.......................... 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)... . ( 4 sec) [ -15365.1345] [GTR parameters ] . ( 4 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 5 sec) [ -15101.1009] [ 2403] [depth= 1] . ( 5 sec) [ -15098.8715] [ 2402] [depth= 1] . ( 6 sec) [ -15093.6818] [ 2401] [depth= 1] . ( 6 sec) [ -15092.8612] [ 2406] [depth= 1] . ( 6 sec) [ -15081.3237] [ 2407] [depth= 1] . ( 7 sec) [ -15080.2997] [ 2406] [depth= 1] . ( 7 sec) [ -15077.9949] [ 2407] [depth= 1] . ( 7 sec) [ -15067.1487] [ 2405] [depth= 1] . ( 7 sec) [ -15065.0067] [ 2407] [depth= 1] . ( 7 sec) [ -15048.7396] [ 2410] [depth= 1] . ( 8 sec) [ -15048.7123] [ 2408] [depth= 1] . ( 8 sec) [ -15044.3314] [ 2413] [depth= 1] . ( 8 sec) [ -15039.7874] [ 2408] [depth= 1] . ( 8 sec) [ -15025.8176] [ 2410] [depth= 1] . ( 8 sec) [ -15017.5989] [ 2415] [depth= 1] . ( 9 sec) [ -15006.7315] [ 2413] [depth= 1] . ( 9 sec) [ -15005.5309] [ 2412] [depth= 1] . ( 9 sec) [ -15000.6955] [ 2413] [depth= 1] . ( 10 sec) [ -14998.6483] [ 2408] [depth= 2] . ( 10 sec) [ -14985.9747] [ 2405] [depth= 1] . ( 10 sec) [ -14977.2182] [ 2410] [depth= 2] . ( 10 sec) [ -14974.8949] [ 2409] [depth= 1] . ( 10 sec) [ -14955.3891] [ 2407] [depth= 1] . ( 11 sec) [ -14944.4462] [ 2409] [depth= 1] . ( 11 sec) [ -14943.9470] [ 2407] [depth= 1] . ( 11 sec) [ -14936.5164] [ 2409] [depth= 1] . ( 11 sec) [ -14924.6699] [ 2407] [depth= 1] . ( 11 sec) [ -14921.7876] [ 2409] [depth= 1] . ( 11 sec) [ -14921.4163] [ 2408] [depth= 1] . ( 11 sec) [ -14919.4722] [ 2409] [depth= 1] . ( 11 sec) [ -14919.3492] [ 2408] [depth= 1] . ( 12 sec) [ -14918.2838] [ 2411] [depth= 3] . ( 12 sec) [ -14917.5834] [ 2411] [depth= 1] . ( 12 sec) [ -14917.5138] [ 2411] [depth= 1] . ( 12 sec) [ -14917.4237] [ 2411] [depth= 1] . ( 13 sec) [ -14915.5893] [ 2411] [depth= 1] . ( 13 sec) [ -14912.2617] [ 2410] [depth= 2] . ( 14 sec) [ -14824.2241] [Branch lengths ] . ( 16 sec) [ -14822.7007] [GTR parameters ] . ( 16 sec) [ -14689.8952] [Alpha ][ 0.250961] . ( 17 sec) [ -14686.1825] [ 2405] [depth= 1] . ( 18 sec) [ -14684.5045] [ 2400] [depth= 2] . ( 19 sec) [ -14684.4170] [ 2403] [depth= 1] . ( 19 sec) [ -14683.9171] [ 2400] [depth= 1] . ( 20 sec) [ -14682.4409] [ 2403] [depth= 1] . ( 21 sec) [ -14682.3745] [ 2404] [depth= 1] . ( 21 sec) [ -14681.3036] [ 2400] [depth= 3] . ( 22 sec) [ -14681.1306] [ 2400] [depth= 1] . ( 23 sec) [ -14669.9422] [Branch lengths ] . ( 25 sec) [ -14669.5463] [GTR parameters ] . ( 25 sec) [ -14669.1978] [Alpha ][ 0.242554] . ( 30 sec) [ -14669.1761] [ 2400] [depth= 1] . ( 31 sec) [ -14668.1519] [Branch lengths ] . ( 33 sec) [ -14668.1431] [GTR parameters ] . ( 34 sec) [ -14668.1347] [Alpha ][ 0.243824] . ( 41 sec) [ -14667.9466] [Branch lengths ] . ( 60 sec) [ -14666.5482] [ 2402] [depth= 2] . ( 90 sec) [ -14662.4468] [Branch lengths ] . ( 92 sec) [ -14662.3846] [GTR parameters ] . ( 92 sec) [ -14662.3838] [Alpha ][ 0.244187] . ( 143 sec) [ -14662.2590] [Branch lengths ] . ( 143 sec) [ -14662.2590] [Topology ] . ( 144 sec) [ -14661.6987] [Topology ] . ( 146 sec) [ -14660.0087] [Topology ] . ( 147 sec) [ -14658.1858] [Topology ] . ( 149 sec) [ -14657.8614] [Topology ] . ( 151 sec) [ -14657.7915] [Topology ] . ( 153 sec) [ -14657.7749] [Topology ] . ( 155 sec) [ -14657.7708] [Topology ] . ( 156 sec) [ -14657.7698] [Topology ] . ( 157 sec) [ -14657.7681] [GTR parameters ] . ( 158 sec) [ -14657.7669] [Alpha ][ 0.244628] . ( 158 sec) [ -14657.7669] [Topology ] . ( 159 sec) [ -14657.7666] [Topology ] . ( 160 sec) [ -14657.7666] [GTR parameters ] . ( 160 sec) [ -14657.7666] [Alpha ][ 0.244628] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -14657.766618. . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Time used 0h2m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 169.44user 0.00system 2:53.48elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps