.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2764_57x803_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 628 patterns found. (out of a total of 803 sites) . 286 sites without polymorphism (35.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10371.9103] [Ts/ts ratio ][ 1.920862] . ( 1 sec) [ -10368.8808] [ 1955] [depth= 1] . ( 1 sec) [ -10360.9028] [ 1953] [depth= 2] . ( 3 sec) [ -10360.3038] [ 1957] [depth= 1] . ( 3 sec) [ -10357.3237] [ 1953] [depth= 1] . ( 3 sec) [ -10356.5329] [ 1953] [depth= 1] . ( 3 sec) [ -10355.6924] [ 1954] [depth= 1] . ( 3 sec) [ -10354.1988] [ 1954] [depth= 1] . ( 4 sec) [ -10353.9535] [ 1954] [depth= 1] . ( 4 sec) [ -10353.7144] [ 1954] [depth= 1] . ( 4 sec) [ -10353.6824] [ 1954] [depth= 1] . ( 4 sec) [ -10341.5307] [ 1950] [depth= 1] . ( 4 sec) [ -10340.8153] [ 1952] [depth= 1] . ( 4 sec) [ -10337.3673] [ 1954] [depth= 2] . ( 5 sec) [ -10336.1400] [ 1955] [depth= 1] . ( 5 sec) [ -10333.6528] [ 1954] [depth= 1] . ( 5 sec) [ -10333.4225] [ 1955] [depth= 1] . ( 6 sec) [ -10333.1919] [ 1955] [depth= 1] . ( 6 sec) [ -10330.5650] [ 1958] [depth= 2] . ( 6 sec) [ -10330.4135] [ 1958] [depth= 1] . ( 6 sec) [ -10327.4213] [ 1956] [depth= 2] . ( 6 sec) [ -10327.3176] [ 1956] [depth= 1] . ( 7 sec) [ -10325.9091] [ 1959] [depth= 2] . ( 7 sec) [ -10324.6339] [ 1957] [depth= 1] . ( 7 sec) [ -10315.9611] [ 1953] [depth= 1] . ( 8 sec) [ -10312.8714] [ 1952] [depth= 1] . ( 8 sec) [ -10312.7589] [ 1953] [depth= 1] . ( 8 sec) [ -10311.5974] [ 1954] [depth= 1] . ( 9 sec) [ -10311.0164] [ 1954] [depth= 1] . ( 9 sec) [ -10306.8879] [ 1954] [depth= 1] . ( 9 sec) [ -10305.6952] [ 1954] [depth= 1] . ( 9 sec) [ -10303.0164] [ 1954] [depth= 1] . ( 9 sec) [ -10298.5451] [ 1950] [depth= 1] . ( 9 sec) [ -10297.8964] [ 1953] [depth= 1] . ( 10 sec) [ -10296.5630] [ 1950] [depth= 1] . ( 10 sec) [ -10296.4957] [ 1950] [depth= 1] . ( 10 sec) [ -10296.3615] [ 1950] [depth= 1] . ( 11 sec) [ -10294.9784] [ 1952] [depth= 1] . ( 11 sec) [ -10292.2274] [ 1953] [depth= 1] . ( 11 sec) [ -10291.8438] [ 1955] [depth= 1] . ( 11 sec) [ -10291.3693] [ 1955] [depth= 2] . ( 11 sec) [ -10291.0589] [ 1956] [depth= 1] . ( 12 sec) [ -10290.6036] [ 1956] [depth= 1] . ( 12 sec) [ -10289.4283] [ 1956] [depth= 1] . ( 13 sec) [ -10289.1694] [ 1956] [depth= 1] . ( 14 sec) [ -10236.7530] [Branch lengths ] . ( 14 sec) [ -10236.6307] [Ts/ts ratio ][ 1.969459] . ( 14 sec) [ -10236.3397] [ 1956] [depth= 1] . ( 16 sec) [ -10234.8651] [ 1954] [depth= 1] . ( 17 sec) [ -10234.5659] [ 1955] [depth= 1] . ( 17 sec) [ -10234.0471] [ 1955] [depth= 1] . ( 17 sec) [ -10233.9473] [ 1955] [depth= 2] . ( 17 sec) [ -10232.7174] [ 1954] [depth= 2] . ( 19 sec) [ -10232.4993] [ 1954] [depth= 1] . ( 19 sec) [ -10229.6174] [ 1952] [depth= 1] . ( 20 sec) [ -10229.4793] [ 1952] [depth= 1] . ( 20 sec) [ -10229.4075] [ 1954] [depth= 1] . ( 21 sec) [ -10229.1355] [ 1956] [depth= 1] . ( 23 sec) [ -10229.0714] [ 1954] [depth= 1] . ( 23 sec) [ -10228.5145] [ 1952] [depth= 1] . ( 24 sec) [ -10227.6462] [ 1951] [depth= 1] . ( 28 sec) [ -10227.0565] [ 1951] [depth= 1] . ( 30 sec) [ -10226.8616] [ 1950] [depth= 1] . ( 31 sec) [ -10218.7824] [Branch lengths ] . ( 31 sec) [ -10218.7423] [Ts/ts ratio ][ 1.998078] . ( 49 sec) [ -10217.9397] [Branch lengths ] . ( 77 sec) [ -10217.5902] [ 1948] [depth= 1] . ( 78 sec) [ -10217.5098] [ 1947] [depth= 1] . ( 112 sec) [ -10216.9727] [Branch lengths ] . ( 112 sec) [ -10216.9725] [Ts/ts ratio ][ 2.000233] . ( 112 sec) [ -10216.9725] [Topology ] . ( 114 sec) [ -10216.9448] [Topology ] . ( 115 sec) [ -10216.9359] [Topology ] . ( 117 sec) [ -10216.9314] [Topology ] . ( 119 sec) [ -10216.9291] [Topology ] . ( 120 sec) [ -10216.9278] [Topology ] . ( 122 sec) [ -10216.9272] [Topology ] . ( 122 sec) [ -10216.9271] [Ts/ts ratio ][ 2.002233] . ( 122 sec) [ -10216.9271] [Topology ] . ( 124 sec) [ -10216.9267] [Topology ] . ( 124 sec) [ -10216.9267] [Ts/ts ratio ][ 2.002233] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10216.926662. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 149.197403 1.000000 0.050881 48 0.439531 0.047000 0.005816 100 73.005568 0.997000 0.038787 99 44.947961 0.990000 0.024380 54 1.608570 0.397000 0.002713 73 2.408712 0.729000 0.003357 91 19.509243 0.936000 0.019602 39 0.019583 0.000000 0.003953 100 42.150756 0.998000 0.041918 61 4.760787 0.655000 0.009786 90 25.277968 0.950000 0.020067 100 134.787214 1.000000 0.110726 48 0.070312 0.000000 0.001152 59 22.670500 0.918000 0.024896 96 28.177882 0.979000 0.053090 100 27.197519 0.977000 0.042794 93 7.457128 0.852000 0.010762 47 1.441428 0.684000 0.004696 91 50.145665 0.996000 0.103576 82 17.424315 0.933000 0.070797 89 18.476434 0.951000 0.070556 93 29.041482 0.972000 0.029886 61 3.274787 0.445000 0.010366 99 37.911647 0.974000 0.024423 100 29.977355 0.971000 0.023607 96 27.003598 0.958000 0.019604 49 7.197983 0.838000 0.013415 22 0.278238 0.574000 0.002566 52 8.866345 0.882000 0.015718 48 10.709843 0.909000 0.012741 100 103.820872 1.000000 0.066932 79 3.860278 0.792000 0.006719 94 17.991795 0.926000 0.012389 64 1.880584 0.737000 0.003358 30 0.540803 0.130000 0.006635 78 19.833455 0.952000 0.020701 88 34.493834 0.986000 0.028810 74 4.693951 0.766000 0.003603 27 -1.000000 0.000000 0.000000 89 25.916075 0.984000 0.043700 27 0.544670 0.650000 0.005369 65 30.440395 0.965000 0.020939 54 15.684210 0.906000 0.017396 94 37.906492 0.972000 0.022530 38 2.035124 0.294000 0.013033 55 4.700527 0.773000 0.008755 26 3.163135 0.547000 0.004114 20 3.978315 0.815000 0.008612 41 6.671850 0.837000 0.012545 87 42.822853 0.990000 0.032798 9 0.759317 0.701000 0.001351 59 16.140676 0.908000 0.009773 100 147.770446 1.000000 0.053806 65 1.165308 0.694000 0.004307 . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Time used 3h43m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo