.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2572_191x990_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 . Compressing sequences... . 285 patterns found. (out of a total of 990 sites) . 729 sites without polymorphism (73.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 29Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -3531.0072] [GTR parameters ] . ( 5 sec) [ -3527.8965] [Alpha ][ 0.577459] . ( 5 sec) [ -3527.8965] [Topology ] . ( 7 sec) [ -3510.2444] [Topology ] . ( 9 sec) [ -3508.5708] [Topology ] . ( 12 sec) [ -3508.2867] [Topology ] . ( 14 sec) [ -3508.2234] [Topology ] . ( 16 sec) [ -3508.2072] [Topology ] . ( 18 sec) [ -3508.2027] [Topology ] . ( 20 sec) [ -3508.2013] [Topology ] . Checking for NNIs, optimizing five branches... . ( 32 sec) [ -3508.0718] [GTR parameters ] . ( 32 sec) [ -3508.0712] [Alpha ][ 0.573895] . ( 32 sec) [ -3508.0712] [Topology ] . ( 34 sec) [ -3508.0703] [Topology ] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -3508.0703] [GTR parameters ] . ( 44 sec) [ -3508.0703] [Alpha ][ 0.573191] . ( 44 sec) [ -3508.0703] [Topology ] . ( 46 sec) [ -3508.0702] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 68 sec) [ -3531.0072] [GTR parameters ] . ( 68 sec) [ -3527.8965] [Alpha ][ 0.577459] . ( 69 sec) [ -3527.8479] [ 369] [depth= 1] . ( 69 sec) [ -3527.8239] [ 369] [depth= 1] . ( 69 sec) [ -3527.8118] [ 369] [depth= 1] . ( 69 sec) [ -3527.7895] [ 369] [depth= 2] . ( 70 sec) [ -3527.5963] [ 369] [depth= 1] . ( 70 sec) [ -3527.5160] [ 369] [depth= 1] . ( 70 sec) [ -3527.4234] [ 369] [depth= 1] . ( 70 sec) [ -3527.3767] [ 369] [depth= 1] . ( 72 sec) [ -3527.3454] [ 369] [depth= 1] . ( 72 sec) [ -3526.6627] [ 369] [depth= 1] . ( 72 sec) [ -3526.5187] [ 369] [depth= 1] . ( 73 sec) [ -3525.6629] [ 371] [depth= 2] . ( 73 sec) [ -3525.3201] [ 371] [depth= 1] . ( 75 sec) [ -3525.2826] [ 371] [depth= 1] . ( 75 sec) [ -3525.1647] [ 371] [depth= 9] . ( 76 sec) [ -3525.1288] [ 371] [depth= 1] . ( 76 sec) [ -3525.0164] [ 371] [depth= 6] . ( 76 sec) [ -3524.9966] [ 371] [depth= 1] . ( 76 sec) [ -3524.9866] [ 371] [depth= 2] . ( 82 sec) [ -3524.9735] [ 371] [depth= 1] . ( 83 sec) [ -3524.9627] [ 371] [depth= 1] . ( 83 sec) [ -3523.8521] [ 371] [depth= 1] . ( 83 sec) [ -3523.0114] [ 371] [depth= 1] . ( 84 sec) [ -3522.9783] [ 371] [depth= 1] . ( 84 sec) [ -3522.8374] [ 371] [depth= 1] . ( 106 sec) [ -3522.8214] [ 371] [depth= 1] . ( 107 sec) [ -3522.8100] [ 371] [depth= 1] . ( 130 sec) [ -3522.7923] [ 371] [depth= 2] . ( 130 sec) [ -3522.7272] [ 371] [depth= 9] . ( 131 sec) [ -3522.6714] [ 371] [depth= 7] . ( 131 sec) [ -3522.6361] [ 371] [depth= 3] . ( 147 sec) [ -3522.6060] [ 371] [depth= 5] . ( 149 sec) [ -3522.4612] [ 371] [depth= 4] . ( 153 sec) [ -3522.4477] [ 371] [depth= 1] . ( 153 sec) [ -3522.3715] [ 371] [depth= 28] . ( 153 sec) [ -3522.3332] [ 371] [depth= 27] . ( 154 sec) [ -3521.9724] [ 371] [depth= 2] . ( 154 sec) [ -3521.9393] [ 371] [depth= 2] . ( 155 sec) [ -3521.9117] [ 371] [depth= 27] . ( 187 sec) [ -3521.8083] [ 371] [depth= 3] . ( 187 sec) [ -3521.6973] [ 371] [depth= 3] . ( 188 sec) [ -3521.0631] [ 371] [depth= 3] . ( 188 sec) [ -3520.9156] [ 371] [depth= 1] . ( 189 sec) [ -3519.9119] [ 371] [depth= 4] . ( 189 sec) [ -3517.6696] [ 370] [depth= 1] . ( 209 sec) [ -3517.4609] [ 370] [depth= 4] . ( 209 sec) [ -3517.4300] [ 370] [depth= 4] . ( 209 sec) [ -3517.4065] [ 370] [depth= 2] . ( 209 sec) [ -3517.3814] [ 370] [depth= 2] . ( 219 sec) [ -3512.8983] [ 369] [depth= 1] . ( 221 sec) [ -3512.4324] [ 369] [depth= 1] . ( 221 sec) [ -3512.3180] [ 369] [depth= 4] . ( 222 sec) [ -3512.3034] [ 369] [depth= 4] . ( 226 sec) [ -3512.2889] [ 369] [depth= 4] . ( 269 sec) [ -3508.2210] [Branch lengths ] . ( 270 sec) [ -3508.0541] [GTR parameters ] . ( 271 sec) [ -3508.0535] [Alpha ][ 0.573103] . ( 492 sec) [ -3508.0092] [Branch lengths ] . ( 612 sec) [ -3508.0080] [Branch lengths ] . ( 612 sec) [ -3508.0080] [Topology ] . ( 615 sec) [ -3508.0080] [Topology ] . ( 615 sec) [ -3508.0080] [GTR parameters ] . ( 615 sec) [ -3508.0079] [Alpha ][ 0.571928] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3508.070176 . Log likelihood obtained after SPR moves : -3508.007923 . Log likelihood of the current tree: -3508.007923. . Printing the most likely tree in file 'nucleic_M2572_191x990_2006.phy_phyml_tree.txt'... . Time used 0h10m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 624.29user 0.00system 10:27.01elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps