.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2600_69x814_2006.phy . Data type : dna . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 100 . Compute approximate likelihood ratio test : no . Model name : HKY85 . Ts/tv ratio : estimated . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : 0.500000 . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 78 patterns found. (out of a total of 814 sites) . 733 sites without polymorphism (90.05%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -1759.5762] [Ts/ts ratio ][ 2.656398] . ( 1 sec) [ -1759.5603] [ 88] [depth= 1] . ( 1 sec) [ -1759.5459] [ 88] [depth= 1] . ( 2 sec) [ -1759.3588] [ 88] [depth= 2] . ( 2 sec) [ -1759.3207] [ 88] [depth= 1] . ( 2 sec) [ -1759.3072] [ 88] [depth= 1] . ( 3 sec) [ -1759.1893] [ 88] [depth= 2] . ( 7 sec) [ -1759.1787] [ 88] [depth= 3] . ( 10 sec) [ -1759.1519] [ 88] [depth= 1] . ( 12 sec) [ -1756.3561] [ 88] [depth= 3] . ( 13 sec) [ -1756.3369] [ 88] [depth= 1] . ( 15 sec) [ -1756.3208] [ 88] [depth= 5] . ( 19 sec) [ -1756.3104] [ 88] [depth= 2] . ( 19 sec) [ -1756.1566] [ 88] [depth= 2] . ( 19 sec) [ -1756.1218] [ 88] [depth= 2] . ( 23 sec) [ -1754.2546] [Branch lengths ] . ( 23 sec) [ -1754.2310] [Ts/ts ratio ][ 2.782525] . ( 44 sec) [ -1754.0808] [ 88] [depth= 9] . ( 44 sec) [ -1754.0647] [ 88] [depth= 8] . ( 49 sec) [ -1753.9827] [Branch lengths ] . ( 49 sec) [ -1753.9827] [Ts/ts ratio ][ 2.785308] . ( 60 sec) [ -1753.9826] [Branch lengths ] . ( 60 sec) [ -1753.9826] [Topology ] . ( 60 sec) [ -1753.9826] [Topology ] . ( 60 sec) [ -1753.9826] [Ts/ts ratio ][ 2.785308] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -1753.982569. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 37.975946 0.976000 0.007676 100 92.969765 1.000000 0.016747 64 4.589714 0.750000 0.001219 92 36.919490 0.975000 0.005071 83 24.513528 0.917000 0.002522 62 13.462123 0.848000 0.001259 8 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 41 13.585847 0.918000 0.001256 1 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 65 13.991755 0.923000 0.001254 31 -1.000000 0.000000 0.000000 86 19.650154 0.880000 0.003801 43 4.371816 0.722000 0.001249 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 59 14.498645 0.857000 0.001251 69 10.804058 0.852000 0.001248 22 -1.000000 0.000000 0.000000 17 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 14 -1.000000 0.000000 0.000000 43 9.692278 0.807000 0.001245 37 5.125104 0.758000 0.001227 51 11.760442 0.804000 0.001250 63 14.085550 0.840000 0.001249 8 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 60 14.060771 0.902000 0.001247 15 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 56 11.428658 0.862000 0.001246 30 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 14 10.638645 0.764000 0.001252 48 8.980846 0.549000 0.002493 0 -1.000000 0.000000 0.000000 64 11.704604 0.838000 0.001249 98 50.353018 0.974000 0.005044 23 -1.000000 0.000000 0.000000 84 27.130762 0.948000 0.002499 19 -1.000000 0.000000 0.000000 90 20.861068 0.888000 0.002507 69 7.425844 0.799000 0.001244 . Printing the most likely tree in file 'nucleic_M2600_69x814_2006.phy_phyml_tree.txt'... . Time used 1h30m2s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo