.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2675_51x1537_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 . Compressing sequences... . 607 patterns found. (out of a total of 1537 sites) . 978 sites without polymorphism (63.63%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 16Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -8178.2748] [GTR parameters ] . ( 4 sec) [ -8087.4232] [Alpha ][ 0.500960] . ( 4 sec) [ -8087.4232] [Topology ] . ( 6 sec) [ -7959.9720] [Topology ] . ( 7 sec) [ -7936.8427] [Topology ] . ( 8 sec) [ -7933.2782] [Topology ] . ( 10 sec) [ -7932.4736] [Topology ] . ( 11 sec) [ -7932.2115] [Topology ] . ( 13 sec) [ -7931.9493] [Topology ] . ( 14 sec) [ -7930.8733] [Topology ] . ( 15 sec) [ -7927.9431] [Topology ] . Checking for NNIs, optimizing five branches... . ( 27 sec) [ -7926.6478] [GTR parameters ] . ( 27 sec) [ -7886.3932] [Alpha ][ 0.264515] . ( 27 sec) [ -7886.3932] [Topology ] . ( 29 sec) [ -7882.1933] [Topology ] . ( 30 sec) [ -7881.8491] [Topology ] . ( 31 sec) [ -7881.6938] [Topology ] . ( 33 sec) [ -7881.6300] [Topology ] . ( 34 sec) [ -7881.6105] [Topology ] . ( 35 sec) [ -7881.6038] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -7880.9586] [GTR parameters ] . ( 47 sec) [ -7880.7604] [Alpha ][ 0.253715] . ( 47 sec) [ -7880.7604] [Topology ] . ( 48 sec) [ -7880.7346] [Topology ] . ( 50 sec) [ -7880.7314] [Topology ] . ( 51 sec) [ -7880.7299] [Topology ] . ( 52 sec) [ -7880.7292] [Topology ] . Checking for NNIs, optimizing five branches... . ( 64 sec) [ -7880.7245] [GTR parameters ] . ( 64 sec) [ -7880.7226] [Alpha ][ 0.252603] . ( 64 sec) [ -7880.7226] [Topology ] . ( 65 sec) [ -7880.7218] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -7880.7218] [GTR parameters ] . ( 75 sec) [ -7880.7218] [Alpha ][ 0.252603] . ( 75 sec) [ -7880.7218] [Topology ] . ( 77 sec) [ -7880.7215] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 99 sec) [ -8178.2748] [GTR parameters ] . ( 100 sec) [ -8087.4232] [Alpha ][ 0.500960] . ( 100 sec) [ -8087.0972] [ 1200] [depth= 1] . ( 101 sec) [ -8084.7754] [ 1202] [depth= 1] . ( 101 sec) [ -8082.7059] [ 1201] [depth= 1] . ( 101 sec) [ -8082.5110] [ 1201] [depth= 1] . ( 102 sec) [ -8082.2716] [ 1201] [depth= 1] . ( 102 sec) [ -8081.9018] [ 1200] [depth= 2] . ( 102 sec) [ -8079.7678] [ 1200] [depth= 1] . ( 102 sec) [ -8078.9041] [ 1200] [depth= 1] . ( 102 sec) [ -8078.5930] [ 1200] [depth= 1] . ( 102 sec) [ -8078.4987] [ 1200] [depth= 1] . ( 103 sec) [ -8078.4207] [ 1200] [depth= 2] . ( 103 sec) [ -8069.1232] [ 1200] [depth= 1] . ( 103 sec) [ -8055.0493] [ 1198] [depth= 1] . ( 103 sec) [ -8053.5396] [ 1198] [depth= 2] . ( 104 sec) [ -8053.5137] [ 1198] [depth= 2] . ( 104 sec) [ -8049.2586] [ 1197] [depth= 1] . ( 104 sec) [ -8047.0850] [ 1197] [depth= 1] . ( 105 sec) [ -8046.9941] [ 1197] [depth= 2] . ( 105 sec) [ -8046.6394] [ 1197] [depth= 2] . ( 105 sec) [ -8046.5629] [ 1197] [depth= 1] . ( 105 sec) [ -8043.9070] [ 1197] [depth= 5] . ( 105 sec) [ -8034.1401] [ 1195] [depth= 2] . ( 105 sec) [ -8029.8403] [ 1195] [depth= 1] . ( 106 sec) [ -7981.5911] [ 1193] [depth= 1] . ( 106 sec) [ -7981.2213] [ 1193] [depth= 1] . ( 107 sec) [ -7979.5751] [ 1194] [depth= 1] . ( 107 sec) [ -7973.7832] [ 1193] [depth= 1] . ( 107 sec) [ -7973.5404] [ 1193] [depth= 1] . ( 107 sec) [ -7973.5261] [ 1193] [depth= 1] . ( 108 sec) [ -7954.2323] [ 1201] [depth= 1] . ( 108 sec) [ -7953.2675] [ 1202] [depth= 2] . ( 108 sec) [ -7951.8497] [ 1204] [depth= 1] . ( 108 sec) [ -7949.4161] [ 1202] [depth= 1] . ( 108 sec) [ -7942.7037] [ 1201] [depth= 1] . ( 109 sec) [ -7941.8535] [ 1201] [depth= 2] . ( 110 sec) [ -7936.2058] [ 1193] [depth= 1] . ( 110 sec) [ -7929.6872] [ 1192] [depth= 2] . ( 112 sec) [ -7929.6752] [ 1192] [depth= 1] . ( 112 sec) [ -7929.6434] [ 1192] [depth= 2] . ( 114 sec) [ -7929.0723] [ 1192] [depth= 1] . ( 114 sec) [ -7902.7152] [Branch lengths ] . ( 117 sec) [ -7901.2669] [GTR parameters ] . ( 117 sec) [ -7861.2592] [Alpha ][ 0.264044] . ( 118 sec) [ -7861.2490] [ 1192] [depth= 1] . ( 118 sec) [ -7861.1443] [ 1190] [depth= 1] . ( 119 sec) [ -7861.0911] [ 1190] [depth= 2] . ( 120 sec) [ -7860.9953] [ 1190] [depth= 1] . ( 127 sec) [ -7859.7277] [ 1190] [depth= 1] . ( 131 sec) [ -7856.7396] [Branch lengths ] . ( 133 sec) [ -7856.2157] [GTR parameters ] . ( 133 sec) [ -7856.0277] [Alpha ][ 0.253416] . ( 141 sec) [ -7856.0165] [ 1190] [depth= 1] . ( 150 sec) [ -7855.8353] [Branch lengths ] . ( 151 sec) [ -7855.8266] [GTR parameters ] . ( 151 sec) [ -7855.8264] [Alpha ][ 0.253774] . ( 200 sec) [ -7855.8081] [Branch lengths ] . ( 200 sec) [ -7855.8081] [Topology ] . ( 202 sec) [ -7855.8066] [Topology ] . ( 203 sec) [ -7855.8062] [Topology ] . ( 203 sec) [ -7855.8060] [GTR parameters ] . ( 203 sec) [ -7855.8058] [Alpha ][ 0.254136] . ( 203 sec) [ -7855.8058] [Topology ] . ( 205 sec) [ -7855.8055] [Topology ] . ( 205 sec) [ -7855.8055] [GTR parameters ] . ( 206 sec) [ -7855.8055] [Alpha ][ 0.254136] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7880.721493 . Log likelihood obtained after SPR moves : -7855.805506 . Log likelihood of the current tree: -7855.805506. . Printing the most likely tree in file 'nucleic_M2675_51x1537_2006.phy_phyml_tree.txt'... . Time used 0h3m37s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 213.88user 0.00system 3:36.52elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps