.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1380_9x1558_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 1558 sites) . 832 sites without polymorphism (53.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11979.1337] [ 1431] [depth= 1] . ( 2 sec) [ -11967.9342] [ 1431] [depth= 1] . ( 2 sec) [ -11962.9705] [ 1432] [depth= 1] . ( 4 sec) [ -11938.9109] [ 1430] [depth= 5] . ( 6 sec) [ -11935.2807] [ 1427] [depth= 1] . ( 7 sec) [ -11931.4114] [ 1427] [depth= 1] . ( 8 sec) [ -11916.4298] [Branch lengths ] . ( 12 sec) [ -11916.3727] [ 1427] [depth= 1] . ( 15 sec) [ -11914.1473] [Branch lengths ] . ( 24 sec) [ -11914.0399] [Branch lengths ] . ( 24 sec) [ -11914.0399] [Topology ] . ( 25 sec) [ -11914.0374] [Topology ] . ( 26 sec) [ -11914.0368] [Topology ] . ( 26 sec) [ -11914.0368] [Topology ] . ( 27 sec) [ -11914.0366] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11914.036649. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 507.911535 1.000000 0.236265 69 36.545506 0.993000 0.033099 35 3.036194 0.262000 0.009583 66 52.898896 0.998000 0.027317 66 55.136733 0.964000 0.031763 43 1.134838 0.094000 0.008892 . Printing the most likely tree in file 'proteic_M1380_9x1558_2003.phy_phyml_tree.txt'... . Time used 0h42m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo