.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data42.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... . 279 patterns found. (out of a total of 500 sites) . 203 sites without polymorphism (40.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-4232.026270 . ( 0 sec) [ -4230.2548] [GTR parameters ] . ( 0 sec) [ -4230.1853] [Alpha ][ 0.950604] . ( 0 sec) [ -4230.1853] [Topology ] . ( 1 sec) [ -4215.8559] [Topology ] . ( 2 sec) [ -4214.8475] [Topology ] . ( 3 sec) [ -4214.6692] [Topology ] . ( 3 sec) [ -4214.6239] [Topology ] . ( 4 sec) [ -4214.6092] [Topology ] . ( 5 sec) [ -4214.6031] [Topology ] . ( 5 sec) [ -4214.5999] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.599937 . ( 9 sec) [ -4214.5866] [GTR parameters ] . ( 9 sec) [ -4214.5662] [Alpha ][ 0.976114] . ( 9 sec) [ -4214.5662] [Topology ] . ( 9 sec) [ -4214.5632] [Topology ] . ( 10 sec) [ -4214.5614] [Topology ] . ( 11 sec) [ -4214.5600] [Topology ] . ( 11 sec) [ -4214.5589] [Topology ] . ( 12 sec) [ -4214.5581] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-4214.558087 . ( 15 sec) [ -4214.5580] [GTR parameters ] . ( 15 sec) [ -4214.5580] [Alpha ][ 0.977090] . ( 15 sec) [ -4214.5580] [Topology ] . ( 16 sec) [ -4214.5572] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 23 sec) [ -4230.2548] [GTR parameters ] . ( 23 sec) [ -4230.1853] [Alpha ][ 0.950604] . ( 23 sec) [ -4224.0623] [ 648] [depth= 2] . ( 24 sec) [ -4223.5846] [ 648] [depth= 1] . ( 24 sec) [ -4222.3690] [ 648] [depth= 1] . ( 24 sec) [ -4222.2615] [ 648] [depth= 1] . ( 24 sec) [ -4222.1229] [ 648] [depth= 1] . ( 25 sec) [ -4222.0692] [ 648] [depth= 1] . ( 25 sec) [ -4221.9858] [ 648] [depth= 1] . ( 25 sec) [ -4221.0501] [ 647] [depth= 1] . ( 26 sec) [ -4214.7012] [Branch lengths ] . ( 27 sec) [ -4214.6884] [GTR parameters ] . ( 27 sec) [ -4214.6700] [Alpha ][ 0.974743] . ( 27 sec) [ -4214.6599] [ 647] [depth= 1] . ( 30 sec) [ -4214.5723] [Branch lengths ] . ( 30 sec) [ -4214.5722] [GTR parameters ] . ( 30 sec) [ -4214.5721] [Alpha ][ 0.976356] . ( 45 sec) [ -4214.5623] [Branch lengths ] . ( 45 sec) [ -4214.5623] [Topology ] . ( 45 sec) [ -4214.5604] [Topology ] . ( 46 sec) [ -4214.5592] [Topology ] . ( 46 sec) [ -4214.5583] [Topology ] . ( 46 sec) [ -4214.5581] [GTR parameters ] . ( 46 sec) [ -4214.5581] [Alpha ][ 0.976356] . ( 46 sec) [ -4214.5581] [Topology ] . ( 47 sec) [ -4214.5573] [Topology ] . ( 47 sec) [ -4214.5573] [GTR parameters ] . ( 47 sec) [ -4214.5573] [Alpha ][ 0.976356] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -4214.557221 . Log likelihood obtained after SPR moves : -4214.557326 . Log likelihood of the current tree: -4214.557221. . Printing the most likely tree in file 'data42.phy_phyml_tree.txt'... . Time used 0h0m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo