.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data12.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... . 349 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=-6050.947914 . ( 1 sec) [ -6049.3553] [GTR parameters ] . ( 1 sec) [ -6049.3232] [Alpha ][ 0.974396] . ( 1 sec) [ -6049.3232] [Topology ] . ( 2 sec) [ -6034.4456] [Topology ] . ( 2 sec) [ -6032.8652] [Topology ] . ( 3 sec) [ -6032.4749] [Topology ] . ( 4 sec) [ -6032.3420] [Topology ] . ( 4 sec) [ -6032.2915] [Topology ] . ( 5 sec) [ -6032.2714] [Topology ] . ( 6 sec) [ -6032.2632] [Topology ] . Checking for NNIs, optimizing five branches... . ( 10 sec) [ -6031.9929] [Topology ] . Before opt ts/t=1.000000 LK=-6031.992854 . ( 11 sec) [ -6031.9701] [GTR parameters ] . ( 11 sec) [ -6031.9311] [Alpha ][ 1.001414] . ( 11 sec) [ -6031.9311] [Topology ] . ( 11 sec) [ -6031.9038] [Topology ] . ( 12 sec) [ -6031.8983] [Topology ] . ( 13 sec) [ -6031.8966] [Topology ] . ( 13 sec) [ -6031.8959] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6031.895930 . ( 18 sec) [ -6031.8959] [GTR parameters ] . ( 18 sec) [ -6031.8958] [Alpha ][ 1.002853] . ( 18 sec) [ -6031.8958] [Topology ] . ( 19 sec) [ -6031.8955] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 28 sec) [ -6049.3553] [GTR parameters ] . ( 28 sec) [ -6049.3232] [Alpha ][ 0.974396] . ( 28 sec) [ -6047.0883] [ 1080] [depth= 1] . ( 29 sec) [ -6046.1418] [ 1082] [depth= 1] . ( 29 sec) [ -6044.5745] [ 1085] [depth= 1] . ( 29 sec) [ -6042.5194] [ 1085] [depth= 1] . ( 30 sec) [ -6041.2747] [ 1086] [depth= 1] . ( 30 sec) [ -6041.0408] [ 1086] [depth= 1] . ( 30 sec) [ -6040.0915] [ 1086] [depth= 1] . ( 30 sec) [ -6039.8905] [ 1086] [depth= 1] . ( 30 sec) [ -6039.6897] [ 1086] [depth= 1] . ( 30 sec) [ -6039.1390] [ 1086] [depth= 1] . ( 31 sec) [ -6039.1261] [ 1086] [depth= 1] . ( 31 sec) [ -6032.3997] [Branch lengths ] . ( 32 sec) [ -6032.3737] [GTR parameters ] . ( 32 sec) [ -6032.3571] [Alpha ][ 0.992661] . ( 36 sec) [ -6032.0587] [Branch lengths ] . ( 43 sec) [ -6031.9778] [ 1082] [depth= 1] . ( 53 sec) [ -6031.9068] [Branch lengths ] . ( 53 sec) [ -6031.9063] [GTR parameters ] . ( 53 sec) [ -6031.9017] [Alpha ][ 1.002262] . ( 53 sec) [ -6031.9017] [Topology ] . ( 54 sec) [ -6031.8970] [Topology ] . ( 55 sec) [ -6031.8960] [Topology ] . ( 55 sec) [ -6031.8956] [Topology ] . ( 55 sec) [ -6031.8955] [GTR parameters ] . ( 55 sec) [ -6031.8955] [Alpha ][ 1.003264] . ( 55 sec) [ -6031.8955] [Topology ] . ( 56 sec) [ -6031.8953] [Topology ] . ( 56 sec) [ -6031.8953] [GTR parameters ] . ( 56 sec) [ -6031.8953] [Alpha ][ 1.003264] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6031.895482 . Log likelihood obtained after SPR moves : -6031.895324 . Log likelihood of the current tree: -6031.895324. . Printing the most likely tree in file 'data12.phy_phyml_tree.txt'... . Time used 0h1m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo