.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1989_18x173_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 . 7 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 139 patterns found. (out of a total of 173 sites) . 46 sites without polymorphism (26.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -3204.9307] [ 588] [depth= 1] . ( 0 sec) [ -3204.6062] [ 588] [depth= 1] . ( 0 sec) [ -3204.5822] [ 588] [depth= 1] . ( 1 sec) [ -3202.1398] [ 590] [depth= 1] . ( 1 sec) [ -3198.2742] [ 588] [depth= 1] . ( 1 sec) [ -3196.8438] [ 588] [depth= 1] . ( 2 sec) [ -3194.8746] [ 588] [depth= 1] . ( 2 sec) [ -3194.6856] [ 588] [depth= 1] . ( 2 sec) [ -3194.5689] [ 588] [depth= 1] . ( 2 sec) [ -3194.5153] [ 588] [depth= 1] . ( 4 sec) [ -3193.9490] [ 589] [depth= 3] . ( 5 sec) [ -3193.6769] [ 590] [depth= 1] . ( 5 sec) [ -3190.8059] [ 586] [depth= 3] . ( 5 sec) [ -3190.5124] [ 588] [depth= 1] . ( 6 sec) [ -3189.5878] [ 587] [depth= 1] . ( 7 sec) [ -3182.3802] [Branch lengths ] . ( 8 sec) [ -3181.4769] [ 587] [depth= 1] . ( 9 sec) [ -3180.3622] [ 587] [depth= 2] . ( 16 sec) [ -3179.1188] [Branch lengths ] . ( 25 sec) [ -3178.8868] [Branch lengths ] . ( 25 sec) [ -3178.8868] [Topology ] . ( 26 sec) [ -3178.8424] [Topology ] . ( 26 sec) [ -3178.8203] [Topology ] . ( 27 sec) [ -3178.8047] [Topology ] . ( 28 sec) [ -3178.7934] [Topology ] . ( 28 sec) [ -3178.7850] [Topology ] . ( 29 sec) [ -3178.7788] [Topology ] . ( 29 sec) [ -3178.7788] [Topology ] . ( 29 sec) [ -3178.7742] [Topology ] . ( 30 sec) [ -3178.7707] [Topology ] . ( 30 sec) [ -3178.7681] [Topology ] . ( 31 sec) [ -3178.7661] [Topology ] . ( 32 sec) [ -3178.7646] [Topology ] . ( 32 sec) [ -3178.7635] [Topology ] . ( 32 sec) [ -3178.7635] [Topology ] . ( 33 sec) [ -3178.7626] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3178.762621. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 99 30.173413 0.988000 0.437470 42 3.440081 0.804000 0.140411 25 1.062477 0.376000 0.048622 100 75.330959 0.999000 0.540892 23 4.194005 0.818000 0.065885 47 6.925894 0.790000 0.094119 98 37.937735 0.990000 0.215783 98 21.647348 0.960000 0.142844 53 -1.000000 0.000000 0.000001 51 7.346355 0.852000 0.108953 100 30.828623 0.985000 0.242898 41 1.536144 0.627000 0.022129 28 -1.000000 0.000000 0.000002 47 0.700721 0.643000 0.037540 80 9.995920 0.904000 0.194860 . Printing the most likely tree in file 'proteic_M1989_18x173_2004.phy_phyml_tree.txt'... . Time used 1h1m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo