.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1503_23x479_2003.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 . Compressing sequences... . 356 patterns found. (out of a total of 479 sites) . 140 sites without polymorphism (29.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -9863.9546] [ 1748] [depth= 1] . ( 2 sec) [ -9863.4697] [ 1746] [depth= 1] . ( 2 sec) [ -9859.6339] [ 1749] [depth= 1] . ( 4 sec) [ -9854.2666] [ 1750] [depth= 1] . ( 6 sec) [ -9852.6977] [ 1751] [depth= 1] . ( 7 sec) [ -9848.6275] [ 1750] [depth= 2] . ( 7 sec) [ -9844.1985] [ 1750] [depth= 1] . ( 10 sec) [ -9839.6022] [ 1750] [depth= 1] . ( 11 sec) [ -9838.8811] [ 1751] [depth= 1] . ( 11 sec) [ -9836.4921] [ 1750] [depth= 1] . ( 13 sec) [ -9830.8368] [ 1750] [depth= 1] . ( 17 sec) [ -9804.3791] [Branch lengths ] . ( 23 sec) [ -9795.8228] [ 1747] [depth= 3] . ( 24 sec) [ -9794.2798] [ 1747] [depth= 1] . ( 27 sec) [ -9794.1438] [ 1748] [depth= 1] . ( 27 sec) [ -9793.8973] [ 1745] [depth= 1] . ( 33 sec) [ -9788.5594] [Branch lengths ] . ( 50 sec) [ -9788.1633] [Branch lengths ] . ( 50 sec) [ -9788.1633] [Topology ] . ( 52 sec) [ -9787.8114] [Topology ] . ( 54 sec) [ -9787.4787] [Topology ] . ( 56 sec) [ -9787.4196] [Topology ] . ( 57 sec) [ -9787.3997] [Topology ] . ( 59 sec) [ -9787.3912] [Topology ] . ( 61 sec) [ -9787.3870] [Topology ] . ( 62 sec) [ -9787.3849] [Topology ] . ( 63 sec) [ -9787.3849] [Topology ] . ( 64 sec) [ -9787.3838] [Topology ] . ( 66 sec) [ -9787.3833] [Topology ] . ( 66 sec) [ -9787.3833] [Topology ] . ( 68 sec) [ -9787.3830] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -9787.3827] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -9787.3537] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9787.353703. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 164.878791 1.000000 0.226784 53 7.648763 0.785000 0.044280 76 21.299642 0.955000 0.051064 100 159.459270 1.000000 0.172350 93 15.051765 0.915000 0.044743 51 6.552288 0.445000 0.025233 90 56.995863 0.992000 0.069613 54 6.983205 0.827000 0.048822 41 1.709873 0.225000 0.013939 58 11.289785 0.900000 0.028798 61 12.051896 0.864000 0.032466 43 3.585430 0.611000 0.015475 72 6.358072 0.676000 0.026210 78 33.574093 0.966000 0.050915 100 72.540377 0.999000 0.105088 68 6.182383 0.429000 0.040100 99 52.130072 0.993000 0.086410 97 20.440133 0.921000 0.042966 30 0.029191 0.000000 0.003792 100 150.777948 1.000000 0.166121 . Printing the most likely tree in file 'proteic_M1503_23x479_2003.phy_phyml_tree.txt'... . Time used 2h19m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo