.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2733_60x1207_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... . 564 patterns found. (out of a total of 1207 sites) . 771 sites without polymorphism (63.88%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 18Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 2 sec) [ -11527.8412] [GTR parameters ] . ( 2 sec) [ -11290.9171] [Alpha ][ 0.500960] . ( 3 sec) [ -11290.9171] [Topology ] . ( 4 sec) [ -11117.8710] [Topology ] . ( 5 sec) [ -11094.1516] [Topology ] . ( 7 sec) [ -11082.0348] [Topology ] . ( 8 sec) [ -11077.9788] [Topology ] . ( 10 sec) [ -11076.4776] [Topology ] . ( 11 sec) [ -11076.4553] [Topology ] . ( 12 sec) [ -11075.8479] [Topology ] . ( 14 sec) [ -11076.2332] [Topology ] . Moving backward . ( 14 sec) [ -11075.1093] [Topology ] . ( 16 sec) [ -11068.4643] [GTR parameters ] . ( 16 sec) [ -10959.7071] [Alpha ][ 0.250961] . ( 16 sec) [ -10959.7071] [Topology ] . ( 18 sec) [ -10957.4372] [Topology ] . ( 19 sec) [ -10954.7582] [Topology ] . ( 21 sec) [ -10953.6852] [Topology ] . ( 22 sec) [ -10953.4971] [Topology ] . ( 24 sec) [ -10953.4414] [Topology ] . ( 25 sec) [ -10953.4210] [Topology ] . ( 26 sec) [ -10953.4130] [Topology ] . ( 28 sec) [ -10953.4098] [Topology ] . Checking for NNIs, optimizing five branches... . ( 39 sec) [ -10951.3573] [GTR parameters ] . ( 39 sec) [ -10948.0561] [Alpha ][ 0.220954] . ( 39 sec) [ -10948.0561] [Topology ] . ( 41 sec) [ -10947.8648] [Topology ] . ( 42 sec) [ -10947.8045] [Topology ] . ( 44 sec) [ -10947.7823] [Topology ] . ( 45 sec) [ -10947.7737] [Topology ] . ( 46 sec) [ -10947.7704] [Topology ] . ( 48 sec) [ -10947.7691] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -10947.6913] [GTR parameters ] . ( 60 sec) [ -10947.6238] [Alpha ][ 0.217056] . ( 60 sec) [ -10947.6238] [Topology ] . ( 61 sec) [ -10947.6183] [Topology ] . ( 62 sec) [ -10947.6165] [Topology ] . ( 64 sec) [ -10947.6159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -10947.6141] [GTR parameters ] . ( 75 sec) [ -10947.6123] [Alpha ][ 0.216373] . ( 75 sec) [ -10947.6123] [Topology ] . ( 77 sec) [ -10947.6117] [Topology ] . Checking for NNIs, optimizing five branches... . ( 88 sec) [ -10947.6116] [GTR parameters ] . ( 88 sec) [ -10947.6116] [Alpha ][ 0.216373] . ( 88 sec) [ -10947.6116] [Topology ] . ( 89 sec) [ -10947.6114] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 113 sec) [ -11527.8412] [GTR parameters ] . ( 113 sec) [ -11290.9171] [Alpha ][ 0.500960] . ( 114 sec) [ -11290.4691] [ 1959] [depth= 1] . ( 114 sec) [ -11290.1769] [ 1959] [depth= 1] . ( 114 sec) [ -11290.1047] [ 1959] [depth= 1] . ( 114 sec) [ -11289.2190] [ 1959] [depth= 1] . ( 115 sec) [ -11270.6339] [ 1959] [depth= 1] . ( 115 sec) [ -11268.5424] [ 1960] [depth= 1] . ( 115 sec) [ -11255.4173] [ 1959] [depth= 1] . ( 115 sec) [ -11242.4770] [ 1954] [depth= 1] . ( 115 sec) [ -11238.3344] [ 1955] [depth= 3] . ( 116 sec) [ -11219.1425] [ 1953] [depth= 1] . ( 116 sec) [ -11208.3575] [ 1949] [depth= 1] . ( 116 sec) [ -11206.4026] [ 1953] [depth= 1] . ( 116 sec) [ -11204.6450] [ 1952] [depth= 1] . ( 116 sec) [ -11202.1311] [ 1952] [depth= 1] . ( 116 sec) [ -11199.3473] [ 1952] [depth= 1] . ( 117 sec) [ -11196.7907] [ 1953] [depth= 1] . ( 117 sec) [ -11195.3227] [ 1951] [depth= 1] . ( 117 sec) [ -11194.2373] [ 1951] [depth= 1] . ( 117 sec) [ -11194.0336] [ 1951] [depth= 1] . ( 117 sec) [ -11193.6108] [ 1951] [depth= 1] . ( 118 sec) [ -11183.1743] [ 1951] [depth= 1] . ( 118 sec) [ -11181.3775] [ 1951] [depth= 5] . ( 119 sec) [ -11173.5900] [ 1948] [depth= 1] . ( 120 sec) [ -11168.5497] [ 1946] [depth= 1] . ( 120 sec) [ -11166.7899] [ 1946] [depth= 1] . ( 120 sec) [ -11165.7946] [ 1945] [depth= 1] . ( 121 sec) [ -11165.2185] [ 1946] [depth= 1] . ( 121 sec) [ -11164.7793] [ 1945] [depth= 1] . ( 121 sec) [ -11154.6777] [ 1943] [depth= 1] . ( 121 sec) [ -11150.9104] [ 1944] [depth= 1] . ( 121 sec) [ -11148.2190] [ 1942] [depth= 1] . ( 121 sec) [ -11144.7992] [ 1943] [depth= 1] . ( 121 sec) [ -11143.3429] [ 1942] [depth= 1] . ( 122 sec) [ -11141.9461] [ 1945] [depth= 2] . ( 123 sec) [ -11132.2577] [ 1942] [depth= 3] . ( 123 sec) [ -11130.7274] [ 1943] [depth= 1] . ( 123 sec) [ -11130.6639] [ 1943] [depth= 1] . ( 123 sec) [ -11129.0690] [ 1942] [depth= 1] . ( 124 sec) [ -11127.8207] [ 1944] [depth= 1] . ( 124 sec) [ -11127.5787] [ 1947] [depth= 2] . ( 124 sec) [ -11126.6961] [ 1945] [depth= 1] . ( 124 sec) [ -11126.4153] [ 1945] [depth= 2] . ( 124 sec) [ -11125.3180] [ 1941] [depth= 1] . ( 125 sec) [ -11122.2360] [ 1941] [depth= 2] . ( 125 sec) [ -11121.1897] [ 1939] [depth= 1] . ( 126 sec) [ -11120.7593] [ 1939] [depth= 1] . ( 126 sec) [ -11070.5794] [Branch lengths ] . ( 127 sec) [ -11064.6553] [GTR parameters ] . ( 127 sec) [ -10953.2523] [Alpha ][ 0.250961] . ( 135 sec) [ -10952.1908] [ 1940] [depth= 1] . ( 137 sec) [ -10951.4860] [ 1939] [depth= 2] . ( 140 sec) [ -10951.2582] [ 1939] [depth= 1] . ( 143 sec) [ -10946.8764] [Branch lengths ] . ( 144 sec) [ -10944.3053] [GTR parameters ] . ( 144 sec) [ -10941.0273] [Alpha ][ 0.221104] . ( 160 sec) [ -10940.4546] [Branch lengths ] . ( 219 sec) [ -10940.4113] [Branch lengths ] . ( 219 sec) [ -10940.4113] [Topology ] . ( 220 sec) [ -10940.4090] [Topology ] . ( 222 sec) [ -10940.4085] [Topology ] . ( 222 sec) [ -10940.3372] [GTR parameters ] . ( 223 sec) [ -10940.2696] [Alpha ][ 0.217206] . ( 223 sec) [ -10940.2696] [Topology ] . ( 224 sec) [ -10940.2654] [Topology ] . ( 225 sec) [ -10940.2639] [Topology ] . ( 227 sec) [ -10940.2634] [Topology ] . ( 227 sec) [ -10940.2616] [GTR parameters ] . ( 228 sec) [ -10940.2600] [Alpha ][ 0.216571] . ( 228 sec) [ -10940.2600] [Topology ] . ( 229 sec) [ -10940.2595] [Topology ] . ( 229 sec) [ -10940.2594] [GTR parameters ] . ( 229 sec) [ -10940.2594] [Alpha ][ 0.216571] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -10947.611398 . Log likelihood obtained after SPR moves : -10940.259448 . Log likelihood of the current tree: -10940.259448. . Printing the most likely tree in file 'nucleic_M2733_60x1207_2006.phy_phyml_tree.txt'... . Time used 0h4m1s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 239.72user 0.00system 4:01.68elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps