.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data70.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... . 363 patterns found. (out of a total of 500 sites) . 131 sites without polymorphism (26.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-6467.237369 . ( 1 sec) [ -6462.6699] [GTR parameters ] . ( 1 sec) [ -6462.3038] [Alpha ][ 0.921661] . ( 1 sec) [ -6462.3038] [Topology ] . ( 2 sec) [ -6425.9501] [Topology ] . ( 3 sec) [ -6416.9065] [Topology ] . ( 4 sec) [ -6415.5687] [Topology ] . ( 5 sec) [ -6415.2570] [Topology ] . ( 5 sec) [ -6415.1499] [Topology ] . ( 6 sec) [ -6415.1064] [Topology ] . ( 7 sec) [ -6415.0871] [Topology ] . ( 8 sec) [ -6415.0781] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6415.078064 . ( 12 sec) [ -6415.0578] [GTR parameters ] . ( 12 sec) [ -6415.0525] [Alpha ][ 0.930619] . ( 12 sec) [ -6415.0525] [Topology ] . ( 13 sec) [ -6415.0475] [Topology ] . ( 14 sec) [ -6415.0453] [Topology ] . ( 14 sec) [ -6415.0442] [Topology ] . ( 15 sec) [ -6415.0436] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6415.043635 . ( 20 sec) [ -6415.0436] [GTR parameters ] . ( 20 sec) [ -6415.0436] [Alpha ][ 0.931550] . ( 20 sec) [ -6415.0436] [Topology ] . ( 20 sec) [ -6415.0433] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 30 sec) [ -6462.6699] [GTR parameters ] . ( 30 sec) [ -6462.3038] [Alpha ][ 0.921661] . ( 30 sec) [ -6461.4406] [ 1246] [depth= 1] . ( 30 sec) [ -6456.1352] [ 1247] [depth= 1] . ( 30 sec) [ -6445.7262] [ 1243] [depth= 1] . ( 30 sec) [ -6444.4661] [ 1241] [depth= 1] . ( 30 sec) [ -6442.0207] [ 1243] [depth= 1] . ( 30 sec) [ -6439.4050] [ 1241] [depth= 1] . ( 31 sec) [ -6435.9409] [ 1244] [depth= 1] . ( 31 sec) [ -6435.3430] [ 1240] [depth= 1] . ( 31 sec) [ -6429.9547] [ 1252] [depth= 1] . ( 31 sec) [ -6429.0249] [ 1252] [depth= 1] . ( 31 sec) [ -6428.9904] [ 1252] [depth= 1] . ( 31 sec) [ -6428.8664] [ 1252] [depth= 1] . ( 31 sec) [ -6428.7780] [ 1252] [depth= 1] . ( 31 sec) [ -6428.3956] [ 1252] [depth= 1] . ( 32 sec) [ -6428.3071] [ 1252] [depth= 1] . ( 32 sec) [ -6427.8907] [ 1254] [depth= 1] . ( 32 sec) [ -6427.0708] [ 1252] [depth= 1] . ( 32 sec) [ -6426.5595] [ 1253] [depth= 1] . ( 33 sec) [ -6418.9227] [Branch lengths ] . ( 33 sec) [ -6418.8818] [GTR parameters ] . ( 34 sec) [ -6418.8815] [Alpha ][ 0.923677] . ( 34 sec) [ -6417.1265] [ 1241] [depth= 1] . ( 37 sec) [ -6415.1542] [Branch lengths ] . ( 37 sec) [ -6415.1508] [GTR parameters ] . ( 37 sec) [ -6415.1482] [Alpha ][ 0.929877] . ( 41 sec) [ -6415.0460] [Branch lengths ] . ( 61 sec) [ -6415.0435] [Branch lengths ] . ( 61 sec) [ -6415.0435] [Topology ] . ( 62 sec) [ -6415.0434] [Topology ] . ( 62 sec) [ -6415.0433] [GTR parameters ] . ( 62 sec) [ -6415.0431] [Alpha ][ 0.931570] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6415.043293 . Log likelihood obtained after SPR moves : -6415.043112 . Log likelihood of the current tree: -6415.043112. . Printing the most likely tree in file 'data70.phy_phyml_tree.txt'... . Time used 0h1m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo