.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : data40.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... . 426 patterns found. (out of a total of 500 sites) . 70 sites without polymorphism (14.00%). . 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=-9827.155972 . ( 2 sec) [ -9824.3441] [GTR parameters ] . ( 2 sec) [ -9824.0535] [Alpha ][ 0.943410] . ( 2 sec) [ -9824.0535] [Topology ] . ( 3 sec) [ -9781.0533] [Topology ] . ( 4 sec) [ -9771.4895] [Topology ] . ( 5 sec) [ -9769.0992] [Topology ] . ( 6 sec) [ -9768.2834] [Topology ] . ( 7 sec) [ -9767.8984] [Topology ] . ( 8 sec) [ -9767.7052] [Topology ] . ( 9 sec) [ -9767.6057] [Topology ] . ( 10 sec) [ -9767.5536] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9767.553606 . ( 19 sec) [ -9767.4435] [GTR parameters ] . ( 19 sec) [ -9767.0408] [Alpha ][ 1.007628] . ( 19 sec) [ -9767.0408] [Topology ] . ( 21 sec) [ -9766.9849] [Topology ] . ( 22 sec) [ -9766.9584] [Topology ] . ( 23 sec) [ -9766.9447] [Topology ] . ( 24 sec) [ -9766.9375] [Topology ] . ( 26 sec) [ -9766.9336] [Topology ] . ( 27 sec) [ -9766.9315] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.931452 . ( 36 sec) [ -9766.9314] [GTR parameters ] . ( 36 sec) [ -9766.9301] [Alpha ][ 1.011385] . ( 36 sec) [ -9766.9301] [Topology ] . ( 37 sec) [ -9766.9288] [Topology ] . ( 38 sec) [ -9766.9280] [Topology ] . Checking for NNIs, optimizing five branches... . Before opt ts/t=1.000000 LK=-9766.928011 . ( 47 sec) [ -9766.9280] [GTR parameters ] . ( 47 sec) [ -9766.9280] [Alpha ][ 1.011385] . ( 47 sec) [ -9766.9280] [Topology ] . ( 48 sec) [ -9766.9276] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 68 sec) [ -9824.3441] [GTR parameters ] . ( 68 sec) [ -9824.0535] [Alpha ][ 0.943410] . ( 70 sec) [ -9822.6627] [ 2112] [depth= 1] . ( 70 sec) [ -9821.9513] [ 2111] [depth= 1] . ( 70 sec) [ -9821.4004] [ 2112] [depth= 1] . ( 71 sec) [ -9821.0707] [ 2112] [depth= 1] . ( 71 sec) [ -9819.9794] [ 2112] [depth= 1] . ( 71 sec) [ -9818.3978] [ 2115] [depth= 1] . ( 71 sec) [ -9815.7389] [ 2112] [depth= 1] . ( 71 sec) [ -9815.7194] [ 2117] [depth= 2] . ( 71 sec) [ -9810.5380] [ 2110] [depth= 3] . ( 72 sec) [ -9803.8708] [ 2108] [depth= 1] . ( 72 sec) [ -9803.6585] [ 2107] [depth= 1] . ( 72 sec) [ -9803.3043] [ 2109] [depth= 1] . ( 72 sec) [ -9800.2978] [ 2114] [depth= 1] . ( 72 sec) [ -9797.4250] [ 2114] [depth= 2] . ( 72 sec) [ -9795.1512] [ 2107] [depth= 1] . ( 72 sec) [ -9795.0851] [ 2109] [depth= 2] . ( 73 sec) [ -9794.8636] [ 2112] [depth= 1] . ( 73 sec) [ -9794.3837] [ 2109] [depth= 1] . ( 74 sec) [ -9773.0167] [Branch lengths ] . ( 74 sec) [ -9772.9113] [GTR parameters ] . ( 75 sec) [ -9772.6790] [Alpha ][ 0.992215] . ( 76 sec) [ -9772.3306] [ 2103] [depth= 1] . ( 79 sec) [ -9769.6066] [Branch lengths ] . ( 79 sec) [ -9769.5999] [GTR parameters ] . ( 79 sec) [ -9769.5822] [Alpha ][ 1.006393] . ( 83 sec) [ -9769.2523] [Branch lengths ] . ( 112 sec) [ -9767.6878] [ 2101] [depth= 2] . ( 113 sec) [ -9767.2244] [ 2101] [depth= 1] . ( 114 sec) [ -9767.1671] [ 2102] [depth= 1] . ( 115 sec) [ -9766.9640] [Branch lengths ] . ( 115 sec) [ -9766.9591] [GTR parameters ] . ( 115 sec) [ -9766.9576] [Alpha ][ 1.010436] . ( 147 sec) [ -9766.9362] [Branch lengths ] . ( 147 sec) [ -9766.9362] [Topology ] . ( 148 sec) [ -9766.9332] [Topology ] . ( 150 sec) [ -9766.9321] [Topology ] . ( 151 sec) [ -9766.9314] [Topology ] . ( 151 sec) [ -9766.9313] [GTR parameters ] . ( 151 sec) [ -9766.9312] [Alpha ][ 1.011457] . ( 151 sec) [ -9766.9312] [Topology ] . ( 152 sec) [ -9766.9308] [Topology ] . ( 152 sec) [ -9766.9308] [GTR parameters ] . ( 153 sec) [ -9766.9308] [Alpha ][ 1.011457] . Checking for NNIs, optimizing five branches... . ( 160 sec) [ -9766.9307] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -9766.927571 . Log likelihood obtained after SPR moves : -9766.930704 . Log likelihood of the current tree: -9766.927571. . Printing the most likely tree in file 'data40.phy_phyml_tree.txt'... . Time used 0h2m48s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo