.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data27.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... . 349 patterns found. (out of a total of 500 sites) . 141 sites without polymorphism (28.20%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-5986.650611 . ( 0 sec) [ -5984.4472] [GTR parameters ] . ( 0 sec) [ -5984.4385] [Alpha ][ 0.986858] . ( 0 sec) [ -5984.4385] [Topology ] . ( 2 sec) [ -5969.4084] [Topology ] . ( 3 sec) [ -5967.7631] [Topology ] . ( 4 sec) [ -5967.0781] [Topology ] . Moving backward . ( 4 sec) [ -5966.5799] [Topology ] . ( 5 sec) [ -5966.2404] [Topology ] . ( 6 sec) [ -5966.1746] [Topology ] . ( 6 sec) [ -5966.1529] [Topology ] . ( 7 sec) [ -5966.1448] [Topology ] . ( 8 sec) [ -5966.1417] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5966.140439 . ( 13 sec) [ -5966.1288] [GTR parameters ] . ( 13 sec) [ -5966.1175] [Alpha ][ 1.002142] . ( 13 sec) [ -5966.1175] [Topology ] . ( 14 sec) [ -5966.1163] [Topology ] . ( 15 sec) [ -5966.1159] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-5966.115860 . ( 19 sec) [ -5966.1159] [GTR parameters ] . ( 19 sec) [ -5966.1159] [Alpha ][ 1.002142] . ( 19 sec) [ -5966.1159] [Topology ] . ( 20 sec) [ -5966.1157] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 29 sec) [ -5984.4472] [GTR parameters ] . ( 29 sec) [ -5984.4385] [Alpha ][ 0.986858] . ( 29 sec) [ -5983.9445] [ 1080] [depth= 1] . ( 29 sec) [ -5983.5588] [ 1078] [depth= 1] . ( 29 sec) [ -5979.7326] [ 1080] [depth= 1] . ( 30 sec) [ -5977.6685] [ 1084] [depth= 1] . ( 31 sec) [ -5977.3826] [ 1082] [depth= 1] . ( 31 sec) [ -5975.1296] [ 1084] [depth= 1] . ( 31 sec) [ -5974.8690] [ 1087] [depth= 1] . ( 31 sec) [ -5974.4485] [ 1087] [depth= 1] . ( 32 sec) [ -5974.4308] [ 1087] [depth= 1] . ( 33 sec) [ -5973.9120] [ 1087] [depth= 1] . ( 33 sec) [ -5973.9017] [ 1087] [depth= 1] . ( 33 sec) [ -5966.6691] [Branch lengths ] . ( 34 sec) [ -5966.6477] [GTR parameters ] . ( 34 sec) [ -5966.6434] [Alpha ][ 0.996132] . ( 39 sec) [ -5966.4650] [Branch lengths ] . ( 61 sec) [ -5966.4548] [Branch lengths ] . ( 61 sec) [ -5966.4548] [Topology ] . ( 62 sec) [ -5966.4543] [Topology ] . ( 62 sec) [ -5966.4541] [GTR parameters ] . ( 62 sec) [ -5966.4538] [Alpha ][ 0.998225] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -5966.1738] [Topology ] . Checking for NNIs, optimizing five branches... . ( 71 sec) [ -5966.1185] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -5966.115680 . Log likelihood obtained after SPR moves : -5966.118526 . Log likelihood of the current tree: -5966.115680. . Printing the most likely tree in file 'data27.phy_phyml_tree.txt'... . Time used 0h1m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo