.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2879_70x800_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... . 466 patterns found. (out of a total of 800 sites) . 405 sites without polymorphism (50.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 17Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 3 sec) [ -5870.6391] [GTR parameters ] . ( 3 sec) [ -5850.1279] [Alpha ][ 0.500960] . ( 3 sec) [ -5850.1279] [Topology ] . ( 5 sec) [ -5802.4192] [Topology ] . ( 7 sec) [ -5794.8150] [Topology ] . ( 8 sec) [ -5792.6224] [Topology ] . ( 10 sec) [ -5791.9272] [Topology ] . ( 11 sec) [ -5791.6644] [Topology ] . ( 13 sec) [ -5791.5565] [Topology ] . ( 14 sec) [ -5791.5112] [Topology ] . ( 15 sec) [ -5791.4918] [Topology ] . Checking for NNIs, optimizing five branches... . ( 25 sec) [ -5791.4140] [Topology ] . ( 26 sec) [ -5790.8079] [GTR parameters ] . ( 27 sec) [ -5789.8818] [Alpha ][ 0.567522] . ( 27 sec) [ -5789.8818] [Topology ] . ( 28 sec) [ -5789.8160] [Topology ] . ( 29 sec) [ -5789.7926] [Topology ] . ( 31 sec) [ -5789.7832] [Topology ] . ( 32 sec) [ -5789.7793] [Topology ] . ( 34 sec) [ -5789.7776] [Topology ] . ( 35 sec) [ -5789.7768] [Topology ] . Checking for NNIs, optimizing five branches... . ( 45 sec) [ -5789.7143] [Topology ] . ( 46 sec) [ -5789.7090] [GTR parameters ] . ( 46 sec) [ -5789.7079] [Alpha ][ 0.569973] . ( 46 sec) [ -5789.7079] [Topology ] . ( 48 sec) [ -5789.7000] [Topology ] . ( 49 sec) [ -5789.6938] [Topology ] . ( 50 sec) [ -5789.6880] [Topology ] . ( 52 sec) [ -5789.6824] [Topology ] . ( 53 sec) [ -5789.6770] [Topology ] . ( 55 sec) [ -5789.6720] [Topology ] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -5789.6719] [Topology ] . ( 65 sec) [ -5789.6709] [GTR parameters ] . ( 65 sec) [ -5789.6709] [Alpha ][ 0.569973] . ( 65 sec) [ -5789.6709] [Topology ] . ( 66 sec) [ -5789.6655] [Topology ] . ( 68 sec) [ -5789.6605] [Topology ] . ( 69 sec) [ -5789.6554] [Topology ] . ( 71 sec) [ -5789.6504] [Topology ] . ( 72 sec) [ -5789.6457] [Topology ] . ( 73 sec) [ -5789.6430] [Topology ] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -5789.6157] [Topology ] . ( 83 sec) [ -5789.6150] [GTR parameters ] . ( 84 sec) [ -5789.6150] [Alpha ][ 0.569973] . ( 84 sec) [ -5789.6150] [Topology ] . ( 85 sec) [ -5789.6140] [Topology ] . Checking for NNIs, optimizing five branches... . ( 95 sec) [ -5789.6140] [GTR parameters ] . ( 95 sec) [ -5789.6140] [Alpha ][ 0.569973] . ( 95 sec) [ -5789.6140] [Topology ] . ( 97 sec) [ -5789.6138] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 119 sec) [ -5870.6391] [GTR parameters ] . ( 119 sec) [ -5850.1279] [Alpha ][ 0.500960] . ( 119 sec) [ -5849.9737] [ 882] [depth= 1] . ( 119 sec) [ -5848.7541] [ 879] [depth= 1] . ( 119 sec) [ -5847.5939] [ 882] [depth= 1] . ( 119 sec) [ -5843.6899] [ 889] [depth= 1] . ( 119 sec) [ -5840.6196] [ 882] [depth= 1] . ( 120 sec) [ -5839.1947] [ 879] [depth= 1] . ( 120 sec) [ -5838.7428] [ 879] [depth= 1] . ( 122 sec) [ -5830.8751] [ 876] [depth= 1] . ( 123 sec) [ -5830.8528] [ 877] [depth= 1] . ( 123 sec) [ -5829.5369] [ 877] [depth= 1] . ( 124 sec) [ -5826.3186] [ 876] [depth= 1] . ( 124 sec) [ -5825.9962] [ 876] [depth= 1] . ( 124 sec) [ -5825.3306] [ 876] [depth= 1] . ( 125 sec) [ -5824.9277] [ 877] [depth= 2] . ( 126 sec) [ -5824.8726] [ 877] [depth= 2] . ( 126 sec) [ -5824.8092] [ 877] [depth= 2] . ( 126 sec) [ -5824.6090] [ 877] [depth= 1] . ( 126 sec) [ -5824.4482] [ 877] [depth= 2] . ( 126 sec) [ -5824.4342] [ 877] [depth= 1] . ( 127 sec) [ -5824.4228] [ 877] [depth= 1] . ( 129 sec) [ -5821.0821] [ 878] [depth= 2] . ( 129 sec) [ -5820.1690] [ 878] [depth= 1] . ( 129 sec) [ -5819.9979] [ 878] [depth= 1] . ( 132 sec) [ -5819.8394] [ 878] [depth= 1] . ( 133 sec) [ -5819.7150] [ 878] [depth= 1] . ( 133 sec) [ -5819.3486] [ 878] [depth= 1] . ( 133 sec) [ -5818.9385] [ 878] [depth= 1] . ( 133 sec) [ -5818.9002] [ 878] [depth= 1] . ( 133 sec) [ -5817.8489] [ 878] [depth= 1] . ( 133 sec) [ -5817.8106] [ 878] [depth= 1] . ( 135 sec) [ -5816.4499] [ 877] [depth= 4] . ( 135 sec) [ -5814.0862] [ 877] [depth= 2] . ( 136 sec) [ -5813.4570] [ 877] [depth= 2] . ( 137 sec) [ -5810.4352] [ 876] [depth= 1] . ( 138 sec) [ -5810.2274] [ 876] [depth= 1] . ( 140 sec) [ -5810.1652] [ 876] [depth= 1] . ( 149 sec) [ -5809.1649] [ 876] [depth= 1] . ( 149 sec) [ -5808.5688] [ 876] [depth= 1] . ( 151 sec) [ -5806.3912] [ 876] [depth= 5] . ( 151 sec) [ -5806.3190] [ 876] [depth= 2] . ( 152 sec) [ -5805.9813] [ 876] [depth= 2] . ( 152 sec) [ -5805.0200] [ 876] [depth= 1] . ( 152 sec) [ -5805.0041] [ 876] [depth= 1] . ( 153 sec) [ -5804.9365] [ 876] [depth= 1] . ( 154 sec) [ -5804.7963] [ 876] [depth= 1] . ( 154 sec) [ -5804.7134] [ 876] [depth= 2] . ( 154 sec) [ -5804.6206] [ 876] [depth= 2] . ( 155 sec) [ -5804.1794] [ 876] [depth= 1] . ( 155 sec) [ -5803.9694] [ 876] [depth= 2] . ( 155 sec) [ -5803.7284] [ 876] [depth= 2] . ( 155 sec) [ -5803.6712] [ 876] [depth= 4] . ( 155 sec) [ -5803.5317] [ 876] [depth= 3] . ( 156 sec) [ -5803.5098] [ 876] [depth= 3] . ( 158 sec) [ -5803.4980] [ 876] [depth= 1] . ( 159 sec) [ -5785.6478] [Branch lengths ] . ( 160 sec) [ -5785.2072] [GTR parameters ] . ( 161 sec) [ -5784.4723] [Alpha ][ 0.560934] . ( 172 sec) [ -5784.4375] [ 876] [depth= 1] . ( 178 sec) [ -5784.4207] [ 876] [depth= 2] . ( 182 sec) [ -5784.3984] [ 876] [depth= 1] . ( 183 sec) [ -5784.3704] [ 876] [depth= 1] . ( 187 sec) [ -5784.3479] [ 876] [depth= 1] . ( 196 sec) [ -5784.2428] [ 876] [depth= 4] . ( 197 sec) [ -5784.1539] [ 876] [depth= 3] . ( 197 sec) [ -5784.1301] [ 876] [depth= 2] . ( 198 sec) [ -5784.1064] [ 876] [depth= 3] . ( 201 sec) [ -5784.0752] [ 876] [depth= 2] . ( 208 sec) [ -5782.4376] [Branch lengths ] . ( 210 sec) [ -5782.4125] [GTR parameters ] . ( 210 sec) [ -5782.4065] [Alpha ][ 0.566844] . ( 256 sec) [ -5782.3794] [ 876] [depth= 1] . ( 268 sec) [ -5782.1995] [Branch lengths ] . ( 268 sec) [ -5782.1985] [GTR parameters ] . ( 268 sec) [ -5782.1984] [Alpha ][ 0.567795] . ( 340 sec) [ -5782.1747] [Branch lengths ] . ( 340 sec) [ -5782.1747] [Topology ] . ( 342 sec) [ -5782.1719] [Topology ] . ( 343 sec) [ -5782.1707] [Topology ] . ( 345 sec) [ -5782.1699] [Topology ] . ( 345 sec) [ -5782.1695] [GTR parameters ] . ( 345 sec) [ -5782.1695] [Alpha ][ 0.568363] . ( 345 sec) [ -5782.1695] [Topology ] . ( 347 sec) [ -5782.1688] [Topology ] . ( 347 sec) [ -5782.1688] [GTR parameters ] . ( 347 sec) [ -5782.1688] [Alpha ][ 0.568363] . Checking for NNIs, optimizing five branches... . ( 356 sec) [ -5782.1686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 366 sec) [ -5782.1678] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5789.613810 . Log likelihood obtained after SPR moves : -5782.167774 . Log likelihood of the current tree: -5782.167774. . Printing the most likely tree in file 'nucleic_M2879_70x800_2006.phy_phyml_tree.txt'... . Time used 0h6m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 370.00user 0.00system 6:16.34elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps