.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2975_93x982_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 . Compressing sequences... . 725 patterns found. (out of a total of 982 sites) . 454 sites without polymorphism (46.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -12806.7417] [GTR parameters ] . ( 2 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 2 sec) [ -12644.1413] [Topology ] . ( 5 sec) [ -12429.9217] [Topology ] . ( 8 sec) [ -12393.9974] [Topology ] . ( 12 sec) [ -12384.0402] [Topology ] . ( 15 sec) [ -12379.8706] [Topology ] . ( 18 sec) [ -12375.5020] [Topology ] . ( 21 sec) [ -12372.0127] [Topology ] . ( 24 sec) [ -12367.8036] [Topology ] . ( 27 sec) [ -12358.6163] [Topology ] . ( 30 sec) [ -12347.6738] [Topology ] . ( 39 sec) [ -12325.5729] [GTR parameters ] . ( 39 sec) [ -12316.6221] [Alpha ][ 0.402047] . ( 39 sec) [ -12316.6221] [Topology ] . ( 42 sec) [ -12311.6903] [Topology ] . ( 45 sec) [ -12310.8725] [Topology ] . ( 48 sec) [ -12310.7349] [Topology ] . ( 52 sec) [ -12310.6936] [Topology ] . ( 55 sec) [ -12310.6783] [Topology ] . ( 58 sec) [ -12310.6717] [Topology ] . ( 61 sec) [ -12310.6688] [Topology ] . Checking for NNIs, optimizing five branches... . ( 82 sec) [ -12310.6353] [Topology ] . ( 86 sec) [ -12310.5799] [GTR parameters ] . ( 86 sec) [ -12310.5503] [Alpha ][ 0.397259] . ( 86 sec) [ -12310.5503] [Topology ] . ( 89 sec) [ -12309.9367] [Topology ] . ( 92 sec) [ -12309.5523] [Topology ] . ( 95 sec) [ -12309.4877] [Topology ] . ( 99 sec) [ -12309.4700] [Topology ] . ( 102 sec) [ -12309.4642] [Topology ] . ( 105 sec) [ -12309.4621] [Topology ] . ( 108 sec) [ -12309.4611] [Topology ] . Checking for NNIs, optimizing five branches... . ( 129 sec) [ -12308.9047] [Topology ] . ( 130 sec) [ -12308.9028] [GTR parameters ] . ( 131 sec) [ -12308.9010] [Alpha ][ 0.395957] . ( 131 sec) [ -12308.9010] [Topology ] . ( 134 sec) [ -12308.8597] [Topology ] . ( 137 sec) [ -12308.8541] [Topology ] . ( 140 sec) [ -12308.8529] [Topology ] . ( 143 sec) [ -12308.8526] [Topology ] . Checking for NNIs, optimizing five branches... . ( 164 sec) [ -12308.8520] [Topology ] . ( 166 sec) [ -12308.8516] [GTR parameters ] . ( 166 sec) [ -12308.8516] [Alpha ][ 0.395957] . ( 167 sec) [ -12308.8516] [Topology ] . ( 170 sec) [ -12308.8485] [Topology ] . ( 173 sec) [ -12308.8392] [Topology ] . ( 176 sec) [ -12308.8360] [Topology ] . ( 179 sec) [ -12308.8347] [Topology ] . ( 182 sec) [ -12308.8342] [Topology ] . Checking for NNIs, optimizing five branches... . ( 203 sec) [ -12308.8340] [Topology ] . ( 203 sec) [ -12308.8340] [GTR parameters ] . ( 204 sec) [ -12308.8340] [Alpha ][ 0.395957] . ( 204 sec) [ -12308.8340] [Topology ] . ( 207 sec) [ -12308.8338] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 250 sec) [ -12806.7417] [GTR parameters ] . ( 251 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 251 sec) [ -12640.5693] [ 2378] [depth= 1] . ( 251 sec) [ -12635.2836] [ 2377] [depth= 1] . ( 252 sec) [ -12633.3264] [ 2376] [depth= 1] . ( 253 sec) [ -12632.1744] [ 2375] [depth= 1] . ( 253 sec) [ -12631.1947] [ 2375] [depth= 1] . ( 254 sec) [ -12631.0543] [ 2377] [depth= 2] . ( 254 sec) [ -12621.1528] [ 2373] [depth= 1] . ( 255 sec) [ -12616.5645] [ 2371] [depth= 2] . ( 255 sec) [ -12615.3601] [ 2371] [depth= 1] . ( 255 sec) [ -12613.0246] [ 2371] [depth= 1] . ( 255 sec) [ -12613.0102] [ 2371] [depth= 1] . ( 256 sec) [ -12612.9641] [ 2376] [depth= 2] . ( 256 sec) [ -12597.5377] [ 2374] [depth= 2] . ( 257 sec) [ -12594.2473] [ 2374] [depth= 1] . ( 257 sec) [ -12588.6016] [ 2374] [depth= 1] . ( 257 sec) [ -12584.6516] [ 2376] [depth= 1] . ( 258 sec) [ -12584.1393] [ 2376] [depth= 1] . ( 258 sec) [ -12581.1476] [ 2376] [depth= 1] . ( 259 sec) [ -12579.9040] [ 2378] [depth= 1] . ( 259 sec) [ -12576.6041] [ 2374] [depth= 1] . ( 259 sec) [ -12573.8256] [ 2374] [depth= 1] . ( 260 sec) [ -12573.0713] [ 2374] [depth= 1] . ( 260 sec) [ -12569.5781] [ 2374] [depth= 1] . ( 260 sec) [ -12569.3060] [ 2374] [depth= 1] . ( 261 sec) [ -12568.6374] [ 2379] [depth= 1] . ( 261 sec) [ -12561.5306] [ 2374] [depth= 1] . ( 262 sec) [ -12554.0244] [ 2374] [depth= 1] . ( 262 sec) [ -12553.6436] [ 2374] [depth= 1] . ( 264 sec) [ -12550.0187] [ 2373] [depth= 1] . ( 264 sec) [ -12549.6405] [ 2373] [depth= 1] . ( 264 sec) [ -12549.5125] [ 2373] [depth= 1] . ( 266 sec) [ -12543.0054] [ 2377] [depth= 2] . ( 266 sec) [ -12538.7970] [ 2375] [depth= 1] . ( 267 sec) [ -12533.1491] [ 2379] [depth= 4] . ( 267 sec) [ -12522.1439] [ 2377] [depth= 1] . ( 268 sec) [ -12521.9624] [ 2377] [depth= 1] . ( 268 sec) [ -12519.4216] [ 2377] [depth= 4] . ( 269 sec) [ -12518.5251] [ 2378] [depth= 1] . ( 269 sec) [ -12514.8310] [ 2377] [depth= 2] . ( 269 sec) [ -12514.6170] [ 2379] [depth= 3] . ( 270 sec) [ -12512.8933] [ 2381] [depth= 1] . ( 271 sec) [ -12511.8103] [ 2380] [depth= 2] . ( 272 sec) [ -12506.6788] [ 2380] [depth= 1] . ( 272 sec) [ -12495.4536] [ 2375] [depth= 1] . ( 272 sec) [ -12493.4723] [ 2376] [depth= 1] . ( 273 sec) [ -12491.2285] [ 2373] [depth= 1] . ( 275 sec) [ -12489.6622] [ 2372] [depth= 1] . ( 275 sec) [ -12488.3437] [ 2372] [depth= 1] . ( 275 sec) [ -12487.5915] [ 2372] [depth= 2] . ( 275 sec) [ -12482.1687] [ 2368] [depth= 2] . ( 276 sec) [ -12478.3744] [ 2368] [depth= 1] . ( 277 sec) [ -12477.9765] [ 2369] [depth= 1] . ( 277 sec) [ -12472.8172] [ 2369] [depth= 1] . ( 277 sec) [ -12471.7730] [ 2365] [depth= 6] . ( 278 sec) [ -12469.9536] [ 2369] [depth= 1] . ( 278 sec) [ -12467.8135] [ 2368] [depth= 4] . ( 278 sec) [ -12458.2790] [ 2367] [depth= 6] . ( 279 sec) [ -12458.1156] [ 2369] [depth= 1] . ( 279 sec) [ -12457.9181] [ 2369] [depth= 1] . ( 280 sec) [ -12457.0392] [ 2368] [depth= 1] . ( 280 sec) [ -12448.8020] [ 2366] [depth= 4] . ( 280 sec) [ -12445.6451] [ 2359] [depth= 6] . ( 281 sec) [ -12442.9493] [ 2358] [depth= 1] . ( 281 sec) [ -12442.8119] [ 2359] [depth= 1] . ( 281 sec) [ -12438.9573] [ 2358] [depth= 1] . ( 282 sec) [ -12437.4520] [ 2357] [depth= 1] . ( 282 sec) [ -12436.2481] [ 2356] [depth= 1] . ( 283 sec) [ -12435.9965] [ 2357] [depth= 1] . ( 283 sec) [ -12431.0452] [ 2360] [depth= 5] . ( 284 sec) [ -12430.6763] [ 2361] [depth= 1] . ( 284 sec) [ -12429.9133] [ 2363] [depth= 1] . ( 285 sec) [ -12429.5187] [ 2362] [depth= 1] . ( 286 sec) [ -12428.2098] [ 2367] [depth= 1] . ( 287 sec) [ -12426.7986] [ 2367] [depth= 1] . ( 288 sec) [ -12426.3159] [ 2363] [depth= 3] . ( 289 sec) [ -12424.6844] [ 2363] [depth= 1] . ( 289 sec) [ -12423.8755] [ 2364] [depth= 4] . ( 289 sec) [ -12419.8666] [ 2365] [depth= 5] . ( 290 sec) [ -12414.1931] [ 2363] [depth= 4] . ( 290 sec) [ -12413.8846] [ 2358] [depth= 1] . ( 291 sec) [ -12413.0258] [ 2359] [depth= 1] . ( 291 sec) [ -12412.3386] [ 2358] [depth= 1] . ( 291 sec) [ -12411.9320] [ 2354] [depth= 1] . ( 292 sec) [ -12411.2544] [ 2356] [depth= 1] . ( 292 sec) [ -12410.2268] [ 2357] [depth= 3] . ( 294 sec) [ -12349.3503] [Branch lengths ] . ( 300 sec) [ -12332.5440] [GTR parameters ] . ( 300 sec) [ -12320.3894] [Alpha ][ 0.384885] . ( 303 sec) [ -12319.8239] [ 2356] [depth= 1] . ( 305 sec) [ -12319.8106] [ 2356] [depth= 1] . ( 308 sec) [ -12319.7713] [ 2356] [depth= 1] . ( 311 sec) [ -12319.7603] [ 2356] [depth= 1] . ( 313 sec) [ -12314.6753] [ 2354] [depth= 2] . ( 314 sec) [ -12307.1725] [ 2349] [depth= 3] . ( 324 sec) [ -12305.4347] [ 2347] [depth= 1] . ( 324 sec) [ -12305.2827] [ 2345] [depth= 1] . ( 328 sec) [ -12304.7428] [ 2349] [depth= 4] . ( 328 sec) [ -12301.8262] [ 2348] [depth= 5] . ( 329 sec) [ -12301.3594] [ 2349] [depth= 1] . ( 333 sec) [ -12301.0713] [ 2352] [depth= 1] . ( 334 sec) [ -12300.6510] [ 2351] [depth= 1] . ( 337 sec) [ -12299.7754] [ 2350] [depth= 1] . ( 337 sec) [ -12299.6027] [ 2348] [depth= 1] . ( 344 sec) [ -12299.3527] [ 2348] [depth= 1] . ( 349 sec) [ -12299.0501] [ 2350] [depth= 2] . ( 349 sec) [ -12297.3192] [ 2348] [depth= 2] . ( 351 sec) [ -12297.0273] [ 2348] [depth= 1] . ( 351 sec) [ -12296.0859] [ 2347] [depth= 1] . ( 351 sec) [ -12296.0601] [ 2345] [depth= 1] . ( 353 sec) [ -12289.9001] [Branch lengths ] . ( 357 sec) [ -12289.6398] [GTR parameters ] . ( 357 sec) [ -12289.6101] [Alpha ][ 0.389881] . ( 359 sec) [ -12289.2025] [ 2346] [depth= 1] . ( 379 sec) [ -12289.1551] [ 2347] [depth= 1] . ( 403 sec) [ -12288.9393] [ 2348] [depth= 7] . ( 407 sec) [ -12288.8465] [ 2348] [depth= 1] . ( 408 sec) [ -12288.5863] [ 2350] [depth= 1] . ( 409 sec) [ -12286.9888] [Branch lengths ] . ( 413 sec) [ -12286.9774] [GTR parameters ] . ( 413 sec) [ -12286.9697] [Alpha ][ 0.392411] . ( 473 sec) [ -12286.7521] [Branch lengths ] . ( 585 sec) [ -12286.2441] [ 2346] [depth= 1] . ( 587 sec) [ -12286.0356] [ 2346] [depth= 1] . ( 622 sec) [ -12285.8079] [Branch lengths ] . ( 627 sec) [ -12285.7957] [GTR parameters ] . ( 627 sec) [ -12285.7889] [Alpha ][ 0.394808] . ( 627 sec) [ -12285.7889] [Topology ] . ( 630 sec) [ -12285.7576] [Topology ] . ( 633 sec) [ -12285.7488] [Topology ] . ( 636 sec) [ -12285.7452] [Topology ] . ( 639 sec) [ -12285.7436] [Topology ] . ( 642 sec) [ -12285.7429] [Topology ] . ( 643 sec) [ -12285.7429] [GTR parameters ] . ( 643 sec) [ -12285.7429] [Alpha ][ 0.394808] . ( 643 sec) [ -12285.7429] [Topology ] . ( 646 sec) [ -12285.7426] [Topology ] . ( 647 sec) [ -12285.7425] [GTR parameters ] . ( 647 sec) [ -12285.7425] [Alpha ][ 0.394808] . Checking for NNIs, optimizing five branches... . ( 668 sec) [ -12285.6121] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12308.833763 . Log likelihood obtained after SPR moves : -12285.612068 . Log likelihood of the current tree: -12285.612068. . Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'... . Time used 0h11m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 688.73user 0.00system 11:31.45elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps