.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2711_123x1181_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 . 18 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 617 patterns found. (out of a total of 1181 sites) . 633 sites without polymorphism (53.60%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 40Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 9 sec) [ -11331.0777] [GTR parameters ] . ( 9 sec) [ -11137.6083] [Alpha ][ 0.500960] . ( 42 sec) [ -11136.4430] [ 2014] [depth= 1] . ( 42 sec) [ -11133.4793] [ 2014] [depth= 1] . ( 43 sec) [ -11116.3234] [ 2007] [depth= 1] . ( 43 sec) [ -11116.1090] [ 2007] [depth= 1] . ( 51 sec) [ -11115.0846] [ 2007] [depth= 1] . ( 51 sec) [ -11114.5969] [ 2006] [depth= 1] . ( 51 sec) [ -11113.9350] [ 2005] [depth= 1] . ( 55 sec) [ -11113.7647] [ 2006] [depth= 2] . ( 55 sec) [ -11108.3844] [ 2003] [depth= 1] . ( 56 sec) [ -11107.2501] [ 2003] [depth= 2] . ( 83 sec) [ -11106.0105] [ 2003] [depth= 1] . ( 83 sec) [ -11105.1080] [ 2003] [depth= 1] . ( 84 sec) [ -11105.0588] [ 2003] [depth= 1] . ( 87 sec) [ -11104.8599] [ 2003] [depth= 1] . ( 88 sec) [ -11104.6092] [ 2003] [depth= 1] . ( 88 sec) [ -11104.5901] [ 2003] [depth= 1] . ( 88 sec) [ -11103.6079] [ 2003] [depth= 1] . ( 89 sec) [ -11103.5268] [ 2003] [depth= 1] . ( 89 sec) [ -11102.3631] [ 2003] [depth= 1] . ( 89 sec) [ -11102.2977] [ 2003] [depth= 2] . ( 89 sec) [ -11102.1355] [ 2003] [depth= 1] . ( 90 sec) [ -11101.3620] [ 2003] [depth= 1] . ( 94 sec) [ -11101.2542] [ 2003] [depth= 1] . ( 94 sec) [ -11101.2409] [ 2003] [depth= 1] . ( 110 sec) [ -11101.2252] [ 2003] [depth= 1] . ( 110 sec) [ -11101.1937] [ 2003] [depth= 1] . ( 114 sec) [ -11101.1179] [ 2003] [depth= 3] . ( 139 sec) [ -11101.0912] [ 2003] [depth= 1] . ( 140 sec) [ -11100.7686] [ 2009] [depth= 1] . ( 140 sec) [ -11094.5767] [ 2003] [depth= 1] . ( 140 sec) [ -11092.6992] [ 2011] [depth= 1] . ( 141 sec) [ -11078.7166] [ 2003] [depth= 1] . ( 149 sec) [ -11073.3338] [ 2005] [depth= 1] . ( 154 sec) [ -11073.2035] [ 2005] [depth= 1] . ( 154 sec) [ -11068.4475] [ 2005] [depth= 1] . ( 154 sec) [ -11053.3636] [ 2002] [depth= 4] . ( 155 sec) [ -11053.2727] [ 2002] [depth= 1] . ( 165 sec) [ -11053.1015] [ 2002] [depth= 1] . ( 166 sec) [ -11052.7807] [ 2002] [depth= 1] . ( 166 sec) [ -11051.4017] [ 2001] [depth= 1] . ( 166 sec) [ -11051.3418] [ 2001] [depth= 1] . ( 206 sec) [ -11047.1443] [ 2000] [depth= 1] . ( 211 sec) [ -11045.5908] [ 2001] [depth= 2] . ( 216 sec) [ -11043.8865] [ 2001] [depth= 2] . ( 217 sec) [ -11041.6856] [ 1999] [depth= 2] . ( 217 sec) [ -11041.6109] [ 1999] [depth= 1] . ( 217 sec) [ -11032.7987] [ 1999] [depth= 1] . ( 227 sec) [ -11032.3057] [ 2001] [depth= 2] . ( 228 sec) [ -11032.2896] [ 2001] [depth= 1] . ( 237 sec) [ -11024.3891] [ 2001] [depth= 1] . ( 237 sec) [ -11017.5804] [ 2002] [depth= 1] . ( 237 sec) [ -11015.8046] [ 2002] [depth= 2] . ( 242 sec) [ -11009.9472] [ 2002] [depth= 1] . ( 246 sec) [ -11009.7483] [ 2002] [depth= 2] . ( 247 sec) [ -11009.3632] [ 2002] [depth= 1] . ( 247 sec) [ -11007.1665] [ 2002] [depth= 1] . ( 251 sec) [ -11005.6550] [ 2001] [depth= 1] . ( 252 sec) [ -10996.6804] [ 1999] [depth= 1] . ( 258 sec) [ -10996.0998] [ 2004] [depth= 1] . ( 259 sec) [ -10990.9892] [ 2016] [depth= 6] . ( 259 sec) [ -10989.8320] [ 2016] [depth= 1] . ( 259 sec) [ -10989.2253] [ 2016] [depth= 1] . ( 260 sec) [ -10989.2035] [ 2016] [depth= 2] . ( 260 sec) [ -10989.1605] [ 2016] [depth= 1] . ( 274 sec) [ -10983.1614] [ 2016] [depth= 2] . ( 275 sec) [ -10981.6710] [ 2016] [depth= 1] . ( 275 sec) [ -10981.6448] [ 2016] [depth= 1] . ( 276 sec) [ -10981.6188] [ 2016] [depth= 1] . ( 302 sec) [ -10980.7596] [ 2016] [depth= 1] . ( 302 sec) [ -10979.8154] [ 2016] [depth= 1] . ( 303 sec) [ -10979.7396] [ 2016] [depth= 1] . ( 314 sec) [ -10979.7146] [ 2016] [depth= 2] . ( 328 sec) [ -10976.2586] [ 2016] [depth= 1] . ( 329 sec) [ -10970.6380] [ 2017] [depth= 2] . ( 329 sec) [ -10965.8267] [ 2016] [depth= 4] . ( 334 sec) [ -10954.0120] [ 2017] [depth= 1] . ( 373 sec) [ -10950.7235] [ 2024] [depth= 2] . ( 373 sec) [ -10950.5989] [ 2024] [depth= 1] . ( 373 sec) [ -10940.7466] [ 2025] [depth= 1] . ( 374 sec) [ -10940.5993] [ 2029] [depth= 1] . ( 374 sec) [ -10940.5571] [ 2031] [depth= 1] . ( 387 sec) [ -10938.0853] [ 2038] [depth= 1] . ( 387 sec) [ -10933.6762] [ 2037] [depth= 2] . ( 388 sec) [ -10918.9287] [ 2042] [depth= 1] . ( 388 sec) [ -10915.6282] [ 2039] [depth= 2] . ( 388 sec) [ -10912.6684] [ 2037] [depth= 1] . ( 389 sec) [ -10908.5443] [ 2032] [depth= 2] . ( 396 sec) [ -10908.1861] [ 2031] [depth= 3] . ( 401 sec) [ -10908.0671] [ 2031] [depth= 3] . ( 402 sec) [ -10906.5484] [ 2034] [depth= 1] . ( 403 sec) [ -10905.9230] [ 2037] [depth= 1] . ( 403 sec) [ -10904.1689] [ 2037] [depth= 1] . ( 419 sec) [ -10899.0716] [ 2029] [depth= 2] . ( 419 sec) [ -10896.9378] [ 2031] [depth= 1] . ( 419 sec) [ -10896.6702] [ 2034] [depth= 1] . ( 425 sec) [ -10893.5991] [ 2029] [depth= 2] . ( 425 sec) [ -10890.9188] [ 2032] [depth= 2] . ( 435 sec) [ -10890.7232] [ 2032] [depth= 1] . ( 436 sec) [ -10890.6916] [ 2032] [depth= 1] . ( 436 sec) [ -10890.6575] [ 2032] [depth= 1] . ( 436 sec) [ -10890.6473] [ 2032] [depth= 3] . ( 436 sec) [ -10890.6297] [ 2032] [depth= 1] . ( 437 sec) [ -10890.4539] [ 2032] [depth= 4] . ( 447 sec) [ -10890.4438] [ 2032] [depth= 1] . ( 460 sec) [ -10890.1916] [ 2032] [depth= 1] . ( 460 sec) [ -10889.7245] [ 2032] [depth= 1] . ( 466 sec) [ -10886.5706] [ 2032] [depth= 1] . ( 467 sec) [ -10886.1070] [ 2032] [depth= 1] . ( 483 sec) [ -10885.9594] [ 2030] [depth= 1] . ( 484 sec) [ -10885.9372] [ 2029] [depth= 1] . ( 484 sec) [ -10885.8993] [ 2029] [depth= 1] . ( 484 sec) [ -10884.5383] [ 2030] [depth= 1] . ( 485 sec) [ -10882.1418] [ 2027] [depth= 1] . ( 490 sec) [ -10880.6899] [ 2030] [depth= 2] . ( 490 sec) [ -10880.5303] [ 2031] [depth= 1] . ( 496 sec) [ -10879.1862] [ 2034] [depth= 1] . ( 497 sec) [ -10878.2653] [ 2036] [depth= 1] . ( 505 sec) [ -10876.8190] [ 2034] [depth= 1] . ( 515 sec) [ -10873.7996] [ 2034] [depth= 1] . ( 515 sec) [ -10873.6267] [ 2034] [depth= 1] . ( 544 sec) [ -10873.5663] [ 2034] [depth= 2] . ( 544 sec) [ -10873.3994] [ 2034] [depth= 2] . ( 544 sec) [ -10873.3312] [ 2034] [depth= 2] . ( 545 sec) [ -10873.0992] [ 2034] [depth= 2] . ( 559 sec) [ -10873.0286] [ 2034] [depth= 2] . ( 559 sec) [ -10872.3843] [ 2034] [depth= 2] . ( 560 sec) [ -10872.2628] [ 2034] [depth= 1] . ( 560 sec) [ -10872.2109] [ 2034] [depth= 1] . ( 560 sec) [ -10872.1962] [ 2034] [depth= 1] . ( 575 sec) [ -10872.1687] [ 2034] [depth= 1] . ( 663 sec) [ -10793.5803] [Branch lengths ] . ( 672 sec) [ -10787.9862] [GTR parameters ] . ( 673 sec) [ -10724.5134] [Alpha ][ 0.281103] . ( 736 sec) [ -10724.0950] [ 2031] [depth= 1] . ( 737 sec) [ -10722.6490] [ 2030] [depth= 1] . ( 843 sec) [ -10722.6384] [ 2030] [depth= 2] . ( 915 sec) [ -10691.7884] [ 2011] [depth= 8] . ( 942 sec) [ -10691.7524] [ 2011] [depth= 1] . ( 1099 sec) [ -10691.6921] [ 2011] [depth= 2] . ( 1126 sec) [ -10689.5419] [ 2009] [depth= 4] . ( 1126 sec) [ -10688.4739] [ 2007] [depth= 1] . ( 1219 sec) [ -10685.1048] [ 2005] [depth= 1] . ( 1224 sec) [ -10685.0167] [ 2005] [depth= 2] . ( 1317 sec) [ -10684.9821] [ 2002] [depth= 2] . ( 1350 sec) [ -10684.9371] [ 2002] [depth= 1] . ( 1357 sec) [ -10683.3797] [ 2000] [depth= 2] . ( 1370 sec) [ -10683.3599] [ 2000] [depth= 1] . ( 1374 sec) [ -10682.9685] [ 2001] [depth= 2] . ( 1394 sec) [ -10682.8453] [ 1996] [depth= 1] . ( 1399 sec) [ -10682.4339] [ 2001] [depth= 1] . ( 1713 sec) [ -10671.4471] [Branch lengths ] . ( 1721 sec) [ -10669.8803] [GTR parameters ] . ( 1721 sec) [ -10669.8031] [Alpha ][ 0.275947] . ( 2005 sec) [ -10669.7927] [ 2001] [depth= 1] . ( 2198 sec) [ -10668.5745] [ 2009] [depth= 4] . ( 2198 sec) [ -10668.0704] [ 2008] [depth= 1] . ( 2234 sec) [ -10667.3603] [ 2008] [depth= 3] . ( 2339 sec) [ -10667.2949] [ 2005] [depth= 1] . ( 2834 sec) [ -10665.6842] [Branch lengths ] . ( 2843 sec) [ -10665.5773] [GTR parameters ] . ( 2843 sec) [ -10665.5770] [Alpha ][ 0.275542] . ( 3272 sec) [ -10665.2260] [ 2018] [depth= 1] . ( 3865 sec) [ -10664.8558] [Branch lengths ] . ( 3872 sec) [ -10664.8535] [GTR parameters ] . ( 3872 sec) [ -10664.8530] [Alpha ][ 0.275896] . ( 3959 sec) [ -10664.8408] [ 2019] [depth= 1] . ( 4114 sec) [ -10664.5538] [Branch lengths ] . ( 4115 sec) [ -10664.5538] [GTR parameters ] . ( 4116 sec) [ -10664.5536] [Alpha ][ 0.276171] . ( 4116 sec) [ -10664.5536] [Topology ] . ( 4121 sec) [ -10663.5024] [Topology ] . ( 4125 sec) [ -10660.8268] [Topology ] . ( 4130 sec) [ -10657.9982] [Topology ] . ( 4135 sec) [ -10656.4290] [Topology ] . ( 4140 sec) [ -10656.2912] [Topology ] . ( 4144 sec) [ -10656.2621] [Topology ] . ( 4146 sec) [ -10656.2620] [GTR parameters ] . ( 4146 sec) [ -10656.2619] [Alpha ][ 0.276448] . ( 4146 sec) [ -10656.2619] [Topology ] . ( 4151 sec) [ -10656.2550] [Topology ] . ( 4155 sec) [ -10656.2533] [Topology ] . ( 4160 sec) [ -10656.2528] [Topology ] . ( 4162 sec) [ -10656.2528] [GTR parameters ] . ( 4162 sec) [ -10656.2528] [Alpha ][ 0.276448] . ( 4162 sec) [ -10656.2528] [Topology ] . ( 4167 sec) [ -10656.2527] [Topology ] . ( 4168 sec) [ -10656.2526] [GTR parameters ] . ( 4169 sec) [ -10656.2526] [Alpha ][ 0.276448] . Checking for NNIs, optimizing five branches... . ( 4201 sec) [ -10655.8928] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4233 sec) [ -10655.6113] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4265 sec) [ -10655.3740] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4297 sec) [ -10655.1822] [Topology ] . Checking for NNIs, optimizing five branches... . ( 4328 sec) [ -10655.1820] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10655.181955. . Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'... . Time used 1h12m38s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 2687.75user 0.00system 1:12:40elapsed 61%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps