.......................... 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 : 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 SPR moves)... . ( 3 sec) [ -5870.6391] [GTR parameters ] . ( 3 sec) [ -5850.1279] [Alpha ][ 0.500960] . ( 3 sec) [ -5849.9737] [ 882] [depth= 1] . ( 4 sec) [ -5848.7541] [ 879] [depth= 1] . ( 4 sec) [ -5847.5939] [ 882] [depth= 1] . ( 4 sec) [ -5843.6899] [ 889] [depth= 1] . ( 4 sec) [ -5840.6196] [ 882] [depth= 1] . ( 4 sec) [ -5839.1947] [ 879] [depth= 1] . ( 5 sec) [ -5838.7428] [ 879] [depth= 1] . ( 7 sec) [ -5830.8751] [ 876] [depth= 1] . ( 7 sec) [ -5830.8528] [ 877] [depth= 1] . ( 8 sec) [ -5829.5369] [ 877] [depth= 1] . ( 8 sec) [ -5826.3186] [ 876] [depth= 1] . ( 9 sec) [ -5825.9962] [ 876] [depth= 1] . ( 9 sec) [ -5825.3306] [ 876] [depth= 1] . ( 9 sec) [ -5824.9277] [ 877] [depth= 2] . ( 10 sec) [ -5824.8726] [ 877] [depth= 2] . ( 10 sec) [ -5824.8092] [ 877] [depth= 2] . ( 10 sec) [ -5824.6090] [ 877] [depth= 1] . ( 11 sec) [ -5824.4482] [ 877] [depth= 2] . ( 11 sec) [ -5824.4342] [ 877] [depth= 1] . ( 11 sec) [ -5824.4228] [ 877] [depth= 1] . ( 13 sec) [ -5821.0821] [ 878] [depth= 2] . ( 14 sec) [ -5820.1690] [ 878] [depth= 1] . ( 14 sec) [ -5819.9979] [ 878] [depth= 1] . ( 17 sec) [ -5819.8394] [ 878] [depth= 1] . ( 17 sec) [ -5819.7150] [ 878] [depth= 1] . ( 17 sec) [ -5819.3486] [ 878] [depth= 1] . ( 17 sec) [ -5818.9385] [ 878] [depth= 1] . ( 18 sec) [ -5818.9002] [ 878] [depth= 1] . ( 18 sec) [ -5817.8489] [ 878] [depth= 1] . ( 18 sec) [ -5817.8106] [ 878] [depth= 1] . ( 20 sec) [ -5816.4499] [ 877] [depth= 4] . ( 20 sec) [ -5814.0862] [ 877] [depth= 2] . ( 20 sec) [ -5813.4570] [ 877] [depth= 2] . ( 22 sec) [ -5810.4352] [ 876] [depth= 1] . ( 22 sec) [ -5810.2274] [ 876] [depth= 1] . ( 24 sec) [ -5810.1652] [ 876] [depth= 1] . ( 34 sec) [ -5809.1649] [ 876] [depth= 1] . ( 34 sec) [ -5808.5688] [ 876] [depth= 1] . ( 35 sec) [ -5806.3912] [ 876] [depth= 5] . ( 36 sec) [ -5806.3190] [ 876] [depth= 2] . ( 36 sec) [ -5805.9813] [ 876] [depth= 2] . ( 36 sec) [ -5805.0200] [ 876] [depth= 1] . ( 37 sec) [ -5805.0041] [ 876] [depth= 1] . ( 37 sec) [ -5804.9365] [ 876] [depth= 1] . ( 38 sec) [ -5804.7963] [ 876] [depth= 1] . ( 38 sec) [ -5804.7134] [ 876] [depth= 2] . ( 38 sec) [ -5804.6206] [ 876] [depth= 2] . ( 39 sec) [ -5804.1794] [ 876] [depth= 1] . ( 39 sec) [ -5803.9694] [ 876] [depth= 2] . ( 39 sec) [ -5803.7284] [ 876] [depth= 2] . ( 40 sec) [ -5803.6712] [ 876] [depth= 4] . ( 40 sec) [ -5803.5317] [ 876] [depth= 3] . ( 40 sec) [ -5803.5098] [ 876] [depth= 3] . ( 43 sec) [ -5803.4980] [ 876] [depth= 1] . ( 43 sec) [ -5785.6478] [Branch lengths ] . ( 45 sec) [ -5785.2072] [GTR parameters ] . ( 45 sec) [ -5784.4723] [Alpha ][ 0.560934] . ( 56 sec) [ -5784.4375] [ 876] [depth= 1] . ( 62 sec) [ -5784.4207] [ 876] [depth= 2] . ( 66 sec) [ -5784.3984] [ 876] [depth= 1] . ( 67 sec) [ -5784.3704] [ 876] [depth= 1] . ( 71 sec) [ -5784.3479] [ 876] [depth= 1] . ( 80 sec) [ -5784.2428] [ 876] [depth= 4] . ( 81 sec) [ -5784.1539] [ 876] [depth= 3] . ( 81 sec) [ -5784.1301] [ 876] [depth= 2] . ( 82 sec) [ -5784.1064] [ 876] [depth= 3] . ( 85 sec) [ -5784.0752] [ 876] [depth= 2] . ( 92 sec) [ -5782.4376] [Branch lengths ] . ( 94 sec) [ -5782.4125] [GTR parameters ] . ( 94 sec) [ -5782.4065] [Alpha ][ 0.566844] . ( 139 sec) [ -5782.3794] [ 876] [depth= 1] . ( 151 sec) [ -5782.1995] [Branch lengths ] . ( 152 sec) [ -5782.1985] [GTR parameters ] . ( 152 sec) [ -5782.1984] [Alpha ][ 0.567795] . ( 223 sec) [ -5782.1747] [Branch lengths ] . ( 223 sec) [ -5782.1747] [Topology ] . ( 224 sec) [ -5782.1719] [Topology ] . ( 226 sec) [ -5782.1707] [Topology ] . ( 227 sec) [ -5782.1699] [Topology ] . ( 228 sec) [ -5782.1695] [GTR parameters ] . ( 228 sec) [ -5782.1695] [Alpha ][ 0.568363] . ( 228 sec) [ -5782.1695] [Topology ] . ( 229 sec) [ -5782.1688] [Topology ] . ( 230 sec) [ -5782.1688] [GTR parameters ] . ( 230 sec) [ -5782.1688] [Alpha ][ 0.568363] . Checking for NNIs, optimizing five branches... . ( 239 sec) [ -5782.1686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 249 sec) [ -5782.1678] [Topology ] . Checking for NNIs, optimizing five branches... . 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 0h4m19s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 257.14user 0.00system 4:18.72elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps