.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data71.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... . 455 patterns found. (out of a total of 500 sites) . 44 sites without polymorphism (8.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-11033.487122 . ( 1 sec) [ -11032.9128] [GTR parameters ] . ( 1 sec) [ -11030.8409] [Alpha ][ 1.162653] . ( 1 sec) [ -11030.8409] [Topology ] . ( 2 sec) [ -10949.5341] [Topology ] . ( 3 sec) [ -10930.4633] [Topology ] . ( 4 sec) [ -10926.6486] [Topology ] . ( 4 sec) [ -10925.5193] [Topology ] . ( 5 sec) [ -10925.0495] [Topology ] . ( 6 sec) [ -10924.8277] [Topology ] . ( 7 sec) [ -10924.7164] [Topology ] . ( 8 sec) [ -10924.6577] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.657736 . ( 15 sec) [ -10924.5882] [GTR parameters ] . ( 16 sec) [ -10924.3961] [Alpha ][ 1.113397] . ( 16 sec) [ -10924.3961] [Topology ] . ( 16 sec) [ -10924.3525] [Topology ] . ( 17 sec) [ -10924.3339] [Topology ] . ( 18 sec) [ -10924.3239] [Topology ] . ( 19 sec) [ -10924.3183] [Topology ] . ( 20 sec) [ -10924.3151] [Topology ] . ( 21 sec) [ -10924.3133] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.313310 . ( 28 sec) [ -10924.3131] [GTR parameters ] . ( 28 sec) [ -10924.3124] [Alpha ][ 1.110450] . ( 28 sec) [ -10924.3124] [Topology ] . ( 29 sec) [ -10924.3113] [Topology ] . ( 30 sec) [ -10924.3107] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10924.310696 . ( 37 sec) [ -10924.3107] [GTR parameters ] . ( 38 sec) [ -10924.3107] [Alpha ][ 1.110450] . ( 38 sec) [ -10924.3107] [Topology ] . ( 38 sec) [ -10924.3103] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 54 sec) [ -11032.9128] [GTR parameters ] . ( 54 sec) [ -11030.8409] [Alpha ][ 1.162653] . ( 55 sec) [ -11027.8222] [ 2511] [depth= 1] . ( 55 sec) [ -11015.2292] [ 2496] [depth= 1] . ( 55 sec) [ -11013.5463] [ 2501] [depth= 1] . ( 55 sec) [ -10995.1740] [ 2506] [depth= 1] . ( 55 sec) [ -10994.9317] [ 2508] [depth= 1] . ( 55 sec) [ -10992.7866] [ 2506] [depth= 1] . ( 55 sec) [ -10991.4563] [ 2508] [depth= 1] . ( 56 sec) [ -10990.8017] [ 2511] [depth= 1] . ( 56 sec) [ -10988.5056] [ 2515] [depth= 1] . ( 56 sec) [ -10984.9145] [ 2511] [depth= 1] . ( 56 sec) [ -10980.2992] [ 2514] [depth= 2] . ( 56 sec) [ -10980.1407] [ 2514] [depth= 1] . ( 56 sec) [ -10978.5828] [ 2515] [depth= 1] . ( 57 sec) [ -10964.8826] [ 2521] [depth= 2] . ( 57 sec) [ -10932.2004] [Branch lengths ] . ( 58 sec) [ -10932.1336] [GTR parameters ] . ( 58 sec) [ -10931.8741] [Alpha ][ 1.105045] . ( 59 sec) [ -10930.3061] [ 2517] [depth= 1] . ( 59 sec) [ -10929.6557] [ 2514] [depth= 1] . ( 60 sec) [ -10929.3083] [ 2523] [depth= 1] . ( 60 sec) [ -10928.3874] [ 2513] [depth= 2] . ( 61 sec) [ -10924.9659] [Branch lengths ] . ( 61 sec) [ -10924.9621] [GTR parameters ] . ( 61 sec) [ -10924.9610] [Alpha ][ 1.108696] . ( 65 sec) [ -10924.4729] [Branch lengths ] . ( 87 sec) [ -10924.3586] [Branch lengths ] . ( 87 sec) [ -10924.3586] [Topology ] . ( 88 sec) [ -10924.3398] [Topology ] . ( 88 sec) [ -10924.3276] [Topology ] . ( 89 sec) [ -10924.3214] [Topology ] . ( 90 sec) [ -10924.3179] [Topology ] . ( 91 sec) [ -10924.3157] [Topology ] . ( 92 sec) [ -10924.3144] [Topology ] . ( 92 sec) [ -10924.3124] [GTR parameters ] . ( 92 sec) [ -10924.3122] [Alpha ][ 1.110175] . ( 92 sec) [ -10924.3122] [Topology ] . ( 93 sec) [ -10924.3113] [Topology ] . ( 93 sec) [ -10924.3113] [GTR parameters ] . ( 93 sec) [ -10924.3113] [Alpha ][ 1.110175] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10924.310330 . Log likelihood obtained after SPR moves : -10924.311344 . Log likelihood of the current tree: -10924.310330. . Printing the most likely tree in file 'data71.phy_phyml_tree.txt'... . Time used 0h1m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo