.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data84.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... . 161 patterns found. (out of a total of 500 sites) . 326 sites without polymorphism (65.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-2307.077771 . ( 0 sec) [ -2305.6179] [GTR parameters ] . ( 1 sec) [ -2305.6153] [Alpha ][ 0.979430] . ( 1 sec) [ -2305.6153] [Topology ] . ( 1 sec) [ -2301.4733] [Topology ] . ( 2 sec) [ -2298.8976] [Topology ] . ( 2 sec) [ -2298.5891] [Topology ] . ( 2 sec) [ -2298.5280] [Topology ] . ( 3 sec) [ -2298.5139] [Topology ] . ( 3 sec) [ -2298.5104] [Topology ] . ( 3 sec) [ -2298.5095] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2298.509471 . ( 5 sec) [ -2298.4914] [GTR parameters ] . ( 5 sec) [ -2298.4808] [Alpha ][ 1.021256] . ( 5 sec) [ -2298.4808] [Topology ] . ( 6 sec) [ -2298.4805] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-2298.480485 . ( 7 sec) [ -2298.4805] [GTR parameters ] . ( 7 sec) [ -2298.4805] [Alpha ][ 1.021256] . ( 7 sec) [ -2298.4805] [Topology ] . ( 8 sec) [ -2298.4804] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 11 sec) [ -2305.6179] [GTR parameters ] . ( 11 sec) [ -2305.6153] [Alpha ][ 0.979430] . ( 11 sec) [ -2305.5720] [ 254] [depth= 1] . ( 11 sec) [ -2305.5596] [ 254] [depth= 1] . ( 12 sec) [ -2305.2005] [ 254] [depth= 1] . ( 12 sec) [ -2305.1783] [ 254] [depth= 1] . ( 12 sec) [ -2305.1256] [ 254] [depth= 1] . ( 12 sec) [ -2305.0988] [ 254] [depth= 1] . ( 12 sec) [ -2305.0154] [ 254] [depth= 1] . ( 15 sec) [ -2302.8322] [ 254] [depth= 2] . ( 15 sec) [ -2300.3373] [ 253] [depth= 1] . ( 15 sec) [ -2299.8618] [ 253] [depth= 1] . ( 15 sec) [ -2299.6790] [ 253] [depth= 1] . ( 15 sec) [ -2299.6676] [ 253] [depth= 1] . ( 15 sec) [ -2299.5345] [ 253] [depth= 1] . ( 16 sec) [ -2299.5066] [ 253] [depth= 1] . ( 16 sec) [ -2298.5342] [Branch lengths ] . ( 16 sec) [ -2298.5161] [GTR parameters ] . ( 16 sec) [ -2298.5056] [Alpha ][ 1.020865] . ( 21 sec) [ -2298.4801] [Branch lengths ] . ( 32 sec) [ -2298.4800] [Branch lengths ] . ( 32 sec) [ -2298.4800] [Topology ] . ( 32 sec) [ -2298.4800] [Topology ] . ( 32 sec) [ -2298.4799] [GTR parameters ] . ( 32 sec) [ -2298.4799] [Alpha ][ 1.021886] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2298.480372 . Log likelihood obtained after SPR moves : -2298.479933 . Log likelihood of the current tree: -2298.479933. . Printing the most likely tree in file 'data84.phy_phyml_tree.txt'... . Time used 0h0m34s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo