.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1181 sites) . 633 sites without polymorphism (53.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 40Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -11163.4347] [Ts/ts ratio ][ 3.087781] . ( 2 sec) [ -11162.2630] [ 2014] [depth= 1] . ( 2 sec) [ -11159.2694] [ 2014] [depth= 1] . ( 2 sec) [ -11142.5980] [ 2007] [depth= 1] . ( 2 sec) [ -11142.3839] [ 2007] [depth= 1] . ( 3 sec) [ -11141.2490] [ 2007] [depth= 1] . ( 3 sec) [ -11140.6719] [ 2006] [depth= 1] . ( 3 sec) [ -11139.6339] [ 2005] [depth= 1] . ( 3 sec) [ -11139.5566] [ 2006] [depth= 2] . ( 4 sec) [ -11133.8483] [ 2003] [depth= 1] . ( 4 sec) [ -11132.6915] [ 2003] [depth= 2] . ( 6 sec) [ -11125.3326] [ 2003] [depth= 1] . ( 6 sec) [ -11124.3094] [ 2003] [depth= 1] . ( 6 sec) [ -11124.2166] [ 2003] [depth= 1] . ( 6 sec) [ -11124.2041] [ 2003] [depth= 1] . ( 6 sec) [ -11123.8771] [ 2003] [depth= 1] . ( 7 sec) [ -11123.7095] [ 2003] [depth= 1] . ( 7 sec) [ -11122.7375] [ 2003] [depth= 1] . ( 7 sec) [ -11122.6388] [ 2003] [depth= 1] . ( 7 sec) [ -11121.2109] [ 2003] [depth= 1] . ( 7 sec) [ -11121.1443] [ 2003] [depth= 2] . ( 8 sec) [ -11120.9796] [ 2003] [depth= 1] . ( 8 sec) [ -11120.2049] [ 2003] [depth= 1] . ( 9 sec) [ -11120.0979] [ 2003] [depth= 1] . ( 9 sec) [ -11120.0849] [ 2003] [depth= 1] . ( 9 sec) [ -11120.0694] [ 2003] [depth= 1] . ( 9 sec) [ -11120.0374] [ 2003] [depth= 1] . ( 10 sec) [ -11119.9791] [ 2003] [depth= 3] . ( 11 sec) [ -11115.8765] [ 2008] [depth= 1] . ( 11 sec) [ -11114.3831] [ 2008] [depth= 1] . ( 11 sec) [ -11114.0742] [ 2008] [depth= 1] . ( 11 sec) [ -11109.5705] [ 2010] [depth= 1] . ( 12 sec) [ -11109.4799] [ 2010] [depth= 1] . ( 12 sec) [ -11105.2077] [ 2010] [depth= 1] . ( 12 sec) [ -11091.7856] [ 2007] [depth= 4] . ( 12 sec) [ -11091.7097] [ 2007] [depth= 1] . ( 13 sec) [ -11091.5252] [ 2007] [depth= 1] . ( 13 sec) [ -11091.2231] [ 2007] [depth= 1] . ( 13 sec) [ -11089.8786] [ 2006] [depth= 1] . ( 14 sec) [ -11089.8261] [ 2006] [depth= 1] . ( 16 sec) [ -11085.9919] [ 2005] [depth= 1] . ( 17 sec) [ -11084.6901] [ 2006] [depth= 2] . ( 18 sec) [ -11083.0855] [ 2006] [depth= 2] . ( 18 sec) [ -11081.2879] [ 2004] [depth= 2] . ( 18 sec) [ -11081.2149] [ 2004] [depth= 1] . ( 18 sec) [ -11076.2437] [ 2004] [depth= 1] . ( 19 sec) [ -11075.0176] [ 2006] [depth= 1] . ( 19 sec) [ -11072.7404] [ 2006] [depth= 2] . ( 19 sec) [ -11072.7265] [ 2006] [depth= 1] . ( 19 sec) [ -11072.0490] [ 2006] [depth= 2] . ( 20 sec) [ -11062.5649] [ 2006] [depth= 3] . ( 20 sec) [ -11057.2536] [ 2006] [depth= 1] . ( 21 sec) [ -11057.2423] [ 2006] [depth= 1] . ( 21 sec) [ -11056.8621] [ 2006] [depth= 1] . ( 21 sec) [ -11054.9488] [ 2006] [depth= 1] . ( 22 sec) [ -11050.0032] [ 2006] [depth= 1] . ( 22 sec) [ -11041.4501] [ 2003] [depth= 1] . ( 22 sec) [ -11021.2105] [ 1998] [depth= 1] . ( 22 sec) [ -10989.4452] [ 1996] [depth= 5] . ( 22 sec) [ -10988.2634] [ 1996] [depth= 1] . ( 23 sec) [ -10987.6474] [ 1996] [depth= 1] . ( 23 sec) [ -10987.6275] [ 1996] [depth= 2] . ( 23 sec) [ -10987.5746] [ 1996] [depth= 1] . ( 25 sec) [ -10982.0017] [ 1996] [depth= 2] . ( 25 sec) [ -10980.5278] [ 1996] [depth= 1] . ( 25 sec) [ -10980.5023] [ 1996] [depth= 1] . ( 25 sec) [ -10980.4748] [ 1996] [depth= 1] . ( 29 sec) [ -10979.6797] [ 1996] [depth= 1] . ( 29 sec) [ -10978.6722] [ 1996] [depth= 1] . ( 29 sec) [ -10978.6028] [ 1996] [depth= 1] . ( 31 sec) [ -10977.9150] [ 1995] [depth= 3] . ( 31 sec) [ -10977.3992] [ 1995] [depth= 1] . ( 32 sec) [ -10977.0803] [ 1995] [depth= 1] . ( 32 sec) [ -10976.7124] [ 1995] [depth= 1] . ( 32 sec) [ -10976.7013] [ 1995] [depth= 1] . ( 33 sec) [ -10969.4442] [ 1994] [depth= 5] . ( 33 sec) [ -10948.2604] [ 1994] [depth= 1] . ( 35 sec) [ -10948.0125] [ 1998] [depth= 1] . ( 35 sec) [ -10947.7131] [ 1998] [depth= 1] . ( 35 sec) [ -10936.4075] [ 1998] [depth= 1] . ( 35 sec) [ -10936.3806] [ 2002] [depth= 2] . ( 35 sec) [ -10934.9598] [ 2002] [depth= 1] . ( 36 sec) [ -10931.4129] [ 1999] [depth= 2] . ( 36 sec) [ -10922.4178] [ 1998] [depth= 1] . ( 36 sec) [ -10919.2890] [ 1999] [depth= 1] . ( 37 sec) [ -10919.2698] [ 2003] [depth= 6] . ( 37 sec) [ -10916.8529] [ 2003] [depth= 1] . ( 37 sec) [ -10916.4404] [ 2006] [depth= 1] . ( 37 sec) [ -10908.7807] [ 2003] [depth= 1] . ( 38 sec) [ -10905.3183] [ 2006] [depth= 1] . ( 38 sec) [ -10903.0744] [ 2007] [depth= 1] . ( 38 sec) [ -10903.0327] [ 2007] [depth= 1] . ( 39 sec) [ -10901.7496] [ 2006] [depth= 1] . ( 39 sec) [ -10892.9336] [ 2006] [depth= 1] . ( 39 sec) [ -10884.6445] [ 2011] [depth= 2] . ( 40 sec) [ -10884.6269] [ 2011] [depth= 1] . ( 40 sec) [ -10883.7808] [ 2007] [depth= 2] . ( 40 sec) [ -10879.7992] [ 2007] [depth= 1] . ( 41 sec) [ -10879.5706] [ 2007] [depth= 1] . ( 41 sec) [ -10879.5406] [ 2007] [depth= 1] . ( 41 sec) [ -10879.5090] [ 2007] [depth= 1] . ( 42 sec) [ -10879.4973] [ 2007] [depth= 3] . ( 42 sec) [ -10879.4809] [ 2007] [depth= 1] . ( 42 sec) [ -10879.2666] [ 2007] [depth= 4] . ( 43 sec) [ -10879.2551] [ 2007] [depth= 2] . ( 44 sec) [ -10878.9827] [ 2007] [depth= 1] . ( 44 sec) [ -10878.2150] [ 2007] [depth= 1] . ( 45 sec) [ -10874.0162] [ 2007] [depth= 1] . ( 45 sec) [ -10873.8761] [ 2007] [depth= 1] . ( 45 sec) [ -10873.0025] [ 2010] [depth= 1] . ( 46 sec) [ -10871.2937] [ 2002] [depth= 5] . ( 46 sec) [ -10869.4666] [ 2002] [depth= 1] . ( 46 sec) [ -10868.8128] [ 2003] [depth= 1] . ( 46 sec) [ -10867.7487] [ 2002] [depth= 1] . ( 46 sec) [ -10865.8243] [ 2002] [depth= 1] . ( 47 sec) [ -10865.7464] [ 2002] [depth= 1] . ( 47 sec) [ -10861.9970] [ 1999] [depth= 1] . ( 47 sec) [ -10860.7560] [ 2003] [depth= 1] . ( 48 sec) [ -10860.1889] [ 2003] [depth= 1] . ( 49 sec) [ -10857.2306] [ 2003] [depth= 1] . ( 49 sec) [ -10857.0440] [ 2003] [depth= 1] . ( 54 sec) [ -10856.9643] [ 2003] [depth= 2] . ( 54 sec) [ -10856.8068] [ 2003] [depth= 2] . ( 55 sec) [ -10856.7187] [ 2003] [depth= 2] . ( 55 sec) [ -10856.4888] [ 2003] [depth= 2] . ( 57 sec) [ -10856.4300] [ 2003] [depth= 2] . ( 57 sec) [ -10855.6797] [ 2003] [depth= 2] . ( 57 sec) [ -10855.5455] [ 2003] [depth= 1] . ( 57 sec) [ -10855.4926] [ 2003] [depth= 1] . ( 58 sec) [ -10855.4771] [ 2003] [depth= 1] . ( 60 sec) [ -10855.4412] [ 2003] [depth= 1] . ( 74 sec) [ -10794.8136] [Branch lengths ] . ( 75 sec) [ -10792.9878] [Ts/ts ratio ][ 3.390733] . ( 76 sec) [ -10792.9627] [ 2003] [depth= 1] . ( 77 sec) [ -10792.9411] [ 2003] [depth= 2] . ( 79 sec) [ -10792.9300] [ 2003] [depth= 1] . ( 79 sec) [ -10792.9011] [ 2003] [depth= 3] . ( 82 sec) [ -10792.8908] [ 2003] [depth= 2] . ( 85 sec) [ -10792.8635] [ 2003] [depth= 1] . ( 91 sec) [ -10792.8270] [ 2003] [depth= 1] . ( 93 sec) [ -10791.2971] [ 2002] [depth= 2] . ( 95 sec) [ -10791.2759] [ 2002] [depth= 1] . ( 96 sec) [ -10786.6900] [ 2001] [depth= 1] . ( 103 sec) [ -10786.5809] [ 2002] [depth= 1] . ( 103 sec) [ -10783.0986] [ 2001] [depth= 1] . ( 107 sec) [ -10781.5326] [ 2000] [depth= 2] . ( 107 sec) [ -10781.4980] [ 2000] [depth= 2] . ( 110 sec) [ -10781.3605] [ 2000] [depth= 4] . ( 110 sec) [ -10780.9445] [ 2001] [depth= 1] . ( 112 sec) [ -10770.9864] [ 1997] [depth= 2] . ( 113 sec) [ -10770.6745] [ 1996] [depth= 1] . ( 113 sec) [ -10770.0124] [ 1992] [depth= 2] . ( 115 sec) [ -10769.9821] [ 1992] [depth= 1] . ( 115 sec) [ -10769.9710] [ 1992] [depth= 1] . ( 116 sec) [ -10769.9335] [ 1995] [depth= 1] . ( 117 sec) [ -10769.8925] [ 1995] [depth= 1] . ( 125 sec) [ -10769.0717] [ 1996] [depth= 1] . ( 125 sec) [ -10768.9285] [ 1998] [depth= 1] . ( 160 sec) [ -10761.9857] [Branch lengths ] . ( 160 sec) [ -10761.8519] [Ts/ts ratio ][ 3.477724] . ( 180 sec) [ -10761.8343] [ 1998] [depth= 1] . ( 185 sec) [ -10761.4439] [ 1998] [depth= 1] . ( 197 sec) [ -10760.7656] [ 1991] [depth= 1] . ( 247 sec) [ -10759.4494] [Branch lengths ] . ( 247 sec) [ -10759.4490] [Ts/ts ratio ][ 3.471036] . ( 334 sec) [ -10759.2897] [Branch lengths ] . ( 432 sec) [ -10759.2097] [ 1990] [depth= 1] . ( 483 sec) [ -10758.7412] [Branch lengths ] . ( 483 sec) [ -10758.7412] [Ts/ts ratio ][ 3.471036] . ( 483 sec) [ -10758.7412] [Topology ] . ( 486 sec) [ -10757.2342] [Topology ] . ( 489 sec) [ -10754.1673] [Topology ] . ( 492 sec) [ -10750.9148] [Topology ] . ( 495 sec) [ -10749.8998] [Topology ] . ( 498 sec) [ -10749.8187] [Topology ] . ( 501 sec) [ -10749.7996] [Topology ] . ( 504 sec) [ -10749.7933] [Topology ] . ( 505 sec) [ -10749.7933] [Ts/ts ratio ][ 3.471036] . ( 505 sec) [ -10749.7933] [Topology ] . ( 508 sec) [ -10749.7908] [Topology ] . ( 511 sec) [ -10749.7897] [Topology ] . ( 514 sec) [ -10749.7891] [Topology ] . ( 514 sec) [ -10749.7891] [Ts/ts ratio ][ 3.471036] . ( 515 sec) [ -10749.7891] [Topology ] . ( 518 sec) [ -10749.7888] [Topology ] . ( 518 sec) [ -10749.7888] [Ts/ts ratio ][ 3.471036] . Checking for NNIs, optimizing five branches... . ( 539 sec) [ -10749.7886] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10749.788603. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 259.159003 1.000000 0.426429 99 22.598976 0.955000 0.108075 100 43.372599 0.997000 0.154396 41 11.487326 0.901000 0.074409 13 5.814249 0.678000 0.019980 71 51.777660 0.996000 0.043105 86 63.772461 0.997000 0.041929 49 1.421172 0.706000 0.001158 97 45.212342 0.961000 0.005603 21 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 43 0.836461 0.143000 0.001403 46 12.841365 0.870000 0.002797 21 6.784615 0.779000 0.001409 6 -1.000000 0.000000 0.000000 26 9.028573 0.854000 0.001436 32 6.238197 0.733000 0.001393 86 19.564047 0.908000 0.002797 9 -1.000000 0.000000 0.000000 10 -1.000000 0.000000 0.000000 7 0.440299 0.615000 0.004312 5 3.778736 0.551000 0.011048 100 207.502922 1.000000 0.106548 73 28.451349 0.970000 0.010635 37 -1.000000 0.000000 0.000000 34 3.246411 0.441000 0.001756 27 17.658007 0.928000 0.031002 53 12.738173 0.933000 0.025302 97 18.027323 0.950000 0.049248 97 18.302776 0.923000 0.033409 32 -1.000000 0.000000 0.000000 52 2.445926 0.380000 0.016746 100 178.320772 1.000000 0.118439 100 64.025664 0.998000 0.053411 100 25.858442 0.947000 0.011012 28 -1.000000 0.000000 0.000000 76 3.184144 0.757000 0.003184 89 20.053573 0.906000 0.008140 91 15.857090 0.905000 0.002957 45 -1.000000 0.000000 0.000000 78 5.879145 0.770000 0.001508 54 5.847412 0.742000 0.001492 71 29.233731 0.932000 0.004273 74 8.435016 0.772000 0.001420 59 9.291607 0.759000 0.001477 22 2.151296 0.724000 0.012792 99 41.626608 0.994000 0.050831 100 121.284475 1.000000 0.079849 100 36.850208 0.975000 0.014299 58 -1.000000 0.000000 0.000000 100 31.578760 0.983000 0.016120 94 14.083092 0.934000 0.028380 52 5.470037 0.507000 0.015284 64 10.974279 0.819000 0.011328 100 47.582451 0.990000 0.022026 84 15.116499 0.916000 0.005438 79 23.465352 0.875000 0.003468 22 -1.000000 0.000000 0.000000 21 -1.000000 0.000000 0.000000 9 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 97 33.811673 0.977000 0.019305 100 51.608750 0.976000 0.010830 78 6.805391 0.771000 0.001420 85 6.629560 0.818000 0.003778 56 9.719860 0.878000 0.030613 8 10.903920 0.847000 0.013874 22 6.379642 0.839000 0.015549 81 33.566867 0.988000 0.043750 82 32.448492 0.973000 0.037351 100 115.415560 1.000000 0.066470 6 -1.000000 0.000000 0.000000 13 -1.000000 0.000000 0.000000 42 0.613625 0.258000 0.005951 100 98.220880 1.000000 0.080029 65 4.978794 0.826000 0.004959 46 1.896161 0.761000 0.001230 100 114.147010 1.000000 0.078997 100 51.039054 0.997000 0.038479 22 0.511052 0.602000 0.009262 100 39.322079 0.995000 0.084172 36 -1.000000 0.000000 0.000000 36 21.919829 0.935000 0.019473 21 4.384611 0.685000 0.009966 100 161.655380 1.000000 0.070357 47 -1.000000 0.000000 0.000000 99 43.605800 0.993000 0.032751 96 15.199659 0.938000 0.009969 79 3.223777 0.767000 0.001401 74 10.813815 0.803000 0.001434 78 8.497997 0.801000 0.001427 86 18.410800 0.935000 0.017603 100 106.384146 1.000000 0.041072 7 -1.000000 0.000000 0.000000 80 30.441311 0.920000 0.003584 10 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 64 11.296533 0.846000 0.001874 100 39.230924 0.985000 0.023107 1 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 49 8.477968 0.763000 0.001408 56 13.012732 0.857000 0.001408 31 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 52 15.868931 0.925000 0.001398 5 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 18 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 3 -1.000000 0.000000 0.000000 43 8.950536 0.790000 0.001394 75 11.612684 0.792000 0.001397 . Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'... . Time used 15h47m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo