . ( 2 sec) [ -19265.3818] [ 4527] [depth= 8] . ( 2 sec) [ -19167.0142] [ 4459] [depth= 7] . ( 2 sec) [ -19141.1879] [ 4447] [depth= 1] . ( 2 sec) [ -18836.8002] [ 4335] [depth= 5] . ( 2 sec) [ -18743.8478] [ 4332] [depth= 8] . ( 2 sec) [ -18502.0170] [ 4300] [depth= 1] . ( 2 sec) [ -18252.5726] [ 4297] [depth= 6] . ( 2 sec) [ -17992.8421] [ 4239] [depth= 4] . ( 3 sec) [ -17939.7537] [ 4216] [depth= 3] . ( 3 sec) [ -17917.2444] [ 4213] [depth= 4] . ( 3 sec) [ -17914.1212] [ 4077] [depth= 9] . ( 3 sec) [ -17821.5528] [ 4081] [depth= 1] . ( 3 sec) [ -17268.0428] [ 4043] [depth= 3] . ( 3 sec) [ -17137.5490] [ 3968] [depth= 1] . ( 3 sec) [ -17009.1230] [ 3950] [depth= 6] . ( 3 sec) [ -16640.1944] [ 3898] [depth= 15] . ( 3 sec) [ -16484.2750] [ 3851] [depth= 9] . ( 3 sec) [ -16296.9858] [ 3823] [depth= 11] . ( 4 sec) [ -16048.2912] [ 3798] [depth= 1] . ( 4 sec) [ -15851.4209] [ 3711] [depth= 10] . ( 4 sec) [ -15540.2310] [ 3632] [depth= 16] . ( 4 sec) [ -15429.6038] [ 3632] [depth= 3] . ( 4 sec) [ -15377.4362] [ 3620] [depth= 1] . ( 4 sec) [ -15356.7252] [ 3585] [depth= 4] . ( 4 sec) [ -15259.3192] [ 3534] [depth= 1] . ( 4 sec) [ -15256.5224] [ 3543] [depth= 10] . ( 4 sec) [ -14928.1142] [ 3540] [depth= 1] . ( 4 sec) [ -14842.0776] [ 3532] [depth= 1] . ( 4 sec) [ -14534.2767] [ 3434] [depth= 5] . ( 4 sec) [ -14131.7388] [ 3358] [depth= 1] . ( 4 sec) [ -13951.0730] [ 3286] [depth= 4] . ( 4 sec) [ -13945.4249] [ 3284] [depth= 1] . ( 4 sec) [ -13753.9395] [ 3256] [depth= 4] . ( 4 sec) [ -12846.0037] [ 3264] [depth= 9] . ( 5 sec) [ -12717.3596] [ 3272] [depth= 1] . ( 5 sec) [ -12712.9387] [ 3234] [depth= 4] . ( 5 sec) [ -12709.1564] [ 3234] [depth= 1] . ( 5 sec) [ -12485.0668] [ 3090] [depth= 11] . ( 5 sec) [ -12337.9694] [ 3070] [depth= 6] . ( 5 sec) [ -12310.9978] [ 3078] [depth= 1] . ( 5 sec) [ -12169.3695] [ 3051] [depth= 1] . ( 5 sec) [ -11941.0502] [ 3122] [depth= 9] . ( 5 sec) [ -11914.0367] [ 3104] [depth= 1] . ( 5 sec) [ -11913.3445] [ 3104] [depth= 1] . ( 5 sec) [ -11786.0565] [ 3075] [depth= 2] . ( 6 sec) [ -11674.0299] [ 2930] [depth= 11] . ( 6 sec) [ -11650.0962] [ 2933] [depth= 2] . ( 6 sec) [ -11638.2183] [ 2928] [depth= 1] . ( 6 sec) [ -11273.7077] [ 2870] [depth= 6] . ( 6 sec) [ -11194.1231] [ 2789] [depth= 1] . ( 6 sec) [ -10939.0523] [ 2626] [depth= 5] . ( 6 sec) [ -10918.5591] [ 2634] [depth= 1] . ( 6 sec) [ -10911.9923] [ 2626] [depth= 1] . ( 6 sec) [ -10863.1403] [ 2625] [depth= 1] . ( 6 sec) [ -10858.6497] [ 2627] [depth= 1] . ( 6 sec) [ -10851.1805] [ 2539] [depth= 1] . ( 6 sec) [ -10813.7873] [ 2534] [depth= 9] . ( 6 sec) [ -10808.6809] [ 2535] [depth= 1] . ( 6 sec) [ -10621.2672] [ 2510] [depth= 1] . ( 7 sec) [ -10620.5516] [ 2507] [depth= 1] . ( 7 sec) [ -10488.0647] [ 2467] [depth= 1] . ( 7 sec) [ -10480.7076] [ 2474] [depth= 1] . ( 7 sec) [ -10473.8664] [ 2467] [depth= 1] . ( 7 sec) [ -10471.8123] [ 2466] [depth= 1] . ( 7 sec) [ -10469.2567] [ 2467] [depth= 1] . ( 7 sec) [ -10389.6185] [ 2402] [depth= 1] . ( 7 sec) [ -10377.3482] [ 2401] [depth= 1] . ( 7 sec) [ -10364.4667] [ 2400] [depth= 2] . ( 7 sec) [ -10118.8723] [ 2314] [depth= 4] . ( 7 sec) [ -10114.3395] [ 2325] [depth= 2] . ( 7 sec) [ -9965.2802] [ 2250] [depth= 6] . ( 7 sec) [ -9897.6763] [ 2175] [depth= 3] . ( 7 sec) [ -9818.9936] [ 2173] [depth= 1] . ( 7 sec) [ -9806.1647] [ 2189] [depth= 1] . ( 7 sec) [ -9759.5128] [ 2171] [depth= 2] . ( 7 sec) [ -9696.6185] [ 2163] [depth= 1] . ( 7 sec) [ -9683.9146] [ 2157] [depth= 2] . ( 7 sec) [ -9683.7760] [ 2157] [depth= 2] . ( 7 sec) [ -9660.9153] [ 2152] [depth= 4] . ( 8 sec) [ -9654.1476] [ 2150] [depth= 1] . ( 8 sec) [ -9516.5527] [Branch lengths ] . ( 9 sec) [ -9515.1423] [GTR parameters ] . ( 9 sec) [ -9475.2718] [Alpha ][ 0.953502] . ( 9 sec) [ -9472.2990] [ 2153] [depth= 1] . ( 10 sec) [ -9451.9751] [ 2105] [depth= 1] . ( 10 sec) [ -9403.9817] [ 2086] [depth= 3] . ( 10 sec) [ -9403.6602] [ 2086] [depth= 1] . ( 10 sec) [ -9403.6164] [ 2086] [depth= 1] . ( 10 sec) [ -9394.1890] [ 2082] [depth= 1] . ( 11 sec) [ -9393.2853] [ 2086] [depth= 3] . ( 11 sec) [ -9382.4424] [ 2082] [depth= 1] . ( 11 sec) [ -9381.5224] [ 2083] [depth= 1] . ( 11 sec) [ -9380.3097] [ 2083] [depth= 1] . ( 12 sec) [ -9376.5749] [ 2085] [depth= 1] . ( 12 sec) [ -9361.7468] [ 2079] [depth= 3] . ( 12 sec) [ -9360.6248] [ 2078] [depth= 1] . ( 13 sec) [ -9360.0845] [ 2079] [depth= 1] . ( 13 sec) [ -9359.5740] [ 2078] [depth= 1] . ( 13 sec) [ -9355.3375] [ 2070] [depth= 2] . ( 13 sec) [ -9351.4231] [ 2068] [depth= 1] . ( 14 sec) [ -9343.7190] [ 2067] [depth= 1] . ( 15 sec) [ -9342.9420] [ 2069] [depth= 1] . ( 16 sec) [ -9342.9290] [ 2069] [depth= 1] . ( 16 sec) [ -9342.4366] [ 2071] [depth= 1] . ( 16 sec) [ -9337.1619] [ 2071] [depth= 1] . ( 16 sec) [ -9336.3451] [ 2077] [depth= 2] . ( 17 sec) [ -9335.6914] [ 2080] [depth= 1] . ( 18 sec) [ -9313.0566] [Branch lengths ] . ( 19 sec) [ -9312.8546] [GTR parameters ] . ( 19 sec) [ -9311.6667] [Alpha ][ 1.071172] . ( 24 sec) [ -9311.2986] [ 2076] [depth= 2] . ( 24 sec) [ -9311.1931] [ 2075] [depth= 2] . ( 25 sec) [ -9310.9154] [ 2073] [depth= 1] . ( 25 sec) [ -9310.3191] [ 2075] [depth= 1] . ( 26 sec) [ -9307.4765] [Branch lengths ] . ( 27 sec) [ -9307.4648] [GTR parameters ] . ( 27 sec) [ -9307.4533] [Alpha ][ 1.083823] . ( 33 sec) [ -9307.2668] [Branch lengths ] . ( 37 sec) [ -9307.0311] [ 2083] [depth= 1] . ( 41 sec) [ -9306.8371] [ 2078] [depth= 1] . ( 57 sec) [ -9306.7409] [ 2076] [depth= 1] . ( 61 sec) [ -9306.4483] [Branch lengths ] . ( 61 sec) [ -9306.4418] [GTR parameters ] . ( 61 sec) [ -9306.4414] [Alpha ][ 1.086128] . ( 61 sec) [ -9306.4414] [Topology ] . ( 62 sec) [ -9306.4367] [Topology ] . ( 63 sec) [ -9306.4352] [Topology ] . ( 63 sec) [ -9306.4347] [Topology ] . ( 63 sec) [ -9306.4346] [GTR parameters ] . ( 64 sec) [ -9306.4346] [Alpha ][ 1.086128] . ( 64 sec) [ -9306.4346] [Topology ] . ( 64 sec) [ -9306.4344] [Topology ] . ( 65 sec) [ -9306.4344] [GTR parameters ] . ( 65 sec) [ -9306.4344] [Alpha ][ 1.086128] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -9306.4343] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9306.434256. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21304.5950] [GTR parameters ] . ( 1 sec) [ -20897.0175] [Alpha ][ 0.500960] . ( 1 sec) [ -20547.6784] [ 4850] [depth= 3] . ( 2 sec) [ -19967.4469] [ 4728] [depth= 3] . ( 2 sec) [ -19897.0790] [ 4713] [depth= 3] . ( 2 sec) [ -19797.7901] [ 4696] [depth= 9] . ( 2 sec) [ -19765.1956] [ 4678] [depth= 5] . ( 2 sec) [ -19487.3586] [ 4678] [depth= 5] . ( 2 sec) [ -19307.7713] [ 4655] [depth= 1] . ( 2 sec) [ -19181.1228] [ 4642] [depth= 4] . ( 2 sec) [ -19102.7859] [ 4576] [depth= 1] . ( 2 sec) [ -18963.6975] [ 4568] [depth= 2] . ( 2 sec) [ -18774.8847] [ 4551] [depth= 4] . ( 2 sec) [ -18663.3356] [ 4546] [depth= 10] . ( 2 sec) [ -18628.7167] [ 4519] [depth= 6] . ( 2 sec) [ -18576.4085] [ 4545] [depth= 5] . ( 3 sec) [ -18322.0037] [ 4483] [depth= 12] . ( 3 sec) [ -17685.9600] [ 4343] [depth= 13] . ( 3 sec) [ -17560.0680] [ 4333] [depth= 14] . ( 3 sec) [ -17521.8395] [ 4319] [depth= 2] . ( 3 sec) [ -17480.9786] [ 4310] [depth= 2] . ( 3 sec) [ -17305.4316] [ 4226] [depth= 6] . ( 3 sec) [ -16928.1544] [ 4113] [depth= 6] . ( 3 sec) [ -16847.6345] [ 4107] [depth= 2] . ( 3 sec) [ -16434.6770] [ 4023] [depth= 12] . ( 3 sec) [ -16183.8792] [ 3998] [depth= 5] . ( 3 sec) [ -15787.5191] [ 3874] [depth= 6] . ( 3 sec) [ -15738.6662] [ 3828] [depth= 1] . ( 4 sec) [ -15716.0340] [ 3814] [depth= 3] . ( 4 sec) [ -15685.4421] [ 3805] [depth= 10] . ( 4 sec) [ -15481.2976] [ 3736] [depth= 5] . ( 4 sec) [ -15347.7390] [ 3695] [depth= 3] . ( 4 sec) [ -15205.2509] [ 3647] [depth= 7] . ( 4 sec) [ -15203.1416] [ 3646] [depth= 1] . ( 4 sec) [ -14922.8502] [ 3564] [depth= 2] . ( 4 sec) [ -14901.3736] [ 3552] [depth= 1] . ( 4 sec) [ -14862.5809] [ 3550] [depth= 2] . ( 4 sec) [ -14571.5819] [ 3437] [depth= 8] . ( 4 sec) [ -14440.6449] [ 3408] [depth= 4] . ( 5 sec) [ -14217.7668] [ 3390] [depth= 7] . ( 5 sec) [ -13973.9189] [ 3296] [depth= 8] . ( 5 sec) [ -13973.1083] [ 3298] [depth= 1] . ( 5 sec) [ -13680.8067] [ 3192] [depth= 9] . ( 5 sec) [ -13643.3232] [ 3182] [depth= 1] . ( 5 sec) [ -13621.4022] [ 3150] [depth= 7] . ( 5 sec) [ -13454.4349] [ 3108] [depth= 8] . ( 5 sec) [ -13447.2130] [ 3079] [depth= 5] . ( 5 sec) [ -13306.9246] [ 3049] [depth= 7] . ( 5 sec) [ -13287.4296] [ 3034] [depth= 1] . ( 6 sec) [ -12941.0041] [ 3013] [depth= 1] . ( 6 sec) [ -12832.0866] [ 2973] [depth= 4] . ( 6 sec) [ -11831.9255] [ 2966] [depth= 4] . ( 6 sec) [ -11715.8817] [ 2866] [depth= 1] . ( 6 sec) [ -11250.0971] [ 2733] [depth= 4] . ( 6 sec) [ -11164.6782] [ 2723] [depth= 2] . ( 6 sec) [ -10937.8535] [ 2568] [depth= 5] . ( 6 sec) [ -10696.3383] [ 2538] [depth= 7] . ( 6 sec) [ -10655.5035] [ 2538] [depth= 1] . ( 6 sec) [ -10535.3935] [ 2474] [depth= 12] . ( 6 sec) [ -10502.9977] [ 2470] [depth= 1] . ( 6 sec) [ -10493.8224] [ 2473] [depth= 1] . ( 6 sec) [ -10463.3396] [ 2453] [depth= 1] . ( 7 sec) [ -10240.0911] [ 2365] [depth= 3] . ( 7 sec) [ -10215.2867] [ 2391] [depth= 2] . ( 7 sec) [ -10215.0923] [ 2391] [depth= 1] . ( 7 sec) [ -10205.6075] [ 2386] [depth= 1] . ( 7 sec) [ -10201.3365] [ 2383] [depth= 1] . ( 7 sec) [ -10118.4824] [ 2319] [depth= 2] . ( 7 sec) [ -10100.3027] [ 2315] [depth= 2] . ( 7 sec) [ -10054.3752] [ 2299] [depth= 11] . ( 8 sec) [ -9959.3284] [ 2258] [depth= 1] . ( 8 sec) [ -9772.4472] [ 2185] [depth= 9] . ( 8 sec) [ -9741.8913] [ 2178] [depth= 1] . ( 8 sec) [ -9736.1639] [ 2179] [depth= 1] . ( 8 sec) [ -9714.8738] [ 2167] [depth= 1] . ( 8 sec) [ -9700.8201] [ 2163] [depth= 5] . ( 8 sec) [ -9696.8510] [ 2153] [depth= 1] . ( 8 sec) [ -9649.0491] [ 2116] [depth= 3] . ( 8 sec) [ -9637.8206] [ 2115] [depth= 1] . ( 8 sec) [ -9630.5503] [ 2115] [depth= 1] . ( 9 sec) [ -9414.0931] [Branch lengths ] . ( 9 sec) [ -9412.6743] [GTR parameters ] . ( 10 sec) [ -9367.4540] [Alpha ][ 1.000014] . ( 10 sec) [ -9367.1534] [ 2120] [depth= 1] . ( 10 sec) [ -9364.6409] [ 2117] [depth= 1] . ( 11 sec) [ -9364.6184] [ 2115] [depth= 1] . ( 11 sec) [ -9364.5883] [ 2113] [depth= 1] . ( 11 sec) [ -9362.9738] [ 2115] [depth= 1] . ( 12 sec) [ -9362.2565] [ 2113] [depth= 2] . ( 12 sec) [ -9361.7430] [ 2112] [depth= 1] . ( 13 sec) [ -9354.8275] [ 2087] [depth= 1] . ( 13 sec) [ -9354.7697] [ 2087] [depth= 1] . ( 14 sec) [ -9346.2757] [ 2070] [depth= 2] . ( 14 sec) [ -9346.0593] [ 2071] [depth= 1] . ( 15 sec) [ -9345.8377] [ 2076] [depth= 2] . ( 15 sec) [ -9312.4227] [Branch lengths ] . ( 16 sec) [ -9312.2737] [GTR parameters ] . ( 16 sec) [ -9311.7396] [Alpha ][ 1.081269] . ( 16 sec) [ -9311.1426] [ 2074] [depth= 1] . ( 17 sec) [ -9311.0652] [ 2075] [depth= 1] . ( 19 sec) [ -9310.8911] [ 2077] [depth= 1] . ( 19 sec) [ -9309.5998] [ 2073] [depth= 1] . ( 21 sec) [ -9309.5258] [ 2071] [depth= 1] . ( 21 sec) [ -9307.0964] [Branch lengths ] . ( 22 sec) [ -9307.0886] [GTR parameters ] . ( 22 sec) [ -9307.0881] [Alpha ][ 1.083871] . ( 27 sec) [ -9306.9327] [Branch lengths ] . ( 52 sec) [ -9306.6326] [ 2078] [depth= 1] . ( 54 sec) [ -9306.4535] [Branch lengths ] . ( 55 sec) [ -9306.4486] [GTR parameters ] . ( 55 sec) [ -9306.4483] [Alpha ][ 1.085935] . ( 55 sec) [ -9306.4483] [Topology ] . ( 56 sec) [ -9306.4370] [Topology ] . ( 57 sec) [ -9306.4350] [Topology ] . ( 58 sec) [ -9306.4344] [Topology ] . ( 58 sec) [ -9306.4344] [GTR parameters ] . ( 58 sec) [ -9306.4344] [Alpha ][ 1.087021] . ( 58 sec) [ -9306.4344] [Topology ] . ( 59 sec) [ -9306.4342] [Topology ] . ( 60 sec) [ -9306.4342] [GTR parameters ] . ( 60 sec) [ -9306.4342] [Alpha ][ 1.087021] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9306.434185. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21839.7445] [GTR parameters ] . ( 0 sec) [ -21419.2414] [Alpha ][ 0.500960] . ( 0 sec) [ -21133.3315] [ 4817] [depth= 8] . ( 0 sec) [ -20487.9675] [ 4684] [depth= 8] . ( 0 sec) [ -20430.9569] [ 4672] [depth= 4] . ( 1 sec) [ -20265.6976] [ 4665] [depth= 2] . ( 1 sec) [ -19842.6890] [ 4578] [depth= 2] . ( 1 sec) [ -19678.7399] [ 4573] [depth= 6] . ( 1 sec) [ -19501.1443] [ 4509] [depth= 10] . ( 1 sec) [ -19111.3951] [ 4412] [depth= 9] . ( 1 sec) [ -18620.1394] [ 4411] [depth= 7] . ( 1 sec) [ -18479.7098] [ 4410] [depth= 8] . ( 1 sec) [ -18140.9597] [ 4276] [depth= 15] . ( 1 sec) [ -17784.4214] [ 4201] [depth= 5] . ( 1 sec) [ -17643.1089] [ 4179] [depth= 2] . ( 1 sec) [ -17572.4545] [ 4175] [depth= 12] . ( 1 sec) [ -17494.2559] [ 4092] [depth= 2] . ( 1 sec) [ -17307.9028] [ 4086] [depth= 1] . ( 1 sec) [ -17052.6155] [ 4035] [depth= 1] . ( 1 sec) [ -16951.1016] [ 4007] [depth= 11] . ( 1 sec) [ -16791.8545] [ 4001] [depth= 1] . ( 1 sec) [ -16351.8028] [ 3966] [depth= 8] . ( 1 sec) [ -15933.2556] [ 3791] [depth= 7] . ( 1 sec) [ -15666.0224] [ 3781] [depth= 7] . ( 1 sec) [ -15466.5190] [ 3757] [depth= 1] . ( 1 sec) [ -15338.5360] [ 3750] [depth= 7] . ( 1 sec) [ -15018.9890] [ 3671] [depth= 4] . ( 1 sec) [ -14821.0199] [ 3616] [depth= 8] . ( 2 sec) [ -14516.8352] [ 3437] [depth= 10] . ( 2 sec) [ -14222.0564] [ 3374] [depth= 2] . ( 2 sec) [ -13964.0672] [ 3295] [depth= 10] . ( 2 sec) [ -13925.5011] [ 3300] [depth= 11] . ( 2 sec) [ -13825.8996] [ 3287] [depth= 4] . ( 2 sec) [ -13541.3255] [ 3203] [depth= 10] . ( 2 sec) [ -13455.2530] [ 3160] [depth= 8] . ( 2 sec) [ -13068.7441] [ 3119] [depth= 4] . ( 2 sec) [ -13051.7791] [ 3125] [depth= 1] . ( 2 sec) [ -12973.9508] [ 3113] [depth= 1] . ( 2 sec) [ -12519.4700] [ 2995] [depth= 3] . ( 2 sec) [ -12452.8895] [ 2963] [depth= 1] . ( 2 sec) [ -12327.3845] [ 2943] [depth= 7] . ( 2 sec) [ -11990.0722] [ 2891] [depth= 1] . ( 2 sec) [ -11779.6077] [ 2816] [depth= 1] . ( 2 sec) [ -11655.5087] [ 2799] [depth= 5] . ( 2 sec) [ -11654.5560] [ 2801] [depth= 2] . ( 2 sec) [ -11610.6573] [ 2786] [depth= 2] . ( 3 sec) [ -11487.1754] [ 2714] [depth= 3] . ( 3 sec) [ -11469.5746] [ 2717] [depth= 2] . ( 3 sec) [ -11334.2752] [ 2668] [depth= 1] . ( 3 sec) [ -11302.6840] [ 2644] [depth= 3] . ( 3 sec) [ -11022.6152] [ 2538] [depth= 5] . ( 3 sec) [ -10885.3000] [ 2511] [depth= 1] . ( 3 sec) [ -10877.8572] [ 2509] [depth= 1] . ( 3 sec) [ -10854.7694] [ 2508] [depth= 1] . ( 3 sec) [ -10830.2956] [ 2486] [depth= 3] . ( 3 sec) [ -10774.2483] [ 2474] [depth= 7] . ( 3 sec) [ -10685.5185] [ 2409] [depth= 8] . ( 3 sec) [ -10683.4258] [ 2406] [depth= 2] . ( 3 sec) [ -10538.6098] [ 2411] [depth= 1] . ( 3 sec) [ -10533.4621] [ 2411] [depth= 1] . ( 3 sec) [ -10532.3540] [ 2414] [depth= 1] . ( 3 sec) [ -10352.0487] [ 2362] [depth= 5] . ( 3 sec) [ -10292.2783] [ 2366] [depth= 1] . ( 3 sec) [ -10212.5523] [ 2327] [depth= 1] . ( 3 sec) [ -10195.6442] [ 2327] [depth= 1] . ( 4 sec) [ -9840.3673] [ 2240] [depth= 4] . ( 4 sec) [ -9802.9111] [ 2242] [depth= 2] . ( 4 sec) [ -9783.0888] [ 2246] [depth= 1] . ( 4 sec) [ -9778.8838] [ 2236] [depth= 4] . ( 4 sec) [ -9772.2478] [ 2235] [depth= 1] . ( 4 sec) [ -9772.1928] [ 2233] [depth= 1] . ( 4 sec) [ -9764.5403] [ 2226] [depth= 3] . ( 4 sec) [ -9735.7545] [ 2218] [depth= 1] . ( 4 sec) [ -9735.2040] [ 2218] [depth= 1] . ( 4 sec) [ -9730.3733] [ 2223] [depth= 3] . ( 4 sec) [ -9552.7958] [ 2156] [depth= 6] . ( 4 sec) [ -9541.9541] [ 2158] [depth= 2] . ( 4 sec) [ -9537.1718] [ 2156] [depth= 2] . ( 4 sec) [ -9520.9266] [ 2147] [depth= 1] . ( 5 sec) [ -9416.8230] [Branch lengths ] . ( 5 sec) [ -9415.1561] [GTR parameters ] . ( 5 sec) [ -9372.0015] [Alpha ][ 0.976644] . ( 6 sec) [ -9371.7993] [ 2146] [depth= 1] . ( 6 sec) [ -9371.7838] [ 2146] [depth= 1] . ( 6 sec) [ -9371.7467] [ 2146] [depth= 1] . ( 6 sec) [ -9352.5575] [ 2107] [depth= 4] . ( 6 sec) [ -9352.5315] [ 2106] [depth= 1] . ( 6 sec) [ -9351.1589] [ 2109] [depth= 1] . ( 6 sec) [ -9350.9450] [ 2110] [depth= 1] . ( 6 sec) [ -9350.0520] [ 2112] [depth= 1] . ( 7 sec) [ -9348.2113] [ 2102] [depth= 2] . ( 7 sec) [ -9347.5093] [ 2104] [depth= 1] . ( 7 sec) [ -9337.0156] [ 2084] [depth= 2] . ( 8 sec) [ -9335.1038] [ 2082] [depth= 1] . ( 8 sec) [ -9334.7899] [ 2082] [depth= 1] . ( 8 sec) [ -9334.7033] [ 2082] [depth= 1] . ( 8 sec) [ -9333.2658] [ 2084] [depth= 1] . ( 10 sec) [ -9333.2556] [ 2084] [depth= 1] . ( 11 sec) [ -9324.3545] [Branch lengths ] . ( 12 sec) [ -9324.1358] [GTR parameters ] . ( 12 sec) [ -9323.4183] [Alpha ][ 1.068835] . ( 13 sec) [ -9323.3924] [ 2079] [depth= 1] . ( 14 sec) [ -9323.3142] [ 2077] [depth= 1] . ( 19 sec) [ -9314.6726] [Branch lengths ] . ( 19 sec) [ -9314.6639] [GTR parameters ] . ( 19 sec) [ -9314.6471] [Alpha ][ 1.084141] . ( 26 sec) [ -9307.4004] [Branch lengths ] . ( 55 sec) [ -9306.4485] [Branch lengths ] . ( 55 sec) [ -9306.4485] [Topology ] . ( 56 sec) [ -9306.4382] [Topology ] . ( 57 sec) [ -9306.4361] [Topology ] . ( 59 sec) [ -9306.4355] [Topology ] . ( 59 sec) [ -9306.4349] [GTR parameters ] . ( 59 sec) [ -9306.4345] [Alpha ][ 1.086549] . ( 60 sec) [ -9306.4345] [Topology ] . ( 61 sec) [ -9306.4342] [Topology ] . ( 61 sec) [ -9306.4342] [GTR parameters ] . ( 61 sec) [ -9306.4342] [Alpha ][ 1.086549] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9306.434211. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20695.3399] [GTR parameters ] . ( 1 sec) [ -20269.7251] [Alpha ][ 0.500960] . ( 1 sec) [ -19747.6706] [ 4734] [depth= 8] . ( 1 sec) [ -19061.4712] [ 4582] [depth= 9] . ( 1 sec) [ -18687.9405] [ 4521] [depth= 8] . ( 1 sec) [ -18641.6180] [ 4475] [depth= 1] . ( 1 sec) [ -18466.6190] [ 4416] [depth= 5] . ( 1 sec) [ -18407.0002] [ 4409] [depth= 2] . ( 1 sec) [ -17991.2741] [ 4404] [depth= 2] . ( 1 sec) [ -17856.8795] [ 4360] [depth= 3] . ( 1 sec) [ -17856.1647] [ 4356] [depth= 5] . ( 2 sec) [ -17790.6767] [ 4282] [depth= 3] . ( 2 sec) [ -17743.1100] [ 4277] [depth= 2] . ( 2 sec) [ -17560.7494] [ 4233] [depth= 2] . ( 2 sec) [ -17453.3103] [ 4220] [depth= 9] . ( 2 sec) [ -17385.7553] [ 4215] [depth= 2] . ( 2 sec) [ -17254.3725] [ 4153] [depth= 10] . ( 2 sec) [ -17132.2559] [ 4123] [depth= 3] . ( 2 sec) [ -17035.3859] [ 4075] [depth= 9] . ( 2 sec) [ -17002.0884] [ 4072] [depth= 2] . ( 2 sec) [ -16937.1656] [ 4041] [depth= 2] . ( 2 sec) [ -16766.2448] [ 3998] [depth= 10] . ( 2 sec) [ -16758.1889] [ 3994] [depth= 13] . ( 3 sec) [ -16702.0433] [ 3987] [depth= 5] . ( 3 sec) [ -16566.7679] [ 3943] [depth= 2] . ( 3 sec) [ -16443.1679] [ 3944] [depth= 3] . ( 3 sec) [ -16322.5216] [ 3882] [depth= 3] . ( 3 sec) [ -16133.5123] [ 3795] [depth= 5] . ( 3 sec) [ -15936.7298] [ 3755] [depth= 4] . ( 3 sec) [ -15595.0861] [ 3700] [depth= 14] . ( 3 sec) [ -15503.2131] [ 3655] [depth= 1] . ( 3 sec) [ -15039.1687] [ 3606] [depth= 16] . ( 3 sec) [ -14870.2173] [ 3530] [depth= 1] . ( 3 sec) [ -14848.4127] [ 3515] [depth= 1] . ( 4 sec) [ -14263.7438] [ 3398] [depth= 9] . ( 4 sec) [ -14131.0403] [ 3376] [depth= 1] . ( 4 sec) [ -14015.5119] [ 3368] [depth= 1] . ( 4 sec) [ -14013.5697] [ 3371] [depth= 1] . ( 4 sec) [ -13752.6239] [ 3289] [depth= 4] . ( 4 sec) [ -13752.4167] [ 3294] [depth= 1] . ( 5 sec) [ -13746.3236] [ 3297] [depth= 1] . ( 5 sec) [ -13639.5395] [ 3252] [depth= 4] . ( 5 sec) [ -13512.3474] [ 3237] [depth= 8] . ( 5 sec) [ -13461.2092] [ 3196] [depth= 9] . ( 5 sec) [ -13250.4313] [ 3194] [depth= 1] . ( 5 sec) [ -13111.8222] [ 3186] [depth= 1] . ( 5 sec) [ -13047.2923] [ 3041] [depth= 10] . ( 5 sec) [ -12249.7875] [ 2907] [depth= 5] . ( 5 sec) [ -12158.0157] [ 2909] [depth= 4] . ( 5 sec) [ -12125.2591] [ 2872] [depth= 1] . ( 5 sec) [ -12098.6720] [ 2857] [depth= 2] . ( 5 sec) [ -11996.5974] [ 2852] [depth= 2] . ( 6 sec) [ -11300.4972] [ 2850] [depth= 1] . ( 6 sec) [ -11264.5713] [ 2851] [depth= 2] . ( 6 sec) [ -11128.7528] [ 2686] [depth= 4] . ( 6 sec) [ -11087.8580] [ 2674] [depth= 4] . ( 6 sec) [ -11087.4288] [ 2678] [depth= 1] . ( 6 sec) [ -11015.5417] [ 2673] [depth= 1] . ( 6 sec) [ -11009.2123] [ 2675] [depth= 1] . ( 6 sec) [ -10804.5896] [ 2550] [depth= 4] . ( 6 sec) [ -10804.3241] [ 2550] [depth= 1] . ( 6 sec) [ -10791.0359] [ 2547] [depth= 2] . ( 7 sec) [ -10777.3631] [ 2546] [depth= 1] . ( 7 sec) [ -10725.5738] [ 2541] [depth= 8] . ( 7 sec) [ -10725.1908] [ 2540] [depth= 1] . ( 7 sec) [ -10725.0702] [ 2541] [depth= 1] . ( 7 sec) [ -10418.9566] [ 2395] [depth= 8] . ( 7 sec) [ -10409.9883] [ 2386] [depth= 1] . ( 8 sec) [ -10396.2179] [ 2390] [depth= 1] . ( 8 sec) [ -10336.5772] [ 2376] [depth= 3] . ( 8 sec) [ -10324.3045] [ 2370] [depth= 1] . ( 8 sec) [ -10265.2565] [ 2353] [depth= 1] . ( 8 sec) [ -10093.3182] [ 2309] [depth= 2] . ( 8 sec) [ -9999.9924] [ 2274] [depth= 1] . ( 8 sec) [ -9955.9153] [ 2239] [depth= 1] . ( 8 sec) [ -9950.8175] [ 2247] [depth= 1] . ( 8 sec) [ -9915.0676] [ 2250] [depth= 4] . ( 8 sec) [ -9795.4649] [ 2225] [depth= 2] . ( 8 sec) [ -9781.0266] [ 2193] [depth= 1] . ( 8 sec) [ -9757.1456] [ 2195] [depth= 1] . ( 9 sec) [ -9752.8254] [ 2194] [depth= 2] . ( 9 sec) [ -9751.5251] [ 2198] [depth= 1] . ( 9 sec) [ -9689.7676] [ 2156] [depth= 3] . ( 9 sec) [ -9462.2203] [Branch lengths ] . ( 10 sec) [ -9461.1065] [GTR parameters ] . ( 10 sec) [ -9422.0645] [Alpha ][ 0.938576] . ( 10 sec) [ -9418.1800] [ 2144] [depth= 1] . ( 11 sec) [ -9411.8216] [ 2140] [depth= 1] . ( 11 sec) [ -9406.6715] [ 2133] [depth= 1] . ( 11 sec) [ -9399.9138] [ 2104] [depth= 1] . ( 11 sec) [ -9391.5184] [ 2103] [depth= 1] . ( 11 sec) [ -9389.8084] [ 2104] [depth= 1] . ( 11 sec) [ -9388.0569] [ 2101] [depth= 1] . ( 12 sec) [ -9386.4859] [ 2103] [depth= 1] . ( 12 sec) [ -9384.7591] [ 2108] [depth= 2] . ( 12 sec) [ -9384.6477] [ 2110] [depth= 1] . ( 13 sec) [ -9384.2567] [ 2109] [depth= 1] . ( 13 sec) [ -9377.4967] [ 2103] [depth= 2] . ( 13 sec) [ -9377.4358] [ 2103] [depth= 1] . ( 13 sec) [ -9377.4125] [ 2103] [depth= 1] . ( 13 sec) [ -9376.6515] [ 2106] [depth= 1] . ( 14 sec) [ -9376.6315] [ 2106] [depth= 1] . ( 14 sec) [ -9371.7869] [ 2068] [depth= 7] . ( 14 sec) [ -9369.4939] [ 2074] [depth= 2] . ( 15 sec) [ -9367.8990] [ 2074] [depth= 1] . ( 15 sec) [ -9355.7880] [ 2069] [depth= 1] . ( 15 sec) [ -9347.7179] [ 2068] [depth= 1] . ( 15 sec) [ -9344.8653] [ 2069] [depth= 1] . ( 15 sec) [ -9344.7925] [ 2071] [depth= 1] . ( 15 sec) [ -9344.3651] [ 2068] [depth= 1] . ( 16 sec) [ -9315.3364] [Branch lengths ] . ( 16 sec) [ -9315.1993] [GTR parameters ] . ( 17 sec) [ -9313.7536] [Alpha ][ 1.065610] . ( 17 sec) [ -9313.6559] [ 2071] [depth= 1] . ( 17 sec) [ -9313.4061] [ 2068] [depth= 1] . ( 18 sec) [ -9312.7473] [ 2072] [depth= 1] . ( 18 sec) [ -9312.0467] [ 2074] [depth= 1] . ( 21 sec) [ -9311.5807] [ 2070] [depth= 2] . ( 22 sec) [ -9311.4205] [ 2075] [depth= 1] . ( 23 sec) [ -9307.5311] [Branch lengths ] . ( 24 sec) [ -9307.5275] [GTR parameters ] . ( 24 sec) [ -9307.5010] [Alpha ][ 1.084832] . ( 24 sec) [ -9307.4809] [ 2070] [depth= 1] . ( 30 sec) [ -9307.0359] [Branch lengths ] . ( 30 sec) [ -9307.0348] [GTR parameters ] . ( 30 sec) [ -9307.0342] [Alpha ][ 1.087476] . ( 47 sec) [ -9306.8382] [ 2078] [depth= 3] . ( 55 sec) [ -9306.4655] [Branch lengths ] . ( 55 sec) [ -9306.4621] [GTR parameters ] . ( 55 sec) [ -9306.4621] [Alpha ][ 1.087476] . ( 55 sec) [ -9306.4621] [Topology ] . ( 56 sec) [ -9306.4451] [Topology ] . ( 57 sec) [ -9306.4394] [Topology ] . ( 58 sec) [ -9306.4369] [Topology ] . ( 59 sec) [ -9306.4356] [Topology ] . ( 59 sec) [ -9306.4349] [Topology ] . ( 59 sec) [ -9306.4349] [GTR parameters ] . ( 60 sec) [ -9306.4349] [Alpha ][ 1.086388] . ( 60 sec) [ -9306.4349] [Topology ] . ( 60 sec) [ -9306.4345] [Topology ] . ( 60 sec) [ -9306.4345] [GTR parameters ] . ( 61 sec) [ -9306.4345] [Alpha ][ 1.086388] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9306.434499. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21757.7741] [GTR parameters ] . ( 1 sec) [ -21329.9403] [Alpha ][ 0.500960] . ( 1 sec) [ -20947.9643] [ 4847] [depth= 6] . ( 1 sec) [ -20566.6165] [ 4711] [depth= 11] . ( 1 sec) [ -20039.5583] [ 4689] [depth= 6] . ( 1 sec) [ -19925.2950] [ 4683] [depth= 1] . ( 1 sec) [ -19819.3813] [ 4540] [depth= 10] . ( 1 sec) [ -19793.8186] [ 4536] [depth= 2] . ( 1 sec) [ -19671.7027] [ 4511] [depth= 6] . ( 1 sec) [ -19651.2662] [ 4510] [depth= 10] . ( 1 sec) [ -19440.1530] [ 4448] [depth= 10] . ( 1 sec) [ -19284.0383] [ 4386] [depth= 5] . ( 1 sec) [ -18744.7037] [ 4211] [depth= 22] . ( 1 sec) [ -18304.8555] [ 4125] [depth= 3] . ( 1 sec) [ -18199.0847] [ 4117] [depth= 6] . ( 1 sec) [ -17861.9371] [ 4121] [depth= 1] . ( 1 sec) [ -17549.5687] [ 4098] [depth= 12] . ( 1 sec) [ -17534.7661] [ 4069] [depth= 11] . ( 2 sec) [ -17460.1374] [ 4068] [depth= 2] . ( 2 sec) [ -17346.3053] [ 3996] [depth= 1] . ( 2 sec) [ -17158.7290] [ 3991] [depth= 3] . ( 2 sec) [ -17069.3293] [ 3908] [depth= 3] . ( 2 sec) [ -16661.3090] [ 3908] [depth= 1] . ( 2 sec) [ -16601.3764] [ 3904] [depth= 2] . ( 2 sec) [ -16511.0562] [ 3864] [depth= 4] . ( 2 sec) [ -16239.1061] [ 3921] [depth= 7] . ( 2 sec) [ -16027.8722] [ 3832] [depth= 3] . ( 2 sec) [ -15765.4160] [ 3704] [depth= 7] . ( 2 sec) [ -15661.4873] [ 3692] [depth= 1] . ( 2 sec) [ -15478.6592] [ 3625] [depth= 11] . ( 2 sec) [ -15447.6764] [ 3626] [depth= 1] . ( 2 sec) [ -15160.2050] [ 3560] [depth= 1] . ( 2 sec) [ -14491.8080] [ 3428] [depth= 8] . ( 2 sec) [ -14163.4036] [ 3293] [depth= 8] . ( 2 sec) [ -13873.8808] [ 3307] [depth= 11] . ( 2 sec) [ -13837.1995] [ 3261] [depth= 12] . ( 2 sec) [ -13827.3965] [ 3252] [depth= 11] . ( 2 sec) [ -13358.6501] [ 3169] [depth= 6] . ( 2 sec) [ -13099.8464] [ 3161] [depth= 6] . ( 2 sec) [ -12773.2404] [ 3111] [depth= 3] . ( 3 sec) [ -12748.5947] [ 3102] [depth= 1] . ( 3 sec) [ -12688.1979] [ 3106] [depth= 1] . ( 3 sec) [ -12626.4485] [ 3107] [depth= 6] . ( 3 sec) [ -12595.1269] [ 3082] [depth= 2] . ( 3 sec) [ -12585.4338] [ 3055] [depth= 1] . ( 3 sec) [ -12407.7258] [ 2969] [depth= 9] . ( 3 sec) [ -12182.1887] [ 2918] [depth= 9] . ( 3 sec) [ -11871.1945] [ 2836] [depth= 7] . ( 3 sec) [ -11859.9023] [ 2780] [depth= 5] . ( 3 sec) [ -11842.7272] [ 2833] [depth= 1] . ( 3 sec) [ -11834.9668] [ 2809] [depth= 2] . ( 3 sec) [ -11710.9389] [ 2775] [depth= 7] . ( 3 sec) [ -11681.0101] [ 2760] [depth= 4] . ( 3 sec) [ -11504.7678] [ 2731] [depth= 2] . ( 3 sec) [ -11191.4276] [ 2693] [depth= 1] . ( 3 sec) [ -11189.7921] [ 2690] [depth= 1] . ( 3 sec) [ -10930.5229] [ 2601] [depth= 3] . ( 3 sec) [ -10744.2130] [ 2522] [depth= 5] . ( 3 sec) [ -10626.8478] [ 2432] [depth= 1] . ( 3 sec) [ -10533.8212] [ 2397] [depth= 6] . ( 4 sec) [ -10520.1895] [ 2388] [depth= 1] . ( 4 sec) [ -10516.9692] [ 2370] [depth= 5] . ( 4 sec) [ -10500.9404] [ 2370] [depth= 1] . ( 4 sec) [ -10500.6952] [ 2370] [depth= 1] . ( 4 sec) [ -10455.2964] [ 2371] [depth= 1] . ( 4 sec) [ -10446.3069] [ 2370] [depth= 1] . ( 4 sec) [ -10328.0245] [ 2428] [depth= 5] . ( 4 sec) [ -10153.6672] [ 2352] [depth= 3] . ( 4 sec) [ -10071.9251] [ 2338] [depth= 1] . ( 4 sec) [ -10046.2850] [ 2336] [depth= 2] . ( 4 sec) [ -10026.3747] [ 2292] [depth= 3] . ( 4 sec) [ -10025.2437] [ 2292] [depth= 1] . ( 4 sec) [ -10024.5838] [ 2290] [depth= 1] . ( 4 sec) [ -10023.1342] [ 2298] [depth= 1] . ( 4 sec) [ -10020.6401] [ 2295] [depth= 1] . ( 4 sec) [ -10020.5484] [ 2277] [depth= 1] . ( 4 sec) [ -10006.7162] [ 2271] [depth= 1] . ( 4 sec) [ -9996.1144] [ 2263] [depth= 1] . ( 4 sec) [ -9821.4533] [ 2196] [depth= 5] . ( 5 sec) [ -9804.4167] [ 2191] [depth= 1] . ( 5 sec) [ -9771.4282] [ 2193] [depth= 5] . ( 5 sec) [ -9771.3544] [ 2193] [depth= 2] . ( 5 sec) [ -9761.8371] [ 2188] [depth= 1] . ( 5 sec) [ -9650.0634] [ 2144] [depth= 2] . ( 5 sec) [ -9604.3063] [ 2144] [depth= 1] . ( 5 sec) [ -9459.9593] [Branch lengths ] . ( 6 sec) [ -9457.5880] [GTR parameters ] . ( 6 sec) [ -9417.2435] [Alpha ][ 0.958351] . ( 6 sec) [ -9406.7973] [ 2141] [depth= 5] . ( 6 sec) [ -9406.0734] [ 2117] [depth= 3] . ( 6 sec) [ -9405.9864] [ 2116] [depth= 3] . ( 6 sec) [ -9405.9513] [ 2116] [depth= 1] . ( 6 sec) [ -9404.7031] [ 2114] [depth= 1] . ( 6 sec) [ -9385.1653] [ 2080] [depth= 1] . ( 6 sec) [ -9384.1865] [ 2078] [depth= 2] . ( 7 sec) [ -9367.8303] [ 2070] [depth= 1] . ( 7 sec) [ -9366.3572] [ 2068] [depth= 2] . ( 7 sec) [ -9366.1920] [ 2072] [depth= 1] . ( 7 sec) [ -9363.0681] [ 2070] [depth= 2] . ( 7 sec) [ -9345.7948] [ 2073] [depth= 1] . ( 7 sec) [ -9345.7313] [ 2075] [depth= 1] . ( 7 sec) [ -9345.6291] [ 2076] [depth= 1] . ( 7 sec) [ -9344.1053] [ 2075] [depth= 1] . ( 7 sec) [ -9344.0926] [ 2075] [depth= 1] . ( 7 sec) [ -9343.9222] [ 2074] [depth= 1] . ( 7 sec) [ -9334.0665] [ 2072] [depth= 1] . ( 8 sec) [ -9331.7470] [ 2071] [depth= 1] . ( 8 sec) [ -9329.3662] [ 2072] [depth= 1] . ( 8 sec) [ -9329.1282] [ 2075] [depth= 1] . ( 8 sec) [ -9327.6054] [ 2071] [depth= 3] . ( 9 sec) [ -9327.3990] [ 2073] [depth= 1] . ( 9 sec) [ -9325.8157] [ 2075] [depth= 3] . ( 9 sec) [ -9325.0079] [ 2071] [depth= 1] . ( 9 sec) [ -9324.1447] [ 2073] [depth= 1] . ( 10 sec) [ -9312.0283] [Branch lengths ] . ( 11 sec) [ -9311.5656] [GTR parameters ] . ( 11 sec) [ -9310.5918] [Alpha ][ 1.064904] . ( 11 sec) [ -9309.7450] [ 2073] [depth= 1] . ( 12 sec) [ -9309.5951] [ 2072] [depth= 1] . ( 12 sec) [ -9309.0002] [ 2075] [depth= 1] . ( 16 sec) [ -9307.5513] [Branch lengths ] . ( 16 sec) [ -9307.5414] [GTR parameters ] . ( 16 sec) [ -9307.5238] [Alpha ][ 1.080527] . ( 22 sec) [ -9307.3348] [Branch lengths ] . ( 23 sec) [ -9307.0098] [ 2083] [depth= 1] . ( 26 sec) [ -9306.7500] [ 2079] [depth= 1] . ( 46 sec) [ -9306.5565] [Branch lengths ] . ( 46 sec) [ -9306.5488] [GTR parameters ] . ( 46 sec) [ -9306.5477] [Alpha ][ 1.084420] . ( 46 sec) [ -9306.5477] [Topology ] . ( 47 sec) [ -9306.5403] [Topology ] . ( 47 sec) [ -9306.5383] [Topology ] . ( 48 sec) [ -9306.5373] [Topology ] . ( 48 sec) [ -9306.5373] [GTR parameters ] . ( 48 sec) [ -9306.5373] [Alpha ][ 1.084420] . ( 48 sec) [ -9306.5373] [Topology ] . ( 49 sec) [ -9306.5368] [Topology ] . ( 49 sec) [ -9306.5368] [GTR parameters ] . ( 49 sec) [ -9306.5368] [Alpha ][ 1.085505] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -9306.4526] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9306.452613. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9376.938197 . ( 1 sec) [ -9375.7050] [GTR parameters ] . ( 1 sec) [ -9374.9931] [Alpha ][ 1.100032] . ( 1 sec) [ -9374.9931] [Topology ] . ( 2 sec) [ -9323.1811] [Topology ] . ( 3 sec) [ -9311.1208] [Topology ] . ( 3 sec) [ -9308.4117] [Topology ] . ( 4 sec) [ -9307.4202] [Topology ] . ( 5 sec) [ -9306.9793] [Topology ] . ( 6 sec) [ -9306.7594] [Topology ] . ( 7 sec) [ -9306.6429] [Topology ] . ( 7 sec) [ -9306.5784] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9306.578440 . ( 15 sec) [ -9306.5318] [GTR parameters ] . ( 15 sec) [ -9306.5244] [Alpha ][ 1.089431] . ( 15 sec) [ -9306.5244] [Topology ] . ( 16 sec) [ -9306.4867] [Topology ] . ( 17 sec) [ -9306.4652] [Topology ] . ( 17 sec) [ -9306.4527] [Topology ] . ( 18 sec) [ -9306.4453] [Topology ] . ( 19 sec) [ -9306.4408] [Topology ] . ( 20 sec) [ -9306.4381] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -9306.4353] [Topology ] . Before opt ts/t=1.000000 LK=-9306.435340 . ( 27 sec) [ -9306.4353] [GTR parameters ] . ( 27 sec) [ -9306.4352] [Alpha ][ 1.087965] . ( 27 sec) [ -9306.4352] [Topology ] . ( 28 sec) [ -9306.4345] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 41 sec) [ -9375.7050] [GTR parameters ] . ( 41 sec) [ -9374.9931] [Alpha ][ 1.100032] . ( 42 sec) [ -9372.9122] [ 2070] [depth= 1] . ( 42 sec) [ -9372.4222] [ 2065] [depth= 1] . ( 42 sec) [ -9371.4415] [ 2066] [depth= 1] . ( 42 sec) [ -9369.5389] [ 2071] [depth= 1] . ( 43 sec) [ -9354.6843] [ 2068] [depth= 2] . ( 43 sec) [ -9351.5360] [ 2070] [depth= 2] . ( 43 sec) [ -9351.5043] [ 2067] [depth= 1] . ( 43 sec) [ -9351.0220] [ 2071] [depth= 1] . ( 43 sec) [ -9350.9645] [ 2070] [depth= 1] . ( 43 sec) [ -9349.9678] [ 2070] [depth= 1] . ( 43 sec) [ -9349.7910] [ 2070] [depth= 1] . ( 44 sec) [ -9349.2850] [ 2078] [depth= 1] . ( 44 sec) [ -9348.5086] [ 2075] [depth= 2] . ( 44 sec) [ -9347.1889] [ 2074] [depth= 1] . ( 44 sec) [ -9346.6661] [ 2077] [depth= 2] . ( 44 sec) [ -9346.0125] [ 2078] [depth= 1] . ( 45 sec) [ -9344.4429] [ 2079] [depth= 1] . ( 45 sec) [ -9344.3534] [ 2078] [depth= 1] . ( 45 sec) [ -9312.8308] [Branch lengths ] . ( 46 sec) [ -9312.7562] [GTR parameters ] . ( 46 sec) [ -9312.7544] [Alpha ][ 1.094700] . ( 46 sec) [ -9312.4864] [ 2079] [depth= 1] . ( 47 sec) [ -9312.4599] [ 2083] [depth= 1] . ( 47 sec) [ -9310.9360] [ 2083] [depth= 1] . ( 48 sec) [ -9309.8602] [ 2082] [depth= 2] . ( 51 sec) [ -9306.9829] [Branch lengths ] . ( 51 sec) [ -9306.9694] [GTR parameters ] . ( 51 sec) [ -9306.9663] [Alpha ][ 1.087741] . ( 56 sec) [ -9306.8305] [Branch lengths ] . ( 62 sec) [ -9306.5693] [ 2077] [depth= 1] . ( 80 sec) [ -9306.4422] [Branch lengths ] . ( 80 sec) [ -9306.4403] [GTR parameters ] . ( 80 sec) [ -9306.4403] [Alpha ][ 1.086654] . ( 80 sec) [ -9306.4403] [Topology ] . ( 81 sec) [ -9306.4355] [Topology ] . ( 82 sec) [ -9306.4347] [Topology ] . ( 82 sec) [ -9306.4347] [GTR parameters ] . ( 82 sec) [ -9306.4347] [Alpha ][ 1.086654] . ( 82 sec) [ -9306.4347] [Topology ] . ( 83 sec) [ -9306.4344] [Topology ] . ( 83 sec) [ -9306.4344] [GTR parameters ] . ( 83 sec) [ -9306.4344] [Alpha ][ 1.086654] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9306.434540 . Log likelihood obtained after SPR moves : -9306.434387 . Log likelihood of the current tree: -9306.434387. . Printing the most likely tree in file 'data96.phy_phyml_tree.txt'... . Best log likelihood : -9306.434185 . Time used 0h1m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo