.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data99.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... . 435 patterns found. (out of a total of 500 sites) . 62 sites without polymorphism (12.40%). . 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=-9344.513092 . ( 1 sec) [ -9340.2121] [GTR parameters ] . ( 2 sec) [ -9340.0840] [Alpha ][ 0.961734] . ( 2 sec) [ -9340.0840] [Topology ] . ( 3 sec) [ -9287.2686] [Topology ] . ( 4 sec) [ -9278.1083] [Topology ] . ( 6 sec) [ -9274.7836] [Topology ] . ( 7 sec) [ -9273.3477] [Topology ] . ( 7 sec) [ -9272.6564] [Topology ] . ( 8 sec) [ -9272.3013] [Topology ] . ( 9 sec) [ -9272.1066] [Topology ] . ( 10 sec) [ -9271.9490] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9271.949043 . ( 21 sec) [ -9271.7805] [GTR parameters ] . ( 21 sec) [ -9271.6934] [Alpha ][ 0.991117] . ( 21 sec) [ -9271.6934] [Topology ] . ( 22 sec) [ -9271.2852] [Topology ] . ( 23 sec) [ -9270.4779] [Topology ] . ( 24 sec) [ -9270.1417] [Topology ] . ( 25 sec) [ -9270.0517] [Topology ] . ( 26 sec) [ -9270.0278] [Topology ] . ( 27 sec) [ -9270.0205] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.020474 . ( 39 sec) [ -9270.0170] [GTR parameters ] . ( 39 sec) [ -9270.0164] [Alpha ][ 0.993723] . ( 39 sec) [ -9270.0164] [Topology ] . ( 40 sec) [ -9270.0135] [Topology ] . ( 41 sec) [ -9270.0123] [Topology ] . ( 42 sec) [ -9270.0117] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9270.011651 . ( 53 sec) [ -9270.0117] [GTR parameters ] . ( 53 sec) [ -9270.0117] [Alpha ][ 0.993723] . ( 53 sec) [ -9270.0117] [Topology ] . ( 54 sec) [ -9270.0113] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9270.011349. . Printing the most likely tree in file 'data99.phy_phyml_tree.txt'... . Time used 0h1m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo