.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data98.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... . 427 patterns found. (out of a total of 500 sites) . 71 sites without polymorphism (14.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-8768.396920 . ( 1 sec) [ -8765.3410] [GTR parameters ] . ( 1 sec) [ -8763.4873] [Alpha ][ 1.174574] . ( 1 sec) [ -8763.4873] [Topology ] . ( 2 sec) [ -8706.9612] [Topology ] . ( 3 sec) [ -8694.4275] [Topology ] . ( 4 sec) [ -8691.9231] [Topology ] . ( 5 sec) [ -8691.1687] [Topology ] . ( 5 sec) [ -8690.8831] [Topology ] . ( 6 sec) [ -8690.7542] [Topology ] . ( 7 sec) [ -8690.6895] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -8690.1883] [Topology ] . Before opt ts/t=1.000000 LK=-8690.188347 . ( 14 sec) [ -8690.1757] [GTR parameters ] . ( 15 sec) [ -8690.1739] [Alpha ][ 1.168506] . ( 15 sec) [ -8690.1739] [Topology ] . ( 15 sec) [ -8690.1317] [Topology ] . ( 16 sec) [ -8690.1094] [Topology ] . ( 17 sec) [ -8690.0966] [Topology ] . ( 19 sec) [ -8690.0892] [Topology ] . ( 20 sec) [ -8690.0847] [Topology ] . ( 22 sec) [ -8690.0821] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8690.082072 . ( 33 sec) [ -8690.0819] [GTR parameters ] . ( 33 sec) [ -8690.0818] [Alpha ][ 1.169955] . ( 33 sec) [ -8690.0818] [Topology ] . ( 34 sec) [ -8690.0802] [Topology ] . ( 35 sec) [ -8690.0792] [Topology ] . ( 37 sec) [ -8690.0785] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8690.078535 . ( 46 sec) [ -8690.0785] [GTR parameters ] . ( 46 sec) [ -8690.0785] [Alpha ][ 1.169955] . ( 46 sec) [ -8690.0785] [Topology ] . ( 47 sec) [ -8690.0781] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 67 sec) [ -8765.3410] [GTR parameters ] . ( 67 sec) [ -8763.4873] [Alpha ][ 1.174574] . ( 68 sec) [ -8736.7899] [ 1825] [depth= 1] . ( 68 sec) [ -8724.8039] [ 1828] [depth= 1] . ( 69 sec) [ -8724.3963] [ 1830] [depth= 1] . ( 69 sec) [ -8723.9811] [ 1828] [depth= 1] . ( 70 sec) [ -8723.2369] [ 1828] [depth= 1] . ( 70 sec) [ -8723.0275] [ 1828] [depth= 1] . ( 70 sec) [ -8720.9832] [ 1833] [depth= 1] . ( 71 sec) [ -8718.5935] [ 1828] [depth= 1] . ( 72 sec) [ -8717.6825] [ 1828] [depth= 1] . ( 72 sec) [ -8691.9707] [Branch lengths ] . ( 73 sec) [ -8691.9562] [GTR parameters ] . ( 73 sec) [ -8691.9438] [Alpha ][ 1.160058] . ( 78 sec) [ -8690.5056] [Branch lengths ] . ( 83 sec) [ -8689.3639] [ 1840] [depth= 2] . ( 96 sec) [ -8689.2582] [ 1836] [depth= 1] . ( 99 sec) [ -8688.9077] [ 1836] [depth= 1] . ( 106 sec) [ -8688.5935] [Branch lengths ] . ( 107 sec) [ -8688.5881] [GTR parameters ] . ( 107 sec) [ -8688.5881] [Alpha ][ 1.160058] . ( 136 sec) [ -8688.4922] [Branch lengths ] . ( 136 sec) [ -8688.4922] [Topology ] . ( 137 sec) [ -8688.4688] [Topology ] . ( 138 sec) [ -8688.4551] [Topology ] . ( 139 sec) [ -8688.4451] [Topology ] . ( 140 sec) [ -8688.4374] [Topology ] . ( 141 sec) [ -8688.4314] [Topology ] . ( 142 sec) [ -8688.4266] [Topology ] . ( 143 sec) [ -8688.4266] [GTR parameters ] . ( 143 sec) [ -8688.4266] [Alpha ][ 1.160058] . ( 143 sec) [ -8688.4266] [Topology ] . ( 144 sec) [ -8688.4229] [Topology ] . ( 145 sec) [ -8688.4199] [Topology ] . ( 146 sec) [ -8688.4176] [Topology ] . ( 147 sec) [ -8688.4157] [Topology ] . ( 149 sec) [ -8688.4142] [Topology ] . ( 150 sec) [ -8688.4131] [Topology ] . ( 150 sec) [ -8688.4131] [GTR parameters ] . ( 150 sec) [ -8688.4131] [Alpha ][ 1.160058] . ( 150 sec) [ -8688.4131] [Topology ] . ( 152 sec) [ -8688.4121] [Topology ] . ( 152 sec) [ -8688.4121] [GTR parameters ] . ( 152 sec) [ -8688.4121] [Alpha ][ 1.160058] . Checking for NNIs, optimizing five branches... . ( 163 sec) [ -8688.4111] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8690.078147 . Log likelihood obtained after SPR moves : -8688.411078 . Log likelihood of the current tree: -8688.411078. . Printing the most likely tree in file 'data98.phy_phyml_tree.txt'... . Time used 0h2m54s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo