.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data11.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... . 459 patterns found. (out of a total of 500 sites) . 37 sites without polymorphism (7.40%). . 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=-10696.571610 . ( 1 sec) [ -10694.6353] [GTR parameters ] . ( 1 sec) [ -10693.9844] [Alpha ][ 1.087154] . ( 1 sec) [ -10693.9844] [Topology ] . ( 3 sec) [ -10617.6895] [Topology ] . ( 4 sec) [ -10603.4090] [Topology ] . ( 5 sec) [ -10598.1320] [Topology ] . ( 6 sec) [ -10595.6592] [Topology ] . ( 7 sec) [ -10594.3258] [Topology ] . ( 8 sec) [ -10593.6099] [Topology ] . ( 9 sec) [ -10593.2291] [Topology ] . ( 10 sec) [ -10593.0135] [Topology ] . ( 11 sec) [ -10592.8883] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.814399 . ( 19 sec) [ -10592.7141] [GTR parameters ] . ( 19 sec) [ -10592.6699] [Alpha ][ 1.066035] . ( 19 sec) [ -10592.6699] [Topology ] . ( 21 sec) [ -10592.6165] [Topology ] . ( 22 sec) [ -10592.5856] [Topology ] . ( 24 sec) [ -10592.5669] [Topology ] . ( 25 sec) [ -10592.5554] [Topology ] . ( 26 sec) [ -10592.5483] [Topology ] . ( 28 sec) [ -10592.5439] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.543867 . ( 38 sec) [ -10592.5435] [GTR parameters ] . ( 38 sec) [ -10592.5422] [Alpha ][ 1.062217] . ( 38 sec) [ -10592.5422] [Topology ] . ( 39 sec) [ -10592.5391] [Topology ] . ( 41 sec) [ -10592.5372] [Topology ] . ( 43 sec) [ -10592.5360] [Topology ] . ( 44 sec) [ -10592.5353] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10592.535251 . ( 55 sec) [ -10592.5352] [GTR parameters ] . ( 55 sec) [ -10592.5352] [Alpha ][ 1.062217] . ( 55 sec) [ -10592.5352] [Topology ] . ( 56 sec) [ -10592.5347] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 75 sec) [ -10694.6353] [GTR parameters ] . ( 75 sec) [ -10693.9844] [Alpha ][ 1.087154] . ( 75 sec) [ -10692.5984] [ 2491] [depth= 1] . ( 76 sec) [ -10692.4701] [ 2490] [depth= 1] . ( 76 sec) [ -10692.1352] [ 2491] [depth= 1] . ( 76 sec) [ -10690.2151] [ 2492] [depth= 2] . ( 76 sec) [ -10688.6342] [ 2492] [depth= 1] . ( 76 sec) [ -10685.3503] [ 2497] [depth= 1] . ( 76 sec) [ -10672.2878] [ 2498] [depth= 1] . ( 77 sec) [ -10671.1974] [ 2497] [depth= 1] . ( 77 sec) [ -10665.1161] [ 2502] [depth= 1] . ( 77 sec) [ -10661.0885] [ 2514] [depth= 1] . ( 77 sec) [ -10658.8661] [ 2511] [depth= 1] . ( 77 sec) [ -10657.3290] [ 2511] [depth= 1] . ( 78 sec) [ -10657.3187] [ 2511] [depth= 1] . ( 78 sec) [ -10656.8438] [ 2511] [depth= 1] . ( 78 sec) [ -10652.9075] [ 2502] [depth= 1] . ( 79 sec) [ -10649.8132] [ 2505] [depth= 1] . ( 79 sec) [ -10648.2321] [ 2505] [depth= 1] . ( 79 sec) [ -10645.8625] [ 2505] [depth= 1] . ( 79 sec) [ -10645.7963] [ 2509] [depth= 1] . ( 79 sec) [ -10645.6961] [ 2511] [depth= 1] . ( 80 sec) [ -10598.2174] [Branch lengths ] . ( 81 sec) [ -10598.1359] [GTR parameters ] . ( 81 sec) [ -10598.1269] [Alpha ][ 1.076709] . ( 82 sec) [ -10597.7301] [ 2513] [depth= 1] . ( 83 sec) [ -10597.7137] [ 2514] [depth= 1] . ( 84 sec) [ -10597.5528] [ 2516] [depth= 1] . ( 87 sec) [ -10593.5177] [Branch lengths ] . ( 87 sec) [ -10593.5111] [GTR parameters ] . ( 88 sec) [ -10593.5060] [Alpha ][ 1.069079] . ( 94 sec) [ -10592.7190] [Branch lengths ] . ( 109 sec) [ -10592.5598] [ 2516] [depth= 1] . ( 126 sec) [ -10592.3160] [Branch lengths ] . ( 126 sec) [ -10592.3146] [GTR parameters ] . ( 127 sec) [ -10592.3103] [Alpha ][ 1.062209] . ( 127 sec) [ -10592.3103] [Topology ] . ( 128 sec) [ -10592.2693] [Topology ] . ( 129 sec) [ -10592.2493] [Topology ] . ( 130 sec) [ -10592.2374] [Topology ] . ( 131 sec) [ -10592.2301] [Topology ] . ( 132 sec) [ -10592.2256] [Topology ] . ( 133 sec) [ -10592.2227] [Topology ] . ( 133 sec) [ -10592.2227] [GTR parameters ] . ( 134 sec) [ -10592.2224] [Alpha ][ 1.060463] . ( 134 sec) [ -10592.2224] [Topology ] . ( 135 sec) [ -10592.2205] [Topology ] . ( 136 sec) [ -10592.2193] [Topology ] . ( 137 sec) [ -10592.2186] [Topology ] . ( 137 sec) [ -10592.2186] [GTR parameters ] . ( 137 sec) [ -10592.2186] [Alpha ][ 1.060463] . ( 137 sec) [ -10592.2186] [Topology ] . ( 138 sec) [ -10592.2181] [Topology ] . ( 139 sec) [ -10592.2181] [GTR parameters ] . ( 139 sec) [ -10592.2181] [Alpha ][ 1.060463] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10592.534732 . Log likelihood obtained after SPR moves : -10592.218086 . Log likelihood of the current tree: -10592.218086. . Printing the most likely tree in file 'data11.phy_phyml_tree.txt'... . Time used 0h2m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo