.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1768_31x228_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 . Compressing sequences... . 60 patterns found. (out of a total of 228 sites) . 185 sites without polymorphism (81.14%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -1053.4853] [ 52] [depth= 2] . ( 7 sec) [ -1053.0415] [ 52] [depth= 2] . ( 7 sec) [ -1053.0095] [ 52] [depth= 1] . ( 7 sec) [ -1052.9110] [ 52] [depth= 1] . ( 7 sec) [ -1052.7073] [ 52] [depth= 3] . ( 10 sec) [ -1052.6719] [ 52] [depth= 1] . ( 14 sec) [ -1052.6490] [ 52] [depth= 2] . ( 14 sec) [ -1052.6364] [ 52] [depth= 1] . ( 38 sec) [ -1052.6036] [ 52] [depth= 1] . ( 38 sec) [ -1052.5682] [ 52] [depth= 1] . ( 42 sec) [ -1052.4749] [ 52] [depth= 3] . ( 45 sec) [ -1052.4623] [ 52] [depth= 3] . ( 45 sec) [ -1052.4510] [ 52] [depth= 1] . ( 45 sec) [ -1052.4334] [ 52] [depth= 1] . ( 76 sec) [ -1052.3897] [Branch lengths ] . ( 218 sec) [ -1052.3890] [Branch lengths ] . ( 218 sec) [ -1052.3890] [Topology ] . ( 218 sec) [ -1052.3890] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1052.389028. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 21.952741 0.976000 0.021218 5 -1.000000 0.000000 0.000001 12 -1.000000 0.000000 0.000000 30 -1.000000 0.000000 0.000001 40 0.409516 0.354000 0.003072 29 0.488362 0.760000 0.002695 9 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 65 19.841599 0.943000 0.004204 40 0.459448 0.754000 0.002638 5 -1.000000 0.000000 0.000000 44 9.646847 0.837000 0.004196 8 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'proteic_M1768_31x228_2004.phy_phyml_tree.txt'... . Time used 7h30m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo