.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data6.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... . 376 patterns found. (out of a total of 500 sites) . 113 sites without polymorphism (22.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-7048.952922 . ( 1 sec) [ -7048.3387] [GTR parameters ] . ( 1 sec) [ -7048.3296] [Alpha ][ 0.988108] . ( 1 sec) [ -7048.3296] [Topology ] . ( 2 sec) [ -7027.3699] [Topology ] . ( 3 sec) [ -7025.2151] [Topology ] . ( 4 sec) [ -7024.6546] [Topology ] . ( 5 sec) [ -7024.4334] [Topology ] . ( 5 sec) [ -7024.3338] [Topology ] . ( 6 sec) [ -7024.2861] [Topology ] . ( 7 sec) [ -7024.2626] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.262628 . ( 14 sec) [ -7024.2478] [GTR parameters ] . ( 14 sec) [ -7024.2259] [Alpha ][ 1.007084] . ( 14 sec) [ -7024.2259] [Topology ] . ( 15 sec) [ -7024.2117] [Topology ] . ( 16 sec) [ -7024.2049] [Topology ] . ( 17 sec) [ -7024.2015] [Topology ] . ( 18 sec) [ -7024.1998] [Topology ] . ( 19 sec) [ -7024.1989] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7024.198936 . ( 26 sec) [ -7024.1989] [GTR parameters ] . ( 26 sec) [ -7024.1988] [Alpha ][ 1.008092] . ( 26 sec) [ -7024.1988] [Topology ] . ( 27 sec) [ -7024.1984] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 39 sec) [ -7048.3387] [GTR parameters ] . ( 39 sec) [ -7048.3296] [Alpha ][ 0.988108] . ( 39 sec) [ -7047.5203] [ 1348] [depth= 1] . ( 39 sec) [ -7046.7389] [ 1347] [depth= 1] . ( 39 sec) [ -7044.1362] [ 1345] [depth= 1] . ( 40 sec) [ -7043.6371] [ 1347] [depth= 1] . ( 40 sec) [ -7040.2878] [ 1340] [depth= 1] . ( 40 sec) [ -7039.2313] [ 1345] [depth= 1] . ( 41 sec) [ -7039.2168] [ 1345] [depth= 1] . ( 41 sec) [ -7039.1872] [ 1345] [depth= 1] . ( 41 sec) [ -7039.1698] [ 1345] [depth= 1] . ( 41 sec) [ -7025.3933] [Branch lengths ] . ( 42 sec) [ -7025.3775] [GTR parameters ] . ( 42 sec) [ -7025.3672] [Alpha ][ 1.001105] . ( 44 sec) [ -7025.1652] [ 1347] [depth= 1] . ( 45 sec) [ -7024.3992] [Branch lengths ] . ( 45 sec) [ -7024.3984] [GTR parameters ] . ( 46 sec) [ -7024.3978] [Alpha ][ 1.003902] . ( 72 sec) [ -7024.3621] [Branch lengths ] . ( 72 sec) [ -7024.3621] [Topology ] . ( 73 sec) [ -7024.3589] [Topology ] . ( 74 sec) [ -7024.3578] [Topology ] . ( 75 sec) [ -7024.3573] [Topology ] . ( 75 sec) [ -7024.3573] [GTR parameters ] . ( 75 sec) [ -7024.3572] [Alpha ][ 1.004905] . ( 75 sec) [ -7024.3572] [Topology ] . ( 76 sec) [ -7024.3569] [Topology ] . ( 76 sec) [ -7024.3569] [GTR parameters ] . ( 76 sec) [ -7024.3569] [Alpha ][ 1.004905] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -7024.3563] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7024.198384 . Log likelihood obtained after SPR moves : -7024.356342 . Log likelihood of the current tree: -7024.198384. . Printing the most likely tree in file 'data6.phy_phyml_tree.txt'... . Time used 0h1m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo