.......................... 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 : 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)... . ( 5 sec) [ -36495.9506] [GTR parameters ] . ( 5 sec) [ -36002.5932] [Alpha ][ 0.500960] . ( 7 sec) [ -35998.6346] [ 9298] [depth= 1] . ( 9 sec) [ -35996.9518] [ 9294] [depth= 1] . ( 9 sec) [ -35993.4197] [ 9298] [depth= 1] . ( 9 sec) [ -35990.0069] [ 9296] [depth= 1] . ( 10 sec) [ -35989.6571] [ 9298] [depth= 1] . ( 10 sec) [ -35988.6791] [ 9301] [depth= 1] . ( 10 sec) [ -35975.2493] [ 9298] [depth= 1] . ( 11 sec) [ -35968.7763] [ 9315] [depth= 1] . ( 11 sec) [ -35938.7796] [ 9298] [depth= 1] . ( 11 sec) [ -35887.6023] [ 9304] [depth= 2] . ( 11 sec) [ -35884.2680] [ 9303] [depth= 1] . ( 11 sec) [ -35880.5717] [ 9297] [depth= 1] . ( 11 sec) [ -35875.1233] [ 9303] [depth= 1] . ( 11 sec) [ -35874.6465] [ 9305] [depth= 1] . ( 12 sec) [ -35864.8674] [ 9297] [depth= 1] . ( 12 sec) [ -35863.5423] [ 9306] [depth= 1] . ( 12 sec) [ -35858.6607] [ 9306] [depth= 1] . ( 12 sec) [ -35852.2611] [ 9306] [depth= 1] . ( 12 sec) [ -35852.0001] [ 9315] [depth= 2] . ( 13 sec) [ -35846.9135] [ 9311] [depth= 1] . ( 13 sec) [ -35829.6825] [ 9315] [depth= 3] . ( 13 sec) [ -35827.8920] [ 9310] [depth= 1] . ( 13 sec) [ -35827.7338] [ 9321] [depth= 1] . ( 14 sec) [ -35824.8258] [ 9325] [depth= 3] . ( 14 sec) [ -35819.8487] [ 9325] [depth= 1] . ( 14 sec) [ -35815.7843] [ 9342] [depth= 2] . ( 14 sec) [ -35775.2913] [ 9308] [depth= 2] . ( 14 sec) [ -35760.4541] [ 9306] [depth= 1] . ( 15 sec) [ -35760.0837] [ 9308] [depth= 1] . ( 15 sec) [ -35751.5615] [ 9293] [depth= 1] . ( 15 sec) [ -35751.2427] [ 9297] [depth= 1] . ( 15 sec) [ -35710.4660] [ 9305] [depth= 2] . ( 15 sec) [ -35689.9691] [ 9317] [depth= 1] . ( 15 sec) [ -35688.5777] [ 9305] [depth= 1] . ( 16 sec) [ -35682.1110] [ 9313] [depth= 1] . ( 16 sec) [ -35656.4096] [ 9305] [depth= 1] . ( 16 sec) [ -35655.5026] [ 9312] [depth= 1] . ( 16 sec) [ -35631.6799] [ 9305] [depth= 1] . ( 17 sec) [ -35625.7289] [ 9308] [depth= 2] . ( 17 sec) [ -35625.0817] [ 9310] [depth= 1] . ( 17 sec) [ -35607.5665] [ 9307] [depth= 2] . ( 18 sec) [ -35605.1079] [ 9300] [depth= 1] . ( 18 sec) [ -35599.8424] [ 9297] [depth= 1] . ( 18 sec) [ -35592.2210] [ 9296] [depth= 1] . ( 19 sec) [ -35591.1458] [ 9293] [depth= 4] . ( 19 sec) [ -35585.1968] [ 9298] [depth= 1] . ( 19 sec) [ -35574.7206] [ 9293] [depth= 1] . ( 19 sec) [ -35574.2143] [ 9294] [depth= 1] . ( 19 sec) [ -35572.8797] [ 9293] [depth= 1] . ( 20 sec) [ -35562.7145] [ 9292] [depth= 1] . ( 20 sec) [ -35540.5258] [ 9293] [depth= 4] . ( 20 sec) [ -35539.9085] [ 9296] [depth= 1] . ( 20 sec) [ -35538.6142] [ 9293] [depth= 1] . ( 21 sec) [ -35536.1295] [ 9297] [depth= 1] . ( 21 sec) [ -35535.8295] [ 9293] [depth= 1] . ( 22 sec) [ -35307.7251] [Branch lengths ] . ( 26 sec) [ -35261.3733] [GTR parameters ] . ( 26 sec) [ -35253.2992] [Alpha ][ 0.446766] . ( 28 sec) [ -35252.6688] [ 9291] [depth= 1] . ( 30 sec) [ -35250.7935] [ 9286] [depth= 1] . ( 31 sec) [ -35250.2314] [ 9301] [depth= 1] . ( 33 sec) [ -35248.4647] [ 9297] [depth= 2] . ( 35 sec) [ -35246.5006] [ 9294] [depth= 1] . ( 36 sec) [ -35244.2970] [ 9296] [depth= 1] . ( 40 sec) [ -35241.2339] [ 9300] [depth= 2] . ( 43 sec) [ -35190.3187] [Branch lengths ] . ( 47 sec) [ -35185.9729] [GTR parameters ] . ( 47 sec) [ -35185.8197] [Alpha ][ 0.453722] . ( 65 sec) [ -35164.7563] [Branch lengths ] . ( 120 sec) [ -35164.6971] [ 9316] [depth= 2] . ( 155 sec) [ -35153.5642] [Branch lengths ] . ( 158 sec) [ -35148.5085] [GTR parameters ] . ( 159 sec) [ -35148.5075] [Alpha ][ 0.454222] . ( 180 sec) [ -35147.8960] [ 9320] [depth= 2] . ( 198 sec) [ -35146.8259] [ 9313] [depth= 1] . ( 203 sec) [ -35146.5948] [ 9312] [depth= 1] . ( 246 sec) [ -35129.9511] [Branch lengths ] . ( 249 sec) [ -35129.0559] [GTR parameters ] . ( 249 sec) [ -35128.9617] [Alpha ][ 0.449161] . ( 337 sec) [ -35120.6288] [Branch lengths ] . ( 337 sec) [ -35120.6288] [Topology ] . ( 339 sec) [ -35118.3724] [Topology ] . ( 341 sec) [ -35117.2532] [Topology ] . ( 344 sec) [ -35116.4904] [Topology ] . ( 346 sec) [ -35115.9462] [Topology ] . ( 348 sec) [ -35115.5520] [Topology ] . ( 350 sec) [ -35115.2638] [Topology ] . ( 352 sec) [ -35113.4848] [GTR parameters ] . ( 353 sec) [ -35112.9793] [Alpha ][ 0.438143] . ( 353 sec) [ -35112.9793] [Topology ] . ( 355 sec) [ -35112.1231] [Topology ] . ( 358 sec) [ -35111.5575] [Topology ] . ( 360 sec) [ -35111.1487] [Topology ] . ( 362 sec) [ -35110.8490] [Topology ] . ( 365 sec) [ -35110.3984] [Topology ] . ( 367 sec) [ -35109.6908] [Topology ] . ( 369 sec) [ -35109.3750] [Topology ] . ( 372 sec) [ -35109.1688] [Topology ] . ( 374 sec) [ -35109.0240] [Topology ] . ( 380 sec) [ -35108.1575] [GTR parameters ] . ( 380 sec) [ -35107.7963] [Alpha ][ 0.429303] . ( 380 sec) [ -35107.7963] [Topology ] . ( 382 sec) [ -35107.4307] [Topology ] . ( 385 sec) [ -35107.1969] [Topology ] . ( 387 sec) [ -35107.0320] [Topology ] . ( 389 sec) [ -35106.9141] [Topology ] . ( 392 sec) [ -35106.8300] [Topology ] . ( 394 sec) [ -35106.7699] [Topology ] . ( 397 sec) [ -35106.6321] [GTR parameters ] . ( 397 sec) [ -35106.5436] [Alpha ][ 0.425027] . ( 397 sec) [ -35106.5436] [Topology ] . ( 400 sec) [ -35106.4210] [Topology ] . ( 402 sec) [ -35106.3406] [Topology ] . ( 404 sec) [ -35106.2841] [Topology ] . ( 407 sec) [ -35106.2441] [Topology ] . ( 409 sec) [ -35106.2158] [Topology ] . ( 411 sec) [ -35106.1958] [Topology ] . ( 413 sec) [ -35106.1554] [GTR parameters ] . ( 413 sec) [ -35106.1236] [Alpha ][ 0.422499] . ( 413 sec) [ -35106.1236] [Topology ] . ( 416 sec) [ -35106.0824] [Topology ] . ( 418 sec) [ -35106.0556] [Topology ] . ( 420 sec) [ -35106.0370] [Topology ] . ( 423 sec) [ -35106.0238] [Topology ] . ( 425 sec) [ -35106.0146] [Topology ] . ( 427 sec) [ -35106.0081] [Topology ] . ( 429 sec) [ -35105.9977] [GTR parameters ] . ( 429 sec) [ -35105.9870] [Alpha ][ 0.421041] . ( 429 sec) [ -35105.9870] [Topology ] . ( 431 sec) [ -35105.9749] [Topology ] . ( 434 sec) [ -35105.9669] [Topology ] . ( 436 sec) [ -35105.9614] [Topology ] . ( 438 sec) [ -35105.9576] [Topology ] . ( 441 sec) [ -35105.9549] [Topology ] . ( 443 sec) [ -35105.9530] [Topology ] . ( 445 sec) [ -35105.9485] [GTR parameters ] . ( 445 sec) [ -35105.9451] [Alpha ][ 0.420199] . ( 445 sec) [ -35105.9451] [Topology ] . ( 448 sec) [ -35105.9408] [Topology ] . ( 450 sec) [ -35105.9381] [Topology ] . ( 452 sec) [ -35105.9362] [Topology ] . ( 455 sec) [ -35105.9349] [Topology ] . ( 457 sec) [ -35105.9339] [Topology ] . ( 459 sec) [ -35105.9332] [GTR parameters ] . ( 459 sec) [ -35105.9325] [Alpha ][ 0.419779] . ( 459 sec) [ -35105.9325] [Topology ] . ( 461 sec) [ -35105.9311] [Topology ] . ( 464 sec) [ -35105.9303] [Topology ] . ( 465 sec) [ -35105.9299] [GTR parameters ] . ( 465 sec) [ -35105.9299] [Alpha ][ 0.419779] . ( 465 sec) [ -35105.9299] [Topology ] . ( 467 sec) [ -35105.9292] [Topology ] . ( 468 sec) [ -35105.9292] [GTR parameters ] . ( 468 sec) [ -35105.9292] [Alpha ][ 0.419779] . Checking for NNIs, optimizing five branches... . 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 0h8m10s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 487.24user 0.00system 8:09.95elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps