.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M2638_18x378_2006.phy . Data type : aa . Sequence format : interleaved . Number of data sets : 1 . Nb of bootstrapped data sets : 0 . Model name : WAG . Proportion of invariable sites : 0.000000 . Number of subst. rate categs : 4 . Gamma distribution parameter : estimated . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : no . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 75 patterns found. (out of a total of 378 sites) . 321 sites without polymorphism (84.92%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 3Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -1700.8671] [Alpha ][ 0.500960] . ( 0 sec) [ -1700.8671] [Topology ] . ( 1 sec) [ -1697.1437] [Topology ] . ( 1 sec) [ -1696.5765] [Topology ] . ( 1 sec) [ -1696.4520] [Topology ] . ( 2 sec) [ -1696.4234] [Topology ] . ( 2 sec) [ -1696.4165] [Topology ] . ( 3 sec) [ -1696.4149] [Topology ] . Checking for NNIs, optimizing five branches... . ( 5 sec) [ -1693.8018] [Alpha ][ 0.250961] . ( 5 sec) [ -1693.8018] [Topology ] . ( 5 sec) [ -1693.7994] [Topology ] . ( 5 sec) [ -1693.7989] [Topology ] . Checking for NNIs, optimizing five branches... . ( 8 sec) [ -1693.3291] [Alpha ][ 0.159379] . ( 8 sec) [ -1693.3291] [Topology ] . ( 8 sec) [ -1693.3244] [Topology ] . ( 8 sec) [ -1693.3235] [Topology ] . Checking for NNIs, optimizing five branches... . ( 10 sec) [ -1693.3234] [Alpha ][ 0.157847] . ( 10 sec) [ -1693.3234] [Topology ] . ( 11 sec) [ -1693.3231] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 15 sec) [ -1700.8671] [Alpha ][ 0.500960] . ( 21 sec) [ -1700.1272] [ 82] [depth= 1] . ( 21 sec) [ -1699.4578] [ 82] [depth= 1] . ( 21 sec) [ -1698.1292] [ 80] [depth= 3] . ( 22 sec) [ -1697.8197] [ 81] [depth= 3] . ( 23 sec) [ -1696.9534] [ 81] [depth= 2] . ( 26 sec) [ -1696.8905] [ 81] [depth= 5] . ( 27 sec) [ -1696.2921] [ 81] [depth= 3] . ( 28 sec) [ -1696.2548] [ 82] [depth= 1] . ( 28 sec) [ -1696.0512] [ 82] [depth= 1] . ( 29 sec) [ -1695.9506] [ 82] [depth= 1] . ( 29 sec) [ -1695.8680] [ 82] [depth= 1] . ( 32 sec) [ -1695.0532] [Branch lengths ] . ( 32 sec) [ -1692.5539] [Alpha ][ 0.250961] . ( 37 sec) [ -1692.0332] [ 81] [depth= 1] . ( 56 sec) [ -1691.8160] [Branch lengths ] . ( 56 sec) [ -1691.4946] [Alpha ][ 0.172623] . ( 80 sec) [ -1691.4860] [Branch lengths ] . ( 80 sec) [ -1691.4860] [Topology ] . ( 81 sec) [ -1691.4857] [Topology ] . ( 81 sec) [ -1691.4855] [Alpha ][ 0.170926] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -1693.323129 . Log likelihood obtained after SPR moves : -1691.485546 . Log likelihood of the current tree: -1691.485546. . Printing the most likely tree in file 'proteic_M2638_18x378_2006.phy_phyml_tree.txt'... . Time used 0h1m23s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 82.80user 0.00system 1:23.32elapsed 99%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps