.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data70.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... . 363 patterns found. (out of a total of 500 sites) . 131 sites without polymorphism (26.20%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -20567.5892] [GTR parameters ] . ( 0 sec) [ -20162.8506] [Alpha ][ 0.500960] . ( 0 sec) [ -19567.6381] [ 3288] [depth= 8] . ( 0 sec) [ -19198.4667] [ 3276] [depth= 11] . ( 0 sec) [ -19112.4787] [ 3262] [depth= 4] . ( 0 sec) [ -19087.6944] [ 3256] [depth= 4] . ( 0 sec) [ -15258.3127] [ 3240] [depth= 4] . ( 0 sec) [ -15160.5798] [ 3235] [depth= 2] . ( 0 sec) [ -14975.1480] [ 3218] [depth= 5] . ( 0 sec) [ -14528.8303] [ 3211] [depth= 1] . ( 0 sec) [ -13846.9824] [ 3153] [depth= 6] . ( 0 sec) [ -13509.2201] [ 3037] [depth= 9] . ( 1 sec) [ -13331.5786] [ 2998] [depth= 1] . ( 1 sec) [ -13146.6636] [ 2962] [depth= 13] . ( 1 sec) [ -12847.9118] [ 2932] [depth= 11] . ( 1 sec) [ -12752.7265] [ 2905] [depth= 3] . ( 1 sec) [ -12709.0620] [ 2901] [depth= 1] . ( 1 sec) [ -12448.0550] [ 2792] [depth= 3] . ( 1 sec) [ -12217.0237] [ 2787] [depth= 1] . ( 1 sec) [ -12055.3340] [ 2785] [depth= 1] . ( 1 sec) [ -11955.9367] [ 2767] [depth= 1] . ( 1 sec) [ -11648.9614] [ 2650] [depth= 14] . ( 1 sec) [ -11580.2682] [ 2649] [depth= 1] . ( 1 sec) [ -11548.2169] [ 2617] [depth= 17] . ( 1 sec) [ -11500.2016] [ 2565] [depth= 2] . ( 1 sec) [ -11327.9514] [ 2561] [depth= 10] . ( 1 sec) [ -10916.6492] [ 2481] [depth= 1] . ( 1 sec) [ -10544.0955] [ 2443] [depth= 10] . ( 1 sec) [ -10305.8491] [ 2407] [depth= 17] . ( 1 sec) [ -10017.5819] [ 2291] [depth= 14] . ( 1 sec) [ -9912.5907] [ 2295] [depth= 7] . ( 1 sec) [ -9909.9579] [ 2260] [depth= 1] . ( 1 sec) [ -9813.6550] [ 2169] [depth= 1] . ( 1 sec) [ -9741.7519] [ 2165] [depth= 1] . ( 1 sec) [ -9642.8127] [ 2140] [depth= 9] . ( 1 sec) [ -9538.4848] [ 2139] [depth= 1] . ( 2 sec) [ -9406.1701] [ 2123] [depth= 6] . ( 2 sec) [ -9380.1267] [ 2118] [depth= 2] . ( 2 sec) [ -9363.6676] [ 2107] [depth= 1] . ( 2 sec) [ -9275.2422] [ 2070] [depth= 1] . ( 2 sec) [ -9264.6145] [ 2066] [depth= 1] . ( 2 sec) [ -9207.9277] [ 2063] [depth= 2] . ( 2 sec) [ -9145.0974] [ 2039] [depth= 1] . ( 2 sec) [ -8983.9071] [ 2001] [depth= 5] . ( 2 sec) [ -8808.1348] [ 1949] [depth= 6] . ( 2 sec) [ -8794.4479] [ 1944] [depth= 1] . ( 2 sec) [ -8758.0733] [ 1930] [depth= 8] . ( 2 sec) [ -8642.1039] [ 1927] [depth= 3] . ( 2 sec) [ -7849.3286] [ 1779] [depth= 6] . ( 2 sec) [ -7658.4823] [ 1754] [depth= 3] . ( 2 sec) [ -7649.7908] [ 1739] [depth= 2] . ( 2 sec) [ -7645.0038] [ 1725] [depth= 6] . ( 2 sec) [ -7545.8235] [ 1631] [depth= 6] . ( 2 sec) [ -7535.2151] [ 1648] [depth= 1] . ( 2 sec) [ -7447.6242] [ 1583] [depth= 9] . ( 2 sec) [ -7441.3798] [ 1543] [depth= 1] . ( 2 sec) [ -7260.1765] [ 1428] [depth= 8] . ( 3 sec) [ -7258.5980] [ 1421] [depth= 3] . ( 3 sec) [ -7223.4992] [ 1405] [depth= 5] . ( 3 sec) [ -7187.0390] [ 1400] [depth= 8] . ( 3 sec) [ -7168.2536] [ 1400] [depth= 3] . ( 3 sec) [ -7167.7117] [ 1400] [depth= 3] . ( 3 sec) [ -7039.0063] [ 1386] [depth= 2] . ( 3 sec) [ -7033.1301] [ 1385] [depth= 1] . ( 3 sec) [ -7020.4560] [ 1384] [depth= 1] . ( 3 sec) [ -7019.6282] [ 1384] [depth= 1] . ( 3 sec) [ -7008.2480] [ 1380] [depth= 2] . ( 3 sec) [ -6985.5034] [ 1370] [depth= 5] . ( 3 sec) [ -6961.8689] [ 1358] [depth= 2] . ( 3 sec) [ -6960.4082] [ 1361] [depth= 2] . ( 3 sec) [ -6953.7309] [ 1359] [depth= 3] . ( 3 sec) [ -6928.4510] [ 1358] [depth= 2] . ( 3 sec) [ -6900.3594] [ 1346] [depth= 4] . ( 3 sec) [ -6809.3960] [ 1339] [depth= 2] . ( 3 sec) [ -6724.6796] [ 1332] [depth= 3] . ( 3 sec) [ -6722.9385] [ 1326] [depth= 1] . ( 3 sec) [ -6709.1437] [ 1320] [depth= 1] . ( 4 sec) [ -6597.3761] [Branch lengths ] . ( 4 sec) [ -6593.1353] [GTR parameters ] . ( 4 sec) [ -6577.4727] [Alpha ][ 0.802448] . ( 5 sec) [ -6540.5633] [ 1305] [depth= 1] . ( 5 sec) [ -6515.8552] [ 1285] [depth= 6] . ( 5 sec) [ -6494.0329] [ 1257] [depth= 2] . ( 5 sec) [ -6493.5931] [ 1256] [depth= 1] . ( 5 sec) [ -6476.4822] [ 1259] [depth= 1] . ( 5 sec) [ -6476.1171] [ 1257] [depth= 1] . ( 5 sec) [ -6471.7300] [ 1255] [depth= 1] . ( 5 sec) [ -6468.8676] [ 1254] [depth= 1] . ( 5 sec) [ -6461.8574] [ 1252] [depth= 1] . ( 5 sec) [ -6457.4129] [ 1250] [depth= 1] . ( 5 sec) [ -6453.7560] [ 1247] [depth= 1] . ( 5 sec) [ -6446.7945] [ 1244] [depth= 1] . ( 6 sec) [ -6446.7661] [ 1244] [depth= 1] . ( 6 sec) [ -6438.3569] [ 1247] [depth= 1] . ( 6 sec) [ -6437.3494] [ 1245] [depth= 1] . ( 6 sec) [ -6436.5647] [ 1248] [depth= 2] . ( 6 sec) [ -6434.5471] [ 1245] [depth= 1] . ( 6 sec) [ -6428.8734] [ 1242] [depth= 1] . ( 6 sec) [ -6427.0747] [ 1241] [depth= 1] . ( 6 sec) [ -6423.9956] [ 1244] [depth= 1] . ( 7 sec) [ -6423.4184] [ 1244] [depth= 1] . ( 7 sec) [ -6422.7930] [ 1246] [depth= 1] . ( 7 sec) [ -6422.3958] [ 1246] [depth= 1] . ( 7 sec) [ -6422.1783] [ 1246] [depth= 1] . ( 7 sec) [ -6422.0755] [ 1244] [depth= 1] . ( 8 sec) [ -6418.7293] [Branch lengths ] . ( 8 sec) [ -6418.4483] [GTR parameters ] . ( 8 sec) [ -6417.2641] [Alpha ][ 0.922046] . ( 8 sec) [ -6416.6607] [ 1240] [depth= 1] . ( 10 sec) [ -6416.0571] [ 1241] [depth= 1] . ( 12 sec) [ -6415.1323] [Branch lengths ] . ( 12 sec) [ -6415.1246] [GTR parameters ] . ( 12 sec) [ -6415.1209] [Alpha ][ 0.929453] . ( 15 sec) [ -6415.0518] [Branch lengths ] . ( 35 sec) [ -6415.0443] [Branch lengths ] . ( 35 sec) [ -6415.0443] [Topology ] . ( 36 sec) [ -6415.0439] [Topology ] . ( 36 sec) [ -6415.0438] [GTR parameters ] . ( 36 sec) [ -6415.0435] [Alpha ][ 0.931563] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6415.043472. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -21053.4405] [GTR parameters ] . ( 1 sec) [ -20619.1489] [Alpha ][ 0.500960] . ( 1 sec) [ -20097.8055] [ 3405] [depth= 3] . ( 1 sec) [ -19632.6938] [ 3343] [depth= 10] . ( 1 sec) [ -19495.8375] [ 3318] [depth= 4] . ( 1 sec) [ -19463.1463] [ 3310] [depth= 2] . ( 1 sec) [ -19013.2921] [ 3279] [depth= 3] . ( 1 sec) [ -18243.5708] [ 3277] [depth= 5] . ( 1 sec) [ -17989.1797] [ 3258] [depth= 3] . ( 1 sec) [ -17936.6833] [ 3217] [depth= 1] . ( 1 sec) [ -17536.4638] [ 3197] [depth= 7] . ( 1 sec) [ -17296.2309] [ 3103] [depth= 2] . ( 1 sec) [ -14101.8201] [ 3100] [depth= 3] . ( 1 sec) [ -13586.7022] [ 3000] [depth= 1] . ( 1 sec) [ -12998.5699] [ 2988] [depth= 6] . ( 1 sec) [ -12838.8594] [ 2837] [depth= 12] . ( 1 sec) [ -12646.9064] [ 2822] [depth= 1] . ( 1 sec) [ -12459.4721] [ 2789] [depth= 14] . ( 1 sec) [ -12376.2116] [ 2770] [depth= 2] . ( 1 sec) [ -12259.8553] [ 2678] [depth= 1] . ( 1 sec) [ -12224.4861] [ 2672] [depth= 7] . ( 1 sec) [ -11982.1715] [ 2644] [depth= 1] . ( 2 sec) [ -11767.1059] [ 2638] [depth= 6] . ( 2 sec) [ -11700.9187] [ 2630] [depth= 8] . ( 2 sec) [ -11555.6175] [ 2630] [depth= 6] . ( 2 sec) [ -11517.2039] [ 2620] [depth= 1] . ( 2 sec) [ -11472.8881] [ 2622] [depth= 1] . ( 2 sec) [ -11471.3954] [ 2620] [depth= 1] . ( 2 sec) [ -11311.5926] [ 2589] [depth= 10] . ( 2 sec) [ -11189.9900] [ 2583] [depth= 3] . ( 2 sec) [ -10969.5813] [ 2527] [depth= 9] . ( 2 sec) [ -10797.4911] [ 2493] [depth= 8] . ( 2 sec) [ -10632.3403] [ 2367] [depth= 17] . ( 2 sec) [ -9959.3002] [ 2337] [depth= 1] . ( 2 sec) [ -9881.9534] [ 2329] [depth= 14] . ( 2 sec) [ -9636.6163] [ 2224] [depth= 2] . ( 2 sec) [ -9636.1728] [ 2226] [depth= 1] . ( 2 sec) [ -9545.9998] [ 2221] [depth= 3] . ( 2 sec) [ -9526.8765] [ 2224] [depth= 1] . ( 2 sec) [ -9495.6892] [ 2209] [depth= 2] . ( 2 sec) [ -9403.8600] [ 2076] [depth= 1] . ( 2 sec) [ -9392.0707] [ 2059] [depth= 10] . ( 2 sec) [ -9306.7734] [ 2039] [depth= 2] . ( 2 sec) [ -9270.2990] [ 2026] [depth= 8] . ( 2 sec) [ -9128.6692] [ 2027] [depth= 1] . ( 2 sec) [ -9025.3666] [ 1969] [depth= 6] . ( 2 sec) [ -8986.4663] [ 1959] [depth= 10] . ( 2 sec) [ -8961.4911] [ 1954] [depth= 1] . ( 3 sec) [ -8885.5845] [ 1939] [depth= 1] . ( 3 sec) [ -8848.7785] [ 1932] [depth= 5] . ( 3 sec) [ -8838.1158] [ 1928] [depth= 1] . ( 3 sec) [ -8789.2200] [ 1916] [depth= 2] . ( 3 sec) [ -8717.1836] [ 1913] [depth= 9] . ( 3 sec) [ -8662.1396] [ 1900] [depth= 8] . ( 3 sec) [ -8648.7474] [ 1892] [depth= 7] . ( 3 sec) [ -8599.8095] [ 1891] [depth= 1] . ( 3 sec) [ -8454.9689] [ 1857] [depth= 4] . ( 3 sec) [ -8405.8015] [ 1857] [depth= 1] . ( 3 sec) [ -8315.5255] [ 1840] [depth= 8] . ( 3 sec) [ -8185.3055] [ 1785] [depth= 2] . ( 3 sec) [ -8115.5766] [ 1773] [depth= 2] . ( 3 sec) [ -8115.0643] [ 1773] [depth= 1] . ( 3 sec) [ -7774.9247] [ 1639] [depth= 7] . ( 3 sec) [ -7772.7089] [ 1638] [depth= 1] . ( 3 sec) [ -7576.1865] [ 1643] [depth= 8] . ( 3 sec) [ -7455.0992] [ 1615] [depth= 4] . ( 4 sec) [ -7137.4050] [ 1458] [depth= 8] . ( 4 sec) [ -7136.6912] [ 1458] [depth= 1] . ( 4 sec) [ -7066.6820] [ 1451] [depth= 7] . ( 4 sec) [ -7060.6218] [ 1452] [depth= 1] . ( 4 sec) [ -7052.3712] [ 1449] [depth= 1] . ( 4 sec) [ -7050.7973] [ 1450] [depth= 1] . ( 4 sec) [ -6971.1821] [ 1432] [depth= 1] . ( 4 sec) [ -6970.1747] [ 1426] [depth= 1] . ( 4 sec) [ -6966.6795] [ 1419] [depth= 3] . ( 4 sec) [ -6956.0585] [ 1413] [depth= 4] . ( 4 sec) [ -6955.9215] [ 1415] [depth= 1] . ( 4 sec) [ -6922.4887] [ 1430] [depth= 2] . ( 4 sec) [ -6919.7120] [ 1379] [depth= 1] . ( 5 sec) [ -6825.6290] [Branch lengths ] . ( 5 sec) [ -6820.6969] [GTR parameters ] . ( 5 sec) [ -6806.8103] [Alpha ][ 0.758658] . ( 5 sec) [ -6766.8466] [ 1370] [depth= 1] . ( 5 sec) [ -6753.6257] [ 1375] [depth= 2] . ( 5 sec) [ -6727.8113] [ 1374] [depth= 2] . ( 6 sec) [ -6726.7279] [ 1378] [depth= 1] . ( 6 sec) [ -6724.1085] [ 1377] [depth= 2] . ( 6 sec) [ -6716.9324] [ 1371] [depth= 1] . ( 6 sec) [ -6614.9501] [ 1327] [depth= 4] . ( 6 sec) [ -6547.8130] [ 1313] [depth= 3] . ( 6 sec) [ -6520.1196] [ 1312] [depth= 1] . ( 6 sec) [ -6518.9100] [ 1313] [depth= 1] . ( 6 sec) [ -6516.1814] [ 1312] [depth= 1] . ( 6 sec) [ -6511.0211] [ 1309] [depth= 1] . ( 6 sec) [ -6506.8956] [ 1320] [depth= 1] . ( 6 sec) [ -6471.7952] [ 1272] [depth= 2] . ( 6 sec) [ -6471.2619] [ 1272] [depth= 1] . ( 6 sec) [ -6467.1607] [ 1268] [depth= 1] . ( 6 sec) [ -6465.5227] [ 1266] [depth= 1] . ( 7 sec) [ -6465.4806] [ 1266] [depth= 1] . ( 7 sec) [ -6453.4785] [ 1259] [depth= 1] . ( 7 sec) [ -6451.4925] [ 1257] [depth= 1] . ( 7 sec) [ -6450.4318] [ 1256] [depth= 1] . ( 7 sec) [ -6442.7763] [ 1253] [depth= 1] . ( 7 sec) [ -6442.7416] [ 1253] [depth= 1] . ( 8 sec) [ -6441.9994] [ 1255] [depth= 1] . ( 8 sec) [ -6428.7188] [ 1256] [depth= 2] . ( 8 sec) [ -6426.9921] [ 1247] [depth= 1] . ( 9 sec) [ -6420.6511] [Branch lengths ] . ( 9 sec) [ -6419.7791] [GTR parameters ] . ( 9 sec) [ -6417.3968] [Alpha ][ 0.922203] . ( 13 sec) [ -6416.9085] [Branch lengths ] . ( 19 sec) [ -6416.2829] [ 1244] [depth= 2] . ( 24 sec) [ -6415.1786] [ 1243] [depth= 1] . ( 32 sec) [ -6415.0817] [Branch lengths ] . ( 32 sec) [ -6415.0758] [GTR parameters ] . ( 32 sec) [ -6415.0702] [Alpha ][ 0.931338] . ( 52 sec) [ -6415.0603] [Branch lengths ] . ( 52 sec) [ -6415.0603] [Topology ] . ( 53 sec) [ -6415.0598] [Topology ] . ( 53 sec) [ -6415.0597] [GTR parameters ] . ( 53 sec) [ -6415.0597] [Alpha ][ 0.931338] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -6415.0434] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6415.043444. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -21438.2775] [GTR parameters ] . ( 0 sec) [ -21004.5283] [Alpha ][ 0.500960] . ( 0 sec) [ -20452.4987] [ 3407] [depth= 8] . ( 0 sec) [ -20057.7918] [ 3395] [depth= 8] . ( 1 sec) [ -20023.8326] [ 3388] [depth= 4] . ( 1 sec) [ -19951.2602] [ 3386] [depth= 2] . ( 1 sec) [ -19699.4298] [ 3328] [depth= 2] . ( 1 sec) [ -19462.2719] [ 3323] [depth= 4] . ( 1 sec) [ -19132.6700] [ 3210] [depth= 13] . ( 1 sec) [ -15118.9248] [ 3158] [depth= 8] . ( 1 sec) [ -14806.3764] [ 3160] [depth= 3] . ( 1 sec) [ -14738.9965] [ 3159] [depth= 7] . ( 1 sec) [ -14249.4705] [ 3106] [depth= 4] . ( 1 sec) [ -13560.5229] [ 3072] [depth= 14] . ( 1 sec) [ -13530.7411] [ 3013] [depth= 4] . ( 1 sec) [ -13450.5321] [ 3014] [depth= 2] . ( 1 sec) [ -13189.2576] [ 2974] [depth= 8] . ( 1 sec) [ -13183.3890] [ 2976] [depth= 1] . ( 1 sec) [ -12844.1004] [ 2868] [depth= 4] . ( 1 sec) [ -12462.3437] [ 2871] [depth= 1] . ( 1 sec) [ -12327.2782] [ 2863] [depth= 3] . ( 1 sec) [ -12263.0100] [ 2863] [depth= 1] . ( 1 sec) [ -12224.4133] [ 2854] [depth= 6] . ( 1 sec) [ -12166.1644] [ 2837] [depth= 5] . ( 1 sec) [ -12057.8176] [ 2818] [depth= 5] . ( 1 sec) [ -12003.3598] [ 2796] [depth= 1] . ( 1 sec) [ -11939.1606] [ 2785] [depth= 8] . ( 1 sec) [ -11578.5143] [ 2684] [depth= 4] . ( 1 sec) [ -11385.0949] [ 2672] [depth= 8] . ( 2 sec) [ -11354.5665] [ 2665] [depth= 11] . ( 2 sec) [ -11337.0053] [ 2659] [depth= 10] . ( 2 sec) [ -11164.4620] [ 2657] [depth= 1] . ( 2 sec) [ -10636.7335] [ 2534] [depth= 11] . ( 2 sec) [ -10452.8130] [ 2441] [depth= 5] . ( 2 sec) [ -10326.0224] [ 2421] [depth= 8] . ( 2 sec) [ -10171.7174] [ 2416] [depth= 5] . ( 2 sec) [ -10168.3815] [ 2418] [depth= 1] . ( 2 sec) [ -10157.1723] [ 2408] [depth= 1] . ( 2 sec) [ -10040.5792] [ 2377] [depth= 7] . ( 2 sec) [ -9887.7126] [ 2360] [depth= 4] . ( 2 sec) [ -9668.6220] [ 2237] [depth= 14] . ( 2 sec) [ -9592.5167] [ 2134] [depth= 9] . ( 2 sec) [ -9571.1613] [ 2136] [depth= 7] . ( 2 sec) [ -9154.9419] [ 2137] [depth= 6] . ( 2 sec) [ -9150.2582] [ 2137] [depth= 1] . ( 2 sec) [ -9056.5992] [ 2113] [depth= 6] . ( 2 sec) [ -8774.0148] [ 1996] [depth= 4] . ( 2 sec) [ -8748.4880] [ 1994] [depth= 1] . ( 2 sec) [ -8741.1633] [ 1984] [depth= 2] . ( 2 sec) [ -8665.1486] [ 1983] [depth= 1] . ( 2 sec) [ -8634.4829] [ 1980] [depth= 1] . ( 2 sec) [ -8627.5165] [ 1976] [depth= 1] . ( 2 sec) [ -8595.0283] [ 1969] [depth= 2] . ( 2 sec) [ -8552.7133] [ 1955] [depth= 1] . ( 3 sec) [ -8546.8363] [ 1939] [depth= 4] . ( 3 sec) [ -8459.3653] [ 1937] [depth= 1] . ( 3 sec) [ -8344.4438] [ 1935] [depth= 2] . ( 3 sec) [ -8307.5086] [ 1932] [depth= 6] . ( 3 sec) [ -8040.4073] [ 1777] [depth= 1] . ( 3 sec) [ -7986.8853] [ 1769] [depth= 4] . ( 3 sec) [ -7920.6487] [ 1764] [depth= 4] . ( 3 sec) [ -7616.3605] [ 1721] [depth= 4] . ( 3 sec) [ -7593.4818] [ 1677] [depth= 1] . ( 3 sec) [ -7593.1439] [ 1682] [depth= 2] . ( 3 sec) [ -7268.2964] [ 1541] [depth= 8] . ( 3 sec) [ -7247.4552] [ 1535] [depth= 6] . ( 3 sec) [ -7247.3124] [ 1536] [depth= 2] . ( 3 sec) [ -7202.6396] [ 1526] [depth= 1] . ( 3 sec) [ -7118.8150] [ 1528] [depth= 1] . ( 3 sec) [ -7117.5307] [ 1528] [depth= 1] . ( 3 sec) [ -7025.5915] [ 1500] [depth= 2] . ( 3 sec) [ -7024.3550] [ 1504] [depth= 1] . ( 3 sec) [ -7011.5336] [ 1500] [depth= 1] . ( 3 sec) [ -7009.1982] [ 1514] [depth= 1] . ( 3 sec) [ -6998.6290] [ 1511] [depth= 3] . ( 4 sec) [ -6989.4480] [ 1496] [depth= 1] . ( 4 sec) [ -6856.1614] [ 1414] [depth= 5] . ( 4 sec) [ -6844.8002] [ 1415] [depth= 3] . ( 4 sec) [ -6803.3304] [ 1405] [depth= 2] . ( 4 sec) [ -6802.3245] [ 1406] [depth= 1] . ( 4 sec) [ -6793.8275] [ 1406] [depth= 1] . ( 4 sec) [ -6780.9424] [ 1402] [depth= 2] . ( 4 sec) [ -6780.6302] [ 1398] [depth= 1] . ( 4 sec) [ -6779.8993] [ 1397] [depth= 2] . ( 4 sec) [ -6735.2373] [ 1347] [depth= 4] . ( 4 sec) [ -6646.1881] [Branch lengths ] . ( 5 sec) [ -6639.8461] [GTR parameters ] . ( 5 sec) [ -6624.3200] [Alpha ][ 0.781542] . ( 5 sec) [ -6622.1240] [ 1346] [depth= 1] . ( 5 sec) [ -6592.1274] [ 1329] [depth= 4] . ( 5 sec) [ -6588.6625] [ 1328] [depth= 1] . ( 5 sec) [ -6556.4789] [ 1315] [depth= 1] . ( 5 sec) [ -6551.6492] [ 1306] [depth= 4] . ( 6 sec) [ -6549.0039] [ 1307] [depth= 1] . ( 6 sec) [ -6527.8607] [ 1301] [depth= 1] . ( 6 sec) [ -6527.7774] [ 1302] [depth= 1] . ( 6 sec) [ -6523.8408] [ 1299] [depth= 1] . ( 6 sec) [ -6518.2258] [ 1292] [depth= 1] . ( 6 sec) [ -6478.5190] [ 1257] [depth= 2] . ( 7 sec) [ -6478.1688] [ 1256] [depth= 1] . ( 7 sec) [ -6474.0837] [ 1253] [depth= 1] . ( 7 sec) [ -6473.8130] [ 1253] [depth= 1] . ( 7 sec) [ -6473.5215] [ 1256] [depth= 1] . ( 7 sec) [ -6455.5788] [ 1260] [depth= 1] . ( 7 sec) [ -6433.2514] [ 1244] [depth= 4] . ( 8 sec) [ -6433.2045] [ 1244] [depth= 1] . ( 8 sec) [ -6431.0932] [ 1246] [depth= 1] . ( 8 sec) [ -6420.0529] [Branch lengths ] . ( 9 sec) [ -6419.9033] [GTR parameters ] . ( 9 sec) [ -6418.1435] [Alpha ][ 0.924088] . ( 10 sec) [ -6415.5241] [ 1243] [depth= 1] . ( 13 sec) [ -6415.0977] [Branch lengths ] . ( 13 sec) [ -6415.0845] [GTR parameters ] . ( 13 sec) [ -6415.0798] [Alpha ][ 0.932425] . ( 16 sec) [ -6415.0610] [Branch lengths ] . ( 36 sec) [ -6415.0597] [Branch lengths ] . ( 36 sec) [ -6415.0597] [Topology ] . ( 37 sec) [ -6415.0597] [Topology ] . ( 37 sec) [ -6415.0596] [GTR parameters ] . ( 37 sec) [ -6415.0596] [Alpha ][ 0.931493] . Checking for NNIs, optimizing five branches... . ( 41 sec) [ -6415.0590] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6415.058989. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -16922.1438] [GTR parameters ] . ( 1 sec) [ -16549.4572] [Alpha ][ 0.500960] . ( 1 sec) [ -15926.0548] [ 3178] [depth= 8] . ( 1 sec) [ -15816.4907] [ 3114] [depth= 6] . ( 1 sec) [ -15428.5948] [ 3058] [depth= 9] . ( 1 sec) [ -15176.6809] [ 3049] [depth= 2] . ( 1 sec) [ -14731.9096] [ 3047] [depth= 1] . ( 1 sec) [ -14700.8652] [ 2917] [depth= 3] . ( 1 sec) [ -14686.1538] [ 2915] [depth= 5] . ( 1 sec) [ -14647.3295] [ 2899] [depth= 2] . ( 1 sec) [ -14621.9468] [ 2897] [depth= 1] . ( 1 sec) [ -14617.3491] [ 2889] [depth= 2] . ( 2 sec) [ -14615.4257] [ 2889] [depth= 1] . ( 2 sec) [ -13725.0853] [ 2829] [depth= 7] . ( 2 sec) [ -13307.5626] [ 2805] [depth= 6] . ( 2 sec) [ -13076.8008] [ 2739] [depth= 5] . ( 2 sec) [ -13021.9031] [ 2740] [depth= 1] . ( 2 sec) [ -12985.3998] [ 2714] [depth= 1] . ( 2 sec) [ -12716.7444] [ 2719] [depth= 1] . ( 2 sec) [ -12624.2269] [ 2710] [depth= 2] . ( 2 sec) [ -12124.5000] [ 2552] [depth= 9] . ( 2 sec) [ -12065.5649] [ 2549] [depth= 1] . ( 2 sec) [ -12053.5406] [ 2545] [depth= 9] . ( 2 sec) [ -11884.6642] [ 2420] [depth= 8] . ( 2 sec) [ -11826.8901] [ 2413] [depth= 6] . ( 2 sec) [ -11194.7737] [ 2303] [depth= 10] . ( 2 sec) [ -11127.3550] [ 2292] [depth= 4] . ( 2 sec) [ -11058.4125] [ 2290] [depth= 7] . ( 2 sec) [ -10937.6935] [ 2287] [depth= 1] . ( 2 sec) [ -10871.4775] [ 2233] [depth= 5] . ( 2 sec) [ -10824.7053] [ 2231] [depth= 1] . ( 2 sec) [ -10814.0372] [ 2227] [depth= 1] . ( 2 sec) [ -10553.3724] [ 2228] [depth= 1] . ( 2 sec) [ -10440.1763] [ 2190] [depth= 4] . ( 2 sec) [ -10360.2895] [ 2167] [depth= 1] . ( 2 sec) [ -10310.6120] [ 2154] [depth= 4] . ( 2 sec) [ -10112.3483] [ 2096] [depth= 8] . ( 3 sec) [ -9722.3477] [ 2072] [depth= 10] . ( 3 sec) [ -9720.4568] [ 2046] [depth= 1] . ( 3 sec) [ -9669.8646] [ 2018] [depth= 1] . ( 3 sec) [ -9508.6650] [ 1948] [depth= 2] . ( 3 sec) [ -9409.1492] [ 1928] [depth= 8] . ( 3 sec) [ -9266.7055] [ 1924] [depth= 1] . ( 3 sec) [ -9161.0757] [ 1920] [depth= 2] . ( 3 sec) [ -9074.8849] [ 1813] [depth= 5] . ( 3 sec) [ -9042.9572] [ 1807] [depth= 5] . ( 3 sec) [ -8614.6902] [ 1747] [depth= 8] . ( 3 sec) [ -8587.9463] [ 1746] [depth= 2] . ( 3 sec) [ -8156.3410] [ 1619] [depth= 15] . ( 3 sec) [ -8002.6206] [ 1584] [depth= 2] . ( 3 sec) [ -7893.0516] [ 1587] [depth= 1] . ( 3 sec) [ -7624.3959] [ 1578] [depth= 2] . ( 3 sec) [ -7579.0111] [ 1579] [depth= 1] . ( 3 sec) [ -7452.1122] [ 1526] [depth= 1] . ( 3 sec) [ -7429.9516] [ 1529] [depth= 1] . ( 3 sec) [ -7311.1103] [ 1523] [depth= 1] . ( 3 sec) [ -7301.8849] [ 1517] [depth= 2] . ( 3 sec) [ -7295.0323] [ 1515] [depth= 2] . ( 3 sec) [ -7281.8979] [ 1519] [depth= 2] . ( 3 sec) [ -7087.8666] [ 1476] [depth= 7] . ( 4 sec) [ -7069.0715] [ 1472] [depth= 3] . ( 4 sec) [ -7062.9346] [ 1472] [depth= 3] . ( 4 sec) [ -6868.5159] [ 1428] [depth= 4] . ( 4 sec) [ -6857.6429] [ 1422] [depth= 1] . ( 4 sec) [ -6852.6075] [ 1407] [depth= 4] . ( 4 sec) [ -6829.4017] [ 1392] [depth= 2] . ( 4 sec) [ -6818.0441] [ 1394] [depth= 1] . ( 4 sec) [ -6751.5341] [ 1372] [depth= 2] . ( 4 sec) [ -6742.6515] [ 1375] [depth= 1] . ( 4 sec) [ -6732.7470] [ 1379] [depth= 1] . ( 4 sec) [ -6730.6954] [ 1379] [depth= 1] . ( 4 sec) [ -6682.3489] [ 1365] [depth= 2] . ( 4 sec) [ -6676.5861] [ 1365] [depth= 1] . ( 4 sec) [ -6670.2267] [ 1332] [depth= 4] . ( 4 sec) [ -6661.1826] [ 1319] [depth= 1] . ( 4 sec) [ -6656.8573] [ 1322] [depth= 3] . ( 4 sec) [ -6654.1925] [ 1321] [depth= 1] . ( 4 sec) [ -6646.0071] [ 1318] [depth= 2] . ( 5 sec) [ -6643.5942] [ 1316] [depth= 2] . ( 5 sec) [ -6640.3474] [ 1308] [depth= 2] . ( 5 sec) [ -6627.6331] [ 1303] [depth= 1] . ( 5 sec) [ -6570.9601] [Branch lengths ] . ( 6 sec) [ -6565.8071] [GTR parameters ] . ( 6 sec) [ -6545.7414] [Alpha ][ 0.848471] . ( 6 sec) [ -6497.2370] [ 1275] [depth= 1] . ( 6 sec) [ -6495.7752] [ 1272] [depth= 1] . ( 6 sec) [ -6492.9728] [ 1269] [depth= 2] . ( 6 sec) [ -6490.2471] [ 1265] [depth= 1] . ( 6 sec) [ -6477.6483] [ 1261] [depth= 1] . ( 7 sec) [ -6466.8317] [ 1258] [depth= 1] . ( 7 sec) [ -6457.6535] [ 1251] [depth= 1] . ( 7 sec) [ -6454.8351] [ 1250] [depth= 1] . ( 7 sec) [ -6454.7791] [ 1255] [depth= 1] . ( 7 sec) [ -6454.5188] [ 1254] [depth= 1] . ( 7 sec) [ -6430.1389] [ 1243] [depth= 1] . ( 8 sec) [ -6428.3152] [ 1246] [depth= 1] . ( 8 sec) [ -6428.2619] [ 1246] [depth= 1] . ( 8 sec) [ -6427.6218] [ 1250] [depth= 1] . ( 9 sec) [ -6427.1843] [ 1251] [depth= 2] . ( 9 sec) [ -6425.3768] [ 1252] [depth= 1] . ( 9 sec) [ -6419.2095] [Branch lengths ] . ( 10 sec) [ -6419.0242] [GTR parameters ] . ( 10 sec) [ -6418.6297] [Alpha ][ 0.919132] . ( 10 sec) [ -6418.0889] [ 1247] [depth= 1] . ( 11 sec) [ -6417.7078] [ 1243] [depth= 1] . ( 13 sec) [ -6416.5212] [Branch lengths ] . ( 14 sec) [ -6416.5182] [GTR parameters ] . ( 14 sec) [ -6416.5134] [Alpha ][ 0.927594] . ( 17 sec) [ -6416.4203] [Branch lengths ] . ( 37 sec) [ -6416.4096] [Branch lengths ] . ( 37 sec) [ -6416.4096] [Topology ] . ( 37 sec) [ -6416.3969] [Topology ] . ( 38 sec) [ -6416.3084] [Topology ] . ( 39 sec) [ -6415.8424] [Topology ] . ( 40 sec) [ -6415.1310] [Topology ] . ( 40 sec) [ -6415.0697] [Topology ] . ( 41 sec) [ -6415.0640] [Topology ] . ( 41 sec) [ -6415.0615] [GTR parameters ] . ( 41 sec) [ -6415.0604] [Alpha ][ 0.931642] . ( 41 sec) [ -6415.0604] [Topology ] . ( 42 sec) [ -6415.0598] [Topology ] . ( 42 sec) [ -6415.0597] [GTR parameters ] . ( 42 sec) [ -6415.0597] [Alpha ][ 0.931642] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -6415.0435] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6415.043460. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -19035.0371] [GTR parameters ] . ( 0 sec) [ -18613.7834] [Alpha ][ 0.500960] . ( 0 sec) [ -18059.6427] [ 3355] [depth= 6] . ( 0 sec) [ -17831.7853] [ 3272] [depth= 8] . ( 0 sec) [ -17757.2066] [ 3264] [depth= 5] . ( 0 sec) [ -17609.6239] [ 3262] [depth= 1] . ( 0 sec) [ -17420.8278] [ 3218] [depth= 9] . ( 0 sec) [ -17364.7998] [ 3222] [depth= 3] . ( 0 sec) [ -17149.1374] [ 3219] [depth= 5] . ( 1 sec) [ -16981.7328] [ 3112] [depth= 9] . ( 1 sec) [ -16400.2370] [ 3071] [depth= 13] . ( 1 sec) [ -16149.5201] [ 3035] [depth= 14] . ( 1 sec) [ -15072.5207] [ 2983] [depth= 6] . ( 1 sec) [ -15039.5262] [ 2998] [depth= 1] . ( 1 sec) [ -14832.6501] [ 2931] [depth= 4] . ( 1 sec) [ -14725.5845] [ 2926] [depth= 4] . ( 1 sec) [ -14687.3477] [ 2924] [depth= 2] . ( 1 sec) [ -14525.7051] [ 2918] [depth= 1] . ( 1 sec) [ -14514.9594] [ 2904] [depth= 2] . ( 1 sec) [ -14398.2023] [ 2868] [depth= 1] . ( 1 sec) [ -13063.2917] [ 2852] [depth= 7] . ( 1 sec) [ -12875.3948] [ 2820] [depth= 1] . ( 1 sec) [ -12548.9823] [ 2809] [depth= 6] . ( 1 sec) [ -12521.1809] [ 2811] [depth= 1] . ( 1 sec) [ -11991.4359] [ 2752] [depth= 5] . ( 1 sec) [ -11988.1355] [ 2748] [depth= 4] . ( 1 sec) [ -11817.6253] [ 2742] [depth= 11] . ( 1 sec) [ -11662.6987] [ 2626] [depth= 12] . ( 1 sec) [ -11403.5481] [ 2617] [depth= 14] . ( 1 sec) [ -11299.2392] [ 2589] [depth= 4] . ( 1 sec) [ -10876.2761] [ 2458] [depth= 11] . ( 1 sec) [ -10811.4704] [ 2436] [depth= 5] . ( 1 sec) [ -10769.2565] [ 2334] [depth= 2] . ( 1 sec) [ -10676.1347] [ 2301] [depth= 7] . ( 2 sec) [ -10661.9396] [ 2294] [depth= 2] . ( 2 sec) [ -10550.5211] [ 2197] [depth= 2] . ( 2 sec) [ -10445.8607] [ 2173] [depth= 3] . ( 2 sec) [ -10383.7506] [ 2174] [depth= 1] . ( 2 sec) [ -10223.4680] [ 2128] [depth= 12] . ( 2 sec) [ -9672.7320] [ 2076] [depth= 12] . ( 2 sec) [ -9663.1961] [ 2073] [depth= 1] . ( 2 sec) [ -9525.2014] [ 2026] [depth= 7] . ( 2 sec) [ -9501.3986] [ 2012] [depth= 2] . ( 2 sec) [ -9015.0796] [ 1979] [depth= 7] . ( 2 sec) [ -8970.4967] [ 1969] [depth= 9] . ( 2 sec) [ -8846.4726] [ 1928] [depth= 4] . ( 2 sec) [ -8846.4448] [ 1929] [depth= 1] . ( 2 sec) [ -8787.1341] [ 1793] [depth= 9] . ( 2 sec) [ -8756.9152] [ 1773] [depth= 4] . ( 2 sec) [ -8692.1457] [ 1773] [depth= 2] . ( 2 sec) [ -8689.5349] [ 1769] [depth= 1] . ( 2 sec) [ -8582.4028] [ 1724] [depth= 4] . ( 3 sec) [ -8582.2422] [ 1726] [depth= 1] . ( 3 sec) [ -8559.5425] [ 1720] [depth= 12] . ( 3 sec) [ -8554.7887] [ 1712] [depth= 2] . ( 3 sec) [ -8421.6024] [ 1727] [depth= 1] . ( 3 sec) [ -8098.3687] [ 1688] [depth= 5] . ( 3 sec) [ -8036.6146] [ 1690] [depth= 6] . ( 3 sec) [ -8025.2129] [ 1685] [depth= 1] . ( 3 sec) [ -8017.0350] [ 1684] [depth= 1] . ( 3 sec) [ -7995.0595] [ 1687] [depth= 11] . ( 3 sec) [ -7979.9635] [ 1688] [depth= 1] . ( 3 sec) [ -7960.8337] [ 1684] [depth= 2] . ( 3 sec) [ -7956.6818] [ 1682] [depth= 1] . ( 3 sec) [ -7383.5874] [ 1593] [depth= 2] . ( 3 sec) [ -7375.8722] [ 1594] [depth= 1] . ( 3 sec) [ -7370.8449] [ 1609] [depth= 1] . ( 3 sec) [ -7356.6734] [ 1594] [depth= 1] . ( 3 sec) [ -7350.8143] [ 1580] [depth= 1] . ( 4 sec) [ -7350.0706] [ 1583] [depth= 2] . ( 4 sec) [ -7336.7071] [ 1581] [depth= 2] . ( 4 sec) [ -7196.1010] [ 1554] [depth= 5] . ( 4 sec) [ -7188.3024] [ 1551] [depth= 3] . ( 4 sec) [ -7187.6132] [ 1551] [depth= 2] . ( 4 sec) [ -7187.2779] [ 1556] [depth= 3] . ( 4 sec) [ -7098.1185] [ 1556] [depth= 2] . ( 4 sec) [ -6975.0336] [Branch lengths ] . ( 5 sec) [ -6970.6939] [GTR parameters ] . ( 5 sec) [ -6966.6890] [Alpha ][ 0.619068] . ( 5 sec) [ -6940.2586] [ 1551] [depth= 2] . ( 5 sec) [ -6937.6098] [ 1552] [depth= 1] . ( 5 sec) [ -6934.7212] [ 1466] [depth= 1] . ( 5 sec) [ -6934.5912] [ 1464] [depth= 1] . ( 6 sec) [ -6894.0166] [ 1426] [depth= 1] . ( 6 sec) [ -6800.7579] [ 1408] [depth= 5] . ( 6 sec) [ -6799.2261] [ 1405] [depth= 1] . ( 6 sec) [ -6744.9738] [ 1382] [depth= 1] . ( 6 sec) [ -6702.9681] [ 1397] [depth= 1] . ( 6 sec) [ -6702.4732] [ 1394] [depth= 2] . ( 6 sec) [ -6693.9394] [ 1378] [depth= 3] . ( 6 sec) [ -6689.0344] [ 1376] [depth= 1] . ( 6 sec) [ -6660.4819] [ 1365] [depth= 3] . ( 6 sec) [ -6513.7814] [ 1276] [depth= 5] . ( 6 sec) [ -6513.6264] [ 1276] [depth= 1] . ( 6 sec) [ -6502.3138] [ 1273] [depth= 2] . ( 6 sec) [ -6497.2446] [ 1278] [depth= 1] . ( 6 sec) [ -6494.1800] [ 1281] [depth= 1] . ( 6 sec) [ -6492.0000] [ 1261] [depth= 2] . ( 7 sec) [ -6486.3307] [ 1272] [depth= 1] . ( 7 sec) [ -6486.3123] [ 1272] [depth= 1] . ( 7 sec) [ -6479.9604] [ 1267] [depth= 2] . ( 7 sec) [ -6477.0590] [ 1266] [depth= 1] . ( 7 sec) [ -6474.4549] [ 1266] [depth= 1] . ( 7 sec) [ -6474.4319] [ 1266] [depth= 1] . ( 7 sec) [ -6474.1702] [ 1266] [depth= 1] . ( 7 sec) [ -6468.9943] [ 1261] [depth= 1] . ( 7 sec) [ -6461.6228] [ 1258] [depth= 1] . ( 8 sec) [ -6461.3520] [ 1260] [depth= 2] . ( 8 sec) [ -6459.5354] [ 1247] [depth= 1] . ( 8 sec) [ -6459.0103] [ 1247] [depth= 2] . ( 8 sec) [ -6457.8396] [ 1250] [depth= 1] . ( 9 sec) [ -6435.3015] [Branch lengths ] . ( 9 sec) [ -6434.5126] [GTR parameters ] . ( 9 sec) [ -6425.1957] [Alpha ][ 0.905063] . ( 10 sec) [ -6425.1856] [ 1247] [depth= 1] . ( 10 sec) [ -6424.9337] [ 1246] [depth= 1] . ( 10 sec) [ -6424.9136] [ 1246] [depth= 1] . ( 11 sec) [ -6423.7773] [ 1243] [depth= 1] . ( 12 sec) [ -6420.0854] [Branch lengths ] . ( 13 sec) [ -6420.0646] [GTR parameters ] . ( 13 sec) [ -6420.0284] [Alpha ][ 0.927264] . ( 16 sec) [ -6419.7690] [Branch lengths ] . ( 36 sec) [ -6419.0392] [Branch lengths ] . ( 36 sec) [ -6419.0392] [Topology ] . ( 37 sec) [ -6416.6130] [Topology ] . ( 37 sec) [ -6415.3272] [Topology ] . ( 38 sec) [ -6415.1050] [Topology ] . ( 39 sec) [ -6415.0702] [Topology ] . ( 39 sec) [ -6415.0651] [Topology ] . ( 40 sec) [ -6415.0643] [Topology ] . ( 41 sec) [ -6415.0610] [GTR parameters ] . ( 41 sec) [ -6415.0597] [Alpha ][ 0.931636] . ( 41 sec) [ -6415.0597] [Topology ] . ( 41 sec) [ -6415.0595] [Topology ] . ( 41 sec) [ -6415.0595] [GTR parameters ] . ( 41 sec) [ -6415.0595] [Alpha ][ 0.931636] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -6415.0588] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6415.058826. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6467.237369 . ( 1 sec) [ -6462.6699] [GTR parameters ] . ( 1 sec) [ -6462.3038] [Alpha ][ 0.921661] . ( 1 sec) [ -6462.3038] [Topology ] . ( 1 sec) [ -6425.9501] [Topology ] . ( 2 sec) [ -6416.9065] [Topology ] . ( 3 sec) [ -6415.5687] [Topology ] . ( 4 sec) [ -6415.2570] [Topology ] . ( 4 sec) [ -6415.1499] [Topology ] . ( 5 sec) [ -6415.1064] [Topology ] . ( 6 sec) [ -6415.0871] [Topology ] . ( 6 sec) [ -6415.0781] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6415.078064 . ( 11 sec) [ -6415.0578] [GTR parameters ] . ( 11 sec) [ -6415.0525] [Alpha ][ 0.930619] . ( 11 sec) [ -6415.0525] [Topology ] . ( 12 sec) [ -6415.0475] [Topology ] . ( 13 sec) [ -6415.0453] [Topology ] . ( 13 sec) [ -6415.0442] [Topology ] . ( 14 sec) [ -6415.0436] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6415.043635 . ( 19 sec) [ -6415.0436] [GTR parameters ] . ( 19 sec) [ -6415.0436] [Alpha ][ 0.931550] . ( 19 sec) [ -6415.0436] [Topology ] . ( 19 sec) [ -6415.0433] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 29 sec) [ -6462.6699] [GTR parameters ] . ( 29 sec) [ -6462.3038] [Alpha ][ 0.921661] . ( 29 sec) [ -6461.4406] [ 1246] [depth= 1] . ( 29 sec) [ -6456.1352] [ 1247] [depth= 1] . ( 29 sec) [ -6445.7262] [ 1243] [depth= 1] . ( 29 sec) [ -6444.4661] [ 1241] [depth= 1] . ( 30 sec) [ -6442.0207] [ 1243] [depth= 1] . ( 30 sec) [ -6439.4050] [ 1241] [depth= 1] . ( 30 sec) [ -6435.9409] [ 1244] [depth= 1] . ( 30 sec) [ -6435.3430] [ 1240] [depth= 1] . ( 30 sec) [ -6429.9547] [ 1252] [depth= 1] . ( 30 sec) [ -6429.0249] [ 1252] [depth= 1] . ( 30 sec) [ -6428.9904] [ 1252] [depth= 1] . ( 31 sec) [ -6428.8664] [ 1252] [depth= 1] . ( 31 sec) [ -6428.7780] [ 1252] [depth= 1] . ( 31 sec) [ -6428.3956] [ 1252] [depth= 1] . ( 31 sec) [ -6428.3071] [ 1252] [depth= 1] . ( 31 sec) [ -6427.8907] [ 1254] [depth= 1] . ( 31 sec) [ -6427.0708] [ 1252] [depth= 1] . ( 31 sec) [ -6426.5595] [ 1253] [depth= 1] . ( 32 sec) [ -6418.9227] [Branch lengths ] . ( 33 sec) [ -6418.8818] [GTR parameters ] . ( 33 sec) [ -6418.8815] [Alpha ][ 0.923677] . ( 34 sec) [ -6417.1265] [ 1241] [depth= 1] . ( 36 sec) [ -6415.1542] [Branch lengths ] . ( 37 sec) [ -6415.1508] [GTR parameters ] . ( 37 sec) [ -6415.1482] [Alpha ][ 0.929877] . ( 40 sec) [ -6415.0460] [Branch lengths ] . ( 60 sec) [ -6415.0435] [Branch lengths ] . ( 60 sec) [ -6415.0435] [Topology ] . ( 61 sec) [ -6415.0434] [Topology ] . ( 61 sec) [ -6415.0433] [GTR parameters ] . ( 61 sec) [ -6415.0431] [Alpha ][ 0.931570] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6415.043293 . Log likelihood obtained after SPR moves : -6415.043112 . Log likelihood of the current tree: -6415.043112. . Printing the most likely tree in file 'data70.phy_phyml_tree.txt'... . Best log likelihood : -6415.043112 . Time used 0h1m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo