.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data14.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... . 387 patterns found. (out of a total of 500 sites) . 105 sites without polymorphism (21.00%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19146.8995] [GTR parameters ] . ( 1 sec) [ -18710.6309] [Alpha ][ 0.500960] . ( 1 sec) [ -18439.7643] [ 3819] [depth= 8] . ( 1 sec) [ -18158.5531] [ 3807] [depth= 9] . ( 1 sec) [ -17869.5460] [ 3789] [depth= 1] . ( 1 sec) [ -17532.0479] [ 3783] [depth= 7] . ( 1 sec) [ -17259.4086] [ 3690] [depth= 1] . ( 1 sec) [ -17069.6448] [ 3687] [depth= 1] . ( 1 sec) [ -16914.9187] [ 3647] [depth= 4] . ( 1 sec) [ -16816.6618] [ 3617] [depth= 1] . ( 1 sec) [ -16526.7636] [ 3604] [depth= 8] . ( 1 sec) [ -16300.0675] [ 3512] [depth= 11] . ( 1 sec) [ -16019.2728] [ 3520] [depth= 10] . ( 1 sec) [ -15763.5155] [ 3413] [depth= 9] . ( 1 sec) [ -15729.6887] [ 3392] [depth= 1] . ( 1 sec) [ -15663.0752] [ 3389] [depth= 2] . ( 1 sec) [ -15486.6190] [ 3274] [depth= 6] . ( 1 sec) [ -15438.4862] [ 3270] [depth= 3] . ( 1 sec) [ -15333.5636] [ 3239] [depth= 3] . ( 1 sec) [ -15330.8552] [ 3240] [depth= 1] . ( 1 sec) [ -15245.5612] [ 3223] [depth= 2] . ( 1 sec) [ -15153.7660] [ 3203] [depth= 13] . ( 2 sec) [ -14695.3536] [ 3165] [depth= 10] . ( 2 sec) [ -14341.5698] [ 3002] [depth= 14] . ( 2 sec) [ -13890.9069] [ 3001] [depth= 10] . ( 2 sec) [ -13879.1552] [ 2999] [depth= 2] . ( 2 sec) [ -13516.4645] [ 2904] [depth= 11] . ( 2 sec) [ -13458.7549] [ 2887] [depth= 7] . ( 2 sec) [ -13371.5630] [ 2877] [depth= 6] . ( 2 sec) [ -13312.9633] [ 2858] [depth= 3] . ( 2 sec) [ -12840.5792] [ 2859] [depth= 9] . ( 2 sec) [ -12782.3028] [ 2856] [depth= 2] . ( 2 sec) [ -12659.3692] [ 2856] [depth= 1] . ( 2 sec) [ -12372.9868] [ 2761] [depth= 17] . ( 2 sec) [ -12371.7423] [ 2761] [depth= 1] . ( 2 sec) [ -12053.9670] [ 2741] [depth= 4] . ( 2 sec) [ -12050.4845] [ 2742] [depth= 1] . ( 2 sec) [ -12036.2785] [ 2740] [depth= 1] . ( 2 sec) [ -12003.4497] [ 2730] [depth= 3] . ( 2 sec) [ -11963.9419] [ 2728] [depth= 11] . ( 2 sec) [ -11036.6838] [ 2620] [depth= 7] . ( 2 sec) [ -10817.3253] [ 2548] [depth= 3] . ( 2 sec) [ -10743.3380] [ 2545] [depth= 1] . ( 2 sec) [ -10742.1855] [ 2546] [depth= 1] . ( 2 sec) [ -10607.2853] [ 2488] [depth= 15] . ( 2 sec) [ -10436.7004] [ 2443] [depth= 7] . ( 2 sec) [ -9627.1649] [ 2392] [depth= 15] . ( 3 sec) [ -9622.6820] [ 2390] [depth= 1] . ( 3 sec) [ -9611.8653] [ 2380] [depth= 1] . ( 3 sec) [ -9314.8320] [ 2205] [depth= 12] . ( 3 sec) [ -9313.1591] [ 2215] [depth= 1] . ( 3 sec) [ -9181.3963] [ 2158] [depth= 11] . ( 3 sec) [ -9131.5235] [ 2158] [depth= 2] . ( 3 sec) [ -8979.8546] [ 2077] [depth= 1] . ( 3 sec) [ -8951.1529] [ 2063] [depth= 16] . ( 3 sec) [ -8946.9326] [ 2088] [depth= 1] . ( 3 sec) [ -8625.2277] [ 1956] [depth= 14] . ( 3 sec) [ -8610.1119] [ 1946] [depth= 2] . ( 3 sec) [ -8475.1313] [ 1912] [depth= 1] . ( 3 sec) [ -8460.7370] [ 1912] [depth= 1] . ( 3 sec) [ -8452.0089] [ 1906] [depth= 1] . ( 3 sec) [ -8392.2357] [ 1893] [depth= 4] . ( 3 sec) [ -8390.8633] [ 1871] [depth= 4] . ( 3 sec) [ -8344.3416] [ 1821] [depth= 2] . ( 3 sec) [ -8312.5834] [ 1820] [depth= 1] . ( 3 sec) [ -8300.8116] [ 1820] [depth= 1] . ( 3 sec) [ -8296.2936] [ 1822] [depth= 1] . ( 3 sec) [ -8296.1385] [ 1822] [depth= 1] . ( 4 sec) [ -8295.9483] [ 1822] [depth= 2] . ( 4 sec) [ -8295.7737] [ 1822] [depth= 1] . ( 4 sec) [ -8295.7310] [ 1822] [depth= 1] . ( 4 sec) [ -8294.8641] [ 1825] [depth= 1] . ( 4 sec) [ -8288.7839] [ 1822] [depth= 1] . ( 4 sec) [ -8274.6167] [ 1822] [depth= 2] . ( 4 sec) [ -8240.8280] [ 1814] [depth= 2] . ( 4 sec) [ -8236.2985] [ 1812] [depth= 1] . ( 4 sec) [ -8217.9331] [ 1812] [depth= 2] . ( 4 sec) [ -8189.5243] [ 1811] [depth= 1] . ( 4 sec) [ -8128.7202] [ 1808] [depth= 4] . ( 4 sec) [ -8127.5000] [ 1807] [depth= 2] . ( 4 sec) [ -7996.3854] [ 1793] [depth= 8] . ( 4 sec) [ -7969.4595] [ 1788] [depth= 2] . ( 4 sec) [ -7961.6785] [ 1780] [depth= 1] . ( 4 sec) [ -7959.4143] [ 1780] [depth= 1] . ( 4 sec) [ -7912.2988] [ 1754] [depth= 5] . ( 5 sec) [ -7801.2776] [Branch lengths ] . ( 5 sec) [ -7800.2895] [GTR parameters ] . ( 5 sec) [ -7786.7659] [Alpha ][ 0.734026] . ( 5 sec) [ -7771.0515] [ 1748] [depth= 1] . ( 5 sec) [ -7771.0326] [ 1748] [depth= 1] . ( 5 sec) [ -7770.4023] [ 1751] [depth= 1] . ( 5 sec) [ -7764.0875] [ 1747] [depth= 2] . ( 5 sec) [ -7761.6883] [ 1747] [depth= 3] . ( 6 sec) [ -7761.2479] [ 1751] [depth= 1] . ( 6 sec) [ -7757.3185] [ 1751] [depth= 2] . ( 6 sec) [ -7669.5116] [ 1700] [depth= 9] . ( 6 sec) [ -7665.9853] [ 1700] [depth= 1] . ( 6 sec) [ -7573.3510] [ 1679] [depth= 2] . ( 6 sec) [ -7573.2569] [ 1684] [depth= 1] . ( 6 sec) [ -7498.0249] [ 1612] [depth= 1] . ( 6 sec) [ -7497.4051] [ 1610] [depth= 1] . ( 6 sec) [ -7491.5979] [ 1602] [depth= 1] . ( 6 sec) [ -7491.4287] [ 1602] [depth= 1] . ( 6 sec) [ -7491.4115] [ 1602] [depth= 1] . ( 6 sec) [ -7485.1506] [ 1598] [depth= 1] . ( 6 sec) [ -7484.6106] [ 1599] [depth= 3] . ( 6 sec) [ -7484.5686] [ 1597] [depth= 1] . ( 7 sec) [ -7483.3639] [ 1597] [depth= 1] . ( 7 sec) [ -7481.7145] [ 1594] [depth= 1] . ( 7 sec) [ -7481.1568] [ 1594] [depth= 1] . ( 7 sec) [ -7479.6135] [ 1590] [depth= 1] . ( 7 sec) [ -7423.3666] [ 1580] [depth= 1] . ( 7 sec) [ -7423.3532] [ 1580] [depth= 1] . ( 7 sec) [ -7423.1039] [ 1581] [depth= 1] . ( 8 sec) [ -7415.9784] [ 1578] [depth= 1] . ( 8 sec) [ -7392.0353] [ 1547] [depth= 5] . ( 8 sec) [ -7373.3486] [ 1508] [depth= 6] . ( 8 sec) [ -7373.3191] [ 1508] [depth= 1] . ( 8 sec) [ -7371.2224] [ 1505] [depth= 2] . ( 8 sec) [ -7361.0246] [ 1494] [depth= 4] . ( 8 sec) [ -7357.5427] [ 1503] [depth= 1] . ( 9 sec) [ -7356.6295] [ 1499] [depth= 1] . ( 9 sec) [ -7350.1660] [Branch lengths ] . ( 10 sec) [ -7349.7442] [GTR parameters ] . ( 10 sec) [ -7345.2906] [Alpha ][ 0.939196] . ( 13 sec) [ -7344.3021] [ 1491] [depth= 1] . ( 13 sec) [ -7344.2645] [ 1493] [depth= 2] . ( 14 sec) [ -7342.6634] [Branch lengths ] . ( 14 sec) [ -7342.6499] [GTR parameters ] . ( 14 sec) [ -7342.6099] [Alpha ][ 0.961494] . ( 19 sec) [ -7342.4358] [Branch lengths ] . ( 42 sec) [ -7342.4109] [Branch lengths ] . ( 42 sec) [ -7342.4109] [Topology ] . ( 43 sec) [ -7342.4083] [Topology ] . ( 43 sec) [ -7342.4074] [Topology ] . ( 43 sec) [ -7342.4072] [GTR parameters ] . ( 44 sec) [ -7342.4063] [Alpha ][ 0.965039] . ( 44 sec) [ -7342.4063] [Topology ] . ( 44 sec) [ -7342.4057] [Topology ] . ( 44 sec) [ -7342.4057] [GTR parameters ] . ( 44 sec) [ -7342.4057] [Alpha ][ 0.965039] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7342.405712. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -18705.3444] [GTR parameters ] . ( 0 sec) [ -18287.1139] [Alpha ][ 0.500960] . ( 0 sec) [ -17985.5999] [ 3918] [depth= 3] . ( 1 sec) [ -17386.0368] [ 3903] [depth= 10] . ( 1 sec) [ -17250.7892] [ 3850] [depth= 3] . ( 1 sec) [ -17069.8715] [ 3843] [depth= 2] . ( 1 sec) [ -16997.1521] [ 3811] [depth= 1] . ( 1 sec) [ -16634.9313] [ 3799] [depth= 7] . ( 1 sec) [ -16589.5473] [ 3793] [depth= 3] . ( 1 sec) [ -16504.5724] [ 3717] [depth= 1] . ( 1 sec) [ -16498.4229] [ 3710] [depth= 5] . ( 1 sec) [ -16399.4384] [ 3688] [depth= 2] . ( 1 sec) [ -16362.3481] [ 3687] [depth= 1] . ( 1 sec) [ -16222.2712] [ 3676] [depth= 7] . ( 1 sec) [ -15556.1961] [ 3671] [depth= 5] . ( 1 sec) [ -15386.6871] [ 3584] [depth= 7] . ( 1 sec) [ -15360.2760] [ 3584] [depth= 9] . ( 1 sec) [ -15030.4187] [ 3522] [depth= 7] . ( 1 sec) [ -15014.1955] [ 3521] [depth= 1] . ( 1 sec) [ -15011.0455] [ 3519] [depth= 18] . ( 1 sec) [ -14552.3534] [ 3515] [depth= 1] . ( 1 sec) [ -14446.0969] [ 3366] [depth= 19] . ( 1 sec) [ -14259.2597] [ 3357] [depth= 20] . ( 1 sec) [ -13924.4175] [ 3351] [depth= 1] . ( 1 sec) [ -13922.6447] [ 3352] [depth= 3] . ( 1 sec) [ -13620.2420] [ 3292] [depth= 3] . ( 1 sec) [ -13618.5656] [ 3289] [depth= 3] . ( 1 sec) [ -13436.9386] [ 3258] [depth= 14] . ( 2 sec) [ -13435.0362] [ 3255] [depth= 1] . ( 2 sec) [ -13036.5864] [ 3092] [depth= 12] . ( 2 sec) [ -12661.7485] [ 2942] [depth= 11] . ( 2 sec) [ -12480.6059] [ 2787] [depth= 5] . ( 2 sec) [ -11921.3338] [ 2783] [depth= 11] . ( 2 sec) [ -11570.8022] [ 2635] [depth= 11] . ( 2 sec) [ -11556.2445] [ 2636] [depth= 2] . ( 2 sec) [ -11338.5152] [ 2633] [depth= 2] . ( 2 sec) [ -11282.9432] [ 2634] [depth= 1] . ( 2 sec) [ -11150.8017] [ 2593] [depth= 2] . ( 2 sec) [ -11138.9368] [ 2590] [depth= 1] . ( 2 sec) [ -11131.6358] [ 2587] [depth= 1] . ( 2 sec) [ -11090.9512] [ 2564] [depth= 3] . ( 2 sec) [ -10985.2332] [ 2528] [depth= 5] . ( 2 sec) [ -10709.5423] [ 2529] [depth= 1] . ( 2 sec) [ -10503.9539] [ 2418] [depth= 6] . ( 2 sec) [ -10487.6330] [ 2412] [depth= 2] . ( 2 sec) [ -10470.2425] [ 2413] [depth= 1] . ( 2 sec) [ -10466.2646] [ 2410] [depth= 1] . ( 2 sec) [ -10251.0033] [ 2389] [depth= 8] . ( 2 sec) [ -10179.7853] [ 2365] [depth= 2] . ( 2 sec) [ -10165.5392] [ 2364] [depth= 9] . ( 3 sec) [ -10118.6741] [ 2362] [depth= 1] . ( 3 sec) [ -10114.3412] [ 2355] [depth= 1] . ( 3 sec) [ -10035.8507] [ 2351] [depth= 3] . ( 3 sec) [ -9612.3580] [ 2189] [depth= 8] . ( 3 sec) [ -9404.9686] [ 2164] [depth= 3] . ( 3 sec) [ -9243.3106] [ 2094] [depth= 1] . ( 3 sec) [ -9202.7305] [ 2089] [depth= 2] . ( 3 sec) [ -8904.3675] [ 1980] [depth= 1] . ( 3 sec) [ -8889.2129] [ 1978] [depth= 3] . ( 3 sec) [ -8657.2125] [ 1972] [depth= 5] . ( 3 sec) [ -8615.0105] [ 1924] [depth= 2] . ( 3 sec) [ -8593.6609] [ 1921] [depth= 2] . ( 3 sec) [ -8593.2222] [ 1921] [depth= 2] . ( 3 sec) [ -8472.8384] [ 1840] [depth= 1] . ( 3 sec) [ -8442.9127] [ 1840] [depth= 1] . ( 3 sec) [ -8438.4628] [ 1840] [depth= 3] . ( 3 sec) [ -8407.2455] [ 1842] [depth= 3] . ( 3 sec) [ -8386.2384] [ 1847] [depth= 2] . ( 3 sec) [ -8354.0513] [ 1833] [depth= 1] . ( 4 sec) [ -8230.7045] [ 1830] [depth= 2] . ( 4 sec) [ -7918.6081] [ 1719] [depth= 3] . ( 4 sec) [ -7771.2224] [ 1614] [depth= 7] . ( 4 sec) [ -7732.7584] [ 1655] [depth= 2] . ( 4 sec) [ -7617.4097] [ 1591] [depth= 6] . ( 4 sec) [ -7615.2175] [ 1590] [depth= 1] . ( 4 sec) [ -7581.9424] [ 1584] [depth= 2] . ( 4 sec) [ -7578.2148] [ 1581] [depth= 3] . ( 4 sec) [ -7577.1451] [ 1581] [depth= 2] . ( 4 sec) [ -7576.7310] [ 1580] [depth= 1] . ( 4 sec) [ -7576.5042] [ 1580] [depth= 2] . ( 4 sec) [ -7570.2362] [ 1581] [depth= 1] . ( 4 sec) [ -7564.0659] [ 1582] [depth= 1] . ( 5 sec) [ -7434.3659] [Branch lengths ] . ( 5 sec) [ -7432.9499] [GTR parameters ] . ( 5 sec) [ -7411.0049] [Alpha ][ 0.845536] . ( 5 sec) [ -7387.4148] [ 1534] [depth= 7] . ( 5 sec) [ -7387.3221] [ 1532] [depth= 1] . ( 5 sec) [ -7383.9128] [ 1530] [depth= 3] . ( 5 sec) [ -7382.5116] [ 1526] [depth= 2] . ( 5 sec) [ -7378.9419] [ 1522] [depth= 1] . ( 6 sec) [ -7376.4029] [ 1520] [depth= 2] . ( 6 sec) [ -7372.0388] [ 1504] [depth= 1] . ( 6 sec) [ -7371.7489] [ 1508] [depth= 1] . ( 6 sec) [ -7371.7306] [ 1504] [depth= 1] . ( 6 sec) [ -7368.8278] [ 1503] [depth= 1] . ( 6 sec) [ -7368.6214] [ 1504] [depth= 2] . ( 6 sec) [ -7368.5529] [ 1501] [depth= 1] . ( 6 sec) [ -7367.0374] [ 1499] [depth= 2] . ( 6 sec) [ -7367.0010] [ 1499] [depth= 2] . ( 6 sec) [ -7366.9767] [ 1499] [depth= 1] . ( 6 sec) [ -7364.9802] [ 1499] [depth= 2] . ( 6 sec) [ -7363.0619] [ 1495] [depth= 1] . ( 7 sec) [ -7361.7340] [ 1496] [depth= 1] . ( 7 sec) [ -7361.4677] [ 1496] [depth= 1] . ( 7 sec) [ -7361.2791] [ 1496] [depth= 1] . ( 7 sec) [ -7360.4563] [ 1492] [depth= 1] . ( 8 sec) [ -7360.2691] [ 1492] [depth= 1] . ( 8 sec) [ -7359.9616] [ 1493] [depth= 1] . ( 8 sec) [ -7359.9394] [ 1493] [depth= 1] . ( 9 sec) [ -7345.6130] [Branch lengths ] . ( 9 sec) [ -7345.3978] [GTR parameters ] . ( 9 sec) [ -7344.3250] [Alpha ][ 0.955645] . ( 13 sec) [ -7342.5928] [Branch lengths ] . ( 35 sec) [ -7342.4396] [Branch lengths ] . ( 35 sec) [ -7342.4396] [Topology ] . ( 36 sec) [ -7342.4249] [Topology ] . ( 37 sec) [ -7342.4197] [Topology ] . ( 37 sec) [ -7342.4173] [Topology ] . ( 38 sec) [ -7342.4161] [Topology ] . ( 39 sec) [ -7342.4154] [Topology ] . ( 39 sec) [ -7342.4126] [GTR parameters ] . ( 39 sec) [ -7342.4063] [Alpha ][ 0.964905] . ( 39 sec) [ -7342.4063] [Topology ] . ( 40 sec) [ -7342.4056] [Topology ] . ( 40 sec) [ -7342.4056] [GTR parameters ] . ( 40 sec) [ -7342.4056] [Alpha ][ 0.964905] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7342.405609. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19136.9286] [GTR parameters ] . ( 1 sec) [ -18714.1626] [Alpha ][ 0.500960] . ( 1 sec) [ -18571.6189] [ 3866] [depth= 8] . ( 1 sec) [ -18224.2840] [ 3871] [depth= 6] . ( 1 sec) [ -17781.8250] [ 3870] [depth= 4] . ( 1 sec) [ -17727.9184] [ 3867] [depth= 5] . ( 1 sec) [ -17656.4994] [ 3745] [depth= 4] . ( 1 sec) [ -17492.9908] [ 3747] [depth= 1] . ( 1 sec) [ -16259.8927] [ 3576] [depth= 14] . ( 1 sec) [ -16212.4610] [ 3555] [depth= 6] . ( 1 sec) [ -15443.8502] [ 3432] [depth= 18] . ( 1 sec) [ -14743.6471] [ 3286] [depth= 16] . ( 2 sec) [ -14650.0661] [ 3266] [depth= 18] . ( 2 sec) [ -14596.8682] [ 3263] [depth= 11] . ( 2 sec) [ -14547.8550] [ 3261] [depth= 3] . ( 2 sec) [ -14473.8828] [ 3235] [depth= 6] . ( 2 sec) [ -14197.8595] [ 3231] [depth= 2] . ( 2 sec) [ -13690.0226] [ 3182] [depth= 1] . ( 2 sec) [ -13564.4241] [ 3165] [depth= 12] . ( 2 sec) [ -13040.3809] [ 3035] [depth= 8] . ( 2 sec) [ -12751.5150] [ 2935] [depth= 6] . ( 2 sec) [ -12673.7765] [ 2934] [depth= 1] . ( 2 sec) [ -12264.2614] [ 2899] [depth= 7] . ( 2 sec) [ -12099.3374] [ 2787] [depth= 9] . ( 2 sec) [ -12098.2731] [ 2799] [depth= 1] . ( 2 sec) [ -11794.4853] [ 2754] [depth= 9] . ( 2 sec) [ -11724.0857] [ 2754] [depth= 9] . ( 2 sec) [ -11684.4547] [ 2739] [depth= 1] . ( 2 sec) [ -11671.6272] [ 2734] [depth= 6] . ( 2 sec) [ -11613.7930] [ 2734] [depth= 2] . ( 2 sec) [ -11232.3022] [ 2560] [depth= 10] . ( 2 sec) [ -11225.3577] [ 2557] [depth= 4] . ( 2 sec) [ -10995.8894] [ 2465] [depth= 8] . ( 2 sec) [ -10994.3902] [ 2468] [depth= 1] . ( 2 sec) [ -10921.2993] [ 2454] [depth= 2] . ( 2 sec) [ -10871.4909] [ 2444] [depth= 4] . ( 2 sec) [ -10820.9885] [ 2434] [depth= 1] . ( 3 sec) [ -10758.2766] [ 2418] [depth= 8] . ( 3 sec) [ -10719.0603] [ 2418] [depth= 1] . ( 3 sec) [ -10623.4944] [ 2389] [depth= 1] . ( 3 sec) [ -10616.0037] [ 2386] [depth= 1] . ( 3 sec) [ -10613.6844] [ 2384] [depth= 1] . ( 3 sec) [ -10209.1985] [ 2240] [depth= 8] . ( 3 sec) [ -10204.8925] [ 2232] [depth= 2] . ( 3 sec) [ -10161.2525] [ 2219] [depth= 7] . ( 3 sec) [ -10124.7272] [ 2211] [depth= 1] . ( 3 sec) [ -9967.9083] [ 2208] [depth= 3] . ( 3 sec) [ -9774.0034] [ 2157] [depth= 1] . ( 3 sec) [ -9572.1202] [ 2141] [depth= 2] . ( 3 sec) [ -9556.6192] [ 2159] [depth= 1] . ( 3 sec) [ -9475.7019] [ 2152] [depth= 2] . ( 3 sec) [ -9475.6204] [ 2134] [depth= 1] . ( 3 sec) [ -9322.0033] [ 2069] [depth= 4] . ( 3 sec) [ -9284.6759] [ 2037] [depth= 5] . ( 3 sec) [ -9076.9124] [ 2033] [depth= 2] . ( 3 sec) [ -9073.2413] [ 1995] [depth= 3] . ( 3 sec) [ -8882.8325] [ 1899] [depth= 6] . ( 3 sec) [ -8740.8250] [ 1867] [depth= 1] . ( 3 sec) [ -8700.7507] [ 1871] [depth= 1] . ( 4 sec) [ -8686.1528] [ 1863] [depth= 2] . ( 4 sec) [ -8678.6425] [ 1862] [depth= 2] . ( 4 sec) [ -8498.1428] [ 1861] [depth= 2] . ( 4 sec) [ -8478.9748] [ 1868] [depth= 1] . ( 4 sec) [ -8469.1056] [ 1855] [depth= 2] . ( 4 sec) [ -8469.0402] [ 1859] [depth= 2] . ( 4 sec) [ -8467.7490] [ 1859] [depth= 1] . ( 4 sec) [ -8340.6925] [ 1776] [depth= 1] . ( 4 sec) [ -8339.0195] [ 1775] [depth= 1] . ( 4 sec) [ -8242.0983] [ 1770] [depth= 1] . ( 4 sec) [ -8222.0396] [ 1749] [depth= 1] . ( 4 sec) [ -8219.7887] [ 1749] [depth= 1] . ( 4 sec) [ -8073.6953] [ 1669] [depth= 2] . ( 4 sec) [ -8040.2587] [ 1647] [depth= 1] . ( 4 sec) [ -8034.7148] [ 1645] [depth= 1] . ( 4 sec) [ -8026.1299] [ 1619] [depth= 6] . ( 4 sec) [ -8011.1834] [ 1616] [depth= 2] . ( 4 sec) [ -8010.0203] [ 1622] [depth= 4] . ( 4 sec) [ -7986.6080] [ 1628] [depth= 6] . ( 4 sec) [ -7979.1082] [ 1626] [depth= 1] . ( 4 sec) [ -7853.9796] [ 1619] [depth= 2] . ( 4 sec) [ -7824.4523] [ 1615] [depth= 2] . ( 5 sec) [ -7820.7822] [ 1612] [depth= 1] . ( 5 sec) [ -7813.8172] [ 1610] [depth= 1] . ( 5 sec) [ -7813.0625] [ 1609] [depth= 1] . ( 5 sec) [ -7759.0739] [ 1592] [depth= 4] . ( 5 sec) [ -7752.6343] [ 1594] [depth= 1] . ( 5 sec) [ -7673.4470] [ 1606] [depth= 1] . ( 5 sec) [ -7580.0607] [Branch lengths ] . ( 6 sec) [ -7579.5642] [GTR parameters ] . ( 6 sec) [ -7555.6581] [Alpha ][ 0.858306] . ( 6 sec) [ -7551.0826] [ 1611] [depth= 1] . ( 6 sec) [ -7551.0602] [ 1611] [depth= 1] . ( 6 sec) [ -7550.6082] [ 1610] [depth= 1] . ( 6 sec) [ -7550.5730] [ 1610] [depth= 1] . ( 6 sec) [ -7550.5481] [ 1610] [depth= 2] . ( 6 sec) [ -7550.0638] [ 1609] [depth= 1] . ( 7 sec) [ -7547.5342] [ 1609] [depth= 1] . ( 7 sec) [ -7546.3561] [ 1609] [depth= 1] . ( 7 sec) [ -7545.4640] [ 1609] [depth= 1] . ( 7 sec) [ -7545.1259] [ 1609] [depth= 1] . ( 7 sec) [ -7543.7950] [ 1608] [depth= 1] . ( 8 sec) [ -7543.2074] [ 1609] [depth= 1] . ( 8 sec) [ -7426.5252] [ 1570] [depth= 6] . ( 8 sec) [ -7426.5114] [ 1570] [depth= 1] . ( 8 sec) [ -7416.4513] [ 1566] [depth= 1] . ( 8 sec) [ -7416.2953] [ 1567] [depth= 1] . ( 8 sec) [ -7415.5740] [ 1568] [depth= 1] . ( 8 sec) [ -7415.4271] [ 1573] [depth= 1] . ( 8 sec) [ -7414.8437] [ 1574] [depth= 1] . ( 8 sec) [ -7414.7525] [ 1578] [depth= 1] . ( 8 sec) [ -7409.0581] [ 1562] [depth= 1] . ( 9 sec) [ -7389.0447] [ 1523] [depth= 3] . ( 9 sec) [ -7386.2981] [ 1521] [depth= 2] . ( 9 sec) [ -7385.8076] [ 1518] [depth= 1] . ( 9 sec) [ -7385.3747] [ 1521] [depth= 1] . ( 9 sec) [ -7384.2895] [ 1524] [depth= 2] . ( 10 sec) [ -7364.3756] [Branch lengths ] . ( 10 sec) [ -7364.2840] [GTR parameters ] . ( 10 sec) [ -7363.8008] [Alpha ][ 0.930610] . ( 10 sec) [ -7352.2139] [ 1504] [depth= 4] . ( 10 sec) [ -7352.0814] [ 1500] [depth= 1] . ( 11 sec) [ -7351.4367] [ 1495] [depth= 2] . ( 11 sec) [ -7351.1603] [ 1496] [depth= 1] . ( 11 sec) [ -7350.8719] [ 1500] [depth= 1] . ( 11 sec) [ -7350.6470] [ 1497] [depth= 1] . ( 12 sec) [ -7349.9571] [ 1502] [depth= 1] . ( 12 sec) [ -7349.7459] [ 1497] [depth= 1] . ( 12 sec) [ -7348.9906] [ 1496] [depth= 1] . ( 13 sec) [ -7348.9794] [ 1497] [depth= 1] . ( 13 sec) [ -7348.8763] [ 1495] [depth= 1] . ( 13 sec) [ -7348.3368] [ 1492] [depth= 1] . ( 13 sec) [ -7347.9348] [ 1493] [depth= 1] . ( 14 sec) [ -7344.4012] [Branch lengths ] . ( 14 sec) [ -7344.3581] [GTR parameters ] . ( 14 sec) [ -7344.3060] [Alpha ][ 0.955752] . ( 18 sec) [ -7343.1959] [Branch lengths ] . ( 40 sec) [ -7342.9624] [Branch lengths ] . ( 40 sec) [ -7342.9624] [Topology ] . ( 41 sec) [ -7342.9390] [Topology ] . ( 42 sec) [ -7342.9314] [Topology ] . ( 42 sec) [ -7342.9283] [Topology ] . ( 43 sec) [ -7342.9270] [Topology ] . ( 44 sec) [ -7342.9265] [Topology ] . ( 44 sec) [ -7342.9242] [GTR parameters ] . ( 44 sec) [ -7342.9199] [Alpha ][ 0.963321] . ( 44 sec) [ -7342.9199] [Topology ] . ( 45 sec) [ -7342.9195] [Topology ] . ( 45 sec) [ -7342.9194] [GTR parameters ] . ( 45 sec) [ -7342.9194] [Alpha ][ 0.963321] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -7342.7383] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7342.4781] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -7342.4769] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7342.476938. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -17296.9717] [GTR parameters ] . ( 0 sec) [ -16912.8118] [Alpha ][ 0.500960] . ( 0 sec) [ -16525.1386] [ 3675] [depth= 8] . ( 0 sec) [ -16050.7776] [ 3575] [depth= 6] . ( 0 sec) [ -15846.2235] [ 3527] [depth= 8] . ( 0 sec) [ -15801.3482] [ 3512] [depth= 1] . ( 1 sec) [ -15652.6188] [ 3498] [depth= 6] . ( 1 sec) [ -15564.5545] [ 3470] [depth= 2] . ( 1 sec) [ -15152.5778] [ 3463] [depth= 5] . ( 1 sec) [ -14968.3360] [ 3407] [depth= 5] . ( 1 sec) [ -14715.3798] [ 3404] [depth= 5] . ( 1 sec) [ -14665.6564] [ 3400] [depth= 2] . ( 1 sec) [ -14440.0208] [ 3400] [depth= 11] . ( 1 sec) [ -14239.8514] [ 3314] [depth= 10] . ( 1 sec) [ -13886.7632] [ 3211] [depth= 4] . ( 1 sec) [ -13819.6577] [ 3209] [depth= 1] . ( 1 sec) [ -13526.7002] [ 3161] [depth= 7] . ( 1 sec) [ -13439.3259] [ 3067] [depth= 10] . ( 1 sec) [ -13398.5826] [ 3054] [depth= 7] . ( 1 sec) [ -13327.9899] [ 3035] [depth= 6] . ( 1 sec) [ -13128.7161] [ 2999] [depth= 2] . ( 1 sec) [ -13121.4241] [ 3000] [depth= 1] . ( 1 sec) [ -13114.0485] [ 2999] [depth= 1] . ( 1 sec) [ -13050.6366] [ 2993] [depth= 2] . ( 1 sec) [ -12961.2079] [ 2985] [depth= 1] . ( 1 sec) [ -12784.0378] [ 2947] [depth= 14] . ( 1 sec) [ -12493.7886] [ 2780] [depth= 14] . ( 1 sec) [ -12485.9841] [ 2779] [depth= 4] . ( 1 sec) [ -12317.1252] [ 2731] [depth= 1] . ( 1 sec) [ -12225.3562] [ 2723] [depth= 11] . ( 1 sec) [ -12101.1205] [ 2668] [depth= 7] . ( 2 sec) [ -12088.3725] [ 2662] [depth= 3] . ( 2 sec) [ -11812.3232] [ 2657] [depth= 1] . ( 2 sec) [ -11479.3845] [ 2552] [depth= 3] . ( 2 sec) [ -11449.3822] [ 2524] [depth= 11] . ( 2 sec) [ -11374.8503] [ 2564] [depth= 11] . ( 2 sec) [ -10947.8881] [ 2451] [depth= 10] . ( 2 sec) [ -10870.3991] [ 2454] [depth= 5] . ( 2 sec) [ -10848.5176] [ 2446] [depth= 2] . ( 2 sec) [ -10699.4647] [ 2309] [depth= 13] . ( 2 sec) [ -10696.6176] [ 2308] [depth= 1] . ( 2 sec) [ -10684.2950] [ 2309] [depth= 1] . ( 2 sec) [ -10682.2996] [ 2310] [depth= 1] . ( 2 sec) [ -10630.9154] [ 2292] [depth= 2] . ( 2 sec) [ -10236.3227] [ 2228] [depth= 1] . ( 2 sec) [ -10214.4011] [ 2219] [depth= 1] . ( 2 sec) [ -10188.2493] [ 2213] [depth= 7] . ( 2 sec) [ -9962.5600] [ 2137] [depth= 9] . ( 2 sec) [ -9906.1030] [ 2138] [depth= 1] . ( 2 sec) [ -9902.5120] [ 2137] [depth= 1] . ( 2 sec) [ -9902.1294] [ 2138] [depth= 1] . ( 2 sec) [ -9808.3152] [ 2129] [depth= 3] . ( 3 sec) [ -9168.3702] [ 1966] [depth= 4] . ( 3 sec) [ -8870.4968] [ 1936] [depth= 7] . ( 3 sec) [ -8864.1534] [ 1936] [depth= 1] . ( 3 sec) [ -8756.2188] [ 1896] [depth= 2] . ( 3 sec) [ -8755.1871] [ 1895] [depth= 2] . ( 3 sec) [ -8749.1766] [ 1893] [depth= 1] . ( 3 sec) [ -8740.2350] [ 1893] [depth= 1] . ( 3 sec) [ -8739.5521] [ 1894] [depth= 4] . ( 3 sec) [ -8721.1732] [ 1908] [depth= 1] . ( 3 sec) [ -8591.6916] [ 1876] [depth= 6] . ( 3 sec) [ -8555.3903] [ 1890] [depth= 3] . ( 3 sec) [ -8505.5941] [ 1826] [depth= 2] . ( 3 sec) [ -8285.0119] [ 1759] [depth= 4] . ( 3 sec) [ -8141.1881] [ 1719] [depth= 3] . ( 3 sec) [ -8091.2653] [ 1763] [depth= 3] . ( 3 sec) [ -8057.3971] [ 1743] [depth= 1] . ( 3 sec) [ -8056.5475] [ 1739] [depth= 1] . ( 3 sec) [ -7964.9408] [ 1737] [depth= 2] . ( 4 sec) [ -7930.1444] [ 1674] [depth= 1] . ( 4 sec) [ -7872.5181] [ 1663] [depth= 2] . ( 4 sec) [ -7710.9329] [ 1563] [depth= 6] . ( 4 sec) [ -7704.3440] [ 1556] [depth= 1] . ( 4 sec) [ -7703.3178] [ 1556] [depth= 2] . ( 4 sec) [ -7703.2766] [ 1556] [depth= 1] . ( 4 sec) [ -7700.2266] [ 1556] [depth= 3] . ( 4 sec) [ -7574.3578] [Branch lengths ] . ( 5 sec) [ -7573.8098] [GTR parameters ] . ( 5 sec) [ -7552.2487] [Alpha ][ 0.840467] . ( 5 sec) [ -7442.0770] [ 1534] [depth= 1] . ( 5 sec) [ -7397.1952] [ 1521] [depth= 1] . ( 5 sec) [ -7397.1340] [ 1522] [depth= 1] . ( 5 sec) [ -7396.2498] [ 1521] [depth= 2] . ( 5 sec) [ -7390.5226] [ 1499] [depth= 1] . ( 5 sec) [ -7390.3904] [ 1504] [depth= 1] . ( 5 sec) [ -7389.5681] [ 1503] [depth= 1] . ( 5 sec) [ -7389.2644] [ 1502] [depth= 1] . ( 6 sec) [ -7388.9591] [ 1500] [depth= 1] . ( 6 sec) [ -7388.9202] [ 1505] [depth= 1] . ( 6 sec) [ -7381.5386] [ 1508] [depth= 1] . ( 6 sec) [ -7381.4401] [ 1507] [depth= 1] . ( 6 sec) [ -7380.7175] [ 1507] [depth= 1] . ( 6 sec) [ -7364.4323] [ 1504] [depth= 2] . ( 7 sec) [ -7364.1396] [ 1495] [depth= 1] . ( 7 sec) [ -7363.9471] [ 1493] [depth= 1] . ( 7 sec) [ -7363.9348] [ 1493] [depth= 2] . ( 7 sec) [ -7363.9229] [ 1493] [depth= 1] . ( 8 sec) [ -7363.8949] [ 1493] [depth= 2] . ( 9 sec) [ -7351.0100] [Branch lengths ] . ( 9 sec) [ -7350.8398] [GTR parameters ] . ( 9 sec) [ -7349.7403] [Alpha ][ 0.950508] . ( 10 sec) [ -7349.5716] [ 1493] [depth= 1] . ( 12 sec) [ -7349.5592] [ 1491] [depth= 1] . ( 13 sec) [ -7343.7847] [Branch lengths ] . ( 13 sec) [ -7343.7773] [GTR parameters ] . ( 13 sec) [ -7343.7512] [Alpha ][ 0.969353] . ( 17 sec) [ -7343.0113] [Branch lengths ] . ( 39 sec) [ -7342.9111] [Branch lengths ] . ( 39 sec) [ -7342.9111] [Topology ] . ( 40 sec) [ -7342.9010] [Topology ] . ( 40 sec) [ -7342.8974] [Topology ] . ( 41 sec) [ -7342.8957] [Topology ] . ( 42 sec) [ -7342.8949] [Topology ] . ( 42 sec) [ -7342.8945] [GTR parameters ] . ( 42 sec) [ -7342.8930] [Alpha ][ 0.964489] . ( 42 sec) [ -7342.8930] [Topology ] . ( 43 sec) [ -7342.8924] [Topology ] . ( 43 sec) [ -7342.8924] [GTR parameters ] . ( 43 sec) [ -7342.8924] [Alpha ][ 0.964489] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -7342.7139] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -7342.4540] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7342.454048. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -19615.3428] [GTR parameters ] . ( 1 sec) [ -19162.5423] [Alpha ][ 0.500960] . ( 1 sec) [ -18830.7904] [ 3997] [depth= 6] . ( 1 sec) [ -18442.0356] [ 3976] [depth= 5] . ( 1 sec) [ -18338.9361] [ 3955] [depth= 4] . ( 1 sec) [ -18272.9178] [ 3950] [depth= 5] . ( 1 sec) [ -18238.9436] [ 3938] [depth= 1] . ( 1 sec) [ -18117.4089] [ 3936] [depth= 5] . ( 1 sec) [ -18086.0507] [ 3930] [depth= 1] . ( 1 sec) [ -17945.2178] [ 3932] [depth= 1] . ( 1 sec) [ -17747.2170] [ 3819] [depth= 9] . ( 1 sec) [ -17585.2969] [ 3730] [depth= 3] . ( 1 sec) [ -17494.0027] [ 3700] [depth= 5] . ( 1 sec) [ -17315.6011] [ 3681] [depth= 5] . ( 1 sec) [ -17311.5977] [ 3669] [depth= 10] . ( 1 sec) [ -17300.5859] [ 3663] [depth= 3] . ( 1 sec) [ -17265.6253] [ 3660] [depth= 1] . ( 1 sec) [ -17181.6160] [ 3682] [depth= 1] . ( 1 sec) [ -16779.2139] [ 3649] [depth= 7] . ( 1 sec) [ -16554.7461] [ 3628] [depth= 4] . ( 1 sec) [ -16441.6697] [ 3625] [depth= 2] . ( 1 sec) [ -16341.8757] [ 3545] [depth= 12] . ( 2 sec) [ -16159.8844] [ 3504] [depth= 3] . ( 2 sec) [ -15995.0918] [ 3458] [depth= 11] . ( 2 sec) [ -15712.3635] [ 3353] [depth= 10] . ( 2 sec) [ -15626.8982] [ 3350] [depth= 1] . ( 2 sec) [ -15479.5295] [ 3319] [depth= 1] . ( 2 sec) [ -15302.5201] [ 3280] [depth= 10] . ( 2 sec) [ -15251.1643] [ 3282] [depth= 1] . ( 2 sec) [ -15225.7664] [ 3312] [depth= 1] . ( 2 sec) [ -15201.1356] [ 3330] [depth= 3] . ( 2 sec) [ -15189.2488] [ 3335] [depth= 1] . ( 2 sec) [ -14892.6592] [ 3330] [depth= 4] . ( 2 sec) [ -14750.7674] [ 3339] [depth= 1] . ( 2 sec) [ -14404.1172] [ 3291] [depth= 2] . ( 2 sec) [ -13962.0947] [ 3242] [depth= 8] . ( 2 sec) [ -13685.9234] [ 3127] [depth= 11] . ( 2 sec) [ -13359.0426] [ 3094] [depth= 7] . ( 2 sec) [ -13112.7203] [ 2993] [depth= 4] . ( 2 sec) [ -12489.4724] [ 2985] [depth= 10] . ( 2 sec) [ -12286.7059] [ 2912] [depth= 4] . ( 2 sec) [ -12091.4385] [ 2883] [depth= 9] . ( 2 sec) [ -12026.1895] [ 2883] [depth= 1] . ( 2 sec) [ -12017.8799] [ 2883] [depth= 2] . ( 2 sec) [ -11750.4023] [ 2763] [depth= 9] . ( 3 sec) [ -11355.9921] [ 2679] [depth= 5] . ( 3 sec) [ -11194.0966] [ 2594] [depth= 5] . ( 3 sec) [ -10791.3015] [ 2474] [depth= 8] . ( 3 sec) [ -10782.9709] [ 2473] [depth= 1] . ( 3 sec) [ -10747.7552] [ 2468] [depth= 10] . ( 3 sec) [ -10696.1401] [ 2467] [depth= 1] . ( 3 sec) [ -10296.6136] [ 2323] [depth= 3] . ( 3 sec) [ -9954.0014] [ 2307] [depth= 5] . ( 3 sec) [ -9875.5531] [ 2151] [depth= 1] . ( 3 sec) [ -9755.9569] [ 2139] [depth= 5] . ( 3 sec) [ -9719.8472] [ 2153] [depth= 2] . ( 3 sec) [ -9698.1903] [ 2149] [depth= 2] . ( 3 sec) [ -9658.1252] [ 2149] [depth= 6] . ( 3 sec) [ -9638.8280] [ 2140] [depth= 6] . ( 3 sec) [ -9627.9828] [ 2129] [depth= 1] . ( 3 sec) [ -9558.0354] [ 2124] [depth= 2] . ( 3 sec) [ -9525.3824] [ 2120] [depth= 1] . ( 3 sec) [ -9521.7019] [ 2119] [depth= 2] . ( 3 sec) [ -9353.7380] [ 2043] [depth= 9] . ( 3 sec) [ -9351.0281] [ 2041] [depth= 2] . ( 3 sec) [ -9348.0791] [ 2038] [depth= 2] . ( 3 sec) [ -8994.2774] [ 2031] [depth= 4] . ( 3 sec) [ -8976.0512] [ 2029] [depth= 1] . ( 3 sec) [ -8868.5883] [ 2009] [depth= 6] . ( 4 sec) [ -8864.1337] [ 2006] [depth= 4] . ( 4 sec) [ -8847.0177] [ 1983] [depth= 2] . ( 4 sec) [ -8622.5602] [ 1856] [depth= 4] . ( 4 sec) [ -8473.6175] [ 1856] [depth= 1] . ( 4 sec) [ -8369.3590] [ 1761] [depth= 2] . ( 4 sec) [ -8369.2906] [ 1761] [depth= 1] . ( 4 sec) [ -8337.6003] [ 1747] [depth= 2] . ( 4 sec) [ -8311.3135] [ 1749] [depth= 1] . ( 4 sec) [ -8288.5721] [ 1741] [depth= 2] . ( 4 sec) [ -8271.7152] [ 1736] [depth= 3] . ( 4 sec) [ -8080.0154] [ 1663] [depth= 10] . ( 4 sec) [ -8076.9671] [ 1664] [depth= 2] . ( 4 sec) [ -7879.7334] [ 1651] [depth= 3] . ( 4 sec) [ -7875.6283] [ 1648] [depth= 2] . ( 4 sec) [ -7861.9117] [ 1642] [depth= 4] . ( 4 sec) [ -7850.9113] [ 1638] [depth= 1] . ( 4 sec) [ -7847.3405] [ 1631] [depth= 3] . ( 4 sec) [ -7814.2854] [ 1637] [depth= 1] . ( 4 sec) [ -7813.1543] [ 1636] [depth= 1] . ( 4 sec) [ -7812.5273] [ 1635] [depth= 1] . ( 4 sec) [ -7713.8945] [ 1609] [depth= 2] . ( 4 sec) [ -7696.7868] [ 1609] [depth= 3] . ( 4 sec) [ -7695.9130] [ 1610] [depth= 1] . ( 4 sec) [ -7675.6994] [ 1611] [depth= 1] . ( 5 sec) [ -7672.2238] [ 1610] [depth= 1] . ( 5 sec) [ -7671.0947] [ 1610] [depth= 1] . ( 5 sec) [ -7596.2710] [Branch lengths ] . ( 5 sec) [ -7594.9108] [GTR parameters ] . ( 5 sec) [ -7571.3658] [Alpha ][ 0.852764] . ( 6 sec) [ -7570.1660] [ 1608] [depth= 1] . ( 6 sec) [ -7556.0576] [ 1585] [depth= 1] . ( 6 sec) [ -7547.7042] [ 1585] [depth= 1] . ( 6 sec) [ -7545.1814] [ 1586] [depth= 1] . ( 6 sec) [ -7534.0055] [ 1547] [depth= 1] . ( 6 sec) [ -7533.9689] [ 1551] [depth= 1] . ( 6 sec) [ -7412.4250] [ 1522] [depth= 1] . ( 6 sec) [ -7412.3733] [ 1520] [depth= 1] . ( 6 sec) [ -7410.0157] [ 1512] [depth= 1] . ( 6 sec) [ -7409.9654] [ 1513] [depth= 1] . ( 6 sec) [ -7409.8586] [ 1514] [depth= 1] . ( 6 sec) [ -7401.8201] [ 1511] [depth= 2] . ( 7 sec) [ -7398.3587] [ 1513] [depth= 1] . ( 7 sec) [ -7398.3112] [ 1519] [depth= 2] . ( 7 sec) [ -7398.2908] [ 1519] [depth= 1] . ( 7 sec) [ -7394.3013] [ 1518] [depth= 1] . ( 7 sec) [ -7384.8204] [ 1515] [depth= 2] . ( 7 sec) [ -7384.8036] [ 1515] [depth= 1] . ( 7 sec) [ -7384.0439] [ 1520] [depth= 1] . ( 7 sec) [ -7382.0981] [ 1530] [depth= 1] . ( 8 sec) [ -7381.8127] [ 1533] [depth= 1] . ( 8 sec) [ -7380.5444] [ 1530] [depth= 1] . ( 8 sec) [ -7378.6558] [ 1528] [depth= 1] . ( 8 sec) [ -7378.6353] [ 1528] [depth= 1] . ( 8 sec) [ -7378.5999] [ 1528] [depth= 1] . ( 8 sec) [ -7378.5626] [ 1528] [depth= 1] . ( 8 sec) [ -7368.1254] [ 1522] [depth= 4] . ( 8 sec) [ -7366.9785] [ 1519] [depth= 1] . ( 8 sec) [ -7363.4957] [ 1522] [depth= 1] . ( 8 sec) [ -7361.4297] [ 1511] [depth= 1] . ( 9 sec) [ -7358.7625] [ 1509] [depth= 2] . ( 9 sec) [ -7358.5524] [ 1509] [depth= 1] . ( 9 sec) [ -7347.3679] [Branch lengths ] . ( 10 sec) [ -7347.0496] [GTR parameters ] . ( 10 sec) [ -7346.2881] [Alpha ][ 0.944716] . ( 11 sec) [ -7346.2439] [ 1512] [depth= 1] . ( 11 sec) [ -7345.7322] [ 1502] [depth= 1] . ( 11 sec) [ -7345.0208] [ 1503] [depth= 1] . ( 14 sec) [ -7343.7473] [Branch lengths ] . ( 15 sec) [ -7343.7417] [GTR parameters ] . ( 15 sec) [ -7343.7312] [Alpha ][ 0.956476] . ( 19 sec) [ -7343.6170] [Branch lengths ] . ( 23 sec) [ -7342.6739] [ 1493] [depth= 2] . ( 41 sec) [ -7342.4393] [Branch lengths ] . ( 41 sec) [ -7342.4371] [GTR parameters ] . ( 41 sec) [ -7342.4314] [Alpha ][ 0.965282] . ( 63 sec) [ -7342.4073] [Branch lengths ] . ( 63 sec) [ -7342.4073] [Topology ] . ( 64 sec) [ -7342.4059] [Topology ] . ( 64 sec) [ -7342.4055] [Topology ] . ( 64 sec) [ -7342.4055] [GTR parameters ] . ( 64 sec) [ -7342.4055] [Alpha ][ 0.965282] . ( 64 sec) [ -7342.4055] [Topology ] . ( 65 sec) [ -7342.4053] [Topology ] . ( 65 sec) [ -7342.4053] [GTR parameters ] . ( 65 sec) [ -7342.4053] [Alpha ][ 0.965282] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7342.405337. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7395.141666 . ( 0 sec) [ -7393.3350] [GTR parameters ] . ( 0 sec) [ -7393.1441] [Alpha ][ 0.947123] . ( 0 sec) [ -7393.1441] [Topology ] . ( 1 sec) [ -7351.5864] [Topology ] . ( 2 sec) [ -7345.3795] [Topology ] . ( 2 sec) [ -7343.3033] [Topology ] . ( 3 sec) [ -7342.8241] [Topology ] . ( 4 sec) [ -7342.6261] [Topology ] . ( 5 sec) [ -7342.5346] [Topology ] . ( 5 sec) [ -7342.4901] [Topology ] . ( 6 sec) [ -7342.4678] [Topology ] . ( 7 sec) [ -7342.4564] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7342.456420 . ( 12 sec) [ -7342.4419] [GTR parameters ] . ( 12 sec) [ -7342.4218] [Alpha ][ 0.963635] . ( 12 sec) [ -7342.4218] [Topology ] . ( 13 sec) [ -7342.4135] [Topology ] . ( 14 sec) [ -7342.4095] [Topology ] . ( 14 sec) [ -7342.4075] [Topology ] . ( 15 sec) [ -7342.4065] [Topology ] . ( 16 sec) [ -7342.4060] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7342.405994 . ( 21 sec) [ -7342.4060] [GTR parameters ] . ( 21 sec) [ -7342.4058] [Alpha ][ 0.965001] . ( 21 sec) [ -7342.4058] [Topology ] . ( 21 sec) [ -7342.4055] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -7393.3350] [GTR parameters ] . ( 32 sec) [ -7393.1441] [Alpha ][ 0.947123] . ( 32 sec) [ -7389.9580] [ 1489] [depth= 1] . ( 32 sec) [ -7388.2503] [ 1489] [depth= 1] . ( 32 sec) [ -7387.7091] [ 1489] [depth= 1] . ( 32 sec) [ -7387.6434] [ 1489] [depth= 1] . ( 33 sec) [ -7385.8140] [ 1490] [depth= 1] . ( 33 sec) [ -7384.5889] [ 1493] [depth= 1] . ( 33 sec) [ -7383.5378] [ 1490] [depth= 1] . ( 33 sec) [ -7383.1092] [ 1492] [depth= 1] . ( 33 sec) [ -7381.7062] [ 1496] [depth= 3] . ( 33 sec) [ -7380.3578] [ 1492] [depth= 3] . ( 34 sec) [ -7378.9339] [ 1496] [depth= 1] . ( 34 sec) [ -7378.8880] [ 1500] [depth= 1] . ( 34 sec) [ -7378.6404] [ 1492] [depth= 1] . ( 34 sec) [ -7378.1273] [ 1497] [depth= 1] . ( 34 sec) [ -7378.0184] [ 1499] [depth= 1] . ( 34 sec) [ -7377.8882] [ 1501] [depth= 1] . ( 34 sec) [ -7377.3765] [ 1497] [depth= 1] . ( 35 sec) [ -7377.3367] [ 1497] [depth= 1] . ( 35 sec) [ -7377.3191] [ 1497] [depth= 1] . ( 35 sec) [ -7377.0085] [ 1497] [depth= 1] . ( 35 sec) [ -7347.0344] [Branch lengths ] . ( 36 sec) [ -7347.0125] [GTR parameters ] . ( 36 sec) [ -7347.0125] [Alpha ][ 0.948070] . ( 37 sec) [ -7346.8626] [ 1497] [depth= 1] . ( 38 sec) [ -7345.5409] [ 1493] [depth= 1] . ( 40 sec) [ -7343.4209] [Branch lengths ] . ( 40 sec) [ -7343.4146] [GTR parameters ] . ( 40 sec) [ -7343.4054] [Alpha ][ 0.959187] . ( 44 sec) [ -7342.6060] [Branch lengths ] . ( 66 sec) [ -7342.4283] [Branch lengths ] . ( 66 sec) [ -7342.4283] [Topology ] . ( 67 sec) [ -7342.4162] [Topology ] . ( 68 sec) [ -7342.4122] [Topology ] . ( 69 sec) [ -7342.4106] [Topology ] . ( 69 sec) [ -7342.4099] [Topology ] . ( 70 sec) [ -7342.4086] [GTR parameters ] . ( 70 sec) [ -7342.4059] [Alpha ][ 0.965158] . ( 70 sec) [ -7342.4059] [Topology ] . ( 71 sec) [ -7342.4055] [Topology ] . ( 71 sec) [ -7342.4055] [GTR parameters ] . ( 71 sec) [ -7342.4055] [Alpha ][ 0.965158] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7342.405517 . Log likelihood obtained after SPR moves : -7342.405475 . Log likelihood of the current tree: -7342.405475. . Printing the most likely tree in file 'data14.phy_phyml_tree.txt'... . Best log likelihood : -7342.405337 . Time used 0h1m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo