.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2708_78x1107_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 15 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 1107 sites) . 505 sites without polymorphism (45.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 25Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6919.1804] [Ts/ts ratio ][ 2.356971] . ( 0 sec) [ -6918.3027] [ 1256] [depth= 1] . ( 1 sec) [ -6918.2759] [ 1256] [depth= 1] . ( 1 sec) [ -6917.8548] [ 1257] [depth= 2] . ( 1 sec) [ -6917.8440] [ 1257] [depth= 1] . ( 2 sec) [ -6884.2602] [ 1255] [depth= 1] . ( 2 sec) [ -6832.7211] [ 1268] [depth= 1] . ( 2 sec) [ -6830.6934] [ 1268] [depth= 1] . ( 2 sec) [ -6830.3183] [ 1268] [depth= 1] . ( 2 sec) [ -6830.2880] [ 1268] [depth= 1] . ( 3 sec) [ -6827.4245] [ 1268] [depth= 1] . ( 3 sec) [ -6827.3802] [ 1268] [depth= 1] . ( 3 sec) [ -6826.5412] [ 1267] [depth= 4] . ( 3 sec) [ -6807.1298] [ 1265] [depth= 2] . ( 3 sec) [ -6800.2051] [ 1265] [depth= 3] . ( 3 sec) [ -6792.8404] [ 1264] [depth= 1] . ( 3 sec) [ -6791.2864] [ 1265] [depth= 1] . ( 4 sec) [ -6791.0529] [ 1264] [depth= 1] . ( 4 sec) [ -6790.6652] [ 1264] [depth= 1] . ( 4 sec) [ -6790.2873] [ 1264] [depth= 1] . ( 4 sec) [ -6790.0938] [ 1264] [depth= 1] . ( 4 sec) [ -6789.9868] [ 1264] [depth= 3] . ( 5 sec) [ -6788.4636] [ 1265] [depth= 3] . ( 5 sec) [ -6788.3666] [ 1265] [depth= 3] . ( 6 sec) [ -6771.2155] [ 1263] [depth= 2] . ( 6 sec) [ -6768.3136] [ 1263] [depth= 2] . ( 7 sec) [ -6768.2987] [ 1263] [depth= 1] . ( 7 sec) [ -6764.4530] [ 1263] [depth= 4] . ( 7 sec) [ -6764.1603] [ 1263] [depth= 2] . ( 9 sec) [ -6763.9115] [ 1263] [depth= 1] . ( 9 sec) [ -6756.3597] [ 1262] [depth= 2] . ( 10 sec) [ -6756.2165] [ 1262] [depth= 1] . ( 10 sec) [ -6756.0845] [ 1262] [depth= 1] . ( 10 sec) [ -6755.9594] [ 1259] [depth= 1] . ( 11 sec) [ -6751.0906] [ 1262] [depth= 2] . ( 11 sec) [ -6749.0164] [ 1259] [depth= 1] . ( 11 sec) [ -6748.4968] [ 1262] [depth= 2] . ( 12 sec) [ -6748.4484] [ 1262] [depth= 1] . ( 12 sec) [ -6748.0904] [ 1262] [depth= 2] . ( 13 sec) [ -6745.5832] [ 1263] [depth= 1] . ( 13 sec) [ -6744.0040] [ 1262] [depth= 1] . ( 13 sec) [ -6734.8948] [ 1261] [depth= 1] . ( 13 sec) [ -6719.8465] [ 1248] [depth= 1] . ( 13 sec) [ -6714.4491] [ 1243] [depth= 1] . ( 13 sec) [ -6707.7580] [ 1243] [depth= 2] . ( 15 sec) [ -6706.0006] [ 1244] [depth= 1] . ( 15 sec) [ -6705.8277] [ 1244] [depth= 1] . ( 15 sec) [ -6705.6588] [ 1244] [depth= 1] . ( 15 sec) [ -6705.4048] [ 1244] [depth= 2] . ( 15 sec) [ -6705.1109] [ 1244] [depth= 1] . ( 16 sec) [ -6705.0925] [ 1244] [depth= 1] . ( 18 sec) [ -6703.3275] [ 1244] [depth= 2] . ( 18 sec) [ -6697.0445] [ 1242] [depth= 1] . ( 19 sec) [ -6689.4857] [ 1241] [depth= 2] . ( 19 sec) [ -6686.0425] [ 1243] [depth= 1] . ( 20 sec) [ -6685.4655] [ 1243] [depth= 1] . ( 20 sec) [ -6684.8644] [ 1240] [depth= 1] . ( 20 sec) [ -6684.8130] [ 1240] [depth= 1] . ( 20 sec) [ -6683.3896] [ 1242] [depth= 1] . ( 21 sec) [ -6682.2741] [ 1242] [depth= 1] . ( 22 sec) [ -6678.7313] [ 1244] [depth= 1] . ( 22 sec) [ -6677.8110] [ 1244] [depth= 1] . ( 23 sec) [ -6676.8541] [ 1244] [depth= 1] . ( 23 sec) [ -6670.8658] [ 1242] [depth= 1] . ( 23 sec) [ -6666.2352] [ 1243] [depth= 1] . ( 23 sec) [ -6665.1888] [ 1243] [depth= 1] . ( 23 sec) [ -6665.1643] [ 1243] [depth= 1] . ( 24 sec) [ -6663.5465] [ 1244] [depth= 2] . ( 24 sec) [ -6659.5060] [ 1242] [depth= 3] . ( 25 sec) [ -6654.0246] [ 1240] [depth= 1] . ( 25 sec) [ -6652.6270] [ 1243] [depth= 1] . ( 25 sec) [ -6651.7864] [ 1243] [depth= 1] . ( 25 sec) [ -6651.7680] [ 1243] [depth= 2] . ( 25 sec) [ -6651.6914] [ 1243] [depth= 2] . ( 26 sec) [ -6651.6802] [ 1243] [depth= 2] . ( 26 sec) [ -6651.6601] [ 1243] [depth= 5] . ( 28 sec) [ -6651.4885] [ 1243] [depth= 8] . ( 28 sec) [ -6651.3178] [ 1243] [depth= 2] . ( 28 sec) [ -6651.2114] [ 1243] [depth= 1] . ( 28 sec) [ -6651.1936] [ 1243] [depth= 2] . ( 28 sec) [ -6650.2279] [ 1243] [depth= 6] . ( 29 sec) [ -6650.1255] [ 1243] [depth= 4] . ( 29 sec) [ -6650.0625] [ 1243] [depth= 1] . ( 29 sec) [ -6650.0521] [ 1243] [depth= 2] . ( 29 sec) [ -6649.9430] [ 1243] [depth= 1] . ( 32 sec) [ -6649.7107] [ 1243] [depth= 4] . ( 32 sec) [ -6649.6986] [ 1243] [depth= 3] . ( 32 sec) [ -6648.2668] [ 1240] [depth= 1] . ( 33 sec) [ -6648.2549] [ 1240] [depth= 5] . ( 34 sec) [ -6648.1257] [ 1240] [depth= 4] . ( 35 sec) [ -6608.7835] [Branch lengths ] . ( 36 sec) [ -6606.0463] [Ts/ts ratio ][ 2.786159] . ( 36 sec) [ -6605.9799] [ 1240] [depth= 2] . ( 36 sec) [ -6605.9306] [ 1239] [depth= 1] . ( 36 sec) [ -6605.4009] [ 1239] [depth= 1] . ( 37 sec) [ -6604.4450] [ 1243] [depth= 1] . ( 37 sec) [ -6604.1312] [ 1242] [depth= 1] . ( 37 sec) [ -6599.4296] [ 1265] [depth= 5] . ( 39 sec) [ -6597.7400] [ 1264] [depth= 2] . ( 39 sec) [ -6596.6128] [ 1264] [depth= 1] . ( 39 sec) [ -6596.4251] [ 1264] [depth= 1] . ( 44 sec) [ -6592.8960] [ 1264] [depth= 5] . ( 46 sec) [ -6590.2935] [ 1264] [depth= 4] . ( 46 sec) [ -6588.3327] [ 1264] [depth= 1] . ( 46 sec) [ -6588.0311] [ 1264] [depth= 1] . ( 46 sec) [ -6587.9142] [ 1264] [depth= 1] . ( 46 sec) [ -6587.5898] [ 1264] [depth= 1] . ( 47 sec) [ -6587.5103] [ 1264] [depth= 1] . ( 47 sec) [ -6586.7251] [ 1264] [depth= 5] . ( 47 sec) [ -6586.2941] [ 1264] [depth= 1] . ( 47 sec) [ -6586.0750] [ 1264] [depth= 1] . ( 48 sec) [ -6586.0648] [ 1264] [depth= 1] . ( 50 sec) [ -6585.4948] [ 1264] [depth= 2] . ( 50 sec) [ -6584.0605] [ 1263] [depth= 1] . ( 51 sec) [ -6584.0207] [ 1263] [depth= 1] . ( 51 sec) [ -6583.6144] [ 1264] [depth= 1] . ( 59 sec) [ -6583.3623] [ 1264] [depth= 1] . ( 60 sec) [ -6583.3340] [ 1264] [depth= 1] . ( 62 sec) [ -6583.2848] [ 1264] [depth= 2] . ( 78 sec) [ -6578.7861] [Branch lengths ] . ( 78 sec) [ -6578.7535] [Ts/ts ratio ][ 2.838723] . ( 78 sec) [ -6577.9271] [ 1264] [depth= 1] . ( 79 sec) [ -6577.9033] [ 1264] [depth= 1] . ( 79 sec) [ -6577.8552] [ 1264] [depth= 1] . ( 80 sec) [ -6577.7168] [ 1263] [depth= 1] . ( 122 sec) [ -6577.0784] [Branch lengths ] . ( 123 sec) [ -6577.0784] [Ts/ts ratio ][ 2.838723] . ( 151 sec) [ -6577.0131] [ 1265] [depth= 1] . ( 167 sec) [ -6576.5859] [Branch lengths ] . ( 167 sec) [ -6576.5857] [Ts/ts ratio ][ 2.833631] . ( 170 sec) [ -6576.2080] [ 1264] [depth= 1] . ( 172 sec) [ -6576.0811] [ 1275] [depth= 1] . ( 172 sec) [ -6575.5419] [ 1269] [depth= 5] . ( 204 sec) [ -6574.1435] [ 1268] [depth= 1] . ( 206 sec) [ -6573.9934] [ 1268] [depth= 1] . ( 207 sec) [ -6573.7980] [ 1268] [depth= 1] . ( 241 sec) [ -6573.6776] [ 1269] [depth= 1] . ( 243 sec) [ -6573.4445] [ 1269] [depth= 2] . ( 249 sec) [ -6573.3582] [ 1269] [depth= 3] . ( 249 sec) [ -6573.3377] [ 1269] [depth= 2] . ( 260 sec) [ -6571.1833] [Branch lengths ] . ( 260 sec) [ -6571.1701] [Ts/ts ratio ][ 2.866648] . ( 354 sec) [ -6570.8840] [Branch lengths ] . ( 354 sec) [ -6570.8840] [Topology ] . ( 356 sec) [ -6570.5514] [Topology ] . ( 358 sec) [ -6570.4337] [Topology ] . ( 359 sec) [ -6570.3736] [Topology ] . ( 361 sec) [ -6570.3362] [Topology ] . ( 363 sec) [ -6570.3113] [Topology ] . ( 365 sec) [ -6570.2939] [Topology ] . ( 366 sec) [ -6570.2810] [Topology ] . ( 367 sec) [ -6570.2810] [Ts/ts ratio ][ 2.866648] . ( 367 sec) [ -6570.2810] [Topology ] . ( 369 sec) [ -6570.2711] [Topology ] . ( 370 sec) [ -6570.2628] [Topology ] . ( 372 sec) [ -6570.2567] [Topology ] . ( 374 sec) [ -6570.2515] [Topology ] . ( 376 sec) [ -6570.2476] [Topology ] . ( 377 sec) [ -6570.2456] [Topology ] . ( 378 sec) [ -6570.2456] [Ts/ts ratio ][ 2.866648] . ( 378 sec) [ -6570.2456] [Topology ] . ( 379 sec) [ -6570.2444] [Topology ] . ( 381 sec) [ -6570.2437] [Topology ] . ( 381 sec) [ -6570.2437] [Ts/ts ratio ][ 2.866648] . ( 381 sec) [ -6570.2437] [Topology ] . ( 383 sec) [ -6570.2433] [Topology ] . ( 383 sec) [ -6570.2433] [Ts/ts ratio ][ 2.866648] . Checking for NNIs, optimizing five branches... . ( 398 sec) [ -6570.1330] [Topology ] . Checking for NNIs, optimizing five branches... . ( 412 sec) [ -6570.1304] [Topology ] . Checking for NNIs, optimizing five branches... . ( 426 sec) [ -6570.1301] [Topology ] . Checking for NNIs, optimizing five branches... . ( 441 sec) [ -6570.1300] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6570.130018. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 27 -1.000000 0.000000 0.000000 67 8.338551 0.795000 0.001295 87 2.653426 0.775000 0.035580 49 1.042118 0.216000 0.036210 100 351.829267 1.000000 0.695403 83 2.533320 0.445000 0.044377 93 12.400981 0.907000 0.016566 20 2.880919 0.758000 0.024400 0 -1.000000 0.000000 0.000000 95 72.414695 0.997000 0.055040 18 20.414354 0.925000 0.023786 59 11.410481 0.916000 0.031732 92 19.944607 0.948000 0.036039 6 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 96 50.933260 0.962000 0.010290 28 -1.000000 0.000000 0.000000 99 43.372635 0.990000 0.050017 55 -1.000000 0.000000 0.000001 25 0.224570 0.256000 0.003243 23 -1.000000 0.000000 0.000000 11 0.945265 0.668000 0.009896 27 14.503908 0.921000 0.047596 50 3.830442 0.689000 0.018042 73 16.401015 0.938000 0.043982 65 22.574008 0.965000 0.040152 23 3.031064 0.756000 0.001740 68 7.559173 0.758000 0.001669 30 7.273332 0.794000 0.001404 33 5.562297 0.774000 0.002080 32 1.131211 0.208000 0.003432 17 0.031811 0.000000 0.000751 66 40.085481 0.985000 0.061396 100 40.185076 0.986000 0.049231 68 8.722376 0.807000 0.003402 79 11.135100 0.792000 0.003438 31 -1.000000 0.000000 0.000000 50 8.225624 0.892000 0.028160 52 18.588121 0.959000 0.034123 14 0.001764 0.000000 0.000248 31 5.860599 0.770000 0.033739 92 13.153647 0.930000 0.022209 23 -1.000000 0.000000 0.000000 28 0.227228 0.011000 0.009344 96 12.278417 0.913000 0.023522 30 -1.000000 0.000000 0.000000 99 102.123710 1.000000 0.063147 99 40.111593 0.986000 0.038002 31 -1.000000 0.000000 0.000000 58 7.079205 0.849000 0.043195 97 52.592216 0.996000 0.067699 1 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 42 14.311858 0.915000 0.001255 18 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 9 0.000241 0.000000 0.000000 12 -1.000000 0.000000 0.002519 5 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 75 9.683997 0.756000 0.018437 61 2.467859 0.737000 0.003382 38 3.234091 0.759000 0.006228 100 61.793259 0.997000 0.049711 95 10.706676 0.885000 0.012530 100 24.210449 0.940000 0.013367 70 2.687502 0.746000 0.003144 88 2.010808 0.756000 0.005052 . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 8h47m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo