.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2304_31x429_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 . 35 sites are made from completely undetermined states ('X', '-', '?')... . Compressing sequences... . 305 patterns found. (out of a total of 429 sites) . 122 sites without polymorphism (28.44%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -5585.2867] [ 799] [depth= 1] . ( 2 sec) [ -5580.7076] [ 794] [depth= 1] . ( 4 sec) [ -5579.7177] [ 795] [depth= 1] . ( 7 sec) [ -5579.2525] [ 795] [depth= 1] . ( 8 sec) [ -5578.9710] [ 795] [depth= 1] . ( 8 sec) [ -5578.4383] [ 794] [depth= 1] . ( 10 sec) [ -5576.1957] [ 795] [depth= 1] . ( 16 sec) [ -5576.1272] [ 795] [depth= 1] . ( 22 sec) [ -5575.9999] [ 795] [depth= 1] . ( 22 sec) [ -5575.9378] [ 795] [depth= 1] . ( 49 sec) [ -5575.2675] [ 795] [depth= 1] . ( 49 sec) [ -5575.0547] [ 795] [depth= 1] . ( 51 sec) [ -5574.9781] [ 795] [depth= 2] . ( 53 sec) [ -5574.8430] [ 795] [depth= 1] . ( 59 sec) [ -5574.6263] [ 795] [depth= 1] . ( 59 sec) [ -5574.2578] [ 795] [depth= 1] . ( 61 sec) [ -5574.2237] [ 795] [depth= 2] . ( 62 sec) [ -5568.3276] [Branch lengths ] . ( 146 sec) [ -5567.9517] [Branch lengths ] . ( 146 sec) [ -5567.9517] [Topology ] . ( 148 sec) [ -5567.9274] [Topology ] . ( 150 sec) [ -5567.9217] [Topology ] . ( 153 sec) [ -5567.9198] [Topology ] . ( 155 sec) [ -5567.9189] [Topology ] . ( 155 sec) [ -5567.9189] [Topology ] . ( 158 sec) [ -5567.9186] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5567.918577. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 238.205232 1.000000 0.548207 100 55.249522 0.996000 0.171818 98 11.122605 0.919000 0.086189 91 11.244122 0.920000 0.075170 97 30.387740 0.974000 0.041316 49 2.513264 0.699000 0.003685 98 21.312956 0.924000 0.013410 100 122.884969 0.999000 0.040066 88 21.705833 0.947000 0.033234 55 2.768188 0.736000 0.002602 54 2.583522 0.759000 0.003341 100 65.584102 0.995000 0.027796 100 69.205164 0.992000 0.026110 80 30.455580 0.910000 0.009097 100 172.247193 1.000000 0.048953 32 -1.000000 0.000000 0.000000 99 72.485569 1.000000 0.035258 16 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 71 9.848346 0.791000 0.002368 85 23.532153 0.898000 0.004771 67 10.757819 0.776000 0.002379 98 44.634517 0.975000 0.009532 47 -1.000000 0.000000 0.000000 24 -1.000000 0.000000 0.000000 71 14.319944 0.772000 0.002378 78 11.600045 0.762000 0.002383 70 3.479156 0.748000 0.002303 . Printing the most likely tree in file 'proteic_M2304_31x429_2005.phy_phyml_tree.txt'... . Time used 4h35m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo