.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2764_57x803_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 . 3 sites are made from completely undetermined states ('X', '-', '?' or 'N')... . Compressing sequences... . 628 patterns found. (out of a total of 803 sites) . 286 sites without polymorphism (35.62%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 19Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 4 sec) [ -10411.1053] [GTR parameters ] . ( 4 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 4 sec) [ -10332.5377] [ 1957] [depth= 1] . ( 4 sec) [ -10328.1906] [ 1951] [depth= 1] . ( 6 sec) [ -10328.1000] [ 1957] [depth= 1] . ( 6 sec) [ -10322.0485] [ 1953] [depth= 2] . ( 6 sec) [ -10321.5223] [ 1957] [depth= 1] . ( 6 sec) [ -10318.8466] [ 1953] [depth= 1] . ( 6 sec) [ -10318.7421] [ 1953] [depth= 1] . ( 6 sec) [ -10318.5053] [ 1953] [depth= 1] . ( 7 sec) [ -10317.9252] [ 1954] [depth= 1] . ( 7 sec) [ -10317.3941] [ 1954] [depth= 1] . ( 7 sec) [ -10317.1936] [ 1953] [depth= 1] . ( 7 sec) [ -10317.1467] [ 1952] [depth= 1] . ( 7 sec) [ -10316.1576] [ 1952] [depth= 1] . ( 7 sec) [ -10315.7973] [ 1952] [depth= 1] . ( 7 sec) [ -10315.6060] [ 1952] [depth= 1] . ( 8 sec) [ -10315.5532] [ 1952] [depth= 1] . ( 8 sec) [ -10314.4237] [ 1954] [depth= 1] . ( 8 sec) [ -10311.8066] [ 1956] [depth= 2] . ( 8 sec) [ -10298.4200] [ 1960] [depth= 1] . ( 9 sec) [ -10296.7188] [ 1964] [depth= 3] . ( 9 sec) [ -10290.8688] [ 1958] [depth= 3] . ( 9 sec) [ -10287.8786] [ 1957] [depth= 1] . ( 9 sec) [ -10287.2467] [ 1958] [depth= 1] . ( 10 sec) [ -10286.6646] [ 1960] [depth= 2] . ( 10 sec) [ -10285.3626] [ 1958] [depth= 1] . ( 10 sec) [ -10284.7476] [ 1960] [depth= 1] . ( 10 sec) [ -10284.4485] [ 1962] [depth= 1] . ( 10 sec) [ -10283.5669] [ 1962] [depth= 1] . ( 11 sec) [ -10282.5503] [ 1961] [depth= 1] . ( 11 sec) [ -10280.7221] [ 1959] [depth= 1] . ( 11 sec) [ -10275.0930] [ 1961] [depth= 1] . ( 11 sec) [ -10271.5810] [ 1959] [depth= 1] . ( 11 sec) [ -10269.1582] [ 1960] [depth= 1] . ( 12 sec) [ -10265.8986] [ 1959] [depth= 1] . ( 12 sec) [ -10255.9269] [ 1954] [depth= 1] . ( 12 sec) [ -10255.6999] [ 1954] [depth= 1] . ( 13 sec) [ -10255.0256] [ 1955] [depth= 1] . ( 13 sec) [ -10254.3015] [ 1957] [depth= 1] . ( 13 sec) [ -10254.0739] [ 1955] [depth= 1] . ( 13 sec) [ -10252.2304] [ 1955] [depth= 1] . ( 13 sec) [ -10249.1318] [ 1956] [depth= 1] . ( 13 sec) [ -10248.1783] [ 1956] [depth= 1] . ( 14 sec) [ -10245.7845] [ 1956] [depth= 1] . ( 14 sec) [ -10241.9436] [ 1952] [depth= 1] . ( 14 sec) [ -10241.4605] [ 1955] [depth= 1] . ( 14 sec) [ -10241.4040] [ 1956] [depth= 1] . ( 14 sec) [ -10239.7131] [ 1952] [depth= 1] . ( 14 sec) [ -10239.0104] [ 1952] [depth= 1] . ( 15 sec) [ -10238.1532] [ 1957] [depth= 2] . ( 15 sec) [ -10237.2127] [ 1957] [depth= 1] . ( 15 sec) [ -10236.9476] [ 1957] [depth= 1] . ( 16 sec) [ -10236.7877] [ 1958] [depth= 1] . ( 17 sec) [ -10235.0013] [ 1960] [depth= 1] . ( 17 sec) [ -10234.7534] [ 1958] [depth= 1] . ( 17 sec) [ -10233.4427] [ 1959] [depth= 1] . ( 18 sec) [ -10232.8847] [ 1959] [depth= 1] . ( 18 sec) [ -10174.7437] [Branch lengths ] . ( 19 sec) [ -10173.5724] [GTR parameters ] . ( 19 sec) [ -10173.1806] [Alpha ][ 0.529333] . ( 20 sec) [ -10172.0753] [ 1954] [depth= 1] . ( 22 sec) [ -10170.8253] [ 1952] [depth= 1] . ( 23 sec) [ -10170.3291] [ 1952] [depth= 1] . ( 23 sec) [ -10170.0245] [ 1952] [depth= 2] . ( 23 sec) [ -10168.8694] [ 1950] [depth= 2] . ( 32 sec) [ -10168.2110] [ 1950] [depth= 1] . ( 38 sec) [ -10167.9359] [ 1950] [depth= 1] . ( 38 sec) [ -10160.5292] [Branch lengths ] . ( 39 sec) [ -10160.4897] [GTR parameters ] . ( 40 sec) [ -10160.3695] [Alpha ][ 0.545447] . ( 58 sec) [ -10159.0871] [Branch lengths ] . ( 91 sec) [ -10159.0322] [ 1949] [depth= 1] . ( 126 sec) [ -10158.8062] [Branch lengths ] . ( 126 sec) [ -10158.7858] [GTR parameters ] . ( 127 sec) [ -10158.7576] [Alpha ][ 0.553586] . ( 127 sec) [ -10158.7576] [Topology ] . ( 128 sec) [ -10158.6050] [Topology ] . ( 130 sec) [ -10158.3544] [Topology ] . ( 131 sec) [ -10158.3113] [Topology ] . ( 133 sec) [ -10158.2964] [Topology ] . ( 135 sec) [ -10158.2902] [Topology ] . ( 136 sec) [ -10158.2873] [Topology ] . ( 138 sec) [ -10158.2857] [Topology ] . ( 139 sec) [ -10158.2808] [GTR parameters ] . ( 139 sec) [ -10158.2786] [Alpha ][ 0.555807] . ( 139 sec) [ -10158.2786] [Topology ] . ( 140 sec) [ -10158.2773] [Topology ] . ( 142 sec) [ -10158.2765] [Topology ] . ( 142 sec) [ -10158.2765] [GTR parameters ] . ( 142 sec) [ -10158.2765] [Alpha ][ 0.555807] . ( 142 sec) [ -10158.2765] [Topology ] . ( 144 sec) [ -10158.2760] [Topology ] . ( 144 sec) [ -10158.2760] [GTR parameters ] . ( 144 sec) [ -10158.2760] [Alpha ][ 0.555807] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10158.276012. . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Time used 0h2m36s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 151.29user 0.00system 2:36.22elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps