.......................... 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)... . ( 3 sec) [ -10411.1053] [GTR parameters ] . ( 3 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 6 sec) [ -10332.5377] [ 1957] [depth= 1] . ( 6 sec) [ -10328.1906] [ 1951] [depth= 1] . ( 11 sec) [ -10321.2816] [ 1960] [depth= 1] . ( 24 sec) [ -10321.1750] [ 1966] [depth= 1] . ( 25 sec) [ -10315.0354] [ 1962] [depth= 2] . ( 29 sec) [ -10314.3880] [ 1966] [depth= 1] . ( 29 sec) [ -10311.7727] [ 1962] [depth= 1] . ( 31 sec) [ -10311.6562] [ 1962] [depth= 1] . ( 31 sec) [ -10311.4408] [ 1962] [depth= 1] . ( 35 sec) [ -10310.8401] [ 1963] [depth= 1] . ( 35 sec) [ -10310.2658] [ 1963] [depth= 1] . ( 35 sec) [ -10310.0322] [ 1962] [depth= 1] . ( 36 sec) [ -10308.9502] [ 1962] [depth= 1] . ( 36 sec) [ -10308.5580] [ 1962] [depth= 1] . ( 36 sec) [ -10308.3523] [ 1962] [depth= 1] . ( 38 sec) [ -10308.3031] [ 1962] [depth= 1] . ( 39 sec) [ -10307.0547] [ 1964] [depth= 1] . ( 39 sec) [ -10304.0308] [ 1966] [depth= 2] . ( 43 sec) [ -10293.9561] [ 1957] [depth= 1] . ( 43 sec) [ -10291.0898] [ 1961] [depth= 1] . ( 55 sec) [ -10289.5941] [ 1965] [depth= 3] . ( 55 sec) [ -10283.7405] [ 1959] [depth= 3] . ( 61 sec) [ -10280.6849] [ 1958] [depth= 1] . ( 61 sec) [ -10279.9494] [ 1959] [depth= 1] . ( 63 sec) [ -10279.4309] [ 1961] [depth= 2] . ( 63 sec) [ -10278.1906] [ 1959] [depth= 1] . ( 64 sec) [ -10278.0911] [ 1960] [depth= 1] . ( 64 sec) [ -10277.2880] [ 1960] [depth= 1] . ( 67 sec) [ -10275.9106] [ 1960] [depth= 1] . ( 68 sec) [ -10270.4687] [ 1962] [depth= 1] . ( 68 sec) [ -10266.9804] [ 1960] [depth= 1] . ( 68 sec) [ -10264.6338] [ 1961] [depth= 1] . ( 70 sec) [ -10261.2045] [ 1960] [depth= 1] . ( 75 sec) [ -10261.0727] [ 1960] [depth= 1] . ( 77 sec) [ -10260.3427] [ 1959] [depth= 1] . ( 78 sec) [ -10259.3010] [ 1961] [depth= 1] . ( 79 sec) [ -10259.0314] [ 1964] [depth= 1] . ( 79 sec) [ -10258.8735] [ 1964] [depth= 1] . ( 79 sec) [ -10257.7183] [ 1963] [depth= 1] . ( 81 sec) [ -10257.5255] [ 1965] [depth= 1] . ( 82 sec) [ -10256.2389] [ 1965] [depth= 1] . ( 82 sec) [ -10253.9635] [ 1965] [depth= 1] . ( 82 sec) [ -10250.4304] [ 1961] [depth= 1] . ( 82 sec) [ -10250.0081] [ 1964] [depth= 1] . ( 85 sec) [ -10248.5194] [ 1961] [depth= 1] . ( 85 sec) [ -10248.2141] [ 1961] [depth= 1] . ( 91 sec) [ -10248.1966] [ 1967] [depth= 2] . ( 91 sec) [ -10247.1717] [ 1968] [depth= 1] . ( 91 sec) [ -10245.4404] [ 1969] [depth= 1] . ( 93 sec) [ -10244.6743] [ 1968] [depth= 1] . ( 93 sec) [ -10243.3522] [ 1969] [depth= 1] . ( 93 sec) [ -10242.4007] [ 1969] [depth= 1] . ( 93 sec) [ -10242.0683] [ 1968] [depth= 1] . ( 100 sec) [ -10241.7457] [ 1969] [depth= 1] . ( 100 sec) [ -10240.7455] [ 1969] [depth= 1] . ( 104 sec) [ -10186.4855] [Branch lengths ] . ( 105 sec) [ -10185.5400] [GTR parameters ] . ( 105 sec) [ -10185.1234] [Alpha ][ 0.530091] . ( 115 sec) [ -10177.7712] [ 1963] [depth= 1] . ( 119 sec) [ -10176.9940] [ 1958] [depth= 1] . ( 141 sec) [ -10175.7184] [ 1956] [depth= 1] . ( 142 sec) [ -10175.6956] [ 1958] [depth= 1] . ( 144 sec) [ -10174.7077] [ 1957] [depth= 1] . ( 145 sec) [ -10174.2821] [ 1957] [depth= 1] . ( 145 sec) [ -10174.0778] [ 1957] [depth= 2] . ( 146 sec) [ -10172.9703] [ 1956] [depth= 2] . ( 150 sec) [ -10172.7968] [ 1954] [depth= 1] . ( 185 sec) [ -10172.7253] [ 1952] [depth= 1] . ( 185 sec) [ -10172.6806] [ 1954] [depth= 1] . ( 203 sec) [ -10172.4551] [ 1952] [depth= 1] . ( 206 sec) [ -10171.8968] [ 1949] [depth= 1] . ( 224 sec) [ -10171.7911] [ 1945] [depth= 3] . ( 231 sec) [ -10171.6787] [ 1944] [depth= 1] . ( 231 sec) [ -10171.5272] [ 1945] [depth= 1] . ( 246 sec) [ -10160.2735] [Branch lengths ] . ( 247 sec) [ -10160.1919] [GTR parameters ] . ( 247 sec) [ -10160.0082] [Alpha ][ 0.550524] . ( 402 sec) [ -10158.5699] [Branch lengths ] . ( 434 sec) [ -10158.5149] [ 1944] [depth= 1] . ( 445 sec) [ -10158.3948] [ 1941] [depth= 1] . ( 466 sec) [ -10158.1025] [Branch lengths ] . ( 467 sec) [ -10158.0781] [GTR parameters ] . ( 467 sec) [ -10158.0548] [Alpha ][ 0.557993] . ( 467 sec) [ -10158.0548] [Topology ] . ( 469 sec) [ -10157.9197] [Topology ] . ( 470 sec) [ -10157.7007] [Topology ] . ( 472 sec) [ -10157.6695] [Topology ] . ( 473 sec) [ -10157.6588] [Topology ] . ( 475 sec) [ -10157.6536] [Topology ] . ( 477 sec) [ -10157.6508] [Topology ] . ( 478 sec) [ -10157.6493] [Topology ] . ( 479 sec) [ -10157.6473] [GTR parameters ] . ( 479 sec) [ -10157.6473] [Alpha ][ 0.557993] . ( 479 sec) [ -10157.6473] [Topology ] . ( 481 sec) [ -10157.6462] [Topology ] . ( 482 sec) [ -10157.6455] [Topology ] . ( 482 sec) [ -10157.6455] [GTR parameters ] . ( 483 sec) [ -10157.6454] [Alpha ][ 0.558551] . ( 483 sec) [ -10157.6454] [Topology ] . ( 484 sec) [ -10157.6450] [Topology ] . ( 485 sec) [ -10157.6450] [GTR parameters ] . ( 485 sec) [ -10157.6450] [Alpha ][ 0.558551] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.644996. . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Time used 0h8m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 493.89user 0.00system 8:17.16elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps