.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data91.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... . 436 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22531.2638] [GTR parameters ] . ( 1 sec) [ -22048.3893] [Alpha ][ 0.500960] . ( 1 sec) [ -21429.8936] [ 4977] [depth= 8] . ( 1 sec) [ -21062.1603] [ 4950] [depth= 6] . ( 1 sec) [ -20939.2316] [ 4928] [depth= 2] . ( 1 sec) [ -20767.6906] [ 4916] [depth= 3] . ( 1 sec) [ -20690.2854] [ 4849] [depth= 5] . ( 1 sec) [ -20240.3111] [ 4821] [depth= 6] . ( 1 sec) [ -19759.0431] [ 4720] [depth= 6] . ( 1 sec) [ -19756.9026] [ 4727] [depth= 1] . ( 1 sec) [ -19537.8540] [ 4654] [depth= 4] . ( 1 sec) [ -19358.3992] [ 4648] [depth= 8] . ( 2 sec) [ -19050.9305] [ 4515] [depth= 1] . ( 2 sec) [ -18909.0561] [ 4516] [depth= 1] . ( 2 sec) [ -18711.5986] [ 4431] [depth= 5] . ( 2 sec) [ -18560.8314] [ 4429] [depth= 3] . ( 2 sec) [ -18430.8561] [ 4424] [depth= 1] . ( 2 sec) [ -17929.2350] [ 4369] [depth= 5] . ( 2 sec) [ -17899.4128] [ 4351] [depth= 2] . ( 2 sec) [ -17850.3294] [ 4324] [depth= 8] . ( 2 sec) [ -17615.1806] [ 4311] [depth= 1] . ( 2 sec) [ -17468.6334] [ 4244] [depth= 12] . ( 2 sec) [ -17237.8035] [ 4190] [depth= 3] . ( 2 sec) [ -17114.6559] [ 4079] [depth= 1] . ( 2 sec) [ -16725.1919] [ 3989] [depth= 10] . ( 2 sec) [ -16391.9672] [ 4016] [depth= 1] . ( 2 sec) [ -16271.5273] [ 3973] [depth= 1] . ( 2 sec) [ -16205.4635] [ 3971] [depth= 10] . ( 3 sec) [ -15847.5993] [ 3922] [depth= 10] . ( 3 sec) [ -15758.0723] [ 3893] [depth= 2] . ( 3 sec) [ -15426.2315] [ 3758] [depth= 9] . ( 3 sec) [ -15412.2274] [ 3758] [depth= 1] . ( 3 sec) [ -15098.7313] [ 3633] [depth= 1] . ( 3 sec) [ -14863.4349] [ 3574] [depth= 15] . ( 3 sec) [ -14794.5129] [ 3562] [depth= 7] . ( 3 sec) [ -14669.1821] [ 3529] [depth= 1] . ( 3 sec) [ -14429.0439] [ 3454] [depth= 5] . ( 3 sec) [ -14246.2819] [ 3401] [depth= 7] . ( 3 sec) [ -14199.8065] [ 3374] [depth= 1] . ( 3 sec) [ -14129.7778] [ 3363] [depth= 6] . ( 3 sec) [ -14000.3175] [ 3314] [depth= 2] . ( 3 sec) [ -13984.8341] [ 3312] [depth= 1] . ( 4 sec) [ -13746.9743] [ 3155] [depth= 9] . ( 4 sec) [ -13511.7382] [ 3078] [depth= 1] . ( 4 sec) [ -13269.9320] [ 3027] [depth= 7] . ( 4 sec) [ -13265.0951] [ 3031] [depth= 1] . ( 4 sec) [ -13198.0884] [ 3005] [depth= 1] . ( 4 sec) [ -13142.6306] [ 2949] [depth= 2] . ( 4 sec) [ -12826.2262] [ 2982] [depth= 9] . ( 4 sec) [ -12703.9446] [ 2947] [depth= 3] . ( 4 sec) [ -12447.1277] [ 2910] [depth= 3] . ( 4 sec) [ -11999.1148] [ 2699] [depth= 11] . ( 4 sec) [ -11988.3456] [ 2699] [depth= 2] . ( 4 sec) [ -11977.8901] [ 2695] [depth= 2] . ( 4 sec) [ -11915.1814] [ 2674] [depth= 1] . ( 4 sec) [ -11770.2818] [ 2688] [depth= 1] . ( 4 sec) [ -11751.3096] [ 2661] [depth= 7] . ( 4 sec) [ -11704.6330] [ 2640] [depth= 1] . ( 4 sec) [ -11684.9450] [ 2635] [depth= 1] . ( 5 sec) [ -11483.7025] [ 2595] [depth= 2] . ( 5 sec) [ -11478.0201] [ 2590] [depth= 1] . ( 5 sec) [ -11454.3134] [ 2584] [depth= 1] . ( 5 sec) [ -10824.8206] [ 2544] [depth= 2] . ( 5 sec) [ -10763.4135] [ 2524] [depth= 3] . ( 5 sec) [ -10662.2620] [ 2502] [depth= 1] . ( 5 sec) [ -10659.9252] [ 2504] [depth= 1] . ( 5 sec) [ -10524.2339] [ 2498] [depth= 3] . ( 5 sec) [ -10521.2149] [ 2497] [depth= 1] . ( 5 sec) [ -10455.1358] [ 2462] [depth= 1] . ( 5 sec) [ -10330.5800] [ 2439] [depth= 2] . ( 5 sec) [ -10271.0825] [ 2412] [depth= 1] . ( 5 sec) [ -10255.9854] [ 2410] [depth= 2] . ( 6 sec) [ -10112.3760] [ 2359] [depth= 4] . ( 6 sec) [ -10032.1583] [ 2331] [depth= 1] . ( 6 sec) [ -9918.4397] [Branch lengths ] . ( 7 sec) [ -9916.3558] [GTR parameters ] . ( 7 sec) [ -9889.4646] [Alpha ][ 0.835097] . ( 7 sec) [ -9888.8638] [ 2335] [depth= 2] . ( 7 sec) [ -9888.1132] [ 2339] [depth= 1] . ( 7 sec) [ -9887.6978] [ 2318] [depth= 1] . ( 7 sec) [ -9885.6902] [ 2317] [depth= 1] . ( 7 sec) [ -9884.6042] [ 2313] [depth= 1] . ( 8 sec) [ -9884.4830] [ 2307] [depth= 1] . ( 8 sec) [ -9884.4336] [ 2305] [depth= 1] . ( 8 sec) [ -9882.1841] [ 2307] [depth= 1] . ( 8 sec) [ -9881.5259] [ 2296] [depth= 1] . ( 8 sec) [ -9881.4358] [ 2296] [depth= 1] . ( 8 sec) [ -9876.4663] [ 2300] [depth= 1] . ( 9 sec) [ -9872.5558] [ 2296] [depth= 1] . ( 9 sec) [ -9870.4109] [ 2297] [depth= 1] . ( 9 sec) [ -9864.2177] [ 2297] [depth= 2] . ( 10 sec) [ -9852.1580] [Branch lengths ] . ( 11 sec) [ -9852.1266] [GTR parameters ] . ( 11 sec) [ -9851.3769] [Alpha ][ 0.908727] . ( 11 sec) [ -9851.3426] [ 2309] [depth= 1] . ( 11 sec) [ -9851.3165] [ 2314] [depth= 1] . ( 12 sec) [ -9851.2899] [ 2314] [depth= 1] . ( 16 sec) [ -9849.3986] [Branch lengths ] . ( 16 sec) [ -9849.3979] [GTR parameters ] . ( 17 sec) [ -9849.3747] [Alpha ][ 0.922397] . ( 20 sec) [ -9848.8438] [Branch lengths ] . ( 45 sec) [ -9848.7449] [Branch lengths ] . ( 45 sec) [ -9848.7449] [Topology ] . ( 46 sec) [ -9848.7322] [Topology ] . ( 47 sec) [ -9848.7234] [Topology ] . ( 48 sec) [ -9848.7050] [Topology ] . ( 49 sec) [ -9848.6906] [Topology ] . ( 49 sec) [ -9848.6814] [Topology ] . ( 50 sec) [ -9848.6751] [Topology ] . ( 51 sec) [ -9848.6707] [Topology ] . ( 52 sec) [ -9848.6676] [Topology ] . ( 52 sec) [ -9848.6654] [Topology ] . ( 53 sec) [ -9848.6633] [GTR parameters ] . ( 53 sec) [ -9848.6607] [Alpha ][ 0.926885] . ( 53 sec) [ -9848.6607] [Topology ] . ( 54 sec) [ -9848.6589] [Topology ] . ( 55 sec) [ -9848.6577] [Topology ] . ( 56 sec) [ -9848.6569] [Topology ] . ( 57 sec) [ -9848.6569] [GTR parameters ] . ( 57 sec) [ -9848.6569] [Alpha ][ 0.926885] . ( 57 sec) [ -9848.6569] [Topology ] . ( 57 sec) [ -9848.6563] [Topology ] . ( 58 sec) [ -9848.6563] [GTR parameters ] . ( 58 sec) [ -9848.6563] [Alpha ][ 0.926885] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -9847.9914] [Topology ] . Checking for NNIs, optimizing five branches... . ( 77 sec) [ -9847.8147] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.814650. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22538.4812] [GTR parameters ] . ( 1 sec) [ -22012.7494] [Alpha ][ 0.500960] . ( 1 sec) [ -21512.7839] [ 5151] [depth= 3] . ( 1 sec) [ -21034.2961] [ 5043] [depth= 3] . ( 1 sec) [ -20719.7554] [ 5020] [depth= 3] . ( 1 sec) [ -20421.2078] [ 5002] [depth= 5] . ( 1 sec) [ -20262.7158] [ 4943] [depth= 3] . ( 1 sec) [ -20245.0526] [ 4943] [depth= 8] . ( 1 sec) [ -20162.9120] [ 4937] [depth= 1] . ( 1 sec) [ -20059.1132] [ 4908] [depth= 5] . ( 1 sec) [ -19911.1282] [ 4808] [depth= 2] . ( 1 sec) [ -19707.5161] [ 4782] [depth= 3] . ( 2 sec) [ -19649.1388] [ 4750] [depth= 5] . ( 2 sec) [ -19358.6004] [ 4756] [depth= 3] . ( 2 sec) [ -19286.8930] [ 4719] [depth= 1] . ( 2 sec) [ -19146.4497] [ 4679] [depth= 5] . ( 2 sec) [ -18718.5555] [ 4496] [depth= 4] . ( 2 sec) [ -18427.2644] [ 4486] [depth= 4] . ( 2 sec) [ -18122.4221] [ 4319] [depth= 7] . ( 2 sec) [ -17880.0039] [ 4294] [depth= 3] . ( 2 sec) [ -17845.0684] [ 4293] [depth= 1] . ( 2 sec) [ -17818.8091] [ 4292] [depth= 1] . ( 2 sec) [ -17732.7914] [ 4281] [depth= 1] . ( 2 sec) [ -17679.9847] [ 4264] [depth= 1] . ( 2 sec) [ -17292.1246] [ 4094] [depth= 5] . ( 3 sec) [ -17283.0962] [ 4088] [depth= 1] . ( 3 sec) [ -17219.9522] [ 4104] [depth= 1] . ( 3 sec) [ -16840.7046] [ 3978] [depth= 14] . ( 3 sec) [ -16725.0266] [ 4001] [depth= 1] . ( 3 sec) [ -16180.1048] [ 3899] [depth= 2] . ( 3 sec) [ -16021.5551] [ 3828] [depth= 5] . ( 3 sec) [ -15742.2303] [ 3744] [depth= 10] . ( 3 sec) [ -15574.0335] [ 3675] [depth= 9] . ( 3 sec) [ -15571.4221] [ 3676] [depth= 1] . ( 4 sec) [ -15163.1189] [ 3604] [depth= 3] . ( 4 sec) [ -14938.7354] [ 3634] [depth= 3] . ( 4 sec) [ -14326.6504] [ 3486] [depth= 4] . ( 4 sec) [ -13638.4027] [ 3307] [depth= 3] . ( 4 sec) [ -13520.5421] [ 3286] [depth= 1] . ( 4 sec) [ -13329.9859] [ 3188] [depth= 5] . ( 4 sec) [ -13126.4964] [ 3074] [depth= 8] . ( 4 sec) [ -13033.7945] [ 3091] [depth= 1] . ( 4 sec) [ -12961.7382] [ 3083] [depth= 10] . ( 4 sec) [ -12644.6055] [ 3020] [depth= 9] . ( 4 sec) [ -12406.8382] [ 3003] [depth= 1] . ( 4 sec) [ -12398.0794] [ 3008] [depth= 1] . ( 5 sec) [ -12053.3622] [ 2956] [depth= 3] . ( 5 sec) [ -11928.1242] [ 2972] [depth= 1] . ( 5 sec) [ -11722.9640] [ 2897] [depth= 3] . ( 5 sec) [ -11645.8743] [ 2888] [depth= 2] . ( 5 sec) [ -11634.0436] [ 2882] [depth= 1] . ( 5 sec) [ -11625.1220] [ 2888] [depth= 1] . ( 5 sec) [ -11599.8413] [ 2882] [depth= 1] . ( 5 sec) [ -11556.2553] [ 2835] [depth= 2] . ( 5 sec) [ -11552.0189] [ 2825] [depth= 1] . ( 5 sec) [ -11375.3967] [ 2820] [depth= 5] . ( 5 sec) [ -11368.9271] [ 2844] [depth= 1] . ( 6 sec) [ -11244.1690] [ 2800] [depth= 3] . ( 6 sec) [ -11243.8853] [ 2800] [depth= 1] . ( 6 sec) [ -11199.1779] [ 2794] [depth= 6] . ( 6 sec) [ -11185.3986] [ 2808] [depth= 5] . ( 6 sec) [ -11183.9303] [ 2810] [depth= 1] . ( 6 sec) [ -11183.2709] [ 2816] [depth= 1] . ( 6 sec) [ -10635.5484] [ 2561] [depth= 5] . ( 6 sec) [ -10632.2535] [ 2563] [depth= 1] . ( 6 sec) [ -10572.9729] [ 2534] [depth= 4] . ( 6 sec) [ -10567.3263] [ 2550] [depth= 1] . ( 7 sec) [ -10347.2434] [ 2483] [depth= 4] . ( 7 sec) [ -10318.3485] [ 2454] [depth= 3] . ( 7 sec) [ -10260.1988] [ 2393] [depth= 5] . ( 7 sec) [ -10243.7819] [ 2366] [depth= 1] . ( 7 sec) [ -10242.0457] [ 2368] [depth= 1] . ( 7 sec) [ -10228.3315] [ 2371] [depth= 2] . ( 7 sec) [ -10225.2002] [ 2363] [depth= 1] . ( 7 sec) [ -10221.8275] [ 2365] [depth= 1] . ( 7 sec) [ -10218.1591] [ 2358] [depth= 4] . ( 8 sec) [ -10214.3565] [ 2358] [depth= 1] . ( 8 sec) [ -9961.6453] [Branch lengths ] . ( 9 sec) [ -9958.2460] [GTR parameters ] . ( 9 sec) [ -9928.6104] [Alpha ][ 0.851338] . ( 9 sec) [ -9925.6131] [ 2354] [depth= 1] . ( 9 sec) [ -9925.5149] [ 2354] [depth= 1] . ( 10 sec) [ -9925.1601] [ 2360] [depth= 1] . ( 10 sec) [ -9921.3389] [ 2360] [depth= 4] . ( 10 sec) [ -9919.9486] [ 2350] [depth= 1] . ( 10 sec) [ -9915.9006] [ 2349] [depth= 1] . ( 10 sec) [ -9915.8211] [ 2349] [depth= 1] . ( 11 sec) [ -9892.6701] [ 2318] [depth= 1] . ( 11 sec) [ -9890.0666] [ 2326] [depth= 2] . ( 11 sec) [ -9889.7920] [ 2321] [depth= 1] . ( 11 sec) [ -9888.9184] [ 2321] [depth= 1] . ( 11 sec) [ -9888.5766] [ 2324] [depth= 1] . ( 12 sec) [ -9888.1318] [ 2327] [depth= 1] . ( 12 sec) [ -9888.0566] [ 2327] [depth= 1] . ( 13 sec) [ -9887.7882] [ 2328] [depth= 1] . ( 13 sec) [ -9883.1693] [ 2329] [depth= 1] . ( 13 sec) [ -9883.0849] [ 2316] [depth= 1] . ( 13 sec) [ -9881.6416] [ 2319] [depth= 1] . ( 14 sec) [ -9880.9613] [ 2318] [depth= 1] . ( 14 sec) [ -9880.9219] [ 2301] [depth= 2] . ( 15 sec) [ -9860.8651] [Branch lengths ] . ( 16 sec) [ -9860.7131] [GTR parameters ] . ( 16 sec) [ -9860.1553] [Alpha ][ 0.914072] . ( 16 sec) [ -9859.7672] [ 2299] [depth= 1] . ( 18 sec) [ -9859.7542] [ 2311] [depth= 1] . ( 20 sec) [ -9857.7565] [Branch lengths ] . ( 21 sec) [ -9857.7513] [GTR parameters ] . ( 21 sec) [ -9857.7484] [Alpha ][ 0.918847] . ( 23 sec) [ -9857.2163] [ 2316] [depth= 5] . ( 24 sec) [ -9851.2807] [Branch lengths ] . ( 24 sec) [ -9851.2687] [GTR parameters ] . ( 24 sec) [ -9851.2674] [Alpha ][ 0.921916] . ( 25 sec) [ -9850.8111] [ 2320] [depth= 1] . ( 25 sec) [ -9850.7446] [ 2316] [depth= 1] . ( 26 sec) [ -9850.4989] [ 2320] [depth= 1] . ( 27 sec) [ -9850.4434] [ 2311] [depth= 1] . ( 28 sec) [ -9848.5016] [Branch lengths ] . ( 28 sec) [ -9848.4992] [GTR parameters ] . ( 28 sec) [ -9848.4968] [Alpha ][ 0.926250] . ( 32 sec) [ -9848.1398] [Branch lengths ] . ( 59 sec) [ -9848.0007] [Branch lengths ] . ( 59 sec) [ -9848.0007] [Topology ] . ( 60 sec) [ -9847.9636] [Topology ] . ( 61 sec) [ -9847.9400] [Topology ] . ( 62 sec) [ -9847.9230] [Topology ] . ( 63 sec) [ -9847.9099] [Topology ] . ( 65 sec) [ -9847.8997] [Topology ] . ( 65 sec) [ -9847.8914] [Topology ] . ( 66 sec) [ -9847.8910] [GTR parameters ] . ( 66 sec) [ -9847.8904] [Alpha ][ 0.928522] . ( 66 sec) [ -9847.8904] [Topology ] . ( 67 sec) [ -9847.8834] [Topology ] . ( 68 sec) [ -9847.8776] [Topology ] . ( 69 sec) [ -9847.8726] [Topology ] . ( 70 sec) [ -9847.8681] [Topology ] . ( 71 sec) [ -9847.8640] [Topology ] . ( 72 sec) [ -9847.8602] [Topology ] . ( 72 sec) [ -9847.8602] [GTR parameters ] . ( 73 sec) [ -9847.8602] [Alpha ][ 0.928522] . ( 73 sec) [ -9847.8602] [Topology ] . ( 74 sec) [ -9847.8566] [Topology ] . ( 75 sec) [ -9847.8532] [Topology ] . ( 76 sec) [ -9847.8499] [Topology ] . ( 77 sec) [ -9847.8467] [Topology ] . ( 78 sec) [ -9847.8436] [Topology ] . ( 78 sec) [ -9847.8406] [Topology ] . ( 78 sec) [ -9847.8406] [GTR parameters ] . ( 79 sec) [ -9847.8406] [Alpha ][ 0.928522] . ( 79 sec) [ -9847.8406] [Topology ] . ( 79 sec) [ -9847.8377] [Topology ] . ( 80 sec) [ -9847.8348] [Topology ] . ( 81 sec) [ -9847.8319] [Topology ] . ( 82 sec) [ -9847.8290] [Topology ] . ( 82 sec) [ -9847.8262] [Topology ] . ( 83 sec) [ -9847.8234] [Topology ] . ( 83 sec) [ -9847.8234] [GTR parameters ] . ( 83 sec) [ -9847.8234] [Alpha ][ 0.928522] . ( 83 sec) [ -9847.8234] [Topology ] . ( 84 sec) [ -9847.8206] [Topology ] . ( 85 sec) [ -9847.8179] [Topology ] . ( 86 sec) [ -9847.8152] [Topology ] . ( 87 sec) [ -9847.8125] [Topology ] . ( 87 sec) [ -9847.8098] [Topology ] . ( 88 sec) [ -9847.8077] [Topology ] . ( 88 sec) [ -9847.8077] [GTR parameters ] . ( 88 sec) [ -9847.8077] [Alpha ][ 0.928522] . ( 88 sec) [ -9847.8077] [Topology ] . ( 89 sec) [ -9847.8067] [Topology ] . ( 89 sec) [ -9847.8067] [GTR parameters ] . ( 89 sec) [ -9847.8067] [Alpha ][ 0.928522] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.806748. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -26792.4053] [GTR parameters ] . ( 1 sec) [ -26276.3190] [Alpha ][ 0.500960] . ( 1 sec) [ -22749.1818] [ 5265] [depth= 8] . ( 1 sec) [ -21605.5722] [ 5173] [depth= 8] . ( 1 sec) [ -21251.0195] [ 5156] [depth= 4] . ( 1 sec) [ -21126.8310] [ 5146] [depth= 3] . ( 1 sec) [ -21004.7497] [ 5058] [depth= 2] . ( 1 sec) [ -20825.9566] [ 5044] [depth= 2] . ( 1 sec) [ -20208.4442] [ 4962] [depth= 14] . ( 1 sec) [ -19876.4593] [ 4920] [depth= 6] . ( 1 sec) [ -19740.4783] [ 4841] [depth= 1] . ( 1 sec) [ -19463.6210] [ 4789] [depth= 11] . ( 2 sec) [ -18709.5411] [ 4667] [depth= 16] . ( 2 sec) [ -18495.8664] [ 4635] [depth= 18] . ( 2 sec) [ -18126.9480] [ 4611] [depth= 13] . ( 2 sec) [ -18051.5318] [ 4603] [depth= 1] . ( 2 sec) [ -17909.1247] [ 4483] [depth= 5] . ( 2 sec) [ -17866.3111] [ 4481] [depth= 3] . ( 2 sec) [ -17687.0669] [ 4470] [depth= 7] . ( 2 sec) [ -17121.9912] [ 4427] [depth= 10] . ( 2 sec) [ -16517.7014] [ 4262] [depth= 1] . ( 2 sec) [ -16494.6908] [ 4254] [depth= 1] . ( 2 sec) [ -16194.4291] [ 4172] [depth= 1] . ( 2 sec) [ -16169.5255] [ 4138] [depth= 5] . ( 2 sec) [ -16084.2143] [ 4088] [depth= 1] . ( 2 sec) [ -15816.1731] [ 4031] [depth= 3] . ( 2 sec) [ -15677.3103] [ 3954] [depth= 1] . ( 2 sec) [ -15631.8938] [ 3949] [depth= 8] . ( 2 sec) [ -15572.5222] [ 3966] [depth= 1] . ( 2 sec) [ -15424.6767] [ 3936] [depth= 5] . ( 2 sec) [ -15367.1006] [ 3931] [depth= 6] . ( 2 sec) [ -15184.5757] [ 3927] [depth= 3] . ( 2 sec) [ -15157.7328] [ 3865] [depth= 8] . ( 2 sec) [ -14705.0214] [ 3836] [depth= 2] . ( 3 sec) [ -14645.0909] [ 3839] [depth= 1] . ( 3 sec) [ -14530.8029] [ 3788] [depth= 3] . ( 3 sec) [ -13993.0960] [ 3647] [depth= 4] . ( 3 sec) [ -13965.3033] [ 3624] [depth= 1] . ( 3 sec) [ -13858.9995] [ 3643] [depth= 1] . ( 3 sec) [ -13745.0145] [ 3624] [depth= 1] . ( 3 sec) [ -13526.5875] [ 3581] [depth= 10] . ( 3 sec) [ -13471.3094] [ 3443] [depth= 5] . ( 3 sec) [ -13468.0768] [ 3440] [depth= 1] . ( 3 sec) [ -13346.3216] [ 3394] [depth= 5] . ( 3 sec) [ -13096.4685] [ 3383] [depth= 2] . ( 3 sec) [ -12962.2236] [ 3331] [depth= 2] . ( 3 sec) [ -12908.8245] [ 3326] [depth= 1] . ( 3 sec) [ -12821.7927] [ 3309] [depth= 4] . ( 3 sec) [ -12722.7844] [ 3306] [depth= 2] . ( 3 sec) [ -12663.0594] [ 3284] [depth= 1] . ( 3 sec) [ -12659.0498] [ 3284] [depth= 1] . ( 3 sec) [ -12176.1386] [ 3240] [depth= 2] . ( 4 sec) [ -12159.7705] [ 3264] [depth= 1] . ( 4 sec) [ -12133.9719] [ 3213] [depth= 1] . ( 4 sec) [ -12131.3162] [ 3212] [depth= 1] . ( 4 sec) [ -11987.2882] [ 3182] [depth= 3] . ( 4 sec) [ -11897.3447] [ 3159] [depth= 1] . ( 4 sec) [ -11882.5265] [ 3160] [depth= 3] . ( 4 sec) [ -11879.1362] [ 3160] [depth= 1] . ( 4 sec) [ -11681.6592] [ 3012] [depth= 1] . ( 4 sec) [ -11534.0544] [ 2992] [depth= 5] . ( 4 sec) [ -11448.0338] [ 2954] [depth= 8] . ( 4 sec) [ -11438.6585] [ 2951] [depth= 1] . ( 4 sec) [ -11343.3252] [ 2907] [depth= 3] . ( 4 sec) [ -11170.9824] [ 2887] [depth= 2] . ( 4 sec) [ -11158.6236] [ 2860] [depth= 1] . ( 4 sec) [ -11000.9417] [ 2785] [depth= 8] . ( 5 sec) [ -10935.2479] [ 2761] [depth= 1] . ( 5 sec) [ -10933.6901] [ 2750] [depth= 1] . ( 5 sec) [ -10891.7390] [ 2771] [depth= 1] . ( 5 sec) [ -10844.5079] [ 2770] [depth= 3] . ( 5 sec) [ -10805.9146] [ 2741] [depth= 4] . ( 5 sec) [ -10792.1139] [ 2701] [depth= 4] . ( 5 sec) [ -10771.7047] [ 2664] [depth= 5] . ( 5 sec) [ -10771.6683] [ 2671] [depth= 1] . ( 5 sec) [ -10403.8271] [Branch lengths ] . ( 6 sec) [ -10400.7455] [GTR parameters ] . ( 6 sec) [ -10385.9830] [Alpha ][ 0.703665] . ( 6 sec) [ -10363.9095] [ 2649] [depth= 2] . ( 6 sec) [ -10361.3899] [ 2643] [depth= 1] . ( 6 sec) [ -10303.0139] [ 2614] [depth= 4] . ( 6 sec) [ -10262.4192] [ 2553] [depth= 7] . ( 7 sec) [ -10260.5551] [ 2568] [depth= 3] . ( 7 sec) [ -10260.5020] [ 2568] [depth= 1] . ( 7 sec) [ -10252.1519] [ 2573] [depth= 1] . ( 7 sec) [ -10248.6338] [ 2573] [depth= 1] . ( 7 sec) [ -10248.6125] [ 2573] [depth= 1] . ( 7 sec) [ -10247.3911] [ 2573] [depth= 1] . ( 7 sec) [ -10241.9356] [ 2577] [depth= 1] . ( 7 sec) [ -10239.3287] [ 2577] [depth= 1] . ( 7 sec) [ -10239.2339] [ 2577] [depth= 1] . ( 7 sec) [ -10237.2373] [ 2561] [depth= 2] . ( 7 sec) [ -10237.1942] [ 2560] [depth= 1] . ( 7 sec) [ -10185.7943] [ 2535] [depth= 3] . ( 7 sec) [ -10185.5355] [ 2548] [depth= 1] . ( 8 sec) [ -10129.5512] [ 2509] [depth= 3] . ( 8 sec) [ -9965.6999] [ 2342] [depth= 3] . ( 8 sec) [ -9954.4274] [ 2334] [depth= 3] . ( 8 sec) [ -9954.1624] [ 2340] [depth= 1] . ( 8 sec) [ -9954.1390] [ 2339] [depth= 2] . ( 8 sec) [ -9952.9776] [ 2333] [depth= 1] . ( 8 sec) [ -9913.5399] [ 2335] [depth= 1] . ( 8 sec) [ -9906.2288] [ 2336] [depth= 1] . ( 9 sec) [ -9905.1712] [ 2338] [depth= 1] . ( 9 sec) [ -9904.6189] [ 2340] [depth= 1] . ( 9 sec) [ -9904.5557] [ 2342] [depth= 1] . ( 9 sec) [ -9904.3759] [ 2331] [depth= 2] . ( 10 sec) [ -9869.8900] [Branch lengths ] . ( 10 sec) [ -9869.2761] [GTR parameters ] . ( 10 sec) [ -9863.0369] [Alpha ][ 0.892111] . ( 11 sec) [ -9862.7905] [ 2333] [depth= 1] . ( 11 sec) [ -9862.5199] [ 2318] [depth= 1] . ( 11 sec) [ -9862.3996] [ 2319] [depth= 1] . ( 12 sec) [ -9861.9532] [ 2313] [depth= 2] . ( 12 sec) [ -9859.8970] [ 2314] [depth= 1] . ( 12 sec) [ -9854.8741] [ 2308] [depth= 1] . ( 12 sec) [ -9854.8461] [ 2320] [depth= 1] . ( 12 sec) [ -9850.9740] [ 2317] [depth= 1] . ( 14 sec) [ -9849.1730] [Branch lengths ] . ( 14 sec) [ -9849.1507] [GTR parameters ] . ( 14 sec) [ -9849.0232] [Alpha ][ 0.923081] . ( 17 sec) [ -9848.7215] [Branch lengths ] . ( 40 sec) [ -9848.6173] [Branch lengths ] . ( 40 sec) [ -9848.6173] [Topology ] . ( 41 sec) [ -9848.5953] [Topology ] . ( 42 sec) [ -9848.5821] [Topology ] . ( 43 sec) [ -9848.5724] [Topology ] . ( 44 sec) [ -9848.5648] [Topology ] . ( 44 sec) [ -9848.5585] [Topology ] . ( 45 sec) [ -9848.5531] [Topology ] . ( 45 sec) [ -9848.5528] [GTR parameters ] . ( 45 sec) [ -9848.5507] [Alpha ][ 0.927068] . ( 45 sec) [ -9848.5507] [Topology ] . ( 46 sec) [ -9848.5458] [Topology ] . ( 47 sec) [ -9848.5415] [Topology ] . ( 48 sec) [ -9848.5376] [Topology ] . ( 48 sec) [ -9848.5339] [Topology ] . ( 49 sec) [ -9848.5303] [Topology ] . ( 50 sec) [ -9848.5269] [Topology ] . ( 50 sec) [ -9848.5269] [GTR parameters ] . ( 50 sec) [ -9848.5269] [Alpha ][ 0.927068] . ( 50 sec) [ -9848.5269] [Topology ] . ( 51 sec) [ -9848.5236] [Topology ] . ( 52 sec) [ -9848.5204] [Topology ] . ( 53 sec) [ -9848.5173] [Topology ] . ( 53 sec) [ -9848.5142] [Topology ] . ( 54 sec) [ -9848.5112] [Topology ] . ( 55 sec) [ -9848.5082] [Topology ] . ( 55 sec) [ -9848.5082] [GTR parameters ] . ( 55 sec) [ -9848.5082] [Alpha ][ 0.927068] . ( 55 sec) [ -9848.5082] [Topology ] . ( 56 sec) [ -9848.5053] [Topology ] . ( 57 sec) [ -9848.5024] [Topology ] . ( 57 sec) [ -9848.4995] [Topology ] . ( 58 sec) [ -9848.4967] [Topology ] . ( 59 sec) [ -9848.4939] [Topology ] . ( 60 sec) [ -9848.4911] [Topology ] . ( 60 sec) [ -9848.4911] [GTR parameters ] . ( 60 sec) [ -9848.4911] [Alpha ][ 0.927068] . ( 60 sec) [ -9848.4911] [Topology ] . ( 61 sec) [ -9848.4883] [Topology ] . ( 62 sec) [ -9848.4855] [Topology ] . ( 62 sec) [ -9848.4828] [Topology ] . ( 63 sec) [ -9848.4801] [Topology ] . ( 64 sec) [ -9848.4774] [Topology ] . ( 65 sec) [ -9848.4752] [Topology ] . ( 65 sec) [ -9848.4752] [GTR parameters ] . ( 65 sec) [ -9848.4752] [Alpha ][ 0.927068] . ( 65 sec) [ -9848.4752] [Topology ] . ( 66 sec) [ -9848.4741] [Topology ] . ( 66 sec) [ -9848.4736] [Topology ] . ( 66 sec) [ -9848.4736] [GTR parameters ] . ( 67 sec) [ -9848.4736] [Alpha ][ 0.927068] . ( 67 sec) [ -9848.4736] [Topology ] . ( 67 sec) [ -9848.4735] [Topology ] . ( 67 sec) [ -9848.4735] [GTR parameters ] . ( 68 sec) [ -9848.4735] [Alpha ][ 0.927068] . Checking for NNIs, optimizing five branches... . ( 74 sec) [ -9847.8089] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -9847.8087] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.808699. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22700.9380] [GTR parameters ] . ( 1 sec) [ -22197.7102] [Alpha ][ 0.500960] . ( 1 sec) [ -21793.5062] [ 5155] [depth= 8] . ( 1 sec) [ -21482.9433] [ 5013] [depth= 9] . ( 1 sec) [ -21039.6299] [ 4918] [depth= 7] . ( 1 sec) [ -20814.7371] [ 4857] [depth= 1] . ( 1 sec) [ -20468.4894] [ 4770] [depth= 9] . ( 1 sec) [ -20340.4739] [ 4763] [depth= 1] . ( 1 sec) [ -20085.1303] [ 4746] [depth= 5] . ( 1 sec) [ -19939.2927] [ 4703] [depth= 4] . ( 1 sec) [ -19849.9161] [ 4689] [depth= 5] . ( 1 sec) [ -19747.7728] [ 4671] [depth= 3] . ( 1 sec) [ -19684.9215] [ 4615] [depth= 1] . ( 2 sec) [ -19584.1476] [ 4591] [depth= 9] . ( 2 sec) [ -19531.8620] [ 4582] [depth= 2] . ( 2 sec) [ -19260.6983] [ 4557] [depth= 7] . ( 2 sec) [ -19106.5948] [ 4521] [depth= 1] . ( 2 sec) [ -19046.7278] [ 4502] [depth= 3] . ( 2 sec) [ -18966.2004] [ 4487] [depth= 1] . ( 2 sec) [ -18632.3641] [ 4414] [depth= 8] . ( 2 sec) [ -18100.7286] [ 4366] [depth= 4] . ( 2 sec) [ -17942.5656] [ 4328] [depth= 5] . ( 2 sec) [ -17433.9465] [ 4210] [depth= 11] . ( 2 sec) [ -17038.7060] [ 4147] [depth= 9] . ( 2 sec) [ -16755.7208] [ 4128] [depth= 3] . ( 2 sec) [ -16731.6087] [ 4158] [depth= 7] . ( 2 sec) [ -16715.9019] [ 4084] [depth= 6] . ( 2 sec) [ -16657.0037] [ 4076] [depth= 5] . ( 2 sec) [ -16623.8041] [ 4059] [depth= 1] . ( 2 sec) [ -15960.1900] [ 3991] [depth= 15] . ( 2 sec) [ -15945.7086] [ 3974] [depth= 5] . ( 2 sec) [ -15886.6929] [ 3945] [depth= 1] . ( 2 sec) [ -15770.8650] [ 3924] [depth= 5] . ( 2 sec) [ -15754.1135] [ 3924] [depth= 2] . ( 2 sec) [ -15619.8079] [ 3906] [depth= 1] . ( 3 sec) [ -15474.3795] [ 3757] [depth= 6] . ( 3 sec) [ -15440.7497] [ 3754] [depth= 4] . ( 3 sec) [ -14794.9043] [ 3709] [depth= 15] . ( 3 sec) [ -14780.8780] [ 3722] [depth= 1] . ( 3 sec) [ -14734.2085] [ 3707] [depth= 1] . ( 3 sec) [ -14629.9177] [ 3597] [depth= 5] . ( 3 sec) [ -14619.6735] [ 3597] [depth= 1] . ( 3 sec) [ -14517.4150] [ 3540] [depth= 1] . ( 3 sec) [ -14055.1952] [ 3450] [depth= 3] . ( 3 sec) [ -14042.2420] [ 3462] [depth= 3] . ( 3 sec) [ -13841.6521] [ 3457] [depth= 2] . ( 3 sec) [ -13654.6719] [ 3461] [depth= 1] . ( 3 sec) [ -13104.9603] [ 3422] [depth= 13] . ( 3 sec) [ -12860.8345] [ 3259] [depth= 6] . ( 3 sec) [ -12528.8752] [ 3131] [depth= 13] . ( 3 sec) [ -12512.7116] [ 3126] [depth= 1] . ( 3 sec) [ -12463.2143] [ 3078] [depth= 10] . ( 3 sec) [ -12306.8854] [ 3020] [depth= 8] . ( 3 sec) [ -12295.5333] [ 3024] [depth= 1] . ( 3 sec) [ -11886.8651] [ 2840] [depth= 3] . ( 4 sec) [ -11878.4586] [ 2837] [depth= 2] . ( 4 sec) [ -11849.7641] [ 2836] [depth= 1] . ( 4 sec) [ -11694.5960] [ 2814] [depth= 1] . ( 4 sec) [ -11515.5256] [ 2727] [depth= 3] . ( 4 sec) [ -11395.1725] [ 2685] [depth= 4] . ( 4 sec) [ -11377.5363] [ 2699] [depth= 1] . ( 4 sec) [ -11336.2309] [ 2694] [depth= 5] . ( 4 sec) [ -11334.6153] [ 2720] [depth= 1] . ( 4 sec) [ -11333.3546] [ 2707] [depth= 1] . ( 4 sec) [ -11317.1716] [ 2704] [depth= 3] . ( 4 sec) [ -11134.1697] [ 2654] [depth= 5] . ( 4 sec) [ -11115.6314] [ 2646] [depth= 3] . ( 4 sec) [ -10919.0686] [ 2511] [depth= 4] . ( 4 sec) [ -10914.2718] [ 2511] [depth= 1] . ( 4 sec) [ -10866.1875] [ 2501] [depth= 1] . ( 4 sec) [ -10866.0144] [ 2501] [depth= 1] . ( 4 sec) [ -10850.2636] [ 2503] [depth= 1] . ( 4 sec) [ -10848.7149] [ 2524] [depth= 1] . ( 4 sec) [ -10482.0496] [ 2463] [depth= 11] . ( 4 sec) [ -10430.2190] [ 2468] [depth= 1] . ( 5 sec) [ -10396.8559] [ 2442] [depth= 1] . ( 5 sec) [ -10394.4770] [ 2447] [depth= 1] . ( 5 sec) [ -10394.2617] [ 2451] [depth= 1] . ( 5 sec) [ -10392.5050] [ 2452] [depth= 1] . ( 5 sec) [ -10387.3362] [ 2451] [depth= 1] . ( 5 sec) [ -10387.2089] [ 2451] [depth= 1] . ( 5 sec) [ -10373.5283] [ 2442] [depth= 2] . ( 5 sec) [ -10361.5783] [ 2416] [depth= 1] . ( 5 sec) [ -10356.7025] [ 2406] [depth= 5] . ( 5 sec) [ -10338.9557] [ 2400] [depth= 1] . ( 5 sec) [ -10336.9367] [ 2396] [depth= 4] . ( 5 sec) [ -10299.8498] [ 2364] [depth= 3] . ( 6 sec) [ -10001.2549] [Branch lengths ] . ( 6 sec) [ -9998.8856] [GTR parameters ] . ( 6 sec) [ -9966.5788] [Alpha ][ 0.824827] . ( 6 sec) [ -9951.5459] [ 2345] [depth= 1] . ( 6 sec) [ -9951.2747] [ 2340] [depth= 1] . ( 7 sec) [ -9950.9201] [ 2340] [depth= 1] . ( 7 sec) [ -9949.3760] [ 2330] [depth= 1] . ( 7 sec) [ -9945.3167] [ 2325] [depth= 1] . ( 7 sec) [ -9942.3569] [ 2332] [depth= 1] . ( 7 sec) [ -9906.9414] [ 2320] [depth= 2] . ( 7 sec) [ -9906.6798] [ 2322] [depth= 1] . ( 7 sec) [ -9905.2655] [ 2316] [depth= 2] . ( 7 sec) [ -9904.2244] [ 2307] [depth= 3] . ( 8 sec) [ -9900.2662] [ 2311] [depth= 1] . ( 8 sec) [ -9899.6061] [ 2325] [depth= 1] . ( 8 sec) [ -9896.4262] [ 2318] [depth= 1] . ( 8 sec) [ -9895.5543] [ 2312] [depth= 1] . ( 8 sec) [ -9893.3333] [ 2319] [depth= 1] . ( 8 sec) [ -9893.2943] [ 2319] [depth= 1] . ( 9 sec) [ -9892.2329] [ 2324] [depth= 1] . ( 9 sec) [ -9891.7087] [ 2328] [depth= 1] . ( 9 sec) [ -9888.3359] [ 2322] [depth= 1] . ( 9 sec) [ -9887.7013] [ 2317] [depth= 1] . ( 9 sec) [ -9887.5960] [ 2322] [depth= 1] . ( 9 sec) [ -9887.4809] [ 2325] [depth= 1] . ( 10 sec) [ -9871.6224] [Branch lengths ] . ( 10 sec) [ -9871.2992] [GTR parameters ] . ( 10 sec) [ -9870.2592] [Alpha ][ 0.904629] . ( 11 sec) [ -9870.0976] [ 2325] [depth= 1] . ( 11 sec) [ -9864.8149] [ 2324] [depth= 3] . ( 11 sec) [ -9864.5699] [ 2326] [depth= 1] . ( 12 sec) [ -9864.4196] [ 2324] [depth= 1] . ( 12 sec) [ -9864.0926] [ 2329] [depth= 1] . ( 13 sec) [ -9864.0410] [ 2332] [depth= 1] . ( 13 sec) [ -9862.3749] [ 2332] [depth= 3] . ( 14 sec) [ -9856.1567] [Branch lengths ] . ( 14 sec) [ -9856.1391] [GTR parameters ] . ( 14 sec) [ -9856.0846] [Alpha ][ 0.924906] . ( 15 sec) [ -9853.8365] [ 2333] [depth= 1] . ( 16 sec) [ -9853.8241] [ 2329] [depth= 1] . ( 17 sec) [ -9853.7453] [ 2330] [depth= 2] . ( 18 sec) [ -9850.9221] [Branch lengths ] . ( 18 sec) [ -9850.9161] [GTR parameters ] . ( 18 sec) [ -9850.9144] [Alpha ][ 0.921213] . ( 22 sec) [ -9849.5328] [Branch lengths ] . ( 35 sec) [ -9849.3490] [ 2317] [depth= 2] . ( 40 sec) [ -9849.0890] [ 2322] [depth= 1] . ( 43 sec) [ -9848.6027] [Branch lengths ] . ( 43 sec) [ -9848.6020] [GTR parameters ] . ( 43 sec) [ -9848.5969] [Alpha ][ 0.927570] . ( 43 sec) [ -9848.5969] [Topology ] . ( 44 sec) [ -9848.5596] [Topology ] . ( 45 sec) [ -9848.5434] [Topology ] . ( 45 sec) [ -9848.5340] [Topology ] . ( 46 sec) [ -9848.5279] [Topology ] . ( 47 sec) [ -9848.5232] [Topology ] . ( 48 sec) [ -9848.5193] [Topology ] . ( 48 sec) [ -9848.5191] [GTR parameters ] . ( 48 sec) [ -9848.5191] [Alpha ][ 0.927570] . ( 48 sec) [ -9848.5191] [Topology ] . ( 49 sec) [ -9848.5157] [Topology ] . ( 50 sec) [ -9848.5125] [Topology ] . ( 50 sec) [ -9848.5094] [Topology ] . ( 51 sec) [ -9848.5064] [Topology ] . ( 52 sec) [ -9848.5035] [Topology ] . ( 53 sec) [ -9848.5006] [Topology ] . ( 53 sec) [ -9848.5006] [GTR parameters ] . ( 53 sec) [ -9848.5006] [Alpha ][ 0.927570] . ( 53 sec) [ -9848.5006] [Topology ] . ( 54 sec) [ -9848.4977] [Topology ] . ( 55 sec) [ -9848.4949] [Topology ] . ( 55 sec) [ -9848.4921] [Topology ] . ( 56 sec) [ -9848.4893] [Topology ] . ( 57 sec) [ -9848.4866] [Topology ] . ( 58 sec) [ -9848.4838] [Topology ] . ( 58 sec) [ -9848.4838] [GTR parameters ] . ( 58 sec) [ -9848.4838] [Alpha ][ 0.927570] . ( 58 sec) [ -9848.4838] [Topology ] . ( 59 sec) [ -9848.4811] [Topology ] . ( 60 sec) [ -9848.4784] [Topology ] . ( 61 sec) [ -9848.4757] [Topology ] . ( 62 sec) [ -9848.4743] [Topology ] . ( 63 sec) [ -9848.4737] [Topology ] . ( 63 sec) [ -9848.4737] [GTR parameters ] . ( 63 sec) [ -9848.4737] [Alpha ][ 0.927570] . ( 63 sec) [ -9848.4737] [Topology ] . ( 64 sec) [ -9848.4736] [Topology ] . ( 65 sec) [ -9848.4736] [GTR parameters ] . ( 65 sec) [ -9848.4736] [Alpha ][ 0.927570] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -9847.8087] [Topology ] . Checking for NNIs, optimizing five branches... . ( 78 sec) [ -9847.8086] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.808592. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -28442.9758] [GTR parameters ] . ( 1 sec) [ -27914.5076] [Alpha ][ 0.500960] . ( 1 sec) [ -27276.1963] [ 5271] [depth= 6] . ( 1 sec) [ -26943.6184] [ 5149] [depth= 11] . ( 1 sec) [ -26745.0969] [ 5126] [depth= 3] . ( 1 sec) [ -26534.3222] [ 5097] [depth= 6] . ( 1 sec) [ -26020.2734] [ 4957] [depth= 7] . ( 1 sec) [ -25987.6441] [ 4955] [depth= 1] . ( 1 sec) [ -25788.0798] [ 4929] [depth= 12] . ( 1 sec) [ -25593.0111] [ 4919] [depth= 1] . ( 1 sec) [ -25120.4687] [ 4813] [depth= 15] . ( 1 sec) [ -24720.8884] [ 4704] [depth= 15] . ( 1 sec) [ -24582.2389] [ 4653] [depth= 14] . ( 1 sec) [ -24072.9675] [ 4586] [depth= 8] . ( 1 sec) [ -23685.9797] [ 4511] [depth= 10] . ( 1 sec) [ -23102.5078] [ 4464] [depth= 1] . ( 1 sec) [ -22768.7410] [ 4412] [depth= 12] . ( 1 sec) [ -22639.3744] [ 4421] [depth= 1] . ( 1 sec) [ -22573.4877] [ 4392] [depth= 9] . ( 1 sec) [ -22509.4182] [ 4330] [depth= 2] . ( 2 sec) [ -22503.2704] [ 4327] [depth= 5] . ( 2 sec) [ -22322.4300] [ 4252] [depth= 12] . ( 2 sec) [ -16382.7124] [ 4203] [depth= 8] . ( 2 sec) [ -15962.7716] [ 4022] [depth= 6] . ( 2 sec) [ -15383.4829] [ 3935] [depth= 1] . ( 2 sec) [ -15210.9274] [ 3893] [depth= 10] . ( 2 sec) [ -15182.5664] [ 3899] [depth= 5] . ( 2 sec) [ -15147.7993] [ 3839] [depth= 1] . ( 2 sec) [ -15095.9129] [ 3811] [depth= 1] . ( 2 sec) [ -15091.9147] [ 3800] [depth= 11] . ( 2 sec) [ -14976.7368] [ 3771] [depth= 5] . ( 2 sec) [ -14971.6652] [ 3743] [depth= 2] . ( 2 sec) [ -14496.6910] [ 3605] [depth= 2] . ( 2 sec) [ -14284.4596] [ 3559] [depth= 2] . ( 2 sec) [ -14209.7424] [ 3523] [depth= 1] . ( 2 sec) [ -14174.8018] [ 3544] [depth= 1] . ( 2 sec) [ -13524.6800] [ 3470] [depth= 1] . ( 2 sec) [ -13451.7437] [ 3455] [depth= 8] . ( 2 sec) [ -13248.3803] [ 3363] [depth= 2] . ( 3 sec) [ -13195.2114] [ 3373] [depth= 1] . ( 3 sec) [ -13090.2542] [ 3334] [depth= 1] . ( 3 sec) [ -13009.9681] [ 3331] [depth= 1] . ( 3 sec) [ -12931.5889] [ 3315] [depth= 2] . ( 3 sec) [ -12707.3970] [ 3257] [depth= 5] . ( 3 sec) [ -12619.7906] [ 3266] [depth= 1] . ( 3 sec) [ -12579.3196] [ 3127] [depth= 1] . ( 3 sec) [ -12572.0295] [ 3116] [depth= 1] . ( 3 sec) [ -12538.3247] [ 3088] [depth= 3] . ( 3 sec) [ -12388.9182] [ 3083] [depth= 10] . ( 3 sec) [ -12273.8241] [ 2987] [depth= 10] . ( 3 sec) [ -11972.6362] [ 2907] [depth= 4] . ( 3 sec) [ -11843.7577] [ 2836] [depth= 3] . ( 3 sec) [ -11821.6451] [ 2823] [depth= 4] . ( 3 sec) [ -11746.1004] [ 2803] [depth= 2] . ( 3 sec) [ -11673.1338] [ 2768] [depth= 1] . ( 3 sec) [ -11595.4303] [ 2757] [depth= 1] . ( 3 sec) [ -11561.7229] [ 2758] [depth= 1] . ( 4 sec) [ -11559.6731] [ 2759] [depth= 1] . ( 4 sec) [ -11474.9194] [ 2756] [depth= 1] . ( 4 sec) [ -11373.3539] [ 2715] [depth= 9] . ( 4 sec) [ -11365.1953] [ 2711] [depth= 1] . ( 4 sec) [ -11318.5792] [ 2704] [depth= 3] . ( 4 sec) [ -11302.4440] [ 2717] [depth= 5] . ( 4 sec) [ -11207.1435] [ 2710] [depth= 1] . ( 4 sec) [ -11185.3967] [ 2707] [depth= 5] . ( 4 sec) [ -11180.5679] [ 2702] [depth= 2] . ( 4 sec) [ -11169.2998] [ 2705] [depth= 5] . ( 4 sec) [ -11165.3819] [ 2707] [depth= 1] . ( 4 sec) [ -11158.6629] [ 2700] [depth= 6] . ( 4 sec) [ -11152.0948] [ 2700] [depth= 1] . ( 4 sec) [ -11083.8021] [ 2655] [depth= 1] . ( 4 sec) [ -11083.2724] [ 2659] [depth= 1] . ( 4 sec) [ -11080.9984] [ 2666] [depth= 1] . ( 5 sec) [ -11032.4432] [ 2610] [depth= 6] . ( 5 sec) [ -11026.1593] [ 2607] [depth= 2] . ( 5 sec) [ -11025.4258] [ 2606] [depth= 1] . ( 5 sec) [ -11018.7037] [ 2588] [depth= 1] . ( 5 sec) [ -11007.9217] [ 2593] [depth= 1] . ( 5 sec) [ -10777.9189] [ 2510] [depth= 2] . ( 5 sec) [ -10686.6093] [ 2483] [depth= 1] . ( 5 sec) [ -10655.3635] [ 2479] [depth= 2] . ( 5 sec) [ -10197.6620] [Branch lengths ] . ( 6 sec) [ -10192.9535] [GTR parameters ] . ( 6 sec) [ -10166.2131] [Alpha ][ 0.805316] . ( 6 sec) [ -10164.5061] [ 2483] [depth= 1] . ( 6 sec) [ -10163.9601] [ 2486] [depth= 1] . ( 6 sec) [ -10157.9869] [ 2483] [depth= 1] . ( 6 sec) [ -10136.6450] [ 2447] [depth= 2] . ( 6 sec) [ -10092.2800] [ 2424] [depth= 1] . ( 6 sec) [ -10082.2398] [ 2409] [depth= 1] . ( 7 sec) [ -10081.3412] [ 2407] [depth= 1] . ( 7 sec) [ -10068.6615] [ 2379] [depth= 1] . ( 7 sec) [ -10065.6905] [ 2383] [depth= 1] . ( 7 sec) [ -10062.0984] [ 2398] [depth= 1] . ( 7 sec) [ -10061.3609] [ 2393] [depth= 1] . ( 7 sec) [ -10060.5981] [ 2395] [depth= 2] . ( 7 sec) [ -10059.5458] [ 2385] [depth= 2] . ( 7 sec) [ -10057.1828] [ 2380] [depth= 1] . ( 7 sec) [ -10055.1219] [ 2382] [depth= 1] . ( 8 sec) [ -10041.0569] [ 2370] [depth= 1] . ( 8 sec) [ -10040.6949] [ 2372] [depth= 1] . ( 8 sec) [ -9938.1207] [ 2334] [depth= 5] . ( 8 sec) [ -9937.4468] [ 2332] [depth= 1] . ( 8 sec) [ -9918.6224] [ 2333] [depth= 1] . ( 8 sec) [ -9917.9185] [ 2334] [depth= 1] . ( 8 sec) [ -9915.6416] [ 2336] [depth= 1] . ( 8 sec) [ -9915.5219] [ 2338] [depth= 1] . ( 8 sec) [ -9906.4758] [ 2343] [depth= 5] . ( 8 sec) [ -9904.3325] [ 2336] [depth= 2] . ( 9 sec) [ -9904.3188] [ 2336] [depth= 1] . ( 9 sec) [ -9902.9167] [ 2337] [depth= 1] . ( 9 sec) [ -9901.4738] [ 2337] [depth= 1] . ( 9 sec) [ -9901.3324] [ 2321] [depth= 1] . ( 9 sec) [ -9901.2350] [ 2321] [depth= 1] . ( 9 sec) [ -9878.6274] [ 2318] [depth= 1] . ( 10 sec) [ -9855.9410] [Branch lengths ] . ( 10 sec) [ -9855.5875] [GTR parameters ] . ( 10 sec) [ -9853.7840] [Alpha ][ 0.913640] . ( 11 sec) [ -9853.7143] [ 2331] [depth= 1] . ( 11 sec) [ -9852.9323] [ 2331] [depth= 1] . ( 12 sec) [ -9849.5882] [ 2311] [depth= 2] . ( 13 sec) [ -9849.5752] [ 2298] [depth= 1] . ( 14 sec) [ -9848.3527] [Branch lengths ] . ( 14 sec) [ -9848.3477] [GTR parameters ] . ( 14 sec) [ -9848.3224] [Alpha ][ 0.927788] . ( 16 sec) [ -9848.2275] [ 2311] [depth= 1] . ( 18 sec) [ -9848.0257] [Branch lengths ] . ( 18 sec) [ -9848.0256] [GTR parameters ] . ( 18 sec) [ -9848.0253] [Alpha ][ 0.929135] . ( 39 sec) [ -9847.9539] [Branch lengths ] . ( 39 sec) [ -9847.9539] [Topology ] . ( 40 sec) [ -9847.9332] [Topology ] . ( 41 sec) [ -9847.9196] [Topology ] . ( 42 sec) [ -9847.9092] [Topology ] . ( 42 sec) [ -9847.9009] [Topology ] . ( 43 sec) [ -9847.8941] [Topology ] . ( 44 sec) [ -9847.8882] [Topology ] . ( 44 sec) [ -9847.8881] [GTR parameters ] . ( 44 sec) [ -9847.8881] [Alpha ][ 0.929135] . ( 44 sec) [ -9847.8881] [Topology ] . ( 45 sec) [ -9847.8830] [Topology ] . ( 46 sec) [ -9847.8784] [Topology ] . ( 47 sec) [ -9847.8743] [Topology ] . ( 47 sec) [ -9847.8704] [Topology ] . ( 48 sec) [ -9847.8667] [Topology ] . ( 49 sec) [ -9847.8632] [Topology ] . ( 49 sec) [ -9847.8632] [GTR parameters ] . ( 49 sec) [ -9847.8632] [Alpha ][ 0.929135] . ( 49 sec) [ -9847.8632] [Topology ] . ( 50 sec) [ -9847.8599] [Topology ] . ( 51 sec) [ -9847.8566] [Topology ] . ( 52 sec) [ -9847.8534] [Topology ] . ( 52 sec) [ -9847.8503] [Topology ] . ( 53 sec) [ -9847.8472] [Topology ] . ( 54 sec) [ -9847.8442] [Topology ] . ( 54 sec) [ -9847.8442] [GTR parameters ] . ( 54 sec) [ -9847.8442] [Alpha ][ 0.929135] . ( 54 sec) [ -9847.8442] [Topology ] . ( 55 sec) [ -9847.8413] [Topology ] . ( 56 sec) [ -9847.8383] [Topology ] . ( 57 sec) [ -9847.8354] [Topology ] . ( 57 sec) [ -9847.8326] [Topology ] . ( 58 sec) [ -9847.8297] [Topology ] . ( 59 sec) [ -9847.8269] [Topology ] . ( 59 sec) [ -9847.8269] [GTR parameters ] . ( 59 sec) [ -9847.8269] [Alpha ][ 0.928206] . ( 59 sec) [ -9847.8269] [Topology ] . ( 60 sec) [ -9847.8241] [Topology ] . ( 61 sec) [ -9847.8213] [Topology ] . ( 62 sec) [ -9847.8186] [Topology ] . ( 62 sec) [ -9847.8159] [Topology ] . ( 63 sec) [ -9847.8132] [Topology ] . ( 64 sec) [ -9847.8105] [Topology ] . ( 64 sec) [ -9847.8105] [GTR parameters ] . ( 64 sec) [ -9847.8105] [Alpha ][ 0.928206] . ( 64 sec) [ -9847.8105] [Topology ] . ( 65 sec) [ -9847.8082] [Topology ] . ( 66 sec) [ -9847.8069] [Topology ] . ( 66 sec) [ -9847.8064] [Topology ] . ( 67 sec) [ -9847.8064] [GTR parameters ] . ( 67 sec) [ -9847.8064] [Alpha ][ 0.928206] . ( 67 sec) [ -9847.8064] [Topology ] . ( 67 sec) [ -9847.8063] [Topology ] . ( 68 sec) [ -9847.8063] [GTR parameters ] . ( 68 sec) [ -9847.8063] [Alpha ][ 0.928206] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.806262. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9969.108107 . ( 0 sec) [ -9965.2502] [GTR parameters ] . ( 0 sec) [ -9965.2156] [Alpha ][ 0.980951] . ( 0 sec) [ -9965.2156] [Topology ] . ( 1 sec) [ -9880.6273] [Topology ] . ( 2 sec) [ -9863.6476] [Topology ] . ( 3 sec) [ -9857.7578] [Topology ] . ( 4 sec) [ -9852.1065] [Topology ] . ( 4 sec) [ -9850.2448] [Topology ] . ( 5 sec) [ -9849.4495] [Topology ] . ( 6 sec) [ -9849.0220] [Topology ] . ( 7 sec) [ -9848.7813] [Topology ] . ( 7 sec) [ -9848.6392] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -9848.2987] [Topology ] . Before opt ts/t=1.000000 LK=-9848.298747 . ( 16 sec) [ -9848.1993] [GTR parameters ] . ( 16 sec) [ -9847.9291] [Alpha ][ 0.933397] . ( 16 sec) [ -9847.9291] [Topology ] . ( 17 sec) [ -9847.8717] [Topology ] . ( 18 sec) [ -9847.8482] [Topology ] . ( 19 sec) [ -9847.8347] [Topology ] . ( 19 sec) [ -9847.8264] [Topology ] . ( 20 sec) [ -9847.8212] [Topology ] . ( 21 sec) [ -9847.8178] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.817810 . ( 28 sec) [ -9847.8160] [GTR parameters ] . ( 28 sec) [ -9847.8138] [Alpha ][ 0.929063] . ( 28 sec) [ -9847.8138] [Topology ] . ( 29 sec) [ -9847.8113] [Topology ] . ( 30 sec) [ -9847.8097] [Topology ] . ( 30 sec) [ -9847.8086] [Topology ] . ( 31 sec) [ -9847.8079] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.807881 . ( 38 sec) [ -9847.8078] [GTR parameters ] . ( 38 sec) [ -9847.8078] [Alpha ][ 0.929063] . ( 38 sec) [ -9847.8078] [Topology ] . ( 39 sec) [ -9847.8073] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 53 sec) [ -9965.2502] [GTR parameters ] . ( 53 sec) [ -9965.2156] [Alpha ][ 0.980951] . ( 53 sec) [ -9945.2695] [ 2314] [depth= 1] . ( 53 sec) [ -9939.2778] [ 2310] [depth= 2] . ( 54 sec) [ -9935.7886] [ 2305] [depth= 1] . ( 54 sec) [ -9934.9568] [ 2304] [depth= 1] . ( 54 sec) [ -9932.2891] [ 2306] [depth= 1] . ( 55 sec) [ -9931.7504] [ 2303] [depth= 1] . ( 55 sec) [ -9931.4114] [ 2303] [depth= 1] . ( 55 sec) [ -9930.8885] [ 2303] [depth= 1] . ( 55 sec) [ -9927.3884] [ 2306] [depth= 1] . ( 55 sec) [ -9901.3985] [ 2321] [depth= 4] . ( 55 sec) [ -9900.8488] [ 2331] [depth= 1] . ( 56 sec) [ -9900.3341] [ 2335] [depth= 1] . ( 56 sec) [ -9898.9125] [ 2331] [depth= 1] . ( 56 sec) [ -9855.8572] [Branch lengths ] . ( 56 sec) [ -9855.7844] [GTR parameters ] . ( 56 sec) [ -9855.3795] [Alpha ][ 0.921868] . ( 56 sec) [ -9855.2780] [ 2316] [depth= 1] . ( 57 sec) [ -9855.2484] [ 2331] [depth= 1] . ( 57 sec) [ -9852.9606] [ 2317] [depth= 2] . ( 57 sec) [ -9852.6223] [ 2314] [depth= 1] . ( 57 sec) [ -9852.4283] [ 2317] [depth= 1] . ( 58 sec) [ -9851.9184] [ 2322] [depth= 1] . ( 60 sec) [ -9849.3188] [Branch lengths ] . ( 60 sec) [ -9849.3094] [GTR parameters ] . ( 61 sec) [ -9849.3086] [Alpha ][ 0.924310] . ( 64 sec) [ -9848.8603] [Branch lengths ] . ( 85 sec) [ -9848.7594] [Branch lengths ] . ( 85 sec) [ -9848.7594] [Topology ] . ( 86 sec) [ -9848.7435] [Topology ] . ( 87 sec) [ -9848.7313] [Topology ] . ( 88 sec) [ -9848.7099] [Topology ] . ( 88 sec) [ -9848.6936] [Topology ] . ( 89 sec) [ -9848.6830] [Topology ] . ( 90 sec) [ -9848.6758] [Topology ] . ( 91 sec) [ -9848.6706] [Topology ] . ( 91 sec) [ -9848.6668] [Topology ] . ( 92 sec) [ -9848.6641] [Topology ] . ( 92 sec) [ -9848.6631] [GTR parameters ] . ( 92 sec) [ -9848.6621] [Alpha ][ 0.927075] . ( 92 sec) [ -9848.6621] [Topology ] . ( 93 sec) [ -9848.6601] [Topology ] . ( 94 sec) [ -9848.6586] [Topology ] . ( 95 sec) [ -9848.6576] [Topology ] . ( 95 sec) [ -9848.6568] [Topology ] . ( 96 sec) [ -9848.6568] [GTR parameters ] . ( 96 sec) [ -9848.6568] [Alpha ][ 0.927075] . ( 96 sec) [ -9848.6568] [Topology ] . ( 96 sec) [ -9848.6562] [Topology ] . ( 97 sec) [ -9848.6562] [GTR parameters ] . ( 97 sec) [ -9848.6562] [Alpha ][ 0.927075] . Checking for NNIs, optimizing five branches... . ( 104 sec) [ -9847.9913] [Topology ] . Checking for NNIs, optimizing five branches... . ( 110 sec) [ -9847.8159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -9847.8158] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9847.807318 . Log likelihood obtained after SPR moves : -9847.815789 . Log likelihood of the current tree: -9847.807318. . Printing the most likely tree in file 'data91.phy_phyml_tree.txt'... . Best log likelihood : -9847.806262 . Time used 0h2m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo