.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data90.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 . Compressing sequences... . 399 patterns found. (out of a total of 500 sites) . 100 sites without polymorphism (20.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7804.366693 . ( 1 sec) [ -7802.1644] [GTR parameters ] . ( 1 sec) [ -7801.9691] [Alpha ][ 0.948006] . ( 1 sec) [ -7801.9691] [Topology ] . ( 2 sec) [ -7762.6758] [Topology ] . ( 3 sec) [ -7752.3946] [Topology ] . ( 5 sec) [ -7747.7755] [Topology ] . ( 6 sec) [ -7744.2828] [Topology ] . ( 6 sec) [ -7742.8247] [Topology ] . ( 7 sec) [ -7742.5889] [Topology ] . ( 8 sec) [ -7742.5291] [Topology ] . ( 9 sec) [ -7742.5065] [Topology ] . ( 10 sec) [ -7742.4959] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -7742.4158] [Topology ] . Before opt ts/t=1.000000 LK=-7742.415787 . ( 18 sec) [ -7742.4033] [GTR parameters ] . ( 18 sec) [ -7742.1531] [Alpha ][ 1.005038] . ( 18 sec) [ -7742.1531] [Topology ] . ( 19 sec) [ -7742.1429] [Topology ] . ( 20 sec) [ -7742.1399] [Topology ] . ( 21 sec) [ -7742.1387] [Topology ] . ( 22 sec) [ -7742.1382] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7742.138223 . ( 31 sec) [ -7742.1382] [GTR parameters ] . ( 31 sec) [ -7742.1378] [Alpha ][ 1.007282] . ( 31 sec) [ -7742.1378] [Topology ] . ( 33 sec) [ -7742.1375] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7742.137484. . Printing the most likely tree in file 'data90.phy_phyml_tree.txt'... . Time used 0h0m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo