.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data63.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... . 407 patterns found. (out of a total of 500 sites) . 77 sites without polymorphism (15.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8115.972555 . ( 0 sec) [ -8113.9827] [GTR parameters ] . ( 0 sec) [ -8113.8648] [Alpha ][ 1.041976] . ( 0 sec) [ -8113.8648] [Topology ] . ( 1 sec) [ -8081.6555] [Topology ] . ( 2 sec) [ -8076.8135] [Topology ] . ( 3 sec) [ -8075.2238] [Topology ] . ( 4 sec) [ -8074.5381] [Topology ] . ( 4 sec) [ -8074.2089] [Topology ] . ( 5 sec) [ -8074.0419] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8074.041867 . ( 11 sec) [ -8074.0065] [GTR parameters ] . ( 12 sec) [ -8073.9835] [Alpha ][ 1.024630] . ( 12 sec) [ -8073.9835] [Topology ] . ( 13 sec) [ -8073.8911] [Topology ] . ( 14 sec) [ -8073.8417] [Topology ] . ( 15 sec) [ -8073.8141] [Topology ] . ( 16 sec) [ -8073.7984] [Topology ] . ( 17 sec) [ -8073.7893] [Topology ] . ( 19 sec) [ -8073.7839] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8073.783940 . ( 28 sec) [ -8073.7837] [GTR parameters ] . ( 28 sec) [ -8073.7832] [Alpha ][ 1.021692] . ( 28 sec) [ -8073.7832] [Topology ] . ( 29 sec) [ -8073.7798] [Topology ] . ( 30 sec) [ -8073.7777] [Topology ] . ( 31 sec) [ -8073.7764] [Topology ] . ( 32 sec) [ -8073.7756] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8073.775626 . ( 40 sec) [ -8073.7756] [GTR parameters ] . ( 40 sec) [ -8073.7756] [Alpha ][ 1.021692] . ( 40 sec) [ -8073.7756] [Topology ] . ( 41 sec) [ -8073.7751] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 55 sec) [ -8113.9827] [GTR parameters ] . ( 56 sec) [ -8113.8648] [Alpha ][ 1.041976] . ( 56 sec) [ -8112.9208] [ 1713] [depth= 1] . ( 56 sec) [ -8112.7853] [ 1714] [depth= 1] . ( 57 sec) [ -8111.9149] [ 1716] [depth= 1] . ( 57 sec) [ -8111.1914] [ 1714] [depth= 1] . ( 58 sec) [ -8111.1500] [ 1716] [depth= 1] . ( 58 sec) [ -8105.6202] [ 1715] [depth= 1] . ( 58 sec) [ -8105.5369] [ 1715] [depth= 1] . ( 58 sec) [ -8103.2695] [ 1716] [depth= 1] . ( 58 sec) [ -8099.2427] [ 1720] [depth= 1] . ( 58 sec) [ -8095.6583] [ 1716] [depth= 1] . ( 59 sec) [ -8093.3924] [ 1719] [depth= 1] . ( 59 sec) [ -8090.8734] [ 1716] [depth= 1] . ( 60 sec) [ -8090.7461] [ 1716] [depth= 1] . ( 60 sec) [ -8090.5215] [ 1716] [depth= 1] . ( 61 sec) [ -8074.6676] [Branch lengths ] . ( 62 sec) [ -8074.6182] [GTR parameters ] . ( 62 sec) [ -8074.5825] [Alpha ][ 1.020159] . ( 62 sec) [ -8074.4862] [ 1708] [depth= 1] . ( 67 sec) [ -8073.8581] [Branch lengths ] . ( 67 sec) [ -8073.8569] [GTR parameters ] . ( 67 sec) [ -8073.8566] [Alpha ][ 1.022149] . ( 83 sec) [ -8073.6190] [ 1714] [depth= 3] . ( 100 sec) [ -8073.3900] [Branch lengths ] . ( 101 sec) [ -8073.3810] [GTR parameters ] . ( 101 sec) [ -8073.3804] [Alpha ][ 1.019209] . ( 101 sec) [ -8073.3804] [Topology ] . ( 103 sec) [ -8073.3735] [Topology ] . ( 104 sec) [ -8073.3715] [Topology ] . ( 106 sec) [ -8073.3706] [Topology ] . ( 106 sec) [ -8073.3706] [GTR parameters ] . ( 106 sec) [ -8073.3706] [Alpha ][ 1.019209] . ( 106 sec) [ -8073.3706] [Topology ] . ( 108 sec) [ -8073.3702] [Topology ] . ( 108 sec) [ -8073.3702] [GTR parameters ] . ( 108 sec) [ -8073.3702] [Alpha ][ 1.019209] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -8073.3699] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8073.775106 . Log likelihood obtained after SPR moves : -8073.369886 . Log likelihood of the current tree: -8073.369886. . Printing the most likely tree in file 'data63.phy_phyml_tree.txt'... . Time used 0h2m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo