.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2675_51x1537_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... . 607 patterns found. (out of a total of 1537 sites) . 978 sites without polymorphism (63.63%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8099.9867] [Ts/ts ratio ][ 3.275679] . ( 1 sec) [ -8099.6386] [ 1200] [depth= 1] . ( 2 sec) [ -8097.5677] [ 1202] [depth= 1] . ( 2 sec) [ -8095.3732] [ 1201] [depth= 1] . ( 2 sec) [ -8095.1721] [ 1201] [depth= 1] . ( 2 sec) [ -8094.9373] [ 1201] [depth= 1] . ( 2 sec) [ -8094.3744] [ 1200] [depth= 2] . ( 3 sec) [ -8092.1575] [ 1200] [depth= 1] . ( 3 sec) [ -8091.2432] [ 1200] [depth= 1] . ( 3 sec) [ -8090.9380] [ 1200] [depth= 1] . ( 3 sec) [ -8090.8454] [ 1200] [depth= 1] . ( 3 sec) [ -8090.7711] [ 1200] [depth= 2] . ( 4 sec) [ -8081.3682] [ 1200] [depth= 1] . ( 4 sec) [ -8073.3512] [ 1198] [depth= 1] . ( 4 sec) [ -8058.3249] [ 1198] [depth= 1] . ( 4 sec) [ -8058.2170] [ 1198] [depth= 2] . ( 4 sec) [ -8055.0593] [ 1197] [depth= 3] . ( 4 sec) [ -8052.9233] [ 1197] [depth= 1] . ( 5 sec) [ -8052.8971] [ 1197] [depth= 2] . ( 5 sec) [ -8051.3004] [ 1197] [depth= 1] . ( 5 sec) [ -8051.2348] [ 1197] [depth= 2] . ( 5 sec) [ -8051.2145] [ 1197] [depth= 1] . ( 5 sec) [ -8047.6723] [ 1197] [depth= 4] . ( 5 sec) [ -8037.6996] [ 1195] [depth= 2] . ( 5 sec) [ -8037.6399] [ 1195] [depth= 2] . ( 6 sec) [ -8037.4497] [ 1195] [depth= 1] . ( 6 sec) [ -8021.7534] [ 1194] [depth= 1] . ( 6 sec) [ -8015.1808] [ 1193] [depth= 2] . ( 6 sec) [ -7987.6931] [ 1194] [depth= 1] . ( 7 sec) [ -7970.9834] [ 1205] [depth= 2] . ( 7 sec) [ -7964.2815] [ 1202] [depth= 1] . ( 7 sec) [ -7956.6025] [ 1192] [depth= 2] . ( 7 sec) [ -7953.1012] [ 1193] [depth= 1] . ( 8 sec) [ -7950.4101] [ 1195] [depth= 1] . ( 8 sec) [ -7948.0290] [ 1194] [depth= 2] . ( 10 sec) [ -7948.0186] [ 1194] [depth= 1] . ( 10 sec) [ -7947.9950] [ 1194] [depth= 2] . ( 11 sec) [ -7947.3400] [ 1194] [depth= 1] . ( 12 sec) [ -7915.3361] [Branch lengths ] . ( 12 sec) [ -7914.5277] [Ts/ts ratio ][ 3.551642] . ( 13 sec) [ -7913.8446] [ 1192] [depth= 1] . ( 14 sec) [ -7913.8274] [ 1192] [depth= 2] . ( 15 sec) [ -7913.7072] [ 1192] [depth= 1] . ( 20 sec) [ -7911.7002] [ 1190] [depth= 1] . ( 22 sec) [ -7910.8555] [ 1190] [depth= 1] . ( 25 sec) [ -7908.1953] [Branch lengths ] . ( 26 sec) [ -7908.1948] [Ts/ts ratio ][ 3.542545] . ( 40 sec) [ -7908.0796] [Branch lengths ] . ( 81 sec) [ -7908.0694] [Branch lengths ] . ( 81 sec) [ -7908.0694] [Topology ] . ( 82 sec) [ -7908.0685] [Topology ] . ( 82 sec) [ -7908.0680] [Ts/ts ratio ][ 3.549188] . ( 82 sec) [ -7908.0680] [Topology ] . ( 84 sec) [ -7908.0677] [Topology ] . ( 84 sec) [ -7908.0677] [Ts/ts ratio ][ 3.549188] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7908.067701. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 499.998765 1.000000 0.286302 81 26.547726 0.979000 0.053908 74 10.624918 0.881000 0.018813 100 78.171601 1.000000 0.046243 80 3.480750 0.751000 0.000886 100 204.732785 1.000000 0.096125 54 -1.000000 0.000000 0.000000 66 6.073526 0.763000 0.001667 13 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 53 15.160987 0.865000 0.000826 49 5.546022 0.743000 0.000828 71 19.953725 0.917000 0.001662 56 8.801152 0.864000 0.019999 99 189.070502 1.000000 0.074804 100 28.559533 0.959000 0.007307 97 44.287106 0.969000 0.004227 27 -1.000000 0.000000 0.000000 62 1.208487 0.166000 0.004629 94 25.735345 0.952000 0.026001 100 90.153890 1.000000 0.046116 100 68.046139 0.995000 0.030303 100 55.061648 0.997000 0.025823 99 26.439736 0.983000 0.023486 100 102.593326 1.000000 0.039866 24 -1.000000 0.000000 0.000000 19 -1.000000 0.000000 0.000000 100 65.366907 0.996000 0.030672 100 59.256685 0.995000 0.020038 52 1.642583 0.435000 0.000927 26 1.721850 0.113000 0.001608 100 49.997131 0.995000 0.019430 76 10.184397 0.925000 0.037199 63 7.098597 0.791000 0.017695 100 155.451304 1.000000 0.068310 98 92.798522 1.000000 0.048967 97 9.716239 0.898000 0.004387 55 2.834604 0.525000 0.003051 47 1.880231 0.220000 0.001015 100 52.018719 0.983000 0.006934 84 14.901840 0.878000 0.003078 93 28.444253 0.945000 0.004532 7 -1.000000 0.000000 0.000000 12 -1.000000 0.000000 0.000000 16 -1.000000 0.000000 0.000000 75 7.275727 0.858000 0.014474 100 205.823693 1.000000 0.084922 100 61.233879 0.997000 0.034389 . Printing the most likely tree in file 'nucleic_M2675_51x1537_2006.phy_phyml_tree.txt'... . Time used 2h31m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo