.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_2006.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... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21997.5202] [GTR parameters ] . ( 1 sec) [ -21523.9600] [Alpha ][ 0.500960] . ( 1 sec) [ -21396.7252] [ 3466] [depth= 11] . ( 1 sec) [ -21298.6063] [ 3441] [depth= 6] . ( 1 sec) [ -21024.7354] [ 3428] [depth= 2] . ( 1 sec) [ -20975.6095] [ 3425] [depth= 1] . ( 1 sec) [ -20785.1332] [ 3398] [depth= 15] . ( 1 sec) [ -20579.9768] [ 3388] [depth= 8] . ( 1 sec) [ -20498.2861] [ 3368] [depth= 1] . ( 1 sec) [ -20246.9471] [ 3354] [depth= 2] . ( 1 sec) [ -20169.8680] [ 3354] [depth= 3] . ( 1 sec) [ -20111.7087] [ 3352] [depth= 11] . ( 2 sec) [ -20079.3739] [ 3335] [depth= 2] . ( 2 sec) [ -20057.1580] [ 3332] [depth= 1] . ( 2 sec) [ -20026.3631] [ 3332] [depth= 7] . ( 2 sec) [ -20021.0886] [ 3330] [depth= 2] . ( 2 sec) [ -19969.5509] [ 3327] [depth= 2] . ( 2 sec) [ -19894.7259] [ 3326] [depth= 1] . ( 2 sec) [ -19860.7653] [ 3323] [depth= 9] . ( 2 sec) [ -19660.5397] [ 3310] [depth= 18] . ( 2 sec) [ -19646.6760] [ 3309] [depth= 1] . ( 2 sec) [ -19614.4708] [ 3301] [depth= 10] . ( 3 sec) [ -19394.4419] [ 3299] [depth= 10] . ( 3 sec) [ -19327.2155] [ 3291] [depth= 11] . ( 3 sec) [ -19290.8761] [ 3283] [depth= 13] . ( 3 sec) [ -19280.7184] [ 3286] [depth= 1] . ( 3 sec) [ -19274.1319] [ 3286] [depth= 1] . ( 3 sec) [ -19218.3750] [ 3277] [depth= 15] . ( 3 sec) [ -19061.7024] [ 3249] [depth= 7] . ( 3 sec) [ -19059.5464] [ 3248] [depth= 1] . ( 3 sec) [ -18960.2816] [ 3227] [depth= 10] . ( 4 sec) [ -18951.3799] [ 3224] [depth= 2] . ( 4 sec) [ -18930.6518] [ 3221] [depth= 8] . ( 4 sec) [ -18765.1293] [ 3217] [depth= 4] . ( 4 sec) [ -18744.9968] [ 3223] [depth= 3] . ( 4 sec) [ -18707.7489] [ 3208] [depth= 20] . ( 4 sec) [ -18548.3135] [ 3187] [depth= 9] . ( 4 sec) [ -18529.8477] [ 3189] [depth= 10] . ( 4 sec) [ -18415.3668] [ 3182] [depth= 9] . ( 4 sec) [ -18410.8747] [ 3180] [depth= 2] . ( 4 sec) [ -18260.6677] [ 3136] [depth= 9] . ( 5 sec) [ -18237.1513] [ 3130] [depth= 6] . ( 5 sec) [ -17941.1516] [ 3070] [depth= 8] . ( 5 sec) [ -17893.0376] [ 3055] [depth= 1] . ( 5 sec) [ -17816.0242] [ 3049] [depth= 4] . ( 5 sec) [ -17746.0801] [ 3039] [depth= 1] . ( 5 sec) [ -17643.7297] [ 3035] [depth= 1] . ( 5 sec) [ -17590.2018] [ 3028] [depth= 17] . ( 5 sec) [ -17574.1301] [ 3028] [depth= 1] . ( 5 sec) [ -17547.2273] [ 3024] [depth= 5] . ( 5 sec) [ -17516.4138] [ 3025] [depth= 1] . ( 6 sec) [ -17506.9086] [ 3022] [depth= 7] . ( 6 sec) [ -17487.2819] [ 3023] [depth= 1] . ( 6 sec) [ -17464.7961] [ 3026] [depth= 1] . ( 6 sec) [ -17442.7030] [ 3018] [depth= 2] . ( 6 sec) [ -17319.5214] [ 3012] [depth= 4] . ( 6 sec) [ -17311.5459] [ 3029] [depth= 1] . ( 6 sec) [ -17283.7622] [ 3012] [depth= 1] . ( 6 sec) [ -17240.1496] [ 2994] [depth= 1] . ( 6 sec) [ -17228.3545] [ 2982] [depth= 5] . ( 6 sec) [ -17179.8028] [ 2976] [depth= 10] . ( 6 sec) [ -17165.4206] [ 2976] [depth= 6] . ( 7 sec) [ -17163.9865] [ 2978] [depth= 5] . ( 7 sec) [ -17011.9050] [ 2974] [depth= 6] . ( 7 sec) [ -17009.0753] [ 2971] [depth= 1] . ( 7 sec) [ -16990.1189] [ 2960] [depth= 6] . ( 7 sec) [ -16958.4712] [ 2947] [depth= 2] . ( 7 sec) [ -16854.2719] [ 2923] [depth= 14] . ( 7 sec) [ -16833.6537] [ 2918] [depth= 7] . ( 7 sec) [ -16794.8580] [ 2899] [depth= 1] . ( 7 sec) [ -16725.9054] [ 2897] [depth= 2] . ( 7 sec) [ -16674.4903] [ 2880] [depth= 8] . ( 8 sec) [ -16533.8018] [ 2852] [depth= 13] . ( 8 sec) [ -16517.5998] [ 2845] [depth= 5] . ( 8 sec) [ -16509.2838] [ 2839] [depth= 1] . ( 8 sec) [ -16506.2471] [ 2838] [depth= 9] . ( 8 sec) [ -16431.7188] [ 2827] [depth= 8] . ( 8 sec) [ -16430.0194] [ 2836] [depth= 1] . ( 8 sec) [ -16396.2810] [ 2829] [depth= 4] . ( 8 sec) [ -16361.0950] [ 2821] [depth= 3] . ( 8 sec) [ -16346.3973] [ 2813] [depth= 2] . ( 9 sec) [ -16142.4619] [ 2806] [depth= 4] . ( 9 sec) [ -16128.2671] [ 2806] [depth= 2] . ( 9 sec) [ -16115.5613] [ 2801] [depth= 3] . ( 9 sec) [ -16099.3329] [ 2798] [depth= 4] . ( 9 sec) [ -16094.7357] [ 2797] [depth= 1] . ( 9 sec) [ -16080.3710] [ 2789] [depth= 15] . ( 9 sec) [ -16080.3139] [ 2788] [depth= 1] . ( 10 sec) [ -16079.0634] [ 2790] [depth= 1] . ( 10 sec) [ -16076.5949] [ 2789] [depth= 1] . ( 10 sec) [ -16053.4544] [ 2784] [depth= 4] . ( 10 sec) [ -15971.7328] [ 2785] [depth= 2] . ( 10 sec) [ -15917.6337] [ 2770] [depth= 15] . ( 10 sec) [ -15864.2810] [ 2748] [depth= 7] . ( 10 sec) [ -15855.8040] [ 2747] [depth= 3] . ( 10 sec) [ -15829.9016] [ 2747] [depth= 1] . ( 10 sec) [ -15825.2442] [ 2746] [depth= 1] . ( 11 sec) [ -15822.6761] [ 2747] [depth= 2] . ( 11 sec) [ -15822.2135] [ 2751] [depth= 3] . ( 11 sec) [ -15818.3975] [ 2748] [depth= 2] . ( 11 sec) [ -15742.3904] [ 2723] [depth= 6] . ( 11 sec) [ -15721.4523] [ 2716] [depth= 2] . ( 11 sec) [ -15695.1448] [ 2711] [depth= 8] . ( 11 sec) [ -15616.7594] [ 2716] [depth= 12] . ( 11 sec) [ -15609.2634] [ 2714] [depth= 5] . ( 12 sec) [ -15539.9590] [ 2684] [depth= 5] . ( 12 sec) [ -15535.3889] [ 2681] [depth= 1] . ( 12 sec) [ -15487.5569] [ 2663] [depth= 9] . ( 12 sec) [ -15486.7127] [ 2663] [depth= 1] . ( 12 sec) [ -15466.4024] [ 2657] [depth= 1] . ( 12 sec) [ -15224.5340] [ 2632] [depth= 4] . ( 12 sec) [ -15224.2293] [ 2633] [depth= 1] . ( 12 sec) [ -15223.9912] [ 2633] [depth= 1] . ( 12 sec) [ -15210.3001] [ 2633] [depth= 9] . ( 13 sec) [ -15184.6708] [ 2628] [depth= 2] . ( 13 sec) [ -15158.0682] [ 2616] [depth= 1] . ( 13 sec) [ -15146.5073] [ 2614] [depth= 4] . ( 13 sec) [ -15122.0364] [ 2611] [depth= 4] . ( 13 sec) [ -15120.8807] [ 2610] [depth= 1] . ( 13 sec) [ -15093.9184] [ 2611] [depth= 1] . ( 13 sec) [ -15091.3521] [ 2613] [depth= 1] . ( 13 sec) [ -15081.6524] [ 2605] [depth= 3] . ( 13 sec) [ -15076.3119] [ 2603] [depth= 1] . ( 14 sec) [ -15075.1494] [ 2604] [depth= 1] . ( 14 sec) [ -15073.3142] [ 2606] [depth= 1] . ( 14 sec) [ -15068.6748] [ 2606] [depth= 4] . ( 14 sec) [ -15067.3435] [ 2599] [depth= 8] . ( 14 sec) [ -15060.0436] [ 2598] [depth= 9] . ( 15 sec) [ -15056.0394] [ 2595] [depth= 2] . ( 15 sec) [ -14980.9850] [Branch lengths ] . ( 20 sec) [ -14603.2834] [GTR parameters ] . ( 20 sec) [ -14507.6996] [Alpha ][ 0.275590] . ( 20 sec) [ -14507.6136] [ 2594] [depth= 1] . ( 20 sec) [ -14505.7135] [ 2593] [depth= 1] . ( 20 sec) [ -14455.2239] [ 2577] [depth= 6] . ( 20 sec) [ -14437.8519] [ 2570] [depth= 2] . ( 21 sec) [ -14437.4977] [ 2572] [depth= 1] . ( 21 sec) [ -14436.1912] [ 2572] [depth= 1] . ( 21 sec) [ -14436.0985] [ 2569] [depth= 1] . ( 21 sec) [ -14428.5099] [ 2562] [depth= 11] . ( 22 sec) [ -14419.0285] [ 2558] [depth= 6] . ( 22 sec) [ -14418.8105] [ 2557] [depth= 2] . ( 22 sec) [ -14417.0249] [ 2557] [depth= 1] . ( 22 sec) [ -14415.8670] [ 2558] [depth= 1] . ( 22 sec) [ -14405.5048] [ 2560] [depth= 8] . ( 22 sec) [ -14400.9586] [ 2558] [depth= 1] . ( 23 sec) [ -14398.8605] [ 2554] [depth= 2] . ( 23 sec) [ -14398.8154] [ 2552] [depth= 1] . ( 23 sec) [ -14397.4714] [ 2555] [depth= 1] . ( 23 sec) [ -14396.6155] [ 2554] [depth= 3] . ( 23 sec) [ -14396.3300] [ 2554] [depth= 1] . ( 24 sec) [ -14395.8934] [ 2554] [depth= 1] . ( 24 sec) [ -14392.4160] [ 2552] [depth= 5] . ( 25 sec) [ -14389.5971] [ 2546] [depth= 1] . ( 25 sec) [ -14389.5760] [ 2545] [depth= 1] . ( 25 sec) [ -14388.6782] [ 2546] [depth= 1] . ( 26 sec) [ -14387.8590] [ 2547] [depth= 1] . ( 26 sec) [ -14377.3794] [ 2546] [depth= 2] . ( 26 sec) [ -14376.8455] [ 2546] [depth= 1] . ( 27 sec) [ -14376.5039] [ 2549] [depth= 1] . ( 27 sec) [ -14373.6571] [ 2549] [depth= 6] . ( 27 sec) [ -14373.4072] [ 2546] [depth= 1] . ( 27 sec) [ -14373.3224] [ 2548] [depth= 1] . ( 28 sec) [ -14373.1090] [ 2549] [depth= 2] . ( 28 sec) [ -14372.6412] [ 2549] [depth= 2] . ( 28 sec) [ -14368.3319] [ 2546] [depth= 1] . ( 29 sec) [ -14366.0774] [ 2545] [depth= 7] . ( 29 sec) [ -14365.7785] [ 2545] [depth= 1] . ( 29 sec) [ -14363.0371] [ 2545] [depth= 2] . ( 30 sec) [ -14360.4778] [ 2545] [depth= 1] . ( 30 sec) [ -14359.9592] [ 2543] [depth= 1] . ( 30 sec) [ -14358.0501] [ 2541] [depth= 1] . ( 31 sec) [ -14357.1532] [ 2543] [depth= 2] . ( 33 sec) [ -14353.9864] [ 2541] [depth= 1] . ( 36 sec) [ -14341.3488] [Branch lengths ] . ( 39 sec) [ -14340.9864] [GTR parameters ] . ( 39 sec) [ -14340.9857] [Alpha ][ 0.275969] . ( 51 sec) [ -14339.0747] [ 2541] [depth= 6] . ( 52 sec) [ -14338.9470] [ 2541] [depth= 1] . ( 60 sec) [ -14338.4965] [Branch lengths ] . ( 62 sec) [ -14338.4778] [GTR parameters ] . ( 62 sec) [ -14338.4778] [Alpha ][ 0.275969] . ( 83 sec) [ -14338.4363] [Branch lengths ] . ( 93 sec) [ -14336.9447] [ 2547] [depth= 4] . ( 97 sec) [ -14336.8943] [ 2547] [depth= 1] . ( 99 sec) [ -14336.3997] [ 2543] [depth= 1] . ( 128 sec) [ -14336.3099] [ 2543] [depth= 1] . ( 154 sec) [ -14335.4846] [Branch lengths ] . ( 155 sec) [ -14335.4647] [GTR parameters ] . ( 155 sec) [ -14335.4603] [Alpha ][ 0.274844] . ( 228 sec) [ -14335.4383] [Branch lengths ] . ( 228 sec) [ -14335.4383] [Topology ] . ( 229 sec) [ -14335.4377] [Topology ] . ( 231 sec) [ -14335.4356] [GTR parameters ] . ( 231 sec) [ -14335.4356] [Alpha ][ 0.274844] . ( 231 sec) [ -14335.4356] [Topology ] . ( 233 sec) [ -14335.4355] [Topology ] . ( 234 sec) [ -14335.4353] [GTR parameters ] . ( 234 sec) [ -14335.4353] [Alpha ][ 0.274844] . Checking for NNIs, optimizing five branches... . ( 246 sec) [ -14335.4352] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14335.435151. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22859.7784] [GTR parameters ] . ( 1 sec) [ -22376.4708] [Alpha ][ 0.500960] . ( 1 sec) [ -22313.7819] [ 3528] [depth= 6] . ( 1 sec) [ -22078.2893] [ 3491] [depth= 4] . ( 1 sec) [ -22045.4447] [ 3482] [depth= 4] . ( 1 sec) [ -21911.8357] [ 3455] [depth= 1] . ( 1 sec) [ -21744.2067] [ 3439] [depth= 4] . ( 2 sec) [ -21706.4189] [ 3435] [depth= 3] . ( 2 sec) [ -21685.6850] [ 3432] [depth= 5] . ( 2 sec) [ -21675.5841] [ 3431] [depth= 1] . ( 2 sec) [ -21636.6748] [ 3427] [depth= 5] . ( 2 sec) [ -21635.3290] [ 3424] [depth= 1] . ( 2 sec) [ -21390.9084] [ 3422] [depth= 2] . ( 2 sec) [ -21364.8084] [ 3421] [depth= 1] . ( 2 sec) [ -21340.1238] [ 3420] [depth= 2] . ( 2 sec) [ -21335.7369] [ 3422] [depth= 1] . ( 2 sec) [ -21222.0774] [ 3418] [depth= 5] . ( 2 sec) [ -21067.4604] [ 3401] [depth= 9] . ( 2 sec) [ -20987.9372] [ 3396] [depth= 2] . ( 3 sec) [ -20969.5839] [ 3397] [depth= 2] . ( 3 sec) [ -20886.4719] [ 3375] [depth= 7] . ( 3 sec) [ -20730.8021] [ 3341] [depth= 1] . ( 3 sec) [ -20447.3166] [ 3329] [depth= 9] . ( 3 sec) [ -20388.6434] [ 3328] [depth= 6] . ( 3 sec) [ -20255.3520] [ 3310] [depth= 9] . ( 3 sec) [ -20207.3192] [ 3297] [depth= 8] . ( 3 sec) [ -20107.1779] [ 3280] [depth= 9] . ( 3 sec) [ -20096.0392] [ 3278] [depth= 1] . ( 3 sec) [ -19904.8341] [ 3278] [depth= 10] . ( 4 sec) [ -19734.1399] [ 3245] [depth= 2] . ( 4 sec) [ -19698.5501] [ 3240] [depth= 17] . ( 4 sec) [ -19653.1494] [ 3242] [depth= 1] . ( 4 sec) [ -19606.9037] [ 3222] [depth= 16] . ( 4 sec) [ -19570.2071] [ 3205] [depth= 20] . ( 4 sec) [ -19541.9915] [ 3222] [depth= 1] . ( 4 sec) [ -19506.2320] [ 3205] [depth= 1] . ( 4 sec) [ -19348.6877] [ 3176] [depth= 4] . ( 4 sec) [ -19303.4912] [ 3169] [depth= 3] . ( 4 sec) [ -19292.6982] [ 3170] [depth= 1] . ( 4 sec) [ -19287.2175] [ 3167] [depth= 1] . ( 4 sec) [ -19122.9815] [ 3141] [depth= 9] . ( 5 sec) [ -19076.0017] [ 3136] [depth= 9] . ( 5 sec) [ -19072.8005] [ 3133] [depth= 1] . ( 5 sec) [ -18941.1671] [ 3132] [depth= 1] . ( 5 sec) [ -18938.3893] [ 3131] [depth= 1] . ( 5 sec) [ -18832.0677] [ 3130] [depth= 3] . ( 5 sec) [ -18822.8312] [ 3130] [depth= 2] . ( 5 sec) [ -18822.7410] [ 3131] [depth= 2] . ( 5 sec) [ -18813.5087] [ 3130] [depth= 1] . ( 5 sec) [ -18795.7183] [ 3129] [depth= 3] . ( 5 sec) [ -18590.9414] [ 3113] [depth= 4] . ( 5 sec) [ -18566.8673] [ 3108] [depth= 8] . ( 6 sec) [ -18396.5495] [ 3095] [depth= 17] . ( 6 sec) [ -18322.5036] [ 3067] [depth= 6] . ( 6 sec) [ -18317.8663] [ 3066] [depth= 2] . ( 6 sec) [ -18296.7752] [ 3064] [depth= 2] . ( 6 sec) [ -18255.9222] [ 3055] [depth= 8] . ( 6 sec) [ -18222.1700] [ 3053] [depth= 12] . ( 6 sec) [ -18199.0400] [ 3054] [depth= 12] . ( 6 sec) [ -18135.6402] [ 3041] [depth= 4] . ( 6 sec) [ -18097.2934] [ 3030] [depth= 6] . ( 6 sec) [ -17879.8148] [ 3026] [depth= 6] . ( 7 sec) [ -17869.9210] [ 3029] [depth= 1] . ( 7 sec) [ -17760.7071] [ 3017] [depth= 13] . ( 7 sec) [ -17652.4465] [ 2982] [depth= 9] . ( 7 sec) [ -17529.0397] [ 2978] [depth= 7] . ( 7 sec) [ -17455.7280] [ 2959] [depth= 1] . ( 7 sec) [ -17450.7602] [ 2956] [depth= 7] . ( 7 sec) [ -17394.1366] [ 2957] [depth= 1] . ( 7 sec) [ -17385.7021] [ 2956] [depth= 3] . ( 7 sec) [ -17378.8479] [ 2952] [depth= 1] . ( 8 sec) [ -17372.6942] [ 2951] [depth= 1] . ( 8 sec) [ -17310.9073] [ 2940] [depth= 10] . ( 8 sec) [ -17280.5187] [ 2933] [depth= 6] . ( 8 sec) [ -16984.2609] [ 2936] [depth= 8] . ( 8 sec) [ -16791.9480] [ 2913] [depth= 2] . ( 9 sec) [ -16786.7300] [ 2905] [depth= 1] . ( 9 sec) [ -16742.2952] [ 2897] [depth= 4] . ( 9 sec) [ -16732.0668] [ 2898] [depth= 2] . ( 9 sec) [ -16691.5447] [ 2883] [depth= 12] . ( 9 sec) [ -16521.2412] [ 2872] [depth= 2] . ( 9 sec) [ -16514.7029] [ 2878] [depth= 5] . ( 9 sec) [ -16471.8216] [ 2858] [depth= 2] . ( 9 sec) [ -16342.5213] [ 2845] [depth= 3] . ( 9 sec) [ -16340.7348] [ 2844] [depth= 1] . ( 9 sec) [ -16319.3029] [ 2841] [depth= 7] . ( 10 sec) [ -16318.7018] [ 2839] [depth= 1] . ( 10 sec) [ -16314.5647] [ 2840] [depth= 1] . ( 10 sec) [ -16279.1087] [ 2832] [depth= 4] . ( 10 sec) [ -16077.7311] [ 2833] [depth= 1] . ( 10 sec) [ -16007.5440] [ 2800] [depth= 11] . ( 10 sec) [ -16005.2858] [ 2799] [depth= 1] . ( 10 sec) [ -16002.9166] [ 2799] [depth= 2] . ( 10 sec) [ -15966.8827] [ 2791] [depth= 4] . ( 10 sec) [ -15948.3130] [ 2787] [depth= 5] . ( 10 sec) [ -15924.9545] [ 2791] [depth= 1] . ( 10 sec) [ -15902.9318] [ 2790] [depth= 2] . ( 11 sec) [ -15847.1867] [ 2778] [depth= 8] . ( 11 sec) [ -15828.2912] [ 2773] [depth= 3] . ( 11 sec) [ -15822.0772] [ 2772] [depth= 8] . ( 11 sec) [ -15789.8785] [ 2764] [depth= 4] . ( 11 sec) [ -15773.7435] [ 2762] [depth= 1] . ( 11 sec) [ -15772.6863] [ 2764] [depth= 1] . ( 11 sec) [ -15755.4290] [ 2758] [depth= 6] . ( 11 sec) [ -15745.6100] [ 2755] [depth= 2] . ( 11 sec) [ -15700.1822] [ 2745] [depth= 11] . ( 11 sec) [ -15653.1864] [ 2732] [depth= 2] . ( 11 sec) [ -15599.6116] [ 2730] [depth= 1] . ( 12 sec) [ -15518.6385] [ 2721] [depth= 9] . ( 12 sec) [ -15517.7449] [ 2722] [depth= 1] . ( 12 sec) [ -15476.8093] [ 2722] [depth= 2] . ( 12 sec) [ -15475.8489] [ 2721] [depth= 1] . ( 12 sec) [ -15472.1499] [ 2721] [depth= 1] . ( 12 sec) [ -15462.3109] [ 2716] [depth= 3] . ( 12 sec) [ -15462.2568] [ 2713] [depth= 6] . ( 12 sec) [ -15391.9590] [ 2692] [depth= 1] . ( 12 sec) [ -15338.4200] [ 2677] [depth= 1] . ( 12 sec) [ -15337.7605] [ 2677] [depth= 1] . ( 13 sec) [ -15337.3759] [ 2677] [depth= 1] . ( 13 sec) [ -15334.3060] [ 2683] [depth= 1] . ( 13 sec) [ -15331.3189] [ 2685] [depth= 5] . ( 13 sec) [ -15326.8304] [ 2683] [depth= 1] . ( 13 sec) [ -15314.5242] [ 2684] [depth= 2] . ( 14 sec) [ -15308.0273] [ 2684] [depth= 1] . ( 15 sec) [ -15195.2675] [ 2659] [depth= 7] . ( 15 sec) [ -15191.2278] [ 2656] [depth= 1] . ( 15 sec) [ -15189.8898] [ 2655] [depth= 1] . ( 16 sec) [ -15187.4402] [ 2654] [depth= 1] . ( 16 sec) [ -15181.9477] [ 2651] [depth= 1] . ( 16 sec) [ -15180.0974] [ 2649] [depth= 1] . ( 16 sec) [ -15179.8565] [ 2650] [depth= 1] . ( 16 sec) [ -15165.5635] [ 2652] [depth= 6] . ( 16 sec) [ -15155.5206] [ 2652] [depth= 5] . ( 16 sec) [ -15119.1237] [ 2645] [depth= 6] . ( 18 sec) [ -15102.8260] [ 2639] [depth= 1] . ( 18 sec) [ -15038.8245] [Branch lengths ] . ( 23 sec) [ -14665.3130] [GTR parameters ] . ( 23 sec) [ -14567.4658] [Alpha ][ 0.275052] . ( 23 sec) [ -14566.8910] [ 2637] [depth= 1] . ( 24 sec) [ -14559.8956] [ 2637] [depth= 4] . ( 24 sec) [ -14559.8046] [ 2637] [depth= 1] . ( 25 sec) [ -14559.6266] [ 2636] [depth= 2] . ( 25 sec) [ -14557.1324] [ 2628] [depth= 1] . ( 25 sec) [ -14550.7671] [ 2625] [depth= 3] . ( 25 sec) [ -14543.1665] [ 2622] [depth= 1] . ( 25 sec) [ -14535.7999] [ 2619] [depth= 3] . ( 25 sec) [ -14523.9612] [ 2608] [depth= 6] . ( 26 sec) [ -14497.1191] [ 2598] [depth= 4] . ( 26 sec) [ -14495.2733] [ 2595] [depth= 2] . ( 27 sec) [ -14494.3606] [ 2594] [depth= 1] . ( 27 sec) [ -14494.0703] [ 2588] [depth= 2] . ( 27 sec) [ -14474.6006] [ 2583] [depth= 6] . ( 28 sec) [ -14472.5987] [ 2582] [depth= 2] . ( 28 sec) [ -14470.4925] [ 2580] [depth= 2] . ( 28 sec) [ -14463.1958] [ 2576] [depth= 1] . ( 28 sec) [ -14462.2543] [ 2575] [depth= 2] . ( 28 sec) [ -14457.0814] [ 2568] [depth= 1] . ( 28 sec) [ -14456.1298] [ 2567] [depth= 1] . ( 28 sec) [ -14455.1098] [ 2567] [depth= 1] . ( 29 sec) [ -14454.2786] [ 2564] [depth= 2] . ( 30 sec) [ -14450.8368] [ 2563] [depth= 2] . ( 30 sec) [ -14432.0279] [ 2558] [depth= 2] . ( 30 sec) [ -14430.9019] [ 2556] [depth= 2] . ( 30 sec) [ -14429.3972] [ 2555] [depth= 1] . ( 31 sec) [ -14427.7335] [ 2556] [depth= 1] . ( 31 sec) [ -14423.9665] [ 2557] [depth= 1] . ( 31 sec) [ -14423.8059] [ 2557] [depth= 1] . ( 31 sec) [ -14423.1008] [ 2558] [depth= 1] . ( 31 sec) [ -14416.5484] [ 2553] [depth= 1] . ( 32 sec) [ -14413.6465] [ 2549] [depth= 2] . ( 32 sec) [ -14412.9289] [ 2550] [depth= 1] . ( 32 sec) [ -14410.7776] [ 2552] [depth= 1] . ( 32 sec) [ -14410.2393] [ 2551] [depth= 1] . ( 33 sec) [ -14409.2427] [ 2551] [depth= 1] . ( 33 sec) [ -14408.6110] [ 2551] [depth= 1] . ( 33 sec) [ -14408.4242] [ 2554] [depth= 1] . ( 34 sec) [ -14404.4701] [ 2552] [depth= 1] . ( 34 sec) [ -14404.1914] [ 2554] [depth= 2] . ( 36 sec) [ -14403.3999] [ 2557] [depth= 5] . ( 36 sec) [ -14402.9941] [ 2556] [depth= 1] . ( 37 sec) [ -14402.9614] [ 2557] [depth= 1] . ( 37 sec) [ -14402.4971] [ 2556] [depth= 1] . ( 38 sec) [ -14398.4848] [ 2556] [depth= 6] . ( 39 sec) [ -14397.9830] [ 2557] [depth= 1] . ( 39 sec) [ -14396.5309] [ 2556] [depth= 2] . ( 39 sec) [ -14395.6230] [ 2555] [depth= 1] . ( 39 sec) [ -14392.1063] [ 2557] [depth= 5] . ( 39 sec) [ -14391.2046] [ 2558] [depth= 1] . ( 39 sec) [ -14390.8286] [ 2558] [depth= 1] . ( 39 sec) [ -14383.4992] [ 2559] [depth= 6] . ( 40 sec) [ -14380.5826] [ 2559] [depth= 1] . ( 40 sec) [ -14378.0354] [ 2558] [depth= 1] . ( 40 sec) [ -14377.5073] [ 2557] [depth= 1] . ( 40 sec) [ -14366.8548] [ 2552] [depth= 1] . ( 41 sec) [ -14344.3573] [Branch lengths ] . ( 44 sec) [ -14343.5840] [GTR parameters ] . ( 44 sec) [ -14343.5774] [Alpha ][ 0.273675] . ( 48 sec) [ -14342.9318] [ 2548] [depth= 1] . ( 49 sec) [ -14342.0213] [ 2547] [depth= 1] . ( 50 sec) [ -14341.3394] [ 2547] [depth= 1] . ( 50 sec) [ -14340.2410] [ 2547] [depth= 1] . ( 51 sec) [ -14340.1809] [ 2546] [depth= 1] . ( 51 sec) [ -14338.5435] [ 2547] [depth= 2] . ( 52 sec) [ -14337.1879] [ 2544] [depth= 1] . ( 53 sec) [ -14337.1442] [ 2544] [depth= 1] . ( 55 sec) [ -14336.8435] [ 2544] [depth= 1] . ( 56 sec) [ -14336.7498] [ 2544] [depth= 2] . ( 60 sec) [ -14335.6006] [ 2542] [depth= 1] . ( 61 sec) [ -14335.5395] [ 2543] [depth= 1] . ( 62 sec) [ -14334.1809] [ 2542] [depth= 1] . ( 65 sec) [ -14333.8460] [ 2541] [depth= 1] . ( 66 sec) [ -14330.3721] [Branch lengths ] . ( 69 sec) [ -14330.3184] [GTR parameters ] . ( 69 sec) [ -14330.3123] [Alpha ][ 0.274922] . ( 72 sec) [ -14330.1754] [ 2542] [depth= 1] . ( 77 sec) [ -14329.3178] [ 2543] [depth= 1] . ( 82 sec) [ -14328.7602] [ 2549] [depth= 4] . ( 91 sec) [ -14328.1181] [Branch lengths ] . ( 92 sec) [ -14328.1180] [GTR parameters ] . ( 92 sec) [ -14328.1178] [Alpha ][ 0.275197] . ( 115 sec) [ -14328.0655] [Branch lengths ] . ( 186 sec) [ -14328.0517] [Branch lengths ] . ( 186 sec) [ -14328.0517] [Topology ] . ( 188 sec) [ -14328.0493] [Topology ] . ( 190 sec) [ -14328.0483] [Topology ] . ( 191 sec) [ -14328.0477] [Topology ] . ( 192 sec) [ -14328.0444] [GTR parameters ] . ( 193 sec) [ -14328.0410] [Alpha ][ 0.276114] . ( 193 sec) [ -14328.0410] [Topology ] . ( 194 sec) [ -14328.0400] [Topology ] . ( 195 sec) [ -14328.0400] [GTR parameters ] . ( 195 sec) [ -14328.0400] [Alpha ][ 0.276114] . Checking for NNIs, optimizing five branches... . ( 207 sec) [ -14327.9310] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14327.931016. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22180.3710] [GTR parameters ] . ( 1 sec) [ -21709.9938] [Alpha ][ 0.500960] . ( 1 sec) [ -21554.2751] [ 3455] [depth= 14] . ( 1 sec) [ -21407.7418] [ 3439] [depth= 9] . ( 1 sec) [ -21220.9006] [ 3444] [depth= 1] . ( 1 sec) [ -20993.1968] [ 3436] [depth= 7] . ( 1 sec) [ -20985.5864] [ 3424] [depth= 2] . ( 1 sec) [ -20958.2442] [ 3422] [depth= 5] . ( 1 sec) [ -20940.8862] [ 3413] [depth= 2] . ( 1 sec) [ -20924.7479] [ 3411] [depth= 1] . ( 1 sec) [ -20915.0316] [ 3404] [depth= 1] . ( 1 sec) [ -20889.7004] [ 3400] [depth= 7] . ( 2 sec) [ -20819.5774] [ 3397] [depth= 2] . ( 2 sec) [ -20748.4635] [ 3396] [depth= 1] . ( 2 sec) [ -20741.3806] [ 3395] [depth= 1] . ( 2 sec) [ -20738.0654] [ 3393] [depth= 3] . ( 2 sec) [ -20706.9462] [ 3389] [depth= 3] . ( 2 sec) [ -20668.3857] [ 3387] [depth= 5] . ( 2 sec) [ -20535.5819] [ 3382] [depth= 7] . ( 2 sec) [ -20503.1021] [ 3380] [depth= 1] . ( 2 sec) [ -20161.1647] [ 3360] [depth= 10] . ( 2 sec) [ -20034.7653] [ 3336] [depth= 7] . ( 2 sec) [ -19826.8634] [ 3336] [depth= 4] . ( 3 sec) [ -19799.5827] [ 3332] [depth= 7] . ( 3 sec) [ -19604.7211] [ 3323] [depth= 4] . ( 3 sec) [ -19511.6970] [ 3327] [depth= 1] . ( 3 sec) [ -19383.9897] [ 3302] [depth= 2] . ( 3 sec) [ -19277.0738] [ 3276] [depth= 6] . ( 3 sec) [ -19252.0205] [ 3267] [depth= 7] . ( 3 sec) [ -19200.9151] [ 3260] [depth= 1] . ( 3 sec) [ -19029.6745] [ 3232] [depth= 14] . ( 3 sec) [ -18987.1240] [ 3230] [depth= 1] . ( 3 sec) [ -18968.2574] [ 3230] [depth= 2] . ( 3 sec) [ -18925.5547] [ 3227] [depth= 3] . ( 3 sec) [ -18902.2584] [ 3222] [depth= 11] . ( 4 sec) [ -18845.6618] [ 3218] [depth= 12] . ( 4 sec) [ -18807.6712] [ 3213] [depth= 2] . ( 4 sec) [ -18733.5219] [ 3209] [depth= 14] . ( 4 sec) [ -18688.7670] [ 3184] [depth= 1] . ( 4 sec) [ -18660.1186] [ 3178] [depth= 5] . ( 4 sec) [ -18629.5261] [ 3164] [depth= 13] . ( 4 sec) [ -18481.4601] [ 3160] [depth= 1] . ( 4 sec) [ -18477.5063] [ 3155] [depth= 2] . ( 4 sec) [ -18468.5362] [ 3152] [depth= 10] . ( 4 sec) [ -18453.9363] [ 3139] [depth= 4] . ( 4 sec) [ -18440.8788] [ 3157] [depth= 1] . ( 5 sec) [ -18397.8959] [ 3141] [depth= 9] . ( 5 sec) [ -18333.3069] [ 3123] [depth= 1] . ( 5 sec) [ -18239.7605] [ 3094] [depth= 6] . ( 5 sec) [ -18224.1363] [ 3091] [depth= 8] . ( 5 sec) [ -18138.4956] [ 3086] [depth= 7] . ( 5 sec) [ -18084.1533] [ 3079] [depth= 7] . ( 5 sec) [ -18083.1407] [ 3077] [depth= 1] . ( 5 sec) [ -18033.4218] [ 3062] [depth= 3] . ( 5 sec) [ -18003.9325] [ 3061] [depth= 2] . ( 5 sec) [ -17876.8311] [ 3051] [depth= 13] . ( 6 sec) [ -17858.4395] [ 3043] [depth= 1] . ( 6 sec) [ -17831.5774] [ 3037] [depth= 8] . ( 6 sec) [ -17720.4370] [ 3023] [depth= 10] . ( 6 sec) [ -17703.4017] [ 3022] [depth= 4] . ( 6 sec) [ -17692.8242] [ 3019] [depth= 2] . ( 6 sec) [ -17663.2935] [ 3016] [depth= 7] . ( 6 sec) [ -17635.6628] [ 3017] [depth= 1] . ( 6 sec) [ -17572.1270] [ 2988] [depth= 7] . ( 6 sec) [ -17546.3666] [ 2985] [depth= 1] . ( 6 sec) [ -17526.9239] [ 2983] [depth= 8] . ( 7 sec) [ -17482.4531] [ 2996] [depth= 1] . ( 7 sec) [ -17433.1936] [ 2980] [depth= 10] . ( 7 sec) [ -17422.5289] [ 2977] [depth= 2] . ( 7 sec) [ -17398.2024] [ 2976] [depth= 2] . ( 7 sec) [ -17353.0114] [ 2960] [depth= 2] . ( 7 sec) [ -17218.1278] [ 2926] [depth= 2] . ( 7 sec) [ -17191.9052] [ 2916] [depth= 9] . ( 7 sec) [ -17116.4723] [ 2911] [depth= 4] . ( 7 sec) [ -17072.9113] [ 2903] [depth= 7] . ( 7 sec) [ -17028.6767] [ 2900] [depth= 1] . ( 7 sec) [ -17017.1618] [ 2895] [depth= 5] . ( 8 sec) [ -17007.7413] [ 2892] [depth= 2] . ( 8 sec) [ -17000.3122] [ 2891] [depth= 1] . ( 8 sec) [ -16918.9320] [ 2882] [depth= 15] . ( 8 sec) [ -16914.9444] [ 2882] [depth= 1] . ( 8 sec) [ -16883.3089] [ 2872] [depth= 2] . ( 8 sec) [ -16823.0258] [ 2856] [depth= 15] . ( 8 sec) [ -16820.1035] [ 2855] [depth= 1] . ( 8 sec) [ -16814.6420] [ 2857] [depth= 2] . ( 9 sec) [ -16773.8244] [ 2848] [depth= 6] . ( 9 sec) [ -16733.4279] [ 2851] [depth= 1] . ( 9 sec) [ -16732.4874] [ 2851] [depth= 1] . ( 9 sec) [ -16727.3539] [ 2846] [depth= 11] . ( 9 sec) [ -16654.6688] [ 2854] [depth= 1] . ( 9 sec) [ -16601.9285] [ 2822] [depth= 5] . ( 9 sec) [ -16509.1546] [ 2819] [depth= 5] . ( 9 sec) [ -16455.0732] [ 2807] [depth= 4] . ( 9 sec) [ -16432.5003] [ 2800] [depth= 15] . ( 9 sec) [ -16331.0586] [ 2774] [depth= 13] . ( 10 sec) [ -16284.6212] [ 2763] [depth= 5] . ( 10 sec) [ -16277.4028] [ 2764] [depth= 1] . ( 10 sec) [ -16268.6995] [ 2761] [depth= 1] . ( 10 sec) [ -16252.8341] [ 2761] [depth= 1] . ( 10 sec) [ -16252.6880] [ 2761] [depth= 2] . ( 10 sec) [ -16238.9467] [ 2759] [depth= 5] . ( 10 sec) [ -16206.0040] [ 2764] [depth= 1] . ( 10 sec) [ -16163.7431] [ 2749] [depth= 8] . ( 10 sec) [ -16047.0992] [ 2716] [depth= 14] . ( 10 sec) [ -16042.2731] [ 2716] [depth= 1] . ( 10 sec) [ -16024.8804] [ 2711] [depth= 1] . ( 11 sec) [ -15841.4737] [ 2708] [depth= 5] . ( 11 sec) [ -15839.3155] [ 2707] [depth= 1] . ( 11 sec) [ -15805.3169] [ 2707] [depth= 1] . ( 11 sec) [ -15795.5728] [ 2708] [depth= 1] . ( 11 sec) [ -15770.5545] [ 2701] [depth= 8] . ( 11 sec) [ -15519.3134] [ 2709] [depth= 1] . ( 11 sec) [ -15501.4904] [ 2701] [depth= 1] . ( 11 sec) [ -15335.8381] [ 2694] [depth= 11] . ( 11 sec) [ -15329.7324] [ 2691] [depth= 2] . ( 11 sec) [ -15313.9558] [ 2687] [depth= 2] . ( 11 sec) [ -15284.8755] [ 2679] [depth= 13] . ( 12 sec) [ -15265.5682] [ 2672] [depth= 9] . ( 12 sec) [ -15253.5732] [ 2664] [depth= 6] . ( 12 sec) [ -15223.1767] [ 2655] [depth= 9] . ( 12 sec) [ -15217.6118] [ 2653] [depth= 1] . ( 12 sec) [ -15188.3371] [ 2647] [depth= 4] . ( 12 sec) [ -15177.3227] [ 2647] [depth= 1] . ( 13 sec) [ -15173.1014] [ 2646] [depth= 1] . ( 13 sec) [ -15140.2493] [ 2637] [depth= 4] . ( 13 sec) [ -15131.9607] [ 2633] [depth= 4] . ( 13 sec) [ -15122.0216] [ 2637] [depth= 1] . ( 13 sec) [ -15099.0306] [ 2630] [depth= 2] . ( 13 sec) [ -15097.6319] [ 2626] [depth= 1] . ( 13 sec) [ -15094.5875] [ 2627] [depth= 1] . ( 14 sec) [ -15084.9878] [ 2628] [depth= 1] . ( 14 sec) [ -15081.5622] [ 2627] [depth= 2] . ( 14 sec) [ -15080.6379] [ 2627] [depth= 1] . ( 14 sec) [ -15060.1744] [ 2620] [depth= 2] . ( 14 sec) [ -15056.7683] [ 2621] [depth= 2] . ( 15 sec) [ -15037.2633] [ 2600] [depth= 7] . ( 15 sec) [ -15034.7629] [ 2600] [depth= 1] . ( 16 sec) [ -14972.0744] [Branch lengths ] . ( 20 sec) [ -14597.9198] [GTR parameters ] . ( 21 sec) [ -14501.3207] [Alpha ][ 0.274963] . ( 21 sec) [ -14486.0507] [ 2595] [depth= 1] . ( 21 sec) [ -14482.4158] [ 2591] [depth= 1] . ( 21 sec) [ -14465.8287] [ 2590] [depth= 1] . ( 22 sec) [ -14453.8413] [ 2583] [depth= 8] . ( 22 sec) [ -14453.8128] [ 2584] [depth= 1] . ( 23 sec) [ -14452.7398] [ 2582] [depth= 2] . ( 24 sec) [ -14451.7807] [ 2584] [depth= 1] . ( 24 sec) [ -14451.7415] [ 2584] [depth= 1] . ( 24 sec) [ -14451.1135] [ 2585] [depth= 3] . ( 25 sec) [ -14445.7687] [ 2579] [depth= 3] . ( 25 sec) [ -14441.4333] [ 2573] [depth= 2] . ( 25 sec) [ -14440.4213] [ 2572] [depth= 1] . ( 25 sec) [ -14440.2000] [ 2570] [depth= 1] . ( 25 sec) [ -14430.4412] [ 2566] [depth= 2] . ( 25 sec) [ -14422.7902] [ 2562] [depth= 1] . ( 26 sec) [ -14420.5127] [ 2564] [depth= 4] . ( 27 sec) [ -14420.2355] [ 2565] [depth= 2] . ( 27 sec) [ -14405.3923] [ 2558] [depth= 7] . ( 28 sec) [ -14404.5917] [ 2560] [depth= 1] . ( 28 sec) [ -14403.1201] [ 2560] [depth= 1] . ( 29 sec) [ -14372.4635] [ 2545] [depth= 6] . ( 30 sec) [ -14372.0604] [ 2548] [depth= 1] . ( 30 sec) [ -14368.0058] [ 2545] [depth= 1] . ( 31 sec) [ -14366.8743] [ 2545] [depth= 1] . ( 33 sec) [ -14366.8633] [ 2546] [depth= 1] . ( 33 sec) [ -14363.9623] [ 2548] [depth= 1] . ( 35 sec) [ -14363.2884] [ 2549] [depth= 1] . ( 35 sec) [ -14359.3087] [ 2548] [depth= 1] . ( 35 sec) [ -14359.0145] [ 2548] [depth= 3] . ( 35 sec) [ -14354.0025] [ 2546] [depth= 1] . ( 38 sec) [ -14353.4508] [ 2546] [depth= 1] . ( 38 sec) [ -14353.2504] [ 2544] [depth= 1] . ( 39 sec) [ -14351.8547] [ 2546] [depth= 1] . ( 39 sec) [ -14351.8305] [ 2546] [depth= 1] . ( 40 sec) [ -14343.2392] [Branch lengths ] . ( 43 sec) [ -14342.8707] [GTR parameters ] . ( 43 sec) [ -14342.8659] [Alpha ][ 0.273782] . ( 46 sec) [ -14341.5491] [ 2548] [depth= 4] . ( 50 sec) [ -14341.4672] [ 2548] [depth= 1] . ( 53 sec) [ -14341.4426] [ 2549] [depth= 1] . ( 62 sec) [ -14341.3425] [ 2549] [depth= 1] . ( 66 sec) [ -14341.2573] [ 2550] [depth= 5] . ( 67 sec) [ -14338.0368] [Branch lengths ] . ( 70 sec) [ -14337.9162] [GTR parameters ] . ( 70 sec) [ -14337.9154] [Alpha ][ 0.274214] . ( 72 sec) [ -14337.1834] [ 2551] [depth= 3] . ( 72 sec) [ -14334.9184] [ 2550] [depth= 1] . ( 73 sec) [ -14333.8031] [ 2548] [depth= 1] . ( 76 sec) [ -14333.4512] [ 2546] [depth= 1] . ( 79 sec) [ -14333.3986] [ 2547] [depth= 1] . ( 90 sec) [ -14333.2139] [ 2547] [depth= 1] . ( 92 sec) [ -14331.5289] [Branch lengths ] . ( 95 sec) [ -14331.5141] [GTR parameters ] . ( 95 sec) [ -14331.5121] [Alpha ][ 0.274926] . ( 117 sec) [ -14331.3186] [Branch lengths ] . ( 190 sec) [ -14331.2951] [Branch lengths ] . ( 190 sec) [ -14331.2951] [Topology ] . ( 191 sec) [ -14331.2942] [Topology ] . ( 192 sec) [ -14331.2940] [GTR parameters ] . ( 192 sec) [ -14331.2930] [Alpha ][ 0.275427] . ( 192 sec) [ -14331.2930] [Topology ] . ( 194 sec) [ -14331.2926] [Topology ] . ( 195 sec) [ -14331.2926] [GTR parameters ] . ( 195 sec) [ -14331.2926] [Alpha ][ 0.275427] . Checking for NNIs, optimizing five branches... . ( 207 sec) [ -14331.1123] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14331.112311. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22294.8690] [GTR parameters ] . ( 1 sec) [ -21834.9041] [Alpha ][ 0.500960] . ( 1 sec) [ -21641.7823] [ 3409] [depth= 2] . ( 1 sec) [ -21533.9662] [ 3397] [depth= 9] . ( 1 sec) [ -21315.0862] [ 3387] [depth= 3] . ( 1 sec) [ -21217.0475] [ 3354] [depth= 1] . ( 1 sec) [ -21176.4915] [ 3350] [depth= 3] . ( 1 sec) [ -21111.0215] [ 3335] [depth= 5] . ( 1 sec) [ -21093.4829] [ 3334] [depth= 5] . ( 1 sec) [ -20715.4183] [ 3325] [depth= 14] . ( 1 sec) [ -20695.1585] [ 3326] [depth= 1] . ( 2 sec) [ -20671.4971] [ 3319] [depth= 1] . ( 2 sec) [ -20662.4583] [ 3317] [depth= 1] . ( 2 sec) [ -20633.2399] [ 3307] [depth= 16] . ( 2 sec) [ -20444.7489] [ 3303] [depth= 3] . ( 2 sec) [ -20403.9416] [ 3293] [depth= 18] . ( 2 sec) [ -20152.5399] [ 3287] [depth= 21] . ( 2 sec) [ -20072.5293] [ 3278] [depth= 1] . ( 2 sec) [ -20040.3939] [ 3269] [depth= 20] . ( 2 sec) [ -19925.0582] [ 3257] [depth= 22] . ( 2 sec) [ -19917.2753] [ 3251] [depth= 18] . ( 3 sec) [ -19907.0922] [ 3249] [depth= 1] . ( 3 sec) [ -19665.6476] [ 3255] [depth= 23] . ( 3 sec) [ -19657.9625] [ 3258] [depth= 1] . ( 3 sec) [ -19454.3905] [ 3256] [depth= 3] . ( 3 sec) [ -19407.7320] [ 3255] [depth= 1] . ( 3 sec) [ -19348.5674] [ 3246] [depth= 10] . ( 3 sec) [ -19215.3123] [ 3226] [depth= 3] . ( 3 sec) [ -18973.4068] [ 3217] [depth= 5] . ( 3 sec) [ -18880.3623] [ 3219] [depth= 3] . ( 3 sec) [ -18874.8063] [ 3217] [depth= 1] . ( 3 sec) [ -18688.3864] [ 3218] [depth= 6] . ( 4 sec) [ -18687.7111] [ 3205] [depth= 11] . ( 4 sec) [ -18626.5395] [ 3207] [depth= 7] . ( 4 sec) [ -18421.0491] [ 3182] [depth= 13] . ( 4 sec) [ -18403.0270] [ 3179] [depth= 1] . ( 4 sec) [ -18385.0218] [ 3177] [depth= 1] . ( 4 sec) [ -18321.6431] [ 3168] [depth= 8] . ( 4 sec) [ -18290.3737] [ 3164] [depth= 3] . ( 4 sec) [ -18199.0489] [ 3151] [depth= 5] . ( 4 sec) [ -18165.6591] [ 3138] [depth= 6] . ( 4 sec) [ -18123.2192] [ 3132] [depth= 2] . ( 5 sec) [ -18114.3672] [ 3136] [depth= 1] . ( 5 sec) [ -18086.6122] [ 3141] [depth= 17] . ( 5 sec) [ -18031.9053] [ 3121] [depth= 11] . ( 5 sec) [ -17992.1632] [ 3107] [depth= 10] . ( 5 sec) [ -17916.5980] [ 3090] [depth= 5] . ( 5 sec) [ -17832.4661] [ 3100] [depth= 1] . ( 5 sec) [ -17717.8103] [ 3070] [depth= 9] . ( 5 sec) [ -17716.9025] [ 3068] [depth= 1] . ( 6 sec) [ -17699.3471] [ 3070] [depth= 6] . ( 6 sec) [ -17632.3400] [ 3046] [depth= 10] . ( 6 sec) [ -17611.3569] [ 3057] [depth= 11] . ( 6 sec) [ -17602.2393] [ 3056] [depth= 9] . ( 6 sec) [ -17598.2569] [ 3056] [depth= 1] . ( 6 sec) [ -17593.8657] [ 3053] [depth= 1] . ( 6 sec) [ -17255.3958] [ 3008] [depth= 5] . ( 6 sec) [ -16890.1048] [ 2994] [depth= 6] . ( 6 sec) [ -16740.6420] [ 2957] [depth= 5] . ( 6 sec) [ -16704.3050] [ 2953] [depth= 1] . ( 6 sec) [ -16666.9369] [ 2939] [depth= 5] . ( 7 sec) [ -16652.3403] [ 2936] [depth= 5] . ( 7 sec) [ -16570.1951] [ 2917] [depth= 1] . ( 7 sec) [ -16534.1180] [ 2917] [depth= 2] . ( 7 sec) [ -16488.8768] [ 2911] [depth= 5] . ( 7 sec) [ -16452.1486] [ 2908] [depth= 1] . ( 7 sec) [ -16416.1160] [ 2901] [depth= 9] . ( 7 sec) [ -16412.5956] [ 2901] [depth= 1] . ( 7 sec) [ -16408.1692] [ 2899] [depth= 1] . ( 7 sec) [ -16242.3234] [ 2848] [depth= 11] . ( 8 sec) [ -16216.0639] [ 2854] [depth= 8] . ( 8 sec) [ -16214.3630] [ 2851] [depth= 3] . ( 8 sec) [ -16160.4920] [ 2826] [depth= 8] . ( 8 sec) [ -16147.1869] [ 2827] [depth= 1] . ( 8 sec) [ -16138.1622] [ 2824] [depth= 1] . ( 8 sec) [ -16122.5221] [ 2820] [depth= 1] . ( 8 sec) [ -16110.3578] [ 2815] [depth= 1] . ( 8 sec) [ -16103.7322] [ 2815] [depth= 3] . ( 8 sec) [ -16101.5704] [ 2814] [depth= 3] . ( 8 sec) [ -16034.2122] [ 2814] [depth= 1] . ( 9 sec) [ -15975.0568] [ 2793] [depth= 2] . ( 9 sec) [ -15889.2535] [ 2790] [depth= 5] . ( 9 sec) [ -15883.5003] [ 2787] [depth= 3] . ( 9 sec) [ -15878.2757] [ 2781] [depth= 4] . ( 9 sec) [ -15857.5198] [ 2766] [depth= 1] . ( 9 sec) [ -15850.6557] [ 2765] [depth= 3] . ( 9 sec) [ -15763.9095] [ 2739] [depth= 2] . ( 9 sec) [ -15745.1890] [ 2735] [depth= 1] . ( 9 sec) [ -15723.2423] [ 2727] [depth= 10] . ( 10 sec) [ -15714.7600] [ 2724] [depth= 11] . ( 10 sec) [ -15703.2825] [ 2728] [depth= 10] . ( 10 sec) [ -15696.3256] [ 2727] [depth= 1] . ( 10 sec) [ -15663.7975] [ 2725] [depth= 2] . ( 10 sec) [ -15657.4926] [ 2724] [depth= 2] . ( 10 sec) [ -15641.9100] [ 2729] [depth= 1] . ( 10 sec) [ -15605.7004] [ 2722] [depth= 1] . ( 11 sec) [ -15603.8865] [ 2719] [depth= 4] . ( 11 sec) [ -15596.9663] [ 2716] [depth= 1] . ( 11 sec) [ -15587.4938] [ 2712] [depth= 5] . ( 11 sec) [ -15587.3324] [ 2714] [depth= 1] . ( 11 sec) [ -15539.6944] [ 2700] [depth= 3] . ( 11 sec) [ -15536.1243] [ 2699] [depth= 1] . ( 11 sec) [ -15535.9764] [ 2699] [depth= 1] . ( 11 sec) [ -15452.7888] [ 2701] [depth= 2] . ( 11 sec) [ -15436.6179] [ 2697] [depth= 2] . ( 12 sec) [ -15428.7521] [ 2694] [depth= 5] . ( 12 sec) [ -15342.2361] [ 2679] [depth= 1] . ( 12 sec) [ -15333.0058] [ 2677] [depth= 1] . ( 12 sec) [ -15314.3756] [ 2672] [depth= 1] . ( 12 sec) [ -15311.9453] [ 2670] [depth= 1] . ( 12 sec) [ -15308.8480] [ 2667] [depth= 2] . ( 12 sec) [ -15288.8568] [ 2664] [depth= 1] . ( 12 sec) [ -15288.1182] [ 2660] [depth= 2] . ( 12 sec) [ -15269.6162] [ 2664] [depth= 1] . ( 13 sec) [ -15260.6549] [ 2660] [depth= 1] . ( 13 sec) [ -15260.3095] [ 2658] [depth= 3] . ( 13 sec) [ -15251.2854] [ 2659] [depth= 1] . ( 13 sec) [ -15250.1650] [ 2654] [depth= 2] . ( 13 sec) [ -15249.9313] [ 2654] [depth= 1] . ( 13 sec) [ -15249.6920] [ 2656] [depth= 2] . ( 13 sec) [ -15235.2977] [ 2660] [depth= 1] . ( 13 sec) [ -15231.5101] [ 2653] [depth= 1] . ( 13 sec) [ -15229.4580] [ 2654] [depth= 7] . ( 14 sec) [ -15222.4716] [ 2648] [depth= 3] . ( 14 sec) [ -15219.1780] [ 2648] [depth= 1] . ( 14 sec) [ -15216.0716] [ 2649] [depth= 3] . ( 14 sec) [ -15209.8797] [ 2648] [depth= 2] . ( 15 sec) [ -15147.0968] [ 2624] [depth= 15] . ( 15 sec) [ -15036.6298] [Branch lengths ] . ( 19 sec) [ -14639.4684] [GTR parameters ] . ( 20 sec) [ -14542.1481] [Alpha ][ 0.275607] . ( 20 sec) [ -14535.3673] [ 2622] [depth= 7] . ( 20 sec) [ -14515.5591] [ 2613] [depth= 6] . ( 20 sec) [ -14463.8667] [ 2600] [depth= 1] . ( 20 sec) [ -14463.3245] [ 2594] [depth= 1] . ( 20 sec) [ -14454.3674] [ 2589] [depth= 2] . ( 21 sec) [ -14453.8568] [ 2588] [depth= 1] . ( 21 sec) [ -14451.7065] [ 2588] [depth= 1] . ( 22 sec) [ -14442.5042] [ 2581] [depth= 1] . ( 22 sec) [ -14441.2003] [ 2581] [depth= 1] . ( 23 sec) [ -14440.5728] [ 2582] [depth= 1] . ( 23 sec) [ -14427.3274] [ 2574] [depth= 8] . ( 24 sec) [ -14422.8949] [ 2574] [depth= 1] . ( 26 sec) [ -14422.5301] [ 2573] [depth= 1] . ( 26 sec) [ -14422.3658] [ 2578] [depth= 1] . ( 27 sec) [ -14420.9652] [ 2576] [depth= 1] . ( 27 sec) [ -14420.1682] [ 2578] [depth= 9] . ( 28 sec) [ -14417.1980] [ 2583] [depth= 1] . ( 28 sec) [ -14412.4734] [ 2587] [depth= 5] . ( 28 sec) [ -14400.2365] [ 2581] [depth= 8] . ( 28 sec) [ -14399.9294] [ 2581] [depth= 1] . ( 29 sec) [ -14387.7378] [ 2576] [depth= 1] . ( 31 sec) [ -14373.3722] [ 2570] [depth= 6] . ( 31 sec) [ -14372.1250] [ 2566] [depth= 2] . ( 32 sec) [ -14371.5980] [ 2566] [depth= 1] . ( 32 sec) [ -14370.5969] [ 2563] [depth= 3] . ( 33 sec) [ -14362.7968] [ 2562] [depth= 3] . ( 33 sec) [ -14362.2873] [ 2561] [depth= 1] . ( 34 sec) [ -14361.3064] [ 2560] [depth= 1] . ( 34 sec) [ -14361.0633] [ 2560] [depth= 1] . ( 35 sec) [ -14359.9565] [ 2559] [depth= 1] . ( 35 sec) [ -14358.7113] [ 2558] [depth= 1] . ( 36 sec) [ -14356.4172] [ 2560] [depth= 1] . ( 37 sec) [ -14356.0993] [ 2561] [depth= 1] . ( 37 sec) [ -14355.9968] [ 2560] [depth= 1] . ( 38 sec) [ -14355.5250] [ 2559] [depth= 1] . ( 40 sec) [ -14342.7215] [Branch lengths ] . ( 42 sec) [ -14342.3849] [GTR parameters ] . ( 42 sec) [ -14342.3847] [Alpha ][ 0.275308] . ( 46 sec) [ -14339.9235] [ 2548] [depth= 12] . ( 47 sec) [ -14339.4001] [ 2547] [depth= 1] . ( 49 sec) [ -14339.2276] [ 2548] [depth= 1] . ( 53 sec) [ -14337.1435] [ 2546] [depth= 2] . ( 53 sec) [ -14336.6681] [ 2548] [depth= 2] . ( 55 sec) [ -14336.1956] [ 2550] [depth= 1] . ( 58 sec) [ -14335.8931] [ 2549] [depth= 1] . ( 60 sec) [ -14335.7141] [ 2550] [depth= 1] . ( 62 sec) [ -14335.6104] [ 2549] [depth= 1] . ( 62 sec) [ -14332.0941] [Branch lengths ] . ( 65 sec) [ -14331.9734] [GTR parameters ] . ( 66 sec) [ -14331.9664] [Alpha ][ 0.273889] . ( 66 sec) [ -14331.9406] [ 2550] [depth= 1] . ( 70 sec) [ -14331.9096] [ 2549] [depth= 1] . ( 87 sec) [ -14331.4378] [Branch lengths ] . ( 87 sec) [ -14331.4378] [GTR parameters ] . ( 87 sec) [ -14331.4345] [Alpha ][ 0.274779] . ( 159 sec) [ -14331.2228] [Branch lengths ] . ( 159 sec) [ -14331.2228] [Topology ] . ( 161 sec) [ -14331.0423] [Topology ] . ( 162 sec) [ -14331.0022] [Topology ] . ( 164 sec) [ -14330.9920] [Topology ] . ( 166 sec) [ -14330.9893] [Topology ] . ( 168 sec) [ -14330.9885] [Topology ] . ( 171 sec) [ -14330.9852] [GTR parameters ] . ( 171 sec) [ -14330.9847] [Alpha ][ 0.275113] . ( 171 sec) [ -14330.9847] [Topology ] . ( 173 sec) [ -14330.9844] [Topology ] . ( 173 sec) [ -14330.9844] [GTR parameters ] . ( 173 sec) [ -14330.9844] [Alpha ][ 0.275113] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -14330.8605] [Topology ] . Checking for NNIs, optimizing five branches... . ( 196 sec) [ -14330.8589] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14330.858896. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -22511.1917] [GTR parameters ] . ( 1 sec) [ -22034.5541] [Alpha ][ 0.500960] . ( 1 sec) [ -21847.4426] [ 3450] [depth= 7] . ( 1 sec) [ -21693.9052] [ 3427] [depth= 9] . ( 1 sec) [ -21536.1963] [ 3423] [depth= 3] . ( 1 sec) [ -21528.3188] [ 3422] [depth= 4] . ( 1 sec) [ -21499.3104] [ 3421] [depth= 2] . ( 1 sec) [ -21459.8071] [ 3421] [depth= 1] . ( 1 sec) [ -21386.1181] [ 3413] [depth= 3] . ( 1 sec) [ -21376.3143] [ 3411] [depth= 3] . ( 1 sec) [ -21371.2620] [ 3406] [depth= 1] . ( 2 sec) [ -21287.7282] [ 3405] [depth= 1] . ( 2 sec) [ -21259.3023] [ 3406] [depth= 3] . ( 2 sec) [ -21208.4858] [ 3405] [depth= 4] . ( 2 sec) [ -21186.6043] [ 3401] [depth= 2] . ( 2 sec) [ -21167.8396] [ 3398] [depth= 11] . ( 2 sec) [ -21118.9087] [ 3379] [depth= 3] . ( 2 sec) [ -21110.9862] [ 3378] [depth= 8] . ( 2 sec) [ -20794.8680] [ 3368] [depth= 9] . ( 2 sec) [ -20738.0946] [ 3340] [depth= 3] . ( 2 sec) [ -20716.6892] [ 3346] [depth= 15] . ( 2 sec) [ -20625.4371] [ 3369] [depth= 1] . ( 2 sec) [ -20407.2626] [ 3344] [depth= 14] . ( 3 sec) [ -20327.0224] [ 3306] [depth= 2] . ( 3 sec) [ -20027.7266] [ 3298] [depth= 13] . ( 3 sec) [ -19532.9197] [ 3282] [depth= 3] . ( 3 sec) [ -19281.4375] [ 3258] [depth= 12] . ( 3 sec) [ -19158.9848] [ 3225] [depth= 12] . ( 3 sec) [ -19111.6616] [ 3217] [depth= 14] . ( 3 sec) [ -19060.8674] [ 3177] [depth= 8] . ( 3 sec) [ -18912.9096] [ 3161] [depth= 16] . ( 3 sec) [ -18900.9682] [ 3159] [depth= 2] . ( 3 sec) [ -18890.0958] [ 3167] [depth= 1] . ( 4 sec) [ -18637.5954] [ 3141] [depth= 13] . ( 4 sec) [ -18624.9709] [ 3138] [depth= 1] . ( 4 sec) [ -18405.2003] [ 3113] [depth= 10] . ( 4 sec) [ -18347.3230] [ 3094] [depth= 2] . ( 4 sec) [ -18221.7223] [ 3064] [depth= 8] . ( 4 sec) [ -18115.7172] [ 3062] [depth= 3] . ( 4 sec) [ -18062.4832] [ 3055] [depth= 12] . ( 4 sec) [ -18048.3237] [ 3050] [depth= 1] . ( 4 sec) [ -18037.2733] [ 3043] [depth= 1] . ( 4 sec) [ -18030.4833] [ 3041] [depth= 1] . ( 4 sec) [ -17948.5508] [ 3021] [depth= 12] . ( 4 sec) [ -17910.8590] [ 3023] [depth= 1] . ( 5 sec) [ -17740.7943] [ 2997] [depth= 16] . ( 5 sec) [ -17672.1251] [ 2987] [depth= 12] . ( 5 sec) [ -17628.5394] [ 2982] [depth= 11] . ( 5 sec) [ -17426.5044] [ 2959] [depth= 10] . ( 5 sec) [ -17391.4630] [ 2949] [depth= 3] . ( 5 sec) [ -17259.9364] [ 2922] [depth= 11] . ( 5 sec) [ -17249.2238] [ 2922] [depth= 2] . ( 5 sec) [ -17222.4472] [ 2914] [depth= 4] . ( 5 sec) [ -17195.9127] [ 2904] [depth= 1] . ( 5 sec) [ -17192.8664] [ 2898] [depth= 6] . ( 5 sec) [ -17188.2741] [ 2896] [depth= 1] . ( 6 sec) [ -17082.7759] [ 2891] [depth= 10] . ( 6 sec) [ -16808.7215] [ 2844] [depth= 15] . ( 6 sec) [ -16760.2142] [ 2832] [depth= 11] . ( 6 sec) [ -16747.5436] [ 2830] [depth= 1] . ( 6 sec) [ -16628.4301] [ 2835] [depth= 5] . ( 6 sec) [ -16619.4838] [ 2832] [depth= 6] . ( 6 sec) [ -16612.6475] [ 2831] [depth= 1] . ( 6 sec) [ -16579.9630] [ 2818] [depth= 11] . ( 6 sec) [ -16575.2891] [ 2814] [depth= 9] . ( 7 sec) [ -16557.7985] [ 2807] [depth= 6] . ( 7 sec) [ -16536.7684] [ 2801] [depth= 1] . ( 7 sec) [ -16535.8270] [ 2800] [depth= 1] . ( 7 sec) [ -16524.2847] [ 2800] [depth= 8] . ( 7 sec) [ -16520.4449] [ 2801] [depth= 1] . ( 7 sec) [ -16455.4096] [ 2798] [depth= 9] . ( 7 sec) [ -16412.2802] [ 2780] [depth= 11] . ( 7 sec) [ -16391.9139] [ 2773] [depth= 5] . ( 7 sec) [ -16373.8401] [ 2775] [depth= 7] . ( 7 sec) [ -16216.7050] [ 2767] [depth= 8] . ( 8 sec) [ -16204.2422] [ 2764] [depth= 7] . ( 8 sec) [ -16202.1180] [ 2764] [depth= 2] . ( 8 sec) [ -16192.5158] [ 2764] [depth= 1] . ( 8 sec) [ -16186.6951] [ 2760] [depth= 3] . ( 8 sec) [ -16176.9572] [ 2757] [depth= 4] . ( 8 sec) [ -16167.8200] [ 2754] [depth= 3] . ( 8 sec) [ -16159.7425] [ 2753] [depth= 1] . ( 8 sec) [ -16149.7963] [ 2758] [depth= 9] . ( 8 sec) [ -16006.7652] [ 2717] [depth= 9] . ( 9 sec) [ -15986.8547] [ 2706] [depth= 5] . ( 9 sec) [ -15984.4603] [ 2702] [depth= 3] . ( 9 sec) [ -15977.5136] [ 2700] [depth= 2] . ( 9 sec) [ -15958.5015] [ 2700] [depth= 1] . ( 9 sec) [ -15667.0050] [ 2693] [depth= 2] . ( 9 sec) [ -15589.9220] [ 2698] [depth= 1] . ( 9 sec) [ -15558.9442] [ 2690] [depth= 2] . ( 9 sec) [ -15528.6010] [ 2690] [depth= 7] . ( 9 sec) [ -15515.4896] [ 2686] [depth= 3] . ( 9 sec) [ -15513.1862] [ 2685] [depth= 3] . ( 9 sec) [ -15504.1826] [ 2682] [depth= 1] . ( 9 sec) [ -15486.7553] [ 2675] [depth= 1] . ( 10 sec) [ -15465.5271] [ 2671] [depth= 1] . ( 10 sec) [ -15455.4981] [ 2659] [depth= 2] . ( 10 sec) [ -15455.4295] [ 2659] [depth= 1] . ( 10 sec) [ -15448.9489] [ 2661] [depth= 1] . ( 10 sec) [ -15442.3013] [ 2660] [depth= 4] . ( 10 sec) [ -15441.4325] [ 2660] [depth= 1] . ( 10 sec) [ -15417.6388] [ 2656] [depth= 3] . ( 10 sec) [ -15416.9541] [ 2655] [depth= 1] . ( 10 sec) [ -15363.7980] [ 2644] [depth= 3] . ( 11 sec) [ -15277.5644] [ 2627] [depth= 1] . ( 11 sec) [ -15276.1030] [ 2628] [depth= 2] . ( 11 sec) [ -15271.3277] [ 2630] [depth= 5] . ( 11 sec) [ -15267.0875] [ 2628] [depth= 1] . ( 11 sec) [ -15258.7781] [ 2629] [depth= 1] . ( 11 sec) [ -15257.9029] [ 2629] [depth= 1] . ( 11 sec) [ -15245.6266] [ 2626] [depth= 2] . ( 11 sec) [ -15244.5628] [ 2625] [depth= 2] . ( 12 sec) [ -15212.8608] [ 2624] [depth= 4] . ( 12 sec) [ -15207.1813] [ 2623] [depth= 4] . ( 12 sec) [ -15204.6742] [ 2623] [depth= 2] . ( 12 sec) [ -15152.7468] [ 2626] [depth= 2] . ( 13 sec) [ -15152.4473] [ 2628] [depth= 2] . ( 13 sec) [ -15147.0922] [ 2626] [depth= 4] . ( 13 sec) [ -15144.7887] [ 2625] [depth= 1] . ( 13 sec) [ -15047.8368] [ 2621] [depth= 5] . ( 13 sec) [ -15046.7009] [ 2621] [depth= 1] . ( 14 sec) [ -15041.5381] [ 2620] [depth= 2] . ( 14 sec) [ -15036.1337] [ 2615] [depth= 3] . ( 14 sec) [ -15035.4162] [ 2620] [depth= 1] . ( 14 sec) [ -15029.4291] [ 2615] [depth= 1] . ( 14 sec) [ -15015.0205] [ 2612] [depth= 5] . ( 14 sec) [ -15014.9830] [ 2613] [depth= 1] . ( 14 sec) [ -15013.9798] [ 2614] [depth= 1] . ( 14 sec) [ -15012.6249] [ 2606] [depth= 5] . ( 14 sec) [ -15000.9856] [ 2601] [depth= 6] . ( 14 sec) [ -15000.5661] [ 2599] [depth= 1] . ( 15 sec) [ -14991.3588] [ 2594] [depth= 2] . ( 15 sec) [ -14990.9279] [ 2599] [depth= 8] . ( 15 sec) [ -14989.2583] [ 2600] [depth= 1] . ( 15 sec) [ -14988.3441] [ 2598] [depth= 1] . ( 15 sec) [ -14988.2302] [ 2599] [depth= 1] . ( 15 sec) [ -14986.1843] [ 2599] [depth= 2] . ( 15 sec) [ -14985.9831] [ 2592] [depth= 2] . ( 16 sec) [ -14929.4449] [Branch lengths ] . ( 20 sec) [ -14568.2763] [GTR parameters ] . ( 20 sec) [ -14471.1705] [Alpha ][ 0.273295] . ( 20 sec) [ -14460.3463] [ 2587] [depth= 2] . ( 21 sec) [ -14459.7448] [ 2591] [depth= 7] . ( 21 sec) [ -14458.6290] [ 2591] [depth= 1] . ( 22 sec) [ -14453.2832] [ 2587] [depth= 1] . ( 22 sec) [ -14453.2722] [ 2588] [depth= 1] . ( 22 sec) [ -14442.8832] [ 2583] [depth= 2] . ( 22 sec) [ -14432.5231] [ 2578] [depth= 1] . ( 22 sec) [ -14430.6803] [ 2577] [depth= 1] . ( 22 sec) [ -14421.0470] [ 2573] [depth= 6] . ( 23 sec) [ -14418.0533] [ 2570] [depth= 1] . ( 23 sec) [ -14416.9030] [ 2571] [depth= 1] . ( 23 sec) [ -14416.5891] [ 2572] [depth= 5] . ( 24 sec) [ -14413.6049] [ 2574] [depth= 1] . ( 24 sec) [ -14413.2061] [ 2573] [depth= 1] . ( 24 sec) [ -14411.7329] [ 2571] [depth= 2] . ( 25 sec) [ -14411.4654] [ 2573] [depth= 1] . ( 25 sec) [ -14399.2503] [ 2571] [depth= 8] . ( 25 sec) [ -14397.0890] [ 2573] [depth= 2] . ( 25 sec) [ -14385.4176] [ 2565] [depth= 7] . ( 26 sec) [ -14383.9254] [ 2563] [depth= 1] . ( 26 sec) [ -14383.5997] [ 2564] [depth= 4] . ( 27 sec) [ -14381.7096] [ 2564] [depth= 1] . ( 27 sec) [ -14379.2149] [ 2569] [depth= 2] . ( 28 sec) [ -14373.4020] [ 2568] [depth= 3] . ( 28 sec) [ -14373.0722] [ 2567] [depth= 1] . ( 28 sec) [ -14369.5314] [ 2566] [depth= 2] . ( 28 sec) [ -14367.2719] [ 2564] [depth= 1] . ( 28 sec) [ -14362.1368] [ 2565] [depth= 1] . ( 29 sec) [ -14361.9524] [ 2568] [depth= 1] . ( 30 sec) [ -14359.1955] [ 2567] [depth= 1] . ( 30 sec) [ -14356.9890] [ 2565] [depth= 3] . ( 31 sec) [ -14355.9077] [ 2564] [depth= 2] . ( 33 sec) [ -14354.5481] [ 2554] [depth= 2] . ( 33 sec) [ -14353.8776] [ 2554] [depth= 1] . ( 33 sec) [ -14353.7522] [ 2553] [depth= 1] . ( 35 sec) [ -14352.2914] [ 2552] [depth= 1] . ( 35 sec) [ -14350.3956] [ 2553] [depth= 1] . ( 36 sec) [ -14350.3666] [ 2555] [depth= 2] . ( 36 sec) [ -14349.3175] [ 2556] [depth= 1] . ( 36 sec) [ -14349.0995] [ 2556] [depth= 1] . ( 37 sec) [ -14348.1861] [ 2558] [depth= 2] . ( 39 sec) [ -14334.3206] [Branch lengths ] . ( 42 sec) [ -14333.4962] [GTR parameters ] . ( 42 sec) [ -14333.4959] [Alpha ][ 0.272964] . ( 45 sec) [ -14333.4152] [ 2557] [depth= 1] . ( 51 sec) [ -14332.1120] [ 2549] [depth= 2] . ( 54 sec) [ -14331.7952] [ 2549] [depth= 1] . ( 64 sec) [ -14331.2782] [Branch lengths ] . ( 66 sec) [ -14331.2682] [GTR parameters ] . ( 66 sec) [ -14331.2657] [Alpha ][ 0.273757] . ( 87 sec) [ -14331.2444] [Branch lengths ] . ( 154 sec) [ -14330.6698] [ 2555] [depth= 3] . ( 159 sec) [ -14330.3957] [Branch lengths ] . ( 161 sec) [ -14330.3922] [GTR parameters ] . ( 161 sec) [ -14330.3885] [Alpha ][ 0.274715] . ( 162 sec) [ -14330.3885] [Topology ] . ( 163 sec) [ -14330.3655] [Topology ] . ( 165 sec) [ -14330.3551] [Topology ] . ( 166 sec) [ -14330.3490] [Topology ] . ( 168 sec) [ -14330.3454] [Topology ] . ( 170 sec) [ -14330.3431] [Topology ] . ( 171 sec) [ -14330.3418] [Topology ] . ( 172 sec) [ -14330.3415] [GTR parameters ] . ( 172 sec) [ -14330.3392] [Alpha ][ 0.275470] . ( 172 sec) [ -14330.3392] [Topology ] . ( 174 sec) [ -14330.3376] [Topology ] . ( 175 sec) [ -14330.3367] [Topology ] . ( 176 sec) [ -14330.3366] [GTR parameters ] . ( 176 sec) [ -14330.3366] [Alpha ][ 0.275746] . ( 176 sec) [ -14330.3366] [Topology ] . ( 178 sec) [ -14330.3358] [Topology ] . ( 179 sec) [ -14330.3358] [GTR parameters ] . ( 179 sec) [ -14330.3358] [Alpha ][ 0.275746] . Checking for NNIs, optimizing five branches... . ( 191 sec) [ -14330.2525] [Topology ] . Checking for NNIs, optimizing five branches... . ( 203 sec) [ -14330.2461] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14330.246126. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -15009.3920] [GTR parameters ] . ( 4 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 4 sec) [ -14725.6209] [Topology ] . ( 5 sec) [ -14531.9053] [Topology ] . ( 7 sec) [ -14493.0754] [Topology ] . ( 9 sec) [ -14474.2240] [Topology ] . ( 10 sec) [ -14466.5015] [Topology ] . ( 12 sec) [ -14464.3817] [Topology ] . ( 14 sec) [ -14463.4422] [Topology ] . ( 15 sec) [ -14462.9907] [Topology ] . ( 17 sec) [ -14462.7666] [Topology ] . ( 18 sec) [ -14462.6528] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -14460.8041] [GTR parameters ] . ( 34 sec) [ -14371.0264] [Alpha ][ 0.279990] . ( 34 sec) [ -14371.0264] [Topology ] . ( 36 sec) [ -14370.0783] [Topology ] . ( 37 sec) [ -14369.8437] [Topology ] . ( 39 sec) [ -14369.4994] [Topology ] . ( 41 sec) [ -14369.4254] [Topology ] . ( 42 sec) [ -14369.3901] [Topology ] . ( 44 sec) [ -14369.3698] [Topology ] . ( 46 sec) [ -14369.3578] [Topology ] . ( 47 sec) [ -14369.3507] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -14368.8958] [GTR parameters ] . ( 61 sec) [ -14368.7192] [Alpha ][ 0.273158] . ( 61 sec) [ -14368.7192] [Topology ] . ( 63 sec) [ -14368.6894] [Topology ] . ( 64 sec) [ -14368.6736] [Topology ] . ( 66 sec) [ -14368.6645] [Topology ] . ( 67 sec) [ -14368.6593] [Topology ] . ( 69 sec) [ -14368.6562] [Topology ] . ( 71 sec) [ -14368.6545] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -14368.6527] [GTR parameters ] . ( 83 sec) [ -14368.6463] [Alpha ][ 0.271777] . ( 83 sec) [ -14368.6463] [Topology ] . ( 85 sec) [ -14368.6434] [Topology ] . ( 87 sec) [ -14368.6418] [Topology ] . ( 88 sec) [ -14368.6408] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -14368.6398] [GTR parameters ] . ( 102 sec) [ -14368.6396] [Alpha ][ 0.271504] . ( 102 sec) [ -14368.6396] [Topology ] . ( 103 sec) [ -14368.6388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 115 sec) [ -14368.6388] [GTR parameters ] . ( 115 sec) [ -14368.6388] [Alpha ][ 0.271504] . ( 116 sec) [ -14368.6388] [Topology ] . ( 117 sec) [ -14368.6384] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 144 sec) [ -15009.3920] [GTR parameters ] . ( 144 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 144 sec) [ -14724.6451] [ 2562] [depth= 2] . ( 144 sec) [ -14721.3879] [ 2562] [depth= 1] . ( 144 sec) [ -14721.0926] [ 2562] [depth= 1] . ( 145 sec) [ -14717.3225] [ 2562] [depth= 2] . ( 145 sec) [ -14714.6002] [ 2561] [depth= 2] . ( 146 sec) [ -14714.3106] [ 2561] [depth= 1] . ( 146 sec) [ -14713.7025] [ 2562] [depth= 1] . ( 146 sec) [ -14713.3967] [ 2561] [depth= 1] . ( 146 sec) [ -14704.7688] [ 2559] [depth= 2] . ( 147 sec) [ -14704.3651] [ 2563] [depth= 1] . ( 147 sec) [ -14695.9944] [ 2562] [depth= 1] . ( 148 sec) [ -14695.9146] [ 2563] [depth= 1] . ( 148 sec) [ -14690.7071] [ 2561] [depth= 1] . ( 148 sec) [ -14690.0098] [ 2562] [depth= 1] . ( 148 sec) [ -14686.3531] [ 2561] [depth= 1] . ( 149 sec) [ -14684.1260] [ 2567] [depth= 1] . ( 149 sec) [ -14677.8669] [ 2561] [depth= 1] . ( 149 sec) [ -14676.6694] [ 2560] [depth= 1] . ( 149 sec) [ -14674.4483] [ 2561] [depth= 1] . ( 149 sec) [ -14660.3956] [ 2567] [depth= 1] . ( 149 sec) [ -14659.0069] [ 2561] [depth= 1] . ( 149 sec) [ -14647.2826] [ 2564] [depth= 5] . ( 149 sec) [ -14641.6838] [ 2560] [depth= 2] . ( 149 sec) [ -14640.9537] [ 2563] [depth= 1] . ( 150 sec) [ -14639.3847] [ 2560] [depth= 1] . ( 150 sec) [ -14637.2516] [ 2560] [depth= 1] . ( 150 sec) [ -14632.7965] [ 2560] [depth= 1] . ( 150 sec) [ -14627.6486] [ 2556] [depth= 1] . ( 150 sec) [ -14624.5125] [ 2560] [depth= 2] . ( 150 sec) [ -14616.8912] [ 2557] [depth= 2] . ( 150 sec) [ -14613.0179] [ 2560] [depth= 1] . ( 150 sec) [ -14611.8228] [ 2557] [depth= 1] . ( 151 sec) [ -14608.7228] [ 2561] [depth= 1] . ( 151 sec) [ -14604.5800] [ 2557] [depth= 3] . ( 151 sec) [ -14587.9009] [ 2557] [depth= 2] . ( 151 sec) [ -14585.8415] [ 2553] [depth= 1] . ( 151 sec) [ -14583.3343] [ 2553] [depth= 1] . ( 152 sec) [ -14562.1720] [ 2545] [depth= 4] . ( 152 sec) [ -14551.6166] [ 2544] [depth= 1] . ( 152 sec) [ -14547.2622] [ 2546] [depth= 1] . ( 152 sec) [ -14539.0044] [ 2542] [depth= 4] . ( 153 sec) [ -14527.5500] [ 2544] [depth= 3] . ( 153 sec) [ -14526.7659] [ 2542] [depth= 3] . ( 153 sec) [ -14526.6286] [ 2542] [depth= 1] . ( 153 sec) [ -14522.6486] [ 2540] [depth= 2] . ( 153 sec) [ -14516.3579] [ 2539] [depth= 1] . ( 153 sec) [ -14507.3997] [ 2534] [depth= 2] . ( 154 sec) [ -14507.2432] [ 2534] [depth= 1] . ( 154 sec) [ -14506.5689] [ 2536] [depth= 1] . ( 155 sec) [ -14505.9348] [ 2536] [depth= 1] . ( 155 sec) [ -14503.9401] [ 2534] [depth= 1] . ( 155 sec) [ -14503.9059] [ 2534] [depth= 1] . ( 156 sec) [ -14503.2496] [ 2535] [depth= 1] . ( 156 sec) [ -14503.0758] [ 2536] [depth= 1] . ( 157 sec) [ -14501.9580] [ 2535] [depth= 1] . ( 157 sec) [ -14501.3985] [ 2536] [depth= 1] . ( 157 sec) [ -14500.9434] [ 2538] [depth= 1] . ( 157 sec) [ -14500.7891] [ 2538] [depth= 1] . ( 157 sec) [ -14499.6083] [ 2539] [depth= 1] . ( 158 sec) [ -14496.2386] [ 2539] [depth= 2] . ( 159 sec) [ -14495.1641] [ 2538] [depth= 1] . ( 160 sec) [ -14435.2965] [Branch lengths ] . ( 162 sec) [ -14434.5167] [GTR parameters ] . ( 163 sec) [ -14339.6216] [Alpha ][ 0.269840] . ( 165 sec) [ -14339.4127] [ 2535] [depth= 1] . ( 168 sec) [ -14337.8490] [ 2540] [depth= 5] . ( 169 sec) [ -14337.5930] [ 2539] [depth= 1] . ( 170 sec) [ -14337.0348] [ 2541] [depth= 1] . ( 172 sec) [ -14336.8992] [ 2541] [depth= 1] . ( 173 sec) [ -14336.8418] [ 2541] [depth= 1] . ( 178 sec) [ -14336.6492] [ 2542] [depth= 1] . ( 184 sec) [ -14336.5738] [ 2542] [depth= 1] . ( 184 sec) [ -14335.8282] [ 2542] [depth= 2] . ( 185 sec) [ -14330.7728] [Branch lengths ] . ( 187 sec) [ -14330.3911] [GTR parameters ] . ( 187 sec) [ -14330.3908] [Alpha ][ 0.270109] . ( 187 sec) [ -14330.3207] [ 2543] [depth= 2] . ( 207 sec) [ -14330.2994] [ 2543] [depth= 1] . ( 208 sec) [ -14329.5544] [Branch lengths ] . ( 210 sec) [ -14329.5291] [GTR parameters ] . ( 210 sec) [ -14329.5125] [Alpha ][ 0.272182] . ( 264 sec) [ -14329.0882] [ 2549] [depth= 2] . ( 266 sec) [ -14329.0544] [ 2550] [depth= 1] . ( 266 sec) [ -14329.0250] [ 2550] [depth= 1] . ( 281 sec) [ -14328.5254] [Branch lengths ] . ( 281 sec) [ -14328.5190] [GTR parameters ] . ( 282 sec) [ -14328.5056] [Alpha ][ 0.274026] . ( 353 sec) [ -14328.3220] [Branch lengths ] . ( 353 sec) [ -14328.3220] [Topology ] . ( 355 sec) [ -14328.2030] [Topology ] . ( 357 sec) [ -14328.1053] [Topology ] . ( 358 sec) [ -14328.0777] [Topology ] . ( 360 sec) [ -14328.0680] [Topology ] . ( 362 sec) [ -14328.0642] [Topology ] . ( 363 sec) [ -14328.0624] [Topology ] . ( 364 sec) [ -14328.0611] [GTR parameters ] . ( 365 sec) [ -14328.0467] [Alpha ][ 0.275942] . ( 365 sec) [ -14328.0467] [Topology ] . ( 366 sec) [ -14328.0437] [Topology ] . ( 368 sec) [ -14328.0419] [Topology ] . ( 370 sec) [ -14328.0408] [Topology ] . ( 371 sec) [ -14328.0402] [Topology ] . ( 372 sec) [ -14328.0399] [GTR parameters ] . ( 372 sec) [ -14328.0397] [Alpha ][ 0.276218] . ( 372 sec) [ -14328.0397] [Topology ] . ( 374 sec) [ -14328.0391] [Topology ] . ( 374 sec) [ -14328.0391] [GTR parameters ] . ( 375 sec) [ -14328.0391] [Alpha ][ 0.276218] . Checking for NNIs, optimizing five branches... . ( 387 sec) [ -14327.9302] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -14368.638364 . Log likelihood obtained after SPR moves : -14327.930250 . Log likelihood of the current tree: -14327.930250. . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Best log likelihood : -14327.930250 . Time used 0h6m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1519.06user 0.00system 25:27.41elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps