.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1504_37x547_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... . 429 patterns found. (out of a total of 547 sites) . 136 sites without polymorphism (24.86%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 38Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 11 sec) [ -12564.8178] [ 2077] [depth= 1] . ( 11 sec) [ -12557.9134] [ 2073] [depth= 1] . ( 12 sec) [ -12556.1707] [ 2075] [depth= 1] . ( 12 sec) [ -12555.6245] [ 2073] [depth= 1] . ( 13 sec) [ -12550.6492] [ 2074] [depth= 2] . ( 14 sec) [ -12545.7589] [ 2079] [depth= 1] . ( 15 sec) [ -12544.3600] [ 2077] [depth= 2] . ( 15 sec) [ -12538.3133] [ 2074] [depth= 1] . ( 16 sec) [ -12530.3034] [ 2068] [depth= 3] . ( 21 sec) [ -12528.8675] [ 2068] [depth= 1] . ( 21 sec) [ -12526.4384] [ 2068] [depth= 1] . ( 24 sec) [ -12525.1279] [ 2072] [depth= 1] . ( 28 sec) [ -12524.0781] [ 2073] [depth= 1] . ( 28 sec) [ -12517.5328] [ 2072] [depth= 1] . ( 29 sec) [ -12515.3045] [ 2071] [depth= 3] . ( 29 sec) [ -12514.3455] [ 2078] [depth= 1] . ( 31 sec) [ -12513.0907] [ 2078] [depth= 1] . ( 32 sec) [ -12481.6476] [Branch lengths ] . ( 43 sec) [ -12480.4890] [ 2072] [depth= 1] . ( 60 sec) [ -12479.9676] [ 2067] [depth= 1] . ( 64 sec) [ -12479.5785] [ 2068] [depth= 3] . ( 68 sec) [ -12475.2527] [Branch lengths ] . ( 103 sec) [ -12474.7406] [Branch lengths ] . ( 104 sec) [ -12474.7406] [Topology ] . ( 107 sec) [ -12474.5847] [Topology ] . ( 111 sec) [ -12474.4952] [Topology ] . ( 115 sec) [ -12474.4251] [Topology ] . ( 119 sec) [ -12474.3695] [Topology ] . ( 122 sec) [ -12474.3249] [Topology ] . ( 126 sec) [ -12474.2890] [Topology ] . ( 126 sec) [ -12474.2890] [Topology ] . ( 130 sec) [ -12474.2599] [Topology ] . ( 134 sec) [ -12474.2364] [Topology ] . ( 138 sec) [ -12474.2172] [Topology ] . ( 141 sec) [ -12474.2015] [Topology ] . ( 145 sec) [ -12474.1887] [Topology ] . ( 149 sec) [ -12474.1782] [Topology ] . ( 149 sec) [ -12474.1782] [Topology ] . ( 153 sec) [ -12474.1695] [Topology ] . ( 157 sec) [ -12474.1624] [Topology ] . ( 160 sec) [ -12474.1565] [Topology ] . ( 164 sec) [ -12474.1517] [Topology ] . ( 168 sec) [ -12474.1476] [Topology ] . ( 172 sec) [ -12474.1443] [Topology ] . ( 172 sec) [ -12474.1443] [Topology ] . ( 176 sec) [ -12474.1415] [Topology ] . ( 179 sec) [ -12474.1392] [Topology ] . ( 183 sec) [ -12474.1372] [Topology ] . ( 187 sec) [ -12474.1356] [Topology ] . ( 191 sec) [ -12474.1343] [Topology ] . ( 194 sec) [ -12474.1332] [Topology ] . ( 195 sec) [ -12474.1332] [Topology ] . ( 198 sec) [ -12474.1323] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12474.132252. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 59.260593 0.999000 0.069749 98 23.174959 0.968000 0.039776 100 279.053071 1.000000 0.257633 16 1.399332 0.173000 0.022415 63 9.598692 0.900000 0.039757 100 165.003068 1.000000 0.173584 52 6.295771 0.388000 0.052031 100 118.362654 1.000000 0.092167 100 52.995646 0.995000 0.045121 100 115.325433 1.000000 0.101116 73 14.956153 0.857000 0.027690 100 147.178007 1.000000 0.150188 100 113.170583 1.000000 0.093198 55 3.187193 0.354000 0.020706 100 93.724959 0.998000 0.072075 100 75.269418 1.000000 0.065538 100 69.985522 0.998000 0.048235 100 72.137469 0.997000 0.051905 100 52.129048 0.990000 0.033516 71 8.698905 0.729000 0.016737 20 4.578754 0.403000 0.025358 84 53.614905 0.990000 0.070552 95 31.796419 0.981000 0.068032 39 1.854061 0.169000 0.029251 100 194.935462 1.000000 0.165827 39 7.593578 0.578000 0.041538 100 82.309747 0.996000 0.085112 89 37.334375 0.976000 0.049372 81 36.989416 0.979000 0.048526 83 23.933791 0.932000 0.028094 100 56.399998 0.993000 0.030179 75 11.282713 0.796000 0.007650 35 1.596842 0.126000 0.012982 97 52.970038 0.995000 0.094262 . Printing the most likely tree in file 'proteic_M1504_37x547_2003.phy_phyml_tree.txt'... . Time used 5h12m55s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo