.......................... 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 : 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 . 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 NNI moves)... . ( 4 sec) [ -15365.1345] [GTR parameters ] . ( 4 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 4 sec) [ -15101.1310] [Topology ] . ( 6 sec) [ -14867.9767] [Topology ] . ( 7 sec) [ -14827.6590] [Topology ] . ( 9 sec) [ -14813.5467] [Topology ] . ( 11 sec) [ -14806.6086] [Topology ] . ( 12 sec) [ -14803.6705] [Topology ] . ( 14 sec) [ -14802.4499] [Topology ] . ( 15 sec) [ -14801.9650] [Topology ] . ( 17 sec) [ -14801.0546] [Topology ] . ( 19 sec) [ -14798.5980] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -14797.1571] [Topology ] . ( 36 sec) [ -14794.9999] [GTR parameters ] . ( 36 sec) [ -14662.2856] [Alpha ][ 0.250961] . ( 36 sec) [ -14662.2856] [Topology ] . ( 38 sec) [ -14660.9408] [Topology ] . ( 39 sec) [ -14660.5526] [Topology ] . ( 41 sec) [ -14660.3874] [Topology ] . ( 42 sec) [ -14660.3135] [Topology ] . ( 44 sec) [ -14660.2777] [Topology ] . ( 46 sec) [ -14660.2591] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -14659.7059] [GTR parameters ] . ( 61 sec) [ -14659.4964] [Alpha ][ 0.244536] . ( 61 sec) [ -14659.4964] [Topology ] . ( 63 sec) [ -14659.4851] [Topology ] . ( 64 sec) [ -14659.4811] [Topology ] . ( 66 sec) [ -14659.4791] [Topology ] . ( 67 sec) [ -14659.4781] [Topology ] . ( 69 sec) [ -14659.4775] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -14659.4757] [GTR parameters ] . ( 83 sec) [ -14659.4757] [Alpha ][ 0.244536] . ( 83 sec) [ -14659.4757] [Topology ] . ( 84 sec) [ -14659.4753] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -14659.4752] [GTR parameters ] . ( 98 sec) [ -14659.4752] [Alpha ][ 0.244536] . ( 98 sec) [ -14659.4752] [Topology ] . ( 100 sec) [ -14659.4750] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 130 sec) [ -15365.1345] [GTR parameters ] . ( 130 sec) [ -15101.1310] [Alpha ][ 0.500960] . ( 130 sec) [ -15101.1009] [ 2403] [depth= 1] . ( 131 sec) [ -15098.8715] [ 2402] [depth= 1] . ( 131 sec) [ -15093.6818] [ 2401] [depth= 1] . ( 133 sec) [ -15092.8612] [ 2406] [depth= 1] . ( 133 sec) [ -15081.3237] [ 2407] [depth= 1] . ( 133 sec) [ -15080.2997] [ 2406] [depth= 1] . ( 133 sec) [ -15077.9949] [ 2407] [depth= 1] . ( 133 sec) [ -15075.3447] [ 2409] [depth= 2] . ( 133 sec) [ -15066.2616] [ 2405] [depth= 2] . ( 134 sec) [ -15042.6033] [ 2407] [depth= 1] . ( 134 sec) [ -15042.2844] [ 2409] [depth= 1] . ( 134 sec) [ -15037.4363] [ 2414] [depth= 2] . ( 134 sec) [ -15034.8203] [ 2407] [depth= 2] . ( 134 sec) [ -15033.3611] [ 2405] [depth= 1] . ( 134 sec) [ -15028.4546] [ 2411] [depth= 1] . ( 134 sec) [ -15024.4674] [ 2405] [depth= 1] . ( 134 sec) [ -15013.3167] [ 2407] [depth= 1] . ( 135 sec) [ -15010.1207] [ 2410] [depth= 1] . ( 135 sec) [ -14999.2240] [ 2408] [depth= 1] . ( 135 sec) [ -14998.0467] [ 2407] [depth= 1] . ( 136 sec) [ -14993.0069] [ 2408] [depth= 1] . ( 137 sec) [ -14990.9335] [ 2404] [depth= 2] . ( 137 sec) [ -14984.5772] [ 2399] [depth= 1] . ( 137 sec) [ -14983.2566] [ 2404] [depth= 1] . ( 137 sec) [ -14957.0542] [ 2403] [depth= 1] . ( 137 sec) [ -14948.7024] [ 2400] [depth= 1] . ( 137 sec) [ -14944.2341] [ 2404] [depth= 2] . ( 138 sec) [ -14942.0251] [ 2404] [depth= 1] . ( 138 sec) [ -14935.9613] [ 2405] [depth= 1] . ( 138 sec) [ -14932.2116] [ 2408] [depth= 1] . ( 138 sec) [ -14930.9248] [ 2405] [depth= 1] . ( 138 sec) [ -14924.1668] [ 2404] [depth= 1] . ( 138 sec) [ -14923.1236] [ 2407] [depth= 1] . ( 139 sec) [ -14921.4219] [ 2410] [depth= 1] . ( 139 sec) [ -14920.9806] [ 2407] [depth= 1] . ( 140 sec) [ -14919.6076] [ 2410] [depth= 3] . ( 140 sec) [ -14918.9091] [ 2410] [depth= 1] . ( 140 sec) [ -14918.8393] [ 2410] [depth= 1] . ( 140 sec) [ -14918.7493] [ 2410] [depth= 1] . ( 140 sec) [ -14916.7639] [ 2410] [depth= 1] . ( 141 sec) [ -14913.6688] [ 2409] [depth= 2] . ( 142 sec) [ -14818.6887] [Branch lengths ] . ( 144 sec) [ -14816.9403] [GTR parameters ] . ( 144 sec) [ -14684.1683] [Alpha ][ 0.250961] . ( 146 sec) [ -14680.5537] [ 2404] [depth= 1] . ( 149 sec) [ -14680.3275] [ 2408] [depth= 1] . ( 151 sec) [ -14680.2820] [ 2404] [depth= 1] . ( 151 sec) [ -14677.0815] [ 2406] [depth= 1] . ( 152 sec) [ -14675.9054] [ 2410] [depth= 1] . ( 154 sec) [ -14674.7975] [ 2406] [depth= 3] . ( 154 sec) [ -14674.6222] [ 2406] [depth= 1] . ( 157 sec) [ -14664.5296] [Branch lengths ] . ( 159 sec) [ -14664.1216] [GTR parameters ] . ( 159 sec) [ -14663.7831] [Alpha ][ 0.242689] . ( 169 sec) [ -14663.7647] [ 2406] [depth= 1] . ( 170 sec) [ -14662.5765] [Branch lengths ] . ( 173 sec) [ -14662.5623] [GTR parameters ] . ( 173 sec) [ -14662.5565] [Alpha ][ 0.243734] . ( 184 sec) [ -14662.3659] [Branch lengths ] . ( 233 sec) [ -14662.3234] [Branch lengths ] . ( 233 sec) [ -14662.3234] [Topology ] . ( 235 sec) [ -14662.0968] [Topology ] . ( 236 sec) [ -14661.6754] [Topology ] . ( 238 sec) [ -14660.2749] [Topology ] . ( 240 sec) [ -14658.2223] [Topology ] . ( 241 sec) [ -14657.8743] [Topology ] . ( 243 sec) [ -14657.7992] [Topology ] . ( 245 sec) [ -14657.7815] [Topology ] . ( 246 sec) [ -14657.7771] [Topology ] . ( 247 sec) [ -14657.7732] [GTR parameters ] . ( 247 sec) [ -14657.7689] [Alpha ][ 0.244620] . ( 247 sec) [ -14657.7689] [Topology ] . ( 249 sec) [ -14657.7678] [Topology ] . ( 250 sec) [ -14657.7675] [Topology ] . ( 251 sec) [ -14657.7667] [GTR parameters ] . ( 251 sec) [ -14657.7667] [Alpha ][ 0.244620] . ( 251 sec) [ -14657.7667] [Topology ] . ( 253 sec) [ -14657.7666] [Topology ] . ( 254 sec) [ -14657.7665] [GTR parameters ] . ( 254 sec) [ -14657.7665] [Alpha ][ 0.244620] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -14659.474973 . Log likelihood obtained after SPR moves : -14657.766539 . Log likelihood of the current tree: -14657.766539. . Printing the most likely tree in file 'nucleic_M2565_51x1951_2006.phy_phyml_tree.txt'... . Time used 0h4m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 264.40user 0.00system 4:27.46elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps