.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data97.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 : 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 . Compressing sequences... . 269 patterns found. (out of a total of 500 sites) . 214 sites without polymorphism (42.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4111.471889 . ( 1 sec) [ -4110.4914] [GTR parameters ] . ( 1 sec) [ -4110.4093] [Alpha ][ 0.944284] . ( 1 sec) [ -4110.4093] [Topology ] . ( 2 sec) [ -4104.9272] [Topology ] . ( 3 sec) [ -4104.3231] [Topology ] . ( 4 sec) [ -4104.2064] [Topology ] . ( 5 sec) [ -4104.1784] [Topology ] . ( 6 sec) [ -4104.1711] [Topology ] . ( 6 sec) [ -4104.1691] [Topology ] . ( 7 sec) [ -4104.1685] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4104.168519 . ( 12 sec) [ -4104.1638] [GTR parameters ] . ( 12 sec) [ -4104.1535] [Alpha ][ 0.962692] . ( 12 sec) [ -4104.1535] [Topology ] . ( 13 sec) [ -4104.1529] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4104.152929 . ( 19 sec) [ -4104.1529] [GTR parameters ] . ( 19 sec) [ -4104.1529] [Alpha ][ 0.963655] . ( 19 sec) [ -4104.1529] [Topology ] . ( 20 sec) [ -4104.1528] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -4110.4914] [GTR parameters ] . ( 32 sec) [ -4110.4093] [Alpha ][ 0.944284] . ( 35 sec) [ -4109.8399] [ 611] [depth= 1] . ( 35 sec) [ -4109.7768] [ 612] [depth= 1] . ( 35 sec) [ -4109.6872] [ 612] [depth= 1] . ( 35 sec) [ -4109.6429] [ 612] [depth= 1] . ( 36 sec) [ -4104.4713] [Branch lengths ] . ( 37 sec) [ -4104.4705] [GTR parameters ] . ( 37 sec) [ -4104.4652] [Alpha ][ 0.958101] . ( 39 sec) [ -4104.4060] [ 611] [depth= 1] . ( 40 sec) [ -4104.1627] [Branch lengths ] . ( 40 sec) [ -4104.1609] [GTR parameters ] . ( 41 sec) [ -4104.1603] [Alpha ][ 0.962574] . ( 63 sec) [ -4104.1529] [Branch lengths ] . ( 63 sec) [ -4104.1529] [Topology ] . ( 63 sec) [ -4104.1527] [Topology ] . ( 64 sec) [ -4104.1527] [GTR parameters ] . ( 64 sec) [ -4104.1527] [Alpha ][ 0.963537] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4104.152764 . Log likelihood obtained after SPR moves : -4104.152700 . Log likelihood of the current tree: -4104.152700. . Printing the most likely tree in file 'data97.phy_phyml_tree.txt'... . Time used 0h1m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo