.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data85.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... . 460 patterns found. (out of a total of 500 sites) . 40 sites without polymorphism (8.00%). . 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=-12046.112397 . ( 1 sec) [ -12041.9616] [GTR parameters ] . ( 1 sec) [ -12041.7961] [Alpha ][ 0.960910] . ( 1 sec) [ -12041.7961] [Topology ] . ( 2 sec) [ -11980.6757] [Topology ] . ( 3 sec) [ -11972.0740] [Topology ] . ( 4 sec) [ -11969.8220] [Topology ] . ( 5 sec) [ -11968.8175] [Topology ] . ( 5 sec) [ -11968.3196] [Topology ] . ( 6 sec) [ -11968.0585] [Topology ] . ( 7 sec) [ -11967.9172] [Topology ] . ( 8 sec) [ -11967.8397] [Topology ] . Checking for NNIs, optimizing five branches... . ( 15 sec) [ -11967.8180] [Topology ] . Before opt ts/t=1.000000 LK=-11967.817956 . ( 16 sec) [ -11967.6718] [GTR parameters ] . ( 16 sec) [ -11967.0266] [Alpha ][ 1.035749] . ( 16 sec) [ -11967.0266] [Topology ] . ( 16 sec) [ -11966.9204] [Topology ] . ( 17 sec) [ -11966.8765] [Topology ] . ( 18 sec) [ -11966.8537] [Topology ] . ( 19 sec) [ -11966.8415] [Topology ] . ( 20 sec) [ -11966.8348] [Topology ] . ( 21 sec) [ -11966.8311] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.831138 . ( 27 sec) [ -11966.8304] [GTR parameters ] . ( 27 sec) [ -11966.8252] [Alpha ][ 1.042902] . ( 27 sec) [ -11966.8252] [Topology ] . ( 28 sec) [ -11966.8224] [Topology ] . ( 29 sec) [ -11966.8210] [Topology ] . ( 30 sec) [ -11966.8203] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-11966.820258 . ( 36 sec) [ -11966.8202] [GTR parameters ] . ( 36 sec) [ -11966.8202] [Alpha ][ 1.043945] . ( 36 sec) [ -11966.8202] [Topology ] . ( 37 sec) [ -11966.8197] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 50 sec) [ -12041.9616] [GTR parameters ] . ( 50 sec) [ -12041.7961] [Alpha ][ 0.960910] . ( 51 sec) [ -12041.2513] [ 2830] [depth= 2] . ( 51 sec) [ -12039.5922] [ 2832] [depth= 1] . ( 51 sec) [ -12039.3732] [ 2830] [depth= 1] . ( 51 sec) [ -12035.0220] [ 2830] [depth= 2] . ( 52 sec) [ -12032.6794] [ 2825] [depth= 1] . ( 52 sec) [ -12014.8516] [ 2828] [depth= 1] . ( 52 sec) [ -12014.4231] [ 2832] [depth= 2] . ( 53 sec) [ -12010.0128] [ 2833] [depth= 1] . ( 53 sec) [ -12009.4667] [ 2831] [depth= 1] . ( 53 sec) [ -12007.4819] [ 2831] [depth= 2] . ( 53 sec) [ -12003.0060] [ 2828] [depth= 2] . ( 53 sec) [ -12002.7254] [ 2828] [depth= 1] . ( 53 sec) [ -12001.6902] [ 2829] [depth= 1] . ( 53 sec) [ -12001.2296] [ 2834] [depth= 1] . ( 54 sec) [ -11973.7262] [Branch lengths ] . ( 54 sec) [ -11973.5526] [GTR parameters ] . ( 54 sec) [ -11973.1450] [Alpha ][ 1.020335] . ( 56 sec) [ -11971.5100] [ 2833] [depth= 1] . ( 57 sec) [ -11970.2621] [ 2832] [depth= 1] . ( 57 sec) [ -11970.2030] [ 2830] [depth= 1] . ( 57 sec) [ -11970.0801] [ 2832] [depth= 1] . ( 58 sec) [ -11967.5488] [Branch lengths ] . ( 58 sec) [ -11967.5413] [GTR parameters ] . ( 58 sec) [ -11967.5116] [Alpha ][ 1.037303] . ( 62 sec) [ -11967.1131] [Branch lengths ] . ( 86 sec) [ -11967.0211] [Branch lengths ] . ( 86 sec) [ -11967.0211] [Topology ] . ( 87 sec) [ -11966.9430] [Topology ] . ( 88 sec) [ -11966.8850] [Topology ] . ( 89 sec) [ -11966.8756] [Topology ] . ( 89 sec) [ -11966.8713] [Topology ] . ( 90 sec) [ -11966.8693] [Topology ] . ( 91 sec) [ -11966.8683] [Topology ] . ( 91 sec) [ -11966.8668] [GTR parameters ] . ( 91 sec) [ -11966.8630] [Alpha ][ 1.043364] . ( 91 sec) [ -11966.8630] [Topology ] . ( 92 sec) [ -11966.8622] [Topology ] . ( 92 sec) [ -11966.8621] [GTR parameters ] . ( 92 sec) [ -11966.8621] [Alpha ][ 1.043364] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -11966.8618] [Topology ] . Checking for NNIs, optimizing five branches... . ( 105 sec) [ -11966.8615] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11966.819701 . Log likelihood obtained after SPR moves : -11966.861461 . Log likelihood of the current tree: -11966.819701. . Printing the most likely tree in file 'data85.phy_phyml_tree.txt'... . Time used 0h1m53s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo