.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -15011.6040] [GTR parameters ] . ( 2 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 2 sec) [ -14780.7799] [Topology ] . ( 4 sec) [ -14624.4043] [Topology ] . ( 6 sec) [ -14602.8474] [Topology ] . ( 8 sec) [ -14597.0947] [Topology ] . ( 10 sec) [ -14595.2996] [Topology ] . ( 12 sec) [ -14594.6333] [Topology ] . ( 14 sec) [ -14594.3799] [Topology ] . ( 16 sec) [ -14594.2815] [Topology ] . ( 18 sec) [ -14594.2428] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -14114.5883] [GTR parameters ] . ( 37 sec) [ -14006.0829] [Alpha ][ 0.250961] . ( 38 sec) [ -14006.0829] [Topology ] . ( 40 sec) [ -14001.9646] [Topology ] . ( 41 sec) [ -14000.6200] [Topology ] . ( 43 sec) [ -14000.2713] [Topology ] . ( 45 sec) [ -14000.1289] [Topology ] . ( 47 sec) [ -14000.0645] [Topology ] . ( 49 sec) [ -14000.0344] [Topology ] . ( 51 sec) [ -14000.0201] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -13998.9233] [GTR parameters ] . ( 71 sec) [ -13998.9208] [Alpha ][ 0.250133] . ( 71 sec) [ -13998.9208] [Topology ] . ( 73 sec) [ -13998.8831] [Topology ] . ( 75 sec) [ -13998.8674] [Topology ] . ( 77 sec) [ -13998.8600] [Topology ] . ( 79 sec) [ -13998.8564] [Topology ] . ( 81 sec) [ -13998.8547] [Topology ] . ( 83 sec) [ -13998.8539] [Topology ] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -13998.8521] [GTR parameters ] . ( 99 sec) [ -13998.8503] [Alpha ][ 0.250757] . ( 99 sec) [ -13998.8503] [Topology ] . ( 101 sec) [ -13998.8493] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -13998.8493] [GTR parameters ] . ( 117 sec) [ -13998.8493] [Alpha ][ 0.250757] . ( 117 sec) [ -13998.8493] [Topology ] . ( 119 sec) [ -13998.8488] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 151 sec) [ -15011.6040] [GTR parameters ] . ( 151 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 151 sec) [ -14763.5982] [ 2324] [depth= 1] . ( 152 sec) [ -14761.9657] [ 2324] [depth= 1] . ( 152 sec) [ -14761.4417] [ 2324] [depth= 1] . ( 152 sec) [ -14758.9385] [ 2324] [depth= 1] . ( 154 sec) [ -14754.4887] [ 2324] [depth= 1] . ( 154 sec) [ -14748.4513] [ 2324] [depth= 1] . ( 154 sec) [ -14747.6244] [ 2326] [depth= 1] . ( 155 sec) [ -14747.5440] [ 2328] [depth= 1] . ( 155 sec) [ -14746.2770] [ 2326] [depth= 1] . ( 155 sec) [ -14745.4215] [ 2324] [depth= 1] . ( 156 sec) [ -14739.8437] [ 2319] [depth= 1] . ( 156 sec) [ -14735.4461] [ 2319] [depth= 2] . ( 156 sec) [ -14733.8271] [ 2315] [depth= 2] . ( 156 sec) [ -14733.4227] [ 2319] [depth= 1] . ( 157 sec) [ -14733.2549] [ 2320] [depth= 1] . ( 157 sec) [ -14731.6522] [ 2320] [depth= 1] . ( 158 sec) [ -14727.5651] [ 2319] [depth= 1] . ( 158 sec) [ -14718.8341] [ 2318] [depth= 2] . ( 159 sec) [ -14717.4738] [ 2320] [depth= 1] . ( 160 sec) [ -14705.6155] [ 2324] [depth= 2] . ( 160 sec) [ -14696.6055] [ 2318] [depth= 2] . ( 160 sec) [ -14692.9109] [ 2318] [depth= 1] . ( 160 sec) [ -14692.2380] [ 2318] [depth= 1] . ( 161 sec) [ -14691.2322] [ 2320] [depth= 1] . ( 161 sec) [ -14683.0303] [ 2318] [depth= 1] . ( 163 sec) [ -14681.9770] [ 2319] [depth= 1] . ( 163 sec) [ -14680.2524] [ 2319] [depth= 2] . ( 164 sec) [ -14679.7118] [ 2320] [depth= 1] . ( 164 sec) [ -14679.3119] [ 2324] [depth= 4] . ( 164 sec) [ -14676.9398] [ 2323] [depth= 1] . ( 164 sec) [ -14676.6320] [ 2326] [depth= 1] . ( 165 sec) [ -14676.5942] [ 2331] [depth= 5] . ( 165 sec) [ -14675.0120] [ 2325] [depth= 2] . ( 165 sec) [ -14671.4546] [ 2325] [depth= 1] . ( 166 sec) [ -14668.0383] [ 2325] [depth= 1] . ( 166 sec) [ -14665.0324] [ 2325] [depth= 1] . ( 168 sec) [ -14620.0875] [Branch lengths ] . ( 172 sec) [ -14145.3710] [GTR parameters ] . ( 172 sec) [ -14030.6974] [Alpha ][ 0.250961] . ( 173 sec) [ -14030.5817] [ 2324] [depth= 1] . ( 174 sec) [ -14030.5434] [ 2327] [depth= 1] . ( 175 sec) [ -14028.9277] [ 2327] [depth= 2] . ( 176 sec) [ -14026.9323] [ 2327] [depth= 1] . ( 178 sec) [ -14025.9535] [ 2325] [depth= 1] . ( 178 sec) [ -14024.4685] [ 2322] [depth= 1] . ( 181 sec) [ -14019.0906] [ 2315] [depth= 4] . ( 181 sec) [ -14018.2908] [ 2313] [depth= 1] . ( 183 sec) [ -14018.0722] [ 2314] [depth= 1] . ( 187 sec) [ -14016.4404] [ 2316] [depth= 1] . ( 187 sec) [ -14011.6093] [ 2314] [depth= 2] . ( 188 sec) [ -14010.9861] [ 2316] [depth= 1] . ( 188 sec) [ -14010.6796] [ 2318] [depth= 1] . ( 188 sec) [ -14007.6593] [ 2313] [depth= 2] . ( 189 sec) [ -14007.6479] [ 2313] [depth= 2] . ( 190 sec) [ -14006.4128] [ 2316] [depth= 1] . ( 191 sec) [ -14005.9963] [ 2313] [depth= 1] . ( 192 sec) [ -13997.3082] [Branch lengths ] . ( 197 sec) [ -13996.3161] [GTR parameters ] . ( 197 sec) [ -13996.2355] [Alpha ][ 0.246642] . ( 206 sec) [ -13995.8097] [ 2311] [depth= 1] . ( 217 sec) [ -13993.9109] [Branch lengths ] . ( 222 sec) [ -13993.8880] [GTR parameters ] . ( 222 sec) [ -13993.8731] [Alpha ][ 0.248524] . ( 242 sec) [ -13993.6177] [Branch lengths ] . ( 320 sec) [ -13993.5906] [Branch lengths ] . ( 320 sec) [ -13993.5906] [Topology ] . ( 322 sec) [ -13993.5883] [Topology ] . ( 324 sec) [ -13993.5876] [Topology ] . ( 327 sec) [ -13993.5844] [GTR parameters ] . ( 327 sec) [ -13993.5791] [Alpha ][ 0.249640] . ( 327 sec) [ -13993.5791] [Topology ] . ( 329 sec) [ -13993.5779] [Topology ] . ( 331 sec) [ -13993.5774] [Topology ] . ( 334 sec) [ -13993.5771] [GTR parameters ] . ( 334 sec) [ -13993.5771] [Alpha ][ 0.249640] . ( 334 sec) [ -13993.5771] [Topology ] . ( 336 sec) [ -13993.5768] [Topology ] . ( 337 sec) [ -13993.5768] [GTR parameters ] . ( 337 sec) [ -13993.5768] [Alpha ][ 0.249640] . Checking for NNIs, optimizing five branches... . ( 352 sec) [ -13993.2261] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -13998.848836 . Log likelihood obtained after SPR moves : -13993.226072 . Log likelihood of the current tree: -13993.226072. . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Time used 0h6m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 365.85user 0.00system 6:08.37elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps