.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2770_86x1628_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... . 571 patterns found. (out of a total of 1628 sites) . 1267 sites without polymorphism (77.83%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -5936.1502] [Ts/ts ratio ][ 1.581383] . ( 1 sec) [ -5935.3395] [ 518] [depth= 1] . ( 1 sec) [ -5934.8017] [ 518] [depth= 1] . ( 1 sec) [ -5934.3598] [ 518] [depth= 1] . ( 1 sec) [ -5934.3231] [ 518] [depth= 1] . ( 2 sec) [ -5929.3204] [ 517] [depth= 1] . ( 2 sec) [ -5928.8848] [ 517] [depth= 1] . ( 2 sec) [ -5928.6452] [ 517] [depth= 1] . ( 3 sec) [ -5927.8875] [ 517] [depth= 3] . ( 3 sec) [ -5927.7660] [ 517] [depth= 1] . ( 3 sec) [ -5927.6271] [ 517] [depth= 1] . ( 3 sec) [ -5927.5999] [ 517] [depth= 1] . ( 4 sec) [ -5926.1288] [ 517] [depth= 1] . ( 5 sec) [ -5926.1013] [ 517] [depth= 2] . ( 5 sec) [ -5925.9520] [ 517] [depth= 2] . ( 6 sec) [ -5925.7833] [ 517] [depth= 2] . ( 6 sec) [ -5925.7716] [ 517] [depth= 2] . ( 7 sec) [ -5925.4073] [ 517] [depth= 1] . ( 9 sec) [ -5914.0203] [ 515] [depth= 4] . ( 11 sec) [ -5913.4990] [ 515] [depth= 1] . ( 11 sec) [ -5913.0382] [ 515] [depth= 1] . ( 11 sec) [ -5906.6273] [ 513] [depth= 1] . ( 12 sec) [ -5902.3328] [ 512] [depth= 2] . ( 12 sec) [ -5902.3021] [ 512] [depth= 1] . ( 13 sec) [ -5902.0814] [ 512] [depth= 1] . ( 14 sec) [ -5902.0554] [ 512] [depth= 1] . ( 19 sec) [ -5901.9859] [ 512] [depth= 1] . ( 19 sec) [ -5901.8466] [ 512] [depth= 1] . ( 21 sec) [ -5901.8168] [ 512] [depth= 1] . ( 23 sec) [ -5901.1691] [ 512] [depth= 1] . ( 24 sec) [ -5901.1514] [ 512] [depth= 1] . ( 24 sec) [ -5900.8440] [ 512] [depth= 1] . ( 24 sec) [ -5900.8251] [ 512] [depth= 1] . ( 24 sec) [ -5900.7818] [ 512] [depth= 1] . ( 26 sec) [ -5900.5292] [ 512] [depth= 2] . ( 26 sec) [ -5900.3725] [ 512] [depth= 2] . ( 26 sec) [ -5900.1062] [ 512] [depth= 1] . ( 26 sec) [ -5900.0852] [ 512] [depth= 2] . ( 27 sec) [ -5900.0346] [ 512] [depth= 1] . ( 28 sec) [ -5899.5776] [ 512] [depth= 1] . ( 28 sec) [ -5899.5633] [ 512] [depth= 1] . ( 33 sec) [ -5898.3206] [ 510] [depth= 1] . ( 37 sec) [ -5897.5516] [ 510] [depth= 5] . ( 42 sec) [ -5896.8030] [ 510] [depth= 1] . ( 42 sec) [ -5895.1226] [ 510] [depth= 2] . ( 42 sec) [ -5891.1572] [ 509] [depth= 1] . ( 42 sec) [ -5890.8629] [ 509] [depth= 1] . ( 44 sec) [ -5890.2246] [ 509] [depth= 2] . ( 48 sec) [ -5890.1775] [ 509] [depth= 1] . ( 49 sec) [ -5888.4699] [ 509] [depth= 1] . ( 49 sec) [ -5883.6131] [ 508] [depth= 1] . ( 49 sec) [ -5882.6360] [ 508] [depth= 2] . ( 50 sec) [ -5882.5798] [ 508] [depth= 1] . ( 50 sec) [ -5882.3208] [ 508] [depth= 1] . ( 50 sec) [ -5882.2143] [ 508] [depth= 1] . ( 53 sec) [ -5882.1728] [ 508] [depth= 1] . ( 57 sec) [ -5871.6428] [Branch lengths ] . ( 57 sec) [ -5871.6300] [Ts/ts ratio ][ 1.559018] . ( 61 sec) [ -5871.5436] [ 508] [depth= 1] . ( 72 sec) [ -5871.5157] [ 508] [depth= 1] . ( 98 sec) [ -5871.2980] [ 508] [depth= 1] . ( 102 sec) [ -5868.6995] [ 507] [depth= 1] . ( 104 sec) [ -5868.5938] [ 507] [depth= 1] . ( 124 sec) [ -5867.8717] [Branch lengths ] . ( 124 sec) [ -5867.8710] [Ts/ts ratio ][ 1.553882] . ( 191 sec) [ -5867.8548] [Branch lengths ] . ( 293 sec) [ -5867.8534] [Branch lengths ] . ( 293 sec) [ -5867.8534] [Topology ] . ( 296 sec) [ -5867.8533] [Topology ] . ( 296 sec) [ -5867.8533] [Ts/ts ratio ][ 1.553882] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5867.853286. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 163.085341 1.000000 0.030139 100 73.734849 0.997000 0.017981 95 26.982371 0.944000 0.006663 71 30.593589 0.959000 0.004528 80 10.551074 0.850000 0.001787 65 8.740641 0.760000 0.000904 78 15.258586 0.872000 0.002179 36 3.871976 0.750000 0.000918 96 36.435564 0.941000 0.002804 27 7.265076 0.759000 0.000874 8 -1.000000 0.000000 0.000000 73 27.188627 0.921000 0.002644 46 15.963909 0.855000 0.001847 19 0.540635 0.080000 0.000918 60 -1.000000 0.000000 0.000000 43 22.770460 0.911000 0.002652 91 34.663748 0.959000 0.003544 36 -1.000000 0.000000 0.000000 35 6.675622 0.734000 0.000892 79 60.719953 0.986000 0.005429 12 -1.000000 0.000000 0.000000 29 4.649645 0.742000 0.000876 3 -1.000000 0.000000 0.000000 40 10.046347 0.831000 0.000938 11 -1.000000 0.000000 0.000000 21 -1.000000 0.000000 0.000000 97 15.246833 0.896000 0.004694 98 34.259523 0.946000 0.004356 89 12.940924 0.879000 0.002516 30 -1.000000 0.000000 0.000000 66 4.391731 0.415000 0.001868 91 31.339340 0.973000 0.009205 62 5.699079 0.803000 0.001762 88 24.728935 0.943000 0.004725 93 19.476438 0.902000 0.004061 100 114.529255 1.000000 0.014225 80 5.042421 0.758000 0.001270 69 11.022193 0.850000 0.001845 70 22.411379 0.925000 0.002943 95 46.293053 0.977000 0.005761 62 6.474634 0.742000 0.001132 67 12.133858 0.831000 0.000973 15 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 94 34.952526 0.947000 0.002926 88 12.813866 0.865000 0.001979 39 -1.000000 0.000000 0.000000 38 6.903530 0.750000 0.000944 28 6.820998 0.782000 0.000986 100 86.210074 0.997000 0.009567 16 0.489943 0.084000 0.000971 98 76.509126 0.996000 0.007859 71 6.914701 0.747000 0.000969 60 9.424639 0.785000 0.000972 14 -1.000000 0.000000 0.000000 77 24.815920 0.911000 0.001947 28 -1.000000 0.000000 0.000000 42 13.040519 0.844000 0.000972 89 26.479993 0.924000 0.001949 10 -1.000000 0.000000 0.000000 29 -1.000000 0.000000 0.000000 19 4.064888 0.749000 0.001026 41 7.190206 0.795000 0.001572 57 11.279999 0.795000 0.001546 22 -1.000000 0.000000 0.000000 61 9.404219 0.731000 0.001039 100 64.380795 0.986000 0.006362 8 -1.000000 0.000000 0.000000 94 38.647443 0.955000 0.003172 27 7.271881 0.759000 0.001035 93 20.407619 0.919000 0.003136 100 37.887922 0.979000 0.005261 88 16.348459 0.873000 0.002092 94 18.314905 0.871000 0.002087 10 7.632492 0.767000 0.000950 7 6.301549 0.741000 0.000947 28 14.186993 0.859000 0.002126 95 30.404683 0.947000 0.003745 69 10.626041 0.806000 0.000972 38 5.785831 0.437000 0.001979 80 10.842179 0.684000 0.003145 36 4.798225 0.745000 0.001634 99 70.088378 0.989000 0.008693 . Printing the most likely tree in file 'nucleic_M2770_86x1628_2006.phy_phyml_tree.txt'... . Time used 6h56m6s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo