.......................... 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)... . ( 2 sec) [ -6941.4211] [GTR parameters ] . ( 3 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 3 sec) [ -6898.9682] [ 1256] [depth= 1] . ( 3 sec) [ -6862.0921] [ 1254] [depth= 1] . ( 4 sec) [ -6800.8822] [ 1267] [depth= 1] . ( 4 sec) [ -6798.9513] [ 1267] [depth= 1] . ( 4 sec) [ -6798.5548] [ 1267] [depth= 1] . ( 4 sec) [ -6798.5334] [ 1267] [depth= 1] . ( 4 sec) [ -6795.8395] [ 1267] [depth= 1] . ( 4 sec) [ -6795.7936] [ 1267] [depth= 1] . ( 4 sec) [ -6794.1363] [ 1266] [depth= 4] . ( 4 sec) [ -6774.7401] [ 1264] [depth= 2] . ( 5 sec) [ -6768.7610] [ 1264] [depth= 3] . ( 5 sec) [ -6761.2730] [ 1263] [depth= 1] . ( 5 sec) [ -6760.9157] [ 1263] [depth= 1] . ( 5 sec) [ -6760.5490] [ 1263] [depth= 1] . ( 5 sec) [ -6760.3612] [ 1263] [depth= 1] . ( 6 sec) [ -6760.2626] [ 1263] [depth= 3] . ( 6 sec) [ -6760.2523] [ 1263] [depth= 1] . ( 6 sec) [ -6755.8202] [ 1264] [depth= 1] . ( 7 sec) [ -6755.6585] [ 1264] [depth= 1] . ( 7 sec) [ -6755.5331] [ 1264] [depth= 1] . ( 7 sec) [ -6737.4835] [ 1262] [depth= 2] . ( 7 sec) [ -6734.3279] [ 1262] [depth= 2] . ( 8 sec) [ -6730.5908] [ 1262] [depth= 4] . ( 9 sec) [ -6730.3512] [ 1262] [depth= 1] . ( 9 sec) [ -6723.0317] [ 1261] [depth= 2] . ( 9 sec) [ -6722.8919] [ 1261] [depth= 1] . ( 9 sec) [ -6722.7601] [ 1261] [depth= 1] . ( 9 sec) [ -6722.6363] [ 1258] [depth= 1] . ( 10 sec) [ -6709.0406] [ 1258] [depth= 5] . ( 10 sec) [ -6707.6632] [ 1258] [depth= 1] . ( 10 sec) [ -6707.6102] [ 1258] [depth= 1] . ( 10 sec) [ -6707.4169] [ 1258] [depth= 2] . ( 10 sec) [ -6705.3906] [ 1259] [depth= 1] . ( 10 sec) [ -6703.5796] [ 1258] [depth= 1] . ( 10 sec) [ -6693.2047] [ 1257] [depth= 1] . ( 10 sec) [ -6676.3545] [ 1244] [depth= 1] . ( 11 sec) [ -6675.9160] [ 1239] [depth= 3] . ( 11 sec) [ -6664.5759] [ 1238] [depth= 4] . ( 11 sec) [ -6663.7723] [ 1238] [depth= 1] . ( 11 sec) [ -6662.0884] [ 1239] [depth= 1] . ( 12 sec) [ -6661.8838] [ 1239] [depth= 1] . ( 12 sec) [ -6660.7282] [ 1239] [depth= 2] . ( 12 sec) [ -6660.4369] [ 1239] [depth= 1] . ( 12 sec) [ -6660.4184] [ 1239] [depth= 1] . ( 13 sec) [ -6658.3618] [ 1238] [depth= 1] . ( 13 sec) [ -6652.5836] [ 1236] [depth= 1] . ( 13 sec) [ -6652.0442] [ 1237] [depth= 2] . ( 13 sec) [ -6650.0021] [ 1238] [depth= 1] . ( 14 sec) [ -6649.9572] [ 1238] [depth= 1] . ( 14 sec) [ -6645.6943] [ 1238] [depth= 2] . ( 14 sec) [ -6644.1904] [ 1243] [depth= 1] . ( 14 sec) [ -6641.8149] [ 1238] [depth= 3] . ( 14 sec) [ -6641.2940] [ 1238] [depth= 1] . ( 15 sec) [ -6640.6465] [ 1238] [depth= 1] . ( 15 sec) [ -6636.9576] [ 1238] [depth= 1] . ( 15 sec) [ -6636.9404] [ 1238] [depth= 1] . ( 15 sec) [ -6633.4446] [ 1238] [depth= 2] . ( 15 sec) [ -6631.7744] [ 1237] [depth= 2] . ( 16 sec) [ -6616.6821] [ 1237] [depth= 1] . ( 16 sec) [ -6616.1592] [ 1241] [depth= 1] . ( 16 sec) [ -6615.6594] [ 1237] [depth= 1] . ( 16 sec) [ -6615.6486] [ 1237] [depth= 2] . ( 16 sec) [ -6615.4934] [ 1237] [depth= 2] . ( 16 sec) [ -6615.4816] [ 1237] [depth= 2] . ( 17 sec) [ -6615.3963] [ 1237] [depth= 2] . ( 17 sec) [ -6615.3824] [ 1237] [depth= 2] . ( 17 sec) [ -6615.1932] [ 1237] [depth= 1] . ( 17 sec) [ -6615.0822] [ 1237] [depth= 1] . ( 17 sec) [ -6615.0164] [ 1237] [depth= 1] . ( 18 sec) [ -6614.6900] [ 1237] [depth= 2] . ( 18 sec) [ -6614.6520] [ 1237] [depth= 2] . ( 18 sec) [ -6614.6419] [ 1237] [depth= 3] . ( 18 sec) [ -6614.6305] [ 1237] [depth= 2] . ( 19 sec) [ -6614.5924] [ 1237] [depth= 1] . ( 19 sec) [ -6614.5399] [ 1237] [depth= 1] . ( 20 sec) [ -6614.5096] [ 1237] [depth= 1] . ( 20 sec) [ -6613.2829] [ 1237] [depth= 5] . ( 20 sec) [ -6613.1899] [ 1237] [depth= 2] . ( 20 sec) [ -6613.1762] [ 1237] [depth= 3] . ( 21 sec) [ -6613.1618] [ 1237] [depth= 1] . ( 23 sec) [ -6570.9410] [Branch lengths ] . ( 25 sec) [ -6563.1084] [GTR parameters ] . ( 25 sec) [ -6559.9654] [Alpha ][ 0.421531] . ( 26 sec) [ -6555.4525] [ 1254] [depth= 3] . ( 26 sec) [ -6555.2684] [ 1254] [depth= 2] . ( 27 sec) [ -6554.9687] [ 1254] [depth= 1] . ( 27 sec) [ -6554.8627] [ 1254] [depth= 1] . ( 27 sec) [ -6552.5574] [ 1253] [depth= 4] . ( 27 sec) [ -6552.4850] [ 1253] [depth= 1] . ( 28 sec) [ -6552.4747] [ 1253] [depth= 5] . ( 29 sec) [ -6552.4615] [ 1253] [depth= 1] . ( 29 sec) [ -6552.3797] [ 1253] [depth= 1] . ( 31 sec) [ -6552.1886] [ 1253] [depth= 1] . ( 31 sec) [ -6551.8520] [ 1253] [depth= 1] . ( 32 sec) [ -6551.7811] [ 1253] [depth= 1] . ( 32 sec) [ -6551.7100] [ 1253] [depth= 1] . ( 35 sec) [ -6551.5802] [ 1254] [depth= 1] . ( 35 sec) [ -6551.3776] [ 1254] [depth= 1] . ( 36 sec) [ -6550.6166] [ 1253] [depth= 1] . ( 36 sec) [ -6546.6377] [ 1253] [depth= 1] . ( 36 sec) [ -6546.4150] [ 1253] [depth= 2] . ( 44 sec) [ -6539.8103] [Branch lengths ] . ( 45 sec) [ -6539.5109] [GTR parameters ] . ( 46 sec) [ -6538.2025] [Alpha ][ 0.379800] . ( 52 sec) [ -6538.0228] [ 1253] [depth= 1] . ( 56 sec) [ -6537.5857] [ 1252] [depth= 1] . ( 57 sec) [ -6537.4343] [ 1252] [depth= 4] . ( 60 sec) [ -6537.4242] [ 1252] [depth= 5] . ( 60 sec) [ -6536.5958] [ 1252] [depth= 3] . ( 63 sec) [ -6533.7821] [Branch lengths ] . ( 65 sec) [ -6533.7427] [GTR parameters ] . ( 65 sec) [ -6533.4299] [Alpha ][ 0.361308] . ( 73 sec) [ -6533.2716] [ 1252] [depth= 1] . ( 85 sec) [ -6532.5618] [Branch lengths ] . ( 87 sec) [ -6532.5496] [GTR parameters ] . ( 87 sec) [ -6532.4531] [Alpha ][ 0.351664] . ( 91 sec) [ -6532.1146] [ 1256] [depth= 3] . ( 91 sec) [ -6531.7307] [ 1258] [depth= 1] . ( 158 sec) [ -6531.6929] [ 1259] [depth= 1] . ( 177 sec) [ -6530.9360] [Branch lengths ] . ( 179 sec) [ -6530.9162] [GTR parameters ] . ( 179 sec) [ -6530.8783] [Alpha ][ 0.345558] . ( 183 sec) [ -6530.5483] [ 1269] [depth= 3] . ( 184 sec) [ -6530.3973] [ 1274] [depth= 4] . ( 190 sec) [ -6530.3683] [ 1274] [depth= 2] . ( 193 sec) [ -6530.3565] [ 1274] [depth= 1] . ( 207 sec) [ -6530.3204] [ 1274] [depth= 3] . ( 248 sec) [ -6530.2273] [ 1274] [depth= 1] . ( 248 sec) [ -6530.2169] [ 1274] [depth= 1] . ( 270 sec) [ -6529.5991] [Branch lengths ] . ( 272 sec) [ -6529.5840] [GTR parameters ] . ( 272 sec) [ -6529.5776] [Alpha ][ 0.343072] . ( 277 sec) [ -6529.0578] [ 1265] [depth= 6] . ( 283 sec) [ -6529.0406] [ 1265] [depth= 1] . ( 387 sec) [ -6528.6027] [Branch lengths ] . ( 389 sec) [ -6528.5966] [GTR parameters ] . ( 389 sec) [ -6528.5949] [Alpha ][ 0.341772] . ( 389 sec) [ -6528.5949] [Topology ] . ( 392 sec) [ -6528.4676] [Topology ] . ( 395 sec) [ -6528.4246] [Topology ] . ( 398 sec) [ -6528.4047] [Topology ] . ( 402 sec) [ -6528.3940] [Topology ] . ( 405 sec) [ -6528.3878] [Topology ] . ( 407 sec) [ -6528.3839] [Topology ] . ( 410 sec) [ -6528.3836] [GTR parameters ] . ( 411 sec) [ -6528.3833] [Alpha ][ 0.341236] . ( 411 sec) [ -6528.3833] [Topology ] . ( 414 sec) [ -6528.3807] [Topology ] . ( 417 sec) [ -6528.3790] [Topology ] . ( 420 sec) [ -6528.3779] [Topology ] . ( 424 sec) [ -6528.3771] [Topology ] . ( 425 sec) [ -6528.3771] [GTR parameters ] . ( 425 sec) [ -6528.3771] [Alpha ][ 0.341236] . ( 425 sec) [ -6528.3771] [Topology ] . ( 428 sec) [ -6528.3765] [Topology ] . ( 429 sec) [ -6528.3765] [GTR parameters ] . ( 429 sec) [ -6528.3765] [Alpha ][ 0.341236] . Checking for NNIs, optimizing five branches... . ( 456 sec) [ -6527.8353] [Topology ] . Checking for NNIs, optimizing five branches... . ( 486 sec) [ -6527.5528] [Topology ] . Checking for NNIs, optimizing five branches... . ( 514 sec) [ -6527.5507] [Topology ] . Checking for NNIs, optimizing five branches... . ( 542 sec) [ -6527.5502] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6527.550241. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h9m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 470.05user 0.00system 9:31.39elapsed 82%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps