.......................... 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 : 0 . Model name : GTR . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Nucleotide equilibrium frequencies : empirical . Optimise tree topology : yes . Tree topology search : Best of NNIs and 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 NNI moves)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 5 sec) [ -36002.5932] [Topology ] . ( 7 sec) [ -35423.6231] [Topology ] . ( 10 sec) [ -35317.4470] [Topology ] . ( 12 sec) [ -35293.7583] [Topology ] . ( 14 sec) [ -35285.1407] [Topology ] . ( 16 sec) [ -35280.7055] [Topology ] . ( 19 sec) [ -35278.0935] [Topology ] . ( 21 sec) [ -35276.2739] [Topology ] . ( 23 sec) [ -35275.3266] [Topology ] . ( 25 sec) [ -35274.2363] [Topology ] . Checking for NNIs, optimizing five branches... . ( 49 sec) [ -35272.9942] [Topology ] . ( 54 sec) [ -35208.5581] [GTR parameters ] . ( 54 sec) [ -35204.6841] [Alpha ][ 0.464402] . ( 54 sec) [ -35204.6841] [Topology ] . ( 57 sec) [ -35193.4410] [Topology ] . ( 59 sec) [ -35186.4924] [Topology ] . ( 61 sec) [ -35181.2926] [Topology ] . ( 63 sec) [ -35177.0730] [Topology ] . ( 65 sec) [ -35173.4542] [Topology ] . ( 68 sec) [ -35170.3629] [Topology ] . ( 70 sec) [ -35167.7702] [Topology ] . ( 72 sec) [ -35165.6380] [Topology ] . Checking for NNIs, optimizing five branches... . ( 98 sec) [ -35155.5880] [GTR parameters ] . ( 98 sec) [ -35155.2055] [Alpha ][ 0.454189] . ( 98 sec) [ -35155.2055] [Topology ] . ( 101 sec) [ -35150.8159] [Topology ] . ( 103 sec) [ -35147.8747] [Topology ] . ( 105 sec) [ -35145.7696] [Topology ] . ( 107 sec) [ -35144.2357] [Topology ] . ( 110 sec) [ -35143.1072] [Topology ] . ( 112 sec) [ -35142.2702] [Topology ] . Checking for NNIs, optimizing five branches... . ( 137 sec) [ -35140.5502] [GTR parameters ] . ( 137 sec) [ -35140.0006] [Alpha ][ 0.442745] . ( 137 sec) [ -35140.0006] [Topology ] . ( 139 sec) [ -35138.4908] [Topology ] . ( 141 sec) [ -35137.4503] [Topology ] . ( 144 sec) [ -35136.6902] [Topology ] . ( 146 sec) [ -35136.1303] [Topology ] . ( 148 sec) [ -35135.7172] [Topology ] . ( 151 sec) [ -35135.4120] [Topology ] . Checking for NNIs, optimizing five branches... . ( 172 sec) [ -35135.3839] [Topology ] . ( 176 sec) [ -35134.7559] [GTR parameters ] . ( 176 sec) [ -35134.4189] [Alpha ][ 0.434211] . ( 176 sec) [ -35134.4189] [Topology ] . ( 179 sec) [ -35128.0537] [Topology ] . ( 181 sec) [ -35126.6368] [Topology ] . ( 183 sec) [ -35126.3037] [Topology ] . ( 185 sec) [ -35126.1149] [Topology ] . ( 188 sec) [ -35125.9887] [Topology ] . ( 190 sec) [ -35125.9007] [Topology ] . ( 192 sec) [ -35125.8389] [Topology ] . Checking for NNIs, optimizing five branches... . ( 216 sec) [ -35125.6522] [GTR parameters ] . ( 216 sec) [ -35125.4511] [Alpha ][ 0.427834] . ( 216 sec) [ -35125.4511] [Topology ] . ( 218 sec) [ -35125.2913] [Topology ] . ( 221 sec) [ -35125.1900] [Topology ] . ( 223 sec) [ -35125.1191] [Topology ] . ( 225 sec) [ -35125.0689] [Topology ] . ( 228 sec) [ -35125.0332] [Topology ] . ( 230 sec) [ -35125.0077] [Topology ] . Checking for NNIs, optimizing five branches... . ( 253 sec) [ -35124.9480] [GTR parameters ] . ( 254 sec) [ -35124.9013] [Alpha ][ 0.424805] . ( 254 sec) [ -35124.9013] [Topology ] . ( 256 sec) [ -35124.8461] [Topology ] . ( 258 sec) [ -35124.8103] [Topology ] . ( 261 sec) [ -35124.7850] [Topology ] . ( 263 sec) [ -35124.7670] [Topology ] . ( 265 sec) [ -35124.7541] [Topology ] . ( 267 sec) [ -35124.7449] [Topology ] . Checking for NNIs, optimizing five branches... . ( 290 sec) [ -35124.7299] [GTR parameters ] . ( 291 sec) [ -35124.7141] [Alpha ][ 0.423056] . ( 291 sec) [ -35124.7141] [Topology ] . ( 293 sec) [ -35124.6957] [Topology ] . ( 295 sec) [ -35124.6836] [Topology ] . ( 298 sec) [ -35124.6750] [Topology ] . ( 300 sec) [ -35124.6688] [Topology ] . ( 302 sec) [ -35124.6644] [Topology ] . ( 305 sec) [ -35124.6612] [Topology ] . Checking for NNIs, optimizing five branches... . ( 327 sec) [ -35124.6565] [GTR parameters ] . ( 328 sec) [ -35124.6511] [Alpha ][ 0.422039] . ( 328 sec) [ -35124.6511] [Topology ] . ( 330 sec) [ -35124.6451] [Topology ] . ( 332 sec) [ -35124.6411] [Topology ] . ( 335 sec) [ -35124.6382] [Topology ] . ( 337 sec) [ -35124.6362] [Topology ] . ( 339 sec) [ -35124.6348] [Topology ] . ( 341 sec) [ -35124.6337] [Topology ] . Checking for NNIs, optimizing five branches... . ( 364 sec) [ -35124.6310] [GTR parameters ] . ( 364 sec) [ -35124.6295] [Alpha ][ 0.421498] . ( 364 sec) [ -35124.6295] [Topology ] . ( 367 sec) [ -35124.6275] [Topology ] . ( 369 sec) [ -35124.6261] [Topology ] . ( 371 sec) [ -35124.6251] [Topology ] . Checking for NNIs, optimizing five branches... . ( 393 sec) [ -35124.6243] [GTR parameters ] . ( 393 sec) [ -35124.6243] [Alpha ][ 0.421077] . ( 393 sec) [ -35124.6243] [Topology ] . ( 395 sec) [ -35124.6228] [Topology ] . ( 398 sec) [ -35124.6219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 419 sec) [ -35124.6216] [GTR parameters ] . ( 420 sec) [ -35124.6216] [Alpha ][ 0.421077] . ( 420 sec) [ -35124.6216] [Topology ] . ( 422 sec) [ -35124.6208] [Topology ] . Checking for NNIs, optimizing five branches... . ( 444 sec) [ -35124.6208] [GTR parameters ] . ( 444 sec) [ -35124.6208] [Alpha ][ 0.421077] . ( 444 sec) [ -35124.6208] [Topology ] . ( 446 sec) [ -35124.6201] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 494 sec) [ -36495.9506] [GTR parameters ] . ( 494 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 496 sec) [ -35998.6346] [ 9298] [depth= 1] . ( 497 sec) [ -35996.9518] [ 9294] [depth= 1] . ( 498 sec) [ -35993.4197] [ 9298] [depth= 1] . ( 498 sec) [ -35990.0069] [ 9296] [depth= 1] . ( 499 sec) [ -35989.6571] [ 9298] [depth= 1] . ( 499 sec) [ -35988.6791] [ 9301] [depth= 1] . ( 499 sec) [ -35975.2493] [ 9298] [depth= 1] . ( 499 sec) [ -35968.7763] [ 9315] [depth= 1] . ( 499 sec) [ -35938.7796] [ 9298] [depth= 1] . ( 500 sec) [ -35887.6023] [ 9304] [depth= 2] . ( 500 sec) [ -35884.2680] [ 9303] [depth= 1] . ( 500 sec) [ -35880.5717] [ 9297] [depth= 1] . ( 500 sec) [ -35875.1233] [ 9303] [depth= 1] . ( 500 sec) [ -35874.6465] [ 9305] [depth= 1] . ( 501 sec) [ -35864.8674] [ 9297] [depth= 1] . ( 501 sec) [ -35863.5423] [ 9306] [depth= 1] . ( 501 sec) [ -35858.6607] [ 9306] [depth= 1] . ( 501 sec) [ -35852.2611] [ 9306] [depth= 1] . ( 501 sec) [ -35852.0001] [ 9315] [depth= 2] . ( 501 sec) [ -35846.9135] [ 9311] [depth= 1] . ( 502 sec) [ -35829.6825] [ 9315] [depth= 3] . ( 502 sec) [ -35827.8920] [ 9310] [depth= 1] . ( 502 sec) [ -35827.7338] [ 9321] [depth= 1] . ( 502 sec) [ -35824.8258] [ 9325] [depth= 3] . ( 503 sec) [ -35819.8487] [ 9325] [depth= 1] . ( 503 sec) [ -35815.7843] [ 9342] [depth= 2] . ( 503 sec) [ -35775.2913] [ 9308] [depth= 2] . ( 503 sec) [ -35760.4541] [ 9306] [depth= 1] . ( 503 sec) [ -35760.0837] [ 9308] [depth= 1] . ( 504 sec) [ -35751.5615] [ 9293] [depth= 1] . ( 504 sec) [ -35751.2427] [ 9297] [depth= 1] . ( 504 sec) [ -35710.4660] [ 9305] [depth= 2] . ( 504 sec) [ -35689.9691] [ 9317] [depth= 1] . ( 504 sec) [ -35688.5777] [ 9305] [depth= 1] . ( 504 sec) [ -35682.1110] [ 9313] [depth= 1] . ( 504 sec) [ -35656.4096] [ 9305] [depth= 1] . ( 505 sec) [ -35655.5026] [ 9312] [depth= 1] . ( 505 sec) [ -35631.6799] [ 9305] [depth= 1] . ( 506 sec) [ -35625.7289] [ 9308] [depth= 2] . ( 506 sec) [ -35625.0817] [ 9310] [depth= 1] . ( 506 sec) [ -35607.5665] [ 9307] [depth= 2] . ( 506 sec) [ -35605.1079] [ 9300] [depth= 1] . ( 506 sec) [ -35599.8424] [ 9297] [depth= 1] . ( 507 sec) [ -35592.2210] [ 9296] [depth= 1] . ( 507 sec) [ -35591.1458] [ 9293] [depth= 4] . ( 507 sec) [ -35585.1968] [ 9298] [depth= 1] . ( 508 sec) [ -35574.7206] [ 9293] [depth= 1] . ( 508 sec) [ -35574.2143] [ 9294] [depth= 1] . ( 508 sec) [ -35572.8797] [ 9293] [depth= 1] . ( 508 sec) [ -35562.7145] [ 9292] [depth= 1] . ( 508 sec) [ -35540.5258] [ 9293] [depth= 4] . ( 509 sec) [ -35539.9085] [ 9296] [depth= 1] . ( 509 sec) [ -35538.6142] [ 9293] [depth= 1] . ( 509 sec) [ -35536.1295] [ 9297] [depth= 1] . ( 509 sec) [ -35535.8295] [ 9293] [depth= 1] . ( 510 sec) [ -35307.7251] [Branch lengths ] . ( 515 sec) [ -35261.3733] [GTR parameters ] . ( 515 sec) [ -35253.2992] [Alpha ][ 0.446766] . ( 517 sec) [ -35252.6688] [ 9291] [depth= 1] . ( 518 sec) [ -35250.7935] [ 9286] [depth= 1] . ( 519 sec) [ -35250.2314] [ 9301] [depth= 1] . ( 521 sec) [ -35248.4647] [ 9297] [depth= 2] . ( 523 sec) [ -35246.5006] [ 9294] [depth= 1] . ( 525 sec) [ -35244.2970] [ 9296] [depth= 1] . ( 528 sec) [ -35241.2339] [ 9300] [depth= 2] . ( 532 sec) [ -35190.3187] [Branch lengths ] . ( 535 sec) [ -35185.9729] [GTR parameters ] . ( 536 sec) [ -35185.8197] [Alpha ][ 0.453722] . ( 553 sec) [ -35164.7563] [Branch lengths ] . ( 608 sec) [ -35164.6971] [ 9316] [depth= 2] . ( 643 sec) [ -35153.5642] [Branch lengths ] . ( 646 sec) [ -35148.5085] [GTR parameters ] . ( 646 sec) [ -35148.5075] [Alpha ][ 0.454222] . ( 667 sec) [ -35147.8960] [ 9320] [depth= 2] . ( 685 sec) [ -35146.8259] [ 9313] [depth= 1] . ( 690 sec) [ -35146.5948] [ 9312] [depth= 1] . ( 733 sec) [ -35129.9511] [Branch lengths ] . ( 736 sec) [ -35129.0559] [GTR parameters ] . ( 736 sec) [ -35128.9617] [Alpha ][ 0.449161] . ( 824 sec) [ -35120.6288] [Branch lengths ] . ( 824 sec) [ -35120.6288] [Topology ] . ( 826 sec) [ -35118.3724] [Topology ] . ( 829 sec) [ -35117.2532] [Topology ] . ( 831 sec) [ -35116.4904] [Topology ] . ( 833 sec) [ -35115.9462] [Topology ] . ( 835 sec) [ -35115.5520] [Topology ] . ( 838 sec) [ -35115.2638] [Topology ] . ( 840 sec) [ -35113.4848] [GTR parameters ] . ( 840 sec) [ -35112.9793] [Alpha ][ 0.438143] . ( 840 sec) [ -35112.9793] [Topology ] . ( 842 sec) [ -35112.1231] [Topology ] . ( 845 sec) [ -35111.5575] [Topology ] . ( 847 sec) [ -35111.1487] [Topology ] . ( 849 sec) [ -35110.8490] [Topology ] . ( 852 sec) [ -35110.3984] [Topology ] . ( 854 sec) [ -35109.6908] [Topology ] . ( 856 sec) [ -35109.3750] [Topology ] . ( 859 sec) [ -35109.1688] [Topology ] . ( 861 sec) [ -35109.0240] [Topology ] . ( 867 sec) [ -35108.1575] [GTR parameters ] . ( 867 sec) [ -35107.7963] [Alpha ][ 0.429303] . ( 867 sec) [ -35107.7963] [Topology ] . ( 870 sec) [ -35107.4307] [Topology ] . ( 872 sec) [ -35107.1969] [Topology ] . ( 874 sec) [ -35107.0320] [Topology ] . ( 876 sec) [ -35106.9141] [Topology ] . ( 879 sec) [ -35106.8300] [Topology ] . ( 881 sec) [ -35106.7699] [Topology ] . ( 884 sec) [ -35106.6321] [GTR parameters ] . ( 884 sec) [ -35106.5436] [Alpha ][ 0.425027] . ( 884 sec) [ -35106.5436] [Topology ] . ( 887 sec) [ -35106.4210] [Topology ] . ( 889 sec) [ -35106.3406] [Topology ] . ( 891 sec) [ -35106.2841] [Topology ] . ( 894 sec) [ -35106.2441] [Topology ] . ( 896 sec) [ -35106.2158] [Topology ] . ( 898 sec) [ -35106.1958] [Topology ] . ( 900 sec) [ -35106.1554] [GTR parameters ] . ( 900 sec) [ -35106.1236] [Alpha ][ 0.422499] . ( 900 sec) [ -35106.1236] [Topology ] . ( 902 sec) [ -35106.0824] [Topology ] . ( 905 sec) [ -35106.0556] [Topology ] . ( 907 sec) [ -35106.0370] [Topology ] . ( 909 sec) [ -35106.0238] [Topology ] . ( 912 sec) [ -35106.0146] [Topology ] . ( 914 sec) [ -35106.0081] [Topology ] . ( 915 sec) [ -35105.9977] [GTR parameters ] . ( 916 sec) [ -35105.9870] [Alpha ][ 0.421041] . ( 916 sec) [ -35105.9870] [Topology ] . ( 918 sec) [ -35105.9749] [Topology ] . ( 920 sec) [ -35105.9669] [Topology ] . ( 923 sec) [ -35105.9614] [Topology ] . ( 925 sec) [ -35105.9576] [Topology ] . ( 927 sec) [ -35105.9549] [Topology ] . ( 930 sec) [ -35105.9530] [Topology ] . ( 931 sec) [ -35105.9485] [GTR parameters ] . ( 932 sec) [ -35105.9451] [Alpha ][ 0.420199] . ( 932 sec) [ -35105.9451] [Topology ] . ( 934 sec) [ -35105.9408] [Topology ] . ( 936 sec) [ -35105.9381] [Topology ] . ( 939 sec) [ -35105.9362] [Topology ] . ( 941 sec) [ -35105.9349] [Topology ] . ( 943 sec) [ -35105.9339] [Topology ] . ( 945 sec) [ -35105.9332] [GTR parameters ] . ( 945 sec) [ -35105.9325] [Alpha ][ 0.419779] . ( 945 sec) [ -35105.9325] [Topology ] . ( 948 sec) [ -35105.9311] [Topology ] . ( 950 sec) [ -35105.9303] [Topology ] . ( 951 sec) [ -35105.9299] [GTR parameters ] . ( 951 sec) [ -35105.9299] [Alpha ][ 0.419779] . ( 951 sec) [ -35105.9299] [Topology ] . ( 954 sec) [ -35105.9292] [Topology ] . ( 954 sec) [ -35105.9292] [GTR parameters ] . ( 954 sec) [ -35105.9292] [Alpha ][ 0.419779] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -35124.620116 . Log likelihood obtained after SPR moves : -35105.929217 . Log likelihood of the current tree: -35105.929217. . Printing the most likely tree in file 'nucleic_M2945_62x1271_2006.phy_phyml_tree.txt'... . Time used 0h16m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 973.36user 0.00system 16:16.89elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps