.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1499_22x513_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... . 440 patterns found. (out of a total of 513 sites) . 87 sites without polymorphism (16.96%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -12473.4159] [ 2338] [depth= 2] . ( 5 sec) [ -12469.4979] [ 2339] [depth= 2] . ( 5 sec) [ -12468.0860] [ 2341] [depth= 1] . ( 5 sec) [ -12467.8266] [ 2341] [depth= 1] . ( 6 sec) [ -12462.4608] [ 2338] [depth= 2] . ( 6 sec) [ -12460.1031] [ 2341] [depth= 1] . ( 7 sec) [ -12459.1020] [ 2339] [depth= 1] . ( 8 sec) [ -12458.2097] [ 2339] [depth= 1] . ( 9 sec) [ -12456.7297] [ 2340] [depth= 1] . ( 9 sec) [ -12455.4426] [ 2341] [depth= 1] . ( 9 sec) [ -12449.9796] [ 2340] [depth= 1] . ( 14 sec) [ -12447.8478] [ 2344] [depth= 1] . ( 17 sec) [ -12444.3332] [ 2340] [depth= 1] . ( 19 sec) [ -12412.0064] [Branch lengths ] . ( 26 sec) [ -12411.6230] [ 2339] [depth= 1] . ( 27 sec) [ -12411.1273] [ 2341] [depth= 1] . ( 28 sec) [ -12410.7866] [ 2341] [depth= 1] . ( 39 sec) [ -12407.2047] [Branch lengths ] . ( 61 sec) [ -12406.0827] [Branch lengths ] . ( 61 sec) [ -12406.0827] [Topology ] . ( 63 sec) [ -12405.8070] [Topology ] . ( 65 sec) [ -12405.6563] [Topology ] . ( 67 sec) [ -12405.5471] [Topology ] . ( 69 sec) [ -12405.4666] [Topology ] . ( 71 sec) [ -12405.4071] [Topology ] . ( 73 sec) [ -12405.3631] [Topology ] . ( 73 sec) [ -12405.3631] [Topology ] . ( 75 sec) [ -12405.3302] [Topology ] . ( 76 sec) [ -12405.3059] [Topology ] . ( 78 sec) [ -12405.2879] [Topology ] . ( 80 sec) [ -12405.2745] [Topology ] . ( 82 sec) [ -12405.2646] [Topology ] . ( 84 sec) [ -12405.2573] [Topology ] . ( 84 sec) [ -12405.2573] [Topology ] . ( 86 sec) [ -12405.2519] [Topology ] . ( 88 sec) [ -12405.2479] [Topology ] . ( 90 sec) [ -12405.2449] [Topology ] . ( 91 sec) [ -12405.2427] [Topology ] . ( 93 sec) [ -12405.2411] [Topology ] . ( 95 sec) [ -12405.2398] [Topology ] . ( 95 sec) [ -12405.2398] [Topology ] . ( 97 sec) [ -12405.2389] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12405.238935. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 170.454264 1.000000 0.306038 100 87.813323 0.999000 0.194995 97 39.040000 0.979000 0.114510 30 1.244834 0.139000 0.031136 100 140.761927 1.000000 0.192687 25 2.516603 0.353000 0.037314 37 1.268692 0.173000 0.033536 99 60.393756 0.999000 0.156693 100 141.111721 1.000000 0.202848 94 36.071700 0.957000 0.083147 100 77.098955 0.994000 0.108038 81 22.266045 0.928000 0.038540 54 1.897428 0.189000 0.031719 93 25.260425 0.949000 0.076902 66 11.532931 0.714000 0.063448 80 24.193173 0.968000 0.057048 45 7.711047 0.693000 0.040133 48 5.550367 0.657000 0.028935 59 12.963411 0.910000 0.031427 . Printing the most likely tree in file 'proteic_M1499_22x513_2003.phy_phyml_tree.txt'... . Time used 2h58m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo