.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2792_166x812_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 . 1 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 616 patterns found. (out of a total of 812 sites) . 322 sites without polymorphism (39.66%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 54Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 12 sec) [ -10920.5693] [GTR parameters ] . ( 13 sec) [ -10843.4467] [Alpha ][ 0.500960] . ( 14 sec) [ -10833.0450] [ 1899] [depth= 1] . ( 15 sec) [ -10824.3371] [ 1899] [depth= 1] . ( 16 sec) [ -10822.9897] [ 1899] [depth= 1] . ( 16 sec) [ -10791.3332] [ 1894] [depth= 4] . ( 18 sec) [ -10785.2574] [ 1895] [depth= 2] . ( 19 sec) [ -10781.0168] [ 1894] [depth= 1] . ( 20 sec) [ -10780.4294] [ 1893] [depth= 2] . ( 20 sec) [ -10780.4015] [ 1893] [depth= 1] . ( 21 sec) [ -10779.1848] [ 1892] [depth= 1] . ( 21 sec) [ -10774.9384] [ 1892] [depth= 2] . ( 22 sec) [ -10772.2351] [ 1890] [depth= 1] . ( 23 sec) [ -10771.8908] [ 1890] [depth= 1] . ( 23 sec) [ -10771.5687] [ 1890] [depth= 1] . ( 24 sec) [ -10771.5304] [ 1890] [depth= 1] . ( 24 sec) [ -10771.5160] [ 1890] [depth= 2] . ( 25 sec) [ -10761.9896] [ 1889] [depth= 1] . ( 25 sec) [ -10760.7392] [ 1889] [depth= 1] . ( 26 sec) [ -10757.8824] [ 1888] [depth= 1] . ( 27 sec) [ -10757.7449] [ 1888] [depth= 1] . ( 27 sec) [ -10757.4668] [ 1888] [depth= 1] . ( 28 sec) [ -10756.2480] [ 1888] [depth= 2] . ( 29 sec) [ -10756.0455] [ 1888] [depth= 2] . ( 30 sec) [ -10756.0112] [ 1888] [depth= 1] . ( 30 sec) [ -10755.5710] [ 1888] [depth= 4] . ( 31 sec) [ -10749.0133] [ 1887] [depth= 2] . ( 31 sec) [ -10748.9217] [ 1887] [depth= 2] . ( 31 sec) [ -10748.6085] [ 1887] [depth= 1] . ( 32 sec) [ -10748.4578] [ 1887] [depth= 1] . ( 33 sec) [ -10748.4196] [ 1887] [depth= 2] . ( 34 sec) [ -10746.3605] [ 1886] [depth= 3] . ( 34 sec) [ -10742.2910] [ 1886] [depth= 1] . ( 35 sec) [ -10742.2764] [ 1886] [depth= 3] . ( 36 sec) [ -10739.6425] [ 1886] [depth= 1] . ( 37 sec) [ -10739.6097] [ 1886] [depth= 2] . ( 37 sec) [ -10733.4462] [ 1889] [depth= 1] . ( 40 sec) [ -10728.8584] [ 1891] [depth= 1] . ( 41 sec) [ -10728.4149] [ 1889] [depth= 1] . ( 41 sec) [ -10727.5834] [ 1886] [depth= 1] . ( 42 sec) [ -10725.5198] [ 1887] [depth= 1] . ( 42 sec) [ -10724.4469] [ 1887] [depth= 1] . ( 42 sec) [ -10724.1001] [ 1887] [depth= 1] . ( 43 sec) [ -10721.6182] [ 1886] [depth= 1] . ( 47 sec) [ -10721.5075] [ 1886] [depth= 1] . ( 48 sec) [ -10720.9216] [ 1886] [depth= 1] . ( 48 sec) [ -10720.0930] [ 1886] [depth= 1] . ( 49 sec) [ -10719.7078] [ 1886] [depth= 1] . ( 50 sec) [ -10719.6593] [ 1886] [depth= 1] . ( 51 sec) [ -10719.1513] [ 1887] [depth= 1] . ( 52 sec) [ -10718.3469] [ 1887] [depth= 1] . ( 53 sec) [ -10717.8075] [ 1887] [depth= 1] . ( 54 sec) [ -10717.7697] [ 1887] [depth= 1] . ( 54 sec) [ -10717.7432] [ 1887] [depth= 1] . ( 55 sec) [ -10717.6566] [ 1887] [depth= 1] . ( 57 sec) [ -10717.6320] [ 1887] [depth= 1] . ( 57 sec) [ -10717.1332] [ 1887] [depth= 1] . ( 57 sec) [ -10716.7813] [ 1887] [depth= 1] . ( 59 sec) [ -10716.7435] [ 1887] [depth= 1] . ( 60 sec) [ -10716.6407] [ 1887] [depth= 1] . ( 61 sec) [ -10716.6182] [ 1887] [depth= 2] . ( 62 sec) [ -10716.6060] [ 1887] [depth= 1] . ( 62 sec) [ -10715.0578] [ 1887] [depth= 1] . ( 63 sec) [ -10714.1974] [ 1887] [depth= 1] . ( 64 sec) [ -10713.7485] [ 1887] [depth= 1] . ( 64 sec) [ -10713.6835] [ 1887] [depth= 1] . ( 65 sec) [ -10713.5283] [ 1887] [depth= 2] . ( 66 sec) [ -10712.1967] [ 1887] [depth= 1] . ( 66 sec) [ -10711.8075] [ 1886] [depth= 2] . ( 67 sec) [ -10711.6304] [ 1886] [depth= 1] . ( 67 sec) [ -10711.3366] [ 1886] [depth= 1] . ( 68 sec) [ -10711.1143] [ 1886] [depth= 1] . ( 68 sec) [ -10710.9944] [ 1886] [depth= 2] . ( 69 sec) [ -10710.6670] [ 1886] [depth= 2] . ( 69 sec) [ -10710.3335] [ 1886] [depth= 2] . ( 70 sec) [ -10710.3116] [ 1886] [depth= 2] . ( 71 sec) [ -10710.2584] [ 1886] [depth= 1] . ( 71 sec) [ -10710.0941] [ 1886] [depth= 2] . ( 72 sec) [ -10710.0526] [ 1886] [depth= 3] . ( 73 sec) [ -10709.8422] [ 1886] [depth= 4] . ( 74 sec) [ -10708.8116] [ 1888] [depth= 1] . ( 75 sec) [ -10708.4296] [ 1890] [depth= 1] . ( 75 sec) [ -10695.1054] [ 1888] [depth= 1] . ( 78 sec) [ -10694.5174] [ 1889] [depth= 1] . ( 78 sec) [ -10693.5467] [ 1888] [depth= 1] . ( 79 sec) [ -10691.4544] [ 1887] [depth= 1] . ( 79 sec) [ -10685.7084] [ 1887] [depth= 1] . ( 80 sec) [ -10682.5089] [ 1885] [depth= 1] . ( 81 sec) [ -10680.1775] [ 1885] [depth= 3] . ( 81 sec) [ -10678.2816] [ 1889] [depth= 1] . ( 82 sec) [ -10674.0766] [ 1888] [depth= 1] . ( 83 sec) [ -10671.7642] [ 1888] [depth= 1] . ( 83 sec) [ -10671.6773] [ 1888] [depth= 1] . ( 84 sec) [ -10671.4354] [ 1888] [depth= 1] . ( 84 sec) [ -10671.0498] [ 1888] [depth= 1] . ( 84 sec) [ -10671.0336] [ 1888] [depth= 2] . ( 85 sec) [ -10670.6980] [ 1888] [depth= 1] . ( 86 sec) [ -10670.5879] [ 1888] [depth= 1] . ( 86 sec) [ -10670.5653] [ 1888] [depth= 1] . ( 89 sec) [ -10669.5982] [ 1888] [depth= 1] . ( 93 sec) [ -10665.5708] [ 1889] [depth= 3] . ( 93 sec) [ -10665.3431] [ 1889] [depth= 1] . ( 94 sec) [ -10664.9679] [ 1889] [depth= 1] . ( 94 sec) [ -10664.4759] [ 1889] [depth= 1] . ( 95 sec) [ -10664.2852] [ 1890] [depth= 1] . ( 95 sec) [ -10662.8460] [ 1888] [depth= 1] . ( 96 sec) [ -10662.8322] [ 1888] [depth= 1] . ( 97 sec) [ -10662.4253] [ 1888] [depth= 2] . ( 98 sec) [ -10662.0266] [ 1888] [depth= 3] . ( 99 sec) [ -10660.6728] [ 1888] [depth= 2] . ( 99 sec) [ -10659.6556] [ 1888] [depth= 1] . ( 100 sec) [ -10658.0055] [ 1889] [depth= 1] . ( 101 sec) [ -10656.3790] [ 1888] [depth= 2] . ( 102 sec) [ -10652.2507] [ 1887] [depth= 2] . ( 103 sec) [ -10651.6978] [ 1887] [depth= 1] . ( 104 sec) [ -10651.5920] [ 1887] [depth= 2] . ( 105 sec) [ -10651.4774] [ 1887] [depth= 1] . ( 106 sec) [ -10651.4553] [ 1887] [depth= 3] . ( 106 sec) [ -10651.1100] [ 1887] [depth= 1] . ( 106 sec) [ -10651.0694] [ 1887] [depth= 1] . ( 107 sec) [ -10651.0407] [ 1887] [depth= 2] . ( 112 sec) [ -10587.1335] [Branch lengths ] . ( 123 sec) [ -10585.9261] [GTR parameters ] . ( 123 sec) [ -10585.8506] [Alpha ][ 0.489315] . ( 127 sec) [ -10584.9711] [ 1885] [depth= 1] . ( 143 sec) [ -10583.9280] [ 1885] [depth= 5] . ( 144 sec) [ -10583.6819] [ 1885] [depth= 3] . ( 144 sec) [ -10583.6627] [ 1885] [depth= 4] . ( 146 sec) [ -10581.9258] [ 1886] [depth= 1] . ( 147 sec) [ -10581.8651] [ 1886] [depth= 2] . ( 150 sec) [ -10581.8487] [ 1885] [depth= 1] . ( 152 sec) [ -10581.8384] [ 1885] [depth= 1] . ( 186 sec) [ -10581.3317] [ 1884] [depth= 1] . ( 193 sec) [ -10581.2218] [ 1884] [depth= 1] . ( 198 sec) [ -10581.2034] [ 1884] [depth= 4] . ( 205 sec) [ -10574.6481] [Branch lengths ] . ( 213 sec) [ -10574.6359] [GTR parameters ] . ( 214 sec) [ -10574.6020] [Alpha ][ 0.497182] . ( 223 sec) [ -10574.5736] [ 1886] [depth= 2] . ( 235 sec) [ -10574.5134] [ 1886] [depth= 2] . ( 286 sec) [ -10574.0998] [ 1886] [depth= 2] . ( 293 sec) [ -10574.0720] [ 1886] [depth= 3] . ( 303 sec) [ -10571.8043] [Branch lengths ] . ( 312 sec) [ -10571.7556] [GTR parameters ] . ( 313 sec) [ -10571.7520] [Alpha ][ 0.499728] . ( 406 sec) [ -10569.7344] [Branch lengths ] . ( 452 sec) [ -10569.7004] [ 1886] [depth= 1] . ( 853 sec) [ -10568.2906] [Branch lengths ] . ( 864 sec) [ -10568.2845] [GTR parameters ] . ( 865 sec) [ -10568.2831] [Alpha ][ 0.501312] . ( 1306 sec) [ -10567.5742] [Branch lengths ] . ( 1306 sec) [ -10567.5742] [Topology ] . ( 1315 sec) [ -10565.7723] [Topology ] . ( 1323 sec) [ -10564.0712] [Topology ] . ( 1332 sec) [ -10563.8975] [Topology ] . ( 1340 sec) [ -10563.8803] [Topology ] . ( 1348 sec) [ -10563.8766] [Topology ] . ( 1357 sec) [ -10563.8753] [Topology ] . ( 1360 sec) [ -10563.8716] [GTR parameters ] . ( 1360 sec) [ -10563.8715] [Alpha ][ 0.501813] . ( 1360 sec) [ -10563.8715] [Topology ] . ( 1369 sec) [ -10563.8707] [Topology ] . ( 1371 sec) [ -10563.8707] [GTR parameters ] . ( 1371 sec) [ -10563.8707] [Alpha ][ 0.501813] . Checking for NNIs, optimizing five branches... . ( 1427 sec) [ -10563.8696] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1475 sec) [ -10563.7795] [Topology ] . Checking for NNIs, optimizing five branches... . ( 1523 sec) [ -10563.7777] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10563.777651. . Printing the most likely tree in file 'nucleic_M2792_166x812_2006.phy_phyml_tree.txt'... . Time used 0h26m11s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 926.50user 0.00system 26:13.24elapsed 58%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps