.......................... 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 : 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 . 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 NNI moves)... . ( 0 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 0 sec) [ -4512.1912] [Topology ] . ( 1 sec) [ -4483.0594] [Topology ] . ( 3 sec) [ -4477.9104] [Topology ] . ( 4 sec) [ -4476.3403] [Topology ] . ( 5 sec) [ -4475.2627] [Topology ] . ( 7 sec) [ -4474.9882] [Topology ] . ( 8 sec) [ -4474.9096] [Topology ] . ( 9 sec) [ -4474.8846] [Topology ] . ( 11 sec) [ -4474.8756] [Topology ] . ( 12 sec) [ -4474.8722] [Topology ] . Checking for NNIs, optimizing five branches... . ( 21 sec) [ -4474.5121] [Alpha ][ 0.655762] . ( 21 sec) [ -4474.5121] [Topology ] . ( 23 sec) [ -4474.4958] [Topology ] . ( 24 sec) [ -4474.4919] [Topology ] . ( 25 sec) [ -4474.4903] [Topology ] . ( 26 sec) [ -4474.4896] [Topology ] . Checking for NNIs, optimizing five branches... . ( 36 sec) [ -4474.4890] [Alpha ][ 0.658482] . ( 36 sec) [ -4474.4890] [Topology ] . ( 37 sec) [ -4474.4886] [Topology ] . Checking for NNIs, optimizing five branches... . ( 46 sec) [ -4474.4886] [Alpha ][ 0.658482] . ( 46 sec) [ -4474.4886] [Topology ] . ( 48 sec) [ -4474.4884] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 66 sec) [ -4512.1912] [Alpha ][ 0.596203] . ( 67 sec) [ -4510.7574] [ 648] [depth= 2] . ( 68 sec) [ -4509.8214] [ 651] [depth= 1] . ( 70 sec) [ -4507.5758] [ 648] [depth= 1] . ( 70 sec) [ -4504.4834] [ 648] [depth= 2] . ( 70 sec) [ -4494.0203] [ 645] [depth= 5] . ( 70 sec) [ -4493.9133] [ 646] [depth= 1] . ( 71 sec) [ -4493.5419] [ 643] [depth= 4] . ( 71 sec) [ -4492.5401] [ 643] [depth= 1] . ( 71 sec) [ -4492.0982] [ 643] [depth= 1] . ( 71 sec) [ -4491.8533] [ 643] [depth= 1] . ( 71 sec) [ -4491.6218] [ 643] [depth= 1] . ( 72 sec) [ -4490.2200] [ 643] [depth= 1] . ( 81 sec) [ -4487.3781] [ 644] [depth= 1] . ( 83 sec) [ -4485.5060] [ 643] [depth= 2] . ( 85 sec) [ -4485.3798] [ 643] [depth= 1] . ( 87 sec) [ -4483.1302] [ 643] [depth= 1] . ( 88 sec) [ -4483.0009] [ 643] [depth= 1] . ( 89 sec) [ -4482.7074] [ 643] [depth= 1] . ( 93 sec) [ -4473.1385] [Branch lengths ] . ( 93 sec) [ -4472.7653] [Alpha ][ 0.657460] . ( 94 sec) [ -4469.6521] [ 645] [depth= 2] . ( 100 sec) [ -4468.8713] [ 647] [depth= 1] . ( 100 sec) [ -4467.9178] [ 648] [depth= 7] . ( 101 sec) [ -4466.7216] [ 648] [depth= 6] . ( 101 sec) [ -4464.9578] [ 647] [depth= 1] . ( 138 sec) [ -4463.3848] [Branch lengths ] . ( 138 sec) [ -4463.3839] [Alpha ][ 0.660589] . ( 143 sec) [ -4462.6943] [ 648] [depth= 6] . ( 146 sec) [ -4461.7266] [ 648] [depth= 7] . ( 151 sec) [ -4461.0059] [ 648] [depth= 1] . ( 185 sec) [ -4460.4822] [Branch lengths ] . ( 185 sec) [ -4460.4765] [Alpha ][ 0.652976] . ( 240 sec) [ -4460.4577] [Branch lengths ] . ( 240 sec) [ -4460.4577] [Topology ] . ( 241 sec) [ -4460.4567] [Topology ] . ( 241 sec) [ -4460.4567] [Alpha ][ 0.653629] . ( 241 sec) [ -4460.4567] [Topology ] . ( 243 sec) [ -4460.4564] [Topology ] . ( 243 sec) [ -4460.4564] [Alpha ][ 0.653629] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4474.488419 . Log likelihood obtained after SPR moves : -4460.456367 . 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 0h4m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 253.12user 0.00system 4:13.96elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps