.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data80.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... . 409 patterns found. (out of a total of 500 sites) . 90 sites without polymorphism (18.00%). . 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=-9414.383223 . ( 2 sec) [ -9401.9651] [GTR parameters ] . ( 2 sec) [ -9400.9169] [Alpha ][ 0.893448] . ( 2 sec) [ -9400.9169] [Topology ] . ( 3 sec) [ -9356.1912] [Topology ] . ( 5 sec) [ -9350.5757] [Topology ] . ( 6 sec) [ -9349.4320] [Topology ] . ( 7 sec) [ -9348.9751] [Topology ] . ( 8 sec) [ -9348.7678] [Topology ] . ( 8 sec) [ -9348.6682] [Topology ] . ( 9 sec) [ -9348.6185] [Topology ] . ( 10 sec) [ -9348.5933] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.593346 . ( 17 sec) [ -9348.5517] [GTR parameters ] . ( 17 sec) [ -9348.5034] [Alpha ][ 0.914037] . ( 17 sec) [ -9348.5034] [Topology ] . ( 19 sec) [ -9348.4836] [Topology ] . ( 20 sec) [ -9348.4746] [Topology ] . ( 21 sec) [ -9348.4701] [Topology ] . ( 23 sec) [ -9348.4678] [Topology ] . ( 24 sec) [ -9348.4666] [Topology ] . ( 26 sec) [ -9348.4660] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.466014 . ( 35 sec) [ -9348.4660] [GTR parameters ] . ( 35 sec) [ -9348.4650] [Alpha ][ 0.917096] . ( 35 sec) [ -9348.4650] [Topology ] . ( 36 sec) [ -9348.4645] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9348.464522 . ( 45 sec) [ -9348.4645] [GTR parameters ] . ( 45 sec) [ -9348.4645] [Alpha ][ 0.917096] . ( 45 sec) [ -9348.4645] [Topology ] . ( 46 sec) [ -9348.4643] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 65 sec) [ -9401.9651] [GTR parameters ] . ( 65 sec) [ -9400.9169] [Alpha ][ 0.893448] . ( 67 sec) [ -9397.6475] [ 2046] [depth= 1] . ( 68 sec) [ -9396.2183] [ 2042] [depth= 1] . ( 68 sec) [ -9395.8159] [ 2046] [depth= 1] . ( 68 sec) [ -9395.2251] [ 2045] [depth= 1] . ( 69 sec) [ -9394.6189] [ 2048] [depth= 1] . ( 69 sec) [ -9390.0440] [ 2045] [depth= 1] . ( 69 sec) [ -9384.6865] [ 2043] [depth= 1] . ( 69 sec) [ -9384.3506] [ 2043] [depth= 1] . ( 69 sec) [ -9383.7166] [ 2043] [depth= 1] . ( 69 sec) [ -9382.9420] [ 2040] [depth= 1] . ( 70 sec) [ -9352.8625] [Branch lengths ] . ( 71 sec) [ -9352.8058] [GTR parameters ] . ( 71 sec) [ -9352.7891] [Alpha ][ 0.906140] . ( 75 sec) [ -9349.7908] [Branch lengths ] . ( 101 sec) [ -9349.5138] [Branch lengths ] . ( 101 sec) [ -9349.5138] [Topology ] . ( 103 sec) [ -9349.4923] [Topology ] . ( 104 sec) [ -9349.4850] [Topology ] . ( 105 sec) [ -9349.4817] [Topology ] . ( 107 sec) [ -9349.4800] [Topology ] . ( 108 sec) [ -9349.4792] [Topology ] . ( 108 sec) [ -9349.4774] [GTR parameters ] . ( 108 sec) [ -9349.4634] [Alpha ][ 0.917735] . ( 108 sec) [ -9349.4634] [Topology ] . ( 110 sec) [ -9349.4622] [Topology ] . ( 111 sec) [ -9349.4618] [Topology ] . ( 111 sec) [ -9349.4618] [GTR parameters ] . ( 111 sec) [ -9349.4618] [Alpha ][ 0.917735] . ( 111 sec) [ -9349.4618] [Topology ] . ( 112 sec) [ -9349.4616] [Topology ] . ( 112 sec) [ -9349.4616] [GTR parameters ] . ( 112 sec) [ -9349.4616] [Alpha ][ 0.917735] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -9348.4715] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9348.464309 . Log likelihood obtained after SPR moves : -9348.471488 . Log likelihood of the current tree: -9348.464309. . Printing the most likely tree in file 'data80.phy_phyml_tree.txt'... . Time used 0h2m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo