.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2707_115x1677_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 759 patterns found. (out of a total of 1677 sites) . 924 sites without polymorphism (55.10%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 46Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 5 sec) [ -11652.5156] [GTR parameters ] . ( 5 sec) [ -11452.6188] [Alpha ][ 0.500960] . ( 5 sec) [ -11452.6188] [Topology ] . ( 10 sec) [ -10365.2625] [Topology ] . ( 14 sec) [ -10031.8375] [Topology ] . ( 18 sec) [ -10010.6258] [Topology ] . ( 22 sec) [ -10000.4939] [Topology ] . ( 25 sec) [ -10078.8663] [Topology ] . Moving backward . ( 25 sec) [ -9998.0838] [Topology ] . ( 29 sec) [ -9978.6205] [Topology ] . ( 33 sec) [ -10082.5053] [Topology ] . Moving backward . ( 33 sec) [ -9970.6332] [Topology ] . ( 42 sec) [ -9952.5716] [GTR parameters ] . ( 43 sec) [ -9875.4361] [Alpha ][ 0.259706] . ( 43 sec) [ -9875.4361] [Topology ] . ( 46 sec) [ -9932.2170] [Topology ] . Moving backward . ( 47 sec) [ -9874.3108] [Topology ] . ( 50 sec) [ -9863.8641] [Topology ] . ( 54 sec) [ -9930.4278] [Topology ] . Moving backward . ( 54 sec) [ -9853.3092] [Topology ] . ( 58 sec) [ -9848.7910] [Topology ] . ( 61 sec) [ -9895.9855] [Topology ] . Moving backward . ( 62 sec) [ -9846.4683] [Topology ] . ( 65 sec) [ -9842.2614] [Topology ] . ( 72 sec) [ -9850.4471] [GTR parameters ] . ( 73 sec) [ -9850.3708] [Alpha ][ 0.255177] . ( 73 sec) [ -9850.3708] [Topology ] . ( 76 sec) [ -9839.3721] [Topology ] . ( 80 sec) [ -9894.3038] [Topology ] . Moving backward . ( 80 sec) [ -9832.5169] [Topology ] . ( 83 sec) [ -9828.9871] [Topology ] . ( 87 sec) [ -9848.9864] [Topology ] . Moving backward . ( 87 sec) [ -9828.5015] [Topology ] . ( 91 sec) [ -9828.1237] [Topology ] . ( 94 sec) [ -9853.2397] [Topology ] . Moving backward . ( 94 sec) [ -9823.8735] [Topology ] . Checking for NNIs, optimizing five branches... . ( 128 sec) [ -9822.3410] [Topology ] . ( 131 sec) [ -9822.1675] [GTR parameters ] . ( 131 sec) [ -9819.7744] [Alpha ][ 0.231992] . ( 131 sec) [ -9819.7744] [Topology ] . ( 135 sec) [ -9824.8512] [Topology ] . Moving backward . ( 135 sec) [ -9817.6700] [Topology ] . ( 138 sec) [ -9817.3750] [Topology ] . ( 141 sec) [ -9824.1131] [Topology ] . Moving backward . ( 142 sec) [ -9816.1565] [Topology ] . ( 145 sec) [ -9816.4149] [Topology ] . Moving backward . ( 145 sec) [ -9814.5736] [Topology ] . ( 149 sec) [ -9814.0199] [Topology ] . ( 152 sec) [ -9813.6959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 182 sec) [ -9812.9284] [Topology ] . ( 185 sec) [ -9812.4685] [GTR parameters ] . ( 185 sec) [ -9812.0924] [Alpha ][ 0.223570] . ( 186 sec) [ -9812.0924] [Topology ] . ( 189 sec) [ -9811.0097] [Topology ] . ( 192 sec) [ -9810.6491] [Topology ] . ( 195 sec) [ -9810.6447] [Topology ] . ( 198 sec) [ -9814.1610] [Topology ] . Moving backward . ( 199 sec) [ -9809.4865] [Topology ] . ( 202 sec) [ -9809.4931] [Topology ] . Moving backward . ( 202 sec) [ -9808.5732] [Topology ] . ( 206 sec) [ -9808.0614] [Topology ] . Checking for NNIs, optimizing five branches... . ( 232 sec) [ -9807.9271] [Topology ] . ( 236 sec) [ -9807.8015] [GTR parameters ] . ( 236 sec) [ -9807.3598] [Alpha ][ 0.214946] . ( 236 sec) [ -9807.3598] [Topology ] . ( 239 sec) [ -9806.6399] [Topology ] . ( 243 sec) [ -9806.2793] [Topology ] . ( 246 sec) [ -9806.1576] [Topology ] . ( 249 sec) [ -9807.5394] [Topology ] . Moving backward . ( 249 sec) [ -9805.4493] [Topology ] . ( 253 sec) [ -9805.3474] [Topology ] . ( 256 sec) [ -9805.9623] [Topology ] . Checking for NNIs, optimizing five branches... . ( 282 sec) [ -9805.1128] [Topology ] . ( 286 sec) [ -9805.0099] [GTR parameters ] . ( 286 sec) [ -9804.6287] [Alpha ][ 0.207349] . ( 286 sec) [ -9804.6287] [Topology ] . ( 289 sec) [ -9802.2333] [Topology ] . ( 293 sec) [ -9802.9608] [Topology ] . Moving backward . ( 293 sec) [ -9801.3804] [Topology ] . ( 296 sec) [ -9800.7142] [Topology ] . ( 299 sec) [ -9800.3920] [Topology ] . ( 303 sec) [ -9800.4421] [Topology ] . Moving backward . ( 303 sec) [ -9799.3829] [Topology ] . ( 306 sec) [ -9799.1803] [Topology ] . ( 310 sec) [ -9799.0856] [Topology ] . Checking for NNIs, optimizing five branches... . ( 336 sec) [ -9799.0828] [Topology ] . ( 339 sec) [ -9799.0160] [GTR parameters ] . ( 340 sec) [ -9798.6946] [Alpha ][ 0.200634] . ( 340 sec) [ -9798.6946] [Topology ] . ( 343 sec) [ -9798.4749] [Topology ] . ( 346 sec) [ -9798.3588] [Topology ] . ( 349 sec) [ -9798.2947] [Topology ] . ( 353 sec) [ -9798.2596] [Topology ] . ( 356 sec) [ -9798.2430] [Topology ] . ( 359 sec) [ -9798.2384] [Topology ] . Checking for NNIs, optimizing five branches... . ( 385 sec) [ -9798.2256] [Topology ] . ( 388 sec) [ -9798.1963] [GTR parameters ] . ( 389 sec) [ -9798.0724] [Alpha ][ 0.196577] . ( 389 sec) [ -9798.0724] [Topology ] . ( 392 sec) [ -9798.0224] [Topology ] . ( 395 sec) [ -9798.0187] [Topology ] . ( 398 sec) [ -9798.0873] [Topology ] . Moving backward . ( 399 sec) [ -9797.9429] [Topology ] . ( 402 sec) [ -9797.9340] [Topology ] . ( 405 sec) [ -9797.9378] [Topology ] . Moving backward . ( 405 sec) [ -9797.9210] [Topology ] . ( 409 sec) [ -9797.9162] [Topology ] . Checking for NNIs, optimizing five branches... . ( 434 sec) [ -9797.9151] [Topology ] . ( 438 sec) [ -9797.9040] [GTR parameters ] . ( 438 sec) [ -9797.8693] [Alpha ][ 0.194506] . ( 438 sec) [ -9797.8693] [Topology ] . ( 441 sec) [ -9797.8490] [Topology ] . ( 444 sec) [ -9797.8406] [Topology ] . ( 448 sec) [ -9797.8393] [Topology ] . ( 451 sec) [ -9797.8428] [Topology ] . Moving backward . ( 451 sec) [ -9797.8300] [Topology ] . ( 454 sec) [ -9797.8281] [Topology ] . ( 458 sec) [ -9797.8274] [Topology ] . Checking for NNIs, optimizing five branches... . ( 484 sec) [ -9797.8245] [GTR parameters ] . ( 485 sec) [ -9797.8118] [Alpha ][ 0.193307] . ( 485 sec) [ -9797.8118] [Topology ] . ( 488 sec) [ -9797.8064] [Topology ] . ( 491 sec) [ -9797.8047] [Topology ] . ( 494 sec) [ -9797.8056] [Topology ] . Checking for NNIs, optimizing five branches... . ( 521 sec) [ -9797.8044] [GTR parameters ] . ( 521 sec) [ -9797.8022] [Alpha ][ 0.192686] . ( 521 sec) [ -9797.8022] [Topology ] . ( 524 sec) [ -9797.8030] [Topology ] . Checking for NNIs, optimizing five branches... . ( 551 sec) [ -9797.8029] [GTR parameters ] . ( 551 sec) [ -9797.8027] [Alpha ][ 0.192434] . ( 551 sec) [ -9797.8027] [Topology ] . ( 554 sec) [ -9797.8092] [Topology ] . Moving backward . ( 555 sec) [ -9797.7933] [Topology ] . ( 558 sec) [ -9797.7920] [Topology ] . ( 561 sec) [ -9797.7919] [Topology ] . Checking for NNIs, optimizing five branches... . ( 587 sec) [ -9797.7913] [GTR parameters ] . ( 588 sec) [ -9797.7912] [Alpha ][ 0.192235] . ( 588 sec) [ -9797.7912] [Topology ] . ( 591 sec) [ -9797.7912] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9797.791236. . Printing the most likely tree in file 'nucleic_M2707_115x1677_2006.phy_phyml_tree.txt'... . Time used 0h10m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 639.82user 0.00system 10:44.51elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps