.......................... 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 : 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 . 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 NNI moves)... . ( 2 sec) [ -3429.4082] [GTR parameters ] . ( 2 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 2 sec) [ -3418.4507] [Topology ] . ( 3 sec) [ -3383.7580] [Topology ] . ( 4 sec) [ -3375.4885] [Topology ] . ( 5 sec) [ -3373.8574] [Topology ] . ( 6 sec) [ -3375.5743] [Topology ] . Moving backward . ( 6 sec) [ -3372.6560] [Topology ] . ( 6 sec) [ -3373.0305] [Topology ] . Moving backward . ( 7 sec) [ -3371.8967] [Topology ] . ( 7 sec) [ -3371.9248] [Topology ] . Moving backward . ( 7 sec) [ -3371.5939] [Topology ] . ( 9 sec) [ -3371.1516] [GTR parameters ] . ( 9 sec) [ -3365.0485] [Alpha ][ 0.259276] . ( 9 sec) [ -3365.0485] [Topology ] . ( 10 sec) [ -3364.5439] [Topology ] . ( 10 sec) [ -3364.9588] [Topology ] . Moving backward . ( 11 sec) [ -3363.9789] [Topology ] . ( 11 sec) [ -3364.1521] [Topology ] . Moving backward . ( 11 sec) [ -3363.9097] [Topology ] . ( 12 sec) [ -3363.9390] [Topology ] . Moving backward . ( 12 sec) [ -3363.8773] [Topology ] . ( 13 sec) [ -3363.9045] [Topology ] . Moving backward . ( 13 sec) [ -3363.8521] [Topology ] . Checking for NNIs, optimizing five branches... . ( 19 sec) [ -3363.8103] [Topology ] . ( 20 sec) [ -3363.6958] [GTR parameters ] . ( 20 sec) [ -3363.6179] [Alpha ][ 0.242419] . ( 20 sec) [ -3363.6179] [Topology ] . ( 21 sec) [ -3363.5719] [Topology ] . ( 21 sec) [ -3363.5643] [Topology ] . ( 22 sec) [ -3363.6368] [Topology ] . Moving backward . ( 22 sec) [ -3363.5567] [Topology ] . ( 23 sec) [ -3363.5928] [Topology ] . Moving backward . ( 23 sec) [ -3363.5488] [Topology ] . ( 23 sec) [ -3363.5884] [Topology ] . Moving backward . ( 24 sec) [ -3363.5425] [Topology ] . ( 24 sec) [ -3363.5619] [Topology ] . Checking for NNIs, optimizing five branches... . ( 29 sec) [ -3363.5617] [Topology ] . ( 29 sec) [ -3363.5577] [GTR parameters ] . ( 29 sec) [ -3363.5548] [Alpha ][ 0.239253] . ( 30 sec) [ -3363.5548] [Topology ] . ( 30 sec) [ -3363.9067] [Topology ] . Moving backward . ( 30 sec) [ -3363.5441] [Topology ] . ( 31 sec) [ -3363.6769] [Topology ] . Moving backward . ( 31 sec) [ -3363.5300] [Topology ] . ( 32 sec) [ -3363.7362] [Topology ] . Moving backward . ( 32 sec) [ -3363.5250] [Topology ] . ( 32 sec) [ -3363.6144] [Topology ] . Moving backward . ( 33 sec) [ -3363.5137] [Topology ] . ( 33 sec) [ -3363.6283] [Topology ] . Moving backward . Checking for NNIs, optimizing five branches... . ( 38 sec) [ -3363.4943] [Topology ] . ( 38 sec) [ -3363.4941] [GTR parameters ] . ( 38 sec) [ -3363.4939] [Alpha ][ 0.238325] . ( 38 sec) [ -3363.4939] [Topology ] . ( 39 sec) [ -3363.4851] [Topology ] . ( 40 sec) [ -3363.4793] [Topology ] . ( 40 sec) [ -3363.4779] [Topology ] . ( 41 sec) [ -3363.4819] [Topology ] . Moving backward . ( 41 sec) [ -3363.4758] [Topology ] . ( 42 sec) [ -3363.4760] [Topology ] . Checking for NNIs, optimizing five branches... . ( 47 sec) [ -3363.4729] [Topology ] . ( 47 sec) [ -3363.4729] [GTR parameters ] . ( 47 sec) [ -3363.4729] [Alpha ][ 0.238087] . ( 47 sec) [ -3363.4729] [Topology ] . ( 48 sec) [ -3363.4717] [Topology ] . ( 48 sec) [ -3363.4707] [Topology ] . ( 49 sec) [ -3363.4697] [Topology ] . ( 50 sec) [ -3363.4687] [Topology ] . Checking for NNIs, optimizing five branches... . ( 55 sec) [ -3363.4497] [Topology ] . ( 55 sec) [ -3363.4497] [GTR parameters ] . ( 55 sec) [ -3363.4497] [Alpha ][ 0.238087] . ( 55 sec) [ -3363.4497] [Topology ] . ( 56 sec) [ -3363.4489] [Topology ] . Checking for NNIs, optimizing five branches... . ( 60 sec) [ -3363.4487] [Topology ] . Checking for NNIs, optimizing five branches... . ( 65 sec) [ -3363.4294] [Topology ] . Checking for NNIs, optimizing five branches... . ( 70 sec) [ -3363.4235] [Topology ] . Checking for NNIs, optimizing five branches... . ( 75 sec) [ -3363.4219] [Topology ] . Checking for NNIs, optimizing five branches... . ( 80 sec) [ -3363.4203] [Topology ] . Checking for NNIs, optimizing five branches... . ( 85 sec) [ -3363.3839] [Topology ] . Checking for NNIs, optimizing five branches... . ( 89 sec) [ -3363.3837] [Topology ] . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 96 sec) [ -3429.4082] [GTR parameters ] . ( 96 sec) [ -3418.4507] [Alpha ][ 0.500960] . ( 96 sec) [ -3418.0700] [ 336] [depth= 1] . ( 96 sec) [ -3417.9931] [ 336] [depth= 1] . ( 97 sec) [ -3417.0232] [ 340] [depth= 1] . ( 97 sec) [ -3414.9815] [ 340] [depth= 1] . ( 97 sec) [ -3414.6607] [ 340] [depth= 1] . ( 97 sec) [ -3413.6439] [ 340] [depth= 1] . ( 97 sec) [ -3413.6013] [ 340] [depth= 1] . ( 98 sec) [ -3413.5823] [ 340] [depth= 2] . ( 98 sec) [ -3413.5625] [ 340] [depth= 2] . ( 99 sec) [ -3413.4774] [ 340] [depth= 2] . ( 99 sec) [ -3413.2737] [ 340] [depth= 3] . ( 99 sec) [ -3413.1917] [ 340] [depth= 1] . ( 99 sec) [ -3412.8933] [ 340] [depth= 1] . ( 99 sec) [ -3412.5965] [ 340] [depth= 1] . ( 100 sec) [ -3412.5584] [ 340] [depth= 3] . ( 100 sec) [ -3410.8766] [ 340] [depth= 8] . ( 100 sec) [ -3406.7619] [ 339] [depth= 8] . ( 100 sec) [ -3406.6175] [ 339] [depth= 1] . ( 100 sec) [ -3402.2669] [ 335] [depth= 1] . ( 100 sec) [ -3399.0047] [ 333] [depth= 1] . ( 101 sec) [ -3398.9267] [ 333] [depth= 2] . ( 103 sec) [ -3397.9709] [ 333] [depth= 1] . ( 103 sec) [ -3397.1404] [ 333] [depth= 1] . ( 104 sec) [ -3397.1210] [ 333] [depth= 1] . ( 104 sec) [ -3396.9412] [ 333] [depth= 1] . ( 105 sec) [ -3396.8891] [ 333] [depth= 1] . ( 105 sec) [ -3396.8753] [ 333] [depth= 2] . ( 105 sec) [ -3396.1252] [ 333] [depth= 1] . ( 105 sec) [ -3396.0723] [ 333] [depth= 1] . ( 105 sec) [ -3395.9211] [ 333] [depth= 3] . ( 105 sec) [ -3395.8836] [ 333] [depth= 1] . ( 105 sec) [ -3395.8563] [ 333] [depth= 1] . ( 106 sec) [ -3395.8398] [ 333] [depth= 9] . ( 106 sec) [ -3395.8258] [ 333] [depth= 1] . ( 106 sec) [ -3395.7835] [ 333] [depth= 6] . ( 106 sec) [ -3395.2384] [ 333] [depth= 1] . ( 106 sec) [ -3395.1397] [ 333] [depth= 4] . ( 106 sec) [ -3394.7715] [ 333] [depth= 1] . ( 106 sec) [ -3394.5784] [ 333] [depth= 2] . ( 107 sec) [ -3394.5632] [ 333] [depth= 1] . ( 107 sec) [ -3394.5504] [ 333] [depth= 3] . ( 108 sec) [ -3394.5376] [ 333] [depth= 2] . ( 109 sec) [ -3386.5760] [ 332] [depth= 4] . ( 109 sec) [ -3386.5168] [ 333] [depth= 1] . ( 110 sec) [ -3381.5448] [ 333] [depth= 2] . ( 110 sec) [ -3381.3991] [ 333] [depth= 1] . ( 111 sec) [ -3380.8694] [ 332] [depth= 1] . ( 111 sec) [ -3378.2572] [ 331] [depth= 1] . ( 112 sec) [ -3377.5295] [ 331] [depth= 1] . ( 112 sec) [ -3376.7550] [ 331] [depth= 1] . ( 112 sec) [ -3376.0843] [ 332] [depth= 5] . ( 113 sec) [ -3376.0700] [ 332] [depth= 2] . ( 113 sec) [ -3375.9891] [ 332] [depth= 1] . ( 113 sec) [ -3375.6208] [ 332] [depth= 4] . ( 113 sec) [ -3375.3710] [ 332] [depth= 1] . ( 113 sec) [ -3374.9783] [ 332] [depth= 1] . ( 113 sec) [ -3373.1937] [ 332] [depth= 4] . ( 113 sec) [ -3372.6258] [ 332] [depth= 1] . ( 113 sec) [ -3372.3898] [ 332] [depth= 1] . ( 113 sec) [ -3372.1519] [ 332] [depth= 2] . ( 113 sec) [ -3371.9848] [ 332] [depth= 4] . ( 114 sec) [ -3371.7360] [ 332] [depth= 3] . ( 114 sec) [ -3371.7198] [ 332] [depth= 4] . ( 115 sec) [ -3371.6999] [ 332] [depth= 1] . ( 115 sec) [ -3371.5829] [ 332] [depth= 3] . ( 115 sec) [ -3371.4835] [ 332] [depth= 3] . ( 117 sec) [ -3368.4015] [ 331] [depth= 1] . ( 117 sec) [ -3368.0489] [ 331] [depth= 3] . ( 117 sec) [ -3367.9113] [ 331] [depth= 6] . ( 117 sec) [ -3367.7666] [ 331] [depth= 4] . ( 118 sec) [ -3367.7274] [ 331] [depth= 2] . ( 118 sec) [ -3367.6900] [ 331] [depth= 2] . ( 118 sec) [ -3367.6727] [ 331] [depth= 3] . ( 118 sec) [ -3367.6524] [ 331] [depth= 1] . ( 118 sec) [ -3364.9507] [ 331] [depth= 1] . ( 118 sec) [ -3364.8801] [ 331] [depth= 6] . ( 118 sec) [ -3364.8181] [ 331] [depth= 1] . ( 118 sec) [ -3364.7366] [ 331] [depth= 3] . ( 119 sec) [ -3361.9486] [ 330] [depth= 1] . ( 120 sec) [ -3361.9264] [ 330] [depth= 5] . ( 121 sec) [ -3361.9098] [ 330] [depth= 2] . ( 121 sec) [ -3360.4111] [ 330] [depth= 1] . ( 121 sec) [ -3360.3954] [ 330] [depth= 5] . ( 121 sec) [ -3359.6347] [ 330] [depth= 1] . ( 122 sec) [ -3359.5920] [ 330] [depth= 3] . ( 122 sec) [ -3359.1840] [ 330] [depth= 1] . ( 123 sec) [ -3359.1667] [ 330] [depth= 4] . ( 123 sec) [ -3359.1552] [ 330] [depth= 1] . ( 123 sec) [ -3359.1345] [ 330] [depth= 1] . ( 135 sec) [ -3351.5540] [Branch lengths ] . ( 136 sec) [ -3351.3432] [GTR parameters ] . ( 136 sec) [ -3346.1094] [Alpha ][ 0.269884] . ( 138 sec) [ -3346.0945] [ 330] [depth= 1] . ( 138 sec) [ -3346.0798] [ 330] [depth= 3] . ( 141 sec) [ -3345.9716] [ 330] [depth= 2] . ( 142 sec) [ -3345.9603] [ 330] [depth= 2] . ( 144 sec) [ -3345.9380] [ 330] [depth= 1] . ( 197 sec) [ -3345.1355] [Branch lengths ] . ( 198 sec) [ -3345.0529] [GTR parameters ] . ( 198 sec) [ -3344.9773] [Alpha ][ 0.252061] . ( 202 sec) [ -3344.9610] [ 330] [depth= 2] . ( 258 sec) [ -3344.8643] [Branch lengths ] . ( 258 sec) [ -3344.8610] [GTR parameters ] . ( 258 sec) [ -3344.8585] [Alpha ][ 0.248914] . ( 301 sec) [ -3344.8441] [Branch lengths ] . ( 301 sec) [ -3344.8441] [Topology ] . ( 302 sec) [ -3344.7927] [Topology ] . ( 303 sec) [ -3344.7677] [Topology ] . ( 303 sec) [ -3344.7626] [Topology ] . ( 304 sec) [ -3344.7608] [Topology ] . ( 304 sec) [ -3344.7602] [Topology ] . ( 305 sec) [ -3344.7595] [GTR parameters ] . ( 305 sec) [ -3344.7589] [Alpha ][ 0.247340] . ( 305 sec) [ -3344.7589] [Topology ] . ( 305 sec) [ -3344.7585] [Topology ] . ( 306 sec) [ -3344.7584] [GTR parameters ] . ( 306 sec) [ -3344.7584] [Alpha ][ 0.247092] . Checking for NNIs, optimizing five branches... . ( 310 sec) [ -3344.7583] [Topology ] . Checking for NNIs, optimizing five branches... . ( 315 sec) [ -3344.7582] [Topology ] . Checking for NNIs, optimizing five branches... . ( 320 sec) [ -3344.7500] [Topology ] . Checking for NNIs, optimizing five branches... . ( 324 sec) [ -3344.7479] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -3363.383651 . Log likelihood obtained after SPR moves : -3344.747935 . 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 0h5m30s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 326.55user 0.00system 5:30.70elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps