.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1990_35x153_2004.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 . 5 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 104 patterns found. (out of a total of 153 sites) . 83 sites without polymorphism (54.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -1475.6886] [Alpha ][ 0.500960] . ( 1 sec) [ -1475.6886] [Topology ] . ( 2 sec) [ -1458.9478] [Topology ] . ( 3 sec) [ -1456.3850] [Topology ] . ( 4 sec) [ -1455.6479] [Topology ] . ( 5 sec) [ -1455.3351] [Topology ] . ( 6 sec) [ -1455.1478] [Topology ] . ( 7 sec) [ -1455.0229] [Topology ] . ( 8 sec) [ -1454.9621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -1454.8907] [Topology ] . ( 16 sec) [ -1454.4162] [Alpha ][ 0.419100] . ( 16 sec) [ -1454.4162] [Topology ] . ( 17 sec) [ -1454.3127] [Topology ] . ( 18 sec) [ -1454.2962] [Topology ] . ( 19 sec) [ -1454.2898] [Topology ] . ( 20 sec) [ -1454.2869] [Topology ] . ( 21 sec) [ -1454.2855] [Topology ] . ( 22 sec) [ -1454.2845] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -1454.2697] [Alpha ][ 0.406420] . ( 29 sec) [ -1454.2697] [Topology ] . ( 30 sec) [ -1454.2659] [Topology ] . ( 31 sec) [ -1454.2653] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -1454.2647] [Alpha ][ 0.403661] . ( 39 sec) [ -1454.2647] [Topology ] . ( 40 sec) [ -1454.2640] [Topology ] . Checking for NNIs, optimizing five branches... . ( 48 sec) [ -1454.2639] [Alpha ][ 0.403166] . ( 48 sec) [ -1454.2639] [Topology ] . ( 49 sec) [ -1454.2635] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 63 sec) [ -1475.6886] [Alpha ][ 0.500960] . ( 66 sec) [ -1475.5479] [ 181] [depth= 1] . ( 66 sec) [ -1474.1794] [ 180] [depth= 2] . ( 72 sec) [ -1473.3210] [ 180] [depth= 2] . ( 72 sec) [ -1468.9409] [ 183] [depth= 1] . ( 72 sec) [ -1466.3719] [ 180] [depth= 1] . ( 73 sec) [ -1466.1893] [ 180] [depth= 2] . ( 73 sec) [ -1465.7909] [ 180] [depth= 2] . ( 81 sec) [ -1465.7130] [ 180] [depth= 1] . ( 98 sec) [ -1465.4483] [ 181] [depth= 1] . ( 98 sec) [ -1464.5404] [ 180] [depth= 1] . ( 98 sec) [ -1464.1279] [ 180] [depth= 1] . ( 103 sec) [ -1464.0944] [ 180] [depth= 1] . ( 106 sec) [ -1463.9398] [ 180] [depth= 1] . ( 106 sec) [ -1463.2948] [ 180] [depth= 1] . ( 114 sec) [ -1458.0849] [Branch lengths ] . ( 114 sec) [ -1457.8962] [Alpha ][ 0.446406] . ( 123 sec) [ -1457.8769] [ 180] [depth= 2] . ( 126 sec) [ -1457.8074] [ 185] [depth= 3] . ( 128 sec) [ -1457.7805] [ 185] [depth= 2] . ( 133 sec) [ -1457.1222] [ 185] [depth= 1] . ( 135 sec) [ -1456.9249] [ 185] [depth= 1] . ( 171 sec) [ -1454.4562] [Branch lengths ] . ( 171 sec) [ -1454.3192] [Alpha ][ 0.406113] . ( 234 sec) [ -1454.1176] [Branch lengths ] . ( 234 sec) [ -1454.1176] [Topology ] . ( 235 sec) [ -1454.0674] [Topology ] . ( 236 sec) [ -1454.0310] [Topology ] . ( 237 sec) [ -1454.0017] [Topology ] . ( 238 sec) [ -1453.9747] [Topology ] . ( 239 sec) [ -1453.9504] [Topology ] . ( 240 sec) [ -1453.9314] [Topology ] . ( 240 sec) [ -1453.9279] [Alpha ][ 0.399938] . ( 240 sec) [ -1453.9279] [Topology ] . ( 241 sec) [ -1453.9193] [Topology ] . ( 242 sec) [ -1453.9172] [Topology ] . ( 243 sec) [ -1453.9166] [Topology ] . ( 243 sec) [ -1453.9166] [Alpha ][ 0.398949] . ( 243 sec) [ -1453.9166] [Topology ] . ( 244 sec) [ -1453.9164] [Topology ] . ( 245 sec) [ -1453.9164] [Alpha ][ 0.398949] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1454.263454 . Log likelihood obtained after SPR moves : -1453.916361 . Log likelihood of the current tree: -1453.916361. . Printing the most likely tree in file 'proteic_M1990_35x153_2004.phy_phyml_tree.txt'... . Time used 0h4m12s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 251.18user 0.00system 4:12.25elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps