.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2932_68x1712_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 . 5 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 1264 patterns found. (out of a total of 1712 sites) . 601 sites without polymorphism (35.11%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 45Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 8 sec) [ -15465.7212] [GTR parameters ] . ( 8 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 8 sec) [ -15431.9484] [Topology ] . ( 12 sec) [ -15123.7998] [Topology ] . ( 16 sec) [ -15045.1303] [Topology ] . ( 20 sec) [ -15019.2652] [Topology ] . ( 24 sec) [ -15009.7959] [Topology ] . ( 27 sec) [ -15006.3124] [Topology ] . ( 31 sec) [ -15003.2852] [Topology ] . ( 34 sec) [ -14997.0189] [Topology ] . ( 38 sec) [ -14981.6104] [Topology ] . ( 41 sec) [ -14966.8514] [Topology ] . ( 54 sec) [ -14941.8760] [GTR parameters ] . ( 54 sec) [ -14941.7245] [Alpha ][ 0.597689] . ( 54 sec) [ -14941.7245] [Topology ] . ( 58 sec) [ -14938.9688] [Topology ] . ( 61 sec) [ -14938.5298] [Topology ] . ( 64 sec) [ -14938.0933] [Topology ] . ( 68 sec) [ -14937.9609] [Topology ] . ( 71 sec) [ -14937.9156] [Topology ] . ( 75 sec) [ -14937.6606] [Topology ] . ( 78 sec) [ -14937.8851] [Topology ] . Moving backward . ( 78 sec) [ -14932.9840] [Topology ] . ( 82 sec) [ -14932.5999] [Topology ] . Checking for NNIs, optimizing five branches... . ( 117 sec) [ -14932.8775] [Topology ] . ( 123 sec) [ -14932.6234] [GTR parameters ] . ( 123 sec) [ -14932.3411] [Alpha ][ 0.576687] . ( 124 sec) [ -14932.3411] [Topology ] . ( 127 sec) [ -14931.4471] [Topology ] . ( 131 sec) [ -14931.6178] [Topology ] . Moving backward . ( 131 sec) [ -14931.3953] [Topology ] . ( 134 sec) [ -14931.7351] [Topology ] . Moving backward . ( 135 sec) [ -14931.3471] [Topology ] . ( 138 sec) [ -14931.4047] [Topology ] . Moving backward . ( 138 sec) [ -14931.3258] [Topology ] . ( 142 sec) [ -14931.5111] [Topology ] . Moving backward . ( 142 sec) [ -14931.3137] [Topology ] . Checking for NNIs, optimizing five branches... . ( 176 sec) [ -14930.6260] [Topology ] . ( 178 sec) [ -14930.6075] [GTR parameters ] . ( 179 sec) [ -14930.5855] [Alpha ][ 0.570794] . ( 179 sec) [ -14930.5855] [Topology ] . ( 182 sec) [ -14930.1129] [Topology ] . ( 186 sec) [ -14930.3959] [Topology ] . Moving backward . ( 186 sec) [ -14929.8056] [Topology ] . ( 190 sec) [ -14929.9694] [Topology ] . Moving backward . ( 190 sec) [ -14929.6610] [Topology ] . ( 193 sec) [ -14929.6374] [Topology ] . ( 197 sec) [ -14929.6416] [Topology ] . Moving backward . ( 197 sec) [ -14929.6332] [Topology ] . ( 200 sec) [ -14929.6352] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 230 sec) [ -14929.6291] [Topology ] . ( 235 sec) [ -14929.6260] [GTR parameters ] . ( 235 sec) [ -14929.6239] [Alpha ][ 0.568931] . ( 236 sec) [ -14929.6239] [Topology ] . ( 239 sec) [ -14929.6195] [Topology ] . ( 242 sec) [ -14929.6177] [Topology ] . ( 246 sec) [ -14929.6180] [Topology ] . Checking for NNIs, optimizing five branches... . ( 276 sec) [ -14929.6162] [Topology ] . ( 278 sec) [ -14929.6157] [GTR parameters ] . ( 279 sec) [ -14929.6154] [Alpha ][ 0.568261] . ( 279 sec) [ -14929.6154] [Topology ] . ( 282 sec) [ -14929.6146] [Topology ] . Checking for NNIs, optimizing five branches... . ( 312 sec) [ -14929.6140] [Topology ] . ( 313 sec) [ -14929.6139] [GTR parameters ] . ( 313 sec) [ -14929.6139] [Alpha ][ 0.568261] . ( 314 sec) [ -14929.6139] [Topology ] . ( 317 sec) [ -14929.6134] [Topology ] . Checking for NNIs, optimizing five branches... . ( 347 sec) [ -14929.6131] [Topology ] . Checking for NNIs, optimizing five branches... . ( 379 sec) [ -14929.6092] [Topology ] . Checking for NNIs, optimizing five branches... . ( 410 sec) [ -14929.6091] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 449 sec) [ -15465.7212] [GTR parameters ] . ( 449 sec) [ -15431.9484] [Alpha ][ 0.613860] . ( 449 sec) [ -15431.3316] [ 3250] [depth= 1] . ( 452 sec) [ -15430.9760] [ 3252] [depth= 1] . ( 452 sec) [ -15430.5960] [ 3255] [depth= 1] . ( 452 sec) [ -15402.3780] [ 3252] [depth= 1] . ( 452 sec) [ -15387.4679] [ 3269] [depth= 1] . ( 453 sec) [ -15376.8933] [ 3271] [depth= 1] . ( 453 sec) [ -15368.7103] [ 3289] [depth= 2] . ( 454 sec) [ -15360.7370] [ 3290] [depth= 1] . ( 455 sec) [ -15342.9301] [ 3286] [depth= 1] . ( 455 sec) [ -15342.2817] [ 3286] [depth= 1] . ( 456 sec) [ -15337.1367] [ 3286] [depth= 1] . ( 456 sec) [ -15328.5284] [ 3286] [depth= 1] . ( 456 sec) [ -15324.4261] [ 3286] [depth= 2] . ( 456 sec) [ -15299.4630] [ 3260] [depth= 2] . ( 457 sec) [ -15297.9546] [ 3260] [depth= 1] . ( 457 sec) [ -15226.6796] [ 3246] [depth= 2] . ( 457 sec) [ -15223.5302] [ 3246] [depth= 1] . ( 458 sec) [ -15219.9536] [ 3249] [depth= 1] . ( 458 sec) [ -15218.0654] [ 3246] [depth= 1] . ( 459 sec) [ -15215.1312] [ 3242] [depth= 1] . ( 459 sec) [ -15207.1548] [ 3241] [depth= 1] . ( 460 sec) [ -15178.2131] [ 3238] [depth= 1] . ( 460 sec) [ -15177.5438] [ 3238] [depth= 1] . ( 460 sec) [ -15176.6334] [ 3238] [depth= 1] . ( 460 sec) [ -15176.6148] [ 3238] [depth= 5] . ( 461 sec) [ -15174.4771] [ 3238] [depth= 7] . ( 462 sec) [ -15169.9818] [ 3237] [depth= 5] . ( 462 sec) [ -15168.4855] [ 3237] [depth= 3] . ( 462 sec) [ -15159.0500] [ 3237] [depth= 1] . ( 462 sec) [ -15152.2342] [ 3236] [depth= 1] . ( 463 sec) [ -15149.8557] [ 3237] [depth= 3] . ( 463 sec) [ -15149.4975] [ 3237] [depth= 2] . ( 464 sec) [ -15149.1815] [ 3237] [depth= 2] . ( 465 sec) [ -15144.5080] [ 3237] [depth= 1] . ( 465 sec) [ -15144.2312] [ 3236] [depth= 2] . ( 466 sec) [ -15141.4441] [ 3236] [depth= 4] . ( 467 sec) [ -15138.9343] [ 3236] [depth= 3] . ( 467 sec) [ -15137.4369] [ 3237] [depth= 2] . ( 467 sec) [ -15134.6409] [ 3240] [depth= 1] . ( 468 sec) [ -15125.1651] [ 3247] [depth= 1] . ( 468 sec) [ -15124.8924] [ 3268] [depth= 1] . ( 468 sec) [ -15121.4875] [ 3271] [depth= 1] . ( 468 sec) [ -15111.7082] [ 3268] [depth= 1] . ( 469 sec) [ -15110.3915] [ 3259] [depth= 1] . ( 470 sec) [ -15110.3108] [ 3259] [depth= 1] . ( 470 sec) [ -15106.8144] [ 3267] [depth= 1] . ( 471 sec) [ -15104.1425] [ 3268] [depth= 1] . ( 471 sec) [ -15089.5291] [ 3266] [depth= 1] . ( 472 sec) [ -15087.3993] [ 3266] [depth= 1] . ( 472 sec) [ -15086.2127] [ 3267] [depth= 1] . ( 473 sec) [ -15075.8849] [ 3255] [depth= 2] . ( 473 sec) [ -15074.6378] [ 3256] [depth= 1] . ( 477 sec) [ -15072.7604] [ 3256] [depth= 1] . ( 478 sec) [ -15072.6756] [ 3256] [depth= 1] . ( 481 sec) [ -15071.9309] [ 3255] [depth= 2] . ( 483 sec) [ -15066.7065] [ 3254] [depth= 4] . ( 483 sec) [ -15066.6527] [ 3254] [depth= 2] . ( 484 sec) [ -15066.6317] [ 3254] [depth= 3] . ( 485 sec) [ -15066.4662] [ 3254] [depth= 1] . ( 485 sec) [ -15066.4475] [ 3254] [depth= 2] . ( 486 sec) [ -15065.8339] [ 3254] [depth= 2] . ( 487 sec) [ -15065.7142] [ 3254] [depth= 2] . ( 490 sec) [ -15065.4899] [ 3254] [depth= 2] . ( 490 sec) [ -15065.4663] [ 3254] [depth= 1] . ( 491 sec) [ -15065.4080] [ 3254] [depth= 2] . ( 493 sec) [ -15065.3606] [ 3254] [depth= 5] . ( 499 sec) [ -14985.5307] [Branch lengths ] . ( 507 sec) [ -14972.2412] [GTR parameters ] . ( 508 sec) [ -14972.0099] [Alpha ][ 0.593758] . ( 508 sec) [ -14971.2118] [ 3252] [depth= 1] . ( 510 sec) [ -14969.6020] [ 3242] [depth= 1] . ( 512 sec) [ -14964.8776] [ 3239] [depth= 1] . ( 512 sec) [ -14963.6740] [ 3215] [depth= 1] . ( 512 sec) [ -14955.9309] [ 3219] [depth= 2] . ( 515 sec) [ -14955.9034] [ 3219] [depth= 1] . ( 516 sec) [ -14955.8487] [ 3219] [depth= 1] . ( 525 sec) [ -14955.8278] [ 3219] [depth= 2] . ( 530 sec) [ -14955.7823] [ 3219] [depth= 1] . ( 531 sec) [ -14955.5209] [ 3219] [depth= 1] . ( 531 sec) [ -14953.5216] [ 3219] [depth= 2] . ( 531 sec) [ -14953.4906] [ 3219] [depth= 5] . ( 535 sec) [ -14952.2332] [ 3216] [depth= 1] . ( 539 sec) [ -14949.0679] [ 3216] [depth= 1] . ( 539 sec) [ -14949.0018] [ 3216] [depth= 1] . ( 539 sec) [ -14948.7168] [ 3216] [depth= 1] . ( 539 sec) [ -14948.6794] [ 3216] [depth= 1] . ( 542 sec) [ -14948.4115] [ 3216] [depth= 1] . ( 543 sec) [ -14948.2911] [ 3216] [depth= 1] . ( 549 sec) [ -14948.1888] [ 3216] [depth= 1] . ( 570 sec) [ -14936.0711] [Branch lengths ] . ( 576 sec) [ -14935.1236] [GTR parameters ] . ( 577 sec) [ -14935.0638] [Alpha ][ 0.583612] . ( 583 sec) [ -14935.0222] [ 3216] [depth= 1] . ( 589 sec) [ -14935.0078] [ 3216] [depth= 2] . ( 593 sec) [ -14934.9974] [ 3216] [depth= 3] . ( 638 sec) [ -14932.5067] [Branch lengths ] . ( 644 sec) [ -14932.4659] [GTR parameters ] . ( 644 sec) [ -14932.4100] [Alpha ][ 0.574091] . ( 706 sec) [ -14931.9789] [Branch lengths ] . ( 731 sec) [ -14930.9015] [ 3215] [depth= 2] . ( 777 sec) [ -14929.9518] [ 3224] [depth= 2] . ( 848 sec) [ -14928.7571] [Branch lengths ] . ( 854 sec) [ -14928.7327] [GTR parameters ] . ( 854 sec) [ -14928.7187] [Alpha ][ 0.569395] . ( 997 sec) [ -14928.6317] [Branch lengths ] . ( 997 sec) [ -14928.6317] [Topology ] . ( 1001 sec) [ -14928.2402] [Topology ] . ( 1004 sec) [ -14926.2670] [Topology ] . ( 1007 sec) [ -14922.4720] [Topology ] . ( 1011 sec) [ -14921.7838] [Topology ] . ( 1014 sec) [ -14921.6095] [Topology ] . ( 1018 sec) [ -14921.5273] [Topology ] . ( 1019 sec) [ -14921.5272] [GTR parameters ] . ( 1019 sec) [ -14921.5249] [Alpha ][ 0.567474] . ( 1020 sec) [ -14921.5249] [Topology ] . ( 1023 sec) [ -14921.4776] [Topology ] . ( 1026 sec) [ -14921.4501] [Topology ] . ( 1030 sec) [ -14921.4344] [Topology ] . ( 1033 sec) [ -14921.4271] [Topology ] . ( 1037 sec) [ -14921.4301] [Topology ] . Moving backward . ( 1037 sec) [ -14921.4225] [Topology ] . ( 1040 sec) [ -14921.4202] [Topology ] . ( 1042 sec) [ -14921.4201] [GTR parameters ] . ( 1042 sec) [ -14921.4201] [Alpha ][ 0.567474] . ( 1042 sec) [ -14921.4201] [Topology ] . ( 1045 sec) [ -14921.4253] [Topology ] . Moving backward . ( 1046 sec) [ -14921.4171] [Topology ] . ( 1049 sec) [ -14921.4168] [Topology ] . ( 1053 sec) [ -14921.4126] [GTR parameters ] . ( 1053 sec) [ -14921.4126] [Alpha ][ 0.567474] . ( 1053 sec) [ -14921.4126] [Topology ] . ( 1057 sec) [ -14921.4180] [Topology ] . Moving backward . ( 1057 sec) [ -14921.4104] [Topology ] . ( 1060 sec) [ -14921.4109] [Topology ] . ( 1062 sec) [ -14921.4109] [GTR parameters ] . ( 1062 sec) [ -14921.4109] [Alpha ][ 0.567474] . ( 1062 sec) [ -14921.4109] [Topology ] . ( 1066 sec) [ -14921.4162] [Topology ] . Moving backward . ( 1066 sec) [ -14921.4093] [Topology ] . ( 1070 sec) [ -14921.4101] [Topology ] . ( 1071 sec) [ -14921.4100] [GTR parameters ] . ( 1071 sec) [ -14921.4100] [Alpha ][ 0.567474] . Checking for NNIs, optimizing five branches... . ( 1103 sec) [ -14921.3056] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1135 sec) [ -14921.3024] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -14929.609064 . Log likelihood obtained after SPR moves : -14921.302358 . Log likelihood of the current tree: -14921.302358. . Printing the most likely tree in file 'nucleic_M2932_68x1712_2006.phy_phyml_tree.txt'... . Time used 0h19m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1161.55user 0.00system 19:27.96elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps