.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2565_51x1951_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 763 patterns found. (out of a total of 1951 sites) . 1244 sites without polymorphism (63.76%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -15365.1345] [GTR parameters ] . ( 3 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 5 sec) [ -15101.1009] [ 2403] [depth= 1] . ( 15 sec) [ -15098.8715] [ 2402] [depth= 1] . ( 19 sec) [ -15093.6818] [ 2401] [depth= 1] . ( 30 sec) [ -15092.8612] [ 2406] [depth= 1] . ( 30 sec) [ -15081.3237] [ 2407] [depth= 1] . ( 30 sec) [ -15080.2997] [ 2406] [depth= 1] . ( 31 sec) [ -15077.9949] [ 2407] [depth= 1] . ( 32 sec) [ -15075.3447] [ 2409] [depth= 2] . ( 32 sec) [ -15066.2616] [ 2405] [depth= 2] . ( 34 sec) [ -15042.6033] [ 2407] [depth= 1] . ( 34 sec) [ -15042.2844] [ 2409] [depth= 1] . ( 35 sec) [ -15037.4363] [ 2414] [depth= 2] . ( 35 sec) [ -15034.8203] [ 2407] [depth= 2] . ( 35 sec) [ -15033.3611] [ 2405] [depth= 1] . ( 36 sec) [ -15032.9398] [ 2412] [depth= 1] . ( 36 sec) [ -15023.6084] [ 2405] [depth= 1] . ( 37 sec) [ -15012.2073] [ 2407] [depth= 1] . ( 37 sec) [ -15008.9351] [ 2410] [depth= 1] . ( 43 sec) [ -14997.9787] [ 2408] [depth= 1] . ( 44 sec) [ -14996.7726] [ 2407] [depth= 1] . ( 45 sec) [ -14991.6751] [ 2408] [depth= 1] . ( 53 sec) [ -14989.4243] [ 2404] [depth= 2] . ( 56 sec) [ -14982.9679] [ 2399] [depth= 1] . ( 56 sec) [ -14981.8184] [ 2404] [depth= 1] . ( 56 sec) [ -14955.6978] [ 2403] [depth= 1] . ( 56 sec) [ -14947.0574] [ 2400] [depth= 1] . ( 56 sec) [ -14942.7612] [ 2404] [depth= 2] . ( 57 sec) [ -14940.5282] [ 2404] [depth= 1] . ( 57 sec) [ -14934.3842] [ 2405] [depth= 1] . ( 58 sec) [ -14930.6059] [ 2408] [depth= 1] . ( 59 sec) [ -14929.3073] [ 2405] [depth= 1] . ( 60 sec) [ -14922.4497] [ 2404] [depth= 1] . ( 60 sec) [ -14921.4297] [ 2407] [depth= 1] . ( 64 sec) [ -14919.6825] [ 2410] [depth= 1] . ( 64 sec) [ -14919.2516] [ 2407] [depth= 1] . ( 72 sec) [ -14917.8229] [ 2410] [depth= 3] . ( 72 sec) [ -14917.1130] [ 2410] [depth= 1] . ( 72 sec) [ -14917.0495] [ 2410] [depth= 1] . ( 73 sec) [ -14916.9593] [ 2410] [depth= 1] . ( 75 sec) [ -14914.9730] [ 2410] [depth= 1] . ( 75 sec) [ -14911.8756] [ 2409] [depth= 2] . ( 80 sec) [ -14818.6752] [Branch lengths ] . ( 82 sec) [ -14816.9252] [GTR parameters ] . ( 82 sec) [ -14684.1210] [Alpha ][ 0.250961] . ( 105 sec) [ -14680.5075] [ 2404] [depth= 1] . ( 132 sec) [ -14680.3101] [ 2408] [depth= 1] . ( 151 sec) [ -14680.2479] [ 2404] [depth= 1] . ( 155 sec) [ -14677.0268] [ 2406] [depth= 1] . ( 157 sec) [ -14675.8522] [ 2410] [depth= 1] . ( 177 sec) [ -14674.7452] [ 2406] [depth= 3] . ( 178 sec) [ -14674.5699] [ 2406] [depth= 1] . ( 191 sec) [ -14664.5222] [Branch lengths ] . ( 193 sec) [ -14664.1173] [GTR parameters ] . ( 193 sec) [ -14663.7794] [Alpha ][ 0.242695] . ( 296 sec) [ -14663.7609] [ 2406] [depth= 1] . ( 305 sec) [ -14662.5777] [Branch lengths ] . ( 307 sec) [ -14662.5624] [GTR parameters ] . ( 307 sec) [ -14662.5567] [Alpha ][ 0.243728] . ( 422 sec) [ -14662.3655] [Branch lengths ] . ( 474 sec) [ -14662.3228] [Branch lengths ] . ( 474 sec) [ -14662.3228] [Topology ] . ( 476 sec) [ -14662.0962] [Topology ] . ( 477 sec) [ -14661.6747] [Topology ] . ( 479 sec) [ -14660.2744] [Topology ] . ( 480 sec) [ -14658.2219] [Topology ] . ( 482 sec) [ -14657.8739] [Topology ] . ( 484 sec) [ -14657.7988] [Topology ] . ( 485 sec) [ -14657.7811] [Topology ] . ( 487 sec) [ -14657.7767] [Topology ] . ( 488 sec) [ -14657.7725] [GTR parameters ] . ( 488 sec) [ -14657.7681] [Alpha ][ 0.244631] . ( 488 sec) [ -14657.7681] [Topology ] . ( 490 sec) [ -14657.7670] [Topology ] . ( 492 sec) [ -14657.7667] [Topology ] . ( 492 sec) [ -14657.7667] [GTR parameters ] . ( 492 sec) [ -14657.7667] [Alpha ][ 0.244631] . ( 492 sec) [ -14657.7667] [Topology ] . ( 494 sec) [ -14657.7666] [Topology ] . ( 494 sec) [ -14657.7666] [GTR parameters ] . ( 494 sec) [ -14657.7666] [Alpha ][ 0.244631] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14657.766568. . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Time used 0h8m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 507.05user 0.00system 8:29.15elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps