.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2302_24x365_2005.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 . 19 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 261 patterns found. (out of a total of 365 sites) . 103 sites without polymorphism (28.22%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 15Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -4258.7919] [ 592] [depth= 1] . ( 6 sec) [ -4258.7394] [ 592] [depth= 1] . ( 6 sec) [ -4257.9005] [ 592] [depth= 1] . ( 6 sec) [ -4257.7663] [ 592] [depth= 1] . ( 7 sec) [ -4257.5705] [ 592] [depth= 2] . ( 9 sec) [ -4257.4685] [ 592] [depth= 2] . ( 19 sec) [ -4257.0969] [ 592] [depth= 1] . ( 19 sec) [ -4256.9275] [ 592] [depth= 1] . ( 20 sec) [ -4256.8775] [ 592] [depth= 1] . ( 20 sec) [ -4256.6098] [ 592] [depth= 2] . ( 20 sec) [ -4256.4302] [ 592] [depth= 2] . ( 21 sec) [ -4256.4180] [ 592] [depth= 3] . ( 21 sec) [ -4256.3794] [ 592] [depth= 1] . ( 22 sec) [ -4256.3261] [ 592] [depth= 1] . ( 29 sec) [ -4247.4596] [Branch lengths ] . ( 81 sec) [ -4247.3033] [Branch lengths ] . ( 81 sec) [ -4247.3033] [Topology ] . ( 83 sec) [ -4247.2924] [Topology ] . ( 84 sec) [ -4247.2883] [Topology ] . ( 85 sec) [ -4247.2861] [Topology ] . ( 87 sec) [ -4247.2849] [Topology ] . ( 88 sec) [ -4247.2843] [Topology ] . ( 88 sec) [ -4247.2843] [Topology ] . ( 90 sec) [ -4247.2839] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -4247.283869. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 109.808768 0.999000 0.220513 100 38.182584 0.991000 0.101550 100 27.883319 0.983000 0.139119 100 33.003034 0.981000 0.140211 100 38.874721 0.980000 0.057589 67 8.357538 0.803000 0.024393 75 42.695619 0.982000 0.028864 89 4.605494 0.796000 0.006671 100 112.994411 0.998000 0.042195 100 93.153973 0.999000 0.040621 1 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 59 7.764335 0.751000 0.002645 73 20.092778 0.892000 0.005310 50 3.552747 0.746000 0.002504 100 62.644297 0.987000 0.016339 2 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 15 -1.000000 0.000000 0.000000 96 54.179238 0.983000 0.016096 . Printing the most likely tree in file 'proteic_M2302_24x365_2005.phy_phyml_tree.txt'... . Time used 2h50m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo