.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24842.7709] [GTR parameters ] . ( 2 sec) [ -24265.9035] [Alpha ][ 0.500960] . ( 2 sec) [ -24057.1181] [ 3978] [depth= 8] . ( 2 sec) [ -23979.8401] [ 3957] [depth= 6] . ( 2 sec) [ -23736.7453] [ 3928] [depth= 5] . ( 2 sec) [ -23711.5787] [ 3918] [depth= 1] . ( 2 sec) [ -23597.1382] [ 3893] [depth= 9] . ( 2 sec) [ -23261.2178] [ 3861] [depth= 2] . ( 2 sec) [ -23022.0264] [ 3775] [depth= 1] . ( 2 sec) [ -22556.6336] [ 3756] [depth= 6] . ( 3 sec) [ -22397.4493] [ 3744] [depth= 2] . ( 3 sec) [ -22384.7631] [ 3739] [depth= 2] . ( 3 sec) [ -22363.3569] [ 3728] [depth= 1] . ( 3 sec) [ -22331.5562] [ 3723] [depth= 2] . ( 3 sec) [ -22223.7910] [ 3708] [depth= 3] . ( 3 sec) [ -22114.9176] [ 3698] [depth= 3] . ( 3 sec) [ -22101.7878] [ 3693] [depth= 1] . ( 3 sec) [ -20645.5087] [ 3685] [depth= 2] . ( 3 sec) [ -20152.6341] [ 3658] [depth= 10] . ( 3 sec) [ -20121.1335] [ 3643] [depth= 1] . ( 3 sec) [ -19985.0121] [ 3639] [depth= 4] . ( 4 sec) [ -19850.4115] [ 3637] [depth= 1] . ( 4 sec) [ -19250.6589] [ 3610] [depth= 5] . ( 4 sec) [ -19009.0640] [ 3513] [depth= 14] . ( 4 sec) [ -18639.0176] [ 3484] [depth= 9] . ( 4 sec) [ -18572.7288] [ 3467] [depth= 2] . ( 4 sec) [ -18503.0126] [ 3449] [depth= 3] . ( 4 sec) [ -18381.5195] [ 3446] [depth= 1] . ( 5 sec) [ -18299.6616] [ 3429] [depth= 11] . ( 5 sec) [ -18090.4135] [ 3387] [depth= 8] . ( 5 sec) [ -17917.0934] [ 3340] [depth= 16] . ( 5 sec) [ -17859.7436] [ 3332] [depth= 3] . ( 5 sec) [ -17795.8986] [ 3318] [depth= 4] . ( 5 sec) [ -17787.9036] [ 3318] [depth= 3] . ( 5 sec) [ -17681.2622] [ 3291] [depth= 3] . ( 5 sec) [ -17593.2412] [ 3265] [depth= 7] . ( 5 sec) [ -17415.9956] [ 3248] [depth= 4] . ( 5 sec) [ -17386.1078] [ 3244] [depth= 2] . ( 6 sec) [ -17237.6506] [ 3206] [depth= 9] . ( 6 sec) [ -17175.0075] [ 3194] [depth= 1] . ( 6 sec) [ -17167.7742] [ 3196] [depth= 1] . ( 6 sec) [ -17149.6195] [ 3197] [depth= 1] . ( 6 sec) [ -17135.7339] [ 3191] [depth= 2] . ( 6 sec) [ -16973.4558] [ 3139] [depth= 6] . ( 6 sec) [ -16964.7022] [ 3137] [depth= 1] . ( 6 sec) [ -16900.7950] [ 3139] [depth= 1] . ( 6 sec) [ -16898.1239] [ 3139] [depth= 1] . ( 6 sec) [ -16790.3026] [ 3129] [depth= 1] . ( 6 sec) [ -16689.7731] [ 3101] [depth= 1] . ( 7 sec) [ -16644.1388] [ 3078] [depth= 4] . ( 7 sec) [ -16552.7507] [ 3038] [depth= 7] . ( 7 sec) [ -16437.3534] [ 3012] [depth= 1] . ( 7 sec) [ -16325.9708] [ 2984] [depth= 4] . ( 7 sec) [ -16295.0091] [ 2976] [depth= 5] . ( 7 sec) [ -16169.0396] [ 2929] [depth= 13] . ( 7 sec) [ -16123.0136] [ 2922] [depth= 5] . ( 7 sec) [ -15957.6441] [ 2902] [depth= 8] . ( 7 sec) [ -15837.7630] [ 2870] [depth= 12] . ( 8 sec) [ -15750.0883] [ 2843] [depth= 1] . ( 8 sec) [ -15675.6795] [ 2814] [depth= 2] . ( 8 sec) [ -15502.9149] [ 2796] [depth= 8] . ( 8 sec) [ -15456.9368] [ 2774] [depth= 5] . ( 8 sec) [ -15432.3224] [ 2765] [depth= 1] . ( 8 sec) [ -15431.5785] [ 2769] [depth= 2] . ( 8 sec) [ -15409.9523] [ 2754] [depth= 7] . ( 8 sec) [ -15387.5031] [ 2745] [depth= 3] . ( 8 sec) [ -15347.5898] [ 2738] [depth= 2] . ( 9 sec) [ -15297.4261] [ 2720] [depth= 2] . ( 9 sec) [ -15257.7331] [ 2714] [depth= 2] . ( 9 sec) [ -15147.3454] [ 2713] [depth= 1] . ( 9 sec) [ -15068.6605] [ 2692] [depth= 1] . ( 9 sec) [ -14973.5440] [ 2673] [depth= 1] . ( 9 sec) [ -14971.1422] [ 2673] [depth= 16] . ( 9 sec) [ -14950.2935] [ 2667] [depth= 1] . ( 9 sec) [ -14738.6196] [ 2640] [depth= 19] . ( 9 sec) [ -14669.5145] [ 2614] [depth= 3] . ( 9 sec) [ -14582.0409] [ 2620] [depth= 1] . ( 10 sec) [ -14512.0887] [ 2598] [depth= 4] . ( 10 sec) [ -14264.8845] [ 2540] [depth= 10] . ( 10 sec) [ -14181.3722] [ 2523] [depth= 2] . ( 10 sec) [ -14138.6839] [ 2519] [depth= 3] . ( 10 sec) [ -14126.9532] [ 2519] [depth= 11] . ( 10 sec) [ -14117.8374] [ 2519] [depth= 1] . ( 10 sec) [ -14044.9596] [ 2490] [depth= 12] . ( 11 sec) [ -14030.4191] [ 2488] [depth= 1] . ( 11 sec) [ -13977.4075] [ 2466] [depth= 1] . ( 11 sec) [ -13973.4670] [ 2463] [depth= 1] . ( 11 sec) [ -13968.9899] [ 2464] [depth= 1] . ( 11 sec) [ -13968.2376] [ 2466] [depth= 1] . ( 11 sec) [ -13967.7874] [ 2469] [depth= 1] . ( 12 sec) [ -13913.3048] [ 2452] [depth= 2] . ( 12 sec) [ -13903.0560] [ 2451] [depth= 1] . ( 12 sec) [ -13896.0989] [ 2448] [depth= 1] . ( 12 sec) [ -13884.5699] [ 2445] [depth= 1] . ( 12 sec) [ -13877.3341] [ 2443] [depth= 4] . ( 12 sec) [ -13694.3750] [ 2435] [depth= 5] . ( 12 sec) [ -13630.9728] [ 2405] [depth= 1] . ( 12 sec) [ -13506.4427] [ 2363] [depth= 4] . ( 13 sec) [ -13504.2805] [ 2362] [depth= 1] . ( 13 sec) [ -13473.2521] [ 2362] [depth= 1] . ( 13 sec) [ -13432.3727] [ 2349] [depth= 1] . ( 13 sec) [ -13428.2832] [ 2347] [depth= 1] . ( 13 sec) [ -13426.1790] [ 2345] [depth= 1] . ( 13 sec) [ -13399.6398] [ 2343] [depth= 1] . ( 13 sec) [ -13367.3895] [ 2340] [depth= 1] . ( 13 sec) [ -13304.9158] [ 2346] [depth= 1] . ( 13 sec) [ -13304.4427] [ 2346] [depth= 1] . ( 14 sec) [ -13258.5534] [ 2322] [depth= 2] . ( 14 sec) [ -13257.1722] [ 2319] [depth= 1] . ( 14 sec) [ -13256.3383] [ 2324] [depth= 1] . ( 14 sec) [ -13248.2199] [ 2319] [depth= 1] . ( 14 sec) [ -13248.0258] [ 2319] [depth= 1] . ( 14 sec) [ -13244.6935] [ 2321] [depth= 1] . ( 14 sec) [ -13241.1310] [ 2321] [depth= 1] . ( 14 sec) [ -13232.5043] [ 2319] [depth= 5] . ( 15 sec) [ -13138.8219] [ 2291] [depth= 10] . ( 15 sec) [ -13132.6602] [ 2291] [depth= 1] . ( 15 sec) [ -13127.5760] [ 2293] [depth= 1] . ( 16 sec) [ -12865.1769] [Branch lengths ] . ( 20 sec) [ -12728.4315] [GTR parameters ] . ( 20 sec) [ -12660.5365] [Alpha ][ 0.289391] . ( 20 sec) [ -12657.3853] [ 2290] [depth= 1] . ( 20 sec) [ -12656.9977] [ 2285] [depth= 1] . ( 20 sec) [ -12654.7510] [ 2282] [depth= 1] . ( 21 sec) [ -12628.7298] [ 2270] [depth= 8] . ( 21 sec) [ -12627.4446] [ 2268] [depth= 1] . ( 21 sec) [ -12625.1603] [ 2268] [depth= 1] . ( 21 sec) [ -12582.8263] [ 2248] [depth= 3] . ( 21 sec) [ -12582.7058] [ 2249] [depth= 2] . ( 21 sec) [ -12582.6047] [ 2240] [depth= 2] . ( 22 sec) [ -12580.3232] [ 2240] [depth= 1] . ( 22 sec) [ -12512.6501] [ 2221] [depth= 2] . ( 23 sec) [ -12512.2069] [ 2223] [depth= 1] . ( 23 sec) [ -12497.7298] [ 2220] [depth= 5] . ( 24 sec) [ -12494.0027] [ 2218] [depth= 1] . ( 24 sec) [ -12488.3587] [ 2223] [depth= 1] . ( 24 sec) [ -12484.7021] [ 2217] [depth= 1] . ( 24 sec) [ -12476.6961] [ 2213] [depth= 2] . ( 25 sec) [ -12474.7198] [ 2212] [depth= 2] . ( 26 sec) [ -12470.1956] [ 2205] [depth= 3] . ( 27 sec) [ -12443.6096] [ 2207] [depth= 4] . ( 29 sec) [ -12407.5865] [ 2210] [depth= 1] . ( 29 sec) [ -12406.7021] [ 2211] [depth= 1] . ( 29 sec) [ -12405.3512] [ 2211] [depth= 1] . ( 30 sec) [ -12405.1455] [ 2211] [depth= 1] . ( 30 sec) [ -12403.8994] [ 2212] [depth= 1] . ( 31 sec) [ -12401.6687] [ 2211] [depth= 1] . ( 31 sec) [ -12395.2694] [ 2205] [depth= 2] . ( 31 sec) [ -12382.4880] [ 2202] [depth= 1] . ( 32 sec) [ -12355.5465] [Branch lengths ] . ( 35 sec) [ -12353.5144] [GTR parameters ] . ( 35 sec) [ -12353.4772] [Alpha ][ 0.293049] . ( 35 sec) [ -12352.1965] [ 2202] [depth= 1] . ( 36 sec) [ -12350.1722] [ 2206] [depth= 1] . ( 37 sec) [ -12348.9619] [ 2202] [depth= 1] . ( 38 sec) [ -12348.9458] [ 2202] [depth= 1] . ( 51 sec) [ -12346.9969] [Branch lengths ] . ( 52 sec) [ -12346.9727] [GTR parameters ] . ( 52 sec) [ -12346.9724] [Alpha ][ 0.292669] . ( 68 sec) [ -12346.7478] [Branch lengths ] . ( 138 sec) [ -12346.7144] [Branch lengths ] . ( 138 sec) [ -12346.7144] [Topology ] . ( 139 sec) [ -12346.7107] [Topology ] . ( 141 sec) [ -12346.7095] [Topology ] . ( 143 sec) [ -12346.7091] [Topology ] . ( 144 sec) [ -12346.7070] [GTR parameters ] . ( 144 sec) [ -12346.7062] [Alpha ][ 0.293158] . ( 145 sec) [ -12346.7062] [Topology ] . ( 146 sec) [ -12346.7057] [Topology ] . ( 147 sec) [ -12346.7057] [GTR parameters ] . ( 147 sec) [ -12346.7057] [Alpha ][ 0.293158] . Checking for NNIs, optimizing five branches... . ( 160 sec) [ -12346.2915] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.291504. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -24691.4720] [GTR parameters ] . ( 1 sec) [ -24137.4394] [Alpha ][ 0.500960] . ( 1 sec) [ -23912.2902] [ 3910] [depth= 6] . ( 1 sec) [ -23558.4174] [ 3889] [depth= 11] . ( 1 sec) [ -23554.6370] [ 3884] [depth= 1] . ( 1 sec) [ -23479.5967] [ 3877] [depth= 3] . ( 1 sec) [ -23462.8341] [ 3874] [depth= 1] . ( 1 sec) [ -23404.6386] [ 3876] [depth= 1] . ( 1 sec) [ -23398.2656] [ 3879] [depth= 1] . ( 1 sec) [ -23241.3355] [ 3865] [depth= 8] . ( 2 sec) [ -22883.1078] [ 3793] [depth= 2] . ( 2 sec) [ -22774.6234] [ 3778] [depth= 10] . ( 2 sec) [ -22740.0892] [ 3777] [depth= 1] . ( 2 sec) [ -22622.2644] [ 3740] [depth= 5] . ( 2 sec) [ -22601.0776] [ 3737] [depth= 2] . ( 2 sec) [ -22502.0158] [ 3731] [depth= 9] . ( 2 sec) [ -22116.9332] [ 3646] [depth= 1] . ( 2 sec) [ -21879.0243] [ 3589] [depth= 7] . ( 2 sec) [ -21786.7650] [ 3571] [depth= 16] . ( 2 sec) [ -21687.2408] [ 3554] [depth= 3] . ( 3 sec) [ -21670.8877] [ 3554] [depth= 6] . ( 3 sec) [ -21609.0940] [ 3559] [depth= 10] . ( 3 sec) [ -21550.4919] [ 3542] [depth= 1] . ( 3 sec) [ -21473.4911] [ 3545] [depth= 1] . ( 3 sec) [ -21281.1664] [ 3513] [depth= 9] . ( 3 sec) [ -21276.5321] [ 3511] [depth= 1] . ( 3 sec) [ -21133.0600] [ 3473] [depth= 10] . ( 3 sec) [ -20931.6296] [ 3465] [depth= 8] . ( 3 sec) [ -20791.1734] [ 3418] [depth= 3] . ( 4 sec) [ -20718.4239] [ 3398] [depth= 6] . ( 4 sec) [ -20706.9930] [ 3386] [depth= 5] . ( 4 sec) [ -19268.8179] [ 3350] [depth= 5] . ( 4 sec) [ -19150.1814] [ 3341] [depth= 2] . ( 4 sec) [ -19099.4736] [ 3335] [depth= 1] . ( 4 sec) [ -19093.0295] [ 3326] [depth= 13] . ( 4 sec) [ -18850.1501] [ 3308] [depth= 2] . ( 4 sec) [ -18609.7346] [ 3304] [depth= 1] . ( 4 sec) [ -18508.4716] [ 3287] [depth= 13] . ( 4 sec) [ -18495.6619] [ 3288] [depth= 3] . ( 4 sec) [ -18473.7973] [ 3285] [depth= 1] . ( 4 sec) [ -18466.8833] [ 3288] [depth= 1] . ( 5 sec) [ -18398.4808] [ 3291] [depth= 14] . ( 5 sec) [ -18283.6374] [ 3269] [depth= 11] . ( 5 sec) [ -18230.2803] [ 3273] [depth= 2] . ( 5 sec) [ -18175.3048] [ 3260] [depth= 2] . ( 5 sec) [ -18133.8935] [ 3241] [depth= 1] . ( 5 sec) [ -18119.5987] [ 3250] [depth= 1] . ( 5 sec) [ -18075.3207] [ 3228] [depth= 3] . ( 5 sec) [ -18059.7256] [ 3233] [depth= 12] . ( 5 sec) [ -17991.8867] [ 3218] [depth= 2] . ( 5 sec) [ -17963.9189] [ 3202] [depth= 1] . ( 6 sec) [ -17962.7800] [ 3196] [depth= 1] . ( 6 sec) [ -17874.5694] [ 3171] [depth= 1] . ( 6 sec) [ -17873.5182] [ 3176] [depth= 1] . ( 6 sec) [ -17836.7113] [ 3165] [depth= 20] . ( 6 sec) [ -17826.1432] [ 3166] [depth= 1] . ( 6 sec) [ -17739.5488] [ 3146] [depth= 7] . ( 6 sec) [ -17735.9809] [ 3146] [depth= 1] . ( 6 sec) [ -17725.1812] [ 3141] [depth= 1] . ( 6 sec) [ -17268.7376] [ 3071] [depth= 12] . ( 6 sec) [ -17259.6010] [ 3067] [depth= 2] . ( 7 sec) [ -17238.4824] [ 3066] [depth= 2] . ( 7 sec) [ -17189.5810] [ 3066] [depth= 13] . ( 7 sec) [ -17154.5886] [ 3060] [depth= 3] . ( 7 sec) [ -16835.5054] [ 3056] [depth= 1] . ( 7 sec) [ -16574.9952] [ 3039] [depth= 17] . ( 7 sec) [ -16494.6880] [ 3016] [depth= 13] . ( 7 sec) [ -16263.0220] [ 2913] [depth= 10] . ( 7 sec) [ -16085.9483] [ 2899] [depth= 5] . ( 7 sec) [ -15932.4091] [ 2883] [depth= 4] . ( 7 sec) [ -15905.5456] [ 2879] [depth= 2] . ( 8 sec) [ -15890.6050] [ 2867] [depth= 4] . ( 8 sec) [ -15818.3462] [ 2845] [depth= 13] . ( 8 sec) [ -15756.8774] [ 2828] [depth= 20] . ( 8 sec) [ -15617.2048] [ 2796] [depth= 10] . ( 8 sec) [ -15565.1696] [ 2789] [depth= 10] . ( 8 sec) [ -15554.2948] [ 2789] [depth= 1] . ( 8 sec) [ -15550.9407] [ 2786] [depth= 1] . ( 8 sec) [ -15524.2950] [ 2783] [depth= 11] . ( 8 sec) [ -15352.3425] [ 2749] [depth= 16] . ( 9 sec) [ -15048.6793] [ 2726] [depth= 6] . ( 9 sec) [ -15014.7311] [ 2726] [depth= 1] . ( 9 sec) [ -14980.3626] [ 2719] [depth= 1] . ( 9 sec) [ -14879.6770] [ 2684] [depth= 9] . ( 9 sec) [ -14742.4487] [ 2632] [depth= 14] . ( 9 sec) [ -14607.6272] [ 2598] [depth= 2] . ( 9 sec) [ -14600.1332] [ 2590] [depth= 4] . ( 9 sec) [ -14555.7995] [ 2582] [depth= 3] . ( 9 sec) [ -14485.8156] [ 2559] [depth= 5] . ( 10 sec) [ -14455.1464] [ 2552] [depth= 9] . ( 10 sec) [ -14327.4147] [ 2516] [depth= 5] . ( 10 sec) [ -14286.3776] [ 2507] [depth= 1] . ( 10 sec) [ -14159.1761] [ 2472] [depth= 2] . ( 10 sec) [ -14135.0909] [ 2471] [depth= 1] . ( 10 sec) [ -14108.9463] [ 2468] [depth= 1] . ( 11 sec) [ -14108.8137] [ 2467] [depth= 1] . ( 11 sec) [ -14048.7425] [ 2448] [depth= 2] . ( 11 sec) [ -14040.1987] [ 2447] [depth= 1] . ( 11 sec) [ -14035.0497] [ 2449] [depth= 5] . ( 11 sec) [ -14014.6728] [ 2443] [depth= 1] . ( 11 sec) [ -13908.0876] [ 2440] [depth= 4] . ( 12 sec) [ -13841.0438] [ 2436] [depth= 1] . ( 12 sec) [ -13735.1087] [ 2404] [depth= 6] . ( 12 sec) [ -13649.1397] [ 2390] [depth= 4] . ( 12 sec) [ -13564.3611] [ 2387] [depth= 2] . ( 12 sec) [ -13546.4407] [ 2388] [depth= 1] . ( 12 sec) [ -13443.7525] [ 2362] [depth= 1] . ( 12 sec) [ -13363.5055] [ 2334] [depth= 7] . ( 12 sec) [ -13343.6641] [ 2327] [depth= 6] . ( 12 sec) [ -13270.3648] [ 2306] [depth= 2] . ( 13 sec) [ -13256.2545] [ 2305] [depth= 1] . ( 13 sec) [ -13253.2241] [ 2305] [depth= 1] . ( 13 sec) [ -13232.3714] [ 2301] [depth= 2] . ( 13 sec) [ -13216.8055] [ 2302] [depth= 4] . ( 13 sec) [ -13189.5928] [ 2298] [depth= 2] . ( 13 sec) [ -13141.9577] [ 2286] [depth= 5] . ( 13 sec) [ -13059.5867] [ 2242] [depth= 9] . ( 14 sec) [ -13053.2127] [ 2239] [depth= 3] . ( 14 sec) [ -13052.4079] [ 2239] [depth= 1] . ( 14 sec) [ -13042.6823] [ 2234] [depth= 3] . ( 14 sec) [ -12989.2031] [ 2220] [depth= 1] . ( 14 sec) [ -12975.0097] [ 2218] [depth= 2] . ( 14 sec) [ -12967.2095] [ 2214] [depth= 1] . ( 14 sec) [ -12962.1985] [ 2216] [depth= 1] . ( 15 sec) [ -12807.1265] [Branch lengths ] . ( 19 sec) [ -12464.7983] [GTR parameters ] . ( 19 sec) [ -12407.8746] [Alpha ][ 0.300941] . ( 20 sec) [ -12406.2060] [ 2216] [depth= 1] . ( 20 sec) [ -12405.4834] [ 2218] [depth= 1] . ( 20 sec) [ -12402.7099] [ 2220] [depth= 1] . ( 20 sec) [ -12401.2069] [ 2223] [depth= 2] . ( 20 sec) [ -12400.9317] [ 2223] [depth= 1] . ( 21 sec) [ -12396.5971] [ 2221] [depth= 1] . ( 21 sec) [ -12393.1568] [ 2222] [depth= 1] . ( 21 sec) [ -12390.8950] [ 2223] [depth= 1] . ( 22 sec) [ -12389.8524] [ 2217] [depth= 1] . ( 22 sec) [ -12388.6395] [ 2219] [depth= 1] . ( 23 sec) [ -12380.9087] [ 2216] [depth= 1] . ( 23 sec) [ -12380.8397] [ 2220] [depth= 1] . ( 25 sec) [ -12375.1062] [ 2219] [depth= 1] . ( 26 sec) [ -12373.0741] [ 2218] [depth= 1] . ( 26 sec) [ -12372.9598] [ 2219] [depth= 1] . ( 27 sec) [ -12372.2642] [ 2215] [depth= 1] . ( 28 sec) [ -12372.0468] [ 2216] [depth= 1] . ( 31 sec) [ -12370.4599] [ 2216] [depth= 1] . ( 32 sec) [ -12368.5843] [ 2217] [depth= 1] . ( 32 sec) [ -12367.7849] [ 2217] [depth= 1] . ( 32 sec) [ -12367.5387] [ 2217] [depth= 1] . ( 33 sec) [ -12367.5145] [ 2217] [depth= 1] . ( 34 sec) [ -12363.6800] [ 2207] [depth= 2] . ( 34 sec) [ -12350.5462] [Branch lengths ] . ( 37 sec) [ -12349.5603] [GTR parameters ] . ( 38 sec) [ -12349.3553] [Alpha ][ 0.292285] . ( 50 sec) [ -12348.9452] [ 2207] [depth= 2] . ( 54 sec) [ -12347.0388] [Branch lengths ] . ( 56 sec) [ -12346.9580] [GTR parameters ] . ( 56 sec) [ -12346.9548] [Alpha ][ 0.291148] . ( 64 sec) [ -12346.8852] [ 2203] [depth= 1] . ( 70 sec) [ -12346.3556] [Branch lengths ] . ( 73 sec) [ -12346.3255] [GTR parameters ] . ( 73 sec) [ -12346.3240] [Alpha ][ 0.291832] . ( 140 sec) [ -12346.2619] [Branch lengths ] . ( 140 sec) [ -12346.2619] [Topology ] . ( 142 sec) [ -12346.2570] [Topology ] . ( 143 sec) [ -12346.2552] [Topology ] . ( 145 sec) [ -12346.2544] [Topology ] . ( 146 sec) [ -12346.2544] [GTR parameters ] . ( 146 sec) [ -12346.2542] [Alpha ][ 0.292124] . ( 146 sec) [ -12346.2542] [Topology ] . ( 148 sec) [ -12346.2537] [Topology ] . ( 148 sec) [ -12346.2534] [GTR parameters ] . ( 148 sec) [ -12346.2534] [Alpha ][ 0.292124] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.253373. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -24169.0537] [GTR parameters ] . ( 1 sec) [ -23590.6219] [Alpha ][ 0.500960] . ( 2 sec) [ -23421.6309] [ 4045] [depth= 9] . ( 2 sec) [ -23155.8043] [ 4019] [depth= 10] . ( 2 sec) [ -23103.6812] [ 4008] [depth= 2] . ( 2 sec) [ -23041.5172] [ 4008] [depth= 8] . ( 2 sec) [ -22995.8530] [ 3988] [depth= 1] . ( 2 sec) [ -22631.8531] [ 3967] [depth= 8] . ( 2 sec) [ -22625.8186] [ 3960] [depth= 4] . ( 2 sec) [ -22575.8588] [ 3945] [depth= 4] . ( 2 sec) [ -22502.9555] [ 3930] [depth= 5] . ( 3 sec) [ -22370.0580] [ 3918] [depth= 7] . ( 3 sec) [ -22287.4147] [ 3911] [depth= 5] . ( 3 sec) [ -22260.7693] [ 3907] [depth= 2] . ( 3 sec) [ -22192.3894] [ 3885] [depth= 9] . ( 3 sec) [ -22138.5368] [ 3893] [depth= 1] . ( 3 sec) [ -22032.7306] [ 3872] [depth= 2] . ( 3 sec) [ -21960.8910] [ 3852] [depth= 14] . ( 3 sec) [ -21847.8710] [ 3829] [depth= 2] . ( 3 sec) [ -21625.4159] [ 3755] [depth= 11] . ( 4 sec) [ -21565.9794] [ 3724] [depth= 8] . ( 4 sec) [ -21532.3444] [ 3727] [depth= 1] . ( 4 sec) [ -21439.7052] [ 3701] [depth= 20] . ( 4 sec) [ -21353.9791] [ 3693] [depth= 1] . ( 4 sec) [ -21300.5149] [ 3680] [depth= 9] . ( 4 sec) [ -21215.5020] [ 3679] [depth= 1] . ( 4 sec) [ -21046.2172] [ 3654] [depth= 2] . ( 4 sec) [ -20921.9434] [ 3622] [depth= 13] . ( 4 sec) [ -20841.2160] [ 3597] [depth= 1] . ( 5 sec) [ -20746.6454] [ 3564] [depth= 20] . ( 5 sec) [ -20679.2373] [ 3519] [depth= 2] . ( 5 sec) [ -20574.5693] [ 3507] [depth= 2] . ( 5 sec) [ -20549.2318] [ 3509] [depth= 1] . ( 5 sec) [ -20403.7960] [ 3460] [depth= 11] . ( 5 sec) [ -20293.7280] [ 3420] [depth= 8] . ( 5 sec) [ -20287.8516] [ 3420] [depth= 1] . ( 5 sec) [ -20246.9455] [ 3422] [depth= 4] . ( 5 sec) [ -20120.4030] [ 3426] [depth= 7] . ( 5 sec) [ -19940.3794] [ 3388] [depth= 4] . ( 6 sec) [ -19676.7328] [ 3349] [depth= 5] . ( 6 sec) [ -19603.6866] [ 3322] [depth= 13] . ( 6 sec) [ -19596.0342] [ 3322] [depth= 5] . ( 6 sec) [ -19417.4002] [ 3266] [depth= 6] . ( 6 sec) [ -19312.8432] [ 3245] [depth= 1] . ( 6 sec) [ -19293.4061] [ 3235] [depth= 2] . ( 6 sec) [ -19290.4413] [ 3233] [depth= 3] . ( 6 sec) [ -19189.4495] [ 3208] [depth= 1] . ( 7 sec) [ -19173.8370] [ 3206] [depth= 5] . ( 7 sec) [ -19163.0609] [ 3205] [depth= 1] . ( 7 sec) [ -19106.5355] [ 3186] [depth= 4] . ( 7 sec) [ -19088.0877] [ 3184] [depth= 3] . ( 7 sec) [ -19087.2697] [ 3184] [depth= 2] . ( 7 sec) [ -19085.7699] [ 3184] [depth= 1] . ( 7 sec) [ -19045.1521] [ 3177] [depth= 6] . ( 7 sec) [ -18960.6320] [ 3169] [depth= 5] . ( 7 sec) [ -18820.5700] [ 3144] [depth= 2] . ( 7 sec) [ -18716.0582] [ 3149] [depth= 8] . ( 8 sec) [ -18707.8960] [ 3150] [depth= 1] . ( 8 sec) [ -18594.4101] [ 3131] [depth= 2] . ( 8 sec) [ -18537.8381] [ 3147] [depth= 1] . ( 8 sec) [ -18328.0944] [ 3092] [depth= 15] . ( 8 sec) [ -18032.3567] [ 3083] [depth= 16] . ( 8 sec) [ -17949.6200] [ 3056] [depth= 1] . ( 8 sec) [ -17758.2166] [ 2986] [depth= 1] . ( 8 sec) [ -17724.4057] [ 3002] [depth= 1] . ( 9 sec) [ -17639.2174] [ 2976] [depth= 6] . ( 9 sec) [ -17480.8728] [ 2973] [depth= 8] . ( 9 sec) [ -17436.4736] [ 2974] [depth= 2] . ( 9 sec) [ -17287.4668] [ 2953] [depth= 12] . ( 9 sec) [ -17154.5321] [ 2925] [depth= 1] . ( 9 sec) [ -16982.1256] [ 2883] [depth= 8] . ( 9 sec) [ -16762.9745] [ 2843] [depth= 3] . ( 9 sec) [ -16741.3094] [ 2838] [depth= 2] . ( 10 sec) [ -16720.1635] [ 2837] [depth= 2] . ( 10 sec) [ -16599.4840] [ 2797] [depth= 9] . ( 10 sec) [ -16478.3251] [ 2771] [depth= 5] . ( 10 sec) [ -16267.6941] [ 2756] [depth= 11] . ( 10 sec) [ -16090.9988] [ 2727] [depth= 8] . ( 10 sec) [ -16009.3856] [ 2692] [depth= 1] . ( 11 sec) [ -15851.8493] [ 2671] [depth= 6] . ( 11 sec) [ -15824.4568] [ 2655] [depth= 1] . ( 11 sec) [ -15782.9193] [ 2650] [depth= 1] . ( 11 sec) [ -15658.6840] [ 2653] [depth= 1] . ( 11 sec) [ -15545.5893] [ 2608] [depth= 5] . ( 11 sec) [ -15506.1100] [ 2588] [depth= 6] . ( 11 sec) [ -15443.0175] [ 2577] [depth= 10] . ( 12 sec) [ -15430.0882] [ 2587] [depth= 1] . ( 12 sec) [ -14247.4599] [ 2556] [depth= 13] . ( 12 sec) [ -14161.1509] [ 2528] [depth= 5] . ( 12 sec) [ -14136.6052] [ 2515] [depth= 1] . ( 12 sec) [ -14099.0871] [ 2517] [depth= 2] . ( 12 sec) [ -14092.8913] [ 2510] [depth= 1] . ( 12 sec) [ -14025.2649] [ 2503] [depth= 1] . ( 12 sec) [ -14020.0962] [ 2505] [depth= 3] . ( 13 sec) [ -13975.1490] [ 2484] [depth= 4] . ( 13 sec) [ -13830.5499] [ 2467] [depth= 2] . ( 13 sec) [ -13806.0870] [ 2454] [depth= 7] . ( 13 sec) [ -13790.1985] [ 2486] [depth= 1] . ( 13 sec) [ -13688.3150] [ 2454] [depth= 1] . ( 13 sec) [ -13611.8820] [ 2433] [depth= 5] . ( 13 sec) [ -13609.9244] [ 2433] [depth= 1] . ( 14 sec) [ -13547.1740] [ 2422] [depth= 4] . ( 14 sec) [ -13540.0494] [ 2423] [depth= 1] . ( 14 sec) [ -13482.2849] [ 2404] [depth= 8] . ( 14 sec) [ -13427.4142] [ 2381] [depth= 5] . ( 14 sec) [ -13424.9298] [ 2386] [depth= 1] . ( 15 sec) [ -13400.2800] [ 2378] [depth= 3] . ( 15 sec) [ -13389.3200] [ 2376] [depth= 1] . ( 15 sec) [ -13274.7115] [ 2348] [depth= 4] . ( 15 sec) [ -13178.8460] [ 2319] [depth= 4] . ( 15 sec) [ -13176.3296] [ 2319] [depth= 1] . ( 15 sec) [ -13176.1034] [ 2319] [depth= 1] . ( 16 sec) [ -13173.6359] [ 2320] [depth= 1] . ( 16 sec) [ -13165.9755] [ 2320] [depth= 2] . ( 16 sec) [ -13149.0288] [ 2316] [depth= 3] . ( 16 sec) [ -13127.7822] [ 2310] [depth= 3] . ( 16 sec) [ -13119.3442] [ 2308] [depth= 2] . ( 16 sec) [ -13109.9117] [ 2306] [depth= 1] . ( 17 sec) [ -13054.3075] [ 2288] [depth= 1] . ( 17 sec) [ -13018.9579] [ 2280] [depth= 1] . ( 17 sec) [ -13015.3376] [ 2281] [depth= 1] . ( 18 sec) [ -12852.0615] [Branch lengths ] . ( 21 sec) [ -12651.8977] [GTR parameters ] . ( 21 sec) [ -12588.7072] [Alpha ][ 0.296820] . ( 22 sec) [ -12588.3507] [ 2280] [depth= 1] . ( 22 sec) [ -12546.4694] [ 2265] [depth= 1] . ( 23 sec) [ -12546.4035] [ 2264] [depth= 1] . ( 23 sec) [ -12518.1987] [ 2252] [depth= 1] . ( 24 sec) [ -12513.8542] [ 2250] [depth= 1] . ( 25 sec) [ -12511.9374] [ 2251] [depth= 1] . ( 26 sec) [ -12455.4968] [ 2223] [depth= 6] . ( 26 sec) [ -12435.1839] [ 2217] [depth= 3] . ( 26 sec) [ -12434.9167] [ 2219] [depth= 1] . ( 26 sec) [ -12434.5485] [ 2218] [depth= 1] . ( 27 sec) [ -12433.1228] [ 2218] [depth= 1] . ( 27 sec) [ -12430.0448] [ 2217] [depth= 1] . ( 27 sec) [ -12406.7621] [ 2220] [depth= 4] . ( 27 sec) [ -12400.7810] [ 2224] [depth= 1] . ( 28 sec) [ -12400.1155] [ 2223] [depth= 2] . ( 28 sec) [ -12399.7713] [ 2222] [depth= 1] . ( 29 sec) [ -12399.3479] [ 2221] [depth= 1] . ( 29 sec) [ -12395.5443] [ 2219] [depth= 3] . ( 29 sec) [ -12394.6644] [ 2219] [depth= 1] . ( 29 sec) [ -12391.1932] [ 2210] [depth= 3] . ( 30 sec) [ -12391.1369] [ 2210] [depth= 1] . ( 30 sec) [ -12389.1421] [ 2207] [depth= 1] . ( 30 sec) [ -12388.5396] [ 2206] [depth= 1] . ( 32 sec) [ -12387.2351] [ 2205] [depth= 1] . ( 32 sec) [ -12385.2718] [ 2204] [depth= 2] . ( 32 sec) [ -12382.2850] [ 2205] [depth= 1] . ( 33 sec) [ -12382.0727] [ 2205] [depth= 1] . ( 33 sec) [ -12381.8944] [ 2206] [depth= 1] . ( 33 sec) [ -12380.0167] [ 2210] [depth= 1] . ( 34 sec) [ -12379.0385] [ 2209] [depth= 1] . ( 35 sec) [ -12363.3820] [Branch lengths ] . ( 38 sec) [ -12361.7059] [GTR parameters ] . ( 38 sec) [ -12361.6121] [Alpha ][ 0.291133] . ( 39 sec) [ -12357.7257] [ 2211] [depth= 2] . ( 41 sec) [ -12357.1141] [ 2208] [depth= 1] . ( 43 sec) [ -12356.5441] [ 2208] [depth= 1] . ( 44 sec) [ -12356.2598] [ 2202] [depth= 1] . ( 45 sec) [ -12354.9326] [ 2202] [depth= 1] . ( 45 sec) [ -12354.3381] [ 2205] [depth= 1] . ( 46 sec) [ -12351.8779] [ 2207] [depth= 1] . ( 48 sec) [ -12351.8363] [ 2207] [depth= 1] . ( 51 sec) [ -12347.5096] [Branch lengths ] . ( 54 sec) [ -12347.3434] [GTR parameters ] . ( 54 sec) [ -12347.3432] [Alpha ][ 0.291424] . ( 64 sec) [ -12346.9434] [ 2203] [depth= 1] . ( 71 sec) [ -12346.3276] [Branch lengths ] . ( 73 sec) [ -12346.3037] [GTR parameters ] . ( 73 sec) [ -12346.3032] [Alpha ][ 0.291810] . ( 90 sec) [ -12346.2569] [Branch lengths ] . ( 159 sec) [ -12346.2536] [Branch lengths ] . ( 159 sec) [ -12346.2536] [Topology ] . ( 161 sec) [ -12346.2533] [Topology ] . ( 162 sec) [ -12346.2530] [GTR parameters ] . ( 162 sec) [ -12346.2529] [Alpha ][ 0.292102] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.252884. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -23361.0577] [GTR parameters ] . ( 1 sec) [ -22788.6712] [Alpha ][ 0.500960] . ( 1 sec) [ -22569.0177] [ 3972] [depth= 9] . ( 2 sec) [ -22429.5745] [ 3945] [depth= 8] . ( 2 sec) [ -22314.8196] [ 3919] [depth= 9] . ( 2 sec) [ -22157.5584] [ 3879] [depth= 1] . ( 2 sec) [ -22055.6904] [ 3873] [depth= 9] . ( 2 sec) [ -21780.3667] [ 3871] [depth= 1] . ( 2 sec) [ -21720.2686] [ 3859] [depth= 5] . ( 2 sec) [ -21658.9715] [ 3852] [depth= 1] . ( 2 sec) [ -21532.8719] [ 3855] [depth= 11] . ( 2 sec) [ -21464.7562] [ 3846] [depth= 6] . ( 2 sec) [ -21368.8017] [ 3837] [depth= 4] . ( 3 sec) [ -21103.5957] [ 3822] [depth= 16] . ( 3 sec) [ -20963.2782] [ 3788] [depth= 5] . ( 3 sec) [ -20792.7915] [ 3771] [depth= 3] . ( 3 sec) [ -20754.4434] [ 3784] [depth= 3] . ( 3 sec) [ -20658.7891] [ 3775] [depth= 15] . ( 3 sec) [ -20657.9450] [ 3765] [depth= 13] . ( 3 sec) [ -20436.8672] [ 3716] [depth= 11] . ( 3 sec) [ -20407.9899] [ 3684] [depth= 2] . ( 3 sec) [ -20402.2863] [ 3678] [depth= 11] . ( 4 sec) [ -19931.7965] [ 3603] [depth= 13] . ( 4 sec) [ -19878.7673] [ 3591] [depth= 12] . ( 4 sec) [ -19453.5828] [ 3596] [depth= 1] . ( 4 sec) [ -19143.4106] [ 3520] [depth= 13] . ( 4 sec) [ -18998.5359] [ 3481] [depth= 10] . ( 4 sec) [ -18864.4755] [ 3456] [depth= 10] . ( 4 sec) [ -18659.2971] [ 3415] [depth= 2] . ( 4 sec) [ -18646.3093] [ 3416] [depth= 9] . ( 4 sec) [ -18594.0589] [ 3414] [depth= 1] . ( 4 sec) [ -18543.7525] [ 3414] [depth= 2] . ( 5 sec) [ -18529.2489] [ 3413] [depth= 2] . ( 5 sec) [ -18468.8414] [ 3403] [depth= 4] . ( 5 sec) [ -18442.5236] [ 3398] [depth= 2] . ( 5 sec) [ -18118.4254] [ 3383] [depth= 4] . ( 5 sec) [ -18044.1074] [ 3363] [depth= 6] . ( 5 sec) [ -17947.8863] [ 3340] [depth= 2] . ( 5 sec) [ -17912.5382] [ 3337] [depth= 2] . ( 5 sec) [ -17858.9632] [ 3330] [depth= 1] . ( 5 sec) [ -17783.0319] [ 3332] [depth= 3] . ( 5 sec) [ -17656.7183] [ 3302] [depth= 7] . ( 6 sec) [ -17653.4348] [ 3302] [depth= 1] . ( 6 sec) [ -17528.4306] [ 3250] [depth= 3] . ( 6 sec) [ -17486.5880] [ 3241] [depth= 1] . ( 6 sec) [ -17439.8195] [ 3228] [depth= 15] . ( 6 sec) [ -17399.9538] [ 3217] [depth= 1] . ( 6 sec) [ -17399.0845] [ 3216] [depth= 1] . ( 6 sec) [ -17395.3623] [ 3217] [depth= 1] . ( 6 sec) [ -17384.6042] [ 3212] [depth= 1] . ( 7 sec) [ -17298.4757] [ 3188] [depth= 9] . ( 7 sec) [ -17226.5100] [ 3161] [depth= 3] . ( 7 sec) [ -17170.7911] [ 3154] [depth= 5] . ( 7 sec) [ -17041.1098] [ 3124] [depth= 8] . ( 7 sec) [ -16811.4364] [ 3080] [depth= 10] . ( 7 sec) [ -16692.7473] [ 3048] [depth= 6] . ( 7 sec) [ -16641.2126] [ 3030] [depth= 2] . ( 8 sec) [ -16639.9787] [ 3030] [depth= 1] . ( 8 sec) [ -16525.0752] [ 2993] [depth= 1] . ( 8 sec) [ -16524.2510] [ 2993] [depth= 1] . ( 8 sec) [ -16513.4978] [ 3001] [depth= 1] . ( 8 sec) [ -16075.3065] [ 2892] [depth= 13] . ( 8 sec) [ -15731.9208] [ 2845] [depth= 8] . ( 8 sec) [ -15600.5800] [ 2811] [depth= 2] . ( 8 sec) [ -15464.6379] [ 2801] [depth= 6] . ( 8 sec) [ -15156.3185] [ 2701] [depth= 12] . ( 9 sec) [ -15122.4192] [ 2675] [depth= 4] . ( 9 sec) [ -14992.9200] [ 2644] [depth= 2] . ( 9 sec) [ -14973.1490] [ 2642] [depth= 1] . ( 9 sec) [ -14922.7755] [ 2617] [depth= 9] . ( 9 sec) [ -14851.0618] [ 2639] [depth= 4] . ( 9 sec) [ -14836.8315] [ 2636] [depth= 1] . ( 9 sec) [ -14720.5093] [ 2599] [depth= 4] . ( 9 sec) [ -14702.9409] [ 2590] [depth= 1] . ( 10 sec) [ -14691.8513] [ 2581] [depth= 1] . ( 10 sec) [ -14591.1281] [ 2560] [depth= 3] . ( 10 sec) [ -14562.4163] [ 2553] [depth= 1] . ( 10 sec) [ -14511.7429] [ 2539] [depth= 3] . ( 10 sec) [ -14506.7251] [ 2538] [depth= 1] . ( 10 sec) [ -14488.6003] [ 2543] [depth= 3] . ( 10 sec) [ -14414.8454] [ 2517] [depth= 7] . ( 10 sec) [ -14398.6925] [ 2512] [depth= 2] . ( 10 sec) [ -14021.0428] [ 2491] [depth= 4] . ( 11 sec) [ -13930.7702] [ 2475] [depth= 1] . ( 11 sec) [ -13925.7053] [ 2472] [depth= 1] . ( 11 sec) [ -13885.3376] [ 2461] [depth= 7] . ( 11 sec) [ -13712.4020] [ 2429] [depth= 4] . ( 11 sec) [ -13646.8756] [ 2393] [depth= 1] . ( 11 sec) [ -13609.5906] [ 2383] [depth= 1] . ( 11 sec) [ -13475.1271] [ 2377] [depth= 2] . ( 12 sec) [ -13435.7627] [ 2372] [depth= 4] . ( 12 sec) [ -13425.8416] [ 2365] [depth= 4] . ( 12 sec) [ -13412.3531] [ 2355] [depth= 1] . ( 12 sec) [ -13409.5166] [ 2352] [depth= 2] . ( 12 sec) [ -13377.1351] [ 2343] [depth= 2] . ( 12 sec) [ -13291.3818] [ 2329] [depth= 6] . ( 13 sec) [ -13280.7488] [ 2344] [depth= 1] . ( 13 sec) [ -13197.0562] [ 2311] [depth= 4] . ( 13 sec) [ -13188.7372] [ 2309] [depth= 2] . ( 13 sec) [ -13150.1348] [ 2298] [depth= 3] . ( 13 sec) [ -13103.3392] [ 2278] [depth= 2] . ( 13 sec) [ -13082.4460] [ 2284] [depth= 2] . ( 13 sec) [ -13080.7845] [ 2274] [depth= 1] . ( 14 sec) [ -13062.7449] [ 2265] [depth= 1] . ( 14 sec) [ -13060.7695] [ 2265] [depth= 2] . ( 14 sec) [ -13006.8889] [ 2251] [depth= 3] . ( 14 sec) [ -12991.3850] [ 2252] [depth= 1] . ( 14 sec) [ -12989.3382] [ 2254] [depth= 2] . ( 14 sec) [ -12983.9701] [ 2253] [depth= 2] . ( 14 sec) [ -12981.5004] [ 2256] [depth= 1] . ( 14 sec) [ -12978.8045] [ 2259] [depth= 4] . ( 15 sec) [ -12977.7532] [ 2257] [depth= 1] . ( 15 sec) [ -12976.7427] [ 2257] [depth= 1] . ( 15 sec) [ -12970.5978] [ 2257] [depth= 1] . ( 15 sec) [ -12969.1927] [ 2265] [depth= 1] . ( 15 sec) [ -12968.8038] [ 2264] [depth= 2] . ( 15 sec) [ -12967.8878] [ 2261] [depth= 2] . ( 16 sec) [ -12964.1873] [ 2263] [depth= 1] . ( 17 sec) [ -12800.8740] [Branch lengths ] . ( 22 sec) [ -12595.6339] [GTR parameters ] . ( 22 sec) [ -12533.9649] [Alpha ][ 0.296928] . ( 23 sec) [ -12528.8587] [ 2262] [depth= 2] . ( 24 sec) [ -12507.8588] [ 2256] [depth= 1] . ( 24 sec) [ -12479.0717] [ 2247] [depth= 5] . ( 25 sec) [ -12478.8666] [ 2245] [depth= 1] . ( 26 sec) [ -12469.7011] [ 2241] [depth= 2] . ( 26 sec) [ -12467.9894] [ 2236] [depth= 1] . ( 26 sec) [ -12467.0915] [ 2237] [depth= 2] . ( 26 sec) [ -12463.9470] [ 2239] [depth= 1] . ( 27 sec) [ -12463.7050] [ 2233] [depth= 1] . ( 28 sec) [ -12461.7644] [ 2231] [depth= 1] . ( 29 sec) [ -12459.4603] [ 2229] [depth= 1] . ( 29 sec) [ -12458.4544] [ 2227] [depth= 1] . ( 29 sec) [ -12457.8568] [ 2231] [depth= 1] . ( 30 sec) [ -12455.6814] [ 2227] [depth= 1] . ( 30 sec) [ -12422.7744] [ 2214] [depth= 5] . ( 31 sec) [ -12417.4298] [ 2214] [depth= 2] . ( 32 sec) [ -12413.5129] [ 2212] [depth= 1] . ( 33 sec) [ -12409.8923] [ 2211] [depth= 1] . ( 34 sec) [ -12401.9734] [ 2213] [depth= 5] . ( 34 sec) [ -12396.6432] [ 2215] [depth= 1] . ( 34 sec) [ -12396.2066] [ 2209] [depth= 1] . ( 36 sec) [ -12395.3357] [ 2210] [depth= 1] . ( 36 sec) [ -12394.1353] [ 2210] [depth= 5] . ( 36 sec) [ -12392.2696] [ 2211] [depth= 1] . ( 36 sec) [ -12389.6869] [ 2208] [depth= 2] . ( 36 sec) [ -12387.3710] [ 2211] [depth= 1] . ( 39 sec) [ -12369.0766] [Branch lengths ] . ( 43 sec) [ -12366.9196] [GTR parameters ] . ( 43 sec) [ -12366.8569] [Alpha ][ 0.292344] . ( 44 sec) [ -12360.5143] [ 2207] [depth= 1] . ( 44 sec) [ -12359.3906] [ 2212] [depth= 1] . ( 44 sec) [ -12358.0173] [ 2214] [depth= 1] . ( 46 sec) [ -12355.4991] [ 2216] [depth= 2] . ( 47 sec) [ -12355.2728] [ 2216] [depth= 1] . ( 50 sec) [ -12354.6748] [ 2215] [depth= 1] . ( 55 sec) [ -12351.7009] [ 2208] [depth= 1] . ( 55 sec) [ -12350.9930] [ 2204] [depth= 1] . ( 58 sec) [ -12347.6316] [Branch lengths ] . ( 64 sec) [ -12347.4238] [GTR parameters ] . ( 64 sec) [ -12347.4230] [Alpha ][ 0.292847] . ( 83 sec) [ -12347.1010] [Branch lengths ] . ( 154 sec) [ -12347.0556] [Branch lengths ] . ( 154 sec) [ -12347.0556] [Topology ] . ( 156 sec) [ -12347.0180] [Topology ] . ( 158 sec) [ -12346.7693] [Topology ] . ( 159 sec) [ -12346.7276] [Topology ] . ( 161 sec) [ -12346.7164] [Topology ] . ( 163 sec) [ -12346.7132] [Topology ] . ( 165 sec) [ -12346.7123] [Topology ] . ( 165 sec) [ -12346.7123] [GTR parameters ] . ( 165 sec) [ -12346.7116] [Alpha ][ 0.293298] . ( 165 sec) [ -12346.7116] [Topology ] . ( 167 sec) [ -12346.7113] [Topology ] . ( 168 sec) [ -12346.7058] [GTR parameters ] . ( 168 sec) [ -12346.7058] [Alpha ][ 0.293298] . ( 169 sec) [ -12346.7058] [Topology ] . ( 170 sec) [ -12346.7056] [Topology ] . ( 171 sec) [ -12346.7056] [GTR parameters ] . ( 171 sec) [ -12346.7056] [Alpha ][ 0.293298] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -12346.2936] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.293608. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -24861.7357] [GTR parameters ] . ( 2 sec) [ -24283.7910] [Alpha ][ 0.500960] . ( 2 sec) [ -24054.9914] [ 3973] [depth= 6] . ( 2 sec) [ -23808.4447] [ 3943] [depth= 10] . ( 2 sec) [ -23669.6442] [ 3938] [depth= 1] . ( 2 sec) [ -23644.0015] [ 3928] [depth= 10] . ( 2 sec) [ -21792.8415] [ 3895] [depth= 4] . ( 3 sec) [ -21457.2947] [ 3892] [depth= 2] . ( 3 sec) [ -21389.1761] [ 3890] [depth= 1] . ( 3 sec) [ -21283.7966] [ 3872] [depth= 10] . ( 3 sec) [ -21189.5089] [ 3850] [depth= 3] . ( 3 sec) [ -21055.0280] [ 3834] [depth= 13] . ( 3 sec) [ -20998.1094] [ 3818] [depth= 6] . ( 3 sec) [ -20984.9941] [ 3816] [depth= 6] . ( 3 sec) [ -20876.9083] [ 3782] [depth= 9] . ( 3 sec) [ -20871.5724] [ 3777] [depth= 1] . ( 3 sec) [ -20818.2522] [ 3766] [depth= 2] . ( 3 sec) [ -20634.2017] [ 3723] [depth= 12] . ( 4 sec) [ -20571.7163] [ 3721] [depth= 1] . ( 4 sec) [ -20460.4592] [ 3687] [depth= 7] . ( 4 sec) [ -20410.5893] [ 3688] [depth= 1] . ( 4 sec) [ -20129.5626] [ 3620] [depth= 11] . ( 4 sec) [ -20058.2747] [ 3604] [depth= 1] . ( 4 sec) [ -19855.5457] [ 3564] [depth= 6] . ( 4 sec) [ -19766.8007] [ 3535] [depth= 7] . ( 4 sec) [ -19621.7713] [ 3510] [depth= 13] . ( 4 sec) [ -19611.0322] [ 3510] [depth= 4] . ( 4 sec) [ -19526.2583] [ 3491] [depth= 8] . ( 4 sec) [ -19491.4173] [ 3487] [depth= 4] . ( 5 sec) [ -19293.6624] [ 3470] [depth= 18] . ( 5 sec) [ -19280.4896] [ 3487] [depth= 19] . ( 5 sec) [ -19121.4554] [ 3418] [depth= 1] . ( 5 sec) [ -19082.2178] [ 3398] [depth= 1] . ( 5 sec) [ -18980.1196] [ 3394] [depth= 1] . ( 5 sec) [ -18710.5189] [ 3375] [depth= 17] . ( 5 sec) [ -18117.2777] [ 3266] [depth= 6] . ( 5 sec) [ -17957.8315] [ 3266] [depth= 2] . ( 5 sec) [ -17909.0594] [ 3254] [depth= 12] . ( 6 sec) [ -17824.4902] [ 3250] [depth= 1] . ( 6 sec) [ -17813.3441] [ 3248] [depth= 2] . ( 6 sec) [ -17770.8909] [ 3275] [depth= 5] . ( 6 sec) [ -17710.0020] [ 3244] [depth= 18] . ( 6 sec) [ -17689.8994] [ 3239] [depth= 1] . ( 6 sec) [ -17601.6559] [ 3214] [depth= 8] . ( 6 sec) [ -17463.2573] [ 3203] [depth= 3] . ( 6 sec) [ -17337.5649] [ 3180] [depth= 3] . ( 6 sec) [ -17316.6282] [ 3180] [depth= 1] . ( 6 sec) [ -17246.2300] [ 3177] [depth= 11] . ( 7 sec) [ -17191.6080] [ 3163] [depth= 1] . ( 7 sec) [ -17115.7320] [ 3133] [depth= 7] . ( 7 sec) [ -17043.4621] [ 3132] [depth= 1] . ( 7 sec) [ -16881.1753] [ 3084] [depth= 16] . ( 7 sec) [ -16876.9793] [ 3083] [depth= 1] . ( 7 sec) [ -16824.9076] [ 3081] [depth= 4] . ( 7 sec) [ -16648.1760] [ 3033] [depth= 8] . ( 7 sec) [ -16594.4543] [ 3035] [depth= 1] . ( 7 sec) [ -16571.0320] [ 3030] [depth= 1] . ( 8 sec) [ -16390.4972] [ 2999] [depth= 2] . ( 8 sec) [ -16381.7065] [ 2994] [depth= 4] . ( 8 sec) [ -16313.0895] [ 2991] [depth= 9] . ( 8 sec) [ -16306.7795] [ 2986] [depth= 10] . ( 8 sec) [ -16183.2806] [ 2960] [depth= 11] . ( 8 sec) [ -16169.1320] [ 2956] [depth= 1] . ( 8 sec) [ -16160.5388] [ 2954] [depth= 1] . ( 8 sec) [ -16160.4425] [ 2956] [depth= 1] . ( 8 sec) [ -16028.9160] [ 2918] [depth= 11] . ( 8 sec) [ -16020.1729] [ 2914] [depth= 3] . ( 8 sec) [ -15885.8790] [ 2929] [depth= 2] . ( 9 sec) [ -15772.9506] [ 2863] [depth= 13] . ( 9 sec) [ -15750.1254] [ 2865] [depth= 1] . ( 9 sec) [ -15733.9171] [ 2863] [depth= 3] . ( 9 sec) [ -15665.1419] [ 2838] [depth= 12] . ( 9 sec) [ -15660.3494] [ 2836] [depth= 1] . ( 9 sec) [ -15657.1057] [ 2838] [depth= 2] . ( 9 sec) [ -15525.1096] [ 2777] [depth= 22] . ( 9 sec) [ -15515.5832] [ 2776] [depth= 1] . ( 10 sec) [ -15386.7346] [ 2735] [depth= 3] . ( 10 sec) [ -15305.0080] [ 2726] [depth= 1] . ( 10 sec) [ -15293.1043] [ 2730] [depth= 1] . ( 10 sec) [ -15232.4445] [ 2719] [depth= 15] . ( 10 sec) [ -15023.9046] [ 2654] [depth= 12] . ( 10 sec) [ -14906.5756] [ 2643] [depth= 10] . ( 10 sec) [ -14879.4683] [ 2648] [depth= 1] . ( 10 sec) [ -14835.3922] [ 2644] [depth= 1] . ( 10 sec) [ -14719.7243] [ 2635] [depth= 3] . ( 11 sec) [ -14706.4295] [ 2630] [depth= 1] . ( 11 sec) [ -14705.9554] [ 2632] [depth= 1] . ( 11 sec) [ -14559.7247] [ 2609] [depth= 13] . ( 11 sec) [ -14531.1306] [ 2603] [depth= 4] . ( 11 sec) [ -14519.5305] [ 2597] [depth= 1] . ( 11 sec) [ -14471.1254] [ 2586] [depth= 1] . ( 11 sec) [ -14453.8905] [ 2576] [depth= 8] . ( 11 sec) [ -14402.0962] [ 2566] [depth= 1] . ( 12 sec) [ -14354.6877] [ 2566] [depth= 2] . ( 12 sec) [ -14261.0925] [ 2558] [depth= 3] . ( 12 sec) [ -14175.8244] [ 2529] [depth= 1] . ( 12 sec) [ -14136.7819] [ 2526] [depth= 3] . ( 12 sec) [ -14002.3977] [ 2499] [depth= 1] . ( 12 sec) [ -13959.3401] [ 2466] [depth= 7] . ( 12 sec) [ -13930.1423] [ 2462] [depth= 3] . ( 12 sec) [ -13869.2504] [ 2460] [depth= 3] . ( 12 sec) [ -13863.5702] [ 2453] [depth= 1] . ( 13 sec) [ -13846.7886] [ 2452] [depth= 2] . ( 13 sec) [ -13838.5465] [ 2443] [depth= 6] . ( 13 sec) [ -13837.6286] [ 2447] [depth= 1] . ( 13 sec) [ -13786.6024] [ 2449] [depth= 11] . ( 13 sec) [ -13778.0065] [ 2442] [depth= 1] . ( 13 sec) [ -13725.5719] [ 2428] [depth= 1] . ( 13 sec) [ -13674.3883] [ 2426] [depth= 1] . ( 13 sec) [ -13664.4713] [ 2423] [depth= 1] . ( 13 sec) [ -13647.3166] [ 2413] [depth= 14] . ( 14 sec) [ -13589.8382] [ 2389] [depth= 4] . ( 14 sec) [ -13588.1540] [ 2392] [depth= 1] . ( 14 sec) [ -13585.8230] [ 2397] [depth= 1] . ( 14 sec) [ -13581.9826] [ 2396] [depth= 1] . ( 14 sec) [ -13542.4624] [ 2378] [depth= 2] . ( 14 sec) [ -13533.2605] [ 2376] [depth= 1] . ( 14 sec) [ -13529.7467] [ 2374] [depth= 1] . ( 14 sec) [ -13467.1615] [ 2359] [depth= 1] . ( 14 sec) [ -13464.2454] [ 2366] [depth= 1] . ( 14 sec) [ -13445.9586] [ 2352] [depth= 3] . ( 15 sec) [ -13417.3791] [ 2344] [depth= 2] . ( 15 sec) [ -13416.3655] [ 2372] [depth= 1] . ( 15 sec) [ -13395.4426] [ 2370] [depth= 1] . ( 15 sec) [ -13394.1745] [ 2371] [depth= 3] . ( 15 sec) [ -13352.9729] [ 2342] [depth= 1] . ( 15 sec) [ -13336.9064] [ 2335] [depth= 1] . ( 15 sec) [ -13272.0086] [ 2319] [depth= 1] . ( 15 sec) [ -13221.1149] [ 2303] [depth= 1] . ( 16 sec) [ -13215.2962] [ 2302] [depth= 1] . ( 16 sec) [ -13212.3578] [ 2307] [depth= 2] . ( 16 sec) [ -13175.6951] [ 2300] [depth= 1] . ( 17 sec) [ -12995.0273] [Branch lengths ] . ( 21 sec) [ -12749.3685] [GTR parameters ] . ( 21 sec) [ -12687.0977] [Alpha ][ 0.293089] . ( 21 sec) [ -12678.5948] [ 2292] [depth= 1] . ( 21 sec) [ -12653.6168] [ 2281] [depth= 3] . ( 22 sec) [ -12628.4491] [ 2267] [depth= 6] . ( 22 sec) [ -12628.0033] [ 2268] [depth= 1] . ( 22 sec) [ -12615.1903] [ 2262] [depth= 2] . ( 22 sec) [ -12599.9900] [ 2255] [depth= 2] . ( 22 sec) [ -12593.8908] [ 2255] [depth= 1] . ( 22 sec) [ -12580.0517] [ 2248] [depth= 3] . ( 23 sec) [ -12545.0622] [ 2239] [depth= 1] . ( 23 sec) [ -12544.5709] [ 2240] [depth= 1] . ( 24 sec) [ -12542.2155] [ 2239] [depth= 2] . ( 24 sec) [ -12530.7876] [ 2237] [depth= 3] . ( 24 sec) [ -12529.1937] [ 2237] [depth= 1] . ( 25 sec) [ -12527.6474] [ 2237] [depth= 1] . ( 25 sec) [ -12527.6272] [ 2239] [depth= 2] . ( 26 sec) [ -12512.0609] [ 2234] [depth= 5] . ( 26 sec) [ -12496.7616] [ 2224] [depth= 10] . ( 26 sec) [ -12493.5750] [ 2225] [depth= 1] . ( 26 sec) [ -12445.6504] [ 2210] [depth= 2] . ( 27 sec) [ -12444.4066] [ 2214] [depth= 1] . ( 27 sec) [ -12444.3393] [ 2214] [depth= 1] . ( 28 sec) [ -12440.2907] [ 2213] [depth= 1] . ( 28 sec) [ -12421.9273] [ 2210] [depth= 1] . ( 29 sec) [ -12421.8457] [ 2210] [depth= 1] . ( 29 sec) [ -12421.0940] [ 2211] [depth= 1] . ( 30 sec) [ -12420.9576] [ 2210] [depth= 1] . ( 30 sec) [ -12408.8418] [ 2206] [depth= 4] . ( 30 sec) [ -12405.8414] [ 2214] [depth= 3] . ( 31 sec) [ -12404.9333] [ 2214] [depth= 1] . ( 31 sec) [ -12404.7391] [ 2215] [depth= 1] . ( 31 sec) [ -12404.2528] [ 2215] [depth= 1] . ( 32 sec) [ -12403.9349] [ 2214] [depth= 1] . ( 32 sec) [ -12403.2534] [ 2214] [depth= 1] . ( 33 sec) [ -12402.2334] [ 2216] [depth= 2] . ( 34 sec) [ -12394.6874] [ 2208] [depth= 4] . ( 34 sec) [ -12364.1710] [Branch lengths ] . ( 38 sec) [ -12361.1647] [GTR parameters ] . ( 38 sec) [ -12361.1463] [Alpha ][ 0.290408] . ( 39 sec) [ -12361.1060] [ 2209] [depth= 1] . ( 39 sec) [ -12360.8399] [ 2208] [depth= 1] . ( 42 sec) [ -12356.5012] [ 2204] [depth= 2] . ( 46 sec) [ -12354.7885] [ 2207] [depth= 1] . ( 46 sec) [ -12353.9905] [ 2208] [depth= 1] . ( 48 sec) [ -12351.9872] [ 2209] [depth= 1] . ( 52 sec) [ -12351.4015] [ 2205] [depth= 1] . ( 54 sec) [ -12347.0720] [Branch lengths ] . ( 55 sec) [ -12347.0288] [GTR parameters ] . ( 55 sec) [ -12347.0277] [Alpha ][ 0.290993] . ( 74 sec) [ -12346.6710] [Branch lengths ] . ( 143 sec) [ -12346.6193] [Branch lengths ] . ( 143 sec) [ -12346.6193] [Topology ] . ( 145 sec) [ -12346.5771] [Topology ] . ( 147 sec) [ -12346.3275] [Topology ] . ( 149 sec) [ -12346.2858] [Topology ] . ( 151 sec) [ -12346.2747] [Topology ] . ( 152 sec) [ -12346.2716] [Topology ] . ( 154 sec) [ -12346.2707] [Topology ] . ( 156 sec) [ -12346.2568] [GTR parameters ] . ( 157 sec) [ -12346.2537] [Alpha ][ 0.292011] . ( 157 sec) [ -12346.2537] [Topology ] . ( 158 sec) [ -12346.2530] [Topology ] . ( 159 sec) [ -12346.2530] [GTR parameters ] . ( 159 sec) [ -12346.2530] [Alpha ][ 0.292011] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12346.252987. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -12871.6129] [GTR parameters ] . ( 4 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 4 sec) [ -12665.7546] [Topology ] . ( 6 sec) [ -12467.2258] [Topology ] . ( 8 sec) [ -12431.6435] [Topology ] . ( 9 sec) [ -12420.9779] [Topology ] . ( 11 sec) [ -12417.1150] [Topology ] . ( 13 sec) [ -12415.5191] [Topology ] . ( 15 sec) [ -12414.8202] [Topology ] . ( 16 sec) [ -12414.5047] [Topology ] . ( 18 sec) [ -12414.3440] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -12413.0509] [Topology ] . ( 34 sec) [ -12409.7217] [GTR parameters ] . ( 35 sec) [ -12350.3670] [Alpha ][ 0.296953] . ( 35 sec) [ -12350.3670] [Topology ] . ( 36 sec) [ -12349.1010] [Topology ] . ( 38 sec) [ -12348.8323] [Topology ] . ( 40 sec) [ -12348.7770] [Topology ] . ( 42 sec) [ -12348.7575] [Topology ] . ( 44 sec) [ -12348.7485] [Topology ] . ( 45 sec) [ -12348.7439] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -12348.4350] [Topology ] . ( 61 sec) [ -12348.0258] [GTR parameters ] . ( 62 sec) [ -12347.9937] [Alpha ][ 0.293713] . ( 62 sec) [ -12347.9937] [Topology ] . ( 63 sec) [ -12347.9651] [Topology ] . ( 65 sec) [ -12347.9570] [Topology ] . ( 67 sec) [ -12347.9532] [Topology ] . ( 69 sec) [ -12347.9512] [Topology ] . ( 70 sec) [ -12347.9501] [Topology ] . ( 72 sec) [ -12347.9495] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -12347.8637] [Topology ] . ( 86 sec) [ -12347.8612] [GTR parameters ] . ( 87 sec) [ -12347.8612] [Alpha ][ 0.293713] . ( 87 sec) [ -12347.8612] [Topology ] . ( 88 sec) [ -12347.8510] [Topology ] . ( 90 sec) [ -12347.8483] [Topology ] . ( 92 sec) [ -12347.8471] [Topology ] . ( 94 sec) [ -12347.8465] [Topology ] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -12347.8461] [GTR parameters ] . ( 108 sec) [ -12347.8461] [Alpha ][ 0.293713] . ( 109 sec) [ -12347.8461] [Topology ] . ( 110 sec) [ -12347.8457] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 141 sec) [ -12871.6129] [GTR parameters ] . ( 141 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 141 sec) [ -12665.5249] [ 2217] [depth= 1] . ( 142 sec) [ -12664.1456] [ 2216] [depth= 1] . ( 142 sec) [ -12663.3354] [ 2216] [depth= 1] . ( 143 sec) [ -12661.6311] [ 2218] [depth= 2] . ( 143 sec) [ -12661.0790] [ 2219] [depth= 1] . ( 143 sec) [ -12653.9924] [ 2215] [depth= 1] . ( 143 sec) [ -12652.7357] [ 2219] [depth= 1] . ( 144 sec) [ -12650.1454] [ 2220] [depth= 1] . ( 144 sec) [ -12650.0086] [ 2219] [depth= 1] . ( 144 sec) [ -12648.4386] [ 2216] [depth= 2] . ( 144 sec) [ -12634.9783] [ 2220] [depth= 1] . ( 144 sec) [ -12633.2061] [ 2217] [depth= 1] . ( 144 sec) [ -12632.7527] [ 2218] [depth= 1] . ( 145 sec) [ -12620.6039] [ 2214] [depth= 1] . ( 145 sec) [ -12617.7329] [ 2214] [depth= 1] . ( 146 sec) [ -12617.3662] [ 2215] [depth= 1] . ( 147 sec) [ -12612.2385] [ 2218] [depth= 1] . ( 147 sec) [ -12612.1646] [ 2218] [depth= 1] . ( 147 sec) [ -12609.2459] [ 2215] [depth= 1] . ( 147 sec) [ -12608.8805] [ 2214] [depth= 2] . ( 147 sec) [ -12601.4986] [ 2210] [depth= 1] . ( 148 sec) [ -12599.7595] [ 2212] [depth= 1] . ( 148 sec) [ -12597.2574] [ 2210] [depth= 1] . ( 148 sec) [ -12593.6539] [ 2209] [depth= 1] . ( 148 sec) [ -12591.8308] [ 2210] [depth= 1] . ( 148 sec) [ -12589.3679] [ 2207] [depth= 6] . ( 149 sec) [ -12581.3551] [ 2209] [depth= 1] . ( 149 sec) [ -12570.3569] [ 2207] [depth= 1] . ( 149 sec) [ -12570.3300] [ 2210] [depth= 1] . ( 149 sec) [ -12566.7592] [ 2210] [depth= 1] . ( 149 sec) [ -12564.5110] [ 2210] [depth= 1] . ( 150 sec) [ -12555.9968] [ 2212] [depth= 1] . ( 150 sec) [ -12548.2701] [ 2210] [depth= 1] . ( 150 sec) [ -12546.6607] [ 2212] [depth= 1] . ( 150 sec) [ -12538.8293] [ 2210] [depth= 1] . ( 151 sec) [ -12533.6674] [ 2213] [depth= 1] . ( 152 sec) [ -12531.1873] [ 2211] [depth= 1] . ( 153 sec) [ -12433.6326] [Branch lengths ] . ( 156 sec) [ -12431.2092] [GTR parameters ] . ( 156 sec) [ -12369.5247] [Alpha ][ 0.289385] . ( 158 sec) [ -12368.6080] [ 2212] [depth= 1] . ( 159 sec) [ -12368.1523] [ 2211] [depth= 1] . ( 159 sec) [ -12368.0217] [ 2213] [depth= 1] . ( 161 sec) [ -12366.5513] [ 2212] [depth= 1] . ( 163 sec) [ -12364.6889] [ 2211] [depth= 1] . ( 163 sec) [ -12364.6608] [ 2211] [depth= 1] . ( 165 sec) [ -12361.5436] [ 2206] [depth= 6] . ( 172 sec) [ -12351.1994] [Branch lengths ] . ( 174 sec) [ -12350.6970] [GTR parameters ] . ( 174 sec) [ -12350.6675] [Alpha ][ 0.292660] . ( 176 sec) [ -12350.2335] [ 2206] [depth= 2] . ( 177 sec) [ -12350.1842] [ 2202] [depth= 1] . ( 191 sec) [ -12347.5370] [Branch lengths ] . ( 193 sec) [ -12347.3568] [GTR parameters ] . ( 193 sec) [ -12347.3566] [Alpha ][ 0.292338] . ( 210 sec) [ -12347.0564] [Branch lengths ] . ( 281 sec) [ -12347.0003] [Branch lengths ] . ( 281 sec) [ -12347.0003] [Topology ] . ( 283 sec) [ -12346.9930] [Topology ] . ( 285 sec) [ -12346.9851] [Topology ] . ( 286 sec) [ -12346.9460] [Topology ] . ( 288 sec) [ -12346.7774] [Topology ] . ( 290 sec) [ -12346.7270] [Topology ] . ( 292 sec) [ -12346.7178] [Topology ] . ( 293 sec) [ -12346.7115] [GTR parameters ] . ( 294 sec) [ -12346.7093] [Alpha ][ 0.293194] . ( 294 sec) [ -12346.7093] [Topology ] . ( 295 sec) [ -12346.7067] [Topology ] . ( 297 sec) [ -12346.7058] [Topology ] . ( 297 sec) [ -12346.7058] [GTR parameters ] . ( 298 sec) [ -12346.7058] [Alpha ][ 0.293194] . ( 298 sec) [ -12346.7058] [Topology ] . ( 300 sec) [ -12346.7054] [Topology ] . ( 300 sec) [ -12346.7054] [GTR parameters ] . ( 300 sec) [ -12346.7054] [Alpha ][ 0.293194] . Checking for NNIs, optimizing five branches... . ( 313 sec) [ -12346.2906] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12347.845692 . Log likelihood obtained after SPR moves : -12346.290635 . Log likelihood of the current tree: -12346.290635. . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Best log likelihood : -12346.252884 . Time used 0h5m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1205.54user 0.00system 20:13.50elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps