.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data33.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... . 449 patterns found. (out of a total of 500 sites) . 47 sites without polymorphism (9.40%). . 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=-10151.781372 . ( 1 sec) [ -10150.4304] [GTR parameters ] . ( 2 sec) [ -10149.1164] [Alpha ][ 1.135049] . ( 2 sec) [ -10149.1164] [Topology ] . ( 4 sec) [ -10097.5748] [Topology ] . ( 5 sec) [ -10087.6357] [Topology ] . ( 6 sec) [ -10084.4119] [Topology ] . ( 7 sec) [ -10083.0900] [Topology ] . ( 8 sec) [ -10082.4992] [Topology ] . ( 9 sec) [ -10082.2214] [Topology ] . ( 10 sec) [ -10082.0866] [Topology ] . ( 10 sec) [ -10082.0197] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -10081.9079] [Topology ] . Before opt ts/t=1.000000 LK=-10081.907934 . ( 20 sec) [ -10081.8414] [GTR parameters ] . ( 20 sec) [ -10081.8402] [Alpha ][ 1.130698] . ( 20 sec) [ -10081.8402] [Topology ] . ( 21 sec) [ -10081.7853] [Topology ] . ( 23 sec) [ -10081.7664] [Topology ] . ( 24 sec) [ -10081.7508] [Topology ] . ( 25 sec) [ -10081.7394] [Topology ] . ( 26 sec) [ -10081.7319] [Topology ] . ( 27 sec) [ -10081.7267] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10081.726687 . ( 38 sec) [ -10081.7266] [GTR parameters ] . ( 38 sec) [ -10081.7266] [Alpha ][ 1.131828] . ( 38 sec) [ -10081.7266] [Topology ] . ( 39 sec) [ -10081.7228] [Topology ] . ( 40 sec) [ -10081.7199] [Topology ] . ( 42 sec) [ -10081.7177] [Topology ] . ( 43 sec) [ -10081.7159] [Topology ] . ( 44 sec) [ -10081.7145] [Topology ] . ( 45 sec) [ -10081.7133] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-10081.713323 . ( 56 sec) [ -10081.7133] [GTR parameters ] . ( 56 sec) [ -10081.7133] [Alpha ][ 1.131828] . ( 56 sec) [ -10081.7133] [Topology ] . ( 57 sec) [ -10081.7124] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 77 sec) [ -10150.4304] [GTR parameters ] . ( 77 sec) [ -10149.1164] [Alpha ][ 1.135049] . ( 78 sec) [ -10147.4557] [ 2331] [depth= 1] . ( 78 sec) [ -10147.2494] [ 2330] [depth= 1] . ( 78 sec) [ -10147.0769] [ 2331] [depth= 1] . ( 78 sec) [ -10146.8627] [ 2330] [depth= 1] . ( 79 sec) [ -10133.0958] [ 2339] [depth= 1] . ( 79 sec) [ -10132.9135] [ 2330] [depth= 1] . ( 79 sec) [ -10131.9798] [ 2339] [depth= 1] . ( 79 sec) [ -10128.7436] [ 2330] [depth= 1] . ( 79 sec) [ -10127.5067] [ 2333] [depth= 1] . ( 80 sec) [ -10127.3508] [ 2330] [depth= 1] . ( 80 sec) [ -10088.5205] [Branch lengths ] . ( 80 sec) [ -10088.4932] [GTR parameters ] . ( 80 sec) [ -10088.4922] [Alpha ][ 1.131203] . ( 80 sec) [ -10088.4612] [ 2319] [depth= 1] . ( 81 sec) [ -10088.3981] [ 2330] [depth= 1] . ( 82 sec) [ -10087.5956] [ 2339] [depth= 1] . ( 83 sec) [ -10084.5132] [Branch lengths ] . ( 84 sec) [ -10084.4925] [GTR parameters ] . ( 84 sec) [ -10084.4911] [Alpha ][ 1.126565] . ( 84 sec) [ -10083.9318] [ 2328] [depth= 1] . ( 87 sec) [ -10082.1710] [Branch lengths ] . ( 87 sec) [ -10082.1696] [GTR parameters ] . ( 87 sec) [ -10082.1647] [Alpha ][ 1.134865] . ( 90 sec) [ -10081.7698] [Branch lengths ] . ( 112 sec) [ -10081.7335] [Branch lengths ] . ( 112 sec) [ -10081.7335] [Topology ] . ( 113 sec) [ -10081.7279] [Topology ] . ( 114 sec) [ -10081.7245] [Topology ] . ( 115 sec) [ -10081.7218] [Topology ] . ( 116 sec) [ -10081.7196] [Topology ] . ( 117 sec) [ -10081.7178] [Topology ] . ( 118 sec) [ -10081.7163] [Topology ] . ( 118 sec) [ -10081.7161] [GTR parameters ] . ( 119 sec) [ -10081.7154] [Alpha ][ 1.131481] . ( 119 sec) [ -10081.7154] [Topology ] . ( 120 sec) [ -10081.7141] [Topology ] . ( 121 sec) [ -10081.7130] [Topology ] . ( 122 sec) [ -10081.7121] [Topology ] . ( 122 sec) [ -10081.7121] [GTR parameters ] . ( 122 sec) [ -10081.7121] [Alpha ][ 1.131481] . ( 122 sec) [ -10081.7121] [Topology ] . ( 124 sec) [ -10081.7114] [Topology ] . ( 124 sec) [ -10081.7114] [GTR parameters ] . ( 124 sec) [ -10081.7114] [Alpha ][ 1.131481] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10081.712370 . Log likelihood obtained after SPR moves : -10081.711411 . Log likelihood of the current tree: -10081.711411. . Printing the most likely tree in file 'data33.phy_phyml_tree.txt'... . Time used 0h2m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo