.......................... 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 ] . ( 4 sec) [ -10335.0128] [Alpha ][ 0.500960] . ( 4 sec) [ -10332.5377] [ 1957] [depth= 1] . ( 4 sec) [ -10328.1906] [ 1951] [depth= 1] . ( 5 sec) [ -10328.1000] [ 1957] [depth= 1] . ( 5 sec) [ -10322.0485] [ 1953] [depth= 2] . ( 5 sec) [ -10321.5223] [ 1957] [depth= 1] . ( 5 sec) [ -10318.8466] [ 1953] [depth= 1] . ( 6 sec) [ -10318.7421] [ 1953] [depth= 1] . ( 6 sec) [ -10318.5053] [ 1953] [depth= 1] . ( 6 sec) [ -10317.9252] [ 1954] [depth= 1] . ( 6 sec) [ -10317.3941] [ 1954] [depth= 1] . ( 6 sec) [ -10317.1936] [ 1953] [depth= 1] . ( 6 sec) [ -10317.1467] [ 1952] [depth= 1] . ( 6 sec) [ -10316.1576] [ 1952] [depth= 1] . ( 6 sec) [ -10315.7973] [ 1952] [depth= 1] . ( 6 sec) [ -10315.6060] [ 1952] [depth= 1] . ( 6 sec) [ -10315.5532] [ 1952] [depth= 1] . ( 7 sec) [ -10314.4237] [ 1954] [depth= 1] . ( 7 sec) [ -10311.8066] [ 1956] [depth= 2] . ( 7 sec) [ -10298.4200] [ 1960] [depth= 1] . ( 8 sec) [ -10289.7401] [ 1957] [depth= 1] . ( 8 sec) [ -10289.6879] [ 1959] [depth= 2] . ( 8 sec) [ -10289.0089] [ 1958] [depth= 1] . ( 8 sec) [ -10288.5616] [ 1957] [depth= 1] . ( 9 sec) [ -10286.7576] [ 1959] [depth= 1] . ( 9 sec) [ -10282.8478] [ 1961] [depth= 1] . ( 9 sec) [ -10279.3729] [ 1959] [depth= 1] . ( 9 sec) [ -10277.0324] [ 1959] [depth= 1] . ( 9 sec) [ -10273.5485] [ 1959] [depth= 1] . ( 10 sec) [ -10263.5614] [ 1954] [depth= 1] . ( 10 sec) [ -10262.5370] [ 1954] [depth= 1] . ( 10 sec) [ -10262.5206] [ 1956] [depth= 1] . ( 10 sec) [ -10260.5546] [ 1956] [depth= 1] . ( 10 sec) [ -10259.3101] [ 1956] [depth= 1] . ( 11 sec) [ -10256.9944] [ 1956] [depth= 1] . ( 11 sec) [ -10253.4037] [ 1952] [depth= 1] . ( 11 sec) [ -10252.7925] [ 1955] [depth= 1] . ( 11 sec) [ -10251.8154] [ 1952] [depth= 1] . ( 11 sec) [ -10251.5620] [ 1952] [depth= 1] . ( 11 sec) [ -10248.9677] [ 1952] [depth= 1] . ( 12 sec) [ -10245.1368] [ 1954] [depth= 1] . ( 12 sec) [ -10244.6777] [ 1954] [depth= 1] . ( 12 sec) [ -10244.3453] [ 1954] [depth= 1] . ( 12 sec) [ -10243.7468] [ 1954] [depth= 1] . ( 12 sec) [ -10243.0409] [ 1954] [depth= 1] . ( 13 sec) [ -10242.9194] [ 1954] [depth= 1] . ( 13 sec) [ -10176.2018] [Branch lengths ] . ( 14 sec) [ -10175.3323] [GTR parameters ] . ( 15 sec) [ -10174.9626] [Alpha ][ 0.528629] . ( 15 sec) [ -10174.8386] [ 1952] [depth= 1] . ( 15 sec) [ -10173.8735] [ 1947] [depth= 1] . ( 16 sec) [ -10172.8929] [ 1945] [depth= 1] . ( 17 sec) [ -10172.4237] [ 1945] [depth= 1] . ( 17 sec) [ -10172.1357] [ 1945] [depth= 2] . ( 17 sec) [ -10170.9851] [ 1943] [depth= 2] . ( 18 sec) [ -10170.9636] [ 1942] [depth= 1] . ( 21 sec) [ -10170.9290] [ 1942] [depth= 2] . ( 21 sec) [ -10170.5737] [ 1942] [depth= 1] . ( 22 sec) [ -10160.4203] [Branch lengths ] . ( 22 sec) [ -10160.3809] [GTR parameters ] . ( 22 sec) [ -10160.2034] [Alpha ][ 0.548769] . ( 30 sec) [ -10158.7556] [Branch lengths ] . ( 75 sec) [ -10158.6458] [ 1939] [depth= 1] . ( 105 sec) [ -10158.3395] [Branch lengths ] . ( 106 sec) [ -10158.3141] [GTR parameters ] . ( 106 sec) [ -10158.2829] [Alpha ][ 0.557419] . ( 106 sec) [ -10158.2829] [Topology ] . ( 109 sec) [ -10158.2379] [Topology ] . ( 112 sec) [ -10158.2184] [Topology ] . ( 115 sec) [ -10158.2076] [Topology ] . ( 117 sec) [ -10158.2014] [Topology ] . ( 119 sec) [ -10158.1977] [Topology ] . ( 122 sec) [ -10158.1956] [Topology ] . ( 123 sec) [ -10158.1944] [GTR parameters ] . ( 123 sec) [ -10158.1936] [Alpha ][ 0.558818] . ( 123 sec) [ -10158.1936] [Topology ] . ( 125 sec) [ -10158.1918] [Topology ] . ( 127 sec) [ -10158.1907] [Topology ] . ( 130 sec) [ -10158.1771] [Topology ] . ( 132 sec) [ -10158.0103] [Topology ] . ( 134 sec) [ -10157.9932] [Topology ] . ( 136 sec) [ -10157.9901] [Topology ] . ( 138 sec) [ -10157.9889] [Topology ] . ( 141 sec) [ -10157.9883] [Topology ] . ( 142 sec) [ -10157.9864] [GTR parameters ] . ( 142 sec) [ -10157.9864] [Alpha ][ 0.558818] . ( 142 sec) [ -10157.9864] [Topology ] . ( 145 sec) [ -10157.9862] [Topology ] . ( 145 sec) [ -10157.9862] [GTR parameters ] . ( 145 sec) [ -10157.9862] [Alpha ][ 0.558818] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -10157.986154. . Printing the most likely tree in file 'nucleic_M2764_57x803_2006.phy_phyml_tree.txt'... . Time used 0h2m43s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 130.32user 0.00system 2:43.17elapsed 79%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps