.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1372_23x394_2003.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 : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 3 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 246 patterns found. (out of a total of 394 sites) . 162 sites without polymorphism (41.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 8 sec) [ -4510.7574] [ 648] [depth= 2] . ( 21 sec) [ -4509.8214] [ 651] [depth= 1] . ( 61 sec) [ -4507.5758] [ 648] [depth= 1] . ( 61 sec) [ -4504.4834] [ 648] [depth= 2] . ( 62 sec) [ -4494.0203] [ 645] [depth= 5] . ( 63 sec) [ -4493.9133] [ 646] [depth= 1] . ( 64 sec) [ -4493.5419] [ 643] [depth= 4] . ( 64 sec) [ -4492.5401] [ 643] [depth= 1] . ( 64 sec) [ -4492.0982] [ 643] [depth= 1] . ( 64 sec) [ -4491.8533] [ 643] [depth= 1] . ( 64 sec) [ -4491.6218] [ 643] [depth= 1] . ( 65 sec) [ -4490.2200] [ 643] [depth= 1] . ( 88 sec) [ -4487.3781] [ 644] [depth= 1] . ( 92 sec) [ -4485.5060] [ 643] [depth= 2] . ( 96 sec) [ -4485.3798] [ 643] [depth= 1] . ( 101 sec) [ -4483.1302] [ 643] [depth= 1] . ( 105 sec) [ -4483.0009] [ 643] [depth= 1] . ( 108 sec) [ -4482.7074] [ 643] [depth= 1] . ( 115 sec) [ -4473.1385] [Branch lengths ] . ( 116 sec) [ -4472.7653] [Alpha ][ 0.657460] . ( 123 sec) [ -4469.6521] [ 645] [depth= 2] . ( 182 sec) [ -4468.8713] [ 647] [depth= 1] . ( 184 sec) [ -4467.9178] [ 648] [depth= 7] . ( 184 sec) [ -4466.7216] [ 648] [depth= 6] . ( 184 sec) [ -4464.9578] [ 647] [depth= 1] . ( 277 sec) [ -4463.3848] [Branch lengths ] . ( 277 sec) [ -4463.3839] [Alpha ][ 0.660589] . ( 362 sec) [ -4462.6943] [ 648] [depth= 6] . ( 374 sec) [ -4461.7266] [ 648] [depth= 7] . ( 395 sec) [ -4461.0059] [ 648] [depth= 1] . ( 489 sec) [ -4460.4822] [Branch lengths ] . ( 490 sec) [ -4460.4765] [Alpha ][ 0.652976] . ( 731 sec) [ -4460.4577] [Branch lengths ] . ( 731 sec) [ -4460.4577] [Topology ] . ( 733 sec) [ -4460.4567] [Topology ] . ( 733 sec) [ -4460.4567] [Alpha ][ 0.653629] . ( 734 sec) [ -4460.4567] [Topology ] . ( 735 sec) [ -4460.4564] [Topology ] . ( 736 sec) [ -4460.4564] [Alpha ][ 0.653629] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4460.456367. . Printing the most likely tree in file 'proteic_M1372_23x394_2003.phy_phyml_tree.txt'... . Time used 0h12m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 583.79user 0.00system 12:31.76elapsed 77%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps