.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data58.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... . 375 patterns found. (out of a total of 500 sites) . 121 sites without polymorphism (24.20%). . [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) [ -14097.1707] [GTR parameters ] . ( 1 sec) [ -13833.7748] [Alpha ][ 0.500960] . ( 1 sec) [ -13649.8236] [ 2794] [depth= 8] . ( 1 sec) [ -13314.7726] [ 2755] [depth= 6] . ( 1 sec) [ -13180.9607] [ 2739] [depth= 4] . ( 1 sec) [ -13168.4038] [ 2733] [depth= 3] . ( 1 sec) [ -13003.3492] [ 2727] [depth= 4] . ( 1 sec) [ -12935.8922] [ 2720] [depth= 4] . ( 1 sec) [ -12668.0673] [ 2694] [depth= 5] . ( 1 sec) [ -12510.8968] [ 2692] [depth= 1] . ( 1 sec) [ -12146.8956] [ 2594] [depth= 14] . ( 1 sec) [ -12063.4501] [ 2542] [depth= 1] . ( 1 sec) [ -11990.8830] [ 2525] [depth= 13] . ( 1 sec) [ -11952.7618] [ 2552] [depth= 4] . ( 1 sec) [ -11909.0077] [ 2486] [depth= 7] . ( 1 sec) [ -11906.7815] [ 2489] [depth= 1] . ( 1 sec) [ -11899.1636] [ 2492] [depth= 2] . ( 1 sec) [ -11877.7623] [ 2489] [depth= 1] . ( 1 sec) [ -11812.9510] [ 2471] [depth= 4] . ( 1 sec) [ -11738.7631] [ 2474] [depth= 5] . ( 1 sec) [ -11567.4266] [ 2422] [depth= 6] . ( 2 sec) [ -11555.9094] [ 2418] [depth= 10] . ( 2 sec) [ -11532.4643] [ 2419] [depth= 1] . ( 2 sec) [ -11467.6519] [ 2396] [depth= 13] . ( 2 sec) [ -11416.3652] [ 2415] [depth= 1] . ( 2 sec) [ -11401.2771] [ 2396] [depth= 1] . ( 2 sec) [ -11141.0254] [ 2289] [depth= 13] . ( 2 sec) [ -11111.3373] [ 2311] [depth= 1] . ( 2 sec) [ -11051.4529] [ 2288] [depth= 11] . ( 2 sec) [ -11023.6477] [ 2268] [depth= 8] . ( 2 sec) [ -10912.5132] [ 2227] [depth= 10] . ( 2 sec) [ -10882.7647] [ 2214] [depth= 5] . ( 2 sec) [ -10855.2913] [ 2213] [depth= 9] . ( 2 sec) [ -10630.7211] [ 2141] [depth= 14] . ( 2 sec) [ -10618.6503] [ 2137] [depth= 1] . ( 2 sec) [ -10406.5808] [ 2083] [depth= 7] . ( 2 sec) [ -10369.3325] [ 2080] [depth= 9] . ( 2 sec) [ -10319.7935] [ 2068] [depth= 8] . ( 2 sec) [ -10140.7908] [ 2030] [depth= 11] . ( 2 sec) [ -10137.8320] [ 2032] [depth= 1] . ( 2 sec) [ -10102.2840] [ 2008] [depth= 1] . ( 2 sec) [ -10050.8050] [ 2005] [depth= 1] . ( 3 sec) [ -10020.2544] [ 2010] [depth= 3] . ( 3 sec) [ -9853.5099] [ 1950] [depth= 4] . ( 3 sec) [ -9674.7553] [ 1892] [depth= 9] . ( 3 sec) [ -9674.0332] [ 1888] [depth= 2] . ( 3 sec) [ -9582.3941] [ 1887] [depth= 6] . ( 3 sec) [ -9518.6917] [ 1857] [depth= 3] . ( 3 sec) [ -9457.9993] [ 1857] [depth= 6] . ( 3 sec) [ -9455.1573] [ 1853] [depth= 1] . ( 3 sec) [ -9440.7320] [ 1862] [depth= 2] . ( 3 sec) [ -9365.1463] [ 1848] [depth= 2] . ( 3 sec) [ -9350.1392] [ 1843] [depth= 2] . ( 3 sec) [ -9207.2857] [ 1800] [depth= 9] . ( 3 sec) [ -9180.1400] [ 1792] [depth= 1] . ( 3 sec) [ -9179.8584] [ 1791] [depth= 2] . ( 3 sec) [ -9177.0777] [ 1794] [depth= 1] . ( 3 sec) [ -9152.6134] [ 1788] [depth= 9] . ( 3 sec) [ -8724.0725] [ 1787] [depth= 1] . ( 3 sec) [ -8491.4691] [ 1745] [depth= 10] . ( 3 sec) [ -8215.5484] [ 1674] [depth= 3] . ( 4 sec) [ -8171.1737] [ 1669] [depth= 7] . ( 4 sec) [ -8126.5170] [ 1645] [depth= 1] . ( 4 sec) [ -8023.5559] [ 1619] [depth= 3] . ( 4 sec) [ -8004.8559] [ 1595] [depth= 1] . ( 4 sec) [ -7879.9147] [ 1560] [depth= 4] . ( 4 sec) [ -7855.0672] [ 1551] [depth= 1] . ( 4 sec) [ -7852.8318] [ 1552] [depth= 5] . ( 4 sec) [ -7830.6320] [ 1541] [depth= 1] . ( 4 sec) [ -7811.0259] [ 1539] [depth= 2] . ( 4 sec) [ -7775.4602] [ 1525] [depth= 2] . ( 4 sec) [ -7592.5889] [ 1461] [depth= 12] . ( 4 sec) [ -7589.9502] [ 1462] [depth= 3] . ( 4 sec) [ -7450.9748] [ 1430] [depth= 6] . ( 4 sec) [ -7449.4105] [ 1430] [depth= 1] . ( 4 sec) [ -7405.5287] [ 1411] [depth= 1] . ( 4 sec) [ -7395.0785] [ 1411] [depth= 3] . ( 4 sec) [ -7365.9664] [ 1421] [depth= 3] . ( 4 sec) [ -7365.5324] [ 1423] [depth= 1] . ( 5 sec) [ -7345.1630] [ 1423] [depth= 4] . ( 5 sec) [ -7289.9346] [ 1411] [depth= 3] . ( 5 sec) [ -7282.1084] [ 1409] [depth= 2] . ( 5 sec) [ -7246.4854] [ 1411] [depth= 1] . ( 5 sec) [ -7234.9763] [ 1412] [depth= 1] . ( 5 sec) [ -7206.5939] [ 1402] [depth= 5] . ( 5 sec) [ -7206.0375] [ 1402] [depth= 1] . ( 5 sec) [ -7195.0526] [ 1402] [depth= 1] . ( 5 sec) [ -7124.2683] [Branch lengths ] . ( 6 sec) [ -7122.2046] [GTR parameters ] . ( 6 sec) [ -7096.8757] [Alpha ][ 0.890562] . ( 6 sec) [ -7096.7043] [ 1402] [depth= 1] . ( 6 sec) [ -7096.4521] [ 1402] [depth= 1] . ( 6 sec) [ -7096.1021] [ 1406] [depth= 1] . ( 6 sec) [ -7071.1511] [ 1383] [depth= 2] . ( 6 sec) [ -7064.8206] [ 1365] [depth= 2] . ( 6 sec) [ -7046.8630] [ 1350] [depth= 3] . ( 6 sec) [ -7041.0822] [ 1343] [depth= 2] . ( 7 sec) [ -7040.8732] [ 1343] [depth= 1] . ( 7 sec) [ -7039.8680] [ 1339] [depth= 2] . ( 7 sec) [ -7039.2029] [ 1341] [depth= 1] . ( 7 sec) [ -7038.0149] [ 1341] [depth= 1] . ( 7 sec) [ -7037.9969] [ 1343] [depth= 1] . ( 7 sec) [ -7036.7515] [ 1342] [depth= 1] . ( 7 sec) [ -7036.3019] [ 1342] [depth= 1] . ( 7 sec) [ -7034.1895] [ 1340] [depth= 1] . ( 7 sec) [ -7030.3518] [ 1338] [depth= 1] . ( 7 sec) [ -7030.0267] [ 1340] [depth= 1] . ( 8 sec) [ -7018.0793] [ 1341] [depth= 2] . ( 8 sec) [ -7016.5590] [ 1342] [depth= 1] . ( 8 sec) [ -7010.5056] [ 1340] [depth= 1] . ( 8 sec) [ -7010.4833] [ 1341] [depth= 1] . ( 9 sec) [ -7009.2934] [ 1342] [depth= 1] . ( 9 sec) [ -7008.9373] [ 1340] [depth= 1] . ( 9 sec) [ -7005.1925] [ 1338] [depth= 2] . ( 9 sec) [ -7003.2426] [ 1339] [depth= 1] . ( 9 sec) [ -7002.5627] [ 1338] [depth= 1] . ( 9 sec) [ -6989.6212] [Branch lengths ] . ( 10 sec) [ -6989.4640] [GTR parameters ] . ( 10 sec) [ -6989.1500] [Alpha ][ 0.954045] . ( 10 sec) [ -6985.4017] [ 1339] [depth= 1] . ( 12 sec) [ -6984.4339] [ 1336] [depth= 1] . ( 12 sec) [ -6984.0556] [ 1339] [depth= 1] . ( 13 sec) [ -6983.4336] [Branch lengths ] . ( 14 sec) [ -6983.4234] [GTR parameters ] . ( 14 sec) [ -6983.4225] [Alpha ][ 0.957560] . ( 18 sec) [ -6983.3980] [Branch lengths ] . ( 31 sec) [ -6983.3841] [ 1336] [depth= 1] . ( 37 sec) [ -6983.3359] [Branch lengths ] . ( 37 sec) [ -6983.3357] [GTR parameters ] . ( 37 sec) [ -6983.3353] [Alpha ][ 0.959961] . ( 37 sec) [ -6983.3353] [Topology ] . ( 38 sec) [ -6983.3322] [Topology ] . ( 39 sec) [ -6983.3316] [Topology ] . ( 39 sec) [ -6983.3315] [GTR parameters ] . ( 39 sec) [ -6983.3315] [Alpha ][ 0.959961] . ( 39 sec) [ -6983.3315] [Topology ] . ( 39 sec) [ -6983.3313] [Topology ] . ( 40 sec) [ -6983.3313] [GTR parameters ] . ( 40 sec) [ -6983.3313] [Alpha ][ 0.959961] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.331321. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14071.2862] [GTR parameters ] . ( 0 sec) [ -13828.5205] [Alpha ][ 0.500960] . ( 0 sec) [ -13675.6549] [ 2782] [depth= 9] . ( 0 sec) [ -13519.6295] [ 2754] [depth= 9] . ( 0 sec) [ -13387.6214] [ 2737] [depth= 3] . ( 0 sec) [ -13267.8477] [ 2730] [depth= 2] . ( 0 sec) [ -13127.2189] [ 2683] [depth= 1] . ( 1 sec) [ -12852.5606] [ 2670] [depth= 6] . ( 1 sec) [ -12552.1884] [ 2640] [depth= 3] . ( 1 sec) [ -12386.8785] [ 2586] [depth= 1] . ( 1 sec) [ -12318.6153] [ 2563] [depth= 5] . ( 1 sec) [ -12091.0585] [ 2537] [depth= 10] . ( 1 sec) [ -12065.4385] [ 2537] [depth= 3] . ( 1 sec) [ -11845.6061] [ 2498] [depth= 5] . ( 1 sec) [ -11681.2276] [ 2503] [depth= 4] . ( 1 sec) [ -11463.1073] [ 2439] [depth= 11] . ( 1 sec) [ -11135.3919] [ 2353] [depth= 16] . ( 1 sec) [ -10901.4071] [ 2281] [depth= 12] . ( 1 sec) [ -10850.2979] [ 2274] [depth= 3] . ( 1 sec) [ -10765.1048] [ 2249] [depth= 1] . ( 1 sec) [ -10710.2244] [ 2200] [depth= 2] . ( 1 sec) [ -10627.8968] [ 2194] [depth= 1] . ( 1 sec) [ -10575.5675] [ 2181] [depth= 4] . ( 1 sec) [ -10564.9793] [ 2185] [depth= 5] . ( 1 sec) [ -10374.2756] [ 2134] [depth= 14] . ( 1 sec) [ -10180.3861] [ 2085] [depth= 5] . ( 1 sec) [ -10124.0756] [ 2087] [depth= 1] . ( 1 sec) [ -10123.2331] [ 2087] [depth= 1] . ( 1 sec) [ -10110.1393] [ 2086] [depth= 1] . ( 1 sec) [ -9747.3324] [ 2015] [depth= 8] . ( 1 sec) [ -9715.7498] [ 2014] [depth= 1] . ( 1 sec) [ -9673.3398] [ 2011] [depth= 3] . ( 2 sec) [ -9626.9163] [ 1988] [depth= 1] . ( 2 sec) [ -9626.2778] [ 1992] [depth= 1] . ( 2 sec) [ -9498.9685] [ 1946] [depth= 1] . ( 2 sec) [ -9367.6166] [ 1914] [depth= 9] . ( 2 sec) [ -9315.0442] [ 1927] [depth= 1] . ( 2 sec) [ -9308.7256] [ 1938] [depth= 3] . ( 2 sec) [ -9166.1766] [ 1921] [depth= 4] . ( 2 sec) [ -9134.1458] [ 1914] [depth= 1] . ( 2 sec) [ -9096.6779] [ 1906] [depth= 5] . ( 2 sec) [ -9072.8293] [ 1902] [depth= 1] . ( 2 sec) [ -9017.4857] [ 1867] [depth= 1] . ( 2 sec) [ -8945.8299] [ 1860] [depth= 3] . ( 2 sec) [ -8810.6445] [ 1799] [depth= 6] . ( 2 sec) [ -8762.8334] [ 1793] [depth= 10] . ( 2 sec) [ -8760.5558] [ 1790] [depth= 1] . ( 2 sec) [ -8705.4272] [ 1814] [depth= 1] . ( 2 sec) [ -8656.5386] [ 1809] [depth= 2] . ( 2 sec) [ -8593.4601] [ 1806] [depth= 1] . ( 2 sec) [ -8428.7099] [ 1749] [depth= 7] . ( 2 sec) [ -8427.4839] [ 1748] [depth= 1] . ( 2 sec) [ -8396.3048] [ 1735] [depth= 3] . ( 2 sec) [ -8296.4576] [ 1729] [depth= 4] . ( 2 sec) [ -8225.9629] [ 1704] [depth= 2] . ( 2 sec) [ -8212.4447] [ 1687] [depth= 2] . ( 2 sec) [ -8203.7896] [ 1687] [depth= 1] . ( 3 sec) [ -8201.7048] [ 1685] [depth= 1] . ( 3 sec) [ -8117.2067] [ 1671] [depth= 4] . ( 3 sec) [ -8115.4570] [ 1670] [depth= 1] . ( 3 sec) [ -8075.8017] [ 1660] [depth= 3] . ( 3 sec) [ -8072.3139] [ 1661] [depth= 2] . ( 3 sec) [ -8026.5793] [ 1644] [depth= 3] . ( 3 sec) [ -7962.8474] [ 1647] [depth= 1] . ( 3 sec) [ -7906.7447] [ 1619] [depth= 5] . ( 3 sec) [ -7899.8542] [ 1616] [depth= 1] . ( 3 sec) [ -7857.2017] [ 1617] [depth= 1] . ( 3 sec) [ -7792.1763] [ 1600] [depth= 5] . ( 3 sec) [ -7788.2927] [ 1584] [depth= 3] . ( 3 sec) [ -7736.9514] [ 1556] [depth= 2] . ( 3 sec) [ -7696.2735] [ 1545] [depth= 2] . ( 3 sec) [ -7670.8581] [ 1521] [depth= 1] . ( 3 sec) [ -7664.3498] [ 1518] [depth= 1] . ( 3 sec) [ -7616.8957] [ 1507] [depth= 5] . ( 3 sec) [ -7557.5321] [ 1491] [depth= 1] . ( 3 sec) [ -7556.3096] [ 1489] [depth= 1] . ( 3 sec) [ -7543.7269] [ 1482] [depth= 2] . ( 3 sec) [ -7538.2825] [ 1485] [depth= 1] . ( 4 sec) [ -7535.0327] [ 1484] [depth= 3] . ( 4 sec) [ -7524.7838] [ 1482] [depth= 2] . ( 4 sec) [ -7403.4321] [ 1447] [depth= 1] . ( 4 sec) [ -7351.8473] [ 1419] [depth= 1] . ( 4 sec) [ -7351.6504] [ 1415] [depth= 2] . ( 4 sec) [ -7349.0940] [ 1416] [depth= 1] . ( 4 sec) [ -7328.2141] [ 1414] [depth= 1] . ( 4 sec) [ -7264.8784] [ 1395] [depth= 1] . ( 4 sec) [ -7167.4560] [Branch lengths ] . ( 5 sec) [ -7166.2269] [GTR parameters ] . ( 5 sec) [ -7141.3067] [Alpha ][ 0.889972] . ( 5 sec) [ -7104.7124] [ 1379] [depth= 1] . ( 5 sec) [ -7104.3618] [ 1379] [depth= 1] . ( 5 sec) [ -7056.0223] [ 1359] [depth= 2] . ( 5 sec) [ -7022.7067] [ 1350] [depth= 1] . ( 5 sec) [ -7022.6961] [ 1350] [depth= 1] . ( 5 sec) [ -7004.8558] [ 1340] [depth= 1] . ( 5 sec) [ -7004.7101] [ 1339] [depth= 1] . ( 5 sec) [ -7004.2219] [ 1341] [depth= 1] . ( 6 sec) [ -7004.1286] [ 1340] [depth= 1] . ( 6 sec) [ -6999.2816] [ 1338] [depth= 1] . ( 6 sec) [ -6995.8826] [ 1337] [depth= 1] . ( 6 sec) [ -6994.9160] [ 1337] [depth= 1] . ( 6 sec) [ -6994.2946] [ 1338] [depth= 1] . ( 6 sec) [ -6994.0044] [ 1339] [depth= 1] . ( 7 sec) [ -6993.6921] [ 1342] [depth= 1] . ( 7 sec) [ -6993.5023] [ 1341] [depth= 1] . ( 7 sec) [ -6993.4596] [ 1341] [depth= 1] . ( 7 sec) [ -6993.3299] [ 1340] [depth= 2] . ( 8 sec) [ -6991.7573] [ 1339] [depth= 1] . ( 8 sec) [ -6989.9391] [ 1341] [depth= 1] . ( 8 sec) [ -6984.1218] [Branch lengths ] . ( 9 sec) [ -6983.9262] [GTR parameters ] . ( 9 sec) [ -6983.6070] [Alpha ][ 0.954078] . ( 13 sec) [ -6983.4528] [Branch lengths ] . ( 28 sec) [ -6983.4420] [ 1338] [depth= 1] . ( 31 sec) [ -6983.3931] [Branch lengths ] . ( 31 sec) [ -6983.3927] [GTR parameters ] . ( 31 sec) [ -6983.3893] [Alpha ][ 0.961069] . ( 31 sec) [ -6983.3893] [Topology ] . ( 32 sec) [ -6983.3854] [Topology ] . ( 33 sec) [ -6983.3843] [Topology ] . ( 33 sec) [ -6983.3838] [Topology ] . ( 34 sec) [ -6983.3838] [GTR parameters ] . ( 34 sec) [ -6983.3838] [Alpha ][ 0.962031] . ( 34 sec) [ -6983.3838] [Topology ] . ( 34 sec) [ -6983.3836] [Topology ] . ( 34 sec) [ -6983.3836] [GTR parameters ] . ( 35 sec) [ -6983.3836] [Alpha ][ 0.962031] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -6983.3824] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.382402. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14737.5144] [GTR parameters ] . ( 0 sec) [ -14456.1301] [Alpha ][ 0.500960] . ( 1 sec) [ -14408.5007] [ 2868] [depth= 4] . ( 1 sec) [ -14189.2312] [ 2833] [depth= 8] . ( 1 sec) [ -14094.3749] [ 2827] [depth= 4] . ( 1 sec) [ -14073.4954] [ 2827] [depth= 1] . ( 1 sec) [ -14006.2217] [ 2795] [depth= 8] . ( 1 sec) [ -13969.3010] [ 2791] [depth= 2] . ( 1 sec) [ -13880.0975] [ 2788] [depth= 14] . ( 1 sec) [ -13833.5966] [ 2773] [depth= 4] . ( 1 sec) [ -13562.1590] [ 2742] [depth= 2] . ( 1 sec) [ -13453.7351] [ 2755] [depth= 10] . ( 1 sec) [ -13357.7290] [ 2721] [depth= 9] . ( 1 sec) [ -13325.2090] [ 2719] [depth= 1] . ( 1 sec) [ -13140.2716] [ 2690] [depth= 3] . ( 1 sec) [ -13095.5888] [ 2684] [depth= 7] . ( 1 sec) [ -13019.2211] [ 2680] [depth= 1] . ( 1 sec) [ -12873.1847] [ 2623] [depth= 8] . ( 1 sec) [ -12749.6783] [ 2624] [depth= 2] . ( 1 sec) [ -12451.7145] [ 2569] [depth= 7] . ( 1 sec) [ -12440.0981] [ 2569] [depth= 1] . ( 1 sec) [ -12298.1496] [ 2545] [depth= 8] . ( 1 sec) [ -11980.8269] [ 2466] [depth= 1] . ( 1 sec) [ -11887.4957] [ 2457] [depth= 8] . ( 1 sec) [ -11789.4725] [ 2427] [depth= 3] . ( 1 sec) [ -11768.6882] [ 2424] [depth= 8] . ( 1 sec) [ -11745.2155] [ 2410] [depth= 5] . ( 1 sec) [ -11668.5185] [ 2370] [depth= 1] . ( 2 sec) [ -11584.7379] [ 2358] [depth= 5] . ( 2 sec) [ -11575.7076] [ 2362] [depth= 1] . ( 2 sec) [ -11491.6951] [ 2352] [depth= 8] . ( 2 sec) [ -11138.5410] [ 2258] [depth= 9] . ( 2 sec) [ -11118.2539] [ 2281] [depth= 8] . ( 2 sec) [ -11037.8124] [ 2276] [depth= 2] . ( 2 sec) [ -10969.8227] [ 2304] [depth= 2] . ( 2 sec) [ -10686.0241] [ 2211] [depth= 3] . ( 2 sec) [ -10642.7271] [ 2192] [depth= 3] . ( 2 sec) [ -10132.0572] [ 2149] [depth= 7] . ( 2 sec) [ -10096.1041] [ 2128] [depth= 3] . ( 2 sec) [ -9738.7720] [ 2071] [depth= 1] . ( 2 sec) [ -9695.3245] [ 2053] [depth= 6] . ( 2 sec) [ -9601.1465] [ 2008] [depth= 6] . ( 2 sec) [ -9423.9551] [ 1943] [depth= 5] . ( 2 sec) [ -9405.5452] [ 1931] [depth= 1] . ( 2 sec) [ -9270.5155] [ 1874] [depth= 1] . ( 2 sec) [ -9174.2880] [ 1866] [depth= 3] . ( 2 sec) [ -9148.1140] [ 1864] [depth= 2] . ( 2 sec) [ -8948.7832] [ 1811] [depth= 2] . ( 2 sec) [ -8940.2632] [ 1809] [depth= 1] . ( 2 sec) [ -8890.0383] [ 1789] [depth= 5] . ( 2 sec) [ -8870.5772] [ 1800] [depth= 1] . ( 3 sec) [ -8803.5334] [ 1770] [depth= 6] . ( 3 sec) [ -8692.4466] [ 1713] [depth= 8] . ( 3 sec) [ -8624.7433] [ 1707] [depth= 2] . ( 3 sec) [ -8525.4667] [ 1707] [depth= 2] . ( 3 sec) [ -8373.2030] [ 1674] [depth= 2] . ( 3 sec) [ -8372.9087] [ 1678] [depth= 2] . ( 3 sec) [ -8255.5295] [ 1660] [depth= 5] . ( 3 sec) [ -8251.9959] [ 1663] [depth= 12] . ( 3 sec) [ -8248.4495] [ 1666] [depth= 2] . ( 3 sec) [ -8215.8055] [ 1647] [depth= 3] . ( 3 sec) [ -8203.5223] [ 1641] [depth= 1] . ( 3 sec) [ -8150.8319] [ 1623] [depth= 4] . ( 3 sec) [ -8150.5949] [ 1625] [depth= 1] . ( 3 sec) [ -8145.3349] [ 1623] [depth= 10] . ( 3 sec) [ -8100.0894] [ 1611] [depth= 1] . ( 3 sec) [ -8068.7826] [ 1597] [depth= 7] . ( 3 sec) [ -8058.6081] [ 1594] [depth= 3] . ( 3 sec) [ -8052.3874] [ 1588] [depth= 1] . ( 3 sec) [ -7917.4492] [ 1557] [depth= 3] . ( 4 sec) [ -7913.3031] [ 1559] [depth= 1] . ( 4 sec) [ -7767.1723] [ 1521] [depth= 6] . ( 4 sec) [ -7739.2225] [ 1511] [depth= 2] . ( 4 sec) [ -7724.7466] [ 1501] [depth= 1] . ( 4 sec) [ -7403.0404] [ 1427] [depth= 8] . ( 4 sec) [ -7327.6965] [ 1404] [depth= 2] . ( 4 sec) [ -7324.3457] [ 1407] [depth= 1] . ( 4 sec) [ -7319.8493] [ 1407] [depth= 1] . ( 4 sec) [ -7266.2454] [ 1391] [depth= 2] . ( 4 sec) [ -7262.2944] [ 1389] [depth= 1] . ( 4 sec) [ -7260.9308] [ 1387] [depth= 1] . ( 4 sec) [ -7218.3678] [ 1377] [depth= 2] . ( 4 sec) [ -7217.1505] [ 1376] [depth= 1] . ( 4 sec) [ -7195.5917] [ 1380] [depth= 1] . ( 4 sec) [ -7191.5910] [ 1378] [depth= 1] . ( 4 sec) [ -7179.6382] [ 1372] [depth= 1] . ( 4 sec) [ -7087.8251] [Branch lengths ] . ( 5 sec) [ -7084.7282] [GTR parameters ] . ( 5 sec) [ -7058.6782] [Alpha ][ 0.908228] . ( 5 sec) [ -7058.2624] [ 1367] [depth= 2] . ( 5 sec) [ -7030.2955] [ 1356] [depth= 1] . ( 5 sec) [ -7023.6000] [ 1353] [depth= 1] . ( 5 sec) [ -7021.6147] [ 1349] [depth= 1] . ( 5 sec) [ -7021.6017] [ 1349] [depth= 1] . ( 5 sec) [ -7015.5681] [ 1349] [depth= 2] . ( 5 sec) [ -7014.4076] [ 1348] [depth= 1] . ( 6 sec) [ -7014.1252] [ 1349] [depth= 1] . ( 6 sec) [ -6996.7056] [ 1337] [depth= 1] . ( 6 sec) [ -6996.6139] [ 1337] [depth= 1] . ( 6 sec) [ -6995.3366] [ 1339] [depth= 1] . ( 6 sec) [ -6994.1903] [ 1339] [depth= 1] . ( 6 sec) [ -6991.7575] [ 1341] [depth= 1] . ( 7 sec) [ -6990.8829] [ 1342] [depth= 1] . ( 7 sec) [ -6990.2995] [ 1340] [depth= 1] . ( 7 sec) [ -6990.0588] [ 1340] [depth= 1] . ( 7 sec) [ -6989.8797] [ 1339] [depth= 1] . ( 8 sec) [ -6989.2021] [ 1339] [depth= 1] . ( 9 sec) [ -6989.1862] [ 1340] [depth= 1] . ( 9 sec) [ -6984.6320] [Branch lengths ] . ( 10 sec) [ -6984.5381] [GTR parameters ] . ( 10 sec) [ -6984.3766] [Alpha ][ 0.954504] . ( 10 sec) [ -6984.1079] [ 1339] [depth= 1] . ( 13 sec) [ -6983.7565] [ 1340] [depth= 1] . ( 15 sec) [ -6983.4618] [Branch lengths ] . ( 15 sec) [ -6983.4223] [GTR parameters ] . ( 16 sec) [ -6983.4216] [Alpha ][ 0.957622] . ( 35 sec) [ -6983.3978] [Branch lengths ] . ( 35 sec) [ -6983.3978] [Topology ] . ( 35 sec) [ -6983.3955] [Topology ] . ( 36 sec) [ -6983.3947] [Topology ] . ( 36 sec) [ -6983.3947] [GTR parameters ] . ( 36 sec) [ -6983.3943] [Alpha ][ 0.959866] . ( 36 sec) [ -6983.3943] [Topology ] . ( 37 sec) [ -6983.3938] [Topology ] . ( 37 sec) [ -6983.3938] [GTR parameters ] . ( 37 sec) [ -6983.3938] [Alpha ][ 0.959866] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -6983.3327] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.332707. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -13953.0272] [GTR parameters ] . ( 1 sec) [ -13724.2115] [Alpha ][ 0.500960] . ( 1 sec) [ -13533.5081] [ 2777] [depth= 8] . ( 1 sec) [ -13305.0549] [ 2743] [depth= 8] . ( 1 sec) [ -13137.1781] [ 2724] [depth= 7] . ( 1 sec) [ -13121.3907] [ 2678] [depth= 1] . ( 1 sec) [ -12988.3915] [ 2666] [depth= 5] . ( 1 sec) [ -12918.7813] [ 2655] [depth= 3] . ( 1 sec) [ -12874.0807] [ 2651] [depth= 4] . ( 1 sec) [ -12817.0617] [ 2633] [depth= 1] . ( 1 sec) [ -12759.3185] [ 2627] [depth= 3] . ( 1 sec) [ -12661.8971] [ 2616] [depth= 11] . ( 1 sec) [ -12589.6047] [ 2595] [depth= 14] . ( 1 sec) [ -12478.4914] [ 2568] [depth= 10] . ( 1 sec) [ -12377.9757] [ 2568] [depth= 1] . ( 2 sec) [ -12324.7901] [ 2556] [depth= 9] . ( 2 sec) [ -12290.9310] [ 2552] [depth= 2] . ( 2 sec) [ -12249.5371] [ 2541] [depth= 2] . ( 2 sec) [ -12208.9730] [ 2539] [depth= 6] . ( 2 sec) [ -12137.5647] [ 2500] [depth= 5] . ( 2 sec) [ -11832.6807] [ 2441] [depth= 7] . ( 2 sec) [ -11676.9032] [ 2435] [depth= 6] . ( 2 sec) [ -11671.0328] [ 2435] [depth= 5] . ( 2 sec) [ -11516.4401] [ 2401] [depth= 16] . ( 2 sec) [ -11496.2032] [ 2401] [depth= 1] . ( 2 sec) [ -11401.8536] [ 2388] [depth= 2] . ( 2 sec) [ -11390.2129] [ 2375] [depth= 3] . ( 2 sec) [ -11311.0010] [ 2323] [depth= 18] . ( 2 sec) [ -11241.1203] [ 2294] [depth= 5] . ( 2 sec) [ -11109.2559] [ 2260] [depth= 2] . ( 2 sec) [ -10988.8024] [ 2245] [depth= 3] . ( 2 sec) [ -10904.8039] [ 2188] [depth= 13] . ( 2 sec) [ -10606.6290] [ 2177] [depth= 2] . ( 2 sec) [ -10593.6463] [ 2162] [depth= 1] . ( 2 sec) [ -10437.3908] [ 2142] [depth= 1] . ( 2 sec) [ -10102.8283] [ 2048] [depth= 10] . ( 2 sec) [ -10068.8545] [ 2021] [depth= 2] . ( 2 sec) [ -10020.4692] [ 1979] [depth= 1] . ( 2 sec) [ -9588.9279] [ 1901] [depth= 11] . ( 2 sec) [ -9572.5956] [ 1898] [depth= 1] . ( 2 sec) [ -9561.2309] [ 1885] [depth= 2] . ( 2 sec) [ -9543.6646] [ 1883] [depth= 8] . ( 3 sec) [ -9536.4381] [ 1883] [depth= 1] . ( 3 sec) [ -9525.2755] [ 1886] [depth= 1] . ( 3 sec) [ -9481.8670] [ 1878] [depth= 8] . ( 3 sec) [ -9468.2126] [ 1867] [depth= 5] . ( 3 sec) [ -9298.5041] [ 1827] [depth= 8] . ( 3 sec) [ -9276.1085] [ 1827] [depth= 1] . ( 3 sec) [ -9265.2236] [ 1824] [depth= 1] . ( 3 sec) [ -9187.0078] [ 1836] [depth= 1] . ( 3 sec) [ -9077.4472] [ 1799] [depth= 8] . ( 3 sec) [ -8925.2185] [ 1809] [depth= 3] . ( 3 sec) [ -8916.8950] [ 1813] [depth= 3] . ( 3 sec) [ -8711.4150] [ 1804] [depth= 2] . ( 3 sec) [ -8692.0750] [ 1808] [depth= 8] . ( 3 sec) [ -8664.7293] [ 1810] [depth= 1] . ( 3 sec) [ -8632.9162] [ 1789] [depth= 3] . ( 3 sec) [ -8489.1231] [ 1729] [depth= 3] . ( 3 sec) [ -8462.6164] [ 1727] [depth= 2] . ( 3 sec) [ -8383.0808] [ 1713] [depth= 4] . ( 3 sec) [ -8365.9016] [ 1701] [depth= 1] . ( 3 sec) [ -8166.8436] [ 1646] [depth= 2] . ( 3 sec) [ -8052.5544] [ 1622] [depth= 4] . ( 3 sec) [ -8050.8157] [ 1622] [depth= 2] . ( 3 sec) [ -8046.3979] [ 1616] [depth= 3] . ( 3 sec) [ -8045.3838] [ 1613] [depth= 1] . ( 4 sec) [ -8041.9217] [ 1610] [depth= 1] . ( 4 sec) [ -8016.9533] [ 1586] [depth= 2] . ( 4 sec) [ -7827.6008] [ 1530] [depth= 1] . ( 4 sec) [ -7823.7209] [ 1527] [depth= 1] . ( 4 sec) [ -7709.5777] [ 1521] [depth= 3] . ( 4 sec) [ -7647.4684] [ 1487] [depth= 1] . ( 4 sec) [ -7505.2778] [ 1451] [depth= 4] . ( 4 sec) [ -7472.7520] [ 1447] [depth= 2] . ( 4 sec) [ -7472.3624] [ 1447] [depth= 1] . ( 4 sec) [ -7460.2715] [ 1446] [depth= 1] . ( 4 sec) [ -7444.4286] [ 1443] [depth= 3] . ( 4 sec) [ -7352.0179] [ 1408] [depth= 2] . ( 4 sec) [ -7351.7031] [ 1408] [depth= 1] . ( 4 sec) [ -7349.8605] [ 1406] [depth= 1] . ( 4 sec) [ -7341.0397] [ 1403] [depth= 2] . ( 4 sec) [ -7335.8482] [ 1401] [depth= 2] . ( 4 sec) [ -7334.2920] [ 1401] [depth= 1] . ( 4 sec) [ -7332.9480] [ 1402] [depth= 1] . ( 4 sec) [ -7256.5155] [ 1376] [depth= 7] . ( 5 sec) [ -7242.9350] [ 1376] [depth= 1] . ( 5 sec) [ -7164.1726] [ 1360] [depth= 3] . ( 5 sec) [ -7096.9165] [Branch lengths ] . ( 5 sec) [ -7095.1817] [GTR parameters ] . ( 5 sec) [ -7068.8845] [Alpha ][ 0.914442] . ( 5 sec) [ -7068.8544] [ 1361] [depth= 1] . ( 6 sec) [ -7043.7608] [ 1354] [depth= 1] . ( 6 sec) [ -7043.7384] [ 1354] [depth= 1] . ( 6 sec) [ -6999.2837] [ 1341] [depth= 1] . ( 6 sec) [ -6997.4445] [ 1341] [depth= 1] . ( 6 sec) [ -6997.2411] [ 1341] [depth= 1] . ( 6 sec) [ -6997.0896] [ 1341] [depth= 1] . ( 7 sec) [ -6995.2071] [ 1340] [depth= 1] . ( 7 sec) [ -6994.9789] [ 1340] [depth= 1] . ( 7 sec) [ -6994.4403] [ 1340] [depth= 1] . ( 7 sec) [ -6992.4423] [ 1337] [depth= 1] . ( 7 sec) [ -6992.3596] [ 1338] [depth= 1] . ( 7 sec) [ -6991.7024] [ 1339] [depth= 1] . ( 7 sec) [ -6990.9953] [ 1338] [depth= 1] . ( 7 sec) [ -6989.9917] [ 1339] [depth= 1] . ( 8 sec) [ -6989.3075] [ 1337] [depth= 1] . ( 8 sec) [ -6988.8936] [ 1340] [depth= 1] . ( 8 sec) [ -6988.5671] [ 1340] [depth= 1] . ( 9 sec) [ -6988.3239] [ 1341] [depth= 1] . ( 9 sec) [ -6984.7440] [Branch lengths ] . ( 9 sec) [ -6984.5415] [GTR parameters ] . ( 10 sec) [ -6984.4035] [Alpha ][ 0.957403] . ( 10 sec) [ -6984.2675] [ 1340] [depth= 1] . ( 13 sec) [ -6983.4389] [Branch lengths ] . ( 14 sec) [ -6983.4313] [GTR parameters ] . ( 14 sec) [ -6983.4312] [Alpha ][ 0.958521] . ( 32 sec) [ -6983.3964] [Branch lengths ] . ( 32 sec) [ -6983.3964] [Topology ] . ( 33 sec) [ -6983.3947] [Topology ] . ( 34 sec) [ -6983.3941] [Topology ] . ( 34 sec) [ -6983.3941] [GTR parameters ] . ( 34 sec) [ -6983.3939] [Alpha ][ 0.960009] . ( 34 sec) [ -6983.3939] [Topology ] . ( 34 sec) [ -6983.3937] [Topology ] . ( 34 sec) [ -6983.3937] [GTR parameters ] . ( 35 sec) [ -6983.3937] [Alpha ][ 0.960009] . Checking for NNIs, optimizing five branches... . ( 40 sec) [ -6983.3325] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.332512. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -14251.4103] [GTR parameters ] . ( 0 sec) [ -14015.8998] [Alpha ][ 0.500960] . ( 1 sec) [ -13844.1381] [ 2820] [depth= 4] . ( 1 sec) [ -13689.7168] [ 2780] [depth= 10] . ( 1 sec) [ -13602.0083] [ 2769] [depth= 4] . ( 1 sec) [ -13581.5743] [ 2768] [depth= 2] . ( 1 sec) [ -13467.9656] [ 2764] [depth= 10] . ( 1 sec) [ -13418.4996] [ 2765] [depth= 2] . ( 1 sec) [ -13405.5890] [ 2763] [depth= 3] . ( 1 sec) [ -13321.3222] [ 2759] [depth= 1] . ( 1 sec) [ -13181.2232] [ 2730] [depth= 4] . ( 1 sec) [ -13035.8150] [ 2703] [depth= 8] . ( 1 sec) [ -12729.5209] [ 2594] [depth= 7] . ( 1 sec) [ -12604.8996] [ 2593] [depth= 1] . ( 1 sec) [ -12486.0819] [ 2547] [depth= 12] . ( 1 sec) [ -12463.0415] [ 2555] [depth= 5] . ( 1 sec) [ -12419.2163] [ 2558] [depth= 9] . ( 1 sec) [ -12313.4561] [ 2556] [depth= 1] . ( 1 sec) [ -12229.4722] [ 2548] [depth= 11] . ( 1 sec) [ -12161.2983] [ 2537] [depth= 12] . ( 1 sec) [ -12131.1045] [ 2534] [depth= 1] . ( 1 sec) [ -11939.2883] [ 2513] [depth= 10] . ( 1 sec) [ -11428.4553] [ 2410] [depth= 8] . ( 1 sec) [ -11316.2761] [ 2408] [depth= 5] . ( 1 sec) [ -11064.9207] [ 2338] [depth= 4] . ( 1 sec) [ -11013.4170] [ 2327] [depth= 4] . ( 1 sec) [ -10737.0445] [ 2326] [depth= 3] . ( 1 sec) [ -10651.3397] [ 2277] [depth= 10] . ( 1 sec) [ -10491.7121] [ 2234] [depth= 12] . ( 2 sec) [ -10480.9535] [ 2233] [depth= 1] . ( 2 sec) [ -10351.2811] [ 2205] [depth= 6] . ( 2 sec) [ -10350.5138] [ 2205] [depth= 1] . ( 2 sec) [ -10257.7743] [ 2182] [depth= 13] . ( 2 sec) [ -10226.3338] [ 2156] [depth= 1] . ( 2 sec) [ -10137.8004] [ 2138] [depth= 10] . ( 2 sec) [ -10116.1189] [ 2123] [depth= 7] . ( 2 sec) [ -10092.6178] [ 2111] [depth= 1] . ( 2 sec) [ -10043.7111] [ 2104] [depth= 8] . ( 2 sec) [ -10033.5413] [ 2085] [depth= 6] . ( 2 sec) [ -9883.6478] [ 2088] [depth= 1] . ( 2 sec) [ -9866.8268] [ 2085] [depth= 1] . ( 2 sec) [ -9553.6420] [ 1965] [depth= 8] . ( 2 sec) [ -9488.6670] [ 1964] [depth= 7] . ( 2 sec) [ -9417.4461] [ 1945] [depth= 2] . ( 2 sec) [ -9202.1255] [ 1875] [depth= 7] . ( 2 sec) [ -9153.2250] [ 1856] [depth= 1] . ( 2 sec) [ -9052.8553] [ 1827] [depth= 7] . ( 2 sec) [ -8979.3165] [ 1825] [depth= 2] . ( 2 sec) [ -8936.8921] [ 1811] [depth= 2] . ( 2 sec) [ -8861.5872] [ 1793] [depth= 3] . ( 2 sec) [ -8653.3240] [ 1740] [depth= 8] . ( 2 sec) [ -8602.0544] [ 1726] [depth= 4] . ( 3 sec) [ -8472.7607] [ 1697] [depth= 2] . ( 3 sec) [ -8456.7114] [ 1695] [depth= 2] . ( 3 sec) [ -8273.6730] [ 1601] [depth= 8] . ( 3 sec) [ -8242.9361] [ 1599] [depth= 2] . ( 3 sec) [ -8202.7737] [ 1622] [depth= 5] . ( 3 sec) [ -8198.0016] [ 1622] [depth= 1] . ( 3 sec) [ -8017.4582] [ 1599] [depth= 4] . ( 3 sec) [ -8001.0318] [ 1589] [depth= 5] . ( 3 sec) [ -7999.3709] [ 1590] [depth= 2] . ( 3 sec) [ -7996.0109] [ 1592] [depth= 1] . ( 3 sec) [ -7993.7795] [ 1592] [depth= 1] . ( 3 sec) [ -7993.7695] [ 1594] [depth= 1] . ( 3 sec) [ -7993.1568] [ 1594] [depth= 1] . ( 3 sec) [ -7982.7820] [ 1587] [depth= 1] . ( 3 sec) [ -7901.2453] [ 1573] [depth= 2] . ( 3 sec) [ -7886.0129] [ 1561] [depth= 1] . ( 3 sec) [ -7805.6706] [ 1542] [depth= 2] . ( 3 sec) [ -7781.6776] [ 1533] [depth= 5] . ( 3 sec) [ -7765.9393] [ 1532] [depth= 2] . ( 3 sec) [ -7659.2174] [ 1504] [depth= 1] . ( 3 sec) [ -7577.8423] [ 1490] [depth= 1] . ( 3 sec) [ -7577.1481] [ 1490] [depth= 2] . ( 3 sec) [ -7575.7485] [ 1487] [depth= 1] . ( 3 sec) [ -7554.0559] [ 1482] [depth= 1] . ( 4 sec) [ -7542.3368] [ 1485] [depth= 3] . ( 4 sec) [ -7509.5670] [ 1469] [depth= 3] . ( 4 sec) [ -7506.2536] [ 1470] [depth= 1] . ( 4 sec) [ -7424.1677] [ 1427] [depth= 1] . ( 4 sec) [ -7408.0042] [ 1427] [depth= 1] . ( 4 sec) [ -7404.2313] [ 1430] [depth= 1] . ( 4 sec) [ -7404.0613] [ 1428] [depth= 2] . ( 4 sec) [ -7388.3737] [ 1424] [depth= 2] . ( 4 sec) [ -7354.3817] [ 1424] [depth= 1] . ( 4 sec) [ -7312.7233] [ 1408] [depth= 1] . ( 4 sec) [ -7292.6926] [ 1411] [depth= 1] . ( 4 sec) [ -7289.3703] [ 1408] [depth= 1] . ( 4 sec) [ -7275.5847] [ 1403] [depth= 1] . ( 4 sec) [ -7172.7208] [Branch lengths ] . ( 5 sec) [ -7168.6689] [GTR parameters ] . ( 5 sec) [ -7147.1542] [Alpha ][ 0.854799] . ( 5 sec) [ -7145.5073] [ 1406] [depth= 1] . ( 5 sec) [ -7145.4266] [ 1408] [depth= 1] . ( 5 sec) [ -7145.3830] [ 1407] [depth= 1] . ( 5 sec) [ -7126.5550] [ 1394] [depth= 1] . ( 5 sec) [ -7124.1676] [ 1395] [depth= 1] . ( 5 sec) [ -7124.0806] [ 1396] [depth= 1] . ( 5 sec) [ -7122.2426] [ 1395] [depth= 1] . ( 6 sec) [ -7114.8586] [ 1388] [depth= 2] . ( 6 sec) [ -7114.7032] [ 1386] [depth= 1] . ( 6 sec) [ -7109.7846] [ 1384] [depth= 1] . ( 6 sec) [ -7109.6835] [ 1385] [depth= 1] . ( 6 sec) [ -7095.7536] [ 1375] [depth= 1] . ( 6 sec) [ -7095.1117] [ 1376] [depth= 1] . ( 6 sec) [ -7048.0725] [ 1340] [depth= 3] . ( 7 sec) [ -7020.8117] [ 1354] [depth= 1] . ( 7 sec) [ -7017.8096] [ 1354] [depth= 1] . ( 7 sec) [ -7003.1354] [ 1341] [depth= 1] . ( 7 sec) [ -7002.4226] [ 1341] [depth= 1] . ( 7 sec) [ -7002.2507] [ 1341] [depth= 1] . ( 7 sec) [ -7002.0979] [ 1339] [depth= 1] . ( 7 sec) [ -7001.9029] [ 1339] [depth= 1] . ( 7 sec) [ -7001.8387] [ 1341] [depth= 1] . ( 7 sec) [ -7001.2133] [ 1340] [depth= 1] . ( 7 sec) [ -7000.0974] [ 1342] [depth= 1] . ( 8 sec) [ -6998.1743] [ 1340] [depth= 1] . ( 8 sec) [ -6996.7554] [ 1341] [depth= 1] . ( 8 sec) [ -6995.3443] [ 1342] [depth= 1] . ( 8 sec) [ -6994.8807] [ 1341] [depth= 1] . ( 8 sec) [ -6994.5565] [ 1342] [depth= 1] . ( 8 sec) [ -6994.4430] [ 1342] [depth= 1] . ( 9 sec) [ -6985.3423] [Branch lengths ] . ( 9 sec) [ -6985.0000] [GTR parameters ] . ( 9 sec) [ -6984.3336] [Alpha ][ 0.944982] . ( 11 sec) [ -6984.1961] [ 1341] [depth= 1] . ( 12 sec) [ -6984.0234] [ 1341] [depth= 1] . ( 13 sec) [ -6983.5403] [Branch lengths ] . ( 14 sec) [ -6983.5397] [GTR parameters ] . ( 14 sec) [ -6983.5327] [Alpha ][ 0.955051] . ( 17 sec) [ -6983.5096] [ 1338] [depth= 1] . ( 25 sec) [ -6983.4779] [ 1337] [depth= 1] . ( 32 sec) [ -6983.3490] [Branch lengths ] . ( 32 sec) [ -6983.3475] [GTR parameters ] . ( 32 sec) [ -6983.3464] [Alpha ][ 0.958934] . ( 32 sec) [ -6983.3464] [Topology ] . ( 33 sec) [ -6983.3364] [Topology ] . ( 34 sec) [ -6983.3337] [Topology ] . ( 34 sec) [ -6983.3325] [Topology ] . ( 35 sec) [ -6983.3320] [Topology ] . ( 35 sec) [ -6983.3320] [GTR parameters ] . ( 35 sec) [ -6983.3318] [Alpha ][ 0.960107] . ( 35 sec) [ -6983.3318] [Topology ] . ( 36 sec) [ -6983.3316] [Topology ] . ( 36 sec) [ -6983.3316] [GTR parameters ] . ( 36 sec) [ -6983.3316] [Alpha ][ 0.960107] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6983.331560. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7012.025245 . ( 1 sec) [ -7007.8352] [GTR parameters ] . ( 1 sec) [ -7007.3705] [Alpha ][ 0.916448] . ( 1 sec) [ -7007.3705] [Topology ] . ( 2 sec) [ -6988.1007] [Topology ] . ( 3 sec) [ -6984.6001] [Topology ] . ( 3 sec) [ -6983.9065] [Topology ] . ( 4 sec) [ -6983.6870] [Topology ] . ( 5 sec) [ -6983.6010] [Topology ] . ( 5 sec) [ -6983.5643] [Topology ] . ( 6 sec) [ -6983.5477] [Topology ] . ( 7 sec) [ -6983.5401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -6983.5348] [Topology ] . Before opt ts/t=1.000000 LK=-6983.534791 . ( 12 sec) [ -6983.5212] [GTR parameters ] . ( 12 sec) [ -6983.3866] [Alpha ][ 0.958886] . ( 12 sec) [ -6983.3866] [Topology ] . ( 13 sec) [ -6983.3741] [Topology ] . ( 13 sec) [ -6983.3691] [Topology ] . ( 14 sec) [ -6983.3669] [Topology ] . ( 15 sec) [ -6983.3659] [Topology ] . ( 16 sec) [ -6983.3654] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.365373 . ( 20 sec) [ -6983.3652] [GTR parameters ] . ( 21 sec) [ -6983.3646] [Alpha ][ 0.961784] . ( 21 sec) [ -6983.3646] [Topology ] . ( 21 sec) [ -6983.3642] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.364241 . ( 26 sec) [ -6983.3642] [GTR parameters ] . ( 26 sec) [ -6983.3642] [Alpha ][ 0.961784] . ( 26 sec) [ -6983.3642] [Topology ] . ( 27 sec) [ -6983.3641] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 37 sec) [ -7007.8352] [GTR parameters ] . ( 37 sec) [ -7007.3705] [Alpha ][ 0.916448] . ( 37 sec) [ -7006.2744] [ 1337] [depth= 1] . ( 37 sec) [ -7005.7672] [ 1338] [depth= 1] . ( 38 sec) [ -7004.4540] [ 1337] [depth= 1] . ( 38 sec) [ -7004.3722] [ 1339] [depth= 1] . ( 38 sec) [ -7004.2689] [ 1337] [depth= 1] . ( 38 sec) [ -7002.6433] [ 1339] [depth= 1] . ( 39 sec) [ -7001.7142] [ 1339] [depth= 1] . ( 39 sec) [ -7001.6146] [ 1339] [depth= 1] . ( 39 sec) [ -7001.5759] [ 1340] [depth= 1] . ( 40 sec) [ -7001.3080] [ 1339] [depth= 1] . ( 40 sec) [ -6999.9083] [ 1341] [depth= 1] . ( 40 sec) [ -6999.2829] [ 1341] [depth= 1] . ( 40 sec) [ -6993.5320] [ 1337] [depth= 2] . ( 40 sec) [ -6993.4556] [ 1341] [depth= 1] . ( 40 sec) [ -6993.2368] [ 1337] [depth= 1] . ( 40 sec) [ -6993.1190] [ 1339] [depth= 2] . ( 41 sec) [ -6983.9488] [Branch lengths ] . ( 41 sec) [ -6983.9341] [GTR parameters ] . ( 41 sec) [ -6983.8540] [Alpha ][ 0.949191] . ( 45 sec) [ -6983.5237] [Branch lengths ] . ( 56 sec) [ -6983.4936] [ 1338] [depth= 1] . ( 63 sec) [ -6983.4306] [Branch lengths ] . ( 63 sec) [ -6983.4297] [GTR parameters ] . ( 64 sec) [ -6983.4206] [Alpha ][ 0.960696] . ( 64 sec) [ -6983.4206] [Topology ] . ( 64 sec) [ -6983.4138] [Topology ] . ( 65 sec) [ -6983.4117] [Topology ] . ( 66 sec) [ -6983.4107] [Topology ] . ( 66 sec) [ -6983.4107] [GTR parameters ] . ( 66 sec) [ -6983.4106] [Alpha ][ 0.961656] . ( 66 sec) [ -6983.4106] [Topology ] . ( 66 sec) [ -6983.4102] [Topology ] . ( 67 sec) [ -6983.4102] [GTR parameters ] . ( 67 sec) [ -6983.4102] [Alpha ][ 0.961656] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -6983.3653] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6983.364091 . Log likelihood obtained after SPR moves : -6983.365345 . Log likelihood of the current tree: -6983.364091. . Printing the most likely tree in file 'data58.phy_phyml_tree.txt'... . Best log likelihood : -6983.331321 . Time used 0h1m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo