.......................... 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)... . ( 3 sec) [ -9359.5522] [GTR parameters ] . ( 3 sec) [ -9317.1831] [Alpha ][ 0.504181] . ( 10 sec) [ -9317.1645] [ 1834] [depth= 1] . ( 11 sec) [ -9315.6040] [ 1834] [depth= 1] . ( 11 sec) [ -9315.1052] [ 1833] [depth= 1] . ( 20 sec) [ -9315.0255] [ 1833] [depth= 1] . ( 20 sec) [ -9314.3793] [ 1833] [depth= 1] . ( 20 sec) [ -9314.2353] [ 1833] [depth= 1] . ( 23 sec) [ -9262.9945] [ 1860] [depth= 1] . ( 23 sec) [ -9248.7438] [ 1833] [depth= 1] . ( 25 sec) [ -9247.9524] [ 1833] [depth= 1] . ( 25 sec) [ -9247.8331] [ 1833] [depth= 1] . ( 27 sec) [ -9247.8211] [ 1833] [depth= 1] . ( 27 sec) [ -9246.7479] [ 1844] [depth= 1] . ( 29 sec) [ -9234.3055] [ 1841] [depth= 1] . ( 29 sec) [ -9233.2641] [ 1844] [depth= 1] . ( 29 sec) [ -9232.7790] [ 1841] [depth= 1] . ( 31 sec) [ -9227.5086] [ 1854] [depth= 3] . ( 35 sec) [ -9226.5593] [ 1854] [depth= 2] . ( 36 sec) [ -9226.4531] [ 1854] [depth= 1] . ( 36 sec) [ -9226.4102] [ 1854] [depth= 1] . ( 43 sec) [ -9226.3938] [ 1854] [depth= 3] . ( 54 sec) [ -9225.2379] [ 1856] [depth= 1] . ( 54 sec) [ -9223.0768] [ 1854] [depth= 1] . ( 70 sec) [ -9219.8931] [ 1860] [depth= 1] . ( 70 sec) [ -9219.7933] [ 1860] [depth= 1] . ( 70 sec) [ -9219.7819] [ 1860] [depth= 1] . ( 71 sec) [ -9218.9207] [ 1860] [depth= 1] . ( 72 sec) [ -9218.8751] [ 1860] [depth= 1] . ( 76 sec) [ -9215.3501] [ 1860] [depth= 1] . ( 76 sec) [ -9200.1084] [ 1857] [depth= 2] . ( 76 sec) [ -9187.7485] [ 1852] [depth= 2] . ( 78 sec) [ -9182.6876] [ 1839] [depth= 3] . ( 78 sec) [ -9176.2340] [ 1837] [depth= 1] . ( 84 sec) [ -9175.9509] [ 1837] [depth= 1] . ( 87 sec) [ -9173.3343] [ 1837] [depth= 1] . ( 89 sec) [ -9173.2222] [ 1837] [depth= 1] . ( 89 sec) [ -9172.8926] [ 1837] [depth= 1] . ( 90 sec) [ -9172.6494] [ 1837] [depth= 1] . ( 99 sec) [ -9172.6320] [ 1837] [depth= 1] . ( 103 sec) [ -9170.4392] [ 1840] [depth= 1] . ( 103 sec) [ -9169.3339] [ 1837] [depth= 1] . ( 105 sec) [ -9169.3070] [ 1837] [depth= 1] . ( 105 sec) [ -9169.2755] [ 1837] [depth= 1] . ( 116 sec) [ -9145.8355] [Branch lengths ] . ( 119 sec) [ -9139.4833] [GTR parameters ] . ( 119 sec) [ -9139.3890] [Alpha ][ 0.491064] . ( 132 sec) [ -9139.3769] [ 1837] [depth= 1] . ( 145 sec) [ -9139.0367] [ 1889] [depth= 7] . ( 161 sec) [ -9138.0060] [ 1889] [depth= 1] . ( 167 sec) [ -9137.9823] [ 1889] [depth= 1] . ( 198 sec) [ -9137.9654] [ 1884] [depth= 1] . ( 209 sec) [ -9137.8630] [ 1884] [depth= 1] . ( 266 sec) [ -9134.4274] [Branch lengths ] . ( 267 sec) [ -9134.3578] [GTR parameters ] . ( 267 sec) [ -9134.2824] [Alpha ][ 0.479965] . ( 270 sec) [ -9134.2456] [ 1877] [depth= 1] . ( 293 sec) [ -9132.1384] [ 1829] [depth= 6] . ( 416 sec) [ -9131.6999] [Branch lengths ] . ( 418 sec) [ -9131.6703] [GTR parameters ] . ( 418 sec) [ -9131.6505] [Alpha ][ 0.485862] . ( 573 sec) [ -9131.5680] [Branch lengths ] . ( 633 sec) [ -9131.5557] [Branch lengths ] . ( 633 sec) [ -9131.5557] [Topology ] . ( 634 sec) [ -9131.5544] [Topology ] . ( 636 sec) [ -9131.5538] [Topology ] . ( 636 sec) [ -9131.5535] [GTR parameters ] . ( 637 sec) [ -9131.5533] [Alpha ][ 0.486473] . ( 637 sec) [ -9131.5533] [Topology ] . ( 638 sec) [ -9131.5529] [Topology ] . ( 639 sec) [ -9131.5529] [GTR parameters ] . ( 639 sec) [ -9131.5529] [Alpha ][ 0.486473] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9131.552931. . Printing the most likely tree in file 'nucleic_M2661_66x1027_2006.phy_phyml_tree.txt'... . Time used 0h10m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 648.93user 0.00system 10:50.95elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps