.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data64.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... . 433 patterns found. (out of a total of 500 sites) . 61 sites without polymorphism (12.20%). . 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=-9633.594476 . ( 0 sec) [ -9633.1925] [GTR parameters ] . ( 1 sec) [ -9631.5367] [Alpha ][ 1.149448] . ( 1 sec) [ -9631.5367] [Topology ] . ( 2 sec) [ -9584.1716] [Topology ] . ( 3 sec) [ -9574.1907] [Topology ] . ( 5 sec) [ -9571.8821] [Topology ] . ( 6 sec) [ -9571.1460] [Topology ] . ( 7 sec) [ -9570.8312] [Topology ] . ( 9 sec) [ -9570.6829] [Topology ] . ( 10 sec) [ -9570.6084] [Topology ] . ( 11 sec) [ -9570.5694] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.569422 . ( 23 sec) [ -9570.5359] [GTR parameters ] . ( 23 sec) [ -9570.5256] [Alpha ][ 1.162201] . ( 23 sec) [ -9570.5256] [Topology ] . ( 24 sec) [ -9570.5023] [Topology ] . ( 26 sec) [ -9570.4906] [Topology ] . ( 27 sec) [ -9570.4847] [Topology ] . ( 28 sec) [ -9570.4816] [Topology ] . ( 29 sec) [ -9570.4800] [Topology ] . ( 30 sec) [ -9570.4792] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.479199 . ( 41 sec) [ -9570.4792] [GTR parameters ] . ( 41 sec) [ -9570.4787] [Alpha ][ 1.164851] . ( 41 sec) [ -9570.4787] [Topology ] . ( 42 sec) [ -9570.4782] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9570.478181 . ( 52 sec) [ -9570.4782] [GTR parameters ] . ( 52 sec) [ -9570.4782] [Alpha ][ 1.164851] . ( 52 sec) [ -9570.4782] [Topology ] . ( 53 sec) [ -9570.4779] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 74 sec) [ -9633.1925] [GTR parameters ] . ( 74 sec) [ -9631.5367] [Alpha ][ 1.149448] . ( 75 sec) [ -9630.8308] [ 2120] [depth= 1] . ( 75 sec) [ -9628.5460] [ 2119] [depth= 1] . ( 75 sec) [ -9627.9684] [ 2120] [depth= 1] . ( 75 sec) [ -9626.3291] [ 2120] [depth= 1] . ( 77 sec) [ -9624.9462] [ 2121] [depth= 1] . ( 77 sec) [ -9622.4295] [ 2120] [depth= 1] . ( 77 sec) [ -9618.5712] [ 2121] [depth= 1] . ( 77 sec) [ -9613.9623] [ 2116] [depth= 1] . ( 77 sec) [ -9612.3173] [ 2116] [depth= 1] . ( 77 sec) [ -9611.5887] [ 2116] [depth= 1] . ( 78 sec) [ -9611.1207] [ 2116] [depth= 1] . ( 78 sec) [ -9609.9239] [ 2115] [depth= 1] . ( 78 sec) [ -9608.7957] [ 2120] [depth= 2] . ( 78 sec) [ -9607.4962] [ 2121] [depth= 1] . ( 79 sec) [ -9607.4603] [ 2121] [depth= 1] . ( 79 sec) [ -9607.4126] [ 2116] [depth= 1] . ( 79 sec) [ -9607.3899] [ 2119] [depth= 1] . ( 81 sec) [ -9579.1170] [Branch lengths ] . ( 81 sec) [ -9579.0908] [GTR parameters ] . ( 82 sec) [ -9579.0906] [Alpha ][ 1.147681] . ( 83 sec) [ -9577.7436] [ 2124] [depth= 1] . ( 84 sec) [ -9576.0336] [ 2121] [depth= 1] . ( 85 sec) [ -9575.8884] [ 2122] [depth= 1] . ( 85 sec) [ -9575.8388] [ 2117] [depth= 1] . ( 86 sec) [ -9570.8584] [Branch lengths ] . ( 87 sec) [ -9570.8509] [GTR parameters ] . ( 87 sec) [ -9570.8385] [Alpha ][ 1.161660] . ( 91 sec) [ -9570.4958] [Branch lengths ] . ( 122 sec) [ -9570.4804] [Branch lengths ] . ( 122 sec) [ -9570.4804] [Topology ] . ( 124 sec) [ -9570.4793] [Topology ] . ( 125 sec) [ -9570.4790] [Topology ] . ( 125 sec) [ -9570.4789] [GTR parameters ] . ( 125 sec) [ -9570.4782] [Alpha ][ 1.164980] . ( 125 sec) [ -9570.4782] [Topology ] . ( 126 sec) [ -9570.4779] [Topology ] . ( 126 sec) [ -9570.4779] [GTR parameters ] . ( 126 sec) [ -9570.4779] [Alpha ][ 1.164980] . Checking for NNIs, optimizing five branches... . ( 135 sec) [ -9570.4778] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9570.477914 . Log likelihood obtained after SPR moves : -9570.477755 . Log likelihood of the current tree: -9570.477755. . Printing the most likely tree in file 'data64.phy_phyml_tree.txt'... . Time used 0h2m25s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo