.......................... 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 : 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 SPR moves)... . ( 1 sec) [ -2523.3266] [GTR parameters ] . ( 1 sec) [ -2508.5261] [Alpha ][ 0.500960] . ( 1 sec) [ -2507.9522] [ 220] [depth= 1] . ( 1 sec) [ -2507.8060] [ 220] [depth= 1] . ( 1 sec) [ -2507.6883] [ 220] [depth= 1] . ( 2 sec) [ -2502.5950] [ 220] [depth= 1] . ( 2 sec) [ -2502.4563] [ 220] [depth= 1] . ( 2 sec) [ -2501.6969] [ 220] [depth= 14] . ( 2 sec) [ -2499.2974] [ 220] [depth= 14] . ( 2 sec) [ -2499.2829] [ 220] [depth= 2] . ( 2 sec) [ -2499.2106] [ 220] [depth= 1] . ( 2 sec) [ -2499.0270] [ 220] [depth= 3] . ( 2 sec) [ -2498.9641] [ 220] [depth= 1] . ( 2 sec) [ -2498.9230] [ 220] [depth= 1] . ( 3 sec) [ -2498.5762] [ 220] [depth= 2] . ( 3 sec) [ -2493.9000] [ 219] [depth= 5] . ( 3 sec) [ -2490.6073] [ 220] [depth= 1] . ( 3 sec) [ -2486.8545] [ 219] [depth= 2] . ( 3 sec) [ -2486.8427] [ 219] [depth= 2] . ( 3 sec) [ -2486.8268] [ 219] [depth= 2] . ( 3 sec) [ -2486.7895] [ 219] [depth= 5] . ( 3 sec) [ -2486.6785] [ 219] [depth= 1] . ( 3 sec) [ -2486.6421] [ 219] [depth= 1] . ( 3 sec) [ -2486.5227] [ 219] [depth= 2] . ( 3 sec) [ -2486.5082] [ 219] [depth= 1] . ( 3 sec) [ -2486.4944] [ 219] [depth= 3] . ( 3 sec) [ -2485.6728] [ 219] [depth= 1] . ( 3 sec) [ -2485.0316] [ 219] [depth= 7] . ( 4 sec) [ -2485.0192] [ 219] [depth= 1] . ( 4 sec) [ -2484.4731] [ 219] [depth= 1] . ( 4 sec) [ -2484.4189] [ 219] [depth= 2] . ( 4 sec) [ -2484.4081] [ 219] [depth= 3] . ( 4 sec) [ -2478.0949] [ 218] [depth= 3] . ( 4 sec) [ -2470.8201] [ 217] [depth= 2] . ( 4 sec) [ -2467.3365] [ 216] [depth= 5] . ( 4 sec) [ -2467.2687] [ 216] [depth= 1] . ( 5 sec) [ -2466.5602] [ 216] [depth= 3] . ( 5 sec) [ -2465.7114] [ 216] [depth= 2] . ( 5 sec) [ -2465.6458] [ 216] [depth= 3] . ( 5 sec) [ -2465.2651] [ 216] [depth= 1] . ( 5 sec) [ -2462.8497] [ 215] [depth= 2] . ( 5 sec) [ -2462.7569] [ 215] [depth= 1] . ( 5 sec) [ -2462.7231] [ 215] [depth= 1] . ( 5 sec) [ -2462.6711] [ 215] [depth= 1] . ( 5 sec) [ -2462.5883] [ 215] [depth= 1] . ( 5 sec) [ -2462.4027] [ 215] [depth= 1] . ( 5 sec) [ -2462.1675] [ 215] [depth= 1] . ( 5 sec) [ -2462.0100] [ 215] [depth= 1] . ( 5 sec) [ -2461.8612] [ 215] [depth= 1] . ( 5 sec) [ -2461.7877] [ 215] [depth= 1] . ( 5 sec) [ -2461.2697] [ 215] [depth= 1] . ( 5 sec) [ -2460.7435] [ 215] [depth= 2] . ( 5 sec) [ -2460.7333] [ 215] [depth= 8] . ( 6 sec) [ -2460.4716] [ 215] [depth= 1] . ( 6 sec) [ -2460.4328] [ 215] [depth= 7] . ( 6 sec) [ -2460.4019] [ 215] [depth= 3] . ( 6 sec) [ -2460.2186] [ 215] [depth= 1] . ( 6 sec) [ -2459.8731] [ 215] [depth= 1] . ( 6 sec) [ -2459.8430] [ 215] [depth= 3] . ( 6 sec) [ -2459.7072] [ 215] [depth= 1] . ( 6 sec) [ -2459.6557] [ 215] [depth= 1] . ( 6 sec) [ -2459.4782] [ 215] [depth= 2] . ( 6 sec) [ -2459.4580] [ 215] [depth= 3] . ( 6 sec) [ -2452.8034] [ 215] [depth= 2] . ( 6 sec) [ -2447.0163] [ 214] [depth= 6] . ( 6 sec) [ -2446.9724] [ 214] [depth= 2] . ( 6 sec) [ -2446.8958] [ 214] [depth= 1] . ( 6 sec) [ -2446.4040] [ 214] [depth= 2] . ( 6 sec) [ -2446.3734] [ 214] [depth= 3] . ( 7 sec) [ -2446.1657] [ 214] [depth= 3] . ( 7 sec) [ -2445.5889] [ 214] [depth= 1] . ( 7 sec) [ -2445.4182] [ 214] [depth= 1] . ( 7 sec) [ -2445.2890] [ 214] [depth= 1] . ( 7 sec) [ -2445.2011] [ 214] [depth= 2] . ( 7 sec) [ -2445.1651] [ 214] [depth= 1] . ( 7 sec) [ -2437.2963] [ 213] [depth= 5] . ( 7 sec) [ -2437.2056] [ 213] [depth= 3] . ( 7 sec) [ -2437.1547] [ 213] [depth= 5] . ( 7 sec) [ -2437.1401] [ 213] [depth= 4] . ( 7 sec) [ -2437.0582] [ 213] [depth= 3] . ( 7 sec) [ -2435.6076] [ 213] [depth= 1] . ( 7 sec) [ -2435.3074] [ 213] [depth= 1] . ( 7 sec) [ -2435.2941] [ 213] [depth= 2] . ( 7 sec) [ -2435.1932] [ 213] [depth= 2] . ( 7 sec) [ -2435.0304] [ 213] [depth= 1] . ( 7 sec) [ -2435.0103] [ 213] [depth= 1] . ( 7 sec) [ -2434.9798] [ 213] [depth= 3] . ( 7 sec) [ -2434.9286] [ 213] [depth= 4] . ( 8 sec) [ -2434.9126] [ 213] [depth= 8] . ( 8 sec) [ -2434.8946] [ 213] [depth= 2] . ( 8 sec) [ -2434.8763] [ 213] [depth= 5] . ( 8 sec) [ -2434.8265] [ 213] [depth= 5] . ( 8 sec) [ -2434.8157] [ 213] [depth= 3] . ( 8 sec) [ -2434.7376] [ 213] [depth= 2] . ( 8 sec) [ -2434.6850] [ 213] [depth= 3] . ( 8 sec) [ -2434.6735] [ 213] [depth= 7] . ( 8 sec) [ -2434.6590] [ 213] [depth= 7] . ( 9 sec) [ -2434.6111] [ 213] [depth= 9] . ( 9 sec) [ -2434.0315] [ 213] [depth= 2] . ( 9 sec) [ -2433.9130] [ 213] [depth= 8] . ( 9 sec) [ -2433.9018] [ 213] [depth= 2] . ( 10 sec) [ -2431.0256] [Branch lengths ] . ( 10 sec) [ -2431.0029] [GTR parameters ] . ( 10 sec) [ -2421.0807] [Alpha ][ 0.250961] . ( 10 sec) [ -2421.0682] [ 213] [depth= 1] . ( 13 sec) [ -2420.6814] [ 213] [depth= 8] . ( 13 sec) [ -2420.6402] [ 213] [depth= 1] . ( 13 sec) [ -2418.5486] [ 212] [depth= 9] . ( 14 sec) [ -2418.0657] [ 212] [depth= 13] . ( 22 sec) [ -2417.2310] [Branch lengths ] . ( 22 sec) [ -2417.1766] [GTR parameters ] . ( 22 sec) [ -2414.7024] [Alpha ][ 0.142714] . ( 25 sec) [ -2413.4713] [ 212] [depth= 2] . ( 25 sec) [ -2411.9113] [ 212] [depth= 7] . ( 27 sec) [ -2410.7513] [ 211] [depth= 14] . ( 28 sec) [ -2410.6783] [ 211] [depth= 4] . ( 29 sec) [ -2410.6536] [ 211] [depth= 5] . ( 31 sec) [ -2410.6401] [ 211] [depth= 5] . ( 31 sec) [ -2410.6224] [ 211] [depth= 5] . ( 33 sec) [ -2410.5440] [Branch lengths ] . ( 33 sec) [ -2410.2904] [GTR parameters ] . ( 33 sec) [ -2410.2894] [Alpha ][ 0.140939] . ( 38 sec) [ -2410.2763] [ 211] [depth= 1] . ( 38 sec) [ -2410.2654] [ 211] [depth= 6] . ( 43 sec) [ -2410.2639] [Branch lengths ] . ( 44 sec) [ -2410.2639] [GTR parameters ] . ( 44 sec) [ -2410.2639] [Alpha ][ 0.140737] . ( 75 sec) [ -2410.2633] [Branch lengths ] . ( 75 sec) [ -2410.2633] [Topology ] . ( 76 sec) [ -2410.2631] [Topology ] . ( 76 sec) [ -2410.2631] [GTR parameters ] . ( 76 sec) [ -2410.2631] [Alpha ][ 0.140737] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -2410.2621] [Topology ] . Checking for NNIs, optimizing five branches... . ( 84 sec) [ -2410.2573] [Topology ] . Checking for NNIs, optimizing five branches... . ( 87 sec) [ -2410.2572] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -2410.257237. . Printing the most likely tree in file 'nucleic_M2913_81x897_2006.phy_phyml_tree.txt'... . Time used 0h1m32s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 91.06user 0.00system 1:32.37elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps