.......................... 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 : Best of NNIs and 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 NNI moves)... . ( 3 sec) [ -6941.4211] [GTR parameters ] . ( 3 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 3 sec) [ -6899.8793] [Topology ] . ( 5 sec) [ -6669.7753] [Topology ] . ( 7 sec) [ -6620.7511] [Topology ] . ( 9 sec) [ -6610.4959] [Topology ] . ( 11 sec) [ -6599.3357] [Topology ] . ( 13 sec) [ -6609.3373] [Topology ] . Moving backward . ( 14 sec) [ -6597.4246] [Topology ] . ( 16 sec) [ -6595.4764] [Topology ] . ( 18 sec) [ -6607.0982] [Topology ] . Moving backward . ( 18 sec) [ -6590.6067] [Topology ] . ( 23 sec) [ -6576.6676] [GTR parameters ] . ( 23 sec) [ -6570.7826] [Alpha ][ 0.397913] . ( 23 sec) [ -6570.7826] [Topology ] . ( 25 sec) [ -6564.4184] [Topology ] . ( 27 sec) [ -6560.3072] [Topology ] . ( 29 sec) [ -6558.6608] [Topology ] . ( 31 sec) [ -6554.1380] [Topology ] . ( 33 sec) [ -6555.8576] [Topology ] . Moving backward . ( 33 sec) [ -6547.5431] [Topology ] . ( 34 sec) [ -6546.5753] [Topology ] . ( 36 sec) [ -6545.8661] [Topology ] . ( 38 sec) [ -6545.4234] [Topology ] . Checking for NNIs, optimizing five branches... . ( 57 sec) [ -6544.7079] [Topology ] . ( 58 sec) [ -6544.4729] [GTR parameters ] . ( 59 sec) [ -6543.5007] [Alpha ][ 0.364367] . ( 59 sec) [ -6543.5007] [Topology ] . ( 60 sec) [ -6543.0475] [Topology ] . ( 62 sec) [ -6542.9259] [Topology ] . ( 64 sec) [ -6542.8611] [Topology ] . ( 66 sec) [ -6542.8201] [Topology ] . ( 68 sec) [ -6542.7894] [Topology ] . ( 69 sec) [ -6542.7655] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -6542.3276] [Topology ] . ( 87 sec) [ -6542.3035] [GTR parameters ] . ( 87 sec) [ -6542.1103] [Alpha ][ 0.350598] . ( 88 sec) [ -6542.1103] [Topology ] . ( 89 sec) [ -6541.8049] [Topology ] . ( 91 sec) [ -6541.7034] [Topology ] . ( 93 sec) [ -6541.6334] [Topology ] . ( 95 sec) [ -6541.6074] [Topology ] . ( 96 sec) [ -6541.5899] [Topology ] . ( 98 sec) [ -6541.5776] [Topology ] . ( 100 sec) [ -6541.5669] [Topology ] . ( 102 sec) [ -6541.5598] [Topology ] . Checking for NNIs, optimizing five branches... . ( 119 sec) [ -6541.0115] [Topology ] . ( 120 sec) [ -6541.0040] [GTR parameters ] . ( 120 sec) [ -6540.9757] [Alpha ][ 0.345346] . ( 120 sec) [ -6540.9757] [Topology ] . ( 122 sec) [ -6540.9545] [Topology ] . ( 124 sec) [ -6540.9485] [Topology ] . ( 126 sec) [ -6540.9454] [Topology ] . ( 127 sec) [ -6540.9436] [Topology ] . ( 129 sec) [ -6540.9428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 145 sec) [ -6540.7077] [Topology ] . ( 145 sec) [ -6540.7072] [GTR parameters ] . ( 146 sec) [ -6540.7023] [Alpha ][ 0.343170] . ( 146 sec) [ -6540.7023] [Topology ] . ( 148 sec) [ -6540.6981] [Topology ] . ( 149 sec) [ -6540.6973] [Topology ] . Checking for NNIs, optimizing five branches... . ( 165 sec) [ -6540.5640] [Topology ] . ( 165 sec) [ -6540.5638] [GTR parameters ] . ( 165 sec) [ -6540.5634] [Alpha ][ 0.342534] . ( 165 sec) [ -6540.5634] [Topology ] . ( 167 sec) [ -6540.5620] [Topology ] . ( 169 sec) [ -6540.5615] [Topology ] . Checking for NNIs, optimizing five branches... . ( 184 sec) [ -6540.5611] [Topology ] . ( 184 sec) [ -6540.5611] [GTR parameters ] . ( 184 sec) [ -6540.5610] [Alpha ][ 0.342191] . ( 184 sec) [ -6540.5610] [Topology ] . ( 186 sec) [ -6540.5602] [Topology ] . Checking for NNIs, optimizing five branches... . ( 201 sec) [ -6540.5596] [Topology ] . ( 201 sec) [ -6540.5596] [GTR parameters ] . ( 202 sec) [ -6540.5594] [Alpha ][ 0.341744] . ( 202 sec) [ -6540.5594] [Topology ] . ( 203 sec) [ -6540.5589] [Topology ] . Checking for NNIs, optimizing five branches... . ( 218 sec) [ -6540.5581] [Topology ] . ( 219 sec) [ -6540.5581] [GTR parameters ] . ( 219 sec) [ -6540.5581] [Alpha ][ 0.342085] . ( 219 sec) [ -6540.5581] [Topology ] . ( 221 sec) [ -6540.5569] [Topology ] . ( 223 sec) [ -6540.5564] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -6540.5564] [GTR parameters ] . ( 238 sec) [ -6540.5564] [Alpha ][ 0.342085] . ( 238 sec) [ -6540.5564] [Topology ] . ( 239 sec) [ -6540.5559] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 271 sec) [ -6941.4211] [GTR parameters ] . ( 271 sec) [ -6899.8793] [Alpha ][ 0.500960] . ( 271 sec) [ -6898.9682] [ 1256] [depth= 1] . ( 272 sec) [ -6898.6922] [ 1257] [depth= 1] . ( 272 sec) [ -6862.0853] [ 1254] [depth= 1] . ( 272 sec) [ -6859.2450] [ 1256] [depth= 1] . ( 272 sec) [ -6783.6394] [ 1270] [depth= 1] . ( 272 sec) [ -6781.8295] [ 1267] [depth= 1] . ( 273 sec) [ -6779.1598] [ 1269] [depth= 1] . ( 273 sec) [ -6778.4840] [ 1271] [depth= 1] . ( 273 sec) [ -6776.5967] [ 1271] [depth= 1] . ( 273 sec) [ -6776.3316] [ 1271] [depth= 1] . ( 273 sec) [ -6776.3003] [ 1271] [depth= 1] . ( 273 sec) [ -6773.2248] [ 1271] [depth= 1] . ( 273 sec) [ -6773.1883] [ 1271] [depth= 1] . ( 273 sec) [ -6770.0884] [ 1270] [depth= 4] . ( 274 sec) [ -6751.0122] [ 1268] [depth= 2] . ( 274 sec) [ -6744.9013] [ 1268] [depth= 3] . ( 274 sec) [ -6737.5008] [ 1267] [depth= 1] . ( 274 sec) [ -6735.8779] [ 1268] [depth= 1] . ( 275 sec) [ -6735.8203] [ 1267] [depth= 1] . ( 275 sec) [ -6735.4932] [ 1267] [depth= 1] . ( 275 sec) [ -6735.1440] [ 1267] [depth= 1] . ( 275 sec) [ -6734.9653] [ 1267] [depth= 1] . ( 276 sec) [ -6734.8702] [ 1267] [depth= 3] . ( 276 sec) [ -6734.7178] [ 1267] [depth= 1] . ( 277 sec) [ -6734.0950] [ 1268] [depth= 3] . ( 277 sec) [ -6733.2735] [ 1268] [depth= 3] . ( 278 sec) [ -6713.8518] [ 1266] [depth= 2] . ( 278 sec) [ -6710.1101] [ 1266] [depth= 2] . ( 279 sec) [ -6705.9172] [ 1266] [depth= 4] . ( 279 sec) [ -6705.4473] [ 1266] [depth= 2] . ( 281 sec) [ -6705.2219] [ 1266] [depth= 1] . ( 281 sec) [ -6697.9578] [ 1265] [depth= 2] . ( 281 sec) [ -6697.4188] [ 1265] [depth= 1] . ( 281 sec) [ -6695.8394] [ 1265] [depth= 2] . ( 281 sec) [ -6695.2354] [ 1265] [depth= 1] . ( 282 sec) [ -6695.1205] [ 1262] [depth= 1] . ( 282 sec) [ -6689.8948] [ 1265] [depth= 2] . ( 282 sec) [ -6687.6406] [ 1262] [depth= 1] . ( 282 sec) [ -6687.0497] [ 1265] [depth= 2] . ( 282 sec) [ -6682.7669] [ 1266] [depth= 2] . ( 283 sec) [ -6680.4923] [ 1268] [depth= 1] . ( 283 sec) [ -6678.4931] [ 1266] [depth= 1] . ( 283 sec) [ -6670.3979] [ 1265] [depth= 1] . ( 283 sec) [ -6669.2846] [ 1264] [depth= 1] . ( 283 sec) [ -6663.6149] [ 1259] [depth= 2] . ( 283 sec) [ -6657.6884] [ 1245] [depth= 4] . ( 284 sec) [ -6657.4562] [ 1246] [depth= 1] . ( 284 sec) [ -6655.2062] [ 1246] [depth= 1] . ( 284 sec) [ -6655.1025] [ 1246] [depth= 1] . ( 285 sec) [ -6654.8410] [ 1246] [depth= 1] . ( 285 sec) [ -6653.7394] [ 1246] [depth= 2] . ( 285 sec) [ -6653.4680] [ 1246] [depth= 1] . ( 285 sec) [ -6653.4560] [ 1246] [depth= 1] . ( 286 sec) [ -6651.9113] [ 1246] [depth= 2] . ( 287 sec) [ -6646.1350] [ 1244] [depth= 1] . ( 287 sec) [ -6640.3984] [ 1245] [depth= 2] . ( 288 sec) [ -6640.3662] [ 1245] [depth= 1] . ( 288 sec) [ -6639.7977] [ 1242] [depth= 1] . ( 288 sec) [ -6638.1003] [ 1242] [depth= 2] . ( 288 sec) [ -6635.8135] [ 1241] [depth= 1] . ( 289 sec) [ -6635.3102] [ 1242] [depth= 1] . ( 289 sec) [ -6632.8656] [ 1244] [depth= 2] . ( 289 sec) [ -6628.7609] [ 1245] [depth= 1] . ( 289 sec) [ -6628.2487] [ 1245] [depth= 1] . ( 290 sec) [ -6627.4075] [ 1245] [depth= 1] . ( 290 sec) [ -6621.8047] [ 1244] [depth= 1] . ( 290 sec) [ -6615.9361] [ 1244] [depth= 1] . ( 290 sec) [ -6613.4872] [ 1244] [depth= 1] . ( 290 sec) [ -6613.4705] [ 1244] [depth= 1] . ( 291 sec) [ -6612.8261] [ 1245] [depth= 1] . ( 291 sec) [ -6608.4187] [ 1243] [depth= 1] . ( 292 sec) [ -6608.2166] [ 1243] [depth= 1] . ( 292 sec) [ -6603.3294] [ 1243] [depth= 1] . ( 292 sec) [ -6602.9630] [ 1243] [depth= 2] . ( 292 sec) [ -6602.9450] [ 1243] [depth= 2] . ( 292 sec) [ -6602.6752] [ 1243] [depth= 2] . ( 292 sec) [ -6602.6639] [ 1243] [depth= 2] . ( 293 sec) [ -6602.4765] [ 1243] [depth= 1] . ( 294 sec) [ -6602.2208] [ 1243] [depth= 5] . ( 294 sec) [ -6602.0498] [ 1243] [depth= 1] . ( 295 sec) [ -6601.9435] [ 1243] [depth= 1] . ( 295 sec) [ -6601.8804] [ 1243] [depth= 1] . ( 295 sec) [ -6601.8551] [ 1243] [depth= 3] . ( 295 sec) [ -6601.8432] [ 1243] [depth= 3] . ( 295 sec) [ -6601.5227] [ 1243] [depth= 2] . ( 295 sec) [ -6601.4694] [ 1243] [depth= 3] . ( 295 sec) [ -6601.4555] [ 1243] [depth= 1] . ( 296 sec) [ -6601.3631] [ 1243] [depth= 1] . ( 299 sec) [ -6601.3487] [ 1243] [depth= 4] . ( 299 sec) [ -6601.3128] [ 1243] [depth= 4] . ( 300 sec) [ -6601.2918] [ 1243] [depth= 3] . ( 301 sec) [ -6601.2759] [ 1243] [depth= 4] . ( 302 sec) [ -6575.1063] [Branch lengths ] . ( 304 sec) [ -6567.9357] [GTR parameters ] . ( 304 sec) [ -6563.3657] [Alpha ][ 0.408141] . ( 305 sec) [ -6563.2053] [ 1240] [depth= 1] . ( 306 sec) [ -6557.8033] [ 1263] [depth= 6] . ( 307 sec) [ -6555.4393] [ 1262] [depth= 2] . ( 307 sec) [ -6554.9281] [ 1262] [depth= 1] . ( 307 sec) [ -6554.7742] [ 1262] [depth= 1] . ( 310 sec) [ -6549.2579] [ 1267] [depth= 1] . ( 312 sec) [ -6549.0624] [ 1267] [depth= 4] . ( 314 sec) [ -6548.3324] [ 1267] [depth= 4] . ( 315 sec) [ -6547.7906] [ 1267] [depth= 1] . ( 316 sec) [ -6546.3981] [ 1262] [depth= 6] . ( 316 sec) [ -6544.4423] [ 1263] [depth= 2] . ( 318 sec) [ -6543.0174] [ 1263] [depth= 2] . ( 319 sec) [ -6540.8938] [ 1263] [depth= 1] . ( 320 sec) [ -6540.8699] [ 1263] [depth= 1] . ( 320 sec) [ -6540.3401] [ 1265] [depth= 1] . ( 331 sec) [ -6540.1386] [ 1265] [depth= 1] . ( 331 sec) [ -6540.1026] [ 1265] [depth= 1] . ( 333 sec) [ -6540.0852] [ 1266] [depth= 1] . ( 334 sec) [ -6540.0749] [ 1266] [depth= 5] . ( 342 sec) [ -6540.0588] [ 1266] [depth= 5] . ( 349 sec) [ -6533.1237] [Branch lengths ] . ( 351 sec) [ -6532.5713] [GTR parameters ] . ( 351 sec) [ -6531.6534] [Alpha ][ 0.374202] . ( 352 sec) [ -6531.4907] [ 1267] [depth= 5] . ( 353 sec) [ -6530.9669] [ 1265] [depth= 1] . ( 356 sec) [ -6530.8641] [ 1265] [depth= 5] . ( 367 sec) [ -6530.6974] [ 1264] [depth= 1] . ( 393 sec) [ -6529.1374] [Branch lengths ] . ( 394 sec) [ -6529.0886] [GTR parameters ] . ( 394 sec) [ -6528.8876] [Alpha ][ 0.359592] . ( 396 sec) [ -6528.8344] [ 1264] [depth= 1] . ( 412 sec) [ -6528.8241] [ 1264] [depth= 1] . ( 423 sec) [ -6528.7659] [ 1264] [depth= 1] . ( 423 sec) [ -6528.7502] [ 1264] [depth= 1] . ( 441 sec) [ -6528.2640] [Branch lengths ] . ( 443 sec) [ -6528.2564] [GTR parameters ] . ( 443 sec) [ -6528.2091] [Alpha ][ 0.352922] . ( 446 sec) [ -6528.1898] [ 1264] [depth= 1] . ( 447 sec) [ -6528.0575] [ 1274] [depth= 1] . ( 527 sec) [ -6527.8437] [Branch lengths ] . ( 529 sec) [ -6527.8415] [GTR parameters ] . ( 529 sec) [ -6527.8248] [Alpha ][ 0.348823] . ( 529 sec) [ -6527.8248] [Topology ] . ( 531 sec) [ -6527.7609] [Topology ] . ( 533 sec) [ -6527.7334] [Topology ] . ( 535 sec) [ -6527.7165] [Topology ] . ( 536 sec) [ -6527.7055] [Topology ] . ( 538 sec) [ -6527.6980] [Topology ] . ( 540 sec) [ -6527.6930] [Topology ] . ( 542 sec) [ -6527.6922] [GTR parameters ] . ( 542 sec) [ -6527.6855] [Alpha ][ 0.346244] . ( 542 sec) [ -6527.6855] [Topology ] . ( 544 sec) [ -6527.6787] [Topology ] . ( 545 sec) [ -6527.6756] [Topology ] . ( 547 sec) [ -6527.6736] [Topology ] . ( 549 sec) [ -6527.6722] [Topology ] . ( 551 sec) [ -6527.6713] [Topology ] . ( 551 sec) [ -6527.6711] [GTR parameters ] . ( 551 sec) [ -6527.6696] [Alpha ][ 0.345026] . ( 552 sec) [ -6527.6696] [Topology ] . ( 553 sec) [ -6527.6682] [Topology ] . ( 555 sec) [ -6527.6676] [Topology ] . ( 556 sec) [ -6527.6676] [GTR parameters ] . ( 556 sec) [ -6527.6674] [Alpha ][ 0.344575] . ( 556 sec) [ -6527.6674] [Topology ] . ( 558 sec) [ -6527.6667] [Topology ] . ( 559 sec) [ -6527.6667] [GTR parameters ] . ( 559 sec) [ -6527.6667] [Alpha ][ 0.344575] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6540.555880 . Log likelihood obtained after SPR moves : -6527.666726 . Log likelihood of the current tree: -6527.666726. . Printing the most likely tree in file 'nucleic_M2708_78x1107_2006.phy_phyml_tree.txt'... . Time used 0h9m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 571.59user 0.00system 9:34.19elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps