.......................... 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 : 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 SPR moves)... . ( 1 sec) [ -7535.7731] [GTR parameters ] . ( 2 sec) [ -7436.5581] [Alpha ][ 0.500960] . ( 2 sec) [ -7431.0273] [ 1225] [depth= 1] . ( 2 sec) [ -7429.9233] [ 1225] [depth= 1] . ( 2 sec) [ -7410.2809] [ 1223] [depth= 1] . ( 11 sec) [ -7410.1458] [ 1223] [depth= 1] . ( 11 sec) [ -7410.1041] [ 1223] [depth= 1] . ( 11 sec) [ -7409.8023] [ 1223] [depth= 2] . ( 11 sec) [ -7408.9585] [ 1224] [depth= 1] . ( 12 sec) [ -7406.9594] [ 1224] [depth= 2] . ( 12 sec) [ -7404.9846] [ 1223] [depth= 1] . ( 21 sec) [ -7401.0463] [ 1222] [depth= 1] . ( 33 sec) [ -7400.6838] [ 1222] [depth= 1] . ( 33 sec) [ -7398.0154] [ 1225] [depth= 2] . ( 34 sec) [ -7397.8300] [ 1225] [depth= 1] . ( 34 sec) [ -7395.7624] [ 1225] [depth= 1] . ( 34 sec) [ -7395.5684] [ 1225] [depth= 1] . ( 34 sec) [ -7393.7285] [ 1225] [depth= 1] . ( 38 sec) [ -7392.9397] [ 1225] [depth= 1] . ( 39 sec) [ -7383.7269] [ 1222] [depth= 1] . ( 39 sec) [ -7383.0988] [ 1222] [depth= 1] . ( 41 sec) [ -7383.0734] [ 1222] [depth= 1] . ( 41 sec) [ -7381.2424] [ 1222] [depth= 1] . ( 43 sec) [ -7378.2043] [ 1221] [depth= 1] . ( 43 sec) [ -7375.9504] [ 1218] [depth= 2] . ( 51 sec) [ -7375.2050] [ 1219] [depth= 1] . ( 61 sec) [ -7372.3325] [ 1221] [depth= 1] . ( 64 sec) [ -7370.9400] [ 1229] [depth= 1] . ( 68 sec) [ -7363.7333] [ 1232] [depth= 1] . ( 70 sec) [ -7355.2691] [ 1235] [depth= 1] . ( 70 sec) [ -7348.2307] [ 1232] [depth= 1] . ( 70 sec) [ -7342.6343] [ 1231] [depth= 1] . ( 70 sec) [ -7342.3487] [ 1231] [depth= 1] . ( 70 sec) [ -7339.7361] [ 1224] [depth= 1] . ( 70 sec) [ -7328.6131] [ 1223] [depth= 6] . ( 83 sec) [ -7327.0184] [ 1220] [depth= 1] . ( 83 sec) [ -7324.7332] [ 1223] [depth= 1] . ( 83 sec) [ -7322.1135] [ 1221] [depth= 1] . ( 83 sec) [ -7320.1814] [ 1222] [depth= 2] . ( 85 sec) [ -7309.7187] [ 1219] [depth= 2] . ( 85 sec) [ -7307.8922] [ 1223] [depth= 1] . ( 85 sec) [ -7306.6613] [ 1233] [depth= 1] . ( 85 sec) [ -7304.4025] [ 1233] [depth= 1] . ( 103 sec) [ -7300.1247] [ 1232] [depth= 1] . ( 103 sec) [ -7299.3413] [ 1232] [depth= 1] . ( 103 sec) [ -7296.0984] [ 1231] [depth= 2] . ( 103 sec) [ -7295.5170] [ 1231] [depth= 1] . ( 107 sec) [ -7295.4323] [ 1231] [depth= 1] . ( 108 sec) [ -7288.6927] [ 1231] [depth= 2] . ( 108 sec) [ -7287.6821] [ 1231] [depth= 1] . ( 108 sec) [ -7287.2436] [ 1231] [depth= 1] . ( 109 sec) [ -7287.0776] [ 1231] [depth= 1] . ( 109 sec) [ -7286.8479] [ 1231] [depth= 1] . ( 112 sec) [ -7286.6382] [ 1231] [depth= 2] . ( 112 sec) [ -7286.5717] [ 1231] [depth= 1] . ( 112 sec) [ -7286.5382] [ 1231] [depth= 1] . ( 118 sec) [ -7286.2962] [ 1231] [depth= 1] . ( 118 sec) [ -7286.0920] [ 1231] [depth= 1] . ( 118 sec) [ -7285.9354] [ 1231] [depth= 1] . ( 122 sec) [ -7284.9194] [ 1231] [depth= 1] . ( 123 sec) [ -7282.9733] [ 1231] [depth= 1] . ( 123 sec) [ -7280.4016] [ 1231] [depth= 1] . ( 125 sec) [ -7277.6923] [ 1230] [depth= 1] . ( 133 sec) [ -7276.2051] [ 1229] [depth= 2] . ( 133 sec) [ -7276.1827] [ 1229] [depth= 3] . ( 133 sec) [ -7266.2538] [ 1227] [depth= 2] . ( 149 sec) [ -7265.9950] [ 1230] [depth= 1] . ( 153 sec) [ -7264.1554] [ 1230] [depth= 1] . ( 174 sec) [ -7231.9913] [Branch lengths ] . ( 176 sec) [ -7230.3034] [GTR parameters ] . ( 176 sec) [ -7209.1197] [Alpha ][ 0.316823] . ( 189 sec) [ -7206.2415] [ 1220] [depth= 1] . ( 220 sec) [ -7206.0457] [ 1220] [depth= 1] . ( 240 sec) [ -7204.4176] [ 1218] [depth= 1] . ( 240 sec) [ -7204.2371] [ 1218] [depth= 1] . ( 250 sec) [ -7203.2606] [ 1217] [depth= 1] . ( 289 sec) [ -7202.9370] [ 1216] [depth= 2] . ( 389 sec) [ -7200.2289] [ 1213] [depth= 2] . ( 430 sec) [ -7194.8724] [Branch lengths ] . ( 432 sec) [ -7194.6860] [GTR parameters ] . ( 432 sec) [ -7194.6849] [Alpha ][ 0.315748] . ( 581 sec) [ -7194.4165] [ 1210] [depth= 1] . ( 699 sec) [ -7193.3987] [Branch lengths ] . ( 700 sec) [ -7193.3854] [GTR parameters ] . ( 700 sec) [ -7193.3838] [Alpha ][ 0.316940] . ( 961 sec) [ -7193.3138] [Branch lengths ] . ( 1050 sec) [ -7193.3078] [Branch lengths ] . ( 1050 sec) [ -7193.3078] [Topology ] . ( 1052 sec) [ -7193.3074] [Topology ] . ( 1053 sec) [ -7193.3072] [GTR parameters ] . ( 1053 sec) [ -7193.3072] [Alpha ][ 0.317257] . Checking for NNIs, optimizing five branches... . ( 1066 sec) [ -7193.3071] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7193.307076. . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Time used 0h18m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1078.94user 0.00system 18:01.18elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps