.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data1.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... . 437 patterns found. (out of a total of 500 sites) . 64 sites without polymorphism (12.80%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-10670.638885 . ( 1 sec) [ -10666.7778] [GTR parameters ] . ( 1 sec) [ -10666.2120] [Alpha ][ 0.925980] . ( 1 sec) [ -10666.2120] [Topology ] . ( 2 sec) [ -10610.0666] [Topology ] . ( 3 sec) [ -10586.1511] [Topology ] . ( 4 sec) [ -10581.2066] [Topology ] . ( 6 sec) [ -10580.2747] [Topology ] . ( 7 sec) [ -10579.9449] [Topology ] . ( 7 sec) [ -10579.7943] [Topology ] . ( 8 sec) [ -10579.7182] [Topology ] . ( 9 sec) [ -10579.6779] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.677901 . ( 16 sec) [ -10579.6411] [GTR parameters ] . ( 16 sec) [ -10579.3155] [Alpha ][ 0.979846] . ( 16 sec) [ -10579.3155] [Topology ] . ( 17 sec) [ -10579.2624] [Topology ] . ( 18 sec) [ -10579.2389] [Topology ] . ( 19 sec) [ -10579.2266] [Topology ] . ( 20 sec) [ -10579.2199] [Topology ] . ( 21 sec) [ -10579.2162] [Topology ] . ( 22 sec) [ -10579.2142] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.214195 . ( 32 sec) [ -10579.2140] [GTR parameters ] . ( 32 sec) [ -10579.2110] [Alpha ][ 0.985268] . ( 32 sec) [ -10579.2110] [Topology ] . ( 34 sec) [ -10579.2094] [Topology ] . ( 35 sec) [ -10579.2086] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10579.208575 . ( 45 sec) [ -10579.2086] [GTR parameters ] . ( 45 sec) [ -10579.2086] [Alpha ][ 0.985268] . ( 45 sec) [ -10579.2086] [Topology ] . ( 46 sec) [ -10579.2081] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 65 sec) [ -10666.7778] [GTR parameters ] . ( 65 sec) [ -10666.2120] [Alpha ][ 0.925980] . ( 65 sec) [ -10663.6745] [ 2444] [depth= 1] . ( 66 sec) [ -10662.8854] [ 2438] [depth= 1] . ( 66 sec) [ -10661.8404] [ 2433] [depth= 1] . ( 66 sec) [ -10659.2880] [ 2436] [depth= 2] . ( 66 sec) [ -10657.3191] [ 2436] [depth= 1] . ( 66 sec) [ -10655.7531] [ 2441] [depth= 1] . ( 66 sec) [ -10655.1393] [ 2441] [depth= 1] . ( 66 sec) [ -10654.1761] [ 2439] [depth= 1] . ( 67 sec) [ -10650.3920] [ 2436] [depth= 1] . ( 67 sec) [ -10636.8133] [ 2432] [depth= 1] . ( 67 sec) [ -10634.0615] [ 2427] [depth= 1] . ( 67 sec) [ -10632.0786] [ 2432] [depth= 1] . ( 67 sec) [ -10632.0400] [ 2430] [depth= 1] . ( 67 sec) [ -10631.8002] [ 2431] [depth= 1] . ( 68 sec) [ -10627.8761] [ 2426] [depth= 1] . ( 68 sec) [ -10625.7284] [ 2424] [depth= 1] . ( 68 sec) [ -10623.8041] [ 2420] [depth= 1] . ( 69 sec) [ -10619.1472] [ 2418] [depth= 1] . ( 70 sec) [ -10616.3551] [ 2418] [depth= 1] . ( 70 sec) [ -10616.1510] [ 2422] [depth= 1] . ( 70 sec) [ -10616.1397] [ 2422] [depth= 1] . ( 71 sec) [ -10615.8397] [ 2422] [depth= 1] . ( 71 sec) [ -10582.1024] [Branch lengths ] . ( 72 sec) [ -10582.0651] [GTR parameters ] . ( 72 sec) [ -10581.8459] [Alpha ][ 0.970479] . ( 74 sec) [ -10581.8150] [ 2422] [depth= 1] . ( 78 sec) [ -10579.5289] [Branch lengths ] . ( 78 sec) [ -10579.5256] [GTR parameters ] . ( 78 sec) [ -10579.5159] [Alpha ][ 0.980181] . ( 84 sec) [ -10579.2606] [Branch lengths ] . ( 115 sec) [ -10579.2212] [Branch lengths ] . ( 115 sec) [ -10579.2212] [Topology ] . ( 117 sec) [ -10579.2162] [Topology ] . ( 118 sec) [ -10579.2142] [Topology ] . ( 119 sec) [ -10579.2131] [Topology ] . ( 120 sec) [ -10579.2124] [Topology ] . ( 121 sec) [ -10579.2118] [GTR parameters ] . ( 121 sec) [ -10579.2088] [Alpha ][ 0.985571] . ( 121 sec) [ -10579.2088] [Topology ] . ( 122 sec) [ -10579.2081] [Topology ] . ( 122 sec) [ -10579.2081] [GTR parameters ] . ( 122 sec) [ -10579.2081] [Alpha ][ 0.985571] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10579.208118 . Log likelihood obtained after SPR moves : -10579.208104 . Log likelihood of the current tree: -10579.208104. . Printing the most likely tree in file 'data1.phy_phyml_tree.txt'... . Time used 0h2m13s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo