.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2752_106x1292_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 . 11 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 427 patterns found. (out of a total of 1292 sites) . 807 sites without polymorphism (62.46%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -7952.3607] [GTR parameters ] . ( 2 sec) [ -7922.0045] [Alpha ][ 0.500960] . ( 2 sec) [ -7922.0045] [Topology ] . ( 5 sec) [ -7888.2427] [Topology ] . ( 7 sec) [ -7882.0784] [Topology ] . ( 9 sec) [ -7877.5421] [Topology ] . ( 12 sec) [ -7874.9338] [Topology ] . ( 14 sec) [ -7873.6053] [Topology ] . ( 17 sec) [ -7873.2530] [Topology ] . ( 19 sec) [ -7873.0995] [Topology ] . ( 21 sec) [ -7872.9835] [Topology ] . ( 23 sec) [ -7872.9341] [Topology ] . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -7872.6117] [GTR parameters ] . ( 38 sec) [ -7872.4034] [Alpha ][ 0.474317] . ( 38 sec) [ -7872.4034] [Topology ] . ( 41 sec) [ -7872.3979] [Topology ] . ( 43 sec) [ -7872.3966] [Topology ] . ( 45 sec) [ -7872.3961] [Topology ] . Checking for NNIs, optimizing five branches... . ( 58 sec) [ -7872.3933] [GTR parameters ] . ( 58 sec) [ -7872.3933] [Alpha ][ 0.473843] . ( 58 sec) [ -7872.3933] [Topology ] . ( 60 sec) [ -7872.3931] [Topology ] . Checking for NNIs, optimizing five branches... . ( 72 sec) [ -7872.3931] [GTR parameters ] . ( 72 sec) [ -7872.3931] [Alpha ][ 0.473843] . ( 73 sec) [ -7872.3931] [Topology ] . ( 75 sec) [ -7872.3930] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 101 sec) [ -7952.3607] [GTR parameters ] . ( 101 sec) [ -7922.0045] [Alpha ][ 0.500960] . ( 102 sec) [ -7921.9865] [ 1008] [depth= 1] . ( 102 sec) [ -7921.9299] [ 1008] [depth= 3] . ( 103 sec) [ -7921.9117] [ 1008] [depth= 3] . ( 103 sec) [ -7921.4488] [ 1008] [depth= 1] . ( 103 sec) [ -7921.4128] [ 1008] [depth= 1] . ( 103 sec) [ -7921.3866] [ 1008] [depth= 4] . ( 103 sec) [ -7921.3643] [ 1008] [depth= 2] . ( 103 sec) [ -7921.3426] [ 1008] [depth= 3] . ( 103 sec) [ -7921.2586] [ 1008] [depth= 2] . ( 104 sec) [ -7921.2289] [ 1008] [depth= 4] . ( 104 sec) [ -7921.2100] [ 1008] [depth= 4] . ( 105 sec) [ -7921.1496] [ 1008] [depth= 1] . ( 105 sec) [ -7920.5718] [ 1008] [depth= 1] . ( 105 sec) [ -7920.5516] [ 1008] [depth= 1] . ( 109 sec) [ -7920.0296] [ 1008] [depth= 1] . ( 109 sec) [ -7919.9843] [ 1008] [depth= 4] . ( 110 sec) [ -7912.5704] [ 1007] [depth= 4] . ( 110 sec) [ -7912.4582] [ 1007] [depth= 3] . ( 110 sec) [ -7912.0542] [ 1007] [depth= 2] . ( 110 sec) [ -7911.7589] [ 1007] [depth= 2] . ( 110 sec) [ -7911.5610] [ 1007] [depth= 1] . ( 110 sec) [ -7911.5009] [ 1007] [depth= 1] . ( 110 sec) [ -7911.4639] [ 1007] [depth= 2] . ( 111 sec) [ -7911.2940] [ 1007] [depth= 1] . ( 111 sec) [ -7911.2596] [ 1007] [depth= 1] . ( 117 sec) [ -7911.0809] [ 1006] [depth= 1] . ( 117 sec) [ -7910.9846] [ 1007] [depth= 1] . ( 118 sec) [ -7910.8110] [ 1007] [depth= 1] . ( 118 sec) [ -7910.6836] [ 1007] [depth= 1] . ( 118 sec) [ -7909.0155] [ 1006] [depth= 1] . ( 122 sec) [ -7908.9445] [ 1006] [depth= 1] . ( 122 sec) [ -7908.8908] [ 1006] [depth= 1] . ( 124 sec) [ -7908.4862] [ 1006] [depth= 4] . ( 124 sec) [ -7906.0923] [ 1006] [depth= 1] . ( 125 sec) [ -7904.4661] [ 1006] [depth= 2] . ( 125 sec) [ -7904.3943] [ 1006] [depth= 1] . ( 125 sec) [ -7902.9703] [ 1006] [depth= 1] . ( 126 sec) [ -7902.9463] [ 1006] [depth= 1] . ( 126 sec) [ -7902.2082] [ 1006] [depth= 1] . ( 130 sec) [ -7899.3771] [ 1006] [depth= 1] . ( 131 sec) [ -7898.8193] [ 1006] [depth= 1] . ( 131 sec) [ -7898.3429] [ 1006] [depth= 1] . ( 131 sec) [ -7895.5364] [ 1005] [depth= 1] . ( 132 sec) [ -7893.3002] [ 1005] [depth= 1] . ( 135 sec) [ -7892.8554] [ 1005] [depth= 1] . ( 135 sec) [ -7892.8389] [ 1005] [depth= 1] . ( 136 sec) [ -7892.7471] [ 1005] [depth= 1] . ( 137 sec) [ -7892.7226] [ 1005] [depth= 2] . ( 137 sec) [ -7892.6897] [ 1005] [depth= 2] . ( 138 sec) [ -7892.5157] [ 1005] [depth= 1] . ( 139 sec) [ -7891.9373] [ 1005] [depth= 1] . ( 140 sec) [ -7891.8842] [ 1005] [depth= 1] . ( 142 sec) [ -7891.8361] [ 1005] [depth= 1] . ( 143 sec) [ -7891.5740] [ 1004] [depth= 2] . ( 144 sec) [ -7888.9031] [ 1004] [depth= 1] . ( 144 sec) [ -7888.8135] [ 1004] [depth= 1] . ( 145 sec) [ -7888.7653] [ 1004] [depth= 1] . ( 147 sec) [ -7888.6147] [ 1004] [depth= 1] . ( 149 sec) [ -7872.1766] [Branch lengths ] . ( 150 sec) [ -7871.8928] [GTR parameters ] . ( 150 sec) [ -7871.6574] [Alpha ][ 0.472364] . ( 171 sec) [ -7871.4930] [ 1003] [depth= 1] . ( 200 sec) [ -7871.4683] [ 1003] [depth= 1] . ( 209 sec) [ -7869.2208] [Branch lengths ] . ( 210 sec) [ -7869.2074] [GTR parameters ] . ( 210 sec) [ -7869.2072] [Alpha ][ 0.473062] . ( 268 sec) [ -7869.0851] [Branch lengths ] . ( 359 sec) [ -7869.0777] [Branch lengths ] . ( 359 sec) [ -7869.0777] [Topology ] . ( 361 sec) [ -7869.0774] [Topology ] . ( 362 sec) [ -7869.0773] [GTR parameters ] . ( 362 sec) [ -7869.0773] [Alpha ][ 0.473062] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7872.392970 . Log likelihood obtained after SPR moves : -7869.077264 . Log likelihood of the current tree: -7869.077264. . Printing the most likely tree in file 'nucleic_M2752_106x1292_2006.phy_phyml_tree.txt'... . Time used 0h6m15s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 373.56user 0.00system 6:15.64elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps