.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -12810.0811] [Ts/ts ratio ][ 3.359093] . ( 1 sec) [ -12809.3021] [ 2217] [depth= 1] . ( 1 sec) [ -12808.8072] [ 2216] [depth= 1] . ( 1 sec) [ -12808.6145] [ 2217] [depth= 1] . ( 1 sec) [ -12808.4698] [ 2216] [depth= 1] . ( 2 sec) [ -12806.9554] [ 2216] [depth= 1] . ( 2 sec) [ -12806.8378] [ 2219] [depth= 1] . ( 3 sec) [ -12795.9121] [ 2215] [depth= 1] . ( 3 sec) [ -12791.4474] [ 2214] [depth= 1] . ( 4 sec) [ -12791.3363] [ 2215] [depth= 1] . ( 4 sec) [ -12789.6150] [ 2215] [depth= 2] . ( 4 sec) [ -12785.1881] [ 2214] [depth= 1] . ( 5 sec) [ -12774.9163] [ 2216] [depth= 1] . ( 5 sec) [ -12774.4071] [ 2217] [depth= 1] . ( 5 sec) [ -12774.2808] [ 2216] [depth= 1] . ( 6 sec) [ -12762.3171] [ 2212] [depth= 1] . ( 6 sec) [ -12761.7143] [ 2215] [depth= 1] . ( 7 sec) [ -12756.1050] [ 2212] [depth= 1] . ( 7 sec) [ -12749.2577] [ 2208] [depth= 1] . ( 8 sec) [ -12745.1605] [ 2210] [depth= 1] . ( 8 sec) [ -12744.5091] [ 2208] [depth= 1] . ( 8 sec) [ -12739.0014] [ 2204] [depth= 1] . ( 9 sec) [ -12738.3598] [ 2206] [depth= 1] . ( 9 sec) [ -12734.1769] [ 2204] [depth= 1] . ( 9 sec) [ -12730.8456] [ 2203] [depth= 1] . ( 9 sec) [ -12730.8328] [ 2204] [depth= 1] . ( 10 sec) [ -12726.5920] [ 2201] [depth= 1] . ( 10 sec) [ -12725.2356] [ 2204] [depth= 1] . ( 10 sec) [ -12724.2794] [ 2208] [depth= 1] . ( 10 sec) [ -12719.2568] [ 2213] [depth= 2] . ( 10 sec) [ -12718.9227] [ 2213] [depth= 1] . ( 10 sec) [ -12710.8309] [ 2207] [depth= 1] . ( 10 sec) [ -12706.4515] [ 2209] [depth= 3] . ( 11 sec) [ -12701.4028] [ 2207] [depth= 1] . ( 11 sec) [ -12699.3030] [ 2209] [depth= 1] . ( 11 sec) [ -12689.7071] [ 2206] [depth= 1] . ( 11 sec) [ -12681.0210] [ 2206] [depth= 1] . ( 12 sec) [ -12679.9111] [ 2207] [depth= 1] . ( 12 sec) [ -12679.4006] [ 2206] [depth= 2] . ( 13 sec) [ -12678.5862] [ 2205] [depth= 1] . ( 13 sec) [ -12677.8000] [ 2202] [depth= 1] . ( 14 sec) [ -12677.3352] [ 2202] [depth= 1] . ( 14 sec) [ -12670.8720] [ 2199] [depth= 1] . ( 14 sec) [ -12669.5550] [ 2199] [depth= 1] . ( 15 sec) [ -12563.7633] [Branch lengths ] . ( 15 sec) [ -12562.5862] [Ts/ts ratio ][ 3.602896] . ( 16 sec) [ -12558.3816] [ 2199] [depth= 1] . ( 16 sec) [ -12557.0803] [ 2200] [depth= 1] . ( 18 sec) [ -12555.3992] [ 2199] [depth= 1] . ( 20 sec) [ -12550.2708] [ 2196] [depth= 1] . ( 23 sec) [ -12549.5505] [ 2202] [depth= 1] . ( 26 sec) [ -12549.0791] [ 2200] [depth= 2] . ( 30 sec) [ -12533.4262] [Branch lengths ] . ( 30 sec) [ -12533.2124] [Ts/ts ratio ][ 3.711765] . ( 46 sec) [ -12531.3288] [Branch lengths ] . ( 113 sec) [ -12531.0803] [Branch lengths ] . ( 113 sec) [ -12531.0803] [Topology ] . ( 115 sec) [ -12531.0589] [Topology ] . ( 117 sec) [ -12531.0517] [Topology ] . ( 119 sec) [ -12531.0482] [Topology ] . ( 120 sec) [ -12531.0443] [Topology ] . ( 122 sec) [ -12531.0304] [Topology ] . ( 124 sec) [ -12531.0232] [Topology ] . ( 124 sec) [ -12530.9976] [Ts/ts ratio ][ 3.750254] . ( 124 sec) [ -12530.9976] [Topology ] . ( 126 sec) [ -12530.9955] [Topology ] . ( 128 sec) [ -12530.9949] [Topology ] . ( 128 sec) [ -12530.9949] [Ts/ts ratio ][ 3.750254] . ( 128 sec) [ -12530.9949] [Topology ] . ( 130 sec) [ -12530.9947] [Topology ] . ( 130 sec) [ -12530.9947] [Ts/ts ratio ][ 3.750254] . Checking for NNIs, optimizing five branches... . ( 143 sec) [ -12530.8261] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12530.826104. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 420.187588 1.000000 0.282357 64 8.137954 0.843000 0.034084 53 13.470117 0.913000 0.015559 43 17.510917 0.847000 0.015033 100 82.265449 0.999000 0.041117 23 2.637840 0.496000 0.009225 55 14.666014 0.872000 0.012943 29 4.049141 0.649000 0.006792 68 11.820718 0.910000 0.014592 84 13.761359 0.928000 0.037909 31 5.008726 0.809000 0.006446 88 41.730789 0.970000 0.023210 93 38.637846 0.982000 0.025187 73 15.300635 0.905000 0.014022 99 17.173204 0.942000 0.019049 56 6.698635 0.627000 0.016656 60 5.519165 0.792000 0.012426 100 85.698196 0.999000 0.053416 100 56.775989 0.994000 0.038656 98 31.502167 0.975000 0.029037 29 0.058584 0.000000 0.008973 69 27.517597 0.969000 0.025279 89 9.314836 0.896000 0.029259 100 12.824947 0.922000 0.031255 100 37.485375 0.986000 0.030319 87 9.277019 0.896000 0.015569 94 24.035832 0.948000 0.023736 100 54.077434 0.985000 0.024479 99 44.433121 0.989000 0.023767 62 17.385006 0.884000 0.015416 99 115.136480 1.000000 0.061858 100 94.596999 0.999000 0.055508 67 3.050451 0.770000 0.007954 100 68.026461 1.000000 0.096043 75 11.539725 0.886000 0.015413 56 4.907808 0.829000 0.008981 55 5.190854 0.644000 0.014998 49 11.055846 0.737000 0.015754 72 25.763250 0.968000 0.019175 100 220.110366 1.000000 0.096628 27 2.001846 0.559000 0.004312 100 116.838413 1.000000 0.045856 76 0.097680 0.000000 0.000961 50 0.337209 0.013000 0.004132 99 72.136314 0.997000 0.015371 42 5.427039 0.800000 0.008814 100 84.005996 1.000000 0.046767 96 28.552861 0.973000 0.030847 100 160.505192 1.000000 0.060357 84 15.811833 0.943000 0.015665 50 2.299809 0.158000 0.005803 91 25.635310 0.931000 0.019716 68 18.534522 0.913000 0.016557 100 81.803525 1.000000 0.052612 100 121.559169 1.000000 0.063114 100 43.471603 0.988000 0.024680 68 4.790131 0.481000 0.005726 . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Time used 3h47m31s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo