.......................... 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 : 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 . 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 NNI moves)... . ( 7 sec) [ -11331.0777] [GTR parameters ] . ( 8 sec) [ -11137.6083] [Alpha ][ 0.500960] . ( 8 sec) [ -11137.6083] [Topology ] . ( 13 sec) [ -10846.7133] [Topology ] . ( 16 sec) [ -10788.2050] [Topology ] . ( 20 sec) [ -10770.4417] [Topology ] . ( 23 sec) [ -10764.1705] [Topology ] . ( 26 sec) [ -10761.8527] [Topology ] . ( 29 sec) [ -10760.1538] [Topology ] . ( 32 sec) [ -10756.2242] [Topology ] . ( 36 sec) [ -10751.2212] [Topology ] . ( 39 sec) [ -10746.7046] [Topology ] . Checking for NNIs, optimizing five branches... . ( 63 sec) [ -10745.2234] [Topology ] . ( 69 sec) [ -10738.9458] [GTR parameters ] . ( 69 sec) [ -10676.9327] [Alpha ][ 0.283794] . ( 69 sec) [ -10676.9327] [Topology ] . ( 72 sec) [ -10673.0638] [Topology ] . ( 75 sec) [ -10672.5895] [Topology ] . ( 78 sec) [ -10672.4366] [Topology ] . ( 81 sec) [ -10672.3670] [Topology ] . ( 84 sec) [ -10672.3314] [Topology ] . ( 87 sec) [ -10672.3125] [Topology ] . Checking for NNIs, optimizing five branches... . ( 109 sec) [ -10672.1784] [Topology ] . ( 115 sec) [ -10671.1857] [GTR parameters ] . ( 115 sec) [ -10670.9081] [Alpha ][ 0.273953] . ( 115 sec) [ -10670.9081] [Topology ] . ( 118 sec) [ -10670.8062] [Topology ] . ( 121 sec) [ -10670.7758] [Topology ] . ( 124 sec) [ -10670.7613] [Topology ] . ( 127 sec) [ -10670.7537] [Topology ] . ( 130 sec) [ -10670.7496] [Topology ] . ( 133 sec) [ -10670.7474] [Topology ] . Checking for NNIs, optimizing five branches... . ( 155 sec) [ -10670.6067] [Topology ] . ( 160 sec) [ -10670.5596] [GTR parameters ] . ( 160 sec) [ -10670.5518] [Alpha ][ 0.272238] . ( 160 sec) [ -10670.5518] [Topology ] . ( 163 sec) [ -10670.4424] [Topology ] . ( 166 sec) [ -10670.4221] [Topology ] . ( 169 sec) [ -10670.4162] [Topology ] . ( 172 sec) [ -10670.4142] [Topology ] . ( 175 sec) [ -10670.4134] [Topology ] . Checking for NNIs, optimizing five branches... . ( 197 sec) [ -10670.4133] [GTR parameters ] . ( 198 sec) [ -10670.4130] [Alpha ][ 0.272549] . ( 198 sec) [ -10670.4130] [Topology ] . ( 201 sec) [ -10670.4126] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 250 sec) [ -11331.0777] [GTR parameters ] . ( 251 sec) [ -11137.6083] [Alpha ][ 0.500960] . ( 251 sec) [ -11136.4430] [ 2014] [depth= 1] . ( 252 sec) [ -11133.4793] [ 2014] [depth= 1] . ( 252 sec) [ -11116.3234] [ 2007] [depth= 1] . ( 252 sec) [ -11116.1090] [ 2007] [depth= 1] . ( 252 sec) [ -11115.0846] [ 2007] [depth= 1] . ( 253 sec) [ -11114.5969] [ 2006] [depth= 1] . ( 253 sec) [ -11113.9350] [ 2005] [depth= 1] . ( 253 sec) [ -11113.7647] [ 2006] [depth= 2] . ( 253 sec) [ -11108.3844] [ 2003] [depth= 1] . ( 254 sec) [ -11107.2501] [ 2003] [depth= 2] . ( 255 sec) [ -11106.0105] [ 2003] [depth= 1] . ( 255 sec) [ -11105.1080] [ 2003] [depth= 1] . ( 255 sec) [ -11105.0588] [ 2003] [depth= 1] . ( 255 sec) [ -11104.8599] [ 2003] [depth= 1] . ( 255 sec) [ -11104.6092] [ 2003] [depth= 1] . ( 256 sec) [ -11104.5901] [ 2003] [depth= 1] . ( 256 sec) [ -11103.6079] [ 2003] [depth= 1] . ( 256 sec) [ -11103.5268] [ 2003] [depth= 1] . ( 256 sec) [ -11102.3631] [ 2003] [depth= 1] . ( 256 sec) [ -11102.2977] [ 2003] [depth= 2] . ( 256 sec) [ -11102.1355] [ 2003] [depth= 1] . ( 257 sec) [ -11101.3620] [ 2003] [depth= 1] . ( 257 sec) [ -11101.2542] [ 2003] [depth= 1] . ( 257 sec) [ -11101.2409] [ 2003] [depth= 1] . ( 258 sec) [ -11101.2252] [ 2003] [depth= 1] . ( 258 sec) [ -11101.1937] [ 2003] [depth= 1] . ( 258 sec) [ -11101.1179] [ 2003] [depth= 3] . ( 259 sec) [ -11101.0912] [ 2003] [depth= 1] . ( 260 sec) [ -11098.1667] [ 2004] [depth= 1] . ( 260 sec) [ -11091.1431] [ 2009] [depth= 1] . ( 260 sec) [ -11086.4029] [ 2011] [depth= 1] . ( 261 sec) [ -11086.2805] [ 2011] [depth= 1] . ( 261 sec) [ -11081.6850] [ 2011] [depth= 1] . ( 261 sec) [ -11068.4600] [ 2007] [depth= 4] . ( 261 sec) [ -11068.3726] [ 2007] [depth= 1] . ( 262 sec) [ -11068.1988] [ 2007] [depth= 1] . ( 262 sec) [ -11067.9164] [ 2007] [depth= 1] . ( 262 sec) [ -11066.2698] [ 2006] [depth= 1] . ( 263 sec) [ -11066.2105] [ 2006] [depth= 1] . ( 265 sec) [ -11062.0386] [ 2005] [depth= 1] . ( 266 sec) [ -11060.6392] [ 2006] [depth= 2] . ( 267 sec) [ -11058.9426] [ 2006] [depth= 2] . ( 267 sec) [ -11056.9381] [ 2004] [depth= 2] . ( 267 sec) [ -11056.8651] [ 2004] [depth= 1] . ( 267 sec) [ -11050.1487] [ 2004] [depth= 1] . ( 268 sec) [ -11049.4134] [ 2006] [depth= 1] . ( 268 sec) [ -11049.1043] [ 2004] [depth= 1] . ( 269 sec) [ -11049.0938] [ 2004] [depth= 1] . ( 269 sec) [ -11047.6221] [ 2004] [depth= 1] . ( 269 sec) [ -11031.6174] [ 2003] [depth= 3] . ( 269 sec) [ -11023.9100] [ 2005] [depth= 3] . ( 269 sec) [ -11018.7080] [ 2005] [depth= 1] . ( 270 sec) [ -11018.4393] [ 2007] [depth= 2] . ( 270 sec) [ -11007.3238] [ 2007] [depth= 1] . ( 271 sec) [ -11006.9383] [ 2007] [depth= 1] . ( 271 sec) [ -11004.8620] [ 2007] [depth= 1] . ( 271 sec) [ -11004.2700] [ 2006] [depth= 1] . ( 271 sec) [ -10995.6026] [ 2001] [depth= 1] . ( 272 sec) [ -10970.7194] [ 1996] [depth= 1] . ( 272 sec) [ -10937.6845] [ 1997] [depth= 4] . ( 272 sec) [ -10936.5689] [ 1997] [depth= 1] . ( 272 sec) [ -10935.9874] [ 1997] [depth= 1] . ( 272 sec) [ -10935.9659] [ 1997] [depth= 2] . ( 273 sec) [ -10935.8929] [ 1997] [depth= 1] . ( 274 sec) [ -10929.9521] [ 1997] [depth= 2] . ( 274 sec) [ -10928.4798] [ 1997] [depth= 1] . ( 274 sec) [ -10928.4544] [ 1997] [depth= 1] . ( 275 sec) [ -10928.4261] [ 1997] [depth= 1] . ( 278 sec) [ -10927.5954] [ 1997] [depth= 1] . ( 278 sec) [ -10926.6530] [ 1997] [depth= 1] . ( 278 sec) [ -10926.5779] [ 1997] [depth= 1] . ( 280 sec) [ -10926.5514] [ 1997] [depth= 2] . ( 282 sec) [ -10923.4964] [ 1997] [depth= 1] . ( 283 sec) [ -10916.9544] [ 1998] [depth= 2] . ( 283 sec) [ -10912.2097] [ 1997] [depth= 4] . ( 283 sec) [ -10900.3539] [ 1999] [depth= 1] . ( 285 sec) [ -10900.0813] [ 1999] [depth= 1] . ( 285 sec) [ -10889.1459] [ 1998] [depth= 1] . ( 285 sec) [ -10889.1047] [ 2002] [depth= 2] . ( 286 sec) [ -10887.9591] [ 2003] [depth= 1] . ( 286 sec) [ -10883.0860] [ 2009] [depth= 7] . ( 286 sec) [ -10882.8314] [ 2008] [depth= 1] . ( 287 sec) [ -10879.9395] [ 2007] [depth= 1] . ( 287 sec) [ -10878.3707] [ 2012] [depth= 1] . ( 287 sec) [ -10878.2563] [ 2012] [depth= 3] . ( 288 sec) [ -10868.6095] [ 2016] [depth= 1] . ( 288 sec) [ -10867.4555] [ 2012] [depth= 1] . ( 288 sec) [ -10866.4750] [ 2012] [depth= 1] . ( 289 sec) [ -10862.1974] [ 2011] [depth= 1] . ( 289 sec) [ -10861.6700] [ 2009] [depth= 3] . ( 289 sec) [ -10859.4837] [ 2005] [depth= 1] . ( 290 sec) [ -10849.0100] [ 2005] [depth= 1] . ( 290 sec) [ -10847.1820] [ 2006] [depth= 2] . ( 291 sec) [ -10846.9757] [ 2006] [depth= 1] . ( 291 sec) [ -10846.9449] [ 2006] [depth= 1] . ( 291 sec) [ -10846.9115] [ 2006] [depth= 1] . ( 291 sec) [ -10846.9015] [ 2006] [depth= 3] . ( 292 sec) [ -10846.8842] [ 2006] [depth= 1] . ( 292 sec) [ -10846.6930] [ 2006] [depth= 4] . ( 293 sec) [ -10846.6809] [ 2006] [depth= 2] . ( 294 sec) [ -10846.4099] [ 2006] [depth= 1] . ( 294 sec) [ -10845.8168] [ 2006] [depth= 1] . ( 295 sec) [ -10845.7093] [ 2006] [depth= 1] . ( 296 sec) [ -10845.4337] [ 2005] [depth= 3] . ( 297 sec) [ -10840.7191] [ 2004] [depth= 1] . ( 297 sec) [ -10837.6492] [ 2005] [depth= 1] . ( 298 sec) [ -10835.1282] [ 2003] [depth= 1] . ( 298 sec) [ -10833.3392] [ 2006] [depth= 1] . ( 298 sec) [ -10832.5984] [ 2009] [depth= 1] . ( 299 sec) [ -10830.9069] [ 2006] [depth= 1] . ( 299 sec) [ -10828.0262] [ 2006] [depth= 1] . ( 300 sec) [ -10827.8474] [ 2006] [depth= 1] . ( 305 sec) [ -10827.7776] [ 2006] [depth= 2] . ( 305 sec) [ -10827.6156] [ 2006] [depth= 2] . ( 306 sec) [ -10827.5377] [ 2006] [depth= 2] . ( 306 sec) [ -10827.3078] [ 2006] [depth= 2] . ( 308 sec) [ -10827.2428] [ 2006] [depth= 2] . ( 308 sec) [ -10826.6096] [ 2006] [depth= 2] . ( 308 sec) [ -10826.4818] [ 2006] [depth= 1] . ( 308 sec) [ -10826.4295] [ 2006] [depth= 1] . ( 309 sec) [ -10826.4144] [ 2006] [depth= 1] . ( 311 sec) [ -10826.3827] [ 2006] [depth= 1] . ( 326 sec) [ -10755.9989] [Branch lengths ] . ( 331 sec) [ -10751.1100] [GTR parameters ] . ( 331 sec) [ -10690.4387] [Alpha ][ 0.282892] . ( 333 sec) [ -10690.4003] [ 2006] [depth= 2] . ( 338 sec) [ -10690.3902] [ 2006] [depth= 2] . ( 347 sec) [ -10690.3401] [ 2006] [depth= 1] . ( 348 sec) [ -10688.8919] [ 2005] [depth= 1] . ( 349 sec) [ -10688.7987] [ 2005] [depth= 1] . ( 350 sec) [ -10688.6865] [ 2010] [depth= 1] . ( 351 sec) [ -10688.6759] [ 2010] [depth= 1] . ( 352 sec) [ -10686.1465] [ 2002] [depth= 4] . ( 352 sec) [ -10685.8054] [ 2003] [depth= 2] . ( 363 sec) [ -10682.4571] [ 2001] [depth= 1] . ( 364 sec) [ -10682.3720] [ 2001] [depth= 2] . ( 371 sec) [ -10680.9399] [ 1996] [depth= 2] . ( 372 sec) [ -10680.9210] [ 1996] [depth= 1] . ( 374 sec) [ -10679.2405] [ 1995] [depth= 1] . ( 380 sec) [ -10679.2267] [ 1995] [depth= 1] . ( 416 sec) [ -10670.9758] [Branch lengths ] . ( 423 sec) [ -10669.8049] [GTR parameters ] . ( 423 sec) [ -10669.6099] [Alpha ][ 0.274547] . ( 447 sec) [ -10668.9000] [ 1995] [depth= 3] . ( 462 sec) [ -10668.8679] [ 1992] [depth= 2] . ( 510 sec) [ -10666.7579] [Branch lengths ] . ( 515 sec) [ -10666.7050] [GTR parameters ] . ( 515 sec) [ -10666.7050] [Alpha ][ 0.274547] . ( 605 sec) [ -10666.3795] [Branch lengths ] . ( 663 sec) [ -10666.1506] [ 2002] [depth= 6] . ( 763 sec) [ -10665.2915] [Branch lengths ] . ( 769 sec) [ -10665.2456] [GTR parameters ] . ( 769 sec) [ -10665.2455] [Alpha ][ 0.274273] . ( 824 sec) [ -10664.8532] [ 2015] [depth= 1] . ( 862 sec) [ -10664.8389] [ 2017] [depth= 2] . ( 922 sec) [ -10662.7767] [Branch lengths ] . ( 928 sec) [ -10662.7633] [GTR parameters ] . ( 928 sec) [ -10662.7633] [Alpha ][ 0.274547] . ( 984 sec) [ -10662.7521] [ 2017] [depth= 1] . ( 1083 sec) [ -10659.6700] [Branch lengths ] . ( 1084 sec) [ -10659.6699] [GTR parameters ] . ( 1085 sec) [ -10659.6699] [Alpha ][ 0.274547] . ( 1235 sec) [ -10656.7916] [Branch lengths ] . ( 1236 sec) [ -10656.7916] [Topology ] . ( 1239 sec) [ -10656.2104] [Topology ] . ( 1242 sec) [ -10656.1915] [Topology ] . ( 1245 sec) [ -10656.1899] [Topology ] . ( 1248 sec) [ -10656.1895] [Topology ] . ( 1249 sec) [ -10656.1893] [GTR parameters ] . ( 1249 sec) [ -10656.1893] [Alpha ][ 0.274547] . ( 1249 sec) [ -10656.1893] [Topology ] . ( 1252 sec) [ -10656.1891] [Topology ] . ( 1254 sec) [ -10656.1891] [GTR parameters ] . ( 1254 sec) [ -10656.1891] [Alpha ][ 0.274547] . Checking for NNIs, optimizing five branches... . ( 1275 sec) [ -10656.1889] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1296 sec) [ -10656.1887] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10670.412606 . Log likelihood obtained after SPR moves : -10656.188722 . Log likelihood of the current tree: -10656.188722. . Printing the most likely tree in file 'nucleic_M2711_123x1181_2006.phy_phyml_tree.txt'... . Time used 0h21m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1315.87user 0.00system 21:59.34elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps