.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data31.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... . 380 patterns found. (out of a total of 500 sites) . 109 sites without polymorphism (21.80%). . 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=-7232.842533 . ( 1 sec) [ -7230.4040] [GTR parameters ] . ( 1 sec) [ -7229.6204] [Alpha ][ 0.896021] . ( 1 sec) [ -7229.6204] [Topology ] . ( 2 sec) [ -7192.0939] [Topology ] . ( 3 sec) [ -7187.0334] [Topology ] . ( 3 sec) [ -7185.9593] [Topology ] . ( 4 sec) [ -7185.6067] [Topology ] . ( 5 sec) [ -7185.4697] [Topology ] . ( 6 sec) [ -7185.4114] [Topology ] . ( 6 sec) [ -7185.3852] [Topology ] . ( 7 sec) [ -7185.3059] [Topology ] . ( 8 sec) [ -7182.8083] [Topology ] . Before opt ts/t=1.000000 LK=-7182.649243 . ( 9 sec) [ -7182.5732] [GTR parameters ] . ( 9 sec) [ -7182.4728] [Alpha ][ 0.929875] . ( 9 sec) [ -7182.4728] [Topology ] . ( 10 sec) [ -7181.7891] [Topology ] . ( 10 sec) [ -7179.9913] [Topology ] . ( 11 sec) [ -7179.6157] [Topology ] . ( 12 sec) [ -7179.5869] [Topology ] . ( 13 sec) [ -7179.5798] [Topology ] . ( 13 sec) [ -7179.5776] [Topology ] . ( 14 sec) [ -7179.5769] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.576932 . ( 19 sec) [ -7179.5752] [GTR parameters ] . ( 19 sec) [ -7179.5673] [Alpha ][ 0.939938] . ( 19 sec) [ -7179.5673] [Topology ] . ( 20 sec) [ -7179.5669] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-7179.566930 . ( 25 sec) [ -7179.5669] [GTR parameters ] . ( 25 sec) [ -7179.5669] [Alpha ][ 0.939938] . ( 25 sec) [ -7179.5669] [Topology ] . ( 26 sec) [ -7179.5668] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 37 sec) [ -7230.4040] [GTR parameters ] . ( 37 sec) [ -7229.6204] [Alpha ][ 0.896021] . ( 37 sec) [ -7229.5500] [ 1446] [depth= 1] . ( 37 sec) [ -7228.5236] [ 1445] [depth= 1] . ( 37 sec) [ -7227.7082] [ 1447] [depth= 1] . ( 37 sec) [ -7224.8975] [ 1445] [depth= 1] . ( 38 sec) [ -7224.7264] [ 1445] [depth= 1] . ( 38 sec) [ -7224.2540] [ 1445] [depth= 1] . ( 38 sec) [ -7224.0131] [ 1445] [depth= 1] . ( 38 sec) [ -7223.9768] [ 1445] [depth= 1] . ( 38 sec) [ -7222.4071] [ 1445] [depth= 1] . ( 38 sec) [ -7222.3622] [ 1445] [depth= 1] . ( 38 sec) [ -7221.8243] [ 1446] [depth= 1] . ( 38 sec) [ -7221.2932] [ 1445] [depth= 1] . ( 39 sec) [ -7220.3057] [ 1446] [depth= 1] . ( 39 sec) [ -7215.1876] [ 1445] [depth= 1] . ( 40 sec) [ -7210.9794] [ 1444] [depth= 1] . ( 40 sec) [ -7207.7011] [ 1445] [depth= 1] . ( 40 sec) [ -7206.6468] [ 1444] [depth= 1] . ( 40 sec) [ -7206.3219] [ 1444] [depth= 1] . ( 40 sec) [ -7206.1998] [ 1446] [depth= 2] . ( 40 sec) [ -7204.7896] [ 1449] [depth= 2] . ( 41 sec) [ -7200.3620] [ 1450] [depth= 1] . ( 41 sec) [ -7186.3168] [Branch lengths ] . ( 42 sec) [ -7186.2890] [GTR parameters ] . ( 42 sec) [ -7186.2249] [Alpha ][ 0.923339] . ( 44 sec) [ -7186.2014] [ 1448] [depth= 1] . ( 45 sec) [ -7185.5295] [ 1452] [depth= 1] . ( 45 sec) [ -7183.5661] [ 1447] [depth= 2] . ( 46 sec) [ -7182.8653] [ 1450] [depth= 1] . ( 47 sec) [ -7180.9195] [ 1448] [depth= 1] . ( 47 sec) [ -7179.8380] [Branch lengths ] . ( 47 sec) [ -7179.8137] [GTR parameters ] . ( 47 sec) [ -7179.8012] [Alpha ][ 0.935945] . ( 53 sec) [ -7179.7267] [Branch lengths ] . ( 74 sec) [ -7179.7190] [Branch lengths ] . ( 74 sec) [ -7179.7190] [Topology ] . ( 75 sec) [ -7179.5787] [Topology ] . ( 76 sec) [ -7179.5698] [Topology ] . ( 77 sec) [ -7179.5687] [Topology ] . ( 77 sec) [ -7179.5685] [Topology ] . ( 78 sec) [ -7179.5682] [GTR parameters ] . ( 78 sec) [ -7179.5670] [Alpha ][ 0.939863] . ( 78 sec) [ -7179.5670] [Topology ] . ( 78 sec) [ -7179.5669] [Topology ] . ( 78 sec) [ -7179.5669] [GTR parameters ] . ( 78 sec) [ -7179.5669] [Alpha ][ 0.939863] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7179.566849 . Log likelihood obtained after SPR moves : -7179.566904 . Log likelihood of the current tree: -7179.566849. . Printing the most likely tree in file 'data31.phy_phyml_tree.txt'... . Time used 0h1m24s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo