.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2752_106x1292_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 . 11 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 427 patterns found. (out of a total of 1292 sites) . 807 sites without polymorphism (62.46%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -7955.8143] [Ts/ts ratio ][ 2.240794] . ( 2 sec) [ -7955.7789] [ 1008] [depth= 1] . ( 2 sec) [ -7955.7620] [ 1008] [depth= 1] . ( 2 sec) [ -7955.7000] [ 1008] [depth= 2] . ( 2 sec) [ -7955.3926] [ 1008] [depth= 2] . ( 2 sec) [ -7955.3661] [ 1008] [depth= 2] . ( 2 sec) [ -7955.3357] [ 1008] [depth= 3] . ( 2 sec) [ -7955.3079] [ 1008] [depth= 2] . ( 3 sec) [ -7955.2856] [ 1008] [depth= 3] . ( 3 sec) [ -7955.1719] [ 1008] [depth= 2] . ( 3 sec) [ -7955.0118] [ 1008] [depth= 4] . ( 5 sec) [ -7954.9601] [ 1008] [depth= 1] . ( 5 sec) [ -7954.3713] [ 1008] [depth= 1] . ( 5 sec) [ -7954.3531] [ 1008] [depth= 1] . ( 9 sec) [ -7953.8196] [ 1008] [depth= 1] . ( 9 sec) [ -7953.7764] [ 1008] [depth= 4] . ( 9 sec) [ -7946.0067] [ 1007] [depth= 4] . ( 9 sec) [ -7945.9152] [ 1007] [depth= 3] . ( 10 sec) [ -7945.5181] [ 1007] [depth= 2] . ( 10 sec) [ -7945.1953] [ 1007] [depth= 2] . ( 10 sec) [ -7944.9913] [ 1007] [depth= 1] . ( 10 sec) [ -7944.9308] [ 1007] [depth= 1] . ( 10 sec) [ -7944.8860] [ 1007] [depth= 2] . ( 10 sec) [ -7944.7316] [ 1007] [depth= 1] . ( 11 sec) [ -7944.7048] [ 1007] [depth= 1] . ( 17 sec) [ -7944.0588] [ 1006] [depth= 1] . ( 18 sec) [ -7943.8977] [ 1006] [depth= 1] . ( 18 sec) [ -7943.7691] [ 1006] [depth= 1] . ( 18 sec) [ -7942.6173] [ 1005] [depth= 1] . ( 22 sec) [ -7942.5982] [ 1005] [depth= 1] . ( 22 sec) [ -7942.5228] [ 1005] [depth= 1] . ( 24 sec) [ -7941.7738] [ 1005] [depth= 3] . ( 24 sec) [ -7941.5650] [ 1005] [depth= 1] . ( 24 sec) [ -7939.7130] [ 1005] [depth= 1] . ( 25 sec) [ -7939.6133] [ 1005] [depth= 1] . ( 25 sec) [ -7939.4537] [ 1005] [depth= 1] . ( 26 sec) [ -7939.4127] [ 1005] [depth= 1] . ( 26 sec) [ -7938.9865] [ 1005] [depth= 1] . ( 26 sec) [ -7938.5954] [ 1005] [depth= 1] . ( 27 sec) [ -7938.5430] [ 1005] [depth= 1] . ( 29 sec) [ -7935.5697] [ 1005] [depth= 1] . ( 31 sec) [ -7935.0101] [ 1005] [depth= 1] . ( 31 sec) [ -7934.5108] [ 1005] [depth= 1] . ( 31 sec) [ -7931.6698] [ 1004] [depth= 1] . ( 32 sec) [ -7929.8254] [ 1004] [depth= 1] . ( 35 sec) [ -7929.3873] [ 1004] [depth= 1] . ( 36 sec) [ -7929.3063] [ 1004] [depth= 1] . ( 36 sec) [ -7929.2924] [ 1004] [depth= 1] . ( 37 sec) [ -7929.2691] [ 1004] [depth= 1] . ( 37 sec) [ -7929.2541] [ 1004] [depth= 1] . ( 38 sec) [ -7929.1214] [ 1004] [depth= 1] . ( 39 sec) [ -7928.7884] [ 1004] [depth= 1] . ( 42 sec) [ -7928.4592] [ 1004] [depth= 1] . ( 44 sec) [ -7928.0604] [ 1004] [depth= 1] . ( 44 sec) [ -7928.0441] [ 1004] [depth= 1] . ( 44 sec) [ -7928.0196] [ 1004] [depth= 1] . ( 45 sec) [ -7925.7698] [ 1004] [depth= 1] . ( 46 sec) [ -7925.6811] [ 1004] [depth= 1] . ( 48 sec) [ -7910.7819] [Branch lengths ] . ( 48 sec) [ -7910.7814] [Ts/ts ratio ][ 2.245485] . ( 70 sec) [ -7907.4529] [ 1004] [depth= 2] . ( 77 sec) [ -7907.4103] [ 1004] [depth= 1] . ( 97 sec) [ -7907.3815] [ 1004] [depth= 1] . ( 105 sec) [ -7906.6918] [Branch lengths ] . ( 106 sec) [ -7906.6909] [Ts/ts ratio ][ 2.252007] . ( 163 sec) [ -7906.6364] [Branch lengths ] . ( 253 sec) [ -7906.6322] [Branch lengths ] . ( 253 sec) [ -7906.6322] [Topology ] . ( 255 sec) [ -7906.6320] [Topology ] . ( 255 sec) [ -7906.6320] [Ts/ts ratio ][ 2.252007] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7906.631973. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 30.856958 0.965000 0.011595 100 162.591910 1.000000 0.072322 100 41.451741 0.994000 0.033318 100 181.615615 1.000000 0.054516 99 31.925382 0.977000 0.009815 100 62.170818 0.999000 0.027340 100 93.017135 1.000000 0.024549 100 93.944022 0.998000 0.016889 81 10.811072 0.886000 0.003992 97 52.136407 0.977000 0.006539 90 12.536942 0.867000 0.002472 97 22.442167 0.900000 0.002650 67 10.522828 0.865000 0.001830 75 22.666465 0.881000 0.001871 3 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 57 9.684565 0.778000 0.000917 64 21.407919 0.879000 0.001844 16 -1.000000 0.000000 0.000000 17 -1.000000 0.000000 0.000000 19 12.208099 0.856000 0.000917 16 -1.000000 0.000000 0.000000 90 20.361022 0.932000 0.002760 8 -1.000000 0.000000 0.000000 87 41.473336 0.968000 0.004630 78 6.942421 0.746000 0.000919 0 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 92 21.869405 0.899000 0.002782 80 11.451336 0.771000 0.001852 96 36.330986 0.982000 0.013356 78 9.873794 0.865000 0.002934 100 114.309594 0.999000 0.013858 81 18.499916 0.881000 0.003525 45 3.993513 0.704000 0.000936 99 83.515308 1.000000 0.013385 91 14.433949 0.899000 0.003577 56 6.075966 0.782000 0.001516 100 55.385433 0.989000 0.010153 100 75.861572 0.999000 0.011853 84 0.936816 0.710000 0.000669 69 4.705089 0.769000 0.001740 55 0.692916 0.075000 0.002117 100 96.096969 1.000000 0.013165 100 62.294584 0.994000 0.010511 54 3.304168 0.747000 0.000926 68 10.405730 0.844000 0.002367 95 10.475787 0.875000 0.003307 48 7.877739 0.717000 0.001728 60 5.246654 0.764000 0.001524 36 2.468873 0.760000 0.001330 53 7.264747 0.862000 0.001946 97 25.863485 0.938000 0.005187 100 45.233454 0.970000 0.007015 100 72.407866 0.996000 0.008538 90 31.259706 0.961000 0.004726 26 -1.000000 0.000000 0.000000 40 11.473434 0.752000 0.000936 8 -1.000000 0.000000 0.000000 23 6.579305 0.697000 0.000938 100 90.025322 0.992000 0.006643 68 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 70 9.558859 0.748000 0.000940 90 18.639674 0.900000 0.001879 30 -1.000000 0.000000 0.000000 98 76.962800 0.995000 0.008871 96 20.135427 0.931000 0.004290 100 30.911222 0.947000 0.003796 54 9.969936 0.861000 0.002081 99 47.964585 0.979000 0.004627 34 6.554357 0.757000 0.000925 27 8.212382 0.774000 0.000917 74 38.933268 0.955000 0.003596 69 13.210426 0.837000 0.000920 20 -1.000000 0.000000 0.000000 27 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 84 35.735468 0.957000 0.003690 98 16.417559 0.872000 0.001842 87 23.166796 0.885000 0.001846 64 9.743992 0.753000 0.000919 41 -1.000000 0.000000 0.000000 60 9.035403 0.787000 0.000919 70 13.162250 0.859000 0.000920 4 -1.000000 0.000000 0.000000 20 2.615197 0.785000 0.000960 13 3.371104 0.446000 0.000992 14 0.112086 0.000000 0.000339 26 2.464018 0.448000 0.001531 12 1.067393 0.316000 0.001035 93 45.141721 0.970000 0.006439 48 2.143622 0.738000 0.000830 78 19.665678 0.893000 0.001845 82 23.914821 0.860000 0.002772 58 8.774687 0.766000 0.000925 71 9.718211 0.790000 0.000922 75 23.992333 0.926000 0.004757 . Printing the most likely tree in file 'nucleic_M2752_106x1292_2006.phy_phyml_tree.txt'... . Time used 6h20m22s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo