.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2478_30x276_2005.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . 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... . 249 patterns found. (out of a total of 276 sites) . 41 sites without polymorphism (14.86%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -8811.1519] [Alpha ][ 0.880454] . ( 1 sec) [ -8811.1519] [Topology ] . ( 3 sec) [ -8746.8962] [Topology ] . ( 4 sec) [ -8734.3709] [Topology ] . ( 6 sec) [ -8732.6388] [Topology ] . ( 8 sec) [ -8732.0970] [Topology ] . ( 9 sec) [ -8730.9948] [Topology ] . ( 11 sec) [ -8728.4784] [Topology ] . ( 13 sec) [ -8726.6266] [Topology ] . ( 14 sec) [ -8726.2606] [Topology ] . ( 16 sec) [ -8726.1914] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -8725.4787] [Alpha ][ 0.974173] . ( 31 sec) [ -8725.4787] [Topology ] . ( 33 sec) [ -8725.4256] [Topology ] . ( 35 sec) [ -8725.4069] [Topology ] . ( 36 sec) [ -8725.3977] [Topology ] . ( 38 sec) [ -8725.3930] [Topology ] . ( 40 sec) [ -8725.3904] [Topology ] . ( 41 sec) [ -8725.3890] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -8725.3805] [Alpha ][ 0.985455] . ( 55 sec) [ -8725.3805] [Topology ] . ( 57 sec) [ -8725.3781] [Topology ] . ( 58 sec) [ -8725.3770] [Topology ] . ( 60 sec) [ -8725.3763] [Topology ] . Checking for NNIs, optimizing five branches... . ( 74 sec) [ -8725.3762] [Alpha ][ 0.986897] . ( 74 sec) [ -8725.3762] [Topology ] . ( 75 sec) [ -8725.3758] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 102 sec) [ -8811.1519] [Alpha ][ 0.880454] . ( 103 sec) [ -8799.7211] [ 1681] [depth= 1] . ( 106 sec) [ -8794.0723] [ 1678] [depth= 1] . ( 108 sec) [ -8792.5920] [ 1678] [depth= 1] . ( 109 sec) [ -8791.5164] [ 1678] [depth= 1] . ( 109 sec) [ -8788.1612] [ 1678] [depth= 1] . ( 110 sec) [ -8787.8672] [ 1678] [depth= 1] . ( 111 sec) [ -8787.5915] [ 1679] [depth= 1] . ( 112 sec) [ -8787.1394] [ 1675] [depth= 2] . ( 112 sec) [ -8782.1493] [ 1675] [depth= 1] . ( 112 sec) [ -8781.7047] [ 1675] [depth= 1] . ( 113 sec) [ -8776.8288] [ 1677] [depth= 1] . ( 113 sec) [ -8770.1167] [ 1671] [depth= 1] . ( 116 sec) [ -8768.2046] [ 1672] [depth= 1] . ( 117 sec) [ -8765.3032] [ 1672] [depth= 1] . ( 118 sec) [ -8762.6609] [ 1672] [depth= 1] . ( 118 sec) [ -8761.2050] [ 1671] [depth= 1] . ( 119 sec) [ -8761.0174] [ 1672] [depth= 1] . ( 120 sec) [ -8760.0796] [ 1671] [depth= 1] . ( 123 sec) [ -8729.5163] [Branch lengths ] . ( 124 sec) [ -8728.7833] [Alpha ][ 0.976436] . ( 130 sec) [ -8728.6757] [ 1668] [depth= 1] . ( 148 sec) [ -8726.7933] [Branch lengths ] . ( 148 sec) [ -8726.7915] [Alpha ][ 0.981506] . ( 173 sec) [ -8726.7047] [Branch lengths ] . ( 173 sec) [ -8726.7047] [Topology ] . ( 175 sec) [ -8725.4580] [Topology ] . ( 177 sec) [ -8725.3897] [Topology ] . ( 178 sec) [ -8725.3804] [Topology ] . ( 180 sec) [ -8725.3785] [Topology ] . ( 182 sec) [ -8725.3781] [Topology ] . ( 182 sec) [ -8725.3757] [Alpha ][ 0.987405] . ( 182 sec) [ -8725.3757] [Topology ] . ( 184 sec) [ -8725.3754] [Topology ] . ( 184 sec) [ -8725.3754] [Alpha ][ 0.987405] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8725.375765 . Log likelihood obtained after SPR moves : -8725.375398 . Log likelihood of the current tree: -8725.375398. . Printing the most likely tree in file 'proteic_M2478_30x276_2005.phy_phyml_tree.txt'... . Time used 0h3m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 193.60user 0.00system 3:17.69elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps