.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2856_61x970_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 686 patterns found. (out of a total of 970 sites) . 322 sites without polymorphism (33.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 22Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 3 sec) [ -26079.2058] [GTR parameters ] . ( 3 sec) [ -25728.9409] [Alpha ][ 0.500960] . ( 19 sec) [ -25726.2013] [ 6340] [depth= 1] . ( 20 sec) [ -25715.3178] [ 6339] [depth= 1] . ( 26 sec) [ -25709.8673] [ 6334] [depth= 1] . ( 26 sec) [ -25700.1364] [ 6331] [depth= 1] . ( 41 sec) [ -25699.7942] [ 6333] [depth= 1] . ( 41 sec) [ -25695.6843] [ 6329] [depth= 1] . ( 41 sec) [ -25682.5744] [ 6317] [depth= 2] . ( 42 sec) [ -25682.3575] [ 6318] [depth= 1] . ( 42 sec) [ -25681.9471] [ 6322] [depth= 1] . ( 46 sec) [ -25667.9534] [ 6328] [depth= 1] . ( 46 sec) [ -25663.2486] [ 6322] [depth= 1] . ( 46 sec) [ -25645.8279] [ 6321] [depth= 1] . ( 56 sec) [ -25644.9872] [ 6344] [depth= 2] . ( 56 sec) [ -25620.6856] [ 6325] [depth= 2] . ( 61 sec) [ -25620.1891] [ 6335] [depth= 1] . ( 61 sec) [ -25595.1045] [ 6325] [depth= 1] . ( 66 sec) [ -25577.1825] [ 6321] [depth= 1] . ( 67 sec) [ -25572.0381] [ 6331] [depth= 1] . ( 67 sec) [ -25568.1996] [ 6325] [depth= 1] . ( 67 sec) [ -25567.6514] [ 6331] [depth= 1] . ( 67 sec) [ -25566.1507] [ 6337] [depth= 1] . ( 67 sec) [ -25558.3831] [ 6331] [depth= 1] . ( 67 sec) [ -25555.1766] [ 6325] [depth= 1] . ( 67 sec) [ -25547.0947] [ 6329] [depth= 1] . ( 67 sec) [ -25545.5267] [ 6337] [depth= 1] . ( 71 sec) [ -25541.5248] [ 6337] [depth= 1] . ( 71 sec) [ -25512.2032] [ 6328] [depth= 1] . ( 75 sec) [ -25503.1096] [ 6346] [depth= 1] . ( 75 sec) [ -25480.9900] [ 6328] [depth= 1] . ( 75 sec) [ -25473.1136] [ 6334] [depth= 1] . ( 77 sec) [ -25471.1514] [ 6331] [depth= 3] . ( 79 sec) [ -25468.6752] [ 6321] [depth= 2] . ( 79 sec) [ -25465.4246] [ 6336] [depth= 1] . ( 86 sec) [ -25458.4987] [ 6330] [depth= 1] . ( 86 sec) [ -25456.7205] [ 6331] [depth= 1] . ( 86 sec) [ -25456.2729] [ 6328] [depth= 1] . ( 87 sec) [ -25443.9256] [ 6320] [depth= 2] . ( 87 sec) [ -25431.9593] [ 6329] [depth= 5] . ( 87 sec) [ -25430.4240] [ 6328] [depth= 1] . ( 87 sec) [ -25427.8747] [ 6328] [depth= 1] . ( 88 sec) [ -25426.8904] [ 6349] [depth= 4] . ( 89 sec) [ -25420.1612] [ 6343] [depth= 3] . ( 89 sec) [ -25410.7057] [ 6347] [depth= 3] . ( 89 sec) [ -25405.2249] [ 6349] [depth= 4] . ( 89 sec) [ -25401.0393] [ 6347] [depth= 4] . ( 89 sec) [ -25396.7059] [ 6345] [depth= 1] . ( 90 sec) [ -25391.2251] [ 6337] [depth= 3] . ( 90 sec) [ -25387.5471] [ 6337] [depth= 4] . ( 90 sec) [ -25380.9523] [ 6341] [depth= 2] . ( 90 sec) [ -25380.8338] [ 6338] [depth= 2] . ( 92 sec) [ -25366.5133] [ 6340] [depth= 1] . ( 92 sec) [ -25354.9524] [ 6329] [depth= 3] . ( 94 sec) [ -25351.2681] [ 6326] [depth= 1] . ( 94 sec) [ -25330.6871] [ 6320] [depth= 1] . ( 95 sec) [ -25327.4156] [ 6322] [depth= 1] . ( 95 sec) [ -25320.9342] [ 6324] [depth= 1] . ( 96 sec) [ -25203.1207] [Branch lengths ] . ( 99 sec) [ -25170.5085] [GTR parameters ] . ( 99 sec) [ -25156.9500] [Alpha ][ 0.419328] . ( 179 sec) [ -25155.3952] [ 6324] [depth= 1] . ( 186 sec) [ -25154.2086] [ 6323] [depth= 1] . ( 188 sec) [ -25154.0398] [ 6328] [depth= 1] . ( 210 sec) [ -25152.0400] [ 6326] [depth= 1] . ( 243 sec) [ -25135.1953] [Branch lengths ] . ( 245 sec) [ -25132.2047] [GTR parameters ] . ( 246 sec) [ -25132.2037] [Alpha ][ 0.419919] . ( 333 sec) [ -25131.4128] [ 6322] [depth= 1] . ( 392 sec) [ -25126.2120] [Branch lengths ] . ( 394 sec) [ -25125.6852] [GTR parameters ] . ( 394 sec) [ -25125.6848] [Alpha ][ 0.420339] . ( 542 sec) [ -25123.7326] [Branch lengths ] . ( 601 sec) [ -25123.1087] [Branch lengths ] . ( 601 sec) [ -25123.1087] [Topology ] . ( 602 sec) [ -25121.3580] [Topology ] . ( 604 sec) [ -25119.5834] [Topology ] . ( 606 sec) [ -25119.1624] [Topology ] . ( 608 sec) [ -25119.0846] [Topology ] . ( 609 sec) [ -25119.0581] [Topology ] . ( 611 sec) [ -25119.0460] [Topology ] . ( 613 sec) [ -25119.0398] [Topology ] . ( 615 sec) [ -25119.0365] [Topology ] . ( 617 sec) [ -25118.4522] [GTR parameters ] . ( 618 sec) [ -25118.4488] [Alpha ][ 0.419092] . ( 618 sec) [ -25118.4488] [Topology ] . ( 619 sec) [ -25118.3294] [Topology ] . ( 621 sec) [ -25118.2713] [Topology ] . ( 623 sec) [ -25118.2368] [Topology ] . ( 625 sec) [ -25118.2158] [Topology ] . ( 626 sec) [ -25118.2028] [Topology ] . ( 628 sec) [ -25118.1947] [Topology ] . ( 630 sec) [ -25118.1162] [GTR parameters ] . ( 630 sec) [ -25118.1159] [Alpha ][ 0.418673] . ( 630 sec) [ -25118.1159] [Topology ] . ( 631 sec) [ -25118.0826] [Topology ] . ( 633 sec) [ -25118.0640] [Topology ] . ( 635 sec) [ -25118.0526] [Topology ] . ( 637 sec) [ -25118.0454] [Topology ] . ( 638 sec) [ -25118.0409] [Topology ] . ( 640 sec) [ -25118.0380] [Topology ] . ( 642 sec) [ -25118.0163] [GTR parameters ] . ( 642 sec) [ -25118.0163] [Alpha ][ 0.418673] . ( 642 sec) [ -25118.0163] [Topology ] . ( 644 sec) [ -25118.0063] [Topology ] . ( 645 sec) [ -25118.0006] [Topology ] . ( 647 sec) [ -25117.9970] [Topology ] . ( 649 sec) [ -25117.9948] [Topology ] . ( 651 sec) [ -25117.9933] [Topology ] . ( 652 sec) [ -25117.9924] [Topology ] . ( 654 sec) [ -25117.9860] [GTR parameters ] . ( 654 sec) [ -25117.9860] [Alpha ][ 0.418673] . ( 654 sec) [ -25117.9860] [Topology ] . ( 656 sec) [ -25117.9832] [Topology ] . ( 657 sec) [ -25117.9816] [Topology ] . ( 659 sec) [ -25117.9805] [Topology ] . ( 661 sec) [ -25117.9799] [Topology ] . ( 662 sec) [ -25117.9783] [GTR parameters ] . ( 662 sec) [ -25117.9783] [Alpha ][ 0.418254] . ( 662 sec) [ -25117.9783] [Topology ] . ( 664 sec) [ -25117.9771] [Topology ] . ( 665 sec) [ -25117.9765] [Topology ] . ( 667 sec) [ -25117.9756] [GTR parameters ] . ( 667 sec) [ -25117.9756] [Alpha ][ 0.418254] . ( 667 sec) [ -25117.9756] [Topology ] . ( 669 sec) [ -25117.9747] [Topology ] . ( 669 sec) [ -25117.9746] [GTR parameters ] . ( 669 sec) [ -25117.9746] [Alpha ][ 0.418254] . ( 669 sec) [ -25117.9746] [Topology ] . ( 671 sec) [ -25117.9739] [Topology ] . ( 671 sec) [ -25117.9739] [GTR parameters ] . ( 671 sec) [ -25117.9739] [Alpha ][ 0.418254] . Checking for NNIs, optimizing five branches... . ( 687 sec) [ -25117.9338] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -25117.933785. . Printing the most likely tree in file 'nucleic_M2856_61x970_2006.phy_phyml_tree.txt'... . Time used 0h11m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 700.37user 0.00system 11:43.55elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps