.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data54.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... . 272 patterns found. (out of a total of 500 sites) . 217 sites without polymorphism (43.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4435.128913 . ( 1 sec) [ -4434.0770] [GTR parameters ] . ( 1 sec) [ -4431.3121] [Alpha ][ 0.745784] . ( 1 sec) [ -4431.3121] [Topology ] . ( 1 sec) [ -4425.7334] [Topology ] . ( 2 sec) [ -4425.1425] [Topology ] . ( 3 sec) [ -4424.9939] [Topology ] . ( 3 sec) [ -4424.9398] [Topology ] . ( 4 sec) [ -4424.9144] [Topology ] . ( 5 sec) [ -4424.8984] [Topology ] . ( 5 sec) [ -4424.8861] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4424.886111 . ( 9 sec) [ -4424.8579] [GTR parameters ] . ( 9 sec) [ -4424.8340] [Alpha ][ 0.764840] . ( 9 sec) [ -4424.8340] [Topology ] . ( 10 sec) [ -4424.8188] [Topology ] . ( 10 sec) [ -4424.8065] [Topology ] . ( 11 sec) [ -4424.7967] [Topology ] . ( 11 sec) [ -4424.7921] [Topology ] . ( 12 sec) [ -4424.7910] [Topology ] . ( 12 sec) [ -4424.7907] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4424.790725 . ( 16 sec) [ -4424.7904] [GTR parameters ] . ( 16 sec) [ -4424.7902] [Alpha ][ 0.766147] . ( 16 sec) [ -4424.7902] [Topology ] . ( 16 sec) [ -4424.7901] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 24 sec) [ -4434.0770] [GTR parameters ] . ( 24 sec) [ -4431.3121] [Alpha ][ 0.745784] . ( 24 sec) [ -4430.8322] [ 683] [depth= 1] . ( 25 sec) [ -4430.6063] [ 684] [depth= 1] . ( 25 sec) [ -4429.0542] [ 684] [depth= 1] . ( 25 sec) [ -4429.0222] [ 683] [depth= 1] . ( 26 sec) [ -4429.0106] [ 683] [depth= 1] . ( 26 sec) [ -4428.7210] [ 685] [depth= 1] . ( 26 sec) [ -4428.6819] [ 683] [depth= 1] . ( 26 sec) [ -4425.8767] [Branch lengths ] . ( 27 sec) [ -4425.8604] [GTR parameters ] . ( 27 sec) [ -4425.8410] [Alpha ][ 0.762873] . ( 28 sec) [ -4425.7080] [ 683] [depth= 1] . ( 29 sec) [ -4425.0740] [Branch lengths ] . ( 29 sec) [ -4425.0712] [GTR parameters ] . ( 29 sec) [ -4425.0708] [Alpha ][ 0.765193] . ( 45 sec) [ -4425.0308] [Branch lengths ] . ( 45 sec) [ -4425.0308] [Topology ] . ( 45 sec) [ -4425.0143] [Topology ] . ( 46 sec) [ -4425.0024] [Topology ] . ( 46 sec) [ -4424.9908] [Topology ] . ( 47 sec) [ -4424.9836] [Topology ] . ( 47 sec) [ -4424.9815] [Topology ] . ( 48 sec) [ -4424.9810] [Topology ] . ( 48 sec) [ -4424.9796] [GTR parameters ] . ( 48 sec) [ -4424.9796] [Alpha ][ 0.765193] . ( 48 sec) [ -4424.9796] [Topology ] . ( 49 sec) [ -4424.9795] [Topology ] . ( 49 sec) [ -4424.9795] [GTR parameters ] . ( 49 sec) [ -4424.9795] [Alpha ][ 0.765193] . Checking for NNIs, optimizing five branches... . ( 52 sec) [ -4424.7911] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4424.790112 . Log likelihood obtained after SPR moves : -4424.791060 . Log likelihood of the current tree: -4424.790112. . Printing the most likely tree in file 'data54.phy_phyml_tree.txt'... . Time used 0h0m56s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo