.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data58.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... . 375 patterns found. (out of a total of 500 sites) . 121 sites without polymorphism (24.20%). . 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=-7012.025245 . ( 1 sec) [ -7007.8352] [GTR parameters ] . ( 1 sec) [ -7007.3705] [Alpha ][ 0.916448] . ( 1 sec) [ -7007.3705] [Topology ] . ( 3 sec) [ -6988.1007] [Topology ] . ( 4 sec) [ -6984.6001] [Topology ] . ( 5 sec) [ -6983.9065] [Topology ] . ( 5 sec) [ -6983.6870] [Topology ] . ( 6 sec) [ -6983.6010] [Topology ] . ( 7 sec) [ -6983.5643] [Topology ] . ( 8 sec) [ -6983.5477] [Topology ] . ( 8 sec) [ -6983.5401] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -6983.5348] [Topology ] . Before opt ts/t=1.000000 LK=-6983.534791 . ( 15 sec) [ -6983.5212] [GTR parameters ] . ( 15 sec) [ -6983.3866] [Alpha ][ 0.958886] . ( 15 sec) [ -6983.3866] [Topology ] . ( 16 sec) [ -6983.3741] [Topology ] . ( 17 sec) [ -6983.3691] [Topology ] . ( 19 sec) [ -6983.3669] [Topology ] . ( 20 sec) [ -6983.3659] [Topology ] . ( 21 sec) [ -6983.3654] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.365373 . ( 30 sec) [ -6983.3652] [GTR parameters ] . ( 30 sec) [ -6983.3646] [Alpha ][ 0.961784] . ( 30 sec) [ -6983.3646] [Topology ] . ( 31 sec) [ -6983.3642] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-6983.364241 . ( 37 sec) [ -6983.3642] [GTR parameters ] . ( 37 sec) [ -6983.3642] [Alpha ][ 0.961784] . ( 38 sec) [ -6983.3642] [Topology ] . ( 38 sec) [ -6983.3641] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 52 sec) [ -7007.8352] [GTR parameters ] . ( 52 sec) [ -7007.3705] [Alpha ][ 0.916448] . ( 52 sec) [ -7006.2744] [ 1337] [depth= 1] . ( 52 sec) [ -7005.7672] [ 1338] [depth= 1] . ( 53 sec) [ -7004.4540] [ 1337] [depth= 1] . ( 54 sec) [ -7004.3722] [ 1339] [depth= 1] . ( 54 sec) [ -7004.2689] [ 1337] [depth= 1] . ( 54 sec) [ -7002.6433] [ 1339] [depth= 1] . ( 55 sec) [ -7001.7142] [ 1339] [depth= 1] . ( 55 sec) [ -7001.6146] [ 1339] [depth= 1] . ( 56 sec) [ -7001.5759] [ 1340] [depth= 1] . ( 56 sec) [ -7001.3080] [ 1339] [depth= 1] . ( 57 sec) [ -6999.9083] [ 1341] [depth= 1] . ( 57 sec) [ -6999.2829] [ 1341] [depth= 1] . ( 58 sec) [ -6993.5320] [ 1337] [depth= 2] . ( 58 sec) [ -6993.4556] [ 1341] [depth= 1] . ( 58 sec) [ -6993.2368] [ 1337] [depth= 1] . ( 58 sec) [ -6993.1190] [ 1339] [depth= 2] . ( 59 sec) [ -6983.9488] [Branch lengths ] . ( 59 sec) [ -6983.9341] [GTR parameters ] . ( 59 sec) [ -6983.8540] [Alpha ][ 0.949191] . ( 65 sec) [ -6983.5237] [Branch lengths ] . ( 82 sec) [ -6983.4936] [ 1338] [depth= 1] . ( 92 sec) [ -6983.4306] [Branch lengths ] . ( 92 sec) [ -6983.4297] [GTR parameters ] . ( 92 sec) [ -6983.4206] [Alpha ][ 0.960696] . ( 93 sec) [ -6983.4206] [Topology ] . ( 93 sec) [ -6983.4138] [Topology ] . ( 95 sec) [ -6983.4117] [Topology ] . ( 96 sec) [ -6983.4107] [Topology ] . ( 96 sec) [ -6983.4107] [GTR parameters ] . ( 96 sec) [ -6983.4106] [Alpha ][ 0.961656] . ( 96 sec) [ -6983.4106] [Topology ] . ( 97 sec) [ -6983.4102] [Topology ] . ( 97 sec) [ -6983.4102] [GTR parameters ] . ( 97 sec) [ -6983.4102] [Alpha ][ 0.961656] . Checking for NNIs, optimizing five branches... . ( 105 sec) [ -6983.3653] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -6983.364091 . Log likelihood obtained after SPR moves : -6983.365345 . Log likelihood of the current tree: -6983.364091. . Printing the most likely tree in file 'data58.phy_phyml_tree.txt'... . Time used 0h1m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo