.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1508_22x431_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... . 172 patterns found. (out of a total of 431 sites) . 298 sites without polymorphism (69.14%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -3147.4178] [ 318] [depth= 1] . ( 7 sec) [ -3147.1552] [ 318] [depth= 1] . ( 7 sec) [ -3144.5653] [ 318] [depth= 1] . ( 8 sec) [ -3142.1097] [ 317] [depth= 4] . ( 8 sec) [ -3138.7070] [ 315] [depth= 2] . ( 10 sec) [ -3138.6386] [ 316] [depth= 1] . ( 10 sec) [ -3137.5181] [ 317] [depth= 1] . ( 10 sec) [ -3137.2917] [ 317] [depth= 1] . ( 10 sec) [ -3137.2747] [ 316] [depth= 1] . ( 12 sec) [ -3137.1335] [ 317] [depth= 1] . ( 14 sec) [ -3136.4709] [ 322] [depth= 3] . ( 15 sec) [ -3134.9586] [ 320] [depth= 2] . ( 15 sec) [ -3132.4612] [ 321] [depth= 3] . ( 15 sec) [ -3132.4035] [ 321] [depth= 1] . ( 15 sec) [ -3132.3053] [ 322] [depth= 1] . ( 16 sec) [ -3130.0109] [ 319] [depth= 3] . ( 20 sec) [ -3129.8071] [ 318] [depth= 1] . ( 21 sec) [ -3129.0870] [ 318] [depth= 1] . ( 22 sec) [ -3128.4822] [ 318] [depth= 1] . ( 22 sec) [ -3128.3474] [ 318] [depth= 1] . ( 24 sec) [ -3123.5248] [Branch lengths ] . ( 33 sec) [ -3121.9705] [ 316] [depth= 3] . ( 35 sec) [ -3120.2914] [ 315] [depth= 3] . ( 44 sec) [ -3117.2695] [ 315] [depth= 1] . ( 59 sec) [ -3115.9504] [Branch lengths ] . ( 63 sec) [ -3115.3735] [ 313] [depth= 1] . ( 95 sec) [ -3115.1278] [Branch lengths ] . ( 95 sec) [ -3115.1278] [Topology ] . ( 96 sec) [ -3115.1263] [Topology ] . ( 97 sec) [ -3115.1261] [Topology ] . ( 97 sec) [ -3115.1261] [Topology ] . ( 98 sec) [ -3115.1261] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3115.126120. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 44 8.842460 0.741000 0.008329 70 12.601396 0.899000 0.014757 93 48.991434 0.989000 0.026320 78 9.665074 0.867000 0.008339 38 4.373367 0.702000 0.005843 24 13.955741 0.887000 0.011601 91 32.929137 0.976000 0.028844 34 2.126226 0.639000 0.007088 8 17.444997 0.901000 0.011070 33 14.001169 0.896000 0.006655 16 -1.000000 0.000000 0.000000 48 15.681049 0.920000 0.007806 33 0.125737 0.000000 0.000904 20 7.032740 0.856000 0.008711 61 29.551169 0.963000 0.016938 48 9.697433 0.849000 0.008606 41 1.695296 0.168000 0.008503 32 0.685365 0.206000 0.003071 60 6.100581 0.841000 0.010257 . Printing the most likely tree in file 'proteic_M1508_22x431_2003.phy_phyml_tree.txt'... . Time used 2h38m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo