.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2662_60x1348_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 . 7 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 664 patterns found. (out of a total of 1348 sites) . 794 sites without polymorphism (58.90%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 21Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 4 sec) [ -12871.6129] [GTR parameters ] . ( 5 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 5 sec) [ -12665.7546] [Topology ] . ( 6 sec) [ -12467.2258] [Topology ] . ( 8 sec) [ -12431.6435] [Topology ] . ( 10 sec) [ -12420.9779] [Topology ] . ( 11 sec) [ -12417.1150] [Topology ] . ( 13 sec) [ -12415.5191] [Topology ] . ( 15 sec) [ -12414.8202] [Topology ] . ( 17 sec) [ -12414.5047] [Topology ] . ( 18 sec) [ -12414.3440] [Topology ] . Checking for NNIs, optimizing five branches... . ( 32 sec) [ -12413.0509] [Topology ] . ( 35 sec) [ -12409.7217] [GTR parameters ] . ( 35 sec) [ -12350.3670] [Alpha ][ 0.296953] . ( 35 sec) [ -12350.3670] [Topology ] . ( 37 sec) [ -12349.1010] [Topology ] . ( 39 sec) [ -12348.8323] [Topology ] . ( 41 sec) [ -12348.7770] [Topology ] . ( 42 sec) [ -12348.7575] [Topology ] . ( 44 sec) [ -12348.7485] [Topology ] . ( 46 sec) [ -12348.7439] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -12348.4350] [Topology ] . ( 62 sec) [ -12348.0258] [GTR parameters ] . ( 62 sec) [ -12347.9937] [Alpha ][ 0.293713] . ( 62 sec) [ -12347.9937] [Topology ] . ( 64 sec) [ -12347.9651] [Topology ] . ( 66 sec) [ -12347.9570] [Topology ] . ( 68 sec) [ -12347.9532] [Topology ] . ( 70 sec) [ -12347.9512] [Topology ] . ( 71 sec) [ -12347.9501] [Topology ] . ( 73 sec) [ -12347.9495] [Topology ] . Checking for NNIs, optimizing five branches... . ( 86 sec) [ -12347.8637] [Topology ] . ( 87 sec) [ -12347.8612] [GTR parameters ] . ( 87 sec) [ -12347.8612] [Alpha ][ 0.293713] . ( 87 sec) [ -12347.8612] [Topology ] . ( 89 sec) [ -12347.8510] [Topology ] . ( 91 sec) [ -12347.8483] [Topology ] . ( 93 sec) [ -12347.8471] [Topology ] . ( 95 sec) [ -12347.8465] [Topology ] . Checking for NNIs, optimizing five branches... . ( 109 sec) [ -12347.8461] [GTR parameters ] . ( 109 sec) [ -12347.8461] [Alpha ][ 0.293713] . ( 109 sec) [ -12347.8461] [Topology ] . ( 111 sec) [ -12347.8457] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 141 sec) [ -12871.6129] [GTR parameters ] . ( 142 sec) [ -12665.7546] [Alpha ][ 0.500960] . ( 142 sec) [ -12665.5249] [ 2217] [depth= 1] . ( 142 sec) [ -12664.1456] [ 2216] [depth= 1] . ( 143 sec) [ -12663.3354] [ 2216] [depth= 1] . ( 144 sec) [ -12661.6311] [ 2218] [depth= 2] . ( 144 sec) [ -12661.0790] [ 2219] [depth= 1] . ( 144 sec) [ -12653.9924] [ 2215] [depth= 1] . ( 144 sec) [ -12652.7357] [ 2219] [depth= 1] . ( 144 sec) [ -12650.1454] [ 2220] [depth= 1] . ( 145 sec) [ -12650.0086] [ 2219] [depth= 1] . ( 145 sec) [ -12648.4386] [ 2216] [depth= 2] . ( 145 sec) [ -12634.9783] [ 2220] [depth= 1] . ( 145 sec) [ -12633.2061] [ 2217] [depth= 1] . ( 145 sec) [ -12632.7527] [ 2218] [depth= 1] . ( 145 sec) [ -12620.6039] [ 2214] [depth= 1] . ( 146 sec) [ -12617.7329] [ 2214] [depth= 1] . ( 147 sec) [ -12617.3662] [ 2215] [depth= 1] . ( 147 sec) [ -12612.2385] [ 2218] [depth= 1] . ( 147 sec) [ -12612.1646] [ 2218] [depth= 1] . ( 148 sec) [ -12609.2459] [ 2215] [depth= 1] . ( 148 sec) [ -12608.8805] [ 2214] [depth= 2] . ( 148 sec) [ -12601.4986] [ 2210] [depth= 1] . ( 148 sec) [ -12599.7595] [ 2212] [depth= 1] . ( 148 sec) [ -12597.2574] [ 2210] [depth= 1] . ( 149 sec) [ -12593.6539] [ 2209] [depth= 1] . ( 149 sec) [ -12591.8308] [ 2210] [depth= 1] . ( 149 sec) [ -12589.3679] [ 2207] [depth= 6] . ( 149 sec) [ -12581.3551] [ 2209] [depth= 1] . ( 150 sec) [ -12570.3569] [ 2207] [depth= 1] . ( 150 sec) [ -12570.3300] [ 2210] [depth= 1] . ( 150 sec) [ -12566.7592] [ 2210] [depth= 1] . ( 150 sec) [ -12564.5110] [ 2210] [depth= 1] . ( 150 sec) [ -12555.9968] [ 2212] [depth= 1] . ( 150 sec) [ -12548.2701] [ 2210] [depth= 1] . ( 151 sec) [ -12546.6607] [ 2212] [depth= 1] . ( 151 sec) [ -12538.8293] [ 2210] [depth= 1] . ( 152 sec) [ -12533.6674] [ 2213] [depth= 1] . ( 152 sec) [ -12531.1873] [ 2211] [depth= 1] . ( 154 sec) [ -12433.6326] [Branch lengths ] . ( 157 sec) [ -12431.2092] [GTR parameters ] . ( 157 sec) [ -12369.5247] [Alpha ][ 0.289385] . ( 159 sec) [ -12368.6080] [ 2212] [depth= 1] . ( 159 sec) [ -12368.1523] [ 2211] [depth= 1] . ( 160 sec) [ -12368.0217] [ 2213] [depth= 1] . ( 162 sec) [ -12366.5513] [ 2212] [depth= 1] . ( 163 sec) [ -12364.6889] [ 2211] [depth= 1] . ( 164 sec) [ -12364.6608] [ 2211] [depth= 1] . ( 166 sec) [ -12361.5436] [ 2206] [depth= 6] . ( 173 sec) [ -12351.1994] [Branch lengths ] . ( 175 sec) [ -12350.6970] [GTR parameters ] . ( 175 sec) [ -12350.6675] [Alpha ][ 0.292660] . ( 177 sec) [ -12350.2335] [ 2206] [depth= 2] . ( 178 sec) [ -12350.1842] [ 2202] [depth= 1] . ( 192 sec) [ -12347.5370] [Branch lengths ] . ( 194 sec) [ -12347.3568] [GTR parameters ] . ( 194 sec) [ -12347.3566] [Alpha ][ 0.292338] . ( 211 sec) [ -12347.0564] [Branch lengths ] . ( 282 sec) [ -12347.0003] [Branch lengths ] . ( 282 sec) [ -12347.0003] [Topology ] . ( 284 sec) [ -12346.9930] [Topology ] . ( 286 sec) [ -12346.9851] [Topology ] . ( 287 sec) [ -12346.9460] [Topology ] . ( 289 sec) [ -12346.7774] [Topology ] . ( 291 sec) [ -12346.7270] [Topology ] . ( 293 sec) [ -12346.7178] [Topology ] . ( 294 sec) [ -12346.7115] [GTR parameters ] . ( 295 sec) [ -12346.7093] [Alpha ][ 0.293194] . ( 295 sec) [ -12346.7093] [Topology ] . ( 296 sec) [ -12346.7067] [Topology ] . ( 298 sec) [ -12346.7058] [Topology ] . ( 299 sec) [ -12346.7058] [GTR parameters ] . ( 299 sec) [ -12346.7058] [Alpha ][ 0.293194] . ( 299 sec) [ -12346.7058] [Topology ] . ( 301 sec) [ -12346.7054] [Topology ] . ( 301 sec) [ -12346.7054] [GTR parameters ] . ( 301 sec) [ -12346.7054] [Alpha ][ 0.293194] . Checking for NNIs, optimizing five branches... . ( 314 sec) [ -12346.2906] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -12347.845692 . Log likelihood obtained after SPR moves : -12346.290635 . Log likelihood of the current tree: -12346.290635. . Printing the most likely tree in file 'nucleic_M2662_60x1348_2006.phy_phyml_tree.txt'... . Time used 0h5m28s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 324.46user 0.00system 5:27.78elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps