.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data100.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... . 450 patterns found. (out of a total of 500 sites) . 47 sites without polymorphism (9.40%). . [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) [ -21370.5219] [GTR parameters ] . ( 2 sec) [ -20934.1511] [Alpha ][ 0.500960] . ( 2 sec) [ -20842.2735] [ 5289] [depth= 7] . ( 2 sec) [ -20519.2044] [ 5224] [depth= 5] . ( 2 sec) [ -20209.3471] [ 5165] [depth= 1] . ( 2 sec) [ -20151.6395] [ 5131] [depth= 7] . ( 2 sec) [ -19745.8114] [ 5004] [depth= 5] . ( 2 sec) [ -19653.5204] [ 4981] [depth= 2] . ( 2 sec) [ -19229.0797] [ 4916] [depth= 5] . ( 2 sec) [ -19100.7008] [ 4901] [depth= 1] . ( 2 sec) [ -18888.5176] [ 4846] [depth= 2] . ( 3 sec) [ -18625.1005] [ 4770] [depth= 9] . ( 3 sec) [ -18561.4410] [ 4721] [depth= 8] . ( 3 sec) [ -18397.2588] [ 4722] [depth= 15] . ( 3 sec) [ -17993.3700] [ 4593] [depth= 14] . ( 3 sec) [ -17896.8815] [ 4585] [depth= 1] . ( 3 sec) [ -17747.5450] [ 4563] [depth= 4] . ( 3 sec) [ -17702.6850] [ 4478] [depth= 3] . ( 3 sec) [ -17582.2662] [ 4472] [depth= 4] . ( 3 sec) [ -17512.8716] [ 4451] [depth= 2] . ( 3 sec) [ -17378.2732] [ 4438] [depth= 1] . ( 3 sec) [ -17345.7978] [ 4419] [depth= 17] . ( 3 sec) [ -17048.7216] [ 4339] [depth= 8] . ( 3 sec) [ -16766.7463] [ 4236] [depth= 13] . ( 3 sec) [ -16695.6144] [ 4226] [depth= 2] . ( 3 sec) [ -16671.6671] [ 4208] [depth= 1] . ( 3 sec) [ -16347.9718] [ 4065] [depth= 17] . ( 3 sec) [ -16201.5718] [ 4031] [depth= 9] . ( 3 sec) [ -15825.1244] [ 3955] [depth= 12] . ( 4 sec) [ -15427.8511] [ 3953] [depth= 9] . ( 4 sec) [ -15229.5631] [ 3851] [depth= 3] . ( 4 sec) [ -15106.8046] [ 3860] [depth= 1] . ( 4 sec) [ -14961.6181] [ 3824] [depth= 5] . ( 4 sec) [ -14928.3816] [ 3804] [depth= 1] . ( 4 sec) [ -14836.1228] [ 3746] [depth= 8] . ( 4 sec) [ -14599.8803] [ 3680] [depth= 4] . ( 4 sec) [ -14344.1304] [ 3537] [depth= 9] . ( 4 sec) [ -14227.3305] [ 3508] [depth= 1] . ( 4 sec) [ -14100.5755] [ 3459] [depth= 5] . ( 4 sec) [ -13901.2693] [ 3386] [depth= 12] . ( 4 sec) [ -13786.4515] [ 3377] [depth= 1] . ( 4 sec) [ -13783.6800] [ 3359] [depth= 2] . ( 4 sec) [ -13678.5088] [ 3358] [depth= 1] . ( 5 sec) [ -13445.1848] [ 3283] [depth= 1] . ( 5 sec) [ -13425.4327] [ 3280] [depth= 1] . ( 5 sec) [ -13330.7030] [ 3250] [depth= 4] . ( 5 sec) [ -13216.4141] [ 3152] [depth= 14] . ( 5 sec) [ -13181.4178] [ 3141] [depth= 2] . ( 5 sec) [ -13103.9072] [ 3110] [depth= 1] . ( 5 sec) [ -13084.6909] [ 3113] [depth= 2] . ( 5 sec) [ -13083.3247] [ 3111] [depth= 1] . ( 5 sec) [ -12691.0436] [ 3014] [depth= 12] . ( 5 sec) [ -12578.7516] [ 2980] [depth= 1] . ( 5 sec) [ -12568.3098] [ 2973] [depth= 2] . ( 5 sec) [ -12414.4692] [ 2977] [depth= 1] . ( 5 sec) [ -12412.5031] [ 2974] [depth= 2] . ( 5 sec) [ -12384.2182] [ 2967] [depth= 1] . ( 6 sec) [ -12010.3443] [ 2923] [depth= 3] . ( 6 sec) [ -12009.3629] [ 2927] [depth= 1] . ( 6 sec) [ -12006.8642] [ 2934] [depth= 1] . ( 6 sec) [ -11993.4070] [ 2927] [depth= 1] . ( 6 sec) [ -11667.5526] [ 2773] [depth= 3] . ( 6 sec) [ -11416.8043] [ 2750] [depth= 1] . ( 6 sec) [ -11314.6508] [ 2665] [depth= 9] . ( 6 sec) [ -11294.0040] [ 2683] [depth= 2] . ( 6 sec) [ -11292.6638] [ 2664] [depth= 1] . ( 6 sec) [ -11224.4595] [ 2665] [depth= 2] . ( 6 sec) [ -11221.8287] [ 2647] [depth= 1] . ( 6 sec) [ -11220.9636] [ 2648] [depth= 1] . ( 7 sec) [ -11218.8703] [ 2631] [depth= 2] . ( 7 sec) [ -11217.3726] [ 2631] [depth= 1] . ( 7 sec) [ -10999.7796] [ 2626] [depth= 2] . ( 7 sec) [ -10988.5712] [ 2626] [depth= 1] . ( 7 sec) [ -10967.7269] [ 2615] [depth= 4] . ( 7 sec) [ -10956.4848] [ 2611] [depth= 1] . ( 7 sec) [ -10944.6415] [ 2611] [depth= 1] . ( 8 sec) [ -10919.3046] [ 2600] [depth= 1] . ( 8 sec) [ -10730.9444] [Branch lengths ] . ( 9 sec) [ -10724.2929] [GTR parameters ] . ( 9 sec) [ -10687.7153] [Alpha ][ 0.878171] . ( 10 sec) [ -10687.4292] [ 2595] [depth= 1] . ( 10 sec) [ -10685.8575] [ 2587] [depth= 2] . ( 10 sec) [ -10685.8394] [ 2588] [depth= 1] . ( 10 sec) [ -10679.5841] [ 2589] [depth= 1] . ( 10 sec) [ -10660.7630] [ 2558] [depth= 1] . ( 11 sec) [ -10660.4710] [ 2557] [depth= 1] . ( 11 sec) [ -10651.4879] [ 2558] [depth= 2] . ( 11 sec) [ -10536.2288] [ 2513] [depth= 2] . ( 11 sec) [ -10536.1325] [ 2513] [depth= 1] . ( 11 sec) [ -10535.4804] [ 2514] [depth= 2] . ( 12 sec) [ -10535.2958] [ 2519] [depth= 1] . ( 12 sec) [ -10534.6161] [ 2512] [depth= 2] . ( 12 sec) [ -10529.1024] [ 2508] [depth= 1] . ( 13 sec) [ -10529.0289] [ 2512] [depth= 1] . ( 13 sec) [ -10527.8632] [ 2515] [depth= 1] . ( 13 sec) [ -10527.8240] [ 2515] [depth= 2] . ( 13 sec) [ -10524.1503] [ 2519] [depth= 1] . ( 14 sec) [ -10523.9631] [ 2519] [depth= 1] . ( 15 sec) [ -10523.6346] [ 2524] [depth= 2] . ( 16 sec) [ -10523.1364] [ 2522] [depth= 1] . ( 17 sec) [ -10504.7271] [Branch lengths ] . ( 17 sec) [ -10504.0615] [GTR parameters ] . ( 17 sec) [ -10503.3056] [Alpha ][ 0.953588] . ( 19 sec) [ -10503.0893] [ 2515] [depth= 1] . ( 19 sec) [ -10502.7383] [ 2513] [depth= 1] . ( 20 sec) [ -10502.1561] [ 2515] [depth= 2] . ( 20 sec) [ -10502.1402] [ 2519] [depth= 1] . ( 23 sec) [ -10500.2119] [Branch lengths ] . ( 23 sec) [ -10500.2015] [GTR parameters ] . ( 24 sec) [ -10500.1834] [Alpha ][ 0.966152] . ( 27 sec) [ -10499.7957] [ 2515] [depth= 1] . ( 30 sec) [ -10499.5596] [Branch lengths ] . ( 31 sec) [ -10499.5583] [GTR parameters ] . ( 31 sec) [ -10499.5583] [Alpha ][ 0.966152] . ( 63 sec) [ -10499.5415] [Branch lengths ] . ( 63 sec) [ -10499.5415] [Topology ] . ( 64 sec) [ -10499.5397] [Topology ] . ( 65 sec) [ -10499.5390] [Topology ] . ( 65 sec) [ -10499.5389] [GTR parameters ] . ( 65 sec) [ -10499.5389] [Alpha ][ 0.967118] . ( 65 sec) [ -10499.5389] [Topology ] . ( 66 sec) [ -10499.5385] [Topology ] . ( 66 sec) [ -10499.5385] [GTR parameters ] . ( 66 sec) [ -10499.5385] [Alpha ][ 0.967118] . Checking for NNIs, optimizing five branches... . ( 74 sec) [ -10498.9876] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10498.987583. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22385.5252] [GTR parameters ] . ( 1 sec) [ -21952.1186] [Alpha ][ 0.500960] . ( 1 sec) [ -21849.7624] [ 5389] [depth= 9] . ( 1 sec) [ -21541.4620] [ 5312] [depth= 10] . ( 1 sec) [ -21165.7399] [ 5220] [depth= 4] . ( 1 sec) [ -20948.1826] [ 5210] [depth= 6] . ( 1 sec) [ -20766.1583] [ 5156] [depth= 1] . ( 2 sec) [ -20539.8820] [ 5109] [depth= 9] . ( 2 sec) [ -20185.3075] [ 5096] [depth= 1] . ( 2 sec) [ -20134.4041] [ 5072] [depth= 3] . ( 2 sec) [ -20047.9325] [ 5029] [depth= 1] . ( 2 sec) [ -19850.3844] [ 4998] [depth= 2] . ( 2 sec) [ -19665.1904] [ 4945] [depth= 2] . ( 2 sec) [ -19611.9101] [ 4930] [depth= 1] . ( 2 sec) [ -19327.4885] [ 4835] [depth= 11] . ( 2 sec) [ -19232.2360] [ 4829] [depth= 3] . ( 2 sec) [ -18941.8924] [ 4726] [depth= 4] . ( 2 sec) [ -18914.7285] [ 4777] [depth= 17] . ( 3 sec) [ -18720.4127] [ 4642] [depth= 12] . ( 3 sec) [ -18670.8248] [ 4623] [depth= 4] . ( 3 sec) [ -18538.7590] [ 4595] [depth= 3] . ( 3 sec) [ -17811.2684] [ 4472] [depth= 10] . ( 3 sec) [ -17494.8146] [ 4325] [depth= 18] . ( 3 sec) [ -17366.7290] [ 4346] [depth= 10] . ( 3 sec) [ -16641.7452] [ 4318] [depth= 16] . ( 3 sec) [ -16574.9983] [ 4277] [depth= 1] . ( 3 sec) [ -16137.1378] [ 4184] [depth= 3] . ( 3 sec) [ -16132.5852] [ 4179] [depth= 2] . ( 4 sec) [ -15714.6176] [ 4015] [depth= 7] . ( 4 sec) [ -15544.2162] [ 4012] [depth= 2] . ( 4 sec) [ -15539.1859] [ 4003] [depth= 9] . ( 4 sec) [ -15320.1720] [ 3992] [depth= 8] . ( 4 sec) [ -15124.7082] [ 3990] [depth= 1] . ( 4 sec) [ -15086.0496] [ 3990] [depth= 1] . ( 4 sec) [ -15067.4835] [ 4010] [depth= 1] . ( 4 sec) [ -14835.2444] [ 3919] [depth= 3] . ( 4 sec) [ -14622.3787] [ 3850] [depth= 3] . ( 4 sec) [ -14487.4426] [ 3848] [depth= 1] . ( 4 sec) [ -14453.5073] [ 3811] [depth= 4] . ( 5 sec) [ -14421.5757] [ 3798] [depth= 2] . ( 5 sec) [ -14229.6633] [ 3762] [depth= 4] . ( 5 sec) [ -14196.8192] [ 3764] [depth= 1] . ( 5 sec) [ -14149.9342] [ 3762] [depth= 8] . ( 5 sec) [ -14106.8605] [ 3742] [depth= 1] . ( 5 sec) [ -14054.6773] [ 3734] [depth= 3] . ( 5 sec) [ -13833.3911] [ 3581] [depth= 3] . ( 5 sec) [ -13822.5620] [ 3586] [depth= 2] . ( 5 sec) [ -13682.2367] [ 3576] [depth= 1] . ( 5 sec) [ -13461.5923] [ 3509] [depth= 3] . ( 5 sec) [ -13446.5579] [ 3500] [depth= 1] . ( 6 sec) [ -13446.2829] [ 3497] [depth= 1] . ( 6 sec) [ -13179.5643] [ 3380] [depth= 3] . ( 6 sec) [ -13167.3548] [ 3363] [depth= 2] . ( 6 sec) [ -13163.4547] [ 3375] [depth= 1] . ( 6 sec) [ -13152.2717] [ 3373] [depth= 1] . ( 6 sec) [ -13018.7591] [ 3340] [depth= 3] . ( 6 sec) [ -12927.9436] [ 3328] [depth= 8] . ( 6 sec) [ -12804.5844] [ 3319] [depth= 2] . ( 6 sec) [ -12725.6785] [ 3271] [depth= 1] . ( 6 sec) [ -12606.8422] [ 3268] [depth= 2] . ( 7 sec) [ -12586.7233] [ 3279] [depth= 3] . ( 7 sec) [ -12422.4011] [ 3265] [depth= 1] . ( 7 sec) [ -12357.7027] [ 3234] [depth= 2] . ( 7 sec) [ -12347.1141] [ 3227] [depth= 1] . ( 7 sec) [ -12338.4584] [ 3227] [depth= 1] . ( 7 sec) [ -12272.6660] [ 3120] [depth= 8] . ( 7 sec) [ -12267.9845] [ 3094] [depth= 3] . ( 8 sec) [ -11990.5031] [ 2946] [depth= 4] . ( 8 sec) [ -11905.1224] [ 2933] [depth= 1] . ( 8 sec) [ -11746.9460] [ 2855] [depth= 4] . ( 8 sec) [ -11616.1294] [ 2807] [depth= 1] . ( 8 sec) [ -11540.3279] [ 2769] [depth= 2] . ( 8 sec) [ -11353.5069] [ 2785] [depth= 2] . ( 8 sec) [ -11290.2196] [ 2789] [depth= 1] . ( 8 sec) [ -11285.0835] [ 2779] [depth= 3] . ( 8 sec) [ -11233.5419] [ 2690] [depth= 6] . ( 8 sec) [ -11124.9910] [ 2654] [depth= 1] . ( 9 sec) [ -11067.0681] [ 2651] [depth= 1] . ( 9 sec) [ -11055.0776] [ 2645] [depth= 1] . ( 9 sec) [ -11054.1319] [ 2656] [depth= 1] . ( 9 sec) [ -10978.6402] [ 2641] [depth= 2] . ( 9 sec) [ -10966.3070] [ 2640] [depth= 1] . ( 9 sec) [ -10770.9777] [Branch lengths ] . ( 11 sec) [ -10765.5498] [GTR parameters ] . ( 11 sec) [ -10728.6109] [Alpha ][ 0.908083] . ( 11 sec) [ -10727.9614] [ 2639] [depth= 1] . ( 11 sec) [ -10719.5826] [ 2610] [depth= 2] . ( 11 sec) [ -10717.7696] [ 2611] [depth= 2] . ( 12 sec) [ -10694.4574] [ 2578] [depth= 1] . ( 12 sec) [ -10688.5081] [ 2578] [depth= 1] . ( 12 sec) [ -10687.5546] [ 2582] [depth= 1] . ( 12 sec) [ -10687.1479] [ 2579] [depth= 1] . ( 13 sec) [ -10687.0262] [ 2576] [depth= 1] . ( 13 sec) [ -10686.9737] [ 2576] [depth= 1] . ( 14 sec) [ -10686.6511] [ 2579] [depth= 1] . ( 14 sec) [ -10672.6948] [ 2565] [depth= 1] . ( 14 sec) [ -10669.1408] [ 2557] [depth= 1] . ( 14 sec) [ -10648.4069] [ 2548] [depth= 1] . ( 14 sec) [ -10648.0014] [ 2547] [depth= 1] . ( 15 sec) [ -10643.3630] [ 2529] [depth= 1] . ( 16 sec) [ -10628.1568] [ 2528] [depth= 1] . ( 16 sec) [ -10626.9067] [ 2526] [depth= 1] . ( 16 sec) [ -10614.8598] [ 2510] [depth= 1] . ( 17 sec) [ -10598.5835] [ 2513] [depth= 3] . ( 17 sec) [ -10595.7242] [ 2516] [depth= 2] . ( 17 sec) [ -10556.3411] [ 2526] [depth= 1] . ( 17 sec) [ -10556.1582] [ 2528] [depth= 1] . ( 18 sec) [ -10554.0151] [ 2512] [depth= 2] . ( 19 sec) [ -10516.0438] [Branch lengths ] . ( 19 sec) [ -10515.4826] [GTR parameters ] . ( 19 sec) [ -10514.9887] [Alpha ][ 0.971786] . ( 20 sec) [ -10502.2838] [ 2502] [depth= 1] . ( 20 sec) [ -10502.2621] [ 2506] [depth= 1] . ( 23 sec) [ -10502.2039] [ 2508] [depth= 1] . ( 23 sec) [ -10502.0419] [ 2507] [depth= 1] . ( 24 sec) [ -10502.0284] [ 2511] [depth= 1] . ( 25 sec) [ -10499.9148] [Branch lengths ] . ( 25 sec) [ -10499.8859] [GTR parameters ] . ( 25 sec) [ -10499.8841] [Alpha ][ 0.967719] . ( 31 sec) [ -10499.7411] [Branch lengths ] . ( 64 sec) [ -10499.7316] [Branch lengths ] . ( 64 sec) [ -10499.7316] [Topology ] . ( 65 sec) [ -10499.7308] [Topology ] . ( 65 sec) [ -10499.7306] [GTR parameters ] . ( 65 sec) [ -10499.7303] [Alpha ][ 0.966139] . ( 65 sec) [ -10499.7303] [Topology ] . ( 66 sec) [ -10499.7300] [Topology ] . ( 67 sec) [ -10499.7300] [GTR parameters ] . ( 67 sec) [ -10499.7300] [Alpha ][ 0.966139] . Checking for NNIs, optimizing five branches... . ( 77 sec) [ -10499.0921] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -10499.0889] [Topology ] . Checking for NNIs, optimizing five branches... . ( 96 sec) [ -10499.0880] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10499.087984. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21458.0265] [GTR parameters ] . ( 1 sec) [ -20999.3774] [Alpha ][ 0.500960] . ( 1 sec) [ -20715.9151] [ 5567] [depth= 6] . ( 1 sec) [ -20517.8197] [ 5485] [depth= 12] . ( 2 sec) [ -20489.2405] [ 5475] [depth= 3] . ( 2 sec) [ -20446.6986] [ 5471] [depth= 3] . ( 2 sec) [ -20330.0783] [ 5409] [depth= 2] . ( 2 sec) [ -20258.0210] [ 5391] [depth= 3] . ( 2 sec) [ -19797.6992] [ 5235] [depth= 10] . ( 2 sec) [ -19765.6962] [ 5171] [depth= 7] . ( 2 sec) [ -19176.2067] [ 5119] [depth= 1] . ( 2 sec) [ -18996.1089] [ 5016] [depth= 4] . ( 2 sec) [ -18833.1414] [ 5032] [depth= 9] . ( 2 sec) [ -18699.1232] [ 5017] [depth= 1] . ( 2 sec) [ -18530.0689] [ 4941] [depth= 10] . ( 2 sec) [ -18428.0782] [ 4918] [depth= 3] . ( 2 sec) [ -18422.3530] [ 4917] [depth= 1] . ( 3 sec) [ -18110.4990] [ 4911] [depth= 1] . ( 3 sec) [ -18052.1685] [ 4892] [depth= 2] . ( 3 sec) [ -18046.4012] [ 4886] [depth= 1] . ( 3 sec) [ -17856.2833] [ 4820] [depth= 10] . ( 3 sec) [ -17781.3348] [ 4810] [depth= 2] . ( 3 sec) [ -17508.8457] [ 4780] [depth= 5] . ( 3 sec) [ -16547.7420] [ 4594] [depth= 6] . ( 3 sec) [ -16091.1341] [ 4480] [depth= 11] . ( 3 sec) [ -15775.7473] [ 4305] [depth= 12] . ( 3 sec) [ -15426.8393] [ 4275] [depth= 7] . ( 3 sec) [ -15322.0785] [ 4246] [depth= 1] . ( 4 sec) [ -15268.0414] [ 4228] [depth= 1] . ( 4 sec) [ -15178.2832] [ 4211] [depth= 4] . ( 4 sec) [ -14779.6251] [ 4056] [depth= 13] . ( 4 sec) [ -14693.5225] [ 3992] [depth= 6] . ( 4 sec) [ -14569.0894] [ 3931] [depth= 7] . ( 4 sec) [ -14383.7296] [ 3901] [depth= 8] . ( 4 sec) [ -14236.6575] [ 3883] [depth= 8] . ( 4 sec) [ -14121.8860] [ 3858] [depth= 2] . ( 4 sec) [ -14022.3286] [ 3831] [depth= 8] . ( 4 sec) [ -13961.1352] [ 3775] [depth= 6] . ( 4 sec) [ -13658.5793] [ 3778] [depth= 4] . ( 5 sec) [ -13634.3505] [ 3763] [depth= 1] . ( 5 sec) [ -13597.1262] [ 3749] [depth= 14] . ( 5 sec) [ -13467.1198] [ 3667] [depth= 8] . ( 5 sec) [ -13467.0208] [ 3668] [depth= 1] . ( 5 sec) [ -12986.3750] [ 3571] [depth= 6] . ( 5 sec) [ -12975.3534] [ 3550] [depth= 2] . ( 5 sec) [ -12905.8948] [ 3537] [depth= 1] . ( 5 sec) [ -12864.5428] [ 3465] [depth= 5] . ( 5 sec) [ -12844.0361] [ 3459] [depth= 2] . ( 5 sec) [ -12841.0130] [ 3461] [depth= 1] . ( 6 sec) [ -12663.2300] [ 3282] [depth= 3] . ( 6 sec) [ -12654.0359] [ 3280] [depth= 1] . ( 6 sec) [ -12619.3481] [ 3272] [depth= 1] . ( 6 sec) [ -12559.6776] [ 3267] [depth= 4] . ( 6 sec) [ -12559.2591] [ 3269] [depth= 1] . ( 6 sec) [ -12532.8271] [ 3273] [depth= 7] . ( 6 sec) [ -12403.2097] [ 3200] [depth= 5] . ( 6 sec) [ -12302.8721] [ 3204] [depth= 2] . ( 6 sec) [ -12172.7542] [ 3100] [depth= 12] . ( 6 sec) [ -12137.2298] [ 3113] [depth= 1] . ( 7 sec) [ -12133.1656] [ 3112] [depth= 1] . ( 7 sec) [ -11989.7365] [ 3054] [depth= 4] . ( 7 sec) [ -11983.1329] [ 3053] [depth= 1] . ( 7 sec) [ -11853.4788] [ 3022] [depth= 1] . ( 7 sec) [ -11853.0856] [ 3022] [depth= 1] . ( 7 sec) [ -11734.4364] [ 3003] [depth= 1] . ( 7 sec) [ -11601.6929] [ 2946] [depth= 3] . ( 8 sec) [ -11492.9520] [ 2903] [depth= 8] . ( 8 sec) [ -11487.9482] [ 2901] [depth= 3] . ( 8 sec) [ -11487.7649] [ 2902] [depth= 1] . ( 8 sec) [ -11468.5784] [ 2901] [depth= 1] . ( 8 sec) [ -11283.8047] [ 2837] [depth= 5] . ( 8 sec) [ -11257.2541] [ 2737] [depth= 1] . ( 8 sec) [ -11190.4901] [ 2699] [depth= 1] . ( 8 sec) [ -11187.5806] [ 2690] [depth= 2] . ( 8 sec) [ -11183.7562] [ 2689] [depth= 1] . ( 8 sec) [ -11179.7862] [ 2690] [depth= 1] . ( 9 sec) [ -11012.6299] [ 2688] [depth= 1] . ( 9 sec) [ -10906.9648] [ 2646] [depth= 3] . ( 9 sec) [ -10847.2620] [ 2609] [depth= 3] . ( 9 sec) [ -10688.9789] [Branch lengths ] . ( 10 sec) [ -10683.7052] [GTR parameters ] . ( 10 sec) [ -10651.8299] [Alpha ][ 0.872069] . ( 10 sec) [ -10644.9874] [ 2601] [depth= 2] . ( 11 sec) [ -10644.8788] [ 2588] [depth= 1] . ( 11 sec) [ -10641.0722] [ 2582] [depth= 1] . ( 11 sec) [ -10611.0049] [ 2559] [depth= 1] . ( 11 sec) [ -10610.5184] [ 2546] [depth= 1] . ( 11 sec) [ -10579.9817] [ 2521] [depth= 1] . ( 11 sec) [ -10574.2169] [ 2525] [depth= 1] . ( 11 sec) [ -10574.0101] [ 2521] [depth= 1] . ( 12 sec) [ -10573.7063] [ 2521] [depth= 1] . ( 12 sec) [ -10569.8787] [ 2517] [depth= 2] . ( 12 sec) [ -10569.5684] [ 2517] [depth= 1] . ( 13 sec) [ -10565.2849] [ 2518] [depth= 1] . ( 13 sec) [ -10565.0716] [ 2518] [depth= 1] . ( 13 sec) [ -10564.9814] [ 2517] [depth= 1] . ( 13 sec) [ -10564.5144] [ 2518] [depth= 2] . ( 14 sec) [ -10564.4998] [ 2522] [depth= 1] . ( 14 sec) [ -10562.4779] [ 2523] [depth= 1] . ( 15 sec) [ -10562.4254] [ 2523] [depth= 1] . ( 16 sec) [ -10546.3447] [ 2521] [depth= 2] . ( 16 sec) [ -10536.4027] [ 2508] [depth= 1] . ( 17 sec) [ -10536.2611] [ 2508] [depth= 2] . ( 17 sec) [ -10535.6847] [ 2504] [depth= 1] . ( 17 sec) [ -10535.2399] [ 2524] [depth= 1] . ( 18 sec) [ -10520.6719] [Branch lengths ] . ( 18 sec) [ -10520.5077] [GTR parameters ] . ( 18 sec) [ -10519.5867] [Alpha ][ 0.957050] . ( 19 sec) [ -10519.3741] [ 2523] [depth= 1] . ( 19 sec) [ -10518.9644] [ 2514] [depth= 2] . ( 19 sec) [ -10518.2276] [ 2534] [depth= 2] . ( 19 sec) [ -10518.1280] [ 2534] [depth= 1] . ( 20 sec) [ -10513.5776] [ 2523] [depth= 1] . ( 20 sec) [ -10509.8464] [ 2505] [depth= 1] . ( 21 sec) [ -10509.8277] [ 2508] [depth= 1] . ( 21 sec) [ -10509.7694] [ 2509] [depth= 1] . ( 21 sec) [ -10508.6839] [ 2510] [depth= 2] . ( 22 sec) [ -10508.0436] [ 2514] [depth= 1] . ( 22 sec) [ -10508.0032] [ 2518] [depth= 1] . ( 24 sec) [ -10507.5519] [ 2514] [depth= 1] . ( 24 sec) [ -10506.6029] [ 2516] [depth= 1] . ( 25 sec) [ -10500.7540] [Branch lengths ] . ( 26 sec) [ -10500.7328] [GTR parameters ] . ( 26 sec) [ -10500.7084] [Alpha ][ 0.971968] . ( 27 sec) [ -10500.6254] [ 2513] [depth= 1] . ( 32 sec) [ -10500.5642] [ 2514] [depth= 1] . ( 32 sec) [ -10499.9181] [Branch lengths ] . ( 32 sec) [ -10499.9165] [GTR parameters ] . ( 33 sec) [ -10499.9156] [Alpha ][ 0.969074] . ( 64 sec) [ -10499.7693] [Branch lengths ] . ( 64 sec) [ -10499.7693] [Topology ] . ( 66 sec) [ -10499.7483] [Topology ] . ( 67 sec) [ -10499.7389] [Topology ] . ( 68 sec) [ -10499.7349] [Topology ] . ( 69 sec) [ -10499.7332] [Topology ] . ( 70 sec) [ -10499.7324] [Topology ] . ( 71 sec) [ -10499.7317] [GTR parameters ] . ( 71 sec) [ -10499.7309] [Alpha ][ 0.966316] . ( 71 sec) [ -10499.7309] [Topology ] . ( 72 sec) [ -10499.7304] [Topology ] . ( 72 sec) [ -10499.7304] [GTR parameters ] . ( 72 sec) [ -10499.7304] [Alpha ][ 0.966316] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -10499.0922] [Topology ] . Checking for NNIs, optimizing five branches... . ( 91 sec) [ -10499.0894] [Topology ] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -10499.0885] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10499.088460. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21946.9547] [GTR parameters ] . ( 1 sec) [ -21562.7413] [Alpha ][ 0.500960] . ( 1 sec) [ -21294.3839] [ 5208] [depth= 9] . ( 1 sec) [ -20854.4008] [ 5114] [depth= 10] . ( 1 sec) [ -20797.6572] [ 5047] [depth= 8] . ( 1 sec) [ -20380.2357] [ 4922] [depth= 3] . ( 1 sec) [ -20321.8889] [ 4858] [depth= 2] . ( 1 sec) [ -19785.8100] [ 4851] [depth= 7] . ( 1 sec) [ -19716.7682] [ 4830] [depth= 1] . ( 1 sec) [ -19562.4910] [ 4810] [depth= 4] . ( 1 sec) [ -19394.5117] [ 4778] [depth= 3] . ( 1 sec) [ -19208.2756] [ 4795] [depth= 4] . ( 2 sec) [ -18793.5073] [ 4664] [depth= 5] . ( 2 sec) [ -18129.0863] [ 4549] [depth= 8] . ( 2 sec) [ -17766.3424] [ 4543] [depth= 5] . ( 2 sec) [ -17620.6924] [ 4518] [depth= 8] . ( 2 sec) [ -17598.0260] [ 4466] [depth= 5] . ( 2 sec) [ -17538.6863] [ 4438] [depth= 1] . ( 2 sec) [ -17330.5910] [ 4315] [depth= 16] . ( 2 sec) [ -17191.0723] [ 4290] [depth= 1] . ( 2 sec) [ -17000.5987] [ 4196] [depth= 4] . ( 2 sec) [ -16563.6873] [ 4123] [depth= 4] . ( 2 sec) [ -16301.2476] [ 4046] [depth= 3] . ( 3 sec) [ -16208.9697] [ 4017] [depth= 3] . ( 3 sec) [ -16077.7085] [ 3955] [depth= 3] . ( 3 sec) [ -15443.3705] [ 3900] [depth= 11] . ( 3 sec) [ -15395.4071] [ 3922] [depth= 2] . ( 3 sec) [ -15122.0449] [ 3805] [depth= 5] . ( 3 sec) [ -14977.5291] [ 3789] [depth= 1] . ( 3 sec) [ -14870.4827] [ 3692] [depth= 13] . ( 3 sec) [ -14801.5882] [ 3682] [depth= 1] . ( 3 sec) [ -14729.7554] [ 3682] [depth= 2] . ( 3 sec) [ -14673.5387] [ 3645] [depth= 1] . ( 3 sec) [ -14578.4043] [ 3616] [depth= 2] . ( 4 sec) [ -14453.9397] [ 3623] [depth= 1] . ( 4 sec) [ -14320.0596] [ 3627] [depth= 8] . ( 4 sec) [ -14211.3859] [ 3520] [depth= 14] . ( 4 sec) [ -14136.5356] [ 3527] [depth= 3] . ( 4 sec) [ -13948.9745] [ 3511] [depth= 3] . ( 4 sec) [ -13799.1450] [ 3509] [depth= 1] . ( 4 sec) [ -13497.9780] [ 3479] [depth= 10] . ( 4 sec) [ -13393.6711] [ 3446] [depth= 2] . ( 4 sec) [ -13326.2033] [ 3396] [depth= 12] . ( 4 sec) [ -13112.0090] [ 3317] [depth= 11] . ( 5 sec) [ -13091.2407] [ 3328] [depth= 8] . ( 5 sec) [ -12745.1457] [ 3217] [depth= 11] . ( 5 sec) [ -12743.3322] [ 3225] [depth= 1] . ( 5 sec) [ -12741.1663] [ 3224] [depth= 1] . ( 5 sec) [ -12707.5426] [ 3220] [depth= 1] . ( 5 sec) [ -12669.6699] [ 3217] [depth= 1] . ( 5 sec) [ -12632.7194] [ 3185] [depth= 1] . ( 5 sec) [ -12588.6289] [ 3174] [depth= 5] . ( 5 sec) [ -12578.5303] [ 3166] [depth= 1] . ( 5 sec) [ -12575.7565] [ 3166] [depth= 1] . ( 6 sec) [ -12567.3707] [ 3173] [depth= 3] . ( 6 sec) [ -12313.4373] [ 3132] [depth= 2] . ( 6 sec) [ -12274.0979] [ 3072] [depth= 1] . ( 6 sec) [ -12239.9375] [ 3074] [depth= 2] . ( 6 sec) [ -12126.4970] [ 3024] [depth= 5] . ( 6 sec) [ -12111.8239] [ 3023] [depth= 1] . ( 6 sec) [ -12000.7158] [ 3011] [depth= 1] . ( 6 sec) [ -11814.2002] [ 2946] [depth= 4] . ( 6 sec) [ -11752.1649] [ 2946] [depth= 1] . ( 6 sec) [ -11743.2598] [ 2946] [depth= 1] . ( 6 sec) [ -11677.6893] [ 2934] [depth= 1] . ( 6 sec) [ -11668.4921] [ 2936] [depth= 2] . ( 7 sec) [ -11554.3519] [ 2895] [depth= 7] . ( 7 sec) [ -11499.6318] [ 2860] [depth= 1] . ( 7 sec) [ -11299.3973] [ 2779] [depth= 5] . ( 7 sec) [ -11283.1651] [ 2751] [depth= 3] . ( 7 sec) [ -11211.4856] [ 2728] [depth= 2] . ( 7 sec) [ -11211.1609] [ 2728] [depth= 1] . ( 7 sec) [ -11160.4538] [ 2736] [depth= 1] . ( 7 sec) [ -11140.4203] [ 2724] [depth= 1] . ( 8 sec) [ -11096.0001] [ 2689] [depth= 3] . ( 8 sec) [ -11043.4031] [ 2713] [depth= 1] . ( 8 sec) [ -10884.8408] [ 2647] [depth= 5] . ( 8 sec) [ -10879.6060] [ 2640] [depth= 1] . ( 8 sec) [ -10856.0018] [ 2616] [depth= 1] . ( 8 sec) [ -10842.9932] [ 2597] [depth= 1] . ( 8 sec) [ -10834.9506] [ 2591] [depth= 2] . ( 8 sec) [ -10834.4421] [ 2586] [depth= 2] . ( 8 sec) [ -10821.8987] [ 2574] [depth= 1] . ( 8 sec) [ -10782.1294] [ 2564] [depth= 1] . ( 8 sec) [ -10769.0276] [ 2559] [depth= 1] . ( 9 sec) [ -10622.0141] [Branch lengths ] . ( 10 sec) [ -10618.8745] [GTR parameters ] . ( 10 sec) [ -10579.7193] [Alpha ][ 0.920072] . ( 10 sec) [ -10579.6303] [ 2564] [depth= 1] . ( 11 sec) [ -10578.4993] [ 2562] [depth= 1] . ( 11 sec) [ -10577.3145] [ 2562] [depth= 2] . ( 11 sec) [ -10576.6237] [ 2566] [depth= 1] . ( 11 sec) [ -10575.3933] [ 2573] [depth= 2] . ( 11 sec) [ -10571.7711] [ 2562] [depth= 1] . ( 12 sec) [ -10566.7302] [ 2545] [depth= 1] . ( 12 sec) [ -10566.0027] [ 2538] [depth= 1] . ( 12 sec) [ -10565.8834] [ 2538] [depth= 1] . ( 12 sec) [ -10561.5330] [ 2535] [depth= 1] . ( 13 sec) [ -10560.6366] [ 2531] [depth= 1] . ( 13 sec) [ -10540.3210] [ 2524] [depth= 1] . ( 13 sec) [ -10522.2040] [ 2512] [depth= 2] . ( 13 sec) [ -10518.6901] [ 2511] [depth= 1] . ( 14 sec) [ -10518.3901] [ 2514] [depth= 1] . ( 14 sec) [ -10518.2323] [ 2517] [depth= 1] . ( 14 sec) [ -10517.4506] [ 2514] [depth= 1] . ( 15 sec) [ -10517.3592] [ 2514] [depth= 1] . ( 15 sec) [ -10517.0445] [ 2519] [depth= 2] . ( 15 sec) [ -10516.8777] [ 2514] [depth= 1] . ( 16 sec) [ -10516.6455] [ 2512] [depth= 1] . ( 16 sec) [ -10516.5955] [ 2512] [depth= 1] . ( 17 sec) [ -10503.7864] [Branch lengths ] . ( 17 sec) [ -10503.7396] [GTR parameters ] . ( 17 sec) [ -10503.4009] [Alpha ][ 0.973386] . ( 20 sec) [ -10503.0201] [ 2512] [depth= 1] . ( 21 sec) [ -10502.9694] [ 2510] [depth= 1] . ( 21 sec) [ -10502.9372] [ 2512] [depth= 1] . ( 23 sec) [ -10501.3776] [Branch lengths ] . ( 23 sec) [ -10501.3770] [GTR parameters ] . ( 24 sec) [ -10501.3753] [Alpha ][ 0.969374] . ( 29 sec) [ -10501.1988] [Branch lengths ] . ( 30 sec) [ -10501.1715] [ 2518] [depth= 2] . ( 58 sec) [ -10501.1269] [Branch lengths ] . ( 58 sec) [ -10501.1264] [GTR parameters ] . ( 59 sec) [ -10501.1250] [Alpha ][ 0.965784] . ( 59 sec) [ -10501.1250] [Topology ] . ( 60 sec) [ -10501.1187] [Topology ] . ( 61 sec) [ -10501.1163] [Topology ] . ( 62 sec) [ -10501.1151] [Topology ] . ( 64 sec) [ -10501.1144] [Topology ] . ( 64 sec) [ -10501.1143] [GTR parameters ] . ( 64 sec) [ -10501.1142] [Alpha ][ 0.964686] . ( 64 sec) [ -10501.1142] [Topology ] . ( 65 sec) [ -10501.1137] [Topology ] . ( 65 sec) [ -10501.1137] [GTR parameters ] . ( 65 sec) [ -10501.1137] [Alpha ][ 0.964686] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10501.113688. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21970.5936] [GTR parameters ] . ( 1 sec) [ -21471.9803] [Alpha ][ 0.500960] . ( 1 sec) [ -21186.8716] [ 5572] [depth= 8] . ( 1 sec) [ -20905.4462] [ 5513] [depth= 12] . ( 1 sec) [ -20550.3252] [ 5436] [depth= 5] . ( 2 sec) [ -20488.9046] [ 5429] [depth= 1] . ( 2 sec) [ -20148.2700] [ 5356] [depth= 3] . ( 2 sec) [ -20029.3563] [ 5360] [depth= 5] . ( 2 sec) [ -19694.8999] [ 5316] [depth= 6] . ( 2 sec) [ -19669.1878] [ 5262] [depth= 1] . ( 2 sec) [ -19449.0280] [ 5189] [depth= 20] . ( 2 sec) [ -19208.0276] [ 5142] [depth= 1] . ( 2 sec) [ -19035.7442] [ 5078] [depth= 6] . ( 2 sec) [ -18558.5789] [ 4986] [depth= 2] . ( 2 sec) [ -18556.9229] [ 4985] [depth= 1] . ( 2 sec) [ -18455.5708] [ 4962] [depth= 4] . ( 3 sec) [ -18391.2769] [ 4946] [depth= 5] . ( 3 sec) [ -18357.2686] [ 4944] [depth= 1] . ( 3 sec) [ -18078.6358] [ 4900] [depth= 4] . ( 3 sec) [ -18047.5642] [ 4896] [depth= 5] . ( 3 sec) [ -17867.7577] [ 4882] [depth= 10] . ( 3 sec) [ -17440.4773] [ 4732] [depth= 11] . ( 3 sec) [ -17203.2043] [ 4695] [depth= 4] . ( 3 sec) [ -17021.0804] [ 4603] [depth= 7] . ( 3 sec) [ -16968.0844] [ 4577] [depth= 1] . ( 3 sec) [ -16777.1217] [ 4503] [depth= 6] . ( 4 sec) [ -16382.0142] [ 4397] [depth= 15] . ( 4 sec) [ -16336.9676] [ 4395] [depth= 1] . ( 4 sec) [ -16264.3583] [ 4381] [depth= 7] . ( 4 sec) [ -16264.3352] [ 4383] [depth= 1] . ( 4 sec) [ -15970.7890] [ 4287] [depth= 3] . ( 4 sec) [ -15517.7768] [ 4097] [depth= 7] . ( 4 sec) [ -15511.6848] [ 4097] [depth= 1] . ( 4 sec) [ -15306.9612] [ 4009] [depth= 12] . ( 4 sec) [ -15254.0256] [ 4025] [depth= 3] . ( 4 sec) [ -15147.7262] [ 4004] [depth= 1] . ( 5 sec) [ -14816.2881] [ 3890] [depth= 2] . ( 5 sec) [ -14784.8536] [ 3843] [depth= 3] . ( 5 sec) [ -14742.5691] [ 3865] [depth= 3] . ( 5 sec) [ -14681.5643] [ 3830] [depth= 1] . ( 5 sec) [ -14583.2925] [ 3783] [depth= 15] . ( 5 sec) [ -14347.8676] [ 3718] [depth= 7] . ( 5 sec) [ -14165.8282] [ 3625] [depth= 9] . ( 6 sec) [ -14117.5415] [ 3615] [depth= 1] . ( 6 sec) [ -13879.6667] [ 3554] [depth= 3] . ( 6 sec) [ -13781.3907] [ 3517] [depth= 1] . ( 6 sec) [ -13704.8882] [ 3525] [depth= 4] . ( 6 sec) [ -13496.9135] [ 3447] [depth= 11] . ( 7 sec) [ -13472.5984] [ 3447] [depth= 2] . ( 7 sec) [ -13374.2825] [ 3390] [depth= 1] . ( 7 sec) [ -13228.4215] [ 3332] [depth= 7] . ( 7 sec) [ -13185.9619] [ 3317] [depth= 1] . ( 7 sec) [ -13125.0601] [ 3326] [depth= 1] . ( 7 sec) [ -13109.1655] [ 3320] [depth= 4] . ( 7 sec) [ -12892.2521] [ 3285] [depth= 2] . ( 7 sec) [ -12775.9480] [ 3279] [depth= 1] . ( 8 sec) [ -12659.7696] [ 3262] [depth= 7] . ( 8 sec) [ -12579.0472] [ 3255] [depth= 1] . ( 8 sec) [ -12568.4665] [ 3273] [depth= 1] . ( 8 sec) [ -12516.5012] [ 3231] [depth= 8] . ( 8 sec) [ -12398.1266] [ 3185] [depth= 1] . ( 8 sec) [ -12372.9339] [ 3179] [depth= 2] . ( 8 sec) [ -12324.7737] [ 3150] [depth= 1] . ( 8 sec) [ -12274.5414] [ 3131] [depth= 1] . ( 8 sec) [ -12225.6547] [ 3064] [depth= 1] . ( 9 sec) [ -12085.2765] [ 3003] [depth= 3] . ( 9 sec) [ -11991.6221] [ 2980] [depth= 1] . ( 9 sec) [ -11916.1599] [ 2961] [depth= 2] . ( 9 sec) [ -11753.6432] [ 2881] [depth= 2] . ( 9 sec) [ -11744.1147] [ 2868] [depth= 1] . ( 9 sec) [ -11697.1792] [ 2831] [depth= 2] . ( 9 sec) [ -11671.8698] [ 2828] [depth= 1] . ( 9 sec) [ -11647.0568] [ 2817] [depth= 1] . ( 9 sec) [ -11210.4172] [ 2701] [depth= 6] . ( 9 sec) [ -11210.3186] [ 2700] [depth= 1] . ( 10 sec) [ -11198.8838] [ 2700] [depth= 1] . ( 10 sec) [ -11158.9002] [ 2671] [depth= 1] . ( 10 sec) [ -11137.5281] [ 2664] [depth= 2] . ( 10 sec) [ -11122.3627] [ 2669] [depth= 2] . ( 10 sec) [ -11092.7844] [ 2661] [depth= 1] . ( 10 sec) [ -11030.4102] [ 2639] [depth= 2] . ( 11 sec) [ -10954.6295] [ 2610] [depth= 4] . ( 11 sec) [ -10939.9911] [ 2604] [depth= 2] . ( 11 sec) [ -10910.3705] [ 2596] [depth= 3] . ( 11 sec) [ -10664.2530] [Branch lengths ] . ( 12 sec) [ -10657.2358] [GTR parameters ] . ( 13 sec) [ -10623.7009] [Alpha ][ 0.891108] . ( 13 sec) [ -10601.7991] [ 2569] [depth= 2] . ( 13 sec) [ -10598.7267] [ 2570] [depth= 1] . ( 14 sec) [ -10597.3276] [ 2568] [depth= 1] . ( 14 sec) [ -10591.8121] [ 2560] [depth= 1] . ( 14 sec) [ -10565.6967] [ 2543] [depth= 2] . ( 14 sec) [ -10564.0576] [ 2531] [depth= 1] . ( 15 sec) [ -10563.8313] [ 2532] [depth= 1] . ( 16 sec) [ -10563.6176] [ 2532] [depth= 1] . ( 16 sec) [ -10548.7547] [ 2497] [depth= 1] . ( 17 sec) [ -10544.3184] [ 2499] [depth= 1] . ( 17 sec) [ -10530.4400] [ 2508] [depth= 1] . ( 17 sec) [ -10524.2559] [ 2499] [depth= 1] . ( 18 sec) [ -10524.1136] [ 2501] [depth= 1] . ( 18 sec) [ -10524.1008] [ 2501] [depth= 1] . ( 18 sec) [ -10503.5394] [Branch lengths ] . ( 20 sec) [ -10502.9555] [GTR parameters ] . ( 20 sec) [ -10502.0614] [Alpha ][ 0.977468] . ( 20 sec) [ -10502.0497] [ 2502] [depth= 1] . ( 21 sec) [ -10502.0302] [ 2501] [depth= 1] . ( 21 sec) [ -10502.0170] [ 2501] [depth= 1] . ( 23 sec) [ -10501.7991] [ 2504] [depth= 2] . ( 24 sec) [ -10501.6887] [ 2505] [depth= 1] . ( 25 sec) [ -10499.4615] [Branch lengths ] . ( 25 sec) [ -10499.4599] [GTR parameters ] . ( 26 sec) [ -10499.4596] [Alpha ][ 0.975496] . ( 31 sec) [ -10499.1050] [Branch lengths ] . ( 59 sec) [ -10499.0068] [Branch lengths ] . ( 60 sec) [ -10499.0068] [Topology ] . ( 61 sec) [ -10498.9939] [Topology ] . ( 62 sec) [ -10498.9888] [Topology ] . ( 63 sec) [ -10498.9862] [Topology ] . ( 64 sec) [ -10498.9847] [Topology ] . ( 65 sec) [ -10498.9839] [Topology ] . ( 65 sec) [ -10498.9826] [GTR parameters ] . ( 65 sec) [ -10498.9770] [Alpha ][ 0.968262] . ( 65 sec) [ -10498.9770] [Topology ] . ( 66 sec) [ -10498.9759] [Topology ] . ( 67 sec) [ -10498.9754] [Topology ] . ( 67 sec) [ -10498.9753] [GTR parameters ] . ( 67 sec) [ -10498.9753] [Alpha ][ 0.968262] . ( 67 sec) [ -10498.9753] [Topology ] . ( 68 sec) [ -10498.9750] [Topology ] . ( 69 sec) [ -10498.9750] [GTR parameters ] . ( 69 sec) [ -10498.9750] [Alpha ][ 0.968262] . Checking for NNIs, optimizing five branches... . ( 76 sec) [ -10498.9747] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10498.974725. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10614.462202 . ( 1 sec) [ -10610.1657] [GTR parameters ] . ( 1 sec) [ -10610.1656] [Alpha ][ 1.001154] . ( 1 sec) [ -10610.1656] [Topology ] . ( 3 sec) [ -10531.3624] [Topology ] . ( 4 sec) [ -10511.2075] [Topology ] . ( 4 sec) [ -10505.1369] [Topology ] . ( 6 sec) [ -10502.3616] [Topology ] . ( 6 sec) [ -10500.9767] [Topology ] . ( 7 sec) [ -10500.2834] [Topology ] . ( 9 sec) [ -10499.9077] [Topology ] . ( 10 sec) [ -10499.6992] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10499.699178 . ( 17 sec) [ -10499.3949] [GTR parameters ] . ( 17 sec) [ -10499.3214] [Alpha ][ 0.975377] . ( 17 sec) [ -10499.3214] [Topology ] . ( 18 sec) [ -10499.1740] [Topology ] . ( 19 sec) [ -10499.0934] [Topology ] . ( 20 sec) [ -10499.0472] [Topology ] . ( 21 sec) [ -10499.0204] [Topology ] . ( 22 sec) [ -10499.0049] [Topology ] . ( 23 sec) [ -10498.9959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.995947 . ( 31 sec) [ -10498.9941] [GTR parameters ] . ( 31 sec) [ -10498.9900] [Alpha ][ 0.969090] . ( 31 sec) [ -10498.9900] [Topology ] . ( 32 sec) [ -10498.9835] [Topology ] . ( 33 sec) [ -10498.9798] [Topology ] . ( 34 sec) [ -10498.9777] [Topology ] . ( 35 sec) [ -10498.9765] [Topology ] . ( 36 sec) [ -10498.9757] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10498.975740 . ( 44 sec) [ -10498.9757] [GTR parameters ] . ( 44 sec) [ -10498.9755] [Alpha ][ 0.967885] . ( 44 sec) [ -10498.9755] [Topology ] . ( 45 sec) [ -10498.9750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 61 sec) [ -10610.1657] [GTR parameters ] . ( 61 sec) [ -10610.1656] [Alpha ][ 1.001154] . ( 61 sec) [ -10608.0965] [ 2507] [depth= 1] . ( 61 sec) [ -10607.2250] [ 2507] [depth= 1] . ( 61 sec) [ -10606.9712] [ 2507] [depth= 1] . ( 62 sec) [ -10606.9582] [ 2507] [depth= 1] . ( 62 sec) [ -10601.5769] [ 2508] [depth= 1] . ( 63 sec) [ -10597.1747] [ 2513] [depth= 1] . ( 63 sec) [ -10595.2247] [ 2508] [depth= 1] . ( 63 sec) [ -10591.5719] [ 2510] [depth= 1] . ( 63 sec) [ -10591.3353] [ 2515] [depth= 1] . ( 63 sec) [ -10589.1863] [ 2529] [depth= 1] . ( 63 sec) [ -10587.6234] [ 2532] [depth= 1] . ( 63 sec) [ -10587.0615] [ 2529] [depth= 1] . ( 64 sec) [ -10584.0384] [ 2525] [depth= 1] . ( 64 sec) [ -10582.3196] [ 2528] [depth= 1] . ( 64 sec) [ -10579.6436] [ 2525] [depth= 1] . ( 64 sec) [ -10569.8342] [ 2525] [depth= 1] . ( 64 sec) [ -10569.0272] [ 2525] [depth= 1] . ( 65 sec) [ -10563.4355] [ 2525] [depth= 1] . ( 65 sec) [ -10562.6789] [ 2524] [depth= 1] . ( 65 sec) [ -10558.0434] [ 2536] [depth= 1] . ( 66 sec) [ -10557.6969] [ 2535] [depth= 1] . ( 67 sec) [ -10512.1811] [Branch lengths ] . ( 68 sec) [ -10511.9068] [GTR parameters ] . ( 68 sec) [ -10511.8032] [Alpha ][ 0.970150] . ( 69 sec) [ -10510.4104] [ 2523] [depth= 1] . ( 70 sec) [ -10506.7544] [ 2505] [depth= 1] . ( 70 sec) [ -10506.6295] [ 2508] [depth= 1] . ( 70 sec) [ -10506.5790] [ 2505] [depth= 1] . ( 70 sec) [ -10506.5582] [ 2508] [depth= 1] . ( 71 sec) [ -10506.0693] [ 2505] [depth= 1] . ( 72 sec) [ -10500.4665] [Branch lengths ] . ( 73 sec) [ -10500.4513] [GTR parameters ] . ( 73 sec) [ -10500.4513] [Alpha ][ 0.971121] . ( 77 sec) [ -10499.8005] [Branch lengths ] . ( 105 sec) [ -10499.7411] [Branch lengths ] . ( 105 sec) [ -10499.7411] [Topology ] . ( 106 sec) [ -10499.2211] [Topology ] . ( 107 sec) [ -10499.1183] [Topology ] . ( 108 sec) [ -10499.0997] [Topology ] . ( 109 sec) [ -10499.0948] [Topology ] . ( 111 sec) [ -10499.0933] [Topology ] . ( 112 sec) [ -10499.0928] [Topology ] . ( 112 sec) [ -10499.0889] [GTR parameters ] . ( 112 sec) [ -10499.0869] [Alpha ][ 0.966770] . ( 112 sec) [ -10499.0869] [Topology ] . ( 113 sec) [ -10499.0866] [Topology ] . ( 113 sec) [ -10499.0865] [GTR parameters ] . ( 113 sec) [ -10499.0865] [Alpha ][ 0.966770] . Checking for NNIs, optimizing five branches... . ( 122 sec) [ -10499.0857] [Topology ] . Checking for NNIs, optimizing five branches... . ( 130 sec) [ -10499.0856] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10498.975038 . Log likelihood obtained after SPR moves : -10499.085559 . Log likelihood of the current tree: -10498.975038. . Printing the most likely tree in file 'data100.phy_phyml_tree.txt'... . Best log likelihood : -10498.974725 . Time used 0h2m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo