.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2975_93x982_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 . Compressing sequences... . 725 patterns found. (out of a total of 982 sites) . 454 sites without polymorphism (46.23%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 36Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -12806.7417] [GTR parameters ] . ( 2 sec) [ -12644.1413] [Alpha ][ 0.500960] . ( 3 sec) [ -12640.5693] [ 2378] [depth= 1] . ( 3 sec) [ -12635.2836] [ 2377] [depth= 1] . ( 19 sec) [ -12633.3264] [ 2376] [depth= 1] . ( 19 sec) [ -12632.1744] [ 2375] [depth= 1] . ( 23 sec) [ -12631.1947] [ 2375] [depth= 1] . ( 24 sec) [ -12631.0543] [ 2377] [depth= 2] . ( 24 sec) [ -12621.1528] [ 2373] [depth= 1] . ( 35 sec) [ -12616.5645] [ 2371] [depth= 2] . ( 35 sec) [ -12615.3601] [ 2371] [depth= 1] . ( 35 sec) [ -12613.0246] [ 2371] [depth= 1] . ( 36 sec) [ -12613.0102] [ 2371] [depth= 1] . ( 44 sec) [ -12612.9641] [ 2376] [depth= 2] . ( 45 sec) [ -12597.5377] [ 2374] [depth= 2] . ( 55 sec) [ -12594.2473] [ 2374] [depth= 1] . ( 55 sec) [ -12588.6016] [ 2374] [depth= 1] . ( 57 sec) [ -12584.6516] [ 2376] [depth= 1] . ( 63 sec) [ -12584.1393] [ 2376] [depth= 1] . ( 66 sec) [ -12581.1476] [ 2376] [depth= 1] . ( 71 sec) [ -12579.9040] [ 2378] [depth= 1] . ( 71 sec) [ -12576.6041] [ 2374] [depth= 1] . ( 73 sec) [ -12573.8256] [ 2374] [depth= 1] . ( 73 sec) [ -12573.0713] [ 2374] [depth= 1] . ( 74 sec) [ -12569.5781] [ 2374] [depth= 1] . ( 76 sec) [ -12569.3060] [ 2374] [depth= 1] . ( 85 sec) [ -12568.6374] [ 2379] [depth= 1] . ( 85 sec) [ -12561.5306] [ 2374] [depth= 1] . ( 92 sec) [ -12554.0244] [ 2374] [depth= 1] . ( 100 sec) [ -12553.6436] [ 2374] [depth= 1] . ( 123 sec) [ -12550.0187] [ 2373] [depth= 1] . ( 126 sec) [ -12549.6405] [ 2373] [depth= 1] . ( 126 sec) [ -12549.5125] [ 2373] [depth= 1] . ( 141 sec) [ -12543.0054] [ 2377] [depth= 2] . ( 142 sec) [ -12538.7970] [ 2375] [depth= 1] . ( 147 sec) [ -12533.1491] [ 2379] [depth= 4] . ( 147 sec) [ -12522.1439] [ 2377] [depth= 1] . ( 154 sec) [ -12521.9624] [ 2377] [depth= 1] . ( 154 sec) [ -12519.4216] [ 2377] [depth= 4] . ( 159 sec) [ -12519.1581] [ 2387] [depth= 3] . ( 160 sec) [ -12518.9392] [ 2390] [depth= 1] . ( 160 sec) [ -12518.3357] [ 2392] [depth= 1] . ( 161 sec) [ -12517.2420] [ 2389] [depth= 4] . ( 161 sec) [ -12508.5557] [ 2381] [depth= 2] . ( 163 sec) [ -12506.9163] [ 2374] [depth= 2] . ( 163 sec) [ -12505.0292] [ 2376] [depth= 1] . ( 177 sec) [ -12504.5087] [ 2375] [depth= 2] . ( 181 sec) [ -12500.5077] [ 2376] [depth= 2] . ( 181 sec) [ -12499.6102] [ 2376] [depth= 1] . ( 184 sec) [ -12491.0121] [ 2372] [depth= 1] . ( 184 sec) [ -12488.9846] [ 2373] [depth= 1] . ( 184 sec) [ -12484.9595] [ 2373] [depth= 1] . ( 187 sec) [ -12484.9028] [ 2376] [depth= 1] . ( 191 sec) [ -12484.0366] [ 2383] [depth= 2] . ( 191 sec) [ -12483.9072] [ 2384] [depth= 1] . ( 210 sec) [ -12482.3492] [ 2382] [depth= 1] . ( 222 sec) [ -12478.9299] [ 2377] [depth= 2] . ( 222 sec) [ -12475.0003] [ 2377] [depth= 1] . ( 236 sec) [ -12474.6347] [ 2378] [depth= 1] . ( 237 sec) [ -12468.9058] [ 2378] [depth= 1] . ( 237 sec) [ -12468.1726] [ 2374] [depth= 6] . ( 238 sec) [ -12467.4131] [ 2378] [depth= 1] . ( 238 sec) [ -12457.6857] [ 2375] [depth= 7] . ( 242 sec) [ -12457.5423] [ 2377] [depth= 1] . ( 245 sec) [ -12457.3376] [ 2377] [depth= 1] . ( 249 sec) [ -12457.1781] [ 2377] [depth= 5] . ( 250 sec) [ -12454.8775] [ 2374] [depth= 1] . ( 250 sec) [ -12448.1276] [ 2369] [depth= 5] . ( 257 sec) [ -12445.0897] [ 2368] [depth= 1] . ( 261 sec) [ -12443.5848] [ 2368] [depth= 1] . ( 272 sec) [ -12441.7135] [ 2367] [depth= 1] . ( 277 sec) [ -12441.3273] [ 2374] [depth= 5] . ( 281 sec) [ -12441.2925] [ 2375] [depth= 1] . ( 282 sec) [ -12440.1669] [ 2374] [depth= 1] . ( 283 sec) [ -12436.2625] [ 2373] [depth= 1] . ( 287 sec) [ -12434.4087] [ 2378] [depth= 1] . ( 294 sec) [ -12431.5725] [ 2376] [depth= 5] . ( 294 sec) [ -12429.6432] [ 2376] [depth= 2] . ( 297 sec) [ -12429.4128] [ 2375] [depth= 1] . ( 298 sec) [ -12429.2549] [ 2374] [depth= 1] . ( 298 sec) [ -12426.2277] [ 2375] [depth= 2] . ( 298 sec) [ -12424.0415] [ 2375] [depth= 1] . ( 298 sec) [ -12422.1603] [ 2373] [depth= 1] . ( 302 sec) [ -12417.8026] [ 2372] [depth= 3] . ( 309 sec) [ -12417.0940] [ 2374] [depth= 2] . ( 312 sec) [ -12416.9297] [ 2375] [depth= 1] . ( 314 sec) [ -12416.3418] [ 2375] [depth= 2] . ( 319 sec) [ -12360.8053] [Branch lengths ] . ( 326 sec) [ -12344.4876] [GTR parameters ] . ( 327 sec) [ -12332.4293] [Alpha ][ 0.386271] . ( 355 sec) [ -12331.8850] [ 2374] [depth= 1] . ( 505 sec) [ -12331.8697] [ 2374] [depth= 1] . ( 521 sec) [ -12326.7213] [ 2367] [depth= 1] . ( 528 sec) [ -12318.8226] [ 2363] [depth= 4] . ( 545 sec) [ -12316.6093] [ 2360] [depth= 1] . ( 588 sec) [ -12316.4990] [ 2358] [depth= 1] . ( 588 sec) [ -12315.4250] [ 2359] [depth= 1] . ( 614 sec) [ -12313.7096] [ 2358] [depth= 1] . ( 620 sec) [ -12313.4226] [ 2356] [depth= 1] . ( 648 sec) [ -12312.4477] [ 2355] [depth= 3] . ( 652 sec) [ -12312.3100] [ 2354] [depth= 1] . ( 652 sec) [ -12311.9696] [ 2349] [depth= 2] . ( 668 sec) [ -12311.9399] [ 2349] [depth= 1] . ( 676 sec) [ -12311.5616] [ 2350] [depth= 2] . ( 676 sec) [ -12310.9846] [ 2350] [depth= 1] . ( 714 sec) [ -12309.8729] [ 2357] [depth= 3] . ( 718 sec) [ -12309.6718] [ 2357] [depth= 1] . ( 723 sec) [ -12309.5384] [ 2358] [depth= 3] . ( 726 sec) [ -12308.7958] [ 2353] [depth= 1] . ( 733 sec) [ -12308.5371] [ 2354] [depth= 1] . ( 741 sec) [ -12308.5045] [ 2352] [depth= 2] . ( 742 sec) [ -12305.5595] [ 2352] [depth= 1] . ( 746 sec) [ -12300.0489] [ 2354] [depth= 5] . ( 747 sec) [ -12299.1632] [ 2352] [depth= 2] . ( 751 sec) [ -12298.8837] [ 2351] [depth= 1] . ( 754 sec) [ -12298.4874] [ 2351] [depth= 1] . ( 755 sec) [ -12298.0603] [ 2352] [depth= 1] . ( 766 sec) [ -12289.9401] [Branch lengths ] . ( 771 sec) [ -12289.4249] [GTR parameters ] . ( 772 sec) [ -12289.4059] [Alpha ][ 0.390253] . ( 800 sec) [ -12289.0036] [ 2353] [depth= 1] . ( 1172 sec) [ -12288.0418] [ 2349] [depth= 3] . ( 1260 sec) [ -12287.8822] [ 2351] [depth= 1] . ( 1274 sec) [ -12286.6582] [Branch lengths ] . ( 1277 sec) [ -12286.6504] [GTR parameters ] . ( 1277 sec) [ -12286.6446] [Alpha ][ 0.392449] . ( 1781 sec) [ -12286.4617] [Branch lengths ] . ( 1920 sec) [ -12286.4289] [Branch lengths ] . ( 1920 sec) [ -12286.4289] [Topology ] . ( 1923 sec) [ -12286.3474] [Topology ] . ( 1926 sec) [ -12285.7813] [Topology ] . ( 1929 sec) [ -12285.6755] [Topology ] . ( 1932 sec) [ -12285.6293] [Topology ] . ( 1935 sec) [ -12285.6073] [Topology ] . ( 1938 sec) [ -12285.5964] [Topology ] . ( 1941 sec) [ -12285.5912] [Topology ] . ( 1945 sec) [ -12285.5884] [GTR parameters ] . ( 1945 sec) [ -12285.5817] [Alpha ][ 0.394824] . ( 1945 sec) [ -12285.5817] [Topology ] . ( 1948 sec) [ -12285.5792] [Topology ] . ( 1951 sec) [ -12285.5783] [Topology ] . ( 1952 sec) [ -12285.5783] [GTR parameters ] . ( 1952 sec) [ -12285.5783] [Alpha ][ 0.394824] . ( 1952 sec) [ -12285.5783] [Topology ] . ( 1955 sec) [ -12285.5779] [Topology ] . ( 1956 sec) [ -12285.5779] [GTR parameters ] . ( 1957 sec) [ -12285.5779] [Alpha ][ 0.394824] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12285.577896. . Printing the most likely tree in file 'nucleic_M2975_93x982_2006.phy_phyml_tree.txt'... . Time used 0h32m58s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1973.38user 0.00system 32:59.07elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps