.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data56.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... . 403 patterns found. (out of a total of 500 sites) . 86 sites without polymorphism (17.20%). . 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=-8289.945444 . ( 1 sec) [ -8288.3499] [GTR parameters ] . ( 2 sec) [ -8288.3411] [Alpha ][ 0.988651] . ( 2 sec) [ -8288.3411] [Topology ] . ( 3 sec) [ -8244.1423] [Topology ] . ( 4 sec) [ -8236.4087] [Topology ] . ( 5 sec) [ -8234.2678] [Topology ] . ( 6 sec) [ -8233.3628] [Topology ] . ( 7 sec) [ -8232.9429] [Topology ] . ( 8 sec) [ -8232.6466] [Topology ] . ( 8 sec) [ -8232.4177] [Topology ] . ( 9 sec) [ -8232.3566] [Topology ] . ( 10 sec) [ -8232.3295] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8232.316719 . ( 17 sec) [ -8232.2915] [GTR parameters ] . ( 17 sec) [ -8232.2787] [Alpha ][ 1.001505] . ( 18 sec) [ -8232.2787] [Topology ] . ( 18 sec) [ -8232.2703] [Topology ] . ( 19 sec) [ -8232.2664] [Topology ] . ( 20 sec) [ -8232.2645] [Topology ] . ( 21 sec) [ -8232.2636] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8232.263567 . ( 30 sec) [ -8232.2635] [GTR parameters ] . ( 30 sec) [ -8232.2634] [Alpha ][ 1.002599] . ( 30 sec) [ -8232.2634] [Topology ] . ( 32 sec) [ -8232.2629] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 48 sec) [ -8288.3499] [GTR parameters ] . ( 48 sec) [ -8288.3411] [Alpha ][ 0.988651] . ( 49 sec) [ -8277.2816] [ 1708] [depth= 1] . ( 49 sec) [ -8276.1095] [ 1703] [depth= 1] . ( 49 sec) [ -8269.1435] [ 1701] [depth= 2] . ( 50 sec) [ -8262.5412] [ 1711] [depth= 1] . ( 51 sec) [ -8262.0841] [ 1714] [depth= 1] . ( 51 sec) [ -8261.5964] [ 1717] [depth= 1] . ( 52 sec) [ -8258.4061] [ 1718] [depth= 1] . ( 52 sec) [ -8256.9569] [ 1718] [depth= 3] . ( 53 sec) [ -8256.3808] [ 1717] [depth= 2] . ( 53 sec) [ -8255.6193] [ 1717] [depth= 1] . ( 54 sec) [ -8255.4415] [ 1718] [depth= 1] . ( 55 sec) [ -8232.0786] [Branch lengths ] . ( 55 sec) [ -8232.0481] [GTR parameters ] . ( 55 sec) [ -8232.0472] [Alpha ][ 0.992001] . ( 57 sec) [ -8231.9472] [ 1718] [depth= 1] . ( 61 sec) [ -8231.0530] [Branch lengths ] . ( 61 sec) [ -8231.0526] [GTR parameters ] . ( 61 sec) [ -8231.0512] [Alpha ][ 0.996082] . ( 95 sec) [ -8230.9774] [Branch lengths ] . ( 95 sec) [ -8230.9774] [Topology ] . ( 96 sec) [ -8230.7117] [Topology ] . ( 98 sec) [ -8230.4978] [Topology ] . ( 99 sec) [ -8230.4656] [Topology ] . ( 100 sec) [ -8230.4537] [Topology ] . ( 102 sec) [ -8230.4482] [Topology ] . ( 103 sec) [ -8230.4455] [Topology ] . ( 104 sec) [ -8230.4441] [Topology ] . ( 104 sec) [ -8230.4350] [GTR parameters ] . ( 104 sec) [ -8230.4332] [Alpha ][ 1.000787] . ( 105 sec) [ -8230.4332] [Topology ] . ( 106 sec) [ -8230.4325] [Topology ] . ( 106 sec) [ -8230.4325] [GTR parameters ] . ( 106 sec) [ -8230.4325] [Alpha ][ 1.000787] . Checking for NNIs, optimizing five branches... . ( 114 sec) [ -8230.4242] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8232.262930 . Log likelihood obtained after SPR moves : -8230.424162 . Log likelihood of the current tree: -8230.424162. . Printing the most likely tree in file 'data56.phy_phyml_tree.txt'... . Time used 0h2m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo