.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2588_68x1196_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 . 6 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 730 patterns found. (out of a total of 1196 sites) . 526 sites without polymorphism (43.98%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 26Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 6 sec) [ -12703.7048] [GTR parameters ] . ( 6 sec) [ -12506.3721] [Alpha ][ 0.500960] . ( 7 sec) [ -12504.9636] [ 2715] [depth= 1] . ( 7 sec) [ -12504.7654] [ 2715] [depth= 1] . ( 7 sec) [ -12497.1136] [ 2715] [depth= 1] . ( 7 sec) [ -12493.5302] [ 2715] [depth= 1] . ( 7 sec) [ -12491.3616] [ 2715] [depth= 1] . ( 8 sec) [ -12483.4602] [ 2713] [depth= 2] . ( 8 sec) [ -12482.5118] [ 2713] [depth= 1] . ( 8 sec) [ -12482.4575] [ 2713] [depth= 1] . ( 8 sec) [ -12470.4830] [ 2713] [depth= 1] . ( 8 sec) [ -12466.0686] [ 2713] [depth= 1] . ( 8 sec) [ -12465.9179] [ 2713] [depth= 1] . ( 8 sec) [ -12449.2031] [ 2705] [depth= 1] . ( 8 sec) [ -12449.1587] [ 2705] [depth= 1] . ( 9 sec) [ -12437.2290] [ 2704] [depth= 1] . ( 9 sec) [ -12432.0204] [ 2705] [depth= 1] . ( 9 sec) [ -12431.2264] [ 2705] [depth= 1] . ( 9 sec) [ -12431.1803] [ 2705] [depth= 1] . ( 10 sec) [ -12414.3902] [ 2705] [depth= 1] . ( 10 sec) [ -12397.8831] [ 2704] [depth= 1] . ( 11 sec) [ -12388.4419] [ 2704] [depth= 1] . ( 11 sec) [ -12357.7085] [ 2703] [depth= 4] . ( 11 sec) [ -12340.0539] [ 2692] [depth= 4] . ( 11 sec) [ -12298.9916] [ 2697] [depth= 1] . ( 11 sec) [ -12297.6055] [ 2699] [depth= 1] . ( 11 sec) [ -12295.9158] [ 2693] [depth= 2] . ( 12 sec) [ -12295.6810] [ 2689] [depth= 3] . ( 12 sec) [ -12287.0956] [ 2686] [depth= 2] . ( 12 sec) [ -12286.0143] [ 2681] [depth= 1] . ( 13 sec) [ -12284.1169] [ 2688] [depth= 1] . ( 13 sec) [ -12281.7071] [ 2687] [depth= 1] . ( 14 sec) [ -12281.3732] [ 2692] [depth= 1] . ( 14 sec) [ -12254.7276] [ 2685] [depth= 1] . ( 14 sec) [ -12246.2770] [ 2685] [depth= 1] . ( 15 sec) [ -12244.4031] [ 2685] [depth= 1] . ( 15 sec) [ -12244.3777] [ 2685] [depth= 2] . ( 15 sec) [ -12243.7796] [ 2685] [depth= 1] . ( 15 sec) [ -12243.6505] [ 2685] [depth= 1] . ( 15 sec) [ -12243.4053] [ 2685] [depth= 1] . ( 18 sec) [ -12242.3610] [ 2685] [depth= 1] . ( 18 sec) [ -12240.1649] [ 2685] [depth= 1] . ( 19 sec) [ -12239.8700] [ 2685] [depth= 4] . ( 19 sec) [ -12239.8600] [ 2685] [depth= 7] . ( 20 sec) [ -12237.1446] [ 2684] [depth= 11] . ( 20 sec) [ -12235.6354] [ 2684] [depth= 1] . ( 20 sec) [ -12234.0682] [ 2685] [depth= 1] . ( 20 sec) [ -12233.8001] [ 2685] [depth= 1] . ( 20 sec) [ -12233.7591] [ 2685] [depth= 1] . ( 21 sec) [ -12233.5663] [ 2685] [depth= 7] . ( 21 sec) [ -12233.5275] [ 2685] [depth= 2] . ( 21 sec) [ -12233.3893] [ 2685] [depth= 3] . ( 21 sec) [ -12233.3728] [ 2685] [depth= 2] . ( 21 sec) [ -12233.3331] [ 2685] [depth= 6] . ( 21 sec) [ -12233.3078] [ 2685] [depth= 1] . ( 23 sec) [ -12233.2945] [ 2685] [depth= 2] . ( 29 sec) [ -12145.0069] [Branch lengths ] . ( 31 sec) [ -12126.3144] [GTR parameters ] . ( 31 sec) [ -12090.9741] [Alpha ][ 0.331722] . ( 32 sec) [ -12090.9204] [ 2685] [depth= 1] . ( 33 sec) [ -12089.1043] [ 2684] [depth= 1] . ( 33 sec) [ -12089.0327] [ 2684] [depth= 1] . ( 34 sec) [ -12083.8407] [ 2681] [depth= 1] . ( 35 sec) [ -12081.3871] [ 2687] [depth= 1] . ( 35 sec) [ -12080.8632] [ 2687] [depth= 1] . ( 35 sec) [ -12076.7751] [ 2680] [depth= 2] . ( 36 sec) [ -12076.0754] [ 2687] [depth= 1] . ( 36 sec) [ -12075.0778] [ 2682] [depth= 2] . ( 36 sec) [ -12073.6979] [ 2677] [depth= 2] . ( 37 sec) [ -12073.6215] [ 2676] [depth= 1] . ( 43 sec) [ -12070.6954] [ 2676] [depth= 4] . ( 43 sec) [ -12067.1459] [ 2675] [depth= 4] . ( 44 sec) [ -12067.0194] [ 2675] [depth= 8] . ( 44 sec) [ -12065.8699] [ 2675] [depth= 1] . ( 44 sec) [ -12065.6188] [ 2675] [depth= 3] . ( 46 sec) [ -12065.5958] [ 2675] [depth= 1] . ( 47 sec) [ -12065.5743] [ 2675] [depth= 2] . ( 52 sec) [ -12044.4539] [Branch lengths ] . ( 54 sec) [ -12040.3025] [GTR parameters ] . ( 54 sec) [ -12039.6079] [Alpha ][ 0.314272] . ( 54 sec) [ -12039.5684] [ 2675] [depth= 1] . ( 56 sec) [ -12039.4562] [ 2675] [depth= 1] . ( 58 sec) [ -12038.2630] [ 2676] [depth= 1] . ( 75 sec) [ -12033.2446] [Branch lengths ] . ( 77 sec) [ -12032.8552] [GTR parameters ] . ( 77 sec) [ -12032.7744] [Alpha ][ 0.308746] . ( 96 sec) [ -12031.7249] [Branch lengths ] . ( 105 sec) [ -12031.1492] [ 2675] [depth= 1] . ( 125 sec) [ -12030.9250] [ 2678] [depth= 2] . ( 173 sec) [ -12030.3233] [Branch lengths ] . ( 175 sec) [ -12030.1458] [GTR parameters ] . ( 175 sec) [ -12030.1157] [Alpha ][ 0.305551] . ( 277 sec) [ -12029.1955] [Branch lengths ] . ( 277 sec) [ -12029.1955] [Topology ] . ( 281 sec) [ -12027.5861] [Topology ] . ( 284 sec) [ -12025.5146] [Topology ] . ( 287 sec) [ -12024.7690] [Topology ] . ( 290 sec) [ -12024.5005] [Topology ] . ( 293 sec) [ -12024.4087] [Topology ] . ( 296 sec) [ -12024.3739] [Topology ] . ( 299 sec) [ -12024.2903] [GTR parameters ] . ( 299 sec) [ -12024.2838] [Alpha ][ 0.303916] . ( 299 sec) [ -12024.2838] [Topology ] . ( 303 sec) [ -12024.2612] [Topology ] . ( 306 sec) [ -12024.2522] [Topology ] . ( 309 sec) [ -12024.2480] [Topology ] . ( 312 sec) [ -12024.2459] [Topology ] . ( 316 sec) [ -12024.2449] [Topology ] . ( 319 sec) [ -12024.2444] [Topology ] . ( 321 sec) [ -12024.2406] [GTR parameters ] . ( 321 sec) [ -12024.2401] [Alpha ][ 0.303427] . ( 321 sec) [ -12024.2401] [Topology ] . ( 325 sec) [ -12024.2388] [Topology ] . ( 327 sec) [ -12024.2383] [Topology ] . ( 329 sec) [ -12024.2380] [GTR parameters ] . ( 329 sec) [ -12024.2380] [Alpha ][ 0.303427] . ( 329 sec) [ -12024.2380] [Topology ] . ( 332 sec) [ -12024.2376] [Topology ] . ( 333 sec) [ -12024.2376] [GTR parameters ] . ( 333 sec) [ -12024.2376] [Alpha ][ 0.303427] . Checking for NNIs, optimizing five branches... . ( 359 sec) [ -12024.2375] [Topology ] . Checking for NNIs, optimizing five branches... . ( 384 sec) [ -12024.2373] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -12024.237280. . Printing the most likely tree in file 'nucleic_M2588_68x1196_2006.phy_phyml_tree.txt'... . Time used 0h6m51s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 325.23user 0.00system 6:51.40elapsed 79%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps