.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2945_62x1271_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 . 4 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 935 patterns found. (out of a total of 1271 sites) . 411 sites without polymorphism (32.34%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 30Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -35967.4389] [Ts/ts ratio ][ 2.836691] . ( 3 sec) [ -35966.6277] [ 9306] [depth= 1] . ( 3 sec) [ -35963.4982] [ 9305] [depth= 1] . ( 3 sec) [ -35946.0340] [ 9293] [depth= 3] . ( 4 sec) [ -35943.4495] [ 9288] [depth= 1] . ( 5 sec) [ -35940.0505] [ 9293] [depth= 1] . ( 5 sec) [ -35936.1921] [ 9291] [depth= 1] . ( 5 sec) [ -35935.6157] [ 9288] [depth= 1] . ( 6 sec) [ -35932.2225] [ 9292] [depth= 1] . ( 6 sec) [ -35930.2261] [ 9295] [depth= 1] . ( 6 sec) [ -35928.2576] [ 9293] [depth= 1] . ( 6 sec) [ -35921.8045] [ 9295] [depth= 1] . ( 7 sec) [ -35920.2013] [ 9296] [depth= 1] . ( 7 sec) [ -35903.1376] [ 9294] [depth= 1] . ( 7 sec) [ -35893.7847] [ 9293] [depth= 1] . ( 7 sec) [ -35885.2056] [ 9293] [depth= 1] . ( 7 sec) [ -35841.6050] [ 9297] [depth= 1] . ( 7 sec) [ -35840.2700] [ 9297] [depth= 1] . ( 8 sec) [ -35833.8830] [ 9297] [depth= 1] . ( 8 sec) [ -35820.9138] [ 9296] [depth= 1] . ( 8 sec) [ -35817.2627] [ 9292] [depth= 1] . ( 8 sec) [ -35806.4511] [ 9295] [depth= 1] . ( 8 sec) [ -35806.3646] [ 9292] [depth= 1] . ( 9 sec) [ -35804.1248] [ 9319] [depth= 1] . ( 9 sec) [ -35767.4593] [ 9292] [depth= 1] . ( 9 sec) [ -35756.7777] [ 9296] [depth= 1] . ( 9 sec) [ -35735.5572] [ 9294] [depth= 2] . ( 9 sec) [ -35727.2772] [ 9291] [depth= 1] . ( 10 sec) [ -35725.8758] [ 9292] [depth= 1] . ( 10 sec) [ -35712.9262] [ 9293] [depth= 1] . ( 10 sec) [ -35694.5151] [ 9298] [depth= 1] . ( 10 sec) [ -35691.3125] [ 9293] [depth= 1] . ( 11 sec) [ -35689.5038] [ 9293] [depth= 2] . ( 12 sec) [ -35686.0735] [ 9297] [depth= 1] . ( 12 sec) [ -35685.9482] [ 9293] [depth= 1] . ( 12 sec) [ -35675.1256] [ 9288] [depth= 1] . ( 12 sec) [ -35662.4031] [ 9284] [depth= 2] . ( 13 sec) [ -35660.2791] [ 9286] [depth= 1] . ( 13 sec) [ -35644.4719] [ 9290] [depth= 1] . ( 13 sec) [ -35631.8861] [ 9287] [depth= 1] . ( 13 sec) [ -35615.2632] [ 9284] [depth= 1] . ( 13 sec) [ -35614.1864] [ 9281] [depth= 1] . ( 14 sec) [ -35583.1633] [ 9285] [depth= 4] . ( 14 sec) [ -35577.9682] [ 9286] [depth= 2] . ( 14 sec) [ -35557.5278] [ 9283] [depth= 1] . ( 15 sec) [ -35553.7395] [ 9286] [depth= 1] . ( 15 sec) [ -35551.6280] [ 9286] [depth= 1] . ( 16 sec) [ -35549.9219] [ 9290] [depth= 1] . ( 17 sec) [ -35368.2561] [Branch lengths ] . ( 17 sec) [ -35348.3914] [Ts/ts ratio ][ 3.316066] . ( 22 sec) [ -35346.4566] [ 9287] [depth= 1] . ( 22 sec) [ -35346.3883] [ 9290] [depth= 1] . ( 24 sec) [ -35345.2929] [ 9294] [depth= 1] . ( 24 sec) [ -35343.7305] [ 9295] [depth= 1] . ( 25 sec) [ -35343.3837] [ 9292] [depth= 2] . ( 25 sec) [ -35340.5307] [ 9289] [depth= 1] . ( 25 sec) [ -35339.9285] [ 9290] [depth= 1] . ( 34 sec) [ -35301.4862] [Branch lengths ] . ( 34 sec) [ -35299.9799] [Ts/ts ratio ][ 3.462842] . ( 51 sec) [ -35291.1610] [Branch lengths ] . ( 75 sec) [ -35290.9831] [ 9299] [depth= 2] . ( 78 sec) [ -35290.5650] [ 9294] [depth= 1] . ( 81 sec) [ -35290.2500] [ 9305] [depth= 2] . ( 89 sec) [ -35289.5136] [ 9308] [depth= 1] . ( 99 sec) [ -35289.2713] [ 9306] [depth= 1] . ( 99 sec) [ -35287.6139] [ 9313] [depth= 1] . ( 99 sec) [ -35287.1501] [ 9311] [depth= 1] . ( 100 sec) [ -35286.0455] [ 9308] [depth= 1] . ( 101 sec) [ -35285.7110] [ 9322] [depth= 2] . ( 113 sec) [ -35285.0316] [ 9318] [depth= 1] . ( 133 sec) [ -35277.5928] [Branch lengths ] . ( 134 sec) [ -35276.7634] [Ts/ts ratio ][ 3.577548] . ( 174 sec) [ -35275.4334] [ 9312] [depth= 1] . ( 221 sec) [ -35273.3491] [Branch lengths ] . ( 221 sec) [ -35273.2553] [Ts/ts ratio ][ 3.617005] . ( 308 sec) [ -35272.0815] [Branch lengths ] . ( 308 sec) [ -35272.0815] [Topology ] . ( 311 sec) [ -35271.6623] [Topology ] . ( 313 sec) [ -35271.3855] [Topology ] . ( 315 sec) [ -35271.1403] [Topology ] . ( 317 sec) [ -35270.9118] [Topology ] . ( 320 sec) [ -35270.6930] [Topology ] . ( 322 sec) [ -35270.4796] [Topology ] . ( 322 sec) [ -35270.2503] [Ts/ts ratio ][ 3.680452] . ( 322 sec) [ -35270.2503] [Topology ] . ( 325 sec) [ -35269.9487] [Topology ] . ( 327 sec) [ -35269.6522] [Topology ] . ( 329 sec) [ -35269.3519] [Topology ] . ( 332 sec) [ -35269.0438] [Topology ] . ( 334 sec) [ -35268.7244] [Topology ] . ( 336 sec) [ -35268.3911] [Topology ] . ( 336 sec) [ -35268.3045] [Ts/ts ratio ][ 3.720234] . ( 336 sec) [ -35268.3045] [Topology ] . ( 339 sec) [ -35267.8967] [Topology ] . ( 341 sec) [ -35267.4722] [Topology ] . ( 343 sec) [ -35267.0299] [Topology ] . ( 346 sec) [ -35266.5720] [Topology ] . ( 348 sec) [ -35266.1030] [Topology ] . ( 350 sec) [ -35265.6297] [Topology ] . ( 351 sec) [ -35265.5296] [Ts/ts ratio ][ 3.763714] . ( 351 sec) [ -35265.5296] [Topology ] . ( 353 sec) [ -35264.9901] [Topology ] . ( 355 sec) [ -35264.4686] [Topology ] . ( 357 sec) [ -35263.9746] [Topology ] . ( 360 sec) [ -35263.5182] [Topology ] . ( 362 sec) [ -35263.1071] [Topology ] . ( 364 sec) [ -35262.7457] [Topology ] . ( 365 sec) [ -35262.6340] [Ts/ts ratio ][ 3.810422] . ( 365 sec) [ -35262.6340] [Topology ] . ( 367 sec) [ -35262.2593] [Topology ] . ( 369 sec) [ -35261.9462] [Topology ] . ( 372 sec) [ -35261.6885] [Topology ] . ( 374 sec) [ -35261.4802] [Topology ] . ( 376 sec) [ -35261.3145] [Topology ] . ( 378 sec) [ -35261.1841] [Topology ] . ( 379 sec) [ -35261.1178] [Ts/ts ratio ][ 3.846961] . ( 379 sec) [ -35261.1178] [Topology ] . ( 381 sec) [ -35260.9866] [Topology ] . ( 383 sec) [ -35260.8866] [Topology ] . ( 386 sec) [ -35260.8104] [Topology ] . ( 388 sec) [ -35260.7528] [Topology ] . ( 390 sec) [ -35260.7095] [Topology ] . ( 393 sec) [ -35260.6422] [Topology ] . ( 395 sec) [ -35260.2563] [Topology ] . ( 397 sec) [ -35260.1600] [Topology ] . ( 399 sec) [ -35260.1141] [Topology ] . ( 402 sec) [ -35260.0584] [Ts/ts ratio ][ 3.870753] . ( 402 sec) [ -35260.0584] [Topology ] . ( 404 sec) [ -35260.0308] [Topology ] . ( 406 sec) [ -35260.0115] [Topology ] . ( 409 sec) [ -35259.9977] [Topology ] . ( 411 sec) [ -35259.9876] [Topology ] . ( 413 sec) [ -35259.9804] [Topology ] . ( 416 sec) [ -35259.9751] [Topology ] . ( 416 sec) [ -35259.9711] [Ts/ts ratio ][ 3.879963] . ( 416 sec) [ -35259.9711] [Topology ] . ( 418 sec) [ -35259.9658] [Topology ] . ( 420 sec) [ -35259.9621] [Topology ] . ( 423 sec) [ -35259.9594] [Topology ] . ( 425 sec) [ -35259.9575] [Topology ] . ( 427 sec) [ -35259.9561] [Topology ] . ( 430 sec) [ -35259.9550] [Topology ] . ( 430 sec) [ -35259.9543] [Ts/ts ratio ][ 3.883843] . ( 430 sec) [ -35259.9543] [Topology ] . ( 432 sec) [ -35259.9533] [Topology ] . ( 432 sec) [ -35259.9533] [Ts/ts ratio ][ 3.883843] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35259.953304. . Launch bootstrap analysis on the most likely tree... . Non parametric bootstrap analysis [....................] 20/ 100 [....................] 40/ 100 [....................] 60/ 100 [....................] 80/ 100 [....................] 100/ 100 Graphics: 100 122.879561 1.000000 0.334363 97 77.062907 1.000000 0.239025 19 4.847280 0.572000 0.044924 22 11.861831 0.874000 0.074038 14 0.296169 0.017000 0.049160 41 7.965954 0.847000 0.037808 100 83.974221 1.000000 0.197424 89 29.948730 0.981000 0.118276 94 62.005352 0.996000 0.178775 98 71.959241 0.997000 0.184860 100 164.257360 1.000000 0.335524 70 18.228514 0.917000 0.094247 46 0.497307 0.063000 0.043420 100 68.729308 0.998000 0.209468 100 79.384374 1.000000 0.196631 24 1.955513 0.236000 0.035277 65 18.347475 0.959000 0.186149 83 39.689766 0.983000 0.109710 96 33.728803 0.990000 0.257551 100 80.439446 0.999000 0.392409 47 6.105222 0.777000 0.058943 100 148.761838 1.000000 0.246997 92 29.188557 0.977000 0.111411 81 11.795651 0.903000 0.107513 56 7.838945 0.633000 0.053455 100 184.226836 1.000000 0.273186 75 22.608693 0.944000 0.068934 60 10.459738 0.865000 0.045462 39 12.335575 0.866000 0.051328 44 11.801600 0.913000 0.036756 100 69.471788 0.999000 0.107863 48 2.184916 0.337000 0.037990 29 5.504349 0.807000 0.049639 21 2.196422 0.232000 0.046149 100 128.231627 1.000000 0.287914 100 52.741187 0.994000 0.147655 100 63.402485 0.994000 0.113181 100 74.571614 0.998000 0.118231 97 27.515716 0.960000 0.091957 100 55.077302 0.996000 0.167080 100 49.032964 0.997000 0.131426 98 39.074695 0.978000 0.150511 67 20.968649 0.955000 0.085437 100 294.657475 1.000000 0.398994 40 7.817038 0.839000 0.043309 100 183.614207 1.000000 0.242508 66 0.422540 0.129000 0.006290 92 37.229275 0.968000 0.014903 27 1.964808 0.186000 0.050529 39 9.720488 0.890000 0.068222 32 8.521521 0.741000 0.060527 99 58.665467 0.998000 0.129582 56 8.651976 0.762000 0.076410 64 12.803883 0.873000 0.087495 100 192.129761 1.000000 0.358588 31 1.834620 0.181000 0.027648 100 140.538749 1.000000 0.244600 85 20.291687 0.961000 0.089324 100 75.659566 1.000000 0.186919 . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 9h43m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo