.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data36.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... . 242 patterns found. (out of a total of 500 sites) . 238 sites without polymorphism (47.60%). . 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=-3607.752479 . ( 0 sec) [ -3604.8214] [GTR parameters ] . ( 0 sec) [ -3603.5517] [Alpha ][ 0.788011] . ( 0 sec) [ -3603.5517] [Topology ] . ( 1 sec) [ -3598.3151] [Topology ] . ( 1 sec) [ -3597.5172] [Topology ] . ( 2 sec) [ -3597.3284] [Topology ] . ( 2 sec) [ -3597.2749] [Topology ] . ( 3 sec) [ -3597.2579] [Topology ] . ( 3 sec) [ -3597.2516] [Topology ] . Checking for NNIs, optimizing five branches... . ( 6 sec) [ -3597.1388] [Topology ] . Before opt ts/t=1.000000 LK=-3597.138757 . ( 6 sec) [ -3597.1192] [GTR parameters ] . ( 6 sec) [ -3597.1105] [Alpha ][ 0.802128] . ( 6 sec) [ -3597.1105] [Topology ] . ( 7 sec) [ -3597.0776] [Topology ] . ( 7 sec) [ -3596.9868] [Topology ] . ( 8 sec) [ -3596.8400] [Topology ] . ( 8 sec) [ -3596.7996] [Topology ] . ( 9 sec) [ -3596.7876] [Topology ] . ( 9 sec) [ -3596.7837] [Topology ] . ( 10 sec) [ -3596.7823] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3596.782309 . ( 13 sec) [ -3596.7812] [GTR parameters ] . ( 13 sec) [ -3596.7793] [Alpha ][ 0.809327] . ( 13 sec) [ -3596.7793] [Topology ] . ( 13 sec) [ -3596.7785] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-3596.778495 . ( 16 sec) [ -3596.7785] [GTR parameters ] . ( 16 sec) [ -3596.7785] [Alpha ][ 0.809327] . ( 16 sec) [ -3596.7785] [Topology ] . ( 17 sec) [ -3596.7781] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -3604.8214] [GTR parameters ] . ( 23 sec) [ -3603.5517] [Alpha ][ 0.788011] . ( 23 sec) [ -3603.4041] [ 531] [depth= 1] . ( 23 sec) [ -3603.2726] [ 531] [depth= 1] . ( 23 sec) [ -3602.5869] [ 529] [depth= 2] . ( 24 sec) [ -3602.0030] [ 532] [depth= 1] . ( 24 sec) [ -3601.9340] [ 532] [depth= 1] . ( 24 sec) [ -3601.3957] [ 532] [depth= 1] . ( 24 sec) [ -3601.3651] [ 532] [depth= 1] . ( 25 sec) [ -3601.3541] [ 533] [depth= 1] . ( 26 sec) [ -3598.0565] [Branch lengths ] . ( 26 sec) [ -3598.0338] [GTR parameters ] . ( 26 sec) [ -3598.0313] [Alpha ][ 0.796029] . ( 27 sec) [ -3598.0175] [ 531] [depth= 1] . ( 28 sec) [ -3597.2328] [ 529] [depth= 1] . ( 30 sec) [ -3596.8196] [Branch lengths ] . ( 30 sec) [ -3596.8034] [GTR parameters ] . ( 30 sec) [ -3596.7973] [Alpha ][ 0.808789] . ( 33 sec) [ -3596.7834] [Branch lengths ] . ( 49 sec) [ -3596.7806] [Branch lengths ] . ( 49 sec) [ -3596.7806] [Topology ] . ( 50 sec) [ -3596.7798] [Topology ] . ( 50 sec) [ -3596.7796] [GTR parameters ] . ( 50 sec) [ -3596.7796] [Alpha ][ 0.809598] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3596.778076 . Log likelihood obtained after SPR moves : -3596.779630 . Log likelihood of the current tree: -3596.778076. . Printing the most likely tree in file 'data36.phy_phyml_tree.txt'... . Time used 0h0m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo