.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -15009.3920] [GTR parameters ] . ( 4 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 4 sec) [ -14724.6451] [ 2562] [depth= 2] . ( 4 sec) [ -14721.3879] [ 2562] [depth= 1] . ( 4 sec) [ -14721.0926] [ 2562] [depth= 1] . ( 5 sec) [ -14717.3225] [ 2562] [depth= 2] . ( 5 sec) [ -14714.6002] [ 2561] [depth= 2] . ( 5 sec) [ -14714.3106] [ 2561] [depth= 1] . ( 5 sec) [ -14713.7025] [ 2562] [depth= 1] . ( 5 sec) [ -14713.3967] [ 2561] [depth= 1] . ( 6 sec) [ -14704.7688] [ 2559] [depth= 2] . ( 6 sec) [ -14696.4518] [ 2558] [depth= 1] . ( 6 sec) [ -14696.3993] [ 2559] [depth= 1] . ( 6 sec) [ -14691.0438] [ 2558] [depth= 1] . ( 7 sec) [ -14690.6716] [ 2559] [depth= 1] . ( 7 sec) [ -14686.7771] [ 2558] [depth= 1] . ( 7 sec) [ -14684.6139] [ 2564] [depth= 1] . ( 7 sec) [ -14678.3535] [ 2558] [depth= 1] . ( 7 sec) [ -14677.1496] [ 2557] [depth= 1] . ( 7 sec) [ -14663.9403] [ 2563] [depth= 1] . ( 7 sec) [ -14662.0337] [ 2557] [depth= 1] . ( 7 sec) [ -14655.9153] [ 2559] [depth= 6] . ( 8 sec) [ -14650.4545] [ 2556] [depth= 2] . ( 8 sec) [ -14645.1718] [ 2554] [depth= 1] . ( 8 sec) [ -14643.2938] [ 2556] [depth= 1] . ( 8 sec) [ -14641.1685] [ 2556] [depth= 1] . ( 8 sec) [ -14636.8014] [ 2556] [depth= 1] . ( 8 sec) [ -14631.7827] [ 2552] [depth= 1] . ( 8 sec) [ -14628.0827] [ 2555] [depth= 1] . ( 8 sec) [ -14626.8927] [ 2552] [depth= 1] . ( 9 sec) [ -14624.3086] [ 2555] [depth= 1] . ( 9 sec) [ -14620.8261] [ 2552] [depth= 1] . ( 9 sec) [ -14603.0429] [ 2551] [depth= 2] . ( 9 sec) [ -14600.8108] [ 2548] [depth= 1] . ( 9 sec) [ -14599.9778] [ 2548] [depth= 1] . ( 9 sec) [ -14580.5860] [ 2541] [depth= 5] . ( 9 sec) [ -14575.8934] [ 2540] [depth= 1] . ( 9 sec) [ -14572.2495] [ 2542] [depth= 1] . ( 10 sec) [ -14563.2781] [ 2537] [depth= 4] . ( 10 sec) [ -14559.8106] [ 2536] [depth= 7] . ( 10 sec) [ -14552.0900] [ 2537] [depth= 1] . ( 10 sec) [ -14548.9195] [ 2537] [depth= 1] . ( 10 sec) [ -14545.3326] [ 2536] [depth= 2] . ( 10 sec) [ -14539.3433] [ 2535] [depth= 1] . ( 10 sec) [ -14530.9129] [ 2530] [depth= 2] . ( 11 sec) [ -14530.5370] [ 2532] [depth= 1] . ( 11 sec) [ -14523.9040] [ 2531] [depth= 1] . ( 11 sec) [ -14520.1306] [ 2530] [depth= 1] . ( 11 sec) [ -14519.0497] [ 2533] [depth= 1] . ( 11 sec) [ -14518.4535] [ 2533] [depth= 1] . ( 11 sec) [ -14516.0381] [ 2532] [depth= 1] . ( 11 sec) [ -14515.9920] [ 2532] [depth= 1] . ( 12 sec) [ -14515.8356] [ 2533] [depth= 1] . ( 12 sec) [ -14515.4332] [ 2533] [depth= 1] . ( 12 sec) [ -14512.1680] [ 2534] [depth= 1] . ( 12 sec) [ -14510.7407] [ 2533] [depth= 1] . ( 12 sec) [ -14510.3018] [ 2535] [depth= 1] . ( 12 sec) [ -14508.7010] [ 2539] [depth= 1] . ( 13 sec) [ -14506.8428] [ 2535] [depth= 1] . ( 14 sec) [ -14449.0742] [Branch lengths ] . ( 15 sec) [ -14448.3339] [GTR parameters ] . ( 15 sec) [ -14354.7575] [Alpha ][ 0.269871] . ( 17 sec) [ -14353.9835] [ 2539] [depth= 1] . ( 19 sec) [ -14353.8441] [ 2538] [depth= 1] . ( 20 sec) [ -14353.4687] [ 2534] [depth= 1] . ( 23 sec) [ -14349.3119] [Branch lengths ] . ( 25 sec) [ -14348.9288] [GTR parameters ] . ( 25 sec) [ -14348.8950] [Alpha ][ 0.272890] . ( 28 sec) [ -14344.3385] [ 2534] [depth= 7] . ( 30 sec) [ -14342.7087] [ 2535] [depth= 6] . ( 33 sec) [ -14339.4954] [Branch lengths ] . ( 35 sec) [ -14339.4174] [GTR parameters ] . ( 35 sec) [ -14339.4173] [Alpha ][ 0.273163] . ( 35 sec) [ -14339.3433] [ 2536] [depth= 2] . ( 38 sec) [ -14337.3021] [ 2535] [depth= 1] . ( 42 sec) [ -14336.3748] [Branch lengths ] . ( 44 sec) [ -14336.3537] [GTR parameters ] . ( 44 sec) [ -14336.3515] [Alpha ][ 0.273902] . ( 56 sec) [ -14336.2708] [Branch lengths ] . ( 96 sec) [ -14334.4668] [ 2540] [depth= 4] . ( 111 sec) [ -14334.4117] [ 2540] [depth= 1] . ( 115 sec) [ -14334.1038] [ 2541] [depth= 1] . ( 116 sec) [ -14334.0078] [ 2541] [depth= 1] . ( 135 sec) [ -14333.4132] [ 2547] [depth= 3] . ( 137 sec) [ -14333.2928] [ 2549] [depth= 1] . ( 137 sec) [ -14333.2326] [ 2550] [depth= 1] . ( 157 sec) [ -14332.4635] [ 2550] [depth= 2] . ( 159 sec) [ -14330.8759] [Branch lengths ] . ( 162 sec) [ -14330.8561] [GTR parameters ] . ( 162 sec) [ -14330.8561] [Alpha ][ 0.273902] . ( 275 sec) [ -14330.5886] [Branch lengths ] . ( 275 sec) [ -14330.5886] [Topology ] . ( 277 sec) [ -14330.2210] [Topology ] . ( 280 sec) [ -14329.7706] [Topology ] . ( 283 sec) [ -14329.7336] [Topology ] . ( 285 sec) [ -14329.7269] [Topology ] . ( 288 sec) [ -14329.7244] [Topology ] . ( 290 sec) [ -14329.7231] [Topology ] . ( 293 sec) [ -14329.7224] [Topology ] . ( 295 sec) [ -14329.7125] [GTR parameters ] . ( 295 sec) [ -14329.6996] [Alpha ][ 0.275712] . ( 295 sec) [ -14329.6996] [Topology ] . ( 298 sec) [ -14329.6976] [Topology ] . ( 300 sec) [ -14329.6965] [Topology ] . ( 303 sec) [ -14329.6959] [Topology ] . ( 305 sec) [ -14329.6957] [GTR parameters ] . ( 305 sec) [ -14329.6956] [Alpha ][ 0.275988] . ( 305 sec) [ -14329.6956] [Topology ] . ( 308 sec) [ -14329.6950] [Topology ] . ( 308 sec) [ -14329.6950] [GTR parameters ] . ( 309 sec) [ -14329.6950] [Alpha ][ 0.275988] . Checking for NNIs, optimizing five branches... . ( 328 sec) [ -14329.5881] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14329.588051. . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 0h5m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 239.53user 0.00system 5:47.33elapsed 68%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps