.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2476_30x719_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... . 620 patterns found. (out of a total of 719 sites) . 115 sites without polymorphism (15.99%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 44Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -24774.5534] [Alpha ][ 0.568788] . ( 2 sec) [ -24774.5534] [Topology ] . ( 5 sec) [ -24604.5727] [Topology ] . ( 9 sec) [ -24577.4142] [Topology ] . ( 12 sec) [ -24569.8172] [Topology ] . ( 16 sec) [ -24566.0500] [Topology ] . ( 19 sec) [ -24563.8019] [Topology ] . ( 23 sec) [ -24562.4009] [Topology ] . ( 26 sec) [ -24561.5110] [Topology ] . ( 30 sec) [ -24560.9388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -24551.4355] [Alpha ][ 0.694186] . ( 62 sec) [ -24551.4355] [Topology ] . ( 65 sec) [ -24550.1640] [Topology ] . ( 69 sec) [ -24549.5953] [Topology ] . ( 73 sec) [ -24549.2553] [Topology ] . ( 76 sec) [ -24549.0455] [Topology ] . ( 80 sec) [ -24548.9148] [Topology ] . ( 83 sec) [ -24548.8327] [Topology ] . Checking for NNIs, optimizing five branches... . ( 114 sec) [ -24548.7536] [Alpha ][ 0.707150] . ( 114 sec) [ -24548.7536] [Topology ] . ( 118 sec) [ -24548.6901] [Topology ] . ( 121 sec) [ -24548.6518] [Topology ] . ( 125 sec) [ -24548.6279] [Topology ] . ( 128 sec) [ -24548.6128] [Topology ] . ( 132 sec) [ -24548.6033] [Topology ] . ( 136 sec) [ -24548.5973] [Topology ] . Checking for NNIs, optimizing five branches... . ( 166 sec) [ -24548.5961] [Alpha ][ 0.708722] . ( 166 sec) [ -24548.5961] [Topology ] . ( 170 sec) [ -24548.5920] [Topology ] . ( 174 sec) [ -24548.5894] [Topology ] . ( 177 sec) [ -24548.5878] [Topology ] . ( 181 sec) [ -24548.5867] [Topology ] . ( 184 sec) [ -24548.5861] [Topology ] . Checking for NNIs, optimizing five branches... . ( 215 sec) [ -24548.5861] [Alpha ][ 0.709431] . ( 215 sec) [ -24548.5861] [Topology ] . ( 219 sec) [ -24548.5856] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 280 sec) [ -24774.5534] [Alpha ][ 0.568788] . ( 282 sec) [ -24770.6356] [ 4912] [depth= 2] . ( 283 sec) [ -24754.7924] [ 4911] [depth= 1] . ( 284 sec) [ -24750.8991] [ 4912] [depth= 1] . ( 287 sec) [ -24750.3251] [ 4917] [depth= 1] . ( 288 sec) [ -24749.7088] [ 4922] [depth= 1] . ( 289 sec) [ -24749.1434] [ 4918] [depth= 3] . ( 291 sec) [ -24745.1957] [ 4935] [depth= 1] . ( 292 sec) [ -24735.6770] [ 4918] [depth= 1] . ( 292 sec) [ -24725.4325] [ 4918] [depth= 2] . ( 294 sec) [ -24722.7390] [ 4922] [depth= 1] . ( 295 sec) [ -24720.7531] [ 4918] [depth= 1] . ( 296 sec) [ -24719.3563] [ 4921] [depth= 2] . ( 297 sec) [ -24711.0539] [ 4914] [depth= 2] . ( 298 sec) [ -24709.7604] [ 4917] [depth= 1] . ( 299 sec) [ -24703.2458] [ 4921] [depth= 1] . ( 299 sec) [ -24691.7815] [ 4925] [depth= 1] . ( 302 sec) [ -24682.0022] [ 4926] [depth= 1] . ( 303 sec) [ -24677.6305] [ 4925] [depth= 1] . ( 304 sec) [ -24677.2427] [ 4921] [depth= 1] . ( 305 sec) [ -24666.3676] [ 4923] [depth= 4] . ( 310 sec) [ -24665.7809] [ 4926] [depth= 1] . ( 312 sec) [ -24658.7862] [ 4923] [depth= 1] . ( 313 sec) [ -24658.5416] [ 4926] [depth= 1] . ( 314 sec) [ -24658.1349] [ 4922] [depth= 1] . ( 315 sec) [ -24655.6356] [ 4926] [depth= 1] . ( 315 sec) [ -24655.5104] [ 4925] [depth= 1] . ( 316 sec) [ -24648.1249] [ 4920] [depth= 1] . ( 318 sec) [ -24647.2387] [ 4923] [depth= 1] . ( 319 sec) [ -24643.6939] [ 4927] [depth= 2] . ( 323 sec) [ -24641.3313] [ 4923] [depth= 1] . ( 325 sec) [ -24638.6431] [ 4926] [depth= 2] . ( 327 sec) [ -24581.3651] [Branch lengths ] . ( 328 sec) [ -24573.5916] [Alpha ][ 0.682758] . ( 333 sec) [ -24567.1512] [ 4919] [depth= 1] . ( 344 sec) [ -24558.3976] [ 4921] [depth= 3] . ( 385 sec) [ -24545.7546] [Branch lengths ] . ( 386 sec) [ -24545.6295] [Alpha ][ 0.698976] . ( 389 sec) [ -24544.1948] [ 4920] [depth= 6] . ( 440 sec) [ -24540.7976] [Branch lengths ] . ( 440 sec) [ -24540.7971] [Alpha ][ 0.697836] . ( 500 sec) [ -24539.9444] [Branch lengths ] . ( 500 sec) [ -24539.9444] [Topology ] . ( 504 sec) [ -24534.6494] [Topology ] . ( 508 sec) [ -24530.5271] [Topology ] . ( 511 sec) [ -24529.9490] [Topology ] . ( 515 sec) [ -24529.8280] [Topology ] . ( 519 sec) [ -24529.7965] [Topology ] . ( 522 sec) [ -24529.7876] [Topology ] . ( 526 sec) [ -24529.7850] [Topology ] . ( 526 sec) [ -24529.7722] [Alpha ][ 0.703045] . ( 527 sec) [ -24529.7722] [Topology ] . ( 530 sec) [ -24529.7704] [Topology ] . ( 534 sec) [ -24529.7698] [Topology ] . ( 535 sec) [ -24529.7698] [Alpha ][ 0.703045] . ( 535 sec) [ -24529.7698] [Topology ] . ( 539 sec) [ -24529.7695] [Topology ] . ( 539 sec) [ -24529.7695] [Alpha ][ 0.703045] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -24548.585605 . Log likelihood obtained after SPR moves : -24529.769532 . Log likelihood of the current tree: -24529.769532. . Printing the most likely tree in file 'proteic_M2476_30x719_2005.phy_phyml_tree.txt'... . Time used 0h9m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 550.75user 0.00system 9:32.35elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps