.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2567_64x1044_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 408 patterns found. (out of a total of 1044 sites) . 678 sites without polymorphism (64.94%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 14Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -6956.7675] [Ts/ts ratio ][ 3.482349] . ( 0 sec) [ -6956.7083] [ 965] [depth= 1] . ( 0 sec) [ -6956.6704] [ 965] [depth= 1] . ( 0 sec) [ -6956.6542] [ 965] [depth= 1] . ( 0 sec) [ -6953.6413] [ 965] [depth= 2] . ( 1 sec) [ -6953.5717] [ 965] [depth= 1] . ( 1 sec) [ -6953.2545] [ 965] [depth= 1] . ( 1 sec) [ -6953.0071] [ 965] [depth= 1] . ( 1 sec) [ -6952.9963] [ 965] [depth= 1] . ( 2 sec) [ -6952.5766] [ 964] [depth= 2] . ( 2 sec) [ -6951.1361] [ 964] [depth= 1] . ( 2 sec) [ -6950.6152] [ 964] [depth= 3] . ( 2 sec) [ -6949.4530] [ 964] [depth= 1] . ( 2 sec) [ -6949.0334] [ 964] [depth= 1] . ( 2 sec) [ -6940.2879] [ 965] [depth= 1] . ( 2 sec) [ -6938.6467] [ 967] [depth= 1] . ( 2 sec) [ -6936.8723] [ 965] [depth= 1] . ( 2 sec) [ -6935.5890] [ 965] [depth= 1] . ( 2 sec) [ -6934.7686] [ 965] [depth= 1] . ( 4 sec) [ -6927.2109] [ 963] [depth= 2] . ( 5 sec) [ -6924.3615] [ 961] [depth= 1] . ( 5 sec) [ -6919.4786] [ 961] [depth= 1] . ( 6 sec) [ -6919.4679] [ 961] [depth= 1] . ( 6 sec) [ -6919.1689] [ 962] [depth= 1] . ( 6 sec) [ -6916.3684] [ 961] [depth= 1] . ( 7 sec) [ -6908.7926] [ 958] [depth= 1] . ( 7 sec) [ -6907.4958] [ 958] [depth= 1] . ( 8 sec) [ -6906.0296] [ 960] [depth= 1] . ( 8 sec) [ -6900.5607] [ 958] [depth= 1] . ( 9 sec) [ -6899.9935] [ 958] [depth= 1] . ( 9 sec) [ -6897.9087] [ 958] [depth= 1] . ( 9 sec) [ -6897.8366] [ 958] [depth= 1] . ( 9 sec) [ -6893.8739] [ 957] [depth= 1] . ( 11 sec) [ -6893.6261] [ 957] [depth= 1] . ( 11 sec) [ -6893.5295] [ 957] [depth= 1] . ( 11 sec) [ -6893.4688] [ 957] [depth= 1] . ( 11 sec) [ -6892.7962] [ 957] [depth= 1] . ( 11 sec) [ -6892.7828] [ 957] [depth= 1] . ( 11 sec) [ -6892.7679] [ 957] [depth= 1] . ( 11 sec) [ -6892.7419] [ 957] [depth= 1] . ( 11 sec) [ -6892.7311] [ 957] [depth= 1] . ( 11 sec) [ -6892.7205] [ 957] [depth= 2] . ( 12 sec) [ -6858.3072] [Branch lengths ] . ( 12 sec) [ -6858.3072] [Ts/ts ratio ][ 3.482349] . ( 14 sec) [ -6858.0844] [ 958] [depth= 2] . ( 15 sec) [ -6857.9011] [ 957] [depth= 1] . ( 15 sec) [ -6857.8745] [ 958] [depth= 1] . ( 26 sec) [ -6856.0087] [Branch lengths ] . ( 26 sec) [ -6855.9935] [Ts/ts ratio ][ 3.524679] . ( 36 sec) [ -6855.9831] [ 958] [depth= 1] . ( 36 sec) [ -6855.9565] [ 958] [depth= 1] . ( 37 sec) [ -6855.7400] [ 959] [depth= 2] . ( 40 sec) [ -6855.3511] [Branch lengths ] . ( 40 sec) [ -6855.3421] [Ts/ts ratio ][ 3.557529] . ( 82 sec) [ -6855.3210] [Branch lengths ] . ( 82 sec) [ -6855.3210] [Topology ] . ( 83 sec) [ -6855.3199] [Topology ] . ( 84 sec) [ -6855.3195] [Topology ] . ( 85 sec) [ -6855.3195] [Ts/ts ratio ][ 3.561086] . ( 85 sec) [ -6855.3195] [Topology ] . ( 86 sec) [ -6855.3194] [Topology ] . ( 86 sec) [ -6855.3194] [Ts/ts ratio ][ 3.561086] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -6855.319391. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 96.708428 1.000000 0.069081 99 49.536946 0.985000 0.019110 67 8.922027 0.853000 0.004285 97 44.168275 0.985000 0.017447 77 13.492182 0.902000 0.008143 33 2.346870 0.633000 0.003620 41 1.167996 0.337000 0.002441 97 29.204755 0.971000 0.016647 62 5.612996 0.533000 0.004397 44 4.049145 0.773000 0.003236 69 7.647245 0.855000 0.005932 76 19.931367 0.886000 0.008041 43 2.099074 0.297000 0.001381 42 3.125284 0.569000 0.005873 100 149.585247 1.000000 0.033510 36 -1.000000 0.000000 0.000000 93 28.059690 0.944000 0.011271 52 10.775751 0.877000 0.005060 68 16.325714 0.893000 0.006403 71 10.838199 0.830000 0.007757 64 11.767393 0.789000 0.009489 86 26.202324 0.953000 0.007636 98 54.875030 0.992000 0.016100 99 35.349926 0.985000 0.014284 82 5.084359 0.836000 0.003524 73 10.701428 0.799000 0.003972 92 11.929241 0.866000 0.004302 94 29.094968 0.938000 0.008213 56 7.756997 0.816000 0.006526 100 97.150950 0.999000 0.026350 71 12.956843 0.900000 0.006420 42 8.261846 0.750000 0.004220 80 18.708436 0.914000 0.008133 96 11.845525 0.855000 0.005654 100 65.619988 0.996000 0.016626 99 49.535826 0.976000 0.013168 64 1.511478 0.680000 0.002754 100 102.433821 1.000000 0.021583 82 4.371742 0.733000 0.004571 100 117.420180 1.000000 0.027019 93 44.032684 0.985000 0.014822 100 21.852825 0.952000 0.007870 100 94.082832 0.997000 0.017840 100 62.425625 0.995000 0.013293 12 -1.000000 0.000000 0.000000 47 10.537483 0.838000 0.001309 11 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 24 -1.000000 0.000000 0.000000 100 86.244239 0.998000 0.012067 21 -1.000000 0.000000 0.000000 44 5.544553 0.636000 0.001334 47 18.000066 0.925000 0.005193 15 -1.000000 0.000000 0.000000 92 72.825835 0.996000 0.012094 45 3.049658 0.761000 0.001246 49 10.108384 0.848000 0.001311 16 -1.000000 0.000000 0.000000 84 29.738065 0.933000 0.002631 23 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2567_64x1044_2006.phy_phyml_tree.txt'... . Time used 2h17m4s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo