.......................... 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 : 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 SPR moves)... . ( 2 sec) [ -14871.4533] [GTR parameters ] . ( 2 sec) [ -14653.1273] [Alpha ][ 0.500960] . ( 3 sec) [ -14651.0565] [ 2609] [depth= 1] . ( 3 sec) [ -14639.3400] [ 2603] [depth= 1] . ( 3 sec) [ -14626.0253] [ 2606] [depth= 1] . ( 3 sec) [ -14615.1978] [ 2603] [depth= 1] . ( 3 sec) [ -14605.7753] [ 2606] [depth= 1] . ( 5 sec) [ -14605.6482] [ 2606] [depth= 1] . ( 5 sec) [ -14605.2736] [ 2606] [depth= 1] . ( 5 sec) [ -14602.5720] [ 2606] [depth= 1] . ( 6 sec) [ -14602.5590] [ 2606] [depth= 1] . ( 7 sec) [ -14596.9605] [ 2605] [depth= 1] . ( 7 sec) [ -14588.0827] [ 2606] [depth= 1] . ( 7 sec) [ -14581.4977] [ 2603] [depth= 1] . ( 8 sec) [ -14580.3923] [ 2605] [depth= 1] . ( 8 sec) [ -14576.7139] [ 2611] [depth= 2] . ( 8 sec) [ -14574.3082] [ 2609] [depth= 1] . ( 8 sec) [ -14572.5761] [ 2610] [depth= 1] . ( 9 sec) [ -14565.9474] [ 2612] [depth= 1] . ( 9 sec) [ -14562.6943] [ 2610] [depth= 1] . ( 9 sec) [ -14557.7873] [ 2612] [depth= 1] . ( 9 sec) [ -14552.4619] [ 2609] [depth= 2] . ( 9 sec) [ -14549.3964] [ 2609] [depth= 1] . ( 10 sec) [ -14545.2688] [ 2609] [depth= 2] . ( 10 sec) [ -14544.6011] [ 2608] [depth= 1] . ( 10 sec) [ -14538.8470] [ 2606] [depth= 1] . ( 10 sec) [ -14534.8069] [ 2603] [depth= 1] . ( 10 sec) [ -14531.3793] [ 2605] [depth= 1] . ( 11 sec) [ -14530.8750] [ 2604] [depth= 2] . ( 11 sec) [ -14524.0428] [ 2604] [depth= 2] . ( 11 sec) [ -14509.9312] [ 2603] [depth= 3] . ( 11 sec) [ -14508.7271] [ 2601] [depth= 1] . ( 12 sec) [ -14507.8075] [ 2603] [depth= 1] . ( 13 sec) [ -14440.2406] [Branch lengths ] . ( 17 sec) [ -13989.8298] [GTR parameters ] . ( 17 sec) [ -13934.0837] [Alpha ][ 0.304325] . ( 21 sec) [ -13932.2975] [ 2601] [depth= 1] . ( 21 sec) [ -13932.0226] [ 2601] [depth= 1] . ( 22 sec) [ -13931.8852] [ 2603] [depth= 1] . ( 23 sec) [ -13931.2559] [ 2603] [depth= 1] . ( 24 sec) [ -13930.3854] [ 2601] [depth= 1] . ( 25 sec) [ -13915.9990] [Branch lengths ] . ( 29 sec) [ -13913.6929] [GTR parameters ] . ( 30 sec) [ -13913.5720] [Alpha ][ 0.297811] . ( 38 sec) [ -13911.9958] [Branch lengths ] . ( 68 sec) [ -13911.8613] [ 2614] [depth= 3] . ( 79 sec) [ -13911.3511] [ 2615] [depth= 1] . ( 87 sec) [ -13909.9972] [ 2616] [depth= 1] . ( 101 sec) [ -13908.1512] [Branch lengths ] . ( 105 sec) [ -13908.0577] [GTR parameters ] . ( 105 sec) [ -13908.0561] [Alpha ][ 0.298513] . ( 168 sec) [ -13907.8037] [Branch lengths ] . ( 168 sec) [ -13907.8037] [Topology ] . ( 170 sec) [ -13907.7898] [Topology ] . ( 171 sec) [ -13907.7865] [Topology ] . ( 173 sec) [ -13907.7851] [Topology ] . ( 175 sec) [ -13907.7844] [Topology ] . ( 178 sec) [ -13907.7788] [GTR parameters ] . ( 178 sec) [ -13907.7788] [Alpha ][ 0.298513] . ( 178 sec) [ -13907.7788] [Topology ] . ( 180 sec) [ -13907.7776] [Topology ] . ( 181 sec) [ -13907.7771] [Topology ] . ( 182 sec) [ -13907.7771] [GTR parameters ] . ( 182 sec) [ -13907.7771] [Alpha ][ 0.298513] . ( 182 sec) [ -13907.7771] [Topology ] . ( 184 sec) [ -13907.7768] [Topology ] . ( 187 sec) [ -13907.7766] [GTR parameters ] . ( 187 sec) [ -13907.7766] [Alpha ][ 0.298513] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13907.776574. . Printing the most likely tree in file 'nucleic_M2738_53x1538_2006.phy_phyml_tree.txt'... . Time used 0h3m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 195.92user 0.00system 3:20.03elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps