.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2716_79x1252_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 . 28 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 280 patterns found. (out of a total of 1252 sites) . 984 sites without polymorphism (78.59%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 12Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 2 sec) [ -3429.4082] [GTR parameters ] . ( 2 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 2 sec) [ -3418.0700] [ 336] [depth= 1] . ( 2 sec) [ -3417.9931] [ 336] [depth= 1] . ( 8 sec) [ -3417.0232] [ 340] [depth= 1] . ( 8 sec) [ -3414.9815] [ 340] [depth= 1] . ( 8 sec) [ -3414.6607] [ 340] [depth= 1] . ( 9 sec) [ -3413.6439] [ 340] [depth= 1] . ( 9 sec) [ -3413.6013] [ 340] [depth= 1] . ( 9 sec) [ -3413.5823] [ 340] [depth= 2] . ( 10 sec) [ -3413.5625] [ 340] [depth= 2] . ( 12 sec) [ -3413.4774] [ 340] [depth= 2] . ( 12 sec) [ -3413.2737] [ 340] [depth= 3] . ( 13 sec) [ -3413.1917] [ 340] [depth= 1] . ( 14 sec) [ -3412.8933] [ 340] [depth= 1] . ( 14 sec) [ -3412.5965] [ 340] [depth= 1] . ( 14 sec) [ -3412.5584] [ 340] [depth= 3] . ( 14 sec) [ -3410.8766] [ 340] [depth= 8] . ( 14 sec) [ -3406.7619] [ 339] [depth= 8] . ( 15 sec) [ -3406.6175] [ 339] [depth= 1] . ( 15 sec) [ -3402.2669] [ 335] [depth= 1] . ( 15 sec) [ -3399.0047] [ 333] [depth= 1] . ( 18 sec) [ -3398.9267] [ 333] [depth= 2] . ( 24 sec) [ -3397.9709] [ 333] [depth= 1] . ( 24 sec) [ -3397.1404] [ 333] [depth= 1] . ( 27 sec) [ -3397.1210] [ 333] [depth= 1] . ( 27 sec) [ -3396.9412] [ 333] [depth= 1] . ( 28 sec) [ -3396.8891] [ 333] [depth= 1] . ( 28 sec) [ -3396.8753] [ 333] [depth= 2] . ( 29 sec) [ -3396.1252] [ 333] [depth= 1] . ( 30 sec) [ -3396.0723] [ 333] [depth= 1] . ( 30 sec) [ -3395.9211] [ 333] [depth= 3] . ( 30 sec) [ -3395.8836] [ 333] [depth= 1] . ( 30 sec) [ -3395.8563] [ 333] [depth= 1] . ( 30 sec) [ -3395.8398] [ 333] [depth= 9] . ( 30 sec) [ -3395.8258] [ 333] [depth= 1] . ( 30 sec) [ -3395.7835] [ 333] [depth= 6] . ( 30 sec) [ -3395.2384] [ 333] [depth= 1] . ( 30 sec) [ -3395.1397] [ 333] [depth= 4] . ( 31 sec) [ -3394.7715] [ 333] [depth= 1] . ( 31 sec) [ -3394.5784] [ 333] [depth= 2] . ( 31 sec) [ -3394.5632] [ 333] [depth= 1] . ( 31 sec) [ -3394.5504] [ 333] [depth= 3] . ( 34 sec) [ -3394.5376] [ 333] [depth= 2] . ( 40 sec) [ -3386.5760] [ 332] [depth= 4] . ( 40 sec) [ -3386.5168] [ 333] [depth= 1] . ( 41 sec) [ -3381.5448] [ 333] [depth= 2] . ( 41 sec) [ -3381.3991] [ 333] [depth= 1] . ( 45 sec) [ -3380.8694] [ 332] [depth= 1] . ( 45 sec) [ -3378.2572] [ 331] [depth= 1] . ( 46 sec) [ -3377.5295] [ 331] [depth= 1] . ( 46 sec) [ -3376.7550] [ 331] [depth= 1] . ( 47 sec) [ -3376.0843] [ 332] [depth= 5] . ( 49 sec) [ -3376.0700] [ 332] [depth= 2] . ( 49 sec) [ -3375.9891] [ 332] [depth= 1] . ( 49 sec) [ -3375.6208] [ 332] [depth= 4] . ( 49 sec) [ -3375.3710] [ 332] [depth= 1] . ( 49 sec) [ -3374.9783] [ 332] [depth= 1] . ( 49 sec) [ -3373.1937] [ 332] [depth= 4] . ( 49 sec) [ -3372.6258] [ 332] [depth= 1] . ( 50 sec) [ -3372.3898] [ 332] [depth= 1] . ( 50 sec) [ -3372.1519] [ 332] [depth= 2] . ( 50 sec) [ -3371.9848] [ 332] [depth= 4] . ( 51 sec) [ -3371.7360] [ 332] [depth= 3] . ( 51 sec) [ -3371.7198] [ 332] [depth= 4] . ( 53 sec) [ -3371.6999] [ 332] [depth= 1] . ( 53 sec) [ -3371.5829] [ 332] [depth= 3] . ( 53 sec) [ -3371.4835] [ 332] [depth= 3] . ( 56 sec) [ -3368.4015] [ 331] [depth= 1] . ( 58 sec) [ -3368.0489] [ 331] [depth= 3] . ( 58 sec) [ -3367.9113] [ 331] [depth= 6] . ( 58 sec) [ -3367.7666] [ 331] [depth= 4] . ( 58 sec) [ -3367.7274] [ 331] [depth= 2] . ( 58 sec) [ -3367.6900] [ 331] [depth= 2] . ( 58 sec) [ -3367.6727] [ 331] [depth= 3] . ( 58 sec) [ -3367.6524] [ 331] [depth= 1] . ( 58 sec) [ -3364.9507] [ 331] [depth= 1] . ( 58 sec) [ -3364.8801] [ 331] [depth= 6] . ( 58 sec) [ -3364.8181] [ 331] [depth= 1] . ( 58 sec) [ -3364.7366] [ 331] [depth= 3] . ( 62 sec) [ -3361.9486] [ 330] [depth= 1] . ( 62 sec) [ -3361.9264] [ 330] [depth= 5] . ( 64 sec) [ -3361.9098] [ 330] [depth= 2] . ( 64 sec) [ -3360.4111] [ 330] [depth= 1] . ( 64 sec) [ -3360.3954] [ 330] [depth= 5] . ( 64 sec) [ -3359.6347] [ 330] [depth= 1] . ( 65 sec) [ -3359.5920] [ 330] [depth= 3] . ( 65 sec) [ -3359.1840] [ 330] [depth= 1] . ( 66 sec) [ -3359.1667] [ 330] [depth= 4] . ( 67 sec) [ -3359.1552] [ 330] [depth= 1] . ( 68 sec) [ -3359.1345] [ 330] [depth= 1] . ( 95 sec) [ -3351.5540] [Branch lengths ] . ( 96 sec) [ -3351.3432] [GTR parameters ] . ( 96 sec) [ -3346.1094] [Alpha ][ 0.269884] . ( 108 sec) [ -3346.0945] [ 330] [depth= 1] . ( 108 sec) [ -3346.0798] [ 330] [depth= 3] . ( 117 sec) [ -3345.9716] [ 330] [depth= 2] . ( 120 sec) [ -3345.9603] [ 330] [depth= 2] . ( 127 sec) [ -3345.9380] [ 330] [depth= 1] . ( 272 sec) [ -3345.1355] [Branch lengths ] . ( 273 sec) [ -3345.0529] [GTR parameters ] . ( 273 sec) [ -3344.9773] [Alpha ][ 0.252061] . ( 292 sec) [ -3344.9610] [ 330] [depth= 2] . ( 448 sec) [ -3344.8643] [Branch lengths ] . ( 449 sec) [ -3344.8610] [GTR parameters ] . ( 449 sec) [ -3344.8585] [Alpha ][ 0.248914] . ( 492 sec) [ -3344.8441] [Branch lengths ] . ( 492 sec) [ -3344.8441] [Topology ] . ( 493 sec) [ -3344.7927] [Topology ] . ( 493 sec) [ -3344.7677] [Topology ] . ( 494 sec) [ -3344.7626] [Topology ] . ( 494 sec) [ -3344.7608] [Topology ] . ( 495 sec) [ -3344.7602] [Topology ] . ( 495 sec) [ -3344.7595] [GTR parameters ] . ( 496 sec) [ -3344.7589] [Alpha ][ 0.247340] . ( 496 sec) [ -3344.7589] [Topology ] . ( 496 sec) [ -3344.7585] [Topology ] . ( 496 sec) [ -3344.7584] [GTR parameters ] . ( 496 sec) [ -3344.7584] [Alpha ][ 0.247092] . Checking for NNIs, optimizing five branches... . ( 501 sec) [ -3344.7583] [Topology ] . Checking for NNIs, optimizing five branches... . ( 506 sec) [ -3344.7582] [Topology ] . Checking for NNIs, optimizing five branches... . ( 510 sec) [ -3344.7500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 515 sec) [ -3344.7479] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3344.747935. . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Time used 0h8m40s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 519.38user 0.00system 8:41.04elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps