.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2879_70x800_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... . 466 patterns found. (out of a total of 800 sites) . 405 sites without polymorphism (50.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 17Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -5881.5297] [Ts/ts ratio ][ 3.529319] . ( 1 sec) [ -5877.4706] [ 885] [depth= 3] . ( 1 sec) [ -5876.9023] [ 885] [depth= 1] . ( 1 sec) [ -5876.4137] [ 885] [depth= 1] . ( 1 sec) [ -5876.2556] [ 885] [depth= 1] . ( 1 sec) [ -5874.7156] [ 884] [depth= 1] . ( 1 sec) [ -5874.1565] [ 885] [depth= 1] . ( 3 sec) [ -5873.7893] [ 885] [depth= 1] . ( 4 sec) [ -5866.6538] [ 882] [depth= 1] . ( 4 sec) [ -5866.2595] [ 883] [depth= 1] . ( 6 sec) [ -5865.9729] [ 883] [depth= 1] . ( 6 sec) [ -5865.2718] [ 883] [depth= 1] . ( 6 sec) [ -5865.2527] [ 884] [depth= 2] . ( 8 sec) [ -5865.1967] [ 884] [depth= 2] . ( 8 sec) [ -5865.1257] [ 884] [depth= 2] . ( 8 sec) [ -5864.9264] [ 884] [depth= 1] . ( 8 sec) [ -5864.7695] [ 884] [depth= 2] . ( 8 sec) [ -5864.7566] [ 884] [depth= 1] . ( 8 sec) [ -5864.7448] [ 884] [depth= 1] . ( 10 sec) [ -5863.0147] [ 883] [depth= 1] . ( 10 sec) [ -5862.8455] [ 885] [depth= 2] . ( 10 sec) [ -5858.8101] [ 884] [depth= 1] . ( 10 sec) [ -5857.8389] [ 884] [depth= 1] . ( 10 sec) [ -5857.6843] [ 884] [depth= 1] . ( 12 sec) [ -5854.9402] [ 883] [depth= 4] . ( 13 sec) [ -5854.7820] [ 883] [depth= 1] . ( 13 sec) [ -5854.6472] [ 883] [depth= 1] . ( 13 sec) [ -5854.2489] [ 883] [depth= 1] . ( 13 sec) [ -5853.8978] [ 883] [depth= 1] . ( 13 sec) [ -5853.8624] [ 883] [depth= 1] . ( 14 sec) [ -5852.7631] [ 883] [depth= 1] . ( 14 sec) [ -5852.7278] [ 883] [depth= 1] . ( 15 sec) [ -5852.5752] [ 883] [depth= 1] . ( 19 sec) [ -5850.1133] [ 883] [depth= 1] . ( 20 sec) [ -5847.8768] [ 882] [depth= 2] . ( 20 sec) [ -5847.8636] [ 882] [depth= 2] . ( 20 sec) [ -5847.7878] [ 882] [depth= 1] . ( 30 sec) [ -5846.8224] [ 882] [depth= 1] . ( 30 sec) [ -5846.1936] [ 882] [depth= 1] . ( 32 sec) [ -5843.9500] [ 882] [depth= 5] . ( 32 sec) [ -5843.9076] [ 882] [depth= 2] . ( 33 sec) [ -5843.5832] [ 882] [depth= 2] . ( 33 sec) [ -5842.6616] [ 882] [depth= 1] . ( 33 sec) [ -5842.6458] [ 882] [depth= 1] . ( 33 sec) [ -5842.5721] [ 882] [depth= 1] . ( 34 sec) [ -5842.4244] [ 882] [depth= 1] . ( 34 sec) [ -5842.3468] [ 882] [depth= 2] . ( 34 sec) [ -5842.2608] [ 882] [depth= 2] . ( 35 sec) [ -5841.8536] [ 882] [depth= 1] . ( 35 sec) [ -5841.6486] [ 882] [depth= 2] . ( 35 sec) [ -5841.3762] [ 882] [depth= 2] . ( 35 sec) [ -5841.3187] [ 882] [depth= 4] . ( 36 sec) [ -5841.1780] [ 882] [depth= 3] . ( 36 sec) [ -5841.1563] [ 882] [depth= 3] . ( 38 sec) [ -5841.1442] [ 882] [depth= 1] . ( 39 sec) [ -5819.8409] [Branch lengths ] . ( 39 sec) [ -5819.8289] [Ts/ts ratio ][ 3.489910] . ( 40 sec) [ -5819.1197] [ 884] [depth= 11] . ( 52 sec) [ -5819.0823] [ 883] [depth= 2] . ( 58 sec) [ -5819.0399] [ 883] [depth= 2] . ( 60 sec) [ -5818.9290] [ 883] [depth= 1] . ( 71 sec) [ -5818.5479] [ 883] [depth= 1] . ( 75 sec) [ -5818.3069] [ 883] [depth= 1] . ( 75 sec) [ -5818.2286] [ 883] [depth= 4] . ( 81 sec) [ -5818.0182] [ 883] [depth= 3] . ( 83 sec) [ -5817.9767] [ 883] [depth= 1] . ( 90 sec) [ -5815.8436] [Branch lengths ] . ( 90 sec) [ -5815.8302] [Ts/ts ratio ][ 3.532105] . ( 148 sec) [ -5815.6208] [Branch lengths ] . ( 217 sec) [ -5815.6047] [Branch lengths ] . ( 217 sec) [ -5815.6047] [Topology ] . ( 219 sec) [ -5815.6031] [Topology ] . ( 220 sec) [ -5815.6025] [Topology ] . ( 220 sec) [ -5815.6022] [Ts/ts ratio ][ 3.537554] . ( 220 sec) [ -5815.6022] [Topology ] . ( 222 sec) [ -5815.6017] [Topology ] . ( 222 sec) [ -5815.6017] [Ts/ts ratio ][ 3.537554] . Checking for NNIs, optimizing five branches... . ( 231 sec) [ -5815.6016] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -5815.601592. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 80 6.921993 0.841000 0.012105 83 9.564188 0.891000 0.016089 39 0.549931 0.655000 0.003132 64 50.262941 0.993000 0.031438 51 6.070387 0.690000 0.008447 78 9.895603 0.828000 0.010912 100 26.096398 0.961000 0.020190 94 12.898211 0.884000 0.008914 26 4.689263 0.805000 0.007796 34 3.674925 0.688000 0.002650 87 39.301447 0.975000 0.017431 97 12.762206 0.913000 0.012414 48 6.979552 0.860000 0.008096 89 9.286209 0.857000 0.008946 71 3.809882 0.741000 0.003701 92 20.995069 0.928000 0.007940 100 31.791652 0.960000 0.012475 27 11.588047 0.863000 0.005951 21 7.447886 0.766000 0.002187 40 14.949837 0.889000 0.003709 49 6.264049 0.758000 0.001857 82 35.282670 0.968000 0.011753 7 5.378848 0.788000 0.003518 0 -1.000000 0.000000 0.000000 94 59.066717 0.990000 0.014137 52 0.753835 0.223000 0.001709 66 5.164627 0.749000 0.001786 1 0.512278 0.647000 0.001185 39 6.021393 0.842000 0.006889 98 36.985314 0.969000 0.014559 50 0.411376 0.084000 0.001613 73 6.117408 0.749000 0.001820 6 4.736674 0.796000 0.003607 53 10.563007 0.769000 0.004279 62 9.491576 0.871000 0.004143 29 0.089892 0.000000 0.000763 86 22.154734 0.904000 0.007079 74 7.385940 0.767000 0.003194 64 10.185755 0.907000 0.001916 18 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 45 4.451880 0.747000 0.001764 96 32.434073 0.956000 0.008097 24 29.138100 0.940000 0.008527 9 6.910687 0.805000 0.004863 1 0.053848 0.000000 0.002729 0 -1.000000 0.000000 0.000000 97 38.849187 0.963000 0.007584 52 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 19 9.840917 0.869000 0.003898 96 38.341478 0.979000 0.014782 100 34.429875 0.971000 0.010242 16 1.756061 0.755000 0.001794 71 18.918551 0.916000 0.005255 70 15.917034 0.868000 0.003433 46 -1.000000 0.000000 0.000000 58 7.262883 0.745000 0.001767 19 7.932122 0.844000 0.003479 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.001787 19 -1.000000 0.000000 0.000056 100 58.566872 0.994000 0.012191 5 -1.000000 0.000000 0.000000 61 6.626000 0.774000 0.001673 3 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2879_70x800_2006.phy_phyml_tree.txt'... . Time used 6h7m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo