.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data53.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... . 429 patterns found. (out of a total of 500 sites) . 66 sites without polymorphism (13.20%). . 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=-9648.148083 . ( 1 sec) [ -9645.7865] [GTR parameters ] . ( 1 sec) [ -9645.7819] [Alpha ][ 0.992321] . ( 1 sec) [ -9645.7819] [Topology ] . ( 2 sec) [ -9563.6932] [Topology ] . ( 3 sec) [ -9549.6521] [Topology ] . ( 4 sec) [ -9546.6529] [Topology ] . ( 5 sec) [ -9545.4735] [Topology ] . ( 6 sec) [ -9544.9102] [Topology ] . ( 7 sec) [ -9544.6138] [Topology ] . ( 7 sec) [ -9544.4490] [Topology ] . ( 8 sec) [ -9544.3556] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.355619 . ( 16 sec) [ -9544.3056] [GTR parameters ] . ( 16 sec) [ -9544.1564] [Alpha ][ 0.953985] . ( 16 sec) [ -9544.1564] [Topology ] . ( 16 sec) [ -9544.0946] [Topology ] . ( 17 sec) [ -9544.0660] [Topology ] . ( 18 sec) [ -9544.0497] [Topology ] . ( 19 sec) [ -9544.0399] [Topology ] . ( 20 sec) [ -9544.0336] [Topology ] . ( 20 sec) [ -9544.0296] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.029640 . ( 27 sec) [ -9544.0293] [GTR parameters ] . ( 27 sec) [ -9544.0281] [Alpha ][ 0.950438] . ( 27 sec) [ -9544.0281] [Topology ] . ( 28 sec) [ -9544.0253] [Topology ] . ( 28 sec) [ -9544.0235] [Topology ] . ( 29 sec) [ -9544.0223] [Topology ] . ( 30 sec) [ -9544.0215] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9544.021461 . ( 36 sec) [ -9544.0215] [GTR parameters ] . ( 36 sec) [ -9544.0215] [Alpha ][ 0.950438] . ( 36 sec) [ -9544.0215] [Topology ] . ( 37 sec) [ -9544.0209] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -9645.7865] [GTR parameters ] . ( 51 sec) [ -9645.7819] [Alpha ][ 0.992321] . ( 51 sec) [ -9644.2995] [ 2152] [depth= 1] . ( 51 sec) [ -9641.9088] [ 2151] [depth= 1] . ( 51 sec) [ -9641.3366] [ 2152] [depth= 1] . ( 51 sec) [ -9639.9005] [ 2147] [depth= 1] . ( 51 sec) [ -9637.0774] [ 2146] [depth= 1] . ( 51 sec) [ -9636.7170] [ 2148] [depth= 1] . ( 51 sec) [ -9635.4102] [ 2152] [depth= 1] . ( 51 sec) [ -9633.6675] [ 2157] [depth= 3] . ( 51 sec) [ -9632.4627] [ 2148] [depth= 2] . ( 51 sec) [ -9629.2827] [ 2144] [depth= 2] . ( 51 sec) [ -9627.6369] [ 2147] [depth= 2] . ( 51 sec) [ -9615.3235] [ 2153] [depth= 1] . ( 51 sec) [ -9614.1674] [ 2152] [depth= 1] . ( 52 sec) [ -9597.7284] [ 2149] [depth= 1] . ( 52 sec) [ -9595.1914] [ 2154] [depth= 1] . ( 52 sec) [ -9589.5348] [ 2149] [depth= 1] . ( 52 sec) [ -9589.3482] [ 2141] [depth= 1] . ( 52 sec) [ -9587.8988] [ 2142] [depth= 1] . ( 53 sec) [ -9586.6129] [ 2147] [depth= 1] . ( 53 sec) [ -9585.4572] [ 2142] [depth= 1] . ( 53 sec) [ -9584.8741] [ 2145] [depth= 1] . ( 53 sec) [ -9583.8484] [ 2150] [depth= 1] . ( 53 sec) [ -9583.3635] [ 2145] [depth= 1] . ( 54 sec) [ -9581.6305] [ 2145] [depth= 1] . ( 54 sec) [ -9580.4756] [ 2145] [depth= 2] . ( 54 sec) [ -9580.2402] [ 2144] [depth= 1] . ( 54 sec) [ -9549.4316] [Branch lengths ] . ( 55 sec) [ -9549.3204] [GTR parameters ] . ( 55 sec) [ -9549.1981] [Alpha ][ 0.957325] . ( 55 sec) [ -9549.1577] [ 2143] [depth= 1] . ( 55 sec) [ -9549.1475] [ 2143] [depth= 1] . ( 56 sec) [ -9546.9076] [ 2142] [depth= 3] . ( 57 sec) [ -9546.5598] [ 2140] [depth= 1] . ( 58 sec) [ -9545.1529] [Branch lengths ] . ( 59 sec) [ -9545.1391] [GTR parameters ] . ( 59 sec) [ -9545.1372] [Alpha ][ 0.952957] . ( 59 sec) [ -9544.9224] [ 2144] [depth= 1] . ( 63 sec) [ -9544.4231] [Branch lengths ] . ( 63 sec) [ -9544.4205] [GTR parameters ] . ( 63 sec) [ -9544.4198] [Alpha ][ 0.950249] . ( 65 sec) [ -9544.1385] [ 2141] [depth= 1] . ( 85 sec) [ -9544.0258] [Branch lengths ] . ( 85 sec) [ -9544.0249] [GTR parameters ] . ( 85 sec) [ -9544.0249] [Alpha ][ 0.950249] . ( 85 sec) [ -9544.0249] [Topology ] . ( 86 sec) [ -9544.0211] [Topology ] . ( 87 sec) [ -9544.0203] [Topology ] . ( 87 sec) [ -9544.0203] [GTR parameters ] . ( 87 sec) [ -9544.0203] [Alpha ][ 0.950249] . ( 87 sec) [ -9544.0203] [Topology ] . ( 88 sec) [ -9544.0200] [Topology ] . ( 88 sec) [ -9544.0200] [GTR parameters ] . ( 88 sec) [ -9544.0200] [Alpha ][ 0.950249] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9544.020887 . Log likelihood obtained after SPR moves : -9544.019989 . Log likelihood of the current tree: -9544.019989. . Printing the most likely tree in file 'data53.phy_phyml_tree.txt'... . Time used 0h1m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo