.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data94.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... . 404 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . 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=-8212.880884 . ( 1 sec) [ -8210.1139] [GTR parameters ] . ( 1 sec) [ -8210.0646] [Alpha ][ 0.974422] . ( 1 sec) [ -8210.0646] [Topology ] . ( 1 sec) [ -8156.1994] [Topology ] . ( 2 sec) [ -8148.1552] [Topology ] . ( 3 sec) [ -8142.4795] [Topology ] . ( 4 sec) [ -8134.5723] [Topology ] . ( 4 sec) [ -8132.9551] [Topology ] . ( 5 sec) [ -8132.6711] [Topology ] . ( 6 sec) [ -8132.6161] [Topology ] . ( 7 sec) [ -8132.6018] [Topology ] . ( 8 sec) [ -8132.5970] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8132.597018 . ( 13 sec) [ -8132.5816] [GTR parameters ] . ( 14 sec) [ -8132.5425] [Alpha ][ 0.996004] . ( 14 sec) [ -8132.5425] [Topology ] . ( 14 sec) [ -8132.5376] [Topology ] . ( 15 sec) [ -8132.5358] [Topology ] . ( 16 sec) [ -8132.5350] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8132.534999 . ( 22 sec) [ -8132.5349] [GTR parameters ] . ( 23 sec) [ -8132.5347] [Alpha ][ 0.997812] . ( 23 sec) [ -8132.5347] [Topology ] . ( 23 sec) [ -8132.5342] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -8210.1139] [GTR parameters ] . ( 36 sec) [ -8210.0646] [Alpha ][ 0.974422] . ( 36 sec) [ -8201.8939] [ 1692] [depth= 1] . ( 37 sec) [ -8200.2394] [ 1691] [depth= 1] . ( 37 sec) [ -8198.3227] [ 1692] [depth= 1] . ( 37 sec) [ -8198.1399] [ 1691] [depth= 1] . ( 37 sec) [ -8192.0534] [ 1689] [depth= 1] . ( 37 sec) [ -8191.6431] [ 1688] [depth= 1] . ( 37 sec) [ -8190.1250] [ 1687] [depth= 1] . ( 37 sec) [ -8173.0889] [ 1679] [depth= 1] . ( 37 sec) [ -8172.9441] [ 1682] [depth= 1] . ( 37 sec) [ -8172.8690] [ 1682] [depth= 1] . ( 37 sec) [ -8172.2274] [ 1684] [depth= 1] . ( 37 sec) [ -8166.8175] [ 1682] [depth= 1] . ( 38 sec) [ -8161.9383] [ 1684] [depth= 1] . ( 38 sec) [ -8151.0564] [ 1689] [depth= 1] . ( 38 sec) [ -8150.9687] [ 1693] [depth= 3] . ( 38 sec) [ -8150.6793] [ 1687] [depth= 1] . ( 38 sec) [ -8150.3505] [ 1690] [depth= 1] . ( 38 sec) [ -8150.0049] [ 1687] [depth= 1] . ( 39 sec) [ -8149.7859] [ 1690] [depth= 1] . ( 39 sec) [ -8149.5794] [ 1690] [depth= 1] . ( 39 sec) [ -8149.4249] [ 1690] [depth= 1] . ( 39 sec) [ -8149.0719] [ 1690] [depth= 1] . ( 39 sec) [ -8134.2043] [Branch lengths ] . ( 40 sec) [ -8134.1858] [GTR parameters ] . ( 40 sec) [ -8134.1778] [Alpha ][ 0.984489] . ( 41 sec) [ -8133.6434] [ 1695] [depth= 3] . ( 41 sec) [ -8133.6144] [ 1696] [depth= 1] . ( 41 sec) [ -8133.5610] [ 1692] [depth= 1] . ( 41 sec) [ -8132.8402] [ 1692] [depth= 2] . ( 41 sec) [ -8132.7004] [ 1692] [depth= 2] . ( 42 sec) [ -8132.0979] [ 1691] [depth= 1] . ( 43 sec) [ -8131.3403] [Branch lengths ] . ( 44 sec) [ -8131.3359] [GTR parameters ] . ( 44 sec) [ -8131.3292] [Alpha ][ 0.993850] . ( 47 sec) [ -8131.2978] [Branch lengths ] . ( 58 sec) [ -8129.8985] [ 1699] [depth= 3] . ( 69 sec) [ -8128.9234] [Branch lengths ] . ( 69 sec) [ -8128.9063] [GTR parameters ] . ( 69 sec) [ -8128.9061] [Alpha ][ 0.995243] . ( 91 sec) [ -8128.7614] [Branch lengths ] . ( 91 sec) [ -8128.7614] [Topology ] . ( 92 sec) [ -8128.7073] [Topology ] . ( 93 sec) [ -8128.6958] [Topology ] . ( 93 sec) [ -8128.6939] [Topology ] . ( 94 sec) [ -8128.6934] [Topology ] . ( 95 sec) [ -8128.6923] [GTR parameters ] . ( 95 sec) [ -8128.6923] [Alpha ][ 0.995243] . ( 95 sec) [ -8128.6923] [Topology ] . ( 95 sec) [ -8128.6921] [Topology ] . ( 96 sec) [ -8128.6921] [GTR parameters ] . ( 96 sec) [ -8128.6921] [Alpha ][ 0.995243] . Checking for NNIs, optimizing five branches... . ( 102 sec) [ -8128.4334] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8132.534195 . Log likelihood obtained after SPR moves : -8128.433371 . Log likelihood of the current tree: -8128.433371. . Printing the most likely tree in file 'data94.phy_phyml_tree.txt'... . Time used 0h1m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo