.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2567_64x1044_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 : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 408 patterns found. (out of a total of 1044 sites) . 678 sites without polymorphism (64.94%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -7007.3560] [GTR parameters ] . ( 1 sec) [ -6925.4087] [Alpha ][ 0.500960] . ( 1 sec) [ -6925.4087] [Topology ] . ( 3 sec) [ -6848.6098] [Topology ] . ( 4 sec) [ -6831.2831] [Topology ] . ( 5 sec) [ -6827.5568] [Topology ] . ( 6 sec) [ -6826.0300] [Topology ] . ( 7 sec) [ -6825.4490] [Topology ] . ( 9 sec) [ -6825.2395] [Topology ] . ( 10 sec) [ -6825.1698] [Topology ] . ( 11 sec) [ -6825.1447] [Topology ] . ( 12 sec) [ -6825.1351] [Topology ] . Checking for NNIs, optimizing five branches... . ( 20 sec) [ -6824.9189] [Topology ] . ( 21 sec) [ -6824.8588] [GTR parameters ] . ( 22 sec) [ -6793.4815] [Alpha ][ 0.278369] . ( 22 sec) [ -6793.4815] [Topology ] . ( 23 sec) [ -6793.2337] [Topology ] . ( 24 sec) [ -6793.1641] [Topology ] . ( 25 sec) [ -6793.1308] [Topology ] . ( 26 sec) [ -6793.1140] [Topology ] . ( 27 sec) [ -6793.1054] [Topology ] . ( 28 sec) [ -6793.1011] [Topology ] . Checking for NNIs, optimizing five branches... . ( 36 sec) [ -6792.9534] [Topology ] . ( 38 sec) [ -6792.7485] [GTR parameters ] . ( 38 sec) [ -6792.7442] [Alpha ][ 0.276515] . ( 38 sec) [ -6792.7442] [Topology ] . ( 39 sec) [ -6792.6671] [Topology ] . ( 40 sec) [ -6792.6469] [Topology ] . ( 41 sec) [ -6792.6391] [Topology ] . ( 42 sec) [ -6792.6357] [Topology ] . ( 43 sec) [ -6792.6341] [Topology ] . ( 44 sec) [ -6792.6333] [Topology ] . Checking for NNIs, optimizing five branches... . ( 53 sec) [ -6792.5556] [Topology ] . ( 53 sec) [ -6792.5462] [GTR parameters ] . ( 54 sec) [ -6792.5460] [Alpha ][ 0.276824] . ( 54 sec) [ -6792.5460] [Topology ] . ( 55 sec) [ -6792.0186] [Topology ] . ( 56 sec) [ -6791.9663] [Topology ] . ( 57 sec) [ -6791.9610] [Topology ] . ( 58 sec) [ -6791.9601] [Topology ] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -6791.9559] [GTR parameters ] . ( 67 sec) [ -6791.9559] [Alpha ][ 0.276824] . ( 67 sec) [ -6791.9559] [Topology ] . ( 69 sec) [ -6791.9557] [Topology ] . Checking for NNIs, optimizing five branches... . ( 77 sec) [ -6791.9556] [GTR parameters ] . ( 77 sec) [ -6791.9556] [Alpha ][ 0.276824] . ( 77 sec) [ -6791.9556] [Topology ] . ( 78 sec) [ -6791.9556] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 96 sec) [ -7007.3560] [GTR parameters ] . ( 96 sec) [ -6925.4087] [Alpha ][ 0.500960] . ( 97 sec) [ -6925.3545] [ 965] [depth= 1] . ( 97 sec) [ -6925.3355] [ 965] [depth= 1] . ( 97 sec) [ -6925.3142] [ 965] [depth= 1] . ( 97 sec) [ -6922.0750] [ 965] [depth= 2] . ( 97 sec) [ -6922.0117] [ 965] [depth= 1] . ( 97 sec) [ -6921.6923] [ 965] [depth= 1] . ( 97 sec) [ -6921.4604] [ 965] [depth= 1] . ( 98 sec) [ -6921.4480] [ 965] [depth= 1] . ( 98 sec) [ -6920.0256] [ 965] [depth= 1] . ( 98 sec) [ -6919.4940] [ 965] [depth= 1] . ( 98 sec) [ -6918.9738] [ 965] [depth= 3] . ( 99 sec) [ -6917.6880] [ 965] [depth= 1] . ( 99 sec) [ -6917.3110] [ 965] [depth= 1] . ( 99 sec) [ -6908.0135] [ 966] [depth= 1] . ( 99 sec) [ -6906.1612] [ 968] [depth= 1] . ( 99 sec) [ -6904.1512] [ 966] [depth= 1] . ( 99 sec) [ -6902.8193] [ 966] [depth= 1] . ( 99 sec) [ -6901.8640] [ 966] [depth= 1] . ( 101 sec) [ -6894.5646] [ 964] [depth= 2] . ( 102 sec) [ -6891.9879] [ 962] [depth= 1] . ( 102 sec) [ -6887.2451] [ 962] [depth= 1] . ( 102 sec) [ -6887.1358] [ 962] [depth= 1] . ( 103 sec) [ -6887.0553] [ 963] [depth= 1] . ( 103 sec) [ -6884.1030] [ 962] [depth= 1] . ( 104 sec) [ -6875.8546] [ 959] [depth= 1] . ( 105 sec) [ -6875.7013] [ 961] [depth= 1] . ( 105 sec) [ -6868.8417] [ 959] [depth= 1] . ( 106 sec) [ -6868.2051] [ 959] [depth= 1] . ( 106 sec) [ -6866.2390] [ 959] [depth= 1] . ( 107 sec) [ -6862.1974] [ 958] [depth= 1] . ( 108 sec) [ -6861.9667] [ 958] [depth= 1] . ( 108 sec) [ -6861.8849] [ 958] [depth= 1] . ( 108 sec) [ -6861.8248] [ 958] [depth= 1] . ( 108 sec) [ -6861.1538] [ 958] [depth= 1] . ( 108 sec) [ -6861.1391] [ 958] [depth= 1] . ( 108 sec) [ -6861.1256] [ 958] [depth= 1] . ( 108 sec) [ -6861.1092] [ 958] [depth= 1] . ( 108 sec) [ -6861.0913] [ 958] [depth= 1] . ( 110 sec) [ -6827.2596] [Branch lengths ] . ( 111 sec) [ -6827.2170] [GTR parameters ] . ( 111 sec) [ -6796.4574] [Alpha ][ 0.275898] . ( 113 sec) [ -6796.3034] [ 957] [depth= 1] . ( 115 sec) [ -6795.4649] [ 957] [depth= 1] . ( 125 sec) [ -6792.9270] [Branch lengths ] . ( 126 sec) [ -6792.7223] [GTR parameters ] . ( 126 sec) [ -6792.7202] [Alpha ][ 0.277144] . ( 136 sec) [ -6792.6824] [ 958] [depth= 1] . ( 140 sec) [ -6792.1049] [Branch lengths ] . ( 141 sec) [ -6792.0766] [GTR parameters ] . ( 141 sec) [ -6792.0763] [Alpha ][ 0.276627] . ( 187 sec) [ -6791.9760] [Branch lengths ] . ( 187 sec) [ -6791.9760] [Topology ] . ( 188 sec) [ -6791.9648] [Topology ] . ( 189 sec) [ -6791.9607] [Topology ] . ( 191 sec) [ -6791.9586] [Topology ] . ( 192 sec) [ -6791.9575] [Topology ] . ( 193 sec) [ -6791.9570] [Topology ] . ( 193 sec) [ -6791.9565] [GTR parameters ] . ( 193 sec) [ -6791.9564] [Alpha ][ 0.276904] . ( 193 sec) [ -6791.9564] [Topology ] . ( 195 sec) [ -6791.9561] [Topology ] . ( 195 sec) [ -6791.9561] [GTR parameters ] . ( 195 sec) [ -6791.9561] [Alpha ][ 0.276904] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6791.955578 . Log likelihood obtained after SPR moves : -6791.956055 . Log likelihood of the current tree: -6791.955578. . Printing the most likely tree in file 'nucleic_M2567_64x1044_2006.phy_phyml_tree.txt'... . Time used 0h3m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 203.31user 0.00system 3:24.65elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps