.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : nucleic_M2771_52x1896_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 . Compressing sequences... . 906 patterns found. (out of a total of 1896 sites) . 1193 sites without polymorphism (62.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 24Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15011.6040] [GTR parameters ] . ( 1 sec) [ -14780.7799] [Alpha ][ 0.500960] . ( 10 sec) [ -14763.5982] [ 2324] [depth= 1] . ( 13 sec) [ -14761.9657] [ 2324] [depth= 1] . ( 13 sec) [ -14761.4417] [ 2324] [depth= 1] . ( 15 sec) [ -14758.9385] [ 2324] [depth= 1] . ( 43 sec) [ -14754.4887] [ 2324] [depth= 1] . ( 43 sec) [ -14748.4513] [ 2324] [depth= 1] . ( 46 sec) [ -14747.6244] [ 2326] [depth= 1] . ( 47 sec) [ -14747.5440] [ 2328] [depth= 1] . ( 48 sec) [ -14746.2770] [ 2326] [depth= 1] . ( 48 sec) [ -14745.4215] [ 2324] [depth= 1] . ( 50 sec) [ -14739.8437] [ 2319] [depth= 1] . ( 52 sec) [ -14735.4461] [ 2319] [depth= 2] . ( 52 sec) [ -14733.8271] [ 2315] [depth= 2] . ( 54 sec) [ -14733.7970] [ 2324] [depth= 1] . ( 55 sec) [ -14733.6422] [ 2319] [depth= 1] . ( 61 sec) [ -14730.8109] [ 2319] [depth= 1] . ( 74 sec) [ -14726.7534] [ 2318] [depth= 1] . ( 76 sec) [ -14717.8940] [ 2317] [depth= 2] . ( 76 sec) [ -14716.1366] [ 2318] [depth= 1] . ( 92 sec) [ -14704.3592] [ 2322] [depth= 2] . ( 92 sec) [ -14695.5998] [ 2316] [depth= 2] . ( 93 sec) [ -14691.8977] [ 2316] [depth= 1] . ( 93 sec) [ -14691.2303] [ 2316] [depth= 1] . ( 97 sec) [ -14690.4389] [ 2318] [depth= 1] . ( 97 sec) [ -14681.9966] [ 2316] [depth= 1] . ( 105 sec) [ -14681.8321] [ 2325] [depth= 3] . ( 107 sec) [ -14677.8437] [ 2319] [depth= 1] . ( 107 sec) [ -14672.2554] [ 2316] [depth= 1] . ( 113 sec) [ -14671.0619] [ 2322] [depth= 3] . ( 113 sec) [ -14670.3896] [ 2323] [depth= 1] . ( 114 sec) [ -14669.8481] [ 2320] [depth= 1] . ( 118 sec) [ -14668.4521] [ 2323] [depth= 2] . ( 120 sec) [ -14666.9612] [ 2320] [depth= 2] . ( 122 sec) [ -14664.8637] [ 2320] [depth= 1] . ( 122 sec) [ -14663.0500] [ 2321] [depth= 1] . ( 127 sec) [ -14614.3891] [Branch lengths ] . ( 131 sec) [ -14141.5623] [GTR parameters ] . ( 132 sec) [ -14028.7762] [Alpha ][ 0.250961] . ( 141 sec) [ -14028.5018] [ 2320] [depth= 1] . ( 181 sec) [ -14026.9485] [ 2320] [depth= 2] . ( 186 sec) [ -14024.9951] [ 2319] [depth= 1] . ( 202 sec) [ -14022.7918] [ 2319] [depth= 2] . ( 233 sec) [ -14015.5040] [ 2309] [depth= 4] . ( 234 sec) [ -14015.3562] [ 2311] [depth= 6] . ( 234 sec) [ -14011.3941] [ 2309] [depth= 7] . ( 245 sec) [ -14011.1527] [ 2316] [depth= 1] . ( 245 sec) [ -14011.0996] [ 2316] [depth= 1] . ( 246 sec) [ -14010.8817] [ 2317] [depth= 1] . ( 251 sec) [ -14009.0125] [ 2315] [depth= 1] . ( 260 sec) [ -14005.3767] [ 2312] [depth= 2] . ( 306 sec) [ -13991.3877] [Branch lengths ] . ( 311 sec) [ -13989.9204] [GTR parameters ] . ( 311 sec) [ -13989.8543] [Alpha ][ 0.247062] . ( 370 sec) [ -13989.8107] [ 2315] [depth= 1] . ( 504 sec) [ -13988.1938] [Branch lengths ] . ( 506 sec) [ -13988.1631] [GTR parameters ] . ( 507 sec) [ -13988.1510] [Alpha ][ 0.248750] . ( 702 sec) [ -13987.9086] [Branch lengths ] . ( 780 sec) [ -13987.8736] [Branch lengths ] . ( 781 sec) [ -13987.8736] [Topology ] . ( 782 sec) [ -13987.8704] [Topology ] . ( 784 sec) [ -13987.8693] [Topology ] . ( 786 sec) [ -13987.8688] [Topology ] . ( 789 sec) [ -13987.8649] [GTR parameters ] . ( 789 sec) [ -13987.8590] [Alpha ][ 0.249930] . ( 789 sec) [ -13987.8590] [Topology ] . ( 791 sec) [ -13987.8578] [Topology ] . ( 793 sec) [ -13987.8573] [Topology ] . ( 795 sec) [ -13987.8567] [GTR parameters ] . ( 795 sec) [ -13987.8567] [Alpha ][ 0.249930] . ( 795 sec) [ -13987.8567] [Topology ] . ( 797 sec) [ -13987.8564] [Topology ] . ( 798 sec) [ -13987.8564] [GTR parameters ] . ( 798 sec) [ -13987.8564] [Alpha ][ 0.249930] . Checking for NNIs, optimizing five branches... . ( 813 sec) [ -13987.6759] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -13987.675879. . Printing the most likely tree in file 'nucleic_M2771_52x1896_2006.phy_phyml_tree.txt'... . Time used 0h13m49s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 826.83user 0.00system 13:49.63elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps