.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2975_93x982_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... . 725 patterns found. (out of a total of 982 sites) . 454 sites without polymorphism (46.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12665.3350] [Ts/ts ratio ][ 4.032343] . ( 1 sec) [ -12661.7679] [ 2378] [depth= 1] . ( 1 sec) [ -12655.9657] [ 2377] [depth= 1] . ( 2 sec) [ -12653.6681] [ 2376] [depth= 1] . ( 2 sec) [ -12652.4999] [ 2375] [depth= 1] . ( 3 sec) [ -12651.7623] [ 2375] [depth= 1] . ( 3 sec) [ -12642.4619] [ 2371] [depth= 1] . ( 4 sec) [ -12639.3466] [ 2373] [depth= 2] . ( 5 sec) [ -12636.9808] [ 2373] [depth= 1] . ( 5 sec) [ -12636.9685] [ 2373] [depth= 1] . ( 6 sec) [ -12634.1456] [ 2375] [depth= 1] . ( 6 sec) [ -12626.5696] [ 2375] [depth= 1] . ( 7 sec) [ -12623.6399] [ 2375] [depth= 1] . ( 7 sec) [ -12622.0227] [ 2375] [depth= 1] . ( 7 sec) [ -12621.7874] [ 2375] [depth= 1] . ( 8 sec) [ -12612.6691] [ 2378] [depth= 1] . ( 8 sec) [ -12612.2966] [ 2377] [depth= 2] . ( 8 sec) [ -12611.8797] [ 2377] [depth= 1] . ( 8 sec) [ -12607.2342] [ 2377] [depth= 1] . ( 9 sec) [ -12607.1029] [ 2377] [depth= 1] . ( 10 sec) [ -12603.2376] [ 2374] [depth= 1] . ( 10 sec) [ -12602.7104] [ 2378] [depth= 1] . ( 10 sec) [ -12600.7760] [ 2379] [depth= 1] . ( 11 sec) [ -12600.6265] [ 2378] [depth= 1] . ( 11 sec) [ -12600.2620] [ 2378] [depth= 1] . ( 12 sec) [ -12588.8205] [ 2382] [depth= 2] . ( 12 sec) [ -12584.5775] [ 2380] [depth= 1] . ( 12 sec) [ -12581.4061] [ 2377] [depth= 1] . ( 13 sec) [ -12577.0202] [ 2376] [depth= 1] . ( 13 sec) [ -12574.3066] [ 2376] [depth= 1] . ( 14 sec) [ -12570.2091] [ 2380] [depth= 4] . ( 14 sec) [ -12559.0236] [ 2378] [depth= 1] . ( 15 sec) [ -12555.6677] [ 2379] [depth= 1] . ( 15 sec) [ -12552.1076] [ 2378] [depth= 1] . ( 15 sec) [ -12550.3623] [ 2382] [depth= 1] . ( 15 sec) [ -12547.0301] [ 2378] [depth= 2] . ( 16 sec) [ -12546.2914] [ 2381] [depth= 1] . ( 16 sec) [ -12542.1147] [ 2381] [depth= 1] . ( 16 sec) [ -12537.6880] [ 2383] [depth= 2] . ( 16 sec) [ -12537.4001] [ 2383] [depth= 1] . ( 17 sec) [ -12537.3711] [ 2383] [depth= 1] . ( 17 sec) [ -12537.0368] [ 2383] [depth= 1] . ( 18 sec) [ -12536.8135] [ 2383] [depth= 2] . ( 19 sec) [ -12536.7500] [ 2387] [depth= 1] . ( 20 sec) [ -12527.7890] [ 2380] [depth= 2] . ( 20 sec) [ -12524.9174] [ 2380] [depth= 1] . ( 20 sec) [ -12523.7190] [ 2381] [depth= 1] . ( 21 sec) [ -12523.7076] [ 2382] [depth= 2] . ( 22 sec) [ -12521.6230] [ 2380] [depth= 1] . ( 23 sec) [ -12516.8748] [ 2374] [depth= 2] . ( 23 sec) [ -12513.1241] [ 2374] [depth= 1] . ( 24 sec) [ -12512.6012] [ 2375] [depth= 1] . ( 24 sec) [ -12505.4414] [ 2373] [depth= 1] . ( 24 sec) [ -12504.3096] [ 2372] [depth= 6] . ( 24 sec) [ -12503.3200] [ 2377] [depth= 3] . ( 25 sec) [ -12489.9423] [ 2372] [depth= 8] . ( 25 sec) [ -12489.7529] [ 2374] [depth= 1] . ( 26 sec) [ -12489.5263] [ 2374] [depth= 1] . ( 26 sec) [ -12488.9723] [ 2373] [depth= 1] . ( 26 sec) [ -12488.2877] [ 2373] [depth= 1] . ( 27 sec) [ -12484.6526] [ 2369] [depth= 2] . ( 28 sec) [ -12481.8190] [ 2368] [depth= 1] . ( 28 sec) [ -12481.5200] [ 2369] [depth= 1] . ( 29 sec) [ -12478.0507] [ 2368] [depth= 1] . ( 29 sec) [ -12471.5376] [ 2371] [depth= 5] . ( 29 sec) [ -12470.9796] [ 2371] [depth= 1] . ( 29 sec) [ -12470.5043] [ 2369] [depth= 2] . ( 29 sec) [ -12470.3215] [ 2369] [depth= 2] . ( 30 sec) [ -12468.7776] [ 2368] [depth= 1] . ( 30 sec) [ -12468.1171] [ 2368] [depth= 1] . ( 30 sec) [ -12467.9340] [ 2368] [depth= 1] . ( 32 sec) [ -12466.8857] [ 2371] [depth= 2] . ( 32 sec) [ -12466.5699] [ 2374] [depth= 3] . ( 34 sec) [ -12466.2295] [ 2372] [depth= 2] . ( 35 sec) [ -12462.2623] [ 2372] [depth= 4] . ( 35 sec) [ -12461.6050] [ 2374] [depth= 1] . ( 35 sec) [ -12459.8651] [ 2377] [depth= 3] . ( 36 sec) [ -12455.9293] [ 2373] [depth= 2] . ( 36 sec) [ -12455.0075] [ 2373] [depth= 4] . ( 37 sec) [ -12454.2600] [ 2371] [depth= 1] . ( 37 sec) [ -12449.8105] [ 2370] [depth= 2] . ( 37 sec) [ -12449.6059] [ 2372] [depth= 1] . ( 41 sec) [ -12381.6528] [Branch lengths ] . ( 41 sec) [ -12380.7642] [Ts/ts ratio ][ 4.281683] . ( 44 sec) [ -12378.7889] [ 2372] [depth= 2] . ( 45 sec) [ -12377.0723] [ 2371] [depth= 1] . ( 51 sec) [ -12377.0460] [ 2371] [depth= 1] . ( 52 sec) [ -12371.1075] [ 2365] [depth= 1] . ( 52 sec) [ -12371.0666] [ 2363] [depth= 1] . ( 53 sec) [ -12370.9310] [ 2363] [depth= 1] . ( 53 sec) [ -12370.9056] [ 2365] [depth= 1] . ( 54 sec) [ -12367.2469] [ 2363] [depth= 1] . ( 55 sec) [ -12365.9902] [ 2360] [depth= 1] . ( 57 sec) [ -12365.9794] [ 2360] [depth= 1] . ( 58 sec) [ -12361.0012] [ 2358] [depth= 1] . ( 63 sec) [ -12358.5814] [ 2356] [depth= 1] . ( 64 sec) [ -12358.0811] [ 2354] [depth= 1] . ( 64 sec) [ -12355.8555] [ 2352] [depth= 1] . ( 67 sec) [ -12355.4259] [ 2356] [depth= 3] . ( 67 sec) [ -12355.0991] [ 2356] [depth= 4] . ( 67 sec) [ -12354.3840] [ 2352] [depth= 2] . ( 71 sec) [ -12353.5277] [ 2356] [depth= 5] . ( 72 sec) [ -12353.1921] [ 2358] [depth= 2] . ( 72 sec) [ -12349.4813] [ 2349] [depth= 3] . ( 73 sec) [ -12349.3219] [ 2348] [depth= 1] . ( 74 sec) [ -12349.3051] [ 2348] [depth= 1] . ( 75 sec) [ -12348.5785] [ 2349] [depth= 1] . ( 80 sec) [ -12348.5187] [ 2349] [depth= 1] . ( 83 sec) [ -12348.4315] [ 2349] [depth= 1] . ( 86 sec) [ -12348.1049] [ 2348] [depth= 1] . ( 86 sec) [ -12347.9169] [ 2349] [depth= 1] . ( 86 sec) [ -12346.8439] [ 2346] [depth= 2] . ( 89 sec) [ -12337.3596] [Branch lengths ] . ( 89 sec) [ -12337.3393] [Ts/ts ratio ][ 4.320717] . ( 91 sec) [ -12337.0795] [ 2347] [depth= 1] . ( 112 sec) [ -12337.0247] [ 2347] [depth= 2] . ( 114 sec) [ -12334.6650] [ 2344] [depth= 4] . ( 128 sec) [ -12334.3639] [ 2344] [depth= 1] . ( 135 sec) [ -12333.2827] [Branch lengths ] . ( 136 sec) [ -12333.2804] [Ts/ts ratio ][ 4.334020] . ( 184 sec) [ -12333.1056] [Branch lengths ] . ( 319 sec) [ -12333.0683] [Branch lengths ] . ( 319 sec) [ -12333.0683] [Topology ] . ( 322 sec) [ -12333.0634] [Topology ] . ( 325 sec) [ -12333.0613] [Topology ] . ( 328 sec) [ -12333.0602] [Topology ] . ( 332 sec) [ -12333.0596] [Topology ] . ( 332 sec) [ -12333.0590] [Ts/ts ratio ][ 4.339049] . ( 332 sec) [ -12333.0590] [Topology ] . ( 335 sec) [ -12333.0586] [Topology ] . ( 335 sec) [ -12333.0586] [Ts/ts ratio ][ 4.343388] . Checking for NNIs, optimizing five branches... . ( 356 sec) [ -12333.0585] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12333.058508. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 99 43.169239 0.986000 0.020906 86 5.517595 0.826000 0.006632 58 1.846989 0.710000 0.011249 88 14.383452 0.905000 0.012403 100 97.040491 1.000000 0.087471 89 21.477479 0.937000 0.025301 99 32.621326 0.969000 0.042029 95 17.915279 0.970000 0.036989 38 -1.000000 0.000000 0.000001 96 7.092580 0.864000 0.035375 44 1.067851 0.203000 0.013520 74 4.801052 0.604000 0.016422 95 13.712619 0.870000 0.027959 100 71.976448 0.994000 0.055980 84 14.717591 0.927000 0.022493 95 15.525916 0.913000 0.008446 43 -1.000000 0.000000 0.000000 98 15.392959 0.906000 0.008499 59 2.331925 0.755000 0.007827 100 97.359689 1.000000 0.069865 58 7.795990 0.756000 0.016603 47 4.123875 0.818000 0.019008 74 12.149304 0.931000 0.066639 92 14.420525 0.945000 0.057286 100 88.383581 1.000000 0.061109 70 4.544442 0.769000 0.007663 100 22.566027 0.937000 0.014853 93 17.267314 0.928000 0.014239 44 4.153511 0.668000 0.018864 81 9.317478 0.864000 0.034885 96 52.541339 0.993000 0.037253 50 1.183941 0.276000 0.004617 77 10.495516 0.883000 0.011752 93 38.222957 0.986000 0.031556 100 106.097218 1.000000 0.063710 32 -1.000000 0.000000 0.000000 45 0.721248 0.180000 0.003809 77 7.133358 0.801000 0.014125 75 17.878922 0.900000 0.012989 88 24.027038 0.955000 0.018244 100 33.444536 0.985000 0.017967 95 9.039855 0.873000 0.006412 100 27.504774 0.965000 0.022027 81 10.327363 0.725000 0.013408 98 25.412487 0.948000 0.014545 34 -1.000000 0.000000 0.000000 74 3.381323 0.744000 0.003298 85 6.837416 0.857000 0.019132 97 22.047626 0.965000 0.027797 100 180.277486 1.000000 0.095538 72 8.126540 0.887000 0.015822 49 11.204724 0.931000 0.014025 9 3.566124 0.716000 0.005326 3 -1.000000 0.000000 0.000000 5 14.123567 0.941000 0.008160 0 -1.000000 0.000000 0.000000 12 11.785635 0.902000 0.007966 13 3.096577 0.783000 0.004048 19 3.106833 0.800000 0.003791 41 13.772981 0.912000 0.012441 26 0.335801 0.025000 0.006486 99 73.712104 0.998000 0.032350 11 0.844702 0.475000 0.001693 100 179.011469 1.000000 0.051526 14 0.774255 0.378000 0.002374 54 13.212092 0.868000 0.006702 96 38.164416 0.981000 0.018694 62 6.038677 0.816000 0.008936 8 18.766297 0.927000 0.012277 12 1.590697 0.442000 0.012649 49 5.463178 0.804000 0.005338 64 5.473684 0.782000 0.006236 100 98.476188 1.000000 0.036497 51 0.000214 0.000000 0.000000 99 48.244576 0.996000 0.027076 5 2.202137 0.749000 0.002604 22 3.049644 0.790000 0.011021 74 3.731504 0.665000 0.014805 91 31.100609 0.967000 0.017080 79 9.017002 0.876000 0.010145 91 11.246958 0.848000 0.006851 77 13.714705 0.878000 0.004670 66 3.574488 0.799000 0.005042 27 1.134931 0.728000 0.002053 100 105.730746 1.000000 0.034523 28 -1.000000 0.000000 0.000000 41 6.154258 0.743000 0.009077 58 6.042347 0.840000 0.012700 65 1.126669 0.394000 0.005936 58 4.546088 0.732000 0.010420 . Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'... . Time used 10h9m27s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo