.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2772_77x900_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 . 57 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 575 patterns found. (out of a total of 900 sites) . 459 sites without polymorphism (51.00%). . [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)... . ( 5 sec) [ -21366.1453] [GTR parameters ] . ( 5 sec) [ -20810.2656] [Alpha ][ 0.500960] . ( 5 sec) [ -20681.5990] [ 3257] [depth= 8] . ( 6 sec) [ -20601.0112] [ 3239] [depth= 5] . ( 6 sec) [ -20427.6438] [ 3240] [depth= 1] . ( 6 sec) [ -20348.3553] [ 3235] [depth= 10] . ( 6 sec) [ -20337.4206] [ 3232] [depth= 2] . ( 6 sec) [ -20300.9512] [ 3231] [depth= 2] . ( 6 sec) [ -20234.2791] [ 3219] [depth= 1] . ( 6 sec) [ -20203.3507] [ 3207] [depth= 3] . ( 6 sec) [ -20102.1292] [ 3163] [depth= 2] . ( 6 sec) [ -20062.6963] [ 3159] [depth= 4] . ( 7 sec) [ -20043.1560] [ 3145] [depth= 3] . ( 7 sec) [ -19955.3734] [ 3143] [depth= 1] . ( 7 sec) [ -19879.3984] [ 3123] [depth= 4] . ( 7 sec) [ -19509.1813] [ 3118] [depth= 3] . ( 7 sec) [ -19313.5207] [ 3112] [depth= 9] . ( 7 sec) [ -19208.6028] [ 3110] [depth= 1] . ( 7 sec) [ -19071.5754] [ 3075] [depth= 3] . ( 7 sec) [ -19040.6004] [ 3070] [depth= 6] . ( 7 sec) [ -18815.2164] [ 3015] [depth= 6] . ( 7 sec) [ -18682.9821] [ 3012] [depth= 11] . ( 8 sec) [ -18443.0606] [ 3009] [depth= 2] . ( 8 sec) [ -18327.2638] [ 3009] [depth= 1] . ( 8 sec) [ -18278.1405] [ 3003] [depth= 6] . ( 8 sec) [ -18225.7103] [ 3001] [depth= 1] . ( 8 sec) [ -17972.4959] [ 3000] [depth= 6] . ( 8 sec) [ -17769.5565] [ 3000] [depth= 1] . ( 8 sec) [ -17456.1316] [ 2975] [depth= 8] . ( 8 sec) [ -17319.6864] [ 2961] [depth= 11] . ( 9 sec) [ -17135.8172] [ 2906] [depth= 6] . ( 9 sec) [ -17031.0114] [ 2899] [depth= 5] . ( 9 sec) [ -16977.1777] [ 2889] [depth= 16] . ( 9 sec) [ -16775.5667] [ 2885] [depth= 14] . ( 9 sec) [ -16688.3041] [ 2878] [depth= 5] . ( 9 sec) [ -16440.9941] [ 2895] [depth= 1] . ( 9 sec) [ -16097.7940] [ 2895] [depth= 1] . ( 9 sec) [ -15558.5983] [ 2830] [depth= 5] . ( 10 sec) [ -15301.6157] [ 2767] [depth= 17] . ( 10 sec) [ -15300.3316] [ 2767] [depth= 22] . ( 10 sec) [ -15082.3494] [ 2711] [depth= 10] . ( 10 sec) [ -14972.4792] [ 2673] [depth= 2] . ( 10 sec) [ -14962.6208] [ 2672] [depth= 1] . ( 10 sec) [ -14823.6769] [ 2671] [depth= 1] . ( 10 sec) [ -14786.2779] [ 2650] [depth= 13] . ( 10 sec) [ -14781.9511] [ 2632] [depth= 7] . ( 11 sec) [ -14379.2711] [ 2616] [depth= 18] . ( 11 sec) [ -14143.8187] [ 2558] [depth= 12] . ( 11 sec) [ -13976.5025] [ 2522] [depth= 1] . ( 11 sec) [ -13867.4659] [ 2512] [depth= 6] . ( 11 sec) [ -13698.2886] [ 2467] [depth= 6] . ( 11 sec) [ -13538.3008] [ 2463] [depth= 5] . ( 11 sec) [ -13398.8410] [ 2396] [depth= 8] . ( 11 sec) [ -13306.2845] [ 2377] [depth= 13] . ( 11 sec) [ -13206.2289] [ 2377] [depth= 1] . ( 12 sec) [ -13202.9136] [ 2377] [depth= 7] . ( 12 sec) [ -13174.5702] [ 2377] [depth= 20] . ( 12 sec) [ -13161.7510] [ 2379] [depth= 1] . ( 12 sec) [ -12978.8413] [ 2333] [depth= 20] . ( 12 sec) [ -12928.1290] [ 2328] [depth= 2] . ( 12 sec) [ -12884.1355] [ 2309] [depth= 9] . ( 12 sec) [ -12836.5781] [ 2304] [depth= 6] . ( 12 sec) [ -12818.4237] [ 2298] [depth= 1] . ( 12 sec) [ -12770.1639] [ 2294] [depth= 2] . ( 13 sec) [ -12759.6162] [ 2295] [depth= 5] . ( 13 sec) [ -12571.1372] [ 2256] [depth= 5] . ( 13 sec) [ -12564.9474] [ 2256] [depth= 1] . ( 13 sec) [ -12469.7033] [ 2246] [depth= 3] . ( 13 sec) [ -12455.3014] [ 2244] [depth= 8] . ( 13 sec) [ -12441.4989] [ 2244] [depth= 1] . ( 14 sec) [ -12366.1333] [ 2244] [depth= 5] . ( 14 sec) [ -12363.3689] [ 2246] [depth= 7] . ( 14 sec) [ -12282.5057] [ 2238] [depth= 22] . ( 14 sec) [ -12248.3456] [ 2238] [depth= 12] . ( 14 sec) [ -12247.7063] [ 2238] [depth= 1] . ( 14 sec) [ -12244.5763] [ 2240] [depth= 11] . ( 14 sec) [ -12233.9657] [ 2235] [depth= 4] . ( 14 sec) [ -12206.8587] [ 2235] [depth= 1] . ( 15 sec) [ -12139.3263] [ 2211] [depth= 6] . ( 15 sec) [ -12108.2505] [ 2198] [depth= 14] . ( 15 sec) [ -11971.8749] [ 2188] [depth= 3] . ( 15 sec) [ -11855.2944] [ 2186] [depth= 2] . ( 15 sec) [ -11775.0335] [ 2199] [depth= 1] . ( 15 sec) [ -11661.8979] [ 2177] [depth= 13] . ( 15 sec) [ -11580.5863] [ 2149] [depth= 1] . ( 15 sec) [ -11556.4153] [ 2142] [depth= 1] . ( 16 sec) [ -11545.4264] [ 2142] [depth= 1] . ( 16 sec) [ -11528.2226] [ 2143] [depth= 1] . ( 16 sec) [ -11449.5083] [ 2112] [depth= 5] . ( 16 sec) [ -11428.7407] [ 2109] [depth= 3] . ( 16 sec) [ -11330.3213] [ 2097] [depth= 2] . ( 16 sec) [ -11303.1289] [ 2101] [depth= 8] . ( 16 sec) [ -11264.1488] [ 2081] [depth= 1] . ( 16 sec) [ -11218.7671] [ 2067] [depth= 13] . ( 17 sec) [ -11192.1200] [ 2059] [depth= 7] . ( 17 sec) [ -11170.4082] [ 2050] [depth= 2] . ( 17 sec) [ -11166.0423] [ 2047] [depth= 2] . ( 17 sec) [ -11074.7822] [ 2037] [depth= 6] . ( 17 sec) [ -11042.3917] [ 2027] [depth= 3] . ( 17 sec) [ -10924.9367] [ 1976] [depth= 10] . ( 17 sec) [ -10915.5343] [ 1977] [depth= 1] . ( 17 sec) [ -10820.5503] [ 1965] [depth= 5] . ( 18 sec) [ -10819.4230] [ 1965] [depth= 1] . ( 18 sec) [ -10713.0040] [ 1959] [depth= 6] . ( 18 sec) [ -10690.4186] [ 1953] [depth= 2] . ( 18 sec) [ -10670.9579] [ 1948] [depth= 2] . ( 18 sec) [ -10523.0142] [ 1902] [depth= 6] . ( 18 sec) [ -10490.5457] [ 1884] [depth= 3] . ( 19 sec) [ -10488.8839] [ 1885] [depth= 1] . ( 19 sec) [ -10456.5058] [ 1885] [depth= 1] . ( 19 sec) [ -10232.7415] [ 1866] [depth= 5] . ( 19 sec) [ -10224.9730] [ 1866] [depth= 3] . ( 19 sec) [ -10223.9753] [ 1864] [depth= 6] . ( 19 sec) [ -10221.0064] [ 1863] [depth= 1] . ( 19 sec) [ -10115.2875] [ 1826] [depth= 6] . ( 19 sec) [ -10049.7796] [ 1826] [depth= 1] . ( 19 sec) [ -9969.9391] [ 1807] [depth= 8] . ( 20 sec) [ -9929.6523] [ 1808] [depth= 1] . ( 20 sec) [ -9919.4040] [ 1808] [depth= 1] . ( 20 sec) [ -9915.1436] [ 1808] [depth= 2] . ( 20 sec) [ -9861.2299] [ 1798] [depth= 4] . ( 20 sec) [ -9808.7059] [ 1787] [depth= 8] . ( 20 sec) [ -9729.0391] [ 1769] [depth= 13] . ( 20 sec) [ -9702.2758] [ 1760] [depth= 6] . ( 20 sec) [ -9699.7817] [ 1760] [depth= 1] . ( 21 sec) [ -9684.7495] [ 1758] [depth= 2] . ( 21 sec) [ -9628.9343] [ 1743] [depth= 6] . ( 21 sec) [ -9553.8666] [ 1723] [depth= 3] . ( 21 sec) [ -9521.9093] [ 1725] [depth= 1] . ( 21 sec) [ -9337.8758] [ 1701] [depth= 1] . ( 21 sec) [ -9260.6464] [ 1691] [depth= 6] . ( 21 sec) [ -9074.9349] [ 1669] [depth= 12] . ( 22 sec) [ -9035.1470] [ 1659] [depth= 2] . ( 22 sec) [ -8942.3404] [ 1628] [depth= 7] . ( 22 sec) [ -8942.2222] [ 1627] [depth= 1] . ( 22 sec) [ -8940.8438] [ 1614] [depth= 3] . ( 22 sec) [ -8861.6237] [ 1609] [depth= 4] . ( 22 sec) [ -8833.7136] [ 1603] [depth= 2] . ( 22 sec) [ -8796.0492] [ 1596] [depth= 1] . ( 22 sec) [ -8778.8678] [ 1591] [depth= 2] . ( 23 sec) [ -8777.7741] [ 1591] [depth= 2] . ( 23 sec) [ -8741.1234] [ 1583] [depth= 1] . ( 23 sec) [ -8704.9770] [ 1566] [depth= 1] . ( 23 sec) [ -8694.8535] [ 1566] [depth= 3] . ( 23 sec) [ -8690.0479] [ 1567] [depth= 1] . ( 24 sec) [ -8686.5273] [ 1564] [depth= 1] . ( 24 sec) [ -8680.1416] [ 1564] [depth= 2] . ( 24 sec) [ -8669.0710] [ 1561] [depth= 2] . ( 24 sec) [ -8656.7833] [ 1558] [depth= 2] . ( 24 sec) [ -8616.4568] [ 1542] [depth= 4] . ( 24 sec) [ -8614.3376] [ 1541] [depth= 1] . ( 24 sec) [ -8607.5820] [ 1541] [depth= 1] . ( 25 sec) [ -8557.3007] [ 1520] [depth= 2] . ( 25 sec) [ -8467.6531] [ 1492] [depth= 3] . ( 25 sec) [ -8447.8793] [ 1497] [depth= 1] . ( 25 sec) [ -8441.5191] [ 1496] [depth= 1] . ( 25 sec) [ -8437.4159] [ 1495] [depth= 1] . ( 25 sec) [ -8436.1633] [ 1495] [depth= 1] . ( 25 sec) [ -8400.8134] [ 1480] [depth= 3] . ( 26 sec) [ -8381.9238] [ 1472] [depth= 2] . ( 26 sec) [ -8368.2325] [ 1464] [depth= 2] . ( 26 sec) [ -8249.0903] [ 1442] [depth= 1] . ( 26 sec) [ -8196.3538] [ 1437] [depth= 2] . ( 26 sec) [ -8191.6222] [ 1431] [depth= 2] . ( 26 sec) [ -8158.0342] [ 1433] [depth= 3] . ( 26 sec) [ -8151.8101] [ 1439] [depth= 1] . ( 26 sec) [ -8144.9218] [ 1437] [depth= 1] . ( 26 sec) [ -8139.0549] [ 1436] [depth= 1] . ( 27 sec) [ -8127.7289] [ 1432] [depth= 4] . ( 27 sec) [ -8031.8277] [ 1411] [depth= 4] . ( 27 sec) [ -8009.0929] [ 1413] [depth= 1] . ( 27 sec) [ -8008.4561] [ 1413] [depth= 3] . ( 27 sec) [ -8005.4379] [ 1413] [depth= 1] . ( 28 sec) [ -7948.9720] [ 1396] [depth= 2] . ( 29 sec) [ -7932.8769] [ 1393] [depth= 4] . ( 29 sec) [ -7932.4297] [ 1391] [depth= 4] . ( 29 sec) [ -7928.7375] [ 1391] [depth= 1] . ( 29 sec) [ -7927.6227] [ 1391] [depth= 1] . ( 29 sec) [ -7912.7349] [ 1383] [depth= 7] . ( 30 sec) [ -7767.5727] [ 1336] [depth= 8] . ( 31 sec) [ -7552.8167] [Branch lengths ] . ( 33 sec) [ -7538.7906] [GTR parameters ] . ( 33 sec) [ -7512.2794] [Alpha ][ 0.314272] . ( 34 sec) [ -7485.2204] [ 1329] [depth= 3] . ( 34 sec) [ -7479.6744] [ 1326] [depth= 1] . ( 34 sec) [ -7475.4728] [ 1325] [depth= 3] . ( 34 sec) [ -7471.0539] [ 1322] [depth= 1] . ( 35 sec) [ -7423.5612] [ 1296] [depth= 10] . ( 35 sec) [ -7423.5390] [ 1296] [depth= 1] . ( 35 sec) [ -7368.6505] [ 1275] [depth= 8] . ( 35 sec) [ -7365.5309] [ 1275] [depth= 1] . ( 35 sec) [ -7339.7651] [ 1255] [depth= 7] . ( 35 sec) [ -7339.2607] [ 1254] [depth= 1] . ( 36 sec) [ -7339.2204] [ 1254] [depth= 1] . ( 36 sec) [ -7332.0456] [ 1250] [depth= 3] . ( 36 sec) [ -7331.3642] [ 1250] [depth= 1] . ( 36 sec) [ -7328.9242] [ 1250] [depth= 1] . ( 36 sec) [ -7328.4841] [ 1250] [depth= 1] . ( 36 sec) [ -7328.3895] [ 1250] [depth= 1] . ( 36 sec) [ -7324.4246] [ 1249] [depth= 1] . ( 37 sec) [ -7313.9400] [ 1245] [depth= 4] . ( 38 sec) [ -7313.8033] [ 1245] [depth= 1] . ( 38 sec) [ -7311.4932] [ 1243] [depth= 1] . ( 38 sec) [ -7303.0000] [ 1242] [depth= 1] . ( 39 sec) [ -7302.9072] [ 1242] [depth= 1] . ( 39 sec) [ -7302.7381] [ 1242] [depth= 1] . ( 40 sec) [ -7302.2516] [ 1243] [depth= 1] . ( 40 sec) [ -7300.8041] [ 1241] [depth= 1] . ( 40 sec) [ -7298.9154] [ 1241] [depth= 1] . ( 40 sec) [ -7298.3999] [ 1241] [depth= 1] . ( 41 sec) [ -7297.4409] [ 1241] [depth= 1] . ( 41 sec) [ -7296.8365] [ 1243] [depth= 1] . ( 41 sec) [ -7296.7497] [ 1243] [depth= 1] . ( 42 sec) [ -7296.6002] [ 1243] [depth= 1] . ( 42 sec) [ -7252.6836] [ 1223] [depth= 5] . ( 43 sec) [ -7252.5955] [ 1223] [depth= 1] . ( 43 sec) [ -7250.6679] [ 1223] [depth= 1] . ( 43 sec) [ -7249.1497] [ 1220] [depth= 2] . ( 43 sec) [ -7247.6228] [ 1219] [depth= 2] . ( 44 sec) [ -7246.0085] [ 1220] [depth= 2] . ( 45 sec) [ -7245.4537] [ 1224] [depth= 1] . ( 46 sec) [ -7239.6276] [ 1219] [depth= 1] . ( 46 sec) [ -7236.4063] [ 1218] [depth= 2] . ( 47 sec) [ -7236.3931] [ 1218] [depth= 2] . ( 47 sec) [ -7236.3012] [ 1218] [depth= 1] . ( 50 sec) [ -7236.1985] [ 1218] [depth= 3] . ( 51 sec) [ -7236.1804] [ 1218] [depth= 2] . ( 51 sec) [ -7231.6710] [ 1218] [depth= 1] . ( 52 sec) [ -7231.1332] [ 1218] [depth= 1] . ( 53 sec) [ -7230.8099] [ 1218] [depth= 1] . ( 53 sec) [ -7230.3159] [ 1221] [depth= 1] . ( 53 sec) [ -7228.7640] [ 1217] [depth= 1] . ( 53 sec) [ -7227.4315] [ 1219] [depth= 1] . ( 54 sec) [ -7222.1415] [ 1219] [depth= 1] . ( 54 sec) [ -7222.1278] [ 1219] [depth= 1] . ( 56 sec) [ -7221.1188] [ 1219] [depth= 3] . ( 56 sec) [ -7219.8203] [ 1219] [depth= 2] . ( 56 sec) [ -7219.1912] [ 1220] [depth= 1] . ( 57 sec) [ -7200.5419] [Branch lengths ] . ( 59 sec) [ -7199.5945] [GTR parameters ] . ( 59 sec) [ -7199.5364] [Alpha ][ 0.321337] . ( 61 sec) [ -7195.7920] [ 1224] [depth= 4] . ( 66 sec) [ -7195.7247] [ 1224] [depth= 1] . ( 67 sec) [ -7195.1388] [ 1220] [depth= 1] . ( 72 sec) [ -7192.5574] [ 1220] [depth= 1] . ( 72 sec) [ -7192.2366] [ 1219] [depth= 3] . ( 88 sec) [ -7190.4959] [Branch lengths ] . ( 89 sec) [ -7190.4881] [GTR parameters ] . ( 89 sec) [ -7190.4875] [Alpha ][ 0.320530] . ( 92 sec) [ -7190.3533] [ 1218] [depth= 2] . ( 93 sec) [ -7190.3379] [ 1218] [depth= 1] . ( 99 sec) [ -7190.0034] [ 1218] [depth= 1] . ( 116 sec) [ -7189.5662] [Branch lengths ] . ( 117 sec) [ -7189.5633] [GTR parameters ] . ( 117 sec) [ -7189.5632] [Alpha ][ 0.320107] . ( 216 sec) [ -7189.5483] [Branch lengths ] . ( 216 sec) [ -7189.5483] [Topology ] . ( 218 sec) [ -7189.5477] [Topology ] . ( 218 sec) [ -7189.5477] [GTR parameters ] . ( 218 sec) [ -7189.5477] [Alpha ][ 0.319787] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7189.547650. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -20578.8584] [GTR parameters ] . ( 2 sec) [ -20041.6506] [Alpha ][ 0.500960] . ( 3 sec) [ -19857.3167] [ 3350] [depth= 11] . ( 3 sec) [ -19669.7065] [ 3323] [depth= 11] . ( 3 sec) [ -19638.0698] [ 3296] [depth= 10] . ( 3 sec) [ -19583.4520] [ 3291] [depth= 1] . ( 3 sec) [ -19516.9283] [ 3283] [depth= 4] . ( 3 sec) [ -19447.7866] [ 3283] [depth= 1] . ( 3 sec) [ -19375.3201] [ 3279] [depth= 3] . ( 3 sec) [ -19187.5020] [ 3256] [depth= 3] . ( 4 sec) [ -19008.5360] [ 3253] [depth= 10] . ( 4 sec) [ -18927.8890] [ 3238] [depth= 6] . ( 4 sec) [ -18918.3010] [ 3234] [depth= 2] . ( 4 sec) [ -18863.2535] [ 3229] [depth= 9] . ( 4 sec) [ -18837.3787] [ 3229] [depth= 4] . ( 4 sec) [ -18679.4090] [ 3202] [depth= 5] . ( 4 sec) [ -18338.3546] [ 3171] [depth= 10] . ( 4 sec) [ -18252.6976] [ 3169] [depth= 1] . ( 4 sec) [ -18210.6272] [ 3164] [depth= 10] . ( 5 sec) [ -18134.0248] [ 3157] [depth= 14] . ( 5 sec) [ -18107.2787] [ 3156] [depth= 1] . ( 5 sec) [ -17984.3720] [ 3144] [depth= 8] . ( 5 sec) [ -17759.3229] [ 3073] [depth= 17] . ( 5 sec) [ -17753.7776] [ 3100] [depth= 7] . ( 5 sec) [ -17619.1223] [ 3072] [depth= 1] . ( 5 sec) [ -17613.6651] [ 3066] [depth= 13] . ( 5 sec) [ -17502.3972] [ 3047] [depth= 3] . ( 5 sec) [ -17258.8853] [ 3012] [depth= 13] . ( 6 sec) [ -17044.8983] [ 2973] [depth= 2] . ( 6 sec) [ -16995.3991] [ 2963] [depth= 3] . ( 6 sec) [ -16928.7757] [ 2958] [depth= 1] . ( 6 sec) [ -16800.3496] [ 2935] [depth= 6] . ( 6 sec) [ -16688.4055] [ 2910] [depth= 2] . ( 6 sec) [ -16662.0540] [ 2908] [depth= 1] . ( 6 sec) [ -16471.8694] [ 2845] [depth= 9] . ( 6 sec) [ -16394.2887] [ 2845] [depth= 5] . ( 6 sec) [ -16170.5646] [ 2796] [depth= 6] . ( 7 sec) [ -15805.9104] [ 2755] [depth= 17] . ( 7 sec) [ -15740.4067] [ 2750] [depth= 1] . ( 7 sec) [ -15165.7135] [ 2691] [depth= 5] . ( 7 sec) [ -15144.6771] [ 2692] [depth= 1] . ( 7 sec) [ -14845.6589] [ 2645] [depth= 12] . ( 7 sec) [ -14788.2821] [ 2666] [depth= 4] . ( 7 sec) [ -14662.4353] [ 2639] [depth= 1] . ( 7 sec) [ -14438.5175] [ 2579] [depth= 11] . ( 7 sec) [ -14391.3464] [ 2590] [depth= 12] . ( 8 sec) [ -14369.2473] [ 2587] [depth= 2] . ( 8 sec) [ -14243.1931] [ 2580] [depth= 3] . ( 8 sec) [ -14163.2083] [ 2556] [depth= 14] . ( 8 sec) [ -13892.6818] [ 2547] [depth= 13] . ( 8 sec) [ -13887.2206] [ 2547] [depth= 1] . ( 8 sec) [ -13862.5651] [ 2530] [depth= 8] . ( 8 sec) [ -13808.3762] [ 2542] [depth= 1] . ( 8 sec) [ -13759.2144] [ 2536] [depth= 2] . ( 9 sec) [ -13562.2934] [ 2510] [depth= 15] . ( 9 sec) [ -13204.8878] [ 2454] [depth= 8] . ( 9 sec) [ -13198.3591] [ 2453] [depth= 1] . ( 9 sec) [ -13127.9509] [ 2443] [depth= 10] . ( 9 sec) [ -13099.5310] [ 2438] [depth= 1] . ( 9 sec) [ -13098.8279] [ 2438] [depth= 1] . ( 9 sec) [ -12894.1374] [ 2423] [depth= 9] . ( 9 sec) [ -12625.4566] [ 2395] [depth= 2] . ( 9 sec) [ -12618.6985] [ 2394] [depth= 3] . ( 10 sec) [ -12614.4647] [ 2390] [depth= 10] . ( 10 sec) [ -12605.9285] [ 2388] [depth= 4] . ( 10 sec) [ -12595.2763] [ 2386] [depth= 2] . ( 10 sec) [ -12591.8357] [ 2386] [depth= 1] . ( 10 sec) [ -12549.3188] [ 2382] [depth= 15] . ( 10 sec) [ -12497.0884] [ 2386] [depth= 1] . ( 10 sec) [ -12333.4921] [ 2343] [depth= 3] . ( 10 sec) [ -12173.3451] [ 2317] [depth= 4] . ( 10 sec) [ -12099.0072] [ 2306] [depth= 1] . ( 10 sec) [ -12089.1468] [ 2306] [depth= 3] . ( 11 sec) [ -11986.4181] [ 2267] [depth= 7] . ( 11 sec) [ -11891.7240] [ 2258] [depth= 1] . ( 11 sec) [ -11844.6813] [ 2250] [depth= 7] . ( 11 sec) [ -11793.9297] [ 2245] [depth= 2] . ( 11 sec) [ -11758.0936] [ 2236] [depth= 2] . ( 11 sec) [ -11750.8847] [ 2236] [depth= 1] . ( 11 sec) [ -11556.1633] [ 2213] [depth= 17] . ( 11 sec) [ -11227.0235] [ 2196] [depth= 16] . ( 12 sec) [ -11226.1276] [ 2196] [depth= 1] . ( 12 sec) [ -11194.7246] [ 2193] [depth= 11] . ( 12 sec) [ -11163.3623] [ 2181] [depth= 12] . ( 12 sec) [ -11123.8709] [ 2174] [depth= 2] . ( 12 sec) [ -11046.9581] [ 2165] [depth= 14] . ( 12 sec) [ -11034.7901] [ 2152] [depth= 12] . ( 12 sec) [ -10868.4338] [ 2146] [depth= 11] . ( 12 sec) [ -10822.1574] [ 2147] [depth= 3] . ( 13 sec) [ -10698.4967] [ 2082] [depth= 10] . ( 13 sec) [ -10695.2041] [ 2082] [depth= 1] . ( 13 sec) [ -10694.5672] [ 2082] [depth= 2] . ( 13 sec) [ -10694.3834] [ 2082] [depth= 3] . ( 13 sec) [ -10630.0531] [ 2071] [depth= 6] . ( 13 sec) [ -10629.9245] [ 2071] [depth= 1] . ( 14 sec) [ -10556.8879] [ 2038] [depth= 4] . ( 14 sec) [ -10552.9176] [ 2025] [depth= 5] . ( 14 sec) [ -10491.2895] [ 2025] [depth= 1] . ( 14 sec) [ -10463.4692] [ 2020] [depth= 1] . ( 14 sec) [ -10450.0601] [ 2026] [depth= 1] . ( 14 sec) [ -10427.8028] [ 2021] [depth= 1] . ( 14 sec) [ -10423.5238] [ 2023] [depth= 1] . ( 14 sec) [ -10416.0627] [ 2021] [depth= 2] . ( 14 sec) [ -10221.2264] [ 1975] [depth= 14] . ( 15 sec) [ -10084.0477] [ 1938] [depth= 15] . ( 15 sec) [ -10051.2890] [ 1918] [depth= 1] . ( 15 sec) [ -10048.5481] [ 1919] [depth= 1] . ( 15 sec) [ -9991.1487] [ 1908] [depth= 11] . ( 15 sec) [ -9990.1045] [ 1908] [depth= 1] . ( 15 sec) [ -9873.3359] [ 1853] [depth= 3] . ( 15 sec) [ -9871.3480] [ 1844] [depth= 8] . ( 15 sec) [ -9849.2285] [ 1836] [depth= 1] . ( 15 sec) [ -9716.5338] [ 1798] [depth= 5] . ( 16 sec) [ -9640.7137] [ 1787] [depth= 9] . ( 16 sec) [ -9634.4239] [ 1786] [depth= 4] . ( 16 sec) [ -9633.7394] [ 1786] [depth= 1] . ( 16 sec) [ -9563.8523] [ 1779] [depth= 3] . ( 16 sec) [ -9487.5681] [ 1774] [depth= 4] . ( 16 sec) [ -9475.5518] [ 1774] [depth= 1] . ( 16 sec) [ -9446.7202] [ 1751] [depth= 5] . ( 16 sec) [ -9340.8374] [ 1753] [depth= 1] . ( 17 sec) [ -9340.5850] [ 1754] [depth= 1] . ( 17 sec) [ -9337.8849] [ 1752] [depth= 3] . ( 17 sec) [ -9337.0452] [ 1752] [depth= 1] . ( 17 sec) [ -9216.6218] [ 1709] [depth= 4] . ( 17 sec) [ -9214.6439] [ 1702] [depth= 3] . ( 17 sec) [ -9214.6036] [ 1702] [depth= 1] . ( 17 sec) [ -9213.0516] [ 1702] [depth= 3] . ( 17 sec) [ -9177.7243] [ 1684] [depth= 1] . ( 17 sec) [ -9177.2109] [ 1688] [depth= 3] . ( 18 sec) [ -9146.2871] [ 1688] [depth= 1] . ( 18 sec) [ -9108.9812] [ 1674] [depth= 3] . ( 18 sec) [ -9085.3839] [ 1669] [depth= 3] . ( 18 sec) [ -9066.7788] [ 1661] [depth= 1] . ( 18 sec) [ -8988.9699] [ 1646] [depth= 1] . ( 18 sec) [ -8981.1211] [ 1643] [depth= 1] . ( 19 sec) [ -8970.9801] [ 1644] [depth= 2] . ( 19 sec) [ -8912.0470] [ 1627] [depth= 9] . ( 19 sec) [ -8899.6132] [ 1628] [depth= 1] . ( 19 sec) [ -8889.6274] [ 1627] [depth= 1] . ( 19 sec) [ -8868.8364] [ 1621] [depth= 10] . ( 19 sec) [ -8820.7593] [ 1618] [depth= 1] . ( 19 sec) [ -8816.5777] [ 1618] [depth= 1] . ( 19 sec) [ -8813.9239] [ 1617] [depth= 1] . ( 20 sec) [ -8790.7209] [ 1621] [depth= 1] . ( 20 sec) [ -8789.5894] [ 1621] [depth= 1] . ( 20 sec) [ -8652.7729] [ 1624] [depth= 16] . ( 20 sec) [ -8646.0189] [ 1623] [depth= 1] . ( 20 sec) [ -8564.3036] [ 1601] [depth= 6] . ( 20 sec) [ -8555.8280] [ 1601] [depth= 1] . ( 20 sec) [ -8536.3356] [ 1601] [depth= 4] . ( 21 sec) [ -8513.7296] [ 1591] [depth= 4] . ( 21 sec) [ -8513.2582] [ 1593] [depth= 2] . ( 21 sec) [ -8503.9802] [ 1584] [depth= 8] . ( 21 sec) [ -8463.3466] [ 1570] [depth= 1] . ( 21 sec) [ -8460.3385] [ 1571] [depth= 1] . ( 21 sec) [ -8388.3154] [ 1544] [depth= 2] . ( 21 sec) [ -8372.7611] [ 1544] [depth= 2] . ( 22 sec) [ -8324.1431] [ 1519] [depth= 6] . ( 22 sec) [ -8323.9398] [ 1519] [depth= 1] . ( 22 sec) [ -8320.7336] [ 1516] [depth= 1] . ( 22 sec) [ -8302.4211] [ 1524] [depth= 2] . ( 22 sec) [ -8298.4178] [ 1524] [depth= 1] . ( 22 sec) [ -8297.9861] [ 1524] [depth= 2] . ( 23 sec) [ -8275.4977] [ 1519] [depth= 8] . ( 23 sec) [ -8260.9567] [ 1515] [depth= 2] . ( 23 sec) [ -8241.5036] [ 1509] [depth= 2] . ( 23 sec) [ -8217.0437] [ 1495] [depth= 3] . ( 23 sec) [ -8203.3117] [ 1491] [depth= 2] . ( 23 sec) [ -8179.4211] [ 1474] [depth= 9] . ( 24 sec) [ -8177.6652] [ 1474] [depth= 1] . ( 24 sec) [ -8162.8446] [ 1472] [depth= 1] . ( 24 sec) [ -8147.4662] [ 1469] [depth= 15] . ( 25 sec) [ -8147.0453] [ 1469] [depth= 1] . ( 25 sec) [ -7989.8939] [ 1427] [depth= 12] . ( 25 sec) [ -7975.7715] [ 1425] [depth= 1] . ( 26 sec) [ -7783.6458] [Branch lengths ] . ( 28 sec) [ -7774.4039] [GTR parameters ] . ( 29 sec) [ -7738.6908] [Alpha ][ 0.296462] . ( 29 sec) [ -7710.9163] [ 1400] [depth= 4] . ( 29 sec) [ -7688.4871] [ 1366] [depth= 4] . ( 29 sec) [ -7686.3721] [ 1363] [depth= 1] . ( 30 sec) [ -7675.3925] [ 1356] [depth= 6] . ( 30 sec) [ -7667.8676] [ 1360] [depth= 2] . ( 30 sec) [ -7667.7681] [ 1359] [depth= 1] . ( 31 sec) [ -7655.6683] [ 1350] [depth= 1] . ( 31 sec) [ -7655.0914] [ 1350] [depth= 1] . ( 31 sec) [ -7618.3743] [ 1335] [depth= 2] . ( 31 sec) [ -7589.4962] [ 1323] [depth= 1] . ( 32 sec) [ -7583.3536] [ 1322] [depth= 2] . ( 32 sec) [ -7574.6396] [ 1316] [depth= 3] . ( 33 sec) [ -7574.6118] [ 1316] [depth= 1] . ( 34 sec) [ -7561.1415] [ 1312] [depth= 1] . ( 34 sec) [ -7560.9298] [ 1313] [depth= 1] . ( 34 sec) [ -7537.4690] [ 1302] [depth= 2] . ( 35 sec) [ -7478.6964] [ 1285] [depth= 1] . ( 35 sec) [ -7451.1824] [ 1280] [depth= 12] . ( 36 sec) [ -7451.0987] [ 1280] [depth= 2] . ( 36 sec) [ -7450.8252] [ 1280] [depth= 1] . ( 36 sec) [ -7449.3807] [ 1284] [depth= 1] . ( 37 sec) [ -7442.7385] [ 1285] [depth= 5] . ( 37 sec) [ -7442.6665] [ 1285] [depth= 3] . ( 37 sec) [ -7434.1245] [ 1285] [depth= 1] . ( 37 sec) [ -7407.8306] [ 1275] [depth= 12] . ( 37 sec) [ -7404.6613] [ 1274] [depth= 3] . ( 38 sec) [ -7404.6436] [ 1274] [depth= 1] . ( 38 sec) [ -7399.8721] [ 1276] [depth= 4] . ( 38 sec) [ -7394.9746] [ 1275] [depth= 2] . ( 38 sec) [ -7382.0616] [ 1268] [depth= 1] . ( 38 sec) [ -7377.7830] [ 1265] [depth= 1] . ( 39 sec) [ -7368.7824] [ 1254] [depth= 2] . ( 39 sec) [ -7368.1795] [ 1254] [depth= 1] . ( 40 sec) [ -7353.8325] [ 1247] [depth= 1] . ( 41 sec) [ -7347.9919] [ 1245] [depth= 5] . ( 42 sec) [ -7347.5996] [ 1245] [depth= 2] . ( 43 sec) [ -7346.5505] [ 1245] [depth= 1] . ( 43 sec) [ -7344.3200] [ 1244] [depth= 1] . ( 44 sec) [ -7341.2498] [ 1242] [depth= 2] . ( 44 sec) [ -7340.8327] [ 1240] [depth= 3] . ( 45 sec) [ -7339.2359] [ 1239] [depth= 1] . ( 45 sec) [ -7339.1397] [ 1239] [depth= 1] . ( 46 sec) [ -7338.9893] [ 1238] [depth= 1] . ( 46 sec) [ -7338.2736] [ 1242] [depth= 1] . ( 46 sec) [ -7330.4528] [ 1241] [depth= 1] . ( 46 sec) [ -7327.1608] [ 1241] [depth= 1] . ( 46 sec) [ -7325.1052] [ 1240] [depth= 5] . ( 46 sec) [ -7324.2271] [ 1240] [depth= 1] . ( 47 sec) [ -7320.3234] [ 1239] [depth= 1] . ( 47 sec) [ -7319.2692] [ 1239] [depth= 1] . ( 48 sec) [ -7308.9808] [ 1235] [depth= 1] . ( 48 sec) [ -7308.9360] [ 1235] [depth= 1] . ( 49 sec) [ -7306.2377] [ 1235] [depth= 1] . ( 49 sec) [ -7306.1807] [ 1235] [depth= 1] . ( 49 sec) [ -7301.2635] [ 1233] [depth= 1] . ( 50 sec) [ -7296.8506] [ 1226] [depth= 2] . ( 50 sec) [ -7296.6630] [ 1225] [depth= 2] . ( 50 sec) [ -7293.9078] [ 1224] [depth= 1] . ( 51 sec) [ -7290.2548] [ 1223] [depth= 1] . ( 51 sec) [ -7287.1262] [ 1223] [depth= 1] . ( 51 sec) [ -7286.7604] [ 1225] [depth= 1] . ( 52 sec) [ -7286.6949] [ 1225] [depth= 1] . ( 53 sec) [ -7285.7333] [ 1224] [depth= 2] . ( 53 sec) [ -7285.5514] [ 1225] [depth= 1] . ( 55 sec) [ -7285.2440] [ 1225] [depth= 2] . ( 55 sec) [ -7284.8397] [ 1225] [depth= 1] . ( 56 sec) [ -7284.1741] [ 1233] [depth= 2] . ( 59 sec) [ -7251.3876] [Branch lengths ] . ( 61 sec) [ -7248.8896] [GTR parameters ] . ( 61 sec) [ -7248.5762] [Alpha ][ 0.312325] . ( 61 sec) [ -7244.8944] [ 1233] [depth= 1] . ( 62 sec) [ -7238.5704] [ 1231] [depth= 3] . ( 62 sec) [ -7235.2066] [ 1229] [depth= 1] . ( 63 sec) [ -7217.9762] [ 1222] [depth= 4] . ( 64 sec) [ -7217.1864] [ 1223] [depth= 1] . ( 66 sec) [ -7215.0708] [ 1222] [depth= 2] . ( 70 sec) [ -7215.0493] [ 1222] [depth= 1] . ( 70 sec) [ -7214.5940] [ 1220] [depth= 1] . ( 71 sec) [ -7214.5706] [ 1220] [depth= 2] . ( 73 sec) [ -7214.5601] [ 1220] [depth= 2] . ( 74 sec) [ -7214.5497] [ 1220] [depth= 1] . ( 74 sec) [ -7214.0907] [ 1218] [depth= 2] . ( 79 sec) [ -7210.8346] [ 1217] [depth= 1] . ( 85 sec) [ -7210.5431] [ 1217] [depth= 1] . ( 92 sec) [ -7210.5248] [ 1217] [depth= 1] . ( 93 sec) [ -7206.0540] [ 1210] [depth= 2] . ( 95 sec) [ -7206.0245] [ 1210] [depth= 1] . ( 96 sec) [ -7197.6410] [Branch lengths ] . ( 97 sec) [ -7197.0927] [GTR parameters ] . ( 98 sec) [ -7197.0463] [Alpha ][ 0.319002] . ( 124 sec) [ -7196.4943] [Branch lengths ] . ( 208 sec) [ -7196.4674] [Branch lengths ] . ( 208 sec) [ -7196.4674] [Topology ] . ( 210 sec) [ -7196.4666] [Topology ] . ( 211 sec) [ -7196.4627] [GTR parameters ] . ( 211 sec) [ -7196.4594] [Alpha ][ 0.317155] . ( 211 sec) [ -7196.4594] [Topology ] . ( 213 sec) [ -7196.4588] [Topology ] . ( 213 sec) [ -7196.4588] [GTR parameters ] . ( 214 sec) [ -7196.4588] [Alpha ][ 0.317155] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7196.458766. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -22182.0887] [GTR parameters ] . ( 2 sec) [ -21606.6780] [Alpha ][ 0.500960] . ( 2 sec) [ -21492.0450] [ 3407] [depth= 15] . ( 3 sec) [ -21436.1650] [ 3389] [depth= 13] . ( 3 sec) [ -21418.2802] [ 3384] [depth= 7] . ( 3 sec) [ -21301.3899] [ 3380] [depth= 1] . ( 3 sec) [ -21052.5578] [ 3377] [depth= 15] . ( 3 sec) [ -20576.0093] [ 3364] [depth= 5] . ( 3 sec) [ -20322.9355] [ 3354] [depth= 8] . ( 3 sec) [ -20192.0148] [ 3328] [depth= 4] . ( 3 sec) [ -20150.4622] [ 3325] [depth= 4] . ( 3 sec) [ -20121.0863] [ 3319] [depth= 3] . ( 4 sec) [ -20026.2672] [ 3306] [depth= 9] . ( 4 sec) [ -19748.5873] [ 3264] [depth= 7] . ( 4 sec) [ -19705.2695] [ 3266] [depth= 3] . ( 4 sec) [ -19530.7287] [ 3248] [depth= 6] . ( 4 sec) [ -19466.6108] [ 3236] [depth= 6] . ( 4 sec) [ -19338.3958] [ 3219] [depth= 1] . ( 4 sec) [ -19312.5800] [ 3207] [depth= 1] . ( 4 sec) [ -19290.1221] [ 3204] [depth= 1] . ( 4 sec) [ -19132.9494] [ 3185] [depth= 10] . ( 5 sec) [ -18937.4832] [ 3162] [depth= 22] . ( 5 sec) [ -18810.2455] [ 3164] [depth= 1] . ( 5 sec) [ -18733.7708] [ 3166] [depth= 4] . ( 5 sec) [ -18700.2284] [ 3149] [depth= 3] . ( 5 sec) [ -18461.1200] [ 3097] [depth= 21] . ( 5 sec) [ -18208.2775] [ 3052] [depth= 23] . ( 5 sec) [ -18013.2620] [ 3057] [depth= 12] . ( 5 sec) [ -17825.4887] [ 3026] [depth= 16] . ( 5 sec) [ -17424.9019] [ 2993] [depth= 9] . ( 6 sec) [ -17424.0878] [ 3014] [depth= 3] . ( 6 sec) [ -17234.0284] [ 2965] [depth= 9] . ( 6 sec) [ -17053.2889] [ 2936] [depth= 17] . ( 6 sec) [ -17010.4299] [ 2935] [depth= 1] . ( 6 sec) [ -16916.7566] [ 2936] [depth= 1] . ( 6 sec) [ -16643.5203] [ 2925] [depth= 1] . ( 6 sec) [ -16394.8129] [ 2904] [depth= 26] . ( 6 sec) [ -16321.0918] [ 2899] [depth= 2] . ( 7 sec) [ -16207.7539] [ 2894] [depth= 3] . ( 7 sec) [ -15969.2953] [ 2877] [depth= 3] . ( 7 sec) [ -15728.9377] [ 2879] [depth= 1] . ( 7 sec) [ -15352.2574] [ 2831] [depth= 7] . ( 7 sec) [ -15055.1089] [ 2762] [depth= 7] . ( 7 sec) [ -14848.2017] [ 2706] [depth= 10] . ( 7 sec) [ -14681.8402] [ 2692] [depth= 4] . ( 7 sec) [ -14626.1657] [ 2689] [depth= 1] . ( 7 sec) [ -14393.5958] [ 2639] [depth= 2] . ( 8 sec) [ -14352.9197] [ 2636] [depth= 6] . ( 8 sec) [ -14314.9485] [ 2622] [depth= 6] . ( 8 sec) [ -14299.9874] [ 2619] [depth= 11] . ( 8 sec) [ -14261.4087] [ 2610] [depth= 7] . ( 8 sec) [ -14014.0061] [ 2547] [depth= 11] . ( 8 sec) [ -13697.3148] [ 2510] [depth= 18] . ( 8 sec) [ -13633.4854] [ 2508] [depth= 4] . ( 8 sec) [ -13541.7072] [ 2496] [depth= 23] . ( 8 sec) [ -13467.3111] [ 2474] [depth= 5] . ( 9 sec) [ -13278.2046] [ 2466] [depth= 28] . ( 9 sec) [ -12820.9810] [ 2402] [depth= 19] . ( 9 sec) [ -12799.8537] [ 2412] [depth= 2] . ( 9 sec) [ -12799.7936] [ 2409] [depth= 25] . ( 9 sec) [ -12717.0544] [ 2397] [depth= 14] . ( 9 sec) [ -12534.8588] [ 2367] [depth= 27] . ( 9 sec) [ -12442.1020] [ 2351] [depth= 4] . ( 9 sec) [ -12396.2264] [ 2348] [depth= 14] . ( 9 sec) [ -12381.9808] [ 2358] [depth= 1] . ( 10 sec) [ -12267.9893] [ 2334] [depth= 8] . ( 10 sec) [ -12207.1339] [ 2310] [depth= 15] . ( 10 sec) [ -12090.8819] [ 2299] [depth= 7] . ( 10 sec) [ -12066.3984] [ 2284] [depth= 1] . ( 10 sec) [ -12049.3610] [ 2284] [depth= 1] . ( 10 sec) [ -12036.3484] [ 2281] [depth= 2] . ( 10 sec) [ -11972.5621] [ 2279] [depth= 12] . ( 10 sec) [ -11871.9815] [ 2258] [depth= 8] . ( 11 sec) [ -11852.7382] [ 2259] [depth= 17] . ( 11 sec) [ -11767.7277] [ 2248] [depth= 9] . ( 11 sec) [ -11754.6348] [ 2241] [depth= 1] . ( 11 sec) [ -11706.9289] [ 2231] [depth= 2] . ( 11 sec) [ -11344.7660] [ 2226] [depth= 6] . ( 11 sec) [ -11315.4742] [ 2219] [depth= 12] . ( 11 sec) [ -11297.0043] [ 2208] [depth= 11] . ( 11 sec) [ -11294.7096] [ 2208] [depth= 1] . ( 11 sec) [ -11271.3376] [ 2203] [depth= 1] . ( 12 sec) [ -11268.1810] [ 2206] [depth= 1] . ( 12 sec) [ -11149.8723] [ 2161] [depth= 25] . ( 12 sec) [ -11111.3820] [ 2159] [depth= 20] . ( 12 sec) [ -11111.1074] [ 2161] [depth= 1] . ( 12 sec) [ -10945.2669] [ 2134] [depth= 2] . ( 12 sec) [ -10879.9118] [ 2134] [depth= 4] . ( 12 sec) [ -10835.2690] [ 2108] [depth= 1] . ( 12 sec) [ -10813.7010] [ 2106] [depth= 3] . ( 12 sec) [ -10796.9702] [ 2106] [depth= 1] . ( 13 sec) [ -10724.1165] [ 2061] [depth= 9] . ( 13 sec) [ -10701.6261] [ 2053] [depth= 16] . ( 13 sec) [ -10688.0364] [ 2053] [depth= 1] . ( 13 sec) [ -10682.4872] [ 2053] [depth= 1] . ( 13 sec) [ -10555.6747] [ 2006] [depth= 17] . ( 13 sec) [ -10374.2765] [ 2004] [depth= 5] . ( 13 sec) [ -10289.9431] [ 1993] [depth= 2] . ( 14 sec) [ -10288.9220] [ 2002] [depth= 1] . ( 14 sec) [ -10217.5872] [ 1978] [depth= 7] . ( 14 sec) [ -10151.0672] [ 1967] [depth= 13] . ( 14 sec) [ -10021.2381] [ 1916] [depth= 5] . ( 14 sec) [ -10016.2783] [ 1918] [depth= 4] . ( 14 sec) [ -9974.7168] [ 1917] [depth= 16] . ( 14 sec) [ -9966.1301] [ 1915] [depth= 2] . ( 15 sec) [ -9914.1150] [ 1895] [depth= 18] . ( 15 sec) [ -9904.7921] [ 1897] [depth= 2] . ( 15 sec) [ -9877.1734] [ 1890] [depth= 18] . ( 15 sec) [ -9845.0544] [ 1878] [depth= 1] . ( 15 sec) [ -9758.3778] [ 1867] [depth= 7] . ( 15 sec) [ -9729.7307] [ 1850] [depth= 1] . ( 15 sec) [ -9666.8438] [ 1836] [depth= 15] . ( 15 sec) [ -9648.2955] [ 1836] [depth= 2] . ( 15 sec) [ -9634.8789] [ 1834] [depth= 1] . ( 16 sec) [ -9629.5290] [ 1834] [depth= 1] . ( 16 sec) [ -9564.1514] [ 1797] [depth= 7] . ( 16 sec) [ -9548.8730] [ 1796] [depth= 1] . ( 16 sec) [ -9456.1973] [ 1796] [depth= 10] . ( 16 sec) [ -9410.5481] [ 1782] [depth= 3] . ( 16 sec) [ -9406.6586] [ 1780] [depth= 2] . ( 16 sec) [ -9405.7292] [ 1781] [depth= 5] . ( 16 sec) [ -9403.5268] [ 1780] [depth= 1] . ( 17 sec) [ -9360.7065] [ 1779] [depth= 3] . ( 17 sec) [ -9301.9036] [ 1764] [depth= 4] . ( 17 sec) [ -9273.1846] [ 1755] [depth= 1] . ( 17 sec) [ -9142.4823] [ 1735] [depth= 2] . ( 17 sec) [ -9123.5042] [ 1726] [depth= 2] . ( 17 sec) [ -9083.6531] [ 1705] [depth= 2] . ( 17 sec) [ -9082.1335] [ 1694] [depth= 7] . ( 17 sec) [ -9072.5827] [ 1687] [depth= 3] . ( 18 sec) [ -9072.0898] [ 1687] [depth= 1] . ( 18 sec) [ -9054.2082] [ 1669] [depth= 1] . ( 18 sec) [ -9027.2733] [ 1651] [depth= 10] . ( 18 sec) [ -9017.1567] [ 1648] [depth= 1] . ( 18 sec) [ -9016.7986] [ 1648] [depth= 1] . ( 18 sec) [ -8965.6264] [ 1636] [depth= 14] . ( 18 sec) [ -8947.2397] [ 1633] [depth= 1] . ( 19 sec) [ -8905.7179] [ 1627] [depth= 2] . ( 19 sec) [ -8799.4827] [ 1616] [depth= 17] . ( 19 sec) [ -8687.9417] [ 1613] [depth= 1] . ( 19 sec) [ -8677.6072] [ 1611] [depth= 1] . ( 19 sec) [ -8651.8940] [ 1612] [depth= 1] . ( 19 sec) [ -8641.1979] [ 1611] [depth= 1] . ( 19 sec) [ -8526.3783] [ 1584] [depth= 13] . ( 19 sec) [ -8503.2431] [ 1565] [depth= 17] . ( 20 sec) [ -8496.8788] [ 1565] [depth= 1] . ( 20 sec) [ -8426.3710] [ 1551] [depth= 8] . ( 20 sec) [ -8409.5716] [ 1540] [depth= 1] . ( 20 sec) [ -8371.7513] [ 1514] [depth= 5] . ( 20 sec) [ -8359.7235] [ 1508] [depth= 3] . ( 20 sec) [ -8357.3839] [ 1503] [depth= 3] . ( 20 sec) [ -8290.2874] [ 1477] [depth= 10] . ( 21 sec) [ -8215.6770] [ 1458] [depth= 2] . ( 21 sec) [ -8209.2011] [ 1457] [depth= 1] . ( 21 sec) [ -8141.7147] [ 1431] [depth= 4] . ( 21 sec) [ -8117.3399] [ 1423] [depth= 3] . ( 21 sec) [ -8105.9164] [ 1422] [depth= 2] . ( 21 sec) [ -8087.4197] [ 1420] [depth= 4] . ( 22 sec) [ -8082.6531] [ 1420] [depth= 2] . ( 22 sec) [ -8056.0310] [ 1416] [depth= 6] . ( 22 sec) [ -8056.0008] [ 1416] [depth= 2] . ( 22 sec) [ -8022.3999] [ 1410] [depth= 5] . ( 22 sec) [ -8021.7582] [ 1410] [depth= 2] . ( 22 sec) [ -8001.8318] [ 1408] [depth= 4] . ( 23 sec) [ -8000.3960] [ 1413] [depth= 2] . ( 23 sec) [ -7994.7723] [ 1415] [depth= 1] . ( 23 sec) [ -7991.9207] [ 1413] [depth= 1] . ( 23 sec) [ -7990.8937] [ 1415] [depth= 3] . ( 23 sec) [ -7988.5462] [ 1415] [depth= 1] . ( 23 sec) [ -7988.0013] [ 1415] [depth= 1] . ( 23 sec) [ -7987.7233] [ 1415] [depth= 2] . ( 24 sec) [ -7982.7016] [ 1414] [depth= 1] . ( 24 sec) [ -7982.4418] [ 1414] [depth= 2] . ( 24 sec) [ -7982.0780] [ 1412] [depth= 1] . ( 24 sec) [ -7973.2383] [ 1412] [depth= 2] . ( 25 sec) [ -7953.6377] [ 1407] [depth= 7] . ( 25 sec) [ -7943.6083] [ 1405] [depth= 1] . ( 25 sec) [ -7939.7517] [ 1405] [depth= 1] . ( 25 sec) [ -7939.5935] [ 1405] [depth= 3] . ( 25 sec) [ -7912.0862] [ 1402] [depth= 4] . ( 25 sec) [ -7908.2317] [ 1372] [depth= 1] . ( 25 sec) [ -7853.7428] [ 1356] [depth= 4] . ( 26 sec) [ -7700.4423] [Branch lengths ] . ( 29 sec) [ -7688.4596] [GTR parameters ] . ( 29 sec) [ -7659.3958] [Alpha ][ 0.310234] . ( 29 sec) [ -7658.7845] [ 1358] [depth= 1] . ( 30 sec) [ -7654.7914] [ 1359] [depth= 4] . ( 30 sec) [ -7653.2419] [ 1360] [depth= 2] . ( 30 sec) [ -7650.0088] [ 1359] [depth= 2] . ( 30 sec) [ -7649.9910] [ 1359] [depth= 2] . ( 31 sec) [ -7649.9404] [ 1359] [depth= 1] . ( 31 sec) [ -7648.3749] [ 1359] [depth= 9] . ( 31 sec) [ -7648.3412] [ 1359] [depth= 1] . ( 31 sec) [ -7512.4121] [ 1333] [depth= 3] . ( 32 sec) [ -7512.3612] [ 1334] [depth= 1] . ( 32 sec) [ -7502.0767] [ 1336] [depth= 5] . ( 32 sec) [ -7499.7347] [ 1334] [depth= 3] . ( 32 sec) [ -7497.0448] [ 1333] [depth= 2] . ( 32 sec) [ -7495.9465] [ 1334] [depth= 1] . ( 32 sec) [ -7495.8864] [ 1333] [depth= 1] . ( 32 sec) [ -7495.8395] [ 1333] [depth= 1] . ( 33 sec) [ -7494.5306] [ 1334] [depth= 1] . ( 33 sec) [ -7493.8812] [ 1334] [depth= 1] . ( 33 sec) [ -7487.0088] [ 1332] [depth= 1] . ( 33 sec) [ -7402.8986] [ 1297] [depth= 6] . ( 34 sec) [ -7399.2277] [ 1298] [depth= 1] . ( 34 sec) [ -7395.6214] [ 1296] [depth= 3] . ( 35 sec) [ -7395.4226] [ 1295] [depth= 4] . ( 35 sec) [ -7382.5243] [ 1292] [depth= 2] . ( 35 sec) [ -7379.5781] [ 1291] [depth= 1] . ( 35 sec) [ -7379.5153] [ 1291] [depth= 1] . ( 36 sec) [ -7375.5995] [ 1290] [depth= 1] . ( 36 sec) [ -7374.8224] [ 1290] [depth= 1] . ( 36 sec) [ -7349.0089] [ 1282] [depth= 3] . ( 36 sec) [ -7348.9478] [ 1282] [depth= 4] . ( 37 sec) [ -7344.5489] [ 1283] [depth= 2] . ( 37 sec) [ -7344.5137] [ 1283] [depth= 1] . ( 38 sec) [ -7343.5616] [ 1285] [depth= 2] . ( 38 sec) [ -7341.6649] [ 1287] [depth= 1] . ( 40 sec) [ -7339.6143] [ 1287] [depth= 1] . ( 40 sec) [ -7339.1945] [ 1286] [depth= 1] . ( 40 sec) [ -7336.2156] [ 1285] [depth= 1] . ( 42 sec) [ -7335.6502] [ 1285] [depth= 3] . ( 43 sec) [ -7334.5035] [ 1284] [depth= 2] . ( 43 sec) [ -7312.2260] [ 1275] [depth= 9] . ( 43 sec) [ -7310.1273] [ 1274] [depth= 6] . ( 43 sec) [ -7310.0409] [ 1274] [depth= 2] . ( 44 sec) [ -7305.2520] [ 1273] [depth= 1] . ( 45 sec) [ -7305.1971] [ 1273] [depth= 1] . ( 46 sec) [ -7295.0234] [ 1275] [depth= 6] . ( 47 sec) [ -7258.8156] [ 1241] [depth= 11] . ( 47 sec) [ -7258.7882] [ 1241] [depth= 1] . ( 48 sec) [ -7256.6088] [ 1241] [depth= 1] . ( 48 sec) [ -7256.5819] [ 1241] [depth= 3] . ( 49 sec) [ -7256.5699] [ 1241] [depth= 1] . ( 49 sec) [ -7255.0153] [ 1241] [depth= 1] . ( 50 sec) [ -7254.9915] [ 1241] [depth= 1] . ( 50 sec) [ -7254.9246] [ 1241] [depth= 2] . ( 50 sec) [ -7254.9125] [ 1238] [depth= 1] . ( 51 sec) [ -7252.1946] [ 1238] [depth= 1] . ( 51 sec) [ -7251.7001] [ 1237] [depth= 5] . ( 51 sec) [ -7247.1966] [ 1237] [depth= 1] . ( 52 sec) [ -7247.1094] [ 1239] [depth= 4] . ( 53 sec) [ -7244.1373] [ 1238] [depth= 1] . ( 54 sec) [ -7221.9577] [Branch lengths ] . ( 55 sec) [ -7221.5205] [GTR parameters ] . ( 56 sec) [ -7221.4583] [Alpha ][ 0.317403] . ( 56 sec) [ -7201.4095] [ 1224] [depth= 5] . ( 56 sec) [ -7201.1308] [ 1224] [depth= 1] . ( 56 sec) [ -7198.8610] [ 1221] [depth= 1] . ( 58 sec) [ -7198.8008] [ 1221] [depth= 1] . ( 58 sec) [ -7195.2764] [ 1220] [depth= 1] . ( 59 sec) [ -7194.8414] [ 1220] [depth= 3] . ( 61 sec) [ -7194.6547] [ 1223] [depth= 1] . ( 65 sec) [ -7194.5736] [ 1224] [depth= 1] . ( 72 sec) [ -7194.1558] [ 1223] [depth= 2] . ( 85 sec) [ -7190.5836] [Branch lengths ] . ( 86 sec) [ -7190.4866] [GTR parameters ] . ( 86 sec) [ -7190.4768] [Alpha ][ 0.320424] . ( 90 sec) [ -7190.2638] [ 1222] [depth= 1] . ( 117 sec) [ -7189.9217] [Branch lengths ] . ( 117 sec) [ -7189.9206] [GTR parameters ] . ( 117 sec) [ -7189.9196] [Alpha ][ 0.321373] . ( 208 sec) [ -7189.8937] [Branch lengths ] . ( 208 sec) [ -7189.8937] [Topology ] . ( 210 sec) [ -7189.8928] [Topology ] . ( 210 sec) [ -7189.8928] [GTR parameters ] . ( 210 sec) [ -7189.8928] [Alpha ][ 0.321373] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7189.892765. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -20920.1166] [GTR parameters ] . ( 4 sec) [ -20380.1857] [Alpha ][ 0.500960] . ( 4 sec) [ -20240.5725] [ 3247] [depth= 10] . ( 4 sec) [ -20118.9618] [ 3224] [depth= 9] . ( 4 sec) [ -20100.9373] [ 3203] [depth= 11] . ( 4 sec) [ -20012.6470] [ 3194] [depth= 1] . ( 4 sec) [ -19885.4845] [ 3177] [depth= 17] . ( 5 sec) [ -19864.0912] [ 3175] [depth= 7] . ( 5 sec) [ -19787.7739] [ 3175] [depth= 1] . ( 5 sec) [ -19610.2187] [ 3131] [depth= 10] . ( 5 sec) [ -19548.5565] [ 3129] [depth= 4] . ( 5 sec) [ -19023.4023] [ 3095] [depth= 3] . ( 5 sec) [ -18995.6638] [ 3088] [depth= 8] . ( 5 sec) [ -18951.9817] [ 3068] [depth= 2] . ( 5 sec) [ -18915.0020] [ 3068] [depth= 2] . ( 5 sec) [ -18746.1368] [ 3063] [depth= 3] . ( 5 sec) [ -18610.2046] [ 3038] [depth= 25] . ( 6 sec) [ -18365.4282] [ 3006] [depth= 1] . ( 6 sec) [ -18351.7796] [ 3005] [depth= 1] . ( 6 sec) [ -18350.4625] [ 3006] [depth= 1] . ( 6 sec) [ -18260.4544] [ 2984] [depth= 15] . ( 6 sec) [ -18026.2481] [ 2937] [depth= 7] . ( 6 sec) [ -18003.4719] [ 2933] [depth= 1] . ( 6 sec) [ -17513.1115] [ 2891] [depth= 16] . ( 7 sec) [ -17493.1634] [ 2884] [depth= 3] . ( 7 sec) [ -17300.9719] [ 2848] [depth= 2] . ( 7 sec) [ -17050.5403] [ 2822] [depth= 3] . ( 7 sec) [ -16679.8180] [ 2763] [depth= 21] . ( 7 sec) [ -16518.1347] [ 2744] [depth= 1] . ( 7 sec) [ -16333.7447] [ 2700] [depth= 14] . ( 7 sec) [ -16255.2824] [ 2676] [depth= 2] . ( 7 sec) [ -16246.4779] [ 2674] [depth= 1] . ( 8 sec) [ -16243.2892] [ 2676] [depth= 1] . ( 8 sec) [ -15959.8203] [ 2668] [depth= 24] . ( 8 sec) [ -15806.9063] [ 2626] [depth= 11] . ( 8 sec) [ -15576.0224] [ 2583] [depth= 9] . ( 8 sec) [ -15440.2366] [ 2561] [depth= 7] . ( 8 sec) [ -15351.9509] [ 2552] [depth= 8] . ( 8 sec) [ -15230.1892] [ 2526] [depth= 1] . ( 8 sec) [ -15057.8608] [ 2496] [depth= 12] . ( 9 sec) [ -15040.3240] [ 2493] [depth= 11] . ( 9 sec) [ -14976.8703] [ 2497] [depth= 11] . ( 9 sec) [ -14565.5960] [ 2454] [depth= 3] . ( 9 sec) [ -14557.8187] [ 2447] [depth= 1] . ( 9 sec) [ -14554.3832] [ 2446] [depth= 3] . ( 9 sec) [ -14536.7507] [ 2422] [depth= 1] . ( 9 sec) [ -14519.1714] [ 2418] [depth= 2] . ( 9 sec) [ -14233.0177] [ 2371] [depth= 8] . ( 9 sec) [ -14082.0653] [ 2349] [depth= 4] . ( 10 sec) [ -14080.5517] [ 2349] [depth= 1] . ( 10 sec) [ -13761.6721] [ 2343] [depth= 14] . ( 10 sec) [ -13715.8348] [ 2341] [depth= 1] . ( 10 sec) [ -13590.2058] [ 2336] [depth= 2] . ( 10 sec) [ -13567.5672] [ 2334] [depth= 2] . ( 10 sec) [ -13549.1773] [ 2308] [depth= 7] . ( 10 sec) [ -13386.3738] [ 2306] [depth= 1] . ( 10 sec) [ -13216.5769] [ 2258] [depth= 23] . ( 10 sec) [ -13027.4051] [ 2192] [depth= 6] . ( 11 sec) [ -12995.2251] [ 2192] [depth= 1] . ( 11 sec) [ -12989.1494] [ 2192] [depth= 1] . ( 11 sec) [ -12846.2595] [ 2166] [depth= 19] . ( 11 sec) [ -12733.4281] [ 2127] [depth= 15] . ( 11 sec) [ -12524.0164] [ 2124] [depth= 2] . ( 11 sec) [ -12501.2426] [ 2122] [depth= 1] . ( 11 sec) [ -12476.8497] [ 2122] [depth= 1] . ( 11 sec) [ -12425.4783] [ 2099] [depth= 3] . ( 12 sec) [ -12291.7193] [ 2091] [depth= 3] . ( 12 sec) [ -12290.1493] [ 2091] [depth= 1] . ( 12 sec) [ -12276.0303] [ 2090] [depth= 1] . ( 12 sec) [ -12214.0002] [ 2081] [depth= 6] . ( 12 sec) [ -12206.4847] [ 2080] [depth= 1] . ( 12 sec) [ -12044.5363] [ 2080] [depth= 1] . ( 12 sec) [ -11656.4758] [ 2034] [depth= 8] . ( 12 sec) [ -11641.5476] [ 2033] [depth= 1] . ( 13 sec) [ -11437.7254] [ 1962] [depth= 13] . ( 13 sec) [ -11323.8737] [ 1942] [depth= 16] . ( 13 sec) [ -11247.9334] [ 1929] [depth= 4] . ( 13 sec) [ -11107.5325] [ 1935] [depth= 4] . ( 13 sec) [ -11011.4569] [ 1930] [depth= 12] . ( 13 sec) [ -10890.9101] [ 1916] [depth= 7] . ( 13 sec) [ -10673.0554] [ 1873] [depth= 12] . ( 13 sec) [ -10340.1979] [ 1844] [depth= 18] . ( 14 sec) [ -10318.1934] [ 1845] [depth= 1] . ( 14 sec) [ -10157.6322] [ 1793] [depth= 9] . ( 14 sec) [ -10156.4131] [ 1794] [depth= 1] . ( 14 sec) [ -10048.6969] [ 1783] [depth= 10] . ( 14 sec) [ -10000.5270] [ 1782] [depth= 2] . ( 14 sec) [ -9995.3743] [ 1779] [depth= 1] . ( 15 sec) [ -9980.1177] [ 1774] [depth= 2] . ( 15 sec) [ -9973.3599] [ 1774] [depth= 1] . ( 15 sec) [ -9932.6673] [ 1764] [depth= 1] . ( 15 sec) [ -9928.1740] [ 1771] [depth= 1] . ( 15 sec) [ -9822.2214] [ 1725] [depth= 8] . ( 15 sec) [ -9818.0783] [ 1725] [depth= 1] . ( 15 sec) [ -9813.2224] [ 1711] [depth= 1] . ( 16 sec) [ -9746.4826] [ 1711] [depth= 12] . ( 16 sec) [ -9744.3866] [ 1712] [depth= 1] . ( 16 sec) [ -9706.4520] [ 1703] [depth= 13] . ( 16 sec) [ -9693.6338] [ 1702] [depth= 1] . ( 16 sec) [ -9680.9255] [ 1703] [depth= 1] . ( 16 sec) [ -9493.6089] [ 1656] [depth= 12] . ( 16 sec) [ -9464.0780] [ 1650] [depth= 5] . ( 16 sec) [ -9456.7056] [ 1651] [depth= 1] . ( 17 sec) [ -9455.9053] [ 1654] [depth= 1] . ( 17 sec) [ -9450.0448] [ 1653] [depth= 1] . ( 17 sec) [ -9445.5461] [ 1654] [depth= 1] . ( 17 sec) [ -9352.5106] [ 1627] [depth= 7] . ( 18 sec) [ -9127.0670] [ 1628] [depth= 2] . ( 18 sec) [ -9056.7133] [ 1610] [depth= 7] . ( 18 sec) [ -9046.2027] [ 1611] [depth= 10] . ( 18 sec) [ -9045.9132] [ 1612] [depth= 1] . ( 18 sec) [ -9012.9500] [ 1605] [depth= 4] . ( 18 sec) [ -9007.9893] [ 1605] [depth= 2] . ( 18 sec) [ -8941.0225] [ 1588] [depth= 12] . ( 19 sec) [ -8939.2746] [ 1588] [depth= 3] . ( 19 sec) [ -8829.4680] [ 1572] [depth= 1] . ( 19 sec) [ -8758.1548] [ 1567] [depth= 3] . ( 19 sec) [ -8747.3773] [ 1567] [depth= 1] . ( 19 sec) [ -8744.4808] [ 1567] [depth= 2] . ( 19 sec) [ -8734.5415] [ 1566] [depth= 2] . ( 19 sec) [ -8733.8053] [ 1566] [depth= 1] . ( 20 sec) [ -8731.8439] [ 1566] [depth= 2] . ( 20 sec) [ -8665.2541] [ 1557] [depth= 7] . ( 20 sec) [ -8661.8295] [ 1557] [depth= 1] . ( 20 sec) [ -8657.2867] [ 1557] [depth= 2] . ( 20 sec) [ -8573.9449] [ 1530] [depth= 3] . ( 20 sec) [ -8572.2693] [ 1530] [depth= 2] . ( 20 sec) [ -8572.0224] [ 1530] [depth= 2] . ( 21 sec) [ -8457.8962] [ 1481] [depth= 7] . ( 21 sec) [ -8452.2500] [ 1472] [depth= 3] . ( 21 sec) [ -8410.3455] [ 1450] [depth= 3] . ( 21 sec) [ -8294.4044] [ 1445] [depth= 5] . ( 21 sec) [ -8263.4736] [ 1439] [depth= 2] . ( 21 sec) [ -8202.3797] [ 1438] [depth= 1] . ( 21 sec) [ -8191.3640] [ 1437] [depth= 5] . ( 21 sec) [ -8132.0572] [ 1408] [depth= 6] . ( 22 sec) [ -8130.6663] [ 1408] [depth= 1] . ( 22 sec) [ -8127.1161] [ 1416] [depth= 1] . ( 22 sec) [ -8031.4882] [ 1376] [depth= 8] . ( 22 sec) [ -8021.2391] [ 1375] [depth= 1] . ( 22 sec) [ -8008.5923] [ 1375] [depth= 1] . ( 22 sec) [ -7988.2217] [ 1372] [depth= 3] . ( 22 sec) [ -7968.5093] [ 1371] [depth= 6] . ( 23 sec) [ -7956.4064] [ 1368] [depth= 1] . ( 23 sec) [ -7951.2527] [ 1367] [depth= 2] . ( 23 sec) [ -7938.0877] [ 1361] [depth= 6] . ( 23 sec) [ -7937.3545] [ 1361] [depth= 2] . ( 23 sec) [ -7932.9961] [ 1361] [depth= 4] . ( 23 sec) [ -7899.1779] [ 1353] [depth= 5] . ( 23 sec) [ -7880.9018] [ 1351] [depth= 5] . ( 23 sec) [ -7828.8555] [ 1331] [depth= 4] . ( 24 sec) [ -7811.6072] [ 1329] [depth= 3] . ( 24 sec) [ -7789.3623] [ 1322] [depth= 1] . ( 24 sec) [ -7777.8384] [ 1320] [depth= 2] . ( 24 sec) [ -7775.5219] [ 1320] [depth= 1] . ( 24 sec) [ -7708.5731] [ 1301] [depth= 8] . ( 25 sec) [ -7708.3684] [ 1301] [depth= 2] . ( 25 sec) [ -7695.1709] [ 1298] [depth= 1] . ( 25 sec) [ -7628.0873] [ 1282] [depth= 4] . ( 25 sec) [ -7624.0303] [ 1281] [depth= 1] . ( 25 sec) [ -7623.3787] [ 1281] [depth= 1] . ( 25 sec) [ -7615.6915] [ 1282] [depth= 1] . ( 26 sec) [ -7611.9227] [ 1282] [depth= 2] . ( 26 sec) [ -7605.6083] [ 1283] [depth= 1] . ( 26 sec) [ -7598.5940] [ 1282] [depth= 1] . ( 26 sec) [ -7583.4874] [ 1278] [depth= 2] . ( 26 sec) [ -7582.9721] [ 1282] [depth= 1] . ( 26 sec) [ -7557.5357] [ 1269] [depth= 5] . ( 26 sec) [ -7555.0646] [ 1269] [depth= 2] . ( 26 sec) [ -7549.4421] [ 1271] [depth= 1] . ( 27 sec) [ -7535.7686] [ 1270] [depth= 1] . ( 27 sec) [ -7533.7447] [ 1270] [depth= 1] . ( 27 sec) [ -7532.0135] [ 1268] [depth= 2] . ( 27 sec) [ -7523.9683] [ 1268] [depth= 1] . ( 27 sec) [ -7508.6864] [ 1265] [depth= 2] . ( 27 sec) [ -7507.8553] [ 1267] [depth= 2] . ( 28 sec) [ -7357.8002] [Branch lengths ] . ( 31 sec) [ -7347.9255] [GTR parameters ] . ( 31 sec) [ -7326.1760] [Alpha ][ 0.323694] . ( 31 sec) [ -7325.4157] [ 1260] [depth= 3] . ( 32 sec) [ -7308.7672] [ 1253] [depth= 3] . ( 32 sec) [ -7306.6076] [ 1255] [depth= 1] . ( 32 sec) [ -7305.8368] [ 1252] [depth= 1] . ( 32 sec) [ -7305.4475] [ 1252] [depth= 2] . ( 33 sec) [ -7296.3307] [ 1247] [depth= 1] . ( 34 sec) [ -7296.2461] [ 1244] [depth= 2] . ( 34 sec) [ -7293.9532] [ 1243] [depth= 2] . ( 35 sec) [ -7282.0256] [ 1238] [depth= 2] . ( 36 sec) [ -7280.7173] [ 1237] [depth= 1] . ( 36 sec) [ -7280.6726] [ 1236] [depth= 1] . ( 36 sec) [ -7278.5784] [ 1234] [depth= 1] . ( 37 sec) [ -7278.3103] [ 1234] [depth= 1] . ( 37 sec) [ -7277.9349] [ 1234] [depth= 1] . ( 37 sec) [ -7277.9190] [ 1234] [depth= 2] . ( 38 sec) [ -7269.9007] [ 1230] [depth= 2] . ( 39 sec) [ -7269.8527] [ 1230] [depth= 2] . ( 40 sec) [ -7269.7783] [ 1230] [depth= 1] . ( 40 sec) [ -7269.4261] [ 1230] [depth= 1] . ( 40 sec) [ -7269.4050] [ 1230] [depth= 2] . ( 41 sec) [ -7268.6728] [ 1229] [depth= 2] . ( 41 sec) [ -7268.6474] [ 1229] [depth= 1] . ( 41 sec) [ -7268.4146] [ 1230] [depth= 1] . ( 42 sec) [ -7264.7842] [ 1228] [depth= 1] . ( 42 sec) [ -7264.6788] [ 1228] [depth= 1] . ( 42 sec) [ -7264.6396] [ 1228] [depth= 1] . ( 44 sec) [ -7261.9140] [ 1227] [depth= 3] . ( 44 sec) [ -7259.4961] [ 1224] [depth= 2] . ( 46 sec) [ -7259.4821] [ 1224] [depth= 1] . ( 49 sec) [ -7244.5145] [ 1220] [depth= 3] . ( 49 sec) [ -7241.6067] [ 1218] [depth= 1] . ( 49 sec) [ -7238.2003] [ 1220] [depth= 1] . ( 49 sec) [ -7238.0902] [ 1220] [depth= 1] . ( 50 sec) [ -7238.0635] [ 1220] [depth= 1] . ( 51 sec) [ -7237.8546] [ 1221] [depth= 1] . ( 51 sec) [ -7237.5437] [ 1222] [depth= 1] . ( 52 sec) [ -7235.5713] [ 1219] [depth= 2] . ( 53 sec) [ -7235.3604] [ 1219] [depth= 3] . ( 53 sec) [ -7234.5499] [ 1219] [depth= 1] . ( 53 sec) [ -7231.4698] [ 1218] [depth= 1] . ( 54 sec) [ -7231.2322] [ 1218] [depth= 1] . ( 55 sec) [ -7228.7876] [ 1216] [depth= 7] . ( 55 sec) [ -7228.6983] [ 1216] [depth= 1] . ( 55 sec) [ -7227.9619] [ 1215] [depth= 1] . ( 56 sec) [ -7211.6698] [Branch lengths ] . ( 58 sec) [ -7211.2346] [GTR parameters ] . ( 58 sec) [ -7211.2338] [Alpha ][ 0.324546] . ( 59 sec) [ -7209.9399] [ 1215] [depth= 1] . ( 61 sec) [ -7209.9180] [ 1215] [depth= 1] . ( 64 sec) [ -7209.8797] [ 1215] [depth= 2] . ( 67 sec) [ -7209.6755] [ 1214] [depth= 1] . ( 68 sec) [ -7209.6597] [ 1214] [depth= 3] . ( 68 sec) [ -7206.6960] [ 1213] [depth= 2] . ( 71 sec) [ -7204.7215] [ 1213] [depth= 2] . ( 72 sec) [ -7204.0347] [ 1214] [depth= 3] . ( 73 sec) [ -7204.0214] [ 1214] [depth= 2] . ( 83 sec) [ -7198.5857] [Branch lengths ] . ( 85 sec) [ -7198.5174] [GTR parameters ] . ( 85 sec) [ -7198.5156] [Alpha ][ 0.323153] . ( 86 sec) [ -7196.2374] [ 1212] [depth= 1] . ( 111 sec) [ -7194.6232] [Branch lengths ] . ( 112 sec) [ -7194.6034] [GTR parameters ] . ( 112 sec) [ -7194.6010] [Alpha ][ 0.321531] . ( 144 sec) [ -7194.5751] [Branch lengths ] . ( 235 sec) [ -7194.5731] [Branch lengths ] . ( 235 sec) [ -7194.5731] [Topology ] . ( 237 sec) [ -7194.5730] [Topology ] . ( 237 sec) [ -7194.5730] [GTR parameters ] . ( 237 sec) [ -7194.5728] [Alpha ][ 0.321155] . Checking for NNIs, optimizing five branches... . ( 251 sec) [ -7194.5633] [Topology ] . Checking for NNIs, optimizing five branches... . ( 265 sec) [ -7194.5631] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7194.563139. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 5 sec) [ -21634.4526] [GTR parameters ] . ( 5 sec) [ -21046.0083] [Alpha ][ 0.500960] . ( 5 sec) [ -20821.2401] [ 3404] [depth= 15] . ( 5 sec) [ -20564.1420] [ 3391] [depth= 11] . ( 5 sec) [ -20551.6914] [ 3395] [depth= 1] . ( 5 sec) [ -20381.1634] [ 3379] [depth= 8] . ( 5 sec) [ -20354.2255] [ 3379] [depth= 2] . ( 6 sec) [ -20315.1415] [ 3378] [depth= 9] . ( 6 sec) [ -20116.5050] [ 3373] [depth= 11] . ( 6 sec) [ -19947.9229] [ 3335] [depth= 1] . ( 6 sec) [ -19884.0145] [ 3320] [depth= 13] . ( 6 sec) [ -19786.0284] [ 3300] [depth= 1] . ( 6 sec) [ -19286.1502] [ 3284] [depth= 9] . ( 6 sec) [ -18959.0169] [ 3241] [depth= 1] . ( 6 sec) [ -18900.4973] [ 3234] [depth= 2] . ( 6 sec) [ -18861.9916] [ 3224] [depth= 2] . ( 7 sec) [ -18779.2682] [ 3215] [depth= 4] . ( 7 sec) [ -18640.7259] [ 3183] [depth= 5] . ( 7 sec) [ -18506.1101] [ 3181] [depth= 2] . ( 7 sec) [ -18462.0063] [ 3177] [depth= 1] . ( 7 sec) [ -18407.0463] [ 3167] [depth= 3] . ( 7 sec) [ -18277.3979] [ 3165] [depth= 1] . ( 7 sec) [ -18264.6435] [ 3162] [depth= 5] . ( 7 sec) [ -17768.4008] [ 3127] [depth= 5] . ( 7 sec) [ -17530.1915] [ 3127] [depth= 2] . ( 7 sec) [ -17213.7141] [ 3102] [depth= 5] . ( 8 sec) [ -17110.2523] [ 3093] [depth= 12] . ( 8 sec) [ -17028.0307] [ 3079] [depth= 2] . ( 8 sec) [ -16998.1188] [ 3076] [depth= 3] . ( 8 sec) [ -16660.0092] [ 3051] [depth= 21] . ( 8 sec) [ -16267.0299] [ 3024] [depth= 1] . ( 8 sec) [ -16177.5728] [ 2993] [depth= 16] . ( 8 sec) [ -16063.8119] [ 2981] [depth= 18] . ( 8 sec) [ -15981.9873] [ 2967] [depth= 6] . ( 8 sec) [ -15927.0428] [ 2956] [depth= 2] . ( 9 sec) [ -15756.1938] [ 2923] [depth= 6] . ( 9 sec) [ -15745.0536] [ 2923] [depth= 1] . ( 9 sec) [ -15654.0091] [ 2902] [depth= 4] . ( 9 sec) [ -15649.0417] [ 2902] [depth= 1] . ( 9 sec) [ -15467.2870] [ 2877] [depth= 3] . ( 9 sec) [ -15466.9975] [ 2877] [depth= 1] . ( 9 sec) [ -15303.0700] [ 2838] [depth= 13] . ( 9 sec) [ -15241.1762] [ 2825] [depth= 2] . ( 9 sec) [ -14666.6517] [ 2799] [depth= 24] . ( 10 sec) [ -14431.5292] [ 2765] [depth= 7] . ( 10 sec) [ -14410.2714] [ 2765] [depth= 1] . ( 10 sec) [ -14401.5878] [ 2760] [depth= 4] . ( 10 sec) [ -14251.4137] [ 2762] [depth= 3] . ( 10 sec) [ -14246.7924] [ 2763] [depth= 1] . ( 10 sec) [ -14174.3156] [ 2750] [depth= 2] . ( 10 sec) [ -14059.0661] [ 2713] [depth= 1] . ( 10 sec) [ -14032.2419] [ 2712] [depth= 1] . ( 10 sec) [ -13926.7250] [ 2684] [depth= 12] . ( 11 sec) [ -13736.1465] [ 2668] [depth= 14] . ( 11 sec) [ -13686.9007] [ 2663] [depth= 6] . ( 11 sec) [ -13654.8565] [ 2651] [depth= 5] . ( 11 sec) [ -13593.2507] [ 2609] [depth= 1] . ( 11 sec) [ -13511.6426] [ 2596] [depth= 8] . ( 11 sec) [ -13396.2945] [ 2539] [depth= 11] . ( 11 sec) [ -13207.8443] [ 2492] [depth= 8] . ( 11 sec) [ -13119.4400] [ 2462] [depth= 14] . ( 11 sec) [ -13036.2573] [ 2456] [depth= 12] . ( 12 sec) [ -12893.9223] [ 2421] [depth= 8] . ( 12 sec) [ -12882.0751] [ 2418] [depth= 1] . ( 12 sec) [ -12759.2340] [ 2375] [depth= 20] . ( 12 sec) [ -12736.4315] [ 2372] [depth= 2] . ( 12 sec) [ -12725.3446] [ 2369] [depth= 1] . ( 12 sec) [ -12574.6237] [ 2339] [depth= 3] . ( 12 sec) [ -12503.5731] [ 2337] [depth= 4] . ( 12 sec) [ -12432.2048] [ 2300] [depth= 7] . ( 12 sec) [ -12396.9198] [ 2301] [depth= 1] . ( 13 sec) [ -12390.4360] [ 2301] [depth= 1] . ( 13 sec) [ -12327.2641] [ 2274] [depth= 4] . ( 13 sec) [ -12298.8969] [ 2270] [depth= 4] . ( 13 sec) [ -12251.9294] [ 2256] [depth= 3] . ( 13 sec) [ -12181.9131] [ 2254] [depth= 2] . ( 13 sec) [ -11746.9648] [ 2211] [depth= 11] . ( 13 sec) [ -11736.9460] [ 2212] [depth= 1] . ( 13 sec) [ -11700.4850] [ 2208] [depth= 12] . ( 13 sec) [ -11661.9035] [ 2200] [depth= 1] . ( 13 sec) [ -11541.5441] [ 2198] [depth= 9] . ( 14 sec) [ -11536.1434] [ 2197] [depth= 1] . ( 14 sec) [ -11456.7380] [ 2186] [depth= 6] . ( 14 sec) [ -11448.0389] [ 2186] [depth= 1] . ( 14 sec) [ -11447.9653] [ 2186] [depth= 1] . ( 14 sec) [ -11447.9231] [ 2186] [depth= 1] . ( 14 sec) [ -11339.7369] [ 2170] [depth= 4] . ( 14 sec) [ -11332.9711] [ 2178] [depth= 2] . ( 15 sec) [ -11325.4072] [ 2177] [depth= 1] . ( 15 sec) [ -11322.8824] [ 2176] [depth= 1] . ( 15 sec) [ -11256.8933] [ 2149] [depth= 4] . ( 15 sec) [ -11070.2421] [ 2122] [depth= 9] . ( 15 sec) [ -11018.1464] [ 2108] [depth= 5] . ( 15 sec) [ -10991.7057] [ 2107] [depth= 2] . ( 15 sec) [ -10976.7321] [ 2107] [depth= 2] . ( 15 sec) [ -10976.6531] [ 2107] [depth= 2] . ( 15 sec) [ -10976.4686] [ 2108] [depth= 1] . ( 16 sec) [ -10961.9976] [ 2100] [depth= 12] . ( 16 sec) [ -10890.7818] [ 2074] [depth= 17] . ( 16 sec) [ -10875.9911] [ 2067] [depth= 1] . ( 16 sec) [ -10802.9694] [ 2063] [depth= 2] . ( 16 sec) [ -10727.8669] [ 2057] [depth= 4] . ( 16 sec) [ -10703.7207] [ 2028] [depth= 2] . ( 16 sec) [ -10524.5462] [ 2023] [depth= 3] . ( 16 sec) [ -10494.5954] [ 2022] [depth= 23] . ( 17 sec) [ -10360.6453] [ 2008] [depth= 4] . ( 17 sec) [ -10247.8937] [ 1991] [depth= 10] . ( 17 sec) [ -10232.0409] [ 1990] [depth= 2] . ( 17 sec) [ -10199.8910] [ 1990] [depth= 1] . ( 17 sec) [ -9998.8136] [ 1926] [depth= 10] . ( 17 sec) [ -9991.7563] [ 1926] [depth= 1] . ( 17 sec) [ -9987.8226] [ 1927] [depth= 2] . ( 18 sec) [ -9976.8344] [ 1927] [depth= 1] . ( 18 sec) [ -9962.7711] [ 1932] [depth= 1] . ( 18 sec) [ -9928.1832] [ 1886] [depth= 17] . ( 18 sec) [ -9906.8854] [ 1846] [depth= 2] . ( 18 sec) [ -9905.7325] [ 1844] [depth= 1] . ( 18 sec) [ -9856.8946] [ 1824] [depth= 6] . ( 18 sec) [ -9837.8214] [ 1809] [depth= 6] . ( 18 sec) [ -9807.8108] [ 1802] [depth= 3] . ( 18 sec) [ -9796.3312] [ 1800] [depth= 3] . ( 19 sec) [ -9783.3805] [ 1795] [depth= 1] . ( 19 sec) [ -9665.5990] [ 1770] [depth= 5] . ( 19 sec) [ -9618.6493] [ 1744] [depth= 1] . ( 19 sec) [ -9521.2319] [ 1734] [depth= 10] . ( 19 sec) [ -9507.9750] [ 1728] [depth= 10] . ( 19 sec) [ -9438.1101] [ 1698] [depth= 1] . ( 19 sec) [ -9387.7093] [ 1676] [depth= 4] . ( 20 sec) [ -9347.1795] [ 1676] [depth= 1] . ( 20 sec) [ -9302.7879] [ 1669] [depth= 8] . ( 20 sec) [ -9247.5405] [ 1673] [depth= 1] . ( 20 sec) [ -9199.7331] [ 1648] [depth= 2] . ( 20 sec) [ -9132.1622] [ 1639] [depth= 1] . ( 20 sec) [ -9125.9394] [ 1638] [depth= 1] . ( 20 sec) [ -9094.1561] [ 1640] [depth= 2] . ( 20 sec) [ -9047.6638] [ 1632] [depth= 8] . ( 20 sec) [ -9041.0300] [ 1630] [depth= 6] . ( 21 sec) [ -9015.3313] [ 1630] [depth= 1] . ( 21 sec) [ -8975.2310] [ 1624] [depth= 3] . ( 21 sec) [ -8951.6685] [ 1623] [depth= 1] . ( 21 sec) [ -8937.3244] [ 1620] [depth= 1] . ( 21 sec) [ -8903.6118] [ 1619] [depth= 2] . ( 21 sec) [ -8887.4611] [ 1618] [depth= 1] . ( 21 sec) [ -8744.8260] [ 1567] [depth= 8] . ( 21 sec) [ -8737.2771] [ 1568] [depth= 1] . ( 22 sec) [ -8734.2368] [ 1568] [depth= 1] . ( 22 sec) [ -8729.2818] [ 1566] [depth= 2] . ( 22 sec) [ -8725.5538] [ 1567] [depth= 1] . ( 22 sec) [ -8721.3932] [ 1567] [depth= 1] . ( 22 sec) [ -8648.2825] [ 1548] [depth= 9] . ( 22 sec) [ -8645.3520] [ 1540] [depth= 1] . ( 22 sec) [ -8621.7520] [ 1540] [depth= 1] . ( 22 sec) [ -8481.7395] [ 1494] [depth= 4] . ( 22 sec) [ -8480.2468] [ 1489] [depth= 2] . ( 23 sec) [ -8474.4549] [ 1488] [depth= 1] . ( 23 sec) [ -8472.8952] [ 1488] [depth= 1] . ( 23 sec) [ -8468.9853] [ 1488] [depth= 1] . ( 23 sec) [ -8374.1830] [ 1463] [depth= 7] . ( 23 sec) [ -8356.2189] [ 1465] [depth= 1] . ( 23 sec) [ -8355.1368] [ 1465] [depth= 2] . ( 23 sec) [ -8263.2594] [ 1448] [depth= 2] . ( 24 sec) [ -8257.6017] [ 1448] [depth= 1] . ( 24 sec) [ -8007.1546] [ 1406] [depth= 3] . ( 24 sec) [ -7993.9510] [ 1401] [depth= 4] . ( 24 sec) [ -7993.2933] [ 1401] [depth= 1] . ( 24 sec) [ -7974.0238] [ 1395] [depth= 4] . ( 24 sec) [ -7973.0559] [ 1395] [depth= 1] . ( 24 sec) [ -7970.6096] [ 1397] [depth= 1] . ( 24 sec) [ -7925.5551] [ 1374] [depth= 3] . ( 24 sec) [ -7919.9977] [ 1374] [depth= 2] . ( 25 sec) [ -7907.0833] [ 1373] [depth= 1] . ( 25 sec) [ -7902.3232] [ 1372] [depth= 1] . ( 25 sec) [ -7816.7009] [ 1349] [depth= 5] . ( 25 sec) [ -7800.9272] [ 1343] [depth= 3] . ( 25 sec) [ -7786.0735] [ 1343] [depth= 1] . ( 26 sec) [ -7785.7152] [ 1343] [depth= 1] . ( 26 sec) [ -7784.7640] [ 1343] [depth= 1] . ( 26 sec) [ -7757.8805] [ 1333] [depth= 1] . ( 26 sec) [ -7739.9317] [ 1323] [depth= 1] . ( 26 sec) [ -7694.9881] [ 1308] [depth= 8] . ( 26 sec) [ -7694.9753] [ 1308] [depth= 4] . ( 26 sec) [ -7693.6813] [ 1308] [depth= 1] . ( 27 sec) [ -7509.7472] [Branch lengths ] . ( 30 sec) [ -7492.2301] [GTR parameters ] . ( 30 sec) [ -7463.8478] [Alpha ][ 0.306538] . ( 30 sec) [ -7435.0549] [ 1300] [depth= 11] . ( 30 sec) [ -7434.7147] [ 1300] [depth= 1] . ( 31 sec) [ -7430.3189] [ 1300] [depth= 2] . ( 31 sec) [ -7427.5855] [ 1297] [depth= 1] . ( 31 sec) [ -7389.8486] [ 1265] [depth= 12] . ( 31 sec) [ -7382.7955] [ 1266] [depth= 1] . ( 32 sec) [ -7381.5179] [ 1266] [depth= 1] . ( 32 sec) [ -7380.8829] [ 1268] [depth= 1] . ( 32 sec) [ -7380.4894] [ 1264] [depth= 4] . ( 32 sec) [ -7376.4738] [ 1260] [depth= 2] . ( 33 sec) [ -7375.8374] [ 1259] [depth= 1] . ( 33 sec) [ -7375.6521] [ 1259] [depth= 1] . ( 33 sec) [ -7375.6268] [ 1252] [depth= 1] . ( 34 sec) [ -7375.5560] [ 1252] [depth= 1] . ( 34 sec) [ -7375.5371] [ 1252] [depth= 2] . ( 36 sec) [ -7375.4098] [ 1252] [depth= 1] . ( 36 sec) [ -7367.1695] [ 1249] [depth= 6] . ( 36 sec) [ -7366.3831] [ 1249] [depth= 1] . ( 36 sec) [ -7365.8152] [ 1249] [depth= 1] . ( 37 sec) [ -7365.7921] [ 1248] [depth= 1] . ( 37 sec) [ -7365.6577] [ 1248] [depth= 1] . ( 38 sec) [ -7352.9636] [ 1244] [depth= 1] . ( 38 sec) [ -7330.3804] [ 1241] [depth= 5] . ( 39 sec) [ -7329.6207] [ 1241] [depth= 1] . ( 39 sec) [ -7322.8773] [ 1237] [depth= 1] . ( 39 sec) [ -7316.5994] [ 1225] [depth= 2] . ( 39 sec) [ -7313.8936] [ 1225] [depth= 2] . ( 40 sec) [ -7311.7781] [ 1228] [depth= 1] . ( 40 sec) [ -7310.6448] [ 1227] [depth= 1] . ( 40 sec) [ -7308.5643] [ 1227] [depth= 1] . ( 41 sec) [ -7305.3906] [ 1224] [depth= 6] . ( 41 sec) [ -7302.0562] [ 1223] [depth= 1] . ( 42 sec) [ -7301.0627] [ 1223] [depth= 1] . ( 42 sec) [ -7281.3636] [ 1218] [depth= 1] . ( 42 sec) [ -7281.3304] [ 1218] [depth= 2] . ( 42 sec) [ -7281.3016] [ 1218] [depth= 1] . ( 43 sec) [ -7281.1186] [ 1218] [depth= 1] . ( 43 sec) [ -7281.0619] [ 1218] [depth= 1] . ( 45 sec) [ -7280.5372] [ 1221] [depth= 1] . ( 46 sec) [ -7279.8558] [ 1222] [depth= 1] . ( 46 sec) [ -7279.5452] [ 1222] [depth= 1] . ( 47 sec) [ -7269.5539] [ 1217] [depth= 3] . ( 47 sec) [ -7269.1131] [ 1217] [depth= 1] . ( 48 sec) [ -7269.0168] [ 1217] [depth= 1] . ( 48 sec) [ -7268.8643] [ 1217] [depth= 1] . ( 48 sec) [ -7259.4095] [ 1215] [depth= 1] . ( 49 sec) [ -7258.7348] [ 1215] [depth= 1] . ( 49 sec) [ -7258.0690] [ 1218] [depth= 1] . ( 51 sec) [ -7256.8336] [ 1219] [depth= 1] . ( 51 sec) [ -7256.8193] [ 1219] [depth= 2] . ( 51 sec) [ -7256.8051] [ 1219] [depth= 1] . ( 52 sec) [ -7255.5369] [ 1216] [depth= 1] . ( 52 sec) [ -7255.0730] [ 1215] [depth= 1] . ( 55 sec) [ -7251.8740] [ 1215] [depth= 2] . ( 55 sec) [ -7251.7620] [ 1215] [depth= 2] . ( 56 sec) [ -7228.0936] [Branch lengths ] . ( 58 sec) [ -7227.5350] [GTR parameters ] . ( 58 sec) [ -7227.3106] [Alpha ][ 0.320472] . ( 58 sec) [ -7226.4538] [ 1215] [depth= 1] . ( 60 sec) [ -7225.2115] [ 1213] [depth= 4] . ( 60 sec) [ -7224.9757] [ 1213] [depth= 1] . ( 61 sec) [ -7224.0501] [ 1212] [depth= 1] . ( 63 sec) [ -7223.8844] [ 1213] [depth= 1] . ( 65 sec) [ -7222.0413] [ 1214] [depth= 2] . ( 69 sec) [ -7221.8537] [ 1213] [depth= 1] . ( 70 sec) [ -7221.8346] [ 1213] [depth= 1] . ( 71 sec) [ -7221.3734] [ 1213] [depth= 1] . ( 71 sec) [ -7221.3602] [ 1213] [depth= 1] . ( 72 sec) [ -7221.3342] [ 1213] [depth= 1] . ( 76 sec) [ -7220.6813] [ 1213] [depth= 1] . ( 77 sec) [ -7220.6282] [ 1209] [depth= 1] . ( 79 sec) [ -7220.6054] [ 1209] [depth= 3] . ( 86 sec) [ -7208.2727] [Branch lengths ] . ( 88 sec) [ -7208.0174] [GTR parameters ] . ( 88 sec) [ -7208.0144] [Alpha ][ 0.318692] . ( 89 sec) [ -7207.7209] [ 1209] [depth= 1] . ( 122 sec) [ -7195.6842] [Branch lengths ] . ( 123 sec) [ -7195.6727] [GTR parameters ] . ( 123 sec) [ -7195.6725] [Alpha ][ 0.319124] . ( 158 sec) [ -7193.9559] [Branch lengths ] . ( 255 sec) [ -7193.7318] [Branch lengths ] . ( 255 sec) [ -7193.7318] [Topology ] . ( 257 sec) [ -7193.7151] [Topology ] . ( 259 sec) [ -7193.7100] [Topology ] . ( 261 sec) [ -7193.7080] [Topology ] . ( 262 sec) [ -7193.7071] [Topology ] . ( 263 sec) [ -7193.7064] [GTR parameters ] . ( 263 sec) [ -7193.7060] [Alpha ][ 0.318435] . ( 263 sec) [ -7193.7060] [Topology ] . ( 265 sec) [ -7193.7055] [Topology ] . ( 266 sec) [ -7193.7055] [GTR parameters ] . ( 266 sec) [ -7193.7055] [Alpha ][ 0.318435] . Checking for NNIs, optimizing five branches... . ( 279 sec) [ -7193.4049] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7193.404921. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -7535.7731] [GTR parameters ] . ( 2 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 2 sec) [ -7436.5581] [Topology ] . ( 4 sec) [ -7272.4837] [Topology ] . ( 6 sec) [ -7248.9131] [Topology ] . ( 8 sec) [ -7242.2258] [Topology ] . ( 10 sec) [ -7239.3759] [Topology ] . ( 12 sec) [ -7237.7430] [Topology ] . ( 14 sec) [ -7235.4982] [Topology ] . ( 16 sec) [ -7232.9129] [Topology ] . ( 18 sec) [ -7229.8674] [Topology ] . ( 20 sec) [ -7226.3877] [Topology ] . ( 23 sec) [ -7224.6006] [GTR parameters ] . ( 23 sec) [ -7205.9195] [Alpha ][ 0.327414] . ( 23 sec) [ -7205.9195] [Topology ] . ( 25 sec) [ -7204.3575] [Topology ] . ( 27 sec) [ -7202.4492] [Topology ] . ( 29 sec) [ -7200.1107] [Topology ] . ( 31 sec) [ -7199.6426] [Topology ] . ( 33 sec) [ -7199.5423] [Topology ] . ( 35 sec) [ -7199.5102] [Topology ] . ( 38 sec) [ -7199.4996] [Topology ] . ( 40 sec) [ -7199.4959] [Topology ] . ( 41 sec) [ -7199.4946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7199.4129] [Topology ] . ( 57 sec) [ -7199.2768] [GTR parameters ] . ( 57 sec) [ -7199.1884] [Alpha ][ 0.318202] . ( 57 sec) [ -7199.1884] [Topology ] . ( 59 sec) [ -7199.1112] [Topology ] . ( 61 sec) [ -7199.0965] [Topology ] . ( 62 sec) [ -7199.0928] [Topology ] . ( 64 sec) [ -7199.0918] [Topology ] . ( 66 sec) [ -7199.0916] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -7199.0904] [GTR parameters ] . ( 81 sec) [ -7199.0902] [Alpha ][ 0.317709] . ( 81 sec) [ -7199.0902] [Topology ] . ( 83 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -7199.0900] [GTR parameters ] . ( 97 sec) [ -7199.0900] [Alpha ][ 0.317709] . ( 97 sec) [ -7199.0900] [Topology ] . ( 99 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 127 sec) [ -7535.7731] [GTR parameters ] . ( 128 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 128 sec) [ -7431.0273] [ 1225] [depth= 1] . ( 128 sec) [ -7429.9233] [ 1225] [depth= 1] . ( 128 sec) [ -7410.2809] [ 1223] [depth= 1] . ( 128 sec) [ -7410.1458] [ 1223] [depth= 1] . ( 128 sec) [ -7410.1041] [ 1223] [depth= 1] . ( 129 sec) [ -7409.8023] [ 1223] [depth= 2] . ( 129 sec) [ -7408.9585] [ 1224] [depth= 1] . ( 129 sec) [ -7406.9594] [ 1224] [depth= 2] . ( 129 sec) [ -7404.9846] [ 1223] [depth= 1] . ( 129 sec) [ -7401.0463] [ 1222] [depth= 1] . ( 130 sec) [ -7400.6838] [ 1222] [depth= 1] . ( 130 sec) [ -7398.0154] [ 1225] [depth= 2] . ( 130 sec) [ -7397.8300] [ 1225] [depth= 1] . ( 130 sec) [ -7395.7624] [ 1225] [depth= 1] . ( 131 sec) [ -7395.5684] [ 1225] [depth= 1] . ( 131 sec) [ -7393.7285] [ 1225] [depth= 1] . ( 131 sec) [ -7392.9397] [ 1225] [depth= 1] . ( 131 sec) [ -7383.7269] [ 1222] [depth= 1] . ( 131 sec) [ -7383.0988] [ 1222] [depth= 1] . ( 131 sec) [ -7383.0734] [ 1222] [depth= 1] . ( 132 sec) [ -7381.2424] [ 1222] [depth= 1] . ( 132 sec) [ -7378.2043] [ 1221] [depth= 1] . ( 132 sec) [ -7375.9504] [ 1218] [depth= 2] . ( 133 sec) [ -7375.2050] [ 1219] [depth= 1] . ( 134 sec) [ -7372.3325] [ 1221] [depth= 1] . ( 134 sec) [ -7365.3835] [ 1224] [depth= 1] . ( 135 sec) [ -7357.5601] [ 1227] [depth= 1] . ( 135 sec) [ -7350.6244] [ 1224] [depth= 1] . ( 135 sec) [ -7345.7180] [ 1223] [depth= 1] . ( 135 sec) [ -7345.1969] [ 1224] [depth= 1] . ( 135 sec) [ -7339.3803] [ 1225] [depth= 1] . ( 135 sec) [ -7337.8608] [ 1225] [depth= 1] . ( 136 sec) [ -7335.1324] [ 1222] [depth= 2] . ( 136 sec) [ -7329.5476] [ 1224] [depth= 1] . ( 136 sec) [ -7328.4499] [ 1222] [depth= 3] . ( 136 sec) [ -7326.4817] [ 1222] [depth= 1] . ( 137 sec) [ -7323.6003] [ 1225] [depth= 3] . ( 137 sec) [ -7321.6078] [ 1220] [depth= 1] . ( 137 sec) [ -7321.4654] [ 1222] [depth= 3] . ( 139 sec) [ -7317.2003] [ 1221] [depth= 1] . ( 139 sec) [ -7316.4724] [ 1221] [depth= 1] . ( 139 sec) [ -7313.2630] [ 1220] [depth= 2] . ( 139 sec) [ -7312.6734] [ 1220] [depth= 1] . ( 139 sec) [ -7312.5806] [ 1220] [depth= 1] . ( 140 sec) [ -7305.9445] [ 1220] [depth= 2] . ( 140 sec) [ -7305.0020] [ 1220] [depth= 1] . ( 140 sec) [ -7304.5343] [ 1220] [depth= 1] . ( 140 sec) [ -7304.3698] [ 1220] [depth= 1] . ( 140 sec) [ -7304.1801] [ 1220] [depth= 1] . ( 140 sec) [ -7303.9790] [ 1220] [depth= 2] . ( 141 sec) [ -7303.8950] [ 1220] [depth= 1] . ( 141 sec) [ -7303.8715] [ 1220] [depth= 1] . ( 141 sec) [ -7303.6273] [ 1220] [depth= 1] . ( 141 sec) [ -7303.4188] [ 1220] [depth= 1] . ( 141 sec) [ -7303.2237] [ 1220] [depth= 1] . ( 142 sec) [ -7302.0783] [ 1220] [depth= 1] . ( 142 sec) [ -7300.3856] [ 1220] [depth= 1] . ( 142 sec) [ -7297.6435] [ 1220] [depth= 1] . ( 143 sec) [ -7294.9308] [ 1219] [depth= 1] . ( 143 sec) [ -7294.7546] [ 1223] [depth= 1] . ( 143 sec) [ -7289.1968] [ 1219] [depth= 1] . ( 143 sec) [ -7283.1667] [ 1216] [depth= 1] . ( 144 sec) [ -7277.1827] [ 1216] [depth= 1] . ( 147 sec) [ -7275.2623] [ 1216] [depth= 1] . ( 152 sec) [ -7232.6772] [Branch lengths ] . ( 153 sec) [ -7231.8310] [GTR parameters ] . ( 154 sec) [ -7212.1611] [Alpha ][ 0.321042] . ( 156 sec) [ -7212.0642] [ 1216] [depth= 1] . ( 158 sec) [ -7208.4836] [ 1214] [depth= 1] . ( 158 sec) [ -7208.1432] [ 1214] [depth= 1] . ( 159 sec) [ -7207.3190] [ 1213] [depth= 1] . ( 161 sec) [ -7205.7479] [ 1213] [depth= 2] . ( 162 sec) [ -7203.6592] [ 1211] [depth= 3] . ( 163 sec) [ -7203.0508] [ 1211] [depth= 2] . ( 164 sec) [ -7200.1444] [ 1210] [depth= 1] . ( 179 sec) [ -7195.0134] [Branch lengths ] . ( 180 sec) [ -7194.5060] [GTR parameters ] . ( 180 sec) [ -7194.4992] [Alpha ][ 0.318382] . ( 187 sec) [ -7194.2808] [ 1210] [depth= 1] . ( 205 sec) [ -7193.3440] [Branch lengths ] . ( 206 sec) [ -7193.3395] [GTR parameters ] . ( 206 sec) [ -7193.3387] [Alpha ][ 0.317458] . ( 233 sec) [ -7193.3098] [Branch lengths ] . ( 318 sec) [ -7193.3075] [Branch lengths ] . ( 318 sec) [ -7193.3075] [Topology ] . ( 320 sec) [ -7193.3073] [Topology ] . ( 320 sec) [ -7193.3072] [GTR parameters ] . ( 320 sec) [ -7193.3071] [Alpha ][ 0.317141] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7199.090001 . Log likelihood obtained after SPR moves : -7193.307136 . Log likelihood of the current tree: -7193.307136. . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Best log likelihood : -7189.547650 . Time used 0h5m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1582.51user 0.00system 26:35.59elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps