.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data91.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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 436 patterns found. (out of a total of 500 sites) . 54 sites without polymorphism (10.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9969.108107 . ( 1 sec) [ -9965.2502] [GTR parameters ] . ( 1 sec) [ -9965.2156] [Alpha ][ 0.980951] . ( 1 sec) [ -9965.2156] [Topology ] . ( 2 sec) [ -9880.6273] [Topology ] . ( 3 sec) [ -9863.6476] [Topology ] . ( 4 sec) [ -9857.7578] [Topology ] . ( 4 sec) [ -9852.1065] [Topology ] . ( 5 sec) [ -9850.2448] [Topology ] . ( 6 sec) [ -9849.4495] [Topology ] . ( 7 sec) [ -9849.0220] [Topology ] . ( 8 sec) [ -9848.7813] [Topology ] . ( 8 sec) [ -9848.6392] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -9848.2987] [Topology ] . Before opt ts/t=1.000000 LK=-9848.298747 . ( 17 sec) [ -9848.1993] [GTR parameters ] . ( 17 sec) [ -9847.9291] [Alpha ][ 0.933397] . ( 17 sec) [ -9847.9291] [Topology ] . ( 18 sec) [ -9847.8717] [Topology ] . ( 19 sec) [ -9847.8482] [Topology ] . ( 20 sec) [ -9847.8347] [Topology ] . ( 20 sec) [ -9847.8264] [Topology ] . ( 21 sec) [ -9847.8212] [Topology ] . ( 22 sec) [ -9847.8178] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.817810 . ( 29 sec) [ -9847.8160] [GTR parameters ] . ( 29 sec) [ -9847.8138] [Alpha ][ 0.929063] . ( 29 sec) [ -9847.8138] [Topology ] . ( 30 sec) [ -9847.8113] [Topology ] . ( 31 sec) [ -9847.8097] [Topology ] . ( 31 sec) [ -9847.8086] [Topology ] . ( 32 sec) [ -9847.8079] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9847.807881 . ( 39 sec) [ -9847.8078] [GTR parameters ] . ( 39 sec) [ -9847.8078] [Alpha ][ 0.929063] . ( 39 sec) [ -9847.8078] [Topology ] . ( 40 sec) [ -9847.8073] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9847.807318. . Printing the most likely tree in file 'data91.phy_phyml_tree.txt'... . Time used 0h0m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo