.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -8163.5103] [GTR parameters ] . ( 3 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 3 sec) [ -8080.4464] [Topology ] . ( 4 sec) [ -7998.7983] [Topology ] . ( 6 sec) [ -7955.3559] [Topology ] . ( 8 sec) [ -7942.8529] [Topology ] . ( 9 sec) [ -7938.6627] [Topology ] . ( 11 sec) [ -7938.6180] [Topology ] . ( 13 sec) [ -7936.9159] [Topology ] . ( 14 sec) [ -7937.3880] [Topology ] . Moving backward . ( 14 sec) [ -7936.2310] [Topology ] . ( 16 sec) [ -7935.8656] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -7931.5928] [Topology ] . ( 33 sec) [ -7931.2315] [GTR parameters ] . ( 33 sec) [ -7881.1773] [Alpha ][ 0.250961] . ( 33 sec) [ -7881.1773] [Topology ] . ( 35 sec) [ -7880.5556] [Topology ] . ( 37 sec) [ -7880.3201] [Topology ] . ( 38 sec) [ -7880.2593] [Topology ] . ( 40 sec) [ -7880.2272] [Topology ] . ( 41 sec) [ -7880.2046] [Topology ] . ( 43 sec) [ -7880.1875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -7878.0740] [Topology ] . ( 57 sec) [ -7878.0004] [GTR parameters ] . ( 57 sec) [ -7875.6771] [Alpha ][ 0.212336] . ( 57 sec) [ -7875.6771] [Topology ] . ( 59 sec) [ -7875.5666] [Topology ] . ( 61 sec) [ -7875.2585] [Topology ] . ( 62 sec) [ -7873.6080] [Topology ] . ( 65 sec) [ -7869.6012] [Topology ] . ( 66 sec) [ -7868.4627] [Topology ] . ( 68 sec) [ -7868.3538] [Topology ] . ( 69 sec) [ -7868.3402] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -7868.3399] [Topology ] . ( 83 sec) [ -7868.3159] [GTR parameters ] . ( 83 sec) [ -7868.3141] [Alpha ][ 0.211294] . ( 83 sec) [ -7868.3141] [Topology ] . ( 85 sec) [ -7868.3112] [Topology ] . ( 86 sec) [ -7868.3103] [Topology ] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -7868.3029] [Topology ] . ( 99 sec) [ -7868.3029] [GTR parameters ] . ( 99 sec) [ -7868.3029] [Alpha ][ 0.211294] . ( 99 sec) [ -7868.3029] [Topology ] . ( 101 sec) [ -7868.3022] [Topology ] . Checking for NNIs, optimizing five branches... . ( 113 sec) [ -7868.3021] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 128 sec) [ -8163.5103] [GTR parameters ] . ( 129 sec) [ -8080.4464] [Alpha ][ 0.500960] . ( 129 sec) [ -8077.4988] [ 943] [depth= 1] . ( 130 sec) [ -8074.4226] [ 944] [depth= 1] . ( 130 sec) [ -8069.8592] [ 943] [depth= 1] . ( 130 sec) [ -8065.7549] [ 943] [depth= 2] . ( 130 sec) [ -8035.2996] [ 934] [depth= 12] . ( 131 sec) [ -8035.0145] [ 934] [depth= 1] . ( 131 sec) [ -8033.2509] [ 934] [depth= 1] . ( 131 sec) [ -8032.7544] [ 934] [depth= 1] . ( 131 sec) [ -8032.5127] [ 934] [depth= 2] . ( 131 sec) [ -8031.4073] [ 935] [depth= 1] . ( 131 sec) [ -8030.9440] [ 935] [depth= 2] . ( 132 sec) [ -8018.3883] [ 932] [depth= 3] . ( 133 sec) [ -8013.6878] [ 931] [depth= 1] . ( 137 sec) [ -8004.2182] [ 927] [depth= 3] . ( 137 sec) [ -7995.5703] [ 925] [depth= 3] . ( 137 sec) [ -7993.4724] [ 927] [depth= 3] . ( 139 sec) [ -7993.3462] [ 926] [depth= 1] . ( 139 sec) [ -7992.0605] [ 924] [depth= 1] . ( 139 sec) [ -7985.9831] [ 924] [depth= 3] . ( 139 sec) [ -7975.4984] [ 920] [depth= 1] . ( 139 sec) [ -7973.0920] [ 921] [depth= 1] . ( 140 sec) [ -7962.3801] [ 922] [depth= 2] . ( 140 sec) [ -7955.3368] [ 920] [depth= 1] . ( 141 sec) [ -7946.2442] [ 917] [depth= 6] . ( 142 sec) [ -7945.3685] [ 917] [depth= 1] . ( 143 sec) [ -7945.0053] [ 918] [depth= 1] . ( 143 sec) [ -7943.0299] [ 918] [depth= 2] . ( 143 sec) [ -7940.5241] [ 918] [depth= 3] . ( 143 sec) [ -7936.5351] [ 917] [depth= 2] . ( 144 sec) [ -7936.3747] [ 917] [depth= 2] . ( 145 sec) [ -7936.3609] [ 917] [depth= 2] . ( 145 sec) [ -7935.5532] [ 917] [depth= 1] . ( 145 sec) [ -7935.0894] [ 917] [depth= 2] . ( 145 sec) [ -7934.8823] [ 917] [depth= 4] . ( 146 sec) [ -7931.7450] [ 917] [depth= 5] . ( 147 sec) [ -7930.7373] [ 917] [depth= 1] . ( 147 sec) [ -7928.2193] [ 916] [depth= 1] . ( 147 sec) [ -7927.3382] [ 915] [depth= 8] . ( 147 sec) [ -7925.5620] [ 915] [depth= 1] . ( 149 sec) [ -7923.4738] [ 915] [depth= 4] . ( 149 sec) [ -7919.0905] [ 915] [depth= 1] . ( 149 sec) [ -7916.6878] [ 914] [depth= 2] . ( 149 sec) [ -7916.5886] [ 914] [depth= 1] . ( 150 sec) [ -7913.1575] [ 915] [depth= 10] . ( 154 sec) [ -7912.7043] [ 915] [depth= 1] . ( 154 sec) [ -7912.4281] [ 915] [depth= 1] . ( 154 sec) [ -7912.3920] [ 915] [depth= 1] . ( 154 sec) [ -7912.3295] [ 915] [depth= 1] . ( 158 sec) [ -7888.7799] [Branch lengths ] . ( 160 sec) [ -7888.0247] [GTR parameters ] . ( 160 sec) [ -7840.1979] [Alpha ][ 0.250961] . ( 160 sec) [ -7839.0071] [ 916] [depth= 1] . ( 162 sec) [ -7837.5084] [ 915] [depth= 5] . ( 162 sec) [ -7836.9764] [ 914] [depth= 1] . ( 162 sec) [ -7836.9098] [ 914] [depth= 1] . ( 163 sec) [ -7836.8955] [ 914] [depth= 1] . ( 167 sec) [ -7836.8741] [ 914] [depth= 1] . ( 175 sec) [ -7836.6513] [ 914] [depth= 1] . ( 175 sec) [ -7836.5284] [ 913] [depth= 4] . ( 181 sec) [ -7836.4322] [ 913] [depth= 1] . ( 184 sec) [ -7835.9844] [ 913] [depth= 1] . ( 188 sec) [ -7835.9501] [ 913] [depth= 5] . ( 189 sec) [ -7835.9205] [ 913] [depth= 4] . ( 191 sec) [ -7835.4842] [ 914] [depth= 10] . ( 200 sec) [ -7835.4479] [ 914] [depth= 1] . ( 200 sec) [ -7835.3659] [ 914] [depth= 2] . ( 203 sec) [ -7835.3495] [ 914] [depth= 1] . ( 203 sec) [ -7830.1491] [Branch lengths ] . ( 204 sec) [ -7830.0929] [GTR parameters ] . ( 204 sec) [ -7828.0024] [Alpha ][ 0.213361] . ( 224 sec) [ -7824.4973] [ 915] [depth= 4] . ( 235 sec) [ -7824.3622] [ 915] [depth= 1] . ( 236 sec) [ -7824.3456] [ 915] [depth= 1] . ( 241 sec) [ -7824.2176] [ 915] [depth= 1] . ( 258 sec) [ -7823.7403] [Branch lengths ] . ( 260 sec) [ -7823.7166] [GTR parameters ] . ( 260 sec) [ -7823.7165] [Alpha ][ 0.213039] . ( 315 sec) [ -7823.7128] [Branch lengths ] . ( 386 sec) [ -7823.7126] [Branch lengths ] . ( 386 sec) [ -7823.7126] [Topology ] . ( 388 sec) [ -7823.7126] [Topology ] . ( 388 sec) [ -7823.7126] [GTR parameters ] . ( 388 sec) [ -7823.7126] [Alpha ][ 0.213039] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7868.302081 . Log likelihood obtained after SPR moves : -7823.712571 . Log likelihood of the current tree: -7823.712571. . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 0h6m41s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 396.62user 0.00system 6:41.79elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps