.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2826_60x1398_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... . 652 patterns found. (out of a total of 1398 sites) . 816 sites without polymorphism (58.37%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -15009.3920] [GTR parameters ] . ( 3 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 3 sec) [ -14725.6209] [Topology ] . ( 5 sec) [ -14531.9053] [Topology ] . ( 6 sec) [ -14493.0754] [Topology ] . ( 8 sec) [ -14474.2240] [Topology ] . ( 10 sec) [ -14466.5015] [Topology ] . ( 11 sec) [ -14464.3817] [Topology ] . ( 13 sec) [ -14463.4422] [Topology ] . ( 15 sec) [ -14462.9907] [Topology ] . ( 16 sec) [ -14462.7666] [Topology ] . ( 18 sec) [ -14462.6528] [Topology ] . Checking for NNIs, optimizing five branches... . ( 34 sec) [ -14460.8041] [GTR parameters ] . ( 34 sec) [ -14371.0264] [Alpha ][ 0.279990] . ( 34 sec) [ -14371.0264] [Topology ] . ( 35 sec) [ -14370.0783] [Topology ] . ( 37 sec) [ -14369.8437] [Topology ] . ( 39 sec) [ -14369.4994] [Topology ] . ( 40 sec) [ -14369.4254] [Topology ] . ( 42 sec) [ -14369.3901] [Topology ] . ( 44 sec) [ -14369.3698] [Topology ] . ( 45 sec) [ -14369.3578] [Topology ] . ( 47 sec) [ -14369.3507] [Topology ] . Checking for NNIs, optimizing five branches... . ( 61 sec) [ -14368.8958] [GTR parameters ] . ( 61 sec) [ -14368.7192] [Alpha ][ 0.273158] . ( 61 sec) [ -14368.7192] [Topology ] . ( 62 sec) [ -14368.6894] [Topology ] . ( 64 sec) [ -14368.6736] [Topology ] . ( 66 sec) [ -14368.6645] [Topology ] . ( 67 sec) [ -14368.6593] [Topology ] . ( 69 sec) [ -14368.6562] [Topology ] . ( 71 sec) [ -14368.6545] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -14368.6527] [GTR parameters ] . ( 83 sec) [ -14368.6463] [Alpha ][ 0.271777] . ( 83 sec) [ -14368.6463] [Topology ] . ( 85 sec) [ -14368.6434] [Topology ] . ( 87 sec) [ -14368.6418] [Topology ] . ( 88 sec) [ -14368.6408] [Topology ] . Checking for NNIs, optimizing five branches... . ( 102 sec) [ -14368.6398] [GTR parameters ] . ( 102 sec) [ -14368.6396] [Alpha ][ 0.271504] . ( 102 sec) [ -14368.6396] [Topology ] . ( 103 sec) [ -14368.6388] [Topology ] . Checking for NNIs, optimizing five branches... . ( 116 sec) [ -14368.6388] [GTR parameters ] . ( 116 sec) [ -14368.6388] [Alpha ][ 0.271504] . ( 116 sec) [ -14368.6388] [Topology ] . ( 117 sec) [ -14368.6384] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 144 sec) [ -15009.3920] [GTR parameters ] . ( 145 sec) [ -14725.6209] [Alpha ][ 0.500960] . ( 145 sec) [ -14724.6451] [ 2562] [depth= 2] . ( 145 sec) [ -14721.3879] [ 2562] [depth= 1] . ( 145 sec) [ -14721.0926] [ 2562] [depth= 1] . ( 146 sec) [ -14717.3225] [ 2562] [depth= 2] . ( 146 sec) [ -14714.6002] [ 2561] [depth= 2] . ( 146 sec) [ -14714.3106] [ 2561] [depth= 1] . ( 146 sec) [ -14713.7025] [ 2562] [depth= 1] . ( 146 sec) [ -14713.3967] [ 2561] [depth= 1] . ( 147 sec) [ -14704.7688] [ 2559] [depth= 2] . ( 148 sec) [ -14704.3651] [ 2563] [depth= 1] . ( 148 sec) [ -14695.9944] [ 2562] [depth= 1] . ( 148 sec) [ -14695.9146] [ 2563] [depth= 1] . ( 148 sec) [ -14690.7071] [ 2561] [depth= 1] . ( 149 sec) [ -14690.0098] [ 2562] [depth= 1] . ( 149 sec) [ -14686.3531] [ 2561] [depth= 1] . ( 149 sec) [ -14684.1260] [ 2567] [depth= 1] . ( 149 sec) [ -14677.8669] [ 2561] [depth= 1] . ( 149 sec) [ -14676.6694] [ 2560] [depth= 1] . ( 150 sec) [ -14674.4483] [ 2561] [depth= 1] . ( 150 sec) [ -14660.3956] [ 2567] [depth= 1] . ( 150 sec) [ -14659.0069] [ 2561] [depth= 1] . ( 150 sec) [ -14647.2826] [ 2564] [depth= 5] . ( 150 sec) [ -14641.6838] [ 2560] [depth= 2] . ( 150 sec) [ -14640.9537] [ 2563] [depth= 1] . ( 150 sec) [ -14639.3847] [ 2560] [depth= 1] . ( 150 sec) [ -14637.2516] [ 2560] [depth= 1] . ( 150 sec) [ -14632.7965] [ 2560] [depth= 1] . ( 151 sec) [ -14627.6486] [ 2556] [depth= 1] . ( 151 sec) [ -14624.5125] [ 2560] [depth= 2] . ( 151 sec) [ -14616.8912] [ 2557] [depth= 2] . ( 151 sec) [ -14613.0179] [ 2560] [depth= 1] . ( 151 sec) [ -14611.8228] [ 2557] [depth= 1] . ( 151 sec) [ -14608.7228] [ 2561] [depth= 1] . ( 152 sec) [ -14604.5800] [ 2557] [depth= 3] . ( 152 sec) [ -14587.9009] [ 2557] [depth= 2] . ( 152 sec) [ -14585.8415] [ 2553] [depth= 1] . ( 152 sec) [ -14583.3343] [ 2553] [depth= 1] . ( 152 sec) [ -14562.1720] [ 2545] [depth= 4] . ( 152 sec) [ -14551.6166] [ 2544] [depth= 1] . ( 153 sec) [ -14547.2622] [ 2546] [depth= 1] . ( 153 sec) [ -14539.0044] [ 2542] [depth= 4] . ( 153 sec) [ -14527.5500] [ 2544] [depth= 3] . ( 154 sec) [ -14526.7659] [ 2542] [depth= 3] . ( 154 sec) [ -14526.6286] [ 2542] [depth= 1] . ( 154 sec) [ -14522.6486] [ 2540] [depth= 2] . ( 154 sec) [ -14516.3579] [ 2539] [depth= 1] . ( 154 sec) [ -14507.3997] [ 2534] [depth= 2] . ( 155 sec) [ -14507.2432] [ 2534] [depth= 1] . ( 155 sec) [ -14506.5689] [ 2536] [depth= 1] . ( 155 sec) [ -14505.9348] [ 2536] [depth= 1] . ( 156 sec) [ -14503.9401] [ 2534] [depth= 1] . ( 156 sec) [ -14503.9059] [ 2534] [depth= 1] . ( 156 sec) [ -14503.2496] [ 2535] [depth= 1] . ( 157 sec) [ -14503.0758] [ 2536] [depth= 1] . ( 157 sec) [ -14501.9580] [ 2535] [depth= 1] . ( 157 sec) [ -14501.3985] [ 2536] [depth= 1] . ( 158 sec) [ -14500.9434] [ 2538] [depth= 1] . ( 158 sec) [ -14500.7891] [ 2538] [depth= 1] . ( 158 sec) [ -14499.6083] [ 2539] [depth= 1] . ( 159 sec) [ -14496.2386] [ 2539] [depth= 2] . ( 160 sec) [ -14495.1641] [ 2538] [depth= 1] . ( 161 sec) [ -14435.2965] [Branch lengths ] . ( 163 sec) [ -14434.5167] [GTR parameters ] . ( 163 sec) [ -14339.6216] [Alpha ][ 0.269840] . ( 166 sec) [ -14339.4127] [ 2535] [depth= 1] . ( 168 sec) [ -14337.8490] [ 2540] [depth= 5] . ( 170 sec) [ -14337.5930] [ 2539] [depth= 1] . ( 171 sec) [ -14337.0348] [ 2541] [depth= 1] . ( 172 sec) [ -14336.8992] [ 2541] [depth= 1] . ( 174 sec) [ -14336.8418] [ 2541] [depth= 1] . ( 179 sec) [ -14336.6492] [ 2542] [depth= 1] . ( 185 sec) [ -14336.5738] [ 2542] [depth= 1] . ( 185 sec) [ -14335.8282] [ 2542] [depth= 2] . ( 186 sec) [ -14330.7728] [Branch lengths ] . ( 188 sec) [ -14330.3911] [GTR parameters ] . ( 188 sec) [ -14330.3908] [Alpha ][ 0.270109] . ( 188 sec) [ -14330.3207] [ 2543] [depth= 2] . ( 208 sec) [ -14330.2994] [ 2543] [depth= 1] . ( 209 sec) [ -14329.5544] [Branch lengths ] . ( 211 sec) [ -14329.5291] [GTR parameters ] . ( 211 sec) [ -14329.5125] [Alpha ][ 0.272182] . ( 266 sec) [ -14329.0882] [ 2549] [depth= 2] . ( 267 sec) [ -14329.0544] [ 2550] [depth= 1] . ( 268 sec) [ -14329.0250] [ 2550] [depth= 1] . ( 283 sec) [ -14328.5254] [Branch lengths ] . ( 283 sec) [ -14328.5190] [GTR parameters ] . ( 283 sec) [ -14328.5056] [Alpha ][ 0.274026] . ( 356 sec) [ -14328.3220] [Branch lengths ] . ( 356 sec) [ -14328.3220] [Topology ] . ( 357 sec) [ -14328.2030] [Topology ] . ( 359 sec) [ -14328.1053] [Topology ] . ( 361 sec) [ -14328.0777] [Topology ] . ( 362 sec) [ -14328.0680] [Topology ] . ( 364 sec) [ -14328.0642] [Topology ] . ( 366 sec) [ -14328.0624] [Topology ] . ( 367 sec) [ -14328.0611] [GTR parameters ] . ( 367 sec) [ -14328.0467] [Alpha ][ 0.275942] . ( 367 sec) [ -14328.0467] [Topology ] . ( 369 sec) [ -14328.0437] [Topology ] . ( 370 sec) [ -14328.0419] [Topology ] . ( 372 sec) [ -14328.0408] [Topology ] . ( 374 sec) [ -14328.0402] [Topology ] . ( 375 sec) [ -14328.0399] [GTR parameters ] . ( 375 sec) [ -14328.0397] [Alpha ][ 0.276218] . ( 375 sec) [ -14328.0397] [Topology ] . ( 377 sec) [ -14328.0391] [Topology ] . ( 377 sec) [ -14328.0391] [GTR parameters ] . ( 377 sec) [ -14328.0391] [Alpha ][ 0.276218] . Checking for NNIs, optimizing five branches... . ( 390 sec) [ -14327.9302] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -14368.638364 . Log likelihood obtained after SPR moves : -14327.930250 . Log likelihood of the current tree: -14327.930250. . Printing the most likely tree in file 'nucleic_M2826_60x1398_2006.phy_phyml_tree.txt'... . Time used 0h6m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 392.92user 0.00system 6:44.09elapsed 97%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps