.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2566_73x918_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... . 541 patterns found. (out of a total of 918 sites) . 442 sites without polymorphism (48.15%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -12547.6816] [Ts/ts ratio ][ 3.712991] . ( 1 sec) [ -12546.1576] [ 2346] [depth= 1] . ( 1 sec) [ -12534.7958] [ 2339] [depth= 1] . ( 1 sec) [ -12516.9718] [ 2331] [depth= 3] . ( 2 sec) [ -12504.8249] [ 2329] [depth= 2] . ( 2 sec) [ -12503.9847] [ 2328] [depth= 1] . ( 3 sec) [ -12501.0676] [ 2335] [depth= 1] . ( 3 sec) [ -12493.5787] [ 2328] [depth= 1] . ( 3 sec) [ -12491.9078] [ 2331] [depth= 1] . ( 3 sec) [ -12488.0710] [ 2328] [depth= 1] . ( 4 sec) [ -12487.4054] [ 2329] [depth= 1] . ( 4 sec) [ -12487.3573] [ 2328] [depth= 1] . ( 5 sec) [ -12486.6574] [ 2327] [depth= 1] . ( 5 sec) [ -12482.3520] [ 2328] [depth= 1] . ( 5 sec) [ -12477.8989] [ 2328] [depth= 1] . ( 5 sec) [ -12470.4120] [ 2328] [depth= 1] . ( 6 sec) [ -12465.0536] [ 2328] [depth= 1] . ( 6 sec) [ -12460.6164] [ 2331] [depth= 2] . ( 6 sec) [ -12459.1495] [ 2330] [depth= 1] . ( 6 sec) [ -12452.7720] [ 2330] [depth= 1] . ( 7 sec) [ -12446.9705] [ 2323] [depth= 1] . ( 8 sec) [ -12442.6912] [ 2321] [depth= 1] . ( 8 sec) [ -12439.0284] [ 2321] [depth= 1] . ( 8 sec) [ -12434.3857] [ 2323] [depth= 1] . ( 9 sec) [ -12423.5194] [ 2321] [depth= 1] . ( 9 sec) [ -12419.7560] [ 2321] [depth= 1] . ( 9 sec) [ -12406.5300] [ 2313] [depth= 2] . ( 9 sec) [ -12400.4840] [ 2311] [depth= 1] . ( 9 sec) [ -12399.6199] [ 2312] [depth= 2] . ( 9 sec) [ -12386.7190] [ 2314] [depth= 1] . ( 10 sec) [ -12385.6419] [ 2313] [depth= 1] . ( 10 sec) [ -12379.5962] [ 2314] [depth= 1] . ( 10 sec) [ -12376.0690] [ 2313] [depth= 1] . ( 10 sec) [ -12374.7070] [ 2318] [depth= 1] . ( 10 sec) [ -12363.3372] [ 2319] [depth= 1] . ( 11 sec) [ -12361.6580] [ 2318] [depth= 1] . ( 12 sec) [ -12358.3593] [ 2314] [depth= 2] . ( 12 sec) [ -12356.9088] [ 2314] [depth= 1] . ( 12 sec) [ -12349.7796] [ 2314] [depth= 1] . ( 13 sec) [ -12347.5672] [ 2313] [depth= 2] . ( 13 sec) [ -12346.3397] [ 2314] [depth= 1] . ( 13 sec) [ -12345.3043] [ 2319] [depth= 1] . ( 13 sec) [ -12344.9507] [ 2318] [depth= 1] . ( 13 sec) [ -12343.9060] [ 2319] [depth= 1] . ( 13 sec) [ -12343.0054] [ 2320] [depth= 1] . ( 14 sec) [ -12342.1771] [ 2321] [depth= 1] . ( 14 sec) [ -12341.1529] [ 2330] [depth= 1] . ( 14 sec) [ -12340.3028] [ 2334] [depth= 5] . ( 14 sec) [ -12338.2081] [ 2336] [depth= 1] . ( 14 sec) [ -12327.9797] [ 2334] [depth= 1] . ( 15 sec) [ -12325.8398] [ 2333] [depth= 2] . ( 15 sec) [ -12322.6658] [ 2332] [depth= 1] . ( 15 sec) [ -12316.4183] [ 2332] [depth= 2] . ( 16 sec) [ -12310.5592] [ 2330] [depth= 1] . ( 16 sec) [ -12309.9502] [ 2330] [depth= 1] . ( 16 sec) [ -12309.5241] [ 2330] [depth= 1] . ( 17 sec) [ -12309.4825] [ 2330] [depth= 1] . ( 17 sec) [ -12309.4463] [ 2330] [depth= 1] . ( 19 sec) [ -12213.9057] [Branch lengths ] . ( 20 sec) [ -12210.7551] [Ts/ts ratio ][ 4.154009] . ( 20 sec) [ -12210.6746] [ 2325] [depth= 1] . ( 23 sec) [ -12209.7827] [ 2325] [depth= 1] . ( 25 sec) [ -12207.5101] [ 2324] [depth= 1] . ( 26 sec) [ -12206.6793] [ 2329] [depth= 1] . ( 32 sec) [ -12205.9533] [ 2324] [depth= 1] . ( 34 sec) [ -12197.5020] [ 2321] [depth= 5] . ( 40 sec) [ -12185.9457] [Branch lengths ] . ( 40 sec) [ -12185.8288] [Ts/ts ratio ][ 4.245092] . ( 42 sec) [ -12178.7302] [ 2312] [depth= 1] . ( 42 sec) [ -12178.4069] [ 2313] [depth= 1] . ( 60 sec) [ -12174.5499] [Branch lengths ] . ( 60 sec) [ -12174.5148] [Ts/ts ratio ][ 4.295947] . ( 80 sec) [ -12174.0288] [Branch lengths ] . ( 158 sec) [ -12173.9469] [Branch lengths ] . ( 158 sec) [ -12173.9469] [Topology ] . ( 160 sec) [ -12173.9383] [Topology ] . ( 161 sec) [ -12173.9351] [Topology ] . ( 163 sec) [ -12173.9335] [Topology ] . ( 165 sec) [ -12173.9327] [Topology ] . ( 165 sec) [ -12173.9205] [Ts/ts ratio ][ 4.326195] . ( 165 sec) [ -12173.9205] [Topology ] . ( 167 sec) [ -12173.9194] [Topology ] . ( 168 sec) [ -12173.9188] [Topology ] . ( 169 sec) [ -12173.9188] [Ts/ts ratio ][ 4.326195] . ( 169 sec) [ -12173.9188] [Topology ] . ( 170 sec) [ -12173.9185] [Topology ] . ( 171 sec) [ -12173.9185] [Ts/ts ratio ][ 4.326195] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12173.918492. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 70.723099 0.999000 0.074401 100 92.271840 1.000000 0.081263 99 13.495254 0.906000 0.024930 89 31.255104 0.974000 0.041855 88 31.336829 0.980000 0.037651 49 11.391967 0.886000 0.019671 33 2.339561 0.675000 0.010186 50 3.913082 0.550000 0.018685 80 13.609822 0.900000 0.026738 99 58.737135 0.996000 0.060933 99 73.192763 1.000000 0.061287 88 20.293374 0.939000 0.029345 100 75.671584 1.000000 0.059709 65 5.145706 0.596000 0.014103 90 13.396972 0.925000 0.021996 55 8.495279 0.857000 0.014363 44 1.576333 0.590000 0.003548 90 10.865944 0.887000 0.019102 86 16.473905 0.910000 0.022202 69 2.040718 0.483000 0.005395 99 41.448136 0.977000 0.038624 27 2.211687 0.379000 0.013496 14 4.655400 0.808000 0.016117 100 151.555265 1.000000 0.090637 97 40.246453 0.980000 0.027936 100 85.317520 0.999000 0.053667 66 2.423071 0.743000 0.004409 23 10.166306 0.871000 0.022218 77 39.126338 0.971000 0.039769 68 13.479263 0.895000 0.018367 41 1.951529 0.272000 0.008027 64 2.971483 0.780000 0.003751 82 28.211237 0.971000 0.023078 100 45.203615 0.992000 0.027088 37 1.293795 0.352000 0.006939 67 13.103665 0.895000 0.021476 51 1.607984 0.244000 0.016829 98 89.431084 1.000000 0.092535 100 39.212226 0.986000 0.048054 59 26.783489 0.973000 0.037272 50 8.948233 0.882000 0.013543 71 19.143102 0.962000 0.018218 77 37.027958 0.972000 0.023786 44 15.394564 0.914000 0.014925 73 33.971576 0.974000 0.036066 99 65.225330 0.997000 0.067671 67 16.151921 0.875000 0.031833 100 33.327071 0.969000 0.033995 86 37.048807 0.986000 0.045747 57 5.007816 0.826000 0.006281 36 0.627233 0.059000 0.005356 47 4.234798 0.724000 0.003826 71 9.023737 0.859000 0.007948 69 12.427324 0.817000 0.004454 44 0.983494 0.226000 0.003542 91 41.473038 0.988000 0.018447 37 2.495716 0.272000 0.003758 54 1.860021 0.728000 0.002710 77 28.559102 0.954000 0.007545 24 -1.000000 0.000000 0.000000 52 6.601962 0.780000 0.002658 34 14.095407 0.906000 0.035939 67 0.191279 0.000000 0.006232 100 125.894974 1.000000 0.155016 54 0.830451 0.102000 0.028906 71 26.247879 0.960000 0.058353 89 6.721837 0.861000 0.019212 16 1.371974 0.118000 0.019979 47 8.134981 0.599000 0.019414 39 11.244489 0.741000 0.027262 . Printing the most likely tree in file 'nucleic_M2566_73x918_2006.phy_phyml_tree.txt'... . Time used 4h29m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo