.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data6.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... . 376 patterns found. (out of a total of 500 sites) . 113 sites without polymorphism (22.60%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15223.5672] [GTR parameters ] . ( 1 sec) [ -14919.4897] [Alpha ][ 0.500960] . ( 1 sec) [ -14827.9301] [ 3189] [depth= 7] . ( 1 sec) [ -14566.0888] [ 3165] [depth= 5] . ( 1 sec) [ -14287.1264] [ 3151] [depth= 4] . ( 2 sec) [ -14151.7471] [ 3138] [depth= 5] . ( 2 sec) [ -13974.2623] [ 3072] [depth= 4] . ( 2 sec) [ -13910.9767] [ 3060] [depth= 1] . ( 2 sec) [ -13834.6305] [ 3053] [depth= 6] . ( 2 sec) [ -13814.4727] [ 3050] [depth= 1] . ( 2 sec) [ -13700.0163] [ 3022] [depth= 2] . ( 2 sec) [ -13561.3047] [ 2967] [depth= 14] . ( 2 sec) [ -13477.0102] [ 2941] [depth= 1] . ( 2 sec) [ -13333.0202] [ 2912] [depth= 14] . ( 2 sec) [ -13182.6654] [ 2896] [depth= 5] . ( 2 sec) [ -13078.0198] [ 2878] [depth= 3] . ( 2 sec) [ -13055.6759] [ 2878] [depth= 3] . ( 2 sec) [ -12948.7708] [ 2802] [depth= 2] . ( 2 sec) [ -12899.2671] [ 2798] [depth= 10] . ( 2 sec) [ -12807.0028] [ 2739] [depth= 11] . ( 2 sec) [ -12399.6939] [ 2744] [depth= 1] . ( 2 sec) [ -12227.4670] [ 2732] [depth= 16] . ( 2 sec) [ -12170.2520] [ 2705] [depth= 10] . ( 2 sec) [ -12152.2777] [ 2707] [depth= 3] . ( 2 sec) [ -11945.3926] [ 2664] [depth= 8] . ( 2 sec) [ -11748.7287] [ 2656] [depth= 10] . ( 2 sec) [ -11367.5843] [ 2533] [depth= 6] . ( 2 sec) [ -10974.0380] [ 2363] [depth= 10] . ( 3 sec) [ -10973.4055] [ 2358] [depth= 1] . ( 3 sec) [ -10972.8859] [ 2357] [depth= 1] . ( 3 sec) [ -10669.4282] [ 2272] [depth= 13] . ( 3 sec) [ -10559.2246] [ 2262] [depth= 1] . ( 3 sec) [ -10515.1803] [ 2235] [depth= 1] . ( 3 sec) [ -10513.3631] [ 2235] [depth= 1] . ( 3 sec) [ -10332.9754] [ 2255] [depth= 14] . ( 3 sec) [ -10299.2549] [ 2245] [depth= 1] . ( 3 sec) [ -10015.9846] [ 2228] [depth= 6] . ( 3 sec) [ -9963.8073] [ 2238] [depth= 1] . ( 3 sec) [ -9946.9471] [ 2240] [depth= 1] . ( 3 sec) [ -9946.3660] [ 2233] [depth= 3] . ( 3 sec) [ -9682.7996] [ 2138] [depth= 8] . ( 3 sec) [ -9577.6014] [ 2118] [depth= 2] . ( 3 sec) [ -9507.2943] [ 2097] [depth= 1] . ( 3 sec) [ -9310.9962] [ 2044] [depth= 4] . ( 3 sec) [ -9279.5101] [ 2031] [depth= 1] . ( 3 sec) [ -9183.0420] [ 2009] [depth= 6] . ( 3 sec) [ -9134.8381] [ 2013] [depth= 1] . ( 3 sec) [ -9133.3306] [ 2015] [depth= 2] . ( 3 sec) [ -9111.7197] [ 2015] [depth= 9] . ( 3 sec) [ -9007.0148] [ 1969] [depth= 8] . ( 3 sec) [ -9006.0097] [ 1969] [depth= 1] . ( 4 sec) [ -9005.5789] [ 1974] [depth= 1] . ( 4 sec) [ -9001.4123] [ 1973] [depth= 1] . ( 4 sec) [ -8887.7599] [ 1974] [depth= 1] . ( 4 sec) [ -8496.8877] [ 1874] [depth= 8] . ( 4 sec) [ -8460.8331] [ 1849] [depth= 1] . ( 4 sec) [ -8428.5257] [ 1849] [depth= 1] . ( 4 sec) [ -8421.3488] [ 1826] [depth= 1] . ( 4 sec) [ -8417.0607] [ 1827] [depth= 1] . ( 4 sec) [ -8408.5923] [ 1830] [depth= 1] . ( 4 sec) [ -8406.8562] [ 1827] [depth= 1] . ( 4 sec) [ -8403.7973] [ 1810] [depth= 1] . ( 4 sec) [ -8304.3893] [ 1762] [depth= 3] . ( 4 sec) [ -8294.5464] [ 1759] [depth= 1] . ( 4 sec) [ -8248.5195] [ 1750] [depth= 1] . ( 4 sec) [ -8158.8391] [ 1682] [depth= 6] . ( 4 sec) [ -8138.0452] [ 1673] [depth= 2] . ( 4 sec) [ -8135.7972] [ 1672] [depth= 1] . ( 4 sec) [ -8134.5964] [ 1670] [depth= 2] . ( 5 sec) [ -8121.7407] [ 1653] [depth= 1] . ( 5 sec) [ -8037.2626] [ 1642] [depth= 4] . ( 5 sec) [ -8024.3385] [ 1638] [depth= 3] . ( 5 sec) [ -7997.5253] [ 1605] [depth= 1] . ( 5 sec) [ -7914.9079] [ 1601] [depth= 2] . ( 5 sec) [ -7902.6524] [ 1608] [depth= 1] . ( 5 sec) [ -7729.3850] [ 1591] [depth= 1] . ( 5 sec) [ -7663.8946] [ 1587] [depth= 1] . ( 5 sec) [ -7589.0238] [ 1561] [depth= 1] . ( 5 sec) [ -7536.4796] [ 1549] [depth= 1] . ( 5 sec) [ -7429.5243] [ 1466] [depth= 1] . ( 5 sec) [ -7301.3396] [ 1451] [depth= 1] . ( 5 sec) [ -7290.4356] [ 1454] [depth= 1] . ( 5 sec) [ -7267.4002] [ 1443] [depth= 1] . ( 6 sec) [ -7177.8154] [Branch lengths ] . ( 6 sec) [ -7176.6580] [GTR parameters ] . ( 6 sec) [ -7150.6901] [Alpha ][ 0.894579] . ( 6 sec) [ -7149.0566] [ 1440] [depth= 1] . ( 6 sec) [ -7141.9043] [ 1421] [depth= 3] . ( 6 sec) [ -7131.4692] [ 1417] [depth= 1] . ( 6 sec) [ -7113.4772] [ 1409] [depth= 1] . ( 6 sec) [ -7106.9988] [ 1404] [depth= 1] . ( 7 sec) [ -7070.4742] [ 1374] [depth= 2] . ( 7 sec) [ -7070.3617] [ 1374] [depth= 1] . ( 7 sec) [ -7060.4163] [ 1357] [depth= 1] . ( 9 sec) [ -7044.0792] [ 1345] [depth= 1] . ( 9 sec) [ -7043.6710] [ 1347] [depth= 1] . ( 9 sec) [ -7031.0564] [Branch lengths ] . ( 10 sec) [ -7030.9617] [GTR parameters ] . ( 10 sec) [ -7030.2551] [Alpha ][ 0.992076] . ( 10 sec) [ -7029.3436] [ 1345] [depth= 1] . ( 13 sec) [ -7028.4114] [Branch lengths ] . ( 14 sec) [ -7028.4102] [GTR parameters ] . ( 14 sec) [ -7028.4035] [Alpha ][ 1.002410] . ( 17 sec) [ -7025.8692] [Branch lengths ] . ( 40 sec) [ -7024.3955] [Branch lengths ] . ( 40 sec) [ -7024.3955] [Topology ] . ( 41 sec) [ -7024.2426] [Topology ] . ( 42 sec) [ -7024.2164] [Topology ] . ( 43 sec) [ -7024.2092] [Topology ] . ( 44 sec) [ -7024.2071] [Topology ] . ( 45 sec) [ -7024.2063] [Topology ] . ( 45 sec) [ -7024.2004] [GTR parameters ] . ( 45 sec) [ -7024.1983] [Alpha ][ 1.008246] . ( 46 sec) [ -7024.1983] [Topology ] . ( 47 sec) [ -7024.1980] [Topology ] . ( 47 sec) [ -7024.1980] [GTR parameters ] . ( 47 sec) [ -7024.1980] [Alpha ][ 1.008246] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.197957. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15914.0300] [GTR parameters ] . ( 1 sec) [ -15586.9916] [Alpha ][ 0.500960] . ( 1 sec) [ -15461.4714] [ 3317] [depth= 9] . ( 2 sec) [ -15316.0629] [ 3284] [depth= 10] . ( 2 sec) [ -15162.0221] [ 3249] [depth= 3] . ( 2 sec) [ -15025.9011] [ 3245] [depth= 2] . ( 2 sec) [ -14938.6324] [ 3185] [depth= 2] . ( 2 sec) [ -14938.1528] [ 3182] [depth= 7] . ( 2 sec) [ -14896.9292] [ 3170] [depth= 3] . ( 2 sec) [ -14847.8687] [ 3143] [depth= 1] . ( 2 sec) [ -14684.9578] [ 3132] [depth= 3] . ( 2 sec) [ -14519.5398] [ 3101] [depth= 8] . ( 2 sec) [ -14407.1599] [ 3100] [depth= 1] . ( 2 sec) [ -14131.1202] [ 3057] [depth= 4] . ( 2 sec) [ -14069.9435] [ 3068] [depth= 3] . ( 2 sec) [ -13736.5172] [ 2976] [depth= 4] . ( 3 sec) [ -13620.9879] [ 2963] [depth= 11] . ( 3 sec) [ -13372.4169] [ 2893] [depth= 9] . ( 3 sec) [ -13321.4692] [ 2887] [depth= 1] . ( 3 sec) [ -13127.3756] [ 2867] [depth= 1] . ( 3 sec) [ -12865.6672] [ 2863] [depth= 1] . ( 3 sec) [ -12717.0693] [ 2772] [depth= 1] . ( 3 sec) [ -12666.1117] [ 2764] [depth= 1] . ( 3 sec) [ -12482.5075] [ 2722] [depth= 2] . ( 3 sec) [ -12322.5769] [ 2683] [depth= 3] . ( 3 sec) [ -12283.2625] [ 2662] [depth= 1] . ( 3 sec) [ -12067.5445] [ 2644] [depth= 3] . ( 3 sec) [ -12041.2746] [ 2644] [depth= 1] . ( 3 sec) [ -11634.5218] [ 2545] [depth= 2] . ( 4 sec) [ -11596.5439] [ 2544] [depth= 1] . ( 4 sec) [ -11438.8324] [ 2505] [depth= 6] . ( 4 sec) [ -11184.1493] [ 2462] [depth= 14] . ( 4 sec) [ -11168.7610] [ 2457] [depth= 1] . ( 4 sec) [ -11129.6711] [ 2455] [depth= 5] . ( 4 sec) [ -11126.2501] [ 2460] [depth= 1] . ( 4 sec) [ -10737.9752] [ 2385] [depth= 11] . ( 4 sec) [ -10542.8404] [ 2272] [depth= 1] . ( 4 sec) [ -10508.2712] [ 2259] [depth= 1] . ( 4 sec) [ -10475.1203] [ 2267] [depth= 2] . ( 4 sec) [ -10190.4290] [ 2154] [depth= 3] . ( 4 sec) [ -9966.2205] [ 2076] [depth= 8] . ( 4 sec) [ -9870.3757] [ 2052] [depth= 4] . ( 5 sec) [ -9778.5265] [ 2043] [depth= 12] . ( 5 sec) [ -9082.9660] [ 1893] [depth= 13] . ( 5 sec) [ -9076.8691] [ 1891] [depth= 5] . ( 5 sec) [ -9010.1836] [ 1828] [depth= 2] . ( 5 sec) [ -8856.2393] [ 1804] [depth= 5] . ( 5 sec) [ -8787.8640] [ 1783] [depth= 1] . ( 5 sec) [ -8541.0219] [ 1729] [depth= 4] . ( 6 sec) [ -8509.7087] [ 1718] [depth= 3] . ( 6 sec) [ -8425.0538] [ 1721] [depth= 1] . ( 6 sec) [ -8341.8188] [ 1688] [depth= 7] . ( 6 sec) [ -8320.2338] [ 1686] [depth= 1] . ( 6 sec) [ -8205.2190] [ 1653] [depth= 9] . ( 6 sec) [ -8156.8340] [ 1636] [depth= 4] . ( 6 sec) [ -8092.7062] [ 1617] [depth= 1] . ( 6 sec) [ -8069.4490] [ 1604] [depth= 1] . ( 6 sec) [ -8068.0449] [ 1605] [depth= 1] . ( 6 sec) [ -8045.6288] [ 1593] [depth= 1] . ( 6 sec) [ -7867.9121] [ 1611] [depth= 2] . ( 7 sec) [ -7667.4518] [ 1525] [depth= 5] . ( 7 sec) [ -7655.4477] [ 1515] [depth= 1] . ( 7 sec) [ -7646.6867] [ 1492] [depth= 7] . ( 7 sec) [ -7591.8565] [ 1486] [depth= 1] . ( 7 sec) [ -7476.2033] [ 1475] [depth= 2] . ( 7 sec) [ -7467.1860] [ 1491] [depth= 1] . ( 7 sec) [ -7428.9254] [ 1458] [depth= 6] . ( 7 sec) [ -7428.6111] [ 1458] [depth= 1] . ( 7 sec) [ -7412.3287] [ 1447] [depth= 2] . ( 7 sec) [ -7394.4207] [ 1446] [depth= 1] . ( 8 sec) [ -7393.1599] [ 1445] [depth= 1] . ( 8 sec) [ -7393.1202] [ 1445] [depth= 1] . ( 8 sec) [ -7369.2950] [ 1432] [depth= 2] . ( 8 sec) [ -7274.4679] [ 1404] [depth= 2] . ( 8 sec) [ -7236.9214] [ 1387] [depth= 1] . ( 8 sec) [ -7232.3012] [ 1384] [depth= 1] . ( 9 sec) [ -7122.8782] [Branch lengths ] . ( 9 sec) [ -7120.9625] [GTR parameters ] . ( 10 sec) [ -7087.9683] [Alpha ][ 0.969096] . ( 10 sec) [ -7072.5333] [ 1375] [depth= 1] . ( 10 sec) [ -7053.9373] [ 1368] [depth= 1] . ( 11 sec) [ -7051.4650] [ 1367] [depth= 1] . ( 11 sec) [ -7049.3877] [ 1350] [depth= 1] . ( 12 sec) [ -7045.4120] [ 1340] [depth= 2] . ( 12 sec) [ -7045.1547] [ 1345] [depth= 1] . ( 13 sec) [ -7040.5699] [ 1347] [depth= 1] . ( 13 sec) [ -7038.8806] [ 1340] [depth= 1] . ( 13 sec) [ -7038.8700] [ 1340] [depth= 1] . ( 14 sec) [ -7026.9615] [Branch lengths ] . ( 14 sec) [ -7026.8727] [GTR parameters ] . ( 14 sec) [ -7026.8184] [Alpha ][ 0.997127] . ( 17 sec) [ -7026.6717] [ 1345] [depth= 1] . ( 18 sec) [ -7024.5377] [Branch lengths ] . ( 19 sec) [ -7024.5347] [GTR parameters ] . ( 19 sec) [ -7024.5170] [Alpha ][ 1.014200] . ( 22 sec) [ -7024.2594] [Branch lengths ] . ( 48 sec) [ -7024.2069] [Branch lengths ] . ( 48 sec) [ -7024.2069] [Topology ] . ( 49 sec) [ -7024.2022] [Topology ] . ( 50 sec) [ -7024.2008] [Topology ] . ( 51 sec) [ -7024.2003] [Topology ] . ( 52 sec) [ -7024.2002] [GTR parameters ] . ( 52 sec) [ -7024.1983] [Alpha ][ 1.008364] . ( 52 sec) [ -7024.1983] [Topology ] . ( 53 sec) [ -7024.1980] [Topology ] . ( 53 sec) [ -7024.1980] [GTR parameters ] . ( 53 sec) [ -7024.1980] [Alpha ][ 1.008364] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.197952. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16181.5890] [GTR parameters ] . ( 1 sec) [ -15833.5982] [Alpha ][ 0.500960] . ( 1 sec) [ -15700.8044] [ 3362] [depth= 4] . ( 1 sec) [ -15481.8171] [ 3307] [depth= 10] . ( 1 sec) [ -15389.8084] [ 3306] [depth= 4] . ( 1 sec) [ -15051.4263] [ 3303] [depth= 1] . ( 1 sec) [ -14909.4307] [ 3196] [depth= 2] . ( 1 sec) [ -14867.2652] [ 3190] [depth= 5] . ( 1 sec) [ -14478.9968] [ 3174] [depth= 8] . ( 1 sec) [ -14429.9887] [ 3164] [depth= 9] . ( 1 sec) [ -14056.4040] [ 3061] [depth= 9] . ( 1 sec) [ -14051.5669] [ 3041] [depth= 1] . ( 1 sec) [ -13974.5446] [ 3038] [depth= 1] . ( 2 sec) [ -13742.5244] [ 2985] [depth= 12] . ( 2 sec) [ -13664.9260] [ 2978] [depth= 1] . ( 2 sec) [ -13572.7652] [ 2977] [depth= 1] . ( 2 sec) [ -13327.3475] [ 2945] [depth= 12] . ( 2 sec) [ -13203.3605] [ 2943] [depth= 1] . ( 2 sec) [ -12909.7619] [ 2844] [depth= 15] . ( 2 sec) [ -12902.6966] [ 2848] [depth= 3] . ( 2 sec) [ -12733.9717] [ 2799] [depth= 13] . ( 2 sec) [ -12612.0350] [ 2763] [depth= 1] . ( 2 sec) [ -12526.6919] [ 2688] [depth= 3] . ( 2 sec) [ -12251.4848] [ 2604] [depth= 7] . ( 2 sec) [ -11743.5877] [ 2490] [depth= 15] . ( 2 sec) [ -11518.9442] [ 2429] [depth= 7] . ( 2 sec) [ -11490.3611] [ 2422] [depth= 8] . ( 2 sec) [ -10957.0687] [ 2390] [depth= 7] . ( 3 sec) [ -10865.5932] [ 2362] [depth= 11] . ( 3 sec) [ -10797.9405] [ 2335] [depth= 14] . ( 3 sec) [ -10588.4021] [ 2346] [depth= 14] . ( 3 sec) [ -10524.4678] [ 2395] [depth= 8] . ( 3 sec) [ -10272.1620] [ 2337] [depth= 7] . ( 3 sec) [ -10144.8360] [ 2283] [depth= 11] . ( 3 sec) [ -10143.7660] [ 2283] [depth= 4] . ( 3 sec) [ -10030.6564] [ 2253] [depth= 6] . ( 3 sec) [ -9995.6602] [ 2248] [depth= 2] . ( 3 sec) [ -9962.2355] [ 2248] [depth= 1] . ( 3 sec) [ -9946.3411] [ 2226] [depth= 4] . ( 3 sec) [ -9945.8676] [ 2230] [depth= 1] . ( 4 sec) [ -9875.3998] [ 2233] [depth= 5] . ( 4 sec) [ -9463.7280] [ 2095] [depth= 14] . ( 4 sec) [ -9463.4676] [ 2095] [depth= 1] . ( 4 sec) [ -9307.7049] [ 2082] [depth= 12] . ( 4 sec) [ -9081.2826] [ 1978] [depth= 5] . ( 4 sec) [ -8928.4078] [ 1974] [depth= 1] . ( 4 sec) [ -8875.3111] [ 1950] [depth= 2] . ( 4 sec) [ -8646.5758] [ 1845] [depth= 4] . ( 4 sec) [ -8645.3066] [ 1846] [depth= 1] . ( 4 sec) [ -8639.0951] [ 1832] [depth= 6] . ( 4 sec) [ -8606.4268] [ 1823] [depth= 2] . ( 4 sec) [ -8510.4245] [ 1812] [depth= 1] . ( 4 sec) [ -8142.6766] [ 1717] [depth= 1] . ( 5 sec) [ -8013.0407] [ 1659] [depth= 5] . ( 5 sec) [ -8007.7325] [ 1666] [depth= 1] . ( 5 sec) [ -7861.4100] [ 1656] [depth= 1] . ( 5 sec) [ -7823.8572] [ 1638] [depth= 1] . ( 5 sec) [ -7821.7480] [ 1625] [depth= 2] . ( 5 sec) [ -7820.3372] [ 1623] [depth= 3] . ( 5 sec) [ -7796.2206] [ 1617] [depth= 1] . ( 5 sec) [ -7773.1001] [ 1634] [depth= 1] . ( 5 sec) [ -7768.8372] [ 1633] [depth= 1] . ( 5 sec) [ -7680.5418] [ 1613] [depth= 1] . ( 5 sec) [ -7653.6103] [ 1565] [depth= 8] . ( 5 sec) [ -7612.7172] [ 1538] [depth= 2] . ( 5 sec) [ -7596.4423] [ 1534] [depth= 1] . ( 5 sec) [ -7596.4196] [ 1534] [depth= 1] . ( 5 sec) [ -7577.5001] [ 1530] [depth= 1] . ( 6 sec) [ -7537.4031] [ 1492] [depth= 4] . ( 6 sec) [ -7531.1615] [ 1505] [depth= 1] . ( 6 sec) [ -7469.6050] [ 1494] [depth= 2] . ( 6 sec) [ -7444.6865] [ 1485] [depth= 1] . ( 6 sec) [ -7318.1978] [ 1432] [depth= 3] . ( 6 sec) [ -7268.0638] [ 1420] [depth= 2] . ( 6 sec) [ -7261.6045] [ 1418] [depth= 1] . ( 6 sec) [ -7261.5645] [ 1418] [depth= 1] . ( 7 sec) [ -7255.6441] [ 1404] [depth= 1] . ( 7 sec) [ -7245.6807] [ 1407] [depth= 1] . ( 7 sec) [ -7167.7433] [Branch lengths ] . ( 8 sec) [ -7165.7450] [GTR parameters ] . ( 8 sec) [ -7138.1278] [Alpha ][ 0.920807] . ( 8 sec) [ -7125.0375] [ 1390] [depth= 1] . ( 8 sec) [ -7074.3668] [ 1371] [depth= 2] . ( 8 sec) [ -7056.2191] [ 1365] [depth= 1] . ( 9 sec) [ -7055.3679] [ 1355] [depth= 2] . ( 9 sec) [ -7052.2167] [ 1354] [depth= 1] . ( 9 sec) [ -7043.0495] [ 1351] [depth= 1] . ( 10 sec) [ -7040.4905] [ 1347] [depth= 1] . ( 10 sec) [ -7037.8163] [ 1340] [depth= 1] . ( 10 sec) [ -7036.2523] [ 1345] [depth= 1] . ( 11 sec) [ -7034.7080] [ 1347] [depth= 1] . ( 12 sec) [ -7025.1002] [Branch lengths ] . ( 13 sec) [ -7025.0509] [GTR parameters ] . ( 13 sec) [ -7024.6489] [Alpha ][ 0.996293] . ( 15 sec) [ -7024.6164] [ 1345] [depth= 1] . ( 16 sec) [ -7024.2580] [Branch lengths ] . ( 17 sec) [ -7024.2578] [GTR parameters ] . ( 17 sec) [ -7024.2521] [Alpha ][ 1.005904] . ( 44 sec) [ -7024.2065] [Branch lengths ] . ( 44 sec) [ -7024.2065] [Topology ] . ( 45 sec) [ -7024.2012] [Topology ] . ( 47 sec) [ -7024.1995] [Topology ] . ( 47 sec) [ -7024.1987] [Topology ] . ( 48 sec) [ -7024.1987] [GTR parameters ] . ( 48 sec) [ -7024.1984] [Alpha ][ 1.007921] . ( 48 sec) [ -7024.1984] [Topology ] . ( 49 sec) [ -7024.1981] [Topology ] . ( 49 sec) [ -7024.1981] [GTR parameters ] . ( 49 sec) [ -7024.1981] [Alpha ][ 1.007921] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.198070. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15360.3459] [GTR parameters ] . ( 1 sec) [ -15048.6038] [Alpha ][ 0.500960] . ( 1 sec) [ -14953.7382] [ 3211] [depth= 10] . ( 1 sec) [ -14876.9301] [ 3201] [depth= 8] . ( 1 sec) [ -14684.0577] [ 3169] [depth= 2] . ( 1 sec) [ -14664.8503] [ 3157] [depth= 1] . ( 1 sec) [ -14496.7216] [ 3119] [depth= 5] . ( 1 sec) [ -14448.4484] [ 3109] [depth= 2] . ( 1 sec) [ -14228.2987] [ 3104] [depth= 2] . ( 2 sec) [ -14203.6405] [ 3088] [depth= 1] . ( 2 sec) [ -13999.1862] [ 3045] [depth= 8] . ( 2 sec) [ -13986.6182] [ 3027] [depth= 1] . ( 2 sec) [ -13885.6524] [ 3017] [depth= 4] . ( 2 sec) [ -13596.7778] [ 2961] [depth= 4] . ( 2 sec) [ -13589.0117] [ 2959] [depth= 1] . ( 2 sec) [ -13503.8920] [ 2960] [depth= 3] . ( 2 sec) [ -13295.0212] [ 2891] [depth= 7] . ( 2 sec) [ -13283.6808] [ 2909] [depth= 4] . ( 2 sec) [ -13187.8844] [ 2911] [depth= 1] . ( 2 sec) [ -13130.1090] [ 2906] [depth= 8] . ( 2 sec) [ -12898.1385] [ 2822] [depth= 8] . ( 2 sec) [ -12715.7172] [ 2798] [depth= 2] . ( 2 sec) [ -12575.2998] [ 2769] [depth= 10] . ( 2 sec) [ -12440.9342] [ 2746] [depth= 5] . ( 3 sec) [ -12317.0080] [ 2721] [depth= 1] . ( 3 sec) [ -12154.3343] [ 2655] [depth= 8] . ( 3 sec) [ -12093.3082] [ 2639] [depth= 1] . ( 3 sec) [ -12005.9665] [ 2622] [depth= 5] . ( 3 sec) [ -11333.4794] [ 2487] [depth= 14] . ( 3 sec) [ -11278.7424] [ 2460] [depth= 1] . ( 3 sec) [ -11225.9863] [ 2453] [depth= 3] . ( 3 sec) [ -11220.3441] [ 2448] [depth= 2] . ( 3 sec) [ -10906.8033] [ 2373] [depth= 3] . ( 3 sec) [ -10742.2165] [ 2300] [depth= 8] . ( 3 sec) [ -10217.7168] [ 2163] [depth= 14] . ( 3 sec) [ -10119.4108] [ 2122] [depth= 11] . ( 4 sec) [ -10005.1509] [ 2118] [depth= 1] . ( 4 sec) [ -9951.2784] [ 2093] [depth= 1] . ( 4 sec) [ -9840.4612] [ 2044] [depth= 9] . ( 4 sec) [ -9805.3864] [ 2044] [depth= 1] . ( 4 sec) [ -9801.5030] [ 2047] [depth= 1] . ( 4 sec) [ -9681.8489] [ 2024] [depth= 5] . ( 4 sec) [ -9675.5781] [ 2026] [depth= 1] . ( 4 sec) [ -9674.5843] [ 2023] [depth= 1] . ( 4 sec) [ -9528.0031] [ 2008] [depth= 14] . ( 4 sec) [ -9519.1685] [ 2003] [depth= 3] . ( 4 sec) [ -9504.4968] [ 2006] [depth= 1] . ( 4 sec) [ -9497.4457] [ 2000] [depth= 4] . ( 5 sec) [ -9430.8055] [ 1977] [depth= 3] . ( 5 sec) [ -9430.2215] [ 1979] [depth= 1] . ( 5 sec) [ -9386.0324] [ 1961] [depth= 3] . ( 5 sec) [ -9361.4531] [ 1954] [depth= 1] . ( 5 sec) [ -9361.2329] [ 1955] [depth= 1] . ( 5 sec) [ -9328.0254] [ 1956] [depth= 1] . ( 5 sec) [ -9290.2044] [ 1952] [depth= 7] . ( 5 sec) [ -9132.1007] [ 1874] [depth= 2] . ( 5 sec) [ -9099.1342] [ 1873] [depth= 11] . ( 5 sec) [ -8971.3891] [ 1830] [depth= 9] . ( 5 sec) [ -8711.2111] [ 1734] [depth= 9] . ( 5 sec) [ -8709.7652] [ 1735] [depth= 2] . ( 6 sec) [ -8707.4973] [ 1734] [depth= 1] . ( 6 sec) [ -8529.4740] [ 1715] [depth= 1] . ( 6 sec) [ -8507.4999] [ 1703] [depth= 11] . ( 6 sec) [ -8469.5455] [ 1694] [depth= 1] . ( 6 sec) [ -8387.8569] [ 1661] [depth= 2] . ( 6 sec) [ -8367.5647] [ 1662] [depth= 4] . ( 6 sec) [ -8354.5234] [ 1663] [depth= 2] . ( 6 sec) [ -8324.6499] [ 1651] [depth= 1] . ( 6 sec) [ -8320.9559] [ 1651] [depth= 1] . ( 6 sec) [ -8193.8060] [ 1587] [depth= 1] . ( 6 sec) [ -8164.7781] [ 1576] [depth= 1] . ( 6 sec) [ -8104.2668] [ 1564] [depth= 2] . ( 7 sec) [ -8101.1754] [ 1563] [depth= 1] . ( 7 sec) [ -7888.9996] [ 1522] [depth= 4] . ( 7 sec) [ -7883.3558] [ 1524] [depth= 1] . ( 7 sec) [ -7756.4539] [ 1493] [depth= 4] . ( 7 sec) [ -7753.4181] [ 1492] [depth= 2] . ( 7 sec) [ -7686.6591] [ 1492] [depth= 5] . ( 7 sec) [ -7523.1442] [ 1503] [depth= 1] . ( 7 sec) [ -7496.9703] [ 1492] [depth= 1] . ( 7 sec) [ -7336.1200] [ 1409] [depth= 4] . ( 8 sec) [ -7335.1275] [ 1409] [depth= 1] . ( 8 sec) [ -7315.0474] [ 1400] [depth= 1] . ( 8 sec) [ -7136.2560] [Branch lengths ] . ( 9 sec) [ -7135.2151] [GTR parameters ] . ( 9 sec) [ -7111.0003] [Alpha ][ 0.887592] . ( 9 sec) [ -7110.2482] [ 1398] [depth= 1] . ( 9 sec) [ -7110.2239] [ 1398] [depth= 1] . ( 9 sec) [ -7099.8417] [ 1394] [depth= 1] . ( 9 sec) [ -7095.7758] [ 1383] [depth= 2] . ( 10 sec) [ -7095.5967] [ 1378] [depth= 2] . ( 10 sec) [ -7089.0842] [ 1373] [depth= 2] . ( 10 sec) [ -7071.9820] [ 1340] [depth= 1] . ( 10 sec) [ -7070.5059] [ 1348] [depth= 1] . ( 11 sec) [ -7061.5748] [ 1340] [depth= 1] . ( 11 sec) [ -7061.5634] [ 1340] [depth= 1] . ( 12 sec) [ -7061.1925] [ 1348] [depth= 1] . ( 12 sec) [ -7059.5446] [ 1353] [depth= 1] . ( 13 sec) [ -7057.4770] [ 1353] [depth= 1] . ( 14 sec) [ -7038.7125] [Branch lengths ] . ( 14 sec) [ -7038.5501] [GTR parameters ] . ( 14 sec) [ -7037.9861] [Alpha ][ 0.973623] . ( 15 sec) [ -7031.3552] [ 1347] [depth= 1] . ( 17 sec) [ -7031.2346] [ 1345] [depth= 1] . ( 18 sec) [ -7028.7628] [Branch lengths ] . ( 18 sec) [ -7028.7380] [GTR parameters ] . ( 18 sec) [ -7028.7206] [Alpha ][ 0.990161] . ( 22 sec) [ -7027.5254] [Branch lengths ] . ( 50 sec) [ -7025.2916] [Branch lengths ] . ( 50 sec) [ -7025.2916] [Topology ] . ( 51 sec) [ -7024.6605] [Topology ] . ( 53 sec) [ -7024.4324] [Topology ] . ( 54 sec) [ -7024.3308] [Topology ] . ( 55 sec) [ -7024.2820] [Topology ] . ( 56 sec) [ -7024.2588] [Topology ] . ( 57 sec) [ -7024.2478] [Topology ] . ( 57 sec) [ -7024.2294] [GTR parameters ] . ( 57 sec) [ -7024.2100] [Alpha ][ 1.008011] . ( 57 sec) [ -7024.2100] [Topology ] . ( 59 sec) [ -7024.2033] [Topology ] . ( 60 sec) [ -7024.2004] [Topology ] . ( 61 sec) [ -7024.1990] [Topology ] . ( 62 sec) [ -7024.1984] [Topology ] . ( 63 sec) [ -7024.1983] [GTR parameters ] . ( 63 sec) [ -7024.1983] [Alpha ][ 1.008011] . ( 63 sec) [ -7024.1983] [Topology ] . ( 64 sec) [ -7024.1980] [Topology ] . ( 64 sec) [ -7024.1980] [GTR parameters ] . ( 64 sec) [ -7024.1980] [Alpha ][ 1.008011] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.198043. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15548.9757] [GTR parameters ] . ( 1 sec) [ -15223.4464] [Alpha ][ 0.500960] . ( 1 sec) [ -14945.2532] [ 3340] [depth= 7] . ( 1 sec) [ -14686.5731] [ 3325] [depth= 11] . ( 1 sec) [ -14556.4607] [ 3304] [depth= 6] . ( 1 sec) [ -14506.1556] [ 3299] [depth= 4] . ( 1 sec) [ -14353.7111] [ 3238] [depth= 1] . ( 1 sec) [ -14336.0701] [ 3232] [depth= 5] . ( 1 sec) [ -14174.1258] [ 3219] [depth= 1] . ( 1 sec) [ -14089.8777] [ 3211] [depth= 15] . ( 2 sec) [ -13791.9501] [ 3137] [depth= 23] . ( 2 sec) [ -13400.6898] [ 3065] [depth= 5] . ( 2 sec) [ -13211.7064] [ 2999] [depth= 10] . ( 2 sec) [ -13059.4405] [ 2999] [depth= 2] . ( 2 sec) [ -12700.9339] [ 2915] [depth= 14] . ( 2 sec) [ -12504.4956] [ 2906] [depth= 1] . ( 2 sec) [ -12451.6135] [ 2890] [depth= 11] . ( 2 sec) [ -12294.4051] [ 2872] [depth= 12] . ( 2 sec) [ -12182.9938] [ 2870] [depth= 3] . ( 2 sec) [ -12017.3908] [ 2820] [depth= 10] . ( 2 sec) [ -11766.6932] [ 2824] [depth= 4] . ( 2 sec) [ -11541.5732] [ 2774] [depth= 15] . ( 2 sec) [ -11332.1222] [ 2742] [depth= 12] . ( 2 sec) [ -11181.0700] [ 2698] [depth= 5] . ( 3 sec) [ -11043.0645] [ 2647] [depth= 5] . ( 3 sec) [ -10934.1657] [ 2634] [depth= 10] . ( 3 sec) [ -10805.7198] [ 2591] [depth= 1] . ( 3 sec) [ -10783.5247] [ 2542] [depth= 1] . ( 3 sec) [ -10678.6345] [ 2537] [depth= 1] . ( 3 sec) [ -10629.4669] [ 2521] [depth= 1] . ( 3 sec) [ -10538.3841] [ 2506] [depth= 1] . ( 3 sec) [ -10491.1463] [ 2467] [depth= 7] . ( 3 sec) [ -9984.6151] [ 2352] [depth= 5] . ( 3 sec) [ -9889.6686] [ 2306] [depth= 6] . ( 3 sec) [ -9760.9791] [ 2267] [depth= 4] . ( 3 sec) [ -9682.1352] [ 2252] [depth= 13] . ( 3 sec) [ -9564.2466] [ 2198] [depth= 13] . ( 3 sec) [ -9550.8018] [ 2205] [depth= 3] . ( 4 sec) [ -9425.9296] [ 2177] [depth= 2] . ( 4 sec) [ -9405.8856] [ 2174] [depth= 1] . ( 4 sec) [ -9370.2203] [ 2167] [depth= 2] . ( 4 sec) [ -9295.5376] [ 2053] [depth= 1] . ( 4 sec) [ -9166.4392] [ 2039] [depth= 2] . ( 4 sec) [ -8848.2772] [ 1904] [depth= 11] . ( 4 sec) [ -8831.8353] [ 1899] [depth= 1] . ( 4 sec) [ -8702.4150] [ 1885] [depth= 1] . ( 4 sec) [ -8640.5421] [ 1867] [depth= 1] . ( 4 sec) [ -8633.2477] [ 1865] [depth= 2] . ( 4 sec) [ -8625.1431] [ 1864] [depth= 1] . ( 4 sec) [ -8589.5806] [ 1857] [depth= 2] . ( 5 sec) [ -8584.3244] [ 1818] [depth= 2] . ( 5 sec) [ -8534.3807] [ 1820] [depth= 3] . ( 5 sec) [ -8514.8910] [ 1802] [depth= 1] . ( 5 sec) [ -8486.9215] [ 1797] [depth= 2] . ( 5 sec) [ -8472.8785] [ 1782] [depth= 1] . ( 5 sec) [ -8167.2489] [ 1662] [depth= 4] . ( 5 sec) [ -8152.2332] [ 1658] [depth= 4] . ( 5 sec) [ -8113.3904] [ 1669] [depth= 1] . ( 5 sec) [ -8105.3686] [ 1658] [depth= 1] . ( 5 sec) [ -8098.0437] [ 1658] [depth= 2] . ( 5 sec) [ -8083.1945] [ 1661] [depth= 9] . ( 5 sec) [ -7960.9219] [ 1605] [depth= 2] . ( 6 sec) [ -7955.8196] [ 1610] [depth= 2] . ( 6 sec) [ -7865.4114] [ 1629] [depth= 1] . ( 6 sec) [ -7865.2999] [ 1633] [depth= 1] . ( 6 sec) [ -7857.8945] [ 1618] [depth= 1] . ( 6 sec) [ -7848.1952] [ 1619] [depth= 1] . ( 6 sec) [ -7844.7657] [ 1623] [depth= 1] . ( 6 sec) [ -7832.6545] [ 1619] [depth= 1] . ( 6 sec) [ -7810.9678] [ 1616] [depth= 7] . ( 6 sec) [ -7810.5662] [ 1616] [depth= 1] . ( 7 sec) [ -7807.9236] [ 1613] [depth= 1] . ( 7 sec) [ -7806.9380] [ 1611] [depth= 1] . ( 7 sec) [ -7736.5486] [ 1590] [depth= 2] . ( 7 sec) [ -7665.4278] [ 1571] [depth= 1] . ( 7 sec) [ -7613.4482] [ 1569] [depth= 1] . ( 7 sec) [ -7608.6487] [ 1569] [depth= 2] . ( 7 sec) [ -7597.7025] [ 1546] [depth= 1] . ( 7 sec) [ -7365.4393] [Branch lengths ] . ( 8 sec) [ -7363.9146] [GTR parameters ] . ( 8 sec) [ -7346.2591] [Alpha ][ 0.771966] . ( 8 sec) [ -7343.3959] [ 1517] [depth= 1] . ( 8 sec) [ -7342.4377] [ 1517] [depth= 2] . ( 9 sec) [ -7333.5224] [ 1511] [depth= 2] . ( 9 sec) [ -7291.7955] [ 1459] [depth= 3] . ( 9 sec) [ -7248.6401] [ 1437] [depth= 1] . ( 9 sec) [ -7246.4828] [ 1436] [depth= 1] . ( 10 sec) [ -7095.6712] [ 1358] [depth= 7] . ( 10 sec) [ -7094.4039] [ 1353] [depth= 2] . ( 10 sec) [ -7080.8812] [ 1345] [depth= 1] . ( 10 sec) [ -7076.7552] [ 1340] [depth= 1] . ( 11 sec) [ -7076.5880] [ 1344] [depth= 1] . ( 11 sec) [ -7066.7960] [ 1347] [depth= 1] . ( 11 sec) [ -7066.2555] [ 1352] [depth= 1] . ( 12 sec) [ -7063.9635] [ 1347] [depth= 1] . ( 12 sec) [ -7036.9813] [Branch lengths ] . ( 13 sec) [ -7036.8384] [GTR parameters ] . ( 13 sec) [ -7031.8894] [Alpha ][ 1.007937] . ( 13 sec) [ -7031.1490] [ 1345] [depth= 1] . ( 15 sec) [ -7030.6600] [ 1347] [depth= 1] . ( 16 sec) [ -7030.3275] [ 1345] [depth= 1] . ( 17 sec) [ -7027.8745] [Branch lengths ] . ( 17 sec) [ -7027.8605] [GTR parameters ] . ( 17 sec) [ -7027.8600] [Alpha ][ 1.004897] . ( 20 sec) [ -7027.4467] [Branch lengths ] . ( 47 sec) [ -7025.6661] [Branch lengths ] . ( 47 sec) [ -7025.6661] [Topology ] . ( 48 sec) [ -7024.8102] [Topology ] . ( 49 sec) [ -7024.4853] [Topology ] . ( 50 sec) [ -7024.3405] [Topology ] . ( 52 sec) [ -7024.2713] [Topology ] . ( 53 sec) [ -7024.2390] [Topology ] . ( 54 sec) [ -7024.2236] [Topology ] . ( 55 sec) [ -7024.2136] [GTR parameters ] . ( 55 sec) [ -7024.2129] [Alpha ][ 1.008292] . ( 55 sec) [ -7024.2129] [Topology ] . ( 56 sec) [ -7024.2049] [Topology ] . ( 57 sec) [ -7024.2012] [Topology ] . ( 58 sec) [ -7024.1994] [Topology ] . ( 59 sec) [ -7024.1986] [Topology ] . ( 60 sec) [ -7024.1985] [GTR parameters ] . ( 60 sec) [ -7024.1985] [Alpha ][ 1.008292] . ( 60 sec) [ -7024.1985] [Topology ] . ( 61 sec) [ -7024.1981] [Topology ] . ( 61 sec) [ -7024.1981] [GTR parameters ] . ( 61 sec) [ -7024.1981] [Alpha ][ 1.008292] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7024.198099. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7048.952922 . ( 1 sec) [ -7048.3387] [GTR parameters ] . ( 1 sec) [ -7048.3296] [Alpha ][ 0.988108] . ( 1 sec) [ -7048.3296] [Topology ] . ( 2 sec) [ -7027.3699] [Topology ] . ( 3 sec) [ -7025.2151] [Topology ] . ( 4 sec) [ -7024.6546] [Topology ] . ( 4 sec) [ -7024.4334] [Topology ] . ( 5 sec) [ -7024.3338] [Topology ] . ( 6 sec) [ -7024.2861] [Topology ] . ( 7 sec) [ -7024.2626] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.262628 . ( 13 sec) [ -7024.2478] [GTR parameters ] . ( 13 sec) [ -7024.2259] [Alpha ][ 1.007084] . ( 13 sec) [ -7024.2259] [Topology ] . ( 14 sec) [ -7024.2117] [Topology ] . ( 15 sec) [ -7024.2049] [Topology ] . ( 16 sec) [ -7024.2015] [Topology ] . ( 17 sec) [ -7024.1998] [Topology ] . ( 18 sec) [ -7024.1989] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.198936 . ( 26 sec) [ -7024.1989] [GTR parameters ] . ( 26 sec) [ -7024.1988] [Alpha ][ 1.008092] . ( 26 sec) [ -7024.1988] [Topology ] . ( 27 sec) [ -7024.1984] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -7048.3387] [GTR parameters ] . ( 43 sec) [ -7048.3296] [Alpha ][ 0.988108] . ( 43 sec) [ -7047.5203] [ 1348] [depth= 1] . ( 43 sec) [ -7046.7389] [ 1347] [depth= 1] . ( 44 sec) [ -7044.1362] [ 1345] [depth= 1] . ( 45 sec) [ -7043.6371] [ 1347] [depth= 1] . ( 45 sec) [ -7040.2878] [ 1340] [depth= 1] . ( 45 sec) [ -7039.2313] [ 1345] [depth= 1] . ( 46 sec) [ -7039.2168] [ 1345] [depth= 1] . ( 46 sec) [ -7039.1872] [ 1345] [depth= 1] . ( 46 sec) [ -7039.1698] [ 1345] [depth= 1] . ( 47 sec) [ -7025.3933] [Branch lengths ] . ( 47 sec) [ -7025.3775] [GTR parameters ] . ( 47 sec) [ -7025.3672] [Alpha ][ 1.001105] . ( 50 sec) [ -7025.1652] [ 1347] [depth= 1] . ( 52 sec) [ -7024.3992] [Branch lengths ] . ( 52 sec) [ -7024.3984] [GTR parameters ] . ( 52 sec) [ -7024.3978] [Alpha ][ 1.003902] . ( 82 sec) [ -7024.3621] [Branch lengths ] . ( 82 sec) [ -7024.3621] [Topology ] . ( 83 sec) [ -7024.3589] [Topology ] . ( 84 sec) [ -7024.3578] [Topology ] . ( 86 sec) [ -7024.3573] [Topology ] . ( 86 sec) [ -7024.3573] [GTR parameters ] . ( 86 sec) [ -7024.3572] [Alpha ][ 1.004905] . ( 86 sec) [ -7024.3572] [Topology ] . ( 87 sec) [ -7024.3569] [Topology ] . ( 87 sec) [ -7024.3569] [GTR parameters ] . ( 88 sec) [ -7024.3569] [Alpha ][ 1.004905] . Checking for NNIs, optimizing five branches... . ( 97 sec) [ -7024.3563] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7024.198384 . Log likelihood obtained after SPR moves : -7024.356342 . Log likelihood of the current tree: -7024.198384. . Printing the most likely tree in file 'data6.phy_phyml_tree.txt'... . Best log likelihood : -7024.197952 . Time used 0h1m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo