.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data85.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... . 460 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-12046.112397 . ( 1 sec) [ -12041.9616] [GTR parameters ] . ( 1 sec) [ -12041.7961] [Alpha ][ 0.960910] . ( 1 sec) [ -12041.7961] [Topology ] . ( 2 sec) [ -11980.6757] [Topology ] . ( 3 sec) [ -11972.0740] [Topology ] . ( 4 sec) [ -11969.8220] [Topology ] . ( 5 sec) [ -11968.8175] [Topology ] . ( 5 sec) [ -11968.3196] [Topology ] . ( 6 sec) [ -11968.0585] [Topology ] . ( 8 sec) [ -11967.9172] [Topology ] . ( 9 sec) [ -11967.8397] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -11967.8180] [Topology ] . Before opt ts/t=1.000000 LK=-11967.817956 . ( 21 sec) [ -11967.6718] [GTR parameters ] . ( 21 sec) [ -11967.0266] [Alpha ][ 1.035749] . ( 21 sec) [ -11967.0266] [Topology ] . ( 22 sec) [ -11966.9204] [Topology ] . ( 23 sec) [ -11966.8765] [Topology ] . ( 24 sec) [ -11966.8537] [Topology ] . ( 26 sec) [ -11966.8415] [Topology ] . ( 27 sec) [ -11966.8348] [Topology ] . ( 28 sec) [ -11966.8311] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.831138 . ( 38 sec) [ -11966.8304] [GTR parameters ] . ( 38 sec) [ -11966.8252] [Alpha ][ 1.042902] . ( 39 sec) [ -11966.8252] [Topology ] . ( 40 sec) [ -11966.8224] [Topology ] . ( 41 sec) [ -11966.8210] [Topology ] . ( 42 sec) [ -11966.8203] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.820258 . ( 49 sec) [ -11966.8202] [GTR parameters ] . ( 50 sec) [ -11966.8202] [Alpha ][ 1.043945] . ( 50 sec) [ -11966.8202] [Topology ] . ( 50 sec) [ -11966.8197] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11966.819701. . Printing the most likely tree in file 'data85.phy_phyml_tree.txt'... . Time used 0h1m8s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo