.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2913_81x897_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 84 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 197 patterns found. (out of a total of 897 sites) . 676 sites without polymorphism (75.36%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -2523.3266] [GTR parameters ] . ( 1 sec) [ -2508.5261] [Alpha ][ 0.500960] . ( 1 sec) [ -2508.5261] [Topology ] . ( 1 sec) [ -2475.2275] [Topology ] . ( 2 sec) [ -2462.5552] [Topology ] . ( 3 sec) [ -2464.0611] [Topology ] . Moving backward . ( 3 sec) [ -2459.8744] [Topology ] . ( 4 sec) [ -2457.8355] [Topology ] . ( 5 sec) [ -2460.3467] [Topology ] . Moving backward . ( 5 sec) [ -2456.9884] [Topology ] . ( 5 sec) [ -2458.0589] [Topology ] . Moving backward . ( 5 sec) [ -2456.2108] [Topology ] . ( 6 sec) [ -2455.5442] [GTR parameters ] . ( 7 sec) [ -2444.5627] [Alpha ][ 0.250961] . ( 7 sec) [ -2444.5627] [Topology ] . ( 7 sec) [ -2443.3022] [Topology ] . ( 8 sec) [ -2442.5524] [Topology ] . ( 8 sec) [ -2443.1700] [Topology ] . Moving backward . ( 8 sec) [ -2441.1183] [Topology ] . ( 9 sec) [ -2440.9937] [Topology ] . ( 10 sec) [ -2441.5182] [Topology ] . Moving backward . ( 10 sec) [ -2440.8971] [Topology ] . ( 10 sec) [ -2440.8978] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -2440.0218] [Topology ] . ( 14 sec) [ -2439.6357] [GTR parameters ] . ( 15 sec) [ -2436.5083] [Alpha ][ 0.134987] . ( 15 sec) [ -2436.5083] [Topology ] . ( 15 sec) [ -2436.5113] [Topology ] . Moving backward . ( 15 sec) [ -2436.2451] [Topology ] . ( 16 sec) [ -2436.0366] [Topology ] . ( 16 sec) [ -2436.0412] [Topology ] . Moving backward . ( 16 sec) [ -2435.9470] [Topology ] . ( 17 sec) [ -2435.8884] [Topology ] . ( 18 sec) [ -2435.8703] [Topology ] . ( 18 sec) [ -2435.8875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -2435.8493] [Topology ] . ( 22 sec) [ -2435.8262] [GTR parameters ] . ( 22 sec) [ -2435.8248] [Alpha ][ 0.132931] . ( 22 sec) [ -2435.8248] [Topology ] . ( 23 sec) [ -2435.8227] [Topology ] . ( 23 sec) [ -2435.8221] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -2435.8186] [Topology ] . ( 27 sec) [ -2435.8186] [GTR parameters ] . ( 27 sec) [ -2435.8186] [Alpha ][ 0.132798] . ( 27 sec) [ -2435.8186] [Topology ] . ( 28 sec) [ -2435.8197] [Topology ] . Moving backward . ( 28 sec) [ -2435.8164] [Topology ] . ( 28 sec) [ -2435.8159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 32 sec) [ -2435.8152] [Topology ] . ( 33 sec) [ -2435.8152] [GTR parameters ] . ( 33 sec) [ -2435.8152] [Alpha ][ 0.132931] . ( 33 sec) [ -2435.8152] [Topology ] . ( 33 sec) [ -2435.8164] [Topology ] . Moving backward . ( 33 sec) [ -2435.8143] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -2435.8113] [Topology ] . ( 37 sec) [ -2435.8113] [GTR parameters ] . ( 37 sec) [ -2435.8113] [Alpha ][ 0.132798] . ( 37 sec) [ -2435.8113] [Topology ] . ( 38 sec) [ -2435.8113] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -2435.8086] [Topology ] . ( 42 sec) [ -2435.8086] [GTR parameters ] . ( 42 sec) [ -2435.8086] [Alpha ][ 0.132931] . ( 42 sec) [ -2435.8086] [Topology ] . ( 42 sec) [ -2435.8118] [Topology ] . Moving backward . ( 42 sec) [ -2435.8072] [Topology ] . ( 43 sec) [ -2435.8081] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -2435.8019] [Topology ] . ( 47 sec) [ -2435.8019] [GTR parameters ] . ( 47 sec) [ -2435.8019] [Alpha ][ 0.132931] . ( 47 sec) [ -2435.8019] [Topology ] . ( 48 sec) [ -2435.8123] [Topology ] . Moving backward . ( 48 sec) [ -2435.7996] [Topology ] . ( 48 sec) [ -2435.8038] [Topology ] . Moving backward . ( 48 sec) [ -2435.7986] [Topology ] . ( 49 sec) [ -2435.8010] [Topology ] . Moving backward . ( 49 sec) [ -2435.7975] [Topology ] . ( 49 sec) [ -2435.7982] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -2435.7982] [GTR parameters ] . ( 53 sec) [ -2435.7982] [Alpha ][ 0.132931] . ( 53 sec) [ -2435.7982] [Topology ] . ( 54 sec) [ -2435.8118] [Topology ] . Moving backward . ( 54 sec) [ -2435.7956] [Topology ] . ( 55 sec) [ -2435.8064] [Topology ] . Moving backward . ( 55 sec) [ -2435.7951] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -2435.7951] [GTR parameters ] . ( 59 sec) [ -2435.7951] [Alpha ][ 0.132931] . ( 59 sec) [ -2435.7951] [Topology ] . ( 59 sec) [ -2435.8065] [Topology ] . Moving backward . ( 59 sec) [ -2435.7933] [Topology ] . ( 60 sec) [ -2435.7992] [Topology ] . Moving backward . ( 60 sec) [ -2435.7918] [Topology ] . ( 60 sec) [ -2435.7972] [Topology ] . Moving backward . ( 60 sec) [ -2435.7901] [Topology ] . ( 61 sec) [ -2435.7924] [Topology ] . Moving backward . ( 61 sec) [ -2435.7884] [Topology ] . ( 61 sec) [ -2435.7899] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -2435.7866] [GTR parameters ] . ( 66 sec) [ -2435.7866] [Alpha ][ 0.132785] . ( 66 sec) [ -2435.7866] [Topology ] . ( 66 sec) [ -2435.7863] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2435.786324. . Printing the most likely tree in file 'nucleic_M2913_81x897_2006.phy_phyml_tree.txt'... . Time used 0h1m14s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 73.77user 0.00system 1:14.87elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps