.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data93.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... . 402 patterns found. (out of a total of 500 sites) . 92 sites without polymorphism (18.40%). . 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=-8471.601432 . ( 1 sec) [ -8466.7709] [GTR parameters ] . ( 1 sec) [ -8465.8651] [Alpha ][ 0.896372] . ( 1 sec) [ -8465.8651] [Topology ] . ( 2 sec) [ -8427.9263] [Topology ] . ( 3 sec) [ -8421.9128] [Topology ] . ( 4 sec) [ -8420.1616] [Topology ] . ( 4 sec) [ -8419.4102] [Topology ] . ( 5 sec) [ -8419.0903] [Topology ] . ( 6 sec) [ -8418.9520] [Topology ] . ( 7 sec) [ -8418.8875] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.887512 . ( 13 sec) [ -8418.8409] [GTR parameters ] . ( 13 sec) [ -8418.5825] [Alpha ][ 0.947946] . ( 13 sec) [ -8418.5825] [Topology ] . ( 14 sec) [ -8418.5235] [Topology ] . ( 15 sec) [ -8418.4968] [Topology ] . ( 15 sec) [ -8418.4836] [Topology ] . ( 16 sec) [ -8418.4771] [Topology ] . ( 17 sec) [ -8418.4738] [Topology ] . ( 18 sec) [ -8418.4721] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.472118 . ( 23 sec) [ -8418.4720] [GTR parameters ] . ( 23 sec) [ -8418.4699] [Alpha ][ 0.952739] . ( 23 sec) [ -8418.4699] [Topology ] . ( 24 sec) [ -8418.4688] [Topology ] . ( 25 sec) [ -8418.4683] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-8418.468264 . ( 31 sec) [ -8418.4683] [GTR parameters ] . ( 31 sec) [ -8418.4683] [Alpha ][ 0.952739] . ( 31 sec) [ -8418.4683] [Topology ] . ( 32 sec) [ -8418.4680] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -8466.7709] [GTR parameters ] . ( 44 sec) [ -8465.8651] [Alpha ][ 0.896372] . ( 44 sec) [ -8465.4448] [ 1745] [depth= 1] . ( 44 sec) [ -8462.7015] [ 1743] [depth= 1] . ( 44 sec) [ -8453.4460] [ 1739] [depth= 1] . ( 44 sec) [ -8453.2703] [ 1740] [depth= 1] . ( 44 sec) [ -8453.1350] [ 1739] [depth= 1] . ( 45 sec) [ -8452.6541] [ 1743] [depth= 1] . ( 45 sec) [ -8452.2686] [ 1739] [depth= 1] . ( 46 sec) [ -8449.0090] [ 1743] [depth= 1] . ( 46 sec) [ -8443.6588] [ 1739] [depth= 1] . ( 46 sec) [ -8443.6409] [ 1740] [depth= 1] . ( 46 sec) [ -8441.7570] [ 1739] [depth= 1] . ( 46 sec) [ -8441.5495] [ 1743] [depth= 1] . ( 47 sec) [ -8440.3955] [ 1746] [depth= 1] . ( 47 sec) [ -8421.2535] [Branch lengths ] . ( 48 sec) [ -8421.2189] [GTR parameters ] . ( 48 sec) [ -8421.0096] [Alpha ][ 0.942826] . ( 48 sec) [ -8420.6643] [ 1747] [depth= 1] . ( 49 sec) [ -8420.1888] [ 1742] [depth= 1] . ( 50 sec) [ -8419.9111] [ 1741] [depth= 1] . ( 50 sec) [ -8419.8582] [ 1742] [depth= 1] . ( 51 sec) [ -8418.5925] [Branch lengths ] . ( 51 sec) [ -8418.5910] [GTR parameters ] . ( 51 sec) [ -8418.5874] [Alpha ][ 0.949201] . ( 54 sec) [ -8418.4908] [Branch lengths ] . ( 75 sec) [ -8418.4736] [Branch lengths ] . ( 75 sec) [ -8418.4736] [Topology ] . ( 75 sec) [ -8418.4718] [Topology ] . ( 76 sec) [ -8418.4711] [Topology ] . ( 76 sec) [ -8418.4708] [GTR parameters ] . ( 76 sec) [ -8418.4697] [Alpha ][ 0.952781] . ( 76 sec) [ -8418.4697] [Topology ] . ( 77 sec) [ -8418.4692] [Topology ] . ( 77 sec) [ -8418.4692] [GTR parameters ] . ( 77 sec) [ -8418.4692] [Alpha ][ 0.952781] . Checking for NNIs, optimizing five branches... . ( 83 sec) [ -8418.4690] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -8418.467977 . Log likelihood obtained after SPR moves : -8418.468999 . Log likelihood of the current tree: -8418.467977. . Printing the most likely tree in file 'data93.phy_phyml_tree.txt'... . Time used 0h1m29s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo