.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data39.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... . 451 patterns found. (out of a total of 500 sites) . 50 sites without polymorphism (10.00%). . [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)... . ( 0 sec) [ -20711.7059] [GTR parameters ] . ( 1 sec) [ -20367.3681] [Alpha ][ 0.500960] . ( 1 sec) [ -19823.1653] [ 4528] [depth= 8] . ( 1 sec) [ -19695.4413] [ 4528] [depth= 6] . ( 1 sec) [ -19547.5514] [ 4496] [depth= 4] . ( 1 sec) [ -19533.9619] [ 4480] [depth= 4] . ( 1 sec) [ -19155.6111] [ 4420] [depth= 4] . ( 1 sec) [ -18995.4382] [ 4402] [depth= 5] . ( 1 sec) [ -18991.4653] [ 4388] [depth= 3] . ( 1 sec) [ -18948.2568] [ 4382] [depth= 3] . ( 1 sec) [ -18871.4809] [ 4324] [depth= 8] . ( 1 sec) [ -18658.7035] [ 4271] [depth= 1] . ( 1 sec) [ -18519.4457] [ 4212] [depth= 6] . ( 1 sec) [ -18346.8405] [ 4136] [depth= 1] . ( 1 sec) [ -18149.6586] [ 4100] [depth= 11] . ( 1 sec) [ -18118.6157] [ 4090] [depth= 2] . ( 1 sec) [ -18069.3401] [ 4061] [depth= 4] . ( 1 sec) [ -17977.4600] [ 3996] [depth= 4] . ( 1 sec) [ -17830.1104] [ 3985] [depth= 4] . ( 1 sec) [ -17761.1888] [ 3980] [depth= 1] . ( 1 sec) [ -17616.9768] [ 3970] [depth= 2] . ( 1 sec) [ -17575.6264] [ 3933] [depth= 7] . ( 2 sec) [ -17524.1400] [ 3893] [depth= 4] . ( 2 sec) [ -17453.5537] [ 3884] [depth= 1] . ( 2 sec) [ -17338.8056] [ 3815] [depth= 2] . ( 2 sec) [ -17312.0968] [ 3796] [depth= 1] . ( 2 sec) [ -17207.3683] [ 3776] [depth= 1] . ( 2 sec) [ -16851.3235] [ 3694] [depth= 2] . ( 2 sec) [ -16577.2575] [ 3685] [depth= 16] . ( 2 sec) [ -16165.5078] [ 3555] [depth= 7] . ( 2 sec) [ -16020.9387] [ 3576] [depth= 2] . ( 2 sec) [ -15780.4279] [ 3520] [depth= 10] . ( 2 sec) [ -15672.6569] [ 3502] [depth= 3] . ( 2 sec) [ -15607.9062] [ 3492] [depth= 8] . ( 2 sec) [ -15584.9057] [ 3475] [depth= 5] . ( 2 sec) [ -15527.7652] [ 3474] [depth= 13] . ( 2 sec) [ -15179.2206] [ 3459] [depth= 1] . ( 2 sec) [ -15159.9796] [ 3450] [depth= 11] . ( 2 sec) [ -15066.3118] [ 3385] [depth= 10] . ( 2 sec) [ -15053.2728] [ 3386] [depth= 2] . ( 2 sec) [ -14965.6156] [ 3363] [depth= 5] . ( 2 sec) [ -14897.6252] [ 3368] [depth= 1] . ( 3 sec) [ -14827.9602] [ 3348] [depth= 1] . ( 3 sec) [ -14426.6667] [ 3244] [depth= 4] . ( 3 sec) [ -14406.2315] [ 3237] [depth= 1] . ( 3 sec) [ -14323.0738] [ 3212] [depth= 1] . ( 3 sec) [ -14279.8778] [ 3212] [depth= 7] . ( 3 sec) [ -14206.4323] [ 3152] [depth= 6] . ( 3 sec) [ -13781.5128] [ 3092] [depth= 3] . ( 3 sec) [ -13271.8345] [ 3016] [depth= 1] . ( 3 sec) [ -13157.4892] [ 2994] [depth= 9] . ( 3 sec) [ -13022.6926] [ 2961] [depth= 1] . ( 3 sec) [ -12980.4955] [ 2946] [depth= 1] . ( 3 sec) [ -12963.5595] [ 2918] [depth= 1] . ( 3 sec) [ -12615.9867] [ 2871] [depth= 3] . ( 3 sec) [ -12539.6999] [ 2876] [depth= 1] . ( 3 sec) [ -12530.7207] [ 2876] [depth= 1] . ( 3 sec) [ -12529.6995] [ 2871] [depth= 1] . ( 3 sec) [ -12525.5031] [ 2864] [depth= 1] . ( 3 sec) [ -12448.0675] [ 2834] [depth= 4] . ( 3 sec) [ -12405.2451] [ 2829] [depth= 2] . ( 4 sec) [ -12355.6095] [ 2818] [depth= 3] . ( 4 sec) [ -12334.9245] [ 2807] [depth= 1] . ( 4 sec) [ -12305.4842] [ 2801] [depth= 1] . ( 4 sec) [ -12194.7750] [ 2773] [depth= 4] . ( 4 sec) [ -12186.6646] [ 2770] [depth= 1] . ( 4 sec) [ -12185.0963] [ 2773] [depth= 1] . ( 4 sec) [ -12168.6397] [ 2769] [depth= 1] . ( 4 sec) [ -12070.0193] [ 2740] [depth= 3] . ( 4 sec) [ -11999.5144] [ 2667] [depth= 6] . ( 4 sec) [ -11990.2865] [ 2666] [depth= 1] . ( 4 sec) [ -11932.5647] [ 2650] [depth= 1] . ( 4 sec) [ -11712.1887] [ 2642] [depth= 1] . ( 4 sec) [ -11587.7683] [ 2629] [depth= 1] . ( 4 sec) [ -11580.0254] [ 2628] [depth= 3] . ( 4 sec) [ -11426.7485] [ 2633] [depth= 2] . ( 4 sec) [ -11387.2039] [ 2601] [depth= 3] . ( 4 sec) [ -11374.7943] [ 2593] [depth= 1] . ( 5 sec) [ -11166.9704] [Branch lengths ] . ( 5 sec) [ -11163.8744] [GTR parameters ] . ( 5 sec) [ -11119.5851] [Alpha ][ 0.953650] . ( 6 sec) [ -11113.9084] [ 2582] [depth= 3] . ( 6 sec) [ -11064.1093] [ 2556] [depth= 1] . ( 6 sec) [ -11054.3424] [ 2551] [depth= 1] . ( 6 sec) [ -11053.1956] [ 2556] [depth= 1] . ( 6 sec) [ -11050.7247] [ 2561] [depth= 1] . ( 6 sec) [ -11050.1504] [ 2561] [depth= 1] . ( 6 sec) [ -11029.6997] [ 2552] [depth= 1] . ( 6 sec) [ -11029.5185] [ 2552] [depth= 1] . ( 7 sec) [ -11022.7426] [ 2551] [depth= 2] . ( 7 sec) [ -11019.8950] [ 2563] [depth= 1] . ( 7 sec) [ -11018.6158] [ 2559] [depth= 1] . ( 7 sec) [ -11007.9722] [ 2547] [depth= 1] . ( 7 sec) [ -11004.1568] [ 2547] [depth= 1] . ( 7 sec) [ -11001.8895] [ 2548] [depth= 1] . ( 8 sec) [ -10997.6222] [ 2549] [depth= 1] . ( 8 sec) [ -10994.0765] [ 2545] [depth= 1] . ( 8 sec) [ -10990.8421] [ 2543] [depth= 1] . ( 8 sec) [ -10986.8843] [ 2545] [depth= 1] . ( 9 sec) [ -10965.6868] [Branch lengths ] . ( 9 sec) [ -10965.2415] [GTR parameters ] . ( 9 sec) [ -10964.8072] [Alpha ][ 1.016485] . ( 13 sec) [ -10963.9159] [Branch lengths ] . ( 24 sec) [ -10963.7865] [ 2544] [depth= 1] . ( 29 sec) [ -10963.7426] [ 2539] [depth= 1] . ( 34 sec) [ -10963.4390] [Branch lengths ] . ( 35 sec) [ -10963.4378] [GTR parameters ] . ( 35 sec) [ -10963.4240] [Alpha ][ 1.028300] . ( 35 sec) [ -10963.4240] [Topology ] . ( 36 sec) [ -10963.3807] [Topology ] . ( 37 sec) [ -10963.3280] [Topology ] . ( 37 sec) [ -10963.3190] [Topology ] . ( 38 sec) [ -10963.3162] [Topology ] . ( 39 sec) [ -10963.3152] [Topology ] . ( 40 sec) [ -10963.3147] [Topology ] . ( 40 sec) [ -10963.3130] [GTR parameters ] . ( 40 sec) [ -10963.3125] [Alpha ][ 1.030516] . ( 40 sec) [ -10963.3125] [Topology ] . ( 41 sec) [ -10963.3121] [Topology ] . ( 41 sec) [ -10963.3121] [GTR parameters ] . ( 41 sec) [ -10963.3121] [Alpha ][ 1.030516] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.312136. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21364.5434] [GTR parameters ] . ( 1 sec) [ -21019.7954] [Alpha ][ 0.500960] . ( 1 sec) [ -20475.3193] [ 4672] [depth= 3] . ( 1 sec) [ -20058.7579] [ 4564] [depth= 3] . ( 1 sec) [ -20026.9813] [ 4551] [depth= 2] . ( 1 sec) [ -19927.2403] [ 4545] [depth= 3] . ( 1 sec) [ -19894.5890] [ 4535] [depth= 1] . ( 1 sec) [ -19694.3711] [ 4530] [depth= 6] . ( 1 sec) [ -19692.4180] [ 4530] [depth= 1] . ( 1 sec) [ -19439.3431] [ 4510] [depth= 5] . ( 1 sec) [ -19375.6772] [ 4492] [depth= 2] . ( 1 sec) [ -19166.3590] [ 4485] [depth= 5] . ( 1 sec) [ -19114.1624] [ 4485] [depth= 3] . ( 1 sec) [ -18997.8148] [ 4480] [depth= 4] . ( 1 sec) [ -18788.1235] [ 4434] [depth= 13] . ( 1 sec) [ -18647.6698] [ 4421] [depth= 1] . ( 1 sec) [ -18187.6616] [ 4282] [depth= 15] . ( 1 sec) [ -18054.9011] [ 4223] [depth= 5] . ( 1 sec) [ -17765.1017] [ 4153] [depth= 2] . ( 1 sec) [ -17707.2760] [ 4147] [depth= 1] . ( 1 sec) [ -17114.8286] [ 4116] [depth= 1] . ( 2 sec) [ -16593.6383] [ 4002] [depth= 20] . ( 2 sec) [ -16582.4268] [ 3952] [depth= 6] . ( 2 sec) [ -16537.2339] [ 3943] [depth= 13] . ( 2 sec) [ -16416.8038] [ 3930] [depth= 1] . ( 2 sec) [ -16386.3680] [ 3989] [depth= 1] . ( 2 sec) [ -16307.5807] [ 3994] [depth= 15] . ( 2 sec) [ -15852.1683] [ 3890] [depth= 16] . ( 2 sec) [ -15848.5806] [ 3899] [depth= 1] . ( 2 sec) [ -15645.6567] [ 3812] [depth= 7] . ( 2 sec) [ -15634.1487] [ 3824] [depth= 2] . ( 2 sec) [ -15629.7743] [ 3815] [depth= 1] . ( 2 sec) [ -15561.4915] [ 3742] [depth= 13] . ( 2 sec) [ -15345.7539] [ 3643] [depth= 6] . ( 2 sec) [ -15344.5710] [ 3576] [depth= 1] . ( 2 sec) [ -15267.8861] [ 3563] [depth= 3] . ( 2 sec) [ -15194.2462] [ 3572] [depth= 1] . ( 2 sec) [ -15051.9174] [ 3525] [depth= 3] . ( 3 sec) [ -14701.9090] [ 3507] [depth= 6] . ( 3 sec) [ -14684.2852] [ 3500] [depth= 11] . ( 3 sec) [ -14466.5559] [ 3492] [depth= 1] . ( 3 sec) [ -14320.3823] [ 3460] [depth= 4] . ( 3 sec) [ -14160.6328] [ 3372] [depth= 11] . ( 3 sec) [ -13914.7251] [ 3303] [depth= 1] . ( 3 sec) [ -13730.2523] [ 3230] [depth= 6] . ( 3 sec) [ -13687.0899] [ 3221] [depth= 2] . ( 3 sec) [ -13467.4187] [ 3194] [depth= 4] . ( 3 sec) [ -13377.5918] [ 3158] [depth= 1] . ( 3 sec) [ -13101.9894] [ 3067] [depth= 2] . ( 3 sec) [ -12761.8163] [ 3034] [depth= 5] . ( 3 sec) [ -12641.1109] [ 2957] [depth= 2] . ( 3 sec) [ -12610.4954] [ 2981] [depth= 1] . ( 3 sec) [ -12599.3303] [ 2982] [depth= 1] . ( 3 sec) [ -12390.9314] [ 2949] [depth= 4] . ( 3 sec) [ -12390.7321] [ 2952] [depth= 1] . ( 3 sec) [ -12267.8497] [ 2900] [depth= 3] . ( 3 sec) [ -12179.7535] [ 2872] [depth= 2] . ( 4 sec) [ -12145.6749] [ 2838] [depth= 2] . ( 4 sec) [ -12043.3527] [ 2808] [depth= 8] . ( 4 sec) [ -11978.2278] [ 2789] [depth= 1] . ( 4 sec) [ -11977.7904] [ 2777] [depth= 2] . ( 4 sec) [ -11908.5899] [ 2755] [depth= 3] . ( 4 sec) [ -11901.8316] [ 2752] [depth= 1] . ( 4 sec) [ -11854.9928] [ 2727] [depth= 5] . ( 4 sec) [ -11841.8544] [ 2716] [depth= 1] . ( 4 sec) [ -11827.0676] [ 2713] [depth= 1] . ( 4 sec) [ -11824.9666] [ 2697] [depth= 1] . ( 4 sec) [ -11793.2010] [ 2698] [depth= 3] . ( 4 sec) [ -11672.8964] [ 2659] [depth= 1] . ( 4 sec) [ -11510.1543] [ 2633] [depth= 2] . ( 4 sec) [ -11455.3453] [ 2618] [depth= 1] . ( 4 sec) [ -11410.7123] [ 2609] [depth= 1] . ( 5 sec) [ -11393.8423] [ 2615] [depth= 1] . ( 5 sec) [ -11393.6552] [ 2611] [depth= 2] . ( 5 sec) [ -11385.7073] [ 2615] [depth= 1] . ( 5 sec) [ -11375.7584] [ 2614] [depth= 2] . ( 5 sec) [ -11365.5728] [ 2614] [depth= 2] . ( 5 sec) [ -11192.4667] [Branch lengths ] . ( 6 sec) [ -11189.7518] [GTR parameters ] . ( 6 sec) [ -11149.5782] [Alpha ][ 0.920437] . ( 6 sec) [ -11134.4933] [ 2597] [depth= 1] . ( 6 sec) [ -11132.6842] [ 2603] [depth= 3] . ( 6 sec) [ -11119.0126] [ 2589] [depth= 1] . ( 6 sec) [ -11118.2117] [ 2581] [depth= 1] . ( 7 sec) [ -11117.4811] [ 2579] [depth= 2] . ( 7 sec) [ -11117.4678] [ 2581] [depth= 1] . ( 7 sec) [ -11116.9544] [ 2587] [depth= 1] . ( 7 sec) [ -11071.0034] [ 2600] [depth= 1] . ( 7 sec) [ -11054.0282] [ 2587] [depth= 1] . ( 7 sec) [ -11040.1659] [ 2582] [depth= 1] . ( 8 sec) [ -11035.4606] [ 2574] [depth= 1] . ( 8 sec) [ -11004.3140] [ 2550] [depth= 1] . ( 9 sec) [ -11003.9119] [ 2549] [depth= 1] . ( 9 sec) [ -11000.7243] [ 2553] [depth= 1] . ( 9 sec) [ -10999.2549] [ 2554] [depth= 1] . ( 9 sec) [ -10999.0410] [ 2552] [depth= 1] . ( 9 sec) [ -10996.4476] [ 2546] [depth= 1] . ( 9 sec) [ -10995.0120] [ 2548] [depth= 1] . ( 9 sec) [ -10971.0820] [Branch lengths ] . ( 10 sec) [ -10970.8193] [GTR parameters ] . ( 10 sec) [ -10969.9214] [Alpha ][ 1.009359] . ( 10 sec) [ -10968.1484] [ 2544] [depth= 1] . ( 12 sec) [ -10968.1122] [ 2544] [depth= 1] . ( 13 sec) [ -10964.4671] [Branch lengths ] . ( 13 sec) [ -10964.4476] [GTR parameters ] . ( 13 sec) [ -10964.4244] [Alpha ][ 1.024659] . ( 16 sec) [ -10963.9908] [Branch lengths ] . ( 32 sec) [ -10963.9635] [ 2541] [depth= 1] . ( 38 sec) [ -10963.5944] [Branch lengths ] . ( 38 sec) [ -10963.5937] [GTR parameters ] . ( 39 sec) [ -10963.5919] [Alpha ][ 1.028948] . ( 39 sec) [ -10963.5919] [Topology ] . ( 39 sec) [ -10963.4013] [Topology ] . ( 40 sec) [ -10963.3325] [Topology ] . ( 41 sec) [ -10963.3209] [Topology ] . ( 42 sec) [ -10963.3174] [Topology ] . ( 43 sec) [ -10963.3161] [Topology ] . ( 44 sec) [ -10963.3157] [Topology ] . ( 44 sec) [ -10963.3127] [GTR parameters ] . ( 44 sec) [ -10963.3124] [Alpha ][ 1.030552] . ( 44 sec) [ -10963.3124] [Topology ] . ( 45 sec) [ -10963.3121] [Topology ] . ( 45 sec) [ -10963.3121] [GTR parameters ] . ( 45 sec) [ -10963.3121] [Alpha ][ 1.030552] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.312086. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21631.9998] [GTR parameters ] . ( 1 sec) [ -21274.9006] [Alpha ][ 0.500960] . ( 1 sec) [ -20626.8983] [ 4705] [depth= 8] . ( 1 sec) [ -20145.6590] [ 4593] [depth= 8] . ( 1 sec) [ -20082.9002] [ 4584] [depth= 4] . ( 1 sec) [ -19897.0184] [ 4575] [depth= 2] . ( 1 sec) [ -19842.7997] [ 4526] [depth= 7] . ( 1 sec) [ -19703.9081] [ 4520] [depth= 6] . ( 1 sec) [ -19475.3725] [ 4499] [depth= 16] . ( 1 sec) [ -19296.2054] [ 4474] [depth= 4] . ( 1 sec) [ -19016.2078] [ 4364] [depth= 13] . ( 1 sec) [ -18917.1189] [ 4364] [depth= 17] . ( 1 sec) [ -18491.0630] [ 4302] [depth= 17] . ( 1 sec) [ -18104.2650] [ 4208] [depth= 16] . ( 1 sec) [ -18096.2381] [ 4211] [depth= 1] . ( 1 sec) [ -17991.8567] [ 4180] [depth= 11] . ( 1 sec) [ -17977.1256] [ 4158] [depth= 2] . ( 1 sec) [ -17925.0989] [ 4139] [depth= 5] . ( 1 sec) [ -17695.7788] [ 4120] [depth= 1] . ( 1 sec) [ -17540.5675] [ 4103] [depth= 2] . ( 1 sec) [ -17111.8575] [ 4085] [depth= 6] . ( 2 sec) [ -16942.2681] [ 4077] [depth= 6] . ( 2 sec) [ -16780.0975] [ 4052] [depth= 9] . ( 2 sec) [ -16632.4575] [ 3973] [depth= 1] . ( 2 sec) [ -16379.0066] [ 3968] [depth= 9] . ( 2 sec) [ -16289.9037] [ 3906] [depth= 1] . ( 2 sec) [ -16192.4081] [ 3854] [depth= 1] . ( 2 sec) [ -16082.9771] [ 3833] [depth= 5] . ( 2 sec) [ -15866.5102] [ 3820] [depth= 1] . ( 2 sec) [ -15703.6632] [ 3752] [depth= 8] . ( 2 sec) [ -15614.6077] [ 3777] [depth= 10] . ( 2 sec) [ -15566.3453] [ 3808] [depth= 1] . ( 2 sec) [ -15498.2537] [ 3770] [depth= 2] . ( 2 sec) [ -15424.1062] [ 3726] [depth= 8] . ( 2 sec) [ -15246.5212] [ 3682] [depth= 1] . ( 2 sec) [ -15142.1082] [ 3655] [depth= 10] . ( 2 sec) [ -15141.4143] [ 3658] [depth= 1] . ( 2 sec) [ -15124.0868] [ 3653] [depth= 4] . ( 2 sec) [ -15060.6060] [ 3631] [depth= 1] . ( 2 sec) [ -15053.3514] [ 3642] [depth= 1] . ( 2 sec) [ -14772.9098] [ 3528] [depth= 3] . ( 3 sec) [ -14716.1170] [ 3512] [depth= 1] . ( 3 sec) [ -14500.4630] [ 3447] [depth= 1] . ( 3 sec) [ -14458.0860] [ 3420] [depth= 5] . ( 3 sec) [ -14436.7429] [ 3401] [depth= 3] . ( 3 sec) [ -14429.8857] [ 3402] [depth= 1] . ( 3 sec) [ -14401.2227] [ 3381] [depth= 10] . ( 3 sec) [ -13573.2671] [ 3268] [depth= 1] . ( 3 sec) [ -13458.7336] [ 3223] [depth= 6] . ( 3 sec) [ -13386.6852] [ 3220] [depth= 1] . ( 3 sec) [ -13374.7575] [ 3219] [depth= 1] . ( 3 sec) [ -13346.9817] [ 3214] [depth= 1] . ( 3 sec) [ -13333.8335] [ 3213] [depth= 1] . ( 3 sec) [ -13201.8881] [ 3188] [depth= 3] . ( 3 sec) [ -12806.2691] [ 3075] [depth= 11] . ( 3 sec) [ -12759.0263] [ 3040] [depth= 5] . ( 3 sec) [ -12628.4626] [ 3033] [depth= 3] . ( 3 sec) [ -12610.1086] [ 3050] [depth= 10] . ( 3 sec) [ -12586.8758] [ 3047] [depth= 1] . ( 3 sec) [ -12321.4365] [ 2978] [depth= 2] . ( 3 sec) [ -12301.4325] [ 2971] [depth= 1] . ( 3 sec) [ -12298.5486] [ 2978] [depth= 1] . ( 4 sec) [ -12298.0373] [ 2973] [depth= 1] . ( 4 sec) [ -12265.5610] [ 2978] [depth= 1] . ( 4 sec) [ -12210.8081] [ 2926] [depth= 2] . ( 4 sec) [ -12199.8557] [ 2914] [depth= 1] . ( 4 sec) [ -12036.5385] [ 2862] [depth= 4] . ( 4 sec) [ -11985.7288] [ 2864] [depth= 4] . ( 4 sec) [ -11807.9512] [ 2800] [depth= 11] . ( 4 sec) [ -11806.8176] [ 2801] [depth= 1] . ( 4 sec) [ -11766.9006] [ 2801] [depth= 1] . ( 4 sec) [ -11762.2500] [ 2791] [depth= 6] . ( 4 sec) [ -11712.5671] [ 2770] [depth= 1] . ( 4 sec) [ -11639.5454] [ 2766] [depth= 4] . ( 4 sec) [ -11623.6603] [ 2765] [depth= 1] . ( 4 sec) [ -11527.4250] [ 2729] [depth= 3] . ( 4 sec) [ -11450.9321] [ 2728] [depth= 3] . ( 4 sec) [ -11440.4869] [ 2723] [depth= 3] . ( 5 sec) [ -11415.0168] [ 2712] [depth= 2] . ( 5 sec) [ -11400.8472] [ 2717] [depth= 2] . ( 5 sec) [ -11375.2547] [ 2698] [depth= 1] . ( 5 sec) [ -11372.6341] [ 2697] [depth= 1] . ( 5 sec) [ -11231.1118] [Branch lengths ] . ( 6 sec) [ -11228.0574] [GTR parameters ] . ( 6 sec) [ -11189.3233] [Alpha ][ 0.902842] . ( 6 sec) [ -11187.3639] [ 2696] [depth= 1] . ( 6 sec) [ -11115.7386] [ 2623] [depth= 10] . ( 6 sec) [ -11108.8907] [ 2625] [depth= 1] . ( 6 sec) [ -11099.2175] [ 2613] [depth= 1] . ( 7 sec) [ -11083.8581] [ 2607] [depth= 1] . ( 7 sec) [ -11080.9224] [ 2603] [depth= 1] . ( 7 sec) [ -11076.7758] [ 2595] [depth= 1] . ( 7 sec) [ -11075.7855] [ 2595] [depth= 1] . ( 7 sec) [ -11074.3671] [ 2594] [depth= 1] . ( 7 sec) [ -11043.5858] [ 2575] [depth= 4] . ( 7 sec) [ -11041.2518] [ 2572] [depth= 1] . ( 7 sec) [ -11039.7623] [ 2573] [depth= 1] . ( 7 sec) [ -11039.1247] [ 2572] [depth= 1] . ( 8 sec) [ -11034.1084] [ 2568] [depth= 1] . ( 8 sec) [ -11030.4787] [ 2572] [depth= 1] . ( 8 sec) [ -11026.6672] [ 2569] [depth= 1] . ( 8 sec) [ -11012.6142] [ 2565] [depth= 2] . ( 8 sec) [ -11010.0085] [ 2568] [depth= 1] . ( 8 sec) [ -10994.9687] [ 2562] [depth= 1] . ( 8 sec) [ -10994.7368] [ 2563] [depth= 1] . ( 9 sec) [ -10993.1296] [ 2557] [depth= 1] . ( 9 sec) [ -10992.3033] [ 2557] [depth= 1] . ( 9 sec) [ -10992.1532] [ 2552] [depth= 1] . ( 9 sec) [ -10972.2607] [Branch lengths ] . ( 10 sec) [ -10972.0692] [GTR parameters ] . ( 10 sec) [ -10970.7217] [Alpha ][ 1.010395] . ( 10 sec) [ -10970.2010] [ 2546] [depth= 1] . ( 11 sec) [ -10970.0933] [ 2546] [depth= 1] . ( 11 sec) [ -10969.8533] [ 2546] [depth= 1] . ( 13 sec) [ -10966.0673] [Branch lengths ] . ( 14 sec) [ -10966.0615] [GTR parameters ] . ( 14 sec) [ -10966.0401] [Alpha ][ 1.025097] . ( 17 sec) [ -10965.8210] [Branch lengths ] . ( 19 sec) [ -10963.8876] [ 2544] [depth= 1] . ( 33 sec) [ -10963.8476] [ 2539] [depth= 1] . ( 39 sec) [ -10963.3940] [Branch lengths ] . ( 39 sec) [ -10963.3773] [GTR parameters ] . ( 39 sec) [ -10963.3751] [Alpha ][ 1.029840] . ( 62 sec) [ -10963.3164] [Branch lengths ] . ( 62 sec) [ -10963.3164] [Topology ] . ( 63 sec) [ -10963.3136] [Topology ] . ( 64 sec) [ -10963.3127] [Topology ] . ( 64 sec) [ -10963.3126] [GTR parameters ] . ( 64 sec) [ -10963.3126] [Alpha ][ 1.030870] . ( 64 sec) [ -10963.3126] [Topology ] . ( 65 sec) [ -10963.3122] [Topology ] . ( 65 sec) [ -10963.3122] [GTR parameters ] . ( 65 sec) [ -10963.3122] [Alpha ][ 1.030870] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.312185. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20863.8946] [GTR parameters ] . ( 1 sec) [ -20541.6345] [Alpha ][ 0.500960] . ( 1 sec) [ -19763.4729] [ 4641] [depth= 8] . ( 1 sec) [ -19437.2912] [ 4523] [depth= 8] . ( 1 sec) [ -19211.7041] [ 4474] [depth= 7] . ( 1 sec) [ -19177.9995] [ 4360] [depth= 1] . ( 1 sec) [ -18945.4546] [ 4349] [depth= 7] . ( 1 sec) [ -18924.9516] [ 4338] [depth= 2] . ( 1 sec) [ -18893.8330] [ 4326] [depth= 3] . ( 1 sec) [ -18862.6605] [ 4309] [depth= 2] . ( 1 sec) [ -18767.8461] [ 4287] [depth= 3] . ( 1 sec) [ -18748.4215] [ 4283] [depth= 2] . ( 1 sec) [ -18735.1347] [ 4282] [depth= 1] . ( 1 sec) [ -18490.9265] [ 4195] [depth= 3] . ( 1 sec) [ -18394.1123] [ 4173] [depth= 1] . ( 1 sec) [ -18347.7986] [ 4175] [depth= 7] . ( 1 sec) [ -17945.7285] [ 4121] [depth= 12] . ( 1 sec) [ -17524.6543] [ 4053] [depth= 11] . ( 1 sec) [ -17409.2219] [ 3970] [depth= 1] . ( 1 sec) [ -17284.1761] [ 3911] [depth= 4] . ( 1 sec) [ -17233.7679] [ 3903] [depth= 1] . ( 2 sec) [ -17203.7617] [ 3916] [depth= 1] . ( 2 sec) [ -16937.5830] [ 3827] [depth= 15] . ( 2 sec) [ -16905.7346] [ 3823] [depth= 2] . ( 2 sec) [ -16564.2307] [ 3826] [depth= 1] . ( 2 sec) [ -16365.1150] [ 3793] [depth= 2] . ( 2 sec) [ -16284.0215] [ 3750] [depth= 2] . ( 2 sec) [ -16044.1730] [ 3738] [depth= 11] . ( 2 sec) [ -15840.3167] [ 3691] [depth= 9] . ( 2 sec) [ -15669.6721] [ 3660] [depth= 3] . ( 2 sec) [ -15579.2899] [ 3640] [depth= 1] . ( 2 sec) [ -15328.1529] [ 3538] [depth= 6] . ( 2 sec) [ -15186.9099] [ 3528] [depth= 2] . ( 2 sec) [ -15112.1798] [ 3564] [depth= 1] . ( 2 sec) [ -14839.6016] [ 3492] [depth= 1] . ( 2 sec) [ -14739.3812] [ 3446] [depth= 9] . ( 2 sec) [ -14679.8521] [ 3379] [depth= 2] . ( 2 sec) [ -14649.5950] [ 3348] [depth= 1] . ( 2 sec) [ -14488.5631] [ 3328] [depth= 6] . ( 2 sec) [ -14485.4221] [ 3331] [depth= 1] . ( 2 sec) [ -14256.1477] [ 3274] [depth= 10] . ( 2 sec) [ -14214.6036] [ 3260] [depth= 1] . ( 2 sec) [ -14212.2117] [ 3256] [depth= 1] . ( 3 sec) [ -14139.4992] [ 3217] [depth= 7] . ( 3 sec) [ -14099.9944] [ 3199] [depth= 1] . ( 3 sec) [ -14001.0341] [ 3187] [depth= 3] . ( 3 sec) [ -13943.0170] [ 3205] [depth= 1] . ( 3 sec) [ -13930.5896] [ 3198] [depth= 1] . ( 3 sec) [ -13855.6671] [ 3186] [depth= 6] . ( 3 sec) [ -13848.6843] [ 3282] [depth= 1] . ( 3 sec) [ -13643.2292] [ 3268] [depth= 3] . ( 3 sec) [ -13417.7604] [ 3248] [depth= 2] . ( 3 sec) [ -13379.6984] [ 3263] [depth= 1] . ( 3 sec) [ -13257.3810] [ 3202] [depth= 4] . ( 3 sec) [ -13080.7108] [ 3156] [depth= 3] . ( 3 sec) [ -13016.2669] [ 3158] [depth= 1] . ( 3 sec) [ -12939.2648] [ 3138] [depth= 10] . ( 3 sec) [ -12932.7010] [ 3133] [depth= 1] . ( 3 sec) [ -12926.5750] [ 3139] [depth= 1] . ( 3 sec) [ -12840.4581] [ 3107] [depth= 1] . ( 3 sec) [ -12837.0617] [ 3107] [depth= 5] . ( 3 sec) [ -12713.7540] [ 3090] [depth= 5] . ( 4 sec) [ -12686.5778] [ 3092] [depth= 3] . ( 4 sec) [ -12647.0827] [ 3079] [depth= 1] . ( 4 sec) [ -12606.8739] [ 3063] [depth= 1] . ( 4 sec) [ -12597.8283] [ 3060] [depth= 1] . ( 4 sec) [ -12467.9887] [ 2988] [depth= 5] . ( 4 sec) [ -12430.7468] [ 2966] [depth= 1] . ( 4 sec) [ -12423.7497] [ 2959] [depth= 1] . ( 4 sec) [ -12406.7095] [ 2949] [depth= 3] . ( 4 sec) [ -12388.7373] [ 2942] [depth= 2] . ( 4 sec) [ -12182.0900] [ 2837] [depth= 9] . ( 4 sec) [ -12173.7432] [ 2851] [depth= 1] . ( 4 sec) [ -12173.4125] [ 2864] [depth= 1] . ( 4 sec) [ -12092.8971] [ 2754] [depth= 6] . ( 4 sec) [ -12074.6975] [ 2751] [depth= 5] . ( 4 sec) [ -12042.7819] [ 2740] [depth= 1] . ( 4 sec) [ -12022.5246] [ 2723] [depth= 1] . ( 4 sec) [ -12009.8587] [ 2713] [depth= 1] . ( 5 sec) [ -11979.5617] [ 2710] [depth= 1] . ( 5 sec) [ -11964.7448] [ 2709] [depth= 2] . ( 5 sec) [ -11856.5886] [ 2692] [depth= 1] . ( 5 sec) [ -11696.2995] [ 2695] [depth= 1] . ( 5 sec) [ -11296.4562] [Branch lengths ] . ( 6 sec) [ -11293.5406] [GTR parameters ] . ( 6 sec) [ -11245.7166] [Alpha ][ 0.958220] . ( 6 sec) [ -11245.2640] [ 2692] [depth= 1] . ( 6 sec) [ -11244.1734] [ 2690] [depth= 1] . ( 6 sec) [ -11229.8004] [ 2689] [depth= 3] . ( 6 sec) [ -11219.2671] [ 2689] [depth= 1] . ( 6 sec) [ -11210.4798] [ 2676] [depth= 1] . ( 6 sec) [ -11196.0690] [ 2636] [depth= 5] . ( 6 sec) [ -11165.2013] [ 2618] [depth= 1] . ( 7 sec) [ -11137.6760] [ 2594] [depth= 2] . ( 7 sec) [ -11136.1040] [ 2598] [depth= 1] . ( 7 sec) [ -11127.8954] [ 2610] [depth= 3] . ( 7 sec) [ -11117.7423] [ 2599] [depth= 2] . ( 7 sec) [ -11109.3571] [ 2591] [depth= 5] . ( 7 sec) [ -11075.8604] [ 2572] [depth= 2] . ( 7 sec) [ -11067.8233] [ 2570] [depth= 1] . ( 7 sec) [ -11057.3537] [ 2561] [depth= 1] . ( 8 sec) [ -11057.1452] [ 2563] [depth= 1] . ( 8 sec) [ -11006.1099] [ 2546] [depth= 1] . ( 9 sec) [ -11004.1198] [ 2547] [depth= 1] . ( 9 sec) [ -10977.1338] [Branch lengths ] . ( 9 sec) [ -10976.8011] [GTR parameters ] . ( 9 sec) [ -10976.3642] [Alpha ][ 1.020803] . ( 10 sec) [ -10974.3934] [ 2542] [depth= 1] . ( 10 sec) [ -10974.3236] [ 2541] [depth= 1] . ( 12 sec) [ -10974.1974] [ 2541] [depth= 1] . ( 13 sec) [ -10965.6253] [Branch lengths ] . ( 13 sec) [ -10965.6055] [GTR parameters ] . ( 13 sec) [ -10965.5953] [Alpha ][ 1.030970] . ( 16 sec) [ -10964.4307] [Branch lengths ] . ( 38 sec) [ -10963.9347] [Branch lengths ] . ( 38 sec) [ -10963.9347] [Topology ] . ( 39 sec) [ -10963.6575] [Topology ] . ( 39 sec) [ -10963.5158] [Topology ] . ( 40 sec) [ -10963.4500] [Topology ] . ( 41 sec) [ -10963.4003] [Topology ] . ( 42 sec) [ -10963.3612] [Topology ] . ( 43 sec) [ -10963.3306] [Topology ] . ( 44 sec) [ -10963.3173] [Topology ] . ( 44 sec) [ -10963.3159] [GTR parameters ] . ( 44 sec) [ -10963.3159] [Alpha ][ 1.030970] . ( 44 sec) [ -10963.3159] [Topology ] . ( 45 sec) [ -10963.3127] [Topology ] . ( 46 sec) [ -10963.3121] [Topology ] . ( 46 sec) [ -10963.3121] [GTR parameters ] . ( 46 sec) [ -10963.3121] [Alpha ][ 1.030970] . ( 46 sec) [ -10963.3121] [Topology ] . ( 47 sec) [ -10963.3119] [Topology ] . ( 47 sec) [ -10963.3119] [GTR parameters ] . ( 47 sec) [ -10963.3119] [Alpha ][ 1.030970] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.311915. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20933.2757] [GTR parameters ] . ( 1 sec) [ -20576.5426] [Alpha ][ 0.500960] . ( 1 sec) [ -19875.9304] [ 4646] [depth= 6] . ( 1 sec) [ -19436.0194] [ 4517] [depth= 9] . ( 1 sec) [ -19324.6042] [ 4500] [depth= 5] . ( 1 sec) [ -19233.5928] [ 4491] [depth= 1] . ( 1 sec) [ -19010.3985] [ 4394] [depth= 3] . ( 1 sec) [ -19008.2221] [ 4380] [depth= 3] . ( 1 sec) [ -18883.6508] [ 4348] [depth= 6] . ( 1 sec) [ -18663.6383] [ 4286] [depth= 1] . ( 1 sec) [ -18572.6878] [ 4218] [depth= 7] . ( 1 sec) [ -18357.6222] [ 4216] [depth= 1] . ( 1 sec) [ -18324.7135] [ 4212] [depth= 1] . ( 1 sec) [ -18143.4269] [ 4130] [depth= 10] . ( 1 sec) [ -17937.3532] [ 4080] [depth= 2] . ( 1 sec) [ -17836.3079] [ 4045] [depth= 6] . ( 1 sec) [ -17407.1625] [ 4037] [depth= 3] . ( 1 sec) [ -17381.2652] [ 4035] [depth= 1] . ( 1 sec) [ -17111.3197] [ 4007] [depth= 9] . ( 1 sec) [ -16817.9321] [ 3952] [depth= 1] . ( 1 sec) [ -16723.4315] [ 3924] [depth= 10] . ( 1 sec) [ -16573.9355] [ 3881] [depth= 9] . ( 2 sec) [ -15977.5471] [ 3807] [depth= 1] . ( 2 sec) [ -15643.8989] [ 3719] [depth= 6] . ( 2 sec) [ -15464.3402] [ 3700] [depth= 6] . ( 2 sec) [ -15260.8996] [ 3663] [depth= 9] . ( 2 sec) [ -15148.3923] [ 3684] [depth= 1] . ( 2 sec) [ -15045.3420] [ 3616] [depth= 11] . ( 2 sec) [ -14951.2349] [ 3589] [depth= 1] . ( 2 sec) [ -14949.3894] [ 3593] [depth= 2] . ( 2 sec) [ -14888.5677] [ 3575] [depth= 8] . ( 2 sec) [ -14560.5616] [ 3512] [depth= 5] . ( 2 sec) [ -14498.5260] [ 3457] [depth= 2] . ( 2 sec) [ -14392.7765] [ 3450] [depth= 4] . ( 2 sec) [ -14187.2608] [ 3367] [depth= 5] . ( 2 sec) [ -13999.8388] [ 3270] [depth= 1] . ( 2 sec) [ -13775.4786] [ 3223] [depth= 2] . ( 2 sec) [ -13748.8913] [ 3209] [depth= 5] . ( 2 sec) [ -13692.9829] [ 3226] [depth= 1] . ( 2 sec) [ -13681.4906] [ 3232] [depth= 1] . ( 2 sec) [ -13673.4104] [ 3250] [depth= 1] . ( 2 sec) [ -13670.7855] [ 3270] [depth= 1] . ( 3 sec) [ -13326.9554] [ 3167] [depth= 6] . ( 3 sec) [ -13216.8961] [ 3139] [depth= 3] . ( 3 sec) [ -13209.3182] [ 3133] [depth= 3] . ( 3 sec) [ -12925.4267] [ 3059] [depth= 1] . ( 3 sec) [ -12861.6571] [ 3004] [depth= 4] . ( 3 sec) [ -12844.7683] [ 2996] [depth= 1] . ( 3 sec) [ -12748.4863] [ 3026] [depth= 10] . ( 3 sec) [ -12529.5421] [ 2975] [depth= 7] . ( 3 sec) [ -12528.9521] [ 2966] [depth= 3] . ( 3 sec) [ -12452.4615] [ 2953] [depth= 4] . ( 3 sec) [ -12402.3869] [ 2941] [depth= 3] . ( 3 sec) [ -12346.3371] [ 2937] [depth= 1] . ( 3 sec) [ -12302.0442] [ 2909] [depth= 2] . ( 3 sec) [ -12251.2313] [ 2912] [depth= 1] . ( 3 sec) [ -12216.2789] [ 2890] [depth= 4] . ( 3 sec) [ -12208.8504] [ 2885] [depth= 1] . ( 3 sec) [ -12103.6703] [ 2854] [depth= 1] . ( 3 sec) [ -12041.4783] [ 2834] [depth= 1] . ( 3 sec) [ -11866.6133] [ 2785] [depth= 4] . ( 4 sec) [ -11710.2120] [ 2737] [depth= 2] . ( 4 sec) [ -11686.3883] [ 2722] [depth= 4] . ( 4 sec) [ -11635.1726] [ 2747] [depth= 2] . ( 4 sec) [ -11536.1294] [ 2697] [depth= 3] . ( 4 sec) [ -11522.5000] [ 2689] [depth= 1] . ( 4 sec) [ -11500.2170] [ 2679] [depth= 1] . ( 4 sec) [ -11483.4702] [ 2679] [depth= 1] . ( 4 sec) [ -11483.2384] [ 2681] [depth= 1] . ( 4 sec) [ -11450.6292] [ 2670] [depth= 1] . ( 4 sec) [ -11397.7753] [ 2656] [depth= 1] . ( 4 sec) [ -11396.9154] [ 2651] [depth= 1] . ( 4 sec) [ -11396.2590] [ 2651] [depth= 1] . ( 4 sec) [ -11325.7226] [ 2623] [depth= 5] . ( 4 sec) [ -11321.2260] [ 2620] [depth= 1] . ( 4 sec) [ -11297.1832] [ 2601] [depth= 1] . ( 4 sec) [ -11293.6173] [ 2605] [depth= 1] . ( 4 sec) [ -11289.7720] [ 2601] [depth= 1] . ( 5 sec) [ -11275.8103] [ 2599] [depth= 1] . ( 5 sec) [ -11275.4279] [ 2596] [depth= 2] . ( 5 sec) [ -11133.5738] [Branch lengths ] . ( 5 sec) [ -11131.9026] [GTR parameters ] . ( 6 sec) [ -11089.0804] [Alpha ][ 0.945816] . ( 6 sec) [ -11086.5490] [ 2593] [depth= 1] . ( 6 sec) [ -11043.5175] [ 2563] [depth= 1] . ( 6 sec) [ -11040.3993] [ 2560] [depth= 1] . ( 6 sec) [ -11038.7859] [ 2563] [depth= 1] . ( 6 sec) [ -11030.3371] [ 2567] [depth= 1] . ( 6 sec) [ -10991.9798] [ 2552] [depth= 1] . ( 7 sec) [ -10990.8916] [ 2550] [depth= 1] . ( 7 sec) [ -10989.1704] [ 2550] [depth= 1] . ( 7 sec) [ -10989.0820] [ 2547] [depth= 1] . ( 7 sec) [ -10987.6825] [ 2549] [depth= 1] . ( 7 sec) [ -10985.4613] [ 2544] [depth= 1] . ( 8 sec) [ -10985.2230] [ 2543] [depth= 1] . ( 8 sec) [ -10985.0706] [ 2544] [depth= 1] . ( 8 sec) [ -10981.4677] [ 2544] [depth= 1] . ( 8 sec) [ -10980.9429] [ 2544] [depth= 1] . ( 9 sec) [ -10966.4114] [Branch lengths ] . ( 9 sec) [ -10966.1378] [GTR parameters ] . ( 9 sec) [ -10965.6772] [Alpha ][ 1.010518] . ( 12 sec) [ -10964.0286] [Branch lengths ] . ( 22 sec) [ -10963.9927] [ 2539] [depth= 1] . ( 34 sec) [ -10963.5006] [Branch lengths ] . ( 35 sec) [ -10963.5000] [GTR parameters ] . ( 35 sec) [ -10963.4730] [Alpha ][ 1.027005] . ( 35 sec) [ -10963.4730] [Topology ] . ( 36 sec) [ -10963.3996] [Topology ] . ( 36 sec) [ -10963.3354] [Topology ] . ( 37 sec) [ -10963.3227] [Topology ] . ( 38 sec) [ -10963.3184] [Topology ] . ( 39 sec) [ -10963.3166] [Topology ] . ( 40 sec) [ -10963.3157] [Topology ] . ( 40 sec) [ -10963.3141] [GTR parameters ] . ( 40 sec) [ -10963.3129] [Alpha ][ 1.030400] . ( 40 sec) [ -10963.3129] [Topology ] . ( 41 sec) [ -10963.3124] [Topology ] . ( 41 sec) [ -10963.3124] [GTR parameters ] . ( 41 sec) [ -10963.3124] [Alpha ][ 1.030400] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10963.312370. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11018.795404 . ( 1 sec) [ -11014.7165] [GTR parameters ] . ( 1 sec) [ -11014.2861] [Alpha ][ 0.935530] . ( 1 sec) [ -11014.2861] [Topology ] . ( 1 sec) [ -10972.3241] [Topology ] . ( 2 sec) [ -10967.5469] [Topology ] . ( 3 sec) [ -10965.9215] [Topology ] . ( 4 sec) [ -10965.1673] [Topology ] . ( 5 sec) [ -10964.7837] [Topology ] . ( 6 sec) [ -10964.5763] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10964.576298 . ( 12 sec) [ -10964.5099] [GTR parameters ] . ( 12 sec) [ -10963.7218] [Alpha ][ 1.019586] . ( 13 sec) [ -10963.7218] [Topology ] . ( 13 sec) [ -10963.5142] [Topology ] . ( 14 sec) [ -10963.4215] [Topology ] . ( 15 sec) [ -10963.3752] [Topology ] . ( 16 sec) [ -10963.3512] [Topology ] . ( 17 sec) [ -10963.3387] [Topology ] . ( 18 sec) [ -10963.3321] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.332126 . ( 24 sec) [ -10963.3319] [GTR parameters ] . ( 24 sec) [ -10963.3219] [Alpha ][ 1.029584] . ( 24 sec) [ -10963.3219] [Topology ] . ( 25 sec) [ -10963.3171] [Topology ] . ( 26 sec) [ -10963.3147] [Topology ] . ( 27 sec) [ -10963.3135] [Topology ] . ( 28 sec) [ -10963.3128] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10963.312816 . ( 34 sec) [ -10963.3128] [GTR parameters ] . ( 34 sec) [ -10963.3127] [Alpha ][ 1.030614] . ( 34 sec) [ -10963.3127] [Topology ] . ( 35 sec) [ -10963.3123] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -11014.7165] [GTR parameters ] . ( 49 sec) [ -11014.2861] [Alpha ][ 0.935530] . ( 49 sec) [ -11014.2447] [ 2544] [depth= 1] . ( 49 sec) [ -11011.8548] [ 2539] [depth= 1] . ( 50 sec) [ -11011.5247] [ 2538] [depth= 1] . ( 50 sec) [ -11011.0193] [ 2539] [depth= 1] . ( 50 sec) [ -11006.3603] [ 2541] [depth= 1] . ( 50 sec) [ -11004.7440] [ 2537] [depth= 1] . ( 50 sec) [ -11001.8465] [ 2536] [depth= 1] . ( 51 sec) [ -11001.3172] [ 2544] [depth= 1] . ( 51 sec) [ -11000.3102] [ 2547] [depth= 1] . ( 51 sec) [ -10999.0709] [ 2544] [depth= 1] . ( 51 sec) [ -10998.7147] [ 2551] [depth= 2] . ( 51 sec) [ -10997.6180] [ 2550] [depth= 1] . ( 51 sec) [ -10996.0019] [ 2544] [depth= 2] . ( 51 sec) [ -10991.6144] [ 2546] [depth= 1] . ( 51 sec) [ -10990.0498] [ 2544] [depth= 1] . ( 52 sec) [ -10969.7566] [Branch lengths ] . ( 52 sec) [ -10969.6992] [GTR parameters ] . ( 52 sec) [ -10969.1724] [Alpha ][ 1.003780] . ( 53 sec) [ -10967.8607] [ 2536] [depth= 1] . ( 54 sec) [ -10967.7681] [ 2541] [depth= 1] . ( 54 sec) [ -10967.0988] [ 2541] [depth= 1] . ( 55 sec) [ -10964.1613] [Branch lengths ] . ( 55 sec) [ -10964.1536] [GTR parameters ] . ( 55 sec) [ -10964.1208] [Alpha ][ 1.021875] . ( 57 sec) [ -10963.8059] [ 2541] [depth= 1] . ( 58 sec) [ -10963.5918] [Branch lengths ] . ( 58 sec) [ -10963.5901] [GTR parameters ] . ( 58 sec) [ -10963.5874] [Alpha ][ 1.027002] . ( 81 sec) [ -10963.5461] [Branch lengths ] . ( 81 sec) [ -10963.5461] [Topology ] . ( 82 sec) [ -10963.3897] [Topology ] . ( 83 sec) [ -10963.3293] [Topology ] . ( 83 sec) [ -10963.3209] [Topology ] . ( 84 sec) [ -10963.3186] [Topology ] . ( 85 sec) [ -10963.3179] [Topology ] . ( 85 sec) [ -10963.3138] [GTR parameters ] . ( 85 sec) [ -10963.3125] [Alpha ][ 1.030547] . ( 85 sec) [ -10963.3125] [Topology ] . ( 86 sec) [ -10963.3121] [Topology ] . ( 86 sec) [ -10963.3120] [GTR parameters ] . ( 87 sec) [ -10963.3120] [Alpha ][ 1.030547] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10963.312327 . Log likelihood obtained after SPR moves : -10963.312046 . Log likelihood of the current tree: -10963.312046. . Printing the most likely tree in file 'data39.phy_phyml_tree.txt'... . Best log likelihood : -10963.311915 . Time used 0h1m33s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo