.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data62.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... . 398 patterns found. (out of a total of 500 sites) . 95 sites without polymorphism (19.00%). . 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=-8223.651307 . ( 0 sec) [ -8220.1928] [GTR parameters ] . ( 1 sec) [ -8219.3015] [Alpha ][ 0.896853] . ( 1 sec) [ -8219.3015] [Topology ] . ( 2 sec) [ -8175.9036] [Topology ] . ( 3 sec) [ -8170.0695] [Topology ] . ( 3 sec) [ -8168.4675] [Topology ] . ( 4 sec) [ -8167.8102] [Topology ] . ( 5 sec) [ -8167.5141] [Topology ] . ( 6 sec) [ -8167.3714] [Topology ] . ( 6 sec) [ -8167.3002] [Topology ] . Checking for NNIs, optimizing five branches... . ( 12 sec) [ -8167.2928] [Topology ] . Before opt ts/t=1.000000 LK=-8167.292832 . ( 13 sec) [ -8167.2502] [GTR parameters ] . ( 13 sec) [ -8167.2005] [Alpha ][ 0.918662] . ( 13 sec) [ -8167.2005] [Topology ] . ( 14 sec) [ -8167.1537] [Topology ] . ( 14 sec) [ -8167.1320] [Topology ] . ( 15 sec) [ -8167.1213] [Topology ] . ( 16 sec) [ -8167.1158] [Topology ] . ( 18 sec) [ -8167.1131] [Topology ] . ( 19 sec) [ -8167.1116] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -8167.1003] [Topology ] . Before opt ts/t=1.000000 LK=-8167.100340 . ( 28 sec) [ -8167.0984] [GTR parameters ] . ( 28 sec) [ -8167.0946] [Alpha ][ 0.925005] . ( 28 sec) [ -8167.0946] [Topology ] . ( 29 sec) [ -8167.0901] [Topology ] . ( 30 sec) [ -8167.0892] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8167.089155 . ( 37 sec) [ -8167.0892] [GTR parameters ] . ( 37 sec) [ -8167.0891] [Alpha ][ 0.925930] . ( 37 sec) [ -8167.0891] [Topology ] . ( 38 sec) [ -8167.0887] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 51 sec) [ -8220.1928] [GTR parameters ] . ( 52 sec) [ -8219.3015] [Alpha ][ 0.896853] . ( 52 sec) [ -8215.3168] [ 1703] [depth= 1] . ( 52 sec) [ -8215.0859] [ 1706] [depth= 1] . ( 52 sec) [ -8211.6814] [ 1705] [depth= 1] . ( 53 sec) [ -8207.8637] [ 1708] [depth= 1] . ( 53 sec) [ -8206.1045] [ 1705] [depth= 1] . ( 53 sec) [ -8204.4330] [ 1705] [depth= 1] . ( 53 sec) [ -8200.7552] [ 1705] [depth= 1] . ( 53 sec) [ -8196.4679] [ 1705] [depth= 1] . ( 54 sec) [ -8194.7076] [ 1701] [depth= 1] . ( 54 sec) [ -8194.3972] [ 1705] [depth= 1] . ( 54 sec) [ -8193.6413] [ 1701] [depth= 1] . ( 55 sec) [ -8192.2892] [ 1701] [depth= 1] . ( 55 sec) [ -8191.2104] [ 1701] [depth= 1] . ( 56 sec) [ -8170.0561] [Branch lengths ] . ( 56 sec) [ -8170.0112] [GTR parameters ] . ( 56 sec) [ -8169.9955] [Alpha ][ 0.909592] . ( 56 sec) [ -8168.8160] [ 1690] [depth= 1] . ( 61 sec) [ -8167.4907] [Branch lengths ] . ( 61 sec) [ -8167.4844] [GTR parameters ] . ( 61 sec) [ -8167.4782] [Alpha ][ 0.917576] . ( 65 sec) [ -8167.1703] [Branch lengths ] . ( 87 sec) [ -8167.1212] [Branch lengths ] . ( 87 sec) [ -8167.1212] [Topology ] . ( 88 sec) [ -8167.1157] [Topology ] . ( 89 sec) [ -8167.1136] [Topology ] . ( 90 sec) [ -8167.1125] [Topology ] . ( 91 sec) [ -8167.1120] [Topology ] . ( 91 sec) [ -8167.1116] [GTR parameters ] . ( 92 sec) [ -8167.1086] [Alpha ][ 0.923178] . ( 92 sec) [ -8167.1086] [Topology ] . ( 92 sec) [ -8167.1080] [Topology ] . ( 93 sec) [ -8167.1080] [GTR parameters ] . ( 93 sec) [ -8167.1080] [Alpha ][ 0.923178] . Checking for NNIs, optimizing five branches... . ( 101 sec) [ -8167.0943] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8167.088697 . Log likelihood obtained after SPR moves : -8167.094262 . Log likelihood of the current tree: -8167.088697. . Printing the most likely tree in file 'data62.phy_phyml_tree.txt'... . Time used 0h1m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo