.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data20.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... . 419 patterns found. (out of a total of 500 sites) . 77 sites without polymorphism (15.40%). . [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) [ -18084.0987] [GTR parameters ] . ( 1 sec) [ -17778.9903] [Alpha ][ 0.500960] . ( 1 sec) [ -17585.1184] [ 3942] [depth= 8] . ( 1 sec) [ -17325.2313] [ 3895] [depth= 6] . ( 1 sec) [ -17277.8130] [ 3884] [depth= 2] . ( 1 sec) [ -17232.3179] [ 3884] [depth= 7] . ( 1 sec) [ -17181.5906] [ 3873] [depth= 3] . ( 1 sec) [ -17115.4801] [ 3871] [depth= 5] . ( 1 sec) [ -17077.9630] [ 3856] [depth= 5] . ( 1 sec) [ -16983.8633] [ 3848] [depth= 1] . ( 1 sec) [ -16964.3116] [ 3847] [depth= 1] . ( 1 sec) [ -16845.7841] [ 3770] [depth= 8] . ( 1 sec) [ -16818.9959] [ 3802] [depth= 1] . ( 1 sec) [ -16661.7699] [ 3805] [depth= 10] . ( 1 sec) [ -16599.1716] [ 3759] [depth= 4] . ( 1 sec) [ -16224.1550] [ 3672] [depth= 4] . ( 1 sec) [ -16149.9391] [ 3668] [depth= 1] . ( 1 sec) [ -16053.7015] [ 3658] [depth= 3] . ( 1 sec) [ -15945.1519] [ 3636] [depth= 4] . ( 1 sec) [ -15851.9794] [ 3630] [depth= 6] . ( 2 sec) [ -15777.5273] [ 3619] [depth= 3] . ( 2 sec) [ -15693.7648] [ 3620] [depth= 1] . ( 2 sec) [ -15581.3251] [ 3533] [depth= 3] . ( 2 sec) [ -15469.3338] [ 3471] [depth= 1] . ( 2 sec) [ -15111.1593] [ 3447] [depth= 13] . ( 2 sec) [ -14916.5330] [ 3357] [depth= 1] . ( 2 sec) [ -14766.9200] [ 3312] [depth= 13] . ( 2 sec) [ -14739.2718] [ 3311] [depth= 1] . ( 2 sec) [ -14675.3173] [ 3309] [depth= 2] . ( 2 sec) [ -14631.3505] [ 3293] [depth= 2] . ( 2 sec) [ -14595.4781] [ 3275] [depth= 9] . ( 2 sec) [ -14523.0029] [ 3268] [depth= 1] . ( 2 sec) [ -14507.5658] [ 3267] [depth= 1] . ( 2 sec) [ -14498.7487] [ 3264] [depth= 1] . ( 2 sec) [ -14439.6523] [ 3237] [depth= 3] . ( 2 sec) [ -14433.7310] [ 3236] [depth= 1] . ( 2 sec) [ -14428.6756] [ 3236] [depth= 1] . ( 2 sec) [ -14425.5025] [ 3236] [depth= 1] . ( 2 sec) [ -14204.7272] [ 3224] [depth= 9] . ( 2 sec) [ -13991.9326] [ 3134] [depth= 9] . ( 2 sec) [ -13989.3339] [ 3141] [depth= 5] . ( 3 sec) [ -13956.4197] [ 3131] [depth= 1] . ( 3 sec) [ -13489.2474] [ 3096] [depth= 3] . ( 3 sec) [ -13308.3679] [ 3078] [depth= 2] . ( 3 sec) [ -13128.8100] [ 3064] [depth= 12] . ( 3 sec) [ -13020.0109] [ 3005] [depth= 1] . ( 3 sec) [ -12969.9756] [ 2967] [depth= 6] . ( 3 sec) [ -12808.6866] [ 2921] [depth= 11] . ( 3 sec) [ -12748.5092] [ 2900] [depth= 2] . ( 3 sec) [ -12420.0997] [ 2827] [depth= 2] . ( 3 sec) [ -12298.4789] [ 2779] [depth= 1] . ( 3 sec) [ -12107.1644] [ 2744] [depth= 3] . ( 3 sec) [ -12064.9169] [ 2727] [depth= 8] . ( 3 sec) [ -12027.0924] [ 2711] [depth= 1] . ( 3 sec) [ -11989.3571] [ 2714] [depth= 8] . ( 3 sec) [ -11878.8104] [ 2718] [depth= 4] . ( 3 sec) [ -11875.4957] [ 2716] [depth= 10] . ( 3 sec) [ -11823.1730] [ 2688] [depth= 3] . ( 3 sec) [ -11818.4313] [ 2690] [depth= 2] . ( 4 sec) [ -11746.2146] [ 2676] [depth= 6] . ( 4 sec) [ -11707.9419] [ 2640] [depth= 6] . ( 4 sec) [ -11546.4475] [ 2578] [depth= 1] . ( 4 sec) [ -11530.0342] [ 2575] [depth= 1] . ( 4 sec) [ -11282.5227] [ 2563] [depth= 5] . ( 4 sec) [ -11124.2224] [ 2502] [depth= 6] . ( 4 sec) [ -11118.6626] [ 2502] [depth= 1] . ( 4 sec) [ -11011.1223] [ 2426] [depth= 9] . ( 4 sec) [ -10896.1063] [ 2406] [depth= 1] . ( 4 sec) [ -10888.7953] [ 2405] [depth= 1] . ( 4 sec) [ -10858.1412] [ 2394] [depth= 3] . ( 4 sec) [ -10857.6051] [ 2393] [depth= 1] . ( 4 sec) [ -10855.1989] [ 2404] [depth= 3] . ( 4 sec) [ -10829.4834] [ 2400] [depth= 2] . ( 4 sec) [ -10697.4152] [ 2402] [depth= 1] . ( 4 sec) [ -10692.0864] [ 2402] [depth= 1] . ( 4 sec) [ -10584.0634] [ 2371] [depth= 4] . ( 4 sec) [ -10487.6877] [ 2357] [depth= 5] . ( 4 sec) [ -10439.4744] [ 2351] [depth= 1] . ( 4 sec) [ -10264.3650] [ 2287] [depth= 7] . ( 5 sec) [ -10218.4926] [ 2275] [depth= 1] . ( 5 sec) [ -10218.0733] [ 2273] [depth= 4] . ( 5 sec) [ -10078.3417] [ 2272] [depth= 2] . ( 5 sec) [ -9971.6691] [Branch lengths ] . ( 5 sec) [ -9967.6275] [GTR parameters ] . ( 5 sec) [ -9942.4337] [Alpha ][ 0.819428] . ( 6 sec) [ -9936.8032] [ 2264] [depth= 2] . ( 6 sec) [ -9936.7212] [ 2269] [depth= 1] . ( 6 sec) [ -9896.3506] [ 2248] [depth= 1] . ( 6 sec) [ -9896.3266] [ 2250] [depth= 1] . ( 6 sec) [ -9896.2467] [ 2248] [depth= 1] . ( 6 sec) [ -9879.0961] [ 2239] [depth= 4] . ( 6 sec) [ -9845.7292] [ 2214] [depth= 1] . ( 6 sec) [ -9842.3306] [ 2214] [depth= 1] . ( 6 sec) [ -9832.6110] [ 2213] [depth= 1] . ( 6 sec) [ -9824.0619] [ 2216] [depth= 3] . ( 7 sec) [ -9823.5780] [ 2213] [depth= 1] . ( 7 sec) [ -9822.8848] [ 2214] [depth= 1] . ( 7 sec) [ -9822.7091] [ 2209] [depth= 2] . ( 7 sec) [ -9821.2368] [ 2209] [depth= 1] . ( 7 sec) [ -9819.3815] [ 2211] [depth= 1] . ( 7 sec) [ -9818.8241] [ 2209] [depth= 1] . ( 8 sec) [ -9817.2709] [ 2212] [depth= 1] . ( 8 sec) [ -9802.2656] [ 2209] [depth= 2] . ( 8 sec) [ -9802.1242] [ 2207] [depth= 1] . ( 8 sec) [ -9800.5700] [ 2201] [depth= 1] . ( 8 sec) [ -9799.8759] [ 2203] [depth= 1] . ( 8 sec) [ -9798.4837] [ 2208] [depth= 2] . ( 9 sec) [ -9798.0109] [ 2208] [depth= 1] . ( 9 sec) [ -9796.4721] [ 2194] [depth= 1] . ( 9 sec) [ -9780.2254] [Branch lengths ] . ( 9 sec) [ -9779.9509] [GTR parameters ] . ( 9 sec) [ -9779.3100] [Alpha ][ 0.888056] . ( 10 sec) [ -9779.2570] [ 2198] [depth= 1] . ( 10 sec) [ -9777.3122] [ 2198] [depth= 1] . ( 10 sec) [ -9777.2468] [ 2199] [depth= 1] . ( 10 sec) [ -9776.6256] [ 2197] [depth= 1] . ( 11 sec) [ -9776.6001] [ 2197] [depth= 1] . ( 11 sec) [ -9776.2390] [ 2199] [depth= 1] . ( 11 sec) [ -9758.5847] [ 2175] [depth= 2] . ( 12 sec) [ -9754.0864] [ 2172] [depth= 1] . ( 12 sec) [ -9754.0741] [ 2171] [depth= 1] . ( 12 sec) [ -9753.3022] [ 2176] [depth= 1] . ( 13 sec) [ -9753.1462] [ 2176] [depth= 1] . ( 13 sec) [ -9753.1350] [ 2175] [depth= 1] . ( 13 sec) [ -9749.5693] [Branch lengths ] . ( 13 sec) [ -9749.5357] [GTR parameters ] . ( 13 sec) [ -9749.4482] [Alpha ][ 0.914661] . ( 14 sec) [ -9748.2970] [ 2170] [depth= 1] . ( 17 sec) [ -9746.8576] [Branch lengths ] . ( 17 sec) [ -9746.8536] [GTR parameters ] . ( 17 sec) [ -9746.8474] [Alpha ][ 0.922029] . ( 21 sec) [ -9746.7081] [Branch lengths ] . ( 41 sec) [ -9746.5399] [ 2170] [depth= 1] . ( 44 sec) [ -9746.4898] [Branch lengths ] . ( 44 sec) [ -9746.4883] [GTR parameters ] . ( 44 sec) [ -9746.4858] [Alpha ][ 0.926678] . ( 44 sec) [ -9746.4858] [Topology ] . ( 45 sec) [ -9746.4793] [Topology ] . ( 46 sec) [ -9746.4772] [Topology ] . ( 46 sec) [ -9746.4760] [Topology ] . ( 47 sec) [ -9746.4754] [Topology ] . ( 47 sec) [ -9746.4754] [GTR parameters ] . ( 47 sec) [ -9746.4753] [Alpha ][ 0.927605] . ( 47 sec) [ -9746.4753] [Topology ] . ( 48 sec) [ -9746.4749] [Topology ] . ( 48 sec) [ -9746.4749] [GTR parameters ] . ( 48 sec) [ -9746.4749] [Alpha ][ 0.927605] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -9746.4741] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -9746.4739] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9746.473894. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21088.6802] [GTR parameters ] . ( 1 sec) [ -20787.1432] [Alpha ][ 0.500960] . ( 2 sec) [ -20580.4501] [ 3829] [depth= 4] . ( 2 sec) [ -20372.8824] [ 3782] [depth= 3] . ( 2 sec) [ -20305.6464] [ 3730] [depth= 3] . ( 2 sec) [ -20129.2816] [ 3719] [depth= 2] . ( 2 sec) [ -20015.2553] [ 3677] [depth= 1] . ( 2 sec) [ -16581.4223] [ 3666] [depth= 7] . ( 2 sec) [ -16489.4790] [ 3649] [depth= 3] . ( 2 sec) [ -16471.8044] [ 3606] [depth= 1] . ( 2 sec) [ -16378.2293] [ 3584] [depth= 1] . ( 2 sec) [ -16279.8241] [ 3556] [depth= 9] . ( 2 sec) [ -16251.7104] [ 3555] [depth= 1] . ( 2 sec) [ -16212.4780] [ 3544] [depth= 6] . ( 2 sec) [ -15973.2441] [ 3506] [depth= 1] . ( 2 sec) [ -15918.7267] [ 3479] [depth= 11] . ( 2 sec) [ -15731.4810] [ 3453] [depth= 7] . ( 2 sec) [ -15477.2786] [ 3439] [depth= 2] . ( 2 sec) [ -15382.1450] [ 3439] [depth= 1] . ( 2 sec) [ -15270.9214] [ 3435] [depth= 1] . ( 2 sec) [ -14806.5195] [ 3402] [depth= 3] . ( 2 sec) [ -14792.5034] [ 3386] [depth= 6] . ( 2 sec) [ -14482.8128] [ 3310] [depth= 3] . ( 2 sec) [ -14160.4375] [ 3284] [depth= 12] . ( 2 sec) [ -14101.6950] [ 3288] [depth= 2] . ( 2 sec) [ -14073.9670] [ 3274] [depth= 1] . ( 3 sec) [ -14071.5759] [ 3267] [depth= 1] . ( 3 sec) [ -13961.3642] [ 3264] [depth= 8] . ( 3 sec) [ -13590.3257] [ 3167] [depth= 12] . ( 3 sec) [ -13529.0697] [ 3141] [depth= 1] . ( 3 sec) [ -13161.3678] [ 3127] [depth= 13] . ( 3 sec) [ -13097.7126] [ 3107] [depth= 11] . ( 3 sec) [ -13024.7156] [ 3086] [depth= 11] . ( 3 sec) [ -13022.0383] [ 3087] [depth= 16] . ( 3 sec) [ -12804.8022] [ 3077] [depth= 3] . ( 3 sec) [ -12735.4827] [ 3073] [depth= 1] . ( 3 sec) [ -12575.8272] [ 2996] [depth= 2] . ( 3 sec) [ -12567.9417] [ 2990] [depth= 9] . ( 3 sec) [ -12447.0108] [ 2988] [depth= 1] . ( 3 sec) [ -12378.9792] [ 2948] [depth= 11] . ( 3 sec) [ -12352.5346] [ 2940] [depth= 3] . ( 3 sec) [ -12323.8044] [ 2945] [depth= 1] . ( 3 sec) [ -12290.8892] [ 2920] [depth= 3] . ( 3 sec) [ -12277.5328] [ 2909] [depth= 14] . ( 3 sec) [ -12231.2325] [ 2907] [depth= 7] . ( 3 sec) [ -11981.8629] [ 2797] [depth= 12] . ( 3 sec) [ -11967.5019] [ 2796] [depth= 1] . ( 3 sec) [ -11757.8154] [ 2722] [depth= 2] . ( 4 sec) [ -11636.8064] [ 2731] [depth= 1] . ( 4 sec) [ -11587.4013] [ 2714] [depth= 2] . ( 4 sec) [ -11546.4025] [ 2714] [depth= 1] . ( 4 sec) [ -11503.9038] [ 2693] [depth= 7] . ( 4 sec) [ -11490.2864] [ 2702] [depth= 1] . ( 4 sec) [ -11403.4606] [ 2649] [depth= 7] . ( 4 sec) [ -11387.6974] [ 2652] [depth= 3] . ( 4 sec) [ -11265.9632] [ 2656] [depth= 1] . ( 4 sec) [ -11214.3018] [ 2639] [depth= 4] . ( 4 sec) [ -11205.3518] [ 2641] [depth= 3] . ( 4 sec) [ -11088.9363] [ 2609] [depth= 1] . ( 4 sec) [ -11067.3634] [ 2594] [depth= 12] . ( 4 sec) [ -11051.9681] [ 2587] [depth= 1] . ( 4 sec) [ -10967.4947] [ 2526] [depth= 1] . ( 4 sec) [ -10862.1161] [ 2514] [depth= 2] . ( 4 sec) [ -10763.4161] [ 2471] [depth= 1] . ( 4 sec) [ -10713.4938] [ 2437] [depth= 4] . ( 4 sec) [ -10712.6331] [ 2438] [depth= 1] . ( 5 sec) [ -10678.7680] [ 2429] [depth= 1] . ( 5 sec) [ -10465.1034] [ 2356] [depth= 5] . ( 5 sec) [ -10447.4941] [ 2355] [depth= 2] . ( 5 sec) [ -10407.5094] [ 2353] [depth= 7] . ( 5 sec) [ -10388.2509] [ 2353] [depth= 1] . ( 5 sec) [ -10377.6343] [ 2350] [depth= 2] . ( 5 sec) [ -10363.7665] [ 2338] [depth= 1] . ( 5 sec) [ -10359.9558] [ 2336] [depth= 2] . ( 5 sec) [ -10353.9001] [ 2333] [depth= 4] . ( 5 sec) [ -10352.4198] [ 2332] [depth= 1] . ( 5 sec) [ -10302.3165] [ 2320] [depth= 1] . ( 5 sec) [ -10285.3714] [ 2313] [depth= 1] . ( 5 sec) [ -10277.1944] [ 2310] [depth= 2] . ( 5 sec) [ -10211.9802] [ 2274] [depth= 5] . ( 5 sec) [ -10200.8241] [ 2267] [depth= 2] . ( 5 sec) [ -10199.9560] [ 2271] [depth= 1] . ( 5 sec) [ -10020.8799] [ 2206] [depth= 2] . ( 6 sec) [ -9892.8616] [Branch lengths ] . ( 6 sec) [ -9882.2008] [GTR parameters ] . ( 6 sec) [ -9851.4866] [Alpha ][ 0.866049] . ( 6 sec) [ -9836.9285] [ 2199] [depth= 2] . ( 6 sec) [ -9836.6491] [ 2203] [depth= 1] . ( 7 sec) [ -9836.0658] [ 2204] [depth= 1] . ( 7 sec) [ -9828.3907] [ 2197] [depth= 1] . ( 7 sec) [ -9821.5185] [ 2192] [depth= 1] . ( 7 sec) [ -9780.4561] [ 2175] [depth= 4] . ( 7 sec) [ -9778.7187] [ 2179] [depth= 1] . ( 7 sec) [ -9776.9000] [ 2176] [depth= 1] . ( 7 sec) [ -9775.4591] [ 2179] [depth= 1] . ( 7 sec) [ -9775.3438] [ 2179] [depth= 1] . ( 8 sec) [ -9772.5550] [ 2182] [depth= 1] . ( 8 sec) [ -9769.1116] [ 2183] [depth= 1] . ( 8 sec) [ -9767.7943] [ 2179] [depth= 1] . ( 8 sec) [ -9767.2488] [ 2179] [depth= 1] . ( 8 sec) [ -9766.3228] [ 2177] [depth= 1] . ( 9 sec) [ -9765.0391] [ 2176] [depth= 1] . ( 9 sec) [ -9765.0113] [ 2179] [depth= 1] . ( 10 sec) [ -9751.6189] [Branch lengths ] . ( 10 sec) [ -9751.5271] [GTR parameters ] . ( 10 sec) [ -9751.2937] [Alpha ][ 0.909370] . ( 11 sec) [ -9751.2571] [ 2177] [depth= 1] . ( 11 sec) [ -9751.0590] [ 2177] [depth= 1] . ( 11 sec) [ -9751.0155] [ 2178] [depth= 1] . ( 12 sec) [ -9751.0024] [ 2183] [depth= 1] . ( 12 sec) [ -9750.9223] [ 2185] [depth= 1] . ( 13 sec) [ -9750.9086] [ 2173] [depth= 2] . ( 13 sec) [ -9750.7350] [ 2172] [depth= 1] . ( 13 sec) [ -9748.9999] [ 2173] [depth= 1] . ( 14 sec) [ -9747.1484] [Branch lengths ] . ( 14 sec) [ -9747.1422] [GTR parameters ] . ( 15 sec) [ -9747.1306] [Alpha ][ 0.919453] . ( 15 sec) [ -9746.9160] [ 2172] [depth= 1] . ( 18 sec) [ -9746.7163] [Branch lengths ] . ( 19 sec) [ -9746.7160] [GTR parameters ] . ( 19 sec) [ -9746.7136] [Alpha ][ 0.923971] . ( 19 sec) [ -9746.5701] [ 2170] [depth= 2] . ( 41 sec) [ -9746.4878] [Branch lengths ] . ( 41 sec) [ -9746.4864] [GTR parameters ] . ( 42 sec) [ -9746.4856] [Alpha ][ 0.926467] . ( 42 sec) [ -9746.4856] [Topology ] . ( 42 sec) [ -9746.4799] [Topology ] . ( 43 sec) [ -9746.4776] [Topology ] . ( 44 sec) [ -9746.4763] [Topology ] . ( 45 sec) [ -9746.4755] [Topology ] . ( 45 sec) [ -9746.4755] [GTR parameters ] . ( 45 sec) [ -9746.4754] [Alpha ][ 0.927394] . ( 45 sec) [ -9746.4754] [Topology ] . ( 46 sec) [ -9746.4749] [Topology ] . ( 46 sec) [ -9746.4749] [GTR parameters ] . ( 46 sec) [ -9746.4749] [Alpha ][ 0.927394] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -9746.4746] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9746.474614. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18217.4024] [GTR parameters ] . ( 1 sec) [ -17905.9944] [Alpha ][ 0.500960] . ( 1 sec) [ -17774.5611] [ 3976] [depth= 1] . ( 1 sec) [ -17593.9106] [ 3930] [depth= 8] . ( 1 sec) [ -17588.1925] [ 3916] [depth= 2] . ( 1 sec) [ -17585.0885] [ 3917] [depth= 1] . ( 1 sec) [ -17458.5618] [ 3903] [depth= 6] . ( 1 sec) [ -17404.1869] [ 3892] [depth= 2] . ( 1 sec) [ -17188.7797] [ 3849] [depth= 7] . ( 1 sec) [ -17092.7192] [ 3811] [depth= 4] . ( 1 sec) [ -16815.2359] [ 3749] [depth= 8] . ( 1 sec) [ -16584.0749] [ 3745] [depth= 4] . ( 1 sec) [ -16349.8346] [ 3688] [depth= 3] . ( 1 sec) [ -16281.6769] [ 3688] [depth= 2] . ( 1 sec) [ -16094.6178] [ 3603] [depth= 6] . ( 1 sec) [ -16071.3087] [ 3539] [depth= 2] . ( 1 sec) [ -16012.9197] [ 3522] [depth= 1] . ( 1 sec) [ -15797.7823] [ 3513] [depth= 11] . ( 2 sec) [ -15728.0118] [ 3509] [depth= 2] . ( 2 sec) [ -15532.2350] [ 3477] [depth= 2] . ( 2 sec) [ -15488.1849] [ 3462] [depth= 2] . ( 2 sec) [ -15427.8927] [ 3427] [depth= 1] . ( 2 sec) [ -15373.3654] [ 3428] [depth= 1] . ( 2 sec) [ -15147.1923] [ 3360] [depth= 2] . ( 2 sec) [ -15081.0564] [ 3309] [depth= 13] . ( 2 sec) [ -15027.8592] [ 3311] [depth= 6] . ( 2 sec) [ -14891.1332] [ 3274] [depth= 1] . ( 2 sec) [ -14766.0756] [ 3242] [depth= 7] . ( 2 sec) [ -14672.2029] [ 3242] [depth= 6] . ( 2 sec) [ -14649.5282] [ 3241] [depth= 1] . ( 2 sec) [ -14498.6963] [ 3160] [depth= 6] . ( 2 sec) [ -14304.2808] [ 3153] [depth= 8] . ( 2 sec) [ -13478.8465] [ 3147] [depth= 5] . ( 2 sec) [ -13364.1479] [ 3110] [depth= 5] . ( 2 sec) [ -13354.7851] [ 3117] [depth= 1] . ( 2 sec) [ -13190.3557] [ 3108] [depth= 9] . ( 2 sec) [ -13068.9699] [ 3091] [depth= 8] . ( 2 sec) [ -12966.1087] [ 3080] [depth= 11] . ( 2 sec) [ -12792.2429] [ 3005] [depth= 8] . ( 2 sec) [ -12757.2445] [ 3007] [depth= 1] . ( 3 sec) [ -12740.0213] [ 3002] [depth= 1] . ( 3 sec) [ -12729.1833] [ 3002] [depth= 1] . ( 3 sec) [ -12677.7313] [ 2996] [depth= 1] . ( 3 sec) [ -12641.4390] [ 2990] [depth= 5] . ( 3 sec) [ -12380.6344] [ 2929] [depth= 1] . ( 3 sec) [ -11961.6827] [ 2846] [depth= 6] . ( 3 sec) [ -11949.3432] [ 2840] [depth= 1] . ( 3 sec) [ -11860.0545] [ 2797] [depth= 5] . ( 3 sec) [ -11839.5723] [ 2790] [depth= 1] . ( 3 sec) [ -11714.3227] [ 2779] [depth= 3] . ( 3 sec) [ -11660.9047] [ 2749] [depth= 3] . ( 3 sec) [ -11597.4597] [ 2737] [depth= 2] . ( 3 sec) [ -11590.4923] [ 2712] [depth= 3] . ( 3 sec) [ -11558.0740] [ 2706] [depth= 1] . ( 3 sec) [ -11515.0104] [ 2658] [depth= 1] . ( 3 sec) [ -11421.8283] [ 2632] [depth= 2] . ( 3 sec) [ -11337.7791] [ 2570] [depth= 1] . ( 3 sec) [ -11326.5708] [ 2559] [depth= 3] . ( 3 sec) [ -11055.8867] [ 2502] [depth= 9] . ( 3 sec) [ -11050.0452] [ 2521] [depth= 1] . ( 3 sec) [ -10929.3022] [ 2472] [depth= 1] . ( 3 sec) [ -10888.1079] [ 2459] [depth= 3] . ( 4 sec) [ -10754.6379] [ 2418] [depth= 9] . ( 4 sec) [ -10683.6510] [ 2427] [depth= 3] . ( 4 sec) [ -10609.8821] [ 2400] [depth= 4] . ( 4 sec) [ -10602.4585] [ 2395] [depth= 2] . ( 4 sec) [ -10467.3272] [ 2323] [depth= 10] . ( 4 sec) [ -10440.0145] [ 2314] [depth= 1] . ( 4 sec) [ -10240.9877] [ 2244] [depth= 6] . ( 4 sec) [ -10235.0590] [ 2263] [depth= 1] . ( 4 sec) [ -10224.8276] [ 2260] [depth= 2] . ( 4 sec) [ -10088.5696] [ 2241] [depth= 1] . ( 4 sec) [ -10047.4380] [ 2232] [depth= 1] . ( 4 sec) [ -10044.6464] [ 2233] [depth= 1] . ( 4 sec) [ -10038.2630] [ 2236] [depth= 2] . ( 4 sec) [ -10032.1802] [ 2232] [depth= 2] . ( 4 sec) [ -10023.6618] [ 2233] [depth= 1] . ( 4 sec) [ -10006.1964] [ 2230] [depth= 1] . ( 4 sec) [ -10001.5388] [ 2241] [depth= 3] . ( 4 sec) [ -9991.1231] [ 2236] [depth= 1] . ( 4 sec) [ -9990.6990] [ 2237] [depth= 1] . ( 5 sec) [ -9988.5049] [ 2241] [depth= 1] . ( 5 sec) [ -9986.1008] [ 2243] [depth= 1] . ( 5 sec) [ -9937.7098] [ 2224] [depth= 1] . ( 5 sec) [ -9864.8063] [Branch lengths ] . ( 6 sec) [ -9862.5161] [GTR parameters ] . ( 6 sec) [ -9836.2929] [Alpha ][ 0.828612] . ( 6 sec) [ -9836.0626] [ 2223] [depth= 1] . ( 6 sec) [ -9835.8614] [ 2221] [depth= 1] . ( 7 sec) [ -9824.6030] [ 2210] [depth= 2] . ( 7 sec) [ -9821.7111] [ 2206] [depth= 3] . ( 7 sec) [ -9820.7984] [ 2208] [depth= 1] . ( 7 sec) [ -9816.5911] [ 2196] [depth= 1] . ( 7 sec) [ -9800.9219] [ 2196] [depth= 1] . ( 8 sec) [ -9800.7226] [ 2199] [depth= 1] . ( 8 sec) [ -9776.3943] [ 2191] [depth= 4] . ( 8 sec) [ -9774.8165] [ 2194] [depth= 1] . ( 8 sec) [ -9773.6148] [ 2192] [depth= 2] . ( 9 sec) [ -9773.5053] [ 2195] [depth= 1] . ( 9 sec) [ -9772.8386] [ 2182] [depth= 1] . ( 9 sec) [ -9772.3253] [ 2182] [depth= 1] . ( 9 sec) [ -9771.7439] [ 2184] [depth= 3] . ( 10 sec) [ -9761.9601] [Branch lengths ] . ( 10 sec) [ -9761.9231] [GTR parameters ] . ( 10 sec) [ -9761.3268] [Alpha ][ 0.895566] . ( 11 sec) [ -9761.2296] [ 2185] [depth= 1] . ( 14 sec) [ -9758.1139] [Branch lengths ] . ( 14 sec) [ -9758.1133] [GTR parameters ] . ( 14 sec) [ -9758.0888] [Alpha ][ 0.910041] . ( 19 sec) [ -9752.4270] [Branch lengths ] . ( 26 sec) [ -9751.4617] [ 2187] [depth= 1] . ( 27 sec) [ -9751.0721] [ 2182] [depth= 1] . ( 33 sec) [ -9750.7017] [ 2182] [depth= 1] . ( 34 sec) [ -9750.6425] [ 2182] [depth= 1] . ( 40 sec) [ -9749.0112] [Branch lengths ] . ( 41 sec) [ -9749.0038] [GTR parameters ] . ( 41 sec) [ -9748.9842] [Alpha ][ 0.923106] . ( 56 sec) [ -9748.8477] [ 2182] [depth= 1] . ( 56 sec) [ -9748.8076] [ 2182] [depth= 1] . ( 57 sec) [ -9748.6100] [ 2171] [depth= 3] . ( 59 sec) [ -9747.3491] [ 2170] [depth= 1] . ( 59 sec) [ -9747.2882] [ 2171] [depth= 1] . ( 63 sec) [ -9746.5924] [Branch lengths ] . ( 63 sec) [ -9746.5833] [GTR parameters ] . ( 63 sec) [ -9746.5805] [Alpha ][ 0.928024] . ( 86 sec) [ -9746.4787] [Branch lengths ] . ( 86 sec) [ -9746.4787] [Topology ] . ( 87 sec) [ -9746.4758] [Topology ] . ( 88 sec) [ -9746.4750] [Topology ] . ( 88 sec) [ -9746.4748] [GTR parameters ] . ( 88 sec) [ -9746.4748] [Alpha ][ 0.928024] . ( 88 sec) [ -9746.4748] [Topology ] . ( 88 sec) [ -9746.4745] [Topology ] . ( 89 sec) [ -9746.4745] [GTR parameters ] . ( 89 sec) [ -9746.4745] [Alpha ][ 0.928024] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -9746.4742] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -9746.4740] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9746.474023. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18219.6098] [GTR parameters ] . ( 1 sec) [ -17900.9586] [Alpha ][ 0.500960] . ( 1 sec) [ -17652.4898] [ 3998] [depth= 11] . ( 1 sec) [ -17335.6550] [ 3943] [depth= 9] . ( 1 sec) [ -17197.4253] [ 3901] [depth= 7] . ( 1 sec) [ -17086.1727] [ 3829] [depth= 1] . ( 1 sec) [ -16936.2574] [ 3794] [depth= 5] . ( 1 sec) [ -16936.0073] [ 3789] [depth= 2] . ( 1 sec) [ -16916.2459] [ 3780] [depth= 4] . ( 1 sec) [ -16911.1951] [ 3753] [depth= 2] . ( 1 sec) [ -16818.6416] [ 3745] [depth= 8] . ( 1 sec) [ -16708.4867] [ 3727] [depth= 3] . ( 1 sec) [ -16595.0018] [ 3669] [depth= 1] . ( 1 sec) [ -16567.4790] [ 3638] [depth= 9] . ( 1 sec) [ -16514.9618] [ 3635] [depth= 2] . ( 1 sec) [ -16448.7247] [ 3570] [depth= 1] . ( 1 sec) [ -16400.4454] [ 3559] [depth= 3] . ( 1 sec) [ -16243.5702] [ 3530] [depth= 6] . ( 1 sec) [ -16211.4128] [ 3532] [depth= 1] . ( 2 sec) [ -16018.7238] [ 3503] [depth= 4] . ( 2 sec) [ -15790.8940] [ 3470] [depth= 3] . ( 2 sec) [ -15768.8948] [ 3464] [depth= 2] . ( 2 sec) [ -15298.0422] [ 3368] [depth= 4] . ( 2 sec) [ -15228.9104] [ 3328] [depth= 1] . ( 2 sec) [ -15173.2434] [ 3289] [depth= 12] . ( 2 sec) [ -14978.3241] [ 3283] [depth= 3] . ( 2 sec) [ -14838.6829] [ 3214] [depth= 1] . ( 2 sec) [ -14788.4621] [ 3206] [depth= 1] . ( 2 sec) [ -14438.3467] [ 3117] [depth= 11] . ( 2 sec) [ -14198.6813] [ 3103] [depth= 3] . ( 2 sec) [ -13835.3828] [ 3004] [depth= 6] . ( 2 sec) [ -13709.8820] [ 2992] [depth= 1] . ( 2 sec) [ -13015.4153] [ 2922] [depth= 16] . ( 2 sec) [ -12975.2504] [ 2918] [depth= 5] . ( 2 sec) [ -12955.9450] [ 2901] [depth= 1] . ( 2 sec) [ -12894.8489] [ 2853] [depth= 3] . ( 2 sec) [ -12882.0846] [ 2847] [depth= 1] . ( 2 sec) [ -12821.0416] [ 2841] [depth= 1] . ( 2 sec) [ -12797.7528] [ 2857] [depth= 1] . ( 2 sec) [ -12727.6900] [ 2799] [depth= 1] . ( 2 sec) [ -12709.3145] [ 2783] [depth= 1] . ( 2 sec) [ -12703.6371] [ 2776] [depth= 7] . ( 3 sec) [ -12674.9612] [ 2760] [depth= 12] . ( 3 sec) [ -12629.2801] [ 2736] [depth= 1] . ( 3 sec) [ -12604.9228] [ 2739] [depth= 1] . ( 3 sec) [ -12583.3987] [ 2737] [depth= 9] . ( 3 sec) [ -12380.0237] [ 2679] [depth= 4] . ( 3 sec) [ -12342.8881] [ 2725] [depth= 1] . ( 3 sec) [ -12336.1530] [ 2698] [depth= 10] . ( 3 sec) [ -11944.6130] [ 2631] [depth= 1] . ( 3 sec) [ -11865.5785] [ 2631] [depth= 2] . ( 3 sec) [ -11774.3511] [ 2616] [depth= 3] . ( 3 sec) [ -11769.7311] [ 2632] [depth= 1] . ( 3 sec) [ -11589.5468] [ 2599] [depth= 3] . ( 3 sec) [ -11568.6965] [ 2603] [depth= 10] . ( 3 sec) [ -11364.6429] [ 2575] [depth= 1] . ( 3 sec) [ -11197.3205] [ 2545] [depth= 10] . ( 3 sec) [ -11092.9586] [ 2549] [depth= 1] . ( 3 sec) [ -11047.6931] [ 2486] [depth= 4] . ( 3 sec) [ -11010.4238] [ 2467] [depth= 8] . ( 3 sec) [ -10998.1355] [ 2455] [depth= 9] . ( 3 sec) [ -10984.1623] [ 2455] [depth= 1] . ( 4 sec) [ -10922.7471] [ 2445] [depth= 5] . ( 4 sec) [ -10889.7522] [ 2434] [depth= 1] . ( 4 sec) [ -10797.5733] [ 2401] [depth= 1] . ( 4 sec) [ -10745.1495] [ 2384] [depth= 3] . ( 4 sec) [ -10724.6438] [ 2376] [depth= 2] . ( 4 sec) [ -10707.2693] [ 2388] [depth= 2] . ( 4 sec) [ -10706.3874] [ 2384] [depth= 3] . ( 4 sec) [ -10692.1113] [ 2381] [depth= 1] . ( 4 sec) [ -10672.6212] [ 2372] [depth= 1] . ( 4 sec) [ -10650.7254] [ 2383] [depth= 1] . ( 4 sec) [ -10632.1468] [ 2386] [depth= 2] . ( 4 sec) [ -10576.4683] [ 2354] [depth= 3] . ( 4 sec) [ -10381.4850] [ 2275] [depth= 10] . ( 4 sec) [ -10369.7954] [ 2266] [depth= 3] . ( 4 sec) [ -10325.8013] [ 2270] [depth= 1] . ( 4 sec) [ -10324.3682] [ 2267] [depth= 1] . ( 4 sec) [ -10321.1930] [ 2266] [depth= 1] . ( 5 sec) [ -10317.3745] [ 2269] [depth= 2] . ( 5 sec) [ -10279.3809] [ 2261] [depth= 3] . ( 5 sec) [ -10272.5314] [ 2266] [depth= 1] . ( 5 sec) [ -10268.7157] [ 2267] [depth= 1] . ( 5 sec) [ -10097.9686] [ 2221] [depth= 1] . ( 5 sec) [ -9959.7531] [Branch lengths ] . ( 6 sec) [ -9953.5349] [GTR parameters ] . ( 6 sec) [ -9925.1444] [Alpha ][ 0.844435] . ( 6 sec) [ -9925.0471] [ 2222] [depth= 3] . ( 6 sec) [ -9904.2966] [ 2217] [depth= 4] . ( 6 sec) [ -9830.0020] [ 2224] [depth= 1] . ( 6 sec) [ -9815.6026] [ 2223] [depth= 3] . ( 7 sec) [ -9810.9967] [ 2215] [depth= 1] . ( 7 sec) [ -9805.7422] [ 2205] [depth= 1] . ( 7 sec) [ -9800.2830] [ 2198] [depth= 1] . ( 7 sec) [ -9793.6291] [ 2190] [depth= 1] . ( 7 sec) [ -9792.9114] [ 2190] [depth= 2] . ( 7 sec) [ -9786.9959] [ 2189] [depth= 1] . ( 7 sec) [ -9785.8286] [ 2192] [depth= 1] . ( 7 sec) [ -9780.1102] [ 2192] [depth= 1] . ( 7 sec) [ -9775.1648] [ 2182] [depth= 2] . ( 8 sec) [ -9771.5730] [ 2181] [depth= 1] . ( 8 sec) [ -9769.2784] [ 2173] [depth= 2] . ( 8 sec) [ -9769.1033] [ 2170] [depth= 2] . ( 8 sec) [ -9768.8076] [ 2173] [depth= 2] . ( 9 sec) [ -9767.6735] [ 2163] [depth= 2] . ( 9 sec) [ -9766.4763] [ 2167] [depth= 2] . ( 9 sec) [ -9766.1885] [ 2166] [depth= 1] . ( 9 sec) [ -9765.1132] [ 2166] [depth= 1] . ( 9 sec) [ -9765.0593] [ 2170] [depth= 1] . ( 9 sec) [ -9764.4035] [ 2171] [depth= 1] . ( 9 sec) [ -9749.1905] [Branch lengths ] . ( 10 sec) [ -9748.9874] [GTR parameters ] . ( 10 sec) [ -9748.3772] [Alpha ][ 0.913791] . ( 10 sec) [ -9748.2712] [ 2170] [depth= 1] . ( 11 sec) [ -9748.1893] [ 2169] [depth= 1] . ( 13 sec) [ -9746.9118] [Branch lengths ] . ( 14 sec) [ -9746.9101] [GTR parameters ] . ( 14 sec) [ -9746.9045] [Alpha ][ 0.920814] . ( 17 sec) [ -9746.5866] [Branch lengths ] . ( 40 sec) [ -9746.5060] [Branch lengths ] . ( 40 sec) [ -9746.5060] [Topology ] . ( 41 sec) [ -9746.4931] [Topology ] . ( 42 sec) [ -9746.4878] [Topology ] . ( 43 sec) [ -9746.4847] [Topology ] . ( 43 sec) [ -9746.4829] [Topology ] . ( 44 sec) [ -9746.4819] [Topology ] . ( 45 sec) [ -9746.4813] [Topology ] . ( 45 sec) [ -9746.4806] [GTR parameters ] . ( 45 sec) [ -9746.4758] [Alpha ][ 0.927263] . ( 45 sec) [ -9746.4758] [Topology ] . ( 46 sec) [ -9746.4752] [Topology ] . ( 46 sec) [ -9746.4751] [GTR parameters ] . ( 46 sec) [ -9746.4751] [Alpha ][ 0.927263] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -9746.4744] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -9746.4742] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9746.474169. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18037.9145] [GTR parameters ] . ( 0 sec) [ -17698.2527] [Alpha ][ 0.500960] . ( 0 sec) [ -17496.1024] [ 4045] [depth= 6] . ( 0 sec) [ -17307.2529] [ 3992] [depth= 11] . ( 1 sec) [ -17305.5754] [ 3979] [depth= 4] . ( 1 sec) [ -17221.1814] [ 3975] [depth= 3] . ( 1 sec) [ -17025.2414] [ 3942] [depth= 6] . ( 1 sec) [ -16979.5555] [ 3943] [depth= 4] . ( 1 sec) [ -16945.5879] [ 3927] [depth= 6] . ( 1 sec) [ -16842.4972] [ 3873] [depth= 1] . ( 1 sec) [ -16732.1809] [ 3855] [depth= 7] . ( 1 sec) [ -16518.7447] [ 3767] [depth= 12] . ( 1 sec) [ -16468.1581] [ 3765] [depth= 14] . ( 1 sec) [ -15996.7202] [ 3668] [depth= 14] . ( 1 sec) [ -15903.4503] [ 3674] [depth= 1] . ( 1 sec) [ -15785.9323] [ 3661] [depth= 9] . ( 1 sec) [ -15752.8142] [ 3641] [depth= 1] . ( 1 sec) [ -15483.3148] [ 3616] [depth= 6] . ( 1 sec) [ -15277.8257] [ 3551] [depth= 2] . ( 1 sec) [ -15274.6018] [ 3552] [depth= 6] . ( 1 sec) [ -14852.8728] [ 3547] [depth= 10] . ( 1 sec) [ -14639.6170] [ 3429] [depth= 3] . ( 1 sec) [ -14446.1052] [ 3430] [depth= 11] . ( 1 sec) [ -14277.2000] [ 3359] [depth= 3] . ( 1 sec) [ -14113.4799] [ 3270] [depth= 7] . ( 1 sec) [ -13833.2992] [ 3254] [depth= 2] . ( 1 sec) [ -13713.2987] [ 3235] [depth= 1] . ( 1 sec) [ -13657.2307] [ 3225] [depth= 1] . ( 2 sec) [ -13572.4166] [ 3183] [depth= 6] . ( 2 sec) [ -13570.4076] [ 3188] [depth= 1] . ( 2 sec) [ -13315.5122] [ 3137] [depth= 6] . ( 2 sec) [ -12727.0382] [ 3019] [depth= 4] . ( 2 sec) [ -12620.8697] [ 2970] [depth= 1] . ( 2 sec) [ -12612.0400] [ 2976] [depth= 7] . ( 2 sec) [ -12519.0770] [ 2944] [depth= 4] . ( 2 sec) [ -12468.7415] [ 2924] [depth= 1] . ( 2 sec) [ -12466.2488] [ 2911] [depth= 3] . ( 2 sec) [ -12439.4466] [ 2886] [depth= 6] . ( 2 sec) [ -12368.7759] [ 2894] [depth= 1] . ( 2 sec) [ -12363.3739] [ 2892] [depth= 1] . ( 2 sec) [ -12344.4698] [ 2877] [depth= 2] . ( 2 sec) [ -12328.5976] [ 2876] [depth= 2] . ( 2 sec) [ -12324.7579] [ 2886] [depth= 1] . ( 2 sec) [ -12312.0669] [ 2883] [depth= 8] . ( 2 sec) [ -12301.8221] [ 2848] [depth= 1] . ( 2 sec) [ -12229.9266] [ 2817] [depth= 8] . ( 2 sec) [ -12196.0054] [ 2807] [depth= 2] . ( 2 sec) [ -12163.7395] [ 2787] [depth= 8] . ( 2 sec) [ -12161.7800] [ 2791] [depth= 2] . ( 2 sec) [ -12028.2451] [ 2793] [depth= 2] . ( 2 sec) [ -11971.8229] [ 2719] [depth= 9] . ( 3 sec) [ -11882.7192] [ 2727] [depth= 7] . ( 3 sec) [ -11869.9159] [ 2723] [depth= 3] . ( 3 sec) [ -11806.6857] [ 2716] [depth= 2] . ( 3 sec) [ -11573.3875] [ 2702] [depth= 1] . ( 3 sec) [ -11568.6990] [ 2701] [depth= 1] . ( 3 sec) [ -11399.3288] [ 2622] [depth= 1] . ( 3 sec) [ -11344.8184] [ 2603] [depth= 5] . ( 3 sec) [ -11226.0323] [ 2563] [depth= 6] . ( 3 sec) [ -11173.0766] [ 2573] [depth= 1] . ( 3 sec) [ -11029.7829] [ 2555] [depth= 4] . ( 3 sec) [ -11011.7929] [ 2553] [depth= 1] . ( 3 sec) [ -10987.7327] [ 2542] [depth= 7] . ( 3 sec) [ -10915.6086] [ 2517] [depth= 1] . ( 3 sec) [ -10885.3684] [ 2509] [depth= 1] . ( 3 sec) [ -10841.2440] [ 2507] [depth= 1] . ( 3 sec) [ -10818.9256] [ 2500] [depth= 1] . ( 3 sec) [ -10789.1771] [ 2496] [depth= 3] . ( 3 sec) [ -10772.8019] [ 2494] [depth= 2] . ( 3 sec) [ -10722.2346] [ 2479] [depth= 3] . ( 3 sec) [ -10720.2865] [ 2471] [depth= 1] . ( 3 sec) [ -10719.9051] [ 2470] [depth= 2] . ( 3 sec) [ -10712.6002] [ 2463] [depth= 2] . ( 4 sec) [ -10712.1390] [ 2463] [depth= 3] . ( 4 sec) [ -10703.9539] [ 2461] [depth= 2] . ( 4 sec) [ -10665.2479] [ 2466] [depth= 1] . ( 4 sec) [ -10617.7159] [ 2441] [depth= 1] . ( 4 sec) [ -10474.2449] [ 2373] [depth= 5] . ( 4 sec) [ -10474.2002] [ 2378] [depth= 1] . ( 4 sec) [ -10461.0778] [ 2381] [depth= 1] . ( 4 sec) [ -10402.0409] [ 2379] [depth= 1] . ( 4 sec) [ -10390.9683] [ 2379] [depth= 2] . ( 4 sec) [ -10390.0209] [ 2375] [depth= 1] . ( 4 sec) [ -10376.9888] [ 2370] [depth= 5] . ( 4 sec) [ -10376.5133] [ 2372] [depth= 2] . ( 5 sec) [ -10245.4785] [Branch lengths ] . ( 5 sec) [ -10243.1840] [GTR parameters ] . ( 5 sec) [ -10213.9252] [Alpha ][ 0.836247] . ( 6 sec) [ -10067.3404] [ 2304] [depth= 3] . ( 6 sec) [ -10065.8417] [ 2300] [depth= 2] . ( 6 sec) [ -9907.3786] [ 2242] [depth= 5] . ( 6 sec) [ -9896.4029] [ 2244] [depth= 2] . ( 6 sec) [ -9895.9908] [ 2233] [depth= 1] . ( 6 sec) [ -9882.8719] [ 2219] [depth= 1] . ( 6 sec) [ -9875.6528] [ 2214] [depth= 1] . ( 6 sec) [ -9862.3497] [ 2211] [depth= 1] . ( 6 sec) [ -9842.2576] [ 2200] [depth= 1] . ( 6 sec) [ -9838.9184] [ 2199] [depth= 1] . ( 6 sec) [ -9798.3475] [ 2190] [depth= 1] . ( 6 sec) [ -9798.0065] [ 2184] [depth= 1] . ( 6 sec) [ -9792.3315] [ 2176] [depth= 2] . ( 6 sec) [ -9789.9482] [ 2173] [depth= 1] . ( 7 sec) [ -9788.9130] [ 2175] [depth= 1] . ( 7 sec) [ -9785.3911] [ 2173] [depth= 1] . ( 7 sec) [ -9784.0852] [ 2175] [depth= 1] . ( 7 sec) [ -9777.3699] [ 2173] [depth= 1] . ( 7 sec) [ -9775.0901] [ 2176] [depth= 1] . ( 7 sec) [ -9774.8018] [ 2178] [depth= 1] . ( 7 sec) [ -9774.6778] [ 2182] [depth= 1] . ( 7 sec) [ -9765.3023] [ 2168] [depth= 3] . ( 8 sec) [ -9764.6650] [ 2167] [depth= 2] . ( 8 sec) [ -9763.8880] [ 2172] [depth= 1] . ( 8 sec) [ -9761.1429] [ 2172] [depth= 1] . ( 8 sec) [ -9760.8955] [ 2171] [depth= 1] . ( 9 sec) [ -9749.3729] [Branch lengths ] . ( 9 sec) [ -9748.7947] [GTR parameters ] . ( 9 sec) [ -9748.0054] [Alpha ][ 0.914385] . ( 11 sec) [ -9747.8362] [ 2173] [depth= 1] . ( 11 sec) [ -9747.6127] [ 2171] [depth= 1] . ( 11 sec) [ -9747.5666] [ 2170] [depth= 1] . ( 13 sec) [ -9746.6556] [Branch lengths ] . ( 13 sec) [ -9746.6522] [GTR parameters ] . ( 14 sec) [ -9746.6425] [Alpha ][ 0.923686] . ( 17 sec) [ -9746.5082] [Branch lengths ] . ( 40 sec) [ -9746.4831] [Branch lengths ] . ( 40 sec) [ -9746.4831] [Topology ] . ( 41 sec) [ -9746.4797] [Topology ] . ( 42 sec) [ -9746.4782] [Topology ] . ( 43 sec) [ -9746.4774] [Topology ] . ( 43 sec) [ -9746.4772] [GTR parameters ] . ( 43 sec) [ -9746.4758] [Alpha ][ 0.927265] . ( 43 sec) [ -9746.4758] [Topology ] . ( 44 sec) [ -9746.4752] [Topology ] . ( 44 sec) [ -9746.4751] [GTR parameters ] . ( 44 sec) [ -9746.4751] [Alpha ][ 0.927265] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -9746.4743] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9746.474348. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9819.544236 . ( 1 sec) [ -9818.9780] [GTR parameters ] . ( 1 sec) [ -9817.3593] [Alpha ][ 0.874247] . ( 1 sec) [ -9817.3593] [Topology ] . ( 2 sec) [ -9764.1157] [Topology ] . ( 2 sec) [ -9753.9386] [Topology ] . ( 3 sec) [ -9750.7269] [Topology ] . ( 4 sec) [ -9749.3574] [Topology ] . ( 5 sec) [ -9748.6569] [Topology ] . ( 5 sec) [ -9748.2723] [Topology ] . ( 6 sec) [ -9748.0537] [Topology ] . ( 7 sec) [ -9747.9264] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.926387 . ( 13 sec) [ -9747.8744] [GTR parameters ] . ( 14 sec) [ -9747.5766] [Alpha ][ 0.923577] . ( 14 sec) [ -9747.5766] [Topology ] . ( 14 sec) [ -9747.4687] [Topology ] . ( 15 sec) [ -9747.4098] [Topology ] . ( 16 sec) [ -9747.3755] [Topology ] . ( 17 sec) [ -9747.3552] [Topology ] . ( 17 sec) [ -9747.3432] [Topology ] . ( 18 sec) [ -9747.3361] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.336102 . ( 24 sec) [ -9747.3359] [GTR parameters ] . ( 24 sec) [ -9747.3331] [Alpha ][ 0.928476] . ( 24 sec) [ -9747.3331] [Topology ] . ( 25 sec) [ -9747.3284] [Topology ] . ( 26 sec) [ -9747.3256] [Topology ] . ( 27 sec) [ -9747.3240] [Topology ] . ( 27 sec) [ -9747.3230] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.322977 . ( 34 sec) [ -9747.3230] [GTR parameters ] . ( 34 sec) [ -9747.3229] [Alpha ][ 0.929405] . ( 34 sec) [ -9747.3229] [Topology ] . ( 35 sec) [ -9747.3223] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -9818.9780] [GTR parameters ] . ( 48 sec) [ -9817.3593] [Alpha ][ 0.874247] . ( 49 sec) [ -9813.5091] [ 2171] [depth= 1] . ( 49 sec) [ -9811.7173] [ 2169] [depth= 1] . ( 49 sec) [ -9811.4644] [ 2171] [depth= 1] . ( 49 sec) [ -9811.3944] [ 2173] [depth= 1] . ( 49 sec) [ -9807.9557] [ 2177] [depth= 2] . ( 49 sec) [ -9807.1056] [ 2188] [depth= 1] . ( 49 sec) [ -9806.9336] [ 2189] [depth= 1] . ( 49 sec) [ -9802.8983] [ 2188] [depth= 1] . ( 50 sec) [ -9802.5593] [ 2183] [depth= 1] . ( 50 sec) [ -9802.1604] [ 2180] [depth= 2] . ( 50 sec) [ -9799.5137] [ 2182] [depth= 1] . ( 50 sec) [ -9798.4882] [ 2183] [depth= 1] . ( 50 sec) [ -9797.2458] [ 2184] [depth= 2] . ( 50 sec) [ -9797.2135] [ 2185] [depth= 1] . ( 50 sec) [ -9797.1873] [ 2182] [depth= 1] . ( 50 sec) [ -9796.7182] [ 2183] [depth= 1] . ( 50 sec) [ -9795.2640] [ 2182] [depth= 1] . ( 50 sec) [ -9788.6596] [ 2176] [depth= 1] . ( 51 sec) [ -9788.6304] [ 2179] [depth= 1] . ( 51 sec) [ -9786.9837] [ 2178] [depth= 2] . ( 51 sec) [ -9785.9734] [ 2180] [depth= 1] . ( 51 sec) [ -9785.7605] [ 2181] [depth= 1] . ( 51 sec) [ -9785.0104] [ 2180] [depth= 1] . ( 51 sec) [ -9784.5167] [ 2178] [depth= 1] . ( 51 sec) [ -9753.7468] [Branch lengths ] . ( 52 sec) [ -9753.7185] [GTR parameters ] . ( 52 sec) [ -9753.6107] [Alpha ][ 0.903537] . ( 52 sec) [ -9752.0100] [ 2175] [depth= 2] . ( 53 sec) [ -9751.5220] [ 2165] [depth= 1] . ( 53 sec) [ -9751.3083] [ 2167] [depth= 1] . ( 54 sec) [ -9751.2975] [ 2167] [depth= 1] . ( 54 sec) [ -9751.2825] [ 2167] [depth= 2] . ( 54 sec) [ -9751.2618] [ 2168] [depth= 1] . ( 54 sec) [ -9751.2394] [ 2167] [depth= 1] . ( 54 sec) [ -9751.1821] [ 2167] [depth= 1] . ( 54 sec) [ -9751.1712] [ 2171] [depth= 1] . ( 54 sec) [ -9750.6670] [ 2167] [depth= 1] . ( 55 sec) [ -9750.6482] [ 2172] [depth= 1] . ( 55 sec) [ -9747.4229] [Branch lengths ] . ( 55 sec) [ -9747.4077] [GTR parameters ] . ( 55 sec) [ -9747.3801] [Alpha ][ 0.919132] . ( 59 sec) [ -9746.7453] [Branch lengths ] . ( 75 sec) [ -9746.6014] [ 2171] [depth= 2] . ( 82 sec) [ -9746.4965] [Branch lengths ] . ( 82 sec) [ -9746.4943] [GTR parameters ] . ( 82 sec) [ -9746.4880] [Alpha ][ 0.926620] . ( 82 sec) [ -9746.4880] [Topology ] . ( 83 sec) [ -9746.4804] [Topology ] . ( 84 sec) [ -9746.4777] [Topology ] . ( 84 sec) [ -9746.4763] [Topology ] . ( 85 sec) [ -9746.4755] [Topology ] . ( 85 sec) [ -9746.4754] [GTR parameters ] . ( 85 sec) [ -9746.4754] [Alpha ][ 0.927546] . ( 85 sec) [ -9746.4754] [Topology ] . ( 86 sec) [ -9746.4749] [Topology ] . ( 86 sec) [ -9746.4749] [GTR parameters ] . ( 86 sec) [ -9746.4749] [Alpha ][ 0.927546] . Checking for NNIs, optimizing five branches... . ( 92 sec) [ -9746.4740] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -9746.4738] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9747.322299 . Log likelihood obtained after SPR moves : -9746.473802 . Log likelihood of the current tree: -9746.473802. . Printing the most likely tree in file 'data20.phy_phyml_tree.txt'... . Best log likelihood : -9746.473802 . Time used 0h1m45s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo