.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data80.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... . 409 patterns found. (out of a total of 500 sites) . 90 sites without polymorphism (18.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19836.5409] [GTR parameters ] . ( 1 sec) [ -19386.6497] [Alpha ][ 0.500960] . ( 1 sec) [ -19194.2147] [ 4562] [depth= 8] . ( 1 sec) [ -18842.3970] [ 4553] [depth= 6] . ( 2 sec) [ -18437.6987] [ 4527] [depth= 6] . ( 2 sec) [ -18434.3470] [ 4506] [depth= 3] . ( 2 sec) [ -18288.2909] [ 4413] [depth= 7] . ( 2 sec) [ -18251.2758] [ 4404] [depth= 8] . ( 2 sec) [ -18142.3948] [ 4365] [depth= 5] . ( 2 sec) [ -18101.8068] [ 4379] [depth= 3] . ( 2 sec) [ -17785.2299] [ 4276] [depth= 5] . ( 2 sec) [ -17700.2594] [ 4262] [depth= 4] . ( 2 sec) [ -17618.0242] [ 4207] [depth= 1] . ( 2 sec) [ -17519.7432] [ 4245] [depth= 12] . ( 3 sec) [ -17438.1384] [ 4210] [depth= 7] . ( 3 sec) [ -17418.6943] [ 4206] [depth= 3] . ( 3 sec) [ -17268.6087] [ 4202] [depth= 1] . ( 3 sec) [ -17158.4343] [ 4123] [depth= 2] . ( 3 sec) [ -17113.1632] [ 4114] [depth= 3] . ( 3 sec) [ -16825.0035] [ 4108] [depth= 2] . ( 3 sec) [ -16744.5102] [ 4079] [depth= 1] . ( 3 sec) [ -16529.4916] [ 4016] [depth= 8] . ( 3 sec) [ -16521.8409] [ 4016] [depth= 1] . ( 3 sec) [ -16434.2912] [ 3955] [depth= 9] . ( 3 sec) [ -16151.8012] [ 3876] [depth= 1] . ( 4 sec) [ -15957.7344] [ 3837] [depth= 13] . ( 4 sec) [ -15889.2416] [ 3797] [depth= 7] . ( 4 sec) [ -15664.0169] [ 3723] [depth= 11] . ( 4 sec) [ -15520.1224] [ 3713] [depth= 2] . ( 4 sec) [ -15254.5750] [ 3672] [depth= 5] . ( 4 sec) [ -15159.6085] [ 3666] [depth= 1] . ( 4 sec) [ -14741.5688] [ 3662] [depth= 9] . ( 4 sec) [ -14649.7313] [ 3618] [depth= 4] . ( 4 sec) [ -14634.1594] [ 3609] [depth= 3] . ( 4 sec) [ -14556.2884] [ 3625] [depth= 14] . ( 4 sec) [ -14496.3999] [ 3624] [depth= 1] . ( 4 sec) [ -14231.1703] [ 3474] [depth= 11] . ( 4 sec) [ -14049.9501] [ 3384] [depth= 12] . ( 4 sec) [ -14031.3891] [ 3385] [depth= 1] . ( 4 sec) [ -13804.9740] [ 3291] [depth= 3] . ( 4 sec) [ -13790.7101] [ 3288] [depth= 2] . ( 5 sec) [ -13602.6242] [ 3251] [depth= 3] . ( 5 sec) [ -13501.8220] [ 3239] [depth= 5] . ( 5 sec) [ -13458.9626] [ 3249] [depth= 1] . ( 5 sec) [ -13359.5564] [ 3237] [depth= 14] . ( 5 sec) [ -12761.9898] [ 3167] [depth= 7] . ( 5 sec) [ -12739.8423] [ 3087] [depth= 3] . ( 5 sec) [ -12723.1518] [ 3071] [depth= 6] . ( 5 sec) [ -12696.1561] [ 3021] [depth= 3] . ( 5 sec) [ -12469.3075] [ 2936] [depth= 6] . ( 5 sec) [ -12363.3508] [ 2900] [depth= 1] . ( 5 sec) [ -12295.7761] [ 2882] [depth= 6] . ( 5 sec) [ -12116.4679] [ 2850] [depth= 7] . ( 6 sec) [ -11946.9024] [ 2839] [depth= 3] . ( 6 sec) [ -11605.5903] [ 2747] [depth= 6] . ( 6 sec) [ -11519.6794] [ 2684] [depth= 1] . ( 6 sec) [ -11402.5251] [ 2627] [depth= 9] . ( 6 sec) [ -11319.1602] [ 2627] [depth= 6] . ( 6 sec) [ -11317.4890] [ 2623] [depth= 1] . ( 6 sec) [ -11284.3076] [ 2620] [depth= 1] . ( 6 sec) [ -11197.5736] [ 2606] [depth= 5] . ( 6 sec) [ -11123.2823] [ 2597] [depth= 5] . ( 6 sec) [ -11014.9253] [ 2526] [depth= 1] . ( 6 sec) [ -10991.8215] [ 2506] [depth= 2] . ( 6 sec) [ -10990.9149] [ 2512] [depth= 1] . ( 6 sec) [ -10961.2439] [ 2499] [depth= 1] . ( 6 sec) [ -10893.1378] [ 2496] [depth= 2] . ( 6 sec) [ -10889.8078] [ 2500] [depth= 1] . ( 6 sec) [ -10861.4028] [ 2509] [depth= 1] . ( 6 sec) [ -10793.2875] [ 2500] [depth= 1] . ( 6 sec) [ -10786.4081] [ 2501] [depth= 5] . ( 7 sec) [ -10618.7724] [ 2499] [depth= 4] . ( 7 sec) [ -10610.7630] [ 2498] [depth= 2] . ( 7 sec) [ -10606.0776] [ 2365] [depth= 7] . ( 7 sec) [ -10551.2639] [ 2348] [depth= 1] . ( 7 sec) [ -10137.0907] [ 2251] [depth= 7] . ( 7 sec) [ -9900.5956] [ 2272] [depth= 1] . ( 7 sec) [ -9898.2557] [ 2280] [depth= 1] . ( 7 sec) [ -9876.0758] [ 2271] [depth= 1] . ( 7 sec) [ -9712.0582] [Branch lengths ] . ( 8 sec) [ -9710.0226] [GTR parameters ] . ( 8 sec) [ -9689.4062] [Alpha ][ 0.780803] . ( 8 sec) [ -9620.9919] [ 2224] [depth= 6] . ( 8 sec) [ -9570.8445] [ 2199] [depth= 2] . ( 8 sec) [ -9569.4334] [ 2203] [depth= 2] . ( 8 sec) [ -9490.0019] [ 2146] [depth= 3] . ( 8 sec) [ -9488.7077] [ 2141] [depth= 2] . ( 8 sec) [ -9486.5062] [ 2142] [depth= 1] . ( 8 sec) [ -9485.6594] [ 2140] [depth= 1] . ( 8 sec) [ -9477.4525] [ 2113] [depth= 1] . ( 8 sec) [ -9472.3568] [ 2092] [depth= 1] . ( 9 sec) [ -9465.1653] [ 2090] [depth= 1] . ( 9 sec) [ -9442.9779] [ 2077] [depth= 1] . ( 9 sec) [ -9440.0654] [ 2080] [depth= 1] . ( 9 sec) [ -9432.0938] [ 2081] [depth= 1] . ( 9 sec) [ -9429.5852] [ 2075] [depth= 1] . ( 9 sec) [ -9429.5512] [ 2078] [depth= 1] . ( 9 sec) [ -9425.3489] [ 2075] [depth= 1] . ( 9 sec) [ -9406.6361] [ 2060] [depth= 2] . ( 9 sec) [ -9400.7677] [ 2057] [depth= 1] . ( 9 sec) [ -9390.3621] [ 2054] [depth= 1] . ( 10 sec) [ -9389.7397] [ 2057] [depth= 1] . ( 10 sec) [ -9382.7567] [ 2042] [depth= 2] . ( 10 sec) [ -9381.7399] [ 2046] [depth= 1] . ( 10 sec) [ -9381.3064] [ 2045] [depth= 1] . ( 11 sec) [ -9379.7880] [ 2043] [depth= 1] . ( 11 sec) [ -9353.7150] [Branch lengths ] . ( 12 sec) [ -9352.9793] [GTR parameters ] . ( 12 sec) [ -9351.0073] [Alpha ][ 0.905345] . ( 15 sec) [ -9349.6542] [Branch lengths ] . ( 41 sec) [ -9349.5020] [Branch lengths ] . ( 41 sec) [ -9349.5020] [Topology ] . ( 42 sec) [ -9349.4919] [Topology ] . ( 43 sec) [ -9349.4886] [Topology ] . ( 44 sec) [ -9349.4870] [Topology ] . ( 44 sec) [ -9349.4861] [Topology ] . ( 45 sec) [ -9349.4853] [GTR parameters ] . ( 45 sec) [ -9349.4697] [Alpha ][ 0.917596] . ( 45 sec) [ -9349.4697] [Topology ] . ( 45 sec) [ -9349.4684] [Topology ] . ( 46 sec) [ -9349.4679] [Topology ] . ( 46 sec) [ -9349.4679] [GTR parameters ] . ( 46 sec) [ -9349.4679] [Alpha ][ 0.917596] . ( 46 sec) [ -9349.4679] [Topology ] . ( 47 sec) [ -9349.4677] [Topology ] . ( 47 sec) [ -9349.4677] [GTR parameters ] . ( 47 sec) [ -9349.4677] [Alpha ][ 0.918514] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -9348.4780] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -9348.4776] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.477573. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19975.1184] [GTR parameters ] . ( 1 sec) [ -19572.8367] [Alpha ][ 0.500960] . ( 1 sec) [ -19257.0639] [ 4503] [depth= 3] . ( 1 sec) [ -19032.9186] [ 4465] [depth= 3] . ( 2 sec) [ -18802.9431] [ 4443] [depth= 4] . ( 2 sec) [ -18733.6563] [ 4436] [depth= 6] . ( 2 sec) [ -18522.8846] [ 4395] [depth= 2] . ( 2 sec) [ -18384.0551] [ 4379] [depth= 4] . ( 2 sec) [ -18281.6564] [ 4376] [depth= 1] . ( 2 sec) [ -18200.9683] [ 4357] [depth= 4] . ( 2 sec) [ -17943.0492] [ 4267] [depth= 2] . ( 2 sec) [ -17929.9980] [ 4258] [depth= 1] . ( 2 sec) [ -17841.7245] [ 4220] [depth= 4] . ( 2 sec) [ -17742.5307] [ 4208] [depth= 1] . ( 2 sec) [ -17350.6265] [ 4075] [depth= 8] . ( 2 sec) [ -17277.6547] [ 4090] [depth= 1] . ( 2 sec) [ -17229.4728] [ 4091] [depth= 12] . ( 2 sec) [ -17066.2125] [ 4043] [depth= 2] . ( 2 sec) [ -17026.2322] [ 3997] [depth= 9] . ( 2 sec) [ -16780.2657] [ 3923] [depth= 2] . ( 2 sec) [ -16507.8091] [ 3911] [depth= 1] . ( 3 sec) [ -16078.7549] [ 3867] [depth= 10] . ( 3 sec) [ -16003.3970] [ 3822] [depth= 1] . ( 3 sec) [ -15827.0617] [ 3761] [depth= 9] . ( 3 sec) [ -15822.2455] [ 3785] [depth= 1] . ( 3 sec) [ -15597.7904] [ 3704] [depth= 4] . ( 3 sec) [ -15570.3542] [ 3692] [depth= 12] . ( 3 sec) [ -15432.4719] [ 3678] [depth= 2] . ( 3 sec) [ -15217.4883] [ 3669] [depth= 15] . ( 3 sec) [ -15018.8882] [ 3584] [depth= 2] . ( 3 sec) [ -14738.5242] [ 3477] [depth= 9] . ( 3 sec) [ -14400.7758] [ 3408] [depth= 4] . ( 3 sec) [ -14116.7900] [ 3343] [depth= 4] . ( 3 sec) [ -13967.7431] [ 3344] [depth= 2] . ( 4 sec) [ -13694.0315] [ 3240] [depth= 6] . ( 4 sec) [ -13685.9429] [ 3210] [depth= 1] . ( 4 sec) [ -13563.9363] [ 3172] [depth= 2] . ( 4 sec) [ -13357.4144] [ 3104] [depth= 1] . ( 4 sec) [ -13209.9456] [ 3072] [depth= 8] . ( 4 sec) [ -13194.6550] [ 3078] [depth= 1] . ( 4 sec) [ -12906.7499] [ 2949] [depth= 11] . ( 4 sec) [ -12878.7639] [ 2945] [depth= 1] . ( 4 sec) [ -12679.9387] [ 2943] [depth= 2] . ( 4 sec) [ -12548.9758] [ 2902] [depth= 15] . ( 4 sec) [ -12477.3797] [ 2897] [depth= 1] . ( 4 sec) [ -12475.1183] [ 2899] [depth= 1] . ( 4 sec) [ -12340.4000] [ 2833] [depth= 7] . ( 5 sec) [ -12335.4589] [ 2851] [depth= 1] . ( 5 sec) [ -12267.1074] [ 2832] [depth= 1] . ( 5 sec) [ -12238.8822] [ 2812] [depth= 1] . ( 5 sec) [ -12207.7312] [ 2796] [depth= 6] . ( 5 sec) [ -11761.9060] [ 2688] [depth= 5] . ( 5 sec) [ -11722.9804] [ 2691] [depth= 2] . ( 5 sec) [ -11703.4781] [ 2674] [depth= 1] . ( 5 sec) [ -11497.0850] [ 2626] [depth= 3] . ( 5 sec) [ -11489.7014] [ 2608] [depth= 2] . ( 5 sec) [ -11445.9561] [ 2586] [depth= 1] . ( 5 sec) [ -11353.7802] [ 2593] [depth= 8] . ( 5 sec) [ -11281.8705] [ 2564] [depth= 5] . ( 6 sec) [ -11226.0696] [ 2564] [depth= 1] . ( 6 sec) [ -10935.0093] [ 2530] [depth= 5] . ( 6 sec) [ -10899.2486] [ 2501] [depth= 6] . ( 6 sec) [ -10864.1336] [ 2478] [depth= 1] . ( 6 sec) [ -10811.5909] [ 2479] [depth= 2] . ( 6 sec) [ -10805.4481] [ 2478] [depth= 1] . ( 6 sec) [ -10802.1129] [ 2476] [depth= 1] . ( 6 sec) [ -10715.5474] [ 2489] [depth= 1] . ( 6 sec) [ -10623.9585] [ 2472] [depth= 2] . ( 7 sec) [ -10598.6265] [ 2426] [depth= 2] . ( 7 sec) [ -10598.5385] [ 2416] [depth= 1] . ( 7 sec) [ -10455.8289] [ 2336] [depth= 2] . ( 7 sec) [ -10403.6861] [ 2336] [depth= 1] . ( 7 sec) [ -10379.0306] [ 2331] [depth= 1] . ( 7 sec) [ -10243.2049] [ 2297] [depth= 2] . ( 7 sec) [ -10225.8029] [ 2279] [depth= 1] . ( 7 sec) [ -10154.2746] [ 2269] [depth= 2] . ( 7 sec) [ -10060.9265] [ 2258] [depth= 1] . ( 7 sec) [ -10033.5141] [ 2253] [depth= 3] . ( 7 sec) [ -9970.6238] [ 2230] [depth= 7] . ( 7 sec) [ -9917.7966] [ 2197] [depth= 2] . ( 8 sec) [ -9874.2095] [ 2193] [depth= 2] . ( 8 sec) [ -9868.2571] [ 2191] [depth= 1] . ( 8 sec) [ -9694.7997] [Branch lengths ] . ( 9 sec) [ -9693.3102] [GTR parameters ] . ( 9 sec) [ -9668.9813] [Alpha ][ 0.810570] . ( 9 sec) [ -9571.8016] [ 2135] [depth= 7] . ( 9 sec) [ -9505.0213] [ 2088] [depth= 3] . ( 10 sec) [ -9485.1950] [ 2098] [depth= 2] . ( 10 sec) [ -9449.7784] [ 2089] [depth= 3] . ( 10 sec) [ -9434.9188] [ 2099] [depth= 1] . ( 10 sec) [ -9434.5940] [ 2096] [depth= 1] . ( 10 sec) [ -9412.6417] [ 2086] [depth= 1] . ( 10 sec) [ -9387.2989] [ 2066] [depth= 2] . ( 11 sec) [ -9377.1407] [ 2040] [depth= 2] . ( 11 sec) [ -9376.9074] [ 2043] [depth= 1] . ( 12 sec) [ -9375.7971] [ 2040] [depth= 1] . ( 13 sec) [ -9374.0525] [ 2054] [depth= 1] . ( 13 sec) [ -9369.9925] [ 2040] [depth= 1] . ( 13 sec) [ -9367.7590] [ 2035] [depth= 1] . ( 14 sec) [ -9351.6412] [Branch lengths ] . ( 14 sec) [ -9350.9831] [GTR parameters ] . ( 14 sec) [ -9349.8162] [Alpha ][ 0.907931] . ( 17 sec) [ -9349.2190] [Branch lengths ] . ( 19 sec) [ -9348.6732] [ 2040] [depth= 1] . ( 38 sec) [ -9348.5021] [Branch lengths ] . ( 39 sec) [ -9348.4967] [GTR parameters ] . ( 39 sec) [ -9348.4895] [Alpha ][ 0.916224] . ( 39 sec) [ -9348.4895] [Topology ] . ( 39 sec) [ -9348.4752] [Topology ] . ( 40 sec) [ -9348.4723] [Topology ] . ( 41 sec) [ -9348.4713] [Topology ] . ( 41 sec) [ -9348.4713] [GTR parameters ] . ( 41 sec) [ -9348.4712] [Alpha ][ 0.917140] . ( 41 sec) [ -9348.4712] [Topology ] . ( 42 sec) [ -9348.4708] [Topology ] . ( 42 sec) [ -9348.4708] [GTR parameters ] . ( 42 sec) [ -9348.4708] [Alpha ][ 0.917140] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -9348.4704] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.470413. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19828.8315] [GTR parameters ] . ( 1 sec) [ -19437.1352] [Alpha ][ 0.500960] . ( 1 sec) [ -19180.6518] [ 4502] [depth= 8] . ( 1 sec) [ -18799.9396] [ 4481] [depth= 8] . ( 1 sec) [ -18755.5748] [ 4469] [depth= 5] . ( 1 sec) [ -18685.9781] [ 4463] [depth= 2] . ( 1 sec) [ -18501.8843] [ 4328] [depth= 7] . ( 1 sec) [ -18497.0211] [ 4333] [depth= 1] . ( 1 sec) [ -18312.1546] [ 4279] [depth= 9] . ( 1 sec) [ -18184.7333] [ 4259] [depth= 4] . ( 1 sec) [ -17866.2461] [ 4229] [depth= 1] . ( 1 sec) [ -17555.9541] [ 4087] [depth= 10] . ( 1 sec) [ -17308.0483] [ 4065] [depth= 12] . ( 1 sec) [ -17048.9674] [ 3975] [depth= 7] . ( 1 sec) [ -16989.2213] [ 3974] [depth= 1] . ( 1 sec) [ -16757.7323] [ 3961] [depth= 10] . ( 1 sec) [ -16700.9013] [ 3951] [depth= 1] . ( 1 sec) [ -16332.8371] [ 3850] [depth= 8] . ( 1 sec) [ -16285.1857] [ 3843] [depth= 1] . ( 1 sec) [ -16026.4477] [ 3765] [depth= 5] . ( 1 sec) [ -15849.7784] [ 3760] [depth= 2] . ( 1 sec) [ -15401.1663] [ 3668] [depth= 7] . ( 1 sec) [ -15175.2607] [ 3591] [depth= 1] . ( 2 sec) [ -14629.2895] [ 3485] [depth= 6] . ( 2 sec) [ -14510.9689] [ 3462] [depth= 8] . ( 2 sec) [ -14181.2579] [ 3312] [depth= 10] . ( 2 sec) [ -13928.0475] [ 3298] [depth= 4] . ( 2 sec) [ -13885.6737] [ 3291] [depth= 1] . ( 2 sec) [ -13717.6960] [ 3244] [depth= 5] . ( 2 sec) [ -13638.7303] [ 3221] [depth= 1] . ( 2 sec) [ -13621.2283] [ 3253] [depth= 12] . ( 2 sec) [ -13552.8336] [ 3276] [depth= 1] . ( 2 sec) [ -13412.3103] [ 3211] [depth= 2] . ( 2 sec) [ -13388.3461] [ 3216] [depth= 10] . ( 2 sec) [ -13260.2018] [ 3167] [depth= 11] . ( 2 sec) [ -12975.5574] [ 3018] [depth= 2] . ( 2 sec) [ -12782.3754] [ 2976] [depth= 4] . ( 2 sec) [ -12719.7066] [ 2896] [depth= 1] . ( 2 sec) [ -12655.3454] [ 2872] [depth= 8] . ( 2 sec) [ -12628.7324] [ 2867] [depth= 2] . ( 2 sec) [ -12531.6687] [ 2817] [depth= 5] . ( 2 sec) [ -12366.2108] [ 2738] [depth= 8] . ( 2 sec) [ -12311.7184] [ 2736] [depth= 2] . ( 2 sec) [ -12268.3059] [ 2736] [depth= 1] . ( 2 sec) [ -12172.0514] [ 2702] [depth= 4] . ( 3 sec) [ -12076.4244] [ 2663] [depth= 9] . ( 3 sec) [ -12035.8459] [ 2655] [depth= 1] . ( 3 sec) [ -12007.8724] [ 2652] [depth= 2] . ( 3 sec) [ -11989.6469] [ 2649] [depth= 1] . ( 3 sec) [ -11904.8475] [ 2641] [depth= 1] . ( 3 sec) [ -11682.9832] [ 2600] [depth= 5] . ( 3 sec) [ -11603.4272] [ 2563] [depth= 1] . ( 3 sec) [ -11557.7630] [ 2542] [depth= 1] . ( 3 sec) [ -11446.7830] [ 2532] [depth= 2] . ( 3 sec) [ -11402.6621] [ 2515] [depth= 1] . ( 3 sec) [ -11390.7014] [ 2510] [depth= 1] . ( 3 sec) [ -11336.8964] [ 2502] [depth= 1] . ( 3 sec) [ -11283.7603] [ 2513] [depth= 1] . ( 3 sec) [ -11267.2441] [ 2502] [depth= 1] . ( 3 sec) [ -11042.1250] [ 2429] [depth= 5] . ( 3 sec) [ -11027.1613] [ 2404] [depth= 1] . ( 3 sec) [ -11019.8849] [ 2406] [depth= 1] . ( 4 sec) [ -10924.5211] [ 2391] [depth= 1] . ( 4 sec) [ -10894.3657] [ 2342] [depth= 1] . ( 4 sec) [ -10809.8931] [ 2284] [depth= 3] . ( 4 sec) [ -10783.5885] [ 2273] [depth= 5] . ( 4 sec) [ -10674.9513] [ 2252] [depth= 2] . ( 4 sec) [ -10068.4543] [ 2207] [depth= 8] . ( 4 sec) [ -10051.9739] [ 2207] [depth= 2] . ( 4 sec) [ -10050.3866] [ 2205] [depth= 1] . ( 4 sec) [ -10005.2673] [ 2181] [depth= 1] . ( 4 sec) [ -9990.7332] [ 2170] [depth= 1] . ( 4 sec) [ -9990.2103] [ 2172] [depth= 1] . ( 4 sec) [ -9972.4505] [ 2164] [depth= 1] . ( 4 sec) [ -9959.6087] [ 2166] [depth= 1] . ( 4 sec) [ -9887.5035] [ 2165] [depth= 7] . ( 4 sec) [ -9887.4813] [ 2167] [depth= 1] . ( 4 sec) [ -9885.0564] [ 2165] [depth= 1] . ( 4 sec) [ -9875.0644] [ 2162] [depth= 1] . ( 5 sec) [ -9642.2306] [Branch lengths ] . ( 5 sec) [ -9641.3354] [GTR parameters ] . ( 5 sec) [ -9619.2041] [Alpha ][ 0.805053] . ( 5 sec) [ -9618.8931] [ 2165] [depth= 1] . ( 5 sec) [ -9598.3726] [ 2143] [depth= 2] . ( 6 sec) [ -9587.3244] [ 2131] [depth= 1] . ( 6 sec) [ -9549.4490] [ 2117] [depth= 2] . ( 6 sec) [ -9523.8611] [ 2107] [depth= 1] . ( 6 sec) [ -9520.1134] [ 2102] [depth= 1] . ( 6 sec) [ -9519.9183] [ 2099] [depth= 1] . ( 6 sec) [ -9498.1900] [ 2096] [depth= 1] . ( 6 sec) [ -9497.9744] [ 2099] [depth= 1] . ( 7 sec) [ -9495.3455] [ 2104] [depth= 1] . ( 7 sec) [ -9493.1910] [ 2102] [depth= 1] . ( 7 sec) [ -9491.0519] [ 2104] [depth= 1] . ( 7 sec) [ -9454.3212] [ 2073] [depth= 1] . ( 7 sec) [ -9449.7976] [ 2071] [depth= 1] . ( 7 sec) [ -9443.6135] [ 2071] [depth= 1] . ( 7 sec) [ -9442.6312] [ 2074] [depth= 1] . ( 7 sec) [ -9439.7304] [ 2076] [depth= 1] . ( 7 sec) [ -9427.2964] [ 2075] [depth= 2] . ( 7 sec) [ -9395.8505] [ 2038] [depth= 3] . ( 8 sec) [ -9395.1368] [ 2042] [depth= 1] . ( 8 sec) [ -9394.9518] [ 2041] [depth= 1] . ( 8 sec) [ -9391.0496] [ 2046] [depth= 1] . ( 8 sec) [ -9386.3586] [ 2055] [depth= 1] . ( 8 sec) [ -9378.3195] [ 2052] [depth= 1] . ( 8 sec) [ -9358.2267] [Branch lengths ] . ( 9 sec) [ -9358.1337] [GTR parameters ] . ( 9 sec) [ -9357.0564] [Alpha ][ 0.897941] . ( 9 sec) [ -9353.5069] [ 2043] [depth= 1] . ( 12 sec) [ -9349.8071] [Branch lengths ] . ( 12 sec) [ -9349.8001] [GTR parameters ] . ( 12 sec) [ -9349.7719] [Alpha ][ 0.914389] . ( 15 sec) [ -9349.4909] [Branch lengths ] . ( 35 sec) [ -9349.4712] [Branch lengths ] . ( 35 sec) [ -9349.4712] [Topology ] . ( 35 sec) [ -9349.4701] [Topology ] . ( 36 sec) [ -9349.4697] [Topology ] . ( 36 sec) [ -9349.4694] [GTR parameters ] . ( 37 sec) [ -9349.4680] [Alpha ][ 0.917969] . ( 37 sec) [ -9349.4680] [Topology ] . ( 37 sec) [ -9349.4677] [Topology ] . ( 37 sec) [ -9349.4677] [GTR parameters ] . ( 37 sec) [ -9349.4677] [Alpha ][ 0.917969] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -9348.4780] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -9348.4774] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.477438. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19808.9325] [GTR parameters ] . ( 1 sec) [ -19393.1651] [Alpha ][ 0.500960] . ( 1 sec) [ -19103.6008] [ 4501] [depth= 8] . ( 1 sec) [ -18681.9075] [ 4452] [depth= 9] . ( 1 sec) [ -18387.4728] [ 4376] [depth= 8] . ( 1 sec) [ -18318.2855] [ 4343] [depth= 1] . ( 1 sec) [ -17929.0685] [ 4266] [depth= 8] . ( 2 sec) [ -17811.9253] [ 4257] [depth= 2] . ( 2 sec) [ -17754.0625] [ 4254] [depth= 3] . ( 2 sec) [ -17613.0715] [ 4184] [depth= 4] . ( 2 sec) [ -17479.5550] [ 4175] [depth= 4] . ( 2 sec) [ -17363.2147] [ 4165] [depth= 5] . ( 2 sec) [ -17297.1103] [ 4138] [depth= 1] . ( 2 sec) [ -17272.4632] [ 4114] [depth= 5] . ( 2 sec) [ -17200.2015] [ 4107] [depth= 2] . ( 2 sec) [ -16996.6024] [ 4017] [depth= 10] . ( 2 sec) [ -16976.6250] [ 4018] [depth= 1] . ( 2 sec) [ -16905.7644] [ 3973] [depth= 5] . ( 2 sec) [ -16875.9727] [ 3972] [depth= 1] . ( 2 sec) [ -16862.2560] [ 3970] [depth= 1] . ( 2 sec) [ -16607.3961] [ 3926] [depth= 4] . ( 2 sec) [ -16531.1221] [ 3902] [depth= 1] . ( 2 sec) [ -16205.3390] [ 3881] [depth= 14] . ( 2 sec) [ -16201.4862] [ 3878] [depth= 1] . ( 2 sec) [ -15863.6998] [ 3826] [depth= 10] . ( 2 sec) [ -15591.1576] [ 3796] [depth= 10] . ( 2 sec) [ -15153.7751] [ 3642] [depth= 9] . ( 2 sec) [ -15006.4368] [ 3626] [depth= 11] . ( 2 sec) [ -14844.5940] [ 3613] [depth= 2] . ( 2 sec) [ -14639.7155] [ 3580] [depth= 5] . ( 3 sec) [ -14564.6097] [ 3510] [depth= 8] . ( 3 sec) [ -14559.6032] [ 3513] [depth= 1] . ( 3 sec) [ -14411.3997] [ 3507] [depth= 3] . ( 3 sec) [ -14380.9982] [ 3548] [depth= 1] . ( 3 sec) [ -14343.6466] [ 3507] [depth= 1] . ( 3 sec) [ -14239.4770] [ 3477] [depth= 2] . ( 3 sec) [ -14133.8337] [ 3448] [depth= 2] . ( 3 sec) [ -14040.3371] [ 3449] [depth= 1] . ( 3 sec) [ -14014.3868] [ 3432] [depth= 6] . ( 3 sec) [ -13912.0959] [ 3437] [depth= 4] . ( 3 sec) [ -13595.9067] [ 3331] [depth= 14] . ( 3 sec) [ -13421.0498] [ 3266] [depth= 1] . ( 3 sec) [ -13321.7851] [ 3259] [depth= 1] . ( 3 sec) [ -13231.5180] [ 3228] [depth= 1] . ( 3 sec) [ -13216.2983] [ 3229] [depth= 10] . ( 3 sec) [ -13192.9217] [ 3224] [depth= 4] . ( 3 sec) [ -13089.4620] [ 3223] [depth= 11] . ( 3 sec) [ -13041.0768] [ 3223] [depth= 2] . ( 3 sec) [ -12999.1061] [ 3220] [depth= 1] . ( 3 sec) [ -12853.7207] [ 3203] [depth= 9] . ( 3 sec) [ -12649.3245] [ 3195] [depth= 1] . ( 3 sec) [ -12594.8706] [ 3191] [depth= 1] . ( 3 sec) [ -12473.3919] [ 3166] [depth= 1] . ( 4 sec) [ -12471.6844] [ 3164] [depth= 1] . ( 4 sec) [ -12469.7283] [ 3164] [depth= 2] . ( 4 sec) [ -12108.2150] [ 3013] [depth= 8] . ( 4 sec) [ -12104.8371] [ 3009] [depth= 1] . ( 4 sec) [ -12086.6502] [ 3005] [depth= 4] . ( 4 sec) [ -12049.3600] [ 3002] [depth= 6] . ( 4 sec) [ -11995.5610] [ 2941] [depth= 1] . ( 4 sec) [ -11790.9432] [ 2894] [depth= 6] . ( 4 sec) [ -11735.1389] [ 2883] [depth= 2] . ( 4 sec) [ -11692.5873] [ 2802] [depth= 1] . ( 4 sec) [ -11675.1636] [ 2796] [depth= 1] . ( 4 sec) [ -11588.3731] [ 2750] [depth= 4] . ( 4 sec) [ -11331.8777] [ 2676] [depth= 4] . ( 4 sec) [ -11307.0765] [ 2638] [depth= 3] . ( 4 sec) [ -11303.1443] [ 2659] [depth= 1] . ( 4 sec) [ -11245.2060] [ 2633] [depth= 1] . ( 4 sec) [ -11243.6355] [ 2647] [depth= 3] . ( 4 sec) [ -11049.2214] [ 2557] [depth= 3] . ( 4 sec) [ -10968.7178] [ 2533] [depth= 6] . ( 4 sec) [ -10882.2719] [ 2501] [depth= 4] . ( 5 sec) [ -10867.1589] [ 2503] [depth= 1] . ( 5 sec) [ -10564.4625] [ 2390] [depth= 10] . ( 5 sec) [ -10461.0642] [ 2350] [depth= 3] . ( 5 sec) [ -10456.1717] [ 2350] [depth= 1] . ( 5 sec) [ -10387.7739] [ 2338] [depth= 1] . ( 5 sec) [ -10384.2319] [ 2337] [depth= 2] . ( 5 sec) [ -10379.9414] [ 2343] [depth= 1] . ( 5 sec) [ -10343.1227] [ 2336] [depth= 1] . ( 5 sec) [ -10015.7994] [Branch lengths ] . ( 6 sec) [ -10014.9106] [GTR parameters ] . ( 6 sec) [ -9997.9954] [Alpha ][ 0.752160] . ( 6 sec) [ -9874.7065] [ 2272] [depth= 4] . ( 6 sec) [ -9763.9486] [ 2245] [depth= 2] . ( 6 sec) [ -9731.7476] [ 2230] [depth= 2] . ( 6 sec) [ -9690.0212] [ 2206] [depth= 1] . ( 6 sec) [ -9643.0063] [ 2188] [depth= 3] . ( 6 sec) [ -9642.6197] [ 2185] [depth= 1] . ( 6 sec) [ -9636.6717] [ 2185] [depth= 1] . ( 6 sec) [ -9621.1922] [ 2178] [depth= 1] . ( 7 sec) [ -9586.1839] [ 2155] [depth= 1] . ( 7 sec) [ -9530.7987] [ 2120] [depth= 1] . ( 7 sec) [ -9524.9082] [ 2122] [depth= 1] . ( 7 sec) [ -9523.2806] [ 2121] [depth= 1] . ( 7 sec) [ -9494.1083] [ 2093] [depth= 2] . ( 7 sec) [ -9477.3217] [ 2082] [depth= 2] . ( 7 sec) [ -9476.8621] [ 2086] [depth= 1] . ( 7 sec) [ -9475.7386] [ 2085] [depth= 1] . ( 7 sec) [ -9405.7138] [ 2049] [depth= 1] . ( 7 sec) [ -9403.0377] [ 2047] [depth= 1] . ( 7 sec) [ -9400.7751] [ 2051] [depth= 1] . ( 8 sec) [ -9396.0007] [ 2062] [depth= 1] . ( 8 sec) [ -9384.0439] [ 2055] [depth= 1] . ( 8 sec) [ -9381.4520] [ 2053] [depth= 2] . ( 8 sec) [ -9381.2402] [ 2056] [depth= 1] . ( 8 sec) [ -9381.0749] [ 2060] [depth= 1] . ( 8 sec) [ -9381.0103] [ 2059] [depth= 1] . ( 8 sec) [ -9378.2030] [ 2057] [depth= 1] . ( 9 sec) [ -9356.2797] [Branch lengths ] . ( 10 sec) [ -9355.2624] [GTR parameters ] . ( 10 sec) [ -9352.6048] [Alpha ][ 0.892400] . ( 10 sec) [ -9352.5492] [ 2043] [depth= 1] . ( 10 sec) [ -9352.4824] [ 2045] [depth= 1] . ( 13 sec) [ -9350.5752] [Branch lengths ] . ( 13 sec) [ -9350.5722] [GTR parameters ] . ( 13 sec) [ -9350.5372] [Alpha ][ 0.910646] . ( 13 sec) [ -9350.4341] [ 2043] [depth= 1] . ( 16 sec) [ -9349.5392] [Branch lengths ] . ( 17 sec) [ -9349.5375] [GTR parameters ] . ( 17 sec) [ -9349.5345] [Alpha ][ 0.916001] . ( 20 sec) [ -9349.4745] [Branch lengths ] . ( 39 sec) [ -9349.4690] [Branch lengths ] . ( 39 sec) [ -9349.4690] [Topology ] . ( 40 sec) [ -9349.4685] [Topology ] . ( 40 sec) [ -9349.4683] [GTR parameters ] . ( 40 sec) [ -9349.4679] [Alpha ][ 0.917942] . ( 40 sec) [ -9349.4679] [Topology ] . ( 41 sec) [ -9349.4677] [Topology ] . ( 41 sec) [ -9349.4677] [GTR parameters ] . ( 41 sec) [ -9349.4677] [Alpha ][ 0.917942] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -9348.4777] [Topology ] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -9348.4773] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.477314. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19888.4425] [GTR parameters ] . ( 1 sec) [ -19453.9389] [Alpha ][ 0.500960] . ( 1 sec) [ -19171.3653] [ 4615] [depth= 6] . ( 1 sec) [ -18984.5701] [ 4551] [depth= 11] . ( 1 sec) [ -18702.6651] [ 4533] [depth= 5] . ( 1 sec) [ -18606.6381] [ 4531] [depth= 1] . ( 1 sec) [ -18403.8238] [ 4464] [depth= 10] . ( 1 sec) [ -18295.7303] [ 4461] [depth= 6] . ( 1 sec) [ -18009.6462] [ 4418] [depth= 6] . ( 1 sec) [ -17707.3442] [ 4346] [depth= 1] . ( 2 sec) [ -17469.5812] [ 4275] [depth= 12] . ( 2 sec) [ -16924.8851] [ 4199] [depth= 14] . ( 2 sec) [ -16907.7804] [ 4200] [depth= 9] . ( 2 sec) [ -16645.5062] [ 4135] [depth= 3] . ( 2 sec) [ -16620.8822] [ 4127] [depth= 1] . ( 2 sec) [ -16311.7629] [ 4091] [depth= 2] . ( 2 sec) [ -16208.1034] [ 4086] [depth= 1] . ( 2 sec) [ -16150.3039] [ 4058] [depth= 3] . ( 2 sec) [ -16060.0872] [ 4035] [depth= 1] . ( 2 sec) [ -15959.0832] [ 4015] [depth= 2] . ( 2 sec) [ -15863.4967] [ 4000] [depth= 4] . ( 2 sec) [ -15835.9146] [ 3970] [depth= 1] . ( 2 sec) [ -15488.3875] [ 3840] [depth= 9] . ( 2 sec) [ -15476.3672] [ 3849] [depth= 1] . ( 2 sec) [ -15367.4630] [ 3793] [depth= 1] . ( 2 sec) [ -15301.0675] [ 3777] [depth= 6] . ( 2 sec) [ -15216.8259] [ 3729] [depth= 6] . ( 2 sec) [ -15214.5472] [ 3733] [depth= 2] . ( 2 sec) [ -15189.4643] [ 3750] [depth= 3] . ( 2 sec) [ -14966.0607] [ 3667] [depth= 4] . ( 2 sec) [ -14589.4722] [ 3630] [depth= 6] . ( 2 sec) [ -14566.2465] [ 3620] [depth= 1] . ( 3 sec) [ -14403.7293] [ 3561] [depth= 1] . ( 3 sec) [ -14386.2975] [ 3560] [depth= 1] . ( 3 sec) [ -14277.3979] [ 3525] [depth= 12] . ( 3 sec) [ -14236.8527] [ 3484] [depth= 1] . ( 3 sec) [ -13980.0948] [ 3387] [depth= 5] . ( 3 sec) [ -13686.6280] [ 3341] [depth= 2] . ( 3 sec) [ -13374.5727] [ 3270] [depth= 11] . ( 3 sec) [ -13282.9148] [ 3285] [depth= 8] . ( 3 sec) [ -13231.1364] [ 3283] [depth= 1] . ( 3 sec) [ -13012.9253] [ 3218] [depth= 8] . ( 3 sec) [ -12714.7566] [ 3128] [depth= 6] . ( 3 sec) [ -12506.9447] [ 3117] [depth= 3] . ( 3 sec) [ -12446.0811] [ 3084] [depth= 5] . ( 3 sec) [ -12428.5796] [ 3081] [depth= 1] . ( 3 sec) [ -12383.0196] [ 3084] [depth= 7] . ( 3 sec) [ -12376.9329] [ 3082] [depth= 2] . ( 3 sec) [ -12200.0671] [ 3019] [depth= 2] . ( 3 sec) [ -12112.6103] [ 2936] [depth= 4] . ( 3 sec) [ -12021.7566] [ 2911] [depth= 1] . ( 3 sec) [ -11872.8521] [ 2849] [depth= 5] . ( 3 sec) [ -11835.3331] [ 2848] [depth= 5] . ( 3 sec) [ -11768.5509] [ 2841] [depth= 1] . ( 3 sec) [ -11668.9197] [ 2816] [depth= 6] . ( 4 sec) [ -11454.0870] [ 2733] [depth= 10] . ( 4 sec) [ -11188.7769] [ 2627] [depth= 2] . ( 4 sec) [ -11065.9679] [ 2593] [depth= 6] . ( 4 sec) [ -10952.0935] [ 2586] [depth= 1] . ( 4 sec) [ -10933.5596] [ 2562] [depth= 4] . ( 4 sec) [ -10929.7170] [ 2576] [depth= 1] . ( 4 sec) [ -10924.2684] [ 2562] [depth= 1] . ( 4 sec) [ -10684.0760] [ 2501] [depth= 6] . ( 4 sec) [ -10657.0162] [ 2493] [depth= 1] . ( 4 sec) [ -10610.7550] [ 2501] [depth= 9] . ( 4 sec) [ -10559.3053] [ 2493] [depth= 1] . ( 4 sec) [ -10500.3589] [ 2486] [depth= 1] . ( 4 sec) [ -10386.5186] [ 2427] [depth= 2] . ( 4 sec) [ -10268.2534] [ 2365] [depth= 3] . ( 4 sec) [ -10237.1558] [ 2347] [depth= 5] . ( 4 sec) [ -10198.2267] [ 2330] [depth= 2] . ( 4 sec) [ -10165.4225] [ 2311] [depth= 1] . ( 5 sec) [ -10161.2129] [ 2310] [depth= 1] . ( 5 sec) [ -10156.0665] [ 2308] [depth= 1] . ( 5 sec) [ -10119.7842] [ 2283] [depth= 3] . ( 5 sec) [ -10109.7432] [ 2283] [depth= 1] . ( 5 sec) [ -10108.6851] [ 2282] [depth= 1] . ( 5 sec) [ -10107.9322] [ 2283] [depth= 1] . ( 5 sec) [ -10079.4311] [ 2233] [depth= 2] . ( 6 sec) [ -10034.5304] [ 2184] [depth= 5] . ( 6 sec) [ -10001.4105] [ 2191] [depth= 1] . ( 6 sec) [ -9998.5047] [ 2204] [depth= 6] . ( 6 sec) [ -9977.5833] [ 2197] [depth= 1] . ( 7 sec) [ -9754.7675] [Branch lengths ] . ( 7 sec) [ -9753.8091] [GTR parameters ] . ( 7 sec) [ -9729.8938] [Alpha ][ 0.812658] . ( 7 sec) [ -9713.2492] [ 2167] [depth= 5] . ( 7 sec) [ -9701.5748] [ 2163] [depth= 1] . ( 7 sec) [ -9681.3187] [ 2154] [depth= 4] . ( 8 sec) [ -9653.5051] [ 2145] [depth= 2] . ( 8 sec) [ -9653.0364] [ 2144] [depth= 1] . ( 8 sec) [ -9652.3987] [ 2145] [depth= 1] . ( 8 sec) [ -9639.7246] [ 2134] [depth= 1] . ( 8 sec) [ -9593.0894] [ 2106] [depth= 1] . ( 8 sec) [ -9583.6332] [ 2103] [depth= 2] . ( 9 sec) [ -9576.2585] [ 2100] [depth= 2] . ( 9 sec) [ -9374.7862] [ 2041] [depth= 3] . ( 9 sec) [ -9370.6531] [ 2037] [depth= 1] . ( 10 sec) [ -9370.6352] [ 2040] [depth= 1] . ( 10 sec) [ -9370.0914] [ 2042] [depth= 1] . ( 10 sec) [ -9352.0232] [Branch lengths ] . ( 11 sec) [ -9351.2635] [GTR parameters ] . ( 11 sec) [ -9350.1111] [Alpha ][ 0.909634] . ( 13 sec) [ -9349.5478] [ 2040] [depth= 1] . ( 14 sec) [ -9348.5657] [Branch lengths ] . ( 14 sec) [ -9348.5612] [GTR parameters ] . ( 14 sec) [ -9348.5560] [Alpha ][ 0.916760] . ( 17 sec) [ -9348.4758] [Branch lengths ] . ( 36 sec) [ -9348.4710] [Branch lengths ] . ( 36 sec) [ -9348.4710] [Topology ] . ( 37 sec) [ -9348.4706] [Topology ] . ( 37 sec) [ -9348.4706] [GTR parameters ] . ( 37 sec) [ -9348.4706] [Alpha ][ 0.917677] . Checking for NNIs, optimizing five branches... . ( 43 sec) [ -9348.4704] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9348.470399. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9414.383223 . ( 1 sec) [ -9401.9651] [GTR parameters ] . ( 1 sec) [ -9400.9169] [Alpha ][ 0.893448] . ( 1 sec) [ -9400.9169] [Topology ] . ( 2 sec) [ -9356.1912] [Topology ] . ( 2 sec) [ -9350.5757] [Topology ] . ( 3 sec) [ -9349.4320] [Topology ] . ( 4 sec) [ -9348.9751] [Topology ] . ( 5 sec) [ -9348.7678] [Topology ] . ( 6 sec) [ -9348.6682] [Topology ] . ( 6 sec) [ -9348.6185] [Topology ] . ( 7 sec) [ -9348.5933] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.593346 . ( 13 sec) [ -9348.5517] [GTR parameters ] . ( 13 sec) [ -9348.5034] [Alpha ][ 0.914037] . ( 13 sec) [ -9348.5034] [Topology ] . ( 14 sec) [ -9348.4836] [Topology ] . ( 15 sec) [ -9348.4746] [Topology ] . ( 16 sec) [ -9348.4701] [Topology ] . ( 16 sec) [ -9348.4678] [Topology ] . ( 17 sec) [ -9348.4666] [Topology ] . ( 18 sec) [ -9348.4660] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.466014 . ( 24 sec) [ -9348.4660] [GTR parameters ] . ( 24 sec) [ -9348.4650] [Alpha ][ 0.917096] . ( 24 sec) [ -9348.4650] [Topology ] . ( 25 sec) [ -9348.4645] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.464522 . ( 31 sec) [ -9348.4645] [GTR parameters ] . ( 31 sec) [ -9348.4645] [Alpha ][ 0.917096] . ( 31 sec) [ -9348.4645] [Topology ] . ( 31 sec) [ -9348.4643] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -9401.9651] [GTR parameters ] . ( 44 sec) [ -9400.9169] [Alpha ][ 0.893448] . ( 45 sec) [ -9397.6475] [ 2046] [depth= 1] . ( 45 sec) [ -9396.2183] [ 2042] [depth= 1] . ( 45 sec) [ -9395.8159] [ 2046] [depth= 1] . ( 45 sec) [ -9395.2251] [ 2045] [depth= 1] . ( 46 sec) [ -9394.6189] [ 2048] [depth= 1] . ( 46 sec) [ -9390.0440] [ 2045] [depth= 1] . ( 46 sec) [ -9384.6865] [ 2043] [depth= 1] . ( 46 sec) [ -9384.3506] [ 2043] [depth= 1] . ( 46 sec) [ -9383.7166] [ 2043] [depth= 1] . ( 46 sec) [ -9382.9420] [ 2040] [depth= 1] . ( 46 sec) [ -9352.8625] [Branch lengths ] . ( 47 sec) [ -9352.8058] [GTR parameters ] . ( 47 sec) [ -9352.7891] [Alpha ][ 0.906140] . ( 50 sec) [ -9349.7908] [Branch lengths ] . ( 69 sec) [ -9349.5138] [Branch lengths ] . ( 69 sec) [ -9349.5138] [Topology ] . ( 70 sec) [ -9349.4923] [Topology ] . ( 71 sec) [ -9349.4850] [Topology ] . ( 72 sec) [ -9349.4817] [Topology ] . ( 72 sec) [ -9349.4800] [Topology ] . ( 73 sec) [ -9349.4792] [Topology ] . ( 73 sec) [ -9349.4774] [GTR parameters ] . ( 73 sec) [ -9349.4634] [Alpha ][ 0.917735] . ( 73 sec) [ -9349.4634] [Topology ] . ( 74 sec) [ -9349.4622] [Topology ] . ( 75 sec) [ -9349.4618] [Topology ] . ( 75 sec) [ -9349.4618] [GTR parameters ] . ( 75 sec) [ -9349.4618] [Alpha ][ 0.917735] . ( 75 sec) [ -9349.4618] [Topology ] . ( 76 sec) [ -9349.4616] [Topology ] . ( 76 sec) [ -9349.4616] [GTR parameters ] . ( 76 sec) [ -9349.4616] [Alpha ][ 0.917735] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -9348.4715] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9348.464309 . Log likelihood obtained after SPR moves : -9348.471488 . Log likelihood of the current tree: -9348.464309. . Printing the most likely tree in file 'data80.phy_phyml_tree.txt'... . Best log likelihood : -9348.464309 . Time used 0h1m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo