.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data41.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... . 348 patterns found. (out of a total of 500 sites) . 135 sites without polymorphism (27.00%). . 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=-5599.082085 . ( 1 sec) [ -5595.4304] [GTR parameters ] . ( 1 sec) [ -5594.7581] [Alpha ][ 1.136695] . ( 1 sec) [ -5594.7581] [Topology ] . ( 2 sec) [ -5573.7572] [Topology ] . ( 3 sec) [ -5569.6965] [Topology ] . ( 4 sec) [ -5568.0928] [Topology ] . ( 5 sec) [ -5567.7576] [Topology ] . ( 5 sec) [ -5567.6754] [Topology ] . ( 6 sec) [ -5567.6516] [Topology ] . ( 7 sec) [ -5567.6443] [Topology ] . ( 7 sec) [ -5567.6419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5567.641893 . ( 14 sec) [ -5567.6153] [GTR parameters ] . ( 14 sec) [ -5567.6153] [Alpha ][ 1.136695] . ( 14 sec) [ -5567.6153] [Topology ] . ( 16 sec) [ -5567.6141] [Topology ] . ( 17 sec) [ -5567.6137] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5567.613694 . ( 25 sec) [ -5567.6137] [GTR parameters ] . ( 25 sec) [ -5567.6137] [Alpha ][ 1.136695] . ( 25 sec) [ -5567.6137] [Topology ] . ( 25 sec) [ -5567.6136] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 42 sec) [ -5595.4304] [GTR parameters ] . ( 42 sec) [ -5594.7581] [Alpha ][ 1.136695] . ( 42 sec) [ -5594.0482] [ 989] [depth= 1] . ( 42 sec) [ -5592.4546] [ 989] [depth= 1] . ( 43 sec) [ -5592.3055] [ 990] [depth= 1] . ( 43 sec) [ -5592.2777] [ 989] [depth= 1] . ( 44 sec) [ -5591.1113] [ 988] [depth= 1] . ( 44 sec) [ -5591.0384] [ 989] [depth= 1] . ( 44 sec) [ -5590.9881] [ 988] [depth= 1] . ( 46 sec) [ -5587.3950] [ 987] [depth= 1] . ( 46 sec) [ -5587.0676] [ 987] [depth= 1] . ( 46 sec) [ -5586.6693] [ 987] [depth= 1] . ( 46 sec) [ -5586.3154] [ 987] [depth= 1] . ( 47 sec) [ -5568.6704] [Branch lengths ] . ( 48 sec) [ -5568.6436] [GTR parameters ] . ( 48 sec) [ -5568.6430] [Alpha ][ 1.141000] . ( 49 sec) [ -5568.3735] [ 988] [depth= 1] . ( 54 sec) [ -5567.6563] [Branch lengths ] . ( 54 sec) [ -5567.6509] [GTR parameters ] . ( 54 sec) [ -5567.6503] [Alpha ][ 1.136477] . ( 79 sec) [ -5567.6146] [Branch lengths ] . ( 79 sec) [ -5567.6146] [Topology ] . ( 80 sec) [ -5567.6138] [Topology ] . ( 80 sec) [ -5567.6137] [GTR parameters ] . ( 80 sec) [ -5567.6137] [Alpha ][ 1.136477] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5567.613565 . Log likelihood obtained after SPR moves : -5567.613659 . Log likelihood of the current tree: -5567.613565. . Printing the most likely tree in file 'data41.phy_phyml_tree.txt'... . Time used 0h1m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo