.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2738_53x1538_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... . 762 patterns found. (out of a total of 1538 sites) . 828 sites without polymorphism (53.84%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -14871.4533] [GTR parameters ] . ( 1 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 1 sec) [ -14653.1273] [Topology ] . ( 3 sec) [ -14475.8787] [Topology ] . ( 5 sec) [ -14449.9667] [Topology ] . ( 7 sec) [ -14437.7778] [Topology ] . ( 8 sec) [ -14433.7019] [Topology ] . ( 10 sec) [ -14432.2135] [Topology ] . ( 12 sec) [ -14431.6513] [Topology ] . ( 13 sec) [ -14431.4138] [Topology ] . ( 15 sec) [ -14431.3098] [Topology ] . ( 17 sec) [ -14431.2636] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -13978.0628] [GTR parameters ] . ( 34 sec) [ -13925.0703] [Alpha ][ 0.310835] . ( 35 sec) [ -13925.0703] [Topology ] . ( 36 sec) [ -13913.8490] [Topology ] . ( 38 sec) [ -13912.8086] [Topology ] . ( 40 sec) [ -13912.5969] [Topology ] . ( 42 sec) [ -13912.5496] [Topology ] . ( 43 sec) [ -13912.5342] [Topology ] . ( 45 sec) [ -13912.5281] [Topology ] . ( 47 sec) [ -13912.5254] [Topology ] . ( 49 sec) [ -13912.5242] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -13910.7996] [GTR parameters ] . ( 66 sec) [ -13910.4734] [Alpha ][ 0.299981] . ( 66 sec) [ -13910.4734] [Topology ] . ( 67 sec) [ -13910.3270] [Topology ] . ( 69 sec) [ -13910.3021] [Topology ] . ( 71 sec) [ -13910.2910] [Topology ] . ( 73 sec) [ -13910.2855] [Topology ] . ( 75 sec) [ -13910.2828] [Topology ] . ( 76 sec) [ -13910.2814] [Topology ] . Checking for NNIs, optimizing five branches... . ( 89 sec) [ -13910.2341] [Topology ] . ( 92 sec) [ -13910.1845] [GTR parameters ] . ( 92 sec) [ -13910.1744] [Alpha ][ 0.298017] . ( 92 sec) [ -13910.1744] [Topology ] . ( 94 sec) [ -13910.1474] [Topology ] . ( 96 sec) [ -13910.1430] [Topology ] . ( 98 sec) [ -13910.1416] [Topology ] . ( 99 sec) [ -13910.1410] [Topology ] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -13910.1397] [GTR parameters ] . ( 113 sec) [ -13910.1397] [Alpha ][ 0.298017] . ( 113 sec) [ -13910.1397] [Topology ] . ( 115 sec) [ -13910.1391] [Topology ] . Checking for NNIs, optimizing five branches... . ( 129 sec) [ -13910.1390] [GTR parameters ] . ( 129 sec) [ -13910.1390] [Alpha ][ 0.298017] . ( 129 sec) [ -13910.1390] [Topology ] . ( 131 sec) [ -13910.1388] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 157 sec) [ -14871.4533] [GTR parameters ] . ( 157 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 157 sec) [ -14651.0565] [ 2609] [depth= 1] . ( 157 sec) [ -14639.3400] [ 2603] [depth= 1] . ( 158 sec) [ -14626.0253] [ 2606] [depth= 1] . ( 158 sec) [ -14615.1978] [ 2603] [depth= 1] . ( 158 sec) [ -14605.7753] [ 2606] [depth= 1] . ( 159 sec) [ -14605.6482] [ 2606] [depth= 1] . ( 159 sec) [ -14605.2736] [ 2606] [depth= 1] . ( 159 sec) [ -14602.5720] [ 2606] [depth= 1] . ( 160 sec) [ -14602.5590] [ 2606] [depth= 1] . ( 162 sec) [ -14596.9605] [ 2605] [depth= 1] . ( 162 sec) [ -14588.0827] [ 2606] [depth= 1] . ( 162 sec) [ -14581.4977] [ 2603] [depth= 1] . ( 163 sec) [ -14580.3923] [ 2605] [depth= 1] . ( 163 sec) [ -14576.7139] [ 2611] [depth= 2] . ( 163 sec) [ -14574.3082] [ 2609] [depth= 1] . ( 163 sec) [ -14572.5761] [ 2610] [depth= 1] . ( 163 sec) [ -14572.3718] [ 2611] [depth= 1] . ( 163 sec) [ -14570.4127] [ 2610] [depth= 1] . ( 163 sec) [ -14565.8626] [ 2612] [depth= 2] . ( 164 sec) [ -14559.3115] [ 2614] [depth= 1] . ( 164 sec) [ -14556.0086] [ 2612] [depth= 1] . ( 164 sec) [ -14551.0187] [ 2614] [depth= 1] . ( 165 sec) [ -14545.9264] [ 2611] [depth= 2] . ( 165 sec) [ -14545.7014] [ 2613] [depth= 2] . ( 165 sec) [ -14537.0638] [ 2616] [depth= 1] . ( 165 sec) [ -14532.2768] [ 2616] [depth= 1] . ( 165 sec) [ -14531.0975] [ 2609] [depth= 1] . ( 165 sec) [ -14529.9781] [ 2608] [depth= 1] . ( 166 sec) [ -14528.6283] [ 2609] [depth= 1] . ( 166 sec) [ -14528.1179] [ 2606] [depth= 1] . ( 167 sec) [ -14527.7063] [ 2609] [depth= 1] . ( 167 sec) [ -14527.5902] [ 2609] [depth= 3] . ( 167 sec) [ -14523.2113] [ 2609] [depth= 2] . ( 167 sec) [ -14516.8903] [ 2609] [depth= 3] . ( 167 sec) [ -14513.4038] [ 2610] [depth= 2] . ( 168 sec) [ -14511.7476] [ 2612] [depth= 1] . ( 168 sec) [ -14511.2641] [ 2610] [depth= 1] . ( 169 sec) [ -14504.4392] [ 2607] [depth= 1] . ( 170 sec) [ -14441.3405] [Branch lengths ] . ( 173 sec) [ -13989.7912] [GTR parameters ] . ( 174 sec) [ -13933.4916] [Alpha ][ 0.303968] . ( 178 sec) [ -13931.5205] [ 2606] [depth= 1] . ( 178 sec) [ -13930.9974] [ 2604] [depth= 1] . ( 179 sec) [ -13930.2816] [ 2606] [depth= 1] . ( 181 sec) [ -13928.9740] [ 2606] [depth= 1] . ( 184 sec) [ -13928.3169] [ 2605] [depth= 1] . ( 186 sec) [ -13914.7656] [Branch lengths ] . ( 190 sec) [ -13912.4700] [GTR parameters ] . ( 190 sec) [ -13912.3186] [Alpha ][ 0.296678] . ( 202 sec) [ -13910.6480] [Branch lengths ] . ( 231 sec) [ -13909.9426] [ 2613] [depth= 4] . ( 245 sec) [ -13909.7408] [ 2613] [depth= 2] . ( 263 sec) [ -13908.7738] [Branch lengths ] . ( 268 sec) [ -13908.6859] [GTR parameters ] . ( 268 sec) [ -13908.6781] [Alpha ][ 0.298294] . ( 330 sec) [ -13908.5638] [Branch lengths ] . ( 330 sec) [ -13908.5638] [Topology ] . ( 332 sec) [ -13908.5510] [Topology ] . ( 333 sec) [ -13908.5468] [Topology ] . ( 335 sec) [ -13908.5448] [Topology ] . ( 337 sec) [ -13908.5439] [Topology ] . ( 341 sec) [ -13908.5378] [GTR parameters ] . ( 341 sec) [ -13908.5377] [Alpha ][ 0.298593] . ( 341 sec) [ -13908.5377] [Topology ] . ( 343 sec) [ -13908.5362] [Topology ] . ( 345 sec) [ -13908.5356] [Topology ] . ( 346 sec) [ -13908.5354] [GTR parameters ] . ( 346 sec) [ -13908.5354] [Alpha ][ 0.298593] . ( 346 sec) [ -13908.5354] [Topology ] . ( 348 sec) [ -13908.5350] [Topology ] . ( 348 sec) [ -13908.5350] [GTR parameters ] . ( 349 sec) [ -13908.5350] [Alpha ][ 0.298593] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -13910.138779 . Log likelihood obtained after SPR moves : -13908.535048 . Log likelihood of the current tree: -13908.535048. . Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'... . Time used 0h6m3s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 361.42user 0.00system 6:03.10elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps