.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2573_346x897_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 : NNIs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 649 patterns found. (out of a total of 897 sites) . 315 sites without polymorphism (35.12%). . Computing pairwise distances... . Building BioNJ tree... . WARNING: this analysis will use at least 120Mo of memory space... . Maximizing likelihood (using NNI moves)... . ( 21 sec) [ -10190.7400] [GTR parameters ] . ( 22 sec) [ -10163.7051] [Alpha ][ 0.559325] . ( 23 sec) [ -10163.7051] [Topology ] . ( 41 sec) [ -9922.8401] [Topology ] . ( 59 sec) [ -9837.8116] [Topology ] . ( 76 sec) [ -9794.2293] [Topology ] . ( 93 sec) [ -9773.3154] [Topology ] . ( 110 sec) [ -9770.7227] [Topology ] . ( 126 sec) [ -9759.8165] [Topology ] . ( 141 sec) [ -9759.1894] [Topology ] . ( 157 sec) [ -9752.8371] [Topology ] . ( 172 sec) [ -9756.1633] [Topology ] . Moving backward . ( 183 sec) [ -9742.9321] [GTR parameters ] . ( 184 sec) [ -9742.5466] [Alpha ][ 0.593449] . ( 185 sec) [ -9742.5466] [Topology ] . ( 200 sec) [ -9745.0581] [Topology ] . Moving backward . ( 201 sec) [ -9740.7550] [Topology ] . ( 216 sec) [ -9739.9622] [Topology ] . ( 231 sec) [ -9741.1928] [Topology ] . Moving backward . ( 232 sec) [ -9739.2479] [Topology ] . ( 247 sec) [ -9738.9609] [Topology ] . ( 262 sec) [ -9740.1472] [Topology ] . Moving backward . ( 263 sec) [ -9738.2698] [Topology ] . ( 278 sec) [ -9738.3654] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 332 sec) [ -9737.7065] [Topology ] . ( 336 sec) [ -9737.7013] [GTR parameters ] . ( 337 sec) [ -9737.6997] [Alpha ][ 0.591109] . ( 338 sec) [ -9737.6997] [Topology ] . ( 353 sec) [ -9737.8498] [Topology ] . Moving backward . ( 354 sec) [ -9737.4247] [Topology ] . ( 369 sec) [ -9737.4525] [Topology ] . Moving backward . ( 369 sec) [ -9737.2907] [Topology ] . ( 385 sec) [ -9737.6105] [Topology ] . Moving backward . ( 385 sec) [ -9737.1827] [Topology ] . ( 400 sec) [ -9737.3507] [Topology ] . Moving backward . ( 401 sec) [ -9737.1309] [Topology ] . ( 416 sec) [ -9737.4296] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 469 sec) [ -9737.0350] [Topology ] . ( 473 sec) [ -9737.0342] [GTR parameters ] . ( 474 sec) [ -9737.0340] [Alpha ][ 0.590205] . ( 474 sec) [ -9737.0340] [Topology ] . ( 489 sec) [ -9737.1215] [Topology ] . Moving backward . ( 490 sec) [ -9736.9976] [Topology ] . ( 505 sec) [ -9737.3560] [Topology ] . Moving backward . ( 506 sec) [ -9736.9508] [Topology ] . ( 521 sec) [ -9737.1331] [Topology ] . Moving backward . ( 522 sec) [ -9736.9329] [Topology ] . ( 537 sec) [ -9737.2309] [Topology ] . Moving backward . ( 538 sec) [ -9736.8577] [Topology ] . ( 553 sec) [ -9736.9421] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 606 sec) [ -9736.8331] [Topology ] . ( 612 sec) [ -9736.8328] [GTR parameters ] . ( 613 sec) [ -9736.8328] [Alpha ][ 0.590205] . ( 613 sec) [ -9736.8328] [Topology ] . ( 628 sec) [ -9737.1967] [Topology ] . Moving backward . ( 629 sec) [ -9736.8001] [Topology ] . ( 644 sec) [ -9736.9936] [Topology ] . Moving backward . ( 645 sec) [ -9736.7994] [Topology ] . Checking for NNIs, optimizing five branches... . ( 697 sec) [ -9736.7985] [Topology ] . ( 699 sec) [ -9736.7985] [GTR parameters ] . ( 700 sec) [ -9736.7985] [Alpha ][ 0.590205] . ( 700 sec) [ -9736.7985] [Topology ] . ( 715 sec) [ -9737.1336] [Topology ] . Moving backward . ( 716 sec) [ -9736.7474] [Topology ] . ( 731 sec) [ -9736.8716] [Topology ] . Moving backward . ( 732 sec) [ -9736.7309] [Topology ] . ( 747 sec) [ -9736.8999] [Topology ] . Moving backward . ( 748 sec) [ -9736.7223] [Topology ] . ( 763 sec) [ -9736.7674] [Topology ] . Moving backward . ( 763 sec) [ -9736.7210] [Topology ] . ( 778 sec) [ -9737.0746] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 831 sec) [ -9736.7113] [Topology ] . ( 833 sec) [ -9736.7113] [GTR parameters ] . ( 834 sec) [ -9736.7113] [Alpha ][ 0.589615] . ( 834 sec) [ -9736.7113] [Topology ] . ( 849 sec) [ -9736.7878] [Topology ] . Moving backward . ( 850 sec) [ -9736.7052] [Topology ] . ( 865 sec) [ -9736.7907] [Topology ] . Moving backward . ( 866 sec) [ -9736.7013] [Topology ] . ( 881 sec) [ -9736.7259] [Topology ] . Moving backward . ( 881 sec) [ -9736.7009] [Topology ] . Checking for NNIs, optimizing five branches... . ( 934 sec) [ -9736.6948] [Topology ] . ( 936 sec) [ -9736.6948] [GTR parameters ] . ( 936 sec) [ -9736.6948] [Alpha ][ 0.589615] . ( 937 sec) [ -9736.6948] [Topology ] . ( 952 sec) [ -9736.6898] [Topology ] . ( 967 sec) [ -9736.6873] [Topology ] . ( 982 sec) [ -9736.6970] [Topology ] . Moving backward . ( 982 sec) [ -9736.6864] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1035 sec) [ -9736.6853] [Topology ] . ( 1037 sec) [ -9736.6853] [GTR parameters ] . ( 1037 sec) [ -9736.6853] [Alpha ][ 0.589615] . ( 1038 sec) [ -9736.6853] [Topology ] . ( 1053 sec) [ -9736.7058] [Topology ] . Moving backward . ( 1053 sec) [ -9736.6834] [Topology ] . ( 1068 sec) [ -9736.7070] [Topology ] . Moving backward . ( 1069 sec) [ -9736.6821] [Topology ] . ( 1084 sec) [ -9736.7505] [Topology ] . Moving backward . ( 1085 sec) [ -9736.6770] [Topology ] . ( 1100 sec) [ -9736.6854] [Topology ] . Moving backward . ( 1101 sec) [ -9736.6752] [Topology ] . ( 1116 sec) [ -9736.6984] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 1168 sec) [ -9736.6704] [Topology ] . ( 1170 sec) [ -9736.6704] [GTR parameters ] . ( 1171 sec) [ -9736.6704] [Alpha ][ 0.589615] . ( 1171 sec) [ -9736.6704] [Topology ] . ( 1186 sec) [ -9736.6677] [Topology ] . ( 1201 sec) [ -9736.6671] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1253 sec) [ -9736.6661] [Topology ] . ( 1255 sec) [ -9736.6661] [GTR parameters ] . ( 1256 sec) [ -9736.6661] [Alpha ][ 0.589615] . ( 1256 sec) [ -9736.6661] [Topology ] . ( 1271 sec) [ -9736.6655] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1324 sec) [ -9736.6644] [Topology ] . ( 1325 sec) [ -9736.6644] [GTR parameters ] . ( 1326 sec) [ -9736.6644] [Alpha ][ 0.589615] . ( 1326 sec) [ -9736.6644] [Topology ] . ( 1341 sec) [ -9736.6639] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1394 sec) [ -9736.6626] [Topology ] . ( 1395 sec) [ -9736.6626] [GTR parameters ] . ( 1396 sec) [ -9736.6626] [Alpha ][ 0.589615] . ( 1396 sec) [ -9736.6626] [Topology ] . ( 1411 sec) [ -9736.6621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1464 sec) [ -9736.6592] [Topology ] . ( 1465 sec) [ -9736.6592] [GTR parameters ] . ( 1466 sec) [ -9736.6592] [Alpha ][ 0.589615] . ( 1466 sec) [ -9736.6592] [Topology ] . ( 1481 sec) [ -9736.6588] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1534 sec) [ -9736.6587] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1586 sec) [ -9731.9778] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1638 sec) [ -9731.9777] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1690 sec) [ -9731.9775] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1742 sec) [ -9731.9774] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1794 sec) [ -9731.9755] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1846 sec) [ -9731.9754] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1898 sec) [ -9731.9753] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1950 sec) [ -9731.9724] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2002 sec) [ -9731.9702] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2054 sec) [ -9730.9691] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2106 sec) [ -9730.9414] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2158 sec) [ -9730.9345] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2210 sec) [ -9730.9306] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2263 sec) [ -9730.9304] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2315 sec) [ -9730.9295] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2368 sec) [ -9730.9285] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2420 sec) [ -9730.9263] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2473 sec) [ -9730.9261] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2526 sec) [ -9730.9260] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2578 sec) [ -9730.9252] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2630 sec) [ -9730.9251] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2683 sec) [ -9730.8840] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2736 sec) [ -9729.6386] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2789 sec) [ -9729.6365] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2841 sec) [ -9729.6364] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2894 sec) [ -9729.6361] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2947 sec) [ -9729.6360] [Topology ] . Checking for NNIs, optimizing five branches... . ( 2999 sec) [ -9729.6359] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3052 sec) [ -9729.6353] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3105 sec) [ -9729.6352] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3158 sec) [ -9729.6344] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3210 sec) [ -9729.6321] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3263 sec) [ -9729.6320] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3315 sec) [ -9729.6270] [Topology ] . Checking for NNIs, optimizing five branches... . ( 3368 sec) [ -9729.6269] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -9729.626945. . Printing the most likely tree in file 'nucleic_M2573_346x897_2006.phy_phyml_tree.txt'... . Time used 0h57m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 3428.99user 0.00system 57:10.54elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps