.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data25.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... . 418 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . [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)... . ( 0 sec) [ -17709.7765] [GTR parameters ] . ( 0 sec) [ -17390.8107] [Alpha ][ 0.500960] . ( 0 sec) [ -17208.2441] [ 3947] [depth= 7] . ( 1 sec) [ -16969.7528] [ 3908] [depth= 7] . ( 1 sec) [ -16798.8376] [ 3892] [depth= 1] . ( 1 sec) [ -16666.5720] [ 3873] [depth= 3] . ( 1 sec) [ -16459.5784] [ 3841] [depth= 3] . ( 1 sec) [ -16356.2268] [ 3828] [depth= 7] . ( 1 sec) [ -15995.9591] [ 3786] [depth= 5] . ( 1 sec) [ -15963.3926] [ 3763] [depth= 1] . ( 1 sec) [ -15837.3295] [ 3731] [depth= 5] . ( 1 sec) [ -15797.1666] [ 3725] [depth= 1] . ( 1 sec) [ -15480.6661] [ 3608] [depth= 9] . ( 1 sec) [ -15366.7507] [ 3593] [depth= 1] . ( 1 sec) [ -14969.4776] [ 3573] [depth= 4] . ( 1 sec) [ -14848.8505] [ 3561] [depth= 1] . ( 1 sec) [ -14593.2916] [ 3544] [depth= 4] . ( 1 sec) [ -14346.4717] [ 3408] [depth= 2] . ( 1 sec) [ -14231.9997] [ 3404] [depth= 1] . ( 1 sec) [ -14016.5703] [ 3324] [depth= 3] . ( 1 sec) [ -13951.6249] [ 3318] [depth= 3] . ( 1 sec) [ -13649.1562] [ 3316] [depth= 4] . ( 1 sec) [ -13639.0911] [ 3319] [depth= 1] . ( 1 sec) [ -13583.3195] [ 3303] [depth= 4] . ( 1 sec) [ -13332.7277] [ 3285] [depth= 7] . ( 1 sec) [ -12930.7081] [ 3148] [depth= 9] . ( 1 sec) [ -12830.1548] [ 3179] [depth= 1] . ( 1 sec) [ -12814.9363] [ 3173] [depth= 1] . ( 2 sec) [ -12737.3859] [ 3100] [depth= 10] . ( 2 sec) [ -12735.7541] [ 3104] [depth= 1] . ( 2 sec) [ -12525.2906] [ 3027] [depth= 4] . ( 2 sec) [ -12448.3250] [ 3016] [depth= 2] . ( 2 sec) [ -12295.7700] [ 2956] [depth= 4] . ( 2 sec) [ -12262.9981] [ 2953] [depth= 2] . ( 2 sec) [ -12253.0190] [ 2912] [depth= 1] . ( 2 sec) [ -12246.7018] [ 2913] [depth= 1] . ( 2 sec) [ -12220.0371] [ 2896] [depth= 6] . ( 2 sec) [ -12093.6423] [ 2887] [depth= 2] . ( 2 sec) [ -11866.4405] [ 2856] [depth= 9] . ( 2 sec) [ -11784.4213] [ 2849] [depth= 1] . ( 2 sec) [ -11753.9743] [ 2890] [depth= 18] . ( 2 sec) [ -11667.2602] [ 2862] [depth= 4] . ( 2 sec) [ -11548.0773] [ 2786] [depth= 12] . ( 2 sec) [ -11323.9194] [ 2690] [depth= 17] . ( 2 sec) [ -11205.2253] [ 2656] [depth= 1] . ( 2 sec) [ -11202.4959] [ 2650] [depth= 1] . ( 2 sec) [ -11199.0560] [ 2645] [depth= 1] . ( 2 sec) [ -11180.6379] [ 2646] [depth= 2] . ( 2 sec) [ -11160.9927] [ 2642] [depth= 1] . ( 3 sec) [ -11127.4062] [ 2599] [depth= 3] . ( 3 sec) [ -11121.2628] [ 2597] [depth= 1] . ( 3 sec) [ -11113.5721] [ 2556] [depth= 1] . ( 3 sec) [ -10982.1106] [ 2552] [depth= 2] . ( 3 sec) [ -10970.8156] [ 2562] [depth= 1] . ( 3 sec) [ -10960.9100] [ 2547] [depth= 2] . ( 3 sec) [ -10900.3420] [ 2478] [depth= 2] . ( 3 sec) [ -10819.0551] [ 2460] [depth= 9] . ( 3 sec) [ -10762.8088] [ 2431] [depth= 1] . ( 3 sec) [ -10698.1149] [ 2368] [depth= 9] . ( 3 sec) [ -10650.4751] [ 2306] [depth= 2] . ( 3 sec) [ -10638.5722] [ 2311] [depth= 1] . ( 3 sec) [ -10568.5981] [ 2280] [depth= 1] . ( 3 sec) [ -10559.2228] [ 2269] [depth= 1] . ( 3 sec) [ -10546.3119] [ 2265] [depth= 1] . ( 3 sec) [ -10518.9637] [ 2269] [depth= 1] . ( 3 sec) [ -10285.1029] [ 2202] [depth= 6] . ( 3 sec) [ -10026.9795] [ 2134] [depth= 4] . ( 3 sec) [ -10000.8899] [ 2125] [depth= 1] . ( 3 sec) [ -9777.2822] [ 2068] [depth= 7] . ( 4 sec) [ -9711.0919] [ 2025] [depth= 2] . ( 4 sec) [ -9568.6592] [ 1974] [depth= 3] . ( 4 sec) [ -9507.8551] [ 1952] [depth= 2] . ( 4 sec) [ -9501.0482] [ 1947] [depth= 1] . ( 4 sec) [ -9490.5076] [ 1945] [depth= 1] . ( 4 sec) [ -9479.2376] [ 1942] [depth= 1] . ( 4 sec) [ -9474.7240] [ 1930] [depth= 1] . ( 4 sec) [ -9284.3225] [ 1934] [depth= 1] . ( 4 sec) [ -9094.5595] [ 1831] [depth= 6] . ( 4 sec) [ -8994.9524] [ 1834] [depth= 1] . ( 4 sec) [ -8974.8166] [ 1826] [depth= 1] . ( 5 sec) [ -8796.3100] [Branch lengths ] . ( 5 sec) [ -8792.2717] [GTR parameters ] . ( 5 sec) [ -8740.2128] [Alpha ][ 1.000370] . ( 5 sec) [ -8739.1379] [ 1826] [depth= 4] . ( 5 sec) [ -8698.7246] [ 1801] [depth= 2] . ( 5 sec) [ -8684.4904] [ 1791] [depth= 1] . ( 5 sec) [ -8672.6147] [ 1781] [depth= 1] . ( 5 sec) [ -8670.6310] [ 1781] [depth= 1] . ( 5 sec) [ -8664.1945] [ 1772] [depth= 2] . ( 6 sec) [ -8652.3934] [ 1766] [depth= 1] . ( 6 sec) [ -8587.6157] [ 1741] [depth= 1] . ( 6 sec) [ -8583.8478] [ 1739] [depth= 1] . ( 6 sec) [ -8578.4839] [ 1732] [depth= 2] . ( 8 sec) [ -8578.0815] [ 1736] [depth= 1] . ( 8 sec) [ -8568.8715] [Branch lengths ] . ( 9 sec) [ -8568.5431] [GTR parameters ] . ( 9 sec) [ -8567.1064] [Alpha ][ 1.149848] . ( 12 sec) [ -8566.1040] [Branch lengths ] . ( 18 sec) [ -8566.0297] [ 1732] [depth= 1] . ( 32 sec) [ -8565.6956] [Branch lengths ] . ( 32 sec) [ -8565.6925] [GTR parameters ] . ( 32 sec) [ -8565.6748] [Alpha ][ 1.168353] . ( 32 sec) [ -8565.6748] [Topology ] . ( 33 sec) [ -8565.6526] [Topology ] . ( 34 sec) [ -8565.6459] [Topology ] . ( 34 sec) [ -8565.6431] [Topology ] . ( 35 sec) [ -8565.6418] [Topology ] . ( 36 sec) [ -8565.6413] [Topology ] . ( 36 sec) [ -8565.6412] [GTR parameters ] . ( 36 sec) [ -8565.6412] [Alpha ][ 1.169521] . ( 36 sec) [ -8565.6412] [Topology ] . ( 37 sec) [ -8565.6409] [Topology ] . ( 37 sec) [ -8565.6409] [GTR parameters ] . ( 37 sec) [ -8565.6409] [Alpha ][ 1.169521] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640889. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18416.2739] [GTR parameters ] . ( 1 sec) [ -18065.9369] [Alpha ][ 0.500960] . ( 1 sec) [ -17900.8875] [ 4073] [depth= 8] . ( 1 sec) [ -17568.7946] [ 3984] [depth= 9] . ( 1 sec) [ -17383.1149] [ 3960] [depth= 4] . ( 1 sec) [ -17216.7413] [ 3949] [depth= 7] . ( 1 sec) [ -17018.6869] [ 3867] [depth= 3] . ( 1 sec) [ -16855.8524] [ 3856] [depth= 1] . ( 1 sec) [ -16389.7243] [ 3812] [depth= 1] . ( 1 sec) [ -16300.6623] [ 3798] [depth= 5] . ( 1 sec) [ -16129.7607] [ 3743] [depth= 1] . ( 1 sec) [ -15945.5054] [ 3723] [depth= 3] . ( 1 sec) [ -15782.3820] [ 3686] [depth= 9] . ( 1 sec) [ -15655.5981] [ 3682] [depth= 1] . ( 1 sec) [ -15463.5767] [ 3613] [depth= 6] . ( 1 sec) [ -15344.0940] [ 3627] [depth= 4] . ( 1 sec) [ -15058.2225] [ 3523] [depth= 5] . ( 1 sec) [ -14857.8307] [ 3445] [depth= 6] . ( 2 sec) [ -14437.1038] [ 3435] [depth= 3] . ( 2 sec) [ -14329.7008] [ 3429] [depth= 2] . ( 2 sec) [ -14047.6083] [ 3335] [depth= 6] . ( 2 sec) [ -13789.3093] [ 3213] [depth= 5] . ( 2 sec) [ -13691.8628] [ 3207] [depth= 1] . ( 2 sec) [ -13461.5680] [ 3216] [depth= 3] . ( 2 sec) [ -13394.3374] [ 3210] [depth= 8] . ( 2 sec) [ -13324.9422] [ 3212] [depth= 7] . ( 2 sec) [ -13256.1963] [ 3216] [depth= 1] . ( 2 sec) [ -13132.2760] [ 3195] [depth= 3] . ( 2 sec) [ -12754.9495] [ 3026] [depth= 9] . ( 2 sec) [ -12381.1146] [ 2935] [depth= 9] . ( 2 sec) [ -12214.3560] [ 2893] [depth= 6] . ( 2 sec) [ -12016.3890] [ 2818] [depth= 7] . ( 2 sec) [ -11957.0522] [ 2815] [depth= 1] . ( 2 sec) [ -11953.4030] [ 2820] [depth= 2] . ( 2 sec) [ -11922.1877] [ 2823] [depth= 1] . ( 2 sec) [ -11896.3676] [ 2814] [depth= 2] . ( 2 sec) [ -11815.8484] [ 2806] [depth= 2] . ( 2 sec) [ -11752.9689] [ 2728] [depth= 7] . ( 2 sec) [ -11630.6214] [ 2733] [depth= 5] . ( 3 sec) [ -11578.1923] [ 2708] [depth= 2] . ( 3 sec) [ -11543.7178] [ 2668] [depth= 1] . ( 3 sec) [ -11541.5597] [ 2661] [depth= 1] . ( 3 sec) [ -11492.6060] [ 2662] [depth= 4] . ( 3 sec) [ -11469.0202] [ 2660] [depth= 2] . ( 3 sec) [ -11177.9664] [ 2557] [depth= 5] . ( 3 sec) [ -10813.0411] [ 2473] [depth= 6] . ( 3 sec) [ -10781.3310] [ 2460] [depth= 3] . ( 3 sec) [ -10660.0439] [ 2411] [depth= 2] . ( 3 sec) [ -10537.7874] [ 2409] [depth= 2] . ( 3 sec) [ -10436.9321] [ 2349] [depth= 1] . ( 3 sec) [ -10128.7807] [ 2248] [depth= 3] . ( 3 sec) [ -9930.0949] [ 2183] [depth= 7] . ( 3 sec) [ -9901.8548] [ 2193] [depth= 1] . ( 3 sec) [ -9878.1418] [ 2196] [depth= 1] . ( 3 sec) [ -9774.0533] [ 2160] [depth= 6] . ( 3 sec) [ -9764.9329] [ 2157] [depth= 1] . ( 3 sec) [ -9673.8065] [ 2101] [depth= 5] . ( 4 sec) [ -9661.2487] [ 2090] [depth= 1] . ( 4 sec) [ -9646.3136] [ 2090] [depth= 2] . ( 4 sec) [ -9459.9991] [ 2052] [depth= 1] . ( 4 sec) [ -9397.6582] [ 2041] [depth= 2] . ( 4 sec) [ -9312.2887] [ 2000] [depth= 1] . ( 4 sec) [ -9308.6754] [ 1995] [depth= 1] . ( 4 sec) [ -9274.4975] [ 1985] [depth= 1] . ( 4 sec) [ -9245.6702] [ 1939] [depth= 2] . ( 4 sec) [ -9235.1357] [ 1931] [depth= 1] . ( 4 sec) [ -9135.5666] [ 1908] [depth= 5] . ( 4 sec) [ -9095.6583] [ 1872] [depth= 5] . ( 4 sec) [ -9029.4960] [ 1836] [depth= 1] . ( 4 sec) [ -8990.3271] [ 1814] [depth= 1] . ( 4 sec) [ -8970.2783] [ 1814] [depth= 1] . ( 5 sec) [ -8808.8673] [Branch lengths ] . ( 5 sec) [ -8805.7343] [GTR parameters ] . ( 5 sec) [ -8761.2488] [Alpha ][ 1.000161] . ( 5 sec) [ -8741.0029] [ 1807] [depth= 1] . ( 5 sec) [ -8722.1900] [ 1794] [depth= 1] . ( 6 sec) [ -8701.1482] [ 1783] [depth= 2] . ( 6 sec) [ -8596.5071] [ 1743] [depth= 2] . ( 8 sec) [ -8594.1948] [ 1742] [depth= 1] . ( 8 sec) [ -8584.8640] [ 1738] [depth= 1] . ( 8 sec) [ -8583.9252] [ 1734] [depth= 1] . ( 8 sec) [ -8569.8840] [Branch lengths ] . ( 9 sec) [ -8569.7931] [GTR parameters ] . ( 9 sec) [ -8568.6128] [Alpha ][ 1.135875] . ( 10 sec) [ -8568.5979] [ 1732] [depth= 1] . ( 10 sec) [ -8568.4543] [ 1734] [depth= 1] . ( 12 sec) [ -8566.3208] [Branch lengths ] . ( 12 sec) [ -8566.3191] [GTR parameters ] . ( 12 sec) [ -8566.2846] [Alpha ][ 1.160475] . ( 15 sec) [ -8566.1372] [ 1732] [depth= 1] . ( 15 sec) [ -8565.7073] [Branch lengths ] . ( 15 sec) [ -8565.7053] [GTR parameters ] . ( 15 sec) [ -8565.7027] [Alpha ][ 1.167425] . ( 35 sec) [ -8565.6481] [Branch lengths ] . ( 35 sec) [ -8565.6481] [Topology ] . ( 36 sec) [ -8565.6436] [Topology ] . ( 37 sec) [ -8565.6422] [Topology ] . ( 38 sec) [ -8565.6416] [Topology ] . ( 38 sec) [ -8565.6415] [GTR parameters ] . ( 38 sec) [ -8565.6413] [Alpha ][ 1.169233] . ( 38 sec) [ -8565.6413] [Topology ] . ( 39 sec) [ -8565.6409] [Topology ] . ( 39 sec) [ -8565.6409] [GTR parameters ] . ( 39 sec) [ -8565.6409] [Alpha ][ 1.169233] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640930. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -18937.5587] [GTR parameters ] . ( 1 sec) [ -18578.8910] [Alpha ][ 0.500960] . ( 1 sec) [ -18441.4855] [ 4175] [depth= 1] . ( 1 sec) [ -18204.6877] [ 4135] [depth= 4] . ( 1 sec) [ -18013.5512] [ 4122] [depth= 4] . ( 1 sec) [ -17899.9829] [ 4118] [depth= 1] . ( 1 sec) [ -17690.1914] [ 4069] [depth= 8] . ( 1 sec) [ -17677.6646] [ 4058] [depth= 5] . ( 1 sec) [ -17411.2293] [ 3989] [depth= 1] . ( 1 sec) [ -17248.0310] [ 3954] [depth= 6] . ( 1 sec) [ -16345.1897] [ 3797] [depth= 6] . ( 1 sec) [ -16111.4465] [ 3790] [depth= 11] . ( 1 sec) [ -15841.0562] [ 3716] [depth= 8] . ( 1 sec) [ -15469.6278] [ 3713] [depth= 5] . ( 1 sec) [ -15213.1387] [ 3636] [depth= 14] . ( 1 sec) [ -15145.3141] [ 3616] [depth= 1] . ( 1 sec) [ -15093.2172] [ 3612] [depth= 1] . ( 1 sec) [ -15069.8337] [ 3584] [depth= 1] . ( 1 sec) [ -15004.6598] [ 3571] [depth= 3] . ( 1 sec) [ -14857.4344] [ 3561] [depth= 8] . ( 2 sec) [ -14731.0259] [ 3565] [depth= 1] . ( 2 sec) [ -14428.2698] [ 3557] [depth= 3] . ( 2 sec) [ -14210.6360] [ 3523] [depth= 6] . ( 2 sec) [ -14000.5961] [ 3459] [depth= 1] . ( 2 sec) [ -13917.3924] [ 3400] [depth= 6] . ( 2 sec) [ -13799.8464] [ 3323] [depth= 3] . ( 2 sec) [ -13727.0243] [ 3308] [depth= 5] . ( 2 sec) [ -13447.7716] [ 3155] [depth= 8] . ( 2 sec) [ -13436.7874] [ 3158] [depth= 1] . ( 2 sec) [ -13388.7967] [ 3154] [depth= 1] . ( 2 sec) [ -13386.6187] [ 3151] [depth= 1] . ( 2 sec) [ -13285.5948] [ 3069] [depth= 11] . ( 2 sec) [ -12897.9804] [ 2976] [depth= 10] . ( 2 sec) [ -12588.8624] [ 2911] [depth= 7] . ( 2 sec) [ -12587.5745] [ 2933] [depth= 1] . ( 2 sec) [ -12422.7965] [ 2883] [depth= 7] . ( 2 sec) [ -12409.5868] [ 2901] [depth= 1] . ( 2 sec) [ -12351.7826] [ 2903] [depth= 9] . ( 2 sec) [ -12338.3773] [ 2907] [depth= 1] . ( 2 sec) [ -12065.2911] [ 2844] [depth= 2] . ( 2 sec) [ -12039.0037] [ 2848] [depth= 1] . ( 2 sec) [ -11900.3829] [ 2781] [depth= 8] . ( 2 sec) [ -11703.3356] [ 2749] [depth= 1] . ( 2 sec) [ -11691.8835] [ 2745] [depth= 6] . ( 3 sec) [ -11678.3567] [ 2748] [depth= 1] . ( 3 sec) [ -11666.2124] [ 2745] [depth= 1] . ( 3 sec) [ -11309.1166] [ 2646] [depth= 6] . ( 3 sec) [ -11257.0005] [ 2619] [depth= 1] . ( 3 sec) [ -11256.9896] [ 2623] [depth= 1] . ( 3 sec) [ -11254.8864] [ 2643] [depth= 1] . ( 3 sec) [ -10989.2321] [ 2554] [depth= 5] . ( 3 sec) [ -10972.0746] [ 2548] [depth= 2] . ( 3 sec) [ -10956.4307] [ 2541] [depth= 1] . ( 3 sec) [ -10853.3814] [ 2471] [depth= 8] . ( 3 sec) [ -10717.6806] [ 2471] [depth= 3] . ( 3 sec) [ -10717.4272] [ 2425] [depth= 9] . ( 3 sec) [ -10635.5161] [ 2428] [depth= 3] . ( 3 sec) [ -10609.4752] [ 2424] [depth= 1] . ( 3 sec) [ -10569.1780] [ 2409] [depth= 5] . ( 3 sec) [ -10475.6462] [ 2371] [depth= 9] . ( 3 sec) [ -10416.6532] [ 2345] [depth= 1] . ( 3 sec) [ -10189.0649] [ 2277] [depth= 7] . ( 3 sec) [ -10164.9846] [ 2283] [depth= 1] . ( 3 sec) [ -10103.7357] [ 2244] [depth= 8] . ( 3 sec) [ -10033.1150] [ 2230] [depth= 9] . ( 4 sec) [ -10028.2868] [ 2229] [depth= 9] . ( 4 sec) [ -10002.6769] [ 2228] [depth= 1] . ( 4 sec) [ -9910.1598] [ 2180] [depth= 2] . ( 4 sec) [ -9874.3897] [ 2165] [depth= 2] . ( 4 sec) [ -9576.9560] [ 2068] [depth= 6] . ( 4 sec) [ -9554.4854] [ 2062] [depth= 1] . ( 4 sec) [ -9489.8415] [ 2049] [depth= 1] . ( 4 sec) [ -9457.5171] [ 2018] [depth= 1] . ( 4 sec) [ -9446.8730] [ 2025] [depth= 1] . ( 4 sec) [ -9427.1054] [ 2015] [depth= 1] . ( 4 sec) [ -9285.0473] [ 1977] [depth= 3] . ( 4 sec) [ -9267.4276] [ 1969] [depth= 1] . ( 4 sec) [ -9263.0440] [ 1964] [depth= 1] . ( 4 sec) [ -9249.3012] [ 1958] [depth= 1] . ( 4 sec) [ -9228.1650] [ 1954] [depth= 1] . ( 4 sec) [ -9225.1363] [ 1956] [depth= 2] . ( 4 sec) [ -9208.0120] [ 1960] [depth= 1] . ( 4 sec) [ -9158.6055] [ 1925] [depth= 6] . ( 4 sec) [ -9105.5309] [ 1915] [depth= 1] . ( 4 sec) [ -9087.9560] [ 1914] [depth= 1] . ( 4 sec) [ -9085.6250] [ 1923] [depth= 1] . ( 5 sec) [ -9053.1359] [ 1899] [depth= 2] . ( 5 sec) [ -9023.2823] [ 1877] [depth= 1] . ( 5 sec) [ -9003.9373] [ 1868] [depth= 1] . ( 5 sec) [ -8982.8033] [ 1863] [depth= 1] . ( 5 sec) [ -8851.0469] [Branch lengths ] . ( 6 sec) [ -8846.7656] [GTR parameters ] . ( 6 sec) [ -8801.5988] [Alpha ][ 1.000157] . ( 6 sec) [ -8797.5893] [ 1867] [depth= 1] . ( 6 sec) [ -8792.9886] [ 1855] [depth= 1] . ( 6 sec) [ -8759.9586] [ 1847] [depth= 6] . ( 6 sec) [ -8735.5513] [ 1835] [depth= 2] . ( 6 sec) [ -8720.0680] [ 1815] [depth= 1] . ( 6 sec) [ -8716.9372] [ 1812] [depth= 1] . ( 7 sec) [ -8706.1926] [ 1797] [depth= 1] . ( 7 sec) [ -8623.4312] [ 1741] [depth= 4] . ( 7 sec) [ -8620.5761] [ 1747] [depth= 1] . ( 7 sec) [ -8619.4902] [ 1747] [depth= 1] . ( 7 sec) [ -8594.1723] [ 1743] [depth= 1] . ( 8 sec) [ -8593.8561] [ 1745] [depth= 1] . ( 8 sec) [ -8592.4066] [ 1745] [depth= 2] . ( 8 sec) [ -8590.9916] [ 1750] [depth= 1] . ( 8 sec) [ -8588.8471] [ 1734] [depth= 2] . ( 9 sec) [ -8569.3871] [Branch lengths ] . ( 9 sec) [ -8569.2020] [GTR parameters ] . ( 10 sec) [ -8567.7213] [Alpha ][ 1.151728] . ( 11 sec) [ -8567.4169] [ 1732] [depth= 1] . ( 12 sec) [ -8565.7810] [Branch lengths ] . ( 13 sec) [ -8565.7773] [GTR parameters ] . ( 13 sec) [ -8565.7656] [Alpha ][ 1.166734] . ( 15 sec) [ -8565.6499] [Branch lengths ] . ( 35 sec) [ -8565.6423] [Branch lengths ] . ( 35 sec) [ -8565.6423] [Topology ] . ( 36 sec) [ -8565.6418] [Topology ] . ( 36 sec) [ -8565.6414] [GTR parameters ] . ( 36 sec) [ -8565.6411] [Alpha ][ 1.169298] . ( 36 sec) [ -8565.6411] [Topology ] . ( 37 sec) [ -8565.6408] [Topology ] . ( 37 sec) [ -8565.6408] [GTR parameters ] . ( 37 sec) [ -8565.6408] [Alpha ][ 1.169298] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640822. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -17698.9252] [GTR parameters ] . ( 1 sec) [ -17378.9341] [Alpha ][ 0.500960] . ( 1 sec) [ -17197.2594] [ 3989] [depth= 11] . ( 1 sec) [ -16936.2630] [ 3956] [depth= 3] . ( 1 sec) [ -16622.3160] [ 3877] [depth= 8] . ( 1 sec) [ -16575.3617] [ 3869] [depth= 1] . ( 1 sec) [ -16280.5016] [ 3776] [depth= 3] . ( 1 sec) [ -16209.6035] [ 3752] [depth= 3] . ( 1 sec) [ -16198.3890] [ 3754] [depth= 2] . ( 1 sec) [ -16170.6979] [ 3730] [depth= 1] . ( 1 sec) [ -16065.8258] [ 3717] [depth= 6] . ( 1 sec) [ -16056.4499] [ 3710] [depth= 2] . ( 2 sec) [ -15831.7927] [ 3712] [depth= 9] . ( 2 sec) [ -15514.3391] [ 3595] [depth= 12] . ( 2 sec) [ -15266.6561] [ 3554] [depth= 2] . ( 2 sec) [ -15260.7399] [ 3546] [depth= 9] . ( 2 sec) [ -14958.6415] [ 3470] [depth= 18] . ( 2 sec) [ -14852.6956] [ 3456] [depth= 10] . ( 2 sec) [ -14796.0101] [ 3444] [depth= 2] . ( 2 sec) [ -14650.6021] [ 3402] [depth= 3] . ( 2 sec) [ -14376.0173] [ 3322] [depth= 7] . ( 2 sec) [ -14038.0218] [ 3262] [depth= 9] . ( 2 sec) [ -13836.3452] [ 3213] [depth= 7] . ( 2 sec) [ -13615.3632] [ 3132] [depth= 11] . ( 2 sec) [ -13613.4557] [ 3134] [depth= 1] . ( 2 sec) [ -13524.6861] [ 3126] [depth= 1] . ( 2 sec) [ -13507.8058] [ 3125] [depth= 8] . ( 2 sec) [ -13426.3694] [ 3071] [depth= 1] . ( 2 sec) [ -13426.1015] [ 3055] [depth= 7] . ( 2 sec) [ -13421.0914] [ 3051] [depth= 1] . ( 2 sec) [ -13013.4243] [ 3021] [depth= 6] . ( 2 sec) [ -12921.1324] [ 2921] [depth= 5] . ( 2 sec) [ -12867.9084] [ 2877] [depth= 1] . ( 3 sec) [ -12607.0071] [ 2854] [depth= 17] . ( 3 sec) [ -12378.9260] [ 2811] [depth= 2] . ( 3 sec) [ -12367.9613] [ 2822] [depth= 1] . ( 3 sec) [ -12226.3554] [ 2759] [depth= 1] . ( 3 sec) [ -12208.5815] [ 2747] [depth= 1] . ( 3 sec) [ -12177.6554] [ 2736] [depth= 1] . ( 3 sec) [ -12158.8789] [ 2735] [depth= 3] . ( 3 sec) [ -11874.6520] [ 2600] [depth= 7] . ( 3 sec) [ -11804.7106] [ 2555] [depth= 5] . ( 3 sec) [ -11680.3687] [ 2554] [depth= 2] . ( 3 sec) [ -11657.2839] [ 2554] [depth= 1] . ( 3 sec) [ -11524.7966] [ 2509] [depth= 2] . ( 3 sec) [ -11359.8508] [ 2459] [depth= 3] . ( 3 sec) [ -11168.8576] [ 2435] [depth= 1] . ( 3 sec) [ -11141.4571] [ 2420] [depth= 1] . ( 3 sec) [ -10991.9085] [ 2425] [depth= 10] . ( 3 sec) [ -10637.4727] [ 2292] [depth= 9] . ( 3 sec) [ -10567.8821] [ 2268] [depth= 1] . ( 3 sec) [ -10493.0010] [ 2272] [depth= 1] . ( 3 sec) [ -10272.9587] [ 2168] [depth= 2] . ( 3 sec) [ -10227.2982] [ 2161] [depth= 4] . ( 4 sec) [ -10149.1994] [ 2156] [depth= 7] . ( 4 sec) [ -10036.3398] [ 2155] [depth= 1] . ( 4 sec) [ -9957.1287] [ 2141] [depth= 2] . ( 4 sec) [ -9905.3179] [ 2111] [depth= 1] . ( 4 sec) [ -9885.2002] [ 2092] [depth= 1] . ( 4 sec) [ -9718.7134] [ 2057] [depth= 4] . ( 4 sec) [ -9713.6479] [ 2042] [depth= 3] . ( 4 sec) [ -9505.5157] [ 2044] [depth= 1] . ( 4 sec) [ -9366.1857] [ 1940] [depth= 7] . ( 4 sec) [ -9334.9989] [ 1928] [depth= 1] . ( 4 sec) [ -9328.2924] [ 1921] [depth= 4] . ( 4 sec) [ -9326.7875] [ 1924] [depth= 1] . ( 4 sec) [ -9309.1104] [ 1928] [depth= 3] . ( 4 sec) [ -9301.9302] [ 1924] [depth= 1] . ( 4 sec) [ -9294.8253] [ 1924] [depth= 1] . ( 4 sec) [ -9293.1046] [ 1924] [depth= 1] . ( 4 sec) [ -9284.9886] [ 1921] [depth= 1] . ( 4 sec) [ -9254.0063] [ 1922] [depth= 1] . ( 4 sec) [ -9207.7699] [ 1920] [depth= 1] . ( 5 sec) [ -9030.2885] [ 1863] [depth= 7] . ( 5 sec) [ -8913.9322] [ 1804] [depth= 5] . ( 5 sec) [ -8803.6714] [ 1779] [depth= 1] . ( 5 sec) [ -8781.4897] [ 1768] [depth= 4] . ( 5 sec) [ -8777.8165] [ 1769] [depth= 1] . ( 5 sec) [ -8754.4137] [ 1762] [depth= 3] . ( 5 sec) [ -8751.7204] [ 1760] [depth= 1] . ( 5 sec) [ -8675.3787] [Branch lengths ] . ( 6 sec) [ -8671.7167] [GTR parameters ] . ( 6 sec) [ -8628.2845] [Alpha ][ 1.000146] . ( 6 sec) [ -8625.8618] [ 1762] [depth= 1] . ( 6 sec) [ -8623.2401] [ 1759] [depth= 1] . ( 6 sec) [ -8620.4158] [ 1752] [depth= 1] . ( 6 sec) [ -8619.8990] [ 1750] [depth= 1] . ( 7 sec) [ -8589.5713] [ 1735] [depth= 1] . ( 7 sec) [ -8584.8897] [ 1732] [depth= 1] . ( 7 sec) [ -8584.7231] [ 1736] [depth= 1] . ( 7 sec) [ -8584.2488] [ 1738] [depth= 1] . ( 8 sec) [ -8584.0938] [ 1734] [depth= 1] . ( 8 sec) [ -8584.0661] [ 1732] [depth= 1] . ( 8 sec) [ -8583.7673] [ 1734] [depth= 1] . ( 9 sec) [ -8568.6995] [Branch lengths ] . ( 9 sec) [ -8568.6921] [GTR parameters ] . ( 9 sec) [ -8567.3598] [Alpha ][ 1.144149] . ( 12 sec) [ -8566.0881] [Branch lengths ] . ( 17 sec) [ -8565.9652] [ 1732] [depth= 1] . ( 32 sec) [ -8565.7101] [Branch lengths ] . ( 32 sec) [ -8565.7077] [GTR parameters ] . ( 32 sec) [ -8565.6770] [Alpha ][ 1.167295] . ( 32 sec) [ -8565.6770] [Topology ] . ( 33 sec) [ -8565.6548] [Topology ] . ( 34 sec) [ -8565.6472] [Topology ] . ( 35 sec) [ -8565.6439] [Topology ] . ( 36 sec) [ -8565.6423] [Topology ] . ( 37 sec) [ -8565.6416] [Topology ] . ( 37 sec) [ -8565.6416] [GTR parameters ] . ( 37 sec) [ -8565.6414] [Alpha ][ 1.169222] . ( 37 sec) [ -8565.6414] [Topology ] . ( 38 sec) [ -8565.6410] [Topology ] . ( 38 sec) [ -8565.6410] [GTR parameters ] . ( 38 sec) [ -8565.6410] [Alpha ][ 1.169222] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640988. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19172.8299] [GTR parameters ] . ( 0 sec) [ -18803.3003] [Alpha ][ 0.500960] . ( 0 sec) [ -18509.4412] [ 4216] [depth= 7] . ( 0 sec) [ -18103.5605] [ 4182] [depth= 6] . ( 1 sec) [ -17824.4758] [ 4156] [depth= 5] . ( 1 sec) [ -17802.6074] [ 4150] [depth= 7] . ( 1 sec) [ -17657.6835] [ 4037] [depth= 10] . ( 1 sec) [ -17451.6395] [ 4026] [depth= 4] . ( 1 sec) [ -17365.3212] [ 3990] [depth= 1] . ( 1 sec) [ -17086.7612] [ 3947] [depth= 18] . ( 1 sec) [ -16970.5036] [ 3906] [depth= 1] . ( 1 sec) [ -16761.5363] [ 3847] [depth= 1] . ( 1 sec) [ -16506.3493] [ 3807] [depth= 10] . ( 1 sec) [ -16373.8200] [ 3795] [depth= 1] . ( 1 sec) [ -16234.7349] [ 3787] [depth= 13] . ( 1 sec) [ -16224.4664] [ 3799] [depth= 1] . ( 1 sec) [ -16067.7173] [ 3790] [depth= 12] . ( 1 sec) [ -15748.7422] [ 3719] [depth= 2] . ( 1 sec) [ -15689.9143] [ 3718] [depth= 13] . ( 1 sec) [ -15380.2417] [ 3665] [depth= 9] . ( 1 sec) [ -14982.3720] [ 3546] [depth= 8] . ( 1 sec) [ -14761.9392] [ 3505] [depth= 2] . ( 1 sec) [ -14453.4466] [ 3414] [depth= 8] . ( 1 sec) [ -14345.4871] [ 3411] [depth= 1] . ( 1 sec) [ -14264.0784] [ 3420] [depth= 5] . ( 1 sec) [ -14171.9593] [ 3445] [depth= 9] . ( 2 sec) [ -14096.9515] [ 3388] [depth= 3] . ( 2 sec) [ -14080.5420] [ 3381] [depth= 1] . ( 2 sec) [ -13897.2092] [ 3310] [depth= 2] . ( 2 sec) [ -13427.3182] [ 3197] [depth= 7] . ( 2 sec) [ -13181.4138] [ 3120] [depth= 12] . ( 2 sec) [ -13123.9721] [ 3116] [depth= 1] . ( 2 sec) [ -13117.7142] [ 3105] [depth= 4] . ( 2 sec) [ -13036.8374] [ 3103] [depth= 3] . ( 2 sec) [ -12763.5930] [ 3033] [depth= 3] . ( 2 sec) [ -12563.9642] [ 2970] [depth= 16] . ( 2 sec) [ -12556.7513] [ 2898] [depth= 5] . ( 2 sec) [ -12504.6292] [ 2904] [depth= 1] . ( 2 sec) [ -12299.9763] [ 2838] [depth= 7] . ( 2 sec) [ -11991.1399] [ 2751] [depth= 5] . ( 2 sec) [ -11853.6737] [ 2725] [depth= 2] . ( 2 sec) [ -11776.6748] [ 2722] [depth= 1] . ( 2 sec) [ -11600.5286] [ 2692] [depth= 11] . ( 2 sec) [ -11568.3947] [ 2636] [depth= 1] . ( 2 sec) [ -11511.8276] [ 2619] [depth= 4] . ( 2 sec) [ -11169.3183] [ 2609] [depth= 1] . ( 3 sec) [ -11153.2841] [ 2618] [depth= 1] . ( 3 sec) [ -10814.8744] [ 2470] [depth= 9] . ( 3 sec) [ -10652.3999] [ 2431] [depth= 8] . ( 3 sec) [ -10501.9638] [ 2390] [depth= 3] . ( 3 sec) [ -10418.5492] [ 2337] [depth= 2] . ( 3 sec) [ -10168.1761] [ 2263] [depth= 5] . ( 3 sec) [ -10137.1442] [ 2261] [depth= 2] . ( 3 sec) [ -10116.5273] [ 2248] [depth= 7] . ( 3 sec) [ -10059.4178] [ 2234] [depth= 1] . ( 3 sec) [ -10057.2247] [ 2234] [depth= 1] . ( 3 sec) [ -9979.1152] [ 2189] [depth= 1] . ( 3 sec) [ -9978.8539] [ 2195] [depth= 1] . ( 3 sec) [ -9915.4431] [ 2150] [depth= 1] . ( 3 sec) [ -9878.5297] [ 2144] [depth= 1] . ( 3 sec) [ -9771.6954] [ 2098] [depth= 1] . ( 3 sec) [ -9727.5469] [ 2090] [depth= 3] . ( 4 sec) [ -9708.0483] [ 2068] [depth= 1] . ( 4 sec) [ -9534.1061] [ 2051] [depth= 2] . ( 4 sec) [ -9415.5896] [ 1998] [depth= 8] . ( 4 sec) [ -9361.9252] [ 1988] [depth= 1] . ( 4 sec) [ -9361.2382] [ 1988] [depth= 1] . ( 4 sec) [ -9289.9223] [ 1986] [depth= 1] . ( 4 sec) [ -9139.9138] [ 1934] [depth= 9] . ( 4 sec) [ -9136.5751] [ 1930] [depth= 2] . ( 4 sec) [ -9077.3115] [ 1893] [depth= 4] . ( 4 sec) [ -9062.7446] [ 1903] [depth= 2] . ( 4 sec) [ -9012.8795] [ 1884] [depth= 3] . ( 4 sec) [ -8976.2678] [ 1863] [depth= 1] . ( 4 sec) [ -8975.0366] [ 1867] [depth= 1] . ( 4 sec) [ -8950.5490] [ 1853] [depth= 1] . ( 4 sec) [ -8920.4603] [ 1828] [depth= 1] . ( 5 sec) [ -8812.1192] [Branch lengths ] . ( 5 sec) [ -8807.8728] [GTR parameters ] . ( 5 sec) [ -8764.0045] [Alpha ][ 1.000138] . ( 6 sec) [ -8758.9426] [ 1824] [depth= 1] . ( 6 sec) [ -8726.5231] [ 1815] [depth= 3] . ( 6 sec) [ -8726.2579] [ 1810] [depth= 2] . ( 6 sec) [ -8723.2170] [ 1803] [depth= 1] . ( 6 sec) [ -8722.3887] [ 1796] [depth= 1] . ( 6 sec) [ -8719.1197] [ 1803] [depth= 1] . ( 6 sec) [ -8706.2458] [ 1797] [depth= 1] . ( 7 sec) [ -8613.2998] [ 1748] [depth= 2] . ( 7 sec) [ -8607.9891] [ 1737] [depth= 2] . ( 7 sec) [ -8607.7186] [ 1738] [depth= 1] . ( 7 sec) [ -8585.6625] [ 1732] [depth= 1] . ( 8 sec) [ -8584.5008] [ 1736] [depth= 1] . ( 8 sec) [ -8582.2011] [ 1736] [depth= 1] . ( 8 sec) [ -8569.3450] [Branch lengths ] . ( 9 sec) [ -8569.1018] [GTR parameters ] . ( 9 sec) [ -8567.7822] [Alpha ][ 1.143320] . ( 9 sec) [ -8567.6632] [ 1736] [depth= 1] . ( 9 sec) [ -8567.4730] [ 1736] [depth= 1] . ( 12 sec) [ -8566.1773] [Branch lengths ] . ( 12 sec) [ -8566.1768] [GTR parameters ] . ( 12 sec) [ -8566.1592] [Alpha ][ 1.161696] . ( 15 sec) [ -8565.9816] [Branch lengths ] . ( 32 sec) [ -8565.8586] [ 1732] [depth= 1] . ( 35 sec) [ -8565.6680] [Branch lengths ] . ( 35 sec) [ -8565.6645] [GTR parameters ] . ( 35 sec) [ -8565.6616] [Alpha ][ 1.169147] . ( 35 sec) [ -8565.6616] [Topology ] . ( 36 sec) [ -8565.6462] [Topology ] . ( 36 sec) [ -8565.6428] [Topology ] . ( 37 sec) [ -8565.6416] [Topology ] . ( 38 sec) [ -8565.6411] [Topology ] . ( 38 sec) [ -8565.6410] [GTR parameters ] . ( 38 sec) [ -8565.6410] [Alpha ][ 1.169147] . ( 38 sec) [ -8565.6410] [Topology ] . ( 39 sec) [ -8565.6408] [Topology ] . ( 39 sec) [ -8565.6408] [GTR parameters ] . ( 39 sec) [ -8565.6408] [Alpha ][ 1.169147] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -8565.640820. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8600.808417 . ( 1 sec) [ -8595.7121] [GTR parameters ] . ( 1 sec) [ -8594.7346] [Alpha ][ 1.123703] . ( 1 sec) [ -8594.7346] [Topology ] . ( 2 sec) [ -8569.4203] [Topology ] . ( 2 sec) [ -8566.8728] [Topology ] . ( 3 sec) [ -8566.2596] [Topology ] . ( 4 sec) [ -8566.0287] [Topology ] . ( 5 sec) [ -8565.9291] [Topology ] . ( 6 sec) [ -8565.8840] [Topology ] . ( 6 sec) [ -8565.8630] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.863045 . ( 12 sec) [ -8565.7813] [GTR parameters ] . ( 12 sec) [ -8565.6810] [Alpha ][ 1.165891] . ( 12 sec) [ -8565.6810] [Topology ] . ( 13 sec) [ -8565.6588] [Topology ] . ( 14 sec) [ -8565.6494] [Topology ] . ( 15 sec) [ -8565.6451] [Topology ] . ( 16 sec) [ -8565.6432] [Topology ] . ( 16 sec) [ -8565.6422] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.642239 . ( 22 sec) [ -8565.6422] [GTR parameters ] . ( 22 sec) [ -8565.6416] [Alpha ][ 1.169138] . ( 22 sec) [ -8565.6416] [Topology ] . ( 23 sec) [ -8565.6411] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8565.641103 . ( 29 sec) [ -8565.6411] [GTR parameters ] . ( 29 sec) [ -8565.6411] [Alpha ][ 1.169138] . ( 29 sec) [ -8565.6411] [Topology ] . ( 30 sec) [ -8565.6409] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -8595.7121] [GTR parameters ] . ( 42 sec) [ -8594.7346] [Alpha ][ 1.123703] . ( 43 sec) [ -8594.6607] [ 1736] [depth= 1] . ( 43 sec) [ -8593.7167] [ 1736] [depth= 1] . ( 44 sec) [ -8592.7299] [ 1741] [depth= 1] . ( 44 sec) [ -8589.3249] [ 1743] [depth= 1] . ( 44 sec) [ -8588.3251] [ 1736] [depth= 1] . ( 44 sec) [ -8586.0362] [ 1736] [depth= 1] . ( 44 sec) [ -8584.7148] [ 1732] [depth= 1] . ( 45 sec) [ -8566.7282] [Branch lengths ] . ( 45 sec) [ -8566.6697] [GTR parameters ] . ( 45 sec) [ -8566.6050] [Alpha ][ 1.157614] . ( 48 sec) [ -8565.7079] [Branch lengths ] . ( 68 sec) [ -8565.6551] [Branch lengths ] . ( 68 sec) [ -8565.6551] [Topology ] . ( 69 sec) [ -8565.6524] [Topology ] . ( 69 sec) [ -8565.6517] [Topology ] . ( 70 sec) [ -8565.6491] [GTR parameters ] . ( 70 sec) [ -8565.6421] [Alpha ][ 1.169175] . ( 70 sec) [ -8565.6421] [Topology ] . ( 71 sec) [ -8565.6413] [Topology ] . ( 71 sec) [ -8565.6413] [GTR parameters ] . ( 71 sec) [ -8565.6413] [Alpha ][ 1.169175] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8565.640862 . Log likelihood obtained after SPR moves : -8565.641258 . Log likelihood of the current tree: -8565.640862. . Printing the most likely tree in file 'data25.phy_phyml_tree.txt'... . Best log likelihood : -8565.640820 . Time used 0h1m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo