.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data51.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... . 400 patterns found. (out of a total of 500 sites) . 96 sites without polymorphism (19.20%). . 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=-8457.231258 . ( 1 sec) [ -8451.4738] [GTR parameters ] . ( 1 sec) [ -8450.4220] [Alpha ][ 0.890232] . ( 1 sec) [ -8450.4220] [Topology ] . ( 2 sec) [ -8419.1973] [Topology ] . ( 4 sec) [ -8414.2934] [Topology ] . ( 5 sec) [ -8413.2941] [Topology ] . ( 6 sec) [ -8412.8931] [Topology ] . ( 6 sec) [ -8412.7066] [Topology ] . ( 7 sec) [ -8412.6141] [Topology ] . ( 8 sec) [ -8412.5670] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8412.566967 . ( 16 sec) [ -8412.5049] [GTR parameters ] . ( 16 sec) [ -8412.2671] [Alpha ][ 0.939211] . ( 16 sec) [ -8412.2671] [Topology ] . ( 17 sec) [ -8412.2237] [Topology ] . ( 19 sec) [ -8412.2037] [Topology ] . ( 20 sec) [ -8412.1936] [Topology ] . ( 22 sec) [ -8412.1885] [Topology ] . ( 23 sec) [ -8412.1858] [Topology ] . ( 24 sec) [ -8412.1844] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8412.184397 . ( 32 sec) [ -8412.1844] [GTR parameters ] . ( 32 sec) [ -8412.1835] [Alpha ][ 0.942233] . ( 32 sec) [ -8412.1835] [Topology ] . ( 33 sec) [ -8412.1826] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8412.182644 . ( 39 sec) [ -8412.1826] [GTR parameters ] . ( 39 sec) [ -8412.1826] [Alpha ][ 0.942233] . ( 39 sec) [ -8412.1826] [Topology ] . ( 40 sec) [ -8412.1822] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 55 sec) [ -8451.4738] [GTR parameters ] . ( 56 sec) [ -8450.4220] [Alpha ][ 0.890232] . ( 57 sec) [ -8450.2996] [ 1724] [depth= 1] . ( 57 sec) [ -8450.0608] [ 1725] [depth= 1] . ( 57 sec) [ -8449.6502] [ 1724] [depth= 1] . ( 57 sec) [ -8449.1991] [ 1726] [depth= 1] . ( 57 sec) [ -8448.3430] [ 1729] [depth= 1] . ( 58 sec) [ -8447.9667] [ 1734] [depth= 1] . ( 58 sec) [ -8439.5611] [ 1735] [depth= 1] . ( 58 sec) [ -8439.4611] [ 1734] [depth= 1] . ( 58 sec) [ -8438.6771] [ 1729] [depth= 1] . ( 58 sec) [ -8438.3392] [ 1728] [depth= 1] . ( 60 sec) [ -8436.0651] [ 1729] [depth= 1] . ( 60 sec) [ -8415.4866] [Branch lengths ] . ( 61 sec) [ -8415.4408] [GTR parameters ] . ( 61 sec) [ -8415.3094] [Alpha ][ 0.926795] . ( 63 sec) [ -8415.2778] [ 1728] [depth= 1] . ( 63 sec) [ -8415.1816] [ 1727] [depth= 1] . ( 64 sec) [ -8414.6653] [ 1722] [depth= 1] . ( 67 sec) [ -8412.7777] [Branch lengths ] . ( 68 sec) [ -8412.7730] [GTR parameters ] . ( 68 sec) [ -8412.7603] [Alpha ][ 0.938628] . ( 73 sec) [ -8412.5805] [Branch lengths ] . ( 79 sec) [ -8412.5329] [ 1722] [depth= 1] . ( 81 sec) [ -8412.3178] [ 1718] [depth= 1] . ( 104 sec) [ -8412.1963] [Branch lengths ] . ( 104 sec) [ -8412.1935] [GTR parameters ] . ( 104 sec) [ -8412.1922] [Alpha ][ 0.942378] . ( 104 sec) [ -8412.1922] [Topology ] . ( 105 sec) [ -8412.1851] [Topology ] . ( 106 sec) [ -8412.1834] [Topology ] . ( 108 sec) [ -8412.1826] [Topology ] . ( 108 sec) [ -8412.1826] [GTR parameters ] . ( 108 sec) [ -8412.1826] [Alpha ][ 0.942378] . ( 108 sec) [ -8412.1826] [Topology ] . ( 109 sec) [ -8412.1821] [Topology ] . ( 110 sec) [ -8412.1821] [GTR parameters ] . ( 110 sec) [ -8412.1821] [Alpha ][ 0.942378] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8412.182208 . Log likelihood obtained after SPR moves : -8412.182128 . Log likelihood of the current tree: -8412.182128. . Printing the most likely tree in file 'data51.phy_phyml_tree.txt'... . Time used 0h1m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo