.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2772_77x900_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 . 57 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 575 patterns found. (out of a total of 900 sites) . 459 sites without polymorphism (51.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7535.7731] [GTR parameters ] . ( 3 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 3 sec) [ -7436.5581] [Topology ] . ( 5 sec) [ -7272.4837] [Topology ] . ( 7 sec) [ -7248.9131] [Topology ] . ( 9 sec) [ -7242.2258] [Topology ] . ( 11 sec) [ -7239.3759] [Topology ] . ( 13 sec) [ -7237.7430] [Topology ] . ( 15 sec) [ -7235.4982] [Topology ] . ( 17 sec) [ -7232.9129] [Topology ] . ( 19 sec) [ -7229.8674] [Topology ] . ( 21 sec) [ -7226.3877] [Topology ] . ( 24 sec) [ -7224.6006] [GTR parameters ] . ( 24 sec) [ -7205.9195] [Alpha ][ 0.327414] . ( 24 sec) [ -7205.9195] [Topology ] . ( 26 sec) [ -7204.3575] [Topology ] . ( 28 sec) [ -7202.4492] [Topology ] . ( 30 sec) [ -7200.1107] [Topology ] . ( 32 sec) [ -7199.6426] [Topology ] . ( 34 sec) [ -7199.5423] [Topology ] . ( 37 sec) [ -7199.5102] [Topology ] . ( 39 sec) [ -7199.4996] [Topology ] . ( 41 sec) [ -7199.4959] [Topology ] . ( 42 sec) [ -7199.4946] [Topology ] . Checking for NNIs, optimizing five branches... . ( 56 sec) [ -7199.4129] [Topology ] . ( 58 sec) [ -7199.2768] [GTR parameters ] . ( 58 sec) [ -7199.1884] [Alpha ][ 0.318202] . ( 58 sec) [ -7199.1884] [Topology ] . ( 60 sec) [ -7199.1112] [Topology ] . ( 62 sec) [ -7199.0965] [Topology ] . ( 63 sec) [ -7199.0928] [Topology ] . ( 65 sec) [ -7199.0918] [Topology ] . ( 67 sec) [ -7199.0916] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -7199.0904] [GTR parameters ] . ( 82 sec) [ -7199.0902] [Alpha ][ 0.317709] . ( 82 sec) [ -7199.0902] [Topology ] . ( 84 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -7199.0900] [GTR parameters ] . ( 98 sec) [ -7199.0900] [Alpha ][ 0.317709] . ( 98 sec) [ -7199.0900] [Topology ] . ( 100 sec) [ -7199.0900] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 128 sec) [ -7535.7731] [GTR parameters ] . ( 129 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 129 sec) [ -7431.0273] [ 1225] [depth= 1] . ( 129 sec) [ -7429.9233] [ 1225] [depth= 1] . ( 129 sec) [ -7410.2809] [ 1223] [depth= 1] . ( 129 sec) [ -7410.1458] [ 1223] [depth= 1] . ( 130 sec) [ -7410.1041] [ 1223] [depth= 1] . ( 130 sec) [ -7409.8023] [ 1223] [depth= 2] . ( 130 sec) [ -7408.9585] [ 1224] [depth= 1] . ( 130 sec) [ -7406.9594] [ 1224] [depth= 2] . ( 130 sec) [ -7404.9846] [ 1223] [depth= 1] . ( 130 sec) [ -7401.0463] [ 1222] [depth= 1] . ( 131 sec) [ -7400.6838] [ 1222] [depth= 1] . ( 131 sec) [ -7398.0154] [ 1225] [depth= 2] . ( 131 sec) [ -7397.8300] [ 1225] [depth= 1] . ( 131 sec) [ -7395.7624] [ 1225] [depth= 1] . ( 132 sec) [ -7395.5684] [ 1225] [depth= 1] . ( 132 sec) [ -7393.7285] [ 1225] [depth= 1] . ( 132 sec) [ -7392.9397] [ 1225] [depth= 1] . ( 132 sec) [ -7383.7269] [ 1222] [depth= 1] . ( 132 sec) [ -7383.0988] [ 1222] [depth= 1] . ( 132 sec) [ -7383.0734] [ 1222] [depth= 1] . ( 133 sec) [ -7381.2424] [ 1222] [depth= 1] . ( 133 sec) [ -7378.2043] [ 1221] [depth= 1] . ( 133 sec) [ -7375.9504] [ 1218] [depth= 2] . ( 134 sec) [ -7375.2050] [ 1219] [depth= 1] . ( 135 sec) [ -7372.3325] [ 1221] [depth= 1] . ( 135 sec) [ -7365.3835] [ 1224] [depth= 1] . ( 136 sec) [ -7357.5601] [ 1227] [depth= 1] . ( 136 sec) [ -7350.6244] [ 1224] [depth= 1] . ( 136 sec) [ -7345.7180] [ 1223] [depth= 1] . ( 136 sec) [ -7345.1969] [ 1224] [depth= 1] . ( 136 sec) [ -7339.3803] [ 1225] [depth= 1] . ( 136 sec) [ -7337.8608] [ 1225] [depth= 1] . ( 137 sec) [ -7335.1324] [ 1222] [depth= 2] . ( 137 sec) [ -7329.5476] [ 1224] [depth= 1] . ( 137 sec) [ -7328.4499] [ 1222] [depth= 3] . ( 138 sec) [ -7326.4817] [ 1222] [depth= 1] . ( 138 sec) [ -7323.6003] [ 1225] [depth= 3] . ( 138 sec) [ -7321.6078] [ 1220] [depth= 1] . ( 138 sec) [ -7321.4654] [ 1222] [depth= 3] . ( 140 sec) [ -7317.2003] [ 1221] [depth= 1] . ( 140 sec) [ -7316.4724] [ 1221] [depth= 1] . ( 140 sec) [ -7313.2630] [ 1220] [depth= 2] . ( 140 sec) [ -7312.6734] [ 1220] [depth= 1] . ( 140 sec) [ -7312.5806] [ 1220] [depth= 1] . ( 141 sec) [ -7305.9445] [ 1220] [depth= 2] . ( 141 sec) [ -7305.0020] [ 1220] [depth= 1] . ( 141 sec) [ -7304.5343] [ 1220] [depth= 1] . ( 141 sec) [ -7304.3698] [ 1220] [depth= 1] . ( 141 sec) [ -7304.1801] [ 1220] [depth= 1] . ( 141 sec) [ -7303.9790] [ 1220] [depth= 2] . ( 142 sec) [ -7303.8950] [ 1220] [depth= 1] . ( 142 sec) [ -7303.8715] [ 1220] [depth= 1] . ( 142 sec) [ -7303.6273] [ 1220] [depth= 1] . ( 142 sec) [ -7303.4188] [ 1220] [depth= 1] . ( 142 sec) [ -7303.2237] [ 1220] [depth= 1] . ( 143 sec) [ -7302.0783] [ 1220] [depth= 1] . ( 143 sec) [ -7300.3856] [ 1220] [depth= 1] . ( 143 sec) [ -7297.6435] [ 1220] [depth= 1] . ( 144 sec) [ -7294.9308] [ 1219] [depth= 1] . ( 144 sec) [ -7294.7546] [ 1223] [depth= 1] . ( 144 sec) [ -7289.1968] [ 1219] [depth= 1] . ( 144 sec) [ -7283.1667] [ 1216] [depth= 1] . ( 145 sec) [ -7277.1827] [ 1216] [depth= 1] . ( 148 sec) [ -7275.2623] [ 1216] [depth= 1] . ( 153 sec) [ -7232.6772] [Branch lengths ] . ( 154 sec) [ -7231.8310] [GTR parameters ] . ( 155 sec) [ -7212.1611] [Alpha ][ 0.321042] . ( 157 sec) [ -7212.0642] [ 1216] [depth= 1] . ( 159 sec) [ -7208.4836] [ 1214] [depth= 1] . ( 159 sec) [ -7208.1432] [ 1214] [depth= 1] . ( 160 sec) [ -7207.3190] [ 1213] [depth= 1] . ( 162 sec) [ -7205.7479] [ 1213] [depth= 2] . ( 163 sec) [ -7203.6592] [ 1211] [depth= 3] . ( 164 sec) [ -7203.0508] [ 1211] [depth= 2] . ( 165 sec) [ -7200.1444] [ 1210] [depth= 1] . ( 180 sec) [ -7195.0134] [Branch lengths ] . ( 181 sec) [ -7194.5060] [GTR parameters ] . ( 181 sec) [ -7194.4992] [Alpha ][ 0.318382] . ( 188 sec) [ -7194.2808] [ 1210] [depth= 1] . ( 206 sec) [ -7193.3440] [Branch lengths ] . ( 207 sec) [ -7193.3395] [GTR parameters ] . ( 207 sec) [ -7193.3387] [Alpha ][ 0.317458] . ( 235 sec) [ -7193.3098] [Branch lengths ] . ( 319 sec) [ -7193.3075] [Branch lengths ] . ( 319 sec) [ -7193.3075] [Topology ] . ( 321 sec) [ -7193.3073] [Topology ] . ( 322 sec) [ -7193.3072] [GTR parameters ] . ( 322 sec) [ -7193.3071] [Alpha ][ 0.317141] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7199.090001 . Log likelihood obtained after SPR moves : -7193.307136 . Log likelihood of the current tree: -7193.307136. . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Time used 0h5m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 334.96user 0.00system 5:36.16elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps