.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2922_77x1101_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... . 173 patterns found. (out of a total of 1101 sites) . 906 sites without polymorphism (82.29%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 7Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -3268.3123] [GTR parameters ] . ( 1 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 1 sec) [ -3255.0160] [Topology ] . ( 1 sec) [ -3235.7288] [Topology ] . ( 2 sec) [ -3225.5065] [Topology ] . ( 2 sec) [ -3221.9728] [Topology ] . ( 3 sec) [ -3221.2756] [Topology ] . ( 4 sec) [ -3221.1176] [Topology ] . ( 4 sec) [ -3221.0803] [Topology ] . ( 5 sec) [ -3221.0709] [Topology ] . ( 5 sec) [ -3221.0686] [Topology ] . Checking for NNIs, optimizing five branches... . ( 9 sec) [ -3111.9592] [GTR parameters ] . ( 9 sec) [ -3101.6790] [Alpha ][ 0.250961] . ( 9 sec) [ -3101.6790] [Topology ] . ( 10 sec) [ -3101.2469] [Topology ] . ( 10 sec) [ -3101.1951] [Topology ] . ( 11 sec) [ -3101.1835] [Topology ] . ( 11 sec) [ -3101.1807] [Topology ] . ( 12 sec) [ -3101.1800] [Topology ] . Checking for NNIs, optimizing five branches... . ( 16 sec) [ -3096.7030] [GTR parameters ] . ( 16 sec) [ -3094.6692] [Alpha ][ 0.159093] . ( 16 sec) [ -3094.6692] [Topology ] . ( 16 sec) [ -3094.6282] [Topology ] . ( 17 sec) [ -3094.6257] [Topology ] . ( 17 sec) [ -3094.6253] [Topology ] . Checking for NNIs, optimizing five branches... . ( 21 sec) [ -3089.9543] [GTR parameters ] . ( 22 sec) [ -3089.9515] [Alpha ][ 0.156168] . ( 22 sec) [ -3089.9515] [Topology ] . ( 22 sec) [ -3089.9489] [Topology ] . ( 22 sec) [ -3089.9485] [Topology ] . Checking for NNIs, optimizing five branches... . ( 26 sec) [ -3085.2057] [GTR parameters ] . ( 26 sec) [ -3085.2053] [Alpha ][ 0.154998] . ( 26 sec) [ -3085.2053] [Topology ] . ( 27 sec) [ -3085.2010] [Topology ] . ( 27 sec) [ -3085.2002] [Topology ] . Checking for NNIs, optimizing five branches... . ( 31 sec) [ -3080.3925] [GTR parameters ] . ( 31 sec) [ -3080.3922] [Alpha ][ 0.153972] . ( 31 sec) [ -3080.3922] [Topology ] . ( 32 sec) [ -3080.3863] [Topology ] . ( 32 sec) [ -3080.3852] [Topology ] . ( 33 sec) [ -3080.3848] [Topology ] . Checking for NNIs, optimizing five branches... . ( 36 sec) [ -3075.5240] [GTR parameters ] . ( 36 sec) [ -3075.5237] [Alpha ][ 0.152988] . ( 36 sec) [ -3075.5237] [Topology ] . ( 37 sec) [ -3075.5172] [Topology ] . ( 37 sec) [ -3075.5160] [Topology ] . ( 38 sec) [ -3075.5157] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -3039.0349] [GTR parameters ] . ( 42 sec) [ -3038.7796] [Alpha ][ 0.128324] . ( 42 sec) [ -3038.7796] [Topology ] . ( 43 sec) [ -3037.3507] [Topology ] . ( 43 sec) [ -3037.1439] [Topology ] . ( 44 sec) [ -3037.0788] [Topology ] . ( 44 sec) [ -3037.0592] [Topology ] . ( 45 sec) [ -3037.0539] [Topology ] . ( 46 sec) [ -3037.0525] [Topology ] . Checking for NNIs, optimizing five branches... . ( 50 sec) [ -3036.9165] [GTR parameters ] . ( 50 sec) [ -3036.9104] [Alpha ][ 0.131591] . ( 50 sec) [ -3036.9104] [Topology ] . ( 51 sec) [ -3036.8963] [Topology ] . ( 51 sec) [ -3036.8936] [Topology ] . ( 52 sec) [ -3036.8929] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -3036.8920] [GTR parameters ] . ( 55 sec) [ -3036.8918] [Alpha ][ 0.132183] . ( 56 sec) [ -3036.8918] [Topology ] . ( 56 sec) [ -3036.8913] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -3036.8913] [GTR parameters ] . ( 60 sec) [ -3036.8913] [Alpha ][ 0.132315] . ( 60 sec) [ -3036.8913] [Topology ] . ( 60 sec) [ -3036.8912] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 67 sec) [ -3268.3123] [GTR parameters ] . ( 67 sec) [ -3255.0160] [Alpha ][ 0.500960] . ( 68 sec) [ -3254.2192] [ 285] [depth= 1] . ( 68 sec) [ -3254.0206] [ 285] [depth= 1] . ( 68 sec) [ -3249.8435] [ 287] [depth= 1] . ( 71 sec) [ -3249.7182] [ 287] [depth= 1] . ( 71 sec) [ -3249.6907] [ 287] [depth= 1] . ( 71 sec) [ -3249.6645] [ 287] [depth= 1] . ( 71 sec) [ -3249.5797] [ 287] [depth= 2] . ( 75 sec) [ -3249.5506] [ 287] [depth= 1] . ( 75 sec) [ -3249.4221] [ 287] [depth= 2] . ( 75 sec) [ -3249.0013] [ 287] [depth= 2] . ( 75 sec) [ -3244.7325] [ 287] [depth= 4] . ( 75 sec) [ -3244.2633] [ 287] [depth= 2] . ( 75 sec) [ -3243.7508] [ 287] [depth= 1] . ( 75 sec) [ -3243.7402] [ 287] [depth= 3] . ( 75 sec) [ -3237.5172] [ 286] [depth= 3] . ( 76 sec) [ -3236.8494] [ 286] [depth= 2] . ( 76 sec) [ -3236.8378] [ 286] [depth= 1] . ( 77 sec) [ -3236.7549] [ 286] [depth= 1] . ( 77 sec) [ -3236.2186] [ 286] [depth= 1] . ( 77 sec) [ -3236.1944] [ 286] [depth= 1] . ( 79 sec) [ -3235.2068] [ 286] [depth= 2] . ( 79 sec) [ -3232.8330] [ 286] [depth= 2] . ( 79 sec) [ -3232.8083] [ 286] [depth= 1] . ( 81 sec) [ -3232.7844] [ 286] [depth= 4] . ( 81 sec) [ -3232.7563] [ 286] [depth= 1] . ( 81 sec) [ -3232.7366] [ 286] [depth= 1] . ( 81 sec) [ -3232.5855] [ 286] [depth= 2] . ( 82 sec) [ -3232.4975] [ 286] [depth= 1] . ( 83 sec) [ -3232.4602] [ 286] [depth= 1] . ( 83 sec) [ -3232.4367] [ 286] [depth= 2] . ( 87 sec) [ -3232.4157] [ 286] [depth= 3] . ( 87 sec) [ -3232.2600] [ 286] [depth= 1] . ( 91 sec) [ -3232.1425] [ 286] [depth= 1] . ( 92 sec) [ -3231.3343] [ 286] [depth= 4] . ( 92 sec) [ -3230.5993] [ 286] [depth= 2] . ( 92 sec) [ -3230.5753] [ 286] [depth= 1] . ( 92 sec) [ -3230.4740] [ 286] [depth= 2] . ( 92 sec) [ -3230.4378] [ 286] [depth= 2] . ( 93 sec) [ -3229.9582] [ 286] [depth= 1] . ( 93 sec) [ -3229.7321] [ 286] [depth= 1] . ( 93 sec) [ -3229.6998] [ 286] [depth= 1] . ( 93 sec) [ -3229.6813] [ 286] [depth= 1] . ( 94 sec) [ -3229.5369] [ 286] [depth= 2] . ( 94 sec) [ -3229.5083] [ 286] [depth= 1] . ( 100 sec) [ -3218.7872] [Branch lengths ] . ( 101 sec) [ -3057.8348] [GTR parameters ] . ( 101 sec) [ -3044.6318] [Alpha ][ 0.250961] . ( 102 sec) [ -3044.0260] [ 284] [depth= 1] . ( 102 sec) [ -3043.7893] [ 286] [depth= 1] . ( 135 sec) [ -3042.3307] [ 286] [depth= 4] . ( 146 sec) [ -3039.5370] [Branch lengths ] . ( 147 sec) [ -3039.1025] [GTR parameters ] . ( 147 sec) [ -3034.3465] [Alpha ][ 0.133727] . ( 148 sec) [ -3034.3146] [ 288] [depth= 1] . ( 192 sec) [ -3033.9829] [Branch lengths ] . ( 193 sec) [ -3033.8365] [GTR parameters ] . ( 193 sec) [ -3033.8338] [Alpha ][ 0.131597] . ( 219 sec) [ -3033.8075] [Branch lengths ] . ( 219 sec) [ -3033.8075] [Topology ] . ( 219 sec) [ -3033.8064] [Topology ] . ( 220 sec) [ -3033.8062] [Topology ] . ( 220 sec) [ -3033.8053] [GTR parameters ] . ( 220 sec) [ -3033.8051] [Alpha ][ 0.132170] . ( 220 sec) [ -3033.8051] [Topology ] . ( 221 sec) [ -3033.8049] [Topology ] . ( 221 sec) [ -3033.8049] [GTR parameters ] . ( 221 sec) [ -3033.8049] [Alpha ][ 0.132170] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3036.891188 . Log likelihood obtained after SPR moves : -3033.804930 . Log likelihood of the current tree: -3033.804930. . Printing the most likely tree in file 'nucleic_M2922_77x1101_2006.phy_phyml_tree.txt'... . Time used 0h3m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 222.01user 0.00system 3:45.65elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps