.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data28.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... . 421 patterns found. (out of a total of 500 sites) . 74 sites without polymorphism (14.80%). . 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=-9517.729777 . ( 0 sec) [ -9512.4274] [GTR parameters ] . ( 1 sec) [ -9512.2160] [Alpha ][ 0.951124] . ( 1 sec) [ -9512.2160] [Topology ] . ( 1 sec) [ -9481.7224] [Topology ] . ( 2 sec) [ -9477.1726] [Topology ] . ( 3 sec) [ -9475.9502] [Topology ] . ( 4 sec) [ -9475.4351] [Topology ] . ( 5 sec) [ -9475.1891] [Topology ] . ( 6 sec) [ -9475.0652] [Topology ] . ( 6 sec) [ -9475.0016] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9475.001637 . ( 13 sec) [ -9474.8908] [GTR parameters ] . ( 13 sec) [ -9474.5736] [Alpha ][ 1.008942] . ( 13 sec) [ -9474.5736] [Topology ] . ( 14 sec) [ -9474.5046] [Topology ] . ( 15 sec) [ -9474.4727] [Topology ] . ( 15 sec) [ -9474.4565] [Topology ] . ( 16 sec) [ -9474.4482] [Topology ] . ( 17 sec) [ -9474.4439] [Topology ] . ( 18 sec) [ -9474.4417] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9474.441742 . ( 24 sec) [ -9474.4413] [GTR parameters ] . ( 24 sec) [ -9474.4384] [Alpha ][ 1.014807] . ( 24 sec) [ -9474.4384] [Topology ] . ( 25 sec) [ -9474.4368] [Topology ] . ( 26 sec) [ -9474.4361] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9474.436096 . ( 31 sec) [ -9474.4361] [GTR parameters ] . ( 32 sec) [ -9474.4361] [Alpha ][ 1.014807] . ( 32 sec) [ -9474.4361] [Topology ] . ( 32 sec) [ -9474.4357] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 45 sec) [ -9512.4274] [GTR parameters ] . ( 45 sec) [ -9512.2160] [Alpha ][ 0.951124] . ( 45 sec) [ -9511.2588] [ 2039] [depth= 1] . ( 46 sec) [ -9510.0321] [ 2039] [depth= 1] . ( 46 sec) [ -9509.4415] [ 2044] [depth= 1] . ( 46 sec) [ -9509.2955] [ 2043] [depth= 1] . ( 46 sec) [ -9509.0728] [ 2044] [depth= 1] . ( 47 sec) [ -9507.7938] [ 2049] [depth= 1] . ( 47 sec) [ -9507.0333] [ 2042] [depth= 1] . ( 47 sec) [ -9505.5483] [ 2040] [depth= 1] . ( 47 sec) [ -9504.0519] [ 2042] [depth= 1] . ( 47 sec) [ -9503.6797] [ 2044] [depth= 1] . ( 47 sec) [ -9501.7307] [ 2042] [depth= 1] . ( 47 sec) [ -9500.4782] [ 2045] [depth= 2] . ( 47 sec) [ -9500.0698] [ 2046] [depth= 1] . ( 47 sec) [ -9499.3692] [ 2044] [depth= 2] . ( 47 sec) [ -9498.5631] [ 2048] [depth= 1] . ( 48 sec) [ -9497.9218] [ 2049] [depth= 1] . ( 48 sec) [ -9482.2410] [Branch lengths ] . ( 48 sec) [ -9482.1601] [GTR parameters ] . ( 49 sec) [ -9481.9413] [Alpha ][ 0.999289] . ( 50 sec) [ -9480.1115] [ 2051] [depth= 1] . ( 51 sec) [ -9480.0723] [ 2046] [depth= 1] . ( 52 sec) [ -9477.8086] [Branch lengths ] . ( 52 sec) [ -9477.7994] [GTR parameters ] . ( 52 sec) [ -9477.7926] [Alpha ][ 1.008104] . ( 55 sec) [ -9477.6160] [ 2048] [depth= 2] . ( 56 sec) [ -9477.1848] [ 2048] [depth= 1] . ( 56 sec) [ -9476.8434] [Branch lengths ] . ( 56 sec) [ -9476.8412] [GTR parameters ] . ( 57 sec) [ -9476.8401] [Alpha ][ 1.011670] . ( 61 sec) [ -9475.9728] [ 2045] [depth= 1] . ( 79 sec) [ -9475.7123] [Branch lengths ] . ( 79 sec) [ -9475.7112] [GTR parameters ] . ( 79 sec) [ -9475.7112] [Alpha ][ 1.011670] . ( 100 sec) [ -9475.7024] [Branch lengths ] . ( 100 sec) [ -9475.7024] [Topology ] . ( 101 sec) [ -9475.0963] [Topology ] . ( 102 sec) [ -9475.0575] [Topology ] . ( 102 sec) [ -9475.0541] [Topology ] . ( 103 sec) [ -9475.0535] [Topology ] . ( 104 sec) [ -9475.0521] [GTR parameters ] . ( 104 sec) [ -9475.0519] [Alpha ][ 1.013113] . ( 104 sec) [ -9475.0519] [Topology ] . ( 105 sec) [ -9475.0518] [Topology ] . ( 105 sec) [ -9475.0518] [GTR parameters ] . ( 105 sec) [ -9475.0518] [Alpha ][ 1.013113] . Checking for NNIs, optimizing five branches... . ( 111 sec) [ -9473.7597] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9474.435707 . Log likelihood obtained after SPR moves : -9473.759734 . Log likelihood of the current tree: -9473.759734. . Printing the most likely tree in file 'data28.phy_phyml_tree.txt'... . Time used 0h1m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo