.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data68.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... . 417 patterns found. (out of a total of 500 sites) . 78 sites without polymorphism (15.60%). . 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=-9047.095058 . ( 1 sec) [ -9041.3256] [GTR parameters ] . ( 1 sec) [ -9041.2523] [Alpha ][ 0.970005] . ( 1 sec) [ -9041.2523] [Topology ] . ( 2 sec) [ -8996.4322] [Topology ] . ( 3 sec) [ -8988.7327] [Topology ] . ( 3 sec) [ -8970.9581] [Topology ] . ( 4 sec) [ -8965.6059] [Topology ] . ( 5 sec) [ -8964.7395] [Topology ] . ( 6 sec) [ -8964.4999] [Topology ] . ( 6 sec) [ -8964.4081] [Topology ] . ( 7 sec) [ -8964.3656] [Topology ] . ( 8 sec) [ -8964.3441] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -8964.0843] [Topology ] . Before opt ts/t=1.000000 LK=-8964.084298 . ( 15 sec) [ -8964.0076] [GTR parameters ] . ( 15 sec) [ -8963.7412] [Alpha ][ 1.026015] . ( 15 sec) [ -8963.7412] [Topology ] . ( 16 sec) [ -8963.7104] [Topology ] . ( 17 sec) [ -8963.7021] [Topology ] . ( 18 sec) [ -8963.6987] [Topology ] . ( 18 sec) [ -8963.6971] [Topology ] . ( 19 sec) [ -8963.6963] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.696322 . ( 25 sec) [ -8963.6956] [GTR parameters ] . ( 26 sec) [ -8963.6952] [Alpha ][ 1.028310] . ( 26 sec) [ -8963.6952] [Topology ] . ( 27 sec) [ -8963.6948] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8963.694758 . ( 32 sec) [ -8963.6948] [GTR parameters ] . ( 32 sec) [ -8963.6948] [Alpha ][ 1.028310] . ( 32 sec) [ -8963.6948] [Topology ] . ( 33 sec) [ -8963.6945] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -9041.3256] [GTR parameters ] . ( 44 sec) [ -9041.2523] [Alpha ][ 0.970005] . ( 45 sec) [ -9041.1947] [ 1929] [depth= 1] . ( 45 sec) [ -9040.9304] [ 1932] [depth= 1] . ( 45 sec) [ -9016.4106] [ 1924] [depth= 3] . ( 45 sec) [ -9015.0278] [ 1922] [depth= 2] . ( 45 sec) [ -9014.4302] [ 1926] [depth= 1] . ( 45 sec) [ -9013.9366] [ 1922] [depth= 1] . ( 45 sec) [ -9013.8608] [ 1924] [depth= 2] . ( 45 sec) [ -9012.5102] [ 1922] [depth= 1] . ( 45 sec) [ -9012.1884] [ 1924] [depth= 1] . ( 46 sec) [ -9009.4524] [ 1924] [depth= 1] . ( 46 sec) [ -9009.2256] [ 1923] [depth= 1] . ( 46 sec) [ -9007.0731] [ 1924] [depth= 1] . ( 46 sec) [ -9005.5487] [ 1924] [depth= 1] . ( 46 sec) [ -9002.1786] [ 1922] [depth= 1] . ( 46 sec) [ -8999.7411] [ 1922] [depth= 1] . ( 46 sec) [ -8999.7100] [ 1927] [depth= 1] . ( 47 sec) [ -8998.1731] [ 1928] [depth= 1] . ( 47 sec) [ -8997.9680] [ 1922] [depth= 2] . ( 47 sec) [ -8993.5245] [ 1918] [depth= 1] . ( 47 sec) [ -8992.0611] [ 1923] [depth= 1] . ( 47 sec) [ -8991.6815] [ 1918] [depth= 1] . ( 48 sec) [ -8969.9836] [Branch lengths ] . ( 48 sec) [ -8969.8936] [GTR parameters ] . ( 48 sec) [ -8969.7414] [Alpha ][ 1.012304] . ( 48 sec) [ -8968.6087] [ 1914] [depth= 1] . ( 49 sec) [ -8967.5179] [ 1912] [depth= 1] . ( 49 sec) [ -8967.3678] [ 1912] [depth= 1] . ( 51 sec) [ -8964.6489] [Branch lengths ] . ( 52 sec) [ -8964.6273] [GTR parameters ] . ( 52 sec) [ -8964.6064] [Alpha ][ 1.028833] . ( 52 sec) [ -8964.5824] [ 1913] [depth= 1] . ( 55 sec) [ -8964.3557] [Branch lengths ] . ( 55 sec) [ -8964.3554] [GTR parameters ] . ( 55 sec) [ -8964.3554] [Alpha ][ 1.028833] . ( 77 sec) [ -8964.3272] [Branch lengths ] . ( 77 sec) [ -8964.3272] [Topology ] . ( 78 sec) [ -8964.1244] [Topology ] . ( 78 sec) [ -8964.0823] [Topology ] . ( 79 sec) [ -8964.0739] [Topology ] . ( 80 sec) [ -8964.0716] [Topology ] . ( 81 sec) [ -8964.0708] [Topology ] . ( 82 sec) [ -8964.0693] [GTR parameters ] . ( 82 sec) [ -8964.0693] [Alpha ][ 1.027777] . ( 82 sec) [ -8964.0693] [Topology ] . ( 83 sec) [ -8964.0690] [Topology ] . ( 83 sec) [ -8964.0690] [GTR parameters ] . ( 83 sec) [ -8964.0690] [Alpha ][ 1.027777] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8963.694528 . Log likelihood obtained after SPR moves : -8964.068967 . Log likelihood of the current tree: -8963.694528. . Printing the most likely tree in file 'data68.phy_phyml_tree.txt'... . Time used 0h1m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo