.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data67.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... . 385 patterns found. (out of a total of 500 sites) . 104 sites without polymorphism (20.80%). . 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=-7871.915246 . ( 1 sec) [ -7869.8054] [GTR parameters ] . ( 1 sec) [ -7868.6494] [Alpha ][ 0.879732] . ( 1 sec) [ -7868.6494] [Topology ] . ( 2 sec) [ -7813.0785] [Topology ] . ( 3 sec) [ -7802.9008] [Topology ] . ( 4 sec) [ -7800.8748] [Topology ] . ( 5 sec) [ -7800.3566] [Topology ] . ( 5 sec) [ -7800.1461] [Topology ] . ( 6 sec) [ -7800.0490] [Topology ] . ( 7 sec) [ -7800.0020] [Topology ] . ( 8 sec) [ -7799.9787] [Topology ] . ( 8 sec) [ -7799.9671] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7799.967122 . ( 14 sec) [ -7799.9151] [GTR parameters ] . ( 14 sec) [ -7799.8043] [Alpha ][ 0.914129] . ( 14 sec) [ -7799.8043] [Topology ] . ( 15 sec) [ -7799.7919] [Topology ] . ( 16 sec) [ -7799.7868] [Topology ] . ( 16 sec) [ -7799.7844] [Topology ] . ( 17 sec) [ -7799.7831] [Topology ] . ( 18 sec) [ -7799.7825] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7799.782542 . ( 23 sec) [ -7799.7825] [GTR parameters ] . ( 23 sec) [ -7799.7824] [Alpha ][ 0.915335] . ( 23 sec) [ -7799.7824] [Topology ] . ( 24 sec) [ -7799.7820] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 36 sec) [ -7869.8054] [GTR parameters ] . ( 36 sec) [ -7868.6494] [Alpha ][ 0.879732] . ( 36 sec) [ -7868.1752] [ 1588] [depth= 1] . ( 36 sec) [ -7862.1036] [ 1585] [depth= 1] . ( 36 sec) [ -7860.9390] [ 1588] [depth= 1] . ( 36 sec) [ -7860.0576] [ 1586] [depth= 2] . ( 37 sec) [ -7858.7404] [ 1585] [depth= 1] . ( 37 sec) [ -7856.9567] [ 1587] [depth= 1] . ( 37 sec) [ -7856.7800] [ 1584] [depth= 1] . ( 37 sec) [ -7853.3532] [ 1583] [depth= 1] . ( 37 sec) [ -7850.2592] [ 1586] [depth= 1] . ( 37 sec) [ -7844.3395] [ 1583] [depth= 1] . ( 37 sec) [ -7841.3384] [ 1579] [depth= 1] . ( 37 sec) [ -7841.2790] [ 1583] [depth= 1] . ( 37 sec) [ -7840.0540] [ 1587] [depth= 1] . ( 37 sec) [ -7833.6748] [ 1585] [depth= 1] . ( 38 sec) [ -7831.8112] [ 1585] [depth= 1] . ( 38 sec) [ -7827.2882] [ 1587] [depth= 1] . ( 38 sec) [ -7827.2389] [ 1585] [depth= 1] . ( 38 sec) [ -7825.3832] [ 1589] [depth= 1] . ( 38 sec) [ -7821.8024] [ 1588] [depth= 2] . ( 39 sec) [ -7821.7395] [ 1588] [depth= 1] . ( 39 sec) [ -7821.0773] [ 1588] [depth= 1] . ( 39 sec) [ -7808.1051] [Branch lengths ] . ( 39 sec) [ -7808.0487] [GTR parameters ] . ( 39 sec) [ -7807.9444] [Alpha ][ 0.912418] . ( 40 sec) [ -7807.8354] [ 1593] [depth= 1] . ( 41 sec) [ -7806.4962] [ 1589] [depth= 1] . ( 41 sec) [ -7802.0047] [ 1585] [depth= 1] . ( 42 sec) [ -7801.9614] [ 1582] [depth= 1] . ( 42 sec) [ -7800.0112] [Branch lengths ] . ( 43 sec) [ -7800.0028] [GTR parameters ] . ( 43 sec) [ -7800.0028] [Alpha ][ 0.912418] . ( 46 sec) [ -7799.9230] [Branch lengths ] . ( 65 sec) [ -7799.9186] [Branch lengths ] . ( 65 sec) [ -7799.9186] [Topology ] . ( 65 sec) [ -7799.9183] [Topology ] . ( 65 sec) [ -7799.9183] [GTR parameters ] . ( 65 sec) [ -7799.9182] [Alpha ][ 0.913629] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -7799.7826] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7799.782037 . Log likelihood obtained after SPR moves : -7799.782625 . Log likelihood of the current tree: -7799.782037. . Printing the most likely tree in file 'data67.phy_phyml_tree.txt'... . Time used 0h1m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo