.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data22.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... . 237 patterns found. (out of a total of 500 sites) . 249 sites without polymorphism (49.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-3389.217077 . ( 1 sec) [ -3388.1055] [GTR parameters ] . ( 1 sec) [ -3388.1023] [Alpha ][ 1.014501] . ( 1 sec) [ -3388.1023] [Topology ] . ( 1 sec) [ -3383.8115] [Topology ] . ( 2 sec) [ -3383.2249] [Topology ] . ( 3 sec) [ -3383.1115] [Topology ] . ( 3 sec) [ -3383.0856] [Topology ] . ( 4 sec) [ -3383.0793] [Topology ] . ( 4 sec) [ -3383.0777] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3383.077747 . ( 7 sec) [ -3383.0772] [GTR parameters ] . ( 7 sec) [ -3383.0738] [Alpha ][ 1.029469] . ( 7 sec) [ -3383.0738] [Topology ] . ( 8 sec) [ -3383.0731] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3383.073108 . ( 11 sec) [ -3383.0731] [GTR parameters ] . ( 11 sec) [ -3383.0731] [Alpha ][ 1.029469] . ( 11 sec) [ -3383.0731] [Topology ] . ( 11 sec) [ -3383.0730] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 18 sec) [ -3388.1055] [GTR parameters ] . ( 18 sec) [ -3388.1023] [Alpha ][ 1.014501] . ( 19 sec) [ -3388.0399] [ 459] [depth= 1] . ( 19 sec) [ -3388.0145] [ 459] [depth= 1] . ( 19 sec) [ -3387.9654] [ 459] [depth= 1] . ( 20 sec) [ -3387.4861] [ 459] [depth= 1] . ( 20 sec) [ -3387.4233] [ 459] [depth= 1] . ( 20 sec) [ -3387.2541] [ 459] [depth= 1] . ( 20 sec) [ -3387.1683] [ 459] [depth= 1] . ( 20 sec) [ -3387.1491] [ 459] [depth= 1] . ( 21 sec) [ -3387.0827] [ 459] [depth= 1] . ( 21 sec) [ -3387.0697] [ 459] [depth= 1] . ( 21 sec) [ -3387.0574] [ 459] [depth= 1] . ( 21 sec) [ -3386.6385] [ 459] [depth= 1] . ( 21 sec) [ -3386.5808] [ 459] [depth= 1] . ( 21 sec) [ -3386.3717] [ 459] [depth= 1] . ( 21 sec) [ -3386.2253] [ 459] [depth= 1] . ( 22 sec) [ -3385.9159] [ 459] [depth= 1] . ( 22 sec) [ -3383.0919] [Branch lengths ] . ( 22 sec) [ -3383.0915] [GTR parameters ] . ( 23 sec) [ -3383.0887] [Alpha ][ 1.028080] . ( 29 sec) [ -3383.0731] [Branch lengths ] . ( 51 sec) [ -3383.0729] [Branch lengths ] . ( 51 sec) [ -3383.0729] [Topology ] . ( 52 sec) [ -3383.0729] [Topology ] . ( 52 sec) [ -3383.0729] [GTR parameters ] . ( 52 sec) [ -3383.0728] [Alpha ][ 1.029174] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3383.072958 . Log likelihood obtained after SPR moves : -3383.072831 . Log likelihood of the current tree: -3383.072831. . Printing the most likely tree in file 'data22.phy_phyml_tree.txt'... . Time used 0h0m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo