.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2627_54x1915_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 . Compressing sequences... . 1299 patterns found. (out of a total of 1915 sites) . 625 sites without polymorphism (32.64%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -36710.7724] [GTR parameters ] . ( 2 sec) [ -36466.0989] [Alpha ][ 0.500960] . ( 50 sec) [ -36452.6595] [ 8264] [depth= 2] . ( 50 sec) [ -36445.3008] [ 8262] [depth= 2] . ( 58 sec) [ -36443.1273] [ 8290] [depth= 2] . ( 58 sec) [ -36431.2247] [ 8281] [depth= 1] . ( 73 sec) [ -36427.4762] [ 8296] [depth= 1] . ( 73 sec) [ -36422.7758] [ 8282] [depth= 1] . ( 74 sec) [ -36406.3162] [ 8295] [depth= 1] . ( 76 sec) [ -36376.7240] [ 8270] [depth= 2] . ( 76 sec) [ -36371.7416] [ 8270] [depth= 1] . ( 76 sec) [ -36369.4222] [ 8274] [depth= 1] . ( 79 sec) [ -36337.5522] [ 8250] [depth= 1] . ( 79 sec) [ -36318.4054] [ 8268] [depth= 1] . ( 79 sec) [ -36302.2066] [ 8250] [depth= 1] . ( 80 sec) [ -36301.9903] [ 8256] [depth= 1] . ( 80 sec) [ -36301.9742] [ 8248] [depth= 2] . ( 80 sec) [ -36301.5713] [ 8250] [depth= 1] . ( 81 sec) [ -36299.9598] [ 8251] [depth= 1] . ( 104 sec) [ -36298.0814] [ 8247] [depth= 1] . ( 104 sec) [ -36298.0159] [ 8247] [depth= 1] . ( 111 sec) [ -36290.6410] [ 8244] [depth= 1] . ( 112 sec) [ -36289.8819] [ 8254] [depth= 1] . ( 113 sec) [ -36287.7107] [ 8244] [depth= 1] . ( 129 sec) [ -36277.0176] [ 8243] [depth= 1] . ( 160 sec) [ -36275.1584] [ 8242] [depth= 1] . ( 170 sec) [ -36193.2696] [Branch lengths ] . ( 176 sec) [ -35340.6917] [GTR parameters ] . ( 176 sec) [ -35337.0448] [Alpha ][ 0.459187] . ( 251 sec) [ -35336.6866] [ 8255] [depth= 1] . ( 251 sec) [ -35333.5296] [ 8242] [depth= 1] . ( 251 sec) [ -35329.4154] [ 8238] [depth= 1] . ( 258 sec) [ -35328.5714] [ 8245] [depth= 1] . ( 270 sec) [ -35326.8284] [ 8239] [depth= 1] . ( 276 sec) [ -35323.2550] [ 8231] [depth= 2] . ( 372 sec) [ -35286.6840] [Branch lengths ] . ( 376 sec) [ -35282.2864] [GTR parameters ] . ( 376 sec) [ -35281.1806] [Alpha ][ 0.481280] . ( 581 sec) [ -35266.5241] [Branch lengths ] . ( 662 sec) [ -35261.9751] [Branch lengths ] . ( 662 sec) [ -35261.9751] [Topology ] . ( 665 sec) [ -35261.1133] [Topology ] . ( 668 sec) [ -35260.7084] [Topology ] . ( 671 sec) [ -35260.4382] [Topology ] . ( 674 sec) [ -35260.2507] [Topology ] . ( 676 sec) [ -35260.1180] [Topology ] . ( 679 sec) [ -35260.0230] [Topology ] . ( 683 sec) [ -35256.9336] [GTR parameters ] . ( 684 sec) [ -35256.3189] [Alpha ][ 0.497553] . ( 684 sec) [ -35256.3189] [Topology ] . ( 687 sec) [ -35255.5736] [Topology ] . ( 689 sec) [ -35255.0888] [Topology ] . ( 692 sec) [ -35254.7472] [Topology ] . ( 695 sec) [ -35254.5028] [Topology ] . ( 698 sec) [ -35254.3266] [Topology ] . ( 701 sec) [ -35254.1978] [Topology ] . ( 703 sec) [ -35254.0552] [GTR parameters ] . ( 703 sec) [ -35254.0457] [Alpha ][ 0.499625] . ( 703 sec) [ -35254.0457] [Topology ] . ( 706 sec) [ -35253.8703] [Topology ] . ( 709 sec) [ -35253.7443] [Topology ] . ( 712 sec) [ -35253.6515] [Topology ] . ( 715 sec) [ -35253.5831] [Topology ] . ( 717 sec) [ -35253.5325] [Topology ] . ( 720 sec) [ -35253.4948] [Topology ] . ( 722 sec) [ -35253.4349] [GTR parameters ] . ( 722 sec) [ -35253.4349] [Alpha ][ 0.499625] . ( 722 sec) [ -35253.4349] [Topology ] . ( 725 sec) [ -35253.3791] [Topology ] . ( 728 sec) [ -35253.3390] [Topology ] . ( 731 sec) [ -35253.3092] [Topology ] . ( 733 sec) [ -35253.2868] [Topology ] . ( 736 sec) [ -35253.2700] [Topology ] . ( 739 sec) [ -35253.2574] [Topology ] . ( 743 sec) [ -35253.2340] [GTR parameters ] . ( 743 sec) [ -35253.2340] [Alpha ][ 0.499625] . ( 743 sec) [ -35253.2340] [Topology ] . ( 746 sec) [ -35253.2144] [Topology ] . ( 749 sec) [ -35253.2002] [Topology ] . ( 752 sec) [ -35253.1896] [Topology ] . ( 755 sec) [ -35253.1815] [Topology ] . ( 758 sec) [ -35253.1755] [Topology ] . ( 761 sec) [ -35253.1709] [Topology ] . ( 763 sec) [ -35253.1634] [GTR parameters ] . ( 763 sec) [ -35253.1633] [Alpha ][ 0.499126] . ( 763 sec) [ -35253.1633] [Topology ] . ( 766 sec) [ -35253.1565] [Topology ] . ( 769 sec) [ -35253.1516] [Topology ] . ( 772 sec) [ -35253.1480] [Topology ] . ( 775 sec) [ -35253.1452] [Topology ] . ( 778 sec) [ -35253.1431] [Topology ] . ( 781 sec) [ -35253.1415] [Topology ] . ( 781 sec) [ -35253.1381] [GTR parameters ] . ( 782 sec) [ -35253.1381] [Alpha ][ 0.499126] . ( 782 sec) [ -35253.1381] [Topology ] . ( 785 sec) [ -35253.1356] [Topology ] . ( 787 sec) [ -35253.1337] [Topology ] . ( 790 sec) [ -35253.1323] [Topology ] . ( 793 sec) [ -35253.1312] [Topology ] . ( 796 sec) [ -35253.1304] [Topology ] . ( 797 sec) [ -35253.1296] [GTR parameters ] . ( 797 sec) [ -35253.1296] [Alpha ][ 0.499126] . ( 797 sec) [ -35253.1296] [Topology ] . ( 800 sec) [ -35253.1286] [Topology ] . ( 801 sec) [ -35253.1284] [GTR parameters ] . ( 801 sec) [ -35253.1284] [Alpha ][ 0.499126] . ( 801 sec) [ -35253.1284] [Topology ] . ( 804 sec) [ -35253.1276] [Topology ] . ( 805 sec) [ -35253.1276] [GTR parameters ] . ( 805 sec) [ -35253.1276] [Alpha ][ 0.499126] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -35253.127563. . Printing the most likely tree in file 'nucleic_M2627_54x1915_2006.phy_phyml_tree.txt'... . Time used 0h13m50s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 827.28user 0.00system 13:50.10elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps