.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2786_104x1051_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... . 717 patterns found. (out of a total of 1051 sites) . 402 sites without polymorphism (38.25%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 39Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16121.5433] [Ts/ts ratio ][ 3.373436] . ( 1 sec) [ -16112.4156] [ 3250] [depth= 1] . ( 1 sec) [ -16110.2655] [ 3246] [depth= 1] . ( 1 sec) [ -16079.8906] [ 3236] [depth= 2] . ( 1 sec) [ -16077.9770] [ 3234] [depth= 3] . ( 2 sec) [ -16074.6393] [ 3238] [depth= 2] . ( 3 sec) [ -16073.0584] [ 3243] [depth= 2] . ( 3 sec) [ -16067.5176] [ 3240] [depth= 2] . ( 3 sec) [ -16060.6602] [ 3238] [depth= 1] . ( 3 sec) [ -16057.4353] [ 3233] [depth= 2] . ( 3 sec) [ -16052.1160] [ 3244] [depth= 1] . ( 4 sec) [ -16024.6564] [ 3243] [depth= 1] . ( 4 sec) [ -16006.4374] [ 3240] [depth= 2] . ( 4 sec) [ -15987.9560] [ 3228] [depth= 3] . ( 5 sec) [ -15975.1768] [ 3219] [depth= 1] . ( 6 sec) [ -15973.3297] [ 3221] [depth= 1] . ( 6 sec) [ -15966.0820] [ 3225] [depth= 1] . ( 6 sec) [ -15962.1235] [ 3225] [depth= 1] . ( 7 sec) [ -15960.4342] [ 3225] [depth= 1] . ( 7 sec) [ -15948.5197] [ 3225] [depth= 2] . ( 8 sec) [ -15948.1371] [ 3230] [depth= 1] . ( 8 sec) [ -15947.7950] [ 3236] [depth= 1] . ( 8 sec) [ -15915.3708] [ 3224] [depth= 1] . ( 8 sec) [ -15912.2165] [ 3219] [depth= 1] . ( 9 sec) [ -15911.2455] [ 3218] [depth= 1] . ( 9 sec) [ -15904.9967] [ 3221] [depth= 2] . ( 10 sec) [ -15904.7887] [ 3222] [depth= 1] . ( 10 sec) [ -15900.2076] [ 3217] [depth= 1] . ( 10 sec) [ -15899.3738] [ 3217] [depth= 3] . ( 10 sec) [ -15894.4317] [ 3216] [depth= 3] . ( 11 sec) [ -15892.1360] [ 3215] [depth= 1] . ( 11 sec) [ -15890.8424] [ 3215] [depth= 1] . ( 14 sec) [ -15890.7518] [ 3216] [depth= 1] . ( 15 sec) [ -15887.3845] [ 3215] [depth= 1] . ( 16 sec) [ -15884.1632] [ 3215] [depth= 1] . ( 18 sec) [ -15883.6103] [ 3215] [depth= 1] . ( 19 sec) [ -15882.8412] [ 3215] [depth= 1] . ( 19 sec) [ -15880.2454] [ 3217] [depth= 1] . ( 19 sec) [ -15879.7762] [ 3216] [depth= 1] . ( 20 sec) [ -15877.0190] [ 3218] [depth= 1] . ( 20 sec) [ -15876.6294] [ 3221] [depth= 1] . ( 21 sec) [ -15876.6110] [ 3221] [depth= 1] . ( 22 sec) [ -15876.4212] [ 3222] [depth= 1] . ( 23 sec) [ -15875.8880] [ 3222] [depth= 1] . ( 23 sec) [ -15875.8191] [ 3222] [depth= 1] . ( 23 sec) [ -15867.0349] [ 3222] [depth= 1] . ( 23 sec) [ -15866.9617] [ 3221] [depth= 1] . ( 24 sec) [ -15866.6406] [ 3221] [depth= 1] . ( 24 sec) [ -15866.3876] [ 3221] [depth= 1] . ( 25 sec) [ -15863.9790] [ 3220] [depth= 1] . ( 26 sec) [ -15863.6652] [ 3219] [depth= 1] . ( 30 sec) [ -15860.8566] [ 3218] [depth= 1] . ( 30 sec) [ -15859.9929] [ 3218] [depth= 1] . ( 30 sec) [ -15859.3148] [ 3218] [depth= 1] . ( 30 sec) [ -15858.9150] [ 3218] [depth= 1] . ( 31 sec) [ -15858.5982] [ 3219] [depth= 3] . ( 31 sec) [ -15856.8117] [ 3219] [depth= 1] . ( 32 sec) [ -15856.6920] [ 3219] [depth= 1] . ( 34 sec) [ -15856.1050] [ 3218] [depth= 3] . ( 37 sec) [ -15855.3468] [ 3218] [depth= 1] . ( 37 sec) [ -15854.9635] [ 3218] [depth= 1] . ( 37 sec) [ -15851.3043] [ 3219] [depth= 2] . ( 38 sec) [ -15850.8357] [ 3219] [depth= 1] . ( 38 sec) [ -15850.4524] [ 3218] [depth= 1] . ( 39 sec) [ -15850.1449] [ 3218] [depth= 1] . ( 41 sec) [ -15849.1170] [ 3218] [depth= 1] . ( 43 sec) [ -15848.4571] [ 3218] [depth= 1] . ( 43 sec) [ -15848.1669] [ 3218] [depth= 1] . ( 45 sec) [ -15848.1323] [ 3218] [depth= 1] . ( 45 sec) [ -15847.9844] [ 3218] [depth= 1] . ( 46 sec) [ -15847.8122] [ 3218] [depth= 2] . ( 48 sec) [ -15779.5661] [Branch lengths ] . ( 48 sec) [ -15775.9394] [Ts/ts ratio ][ 3.751133] . ( 49 sec) [ -15775.1241] [ 3216] [depth= 1] . ( 49 sec) [ -15773.1304] [ 3212] [depth= 1] . ( 51 sec) [ -15772.8687] [ 3212] [depth= 1] . ( 52 sec) [ -15771.5922] [ 3210] [depth= 1] . ( 53 sec) [ -15771.1077] [ 3207] [depth= 1] . ( 55 sec) [ -15771.0016] [ 3211] [depth= 1] . ( 56 sec) [ -15770.7072] [ 3211] [depth= 1] . ( 61 sec) [ -15770.1952] [ 3210] [depth= 1] . ( 66 sec) [ -15769.7783] [ 3210] [depth= 1] . ( 68 sec) [ -15769.5690] [ 3210] [depth= 1] . ( 68 sec) [ -15769.5507] [ 3210] [depth= 1] . ( 69 sec) [ -15768.6799] [ 3207] [depth= 1] . ( 70 sec) [ -15766.5311] [ 3206] [depth= 1] . ( 80 sec) [ -15766.5154] [ 3206] [depth= 1] . ( 85 sec) [ -15766.0498] [ 3207] [depth= 1] . ( 92 sec) [ -15765.8149] [ 3206] [depth= 1] . ( 96 sec) [ -15765.7736] [ 3206] [depth= 1] . ( 97 sec) [ -15765.7276] [ 3206] [depth= 1] . ( 102 sec) [ -15753.4350] [Branch lengths ] . ( 102 sec) [ -15753.4350] [Ts/ts ratio ][ 3.751133] . ( 103 sec) [ -15750.6888] [ 3202] [depth= 1] . ( 158 sec) [ -15747.2590] [Branch lengths ] . ( 158 sec) [ -15747.2178] [Ts/ts ratio ][ 3.793704] . ( 213 sec) [ -15745.6951] [Branch lengths ] . ( 359 sec) [ -15744.9661] [Branch lengths ] . ( 359 sec) [ -15744.9661] [Topology ] . ( 363 sec) [ -15744.6158] [Topology ] . ( 366 sec) [ -15743.7096] [Topology ] . ( 369 sec) [ -15741.6616] [Topology ] . ( 373 sec) [ -15741.0465] [Topology ] . ( 376 sec) [ -15740.9460] [Topology ] . ( 380 sec) [ -15740.8983] [Topology ] . ( 380 sec) [ -15740.8060] [Ts/ts ratio ][ 3.858946] . ( 380 sec) [ -15740.8060] [Topology ] . ( 384 sec) [ -15740.7615] [Topology ] . ( 387 sec) [ -15740.7298] [Topology ] . ( 390 sec) [ -15740.7054] [Topology ] . ( 394 sec) [ -15740.6862] [Topology ] . ( 397 sec) [ -15740.6711] [Topology ] . ( 401 sec) [ -15740.6592] [Topology ] . ( 401 sec) [ -15740.6562] [Ts/ts ratio ][ 3.870998] . ( 401 sec) [ -15740.6562] [Topology ] . ( 405 sec) [ -15740.6457] [Topology ] . ( 408 sec) [ -15740.6375] [Topology ] . ( 412 sec) [ -15740.6310] [Topology ] . ( 415 sec) [ -15740.6258] [Topology ] . ( 418 sec) [ -15740.6217] [Topology ] . ( 422 sec) [ -15740.6184] [Topology ] . ( 422 sec) [ -15740.6179] [Ts/ts ratio ][ 3.876236] . ( 422 sec) [ -15740.6179] [Topology ] . ( 426 sec) [ -15740.6151] [Topology ] . ( 429 sec) [ -15740.6128] [Topology ] . ( 433 sec) [ -15740.6110] [Topology ] . ( 436 sec) [ -15740.6096] [Topology ] . ( 439 sec) [ -15740.6084] [Topology ] . ( 443 sec) [ -15740.6075] [Topology ] . ( 443 sec) [ -15740.6074] [Ts/ts ratio ][ 3.880112] . ( 443 sec) [ -15740.6074] [Topology ] . ( 447 sec) [ -15740.6065] [Topology ] . ( 447 sec) [ -15740.6065] [Ts/ts ratio ][ 3.880112] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -15740.606550. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 47.199452 0.997000 0.223006 99 31.633972 0.987000 0.192895 79 27.856674 0.960000 0.140563 55 4.696713 0.807000 0.041084 42 8.147697 0.783000 0.089701 64 11.133085 0.892000 0.064186 100 199.713201 1.000000 0.333296 87 6.425029 0.819000 0.029811 23 2.643357 0.708000 0.030849 93 25.023623 0.967000 0.101501 96 40.676298 0.991000 0.135522 58 1.732468 0.280000 0.027264 68 3.614610 0.743000 0.016969 100 95.014343 1.000000 0.139227 83 9.336497 0.854000 0.023210 100 101.781515 1.000000 0.234782 19 3.110228 0.543000 0.049743 100 90.490357 0.999000 0.214854 100 30.816171 0.988000 0.114068 100 24.570163 0.969000 0.104226 78 3.336476 0.785000 0.014888 100 50.550021 0.994000 0.116528 99 23.248961 0.969000 0.084178 97 23.033500 0.969000 0.059982 67 16.150772 0.905000 0.013854 32 0.711998 0.274000 0.002437 58 3.438681 0.782000 0.007420 85 10.396259 0.917000 0.036639 60 1.863164 0.484000 0.006418 100 126.311593 1.000000 0.059941 10 -1.000000 0.000000 0.000000 28 8.880012 0.776000 0.003914 37 2.665494 0.757000 0.003760 32 2.671912 0.777000 0.001639 86 29.285743 0.939000 0.007028 79 20.719504 0.883000 0.009529 94 15.661558 0.903000 0.011083 91 15.309400 0.893000 0.010283 77 7.090445 0.820000 0.005134 99 70.652970 0.994000 0.021301 99 24.684284 0.957000 0.012269 42 1.155187 0.717000 0.001726 59 19.245895 0.867000 0.005735 96 59.206201 0.999000 0.041706 67 4.586509 0.813000 0.006384 46 11.822096 0.759000 0.014121 100 107.884425 0.998000 0.046086 87 2.397605 0.781000 0.007121 45 6.763455 0.853000 0.010387 39 1.631315 0.640000 0.006535 99 31.211625 0.980000 0.035258 48 3.165473 0.484000 0.002213 54 2.709534 0.749000 0.002117 54 1.662433 0.628000 0.001742 48 11.264953 0.876000 0.011275 45 0.095625 0.000000 0.003655 99 78.198385 0.998000 0.037169 84 10.911117 0.839000 0.013627 98 23.899555 0.927000 0.010145 19 5.482865 0.812000 0.005210 14 3.449096 0.753000 0.002252 12 1.060028 0.317000 0.002532 81 21.689477 0.939000 0.015609 100 156.342228 1.000000 0.078689 75 6.433601 0.619000 0.015335 99 30.658186 0.971000 0.022949 23 4.392468 0.762000 0.002721 100 100.867870 1.000000 0.044838 15 0.575556 0.624000 0.002068 100 64.696349 0.989000 0.018634 100 60.154084 0.995000 0.018592 70 0.140955 0.000000 0.003663 58 2.762435 0.473000 0.003483 32 5.164757 0.710000 0.005646 100 141.262630 1.000000 0.047206 76 17.905618 0.912000 0.007822 17 0.180912 0.000000 0.001625 100 52.354466 0.986000 0.014756 36 -1.000000 0.000000 0.000001 100 99.743907 1.000000 0.021868 49 0.002193 0.000000 0.000347 78 10.704109 0.864000 0.003934 100 48.296113 0.976000 0.011697 47 5.351613 0.764000 0.002341 100 81.885549 0.999000 0.025488 100 47.044809 0.987000 0.014176 17 -1.000000 0.000000 0.000000 22 6.951160 0.847000 0.007701 86 51.643065 0.993000 0.017815 91 10.826135 0.874000 0.005263 82 11.710941 0.887000 0.008211 94 22.920877 0.913000 0.008999 22 -1.000000 0.000000 0.000000 82 23.173536 0.943000 0.008013 79 4.000470 0.713000 0.001758 75 8.856624 0.839000 0.003522 73 8.295075 0.777000 0.001734 53 2.914705 0.513000 0.059847 100 119.569957 1.000000 0.379723 74 3.729715 0.816000 0.018694 100 61.582768 0.999000 0.222816 . Printing the most likely tree in file 'nucleic_M2786_104x1051_2006.phy_phyml_tree.txt'... . Time used 13h28m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo