.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1993_28x93_2004.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... . 79 patterns found. (out of a total of 93 sites) . 26 sites without polymorphism (27.96%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 6Mo of memory space. . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -2041.7950] [Alpha ][ 0.666358] . ( 0 sec) [ -2041.7950] [Topology ] . ( 1 sec) [ -2022.2350] [Topology ] . ( 2 sec) [ -2012.7530] [Topology ] . ( 2 sec) [ -2010.0591] [Topology ] . ( 3 sec) [ -2007.6082] [Topology ] . ( 4 sec) [ -2006.9674] [Topology ] . ( 4 sec) [ -2006.8253] [Topology ] . ( 5 sec) [ -2006.7537] [Topology ] . ( 6 sec) [ -2006.7081] [Topology ] . ( 6 sec) [ -2006.6785] [Topology ] . Checking for NNIs, optimizing five branches... . ( 11 sec) [ -2005.6454] [Topology ] . ( 12 sec) [ -2005.5012] [Alpha ][ 0.729106] . ( 12 sec) [ -2005.5012] [Topology ] . ( 12 sec) [ -2005.4906] [Topology ] . ( 13 sec) [ -2005.4891] [Topology ] . ( 14 sec) [ -2005.4884] [Topology ] . Checking for NNIs, optimizing five branches... . ( 18 sec) [ -2005.4882] [Alpha ][ 0.731508] . ( 18 sec) [ -2005.4882] [Topology ] . ( 19 sec) [ -2005.4878] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 27 sec) [ -2041.7950] [Alpha ][ 0.666358] . ( 28 sec) [ -2040.6879] [ 341] [depth= 1] . ( 28 sec) [ -2038.7596] [ 342] [depth= 1] . ( 31 sec) [ -2038.5780] [ 341] [depth= 1] . ( 32 sec) [ -2038.5557] [ 341] [depth= 1] . ( 32 sec) [ -2038.1903] [ 342] [depth= 1] . ( 32 sec) [ -2037.8703] [ 342] [depth= 1] . ( 32 sec) [ -2030.3424] [ 340] [depth= 3] . ( 33 sec) [ -2026.9676] [ 340] [depth= 3] . ( 33 sec) [ -2026.2127] [ 340] [depth= 1] . ( 33 sec) [ -2024.4980] [ 341] [depth= 1] . ( 33 sec) [ -2024.1418] [ 340] [depth= 1] . ( 34 sec) [ -2023.8722] [ 341] [depth= 1] . ( 37 sec) [ -2023.6288] [ 342] [depth= 1] . ( 37 sec) [ -2022.5545] [ 342] [depth= 1] . ( 39 sec) [ -2021.9073] [ 343] [depth= 3] . ( 39 sec) [ -2021.0324] [ 342] [depth= 1] . ( 46 sec) [ -2018.7943] [ 343] [depth= 1] . ( 46 sec) [ -2014.7372] [ 343] [depth= 2] . ( 46 sec) [ -2013.5744] [ 343] [depth= 1] . ( 47 sec) [ -2013.5637] [ 343] [depth= 1] . ( 47 sec) [ -2013.5271] [ 343] [depth= 1] . ( 50 sec) [ -2008.6305] [Branch lengths ] . ( 50 sec) [ -2008.5365] [Alpha ][ 0.716368] . ( 54 sec) [ -2008.5249] [ 344] [depth= 1] . ( 55 sec) [ -2008.4460] [ 344] [depth= 1] . ( 65 sec) [ -2007.7061] [ 343] [depth= 1] . ( 75 sec) [ -2006.9724] [ 342] [depth= 1] . ( 80 sec) [ -2005.6557] [Branch lengths ] . ( 80 sec) [ -2005.6504] [Alpha ][ 0.729164] . ( 96 sec) [ -2005.6342] [ 343] [depth= 2] . ( 97 sec) [ -2005.5462] [ 342] [depth= 1] . ( 107 sec) [ -2005.1672] [Branch lengths ] . ( 107 sec) [ -2005.1667] [Alpha ][ 0.733039] . ( 108 sec) [ -2005.1667] [Topology ] . ( 108 sec) [ -2005.1496] [Topology ] . ( 109 sec) [ -2005.1443] [Topology ] . ( 109 sec) [ -2005.1417] [Topology ] . ( 110 sec) [ -2005.1404] [Topology ] . ( 111 sec) [ -2005.1397] [Topology ] . ( 111 sec) [ -2005.1396] [Alpha ][ 0.733952] . ( 111 sec) [ -2005.1396] [Topology ] . ( 111 sec) [ -2005.1393] [Topology ] . ( 112 sec) [ -2005.1393] [Alpha ][ 0.733952] . Checking for NNIs, optimizing five branches... . ( 116 sec) [ -2005.0786] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -2005.487783 . Log likelihood obtained after SPR moves : -2005.078648 . Log likelihood of the current tree: -2005.078648. . Printing the most likely tree in file 'proteic_M1993_28x93_2004.phy_phyml_tree.txt'... . Time used 0h2m0s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 118.75user 0.00system 2:00.58elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps