.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data44.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... . 285 patterns found. (out of a total of 500 sites) . 201 sites without polymorphism (40.20%). . 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=-4690.275845 . ( 0 sec) [ -4685.6353] [GTR parameters ] . ( 1 sec) [ -4685.0967] [Alpha ][ 0.878928] . ( 1 sec) [ -4685.0967] [Topology ] . ( 1 sec) [ -4677.5186] [Topology ] . ( 2 sec) [ -4676.6086] [Topology ] . ( 2 sec) [ -4676.4124] [Topology ] . ( 3 sec) [ -4676.3612] [Topology ] . ( 4 sec) [ -4676.3466] [Topology ] . ( 4 sec) [ -4676.3421] [Topology ] . ( 5 sec) [ -4676.3407] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4676.340732 . ( 9 sec) [ -4676.3369] [GTR parameters ] . ( 9 sec) [ -4676.3096] [Alpha ][ 0.903671] . ( 9 sec) [ -4676.3096] [Topology ] . ( 10 sec) [ -4676.3076] [Topology ] . ( 10 sec) [ -4676.3070] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4676.306977 . ( 14 sec) [ -4676.3070] [GTR parameters ] . ( 14 sec) [ -4676.3069] [Alpha ][ 0.904574] . ( 14 sec) [ -4676.3069] [Topology ] . ( 15 sec) [ -4676.3067] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 22 sec) [ -4685.6353] [GTR parameters ] . ( 22 sec) [ -4685.0967] [Alpha ][ 0.878928] . ( 22 sec) [ -4684.1047] [ 718] [depth= 1] . ( 22 sec) [ -4684.0629] [ 718] [depth= 1] . ( 23 sec) [ -4683.4607] [ 718] [depth= 1] . ( 23 sec) [ -4682.6754] [ 718] [depth= 1] . ( 23 sec) [ -4682.4650] [ 718] [depth= 1] . ( 23 sec) [ -4681.9375] [ 718] [depth= 1] . ( 24 sec) [ -4681.7946] [ 719] [depth= 1] . ( 24 sec) [ -4681.3218] [ 718] [depth= 1] . ( 25 sec) [ -4680.6303] [ 718] [depth= 1] . ( 25 sec) [ -4680.4831] [ 718] [depth= 1] . ( 25 sec) [ -4680.4423] [ 718] [depth= 1] . ( 25 sec) [ -4680.3144] [ 718] [depth= 1] . ( 25 sec) [ -4676.4045] [Branch lengths ] . ( 26 sec) [ -4676.4016] [GTR parameters ] . ( 26 sec) [ -4676.3830] [Alpha ][ 0.899229] . ( 29 sec) [ -4676.3125] [Branch lengths ] . ( 46 sec) [ -4676.3083] [Branch lengths ] . ( 46 sec) [ -4676.3083] [Topology ] . ( 47 sec) [ -4676.3081] [Topology ] . ( 47 sec) [ -4676.3080] [GTR parameters ] . ( 47 sec) [ -4676.3067] [Alpha ][ 0.904772] . ( 47 sec) [ -4676.3067] [Topology ] . ( 48 sec) [ -4676.3066] [Topology ] . ( 48 sec) [ -4676.3066] [GTR parameters ] . ( 48 sec) [ -4676.3066] [Alpha ][ 0.904772] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4676.306664 . Log likelihood obtained after SPR moves : -4676.306579 . Log likelihood of the current tree: -4676.306579. . Printing the most likely tree in file 'data44.phy_phyml_tree.txt'... . Time used 0h0m52s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo