.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data37.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... . 450 patterns found. (out of a total of 500 sites) . 49 sites without polymorphism (9.80%). . 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=-11647.550131 . ( 1 sec) [ -11644.9724] [GTR parameters ] . ( 1 sec) [ -11644.5594] [Alpha ][ 0.939814] . ( 1 sec) [ -11644.5594] [Topology ] . ( 2 sec) [ -11553.5851] [Topology ] . ( 3 sec) [ -11534.4428] [Topology ] . ( 4 sec) [ -11529.9584] [Topology ] . ( 5 sec) [ -11527.9639] [Topology ] . ( 6 sec) [ -11526.9049] [Topology ] . ( 6 sec) [ -11526.3062] [Topology ] . ( 7 sec) [ -11525.7263] [Topology ] . ( 8 sec) [ -11525.2686] [Topology ] . ( 9 sec) [ -11525.1291] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11525.057322 . ( 16 sec) [ -11525.0023] [GTR parameters ] . ( 16 sec) [ -11524.9751] [Alpha ][ 0.954125] . ( 16 sec) [ -11524.9751] [Topology ] . ( 17 sec) [ -11524.9319] [Topology ] . ( 18 sec) [ -11524.9078] [Topology ] . ( 19 sec) [ -11524.8939] [Topology ] . ( 20 sec) [ -11524.8857] [Topology ] . ( 21 sec) [ -11524.8809] [Topology ] . ( 21 sec) [ -11524.8780] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11524.878014 . ( 28 sec) [ -11524.8779] [GTR parameters ] . ( 28 sec) [ -11524.8779] [Alpha ][ 0.955079] . ( 28 sec) [ -11524.8779] [Topology ] . ( 29 sec) [ -11524.8761] [Topology ] . ( 30 sec) [ -11524.8751] [Topology ] . ( 30 sec) [ -11524.8745] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11524.874533 . ( 37 sec) [ -11524.8745] [GTR parameters ] . ( 37 sec) [ -11524.8745] [Alpha ][ 0.955079] . ( 37 sec) [ -11524.8745] [Topology ] . ( 38 sec) [ -11524.8742] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 51 sec) [ -11644.9724] [GTR parameters ] . ( 51 sec) [ -11644.5594] [Alpha ][ 0.939814] . ( 51 sec) [ -11643.1295] [ 2734] [depth= 2] . ( 51 sec) [ -11641.6106] [ 2733] [depth= 1] . ( 51 sec) [ -11640.1170] [ 2734] [depth= 1] . ( 51 sec) [ -11639.4533] [ 2733] [depth= 1] . ( 51 sec) [ -11637.9517] [ 2734] [depth= 1] . ( 51 sec) [ -11634.0380] [ 2733] [depth= 1] . ( 51 sec) [ -11631.9918] [ 2733] [depth= 1] . ( 52 sec) [ -11630.1070] [ 2745] [depth= 1] . ( 52 sec) [ -11630.0271] [ 2745] [depth= 1] . ( 52 sec) [ -11628.3776] [ 2745] [depth= 1] . ( 52 sec) [ -11625.2307] [ 2745] [depth= 1] . ( 52 sec) [ -11622.0834] [ 2745] [depth= 1] . ( 52 sec) [ -11605.9065] [ 2761] [depth= 1] . ( 52 sec) [ -11600.6969] [ 2764] [depth= 1] . ( 53 sec) [ -11599.2849] [ 2763] [depth= 1] . ( 53 sec) [ -11596.8586] [ 2763] [depth= 1] . ( 53 sec) [ -11593.6002] [ 2763] [depth= 2] . ( 53 sec) [ -11591.2577] [ 2770] [depth= 1] . ( 53 sec) [ -11590.9509] [ 2769] [depth= 1] . ( 53 sec) [ -11582.6558] [ 2764] [depth= 1] . ( 53 sec) [ -11580.4628] [ 2764] [depth= 1] . ( 54 sec) [ -11574.6233] [ 2764] [depth= 1] . ( 54 sec) [ -11572.7803] [ 2767] [depth= 1] . ( 54 sec) [ -11528.4191] [Branch lengths ] . ( 54 sec) [ -11528.3451] [GTR parameters ] . ( 54 sec) [ -11528.3210] [Alpha ][ 0.953445] . ( 55 sec) [ -11527.5788] [ 2755] [depth= 1] . ( 57 sec) [ -11527.3879] [ 2752] [depth= 1] . ( 58 sec) [ -11524.5705] [Branch lengths ] . ( 58 sec) [ -11524.5697] [GTR parameters ] . ( 58 sec) [ -11524.5693] [Alpha ][ 0.955074] . ( 61 sec) [ -11524.2115] [Branch lengths ] . ( 84 sec) [ -11524.1517] [Branch lengths ] . ( 84 sec) [ -11524.1517] [Topology ] . ( 84 sec) [ -11524.1424] [Topology ] . ( 85 sec) [ -11524.1386] [Topology ] . ( 86 sec) [ -11524.1366] [Topology ] . ( 87 sec) [ -11524.1354] [Topology ] . ( 88 sec) [ -11524.1347] [Topology ] . ( 88 sec) [ -11524.1345] [GTR parameters ] . ( 88 sec) [ -11524.1345] [Alpha ][ 0.956029] . ( 88 sec) [ -11524.1345] [Topology ] . ( 89 sec) [ -11524.1340] [Topology ] . ( 89 sec) [ -11524.1340] [GTR parameters ] . ( 89 sec) [ -11524.1340] [Alpha ][ 0.956029] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -11524.1330] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11524.874160 . Log likelihood obtained after SPR moves : -11524.132987 . Log likelihood of the current tree: -11524.132987. . Printing the most likely tree in file 'data37.phy_phyml_tree.txt'... . Time used 0h1m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo