.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data24.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... . 188 patterns found. (out of a total of 500 sites) . 297 sites without polymorphism (59.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 4Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-2563.890838 . ( 1 sec) [ -2561.1245] [GTR parameters ] . ( 1 sec) [ -2561.1122] [Alpha ][ 0.963403] . ( 1 sec) [ -2561.1122] [Topology ] . ( 1 sec) [ -2557.0915] [Topology ] . ( 2 sec) [ -2556.3937] [Topology ] . ( 2 sec) [ -2556.2503] [Topology ] . ( 2 sec) [ -2556.2171] [Topology ] . ( 3 sec) [ -2556.2091] [Topology ] . ( 3 sec) [ -2556.2070] [Topology ] . ( 4 sec) [ -2556.2063] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2556.206263 . ( 7 sec) [ -2556.1709] [GTR parameters ] . ( 7 sec) [ -2556.1709] [Alpha ][ 0.961410] . ( 7 sec) [ -2556.1709] [Topology ] . ( 7 sec) [ -2556.1706] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2556.170629 . ( 11 sec) [ -2556.1706] [GTR parameters ] . ( 11 sec) [ -2556.1706] [Alpha ][ 0.961410] . ( 11 sec) [ -2556.1706] [Topology ] . ( 12 sec) [ -2556.1706] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 20 sec) [ -2561.1245] [GTR parameters ] . ( 20 sec) [ -2561.1122] [Alpha ][ 0.963403] . ( 20 sec) [ -2560.9395] [ 317] [depth= 1] . ( 20 sec) [ -2560.7924] [ 317] [depth= 1] . ( 21 sec) [ -2560.6722] [ 317] [depth= 1] . ( 21 sec) [ -2560.6174] [ 317] [depth= 1] . ( 22 sec) [ -2560.5276] [ 317] [depth= 1] . ( 22 sec) [ -2560.3906] [ 317] [depth= 1] . ( 22 sec) [ -2560.3155] [ 317] [depth= 1] . ( 23 sec) [ -2560.2124] [ 317] [depth= 1] . ( 23 sec) [ -2560.1996] [ 317] [depth= 1] . ( 23 sec) [ -2559.9676] [ 317] [depth= 1] . ( 23 sec) [ -2559.8910] [ 317] [depth= 1] . ( 24 sec) [ -2559.4269] [ 317] [depth= 2] . ( 25 sec) [ -2559.3169] [ 317] [depth= 2] . ( 25 sec) [ -2557.5061] [ 317] [depth= 2] . ( 25 sec) [ -2557.4937] [ 317] [depth= 2] . ( 26 sec) [ -2556.7195] [ 317] [depth= 1] . ( 26 sec) [ -2556.7041] [ 317] [depth= 1] . ( 26 sec) [ -2556.4906] [ 317] [depth= 1] . ( 27 sec) [ -2555.9054] [Branch lengths ] . ( 28 sec) [ -2555.8171] [GTR parameters ] . ( 28 sec) [ -2555.8163] [Alpha ][ 0.954713] . ( 30 sec) [ -2555.7941] [ 317] [depth= 1] . ( 36 sec) [ -2555.7773] [Branch lengths ] . ( 36 sec) [ -2555.7773] [GTR parameters ] . ( 36 sec) [ -2555.7773] [Alpha ][ 0.954713] . ( 51 sec) [ -2555.7772] [Branch lengths ] . ( 51 sec) [ -2555.7772] [Topology ] . ( 52 sec) [ -2555.7772] [Topology ] . ( 52 sec) [ -2555.7771] [GTR parameters ] . ( 52 sec) [ -2555.7771] [Alpha ][ 0.955667] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2556.170608 . Log likelihood obtained after SPR moves : -2555.777145 . Log likelihood of the current tree: -2555.777145. . Printing the most likely tree in file 'data24.phy_phyml_tree.txt'... . Time used 0h0m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo