.......................... 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] . ( 3 sec) [ -3415.8640] [ 336] [depth= 1] . ( 3 sec) [ -3415.4963] [ 336] [depth= 1] . ( 3 sec) [ -3414.4341] [ 336] [depth= 1] . ( 3 sec) [ -3414.3769] [ 336] [depth= 1] . ( 3 sec) [ -3414.3590] [ 336] [depth= 2] . ( 3 sec) [ -3414.3295] [ 336] [depth= 2] . ( 4 sec) [ -3414.2057] [ 336] [depth= 2] . ( 4 sec) [ -3413.9687] [ 336] [depth= 3] . ( 4 sec) [ -3413.8952] [ 336] [depth= 1] . ( 4 sec) [ -3413.5919] [ 336] [depth= 1] . ( 4 sec) [ -3413.3753] [ 336] [depth= 1] . ( 4 sec) [ -3413.3381] [ 336] [depth= 3] . ( 4 sec) [ -3411.6980] [ 336] [depth= 8] . ( 4 sec) [ -3407.5435] [ 335] [depth= 8] . ( 4 sec) [ -3407.3943] [ 335] [depth= 1] . ( 4 sec) [ -3406.6595] [ 338] [depth= 4] . ( 5 sec) [ -3406.5797] [ 338] [depth= 2] . ( 5 sec) [ -3406.5560] [ 338] [depth= 1] . ( 5 sec) [ -3406.4756] [ 338] [depth= 1] . ( 5 sec) [ -3406.2891] [ 338] [depth= 1] . ( 5 sec) [ -3405.3060] [ 338] [depth= 1] . ( 5 sec) [ -3404.4518] [ 338] [depth= 1] . ( 5 sec) [ -3404.4304] [ 338] [depth= 1] . ( 5 sec) [ -3404.2505] [ 338] [depth= 1] . ( 6 sec) [ -3404.2040] [ 338] [depth= 1] . ( 6 sec) [ -3404.1906] [ 338] [depth= 2] . ( 6 sec) [ -3403.4390] [ 338] [depth= 1] . ( 6 sec) [ -3403.3845] [ 338] [depth= 1] . ( 6 sec) [ -3403.2362] [ 338] [depth= 3] . ( 6 sec) [ -3403.2001] [ 338] [depth= 1] . ( 6 sec) [ -3403.1719] [ 338] [depth= 1] . ( 6 sec) [ -3403.1456] [ 338] [depth= 9] . ( 6 sec) [ -3403.1312] [ 338] [depth= 1] . ( 6 sec) [ -3403.0877] [ 338] [depth= 6] . ( 6 sec) [ -3402.5265] [ 338] [depth= 1] . ( 7 sec) [ -3402.4250] [ 338] [depth= 4] . ( 7 sec) [ -3402.0460] [ 338] [depth= 1] . ( 7 sec) [ -3401.8471] [ 338] [depth= 2] . ( 7 sec) [ -3401.8319] [ 338] [depth= 1] . ( 7 sec) [ -3401.8188] [ 338] [depth= 3] . ( 8 sec) [ -3401.8058] [ 338] [depth= 2] . ( 8 sec) [ -3392.9895] [ 340] [depth= 4] . ( 9 sec) [ -3387.6919] [ 340] [depth= 2] . ( 9 sec) [ -3385.2788] [ 339] [depth= 1] . ( 9 sec) [ -3384.9587] [ 339] [depth= 1] . ( 9 sec) [ -3384.7357] [ 339] [depth= 5] . ( 9 sec) [ -3384.0001] [ 339] [depth= 1] . ( 9 sec) [ -3383.2218] [ 339] [depth= 1] . ( 9 sec) [ -3376.2670] [ 338] [depth= 5] . ( 9 sec) [ -3376.2525] [ 338] [depth= 2] . ( 9 sec) [ -3376.1719] [ 338] [depth= 1] . ( 10 sec) [ -3375.8484] [ 338] [depth= 4] . ( 10 sec) [ -3375.5962] [ 338] [depth= 1] . ( 10 sec) [ -3375.1002] [ 338] [depth= 1] . ( 10 sec) [ -3374.4482] [ 338] [depth= 3] . ( 10 sec) [ -3373.8745] [ 338] [depth= 1] . ( 10 sec) [ -3373.6493] [ 338] [depth= 1] . ( 10 sec) [ -3373.4081] [ 338] [depth= 2] . ( 10 sec) [ -3373.2143] [ 338] [depth= 4] . ( 10 sec) [ -3372.9534] [ 338] [depth= 3] . ( 10 sec) [ -3372.9302] [ 338] [depth= 4] . ( 10 sec) [ -3372.9195] [ 338] [depth= 4] . ( 11 sec) [ -3372.8684] [ 338] [depth= 4] . ( 11 sec) [ -3372.8561] [ 338] [depth= 6] . ( 11 sec) [ -3372.8324] [ 338] [depth= 5] . ( 11 sec) [ -3372.6127] [ 338] [depth= 3] . ( 11 sec) [ -3372.4974] [ 338] [depth= 5] . ( 11 sec) [ -3372.4767] [ 338] [depth= 2] . ( 12 sec) [ -3372.4596] [ 338] [depth= 2] . ( 12 sec) [ -3371.7162] [ 338] [depth= 4] . ( 12 sec) [ -3371.5311] [ 338] [depth= 2] . ( 12 sec) [ -3371.4966] [ 338] [depth= 2] . ( 12 sec) [ -3371.4792] [ 338] [depth= 3] . ( 12 sec) [ -3371.4586] [ 338] [depth= 1] . ( 12 sec) [ -3368.7093] [ 338] [depth= 1] . ( 12 sec) [ -3368.6004] [ 338] [depth= 5] . ( 14 sec) [ -3368.5774] [ 338] [depth= 5] . ( 14 sec) [ -3367.1514] [ 338] [depth= 1] . ( 14 sec) [ -3367.1344] [ 338] [depth= 2] . ( 14 sec) [ -3366.3617] [ 338] [depth= 1] . ( 14 sec) [ -3366.3429] [ 338] [depth= 4] . ( 15 sec) [ -3365.9282] [ 338] [depth= 1] . ( 15 sec) [ -3365.8836] [ 338] [depth= 2] . ( 15 sec) [ -3365.8711] [ 338] [depth= 1] . ( 16 sec) [ -3365.8596] [ 338] [depth= 1] . ( 16 sec) [ -3365.8245] [ 338] [depth= 1] . ( 23 sec) [ -3360.1789] [Branch lengths ] . ( 23 sec) [ -3359.9280] [GTR parameters ] . ( 23 sec) [ -3352.2664] [Alpha ][ 0.250961] . ( 24 sec) [ -3352.2552] [ 338] [depth= 1] . ( 24 sec) [ -3352.2405] [ 338] [depth= 3] . ( 25 sec) [ -3352.1379] [ 338] [depth= 2] . ( 26 sec) [ -3352.1269] [ 338] [depth= 2] . ( 26 sec) [ -3346.2461] [ 331] [depth= 3] . ( 31 sec) [ -3345.3077] [ 331] [depth= 1] . ( 48 sec) [ -3344.9731] [Branch lengths ] . ( 48 sec) [ -3344.8538] [GTR parameters ] . ( 49 sec) [ -3344.8513] [Alpha ][ 0.247804] . ( 50 sec) [ -3344.8368] [ 331] [depth= 2] . ( 70 sec) [ -3344.7680] [Branch lengths ] . ( 70 sec) [ -3344.7675] [GTR parameters ] . ( 70 sec) [ -3344.7675] [Alpha ][ 0.247300] . ( 113 sec) [ -3344.7601] [Branch lengths ] . ( 113 sec) [ -3344.7601] [Topology ] . ( 113 sec) [ -3344.7593] [Topology ] . ( 114 sec) [ -3344.7592] [GTR parameters ] . ( 114 sec) [ -3344.7592] [Alpha ][ 0.247300] . Checking for NNIs, optimizing five branches... . ( 118 sec) [ -3344.7572] [Topology ] . Checking for NNIs, optimizing five branches... . ( 123 sec) [ -3344.7490] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -3344.749024. . Printing the most likely tree in file 'nucleic_M2716_79x1252_2006.phy_phyml_tree.txt'... . Time used 0h2m7s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 125.59user 0.00system 2:08.02elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps