.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2512_14x717_2006.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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 . Compressing sequences... . 703 patterns found. (out of a total of 717 sites) . 39 sites without polymorphism (5.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -20898.1075] [Alpha ][ 1.719622] . ( 0 sec) [ -20898.1075] [Topology ] . ( 2 sec) [ -20323.7506] [Topology ] . ( 4 sec) [ -20209.4899] [Topology ] . ( 5 sec) [ -20190.1580] [Topology ] . ( 7 sec) [ -20183.4133] [Topology ] . ( 9 sec) [ -20179.6054] [Topology ] . ( 11 sec) [ -20178.2734] [Topology ] . ( 12 sec) [ -20177.5990] [Topology ] . ( 14 sec) [ -20177.2069] [Topology ] . ( 16 sec) [ -20176.9503] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -20111.7538] [Topology ] . ( 53 sec) [ -20108.0232] [Alpha ][ 1.456524] . ( 53 sec) [ -20108.0232] [Topology ] . ( 55 sec) [ -20106.2903] [Topology ] . ( 57 sec) [ -20105.8153] [Topology ] . ( 59 sec) [ -20105.6133] [Topology ] . ( 61 sec) [ -20105.5047] [Topology ] . ( 63 sec) [ -20105.4368] [Topology ] . ( 64 sec) [ -20105.3898] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -20104.4147] [Topology ] . ( 88 sec) [ -20103.4762] [Alpha ][ 1.346223] . ( 88 sec) [ -20103.4762] [Topology ] . ( 90 sec) [ -20103.0390] [Topology ] . ( 91 sec) [ -20102.9113] [Topology ] . ( 93 sec) [ -20102.8527] [Topology ] . ( 95 sec) [ -20102.8185] [Topology ] . ( 97 sec) [ -20102.7957] [Topology ] . ( 99 sec) [ -20102.7794] [Topology ] . Checking for NNIs, optimizing five branches... . ( 127 sec) [ -20102.5334] [Alpha ][ 1.294348] . ( 128 sec) [ -20102.5334] [Topology ] . ( 130 sec) [ -20102.4148] [Topology ] . ( 132 sec) [ -20102.3768] [Topology ] . ( 133 sec) [ -20102.3577] [Topology ] . ( 135 sec) [ -20102.3458] [Topology ] . ( 137 sec) [ -20102.3377] [Topology ] . ( 139 sec) [ -20102.3318] [Topology ] . Checking for NNIs, optimizing five branches... . ( 167 sec) [ -20102.2632] [Alpha ][ 1.268600] . ( 167 sec) [ -20102.2632] [Topology ] . ( 169 sec) [ -20102.2296] [Topology ] . ( 171 sec) [ -20102.2181] [Topology ] . ( 173 sec) [ -20102.2122] [Topology ] . ( 175 sec) [ -20102.2084] [Topology ] . ( 177 sec) [ -20102.2060] [Topology ] . ( 179 sec) [ -20102.2042] [Topology ] . Checking for NNIs, optimizing five branches... . ( 206 sec) [ -20102.1834] [Alpha ][ 1.254001] . ( 206 sec) [ -20102.1834] [Topology ] . ( 208 sec) [ -20102.1724] [Topology ] . ( 210 sec) [ -20102.1689] [Topology ] . ( 212 sec) [ -20102.1673] [Topology ] . ( 214 sec) [ -20102.1665] [Topology ] . Checking for NNIs, optimizing five branches... . ( 242 sec) [ -20102.1615] [Alpha ][ 1.246927] . ( 242 sec) [ -20102.1615] [Topology ] . ( 244 sec) [ -20102.1586] [Topology ] . ( 246 sec) [ -20102.1579] [Topology ] . Checking for NNIs, optimizing five branches... . ( 273 sec) [ -20102.1571] [Alpha ][ 1.243876] . ( 274 sec) [ -20102.1571] [Topology ] . ( 275 sec) [ -20102.1565] [Topology ] . Checking for NNIs, optimizing five branches... . ( 302 sec) [ -20102.1551] [Alpha ][ 1.240063] . ( 302 sec) [ -20102.1551] [Topology ] . ( 304 sec) [ -20102.1540] [Topology ] . ( 306 sec) [ -20102.1546] [Topology ] . Checking for NNIs, optimizing five branches... . ( 332 sec) [ -20102.1541] [Alpha ][ 1.237895] . ( 332 sec) [ -20102.1541] [Topology ] . ( 334 sec) [ -20102.1543] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 390 sec) [ -20898.1075] [Alpha ][ 1.719622] . ( 391 sec) [ -20895.9923] [ 4555] [depth= 1] . ( 392 sec) [ -20889.3372] [ 4547] [depth= 2] . ( 393 sec) [ -20888.5728] [ 4552] [depth= 1] . ( 394 sec) [ -20867.7868] [ 4559] [depth= 3] . ( 395 sec) [ -20856.0045] [ 4569] [depth= 1] . ( 396 sec) [ -20765.8045] [ 4559] [depth= 1] . ( 396 sec) [ -20510.5376] [ 4542] [depth= 1] . ( 397 sec) [ -20497.8122] [ 4539] [depth= 1] . ( 397 sec) [ -20290.4169] [ 4535] [depth= 1] . ( 398 sec) [ -20246.4177] [ 4531] [depth= 1] . ( 399 sec) [ -20210.5193] [ 4535] [depth= 2] . ( 401 sec) [ -20210.2034] [ 4539] [depth= 1] . ( 402 sec) [ -20130.0567] [Branch lengths ] . ( 403 sec) [ -20128.9883] [Alpha ][ 1.563589] . ( 406 sec) [ -20127.4467] [ 4540] [depth= 1] . ( 407 sec) [ -20125.9501] [ 4537] [depth= 1] . ( 412 sec) [ -20121.8097] [ 4532] [depth= 1] . ( 414 sec) [ -20120.1590] [ 4532] [depth= 1] . ( 416 sec) [ -20119.7832] [ 4532] [depth= 1] . ( 420 sec) [ -20105.7485] [Branch lengths ] . ( 421 sec) [ -20104.0472] [Alpha ][ 1.399967] . ( 433 sec) [ -20104.0291] [ 4532] [depth= 1] . ( 437 sec) [ -20100.3666] [Branch lengths ] . ( 437 sec) [ -20099.9527] [Alpha ][ 1.328237] . ( 452 sec) [ -20099.8226] [ 4532] [depth= 1] . ( 456 sec) [ -20099.0255] [Branch lengths ] . ( 457 sec) [ -20098.9412] [Alpha ][ 1.298255] . ( 473 sec) [ -20098.5912] [Branch lengths ] . ( 473 sec) [ -20098.5912] [Topology ] . ( 475 sec) [ -20098.5244] [Topology ] . ( 477 sec) [ -20098.4864] [Topology ] . ( 479 sec) [ -20098.4592] [Topology ] . ( 481 sec) [ -20098.4386] [Topology ] . ( 483 sec) [ -20098.4225] [Topology ] . ( 485 sec) [ -20098.4097] [Topology ] . ( 486 sec) [ -20098.3651] [Alpha ][ 1.276249] . ( 486 sec) [ -20098.3651] [Topology ] . ( 488 sec) [ -20098.3366] [Topology ] . ( 490 sec) [ -20098.3233] [Topology ] . ( 492 sec) [ -20098.3143] [Topology ] . ( 494 sec) [ -20098.3074] [Topology ] . ( 496 sec) [ -20098.3019] [Topology ] . ( 498 sec) [ -20098.2973] [Topology ] . ( 498 sec) [ -20098.2870] [Alpha ][ 1.265798] . ( 498 sec) [ -20098.2870] [Topology ] . ( 500 sec) [ -20098.2784] [Topology ] . ( 502 sec) [ -20098.2738] [Topology ] . ( 504 sec) [ -20098.2704] [Topology ] . ( 506 sec) [ -20098.2676] [Topology ] . ( 508 sec) [ -20098.2654] [Topology ] . ( 510 sec) [ -20098.2634] [Topology ] . ( 510 sec) [ -20098.2606] [Alpha ][ 1.260348] . ( 511 sec) [ -20098.2606] [Topology ] . ( 513 sec) [ -20098.2575] [Topology ] . ( 514 sec) [ -20098.2557] [Topology ] . ( 516 sec) [ -20098.2542] [Topology ] . ( 518 sec) [ -20098.2530] [Topology ] . ( 520 sec) [ -20098.2519] [Topology ] . ( 522 sec) [ -20098.2510] [Topology ] . ( 523 sec) [ -20098.2502] [Alpha ][ 1.257423] . ( 523 sec) [ -20098.2502] [Topology ] . ( 525 sec) [ -20098.2490] [Topology ] . ( 527 sec) [ -20098.2482] [Topology ] . ( 527 sec) [ -20098.2481] [Alpha ][ 1.256165] . ( 527 sec) [ -20098.2481] [Topology ] . ( 529 sec) [ -20098.2473] [Topology ] . ( 530 sec) [ -20098.2473] [Alpha ][ 1.254909] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -20102.154256 . Log likelihood obtained after SPR moves : -20098.247253 . Log likelihood of the current tree: -20098.247253. . Printing the most likely tree in file 'proteic_M2512_14x717_2006.phy_phyml_tree.txt'... . Time used 0h9m21s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 558.09user 0.00system 9:21.63elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps