.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data95.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... . 415 patterns found. (out of a total of 500 sites) . 84 sites without polymorphism (16.80%). . 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=-9320.302500 . ( 1 sec) [ -9318.8428] [GTR parameters ] . ( 1 sec) [ -9318.8360] [Alpha ][ 0.990367] . ( 1 sec) [ -9318.8360] [Topology ] . ( 2 sec) [ -9296.9484] [Topology ] . ( 2 sec) [ -9293.9800] [Topology ] . ( 3 sec) [ -9293.0792] [Topology ] . ( 4 sec) [ -9292.6952] [Topology ] . ( 5 sec) [ -9292.5629] [Topology ] . ( 6 sec) [ -9292.5022] [Topology ] . ( 6 sec) [ -9292.4726] [Topology ] . ( 7 sec) [ -9292.4579] [Topology ] . ( 8 sec) [ -9292.4506] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.450570 . ( 14 sec) [ -9292.4042] [GTR parameters ] . ( 14 sec) [ -9292.1729] [Alpha ][ 1.044231] . ( 14 sec) [ -9292.1729] [Topology ] . ( 14 sec) [ -9292.1519] [Topology ] . ( 15 sec) [ -9292.1433] [Topology ] . ( 16 sec) [ -9292.1392] [Topology ] . ( 17 sec) [ -9292.1372] [Topology ] . ( 18 sec) [ -9292.1362] [Topology ] . ( 18 sec) [ -9292.1357] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.135669 . ( 24 sec) [ -9292.1352] [GTR parameters ] . ( 24 sec) [ -9292.1336] [Alpha ][ 1.048822] . ( 24 sec) [ -9292.1336] [Topology ] . ( 25 sec) [ -9292.1332] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9292.133168 . ( 31 sec) [ -9292.1332] [GTR parameters ] . ( 31 sec) [ -9292.1332] [Alpha ][ 1.048822] . ( 31 sec) [ -9292.1332] [Topology ] . ( 31 sec) [ -9292.1330] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 43 sec) [ -9318.8428] [GTR parameters ] . ( 43 sec) [ -9318.8360] [Alpha ][ 0.990367] . ( 44 sec) [ -9318.7079] [ 1957] [depth= 1] . ( 44 sec) [ -9318.2107] [ 1955] [depth= 1] . ( 44 sec) [ -9317.4619] [ 1954] [depth= 1] . ( 44 sec) [ -9315.8366] [ 1956] [depth= 1] . ( 45 sec) [ -9313.4815] [ 1955] [depth= 1] . ( 46 sec) [ -9311.7901] [ 1954] [depth= 1] . ( 46 sec) [ -9311.5774] [ 1955] [depth= 1] . ( 46 sec) [ -9311.5122] [ 1954] [depth= 1] . ( 46 sec) [ -9310.4770] [ 1953] [depth= 1] . ( 46 sec) [ -9309.6563] [ 1954] [depth= 1] . ( 47 sec) [ -9309.2220] [ 1953] [depth= 1] . ( 47 sec) [ -9308.8743] [ 1954] [depth= 1] . ( 47 sec) [ -9293.8832] [Branch lengths ] . ( 47 sec) [ -9293.8583] [GTR parameters ] . ( 47 sec) [ -9293.7452] [Alpha ][ 1.027666] . ( 49 sec) [ -9293.6086] [ 1956] [depth= 1] . ( 49 sec) [ -9293.5646] [ 1953] [depth= 1] . ( 52 sec) [ -9292.3182] [Branch lengths ] . ( 52 sec) [ -9292.3157] [GTR parameters ] . ( 52 sec) [ -9292.3014] [Alpha ][ 1.041686] . ( 58 sec) [ -9292.1693] [Branch lengths ] . ( 81 sec) [ -9292.1418] [Branch lengths ] . ( 81 sec) [ -9292.1418] [Topology ] . ( 82 sec) [ -9292.1391] [Topology ] . ( 82 sec) [ -9292.1381] [Topology ] . ( 83 sec) [ -9292.1380] [GTR parameters ] . ( 83 sec) [ -9292.1345] [Alpha ][ 1.048608] . ( 83 sec) [ -9292.1345] [Topology ] . ( 83 sec) [ -9292.1336] [Topology ] . ( 84 sec) [ -9292.1336] [GTR parameters ] . ( 84 sec) [ -9292.1336] [Alpha ][ 1.048608] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9292.132960 . Log likelihood obtained after SPR moves : -9292.133605 . Log likelihood of the current tree: -9292.132960. . Printing the most likely tree in file 'data95.phy_phyml_tree.txt'... . Time used 0h1m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo