.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data89.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... . 394 patterns found. (out of a total of 500 sites) . 98 sites without polymorphism (19.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7626.759928 . ( 0 sec) [ -7623.0405] [GTR parameters ] . ( 1 sec) [ -7623.0403] [Alpha ][ 0.998309] . ( 1 sec) [ -7623.0403] [Topology ] . ( 2 sec) [ -7584.2163] [Topology ] . ( 3 sec) [ -7580.8218] [Topology ] . ( 4 sec) [ -7580.1370] [Topology ] . ( 5 sec) [ -7579.9092] [Topology ] . ( 5 sec) [ -7579.8162] [Topology ] . ( 6 sec) [ -7579.7754] [Topology ] . ( 8 sec) [ -7579.7569] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.756885 . ( 16 sec) [ -7579.6895] [GTR parameters ] . ( 16 sec) [ -7579.5945] [Alpha ][ 1.035635] . ( 16 sec) [ -7579.5945] [Topology ] . ( 17 sec) [ -7579.5739] [Topology ] . ( 18 sec) [ -7579.5652] [Topology ] . ( 19 sec) [ -7579.5613] [Topology ] . ( 20 sec) [ -7579.5595] [Topology ] . ( 21 sec) [ -7579.5587] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.558706 . ( 29 sec) [ -7579.5585] [GTR parameters ] . ( 29 sec) [ -7579.5576] [Alpha ][ 1.039455] . ( 29 sec) [ -7579.5576] [Topology ] . ( 30 sec) [ -7579.5571] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7579.557055 . ( 39 sec) [ -7579.5570] [GTR parameters ] . ( 39 sec) [ -7579.5570] [Alpha ][ 1.039455] . ( 39 sec) [ -7579.5570] [Topology ] . ( 40 sec) [ -7579.5568] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 56 sec) [ -7623.0405] [GTR parameters ] . ( 56 sec) [ -7623.0403] [Alpha ][ 0.998309] . ( 56 sec) [ -7616.5408] [ 1537] [depth= 1] . ( 56 sec) [ -7616.4135] [ 1539] [depth= 1] . ( 56 sec) [ -7609.9858] [ 1538] [depth= 1] . ( 56 sec) [ -7608.1413] [ 1535] [depth= 1] . ( 57 sec) [ -7607.8058] [ 1537] [depth= 2] . ( 57 sec) [ -7607.5327] [ 1538] [depth= 1] . ( 57 sec) [ -7606.0527] [ 1537] [depth= 1] . ( 58 sec) [ -7605.7705] [ 1538] [depth= 1] . ( 58 sec) [ -7605.1930] [ 1541] [depth= 1] . ( 58 sec) [ -7603.6643] [ 1540] [depth= 1] . ( 58 sec) [ -7602.8445] [ 1539] [depth= 1] . ( 58 sec) [ -7602.8066] [ 1540] [depth= 1] . ( 59 sec) [ -7601.6894] [ 1543] [depth= 1] . ( 59 sec) [ -7601.3458] [ 1544] [depth= 1] . ( 59 sec) [ -7601.2756] [ 1544] [depth= 1] . ( 60 sec) [ -7601.2532] [ 1544] [depth= 1] . ( 60 sec) [ -7601.2270] [ 1544] [depth= 1] . ( 60 sec) [ -7601.1958] [ 1544] [depth= 1] . ( 61 sec) [ -7581.4935] [Branch lengths ] . ( 61 sec) [ -7581.3826] [GTR parameters ] . ( 61 sec) [ -7581.3201] [Alpha ][ 1.028495] . ( 62 sec) [ -7581.0498] [ 1544] [depth= 1] . ( 63 sec) [ -7581.0022] [ 1543] [depth= 1] . ( 65 sec) [ -7580.1785] [Branch lengths ] . ( 65 sec) [ -7580.1738] [GTR parameters ] . ( 65 sec) [ -7580.1688] [Alpha ][ 1.037407] . ( 69 sec) [ -7580.0718] [Branch lengths ] . ( 90 sec) [ -7579.7724] [ 1540] [depth= 1] . ( 93 sec) [ -7579.7605] [ 1540] [depth= 1] . ( 95 sec) [ -7579.6569] [Branch lengths ] . ( 95 sec) [ -7579.6561] [GTR parameters ] . ( 95 sec) [ -7579.6561] [Alpha ][ 1.038444] . ( 96 sec) [ -7579.6561] [Topology ] . ( 97 sec) [ -7579.5662] [Topology ] . ( 98 sec) [ -7579.5582] [Topology ] . ( 99 sec) [ -7579.5572] [Topology ] . ( 100 sec) [ -7579.5570] [Topology ] . ( 100 sec) [ -7579.5568] [GTR parameters ] . ( 100 sec) [ -7579.5566] [Alpha ][ 1.039872] . ( 100 sec) [ -7579.5566] [Topology ] . ( 102 sec) [ -7579.5566] [Topology ] . ( 102 sec) [ -7579.5566] [GTR parameters ] . ( 102 sec) [ -7579.5566] [Alpha ][ 1.039872] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7579.556808 . Log likelihood obtained after SPR moves : -7579.556552 . Log likelihood of the current tree: -7579.556552. . Printing the most likely tree in file 'data89.phy_phyml_tree.txt'... . Time used 0h1m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo