.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data72.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... . 341 patterns found. (out of a total of 500 sites) . 144 sites without polymorphism (28.80%). . 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=-5675.382185 . ( 1 sec) [ -5674.1403] [GTR parameters ] . ( 1 sec) [ -5674.1388] [Alpha ][ 0.993583] . ( 1 sec) [ -5674.1388] [Topology ] . ( 1 sec) [ -5656.4636] [Topology ] . ( 2 sec) [ -5651.5572] [Topology ] . ( 3 sec) [ -5650.8384] [Topology ] . ( 4 sec) [ -5650.6391] [Topology ] . ( 4 sec) [ -5650.5758] [Topology ] . ( 5 sec) [ -5650.5540] [Topology ] . ( 6 sec) [ -5650.5459] [Topology ] . ( 7 sec) [ -5650.5429] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5650.542869 . ( 12 sec) [ -5650.5381] [GTR parameters ] . ( 12 sec) [ -5650.5195] [Alpha ][ 1.013446] . ( 12 sec) [ -5650.5195] [Topology ] . ( 12 sec) [ -5650.5175] [Topology ] . ( 13 sec) [ -5650.5167] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5650.516672 . ( 21 sec) [ -5650.5167] [GTR parameters ] . ( 21 sec) [ -5650.5166] [Alpha ][ 1.014460] . ( 21 sec) [ -5650.5166] [Topology ] . ( 22 sec) [ -5650.5163] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -5674.1403] [GTR parameters ] . ( 36 sec) [ -5674.1388] [Alpha ][ 0.993583] . ( 37 sec) [ -5673.2321] [ 982] [depth= 1] . ( 37 sec) [ -5672.5291] [ 981] [depth= 1] . ( 37 sec) [ -5669.7361] [ 984] [depth= 1] . ( 37 sec) [ -5669.3985] [ 986] [depth= 1] . ( 37 sec) [ -5668.6233] [ 984] [depth= 1] . ( 39 sec) [ -5663.7516] [ 980] [depth= 3] . ( 41 sec) [ -5662.7453] [ 981] [depth= 1] . ( 42 sec) [ -5662.1190] [ 981] [depth= 1] . ( 42 sec) [ -5661.3337] [ 980] [depth= 1] . ( 43 sec) [ -5650.7574] [Branch lengths ] . ( 43 sec) [ -5650.7525] [GTR parameters ] . ( 43 sec) [ -5650.7367] [Alpha ][ 1.011886] . ( 48 sec) [ -5650.5716] [Branch lengths ] . ( 73 sec) [ -5650.5643] [Branch lengths ] . ( 73 sec) [ -5650.5643] [Topology ] . ( 74 sec) [ -5650.5638] [Topology ] . ( 74 sec) [ -5650.5637] [GTR parameters ] . ( 74 sec) [ -5650.5632] [Alpha ][ 1.015386] . ( 74 sec) [ -5650.5632] [Topology ] . ( 75 sec) [ -5650.5630] [Topology ] . ( 75 sec) [ -5650.5630] [GTR parameters ] . ( 76 sec) [ -5650.5630] [Alpha ][ 1.015386] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -5650.5263] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5650.516313 . Log likelihood obtained after SPR moves : -5650.526261 . Log likelihood of the current tree: -5650.516313. . Printing the most likely tree in file 'data72.phy_phyml_tree.txt'... . Time used 0h1m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo