.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2913_81x897_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 . 84 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 197 patterns found. (out of a total of 897 sites) . 676 sites without polymorphism (75.36%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -2529.4301] [Ts/ts ratio ][ 3.177172] . ( 0 sec) [ -2528.8651] [ 220] [depth= 1] . ( 0 sec) [ -2528.7074] [ 220] [depth= 1] . ( 0 sec) [ -2528.5949] [ 220] [depth= 1] . ( 1 sec) [ -2523.5012] [ 220] [depth= 1] . ( 1 sec) [ -2523.3487] [ 220] [depth= 1] . ( 1 sec) [ -2523.2109] [ 220] [depth= 11] . ( 1 sec) [ -2520.4899] [ 220] [depth= 11] . ( 1 sec) [ -2520.2695] [ 220] [depth= 4] . ( 1 sec) [ -2519.0468] [ 220] [depth= 1] . ( 4 sec) [ -2518.9833] [ 220] [depth= 1] . ( 4 sec) [ -2518.9431] [ 220] [depth= 1] . ( 4 sec) [ -2518.5913] [ 220] [depth= 2] . ( 5 sec) [ -2517.3213] [ 219] [depth= 7] . ( 5 sec) [ -2508.1049] [ 218] [depth= 4] . ( 5 sec) [ -2508.0831] [ 218] [depth= 1] . ( 8 sec) [ -2508.0507] [ 218] [depth= 5] . ( 8 sec) [ -2507.9342] [ 218] [depth= 1] . ( 8 sec) [ -2507.8958] [ 218] [depth= 1] . ( 8 sec) [ -2507.4639] [ 218] [depth= 4] . ( 8 sec) [ -2507.4184] [ 218] [depth= 1] . ( 8 sec) [ -2507.2267] [ 218] [depth= 1] . ( 8 sec) [ -2506.3893] [ 218] [depth= 1] . ( 9 sec) [ -2506.3718] [ 218] [depth= 3] . ( 11 sec) [ -2506.0064] [ 218] [depth= 1] . ( 11 sec) [ -2503.7811] [ 217] [depth= 3] . ( 11 sec) [ -2503.7693] [ 217] [depth= 1] . ( 12 sec) [ -2503.2559] [ 217] [depth= 1] . ( 12 sec) [ -2503.2021] [ 217] [depth= 2] . ( 12 sec) [ -2503.1914] [ 217] [depth= 4] . ( 16 sec) [ -2502.5731] [ 217] [depth= 3] . ( 17 sec) [ -2501.7656] [ 217] [depth= 1] . ( 17 sec) [ -2501.1877] [ 217] [depth= 1] . ( 17 sec) [ -2500.7777] [ 217] [depth= 2] . ( 18 sec) [ -2500.3827] [ 217] [depth= 1] . ( 18 sec) [ -2499.6019] [ 217] [depth= 4] . ( 18 sec) [ -2499.4096] [ 217] [depth= 2] . ( 18 sec) [ -2499.1548] [ 217] [depth= 2] . ( 18 sec) [ -2498.9511] [ 217] [depth= 1] . ( 18 sec) [ -2494.5854] [ 216] [depth= 2] . ( 18 sec) [ -2494.4871] [ 216] [depth= 5] . ( 19 sec) [ -2494.4028] [ 216] [depth= 1] . ( 19 sec) [ -2494.3695] [ 216] [depth= 1] . ( 19 sec) [ -2494.3154] [ 216] [depth= 1] . ( 20 sec) [ -2494.1385] [ 216] [depth= 1] . ( 20 sec) [ -2493.1664] [ 216] [depth= 2] . ( 20 sec) [ -2492.9849] [ 216] [depth= 1] . ( 20 sec) [ -2492.7424] [ 216] [depth= 2] . ( 20 sec) [ -2492.1452] [ 216] [depth= 1] . ( 21 sec) [ -2491.9962] [ 216] [depth= 1] . ( 21 sec) [ -2491.9232] [ 216] [depth= 1] . ( 22 sec) [ -2491.4062] [ 216] [depth= 1] . ( 22 sec) [ -2490.6994] [ 216] [depth= 3] . ( 22 sec) [ -2489.9668] [ 216] [depth= 6] . ( 22 sec) [ -2489.7849] [ 216] [depth= 1] . ( 22 sec) [ -2489.7670] [ 216] [depth= 5] . ( 22 sec) [ -2489.6468] [ 216] [depth= 1] . ( 22 sec) [ -2487.4562] [ 217] [depth= 6] . ( 22 sec) [ -2487.1744] [ 217] [depth= 2] . ( 23 sec) [ -2486.8292] [ 217] [depth= 1] . ( 23 sec) [ -2486.7992] [ 217] [depth= 3] . ( 23 sec) [ -2483.0431] [ 216] [depth= 3] . ( 23 sec) [ -2478.3650] [ 216] [depth= 2] . ( 24 sec) [ -2478.3214] [ 216] [depth= 1] . ( 24 sec) [ -2477.3529] [ 216] [depth= 2] . ( 24 sec) [ -2477.1454] [ 216] [depth= 1] . ( 24 sec) [ -2477.1252] [ 216] [depth= 2] . ( 24 sec) [ -2476.9312] [ 216] [depth= 1] . ( 24 sec) [ -2475.0379] [ 216] [depth= 1] . ( 25 sec) [ -2475.0011] [ 216] [depth= 1] . ( 25 sec) [ -2474.4752] [ 216] [depth= 1] . ( 25 sec) [ -2474.3734] [ 216] [depth= 10] . ( 25 sec) [ -2474.3598] [ 216] [depth= 1] . ( 25 sec) [ -2473.6860] [ 216] [depth= 3] . ( 26 sec) [ -2473.4486] [ 216] [depth= 2] . ( 27 sec) [ -2470.5022] [ 216] [depth= 1] . ( 27 sec) [ -2470.1263] [ 216] [depth= 1] . ( 27 sec) [ -2470.0905] [ 216] [depth= 6] . ( 27 sec) [ -2470.0359] [ 216] [depth= 2] . ( 28 sec) [ -2469.7812] [ 216] [depth= 3] . ( 28 sec) [ -2465.4240] [ 215] [depth= 7] . ( 28 sec) [ -2456.8179] [ 214] [depth= 4] . ( 28 sec) [ -2456.8025] [ 214] [depth= 2] . ( 28 sec) [ -2456.7883] [ 214] [depth= 2] . ( 28 sec) [ -2455.7127] [ 214] [depth= 1] . ( 28 sec) [ -2455.2975] [ 214] [depth= 2] . ( 28 sec) [ -2454.9598] [ 214] [depth= 2] . ( 28 sec) [ -2454.9244] [ 214] [depth= 3] . ( 28 sec) [ -2454.8801] [ 214] [depth= 1] . ( 30 sec) [ -2454.8647] [ 214] [depth= 2] . ( 30 sec) [ -2454.8518] [ 214] [depth= 2] . ( 32 sec) [ -2454.7714] [ 214] [depth= 2] . ( 33 sec) [ -2454.7557] [ 214] [depth= 1] . ( 33 sec) [ -2454.5229] [ 214] [depth= 1] . ( 33 sec) [ -2454.3800] [ 214] [depth= 3] . ( 33 sec) [ -2454.2654] [ 214] [depth= 7] . ( 33 sec) [ -2454.2534] [ 214] [depth= 2] . ( 35 sec) [ -2454.1787] [ 214] [depth= 2] . ( 35 sec) [ -2454.1596] [ 214] [depth= 3] . ( 39 sec) [ -2454.1449] [ 214] [depth= 1] . ( 39 sec) [ -2454.1249] [ 214] [depth= 9] . ( 43 sec) [ -2452.0337] [ 213] [depth= 3] . ( 43 sec) [ -2452.0217] [ 213] [depth= 3] . ( 43 sec) [ -2449.5474] [Branch lengths ] . ( 44 sec) [ -2449.5402] [Ts/ts ratio ][ 3.233527] . ( 44 sec) [ -2449.5257] [ 213] [depth= 3] . ( 65 sec) [ -2449.1340] [ 213] [depth= 7] . ( 66 sec) [ -2449.0926] [ 213] [depth= 1] . ( 72 sec) [ -2446.8341] [ 212] [depth= 3] . ( 72 sec) [ -2446.5922] [ 212] [depth= 15] . ( 72 sec) [ -2442.7733] [ 211] [depth= 1] . ( 74 sec) [ -2442.7591] [ 211] [depth= 2] . ( 109 sec) [ -2442.7103] [ 211] [depth= 17] . ( 140 sec) [ -2442.5040] [Branch lengths ] . ( 140 sec) [ -2442.4959] [Ts/ts ratio ][ 3.173992] . ( 242 sec) [ -2442.4955] [Branch lengths ] . ( 260 sec) [ -2442.4259] [ 211] [depth= 3] . ( 265 sec) [ -2442.2258] [ 211] [depth= 1] . ( 265 sec) [ -2442.0758] [ 211] [depth= 3] . ( 265 sec) [ -2442.0625] [ 211] [depth= 1] . ( 265 sec) [ -2442.0491] [ 211] [depth= 10] . ( 271 sec) [ -2441.7192] [ 211] [depth= 1] . ( 272 sec) [ -2441.6965] [Branch lengths ] . ( 272 sec) [ -2441.6965] [Ts/ts ratio ][ 3.173992] . ( 272 sec) [ -2441.6965] [Topology ] . ( 272 sec) [ -2441.6957] [Topology ] . ( 272 sec) [ -2441.6957] [Ts/ts ratio ][ 3.173992] . Checking for NNIs, optimizing five branches... . ( 276 sec) [ -2441.6956] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2441.695611. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 21.757966 0.960000 0.011559 90 8.849167 0.890000 0.007287 52 26.822450 0.963000 0.009450 0 5.101160 0.747000 0.001301 0 19.020327 0.894000 0.002602 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 37 6.234724 0.802000 0.002840 64 1.791246 0.269000 0.002629 85 9.625799 0.823000 0.002535 94 25.828943 0.932000 0.004169 2 11.920195 0.871000 0.002601 2 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 42 17.166466 0.913000 0.003897 24 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 0 4.960607 0.765000 0.001296 0 -1.000000 0.000000 0.000000 30 9.160314 0.772000 0.001304 39 6.282637 0.752000 0.001737 76 7.724711 0.847000 0.002403 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 3 17.301437 0.874000 0.006684 5 -1.000000 0.000000 0.000000 41 1.599895 0.791000 0.010483 9 -1.000000 0.000000 0.000000 6 -1.000000 0.000000 0.000000 4 -1.000000 0.000000 0.000000 7 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 8 -1.000000 0.000000 0.000000 65 18.005765 0.924000 0.002611 0 15.758188 0.921000 0.001298 0 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 58 11.793644 0.841000 0.001298 36 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 0 24.608483 0.920000 0.002600 0 -1.000000 0.000000 0.000000 1 0.000218 0.000000 0.000000 1 -1.000000 0.000000 0.001294 0 -1.000000 0.000000 0.000000 7 16.259758 0.920000 0.001296 1 -1.000000 0.000000 0.000000 0 -1.000000 0.000000 0.000000 54 6.760530 0.758000 0.001294 0 -1.000000 0.000000 0.000000 23 16.487546 0.922000 0.001296 3 -1.000000 0.000000 0.000000 47 18.072177 0.911000 0.001295 12 -1.000000 0.000000 0.000000 52 8.267742 0.800000 0.001298 9 -1.000000 0.000000 0.000000 14 -1.000000 0.000000 0.000000 2 -1.000000 0.000000 0.000000 98 45.546433 0.967000 0.005203 13 6.177038 0.763000 0.001293 1 7.305030 0.780000 0.001300 95 28.444108 0.929000 0.003919 4 24.908335 0.936000 0.003905 1 -1.000000 0.000000 0.000000 1 37.553328 0.958000 0.003918 2 -1.000000 0.000000 0.000000 1 -1.000000 0.000000 0.000000 5 -1.000000 0.000000 0.000000 . Printing the most likely tree in file 'nucleic_M2913_81x897_2006.phy_phyml_tree.txt'... . Time used 6h9m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo