.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2772_77x900_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 . 57 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 575 patterns found. (out of a total of 900 sites) . 459 sites without polymorphism (51.00%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -7444.6384] [Ts/ts ratio ][ 1.645943] . ( 1 sec) [ -7439.2841] [ 1225] [depth= 1] . ( 1 sec) [ -7438.3118] [ 1225] [depth= 1] . ( 1 sec) [ -7421.3467] [ 1223] [depth= 1] . ( 2 sec) [ -7421.0758] [ 1223] [depth= 1] . ( 2 sec) [ -7420.9409] [ 1223] [depth= 1] . ( 2 sec) [ -7420.5799] [ 1223] [depth= 2] . ( 2 sec) [ -7419.9921] [ 1224] [depth= 1] . ( 2 sec) [ -7418.1252] [ 1224] [depth= 2] . ( 2 sec) [ -7416.6089] [ 1223] [depth= 1] . ( 3 sec) [ -7412.3379] [ 1222] [depth= 1] . ( 3 sec) [ -7412.1474] [ 1222] [depth= 1] . ( 3 sec) [ -7411.9530] [ 1222] [depth= 1] . ( 4 sec) [ -7408.9603] [ 1221] [depth= 1] . ( 4 sec) [ -7406.4903] [ 1221] [depth= 1] . ( 4 sec) [ -7406.4672] [ 1221] [depth= 1] . ( 4 sec) [ -7405.7659] [ 1221] [depth= 1] . ( 4 sec) [ -7404.2846] [ 1221] [depth= 1] . ( 4 sec) [ -7404.1032] [ 1221] [depth= 1] . ( 4 sec) [ -7399.6413] [ 1219] [depth= 1] . ( 5 sec) [ -7399.6226] [ 1219] [depth= 1] . ( 5 sec) [ -7396.6961] [ 1218] [depth= 1] . ( 5 sec) [ -7395.0754] [ 1218] [depth= 1] . ( 6 sec) [ -7394.2917] [ 1219] [depth= 1] . ( 6 sec) [ -7393.9361] [ 1218] [depth= 1] . ( 6 sec) [ -7392.4576] [ 1218] [depth= 1] . ( 7 sec) [ -7388.1585] [ 1218] [depth= 1] . ( 7 sec) [ -7387.2222] [ 1221] [depth= 1] . ( 7 sec) [ -7386.2104] [ 1222] [depth= 1] . ( 7 sec) [ -7374.9284] [ 1221] [depth= 1] . ( 8 sec) [ -7373.8503] [ 1224] [depth= 1] . ( 8 sec) [ -7368.0367] [ 1221] [depth= 1] . ( 8 sec) [ -7362.5678] [ 1221] [depth= 1] . ( 8 sec) [ -7356.8395] [ 1221] [depth= 1] . ( 8 sec) [ -7355.5593] [ 1220] [depth= 1] . ( 9 sec) [ -7351.0736] [ 1219] [depth= 1] . ( 9 sec) [ -7350.6538] [ 1220] [depth= 1] . ( 9 sec) [ -7348.8987] [ 1222] [depth= 1] . ( 9 sec) [ -7346.2328] [ 1219] [depth= 3] . ( 10 sec) [ -7340.5053] [ 1219] [depth= 2] . ( 10 sec) [ -7339.3211] [ 1219] [depth= 1] . ( 10 sec) [ -7337.7292] [ 1219] [depth= 1] . ( 10 sec) [ -7332.0244] [ 1218] [depth= 2] . ( 11 sec) [ -7331.6618] [ 1219] [depth= 1] . ( 12 sec) [ -7327.3559] [ 1218] [depth= 1] . ( 12 sec) [ -7326.5856] [ 1218] [depth= 1] . ( 12 sec) [ -7322.9191] [ 1217] [depth= 2] . ( 12 sec) [ -7322.3187] [ 1217] [depth= 1] . ( 12 sec) [ -7322.2083] [ 1217] [depth= 1] . ( 13 sec) [ -7315.9298] [ 1217] [depth= 2] . ( 13 sec) [ -7314.9660] [ 1217] [depth= 1] . ( 13 sec) [ -7314.4795] [ 1217] [depth= 1] . ( 13 sec) [ -7314.3177] [ 1217] [depth= 1] . ( 13 sec) [ -7314.1398] [ 1217] [depth= 1] . ( 13 sec) [ -7313.9420] [ 1217] [depth= 2] . ( 14 sec) [ -7313.8595] [ 1217] [depth= 1] . ( 14 sec) [ -7313.8270] [ 1217] [depth= 1] . ( 14 sec) [ -7313.5815] [ 1217] [depth= 1] . ( 14 sec) [ -7313.3667] [ 1217] [depth= 1] . ( 15 sec) [ -7313.0461] [ 1217] [depth= 1] . ( 15 sec) [ -7312.8050] [ 1217] [depth= 1] . ( 15 sec) [ -7310.3208] [ 1217] [depth= 1] . ( 15 sec) [ -7308.3551] [ 1217] [depth= 1] . ( 16 sec) [ -7305.4418] [ 1216] [depth= 1] . ( 16 sec) [ -7302.8758] [ 1215] [depth= 2] . ( 16 sec) [ -7302.7165] [ 1215] [depth= 3] . ( 17 sec) [ -7290.5188] [ 1213] [depth= 2] . ( 17 sec) [ -7286.2698] [ 1213] [depth= 1] . ( 20 sec) [ -7285.0603] [ 1213] [depth= 1] . ( 20 sec) [ -7285.0301] [ 1213] [depth= 1] . ( 22 sec) [ -7284.8988] [ 1213] [depth= 1] . ( 24 sec) [ -7242.8112] [Branch lengths ] . ( 24 sec) [ -7242.7388] [Ts/ts ratio ][ 1.685216] . ( 27 sec) [ -7241.8533] [ 1212] [depth= 1] . ( 31 sec) [ -7241.1838] [ 1210] [depth= 1] . ( 32 sec) [ -7240.8623] [ 1209] [depth= 6] . ( 48 sec) [ -7237.3151] [Branch lengths ] . ( 48 sec) [ -7237.3024] [Ts/ts ratio ][ 1.702448] . ( 51 sec) [ -7235.6911] [ 1209] [depth= 2] . ( 55 sec) [ -7235.5487] [ 1209] [depth= 1] . ( 74 sec) [ -7234.3132] [Branch lengths ] . ( 74 sec) [ -7234.3124] [Ts/ts ratio ][ 1.697087] . ( 99 sec) [ -7234.2687] [Branch lengths ] . ( 177 sec) [ -7234.2662] [Branch lengths ] . ( 177 sec) [ -7234.2662] [Topology ] . ( 179 sec) [ -7234.2660] [Topology ] . ( 180 sec) [ -7234.2659] [Ts/ts ratio ][ 1.698784] . Checking for NNIs, optimizing five branches... . ( 193 sec) [ -7234.2658] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7234.265774. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 30 -1.000000 0.000000 0.000000 100 108.704520 1.000000 0.118083 27 3.365154 0.648000 0.027915 42 2.376130 0.281000 0.033263 90 30.706376 0.979000 0.047037 30 6.873563 0.873000 0.020711 35 22.539449 0.940000 0.023222 14 4.012343 0.803000 0.006844 24 5.037832 0.767000 0.009828 91 14.849083 0.923000 0.082220 99 37.708450 0.990000 0.126716 99 11.934523 0.904000 0.062241 96 46.444961 1.000000 0.085421 46 1.302784 0.456000 0.005629 100 43.773424 0.988000 0.028772 92 8.018653 0.846000 0.006556 99 17.878950 0.913000 0.008430 43 8.535791 0.867000 0.010305 68 13.713776 0.914000 0.014577 57 3.776873 0.534000 0.007293 90 17.574026 0.927000 0.014526 96 31.217194 0.952000 0.014605 74 7.454242 0.807000 0.001927 41 6.810009 0.557000 0.010486 99 28.663725 0.954000 0.020185 43 -1.000000 0.000000 0.000000 97 34.804356 0.978000 0.026457 59 6.948443 0.813000 0.001934 41 3.187935 0.609000 0.014712 87 15.624848 0.920000 0.039057 56 0.189364 0.000000 0.020986 59 19.644986 0.953000 0.027815 43 8.202008 0.869000 0.015112 36 5.241538 0.826000 0.015069 26 2.219997 0.429000 0.019380 100 61.282842 0.995000 0.057334 93 35.181180 0.986000 0.052394 100 103.134940 1.000000 0.101042 54 0.268118 0.576000 0.001681 63 6.526981 0.728000 0.002126 99 39.905766 0.993000 0.056990 41 3.281218 0.460000 0.011839 46 12.657954 0.855000 0.011393 83 39.435490 0.978000 0.026287 86 14.031904 0.926000 0.016223 59 11.348894 0.858000 0.007592 97 54.643156 0.997000 0.020137 11 -1.000000 0.000000 0.000000 11 -1.000000 0.000000 0.000000 21 0.000218 0.000000 0.000000 75 7.063337 0.837000 0.007918 100 17.207974 0.947000 0.013262 29 -1.000000 0.000000 0.000000 22 -1.000000 0.000000 0.000000 97 41.257509 0.974000 0.023117 59 2.716525 0.311000 0.011352 100 29.055652 0.955000 0.014878 99 32.839450 0.962000 0.022246 37 0.623271 0.125000 0.001957 74 16.688461 0.900000 0.005653 55 4.699277 0.754000 0.002189 44 -1.000000 0.000000 0.000000 55 12.531328 0.898000 0.008924 16 0.503108 0.092000 0.003833 92 46.731066 0.980000 0.014407 85 8.155822 0.852000 0.004135 99 61.937129 0.992000 0.016609 43 -1.000000 0.000000 0.000000 29 0.021072 0.000000 0.000360 34 7.756616 0.779000 0.001938 58 9.019670 0.773000 0.001947 67 8.171015 0.741000 0.001952 29 6.500945 0.718000 0.025158 100 23.412198 0.955000 0.037573 . Printing the most likely tree in file 'nucleic_M2772_77x900_2006.phy_phyml_tree.txt'... . Time used 5h12m35s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo