.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2661_66x1027_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 . 9 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 596 patterns found. (out of a total of 1027 sites) . 417 sites without polymorphism (40.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -9359.5522] [GTR parameters ] . ( 5 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 5 sec) [ -9317.1645] [ 1834] [depth= 1] . ( 6 sec) [ -9315.6040] [ 1834] [depth= 1] . ( 6 sec) [ -9315.1052] [ 1833] [depth= 1] . ( 7 sec) [ -9315.0255] [ 1833] [depth= 1] . ( 7 sec) [ -9314.3793] [ 1833] [depth= 1] . ( 7 sec) [ -9314.2353] [ 1833] [depth= 1] . ( 7 sec) [ -9262.9945] [ 1860] [depth= 1] . ( 7 sec) [ -9248.7438] [ 1833] [depth= 1] . ( 8 sec) [ -9247.9524] [ 1833] [depth= 1] . ( 8 sec) [ -9247.8331] [ 1833] [depth= 1] . ( 8 sec) [ -9247.8211] [ 1833] [depth= 1] . ( 8 sec) [ -9247.8078] [ 1833] [depth= 1] . ( 9 sec) [ -9235.3607] [ 1830] [depth= 1] . ( 9 sec) [ -9234.4634] [ 1833] [depth= 1] . ( 9 sec) [ -9233.6999] [ 1833] [depth= 2] . ( 9 sec) [ -9233.5757] [ 1833] [depth= 1] . ( 9 sec) [ -9233.5303] [ 1833] [depth= 1] . ( 10 sec) [ -9233.5145] [ 1833] [depth= 1] . ( 10 sec) [ -9233.4855] [ 1833] [depth= 3] . ( 11 sec) [ -9232.4355] [ 1835] [depth= 1] . ( 11 sec) [ -9230.2014] [ 1833] [depth= 1] . ( 12 sec) [ -9215.8919] [ 1838] [depth= 1] . ( 12 sec) [ -9205.1720] [ 1833] [depth= 1] . ( 13 sec) [ -9193.7854] [ 1832] [depth= 1] . ( 13 sec) [ -9193.6774] [ 1832] [depth= 1] . ( 13 sec) [ -9192.7879] [ 1832] [depth= 1] . ( 13 sec) [ -9192.7518] [ 1832] [depth= 1] . ( 13 sec) [ -9189.2605] [ 1832] [depth= 1] . ( 14 sec) [ -9184.1708] [ 1838] [depth= 1] . ( 14 sec) [ -9182.2796] [ 1832] [depth= 1] . ( 15 sec) [ -9182.1575] [ 1832] [depth= 1] . ( 15 sec) [ -9181.7760] [ 1832] [depth= 1] . ( 15 sec) [ -9181.5352] [ 1832] [depth= 1] . ( 17 sec) [ -9181.5024] [ 1832] [depth= 1] . ( 18 sec) [ -9149.6098] [Branch lengths ] . ( 21 sec) [ -9144.1912] [GTR parameters ] . ( 21 sec) [ -9144.1488] [Alpha ][ 0.495402] . ( 21 sec) [ -9144.1014] [ 1832] [depth= 1] . ( 22 sec) [ -9144.0467] [ 1832] [depth= 1] . ( 23 sec) [ -9143.6674] [ 1829] [depth= 1] . ( 24 sec) [ -9143.6191] [ 1829] [depth= 2] . ( 27 sec) [ -9139.6807] [ 1829] [depth= 1] . ( 27 sec) [ -9139.6640] [ 1829] [depth= 1] . ( 31 sec) [ -9136.6225] [Branch lengths ] . ( 32 sec) [ -9136.5487] [GTR parameters ] . ( 32 sec) [ -9136.5303] [Alpha ][ 0.489471] . ( 34 sec) [ -9136.5180] [ 1829] [depth= 1] . ( 39 sec) [ -9136.5018] [ 1829] [depth= 1] . ( 43 sec) [ -9136.0963] [Branch lengths ] . ( 44 sec) [ -9136.0894] [GTR parameters ] . ( 44 sec) [ -9136.0859] [Alpha ][ 0.486923] . ( 99 sec) [ -9135.9797] [Branch lengths ] . ( 99 sec) [ -9135.9797] [Topology ] . ( 101 sec) [ -9135.8936] [Topology ] . ( 103 sec) [ -9135.4542] [Topology ] . ( 104 sec) [ -9133.8199] [Topology ] . ( 106 sec) [ -9131.8978] [Topology ] . ( 108 sec) [ -9131.6071] [Topology ] . ( 109 sec) [ -9131.5729] [Topology ] . ( 110 sec) [ -9131.5644] [GTR parameters ] . ( 110 sec) [ -9131.5644] [Alpha ][ 0.486923] . ( 110 sec) [ -9131.5644] [Topology ] . ( 112 sec) [ -9131.5569] [Topology ] . ( 113 sec) [ -9131.5547] [Topology ] . ( 115 sec) [ -9131.5539] [Topology ] . ( 115 sec) [ -9131.5539] [GTR parameters ] . ( 115 sec) [ -9131.5539] [Alpha ][ 0.486923] . ( 115 sec) [ -9131.5539] [Topology ] . ( 117 sec) [ -9131.5534] [Topology ] . ( 117 sec) [ -9131.5534] [GTR parameters ] . ( 118 sec) [ -9131.5534] [Alpha ][ 0.486923] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.553438. . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Time used 0h2m9s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 126.97user 0.00system 2:09.62elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps