.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1381_9x1557_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... . 695 patterns found. (out of a total of 1557 sites) . 829 sites without polymorphism (53.24%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -12047.0977] [ 1445] [depth= 1] . ( 2 sec) [ -12040.4707] [ 1446] [depth= 1] . ( 4 sec) [ -12039.3241] [ 1449] [depth= 1] . ( 5 sec) [ -12036.4723] [ 1448] [depth= 1] . ( 5 sec) [ -12010.0752] [ 1447] [depth= 5] . ( 7 sec) [ -11991.7868] [Branch lengths ] . ( 9 sec) [ -11989.9506] [ 1439] [depth= 1] . ( 12 sec) [ -11984.2134] [Branch lengths ] . ( 18 sec) [ -11984.1056] [Branch lengths ] . ( 18 sec) [ -11984.1056] [Topology ] . ( 19 sec) [ -11984.1037] [Topology ] . ( 20 sec) [ -11984.1034] [Topology ] . ( 20 sec) [ -11984.1034] [Topology ] . ( 21 sec) [ -11984.1033] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11984.103270. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 519.968465 1.000000 0.239830 69 35.840767 0.991000 0.031658 45 7.581789 0.458000 0.018902 76 24.225724 0.964000 0.016856 77 60.433074 0.987000 0.031267 62 9.034475 0.793000 0.010625 . Printing the most likely tree in file 'proteic_M1381_9x1557_2003.phy_phyml_tree.txt'... . Time used 0h39m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo