.......................... 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] . ( 3 sec) [ -5848.7541] [ 879] [depth= 1] . ( 3 sec) [ -5847.5939] [ 882] [depth= 1] . ( 5 sec) [ -5843.6899] [ 889] [depth= 1] . ( 5 sec) [ -5840.6196] [ 882] [depth= 1] . ( 15 sec) [ -5839.1947] [ 879] [depth= 1] . ( 19 sec) [ -5838.7428] [ 879] [depth= 1] . ( 54 sec) [ -5830.8751] [ 876] [depth= 1] . ( 57 sec) [ -5830.8528] [ 877] [depth= 1] . ( 64 sec) [ -5829.5369] [ 877] [depth= 1] . ( 68 sec) [ -5826.3186] [ 876] [depth= 1] . ( 74 sec) [ -5825.9962] [ 876] [depth= 1] . ( 74 sec) [ -5825.3306] [ 876] [depth= 1] . ( 75 sec) [ -5824.9277] [ 877] [depth= 2] . ( 90 sec) [ -5824.8726] [ 877] [depth= 2] . ( 90 sec) [ -5824.8092] [ 877] [depth= 2] . ( 90 sec) [ -5824.6090] [ 877] [depth= 1] . ( 92 sec) [ -5824.4482] [ 877] [depth= 2] . ( 92 sec) [ -5824.4342] [ 877] [depth= 1] . ( 94 sec) [ -5824.4228] [ 877] [depth= 1] . ( 110 sec) [ -5821.0821] [ 878] [depth= 2] . ( 111 sec) [ -5820.1690] [ 878] [depth= 1] . ( 111 sec) [ -5819.9979] [ 878] [depth= 1] . ( 127 sec) [ -5819.8394] [ 878] [depth= 1] . ( 129 sec) [ -5819.7150] [ 878] [depth= 1] . ( 129 sec) [ -5819.3486] [ 878] [depth= 1] . ( 129 sec) [ -5818.9385] [ 878] [depth= 1] . ( 129 sec) [ -5818.9002] [ 878] [depth= 1] . ( 130 sec) [ -5817.8489] [ 878] [depth= 1] . ( 130 sec) [ -5817.8106] [ 878] [depth= 1] . ( 137 sec) [ -5816.4499] [ 877] [depth= 4] . ( 138 sec) [ -5814.0862] [ 877] [depth= 2] . ( 138 sec) [ -5813.4570] [ 877] [depth= 2] . ( 143 sec) [ -5810.4352] [ 876] [depth= 1] . ( 146 sec) [ -5810.2274] [ 876] [depth= 1] . ( 154 sec) [ -5810.1652] [ 876] [depth= 1] . ( 184 sec) [ -5809.1649] [ 876] [depth= 1] . ( 184 sec) [ -5808.5688] [ 876] [depth= 1] . ( 188 sec) [ -5806.3912] [ 876] [depth= 5] . ( 188 sec) [ -5806.3190] [ 876] [depth= 2] . ( 190 sec) [ -5805.9813] [ 876] [depth= 2] . ( 190 sec) [ -5805.0200] [ 876] [depth= 1] . ( 192 sec) [ -5805.0041] [ 876] [depth= 1] . ( 193 sec) [ -5804.9365] [ 876] [depth= 1] . ( 196 sec) [ -5804.7963] [ 876] [depth= 1] . ( 196 sec) [ -5804.7134] [ 876] [depth= 2] . ( 196 sec) [ -5804.6206] [ 876] [depth= 2] . ( 197 sec) [ -5804.1794] [ 876] [depth= 1] . ( 197 sec) [ -5803.9694] [ 876] [depth= 2] . ( 197 sec) [ -5803.7284] [ 876] [depth= 2] . ( 197 sec) [ -5803.6712] [ 876] [depth= 4] . ( 197 sec) [ -5803.5317] [ 876] [depth= 3] . ( 199 sec) [ -5803.5098] [ 876] [depth= 3] . ( 205 sec) [ -5803.4980] [ 876] [depth= 1] . ( 205 sec) [ -5785.6478] [Branch lengths ] . ( 207 sec) [ -5785.2072] [GTR parameters ] . ( 207 sec) [ -5784.4723] [Alpha ][ 0.560934] . ( 344 sec) [ -5784.4375] [ 876] [depth= 1] . ( 373 sec) [ -5784.4207] [ 876] [depth= 2] . ( 387 sec) [ -5784.3984] [ 876] [depth= 1] . ( 391 sec) [ -5784.3704] [ 876] [depth= 1] . ( 408 sec) [ -5784.3479] [ 876] [depth= 1] . ( 433 sec) [ -5784.2428] [ 876] [depth= 4] . ( 437 sec) [ -5784.1539] [ 876] [depth= 3] . ( 437 sec) [ -5784.1301] [ 876] [depth= 2] . ( 439 sec) [ -5784.1064] [ 876] [depth= 3] . ( 447 sec) [ -5784.0752] [ 876] [depth= 2] . ( 464 sec) [ -5782.4376] [Branch lengths ] . ( 466 sec) [ -5782.4125] [GTR parameters ] . ( 466 sec) [ -5782.4065] [Alpha ][ 0.566844] . ( 721 sec) [ -5782.3794] [ 876] [depth= 1] . ( 749 sec) [ -5782.1995] [Branch lengths ] . ( 750 sec) [ -5782.1985] [GTR parameters ] . ( 750 sec) [ -5782.1984] [Alpha ][ 0.567795] . ( 822 sec) [ -5782.1747] [Branch lengths ] . ( 822 sec) [ -5782.1747] [Topology ] . ( 823 sec) [ -5782.1719] [Topology ] . ( 825 sec) [ -5782.1707] [Topology ] . ( 826 sec) [ -5782.1699] [Topology ] . ( 827 sec) [ -5782.1695] [GTR parameters ] . ( 827 sec) [ -5782.1695] [Alpha ][ 0.568363] . ( 827 sec) [ -5782.1695] [Topology ] . ( 828 sec) [ -5782.1688] [Topology ] . ( 829 sec) [ -5782.1688] [GTR parameters ] . ( 829 sec) [ -5782.1688] [Alpha ][ 0.568363] . Checking for NNIs, optimizing five branches... . ( 838 sec) [ -5782.1686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 848 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 0h14m18s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 845.53user 0.00system 14:18.13elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps