.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2702_54x886_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 2 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 382 patterns found. (out of a total of 886 sites) . 582 sites without polymorphism (65.69%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 11Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -5607.7521] [GTR parameters ] . ( 1 sec) [ -5527.3790] [Alpha ][ 0.500960] . ( 1 sec) [ -5527.3790] [Topology ] . ( 2 sec) [ -5448.8222] [Topology ] . ( 3 sec) [ -5438.0985] [Topology ] . ( 4 sec) [ -5434.1096] [Topology ] . ( 5 sec) [ -5433.1507] [Topology ] . ( 6 sec) [ -5432.8467] [Topology ] . ( 7 sec) [ -5432.7452] [Topology ] . ( 8 sec) [ -5432.7100] [Topology ] . ( 9 sec) [ -5432.6977] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -5431.2776] [GTR parameters ] . ( 16 sec) [ -5390.3234] [Alpha ][ 0.250961] . ( 16 sec) [ -5390.3234] [Topology ] . ( 17 sec) [ -5388.8139] [Topology ] . ( 18 sec) [ -5388.5269] [Topology ] . ( 19 sec) [ -5388.2440] [Topology ] . ( 20 sec) [ -5388.1583] [Topology ] . ( 21 sec) [ -5388.0550] [Topology ] . ( 22 sec) [ -5387.7713] [Topology ] . ( 23 sec) [ -5387.7076] [Topology ] . ( 24 sec) [ -5387.6842] [Topology ] . ( 25 sec) [ -5387.6741] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -5386.6889] [GTR parameters ] . ( 33 sec) [ -5386.4426] [Alpha ][ 0.239110] . ( 33 sec) [ -5386.4426] [Topology ] . ( 34 sec) [ -5386.3875] [Topology ] . ( 35 sec) [ -5386.3714] [Topology ] . ( 36 sec) [ -5386.3639] [Topology ] . ( 37 sec) [ -5386.3601] [Topology ] . ( 37 sec) [ -5386.3582] [Topology ] . ( 38 sec) [ -5386.3573] [Topology ] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -5386.3405] [GTR parameters ] . ( 46 sec) [ -5386.3391] [Alpha ][ 0.238200] . ( 46 sec) [ -5386.3391] [Topology ] . ( 46 sec) [ -5386.3364] [Topology ] . ( 47 sec) [ -5386.3353] [Topology ] . ( 48 sec) [ -5386.3348] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -5386.3345] [GTR parameters ] . ( 55 sec) [ -5386.3345] [Alpha ][ 0.238200] . ( 55 sec) [ -5386.3345] [Topology ] . ( 56 sec) [ -5386.3341] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5386.334104. . Printing the most likely tree in file 'nucleic_M2702_54x886_2006.phy_phyml_tree.txt'... . Time used 0h1m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 68.33user 0.00system 1:09.45elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps