.......................... 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 : 100 . Compute approximate likelihood ratio test : no . Model name : LG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : no . 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 SPR moves)... . ( 2 sec) [ -1481.0207] [ 181] [depth= 1] . ( 4 sec) [ -1480.7434] [ 181] [depth= 2] . ( 5 sec) [ -1480.3961] [ 181] [depth= 2] . ( 5 sec) [ -1480.0504] [ 180] [depth= 1] . ( 5 sec) [ -1479.1497] [ 180] [depth= 1] . ( 5 sec) [ -1479.1178] [ 180] [depth= 1] . ( 7 sec) [ -1473.5151] [ 183] [depth= 1] . ( 7 sec) [ -1470.6219] [ 180] [depth= 1] . ( 8 sec) [ -1470.4535] [ 180] [depth= 2] . ( 8 sec) [ -1470.1303] [ 180] [depth= 2] . ( 18 sec) [ -1469.9852] [ 180] [depth= 1] . ( 35 sec) [ -1469.7091] [ 181] [depth= 1] . ( 35 sec) [ -1468.8297] [ 180] [depth= 1] . ( 35 sec) [ -1468.5370] [ 180] [depth= 1] . ( 40 sec) [ -1467.2393] [ 180] [depth= 4] . ( 41 sec) [ -1465.6690] [ 180] [depth= 1] . ( 43 sec) [ -1465.3846] [ 180] [depth= 1] . ( 46 sec) [ -1465.3726] [ 180] [depth= 1] . ( 49 sec) [ -1458.0559] [Branch lengths ] . ( 67 sec) [ -1458.0321] [ 180] [depth= 2] . ( 94 sec) [ -1455.0977] [ 179] [depth= 4] . ( 104 sec) [ -1455.0767] [ 179] [depth= 1] . ( 110 sec) [ -1453.7398] [Branch lengths ] . ( 171 sec) [ -1453.6746] [Branch lengths ] . ( 171 sec) [ -1453.6746] [Topology ] . ( 172 sec) [ -1453.6698] [Topology ] . ( 173 sec) [ -1453.6681] [Topology ] . ( 174 sec) [ -1453.6672] [Topology ] . ( 174 sec) [ -1453.6672] [Topology ] . ( 175 sec) [ -1453.6668] [Topology ] . Checking for NNIs, optimizing five branches... . ( 183 sec) [ -1453.5514] [Topology ] . Checking for NNIs, optimizing five branches... . ( 190 sec) [ -1453.5454] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1453.545404. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 79 20.381802 0.931000 0.062341 79 15.153854 0.911000 0.035075 17 0.011621 0.000000 0.011949 51 7.874657 0.818000 0.024967 17 -1.000000 0.000000 0.000000 42 1.966611 0.458000 0.022093 23 0.198019 0.000000 0.076440 48 90.071786 0.999000 0.297459 60 3.734580 0.781000 0.033450 69 10.030843 0.799000 0.013347 15 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 26 1.452837 0.715000 0.009590 31 7.758238 0.890000 0.087689 63 10.779435 0.875000 0.062128 16 -1.000000 0.000000 0.000002 48 21.270056 0.940000 0.034285 32 5.887157 0.798000 0.010683 30 7.620846 0.870000 0.054248 22 8.854216 0.866000 0.037252 26 30.617545 0.961000 0.054478 17 11.815924 0.862000 0.022562 74 14.853050 0.888000 0.024473 21 27.179917 0.953000 0.048158 4 -1.000000 0.000000 0.000004 15 9.902023 0.836000 0.024257 54 2.567170 0.766000 0.017915 53 0.607193 0.637000 0.007229 27 0.717623 0.149000 0.011389 78 11.629542 0.865000 0.028802 21 -1.000000 0.000000 0.000001 37 10.492715 0.865000 0.010695 . Printing the most likely tree in file 'proteic_M1990_35x153_2004.phy_phyml_tree.txt'... . Time used 4h35m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo