.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2901_56x1802_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... . 642 patterns found. (out of a total of 1802 sites) . 1363 sites without polymorphism (75.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -8111.9346] [Ts/ts ratio ][ 3.118606] . ( 1 sec) [ -8111.8844] [ 947] [depth= 1] . ( 1 sec) [ -8104.3610] [ 944] [depth= 1] . ( 1 sec) [ -8102.6159] [ 947] [depth= 1] . ( 2 sec) [ -8102.4336] [ 944] [depth= 1] . ( 2 sec) [ -8102.4194] [ 947] [depth= 1] . ( 2 sec) [ -8097.6188] [ 944] [depth= 1] . ( 3 sec) [ -8093.2102] [ 944] [depth= 2] . ( 3 sec) [ -8061.1203] [ 935] [depth= 12] . ( 3 sec) [ -8060.8233] [ 935] [depth= 1] . ( 3 sec) [ -8059.0817] [ 935] [depth= 1] . ( 3 sec) [ -8058.5265] [ 935] [depth= 1] . ( 3 sec) [ -8058.2804] [ 935] [depth= 2] . ( 4 sec) [ -8057.8069] [ 935] [depth= 2] . ( 5 sec) [ -8045.4432] [ 932] [depth= 3] . ( 5 sec) [ -8040.5126] [ 931] [depth= 1] . ( 10 sec) [ -8030.0215] [ 927] [depth= 3] . ( 10 sec) [ -8021.0976] [ 925] [depth= 3] . ( 10 sec) [ -8018.2595] [ 926] [depth= 7] . ( 11 sec) [ -8015.4695] [ 924] [depth= 1] . ( 12 sec) [ -8009.1510] [ 924] [depth= 3] . ( 12 sec) [ -7998.9252] [ 920] [depth= 1] . ( 12 sec) [ -7997.2471] [ 921] [depth= 1] . ( 13 sec) [ -7996.7569] [ 923] [depth= 2] . ( 14 sec) [ -7989.4078] [ 921] [depth= 1] . ( 14 sec) [ -7980.9500] [ 918] [depth= 6] . ( 15 sec) [ -7979.9932] [ 918] [depth= 1] . ( 17 sec) [ -7978.9413] [ 918] [depth= 1] . ( 17 sec) [ -7975.5844] [ 918] [depth= 3] . ( 18 sec) [ -7972.9094] [ 917] [depth= 2] . ( 19 sec) [ -7972.8765] [ 917] [depth= 1] . ( 19 sec) [ -7972.0802] [ 917] [depth= 1] . ( 19 sec) [ -7971.6310] [ 917] [depth= 2] . ( 20 sec) [ -7971.5360] [ 917] [depth= 2] . ( 20 sec) [ -7971.3820] [ 917] [depth= 4] . ( 20 sec) [ -7970.9462] [ 917] [depth= 5] . ( 22 sec) [ -7969.9694] [ 917] [depth= 1] . ( 22 sec) [ -7968.1694] [ 917] [depth= 2] . ( 22 sec) [ -7966.1788] [ 916] [depth= 6] . ( 22 sec) [ -7964.4599] [ 916] [depth= 1] . ( 23 sec) [ -7957.7382] [ 914] [depth= 4] . ( 24 sec) [ -7954.3548] [ 914] [depth= 1] . ( 25 sec) [ -7954.3218] [ 914] [depth= 3] . ( 25 sec) [ -7954.1212] [ 914] [depth= 1] . ( 25 sec) [ -7950.7747] [ 915] [depth= 11] . ( 29 sec) [ -7950.5685] [ 915] [depth= 2] . ( 29 sec) [ -7949.8500] [ 913] [depth= 2] . ( 29 sec) [ -7949.1496] [ 913] [depth= 1] . ( 29 sec) [ -7948.8311] [ 912] [depth= 2] . ( 30 sec) [ -7948.6483] [ 912] [depth= 1] . ( 30 sec) [ -7948.6323] [ 913] [depth= 1] . ( 30 sec) [ -7948.5550] [ 913] [depth= 1] . ( 32 sec) [ -7926.8102] [Branch lengths ] . ( 32 sec) [ -7926.8036] [Ts/ts ratio ][ 3.143584] . ( 34 sec) [ -7925.5887] [ 913] [depth= 7] . ( 34 sec) [ -7925.5216] [ 913] [depth= 1] . ( 42 sec) [ -7925.1955] [ 912] [depth= 1] . ( 44 sec) [ -7914.8838] [ 909] [depth= 7] . ( 45 sec) [ -7914.5183] [ 909] [depth= 1] . ( 45 sec) [ -7912.9397] [ 908] [depth= 4] . ( 49 sec) [ -7912.8783] [ 908] [depth= 1] . ( 53 sec) [ -7912.4315] [ 908] [depth= 1] . ( 57 sec) [ -7912.3997] [ 908] [depth= 3] . ( 57 sec) [ -7911.5876] [ 909] [depth= 7] . ( 57 sec) [ -7911.5352] [ 909] [depth= 1] . ( 58 sec) [ -7911.4352] [ 909] [depth= 3] . ( 58 sec) [ -7911.3707] [ 909] [depth= 1] . ( 65 sec) [ -7911.3560] [ 909] [depth= 1] . ( 68 sec) [ -7911.3436] [ 909] [depth= 1] . ( 68 sec) [ -7911.1947] [ 909] [depth= 1] . ( 70 sec) [ -7911.0820] [ 909] [depth= 1] . ( 71 sec) [ -7907.8377] [Branch lengths ] . ( 71 sec) [ -7907.8144] [Ts/ts ratio ][ 3.191131] . ( 87 sec) [ -7907.5525] [ 911] [depth= 3] . ( 94 sec) [ -7907.5195] [ 911] [depth= 1] . ( 121 sec) [ -7906.6996] [Branch lengths ] . ( 121 sec) [ -7906.6914] [Ts/ts ratio ][ 3.218239] . ( 173 sec) [ -7906.6821] [Branch lengths ] . ( 243 sec) [ -7906.6774] [Branch lengths ] . ( 243 sec) [ -7906.6774] [Topology ] . ( 245 sec) [ -7906.6754] [Topology ] . ( 246 sec) [ -7906.6736] [Topology ] . ( 248 sec) [ -7906.6719] [Topology ] . ( 249 sec) [ -7906.6702] [Topology ] . ( 251 sec) [ -7906.6684] [Topology ] . ( 252 sec) [ -7906.6667] [Topology ] . ( 253 sec) [ -7906.6667] [Ts/ts ratio ][ 3.221458] . ( 253 sec) [ -7906.6667] [Topology ] . ( 254 sec) [ -7906.6650] [Topology ] . ( 256 sec) [ -7906.6633] [Topology ] . ( 257 sec) [ -7906.6616] [Topology ] . ( 259 sec) [ -7906.6606] [Topology ] . ( 260 sec) [ -7906.6602] [Topology ] . ( 260 sec) [ -7906.6602] [Ts/ts ratio ][ 3.221458] . ( 261 sec) [ -7906.6602] [Topology ] . ( 262 sec) [ -7906.6600] [Topology ] . ( 262 sec) [ -7906.6600] [Ts/ts ratio ][ 3.221458] . Checking for NNIs, optimizing five branches... . ( 274 sec) [ -7906.6385] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7906.638504. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 73 7.488715 0.716000 0.006364 100 448.355888 1.000000 0.072465 100 48.750214 0.996000 0.016982 65 7.981058 0.643000 0.008746 75 3.853809 0.732000 0.005805 97 47.240120 0.981000 0.012979 100 49.153050 0.977000 0.009470 53 26.352273 0.917000 0.008126 21 2.515649 0.737000 0.002972 23 5.234371 0.822000 0.003820 52 91.033473 1.000000 0.011370 20 -1.000000 0.000000 0.000000 5 0.532982 0.689000 0.001516 1 -1.000000 0.000000 0.000000 1 7.080371 0.428000 0.003758 1 16.751811 0.907000 0.004134 67 41.420814 0.976000 0.006740 36 4.787951 0.460000 0.002570 3 3.229750 0.726000 0.001886 48 43.285705 0.978000 0.013537 19 0.002802 0.000000 0.001415 50 0.000216 0.000000 0.003446 24 8.449933 0.644000 0.005457 9 -1.000000 0.000000 0.000000 39 18.017199 0.888000 0.001358 0 6.371756 0.678000 0.003530 0 2.095934 0.732000 0.000941 15 20.858731 0.905000 0.003868 24 10.811917 0.872000 0.002607 100 70.599599 0.997000 0.017570 26 4.340265 0.771000 0.002311 71 13.752216 0.872000 0.003589 27 0.042996 0.000000 0.003095 0 11.722979 0.878000 0.002351 1 26.271023 0.921000 0.003901 55 16.288645 0.919000 0.005045 100 22.628278 0.929000 0.006036 2 0.116539 0.000000 0.000890 0 -1.000000 0.000000 0.000002 68 130.702500 1.000000 0.011739 43 7.578194 0.793000 0.000672 64 9.442080 0.855000 0.003665 1 -1.000000 0.000000 0.000000 22 18.641775 0.924000 0.003465 64 30.667063 0.955000 0.005301 18 3.850039 0.726000 0.000840 23 2.933787 0.739000 0.000797 38 24.967876 0.892000 0.002373 54 17.241792 0.917000 0.004777 12 -1.000000 0.000000 0.000000 100 152.518137 1.000000 0.025859 47 6.278970 0.800000 0.003388 6 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2901_56x1802_2006.phy_phyml_tree.txt'... . Time used 5h57m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo