.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2572_191x990_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... . 285 patterns found. (out of a total of 990 sites) . 729 sites without polymorphism (73.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 29Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -3534.5172] [Ts/ts ratio ][ 1.406956] . ( 2 sec) [ -3534.4447] [ 371] [depth= 1] . ( 2 sec) [ -3534.4089] [ 371] [depth= 1] . ( 2 sec) [ -3534.3909] [ 371] [depth= 1] . ( 3 sec) [ -3534.3802] [ 371] [depth= 2] . ( 3 sec) [ -3534.1835] [ 371] [depth= 1] . ( 3 sec) [ -3534.1007] [ 371] [depth= 1] . ( 4 sec) [ -3534.0333] [ 371] [depth= 1] . ( 4 sec) [ -3533.9829] [ 371] [depth= 1] . ( 4 sec) [ -3533.9670] [ 371] [depth= 2] . ( 5 sec) [ -3533.9262] [ 371] [depth= 1] . ( 5 sec) [ -3533.2362] [ 371] [depth= 1] . ( 5 sec) [ -3533.0949] [ 371] [depth= 1] . ( 6 sec) [ -3532.6854] [ 373] [depth= 2] . ( 8 sec) [ -3532.2171] [ 373] [depth= 1] . ( 8 sec) [ -3532.1925] [ 373] [depth= 2] . ( 9 sec) [ -3532.1491] [ 373] [depth= 2] . ( 9 sec) [ -3532.1232] [ 373] [depth= 1] . ( 9 sec) [ -3532.1103] [ 373] [depth= 1] . ( 9 sec) [ -3532.0128] [ 373] [depth= 7] . ( 9 sec) [ -3531.9146] [ 373] [depth= 1] . ( 11 sec) [ -3531.9016] [ 373] [depth= 1] . ( 14 sec) [ -3531.8881] [ 373] [depth= 1] . ( 14 sec) [ -3531.8461] [ 373] [depth= 5] . ( 15 sec) [ -3531.2277] [ 373] [depth= 1] . ( 16 sec) [ -3530.4818] [ 373] [depth= 1] . ( 16 sec) [ -3530.2816] [ 373] [depth= 1] . ( 38 sec) [ -3530.2642] [ 373] [depth= 1] . ( 40 sec) [ -3530.2522] [ 373] [depth= 1] . ( 61 sec) [ -3530.2369] [ 373] [depth= 1] . ( 61 sec) [ -3530.2140] [ 373] [depth= 1] . ( 62 sec) [ -3530.2020] [ 373] [depth= 1] . ( 62 sec) [ -3530.1502] [ 373] [depth= 9] . ( 62 sec) [ -3530.1083] [ 373] [depth= 6] . ( 62 sec) [ -3530.0656] [ 373] [depth= 2] . ( 77 sec) [ -3529.9018] [ 373] [depth= 5] . ( 78 sec) [ -3523.9988] [ 371] [depth= 1] . ( 79 sec) [ -3523.8500] [ 371] [depth= 4] . ( 90 sec) [ -3521.7307] [ 370] [depth= 1] . ( 94 sec) [ -3521.7152] [ 370] [depth= 1] . ( 95 sec) [ -3521.4778] [ 370] [depth= 3] . ( 95 sec) [ -3521.3414] [ 370] [depth= 2] . ( 96 sec) [ -3521.3307] [ 370] [depth= 2] . ( 97 sec) [ -3521.3193] [ 370] [depth= 1] . ( 100 sec) [ -3521.3085] [ 370] [depth= 1] . ( 135 sec) [ -3521.2718] [ 370] [depth= 2] . ( 135 sec) [ -3521.2580] [ 370] [depth= 1] . ( 135 sec) [ -3521.2454] [ 370] [depth= 1] . ( 135 sec) [ -3521.0461] [ 370] [depth= 2] . ( 136 sec) [ -3520.9641] [ 370] [depth= 1] . ( 136 sec) [ -3519.7127] [ 370] [depth= 2] . ( 136 sec) [ -3519.6919] [ 370] [depth= 5] . ( 136 sec) [ -3519.6282] [ 370] [depth= 2] . ( 136 sec) [ -3519.5901] [ 370] [depth= 2] . ( 136 sec) [ -3519.5382] [ 370] [depth= 4] . ( 138 sec) [ -3519.4634] [ 370] [depth= 3] . ( 138 sec) [ -3513.4028] [ 369] [depth= 1] . ( 153 sec) [ -3512.9998] [ 369] [depth= 1] . ( 153 sec) [ -3512.8748] [ 369] [depth= 1] . ( 190 sec) [ -3509.2885] [Branch lengths ] . ( 191 sec) [ -3509.2650] [Ts/ts ratio ][ 1.372183] . ( 396 sec) [ -3509.2124] [Branch lengths ] . ( 512 sec) [ -3509.2104] [Branch lengths ] . ( 513 sec) [ -3509.2104] [Topology ] . ( 515 sec) [ -3509.2103] [Topology ] . ( 515 sec) [ -3509.2103] [Ts/ts ratio ][ 1.373555] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3509.210282. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 27 -1.000000 0.000000 0.000000 58 16.022628 0.926000 0.001140 20 -1.000000 0.000000 0.000000 100 104.746673 0.998000 0.021166 82 14.015333 0.871000 0.007135 98 32.226484 0.945000 0.006570 59 9.947019 0.816000 0.001113 76 12.350247 0.848000 0.001112 89 9.329371 0.844000 0.003559 94 14.639744 0.870000 0.002210 98 25.418483 0.930000 0.003332 59 10.435646 0.802000 0.001101 31 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 99 45.652784 0.987000 0.013962 40 -1.000000 0.000000 0.000000 100 145.095391 1.000000 0.021667 19 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 100 68.987614 0.998000 0.010672 69 5.591973 0.757000 0.001152 65 13.277865 0.852000 0.001159 9 -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 1 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 94 13.594925 0.871000 0.002345 99 47.721703 0.973000 0.005870 88 14.767586 0.885000 0.002325 100 52.536519 0.989000 0.012088 100 102.174860 1.000000 0.020198 9 -1.000000 0.000000 0.000000 40 1.826862 0.653000 0.003972 79 17.941662 0.912000 0.005402 98 28.991607 0.946000 0.006260 100 69.871762 0.994000 0.011908 7 -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 4 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 91 25.771384 0.940000 0.005948 83 14.622790 0.879000 0.002562 3 -1.000000 0.000000 0.000000 90 30.496949 0.938000 0.002355 15 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 15 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 68 14.736850 0.910000 0.001174 1 -1.000000 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0.965000 0.006166 15 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 98 43.850986 0.972000 0.008294 39 6.243048 0.776000 0.001175 5 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 91 30.148466 0.948000 0.002363 16 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 40 12.392486 0.834000 0.001178 44 6.324217 0.746000 0.001179 62 7.145953 0.773000 0.001175 57 11.219058 0.812000 0.001173 4 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 33 15.077510 0.908000 0.001181 1 -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 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 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 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 83 27.484261 0.954000 0.002347 8 -1.000000 0.000000 0.000000 74 8.780062 0.762000 0.001190 71 10.214800 0.769000 0.001191 100 105.141880 1.000000 0.017903 58 4.775683 0.751000 0.001203 92 20.396751 0.871000 0.002412 10 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 91 29.253832 0.935000 0.003673 59 4.791791 0.786000 0.001200 6 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 90 21.496226 0.886000 0.002410 97 48.803575 0.974000 0.004823 5 -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 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 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 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 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 2 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2572_191x990_2006.phy_phyml_tree.txt'... . Time used 13h24m17s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo