.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2913_81x897_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 . 84 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 197 patterns found. (out of a total of 897 sites) . 676 sites without polymorphism (75.36%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 8Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -2523.3266] [GTR parameters ] . ( 1 sec) [ -2508.5261] [Alpha ][ 0.500960] . ( 1 sec) [ -2508.5261] [Topology ] . ( 1 sec) [ -2475.2275] [Topology ] . ( 2 sec) [ -2462.5552] [Topology ] . ( 3 sec) [ -2464.0611] [Topology ] . Moving backward . ( 3 sec) [ -2459.8744] [Topology ] . ( 4 sec) [ -2457.8355] [Topology ] . ( 4 sec) [ -2460.3467] [Topology ] . Moving backward . ( 4 sec) [ -2456.9884] [Topology ] . ( 5 sec) [ -2458.0589] [Topology ] . Moving backward . ( 5 sec) [ -2456.2108] [Topology ] . ( 6 sec) [ -2455.5442] [GTR parameters ] . ( 6 sec) [ -2444.5627] [Alpha ][ 0.250961] . ( 6 sec) [ -2444.5627] [Topology ] . ( 7 sec) [ -2443.3022] [Topology ] . ( 8 sec) [ -2442.5524] [Topology ] . ( 8 sec) [ -2443.1700] [Topology ] . Moving backward . ( 8 sec) [ -2441.1183] [Topology ] . ( 9 sec) [ -2440.9937] [Topology ] . ( 10 sec) [ -2441.5182] [Topology ] . Moving backward . ( 10 sec) [ -2440.8971] [Topology ] . ( 10 sec) [ -2440.8978] [Topology ] . Checking for NNIs, optimizing five branches... . ( 14 sec) [ -2440.0218] [Topology ] . ( 15 sec) [ -2439.6357] [GTR parameters ] . ( 15 sec) [ -2436.5083] [Alpha ][ 0.134987] . ( 15 sec) [ -2436.5083] [Topology ] . ( 15 sec) [ -2436.5113] [Topology ] . Moving backward . ( 15 sec) [ -2436.2451] [Topology ] . ( 16 sec) [ -2436.0366] [Topology ] . ( 17 sec) [ -2436.0412] [Topology ] . Moving backward . ( 17 sec) [ -2435.9470] [Topology ] . ( 17 sec) [ -2435.8884] [Topology ] . ( 18 sec) [ -2435.8703] [Topology ] . ( 18 sec) [ -2435.8875] [Topology ] . Checking for NNIs, optimizing five branches... . ( 22 sec) [ -2435.8493] [Topology ] . ( 23 sec) [ -2435.8262] [GTR parameters ] . ( 23 sec) [ -2435.8248] [Alpha ][ 0.132931] . ( 23 sec) [ -2435.8248] [Topology ] . ( 23 sec) [ -2435.8227] [Topology ] . ( 24 sec) [ -2435.8221] [Topology ] . Checking for NNIs, optimizing five branches... . ( 28 sec) [ -2435.8186] [Topology ] . ( 28 sec) [ -2435.8186] [GTR parameters ] . ( 28 sec) [ -2435.8186] [Alpha ][ 0.132798] . ( 28 sec) [ -2435.8186] [Topology ] . ( 28 sec) [ -2435.8197] [Topology ] . Moving backward . ( 28 sec) [ -2435.8164] [Topology ] . ( 29 sec) [ -2435.8159] [Topology ] . Checking for NNIs, optimizing five branches... . ( 33 sec) [ -2435.8152] [Topology ] . ( 33 sec) [ -2435.8152] [GTR parameters ] . ( 33 sec) [ -2435.8152] [Alpha ][ 0.132931] . ( 33 sec) [ -2435.8152] [Topology ] . ( 34 sec) [ -2435.8164] [Topology ] . Moving backward . ( 34 sec) [ -2435.8143] [Topology ] . Checking for NNIs, optimizing five branches... . ( 37 sec) [ -2435.8113] [Topology ] . ( 37 sec) [ -2435.8113] [GTR parameters ] . ( 38 sec) [ -2435.8113] [Alpha ][ 0.132798] . ( 38 sec) [ -2435.8113] [Topology ] . ( 38 sec) [ -2435.8113] [Topology ] . Checking for NNIs, optimizing five branches... . ( 42 sec) [ -2435.8086] [Topology ] . ( 42 sec) [ -2435.8086] [GTR parameters ] . ( 42 sec) [ -2435.8086] [Alpha ][ 0.132931] . ( 42 sec) [ -2435.8086] [Topology ] . ( 43 sec) [ -2435.8118] [Topology ] . Moving backward . ( 43 sec) [ -2435.8072] [Topology ] . ( 43 sec) [ -2435.8081] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -2435.8019] [Topology ] . ( 47 sec) [ -2435.8019] [GTR parameters ] . ( 48 sec) [ -2435.8019] [Alpha ][ 0.132931] . ( 48 sec) [ -2435.8019] [Topology ] . ( 48 sec) [ -2435.8123] [Topology ] . Moving backward . ( 48 sec) [ -2435.7996] [Topology ] . ( 49 sec) [ -2435.8038] [Topology ] . Moving backward . ( 49 sec) [ -2435.7986] [Topology ] . ( 49 sec) [ -2435.8010] [Topology ] . Moving backward . ( 49 sec) [ -2435.7975] [Topology ] . ( 50 sec) [ -2435.7982] [Topology ] . Checking for NNIs, optimizing five branches... . ( 54 sec) [ -2435.7982] [GTR parameters ] . ( 54 sec) [ -2435.7982] [Alpha ][ 0.132931] . ( 54 sec) [ -2435.7982] [Topology ] . ( 54 sec) [ -2435.8118] [Topology ] . Moving backward . ( 54 sec) [ -2435.7956] [Topology ] . ( 55 sec) [ -2435.8064] [Topology ] . Moving backward . ( 55 sec) [ -2435.7951] [Topology ] . Checking for NNIs, optimizing five branches... . ( 59 sec) [ -2435.7951] [GTR parameters ] . ( 59 sec) [ -2435.7951] [Alpha ][ 0.132931] . ( 59 sec) [ -2435.7951] [Topology ] . ( 60 sec) [ -2435.8065] [Topology ] . Moving backward . ( 60 sec) [ -2435.7933] [Topology ] . ( 60 sec) [ -2435.7992] [Topology ] . Moving backward . ( 60 sec) [ -2435.7918] [Topology ] . ( 61 sec) [ -2435.7972] [Topology ] . Moving backward . ( 61 sec) [ -2435.7901] [Topology ] . ( 61 sec) [ -2435.7924] [Topology ] . Moving backward . ( 61 sec) [ -2435.7884] [Topology ] . ( 62 sec) [ -2435.7899] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 66 sec) [ -2435.7866] [GTR parameters ] . ( 66 sec) [ -2435.7866] [Alpha ][ 0.132785] . ( 66 sec) [ -2435.7866] [Topology ] . ( 66 sec) [ -2435.7863] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 75 sec) [ -2523.3266] [GTR parameters ] . ( 75 sec) [ -2508.5261] [Alpha ][ 0.500960] . ( 75 sec) [ -2507.9522] [ 220] [depth= 1] . ( 75 sec) [ -2507.8060] [ 220] [depth= 1] . ( 75 sec) [ -2507.6883] [ 220] [depth= 1] . ( 76 sec) [ -2502.5950] [ 220] [depth= 1] . ( 76 sec) [ -2502.4563] [ 220] [depth= 1] . ( 76 sec) [ -2501.6969] [ 220] [depth= 14] . ( 76 sec) [ -2499.2974] [ 220] [depth= 14] . ( 76 sec) [ -2499.2829] [ 220] [depth= 2] . ( 76 sec) [ -2499.2106] [ 220] [depth= 1] . ( 77 sec) [ -2499.0270] [ 220] [depth= 3] . ( 79 sec) [ -2498.9641] [ 220] [depth= 1] . ( 80 sec) [ -2498.9230] [ 220] [depth= 1] . ( 80 sec) [ -2498.5762] [ 220] [depth= 2] . ( 80 sec) [ -2493.9000] [ 219] [depth= 5] . ( 80 sec) [ -2490.6073] [ 220] [depth= 1] . ( 80 sec) [ -2486.8545] [ 219] [depth= 2] . ( 81 sec) [ -2486.8427] [ 219] [depth= 2] . ( 82 sec) [ -2486.8268] [ 219] [depth= 2] . ( 83 sec) [ -2486.7895] [ 219] [depth= 5] . ( 84 sec) [ -2486.6785] [ 219] [depth= 1] . ( 84 sec) [ -2486.6421] [ 219] [depth= 1] . ( 84 sec) [ -2486.5227] [ 219] [depth= 2] . ( 84 sec) [ -2486.5082] [ 219] [depth= 1] . ( 84 sec) [ -2486.4944] [ 219] [depth= 3] . ( 84 sec) [ -2485.6728] [ 219] [depth= 1] . ( 84 sec) [ -2485.0316] [ 219] [depth= 7] . ( 87 sec) [ -2485.0192] [ 219] [depth= 1] . ( 87 sec) [ -2484.4731] [ 219] [depth= 1] . ( 87 sec) [ -2484.4189] [ 219] [depth= 2] . ( 88 sec) [ -2484.4081] [ 219] [depth= 3] . ( 90 sec) [ -2478.0949] [ 218] [depth= 3] . ( 90 sec) [ -2470.8201] [ 217] [depth= 2] . ( 90 sec) [ -2467.3365] [ 216] [depth= 5] . ( 90 sec) [ -2467.2687] [ 216] [depth= 1] . ( 91 sec) [ -2466.3055] [ 217] [depth= 9] . ( 92 sec) [ -2465.5980] [ 217] [depth= 3] . ( 92 sec) [ -2464.7526] [ 217] [depth= 2] . ( 92 sec) [ -2464.7013] [ 217] [depth= 3] . ( 93 sec) [ -2464.3189] [ 217] [depth= 1] . ( 93 sec) [ -2461.9022] [ 216] [depth= 2] . ( 93 sec) [ -2461.8069] [ 216] [depth= 1] . ( 93 sec) [ -2461.7736] [ 216] [depth= 1] . ( 93 sec) [ -2461.7267] [ 216] [depth= 1] . ( 94 sec) [ -2461.6491] [ 216] [depth= 1] . ( 94 sec) [ -2461.6263] [ 216] [depth= 2] . ( 94 sec) [ -2461.4371] [ 216] [depth= 1] . ( 95 sec) [ -2461.2028] [ 216] [depth= 1] . ( 95 sec) [ -2461.0374] [ 216] [depth= 1] . ( 95 sec) [ -2460.8894] [ 216] [depth= 1] . ( 95 sec) [ -2460.8142] [ 216] [depth= 1] . ( 96 sec) [ -2460.2988] [ 216] [depth= 1] . ( 96 sec) [ -2459.7757] [ 216] [depth= 2] . ( 96 sec) [ -2459.7631] [ 216] [depth= 8] . ( 96 sec) [ -2459.5043] [ 216] [depth= 1] . ( 96 sec) [ -2459.4650] [ 216] [depth= 7] . ( 97 sec) [ -2459.4326] [ 216] [depth= 3] . ( 98 sec) [ -2459.3180] [ 216] [depth= 1] . ( 98 sec) [ -2458.4602] [ 216] [depth= 3] . ( 98 sec) [ -2458.1933] [ 216] [depth= 1] . ( 98 sec) [ -2457.8450] [ 216] [depth= 1] . ( 98 sec) [ -2457.8150] [ 216] [depth= 3] . ( 99 sec) [ -2457.6805] [ 216] [depth= 1] . ( 99 sec) [ -2456.9841] [ 216] [depth= 1] . ( 99 sec) [ -2456.8077] [ 216] [depth= 2] . ( 100 sec) [ -2456.7875] [ 216] [depth= 3] . ( 100 sec) [ -2452.9624] [ 215] [depth= 2] . ( 100 sec) [ -2447.2998] [ 214] [depth= 8] . ( 101 sec) [ -2447.2558] [ 214] [depth= 2] . ( 101 sec) [ -2447.1794] [ 214] [depth= 1] . ( 101 sec) [ -2446.6899] [ 214] [depth= 2] . ( 101 sec) [ -2446.6593] [ 214] [depth= 3] . ( 102 sec) [ -2446.4529] [ 214] [depth= 3] . ( 102 sec) [ -2445.8783] [ 214] [depth= 1] . ( 103 sec) [ -2445.7083] [ 214] [depth= 1] . ( 103 sec) [ -2445.5797] [ 214] [depth= 1] . ( 103 sec) [ -2445.2678] [ 214] [depth= 1] . ( 103 sec) [ -2437.4175] [ 213] [depth= 4] . ( 103 sec) [ -2437.3278] [ 213] [depth= 3] . ( 104 sec) [ -2437.2769] [ 213] [depth= 5] . ( 104 sec) [ -2437.1724] [ 213] [depth= 4] . ( 104 sec) [ -2437.1210] [ 213] [depth= 1] . ( 104 sec) [ -2435.5209] [ 213] [depth= 1] . ( 104 sec) [ -2435.4109] [ 213] [depth= 6] . ( 104 sec) [ -2435.3167] [ 213] [depth= 2] . ( 104 sec) [ -2435.2564] [ 213] [depth= 1] . ( 104 sec) [ -2435.2373] [ 213] [depth= 1] . ( 104 sec) [ -2435.2068] [ 213] [depth= 3] . ( 104 sec) [ -2435.1556] [ 213] [depth= 4] . ( 105 sec) [ -2435.1408] [ 213] [depth= 8] . ( 107 sec) [ -2435.1228] [ 213] [depth= 2] . ( 107 sec) [ -2435.1046] [ 213] [depth= 5] . ( 107 sec) [ -2435.0553] [ 213] [depth= 5] . ( 108 sec) [ -2435.0453] [ 213] [depth= 3] . ( 109 sec) [ -2434.9670] [ 213] [depth= 2] . ( 109 sec) [ -2434.9146] [ 213] [depth= 3] . ( 109 sec) [ -2434.9029] [ 213] [depth= 7] . ( 109 sec) [ -2434.8885] [ 213] [depth= 7] . ( 110 sec) [ -2434.8405] [ 213] [depth= 9] . ( 112 sec) [ -2434.2609] [ 213] [depth= 2] . ( 113 sec) [ -2434.1424] [ 213] [depth= 8] . ( 115 sec) [ -2434.1309] [ 213] [depth= 2] . ( 115 sec) [ -2434.1164] [ 213] [depth= 2] . ( 117 sec) [ -2431.5404] [Branch lengths ] . ( 118 sec) [ -2431.5221] [GTR parameters ] . ( 118 sec) [ -2421.4796] [Alpha ][ 0.250961] . ( 118 sec) [ -2421.4673] [ 213] [depth= 1] . ( 139 sec) [ -2421.0805] [ 213] [depth= 7] . ( 140 sec) [ -2421.0393] [ 213] [depth= 1] . ( 147 sec) [ -2417.4997] [ 212] [depth= 11] . ( 155 sec) [ -2417.2747] [ 212] [depth= 5] . ( 155 sec) [ -2417.1760] [ 212] [depth= 1] . ( 156 sec) [ -2416.7776] [ 212] [depth= 14] . ( 163 sec) [ -2416.7586] [ 212] [depth= 5] . ( 166 sec) [ -2416.7343] [ 212] [depth= 12] . ( 170 sec) [ -2416.6744] [ 212] [depth= 3] . ( 179 sec) [ -2415.5493] [ 212] [depth= 1] . ( 187 sec) [ -2415.5381] [ 212] [depth= 2] . ( 215 sec) [ -2415.1227] [Branch lengths ] . ( 216 sec) [ -2415.0514] [GTR parameters ] . ( 216 sec) [ -2412.5767] [Alpha ][ 0.143038] . ( 248 sec) [ -2410.9826] [ 212] [depth= 5] . ( 249 sec) [ -2410.9302] [ 212] [depth= 2] . ( 264 sec) [ -2409.7826] [ 211] [depth= 13] . ( 286 sec) [ -2409.7724] [ 211] [depth= 4] . ( 297 sec) [ -2409.7589] [ 211] [depth= 5] . ( 297 sec) [ -2409.7289] [ 211] [depth= 5] . ( 297 sec) [ -2409.6806] [ 211] [depth= 1] . ( 301 sec) [ -2409.6469] [ 211] [depth= 3] . ( 305 sec) [ -2409.6369] [ 211] [depth= 1] . ( 310 sec) [ -2409.5571] [Branch lengths ] . ( 310 sec) [ -2409.4409] [GTR parameters ] . ( 310 sec) [ -2409.4397] [Alpha ][ 0.141094] . ( 383 sec) [ -2409.4205] [ 211] [depth= 6] . ( 412 sec) [ -2409.4187] [Branch lengths ] . ( 412 sec) [ -2409.4186] [GTR parameters ] . ( 412 sec) [ -2409.4186] [Alpha ][ 0.140735] . ( 443 sec) [ -2409.4185] [Branch lengths ] . ( 443 sec) [ -2409.4185] [Topology ] . ( 444 sec) [ -2409.4185] [Topology ] . ( 444 sec) [ -2409.4185] [GTR parameters ] . ( 444 sec) [ -2409.4185] [Alpha ][ 0.140594] . Checking for NNIs, optimizing five branches... . ( 448 sec) [ -2409.4184] [Topology ] . Checking for NNIs, optimizing five branches... . ( 452 sec) [ -2409.4177] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2435.786324 . Log likelihood obtained after SPR moves : -2409.417748 . Log likelihood of the current tree: -2409.417748. . Printing the most likely tree in file 'nucleic_M2913_81x897_2006.phy_phyml_tree.txt'... . Time used 0h7m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 454.87user 0.00system 7:36.73elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps