.......................... 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 : 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 : 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)... . ( 3 sec) [ -6941.4211] [GTR parameters ] . ( 3 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 3 sec) [ -6898.9682] [ 1256] [depth= 1] . ( 11 sec) [ -6898.6922] [ 1257] [depth= 1] . ( 11 sec) [ -6862.0853] [ 1254] [depth= 1] . ( 11 sec) [ -6859.2450] [ 1256] [depth= 1] . ( 11 sec) [ -6783.6394] [ 1270] [depth= 1] . ( 12 sec) [ -6781.8295] [ 1267] [depth= 1] . ( 12 sec) [ -6777.2927] [ 1274] [depth= 3] . ( 12 sec) [ -6769.2519] [ 1270] [depth= 7] . ( 12 sec) [ -6767.8517] [ 1271] [depth= 1] . ( 12 sec) [ -6765.9688] [ 1271] [depth= 1] . ( 12 sec) [ -6765.7131] [ 1271] [depth= 1] . ( 12 sec) [ -6765.6809] [ 1271] [depth= 1] . ( 12 sec) [ -6762.5606] [ 1271] [depth= 1] . ( 13 sec) [ -6762.5248] [ 1271] [depth= 1] . ( 13 sec) [ -6761.8884] [ 1271] [depth= 1] . ( 13 sec) [ -6757.3694] [ 1271] [depth= 1] . ( 13 sec) [ -6756.6077] [ 1272] [depth= 3] . ( 13 sec) [ -6748.6641] [ 1271] [depth= 3] . ( 13 sec) [ -6744.3996] [ 1270] [depth= 3] . ( 13 sec) [ -6740.6912] [ 1270] [depth= 1] . ( 17 sec) [ -6740.3634] [ 1270] [depth= 1] . ( 17 sec) [ -6740.0138] [ 1270] [depth= 1] . ( 17 sec) [ -6739.8348] [ 1270] [depth= 1] . ( 17 sec) [ -6739.7397] [ 1270] [depth= 3] . ( 17 sec) [ -6739.5369] [ 1270] [depth= 1] . ( 22 sec) [ -6737.4955] [ 1269] [depth= 1] . ( 22 sec) [ -6735.2060] [ 1269] [depth= 2] . ( 23 sec) [ -6731.2638] [ 1269] [depth= 1] . ( 23 sec) [ -6725.5266] [ 1268] [depth= 1] . ( 31 sec) [ -6706.1985] [ 1266] [depth= 2] . ( 32 sec) [ -6702.5146] [ 1266] [depth= 2] . ( 33 sec) [ -6698.3062] [ 1266] [depth= 4] . ( 35 sec) [ -6692.9249] [ 1265] [depth= 1] . ( 48 sec) [ -6692.7030] [ 1265] [depth= 1] . ( 49 sec) [ -6685.4415] [ 1264] [depth= 2] . ( 50 sec) [ -6684.7965] [ 1264] [depth= 1] . ( 52 sec) [ -6683.2139] [ 1264] [depth= 2] . ( 52 sec) [ -6682.6134] [ 1264] [depth= 1] . ( 52 sec) [ -6682.4994] [ 1261] [depth= 1] . ( 52 sec) [ -6677.2485] [ 1264] [depth= 2] . ( 53 sec) [ -6674.9886] [ 1261] [depth= 1] . ( 53 sec) [ -6674.3930] [ 1264] [depth= 2] . ( 53 sec) [ -6672.6152] [ 1264] [depth= 1] . ( 54 sec) [ -6670.0287] [ 1265] [depth= 1] . ( 55 sec) [ -6668.0751] [ 1264] [depth= 1] . ( 55 sec) [ -6657.9441] [ 1263] [depth= 1] . ( 55 sec) [ -6657.1835] [ 1264] [depth= 1] . ( 55 sec) [ -6653.7979] [ 1265] [depth= 1] . ( 60 sec) [ -6653.7157] [ 1266] [depth= 1] . ( 60 sec) [ -6651.9846] [ 1266] [depth= 2] . ( 62 sec) [ -6650.9471] [ 1271] [depth= 2] . ( 63 sec) [ -6650.5795] [ 1271] [depth= 1] . ( 63 sec) [ -6650.1757] [ 1271] [depth= 1] . ( 63 sec) [ -6648.9971] [ 1271] [depth= 2] . ( 63 sec) [ -6648.7205] [ 1271] [depth= 1] . ( 65 sec) [ -6648.7068] [ 1271] [depth= 1] . ( 73 sec) [ -6648.4784] [ 1270] [depth= 2] . ( 77 sec) [ -6642.8789] [ 1268] [depth= 1] . ( 87 sec) [ -6636.6967] [ 1267] [depth= 1] . ( 92 sec) [ -6635.9669] [ 1264] [depth= 1] . ( 95 sec) [ -6635.8654] [ 1265] [depth= 1] . ( 96 sec) [ -6635.0471] [ 1266] [depth= 1] . ( 96 sec) [ -6634.5868] [ 1269] [depth= 2] . ( 96 sec) [ -6631.9206] [ 1265] [depth= 2] . ( 96 sec) [ -6627.2887] [ 1265] [depth= 1] . ( 97 sec) [ -6623.1432] [ 1266] [depth= 1] . ( 97 sec) [ -6622.6536] [ 1266] [depth= 1] . ( 98 sec) [ -6621.8204] [ 1266] [depth= 1] . ( 98 sec) [ -6617.0707] [ 1265] [depth= 1] . ( 99 sec) [ -6610.0398] [ 1265] [depth= 1] . ( 99 sec) [ -6607.6563] [ 1265] [depth= 1] . ( 99 sec) [ -6607.6394] [ 1265] [depth= 1] . ( 108 sec) [ -6606.8345] [ 1265] [depth= 1] . ( 109 sec) [ -6603.3477] [ 1264] [depth= 2] . ( 110 sec) [ -6597.6950] [ 1262] [depth= 1] . ( 112 sec) [ -6597.1027] [ 1264] [depth= 1] . ( 114 sec) [ -6597.0883] [ 1264] [depth= 2] . ( 114 sec) [ -6596.9394] [ 1264] [depth= 2] . ( 114 sec) [ -6596.9279] [ 1264] [depth= 2] . ( 116 sec) [ -6596.8339] [ 1264] [depth= 6] . ( 120 sec) [ -6596.7790] [ 1264] [depth= 1] . ( 120 sec) [ -6596.5978] [ 1264] [depth= 2] . ( 121 sec) [ -6596.4888] [ 1264] [depth= 1] . ( 121 sec) [ -6596.2799] [ 1264] [depth= 2] . ( 121 sec) [ -6596.2570] [ 1264] [depth= 4] . ( 121 sec) [ -6596.2434] [ 1264] [depth= 4] . ( 121 sec) [ -6595.9539] [ 1264] [depth= 3] . ( 122 sec) [ -6595.9305] [ 1264] [depth= 6] . ( 122 sec) [ -6595.8276] [ 1264] [depth= 5] . ( 129 sec) [ -6595.3074] [ 1262] [depth= 1] . ( 129 sec) [ -6595.2602] [ 1262] [depth= 4] . ( 129 sec) [ -6595.2475] [ 1262] [depth= 1] . ( 141 sec) [ -6566.3581] [Branch lengths ] . ( 144 sec) [ -6559.1575] [GTR parameters ] . ( 144 sec) [ -6555.8737] [Alpha ][ 0.420104] . ( 157 sec) [ -6555.5830] [ 1261] [depth= 1] . ( 157 sec) [ -6555.4764] [ 1256] [depth= 8] . ( 172 sec) [ -6555.4615] [ 1256] [depth= 1] . ( 175 sec) [ -6554.5625] [ 1256] [depth= 2] . ( 175 sec) [ -6554.5386] [ 1256] [depth= 3] . ( 176 sec) [ -6551.4643] [ 1256] [depth= 1] . ( 176 sec) [ -6551.4260] [ 1256] [depth= 2] . ( 176 sec) [ -6551.4157] [ 1256] [depth= 3] . ( 176 sec) [ -6551.3769] [ 1256] [depth= 4] . ( 176 sec) [ -6547.7231] [ 1256] [depth= 2] . ( 176 sec) [ -6546.4703] [ 1256] [depth= 2] . ( 197 sec) [ -6545.9994] [ 1256] [depth= 3] . ( 197 sec) [ -6545.8802] [ 1256] [depth= 3] . ( 214 sec) [ -6545.8429] [ 1256] [depth= 4] . ( 228 sec) [ -6545.0323] [ 1256] [depth= 3] . ( 236 sec) [ -6544.9444] [ 1258] [depth= 1] . ( 237 sec) [ -6544.5389] [ 1259] [depth= 1] . ( 241 sec) [ -6543.7025] [ 1259] [depth= 1] . ( 243 sec) [ -6543.5302] [ 1258] [depth= 1] . ( 248 sec) [ -6543.0185] [ 1271] [depth= 2] . ( 294 sec) [ -6542.9371] [ 1271] [depth= 1] . ( 295 sec) [ -6542.7579] [ 1268] [depth= 1] . ( 298 sec) [ -6542.5902] [ 1269] [depth= 1] . ( 300 sec) [ -6542.3917] [ 1269] [depth= 1] . ( 307 sec) [ -6542.3619] [ 1269] [depth= 1] . ( 354 sec) [ -6542.3309] [ 1269] [depth= 6] . ( 377 sec) [ -6536.9230] [Branch lengths ] . ( 379 sec) [ -6536.4971] [GTR parameters ] . ( 379 sec) [ -6535.2182] [Alpha ][ 0.378846] . ( 391 sec) [ -6534.7807] [ 1255] [depth= 4] . ( 393 sec) [ -6534.3877] [ 1253] [depth= 1] . ( 414 sec) [ -6534.3682] [ 1253] [depth= 3] . ( 485 sec) [ -6534.0510] [ 1255] [depth= 1] . ( 643 sec) [ -6532.9808] [Branch lengths ] . ( 644 sec) [ -6532.9076] [GTR parameters ] . ( 644 sec) [ -6532.5960] [Alpha ][ 0.360443] . ( 657 sec) [ -6531.9590] [ 1268] [depth= 4] . ( 658 sec) [ -6529.4684] [ 1261] [depth= 6] . ( 687 sec) [ -6529.4443] [ 1261] [depth= 4] . ( 854 sec) [ -6529.3727] [ 1262] [depth= 1] . ( 909 sec) [ -6528.4370] [Branch lengths ] . ( 911 sec) [ -6528.4132] [GTR parameters ] . ( 911 sec) [ -6528.3548] [Alpha ][ 0.353007] . ( 923 sec) [ -6528.1354] [ 1264] [depth= 2] . ( 925 sec) [ -6528.0134] [ 1274] [depth= 4] . ( 1094 sec) [ -6527.9799] [ 1274] [depth= 1] . ( 1099 sec) [ -6527.9625] [ 1274] [depth= 1] . ( 1175 sec) [ -6527.6384] [Branch lengths ] . ( 1177 sec) [ -6527.6361] [GTR parameters ] . ( 1177 sec) [ -6527.6120] [Alpha ][ 0.348092] . ( 1181 sec) [ -6527.5789] [ 1275] [depth= 1] . ( 1262 sec) [ -6527.4419] [Branch lengths ] . ( 1264 sec) [ -6527.4413] [GTR parameters ] . ( 1264 sec) [ -6527.4368] [Alpha ][ 0.345991] . ( 1264 sec) [ -6527.4368] [Topology ] . ( 1266 sec) [ -6527.4030] [Topology ] . ( 1267 sec) [ -6527.3874] [Topology ] . ( 1269 sec) [ -6527.3776] [Topology ] . ( 1271 sec) [ -6527.3711] [Topology ] . ( 1273 sec) [ -6527.3668] [Topology ] . ( 1274 sec) [ -6527.3638] [Topology ] . ( 1275 sec) [ -6527.3637] [GTR parameters ] . ( 1276 sec) [ -6527.3623] [Alpha ][ 0.344799] . ( 1276 sec) [ -6527.3623] [Topology ] . ( 1277 sec) [ -6527.3596] [Topology ] . ( 1279 sec) [ -6527.3580] [Topology ] . ( 1281 sec) [ -6527.3570] [Topology ] . ( 1283 sec) [ -6527.3563] [Topology ] . ( 1283 sec) [ -6527.3563] [GTR parameters ] . ( 1283 sec) [ -6527.3560] [Alpha ][ 0.344274] . ( 1283 sec) [ -6527.3560] [Topology ] . ( 1285 sec) [ -6527.3554] [Topology ] . ( 1286 sec) [ -6527.3554] [GTR parameters ] . ( 1286 sec) [ -6527.3554] [Alpha ][ 0.344274] . Checking for NNIs, optimizing five branches... . ( 1301 sec) [ -6527.2190] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1316 sec) [ -6527.2181] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.218095. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h22m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1328.96user 0.00system 22:11.59elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps