.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data81.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... . 322 patterns found. (out of a total of 500 sites) . 167 sites without polymorphism (33.40%). . 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=-5112.589783 . ( 1 sec) [ -5111.9426] [GTR parameters ] . ( 1 sec) [ -5111.9419] [Alpha ][ 1.004062] . ( 1 sec) [ -5111.9419] [Topology ] . ( 2 sec) [ -5099.1697] [Topology ] . ( 3 sec) [ -5097.6528] [Topology ] . ( 5 sec) [ -5097.3802] [Topology ] . ( 5 sec) [ -5097.3097] [Topology ] . ( 6 sec) [ -5097.2897] [Topology ] . ( 7 sec) [ -5097.2835] [Topology ] . ( 8 sec) [ -5097.2815] [Topology ] . ( 9 sec) [ -5097.2806] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5097.280569 . ( 14 sec) [ -5097.2553] [GTR parameters ] . ( 14 sec) [ -5097.2534] [Alpha ][ 1.011239] . ( 15 sec) [ -5097.2534] [Topology ] . ( 15 sec) [ -5097.2527] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5097.252714 . ( 21 sec) [ -5097.2527] [GTR parameters ] . ( 21 sec) [ -5097.2527] [Alpha ][ 1.011239] . ( 21 sec) [ -5097.2527] [Topology ] . ( 22 sec) [ -5097.2525] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 32 sec) [ -5111.9426] [GTR parameters ] . ( 32 sec) [ -5111.9419] [Alpha ][ 1.004062] . ( 33 sec) [ -5110.8380] [ 877] [depth= 1] . ( 33 sec) [ -5110.6570] [ 876] [depth= 1] . ( 33 sec) [ -5109.6050] [ 877] [depth= 1] . ( 33 sec) [ -5109.3363] [ 876] [depth= 1] . ( 34 sec) [ -5108.8254] [ 876] [depth= 1] . ( 34 sec) [ -5108.7209] [ 876] [depth= 1] . ( 34 sec) [ -5108.6451] [ 876] [depth= 1] . ( 34 sec) [ -5108.2606] [ 876] [depth= 1] . ( 34 sec) [ -5108.2137] [ 876] [depth= 1] . ( 34 sec) [ -5108.0193] [ 876] [depth= 1] . ( 34 sec) [ -5107.4271] [ 876] [depth= 1] . ( 35 sec) [ -5107.4005] [ 876] [depth= 1] . ( 35 sec) [ -5107.2415] [ 876] [depth= 1] . ( 35 sec) [ -5106.8456] [ 876] [depth= 1] . ( 35 sec) [ -5106.8008] [ 876] [depth= 1] . ( 35 sec) [ -5106.7321] [ 876] [depth= 1] . ( 35 sec) [ -5106.7009] [ 876] [depth= 1] . ( 37 sec) [ -5103.9016] [ 875] [depth= 1] . ( 38 sec) [ -5102.1506] [ 875] [depth= 1] . ( 40 sec) [ -5097.3507] [Branch lengths ] . ( 40 sec) [ -5097.3285] [GTR parameters ] . ( 40 sec) [ -5097.3277] [Alpha ][ 1.008490] . ( 47 sec) [ -5097.2653] [Branch lengths ] . ( 69 sec) [ -5097.2621] [Branch lengths ] . ( 69 sec) [ -5097.2621] [Topology ] . ( 70 sec) [ -5097.2619] [Topology ] . ( 70 sec) [ -5097.2618] [GTR parameters ] . ( 70 sec) [ -5097.2615] [Alpha ][ 1.011143] . Checking for NNIs, optimizing five branches... . ( 74 sec) [ -5097.2524] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5097.252494 . Log likelihood obtained after SPR moves : -5097.252441 . Log likelihood of the current tree: -5097.252441. . Printing the most likely tree in file 'data81.phy_phyml_tree.txt'... . Time used 0h1m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo