.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data1.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... . 437 patterns found. (out of a total of 500 sites) . 64 sites without polymorphism (12.80%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -21236.9712] [GTR parameters ] . ( 2 sec) [ -20827.4094] [Alpha ][ 0.500960] . ( 2 sec) [ -20732.3358] [ 4885] [depth= 7] . ( 2 sec) [ -20604.0692] [ 4886] [depth= 1] . ( 2 sec) [ -20151.9424] [ 4855] [depth= 12] . ( 2 sec) [ -19594.3379] [ 4809] [depth= 6] . ( 2 sec) [ -19507.9579] [ 4796] [depth= 3] . ( 2 sec) [ -19472.5043] [ 4783] [depth= 1] . ( 2 sec) [ -19431.6057] [ 4756] [depth= 4] . ( 3 sec) [ -19370.8925] [ 4749] [depth= 5] . ( 3 sec) [ -19079.2821] [ 4590] [depth= 6] . ( 3 sec) [ -19049.1112] [ 4573] [depth= 2] . ( 3 sec) [ -19030.4963] [ 4570] [depth= 1] . ( 3 sec) [ -18555.5534] [ 4464] [depth= 11] . ( 3 sec) [ -18437.8663] [ 4554] [depth= 5] . ( 3 sec) [ -18264.8410] [ 4473] [depth= 8] . ( 3 sec) [ -18181.5081] [ 4458] [depth= 1] . ( 3 sec) [ -17907.3019] [ 4448] [depth= 3] . ( 3 sec) [ -17881.7489] [ 4437] [depth= 4] . ( 3 sec) [ -17468.1831] [ 4374] [depth= 5] . ( 3 sec) [ -17466.7846] [ 4351] [depth= 6] . ( 3 sec) [ -17422.6684] [ 4307] [depth= 15] . ( 3 sec) [ -17287.8294] [ 4290] [depth= 3] . ( 4 sec) [ -17109.6262] [ 4236] [depth= 4] . ( 4 sec) [ -16964.6413] [ 4177] [depth= 18] . ( 4 sec) [ -16907.0155] [ 4164] [depth= 1] . ( 4 sec) [ -16796.8725] [ 4112] [depth= 6] . ( 4 sec) [ -16561.5592] [ 4056] [depth= 1] . ( 4 sec) [ -16509.9727] [ 4039] [depth= 4] . ( 4 sec) [ -16280.9885] [ 3958] [depth= 1] . ( 4 sec) [ -16201.2964] [ 3955] [depth= 1] . ( 4 sec) [ -15993.0244] [ 3931] [depth= 14] . ( 4 sec) [ -15714.9364] [ 3884] [depth= 3] . ( 4 sec) [ -15518.3784] [ 3884] [depth= 4] . ( 4 sec) [ -15417.8486] [ 3797] [depth= 8] . ( 4 sec) [ -15302.4386] [ 3783] [depth= 15] . ( 4 sec) [ -15279.8369] [ 3772] [depth= 1] . ( 5 sec) [ -15236.4562] [ 3709] [depth= 5] . ( 5 sec) [ -15047.4761] [ 3647] [depth= 7] . ( 5 sec) [ -14972.3937] [ 3647] [depth= 2] . ( 5 sec) [ -14855.9492] [ 3557] [depth= 10] . ( 5 sec) [ -14759.1991] [ 3549] [depth= 1] . ( 5 sec) [ -14588.5355] [ 3484] [depth= 6] . ( 5 sec) [ -14418.3720] [ 3409] [depth= 7] . ( 5 sec) [ -14347.5038] [ 3407] [depth= 1] . ( 5 sec) [ -13697.0964] [ 3255] [depth= 6] . ( 5 sec) [ -13595.3296] [ 3247] [depth= 1] . ( 5 sec) [ -13593.1384] [ 3245] [depth= 1] . ( 5 sec) [ -13489.2297] [ 3197] [depth= 1] . ( 5 sec) [ -13390.0749] [ 3180] [depth= 2] . ( 5 sec) [ -13302.9252] [ 3176] [depth= 1] . ( 5 sec) [ -13278.9077] [ 3172] [depth= 4] . ( 5 sec) [ -13220.3883] [ 3159] [depth= 1] . ( 5 sec) [ -12933.0061] [ 3106] [depth= 6] . ( 5 sec) [ -12816.6212] [ 3098] [depth= 1] . ( 6 sec) [ -12724.4496] [ 3090] [depth= 1] . ( 6 sec) [ -12624.7909] [ 3077] [depth= 2] . ( 6 sec) [ -12553.0112] [ 3076] [depth= 1] . ( 6 sec) [ -12536.9482] [ 3059] [depth= 2] . ( 6 sec) [ -12402.1566] [ 3037] [depth= 12] . ( 6 sec) [ -12306.8351] [ 3033] [depth= 1] . ( 6 sec) [ -12285.5806] [ 3030] [depth= 1] . ( 6 sec) [ -12270.5537] [ 3028] [depth= 1] . ( 6 sec) [ -12200.7288] [ 2932] [depth= 4] . ( 6 sec) [ -12170.4987] [ 2881] [depth= 4] . ( 6 sec) [ -12159.5618] [ 2884] [depth= 1] . ( 6 sec) [ -12120.6326] [ 2887] [depth= 1] . ( 6 sec) [ -12042.5910] [ 2879] [depth= 1] . ( 6 sec) [ -11917.6382] [ 2817] [depth= 3] . ( 7 sec) [ -11712.4746] [ 2732] [depth= 5] . ( 7 sec) [ -11659.9533] [ 2703] [depth= 2] . ( 7 sec) [ -11634.9674] [ 2699] [depth= 1] . ( 7 sec) [ -11631.8272] [ 2696] [depth= 1] . ( 7 sec) [ -11613.8539] [ 2682] [depth= 1] . ( 7 sec) [ -11587.8266] [ 2684] [depth= 2] . ( 7 sec) [ -11580.7176] [ 2680] [depth= 1] . ( 7 sec) [ -11565.5526] [ 2679] [depth= 1] . ( 7 sec) [ -11340.9972] [ 2604] [depth= 2] . ( 7 sec) [ -11310.9805] [ 2597] [depth= 2] . ( 7 sec) [ -11298.1827] [ 2601] [depth= 1] . ( 7 sec) [ -11280.0559] [ 2601] [depth= 1] . ( 8 sec) [ -10949.0263] [Branch lengths ] . ( 8 sec) [ -10941.4006] [GTR parameters ] . ( 8 sec) [ -10913.2298] [Alpha ][ 0.826809] . ( 8 sec) [ -10907.3115] [ 2582] [depth= 2] . ( 8 sec) [ -10888.2635] [ 2575] [depth= 1] . ( 8 sec) [ -10878.9546] [ 2567] [depth= 1] . ( 9 sec) [ -10804.7281] [ 2486] [depth= 2] . ( 9 sec) [ -10801.7313] [ 2483] [depth= 1] . ( 9 sec) [ -10795.4576] [ 2482] [depth= 1] . ( 9 sec) [ -10795.1527] [ 2487] [depth= 1] . ( 9 sec) [ -10793.9844] [ 2480] [depth= 1] . ( 9 sec) [ -10753.6862] [ 2457] [depth= 2] . ( 9 sec) [ -10733.4560] [ 2465] [depth= 1] . ( 9 sec) [ -10733.0124] [ 2468] [depth= 1] . ( 9 sec) [ -10732.4791] [ 2460] [depth= 1] . ( 10 sec) [ -10715.4122] [ 2434] [depth= 1] . ( 10 sec) [ -10694.0354] [ 2432] [depth= 3] . ( 10 sec) [ -10691.5233] [ 2431] [depth= 1] . ( 10 sec) [ -10686.2786] [ 2439] [depth= 2] . ( 10 sec) [ -10684.7701] [ 2442] [depth= 1] . ( 10 sec) [ -10683.5049] [ 2437] [depth= 1] . ( 10 sec) [ -10683.2467] [ 2435] [depth= 1] . ( 10 sec) [ -10682.4318] [ 2438] [depth= 2] . ( 10 sec) [ -10680.3606] [ 2438] [depth= 2] . ( 10 sec) [ -10677.4419] [ 2439] [depth= 1] . ( 11 sec) [ -10676.3720] [ 2442] [depth= 1] . ( 11 sec) [ -10673.6208] [ 2439] [depth= 1] . ( 11 sec) [ -10672.9143] [ 2447] [depth= 1] . ( 11 sec) [ -10627.4217] [ 2437] [depth= 2] . ( 11 sec) [ -10627.2071] [ 2433] [depth= 1] . ( 11 sec) [ -10624.7368] [ 2439] [depth= 1] . ( 11 sec) [ -10624.4750] [ 2433] [depth= 1] . ( 12 sec) [ -10624.4185] [ 2436] [depth= 1] . ( 12 sec) [ -10621.7997] [ 2434] [depth= 1] . ( 12 sec) [ -10618.4025] [ 2429] [depth= 1] . ( 12 sec) [ -10618.2286] [ 2431] [depth= 2] . ( 12 sec) [ -10616.5526] [ 2430] [depth= 1] . ( 12 sec) [ -10615.3089] [ 2428] [depth= 1] . ( 12 sec) [ -10615.1089] [ 2424] [depth= 1] . ( 13 sec) [ -10614.7207] [ 2423] [depth= 1] . ( 13 sec) [ -10589.4375] [Branch lengths ] . ( 14 sec) [ -10589.0280] [GTR parameters ] . ( 14 sec) [ -10586.8908] [Alpha ][ 0.956795] . ( 14 sec) [ -10586.2610] [ 2424] [depth= 1] . ( 15 sec) [ -10585.9925] [ 2424] [depth= 1] . ( 20 sec) [ -10581.6338] [Branch lengths ] . ( 20 sec) [ -10581.6280] [GTR parameters ] . ( 21 sec) [ -10581.5788] [Alpha ][ 0.978611] . ( 27 sec) [ -10581.1051] [Branch lengths ] . ( 28 sec) [ -10579.7213] [ 2417] [depth= 2] . ( 41 sec) [ -10579.4606] [ 2418] [depth= 1] . ( 61 sec) [ -10579.2443] [Branch lengths ] . ( 61 sec) [ -10579.2402] [GTR parameters ] . ( 61 sec) [ -10579.2357] [Alpha ][ 0.985234] . ( 92 sec) [ -10579.2116] [Branch lengths ] . ( 92 sec) [ -10579.2116] [Topology ] . ( 93 sec) [ -10579.2093] [Topology ] . ( 95 sec) [ -10579.2085] [Topology ] . ( 95 sec) [ -10579.2084] [GTR parameters ] . ( 95 sec) [ -10579.2084] [Alpha ][ 0.986219] . ( 95 sec) [ -10579.2084] [Topology ] . ( 96 sec) [ -10579.2079] [Topology ] . ( 97 sec) [ -10579.2079] [GTR parameters ] . ( 97 sec) [ -10579.2079] [Alpha ][ 0.986219] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.207947. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21871.0809] [GTR parameters ] . ( 1 sec) [ -21429.2301] [Alpha ][ 0.500960] . ( 1 sec) [ -21400.7652] [ 4984] [depth= 1] . ( 1 sec) [ -21251.0882] [ 4925] [depth= 4] . ( 1 sec) [ -20703.1787] [ 4904] [depth= 4] . ( 1 sec) [ -20509.0534] [ 4876] [depth= 7] . ( 1 sec) [ -20257.2765] [ 4726] [depth= 6] . ( 1 sec) [ -20254.4606] [ 4721] [depth= 1] . ( 1 sec) [ -20053.1909] [ 4704] [depth= 4] . ( 1 sec) [ -19840.9368] [ 4657] [depth= 1] . ( 2 sec) [ -19537.7839] [ 4652] [depth= 1] . ( 2 sec) [ -19517.7658] [ 4606] [depth= 9] . ( 2 sec) [ -19516.7247] [ 4607] [depth= 3] . ( 2 sec) [ -19459.2083] [ 4559] [depth= 4] . ( 2 sec) [ -19289.4987] [ 4540] [depth= 4] . ( 2 sec) [ -18552.7204] [ 4380] [depth= 20] . ( 2 sec) [ -18351.4116] [ 4337] [depth= 10] . ( 2 sec) [ -18152.5633] [ 4296] [depth= 4] . ( 2 sec) [ -18102.6535] [ 4300] [depth= 3] . ( 2 sec) [ -17499.6133] [ 4298] [depth= 1] . ( 2 sec) [ -17296.7956] [ 4244] [depth= 4] . ( 3 sec) [ -17057.1186] [ 4229] [depth= 1] . ( 3 sec) [ -16549.7286] [ 4117] [depth= 16] . ( 3 sec) [ -16537.4997] [ 4109] [depth= 2] . ( 3 sec) [ -16348.6102] [ 4040] [depth= 6] . ( 3 sec) [ -15910.8964] [ 3915] [depth= 14] . ( 3 sec) [ -15733.4370] [ 3911] [depth= 1] . ( 3 sec) [ -15698.5280] [ 3925] [depth= 1] . ( 3 sec) [ -15612.4486] [ 3905] [depth= 2] . ( 3 sec) [ -15428.9003] [ 3811] [depth= 14] . ( 3 sec) [ -15404.0201] [ 3809] [depth= 1] . ( 3 sec) [ -15361.5356] [ 3751] [depth= 1] . ( 3 sec) [ -15319.8374] [ 3743] [depth= 1] . ( 4 sec) [ -15094.1070] [ 3672] [depth= 2] . ( 4 sec) [ -15042.4607] [ 3655] [depth= 1] . ( 4 sec) [ -14925.7254] [ 3648] [depth= 3] . ( 4 sec) [ -14883.0197] [ 3646] [depth= 1] . ( 4 sec) [ -14782.8812] [ 3600] [depth= 3] . ( 4 sec) [ -14744.4872] [ 3613] [depth= 1] . ( 4 sec) [ -14543.0379] [ 3556] [depth= 3] . ( 4 sec) [ -14477.5057] [ 3483] [depth= 4] . ( 4 sec) [ -14138.8169] [ 3459] [depth= 3] . ( 4 sec) [ -14043.9862] [ 3428] [depth= 5] . ( 4 sec) [ -13825.0859] [ 3390] [depth= 3] . ( 4 sec) [ -13712.3407] [ 3466] [depth= 5] . ( 4 sec) [ -13675.2569] [ 3418] [depth= 4] . ( 5 sec) [ -13522.9650] [ 3341] [depth= 4] . ( 5 sec) [ -13498.4787] [ 3344] [depth= 1] . ( 5 sec) [ -13492.6663] [ 3342] [depth= 1] . ( 5 sec) [ -13447.3265] [ 3308] [depth= 1] . ( 5 sec) [ -13287.4950] [ 3271] [depth= 1] . ( 5 sec) [ -13265.4436] [ 3272] [depth= 1] . ( 5 sec) [ -13242.4887] [ 3263] [depth= 2] . ( 5 sec) [ -13032.8289] [ 3170] [depth= 4] . ( 5 sec) [ -12850.4310] [ 3163] [depth= 5] . ( 5 sec) [ -12721.6015] [ 3076] [depth= 2] . ( 5 sec) [ -12648.4402] [ 3015] [depth= 6] . ( 6 sec) [ -12553.0667] [ 3017] [depth= 1] . ( 6 sec) [ -12523.5124] [ 3004] [depth= 2] . ( 6 sec) [ -12520.4080] [ 3003] [depth= 4] . ( 6 sec) [ -12443.9871] [ 2931] [depth= 2] . ( 6 sec) [ -12297.6868] [ 2864] [depth= 2] . ( 6 sec) [ -12275.4810] [ 2860] [depth= 1] . ( 6 sec) [ -12248.3906] [ 2855] [depth= 1] . ( 6 sec) [ -12230.7930] [ 2844] [depth= 1] . ( 6 sec) [ -12095.6046] [ 2822] [depth= 8] . ( 6 sec) [ -12091.1640] [ 2823] [depth= 1] . ( 7 sec) [ -11814.0648] [ 2734] [depth= 3] . ( 7 sec) [ -11805.2740] [ 2734] [depth= 1] . ( 7 sec) [ -11769.8440] [ 2731] [depth= 1] . ( 7 sec) [ -11602.3093] [ 2662] [depth= 4] . ( 7 sec) [ -11601.0206] [ 2665] [depth= 2] . ( 7 sec) [ -11434.2170] [ 2634] [depth= 2] . ( 7 sec) [ -11365.6920] [ 2637] [depth= 1] . ( 7 sec) [ -11311.6187] [ 2624] [depth= 3] . ( 7 sec) [ -11216.3355] [ 2612] [depth= 2] . ( 8 sec) [ -11049.5529] [ 2561] [depth= 1] . ( 8 sec) [ -11044.5846] [ 2564] [depth= 1] . ( 8 sec) [ -11007.0314] [ 2564] [depth= 1] . ( 8 sec) [ -11003.3379] [ 2557] [depth= 1] . ( 8 sec) [ -10978.3197] [ 2556] [depth= 2] . ( 8 sec) [ -10914.7496] [ 2525] [depth= 6] . ( 8 sec) [ -10914.0409] [ 2521] [depth= 1] . ( 9 sec) [ -10768.3612] [Branch lengths ] . ( 10 sec) [ -10764.3828] [GTR parameters ] . ( 10 sec) [ -10726.9404] [Alpha ][ 0.900529] . ( 10 sec) [ -10671.6206] [ 2449] [depth= 1] . ( 10 sec) [ -10663.2769] [ 2461] [depth= 1] . ( 11 sec) [ -10661.6942] [ 2449] [depth= 1] . ( 11 sec) [ -10661.2175] [ 2449] [depth= 1] . ( 11 sec) [ -10660.9216] [ 2449] [depth= 1] . ( 12 sec) [ -10658.2937] [ 2445] [depth= 1] . ( 12 sec) [ -10657.9859] [ 2447] [depth= 1] . ( 12 sec) [ -10657.8623] [ 2448] [depth= 1] . ( 12 sec) [ -10633.1860] [ 2437] [depth= 3] . ( 13 sec) [ -10632.6624] [ 2434] [depth= 1] . ( 13 sec) [ -10631.8714] [ 2435] [depth= 1] . ( 13 sec) [ -10629.0209] [ 2430] [depth= 1] . ( 13 sec) [ -10627.9472] [ 2427] [depth= 1] . ( 13 sec) [ -10627.1758] [ 2426] [depth= 1] . ( 14 sec) [ -10602.5865] [ 2419] [depth= 1] . ( 15 sec) [ -10602.5048] [ 2418] [depth= 2] . ( 16 sec) [ -10600.2040] [ 2418] [depth= 1] . ( 16 sec) [ -10581.2295] [Branch lengths ] . ( 17 sec) [ -10581.0401] [GTR parameters ] . ( 17 sec) [ -10580.3987] [Alpha ][ 0.974925] . ( 22 sec) [ -10579.3972] [Branch lengths ] . ( 57 sec) [ -10579.2546] [Branch lengths ] . ( 57 sec) [ -10579.2546] [Topology ] . ( 59 sec) [ -10579.2355] [Topology ] . ( 60 sec) [ -10579.2288] [Topology ] . ( 61 sec) [ -10579.2256] [Topology ] . ( 62 sec) [ -10579.2240] [Topology ] . ( 63 sec) [ -10579.2232] [Topology ] . ( 63 sec) [ -10579.2209] [GTR parameters ] . ( 63 sec) [ -10579.2098] [Alpha ][ 0.985352] . ( 63 sec) [ -10579.2098] [Topology ] . ( 64 sec) [ -10579.2085] [Topology ] . ( 65 sec) [ -10579.2080] [Topology ] . ( 65 sec) [ -10579.2079] [GTR parameters ] . ( 65 sec) [ -10579.2079] [Alpha ][ 0.985352] . ( 65 sec) [ -10579.2079] [Topology ] . ( 67 sec) [ -10579.2077] [Topology ] . ( 67 sec) [ -10579.2077] [GTR parameters ] . ( 67 sec) [ -10579.2077] [Alpha ][ 0.986337] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.207689. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -22636.5205] [GTR parameters ] . ( 2 sec) [ -22160.0278] [Alpha ][ 0.500960] . ( 2 sec) [ -22075.7838] [ 5116] [depth= 4] . ( 2 sec) [ -21860.4702] [ 5064] [depth= 9] . ( 2 sec) [ -21846.4164] [ 5054] [depth= 2] . ( 2 sec) [ -21800.5945] [ 5053] [depth= 2] . ( 2 sec) [ -21598.3163] [ 4994] [depth= 4] . ( 2 sec) [ -21567.3813] [ 4999] [depth= 4] . ( 3 sec) [ -21277.1223] [ 4877] [depth= 15] . ( 3 sec) [ -21133.8152] [ 4811] [depth= 14] . ( 3 sec) [ -20904.5464] [ 4759] [depth= 1] . ( 3 sec) [ -20656.3961] [ 4650] [depth= 17] . ( 3 sec) [ -20154.1190] [ 4541] [depth= 6] . ( 3 sec) [ -20076.6032] [ 4519] [depth= 7] . ( 3 sec) [ -19870.5952] [ 4522] [depth= 1] . ( 3 sec) [ -19788.5714] [ 4512] [depth= 3] . ( 3 sec) [ -19578.3310] [ 4434] [depth= 2] . ( 3 sec) [ -19565.3415] [ 4435] [depth= 1] . ( 3 sec) [ -19016.8436] [ 4362] [depth= 10] . ( 3 sec) [ -18949.2345] [ 4351] [depth= 1] . ( 3 sec) [ -18555.0093] [ 4296] [depth= 3] . ( 4 sec) [ -18211.1366] [ 4108] [depth= 10] . ( 4 sec) [ -17780.9706] [ 4120] [depth= 9] . ( 4 sec) [ -17425.9257] [ 4036] [depth= 1] . ( 4 sec) [ -17405.6738] [ 4030] [depth= 7] . ( 4 sec) [ -17264.8537] [ 3968] [depth= 10] . ( 4 sec) [ -17177.3849] [ 3932] [depth= 1] . ( 4 sec) [ -16888.9616] [ 3930] [depth= 8] . ( 5 sec) [ -16444.7698] [ 3786] [depth= 7] . ( 5 sec) [ -16401.0767] [ 3774] [depth= 1] . ( 5 sec) [ -16162.1295] [ 3590] [depth= 14] . ( 5 sec) [ -15842.4555] [ 3524] [depth= 8] . ( 5 sec) [ -15810.0152] [ 3519] [depth= 1] . ( 5 sec) [ -15571.3856] [ 3431] [depth= 7] . ( 5 sec) [ -15521.4500] [ 3410] [depth= 9] . ( 5 sec) [ -15494.9000] [ 3411] [depth= 2] . ( 5 sec) [ -15467.9822] [ 3410] [depth= 11] . ( 5 sec) [ -14997.2114] [ 3379] [depth= 10] . ( 5 sec) [ -14954.0114] [ 3374] [depth= 1] . ( 6 sec) [ -14903.1766] [ 3366] [depth= 3] . ( 6 sec) [ -14836.9873] [ 3349] [depth= 12] . ( 6 sec) [ -14836.6631] [ 3355] [depth= 1] . ( 6 sec) [ -14817.9286] [ 3353] [depth= 2] . ( 6 sec) [ -14783.5366] [ 3349] [depth= 2] . ( 6 sec) [ -14738.6519] [ 3335] [depth= 2] . ( 6 sec) [ -14645.0833] [ 3326] [depth= 1] . ( 6 sec) [ -14616.7323] [ 3330] [depth= 1] . ( 6 sec) [ -14500.8887] [ 3296] [depth= 4] . ( 7 sec) [ -14482.9404] [ 3298] [depth= 2] . ( 7 sec) [ -14456.3772] [ 3289] [depth= 1] . ( 7 sec) [ -14443.9278] [ 3279] [depth= 6] . ( 7 sec) [ -14305.9961] [ 3232] [depth= 6] . ( 7 sec) [ -14083.4000] [ 3120] [depth= 12] . ( 7 sec) [ -13925.3665] [ 3132] [depth= 1] . ( 7 sec) [ -13787.6640] [ 3081] [depth= 3] . ( 7 sec) [ -13320.9217] [ 3009] [depth= 2] . ( 7 sec) [ -13174.1923] [ 3004] [depth= 8] . ( 7 sec) [ -13103.9695] [ 2989] [depth= 1] . ( 7 sec) [ -12974.8286] [ 2952] [depth= 1] . ( 7 sec) [ -12966.8834] [ 2945] [depth= 1] . ( 8 sec) [ -12965.7906] [ 2947] [depth= 1] . ( 8 sec) [ -12916.2843] [ 2924] [depth= 1] . ( 8 sec) [ -12907.7603] [ 2924] [depth= 1] . ( 8 sec) [ -12643.8193] [ 2857] [depth= 2] . ( 8 sec) [ -12636.2042] [ 2867] [depth= 1] . ( 8 sec) [ -12610.3692] [ 2857] [depth= 1] . ( 8 sec) [ -12425.3394] [ 2798] [depth= 10] . ( 8 sec) [ -12414.3651] [ 2809] [depth= 1] . ( 8 sec) [ -12313.5888] [ 2791] [depth= 1] . ( 8 sec) [ -11312.5575] [ 2620] [depth= 6] . ( 9 sec) [ -11308.3223] [ 2611] [depth= 1] . ( 9 sec) [ -11302.7885] [ 2616] [depth= 1] . ( 9 sec) [ -11301.1746] [ 2621] [depth= 1] . ( 9 sec) [ -11145.2766] [ 2566] [depth= 5] . ( 9 sec) [ -11144.3521] [ 2569] [depth= 1] . ( 9 sec) [ -11132.9291] [ 2561] [depth= 2] . ( 9 sec) [ -11040.4206] [ 2543] [depth= 5] . ( 9 sec) [ -11035.5715] [ 2544] [depth= 1] . ( 10 sec) [ -11032.9278] [ 2544] [depth= 1] . ( 10 sec) [ -11001.2902] [ 2525] [depth= 3] . ( 10 sec) [ -10994.8167] [ 2525] [depth= 1] . ( 10 sec) [ -10782.4940] [Branch lengths ] . ( 11 sec) [ -10775.6937] [GTR parameters ] . ( 11 sec) [ -10742.8107] [Alpha ][ 0.870454] . ( 11 sec) [ -10712.3584] [ 2510] [depth= 2] . ( 12 sec) [ -10711.9811] [ 2513] [depth= 2] . ( 12 sec) [ -10709.0820] [ 2506] [depth= 2] . ( 12 sec) [ -10645.3876] [ 2440] [depth= 3] . ( 13 sec) [ -10644.5548] [ 2435] [depth= 1] . ( 13 sec) [ -10643.0428] [ 2444] [depth= 1] . ( 13 sec) [ -10607.9616] [ 2432] [depth= 2] . ( 14 sec) [ -10607.3228] [ 2436] [depth= 1] . ( 14 sec) [ -10606.9583] [ 2435] [depth= 1] . ( 14 sec) [ -10606.9445] [ 2436] [depth= 1] . ( 15 sec) [ -10606.7103] [ 2435] [depth= 1] . ( 15 sec) [ -10606.2226] [ 2436] [depth= 1] . ( 15 sec) [ -10604.1758] [ 2431] [depth= 1] . ( 15 sec) [ -10602.8146] [ 2431] [depth= 1] . ( 15 sec) [ -10602.5735] [ 2424] [depth= 1] . ( 16 sec) [ -10599.4143] [ 2421] [depth= 1] . ( 17 sec) [ -10583.5482] [Branch lengths ] . ( 18 sec) [ -10583.3131] [GTR parameters ] . ( 18 sec) [ -10582.4404] [Alpha ][ 0.955750] . ( 24 sec) [ -10580.0091] [Branch lengths ] . ( 60 sec) [ -10579.4168] [Branch lengths ] . ( 60 sec) [ -10579.4168] [Topology ] . ( 62 sec) [ -10579.3530] [Topology ] . ( 63 sec) [ -10579.3296] [Topology ] . ( 64 sec) [ -10579.3179] [Topology ] . ( 65 sec) [ -10579.3117] [Topology ] . ( 66 sec) [ -10579.3083] [Topology ] . ( 67 sec) [ -10579.3065] [Topology ] . ( 68 sec) [ -10579.3036] [GTR parameters ] . ( 68 sec) [ -10579.2180] [Alpha ][ 0.983505] . ( 68 sec) [ -10579.2180] [Topology ] . ( 69 sec) [ -10579.2120] [Topology ] . ( 70 sec) [ -10579.2101] [Topology ] . ( 71 sec) [ -10579.2092] [Topology ] . ( 71 sec) [ -10579.2091] [GTR parameters ] . ( 71 sec) [ -10579.2087] [Alpha ][ 0.985524] . ( 71 sec) [ -10579.2087] [Topology ] . ( 73 sec) [ -10579.2081] [Topology ] . ( 73 sec) [ -10579.2081] [GTR parameters ] . ( 73 sec) [ -10579.2081] [Alpha ][ 0.985524] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.208096. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21887.4812] [GTR parameters ] . ( 2 sec) [ -21481.5291] [Alpha ][ 0.500960] . ( 2 sec) [ -21133.1756] [ 4904] [depth= 11] . ( 2 sec) [ -20537.3202] [ 4845] [depth= 3] . ( 2 sec) [ -20068.0084] [ 4773] [depth= 7] . ( 2 sec) [ -19975.3377] [ 4747] [depth= 1] . ( 2 sec) [ -19630.6214] [ 4669] [depth= 9] . ( 2 sec) [ -19622.1168] [ 4649] [depth= 2] . ( 2 sec) [ -19447.8985] [ 4637] [depth= 5] . ( 2 sec) [ -19337.9534] [ 4594] [depth= 4] . ( 2 sec) [ -19154.9128] [ 4570] [depth= 2] . ( 2 sec) [ -18647.8486] [ 4544] [depth= 7] . ( 3 sec) [ -18203.5999] [ 4430] [depth= 1] . ( 3 sec) [ -17979.2446] [ 4383] [depth= 6] . ( 3 sec) [ -17893.6432] [ 4376] [depth= 2] . ( 3 sec) [ -17751.4771] [ 4337] [depth= 9] . ( 3 sec) [ -17627.6541] [ 4323] [depth= 3] . ( 3 sec) [ -17481.0827] [ 4310] [depth= 2] . ( 3 sec) [ -17367.3571] [ 4274] [depth= 1] . ( 3 sec) [ -17205.0236] [ 4171] [depth= 18] . ( 3 sec) [ -17022.3596] [ 4128] [depth= 1] . ( 3 sec) [ -16976.7461] [ 4121] [depth= 12] . ( 3 sec) [ -16900.7501] [ 4137] [depth= 1] . ( 3 sec) [ -16704.6881] [ 4089] [depth= 4] . ( 4 sec) [ -16644.4839] [ 4077] [depth= 1] . ( 4 sec) [ -16582.5409] [ 4075] [depth= 10] . ( 4 sec) [ -16529.7473] [ 4071] [depth= 1] . ( 4 sec) [ -16478.7263] [ 4067] [depth= 1] . ( 4 sec) [ -16213.7747] [ 4047] [depth= 7] . ( 4 sec) [ -16204.4999] [ 4025] [depth= 4] . ( 4 sec) [ -16167.9800] [ 4014] [depth= 2] . ( 4 sec) [ -16123.5952] [ 3981] [depth= 6] . ( 4 sec) [ -15693.7469] [ 3812] [depth= 10] . ( 4 sec) [ -15686.2531] [ 3810] [depth= 1] . ( 5 sec) [ -15231.1077] [ 3831] [depth= 5] . ( 5 sec) [ -15215.1083] [ 3831] [depth= 2] . ( 5 sec) [ -15199.9403] [ 3836] [depth= 2] . ( 5 sec) [ -15183.2226] [ 3823] [depth= 2] . ( 5 sec) [ -14839.4382] [ 3671] [depth= 10] . ( 5 sec) [ -14716.3168] [ 3598] [depth= 8] . ( 5 sec) [ -14619.4779] [ 3572] [depth= 7] . ( 5 sec) [ -14531.6348] [ 3551] [depth= 2] . ( 5 sec) [ -14403.8179] [ 3524] [depth= 10] . ( 5 sec) [ -14290.5503] [ 3489] [depth= 1] . ( 6 sec) [ -14256.8511] [ 3494] [depth= 1] . ( 6 sec) [ -14256.8313] [ 3510] [depth= 1] . ( 6 sec) [ -14212.5601] [ 3493] [depth= 13] . ( 6 sec) [ -13980.3111] [ 3437] [depth= 6] . ( 6 sec) [ -13859.1821] [ 3415] [depth= 1] . ( 6 sec) [ -13775.2458] [ 3408] [depth= 1] . ( 6 sec) [ -13652.1513] [ 3333] [depth= 1] . ( 7 sec) [ -13618.0858] [ 3331] [depth= 3] . ( 7 sec) [ -13455.4841] [ 3301] [depth= 3] . ( 7 sec) [ -13406.6153] [ 3293] [depth= 2] . ( 7 sec) [ -13396.4198] [ 3281] [depth= 1] . ( 8 sec) [ -13333.6604] [ 3265] [depth= 2] . ( 8 sec) [ -13134.5813] [ 3198] [depth= 1] . ( 8 sec) [ -12919.7930] [ 3092] [depth= 8] . ( 8 sec) [ -12737.8196] [ 3040] [depth= 4] . ( 8 sec) [ -12720.1386] [ 3026] [depth= 1] . ( 8 sec) [ -12667.0984] [ 3023] [depth= 2] . ( 9 sec) [ -12481.2860] [ 2966] [depth= 6] . ( 9 sec) [ -12453.7894] [ 2955] [depth= 2] . ( 9 sec) [ -12419.7638] [ 2951] [depth= 3] . ( 9 sec) [ -12404.7964] [ 2966] [depth= 1] . ( 9 sec) [ -12350.9023] [ 2970] [depth= 2] . ( 9 sec) [ -12327.4529] [ 2953] [depth= 1] . ( 9 sec) [ -12262.9705] [ 2940] [depth= 1] . ( 10 sec) [ -12119.1293] [ 2861] [depth= 7] . ( 10 sec) [ -12085.3536] [ 2859] [depth= 2] . ( 10 sec) [ -12007.2397] [ 2805] [depth= 1] . ( 10 sec) [ -11965.9325] [ 2800] [depth= 2] . ( 11 sec) [ -11924.4093] [ 2805] [depth= 1] . ( 11 sec) [ -11814.5386] [ 2801] [depth= 1] . ( 11 sec) [ -11773.8164] [ 2777] [depth= 1] . ( 11 sec) [ -11755.2150] [ 2749] [depth= 1] . ( 11 sec) [ -11749.3421] [ 2693] [depth= 1] . ( 11 sec) [ -11731.0354] [ 2696] [depth= 3] . ( 11 sec) [ -11556.5075] [ 2639] [depth= 11] . ( 11 sec) [ -11427.3751] [ 2629] [depth= 7] . ( 11 sec) [ -11421.3525] [ 2632] [depth= 1] . ( 12 sec) [ -11339.6390] [ 2615] [depth= 1] . ( 12 sec) [ -10997.8285] [Branch lengths ] . ( 13 sec) [ -10992.2637] [GTR parameters ] . ( 13 sec) [ -10956.9088] [Alpha ][ 0.878365] . ( 13 sec) [ -10953.7930] [ 2613] [depth= 2] . ( 14 sec) [ -10854.1530] [ 2546] [depth= 2] . ( 14 sec) [ -10854.0119] [ 2548] [depth= 1] . ( 14 sec) [ -10850.5522] [ 2546] [depth= 1] . ( 14 sec) [ -10828.2898] [ 2537] [depth= 3] . ( 14 sec) [ -10774.1147] [ 2479] [depth= 3] . ( 15 sec) [ -10773.7817] [ 2483] [depth= 1] . ( 15 sec) [ -10772.4423] [ 2485] [depth= 1] . ( 15 sec) [ -10771.8683] [ 2483] [depth= 1] . ( 16 sec) [ -10645.9438] [ 2425] [depth= 1] . ( 16 sec) [ -10645.4600] [ 2423] [depth= 1] . ( 16 sec) [ -10639.5692] [ 2425] [depth= 2] . ( 16 sec) [ -10637.8866] [ 2425] [depth= 1] . ( 16 sec) [ -10627.6444] [ 2427] [depth= 1] . ( 16 sec) [ -10625.2505] [ 2427] [depth= 1] . ( 16 sec) [ -10621.4586] [ 2428] [depth= 1] . ( 17 sec) [ -10620.6288] [ 2433] [depth= 1] . ( 17 sec) [ -10620.2627] [ 2433] [depth= 1] . ( 18 sec) [ -10617.1789] [ 2427] [depth= 2] . ( 18 sec) [ -10612.3362] [ 2426] [depth= 2] . ( 18 sec) [ -10609.2564] [ 2428] [depth= 1] . ( 18 sec) [ -10608.3959] [ 2425] [depth= 2] . ( 18 sec) [ -10605.9528] [ 2421] [depth= 1] . ( 19 sec) [ -10585.2613] [Branch lengths ] . ( 20 sec) [ -10584.9661] [GTR parameters ] . ( 20 sec) [ -10584.0009] [Alpha ][ 0.968772] . ( 21 sec) [ -10581.9829] [ 2422] [depth= 2] . ( 22 sec) [ -10581.9076] [ 2422] [depth= 1] . ( 22 sec) [ -10581.8957] [ 2422] [depth= 1] . ( 25 sec) [ -10581.7374] [ 2422] [depth= 1] . ( 27 sec) [ -10579.5877] [Branch lengths ] . ( 27 sec) [ -10579.5809] [GTR parameters ] . ( 27 sec) [ -10579.5726] [Alpha ][ 0.977756] . ( 33 sec) [ -10579.2724] [Branch lengths ] . ( 69 sec) [ -10579.2245] [Branch lengths ] . ( 69 sec) [ -10579.2245] [Topology ] . ( 70 sec) [ -10579.2193] [Topology ] . ( 72 sec) [ -10579.2173] [Topology ] . ( 73 sec) [ -10579.2162] [Topology ] . ( 74 sec) [ -10579.2157] [Topology ] . ( 74 sec) [ -10579.2151] [GTR parameters ] . ( 74 sec) [ -10579.2090] [Alpha ][ 0.985451] . ( 75 sec) [ -10579.2090] [Topology ] . ( 76 sec) [ -10579.2082] [Topology ] . ( 76 sec) [ -10579.2081] [GTR parameters ] . ( 76 sec) [ -10579.2081] [Alpha ][ 0.985451] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.208136. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -21736.4243] [GTR parameters ] . ( 2 sec) [ -21306.4282] [Alpha ][ 0.500960] . ( 3 sec) [ -21208.5319] [ 4988] [depth= 7] . ( 3 sec) [ -21120.6311] [ 4962] [depth= 6] . ( 3 sec) [ -21067.2298] [ 4943] [depth= 3] . ( 3 sec) [ -21033.4235] [ 4936] [depth= 2] . ( 3 sec) [ -20940.8055] [ 4900] [depth= 4] . ( 3 sec) [ -20865.8442] [ 4889] [depth= 5] . ( 3 sec) [ -20786.7026] [ 4867] [depth= 5] . ( 3 sec) [ -20388.3554] [ 4738] [depth= 1] . ( 3 sec) [ -20324.8395] [ 4702] [depth= 1] . ( 3 sec) [ -20310.5111] [ 4696] [depth= 1] . ( 3 sec) [ -20302.3715] [ 4696] [depth= 1] . ( 3 sec) [ -20208.4370] [ 4618] [depth= 10] . ( 4 sec) [ -20069.0550] [ 4616] [depth= 3] . ( 4 sec) [ -19957.2830] [ 4589] [depth= 4] . ( 4 sec) [ -19949.4836] [ 4584] [depth= 1] . ( 4 sec) [ -19847.9300] [ 4578] [depth= 13] . ( 4 sec) [ -19825.2852] [ 4573] [depth= 1] . ( 4 sec) [ -19810.5599] [ 4565] [depth= 11] . ( 4 sec) [ -19540.8415] [ 4496] [depth= 3] . ( 4 sec) [ -19439.2837] [ 4450] [depth= 1] . ( 4 sec) [ -19250.4943] [ 4383] [depth= 2] . ( 4 sec) [ -19089.0507] [ 4389] [depth= 1] . ( 4 sec) [ -19026.4237] [ 4338] [depth= 8] . ( 4 sec) [ -18841.2855] [ 4288] [depth= 1] . ( 5 sec) [ -18687.2029] [ 4203] [depth= 8] . ( 5 sec) [ -18662.2591] [ 4196] [depth= 1] . ( 5 sec) [ -18533.3207] [ 4186] [depth= 13] . ( 5 sec) [ -18287.2456] [ 4133] [depth= 3] . ( 5 sec) [ -18068.6747] [ 4080] [depth= 13] . ( 5 sec) [ -18056.6247] [ 4078] [depth= 11] . ( 5 sec) [ -17969.8447] [ 4080] [depth= 1] . ( 5 sec) [ -17861.9390] [ 4053] [depth= 2] . ( 5 sec) [ -17668.0582] [ 3989] [depth= 2] . ( 6 sec) [ -17266.8038] [ 3917] [depth= 15] . ( 6 sec) [ -16896.2364] [ 3788] [depth= 3] . ( 6 sec) [ -16380.2613] [ 3702] [depth= 2] . ( 6 sec) [ -16166.8995] [ 3697] [depth= 4] . ( 6 sec) [ -16040.9598] [ 3702] [depth= 3] . ( 6 sec) [ -16038.9621] [ 3698] [depth= 3] . ( 6 sec) [ -15982.1189] [ 3709] [depth= 10] . ( 6 sec) [ -15894.6184] [ 3638] [depth= 4] . ( 6 sec) [ -15657.9744] [ 3552] [depth= 7] . ( 6 sec) [ -15642.6477] [ 3531] [depth= 2] . ( 7 sec) [ -14699.7266] [ 3351] [depth= 7] . ( 7 sec) [ -14670.2774] [ 3349] [depth= 4] . ( 7 sec) [ -14475.3791] [ 3309] [depth= 1] . ( 7 sec) [ -14435.4506] [ 3304] [depth= 1] . ( 7 sec) [ -13662.0725] [ 3236] [depth= 1] . ( 7 sec) [ -13539.0866] [ 3161] [depth= 3] . ( 7 sec) [ -13145.1519] [ 3059] [depth= 3] . ( 7 sec) [ -12793.0420] [ 2954] [depth= 8] . ( 7 sec) [ -12789.8964] [ 2949] [depth= 3] . ( 7 sec) [ -12549.8499] [ 2952] [depth= 8] . ( 7 sec) [ -12455.7885] [ 2839] [depth= 9] . ( 8 sec) [ -12448.2988] [ 2836] [depth= 1] . ( 8 sec) [ -12303.8535] [ 2816] [depth= 6] . ( 8 sec) [ -12208.9076] [ 2798] [depth= 2] . ( 8 sec) [ -11924.4155] [ 2766] [depth= 2] . ( 8 sec) [ -11922.7249] [ 2769] [depth= 1] . ( 8 sec) [ -11904.6357] [ 2730] [depth= 2] . ( 8 sec) [ -11762.9160] [ 2686] [depth= 5] . ( 8 sec) [ -11746.0293] [ 2688] [depth= 1] . ( 8 sec) [ -11708.9161] [ 2675] [depth= 5] . ( 8 sec) [ -11698.3187] [ 2681] [depth= 1] . ( 9 sec) [ -11455.5828] [ 2601] [depth= 2] . ( 9 sec) [ -11423.5953] [ 2584] [depth= 3] . ( 9 sec) [ -11343.2265] [ 2575] [depth= 6] . ( 9 sec) [ -11329.6872] [ 2571] [depth= 1] . ( 9 sec) [ -11319.0467] [ 2573] [depth= 1] . ( 9 sec) [ -11303.1056] [ 2568] [depth= 1] . ( 9 sec) [ -11160.3613] [ 2562] [depth= 1] . ( 9 sec) [ -11135.1285] [ 2549] [depth= 3] . ( 9 sec) [ -11112.4243] [ 2546] [depth= 1] . ( 9 sec) [ -11063.1635] [ 2528] [depth= 1] . ( 9 sec) [ -10993.0719] [ 2485] [depth= 1] . ( 10 sec) [ -10979.3122] [ 2493] [depth= 2] . ( 10 sec) [ -10966.6644] [ 2495] [depth= 1] . ( 10 sec) [ -10963.0275] [ 2494] [depth= 1] . ( 10 sec) [ -10936.0951] [ 2495] [depth= 1] . ( 10 sec) [ -10914.6667] [ 2495] [depth= 1] . ( 10 sec) [ -10914.2905] [ 2499] [depth= 1] . ( 10 sec) [ -10871.3214] [ 2466] [depth= 6] . ( 10 sec) [ -10870.8016] [ 2459] [depth= 1] . ( 11 sec) [ -10690.4060] [Branch lengths ] . ( 12 sec) [ -10685.4138] [GTR parameters ] . ( 12 sec) [ -10649.4074] [Alpha ][ 0.902411] . ( 13 sec) [ -10643.0369] [ 2449] [depth= 1] . ( 13 sec) [ -10635.6355] [ 2443] [depth= 3] . ( 13 sec) [ -10631.9249] [ 2438] [depth= 2] . ( 13 sec) [ -10631.8140] [ 2443] [depth= 1] . ( 13 sec) [ -10631.4072] [ 2443] [depth= 1] . ( 14 sec) [ -10627.3292] [ 2444] [depth= 1] . ( 14 sec) [ -10624.6262] [ 2441] [depth= 1] . ( 14 sec) [ -10623.0351] [ 2438] [depth= 1] . ( 14 sec) [ -10622.0314] [ 2438] [depth= 1] . ( 15 sec) [ -10598.8260] [ 2423] [depth= 2] . ( 16 sec) [ -10595.7204] [ 2418] [depth= 1] . ( 16 sec) [ -10592.7849] [ 2418] [depth= 1] . ( 17 sec) [ -10592.6567] [ 2422] [depth= 1] . ( 18 sec) [ -10592.4713] [ 2422] [depth= 1] . ( 20 sec) [ -10581.3089] [Branch lengths ] . ( 20 sec) [ -10581.1373] [GTR parameters ] . ( 20 sec) [ -10580.6365] [Alpha ][ 0.968183] . ( 27 sec) [ -10579.4933] [Branch lengths ] . ( 57 sec) [ -10579.3358] [Branch lengths ] . ( 57 sec) [ -10579.3358] [Topology ] . ( 58 sec) [ -10579.2893] [Topology ] . ( 59 sec) [ -10579.2692] [Topology ] . ( 60 sec) [ -10579.2584] [Topology ] . ( 62 sec) [ -10579.2521] [Topology ] . ( 63 sec) [ -10579.2485] [Topology ] . ( 65 sec) [ -10579.2464] [Topology ] . ( 65 sec) [ -10579.2429] [GTR parameters ] . ( 65 sec) [ -10579.2133] [Alpha ][ 0.985172] . ( 65 sec) [ -10579.2133] [Topology ] . ( 66 sec) [ -10579.2101] [Topology ] . ( 68 sec) [ -10579.2089] [Topology ] . ( 69 sec) [ -10579.2083] [Topology ] . ( 69 sec) [ -10579.2083] [GTR parameters ] . ( 69 sec) [ -10579.2083] [Alpha ][ 0.986157] . ( 69 sec) [ -10579.2083] [Topology ] . ( 70 sec) [ -10579.2079] [Topology ] . ( 70 sec) [ -10579.2079] [GTR parameters ] . ( 70 sec) [ -10579.2079] [Alpha ][ 0.986157] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10579.207895. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10670.638885 . ( 1 sec) [ -10666.7778] [GTR parameters ] . ( 2 sec) [ -10666.2120] [Alpha ][ 0.925980] . ( 2 sec) [ -10666.2120] [Topology ] . ( 3 sec) [ -10610.0666] [Topology ] . ( 4 sec) [ -10586.1511] [Topology ] . ( 5 sec) [ -10581.2066] [Topology ] . ( 7 sec) [ -10580.2747] [Topology ] . ( 8 sec) [ -10579.9449] [Topology ] . ( 10 sec) [ -10579.7943] [Topology ] . ( 11 sec) [ -10579.7182] [Topology ] . ( 13 sec) [ -10579.6779] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.677901 . ( 23 sec) [ -10579.6411] [GTR parameters ] . ( 23 sec) [ -10579.3155] [Alpha ][ 0.979846] . ( 23 sec) [ -10579.3155] [Topology ] . ( 24 sec) [ -10579.2624] [Topology ] . ( 25 sec) [ -10579.2389] [Topology ] . ( 26 sec) [ -10579.2266] [Topology ] . ( 28 sec) [ -10579.2199] [Topology ] . ( 29 sec) [ -10579.2162] [Topology ] . ( 30 sec) [ -10579.2142] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.214195 . ( 39 sec) [ -10579.2140] [GTR parameters ] . ( 39 sec) [ -10579.2110] [Alpha ][ 0.985268] . ( 39 sec) [ -10579.2110] [Topology ] . ( 40 sec) [ -10579.2094] [Topology ] . ( 42 sec) [ -10579.2086] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.208575 . ( 51 sec) [ -10579.2086] [GTR parameters ] . ( 51 sec) [ -10579.2086] [Alpha ][ 0.985268] . ( 51 sec) [ -10579.2086] [Topology ] . ( 52 sec) [ -10579.2081] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 71 sec) [ -10666.7778] [GTR parameters ] . ( 71 sec) [ -10666.2120] [Alpha ][ 0.925980] . ( 72 sec) [ -10663.6745] [ 2444] [depth= 1] . ( 72 sec) [ -10662.8854] [ 2438] [depth= 1] . ( 72 sec) [ -10661.8404] [ 2433] [depth= 1] . ( 72 sec) [ -10659.2880] [ 2436] [depth= 2] . ( 72 sec) [ -10657.3191] [ 2436] [depth= 1] . ( 72 sec) [ -10655.7531] [ 2441] [depth= 1] . ( 73 sec) [ -10655.1393] [ 2441] [depth= 1] . ( 73 sec) [ -10654.1761] [ 2439] [depth= 1] . ( 73 sec) [ -10650.3920] [ 2436] [depth= 1] . ( 73 sec) [ -10636.8133] [ 2432] [depth= 1] . ( 73 sec) [ -10634.0615] [ 2427] [depth= 1] . ( 73 sec) [ -10632.0786] [ 2432] [depth= 1] . ( 73 sec) [ -10632.0400] [ 2430] [depth= 1] . ( 73 sec) [ -10631.8002] [ 2431] [depth= 1] . ( 74 sec) [ -10627.8761] [ 2426] [depth= 1] . ( 74 sec) [ -10625.7284] [ 2424] [depth= 1] . ( 74 sec) [ -10623.8041] [ 2420] [depth= 1] . ( 75 sec) [ -10619.1472] [ 2418] [depth= 1] . ( 76 sec) [ -10616.3551] [ 2418] [depth= 1] . ( 76 sec) [ -10616.1510] [ 2422] [depth= 1] . ( 77 sec) [ -10616.1397] [ 2422] [depth= 1] . ( 77 sec) [ -10615.8397] [ 2422] [depth= 1] . ( 77 sec) [ -10582.1024] [Branch lengths ] . ( 77 sec) [ -10582.0651] [GTR parameters ] . ( 77 sec) [ -10581.8459] [Alpha ][ 0.970479] . ( 79 sec) [ -10581.8150] [ 2422] [depth= 1] . ( 82 sec) [ -10579.5289] [Branch lengths ] . ( 83 sec) [ -10579.5256] [GTR parameters ] . ( 83 sec) [ -10579.5159] [Alpha ][ 0.980181] . ( 88 sec) [ -10579.2606] [Branch lengths ] . ( 116 sec) [ -10579.2212] [Branch lengths ] . ( 116 sec) [ -10579.2212] [Topology ] . ( 118 sec) [ -10579.2162] [Topology ] . ( 119 sec) [ -10579.2142] [Topology ] . ( 120 sec) [ -10579.2131] [Topology ] . ( 121 sec) [ -10579.2124] [Topology ] . ( 121 sec) [ -10579.2118] [GTR parameters ] . ( 122 sec) [ -10579.2088] [Alpha ][ 0.985571] . ( 122 sec) [ -10579.2088] [Topology ] . ( 123 sec) [ -10579.2081] [Topology ] . ( 123 sec) [ -10579.2081] [GTR parameters ] . ( 123 sec) [ -10579.2081] [Alpha ][ 0.985571] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10579.208118 . Log likelihood obtained after SPR moves : -10579.208104 . Log likelihood of the current tree: -10579.208104. . Printing the most likely tree in file 'data1.phy_phyml_tree.txt'... . Best log likelihood : -10579.207689 . Time used 0h2m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo