.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2916_143x897_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 . 73 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 303 patterns found. (out of a total of 897 sites) . 620 sites without polymorphism (69.12%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 23Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -3593.8681] [GTR parameters ] . ( 2 sec) [ -3572.6148] [Alpha ][ 0.500960] . ( 3 sec) [ -3572.6148] [Topology ] . ( 5 sec) [ -3519.3730] [Topology ] . ( 7 sec) [ -3509.5189] [Topology ] . ( 9 sec) [ -3506.2944] [Topology ] . ( 11 sec) [ -3504.2974] [Topology ] . ( 13 sec) [ -3504.1015] [Topology ] . ( 15 sec) [ -3504.0779] [Topology ] . ( 17 sec) [ -3504.7313] [Topology ] . Moving backward . ( 17 sec) [ -3503.2725] [Topology ] . ( 19 sec) [ -3503.0857] [Topology ] . ( 22 sec) [ -3504.2253] [GTR parameters ] . ( 22 sec) [ -3495.1632] [Alpha ][ 0.267622] . ( 22 sec) [ -3495.1632] [Topology ] . ( 24 sec) [ -3493.0420] [Topology ] . ( 26 sec) [ -3493.1186] [Topology ] . Moving backward . ( 26 sec) [ -3492.9346] [Topology ] . ( 28 sec) [ -3493.3411] [Topology ] . Moving backward . ( 28 sec) [ -3492.9330] [Topology ] . ( 30 sec) [ -3493.4804] [Topology ] . Moving backward . ( 30 sec) [ -3492.9140] [Topology ] . ( 32 sec) [ -3493.3163] [Topology ] . Moving backward . ( 32 sec) [ -3492.9024] [Topology ] . Checking for NNIs, optimizing five branches... . ( 44 sec) [ -3493.0797] [Topology ] . ( 45 sec) [ -3492.8590] [GTR parameters ] . ( 45 sec) [ -3492.8542] [Alpha ][ 0.264260] . ( 46 sec) [ -3492.8542] [Topology ] . ( 47 sec) [ -3492.8481] [Topology ] . ( 49 sec) [ -3494.2271] [Topology ] . Moving backward . ( 49 sec) [ -3492.6788] [Topology ] . ( 51 sec) [ -3493.0008] [Topology ] . Moving backward . ( 51 sec) [ -3492.6040] [Topology ] . ( 53 sec) [ -3492.6918] [Topology ] . Moving backward . ( 53 sec) [ -3492.5978] [Topology ] . ( 55 sec) [ -3492.6979] [Topology ] . Moving backward . ( 55 sec) [ -3492.5942] [Topology ] . Checking for NNIs, optimizing five branches... . ( 67 sec) [ -3492.5890] [Topology ] . ( 67 sec) [ -3492.5873] [GTR parameters ] . ( 68 sec) [ -3492.5873] [Alpha ][ 0.263923] . ( 68 sec) [ -3492.5873] [Topology ] . ( 69 sec) [ -3492.5824] [Topology ] . ( 71 sec) [ -3492.5786] [Topology ] . ( 73 sec) [ -3492.5803] [Topology ] . Moving backward . ( 73 sec) [ -3492.5768] [Topology ] . ( 75 sec) [ -3492.5839] [Topology ] . Moving backward . ( 75 sec) [ -3492.5758] [Topology ] . ( 76 sec) [ -3492.5983] [Topology ] . Moving backward . ( 77 sec) [ -3492.5751] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -3492.5700] [Topology ] . ( 87 sec) [ -3492.5699] [GTR parameters ] . ( 88 sec) [ -3492.5699] [Alpha ][ 0.263923] . ( 88 sec) [ -3492.5699] [Topology ] . ( 89 sec) [ -3492.5657] [Topology ] . ( 91 sec) [ -3492.5632] [Topology ] . ( 93 sec) [ -3492.5785] [Topology ] . Moving backward . ( 93 sec) [ -3492.5615] [Topology ] . ( 95 sec) [ -3492.5855] [Topology ] . Moving backward . ( 95 sec) [ -3492.5595] [Topology ] . ( 96 sec) [ -3492.5860] [Topology ] . Moving backward . ( 97 sec) [ -3492.5564] [Topology ] . ( 98 sec) [ -3492.5628] [Topology ] . Checking for NNIs, optimizing five branches... . ( 108 sec) [ -3492.5521] [Topology ] . ( 109 sec) [ -3492.5521] [GTR parameters ] . ( 109 sec) [ -3492.5521] [Alpha ][ 0.263923] . ( 109 sec) [ -3492.5521] [Topology ] . ( 111 sec) [ -3492.5512] [Topology ] . Checking for NNIs, optimizing five branches... . ( 121 sec) [ -3492.5414] [Topology ] . ( 122 sec) [ -3492.5414] [GTR parameters ] . ( 122 sec) [ -3492.5414] [Alpha ][ 0.263923] . ( 122 sec) [ -3492.5414] [Topology ] . ( 123 sec) [ -3492.5409] [Topology ] . Checking for NNIs, optimizing five branches... . ( 134 sec) [ -3492.5408] [Topology ] . Checking for NNIs, optimizing five branches... . ( 144 sec) [ -3492.5404] [Topology ] . Checking for NNIs, optimizing five branches... . ( 154 sec) [ -3492.5390] [Topology ] . Checking for NNIs, optimizing five branches... . ( 164 sec) [ -3492.5377] [Topology ] . Checking for NNIs, optimizing five branches... . ( 174 sec) [ -3492.5355] [Topology ] . Checking for NNIs, optimizing five branches... . ( 185 sec) [ -3492.5346] [Topology ] . Checking for NNIs, optimizing five branches... . ( 195 sec) [ -3492.5345] [Topology ] . Checking for NNIs, optimizing five branches... . ( 205 sec) [ -3492.5316] [Topology ] . Checking for NNIs, optimizing five branches... . ( 215 sec) [ -3492.5315] [Topology ] . Checking for NNIs, optimizing five branches... . ( 225 sec) [ -3492.5314] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 238 sec) [ -3593.8681] [GTR parameters ] . ( 238 sec) [ -3572.6148] [Alpha ][ 0.500960] . ( 238 sec) [ -3572.4614] [ 353] [depth= 1] . ( 238 sec) [ -3571.6785] [ 353] [depth= 1] . ( 238 sec) [ -3571.5253] [ 353] [depth= 1] . ( 239 sec) [ -3571.0210] [ 353] [depth= 1] . ( 239 sec) [ -3570.9924] [ 353] [depth= 1] . ( 239 sec) [ -3570.9805] [ 353] [depth= 2] . ( 239 sec) [ -3570.6843] [ 353] [depth= 1] . ( 239 sec) [ -3569.8999] [ 353] [depth= 1] . ( 239 sec) [ -3569.6842] [ 353] [depth= 4] . ( 240 sec) [ -3569.6592] [ 353] [depth= 3] . ( 240 sec) [ -3569.4956] [ 353] [depth= 2] . ( 240 sec) [ -3568.7289] [ 353] [depth= 1] . ( 240 sec) [ -3568.4433] [ 353] [depth= 1] . ( 240 sec) [ -3568.3259] [ 353] [depth= 5] . ( 240 sec) [ -3568.0798] [ 353] [depth= 4] . ( 240 sec) [ -3567.5463] [ 353] [depth= 1] . ( 240 sec) [ -3567.0643] [ 353] [depth= 7] . ( 240 sec) [ -3567.0070] [ 353] [depth= 1] . ( 241 sec) [ -3566.3349] [ 353] [depth= 1] . ( 241 sec) [ -3565.9748] [ 353] [depth= 1] . ( 242 sec) [ -3565.9621] [ 353] [depth= 1] . ( 243 sec) [ -3565.9390] [ 353] [depth= 1] . ( 244 sec) [ -3565.9194] [ 353] [depth= 2] . ( 244 sec) [ -3565.9028] [ 353] [depth= 2] . ( 244 sec) [ -3565.8798] [ 353] [depth= 1] . ( 245 sec) [ -3565.3501] [ 353] [depth= 1] . ( 248 sec) [ -3564.7953] [ 353] [depth= 1] . ( 248 sec) [ -3564.5906] [ 353] [depth= 1] . ( 250 sec) [ -3564.5261] [ 353] [depth= 1] . ( 250 sec) [ -3563.5564] [ 353] [depth= 1] . ( 250 sec) [ -3563.5350] [ 353] [depth= 1] . ( 253 sec) [ -3563.5103] [ 353] [depth= 1] . ( 253 sec) [ -3563.4802] [ 353] [depth= 1] . ( 255 sec) [ -3563.4454] [ 353] [depth= 1] . ( 256 sec) [ -3555.7923] [ 351] [depth= 1] . ( 257 sec) [ -3555.7595] [ 351] [depth= 1] . ( 259 sec) [ -3555.2934] [ 351] [depth= 1] . ( 260 sec) [ -3555.1831] [ 351] [depth= 1] . ( 261 sec) [ -3554.9727] [ 351] [depth= 1] . ( 261 sec) [ -3554.9396] [ 351] [depth= 1] . ( 261 sec) [ -3554.7225] [ 351] [depth= 1] . ( 261 sec) [ -3554.6258] [ 351] [depth= 2] . ( 262 sec) [ -3552.9023] [ 351] [depth= 1] . ( 262 sec) [ -3552.8352] [ 351] [depth= 1] . ( 262 sec) [ -3549.9612] [ 350] [depth= 1] . ( 262 sec) [ -3549.9230] [ 350] [depth= 1] . ( 262 sec) [ -3549.8801] [ 350] [depth= 1] . ( 263 sec) [ -3549.8693] [ 350] [depth= 1] . ( 263 sec) [ -3549.7948] [ 350] [depth= 5] . ( 263 sec) [ -3549.7332] [ 350] [depth= 1] . ( 264 sec) [ -3549.7186] [ 350] [depth= 3] . ( 264 sec) [ -3549.7074] [ 350] [depth= 3] . ( 266 sec) [ -3548.3703] [ 350] [depth= 2] . ( 266 sec) [ -3548.2883] [ 350] [depth= 2] . ( 268 sec) [ -3547.5076] [ 350] [depth= 1] . ( 268 sec) [ -3546.3205] [ 350] [depth= 2] . ( 268 sec) [ -3545.3163] [ 350] [depth= 2] . ( 268 sec) [ -3545.3028] [ 350] [depth= 1] . ( 275 sec) [ -3539.7680] [ 349] [depth= 3] . ( 276 sec) [ -3539.3892] [ 349] [depth= 1] . ( 276 sec) [ -3538.0645] [ 349] [depth= 1] . ( 276 sec) [ -3538.0426] [ 349] [depth= 2] . ( 276 sec) [ -3538.0297] [ 349] [depth= 1] . ( 281 sec) [ -3537.9115] [ 349] [depth= 1] . ( 284 sec) [ -3536.7265] [ 349] [depth= 2] . ( 284 sec) [ -3536.6430] [ 349] [depth= 2] . ( 284 sec) [ -3536.2487] [ 349] [depth= 1] . ( 290 sec) [ -3534.9818] [ 349] [depth= 1] . ( 290 sec) [ -3534.7619] [ 349] [depth= 1] . ( 290 sec) [ -3534.7416] [ 349] [depth= 1] . ( 290 sec) [ -3534.6922] [ 349] [depth= 3] . ( 290 sec) [ -3534.6473] [ 349] [depth= 3] . ( 291 sec) [ -3534.4889] [ 349] [depth= 1] . ( 291 sec) [ -3534.4522] [ 349] [depth= 2] . ( 291 sec) [ -3534.3769] [ 349] [depth= 3] . ( 293 sec) [ -3534.1938] [ 349] [depth= 7] . ( 293 sec) [ -3534.1278] [ 349] [depth= 2] . ( 293 sec) [ -3534.1144] [ 349] [depth= 2] . ( 293 sec) [ -3533.6212] [ 349] [depth= 1] . ( 293 sec) [ -3533.4769] [ 349] [depth= 1] . ( 293 sec) [ -3528.1682] [ 348] [depth= 6] . ( 293 sec) [ -3528.0618] [ 348] [depth= 8] . ( 294 sec) [ -3528.0170] [ 348] [depth= 1] . ( 294 sec) [ -3528.0063] [ 348] [depth= 3] . ( 295 sec) [ -3527.8938] [ 348] [depth= 6] . ( 295 sec) [ -3527.8836] [ 348] [depth= 3] . ( 295 sec) [ -3527.8530] [ 348] [depth= 4] . ( 295 sec) [ -3527.5496] [ 348] [depth= 5] . ( 296 sec) [ -3527.1815] [ 348] [depth= 2] . ( 296 sec) [ -3527.1327] [ 348] [depth= 3] . ( 296 sec) [ -3526.4830] [ 348] [depth= 6] . ( 296 sec) [ -3526.4609] [ 348] [depth= 6] . ( 296 sec) [ -3525.8181] [ 348] [depth= 1] . ( 296 sec) [ -3525.8044] [ 348] [depth= 4] . ( 297 sec) [ -3525.6466] [ 348] [depth= 4] . ( 298 sec) [ -3525.5867] [ 348] [depth= 1] . ( 299 sec) [ -3520.2341] [ 347] [depth= 3] . ( 300 sec) [ -3520.2089] [ 347] [depth= 4] . ( 301 sec) [ -3520.0842] [ 347] [depth= 2] . ( 301 sec) [ -3519.4585] [ 347] [depth= 6] . ( 307 sec) [ -3519.3335] [ 347] [depth= 1] . ( 307 sec) [ -3518.9583] [ 347] [depth= 5] . ( 309 sec) [ -3517.5532] [ 347] [depth= 3] . ( 309 sec) [ -3517.5207] [ 347] [depth= 4] . ( 310 sec) [ -3517.4473] [ 347] [depth= 1] . ( 312 sec) [ -3507.6931] [ 346] [depth= 11] . ( 316 sec) [ -3507.6814] [ 346] [depth= 1] . ( 318 sec) [ -3507.5768] [ 346] [depth= 1] . ( 325 sec) [ -3507.3515] [ 346] [depth= 2] . ( 326 sec) [ -3507.3413] [ 346] [depth= 3] . ( 326 sec) [ -3507.3094] [ 346] [depth= 1] . ( 327 sec) [ -3507.2260] [ 346] [depth= 1] . ( 327 sec) [ -3507.1616] [ 346] [depth= 1] . ( 327 sec) [ -3507.1127] [ 346] [depth= 5] . ( 330 sec) [ -3506.8805] [ 346] [depth= 1] . ( 330 sec) [ -3506.8509] [ 346] [depth= 2] . ( 330 sec) [ -3506.5325] [ 346] [depth= 4] . ( 330 sec) [ -3506.3907] [ 346] [depth= 2] . ( 330 sec) [ -3506.2555] [ 346] [depth= 2] . ( 330 sec) [ -3506.0145] [ 346] [depth= 2] . ( 330 sec) [ -3505.5590] [ 346] [depth= 3] . ( 330 sec) [ -3504.3803] [ 345] [depth= 1] . ( 331 sec) [ -3499.1280] [ 345] [depth= 5] . ( 331 sec) [ -3499.1092] [ 345] [depth= 5] . ( 331 sec) [ -3498.9889] [ 345] [depth= 5] . ( 331 sec) [ -3497.7192] [ 345] [depth= 2] . ( 331 sec) [ -3497.0725] [ 345] [depth= 2] . ( 331 sec) [ -3496.7266] [ 345] [depth= 2] . ( 331 sec) [ -3496.6604] [ 345] [depth= 2] . ( 331 sec) [ -3496.6110] [ 345] [depth= 2] . ( 332 sec) [ -3496.5967] [ 345] [depth= 3] . ( 332 sec) [ -3496.5357] [ 345] [depth= 1] . ( 332 sec) [ -3495.2141] [ 345] [depth= 3] . ( 332 sec) [ -3494.9447] [ 345] [depth= 1] . ( 333 sec) [ -3494.8091] [ 345] [depth= 1] . ( 333 sec) [ -3494.4837] [ 345] [depth= 1] . ( 334 sec) [ -3494.4717] [ 345] [depth= 2] . ( 334 sec) [ -3494.4604] [ 345] [depth= 6] . ( 335 sec) [ -3494.4241] [ 345] [depth= 11] . ( 336 sec) [ -3494.3328] [ 345] [depth= 1] . ( 336 sec) [ -3494.3219] [ 345] [depth= 1] . ( 336 sec) [ -3494.2047] [ 345] [depth= 2] . ( 336 sec) [ -3494.1898] [ 345] [depth= 1] . ( 338 sec) [ -3494.1635] [ 345] [depth= 1] . ( 338 sec) [ -3494.1050] [ 345] [depth= 2] . ( 338 sec) [ -3493.6970] [ 345] [depth= 1] . ( 338 sec) [ -3493.6498] [ 345] [depth= 3] . ( 340 sec) [ -3493.5010] [ 345] [depth= 3] . ( 340 sec) [ -3493.4436] [ 345] [depth= 4] . ( 340 sec) [ -3493.3731] [ 345] [depth= 3] . ( 340 sec) [ -3493.3081] [ 345] [depth= 4] . ( 340 sec) [ -3493.2975] [ 345] [depth= 2] . ( 340 sec) [ -3493.2766] [ 345] [depth= 2] . ( 341 sec) [ -3493.2318] [ 345] [depth= 3] . ( 343 sec) [ -3493.2177] [ 345] [depth= 3] . ( 345 sec) [ -3493.0319] [ 345] [depth= 5] . ( 347 sec) [ -3483.6944] [Branch lengths ] . ( 348 sec) [ -3483.0392] [GTR parameters ] . ( 349 sec) [ -3474.7473] [Alpha ][ 0.270921] . ( 378 sec) [ -3474.2795] [ 345] [depth= 4] . ( 378 sec) [ -3474.2688] [ 345] [depth= 2] . ( 379 sec) [ -3473.8635] [ 346] [depth= 18] . ( 379 sec) [ -3473.5325] [ 346] [depth= 2] . ( 381 sec) [ -3473.4741] [ 346] [depth= 1] . ( 381 sec) [ -3473.3155] [ 346] [depth= 4] . ( 381 sec) [ -3473.1497] [ 346] [depth= 1] . ( 381 sec) [ -3473.1393] [ 346] [depth= 1] . ( 383 sec) [ -3473.0695] [ 346] [depth= 5] . ( 390 sec) [ -3473.0351] [ 346] [depth= 1] . ( 390 sec) [ -3472.9870] [ 346] [depth= 3] . ( 396 sec) [ -3472.8178] [ 346] [depth= 1] . ( 396 sec) [ -3472.7510] [ 346] [depth= 1] . ( 402 sec) [ -3472.6761] [ 346] [depth= 3] . ( 411 sec) [ -3472.6407] [ 346] [depth= 1] . ( 435 sec) [ -3469.9367] [ 345] [depth= 1] . ( 440 sec) [ -3469.7765] [ 345] [depth= 5] . ( 451 sec) [ -3469.7408] [ 345] [depth= 1] . ( 454 sec) [ -3468.8517] [ 344] [depth= 2] . ( 454 sec) [ -3468.8389] [ 344] [depth= 1] . ( 471 sec) [ -3468.8260] [ 344] [depth= 1] . ( 479 sec) [ -3468.8109] [ 344] [depth= 7] . ( 514 sec) [ -3468.7854] [ 344] [depth= 2] . ( 516 sec) [ -3468.6898] [ 344] [depth= 1] . ( 520 sec) [ -3468.6418] [ 344] [depth= 2] . ( 520 sec) [ -3468.6216] [ 344] [depth= 6] . ( 520 sec) [ -3468.5713] [ 344] [depth= 4] . ( 539 sec) [ -3465.7730] [Branch lengths ] . ( 541 sec) [ -3465.4756] [GTR parameters ] . ( 541 sec) [ -3465.4752] [Alpha ][ 0.269862] . ( 565 sec) [ -3462.4315] [ 343] [depth= 8] . ( 591 sec) [ -3462.3105] [ 343] [depth= 1] . ( 597 sec) [ -3462.2283] [ 343] [depth= 3] . ( 742 sec) [ -3461.3728] [Branch lengths ] . ( 743 sec) [ -3461.3136] [GTR parameters ] . ( 743 sec) [ -3461.3110] [Alpha ][ 0.272528] . ( 946 sec) [ -3461.1530] [Branch lengths ] . ( 1041 sec) [ -3461.1520] [Branch lengths ] . ( 1041 sec) [ -3461.1520] [Topology ] . ( 1043 sec) [ -3461.1520] [Topology ] . ( 1044 sec) [ -3461.1516] [GTR parameters ] . ( 1044 sec) [ -3461.1516] [Alpha ][ 0.272528] . Checking for NNIs, optimizing five branches... . ( 1055 sec) [ -3461.1515] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3492.531436 . Log likelihood obtained after SPR moves : -3461.151501 . Log likelihood of the current tree: -3461.151501. . Printing the most likely tree in file 'nucleic_M2916_143x897_2006.phy_phyml_tree.txt'... . Time used 0h17m47s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1065.69user 0.00system 17:47.72elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps