.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2845_68x1715_2006.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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 649 patterns found. (out of a total of 1715 sites) . 1119 sites without polymorphism (65.25%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22405.5210] [GTR parameters ] . ( 2 sec) [ -21918.2406] [Alpha ][ 0.500960] . ( 2 sec) [ -21872.5390] [ 3186] [depth= 4] . ( 2 sec) [ -21758.0569] [ 3170] [depth= 7] . ( 2 sec) [ -21677.0386] [ 3162] [depth= 7] . ( 3 sec) [ -21593.5862] [ 3141] [depth= 1] . ( 3 sec) [ -21553.4431] [ 3133] [depth= 3] . ( 3 sec) [ -21473.1716] [ 3130] [depth= 6] . ( 3 sec) [ -21450.7300] [ 3128] [depth= 5] . ( 3 sec) [ -21355.4438] [ 3121] [depth= 2] . ( 3 sec) [ -21323.4389] [ 3120] [depth= 5] . ( 3 sec) [ -21238.9609] [ 3114] [depth= 3] . ( 3 sec) [ -21088.0485] [ 3109] [depth= 4] . ( 3 sec) [ -20998.7327] [ 3083] [depth= 2] . ( 3 sec) [ -20974.2871] [ 3080] [depth= 2] . ( 4 sec) [ -20965.7479] [ 3080] [depth= 3] . ( 4 sec) [ -20918.9176] [ 3086] [depth= 10] . ( 4 sec) [ -20657.0811] [ 3050] [depth= 23] . ( 4 sec) [ -20497.0634] [ 3014] [depth= 13] . ( 4 sec) [ -20481.3341] [ 3009] [depth= 12] . ( 4 sec) [ -20472.7518] [ 3032] [depth= 1] . ( 4 sec) [ -20270.7091] [ 2986] [depth= 27] . ( 4 sec) [ -20066.6699] [ 2975] [depth= 26] . ( 4 sec) [ -19973.2081] [ 2957] [depth= 12] . ( 5 sec) [ -19793.8514] [ 2935] [depth= 16] . ( 5 sec) [ -19784.4379] [ 2934] [depth= 1] . ( 5 sec) [ -19755.9347] [ 2934] [depth= 4] . ( 5 sec) [ -19655.6675] [ 2917] [depth= 6] . ( 5 sec) [ -19604.8969] [ 2908] [depth= 9] . ( 5 sec) [ -19598.1155] [ 2907] [depth= 1] . ( 5 sec) [ -19479.9891] [ 2900] [depth= 3] . ( 5 sec) [ -19475.5437] [ 2900] [depth= 9] . ( 5 sec) [ -19335.8557] [ 2871] [depth= 3] . ( 5 sec) [ -19333.4736] [ 2867] [depth= 1] . ( 6 sec) [ -19326.7073] [ 2867] [depth= 2] . ( 6 sec) [ -19121.0966] [ 2850] [depth= 19] . ( 6 sec) [ -19115.6372] [ 2849] [depth= 1] . ( 6 sec) [ -19025.8075] [ 2838] [depth= 4] . ( 6 sec) [ -18917.3170] [ 2835] [depth= 8] . ( 6 sec) [ -18313.0386] [ 2786] [depth= 4] . ( 6 sec) [ -18149.0389] [ 2785] [depth= 1] . ( 6 sec) [ -18148.5597] [ 2786] [depth= 2] . ( 6 sec) [ -17993.0107] [ 2746] [depth= 1] . ( 7 sec) [ -17948.0620] [ 2725] [depth= 1] . ( 7 sec) [ -17728.2925] [ 2673] [depth= 9] . ( 7 sec) [ -17525.1234] [ 2670] [depth= 4] . ( 7 sec) [ -17359.9669] [ 2662] [depth= 18] . ( 7 sec) [ -17243.5168] [ 2645] [depth= 17] . ( 7 sec) [ -17207.4747] [ 2635] [depth= 1] . ( 7 sec) [ -17096.0161] [ 2617] [depth= 8] . ( 7 sec) [ -16859.7016] [ 2558] [depth= 11] . ( 7 sec) [ -16829.1849] [ 2559] [depth= 6] . ( 8 sec) [ -16743.8045] [ 2553] [depth= 1] . ( 8 sec) [ -16711.6657] [ 2518] [depth= 18] . ( 8 sec) [ -16649.6973] [ 2534] [depth= 1] . ( 8 sec) [ -16201.4815] [ 2449] [depth= 8] . ( 8 sec) [ -16091.3725] [ 2427] [depth= 2] . ( 8 sec) [ -15970.2395] [ 2394] [depth= 18] . ( 8 sec) [ -15964.8704] [ 2394] [depth= 1] . ( 9 sec) [ -15895.8245] [ 2381] [depth= 4] . ( 9 sec) [ -15894.7468] [ 2385] [depth= 1] . ( 9 sec) [ -15889.0210] [ 2383] [depth= 1] . ( 9 sec) [ -15881.6758] [ 2384] [depth= 4] . ( 9 sec) [ -15718.6484] [ 2339] [depth= 2] . ( 9 sec) [ -15655.1209] [ 2324] [depth= 3] . ( 9 sec) [ -15606.2168] [ 2303] [depth= 4] . ( 9 sec) [ -15572.8090] [ 2297] [depth= 8] . ( 10 sec) [ -15539.3578] [ 2285] [depth= 2] . ( 10 sec) [ -15513.7977] [ 2282] [depth= 2] . ( 10 sec) [ -15506.3362] [ 2281] [depth= 1] . ( 10 sec) [ -15490.7334] [ 2278] [depth= 3] . ( 10 sec) [ -15476.8735] [ 2278] [depth= 2] . ( 10 sec) [ -15466.8489] [ 2275] [depth= 2] . ( 10 sec) [ -15466.8144] [ 2276] [depth= 1] . ( 10 sec) [ -15183.1435] [ 2231] [depth= 8] . ( 11 sec) [ -15175.4932] [ 2229] [depth= 1] . ( 11 sec) [ -15158.4650] [ 2222] [depth= 4] . ( 11 sec) [ -15153.0805] [ 2223] [depth= 7] . ( 11 sec) [ -15119.3526] [ 2211] [depth= 2] . ( 11 sec) [ -15023.0341] [ 2196] [depth= 4] . ( 11 sec) [ -15016.5678] [ 2195] [depth= 2] . ( 11 sec) [ -14892.9171] [ 2174] [depth= 10] . ( 12 sec) [ -14827.1019] [ 2157] [depth= 7] . ( 12 sec) [ -14739.9089] [ 2161] [depth= 1] . ( 12 sec) [ -14678.2515] [ 2153] [depth= 9] . ( 12 sec) [ -14663.5617] [ 2170] [depth= 1] . ( 12 sec) [ -14587.1254] [ 2151] [depth= 8] . ( 14 sec) [ -14472.8882] [ 2120] [depth= 5] . ( 14 sec) [ -14461.0865] [ 2119] [depth= 3] . ( 14 sec) [ -14325.4886] [ 2112] [depth= 13] . ( 14 sec) [ -14215.7485] [ 2083] [depth= 2] . ( 14 sec) [ -14167.5923] [ 2077] [depth= 4] . ( 15 sec) [ -14149.9374] [ 2071] [depth= 2] . ( 15 sec) [ -14138.9293] [ 2071] [depth= 14] . ( 15 sec) [ -14015.4844] [ 2042] [depth= 2] . ( 15 sec) [ -13957.6759] [ 2030] [depth= 10] . ( 16 sec) [ -13883.8465] [ 2010] [depth= 7] . ( 16 sec) [ -13878.1602] [ 2011] [depth= 1] . ( 16 sec) [ -13870.2338] [ 2013] [depth= 2] . ( 16 sec) [ -13853.0719] [ 2007] [depth= 2] . ( 17 sec) [ -13719.9883] [ 1995] [depth= 2] . ( 17 sec) [ -13688.7374] [ 1990] [depth= 11] . ( 17 sec) [ -13628.1258] [ 1977] [depth= 1] . ( 17 sec) [ -13623.5605] [ 1975] [depth= 1] . ( 17 sec) [ -13603.1419] [ 1971] [depth= 1] . ( 18 sec) [ -13582.8971] [ 1969] [depth= 1] . ( 18 sec) [ -13538.7692] [ 1950] [depth= 2] . ( 18 sec) [ -13522.6801] [ 1956] [depth= 3] . ( 18 sec) [ -13486.4944] [ 1954] [depth= 2] . ( 18 sec) [ -13272.7625] [ 1955] [depth= 3] . ( 19 sec) [ -13180.1041] [ 1932] [depth= 6] . ( 19 sec) [ -12972.6915] [ 1885] [depth= 12] . ( 19 sec) [ -12947.2069] [ 1882] [depth= 4] . ( 19 sec) [ -12938.6004] [ 1880] [depth= 1] . ( 20 sec) [ -12919.2101] [ 1880] [depth= 1] . ( 20 sec) [ -12913.9515] [ 1879] [depth= 1] . ( 20 sec) [ -12901.3080] [ 1884] [depth= 2] . ( 20 sec) [ -12879.6910] [ 1879] [depth= 4] . ( 20 sec) [ -12873.5690] [ 1872] [depth= 2] . ( 21 sec) [ -12816.1094] [ 1873] [depth= 4] . ( 21 sec) [ -12812.8161] [ 1876] [depth= 2] . ( 21 sec) [ -12732.9332] [ 1862] [depth= 2] . ( 22 sec) [ -12506.6130] [ 1783] [depth= 4] . ( 22 sec) [ -12505.4631] [ 1783] [depth= 2] . ( 22 sec) [ -12489.5138] [ 1778] [depth= 9] . ( 22 sec) [ -12487.8311] [ 1779] [depth= 1] . ( 23 sec) [ -12417.7357] [ 1767] [depth= 7] . ( 23 sec) [ -12402.7880] [ 1764] [depth= 1] . ( 23 sec) [ -12376.9769] [ 1767] [depth= 1] . ( 24 sec) [ -12367.2335] [ 1764] [depth= 1] . ( 24 sec) [ -12361.2216] [ 1762] [depth= 4] . ( 24 sec) [ -12295.2164] [ 1748] [depth= 1] . ( 24 sec) [ -12294.1094] [ 1750] [depth= 1] . ( 24 sec) [ -12262.2890] [ 1746] [depth= 3] . ( 24 sec) [ -12260.9479] [ 1746] [depth= 1] . ( 24 sec) [ -12082.5032] [ 1750] [depth= 2] . ( 25 sec) [ -12026.1438] [ 1727] [depth= 8] . ( 25 sec) [ -11954.2588] [ 1726] [depth= 1] . ( 25 sec) [ -11953.8797] [ 1726] [depth= 1] . ( 25 sec) [ -11912.4694] [ 1713] [depth= 1] . ( 25 sec) [ -11841.6198] [ 1689] [depth= 10] . ( 25 sec) [ -11838.6659] [ 1688] [depth= 1] . ( 25 sec) [ -11826.2711] [ 1686] [depth= 1] . ( 26 sec) [ -11824.5362] [ 1686] [depth= 1] . ( 26 sec) [ -11716.8624] [ 1660] [depth= 5] . ( 26 sec) [ -11707.3056] [ 1656] [depth= 3] . ( 26 sec) [ -11703.9738] [ 1654] [depth= 3] . ( 27 sec) [ -11695.7956] [ 1652] [depth= 1] . ( 27 sec) [ -11686.9289] [ 1653] [depth= 2] . ( 27 sec) [ -11682.3924] [ 1652] [depth= 2] . ( 28 sec) [ -11633.6488] [Branch lengths ] . ( 31 sec) [ -11626.6664] [GTR parameters ] . ( 31 sec) [ -11534.0545] [Alpha ][ 0.250961] . ( 32 sec) [ -11527.6968] [ 1649] [depth= 1] . ( 33 sec) [ -11514.5191] [ 1643] [depth= 1] . ( 33 sec) [ -11512.9460] [ 1641] [depth= 2] . ( 34 sec) [ -11509.2495] [ 1640] [depth= 1] . ( 35 sec) [ -11507.4242] [ 1642] [depth= 3] . ( 35 sec) [ -11506.8747] [ 1640] [depth= 1] . ( 36 sec) [ -11506.6972] [ 1639] [depth= 1] . ( 36 sec) [ -11500.9046] [ 1638] [depth= 1] . ( 38 sec) [ -11494.8756] [ 1629] [depth= 1] . ( 38 sec) [ -11493.7201] [ 1631] [depth= 1] . ( 40 sec) [ -11490.6570] [ 1631] [depth= 1] . ( 41 sec) [ -11433.0039] [ 1618] [depth= 1] . ( 42 sec) [ -11411.7814] [ 1614] [depth= 3] . ( 44 sec) [ -11411.2902] [ 1611] [depth= 2] . ( 44 sec) [ -11409.9406] [ 1608] [depth= 2] . ( 44 sec) [ -11402.8756] [ 1600] [depth= 2] . ( 45 sec) [ -11402.1377] [ 1601] [depth= 1] . ( 45 sec) [ -11398.8163] [ 1602] [depth= 1] . ( 45 sec) [ -11395.4265] [ 1599] [depth= 1] . ( 45 sec) [ -11395.0189] [ 1599] [depth= 1] . ( 45 sec) [ -11394.7804] [ 1598] [depth= 1] . ( 47 sec) [ -11382.4507] [ 1593] [depth= 6] . ( 47 sec) [ -11380.0433] [ 1592] [depth= 2] . ( 49 sec) [ -11379.6935] [ 1594] [depth= 3] . ( 50 sec) [ -11376.7653] [ 1593] [depth= 1] . ( 51 sec) [ -11376.2186] [ 1594] [depth= 1] . ( 54 sec) [ -11366.1773] [Branch lengths ] . ( 58 sec) [ -11365.8840] [GTR parameters ] . ( 58 sec) [ -11365.8722] [Alpha ][ 0.252859] . ( 60 sec) [ -11363.7030] [ 1594] [depth= 2] . ( 64 sec) [ -11363.6815] [ 1593] [depth= 1] . ( 66 sec) [ -11363.2812] [ 1592] [depth= 1] . ( 70 sec) [ -11362.9438] [ 1591] [depth= 1] . ( 72 sec) [ -11361.7546] [ 1591] [depth= 1] . ( 74 sec) [ -11359.6544] [ 1591] [depth= 1] . ( 82 sec) [ -11358.3065] [Branch lengths ] . ( 85 sec) [ -11358.2342] [GTR parameters ] . ( 85 sec) [ -11358.2272] [Alpha ][ 0.254322] . ( 109 sec) [ -11358.1045] [Branch lengths ] . ( 191 sec) [ -11358.0843] [Branch lengths ] . ( 191 sec) [ -11358.0843] [Topology ] . ( 193 sec) [ -11358.0816] [Topology ] . ( 195 sec) [ -11358.0805] [Topology ] . ( 197 sec) [ -11358.0799] [Topology ] . ( 198 sec) [ -11358.0793] [GTR parameters ] . ( 198 sec) [ -11358.0793] [Alpha ][ 0.254322] . ( 198 sec) [ -11358.0793] [Topology ] . ( 200 sec) [ -11358.0789] [Topology ] . ( 202 sec) [ -11358.0786] [GTR parameters ] . ( 202 sec) [ -11358.0786] [Alpha ][ 0.254322] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11358.078632. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -21924.0119] [GTR parameters ] . ( 5 sec) [ -21435.3316] [Alpha ][ 0.500960] . ( 5 sec) [ -21344.3460] [ 3237] [depth= 4] . ( 5 sec) [ -21227.8584] [ 3221] [depth= 14] . ( 5 sec) [ -21148.4550] [ 3220] [depth= 3] . ( 6 sec) [ -20959.0893] [ 3219] [depth= 9] . ( 6 sec) [ -20842.2545] [ 3191] [depth= 6] . ( 6 sec) [ -20758.7129] [ 3188] [depth= 2] . ( 6 sec) [ -20722.2987] [ 3184] [depth= 7] . ( 6 sec) [ -20630.2608] [ 3180] [depth= 2] . ( 6 sec) [ -20563.6767] [ 3166] [depth= 12] . ( 6 sec) [ -20411.5442] [ 3164] [depth= 1] . ( 6 sec) [ -20401.2215] [ 3127] [depth= 19] . ( 6 sec) [ -20282.1612] [ 3123] [depth= 2] . ( 7 sec) [ -19993.2082] [ 3085] [depth= 4] . ( 7 sec) [ -19854.8584] [ 3069] [depth= 7] . ( 7 sec) [ -19626.2898] [ 3063] [depth= 23] . ( 7 sec) [ -19356.3559] [ 3032] [depth= 1] . ( 7 sec) [ -19103.1896] [ 2966] [depth= 11] . ( 7 sec) [ -18697.4461] [ 2913] [depth= 11] . ( 7 sec) [ -18589.2464] [ 2925] [depth= 16] . ( 7 sec) [ -18520.8513] [ 2905] [depth= 5] . ( 8 sec) [ -18365.7926] [ 2874] [depth= 9] . ( 8 sec) [ -18351.8819] [ 2873] [depth= 2] . ( 8 sec) [ -18007.6625] [ 2843] [depth= 15] . ( 8 sec) [ -17979.1022] [ 2851] [depth= 3] . ( 8 sec) [ -17977.7607] [ 2847] [depth= 10] . ( 8 sec) [ -17626.2029] [ 2779] [depth= 11] . ( 8 sec) [ -17597.7444] [ 2781] [depth= 7] . ( 8 sec) [ -17495.8563] [ 2755] [depth= 15] . ( 8 sec) [ -17485.7037] [ 2754] [depth= 1] . ( 9 sec) [ -17367.5111] [ 2745] [depth= 17] . ( 9 sec) [ -17309.4262] [ 2740] [depth= 1] . ( 9 sec) [ -17190.4820] [ 2719] [depth= 1] . ( 9 sec) [ -17076.1964] [ 2696] [depth= 11] . ( 9 sec) [ -16971.9278] [ 2669] [depth= 6] . ( 9 sec) [ -16921.0524] [ 2665] [depth= 6] . ( 9 sec) [ -16832.1850] [ 2643] [depth= 1] . ( 9 sec) [ -16668.6987] [ 2629] [depth= 9] . ( 9 sec) [ -16587.6205] [ 2606] [depth= 11] . ( 10 sec) [ -16544.4448] [ 2592] [depth= 2] . ( 10 sec) [ -16457.1494] [ 2580] [depth= 14] . ( 10 sec) [ -16202.3315] [ 2536] [depth= 15] . ( 10 sec) [ -16153.2420] [ 2531] [depth= 16] . ( 10 sec) [ -15984.1427] [ 2489] [depth= 2] . ( 10 sec) [ -15722.1000] [ 2442] [depth= 14] . ( 10 sec) [ -15717.6159] [ 2441] [depth= 1] . ( 11 sec) [ -15644.6907] [ 2418] [depth= 14] . ( 11 sec) [ -15547.2712] [ 2409] [depth= 6] . ( 11 sec) [ -15477.6669] [ 2412] [depth= 1] . ( 11 sec) [ -15443.7339] [ 2408] [depth= 13] . ( 11 sec) [ -15439.2680] [ 2425] [depth= 1] . ( 11 sec) [ -15391.0971] [ 2422] [depth= 12] . ( 11 sec) [ -15266.2955] [ 2388] [depth= 4] . ( 12 sec) [ -15216.1121] [ 2375] [depth= 13] . ( 12 sec) [ -15151.8489] [ 2358] [depth= 5] . ( 12 sec) [ -15113.6707] [ 2352] [depth= 8] . ( 12 sec) [ -15042.0491] [ 2334] [depth= 1] . ( 12 sec) [ -15033.9689] [ 2337] [depth= 1] . ( 12 sec) [ -14939.1569] [ 2331] [depth= 12] . ( 13 sec) [ -14910.4312] [ 2318] [depth= 5] . ( 13 sec) [ -14830.0670] [ 2284] [depth= 6] . ( 13 sec) [ -14815.1488] [ 2278] [depth= 4] . ( 13 sec) [ -14806.5181] [ 2273] [depth= 7] . ( 13 sec) [ -14772.0430] [ 2272] [depth= 2] . ( 13 sec) [ -14764.6540] [ 2269] [depth= 3] . ( 13 sec) [ -14571.6878] [ 2224] [depth= 7] . ( 13 sec) [ -14543.7930] [ 2231] [depth= 1] . ( 13 sec) [ -14536.0626] [ 2231] [depth= 4] . ( 14 sec) [ -14482.0071] [ 2221] [depth= 8] . ( 14 sec) [ -14399.3360] [ 2201] [depth= 2] . ( 14 sec) [ -14353.9291] [ 2188] [depth= 5] . ( 14 sec) [ -14288.6653] [ 2164] [depth= 7] . ( 14 sec) [ -14258.8760] [ 2163] [depth= 3] . ( 14 sec) [ -14236.8596] [ 2157] [depth= 2] . ( 14 sec) [ -13939.3181] [ 2145] [depth= 12] . ( 14 sec) [ -13721.7868] [ 2095] [depth= 8] . ( 14 sec) [ -13684.7329] [ 2087] [depth= 9] . ( 15 sec) [ -13650.6440] [ 2077] [depth= 8] . ( 15 sec) [ -13613.3163] [ 2078] [depth= 1] . ( 15 sec) [ -13603.8071] [ 2077] [depth= 1] . ( 15 sec) [ -13591.9997] [ 2073] [depth= 3] . ( 15 sec) [ -13589.0083] [ 2072] [depth= 1] . ( 15 sec) [ -13480.2466] [ 2063] [depth= 11] . ( 15 sec) [ -13445.2650] [ 2055] [depth= 8] . ( 16 sec) [ -13444.0522] [ 2057] [depth= 2] . ( 16 sec) [ -13375.9552] [ 2040] [depth= 9] . ( 16 sec) [ -13373.8510] [ 2040] [depth= 1] . ( 16 sec) [ -13364.7984] [ 2038] [depth= 1] . ( 17 sec) [ -13355.3008] [ 2036] [depth= 1] . ( 17 sec) [ -13355.0996] [ 2037] [depth= 4] . ( 17 sec) [ -13353.7951] [ 2034] [depth= 1] . ( 17 sec) [ -13176.4799] [ 2008] [depth= 10] . ( 17 sec) [ -13170.6976] [ 2009] [depth= 1] . ( 17 sec) [ -13108.2877] [ 1995] [depth= 9] . ( 17 sec) [ -13099.5583] [ 1996] [depth= 1] . ( 18 sec) [ -13024.7248] [ 1981] [depth= 2] . ( 18 sec) [ -12937.1851] [ 1957] [depth= 1] . ( 18 sec) [ -12936.2986] [ 1955] [depth= 1] . ( 18 sec) [ -12901.3687] [ 1951] [depth= 6] . ( 18 sec) [ -12860.3862] [ 1946] [depth= 1] . ( 18 sec) [ -12831.9802] [ 1945] [depth= 3] . ( 19 sec) [ -12821.2134] [ 1939] [depth= 1] . ( 19 sec) [ -12717.8198] [ 1906] [depth= 2] . ( 19 sec) [ -12669.0303] [ 1897] [depth= 2] . ( 19 sec) [ -12621.6200] [ 1879] [depth= 13] . ( 19 sec) [ -12620.3031] [ 1879] [depth= 1] . ( 19 sec) [ -12594.9867] [ 1880] [depth= 1] . ( 19 sec) [ -12591.8748] [ 1879] [depth= 2] . ( 19 sec) [ -12572.1749] [ 1877] [depth= 14] . ( 19 sec) [ -12519.6067] [ 1865] [depth= 8] . ( 20 sec) [ -12503.8006] [ 1860] [depth= 1] . ( 20 sec) [ -12413.9551] [ 1839] [depth= 2] . ( 20 sec) [ -12350.7070] [ 1821] [depth= 5] . ( 20 sec) [ -12318.8976] [ 1815] [depth= 2] . ( 20 sec) [ -12311.7809] [ 1814] [depth= 2] . ( 20 sec) [ -12285.8317] [ 1806] [depth= 2] . ( 20 sec) [ -12228.2422] [ 1794] [depth= 3] . ( 20 sec) [ -12195.2125] [ 1781] [depth= 1] . ( 20 sec) [ -12147.8996] [ 1768] [depth= 5] . ( 21 sec) [ -12145.9322] [ 1766] [depth= 2] . ( 21 sec) [ -12139.5707] [ 1761] [depth= 2] . ( 21 sec) [ -12103.6045] [ 1759] [depth= 1] . ( 21 sec) [ -12089.0801] [ 1757] [depth= 1] . ( 21 sec) [ -12077.2503] [ 1755] [depth= 1] . ( 21 sec) [ -12064.7022] [ 1747] [depth= 5] . ( 21 sec) [ -12059.3788] [ 1746] [depth= 1] . ( 21 sec) [ -12040.4910] [ 1740] [depth= 3] . ( 22 sec) [ -12015.6918] [ 1730] [depth= 5] . ( 22 sec) [ -12009.6689] [ 1726] [depth= 2] . ( 22 sec) [ -11990.3132] [ 1719] [depth= 5] . ( 22 sec) [ -11984.5198] [ 1719] [depth= 1] . ( 22 sec) [ -11981.4336] [ 1717] [depth= 2] . ( 23 sec) [ -11980.2896] [ 1718] [depth= 1] . ( 23 sec) [ -11961.3392] [ 1710] [depth= 4] . ( 23 sec) [ -11863.5259] [ 1685] [depth= 1] . ( 23 sec) [ -11835.9146] [ 1679] [depth= 5] . ( 23 sec) [ -11818.7129] [ 1676] [depth= 1] . ( 23 sec) [ -11799.9757] [ 1669] [depth= 5] . ( 24 sec) [ -11798.4251] [ 1668] [depth= 2] . ( 24 sec) [ -11798.2762] [ 1669] [depth= 1] . ( 24 sec) [ -11779.3003] [ 1663] [depth= 2] . ( 24 sec) [ -11773.2015] [ 1659] [depth= 1] . ( 24 sec) [ -11759.9564] [ 1647] [depth= 1] . ( 24 sec) [ -11756.5588] [ 1647] [depth= 1] . ( 24 sec) [ -11755.2841] [ 1647] [depth= 1] . ( 24 sec) [ -11735.0862] [ 1647] [depth= 1] . ( 25 sec) [ -11734.9199] [ 1647] [depth= 1] . ( 26 sec) [ -11673.6132] [Branch lengths ] . ( 28 sec) [ -11665.7750] [GTR parameters ] . ( 29 sec) [ -11574.5841] [Alpha ][ 0.250961] . ( 29 sec) [ -11572.9828] [ 1646] [depth= 1] . ( 30 sec) [ -11530.5959] [ 1639] [depth= 1] . ( 30 sec) [ -11529.5216] [ 1636] [depth= 1] . ( 30 sec) [ -11525.6372] [ 1637] [depth= 6] . ( 32 sec) [ -11524.6066] [ 1638] [depth= 2] . ( 32 sec) [ -11517.7455] [ 1633] [depth= 3] . ( 32 sec) [ -11517.6035] [ 1634] [depth= 1] . ( 32 sec) [ -11514.0983] [ 1633] [depth= 1] . ( 33 sec) [ -11511.5836] [ 1632] [depth= 3] . ( 34 sec) [ -11467.7084] [ 1620] [depth= 3] . ( 34 sec) [ -11467.0666] [ 1623] [depth= 1] . ( 34 sec) [ -11466.7432] [ 1620] [depth= 1] . ( 34 sec) [ -11462.3982] [ 1619] [depth= 1] . ( 34 sec) [ -11434.0453] [ 1610] [depth= 2] . ( 34 sec) [ -11433.8595] [ 1611] [depth= 1] . ( 35 sec) [ -11433.3593] [ 1610] [depth= 1] . ( 35 sec) [ -11427.0029] [ 1610] [depth= 2] . ( 36 sec) [ -11424.6517] [ 1613] [depth= 1] . ( 36 sec) [ -11424.3940] [ 1611] [depth= 1] . ( 36 sec) [ -11423.2295] [ 1610] [depth= 1] . ( 36 sec) [ -11421.3745] [ 1609] [depth= 1] . ( 37 sec) [ -11417.7977] [ 1607] [depth= 1] . ( 38 sec) [ -11415.8334] [ 1603] [depth= 2] . ( 39 sec) [ -11412.9877] [ 1605] [depth= 1] . ( 39 sec) [ -11407.5845] [ 1605] [depth= 1] . ( 39 sec) [ -11405.0207] [ 1602] [depth= 1] . ( 40 sec) [ -11402.2729] [ 1603] [depth= 1] . ( 41 sec) [ -11399.8932] [ 1603] [depth= 1] . ( 41 sec) [ -11378.2758] [ 1595] [depth= 5] . ( 43 sec) [ -11377.4175] [ 1595] [depth= 1] . ( 43 sec) [ -11376.7580] [ 1596] [depth= 1] . ( 44 sec) [ -11376.7343] [ 1596] [depth= 1] . ( 44 sec) [ -11375.7783] [ 1595] [depth= 1] . ( 44 sec) [ -11375.5352] [ 1594] [depth= 1] . ( 45 sec) [ -11372.0858] [ 1591] [depth= 4] . ( 50 sec) [ -11358.9615] [Branch lengths ] . ( 52 sec) [ -11358.6282] [GTR parameters ] . ( 53 sec) [ -11358.5893] [Alpha ][ 0.254455] . ( 77 sec) [ -11358.1480] [Branch lengths ] . ( 164 sec) [ -11358.0962] [Branch lengths ] . ( 164 sec) [ -11358.0962] [Topology ] . ( 166 sec) [ -11358.0879] [Topology ] . ( 168 sec) [ -11358.0844] [Topology ] . ( 170 sec) [ -11358.0824] [Topology ] . ( 172 sec) [ -11358.0813] [Topology ] . ( 174 sec) [ -11358.0807] [Topology ] . ( 174 sec) [ -11358.0806] [GTR parameters ] . ( 174 sec) [ -11358.0805] [Alpha ][ 0.254200] . ( 175 sec) [ -11358.0805] [Topology ] . ( 177 sec) [ -11358.0802] [Topology ] . ( 179 sec) [ -11358.0786] [GTR parameters ] . ( 179 sec) [ -11358.0786] [Alpha ][ 0.254200] . ( 179 sec) [ -11358.0786] [Topology ] . ( 181 sec) [ -11358.0783] [Topology ] . ( 182 sec) [ -11358.0783] [GTR parameters ] . ( 182 sec) [ -11358.0783] [Alpha ][ 0.254200] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11358.078305. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22583.4309] [GTR parameters ] . ( 3 sec) [ -22081.9269] [Alpha ][ 0.500960] . ( 3 sec) [ -21717.1215] [ 3230] [depth= 3] . ( 3 sec) [ -21476.6449] [ 3189] [depth= 12] . ( 3 sec) [ -21181.8439] [ 3190] [depth= 10] . ( 3 sec) [ -21181.2375] [ 3190] [depth= 1] . ( 3 sec) [ -20796.6640] [ 3157] [depth= 9] . ( 3 sec) [ -20776.3470] [ 3158] [depth= 1] . ( 4 sec) [ -20751.0827] [ 3153] [depth= 5] . ( 4 sec) [ -20671.6150] [ 3142] [depth= 2] . ( 4 sec) [ -20572.0927] [ 3136] [depth= 6] . ( 4 sec) [ -20496.0377] [ 3136] [depth= 3] . ( 4 sec) [ -20354.4954] [ 3131] [depth= 6] . ( 4 sec) [ -20345.4569] [ 3125] [depth= 3] . ( 4 sec) [ -20307.0572] [ 3122] [depth= 10] . ( 4 sec) [ -20292.8491] [ 3122] [depth= 1] . ( 4 sec) [ -20292.2647] [ 3122] [depth= 8] . ( 4 sec) [ -20236.2432] [ 3113] [depth= 13] . ( 4 sec) [ -20194.2814] [ 3119] [depth= 1] . ( 5 sec) [ -20069.5463] [ 3117] [depth= 2] . ( 5 sec) [ -19990.5191] [ 3117] [depth= 4] . ( 5 sec) [ -19869.6544] [ 3087] [depth= 22] . ( 5 sec) [ -19803.4402] [ 3060] [depth= 15] . ( 5 sec) [ -19693.9488] [ 3056] [depth= 11] . ( 5 sec) [ -19678.6438] [ 3055] [depth= 1] . ( 5 sec) [ -19672.9283] [ 3054] [depth= 1] . ( 5 sec) [ -19470.1693] [ 3039] [depth= 17] . ( 5 sec) [ -19337.2693] [ 3039] [depth= 1] . ( 5 sec) [ -19021.1076] [ 2961] [depth= 2] . ( 6 sec) [ -18851.6186] [ 2959] [depth= 1] . ( 6 sec) [ -18807.1911] [ 2953] [depth= 2] . ( 6 sec) [ -18461.6597] [ 2905] [depth= 6] . ( 6 sec) [ -18241.2299] [ 2836] [depth= 7] . ( 6 sec) [ -18050.3829] [ 2824] [depth= 4] . ( 6 sec) [ -17991.9321] [ 2818] [depth= 5] . ( 6 sec) [ -17896.5585] [ 2811] [depth= 19] . ( 7 sec) [ -17820.9145] [ 2798] [depth= 7] . ( 7 sec) [ -17700.8133] [ 2765] [depth= 22] . ( 7 sec) [ -17612.7635] [ 2761] [depth= 11] . ( 7 sec) [ -17544.0624] [ 2760] [depth= 1] . ( 7 sec) [ -17403.1527] [ 2745] [depth= 12] . ( 7 sec) [ -17336.7550] [ 2745] [depth= 1] . ( 7 sec) [ -17223.6368] [ 2730] [depth= 18] . ( 7 sec) [ -17209.5726] [ 2729] [depth= 2] . ( 7 sec) [ -17118.7479] [ 2705] [depth= 2] . ( 7 sec) [ -16904.0898] [ 2671] [depth= 17] . ( 8 sec) [ -16857.0369] [ 2641] [depth= 4] . ( 8 sec) [ -16851.7872] [ 2640] [depth= 1] . ( 8 sec) [ -16821.4566] [ 2632] [depth= 3] . ( 8 sec) [ -16818.6479] [ 2631] [depth= 1] . ( 8 sec) [ -16512.7154] [ 2612] [depth= 10] . ( 8 sec) [ -16498.0741] [ 2611] [depth= 2] . ( 8 sec) [ -16405.1203] [ 2594] [depth= 6] . ( 8 sec) [ -16302.1705] [ 2552] [depth= 14] . ( 9 sec) [ -16248.9166] [ 2538] [depth= 9] . ( 9 sec) [ -16204.0592] [ 2541] [depth= 5] . ( 9 sec) [ -16073.6932] [ 2504] [depth= 2] . ( 9 sec) [ -15990.5821] [ 2498] [depth= 7] . ( 9 sec) [ -15897.7542] [ 2468] [depth= 9] . ( 9 sec) [ -15836.1070] [ 2453] [depth= 5] . ( 9 sec) [ -15816.8028] [ 2450] [depth= 6] . ( 9 sec) [ -15692.5803] [ 2429] [depth= 19] . ( 10 sec) [ -15645.4024] [ 2419] [depth= 9] . ( 10 sec) [ -15642.1159] [ 2418] [depth= 7] . ( 10 sec) [ -15151.0994] [ 2365] [depth= 6] . ( 10 sec) [ -14990.7529] [ 2359] [depth= 3] . ( 10 sec) [ -14874.9844] [ 2360] [depth= 8] . ( 10 sec) [ -14778.0408] [ 2335] [depth= 1] . ( 10 sec) [ -14734.0387] [ 2321] [depth= 10] . ( 10 sec) [ -14730.2138] [ 2322] [depth= 1] . ( 10 sec) [ -14717.9834] [ 2309] [depth= 1] . ( 11 sec) [ -14491.9952] [ 2258] [depth= 7] . ( 11 sec) [ -14491.4850] [ 2257] [depth= 1] . ( 11 sec) [ -14353.7898] [ 2220] [depth= 13] . ( 11 sec) [ -14308.7257] [ 2215] [depth= 3] . ( 11 sec) [ -14306.8612] [ 2214] [depth= 1] . ( 11 sec) [ -14202.9204] [ 2173] [depth= 13] . ( 11 sec) [ -14195.3750] [ 2173] [depth= 1] . ( 11 sec) [ -14175.5443] [ 2168] [depth= 2] . ( 11 sec) [ -14105.4211] [ 2168] [depth= 3] . ( 12 sec) [ -14102.9404] [ 2168] [depth= 1] . ( 12 sec) [ -14041.0422] [ 2150] [depth= 9] . ( 12 sec) [ -13945.6231] [ 2143] [depth= 1] . ( 12 sec) [ -13941.0761] [ 2141] [depth= 2] . ( 12 sec) [ -13768.2197] [ 2100] [depth= 14] . ( 12 sec) [ -13734.3942] [ 2100] [depth= 3] . ( 12 sec) [ -13661.1889] [ 2097] [depth= 7] . ( 12 sec) [ -13539.1429] [ 2052] [depth= 9] . ( 12 sec) [ -13523.1736] [ 2046] [depth= 4] . ( 13 sec) [ -13433.8495] [ 2018] [depth= 9] . ( 13 sec) [ -13426.8441] [ 2018] [depth= 1] . ( 13 sec) [ -13425.5099] [ 2018] [depth= 1] . ( 13 sec) [ -13321.2690] [ 1990] [depth= 3] . ( 13 sec) [ -13280.1552] [ 1987] [depth= 14] . ( 13 sec) [ -13259.0339] [ 1985] [depth= 2] . ( 14 sec) [ -13258.7704] [ 1986] [depth= 1] . ( 14 sec) [ -13254.5929] [ 1981] [depth= 6] . ( 14 sec) [ -13095.2104] [ 1954] [depth= 6] . ( 14 sec) [ -13007.7084] [ 1944] [depth= 1] . ( 14 sec) [ -12972.3375] [ 1942] [depth= 3] . ( 14 sec) [ -12867.7087] [ 1929] [depth= 4] . ( 14 sec) [ -12847.6503] [ 1929] [depth= 1] . ( 15 sec) [ -12794.6126] [ 1928] [depth= 2] . ( 15 sec) [ -12786.2151] [ 1925] [depth= 4] . ( 15 sec) [ -12776.8748] [ 1918] [depth= 1] . ( 15 sec) [ -12694.6104] [ 1906] [depth= 9] . ( 15 sec) [ -12655.9390] [ 1898] [depth= 9] . ( 15 sec) [ -12595.6853] [ 1882] [depth= 12] . ( 15 sec) [ -12526.9522] [ 1884] [depth= 4] . ( 15 sec) [ -12511.3387] [ 1872] [depth= 15] . ( 16 sec) [ -12502.8009] [ 1870] [depth= 4] . ( 16 sec) [ -12502.7040] [ 1868] [depth= 1] . ( 16 sec) [ -12499.5375] [ 1870] [depth= 2] . ( 16 sec) [ -12481.1162] [ 1860] [depth= 3] . ( 16 sec) [ -12448.8142] [ 1854] [depth= 3] . ( 16 sec) [ -12403.8154] [ 1841] [depth= 2] . ( 16 sec) [ -12400.7752] [ 1836] [depth= 4] . ( 17 sec) [ -12399.8600] [ 1835] [depth= 1] . ( 17 sec) [ -12396.8278] [ 1836] [depth= 1] . ( 17 sec) [ -12396.3696] [ 1836] [depth= 1] . ( 17 sec) [ -12377.3676] [ 1833] [depth= 5] . ( 17 sec) [ -12374.1421] [ 1831] [depth= 5] . ( 17 sec) [ -12344.9773] [ 1823] [depth= 9] . ( 18 sec) [ -12337.9924] [ 1822] [depth= 2] . ( 18 sec) [ -12337.0092] [ 1821] [depth= 1] . ( 18 sec) [ -12310.7436] [ 1816] [depth= 2] . ( 18 sec) [ -12308.3278] [ 1816] [depth= 3] . ( 18 sec) [ -12304.4390] [ 1816] [depth= 2] . ( 18 sec) [ -12262.9923] [ 1804] [depth= 2] . ( 19 sec) [ -12261.8606] [ 1803] [depth= 2] . ( 19 sec) [ -12258.1973] [ 1800] [depth= 5] . ( 19 sec) [ -12245.6505] [ 1789] [depth= 9] . ( 19 sec) [ -12240.9281] [ 1787] [depth= 2] . ( 20 sec) [ -12210.3344] [ 1785] [depth= 3] . ( 20 sec) [ -12166.6707] [ 1766] [depth= 8] . ( 20 sec) [ -12165.4946] [ 1765] [depth= 4] . ( 20 sec) [ -12164.8525] [ 1766] [depth= 2] . ( 20 sec) [ -12158.4797] [ 1765] [depth= 1] . ( 20 sec) [ -12111.9914] [ 1750] [depth= 3] . ( 20 sec) [ -12104.9935] [ 1750] [depth= 1] . ( 21 sec) [ -12102.2509] [ 1747] [depth= 6] . ( 21 sec) [ -12098.7871] [ 1748] [depth= 1] . ( 21 sec) [ -12072.8808] [ 1740] [depth= 3] . ( 22 sec) [ -12061.0576] [ 1736] [depth= 1] . ( 22 sec) [ -11961.1345] [Branch lengths ] . ( 25 sec) [ -11954.2956] [GTR parameters ] . ( 25 sec) [ -11842.0786] [Alpha ][ 0.250961] . ( 26 sec) [ -11841.8963] [ 1734] [depth= 2] . ( 26 sec) [ -11837.8465] [ 1733] [depth= 1] . ( 26 sec) [ -11818.0211] [ 1722] [depth= 11] . ( 26 sec) [ -11799.0995] [ 1717] [depth= 4] . ( 26 sec) [ -11679.2701] [ 1684] [depth= 11] . ( 26 sec) [ -11676.9437] [ 1684] [depth= 2] . ( 26 sec) [ -11675.3413] [ 1686] [depth= 1] . ( 27 sec) [ -11630.5682] [ 1674] [depth= 8] . ( 27 sec) [ -11628.2564] [ 1675] [depth= 2] . ( 27 sec) [ -11612.0129] [ 1669] [depth= 1] . ( 27 sec) [ -11595.6135] [ 1665] [depth= 1] . ( 27 sec) [ -11594.7296] [ 1665] [depth= 1] . ( 27 sec) [ -11583.3859] [ 1662] [depth= 2] . ( 27 sec) [ -11583.1491] [ 1662] [depth= 1] . ( 28 sec) [ -11572.7393] [ 1656] [depth= 1] . ( 28 sec) [ -11570.3044] [ 1656] [depth= 1] . ( 29 sec) [ -11554.1108] [ 1652] [depth= 7] . ( 30 sec) [ -11533.9915] [ 1645] [depth= 1] . ( 30 sec) [ -11479.2165] [ 1624] [depth= 7] . ( 31 sec) [ -11478.7927] [ 1625] [depth= 1] . ( 31 sec) [ -11477.7808] [ 1626] [depth= 1] . ( 32 sec) [ -11476.9197] [ 1625] [depth= 1] . ( 32 sec) [ -11475.3129] [ 1623] [depth= 1] . ( 32 sec) [ -11456.3191] [ 1615] [depth= 2] . ( 32 sec) [ -11454.3196] [ 1615] [depth= 2] . ( 32 sec) [ -11454.1928] [ 1616] [depth= 1] . ( 33 sec) [ -11454.1475] [ 1616] [depth= 1] . ( 33 sec) [ -11451.0630] [ 1615] [depth= 1] . ( 34 sec) [ -11449.6203] [ 1614] [depth= 1] . ( 34 sec) [ -11449.1988] [ 1614] [depth= 1] . ( 34 sec) [ -11448.6942] [ 1616] [depth= 1] . ( 34 sec) [ -11437.6606] [ 1608] [depth= 2] . ( 34 sec) [ -11432.8691] [ 1607] [depth= 1] . ( 35 sec) [ -11432.6474] [ 1607] [depth= 1] . ( 35 sec) [ -11402.2938] [ 1603] [depth= 1] . ( 36 sec) [ -11402.1876] [ 1602] [depth= 1] . ( 37 sec) [ -11401.9061] [ 1603] [depth= 2] . ( 37 sec) [ -11401.3599] [ 1603] [depth= 1] . ( 38 sec) [ -11400.2194] [ 1606] [depth= 1] . ( 39 sec) [ -11393.8439] [ 1604] [depth= 2] . ( 39 sec) [ -11393.7177] [ 1604] [depth= 2] . ( 39 sec) [ -11392.2568] [ 1600] [depth= 1] . ( 39 sec) [ -11389.8890] [ 1604] [depth= 1] . ( 42 sec) [ -11389.7861] [ 1604] [depth= 1] . ( 43 sec) [ -11388.7267] [ 1603] [depth= 1] . ( 44 sec) [ -11388.6426] [ 1604] [depth= 1] . ( 46 sec) [ -11376.1041] [Branch lengths ] . ( 49 sec) [ -11374.6981] [GTR parameters ] . ( 49 sec) [ -11374.6939] [Alpha ][ 0.252056] . ( 53 sec) [ -11374.5754] [ 1603] [depth= 2] . ( 54 sec) [ -11374.2899] [ 1604] [depth= 2] . ( 57 sec) [ -11373.7182] [ 1604] [depth= 1] . ( 61 sec) [ -11373.5594] [ 1602] [depth= 1] . ( 61 sec) [ -11373.0366] [ 1602] [depth= 1] . ( 64 sec) [ -11372.3158] [ 1601] [depth= 1] . ( 71 sec) [ -11372.2570] [ 1601] [depth= 1] . ( 74 sec) [ -11372.1421] [ 1602] [depth= 1] . ( 77 sec) [ -11370.8775] [Branch lengths ] . ( 78 sec) [ -11370.8698] [GTR parameters ] . ( 78 sec) [ -11370.8698] [Alpha ][ 0.251804] . ( 98 sec) [ -11369.9924] [ 1601] [depth= 1] . ( 107 sec) [ -11369.7794] [Branch lengths ] . ( 108 sec) [ -11369.7780] [GTR parameters ] . ( 108 sec) [ -11369.7777] [Alpha ][ 0.252056] . ( 135 sec) [ -11369.7746] [Branch lengths ] . ( 215 sec) [ -11369.7745] [Branch lengths ] . ( 215 sec) [ -11369.7745] [Topology ] . ( 217 sec) [ -11369.7745] [Topology ] . ( 218 sec) [ -11369.7745] [GTR parameters ] . ( 218 sec) [ -11369.7745] [Alpha ][ 0.252056] . Checking for NNIs, optimizing five branches... . ( 233 sec) [ -11369.7743] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11369.774346. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -22946.3685] [GTR parameters ] . ( 3 sec) [ -22447.1907] [Alpha ][ 0.500960] . ( 3 sec) [ -22271.4996] [ 3277] [depth= 6] . ( 3 sec) [ -22153.5718] [ 3267] [depth= 11] . ( 4 sec) [ -22049.4230] [ 3263] [depth= 2] . ( 4 sec) [ -22001.9558] [ 3253] [depth= 4] . ( 4 sec) [ -21862.8224] [ 3216] [depth= 1] . ( 4 sec) [ -21772.5382] [ 3211] [depth= 5] . ( 4 sec) [ -21742.0140] [ 3209] [depth= 1] . ( 4 sec) [ -21714.2058] [ 3205] [depth= 5] . ( 4 sec) [ -21537.6124] [ 3196] [depth= 2] . ( 4 sec) [ -21363.4412] [ 3190] [depth= 6] . ( 4 sec) [ -21350.0081] [ 3188] [depth= 1] . ( 5 sec) [ -21326.5966] [ 3181] [depth= 3] . ( 5 sec) [ -21188.8927] [ 3142] [depth= 1] . ( 5 sec) [ -21122.8305] [ 3136] [depth= 6] . ( 5 sec) [ -20950.3015] [ 3132] [depth= 7] . ( 5 sec) [ -20889.2377] [ 3131] [depth= 1] . ( 5 sec) [ -20836.3214] [ 3126] [depth= 3] . ( 5 sec) [ -20830.9959] [ 3126] [depth= 1] . ( 5 sec) [ -20669.3846] [ 3094] [depth= 22] . ( 6 sec) [ -20574.9977] [ 3080] [depth= 29] . ( 6 sec) [ -20518.6877] [ 3071] [depth= 23] . ( 6 sec) [ -20514.1153] [ 3066] [depth= 12] . ( 6 sec) [ -20499.2717] [ 3067] [depth= 1] . ( 6 sec) [ -20291.2168] [ 3059] [depth= 7] . ( 6 sec) [ -20155.9559] [ 3058] [depth= 1] . ( 6 sec) [ -20070.5869] [ 3006] [depth= 5] . ( 6 sec) [ -19302.3207] [ 2933] [depth= 12] . ( 6 sec) [ -19165.4066] [ 2979] [depth= 16] . ( 7 sec) [ -19039.2670] [ 2959] [depth= 18] . ( 7 sec) [ -19011.6699] [ 2965] [depth= 1] . ( 7 sec) [ -18994.8170] [ 2963] [depth= 3] . ( 7 sec) [ -18981.7894] [ 2960] [depth= 1] . ( 7 sec) [ -18724.5022] [ 2928] [depth= 16] . ( 7 sec) [ -18611.8138] [ 2893] [depth= 3] . ( 7 sec) [ -18553.3355] [ 2890] [depth= 3] . ( 7 sec) [ -18418.4386] [ 2862] [depth= 10] . ( 7 sec) [ -18351.3577] [ 2856] [depth= 12] . ( 8 sec) [ -18348.8584] [ 2858] [depth= 3] . ( 8 sec) [ -18307.0500] [ 2850] [depth= 2] . ( 8 sec) [ -18127.6899] [ 2850] [depth= 1] . ( 8 sec) [ -18094.9672] [ 2850] [depth= 2] . ( 8 sec) [ -18066.6915] [ 2837] [depth= 1] . ( 8 sec) [ -18037.6912] [ 2809] [depth= 10] . ( 8 sec) [ -17865.5545] [ 2773] [depth= 11] . ( 8 sec) [ -17833.0406] [ 2763] [depth= 5] . ( 8 sec) [ -17818.5932] [ 2762] [depth= 1] . ( 9 sec) [ -17722.8762] [ 2757] [depth= 1] . ( 9 sec) [ -17649.9307] [ 2755] [depth= 5] . ( 9 sec) [ -17482.5616] [ 2711] [depth= 10] . ( 9 sec) [ -17444.8352] [ 2712] [depth= 15] . ( 9 sec) [ -17370.2586] [ 2699] [depth= 6] . ( 9 sec) [ -17282.2423] [ 2697] [depth= 1] . ( 9 sec) [ -17250.1290] [ 2687] [depth= 1] . ( 9 sec) [ -17204.1609] [ 2682] [depth= 1] . ( 10 sec) [ -17109.9789] [ 2656] [depth= 9] . ( 10 sec) [ -17046.0474] [ 2657] [depth= 1] . ( 10 sec) [ -17032.8959] [ 2655] [depth= 2] . ( 10 sec) [ -17030.2136] [ 2655] [depth= 1] . ( 10 sec) [ -16937.9006] [ 2634] [depth= 6] . ( 10 sec) [ -16931.5760] [ 2631] [depth= 1] . ( 10 sec) [ -16764.7477] [ 2594] [depth= 1] . ( 10 sec) [ -16692.3461] [ 2580] [depth= 3] . ( 11 sec) [ -16627.5223] [ 2574] [depth= 1] . ( 11 sec) [ -16511.2239] [ 2556] [depth= 8] . ( 11 sec) [ -16503.6936] [ 2550] [depth= 11] . ( 11 sec) [ -16479.1084] [ 2549] [depth= 1] . ( 11 sec) [ -16412.2711] [ 2537] [depth= 19] . ( 11 sec) [ -16346.7779] [ 2524] [depth= 2] . ( 12 sec) [ -16301.6442] [ 2500] [depth= 5] . ( 12 sec) [ -16206.7754] [ 2496] [depth= 1] . ( 12 sec) [ -16188.9271] [ 2495] [depth= 1] . ( 12 sec) [ -16134.3747] [ 2481] [depth= 10] . ( 12 sec) [ -16033.1044] [ 2454] [depth= 2] . ( 12 sec) [ -15996.5374] [ 2446] [depth= 4] . ( 12 sec) [ -15849.7590] [ 2448] [depth= 6] . ( 12 sec) [ -15848.4026] [ 2449] [depth= 2] . ( 12 sec) [ -15717.0980] [ 2419] [depth= 16] . ( 13 sec) [ -15717.0240] [ 2420] [depth= 1] . ( 13 sec) [ -15715.7643] [ 2423] [depth= 1] . ( 13 sec) [ -15714.1227] [ 2422] [depth= 1] . ( 13 sec) [ -15691.4677] [ 2412] [depth= 11] . ( 13 sec) [ -15663.1714] [ 2422] [depth= 1] . ( 13 sec) [ -15398.6825] [ 2365] [depth= 2] . ( 13 sec) [ -15346.9494] [ 2346] [depth= 2] . ( 13 sec) [ -15250.2148] [ 2325] [depth= 14] . ( 14 sec) [ -15229.8361] [ 2319] [depth= 1] . ( 14 sec) [ -15126.3581] [ 2314] [depth= 5] . ( 14 sec) [ -14900.8903] [ 2277] [depth= 14] . ( 14 sec) [ -14804.6306] [ 2276] [depth= 1] . ( 14 sec) [ -14578.6655] [ 2249] [depth= 13] . ( 14 sec) [ -14577.6464] [ 2249] [depth= 1] . ( 14 sec) [ -14576.0830] [ 2248] [depth= 1] . ( 14 sec) [ -14569.5498] [ 2248] [depth= 2] . ( 14 sec) [ -14509.4836] [ 2241] [depth= 3] . ( 15 sec) [ -14455.8789] [ 2231] [depth= 15] . ( 15 sec) [ -14011.0909] [ 2174] [depth= 1] . ( 15 sec) [ -13877.4395] [ 2144] [depth= 2] . ( 15 sec) [ -13866.2376] [ 2137] [depth= 1] . ( 15 sec) [ -13642.9304] [ 2132] [depth= 6] . ( 15 sec) [ -13599.7564] [ 2121] [depth= 1] . ( 15 sec) [ -13594.4716] [ 2116] [depth= 1] . ( 15 sec) [ -13413.9216] [ 2118] [depth= 1] . ( 15 sec) [ -13397.5366] [ 2113] [depth= 1] . ( 15 sec) [ -13383.7553] [ 2112] [depth= 1] . ( 16 sec) [ -13263.2546] [ 2063] [depth= 17] . ( 16 sec) [ -13251.6236] [ 2061] [depth= 1] . ( 16 sec) [ -13152.2113] [ 2026] [depth= 16] . ( 16 sec) [ -13043.3624] [ 1994] [depth= 21] . ( 16 sec) [ -12993.3537] [ 1973] [depth= 19] . ( 16 sec) [ -12983.7362] [ 1964] [depth= 5] . ( 16 sec) [ -12982.2914] [ 1963] [depth= 1] . ( 16 sec) [ -12942.6373] [ 1956] [depth= 1] . ( 16 sec) [ -12931.4192] [ 1949] [depth= 12] . ( 17 sec) [ -12915.7307] [ 1942] [depth= 1] . ( 17 sec) [ -12750.4467] [ 1913] [depth= 1] . ( 17 sec) [ -12738.8156] [ 1912] [depth= 2] . ( 17 sec) [ -12734.3612] [ 1912] [depth= 10] . ( 17 sec) [ -12690.4207] [ 1902] [depth= 2] . ( 17 sec) [ -12677.3909] [ 1899] [depth= 1] . ( 17 sec) [ -12636.4179] [ 1886] [depth= 1] . ( 18 sec) [ -12518.4346] [ 1858] [depth= 14] . ( 18 sec) [ -12515.4507] [ 1857] [depth= 1] . ( 18 sec) [ -12511.2524] [ 1856] [depth= 2] . ( 18 sec) [ -12508.7867] [ 1856] [depth= 1] . ( 18 sec) [ -12498.8174] [ 1853] [depth= 1] . ( 19 sec) [ -12469.4600] [ 1848] [depth= 2] . ( 19 sec) [ -12431.0825] [ 1842] [depth= 2] . ( 19 sec) [ -12428.5929] [ 1843] [depth= 1] . ( 19 sec) [ -12257.6446] [ 1807] [depth= 11] . ( 19 sec) [ -12213.0066] [ 1784] [depth= 2] . ( 19 sec) [ -12209.1662] [ 1783] [depth= 1] . ( 19 sec) [ -12206.8886] [ 1784] [depth= 1] . ( 20 sec) [ -12206.2826] [ 1785] [depth= 1] . ( 20 sec) [ -12199.0206] [ 1785] [depth= 1] . ( 20 sec) [ -12114.8807] [ 1758] [depth= 3] . ( 20 sec) [ -12084.1029] [ 1752] [depth= 2] . ( 20 sec) [ -12065.7094] [ 1752] [depth= 2] . ( 20 sec) [ -12064.2415] [ 1753] [depth= 1] . ( 20 sec) [ -12058.2032] [ 1752] [depth= 1] . ( 21 sec) [ -12057.5283] [ 1752] [depth= 1] . ( 21 sec) [ -12025.1361] [ 1745] [depth= 1] . ( 21 sec) [ -12017.7534] [ 1743] [depth= 4] . ( 21 sec) [ -12012.5726] [ 1742] [depth= 1] . ( 21 sec) [ -11983.3341] [ 1732] [depth= 3] . ( 21 sec) [ -11962.8556] [ 1717] [depth= 13] . ( 22 sec) [ -11960.2939] [ 1717] [depth= 2] . ( 22 sec) [ -11937.4332] [ 1716] [depth= 4] . ( 22 sec) [ -11932.6662] [ 1716] [depth= 2] . ( 22 sec) [ -11931.4890] [ 1717] [depth= 1] . ( 22 sec) [ -11926.6710] [ 1717] [depth= 1] . ( 22 sec) [ -11856.2345] [ 1703] [depth= 2] . ( 24 sec) [ -11764.0954] [Branch lengths ] . ( 26 sec) [ -11759.0438] [GTR parameters ] . ( 27 sec) [ -11654.6651] [Alpha ][ 0.250961] . ( 27 sec) [ -11648.2665] [ 1697] [depth= 3] . ( 27 sec) [ -11540.9095] [ 1658] [depth= 17] . ( 27 sec) [ -11531.2725] [ 1655] [depth= 3] . ( 27 sec) [ -11529.2411] [ 1656] [depth= 1] . ( 28 sec) [ -11523.5265] [ 1655] [depth= 6] . ( 28 sec) [ -11520.9794] [ 1655] [depth= 1] . ( 28 sec) [ -11512.3565] [ 1650] [depth= 2] . ( 29 sec) [ -11508.8413] [ 1650] [depth= 1] . ( 29 sec) [ -11507.9004] [ 1650] [depth= 1] . ( 29 sec) [ -11507.5952] [ 1652] [depth= 2] . ( 30 sec) [ -11501.8918] [ 1651] [depth= 2] . ( 30 sec) [ -11501.7603] [ 1648] [depth= 1] . ( 30 sec) [ -11501.6219] [ 1647] [depth= 1] . ( 31 sec) [ -11500.8954] [ 1648] [depth= 1] . ( 31 sec) [ -11500.7844] [ 1647] [depth= 1] . ( 31 sec) [ -11499.3032] [ 1645] [depth= 1] . ( 31 sec) [ -11486.1017] [ 1643] [depth= 1] . ( 31 sec) [ -11482.6786] [ 1643] [depth= 1] . ( 31 sec) [ -11482.6555] [ 1643] [depth= 1] . ( 31 sec) [ -11418.7236] [ 1619] [depth= 12] . ( 32 sec) [ -11414.9881] [ 1618] [depth= 1] . ( 33 sec) [ -11413.8747] [ 1618] [depth= 1] . ( 33 sec) [ -11413.8463] [ 1616] [depth= 1] . ( 35 sec) [ -11413.2245] [ 1617] [depth= 1] . ( 35 sec) [ -11411.1500] [ 1616] [depth= 1] . ( 35 sec) [ -11411.0837] [ 1616] [depth= 1] . ( 36 sec) [ -11409.4687] [ 1615] [depth= 1] . ( 36 sec) [ -11409.2933] [ 1615] [depth= 1] . ( 38 sec) [ -11399.4568] [ 1605] [depth= 3] . ( 39 sec) [ -11398.9531] [ 1605] [depth= 1] . ( 40 sec) [ -11396.4009] [ 1600] [depth= 2] . ( 40 sec) [ -11395.2461] [ 1598] [depth= 1] . ( 40 sec) [ -11394.9735] [ 1598] [depth= 1] . ( 41 sec) [ -11392.2368] [ 1597] [depth= 2] . ( 41 sec) [ -11391.2389] [ 1598] [depth= 2] . ( 42 sec) [ -11390.2616] [ 1596] [depth= 2] . ( 43 sec) [ -11390.0417] [ 1597] [depth= 1] . ( 43 sec) [ -11389.4876] [ 1597] [depth= 1] . ( 46 sec) [ -11388.0004] [ 1597] [depth= 2] . ( 47 sec) [ -11384.9246] [ 1596] [depth= 2] . ( 48 sec) [ -11371.1638] [Branch lengths ] . ( 51 sec) [ -11370.6774] [GTR parameters ] . ( 51 sec) [ -11370.6619] [Alpha ][ 0.253140] . ( 52 sec) [ -11369.7153] [ 1595] [depth= 2] . ( 53 sec) [ -11369.5764] [ 1595] [depth= 1] . ( 54 sec) [ -11368.6216] [ 1595] [depth= 1] . ( 59 sec) [ -11368.2305] [ 1594] [depth= 1] . ( 62 sec) [ -11368.0795] [ 1593] [depth= 1] . ( 70 sec) [ -11367.9688] [ 1595] [depth= 1] . ( 74 sec) [ -11367.8865] [ 1595] [depth= 1] . ( 76 sec) [ -11366.6968] [Branch lengths ] . ( 78 sec) [ -11366.6452] [GTR parameters ] . ( 79 sec) [ -11366.6429] [Alpha ][ 0.253953] . ( 97 sec) [ -11366.5666] [ 1593] [depth= 1] . ( 103 sec) [ -11366.3552] [Branch lengths ] . ( 104 sec) [ -11366.3552] [GTR parameters ] . ( 104 sec) [ -11366.3551] [Alpha ][ 0.254207] . ( 191 sec) [ -11366.3422] [Branch lengths ] . ( 191 sec) [ -11366.3422] [Topology ] . ( 193 sec) [ -11366.3411] [Topology ] . ( 195 sec) [ -11366.3406] [Topology ] . ( 196 sec) [ -11366.3406] [GTR parameters ] . ( 196 sec) [ -11366.3406] [Alpha ][ 0.254207] . ( 196 sec) [ -11366.3406] [Topology ] . ( 198 sec) [ -11366.3404] [Topology ] . ( 199 sec) [ -11366.3386] [GTR parameters ] . ( 199 sec) [ -11366.3386] [Alpha ][ 0.253953] . ( 199 sec) [ -11366.3386] [Topology ] . ( 202 sec) [ -11366.3384] [Topology ] . ( 202 sec) [ -11366.3383] [GTR parameters ] . ( 203 sec) [ -11366.3383] [Alpha ][ 0.253953] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11366.338339. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22928.7231] [GTR parameters ] . ( 3 sec) [ -22434.2095] [Alpha ][ 0.500960] . ( 3 sec) [ -22345.3853] [ 3228] [depth= 10] . ( 3 sec) [ -22196.0973] [ 3208] [depth= 9] . ( 3 sec) [ -22012.0057] [ 3174] [depth= 7] . ( 3 sec) [ -21792.7679] [ 3136] [depth= 1] . ( 3 sec) [ -21666.4036] [ 3125] [depth= 6] . ( 3 sec) [ -21401.9646] [ 3102] [depth= 7] . ( 4 sec) [ -21367.9878] [ 3095] [depth= 1] . ( 4 sec) [ -21214.3540] [ 3055] [depth= 11] . ( 4 sec) [ -21205.0563] [ 3059] [depth= 1] . ( 4 sec) [ -21166.0640] [ 3053] [depth= 6] . ( 4 sec) [ -21156.8711] [ 3048] [depth= 2] . ( 4 sec) [ -21061.7114] [ 3047] [depth= 8] . ( 4 sec) [ -21021.4951] [ 3043] [depth= 4] . ( 5 sec) [ -21008.8385] [ 3042] [depth= 2] . ( 5 sec) [ -20911.4445] [ 3035] [depth= 2] . ( 5 sec) [ -20691.0046] [ 3037] [depth= 6] . ( 5 sec) [ -20689.7302] [ 3039] [depth= 1] . ( 5 sec) [ -20631.2540] [ 3031] [depth= 3] . ( 5 sec) [ -20455.1756] [ 2985] [depth= 18] . ( 5 sec) [ -20437.5764] [ 2980] [depth= 2] . ( 5 sec) [ -20396.1638] [ 2976] [depth= 18] . ( 5 sec) [ -20166.5487] [ 2970] [depth= 4] . ( 5 sec) [ -20093.8518] [ 2962] [depth= 11] . ( 6 sec) [ -19990.2507] [ 2926] [depth= 1] . ( 6 sec) [ -19822.1575] [ 2906] [depth= 16] . ( 6 sec) [ -19788.8486] [ 2899] [depth= 1] . ( 6 sec) [ -19764.4310] [ 2878] [depth= 6] . ( 6 sec) [ -19584.2546] [ 2875] [depth= 3] . ( 6 sec) [ -19438.6222] [ 2840] [depth= 1] . ( 6 sec) [ -19387.6970] [ 2838] [depth= 10] . ( 6 sec) [ -18998.8077] [ 2777] [depth= 13] . ( 7 sec) [ -18548.4563] [ 2770] [depth= 9] . ( 7 sec) [ -18408.2443] [ 2725] [depth= 14] . ( 7 sec) [ -18390.2374] [ 2727] [depth= 4] . ( 7 sec) [ -18367.4810] [ 2727] [depth= 3] . ( 7 sec) [ -18316.6027] [ 2720] [depth= 8] . ( 7 sec) [ -18247.4147] [ 2715] [depth= 1] . ( 7 sec) [ -17783.2849] [ 2653] [depth= 18] . ( 7 sec) [ -17612.0268] [ 2640] [depth= 13] . ( 8 sec) [ -17529.0588] [ 2591] [depth= 14] . ( 8 sec) [ -17401.1672] [ 2573] [depth= 1] . ( 8 sec) [ -17241.9573] [ 2561] [depth= 6] . ( 8 sec) [ -17202.4359] [ 2548] [depth= 1] . ( 8 sec) [ -17149.3718] [ 2537] [depth= 4] . ( 8 sec) [ -16996.3845] [ 2525] [depth= 9] . ( 8 sec) [ -16925.6613] [ 2505] [depth= 6] . ( 8 sec) [ -16902.8390] [ 2502] [depth= 1] . ( 9 sec) [ -16817.6962] [ 2482] [depth= 14] . ( 9 sec) [ -16791.5378] [ 2484] [depth= 2] . ( 9 sec) [ -16754.3356] [ 2482] [depth= 7] . ( 9 sec) [ -16419.8161] [ 2439] [depth= 18] . ( 9 sec) [ -16357.2818] [ 2435] [depth= 18] . ( 9 sec) [ -16331.1860] [ 2431] [depth= 9] . ( 9 sec) [ -16203.3621] [ 2393] [depth= 16] . ( 10 sec) [ -16192.6202] [ 2390] [depth= 1] . ( 10 sec) [ -16056.2065] [ 2375] [depth= 8] . ( 10 sec) [ -16018.8093] [ 2373] [depth= 1] . ( 10 sec) [ -15921.7778] [ 2377] [depth= 1] . ( 10 sec) [ -15875.3225] [ 2373] [depth= 1] . ( 10 sec) [ -15800.8430] [ 2355] [depth= 1] . ( 10 sec) [ -15456.9373] [ 2336] [depth= 4] . ( 10 sec) [ -15279.6281] [ 2337] [depth= 4] . ( 11 sec) [ -15238.2664] [ 2334] [depth= 1] . ( 11 sec) [ -15227.9832] [ 2325] [depth= 5] . ( 11 sec) [ -15222.8165] [ 2325] [depth= 2] . ( 11 sec) [ -15141.1650] [ 2307] [depth= 5] . ( 11 sec) [ -15121.2470] [ 2309] [depth= 1] . ( 11 sec) [ -14926.7284] [ 2297] [depth= 7] . ( 11 sec) [ -14837.6962] [ 2277] [depth= 2] . ( 11 sec) [ -14834.5858] [ 2274] [depth= 7] . ( 12 sec) [ -14758.2136] [ 2253] [depth= 6] . ( 12 sec) [ -14754.0233] [ 2253] [depth= 1] . ( 12 sec) [ -14573.1524] [ 2242] [depth= 11] . ( 12 sec) [ -14557.9167] [ 2236] [depth= 4] . ( 12 sec) [ -14530.9555] [ 2229] [depth= 1] . ( 12 sec) [ -14521.7901] [ 2230] [depth= 2] . ( 12 sec) [ -14438.5395] [ 2222] [depth= 2] . ( 12 sec) [ -14404.3867] [ 2217] [depth= 14] . ( 12 sec) [ -14373.6683] [ 2212] [depth= 1] . ( 13 sec) [ -14323.0415] [ 2201] [depth= 2] . ( 13 sec) [ -14277.5128] [ 2186] [depth= 1] . ( 13 sec) [ -14219.4065] [ 2176] [depth= 6] . ( 13 sec) [ -14208.2348] [ 2175] [depth= 2] . ( 13 sec) [ -14111.9806] [ 2167] [depth= 4] . ( 13 sec) [ -14031.4637] [ 2137] [depth= 7] . ( 14 sec) [ -14013.3465] [ 2131] [depth= 3] . ( 14 sec) [ -13982.6204] [ 2128] [depth= 2] . ( 14 sec) [ -13927.2778] [ 2122] [depth= 5] . ( 14 sec) [ -13925.6470] [ 2123] [depth= 1] . ( 14 sec) [ -13852.3898] [ 2097] [depth= 9] . ( 14 sec) [ -13674.4882] [ 2027] [depth= 4] . ( 14 sec) [ -13639.8076] [ 2019] [depth= 1] . ( 15 sec) [ -13521.6091] [ 2011] [depth= 3] . ( 15 sec) [ -13304.9240] [ 1994] [depth= 1] . ( 15 sec) [ -13290.4675] [ 1992] [depth= 1] . ( 15 sec) [ -13272.3980] [ 1991] [depth= 1] . ( 15 sec) [ -13203.5011] [ 1945] [depth= 4] . ( 15 sec) [ -13186.6179] [ 1941] [depth= 2] . ( 15 sec) [ -13077.6921] [ 1922] [depth= 1] . ( 15 sec) [ -13059.6152] [ 1916] [depth= 2] . ( 15 sec) [ -13033.3475] [ 1914] [depth= 2] . ( 15 sec) [ -13009.7535] [ 1907] [depth= 2] . ( 16 sec) [ -12960.5397] [ 1898] [depth= 9] . ( 16 sec) [ -12904.5260] [ 1895] [depth= 2] . ( 16 sec) [ -12722.2894] [ 1862] [depth= 1] . ( 16 sec) [ -12717.1816] [ 1862] [depth= 1] . ( 16 sec) [ -12692.2393] [ 1857] [depth= 3] . ( 16 sec) [ -12685.1727] [ 1859] [depth= 1] . ( 16 sec) [ -12643.8988] [ 1849] [depth= 4] . ( 16 sec) [ -12629.7443] [ 1845] [depth= 1] . ( 16 sec) [ -12627.4351] [ 1847] [depth= 1] . ( 17 sec) [ -12611.9874] [ 1840] [depth= 2] . ( 17 sec) [ -12582.0542] [ 1830] [depth= 2] . ( 17 sec) [ -12580.6145] [ 1828] [depth= 1] . ( 17 sec) [ -12572.3877] [ 1825] [depth= 1] . ( 17 sec) [ -12465.2273] [ 1799] [depth= 9] . ( 18 sec) [ -12462.0247] [ 1799] [depth= 1] . ( 18 sec) [ -12461.8689] [ 1799] [depth= 1] . ( 18 sec) [ -12456.7789] [ 1799] [depth= 1] . ( 18 sec) [ -12454.9916] [ 1800] [depth= 1] . ( 18 sec) [ -12454.7661] [ 1799] [depth= 2] . ( 18 sec) [ -12451.7239] [ 1795] [depth= 1] . ( 19 sec) [ -12388.5588] [ 1781] [depth= 5] . ( 19 sec) [ -12376.7341] [ 1781] [depth= 2] . ( 19 sec) [ -12371.6410] [ 1781] [depth= 2] . ( 19 sec) [ -12358.5413] [ 1777] [depth= 3] . ( 19 sec) [ -12354.2020] [ 1780] [depth= 3] . ( 20 sec) [ -12298.5995] [ 1771] [depth= 6] . ( 20 sec) [ -12295.4606] [ 1768] [depth= 2] . ( 20 sec) [ -12170.0774] [ 1772] [depth= 3] . ( 20 sec) [ -12166.7133] [ 1769] [depth= 1] . ( 20 sec) [ -12133.0636] [ 1767] [depth= 3] . ( 20 sec) [ -12129.7427] [ 1765] [depth= 1] . ( 21 sec) [ -12127.4876] [ 1760] [depth= 3] . ( 21 sec) [ -12095.0937] [ 1762] [depth= 3] . ( 21 sec) [ -12043.6925] [ 1746] [depth= 1] . ( 21 sec) [ -11997.5655] [ 1732] [depth= 12] . ( 21 sec) [ -11991.7937] [ 1731] [depth= 2] . ( 21 sec) [ -11899.6242] [ 1709] [depth= 2] . ( 21 sec) [ -11894.9591] [ 1708] [depth= 1] . ( 22 sec) [ -11828.3360] [ 1692] [depth= 6] . ( 22 sec) [ -11697.4399] [ 1652] [depth= 2] . ( 22 sec) [ -11694.8343] [ 1652] [depth= 1] . ( 22 sec) [ -11692.4260] [ 1652] [depth= 2] . ( 23 sec) [ -11684.6071] [ 1647] [depth= 2] . ( 23 sec) [ -11681.1099] [ 1648] [depth= 1] . ( 23 sec) [ -11681.0870] [ 1649] [depth= 1] . ( 24 sec) [ -11595.6784] [Branch lengths ] . ( 27 sec) [ -11589.3583] [GTR parameters ] . ( 27 sec) [ -11498.4580] [Alpha ][ 0.250961] . ( 27 sec) [ -11493.0618] [ 1645] [depth= 1] . ( 27 sec) [ -11489.1844] [ 1642] [depth= 2] . ( 27 sec) [ -11489.0168] [ 1639] [depth= 2] . ( 28 sec) [ -11488.9041] [ 1639] [depth= 1] . ( 28 sec) [ -11480.6977] [ 1634] [depth= 3] . ( 28 sec) [ -11474.8533] [ 1629] [depth= 2] . ( 28 sec) [ -11472.7015] [ 1627] [depth= 2] . ( 28 sec) [ -11468.3710] [ 1620] [depth= 1] . ( 28 sec) [ -11463.0850] [ 1619] [depth= 1] . ( 29 sec) [ -11458.3125] [ 1618] [depth= 1] . ( 30 sec) [ -11456.8592] [ 1619] [depth= 2] . ( 30 sec) [ -11449.0790] [ 1615] [depth= 4] . ( 30 sec) [ -11448.9912] [ 1617] [depth= 1] . ( 31 sec) [ -11444.3143] [ 1616] [depth= 1] . ( 33 sec) [ -11436.5883] [ 1613] [depth= 1] . ( 33 sec) [ -11433.7199] [ 1613] [depth= 1] . ( 33 sec) [ -11432.4667] [ 1610] [depth= 3] . ( 35 sec) [ -11427.4267] [ 1609] [depth= 1] . ( 35 sec) [ -11427.2492] [ 1611] [depth= 2] . ( 35 sec) [ -11405.7379] [ 1604] [depth= 2] . ( 35 sec) [ -11405.6953] [ 1605] [depth= 1] . ( 35 sec) [ -11404.0188] [ 1607] [depth= 3] . ( 36 sec) [ -11403.9557] [ 1603] [depth= 4] . ( 36 sec) [ -11402.4552] [ 1603] [depth= 1] . ( 37 sec) [ -11401.2259] [ 1602] [depth= 2] . ( 38 sec) [ -11398.3563] [ 1601] [depth= 1] . ( 39 sec) [ -11397.7685] [ 1602] [depth= 1] . ( 39 sec) [ -11396.3889] [ 1600] [depth= 1] . ( 42 sec) [ -11395.0734] [ 1600] [depth= 1] . ( 44 sec) [ -11389.9468] [ 1602] [depth= 2] . ( 45 sec) [ -11387.3642] [ 1600] [depth= 1] . ( 46 sec) [ -11385.2705] [ 1600] [depth= 1] . ( 46 sec) [ -11378.8985] [ 1596] [depth= 2] . ( 46 sec) [ -11378.8299] [ 1596] [depth= 1] . ( 47 sec) [ -11378.7119] [ 1595] [depth= 1] . ( 49 sec) [ -11367.6719] [Branch lengths ] . ( 52 sec) [ -11367.3099] [GTR parameters ] . ( 52 sec) [ -11367.2947] [Alpha ][ 0.253115] . ( 63 sec) [ -11367.1893] [ 1595] [depth= 1] . ( 79 sec) [ -11366.7651] [Branch lengths ] . ( 81 sec) [ -11366.7639] [GTR parameters ] . ( 81 sec) [ -11366.7639] [Alpha ][ 0.253115] . ( 163 sec) [ -11366.6856] [Branch lengths ] . ( 163 sec) [ -11366.6856] [Topology ] . ( 166 sec) [ -11366.6755] [Topology ] . ( 168 sec) [ -11366.6713] [Topology ] . ( 170 sec) [ -11366.6690] [Topology ] . ( 173 sec) [ -11366.6677] [Topology ] . ( 175 sec) [ -11366.6670] [Topology ] . ( 179 sec) [ -11366.6662] [GTR parameters ] . ( 179 sec) [ -11366.6661] [Alpha ][ 0.252862] . ( 179 sec) [ -11366.6661] [Topology ] . ( 181 sec) [ -11366.6655] [Topology ] . ( 182 sec) [ -11366.6655] [GTR parameters ] . ( 182 sec) [ -11366.6655] [Alpha ][ 0.252862] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11366.665547. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -11816.7722] [GTR parameters ] . ( 5 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 5 sec) [ -11662.0849] [Topology ] . ( 7 sec) [ -11513.5370] [Topology ] . ( 10 sec) [ -11479.6099] [Topology ] . ( 12 sec) [ -11468.4331] [Topology ] . ( 15 sec) [ -11460.4879] [Topology ] . ( 18 sec) [ -11454.4989] [Topology ] . ( 20 sec) [ -11448.0247] [Topology ] . ( 23 sec) [ -11444.6531] [Topology ] . ( 25 sec) [ -11443.4847] [Topology ] . ( 28 sec) [ -11443.3898] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -11443.1080] [Topology ] . ( 48 sec) [ -11441.9514] [GTR parameters ] . ( 49 sec) [ -11364.0125] [Alpha ][ 0.254613] . ( 49 sec) [ -11364.0125] [Topology ] . ( 51 sec) [ -11362.8246] [Topology ] . ( 53 sec) [ -11362.2598] [Topology ] . ( 55 sec) [ -11361.9487] [Topology ] . ( 58 sec) [ -11361.7736] [Topology ] . ( 60 sec) [ -11361.6743] [Topology ] . ( 63 sec) [ -11361.6180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -11361.4064] [GTR parameters ] . ( 81 sec) [ -11361.4060] [Alpha ][ 0.254194] . ( 81 sec) [ -11361.4060] [Topology ] . ( 83 sec) [ -11361.3635] [Topology ] . ( 85 sec) [ -11361.3397] [Topology ] . ( 87 sec) [ -11361.3261] [Topology ] . ( 90 sec) [ -11361.3184] [Topology ] . ( 92 sec) [ -11361.3140] [Topology ] . ( 94 sec) [ -11361.3114] [Topology ] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -11361.3108] [GTR parameters ] . ( 112 sec) [ -11361.3108] [Alpha ][ 0.254194] . ( 112 sec) [ -11361.3108] [Topology ] . ( 114 sec) [ -11361.3092] [Topology ] . ( 117 sec) [ -11361.3083] [Topology ] . Checking for NNIs, optimizing five branches... . ( 133 sec) [ -11361.3083] [GTR parameters ] . ( 134 sec) [ -11361.3083] [Alpha ][ 0.254194] . ( 134 sec) [ -11361.3083] [Topology ] . ( 136 sec) [ -11361.3078] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 174 sec) [ -11816.7722] [GTR parameters ] . ( 175 sec) [ -11662.0849] [Alpha ][ 0.500960] . ( 175 sec) [ -11660.9342] [ 1610] [depth= 1] . ( 176 sec) [ -11660.7720] [ 1610] [depth= 1] . ( 176 sec) [ -11660.6848] [ 1610] [depth= 1] . ( 176 sec) [ -11660.5983] [ 1610] [depth= 1] . ( 176 sec) [ -11660.4280] [ 1610] [depth= 1] . ( 176 sec) [ -11659.1195] [ 1610] [depth= 1] . ( 177 sec) [ -11655.5792] [ 1610] [depth= 1] . ( 177 sec) [ -11653.6958] [ 1610] [depth= 1] . ( 178 sec) [ -11653.5560] [ 1617] [depth= 1] . ( 178 sec) [ -11647.5359] [ 1616] [depth= 1] . ( 178 sec) [ -11646.9829] [ 1618] [depth= 1] . ( 178 sec) [ -11645.8122] [ 1616] [depth= 1] . ( 179 sec) [ -11645.5713] [ 1616] [depth= 3] . ( 179 sec) [ -11642.9865] [ 1615] [depth= 2] . ( 179 sec) [ -11639.1255] [ 1615] [depth= 2] . ( 179 sec) [ -11631.4518] [ 1613] [depth= 1] . ( 179 sec) [ -11630.4177] [ 1613] [depth= 1] . ( 179 sec) [ -11629.4935] [ 1614] [depth= 1] . ( 180 sec) [ -11624.7814] [ 1609] [depth= 1] . ( 180 sec) [ -11624.2745] [ 1608] [depth= 1] . ( 180 sec) [ -11615.9658] [ 1607] [depth= 1] . ( 180 sec) [ -11614.0316] [ 1606] [depth= 1] . ( 181 sec) [ -11611.2085] [ 1605] [depth= 1] . ( 181 sec) [ -11608.8003] [ 1605] [depth= 2] . ( 181 sec) [ -11604.5634] [ 1604] [depth= 1] . ( 181 sec) [ -11603.2791] [ 1603] [depth= 2] . ( 182 sec) [ -11601.4508] [ 1604] [depth= 1] . ( 183 sec) [ -11599.4456] [ 1603] [depth= 1] . ( 183 sec) [ -11593.9885] [ 1602] [depth= 1] . ( 184 sec) [ -11593.7677] [ 1603] [depth= 1] . ( 184 sec) [ -11592.7014] [ 1602] [depth= 1] . ( 184 sec) [ -11590.9106] [ 1603] [depth= 1] . ( 185 sec) [ -11588.4466] [ 1602] [depth= 1] . ( 185 sec) [ -11585.1893] [ 1603] [depth= 1] . ( 186 sec) [ -11584.6804] [ 1605] [depth= 2] . ( 187 sec) [ -11580.7398] [ 1604] [depth= 1] . ( 187 sec) [ -11577.4276] [ 1602] [depth= 1] . ( 187 sec) [ -11576.4872] [ 1604] [depth= 1] . ( 187 sec) [ -11569.0564] [ 1602] [depth= 1] . ( 188 sec) [ -11557.9330] [ 1602] [depth= 1] . ( 189 sec) [ -11556.8586] [ 1603] [depth= 1] . ( 190 sec) [ -11554.2881] [ 1602] [depth= 1] . ( 190 sec) [ -11553.8444] [ 1603] [depth= 2] . ( 190 sec) [ -11552.7902] [ 1602] [depth= 1] . ( 191 sec) [ -11552.7192] [ 1603] [depth= 1] . ( 191 sec) [ -11549.1910] [ 1607] [depth= 1] . ( 192 sec) [ -11548.8773] [ 1609] [depth= 1] . ( 192 sec) [ -11548.2278] [ 1606] [depth= 2] . ( 192 sec) [ -11547.0035] [ 1605] [depth= 2] . ( 192 sec) [ -11544.2710] [ 1602] [depth= 1] . ( 193 sec) [ -11542.9243] [ 1602] [depth= 1] . ( 193 sec) [ -11542.7269] [ 1602] [depth= 1] . ( 193 sec) [ -11541.4706] [ 1601] [depth= 1] . ( 193 sec) [ -11541.3664] [ 1603] [depth= 2] . ( 194 sec) [ -11541.3481] [ 1601] [depth= 2] . ( 194 sec) [ -11538.7603] [ 1601] [depth= 1] . ( 194 sec) [ -11536.8803] [ 1602] [depth= 1] . ( 194 sec) [ -11536.0622] [ 1603] [depth= 1] . ( 195 sec) [ -11531.8166] [ 1605] [depth= 1] . ( 195 sec) [ -11531.0573] [ 1604] [depth= 1] . ( 197 sec) [ -11473.7781] [Branch lengths ] . ( 200 sec) [ -11472.9610] [GTR parameters ] . ( 200 sec) [ -11396.0721] [Alpha ][ 0.250755] . ( 200 sec) [ -11394.9082] [ 1604] [depth= 1] . ( 201 sec) [ -11394.8949] [ 1604] [depth= 1] . ( 201 sec) [ -11388.7926] [ 1597] [depth= 1] . ( 201 sec) [ -11388.4168] [ 1598] [depth= 2] . ( 202 sec) [ -11388.4015] [ 1598] [depth= 1] . ( 202 sec) [ -11388.2976] [ 1598] [depth= 1] . ( 203 sec) [ -11388.0823] [ 1597] [depth= 1] . ( 203 sec) [ -11387.4957] [ 1598] [depth= 1] . ( 203 sec) [ -11385.9593] [ 1597] [depth= 1] . ( 211 sec) [ -11383.9251] [ 1593] [depth= 2] . ( 212 sec) [ -11381.9572] [ 1594] [depth= 1] . ( 214 sec) [ -11381.8798] [ 1596] [depth= 1] . ( 216 sec) [ -11380.8797] [ 1596] [depth= 1] . ( 217 sec) [ -11380.5844] [ 1595] [depth= 1] . ( 218 sec) [ -11380.1731] [ 1593] [depth= 1] . ( 220 sec) [ -11379.4205] [ 1592] [depth= 2] . ( 221 sec) [ -11376.4039] [ 1591] [depth= 3] . ( 222 sec) [ -11375.7895] [ 1591] [depth= 1] . ( 223 sec) [ -11375.2708] [ 1591] [depth= 2] . ( 225 sec) [ -11374.0964] [ 1591] [depth= 1] . ( 226 sec) [ -11372.7319] [ 1591] [depth= 1] . ( 227 sec) [ -11360.7021] [Branch lengths ] . ( 229 sec) [ -11360.3432] [GTR parameters ] . ( 229 sec) [ -11360.3110] [Alpha ][ 0.253994] . ( 230 sec) [ -11360.2823] [ 1591] [depth= 1] . ( 256 sec) [ -11358.6957] [Branch lengths ] . ( 258 sec) [ -11358.6920] [GTR parameters ] . ( 258 sec) [ -11358.6920] [Alpha ][ 0.254247] . ( 285 sec) [ -11358.3436] [Branch lengths ] . ( 375 sec) [ -11358.2721] [Branch lengths ] . ( 375 sec) [ -11358.2721] [Topology ] . ( 378 sec) [ -11358.1921] [Topology ] . ( 381 sec) [ -11358.1054] [Topology ] . ( 383 sec) [ -11358.0932] [Topology ] . ( 385 sec) [ -11358.0893] [Topology ] . ( 388 sec) [ -11358.0875] [Topology ] . ( 390 sec) [ -11358.0866] [Topology ] . ( 392 sec) [ -11358.0798] [GTR parameters ] . ( 393 sec) [ -11358.0798] [Alpha ][ 0.254247] . ( 393 sec) [ -11358.0798] [Topology ] . ( 395 sec) [ -11358.0790] [Topology ] . ( 395 sec) [ -11358.0790] [GTR parameters ] . ( 395 sec) [ -11358.0790] [Alpha ][ 0.254247] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11361.307799 . Log likelihood obtained after SPR moves : -11358.079001 . Log likelihood of the current tree: -11358.079001. . Printing the most likely tree in file 'nucleic_M2845_68x1715_2006.phy_phyml_tree.txt'... . Best log likelihood : -11358.078305 . Time used 0h6m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1375.20user 0.00system 24:59.47elapsed 91%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps