.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2733_60x1207_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... . 564 patterns found. (out of a total of 1207 sites) . 771 sites without polymorphism (63.88%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -11455.2362] [Ts/ts ratio ][ 2.934662] . ( 0 sec) [ -11454.8175] [ 1957] [depth= 1] . ( 0 sec) [ -11454.5413] [ 1957] [depth= 1] . ( 0 sec) [ -11454.3478] [ 1957] [depth= 1] . ( 1 sec) [ -11449.6373] [ 1957] [depth= 1] . ( 1 sec) [ -11431.7925] [ 1957] [depth= 1] . ( 1 sec) [ -11426.0828] [ 1958] [depth= 1] . ( 1 sec) [ -11413.2361] [ 1957] [depth= 1] . ( 1 sec) [ -11393.4883] [ 1952] [depth= 1] . ( 2 sec) [ -11393.4535] [ 1952] [depth= 2] . ( 2 sec) [ -11373.7533] [ 1952] [depth= 2] . ( 2 sec) [ -11368.6614] [ 1950] [depth= 2] . ( 2 sec) [ -11365.1107] [ 1951] [depth= 2] . ( 2 sec) [ -11347.0914] [ 1947] [depth= 1] . ( 2 sec) [ -11346.4033] [ 1950] [depth= 1] . ( 3 sec) [ -11343.6704] [ 1947] [depth= 1] . ( 3 sec) [ -11343.6058] [ 1946] [depth= 1] . ( 3 sec) [ -11338.8407] [ 1944] [depth= 1] . ( 3 sec) [ -11338.0845] [ 1945] [depth= 1] . ( 3 sec) [ -11334.4927] [ 1948] [depth= 1] . ( 4 sec) [ -11333.4762] [ 1948] [depth= 1] . ( 4 sec) [ -11332.6796] [ 1948] [depth= 1] . ( 4 sec) [ -11332.3234] [ 1948] [depth= 1] . ( 5 sec) [ -11317.8485] [ 1945] [depth= 1] . ( 5 sec) [ -11315.9963] [ 1945] [depth= 3] . ( 6 sec) [ -11308.9915] [ 1943] [depth= 1] . ( 6 sec) [ -11308.8263] [ 1945] [depth= 1] . ( 6 sec) [ -11305.0828] [ 1945] [depth= 1] . ( 6 sec) [ -11304.9580] [ 1945] [depth= 1] . ( 6 sec) [ -11294.7712] [ 1943] [depth= 1] . ( 7 sec) [ -11287.4328] [ 1941] [depth= 1] . ( 8 sec) [ -11286.1896] [ 1941] [depth= 1] . ( 8 sec) [ -11275.5434] [ 1942] [depth= 1] . ( 8 sec) [ -11271.4213] [ 1938] [depth= 1] . ( 8 sec) [ -11267.3626] [ 1938] [depth= 1] . ( 8 sec) [ -11266.1251] [ 1941] [depth= 8] . ( 9 sec) [ -11263.7089] [ 1943] [depth= 1] . ( 9 sec) [ -11262.5318] [ 1941] [depth= 1] . ( 9 sec) [ -11260.1388] [ 1943] [depth= 2] . ( 10 sec) [ -11246.8692] [ 1937] [depth= 3] . ( 10 sec) [ -11242.1694] [ 1941] [depth= 2] . ( 10 sec) [ -11242.0780] [ 1939] [depth= 1] . ( 11 sec) [ -11240.9293] [ 1941] [depth= 1] . ( 12 sec) [ -11240.7475] [ 1941] [depth= 1] . ( 12 sec) [ -11238.6041] [ 1940] [depth= 1] . ( 15 sec) [ -11188.6009] [Branch lengths ] . ( 15 sec) [ -11186.9317] [Ts/ts ratio ][ 3.201667] . ( 16 sec) [ -11186.9210] [ 1940] [depth= 2] . ( 33 sec) [ -11178.9579] [Branch lengths ] . ( 33 sec) [ -11178.9501] [Ts/ts ratio ][ 3.219915] . ( 51 sec) [ -11176.6794] [Branch lengths ] . ( 107 sec) [ -11176.5388] [Branch lengths ] . ( 107 sec) [ -11176.5388] [Topology ] . ( 109 sec) [ -11176.5368] [Topology ] . ( 110 sec) [ -11176.5353] [Topology ] . ( 111 sec) [ -11176.5273] [Topology ] . ( 113 sec) [ -11176.4673] [Topology ] . ( 114 sec) [ -11176.0566] [Topology ] . ( 116 sec) [ -11174.5420] [Topology ] . ( 116 sec) [ -11174.5398] [Ts/ts ratio ][ 3.228856] . ( 116 sec) [ -11174.5398] [Topology ] . ( 117 sec) [ -11174.1009] [Topology ] . ( 119 sec) [ -11174.0075] [Topology ] . ( 120 sec) [ -11173.9885] [Topology ] . ( 121 sec) [ -11173.9844] [Topology ] . ( 123 sec) [ -11173.9835] [Topology ] . ( 123 sec) [ -11173.9835] [Ts/ts ratio ][ 3.223221] . ( 123 sec) [ -11173.9835] [Topology ] . ( 124 sec) [ -11173.9832] [Topology ] . ( 125 sec) [ -11173.9831] [Ts/ts ratio ][ 3.226444] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11173.983094. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 36.756050 0.993000 0.029267 100 174.013755 1.000000 0.079269 13 1.306300 0.315000 0.008875 37 14.890039 0.867000 0.024942 99 31.781052 0.978000 0.035944 99 43.372112 0.986000 0.066578 92 11.834066 0.914000 0.033727 61 19.587814 0.948000 0.022825 44 5.707034 0.619000 0.015388 98 45.234186 0.986000 0.038772 63 3.568960 0.253000 0.019871 68 15.253323 0.886000 0.018414 100 170.063245 1.000000 0.076869 99 26.137415 0.956000 0.013750 20 -1.000000 0.000000 0.000000 20 -1.000000 0.000000 0.000000 99 8.034859 0.868000 0.007120 65 10.262485 0.833000 0.019847 84 27.584507 0.971000 0.029682 10 6.233702 0.855000 0.011096 17 15.970457 0.917000 0.010567 97 25.611995 0.974000 0.023799 12 0.989914 0.696000 0.001747 41 22.080341 0.908000 0.006757 54 9.841844 0.878000 0.006936 98 47.232525 0.993000 0.017978 26 3.387502 0.629000 0.002035 100 142.924932 1.000000 0.035974 29 1.538640 0.342000 0.004758 21 15.457361 0.925000 0.010025 100 178.767259 1.000000 0.050742 4 0.402897 0.073000 0.004142 46 16.635637 0.935000 0.016435 100 77.729137 1.000000 0.038290 34 7.025634 0.778000 0.005574 16 4.910054 0.840000 0.004365 18 2.712793 0.778000 0.002665 55 27.228421 0.947000 0.009662 98 59.574778 0.990000 0.015605 93 27.031859 0.954000 0.007631 93 12.149444 0.904000 0.005962 20 0.077376 0.000000 0.002408 27 3.145081 0.712000 0.003077 100 82.394520 1.000000 0.029481 37 6.604905 0.798000 0.004944 100 56.493870 0.970000 0.043207 60 11.136903 0.891000 0.007357 100 130.035510 1.000000 0.037373 81 8.560361 0.832000 0.006854 100 57.836317 0.992000 0.019563 53 1.383653 0.447000 0.001335 26 9.754193 0.904000 0.008575 100 124.171460 1.000000 0.041952 13 1.855306 0.296000 0.006063 67 21.079226 0.952000 0.025450 100 106.545627 1.000000 0.066031 43 0.944106 0.177000 0.009401 . Printing the most likely tree in file 'nucleic_M2733_60x1207_2006.phy_phyml_tree.txt'... . Time used 3h28m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo