.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data38.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... . 417 patterns found. (out of a total of 500 sites) . 82 sites without polymorphism (16.40%). . 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=-9766.742204 . ( 1 sec) [ -9764.5406] [GTR parameters ] . ( 1 sec) [ -9762.3882] [Alpha ][ 0.854371] . ( 1 sec) [ -9762.3882] [Topology ] . ( 2 sec) [ -9719.6165] [Topology ] . ( 3 sec) [ -9712.6303] [Topology ] . ( 4 sec) [ -9710.9518] [Topology ] . ( 4 sec) [ -9710.2725] [Topology ] . ( 5 sec) [ -9709.9654] [Topology ] . ( 6 sec) [ -9709.8205] [Topology ] . ( 7 sec) [ -9709.7502] [Topology ] . ( 7 sec) [ -9709.7153] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.715254 . ( 13 sec) [ -9709.6642] [GTR parameters ] . ( 13 sec) [ -9709.2487] [Alpha ][ 0.913010] . ( 13 sec) [ -9709.2487] [Topology ] . ( 14 sec) [ -9709.1890] [Topology ] . ( 15 sec) [ -9709.1643] [Topology ] . ( 16 sec) [ -9709.1525] [Topology ] . ( 16 sec) [ -9709.1467] [Topology ] . ( 17 sec) [ -9709.1438] [Topology ] . ( 18 sec) [ -9709.1423] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.142282 . ( 24 sec) [ -9709.1416] [GTR parameters ] . ( 24 sec) [ -9709.1373] [Alpha ][ 0.919319] . ( 24 sec) [ -9709.1373] [Topology ] . ( 25 sec) [ -9709.1361] [Topology ] . ( 25 sec) [ -9709.1355] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9709.135472 . ( 31 sec) [ -9709.1354] [GTR parameters ] . ( 31 sec) [ -9709.1354] [Alpha ][ 0.919319] . ( 31 sec) [ -9709.1354] [Topology ] . ( 32 sec) [ -9709.1352] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -9764.5406] [GTR parameters ] . ( 44 sec) [ -9762.3882] [Alpha ][ 0.854371] . ( 44 sec) [ -9760.8577] [ 2112] [depth= 1] . ( 45 sec) [ -9757.4661] [ 2113] [depth= 1] . ( 45 sec) [ -9757.2701] [ 2112] [depth= 1] . ( 45 sec) [ -9757.0556] [ 2115] [depth= 1] . ( 46 sec) [ -9749.7870] [ 2112] [depth= 1] . ( 46 sec) [ -9749.0051] [ 2113] [depth= 1] . ( 46 sec) [ -9747.9970] [ 2115] [depth= 1] . ( 46 sec) [ -9746.6938] [ 2115] [depth= 1] . ( 46 sec) [ -9744.3172] [ 2115] [depth= 2] . ( 46 sec) [ -9744.2986] [ 2115] [depth= 2] . ( 47 sec) [ -9742.9163] [ 2116] [depth= 1] . ( 47 sec) [ -9742.5842] [ 2118] [depth= 1] . ( 48 sec) [ -9717.7760] [Branch lengths ] . ( 48 sec) [ -9717.7457] [GTR parameters ] . ( 48 sec) [ -9717.4369] [Alpha ][ 0.905039] . ( 49 sec) [ -9712.8435] [ 2116] [depth= 1] . ( 50 sec) [ -9712.6392] [ 2115] [depth= 1] . ( 51 sec) [ -9712.3262] [ 2114] [depth= 1] . ( 52 sec) [ -9712.2889] [ 2113] [depth= 1] . ( 52 sec) [ -9711.9323] [ 2114] [depth= 1] . ( 52 sec) [ -9709.5417] [Branch lengths ] . ( 53 sec) [ -9709.5293] [GTR parameters ] . ( 53 sec) [ -9709.5173] [Alpha ][ 0.915573] . ( 56 sec) [ -9709.4609] [ 2115] [depth= 1] . ( 57 sec) [ -9709.1755] [Branch lengths ] . ( 57 sec) [ -9709.1753] [GTR parameters ] . ( 57 sec) [ -9709.1743] [Alpha ][ 0.918535] . ( 79 sec) [ -9709.1400] [Branch lengths ] . ( 79 sec) [ -9709.1400] [Topology ] . ( 80 sec) [ -9709.1369] [Topology ] . ( 81 sec) [ -9709.1360] [Topology ] . ( 81 sec) [ -9709.1359] [GTR parameters ] . ( 81 sec) [ -9709.1357] [Alpha ][ 0.919786] . ( 81 sec) [ -9709.1357] [Topology ] . ( 82 sec) [ -9709.1352] [Topology ] . ( 82 sec) [ -9709.1352] [GTR parameters ] . ( 82 sec) [ -9709.1352] [Alpha ][ 0.919786] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9709.135166 . Log likelihood obtained after SPR moves : -9709.135246 . Log likelihood of the current tree: -9709.135166. . Printing the most likely tree in file 'data38.phy_phyml_tree.txt'... . Time used 0h1m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo