.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data26.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... . 317 patterns found. (out of a total of 500 sites) . 165 sites without polymorphism (33.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4865.141674 . ( 1 sec) [ -4860.9842] [GTR parameters ] . ( 1 sec) [ -4860.5234] [Alpha ][ 1.125341] . ( 1 sec) [ -4860.5234] [Topology ] . ( 2 sec) [ -4845.9236] [Topology ] . ( 3 sec) [ -4844.6195] [Topology ] . ( 4 sec) [ -4844.4342] [Topology ] . ( 4 sec) [ -4844.3950] [Topology ] . ( 5 sec) [ -4844.3845] [Topology ] . ( 6 sec) [ -4844.3813] [Topology ] . ( 6 sec) [ -4844.3803] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4844.380302 . ( 11 sec) [ -4844.3571] [GTR parameters ] . ( 11 sec) [ -4844.3447] [Alpha ][ 1.146930] . ( 11 sec) [ -4844.3447] [Topology ] . ( 12 sec) [ -4844.3440] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4844.343980 . ( 16 sec) [ -4844.3440] [GTR parameters ] . ( 16 sec) [ -4844.3439] [Alpha ][ 1.148077] . ( 16 sec) [ -4844.3439] [Topology ] . ( 16 sec) [ -4844.3437] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 24 sec) [ -4860.9842] [GTR parameters ] . ( 25 sec) [ -4860.5234] [Alpha ][ 1.125341] . ( 25 sec) [ -4856.9701] [ 798] [depth= 1] . ( 26 sec) [ -4853.6229] [ 798] [depth= 1] . ( 27 sec) [ -4853.2771] [ 798] [depth= 1] . ( 28 sec) [ -4844.4682] [Branch lengths ] . ( 28 sec) [ -4844.4460] [GTR parameters ] . ( 28 sec) [ -4844.4375] [Alpha ][ 1.144208] . ( 31 sec) [ -4844.3483] [Branch lengths ] . ( 50 sec) [ -4844.3440] [Branch lengths ] . ( 50 sec) [ -4844.3440] [Topology ] . ( 50 sec) [ -4844.3439] [Topology ] . ( 50 sec) [ -4844.3438] [GTR parameters ] . ( 51 sec) [ -4844.3435] [Alpha ][ 1.147835] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4844.343707 . Log likelihood obtained after SPR moves : -4844.343476 . Log likelihood of the current tree: -4844.343476. . Printing the most likely tree in file 'data26.phy_phyml_tree.txt'... . Time used 0h0m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo