.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2599_66x1137_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 . Compressing sequences... . 131 patterns found. (out of a total of 1137 sites) . 1062 sites without polymorphism (93.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 5Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2168.1544] [Ts/ts ratio ][ 2.872170] . ( 0 sec) [ -2167.9744] [ 80] [depth= 5] . ( 0 sec) [ -2167.9315] [ 80] [depth= 1] . ( 0 sec) [ -2167.8647] [ 80] [depth= 1] . ( 0 sec) [ -2167.8335] [ 80] [depth= 2] . ( 0 sec) [ -2167.7859] [ 80] [depth= 2] . ( 1 sec) [ -2167.7000] [ 80] [depth= 1] . ( 1 sec) [ -2167.6556] [ 80] [depth= 1] . ( 2 sec) [ -2167.6179] [ 80] [depth= 3] . ( 2 sec) [ -2167.6019] [ 80] [depth= 3] . ( 2 sec) [ -2167.5489] [ 80] [depth= 1] . ( 2 sec) [ -2167.0308] [ 80] [depth= 5] . ( 2 sec) [ -2167.0182] [ 80] [depth= 5] . ( 2 sec) [ -2166.9252] [ 80] [depth= 3] . ( 2 sec) [ -2166.9016] [ 80] [depth= 2] . ( 3 sec) [ -2166.8005] [ 80] [depth= 2] . ( 4 sec) [ -2166.3764] [ 80] [depth= 2] . ( 4 sec) [ -2166.3588] [ 80] [depth= 1] . ( 4 sec) [ -2166.2602] [ 80] [depth= 3] . ( 4 sec) [ -2166.1754] [ 80] [depth= 4] . ( 4 sec) [ -2166.0223] [ 80] [depth= 4] . ( 4 sec) [ -2165.9894] [ 80] [depth= 4] . ( 4 sec) [ -2165.9487] [ 80] [depth= 3] . ( 5 sec) [ -2165.9376] [ 80] [depth= 5] . ( 7 sec) [ -2165.9154] [ 80] [depth= 1] . ( 10 sec) [ -2165.8773] [ 80] [depth= 2] . ( 10 sec) [ -2165.8139] [ 80] [depth= 2] . ( 10 sec) [ -2165.7487] [ 80] [depth= 1] . ( 11 sec) [ -2165.7333] [ 80] [depth= 1] . ( 11 sec) [ -2165.3027] [ 80] [depth= 1] . ( 11 sec) [ -2165.2641] [ 80] [depth= 3] . ( 11 sec) [ -2165.2486] [ 80] [depth= 2] . ( 11 sec) [ -2165.2253] [ 80] [depth= 3] . ( 12 sec) [ -2165.1885] [ 80] [depth= 1] . ( 12 sec) [ -2165.1439] [ 80] [depth= 2] . ( 12 sec) [ -2165.1134] [ 80] [depth= 1] . ( 14 sec) [ -2165.0691] [ 80] [depth= 4] . ( 14 sec) [ -2164.9213] [ 80] [depth= 5] . ( 14 sec) [ -2164.8924] [ 80] [depth= 6] . ( 14 sec) [ -2164.7575] [ 80] [depth= 2] . ( 14 sec) [ -2164.5575] [ 80] [depth= 1] . ( 14 sec) [ -2164.4844] [ 80] [depth= 1] . ( 20 sec) [ -2164.2398] [ 80] [depth= 1] . ( 24 sec) [ -2164.1877] [ 80] [depth= 6] . ( 24 sec) [ -2164.1397] [ 80] [depth= 5] . ( 31 sec) [ -2163.8875] [Branch lengths ] . ( 31 sec) [ -2163.8875] [Ts/ts ratio ][ 2.872170] . ( 72 sec) [ -2163.8858] [Branch lengths ] . ( 89 sec) [ -2163.8858] [Branch lengths ] . ( 89 sec) [ -2163.8858] [Topology ] . ( 90 sec) [ -2163.8858] [Topology ] . ( 90 sec) [ -2163.8858] [Ts/ts ratio ][ 2.872170] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2163.885793. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 96 40.535849 0.962000 0.005050 63 7.114210 0.699000 0.001248 99 32.227467 0.952000 0.005303 99 31.422164 0.959000 0.005537 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 55 12.058448 0.838000 0.000966 6 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 68 9.131574 0.769000 0.000989 69 9.144862 0.777000 0.000997 0 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 98 67.763182 0.997000 0.010076 73 8.150766 0.830000 0.000986 28 -1.000000 0.000000 0.000000 21 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 61 16.970439 0.914000 0.000987 39 -1.000000 0.000000 0.000000 62 27.710277 0.936000 0.001918 1 -1.000000 0.000000 0.000000 2 -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 5 10.536183 0.860000 0.000983 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 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 56 24.130185 0.920000 0.001971 4 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 55 13.146831 0.858000 0.000985 34 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2599_66x1137_2006.phy_phyml_tree.txt'... . Time used 2h1m20s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo