.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2733_60x1207_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... . 564 patterns found. (out of a total of 1207 sites) . 771 sites without polymorphism (63.88%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -11527.8412] [GTR parameters ] . ( 2 sec) [ -11290.9171] [Alpha ][ 0.500960] . ( 3 sec) [ -11290.4691] [ 1959] [depth= 1] . ( 3 sec) [ -11290.1769] [ 1959] [depth= 1] . ( 3 sec) [ -11290.1047] [ 1959] [depth= 1] . ( 4 sec) [ -11289.2190] [ 1959] [depth= 1] . ( 4 sec) [ -11270.6339] [ 1959] [depth= 1] . ( 4 sec) [ -11268.5424] [ 1960] [depth= 1] . ( 4 sec) [ -11255.4173] [ 1959] [depth= 1] . ( 4 sec) [ -11242.4770] [ 1954] [depth= 1] . ( 5 sec) [ -11231.1177] [ 1952] [depth= 1] . ( 5 sec) [ -11229.5680] [ 1952] [depth= 1] . ( 5 sec) [ -11229.4830] [ 1950] [depth= 1] . ( 5 sec) [ -11225.6830] [ 1954] [depth= 1] . ( 5 sec) [ -11218.3725] [ 1955] [depth= 2] . ( 6 sec) [ -11204.7109] [ 1953] [depth= 1] . ( 6 sec) [ -11203.7032] [ 1953] [depth= 1] . ( 6 sec) [ -11203.5111] [ 1953] [depth= 1] . ( 6 sec) [ -11203.1156] [ 1953] [depth= 1] . ( 7 sec) [ -11200.8713] [ 1951] [depth= 1] . ( 7 sec) [ -11198.8792] [ 1954] [depth= 1] . ( 7 sec) [ -11188.8549] [ 1951] [depth= 1] . ( 7 sec) [ -11182.1049] [ 1952] [depth= 4] . ( 7 sec) [ -11179.3089] [ 1951] [depth= 1] . ( 8 sec) [ -11171.4594] [ 1948] [depth= 1] . ( 8 sec) [ -11166.3739] [ 1946] [depth= 1] . ( 8 sec) [ -11164.4835] [ 1946] [depth= 1] . ( 8 sec) [ -11163.6328] [ 1945] [depth= 1] . ( 8 sec) [ -11160.4337] [ 1945] [depth= 4] . ( 9 sec) [ -11154.5249] [ 1946] [depth= 1] . ( 9 sec) [ -11154.2013] [ 1945] [depth= 2] . ( 9 sec) [ -11152.8169] [ 1948] [depth= 2] . ( 9 sec) [ -11142.7307] [ 1945] [depth= 3] . ( 9 sec) [ -11140.7106] [ 1944] [depth= 1] . ( 9 sec) [ -11135.8214] [ 1945] [depth= 2] . ( 10 sec) [ -11133.4980] [ 1944] [depth= 1] . ( 10 sec) [ -11133.3374] [ 1944] [depth= 1] . ( 10 sec) [ -11132.0226] [ 1944] [depth= 1] . ( 10 sec) [ -11128.9941] [ 1942] [depth= 1] . ( 10 sec) [ -11128.1513] [ 1941] [depth= 2] . ( 10 sec) [ -11127.7123] [ 1941] [depth= 1] . ( 11 sec) [ -11072.3564] [Branch lengths ] . ( 12 sec) [ -11066.0703] [GTR parameters ] . ( 12 sec) [ -10954.4935] [Alpha ][ 0.250961] . ( 14 sec) [ -10953.8237] [ 1940] [depth= 1] . ( 17 sec) [ -10953.1368] [ 1939] [depth= 2] . ( 17 sec) [ -10951.4862] [ 1939] [depth= 1] . ( 17 sec) [ -10951.2058] [ 1939] [depth= 1] . ( 18 sec) [ -10946.6974] [Branch lengths ] . ( 19 sec) [ -10944.3473] [GTR parameters ] . ( 19 sec) [ -10941.0363] [Alpha ][ 0.220947] . ( 26 sec) [ -10940.4524] [Branch lengths ] . ( 85 sec) [ -10940.4107] [Branch lengths ] . ( 85 sec) [ -10940.4107] [Topology ] . ( 86 sec) [ -10940.4086] [Topology ] . ( 88 sec) [ -10940.4082] [Topology ] . ( 89 sec) [ -10940.3324] [GTR parameters ] . ( 89 sec) [ -10940.2686] [Alpha ][ 0.217166] . ( 89 sec) [ -10940.2686] [Topology ] . ( 90 sec) [ -10940.2648] [Topology ] . ( 92 sec) [ -10940.2635] [Topology ] . ( 93 sec) [ -10940.2631] [Topology ] . ( 94 sec) [ -10940.2613] [GTR parameters ] . ( 94 sec) [ -10940.2599] [Alpha ][ 0.216557] . ( 94 sec) [ -10940.2599] [Topology ] . ( 95 sec) [ -10940.2594] [Topology ] . ( 96 sec) [ -10940.2594] [GTR parameters ] . ( 96 sec) [ -10940.2594] [Alpha ][ 0.216557] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10940.259388. . Printing the most likely tree in file 'nucleic_M2733_60x1207_2006.phy_phyml_tree.txt'... . Time used 0h1m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 105.07user 0.00system 1:46.45elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps