.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data20.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 : 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... . 419 patterns found. (out of a total of 500 sites) . 77 sites without polymorphism (15.40%). . Computing pairwise distances... . Building BioNJ tree... . This analysis requires at least 9Mo of memory space. . Maximizing likelihood (using NNI moves)... . Before opt ts/t=1.000000 LK=-9819.544236 . ( 0 sec) [ -9818.9780] [GTR parameters ] . ( 0 sec) [ -9817.3593] [Alpha ][ 0.874247] . ( 0 sec) [ -9817.3593] [Topology ] . ( 1 sec) [ -9764.1157] [Topology ] . ( 2 sec) [ -9753.9386] [Topology ] . ( 2 sec) [ -9750.7269] [Topology ] . ( 3 sec) [ -9749.3574] [Topology ] . ( 4 sec) [ -9748.6569] [Topology ] . ( 5 sec) [ -9748.2723] [Topology ] . ( 5 sec) [ -9748.0537] [Topology ] . ( 6 sec) [ -9747.9264] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.926387 . ( 14 sec) [ -9747.8744] [GTR parameters ] . ( 14 sec) [ -9747.5766] [Alpha ][ 0.923577] . ( 14 sec) [ -9747.5766] [Topology ] . ( 14 sec) [ -9747.4687] [Topology ] . ( 15 sec) [ -9747.4098] [Topology ] . ( 16 sec) [ -9747.3755] [Topology ] . ( 17 sec) [ -9747.3552] [Topology ] . ( 18 sec) [ -9747.3432] [Topology ] . ( 18 sec) [ -9747.3361] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.336102 . ( 25 sec) [ -9747.3359] [GTR parameters ] . ( 25 sec) [ -9747.3331] [Alpha ][ 0.928476] . ( 25 sec) [ -9747.3331] [Topology ] . ( 26 sec) [ -9747.3284] [Topology ] . ( 27 sec) [ -9747.3256] [Topology ] . ( 27 sec) [ -9747.3240] [Topology ] . ( 28 sec) [ -9747.3230] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9747.322977 . ( 35 sec) [ -9747.3230] [GTR parameters ] . ( 35 sec) [ -9747.3229] [Alpha ][ 0.929405] . ( 35 sec) [ -9747.3229] [Topology ] . ( 35 sec) [ -9747.3223] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 49 sec) [ -9818.9780] [GTR parameters ] . ( 49 sec) [ -9817.3593] [Alpha ][ 0.874247] . ( 49 sec) [ -9813.5091] [ 2171] [depth= 1] . ( 49 sec) [ -9811.7173] [ 2169] [depth= 1] . ( 49 sec) [ -9811.4644] [ 2171] [depth= 1] . ( 49 sec) [ -9811.3944] [ 2173] [depth= 1] . ( 50 sec) [ -9807.9557] [ 2177] [depth= 2] . ( 50 sec) [ -9807.1056] [ 2188] [depth= 1] . ( 50 sec) [ -9806.9336] [ 2189] [depth= 1] . ( 50 sec) [ -9802.8983] [ 2188] [depth= 1] . ( 50 sec) [ -9802.5593] [ 2183] [depth= 1] . ( 51 sec) [ -9802.1604] [ 2180] [depth= 2] . ( 51 sec) [ -9799.5137] [ 2182] [depth= 1] . ( 51 sec) [ -9798.4882] [ 2183] [depth= 1] . ( 51 sec) [ -9797.2458] [ 2184] [depth= 2] . ( 51 sec) [ -9797.2135] [ 2185] [depth= 1] . ( 51 sec) [ -9797.1873] [ 2182] [depth= 1] . ( 51 sec) [ -9796.7182] [ 2183] [depth= 1] . ( 51 sec) [ -9795.2640] [ 2182] [depth= 1] . ( 51 sec) [ -9788.6596] [ 2176] [depth= 1] . ( 51 sec) [ -9788.6304] [ 2179] [depth= 1] . ( 51 sec) [ -9786.9837] [ 2178] [depth= 2] . ( 51 sec) [ -9785.9734] [ 2180] [depth= 1] . ( 51 sec) [ -9785.7605] [ 2181] [depth= 1] . ( 52 sec) [ -9785.0104] [ 2180] [depth= 1] . ( 52 sec) [ -9784.5167] [ 2178] [depth= 1] . ( 52 sec) [ -9753.7468] [Branch lengths ] . ( 52 sec) [ -9753.7185] [GTR parameters ] . ( 52 sec) [ -9753.6107] [Alpha ][ 0.903537] . ( 53 sec) [ -9752.0100] [ 2175] [depth= 2] . ( 53 sec) [ -9751.5220] [ 2165] [depth= 1] . ( 54 sec) [ -9751.3083] [ 2167] [depth= 1] . ( 54 sec) [ -9751.2975] [ 2167] [depth= 1] . ( 54 sec) [ -9751.2825] [ 2167] [depth= 2] . ( 54 sec) [ -9751.2618] [ 2168] [depth= 1] . ( 55 sec) [ -9751.2394] [ 2167] [depth= 1] . ( 55 sec) [ -9751.1821] [ 2167] [depth= 1] . ( 55 sec) [ -9751.1712] [ 2171] [depth= 1] . ( 55 sec) [ -9750.6670] [ 2167] [depth= 1] . ( 55 sec) [ -9750.6482] [ 2172] [depth= 1] . ( 56 sec) [ -9747.4229] [Branch lengths ] . ( 56 sec) [ -9747.4077] [GTR parameters ] . ( 56 sec) [ -9747.3801] [Alpha ][ 0.919132] . ( 60 sec) [ -9746.7453] [Branch lengths ] . ( 75 sec) [ -9746.6014] [ 2171] [depth= 2] . ( 83 sec) [ -9746.4965] [Branch lengths ] . ( 83 sec) [ -9746.4943] [GTR parameters ] . ( 83 sec) [ -9746.4880] [Alpha ][ 0.926620] . ( 83 sec) [ -9746.4880] [Topology ] . ( 84 sec) [ -9746.4804] [Topology ] . ( 84 sec) [ -9746.4777] [Topology ] . ( 85 sec) [ -9746.4763] [Topology ] . ( 86 sec) [ -9746.4755] [Topology ] . ( 86 sec) [ -9746.4754] [GTR parameters ] . ( 86 sec) [ -9746.4754] [Alpha ][ 0.927546] . ( 86 sec) [ -9746.4754] [Topology ] . ( 87 sec) [ -9746.4749] [Topology ] . ( 87 sec) [ -9746.4749] [GTR parameters ] . ( 87 sec) [ -9746.4749] [Alpha ][ 0.927546] . Checking for NNIs, optimizing five branches... . ( 93 sec) [ -9746.4740] [Topology ] . Checking for NNIs, optimizing five branches... . ( 99 sec) [ -9746.4738] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9747.322299 . Log likelihood obtained after SPR moves : -9746.473802 . Log likelihood of the current tree: -9746.473802. . Printing the most likely tree in file 'data20.phy_phyml_tree.txt'... . Time used 0h1m46s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo