.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1812_34x176_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... . 173 patterns found. (out of a total of 176 sites) . 16 sites without polymorphism (9.09%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 7 sec) [ -5429.0857] [ 1008] [depth= 2] . ( 8 sec) [ -5428.1965] [ 1009] [depth= 1] . ( 8 sec) [ -5427.7277] [ 1008] [depth= 1] . ( 9 sec) [ -5427.6473] [ 1009] [depth= 1] . ( 10 sec) [ -5427.5161] [ 1011] [depth= 1] . ( 13 sec) [ -5424.4107] [ 1013] [depth= 1] . ( 13 sec) [ -5423.2010] [ 1015] [depth= 1] . ( 13 sec) [ -5422.7190] [ 1013] [depth= 1] . ( 14 sec) [ -5421.9697] [ 1017] [depth= 3] . ( 15 sec) [ -5421.1011] [ 1011] [depth= 3] . ( 22 sec) [ -5420.0011] [ 1011] [depth= 1] . ( 27 sec) [ -5418.0938] [ 1009] [depth= 5] . ( 30 sec) [ -5399.5087] [Branch lengths ] . ( 36 sec) [ -5399.3989] [ 1008] [depth= 1] . ( 59 sec) [ -5398.3954] [Branch lengths ] . ( 90 sec) [ -5398.3654] [Branch lengths ] . ( 90 sec) [ -5398.3654] [Topology ] . ( 92 sec) [ -5398.3639] [Topology ] . ( 93 sec) [ -5398.3635] [Topology ] . ( 93 sec) [ -5398.3635] [Topology ] . ( 95 sec) [ -5398.3634] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5398.363362. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 88 17.194296 0.936000 0.131508 50 3.484384 0.359000 0.084131 46 2.571297 0.316000 0.113508 94 19.531990 0.923000 0.232621 89 14.909059 0.934000 0.256575 97 37.256406 0.988000 0.380340 70 6.686124 0.822000 0.058667 91 24.197412 0.956000 0.115650 100 32.091350 0.966000 0.077020 49 2.799284 0.446000 0.020807 84 33.999531 0.971000 0.147634 100 47.874909 0.991000 0.191778 40 0.676927 0.228000 0.017809 97 35.018453 0.938000 0.059620 48 7.360118 0.656000 0.038228 95 55.351822 0.992000 0.081717 59 1.288031 0.693000 0.011734 100 88.677868 1.000000 0.115722 99 40.543780 0.980000 0.065743 98 33.756474 0.974000 0.146966 100 93.642575 1.000000 0.216588 63 0.743259 0.291000 0.018366 50 11.951320 0.898000 0.071937 21 10.005262 0.831000 0.031877 91 16.079664 0.921000 0.033738 16 4.132608 0.414000 0.022478 20 13.302269 0.852000 0.021540 100 92.098183 0.999000 0.085901 10 3.154171 0.460000 0.015855 29 9.035288 0.758000 0.021063 52 9.745708 0.809000 0.018960 . Printing the most likely tree in file 'proteic_M1812_34x176_2004.phy_phyml_tree.txt'... . Time used 2h56m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo