.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data37.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... . 450 patterns found. (out of a total of 500 sites) . 49 sites without polymorphism (9.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20435.7584] [GTR parameters ] . ( 1 sec) [ -20081.7215] [Alpha ][ 0.500960] . ( 1 sec) [ -19974.7270] [ 4942] [depth= 8] . ( 1 sec) [ -19793.8352] [ 4924] [depth= 8] . ( 1 sec) [ -19698.5508] [ 4908] [depth= 2] . ( 1 sec) [ -19686.7495] [ 4904] [depth= 3] . ( 1 sec) [ -19491.0223] [ 4850] [depth= 4] . ( 1 sec) [ -19318.0535] [ 4832] [depth= 8] . ( 1 sec) [ -19238.8020] [ 4797] [depth= 4] . ( 1 sec) [ -18992.8836] [ 4674] [depth= 2] . ( 1 sec) [ -18778.3857] [ 4556] [depth= 5] . ( 1 sec) [ -18650.7720] [ 4541] [depth= 6] . ( 1 sec) [ -18529.3315] [ 4546] [depth= 13] . ( 2 sec) [ -18402.2486] [ 4527] [depth= 2] . ( 2 sec) [ -18245.6149] [ 4503] [depth= 13] . ( 2 sec) [ -18054.6023] [ 4495] [depth= 2] . ( 2 sec) [ -18045.0663] [ 4495] [depth= 1] . ( 2 sec) [ -17919.8318] [ 4451] [depth= 5] . ( 2 sec) [ -17849.0585] [ 4412] [depth= 4] . ( 2 sec) [ -17748.4412] [ 4401] [depth= 1] . ( 2 sec) [ -17598.0776] [ 4396] [depth= 2] . ( 2 sec) [ -17462.4905] [ 4350] [depth= 4] . ( 2 sec) [ -17323.9234] [ 4268] [depth= 7] . ( 2 sec) [ -16947.6382] [ 4148] [depth= 4] . ( 2 sec) [ -16907.5323] [ 4141] [depth= 1] . ( 2 sec) [ -16905.4767] [ 4162] [depth= 1] . ( 2 sec) [ -16576.2242] [ 4098] [depth= 3] . ( 2 sec) [ -16459.8667] [ 4083] [depth= 6] . ( 2 sec) [ -16174.2572] [ 4007] [depth= 14] . ( 2 sec) [ -16017.1541] [ 3971] [depth= 1] . ( 2 sec) [ -15925.0097] [ 3925] [depth= 1] . ( 2 sec) [ -15784.5879] [ 3896] [depth= 5] . ( 2 sec) [ -15680.0609] [ 3884] [depth= 1] . ( 2 sec) [ -15445.9678] [ 3815] [depth= 14] . ( 2 sec) [ -15425.9066] [ 3807] [depth= 1] . ( 2 sec) [ -15170.8095] [ 3763] [depth= 12] . ( 3 sec) [ -14924.1355] [ 3739] [depth= 7] . ( 3 sec) [ -14817.0201] [ 3729] [depth= 11] . ( 3 sec) [ -14681.9337] [ 3707] [depth= 14] . ( 3 sec) [ -14648.2915] [ 3695] [depth= 1] . ( 3 sec) [ -14631.1962] [ 3681] [depth= 1] . ( 3 sec) [ -14572.9164] [ 3679] [depth= 2] . ( 3 sec) [ -14355.1954] [ 3677] [depth= 8] . ( 3 sec) [ -14223.2071] [ 3606] [depth= 1] . ( 3 sec) [ -14192.5115] [ 3602] [depth= 1] . ( 3 sec) [ -14171.1873] [ 3585] [depth= 1] . ( 3 sec) [ -14163.9062] [ 3588] [depth= 1] . ( 3 sec) [ -14102.7358] [ 3543] [depth= 1] . ( 3 sec) [ -14000.6082] [ 3502] [depth= 4] . ( 3 sec) [ -13998.3583] [ 3502] [depth= 1] . ( 3 sec) [ -13952.2498] [ 3512] [depth= 1] . ( 3 sec) [ -13747.6895] [ 3456] [depth= 2] . ( 3 sec) [ -13688.8054] [ 3437] [depth= 3] . ( 3 sec) [ -13643.9595] [ 3425] [depth= 1] . ( 3 sec) [ -13547.2551] [ 3371] [depth= 9] . ( 3 sec) [ -13538.5712] [ 3360] [depth= 6] . ( 3 sec) [ -13436.1862] [ 3388] [depth= 1] . ( 4 sec) [ -13260.5991] [ 3271] [depth= 9] . ( 4 sec) [ -13117.8750] [ 3229] [depth= 4] . ( 4 sec) [ -13099.9908] [ 3208] [depth= 4] . ( 4 sec) [ -13026.8534] [ 3214] [depth= 2] . ( 4 sec) [ -12931.1172] [ 3178] [depth= 4] . ( 4 sec) [ -12909.6280] [ 3184] [depth= 1] . ( 4 sec) [ -12823.3594] [ 3150] [depth= 6] . ( 4 sec) [ -12712.8042] [ 3069] [depth= 1] . ( 4 sec) [ -12701.2535] [ 3069] [depth= 1] . ( 4 sec) [ -12627.5844] [ 3069] [depth= 3] . ( 4 sec) [ -12565.6332] [ 3055] [depth= 4] . ( 4 sec) [ -12552.4960] [ 3042] [depth= 4] . ( 4 sec) [ -12449.4316] [ 3048] [depth= 5] . ( 4 sec) [ -12424.6211] [ 3048] [depth= 1] . ( 4 sec) [ -12408.5750] [ 3005] [depth= 4] . ( 4 sec) [ -12361.4352] [ 2975] [depth= 4] . ( 4 sec) [ -12361.1234] [ 2973] [depth= 1] . ( 4 sec) [ -12309.8817] [ 2978] [depth= 3] . ( 4 sec) [ -12226.4154] [ 2963] [depth= 1] . ( 5 sec) [ -12131.1319] [ 2964] [depth= 1] . ( 5 sec) [ -12099.5052] [ 2950] [depth= 3] . ( 5 sec) [ -12075.8533] [ 2931] [depth= 1] . ( 5 sec) [ -12072.7422] [ 2936] [depth= 1] . ( 5 sec) [ -12069.6417] [ 2936] [depth= 1] . ( 5 sec) [ -11950.3508] [ 2909] [depth= 1] . ( 5 sec) [ -11927.8992] [ 2914] [depth= 1] . ( 5 sec) [ -11925.5642] [ 2908] [depth= 1] . ( 5 sec) [ -11892.4969] [ 2879] [depth= 3] . ( 5 sec) [ -11881.4152] [ 2872] [depth= 1] . ( 6 sec) [ -11751.9815] [Branch lengths ] . ( 6 sec) [ -11750.9412] [GTR parameters ] . ( 6 sec) [ -11716.8814] [Alpha ][ 0.857297] . ( 6 sec) [ -11707.2945] [ 2861] [depth= 1] . ( 7 sec) [ -11687.2912] [ 2851] [depth= 1] . ( 7 sec) [ -11686.1631] [ 2852] [depth= 1] . ( 7 sec) [ -11685.2848] [ 2852] [depth= 1] . ( 7 sec) [ -11664.1687] [ 2849] [depth= 1] . ( 7 sec) [ -11660.0178] [ 2845] [depth= 1] . ( 7 sec) [ -11659.7146] [ 2843] [depth= 1] . ( 7 sec) [ -11656.3948] [ 2833] [depth= 1] . ( 7 sec) [ -11630.9933] [ 2796] [depth= 3] . ( 7 sec) [ -11610.7821] [ 2776] [depth= 1] . ( 8 sec) [ -11610.3230] [ 2770] [depth= 2] . ( 8 sec) [ -11610.1434] [ 2772] [depth= 1] . ( 8 sec) [ -11609.4600] [ 2771] [depth= 1] . ( 8 sec) [ -11606.4101] [ 2760] [depth= 2] . ( 9 sec) [ -11604.9804] [ 2758] [depth= 1] . ( 9 sec) [ -11604.2826] [ 2752] [depth= 1] . ( 9 sec) [ -11573.0498] [ 2732] [depth= 2] . ( 9 sec) [ -11563.8961] [ 2751] [depth= 1] . ( 9 sec) [ -11562.9153] [ 2755] [depth= 1] . ( 9 sec) [ -11562.1717] [ 2757] [depth= 1] . ( 10 sec) [ -11529.3381] [Branch lengths ] . ( 10 sec) [ -11529.1693] [GTR parameters ] . ( 10 sec) [ -11527.7290] [Alpha ][ 0.955894] . ( 13 sec) [ -11527.2715] [ 2760] [depth= 1] . ( 14 sec) [ -11525.2755] [Branch lengths ] . ( 14 sec) [ -11525.2720] [GTR parameters ] . ( 14 sec) [ -11525.2719] [Alpha ][ 0.954938] . ( 17 sec) [ -11525.0540] [Branch lengths ] . ( 20 sec) [ -11524.2191] [ 2754] [depth= 2] . ( 40 sec) [ -11524.1479] [Branch lengths ] . ( 40 sec) [ -11524.1421] [GTR parameters ] . ( 40 sec) [ -11524.1420] [Alpha ][ 0.955893] . ( 40 sec) [ -11524.1420] [Topology ] . ( 41 sec) [ -11524.1372] [Topology ] . ( 41 sec) [ -11524.1355] [Topology ] . ( 42 sec) [ -11524.1346] [Topology ] . ( 42 sec) [ -11524.1346] [GTR parameters ] . ( 42 sec) [ -11524.1346] [Alpha ][ 0.955893] . ( 42 sec) [ -11524.1346] [Topology ] . ( 43 sec) [ -11524.1341] [Topology ] . ( 43 sec) [ -11524.1341] [GTR parameters ] . ( 43 sec) [ -11524.1341] [Alpha ][ 0.955893] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11524.1336] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11524.133556. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20263.5109] [GTR parameters ] . ( 1 sec) [ -19937.4788] [Alpha ][ 0.500960] . ( 1 sec) [ -19649.4864] [ 4827] [depth= 3] . ( 1 sec) [ -19424.9909] [ 4811] [depth= 9] . ( 1 sec) [ -19394.8767] [ 4803] [depth= 3] . ( 1 sec) [ -19364.5414] [ 4786] [depth= 9] . ( 1 sec) [ -19214.9503] [ 4735] [depth= 5] . ( 1 sec) [ -19074.7141] [ 4734] [depth= 4] . ( 1 sec) [ -19057.0912] [ 4733] [depth= 1] . ( 1 sec) [ -18867.6528] [ 4703] [depth= 4] . ( 1 sec) [ -18734.0977] [ 4634] [depth= 2] . ( 1 sec) [ -18536.5190] [ 4624] [depth= 4] . ( 1 sec) [ -18431.9791] [ 4568] [depth= 4] . ( 1 sec) [ -18355.5199] [ 4543] [depth= 4] . ( 1 sec) [ -17976.4464] [ 4445] [depth= 7] . ( 1 sec) [ -17731.2884] [ 4448] [depth= 4] . ( 1 sec) [ -17698.9232] [ 4437] [depth= 1] . ( 1 sec) [ -17581.7006] [ 4379] [depth= 7] . ( 1 sec) [ -17271.8402] [ 4317] [depth= 6] . ( 1 sec) [ -17122.4397] [ 4291] [depth= 2] . ( 1 sec) [ -17023.7941] [ 4264] [depth= 2] . ( 1 sec) [ -17021.0792] [ 4281] [depth= 1] . ( 2 sec) [ -16980.5306] [ 4251] [depth= 1] . ( 2 sec) [ -16620.4447] [ 4163] [depth= 5] . ( 2 sec) [ -16507.2711] [ 4123] [depth= 12] . ( 2 sec) [ -16391.2139] [ 4082] [depth= 10] . ( 2 sec) [ -16364.0664] [ 4075] [depth= 2] . ( 2 sec) [ -16268.0240] [ 4050] [depth= 2] . ( 2 sec) [ -16132.8494] [ 4035] [depth= 7] . ( 2 sec) [ -16025.0995] [ 4022] [depth= 3] . ( 2 sec) [ -16023.5775] [ 4027] [depth= 1] . ( 2 sec) [ -15729.7411] [ 3967] [depth= 6] . ( 2 sec) [ -15618.3936] [ 3941] [depth= 10] . ( 2 sec) [ -15345.6477] [ 3877] [depth= 3] . ( 2 sec) [ -15328.4675] [ 3853] [depth= 7] . ( 2 sec) [ -15215.4706] [ 3849] [depth= 5] . ( 2 sec) [ -15174.2085] [ 3821] [depth= 1] . ( 2 sec) [ -15172.1576] [ 3817] [depth= 1] . ( 2 sec) [ -14929.4948] [ 3796] [depth= 2] . ( 2 sec) [ -14817.3481] [ 3751] [depth= 1] . ( 2 sec) [ -14773.8821] [ 3749] [depth= 3] . ( 2 sec) [ -14597.9452] [ 3747] [depth= 2] . ( 3 sec) [ -14570.3117] [ 3746] [depth= 1] . ( 3 sec) [ -14474.9261] [ 3740] [depth= 1] . ( 3 sec) [ -14460.8192] [ 3733] [depth= 1] . ( 3 sec) [ -14441.3651] [ 3723] [depth= 1] . ( 3 sec) [ -14269.3557] [ 3647] [depth= 14] . ( 3 sec) [ -14261.3635] [ 3621] [depth= 2] . ( 3 sec) [ -14208.2186] [ 3546] [depth= 6] . ( 3 sec) [ -13576.8318] [ 3379] [depth= 11] . ( 3 sec) [ -13575.5954] [ 3379] [depth= 1] . ( 3 sec) [ -13573.9197] [ 3379] [depth= 1] . ( 3 sec) [ -13553.8935] [ 3377] [depth= 1] . ( 3 sec) [ -13456.9536] [ 3326] [depth= 4] . ( 3 sec) [ -13411.5133] [ 3299] [depth= 1] . ( 3 sec) [ -13290.0832] [ 3296] [depth= 1] . ( 3 sec) [ -13274.0144] [ 3286] [depth= 1] . ( 3 sec) [ -13273.7881] [ 3287] [depth= 1] . ( 3 sec) [ -13270.4169] [ 3292] [depth= 1] . ( 3 sec) [ -13259.4835] [ 3291] [depth= 2] . ( 4 sec) [ -13161.9349] [ 3239] [depth= 4] . ( 4 sec) [ -13107.5316] [ 3204] [depth= 1] . ( 4 sec) [ -13089.0259] [ 3194] [depth= 1] . ( 4 sec) [ -13033.8475] [ 3179] [depth= 1] . ( 4 sec) [ -13016.6961] [ 3173] [depth= 6] . ( 4 sec) [ -12981.1208] [ 3175] [depth= 4] . ( 4 sec) [ -12976.6394] [ 3171] [depth= 1] . ( 4 sec) [ -12976.3821] [ 3170] [depth= 1] . ( 4 sec) [ -12928.0730] [ 3151] [depth= 5] . ( 4 sec) [ -12902.5735] [ 3158] [depth= 1] . ( 4 sec) [ -12882.8841] [ 3166] [depth= 1] . ( 4 sec) [ -12640.0992] [ 3088] [depth= 2] . ( 4 sec) [ -12602.4835] [ 3069] [depth= 1] . ( 4 sec) [ -12548.3807] [ 3061] [depth= 1] . ( 4 sec) [ -12441.8185] [ 3010] [depth= 2] . ( 4 sec) [ -12436.1175] [ 3003] [depth= 1] . ( 4 sec) [ -12399.7158] [ 2993] [depth= 1] . ( 4 sec) [ -12380.2737] [ 2981] [depth= 2] . ( 4 sec) [ -12365.3208] [ 2980] [depth= 1] . ( 4 sec) [ -12332.2713] [ 2972] [depth= 2] . ( 5 sec) [ -12325.5175] [ 2964] [depth= 7] . ( 5 sec) [ -12311.6677] [ 2962] [depth= 1] . ( 5 sec) [ -12270.2683] [ 2948] [depth= 1] . ( 5 sec) [ -12234.9090] [ 2961] [depth= 1] . ( 5 sec) [ -12160.3837] [ 2925] [depth= 6] . ( 5 sec) [ -12140.1641] [ 2910] [depth= 2] . ( 5 sec) [ -11941.3210] [Branch lengths ] . ( 6 sec) [ -11936.7241] [GTR parameters ] . ( 6 sec) [ -11900.9832] [Alpha ][ 0.868860] . ( 6 sec) [ -11874.9823] [ 2899] [depth= 1] . ( 6 sec) [ -11817.6883] [ 2870] [depth= 3] . ( 6 sec) [ -11816.9896] [ 2866] [depth= 1] . ( 6 sec) [ -11764.8319] [ 2825] [depth= 5] . ( 6 sec) [ -11683.7232] [ 2794] [depth= 2] . ( 6 sec) [ -11660.7699] [ 2777] [depth= 1] . ( 6 sec) [ -11650.7658] [ 2773] [depth= 2] . ( 6 sec) [ -11637.1542] [ 2769] [depth= 1] . ( 7 sec) [ -11636.3124] [ 2772] [depth= 1] . ( 7 sec) [ -11582.7671] [ 2740] [depth= 1] . ( 7 sec) [ -11580.3214] [ 2740] [depth= 1] . ( 7 sec) [ -11568.9841] [ 2750] [depth= 1] . ( 7 sec) [ -11560.9268] [ 2740] [depth= 1] . ( 7 sec) [ -11558.3280] [ 2743] [depth= 1] . ( 7 sec) [ -11557.5891] [ 2740] [depth= 1] . ( 7 sec) [ -11556.9172] [ 2740] [depth= 2] . ( 7 sec) [ -11556.1389] [ 2731] [depth= 1] . ( 8 sec) [ -11555.9078] [ 2732] [depth= 1] . ( 8 sec) [ -11548.3061] [ 2747] [depth= 1] . ( 8 sec) [ -11547.3332] [ 2752] [depth= 1] . ( 9 sec) [ -11527.5868] [Branch lengths ] . ( 10 sec) [ -11526.8839] [GTR parameters ] . ( 10 sec) [ -11525.9464] [Alpha ][ 0.948827] . ( 13 sec) [ -11524.5069] [Branch lengths ] . ( 35 sec) [ -11524.2217] [Branch lengths ] . ( 35 sec) [ -11524.2217] [Topology ] . ( 36 sec) [ -11524.1801] [Topology ] . ( 37 sec) [ -11524.1631] [Topology ] . ( 38 sec) [ -11524.1540] [Topology ] . ( 39 sec) [ -11524.1489] [Topology ] . ( 39 sec) [ -11524.1460] [Topology ] . ( 40 sec) [ -11524.1443] [Topology ] . ( 41 sec) [ -11524.1421] [GTR parameters ] . ( 41 sec) [ -11524.1363] [Alpha ][ 0.955405] . ( 41 sec) [ -11524.1363] [Topology ] . ( 42 sec) [ -11524.1350] [Topology ] . ( 42 sec) [ -11524.1343] [Topology ] . ( 42 sec) [ -11524.1343] [GTR parameters ] . ( 42 sec) [ -11524.1343] [Alpha ][ 0.955405] . ( 43 sec) [ -11524.1343] [Topology ] . ( 43 sec) [ -11524.1339] [Topology ] . ( 43 sec) [ -11524.1339] [GTR parameters ] . ( 43 sec) [ -11524.1339] [Alpha ][ 0.955405] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11524.1331] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11524.133137. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20442.1871] [GTR parameters ] . ( 1 sec) [ -20106.2860] [Alpha ][ 0.500960] . ( 1 sec) [ -19933.3304] [ 5028] [depth= 8] . ( 1 sec) [ -19472.2214] [ 5006] [depth= 11] . ( 1 sec) [ -19450.9058] [ 4998] [depth= 2] . ( 1 sec) [ -19395.9088] [ 4997] [depth= 3] . ( 1 sec) [ -19338.3663] [ 4958] [depth= 7] . ( 1 sec) [ -19248.7422] [ 4955] [depth= 2] . ( 1 sec) [ -19124.6977] [ 4918] [depth= 3] . ( 1 sec) [ -19043.5847] [ 4858] [depth= 8] . ( 1 sec) [ -18843.5741] [ 4824] [depth= 1] . ( 1 sec) [ -18629.9005] [ 4728] [depth= 15] . ( 1 sec) [ -18493.3598] [ 4744] [depth= 3] . ( 1 sec) [ -18310.3243] [ 4727] [depth= 3] . ( 1 sec) [ -18170.6478] [ 4675] [depth= 4] . ( 1 sec) [ -17784.0236] [ 4660] [depth= 3] . ( 2 sec) [ -17680.9409] [ 4646] [depth= 1] . ( 2 sec) [ -17670.0229] [ 4637] [depth= 1] . ( 2 sec) [ -17581.5176] [ 4640] [depth= 3] . ( 2 sec) [ -17249.7705] [ 4567] [depth= 12] . ( 2 sec) [ -17221.2073] [ 4555] [depth= 3] . ( 2 sec) [ -17187.7216] [ 4543] [depth= 1] . ( 2 sec) [ -17081.6151] [ 4536] [depth= 12] . ( 2 sec) [ -16837.2284] [ 4454] [depth= 1] . ( 2 sec) [ -16481.6334] [ 4356] [depth= 5] . ( 2 sec) [ -16145.6140] [ 4264] [depth= 12] . ( 2 sec) [ -15926.9140] [ 4126] [depth= 12] . ( 2 sec) [ -15918.8886] [ 4119] [depth= 1] . ( 2 sec) [ -15761.8040] [ 4037] [depth= 3] . ( 2 sec) [ -15570.5540] [ 3988] [depth= 3] . ( 2 sec) [ -15528.1349] [ 3987] [depth= 2] . ( 2 sec) [ -15475.9854] [ 3978] [depth= 1] . ( 2 sec) [ -15329.2223] [ 3918] [depth= 9] . ( 2 sec) [ -15272.8093] [ 3881] [depth= 5] . ( 2 sec) [ -15215.1413] [ 3862] [depth= 3] . ( 2 sec) [ -15090.0364] [ 3805] [depth= 9] . ( 3 sec) [ -14958.1979] [ 3731] [depth= 9] . ( 3 sec) [ -14912.3714] [ 3742] [depth= 1] . ( 3 sec) [ -14760.5464] [ 3728] [depth= 5] . ( 3 sec) [ -14676.6985] [ 3720] [depth= 1] . ( 3 sec) [ -14672.0038] [ 3728] [depth= 1] . ( 3 sec) [ -14646.7265] [ 3739] [depth= 2] . ( 3 sec) [ -14642.3040] [ 3741] [depth= 1] . ( 3 sec) [ -14251.6807] [ 3574] [depth= 9] . ( 3 sec) [ -14249.3532] [ 3570] [depth= 1] . ( 3 sec) [ -14242.4387] [ 3569] [depth= 2] . ( 3 sec) [ -14080.4006] [ 3512] [depth= 5] . ( 3 sec) [ -13936.4604] [ 3474] [depth= 2] . ( 3 sec) [ -13898.2225] [ 3451] [depth= 2] . ( 3 sec) [ -13804.6769] [ 3382] [depth= 4] . ( 3 sec) [ -13659.5432] [ 3341] [depth= 7] . ( 3 sec) [ -13632.9022] [ 3330] [depth= 1] . ( 3 sec) [ -13606.7776] [ 3320] [depth= 2] . ( 3 sec) [ -13591.5006] [ 3320] [depth= 1] . ( 3 sec) [ -13407.0162] [ 3275] [depth= 1] . ( 3 sec) [ -13342.4246] [ 3266] [depth= 1] . ( 3 sec) [ -13000.2807] [ 3171] [depth= 12] . ( 4 sec) [ -12997.0623] [ 3171] [depth= 1] . ( 4 sec) [ -12967.4224] [ 3169] [depth= 1] . ( 4 sec) [ -12947.2695] [ 3200] [depth= 11] . ( 4 sec) [ -12900.9527] [ 3200] [depth= 1] . ( 4 sec) [ -12716.3783] [ 3115] [depth= 3] . ( 4 sec) [ -12675.0419] [ 3109] [depth= 4] . ( 4 sec) [ -12672.6737] [ 3110] [depth= 1] . ( 4 sec) [ -12640.1428] [ 3107] [depth= 3] . ( 4 sec) [ -12612.1228] [ 3096] [depth= 1] . ( 4 sec) [ -12533.3201] [ 3087] [depth= 1] . ( 4 sec) [ -12443.1150] [ 3059] [depth= 8] . ( 4 sec) [ -12315.4463] [ 3014] [depth= 12] . ( 4 sec) [ -12301.2785] [ 3001] [depth= 1] . ( 4 sec) [ -12287.3184] [ 2993] [depth= 3] . ( 4 sec) [ -12254.5936] [ 2993] [depth= 1] . ( 4 sec) [ -12208.4920] [ 2965] [depth= 1] . ( 4 sec) [ -12195.1429] [ 2964] [depth= 1] . ( 4 sec) [ -12166.6662] [ 2954] [depth= 2] . ( 4 sec) [ -12162.1800] [ 2952] [depth= 1] . ( 5 sec) [ -12146.0402] [ 2949] [depth= 1] . ( 5 sec) [ -11958.4616] [ 2863] [depth= 14] . ( 5 sec) [ -11934.6805] [ 2854] [depth= 1] . ( 5 sec) [ -11921.8085] [ 2845] [depth= 1] . ( 5 sec) [ -11919.5331] [ 2845] [depth= 1] . ( 5 sec) [ -11903.9086] [ 2862] [depth= 1] . ( 5 sec) [ -11747.6254] [Branch lengths ] . ( 6 sec) [ -11743.7482] [GTR parameters ] . ( 6 sec) [ -11716.4197] [Alpha ][ 0.818379] . ( 6 sec) [ -11709.0070] [ 2853] [depth= 1] . ( 6 sec) [ -11707.2845] [ 2851] [depth= 1] . ( 7 sec) [ -11702.3321] [ 2827] [depth= 3] . ( 7 sec) [ -11700.7730] [ 2829] [depth= 1] . ( 8 sec) [ -11667.3926] [ 2801] [depth= 7] . ( 8 sec) [ -11607.6590] [ 2762] [depth= 2] . ( 8 sec) [ -11600.9434] [ 2764] [depth= 1] . ( 8 sec) [ -11581.9567] [ 2751] [depth= 1] . ( 8 sec) [ -11581.4120] [ 2751] [depth= 1] . ( 8 sec) [ -11581.0954] [ 2763] [depth= 1] . ( 8 sec) [ -11563.5981] [ 2762] [depth= 2] . ( 8 sec) [ -11561.2345] [ 2760] [depth= 1] . ( 9 sec) [ -11560.1359] [ 2765] [depth= 1] . ( 9 sec) [ -11559.7584] [ 2769] [depth= 1] . ( 9 sec) [ -11559.1305] [ 2765] [depth= 1] . ( 10 sec) [ -11533.8647] [Branch lengths ] . ( 10 sec) [ -11533.7430] [GTR parameters ] . ( 10 sec) [ -11531.4191] [Alpha ][ 0.942419] . ( 12 sec) [ -11531.4081] [ 2762] [depth= 1] . ( 13 sec) [ -11531.2872] [ 2763] [depth= 2] . ( 13 sec) [ -11531.2189] [ 2760] [depth= 1] . ( 13 sec) [ -11529.8246] [ 2755] [depth= 2] . ( 14 sec) [ -11525.3588] [Branch lengths ] . ( 14 sec) [ -11525.3582] [GTR parameters ] . ( 14 sec) [ -11525.3310] [Alpha ][ 0.956941] . ( 18 sec) [ -11524.3869] [Branch lengths ] . ( 40 sec) [ -11524.1858] [Branch lengths ] . ( 40 sec) [ -11524.1858] [Topology ] . ( 40 sec) [ -11524.1590] [Topology ] . ( 41 sec) [ -11524.1483] [Topology ] . ( 42 sec) [ -11524.1425] [Topology ] . ( 43 sec) [ -11524.1393] [Topology ] . ( 44 sec) [ -11524.1375] [Topology ] . ( 44 sec) [ -11524.1364] [Topology ] . ( 45 sec) [ -11524.1353] [GTR parameters ] . ( 45 sec) [ -11524.1351] [Alpha ][ 0.955657] . ( 45 sec) [ -11524.1351] [Topology ] . ( 46 sec) [ -11524.1344] [Topology ] . ( 46 sec) [ -11524.1344] [GTR parameters ] . ( 46 sec) [ -11524.1344] [Alpha ][ 0.955657] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -11524.1342] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11524.134199. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20159.2250] [GTR parameters ] . ( 1 sec) [ -19828.3444] [Alpha ][ 0.500960] . ( 1 sec) [ -19600.6589] [ 4936] [depth= 8] . ( 1 sec) [ -19308.0396] [ 4893] [depth= 8] . ( 1 sec) [ -18978.5803] [ 4819] [depth= 8] . ( 1 sec) [ -18884.9839] [ 4791] [depth= 1] . ( 1 sec) [ -18580.3300] [ 4687] [depth= 6] . ( 2 sec) [ -18574.2901] [ 4680] [depth= 2] . ( 2 sec) [ -18475.3555] [ 4659] [depth= 6] . ( 2 sec) [ -18358.4163] [ 4584] [depth= 3] . ( 2 sec) [ -18342.9600] [ 4571] [depth= 1] . ( 2 sec) [ -18187.6164] [ 4561] [depth= 5] . ( 2 sec) [ -18185.1235] [ 4563] [depth= 2] . ( 2 sec) [ -18022.0918] [ 4499] [depth= 9] . ( 2 sec) [ -17928.0673] [ 4426] [depth= 8] . ( 2 sec) [ -17800.6913] [ 4419] [depth= 1] . ( 2 sec) [ -17269.0926] [ 4343] [depth= 4] . ( 2 sec) [ -17221.3028] [ 4327] [depth= 4] . ( 2 sec) [ -17017.8089] [ 4319] [depth= 2] . ( 2 sec) [ -16847.8620] [ 4268] [depth= 1] . ( 2 sec) [ -16500.0710] [ 4126] [depth= 6] . ( 2 sec) [ -16441.3518] [ 4123] [depth= 1] . ( 2 sec) [ -16223.9907] [ 4102] [depth= 6] . ( 2 sec) [ -16019.3770] [ 4076] [depth= 15] . ( 2 sec) [ -15832.6588] [ 4034] [depth= 14] . ( 2 sec) [ -15704.4351] [ 3983] [depth= 12] . ( 2 sec) [ -15696.4101] [ 3986] [depth= 1] . ( 3 sec) [ -15611.6229] [ 3988] [depth= 2] . ( 3 sec) [ -15519.6005] [ 3970] [depth= 7] . ( 3 sec) [ -15513.0169] [ 3971] [depth= 1] . ( 3 sec) [ -15369.5467] [ 3922] [depth= 3] . ( 3 sec) [ -15211.5439] [ 3853] [depth= 9] . ( 3 sec) [ -15008.4167] [ 3765] [depth= 7] . ( 3 sec) [ -14988.5502] [ 3731] [depth= 1] . ( 3 sec) [ -14789.7156] [ 3653] [depth= 5] . ( 3 sec) [ -14694.9757] [ 3611] [depth= 5] . ( 3 sec) [ -14427.6043] [ 3593] [depth= 3] . ( 3 sec) [ -14406.1643] [ 3570] [depth= 8] . ( 3 sec) [ -14360.1546] [ 3539] [depth= 6] . ( 3 sec) [ -14294.7070] [ 3561] [depth= 1] . ( 3 sec) [ -14254.5872] [ 3533] [depth= 2] . ( 3 sec) [ -14149.2906] [ 3503] [depth= 3] . ( 3 sec) [ -13939.4919] [ 3452] [depth= 4] . ( 3 sec) [ -13816.3629] [ 3440] [depth= 1] . ( 3 sec) [ -13763.2968] [ 3431] [depth= 6] . ( 3 sec) [ -13740.7781] [ 3437] [depth= 1] . ( 4 sec) [ -13619.9501] [ 3399] [depth= 7] . ( 4 sec) [ -13581.7231] [ 3397] [depth= 2] . ( 4 sec) [ -13516.5615] [ 3389] [depth= 6] . ( 4 sec) [ -13495.6967] [ 3374] [depth= 2] . ( 4 sec) [ -13394.4824] [ 3357] [depth= 4] . ( 4 sec) [ -13276.9602] [ 3313] [depth= 7] . ( 4 sec) [ -13194.8523] [ 3310] [depth= 1] . ( 4 sec) [ -13188.9603] [ 3312] [depth= 2] . ( 4 sec) [ -13056.9269] [ 3241] [depth= 1] . ( 4 sec) [ -13030.8155] [ 3238] [depth= 1] . ( 4 sec) [ -12958.2503] [ 3213] [depth= 3] . ( 4 sec) [ -12911.1755] [ 3190] [depth= 3] . ( 4 sec) [ -12880.0037] [ 3209] [depth= 1] . ( 4 sec) [ -12822.4617] [ 3179] [depth= 1] . ( 4 sec) [ -12779.1309] [ 3177] [depth= 1] . ( 4 sec) [ -12729.2772] [ 3159] [depth= 8] . ( 4 sec) [ -12720.9038] [ 3166] [depth= 2] . ( 4 sec) [ -12709.9135] [ 3118] [depth= 6] . ( 5 sec) [ -12675.9106] [ 3112] [depth= 1] . ( 5 sec) [ -12564.3415] [ 3061] [depth= 2] . ( 5 sec) [ -12528.9596] [ 3056] [depth= 2] . ( 5 sec) [ -12507.6862] [ 3060] [depth= 1] . ( 5 sec) [ -12441.1392] [ 3047] [depth= 3] . ( 5 sec) [ -12435.0796] [ 3047] [depth= 1] . ( 5 sec) [ -12410.5170] [ 3039] [depth= 6] . ( 5 sec) [ -12371.1731] [ 3046] [depth= 1] . ( 5 sec) [ -12367.3327] [ 3048] [depth= 1] . ( 5 sec) [ -12350.3838] [ 3039] [depth= 1] . ( 5 sec) [ -12089.6696] [ 2952] [depth= 10] . ( 5 sec) [ -12082.5955] [ 2949] [depth= 1] . ( 5 sec) [ -12080.5364] [ 2947] [depth= 1] . ( 5 sec) [ -12032.8532] [ 2950] [depth= 2] . ( 6 sec) [ -11902.3711] [Branch lengths ] . ( 6 sec) [ -11898.5182] [GTR parameters ] . ( 6 sec) [ -11872.5186] [Alpha ][ 0.796483] . ( 6 sec) [ -11864.1049] [ 2928] [depth= 2] . ( 6 sec) [ -11861.8935] [ 2929] [depth= 1] . ( 7 sec) [ -11825.2775] [ 2901] [depth= 2] . ( 7 sec) [ -11782.5160] [ 2885] [depth= 2] . ( 7 sec) [ -11781.7261] [ 2887] [depth= 1] . ( 7 sec) [ -11773.6610] [ 2881] [depth= 1] . ( 7 sec) [ -11772.3830] [ 2881] [depth= 1] . ( 7 sec) [ -11581.4906] [ 2758] [depth= 5] . ( 7 sec) [ -11580.4911] [ 2758] [depth= 1] . ( 7 sec) [ -11578.9801] [ 2759] [depth= 1] . ( 7 sec) [ -11576.6336] [ 2759] [depth= 2] . ( 8 sec) [ -11572.1185] [ 2755] [depth= 2] . ( 8 sec) [ -11570.9297] [ 2773] [depth= 1] . ( 8 sec) [ -11570.7132] [ 2778] [depth= 1] . ( 8 sec) [ -11569.3855] [ 2780] [depth= 1] . ( 8 sec) [ -11569.1369] [ 2781] [depth= 1] . ( 8 sec) [ -11563.2660] [ 2770] [depth= 1] . ( 8 sec) [ -11562.9176] [ 2767] [depth= 2] . ( 9 sec) [ -11561.8319] [ 2770] [depth= 1] . ( 9 sec) [ -11561.6948] [ 2772] [depth= 1] . ( 9 sec) [ -11558.5804] [ 2761] [depth= 2] . ( 9 sec) [ -11555.8830] [ 2764] [depth= 1] . ( 10 sec) [ -11555.7675] [ 2768] [depth= 1] . ( 10 sec) [ -11533.8388] [Branch lengths ] . ( 10 sec) [ -11533.5526] [GTR parameters ] . ( 10 sec) [ -11530.3174] [Alpha ][ 0.938933] . ( 11 sec) [ -11530.2548] [ 2764] [depth= 2] . ( 11 sec) [ -11530.1506] [ 2762] [depth= 1] . ( 11 sec) [ -11530.0750] [ 2755] [depth= 1] . ( 12 sec) [ -11529.9372] [ 2762] [depth= 2] . ( 12 sec) [ -11529.8871] [ 2764] [depth= 1] . ( 13 sec) [ -11529.6805] [ 2764] [depth= 1] . ( 13 sec) [ -11529.5302] [ 2761] [depth= 1] . ( 14 sec) [ -11527.1137] [Branch lengths ] . ( 14 sec) [ -11527.1101] [GTR parameters ] . ( 14 sec) [ -11527.0868] [Alpha ][ 0.952175] . ( 15 sec) [ -11526.8848] [ 2755] [depth= 2] . ( 17 sec) [ -11526.5931] [ 2755] [depth= 1] . ( 18 sec) [ -11525.0478] [Branch lengths ] . ( 18 sec) [ -11525.0473] [GTR parameters ] . ( 18 sec) [ -11525.0463] [Alpha ][ 0.954787] . ( 21 sec) [ -11524.8939] [Branch lengths ] . ( 32 sec) [ -11524.2300] [ 2752] [depth= 2] . ( 41 sec) [ -11524.1877] [ 2751] [depth= 1] . ( 43 sec) [ -11524.1291] [Branch lengths ] . ( 43 sec) [ -11524.1228] [GTR parameters ] . ( 43 sec) [ -11524.1227] [Alpha ][ 0.955742] . ( 43 sec) [ -11524.1227] [Topology ] . ( 44 sec) [ -11524.1206] [Topology ] . ( 45 sec) [ -11524.1199] [Topology ] . ( 45 sec) [ -11524.1199] [GTR parameters ] . ( 45 sec) [ -11524.1199] [Alpha ][ 0.955742] . ( 45 sec) [ -11524.1199] [Topology ] . ( 46 sec) [ -11524.1195] [Topology ] . ( 46 sec) [ -11524.1195] [GTR parameters ] . ( 46 sec) [ -11524.1195] [Alpha ][ 0.955742] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11524.119487. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -20721.8888] [GTR parameters ] . ( 1 sec) [ -20350.5184] [Alpha ][ 0.500960] . ( 1 sec) [ -20222.7636] [ 5000] [depth= 6] . ( 1 sec) [ -20121.7452] [ 4971] [depth= 7] . ( 1 sec) [ -20070.1443] [ 4955] [depth= 5] . ( 2 sec) [ -19997.7584] [ 4941] [depth= 1] . ( 2 sec) [ -19828.5825] [ 4845] [depth= 7] . ( 2 sec) [ -19720.2983] [ 4828] [depth= 3] . ( 2 sec) [ -19665.3727] [ 4808] [depth= 9] . ( 2 sec) [ -19569.1604] [ 4774] [depth= 9] . ( 2 sec) [ -19452.0403] [ 4730] [depth= 14] . ( 2 sec) [ -19085.4161] [ 4658] [depth= 8] . ( 2 sec) [ -18994.3796] [ 4653] [depth= 16] . ( 2 sec) [ -18827.6423] [ 4590] [depth= 15] . ( 2 sec) [ -18776.2822] [ 4567] [depth= 3] . ( 2 sec) [ -18602.2779] [ 4562] [depth= 2] . ( 2 sec) [ -18569.9312] [ 4560] [depth= 1] . ( 2 sec) [ -18483.3721] [ 4514] [depth= 9] . ( 2 sec) [ -18349.1051] [ 4434] [depth= 2] . ( 2 sec) [ -18096.6725] [ 4405] [depth= 4] . ( 2 sec) [ -17867.6805] [ 4384] [depth= 10] . ( 2 sec) [ -17659.1560] [ 4327] [depth= 1] . ( 2 sec) [ -17508.2278] [ 4265] [depth= 10] . ( 2 sec) [ -17222.6095] [ 4176] [depth= 8] . ( 2 sec) [ -17184.0549] [ 4175] [depth= 1] . ( 2 sec) [ -17154.2934] [ 4125] [depth= 7] . ( 2 sec) [ -17033.5389] [ 4122] [depth= 1] . ( 3 sec) [ -16919.0754] [ 4101] [depth= 1] . ( 3 sec) [ -16609.3886] [ 3979] [depth= 9] . ( 3 sec) [ -16604.9504] [ 3990] [depth= 1] . ( 3 sec) [ -16473.4352] [ 3931] [depth= 3] . ( 3 sec) [ -16139.2674] [ 3881] [depth= 5] . ( 3 sec) [ -15764.2311] [ 3764] [depth= 10] . ( 3 sec) [ -15714.2837] [ 3749] [depth= 2] . ( 3 sec) [ -15601.1179] [ 3688] [depth= 2] . ( 3 sec) [ -15556.9672] [ 3623] [depth= 7] . ( 3 sec) [ -14878.2266] [ 3534] [depth= 11] . ( 3 sec) [ -14812.7929] [ 3544] [depth= 1] . ( 3 sec) [ -14558.8511] [ 3465] [depth= 6] . ( 3 sec) [ -14470.6020] [ 3494] [depth= 2] . ( 3 sec) [ -14459.7396] [ 3482] [depth= 1] . ( 3 sec) [ -14208.1115] [ 3435] [depth= 5] . ( 3 sec) [ -14151.0542] [ 3412] [depth= 1] . ( 3 sec) [ -14109.6631] [ 3414] [depth= 1] . ( 3 sec) [ -14099.3883] [ 3414] [depth= 1] . ( 3 sec) [ -13901.8653] [ 3329] [depth= 4] . ( 4 sec) [ -13622.2575] [ 3248] [depth= 2] . ( 4 sec) [ -13597.3915] [ 3253] [depth= 1] . ( 4 sec) [ -13578.6304] [ 3245] [depth= 1] . ( 4 sec) [ -13455.9538] [ 3216] [depth= 3] . ( 4 sec) [ -13328.8431] [ 3208] [depth= 2] . ( 4 sec) [ -13317.3012] [ 3195] [depth= 1] . ( 4 sec) [ -13266.9485] [ 3174] [depth= 2] . ( 4 sec) [ -13185.2264] [ 3166] [depth= 1] . ( 4 sec) [ -13077.7859] [ 3156] [depth= 4] . ( 4 sec) [ -12923.9118] [ 3088] [depth= 3] . ( 4 sec) [ -12817.5079] [ 3058] [depth= 4] . ( 4 sec) [ -12775.3376] [ 3064] [depth= 1] . ( 4 sec) [ -12731.8410] [ 3048] [depth= 3] . ( 4 sec) [ -12682.6064] [ 3008] [depth= 6] . ( 4 sec) [ -12631.7756] [ 2992] [depth= 5] . ( 4 sec) [ -12585.9545] [ 3002] [depth= 1] . ( 4 sec) [ -12491.8609] [ 2969] [depth= 3] . ( 4 sec) [ -12482.9630] [ 2966] [depth= 2] . ( 4 sec) [ -12452.3786] [ 2974] [depth= 2] . ( 4 sec) [ -12435.0133] [ 2960] [depth= 5] . ( 4 sec) [ -12389.3259] [ 2939] [depth= 1] . ( 5 sec) [ -12344.8375] [ 2905] [depth= 3] . ( 5 sec) [ -12339.2730] [ 2906] [depth= 2] . ( 5 sec) [ -12331.3157] [ 2904] [depth= 1] . ( 5 sec) [ -12321.3849] [ 2897] [depth= 2] . ( 5 sec) [ -12285.4598] [ 2900] [depth= 1] . ( 5 sec) [ -12276.3804] [ 2910] [depth= 1] . ( 5 sec) [ -12268.8616] [ 2910] [depth= 1] . ( 5 sec) [ -12230.5601] [ 2897] [depth= 3] . ( 5 sec) [ -12136.5065] [ 2871] [depth= 1] . ( 5 sec) [ -12133.5424] [ 2858] [depth= 3] . ( 5 sec) [ -12127.9394] [ 2855] [depth= 2] . ( 5 sec) [ -12007.9710] [ 2814] [depth= 1] . ( 5 sec) [ -11998.0983] [ 2808] [depth= 1] . ( 5 sec) [ -11987.7489] [ 2830] [depth= 1] . ( 5 sec) [ -11986.0984] [ 2830] [depth= 2] . ( 5 sec) [ -11983.9804] [ 2826] [depth= 1] . ( 6 sec) [ -11699.1591] [Branch lengths ] . ( 6 sec) [ -11696.6885] [GTR parameters ] . ( 6 sec) [ -11660.2422] [Alpha ][ 0.875063] . ( 6 sec) [ -11654.0222] [ 2818] [depth= 1] . ( 6 sec) [ -11648.4587] [ 2806] [depth= 1] . ( 7 sec) [ -11638.9209] [ 2810] [depth= 2] . ( 7 sec) [ -11611.7587] [ 2792] [depth= 2] . ( 7 sec) [ -11611.2239] [ 2791] [depth= 1] . ( 7 sec) [ -11610.1298] [ 2791] [depth= 1] . ( 7 sec) [ -11609.2519] [ 2792] [depth= 2] . ( 7 sec) [ -11608.9860] [ 2794] [depth= 2] . ( 7 sec) [ -11600.4014] [ 2799] [depth= 1] . ( 7 sec) [ -11574.1672] [ 2784] [depth= 1] . ( 8 sec) [ -11572.4296] [ 2775] [depth= 1] . ( 8 sec) [ -11569.1446] [ 2760] [depth= 2] . ( 8 sec) [ -11564.4314] [ 2740] [depth= 1] . ( 8 sec) [ -11564.2643] [ 2739] [depth= 1] . ( 8 sec) [ -11563.8763] [ 2741] [depth= 1] . ( 8 sec) [ -11562.1245] [ 2760] [depth= 2] . ( 8 sec) [ -11560.6587] [ 2759] [depth= 1] . ( 8 sec) [ -11560.4516] [ 2762] [depth= 1] . ( 8 sec) [ -11555.8160] [ 2763] [depth= 1] . ( 9 sec) [ -11555.5761] [ 2765] [depth= 1] . ( 9 sec) [ -11554.3572] [ 2760] [depth= 1] . ( 9 sec) [ -11551.6383] [ 2767] [depth= 2] . ( 9 sec) [ -11549.6091] [ 2763] [depth= 1] . ( 9 sec) [ -11549.4627] [ 2760] [depth= 2] . ( 10 sec) [ -11534.8309] [Branch lengths ] . ( 10 sec) [ -11534.7909] [GTR parameters ] . ( 10 sec) [ -11534.0386] [Alpha ][ 0.946491] . ( 10 sec) [ -11532.1016] [ 2760] [depth= 1] . ( 11 sec) [ -11531.9709] [ 2759] [depth= 1] . ( 12 sec) [ -11531.8945] [ 2753] [depth= 2] . ( 13 sec) [ -11531.5938] [ 2753] [depth= 1] . ( 13 sec) [ -11531.5713] [ 2755] [depth= 1] . ( 14 sec) [ -11525.7220] [Branch lengths ] . ( 14 sec) [ -11525.7050] [GTR parameters ] . ( 14 sec) [ -11525.6952] [Alpha ][ 0.955087] . ( 18 sec) [ -11524.9757] [Branch lengths ] . ( 31 sec) [ -11524.3106] [ 2752] [depth= 2] . ( 33 sec) [ -11524.2991] [ 2751] [depth= 1] . ( 39 sec) [ -11524.1502] [Branch lengths ] . ( 40 sec) [ -11524.1435] [GTR parameters ] . ( 40 sec) [ -11524.1434] [Alpha ][ 0.956042] . ( 40 sec) [ -11524.1434] [Topology ] . ( 41 sec) [ -11524.1371] [Topology ] . ( 41 sec) [ -11524.1352] [Topology ] . ( 42 sec) [ -11524.1343] [Topology ] . ( 42 sec) [ -11524.1343] [GTR parameters ] . ( 42 sec) [ -11524.1343] [Alpha ][ 0.956042] . ( 42 sec) [ -11524.1343] [Topology ] . ( 43 sec) [ -11524.1339] [Topology ] . ( 43 sec) [ -11524.1339] [GTR parameters ] . ( 43 sec) [ -11524.1339] [Alpha ][ 0.956042] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -11524.1331] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11524.133060. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11647.550131 . ( 1 sec) [ -11644.9724] [GTR parameters ] . ( 1 sec) [ -11644.5594] [Alpha ][ 0.939814] . ( 1 sec) [ -11644.5594] [Topology ] . ( 1 sec) [ -11553.5851] [Topology ] . ( 2 sec) [ -11534.4428] [Topology ] . ( 3 sec) [ -11529.9584] [Topology ] . ( 4 sec) [ -11527.9639] [Topology ] . ( 5 sec) [ -11526.9049] [Topology ] . ( 6 sec) [ -11526.3062] [Topology ] . ( 6 sec) [ -11525.7263] [Topology ] . ( 7 sec) [ -11525.2686] [Topology ] . ( 8 sec) [ -11525.1291] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11525.057322 . ( 15 sec) [ -11525.0023] [GTR parameters ] . ( 15 sec) [ -11524.9751] [Alpha ][ 0.954125] . ( 15 sec) [ -11524.9751] [Topology ] . ( 16 sec) [ -11524.9319] [Topology ] . ( 17 sec) [ -11524.9078] [Topology ] . ( 18 sec) [ -11524.8939] [Topology ] . ( 19 sec) [ -11524.8857] [Topology ] . ( 19 sec) [ -11524.8809] [Topology ] . ( 20 sec) [ -11524.8780] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11524.878014 . ( 26 sec) [ -11524.8779] [GTR parameters ] . ( 27 sec) [ -11524.8779] [Alpha ][ 0.955079] . ( 27 sec) [ -11524.8779] [Topology ] . ( 27 sec) [ -11524.8761] [Topology ] . ( 28 sec) [ -11524.8751] [Topology ] . ( 29 sec) [ -11524.8745] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11524.874533 . ( 35 sec) [ -11524.8745] [GTR parameters ] . ( 35 sec) [ -11524.8745] [Alpha ][ 0.955079] . ( 35 sec) [ -11524.8745] [Topology ] . ( 36 sec) [ -11524.8742] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -11644.9724] [GTR parameters ] . ( 49 sec) [ -11644.5594] [Alpha ][ 0.939814] . ( 49 sec) [ -11643.1295] [ 2734] [depth= 2] . ( 49 sec) [ -11641.6106] [ 2733] [depth= 1] . ( 49 sec) [ -11640.1170] [ 2734] [depth= 1] . ( 49 sec) [ -11639.4533] [ 2733] [depth= 1] . ( 50 sec) [ -11637.9517] [ 2734] [depth= 1] . ( 50 sec) [ -11634.0380] [ 2733] [depth= 1] . ( 50 sec) [ -11631.9918] [ 2733] [depth= 1] . ( 50 sec) [ -11630.1070] [ 2745] [depth= 1] . ( 50 sec) [ -11630.0271] [ 2745] [depth= 1] . ( 50 sec) [ -11628.3776] [ 2745] [depth= 1] . ( 50 sec) [ -11625.2307] [ 2745] [depth= 1] . ( 51 sec) [ -11622.0834] [ 2745] [depth= 1] . ( 51 sec) [ -11605.9065] [ 2761] [depth= 1] . ( 51 sec) [ -11600.6969] [ 2764] [depth= 1] . ( 51 sec) [ -11599.2849] [ 2763] [depth= 1] . ( 51 sec) [ -11596.8586] [ 2763] [depth= 1] . ( 52 sec) [ -11593.6002] [ 2763] [depth= 2] . ( 52 sec) [ -11591.2577] [ 2770] [depth= 1] . ( 52 sec) [ -11590.9509] [ 2769] [depth= 1] . ( 52 sec) [ -11582.6558] [ 2764] [depth= 1] . ( 52 sec) [ -11580.4628] [ 2764] [depth= 1] . ( 52 sec) [ -11574.6233] [ 2764] [depth= 1] . ( 52 sec) [ -11572.7803] [ 2767] [depth= 1] . ( 52 sec) [ -11528.4191] [Branch lengths ] . ( 53 sec) [ -11528.3451] [GTR parameters ] . ( 53 sec) [ -11528.3210] [Alpha ][ 0.953445] . ( 53 sec) [ -11527.5788] [ 2755] [depth= 1] . ( 56 sec) [ -11527.3879] [ 2752] [depth= 1] . ( 56 sec) [ -11524.5705] [Branch lengths ] . ( 56 sec) [ -11524.5697] [GTR parameters ] . ( 56 sec) [ -11524.5693] [Alpha ][ 0.955074] . ( 60 sec) [ -11524.2115] [Branch lengths ] . ( 82 sec) [ -11524.1517] [Branch lengths ] . ( 82 sec) [ -11524.1517] [Topology ] . ( 83 sec) [ -11524.1424] [Topology ] . ( 83 sec) [ -11524.1386] [Topology ] . ( 84 sec) [ -11524.1366] [Topology ] . ( 85 sec) [ -11524.1354] [Topology ] . ( 86 sec) [ -11524.1347] [Topology ] . ( 86 sec) [ -11524.1345] [GTR parameters ] . ( 86 sec) [ -11524.1345] [Alpha ][ 0.956029] . ( 86 sec) [ -11524.1345] [Topology ] . ( 87 sec) [ -11524.1340] [Topology ] . ( 87 sec) [ -11524.1340] [GTR parameters ] . ( 87 sec) [ -11524.1340] [Alpha ][ 0.956029] . Checking for NNIs, optimizing five branches... . ( 93 sec) [ -11524.1330] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11524.874160 . Log likelihood obtained after SPR moves : -11524.132987 . Log likelihood of the current tree: -11524.132987. . Printing the most likely tree in file 'data37.phy_phyml_tree.txt'... . Best log likelihood : -11524.119487 . Time used 0h1m39s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo