.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2946_110x1003_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 614 patterns found. (out of a total of 1003 sites) . 462 sites without polymorphism (46.06%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 6 sec) [ -18030.1538] [GTR parameters ] . ( 7 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 7 sec) [ -17741.2296] [Topology ] . ( 10 sec) [ -17315.9427] [Topology ] . ( 13 sec) [ -17203.4981] [Topology ] . ( 16 sec) [ -17151.0051] [Topology ] . ( 19 sec) [ -17128.8187] [Topology ] . ( 22 sec) [ -17112.6803] [Topology ] . ( 25 sec) [ -17105.8340] [Topology ] . ( 28 sec) [ -17101.2221] [Topology ] . ( 31 sec) [ -17099.3400] [Topology ] . ( 34 sec) [ -17097.6209] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -17091.2429] [Topology ] . ( 65 sec) [ -17076.1281] [GTR parameters ] . ( 65 sec) [ -17046.3688] [Alpha ][ 0.369311] . ( 66 sec) [ -17046.3688] [Topology ] . ( 69 sec) [ -17043.4664] [Topology ] . ( 72 sec) [ -17042.4267] [Topology ] . ( 75 sec) [ -17041.4778] [Topology ] . ( 78 sec) [ -17039.1772] [Topology ] . ( 81 sec) [ -17036.4185] [Topology ] . ( 84 sec) [ -17036.0413] [Topology ] . ( 87 sec) [ -17035.9335] [Topology ] . Checking for NNIs, optimizing five branches... . ( 112 sec) [ -17034.9214] [GTR parameters ] . ( 113 sec) [ -17034.8933] [Alpha ][ 0.365833] . ( 113 sec) [ -17034.8933] [Topology ] . ( 116 sec) [ -17034.7268] [Topology ] . ( 119 sec) [ -17034.6482] [Topology ] . ( 122 sec) [ -17034.5992] [Topology ] . ( 125 sec) [ -17034.5677] [Topology ] . ( 129 sec) [ -17034.5474] [Topology ] . ( 132 sec) [ -17034.5344] [Topology ] . Checking for NNIs, optimizing five branches... . ( 157 sec) [ -17034.5093] [GTR parameters ] . ( 157 sec) [ -17034.5092] [Alpha ][ 0.365468] . ( 157 sec) [ -17034.5092] [Topology ] . ( 160 sec) [ -17034.4950] [Topology ] . ( 163 sec) [ -17034.4865] [Topology ] . ( 166 sec) [ -17034.4811] [Topology ] . ( 170 sec) [ -17034.4776] [Topology ] . ( 173 sec) [ -17034.4753] [Topology ] . ( 176 sec) [ -17034.4739] [Topology ] . Checking for NNIs, optimizing five branches... . ( 199 sec) [ -17034.4722] [GTR parameters ] . ( 199 sec) [ -17034.4722] [Alpha ][ 0.365468] . ( 199 sec) [ -17034.4722] [Topology ] . ( 203 sec) [ -17034.4709] [Topology ] . ( 206 sec) [ -17034.4700] [Topology ] . Checking for NNIs, optimizing five branches... . ( 229 sec) [ -17034.4698] [GTR parameters ] . ( 229 sec) [ -17034.4698] [Alpha ][ 0.365468] . ( 229 sec) [ -17034.4698] [Topology ] . ( 232 sec) [ -17034.4693] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 285 sec) [ -18030.1538] [GTR parameters ] . ( 285 sec) [ -17741.2296] [Alpha ][ 0.500960] . ( 286 sec) [ -17732.2284] [ 3534] [depth= 1] . ( 286 sec) [ -17727.9520] [ 3536] [depth= 1] . ( 286 sec) [ -17720.9232] [ 3536] [depth= 2] . ( 286 sec) [ -17710.1407] [ 3534] [depth= 2] . ( 287 sec) [ -17687.4237] [ 3532] [depth= 1] . ( 287 sec) [ -17673.6169] [ 3523] [depth= 2] . ( 287 sec) [ -17672.1004] [ 3522] [depth= 1] . ( 289 sec) [ -17671.8543] [ 3522] [depth= 1] . ( 289 sec) [ -17668.2870] [ 3521] [depth= 1] . ( 289 sec) [ -17667.7826] [ 3521] [depth= 1] . ( 290 sec) [ -17665.2764] [ 3521] [depth= 1] . ( 290 sec) [ -17665.0808] [ 3521] [depth= 1] . ( 290 sec) [ -17662.2901] [ 3528] [depth= 1] . ( 291 sec) [ -17649.7618] [ 3529] [depth= 1] . ( 291 sec) [ -17647.0321] [ 3528] [depth= 2] . ( 291 sec) [ -17645.8889] [ 3528] [depth= 1] . ( 292 sec) [ -17645.5956] [ 3528] [depth= 1] . ( 292 sec) [ -17641.4722] [ 3525] [depth= 1] . ( 293 sec) [ -17641.0441] [ 3523] [depth= 1] . ( 293 sec) [ -17640.6873] [ 3523] [depth= 1] . ( 294 sec) [ -17638.6764] [ 3523] [depth= 1] . ( 294 sec) [ -17625.5744] [ 3522] [depth= 3] . ( 294 sec) [ -17625.1000] [ 3522] [depth= 1] . ( 294 sec) [ -17614.7584] [ 3520] [depth= 2] . ( 295 sec) [ -17614.6570] [ 3520] [depth= 1] . ( 296 sec) [ -17614.0769] [ 3522] [depth= 1] . ( 296 sec) [ -17606.7578] [ 3525] [depth= 1] . ( 297 sec) [ -17605.8674] [ 3522] [depth= 1] . ( 297 sec) [ -17603.1185] [ 3521] [depth= 1] . ( 297 sec) [ -17595.5106] [ 3522] [depth= 1] . ( 298 sec) [ -17591.3249] [ 3525] [depth= 1] . ( 298 sec) [ -17582.7946] [ 3523] [depth= 2] . ( 298 sec) [ -17581.4385] [ 3524] [depth= 1] . ( 299 sec) [ -17576.5902] [ 3521] [depth= 3] . ( 299 sec) [ -17570.1001] [ 3515] [depth= 2] . ( 299 sec) [ -17568.1545] [ 3514] [depth= 1] . ( 299 sec) [ -17565.9700] [ 3515] [depth= 2] . ( 300 sec) [ -17565.5582] [ 3515] [depth= 1] . ( 300 sec) [ -17556.2693] [ 3513] [depth= 1] . ( 301 sec) [ -17547.3723] [ 3509] [depth= 2] . ( 301 sec) [ -17546.3350] [ 3509] [depth= 1] . ( 301 sec) [ -17541.5026] [ 3509] [depth= 2] . ( 302 sec) [ -17528.9614] [ 3505] [depth= 1] . ( 303 sec) [ -17527.4592] [ 3508] [depth= 1] . ( 303 sec) [ -17527.3316] [ 3508] [depth= 1] . ( 303 sec) [ -17527.3063] [ 3512] [depth= 1] . ( 303 sec) [ -17527.2528] [ 3509] [depth= 1] . ( 303 sec) [ -17525.5769] [ 3510] [depth= 1] . ( 304 sec) [ -17522.0796] [ 3513] [depth= 1] . ( 305 sec) [ -17515.7045] [ 3513] [depth= 1] . ( 305 sec) [ -17512.0364] [ 3512] [depth= 1] . ( 305 sec) [ -17506.2200] [ 3513] [depth= 2] . ( 305 sec) [ -17502.5205] [ 3515] [depth= 1] . ( 306 sec) [ -17501.0224] [ 3515] [depth= 1] . ( 306 sec) [ -17498.9748] [ 3513] [depth= 1] . ( 307 sec) [ -17498.6457] [ 3515] [depth= 1] . ( 307 sec) [ -17497.8277] [ 3518] [depth= 2] . ( 307 sec) [ -17494.5538] [ 3516] [depth= 1] . ( 307 sec) [ -17493.8148] [ 3517] [depth= 1] . ( 307 sec) [ -17487.7673] [ 3516] [depth= 1] . ( 308 sec) [ -17477.0588] [ 3517] [depth= 2] . ( 308 sec) [ -17472.5607] [ 3513] [depth= 1] . ( 309 sec) [ -17447.2737] [ 3509] [depth= 2] . ( 309 sec) [ -17438.2099] [ 3509] [depth= 1] . ( 310 sec) [ -17432.9037] [ 3513] [depth= 1] . ( 310 sec) [ -17430.8153] [ 3509] [depth= 1] . ( 310 sec) [ -17428.4813] [ 3511] [depth= 1] . ( 310 sec) [ -17385.6114] [ 3509] [depth= 6] . ( 310 sec) [ -17383.2046] [ 3510] [depth= 1] . ( 310 sec) [ -17383.0598] [ 3509] [depth= 1] . ( 312 sec) [ -17362.7768] [ 3504] [depth= 1] . ( 313 sec) [ -17360.6969] [ 3508] [depth= 1] . ( 313 sec) [ -17353.4635] [ 3501] [depth= 1] . ( 313 sec) [ -17347.5013] [ 3497] [depth= 2] . ( 314 sec) [ -17344.2898] [ 3500] [depth= 2] . ( 314 sec) [ -17341.7376] [ 3505] [depth= 1] . ( 314 sec) [ -17332.8490] [ 3503] [depth= 1] . ( 314 sec) [ -17327.3566] [ 3499] [depth= 1] . ( 315 sec) [ -17320.9950] [ 3499] [depth= 1] . ( 315 sec) [ -17314.6835] [ 3495] [depth= 2] . ( 316 sec) [ -17314.4520] [ 3494] [depth= 1] . ( 316 sec) [ -17309.5389] [ 3495] [depth= 1] . ( 317 sec) [ -17307.8887] [ 3495] [depth= 1] . ( 317 sec) [ -17303.2636] [ 3494] [depth= 1] . ( 317 sec) [ -17302.2737] [ 3495] [depth= 4] . ( 317 sec) [ -17299.9575] [ 3495] [depth= 1] . ( 317 sec) [ -17297.3650] [ 3495] [depth= 1] . ( 318 sec) [ -17296.1814] [ 3494] [depth= 1] . ( 318 sec) [ -17291.1740] [ 3493] [depth= 1] . ( 319 sec) [ -17290.7274] [ 3494] [depth= 1] . ( 319 sec) [ -17289.4688] [ 3493] [depth= 1] . ( 320 sec) [ -17288.4265] [ 3492] [depth= 1] . ( 320 sec) [ -17288.1997] [ 3494] [depth= 1] . ( 320 sec) [ -17287.8339] [ 3496] [depth= 1] . ( 320 sec) [ -17285.6605] [ 3494] [depth= 1] . ( 321 sec) [ -17284.9520] [ 3496] [depth= 1] . ( 321 sec) [ -17283.8794] [ 3494] [depth= 1] . ( 323 sec) [ -17118.6287] [Branch lengths ] . ( 328 sec) [ -17106.5366] [GTR parameters ] . ( 328 sec) [ -17069.3882] [Alpha ][ 0.348580] . ( 330 sec) [ -17067.7315] [ 3496] [depth= 1] . ( 331 sec) [ -17060.2362] [ 3487] [depth= 1] . ( 333 sec) [ -17058.0829] [ 3483] [depth= 2] . ( 333 sec) [ -17055.7461] [ 3484] [depth= 1] . ( 335 sec) [ -17055.0689] [ 3486] [depth= 1] . ( 336 sec) [ -17052.7666] [ 3484] [depth= 1] . ( 336 sec) [ -17052.2562] [ 3483] [depth= 1] . ( 338 sec) [ -17050.8560] [ 3483] [depth= 1] . ( 346 sec) [ -17050.1894] [ 3486] [depth= 1] . ( 347 sec) [ -17050.0303] [ 3485] [depth= 1] . ( 352 sec) [ -17047.8575] [ 3484] [depth= 1] . ( 354 sec) [ -17047.7667] [ 3483] [depth= 1] . ( 355 sec) [ -17047.5997] [ 3484] [depth= 1] . ( 355 sec) [ -17045.3743] [ 3487] [depth= 1] . ( 357 sec) [ -17044.5819] [ 3487] [depth= 1] . ( 358 sec) [ -17043.8421] [ 3487] [depth= 5] . ( 359 sec) [ -17042.9538] [ 3487] [depth= 1] . ( 361 sec) [ -17042.4450] [ 3487] [depth= 1] . ( 367 sec) [ -17007.0987] [Branch lengths ] . ( 371 sec) [ -17005.3774] [GTR parameters ] . ( 371 sec) [ -17005.2591] [Alpha ][ 0.355080] . ( 379 sec) [ -17005.1982] [ 3485] [depth= 1] . ( 380 sec) [ -17005.1710] [ 3487] [depth= 1] . ( 402 sec) [ -17005.0176] [ 3489] [depth= 2] . ( 412 sec) [ -16996.3325] [Branch lengths ] . ( 416 sec) [ -16996.2585] [GTR parameters ] . ( 416 sec) [ -16996.2221] [Alpha ][ 0.358898] . ( 424 sec) [ -16996.2027] [ 3487] [depth= 1] . ( 456 sec) [ -16994.3391] [Branch lengths ] . ( 459 sec) [ -16994.3141] [GTR parameters ] . ( 460 sec) [ -16994.3061] [Alpha ][ 0.360657] . ( 501 sec) [ -16993.7035] [Branch lengths ] . ( 648 sec) [ -16993.5115] [Branch lengths ] . ( 648 sec) [ -16993.5115] [Topology ] . ( 651 sec) [ -16993.2548] [Topology ] . ( 654 sec) [ -16993.1930] [Topology ] . ( 658 sec) [ -16993.1147] [Topology ] . ( 661 sec) [ -16993.0677] [Topology ] . ( 664 sec) [ -16993.0509] [Topology ] . ( 667 sec) [ -16993.0441] [Topology ] . ( 671 sec) [ -16993.0410] [Topology ] . ( 674 sec) [ -16993.0012] [GTR parameters ] . ( 674 sec) [ -16992.9885] [Alpha ][ 0.362902] . ( 674 sec) [ -16992.9885] [Topology ] . ( 677 sec) [ -16992.9828] [Topology ] . ( 680 sec) [ -16992.9796] [Topology ] . ( 683 sec) [ -16992.9774] [Topology ] . ( 687 sec) [ -16992.9760] [Topology ] . ( 690 sec) [ -16992.9751] [Topology ] . ( 691 sec) [ -16992.9747] [GTR parameters ] . ( 692 sec) [ -16992.9747] [Alpha ][ 0.362902] . ( 692 sec) [ -16992.9747] [Topology ] . ( 695 sec) [ -16992.9739] [Topology ] . ( 696 sec) [ -16992.9739] [GTR parameters ] . ( 696 sec) [ -16992.9739] [Alpha ][ 0.362902] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -17034.469256 . Log likelihood obtained after SPR moves : -16992.973865 . Log likelihood of the current tree: -16992.973865. . Printing the most likely tree in file 'nucleic_M2946_110x1003_2006.phy_phyml_tree.txt'... . Time used 0h12m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 706.53user 0.00system 12:00.57elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps