.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2477_39x888_2005.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... . 638 patterns found. (out of a total of 888 sites) . 262 sites without polymorphism (29.50%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 59Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -21417.6215] [Alpha ][ 0.500960] . ( 3 sec) [ -21417.6215] [Topology ] . ( 8 sec) [ -21227.1384] [Topology ] . ( 13 sec) [ -21194.3140] [Topology ] . ( 19 sec) [ -21178.6341] [Topology ] . ( 24 sec) [ -21171.3173] [Topology ] . ( 29 sec) [ -21167.7367] [Topology ] . ( 34 sec) [ -21165.9194] [Topology ] . ( 39 sec) [ -21164.9681] [Topology ] . ( 45 sec) [ -21164.4654] [Topology ] . ( 50 sec) [ -21164.1966] [Topology ] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -21163.8223] [Alpha ][ 0.520309] . ( 95 sec) [ -21163.8223] [Topology ] . ( 100 sec) [ -21163.6457] [Topology ] . ( 105 sec) [ -21163.5527] [Topology ] . ( 111 sec) [ -21163.5018] [Topology ] . ( 116 sec) [ -21163.4739] [Topology ] . ( 121 sec) [ -21163.4586] [Topology ] . ( 127 sec) [ -21163.4502] [Topology ] . Checking for NNIs, optimizing five branches... . ( 171 sec) [ -21163.4475] [Alpha ][ 0.521963] . ( 171 sec) [ -21163.4475] [Topology ] . ( 177 sec) [ -21163.4425] [Topology ] . ( 182 sec) [ -21163.4397] [Topology ] . ( 187 sec) [ -21163.4382] [Topology ] . ( 192 sec) [ -21163.4373] [Topology ] . Checking for NNIs, optimizing five branches... . ( 237 sec) [ -21163.4373] [Alpha ][ 0.521963] . ( 237 sec) [ -21163.4373] [Topology ] . ( 242 sec) [ -21163.4368] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 335 sec) [ -21417.6215] [Alpha ][ 0.500960] . ( 344 sec) [ -21416.4601] [ 3664] [depth= 1] . ( 347 sec) [ -21410.5283] [ 3661] [depth= 1] . ( 349 sec) [ -21406.6173] [ 3663] [depth= 1] . ( 349 sec) [ -21404.2374] [ 3664] [depth= 1] . ( 351 sec) [ -21401.2712] [ 3661] [depth= 1] . ( 358 sec) [ -21378.0439] [ 3666] [depth= 2] . ( 359 sec) [ -21377.2197] [ 3662] [depth= 2] . ( 360 sec) [ -21363.2171] [ 3661] [depth= 1] . ( 362 sec) [ -21361.9633] [ 3662] [depth= 1] . ( 365 sec) [ -21352.5151] [ 3661] [depth= 1] . ( 378 sec) [ -21351.3660] [ 3665] [depth= 1] . ( 379 sec) [ -21338.3273] [ 3661] [depth= 1] . ( 386 sec) [ -21336.2810] [ 3665] [depth= 1] . ( 387 sec) [ -21327.3395] [ 3661] [depth= 1] . ( 389 sec) [ -21321.8468] [ 3663] [depth= 1] . ( 391 sec) [ -21320.6861] [ 3661] [depth= 1] . ( 394 sec) [ -21318.9662] [ 3667] [depth= 1] . ( 395 sec) [ -21307.7239] [ 3661] [depth= 1] . ( 396 sec) [ -21305.7494] [ 3662] [depth= 1] . ( 400 sec) [ -21305.6432] [ 3661] [depth= 1] . ( 401 sec) [ -21305.1675] [ 3662] [depth= 1] . ( 403 sec) [ -21192.5756] [Branch lengths ] . ( 404 sec) [ -21192.5555] [Alpha ][ 0.505582] . ( 409 sec) [ -21189.2474] [ 3659] [depth= 1] . ( 445 sec) [ -21187.3106] [ 3660] [depth= 1] . ( 455 sec) [ -21167.7756] [Branch lengths ] . ( 456 sec) [ -21167.6534] [Alpha ][ 0.516613] . ( 511 sec) [ -21164.1315] [Branch lengths ] . ( 511 sec) [ -21164.1315] [Topology ] . ( 517 sec) [ -21163.7522] [Topology ] . ( 522 sec) [ -21163.6168] [Topology ] . ( 527 sec) [ -21163.5478] [Topology ] . ( 533 sec) [ -21163.5108] [Topology ] . ( 539 sec) [ -21163.4906] [Topology ] . ( 544 sec) [ -21163.4795] [Topology ] . ( 545 sec) [ -21163.4532] [Alpha ][ 0.521977] . ( 546 sec) [ -21163.4532] [Topology ] . ( 551 sec) [ -21163.4454] [Topology ] . ( 556 sec) [ -21163.4414] [Topology ] . ( 562 sec) [ -21163.4391] [Topology ] . ( 567 sec) [ -21163.4378] [Topology ] . ( 572 sec) [ -21163.4371] [Topology ] . ( 573 sec) [ -21163.4371] [Alpha ][ 0.521977] . ( 574 sec) [ -21163.4371] [Topology ] . ( 579 sec) [ -21163.4367] [Topology ] . ( 580 sec) [ -21163.4367] [Alpha ][ 0.521977] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -21163.436847 . Log likelihood obtained after SPR moves : -21163.436730 . Log likelihood of the current tree: -21163.436730. . Printing the most likely tree in file 'proteic_M2477_39x888_2005.phy_phyml_tree.txt'... . Time used 0h10m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 597.65user 0.00system 10:26.66elapsed 95%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps